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lammps/examples/USER/atc/mesh/gaussianIC1d_hex.screen
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LAMMPS (14 Aug 2013)
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms
boundary f p p
create_box 1 mdRegion
Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
4 by 1 by 1 MPI processor grid
create_atoms 1 region mdRegion
Created 3456 atoms
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
# specify interal/ghost atoms
group internal region mdInternal
2880 atoms in group internal
velocity internal create 40 87287 mom yes loop geom # <<< NOTE
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat
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 gaussianIC1d_hex.mesh
ATC: read 44 nodes
ATC: read 10 HEX8 elements
ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat
fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10
# equilibrate MD field
timestep 5.0
thermo 10
#output
fix_modify AtC output gaussianIC1d_hexFE 10 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
# run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0
run 100 # 400
Setting up run ...
Memory usage per processor = 52.9302 Mbytes
Step Temp PotEng AtC[2] AtC[4]
0 33.331404 -6667.7177 20 21.852118
10 29.605914 -6628.8617 15.526061 21.823928
20 20.144352 -6529.8249 4.1452637 21.728037
30 10.661516 -6429.3908 -7.2917185 21.537517
40 7.6716875 -6394.7484 -10.961235 21.28913
50 11.012891 -6425.2214 -7.0020953 21.050343
60 15.276591 -6465.7767 -1.8390571 20.85387
70 17.15209 -6482.1581 0.55215503 20.688207
80 17.028137 -6478.0796 0.55504167 20.530699
90 16.865355 -6473.5664 0.41999569 20.372106
100 17.920474 -6481.673 1.6267665 20.219157
Loop time of 5.05638 on 4 procs for 100 steps with 3456 atoms
Pair time (%) = 0.947014 (18.7291)
Neigh time (%) = 0.418835 (8.2833)
Comm time (%) = 0.338576 (6.69601)
Outpt time (%) = 0.024951 (0.493455)
Other time (%) = 3.327 (65.7981)
Nlocal: 864 ave 864 max 864 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6741 ave 7924 max 5558 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 272828 ave 288265 max 257696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 545657 ave 575527 max 515800 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2182628
Ave neighs/atom = 631.547
Neighbor list builds = 10
Dangerous builds = 0
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