File: ChangeLog

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meep 1.1.1-6
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file content (10683 lines) | stat: -rw-r--r-- 314,557 bytes
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Mon Aug 24 15:46:01 EDT 2009  stevenj@alum.mit.edu
  * tentative 1.1.1 release date

    M ./NEWS -1 +1

Sat Aug 22 00:36:20 EDT 2009  stevenj@alum.mit.edu
  * whoops

    M ./tests/known_results.cpp -1 +1

Fri Aug 21 12:36:04 EDT 2009  stevenj@alum.mit.edu
  * forgot to change geometric-volume -> volume in casimir.scm

    M ./NEWS +4
    M ./configure.ac -2 +2
    M ./libctl/casimir.scm -15 +15
    M ./tests/known_results.cpp -1 +1

Thu Aug 20 19:57:05 EDT 2009  stevenj@alum.mit.edu
  tagged meep-1.1


Thu Aug 20 19:30:03 EDT 2009  stevenj@alum.mit.edu
  * included planned 1.1 release date

    M ./NEWS -3 +3

Thu Aug 20 19:27:52 EDT 2009  stevenj@alum.mit.edu
  * added Alejandro and Alex M. to authors list for Casimir stuff

    M ./AUTHORS +2

Thu Aug 20 19:27:26 EDT 2009  stevenj@alum.mit.edu
  * more compiler warnings (stemming from incomplete deletion of obsolete SZ0 macro)

    M ./src/step_generic.cpp -6 +6

Thu Aug 20 19:27:07 EDT 2009  stevenj@alum.mit.edu
  * clean up some compiler warnings (thanks Peter)

    M ./libctl/meep.cpp -2 +2
    M ./src/casimir.cpp -3 +3

Thu Aug 20 18:20:24 EDT 2009  stevenj@alum.mit.edu
  * whoops

    M ./libctl/meep.scm.in -1 +1

Thu Aug 20 14:07:23 EDT 2009  stevenj@alum.mit.edu
  * more robust (hopefully) checking for how to combine stdio.h and mpi.h (#undefing SEEK_* conflicts with openmpi, so it can't be done unconditionally)

    M ./configure.ac -4 +10
    M ./src/mympi.cpp -4 +6

Thu Aug 20 01:51:36 EDT 2009  stevenj@alum.mit.edu
  * version bump, NEWS

    M ./NEWS -1 +32
    M ./configure.ac -2 +2

Thu Aug 20 01:35:03 EDT 2009  stevenj@alum.mit.edu
  * rename zero-fields-near-cylorigin? to accurate-fields-near-cylorigin? and reverse meaning

    M ./libctl/meep.scm.in -4 +4

Thu Aug 20 01:29:58 EDT 2009  stevenj@alum.mit.edu
  * fix symmetry in ring.ctl example

    M ./examples/ring.ctl -2 +2

Thu Aug 20 01:25:43 EDT 2009  stevenj@alum.mit.edu
  * whoops, forgot to rename some geometric-volume stuff in scheme interface

    M ./libctl/meep-ctl-swig.hpp -4 +3
    M ./libctl/meep.cpp -2 +1
    M ./libctl/meep.scm.in -14 +14

Thu Aug 20 01:20:43 EDT 2009  stevenj@alum.mit.edu
  * add option to NOT use David's hack of setting fieldsss |m| pixels near r=0 to zero for |m|>2  -- using the hack is the default, and seems to maintain stability for a fixed Courant number ~ 0.62 independent of m, but degrades accuracy near r=0 -- with this disabled, Courant number should be set to around min(0.5, 1/(|m|+0.5)) apparently

    M ./examples/ring.ctl -1 +1
    M ./libctl/meep.scm.in -2 +12
    M ./src/fields.cpp -3 +6
    M ./src/meep.hpp -2 +6
    M ./src/step_db.cpp -23 +58
    M ./tests/cylindrical.cpp -7 +7
    M ./tests/flux.cpp -1 +1

Thu Aug 20 01:04:21 EDT 2009  stevenj@alum.mit.edu
  * delete obsolete rshift-phasing hack (which was added  years ago as an experiment for Alejandro that didn't pan out)

    M ./src/fields.cpp -11
    M ./src/meep.hpp -2 +1
    M ./src/step_db.cpp -2 +2

Wed Aug 19 23:35:45 EDT 2009  stevenj@alum.mit.edu
  * added cylindrical PML scaling test to pml.cpp

    M ./tests/pml.cpp -2 +47

Wed Aug 19 19:13:13 EDT 2009  stevenj@alum.mit.edu
  * fix casimir.scm inclusion in dist and for VPATH builds

    M ./libctl/Makefile.am -3 +2
    M ./libctl/meep.scm.in -1 +1

Wed Aug 19 19:04:31 EDT 2009  stevenj@alum.mit.edu
  * remove obsolete doc directory (all docs are on wiki these days)

    M ./Makefile.am -7 +1
    M ./configure.ac -9
    R ./doc/
    R ./doc/Makefile.am
    R ./doc/README
    R ./doc/Yee_bulk.eps
    R ./doc/complicated.tex
    R ./doc/energy_cons.tex
    R ./doc/energy_cons_1d.tex
    R ./doc/epsilon_polariton_1d.tex
    R ./doc/example.cpp
    R ./doc/gpl.tex
    R ./doc/lossgain_epsilon.tex
    R ./doc/meep.tex
    R ./doc/nonlinear.tex
    R ./doc/omniguide.tex
    R ./doc/polaritonbands.tex
    R ./doc/preproc.pl
    R ./doc/simple.tex
    R ./doc/simplebands.tex

Wed Aug 19 18:56:37 EDT 2009  stevenj@alum.mit.edu
  * rename xv (formerly gv) to v (now volume, formerly grid_volume)

    M ./libctl/meep-ctl-const.hpp r1
    M ./libctl/meep-ctl-swig.hpp r1
    M ./libctl/meep-ctl.hpp r1
    M ./libctl/meep.cpp r1
    M ./libctl/structure.cpp r1
    M ./src/anisotropic_averaging.cpp r1
    M ./src/bands.cpp r1
    M ./src/bicgstab.cpp r1
    M ./src/bicgstab.hpp r1
    M ./src/boundaries.cpp r1
    M ./src/casimir.cpp r1
    M ./src/control_c.cpp r1
    M ./src/cw_fields.cpp r1
    M ./src/dft.cpp r2
    M ./src/energy_and_flux.cpp r1
    M ./src/fields.cpp r1
    M ./src/grace.cpp r1
    M ./src/h5fields.cpp r1
    M ./src/h5file.cpp r1
    M ./src/initialize.cpp r1
    M ./src/integrate.cpp r1
    M ./src/integrate2.cpp r1
    M ./src/loop_in_chunks.cpp r3
    M ./src/meep.hpp r1
    M ./src/meep/mympi.hpp r1
    M ./src/meep/vec.hpp r1
    M ./src/meep_internals.hpp r1
    M ./src/monitor.cpp r1
    M ./src/mpb.cpp r1
    M ./src/mympi.cpp r1
    M ./src/output_directory.cpp r1
    M ./src/polarization.cpp r1
    M ./src/sources.cpp r1
    M ./src/sphere-quad.cpp r1
    M ./src/step.cpp r1
    M ./src/step_db.cpp r1
    M ./src/step_generic.cpp r1
    M ./src/stress.cpp r1
    M ./src/structure.cpp r1
    M ./src/time.cpp r1
    M ./src/update_eh.cpp r1
    M ./src/update_pols.cpp r1
    M ./src/vec.cpp r1
    M ./tests/2D_convergence.cpp r1
    M ./tests/bench.cpp r1
    M ./tests/bragg_transmission.cpp r1
    M ./tests/convergence_cyl_waveguide.cpp r1
    M ./tests/cylindrical.cpp r1
    M ./tests/flux.cpp r1
    M ./tests/h5test.cpp r1
    M ./tests/harmonics.cpp r1
    M ./tests/integrate.cpp r1
    M ./tests/known_results.cpp r1
    M ./tests/one_dimensional.cpp r1
    M ./tests/physical.cpp r1
    M ./tests/pml.cpp r1
    M ./tests/symmetry.cpp r1
    M ./tests/three_d.cpp r1
    M ./tests/two_dimensional.cpp r1

Wed Aug 19 18:53:18 EDT 2009  stevenj@alum.mit.edu
  * rename grid_volume "v" to "gv"

    M ./libctl/meep-ctl-const.hpp r2
    M ./libctl/meep-ctl-swig.hpp r2
    M ./libctl/meep-ctl.hpp r2
    M ./libctl/meep.cpp r2
    M ./libctl/structure.cpp r2
    M ./src/anisotropic_averaging.cpp r2
    M ./src/bands.cpp r2
    M ./src/bicgstab.cpp r2
    M ./src/bicgstab.hpp r2
    M ./src/boundaries.cpp r2
    M ./src/casimir.cpp r2
    M ./src/control_c.cpp r2
    M ./src/cw_fields.cpp r2
    M ./src/dft.cpp r2
    M ./src/energy_and_flux.cpp r2
    M ./src/fields.cpp r2
    M ./src/grace.cpp r2
    M ./src/h5fields.cpp r2
    M ./src/h5file.cpp r2
    M ./src/initialize.cpp r2
    M ./src/integrate.cpp r2
    M ./src/integrate2.cpp r2
    M ./src/loop_in_chunks.cpp r2
    M ./src/meep.hpp r2
    M ./src/meep/mympi.hpp r2
    M ./src/meep/vec.hpp r2
    M ./src/meep_internals.hpp r2
    M ./src/monitor.cpp r2
    M ./src/mpb.cpp r2
    M ./src/mympi.cpp r2
    M ./src/output_directory.cpp r2
    M ./src/polarization.cpp r2
    M ./src/sources.cpp r2
    M ./src/sphere-quad.cpp r2
    M ./src/step.cpp r2
    M ./src/step_db.cpp r2
    M ./src/step_generic.cpp r2
    M ./src/stress.cpp r2
    M ./src/structure.cpp r2
    M ./src/time.cpp r2
    M ./src/update_eh.cpp r2
    M ./src/update_pols.cpp r2
    M ./src/vec.cpp r2
    M ./tests/2D_convergence.cpp r2
    M ./tests/bench.cpp r2
    M ./tests/bragg_transmission.cpp r2
    M ./tests/convergence_cyl_waveguide.cpp r2
    M ./tests/cylindrical.cpp r2
    M ./tests/flux.cpp r2
    M ./tests/h5test.cpp r2
    M ./tests/harmonics.cpp r2
    M ./tests/integrate.cpp r2
    M ./tests/known_results.cpp r2
    M ./tests/one_dimensional.cpp r2
    M ./tests/physical.cpp r2
    M ./tests/pml.cpp r2
    M ./tests/symmetry.cpp r2
    M ./tests/three_d.cpp r2
    M ./tests/two_dimensional.cpp r2

Wed Aug 19 18:51:32 EDT 2009  stevenj@alum.mit.edu
  * don't use "v" as variable name for vector

    M ./libctl/meep-ctl-swig.hpp -1 +1
    M ./libctl/structure.cpp -10 +10
    M ./src/initialize.cpp -4 +4
    M ./src/loop_in_chunks.cpp -14 +14
    M ./src/meep/vec.hpp -22 +22
    M ./src/monitor.cpp -6 +6
    M ./src/mpb.cpp -1 +1
    M ./src/mympi.cpp -5 +5
    M ./src/sources.cpp -1 +1
    M ./src/vec.cpp -2 +2
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -2 +2
    M ./tests/convergence_cyl_waveguide.cpp -1 +1
    M ./tests/cylindrical.cpp -3 +3
    M ./tests/flux.cpp -4 +4
    M ./tests/one_dimensional.cpp -2 +2
    M ./tests/three_d.cpp -2 +2
    M ./tests/two_dimensional.cpp -2 +2

Wed Aug 19 18:33:53 EDT 2009  stevenj@alum.mit.edu
  * temporarily rename "gv" geometric_volume vars to "xv"

    M ./libctl/meep-ctl-const.hpp r1
    M ./libctl/meep-ctl-swig.hpp r1
    M ./libctl/meep-ctl.hpp r1
    M ./libctl/meep.cpp r1
    M ./libctl/structure.cpp r1
    M ./src/anisotropic_averaging.cpp r1
    M ./src/bands.cpp r1
    M ./src/bicgstab.cpp r1
    M ./src/bicgstab.hpp r1
    M ./src/boundaries.cpp r1
    M ./src/casimir.cpp r1
    M ./src/control_c.cpp r1
    M ./src/cw_fields.cpp r1
    M ./src/dft.cpp r2
    M ./src/energy_and_flux.cpp r1
    M ./src/fields.cpp r1
    M ./src/grace.cpp r1
    M ./src/h5fields.cpp r1
    M ./src/h5file.cpp r1
    M ./src/initialize.cpp r1
    M ./src/integrate.cpp r1
    M ./src/integrate2.cpp r1
    M ./src/loop_in_chunks.cpp r2
    M ./src/meep.hpp r1
    M ./src/meep/mympi.hpp r1
    M ./src/meep/vec.hpp r1
    M ./src/meep_internals.hpp r1
    M ./src/monitor.cpp r1
    M ./src/mpb.cpp r1
    M ./src/mympi.cpp r1
    M ./src/output_directory.cpp r1
    M ./src/polarization.cpp r1
    M ./src/sources.cpp r1
    M ./src/sphere-quad.cpp r1
    M ./src/step.cpp r1
    M ./src/step_db.cpp r1
    M ./src/step_generic.cpp r1
    M ./src/stress.cpp r1
    M ./src/structure.cpp r1
    M ./src/time.cpp r1
    M ./src/update_eh.cpp r1
    M ./src/update_pols.cpp r1
    M ./src/vec.cpp r1
    M ./tests/2D_convergence.cpp r1
    M ./tests/bench.cpp r1
    M ./tests/bragg_transmission.cpp r1
    M ./tests/convergence_cyl_waveguide.cpp r1
    M ./tests/cylindrical.cpp r1
    M ./tests/flux.cpp r1
    M ./tests/h5test.cpp r1
    M ./tests/harmonics.cpp r1
    M ./tests/integrate.cpp r1
    M ./tests/known_results.cpp r1
    M ./tests/one_dimensional.cpp r1
    M ./tests/physical.cpp r1
    M ./tests/pml.cpp r1
    M ./tests/symmetry.cpp r1
    M ./tests/three_d.cpp r1
    M ./tests/two_dimensional.cpp r1

Wed Aug 19 18:03:56 EDT 2009  stevenj@alum.mit.edu
  * whoops

    M ./tests/h5test.cpp -1 +1

Wed Aug 19 18:01:42 EDT 2009  stevenj@alum.mit.edu
  * rename geometric_volume to volume

    M ./libctl/meep-ctl-swig.hpp r2
    M ./libctl/meep.cpp r2
    M ./libctl/structure.cpp r1
    M ./src/anisotropic_averaging.cpp r1
    M ./src/casimir.cpp r1
    M ./src/dft.cpp r2
    M ./src/energy_and_flux.cpp r1
    M ./src/fields.cpp r1
    M ./src/h5fields.cpp r1
    M ./src/integrate.cpp r1
    M ./src/integrate2.cpp r1
    M ./src/loop_in_chunks.cpp r1
    M ./src/meep.hpp r2
    M ./src/meep/vec.hpp r2
    M ./src/monitor.cpp r1
    M ./src/mpb.cpp r1
    M ./src/sources.cpp r1
    M ./src/stress.cpp r1
    M ./src/structure.cpp r1
    M ./src/vec.cpp r2
    M ./tests/flux.cpp r1
    M ./tests/h5test.cpp r1
    M ./tests/harmonics.cpp r1
    M ./tests/integrate.cpp r1
    M ./tests/pml.cpp r1

Wed Aug 19 17:54:10 EDT 2009  stevenj@alum.mit.edu
  * rename volume to grid_volume

    M ./doc/complicated.tex r1
    M ./doc/epsilon_polariton_1d.tex r1
    M ./doc/nonlinear.tex r1
    M ./doc/simple.tex r1
    M ./examples/ring.ctl -1 +1
    M ./libctl/meep.cpp r1
    M ./libctl/structure.cpp r1
    M ./src/anisotropic_averaging.cpp r1
    M ./src/boundaries.cpp r1
    M ./src/casimir.cpp r1
    M ./src/dft.cpp r1
    M ./src/energy_and_flux.cpp r1
    M ./src/fields.cpp r1
    M ./src/h5fields.cpp r1
    M ./src/integrate.cpp r1
    M ./src/integrate2.cpp r1
    M ./src/loop_in_chunks.cpp r1
    M ./src/meep.hpp r1
    M ./src/meep/vec.hpp r1
    M ./src/meep_internals.hpp r1
    M ./src/monitor.cpp r1
    M ./src/mpb.cpp r1
    M ./src/polarization.cpp r1
    M ./src/sources.cpp r1
    M ./src/step_generic.cpp r1
    M ./src/structure.cpp r1
    M ./src/vec.cpp r1
    M ./tests/2D_convergence.cpp r1
    M ./tests/bench.cpp r1
    M ./tests/bragg_transmission.cpp r1
    M ./tests/convergence_cyl_waveguide.cpp r1
    M ./tests/cylindrical.cpp r1
    M ./tests/flux.cpp r1
    M ./tests/h5test.cpp r1
    M ./tests/harmonics.cpp r1
    M ./tests/integrate.cpp r1
    M ./tests/known_results.cpp r1
    M ./tests/one_dimensional.cpp r1
    M ./tests/physical.cpp r1
    M ./tests/pml.cpp r1
    M ./tests/symmetry.cpp r1
    M ./tests/three_d.cpp r1
    M ./tests/two_dimensional.cpp r1

Wed Aug 19 16:03:01 EDT 2009  mccauley@mit.edu
  * fixed syntax error in casimir.scm

    M ./libctl/casimir.scm -1 +1

Wed Aug 19 15:58:06 EDT 2009  mccauley@mit.edu
  * add casimir.scm helper functions

    M ./libctl/Makefile.am +1
    A ./libctl/casimir.scm
    M ./libctl/meep.scm.in +4

Wed Aug 19 15:30:05 EDT 2009  mccauley@mit.edu
  * fixed Casimir stress stuff, added k integrations

    M ./libctl/meep-ctl-swig.hpp +2
    M ./libctl/meep.cpp +14
    M ./src/casimir.cpp -26 +100
    M ./src/meep.hpp -2 +5

Wed Aug 19 14:35:54 EDT 2009  stevenj@alum.mit.edu
  * fix solve_cw for new PML

    M ./src/cw_fields.cpp -66 +49
    M ./src/fields.cpp -2 +14
    M ./src/meep.hpp -3 +22
    M ./src/step.cpp -1 +1
    M ./src/update_eh.cpp -15 +18
    M ./tests/physical.cpp -4

Wed Aug 19 11:50:47 EDT 2009  stevenj@alum.mit.edu
  * slight cleanup

    M ./src/step_generic.cpp -19 +11

Mon Aug 17 17:41:11 EDT 2009  stevenj@alum.mit.edu
  * fixed field-backup/synchronization for new PML (must backup internal U and W fields too)

    M ./src/energy_and_flux.cpp -5 +21
    M ./src/fields.cpp -8 +22
    M ./src/meep.hpp +3
    M ./tests/three_d.cpp -3 +2

Mon Aug 17 13:51:40 EDT 2009  stevenj@alum.mit.edu
  * fixed harmonics test for new PML - we slightly changed how PML interacts with nonlinearities, which changes the known results by about 1e-4 in this example

    M ./tests/harmonics.cpp -2 +2

Thu Aug 13 20:01:54 EDT 2009  stevenj@alum.mit.edu
  * swap roles of U and D/B fields in PML, to make the former a quantity that is purely needed locally and removing its interactions with boundary conditions etcetera

    M ./src/boundaries.cpp -9 +3
    M ./src/step.cpp -15
    M ./src/step_db.cpp -13 +13
    M ./src/step_generic.cpp -34 +35
    M ./src/update_eh.cpp -9 +4

Thu Aug 13 19:32:38 EDT 2009  stevenj@alum.mit.edu
  * initial stab at cylindrical code with new PML, not quite working yet

    M ./src/step_db.cpp -63 +158

Tue Aug 11 23:50:46 EDT 2009  stevenj@alum.mit.edu
  * PML test now includes anisotropy (and passes)

    M ./tests/pml.cpp -14 +55

Tue Aug 11 23:49:49 EDT 2009  stevenj@alum.mit.edu
  * fix new PML - need to communicate U field at PML boundaries

    M ./src/boundaries.cpp -4 +10
    M ./src/meep.hpp -1 +1
    M ./src/step.cpp +15
    M ./src/step_db.cpp -2 +11

Tue Aug 11 12:26:57 EDT 2009  stevenj@alum.mit.edu
  * fixed (I think) bug that caused anisotropic mu to be unstable (and was only first-order) ... the treatment of offdiagonal mu components forgot to take into account the shift between the H-yee and E-yee lattices!

    M ./src/anisotropic_averaging.cpp -1 +2
    M ./src/update_eh.cpp -3 +3

Mon Aug 10 19:28:25 EDT 2009  stevenj@alum.mit.edu
  * PML + dispersion seems to be working!

    M ./tests/pml.cpp -7 +20

Mon Aug 10 12:24:09 EDT 2009  stevenj@alum.mit.edu
  * partially rewritten PML , passes tests/pml but still needs testing -- should now be true PML for anisotropic eps/mu and for dispersive P -- cylindrical case not yet updated, also cw_solve needs fixing

    M ./src/energy_and_flux.cpp -12 +3
    M ./src/fields.cpp -6 +23
    M ./src/meep.hpp -1 +4
    M ./src/meep_internals.hpp -25 +15
    M ./src/step_db.cpp -21 +20
    M ./src/step_generic.cpp -215 +317
    M ./src/update_eh.cpp -22 +18
    M ./src/update_pols.cpp -1 +1
    M ./tests/pml.cpp +2

Sat Aug  8 00:00:19 EDT 2009  stevenj@alum.mit.edu
  * use a true PML for conductivity (previously was only y an approximate PML)

    M ./src/fields.cpp +4
    M ./src/meep.hpp +1
    M ./src/meep_internals.hpp -10 +12
    M ./src/step_db.cpp -3 +8
    M ./src/step_generic.cpp -20 +44
    M ./src/structure.cpp -18 +2
    M ./tests/pml.cpp -11 +41

Fri Aug  7 17:30:07 EDT 2009  stevenj@alum.mit.edu
  * note that our PML is not a proper PML for conductivity (sigh)

    M ./src/structure.cpp +3

Thu Aug  6 19:52:07 EDT 2009  stevenj@alum.mit.edu
  * beta feature seems to work

    M ./libctl/meep.scm.in -2 +3

Thu Aug  6 19:24:43 EDT 2009  stevenj@alum.mit.edu
  * units in beta should have 2*pi, just like k

    M ./src/step_db.cpp -1 +1

Thu Aug  6 18:55:08 EDT 2009  stevenj@alum.mit.edu
  * slightly more transparent usage of beta trick

    M ./libctl/meep.scm.in -4 +14
    M ./src/fields.cpp -2 +2

Thu Aug  6 18:40:25 EDT 2009  stevenj@alum.mit.edu
  * initial (untested) implementation of exp(i beta z) in 2d calculations

    M ./libctl/meep.scm.in -1 +2
    M ./src/Makefile.am -1 +1
    M ./src/fields.cpp -4 +13
    M ./src/meep.hpp -2 +4
    M ./src/meep_internals.hpp +16
    M ./src/step_db.cpp +29
    M ./src/step_generic.cpp +27

Thu Aug  6 17:06:25 EDT 2009  stevenj@alum.mit.edu
  * slight code cleanup

    M ./src/update_eh.cpp -4 +3

Thu Aug  6 17:04:10 EDT 2009  stevenj@alum.mit.edu
  * slight performance improvements in polarization code

    M ./src/update_eh.cpp -5 +6
    M ./src/update_pols.cpp -3 +3

Wed Jul 15 15:04:45 EDT 2009  stevenj@alum.mit.edu
  * add option for dft chunks to not use centered grid

    M ./src/dft.cpp -6 +11
    M ./src/meep.hpp -1 +3
    M ./src/stress.cpp -2 +2

Wed Jul 15 14:28:42 EDT 2009  stevenj@alum.mit.edu
  * rename yee2diel_offsets to yee2cent_offsets, following the new convention of "centered grid" instead of the confusing and inaccurate ""dielectric grid"

    M ./src/dft.cpp r1
    M ./src/h5fields.cpp r1
    M ./src/integrate.cpp r1
    M ./src/integrate2.cpp r1
    M ./src/meep/vec.hpp r1
    M ./src/vec.cpp r1

Wed Jul 15 14:23:39 EDT 2009  stevenj@alum.mit.edu
  * added synonym "Centered" for "Dielectric" to use when referring to the centered grid, since the former name is much more accurate nowadays as a grid

    M ./libctl/Makefile.am -1 +1
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/h5fields.cpp -2 +2
    M ./src/integrate.cpp -2 +2
    M ./src/integrate2.cpp -3 +3
    M ./src/loop_in_chunks.cpp -8 +8
    M ./src/meep.hpp -1 +1
    M ./src/meep/vec.hpp +1
    M ./src/mpb.cpp -2 +2
    M ./src/vec.cpp -2 +2

Tue Jul 14 19:27:29 EDT 2009  stevenj@alum.mit.edu
  * when doing dft with Nfreq = 1, use center freq

    M ./src/dft.cpp +2
    M ./src/stress.cpp +1

Mon Jul 13 17:00:18 EDT 2009  mccauley@mit.edu
  * use fields::normal_direction rather than geometric_volume::normal_direction, since the former correctly handles no-size dimensions

    M ./src/casimir.cpp -1 +1

Wed Jul  8 13:16:30 EDT 2009  stevenj@alum.mit.edu
  * avoid squaring integration weights in stress tensor

    M ./src/dft.cpp -2 +14
    M ./src/meep.hpp -1 +14
    M ./src/stress.cpp -5 +6

Wed Jul  8 13:15:49 EDT 2009  stevenj@alum.mit.edu
  * bug fix - perfect metals did not work (failed to set offdiagonal epsilon/mu)

    M ./libctl/structure.cpp +4

Wed Jul  8 10:53:25 EDT 2009  stevenj@alum.mit.edu
  * first stab at force-spectrum computation (compiles, but untested)

    M ./libctl/meep-ctl-swig.hpp +1
    M ./libctl/meep.cpp +8
    M ./libctl/meep.scm.in -6 +58
    M ./src/Makefile.am -2 +2
    M ./src/dft.cpp -6 +14
    M ./src/meep.hpp -1 +37
    A ./src/stress.cpp

Sat Jul  4 13:39:48 EDT 2009  stevenj@alum.mit.edu
  * silence compiler warning

    M ./src/mympi.cpp +2

Sat Jul  4 13:38:35 EDT 2009  stevenj@alum.mit.edu
  * comment fix

    M ./src/casimir.cpp -6 +7

Fri Jul  3 18:58:27 EDT 2009  mccauley@mit.edu
  * for convenience of Casimir calculations, add two new input variables (global-D-conductivity and global-B-conductivity) representing scalar conductivities which are added to the conductivity everywhere

    M ./libctl/meep-ctl-swig.hpp -1 +3
    M ./libctl/meep.scm.in -1 +7
    M ./libctl/structure.cpp -7 +18

Fri Jul  3 18:39:51 EDT 2009  mccauley@mit.edu
  * adapt casimir_make_g to handle H sources (which are shifted by half a timestep); rename meep::make_casimir_g to stop g++ complaints

    M ./libctl/meep-ctl-swig.hpp -1 +1
    M ./libctl/meep.cpp -2 +2
    M ./src/casimir.cpp -6 +20
    M ./src/meep.hpp -1 +1

Fri Jul  3 17:32:08 EDT 2009  mccauley@mit.edu
  * slight optimization

    M ./src/casimir.cpp -7 +4

Fri Jul  3 17:31:46 EDT 2009  stevenj@alum.mit.edu
  * use chunkloop in casimir stress integration to avoid 2*pi*r Jacobian

    M ./src/casimir.cpp -9 +54

Thu Jul  2 19:07:53 EDT 2009  mccauley@mit.edu
  * comment

    M ./src/casimir.cpp -1 +1

Thu Jul  2 18:58:19 EDT 2009  mccauley@mit.edu
  * include 1/2pi normalization in Fourier integral

    M ./src/casimir.cpp -1 +1

Wed Jul  1 15:29:25 EDT 2009  stevenj@alum.mit.edu
  * add first draft of Casimir helper functions

    M ./libctl/meep-ctl-swig.hpp +9
    M ./libctl/meep.cpp +18
    M ./libctl/meep.i +19
    M ./src/Makefile.am -2 +2
    A ./src/casimir.cpp
    M ./src/meep.hpp +11

Tue Jun 30 14:55:07 EDT 2009  stevenj@alum.mit.edu
  * std::remove needs cstdio

    M ./src/h5file.cpp +1

Thu Jun 18 10:50:23 EDT 2009  stevenj@alum.mit.edu
  * change infinity to meep::infinity, to work around weird gcc 3.4.4 bug(?) on Cygwin, thanks to Mischa Megens and Alexandr Sadovnikov  for the bug report

    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/h5test.cpp -3 +3

Sat Jun  6 20:17:35 EDT 2009  stevenj@alum.mit.edu
  * work around problem with MPICH (and other MPI versions?) with SEEK_SET and mpi.h

    M ./NEWS -1 +3
    M ./configure.ac -3 +23
    M ./src/mympi.cpp +4

Sat Jun  6 19:47:13 EDT 2009  stevenj@alum.mit.edu
  * tentative 1.0.4 version bump

    M ./NEWS +4
    M ./configure.ac -2 +2

Sat Jun  6 19:46:47 EDT 2009  stevenj@alum.mit.edu
  * give sensible cross-compiling default for sigfpe test

    M ./configure.ac -2 +1

Fri Jun  5 12:33:18 EDT 2009  stevenj@alum.mit.edu
  tagged meep-1.0.3


Fri Jun  5 12:25:57 EDT 2009  stevenj@alum.mit.edu
  * update NEWS

    M ./NEWS -2 +3

Fri Jun  5 12:12:34 EDT 2009  stevenj@alum.mit.edu
  tagged meep-1.0.2


Thu Jun  4 13:03:42 EDT 2009  stevenj@alum.mit.edu
  * whoops

    M ./configure.ac -2 +2

Thu Jun  4 12:57:59 EDT 2009  stevenj@alum.mit.edu
  * version bump

    M ./NEWS +5
    M ./configure.ac -2 +2

Thu Jun  4 12:51:40 EDT 2009  stevenj@alum.mit.edu
  * allow GUILE_CONFIG var to override location of guile-config

    M ./configure.ac -7 +7

Mon Jun  1 20:13:40 EDT 2009  stevenj@alum.mit.edu
  * version bump for 1.0.2

    M ./NEWS +9
    M ./configure.ac -2 +2

Mon Jun  1 20:08:12 EDT 2009  stevenj@alum.mit.edu
  * we can no longer rely on splitting producing *exactly* the same results, including roundoff, because the exploitation of SSE/SSE2 depends on the splitting (which determines alignments, array lengths, etc), and this affects roundoff error; thanks to Silviu Popescu for the bug report

    M ./tests/flux.cpp -10 +11
    M ./tests/one_dimensional.cpp -2 +8
    M ./tests/three_d.cpp -3 +9
    M ./tests/two_dimensional.cpp -2 +8

Mon Jun  1 19:29:26 EDT 2009  stevenj@alum.mit.edu
  * use meep_internals.hpp in step_generic, since that header contains the declarations for the step_generic functions

    M ./src/step_generic.cpp +1

Thu May 28 17:03:22 EDT 2009  stevenj@alum.mit.edu
  * fix tolerance in symmetry test for icc

    M ./tests/symmetry.cpp -1 +1

Thu May 28 08:37:55 EDT 2009  stevenj@alum.mit.edu
  tagged meep-1.0.1


Wed May 27 22:46:10 EDT 2009  stevenj@alum.mit.edu
  * update news

    M ./NEWS -1 +4

Wed May 27 19:10:41 EDT 2009  stevenj@alum.mit.edu
  * more robust calculation of whether a chunk overlaps with PML; thanks to Alex Prengel for the bug report of how this causes problems withgcc 4.3.2 on Athena Linux/x86 (32-bit)

    M ./src/structure.cpp -6 +17

Wed May 27 19:09:42 EDT 2009  stevenj@alum.mit.edu
  * output computational cell in libctl interface

    M ./libctl/structure.cpp -1 +3

Wed May 27 18:57:41 EDT 2009  stevenj@alum.mit.edu
  * 2D_convergence needs to run a little longer to get reliable results

    M ./tests/2D_convergence.cpp -1 +1

Fri May 22 22:44:07 EDT 2009  stevenj@alum.mit.edu
  * missing string.h header causes failure on linux.mit.edu

    M ./src/h5file.cpp +1

Fri May 22 22:40:02 EDT 2009  stevenj@alum.mit.edu
  * running 2D_convergence for slightly more timesteps fixed spurious failure in 2D_convergence; thanks to Alex Prengel for the bug report and help with Athena

    M ./NEWS -1 +6
    M ./tests/2D_convergence.cpp -1 +1

Fri May 22 22:09:34 EDT 2009  stevenj@alum.mit.edu
  * more standard way to make silent rules the default

    M ./configure.ac -6 +1

Fri May 22 21:35:49 EDT 2009  stevenj@alum.mit.edu
  * version bump for 1.0.1

    M ./configure.ac -2 +2

Fri May 22 21:32:17 EDT 2009  stevenj@alum.mit.edu
  * tentative NEWS for 1.0.1

    M ./NEWS +11

Fri May 22 21:23:20 EDT 2009  stevenj@alum.mit.edu
  * don't regenerate sphere-quad.h unnecessarily, fix make distcheck

    M ./src/Makefile.am -4 +4

Fri May 22 21:00:44 EDT 2009  stevenj@alum.mit.edu
  * cleanfiles

    M ./Makefile.am +1
    M ./src/Makefile.am -2 +1

Fri May 22 19:08:19 EDT 2009  stevenj@alum.mit.edu
  * use RUNCODE for running test programs, so that they ruse mpirun in MPI mode as before

    M ./tests/Makefile.am +2

Fri May 22 19:07:01 EDT 2009  stevenj@alum.mit.edu
  * enable silent rules by default

    M ./configure.ac +5

Fri May 22 18:39:59 EDT 2009  stevenj@alum.mit.edu
  * move boundary communications into mympi.cpp so that mycomm can be used

    M ./src/meep.hpp +2
    M ./src/mympi.cpp +48
    M ./src/step.cpp -48 +1

Fri May 22 18:11:11 EDT 2009  stevenj@alum.mit.edu
  * whoops, most of the MPI functions use double precision even when realnum == float

    M ./src/mympi.cpp -15 +13

Fri May 22 15:53:43 EDT 2009  stevenj@alum.mit.edu
  * replace MPI_DOUBLE with MPI_REALNUM to work in single-precision mode; thanks to Seyoon Kim for the bug report

    M ./src/mympi.cpp -13 +15
    M ./src/step.cpp -2 +4

Fri May 22 14:09:17 EDT 2009  stevenj@alum.mit.edu
  * fixed tests to pass in single precision

    M ./tests/h5test.cpp -1 +1
    M ./tests/symmetry.cpp -3 +11

Fri May 22 13:41:25 EDT 2009  stevenj@alum.mit.edu
  * rm unused variable

    M ./src/h5fields.cpp -3

Wed May 20 19:10:34 EDT 2009  stevenj@alum.mit.edu
  * fix compilation in MEEP_SINGLE mode, thanks to Seyoon Kim for the bug report

    M ./src/step.cpp -1 +1

Wed May 20 19:10:02 EDT 2009  stevenj@alum.mit.edu
  * silence compiler warnings

    M ./src/energy_and_flux.cpp -2 +3
    M ./src/monitor.cpp -1 +1
    M ./src/mpb.cpp -1 +2

Tue May 19 13:48:37 EDT 2009  stevenj@alum.mit.edu
  * whoops

    M ./tests/Makefile.am -1 +1

Tue May 19 13:37:00 EDT 2009  stevenj@alum.mit.edu
  * use new automake options

    M ./configure.ac -1 +2

Tue May 19 13:23:20 EDT 2009  stevenj@alum.mit.edu
  * use new automake TESTS variable

    M ./tests/Makefile.am -3 +46

Thu Apr 30 11:58:29 EDT 2009  stevenj@alum.mit.edu
  * fix header file in h5file to use cstdio, since we call std::remove and not remove, fixing Debian bug #505002

    M ./src/h5file.cpp -3 +1

Wed Apr 29 13:46:19 EDT 2009  stevenj@alum.mit.edu
  * update copyright year in --version string

    M ./libctl/Makefile.am -1 +1

Tue Apr 28 23:39:11 EDT 2009  stevenj@alum.mit.edu
  tagged meep-1-0


Tue Apr 28 23:38:03 EDT 2009  stevenj@alum.mit.edu
  * update TODO

    M ./TODO -5 +5

Tue Apr 28 20:00:50 EDT 2009  stevenj@alum.mit.edu
  * new NEWS

    M ./NEWS -1 +17

Tue Apr 28 19:46:35 EDT 2009  stevenj@alum.mit.edu
  * removed delta_epsilon parameter of polarizability entirely; use only sigma, which is allowed to be anisotropic (although offdiagonal sigma are not yet supported)

    M ./examples/material-dispersion.ctl -2 +2
    M ./libctl/meep.scm.in -3 +2
    M ./libctl/structure.cpp -27 +16
    M ./src/anisotropic_averaging.cpp -1 +1
    M ./src/meep.hpp -24 +19
    M ./src/meep/vec.hpp -2 +13
    M ./src/meep_internals.hpp -1 +1
    M ./src/polarization.cpp -37 +16
    M ./src/vec.cpp -5
    M ./tests/known_results.cpp -2 +4
    M ./tests/symmetry.cpp -2 +4

Tue Apr 28 19:02:46 EDT 2009  stevenj@alum.mit.edu
  * delete obsolete energy-saturation stuff, which was never documented and hence never used, and had bitrotted

    M ./libctl/meep.scm.in -2 +1
    M ./libctl/structure.cpp -13 +10
    M ./src/meep.hpp -19 +14
    M ./src/meep_internals.hpp -3 +1
    M ./src/polarization.cpp -72 +18
    M ./src/update_pols.cpp -11
    M ./tests/known_results.cpp -23
    M ./tests/symmetry.cpp -68

Tue Apr 28 18:45:05 EDT 2009  stevenj@alum.mit.edu
  * round times to floats for time comparisons, e.g. for source cutoffs, to avoid gratuitous sensitivity to slight changes in roundoff behavior (e.g. from different compiler options)

    M ./libctl/meep.scm.in -16 +20
    M ./src/meep.hpp -6 +11
    M ./src/sources.cpp -2 +5
    M ./tests/known_results.cpp -8 +8
    M ./tests/symmetry.cpp -41 +41

Tue Apr 28 17:38:12 EDT 2009  stevenj@alum.mit.edu
  * remove dependence of gaussian cutoff on precision

    M ./src/sources.cpp -2 +2

Tue Apr 28 16:57:19 EDT 2009  stevenj@alum.mit.edu
  * remove half-baked subpixel sigma averaging that was only used for cylindrical coordinates with electric susceptibility

    M ./src/polarization.cpp -25 +6

Tue Apr 28 16:46:35 EDT 2009  stevenj@alum.mit.edu
  * support diagonal anisotropic material dispersion, fix bug in cylindrical mu material dispersion, remove unused sigma[] array

    M ./libctl/meep.scm.in -1 +2
    M ./libctl/structure.cpp -8 +18
    M ./src/meep.hpp -8 +15
    M ./src/meep/vec.hpp -1 +8
    M ./src/meep_internals.hpp -3 +3
    M ./src/polarization.cpp -34 +60
    M ./src/structure.cpp -3
    M ./src/vec.cpp +5

Tue Apr 28 14:28:14 EDT 2009  stevenj@alum.mit.edu
  * update release date (hopefully today)

    M ./NEWS -1 +1

Tue Apr 28 14:27:23 EDT 2009  stevenj@alum.mit.edu
  * use ~irrational points, to avoid failure from slightly differnt rounding in snapping point to the nearest grid point

    M ./tests/h5test.cpp -1 +1

Tue Apr 28 11:05:35 EDT 2009  stevenj@alum.mit.edu
  * increase error threshold on flux_2d test, since actual error was within 0.00002 of threshold and rounding differences sometimes pushed  us over

    M ./tests/flux.cpp -2 +5

Mon Apr 27 20:24:31 EDT 2009  stevenj@alum.mit.edu
  * performance hack: gcc seems to emit significantly bfaster code if we make a specialized version of step_generic for the case when the inner loop is stride-1; fortunately, this is autogenerated and should not make maintainance more difficult

    M ./configure.ac +3
    M ./src/Makefile.am -1 +4
    M ./src/meep/vec.hpp +53
    M ./src/meep_internals.hpp +41
    M ./src/step_db.cpp -1 +1
    M ./src/step_generic.cpp -4 +2
    M ./src/update_eh.cpp -1 +1

Mon Apr 27 19:42:57 EDT 2009  stevenj@alum.mit.edu
  * turn on more aggressive optimization with g++, which seems to help as of gcc 4.3, and I'm not too worried about the bugs in ancient gcc 3.3.x any more

    M ./m4/ax_cxx_maxopt.m4 -9 +3

Mon Apr 27 19:19:12 EDT 2009  stevenj@alum.mit.edu
  * do all configure tests using C++, since that's what we compile/link with

    M ./configure.ac -6 +1

Mon Apr 27 16:10:20 EDT 2009  stevenj@alum.mit.edu
  * whoops, fixed breakage of --enable-debug mode

    M ./configure.ac -15 +16

Fri Apr 24 21:57:00 EDT 2009  stevenj@alum.mit.edu
  * remover redundant lapack check when harminv is found

    M ./configure.ac -1 +1

Fri Apr 24 21:47:31 EDT 2009  stevenj@alum.mit.edu
  * uses gcc -march=native on more architectures where available, and correctly set arch flag in CXXFLAGS not CFLAGS

    M ./m4/ax_gcc_archflag.m4 -4 +4

Fri Apr 24 21:34:32 EDT 2009  stevenj@alum.mit.edu
  * re-enable optimization flags that were accidentally turned off because stupid configure script was setting CXXFLAGS twice

    M ./configure.ac -33 +33

Fri Apr 24 21:23:16 EDT 2009  stevenj@alum.mit.edu
  * updated icc flags (from FFTW)

    M ./m4/ax_cxx_maxopt.m4 -1 +4

Fri Apr 24 21:02:54 EDT 2009  stevenj@alum.mit.edu
  * update macros from FFTW

    M ./m4/ax_gcc_archflag.m4 -6 +8
    M ./m4/ax_gcc_x86_cpuid.m4 -4 +26

Fri Apr 24 21:02:33 EDT 2009  stevenj@alum.mit.edu
  * remove obsolute configure flag --with-saturable-absorbers

    M ./configure.ac -7

Fri Apr 24 17:41:05 EDT 2009  stevenj@alum.mit.edu
  * make 2D_convergence.cpp more insensitive to floating-point rounding for pixels that fall right on the cylinder border (which cause the test to fail with some compiler optimizations that change the rounding of r*r)

    M ./tests/2D_convergence.cpp -1 +1

Tue Apr 21 18:55:34 EDT 2009  stevenj@alum.mit.edu
  * version bump

    M ./configure.ac -3 +4

Tue Apr 21 18:53:26 EDT 2009  stevenj@alum.mit.edu
  * silence compiler warning

    M ./src/sphere-quad.cpp -1 +1

Tue Apr 21 18:51:39 EDT 2009  stevenj@alum.mit.edu
  * tentative Meep 1.0 news

    M ./NEWS +24

Tue Apr 21 18:51:32 EDT 2009  stevenj@alum.mit.edu
  * fix Ardavan's name

    M ./AUTHORS -1 +1

Tue Apr 21 18:48:34 EDT 2009  stevenj@alum.mit.edu
  * disable subpixel averaging for pixels crossing metals

    M ./libctl/structure.cpp +30

Tue Apr 21 18:38:36 EDT 2009  stevenj@alum.mit.edu
  * alloc_f and figure_out_step_plan need to be public so that they can be called from fields::

    M ./src/meep.hpp -2 +3

Tue Apr 21 17:23:42 EDT 2009  hila@math.mit.edu
  * maxabs should be optional in integrate2, fixing broken scheme interface

    M ./src/meep.hpp -2 +2

Tue Apr 21 17:42:03 EDT 2009  stevenj@alum.mit.edu
  * cache trivial chi1inv in structure_chunk, and use it to allocate correct fields when require_component is called (in particular, fixing behavior in 2D when anisotropy couples xy and z)

    M ./src/anisotropic_averaging.cpp +3
    M ./src/fields.cpp -13 +64
    M ./src/meep.hpp -1 +6
    M ./src/sources.cpp -15
    M ./src/structure.cpp +17

Tue Apr 21 17:41:20 EDT 2009  stevenj@alum.mit.edu
  * bug fix in checks for trivial chi1inv

    M ./src/anisotropic_averaging.cpp -8 +12

Tue Apr 21 17:32:36 EDT 2009  stevenj@alum.mit.edu
  * hsrc no longer exists

    M ./autogen.sh -2

Thu Apr 16 19:14:36 EDT 2009  ardfar@mit.edu
  * NEWS synced with Steven's version (resolve merge conflict)

    M ./NEWS -1 +1

Thu Apr 16 19:10:54 EDT 2009  stevenj@alum.mit.edu
  * remove unused {stride/num}_{each/any}_direction vars

    M ./src/fields.cpp -13
    M ./src/meep.hpp -2
    M ./src/update_eh.cpp -6 +6

Thu Apr 16 18:59:26 EDT 2009  stevenj@alum.mit.edu
  * remove unused Haskell code generator

    M ./Makefile.am -23 +2
    M ./autogen.sh -2
    M ./configure.ac -27
    R ./hsrc/
    R ./hsrc/Complex.lhs
    R ./hsrc/Makefile.am
    R ./hsrc/StepGen.lhs
    R ./hsrc/YeeLattice.lhs
    R ./hsrc/step_d_gen.hs
    R ./hsrc/step_h_gen.hs
    R ./hsrc/update_e_from_d_gen.hs
    R ./hsrc/update_from_e_gen.hs
    M ./src/Makefile.am -11 +1

Thu Apr 16 18:50:34 EDT 2009  stevenj@alum.mit.edu
  * remove stride0/stride distinction -- stride0 should always be used

    M ./src/meep/vec.hpp -5 +4
    M ./src/vec.cpp -6 +5

Thu Apr  9 14:21:44 EDT 2009  stevenj@alum.mit.edu
  * fix merge conflict

    M ./src/step.cpp -1 +2

Thu Apr  9 14:16:52 EDT 2009  stevenj@fftw.org
  * some updates to phasein code, to use proper refcounting and to properly phasein polarizations; also use refcounting for fields_chunk copy constructor

    M! ./src/fields.cpp -4 +5
    M! ./src/meep.hpp -2 +2
    M! ./src/step.cpp -1
    M! ./src/structure.cpp -1 +7

Mon Apr  6 16:31:57 EDT 2009  stevenj@alum.mit.edu
  * add fields::integrate2 function for field-overlap integrals between two runs

    M ./libctl/meep.i +29
    M ./libctl/meep.scm.in +5
    M ./src/Makefile.am -4 +5
    M ./src/integrate.cpp -29 +29
    A ./src/integrate2.cpp
    M ./src/meep.hpp +18

Wed Mar 18 22:45:15 EDT 2009  stevenj@alum.mit.edu
  tagged meep-0.20.4


Tue Mar 17 19:28:01 EDT 2009  stevenj@alum.mit.edu
  * date NEWS for release

    M! ./NEWS -1 +1

Tue Apr  7 19:24:02 EDT 2009  ardfar@mit.edu
  * new anisotropic averaging with stable(r) timestepping

    M ./libctl/structure.cpp -74 +93
    M ./src/anisotropic_averaging.cpp -5 +11
    M ./src/h5file.cpp -1 +1
    M ./src/step_generic.cpp -33 +36
    M ./tests/2D_convergence.cpp -1 +1
    M ./tests/h5test.cpp -2 +2
    M ./tests/known_results.cpp -1 +1

Wed Mar 18 18:01:43 EDT 2009  ardfar@mit.edu
  * addition to anisotropic medium averaging to include case of fallback

    M ./libctl/structure.cpp -10 +39

Wed Mar 18 17:28:37 EDT 2009  ardfar@mit.edu
  * anisotropic media averaging in libctl frontend

    M ./libctl/meep.scm.in -2 +7
    M ./libctl/structure.cpp -71 +268

Thu Mar 12 22:20:02 EDT 2009  stevenj@alum.mit.edu
  * date NEWS for release

    M ./NEWS -1 +1

Tue Mar 10 14:46:38 EDT 2009  stevenj@alum.mit.edu
  * copyright year update to 2009

    M ./COPYRIGHT -1 +1
    M ./libctl/meep.scm.in -1 +1
    M ./src/bands.cpp -1 +1
    M ./src/bicgstab.cpp -1 +1
    M ./src/bicgstab.hpp -1 +1
    M ./src/boundaries.cpp -1 +1
    M ./src/control_c.cpp -1 +1
    M ./src/cw_fields.cpp -1 +1
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/fields.cpp -1 +1
    M ./src/grace.cpp -1 +1
    M ./src/h5fields.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/initialize.cpp -1 +1
    M ./src/integrate.cpp -1 +1
    M ./src/loop_in_chunks.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/meep/mympi.hpp -1 +1
    M ./src/meep/vec.hpp -1 +1
    M ./src/meep_internals.hpp -1 +1
    M ./src/monitor.cpp -1 +1
    M ./src/mpb.cpp -1 +1
    M ./src/mympi.cpp -1 +1
    M ./src/output_directory.cpp -1 +1
    M ./src/polarization.cpp -1 +1
    M ./src/sources.cpp -1 +1
    M ./src/sphere-quad.cpp -1 +1
    M ./src/step.cpp -1 +1
    M ./src/step_db.cpp -1 +1
    M ./src/structure.cpp -1 +1
    M ./src/time.cpp -1 +1
    M ./src/update_eh.cpp -1 +1
    M ./src/update_pols.cpp -1 +1
    M ./src/vec.cpp -1 +1
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/harmonics.cpp -1 +1
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Tue Mar 10 14:42:12 EDT 2009  stevenj@alum.mit.edu
  * version bump to 0.20.4 (beta)

    M ./NEWS +18
    M ./configure.ac -2 +2

Mon Feb  9 19:54:14 EST 2009  stevenj@alum.mit.edu
  * merged bug fix in writing strings with parallel HDF5

    M ./src/h5file.cpp -1 +1

Wed Nov 12 21:06:24 EST 2008  stevenj@fftw.org
  * bug fix in writing strings with parallel HDF5, thanks to Zheng Li for the bug report

    M! ./src/h5file.cpp -1 +1

Fri Jan 30 16:24:00 EST 2009  stevenj@alum.mit.edu
  * bug fix in cylindrical code, which was missing im/r term for pixels at 0.5*(delta r) from the origin

    M ./src/step_db.cpp -3 +3

Fri Jan 30 15:38:33 EST 2009  stevenj@alum.mit.edu
  * in initialize_field, update E/H if D/B was set

    M ./src/initialize.cpp +8

Tue Jan 13 17:11:58 EST 2009  mccauley@mit.edu
  * fixed divide_processors to use correct mygroup

    M ./src/mympi.cpp -5 +3

Tue Jan 13 13:06:12 EST 2009  stevenj@alum.mit.edu
  * fix divide_parallel stuff to compile

    M ./src/meep/mympi.hpp +1
    M ./src/mympi.cpp -3 +11

Tue Jan 13 13:04:29 EST 2009  stevenj@alum.mit.edu
  * fix to work properly with latest libtool

    M ./Makefile.am -1 +1
    M ./configure.ac +1

Fri Jan  9 17:44:04 EST 2009  stevenj@alum.mit.edu
  * hack to allow multiple FDTD simulations in parallel from the same MPI job

    M ./src/meep/mympi.hpp +5
    M ./src/mympi.cpp -35 +109

Tue Dec  9 16:20:26 EST 2008  stevenj@alum.mit.edu
  * bug fix (thanks Alejandro): when a non-integrated source is used with a conductivity, the 1/(1+cond) factor needs to be multiplied by the current amplitude to get second-order accuracy in the timestepping

    M ./src/step.cpp -6 +15

Thu Dec  4 16:09:02 EST 2008  stevenj@fftw.org
  * bug fix in writing strings with parallel HDF5, thanks to Zheng Li for the bug report

    M ./src/h5file.cpp -1 +1

Mon Jul 28 18:49:19 EDT 2008  stevenj@alum.mit.edu
  * bug fix in merged interface - libctl was returning eps=1 for eps-averaging?=false

    M ./libctl/structure.cpp -2 +2

Mon Jul 28 00:55:48 EDT 2008  stevenj@alum.mit.edu
  * check for correct MPB header

    M ./configure.ac -1 +1

Mon Jul 28 00:53:58 EDT 2008  stevenj@alum.mit.edu
  * eigenmode sources are mostly working, with a couple glitches (all-components sources don't work right, and including both H and E doesn't seem to give a 1-way source like it should)

    M ./libctl/meep.scm.in -13 +66
    M ./src/fields.cpp -1 +1
    M ./src/meep.hpp -3 +3
    M ./src/meep/vec.hpp +2
    M ./src/mpb.cpp -15 +66

Sun Jul 27 15:50:42 EDT 2008  stevenj@alum.mit.edu
  * include check that PML parameters are sensible (e.g. that total PML thickness is not greater than cell thickness, which seems to be a common mistake)

    M ./src/meep.hpp +1
    M ./src/structure.cpp +20

Sun Jul 27 14:25:03 EDT 2008  stevenj@alum.mit.edu
  * accept NULL for A() function in add_volume_source

    M ./src/sources.cpp -2 +2

Sun Jul 27 13:52:17 EDT 2008  stevenj@alum.mit.edu
  * use new mpb.h header

    M ./src/mpb.cpp -19 +20

Sun Jul 27 02:41:47 EDT 2008  stevenj@alum.mit.edu
  * initial stab at MPB-based eigenmode sources (still untested, but compiles)

    M ./configure.ac -1 +20
    M ./src/Makefile.am -1 +1
    M ./src/meep.hpp +9
    M ./src/meep/vec.hpp +1
    A ./src/mpb.cpp
    M ./src/vec.cpp +4

Sat Jul 26 19:12:33 EDT 2008  stevenj@alum.mit.edu
  * added src_time::set_frequency

    M ./src/meep.hpp +3

Sat Jul 26 17:06:19 EDT 2008  stevenj@alum.mit.edu
  * added new extra-materials input variable, so that you no longer have to use "dummy objects" to specify materials when using material-function types

    M ./TODO -4 +1
    M ./libctl/meep-ctl-swig.hpp +1
    M ./libctl/meep.scm.in -1 +6
    M ./libctl/structure.cpp -24 +31

Thu Jul 24 16:47:10 EDT 2008  stevenj@alum.mit.edu
  * merge 0.20.3 patch

    M ./libctl/Makefile.am -1 +1

Thu Jul 24 16:27:52 EDT 2008  stevenj@fftw.org
  tagged meep-0.20.3


Thu Jul 24 16:25:03 EDT 2008  stevenj@fftw.org
  * removed circular ctl-io.h dependency, bumped version to 0.20.3

    M! ./NEWS +5
    M! ./configure.ac -2 +2
    M! ./libctl/Makefile.am -1 +1

Thu Jul 24 01:10:47 EDT 2008  stevenj@alum.mit.edu
  * make it easy to switch Meep to single precision by changing one #define in meep.hpp

    M ./src/anisotropic_averaging.cpp -1 +1
    M ./src/bicgstab.cpp -21 +11
    M ./src/bicgstab.hpp -4 +6
    M ./src/boundaries.cpp -6 +6
    M ./src/cw_fields.cpp -16 +17
    M ./src/dft.cpp -6 +6
    M ./src/energy_and_flux.cpp -6 +6
    M ./src/fields.cpp -11 +11
    M ./src/h5fields.cpp -4 +4
    M ./src/h5file.cpp -11 +13
    M ./src/integrate.cpp -2 +2
    M ./src/meep.hpp -19 +38
    M ./src/meep_internals.hpp -9 +10
    M ./src/monitor.cpp -1 +1
    M ./src/mympi.cpp +13
    M ./src/polarization.cpp -7 +7
    M ./src/step_db.cpp -16 +16
    M ./src/step_generic.cpp -11 +12
    M ./src/structure.cpp -22 +22
    M ./src/update_eh.cpp -8 +8
    M ./src/update_pols.cpp -3 +3
    M ./tests/cylindrical.cpp -1 +3
    M ./tests/h5test.cpp -6 +5
    M ./tests/harmonics.cpp -2 +3
    M ./tests/known_results.cpp -1 +2
    M ./tests/pml.cpp -1 +1

Wed Jul 23 22:28:07 EDT 2008  stevenj@alum.mit.edu
  * added libctl front-end support for dispersive mu

    M ./libctl/meep.scm.in -1 +3
    M ./libctl/structure.cpp -6 +18
    M ./src/meep.hpp -2 +3
    M ./src/polarization.cpp -1 +1

Wed Jul 23 22:00:27 EDT 2008  stevenj@alum.mit.edu
  * fixed libctl front-end

    M ./libctl/Makefile.am -1 +1
    M ./libctl/meep.scm.in -3 +12
    M ./libctl/structure.cpp -86 +130
    M ./src/anisotropic_averaging.cpp -10 +14
    M ./src/meep.hpp +3
    M ./src/meep/vec.hpp -3 +3

Wed Jul 23 18:14:51 EDT 2008  stevenj@alum.mit.edu
  * initial merge of mu and epsilon support
  
  Merge of update_e_from_d and update_h_from_b, and unified support for
  electric and magnetic susceptibilities.  make check passes, but the
  libctl front-end has not been updated yet.   Magnetic materials now
  support anisotropic averaging, material dispersion, and 
  nonlinearity.
  
  Instead of invmu and inveps arrays, we now have a single chi1inv array
  that stores 1/(1+chi1) for the first-order susceptibilities chi1.  The
  material_function::meaneps function has been replaced by a function
  material_function::eff_chi1inv_row that is used for both mu and epsilon
  and returns a row of the effective-medium 1/(1+chi1) tensor.  This has
  the important consequence that user-specified anisotropic materials are
  now possible.  Also, user-controlled effective-medium averaging is 
  possible, and in particular we can do the proper Kottke averaging for
  anisotropic media.
  
  Also, some (diagonal) anisotropy is now supported in the chi2 and chi3
  nonlinearities.

     ./src/update_e_from_d.cpp -> ./src/update_eh.cpp
     ./src/update_from_e.cpp -> ./src/update_pols.cpp
    M ./doc/polaritonbands.tex -3 +1
    M ./src/Makefile.am -2 +2
    M ./src/anisotropic_averaging.cpp -232 +106 r1
    M ./src/boundaries.cpp -10 +13
    M ./src/cw_fields.cpp -15 +10
    M ./src/energy_and_flux.cpp -4 +6
    M ./src/fields.cpp -21 +27
    M ./src/h5fields.cpp -6 +7 r1
    M ./src/initialize.cpp -37 +1
    M ./src/integrate.cpp -10 +11 r1
    M ./src/meep.hpp -61 +74 r1
    M ./src/meep/vec.hpp -4 +11
    M ./src/meep_internals.hpp -3 +3
    M ./src/monitor.cpp -74 +68 r1
    M ./src/polarization.cpp -118 +49
    M ./src/sources.cpp -6 +6 r1
    M ./src/step.cpp -44 +45
    M ./src/step_generic.cpp r1
    M ./src/structure.cpp -103 +97 r1
    M ./src/update_eh.cpp -51 +87 r1
    R ./src/update_h_from_b.cpp
    M ./src/update_pols.cpp -10 +13
    M ./tests/convergence_cyl_waveguide.cpp -1 +5
    M ./tests/known_results.cpp -2 +2

Mon Jul 21 19:40:53 EDT 2008  stevenj@fftw.org
  tagged meep-0.20.2


Mon Jul 21 19:40:03 EDT 2008  stevenj@fftw.org
  * fix to work with Guile 1.6.x

    M ./NEWS +5
    M ./configure.ac -2 +2
    M ./libctl/meep.scm.in -1 +1

Sun Jul 20 14:35:23 EDT 2008  stevenj@fftw.org
  tagged meep-0.20.1


Sun Jul 20 14:35:13 EDT 2008  stevenj@fftw.org
  * fix libctl dependencies so that parallel builds work

    M ./NEWS +2
    M ./libctl/Makefile.am -5 +9

Sun Jul 20 13:51:21 EDT 2008  stevenj@fftw.org
  * install correct pkgconfig file (meep_mpi.pc) for MPI version; thanks to Majid Sodagar for the bug report; bump version to 0.20.1

     ./meep.pc.in -> ./meep-pkgconfig.in
    M ./Makefile.am -2 +5
    M ./NEWS +7
    M ./configure.ac -3 +3
    M ./meep-pkgconfig.in -1 +1

Sun Jul 20 12:10:59 EDT 2008  stevenj@fftw.org
  * more robust handling of nested synchronizations via count; also, allow (expensive) synchronized timestepping if user timesteps inside a synchronized-field state

    M ./src/energy_and_flux.cpp -4 +6
    M ./src/fields.cpp -2 +1
    M ./src/meep.hpp -1 +1
    M ./src/step.cpp -1 +14

Sat Jul 19 20:02:00 EDT 2008  stevenj@fftw.org
  * typo

    M ./NEWS -2 +2

Sat Jul 19 19:56:20 EDT 2008  stevenj@fftw.org
  tagged meep-0.20


Sat Jul 19 19:53:58 EDT 2008  stevenj@fftw.org
  * added perfect-magnetic/electric-conductor predefined materials; epsilon now defaults to 1 for the medium

    M ./NEWS +6
    M ./libctl/meep.scm.in -1 +3

Sat Jul 19 13:28:06 EDT 2008  stevenj@fftw.org
  * pml test with length is now a little more stringent (checks that dependence is really 1/L^6, and not better)

    M ./tests/pml.cpp -27 +11

Sat Jul 19 12:39:34 EDT 2008  stevenj@fftw.org
  * make sync/restore magnetic fields idempotent, as synchronizations might be nested (especially in libctl UI)

    M ./src/energy_and_flux.cpp +4
    M ./src/fields.cpp +3
    M ./src/meep.hpp +1
    M ./src/step.cpp +2

Fri Jul 18 19:58:06 EDT 2008  stevenj@fftw.org
  * clarification

    M ./NEWS -2 +3

Fri Jul 18 19:49:47 EDT 2008  stevenj@fftw.org
  * copyright year update to 2008

    M ./COPYRIGHT -1 +1
    M ./NEWS -1 +1
    M ./libctl/meep.scm.in -1 +1
    M ./src/bands.cpp -1 +1
    M ./src/bicgstab.cpp -1 +1
    M ./src/bicgstab.hpp -1 +1
    M ./src/boundaries.cpp -1 +1
    M ./src/control_c.cpp -1 +1
    M ./src/cw_fields.cpp -1 +1
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/fields.cpp -1 +1
    M ./src/grace.cpp -1 +1
    M ./src/h5fields.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/initialize.cpp -1 +1
    M ./src/integrate.cpp -1 +1
    M ./src/loop_in_chunks.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/meep/mympi.hpp -1 +1
    M ./src/meep/vec.hpp -1 +1
    M ./src/meep_internals.hpp -1 +1
    M ./src/monitor.cpp -1 +1
    M ./src/mympi.cpp -1 +1
    M ./src/output_directory.cpp -1 +1
    M ./src/polarization.cpp -1 +1
    M ./src/sources.cpp -1 +1
    M ./src/sphere-quad.cpp -1 +1
    M ./src/step.cpp -1 +1
    M ./src/step_db.cpp -1 +1
    M ./src/structure.cpp -1 +1
    M ./src/time.cpp -1 +1
    M ./src/update_e_from_d.cpp -1 +1
    M ./src/update_from_e.cpp -1 +1
    M ./src/update_h_from_b.cpp -1 +1
    M ./src/vec.cpp -1 +1
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/harmonics.cpp -1 +1
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Fri Jul 18 19:46:30 EDT 2008  stevenj@fftw.org
  * missing string.h header (for gcc 4.3; see debian bug #455289)

    M ./src/step_db.cpp +1
    M ./src/update_e_from_d.cpp +2
    M ./src/update_h_from_b.cpp +17

Fri Jul 18 18:58:53 EDT 2008  stevenj@fftw.org
  * fix PML test to test whether reflection converges to zero with increasing resolution

    M ./tests/pml.cpp -201 +127

Fri Jul 18 18:18:23 EDT 2008  stevenj@fftw.org
  * honor quiet flag in structure.cpp

    M ./src/structure.cpp -3 +4

Fri Jul 18 17:17:40 EDT 2008  stevenj@fftw.org
  * updated archflag guesses from fftw

    M ./m4/ax_gcc_archflag.m4 -24 +31

Fri Jul 18 17:11:06 EDT 2008  stevenj@fftw.org
  * 0.20 release date

    M ./NEWS -1 +1

Fri Jul 18 17:09:24 EDT 2008  stevenj@fftw.org
  * updated TODO

    M ./TODO -8 +2

Fri Jul 18 16:58:59 EDT 2008  ardavan@mit.edu
  * libctl 3.0.3 is required, to support boolean object properties

    M ./configure.ac -1 +1

Fri Jul 18 16:34:14 EDT 2008  ardavan@mit.edu
  * check for libctl in /usr/share/libctl3

    M ./configure.ac +3

Fri Jul 18 14:00:57 EDT 2008  stevenj@fftw.org
  * Hx source seems to couple better to modes than Ez src, gives more reliable results for ring example

    M ./examples/ring.ctl -1 +1

Fri Jul 18 13:46:21 EDT 2008  stevenj@fftw.org
  * make is-integrated?=false the default for sources

    M ./NEWS -1 +2
    M ./libctl/meep.scm.in -1 +1

Fri Jul 18 13:12:17 EDT 2008  stevenj@fftw.org
  * made 1d symmetry tests a little bigger so that the tests are big enough to run on 8 processors

    M ./tests/symmetry.cpp -2 +2

Fri Jul 18 12:54:01 EDT 2008  stevenj@fftw.org
  * tolerance was a little too low in cylindrical.cpp for new code (where the roundoff error depends on the splitting)

    M ./tests/cylindrical.cpp -2 +2

Fri Jul 18 12:52:20 EDT 2008  stevenj@fftw.org
  * bug fix in and_to_all/or_to_all - was passing wrong type (bool instead of int); also eliminate a couple of unnecessary memcpy's

    M ./src/mympi.cpp -7 +14

Wed Jul 16 18:51:41 EDT 2008  stevenj@fftw.org
  * slight code simplification

    M ./src/structure.cpp -2 +4

Wed Jul 16 18:40:52 EDT 2008  stevenj@fftw.org
  * typo in comment

    M ./src/boundaries.cpp -1 +1

Wed Jul 16 18:29:56 EDT 2008  stevenj@fftw.org
  * added synchronized-magnetic step func

    M ./NEWS +4
    M ./libctl/meep.scm.in +8

Tue Jul 15 22:51:43 EDT 2008  stevenj@fftw.org
  * version bump

    M ./NEWS +32
    M ./configure.ac -2 +2

Tue Jul 15 22:04:35 EDT 2008  stevenj@fftw.org
  * use master_printf rather than printf in tests

    M ./tests/cylindrical.cpp -11 +11
    M ./tests/flux.cpp -4 +4
    M ./tests/h5test.cpp -1 +1
    M ./tests/physical.cpp -2 +2

Tue Jul 15 22:03:55 EDT 2008  stevenj@fftw.org
  * fix deadlock bug in chunk connection when H is allocated on some processes but not on others

    M ./src/step.cpp -1
    M ./src/update_h_from_b.cpp +4

Mon Jun 30 17:08:02 EDT 2008  ardfar@mit.edu
  * added PML test

    M ./tests/Makefile.am -1 +1
    A ./tests/pml.cpp

Mon Jun 30 18:33:33 EDT 2008  stevenj@alum.mit.edu
  * allow user-specified PML profile function and asymptotic (round-trip) reflection

    M ./libctl/meep.scm.in -1 +3
    M ./libctl/structure.cpp -23 +59
    M ./src/meep.hpp -8 +19
    M ./src/structure.cpp -13 +17

Mon Jun 23 23:09:49 EDT 2008  stevenj@alum.mit.edu
  * added output-bfield etc.

    M ./libctl/meep.scm.in +1

Mon Jun 23 19:19:37 EDT 2008  stevenj@alum.mit.edu
  * slight optimization

    M ./src/step_generic.cpp -3 +3

Mon Jun 23 19:02:01 EDT 2008  stevenj@alum.mit.edu
  * use some clever/ugly macros to greatly speed up ksig[] index calculation in the PML loops (makes a significant difference in small benchmarks)

    M ./src/step_generic.cpp -50 +34

Mon Jun 23 18:20:19 EDT 2008  stevenj@alum.mit.edu
  * a few small optimizations (factoring out siginv[k],  special-casing the most common loop) in update_EDHB

    M ./src/step_generic.cpp -13 +32

Mon Jun 23 17:36:03 EDT 2008  stevenj@alum.mit.edu
  * tried using "restrict" keyword to speed things up, but annoying gcc actually slows things down!

    M ./configure.ac +7
    M ./src/step_generic.cpp -22 +27

Mon Jun 23 17:11:40 EDT 2008  stevenj@alum.mit.edu
  * fixed a typo in the PML offset calculation; this bug apparently doesn't affect the results, but I'm not sure why

    M ./src/step_generic.cpp -3 +3

Mon Jun 23 16:06:45 EDT 2008  stevenj@alum.mit.edu
  * optimization - delete offdiagonal inveps when == 0

    M ./src/anisotropic_averaging.cpp -3 +18

Mon Jun 23 15:22:00 EDT 2008  stevenj@alum.mit.edu
  * fix some floating-point thresholds

    M ./tests/cylindrical.cpp -2 +2

Mon Jun 23 14:53:08 EDT 2008  stevenj@alum.mit.edu
  * fixed solve_cw, re-enable solve_cw in physical.cpp

    M ./src/cw_fields.cpp -25 +80
    M ./src/meep.hpp -4 +4
    M ./src/step.cpp -24
    M ./src/update_e_from_d.cpp -3 +9
    M ./tests/physical.cpp -22 +18

Sat Jun 21 18:30:29 EDT 2008  stevenj@alum.mit.edu
  * fix bug in figuring out curl components in 2d, introduced by cylindrical patch; bypass cw_solve in physical.cpp for now ... make check now passes again!!

    M ./src/fields.cpp -1 +2
    M ./tests/physical.cpp +10

Sat Jun 21 01:56:19 EDT 2008  stevenj@alum.mit.edu
  * verified that changes in known_results were due to changes in PML, and that the new results converge to the old ones as the PML thickens; updated numbers so that known_results passes again

    M ./tests/known_results.cpp -8 +9

Sat Jun 21 01:21:55 EDT 2008  stevenj@alum.mit.edu
  * new value for polariton_energy known_result - difference is due to new scheme for synchronizing magnetic fields (I verified that switching back to the old synchronization gives the old result again, so it's not the new timestepping)

    M ./tests/known_results.cpp -1 +1

Fri Jun 20 21:29:24 EDT 2008  stevenj@alum.mit.edu
  * I'm convinced that the old Meep had a bug in its update code for Dz at r=0 for m=0, where it was off by a factor of 4 (this effectively multipled epsilon by 4 for one pixel at r=0 for m==0, which causesd only small errors in the results, and still converged, so it went unnoticed)

    M ./src/step_db.cpp -1 +1

Fri Jun 20 21:19:49 EDT 2008  stevenj@alum.mit.edu
  * lower tolerance (from zero) in cylindrical.cpp -- because of the new way the (1/r) d(r*f)/dr derivative is computed via a cumsum, the roundoff error depends on the splitting in the r direction

    M ./tests/cylindrical.cpp -2 +2

Fri Jun 20 18:50:53 EDT 2008  stevenj@alum.mit.edu
  * fixed some bugs in step_db for Dcyl (wrong radius used at one point, and also treat negative m properly...the latter problem being a bug in the previous Meep too)

    M ./src/step_db.cpp -7 +8

Fri Jun 20 18:49:34 EDT 2008  stevenj@alum.mit.edu
  * use new LOOP_OVER_VOL_OWNED0 in step_curl, to avoid the r=0 origin which gets special treatment in Dcyl

    M ./src/meep/vec.hpp +10
    M ./src/step_generic.cpp -8 +8
    M ./src/vec.cpp -1 +1

Fri Jun 20 15:42:08 EDT 2008  stevenj@alum.mit.edu
  * some fixes; m=0 case now matches old code, and also mmatches if we manually multiply m terms by zero in both programs, so eremaining bug is in im/r terms

    M ./src/step_db.cpp -20 +32

Fri Jun 20 03:27:38 EDT 2008  stevenj@alum.mit.edu
  * initial stab at re-implementing cylindrical support; compiles, and flux.cpp passes, but cylindrical.cpp still fails

    M ./src/anisotropic_averaging.cpp -4 +4
    M ./src/fields.cpp -3 +13
    M ./src/meep.hpp +3
    M ./src/meep/vec.hpp +9
    M ./src/step_db.cpp -26 +159
    M ./src/step_generic.cpp -1 +1
    M ./src/structure.cpp -1 +1

Thu Jun 19 20:54:57 EDT 2008  stevenj@alum.mit.edu
  * unified step_d and step_b into step_db; also, changed d_minus_p to more-generic f_minus_p (both for step_db and in preparation for more unification of magnetic and electric code)

     ./src/step_d.cpp -> ./src/step_db.cpp
    M ./src/Makefile.am -1 +1
    M ./src/energy_and_flux.cpp -4 +6 r1
    M ./src/fields.cpp -9 +7 r1
    M ./src/meep.hpp -5 +2 r1
    M ./src/meep/vec.hpp -1 +1
    M ./src/step.cpp -2 +2
    R ./src/step_b.cpp
    M ./src/step_db.cpp -13 +22 r1
    M ./src/update_e_from_d.cpp -12 +16 r1

Thu Jun 19 20:54:08 EDT 2008  stevenj@alum.mit.edu
  * silence compiler warning

    M ./tests/symmetry.cpp -2 +2

Thu Jun 19 20:34:04 EDT 2008  stevenj@alum.mit.edu
  * when copying fields_chunks, be careful not to duplicate H==B fields

    M ./src/fields.cpp -5 +11

Thu Jun 19 20:17:01 EDT 2008  stevenj@alum.mit.edu
  * greatly simplified step_d and step_h by allowing step_curl to swap its arguments if g1 is NULL

    M ./src/step_b.cpp -27 +3
    M ./src/step_d.cpp -27 +4
    M ./src/step_generic.cpp -4 +9

Thu Jun 19 20:15:51 EDT 2008  stevenj@alum.mit.edu
  * added FOR_FT_COMPONENTS in preparation for more generic stepping functions

    M ./src/meep/vec.hpp +3
    M ./src/vec.cpp +10

Thu Jun 19 19:39:28 EDT 2008  stevenj@alum.mit.edu
  * bug fix - B is a pseudovector too (not just H), and use B*H for H_EnergyDensity derived component

    M ./src/vec.cpp -2 +2

Thu Jun 19 18:43:46 EDT 2008  stevenj@alum.mit.edu
  * naming consistency (H/E sources vs. B/D sources); also, bug fix in "D" sources, which were supposed to be multiplied by eps but appparently weren't (& implemented similar "B" sources multiplied by mu)

    M ./src/cw_fields.cpp r1
    M ./src/fields.cpp r2
    M ./src/meep.hpp r2
    M ./src/sources.cpp -3 +7 r2
    M ./src/step.cpp -2 +2 r2
    M ./src/update_e_from_d.cpp r1

Thu Jun 19 18:16:54 EDT 2008  stevenj@alum.mit.edu
  * send H, not B, when H==B

    M ./src/boundaries.cpp -15 +17

Thu Jun 19 18:04:45 EDT 2008  stevenj@alum.mit.edu
  * in preparation for Dcyl, use function for cyclic shifts of directions

    M ./src/meep/vec.hpp +11
    M ./src/monitor.cpp -6 +2
    M ./src/step_b.cpp -4 +6
    M ./src/step_d.cpp -4 +5
    M ./src/structure.cpp -1 +1
    M ./src/update_e_from_d.cpp -8 +8
    M ./src/update_h_from_b.cpp -8 +8

Thu Jun 19 18:03:48 EDT 2008  stevenj@alum.mit.edu
  * can't force_consistency for H, only for B

    M ./src/cw_fields.cpp -4 +4
    M ./src/step.cpp -2 +1

Thu Jun 19 17:41:08 EDT 2008  stevenj@alum.mit.edu
  * handle u == NULL in update_EDHB

    M ./src/step_generic.cpp -1 +3

Thu Jun 19 15:58:57 EDT 2008  stevenj@alum.mit.edu
  * use HUGE_VAL for infinity, since this is in c90 standard and in C++, and is equivalent to INFINITY on IEEE754 systems; don't define "infinity" twice in meep.scm

    M ./libctl/meep.scm.in -2
    M ./src/meep.hpp -5 +1

Thu Jun 19 15:49:12 EDT 2008  stevenj@alum.mit.edu
  * implement output-mu and related functions to output/integrate Permeability

    M ./libctl/meep.scm.in +1
    M ./src/h5fields.cpp -4 +34
    M ./src/integrate.cpp -7 +37
    M ./src/loop_in_chunks.cpp +2
    M ./src/monitor.cpp -1 +4

Thu Jun 19 15:48:50 EDT 2008  stevenj@alum.mit.edu
  * whoops, typo (set_mu wrote to inveps instead of invmu)

    M ./src/anisotropic_averaging.cpp -2 +2

Thu Jun 19 02:30:32 EDT 2008  stevenj@alum.mit.edu
  * fix a couple of memory leaks

    M ./src/boundaries.cpp +1
    M ./src/dft.cpp +2

Thu Jun 19 01:17:18 EDT 2008  stevenj@alum.mit.edu
  * only allocate separate B and H fields if necessary + many related changed
  
  now, unnecessary H fields are set == B at the pointer level; H is 
  allocated lazily, just before needed, in PML regions or when mu!=1,
  to guarantee consistency
  
  allow invmu to be NULL
  allow user-specification of mu != 1 (although no averaging is done yet)
  
  don't use PML equations if unnecessary - in the PML regions, some 
  components may still be updated with the ordinary equations
  
  fix potential bug in update_EDHB where the PML equations might not have 
  been used if g1 and g2 were swapped, since that also swaps sigsize_dsig1 
  
  the PML equations in nonlinear materials now use the fields, not the 
  fields multiplied by (1+sigma) etc., to determine the nonlinear 
  coefficient, which seems more correct (and allows us to switch to the 
  non-PML equations in more cases)
  

    M ./src/anisotropic_averaging.cpp -1 +7
    M ./src/boundaries.cpp -2 +21
    M ./src/energy_and_flux.cpp -1 +3
    M ./src/fields.cpp -1 +10
    M ./src/meep.hpp -1 +1
    M ./src/meep/mympi.hpp +2
    M ./src/mympi.cpp +14
    M ./src/step_generic.cpp -19 +29
    M ./src/structure.cpp -1 +1
    M ./src/update_h_from_b.cpp -19 +38

Thu Jun 19 01:12:53 EDT 2008  stevenj@alum.mit.edu
  * in mix_with, handle case where two structures don't have the same inveps/invmu/conductivity allocated

    M ./src/structure.cpp -10 +47

Thu Jun 19 01:04:26 EDT 2008  ardavan@mit.edu
  * updated numbers in harmonics test (slightly changed by new PML)

    M ./tests/harmonics.cpp -4 +4

Thu Jun 19 00:12:11 EDT 2008  stevenj@alum.mit.edu
  * silence compiler warnings

    M ./src/energy_and_flux.cpp -1 +1
    M ./src/integrate.cpp +1

Wed Jun 18 22:14:24 EDT 2008  stevenj@alum.mit.edu
  * silence some compiler warnings

    M ./src/h5file.cpp -4 +3

Wed Jun 18 21:48:59 EDT 2008  stevenj@alum.mit.edu
  * have_component should return true if *any* of the owned chunks have the component, not just the first owned chunk -- this doesn't seem to have caused problems in the past, but it 's a bit unsafe

    M ./src/fields.cpp -2 +2

Wed Jun 18 18:00:46 EDT 2008  stevenj@alum.mit.edu
  * compute magnetic energy as B*H, not |H|^2

    M ./src/energy_and_flux.cpp -2 +3

Wed Jun 18 17:18:50 EDT 2008  stevenj@alum.mit.edu
  * don't use conductivity and chi2/chi3 in chunks where they are zero

    M ./src/anisotropic_averaging.cpp -30
    M ./src/structure.cpp -4 +63

Wed Jun 18 17:16:51 EDT 2008  stevenj@alum.mit.edu
  * bug fix in new PML: f_prev should be D-P, not D

    M ./src/energy_and_flux.cpp +3
    M ./src/step_d.cpp -5 +7

Wed Jun 18 01:17:37 EDT 2008  stevenj@alum.mit.edu
  * added conductivity & mu support to libctl (although   mu support still needs to be enabled in C++); conductivity seems to work in simple tests

    M ./libctl/meep.scm.in -1 +10
    M ./libctl/structure.cpp -69 +142
    M ./src/anisotropic_averaging.cpp -20 +19
    M ./src/meep.hpp -3 +7
    M ./src/structure.cpp +3

Wed Jun 18 00:45:35 EDT 2008  stevenj@alum.mit.edu
  * fix (harmless) compiler warnings

    M ./src/h5fields.cpp -4 +6

Tue Jun 17 23:43:39 EDT 2008  stevenj@alum.mit.edu
  * initial stab at general conductivity support (diagonal anisotropic B or D conductors) - untested (but compiles and shouldn't affect programs not using the conducitivity)

    M ./src/anisotropic_averaging.cpp -1 +31
    M ./src/meep.hpp -21 +12
    M ./src/meep_internals.hpp +24
    M ./src/step.cpp +3
    M ./src/step_b.cpp -5 +10
    M ./src/step_d.cpp -5 +10
    M ./src/step_generic.cpp -19 +63
    M ./src/structure.cpp -27 +83

Tue Jun 17 23:42:49 EDT 2008  stevenj@alum.mit.edu
  * error thresholds were too low (passed on x86 in extended-precision mode, but not on x86_64 with ordinary double precision); also, work around weird gcc problem with array of fields/structures

    M ./tests/symmetry.cpp -23 +27

Tue Jun 17 23:41:47 EDT 2008  stevenj@alum.mit.edu
  * don't forget to call set_volume in set_mu

    M ./src/anisotropic_averaging.cpp -1 +4

Tue Jun 17 23:41:05 EDT 2008  stevenj@alum.mit.edu
  * work around mysterious valgrind complaint about uninitialized var when running bragg_transmission.dac; also, slight code cleanup (PASTE macro was unnecessary)

    M ./src/step_generic.cpp -12 +22

Tue Jun 17 18:04:53 EDT 2008  stevenj@alum.mit.edu
  * slight clarification (behavior unchanged)

    M ./src/structure.cpp -1 +1

Tue Jun 17 17:22:39 EDT 2008  stevenj@alum.mit.edu
  * remove redundnant test

    M ./src/step_generic.cpp -12 +6

Tue Jun 17 17:05:44 EDT 2008  stevenj@alum.mit.edu
  * use macros to reduce cut-and-paste in update_EDHB, and fix several bugs in index computations

    M ./src/step_generic.cpp -172 +82

Tue Jun 17 16:52:16 EDT 2008  stevenj@alum.mit.edu
  * avoid high-symmetry monitor point

    M ./tests/2D_convergence.cpp -1 +1

Tue Jun 17 15:49:34 EDT 2008  stevenj@alum.mit.edu
  * remove unused variables/computations

    M ./src/step_generic.cpp -8

Tue Jun 17 15:18:54 EDT 2008  ardfar@mit.edu
  * added g2 && !g1 case for non-PML nonlinear

    M ./src/step_generic.cpp +8

Tue Jun 17 14:43:25 EDT 2008  ardfar@mit.edu
  * added two more missing files

    A ./src/step_b.cpp
    A ./src/update_h_from_b.cpp

Tue Jun 17 14:42:57 EDT 2008  ardfar@mit.edu
  * added step_generic

    A ./src/step_generic.cpp

Tue Jun 17 11:50:14 EDT 2008  ardfar@mit.edu
  * set default Rabs to 1e-15 (todo: make this user-configurable, along with PML profile)

    M ./src/structure.cpp -1 +1

Tue Jun 17 11:49:50 EDT 2008  ardfar@mit.edu
  * handle off-diagonal inveps

    M ./src/update_e_from_d.cpp -2 +2

Tue Jun 17 11:39:53 EDT 2008  ardfar@mit.edu
  * optimization - only call average_with_backup if is_mine

    M ./src/energy_and_flux.cpp -4 +5

Sun Jun 15 22:09:54 EDT 2008  ardfar@mit.edu
  * lower tolerance still works

    M ./tests/two_dimensional.cpp -1 +1

Thu Jun 12 20:15:18 EDT 2008  ardfar@mit.edu
  * tolerances were too low (the energy numbers fluctuate a little from timestep to timestep, and the old tolerance was right on the borderline)

    M ./tests/two_dimensional.cpp -1 +1

Thu Jun 12 20:07:07 EDT 2008  stevenj@fftw.org
  * fixed relative phase of E and H sources (which were wrong by half a timestep); also, tolerance in two_dimensional.cpp was too low (changing the runtime by half a timestep changed the energy by more than the tolerance for the decay rate)

    M ./src/sources.cpp +3
    M ./src/step.cpp -2 +4
    M ./tests/two_dimensional.cpp -1 +1

Thu Jun 12 19:02:24 EDT 2008  ardfar@mit.edu
  * resolve conflicting patch

    M ./src/update_e_from_d.cpp -60 +12

Tue Nov 13 15:27:02 EST 2007  stevenj@fftw.org
  tagged 0.10.1


Thu Aug 16 13:33:34 EDT 2007  stevenj@fftw.org
  * version bump to 0.10.1 (not final until tag!)

    M ./configure.ac -2 +2

Wed Aug 15 22:41:37 EDT 2007  stevenj@fftw.org
  * update_e_from_d should only update owned E's

    M! ./src/update_e_from_d.cpp -12 +60

Thu Jun 12 18:33:34 EDT 2008  ardfar@mit.edu
  * separate f_prev and f_backup, add synchronize_magnetic_fields function

    M ./src/cw_fields.cpp -2 +2
    M ./src/energy_and_flux.cpp -53 +46
    M ./src/fields.cpp +4
    M ./src/meep.hpp -6 +9
    M ./src/step_d.cpp -1 +6
    M ./src/update_e_from_d.cpp -1 +1

Thu Jun 12 15:23:41 EDT 2008  ardfar@mit.edu
  * forgot to record this

    M ./src/structure.cpp -18

Thu Jun 12 15:22:03 EDT 2008  ardfar@mit.edu
  * slight cleanup

    M ./src/meep.hpp -3 +1

Thu Jun 12 14:44:04 EDT 2008  ardfar@mit.edu
  * big patch to rewrite timestepping and PML, and add mu/B

    M ./src/Makefile.am -12 +3
    M ./src/anisotropic_averaging.cpp -1 +16
    M ./src/cw_fields.cpp -29 +24
    M ./src/energy_and_flux.cpp -35 +50
    M ./src/fields.cpp -43 +4
    M ./src/initialize.cpp +1
    M ./src/meep.hpp -15 +45
    M ./src/meep/vec.hpp -19 +24
    M ./src/step.cpp -8 +16
    M ./src/step_d.cpp -150 +40
    R ./src/step_h.cpp
    M ./src/structure.cpp -69 +93
    M ./src/update_e_from_d.cpp -152 +24
    M ./src/vec.cpp -1 +7
    M ./tests/harmonics.cpp -7 +7
    M ./tests/symmetry.cpp -2

Fri Apr 25 15:42:38 EDT 2008  stevenj@fftw.org
  * is-integrated?, not is-integrated

    M ./libctl/meep.scm.in -4 +4

Thu Apr 24 21:08:03 EDT 2008  stevenj@fftw.org
  * added store-polarization-energy? input variable to support that feature of the polarizations

    M ./libctl/meep.scm.in -3 +5

Thu Apr 24 21:01:49 EDT 2008  stevenj@fftw.org
  * disable slow, undocumented saturable-absorber support by default; use simple hand-written alternative in update_from_e.cpp; computingg polarization energy is now optional (to save memory and time since it is rarely used in practice)

    M ./configure.ac +7
    M ./src/fields.cpp -7 +8
    M ./src/meep.hpp -3 +3
    M ./src/meep_internals.hpp -3 +4
    M ./src/polarization.cpp -4 +11
    M ./src/update_e_from_d.cpp -11 +13
    M ./src/update_from_e.cpp -1 +34
    M ./tests/known_results.cpp -1 +5

Thu Apr 24 20:55:17 EDT 2008  stevenj@fftw.org
  * typo

    M ./configure.ac -1 +1

Thu Apr 24 20:54:49 EDT 2008  stevenj@fftw.org
  * fix thermal_energy to include all polarization contributions

    M ./src/energy_and_flux.cpp -4 +5

Thu Apr 24 20:54:26 EDT 2008  stevenj@fftw.org
  * fixed cw_solve to work with recent patch for non-integrated currents

    M ./src/cw_fields.cpp -1 +1
    M ./src/meep.hpp -2 +2
    M ./src/step.cpp -5 +6

Thu Apr 24 20:40:32 EDT 2008  stevenj@fftw.org
  * disable checks for floating-point exceptions in debugging mode, as some versions of g++ seem to have spurious exceptions in the complexx number routines(?)

    M ./src/mympi.cpp -1 +1

Sun Apr  6 20:28:31 EDT 2008  stevenj@fftw.org
  * support HDF5 1.8

    M ./src/h5file.cpp +4

Sun Apr  6 13:56:43 EDT 2008  stevenj@fftw.org
  * more robust link check for guile when guile-config not available

    M ./configure.ac -1 +2

Sun Apr  6 13:54:52 EDT 2008  stevenj@fftw.org
  * no way to test how to activate readline when cross-compiling

    M ./configure.ac +2

Sun Jan  6 16:37:49 EST 2008  stevenj@fftw.org
  * add to TODO

    M ./TODO +6

Fri Dec 21 20:05:17 EST 2007  stevenj@fftw.org
  * fix h5 filename timestamps for cases where dt is very small or very large (just use the integer time step number in that case)

    M ./src/h5fields.cpp -1 +6

Fri Dec 14 14:19:29 EST 2007  stevenj@fftw.org
  * check for ctl.h in /usr/include/ctl/, which is the default under Fedora (grrr)

    M ./configure.ac -1 +15
    M ./libctl/Makefile.am -1 +1

Thu Dec  6 20:03:02 EST 2007  stevenj@fftw.org
  * added is_integrated option to src_time to allow non-integrated E sources and non-integrated custom sources

    M ./libctl/meep.scm.in -18 +25
    M ./src/meep.hpp -2 +17
    M ./src/step.cpp -4 +2
    M ./src/update_e_from_d.cpp -2 +9

Tue Nov 13 15:15:27 EST 2007  stevenj@fftw.org
  * release date for 0.10.1

    M ./NEWS -1 +1

Tue Nov 13 15:13:59 EST 2007  stevenj@fftw.org
  * update copyright year to 2007

    M ./COPYRIGHT -1 +1
    M ./libctl/meep.scm.in -1 +1
    M ./src/bands.cpp -1 +1
    M ./src/bicgstab.cpp -1 +1
    M ./src/bicgstab.hpp -1 +1
    M ./src/boundaries.cpp -1 +1
    M ./src/control_c.cpp -1 +1
    M ./src/cw_fields.cpp -1 +1
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/fields.cpp -1 +1
    M ./src/grace.cpp -1 +1
    M ./src/h5fields.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/initialize.cpp -1 +1
    M ./src/integrate.cpp -1 +1
    M ./src/loop_in_chunks.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/meep/mympi.hpp -1 +1
    M ./src/meep/vec.hpp -1 +1
    M ./src/meep_internals.hpp -1 +1
    M ./src/monitor.cpp -1 +1
    M ./src/mympi.cpp -1 +1
    M ./src/output_directory.cpp -1 +1
    M ./src/polarization.cpp -1 +1
    M ./src/sources.cpp -1 +1
    M ./src/sphere-quad.cpp -1 +1
    M ./src/step.cpp -1 +1
    M ./src/step_d.cpp -1 +1
    M ./src/step_h.cpp -1 +1
    M ./src/structure.cpp -1 +1
    M ./src/time.cpp -1 +1
    M ./src/update_e_from_d.cpp -1 +1
    M ./src/update_from_e.cpp -1 +1
    M ./src/vec.cpp -1 +1
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/harmonics.cpp -1 +1
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Mon Nov 12 19:34:43 EST 2007  stevenj@fftw.org
  * updated NEWS

    M ./NEWS +33

Mon Nov 12 18:58:32 EST 2007  stevenj@fftw.org
  * shorten long h5test

    M ./tests/h5test.cpp -32 +52

Mon Nov 12 18:30:09 EST 2007  stevenj@fftw.org
  * fix several deadlocks when using serial HDF5 with parallel Meep

    M ./src/h5fields.cpp +1
    M ./src/h5file.cpp -2 +4
    M ./tests/h5test.cpp +3

Sat Nov 10 19:54:33 EST 2007  stevenj@fftw.org
  * fix small mem leak

    M ./src/h5file.cpp -2 +4

Sat Oct 20 13:34:19 EDT 2007  stevenj@fftw.org
  * attempt to auto-detect -package name for ghc stuff, since apparently ghc keeps changing it (grr); thanks to Liang Huo for the bug report

    M ./configure.ac -1 +20
    M ./hsrc/Makefile.am -1 +1

Mon Oct  8 19:02:15 EDT 2007  stevenj@fftw.org
  * bug fix -- dft_chunk objects were improperly disposed of in ~fields due to confusion between next_in_chunk and next_in_dft, thanks to Alex McCauley for the bug report and twinkies

    M ./src/dft.cpp -6 +20
    M ./src/fields.cpp -1 +5
    M ./src/meep.hpp -1 +1

Mon Oct  8 19:00:42 EDT 2007  stevenj@fftw.org
  * eliminate compiler warnings about unused params

    M ./src/meep.hpp -6 +6

Mon Oct  8 18:22:47 EDT 2007  stevenj@fftw.org
  * set fluxes = NULL after remove_fluxes

    M ./src/fields.cpp +1

Thu Aug 16 13:30:18 EDT 2007  stevenj@fftw.org
  * 2D saturated polariton known_results fails on 4 processors; according to darcs trackdown this has failed since at least 2005, so it's not clear that it ever worked

    M ./tests/known_results.cpp -2 +3

Wed Aug 15 22:41:22 EDT 2007  stevenj@fftw.org
  * comment fix

    M ./src/boundaries.cpp -1 +1

Wed Aug 15 17:28:10 EDT 2007  stevenj@fftw.org
  * flux.cpp test case accidentally put flux plane inside PML

    M ./tests/flux.cpp -1 +1

Wed Aug 15 17:27:32 EDT 2007  stevenj@fftw.org
  * fixed bug in flux_in_box: accidentally returned flux * number of processes, instead of flux!  yikes, caused 'make check' to fail with MPI, too

    M ./src/energy_and_flux.cpp -1 +1

Wed Aug 15 16:54:25 EDT 2007  stevenj@fftw.org
  * restored legacy simplistic averaging code, modified slightly to remove potential instability, with comment explaining that this code somehow yields quadratic convergence in one of the test cases (although not in general), indicating that there may be a method behind the madness

    M ./src/anisotropic_averaging.cpp -11 +37
    M ./tests/convergence_cyl_waveguide.cpp -2 +2

Wed Aug 15 16:27:23 EDT 2007  stevenj@fftw.org
  * disable epsilon averaging for pixels that include metals (eps < 0), since this can lead to an 0 < average epsilon < 1, which causes instabilities by changing the Courant condition (apparently)

    M ./libctl/structure.cpp -4 +18
    M ./src/anisotropic_averaging.cpp -1 +21

Wed Aug 15 15:44:07 EDT 2007  stevenj@fftw.org
  * run h5topng only once on multiple CPUs, avoid race condition

    M ./libctl/meep.scm.in -2 +4

Wed Aug 15 15:43:22 EDT 2007  stevenj@fftw.org
  * fix deadlock for output-hfield etc. reported by Lingling Tang (deadlocks when using non-MPI HDF5)

    M ./libctl/meep.scm.in -1 +5
    M ./src/h5file.cpp -8 +11

Fri Aug 10 10:53:06 EDT 2007  stevenj@fftw.org
  * update acx_blas

    M ./m4/acx_blas.m4 -1 +16

Mon Jun 25 17:29:24 EDT 2007  ardfar@mit.edu
  * use delete[] not delete for deallocating new char[] array

    M ./src/h5file.cpp -3 +3

Wed May  9 19:41:29 EDT 2007  stevenj@fftw.org
  * update hsrc/Makefile for ghc-6.6

    M ./hsrc/Makefile.am -1 +1

Wed Apr 18 18:23:01 EDT 2007  stevenj@fftw.org
  * bug fix: subpixel averaging was disabled for dimensions=1 (thanks to Mischa Megens for the bug report)

    M ./libctl/structure.cpp -1 +1

Mon Jan 15 16:45:27 EST 2007  stevenj@fftw.org
  * delete cruft

    M ./examples/pw-source.ctl -2

Thu Jan  4 20:47:38 EST 2007  stevenj@fftw.org
  * MPI_LONG_DOUBLE is optional in the MPI standard, so check before using it in MPI_Allreduce

    M ./src/mympi.cpp -2 +11

Tue Jan  2 21:30:53 EST 2007  stevenj@fftw.org
  * fixed bug that prevented output-tot-pwr from working; thanks to Vyacheslav Sokolov for the bug report

    M ./src/h5fields.cpp -1 +1
    M ./src/integrate.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/vec.cpp -2 +2

Thu Nov  2 15:17:51 EST 2006  stevenj@fftw.org
  * make at-every less susceptible to rounding; thanks to L. Le Guyader for the bug report

    M ./libctl/meep.scm.in -1 +2

Fri Oct 20 18:09:36 EDT 2006  stevenj@fftw.org
  * include -march in pkgconfig flags (g++ requires it, apparently)

    M ./configure.ac +12
    M ./meep.pc.in -1 +1

Sat Sep 30 13:49:40 EDT 2006  stevenj@fftw.org
  * fix bug reported by J. L. Silva, where polarization memory was not parallelized

    M ./src/polarization.cpp -1 +1

Sat Sep 30 13:49:26 EDT 2006  stevenj@fftw.org
  * consistency

    M ./src/anisotropic_averaging.cpp +2

Mon Sep 18 21:50:06 EDT 2006  stevenj@fftw.org
  * custom_src_time should respect start_time

    M ./src/meep.hpp -1 +2

Mon Aug 28 13:54:42 EDT 2006  stevenj@fftw.org
  * bug fix in output-png+h5, thanks to Chad Husko

    M ./libctl/meep.scm.in -1 +1

Mon Aug 21 19:44:04 EDT 2006  stevenj@fftw.org
  tagged 0.10


Mon Aug 21 19:09:43 EDT 2006  stevenj@fftw.org
  * really include meep-enums.scm

    M ./libctl/Makefile.am -1 +1

Mon Aug 21 18:22:18 EDT 2006  stevenj@fftw.org
  * version bump

    M ./NEWS -4 +4
    M ./configure.ac -2 +2

Fri Aug 18 14:01:51 EDT 2006  stevenj@fftw.org
  * avoid printing redundant messages about padding

    M ./src/structure.cpp -2 +2

Tue Aug  8 20:21:33 EDT 2006  stevenj@fftw.org
  * fix test case to handle nlo != 1

    M ./tests/bragg_transmission.cpp -3 +3

Mon Aug  7 13:48:19 EDT 2006  stevenj@fftw.org
  * updated NEWS for upcoming 0.10

    M ./NEWS +49

Sun Aug  6 00:27:57 EDT 2006  stevenj@fftw.org
  * added testcase for 2nd/3rd harmonic generation

    M ./tests/Makefile.am -1 +1
    A ./tests/harmonics.cpp

Sat Aug  5 23:05:58 EDT 2006  stevenj@fftw.org
  * turned on polariton symmetry tests, with slightly increased tolerances

    M ./tests/symmetry.cpp -12 +8

Sat Aug  5 22:39:00 EDT 2006  stevenj@fftw.org
  * add nonlinear symmetry tests
  
  The nonlinear symmetry tests had been disabled because they caused
  the symmmetry.dac test to fail.  I had assumed this was a bug,
  but now I'm not so sure.
  
  First, the nonlinear calculations rely on an averaging of field values
  from adjacent points, and this averaging process will differ by rounding
  errors when using symmetries (e.g. left + right + top + bottom may 
  change to right + left + top + bottom, which differs by rounding).  So,
  I had to decrease the error threshold for the nonlinear tests.
  
  Second, a more serious concern: symmetry is not necessarily preserved
  when rounding is included.  A simple example is that exp(i m phi) modes
  in a cylindrical waveguide may be converted to exp(3 i m phi) modes
  by a Kerr nonlinearity, analogous to 3rd harmonic generation.  I *think*
  that this conversion does not occur for the trivial representation
  (analogous to m=0), but I'm not 100% sure.  So, the nonlinear tests
  (which use the trivial representation, i.e. no phase factor) should
  be okay...
  
  However, e.g. the rot4z symmetry test still fails if I use *both* TM
  and TE sources (which interact due to the nonlinearity).  Outputting
  the fields, it looks like a nonsymmetric pattern really is generated
  after a while in this case.   Perhaps this is a numerical effect,
  related to the rounding mentioned above?

    M ./tests/symmetry.cpp -30 +35

Sat Aug  5 00:59:36 EDT 2006  stevenj@fftw.org
  * turn on epsilon averaging by default in libctl interface -- the speed penalty seems to be only about 10%, and the huge accuracy gains (as well as continuous sensitivity to geometry) are more than worth it

    M ./libctl/meep.scm.in -1 +1

Sat Aug  5 00:56:16 EDT 2006  stevenj@fftw.org
  * slight optimization in handling off-diagonal epsilon
  
  Checking whether the off-diagonal inveps components are zero leads to a
  slight (< 10%) speed increase on our Pentium IVs, probably thanks to
  the avoided loads of the off-diagonal fields.  On the other hand, keeping
  a separate array of flags is definitely not a win--it is better to check
  inveps directly.

    M ./src/update_e_from_d.cpp -8 +15

Sat Aug  5 00:54:56 EDT 2006  stevenj@fftw.org
  * bug fix - set_epsilon should delete off-diagonal inveps components when averaging is not being used (otherwise, doing set_epsilon with averaging followed by set_epsilon with no averaging leads to wrong results)

    M ./src/anisotropic_averaging.cpp +2

Fri Aug  4 20:39:37 EDT 2006  stevenj@fftw.org
  * some explanatory comments for Pade approximant

    M ./src/update_e_from_d.cpp -3 +10

Fri Aug  4 03:15:24 EDT 2006  stevenj@fftw.org
  * merge chi2 (pockels) stuff from Ardavan

    M ./libctl/meep.scm.in +1
    M ./libctl/structure.cpp +52
    M ./src/meep.hpp -2 +7
    M ./src/structure.cpp -10 +54
    M ./src/update_e_from_d.cpp -12 +19

Fri Aug  4 02:21:21 EDT 2006  stevenj@fftw.org
  * rename kerr to chi3 in preparation for Ardavan chi2 merge

    M ./doc/nonlinear.tex -2 +2
    M ./libctl/structure.cpp -9 +9 r1
    M ./src/meep.hpp -1 +1 r3
    M ./src/structure.cpp r3
    M ./src/update_e_from_d.cpp r3
    M ./tests/bench.cpp r1
    M ./tests/symmetry.cpp r1

Fri Aug  4 02:10:52 EDT 2006  stevenj@fftw.org
  * kerr does not require d_minus_p

    M ./src/update_e_from_d.cpp -2 +1

Fri Aug  4 02:02:12 EDT 2006  stevenj@fftw.org
  * eliminate update_e_from_d_update.hpp in favor of much smaller, somewhat faster, and more maintainable hand-written version

    M ./src/Makefile.am -5 +2
    M ./src/meep.hpp -3
    M ./src/update_e_from_d.cpp -3 +225
    R ./src/update_e_from_d_prepare.cpp
    R ./src/update_e_from_d_sources.cpp
    R ./src/update_e_from_d_update.cpp

Thu Aug  3 17:06:49 EDT 2006  stevenj@fftw.org
  * eliminated generated update_e_from_d_prepare.hpp (a lot of pointlessly duplicated code), and sped up somewhat, and eliminated old/unused ran.* files

    M ./src/Makefile.am -8 +5
    R ./src/ran.cpp
    R ./src/ran.hpp
    M ./src/step_d.cpp -1
    M ./src/step_h.cpp -1
    M ./src/update_e_from_d_prepare.cpp -3 +34
    M ./src/update_from_e.cpp -1

Thu Aug  3 15:31:33 EDT 2006  stevenj@fftw.org
  * do correct cylindrical integration for fallback_meaneps

    M ./libctl/structure.cpp -7 +12

Thu Aug  3 14:58:31 EDT 2006  stevenj@fftw.org
  * fixed(?) failure of convergence_cyl_waveguide test

    M ./src/anisotropic_averaging.cpp -7 +7
    M ./tests/convergence_cyl_waveguide.cpp +2

Wed Aug  2 22:24:51 EDT 2006  stevenj@fftw.org
  * fixed libctl fallback to use proper cubature

    M ./libctl/structure.cpp -3 +77

Wed Aug  2 21:48:01 EDT 2006  stevenj@fftw.org
  * minor bugfix to default meaneps routine (shouldn't affect results much)

    M ./src/anisotropic_averaging.cpp -8 +12

Wed Aug  2 21:15:06 EDT 2006  stevenj@fftw.org
  * allowed user control of subpixel tolerance via subpixel-tol and subpixel-maxeval parameters, and set these to more modest values, and output progress indicator during subpixel averaging (since it may be slow in 3d)

    M ./libctl/meep-ctl-swig.hpp +1
    M ./libctl/meep.scm.in -1 +4
    M ./libctl/structure.cpp -4 +10
    M ./src/anisotropic_averaging.cpp -12 +31
    M ./src/meep.hpp -6 +17
    M ./src/meep_internals.hpp +2
    M ./src/step.cpp -2
    M ./src/structure.cpp -4 +6

Wed Aug  2 20:03:23 EDT 2006  stevenj@fftw.org
  * merged Ardavan's much-improved subpixel-averaging code, after deleting a lot of obsolete stuff.

    M ./libctl/structure.cpp -13 +183
    M ./src/Makefile.am -2 +2
    M ./src/anisotropic_averaging.cpp -101 +199
    M ./src/meep.hpp -5 +18
    M ./src/meep/vec.hpp -1 +3
    M ./src/structure.cpp -71 +9
    R ./src/threevec.hpp
    M ./src/vec.cpp -2 +10

Wed Aug  2 19:26:43 EDT 2006  stevenj@fftw.org
  * remove debugging printf

    M ./src/sources.cpp -2

Wed Aug  2 14:08:03 EDT 2006  stevenj@fftw.org
  * remove annoying restriction on symmetries requiring even number of grid points, since this is no longer required (an extra pixel is added as needed)

    M ./src/structure.cpp -2 +2

Fri Jul 28 11:36:03 EDT 2006  stevenj@fftw.org
  * use $(EXEEXT) in dependency, thanks to Christopher Kang for the bug report

    M ./src/Makefile.am -1 +1

Tue Jul 25 23:52:34 EDT 2006  stevenj@fftw.org
  * add structure::print_layout for debugging

    M ./src/meep.hpp +1
    M ./src/sources.cpp +2
    M ./src/structure.cpp +19

Wed Jul  5 17:06:27 EDT 2006  stevenj@fftw.org
  * remove obsolete slice output and (64-bit unclean) file* stuff

    M ./doc/Makefile.am -2 +4
    M ./doc/complicated.tex -8 +8
    M ./doc/energy_cons_1d.tex -1
    M ./doc/example.cpp -2 +2
    M ./doc/lossgain_epsilon.tex -3 +1
    M ./doc/nonlinear.tex -2 +1
    M ./doc/omniguide.tex -1
    M ./doc/simple.tex -9 +7
    M ./doc/simplebands.tex -2 +2
    M ./src/Makefile.am -1 +1
    M ./src/bands.cpp -11 +13
    M ./src/grace.cpp -25 +30
    M ./src/meep.hpp -49 +4
    M ./src/meep/mympi.hpp -11 +3
    M ./src/meep/vec.hpp -4
    M ./src/mympi.cpp -84 +14
    M ./src/output_directory.cpp -2 +2
    R ./src/slices.cpp
    M ./src/vec.cpp -30
    M ./tests/cylindrical.cpp -5
    M ./tests/one_dimensional.cpp -2
    M ./tests/symmetry.cpp -17
    M ./tests/three_d.cpp -10
    M ./tests/two_dimensional.cpp -4

Sun Jun 25 00:47:58 EDT 2006  stevenj@fftw.org
  * fix bug in add-flux for multiple flux-regions (thanks to K. Choi for the bug report)

    M ./libctl/meep-ctl-swig.hpp +6
    M ./libctl/meep.cpp +16
    M ./libctl/meep.scm.in -3 +6

Mon Jun 12 13:01:20 EDT 2006  stevenj@fftw.org
  * added simple angled-planewave source example

    A ./examples/pw-source.ctl

Sat May 20 16:05:11 EDT 2006  stevenj@fftw.org
  * allow source size to exceed cell size by < 1 pixel, to account for rounding (thanks to G. J. Parker for the bug report)

    M ./src/sources.cpp -4 +13

Fri May  5 13:46:43 EDT 2006  stevenj@fftw.org
  * harminv now works even if you call it multiple times for one run loop; added harminv! function so that you can change the output data variables (thanks to Aristos for the suggestion)

    M ./libctl/meep.scm.in -12 +19

Thu May  4 22:57:01 EDT 2006  stevenj@fftw.org
  * quote filenames passed to shell

    M ./libctl/meep.scm.in -2 +2

Thu May  4 20:04:36 EDT 2006  stevenj@fftw.org
  * whoops

    M ./libctl/meep.scm.in -8 +7

Thu May  4 19:45:30 EDT 2006  stevenj@fftw.org
  * added with-prefix function to use extra filename prefix for some outputs (e.g. different prefixes for different in-volumes)

    M ./libctl/meep.scm.in +7

Thu May  4 19:39:04 EDT 2006  stevenj@fftw.org
  * allow per-volume $EPS filenames

    M ./libctl/meep.scm.in -5 +12

Thu May  4 19:01:44 EDT 2006  stevenj@fftw.org
  * two requests from Aristos: added output-png+h5 function that doesn't delete the .h5 file, and now output-png defines $EPS variable that can be used on command line to reference the last epsilon file outputted

    M ./libctl/meep.scm.in -7 +19

Thu May  4 18:38:50 EDT 2006  stevenj@fftw.org
  * fix bug in save-flux/load-flux (filename was screwed up and use-output-directory did not work); thanks to Karl Koch for the bug report

    M ./libctl/meep.scm.in -6 +2
    M ./src/dft.cpp -7 +11
    M ./src/meep.hpp -2 +4

Wed May  3 16:10:34 EDT 2006  stevenj@fftw.org
  * add volume::center_origin()

    M ./libctl/structure.cpp -1 +1
    M ./src/meep/vec.hpp -3 +3

Wed May  3 16:09:08 EDT 2006  stevenj@fftw.org
  * tweaks - include more .i and .scm files in tarball so that they don't need to be generated by user (making complex sed/sh commands portable is hard)

    M ./libctl/Makefile.am -5 +5

Mon Apr 17 17:27:05 EDT 2006  stevenj@fftw.org
  * more symmetry fixes, in preparation for allowing symmetry for sizes that are not an even # of pixels

    M ./libctl/structure.cpp -7 +4
    M ./src/meep/vec.hpp +7
    M ./src/vec.cpp -7 +11

Wed Apr 12 14:12:12 EDT 2006  stevenj@fftw.org
  * added missing output-sfield-z etc. commands, in addition to output-poynting-z etc for MPB compatibility; thanks to X. Y. Ao for the bug report

    M ./libctl/meep.scm.in -1 +2

Wed Apr 12 01:31:53 EDT 2006  stevenj@fftw.org
  * fixed bug: rotate2 symmetry was totally broken, yikes!

    M ./src/structure.cpp -2 +10

Wed Apr 12 00:57:13 EDT 2006  stevenj@fftw.org
  * bug fix in symmetry::operator+ that causes symmetries to be dropped if we added three or more symmetries

    M ./src/vec.cpp -1 +3

Wed Apr 12 00:56:46 EDT 2006  stevenj@fftw.org
  * minor cleanups

    M ./src/vec.cpp -5 +5

Mon Apr 10 13:57:28 EDT 2006  stevenj@fftw.org
  * flux-in-box etc. convenience functions

    M ./libctl/meep.scm.in +17

Fri Apr  7 14:02:17 EDT 2006  stevenj@fftw.org
  * missing string.h headers, thanks to Florencio Garcia

    M ./src/fields.cpp +1
    M ./src/grace.cpp +1
    M ./src/h5fields.cpp +1

Fri Apr  7 12:48:42 EDT 2006  stevenj@fftw.org
  * exit() requires stdlib.h ... reported by Florencio Garcia

    M ./src/mympi.cpp +1
    M ./src/threevec.hpp -2 +1

Wed Apr  5 15:21:50 EDT 2006  stevenj@fftw.org
  * fixed bugs in previous patch; renamed split_specifically to halve since that's all we use it for, remove some old unused functions

    M ./src/meep/vec.hpp -3 +1
    M ./src/structure.cpp -6 +6
    M ./src/vec.cpp -42 +4

Tue Apr  4 23:52:23 EDT 2006  stevenj@fftw.org
  * silence warning

    M ./src/dft.cpp -1

Tue Apr  4 23:50:30 EDT 2006  stevenj@fftw.org
  * don't use C99 round function (replace with more portable my_round); delete some unused cruft

    M ./src/meep_internals.hpp +5
    M ./src/vec.cpp -13 +1

Tue Apr  4 23:41:54 EDT 2006  stevenj@fftw.org
  * fixed bug reported by Andreas von Rhein - failure in intersect_with due to rounding in origin operations...now most origin operations work on the integer origin io; some code cleanups

    M ./src/meep/vec.hpp -5 +6
    M ./src/structure.cpp -7 +7
    M ./src/vec.cpp -51 +51

Tue Apr  4 17:58:27 EDT 2006  stevenj@fftw.org
  * -lgen required for basename/dirname on SGI; thanks to Robyn Landers

    M ./configure.ac +3

Sun Apr  2 00:10:31 EST 2006  stevenj@fftw.org
  tagged 0.9


Sat Apr  1 23:45:10 EST 2006  stevenj@fftw.org
  * updated NEWS

    M ./NEWS -1 +1

Sat Apr  1 22:17:25 EST 2006  stevenj@fftw.org
  * don't use HDF5 when it is not available

    M ./tests/bragg_transmission.cpp +2

Sat Apr  1 22:10:18 EST 2006  stevenj@fftw.org
  * use GEN_CTL_IO env. var if present for gen-ctl-io check

    M ./configure.ac -5 +2

Fri Mar 31 18:07:21 EST 2006  stevenj@fftw.org
  * updated title page of manual

    M ./doc/meep.tex -3 +6

Fri Mar 31 18:01:04 EST 2006  stevenj@fftw.org
  * fixed sign of magnetic current sources (so that continuity equation is satisfied: d(mag. charge density)/dt = -div (magnetic current) )

    M ./src/step.cpp -2 +2

Fri Mar 31 16:48:05 EST 2006  stevenj@fftw.org
  * fixed custom-src

    M ./libctl/meep.i -3 +6
    M ./libctl/meep.scm.in -2 +1

Thu Mar 30 13:20:45 EST 2006  stevenj@fftw.org
  * README updates

    M ./README +11
    A ./doc/README

Thu Mar 30 00:16:10 EST 2006  stevenj@fftw.org
  * add integrate-field-function and max-abs-field-function to libctl interface

    M ./libctl/meep.scm.in +23

Wed Mar 29 23:32:24 EST 2006  stevenj@fftw.org
  * fix output_hdf5 for complex functions; add output-field-function to libctl; add output-single-precision? to libctl

    M ./libctl/meep.i +2
    M ./libctl/meep.scm.in -2 +28
    M ./src/h5fields.cpp -13 +17
    M ./src/meep.hpp -1 +2

Mon Mar 27 23:17:05 EST 2006  stevenj@fftw.org
  * fix invalid "friend class injection" (see http://womble.decadentplace.org.uk/c++/syntax-errors.html)

    M ./src/meep/vec.hpp +24

Mon Mar 27 22:39:25 EST 2006  stevenj@fftw.org
  * backwards-incompatible change: re-order the arguments for all field_function and and field_rfunction arguments so that the callback void* goes immediately after the callback function; this is to enable these functions to be called from the libctl interface (which requires that SWIG be able to recognize the arguments as a group)

    M ./libctl/meep.i +37
    M ./src/energy_and_flux.cpp -5 +5
    M ./src/h5fields.cpp -15 +12
    M ./src/integrate.cpp -11 +11
    M ./src/meep.hpp -16 +9
    M ./tests/integrate.cpp -1 +1

Mon Mar 27 20:59:18 EST 2006  stevenj@fftw.org
  * version bump, copyright year update

    M ./AUTHORS +4
    M ./COPYRIGHT -1 +1
    M ./NEWS -1 +3
    M ./TODO -2
    M ./configure.ac -1 +1
    M ./doc/example.cpp -1 +1
    M ./src/bands.cpp -1 +1
    M ./src/bicgstab.cpp -1 +1
    M ./src/bicgstab.hpp -1 +1
    M ./src/boundaries.cpp -1 +1
    M ./src/control_c.cpp -1 +1
    M ./src/cw_fields.cpp -1 +1
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/fields.cpp -1 +1
    M ./src/grace.cpp -1 +1
    M ./src/h5fields.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/initialize.cpp -1 +1
    M ./src/integrate.cpp -1 +1
    M ./src/loop_in_chunks.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/meep/mympi.hpp -1 +1
    M ./src/meep/vec.hpp -1 +1
    M ./src/meep_internals.hpp -1 +1
    M ./src/monitor.cpp -1 +1
    M ./src/mympi.cpp -1 +1
    M ./src/output_directory.cpp -1 +1
    M ./src/polarization.cpp -1 +1
    M ./src/slices.cpp -1 +1
    M ./src/sources.cpp -1 +1
    M ./src/sphere-quad.cpp -1 +1
    M ./src/step.cpp -1 +1
    M ./src/step_d.cpp -1 +1
    M ./src/step_h.cpp -1 +1
    M ./src/structure.cpp -1 +1
    M ./src/time.cpp -1 +1
    M ./src/update_e_from_d.cpp -1 +1
    M ./src/update_e_from_d_prepare.cpp -1 +1
    M ./src/update_e_from_d_sources.cpp -1 +1
    M ./src/update_e_from_d_update.cpp -1 +1
    M ./src/update_from_e.cpp -1 +1
    M ./src/vec.cpp -1 +1
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Thu Mar  9 17:48:38 EST 2006  stevenj@fftw.org
  * added geometric_volume::integral_volume to get integration volume corresponding to a gv

    M ./src/meep/vec.hpp -1 +2
    M ./src/vec.cpp -4 +11

Wed Mar  8 18:12:16 EST 2006  stevenj@fftw.org
  * multiply cnumbers by 1.0 before passing to SWIG functions, since SWIG gets confused if we pass an integer for a complex arg.

    M ./libctl/meep.scm.in -4 +4

Wed Mar  8 18:11:29 EST 2006  stevenj@fftw.org
  * support derived_components in max_abs for output-png, etcetera

    M ./src/h5fields.cpp -54 +1
    M ./src/integrate.cpp -2 +54
    M ./src/meep.hpp +15
    M ./src/vec.cpp +61

Tue Jan 24 17:00:36 EST 2006  stevenj@fftw.org
  * use pkgdatadir for installing .scm files

    M ./libctl/Makefile.am -13 +5

Tue Jan 24 16:15:41 EST 2006  stevenj@fftw.org
  * create libctl/specs directory if necessary during 'make install'

    M ./libctl/Makefile.am +1

Tue Dec  6 22:08:57 EST 2005  stevenj@fftw.org
  * added epsilon-func convenience wrapper for material-func

    M ./libctl/meep.scm.in +2

Fri Dec  2 15:22:45 EST 2005  stevenj@fftw.org
  * don't use -pedantic, even in maintainer mode, because it can cause compilation failures due to header files not under our control (e.g. the LAM/MPI header file)

    M ./configure.ac -1 +1

Thu Dec  1 23:18:04 EST 2005  stevenj@fftw.org
  * whoops 2*pi*R should be included in loop_in_chunks integration volume even for dR=0

    M ./src/loop_in_chunks.cpp -1 +1

Thu Dec  1 21:18:03 EST 2005  stevenj@fftw.org
  * MPI tweaks for libctl front-end

    M ./libctl/Makefile.am +3
    M ./libctl/meep.scm.in +10
    M ./src/mympi.cpp -1 +2

Thu Dec  1 20:12:38 EST 2005  stevenj@fftw.org
  * update Ep and Ez at r=0 in cylindrical coords

    M ./src/update_e_from_d_update.cpp -2 +16

Thu Dec  1 20:12:24 EST 2005  stevenj@fftw.org
  * eliminate compiler warning

    M ./src/dft.cpp -3 +3

Thu Dec  1 19:13:59 EST 2005  stevenj@fftw.org
  * fixed loop-in-chunks for integrating over dR=0 regions; added FIXME for updating E from D for r=0 special cases

    M ./src/loop_in_chunks.cpp -2 +2
    M ./src/update_e_from_d_update.cpp +3

Thu Dec  1 19:04:08 EST 2005  stevenj@fftw.org
  * whoops, distribute material-dispersion.ctl

    M ./examples/Makefile.am -1 +1

Thu Dec  1 19:03:01 EST 2005  stevenj@fftw.org
  * add material-dispersion.ctl example, run-k-point function, and change-sources!

    A ./examples/material-dispersion.ctl
    M ./libctl/meep.scm.in -23 +31

Wed Nov 23 00:19:11 EST 2005  stevenj@fftw.org
  * some fixes for polarizability

    M ./libctl/structure.cpp -15 +14

Tue Nov 22 23:15:41 EST 2005  stevenj@fftw.org
  * amp-fun now works for sources

    M ./libctl/meep.i +3
    M ./libctl/meep.scm.in +1

Tue Nov 22 22:23:41 EST 2005  stevenj@fftw.org
  * run-kpoints sets all-freqs variable with frequencies, like MPB

    M ./libctl/meep.scm.in -2 +6

Tue Nov 22 22:22:36 EST 2005  stevenj@fftw.org
  * better handling of empty dimensions, more consistent with lower-dimensional computation

    M ./libctl/meep.scm.in -1 +1
    M ./src/dft.cpp -2 +19
    M ./src/fields.cpp +10
    M ./src/loop_in_chunks.cpp -5 +4
    M ./src/meep.hpp -1 +4
    M ./src/sources.cpp -1 +1

Mon Nov 14 19:00:58 EST 2005  stevenj@fftw.org
  * fix weights and units for flux spectra!  (bug!  effect on normalized transmission/reflection spectra should be minimal, however)

    M ./src/dft.cpp -7 +15

Sat Nov 12 17:40:53 EST 2005  stevenj@fftw.org
  * comment typos

    M ./src/loop_in_chunks.cpp -5 +5

Sat Nov 12 17:38:13 EST 2005  stevenj@fftw.org
  * TODO updates

    M ./TODO -25 +31

Sat Nov 12 16:51:37 EST 2005  stevenj@fftw.org
  * typo in Makefile.am

    M ./examples/Makefile.am -1 +1

Fri Nov 11 19:12:31 EST 2005  stevenj@fftw.org
  * has_boundary(Low, R) now returns true if the origin is at r > 0

    M ./src/fields.cpp -1 +3
    M ./src/structure.cpp +2
    M ./src/vec.cpp -1 +1

Fri Nov 11 19:11:27 EST 2005  stevenj@fftw.org
  * added cylindrical ring-resonator example

    M ./examples/Makefile.am -1 +1
    A ./examples/ring-cyl.ctl

Fri Nov 11 18:33:36 EST 2005  stevenj@fftw.org
  * support geometry-center in libctl, fix cylindrical in libctl; support r_to_minus_r_symmetry for non-integer m

    M ./libctl/meep-ctl-swig.hpp -2 +2
    M ./libctl/meep.scm.in -2 +2
    M ./libctl/structure.cpp -8 +12
    M ./src/fields.cpp -2 +2
    M ./src/meep/vec.hpp -1 +1
    M ./src/vec.cpp -2 +5

Fri Nov 11 17:35:48 EST 2005  stevenj@fftw.org
  * add examples/Makefile to list of Makefiles

    M ./configure.ac +1

Fri Nov 11 16:58:54 EST 2005  stevenj@fftw.org
  * use Makefile to specify examples to distribute, instead of whole examples/ directory (which may be cluttered with output files etc.); don't distribute doc/ directory at all unless built with --with-doc

    M ./Makefile.am -2 +8
    A ./examples/Makefile.am

Wed Nov  9 22:05:32 EST 2005  stevenj@fftw.org
  * Make unit directions periodic by default, and don't put PML on them

    M ./src/fields.cpp +6
    M ./src/structure.cpp -2 +4

Wed Nov  9 21:38:31 EST 2005  stevenj@fftw.org
  * added nonlinear example

    A ./examples/3rd-harm-1d.ctl

Wed Nov  9 21:36:25 EST 2005  stevenj@fftw.org
  * some fixes in libctl for 1d cells, Kerr media, stop-when-decayed ...

    M ./libctl/meep.scm.in -3 +6
    M ./libctl/structure.cpp -29 +47

Wed Nov  9 13:42:44 EST 2005  stevenj@fftw.org
  * share structure_chunk between structure and fields_chunkk to save memory in the common case; behavior should be the same as before, however, because I implemented copy-on-write semantics via reference counting

    M ./src/fields.cpp -4 +14
    M ./src/meep.hpp -2 +7
    M ./src/polarization.cpp +1
    M ./src/step.cpp +1
    M ./src/structure.cpp -3 +24

Tue Nov  8 22:17:08 EST 2005  stevenj@fftw.org
  * renamed material_of_unshifted_point_in_tree_inobject function in libctl

    M ./libctl/structure.cpp -3 +3

Tue Nov  8 21:59:59 EST 2005  stevenj@fftw.org
  * renormalized currents: amplitude of J is no longer frequency-dependent, and is ~ 1.0 instead

    M ./src/meep.hpp -1 +1
    M ./src/sources.cpp -3 +11
    M ./tests/known_results.cpp -8 +16

Tue Nov  8 21:27:08 EST 2005  stevenj@fftw.org
  * Don't use -Os, even though it produces slightly faster code; in g++ 3.3.5 (and who knows what other versions) it seems to be buggy, sigh

    M ./m4/ax_cxx_maxopt.m4 -1 +2
    M ./src/Makefile.am -1 +3

Tue Nov  8 21:26:35 EST 2005  stevenj@fftw.org
  * fixed misnumbered chi's, and delete[] instead of delete

    M ./libctl/meep.scm.in -1 +1
    M ./libctl/structure.cpp -7 +7
    M ./src/h5file.cpp -1 +1

Tue Nov  8 20:35:21 EST 2005  stevenj@fftw.org
  * added draft (untested) support for kerr and dispersive materials in the libctl front-end

    M ./libctl/meep.scm.in +1
    M ./libctl/structure.cpp -11 +147

Tue Nov  8 20:33:57 EST 2005  stevenj@fftw.org
  * added fields::remove_polarizabilities, added use_averaging optional argument to end of structure constructor, automatically keep track of current polarization in material_function class, reset polarizabilities in fiels::zero_fields

    M ./src/fields.cpp +14
    M ./src/h5fields.cpp -1 +1
    M ./src/meep.hpp -39 +52
    M ./src/structure.cpp -4 +14

Tue Nov  8 20:32:51 EST 2005  stevenj@fftw.org
  * added polarization::zero_fields, for use in fields::zero_fields, and removed the corresponding code from the constructor

    M ./src/meep_internals.hpp +1
    M ./src/polarization.cpp -28 +39

Tue Nov  8 18:34:45 EST 2005  stevenj@fftw.org
  * fix gen-ctl-io lines for vpath builds (meep.scm is in build dir., not srcdir)

    M ./libctl/Makefile.am -3 +3

Tue Nov  8 18:33:07 EST 2005  stevenj@fftw.org
  * Less aggressive compiler flags (FIXME: why does -fstrict-aliasing cause 'make check' to fail with g++ 3.3.5?  Is this a compiler bug, or a Meep bug?)

    M ./m4/ax_cxx_maxopt.m4 -6 +7

Tue Nov  8 18:05:18 EST 2005  stevenj@fftw.org
  * FFTW-style auto-detection of compiler flags

    M ./configure.ac -46 +12
    M ./darcs_test -2 +2
    A ./m4/ax_check_compiler_flags.m4
    A ./m4/ax_compiler_vendor.m4
    A ./m4/ax_cxx_maxopt.m4
    A ./m4/ax_gcc_archflag.m4
    A ./m4/ax_gcc_x86_cpuid.m4

Mon Nov  7 23:01:31 EST 2005  stevenj@fftw.org
  * build libctl but not doc by default; include missing file in dist

    M ./configure.ac -4 +4
    M ./libctl/Makefile.am -1 +1

Mon Nov  7 22:12:48 EST 2005  stevenj@fftw.org
  * update copyright year, bump version to 0.8

    M ./COPYRIGHT -1 +1
    M ./configure.ac -1 +1
    M ./doc/example.cpp -1 +1
    M ./libctl/Makefile.am -1 +1
    M ./libctl/meep.scm.in -1 +1
    M ./src/bands.cpp -1 +1
    M ./src/bicgstab.cpp -1 +1
    M ./src/bicgstab.hpp -1 +1
    M ./src/boundaries.cpp -1 +1
    M ./src/control_c.cpp -1 +1
    M ./src/cw_fields.cpp -1 +1
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/fields.cpp -1 +1
    M ./src/grace.cpp -1 +1
    M ./src/h5fields.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/initialize.cpp -1 +1
    M ./src/integrate.cpp -1 +1
    M ./src/loop_in_chunks.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/meep/mympi.hpp -1 +1
    M ./src/meep/vec.hpp -1 +1
    M ./src/meep_internals.hpp -1 +1
    M ./src/monitor.cpp -1 +1
    M ./src/mympi.cpp -1 +1
    M ./src/output_directory.cpp -1 +1
    M ./src/polarization.cpp -1 +1
    M ./src/slices.cpp -1 +1
    M ./src/sources.cpp -1 +1
    M ./src/sphere-quad.cpp -1 +1
    M ./src/step.cpp -1 +1
    M ./src/step_d.cpp -1 +1
    M ./src/step_h.cpp -1 +1
    M ./src/structure.cpp -1 +1
    M ./src/time.cpp -1 +1
    M ./src/update_e_from_d.cpp -1 +1
    M ./src/update_e_from_d_prepare.cpp -1 +1
    M ./src/update_e_from_d_sources.cpp -1 +1
    M ./src/update_e_from_d_update.cpp -1 +1
    M ./src/update_from_e.cpp -1 +1
    M ./src/vec.cpp -1 +1
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Mon Nov  7 15:03:30 EST 2005  stevenj@fftw.org
  * added eps-averaging? input var.

    M ./libctl/meep-ctl-swig.hpp +1
    M ./libctl/meep.scm.in +3
    M ./libctl/structure.cpp +3

Mon Nov  7 04:32:20 EST 2005  stevenj@fftw.org
  * some renaming; check for complex symmetry phases in determining whether to use real fields; use (x,y,z) = (r,p,z) in cylindrical coordinates

    M ./libctl/meep.scm.in -5 +12
    M ./libctl/structure.cpp -3 +3

Sun Nov  6 21:28:07 EST 2005  stevenj@fftw.org
  * added band diagram example

    A ./examples/holey-wvg-bands.ctl

Sun Nov  6 18:54:14 EST 2005  stevenj@fftw.org
  * libctl meep now defaults to metal boundaries, ensure-periodicity when k, added run-k-points

    A ./examples/holey-wvg-cavity.ctl
    M ./libctl/meep.scm.in -10 +70
    M ./libctl/structure.cpp +11
    M ./src/boundaries.cpp -7 +6
    M ./src/meep.hpp -2 +1
    M ./tests/symmetry.cpp +2

Fri Nov  4 16:16:13 EST 2005  stevenj@fftw.org
  * tweaks

     ./examples/tut-bend-flux.ctl -> ./examples/bend-flux.ctl
     ./examples/tut-ring.ctl -> ./examples/ring.ctl
    M ./libctl/meep.scm.in -4 +7

Fri Nov  4 15:04:37 EST 2005  stevenj@fftw.org
  * added fields::total_volume to get v"un-symmetrized" volume for output, use mirror sym. in tut-ring.ctl, and include examples/ in tarball

    M ./Makefile.am -1 +1
    M ./examples/tut-ring.ctl +3
    M ./libctl/meep.scm.in -2 +2
    M ./src/fields.cpp +9
    M ./src/meep.hpp +2
    M ./src/meep/vec.hpp +4

Fri Nov  4 02:19:11 EST 2005  stevenj@fftw.org
  * more meep libctl changes, added examples/ directory, added FourierTransforming timesink to performance tracking

    A ./examples/
    A ./examples/tut-bend-flux.ctl
    A ./examples/tut-ring.ctl
    M ./libctl/meep-ctl-swig.hpp +1
    M ./libctl/meep.scm.in -90 +139
    M ./libctl/structure.cpp -9 +14
    M ./src/dft.cpp +2
    M ./src/meep.hpp -1 +1
    M ./src/time.cpp +1

Tue Nov  1 18:20:39 EST 2005  stevenj@fftw.org
  * added max_abs(component, geometric_volume), other libctl updates

    M ./libctl/meep.scm.in -15 +73
    M ./src/h5fields.cpp -2 +9
    M ./src/integrate.cpp +14
    M ./src/meep.hpp +3
    M ./src/vec.cpp +2

Wed Oct 26 14:00:45 EDT 2005  stevenj@fftw.org
  * added volume::interior; respect ensure_periodicity in libctl; some fixes

    M ./libctl/meep-ctl-swig.hpp +1
    M ./libctl/meep.scm.in -14 +22
    M ./libctl/structure.cpp -1 +2
    M ./src/meep/vec.hpp +1
    M ./src/vec.cpp -2 +12

Tue Oct 25 20:57:22 EDT 2005  stevenj@fftw.org
  * output # processors for benchmarking

    M ./tests/bench.cpp -1 +2

Tue Oct 25 20:17:15 EDT 2005  stevenj@fftw.org
  * urg, if NAN is not available we should define it to a number we are not likely to see (it is used to initialize current_time in src_time, for example)

    M ./src/meep.hpp -1 +1

Tue Oct 25 19:41:27 EDT 2005  stevenj@fftw.org
  * SUFFIXES rule should be .SUFFIXES in Makefiles

    M ./doc/Makefile.am -1 +1
    M ./hsrc/Makefile.am -1 +1
    M ./tests/Makefile.am -1 +1

Mon Oct 24 20:43:56 EDT 2005  stevenj@fftw.org
  * whoops

    M ./libctl/Makefile.am -1 +1

Mon Oct 24 20:35:05 EDT 2005  stevenj@fftw.org
  * automatically set dimensions

    M ./libctl/meep.scm.in -4 +11

Mon Oct 24 20:34:47 EDT 2005  stevenj@fftw.org
  * whoops, missing file

    A ./libctl/meep_op_renames.i

Mon Oct 24 16:29:32 EDT 2005  stevenj@fftw.org
  * increase tolerance for crashing on negative weights

    M ./src/vec.cpp -1 +1

Sat Oct 22 23:46:41 EDT 2005  stevenj@fftw.org
  * add _mpi/-mpi suffix when installing MPI version

    M ./configure.ac +8
    M ./libctl/Makefile.am -5 +5
    M ./src/Makefile.am -3 +3
    M ./tests/Makefile.am -1 +1

Sat Oct 22 22:34:45 EDT 2005  stevenj@fftw.org
  * make real fields the default

    M ./libctl/meep.scm.in -2 +5

Fri Oct 21 23:53:06 EDT 2005  stevenj@fftw.org
  * rationalized units: set 4*pi to 1 (no point to keeping 4*pi, especially since we didn't have 4*pi multiplying J anyway)

    M ./hsrc/update_e_from_d_gen.hs -1 +1
    M ./hsrc/update_from_e_gen.hs -2 +2
    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -6 +6
    M ./src/h5fields.cpp -2 +2
    M ./src/monitor.cpp -2 +2
    M ./tests/known_results.cpp -5 +5

Fri Oct 21 23:13:24 EDT 2005  stevenj@fftw.org
  * various more libctl stuff

    M ./libctl/meep.i +6
    M ./libctl/meep.scm.in -16 +40

Fri Oct 21 23:11:13 EDT 2005  stevenj@fftw.org
  * don't need h5file::close since we can use delete; should not have dft_flux destructor since it the class is used by value not as a pointer...added dft_flux::remove for explicit removal of flux lists from the chunks

    M ./src/meep.hpp -3 +2

Fri Oct 21 23:10:31 EDT 2005  stevenj@fftw.org
  * some memory-leak fixes

    M ./src/fields.cpp +1
    M ./src/h5file.cpp -1 +2

Wed Oct 19 12:50:19 EDT 2005  stevenj@fftw.org
  * flux fixes, some rearrangements

    M ./libctl/meep.scm.in -101 +139

Tue Oct 18 22:20:56 EDT 2005  stevenj@fftw.org
  * bug fix - harminv test must use C++ compiler in case harminv was compiled with C++

    M ./configure.ac +5

Tue Oct 18 21:43:22 EDT 2005  stevenj@fftw.org
  * generating update_e_from_d_sources was completely unnecessary

    M ./src/Makefile.am -5 +1
    M ./src/update_e_from_d_sources.cpp -1 +13

Tue Oct 18 20:41:44 EDT 2005  stevenj@fftw.org
  * making infinity and nan by dividing by zero was causing problems on the Alpha

    M ./src/meep.hpp -2 +2

Sun Oct 16 02:06:54 EDT 2005  stevenj@fftw.org
  * deleting a dft_flux should now remove it from the fields chunk; some slight rearrangement of overloaded functions for SWIG

    M ./src/dft.cpp -1 +3
    M ./src/meep.hpp -1 +2
    M ./src/meep/vec.hpp +14

Wed Oct 12 20:26:58 EDT 2005  stevenj@fftw.org
  * fixed harminv, some renaming for consistency

    M ./libctl/meep.scm.in -12 +42

Wed Oct 12 19:50:50 EDT 2005  stevenj@fftw.org
  * new constructor for gaussian_src_time accepts frequency width instead of time width (this is backwards compatible because old code used the old constructor)

    M ./libctl/meep.scm.in +2
    M ./src/meep.hpp -1 +1
    M ./src/sources.cpp -4 +4

Wed Oct 12 19:45:59 EDT 2005  stevenj@fftw.org
  * controllable progress-interval parameter

    M ./libctl/meep.scm.in -1 +5

Wed Oct 12 19:42:07 EDT 2005  stevenj@fftw.org
  * bug fixes

    M ./libctl/meep.i -8 +8
    M ./libctl/meep.scm.in -6 +10

Wed Oct 12 19:16:48 EDT 2005  stevenj@fftw.org
  * many more updates to libctl stuff

    M ./libctl/meep-ctl-swig.hpp -1 +2
    M ./libctl/meep.i -1 +19
    M ./libctl/meep.scm.in -63 +132
    M ./libctl/structure.cpp -10 +30

Tue Oct 11 22:41:33 EDT 2005  stevenj@fftw.org
  * added fluxes, output directory; fields::outdir now is a copy rather than a const char* (which would fail for Scheme)

    M ./libctl/meep-ctl-swig.hpp +2
    M ./libctl/meep.cpp +10
    M ./libctl/meep.scm.in -37 +104
    M ./src/fields.cpp -2 +3
    M ./src/meep.hpp -1 +1
    M ./src/output_directory.cpp -2 +3

Tue Oct 11 20:09:09 EDT 2005  stevenj@fftw.org
  * added harminv, run functions to libctl

    M ./libctl/meep-ctl-swig.hpp +3
    M ./libctl/meep.cpp +28
    M ./libctl/meep.scm.in +92

Tue Oct 11 13:13:58 EDT 2005  stevenj@fftw.org
  * libctl src support; added custom_src_time so that users don't need to declare a class; simpler gaussian_src_time constructor variant

    M ./libctl/Makefile.am -1 +1
    M ./libctl/meep.i +11
    M ./libctl/meep.scm.in -1 +76
    M ./src/meep.hpp +20
    M ./src/sources.cpp -1 +23

Mon Oct 10 22:34:50 EDT 2005  stevenj@fftw.org
  * made origin center (like MPB), added swig typemap for complex(vec) functions

    M ./libctl/meep.i -8 +22
    M ./libctl/structure.cpp +4

Mon Oct 10 17:30:45 EDT 2005  stevenj@fftw.org
  * libctl front-end is slowly approaching usability

    M ./libctl/Makefile.am -6 +34
    M ./libctl/meep-ctl-swig.hpp -2 +4
    M ./libctl/meep.i -1 +3
    M ./libctl/meep.scm.in -6 +117
    M ./libctl/structure.cpp -17 +76

Mon Oct 10 17:24:16 EDT 2005  stevenj@fftw.org
  * don't output in quiet mode

    M ./src/h5fields.cpp -1 +1

Mon Oct 10 17:20:38 EDT 2005  stevenj@fftw.org
  * added symmetry::operator*(complex<double>), coordinate_mismatch(derived_component), FOR_SIDES macro; fixed fields::verbose(); output_hdf5 is now tolerant to component/derived_component confusion; open_hdf5_file prints a message when a file is created for writing

    M ./src/fields.cpp +6
    M ./src/h5fields.cpp -1 +20
    M ./src/meep.hpp -2 +4
    M ./src/meep/vec.hpp -1 +8
    M ./src/vec.cpp -1 +1

Fri Oct  7 17:56:17 EDT 2005  stevenj@fftw.org
  * fixed a couple of small memory leaks reported by valgrind, and one huge one that I introduced accidentally for nonlinear media; added new fields::reset() and fields::remove_fluxes() functions; fixed inconsistency: d_minus_p was declared as an array of length NUM_DIRECTIONS, but was indexed via field components (this wasn't technically a bug, since it was only accessed through E components which fall within NUM_DIRECTIONS), but it was asking for trouble

    M ./src/fields.cpp -5 +20
    M ./src/meep.hpp -1 +3
    M ./src/output_directory.cpp -4 +2
    M ./src/structure.cpp -1 +3
    M ./src/update_e_from_d.cpp -1 +1

Fri Oct  7 00:09:47 EDT 2005  stevenj@fftw.org
  * revive libctl stuff from the dead

     ./libctl/meep-ctl-const.h -> ./libctl/meep-ctl-const.hpp
     ./libctl/meep-ctl-swig.h -> ./libctl/meep-ctl-swig.hpp
     ./libctl/meep-ctl.h -> ./libctl/meep-ctl.hpp
    M ./libctl/Makefile.am -7 +13
    M ./libctl/meep-ctl.hpp -3 +3
    M ./libctl/meep.cpp -1 +1
    M ./libctl/meep.i -6 +7
    M ./libctl/structure.cpp -185 +184

Sun Oct  2 12:14:22 EDT 2005  stevenj@fftw.org
  * resolve merge conflicts

    M ./src/meep.hpp +5
    M ./tests/bragg_transmission.cpp -11 +15

Fri Sep 30 18:57:40 EDT 2005  alexrod7@mit.edu
  * add operator-= for dft_chunk so that we can subtract fields from two simulations in the same run without saving as hdf5

    M! ./src/dft.cpp +12
    M! ./src/meep.hpp -2 +2
    M! ./tests/bragg_transmission.cpp -10 +16

Fri Sep  2 14:54:32 EDT 2005  stevenj@fftw.org
  * added mpicxx check (from Silvestre Zabala) as well as new macro-archive tags

    M ./m4/acx_mpi.m4 -2 +9

Thu Sep  1 22:20:08 EDT 2005  stevenj@fftw.org
  * slightly simplified save_hdf5 and load_hdf5 for dft_flux

    M ./src/dft.cpp +12
    M ./src/meep.hpp +4
    M ./tests/bragg_transmission.cpp -5 +5

Thu Sep  1 20:50:56 EDT 2005  stevenj@fftw.org
  * bug fix in solve_cw - check for zero current amplitudes must include all processors

    M ./src/cw_fields.cpp -3 +6

Mon Aug  8 19:39:55 EDT 2005  stevenj@fftw.org
  * bug fix in fields::initialize - don't try to initialize non-allocated fields

    M ./src/initialize.cpp -5 +7

Mon Aug  8 19:29:48 EDT 2005  stevenj@fftw.org
  * allow phasing of cylindrical radius via fields::set_rshift

    M ./src/fields.cpp +11
    M ./src/meep.hpp -1 +2
    M ./src/step_d.cpp -8 +9
    M ./src/step_h.cpp -8 +9

Mon Aug  8 14:45:12 EDT 2005  stevenj@fftw.org
  * added 3-mirror-plane test

    M ./tests/symmetry.cpp +42

Mon Aug  8 14:39:12 EDT 2005  stevenj@fftw.org
  * added symmetry::operator-

    M ./src/meep/vec.hpp +2
    M ./tests/symmetry.cpp -3 +3

Wed Jul 27 16:17:10 EDT 2005  stevenj@fftw.org
  * initialize mpi(argc,argv) had to be modified to pass those arguments as *references*, since MPI_Init may modify the argument list (fortunately, no changes are required to user code)

    M ./src/meep/mympi.hpp -1 +1
    M ./src/mympi.cpp -1 +1

Mon Jul 25 20:30:59 EDT 2005  stevenj@fftw.org
  * typo (wrong return type)

    M ./src/bicgstab.cpp -1 +1

Mon Jul 25 20:30:49 EDT 2005  stevenj@fftw.org
  * wrong format string now that m is double

    M ./src/bands.cpp -1 +1

Mon Jul 25 17:43:23 EDT 2005  stevenj@fftw.org
  * bugfix in HDF5+MPI (called H5Fopen instead of H5Fcreate)

    M ./src/h5file.cpp -2 +2

Mon Jul 25 17:42:25 EDT 2005  stevenj@fftw.org
  * HDF5 check needs to use MPICXX in case HDF was compiled with MPI (and needs mpi.h for header file)

    M ./configure.ac +5

Mon Jul 18 18:53:51 EDT 2005  stevenj@fftw.org
  * allow non-integer values of "m" in cylindrical coordinates (you probably should only do this for cells that don't include r=0)

    M ./src/fields.cpp -7 +6
    M ./src/initialize.cpp -5 +7
    M ./src/meep.hpp -4 +6
    M ./src/step_d.cpp -3 +3
    M ./src/step_h.cpp -3 +3

Fri Jul  8 17:19:02 EDT 2005  stevenj@fftw.org
  * slightly weakened test (now that we are truly including multiple source frequencies)

    M ./tests/two_dimensional.cpp -1 +1

Fri Jul  8 16:36:36 EDT 2005  stevenj@fftw.org
  * noticed *another* apparent bug in nonlinear code for symmetry, grrr (??); disable test for now

    M ./tests/symmetry.cpp -2 +6

Fri Jul  8 16:36:04 EDT 2005  stevenj@fftw.org
  * add more multiple-source tests to symmetry.cpp

    M ./tests/symmetry.cpp +6

Thu Jul  7 20:21:19 EDT 2005  stevenj@fftw.org
  * fix by Mihai for case with multiple source times

    M ./src/sources.cpp -1 +1

Wed Jun  1 21:19:31 EDT 2005  stevenj@fftw.org
  * another potential bug exposed by my previous patch - polariton_ex test also fails when symmetry is included, so revert with comment for now

    M ./tests/symmetry.cpp -2 +6

Wed Jun  1 20:16:42 EDT 2005  stevenj@fftw.org
  * can't use "darcs changes" to generate ChangeLog during 'make dist', because then 'darcs check' will fail (doesn't run in darcs dir); instead, add new 'make darcs-dist' target that creates the ChangeLog

    M ./ChangeLog -1 +1
    M ./Makefile.am -3 +7

Wed Jun  1 20:10:55 EDT 2005  stevenj@fftw.org
  * silence warning

    M ./src/monitor.cpp +1

Wed Jun  1 20:10:31 EDT 2005  stevenj@fftw.org
  * silence C++ warning

    M ./src/bicgstab.cpp -2 +4

Wed Jun  1 19:46:28 EDT 2005  stevenj@fftw.org
  * Generate ChangeLog automatically during 'make dist'

    M ./ChangeLog -1 +1
    M ./Makefile.am +5

Wed Jun  1 14:15:23 EDT 2005  stevenj@fftw.org
  * add equal_layout method to check whether two fields/structures have same
  chunking, etcetera; testcase in symmetry.cpp
  
  also add == for symmetry and signed_direction, and != for various things
  that already have ==.
  
  also fixed bug in symmetry.cpp (some fields were being compared to
  themselves rather than to symmetrized version)
  
  NOTE: THERE IS STILL A BUG IN symmetry.cpp ... nonlinear_ex() compares
  the field to itself rather than to a symmetrized version, and fails if
  the correct thing is done, which means that there may be a bug in the
  nonlinear code for symmetry

    M ./src/fields.cpp +16
    M ./src/meep.hpp +3
    M ./src/meep/vec.hpp +7
    M ./src/structure.cpp +13
    M ./src/vec.cpp +11
    M ./tests/symmetry.cpp -3 +36

Wed Jun  1 12:46:06 EDT 2005  stevenj@fftw.org
  * pass chunk index to chunkloop function, so that in the future we can easily write functions that e.g. compare two different fields objects

    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -1 +1
    M ./src/h5fields.cpp -2 +2
    M ./src/integrate.cpp -1 +1
    M ./src/loop_in_chunks.cpp -1 +1
    M ./src/meep.hpp -1 +1
    M ./src/sources.cpp -1 +1

Wed Jun  1 00:50:53 EDT 2005  stevenj@fftw.org
  * current unit fix: field update should add current*dt, not current, to fields

    M ./src/step.cpp -2 +2

Wed Jun  1 00:33:49 EDT 2005  stevenj@fftw.org
  * minor update to bicgstab comments

    M ./src/bicgstab.cpp -2 +2

Wed Jun  1 00:27:39 EDT 2005  stevenj@fftw.org
  * whoops, forgot to return a value from solve_cw

    M ./src/cw_fields.cpp -1 +1

Tue May 31 20:20:39 EDT 2005  stevenj@fftw.org
  * need string.h in bicgstab.cpp for memset()

    M ./src/bicgstab.cpp +1

Tue May 31 20:05:00 EDT 2005  stevenj@fftw.org
  * to get current(t) from dipole(t), use forward rather than backward difference (makes slightly more sense with solve_cw since many currents turn on at t = 0, and backwards difference would then give undesired spike at t=0)

    M ./src/meep.hpp -1 +1
    M ./src/meep_internals.hpp -2

Tue May 31 19:55:04 EDT 2005  stevenj@fftw.org
  * get sources directly in solve_cw; add new step_d_source to sidestep current hacks

    M ./src/cw_fields.cpp -10 +5
    M ./src/meep.hpp -1 +3
    M ./src/step.cpp -5 +25

Tue May 31 19:24:53 EDT 2005  stevenj@fftw.org
  * use solve_cw in physical.cpp instead of timestepping

    M ./tests/physical.cpp -53 +21

Tue May 31 19:24:16 EDT 2005  stevenj@fftw.org
  * put -J on right hand side of solve_cw

    M ./src/cw_fields.cpp -3 +3

Tue May 31 18:36:51 EDT 2005  stevenj@fftw.org
  * yikes, silly bug in fields::solve_cw

    M ./src/cw_fields.cpp -1 +1

Tue May 31 18:17:47 EDT 2005  stevenj@fftw.org
  * allow CW sources to have complex frequencies (e.g. exponentially decaying)

    M ./src/meep.hpp -7 +9
    M ./src/sources.cpp -11 +3

Tue May 31 18:07:17 EDT 2005  stevenj@fftw.org
  * increase maxiters default to 10000 in solve_cw

    M ./src/meep.hpp -1 +1

Tue May 31 18:05:13 EDT 2005  stevenj@fftw.org
  * add solve_cw() variant that gets frequency from sources (and has reasonable defaults for the tolerance and maximum iterations)

    M ./src/cw_fields.cpp +15
    M ./src/meep.hpp +4

Tue May 31 17:52:24 EDT 2005  stevenj@fftw.org
  * don't output so often in bicgstab

    M ./src/bicgstab.cpp -1 +7

Tue May 31 17:49:00 EDT 2005  stevenj@fftw.org
  * slight tweak in bicgstab

    M ./src/bicgstab.cpp +5

Tue May 31 17:26:11 EDT 2005  stevenj@fftw.org
  * in fields::solve_cw, use the BiCGSTAB(L) algorithm instead of BiCGSTAB.  With L >= 2, this avoids a known convergence failure in BiCGSTAB for operators (like ours) where the eigenvalues are nearly purely imaginary.  Now, solve_cw converges to arbitrary tolerance (limited by numerical precision, of course) even in > 1d!  Hooray, it works!

    M ./configure.ac -1 +1
    M ./src/bicgstab.cpp -50 +167
    M ./src/bicgstab.hpp -6 +24
    M ./src/cw_fields.cpp -6 +18
    M ./src/meep.hpp -1 +1

Tue May 31 01:12:22 EDT 2005  stevenj@fftw.org
  * whoops, forgot to add cw_fields.cpp

    M ./src/bicgstab.cpp -1 +2
    M ./src/bicgstab.hpp -1 +2
    A ./src/cw_fields.cpp

Mon May 30 22:35:05 EDT 2005  stevenj@fftw.org
  * remove (commented-out) stabilized dnrm2, which doesn't parallelize anyway

    M ./src/bicgstab.cpp -22 +1

Mon May 30 22:34:10 EDT 2005  stevenj@fftw.org
  * whoops

    M ./src/bicgstab.cpp -1 +1

Mon May 30 22:23:05 EDT 2005  stevenj@fftw.org
  * during phasing, don't forget to update the E boundaries as well as E

    M ./src/step.cpp -4 +7

Mon May 30 22:20:06 EDT 2005  stevenj@fftw.org
  * add new fields::solve_cw method that, instead of timestepping, treats the whole FDTD system as a big linear equation (specified implicitly by the fields::step) and solves it by the stabilized bi-conjugate gradient method to get the CW response at a particular frequency.  It seems to work reasonably well, except for some reason I can't fathom you can't set the tolerance very low (less then 1e-2) or it never converges in 2+ dimensions

    M ./configure.ac -1 +1
    M ./src/Makefile.am -7 +7
    A ./src/bicgstab.cpp
    A ./src/bicgstab.hpp
    M ./src/fields.cpp +2
    M ./src/meep.hpp -5 +13
    M ./src/sources.cpp -8 +12
    M ./src/step.cpp -1 +21
    M ./src/update_e_from_d.cpp -1 +5

Thu May 19 15:21:05 EDT 2005  stevenj@fftw.org
  * add FIXME comment to unnecessary allocation

    M ./src/fields.cpp +1

Tue May 17 16:57:48 EDT 2005  stevenj@fftw.org
  * fixed slight bug ... volume::nowned() really returned the minimum nowned over all components, which is slightly less than the actual nowned for some components in cylindrical coords; changed the name to nowned_min() to reflect this, added a new nowned(component) that gives the exact nowned, and added a regression test

    M ./src/meep/vec.hpp -1 +2
    M ./src/vec.cpp -4 +11
    M ./tests/integrate.cpp +3

Tue May 17 16:19:33 EDT 2005  stevenj@fftw.org
  * rename all C++ headers to .hpp, for consistency with .cpp and for clarity

     ./src/meep.h -> ./src/meep.hpp
     ./src/meep/mympi.h -> ./src/meep/mympi.hpp
     ./src/meep/vec.h -> ./src/meep/vec.hpp
     ./src/meep_internals.h -> ./src/meep_internals.hpp
     ./src/ran.h -> ./src/ran.hpp
     ./src/threevec.h -> ./src/threevec.hpp
    M ./doc/complicated.tex -1 +1
    M ./doc/energy_cons.tex -1 +1
    M ./doc/energy_cons_1d.tex -1 +1
    M ./doc/epsilon_polariton_1d.tex -1 +1
    M ./doc/example.cpp -1 +1
    M ./doc/lossgain_epsilon.tex -1 +1
    M ./doc/nonlinear.tex -1 +1
    M ./doc/omniguide.tex -1 +1
    M ./doc/polaritonbands.tex -1 +1
    M ./doc/simple.tex -1 +1
    M ./doc/simplebands.tex -1 +1
    M ./src/Makefile.am -12 +13
    M ./src/anisotropic_averaging.cpp -2 +2
    M ./src/bands.cpp -2 +2
    M ./src/boundaries.cpp -2 +2
    M ./src/control_c.cpp -1 +1
    M ./src/dft.cpp -2 +2
    M ./src/energy_and_flux.cpp -2 +2
    M ./src/fields.cpp -2 +2
    M ./src/grace.cpp -2 +2
    M ./src/h5fields.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/initialize.cpp -2 +2
    M ./src/integrate.cpp -2 +2
    M ./src/loop_in_chunks.cpp -2 +2
    M ./src/meep.hpp -3 +2
    M ./src/meep_internals.hpp -2 +1
    M ./src/monitor.cpp -2 +2
    M ./src/mympi.cpp -1 +1
    M ./src/output_directory.cpp -1 +1
    M ./src/polarization.cpp -2 +2
    M ./src/ran.cpp -1 +1
    M ./src/ran.hpp -1
    M ./src/slices.cpp -2 +2
    M ./src/sources.cpp -2 +2
    M ./src/step.cpp -2 +2
    M ./src/step_d.cpp -4 +4
    M ./src/step_h.cpp -4 +4
    M ./src/structure.cpp -2 +2
    M ./src/threevec.hpp -1
    M ./src/time.cpp -1 +1
    M ./src/update_e_from_d.cpp -2 +2
    M ./src/update_e_from_d_prepare.cpp -4 +4
    M ./src/update_e_from_d_sources.cpp -3 +3
    M ./src/update_e_from_d_update.cpp -3 +3
    M ./src/update_from_e.cpp -4 +4
    M ./src/vec.cpp -1 +1
    M ./tests/2D_convergence.cpp -1 +1
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -1 +1
    M ./tests/convergence_cyl_waveguide.cpp -1 +1
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/h5test.cpp -2 +2
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Mon May 16 18:52:39 EDT 2005  stevenj@fftw.org
  * don't re-allocate d_minus_p array at each timestep

    M ./src/fields.cpp +5
    M ./src/meep.h -3 +6
    M ./src/update_e_from_d.cpp -11 +6
    M ./src/update_e_from_d_prepare.cpp -2 +1
    M ./src/update_e_from_d_sources.cpp -2 +1
    M ./src/update_e_from_d_update.cpp -2 +1

Mon May 16 18:03:20 EDT 2005  stevenj@fftw.org
  * add possibility to change PML strength, e.g. pml(X) * 2.0 will increase PML conductivity by 2 (squaring attenuation for same thickness, in theory, albeit increasing numerical reflection)

    M ./src/meep.h -10 +17
    M ./src/structure.cpp -6 +11

Mon May 16 15:45:01 EDT 2005  stevenj@fftw.org
  * comment regarding accuracy of modal volume calcs

    M ./src/energy_and_flux.cpp -2 +14

Mon May 16 14:58:27 EDT 2005  stevenj@fftw.org
  * Darcs is now right-handed (there was a bug in 1d/2d/3d that caused the curls to have the wrong signs, making the system "left-handed" and giving fluxes the wrong signs, although it didn't affect most other calculations)

    M ./src/fields.cpp -1 +1
    M ./tests/flux.cpp -6 +6

Mon May 16 13:36:37 EDT 2005  stevenj@fftw.org
  * work around datatype change in HDF5 1.6.4 (grrr)

    M ./src/h5file.cpp -2 +13

Mon May 16 13:29:19 EDT 2005  stevenj@fftw.org
  * eliminate unnecessary allocation of PML fields

    M ./src/energy_and_flux.cpp -8 +14
    M ./src/fields.cpp -9 +13

Wed Apr 27 15:33:47 EDT 2005  stevenj@fftw.org
  * whoops, fix compilation failure for --without-hdf5

    M ./src/h5file.cpp +2

Mon Apr 25 17:25:20 EDT 2005  stevenj@fftw.org
  * fixed incorrect types in hdf5 calls

    M ./src/h5file.cpp -2 +2

Mon Apr 25 16:33:34 EDT 2005  stevenj@fftw.org
  * print a little more information from "aack, odd number of grid points"

    M ./src/structure.cpp -1 +2

Mon Apr 25 16:31:35 EDT 2005  stevenj@fftw.org
  * when phasing epsilon, use update_e_from_d to keep E in synch, rather than "manual" division and multiplication by inveps diagonal"

    M ./src/step.cpp -31 +1

Mon Apr 25 16:30:55 EDT 2005  stevenj@fftw.org
  * order spherical quadrature points to maximize spatial separation (to make interface detection more efficient, in future)

    M ./src/sphere-quad.cpp -7 +49

Mon May  2 10:44:24 EDT 2005  droundy@abridgegame.org
  * fix bug when running in cylindrical coordinates with real fields.

    M ./src/step_d.cpp -1 +3
    M ./src/step_h.cpp -1 +3

Sat Feb  5 13:44:55 EST 2005  stevenj@fftw.org
  * output s/step along with time-step status

    M ./src/meep.h +1
    M ./src/step.cpp -2 +8
    M ./src/time.cpp -1 +1

Sat Feb  5 12:46:16 EST 2005  stevenj@fftw.org
  * fix comment

    M ./src/energy_and_flux.cpp -3 +3

Sat Feb  5 12:24:51 EST 2005  stevenj@fftw.org
  * rename Slicing to FieldOutput (since we also count hdf5 output under this)

    M ./src/h5fields.cpp r1
    M ./src/meep.h r1
    M ./src/slices.cpp r1
    M ./src/time.cpp r1

Sat Feb  5 12:19:11 EST 2005  stevenj@fftw.org
  * more verbose output by default, with option to suppress by setting meep::quiet = true

    M ./configure.ac -10
    M ./src/bands.cpp -6 +7
    M ./src/fields.cpp -2 +3
    M ./src/h5fields.cpp +2
    M ./src/meep.h -5 +3
    M ./src/mympi.cpp -2 +4
    M ./src/output_directory.cpp -2 +3
    M ./src/step.cpp -2 +9
    M ./src/structure.cpp +3
    M ./src/time.cpp -6 +6
    M ./tests/2D_convergence.cpp +1
    M ./tests/bench.cpp +1
    M ./tests/bragg_transmission.cpp +1
    M ./tests/convergence_cyl_waveguide.cpp +1
    M ./tests/cylindrical.cpp +1
    M ./tests/flux.cpp +1
    M ./tests/h5test.cpp +1
    M ./tests/integrate.cpp +1
    M ./tests/known_results.cpp +1
    M ./tests/one_dimensional.cpp +1
    M ./tests/physical.cpp +1
    M ./tests/symmetry.cpp +1
    M ./tests/three_d.cpp +1
    M ./tests/two_dimensional.cpp +1

Sat Feb  5 11:22:51 EST 2005  stevenj@fftw.org
  * allocate all fields lazily (not just in 2d), ensure all field arrays are initialized to null, don't allocate imag. part for is_real, add missing is_real check to fields::initialize, various cleanups

    M ./src/boundaries.cpp -9 +12
    M ./src/fields.cpp -82 +61
    M ./src/initialize.cpp -44 +25
    M ./src/meep.h -3 +3
    M ./src/meep_internals.h +1
    M ./src/polarization.cpp -2 +4
    M ./src/sources.cpp -1 +5
    M ./tests/2D_convergence.cpp -1 +1
    M ./tests/h5test.cpp -3 +3
    M ./tests/known_results.cpp -1 +1
    M ./tests/symmetry.cpp -8 +8

Fri Feb  4 19:53:44 EST 2005  stevenj@fftw.org
  * major surgery on connect_the_chunks
  connect_the_chunks was:
     (a) a major performance bottleneck on multiprocessor systems
     (b) very difficult to modify, consisting of the same code
         copy-and-pasted many times
     (c) fairly fragile, with the loops impossible to reorder
         without breaking step.cc
  
  I've tried to fix all of those problems.  Now, instead of calling
  things like locate_point O(nc^2) where np is the number of chunks,
  it only computes it O(nc) times, and a lot of the duplication is
  removed.  It's also much less fragile, because the connections are
  stored per phase type (complex, -1, or +1) rather than in one
  order-sensitive array.
  
  However, this required major changes to boundaries.cpp and related code.

    M ./src/boundaries.cpp -273 +163
    M ./src/fields.cpp -25 +21
    M ./src/meep.h -10 +14
    M ./src/step.cpp -41 +58

Mon Jan 31 19:23:19 EST 2005  stevenj@fftw.org
  * added new methods dft_flux::scale_dfts, fields::require_component, and fields::remove_sources

    M ./src/dft.cpp -6 +6
    M ./src/fields.cpp -7 +22
    M ./src/meep.h -2 +8
    M ./src/sources.cpp -9 +12
    M ./tests/bragg_transmission.cpp -1 +1

Thu Jan 27 00:32:41 EST 2005  stevenj@fftw.org
  * prelimiary support for "D" sources, which multiply J by epsilon

    M ./src/sources.cpp +9

Thu Jan 27 00:30:34 EST 2005  stevenj@fftw.org
  * support symmetry-based reductions of geometric_volume_list for efficient computation e.g. of DFT fluxes etc

    M ./src/dft.cpp -45 +22
    M ./src/meep.h -4 +2
    M ./src/meep/vec.h -8 +24
    M ./src/vec.cpp +63

Thu Jan 27 00:29:49 EST 2005  stevenj@fftw.org
  * bug fix in symmetry::phase_shift for Poynting vector

    M ./src/vec.cpp -1 +3

Thu Jan 27 00:28:26 EST 2005  stevenj@fftw.org
  * force newline in abort messages if one is missing

    M ./src/mympi.cpp +1

Tue Jan 25 20:19:21 EST 2005  stevenj@fftw.org
  * immediately flush master_printf output

    M ./src/mympi.cpp -1 +1

Mon Dec  6 18:04:09 EST 2004  stevenj@fftw.org
  * comment correction

    M ./src/h5fields.cpp -2 +1
    M ./src/integrate.cpp -2 +1

Mon Dec  6 17:25:02 EST 2004  stevenj@fftw.org
  * added new derived_component type for various quantities (Poynting vector, energy density) useful to output in get_field and output_hdf5

    M ./src/h5fields.cpp +68
    M ./src/meep.h +8
    M ./src/meep/vec.h -3 +41
    M ./src/monitor.cpp +36
    M ./src/vec.cpp +42
    M ./tests/h5test.cpp -15 +24

Mon Dec  6 15:08:07 EST 2004  stevenj@fftw.org
  * consolidated min/max/abs functions in meep_internals.h

    M ./src/h5fields.cpp -5 +1
    M ./src/meep_internals.h -13 +2
    M ./src/vec.cpp -6 +1

Mon Dec  6 14:55:50 EST 2004  stevenj@fftw.org
  * whoops (only compute offsets for integration on Dielectric grid)

    M ./src/integrate.cpp -1 +2

Mon Dec  6 14:40:47 EST 2004  stevenj@fftw.org
  * fixed missing namespaces

    M ./src/update_e_from_d_update.cpp -5 +1

Mon Dec  6 14:21:53 EST 2004  stevenj@fftw.org
  * consolidated/simplified fields::output_hdf5 interface

    M ./src/h5fields.cpp -74 +54
    M ./src/meep.h -25 +8
    M ./tests/h5test.cpp -3 +3

Mon Dec  6 13:44:27 EST 2004  stevenj@fftw.org
  * add -*- C++ -*- to top of header files so that emacs will use C++ mode (even though they end with .h and not .hpp or .hh)

    M ./libctl/meep-ctl-const.h +1
    M ./libctl/meep-ctl-swig.h +1
    M ./libctl/meep-ctl.h +1
    M ./src/meep.h +1
    M ./src/meep/mympi.h +1
    M ./src/meep/vec.h +1
    M ./src/meep_internals.h +1
    M ./src/ran.h +1
    M ./src/threevec.h +1

Mon Dec  6 00:54:10 EST 2004  stevenj@fftw.org
  * rewrote hdf5 output again in terms of new generic field_function (to output an arbitrary function of the fields); also, when the Dielectric component is requested we use 3/trace(average inveps) instead of eps[i], since the former is closer to what is actually used for time-stepping

    M ./src/h5fields.cpp -107 +266
    M ./src/integrate.cpp -8 +38
    M ./src/meep.h -14 +57
    M ./src/monitor.cpp -11 +66

Sun Dec  5 14:24:12 EST 2004  stevenj@fftw.org
  * whoops, forgot to add integrate.cpp

    A ./src/integrate.cpp

Sun Dec  5 14:07:52 EST 2004  stevenj@fftw.org
  * rename fields::integrate to fields::loop_in_chunks, to reflect more generic nature; added *new* fields::integrate which *does* just do integration and makes it much much easier; rewrote energy_and_flux.cpp in terms of new integrate function

     ./src/fields_integrate.cpp -> ./src/loop_in_chunks.cpp
    M ./src/Makefile.am -6 +7
    M ./src/dft.cpp -5 +5 r1
    M ./src/energy_and_flux.cpp -231 +46 r2
    M ./src/h5fields.cpp -4 +4 r1
    M ./src/loop_in_chunks.cpp -32 +47 r1
    M ./src/meep.h -7 +21 r2
    M ./src/meep/mympi.h -1 +2
    M ./src/mympi.cpp +8
    M ./src/sources.cpp -5 +5 r1
    M ./tests/integrate.cpp -50 +27

Fri Dec  3 20:02:06 EST 2004  stevenj@fftw.org
  * faster, more easily generalized output_hdf5 based on fields::integrate
  The old version of fields::output_hdf5 pre-dated fields::integrate,
  and had home-brewed code for looping over the chunks and symmetries
  and computing the output from each.  Not only was this complicated (as
  opposed to centralizing the complexity in fields::integrate), but it
  also was based on fields::interpolate onto an arbitrary grid, which
  had the following disadvantages:
  
  * doing an arbitrary interpolation for every point in a large volume
    is very slow.  This is a problem if we want to output often.
  
  * very hard to compute functions of more than one field component,
    e.g. the energy density or the average inveps dielectric, because
    on an arbitrary grid this requires communication in general.
  
  * hard to prevent different chunks/symmetries to write slightly
    overlapping data, which produces undefined results in parallel HDF5.
  
  The new code *always* outputs on the dielectric grid, which (since it
  is a fixed interpolation scheme) is a tight loop for each chunk, and
  is guaranteed by fields::integrate to be non-overlapping.  Perhaps
  even more importantly, it will now be easy to implement output
  functions of more than one field component, since no communication is
  required for the interpolation.
  

    M ./src/h5fields.cpp -206 +174
    M ./src/meep.h -3 +3
    M ./tests/h5test.cpp -25 +36

Fri Dec  3 12:25:35 EST 2004  stevenj@fftw.org
  * whoops, fixed bug in last patch (vec min/max funcs)

    M ./src/vec.cpp +4

Fri Dec  3 00:37:08 EST 2004  stevenj@fftw.org
  * added more min/max functions for vec/ivec

    M ./src/meep/vec.h +6
    M ./src/mympi.cpp +11
    M ./src/vec.cpp -10 +30

Fri Dec  3 00:36:16 EST 2004  stevenj@fftw.org
  * added snap_unit_dims to fields::integrate

    M ./src/fields_integrate.cpp -3 +19
    M ./src/meep.h -1 +2

Fri Dec  3 00:34:09 EST 2004  stevenj@fftw.org
  * comment clarification for yee2diel_offsets

    M ./src/vec.cpp -4 +6

Thu Dec  2 17:49:54 EST 2004  stevenj@fftw.org
  * stopgap fix for PML with non-diagonal inveps...is a longer-term, "proper" fix needed???

    M ./src/structure.cpp +4

Mon Nov 29 21:37:42 EST 2004  stevenj@fftw.org
  * added h5file::prevent_deadlock() for deadlock-prevention hacks in exclusive-access HDF5 mode (maybe we should just ditch support for that and require HDF5 to be compiled with MPI?)

    M ./src/dft.cpp +2
    M ./src/h5file.cpp -4 +10
    M ./src/meep.h +1
    M ./tests/bragg_transmission.cpp +2

Mon Nov 29 19:28:53 EST 2004  stevenj@fftw.org
  * completely revamped structure and structure_chunk initialization
  In the previous version of the code, the typical initialization
  sequence went like this:
  
  1) create structure (initializes chunks, evaluates epsilon)
  2) set PML (re-initializes chunks, shuffles epsilon around)
  
  Step (2) is problematic because the communication of epsilon to the
  new chunks was performed point-by-point.  Not only is this incredibly
  slow, but it actually causes Tungsten's MPI implementation to crash
  (probably because there are too many messages).  Moreover, it is
  completely unnecessary.
  
  In the new version, the PML boundaries are specified when the structure
  is first created, so that the chunks need only be computed once and are
  never re-shuffled around.
  
  INCOMPATIBLE API CHANGE:
  
    old:
       structure s(vol, eps, splitting, symmetries);
       s.use_pml_everywhere(1.0);
  
    new:
       structure s(vol, eps, pml(1.0), symmetries, splitting);
  
  In general, the PML boundary regions are specified by *summing* terms
  of the form pml(thickness, direction, High/Low).  If one or both of
  the last two arguments is omitted, it means *all* sides and *all*
  directions, respectively.  So, a more complicated example is:
  
    old:
       structure s(vol, eps, splitting, symmetries);
       s.use_pml(X, High, 1.0);
       s.use_pml(X, Low, 1.0);
       s.use_pml(Y, High, 1.0);
  
    new:
       structure s(vol, eps, pml(1.0, X) + pml(1.0, Y, High), 
                   symmetries, splitting);
  
  To specify *no* PML, you use:
     
     structure s(vol, eps, no_pml(), symmetries, splitting);
  
  This is actually the default, if you omit the boundary-region argument
  along with splitting (default = 0) and symmetries (default =
  identity).
  
  INCOMPATIBLE API CHANGE:
  
    old:
       s.set_epsilon(eps, minvol, do_aniso_averaging);
  
    new:
       s.set_epsilon(eps, do_aniso_averaging, minvol);
  
  The default for the last two arguments is true and 0, respectively, so
  in the usual case where you are using this function because you want
  to turn on averaging (currently not the default), you just do:
  
     s.set_epsilon(eps);

    M ./doc/complicated.tex -2 +1
    M ./doc/epsilon_polariton_1d.tex -2 +1
    M ./doc/lossgain_epsilon.tex -5 +4
    M ./doc/nonlinear.tex -5 +3
    M ./doc/omniguide.tex -1 +1
    M ./doc/simple.tex -3 +2
    M ./src/meep.h -31 +86
    M ./src/structure.cpp -279 +139
    M ./tests/2D_convergence.cpp -1 +1
    M ./tests/bench.cpp -3 +2
    M ./tests/bragg_transmission.cpp -4 +2
    M ./tests/convergence_cyl_waveguide.cpp -3 +3
    M ./tests/cylindrical.cpp -10 +8
    M ./tests/flux.cpp -12 +6
    M ./tests/h5test.cpp -3 +3
    M ./tests/integrate.cpp -1 +1
    M ./tests/known_results.cpp -5 +2
    M ./tests/one_dimensional.cpp -4 +4
    M ./tests/physical.cpp -4 +2
    M ./tests/symmetry.cpp -42 +38
    M ./tests/three_d.cpp -10 +7
    M ./tests/two_dimensional.cpp -22 +12

Sun Nov 28 19:01:35 EST 2004  stevenj@fftw.org
  * provide high-resolution wall_time() function in lieu of clock().  Automatically print elapsed time upon program completion.  Don't use exit(0) in main()...use return 0 so that ~initialize() is called.

    M ./configure.ac +7
    M ./src/fields.cpp -2 +2
    M ./src/meep.h -1 +1
    M ./src/meep/mympi.h +5
    M ./src/mympi.cpp +31
    M ./src/time.cpp -10 +8
    M ./tests/bench.cpp -20 +19
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/flux.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/three_d.cpp -1 +1
    M ./tests/two_dimensional.cpp -1 +1

Wed Nov 24 20:04:09 EST 2004  stevenj@fftw.org
  * add stride0 function that returns 0, instead of 1, for unused dimensions, so that we can easily distinguish them from "real" dimensions in macros etc.

    M ./src/meep/vec.h -7 +9
    M ./src/vec.cpp -5 +6

Wed Nov 24 20:03:39 EST 2004  stevenj@fftw.org
  * don't use make_average_eps in omniguide.tex

    M ./doc/omniguide.tex -1 +2

Wed Nov 24 17:49:55 EST 2004  stevenj@fftw.org
  * remove structure::make_average_eps (apparently unused, non-functional, pointless function)

    M ./src/meep.h -2
    M ./src/structure.cpp -20

Fri Nov  5 12:45:13 EST 2004  stevenj@fftw.org
  * updated acx_mpi.m4

    M ./m4/acx_mpi.m4 -4 +4

Fri Oct 29 21:30:13 EDT 2004  stevenj@fftw.org
  * added another joke

    M ./README -1 +1

Fri Aug 20 18:08:59 EDT 2004  alexrod7@mit.edu
  * added fields::electric_energy_weighted_integral function

    M ./src/energy_and_flux.cpp -10 +27
    M ./src/meep.h +2

Thu Oct 28 21:51:37 EDT 2004  stevenj@fftw.org
  * resolve conflict

    M ./tests/2D_convergence.cpp -3 +3

Thu Oct 28 21:48:29 EDT 2004  alexrod7@mit.edu
  * bug fix: tensor epsilon averaging missed the z component in 2d (added test case for this)

    M! ./src/structure.cpp -1 +2
    M! ./tests/2D_convergence.cpp -17 +29

Mon Aug  9 15:31:16 EDT 2004  alexrod7@mit.edu
  * add fields::electric_deps_integral_in_box function for perturbation theory etc.

    M ./src/energy_and_flux.cpp +59
    M ./src/meep.h +2

Tue Jul 27 18:24:11 EDT 2004  stevenj@fftw.org
  * when computing max(E dot D), compute product of components *before* averaging, in closer analogue to how energy integral is computed

    M ./src/energy_and_flux.cpp -25 +12

Tue Jul 20 15:37:27 EDT 2004  alexrod7@mit.edu
  * add function to compute modal volume according to Purcell definition

    M ./src/energy_and_flux.cpp +103
    M ./src/meep.h +2

Wed Jul 14 21:02:03 EDT 2004  stevenj@fftw.org
  * removed gratuitous "inline" keyword that confused gcc 3.3

    M ./src/vec.cpp -1 +1

Wed Jul 14 20:02:19 EDT 2004  stevenj@fftw.org
  * correct save_dft_hdf5/load_dft_hdf5 for MPI, add test case to bragg_transmission.cpp (compute reflection by subtracting DFTs)

    M ./src/dft.cpp -11 +8
    M ./src/meep/mympi.h +1
    M ./src/mympi.cpp +8
    M ./tests/bragg_transmission.cpp -24 +52

Wed Jul 14 17:38:18 EDT 2004  stevenj@fftw.org
  * vec(r,z) -> veccyl(r,z); vec2d(x,y) -> vec(x,y)
  as a historical artifact, the code used vec(_, _) to indicate cylindrical
  coordinates, while vec(_) was 1d and vec(_,_,_) was 3d.  2d was handled by
  vec2d(_, _).  It makes much more sense to make cylindrical coordinates the
  exception, and so I have implemented this change.
  
  To insure that this does not introduce any bugs into Meep, I implemented
  the change in 2 stages.  First, implement veccyl and remove vec(_, _)
  constructor -- the compiler catches any uses of the 2 argument vec(_,_)
  and I can replace them with veccyl.  Second, remove vec2d and make
  vec(_,_) produce a 2d vector.
  
  USER CODE WILL NEED TO BE UPDATED, HOWEVER!  Hopefully, the elimination
  of vec2d will clue people in that something has changed.
  

    M ./doc/complicated.tex -3 +3
    M ./doc/energy_cons.tex -3 +3
    M ./doc/example.cpp -3 +3
    M ./doc/lossgain_epsilon.tex -8 +8
    M ./doc/nonlinear.tex -3 +3
    M ./doc/omniguide.tex -6 +6
    M ./doc/polaritonbands.tex -2 +2
    M ./doc/simple.tex -2 +2
    M ./src/anisotropic_averaging.cpp -3 +4
    M ./src/boundaries.cpp -3 +4
    M ./src/meep/vec.h -8 +8
    M ./src/slices.cpp -16 +16
    M ./src/step.cpp -1 +1
    M ./src/vec.cpp -8 +8
    M ./tests/2D_convergence.cpp -9 +9
    M ./tests/bench.cpp -10 +10
    M ./tests/convergence_cyl_waveguide.cpp -4 +4
    M ./tests/cylindrical.cpp -33 +33
    M ./tests/flux.cpp -14 +14
    M ./tests/h5test.cpp -6 +6
    M ./tests/known_results.cpp -2 +2
    M ./tests/physical.cpp -5 +5
    M ./tests/symmetry.cpp -103 +103
    M ./tests/two_dimensional.cpp -42 +42

Wed Jul 14 15:22:17 EDT 2004  stevenj@fftw.org
  * slight change in flux tolerance

    M ./tests/flux.cpp -1 +1

Tue Jul 13 19:33:26 EDT 2004  stevenj@fftw.org
  * rename c -> Courant, make a field of structure instead of global
  First of all, I renamed "c" to "Courant", since that is what it is
  (Courant number = dt/dx) ... it is not the speed of light, which
  should be 1.  (I've run into bugs multiple times now from having "c"
  be shadowed by a local variable, e.g. for the component, and this gets
  rid of that forever.)
  
  Second, since people may want to change the Courant number to reduce
  numerical dispersion (in general, it only has to be < 1 /
  sqrt(#dimensions)), I made it a field of the structure class (and also
  of structure_chunk and fields_chunk).  The default is still 0.5,
  however.
  
  Third, inva is no longer a field of the fields class; instead, we have
  a new field dt which is the timestep.  This is much more intuitive and
  useful to the end-user (and to us) instead of having to compute
  Courant*inva all the time.
  
  There some minor related changes.  e.g. do_harminv takes simply the
  sampling interval dt instead of a scale_factor and a.

    M ./hsrc/step_d_gen.hs -3 +3
    M ./hsrc/step_h_gen.hs -3 +3
    M ./hsrc/update_from_e_gen.hs -1 +1
    M ./src/bands.cpp -16 +14
    M ./src/boundaries.cpp -1 +1
    M ./src/dft.cpp -2 +2
    M ./src/fields.cpp -7 +9
    M ./src/initialize.cpp -5 +4
    M ./src/meep.h -10 +11
    M ./src/meep/vec.h -4 +7
    M ./src/meep_internals.h -1 +1
    M ./src/monitor.cpp -1 +1
    M ./src/polarization.cpp -2 +2
    M ./src/slices.cpp -5 +5
    M ./src/sources.cpp -1 +1
    M ./src/step.cpp -2 +3
    M ./src/step_d.cpp -13 +13
    M ./src/step_h.cpp -12 +12
    M ./src/structure.cpp -11 +23
    M ./src/vec.cpp -32 +28
    M ./tests/bench.cpp -1 +1
    M ./tests/bragg_transmission.cpp -8 +8
    M ./tests/convergence_cyl_waveguide.cpp -2 +2
    M ./tests/flux.cpp -8 +8
    M ./tests/h5test.cpp -1 +1
    M ./tests/physical.cpp -2 +2

Tue Jul 13 18:20:48 EDT 2004  stevenj@fftw.org
  * use delete[] instead of delete in dft.cpp

    M ./src/dft.cpp -1 +1

Tue Jul 13 00:41:36 EDT 2004  stevenj@fftw.org
  * grrrr

    M ./libctl/Makefile.am -8 +7

Tue Jul 13 00:29:32 EDT 2004  stevenj@fftw.org
  * grrr

    M ./libctl/Makefile.am -1 +1

Tue Jul 13 00:14:52 EDT 2004  stevenj@fftw.org
  UNDO: set GEN_CTL_IO even --without-libctl

    M ./configure.ac -3 +3

Tue Jul 13 00:19:32 EDT 2004  stevenj@fftw.org
  * can't buld meep_wrap.cxx without libctl

    M ./libctl/Makefile.am -2 +8

Tue Jul 13 00:14:52 EDT 2004  stevenj@fftw.org
  * set GEN_CTL_IO even --without-libctl

    M ./configure.ac -3 +3

Mon Jul 12 23:38:50 EDT 2004  stevenj@fftw.org
  * disable debugging output in integrate.cpp

    M ./tests/integrate.cpp -1 +1

Mon Jul 12 23:33:53 EDT 2004  stevenj@fftw.org
  * fix bug in dft_flux spectrum, support dft over list of geometric volumes in preparation for exploiting symmetry, add routine to get dft flux through surface of box

    M ./src/dft.cpp -69 +133
    M ./src/energy_and_flux.cpp -10 +10
    M ./src/fields_integrate.cpp -1 +1
    M ./src/h5file.cpp -1 +1
    M ./src/meep.h -19 +27
    M ./src/meep/vec.h -2 +19
    M ./src/vec.cpp +9
    M ./tests/bench.cpp -2 +2
    M ./tests/bragg_transmission.cpp -7
    M ./tests/flux.cpp -32 +93
    M ./tests/integrate.cpp -51 +98

Thu Jul  1 12:02:55 EDT 2004  stevenj@fftw.org
  * note FIXME in dft.cpp (save_hdf5 is wrong for MPI)

    M ./src/dft.cpp +4

Wed Jun 30 19:46:07 EDT 2004  stevenj@fftw.org
  * make cylindrical flux test include r=0 in interior of integration volume

    M ./tests/flux.cpp -7 +7

Wed Jun 30 19:38:06 EDT 2004  stevenj@fftw.org
  * added cylindrical-coord flux test

    M ./tests/flux.cpp -2 +46

Fri Jun 25 14:03:04 EDT 2004  stevenj@fftw.org
  * fields::add_dft_pt, so that we can get the dft of a point without computing field value * dV

    M ./src/dft.cpp -1 +14
    M ./src/meep.h -1 +4

Tue Jun 22 14:53:56 EDT 2004  stevenj@fftw.org
  * update for new libctl, which supports (limited) SWIG integration

    M ./libctl/Makefile.am -3 +3
    A ./libctl/meep-ctl-swig.h
    M ./libctl/meep-ctl.h -3 +1
    M ./libctl/meep.i +8
    M ./libctl/meep.scm.in -2 +5
    M ./libctl/structure.cpp -4 +4

Mon Jun 21 20:08:21 EDT 2004  stevenj@fftw.org
  * append_data option only makes sense for fields::output_hdf5 version that takes an h5file option

    M ./src/h5fields.cpp -3 +2
    M ./src/meep.h -7 +7

Mon Jun 21 19:57:49 EDT 2004  stevenj@fftw.org
  * various modifications to support using SWIG to help generate Guile (libctl) interface, so I don't have to muck around with smobs

    M ./libctl/Makefile.am -4 +12
    M ./libctl/meep-ctl.h -11 +6
    M ./libctl/meep.cpp -2 +3
    A ./libctl/meep.i
    M ./libctl/meep.scm.in -3 +3
    R ./libctl/my-smob.h
    M ./libctl/structure.cpp -100 +5
    M ./src/meep.h -13 +10
    M ./src/meep/vec.h -1 +1

Mon Jun 21 17:26:44 EDT 2004  stevenj@fftw.org
  * print benchmark output in easier format for grepping and tabulating

    M ./tests/bench.cpp -5 +5

Wed Jul 14 16:45:12 EDT 2004  meep@ab-initio.mit.edu
  * don't use --enable-shared in darcs_test (triggers a bug with gcc 2.95, apparently)

    M ./darcs_test -1 +1

Mon Jun 21 00:28:57 EDT 2004  stevenj@fftw.org
  * no need to include mymypi.h and vec.h if already included via meep.h

    M ./src/h5file.cpp -1
    M ./src/vec.cpp -2

Mon Jun 21 00:22:21 EDT 2004  stevenj@fftw.org
  * vec.h and mympi.h should be installed under /usr/local/include/meep, while meep.h is installed under /usr/local/include

     ./src/mympi.h -> ./src/meep/mympi.h
     ./src/vec.h -> ./src/meep/vec.h
    M ./src/Makefile.am -1 +3
    A ./src/meep/
    M ./src/meep.h -2 +2

Sat Jun 19 14:09:48 EDT 2004  stevenj@fftw.org
  * lazy chunk connection: only reconnect chunks once, and do so in step_boundaries, after chunk connections have been invalidated by sources, boundary conditions, etc.

    M ./src/boundaries.cpp -12 +16
    M ./src/fields.cpp -3 +3
    M ./src/initialize.cpp -11 +21
    M ./src/meep.h -10 +8
    M ./src/mympi.cpp +16
    M ./src/mympi.h +2
    M ./src/sources.cpp -1 +1
    M ./src/step.cpp +1
    M ./tests/Makefile.am +2

Fri Jun 18 20:12:48 EDT 2004  stevenj@fftw.org
  * whoops, incorrect return type on new set_origin

    M ./src/vec.h -3 +3

Fri Jun 18 19:59:51 EDT 2004  stevenj@fftw.org
  * only call func() once per point, and use LOOP_OVER_VOL, in initialize_field

    M ./src/initialize.cpp -10 +9

Fri Jun 18 19:47:38 EDT 2004  stevenj@fftw.org
  * optimizations after profiling
  After running the code with profiling (compile with -pg) and analyzing
  the results with gprof, I noticed that a lot of time was being wasted
  calling volume::io() and volume::iloc() during "startup".  (This
  corroborated an earlier observation that the pre-time-stepping code
  was taking a long time, several seconds in 3d.)  I've sped up this
  greatly by several improvements, summarized as follows:
  
  1) Eliminate loops of the form:
  	for (i = 0; i < v.ntot(); ++i) {
  		ivec here = v.iloc(c, i);
  		...
  	}
  replacing them with LOOP_OVER_VOL
  
  2) Add special loops LOOP_OVER_VOL_OWNED and LOOP_OVER_VOL_NOTOWNED to
  loop just over the owned and not-owned (boundary) points,
  respectively.
  
  3) io() was still taking too long, so I replaced it with a io member
     that is recomputed on the rare occasions when the origin is changed.
     To make sure that it gets recomputed, volume::origin is now private,
     and there are functions for getting/setting it.
  
  Plus a few other tricks/optimizations in heavily-called "startup" functions.

    M ./src/boundaries.cpp -209 +199
    M ./src/meep.h -1 +1
    M ./src/polarization.cpp -8 +14
    M ./src/sources.cpp -4 +1
    M ./src/step_d.cpp -13 +13
    M ./src/step_h.cpp -12 +12
    M ./src/structure.cpp -53 +65
    M ./src/vec.cpp -33 +106
    M ./src/vec.h -15 +52
    M ./tests/bench.cpp -1 +1
    M ./tests/flux.cpp -3 +3
    M ./tests/integrate.cpp -4 +94
    M ./tests/symmetry.cpp -1 +1

Thu Jun 17 17:50:06 EDT 2004  stevenj@fftw.org
  * pass shift ivect instead of vec to field integrand, so that ivec coords can be computed without worrying about rounding

    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -3 +3
    M ./src/fields_integrate.cpp -3 +3
    M ./src/meep.h -1 +1
    M ./src/sources.cpp -7 +7
    M ./tests/integrate.cpp -2 +2

Thu Jun 17 13:56:21 EDT 2004  stevenj@fftw.org
  * whoops, bug in h5file::read_size

    M ./src/dft.cpp -1 +1
    M ./src/h5file.cpp +1

Thu Jun 17 03:51:31 EDT 2004  stevenj@fftw.org
  * accept data prefix in dft/flux load/save HDF5

    M ./src/dft.cpp -12 +16
    M ./src/meep.h -4 +6

Thu Jun 17 02:34:46 EDT 2004  stevenj@fftw.org
  * set outdir in fields::set_output_directory(!!)

    M ./src/output_directory.cpp -2 +2

Thu Jun 17 02:33:58 EDT 2004  stevenj@fftw.org
  * removed unused dindex

    M ./tests/bragg_transmission.cpp -2

Thu Jun 17 02:33:37 EDT 2004  stevenj@fftw.org
  * extra check in src_vol integrand

    M ./src/sources.cpp +3

Thu Jun 17 02:32:24 EDT 2004  stevenj@fftw.org
  * add add_volume_source that assumes a constant amplitude

    M ./src/meep.h +3
    M ./src/sources.cpp -2 +8

Thu Jun 10 02:29:06 EDT 2004  stevenj@fftw.org
  * update bragg_transmission for new output_hdf5 syntax, print a little output

    M ./tests/bragg_transmission.cpp -3 +6

Thu Jun 10 02:19:35 EDT 2004  stevenj@fftw.org
  * whoops, some fixes to previous h5file patch

    M ./src/h5file.cpp -7 +8

Thu Jun 10 02:05:50 EDT 2004  stevenj@fftw.org
  * lazy HDF5 creation, closing after data extension, to avoid deadlocks for writing time data

    M ./src/dft.cpp +1
    M ./src/h5fields.cpp +2
    M ./src/h5file.cpp -46 +68
    M ./src/meep.h -1 +6

Thu Jun 10 01:05:33 EDT 2004  stevenj@fftw.org
  * fixed logic bug in hdf5: need to keep a list of extensible datasets; just remembering most recent one is insufficient

    M ./src/h5file.cpp -21 +60
    M ./src/meep.h -1 +10
    M ./tests/h5test.cpp -1 +1

Thu Jun 10 00:09:08 EDT 2004  stevenj@fftw.org
  * reworked HDF5 I/O api, so that file can be kept open until I/O operations are finished

     ./src/h5io.cpp -> ./src/h5file.cpp
    M ./src/Makefile.am -3 +2
    M ./src/dft.cpp -69 +25
    M ./src/h5fields.cpp -39 +25
    M ./src/h5file.cpp -315 +415
    R ./src/h5io.h
    M ./src/meep.h -18 +71
    M ./tests/h5test.cpp -38 +37

Tue Jun  8 17:37:18 EDT 2004  stevenj@fftw.org
  * use "=", not "==" for sh tests

    M ./configure.ac -2 +2

Tue Jun  8 16:43:41 EDT 2004  stevenj@fftw.org
  * lower tolerance to ignore small negative weights

    M ./src/vec.cpp -1 +1

Tue Jun  8 16:43:01 EDT 2004  stevenj@fftw.org
  * according to the GNU libc manual, you should always ignore SIGINT if the parent process wants you to

    M ./src/control_c.cpp -1 +2

Tue Jun  8 16:41:56 EDT 2004  stevenj@fftw.org
  * check whether to catch and ignore SIGFPE, for darn Alpha systems that crash even on innocuous things like exp(-infinity)

    M ./configure.ac +14
    M ./src/mympi.cpp +7

Mon Jun  7 22:13:32 EDT 2004  stevenj@fftw.org
  * check for MPI immediately after getting C++ compiler, so that mpiCC is used for all subsequent tests (for --with-mpi)

    M ./configure.ac -14 +17

Fri Jun  4 18:41:55 EDT 2004  stevenj@fftw.org
  * don't output hdf5 file in bragg_transmission test

    M ./tests/bragg_transmission.cpp -1 +2

Wed Jun  2 16:50:01 EDT 2004  stevenj@fftw.org
  * removed DFT volumes and fluxes from TODO (since done)

    M ./TODO -4 +1

Wed Jun  2 16:42:46 EDT 2004  stevenj@fftw.org
  * added geometric_volume::normal_direction

    M ./src/dft.cpp -28 +2
    M ./src/energy_and_flux.cpp -30 +5
    M ./src/vec.cpp +31
    M ./src/vec.h +1

Wed Jun  2 16:30:08 EDT 2004  stevenj@fftw.org
  * bug fixes in dft, add dft_flux feature, add test case comparing to analytical 1d Bragg transmission spectrum

    M ./src/dft.cpp -1 +125
    M ./src/meep.h +28
    M ./src/mympi.cpp +8
    M ./src/mympi.h +1
    M ./tests/Makefile.am -4 +4
    A ./tests/bragg_transmission.cpp

Tue Jun  1 02:44:45 EDT 2004  stevenj@fftw.org
  * added 2d flux test

    M ./tests/flux.cpp -3 +49

Tue Jun  1 01:00:27 EDT 2004  stevenj@fftw.org
  * IVEC_LOOP_WEIGHT macro cleanup

    M ./src/dft.cpp -1 +1
    M ./src/energy_and_flux.cpp -3 +3
    M ./src/sources.cpp -1 +1
    M ./src/vec.h -3 +3
    M ./tests/integrate.cpp -2 +4

Mon May 31 21:56:30 EDT 2004  stevenj@fftw.org
  * whoops, do I remember how to compute cross products?

    M ./src/energy_and_flux.cpp -10 +19

Mon May 31 20:22:39 EDT 2004  stevenj@fftw.org
  * as long as we have ivec::<=, we should have >=, <, and > too

    M ./src/vec.h +15

Mon May 31 20:22:10 EDT 2004  stevenj@fftw.org
  * whoops, inva instead of a in fields::integrate for source volumes

    M ./src/fields_integrate.cpp -1 +1

Mon May 31 19:58:08 EDT 2004  stevenj@fftw.org
  * added unit_vec function to vec.h

    M ./src/vec.h -1 +7

Mon May 31 18:49:44 EDT 2004  stevenj@fftw.org
  * make sure coordinates are exact in symmetry.cpp
  In symmetry.cpp, we want to check that adding symmetry to a simulation
  produces *exactly* the same result as the simulation without explicit
  use of symmetry.  This, however, requires a great deal of care with
  floating point arithmetic.
  
  In particular, one important requirement is that the sources *exactly*
  obey the symmetry condition.  In order for this to be true, the
  location of the source *as represented within floating point* must be
  symmetric.  (Recall that floating-point can only represent base-2
  rational fractions exactly, i.e. integer * 2^e.)  To impose this
  condition, we employ two tricks:
  
  First, the resolution 'a' should be exactly representable (e.g. a
  power of 2) , so that no surprises occur when converting vecs to ivecs
  etc.
  
  Second, the coordinates, or at least those coordinates which are
  supposed to be symmetric, must be exactly representable.
  
  For example, suppose that something is supposed to be mirror symmetric
  around x=0.5.  You might think that sources at x=0.2 and x=0.8 would
  satisfy this, but they don't because those two coordinates are not
  exactly representable--they are stored as 0.2+eps1 and 0.8+eps2, where
  eps1 and eps2 are ~1e-16, and these coordinates are not symmetric.
  Instead, we use e.g. x=0.25 and x=0.75, which are symmetric because
  they are exactly represented (1 / 2^2 and 3 / 2^2, respectively).
  
  Of course, a user code is not expected to play these games, but in
  such circumstances it is acceptable for the symmetric and
  non-symmetric simulations to differ by errors on the order of the
  machine precision.

    M ./tests/symmetry.cpp -21 +21

Sun May 30 20:31:25 EDT 2004  stevenj@fftw.org
  * only call alloc_f() for is_mine() chunks

    M ./src/sources.cpp -1 +1

Sun May 30 20:30:49 EDT 2004  stevenj@fftw.org
  * LOOP_OVER_IVECS cleanups

    M ./src/dft.cpp -10 +4
    M ./src/energy_and_flux.cpp -22 +7
    M ./src/sources.cpp -5 +1
    M ./src/vec.h -23 +24
    M ./tests/integrate.cpp -17 +13

Sun May 30 19:59:08 EDT 2004  stevenj@fftw.org
  * replace old add_source_volume with new version based on fields::integrate

    M ./src/dft.cpp -7 +5
    M ./src/fields_integrate.cpp -1 +16
    M ./src/meep.h -19 +12
    M ./src/meep_internals.h -2 +2
    M ./src/sources.cpp -109 +94

Sat May 29 03:44:12 EDT 2004  stevenj@fftw.org
  * add max() function for symmetry.cpp, when C++ doesn't provide it

    M ./tests/symmetry.cpp +2

Sat May 29 03:02:24 EDT 2004  stevenj@fftw.org
  * updated "known result" for polariton_energy for new fields::integrate-based energy
  The new field_energy function, using fields::integrate, gives slightly
  different energy results from the old code.  This is because of
  different integration weights for the boundary edges...I think the new
  version is more reasonable, actually.
  
  Basically, the old code just summed up the energy for every point in
  the cell, with uniform integration weight.  The new code is almost the
  same, except that at the boundaries, it integrates the boundary pixels
  assuming linear interpolation to the points just beyond (or at) the
  boundary.  (Points beyond the boundary are assumed zero for
  non-periodic boundary conditions.)  I think this should be more
  accurate.
  
  Of course, the new result and the old result converge to one another
  as the resolution is increased.

    M ./tests/known_results.cpp -3 +3

Sat May 29 02:51:55 EDT 2004  stevenj@fftw.org
  * completely replaced old flux_plane stuff with new flux_box calculation (supports 2d/3d flux integration, not just 1d)

    M ./src/Makefile.am -7 +6
    M ./src/energy_and_flux.cpp +41 r1
    M ./src/fields.cpp -3
    R ./src/fluxes.cpp
    M ./src/meep.h -24 +28 r1
    M ./src/meep_internals.h -31
    M ./src/step.cpp -1 +3
    M ./src/vec.h +1
    M ./tests/bench.cpp r1
    M ./tests/flux.cpp -1 +1 r1

Sat May 29 01:53:07 EDT 2004  stevenj@fftw.org
  * added fields::integrate-based flux and thermo. energy

    M ./src/dft.cpp -9 +7
    M ./src/energy_and_flux.cpp -27 +141
    M ./src/meep.h -2 +3
    M ./src/meep_internals.h -1 +1
    M ./src/polarization.cpp -11

Fri May 28 23:27:41 EDT 2004  stevenj@fftw.org
  * fields::integrate now works over an arbitrary Yee grid

    M ./src/dft.cpp -1 +3
    M ./src/energy_and_flux.cpp -41 +26
    M ./src/fields_integrate.cpp -34 +49
    M ./src/meep.h -2 +4
    M ./src/vec.cpp -1 +12
    M ./src/vec.h +1
    M ./tests/integrate.cpp -5 +15
    M ./tests/symmetry.cpp -1 +2

Fri May 28 21:27:12 EDT 2004  stevenj@fftw.org
  * some code compression in dft.cpp

    M ./src/dft.cpp -52 +34

Fri May 28 20:30:27 EDT 2004  stevenj@fftw.org
  * fixes to fields::integrate and friends (+ more rigorous test), use fields::integrate for energy integration

    M ./src/dft.cpp -29 +20
    M ./src/energy_and_flux.cpp -40 +84
    M ./src/fields_integrate.cpp -87 +147
    M ./src/meep.h -2 +1
    M ./src/vec.cpp +16
    M ./src/vec.h +19
    M ./tests/integrate.cpp -35 +73

Thu May 27 22:20:02 EDT 2004  stevenj@fftw.org
  * added dft.cpp: generic DFT volume support

    M ./src/Makefile.am -1 +1
    A ./src/dft.cpp
    M ./src/fields.cpp +2
    M ./src/meep.h -2 +59
    M ./src/step.cpp +1
    M ./src/vec.h -3 +3

Thu May 27 20:18:02 EDT 2004  stevenj@fftw.org
  * added read_chunk, read_size to h5io

    M ./src/h5io.cpp -41 +203
    M ./src/h5io.h -23 +28

Fri May 28 18:49:43 EDT 2004  michel@mit.edu
  * don't call globals "dirname", since this is a library function in POSIX

    M ./tests/cylindrical.cpp r1
    M ./tests/known_results.cpp r1
    M ./tests/one_dimensional.cpp r1
    M ./tests/symmetry.cpp r1
    M ./tests/three_d.cpp r1
    M ./tests/two_dimensional.cpp r1

Fri May 28 18:41:02 EDT 2004  michel@mit.edu
  * whoops, missing close paren

    M ./configure.ac -1 +1

Fri May 28 18:40:15 EDT 2004  michel@mit.edu
  * check for fftw2 installed as libdfftw

    M ./configure.ac -2 +3
    M ./src/monitor.cpp -1 +3

Thu May 27 04:58:29 EDT 2004  stevenj@fftw.org
  * minor tweak

    M ./src/fields_integrate.cpp -1 +1

Thu May 27 04:54:43 EDT 2004  stevenj@fftw.org
  * whoops

    M ./src/fields_integrate.cpp -1 +1

Thu May 27 04:28:04 EDT 2004  stevenj@fftw.org
  * add fields::integrate and friends (this should make it *much* easier to implement DFT volumes, integration of energy/flux, etcetera)

    M ./src/Makefile.am -6 +8
    A ./src/fields_integrate.cpp
    M ./src/meep.h +12
    M ./src/meep_internals.h +13
    M ./src/mympi.cpp +16
    M ./src/mympi.h +2
    M ./src/vec.cpp -9 +24
    M ./src/vec.h -2 +63
    M ./tests/Makefile.am -2 +3
    A ./tests/integrate.cpp

Mon May 24 20:24:07 EDT 2004  stevenj@fftw.org
  * comments re: src_vol

    M ./TODO +8

Mon May 24 17:50:31 EDT 2004  stevenj@fftw.org
  * whoops, fixed infinite loop introduced by previous patch

    M ./src/h5fields.cpp -1 +2

Mon May 24 17:40:25 EDT 2004  stevenj@fftw.org
  * Support HDF5 output of supercell (or volume not intersecting cell) for periodic boundaries

    M ./TODO -1
    M ./src/h5fields.cpp -76 +151
    M ./src/vec.h +7
    M ./tests/h5test.cpp -15 +25

Sun May 23 19:50:29 EDT 2004  stevenj@fftw.org
  * add h5io::read and h5io::write for string data

    M ./src/h5io.cpp -48 +130
    M ./src/h5io.h +5
    M ./src/mympi.cpp +11
    M ./src/mympi.h +1
    M ./tests/h5test.cpp +16

Sun May 23 18:43:54 EDT 2004  stevenj@fftw.org
  * hdf5 output should be single-precision by default (no reason to waste a factor of 2 in space, since FDTD isn't accurate to 8 decimal places anyway), changed order of output_hdf5 etc. to be somewhat more sensible

    M ./src/h5fields.cpp -9 +12
    M ./src/h5io.cpp -6 +9
    M ./src/h5io.h -5 +5
    M ./src/meep.h -3 +6
    M ./tests/h5test.cpp -3 +3

Sun May 23 18:31:58 EDT 2004  stevenj@fftw.org
  * FIXME: thermo_energy_in_box has a comment saying it is buggy for symmetry & parallel, but it is still being called

    M ./src/energy_and_flux.cpp -2

Sun May 23 14:54:15 EDT 2004  stevenj@fftw.org
  * HDF5 epsilon output is now supported; note how we plan to implement energy density and Poynting vector output

    M ./TODO -1 +3

Sun May 23 14:50:06 EDT 2004  stevenj@fftw.org
  * support Dielectric component in get_field, elsewhere; added NO_DIRECTION direction so that scalars work with symmetry; fixed fields::get_eps so that it gives same results with multiple chunks; silenced numerous gcc 3.4 compiler warnings

    M ./src/boundaries.cpp -2 +2
    M ./src/control_c.cpp -1 +2
    M ./src/energy_and_flux.cpp +2
    M ./src/fluxes.cpp +1
    M ./src/h5fields.cpp -5 +7
    M ./src/meep.h -5 +15
    M ./src/monitor.cpp -51 +78
    M ./src/mympi.h -1 +1
    M ./src/output_directory.cpp -33 +8
    M ./src/sources.cpp -1 +1
    M ./src/structure.cpp -1 +1
    M ./src/threevec.h -1 +1
    M ./src/update_e_from_d_sources.cpp -1
    M ./src/vec.cpp -12 +17
    M ./src/vec.h -2 +4
    M ./tests/h5test.cpp -19 +25

Sun May 23 01:31:44 EDT 2004  stevenj@fftw.org
  * silence warning in bands.cpp

    M ./src/bands.cpp -1 +1

Sat May 22 21:42:00 EDT 2004  stevenj@fftw.org
  * changed prototypes for output_hdf5, add option to automatically name files etc. like for slice output

    M ./src/h5fields.cpp -10 +32
    M ./src/meep.h -4 +8
    M ./tests/h5test.cpp -6 +9

Thu May 20 19:17:50 EDT 2004  michel@mit.edu
  * more TODO

    M ./TODO -3 +12

Thu May 20 17:41:20 EDT 2004  michel@mit.edu
  * set small weight to zero for interpolation, check for negative weights

    M ./src/vec.cpp +10

Thu May 20 00:38:36 EDT 2004  stevenj@fftw.org
  * lower harminv limit

    M ./src/bands.cpp -1 +1

Thu May 20 00:12:01 EDT 2004  stevenj@fftw.org
  * prevent harminv matrices from getting too big

    M ./src/bands.cpp +1

Wed May 19 23:25:47 EDT 2004  stevenj@fftw.org
  * pick closest freq to converged value, instead of last one within 0.03

    M ./tests/convergence_cyl_waveguide.cpp -2 +2

Wed May 19 23:24:33 EDT 2004  stevenj@fftw.org
  * use fixed spectral density instead of fixed number of modes as default in do_harminv, to avoid singular eigenproblems and resulting instabilities, as also described in 'man harminv'

    M ./src/bands.cpp -4 +6
    M ./src/meep.h -2 +2

Wed May 19 03:36:38 EDT 2004  stevenj@fftw.org
  * whoops, merge pre-split harminv-related changes made with Mihai

    M ./TODO -3
    M ./configure.ac -5 +3

Wed May 19 03:10:38 EDT 2004  stevenj@fftw.org
  * whoops, limit nf by maxbands, not numfreqs

    M ./src/bands.cpp -4 +4

Tue May 18 23:55:43 EDT 2004  stevenj@fftw.org
  * rewrite harminv support for harminv 1.1

    M ./configure.ac -2 +2
    M ./src/bands.cpp -108 +117
    M ./src/meep.h -1 +5

Tue May 18 23:52:46 EDT 2004  stevenj@fftw.org
  * bug fix: handle case where harminv returns only 1 frequency

    M ./tests/2D_convergence.cpp -2 +3

Mon May 17 18:42:14 EDT 2004  stevenj@fftw.org
  * give error if ghc is missing in --enable-maintainer-mode

    M ./configure.ac +3

Tue May 18 15:06:53 EDT 2004  michel@mit.edu
  * Fix slice output bug due to buffering

    M ./src/slices.cpp -7 +24

Thu May 13 19:52:53 EDT 2004  michel@mit.edu
  * TODO: split harminv

    M ./TODO +3

Thu May 13 19:32:58 EDT 2004  michel@mit.edu
  * error if no LAPACK (disable harminv instead?), abort if try to save to HDF5 without HDF5

    M! ./configure.ac -3 +6
    M! ./src/h5io.cpp +2

Sat May 15 01:15:25 EDT 2004  stevenj@fftw.org
  * fixed handling of missing pkg-config and/or harminv

    M ./configure.ac -2 +2

Sat May 15 00:28:43 EDT 2004  stevenj@fftw.org
  * use external harminv library

    M ./Makefile.am +2
    M ./configure.ac -13 +21
    A ./m4/pkg.m4
    M ./src/Makefile.am -2 +2
    M ./src/bands.cpp -24 +22
    R ./src/harminv.cpp
    R ./src/harminv.h
    M ./tests/2D_convergence.cpp +3
    M ./tests/convergence_cyl_waveguide.cpp +4

Thu May 13 19:23:05 EDT 2004  michel@mit.edu
  * fix bug: inverse symmetry is S.transform(foo,-sn), not S.transform(foo,S.multiplicity()-sn)

    M ./src/sources.cpp -1 +1

Thu May 13 18:31:44 EDT 2004  stevenj@fftw.org
  * TODO file

    A ./TODO

Thu May 13 18:20:11 EDT 2004  stevenj@fftw.org
  * support compilation without FFTW or GSL

    M ./configure.ac -3 +5
    M ./src/initialize.cpp -3 +20
    M ./src/monitor.cpp -2 +12

Thu May 13 18:15:44 EDT 2004  stevenj@fftw.org
  * prevent floating-point exception from 0/0

    M ./tests/physical.cpp -1 +2

Wed May 12 20:34:36 EDT 2004  stevenj@fftw.org
  * added strategic calls to sync() and all_wait() to get HDF5 output working under MPI

    M ./src/h5io.cpp -1 +3
    M ./tests/h5test.cpp +10

Wed May 12 18:36:35 EDT 2004  stevenj@fftw.org
  * bug fix: h5io::write_chunk forgot to call H5Dclose

    M ./src/h5io.cpp +2
    M ./tests/h5test.cpp -1 +1

Wed May 12 18:01:40 EDT 2004  stevenj@fftw.org
  * fixes so that h5io.cpp compiles without hdf5

    M ./src/h5io.cpp -8 +3

Wed May 12 17:47:15 EDT 2004  stevenj@fftw.org
  * make h5test pass (trivially) in --without-hdf5 case

    M ./tests/h5test.cpp -1 +3

Wed May 12 17:34:16 EDT 2004  stevenj@fftw.org
  * workaround for bug in g++ 2.95

    M ./tests/h5test.cpp -1 +2

Wed May 12 17:30:27 EDT 2004  stevenj@fftw.org
  * more robust checking for feenableexcept declaration

    M ./configure.ac -2 +21
    M ./src/mympi.cpp +3

Wed May 12 17:02:00 EDT 2004  stevenj@fftw.org
  * define _GNU_SOURCE to make sure feenableexcept is declared by fenv.h

    M ./src/mympi.cpp -1 +3

Wed May 12 16:39:45 EDT 2004  stevenj@fftw.org
  * comment re src_vol index comparison

    M ./src/sources.cpp +2

Wed May 12 16:38:12 EDT 2004  stevenj@fftw.org
  * added h5test case for appending data (plus some cleanups/fixes in append case)

    M ./src/h5fields.cpp -1
    M ./src/h5io.cpp -8 +14
    M ./tests/h5test.cpp +76

Wed May 12 14:43:53 EDT 2004  stevenj@fftw.org
  * h5io::write should only execute on master

    M ./src/h5io.cpp -5 +7

Wed May 12 14:43:01 EDT 2004  michel@mit.edu
  * implemented volume sources

    M ./hsrc/update_e_from_d_gen.hs -8 +10
    M ./src/boundaries.cpp +50
    M ./src/meep.h -9 +12
    M ./src/meep_internals.h -12 +16
    M ./src/sources.cpp -53 +121
    M ./src/step.cpp -10 +11
    M ./src/vec.cpp -10 +8
    M ./src/vec.h +1
    M ./tests/known_results.cpp -16 +16
    M ./tests/symmetry.cpp -12 +12

Wed May 12 03:51:24 EDT 2004  stevenj@fftw.org
  * include "meep_internals" for min() and max() functions

    M ./tests/h5test.cpp +1

Wed May 12 03:06:07 EDT 2004  stevenj@fftw.org
  * whoops, forgot to include h5fields.cpp, duhh

    A ./src/h5fields.cpp

Wed May 12 03:00:11 EDT 2004  stevenj@fftw.org
  * whoops, make sure z dir. of h5 output file is non-empty in test

    M ./tests/h5test.cpp -1 +1

Wed May 12 02:58:16 EDT 2004  stevenj@fftw.org
  * slightly smaller h5test

    M ./tests/h5test.cpp -3 +3

Wed May 12 02:54:46 EDT 2004  stevenj@fftw.org
  * get damned HDF5 test program to pass with symmetry

    M ./src/meep.h -1
    M ./src/monitor.cpp -14 +3
    M ./tests/h5test.cpp -59 +147

Tue May 11 21:05:19 EDT 2004  stevenj@fftw.org
  * support inverse transforms in symmetry::transform (denoted by -n)

    M ./src/vec.cpp -3 +3

Tue May 11 20:22:14 EDT 2004  stevenj@fftw.org
  * fixed chunk bug in h5io, check splitting in h5test

    M ./src/h5io.cpp -1 +1
    M ./tests/h5test.cpp -28 +32

Tue May 11 20:04:35 EDT 2004  stevenj@fftw.org
  * 3d h5test

    M ./tests/h5test.cpp -5 +108

Tue May 11 19:15:31 EDT 2004  stevenj@fftw.org
  * fixed various bugs in h5io, got first test case working

    M ./src/h5io.cpp -50 +86
    M ./src/mympi.cpp -4 +18
    M ./src/mympi.h -1 +3
    A ./tests/h5test.cpp

Tue May 11 16:02:51 EDT 2004  stevenj@fftw.org
  * initial h5 output support (no symmetry, not tested much)

    M ./src/Makefile.am -3 +3
    M ./src/h5io.cpp -6 +5
    M ./src/h5io.h -3 +3
    M ./src/meep.h +13
    M ./src/mympi.cpp +8
    M ./src/mympi.h +1
    M ./tests/Makefile.am -1 +1

Tue May 11 14:55:39 EDT 2004  stevenj@fftw.org
  * fix doc/meep.pdf output

    M ./doc/Makefile.am -2 +3
    M ./doc/nonlinear.tex -1 +1

Tue May 11 14:55:18 EDT 2004  stevenj@fftw.org
  * update COPYRIGHT year

    M ./COPYRIGHT -1 +1

Sat May  8 00:46:36 EDT 2004  stevenj@fftw.org
  * silence warnings

    M ./src/mympi.cpp +4

Fri May  7 23:51:14 EDT 2004  stevenj@fftw.org
  * non-collective interpolation

    M ./src/meep.h +6
    M ./src/monitor.cpp +34

Thu May  6 19:49:13 EDT 2004  stevenj@fftw.org
  * add h5io.cpp, basic HDF5 i/o routines (not used yet)

    M ./configure.ac +19
    M ./src/Makefile.am -3 +3
    A ./src/h5io.cpp
    A ./src/h5io.h
    M ./src/mympi.cpp +39
    M ./src/mympi.h +3

Sat May  8 19:42:58 EDT 2004  droundy@abridgegame.org
  * add nonlinear example to documentation.

    M ./doc/Makefile.am -2 +11
    M ./doc/meep.tex +2
    A ./doc/nonlinear.tex

Sat May  8 19:38:12 EDT 2004  droundy@abridgegame.org
  * fix bug in kerr computation.
  I was calculating inveps where I should have been calculating the
  fractional change in inveps.

    M ./src/update_e_from_d_update.cpp -1 +1

Sat May  8 16:53:23 EDT 2004  droundy@abridgegame.org
  * split update_e_from_d into three routines.
  This is to deal with some versions of gcc that would crash trying to
  compile update_e_from_d.

    M ./hsrc/update_e_from_d_gen.hs -31 +22
    M ./src/Makefile.am -5 +13
    M ./src/meep.h +3
    M ./src/update_e_from_d.cpp -16 +14
    A ./src/update_e_from_d_prepare.cpp
    A ./src/update_e_from_d_sources.cpp
    A ./src/update_e_from_d_update.cpp

Fri May  7 23:52:15 EDT 2004  stevenj@fftw.org
  * add geometric_volume::intersects

    M ./src/vec.cpp +11
    M ./src/vec.h +4

Thu May  6 19:42:52 EDT 2004  stevenj@fftw.org
  * include <complex> so that we can use this header alone

    M ./src/mympi.h +3

Thu May  6 14:39:58 EDT 2004  stevenj@fftw.org
  * some fp constant fixes

    M ./src/meep.h -2 +11

Thu May  6 14:26:19 EDT 2004  stevenj@fftw.org
  * whoops, forgot arg for fprintf

    M ./src/mympi.cpp -1 +1

Thu May  6 14:24:52 EDT 2004  stevenj@fftw.org
  * print "meep: " before abort message, to be GNU-ly correct

    M ./src/mympi.cpp +1

Sat May  8 00:43:57 EDT 2004  stevenj@fftw.org
  * use darcs_test for test


Fri May  7 19:11:51 EDT 2004  droundy@abridgegame.org
  * turn on some basic testing.


Fri May  7 19:01:25 EDT 2004  droundy@abridgegame.org
  * fix warning.

    M ./src/structure.cpp -1 +1

Fri May  7 19:00:38 EDT 2004  droundy@abridgegame.org
  * try to get dependencies right in doc and tests.

    M ./doc/Makefile.am +3
    M ./hsrc/Makefile.am -1 +1
    M ./tests/Makefile.am -1 +3

Fri May  7 18:56:45 EDT 2004  droundy@abridgegame.org
  * add support for nonlinear kerr materials.

    M ./hsrc/YeeLattice.lhs -33 +40
    M ./hsrc/update_e_from_d_gen.hs -10 +26
    M ./src/meep.h -2 +11
    M ./src/structure.cpp +45
    M ./src/update_e_from_d.cpp +9
    M ./tests/bench.cpp +50
    M ./tests/symmetry.cpp +33

Fri May  7 11:20:05 EDT 2004  droundy@abridgegame.org
  * add additional kerr tests.

    M ./tests/symmetry.cpp -63 +132

Thu May  6 15:52:24 EDT 2004  droundy@abridgegame.org
  * clean up sum_over_components ever so slightly.

    M ./hsrc/YeeLattice.lhs -17 +22

Fri May  7 14:59:49 EDT 2004  droundy@abridgegame.org
  * fix bug when doing EPS slices with real fields.

    M ./src/slices.cpp -1 +1

Wed May  5 00:57:19 EDT 2004  stevenj@fftw.org
  * disable libctl by default (until it is working better)

    M ./configure.ac -2 +1

Tue May  4 23:18:01 EDT 2004  stevenj@fftw.org
  * re-ified current/dipole distinction in src_time

    M ./hsrc/update_e_from_d_gen.hs -1 +1
    M ./src/meep.h -8 +19
    M ./src/meep_internals.h -4 +4
    M ./src/sources.cpp -4 +4
    M ./src/step.cpp -1 +1
    M ./tests/known_results.cpp -10 +8

Tue May  4 21:21:20 EDT 2004  stevenj@fftw.org
  * FIXME: disable saturated-gain tests until divergence bug is fixed

    M ./tests/symmetry.cpp +3

Thu Dec 18 02:10:46 EST 2003  stevenj@fftw.org
  * for symmetry to work properly, equal sources must be combined
  This requires serious crap in src_time to get an equality test that works
  over inheritance.  Also, the current O(n^2) algorithm in src_pt::add_to has
  got to be revised when source volumes are added.  Ugh.

    M ./src/meep.h -6 +11
    M ./src/meep_internals.h +2
    M ./src/sources.cpp -15 +61
    M ./tests/symmetry.cpp -2 +5

Wed Dec 17 21:10:27 EST 2003  stevenj@fftw.org
  * correct for current renormalization

    M ./tests/known_results.cpp -8 +10

Wed Dec 17 20:58:48 EST 2003  stevenj@fftw.org
  * more backwards compatibility (tiny change in default cutoff, but is enough to fail two_dimensional.dac, grr)

    M ./src/sources.cpp -1 +1

Wed Dec 17 18:35:14 EST 2003  stevenj@fftw.org
  * don't use last_source_time for CW sources (infinity!), print more stuff, use good limits for steady-state (with slow CW turn-on)

    M ./tests/physical.cpp -6 +19

Wed Dec 17 18:34:33 EST 2003  stevenj@fftw.org
  * slow-turn-on for is_continuous add_point_source

    M ./src/sources.cpp -7 +6

Wed Dec 17 16:57:39 EST 2003  stevenj@fftw.org
  * fix fp exception in continuous source

    M ./src/sources.cpp -3 +3

Wed Dec 17 15:45:23 EST 2003  stevenj@fftw.org
  * backwards compatibility for specifying continuous sources (finite last_source_time)

    M ./src/sources.cpp -8 +8

Wed Dec 17 14:54:47 EST 2003  stevenj@fftw.org
  * split src into src_pt and src_time, with many related changes

    M ./doc/complicated.tex r1
    M ./doc/simple.tex r1
    M ./hsrc/Complex.lhs r1
    M ./hsrc/StepGen.lhs r1
    M ./hsrc/YeeLattice.lhs r1
    M ./hsrc/step_d_gen.hs r1
    M ./hsrc/step_h_gen.hs r1
    M ./hsrc/update_e_from_d_gen.hs -4 +12 r1
    M ./hsrc/update_from_e_gen.hs r1
    M ./src/anisotropic_averaging.cpp r1
    M ./src/bands.cpp -15 +6 r2
    M ./src/boundaries.cpp r1
    M ./src/control_c.cpp r1
    M ./src/energy_and_flux.cpp r1
    M ./src/fields.cpp +3 r1
    M ./src/fluxes.cpp r1
    M ./src/grace.cpp r1
    M ./src/harminv.cpp r1
    M ./src/harminv.h r1
    M ./src/initialize.cpp r1
    M ./src/meep.h -12 +79 r3
    M ./src/meep_internals.h -14 +17 r2
    M ./src/monitor.cpp r1
    M ./src/mympi.cpp r1
    M ./src/mympi.h r1
    M ./src/output_directory.cpp r1
    M ./src/polarization.cpp r1
    M ./src/ran.cpp r1
    M ./src/ran.h r1
    M ./src/slices.cpp r1
    M ./src/sources.cpp -74 +97 r2
    M ./src/sphere-quad.cpp r1
    M ./src/step.cpp -17 +16 r3
    M ./src/step_d.cpp r1
    M ./src/step_h.cpp r1
    M ./src/structure.cpp r1
    M ./src/threevec.h r1
    M ./src/time.cpp r1
    M ./src/update_e_from_d.cpp r1
    M ./src/update_from_e.cpp r1
    M ./src/vec.cpp r1
    M ./src/vec.h r1
    M ./tests/2D_convergence.cpp r1
    M ./tests/bench.cpp r1
    M ./tests/convergence_cyl_waveguide.cpp r1
    M ./tests/flux.cpp r1
    M ./tests/physical.cpp r1
    M ./tests/three_d.cpp r1
    M ./tests/two_dimensional.cpp r1

Wed Dec 17 23:14:49 EST 2003  stevenj@fftw.org
  * avoid confusion between formal params and members

    M ./src/polarization.cpp -3 +3

Wed Dec 17 14:54:19 EST 2003  stevenj@fftw.org
  * some more %lg's to replace

    M ./doc/example.cpp -3 +3

Tue Dec 16 18:33:52 EST 2003  stevenj@fftw.org
  * missing dependency on libmeep

    M ./tests/Makefile.am -1 +1

Tue Dec 16 14:00:34 EST 2003  stevenj@fftw.org
  * input converged frequency from MPB, weaken convergence criterion (otherwise test fails because of weird error increase around a=30)

    M ./tests/2D_convergence.cpp -5 +11

Tue Dec 16 13:56:07 EST 2003  stevenj@fftw.org
  * acronym expansions

    M ./README +9

Mon Dec 15 17:48:02 EST 2003  stevenj@fftw.org
  * set_epsilon already calls is_mine; no need to call it twice

    M ./src/structure.cpp -1 +1

Tue Apr  6 12:32:38 EDT 2004  droundy@civet.berkeley.edu
  * add in dependencies amongst haskell sources.

    M ./hsrc/Makefile.am +5

Mon Dec 15 18:14:14 EST 2003  stevenj@fftw.org
  * compilation fixes, use new create_geom_box_tree0

    M ./libctl/structure.cpp -39 +50

Wed Dec 17 19:53:05 EST 2003  stevenj@fftw.org
  * in debug mode, also crash with SIGFPE on overflow (it's not good if something is blowing up)

    M ./src/mympi.cpp -1 +1

Wed Dec 17 16:56:55 EST 2003  stevenj@fftw.org
  * with --enable-debug, trap floating-point exceptions

    M ./configure.ac +2
    M ./src/mympi.cpp +8

Wed Dec 17 14:11:20 EST 2003  stevenj@fftw.org
  * --enable-debug option for configure

    M ./configure.ac +11

Mon Dec 15 17:45:03 EST 2003  stevenj@fftw.org
  * set_epsilon should initialize structure_c

    M ./src/structure.cpp -12 +9

Sun Dec 14 14:23:20 EST 2003  stevenj@fftw.org
  * tee is too slow

    M ./tests/Makefile.am -1 +2

Sun Dec 14 14:23:02 EST 2003  stevenj@fftw.org
  * silence warning

    M ./tests/2D_convergence.cpp -1 +1

Sun Dec 14 13:15:02 EST 2003  stevenj@fftw.org
  * remove tests/Makefile.in (generated by automake)

    R ./tests/Makefile.in

Sun Dec 14 13:14:39 EST 2003  stevenj@fftw.org
  * save test output in .done file

    M ./tests/Makefile.am -2 +1

Sat Dec 13 23:53:02 EST 2003  stevenj@fftw.org
  * comments and niceties

    M ./src/sphere-quad.cpp +6

Sat Dec 13 23:48:53 EST 2003  stevenj@fftw.org
  * typo in comment

    M ./src/sphere-quad.cpp -1 +1

Sat Dec 13 23:41:26 EST 2003  stevenj@fftw.org
  * whoops, wrong index for spherical quad.

    M ./src/anisotropic_averaging.cpp -1 +1

Sat Dec 13 23:39:46 EST 2003  stevenj@fftw.org
  * make it easier to change resolution limits in convergence test

    M ./tests/convergence_cyl_waveguide.cpp -2 +6

Sat Dec 13 23:24:25 EST 2003  stevenj@fftw.org
  * damn, missed another %lg

    M ./src/anisotropic_averaging.cpp -1 +1

Sat Dec 13 23:23:23 EST 2003  stevenj@fftw.org
  * threevec convenience constructor

    M ./src/anisotropic_averaging.cpp -2 +1
    M ./src/threevec.h -1 +2

Sat Dec 13 23:22:39 EST 2003  stevenj@fftw.org
  * more fleshed-out sphere quadrature for aniso. averaging

    M ./src/anisotropic_averaging.cpp -4 +22

Sat Dec 13 23:22:11 EST 2003  stevenj@fftw.org
  * geo_center takes reference arg.

    M ./src/anisotropic_averaging.cpp -1 +1

Sat Dec 13 23:13:28 EST 2003  stevenj@fftw.org
  * whoops, more %lg -> %g replacements

    M ./doc/complicated.tex -3 +3
    M ./src/bands.cpp -8 +8
    M ./src/grace.cpp -3 +3
    M ./src/slices.cpp -30 +30
    M ./src/step.cpp -1 +1
    M ./src/vec.cpp -6 +6
    M ./tests/2D_convergence.cpp -3 +3
    M ./tests/cylindrical.cpp -2 +2
    M ./tests/flux.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/physical.cpp -4 +4
    M ./tests/symmetry.cpp -1 +1
    M ./tests/three_d.cpp -5 +5
    M ./tests/two_dimensional.cpp -5 +5

Sat Dec 13 18:31:44 EST 2003  stevenj@fftw.org
  * %lg is incorrect in a printf statement (because of the default type-promotion rules, float arguments are always passed to printf as double in standard C/C++)

    M ./doc/complicated.tex -3 +3
    M ./doc/energy_cons.tex -2 +2
    M ./doc/energy_cons_1d.tex -3 +3
    M ./doc/epsilon_polariton_1d.tex -2 +2
    M ./doc/lossgain_epsilon.tex -5 +5
    M ./src/bands.cpp -10 +10
    M ./src/grace.cpp -7 +7
    M ./src/harminv.cpp -1 +1
    M ./src/slices.cpp -61 +61
    M ./src/step.cpp -2 +2
    M ./src/threevec.h -1 +1
    M ./src/time.cpp -1 +1
    M ./src/vec.cpp -7 +7
    M ./tests/2D_convergence.cpp -4 +4
    M ./tests/bench.cpp -1 +1
    M ./tests/convergence_cyl_waveguide.cpp -2 +2
    M ./tests/cylindrical.cpp -10 +10
    M ./tests/flux.cpp -11 +11
    M ./tests/known_results.cpp -2 +2
    M ./tests/one_dimensional.cpp -5 +5
    M ./tests/physical.cpp -4 +4
    M ./tests/symmetry.cpp -7 +7
    M ./tests/three_d.cpp -10 +10
    M ./tests/two_dimensional.cpp -11 +11

Sat Dec 13 18:29:02 EST 2003  stevenj@fftw.org
  * add experimental spherical-quadrature code (not used yet)

    M ./src/Makefile.am -3 +11
    M ./src/anisotropic_averaging.cpp +47
    A ./src/sphere-quad.cpp

Fri Dec 12 17:33:23 EST 2003  droundy@civet.berkeley.edu
  * resolve conflicts with automake etc.

    M ./darcs_test -2 +2
    M ./src/anisotropic_averaging.cpp -2 +28
    M ./src/meep.h +2
    M ./src/structure.cpp -5 +11
    M ./src/threevec.h -1 +1
    M ./tests/2D_convergence.cpp -3 +4
    M ./tests/Makefile.am -1 +1
    M ./tests/Makefile.in -35 +378
    M ./tests/convergence_cyl_waveguide.cpp -16 +21

Wed Dec 10 16:19:57 EST 2003  droundy@abridgegame.org
  * if necesary, allocate inveps in redefine_chunks.

    M ./src/structure.cpp -1 +7

Tue Dec  9 12:54:57 EST 2003  droundy@abridgegame.org
  * anisotropic dielectric averaging.

    M! ./src/anisotropic_averaging.cpp -14 +18 r1
    M! ./src/structure.cpp -1 +1
    M! ./src/threevec.h -7 +9
    A! ./tests/2D_convergence.cpp
    A! ./tests/Makefile.in
    M! ./tests/convergence_cyl_waveguide.cpp -44 +108

Thu Dec 11 16:27:18 EST 2003  stevenj@fftw.org
  * use gcc attributes to identify printf-like and abort-like functions

    M ./src/mympi.h -5 +13

Thu Dec 11 15:57:53 EST 2003  stevenj@fftw.org
  * use padded volume for material_function

    M ./src/polarization.cpp -1 +1
    M ./src/structure.cpp -2 +2
    M ./src/vec.h +6

Thu Dec 11 13:47:03 EST 2003  stevenj@fftw.org
  * remember my-smob.h for make dist

    M ./libctl/Makefile.am -1 +3

Thu Dec 11 13:26:46 EST 2003  stevenj@fftw.org
  * expanded material_function class
  Use material_function class (renamed from epsilon_function) for both
  epsilon and sigma functions and, in the future, other things like
  nonlinearity as well.  Add calls to set_volume where appropriate.
  

    M ./libctl/structure.cpp -10 +17 r1
    M ./src/anisotropic_averaging.cpp r1
    M ./src/meep.h -1 +28 r2
    M ./src/meep_internals.h -1 +1
    M ./src/polarization.cpp -9 +26
    M ./src/structure.cpp -1 +4 r2

Thu Dec 11 00:41:39 EST 2003  stevenj@fftw.org
  * add libctl skeleton

    M ./Makefile.am -1 +7
    M ./configure.ac +142
    A ./libctl/
    A ./libctl/Makefile.am
    A ./libctl/meep-ctl-const.h
    A ./libctl/meep-ctl.h
    A ./libctl/meep.cpp
    A ./libctl/meep.scm.in
    A ./libctl/my-smob.h
    A ./libctl/structure.cpp

Thu Dec 11 00:40:52 EST 2003  stevenj@fftw.org
  * allow arbitrary epsilon_function object, not just double eps(r)

    M ./src/anisotropic_averaging.cpp -3 +3
    M ./src/meep.h -4 +30
    M ./src/structure.cpp -16 +36

Wed Dec 10 21:13:00 EST 2003  stevenj@fftw.org
  * rename material.cpp to structure.cpp

     ./src/material.cpp -> ./src/structure.cpp
    M ./src/Makefile.am -3 +3

Wed Dec 10 20:45:53 EST 2003  stevenj@fftw.org
  * enable compiler warnings in maintainer mode, silence/fix some cases

    M ./configure.ac +6
    M ./src/anisotropic_averaging.cpp +1
    M ./src/boundaries.cpp +3
    M ./src/fields.cpp -1 +1
    M ./src/initialize.cpp -1 +1
    M ./src/mympi.cpp +24
    M ./src/output_directory.cpp -4 +4
    M ./src/threevec.h -1 +1
    M ./src/vec.h +1

Wed Dec 10 19:59:04 EST 2003  stevenj@fftw.org
  * residual fixes from mat->structure renaming

    M ./hsrc/update_e_from_d_gen.hs -10 +10
    M ./src/material.cpp -1 +1
    M ./src/monitor.cpp -2 +2
    M ./src/polarization.cpp -2 +2
    M ./tests/Makefile.am +2

Wed Dec 10 19:41:26 EST 2003  stevenj@fftw.org
  * mat -> structure, etc.

    M ./doc/complicated.tex -4 +4 r3
    M ./doc/energy_cons.tex r4
    M ./doc/energy_cons_1d.tex r4
    M ./doc/epsilon_polariton_1d.tex r4
    M ./doc/example.cpp r4
    M ./doc/gpl.tex r3
    M ./doc/lossgain_epsilon.tex r4
    M ./doc/meep.tex r3
    M ./doc/omniguide.tex -5 +5 r2
    M ./doc/polaritonbands.tex -1 +1 r3
    M ./doc/simple.tex -2 +2 r3
    M ./doc/simplebands.tex -2 +2 r2
    M ./src/anisotropic_averaging.cpp r4
    M ./src/bands.cpp r3
    M ./src/boundaries.cpp r4
    M ./src/control_c.cpp r4
    M ./src/energy_and_flux.cpp r4
    M ./src/fields.cpp r7
    M ./src/fluxes.cpp r3
    M ./src/grace.cpp r3
    M ./src/harminv.cpp r3
    M ./src/harminv.h r4
    M ./src/initialize.cpp r4
    M ./src/material.cpp -22 +22 r3
    M ./src/meep.h -5 +5 r4
    M ./src/meep_internals.h -1 +1 r3
    M ./src/monitor.cpp r3
    M ./src/mympi.cpp r3
    M ./src/mympi.h r4
    M ./src/output_directory.cpp r3
    M ./src/polarization.cpp -6 +6 r3
    M ./src/ran.cpp r4
    M ./src/ran.h r4
    M ./src/slices.cpp -6 +6 r4
    M ./src/sources.cpp r3
    M ./src/step.cpp -7 +7 r5
    M ./src/step_d.cpp r4
    M ./src/step_h.cpp r4
    M ./src/threevec.h r3
    M ./src/time.cpp r3
    M ./src/update_e_from_d.cpp r4
    M ./src/update_from_e.cpp r4
    M ./src/vec.cpp r3
    M ./src/vec.h r3
    M ./tests/bench.cpp -15 +15 r3
    M ./tests/convergence_cyl_waveguide.cpp -2 +2 r3
    M ./tests/cylindrical.cpp -16 +16 r4
    M ./tests/flux.cpp -9 +9 r4
    M ./tests/known_results.cpp -22 +22 r3
    M ./tests/one_dimensional.cpp -6 +6 r4
    M ./tests/physical.cpp -6 +6 r3
    M ./tests/symmetry.cpp -58 +58 r7
    M ./tests/three_d.cpp -14 +14 r4
    M ./tests/two_dimensional.cpp -23 +23 r4

Wed Dec 10 18:47:02 EST 2003  stevenj@fftw.org
  * don't build shared libraries by default (only with --enable-shared)

    M ./configure.ac +1

Wed Dec 10 18:06:00 EST 2003  stevenj@fftw.org
  * use vpath build in test

    M ./darcs_test -1 +3

Wed Dec 10 18:04:21 EST 2003  stevenj@fftw.org
  * fix for vpath building

    M ./doc/Makefile.am -1 +1

Wed Dec 10 15:50:21 EST 2003  stevenj@fftw.org
  * don't bother with --enable-shared just for make dist

    M ./darcs_test -1 +1

Wed Dec 10 15:13:16 EST 2003  stevenj@fftw.org
  * autoreconf paranoia

    M ./autogen.sh +3

Wed Dec 10 15:09:12 EST 2003  stevenj@fftw.org
  * COPYING is created by autoreconf; does not need to be in repo

    R ./COPYING

Wed Dec 10 15:02:43 EST 2003  stevenj@fftw.org
  * am_conditional for WITH_DOC

    M ./configure.ac +10

Wed Dec 10 14:58:34 EST 2003  stevenj@fftw.org
  * always make autoreconf verbose, and always replace files

    M ./autogen.sh -5 +1

Wed Dec 10 14:55:14 EST 2003  stevenj@fftw.org
  * remove deleted files from dist

    M ./src/Makefile.am -2 +2

Wed Dec 10 14:53:44 EST 2003  stevenj@fftw.org
  * whoops, handle empty $verbose

    M ./autogen.sh -1 +1

Wed Dec 10 14:49:51 EST 2003  stevenj@fftw.org
  * darcs_test does 'make dist' without docs, other build fixes

    M ./Makefile.am +4
    M ./autogen.sh -7 +15
    M ./configure.ac -1 +1
    M ./darcs_test -2 +3
    M ./doc/Makefile.am -3 +11

Wed Dec 10 14:49:16 EST 2003  stevenj@fftw.org
  * more merge recording

    R ./Makefile.in

Wed Dec 10 13:41:34 EST 2003  stevenj@fftw.org
  * stupid merging with latest pull of stupid whitespace

    M ./AUTHORS -1
    M ./ChangeLog -1
    M ./Makefile.am -1
    M ./NEWS -1
    M ./README -1
    M ./autogen.sh -6 +25
    M ./doc/example.cpp -1
    M ./hsrc/Makefile.am -1
    R ./install-sh
    M ./m4/acx_blas.m4 -1
    M ./m4/acx_lapack.m4 -1
    M ./m4/acx_mpi.m4 -1
    M ./meep.pc.in -1
    M ./src/Makefile.am -1
    M ./src/anisotropic_averaging.cpp +2
    M ./src/bands.cpp -1
    M ./src/boundaries.cpp +2
    R ./src/check.h
    M ./src/control_c.cpp +2
    R ./src/copyright.h
    R ./src/diff_slice.cpp
    M ./src/energy_and_flux.cpp +2
    M ./src/fields.cpp +2
    M ./src/fluxes.cpp +2
    M ./src/grace.cpp +2
    M ./src/harminv.cpp -2 +15
    M ./src/initialize.cpp +2
    M ./src/material.cpp +2
    M ./src/meep.h +2
    M ./src/meep_internals.h +2
    M ./src/monitor.cpp +2
    M ./src/mympi.cpp +2
    M ./src/mympi.h +2
    M ./src/output_directory.cpp +2
    M ./src/polarization.cpp +2
    M ./src/ran.cpp +2
    M ./src/ran.h +2
    M ./src/slices.cpp +2
    M ./src/sources.cpp +2
    M ./src/step.cpp +2
    M ./src/step_d.cpp +2
    R ./src/step_d.h
    M ./src/step_h.cpp +2
    R ./src/step_h.h
    M ./src/threevec.h +2
    M ./src/time.cpp +2
    M ./src/update_e_from_d.cpp +2
    R ./src/update_e_from_d.h
    M ./src/update_from_e.cpp +2
    R ./src/update_from_e.h
    M ./src/vec.cpp +2
    M ./src/vec.h +2
    M ./tests/Makefile.am -1
    R ./tests/Makefile.in

Tue Dec  9 18:14:15 EST 2003  meep@ab-initio.mit.edu
  * record result of convert-repo (bunch of blank lines, go figure)

    M! ./COPYING -1
    M! ./COPYRIGHT -1
    A! ./Makefile.in
    M! ./autogen.sh -30 +8
    M! ./configure.ac -1
    M! ./darcs_test -2
    M! ./doc/Makefile.am -1
    M! ./doc/Yee_bulk.eps -1
    M! ./doc/complicated.tex -1
    M! ./doc/energy_cons.tex -1
    M! ./doc/energy_cons_1d.tex -1
    M! ./doc/epsilon_polariton_1d.tex -1
    M! ./doc/example.cpp -1
    M! ./doc/gpl.tex -1
    M! ./doc/lossgain_epsilon.tex -1
    M! ./doc/meep.tex -1
    M! ./doc/omniguide.tex -1
    M! ./doc/polaritonbands.tex -1
    M! ./doc/preproc.pl -1
    M! ./doc/simple.tex -1
    M! ./doc/simplebands.tex -1
    M! ./hsrc/Complex.lhs -1
    M! ./hsrc/StepGen.lhs -1
    M! ./hsrc/YeeLattice.lhs -1
    M! ./hsrc/step_d_gen.hs -1
    M! ./hsrc/step_h_gen.hs -1
    M! ./hsrc/update_e_from_d_gen.hs -1
    M! ./hsrc/update_from_e_gen.hs -1
    A! ./install-sh
    M! ./src/anisotropic_averaging.cpp -3
    M! ./src/boundaries.cpp -3
    M! ./src/check.h -1
    M! ./src/control_c.cpp -3
    M! ./src/copyright.h -1
    A! ./src/diff_slice.cpp
    M! ./src/energy_and_flux.cpp -3
    M! ./src/fields.cpp -3
    M! ./src/fluxes.cpp -3
    M! ./src/grace.cpp -3
    M! ./src/harminv.cpp -1
    M! ./src/harminv.h -1
    M! ./src/initialize.cpp -3
    M! ./src/material.cpp -3
    M! ./src/meep.h -3
    M! ./src/meep_internals.h -3
    M! ./src/monitor.cpp -3
    M! ./src/mympi.cpp -3
    M! ./src/mympi.h -3
    M! ./src/output_directory.cpp -3
    M! ./src/polarization.cpp -3
    M! ./src/ran.cpp -3
    M! ./src/ran.h -3
    M! ./src/slices.cpp -3
    M! ./src/sources.cpp -3
    M! ./src/step.cpp -3
    M! ./src/step_d.cpp -3
    A! ./src/step_d.h
    M! ./src/step_h.cpp -3
    A! ./src/step_h.h
    M! ./src/threevec.h -3
    M! ./src/time.cpp -3
    M! ./src/update_e_from_d.cpp -3
    A! ./src/update_e_from_d.h
    M! ./src/update_from_e.cpp -3
    A! ./src/update_from_e.h
    M! ./src/vec.cpp -3
    M! ./src/vec.h -3
    A! ./tests/Makefile.in
    M! ./tests/bench.cpp -1
    M! ./tests/convergence_cyl_waveguide.cpp -1
    M! ./tests/cylindrical.cpp -1
    M! ./tests/flux.cpp -1
    M! ./tests/known_results.cpp -1
    M! ./tests/one_dimensional.cpp -1
    M! ./tests/physical.cpp -1
    M! ./tests/symmetry.cpp -1
    M! ./tests/three_d.cpp -1
    M! ./tests/two_dimensional.cpp -1

Tue Dec  9 18:01:15 EST 2003  stevenj@fftw.org
  * use AC_F77_WRAPPERS for harminv

    M ./configure.ac +2
    M ./src/harminv.cpp -15 +1

Tue Dec  9 17:58:44 EST 2003  stevenj@fftw.org
  * use meep namespace for libmeep

    M ./doc/complicated.tex -1 +2
    M ./doc/energy_cons.tex -1 +2
    M ./doc/energy_cons_1d.tex -1 +2
    M ./doc/epsilon_polariton_1d.tex -1 +2
    M ./doc/example.cpp -1 +2
    M ./doc/lossgain_epsilon.tex -1 +2
    M ./doc/omniguide.tex -1 +2
    M ./doc/polaritonbands.tex -1 +2
    M ./doc/simple.tex -2 +3
    M ./doc/simplebands.tex -1 +2
    M ./src/anisotropic_averaging.cpp +4
    M ./src/bands.cpp -1 +3
    M ./src/boundaries.cpp +4
    M ./src/control_c.cpp +4
    M ./src/energy_and_flux.cpp +4
    M ./src/fields.cpp +4
    M ./src/fluxes.cpp +4
    M ./src/grace.cpp +4
    M ./src/initialize.cpp +4
    M ./src/material.cpp +4
    M ./src/meep.h -3 +7
    M ./src/meep_internals.h +4
    M ./src/monitor.cpp -7 +10
    M ./src/mympi.cpp +4
    M ./src/mympi.h -3 +7
    M ./src/output_directory.cpp +4
    M ./src/polarization.cpp +4
    M ./src/ran.cpp +4
    M ./src/ran.h +3
    M ./src/slices.cpp +4
    M ./src/sources.cpp +4
    M ./src/step.cpp -5 +9
    M ./src/step_d.cpp +4
    M ./src/step_h.cpp +4
    M ./src/threevec.h -1 +5
    M ./src/time.cpp +4
    M ./src/update_e_from_d.cpp +4
    M ./src/update_from_e.cpp +3
    M ./src/vec.cpp -2 +5
    M ./src/vec.h -3 +7
    M ./tests/bench.cpp -1 +2
    M ./tests/convergence_cyl_waveguide.cpp -1 +2
    M ./tests/cylindrical.cpp -1 +2
    M ./tests/flux.cpp -1 +2
    M ./tests/known_results.cpp -1 +2
    M ./tests/one_dimensional.cpp -1 +2
    M ./tests/physical.cpp -1 +2
    M ./tests/symmetry.cpp -1 +2
    M ./tests/three_d.cpp -1 +2
    M ./tests/two_dimensional.cpp -1 +2

Tue Dec  9 16:30:27 EST 2003  stevenj@fftw.org
  * add meep.ps.gz target

    M ./doc/Makefile.am +3

Tue Dec  9 16:27:30 EST 2003  stevenj@fftw.org
  * use hyperref package for building pdf

    M ./doc/Makefile.am +2
    M ./doc/energy_cons.tex -1 +1
    M ./doc/energy_cons_1d.tex -1 +1
    M ./doc/meep.tex -1 +1

Tue Dec  9 15:51:47 EST 2003  stevenj@fftw.org
  * AM_PROG_LIBTOOL is required for depcomp to be dist'ed (no mention of this in automake docs, grrr)

    M ./configure.ac -1 +1

Tue Dec  9 15:26:01 EST 2003  stevenj@fftw.org
  * grrr

    M ./darcs_test +1

Tue Dec  9 15:06:18 EST 2003  stevenj@fftw.org
  * use __FILE__ for output directory

    M ./doc/complicated.tex -1 +1
    M ./doc/energy_cons.tex -1 +1
    M ./doc/energy_cons_1d.tex -1 +1
    M ./doc/epsilon_polariton_1d.tex -1 +1
    M ./doc/example.cpp -1 +1
    M ./doc/lossgain_epsilon.tex -1 +1
    M ./doc/omniguide.tex -1 +1
    M ./doc/polaritonbands.tex -1 +1
    M ./doc/simple.tex -1 +1
    M ./src/output_directory.cpp -2 +9

Mon Dec  8 22:25:57 EST 2003  stevenj@fftw.org
  * must build libmeep too for make dist

    M ./Makefile.am -2 +9

Mon Dec  8 21:59:40 EST 2003  stevenj@fftw.org
  * sigh...still trying to fix make dist dependencies

    M ./Makefile.am -2 +3

Mon Dec  8 21:56:41 EST 2003  stevenj@fftw.org
  * less verbose darcs_test now that auto* works

    M ./darcs_test -1 +1

Mon Dec  8 21:37:11 EST 2003  stevenj@fftw.org
  * dist fix

    M ./Makefile.am -1 +4

Mon Dec  8 20:48:21 EST 2003  stevenj@fftw.org
  * fixes to make dist (I hope)

    M ./Makefile.am -1 +3
    M ./darcs_test -4

Mon Dec  8 20:27:17 EST 2003  stevenj@fftw.org
  * 'make' in hsrc before 'make dist'

    M ./darcs_test -2 +6

Mon Dec  8 20:04:03 EST 2003  stevenj@fftw.org
  * darcs_test uses 'make dist'

    M ./darcs_test +13

Mon Dec  8 19:58:44 EST 2003  stevenj@fftw.org
  * add meep.pc file for use with pkg-config

    M ./Makefile.am +3
    M ./configure.ac +7
    A ./meep.pc.in

Mon Dec  8 17:40:50 EST 2003  stevenj@fftw.org
  * use \includegraphics so that pdflatex works

    M ./doc/Makefile.am -5 +5
    M ./doc/energy_cons.tex -1 +1
    M ./doc/energy_cons_1d.tex -1 +1
    M ./doc/epsilon_polariton_1d.tex -1 +1
    M ./doc/lossgain_epsilon.tex -1 +1
    M ./doc/meep.tex -2 +2
    M ./doc/omniguide.tex -1 +1
    M ./doc/polaritonbands.tex -1 +1
    M ./doc/simple.tex -1 +1

Mon Dec  8 16:55:20 EST 2003  stevenj@fftw.org
  * move example.cpp to doc/

     ./src/example.cpp -> ./doc/example.cpp
    M ./doc/Makefile.am -5 +6
    R ./doc/dummy.cpp
    M ./src/Makefile.am -4

Mon Dec  8 16:13:52 EST 2003  stevenj@fftw.org
  * whoop sagain

    A ./src/Makefile.am

Mon Dec  8 15:53:33 EST 2003  stevenj@fftw.org
  * whoops

    A ./Makefile.am

Mon Dec  8 15:33:50 EST 2003  stevenj@fftw.org
  * more verbose darcs_test

    M ./autogen.sh -2 +22
    M ./darcs_test -7 +1

Mon Dec  8 15:24:01 EST 2003  stevenj@fftw.org
  * make dist fixes

    M ./doc/Makefile.am +2

Mon Dec  8 15:00:58 EST 2003  stevenj@fftw.org
  * include config.log in darcs_test output

    M ./autogen.sh +1
    M ./darcs_test +6

Sun Dec  7 19:24:52 EST 2003  stevenj@fftw.org
  * whoops, update test for automake'd version

    M ./darcs_test -2 +2

Sun Dec  7 19:21:26 EST 2003  stevenj@fftw.org
  * automakization

     ./doc/Makefile.in -> ./doc/Makefile.am
    A ./ChangeLog
    A ./NEWS
    A ./README
    A ./autogen.sh
    M ./configure.ac -4 +22
    M ./doc/Makefile.am -45 +38
    A ./doc/dummy.cpp
    M ./hsrc/Makefile.am -4 +7
    M ./src/anisotropic_averaging.cpp +1
    M ./src/bands.cpp +1
    M ./src/boundaries.cpp +2
    M ./src/check.h +1
    M ./src/control_c.cpp +1
    M ./src/copyright.h +1
    R ./src/diff_slice.cpp
    M ./src/energy_and_flux.cpp +1
    M ./src/example.cpp +1
    M ./src/fields.cpp +1
    M ./src/fluxes.cpp +1
    M ./src/grace.cpp +1
    M ./src/harminv.cpp +1
    M ./src/harminv.h +1
    M ./src/initialize.cpp +1
    M ./src/material.cpp +1
    M ./src/meep.h +1
    M ./src/meep_internals.h +1
    M ./src/monitor.cpp -1 +14
    M ./src/mympi.cpp +1
    M ./src/mympi.h +1
    M ./src/output_directory.cpp +1
    M ./src/polarization.cpp +1
    M ./src/ran.cpp +1
    M ./src/ran.h +1
    M ./src/slices.cpp +1
    M ./src/sources.cpp +1
    M ./src/step.cpp +1
    M ./src/step_d.cpp +1
    R ./src/step_d.h
    M ./src/step_h.cpp +1
    R ./src/step_h.h
    M ./src/threevec.h +1
    M ./src/time.cpp +1
    M ./src/update_e_from_d.cpp +1
    R ./src/update_e_from_d.h
    M ./src/update_from_e.cpp +1
    R ./src/update_from_e.h
    M ./src/vec.cpp +1
    M ./src/vec.h +1
    A ./tests/Makefile.am
    R ./tests/Makefile.in

Fri Dec  5 16:57:51 EST 2003  stevenj@fftw.org
  * bunch of moves

     ./Complex.lhs -> ./src/Complex.lhs
     ./StepGen.lhs -> ./src/StepGen.lhs
     ./YeeLattice.lhs -> ./src/YeeLattice.lhs
     ./anisotropic_averaging.cpp -> ./src/anisotropic_averaging.cpp
     ./bands.cpp -> ./src/bands.cpp
     ./boundaries.cpp -> ./src/boundaries.cpp
     ./check.h -> ./src/check.h
     ./control_c.cpp -> ./src/control_c.cpp
     ./copyright.h -> ./src/copyright.h
     ./diff_slice.cpp -> ./src/diff_slice.cpp
     ./energy_and_flux.cpp -> ./src/energy_and_flux.cpp
     ./example.cpp -> ./src/example.cpp
     ./fields.cpp -> ./src/fields.cpp
     ./fluxes.cpp -> ./src/fluxes.cpp
     ./grace.cpp -> ./src/grace.cpp
     ./harminv.cpp -> ./src/harminv.cpp
     ./harminv.h -> ./src/harminv.h
     ./initialize.cpp -> ./src/initialize.cpp
     ./material.cpp -> ./src/material.cpp
     ./meep.h -> ./src/meep.h
     ./meep_internals.h -> ./src/meep_internals.h
     ./monitor.cpp -> ./src/monitor.cpp
     ./mympi.cpp -> ./src/mympi.cpp
     ./mympi.h -> ./src/mympi.h
     ./output_directory.cpp -> ./src/output_directory.cpp
     ./polarization.cpp -> ./src/polarization.cpp
     ./ran.cpp -> ./src/ran.cpp
     ./ran.h -> ./src/ran.h
     ./slices.cpp -> ./src/slices.cpp
     ./sources.cpp -> ./src/sources.cpp
     ./step.cpp -> ./src/step.cpp
     ./step_d.cpp -> ./src/step_d.cpp
     ./step_d.h -> ./src/step_d.h
     ./step_d_gen.hs -> ./src/step_d_gen.hs
     ./step_h.cpp -> ./src/step_h.cpp
     ./step_h.h -> ./src/step_h.h
     ./step_h_gen.hs -> ./src/step_h_gen.hs
     ./threevec.h -> ./src/threevec.h
     ./time.cpp -> ./src/time.cpp
     ./update_e_from_d.cpp -> ./src/update_e_from_d.cpp
     ./update_e_from_d.h -> ./src/update_e_from_d.h
     ./update_e_from_d_gen.hs -> ./src/update_e_from_d_gen.hs
     ./update_from_e.cpp -> ./src/update_from_e.cpp
     ./update_from_e.h -> ./src/update_from_e.h
     ./update_from_e_gen.hs -> ./src/update_from_e_gen.hs
     ./vec.cpp -> ./src/vec.cpp
     ./vec.h -> ./src/vec.h
     ./configure.in -> ./configure.ac
     ./src/step_d_gen.hs -> ./hsrc/step_d_gen.hs
     ./src/step_h_gen.hs -> ./hsrc/step_h_gen.hs
     ./src/update_e_from_d_gen.hs -> ./hsrc/update_e_from_d_gen.hs
     ./src/update_from_e_gen.hs -> ./hsrc/update_from_e_gen.hs
     ./src/Complex.lhs -> ./hsrc/Complex.lhs
     ./src/StepGen.lhs -> ./hsrc/StepGen.lhs
     ./src/YeeLattice.lhs -> ./hsrc/YeeLattice.lhs
    A ./AUTHORS
    R ./Makefile.in
    R ./autogen.sh
    M ./configure.ac -129 +50
    A ./hsrc/
    A ./hsrc/Makefile.am
    R ./install-sh
    A ./m4/
    A ./m4/acx_blas.m4
    A ./m4/acx_lapack.m4
    A ./m4/acx_mpi.m4
    A ./src/

Fri Dec  5 15:13:17 EST 2003  stevenj@fftw.org
  * same as before
  Fix copyright year

    M ./COPYRIGHT -1 +1

Fri Dec  5 11:56:10 EST 2003  droundy@abridgegame.org
  * fix epsilon averaging bug (again).

    M ./material.cpp -10 +20
    M ./tests/known_results.cpp -2 +2

Thu Dec  4 12:07:11 EST 2003  droundy@abridgegame.org
  * fix old epsilon averaging bugs.
  This fix changes where epsilon is evaluated in 2D and 1D.

    M ./material.cpp -44 +15
    M ./tests/flux.cpp -1 +1
    M ./tests/known_results.cpp -1 +1
    M ./vec.cpp -2 +2

Thu Dec  4 13:31:20 EST 2003  michel
  * Added convergence test (waveguide mode frequency in cylindrical)

    M ./tests/Makefile.in -3 +3
    A ./tests/convergence_cyl_waveguide.cpp

Wed Nov 26 16:41:10 EST 2003  michel
  * Fix memory leak in bufprint

    M ./slices.cpp +1

Wed Dec  3 16:24:16 EST 2003  droundy@abridgegame.org
  * fix resolution scaling of 3D sources.

    M ./sources.cpp -1 +1
    M ./tests/known_results.cpp -6 +6

Wed Dec  3 16:23:40 EST 2003  droundy@abridgegame.org
  * fix initialize_A (which was causing crashes).

    M ./fields.cpp -6 +5
    M ./initialize.cpp -2 +2

Wed Dec  3 12:03:32 EST 2003  David Roundy <droundy@abridgegame.org>
  * reorder libraries to work on sarge.

    M ./Makefile.in -1 +1
    M ./doc/Makefile.in -1 +1
    M ./tests/Makefile.in -1 +1

Tue Dec  2 18:07:37 EST 2003  droundy@abridgegame.org
  * change monitor harminv interface.

    M ./doc/complicated.tex -4 +4
    M ./meep.h -1 +1
    M ./monitor.cpp -5 +9

Tue Dec  2 14:20:54 EST 2003  droundy@abridgegame.org
  * add support for anisotropic averaging (untested).
  Also fix a bug in the normal averaging in 3D.  It was evaluating epsilon at
  the wrong locations.

    M ./Makefile.in -1 +2
    A ./anisotropic_averaging.cpp
    M ./material.cpp -47 +76
    M ./meep.h +4
    M ./tests/known_results.cpp -1 +1
    A ./threevec.h

Tue Dec  2 14:16:43 EST 2003  droundy@abridgegame.org
  * fix memory leaks.

    M ./material.cpp -2 +4

Mon Dec  1 15:51:43 EST 2003  droundy@abridgegame.org
  * support anisotropic dielectrics.

    M ./Complex.lhs -2 +4
    M ./StepGen.lhs -1 +8
    M ./YeeLattice.lhs -7 +70
    M ./update_e_from_d.h -994 +2736
    M ./update_e_from_d_gen.hs -22 +41
    M ./update_from_e.h -539 +78

Wed Nov 26 15:31:13 EST 2003  droundy@abridgegame.org
  * fix the fix to sources outside of periodic cells.

    M ./sources.cpp -1 +1

Wed Nov 26 12:36:19 EST 2003  droundy@abridgegame.org
  * speed up EPS output in parallel (hopefully).

    M ./mympi.cpp -3 +7
    M ./slices.cpp -106 +169

Tue Nov 25 17:38:38 EST 2003  droundy@abridgegame.org
  * support sources out of uservolume in periodic directions.

    M ./sources.cpp -1 +4

Tue Nov 25 11:20:47 EST 2003  droundy@abridgegame.org
  * add outputting of EPS polarization slices.

    M ./meep.h +9
    M ./monitor.cpp +11
    M ./slices.cpp +95

Tue Nov 25 12:29:53 EST 2003  michel
  * Added Poynting vector functions to monitor and fixed comment in meep.h

    M ./meep.h -1 +3
    M ./monitor.cpp +27

Tue Nov 25 12:27:02 EST 2003  michel
  * Remove printf for phasing in

    M ./fields.cpp -2

Mon Nov 24 10:05:02 EST 2003  droundy@abridgegame.org
  * don't output zero values in EPS files to save space.

    M ./slices.cpp -1 +2

Fri Nov 21 16:21:56 EST 2003  droundy@abridgegame.org
  * fix saturation condition to avoid overshooting.

    M ./Complex.lhs -3 +7
    M ./StepGen.lhs +8
    M ./YeeLattice.lhs -1 +1
    M ./polarization.cpp -2 +2
    M ./tests/known_results.cpp -3 +3
    M ./update_e_from_d.h -114 +1329
    M ./update_e_from_d_gen.hs -13 +5
    M ./update_from_e.h -1287 +1203
    M ./update_from_e_gen.hs -17 +23

Fri Nov 21 15:18:11 EST 2003  droundy@abridgegame.org
  * fix 4 pi issue with polarization energies.

    M ./energy_and_flux.cpp -1 +1
    M ./polarization.cpp -7 +3
    M ./tests/known_results.cpp -3 +3
    M ./update_e_from_d.h -6 +6
    M ./update_e_from_d_gen.hs -1 +1
    M ./update_from_e.h -54 +54
    M ./update_from_e_gen.hs -1 +1

Tue Nov 18 17:56:35 EST 2003  droundy@abridgegame.org
  * change title color again.

    M ./slices.cpp -1 +1

Wed Nov 19 15:54:10 EST 2003  droundy@abridgegame.org
  * fix known_results test to work in 3D.
  Also change the component-broken energy to sum to the total energy.

    M ./polarization.cpp -3 +12
    M ./tests/known_results.cpp -5 +5

Tue Nov 18 17:36:29 EST 2003  droundy@abridgegame.org
  * change color of EPS title.

    M ./slices.cpp +4

Tue Nov 18 16:03:49 EST 2003  droundy@abridgegame.org
  * fix bugs in saturated gain.

    M ./YeeLattice.lhs -1 +2
    M ./boundaries.cpp -8 +51
    M ./fields.cpp +1
    M ./step.cpp -8 +4
    M ./tests/known_results.cpp -4 +5
    M ./tests/symmetry.cpp +30
    M ./update_e_from_d_gen.hs -1
    M ./update_from_e.h -660 +212

Tue Nov 18 12:43:56 EST 2003  droundy@abridgegame.org
  * output D as well as E and H in real_imaginary_slices.

    M ./slices.cpp -4 +4

Tue Nov 18 12:12:16 EST 2003  droundy@abridgegame.org
  * fix parallel output in symmetry.cpp

    M ./tests/symmetry.cpp -2 +2

Mon Nov 17 18:34:21 EST 2003  droundy@abridgegame.org
  * fix bugs in saturation averaging.

    M ./YeeLattice.lhs -4 +5
    M ./tests/symmetry.cpp -2 +35
    M ./update_from_e.h -13 +19

Mon Nov 17 18:00:07 EST 2003  droundy@abridgegame.org
  * test polariton symmetry in 2D as well as 1D.

    M ./tests/symmetry.cpp -2 +7

Mon Nov 17 15:22:08 EST 2003  droundy@abridgegame.org
  * optimize phase shift on EPS output.

    M ./meep.h -1 +2
    M ./slices.cpp -3 +5

Mon Nov 17 14:38:18 EST 2003  droundy@abridgegame.org
  * print filename on EPS output.

    M ./slices.cpp -9 +9

Mon Nov 17 14:09:01 EST 2003  droundy@abridgegame.org
  * add polariton symmetry test.

    M ./tests/symmetry.cpp +28

Fri Nov 14 14:14:44 EST 2003  droundy@abridgegame.org
  * a few saturation bugfixes.
  This makes saturation run in multiple dimensions.  However, it seems to
  blow up in 3D, and I don't have any idea what it does in other dimensions.

    M ./YeeLattice.lhs -13 +13
    M ./polarization.cpp -5 +6
    M ./tests/known_results.cpp -2 +5
    M ./update_from_e.h -366 +366

Fri Nov 14 13:11:14 EST 2003  droundy@abridgegame.org
  * average energy on yee lattice when updating saturation.

    M ./StepGen.lhs -6 +16
    M ./YeeLattice.lhs -27 +65
    M ./update_from_e.h -2323 +1212
    M ./update_from_e_gen.hs -111 +29

Thu Nov 13 16:25:29 EST 2003  droundy@abridgegame.org
  * rename generating code.

     ./step_d.hs -> ./step_d_gen.hs
     ./step_h.hs -> ./step_h_gen.hs
     ./update_e_from_d.hs -> ./update_e_from_d_gen.hs
     ./update_from_e.hs -> ./update_from_e_gen.hs
    A ./Complex.lhs
    M ./Makefile.in -10 +10 r4
    M ./StepGen.lhs -3 +22
    A ./YeeLattice.lhs
    M ./step_d.h -31 +31
    M ./step_h.h -31 +31
    M ./update_e_from_d.h -7 +7

Thu Nov 13 16:02:31 EST 2003  droundy@abridgegame.org
  * break timestepping into separate files.

    M ./Makefile.in -2 +9
    M ./step.cpp -356
    A ./step_d.cpp
    A ./step_h.cpp
    A ./update_e_from_d.cpp
    A ./update_from_e.cpp

Wed Nov 12 11:19:46 EST 2003  droundy@abridgegame.org
  * Fix mpi polarizability bug.

    M ./polarization.cpp -7 +11

Tue Nov 11 18:55:32 EST 2003  droundy@abridgegame.org
  * sum energy over components when updating saturation.
  Note that this doesn't yet do any averaging.  Most of the work was just in
  creating the sum over components efficiently.  And yes, the code is rather
  scary.

    M ./StepGen.lhs -1 +22
    M ./update_from_e.h -2604 +2731
    M ./update_from_e.hs -12 +67

Tue Nov 11 15:51:37 EST 2003  droundy@abridgegame.org
  * loop over owned points when updating saturating polarization.

    M ./fields.cpp +9
    M ./meep.h +1
    M ./update_from_e.h -22 +3212
    M ./update_from_e.hs -24 +75

Tue Nov 11 13:47:18 EST 2003  droundy@abridgegame.org
  * communicate polarizations.

    M ./boundaries.cpp -1 +110
    M ./meep_internals.h -1 +3
    M ./polarization.cpp -26 +35
    M ./step.cpp +1
    M ./vec.h -3 +3

Mon Nov 10 13:21:54 EST 2003  droundy@abridgegame.org
  * add exponential distribution random number generator.

    M ./ran.cpp +6
    M ./ran.h +1

Fri Nov  7 13:48:16 EST 2003  droundy@abridgegame.org
  * add random number generator.

    M ./Makefile.in -1 +1
    A ./ran.cpp
    A ./ran.h

Fri Nov  7 12:16:53 EST 2003  droundy@abridgegame.org
  * add initialize from vector potential option.

    M ./initialize.cpp +42
    M ./meep.h -1 +2

Thu Nov  6 18:18:34 EST 2003  droundy@abridgegame.org
  * add copy constructor for fields.

    M ./fields.cpp -7 +123
    M ./meep.h -1 +5

Thu Nov  6 16:52:45 EST 2003  droundy@abridgegame.org
  * output D as well as E and H EPS slices.

    M ./slices.cpp -11 +10

Thu Nov  6 15:06:38 EST 2003  droundy@abridgegame.org
  * make alloc_f automatically allocate all the needed fields.

    M ./fields.cpp -15 +29
    M ./sources.cpp -10 +2

Thu Nov  6 14:09:21 EST 2003  droundy@abridgegame.org
  * get rid of empty for loops in generated code.

    M ./StepGen.lhs -3 +6
    M ./update_e_from_d.h -8

Thu Nov  6 13:34:16 EST 2003  droundy@abridgegame.org
  * clean up complex loops in update_...hs

    M ./StepGen.lhs -6 +2
    M ./update_e_from_d.h -35 +129
    M ./update_e_from_d.hs -14 +14
    M ./update_from_e.h -27 +61
    M ./update_from_e.hs -11 +10

Thu Nov  6 12:22:18 EST 2003  droundy@abridgegame.org
  * speed up EPS envelope output.

    M ./slices.cpp -4 +6

Thu Nov  6 11:53:14 EST 2003  droundy@abridgegame.org
  * add envelope-outputting EPS option.

    M ./meep.h +2
    M ./slices.cpp +55

Wed Nov  5 16:22:30 EST 2003  droundy@abridgegame.org
  * use metallic boundary conditions by default.

    M ./boundaries.cpp -8
    M ./doc/complicated.tex -1
    M ./doc/simple.tex -4 +1
    M ./fields.cpp -1 +3
    M ./meep.h -1
    M ./tests/bench.cpp -5
    M ./tests/cylindrical.cpp -5
    M ./tests/known_results.cpp -7 +1
    M ./tests/physical.cpp -1 +1
    M ./tests/symmetry.cpp -27
    M ./tests/three_d.cpp -2
    M ./tests/two_dimensional.cpp -5 +1

Wed Nov  5 15:28:01 EST 2003  droundy@civet.berkeley.edu
  * fix bug in polariton found by Chiyan.

    M ./tests/known_results.cpp -3 +3
    M ./update_from_e.h -3 +3
    M ./update_from_e.hs -1 +1

Tue Nov  4 18:14:29 EST 2003  droundy@abridgegame.org
  * support vol1d and vol2d as well as volone and voltwo.

    M ./vec.cpp +8
    M ./vec.h +2

Tue Nov  4 15:10:32 EST 2003  droundy@abridgegame.org
  * rewrite polarization code using code generator.

    M ./Makefile.in -1 +5
    M ./meep.h -13 +2
    M ./polarization.cpp -117
    M ./step.cpp -28 +12
    M ./update_e_from_d.h +22
    M ./update_e_from_d.hs -3 +27
    A ./update_from_e.h
    A ./update_from_e.hs

Mon Nov  3 17:10:11 EST 2003  droundy@civet.berkeley.edu
  * add two more polariton tests.

    M ./tests/known_results.cpp +28

Mon Nov  3 10:14:33 EST 2003  droundy@abridgegame.org
  * add polariton test in 1D.

    M ./tests/known_results.cpp +15

Mon Nov  3 08:23:03 EST 2003  droundy@abridgegame.org
  * treat source as a polarization.
  This patch also contains a whole slew of gcc --pedantic inspired changes,
  which I'm too lazy to separate out from the critical stuff.

    M ./StepGen.lhs -4 +32
    M ./bands.cpp -3
    M ./boundaries.cpp -20 +9
    M ./energy_and_flux.cpp -19 +10
    M ./fields.cpp -6 +5
    M ./fluxes.cpp +1
    M ./material.cpp -51 +53
    M ./meep.h -6 +7
    M ./meep_internals.h -2 +5
    M ./mympi.cpp +2
    M ./output_directory.cpp -12 +12
    M ./polarization.cpp -4
    M ./slices.cpp -36 +36
    M ./sources.cpp -29 +13
    M ./step.cpp -19 +15
    M ./step_d.h -16
    M ./step_d.hs -4 +9
    M ./tests/flux.cpp -2 +1
    M ./tests/known_results.cpp -11 +11
    M ./tests/physical.cpp -2 +2
    M ./tests/symmetry.cpp -2 +4
    M ./tests/two_dimensional.cpp -2 +2
    M ./time.cpp -1 +2
    M ./update_e_from_d.h -12 +55
    M ./update_e_from_d.hs -26 +55
    M ./vec.cpp -10 +33
    M ./vec.h -2 +12

Mon Nov  3 08:04:39 EST 2003  droundy@abridgegame.org
  * speed up 1D tests.

    M ./tests/one_dimensional.cpp -6

Fri Oct 31 13:01:12 EST 2003  droundy@abridgegame.org
  * don't test mpi (since I'll now test it on superjdj).

    M ./darcs_test -7

Fri Oct 31 09:55:59 EST 2003  droundy@abridgegame.org
  * fix array overrun bug that only bothered gcc 2.95.

    M ./boundaries.cpp -2 +2

Thu Oct 30 08:22:01 EST 2003  droundy@abridgegame.org
  * rename step_e.h to update_e_from_d.h

     ./step_e.h -> ./update_e_from_d.h
     ./step_e.hs -> ./update_e_from_d.hs
    M ./Makefile.in -3 +4
    M ./step.cpp -1 +1

Wed Oct 29 14:13:28 EST 2003  droundy@abridgegame.org
  * generate code for update_e_from_d.

    M ./step.cpp -8 +1
    M ./step_e.h -365 +13
    M ./step_e.hs -68 +27

Wed Oct 29 12:56:27 EST 2003  droundy@abridgegame.org
  * switch to timestepping D rather than E.

    M ./Makefile.in -5 +1
    M ./doc/epsilon_polariton_1d.tex -4 +3
    M ./fields.cpp -7 +13
    M ./meep.h -7 +2
    M ./meep_internals.h -3 +1
    M ./polarization.cpp -72 +25
    M ./sources.cpp -2 +2
    M ./step.cpp -597 +55
    M ./step_d.h -36 +36
    M ./step_d.hs -3 +3
    R ./step_e_old.h
    R ./step_e_old.hs
    M ./tests/Makefile.in -3 +3
    M ./tests/bench.cpp -85
    R ./tests/step_algorithm.cpp
    M ./vec.cpp +5
    M ./vec.h -2 +4

Wed Oct 29 10:11:52 EST 2003  droundy@abridgegame.org
  * add 3D test using soon-to-be-old timestepping.

    M ./Makefile.in -1 +7
    M ./step.cpp -2 +71
    A ./step_d.h
    A ./step_d.hs
    A ./step_e_old.h
    A ./step_e_old.hs
    M ./tests/step_algorithm.cpp +38

Wed Oct 29 09:56:14 EST 2003  droundy@abridgegame.org
  * trivial cleanup.

    M ./fields.cpp -1 +1

Wed Oct 29 09:23:06 EST 2003  droundy@abridgegame.org
  * add D field to fields data structure (but don't actually use it).

    M ./boundaries.cpp -42 +27
    M ./fields.cpp -10 +10
    M ./material.cpp -4 +5
    M ./meep.h -23 +26
    M ./meep_internals.h -4 +6
    M ./step.cpp +144
    M ./vec.h -16 +30

Wed Oct 29 08:58:28 EST 2003  droundy@civet.berkeley.edu
  tagged working version


Wed Oct 29 07:31:08 EST 2003  droundy@abridgegame.org
  * add support for initializing saturation state with saturated gain.

    M ./meep.h +6
    M ./meep_internals.h +1
    M ./polarization.cpp +27

Wed Oct 29 06:51:57 EST 2003  droundy@abridgegame.org
  * add support for outputting any polarization energy we want.

    M ./meep.h -2 +16
    M ./meep_internals.h +1
    M ./monitor.cpp +50
    M ./polarization.cpp -1 +17
    M ./slices.cpp -7 +50

Wed Oct 29 06:51:17 EST 2003  droundy@abridgegame.org
  * start work on methods introduction for manual.

    M ./doc/meep.tex -3 +100

Wed Oct 29 06:50:11 EST 2003  droundy@abridgegame.org
  * fix translate error in EPS output.

    M ./slices.cpp -1 +1

Tue Oct 28 10:05:38 EST 2003  droundy@abridgegame.org
  * remove some commented out code.

    M ./polarization.cpp -1
    M ./slices.cpp -2

Tue Oct 28 08:37:35 EST 2003  droundy@abridgegame.org
  * add EPS output of polarization energy.

    M ./meep.h +10
    M ./meep_internals.h +1
    M ./monitor.cpp +46
    M ./polarization.cpp +9
    M ./slices.cpp +88

Tue Oct 28 15:03:10 EST 2003  droundy@civet.berkeley.edu
  * fix mpi create directory bug.

    M ./output_directory.cpp -8 +8

Mon Oct 27 12:19:53 EST 2003  droundy@abridgegame.org
  * add 1D symmetry test.

    M ./tests/symmetry.cpp +44

Mon Oct 27 11:36:46 EST 2003  droundy@abridgegame.org
  * support symmetry in 1D.

    M ./material.cpp -3
    M ./vec.cpp +1

Mon Oct 27 11:35:50 EST 2003  droundy@abridgegame.org
  * shift EPS output to be on page when printed.

    M ./slices.cpp -3 +3

Mon Oct 27 09:14:17 EST 2003  droundy@abridgegame.org
  * rename dactyl to meep in makefiles.

    M ./Makefile.in -27 +27
    M ./doc/Makefile.in -10 +10
    M ./doc/epsilon_polariton_1d.tex -1 +3
    M ./tests/Makefile.in -2 +2

Mon Oct 27 13:20:57 EST 2003  droundy@civet.berkeley.edu
  * fix bug in make doc.

    M ./doc/Makefile.in -2 +2

Mon Oct 27 07:34:32 EST 2003  droundy@abridgegame.org
  * fix epsilon 1D output.

    M ./doc/epsilon_polariton_1d.tex -6 +6

Mon Oct 27 06:37:55 EST 2003  droundy@abridgegame.org
  * remove redundant is_mine check.

    M ./monitor.cpp -4 +2

Fri Oct 24 13:58:58 EDT 2003  droundy@abridgegame.org
  * never reuse old directories!

    M ./output_directory.cpp -12 +13

Fri Oct 24 13:57:31 EDT 2003  droundy@abridgegame.org
  * allow real fields with k == 0.

    M ./fields.cpp -1 +1

Fri Oct 24 11:16:44 EDT 2003  droundy@abridgegame.org
  * speed up 2D and cylindrical tests.

    M ./tests/cylindrical.cpp -12 +12
    M ./tests/two_dimensional.cpp -11 +11

Fri Oct 24 11:04:06 EDT 2003  droundy@abridgegame.org
  * fix interpolation at r == 0.

    M ./fields.cpp +1
    M ./meep_internals.h +2
    M ./slices.cpp -2 +4
    M ./tests/cylindrical.cpp -1 +50
    M ./vec.cpp -83 +51
    M ./vec.h -6 +3

Fri Oct 24 06:42:35 EDT 2003  droundy@abridgegame.org
  * test both MPI and non-MPI.

    M ./darcs_test -1 +14

Thu Oct 23 12:54:33 EDT 2003  droundy@abridgegame.org
  * fix mpi bug introduced when boundaries were rewritten.

    M ./step.cpp -3 +3

Thu Oct 23 09:12:24 EDT 2003  droundy@abridgegame.org
  * add support for creating files within a directory.

    M ./mympi.cpp +17
    M ./mympi.h +1

Thu Oct 23 08:42:27 EDT 2003  droundy@abridgegame.org
  * optimize phase in slice output.

    M ./meep.h +5
    M ./slices.cpp -31 +41

Thu Oct 23 13:49:09 EDT 2003  droundy@civet.berkeley.edu
  * fix effort volume symmetry bug.

    M ./material.cpp -2 +9

Thu Oct 23 07:30:58 EDT 2003  michel
  * Fix effort_volumes calculation when using symmetry

    M ./material.cpp -3 +3

Thu Oct 23 12:57:37 EDT 2003  droundy@civet.berkeley.edu
  * resolve conflict in tests/symmetry.cpp.

    M ./tests/symmetry.cpp +81

Thu Oct 23 07:32:33 EDT 2003  michel
  * Added support for symmetry in cylindrical + test in tests/symmetry.cpp

    M! ./material.cpp -1 +1
    M! ./tests/symmetry.cpp -42 +7
    M! ./vec.cpp +3

Thu Oct 23 07:27:38 EDT 2003  michel
  * Fix bands output to file and flush file

    M ./bands.cpp -3 +6

Thu Oct 23 07:44:38 EDT 2003  droundy@abridgegame.org
  * add support for symmetry when k == 0.

    M ./energy_and_flux.cpp -24 +9
    M ./fields.cpp -6 +6
    M ./material.cpp -8 +17
    M ./meep.h -10 +10
    M ./monitor.cpp +1
    M ./sources.cpp -73 +18
    M ./step.cpp -10 +7
    M ./tests/symmetry.cpp -14 +105
    M ./vec.cpp -9 +20
    M ./vec.h -2 +8

Thu Oct 23 07:20:49 EDT 2003  droundy@abridgegame.org
  * define complex sum_to_all.

    M ./mympi.cpp +8
    M ./mympi.h +1

Wed Oct 22 11:56:52 EDT 2003  droundy@abridgegame.org
  * floor fix in fluxes.

    M ./fluxes.cpp -2 +2

Wed Oct 22 09:42:33 EDT 2003  droundy@abridgegame.org
  * fix bugs caused by v not being enclosed within user_volume.

    M ./boundaries.cpp -30 +32

Wed Oct 22 14:45:01 EDT 2003  droundy@civet.berkeley.edu
  * speed up 3D tests.

    M ./tests/physical.cpp -4 +5
    M ./tests/three_d.cpp -18 +18

Wed Oct 22 09:36:15 EDT 2003  droundy@abridgegame.org
  * avoid overwriting array in bands.
  Also a couple of formatting fixes...

    M ./bands.cpp -5 +5

Wed Oct 22 12:47:12 EDT 2003  droundy@civet.berkeley.edu
  * replace a few more incidences of dactyl with meep.

    M ./doc/complicated.tex -2 +2
    M ./doc/omniguide.tex -1 +1
    M ./doc/simple.tex -1 +1
    M ./doc/simplebands.tex -1 +1

Wed Oct 22 11:55:25 EDT 2003  droundy@civet.berkeley.edu
  * change name of code from dactyl to meep.

     ./dactyl.h -> ./meep.h
     ./dactyl_internals.h -> ./meep_internals.h
     ./doc/dactyl.tex -> ./doc/meep.tex
    M ./Makefile.in r2
    M ./bands.cpp r2
    M ./boundaries.cpp r2
    M ./check.h r2
    M ./control_c.cpp r2
    M ./copyright.h r2
    M ./diff_slice.cpp r2
    M ./doc/Makefile.in r3
    M ./doc/complicated.tex r3
    M ./doc/energy_cons.tex r3
    M ./doc/energy_cons_1d.tex r3
    M ./doc/epsilon_polariton_1d.tex r3
    M ./doc/gpl.tex r4
    M ./doc/lossgain_epsilon.tex r3
    M ./doc/meep.tex -1 +1 r4
    M ./doc/omniguide.tex r3
    M ./doc/polaritonbands.tex r3
    M ./doc/simple.tex r3
    M ./doc/simplebands.tex r3
    M ./energy_and_flux.cpp r2
    M ./example.cpp r2
    M ./fields.cpp r2
    M ./fluxes.cpp r2
    M ./grace.cpp r2
    M ./harminv.cpp r2
    M ./harminv.h r2
    M ./initialize.cpp r2
    M ./material.cpp r2
    M ./meep.h r2
    M ./meep_internals.h r2
    M ./monitor.cpp r2
    M ./mympi.cpp r2
    M ./mympi.h r2
    M ./output_directory.cpp r2
    M ./polarization.cpp r2
    M ./slices.cpp r2
    M ./sources.cpp r2
    M ./step.cpp r2
    M ./step_e.h r2
    M ./step_h.h r2
    M ./tests/Makefile.in r2
    M ./tests/bench.cpp r2
    M ./tests/cylindrical.cpp r2
    M ./tests/flux.cpp r2
    M ./tests/known_results.cpp r2
    M ./tests/one_dimensional.cpp r2
    M ./tests/physical.cpp r2
    M ./tests/step_algorithm.cpp r2
    M ./tests/symmetry.cpp r2
    M ./tests/three_d.cpp r2
    M ./tests/two_dimensional.cpp r2
    M ./time.cpp r2
    M ./vec.cpp r2
    M ./vec.h r2

Mon Oct 20 12:57:37 EDT 2003  michel
  * Fixed metal/magnetic boundaries in Cylindrical

    M ./boundaries.cpp -13 +5

Mon Oct 20 14:22:08 EDT 2003  droundy@civet.berkeley.edu
  * use floor a few places to round properly.

    M ./vec.cpp -4 +5

Mon Oct 20 07:23:03 EDT 2003  droundy@abridgegame.org
  * don't crash on record_bands just because we didn't prepare.

    M ./bands.cpp +1

Fri Oct 17 08:55:52 EDT 2003  droundy@abridgegame.org
  * add symmetry tests with rods.

    M ./tests/symmetry.cpp -2 +30
    M ./vec.h +2

Thu Oct 16 12:58:51 EDT 2003  droundy@abridgegame.org
  * do epsilon averaging right in 3D.

    M ./material.cpp -1 +11
    M ./tests/known_results.cpp -1 +1

Thu Oct 16 11:57:38 EDT 2003  droundy@abridgegame.org
  * support nice slices on any plane in 3D.

    M ./boundaries.cpp -39 +36
    M ./dactyl.h -1 +10
    M ./monitor.cpp -20 +45
    M ./mympi.cpp +7
    M ./mympi.h +1
    M ./slices.cpp +102
    M ./vec.h +15

Thu Oct 16 06:10:15 EDT 2003  droundy@abridgegame.org
  * increase tolerance in flux test.

    M ./tests/flux.cpp -1 +1

Wed Oct 15 14:24:47 EDT 2003  droundy@abridgegame.org
  * fix bug in periodic boundary conditions.

    M ./step.cpp -1 +1
    M ./tests/known_results.cpp -14 +20

Wed Oct 15 10:54:26 EDT 2003  droundy@abridgegame.org
  * add configure flag to enable timing code.

    M ./configure.in +7
    M ./dactyl.h +5
    M ./time.cpp +2

Wed Oct 15 10:34:50 EDT 2003  droundy@abridgegame.org
  * rewrite boundary condition code.

    M ./boundaries.cpp -42 +83
    M ./dactyl.h -1 +4
    M ./fields.cpp -5 +8
    M ./step.cpp -60 +30

Wed Oct 15 10:33:39 EDT 2003  droundy@abridgegame.org
  * add new test on known results.

    M ./mympi.cpp -1 +1
    M ./mympi.h -1 +1
    M ./tests/Makefile.in -3 +3
    A ./tests/known_results.cpp

Wed Oct 15 07:08:29 EDT 2003  droundy@abridgegame.org
  * treat metals specially in boundaries.

    M ./boundaries.cpp -32 +59
    M ./dactyl.h +5
    M ./fields.cpp +4
    M ./step.cpp -25 +65

Fri Oct 10 12:24:10 EDT 2003  droundy@civet.berkeley.edu
  * increase tolerance in step_algorithm test.

    M ./tests/step_algorithm.cpp -1 +1

Fri Oct 10 11:51:28 EDT 2003  droundy@abridgegame.org
  * parallelize redefine_chunks.

    M ./material.cpp -95 +129
    M ./mympi.cpp +8
    M ./mympi.h -1 +2
    M ./tests/physical.cpp -1 +1
    M ./tests/step_algorithm.cpp -1 +1

Fri Oct 10 11:41:07 EDT 2003  droundy@abridgegame.org
  * fix simplebands example.

    M ./doc/simplebands.tex -2 +2

Fri Oct 10 11:04:37 EDT 2003  droundy@abridgegame.org
  * add nicer explanation to omniguide example.

    M ./doc/omniguide.tex -9 +8

Fri Oct 10 09:28:20 EDT 2003  droundy@abridgegame.org
  * fix bands file fix.

    M ./dactyl.h -1 +1

Fri Oct 10 09:24:30 EDT 2003  droundy@abridgegame.org
  * make bands use file rather than FILE.

    M ./bands.cpp -5 +6
    M ./dactyl.h -2 +2

Fri Oct 10 08:33:40 EDT 2003  droundy@abridgegame.org
  * add 3D benchmarks and support thin volumes in 2D and 3D.

    M ./tests/bench.cpp +60
    M ./vec.cpp -3 +5

Fri Oct 10 08:33:18 EDT 2003  droundy@abridgegame.org
  * add use_bloch interface accepting a double.

    M ./dactyl.h +3

Fri Oct 10 08:33:01 EDT 2003  droundy@abridgegame.org
  * remove debugging code...

    M ./material.cpp -10 +1

Thu Oct  9 13:10:07 EDT 2003  droundy@abridgegame.org
  * define a flush command for the file type.
  This command is a noop when running in parallel...

    M ./mympi.cpp +8
    M ./mympi.h +1

Thu Oct  9 12:57:10 EDT 2003  droundy@abridgegame.org
  * add 3D symmetry support and tests.

    M ./material.cpp -1 +1
    M ./sources.cpp -2 +9
    M ./tests/cylindrical.cpp -3 +3
    M ./tests/physical.cpp -1 +52
    M ./tests/symmetry.cpp -2 +231
    M ./vec.cpp -12 +34
    M ./vec.h -1 +10

Thu Oct  9 12:39:17 EDT 2003  michel
  * Fixed periodic boundary conditions

    M ./boundaries.cpp -4 +3

Thu Oct  9 11:59:57 EDT 2003  droundy@abridgegame.org
  * don't crash on EPS slices in 3D.

    M ./slices.cpp +8
    M ./sources.cpp -1 +1

Thu Oct  9 10:05:07 EDT 2003  droundy@abridgegame.org
  * rewrite monitor points to use new interpolation method.

    M ./dactyl.h -5 +2
    M ./monitor.cpp -36 +20
    M ./slices.cpp -4 +6

Thu Oct  9 08:37:40 EDT 2003  droundy@abridgegame.org
  * fix but in magnetic energy in box.

    M ./energy_and_flux.cpp -7 +6

Thu Oct  9 08:27:00 EDT 2003  droundy@abridgegame.org
  * reorganize interpolation yet again.

    M ./vec.cpp -139 +70
    M ./vec.h -3 +4

Wed Oct  8 10:58:23 EDT 2003  droundy@abridgegame.org
  * fix pml asymmetry by storing both split fields.

    M ./StepGen.lhs -3 +9
    M ./dactyl.h -2 +4
    M ./dactyl_internals.h -1 +1
    M ./energy_and_flux.cpp -4 +8
    M ./fields.cpp -18 +29
    M ./polarization.cpp -17 +33
    M ./slices.cpp -1 +1
    M ./step.cpp -54 +64
    M ./step_e.h -100 +160
    M ./step_e.hs -36 +23
    M ./step_h.h -96 +120
    M ./step_h.hs -32 +15
    M ./tests/symmetry.cpp -39 +11

Tue Oct  7 14:13:07 EDT 2003  michel
  * Added splitting by effort and use it for PML

    M ./dactyl.h -4 +12
    M ./fields.cpp -3 +2
    M ./material.cpp -20 +233
    M ./step.cpp -5 +5
    M ./tests/Makefile.in -4 +4
    A ./tests/physical.cpp
    M ./tests/symmetry.cpp -3 +5
    M ./vec.cpp -19 +141
    M ./vec.h +5

Tue Oct  7 13:47:17 EDT 2003  michel
  * Fix peek_field debug output

    M ./step.cpp -1 +1

Tue Oct  7 13:37:54 EDT 2003  michel
  * Added PML sigma slice output

    M ./slices.cpp +14

Tue Oct  7 13:27:05 EDT 2003  david
  * fix time stepping bug and add more parentheses in generated loop code.

    M ./step_e.h -60 +60
    M ./step_e.hs -3 +3
    M ./step_h.h -52 +52
    M ./step_h.hs -2 +2

Tue Oct  7 13:12:44 EDT 2003  david
  * support ghc 5.02.

    M ./Makefile.in -2 +2
    M ./StepGen.lhs -1 +1

Tue Oct  7 10:32:12 EDT 2003  droundy@abridgegame.org
  * resolve merge conflict in three_d.

    M ./tests/three_d.cpp -1 +1

Tue Oct  7 10:23:25 EDT 2003  droundy@abridgegame.org
  * use fancy new interpolate in all cartesian cases.

    M! ./fluxes.cpp -8 +6
    M! ./tests/step_algorithm.cpp -1 +1
    M! ./tests/symmetry.cpp +1
    M! ./tests/three_d.cpp -1 +1
    M! ./vec.cpp -142 +5
    M! ./vec.h -4

Mon Oct  6 12:26:10 EDT 2003  droundy@civet.berkeley.edu
  * lower accuracy requirements in 3D test.

    M ./tests/three_d.cpp -1 +1

Mon Oct  6 11:12:03 EDT 2003  droundy@abridgegame.org
  * support 3D at last!

    M ./sources.cpp +1
    M ./tests/Makefile.in -3 +3
    A ./tests/three_d.cpp
    M ./tests/two_dimensional.cpp -1 +1
    M ./vec.cpp -18 +53
    M ./vec.h -5 +9

Mon Oct  6 08:31:03 EDT 2003  droundy@abridgegame.org
  * round pml sigma nicely.

    M ./material.cpp -2 +3

Fri Oct  3 09:13:19 EDT 2003  droundy@abridgegame.org
  * fix stride bug in 3D.

    M ./vec.cpp -5 +4

Fri Oct  3 07:19:38 EDT 2003  droundy@civet.berkeley.edu
  * don't use restrict after all, since gcc 2.95 doesn't support it.

    M ./step.cpp -1 +1

Fri Oct  3 07:13:29 EDT 2003  droundy@abridgegame.org
  * use __restrict__ keyword, although it doesn't seem to help.

    M ./step.cpp -17 +19

Thu Oct  2 12:51:20 EDT 2003  droundy@abridgegame.org
  * use generated timestepping code for E.

    M ./Makefile.in -2 +4
    M ./StepGen.lhs -2 +2
    M ./dactyl.h +2
    M ./step.cpp -121 +259
    A ./step_e.h
    A ./step_e.hs
    M ./step_h.h -80 +80
    M ./tests/bench.cpp -7 +42
    M ./tests/flux.cpp -14 +4
    M ./tests/step_algorithm.cpp -4 +74
    M ./vec.cpp -1 +1

Thu Oct  2 10:21:12 EDT 2003  droundy@abridgegame.org
  * step_h optimizations.

    M ./StepGen.lhs -5 +23
    M ./step_h.h -50 +280
    M ./step_h.hs -5 +19
    M ./vec.cpp -1

Thu Oct  2 09:11:05 EDT 2003  droundy@abridgegame.org
  * rewrite step generating code.

    M ./Makefile.in -4 +3
    A ./StepGen.lhs
    M ./step.cpp -1 +1
    A ./step_h.h
    A ./step_h.hs
    R ./stepgen.h
    R ./stepgen.hs

Wed Oct  1 16:19:32 EDT 2003  droundy@abridgegame.org
  * generate timestepping code automatically.

    M ./Makefile.in +5
    M ./step.cpp -15 +14
    A ./stepgen.h
    A ./stepgen.hs
    M ./tests/bench.cpp -1 +1
    M ./tests/step_algorithm.cpp -2 +3

Wed Oct  1 09:08:34 EDT 2003  droundy@abridgegame.org
  * new step_h code which is simpler.

    M ./dactyl.h +14
    M ./fields.cpp +47
    M ./material.cpp -1 +7
    M ./output_directory.cpp -1 +6
    M ./step.cpp -65 +175
    M ./tests/Makefile.in -3 +3
    M ./tests/bench.cpp -2 +55
    M ./tests/cylindrical.cpp +1
    A ./tests/step_algorithm.cpp
    M ./tests/symmetry.cpp +1
    M ./tests/two_dimensional.cpp +1
    M ./vec.cpp -54 +32
    M ./vec.h -3 +39

Tue Sep 30 08:06:08 EDT 2003  droundy@abridgegame.org
  * fix pml bug in H pml.

    M ./material.cpp -6 +7

Mon Sep 29 07:57:26 EDT 2003  droundy@abridgegame.org
  * define stride for a given direction in a field.

    M ./vec.cpp -7 +12
    M ./vec.h +1

Mon Sep 29 07:59:46 EDT 2003  droundy@civet.berkeley.edu
  * resolve merge conflict in vec.cpp.

    M ./vec.cpp -72

Mon Sep 29 07:35:36 EDT 2003  droundy@abridgegame.org
  * remove unused debug code step_right.

    M ./dactyl.h -5
    M ./step.cpp -86

Mon Sep 29 07:26:58 EDT 2003  droundy@abridgegame.org
  * use geometric_volume for energies and slices.

    M! ./dactyl.h -13 +14
    M! ./dactyl_internals.h -1 +1
    M! ./doc/energy_cons.tex -2 +2
    M! ./doc/energy_cons_1d.tex -4 +4
    M! ./energy_and_flux.cpp -20 +19
    M! ./polarization.cpp -4 +3
    M! ./slices.cpp -38 +29
    M! ./tests/cylindrical.cpp -8 +16
    M! ./tests/flux.cpp -8 +8
    M! ./tests/one_dimensional.cpp -4 +8
    M! ./tests/symmetry.cpp -14 +26
    M! ./tests/two_dimensional.cpp -6 +12
    M! ./vec.cpp -22 +52
    M! ./vec.h -5 +5

Fri Sep 26 10:32:25 EDT 2003  droundy@abridgegame.org
  * preliminary work to support anisotropic dielectric tensors.
  This patch just changes the data structures to be capable of holding the
  anisotropic dielectric function.

    M ./dactyl.h -2 +2
    M ./energy_and_flux.cpp -3 +6
    M ./material.cpp -54 +70
    M ./polarization.cpp -3 +5
    M ./step.cpp -59 +61
    M ./vec.h +8

Fri Sep 26 09:13:50 EDT 2003  droundy@abridgegame.org
  * define macros to loop over electric and magnetic field components.

    M ./vec.h +5

Mon Sep 29 07:34:54 EDT 2003  droundy@civet.berkeley.edu
  * define min and max right at top of vec.cpp.
  This is to fix a compile error on gcc 2.95.4.

    M ./vec.cpp -13 +5

Fri Sep 26 11:20:51 EDT 2003  michel
  * Geometric volume

    M ./vec.cpp -2 +34
    M ./vec.h +16

Fri Sep 26 07:20:15 EDT 2003  droundy@abridgegame.org
  * another mpi bug fix.

    M ./tests/bench.cpp -1

Thu Sep 25 12:21:24 EDT 2003  droundy@civet.berkeley.edu
  * fix numerous mpi bugs.

    M ./bands.cpp -9 +6
    M ./dactyl.h -1 +5
    M ./doc/complicated.tex -2 +1
    M ./doc/energy_cons.tex -2 +1
    M ./doc/energy_cons_1d.tex -2 +1
    M ./doc/epsilon_polariton_1d.tex -13 +14
    M ./doc/lossgain_epsilon.tex -2 +1
    M ./doc/omniguide.tex -2 +1
    M ./doc/polaritonbands.tex -8 +2
    M ./doc/simple.tex -8 +7
    M ./doc/simplebands.tex -2 +1
    M ./example.cpp -2 +1
    M ./grace.cpp -3 +3 r2
    M ./material.cpp +22
    M ./mympi.cpp -2 +2
    M ./mympi.h -2 +6
    M ./polarization.cpp -12 +15
    M ./tests/bench.cpp -1 +1
    M ./tests/cylindrical.cpp -2 +1
    M ./tests/flux.cpp -2 +1
    M ./tests/one_dimensional.cpp -2 +1
    M ./tests/symmetry.cpp -2 +1
    M ./tests/two_dimensional.cpp -2 +1

Thu Sep 25 09:22:39 EDT 2003  michel
  * Make volume(void) an empty constructor

    M ./vec.cpp -6
    M ./vec.h -1 +1

Thu Sep 25 09:37:44 EDT 2003  droundy@abridgegame.org
  * fix parallelization bug in bands.

    M ./bands.cpp -3 +6
    M ./mympi.cpp +7
    M ./mympi.h +1

Thu Sep 25 08:52:48 EDT 2003  droundy@abridgegame.org
  * more parallelization of IO fixes.

    M ./dactyl.h -1 +1
    M ./doc/complicated.tex -17 +22
    M ./mympi.cpp +17 r1
    M ./mympi.h +1 r1
    M ./output_directory.cpp -2 +2
    M ./slices.cpp r1
    M ./tests/symmetry.cpp -4 +2
    M ./vec.cpp r1

Thu Sep 25 08:46:08 EDT 2003  michel
  * replace D1,D2 with d1,d2 (directions)

    M ./vec.cpp -5 +5

Thu Sep 25 08:36:56 EDT 2003  michel
  * inline 3 functions: min, max, max

    M ./vec.cpp -3 +3

Thu Sep 25 07:15:38 EDT 2003  michel
  * More automation in vec.cpp: split_specifically, transform, etc.

    M ./vec.cpp -59 +8

Wed Sep 24 18:20:40 EDT 2003  michel
  * Use LOOP_OVER_DIRECTIONS in volume::contains; use bool

    M ./vec.cpp -43 +15
    M ./vec.h -3 +3

Wed Sep 24 14:05:19 EDT 2003  droundy@abridgegame.org
  * rewrite MPI file output to use MPI-2.

    M ./dactyl.h -2 +2
    M ./mympi.cpp -1 +48
    M ./mympi.h -2 +12
    M ./slices.cpp -166 +135
    M ./vec.cpp -6 +8
    M ./vec.h -1 +3

Wed Sep 24 12:52:32 EDT 2003  michel
  * simplify volume.num_direction() and volume.nx() etc.

    M ./vec.cpp -17 +6
    M ./vec.h -17 +8

Wed Sep 24 12:44:11 EDT 2003  michel
  * added vec(ndim) and ivec(ndim) constructors

    M ./vec.h +2

Wed Sep 24 11:56:04 EDT 2003  michel
  * use LOOP_OVER_DIRECTIONS in class ivec

    M ./vec.h -51 +28

Wed Sep 24 11:43:32 EDT 2003  michel
  * in zero_vec only set to 0 meaningful components

    M ./vec.h -1 +1

Wed Sep 24 11:34:54 EDT 2003  michel
  * Make use of LOOP_OVER_DIRECTIONS in vec operators

    M ./vec.h -48 +35

Wed Sep 24 12:06:47 EDT 2003  droundy@abridgegame.org
  * reorganize mpi portion of header file.

    M ./Makefile.in -11 +3
    M ./dactyl.h -20 +1
    A ./mympi.h

Wed Sep 24 10:02:08 EDT 2003  droundy@abridgegame.org
  * test cleanups and new flux plane test.

    M ./tests/cylindrical.cpp -2 +1
    M ./tests/flux.cpp +36
    M ./tests/one_dimensional.cpp -2 +1
    M ./tests/symmetry.cpp -2 +1
    M ./tests/two_dimensional.cpp -2 +1

Wed Sep 24 09:49:13 EDT 2003  droundy@abridgegame.org
  * doc fixes.

    M ./doc/complicated.tex -4 +8
    M ./doc/simple.tex -2 +3

Wed Sep 24 09:38:26 EDT 2003  droundy@abridgegame.org
  * rebuild docs if header files change.

    M ./doc/Makefile.in -1 +1

Wed Sep 24 09:03:40 EDT 2003  michel
  * clean vec() constructor and fix vec with undefined dimension

    M ./material.cpp -4 +2
    M ./sources.cpp -1 +2
    M ./vec.cpp -11 +1
    M ./vec.h -2 +11

Wed Sep 24 07:43:18 EDT 2003  droundy@abridgegame.org
  * fix bug in 1D flux when running in parallel.

    M ./fluxes.cpp -2 +4

Wed Sep 24 07:05:14 EDT 2003  droundy@abridgegame.org
  * don't delete output directories on make clean.

    M ./doc/Makefile.in -2 +2
    M ./tests/Makefile.in -1 +1

Tue Sep 23 13:47:57 EDT 2003  droundy@abridgegame.org
  * make two mirror test use pml.

    M ./tests/symmetry.cpp -10 +13

Tue Sep 23 13:35:30 EDT 2003  michel
  * Added inline functions nd(dim) & dstart(dim)

    M ./vec.h +8

Tue Sep 23 13:11:15 EDT 2003  droundy@abridgegame.org
  * simplify complex.tex example just a tad.

    M ./doc/complicated.tex -10 +5

Tue Sep 23 12:54:32 EDT 2003  droundy@abridgegame.org
  * add support for multiple symmetry operations.

    M ./energy_and_flux.cpp -5 +14
    M ./tests/symmetry.cpp -4 +51
    M ./vec.cpp -8 +68
    M ./vec.h -1 +8

Tue Sep 23 12:18:03 EDT 2003  droundy@abridgegame.org
  * add copy constructor for mat.

    M ./dactyl.h +1
    M ./material.cpp +12

Tue Sep 23 08:21:00 EDT 2003  droundy@abridgegame.org
  * skip redundant chunk boundary draws.
  Also, draw chunk boundaries at electric walls (or where they would be).

    M ./slices.cpp -13 +11

Tue Sep 23 08:04:34 EDT 2003  droundy@abridgegame.org
  * eliminate divides in PML timestepping.

    M ./dactyl.h +1
    M ./material.cpp +14
    M ./step.cpp -30 +35

Tue Sep 23 07:35:53 EDT 2003  droundy@abridgegame.org
  * improve visibility of chunk borders in EPS output.

    M ./slices.cpp -4 +6

Tue Sep 23 07:02:51 EDT 2003  michel
  * Fix chunk splitting and added cylindrical pml test.

    M ./tests/cylindrical.cpp -3 +61
    M ./vec.cpp -2 +2

Tue Sep 23 07:01:15 EDT 2003  michel
  * Fixed boundary location in cylindrical.
  This caused PML problems in cylindrical.

    M ./vec.cpp -2 +2

Mon Sep 22 15:43:22 EDT 2003  michel
  * fix chunk border output in cylindrical EPS output.

    M ./slices.cpp -1 +1

Mon Sep 22 15:42:08 EDT 2003  michel
  * support pentium III.

    M ./configure.in -3 +3

Mon Sep 22 13:36:59 EDT 2003  droundy@abridgegame.org
  * outline chunk boundaries in EPS plots.

    M ./dactyl.h +2
    M ./slices.cpp +39

Mon Sep 22 10:54:05 EDT 2003  droundy@abridgegame.org
  * change d1 etc to D1 etc.

    M ./bands.cpp r4
    M ./boundaries.cpp r4
    M ./check.h r4
    M ./control_c.cpp r4
    M ./copyright.h r4
    M ./dactyl.h r4
    M ./dactyl_internals.h r4
    M ./diff_slice.cpp r4
    M ./doc/complicated.tex r4
    M ./doc/dactyl.tex r4
    M ./doc/energy_cons.tex r4
    M ./doc/energy_cons_1d.tex r4
    M ./doc/epsilon_polariton_1d.tex r4
    M ./doc/gpl.tex r4
    M ./doc/lossgain_epsilon.tex r4
    M ./doc/omniguide.tex r4
    M ./doc/polaritonbands.tex r4
    M ./doc/simple.tex r4
    M ./doc/simplebands.tex r4
    M ./energy_and_flux.cpp r4
    M ./example.cpp r4
    M ./fields.cpp r4
    M ./fluxes.cpp r4
    M ./grace.cpp r4
    M ./harminv.cpp r4
    M ./harminv.h r4
    M ./initialize.cpp r4
    M ./material.cpp r4
    M ./monitor.cpp r4
    M ./mympi.cpp r4
    M ./output_directory.cpp r4
    M ./polarization.cpp r4
    M ./slices.cpp r4
    M ./sources.cpp r4
    M ./step.cpp r4
    M ./tests/bench.cpp r4
    M ./tests/cylindrical.cpp r4
    M ./tests/flux.cpp r4
    M ./tests/one_dimensional.cpp r4
    M ./tests/symmetry.cpp r4
    M ./tests/two_dimensional.cpp r4
    M ./time.cpp r4
    M ./vec.cpp r4
    M ./vec.h r4

Mon Sep 22 10:28:00 EDT 2003  droundy@civet.berkeley.edu
  * add int max function to vec.cpp

    M ./vec.cpp +5

Mon Sep 22 09:47:35 EDT 2003  droundy@abridgegame.org
  * fix up eps output to be more efficient at high resolutions.

    M ./dactyl.h -1 +6
    M ./monitor.cpp -3 +9
    M ./slices.cpp -13 +52
    M ./vec.cpp -1 +27
    M ./vec.h -1 +3

Fri Sep 19 14:46:26 EDT 2003  droundy@abridgegame.org
  * add timing capabilities to fields.

    M ./Makefile.in -1 +1
    M ./boundaries.cpp +2
    M ./dactyl.h -6 +17
    M ./fields.cpp +5
    M ./slices.cpp -6 +10
    M ./step.cpp +8
    M ./tests/Makefile.in -2 +1
    M ./tests/bench.cpp -4 +12
    M ./tests/cylindrical.cpp -1 +1
    M ./tests/one_dimensional.cpp -1 +1
    M ./tests/symmetry.cpp -2 +2
    M ./tests/two_dimensional.cpp -1 +1
    A ./time.cpp

Fri Sep 19 11:44:54 EDT 2003  droundy@abridgegame.org
  * fix 2d example in tutorial and add another.

    M ./doc/Makefile.in -5 +9
    A ./doc/complicated.tex
    M ./doc/dactyl.tex -1 +3
    M ./doc/simple.tex -6 +7

Fri Sep 19 11:42:02 EDT 2003  droundy@abridgegame.org
  * fix postscript output when there are multiple chunks.

    M ./slices.cpp -12 +20

Fri Sep 19 09:48:53 EDT 2003  droundy@abridgegame.org
  * add showpage to postscript output.

    M ./slices.cpp +1

Thu Sep 18 12:48:53 EDT 2003  droundy@abridgegame.org
  * simplify vec transform.

    M ./vec.cpp -15 +5

Thu Sep 18 11:28:25 EDT 2003  droundy@abridgegame.org
  * fix roundoff bugs.
  This patch is rather extreme.  The code now works under the principle of
  trying to never store the location of a lattice point in a vec, but always
  to use an ivec, which is just an integer vector format on the yee lattice.

    M ./boundaries.cpp -15 +30
    M ./dactyl.h -2 +3
    M ./doc/Makefile.in -2 +2
    M ./doc/simple.tex -14 +21
    M ./energy_and_flux.cpp -5 +5
    M ./fluxes.cpp -4 +8
    M ./material.cpp -1 +1
    M ./slices.cpp -22 +22
    M ./step.cpp -2 +7
    M ./vec.cpp -107 +157
    M ./vec.h -11 +109

Wed Sep 17 12:19:27 EDT 2003  droundy@abridgegame.org
  * fix display of epsilon with symmetry.

    M ./slices.cpp -14 +14

Wed Sep 17 11:57:20 EDT 2003  droundy@abridgegame.org
  * don't use pml in chunks that aren't on borders.

    M ./material.cpp +3

Wed Sep 17 11:26:08 EDT 2003  droundy@abridgegame.org
  * support splitting any grid into any number of chunks.

    M ./tests/cylindrical.cpp -1 +1
    M ./tests/two_dimensional.cpp -2 +2
    M ./vec.cpp -16 +53
    M ./vec.h +1

Wed Sep 17 08:56:30 EDT 2003  droundy@abridgegame.org
  * fix symmetry slice output.

    M ./slices.cpp -11 +21

Wed Sep 17 08:52:34 EDT 2003  droundy@abridgegame.org
  * fix pml with symmetry.

    M ./material.cpp -10 +5
    M ./tests/symmetry.cpp -1 +51
    M ./vec.cpp -8 +11

Tue Sep 16 13:45:38 EDT 2003  droundy@civet.berkeley.edu
  * refix TE/TM mpi bug.

    M ./boundaries.cpp -6 +4
    M ./dactyl.h +2
    M ./fields.cpp +8

Tue Sep 16 09:07:50 EDT 2003  droundy@abridgegame.org
  * don't segfault outputting TE/TM slices.

    M ./slices.cpp +5

Tue Sep 16 12:27:45 EDT 2003  droundy@abridgegame.org
  * fix te/tm bug in boundaries.

    M ./boundaries.cpp -6 +8
    M ./tests/bench.cpp +26
    M ./tests/two_dimensional.cpp -5 +152

Tue Sep 16 08:52:23 EDT 2003  droundy@abridgegame.org
  * only use required fields (TE/TM) in 2d.

    M ./boundaries.cpp -2 +2
    M ./dactyl.h -3 +9
    M ./energy_and_flux.cpp -2 +2
    M ./fields.cpp -4 +15
    M ./monitor.cpp -1 +1
    M ./sources.cpp -8 +23
    M ./step.cpp -6 +6
    M ./tests/bench.cpp +51

Mon Sep 15 15:13:32 EDT 2003  droundy@abridgegame.org
  * multiple symmetry bugfixes and new tests.

    M ./boundaries.cpp -2 +2
    M ./energy_and_flux.cpp -2 +2
    M ./sources.cpp -1 +1
    M ./step.cpp -1
    M ./tests/symmetry.cpp -5 +214
    M ./vec.cpp -5 +9

Mon Sep 15 11:18:09 EDT 2003  droundy@abridgegame.org
  * fix bug with mirror plane and metal combined.

    M ./boundaries.cpp -5 +5
    M ./dactyl.h -1 +1

Mon Sep 15 11:14:22 EDT 2003  droundy@abridgegame.org
  * fix bug when metal is in both x and y directions.

    M ./boundaries.cpp -8 +11

Mon Sep 15 09:18:59 EDT 2003  droundy@abridgegame.org
  * get rid of debug output in symmetry test.

    M ./tests/symmetry.cpp -3

Mon Sep 15 09:07:49 EDT 2003  droundy@abridgegame.org
  * fix remaining bugs in symmetry code and add test.

    M ./doc/Makefile.in -1 +5
    M ./doc/dactyl.tex +2
    A ./doc/simple.tex
    M ./energy_and_flux.cpp -4 +4
    M ./material.cpp -2 +2
    M ./tests/Makefile.in -3 +6
    A ./tests/symmetry.cpp
    M ./vec.cpp -28 +80
    M ./vec.h +3

Fri Sep 12 11:22:20 EDT 2003  droundy@abridgegame.org
  * add preliminary incomplete support for symmetries.

    M ./boundaries.cpp -103 +99
    M ./dactyl.h -10 +12
    M ./dactyl_internals.h +2
    M ./energy_and_flux.cpp -19 +33
    M ./fields.cpp +2
    M ./material.cpp -4 +33
    M ./slices.cpp -121 +33
    M ./sources.cpp -25 +53
    M ./tests/flux.cpp +6
    M ./vec.cpp -1 +154
    M ./vec.h -1 +75

Wed Sep 10 14:17:09 EDT 2003  droundy@civet.berkeley.edu
  * eliminate a couple of divides.

    M ./energy_and_flux.cpp -2 +2

Wed Sep 10 14:16:42 EDT 2003  droundy@civet.berkeley.edu
  * check for roundoff errors leading to negative volumes.

    M ./vec.cpp +8

Wed Sep 10 14:16:15 EDT 2003  droundy@civet.berkeley.edu
  * fix MPI tag overflow bug.

    M ./step.cpp -2 +7

Wed Sep 10 07:53:31 EDT 2003  droundy@abridgegame.org
  * vec and volume cleanup.

    M ./vec.cpp -35 +39
    M ./vec.h -34 +35

Tue Sep  9 08:14:19 EDT 2003  droundy@abridgegame.org
  * add 2D bloch boundary condition support.

    M ./bands.cpp -3 +3
    M ./boundaries.cpp -39 +105
    M ./dactyl.h -6 +6
    M ./fields.cpp -20 +4
    M ./initialize.cpp -2 +2
    M ./monitor.cpp -7 +7
    M ./tests/two_dimensional.cpp -3 +48

Mon Sep  8 14:39:36 EDT 2003  droundy@abridgegame.org
  * metal boundary conditions rewrite and 2D support.

    M ./boundaries.cpp -5 +36
    M ./dactyl.h +8
    M ./fields.cpp +1
    M ./material.cpp -19 +18
    M ./tests/cylindrical.cpp +2
    M ./tests/two_dimensional.cpp +2
    M ./vec.h +8

Mon Sep  8 13:24:05 EDT 2003  droundy@abridgegame.org
  * get rid of old use_pml_left etc in favor of use_pml_everywhere.

    M ./dactyl.h -3 +1
    M ./doc/epsilon_polariton_1d.tex -2 +1
    M ./doc/lossgain_epsilon.tex -3 +1
    M ./material.cpp -8 +9
    M ./tests/bench.cpp -2 +1
    M ./tests/flux.cpp -4 +2
    M ./vec.cpp +9
    M ./vec.h +1

Mon Sep  8 11:20:51 EDT 2003  droundy@abridgegame.org
  * support (and test) PML in 2D.
  This also involved a rather large PML cleanup which greatly simplified the
  PML sigma creation code.

    M ./dactyl.h -5 +3
    M ./material.cpp -198 +31
    M ./step.cpp -38 +38
    M ./tests/two_dimensional.cpp -1 +59
    M ./vec.cpp +24
    M ./vec.h +22

Mon Sep  8 10:43:50 EDT 2003  droundy@abridgegame.org
  * add new debug method for examining field contents.

    M ./dactyl.h +2
    M ./step.cpp +17

Mon Sep  8 09:14:35 EDT 2003  droundy@abridgegame.org
  * don't rerun tests without good reason.

    M ./tests/Makefile.in -8 +7

Fri Sep  5 14:23:42 EDT 2003  droundy@abridgegame.org
  * add support for 2D.

    M ./boundaries.cpp -1 +1
    M ./material.cpp +15
    M ./slices.cpp -35 +70
    M ./sources.cpp +1
    M ./step.cpp +139
    M ./tests/Makefile.in -2 +5
    A ./tests/two_dimensional.cpp
    M ./vec.cpp -7 +131
    M ./vec.h +3

Fri Sep  5 14:14:41 EDT 2003  droundy@abridgegame.org
  * postscript formatting changes.

    M ./slices.cpp -28 +28

Fri Sep  5 13:04:36 EDT 2003  droundy@abridgegame.org
  * simplify yee lattice averaging of inveps and sigma.

    M ./material.cpp -23 +5
    M ./polarization.cpp -31 +8

Fri Sep  5 10:28:52 EDT 2003  droundy@abridgegame.org
  * simplify code for recording eps.

    M ./material.cpp -7 +1

Fri Sep  5 10:20:53 EDT 2003  droundy@abridgegame.org
  * fix pml bug in cylindrical coordinates.

    M ./step.cpp -1 +1

Fri Sep  5 09:16:46 EDT 2003  droundy@abridgegame.org
  * extend vec into 2D.

    M ./vec.cpp -2 +49
    M ./vec.h +9

Thu Sep  4 12:00:52 EDT 2003  droundy@abridgegame.org
  * fix roundoff issue with cavity.
  There are still systematic errors in the flux that I'd like to address at
  some point.

    M ./tests/flux.cpp -7 +8

Thu Sep  4 12:00:15 EDT 2003  droundy@abridgegame.org
  * plot 1d eps_slice as a line plot.

    M ./slices.cpp -2 +53

Thu Sep  4 09:56:29 EDT 2003  droundy@abridgegame.org
  * preliminary 3D work.

    M ./vec.cpp +81
    M ./vec.h +12

Thu Sep  4 09:38:53 EDT 2003  droundy@abridgegame.org
  * error message typo fix.

    M ./vec.cpp -1 +1

Thu Sep  4 08:58:05 EDT 2003  droundy@abridgegame.org
  * all object files depend on vec.h...

    M ./Makefile.in -1 +1

Thu Sep  4 08:45:09 EDT 2003  droundy@abridgegame.org
  * shorten the cutoff if it would lead to underflow.

    M ./sources.cpp +2

Thu Sep  4 08:41:15 EDT 2003  droundy@abridgegame.org
  * draw eps boundaries on 1D eps slices.

    M ./slices.cpp -1 +8

Thu Sep  4 08:40:47 EDT 2003  droundy@abridgegame.org
  * include min in flux.cpp.

    M ./tests/flux.cpp +2

Wed Sep  3 13:34:05 EDT 2003  droundy@abridgegame.org
  * add good flux tests.

    M ./tests/flux.cpp -11 +80

Wed Sep  3 12:47:29 EDT 2003  droundy@abridgegame.org
  * fix bugs in flux plane.

    M ./dactyl_internals.h -1 +2
    M ./energy_and_flux.cpp -4 +2
    M ./fluxes.cpp -14 +24

Tue Sep  2 14:14:48 EDT 2003  droundy@abridgegame.org
  * new flux plane mechanism.

    M ./Makefile.in -1 +1
    M ./dactyl.h -2 +24
    M ./dactyl_internals.h +17
    M ./energy_and_flux.cpp -13
    M ./fields.cpp +4
    A ./fluxes.cpp
    M ./step.cpp +2
    M ./tests/bench.cpp -2 +3
    M ./tests/flux.cpp -2 +3

Tue Sep  2 09:32:14 EDT 2003  droundy@abridgegame.org
  * have make clean remove debug output.

    M ./Makefile.in -1 +1
    M ./tests/Makefile.in -1 +1

Tue Sep  2 09:29:42 EDT 2003  droundy@abridgegame.org
  * add debug_printf function to print on all procs to files.

    M ./dactyl.h -1 +2
    M ./mympi.cpp -1 +17

Tue Sep  2 09:28:46 EDT 2003  droundy@abridgegame.org
  * fix bug in find_last_source (parallelization bug).

    M ./bands.cpp -2 +3
    M ./dactyl.h +1
    M ./mympi.cpp +8

Tue Sep  2 08:12:54 EDT 2003  droundy@abridgegame.org
  * interpolate for energy_in_box at edges.

    M ./Makefile.in -1 +1
    M ./energy_and_flux.cpp -2 +4
    M ./tests/Makefile.in -2 +2
    M ./vec.cpp +73
    M ./vec.h +6

Fri Aug 29 12:57:35 EDT 2003  droundy@abridgegame.org
  * add flux code (so far only supporting 1D).

    M ./dactyl.h -16 +4
    M ./energy_and_flux.cpp +13
    M ./tests/Makefile.in -2 +3
    M ./tests/bench.cpp +41
    A ./tests/flux.cpp

Fri Aug 29 12:13:39 EDT 2003  droundy@abridgegame.org
  * fix bug where I was interpolating the fields wrongly.

    M ./monitor.cpp -1 +1

Fri Aug 29 12:12:59 EDT 2003  droundy@abridgegame.org
  * define function for interpolating epsilon.

    M ./dactyl.h +8
    M ./monitor.cpp +51

Fri Aug 29 11:55:27 EDT 2003  droundy@abridgegame.org
  * fix bug in find_last_source.

    M ./bands.cpp -2 +2
    M ./sources.cpp -1 +1

Fri Aug 29 10:03:06 EDT 2003  droundy@abridgegame.org
  * try to guess some good optimization flags.

    M ./configure.in -6 +35

Fri Aug 29 07:23:17 EDT 2003  droundy@abridgegame.org
  * oops g++ 2.95 fix...

    M ./tests/cylindrical.cpp -1 +1

Fri Aug 29 07:17:34 EDT 2003  droundy@abridgegame.org
  * g++3 fixes.

    M ./bands.cpp -3 +3
    M ./control_c.cpp -1 +1
    M ./dactyl.h -2 +4
    M ./doc/epsilon_polariton_1d.tex -1 +1
    M ./doc/lossgain_epsilon.tex -3 +3
    M ./fields.cpp -1 +1
    M ./grace.cpp -6 +6
    M ./harminv.cpp -8 +8
    M ./harminv.h +2
    M ./mympi.cpp -1 +1
    M ./slices.cpp -23 +23
    M ./sources.cpp -4 +4
    M ./step.cpp -1
    M ./vec.cpp -2 +2

Thu Aug 28 13:58:48 EDT 2003  droundy@abridgegame.org
  * add a larger benchmark test.

    M ./tests/bench.cpp +1

Thu Aug 28 13:44:39 EDT 2003  droundy@abridgegame.org
  * add benchmark code.

    M ./Makefile.in -1 +4
    M ./doc/Makefile.in -1 +1
    M ./tests/Makefile.in -5 +9
    A ./tests/bench.cpp

Thu Aug 28 12:52:46 EDT 2003  droundy@abridgegame.org
  * add metallic cylindrical test case for communications.

    M ./tests/cylindrical.cpp +56

Thu Aug 28 12:07:36 EDT 2003  droundy@abridgegame.org
  * actually use mpi when making docs.

    M ./doc/Makefile.in -6 +7

Thu Aug 28 12:00:10 EDT 2003  droundy@abridgegame.org
  * run tests and make docs with all available local procs.

    M ./configure.in -1 +23

Thu Aug 28 11:43:57 EDT 2003  droundy@abridgegame.org
  * if latex2html isn't present, skip html docs.

    M ./configure.in +7
    M ./doc/Makefile.in -1 +1

Thu Aug 28 11:35:14 EDT 2003  droundy@abridgegame.org
  * fix bug in limit on number of requests allocated.

    M ./step.cpp -2 +4

Thu Aug 28 11:13:38 EDT 2003  droundy@abridgegame.org
  * comment in communications code.

    M ./step.cpp -1 +1

Thu Aug 28 11:13:19 EDT 2003  droundy@abridgegame.org
  * don't require latex2html to build ps documentation.

    M ./doc/dactyl.tex -1

Thu Aug 28 11:03:11 EDT 2003  droundy@abridgegame.org
  * parallelize lossgain_epsilon example.

    M ./doc/lossgain_epsilon.tex -11 +14

Thu Aug 28 10:12:19 EDT 2003  droundy@abridgegame.org
  * fix up communication code.
  This change has a bit of reorganization to it, it adds a unique tag to each
  message (which fixes a bug), and reorders the communications so the sends
  and recieves should usually be ordered in a nicer manner.

    M ./step.cpp -28 +30

Thu Aug 28 10:07:05 EDT 2003  droundy@abridgegame.org
  * interpolate correctly under mpi.

    M ./monitor.cpp -8 +11

Thu Aug 28 10:01:46 EDT 2003  droundy@abridgegame.org
  * add extra mympi functionality.

    M ./dactyl.h -4 +6
    M ./mympi.cpp -9 +17

Thu Aug 28 10:00:40 EDT 2003  droundy@abridgegame.org
  * remove redundand cd ..s in Makefile.

    M ./Makefile.in -4 +4

Thu Aug 28 08:11:37 EDT 2003  droundy@abridgegame.org
  * support mpi in make doc.

    M ./bands.cpp -17 +21
    M ./doc/Makefile.in -13 +10
    M ./doc/energy_cons.tex -4 +6
    M ./doc/energy_cons_1d.tex -7 +7
    M ./doc/epsilon_polariton_1d.tex +2
    M ./doc/omniguide.tex +2
    M ./doc/polaritonbands.tex +2
    R ./doc/preproc.hs
    A ./doc/preproc.pl
    M ./doc/simplebands.tex -2 +5

Thu Aug 28 06:51:32 EDT 2003  droundy@abridgegame.org
  * abort should write to stderr, not stdout.

    M ./mympi.cpp -1 +1

Thu Aug 28 06:50:33 EDT 2003  droundy@abridgegame.org
  * make clean should clean tests and doc too.

    M ./Makefile.in +2

Thu Aug 28 06:48:58 EDT 2003  droundy@abridgegame.org
  * fix printing in mpi cylindrical test.

    M ./tests/cylindrical.cpp -21 +9

Wed Aug 27 15:13:46 EDT 2003  droundy@abridgegame.org
  * replace exit with abort throughout.

    M ./bands.cpp -14 +5
    M ./boundaries.cpp -8 +2
    M ./control_c.cpp -1 +1
    M ./fields.cpp -14 +6
    M ./grace.cpp -4 +1
    M ./material.cpp -22 +9
    M ./monitor.cpp -4 +1
    M ./polarization.cpp -14 +6
    M ./slices.cpp -16 +4
    M ./sources.cpp -25 +10
    M ./step.cpp -2 +1
    M ./vec.cpp -34 +21

Wed Aug 27 14:58:46 EDT 2003  droundy@abridgegame.org
  * more mpi work.

    M ./boundaries.cpp -8 +4
    M ./dactyl.h -1 +1
    M ./fields.cpp -7 +5
    M ./output_directory.cpp -5 +3
    M ./step.cpp -8 +36

Wed Aug 27 14:00:00 EDT 2003  droundy@abridgegame.org
  * make mpi actually work (albeit crudely).

    M ./configure.in +4
    M ./dactyl.h -2 +22
    M ./energy_and_flux.cpp -10 +18
    M ./example.cpp -7 +9
    M ./fields.cpp -3 +4
    M ./material.cpp -71 +93
    M ./mympi.cpp -1 +68
    M ./output_directory.cpp -2 +2
    M ./slices.cpp -14 +40
    M ./sources.cpp -4 +6
    M ./step.cpp -20 +42
    M ./tests/Makefile.in -2 +3
    M ./tests/cylindrical.cpp -37 +33
    M ./tests/one_dimensional.cpp -22 +18

Wed Aug 27 09:28:59 EDT 2003  droundy@abridgegame.org
  * add configure --with-mpi option.

    M ./Makefile.in -1 +2
    M ./autogen.sh +1
    R ./config.h.in
    M ./configure.in -5 +33
    M ./dactyl.h +7
    M ./example.cpp -1 +4
    A ./mympi.cpp

Wed Aug 27 08:11:32 EDT 2003  droundy@abridgegame.org
  * print slices with lots more digits.

    M ./slices.cpp -1 +1

Wed Aug 27 07:51:56 EDT 2003  droundy@abridgegame.org
  * turn on a few more tests.

    M ./tests/cylindrical.cpp -6 +4
    M ./tests/one_dimensional.cpp -6 +4

Tue Aug 26 11:11:20 EDT 2003  droundy@abridgegame.org
  * chunk splitting bugfixes!

    M ./boundaries.cpp -298 +101
    M ./dactyl.h -5 +2
    M ./step.cpp -15 +15

Tue Aug 26 08:57:30 EDT 2003  droundy@abridgegame.org
  * another broken step towards mpi.

    M ./boundaries.cpp -161 +253
    M ./dactyl.h -12 +16
    M ./energy_and_flux.cpp -14 +12
    M ./example.cpp -1 +1
    M ./fields.cpp -12 +26
    M ./initialize.cpp -2 +2
    M ./step.cpp -29 +34
    M ./vec.h +5

Mon Aug 25 08:23:28 EDT 2003  droundy@abridgegame.org
  * fix valgrind message when in 1D.

    M ./vec.cpp -3 +6

Fri Aug 22 09:10:47 EDT 2003  droundy@abridgegame.org
  * speed up 1d test.

    M ./tests/one_dimensional.cpp -8 +8

Fri Aug 22 09:00:36 EDT 2003  droundy@abridgegame.org
  * add tests and bugfixes for 1d chunkiness.

    M ./tests/Makefile.in -2 +3
    A ./tests/one_dimensional.cpp
    M ./vec.cpp -22 +28
    M ./vec.h +2

Thu Aug 21 15:24:50 EDT 2003  droundy@abridgegame.org
  * implement nice test for chunks!

    M ./tests/cylindrical.cpp -10 +139

Thu Aug 21 15:23:37 EDT 2003  droundy@abridgegame.org
  * make contains defined properly.

    M ./energy_and_flux.cpp -7 +4
    M ./vec.cpp -4 +9

Thu Aug 21 15:14:57 EDT 2003  droundy@abridgegame.org
  * fix rounding issues with multichunks.

    M ./sources.cpp -1
    M ./step.cpp -25 +23
    M ./vec.cpp -23 +26

Thu Aug 21 10:24:11 EDT 2003  droundy@abridgegame.org
  * fix it so interpolation doesn't give roundoff differences.
  This just avoids roundoff errors being different for different numbers of
  chunks.  It requires that the origin (0,0) lie on a grid point.

    M ./vec.cpp -4 +9

Fri Aug  1 15:14:29 EDT 2003  droundy@abridgegame.org
  * bug fixes in monitor point and interpolate.

    M ./monitor.cpp -1 +3
    M ./vec.cpp -5 +7

Fri Aug  1 14:28:47 EDT 2003  droundy@abridgegame.org
  * fix bug in monitor point.

    M ./monitor.cpp -1 +1

Fri Aug  1 14:19:48 EDT 2003  droundy@abridgegame.org
  * fix bug in stepping at r == 0 and z == 0.

    M ./step.cpp -1 +1

Fri Aug  1 14:16:21 EDT 2003  droundy@abridgegame.org
  * fix bug in interpolation.

    M ./monitor.cpp -1 +1

Fri Aug  1 12:03:03 EDT 2003  droundy@abridgegame.org
  * fix bug in interpolation in eastern quadrant.

    M ./vec.cpp -4 +4

Fri Aug  1 12:01:13 EDT 2003  droundy@abridgegame.org
  * add routine to just integrate the volume of the cell.

    M ./dactyl.h +2
    M ./energy_and_flux.cpp +14

Fri Aug  1 11:04:40 EDT 2003  droundy@abridgegame.org
  * sort terms when summing interpolation in monitor point.

    M ./dactyl.h -2 +3
    M ./fields.cpp -1 +1
    M ./monitor.cpp -11 +41

Fri Aug  1 09:29:50 EDT 2003  droundy@abridgegame.org
  * fix bug in contains and in interpolate.

    M ./vec.cpp -2 +22

Fri Aug  1 09:28:08 EDT 2003  droundy@abridgegame.org
  * fix bug in monitor points at chunk boundaries.

    M ./dactyl.h -2 +1
    M ./monitor.cpp -18 +8

Fri Aug  1 08:42:56 EDT 2003  droundy@abridgegame.org
  * add += operator to vec.

    M ./vec.h +6

Fri Aug  1 08:40:15 EDT 2003  droundy@abridgegame.org
  * dv is zero if a point isn't in the volume.

    M ./vec.cpp +1

Fri Aug  1 08:36:14 EDT 2003  droundy@abridgegame.org
  * comment change in fields.cpp.

    M ./fields.cpp -1 +1

Fri Aug  1 08:33:57 EDT 2003  droundy@abridgegame.org
  * comment change in vec.cpp.

    M ./vec.cpp -1 +1

Fri Aug  1 08:06:39 EDT 2003  droundy@abridgegame.org
  * make interpolate round down a bit more often.

    M ./vec.cpp -1 +1

Fri Aug  1 08:03:25 EDT 2003  droundy@abridgegame.org
  * bugfix: make owns do right thing at r == 0.

    M ./vec.cpp +2

Fri Aug  1 07:59:53 EDT 2003  droundy@abridgegame.org
  * bugfix: two bugs in interpolation.

    M ./vec.cpp -4 +5

Thu Jul 31 15:01:00 EDT 2003  droundy@abridgegame.org
  * make energy_in_box really be in box.

    M ./energy_and_flux.cpp -2 +9

Thu Jul 31 14:57:35 EDT 2003  droundy@abridgegame.org
  * outdir mat fix.

    M ./dactyl.h -14 +13
    M ./fields.cpp -3 +3
    M ./material.cpp -2 +3
    M ./monitor.cpp -4 +4
    M ./output_directory.cpp -6
    M ./slices.cpp -8 +8

Thu Jul 31 08:38:17 EDT 2003  droundy@abridgegame.org
  * remove bogus monitor point constructor from header.

    M ./dactyl.h -1

Thu Jul 31 08:26:02 EDT 2003  droundy@abridgegame.org
  * make mat split recursively (and intelligently).

    M ./material.cpp -5 +1
    M ./tests/cylindrical.cpp -2 +2
    M ./vec.cpp -1 +23
    M ./vec.h +1

Thu Jul 31 08:25:17 EDT 2003  droundy@abridgegame.org
  * just for the heck of it, split chunk in e_p_1d.tex

    M ./doc/epsilon_polariton_1d.tex -1 +1

Thu Jul 31 08:22:40 EDT 2003  droundy@abridgegame.org
  * get rid of excess printf in doc.

    M ./doc/epsilon_polariton_1d.tex -1

Thu Jul 31 08:04:14 EDT 2003  droundy@abridgegame.org
  * make test at least test for failure.

    M ./Makefile.in -1 +1
    M ./tests/cylindrical.cpp -9 +18

Thu Jul 31 07:48:50 EDT 2003  droundy@abridgegame.org
  * remove debug printf.

    M ./vec.cpp -4 +1

Thu Jul 31 07:43:29 EDT 2003  droundy@abridgegame.org
  * remove debug printf.

    M ./sources.cpp -6 +1

Thu Jul 31 07:40:45 EDT 2003  droundy@abridgegame.org
  * add tests dir and one null test.

    M ./Makefile.in -1 +2
    M ./configure.in -1 +1
    A ./tests/
    A ./tests/Makefile.in
    A ./tests/cylindrical.cpp

Wed Jul 30 14:39:48 EDT 2003  droundy@abridgegame.org
  * fix comment in boundaries.

    M ./boundaries.cpp -1 +1

Wed Jul 30 14:38:23 EDT 2003  droundy@abridgegame.org
  * fix bug when origin isn't at r=0.

    M ./step.cpp -20 +20

Wed Jul 30 14:05:32 EDT 2003  droundy@abridgegame.org
  * actually split up into multiple chunks!

    M ./dactyl.h -5 +6
    M ./example.cpp -8 +9
    M ./material.cpp -24 +28
    M ./output_directory.cpp -3 +12
    M ./slices.cpp -1 +1
    M ./sources.cpp +6
    M ./vec.cpp -21 +76
    M ./vec.h -1 +3

Wed Jul 30 14:03:06 EDT 2003  droundy@abridgegame.org
  * fix bugs in propogation when radial origin isn't zero.

    M ./step.cpp -9 +13

Wed Jul 30 09:40:08 EDT 2003  droundy@abridgegame.org
  * break mat chunk creation into a separate method.

    M ./dactyl.h +3
    M ./material.cpp +9

Wed Jul 30 09:39:21 EDT 2003  droundy@abridgegame.org
  * remove debug print statement.

    M ./boundaries.cpp -2

Wed Jul 30 09:16:09 EDT 2003  droundy@abridgegame.org
  * new boundary condition code (preparatory to multiple chunks)

    M ./Makefile.in -1 +1
    A ./boundaries.cpp
    M ./dactyl.h -1 +13
    M ./fields.cpp -146 +22
    M ./vec.cpp -3 +29
    M ./vec.h +1

Tue Jul 29 07:52:24 EDT 2003  droundy@abridgegame.org
  * bugfix: was reading beyond an array occasionally.

    M ./bands.cpp -1 +3

Tue Jul 29 07:19:21 EDT 2003  droundy@abridgegame.org
  * fields_chunk doesn't need kz.

    M ./dactyl.h -5 +5
    M ./fields.cpp -9 +7
    M ./initialize.cpp -6 +6

Mon Jul 28 14:01:36 EDT 2003  droundy@abridgegame.org
  * fields_chunk doesn't need to know the time...

    M ./bands.cpp -5 +5
    M ./dactyl.h -16 +16
    M ./dactyl_internals.h -6 +5
    M ./energy_and_flux.cpp -4 +4
    M ./fields.cpp -1 +1
    M ./monitor.cpp -6 +6
    M ./sources.cpp -30 +35
    M ./step.cpp -16 +16

Mon Jul 28 11:50:15 EDT 2003  droundy@abridgegame.org
  * fields_chunk doesn't need to keep track of phasein_time.

    M ./dactyl.h -4 +3
    M ./fields.cpp -10 +3
    M ./step.cpp -25 +3

Mon Jul 28 11:49:23 EDT 2003  droundy@abridgegame.org
  * makefile improvement.

    M ./Makefile.in -1 +1

Mon Jul 28 11:20:24 EDT 2003  droundy@abridgegame.org
  * fix bug where k was wrong in fields.

    M ./fields.cpp +1

Mon Jul 28 10:40:05 EDT 2003  droundy@abridgegame.org
  * get rid of annowing informational message.

    M ./bands.cpp -1

Mon Jul 28 10:07:38 EDT 2003  droundy@abridgegame.org
  * fix bands bug.

    M ./bands.cpp -5 +5
    M ./dactyl.h -1
    M ./step.cpp -21 +2

Mon Jul 28 09:35:43 EDT 2003  droundy@abridgegame.org
  * convert bands away from fields_chunk to fields.

    M ./bands.cpp -24 +40
    M ./dactyl.h -17 +1
    M ./dactyl_internals.h -1 +3
    M ./doc/omniguide.tex -4 +4
    M ./doc/polaritonbands.tex -2 +2
    M ./doc/simplebands.tex -2 +2
    M ./fields.cpp -5 +17
    M ./initialize.cpp -2 +17
    M ./step.cpp +1

Mon Jul 28 08:26:01 EDT 2003  droundy@abridgegame.org
  * initialize time to zero...

    M ./fields.cpp +1

Mon Jul 28 07:51:22 EDT 2003  droundy@abridgegame.org
  * make the new mat and field actually work.

     ./dactyl.cpp -> ./step.cpp
    M ./Makefile.in -3 +3
    M ./configure.in -1 +1
    M ./dactyl.h -20 +118
    M ./doc/Makefile.in -2 +9
    M ./doc/energy_cons.tex -2 +2
    M ./doc/energy_cons_1d.tex -2 +2
    M ./doc/epsilon_polariton_1d.tex -2 +2
    M ./doc/lossgain_epsilon.tex -3 +3
    M ./energy_and_flux.cpp -3 +31
    M ./example.cpp -2 +2
    A ./fields.cpp
    M ./material.cpp +46
    M ./monitor.cpp -1 +7
    M ./polarization.cpp +43
    M ./slices.cpp -87 +96
    A ./sources.cpp
    M ./step.cpp -389 +85

Fri Jul 25 13:16:25 EDT 2003  droundy@abridgegame.org
  * fix latex errors in docs.

    M ./doc/dactyl.tex -4 +4
    M ./doc/epsilon_polariton_1d.tex -2 +2
    M ./doc/omniguide.tex -1 +1
    M ./doc/simplebands.tex -5 +4

Fri Jul 25 11:53:41 EDT 2003  droundy@abridgegame.org
  * oops, forgot to remove monitor_1d.cpp

    R ./monitor_1d.cpp

Fri Jul 25 11:37:05 EDT 2003  droundy@abridgegame.org
  * rename mat and fields preparatory to splitting them.

    M ./bands.cpp r2
    M ./check.h r2
    M ./control_c.cpp r2
    M ./copyright.h r2
    M ./dactyl.cpp r2
    M ./dactyl.h r2
    M ./dactyl_internals.h r2
    M ./diff_slice.cpp r2
    M ./doc/dactyl.tex r2
    M ./doc/energy_cons.tex r2
    M ./doc/energy_cons_1d.tex r2
    M ./doc/epsilon_polariton_1d.tex r2
    M ./doc/gpl.tex r2
    M ./doc/lossgain_epsilon.tex r2
    M ./doc/omniguide.tex r2
    M ./doc/polaritonbands.tex r2
    M ./doc/simplebands.tex r2
    M ./energy_and_flux.cpp r2
    M ./example.cpp r2
    M ./grace.cpp r2
    M ./harminv.cpp r2
    M ./harminv.h r2
    M ./initialize.cpp r2
    M ./material.cpp r2
    M ./monitor.cpp r2
    M ./monitor_1d.cpp r2
    M ./output_directory.cpp r2
    M ./polarization.cpp r2
    M ./slices.cpp r2
    M ./vec.cpp r2
    M ./vec.h r2

Thu Jul 24 11:59:13 EDT 2003  droundy@abridgegame.org
  * minor improvement in polaritonbands.

    M ./doc/polaritonbands.tex -1 +2

Thu Jul 24 11:53:45 EDT 2003  droundy@abridgegame.org
  * reimplement throwing away bands with too little power.

    M ./bands.cpp +18

Tue Jul 22 09:22:52 EDT 2003  droundy@abridgegame.org
  * bands fixes.

    M ./bands.cpp -2 +5
    M ./doc/omniguide.tex -7 +4
    M ./initialize.cpp +4

Fri Jul 18 14:42:44 EDT 2003  droundy@abridgegame.org
  * fix up bands calculation a bit.

    M ./bands.cpp -31 +47
    M ./dactyl.h -1
    M ./dactyl_internals.h -2 +4
    M ./doc/omniguide.tex -4 +11

Fri Jul 18 09:21:03 EDT 2003  droundy@abridgegame.org
  * fix up the 1d polariton example.

    M ./doc/epsilon_polariton_1d.tex -6 +6

Thu Jul 17 14:20:13 EDT 2003  droundy@abridgegame.org
  * remove old plot.hs and modes.hs files.

    M ./Makefile.in -7 +3
    R ./modes.hs
    R ./plot.hs

Thu Jul 17 14:18:19 EDT 2003  droundy@abridgegame.org
  * fix up lossgain example a bit more.

    M ./doc/lossgain_epsilon.tex -9 +10

Thu Jul 17 12:55:27 EDT 2003  droundy@abridgegame.org
  * fix complex conjugation of source.

    M ./dactyl.cpp -4 +4

Thu Jul 17 10:06:42 EDT 2003  droundy@abridgegame.org
  * fix interpolation bug in analytic_epsilon.

    M ./polarization.cpp -1 +2

Thu Jul 17 06:55:52 EDT 2003  droundy@abridgegame.org
  * improvement in lossgain example, exposing bug somewhere.

    M ./doc/lossgain_epsilon.tex -18 +31

Wed Jul 16 10:10:47 EDT 2003  droundy@abridgegame.org
  * support one dimensional plotting nicely.

    M ./slices.cpp -20 +36

Wed Jul 16 10:04:07 EDT 2003  droundy@abridgegame.org
  * compute analytic epsilon of omega.

    M ./dactyl.h +1
    M ./dactyl_internals.h +1
    M ./doc/epsilon_polariton_1d.tex -4 +16
    M ./polarization.cpp +26

Wed Jul 16 09:09:18 EDT 2003  droundy@abridgegame.org
  * fix up 1d polariton epsilon example.

    M ./doc/epsilon_polariton_1d.tex -32 +35

Wed Jul  9 10:33:27 EDT 2003  droundy@abridgegame.org
  * in grace, if the filename already has .eps, don't add another.

    M ./grace.cpp +5

Wed Jul  9 10:21:08 EDT 2003  droundy@abridgegame.org
  * add eps output in 1D and with real fields.

    M ./dactyl.h -1 +1
    M ./grace.cpp -1 +1
    M ./slices.cpp -20 +33

Wed Jul  9 08:53:08 EDT 2003  droundy@abridgegame.org
  * assorted valgrind-inspired fixes.

    M ./dactyl.cpp +5
    M ./dactyl.h -1 +1
    M ./dactyl_internals.h +1
    M ./grace.cpp -2 +6
    M ./slices.cpp -2 +2

Wed Jul  9 08:52:17 EDT 2003  droundy@abridgegame.org
  * fix bug with sources and real fields.

    M ./dactyl.cpp -12 +3
    M ./dactyl_internals.h -1 +1

Wed Jul  9 08:20:39 EDT 2003  droundy@abridgegame.org
  * redo saturation calculation.

    M ./dactyl.cpp +1
    M ./dactyl.h +1
    M ./dactyl_internals.h -2
    M ./polarization.cpp -20 +27

Wed Jul  9 07:35:04 EDT 2003  droundy@abridgegame.org
  * initial (failed) attempt at supporting real fields.

    M ./dactyl.cpp -5 +19
    M ./dactyl.h -2 +2
    M ./dactyl_internals.h -25 +5
    M ./polarization.cpp -5 +15
    M ./slices.cpp -1 +1

Tue Jul  8 13:43:16 EDT 2003  droundy@abridgegame.org
  * support for gain and loss saturation.

    M ./dactyl.h -1 +1
    M ./dactyl_internals.h -2 +7
    M ./doc/energy_cons_1d.tex -4 +5
    M ./polarization.cpp -10 +56

Tue Jul  8 13:42:16 EDT 2003  droundy@abridgegame.org
  * fix bug in H sources.

    M ./dactyl.cpp -1 +1

Tue Jul  8 11:22:57 EDT 2003  droundy@abridgegame.org
  * fix integrating bug.

    M ./vec.cpp -3 +2

Tue Jul  8 11:22:13 EDT 2003  droundy@abridgegame.org
  * add energy conservation example in cyl.

    M ./doc/Makefile.in -1 +6
    M ./doc/dactyl.tex +2
    A ./doc/energy_cons.tex
    M ./doc/energy_cons_1d.tex -3 +3

Tue Jul  8 10:55:22 EDT 2003  droundy@abridgegame.org
  * minor changes to example.

    M ./example.cpp -8 +7

Tue Jul  8 10:54:02 EDT 2003  droundy@abridgegame.org
  * interpolation fixes.

    M ./vec.cpp -3 +28
    M ./vec.h -8 +1

Tue Jul  8 10:53:35 EDT 2003  droundy@abridgegame.org
  * slice improvements.

    M ./slices.cpp -3 +6

Tue Jul  8 10:52:52 EDT 2003  droundy@abridgegame.org
  * only update P_pml if f_pml exists.

    M ./polarization.cpp -7 +9

Tue Jul  8 10:51:47 EDT 2003  droundy@abridgegame.org
  * fix bugs in energy computation.

    M ./dactyl.cpp -1 +1
    M ./energy_and_flux.cpp -3 +3
    M ./polarization.cpp -1 +1

Tue Jul  8 10:50:23 EDT 2003  droundy@abridgegame.org
  * interpolate in point source.

    M ./dactyl.cpp -2 +10

Tue Jul  8 10:50:07 EDT 2003  droundy@abridgegame.org
  * typos in comments.

    M ./dactyl.cpp -2 +2

Tue Jul  8 10:47:38 EDT 2003  droundy@abridgegame.org
  * fix up examples.

    M ./dactyl.cpp -4 +67
    M ./dactyl.h +4
    M ./doc/Makefile.in -8 +6
    M ./doc/dactyl.tex -1 +1
    M ./doc/energy_cons_1d.tex -12 +16
    R ./doc/epsilon_polariton.tex
    A ./doc/epsilon_polariton_1d.tex

Thu Jul  3 15:16:58 EDT 2003  droundy@abridgegame.org
  * valgrind fix--initialize sigma fields.

    M ./polarization.cpp +2

Thu Jul  3 15:15:52 EDT 2003  droundy@abridgegame.org
  * fix interpolation bugs and use it in lossgain example.

    M ./doc/lossgain_epsilon.tex -6 +4
    M ./monitor.cpp -1 +1
    M ./vec.cpp -20 +103

Thu Jul  3 11:13:15 EDT 2003  droundy@abridgegame.org
  * buggy attempt at cylindrical interpolation.

    M ./monitor.cpp -45
    M ./vec.cpp +41
    M ./vec.h +4

Thu Jul  3 10:44:24 EDT 2003  droundy@abridgegame.org
  * add interface for nice interpolation.

    M ./monitor.cpp -2 +8
    M ./vec.cpp -1 +31
    M ./vec.h -1 +2

Thu Jul  3 10:14:50 EDT 2003  droundy@abridgegame.org
  * make monitor point output field that is closest...

    M ./monitor.cpp -1 +1

Thu Jul  3 10:14:05 EDT 2003  droundy@abridgegame.org
  * include pml boundary in eps file output.

    M ./slices.cpp -3 +36

Thu Jul  3 10:12:47 EDT 2003  droundy@abridgegame.org
  * add support for radial pml.

    M ./dactyl.cpp -8 +53
    M ./dactyl.h +1
    M ./material.cpp +46

Wed Jul  2 11:34:32 EDT 2003  droundy@abridgegame.org
  * mode initialization in cylindrical coords.

    M ./Makefile.in -1 +1
    M ./dactyl.cpp -22
    A ./initialize.cpp

Wed Jul  2 10:30:40 EDT 2003  droundy@abridgegame.org
  * fixes to doc and bugfixes required by docs.

    M ./dactyl.cpp +9
    M ./dactyl.h -5 +10
    M ./dactyl_internals.h -1 +2
    M ./doc/energy_cons_1d.tex -20 +20
    M ./doc/lossgain_epsilon.tex -34 +29
    M ./doc/omniguide.tex -5 +5
    M ./doc/polaritonbands.tex -4 +4
    M ./doc/simplebands.tex -2 +2
    M ./energy_and_flux.cpp -2 +18
    M ./polarization.cpp -4 +53

Wed Jul  2 08:23:27 EDT 2003  droundy@abridgegame.org
  * fix slice naming problem when a == 1.

    M ./slices.cpp -10 +4

Wed Jul  2 08:21:43 EDT 2003  droundy@abridgegame.org
  * spiff up example.

    M ./example.cpp -2 +15

Wed Jul  2 08:21:19 EDT 2003  droundy@abridgegame.org
  * fix m == 1, r == 0 bug.

    M ./dactyl.cpp -1 +1

Wed Jul  2 08:20:55 EDT 2003  droundy@abridgegame.org
  * add initialize_field method.

    M ./dactyl.cpp +8
    M ./dactyl.h -1 +3

Wed Jul  2 08:20:40 EDT 2003  droundy@abridgegame.org
  * fix step_right bug.

    M ./dactyl.cpp -3 +3

Tue Jul  1 11:23:34 EDT 2003  droundy@abridgegame.org
  * add output_real_imaginary_slices without volume argument.

    M ./dactyl.h +1
    M ./slices.cpp +4

Tue Jul  1 11:23:04 EDT 2003  droundy@abridgegame.org
  * add step_right method for debugging.

    M ./dactyl.cpp +69
    M ./dactyl.h +3

Tue Jul  1 09:29:27 EDT 2003  droundy@abridgegame.org
  * oops forgot to add vec.h and vec.cpp...

    A ./vec.cpp
    A ./vec.h

Tue Jul  1 09:27:36 EDT 2003  droundy@abridgegame.org
  * get rid of old unused 1d files.

    R ./bands_1d.cpp
    R ./material_1d.cpp
    R ./polarization_1d.cpp
    R ./slices_1d.cpp
    R ./tidod.cpp
    R ./tidod.h
    R ./tidod_internals.h

Tue Jul  1 09:26:30 EDT 2003  droundy@abridgegame.org
  * get rid of obsolete tests.

    R ./d_eps_pml_m_1.cpp
    R ./d_k_0.1pi_pml_m_0.cpp
    R ./d_k_0.1pi_pml_m_1.cpp
    R ./d_k_0.1pi_pml_m_2.cpp
    R ./d_k_0_pml_m_2.cpp
    R ./d_metal_m_1.cpp
    R ./d_pml_m_0.cpp
    R ./d_pml_m_1.cpp
    R ./d_pml_m_2.cpp
    R ./d_rpml_m_1.cpp
    R ./d_zpml_m_1.cpp

Tue Jul  1 09:25:15 EDT 2003  droundy@abridgegame.org
  * total rewrite to support multiple dimensions.

    M ./Makefile.in -4 +2
    M ./bands.cpp -668 +52
    M ./dactyl.cpp -1015 +444
    M ./dactyl.h -97 +56
    M ./dactyl_internals.h -18 +9
    M ./energy_and_flux.cpp -289 +36
    M ./example.cpp -58 +24
    M ./material.cpp -226 +230
    M ./monitor.cpp -62 +17
    M ./output_directory.cpp -18
    M ./polarization.cpp -284 +104
    M ./slices.cpp -308 +266
    M ./tidod.cpp -2 +2

Wed Jun 18 08:41:43 EDT 2003  droundy@abridgegame.org
  * various doc and poorly tested fixes.

    M ./Makefile.in +1
    M ./bands.cpp +2
    M ./dactyl.cpp +6
    M ./doc/epsilon_polariton.tex -3 +3
    M ./monitor.cpp +6

Tue Jun  3 09:32:41 EDT 2003  droundy@abridgegame.org
  * fix peaktime argument of source adding (was off by c).

    M ./dactyl.cpp -1 +1
    M ./tidod.cpp -1 +1

Tue Jun  3 09:27:58 EDT 2003  droundy@abridgegame.org
  * make energy conserved in 1D.
  This fix adds code to keep track of energy lost (or gained) in polaritonic
  (or plasma, etc) materials in 1D, so energy conservation can be verified
  even in such materials.  This is preliminary to implementing saturated
  gain, and should be ported to the cylindrical code.

    M ./doc/Makefile.in -1 +6
    M ./doc/dactyl.tex +2
    A ./doc/energy_cons_1d.tex
    M ./material_1d.cpp -1 +1
    M ./polarization_1d.cpp -1 +43
    M ./slices_1d.cpp +31
    M ./tidod.cpp -3 +72
    M ./tidod.h +7
    M ./tidod_internals.h -1 +2

Mon May 12 09:32:35 EDT 2003  droundy@abridgegame.org
  * fix for when a peaktime is specified in add_source.

    M ./dactyl.cpp -2 +2

Mon May 12 09:30:39 EDT 2003  droundy@abridgegame.org
  * various 1d fixes.

    M ./Makefile.in -1 +2
    M ./bands_1d.cpp -2 +2
    M ./material_1d.cpp -2 +2
    M ./polarization_1d.cpp -1 +3
    A ./slices_1d.cpp
    M ./tidod.cpp -2 +2

Fri May  9 13:44:37 EDT 2003  droundy@abridgegame.org
  * add 1d code.

    M ./Makefile.in -1 +3
    A ./bands_1d.cpp
    A ./material_1d.cpp
    A ./monitor_1d.cpp
    M ./output_directory.cpp +18
    A ./polarization_1d.cpp
    A ./tidod.cpp
    A ./tidod.h
    A ./tidod_internals.h

Fri May  9 09:02:13 EDT 2003  droundy@abridgegame.org
  * oops, example wasn't superluminal...

     ./doc/superluminal_epsilon.tex -> ./doc/lossgain_epsilon.tex
    M ./doc/Makefile.in r1
    M ./doc/dactyl.tex r1
    M ./doc/lossgain_epsilon.tex -6 +5 r1

Thu May  8 12:14:41 EDT 2003  droundy@abridgegame.org
  * make prepare_for_bands use float time; new bands algorithm.

    M ./bands.cpp -3 +247
    M ./dactyl.h -1 +5
    M ./doc/omniguide.tex -21 +7
    M ./doc/polaritonbands.tex -2 +2

Thu May  1 08:07:56 EDT 2003  droundy@abridgegame.org
  * get rid of white background in omniguide example plot.

    M ./doc/Makefile.in +2

Thu May  1 07:53:12 EDT 2003  droundy@abridgegame.org
  * add superluminal example to docs.

    M ./doc/Makefile.in -2 +13
    M ./doc/dactyl.tex +2
    A ./doc/superluminal_epsilon.tex

Tue Apr 29 10:06:43 EDT 2003  droundy@abridgegame.org
  * implement harminv on monitor point lists.

    M ./dactyl.h -4 +6
    M ./monitor.cpp +27

Tue Apr 29 10:04:22 EDT 2003  droundy@abridgegame.org
  * Flip sign of freq_im so it is correct, when harminving.

    M ./bands.cpp -3 +3

Fri Apr 25 12:11:18 EDT 2003  droundy@abridgegame.org
  * fix bug when there is more than one polarizability.

    M ./polarization.cpp -1 +2

Thu Apr 24 09:14:42 EDT 2003  droundy@abridgegame.org
  * Fix problem introduced in pml reworking.

    M ./material.cpp -5 +10

Wed Apr 23 11:51:17 EDT 2003  droundy@abridgegame.org
  * crude attempt at optimizing pml.

    M ./dactyl.h -2 +3
    M ./material.cpp -14 +99

Wed Apr 23 08:09:35 EDT 2003  droundy@abridgegame.org
  * remove debug printf.

    M ./slices.cpp -1

Wed Apr 23 07:47:44 EDT 2003  droundy@abridgegame.org
  * add continuous wave sources.

    M ./dactyl.cpp -9 +56
    M ./dactyl.h -2 +10
    M ./dactyl_internals.h -1 +1

Tue Apr 22 12:59:29 EDT 2003  michel@mit.edu
  * In output_slices, include epsilon output if new_ma is defined.

    M ./slices.cpp -1 +6

Tue Apr 22 14:19:19 EDT 2003  droundy@civet.berkeley.edu
  * resolve slice filename conflict.

    M ./slices.cpp -47 +2

Tue Apr 22 12:28:53 EDT 2003  michel@mit.edu
  * In output_slices, reduced code by using a time_step_string for a==1

    M ./slices.cpp -18 +60

Fri Apr 18 07:00:25 EDT 2003  droundy@abridgegame.org
  * Fix timestamp units in slices.

    M ./slices.cpp -30 +30

Wed Apr 16 12:17:41 EDT 2003  michel@mit.edu
  * Allow for maxbands = 1 in fourier_transform

    M ./monitor.cpp -2 +3

Wed Apr 16 12:13:59 EDT 2003  michel@mit.edu
  * Fixed potentially infinite loop

    M ./dactyl.cpp -1 +1

Wed Apr 16 08:16:01 EDT 2003  michel@mit.edu
  * Use get_envelope_at_time in get_amplitude_at_time

    M ./dactyl.cpp -4 +3

Wed Apr 16 08:36:34 EDT 2003  droundy@abridgegame.org
  * Nicer energy units in epsilon_polariton.

    M ./doc/epsilon_polariton.tex -1 +1

Thu Apr 10 08:29:53 EDT 2003  droundy@abridgegame.org
  * Use normal distance units for use_pml--CHANGE YOUR CONTROL FILES!!!

    M ./bands.cpp r1
    M ./dactyl.cpp r1
    M ./dactyl.h +1 r1
    M ./dactyl_internals.h r1
    M ./doc/dactyl.tex r1
    M ./doc/epsilon_polariton.tex -1 +2 r1
    M ./doc/omniguide.tex r1
    M ./doc/polaritonbands.tex r1
    M ./doc/simplebands.tex r1
    M ./example.cpp -1 +1 r1
    M ./material.cpp +4 r1
    M ./polarization.cpp r1

Thu Apr 10 07:55:11 EDT 2003  droundy@abridgegame.org
  * Simplify epsilon plotting by using the grace class.

    M ./doc/epsilon_polariton.tex -28 +8

Wed Apr  9 13:34:04 EDT 2003  droundy@abridgegame.org
  * Avoid an infinite loop in bands.

    M ./bands.cpp +3

Wed Apr  9 11:59:18 EDT 2003  droundy@abridgegame.org
  * Fix up polariton bands example, which was wrong.

    M ./doc/Makefile.in -7 +4
    M ./doc/polaritonbands.tex -7 +10
    M ./grace.cpp -1 +2

Wed Apr  9 11:57:13 EDT 2003  droundy@abridgegame.org
  * Be less verbose.

    M ./bands.cpp -2 +2

Wed Apr  9 10:19:32 EDT 2003  droundy@abridgegame.org
  * Omniguide update.

    M ./doc/omniguide.tex -10 +10

Wed Apr  9 10:19:04 EDT 2003  droundy@abridgegame.org
  * More bands tuning.

    M ./bands.cpp -4 +5

Mon Apr  7 12:07:36 EDT 2003  droundy@abridgegame.org
  * Don't make doc when testing.

    M ./Makefile.in -1 +1
    M ./darcs_test -1 +1

Mon Apr  7 11:13:26 EDT 2003  droundy@abridgegame.org
  * Only include dactyl.h once...

    M ./dactyl.h +4

Mon Apr  7 10:41:12 EDT 2003  droundy@abridgegame.org
  * Grace counting fix.

    M ./grace.cpp -10 +10

Mon Apr  7 10:40:22 EDT 2003  droundy@abridgegame.org
  * Bands fixes and omniguide bands example.

    M ./bands.cpp -19 +22
    M ./doc/Makefile.in -2 +8
    M ./doc/dactyl.tex +2
    A ./doc/omniguide.tex

Fri Apr  4 11:36:17 EST 2003  droundy@abridgegame.org
  * Support more output directories.

    M ./output_directory.cpp -1 +1

Thu Apr  3 08:25:32 EST 2003  droundy@abridgegame.org
  * Don't throw out mostly unoccupied bands by default.

    M ./dactyl.h -1 +1

Thu Apr  3 08:24:08 EST 2003  droundy@abridgegame.org
  * Kludge to get initialize_with working again, sort of.

    M ./dactyl.cpp -30 +30

Thu Apr  3 08:23:12 EST 2003  droundy@abridgegame.org
  * Various bands tuneups.

    M ./bands.cpp -6 +32

Thu Apr  3 08:15:14 EST 2003  droundy@abridgegame.org
  * Fix bug in initialize when m > 0 (was missing the ground state!).

    M ./dactyl.cpp -1 +1

Thu Apr  3 07:58:24 EST 2003  droundy@abridgegame.org
  * Create a symlink pointing to latest output.

    M ./output_directory.cpp +9

Wed Apr  2 11:16:32 EST 2003  droundy@abridgegame.org
  * Possibly fixes to initialize_with functions.

    M ./dactyl.cpp -39 +43

Wed Apr  2 10:18:16 EST 2003  droundy@abridgegame.org
  * Spiff up a test.

    M ./Makefile.in +7
    M ./d_k_0.1pi_pml_m_1.cpp -7 +6

Tue Apr  1 13:03:05 EST 2003  droundy@abridgegame.org
  * More bands tuning.

    M ./bands.cpp -7 +26

Tue Apr  1 13:00:42 EST 2003  droundy@abridgegame.org
  * Output approximate power when doing grace_bands.

    M ./bands.cpp -20 +5

Tue Apr  1 12:59:40 EST 2003  droundy@abridgegame.org
  * Make grace able to output one additional datum per point.

    M ./dactyl.h -2 +4
    M ./grace.cpp -6 +12

Tue Apr  1 11:51:08 EST 2003  droundy@abridgegame.org
  * Resolve conflict in merge with find_last_source and prepare_for_bands.

    M ./bands.cpp -6 +2

Tue Apr  1 11:00:19 EST 2003  michel@mit.edu
  * Fix bug in energy calculation (revert h in pml after stepping)

    M ./dactyl.h +2
    M ./energy_and_flux.cpp +41

Tue Apr  1 10:46:58 EST 2003  michel@mit.edu
  * Added fields::find_last_source()

    M ./bands.cpp -2 +11
    M ./dactyl.h +1

Mon Mar 31 11:47:04 EST 2003  michel@mit.edu
  * Wrote energy_in_box(rmin, rmax, zmin, zmax)

    M ./dactyl.h -3 +4
    M ./energy_and_flux.cpp -23 +45

Mon Mar 31 11:41:04 EST 2003  droundy@abridgegame.org
  * Throw out bands which have too little amplitude.

    M ./bands.cpp -1 +21
    M ./dactyl.h -1 +2
    M ./dactyl_internals.h -1 +1

Mon Mar 31 05:49:37 EST 2003  droundy@abridgegame.org
  * Assorted bands fixes.

    M ./bands.cpp -15 +52
    M ./dactyl.cpp -2 +3

Fri Mar 28 10:17:30 EST 2003  michel@mit.edu
  * Changed energy and field units (now independent of a)

    M ./energy_and_flux.cpp -3 +4

Fri Mar 28 10:06:39 EST 2003  michel@mit.edu
  * Fixed units for time()

    M ./dactyl.h -4 +4

Thu Mar 27 09:39:43 EST 2003  bermel@mit.edu
  * Include <complex> rather than <complex.h>.

    M ./harminv.h -1 +1

Thu Mar 27 09:38:13 EST 2003  bermel@mit.edu
  * Get units of k in initialize_with right. (a 2pi)

    M ./dactyl.cpp -9 +9

Thu Mar 27 09:35:52 EST 2003  bermel@mit.edu
  * Output amplitude (actually "approx power") to output of bands.

    M ./bands.cpp -6 +12
    M ./dactyl.h -1 +1

Tue Mar 25 08:24:21 EST 2003  michel@mit.edu
  * New flux planes and moved energy and flux to energy_and_flux.cpp

    M ./Makefile.in -1 +1
    M ./bands.cpp -2
    M ./dactyl.h +20
    M ./dactyl_internals.h +15
    A ./energy_and_flux.cpp
    M ./slices.cpp -93

Tue Mar 25 09:35:26 EST 2003  droundy@abridgegame.org
  * Add more verbosity.

    M ./bands.cpp -10 +20

Wed Mar 19 09:59:02 EST 2003  droundy@abridgegame.org
  * Make err matching requirement less strict at low freqs.

    M ./bands.cpp -1 +3

Wed Mar 19 09:58:35 EST 2003  droundy@abridgegame.org
  * Fixes in commented out printfs in bands calc.

    M ./bands.cpp -18 +18

Wed Mar 19 09:57:57 EST 2003  droundy@abridgegame.org
  * Reduce scale_factor for better results in bands calc.

    M ./bands.cpp -1 +1

Wed Mar 19 09:57:27 EST 2003  droundy@abridgegame.org
  * Ignore amplitude in matching freqs in bands calc.

    M ./bands.cpp -2 +2

Wed Mar 19 09:45:07 EST 2003  droundy@abridgegame.org
  * Get rid of old lowpass filter in bands calc.

    M ./bands.cpp -17 +2

Wed Mar 19 09:37:37 EST 2003  droundy@abridgegame.org
  * Add a verbosity flag which will make dactyl more talkative for debugging purposes.

    M ./bands.cpp -14 +19
    M ./dactyl.cpp +1
    M ./dactyl.h +2
    M ./dactyl_internals.h +1

Tue Mar 18 09:04:40 EST 2003  droundy@abridgegame.org
  * Allow user to set range in a grace plot.

    M ./dactyl.h +1
    M ./grace.cpp -3 +15

Wed Mar 12 13:54:44 EST 2003  michel@mit.edu
  * set sigma_phi to zero again 

    M ./material.cpp -1 +1

Mon Mar 17 13:03:42 EST 2003  droundy@abridgegame.org
  * Add class for outputting to a grace plot.

    M ./Makefile.in -1 +1
    M ./bands.cpp +12
    M ./dactyl.h +23
    A ./grace.cpp

Mon Mar 17 09:26:38 EST 2003  droundy@abridgegame.org
  * Fix units of k.

    M ./dactyl.cpp -2 +2

Mon Mar 17 06:29:37 EST 2003  droundy@abridgegame.org
  * Add epsilon calculation example.

    M ./doc/Makefile.in -2 +9
    M ./doc/dactyl.tex +2
    A ./doc/epsilon_polariton.tex

Fri Mar 14 12:27:17 EST 2003  droundy@abridgegame.org
  * Fix eps file orientation produced by plot.

    M ./doc/Makefile.in -1 +1
    M ./doc/polaritonbands.tex -1 +1
    M ./plot.hs -1 +1

Wed Mar 12 12:51:14 EST 2003  michel@mit.edu
  * improved make_output_directory

    M ./dactyl.h -1 +1
    M ./example.cpp -1
    M ./output_directory.cpp -9 +22

Wed Mar 12 13:41:29 EST 2003  droundy@abridgegame.org
  * Various polariton fixes--still untested in PML.

    M ./polarization.cpp -17 +72

Wed Mar 12 13:38:39 EST 2003  droundy@abridgegame.org
  * Add fancy new interrupt handling, and fix up polariton example.

    M ./Makefile.in -1 +1
    A ./control_c.cpp
    M ./dactyl.h +7
    M ./doc/polaritonbands.tex -33 +11
    M ./example.cpp -11 +5

Wed Mar 12 13:32:28 EST 2003  droundy@abridgegame.org
  * Get fmin right when there is an epsilon.

    M ./bands.cpp -2 +2

Wed Mar 12 11:48:52 EST 2003  droundy@abridgegame.org
  * Check for phonon bands, just in case...

    M ./bands.cpp +15
    M ./dactyl_internals.h +4

Wed Mar 12 10:49:19 EST 2003  droundy@abridgegame.org
  * Another chapter to the manual (incomplete, of course).

    M ./doc/dactyl.tex -2 +39

Wed Mar 12 10:45:39 EST 2003  droundy@abridgegame.org
  * Break out the guts of get_freqs into a separate method.

    M ./bands.cpp -123 +125
    M ./dactyl_internals.h +5

Wed Mar 12 10:41:43 EST 2003  droundy@abridgegame.org
  * Define a handy time method to get the actual floating point time of the simulation.

    M ./dactyl.h +1

Wed Mar 12 10:37:51 EST 2003  droundy@abridgegame.org
  * Fix plane wave source to work better with eps != 1.

    M ./dactyl.cpp -10 +12

Wed Mar 12 10:34:53 EST 2003  droundy@abridgegame.org
  * Fix band structure frequency units.

    M ./bands.cpp -6 +11

Wed Mar 12 10:33:05 EST 2003  droundy@abridgegame.org
  * Don't use libtool any more.

    M ./Makefile.in -1 +2

Wed Mar 12 07:35:36 EST 2003  droundy@abridgegame.org
  * Fix PML derivatives to be self-consistent (hopefully also fixing sigma_phi instability).

    M ./dactyl.cpp -66 +77

Tue Mar 11 12:50:52 EST 2003  michel@mit.edu
  * Made all eps arrays of size (nr+1)*(nz+1)

    M ./material.cpp -10 +10

Tue Mar 11 12:50:04 EST 2003  michel@mit.edu
  * Fixed frequency units bug in do_harminv

    M ./bands.cpp -1 +1

Tue Mar 11 12:49:40 EST 2003  droundy@abridgegame.org
  * Don't crash on initialize_polarizations with no polarization.

    M ./polarization.cpp -1 +1

Tue Mar 11 10:54:49 EST 2003  droundy@abridgegame.org
  * Turn back on sigma_phi (in the PML, that is).

    M ./material.cpp -5

Mon Mar 10 12:14:27 EST 2003  droundy@abridgegame.org
  * Output slices of polarizations.

    M ./slices.cpp -1 +17

Mon Mar 10 12:14:05 EST 2003  droundy@abridgegame.org
  * Update diff_slice to new number of digits in time.

    M ./diff_slice.cpp -2 +2

Mon Mar 10 12:06:50 EST 2003  droundy@abridgegame.org
  * Don't allow bad sources at small r.

    M ./dactyl.cpp +10

Mon Mar 10 08:45:58 EST 2003  droundy@abridgegame.org
  * Get rid of extraneous memory allocation check.

    M ./dactyl.cpp -4

Mon Mar 10 08:37:10 EST 2003  droundy@abridgegame.org
  * Remove extraneous commented out code.

    M ./polarization.cpp -2

Mon Mar 10 08:31:39 EST 2003  droundy@abridgegame.org
  * Make polaritons work (maybe) in PML.

    M ./dactyl.cpp +2
    M ./dactyl.h +2
    M ./dactyl_internals.h -3 +7
    M ./doc/dactyl.tex +52
    M ./material.cpp +1
    M ./polarization.cpp -28 +147

Mon Mar 10 08:21:25 EST 2003  droundy@abridgegame.org
  * Move rmin_bulk to dactyl_internal.h

    M ./dactyl.cpp -10
    M ./dactyl_internals.h +10

Mon Mar 10 08:08:26 EST 2003  droundy@abridgegame.org
  * Makefile fix for doc.

    M ./Makefile.in -1 +3
    M ./doc/Makefile.in -1 +1

Fri Mar  7 11:28:35 EST 2003  droundy@abridgegame.org
  * Make all field arrays the same size.

    M ./dactyl.cpp -6 +6
    M ./slices.cpp -6 +6

Fri Mar  7 08:32:00 EST 2003  michel@mit.edu
  * More exact energy calculation

    M ./dactyl.cpp -12 +18
    M ./dactyl.h +3
    M ./slices.cpp -1 +49

Fri Mar  7 06:46:17 EST 2003  droundy@abridgegame.org
  * Get rid of stupid NaN test in polariton propogation.

    M ./polarization.cpp -4 +1

Fri Mar  7 06:43:26 EST 2003  droundy@abridgegame.org
  * Add polariton bands section to manual and tests.

    M ./doc/Makefile.in -3 +10
    M ./doc/dactyl.tex +2
    A ./doc/polaritonbands.tex

Fri Mar  7 06:22:51 EST 2003  droundy@abridgegame.org
  * Fix polarization propogation bug.

    M ./polarization.cpp -7 +7

Fri Mar  7 06:20:51 EST 2003  droundy@abridgegame.org
  * Fix calculation of start time for bandstruc to deal with t not starting at zero, and also with large qmin.

    M ./bands.cpp -3 +4

Fri Mar  7 06:14:49 EST 2003  droundy@abridgegame.org
  * Improve phasein of epsilon so charge should be conserved.

    M ./dactyl.cpp +53

Thu Mar  6 09:59:57 EST 2003  droundy@abridgegame.org
  * Add new test suite (almost empty) and documentation.

    M ./Makefile.in -13 +4
    M ./configure.in -1 +1
    A ./darcs_test
    A ./doc/Makefile.in
    M ./doc/dactyl.tex +5
    A ./doc/preproc.hs
    A ./doc/simplebands.tex

Thu Mar  6 08:56:43 EST 2003  michel@mit.edu
  * Use plain frequency units for Re and Im parts of freq

    M ./bands.cpp -73 +40
    M ./dactyl.h -2 +4

Thu Mar  6 09:28:26 EST 2003  droundy@abridgegame.org
  * Do fourier transform over limited range with monitor points.

    M ./monitor.cpp -5 +16

Thu Mar  6 09:27:45 EST 2003  droundy@abridgegame.org
  * Fix up the planewave when eps != 1.

    M ./dactyl.cpp -1 +1

Wed Mar  5 11:32:10 EST 2003  michel@mit.edu
  * Made phase_in_material easier to use, changed time units

    M ./dactyl.cpp -4 +9
    M ./dactyl.h -1 +2

Wed Mar  5 11:31:24 EST 2003  michel
  * Added fields::do_harminv

    M ./bands.cpp -1 +61
    M ./dactyl.h +2

Wed Mar  5 11:30:24 EST 2003  droundy@abridgegame.org
  * fourier transform a monitor point list.

    M ./Makefile.in -1 +1
    M ./dactyl.h +21
    M ./monitor.cpp +53

Wed Mar  5 11:24:59 EST 2003  droundy@abridgegame.org
  * Fix time in monitor point stuff.

    M ./monitor.cpp -1 +1

Wed Mar  5 07:36:07 EST 2003  droundy@abridgegame.org
  * New monitor point code.

    M ./Makefile.in -1 +1
    M ./dactyl.h +23
    A ./monitor.cpp
    M ./slices.cpp -17

Tue Mar  4 12:36:40 EST 2003  droundy@abridgegame.org
  * Clean up normal sources.

    M ./dactyl.cpp -36 +18

Tue Mar  4 12:36:23 EST 2003  droundy@abridgegame.org
  * Create a plane wave source.

    M ./dactyl.cpp -1 +33
    M ./dactyl.h +3

Tue Mar  4 08:08:10 EST 2003  droundy@abridgegame.org
  * Get rid of static polarization resulting from short source pulses.

    M ./dactyl.cpp -15 +57
    M ./dactyl_internals.h -1 +3

Tue Mar  4 07:42:18 EST 2003  droundy@abridgegame.org
  * Make name argument to slice functions optional.

    M ./dactyl.h -3 +3

Tue Mar  4 07:19:20 EST 2003  droundy@abridgegame.org
  * Eliminate spurious error message in polarization code.

    M ./polarization.cpp -1 +1

Mon Mar  3 12:57:27 EST 2003  droundy@abridgegame.org
  * Make sources complex.

    M ./dactyl.cpp -107 +77
    M ./dactyl.h -9 +11
    M ./dactyl_internals.h -1 +1
    M ./example.cpp -1 +1

Mon Mar  3 11:46:04 EST 2003  michel@mit.edu
  * Source z location is double (units of a).

    M ./dactyl.cpp -18 +145
    M ./dactyl.h -7 +8

Mon Mar  3 11:39:11 EST 2003  michel@mit.edu
  * Check enough space for PML

    M ./material.cpp +9

Mon Mar  3 10:24:00 EST 2003  droundy@abridgegame.org
  * Implement polarizations (polaritons actually work now) !

    M ./dactyl.cpp +4
    M ./dactyl.h -1 +7
    M ./dactyl_internals.h -1 +3
    M ./material.cpp +12
    M ./polarization.cpp -7 +110

Mon Mar  3 10:23:28 EST 2003  droundy@abridgegame.org
  * Fix memory leaks and a memory error.

    M ./dactyl.cpp +3

Mon Mar  3 10:20:57 EST 2003  droundy@abridgegame.org
  * Reimplement the get_band method.

    M ./bands.cpp -35 +58
    M ./dactyl.h -1 +3
    M ./dactyl_internals.h -3 +1

Mon Mar  3 10:19:07 EST 2003  droundy@abridgegame.org
  * Tune scale_factor.

    M ./bands.cpp -1 +1

Fri Feb 28 14:19:09 EST 2003  droundy@abridgegame.org
  * Fix bug setting up TE modes with nonzero k.

    M ./dactyl.cpp -4 +4

Fri Feb 28 10:28:53 EST 2003  michel@mit.edu
  * Get rid of Big sig comments and fix PML bug

    M ./material.cpp -3 +1

Fri Feb 28 10:33:26 EST 2003  droundy@abridgegame.org
  * Preparatory work towards supporting frequency-dependent polarizations (plus reorganizations).

    M ./Makefile.in -1 +1
    M ./bands.cpp -54 +55
    M ./dactyl.cpp -2 +4
    M ./dactyl.h -35 +10
    M ./dactyl_internals.h +50
    M ./material.cpp -2 +3
    A ./polarization.cpp
    M ./slices.cpp -9

Fri Feb 28 06:13:02 EST 2003  droundy@abridgegame.org
  * Fix bug in units specifying epsilon in z direction.

    M ./material.cpp -1 +1

Thu Feb 27 08:30:17 EST 2003  droundy@abridgegame.org
  * Get rid of some annoying printfs.

    M ./dactyl.cpp -2

Thu Feb 27 08:20:04 EST 2003  droundy@abridgegame.org
  * Add a makefile target for html manual.

    M ./Makefile.in +3

Thu Feb 27 08:14:29 EST 2003  droundy@abridgegame.org
  * Fix misspelling in title...

    M ./doc/dactyl.tex -1 +1

Thu Feb 27 08:13:35 EST 2003  droundy@abridgegame.org
  * Change title and authors of manual.

    M ./doc/dactyl.tex -2 +2

Thu Feb 27 08:10:39 EST 2003  droundy@abridgegame.org
  * Fix phase shift due to freq in initialized modes.

    M ./dactyl.cpp -2 +2

Thu Feb 27 08:10:18 EST 2003  droundy@abridgegame.org
  * Fix indexing problem for TE modes.

    M ./dactyl.cpp -2 +2

Thu Feb 27 07:57:27 EST 2003  droundy@abridgegame.org
  * Replace make_vacuum with make_mean_eps.

    M ./dactyl.h -1 +1
    M ./material.cpp -5 +10

Thu Feb 27 07:57:02 EST 2003  droundy@abridgegame.org
  * Fix bugs in TM initialization.

    M ./dactyl.cpp -8 +6

Thu Feb 27 06:50:55 EST 2003  droundy@abridgegame.org
  * Nicer formatting of some code.

    M ./dactyl.cpp -6 +6

Thu Feb 27 06:50:14 EST 2003  droundy@abridgegame.org
  * Remove old commented out code.

    M ./dactyl.cpp -13

Thu Feb 27 06:49:01 EST 2003  droundy@abridgegame.org
  * Fix initializing of TM and TE states.

    M ./dactyl.cpp -28 +44

Wed Feb 26 13:12:10 EST 2003  droundy@abridgegame.org
  * Partial fixes in field initialization.

    M ./dactyl.cpp -44 +55

Wed Feb 26 13:11:21 EST 2003  droundy@abridgegame.org
  * Mix inverse of eps, not eps itself.

    M ./material.cpp -1 +1

Wed Feb 26 13:10:40 EST 2003  droundy@abridgegame.org
  * Fix up routine to find maximum in Jm.

    M ./dactyl.cpp -2 +3

Wed Feb 26 13:09:53 EST 2003  droundy@abridgegame.org
  * Move definition of pi into darcs_internal.h.

    M ./bands.cpp -2
    M ./dactyl_internals.h +3

Wed Feb 26 10:46:51 EST 2003  droundy@abridgegame.org
  * Add new dactyl_internals.h file.

    A ./dactyl_internals.h

Wed Feb 26 10:45:41 EST 2003  droundy@abridgegame.org
  * Fix up phasing in of epsilon.

    M ./dactyl.cpp -58 +65
    M ./dactyl.h +2

Wed Feb 26 10:44:34 EST 2003  droundy@abridgegame.org
  * Increase number of digits in slice file times.

    M ./slices.cpp -26 +26

Wed Feb 26 08:41:15 EST 2003  droundy@abridgegame.org
  * Create a method to put vacuum in a mat structure.

    M ./dactyl.h +1
    M ./material.cpp +9

Wed Feb 26 08:31:14 EST 2003  droundy@abridgegame.org
  * I forgot to add the materials file...

    A ./material.cpp

Wed Feb 26 08:28:57 EST 2003  droundy@abridgegame.org
  * Move slice code (and rest of output) to a separate file.

    M ./Makefile.in -1 +2
    M ./dactyl.cpp -472
    A ./slices.cpp

Wed Feb 26 08:24:18 EST 2003  droundy@abridgegame.org
  * Support phasing from one material to another adiabatically.

    M ./Makefile.in -2 +2
    M ./bands.cpp +3
    M ./dactyl.cpp -167 +117
    M ./dactyl.h -4 +12

Wed Feb 26 06:39:46 EST 2003  droundy@abridgegame.org
  * Split out macros into a common header file.

    M ./Makefile.in -1 +2
    M ./bands.cpp -13 +2
    M ./dactyl.cpp -25 +1

Wed Feb 26 06:36:11 EST 2003  droundy@abridgegame.org
  * Change copyright to MIT (as it should be).

    M ./bands.cpp -1 +1
    M ./d_eps_pml_m_1.cpp -1 +1
    M ./d_k_0.1pi_pml_m_0.cpp -1 +1
    M ./d_k_0.1pi_pml_m_1.cpp -1 +1
    M ./d_k_0.1pi_pml_m_2.cpp -1 +1
    M ./d_k_0_pml_m_2.cpp -1 +1
    M ./d_metal_m_1.cpp -1 +1
    M ./d_pml_m_0.cpp -1 +1
    M ./d_pml_m_1.cpp -1 +1
    M ./d_pml_m_2.cpp -1 +1
    M ./d_rpml_m_1.cpp -1 +1
    M ./d_zpml_m_1.cpp -1 +1
    M ./dactyl.cpp -1 +1
    M ./dactyl.h -1 +1
    M ./diff_slice.cpp -1 +1
    M ./example.cpp -1 +1
    M ./output_directory.cpp -1 +1

Wed Feb 26 05:52:05 EST 2003  droundy@civet.berkeley.edu
  * Add a script to call autoconf, etc.

    A ./autogen.sh

Mon Feb 24 13:35:17 EST 2003  droundy@abridgegame.org
  * Tune example band structure parameters.

    M ./example.cpp -3 +3

Mon Feb 24 13:34:58 EST 2003  droundy@abridgegame.org
  * Improve commented out debug statements.

    M ./bands.cpp -5 +5

Mon Feb 24 13:34:08 EST 2003  droundy@abridgegame.org
  * Make bands calculation yet more stable...

    M ./bands.cpp -1 +2

Mon Feb 24 11:45:59 EST 2003  droundy@abridgegame.org
  * Fix colors in band structure plot.

    M ./plot.hs -2 +2

Mon Feb 24 11:45:19 EST 2003  droundy@abridgegame.org
  * Patch to make bands calculation more robust to uncertainty in decay time.

    M ./bands.cpp -1 +1

Mon Feb 24 10:25:14 EST 2003  droundy@abridgegame.org
  * Don't record monitor point in bands file, that makes the file too big.

    M ./example.cpp -1 +1

Mon Feb 24 10:22:04 EST 2003  droundy@abridgegame.org
  * Look at larger k values, which are more interesting.

    M ./example.cpp -1 +1

Mon Feb 24 10:21:04 EST 2003  droundy@abridgegame.org
  * Create new interface for files in output dir.

    M ./dactyl.h +1
    M ./example.cpp -14 +6
    M ./output_directory.cpp +12

Mon Feb 24 10:18:54 EST 2003  droundy@abridgegame.org
  * Remove unused code in bands.cpp.

    M ./bands.cpp -17

Mon Feb 24 10:18:14 EST 2003  droundy@abridgegame.org
  * Don't bother initializing band data to zero.

    M ./bands.cpp -18

Mon Feb 24 10:17:43 EST 2003  droundy@abridgegame.org
  * Fix memory leak in bs computation.

    M ./bands.cpp +2

Mon Feb 24 10:14:09 EST 2003  droundy@abridgegame.org
  * Major revision of plot.hs.

    M ./plot.hs -386 +56

Mon Feb 24 06:50:13 EST 2003  droundy@abridgegame.org
  * Untested patch to deal with "example.dac" named executables properly.

    M ./output_directory.cpp -3 +8

Mon Feb 24 06:31:21 EST 2003  droundy@abridgegame.org
  * If source file doesn't exist in existing out dir, use that dir.

    M ./output_directory.cpp +4

Mon Feb 24 06:30:47 EST 2003  droundy@abridgegame.org
  * Spruce up output of example program.

    M ./example.cpp -2 +4

Mon Feb 24 06:29:12 EST 2003  droundy@abridgegame.org
  * Make band structure calculation not always calculate modes.

    M ./bands.cpp -7 +17
    M ./dactyl.h +2

Mon Feb 24 06:19:41 EST 2003  droundy@abridgegame.org
  * Add output directory stuff into dactyl itself.

    M ./Makefile.in -1 +1
    M ./dactyl.cpp -29 +40
    M ./dactyl.h +10
    M ./example.cpp -59 +18
    A ./output_directory.cpp

Mon Feb 24 05:18:34 EST 2003  droundy@abridgegame.org
  * Get rid of some potential buffer overflows.

    M ./dactyl.cpp -32 +35

Mon Feb 24 05:09:14 EST 2003  droundy@abridgegame.org
  * Make modes plot have bigger X's than other shape symbols.

    M ./modes.hs -1 +1

Fri Feb 21 13:12:58 EST 2003  droundy@civet.berkeley.edu
  * Resolve conflict with eps shift patch.

    M ./dactyl.cpp -4

Fri Feb 21 11:49:09 EST 2003  bermel@mit.edu
  * Simple fix for bug setting speed of light to inappropriate value

    M ./example.cpp -2 +2

Fri Feb 21 10:46:34 EST 2003  bermel@mit.edu
  * Fix to example which creates directory and copies source into it

    M ./example.cpp -3 +12

Fri Feb 21 10:29:38 EST 2003  bermel@mit.edu
  * Create target directory + copy source file

    M ./dactyl.cpp -1 +5
    M ./example.cpp -1 +34

Fri Feb 21 10:50:29 EST 2003  bermel@mit.edu
  * Simple fix for crash when flux planes aren't used

    M ./dactyl.cpp -1 +2

Fri Feb 21 13:01:10 EST 2003  droundy@abridgegame.org
  * Yet another test.

    A ./d_eps_pml_m_1.cpp

Fri Feb 21 12:45:30 EST 2003  droundy@abridgegame.org
  * Fix pml in non-one epsilon.

    M ./dactyl.cpp -32 +20

Fri Feb 21 12:45:05 EST 2003  droundy@abridgegame.org
  * Fix shift in epsilon definition.

    M ./dactyl.cpp -1 +1

Fri Feb 21 11:55:24 EST 2003  droundy@abridgegame.org
  * Yet more tests with Mihai.

    A ./d_k_0.1pi_pml_m_0.cpp
    A ./d_k_0.1pi_pml_m_1.cpp
    A ./d_k_0.1pi_pml_m_2.cpp
    A ./d_k_0_pml_m_2.cpp

Fri Feb 21 11:48:58 EST 2003  droundy@abridgegame.org
  * Fix bug in diff_slice.

    M ./diff_slice.cpp -1 +1

Fri Feb 21 11:34:20 EST 2003  droundy@abridgegame.org
  * Fix bugs in m > 1.

    M ./dactyl.cpp -3 +6

Fri Feb 21 11:34:01 EST 2003  droundy@abridgegame.org
  * Two more tests.

    A ./d_pml_m_0.cpp
    A ./d_pml_m_2.cpp

Fri Feb 21 11:09:46 EST 2003  droundy@abridgegame.org
  * Add test for both kinds of pml.

    A ./d_pml_m_1.cpp

Fri Feb 21 11:08:29 EST 2003  droundy@abridgegame.org
  * Change naming scheme for real and imaginary slices.

    M ./dactyl.cpp -14 +14
    M ./diff_slice.cpp -26 +26

Fri Feb 21 11:07:52 EST 2003  droundy@abridgegame.org
  * Fix bugs with radial and axial pml.

    M ./dactyl.cpp -4 +4

Fri Feb 21 10:42:28 EST 2003  droundy@abridgegame.org
  * Checked and fixed bugs in zpml!

    A ./d_zpml_m_1.cpp
    M ./dactyl.cpp -12 +11

Fri Feb 21 09:38:01 EST 2003  droundy@abridgegame.org
  * Allow user to specify a real (not complex) source.

    M ./dactyl.cpp -1 +13
    M ./dactyl.h +3
    M ./example.cpp +1

Fri Feb 21 09:36:26 EST 2003  droundy@abridgegame.org
  * Snapshot of somewhat working bandstructure code.

    M ./bands.cpp -69 +156

Thu Feb 20 08:11:01 EST 2003  droundy@abridgegame.org
  * Change example to a fancy band structure example.

    M ./example.cpp -16 +29

Thu Feb 20 08:08:52 EST 2003  droundy@abridgegame.org
  * Get rid of some printfs in the band structure calc.

    M ./bands.cpp -16 +15

Thu Feb 20 08:08:24 EST 2003  droundy@abridgegame.org
  * Eliminate useless line of code.

    M ./bands.cpp -2 +1

Thu Feb 20 08:06:34 EST 2003  droundy@abridgegame.org
  * Make example deal with control-C nicely.

    M ./example.cpp -5 +12

Thu Feb 20 08:05:22 EST 2003  droundy@abridgegame.org
  * Make monitor point output nicely formatted.

    M ./dactyl.cpp -8 +13

Thu Feb 20 08:03:07 EST 2003  droundy@abridgegame.org
  * Add H sources.

    M ./bands.cpp -3 +7
    M ./dactyl.cpp -28 +70
    M ./dactyl.h -2 +9

Sat Feb 15 13:28:55 EST 2003  bermel@mit.edu
  * Minor source initialization fixes

    M ./dactyl.cpp -2 +1

Sat Feb 15 08:05:31 EST 2003  bermel@mit.edu
  * small but crucial fix to rmin_bulk

    M ./dactyl.cpp -1 +2

Fri Feb 14 10:20:29 EST 2003  droundy@abridgegame.org
  * Redefine d_rpml_m_1.cpp to synchronize with Mihai's test case.

    M ./d_rpml_m_1.cpp -5 +8

Fri Feb 14 10:17:14 EST 2003  droundy@civet.berkeley.edu
  * Set sigma_phi to zero for now, to get rid of blowup.

    M ./dactyl.cpp -3 +8

Fri Feb 14 10:16:36 EST 2003  droundy@civet.berkeley.edu
  * Redefine rmin_bulk to agree with Mihai's terminology.

    M ./dactyl.cpp -2 +6

Fri Feb 14 05:27:45 EST 2003  bermel@mit.edu
  * Declare rflux in dactyl.h.

    M ./dactyl.h +1

Thu Feb 13 09:52:15 EST 2003  
  * Flux patches

    M ./dactyl.cpp -10 +103
    M ./dactyl.h -2 +4
    M ./example.cpp -2 +2

Wed Feb 12 07:15:20 EST 2003  droundy@civet.berkeley.edu
  * Remove dependency on valgrind.

    M ./bands.cpp -2

Thu Feb 13 09:16:28 EST 2003  droundy@civet.berkeley.edu
  * Fix bug in documentation of PML.

    M ./doc/dactyl.tex -12 +12

Thu Feb 13 09:15:52 EST 2003  droundy@civet.berkeley.edu
  * Fix epsilon vs inverse epsilon bug.

    M ./dactyl.cpp -3 +3

Thu Feb 13 08:58:47 EST 2003  droundy@civet.berkeley.edu
  * PML bugfixes.

    M ./dactyl.cpp -59 +76

Thu Feb 13 07:22:32 EST 2003  droundy@civet.berkeley.edu
  * Add documentation.

    M ./Makefile.in -1 +9
    A ./doc/
    A ./doc/Yee_bulk.eps
    A ./doc/dactyl.tex
    A ./doc/gpl.tex

Wed Feb 12 07:50:27 EST 2003  droundy@civet.berkeley.edu
  * Check if source is inside cell before adding.

    M ./dactyl.cpp +5

Wed Feb 12 07:11:52 EST 2003  droundy@civet.berkeley.edu
  * Add check.h...

    A ./check.h

Wed Feb 12 07:09:56 EST 2003  droundy@civet.berkeley.edu
  * Add install-sh.

    A ./install-sh

Wed Feb 12 06:27:30 EST 2003  droundy@civet.berkeley.edu
  * Initial version--0.2

    A ./COPYING
    A ./COPYRIGHT
    A ./Makefile.in
    A ./bands.cpp
    A ./config.h.in
    A ./configure.in
    A ./copyright.h
    A ./d_metal_m_1.cpp
    A ./d_rpml_m_1.cpp
    A ./dactyl.cpp
    A ./dactyl.h
    A ./diff_slice.cpp
    A ./example.cpp
    A ./harminv.cpp
    A ./harminv.h
    A ./modes.hs
    A ./plot.hs