diff --git a/examples/template/in.mol-restart-mix b/examples/template/in.mol-restart-mix index f6fe584e0f..c24857d5d2 100644 --- a/examples/template/in.mol-restart-mix +++ b/examples/template/in.mol-restart-mix @@ -1,6 +1,12 @@ # demo for atom style template simulating a cyclohexane methane mixture # part 3: continuing from restart file +# run the first part and write out restart +include in.molecular-mix +write_restart molecular-mix.restart + +# now restart +clear molecule cychex cyclohexane.mol read_restart molecular-mix.restart @@ -9,3 +15,6 @@ thermo 100 fix 1 all nvt temp 300.0 300.0 1.0 # dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu run 2000 + +# clean up +shell rm molecular-mix.restart diff --git a/examples/template/in.tmpl-restart-mix b/examples/template/in.tmpl-restart-mix index cd9ea605a0..5f527ba362 100644 --- a/examples/template/in.tmpl-restart-mix +++ b/examples/template/in.tmpl-restart-mix @@ -1,6 +1,12 @@ # demo for atom style template simulating a cyclohexane methane mixture # part 3: continuing from restart file +# run the first part and write out restart +include in.template-mix +write_restart template-mix.restart + +# now restart +clear molecule cychex cyclohexane.mol read_restart template-mix.restart @@ -9,3 +15,6 @@ thermo 100 fix 1 all nvt temp 300.0 300.0 1.0 # dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu run 2000 + +# clean up +shell rm template-mix.restart diff --git a/examples/template/log.12Aug24.mol-restart-mix.g++.1 b/examples/template/log.12Aug24.mol-restart-mix.g++.1 new file mode 100644 index 0000000000..9e297dec0b --- /dev/null +++ b/examples/template/log.12Aug24.mol-restart-mix.g++.1 @@ -0,0 +1,302 @@ +LAMMPS (27 Jun 2024) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# demo for atom style template simulating a cyclohexane methane mixture +# part 3: continuing from restart file + +# run the first part and write out restart +include in.molecular-mix +# demo for atom style template simulating a cyclohexane methane mixture + +units real +boundary p p p +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +atom_style molecular + +pair_style lj/cut 12.0 +pair_modify mix geometric tail yes +bond_style harmonic +angle_style harmonic +dihedral_style harmonic + +lattice sc 6.0 +Lattice spacing in x,y,z = 6 6 6 +variable boxlen index 4.0 +region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice +create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2 +Created orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 1 by 1 MPI processor grid + +create_atoms 0 box mol cychex 734594 +Created 3072 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.004 seconds +create_atoms 2 random 800 495437 box +Created 800 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.000 seconds + +mass 1 14.027 +mass 2 16.043 + +pair_coeff 1 1 0.1180 3.905 +pair_coeff 2 2 0.2940 3.730 + +bond_coeff 1 260.00 1.5260 +angle_coeff 1 63.0 112.40 +dihedral_coeff 1 2.0 1 3 + +thermo 100 +minimize 0.001 0.001 500 1000 +Generated 1 of 1 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 = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14 + 100 0 -4351.8383 516.49891 -3835.3394 11635.037 + 190 0 -6191.8196 457.61266 -5734.2069 4365.4279 +Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms + +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + 43897850768892.8 -5729.17409504969 -5734.20694761353 + Force two-norm initial, final = 1.1080994e+15 72.745546 + Force max component initial, final = 4.6607099e+14 17.390179 + Final line search alpha, max atom move = 0.0041638487 0.072410076 + Iterations, force evaluations = 190 297 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2379 | 2.2379 | 2.2379 | 0.0 | 87.19 +Bond | 0.070658 | 0.070658 | 0.070658 | 0.0 | 2.75 +Neigh | 0.21093 | 0.21093 | 0.21093 | 0.0 | 8.22 +Comm | 0.012111 | 0.012111 | 0.012111 | 0.0 | 0.47 +Output | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.03504 | | | 1.37 + +Nlocal: 3872 ave 3872 max 3872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12122 ave 12122 max 12122 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 774375 ave 774375 max 774375 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 774375 +Ave neighs/atom = 199.99354 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 14 +Dangerous builds = 0 +reset_timestep 0 + +velocity all create 100.0 6234235 +fix 1 all nvt temp 100.0 300.0 1.0 +# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu +run 2500 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 100 -6191.8196 457.61266 -4580.3354 4842.371 + 100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321 + 200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619 + 300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123 + 400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393 + 500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524 + 600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889 + 700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164 + 800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503 + 900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352 + 1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354 + 1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244 + 1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439 + 1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716 + 1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061 + 1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408 + 1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728 + 1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923 + 1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241 + 1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835 + 2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701 + 2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632 + 2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546 + 2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574 + 2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435 + 2500 296.10218 -4928.5152 1698.282 186.40572 10946.864 +Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms + +Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.936 | 15.936 | 15.936 | 0.0 | 92.46 +Bond | 0.5636 | 0.5636 | 0.5636 | 0.0 | 3.27 +Neigh | 0.51213 | 0.51213 | 0.51213 | 0.0 | 2.97 +Comm | 0.098127 | 0.098127 | 0.098127 | 0.0 | 0.57 +Output | 0.00072478 | 0.00072478 | 0.00072478 | 0.0 | 0.00 +Modify | 0.10177 | 0.10177 | 0.10177 | 0.0 | 0.59 +Other | | 0.02248 | | | 0.13 + +Nlocal: 3872 ave 3872 max 3872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11821 ave 11821 max 11821 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 770416 ave 770416 max 770416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 770416 +Ave neighs/atom = 198.97107 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 34 +Dangerous builds = 0 +#write_data molecular-mix.data +#write_restart molecular-mix.restart +write_restart molecular-mix.restart +System init for write_restart ... +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule + +# now restart +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +read_restart molecular-mix.restart +Reading restart file ... + restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024 + restoring atom style molecular from restart + orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/cut from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style harmonic from restart + 3872 atoms + 3072 bonds + 3072 angles + 3072 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_restart CPU = 0.003 seconds + +thermo 100 + +fix 1 all nvt temp 300.0 300.0 1.0 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu +run 2000 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +All restart file global fix info was re-assigned +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.12 | 11.12 Mbytes + Step Temp E_pair E_mol TotEng Press + 2500 296.10218 -4928.5152 1698.282 186.40572 10946.864 + 2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357 + 2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67 + 2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997 + 2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823 + 3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636 + 3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576 + 3200 297.34385 -5017.986 1603.4388 16.419054 10451.2 + 3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096 + 3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599 + 3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632 + 3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222 + 3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292 + 3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524 + 3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697 + 4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793 + 4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442 + 4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116 + 4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216 + 4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253 + 4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246 +Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms + +Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.191 | 12.191 | 12.191 | 0.0 | 91.74 +Bond | 0.4224 | 0.4224 | 0.4224 | 0.0 | 3.18 +Neigh | 0.50894 | 0.50894 | 0.50894 | 0.0 | 3.83 +Comm | 0.07309 | 0.07309 | 0.07309 | 0.0 | 0.55 +Output | 0.00057158 | 0.00057158 | 0.00057158 | 0.0 | 0.00 +Modify | 0.077778 | 0.077778 | 0.077778 | 0.0 | 0.59 +Other | | 0.01451 | | | 0.11 + +Nlocal: 3872 ave 3872 max 3872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11685 ave 11685 max 11685 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 770346 ave 770346 max 770346 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 770346 +Ave neighs/atom = 198.953 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 34 +Dangerous builds = 0 + +# clean up +shell rm molecular-mix.restart +Total wall time: 0:00:33 diff --git a/examples/template/log.12Aug24.mol-restart-mix.g++.4 b/examples/template/log.12Aug24.mol-restart-mix.g++.4 new file mode 100644 index 0000000000..a0157eaaa6 --- /dev/null +++ b/examples/template/log.12Aug24.mol-restart-mix.g++.4 @@ -0,0 +1,303 @@ +LAMMPS (27 Jun 2024) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# demo for atom style template simulating a cyclohexane methane mixture +# part 3: continuing from restart file + +# run the first part and write out restart +include in.molecular-mix +# demo for atom style template simulating a cyclohexane methane mixture + +units real +boundary p p p +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +atom_style molecular + +pair_style lj/cut 12.0 +pair_modify mix geometric tail yes +bond_style harmonic +angle_style harmonic +dihedral_style harmonic + +lattice sc 6.0 +Lattice spacing in x,y,z = 6 6 6 +variable boxlen index 4.0 +region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice +create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2 +Created orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 2 by 2 MPI processor grid + +create_atoms 0 box mol cychex 734594 +Created 3072 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.002 seconds +create_atoms 2 random 800 495437 box +Created 800 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.000 seconds + +mass 1 14.027 +mass 2 16.043 + +pair_coeff 1 1 0.1180 3.905 +pair_coeff 2 2 0.2940 3.730 + +bond_coeff 1 260.00 1.5260 +angle_coeff 1 63.0 112.40 +dihedral_coeff 1 2.0 1 3 + +thermo 100 +minimize 0.001 0.001 500 1000 +Generated 1 of 1 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 = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17 + 100 0 -3410.6986 572.28283 -2838.4158 14603.831 + 200 0 -6109.2306 483.67771 -5625.5529 5069.1821 + 204 0 -6137.0238 483.1464 -5653.8774 4952.4083 +Loop time of 0.719327 on 4 procs for 204 steps with 3872 atoms + +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + 7.54300441078755e+16 -5648.75822666276 -5653.87742467986 + Force two-norm initial, final = 8.7430661e+18 74.636836 + Force max component initial, final = 4.1468626e+18 8.680078 + Final line search alpha, max atom move = 0.0032186724 0.027938327 + Iterations, force evaluations = 204 328 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.60273 | 0.60882 | 0.61181 | 0.5 | 84.64 +Bond | 0.018965 | 0.019154 | 0.019363 | 0.1 | 2.66 +Neigh | 0.054004 | 0.054008 | 0.054012 | 0.0 | 7.51 +Comm | 0.022945 | 0.026108 | 0.032071 | 2.2 | 3.63 +Output | 3.4085e-05 | 3.6968e-05 | 4.5055e-05 | 0.0 | 0.01 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.0112 | | | 1.56 + +Nlocal: 968 ave 980 max 954 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 6630 ave 6644 max 6616 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 193550 ave 195957 max 191376 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 774200 +Ave neighs/atom = 199.94835 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 14 +Dangerous builds = 0 +reset_timestep 0 + +velocity all create 100.0 6234235 +fix 1 all nvt temp 100.0 300.0 1.0 +# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu +run 2500 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 100 -6137.0238 483.1464 -4500.0059 5429.3515 + 100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922 + 200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576 + 300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841 + 400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7 + 500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519 + 600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312 + 700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062 + 800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319 + 900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218 + 1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317 + 1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434 + 1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625 + 1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169 + 1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496 + 1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052 + 1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28 + 1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096 + 1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864 + 1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513 + 2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674 + 2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49 + 2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961 + 2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853 + 2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501 + 2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135 +Loop time of 4.32954 on 4 procs for 2500 steps with 3872 atoms + +Performance: 49.890 ns/day, 0.481 hours/ns, 577.429 timesteps/s, 2.236 Matom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.8113 | 3.8529 | 3.8893 | 1.7 | 88.99 +Bond | 0.13153 | 0.13433 | 0.13718 | 0.7 | 3.10 +Neigh | 0.13036 | 0.13039 | 0.13042 | 0.0 | 3.01 +Comm | 0.13688 | 0.1751 | 0.21857 | 8.4 | 4.04 +Output | 0.00032606 | 0.00035873 | 0.00045009 | 0.0 | 0.01 +Modify | 0.027754 | 0.028116 | 0.028735 | 0.2 | 0.65 +Other | | 0.008382 | | | 0.19 + +Nlocal: 968 ave 986 max 944 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 6379.75 ave 6407 max 6352 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 192584 ave 196718 max 188693 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 770338 +Ave neighs/atom = 198.95093 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 34 +Dangerous builds = 0 +#write_data molecular-mix.data +#write_restart molecular-mix.restart +write_restart molecular-mix.restart +System init for write_restart ... +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule + +# now restart +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +read_restart molecular-mix.restart +Reading restart file ... + restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024 + restoring atom style molecular from restart + orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 2 by 2 MPI processor grid + restoring pair style lj/cut from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style harmonic from restart + 3872 atoms + 3072 bonds + 3072 angles + 3072 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_restart CPU = 0.004 seconds + +thermo 100 + +fix 1 all nvt temp 300.0 300.0 1.0 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu +run 2000 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +All restart file global fix info was re-assigned +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.475 | 8.571 | 8.857 Mbytes + Step Temp E_pair E_mol TotEng Press + 2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135 + 2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533 + 2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127 + 2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494 + 2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3 + 3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459 + 3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057 + 3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933 + 3300 297.45744 -4923.6217 1700.537 209.19205 8189.571 + 3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119 + 3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067 + 3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481 + 3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479 + 3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521 + 3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37 + 4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386 + 4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733 + 4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158 + 4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862 + 4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975 + 4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294 +Loop time of 3.58588 on 4 procs for 2000 steps with 3872 atoms + +Performance: 48.189 ns/day, 0.498 hours/ns, 557.743 timesteps/s, 2.160 Matom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0873 | 3.1383 | 3.2136 | 2.7 | 87.52 +Bond | 0.10381 | 0.10769 | 0.11168 | 0.9 | 3.00 +Neigh | 0.13651 | 0.13652 | 0.13654 | 0.0 | 3.81 +Comm | 0.094882 | 0.1741 | 0.22894 | 12.3 | 4.86 +Output | 0.00024683 | 0.00028387 | 0.00038642 | 0.0 | 0.01 +Modify | 0.021974 | 0.022331 | 0.022623 | 0.2 | 0.62 +Other | | 0.006685 | | | 0.19 + +Nlocal: 968 ave 984 max 948 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 6349.5 ave 6370 max 6330 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 192457 ave 196654 max 187154 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 769828 +Ave neighs/atom = 198.81921 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 35 +Dangerous builds = 0 + +# clean up +shell rm molecular-mix.restart +Total wall time: 0:00:08 diff --git a/examples/template/log.12Aug24.tmpl-restart-mix.g++.1 b/examples/template/log.12Aug24.tmpl-restart-mix.g++.1 new file mode 100644 index 0000000000..04c316c02c --- /dev/null +++ b/examples/template/log.12Aug24.tmpl-restart-mix.g++.1 @@ -0,0 +1,295 @@ +LAMMPS (27 Jun 2024) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# demo for atom style template simulating a cyclohexane methane mixture +# part 3: continuing from restart file + +# run the first part and write out restart +include in.template-mix +# demo for atom style template simulating a cyclohexane methane mixture +# part 1: creating system with create_atoms + +units real +boundary p p p +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +atom_style template cychex + +pair_style lj/cut 12.0 +pair_modify mix geometric tail yes +bond_style harmonic +angle_style harmonic +dihedral_style harmonic + +lattice sc 6.0 +Lattice spacing in x,y,z = 6 6 6 +variable boxlen index 4.0 +region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice +create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 +Created orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 1 by 1 MPI processor grid + +create_atoms 0 box mol cychex 734594 +Created 3072 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.000 seconds +create_atoms 2 random 800 495437 box +Created 800 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.000 seconds + +mass 1 14.027 +mass 2 16.043 + +pair_coeff 1 1 0.1180 3.905 +pair_coeff 2 2 0.2940 3.730 + +bond_coeff 1 260.00 1.5260 +angle_coeff 1 63.0 112.40 +dihedral_coeff 1 2.0 1 3 + +thermo 100 +minimize 0.001 0.001 500 1000 +Generated 1 of 1 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 = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.05 | 8.05 | 8.05 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14 + 100 0 -4351.8383 516.49891 -3835.3394 11635.037 + 190 0 -6191.8196 457.61266 -5734.2069 4365.4279 +Loop time of 2.46574 on 1 procs for 190 steps with 3872 atoms + +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + 43897850768892.8 -5729.17409504969 -5734.20694761353 + Force two-norm initial, final = 1.1080994e+15 72.745546 + Force max component initial, final = 4.6607099e+14 17.390179 + Final line search alpha, max atom move = 0.0041638487 0.072410076 + Iterations, force evaluations = 190 297 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1376 | 2.1376 | 2.1376 | 0.0 | 86.69 +Bond | 0.068456 | 0.068456 | 0.068456 | 0.0 | 2.78 +Neigh | 0.21212 | 0.21212 | 0.21212 | 0.0 | 8.60 +Comm | 0.012436 | 0.012436 | 0.012436 | 0.0 | 0.50 +Output | 2.9907e-05 | 2.9907e-05 | 2.9907e-05 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.03511 | | | 1.42 + +Nlocal: 3872 ave 3872 max 3872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 12122 ave 12122 max 12122 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 774375 ave 774375 max 774375 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 774375 +Ave neighs/atom = 199.99354 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 14 +Dangerous builds = 0 +reset_timestep 0 + +velocity all create 100.0 6234235 +fix 1 all nvt temp 100.0 300.0 1.0 +# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu +run 2500 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 100 -6191.8196 457.61266 -4580.3354 4842.371 + 100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321 + 200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619 + 300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123 + 400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393 + 500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524 + 600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889 + 700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164 + 800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503 + 900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352 + 1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354 + 1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244 + 1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439 + 1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716 + 1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061 + 1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408 + 1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728 + 1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923 + 1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241 + 1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835 + 2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701 + 2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632 + 2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546 + 2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574 + 2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435 + 2500 296.10218 -4928.5152 1698.282 186.40572 10946.864 +Loop time of 16.1773 on 1 procs for 2500 steps with 3872 atoms + +Performance: 13.352 ns/day, 1.797 hours/ns, 154.537 timesteps/s, 598.368 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.927 | 14.927 | 14.927 | 0.0 | 92.27 +Bond | 0.52161 | 0.52161 | 0.52161 | 0.0 | 3.22 +Neigh | 0.52299 | 0.52299 | 0.52299 | 0.0 | 3.23 +Comm | 0.090871 | 0.090871 | 0.090871 | 0.0 | 0.56 +Output | 0.00059782 | 0.00059782 | 0.00059782 | 0.0 | 0.00 +Modify | 0.096104 | 0.096104 | 0.096104 | 0.0 | 0.59 +Other | | 0.01791 | | | 0.11 + +Nlocal: 3872 ave 3872 max 3872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11821 ave 11821 max 11821 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 770416 ave 770416 max 770416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 770416 +Ave neighs/atom = 198.97107 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 34 +Dangerous builds = 0 +#write_data template-mix.data +#write_restart template-mix.restart +write_restart template-mix.restart +System init for write_restart ... +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule + +# now restart +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +read_restart template-mix.restart +Reading restart file ... + restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024 + restoring atom style template from restart + orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/cut from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style harmonic from restart + 3872 atoms + 3072 template bonds + 3072 template angles + 3072 template dihedrals + read_restart CPU = 0.001 seconds + +thermo 100 + +fix 1 all nvt temp 300.0 300.0 1.0 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu +run 2000 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +All restart file global fix info was re-assigned +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes + Step Temp E_pair E_mol TotEng Press + 2500 296.10218 -4928.5152 1698.282 186.40572 10946.864 + 2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357 + 2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67 + 2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997 + 2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823 + 3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636 + 3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576 + 3200 297.34385 -5017.986 1603.4388 16.419054 10451.2 + 3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096 + 3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599 + 3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632 + 3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222 + 3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292 + 3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524 + 3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697 + 4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793 + 4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442 + 4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116 + 4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216 + 4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253 + 4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246 +Loop time of 13.2399 on 1 procs for 2000 steps with 3872 atoms + +Performance: 13.051 ns/day, 1.839 hours/ns, 151.058 timesteps/s, 584.898 katom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.13 | 12.13 | 12.13 | 0.0 | 91.61 +Bond | 0.42044 | 0.42044 | 0.42044 | 0.0 | 3.18 +Neigh | 0.52469 | 0.52469 | 0.52469 | 0.0 | 3.96 +Comm | 0.072857 | 0.072857 | 0.072857 | 0.0 | 0.55 +Output | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.00 +Modify | 0.076918 | 0.076918 | 0.076918 | 0.0 | 0.58 +Other | | 0.0148 | | | 0.11 + +Nlocal: 3872 ave 3872 max 3872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11685 ave 11685 max 11685 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 770346 ave 770346 max 770346 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 770346 +Ave neighs/atom = 198.953 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 34 +Dangerous builds = 0 + +# clean up +shell rm template-mix.restart +Total wall time: 0:00:31 diff --git a/examples/template/log.12Aug24.tmpl-restart-mix.g++.4 b/examples/template/log.12Aug24.tmpl-restart-mix.g++.4 new file mode 100644 index 0000000000..7e4302c722 --- /dev/null +++ b/examples/template/log.12Aug24.tmpl-restart-mix.g++.4 @@ -0,0 +1,296 @@ +LAMMPS (27 Jun 2024) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# demo for atom style template simulating a cyclohexane methane mixture +# part 3: continuing from restart file + +# run the first part and write out restart +include in.template-mix +# demo for atom style template simulating a cyclohexane methane mixture +# part 1: creating system with create_atoms + +units real +boundary p p p +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +atom_style template cychex + +pair_style lj/cut 12.0 +pair_modify mix geometric tail yes +bond_style harmonic +angle_style harmonic +dihedral_style harmonic + +lattice sc 6.0 +Lattice spacing in x,y,z = 6 6 6 +variable boxlen index 4.0 +region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice +region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice +create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 +Created orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 2 by 2 MPI processor grid + +create_atoms 0 box mol cychex 734594 +Created 3072 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.001 seconds +create_atoms 2 random 800 495437 box +Created 800 atoms + using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) + create_atoms CPU = 0.000 seconds + +mass 1 14.027 +mass 2 16.043 + +pair_coeff 1 1 0.1180 3.905 +pair_coeff 2 2 0.2940 3.730 + +bond_coeff 1 260.00 1.5260 +angle_coeff 1 63.0 112.40 +dihedral_coeff 1 2.0 1 3 + +thermo 100 +minimize 0.001 0.001 500 1000 +Generated 1 of 1 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 = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17 + 100 0 -3410.6986 572.28283 -2838.4158 14603.831 + 200 0 -6109.2306 483.67771 -5625.5529 5069.1821 + 204 0 -6137.0238 483.1464 -5653.8774 4952.4083 +Loop time of 0.719475 on 4 procs for 204 steps with 3872 atoms + +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + 7.54300441078755e+16 -5648.75822666276 -5653.87742467986 + Force two-norm initial, final = 8.7430661e+18 74.636836 + Force max component initial, final = 4.1468626e+18 8.680078 + Final line search alpha, max atom move = 0.0032186724 0.027938327 + Iterations, force evaluations = 204 328 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.59281 | 0.6027 | 0.60956 | 0.8 | 83.77 +Bond | 0.018776 | 0.020785 | 0.026388 | 2.2 | 2.89 +Neigh | 0.054209 | 0.054242 | 0.054273 | 0.0 | 7.54 +Comm | 0.018189 | 0.03064 | 0.042206 | 4.9 | 4.26 +Output | 3.3034e-05 | 3.5624e-05 | 4.3263e-05 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.01107 | | | 1.54 + +Nlocal: 968 ave 980 max 954 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 6630 ave 6644 max 6616 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 193550 ave 195957 max 191376 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 774200 +Ave neighs/atom = 199.94835 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 14 +Dangerous builds = 0 +reset_timestep 0 + +velocity all create 100.0 6234235 +fix 1 all nvt temp 100.0 300.0 1.0 +# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu +run 2500 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 4.22 | 4.507 | 4.603 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 100 -6137.0238 483.1464 -4500.0059 5429.3515 + 100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922 + 200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576 + 300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841 + 400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7 + 500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519 + 600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312 + 700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062 + 800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319 + 900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218 + 1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317 + 1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434 + 1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625 + 1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169 + 1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496 + 1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052 + 1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28 + 1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096 + 1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864 + 1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513 + 2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674 + 2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49 + 2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961 + 2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853 + 2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501 + 2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135 +Loop time of 4.32742 on 4 procs for 2500 steps with 3872 atoms + +Performance: 49.914 ns/day, 0.481 hours/ns, 577.711 timesteps/s, 2.237 Matom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.7864 | 3.836 | 3.8948 | 2.2 | 88.64 +Bond | 0.13058 | 0.13362 | 0.13735 | 0.8 | 3.09 +Neigh | 0.13597 | 0.13601 | 0.13605 | 0.0 | 3.14 +Comm | 0.12304 | 0.18542 | 0.23763 | 10.5 | 4.28 +Output | 0.00033524 | 0.00036705 | 0.00045513 | 0.0 | 0.01 +Modify | 0.027504 | 0.027917 | 0.028571 | 0.3 | 0.65 +Other | | 0.008118 | | | 0.19 + +Nlocal: 968 ave 986 max 944 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 6379.75 ave 6407 max 6352 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 192584 ave 196718 max 188693 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 770338 +Ave neighs/atom = 198.95093 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 34 +Dangerous builds = 0 +#write_data template-mix.data +#write_restart template-mix.restart +write_restart template-mix.restart +System init for write_restart ... +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule + +# now restart +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +molecule cychex cyclohexane.mol +Read molecule template cychex: +LAMMPS molecule file. Cyclohexane(UA) + 1 molecules + 0 fragments + 6 atoms with max type 1 + 6 bonds with max type 1 + 6 angles with max type 1 + 6 dihedrals with max type 1 + 0 impropers with max type 0 +read_restart template-mix.restart +Reading restart file ... + restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024 + restoring atom style template from restart + orthogonal box = (-24 -24 -24) to (24 24 24) + 1 by 2 by 2 MPI processor grid + restoring pair style lj/cut from restart + restoring bond style harmonic from restart + restoring angle style harmonic from restart + restoring dihedral style harmonic from restart + 3872 atoms + 3072 template bonds + 3072 template angles + 3072 template dihedrals + read_restart CPU = 0.001 seconds + +thermo 100 + +fix 1 all nvt temp 300.0 300.0 1.0 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu +run 2000 +Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule +All restart file global fix info was re-assigned +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.192 | 4.288 | 4.574 Mbytes + Step Temp E_pair E_mol TotEng Press + 2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135 + 2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533 + 2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127 + 2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494 + 2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3 + 3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459 + 3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057 + 3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933 + 3300 297.45744 -4923.6217 1700.537 209.19205 8189.571 + 3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119 + 3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067 + 3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481 + 3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479 + 3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521 + 3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37 + 4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386 + 4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733 + 4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158 + 4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862 + 4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975 + 4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294 +Loop time of 3.5798 on 4 procs for 2000 steps with 3872 atoms + +Performance: 48.271 ns/day, 0.497 hours/ns, 558.691 timesteps/s, 2.163 Matom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0514 | 3.1162 | 3.2058 | 3.3 | 87.05 +Bond | 0.10377 | 0.10776 | 0.11194 | 1.0 | 3.01 +Neigh | 0.14121 | 0.14125 | 0.1413 | 0.0 | 3.95 +Comm | 0.092144 | 0.18542 | 0.25437 | 14.1 | 5.18 +Output | 0.00025632 | 0.00028151 | 0.00035298 | 0.0 | 0.01 +Modify | 0.02193 | 0.022227 | 0.022584 | 0.2 | 0.62 +Other | | 0.006618 | | | 0.18 + +Nlocal: 968 ave 984 max 948 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 6349.5 ave 6370 max 6330 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 192457 ave 196654 max 187154 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 769828 +Ave neighs/atom = 198.81921 +Ave special neighs/atom = 3.9669421 +Neighbor list builds = 35 +Dangerous builds = 0 + +# clean up +shell rm template-mix.restart +Total wall time: 0:00:08 diff --git a/examples/template/log.22Oct20.mol-restart-mix.g++.1 b/examples/template/log.22Oct20.mol-restart-mix.g++.1 deleted file mode 100644 index 2d5120f678..0000000000 --- a/examples/template/log.22Oct20.mol-restart-mix.g++.1 +++ /dev/null @@ -1,106 +0,0 @@ -LAMMPS (22 Oct 2020) - using 1 OpenMP thread(s) per MPI task -# demo for atom style template simulating a cyclohexane methane mixture -# part 3: continuing from restart file - -molecule cychex cyclohexane.mol -Read molecule template cychex: - 1 molecules - 6 atoms with max type 1 - 6 bonds with max type 1 - 6 angles with max type 1 - 6 dihedrals with max type 1 - 0 impropers with max type 0 -read_restart molecular-mix.restart -Reading restart file ... - restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020 - restoring atom style molecular from restart - orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000) - 1 by 1 by 1 MPI processor grid - restoring pair style lj/cut from restart - restoring bond style harmonic from restart - restoring angle style harmonic from restart - restoring dihedral style harmonic from restart - 3872 atoms - 3072 bonds - 3072 angles - 3072 dihedrals -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0.0 0.0 0.0 - special bond factors coul: 0.0 0.0 0.0 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 5 = max # of special neighbors - special bonds CPU = 0.002 seconds - read_restart CPU = 0.008 seconds - -thermo 100 - -fix 1 all nvt temp 300.0 300.0 1.0 -# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu -run 2000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 10.74 | 10.74 | 10.74 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 297.79426 -4928.7403 1686.5107 193.93377 11481.089 - 100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304 - 200 296.49886 -4884.3039 1747.4798 284.39198 11537.322 - 300 295.24937 -4850.2788 1642.4584 198.97822 9160.666 - 400 297.73321 -4952.9967 1660.6439 143.10604 10751.859 - 500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826 - 600 299.50756 -4999.965 1588.0327 44.000269 9233.8621 - 700 295.64728 -4958.2253 1646.2011 99.365838 11089.418 - 800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685 - 900 300.80754 -5033.4853 1727.4591 164.90648 11497.526 - 1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551 - 1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28 - 1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201 - 1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762 - 1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178 - 1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337 - 1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415 - 1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882 - 1800 301.9386 -5068.1221 1755.577 171.43863 11229.315 - 1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348 - 2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209 -Loop time of 15.5879 on 1 procs for 2000 steps with 3872 atoms - -Performance: 11.086 ns/day, 2.165 hours/ns, 128.305 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 | 14.116 | 14.116 | 14.116 | 0.0 | 90.56 -Bond | 0.58742 | 0.58742 | 0.58742 | 0.0 | 3.77 -Neigh | 0.68543 | 0.68543 | 0.68543 | 0.0 | 4.40 -Comm | 0.082574 | 0.082574 | 0.082574 | 0.0 | 0.53 -Output | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.00 -Modify | 0.078446 | 0.078446 | 0.078446 | 0.0 | 0.50 -Other | | 0.03761 | | | 0.24 - -Nlocal: 3872.00 ave 3872 max 3872 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11633.0 ave 11633 max 11633 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 770365.0 ave 770365 max 770365 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 770365 -Ave neighs/atom = 198.95790 -Ave special neighs/atom = 3.9669421 -Neighbor list builds = 35 -Dangerous builds = 0 -Total wall time: 0:00:15 diff --git a/examples/template/log.22Oct20.mol-restart-mix.g++.4 b/examples/template/log.22Oct20.mol-restart-mix.g++.4 deleted file mode 100644 index 1b900d588a..0000000000 --- a/examples/template/log.22Oct20.mol-restart-mix.g++.4 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (22 Oct 2020) - using 1 OpenMP thread(s) per MPI task -# demo for atom style template simulating a cyclohexane methane mixture -# part 3: continuing from restart file - -molecule cychex cyclohexane.mol -Read molecule template cychex: - 1 molecules - 6 atoms with max type 1 - 6 bonds with max type 1 - 6 angles with max type 1 - 6 dihedrals with max type 1 - 0 impropers with max type 0 -read_restart molecular-mix.restart -Reading restart file ... - restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020 -WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:697) - restoring atom style molecular from restart - orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000) - 1 by 2 by 2 MPI processor grid - restoring pair style lj/cut from restart - restoring bond style harmonic from restart - restoring angle style harmonic from restart - restoring dihedral style harmonic from restart - 3872 atoms - 3072 bonds - 3072 angles - 3072 dihedrals -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0.0 0.0 0.0 - special bond factors coul: 0.0 0.0 0.0 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 5 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_restart CPU = 0.031 seconds - -thermo 100 - -fix 1 all nvt temp 300.0 300.0 1.0 -# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu -run 2000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 8.101 | 8.197 | 8.483 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 297.79426 -4928.7403 1686.5107 193.93377 11481.089 - 100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303 - 200 301.9265 -4884.8594 1745.0359 344.02042 11561.79 - 300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245 - 400 302 -4951.4895 1664.5419 197.74463 10784.638 - 500 299.17946 -4983.7996 1615.0068 83.354011 9578.745 - 600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926 - 700 300.90925 -4959.9309 1653.6347 165.81003 11121.514 - 800 293.14833 -4895.5912 1707.8754 194.83943 8397.927 - 900 299.0508 -5032.8395 1726.0885 143.91128 11478.847 - 1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738 - 1100 301.13534 -5004.2113 1761.645 232.14877 11246.198 - 1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178 - 1300 300.79377 -5011.7826 1642.093 101.08422 10390.705 - 1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88 - 1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487 - 1600 298.68972 -4962.1273 1747.402 231.77054 10941.114 - 1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312 - 1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02 - 1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102 - 2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704 -Loop time of 5.2142 on 4 procs for 2000 steps with 3872 atoms - -Performance: 33.140 ns/day, 0.724 hours/ns, 383.568 timesteps/s -94.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.5706 | 3.6724 | 3.7809 | 4.9 | 70.43 -Bond | 0.14654 | 0.1524 | 0.15708 | 1.2 | 2.92 -Neigh | 0.18217 | 0.1822 | 0.18221 | 0.0 | 3.49 -Comm | 0.74346 | 0.8715 | 0.9808 | 10.9 | 16.71 -Output | 0.00034776 | 0.00084716 | 0.0023413 | 0.0 | 0.02 -Modify | 0.12457 | 0.18985 | 0.31013 | 17.4 | 3.64 -Other | | 0.145 | | | 2.78 - -Nlocal: 968.000 ave 979 max 948 min -Histogram: 1 0 0 0 0 0 0 1 1 1 -Nghost: 6321.25 ave 6336 max 6309 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 192540.0 ave 195406 max 187182 min -Histogram: 1 0 0 0 0 0 1 0 0 2 - -Total # of neighbors = 770161 -Ave neighs/atom = 198.90522 -Ave special neighs/atom = 3.9669421 -Neighbor list builds = 35 -Dangerous builds = 0 -Total wall time: 0:00:05 diff --git a/examples/template/log.22Oct20.tmpl-restart-mix.g++.1 b/examples/template/log.22Oct20.tmpl-restart-mix.g++.1 deleted file mode 100644 index 3c28834098..0000000000 --- a/examples/template/log.22Oct20.tmpl-restart-mix.g++.1 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (22 Oct 2020) - using 1 OpenMP thread(s) per MPI task -# demo for atom style template simulating a cyclohexane methane mixture -# part 3: continuing from restart file - -molecule cychex cyclohexane.mol -Read molecule template cychex: - 1 molecules - 6 atoms with max type 1 - 6 bonds with max type 1 - 6 angles with max type 1 - 6 dihedrals with max type 1 - 0 impropers with max type 0 -read_restart template-mix.restart -Reading restart file ... - restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020 -WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697) - restoring atom style template from restart - orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000) - 1 by 1 by 1 MPI processor grid - restoring pair style lj/cut from restart - restoring bond style harmonic from restart - restoring angle style harmonic from restart - restoring dihedral style harmonic from restart - 3872 atoms - 3072 template bonds - 3072 template angles - 3072 template dihedrals - read_restart CPU = 0.002 seconds - -thermo 100 - -fix 1 all nvt temp 300.0 300.0 1.0 -Resetting global fix info from restart file: - fix style: nvt, fix ID: 1 -# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu -run 2000 -All restart file global fix info was re-assigned -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 6.879 | 6.879 | 6.879 Mbytes -Step Temp E_pair E_mol TotEng Press - 2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089 - 2600 303.69861 -4872.1658 1620.5986 252.72467 8824.1501 - 2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748 - 2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133 - 2900 302.323 -4949.4247 1661.0637 200.05824 10788.039 - 3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027 - 3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096 - 3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25 - 3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758 - 3400 308.43113 -5035.583 1732.7837 256.09989 11520.651 - 3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351 - 3600 294.00064 -5011.409 1768.0298 149.01058 11257.53 - 3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281 - 3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396 - 3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891 - 4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067 - 4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757 - 4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093 - 4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023 - 4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256 - 4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338 -Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms - -Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 13.88 | 13.88 | 13.88 | 0.0 | 90.40 -Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78 -Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53 -Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54 -Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00 -Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51 -Other | | 0.03687 | | | 0.24 - -Nlocal: 3872.00 ave 3872 max 3872 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11670.0 ave 11670 max 11670 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 770032.0 ave 770032 max 770032 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 770032 -Ave neighs/atom = 198.87190 -Ave special neighs/atom = 3.9669421 -Neighbor list builds = 35 -Dangerous builds = 0 -Total wall time: 0:00:15 diff --git a/examples/template/log.22Oct20.tmpl-restart-mix.g++.4 b/examples/template/log.22Oct20.tmpl-restart-mix.g++.4 deleted file mode 100644 index 078e7562dc..0000000000 --- a/examples/template/log.22Oct20.tmpl-restart-mix.g++.4 +++ /dev/null @@ -1,101 +0,0 @@ -LAMMPS (22 Oct 2020) - using 1 OpenMP thread(s) per MPI task -# demo for atom style template simulating a cyclohexane methane mixture -# part 3: continuing from restart file - -molecule cychex cyclohexane.mol -Read molecule template cychex: - 1 molecules - 6 atoms with max type 1 - 6 bonds with max type 1 - 6 angles with max type 1 - 6 dihedrals with max type 1 - 0 impropers with max type 0 -read_restart template-mix.restart -Reading restart file ... - restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020 - restoring atom style template from restart - orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000) - 1 by 2 by 2 MPI processor grid - restoring pair style lj/cut from restart - restoring bond style harmonic from restart - restoring angle style harmonic from restart - restoring dihedral style harmonic from restart - 3872 atoms - 3072 template bonds - 3072 template angles - 3072 template dihedrals - read_restart CPU = 0.006 seconds - -thermo 100 - -fix 1 all nvt temp 300.0 300.0 1.0 -Resetting global fix info from restart file: - fix style: nvt, fix ID: 1 -# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu -run 2000 -All restart file global fix info was re-assigned -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 4.193 | 4.289 | 4.575 Mbytes -Step Temp E_pair E_mol TotEng Press - 2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089 - 2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501 - 2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482 - 2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261 - 2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69 - 3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074 - 3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502 - 3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923 - 3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992 - 3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101 - 3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685 - 3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938 - 3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666 - 3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208 - 3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557 - 4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379 - 4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056 - 4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605 - 4300 300.50984 -5082.4128 1742.354 127.43881 11003.298 - 4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004 - 4500 302.62639 -5033.3284 1753.488 212.07956 11150.514 -Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms - -Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 timesteps/s -98.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50 -Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49 -Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04 -Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57 -Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02 -Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96 -Other | | 0.01937 | | | 0.44 - -Nlocal: 968.000 ave 977 max 956 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Nghost: 6322.75 ave 6345 max 6308 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 192555.0 ave 195249 max 188636 min -Histogram: 1 0 0 0 0 1 0 0 1 1 - -Total # of neighbors = 770221 -Ave neighs/atom = 198.92071 -Ave special neighs/atom = 3.9669421 -Neighbor list builds = 34 -Dangerous builds = 0 -Total wall time: 0:00:04