ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

updated summary, comments, and name

Browse Source
This commit is contained in:
Tyler Collins
2024-12-10 21:47:30 -08:00
parent 49938456a3
commit b4acfd1e3b
4 changed files with 431 additions and 116 deletions
Download Patch File Download Diff File Expand all files Collapse all files

113
examples/stress_vcm/in.stress_vcm.lmp Normal file
View File

@ -0,0 +1,113 @@
# Removing Binned Velocities of Center of Mass (VCM) from Stress
# This example shows how to remove rigid body motion from
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute
# stress/atom and fix ave/time. We'll show how these commands
# work in the context of a shockwave experiment on a cube of
# atoms. To shock the cube, a rectangular region of atoms is
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins
# propagating, the body of the cube also moves along the x
# direction. To better understand the stress dynamics of the
# cube we remove the velocity component belonging to the overall
# motion of each bin.
units metal
boundary p p p
atom_style atomic
lattice fcc 5.3589
processors 1 * *
# Defining regions for box and atoms.
# In this experiment an elongated simulation cell is
# defined in the x direction to allow for non-periodic
# motion of the 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, Stress, and VCM removal steps #
#--------------------------------------#
# 1. Create 20 equispaced bins sliced along the x direction.
# -"units reduced" normalizes the distance from 0.0 to 1.0
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 ${fraction} units reduced
# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute ch_temp_vcm all temp/chunk ch_id com yes
# 3. Compute per atom stress with VCM removed via temp-ID.
# -The velocities from specified temp-ID are used to compute stress.
# -Stress/atom units are pressure*volume! Optionally handled next step.
compute atom_stress_vcm all stress/atom ch_temp_vcm
# 4. Divide out bin volume from xx stress component.
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
# 5. Sum the per atom stresses in each bin.
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
# 6. Average and output to file.
# -The average output is every 100 steps with samples collected 20 times with 5 step intervals.
# 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

99
examples/vcm/log.19Nov24.vcm.g++.1 → examples/stress_vcm/log.19Nov24.stress_vcm.g++.1
View File

@ -1,7 +1,20 @@
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
# Removing Binned Center-of-Mass Velocities from Stress Compute
# Removing Binned Velocities of Center of Mass (VCM) from Stress
# This example shows how to remove rigid body motion from
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute
# stress/atom and fix ave/time. We'll show how these commands
# work in the context of a shockwave experiment on a cube of
# atoms. To shock the cube, a rectangular region of atoms is
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins
# propagating, the body of the cube also moves along the x
# direction. To better understand the stress dynamics of the
# cube we remove the velocity component belonging to the overall
# motion of each bin.
units metal
boundary p p p
@ -10,7 +23,10 @@ lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
processors 1 * *
# Defining regions for box and atoms
# Defining regions for box and atoms.
# In this experiment an elongated simulation cell is
# defined in the x direction to allow for non-periodic
# motion of the atoms.
region box1 block -3 24 0 12 0 12 units lattice
region box2 block 0 12 0 12 0 12 units lattice
@ -23,7 +39,7 @@ Created orthogonal box = (-16.0767 0 0) to (128.6136 64.3068 64.3068)
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
create_atoms CPU = 0.002 seconds
mass 1 40.00
@ -64,20 +80,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.721 | 5.721 | 5.721 Mbytes
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
Loop time of 3.01696 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
Performance: 28.638 ns/day, 0.838 hours/ns, 165.730 timesteps/s, 1.193 Matom-step/s
99.4% 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
Pair | 2.8439 | 2.8439 | 2.8439 | 0.0 | 94.26
Neigh | 0.11212 | 0.11212 | 0.11212 | 0.0 | 3.72
Comm | 0.015585 | 0.015585 | 0.015585 | 0.0 | 0.52
Output | 0.003747 | 0.003747 | 0.003747 | 0.0 | 0.12
Modify | 0.026097 | 0.026097 | 0.026097 | 0.0 | 0.87
Other | | 0.01551 | | | 0.51
Nlocal: 7200 ave 7200 max 7200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -91,25 +107,40 @@ Ave neighs/atom = 85.429861
Neighbor list builds = 9
Dangerous builds = 0
# Chunk and stress along x direction
#------------------------------------#
# Chunk, Stress, and VCM removal steps
#------------------------------------#
# 1. Create 20 equispaced bins sliced along the x direction.
# "units reduced" normalizes the distance from 0 to 1
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 ${fraction} units reduced
compute ch_id all chunk/atom bin/1d x lower 0.05 units reduced
# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute ch_temp_vcm all temp/chunk ch_id com yes
# 3. Compute per atom stress with VCM removed via temp-ID.
# The velocities from specified temp-ID are used to compute stress
# Stress/atom units are pressure*volume! Optionally handled next step.
compute atom_stress_vcm all stress/atom ch_temp_vcm
# 4. Divide out bin volume from xx stress component.
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
variable stress atom -(c_atom_stress_vcm[1])/(vol*0.05)
# 5. Sum the per atom stresses in each bin.
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
# Output stress profile in x direction
# 6. Average and output to file.
# The average output is every 100 steps with samples collected 20 times with 5 step intervals
# 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
@ -144,20 +175,20 @@ Per MPI rank memory allocation (min/avg/max) = 6.975 | 6.975 | 6.975 Mbytes
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
Loop time of 3.09383 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
Performance: 27.927 ns/day, 0.859 hours/ns, 161.612 timesteps/s, 1.164 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
Pair | 2.8485 | 2.8485 | 2.8485 | 0.0 | 92.07
Neigh | 0.18767 | 0.18767 | 0.18767 | 0.0 | 6.07
Comm | 0.011533 | 0.011533 | 0.011533 | 0.0 | 0.37
Output | 0.003323 | 0.003323 | 0.003323 | 0.0 | 0.11
Modify | 0.031777 | 0.031777 | 0.031777 | 0.0 | 1.03
Other | | 0.01107 | | | 0.36
Nlocal: 7200 ave 7200 max 7200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -193,20 +224,20 @@ Per MPI rank memory allocation (min/avg/max) = 6.6 | 6.6 | 6.6 Mbytes
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
Loop time of 9.34327 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
Performance: 27.742 ns/day, 0.865 hours/ns, 160.543 timesteps/s, 1.156 Matom-step/s
98.5% 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
Pair | 8.4692 | 8.4692 | 8.4692 | 0.0 | 90.65
Neigh | 0.7512 | 0.7512 | 0.7512 | 0.0 | 8.04
Comm | 0.031189 | 0.031189 | 0.031189 | 0.0 | 0.33
Output | 0.010584 | 0.010584 | 0.010584 | 0.0 | 0.11
Modify | 0.053052 | 0.053052 | 0.053052 | 0.0 | 0.57
Other | | 0.02803 | | | 0.30
Nlocal: 7200 ave 7200 max 7200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -219,4 +250,4 @@ Total # of neighbors = 515773
Ave neighs/atom = 71.635139
Neighbor list builds = 57
Dangerous builds = 0
Total wall time: 0:00:16
Total wall time: 0:00:15

253
examples/stress_vcm/log.19Nov24.stress_vcm.g++.4 Normal file
View File

@ -0,0 +1,253 @@
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
# Removing Binned Velocities of Center of Mass (VCM) from Stress
# This example shows how to remove rigid body motion from
# binned stress calculations. This uses a combination of commands
# from compute chunk/atom, compute temp/chunk, compute
# stress/atom and fix ave/time. We'll show how these commands
# work in the context of a shockwave experiment on a cube of
# atoms. To shock the cube, a rectangular region of atoms is
# frozen, moved into the cube with a constant velocity along the
# x direction, and then unfrozen. As the shockwave begins
# propagating, the body of the cube also moves along the x
# direction. To better understand the stress dynamics of the
# cube we remove the velocity component belonging to the overall
# motion of each bin.
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.
# In this experiment an elongated simulation cell is
# defined in the x direction to allow for non-periodic
# motion of the 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 2 by 2 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 = 0.001 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/opt, 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) = 3.662 | 3.662 | 3.662 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -2252.7567 0 -1694.4304 -974.62456
100 284.1896 -1976.961 0 -1712.5101 2462.6396
200 308.58965 -1998.6349 0 -1711.4787 1789.0033
300 300.55093 -1989.9838 0 -1710.308 1545.8576
400 297.91491 -1986.2519 0 -1709.029 1247.7121
500 294.66041 -1982.1097 0 -1707.9153 961.03073
Loop time of 0.942408 on 4 procs for 500 steps with 7200 atoms
Performance: 91.680 ns/day, 0.262 hours/ns, 530.556 timesteps/s, 3.820 Matom-step/s
82.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.61287 | 0.63781 | 0.65858 | 2.1 | 67.68
Neigh | 0.030246 | 0.031529 | 0.034546 | 1.0 | 3.35
Comm | 0.23074 | 0.25145 | 0.27819 | 3.7 | 26.68
Output | 0.000282 | 0.0003735 | 0.000463 | 0.0 | 0.04
Modify | 0.005566 | 0.0057635 | 0.005989 | 0.2 | 0.61
Other | | 0.01548 | | | 1.64
Nlocal: 1800 ave 1814 max 1787 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 3713.5 ave 3727 max 3699 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 153532 ave 154995 max 152312 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 614128
Ave neighs/atom = 85.295556
Neighbor list builds = 9
Dangerous builds = 0
#------------------------------------#
# Chunk, Stress, and VCM removal steps
#------------------------------------#
# 1. Create 20 equispaced bins sliced along the x direction.
# "units reduced" normalizes the distance from 0 to 1
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 ${fraction} units reduced
compute ch_id all chunk/atom bin/1d x lower 0.05 units reduced
# 2. Calculate temperature bins with VCM aka COM velocities removed.
compute ch_temp_vcm all temp/chunk ch_id com yes
# 3. Compute per atom stress with VCM removed via temp-ID.
# The velocities from specified temp-ID are used to compute stress
# Stress/atom units are pressure*volume! Optionally handled next step.
compute atom_stress_vcm all stress/atom ch_temp_vcm
# 4. Divide out bin volume from xx stress component.
variable stress atom -(c_atom_stress_vcm[1])/(vol*${fraction})
variable stress atom -(c_atom_stress_vcm[1])/(vol*0.05)
# 5. Sum the per atom stresses in each bin.
compute ch_stress_vcm all reduce/chunk ch_id sum v_stress
# 6. Average and output to file.
# The average output is every 100 steps with samples collected 20 times with 5 step intervals
# 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
864 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) = 4.916 | 4.916 | 4.916 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
500 294.66041 274.19441 -1982.1097 144.6903 64.3068 64.3068 645.25795 1119.5337 1118.3006 -1707.9153
600 357.88641 333.02897 -1951.8158 144.6903 64.3068 64.3068 2176.0343 1929.2787 1981.8479 -1618.7869
700 418.41159 389.3503 -1912.8337 144.6903 64.3068 64.3068 3702.2875 3043.7607 3081.1607 -1523.4834
800 483.71102 450.11428 -1875.7955 144.6903 64.3068 64.3068 5254.3875 4190.9789 4158.3561 -1425.6813
900 586.0893 545.38176 -1870.9313 144.6903 64.3068 64.3068 6509.1439 4756.2216 4724.7086 -1325.5495
1000 686.32946 638.65962 -1874.811 144.6903 64.3068 64.3068 7515.1606 5193.049 5261.8688 -1236.1514
Loop time of 0.656417 on 4 procs for 500 steps with 7200 atoms
Performance: 131.624 ns/day, 0.182 hours/ns, 761.711 timesteps/s, 5.484 Matom-step/s
92.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.51672 | 0.52334 | 0.53259 | 0.8 | 79.73
Neigh | 0.045091 | 0.045915 | 0.047402 | 0.4 | 6.99
Comm | 0.060735 | 0.071794 | 0.079302 | 2.6 | 10.94
Output | 0.000208 | 0.000389 | 0.000926 | 0.0 | 0.06
Modify | 0.006007 | 0.0061595 | 0.00626 | 0.1 | 0.94
Other | | 0.008815 | | | 1.34
Nlocal: 1800 ave 1811 max 1785 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 3713.25 ave 3727 max 3702 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 161477 ave 162958 max 159732 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 645909
Ave neighs/atom = 89.709583
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) = 4.541 | 4.541 | 4.541 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Econserve
1000 686.32946 638.65962 -1874.811 144.6903 64.3068 64.3068 7515.1606 5193.049 5261.8688 -1236.1514
1100 709.7333 660.43791 -1898.2844 144.6903 64.3068 64.3068 7932.8638 5334.6171 5364.5335 -1237.8465
1200 713.27253 663.73132 -1902.4588 144.6903 64.3068 64.3068 7957.2574 5500.6231 5538.0516 -1238.7275
1300 705.44796 656.45022 -1895.1575 144.6903 64.3068 64.3068 7996.7265 5584.6233 5538.2494 -1238.7072
1400 711.86463 662.42121 -1899.8416 144.6903 64.3068 64.3068 7674.2462 5292.4915 5294.5366 -1237.4204
1500 742.18946 690.63979 -1924.9562 144.6903 64.3068 64.3068 6047.915 4056.6156 4014.4446 -1234.3164
1600 762.81764 709.83522 -1939.8563 144.6903 64.3068 64.3068 4185.5873 2530.0572 2576.1943 -1230.0211
1700 754.40428 702.00621 -1927.7337 144.6903 64.3068 64.3068 2662.7604 1509.1985 1484.7252 -1225.7275
1800 721.03504 670.95468 -1893.5556 144.6903 64.3068 64.3068 1765.8783 835.89765 861.9432 -1222.6009
1900 689.64162 641.74172 -1861.8886 144.6903 64.3068 64.3068 941.58148 312.93205 409.79901 -1220.1469
2000 650.79664 605.59477 -1823.9889 144.6903 64.3068 64.3068 543.39234 28.48735 80.396505 -1218.3941
2100 616.04072 573.25286 -1790.1764 144.6903 64.3068 64.3068 308.16444 -235.20997 -248.22531 -1216.9235
2200 587.18712 546.40333 -1761.8878 144.6903 64.3068 64.3068 37.044801 -476.50396 -470.83059 -1215.4845
2300 562.84178 523.74892 -1738.2239 144.6903 64.3068 64.3068 -139.28348 -711.17273 -730.80877 -1214.475
2400 540.48362 502.94367 -1716.3529 144.6903 64.3068 64.3068 -320.98222 -951.2066 -943.93966 -1213.4093
2500 519.80431 483.70067 -1696.1896 144.6903 64.3068 64.3068 -471.61317 -1088.8457 -1131.5396 -1212.4889
Loop time of 1.97213 on 4 procs for 1500 steps with 7200 atoms
Performance: 131.431 ns/day, 0.183 hours/ns, 760.598 timesteps/s, 5.476 Matom-step/s
95.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5455 | 1.5599 | 1.5723 | 0.8 | 79.10
Neigh | 0.16844 | 0.1704 | 0.17237 | 0.4 | 8.64
Comm | 0.19002 | 0.2047 | 0.22068 | 2.4 | 10.38
Output | 0.000525 | 0.0006785 | 0.001077 | 0.0 | 0.03
Modify | 0.012434 | 0.012601 | 0.012777 | 0.1 | 0.64
Other | | 0.02388 | | | 1.21
Nlocal: 1800 ave 1833 max 1776 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 3702 ave 3732 max 3674 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 129380 ave 132578 max 127003 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 517520
Ave neighs/atom = 71.877778
Neighbor list builds = 54
Dangerous builds = 0
Total wall time: 0:00:03

82
examples/vcm/in.vcm.lmp
View File

@ -1,82 +0,0 @@
# 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