tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update USER-BOCS example to match LAMMPS style and include reference logs

Browse Source
This commit is contained in:
Axel Kohlmeyer
2018-05-05 11:43:05 -04:00
parent 735bceb468
commit f9f8e2bdbe
3 changed files with 297 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
examples/USER/bocs/in.methanol
View File

@ -47,21 +47,21 @@ thermo_modify press 1_press
## Save some data from simulation to files
fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Uncomment to save some data from simulation to files
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Prints a configuration to dump.txt every 500 steps
dump 1 all custom 500 dump.txt id type x y z fx fy fz
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
# Write restart files to continue simulations
restart 10000 state1.restart state2.restart
#restart 10000 state1.restart state2.restart
## Run for this many steps
run_style verlet

143
examples/USER/bocs/log.20Apr18.methanol.g++.1 Normal file
View File

@ -0,0 +1,143 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
boundary p p p
atom_style atomic
newton on
timestep 1.0
read_data methanol.data
orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
1 by 1 by 1 MPI processor grid
reading atoms ...
968 atoms
velocity all create 300.0 16802 dist gaussian
pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
thermo 500
thermo_style custom step temp pe etotal press vol
variable STEP equal step
variable TEMP equal temp
## volume from cubic angstroms to cubic nm
variable VOL equal vol/1000.0
## pressure from atm to bar
variable PRESS equal press*1.01325
variable PXX equal pxx*1.01325
variable PYY equal pyy*1.01325
variable PZZ equal pzz*1.01325
variable PXY equal pxy*1.01325
variable PXZ equal pxz*1.01325
variable PYZ equal pyz*1.01325
## energy from kcal/mol to kJ/mol
variable KE equal ke*4.184
variable PE equal pe*4.184
variable UVDW equal evdwl*4.184
##### SPECIAL COMMANDS FOR FIX_BOCS #####
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
# Report the modified pressure
thermo_modify press 1_press
## Uncomment to save some data from simulation to files
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Prints a configuration to dump.txt every 500 steps
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
# Write restart files to continue simulations
#restart 10000 state1.restart state2.restart
## Run for this many steps
run_style verlet
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 24
ghost atom cutoff = 24
binsize = 12, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
Other | | 0.1252 | | | 0.36
Nlocal: 968 ave 968 max 968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9112 ave 9112 max 9112 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 404392 ave 404392 max 404392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 404392
Ave neighs/atom = 417.76
Neighbor list builds = 13
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:34

143
examples/USER/bocs/log.20Apr18.methanol.g++.4 Normal file
View File

@ -0,0 +1,143 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
boundary p p p
atom_style atomic
newton on
timestep 1.0
read_data methanol.data
orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
1 by 2 by 2 MPI processor grid
reading atoms ...
968 atoms
velocity all create 300.0 16802 dist gaussian
pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
thermo 500
thermo_style custom step temp pe etotal press vol
variable STEP equal step
variable TEMP equal temp
## volume from cubic angstroms to cubic nm
variable VOL equal vol/1000.0
## pressure from atm to bar
variable PRESS equal press*1.01325
variable PXX equal pxx*1.01325
variable PYY equal pyy*1.01325
variable PZZ equal pzz*1.01325
variable PXY equal pxy*1.01325
variable PXZ equal pxz*1.01325
variable PYZ equal pyz*1.01325
## energy from kcal/mol to kJ/mol
variable KE equal ke*4.184
variable PE equal pe*4.184
variable UVDW equal evdwl*4.184
##### SPECIAL COMMANDS FOR FIX_BOCS #####
# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
# Report the modified pressure
thermo_modify press 1_press
## Uncomment to save some data from simulation to files
#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
## Prints a configuration to dump.txt every 500 steps
#dump 1 all custom 500 dump.txt id type x y z fx fy fz
# Write restart files to continue simulations
#restart 10000 state1.restart state2.restart
## Run for this many steps
run_style verlet
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 24
ghost atom cutoff = 24
binsize = 12, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
Other | | 0.3112 | | | 1.08
Nlocal: 242 ave 244 max 239 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 5718.5 ave 5736 max 5702 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 100703 ave 108064 max 93454 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 402813
Ave neighs/atom = 416.129
Neighbor list builds = 14
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:28