diff --git a/examples/PACKAGES/pimd/langevin_metal_units/in.langevin.metal b/examples/PACKAGES/pimd/langevin_metal_units/in.langevin.metal new file mode 100644 index 0000000000..071b4ad722 --- /dev/null +++ b/examples/PACKAGES/pimd/langevin_metal_units/in.langevin.metal @@ -0,0 +1,28 @@ +variable ibead uloop 99 pad + +units metal +atom_style atomic +atom_modify map yes +boundary p p p +pair_style lj/cut 9.5251 +read_data data.metalnpt${ibead} + +pair_coeff * * 0.00965188 3.4 +pair_modify shift yes + +mass 1 39.948 + +timestep 0.001 + +velocity all create 0.0 ${ibead} + +fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no + +thermo_style custom step temp f_1[*] vol press +thermo 100 +thermo_modify norm no + +# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz +# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f" + +run 1000 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/in.lmp b/examples/PACKAGES/pimd/langevin_metal_units/in.pimd-langevin.metal similarity index 80% rename from examples/PACKAGES/pimd/langevin_metal_units/in.lmp rename to examples/PACKAGES/pimd/langevin_metal_units/in.pimd-langevin.metal index 124063df99..4d1416063c 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/in.lmp +++ b/examples/PACKAGES/pimd/langevin_metal_units/in.pimd-langevin.metal @@ -16,7 +16,7 @@ timestep 0.001 velocity all create 0.0 ${ibead} -fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no +fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no thermo_style custom step temp f_1[*] vol press thermo 100 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++ similarity index 64% rename from examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ rename to examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++ index fa22106766..a05d2d9aa8 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++ @@ -1,2 +1,2 @@ -LAMMPS (28 Mar 2023) +LAMMPS (3 Aug 2023) Running on 4 partitions of processors diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.0 similarity index 70% rename from examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 rename to examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.0 index 00787df8ba..c34bf8e7dd 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.0 @@ -1,5 +1,6 @@ -LAMMPS (28 Mar 2023) +LAMMPS (3 Aug 2023) Processor partition = 0 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task variable ibead uloop 99 pad @@ -29,10 +30,10 @@ timestep 0.001 velocity all create 0.0 ${ibead} velocity all create 0.0 01 -fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no +fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no Initializing PIMD BZP barostat... -The barostat mass is W = 2.3401256650800001e+01 + The barostat mass is W = 2.3401256650800001e+01 thermo_style custom step temp f_1[*] vol press thermo 100 @@ -43,14 +44,13 @@ thermo_modify norm no run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule - Initializing PI Langevin equation thermostat... -Bead ID | omega | tau | c1 | c2 - 0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02 - 1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 - 2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01 - 3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 -PILE_L thermostat successfully initialized! + Bead ID | omega | tau | c1 | c2 + 0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02 + 1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 + 2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01 + 3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 + PILE_L thermostat successfully initialized! Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -66,31 +66,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press - 0 0 0 0 -7.3046601 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373 - 100 149.95804 3.8573359 0 -7.7921375 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374 - 200 245.00113 6.3021074 0 -8.2639651 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426 - 300 300.57486 7.7316177 0 -8.2986331 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889 - 400 368.08438 9.4681493 0 -8.4800193 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398 - 500 419.32066 10.786088 0 -8.640773 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748 - 600 385.4127 9.9138817 0 -8.4356035 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913 - 700 360.14242 9.2638601 0 -8.2900275 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446 - 800 346.92167 8.923786 0 -8.0694169 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123 - 900 364.39442 9.3732334 0 -8.0415668 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868 - 1000 390.77042 10.051697 0 -8.1948009 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799 -Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms + 0 0 0 0 -7.3046601 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373 + 100 149.95804 3.8573359 0 -7.7921375 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374 + 200 245.00113 6.3021074 0 -8.2639651 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426 + 300 300.57486 7.7316177 0 -8.2986331 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889 + 400 368.08438 9.4681493 0 -8.4800193 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398 + 500 419.32066 10.786088 0 -8.640773 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748 + 600 385.4127 9.9138817 0 -8.4356035 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913 + 700 360.14242 9.2638601 0 -8.2900275 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446 + 800 346.92167 8.923786 0 -8.0694169 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123 + 900 364.39442 9.3732334 0 -8.0415668 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868 + 1000 390.77042 10.051697 0 -8.1948009 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799 +Loop time of 0.218442 on 1 procs for 1000 steps with 200 atoms -Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 395.527 ns/day, 0.061 hours/ns, 4577.865 timesteps/s, 915.573 katom-step/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.14541 | 0.14541 | 0.14541 | 0.0 | 58.59 -Neigh | 0.00099082 | 0.00099082 | 0.00099082 | 0.0 | 0.40 -Comm | 0.0039966 | 0.0039966 | 0.0039966 | 0.0 | 1.61 -Output | 0.00016346 | 0.00016346 | 0.00016346 | 0.0 | 0.07 -Modify | 0.096205 | 0.096205 | 0.096205 | 0.0 | 38.76 -Other | | 0.001425 | | | 0.57 +Pair | 0.11918 | 0.11918 | 0.11918 | 0.0 | 54.56 +Neigh | 0.0010314 | 0.0010314 | 0.0010314 | 0.0 | 0.47 +Comm | 0.0046197 | 0.0046197 | 0.0046197 | 0.0 | 2.11 +Output | 0.0001329 | 0.0001329 | 0.0001329 | 0.0 | 0.06 +Modify | 0.092616 | 0.092616 | 0.092616 | 0.0 | 42.40 +Other | | 0.0008616 | | | 0.39 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.1 similarity index 70% rename from examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 rename to examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.1 index 83821cafb7..58f4695d46 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.1 @@ -1,5 +1,6 @@ -LAMMPS (28 Mar 2023) +LAMMPS (3 Aug 2023) Processor partition = 1 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task variable ibead uloop 99 pad @@ -17,7 +18,7 @@ Reading data file ... 200 atoms reading velocities ... 200 velocities - read_data CPU = 0.001 seconds + read_data CPU = 0.002 seconds pair_coeff * * 0.00965188 3.4 pair_modify shift yes @@ -29,10 +30,7 @@ timestep 0.001 velocity all create 0.0 ${ibead} velocity all create 0.0 02 -fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no - -Initializing PIMD BZP barostat... -The barostat mass is W = 2.3401256650800001e+01 +fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no thermo_style custom step temp f_1[*] vol press thermo 100 @@ -43,15 +41,6 @@ thermo_modify norm no run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule - -Initializing PI Langevin equation thermostat... -Bead ID | omega | tau | c1 | c2 - 0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02 - 1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 - 2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01 - 3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 -PILE_L thermostat successfully initialized! - Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 @@ -66,31 +55,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press - 0 0 0 11.920908 -7.3063682 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544 - 100 483.61933 12.440028 11.405863 -7.7749671 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668 - 200 452.03836 11.627678 11.47094 -8.2534927 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476 - 300 470.25997 12.096389 11.739306 -8.3750153 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851 - 400 459.46597 11.818737 12.502421 -8.5240576 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251 - 500 442.73121 11.388273 11.19396 -8.6488583 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119 - 600 493.47034 12.693424 11.91335 -8.4625706 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944 - 700 470.04548 12.090871 10.348757 -8.278182 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796 - 800 458.04928 11.782296 11.152029 -8.0926613 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261 - 900 468.60547 12.05383 10.937315 -8.0319335 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377 - 1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311 -Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms + 0 0 0 11.920908 -7.3063682 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544 + 100 483.61933 12.440028 11.405863 -7.7749671 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668 + 200 452.03836 11.627678 11.47094 -8.2534927 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476 + 300 470.25997 12.096389 11.739306 -8.3750153 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851 + 400 459.46597 11.818737 12.502421 -8.5240576 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251 + 500 442.73121 11.388273 11.19396 -8.6488583 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119 + 600 493.47034 12.693424 11.91335 -8.4625706 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944 + 700 470.04548 12.090871 10.348757 -8.278182 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796 + 800 458.04928 11.782296 11.152029 -8.0926613 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261 + 900 468.60547 12.05383 10.937315 -8.0319335 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377 + 1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311 +Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms -Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 395.541 ns/day, 0.061 hours/ns, 4578.021 timesteps/s, 915.604 katom-step/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.14654 | 0.14654 | 0.14654 | 0.0 | 59.04 -Neigh | 0.00099986 | 0.00099986 | 0.00099986 | 0.0 | 0.40 -Comm | 0.0041628 | 0.0041628 | 0.0041628 | 0.0 | 1.68 -Output | 0.00018019 | 0.00018019 | 0.00018019 | 0.0 | 0.07 -Modify | 0.094878 | 0.094878 | 0.094878 | 0.0 | 38.23 -Other | | 0.001424 | | | 0.57 +Pair | 0.11791 | 0.11791 | 0.11791 | 0.0 | 53.98 +Neigh | 0.0010247 | 0.0010247 | 0.0010247 | 0.0 | 0.47 +Comm | 0.0035577 | 0.0035577 | 0.0035577 | 0.0 | 1.63 +Output | 0.00011003 | 0.00011003 | 0.00011003 | 0.0 | 0.05 +Modify | 0.09496 | 0.09496 | 0.09496 | 0.0 | 43.47 +Other | | 0.0008711 | | | 0.40 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.2 similarity index 70% rename from examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 rename to examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.2 index fd8dd409ae..0b76ce5bbc 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.2 @@ -1,5 +1,6 @@ -LAMMPS (28 Mar 2023) +LAMMPS (3 Aug 2023) Processor partition = 2 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task variable ibead uloop 99 pad @@ -17,7 +18,7 @@ Reading data file ... 200 atoms reading velocities ... 200 velocities - read_data CPU = 0.001 seconds + read_data CPU = 0.002 seconds pair_coeff * * 0.00965188 3.4 pair_modify shift yes @@ -29,10 +30,7 @@ timestep 0.001 velocity all create 0.0 ${ibead} velocity all create 0.0 03 -fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no - -Initializing PIMD BZP barostat... -The barostat mass is W = 2.3401256650800001e+01 +fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no thermo_style custom step temp f_1[*] vol press thermo 100 @@ -43,15 +41,6 @@ thermo_modify norm no run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule - -Initializing PI Langevin equation thermostat... -Bead ID | omega | tau | c1 | c2 - 0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02 - 1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 - 2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01 - 3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 -PILE_L thermostat successfully initialized! - Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 @@ -66,31 +55,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press - 0 0 0 10.862314 -7.320388 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -175.34503 - 100 455.18121 11.708521 11.48472 -7.8033686 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 526.41632 - 200 460.81997 11.853566 10.817157 -8.2276485 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 615.80924 - 300 481.48652 12.385166 10.035423 -8.3866916 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1169.2917 - 400 487.3584 12.536208 11.766522 -8.3643382 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1574.1427 - 500 446.36019 11.48162 12.144202 -8.680266 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 979.68395 - 600 500.3783 12.871115 11.075008 -8.47833 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 912.39361 - 700 435.40634 11.199857 10.923558 -8.3090105 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 617.20857 - 800 446.82793 11.493652 11.599712 -8.0900498 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 652.13243 - 900 448.28506 11.531133 12.130739 -8.0810557 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 674.68073 - 1000 440.94913 11.342433 10.765654 -8.1419484 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 730.67128 -Loop time of 0.248185 on 1 procs for 1000 steps with 200 atoms + 0 0 0 10.862314 -7.320388 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -175.34503 + 100 455.18121 11.708521 11.48472 -7.8033686 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 526.41632 + 200 460.81997 11.853566 10.817157 -8.2276485 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 615.80924 + 300 481.48652 12.385166 10.035423 -8.3866916 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1169.2917 + 400 487.3584 12.536208 11.766522 -8.3643382 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1574.1427 + 500 446.36019 11.48162 12.144202 -8.680266 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 979.68395 + 600 500.3783 12.871115 11.075008 -8.47833 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 912.39361 + 700 435.40634 11.199857 10.923558 -8.3090105 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 617.20857 + 800 446.82793 11.493652 11.599712 -8.0900498 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 652.13243 + 900 448.28506 11.531133 12.130739 -8.0810557 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 674.68073 + 1000 440.94913 11.342433 10.765654 -8.1419484 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 730.67128 +Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms -Performance: 348.128 ns/day, 0.069 hours/ns, 4029.259 timesteps/s, 805.852 katom-step/s -97.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 395.541 ns/day, 0.061 hours/ns, 4578.019 timesteps/s, 915.604 katom-step/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.14702 | 0.14702 | 0.14702 | 0.0 | 59.24 -Neigh | 0.0010003 | 0.0010003 | 0.0010003 | 0.0 | 0.40 -Comm | 0.0039821 | 0.0039821 | 0.0039821 | 0.0 | 1.60 -Output | 0.00023527 | 0.00023527 | 0.00023527 | 0.0 | 0.09 -Modify | 0.094519 | 0.094519 | 0.094519 | 0.0 | 38.08 -Other | | 0.001427 | | | 0.58 +Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 55.30 +Neigh | 0.0010224 | 0.0010224 | 0.0010224 | 0.0 | 0.47 +Comm | 0.0035478 | 0.0035478 | 0.0035478 | 0.0 | 1.62 +Output | 0.00010889 | 0.00010889 | 0.00010889 | 0.0 | 0.05 +Modify | 0.092098 | 0.092098 | 0.092098 | 0.0 | 42.16 +Other | | 0.0008684 | | | 0.40 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.3 similarity index 70% rename from examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3 rename to examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.3 index 423ebb7d63..25578a068c 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3 +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.langevin.metal.g++.3 @@ -1,5 +1,6 @@ -LAMMPS (28 Mar 2023) +LAMMPS (3 Aug 2023) Processor partition = 3 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task variable ibead uloop 99 pad @@ -29,10 +30,7 @@ timestep 0.001 velocity all create 0.0 ${ibead} velocity all create 0.0 04 -fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no - -Initializing PIMD BZP barostat... -The barostat mass is W = 2.3401256650800001e+01 +fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no thermo_style custom step temp f_1[*] vol press thermo 100 @@ -43,15 +41,6 @@ thermo_modify norm no run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule - -Initializing PI Langevin equation thermostat... -Bead ID | omega | tau | c1 | c2 - 0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02 - 1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 - 2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01 - 3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01 -PILE_L thermostat successfully initialized! - Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 @@ -66,31 +55,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press - 0 0 0 10.794425 -7.3457072 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -191.02389 - 100 426.01705 10.958338 12.206372 -7.8040582 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 464.39271 - 200 414.52703 10.662783 11.934129 -8.2331312 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 502.87052 - 300 424.85622 10.928478 11.681713 -8.357621 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1058.1162 - 400 485.80103 12.496148 12.255827 -8.3658975 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1570.2486 - 500 462.99006 11.909386 11.187609 -8.6934698 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1014.2134 - 600 465.24407 11.967366 11.168375 -8.4422887 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 864.12413 - 700 426.16111 10.962044 11.000011 -8.2855512 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 614.76939 - 800 454.53159 11.691811 10.834606 -8.0654281 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 684.85907 - 900 441.72064 11.362278 10.4492 -8.0786302 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 659.68525 - 1000 429.90929 11.058457 11.851933 -8.1578394 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 698.73278 -Loop time of 0.248175 on 1 procs for 1000 steps with 200 atoms + 0 0 0 10.794425 -7.3457072 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -191.02389 + 100 426.01705 10.958338 12.206372 -7.8040582 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 464.39271 + 200 414.52703 10.662783 11.934129 -8.2331312 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 502.87052 + 300 424.85622 10.928478 11.681713 -8.357621 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1058.1162 + 400 485.80103 12.496148 12.255827 -8.3658975 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1570.2486 + 500 462.99006 11.909386 11.187609 -8.6934698 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1014.2134 + 600 465.24407 11.967366 11.168375 -8.4422887 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 864.12413 + 700 426.16111 10.962044 11.000011 -8.2855512 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 614.76939 + 800 454.53159 11.691811 10.834606 -8.0654281 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 684.85907 + 900 441.72064 11.362278 10.4492 -8.0786302 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 659.68525 + 1000 429.90929 11.058457 11.851933 -8.1578394 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 698.73278 +Loop time of 0.218441 on 1 procs for 1000 steps with 200 atoms -Performance: 348.141 ns/day, 0.069 hours/ns, 4029.409 timesteps/s, 805.882 katom-step/s -98.1% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 395.530 ns/day, 0.061 hours/ns, 4577.899 timesteps/s, 915.580 katom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.14919 | 0.14919 | 0.14919 | 0.0 | 60.12 -Neigh | 0.00099112 | 0.00099112 | 0.00099112 | 0.0 | 0.40 -Comm | 0.0040992 | 0.0040992 | 0.0040992 | 0.0 | 1.65 -Output | 0.0001723 | 0.0001723 | 0.0001723 | 0.0 | 0.07 -Modify | 0.092299 | 0.092299 | 0.092299 | 0.0 | 37.19 -Other | | 0.00142 | | | 0.57 +Pair | 0.11655 | 0.11655 | 0.11655 | 0.0 | 53.35 +Neigh | 0.0010236 | 0.0010236 | 0.0010236 | 0.0 | 0.47 +Comm | 0.0035622 | 0.0035622 | 0.0035622 | 0.0 | 1.63 +Output | 0.0001071 | 0.0001071 | 0.0001071 | 0.0 | 0.05 +Modify | 0.096348 | 0.096348 | 0.096348 | 0.0 | 44.11 +Other | | 0.0008537 | | | 0.39 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++ new file mode 100644 index 0000000000..a05d2d9aa8 --- /dev/null +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++ @@ -0,0 +1,2 @@ +LAMMPS (3 Aug 2023) +Running on 4 partitions of processors diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.0 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.0 new file mode 100644 index 0000000000..2d9d049a49 --- /dev/null +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.0 @@ -0,0 +1,103 @@ +LAMMPS (3 Aug 2023) +Processor partition = 0 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 99 pad + +units metal +atom_style atomic +atom_modify map yes +boundary p p p +pair_style lj/cut 9.5251 +read_data data.metalnpt${ibead} +read_data data.metalnpt01 +Reading data file ... + orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 200 atoms + reading velocities ... + 200 velocities + read_data CPU = 0.001 seconds + +pair_coeff * * 0.00965188 3.4 +pair_modify shift yes + +mass 1 39.948 + +timestep 0.001 + +velocity all create 0.0 ${ibead} +velocity all create 0.0 01 + +fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no + +thermo_style custom step temp f_1[*] vol press +thermo 100 +thermo_modify norm no + +# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz +# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f" + +run 1000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Initializing PI Langevin equation thermostat... + Bead ID | omega | tau | c1 | c2 + 0 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02 + 1 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02 + 2 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02 + 3 5.92546167e+01 1.00000000e+00 9.99500125e-01 3.16148726e-02 + PILE_L thermostat successfully initialized! + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5251 + ghost atom cutoff = 11.5251 + binsize = 5.76255, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes + Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press + 0 0 0 8.8893303 -7.3046601 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -164.47373 + 100 248.24141 6.3854564 4.1458616 -7.7546467 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 26.894568 + 200 346.2569 8.9066861 2.6427185 -7.8943744 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 91.225638 + 300 217.65314 5.5986414 7.0223362 -7.788449 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -125.00786 + 400 266.83825 6.8638187 6.2507813 -7.7241546 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 21.104834 + 500 342.40379 8.8075736 5.1959052 -7.7020799 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 208.60351 + 600 280.37754 7.2120867 8.0025846 -7.5954127 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 162.09838 + 700 377.11625 9.700474 6.0049074 -7.5861377 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 389.35575 + 800 378.36221 9.7325237 6.1704761 -7.6170017 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 387.71781 + 900 271.99864 6.9965581 9.037081 -7.4781664 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 266.3664 + 1000 362.4753 9.3238683 8.0266514 -7.4835536 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 433.67079 +Loop time of 0.166656 on 1 procs for 1000 steps with 200 atoms + +Performance: 518.435 ns/day, 0.046 hours/ns, 6000.401 timesteps/s, 1.200 Matom-step/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 | 0.10478 | 0.10478 | 0.10478 | 0.0 | 62.87 +Neigh | 0.00096007 | 0.00096007 | 0.00096007 | 0.0 | 0.58 +Comm | 0.0035065 | 0.0035065 | 0.0035065 | 0.0 | 2.10 +Output | 0.0001037 | 0.0001037 | 0.0001037 | 0.0 | 0.06 +Modify | 0.056454 | 0.056454 | 0.056454 | 0.0 | 33.87 +Other | | 0.0008515 | | | 0.51 + +Nlocal: 200 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9544 ave 9544 max 9544 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9544 +Ave neighs/atom = 47.72 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.1 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.1 new file mode 100644 index 0000000000..9be069b960 --- /dev/null +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.1 @@ -0,0 +1,95 @@ +LAMMPS (3 Aug 2023) +Processor partition = 1 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 99 pad + +units metal +atom_style atomic +atom_modify map yes +boundary p p p +pair_style lj/cut 9.5251 +read_data data.metalnpt${ibead} +read_data data.metalnpt02 +Reading data file ... + orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 200 atoms + reading velocities ... + 200 velocities + read_data CPU = 0.001 seconds + +pair_coeff * * 0.00965188 3.4 +pair_modify shift yes + +mass 1 39.948 + +timestep 0.001 + +velocity all create 0.0 ${ibead} +velocity all create 0.0 02 + +fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no + +thermo_style custom step temp f_1[*] vol press +thermo 100 +thermo_modify norm no + +# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz +# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f" + +run 1000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5251 + ghost atom cutoff = 11.5251 + binsize = 5.76255, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes + Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press + 0 0 0 8.4854554 -7.3063682 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -167.65544 + 100 231.55472 5.9562285 3.9188988 -7.7552569 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 -9.7693407 + 200 366.33366 9.423116 2.3606144 -7.8893287 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 131.05061 + 300 213.74457 5.4981021 6.4391043 -7.7947526 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -136.92734 + 400 273.60832 7.0379636 5.6777233 -7.7709858 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 -0.14681392 + 500 338.99655 8.7199299 5.4335645 -7.7194465 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 190.1705 + 600 298.58126 7.6803369 7.2512164 -7.5741948 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 226.78095 + 700 352.53291 9.0681226 5.4845895 -7.5875298 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 335.39327 + 800 389.70585 10.024313 5.143907 -7.6218106 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 409.36108 + 900 285.3019 7.3387547 7.6228894 -7.5140003 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 266.93105 + 1000 345.35667 8.8835299 6.9652602 -7.5180013 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 368.83819 +Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms + +Performance: 518.420 ns/day, 0.046 hours/ns, 6000.230 timesteps/s, 1.200 Matom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10798 | 0.10798 | 0.10798 | 0.0 | 64.79 +Neigh | 0.00097784 | 0.00097784 | 0.00097784 | 0.0 | 0.59 +Comm | 0.0035304 | 0.0035304 | 0.0035304 | 0.0 | 2.12 +Output | 8.5625e-05 | 8.5625e-05 | 8.5625e-05 | 0.0 | 0.05 +Modify | 0.05322 | 0.05322 | 0.05322 | 0.0 | 31.93 +Other | | 0.0008694 | | | 0.52 + +Nlocal: 200 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9552 ave 9552 max 9552 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9552 +Ave neighs/atom = 47.76 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.2 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.2 new file mode 100644 index 0000000000..f5869bcb03 --- /dev/null +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.2 @@ -0,0 +1,95 @@ +LAMMPS (3 Aug 2023) +Processor partition = 2 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 99 pad + +units metal +atom_style atomic +atom_modify map yes +boundary p p p +pair_style lj/cut 9.5251 +read_data data.metalnpt${ibead} +read_data data.metalnpt03 +Reading data file ... + orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 200 atoms + reading velocities ... + 200 velocities + read_data CPU = 0.001 seconds + +pair_coeff * * 0.00965188 3.4 +pair_modify shift yes + +mass 1 39.948 + +timestep 0.001 + +velocity all create 0.0 ${ibead} +velocity all create 0.0 03 + +fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no + +thermo_style custom step temp f_1[*] vol press +thermo 100 +thermo_modify norm no + +# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz +# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f" + +run 1000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5251 + ghost atom cutoff = 11.5251 + binsize = 5.76255, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes + Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press + 0 0 0 8.4016332 -7.320388 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -175.34503 + 100 235.06814 6.0466034 4.1185166 -7.7660023 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 -7.6578222 + 200 341.9927 8.7969992 2.7767151 -7.9109058 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 69.587081 + 300 206.29873 5.3065745 7.3388955 -7.7440046 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -118.3143 + 400 305.56268 7.8599181 5.7681208 -7.7110516 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 107.63706 + 500 313.47536 8.0634543 5.5086382 -7.7030371 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 145.14899 + 600 258.53638 6.6502715 8.1299001 -7.6530176 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 92.36234 + 700 357.63679 9.1994085 6.539048 -7.6186515 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 329.17147 + 800 391.32883 10.066061 5.7809035 -7.6148923 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 415.13205 + 900 308.61185 7.9383512 8.9544585 -7.4803275 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 341.46691 + 1000 317.70376 8.1722204 7.3013798 -7.4667312 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 352.92253 +Loop time of 0.16666 on 1 procs for 1000 steps with 200 atoms + +Performance: 518.420 ns/day, 0.046 hours/ns, 6000.235 timesteps/s, 1.200 Matom-step/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10509 | 0.10509 | 0.10509 | 0.0 | 63.06 +Neigh | 0.00096379 | 0.00096379 | 0.00096379 | 0.0 | 0.58 +Comm | 0.0035557 | 0.0035557 | 0.0035557 | 0.0 | 2.13 +Output | 7.8072e-05 | 7.8072e-05 | 7.8072e-05 | 0.0 | 0.05 +Modify | 0.05611 | 0.05611 | 0.05611 | 0.0 | 33.67 +Other | | 0.0008601 | | | 0.52 + +Nlocal: 200 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1364 ave 1364 max 1364 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9545 ave 9545 max 9545 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9545 +Ave neighs/atom = 47.725 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.3 b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.3 new file mode 100644 index 0000000000..da0767fe0d --- /dev/null +++ b/examples/PACKAGES/pimd/langevin_metal_units/log.16Nov23.pimd-langevin.metal.g++.3 @@ -0,0 +1,95 @@ +LAMMPS (3 Aug 2023) +Processor partition = 3 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 99 pad + +units metal +atom_style atomic +atom_modify map yes +boundary p p p +pair_style lj/cut 9.5251 +read_data data.metalnpt${ibead} +read_data data.metalnpt04 +Reading data file ... + orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 200 atoms + reading velocities ... + 200 velocities + read_data CPU = 0.001 seconds + +pair_coeff * * 0.00965188 3.4 +pair_modify shift yes + +mass 1 39.948 + +timestep 0.001 + +velocity all create 0.0 ${ibead} +velocity all create 0.0 04 + +fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no + +thermo_style custom step temp f_1[*] vol press +thermo 100 +thermo_modify norm no + +# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz +# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f" + +run 1000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5251 + ghost atom cutoff = 11.5251 + binsize = 5.76255, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes + Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press + 0 0 0 7.8012276 -7.3457072 4.3005229 3.3062167 0 0 -1743.5332 0 0 13402.228 -191.02389 + 100 241.19035 6.2040835 3.9473764 -7.7641902 9.6829291 3.3062167 0 0 -1743.5332 0.00061164884 127.22547 13402.228 3.5720518 + 200 325.21166 8.3653443 2.3529831 -7.9137212 14.016847 3.3062167 0 0 -1743.5332 0.00088274242 177.45909 13402.228 33.184125 + 300 209.19735 5.381135 6.7063061 -7.801056 18.162833 3.3062167 0 0 -1743.5332 0.00054181173 111.54876 13402.228 -154.10632 + 400 280.84513 7.2241142 5.8838331 -7.7320495 21.628032 3.3062167 0 0 -1743.5332 0.0007209203 136.75648 13402.228 45.624285 + 500 367.15726 9.4443014 5.2842629 -7.6643085 25.668758 3.3062167 0 0 -1743.5332 0.00087137898 175.48435 13402.228 283.59979 + 600 294.68254 7.5800508 6.5104311 -7.6234652 28.570788 3.3062167 0 0 -1743.5332 0.00072432598 143.69546 13402.228 183.09906 + 700 356.64514 9.1739005 5.2769462 -7.6204507 30.034627 3.3062167 0 0 -1743.5332 0.00092377441 193.27472 13402.228 334.31754 + 800 360.77353 9.2800941 5.7976264 -7.6946985 31.447502 3.3062167 0 0 -1743.5332 0.00097254954 193.91329 13402.228 299.62001 + 900 291.14241 7.4889889 7.5124196 -7.5102882 32.906719 3.3062167 0 0 -1743.5332 0.00074024142 139.40121 13402.228 277.94834 + 1000 362.48694 9.3241677 6.8711151 -7.4856221 34.914285 3.3062167 0 0 -1743.5332 0.00088800624 185.77114 13402.228 428.98682 +Loop time of 0.166662 on 1 procs for 1000 steps with 200 atoms + +Performance: 518.414 ns/day, 0.046 hours/ns, 6000.167 timesteps/s, 1.200 Matom-step/s +98.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10817 | 0.10817 | 0.10817 | 0.0 | 64.90 +Neigh | 0.00096402 | 0.00096402 | 0.00096402 | 0.0 | 0.58 +Comm | 0.0044991 | 0.0044991 | 0.0044991 | 0.0 | 2.70 +Output | 8.5449e-05 | 8.5449e-05 | 8.5449e-05 | 0.0 | 0.05 +Modify | 0.052066 | 0.052066 | 0.052066 | 0.0 | 31.24 +Other | | 0.00088 | | | 0.53 + +Nlocal: 200 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1368 ave 1368 max 1368 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9541 ave 9541 max 9541 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9541 +Ave neighs/atom = 47.705 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pimd/langevin_metal_units/run.sh b/examples/PACKAGES/pimd/langevin_metal_units/run.sh index 2580ef1a41..8bac9231a3 100644 --- a/examples/PACKAGES/pimd/langevin_metal_units/run.sh +++ b/examples/PACKAGES/pimd/langevin_metal_units/run.sh @@ -1 +1,3 @@ -mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen +mpirun -np 4 $LMP -in in.langevin.metal -p 4x1 -log log.langevin.metal -screen screen +mpirun -np 4 $LMP -in in.pimd-langevin.metal -p 4x1 -log log.pimd-langevin.metal -screen screen +