vcm example script and log added
This commit is contained in:
Tyler Collins
82
examples/vcm/in.vcm.lmp
Normal file
82
examples/vcm/in.vcm.lmp
Normal file
@ -0,0 +1,82 @@
|
||||
# Removing Binned Center-of-Mass Velocities from Stress Compute
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
lattice fcc 5.3589
|
||||
processors 1 * *
|
||||
|
||||
# Defining regions for box and atoms
|
||||
|
||||
region box1 block -3 24 0 12 0 12 units lattice
|
||||
region box2 block 0 12 0 12 0 12 units lattice
|
||||
|
||||
# Creating box and atoms
|
||||
|
||||
create_box 1 box1
|
||||
create_atoms 1 region box2
|
||||
|
||||
mass 1 40.00
|
||||
|
||||
# Adding energy to the system
|
||||
|
||||
velocity all create 600.0 9999
|
||||
|
||||
pair_style lj/cut 10
|
||||
pair_coeff 1 1 0.04 3.405
|
||||
|
||||
# Begin time integration
|
||||
|
||||
timestep 2e-3
|
||||
|
||||
fix fix_nve all nve
|
||||
|
||||
thermo 100
|
||||
|
||||
run 500
|
||||
|
||||
# Chunk and stress along x direction
|
||||
|
||||
variable nbins index 20
|
||||
variable fraction equal 1.0/v_nbins
|
||||
variable volfrac equal 1/(vol*${fraction})
|
||||
|
||||
compute ch_id all chunk/atom bin/1d x lower ${fraction} units reduced
|
||||
compute ch_temp_vcm all temp/chunk ch_id com yes
|
||||
compute atom_stress_vcm all stress/atom ch_temp_vcm
|
||||
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
|
||||
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
|
||||
|
||||
# Output stress profile in x direction
|
||||
|
||||
# fix ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out
|
||||
|
||||
# Piston compressing along x direction
|
||||
|
||||
region piston block -1 1 INF INF INF INF units lattice
|
||||
group piston region piston
|
||||
fix fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve
|
||||
|
||||
# Atom dump
|
||||
|
||||
# dump atom_dump all atom 50 dump.vcm
|
||||
|
||||
# # Image dumps
|
||||
|
||||
# dump 2 all image 250 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
# dump_modify 2 pad 1
|
||||
|
||||
# # Movie dump
|
||||
|
||||
# dump 3 all movie 125 movie.avi type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
# dump_modify 3 pad 1
|
||||
|
||||
run 500
|
||||
|
||||
unfix fix_piston
|
||||
|
||||
run 1500
|
||||
223
examples/vcm/log.19Nov24.vcm.g++.1
Normal file
223
examples/vcm/log.19Nov24.vcm.g++.1
Normal file
@ -0,0 +1,223 @@
|
||||
LAMMPS (19 Nov 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Loaded 1 plugins from C:\Users\tcollins7472\AppData\Local\LAMMPS 64-bit 19Nov2024-MSMPI with Python\plugins
|
||||
# Removing Binned Center-of-Mass Velocities from Stress Compute
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
lattice fcc 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
|
||||
processors 1 * *
|
||||
|
||||
# Defining regions for box and atoms
|
||||
|
||||
region box1 block -3 24 0 12 0 12 units lattice
|
||||
region box2 block 0 12 0 12 0 12 units lattice
|
||||
|
||||
# Creating box and atoms
|
||||
|
||||
create_box 1 box1
|
||||
Created orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box2
|
||||
Created 7200 atoms
|
||||
using lattice units in orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
|
||||
mass 1 40.00
|
||||
|
||||
# Adding energy to the system
|
||||
|
||||
velocity all create 600.0 9999
|
||||
|
||||
pair_style lj/cut 10
|
||||
pair_coeff 1 1 0.04 3.405
|
||||
|
||||
# Begin time integration
|
||||
|
||||
timestep 2e-3
|
||||
|
||||
fix fix_nve all nve
|
||||
|
||||
thermo 100
|
||||
|
||||
run 500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 25 11 11
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.721 | 5.721 | 5.721 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 600 -2252.7567 0 -1694.4304 -974.62456
|
||||
100 284.72172 -1977.4291 0 -1712.483 2453.7429
|
||||
200 304.44519 -1994.7937 0 -1711.4941 1822.2699
|
||||
300 304.28012 -1993.2958 0 -1710.1498 1498.3794
|
||||
400 296.76492 -1985.1364 0 -1708.9836 1259.9474
|
||||
500 295.00895 -1982.4224 0 -1707.9036 964.9526
|
||||
Loop time of 3.07247 on 1 procs for 500 steps with 7200 atoms
|
||||
|
||||
Performance: 28.121 ns/day, 0.853 hours/ns, 162.736 timesteps/s, 1.172 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.8976 | 2.8976 | 2.8976 | 0.0 | 94.31
|
||||
Neigh | 0.11531 | 0.11531 | 0.11531 | 0.0 | 3.75
|
||||
Comm | 0.015167 | 0.015167 | 0.015167 | 0.0 | 0.49
|
||||
Output | 0.003809 | 0.003809 | 0.003809 | 0.0 | 0.12
|
||||
Modify | 0.025306 | 0.025306 | 0.025306 | 0.0 | 0.82
|
||||
Other | | 0.01525 | | | 0.50
|
||||
|
||||
Nlocal: 7200 ave 7200 max 7200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6410 ave 6410 max 6410 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 615095 ave 615095 max 615095 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 615095
|
||||
Ave neighs/atom = 85.429861
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
|
||||
# Chunk and stress along x direction
|
||||
|
||||
variable nbins index 20
|
||||
variable fraction equal 1.0/v_nbins
|
||||
variable volfrac equal 1/(vol*${fraction})
|
||||
variable volfrac equal 1/(vol*0.05)
|
||||
|
||||
compute ch_id all chunk/atom bin/1d x lower ${fraction} units reduced
|
||||
compute ch_id all chunk/atom bin/1d x lower 0.05 units reduced
|
||||
compute ch_temp_vcm all temp/chunk ch_id com yes
|
||||
compute atom_stress_vcm all stress/atom ch_temp_vcm
|
||||
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
|
||||
variable stress atom -(c_atom_stress_vcm[1])/(vol*0.05)
|
||||
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
|
||||
|
||||
# Output stress profile in x direction
|
||||
|
||||
# fix ave_stress_vcm all ave/time 5 20 100 c_ch_stress_vcm mode vector file stress_xx.out
|
||||
|
||||
# Piston compressing along x direction
|
||||
|
||||
region piston block -1 1 INF INF INF INF units lattice
|
||||
group piston region piston
|
||||
863 atoms in group piston
|
||||
fix fix_piston piston move linear 5 0 0 units box # strain rate ~ 8e10 1/s
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz econserve
|
||||
|
||||
# Atom dump
|
||||
|
||||
# dump atom_dump all atom 50 dump.vcm
|
||||
|
||||
# # Image dumps
|
||||
|
||||
# dump 2 all image 250 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
# dump_modify 2 pad 1
|
||||
|
||||
# # Movie dump
|
||||
|
||||
# dump 3 all movie 125 movie.avi type type # axes yes 0.8 0.02 view 60 -30
|
||||
# dump_modify 3 pad 1
|
||||
|
||||
run 500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:296)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.975 | 6.975 | 6.975 Mbytes
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
|
||||
500 295.00895 274.51875 -1982.4224 144.6903 64.3068 64.3068 631.89976 1127.2965 1135.6616 -1707.9036
|
||||
600 357.38902 332.56613 -1951.3422 144.6903 64.3068 64.3068 2236.6706 2003.2726 1943.6815 -1618.7761
|
||||
700 420.30268 391.11005 -1911.8178 144.6903 64.3068 64.3068 3761.5011 3065.4699 3140.3169 -1520.7077
|
||||
800 484.96279 451.27911 -1875.379 144.6903 64.3068 64.3068 5362.254 4174.4201 4166.0818 -1424.0999
|
||||
900 587.78954 546.96391 -1871.217 144.6903 64.3068 64.3068 6481.4714 4875.705 4676.6083 -1324.2531
|
||||
1000 684.07997 636.56636 -1868.1639 144.6903 64.3068 64.3068 7734.6158 5271.3524 5272.1276 -1231.5975
|
||||
Loop time of 3.32746 on 1 procs for 500 steps with 7200 atoms
|
||||
|
||||
Performance: 25.966 ns/day, 0.924 hours/ns, 150.265 timesteps/s, 1.082 Matom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0701 | 3.0701 | 3.0701 | 0.0 | 92.27
|
||||
Neigh | 0.20567 | 0.20567 | 0.20567 | 0.0 | 6.18
|
||||
Comm | 0.010313 | 0.010313 | 0.010313 | 0.0 | 0.31
|
||||
Output | 0.002649 | 0.002649 | 0.002649 | 0.0 | 0.08
|
||||
Modify | 0.029567 | 0.029567 | 0.029567 | 0.0 | 0.89
|
||||
Other | | 0.009157 | | | 0.28
|
||||
|
||||
Nlocal: 7200 ave 7200 max 7200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6409 ave 6409 max 6409 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 646408 ave 646408 max 646408 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 646408
|
||||
Ave neighs/atom = 89.778889
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix fix_piston
|
||||
|
||||
run 1500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.6 | 6.6 | 6.6 Mbytes
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
|
||||
1000 684.07997 636.56636 -1868.1639 144.6903 64.3068 64.3068 7734.6158 5271.3524 5272.1276 -1231.5975
|
||||
1100 710.19886 660.87113 -1894.0485 144.6903 64.3068 64.3068 8048.3485 5396.6668 5376.5956 -1233.1774
|
||||
1200 717.16487 667.35331 -1901.3849 144.6903 64.3068 64.3068 8009.7984 5634.5121 5349.4113 -1234.0316
|
||||
1300 710.26037 660.92837 -1894.9802 144.6903 64.3068 64.3068 8063.4125 5572.1245 5530.174 -1234.0519
|
||||
1400 715.93921 666.21278 -1898.8885 144.6903 64.3068 64.3068 7752.0927 5293.5463 5322.2312 -1232.6757
|
||||
1500 748.85411 696.84154 -1926.4891 144.6903 64.3068 64.3068 6030.5428 4076.8886 4012.7653 -1229.6475
|
||||
1600 767.98982 714.64815 -1939.8556 144.6903 64.3068 64.3068 4200.3475 2532.5711 2530.5518 -1225.2075
|
||||
1700 757.22042 704.62675 -1925.553 144.6903 64.3068 64.3068 2686.7843 1482.2796 1505.8073 -1220.9262
|
||||
1800 727.30327 676.78754 -1894.6635 144.6903 64.3068 64.3068 1764.2793 781.37451 801.18668 -1217.8759
|
||||
1900 688.82146 640.97853 -1856.5007 144.6903 64.3068 64.3068 1022.805 417.32394 359.74951 -1215.5221
|
||||
2000 655.91228 610.35509 -1823.954 144.6903 64.3068 64.3068 551.98825 -20.148643 -56.976652 -1213.5989
|
||||
2100 620.22468 577.14622 -1789.1761 144.6903 64.3068 64.3068 264.05975 -266.8323 -314.45533 -1212.0299
|
||||
2200 589.13325 548.21428 -1758.9252 144.6903 64.3068 64.3068 41.369707 -533.503 -525.69401 -1210.7109
|
||||
2300 563.20394 524.08593 -1733.6036 144.6903 64.3068 64.3068 -220.99189 -810.90513 -774.65084 -1209.5176
|
||||
2400 540.44236 502.90528 -1711.3384 144.6903 64.3068 64.3068 -358.01508 -962.31635 -977.3253 -1208.4332
|
||||
2500 523.5718 487.20648 -1694.7088 144.6903 64.3068 64.3068 -521.87444 -1152.8386 -1231.7615 -1207.5023
|
||||
Loop time of 9.89185 on 1 procs for 1500 steps with 7200 atoms
|
||||
|
||||
Performance: 26.203 ns/day, 0.916 hours/ns, 151.640 timesteps/s, 1.092 Matom-step/s
|
||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.9768 | 8.9768 | 8.9768 | 0.0 | 90.75
|
||||
Neigh | 0.78114 | 0.78114 | 0.78114 | 0.0 | 7.90
|
||||
Comm | 0.035178 | 0.035178 | 0.035178 | 0.0 | 0.36
|
||||
Output | 0.009593 | 0.009593 | 0.009593 | 0.0 | 0.10
|
||||
Modify | 0.057521 | 0.057521 | 0.057521 | 0.0 | 0.58
|
||||
Other | | 0.0316 | | | 0.32
|
||||
|
||||
Nlocal: 7200 ave 7200 max 7200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6380 ave 6380 max 6380 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 515773 ave 515773 max 515773 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 515773
|
||||
Ave neighs/atom = 71.635139
|
||||
Neighbor list builds = 57
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:16
|
||||
Reference in New Issue
Block a user