diff --git a/examples/stress_vcm/in.stress_vcm.lmp b/examples/stress_vcm/in.stress_vcm.lmp new file mode 100644 index 0000000000..24dc86f6fd --- /dev/null +++ b/examples/stress_vcm/in.stress_vcm.lmp @@ -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 diff --git a/examples/vcm/log.19Nov24.vcm.g++.1 b/examples/stress_vcm/log.19Nov24.stress_vcm.g++.1 similarity index 73% rename from examples/vcm/log.19Nov24.vcm.g++.1 rename to examples/stress_vcm/log.19Nov24.stress_vcm.g++.1 index 4b03a771ad..93ae029334 100644 --- a/examples/vcm/log.19Nov24.vcm.g++.1 +++ b/examples/stress_vcm/log.19Nov24.stress_vcm.g++.1 @@ -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 diff --git a/examples/stress_vcm/log.19Nov24.stress_vcm.g++.4 b/examples/stress_vcm/log.19Nov24.stress_vcm.g++.4 new file mode 100644 index 0000000000..d8e7c07536 --- /dev/null +++ b/examples/stress_vcm/log.19Nov24.stress_vcm.g++.4 @@ -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 diff --git a/examples/vcm/in.vcm.lmp b/examples/vcm/in.vcm.lmp deleted file mode 100644 index 41d7665c49..0000000000 --- a/examples/vcm/in.vcm.lmp +++ /dev/null @@ -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