File: release.notes.4.0

package info (click to toggle)
nwchem 7.0.2-1
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 1,134,820 kB
  • sloc: fortran: 4,903,090; ansic: 67,501; f90: 19,555; python: 17,912; java: 12,311; sh: 12,023; cpp: 9,896; perl: 6,123; csh: 4,345; makefile: 1,856; sed: 246; awk: 115; exp: 111; pascal: 76
file content (287 lines) | stat: -rw-r--r-- 12,380 bytes parent folder | download | duplicates (4)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
NWChem Version 4.0 Release Notes
(Also available at 
http://www.emsl.pnl.gov/pub/docs/nwchem/support/release.4.0.html)

NOTE: These release notes are not a substitute for reading the User Manual!
They are meant to give a thumbnail sketch of the new capabilities and bug
fixes that are available in NWChem Version 4.0. When there is a conflict
between the release notes and the User Manual, the User Manual takes
precedence. 

The changes for version 4.0.1 are listed at the bottom of this file.

The TITLE directive is no longer backward compatible.  The syntax is
title <string title>

Several new major capabilities are available in NWChem, including several new
modules. The new modules are: 

  o ONIOM - ONIOM hybrid mthod of Morokuma and co-workers
  o COSMO - the continuum solvation 'Conductor-Like Screening' Model
    of A. Klamt and G. Schuurmann to describe dielectric screening effects in
    solvents.
  o NBO - Natural Bond Orbital analysis is now available inside NWChem (not
    just the interface which was in the previous versions).
  o SODFT - Spin-orbit density functional theory.
  o MD - While this is not a new capability, the MD module has been rewritten
    to allow for new force fields to be incorporated in a modular fashion.

For each of these capabilities, the user is referred to the User Manual for more
information. 

Additional major additions to the capabilities include: 

  o The Douglas-Kroll(-Hess) approach is implemented. It can be used at 
    all levels of theory. Gradients have been implemented allowing geometry 
    optimizations and frequency calculations using the Douglas-Kroll 
    Hamiltonian.
  o Inclusion of code to evaluate relativistic integrals based on Dyall's 
    modified Dirac (DmD) equation.  A one-electron approximation very similar 
    to the Douglas-Kroll-Hess approach has been implemented with gradients. 
    Two-electron scalar relativistic corrections have been implemented for 
    energies only.
  o Vibrational analysis now allows different masses to be used for a
    previously calculated hessian - see VIB description.
  o Input files to standard graphics packages such as RasMol or XMol can 
    be generated to animate vibrational modes - see VIB description.
  o Several new DFT functionals have been added:
    o Exchange-Correlation PBE0, HCTH402 and Becke1997GGA-1 functionals

Again, for each of these capabilities, the user is referred to the User Manual 
for more information. 

A major bug in version 3.3.1 that has been fixed in version 4.0:

  o A bug was found in the distribution of multidimensional Global Array's. 
    This bug created uneven distributions of array elements (i.e. some nodes 
    got many elements and some nodes got a few elements), and this had a 
    significant impact on the parallel performance through-out the code. 
    Note: the final calculated results were correct, the performance was not 
    as good as could be expected. 

Listed below are the other major and many minor changes for each module
with significant changes. These descriptions are somewhat terse and more
information is generally available in the User Manual. 

Top level directives:

  o The TITLE directive has different syntax.  This change is incompatible
    with previous versions of the directive so the user will need to change
    the TITLE directive in any current input files.
  o The CONTINUE directive is no longer supported.
  o Addition of RELATIVISTIC directive to control evaluation of relativistic 
    integrals.
  o The default memory has been increased on most workstations.
  o BUG FIX: Task shell is now working under Linux.
  o BUG FIX: The words start and restart in the TITLE directive no longer cause
    problems.
  o BUG FIX: Linux versions no longer give negative time information.

Initial orbital Guess: 

  o BUG FIX: Projection from a smaller basis set to a larger basis set now 
    works for open shells.

Basis Sets: 

  o Basis set library has been updated to include all new basis sets at the EMSL
    Gaussian Basis Set Order Form page of David Feller 
    (http://www.emsl.pnl.gov:2080/forms/basisform.html)
  o Relativistic contractions of the cc-pvnz, n = 2--5, basis sets for the 
    Douglas-Kroll and DmD approximations.
  o Dyall double-zeta basis sets for the 4p, 5p and 6p elements added
  o Some of the old basis sets were corrected:
    o Basis Set "Ag_Hay-Wadt_VDZ_(n+1)_ECP", correction coefficient in first 
      s-contraction
    o Basis Set "Ag_LANL2DZ_ECP", correction coefficient in first s-contraction
    o Complete Basis Set Family "CRENBS_ECP", complete revision of all basis 
      sets
    o ECP "Ce_SBKJC_VDZ_ECP", correction switched integer powers for d-f 
      component

Geometry: 

  o Inclusion of a finite Gaussian nuclear charge distribution.
  o Inclusion of velocities for QMD and PSPW.
  o More redundant internals are allowed.
  o Allow linear angles.
  o Mixed Cartesians in zmatrix input is more robust.
  o BUG FIX: D5H classification is now correct.
  o BUG FIX: C5H operations are recognized.

DFT: 

  o New functionals: PBE0, HCTH402 and Becke1997GGA-1
  o Self-interaction corrections.
  o Lebedev + Mura grids are now the default.
  o XC fitting can now use sphericals.
  o BUG FIX: Code correctly executes when the number of iterations is 0.

SCF: 

  o CHANGE: New line search for optimizing the wavefunction.  Does not
    abort when the number of steps is exhausted.

Driver: 

  o BUG FIX: Added code to avoid accidental degeneracies in the Hessian.

Properties: 

  o The user is now allowed to choose the point of expansion for dipole,
    quadrupole, and octupole.  See CENTER directive.
  o The center for expansion for dipole, quadrupole and octupole has changed
    from the center of mass to the center of charge.  This behavior can be 
    changed by using the CENTER directive.
  o Relativistic corrections to multipole integrals in the Dyall-modified-Dirac
    approach have been added.
  o Performance fix: GIAO convergence has been improved.
  o BUG FIX: Several parallel bugs that caused calculations to fail have 
    been fixed.
  o BUG FIX: GIAO code now recognizes when an unsupported wavefunction is
    trying to be used with GIAO.

MP2: 

  o BUG FIX: RIMP2 now has more rigorous error handling.

Hessian and Frequencies: 

  o New VIB input group to allow for hessian reuse.

Prepare:

  o PREPARE module can not be used on WIN32 platforms because of problems with
    the Global Array tools.
  o Change in parameter file format. Do not use new files with previous 
    versions of NWChem.
  o Z-matrix rules to assign coordinates of missing atoms.
  o Charge separation data from parameter files.
  o Improved performance for large systems.
  o Optional hydrogen build.
  o User defined default HIS protonation state defined in .nwchemrc.
  o Enhanced options for solute alignment, centering, translation, repeat,
    solvent removal, pmf definitions.
  o Automatic counter ion positioning.
  o Option to read old format restart files.
  o Option to write xyz and pov formats.

MD: 

  o Redesigned MD module.
  o Load balancing takes the cost of I/O into account.
  o New, single trajectory format.
  o Potential of mean force calculations.
  o Improved communication by data packing.
  o Calculation history on restart file.
  o Single point energy calculation prints out solute non-bonded energies, 
    analytic and numerical forces.
  o Positional atom constraints.
  o Profiling information.
  o Anisotropic pressure scaling implemented.
  o Browne-Clark leap frog integration implemented (guided MD).
  o Option to center in selected dimension only.
  o Option to exclude pressure scaling in z-dimension.
  o On-the-fly analysis removed.
  o BUG FIX: Modified sub-box redistribution to prevent 'lbbl increase' errors.
  o BUG FIX: The .nwchemrc file now allows for extraneous white spaces.
  o KNOWN BUG: Free energy calculations can not be performed with 
    polarizable force fields.

Analysis:

  o ANALYSIS module can not be used on WIN32 platforms because of problems with
    the Global Array tools.
  o Essential dynamics analysis.
  o Structural analysis: internal degrees of freedom, RMS deviations, atom 
    and charge distributions, atomic distances.
  o Protein structural analysis: Ramachandran and back-bone hydrogen bonds.
  o Electrostatic potential trajectory generation, including periodic 
    boundary conditions.
  o Output trajectories in pov format with rendering and color options.
  o Option to read old format trajectory files.

Integral changes: 

  o Douglas-Kroll(-Hess) integral routines have been added.
  o Relativistic one- and two-electron integral routines for the DmD approach 
    have been added.
  o General contraction and multipassing have been implemented for the
    Mc-Murchie-Davidson 2e integrals.
  o Spin-orbit integrals for SODFT enabled.
  o Effective charge potential for COSMO added.

DPLOT:

  o Gaussian cube file can now be output.
  o Format for InsightII is compatible with version 97.0.
  o Spherical functions can be plotted for MOs and density.

Tests, manuals and misc script changes: 

  o Updated User's Manual to reflect new and modified functionality in
    NWChem. 
  o QA tests have been updated to reflect the new functionality and the
    TITLE change. 
  o Updated the example directory.
  o INSTALL instructions have been rewritten to be more user friendly.
  o Updates in the contrib directory to reflect more recent machines and
    capabilities, especially the Python capability.

Installation availability: 

The current tested platforms and O/S versions are: 

  o IBM SP with P2SC nodes, AIX 4.3.2, and PSSP 3.1
  o IBM SP with silver nodes (SMP nodes with two 604e processors), AIX
    4.3.2, and PSSP 3.1. 
  o IBM SP with Power 3 nodes (SMP nodes with four processors), AIX 4.3.2
    and PSSP 3.1
  o IBM RS6000 workstation, AIX 4.1 and 4.3 
  o Cray T3E, 2.0.4.61 UNICOSMK 
  o SGI R8000/10000/12000 IRIX 6.5 
  o SUN workstations Solaris 5.6 
  o Compaq DEC alpha workstion (600 MHz EV6), Tru64 V4.0 and V5.0,
    DEC C V5.8-009, Digital Fortran V5.2 
  o Linux with Intel x86 cpus. Since there are at least 8 popular
    distributions of the Linux operating system and numerous others in
    existence, including downloading everything and building your own Linux OS,
    it is impossible to test all possible versions of Linux with NWChem.
    NWChem Release 4.0 has been tested on, RedHat 6.0 and 6.2, Debian 2.2.1,
    Suse 6.4, TurboLinux 6.04, Mandrake based on RedHat 6.0, FreeBSD 4.1.4,
    and RedHat 6.0 for the Power PC Macintosh. These all use the EGCS 
    compilers at different levels. However, the Portland Group Compiler has 
    been tested in a less robust manner.
  o Linux with Alpha cpus has been tested with RedHat 6.1 and 6.2.
    Usage of the Compaq Fortran and C compilers is necessary for compiling.
  o HP 9000/800 workstations with  HPUX B.11.00. f90 must be used for
    compilation.
  o Intel x86 with Windows 98 and NT has been tested with Compaq Visual Fortran
    6.0 and 6.1 with WMPI 1.3 or NT-Mpich.

A general FAQ is available at 
http://www.emsl.pnl.gov:2080/docs/nwchem/support/NWChem_FAQ.html

A list of Known Bugs is available at
http://www.emsl.pnl.gov:2080/docs/nwchem/support/known_bugs.4.0.html

List of Release 4.0.1 changes in the source and binary download files:

  o Fix for PeIGS so cross-compiling works on SP systems.
  o PSPW now works on HP
  o Fix for PSPW simulations of charged system
  o Level shift is now excluded from DFT unoccupied orbital energies 
  o Fix for reading cartesian hessian from a previous frequency calculation
    when run in parallel
  o QM MD restarts no longer fail under MPI
  o MD restart files are no longer overwritten
  o DNA and RNA fragments were missing some ring closure bonds.
  o In the prepare module, the distance restraint definition is fixed.
  o In the MD module, some printing has been removed when performing
    distance restraints.
  o Order of variables for the LINK card in the PDB file is now correct
  o COSMO gradients are now always calculated numerically.
  o UDFT calculations with COSMO behave better.
  o NWChem now dies gracefully when COSMO is run with either spherical
    basis functions or with ECPs.
  o Documentation has been updated based on the above changes.