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LAMMPS (30 Aug 2013)
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
region mdInternal block -$l $l -$l $l -$w $w
region mdInternal block -4 $l -$l $l -$w $w
region mdInternal block -4 4 -$l $l -$w $w
region mdInternal block -4 4 -4 $l -$w $w
region mdInternal block -4 4 -4 4 -$w $w
region mdInternal block -4 4 -4 4 -2 $w
region mdInternal block -4 4 -4 4 -2 2
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
Reading data file ...
orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81)
2 by 2 by 1 MPI processor grid
2304 atoms
2304 velocities
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
1024 atoms in group internal
fix AtC internal atc two_temperature Ar_ttm.mat
ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: 2 materials defined from Ar_ttm.mat
ATC: creating two_temperature extrinsic model
ATC: 2 materials defined from Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
ATC: read 803 nodes
ATC: read 100 HEX20 elements
ATC: created nodeset 11 with 53 nodes
ATC: created nodeset 12 with 53 nodes
ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
Setting up run ...
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
DiagonalMatrix::inv(): Warning: Matrix is badly scaled. RCOND = -0.1875
Memory usage per processor = 115.483 Mbytes
Step Temp PotEng AtC[2] AtC[4]
0 9.9496068 -3732.5766 20 21.685336
10 9.9699944 -3732.6743 20.008305 21.694995
20 9.9879237 -3732.7594 20.015777 21.704833
30 10.002475 -3732.8273 20.02158 21.714852
40 10.013007 -3732.8613 20.025464 21.725057
50 10.019238 -3732.8657 20.027325 21.735449
60 10.021286 -3732.8402 20.027223 21.746031
70 10.019648 -3732.7833 20.025372 21.756808
80 10.015134 -3732.7051 20.022115 21.767782
90 10.008795 -3732.612 20.017899 21.778957
100 10.001827 -3732.5177 20.013234 21.790338
Loop time of 11.401 on 4 procs for 100 steps with 2304 atoms
Pair time (%) = 0.342919 (3.0078)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0145571 (0.127682)
Outpt time (%) = 0.116064 (1.01801)
Other time (%) = 10.9275 (95.8465)
Nlocal: 576 ave 576 max 576 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 720 ave 720 max 720 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 67354.5 ave 67632 max 66958 min
Histogram: 1 0 0 0 0 1 0 0 1 1
FullNghs: 134709 ave 134859 max 134422 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 538836
Ave neighs/atom = 233.87
Neighbor list builds = 0
Dangerous builds = 0
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