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LAMMPS (30 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
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 2304 atoms
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.01202
ATC: computed mass density : 1.01202
ATC: computed mass density : 1.01202
ATC: 3 materials defined from Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 65.7794 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4406.6687 0 -4406.6687 -1155.1752
100 3.8434911e-14 -4406.6687 0 -4406.6687 -1155.1752
200 2.634669e-11 -4406.6687 0 -4406.6687 -1155.1754
300 6.909135e-10 -4406.6685 0 -4406.6685 -1155.1763
400 3.9413859e-09 -4406.6682 0 -4406.6682 -1155.1783
500 8.5603227e-09 -4406.6676 0 -4406.6676 -1155.181
600 1.0143684e-08 -4406.6671 0 -4406.6671 -1155.1835
700 9.8473676e-09 -4406.6667 0 -4406.6667 -1155.1854
800 9.9628095e-09 -4406.6663 0 -4406.6663 -1155.1871
900 1.1034555e-08 -4406.6659 0 -4406.6659 -1155.189
1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191
Loop time of 18.0781 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 5.77584 (31.9495)
Neigh time (%) = 2.46813 (13.6526)
Comm time (%) = 5.5724 (30.8241)
Outpt time (%) = 0.00132889 (0.00735082)
Other time (%) = 4.26036 (23.5665)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288628 max 68417 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# run to equilibrium
timestep 5
thermo 100
run 10000
Setting up run ...
Memory usage per processor = 65.7794 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 1.2796459e-08 -4406.6655 0 -4406.6655 -1155.191
1100 1.3961782e-08 -4406.665 0 -4406.665 -1155.1929
1200 1.4156541e-08 -4406.6646 0 -4406.6646 -1155.1947
1300 1.1743161e-08 -4406.6643 0 -4406.6643 -1155.1961
1400 7.6261191e-09 -4406.6643 0 -4406.6643 -1155.1964
1500 5.4918861e-09 -4406.6644 0 -4406.6644 -1155.1955
1600 3.2067753e-09 -4406.6647 0 -4406.6647 -1155.1942
1700 1.5798693e-09 -4406.6649 0 -4406.6649 -1155.1933
1800 3.4267061e-09 -4406.6649 0 -4406.6649 -1155.1932
1900 5.7984811e-09 -4406.6649 0 -4406.6649 -1155.1934
2000 4.4702416e-09 -4406.6648 0 -4406.6648 -1155.1937
2100 4.110363e-09 -4406.6647 0 -4406.6647 -1155.1943
2200 7.7448231e-09 -4406.6646 0 -4406.6646 -1155.1949
2300 8.9174139e-09 -4406.6645 0 -4406.6645 -1155.1953
2400 4.2475131e-09 -4406.6645 0 -4406.6645 -1155.1951
2500 3.9593952e-09 -4406.6646 0 -4406.6646 -1155.1947
2600 5.0490897e-09 -4406.6646 0 -4406.6646 -1155.1945
2700 3.0091882e-09 -4406.6645 0 -4406.6645 -1155.195
2800 2.8396053e-09 -4406.6644 0 -4406.6644 -1155.1955
2900 3.3590465e-09 -4406.6644 0 -4406.6644 -1155.1957
3000 2.6186659e-09 -4406.6644 0 -4406.6644 -1155.1955
3100 2.8276402e-09 -4406.6645 0 -4406.6645 -1155.1953
3200 3.3651448e-09 -4406.6645 0 -4406.6645 -1155.195
3300 4.8200774e-09 -4406.6647 0 -4406.6647 -1155.1944
3400 2.7178e-09 -4406.6648 0 -4406.6648 -1155.1938
3500 2.8250408e-09 -4406.6648 0 -4406.6648 -1155.1938
3600 4.4426525e-09 -4406.6646 0 -4406.6646 -1155.1946
3700 2.3093452e-09 -4406.6644 0 -4406.6644 -1155.1954
3800 1.0139576e-09 -4406.6644 0 -4406.6644 -1155.1958
3900 3.33486e-09 -4406.6644 0 -4406.6644 -1155.1958
4000 3.6153069e-09 -4406.6644 0 -4406.6644 -1155.1956
4100 4.6993593e-10 -4406.6644 0 -4406.6644 -1155.1954
4200 1.1808552e-09 -4406.6645 0 -4406.6645 -1155.1948
4300 3.1059162e-09 -4406.6647 0 -4406.6647 -1155.1942
4400 2.2356994e-09 -4406.6647 0 -4406.6647 -1155.1942
4500 1.0832e-09 -4406.6646 0 -4406.6646 -1155.1947
4600 3.4691005e-09 -4406.6645 0 -4406.6645 -1155.1954
4700 2.6640925e-09 -4406.6644 0 -4406.6644 -1155.1956
4800 1.8105324e-09 -4406.6644 0 -4406.6644 -1155.1954
4900 3.2865681e-09 -4406.6645 0 -4406.6645 -1155.1951
5000 3.2647654e-09 -4406.6645 0 -4406.6645 -1155.1949
5100 1.9703065e-09 -4406.6646 0 -4406.6646 -1155.1947
5200 1.242015e-09 -4406.6646 0 -4406.6646 -1155.1945
5300 3.0457424e-09 -4406.6646 0 -4406.6646 -1155.1946
5400 1.9560942e-09 -4406.6645 0 -4406.6645 -1155.1951
5500 4.3058633e-10 -4406.6644 0 -4406.6644 -1155.1957
5600 2.3184519e-09 -4406.6644 0 -4406.6644 -1155.1957
5700 3.0207566e-09 -4406.6645 0 -4406.6645 -1155.1953
5800 6.8689369e-10 -4406.6646 0 -4406.6646 -1155.1948
5900 1.5170252e-09 -4406.6646 0 -4406.6646 -1155.1946
6000 3.0629191e-09 -4406.6646 0 -4406.6646 -1155.1946
6100 1.842967e-09 -4406.6646 0 -4406.6646 -1155.1945
6200 6.0033688e-10 -4406.6646 0 -4406.6646 -1155.1946
6300 2.0883931e-09 -4406.6645 0 -4406.6645 -1155.1952
6400 1.8269083e-09 -4406.6644 0 -4406.6644 -1155.1957
6500 5.5810474e-10 -4406.6644 0 -4406.6644 -1155.1957
6600 1.7356452e-09 -4406.6645 0 -4406.6645 -1155.1952
6700 2.6958998e-09 -4406.6646 0 -4406.6646 -1155.1947
6800 8.964107e-10 -4406.6646 0 -4406.6646 -1155.1946
6900 1.1426076e-09 -4406.6646 0 -4406.6646 -1155.1947
7000 2.9188626e-09 -4406.6646 0 -4406.6646 -1155.1947
7100 1.8115562e-09 -4406.6645 0 -4406.6645 -1155.1948
7200 7.4087342e-10 -4406.6645 0 -4406.6645 -1155.1952
7300 1.5779154e-09 -4406.6644 0 -4406.6644 -1155.1956
7400 2.7467977e-09 -4406.6644 0 -4406.6644 -1155.1955
7500 4.2123447e-10 -4406.6645 0 -4406.6645 -1155.195
7600 1.1615418e-09 -4406.6646 0 -4406.6646 -1155.1946
7700 2.5380373e-09 -4406.6646 0 -4406.6646 -1155.1945
7800 1.5068282e-09 -4406.6646 0 -4406.6646 -1155.1948
7900 6.0931799e-10 -4406.6645 0 -4406.6645 -1155.195
8000 2.0802965e-09 -4406.6645 0 -4406.6645 -1155.1951
8100 2.1544428e-09 -4406.6645 0 -4406.6645 -1155.1953
8200 4.4375899e-10 -4406.6644 0 -4406.6644 -1155.1955
8300 1.5879866e-09 -4406.6644 0 -4406.6644 -1155.1954
8400 2.1255967e-09 -4406.6645 0 -4406.6645 -1155.1949
8500 8.5066547e-10 -4406.6646 0 -4406.6646 -1155.1945
8600 4.9764713e-10 -4406.6646 0 -4406.6646 -1155.1945
8700 2.4032931e-09 -4406.6646 0 -4406.6646 -1155.1949
8800 1.5506272e-09 -4406.6645 0 -4406.6645 -1155.1951
8900 2.156996e-10 -4406.6645 0 -4406.6645 -1155.1952
9000 1.5053583e-09 -4406.6645 0 -4406.6645 -1155.1953
9100 2.2313062e-09 -4406.6645 0 -4406.6645 -1155.1954
9200 6.5295769e-10 -4406.6645 0 -4406.6645 -1155.1953
9300 7.1214495e-10 -4406.6646 0 -4406.6646 -1155.1949
9400 2.2525879e-09 -4406.6646 0 -4406.6646 -1155.1945
9500 1.2940878e-09 -4406.6646 0 -4406.6646 -1155.1945
9600 3.7619117e-10 -4406.6645 0 -4406.6645 -1155.195
9700 1.9605412e-09 -4406.6645 0 -4406.6645 -1155.1953
9800 1.7828694e-09 -4406.6645 0 -4406.6645 -1155.1953
9900 5.2324205e-10 -4406.6645 0 -4406.6645 -1155.1952
10000 1.1770899e-09 -4406.6645 0 -4406.6645 -1155.1952
10100 2.0621304e-09 -4406.6645 0 -4406.6645 -1155.1951
10200 9.4046414e-10 -4406.6646 0 -4406.6646 -1155.1948
10300 3.3301061e-10 -4406.6646 0 -4406.6646 -1155.1945
10400 2.2075407e-09 -4406.6646 0 -4406.6646 -1155.1946
10500 1.3556476e-09 -4406.6645 0 -4406.6645 -1155.1951
10600 3.1056944e-10 -4406.6645 0 -4406.6645 -1155.1954
10700 1.2113659e-09 -4406.6645 0 -4406.6645 -1155.1953
10800 2.0914266e-09 -4406.6645 0 -4406.6645 -1155.1951
10900 5.1353017e-10 -4406.6645 0 -4406.6645 -1155.1951
11000 5.470711e-10 -4406.6645 0 -4406.6645 -1155.195
Loop time of 180.295 on 4 procs for 10000 steps with 2304 atoms
Pair time (%) = 57.7011 (32.0037)
Neigh time (%) = 24.6432 (13.6683)
Comm time (%) = 55.7143 (30.9017)
Outpt time (%) = 0.0200394 (0.0111148)
Other time (%) = 42.2164 (23.4152)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 289022 max 67462 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 1000
Dangerous builds = 0
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