diff --git a/examples/relres/README b/examples/relres/README index ebfe65b5b8..1a7c2fe344 100644 --- a/examples/relres/README +++ b/examples/relres/README @@ -1,16 +1,16 @@ -The input script in.22DMH.relres provides an example of a molecular -simulation using the Relative Resolution (RelRes) algorithm. In this -example, 2,2-Dimethylhexane is the molecule in focus. This script -uses the data file Data.22DMH.in.relres, which consists of 8000 +The input script in.22DMH.relres provides an example of a molecular +simulation using the Relative Resolution (RelRes) algorithm. In this +example, 2,2-Dimethylhexane is the molecule in focus. This script +uses the data file Data.22DMH.in.relres, which consists of 8000 molecules. It also generates the RelRes potential for the selected atom types. The input script in.22DMH.respa demonstrates the use of the lj/relres pair -style with r-RESPA applying multi-timestepping between the appropriate atom +style with r-RESPA applying multi-timestepping between the appropriate atom types (using a hybrid pair style configuration). The input script in.22DMH.real demonstrates the use of the lj/relres pair -style with real units (the data file Data.22DMH.in.real). It performs -a set of molecular simulations with different switching distances. Finally, -it performs a molecular simulation with the lj/smooth pair style, allowing -comparison of the thermal characteristics and the running time between the +style with real units (the data file Data.22DMH.in.real). It performs +a set of molecular simulations with different switching distances. Finally, +it performs a molecular simulation with the lj/smooth pair style, allowing +comparison of the thermal characteristics and the running time between the RelRes and the conventional approach. diff --git a/examples/relres/log.05Mar21.22DMH.real.g++.1 b/examples/relres/log.05Mar21.22DMH.real.g++.1 new file mode 100644 index 0000000000..55333da6bd --- /dev/null +++ b/examples/relres/log.05Mar21.22DMH.real.g++.1 @@ -0,0 +1,456 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11 +# with various Rso setting as well as run of reference system for time comparison (real units) +# The first run writes restart file that is used by all subsequent runs. + +# Run relres with Rso=6.25 + +units real +atom_style molecular +boundary p p p +dielectric 1 +special_bonds lj/coul 0.0 0.0 0.5 +bond_style harmonic +angle_style harmonic +dihedral_style fourier + +pair_style lj/relres 5.75 6.25 12.0 14.0 +read_data Data.22DMH.in.real +Reading data file ... + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8000 atoms + reading velocities ... + 8000 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 3 = max dihedrals/atom + reading bonds ... + 7000 bonds + reading angles ... + 9000 angles + reading dihedrals ... + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.003 seconds + read_data CPU = 0.036 seconds + +pair_coeff 6 6 0.175 3.905 0.0 0.0 +pair_coeff 4 4 0.118 3.905 0.0 0.0 +pair_coeff 2 2 0.118 3.905 1.2218 3.905 +pair_coeff 5 5 0.145 3.960 0.0 0.0 +pair_coeff 3 3 0.118 3.905 0.0 0.0 +pair_coeff 1 1 0.05 3.8 2.9128 3.9309 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003 + +@Article{Chaimovich1, + author = {A. Chaimovich, C. Peter, K. Kremer}, + title = {Relative resolution: A hybrid formalism for fluid mixtures}, + journal = {J.~Chem.~Phys.}, + year = 2015, + volume = 143, + pages = {243107} +@Article{Chaimovich2, + author = {M. Chaimovich, A. Chaimovich}, + title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS}, + journal = {J.~Chem.~Theory~Comput.}, + year = 2021, + volume = 17, + pages = {1045--1059} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 20.01 | 20.01 | 20.01 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 0 286.85653 -328.51562 3703.8924 6839.6636 10543.556 -4875.3137 8579.2062 268531.8 + 100 293.231 -55.62132 3520.4874 6991.6533 10512.141 -4797.2633 8317.7507 268531.8 + 200 292.73476 332.40528 3456.3029 6979.8212 10436.124 -4914.7261 8371.0291 268531.8 + 300 292.56511 221.98408 3380.7472 6975.7762 10356.523 -4936.5552 8317.3024 268531.8 + 400 288.42948 117.72433 3428.113 6877.1681 10305.281 -4887.6852 8315.7982 268531.8 + 500 289.20503 -238.73381 3373.758 6895.6601 10269.418 -4947.3214 8321.0795 268531.8 + 600 292.02137 74.370782 3263.4324 6962.8115 10226.244 -4948.3906 8211.823 268531.8 + 700 290.20603 475.24398 3260.0754 6919.5273 10179.603 -4931.4093 8191.4846 268531.8 + 800 293.12504 175.54324 3156.6048 6989.1268 10145.732 -5006.7161 8163.3209 268531.8 + 900 287.78433 63.785361 3251.5393 6861.7855 10113.325 -5029.094 8280.6333 268531.8 + 1000 290.11974 -101.34839 3183.4817 6917.47 10100.952 -5002.9413 8186.423 268531.8 +Loop time of 6.05162 on 1 procs for 1000 steps with 8000 atoms + +Performance: 14.277 ns/day, 1.681 hours/ns, 165.245 timesteps/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 | 4.7637 | 4.7637 | 4.7637 | 0.0 | 78.72 +Bond | 0.693 | 0.693 | 0.693 | 0.0 | 11.45 +Neigh | 0.41311 | 0.41311 | 0.41311 | 0.0 | 6.83 +Comm | 0.070843 | 0.070843 | 0.070843 | 0.0 | 1.17 +Output | 0.00045886 | 0.00045886 | 0.00045886 | 0.0 | 0.01 +Modify | 0.084814 | 0.084814 | 0.084814 | 0.0 | 1.40 +Other | | 0.02564 | | | 0.42 + +Nlocal: 8000.00 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 18934.0 ave 18934 max 18934 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 371920.0 ave 371920 max 371920 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 371920 +Ave neighs/atom = 46.490000 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 13 +Dangerous builds = 0 + +write_restart restart.relres.real +System init for write_restart ... + +# Run relres with Rso=7.25 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.relres.real +Reading restart file ... + restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021 + restoring atom style molecular from restart + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/relres from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style fourier from restart + 8000 atoms + 7000 bonds + 9000 angles + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_restart CPU = 0.004 seconds + +pair_style lj/relres 6.75 7.25 12.0 14.0 + +pair_coeff 6 6 0.175 3.905 0.0 0.0 +pair_coeff 4 4 0.118 3.905 0.0 0.0 +pair_coeff 2 2 0.118 3.905 1.2218 3.905 +pair_coeff 5 5 0.145 3.960 0.0 0.0 +pair_coeff 3 3 0.118 3.905 0.0 0.0 +pair_coeff 1 1 0.05 3.8 2.9128 3.9309 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 2 + +run 1000 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 20.51 | 20.51 | 20.51 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 1000 290.11974 21.86402 3334.7257 6917.47 10252.196 -4851.6973 8186.423 268531.8 + 1100 289.71937 460.00291 3365.0978 6907.9236 10273.021 -4881.5513 8246.6491 268531.8 + 1200 293.0828 194.76483 3348.6267 6988.1197 10336.746 -4743.4894 8092.1162 268531.8 + 1300 291.27785 153.93026 3496.2858 6945.0834 10441.369 -4753.3325 8249.6183 268531.8 + 1400 292.69435 -51.690836 3516.6743 6978.8575 10495.532 -4774.0701 8290.7445 268531.8 + 1500 290.0279 149.43706 3578.8283 6915.2801 10494.108 -4815.5857 8394.414 268531.8 + 1600 292.89473 -109.05125 3487.6652 6983.6354 10471.301 -4839.1407 8326.8059 268531.8 + 1700 290.99802 -146.06465 3496.48 6938.4111 10434.891 -4868.0031 8364.4831 268531.8 + 1800 286.48455 -45.580207 3550.2611 6830.7943 10381.055 -4766.3336 8316.5947 268531.8 + 1900 287.0735 -157.60878 3488.4248 6844.8368 10333.262 -4853.6992 8342.124 268531.8 + 2000 287.38046 -429.32757 3435.8336 6852.1558 10287.989 -4878.4345 8314.2681 268531.8 +Loop time of 7.46943 on 1 procs for 1000 steps with 8000 atoms + +Performance: 11.567 ns/day, 2.075 hours/ns, 133.879 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.1145 | 6.1145 | 6.1145 | 0.0 | 81.86 +Bond | 0.71392 | 0.71392 | 0.71392 | 0.0 | 9.56 +Neigh | 0.45677 | 0.45677 | 0.45677 | 0.0 | 6.12 +Comm | 0.072404 | 0.072404 | 0.072404 | 0.0 | 0.97 +Output | 0.00036481 | 0.00036481 | 0.00036481 | 0.0 | 0.00 +Modify | 0.085956 | 0.085956 | 0.085956 | 0.0 | 1.15 +Other | | 0.02552 | | | 0.34 + +Nlocal: 8000.00 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 18846.0 ave 18846 max 18846 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 475557.0 ave 475557 max 475557 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 475557 +Ave neighs/atom = 59.444625 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 14 +Dangerous builds = 0 + +# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.relres.real +Reading restart file ... + restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021 + restoring atom style molecular from restart + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/relres from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style fourier from restart + 8000 atoms + 7000 bonds + 9000 angles + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_restart CPU = 0.004 seconds + +pair_style lj/relres 6.75 7.25 12.0 14.0 + +pair_coeff 6 6 0.175 3.905 0.0 0.0 5.75 6.25 12.0 14.0 +pair_coeff 4 4 0.118 3.905 0.0 0.0 5.75 6.25 12.0 14.0 +pair_coeff 2 2 0.118 3.905 1.2218 3.905 5.75 6.25 12.0 14.0 +pair_coeff 5 5 0.145 3.960 0.0 0.0 +pair_coeff 3 3 0.118 3.905 0.0 0.0 +pair_coeff 1 1 0.05 3.8 2.9128 3.9309 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 2 + +run 1000 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 20.51 | 20.51 | 20.51 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 1000 290.11974 54.754001 3314.0966 6917.47 10231.567 -4872.3264 8186.423 268531.8 + 1100 289.78217 480.37221 3342.8765 6909.4211 10252.298 -4900.7266 8243.6032 268531.8 + 1200 293.25523 188.46596 3322.6257 6992.2308 10314.857 -4771.3485 8093.9742 268531.8 + 1300 291.59734 146.50303 3465.2113 6952.701 10417.912 -4782.9861 8248.1974 268531.8 + 1400 292.71873 -40.372074 3491.747 6979.4389 10471.186 -4790.7124 8282.4594 268531.8 + 1500 290.60378 120.25863 3539.5538 6929.0112 10468.565 -4849.9813 8389.5351 268531.8 + 1600 293.21218 -143.75501 3452.9516 6991.2046 10444.156 -4885.0192 8337.9708 268531.8 + 1700 291.02865 -207.34728 3465.4131 6939.1416 10404.555 -4887.363 8352.7761 268531.8 + 1800 286.00091 -91.017961 3530.3422 6819.2625 10349.605 -4807.6624 8338.0046 268531.8 + 1900 286.3006 -145.399 3485.1695 6826.4082 10311.578 -4848.263 8333.4325 268531.8 + 2000 288.43931 -469.99712 3409.0906 6877.4025 10286.493 -4905.9002 8314.9907 268531.8 +Loop time of 6.78592 on 1 procs for 1000 steps with 8000 atoms + +Performance: 12.732 ns/day, 1.885 hours/ns, 147.364 timesteps/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 | 5.4637 | 5.4637 | 5.4637 | 0.0 | 80.52 +Bond | 0.68994 | 0.68994 | 0.68994 | 0.0 | 10.17 +Neigh | 0.45166 | 0.45166 | 0.45166 | 0.0 | 6.66 +Comm | 0.070376 | 0.070376 | 0.070376 | 0.0 | 1.04 +Output | 0.000405 | 0.000405 | 0.000405 | 0.0 | 0.01 +Modify | 0.084545 | 0.084545 | 0.084545 | 0.0 | 1.25 +Other | | 0.02527 | | | 0.37 + +Nlocal: 8000.00 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 18820.0 ave 18820 max 18820 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 434269.0 ave 434269 max 434269 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 434269 +Ave neighs/atom = 54.283625 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 14 +Dangerous builds = 0 + +# Run reference system with lj/smooth + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.relres.real +Reading restart file ... + restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021 + restoring atom style molecular from restart + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/relres from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style fourier from restart + 8000 atoms + 7000 bonds + 9000 angles + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_restart CPU = 0.004 seconds + +pair_style lj/smooth 12.0 14.0 + +pair_coeff 6 6 0.175 3.905 +pair_coeff 4 4 0.118 3.905 +pair_coeff 2 2 0.118 3.905 +pair_coeff 5 5 0.145 3.960 +pair_coeff 3 3 0.118 3.905 +pair_coeff 1 1 0.05 3.8 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 2 + +run 1000 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/smooth, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.62 | 26.62 | 26.62 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 1000 290.11974 -80.648214 3258.0256 6917.47 10175.496 -4928.3973 8186.423 268531.8 + 1100 289.70919 358.20314 3288.412 6907.6811 10196.093 -4959.5166 8247.9285 268531.8 + 1200 292.84488 96.692992 3277.1296 6982.4468 10259.576 -4818.7374 8095.867 268531.8 + 1300 291.07262 65.629153 3425.4662 6940.1899 10365.656 -4828.0862 8253.5524 268531.8 + 1400 292.39722 -113.07286 3448.8088 6971.773 10420.582 -4841.3586 8290.1674 268531.8 + 1500 289.80998 90.176596 3510.6526 6910.0843 10420.737 -4884.6145 8395.2671 268531.8 + 1600 292.48452 -180.26543 3426.6967 6973.8544 10400.551 -4903.46 8330.1567 268531.8 + 1700 291.32152 -220.54923 3421.802 6946.1246 10367.927 -4946.101 8367.9031 268531.8 + 1800 286.77292 -101.26406 3475.3166 6837.6701 10312.987 -4830.565 8305.8816 268531.8 + 1900 286.6849 -161.65289 3428.0457 6835.5713 10263.617 -4909.5924 8337.6381 268531.8 + 2000 287.3785 -477.01298 3367.9719 6852.1091 10220.081 -4962.7001 8330.6719 268531.8 +Loop time of 25.7415 on 1 procs for 1000 steps with 8000 atoms + +Performance: 3.356 ns/day, 7.150 hours/ns, 38.848 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.253 | 24.253 | 24.253 | 0.0 | 94.22 +Bond | 0.72224 | 0.72224 | 0.72224 | 0.0 | 2.81 +Neigh | 0.57723 | 0.57723 | 0.57723 | 0.0 | 2.24 +Comm | 0.076624 | 0.076624 | 0.076624 | 0.0 | 0.30 +Output | 0.00035693 | 0.00035693 | 0.00035693 | 0.0 | 0.00 +Modify | 0.087599 | 0.087599 | 0.087599 | 0.0 | 0.34 +Other | | 0.02479 | | | 0.10 + +Nlocal: 8000.00 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 18804.0 ave 18804 max 18804 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.02600e+06 ave 2.026e+06 max 2.026e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2026005 +Ave neighs/atom = 253.25063 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 13 +Dangerous builds = 0 + +Total wall time: 0:00:46 diff --git a/examples/relres/log.05Mar21.22DMH.real.g++.4 b/examples/relres/log.05Mar21.22DMH.real.g++.4 new file mode 100644 index 0000000000..0a906cec4f --- /dev/null +++ b/examples/relres/log.05Mar21.22DMH.real.g++.4 @@ -0,0 +1,456 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11 +# with various Rso setting as well as run of reference system for time comparison (real units) +# The first run writes restart file that is used by all subsequent runs. + +# Run relres with Rso=6.25 + +units real +atom_style molecular +boundary p p p +dielectric 1 +special_bonds lj/coul 0.0 0.0 0.5 +bond_style harmonic +angle_style harmonic +dihedral_style fourier + +pair_style lj/relres 5.75 6.25 12.0 14.0 +read_data Data.22DMH.in.real +Reading data file ... + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 8000 atoms + reading velocities ... + 8000 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 3 = max dihedrals/atom + reading bonds ... + 7000 bonds + reading angles ... + 9000 angles + reading dihedrals ... + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.035 seconds + +pair_coeff 6 6 0.175 3.905 0.0 0.0 +pair_coeff 4 4 0.118 3.905 0.0 0.0 +pair_coeff 2 2 0.118 3.905 1.2218 3.905 +pair_coeff 5 5 0.145 3.960 0.0 0.0 +pair_coeff 3 3 0.118 3.905 0.0 0.0 +pair_coeff 1 1 0.05 3.8 2.9128 3.9309 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003 + +@Article{Chaimovich1, + author = {A. Chaimovich, C. Peter, K. Kremer}, + title = {Relative resolution: A hybrid formalism for fluid mixtures}, + journal = {J.~Chem.~Phys.}, + year = 2015, + volume = 143, + pages = {243107} +@Article{Chaimovich2, + author = {M. Chaimovich, A. Chaimovich}, + title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS}, + journal = {J.~Chem.~Theory~Comput.}, + year = 2021, + volume = 17, + pages = {1045--1059} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.953 | 9.953 | 9.953 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 0 286.85653 -328.51562 3703.8924 6839.6636 10543.556 -4875.3137 8579.2062 268531.8 + 100 293.231 -55.62132 3520.4874 6991.6533 10512.141 -4797.2633 8317.7507 268531.8 + 200 292.73476 332.40528 3456.3029 6979.8212 10436.124 -4914.7261 8371.0291 268531.8 + 300 292.56511 221.98408 3380.7472 6975.7762 10356.523 -4936.5552 8317.3024 268531.8 + 400 288.42948 117.72433 3428.113 6877.1681 10305.281 -4887.6852 8315.7982 268531.8 + 500 289.20503 -238.73381 3373.758 6895.6601 10269.418 -4947.3214 8321.0795 268531.8 + 600 292.02137 74.370782 3263.4324 6962.8115 10226.244 -4948.3906 8211.823 268531.8 + 700 290.20603 475.24398 3260.0754 6919.5273 10179.603 -4931.4093 8191.4846 268531.8 + 800 293.12504 175.54324 3156.6048 6989.1268 10145.732 -5006.7161 8163.3209 268531.8 + 900 287.78433 63.785361 3251.5393 6861.7855 10113.325 -5029.094 8280.6333 268531.8 + 1000 290.11974 -101.34839 3183.4817 6917.47 10100.952 -5002.9413 8186.423 268531.8 +Loop time of 2.12445 on 4 procs for 1000 steps with 8000 atoms + +Performance: 40.669 ns/day, 0.590 hours/ns, 470.709 timesteps/s +91.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2517 | 1.3228 | 1.4636 | 7.2 | 62.27 +Bond | 0.18406 | 0.19356 | 0.20925 | 2.1 | 9.11 +Neigh | 0.12468 | 0.125 | 0.12534 | 0.1 | 5.88 +Comm | 0.25384 | 0.40233 | 0.4919 | 14.1 | 18.94 +Output | 0.00034203 | 0.00061893 | 0.00088527 | 0.0 | 0.03 +Modify | 0.052326 | 0.059507 | 0.066224 | 2.6 | 2.80 +Other | | 0.02066 | | | 0.97 + +Nlocal: 2000.00 ave 2031 max 1964 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 9898.50 ave 9926 max 9869 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 92980.0 ave 94819 max 90517 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 371920 +Ave neighs/atom = 46.490000 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 13 +Dangerous builds = 0 + +write_restart restart.relres.real +System init for write_restart ... + +# Run relres with Rso=7.25 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.relres.real +Reading restart file ... + restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021 + restoring atom style molecular from restart + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 2 by 1 by 2 MPI processor grid + restoring pair style lj/relres from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style fourier from restart + 8000 atoms + 7000 bonds + 9000 angles + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.002 seconds + read_restart CPU = 0.005 seconds + +pair_style lj/relres 6.75 7.25 12.0 14.0 + +pair_coeff 6 6 0.175 3.905 0.0 0.0 +pair_coeff 4 4 0.118 3.905 0.0 0.0 +pair_coeff 2 2 0.118 3.905 1.2218 3.905 +pair_coeff 5 5 0.145 3.960 0.0 0.0 +pair_coeff 3 3 0.118 3.905 0.0 0.0 +pair_coeff 1 1 0.05 3.8 2.9128 3.9309 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 2 + +run 1000 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.34 | 10.34 | 10.34 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 1000 290.11974 21.86402 3334.7257 6917.47 10252.196 -4851.6973 8186.423 268531.8 + 1100 289.71937 460.00291 3365.0978 6907.9236 10273.021 -4881.5513 8246.6491 268531.8 + 1200 293.0828 194.76483 3348.6267 6988.1197 10336.746 -4743.4894 8092.1162 268531.8 + 1300 291.27785 153.93026 3496.2858 6945.0834 10441.369 -4753.3325 8249.6183 268531.8 + 1400 292.69435 -51.690836 3516.6743 6978.8575 10495.532 -4774.0701 8290.7445 268531.8 + 1500 290.0279 149.43706 3578.8283 6915.2801 10494.108 -4815.5857 8394.414 268531.8 + 1600 292.89473 -109.05125 3487.6652 6983.6354 10471.301 -4839.1407 8326.8059 268531.8 + 1700 290.99802 -146.06465 3496.48 6938.4111 10434.891 -4868.0031 8364.4831 268531.8 + 1800 286.48455 -45.580207 3550.2611 6830.7943 10381.055 -4766.3336 8316.5947 268531.8 + 1900 287.0735 -157.60878 3488.4248 6844.8368 10333.262 -4853.6992 8342.124 268531.8 + 2000 287.38046 -429.32757 3435.8336 6852.1558 10287.989 -4878.4345 8314.2681 268531.8 +Loop time of 2.6513 on 4 procs for 1000 steps with 8000 atoms + +Performance: 32.588 ns/day, 0.736 hours/ns, 377.174 timesteps/s +89.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5783 | 1.6371 | 1.7079 | 3.7 | 61.75 +Bond | 0.18196 | 0.19132 | 0.20276 | 1.7 | 7.22 +Neigh | 0.14093 | 0.14128 | 0.14156 | 0.1 | 5.33 +Comm | 0.50333 | 0.5809 | 0.64199 | 6.6 | 21.91 +Output | 0.00023452 | 0.00040924 | 0.00063279 | 0.0 | 0.02 +Modify | 0.066524 | 0.076747 | 0.084331 | 2.5 | 2.89 +Other | | 0.02354 | | | 0.89 + +Nlocal: 2000.00 ave 2009 max 1981 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +Nghost: 9892.50 ave 9923 max 9868 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 118889.0 ave 120387 max 117552 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 475557 +Ave neighs/atom = 59.444625 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 14 +Dangerous builds = 0 + +# Run relres with mixed Rso: 6.25 for C3H7 group and 7.25 for C5H11 group + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.relres.real +Reading restart file ... + restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021 + restoring atom style molecular from restart + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 2 by 1 by 2 MPI processor grid + restoring pair style lj/relres from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style fourier from restart + 8000 atoms + 7000 bonds + 9000 angles + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_restart CPU = 0.004 seconds + +pair_style lj/relres 6.75 7.25 12.0 14.0 + +pair_coeff 6 6 0.175 3.905 0.0 0.0 5.75 6.25 12.0 14.0 +pair_coeff 4 4 0.118 3.905 0.0 0.0 5.75 6.25 12.0 14.0 +pair_coeff 2 2 0.118 3.905 1.2218 3.905 5.75 6.25 12.0 14.0 +pair_coeff 5 5 0.145 3.960 0.0 0.0 +pair_coeff 3 3 0.118 3.905 0.0 0.0 +pair_coeff 1 1 0.05 3.8 2.9128 3.9309 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 2 + +run 1000 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.34 | 10.34 | 10.34 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 1000 290.11974 54.754001 3314.0966 6917.47 10231.567 -4872.3264 8186.423 268531.8 + 1100 289.78217 480.37221 3342.8765 6909.4211 10252.298 -4900.7266 8243.6032 268531.8 + 1200 293.25523 188.46596 3322.6257 6992.2308 10314.857 -4771.3485 8093.9742 268531.8 + 1300 291.59734 146.50303 3465.2113 6952.701 10417.912 -4782.9861 8248.1974 268531.8 + 1400 292.71873 -40.372074 3491.747 6979.4389 10471.186 -4790.7124 8282.4594 268531.8 + 1500 290.60378 120.25863 3539.5538 6929.0112 10468.565 -4849.9813 8389.5351 268531.8 + 1600 293.21218 -143.75501 3452.9516 6991.2046 10444.156 -4885.0192 8337.9708 268531.8 + 1700 291.02865 -207.34728 3465.4131 6939.1416 10404.555 -4887.363 8352.7761 268531.8 + 1800 286.00091 -91.017961 3530.3422 6819.2625 10349.605 -4807.6624 8338.0046 268531.8 + 1900 286.3006 -145.399 3485.1695 6826.4082 10311.578 -4848.263 8333.4325 268531.8 + 2000 288.43931 -469.99712 3409.0906 6877.4025 10286.493 -4905.9002 8314.9907 268531.8 +Loop time of 2.32221 on 4 procs for 1000 steps with 8000 atoms + +Performance: 37.206 ns/day, 0.645 hours/ns, 430.624 timesteps/s +90.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4451 | 1.5022 | 1.555 | 3.7 | 64.69 +Bond | 0.18307 | 0.19206 | 0.20526 | 2.0 | 8.27 +Neigh | 0.12827 | 0.12956 | 0.13074 | 0.3 | 5.58 +Comm | 0.36752 | 0.42006 | 0.48825 | 8.1 | 18.09 +Output | 0.00022658 | 0.00025297 | 0.0003292 | 0.0 | 0.01 +Modify | 0.05223 | 0.057658 | 0.063373 | 2.1 | 2.48 +Other | | 0.02044 | | | 0.88 + +Nlocal: 2000.00 ave 2016 max 1981 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 9878.25 ave 9891 max 9868 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 108567.0 ave 110532 max 107467 min +Histogram: 1 1 1 0 0 0 0 0 0 1 + +Total # of neighbors = 434269 +Ave neighs/atom = 54.283625 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 14 +Dangerous builds = 0 + +# Run reference system with lj/smooth + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.relres.real +Reading restart file ... + restart file = 10 Feb 2021, LAMMPS = 10 Feb 2021 + restoring atom style molecular from restart + orthogonal box = (3.7421629 3.7421629 3.7421629) to (68.257837 68.257837 68.257837) + 2 by 1 by 2 MPI processor grid + restoring pair style lj/relres from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style fourier from restart + 8000 atoms + 7000 bonds + 9000 angles + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_restart CPU = 0.007 seconds + +pair_style lj/smooth 12.0 14.0 + +pair_coeff 6 6 0.175 3.905 +pair_coeff 4 4 0.118 3.905 +pair_coeff 2 2 0.118 3.905 +pair_coeff 5 5 0.145 3.960 +pair_coeff 3 3 0.118 3.905 +pair_coeff 1 1 0.05 3.8 +pair_modify shift yes +neighbor 2.0 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e+02 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 2 + +run 1000 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/smooth, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.86 | 11.86 | 11.86 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 1000 290.11974 -80.648214 3258.0256 6917.47 10175.496 -4928.3973 8186.423 268531.8 + 1100 289.70919 358.20314 3288.412 6907.6811 10196.093 -4959.5166 8247.9285 268531.8 + 1200 292.84488 96.692992 3277.1296 6982.4468 10259.576 -4818.7374 8095.867 268531.8 + 1300 291.07262 65.629153 3425.4662 6940.1899 10365.656 -4828.0862 8253.5524 268531.8 + 1400 292.39722 -113.07286 3448.8088 6971.773 10420.582 -4841.3586 8290.1674 268531.8 + 1500 289.80998 90.176596 3510.6526 6910.0843 10420.737 -4884.6145 8395.2671 268531.8 + 1600 292.48452 -180.26543 3426.6967 6973.8544 10400.551 -4903.46 8330.1567 268531.8 + 1700 291.32152 -220.54923 3421.802 6946.1246 10367.927 -4946.101 8367.9031 268531.8 + 1800 286.77292 -101.26406 3475.3166 6837.6701 10312.987 -4830.565 8305.8816 268531.8 + 1900 286.6849 -161.65289 3428.0457 6835.5713 10263.617 -4909.5924 8337.6381 268531.8 + 2000 287.3785 -477.01298 3367.9719 6852.1091 10220.081 -4962.7001 8330.6719 268531.8 +Loop time of 7.44371 on 4 procs for 1000 steps with 8000 atoms + +Performance: 11.607 ns/day, 2.068 hours/ns, 134.342 timesteps/s +92.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.0092 | 6.1923 | 6.5395 | 8.2 | 83.19 +Bond | 0.18292 | 0.18861 | 0.19918 | 1.5 | 2.53 +Neigh | 0.16826 | 0.16868 | 0.1691 | 0.1 | 2.27 +Comm | 0.47602 | 0.82734 | 1.0097 | 22.7 | 11.11 +Output | 0.00023062 | 0.00025561 | 0.00032727 | 0.0 | 0.00 +Modify | 0.040804 | 0.047642 | 0.054462 | 3.1 | 0.64 +Other | | 0.01893 | | | 0.25 + +Nlocal: 2000.00 ave 2015 max 1972 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 9870.50 ave 9899 max 9855 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Neighs: 506501.0 ave 514030 max 499023 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 2026005 +Ave neighs/atom = 253.25063 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 13 +Dangerous builds = 0 + +Total wall time: 0:00:14 diff --git a/examples/relres/log.09Feb21.22DMH.relres.g++.1 b/examples/relres/log.05Mar21.22DMH.relres.g++.1 similarity index 68% rename from examples/relres/log.09Feb21.22DMH.relres.g++.1 rename to examples/relres/log.05Mar21.22DMH.relres.g++.1 index da3368e6e0..0b3eac595f 100644 --- a/examples/relres/log.09Feb21.22DMH.relres.g++.1 +++ b/examples/relres/log.05Mar21.22DMH.relres.g++.1 @@ -1,5 +1,8 @@ -LAMMPS (24 Dec 2020) +LAMMPS (10 Feb 2021) using 1 OpenMP thread(s) per MPI task +# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11 +# with with mixed Rso: 0.625e-9 for C3H7 group and 0.725e-9 for C5H11 group (si units) + units si atom_style molecular boundary p p p @@ -37,13 +40,13 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors - special bonds CPU = 0.019 seconds - read_data CPU = 0.168 seconds -pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 -pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 + special bonds CPU = 0.003 seconds + read_data CPU = 0.035 seconds +pair_coeff 6 6 1.21585e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 4 4 0.819828e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 5 5 1.00742E-21 0.396E-9 0.0 0.0 +pair_coeff 3 3 0.819828e-21 0.3905e-9 0.0 0.0 pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 pair_modify shift yes neighbor 2.0e-10 bin @@ -55,6 +58,31 @@ thermo_style custom step temp press pe ke etotal epair emol vol fix 2 all nvt temp 290 290 2.0e-13 run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003 + +@Article{Chaimovich1, + author = {A. Chaimovich, C. Peter, K. Kremer}, + title = {Relative resolution: A hybrid formalism for fluid mixtures}, + journal = {J.~Chem.~Phys.}, + year = 2015, + volume = 143, + pages = {243107} +@Article{Chaimovich2, + author = {M. Chaimovich, A. Chaimovich}, + title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS}, + journal = {J.~Chem.~Theory~Comput.}, + year = 2021, + volume = 17, + pages = {1045--1059} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + Neighbor list info ... update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -80,20 +108,20 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25 900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25 1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25 -Loop time of 20.1906 on 1 procs for 1000 steps with 8000 atoms +Loop time of 6.82188 on 1 procs for 1000 steps with 8000 atoms -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +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 | 15.751 | 15.751 | 15.751 | 0.0 | 78.01 -Bond | 1.7612 | 1.7612 | 1.7612 | 0.0 | 8.72 -Neigh | 1.4937 | 1.4937 | 1.4937 | 0.0 | 7.40 -Comm | 0.404 | 0.404 | 0.404 | 0.0 | 2.00 -Output | 0.0013139 | 0.0013139 | 0.0013139 | 0.0 | 0.01 -Modify | 0.72282 | 0.72282 | 0.72282 | 0.0 | 3.58 -Other | | 0.05691 | | | 0.28 +Pair | 5.5321 | 5.5321 | 5.5321 | 0.0 | 81.09 +Bond | 0.69427 | 0.69427 | 0.69427 | 0.0 | 10.18 +Neigh | 0.4138 | 0.4138 | 0.4138 | 0.0 | 6.07 +Comm | 0.070615 | 0.070615 | 0.070615 | 0.0 | 1.04 +Output | 0.00037602 | 0.00037602 | 0.00037602 | 0.0 | 0.01 +Modify | 0.084796 | 0.084796 | 0.084796 | 0.0 | 1.24 +Other | | 0.02591 | | | 0.38 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -111,7 +139,4 @@ Dangerous builds = 0 #pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 #pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 #pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:20 +Total wall time: 0:00:06 diff --git a/examples/relres/log.09Feb21.22DMH.relres.g++.4 b/examples/relres/log.05Mar21.22DMH.relres.g++.4 similarity index 68% rename from examples/relres/log.09Feb21.22DMH.relres.g++.4 rename to examples/relres/log.05Mar21.22DMH.relres.g++.4 index 969b47463a..146bcd3788 100644 --- a/examples/relres/log.09Feb21.22DMH.relres.g++.4 +++ b/examples/relres/log.05Mar21.22DMH.relres.g++.4 @@ -1,5 +1,8 @@ -LAMMPS (24 Dec 2020) +LAMMPS (10 Feb 2021) using 1 OpenMP thread(s) per MPI task +# Example: use of lj/relres for simulation of 2,2-dimethylhexane: C3H7-C5H11 +# with with mixed Rso: 0.625e-9 for C3H7 group and 0.725e-9 for C5H11 group (si units) + units si atom_style molecular boundary p p p @@ -37,13 +40,13 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors - special bonds CPU = 0.010 seconds - read_data CPU = 0.145 seconds -pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 -pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 + special bonds CPU = 0.001 seconds + read_data CPU = 0.037 seconds +pair_coeff 6 6 1.21585e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 4 4 0.819828e-21 0.3905e-9 0.0 0.0 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 5 5 1.00742E-21 0.396E-9 0.0 0.0 +pair_coeff 3 3 0.819828e-21 0.3905e-9 0.0 0.0 pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 pair_modify shift yes neighbor 2.0e-10 bin @@ -55,6 +58,31 @@ thermo_style custom step temp press pe ke etotal epair emol vol fix 2 all nvt temp 290 290 2.0e-13 run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003 + +@Article{Chaimovich1, + author = {A. Chaimovich, C. Peter, K. Kremer}, + title = {Relative resolution: A hybrid formalism for fluid mixtures}, + journal = {J.~Chem.~Phys.}, + year = 2015, + volume = 143, + pages = {243107} +@Article{Chaimovich2, + author = {M. Chaimovich, A. Chaimovich}, + title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS}, + journal = {J.~Chem.~Theory~Comput.}, + year = 2021, + volume = 17, + pages = {1045--1059} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + Neighbor list info ... update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -80,20 +108,20 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25 900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25 1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25 -Loop time of 5.79033 on 4 procs for 1000 steps with 8000 atoms +Loop time of 2.33734 on 4 procs for 1000 steps with 8000 atoms -97.9% CPU use with 4 MPI tasks x 1 OpenMP threads +92.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.0309 | 4.0713 | 4.1247 | 1.7 | 70.31 -Bond | 0.45193 | 0.46562 | 0.49307 | 2.4 | 8.04 -Neigh | 0.40834 | 0.40848 | 0.40871 | 0.0 | 7.05 -Comm | 0.48313 | 0.56787 | 0.60777 | 6.6 | 9.81 -Output | 0.00049329 | 0.0010571 | 0.0020971 | 1.9 | 0.02 -Modify | 0.22813 | 0.25523 | 0.27164 | 3.2 | 4.41 -Other | | 0.02078 | | | 0.36 +Pair | 1.474 | 1.5509 | 1.6662 | 5.7 | 66.35 +Bond | 0.18735 | 0.19226 | 0.20418 | 1.6 | 8.23 +Neigh | 0.11755 | 0.11806 | 0.11861 | 0.1 | 5.05 +Comm | 0.28111 | 0.41325 | 0.49073 | 12.3 | 17.68 +Output | 0.00020343 | 0.00056368 | 0.0016305 | 0.0 | 0.02 +Modify | 0.038727 | 0.044364 | 0.050037 | 2.6 | 1.90 +Other | | 0.01797 | | | 0.77 Nlocal: 2000.00 ave 2013 max 1987 min Histogram: 1 0 0 0 1 1 0 0 0 1 @@ -111,7 +139,4 @@ Dangerous builds = 0 #pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 #pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 #pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:06 +Total wall time: 0:00:02 diff --git a/examples/relres/log.09Feb21.22DMH.respa.g++.1 b/examples/relres/log.05Mar21.22DMH.respa.g++.1 similarity index 81% rename from examples/relres/log.09Feb21.22DMH.respa.g++.1 rename to examples/relres/log.05Mar21.22DMH.respa.g++.1 index 746047f9b1..de9751d1e5 100644 --- a/examples/relres/log.09Feb21.22DMH.respa.g++.1 +++ b/examples/relres/log.05Mar21.22DMH.respa.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Dec 2020) +LAMMPS (10 Feb 2021) using 1 OpenMP thread(s) per MPI task units si atom_style molecular @@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors - special bonds CPU = 0.018 seconds - read_data CPU = 0.170 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.035 seconds pair_coeff 1 1 lj/relres 1 3.47385e-22 3.8e-10 2.02372e-20 3.9309e-10 6.75e-10 7.25e-10 1.2e-09 1.4e-09 pair_coeff 1 2 lj/relres 1 5.33663e-22 3.85214e-10 1.31068e-20 3.91793e-10 6.22997e-10 6.73146e-10 1.2e-09 1.4e-09 pair_coeff 1 3 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10 @@ -76,6 +76,31 @@ Respa levels: 2 = hybrid-2 kspace run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003 + +@Article{Chaimovich1, + author = {A. Chaimovich, C. Peter, K. Kremer}, + title = {Relative resolution: A hybrid formalism for fluid mixtures}, + journal = {J.~Chem.~Phys.}, + year = 2015, + volume = 143, + pages = {243107} +@Article{Chaimovich2, + author = {M. Chaimovich, A. Chaimovich}, + title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS}, + journal = {J.~Chem.~Theory~Comput.}, + year = 2021, + volume = 17, + pages = {1045--1059} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + Neighbor list info ... update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -111,30 +136,30 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 400 293.0168 38268765 2.3173289e-17 4.8540384e-17 7.1713672e-17 -3.3633853e-17 5.6807142e-17 2.685318e-25 450 289.19195 33053376 2.36093e-17 4.7906769e-17 7.151607e-17 -3.3774223e-17 5.7383524e-17 2.685318e-25 500 292.43942 -684078.27 2.2898459e-17 4.8444735e-17 7.1343194e-17 -3.3856946e-17 5.6755405e-17 2.685318e-25 -Loop time of 15.899 on 1 procs for 500 steps with 8000 atoms +Loop time of 4.85018 on 1 procs for 500 steps with 8000 atoms -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +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 | 11.067 | 11.067 | 11.067 | 0.0 | 69.61 -Bond | 1.7933 | 1.7933 | 1.7933 | 0.0 | 11.28 -Neigh | 1.5748 | 1.5748 | 1.5748 | 0.0 | 9.91 -Comm | 0.50431 | 0.50431 | 0.50431 | 0.0 | 3.17 -Output | 0.0013113 | 0.0013113 | 0.0013113 | 0.0 | 0.01 -Modify | 0.69311 | 0.69311 | 0.69311 | 0.0 | 4.36 -Other | | 0.2656 | | | 1.67 +Pair | 3.4622 | 3.4622 | 3.4622 | 0.0 | 71.38 +Bond | 0.68987 | 0.68987 | 0.68987 | 0.0 | 14.22 +Neigh | 0.44102 | 0.44102 | 0.44102 | 0.0 | 9.09 +Comm | 0.087413 | 0.087413 | 0.087413 | 0.0 | 1.80 +Output | 0.00034455 | 0.00034455 | 0.00034455 | 0.0 | 0.01 +Modify | 0.084174 | 0.084174 | 0.084174 | 0.0 | 1.74 +Other | | 0.08514 | | | 1.76 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18908.0 ave 18908 max 18908 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 126950.0 ave 126950 max 126950 min +Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 126950 -Ave neighs/atom = 15.868750 +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 Ave special neighs/atom = 5.2500000 Neighbor list builds = 13 Dangerous builds = 0 @@ -142,7 +167,4 @@ Dangerous builds = 0 #pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 #pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 #pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:16 +Total wall time: 0:00:04 diff --git a/examples/relres/log.09Feb21.22DMH.respa.g++.4 b/examples/relres/log.05Mar21.22DMH.respa.g++.4 similarity index 80% rename from examples/relres/log.09Feb21.22DMH.respa.g++.4 rename to examples/relres/log.05Mar21.22DMH.respa.g++.4 index f2328614a7..01480a5248 100644 --- a/examples/relres/log.09Feb21.22DMH.respa.g++.4 +++ b/examples/relres/log.05Mar21.22DMH.respa.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Dec 2020) +LAMMPS (10 Feb 2021) using 1 OpenMP thread(s) per MPI task units si atom_style molecular @@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors - special bonds CPU = 0.005 seconds - read_data CPU = 0.135 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.036 seconds pair_coeff 1 1 lj/relres 1 3.47385e-22 3.8e-10 2.02372e-20 3.9309e-10 6.75e-10 7.25e-10 1.2e-09 1.4e-09 pair_coeff 1 2 lj/relres 1 5.33663e-22 3.85214e-10 1.31068e-20 3.91793e-10 6.22997e-10 6.73146e-10 1.2e-09 1.4e-09 pair_coeff 1 3 lj/relres 2 5.33663e-22 3.85214e-10 0 3.91793e-10 6.75e-10 7.25e-10 7.25e-10 7.25e-10 @@ -76,6 +76,31 @@ Respa levels: 2 = hybrid-2 kspace run 500 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Pair style lj/relres: doi:10.1021/acs.jctc.0c01003 + +@Article{Chaimovich1, + author = {A. Chaimovich, C. Peter, K. Kremer}, + title = {Relative resolution: A hybrid formalism for fluid mixtures}, + journal = {J.~Chem.~Phys.}, + year = 2015, + volume = 143, + pages = {243107} +@Article{Chaimovich2, + author = {M. Chaimovich, A. Chaimovich}, + title = {Relative Resolution: A Computationally Efficient Implementation in LAMMPS}, + journal = {J.~Chem.~Theory~Comput.}, + year = 2021, + volume = 17, + pages = {1045--1059} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + Neighbor list info ... update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -111,30 +136,30 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 400 293.0168 38268765 2.3173289e-17 4.8540384e-17 7.1713672e-17 -3.3633853e-17 5.6807142e-17 2.685318e-25 450 289.19195 33053376 2.36093e-17 4.7906769e-17 7.151607e-17 -3.3774223e-17 5.7383524e-17 2.685318e-25 500 292.43942 -684078.27 2.2898459e-17 4.8444735e-17 7.1343194e-17 -3.3856946e-17 5.6755405e-17 2.685318e-25 -Loop time of 4.45202 on 4 procs for 500 steps with 8000 atoms +Loop time of 1.76801 on 4 procs for 500 steps with 8000 atoms -98.0% CPU use with 4 MPI tasks x 1 OpenMP threads +91.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.6826 | 2.7363 | 2.7963 | 2.5 | 61.46 -Bond | 0.45619 | 0.46186 | 0.46906 | 0.8 | 10.37 -Neigh | 0.42817 | 0.42863 | 0.4292 | 0.1 | 9.63 -Comm | 0.49036 | 0.56091 | 0.62185 | 6.5 | 12.60 -Output | 0.00049472 | 0.0013556 | 0.0024905 | 2.0 | 0.03 -Modify | 0.1831 | 0.18662 | 0.19193 | 0.8 | 4.19 -Other | | 0.07637 | | | 1.72 +Pair | 0.93397 | 0.97055 | 1.0377 | 4.0 | 54.89 +Bond | 0.18914 | 0.19729 | 0.20727 | 1.5 | 11.16 +Neigh | 0.12623 | 0.12644 | 0.12663 | 0.1 | 7.15 +Comm | 0.31509 | 0.39593 | 0.44272 | 7.7 | 22.39 +Output | 0.00031866 | 0.00034685 | 0.00041755 | 0.0 | 0.02 +Modify | 0.035567 | 0.037833 | 0.039797 | 0.8 | 2.14 +Other | | 0.03963 | | | 2.24 Nlocal: 2000.00 ave 2016 max 1985 min Histogram: 1 0 0 0 1 1 0 0 0 1 Nghost: 9883.00 ave 9895 max 9866 min Histogram: 1 0 0 0 0 1 0 1 0 1 -Neighs: 31737.5 ave 32060 max 31459 min -Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 126950 -Ave neighs/atom = 15.868750 +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 Ave special neighs/atom = 5.2500000 Neighbor list builds = 13 Dangerous builds = 0 @@ -142,7 +167,4 @@ Dangerous builds = 0 #pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 #pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 #pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:04 +Total wall time: 0:00:01