Merge pull request #3976 from akohlmey/collected-small-fixes
Collected small fixes and updates
This commit is contained in:
Axel Kohlmeyer
@ -0,0 +1,28 @@
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variable ibead uloop 99 pad
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units metal
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atom_style atomic
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atom_modify map yes
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boundary p p p
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pair_style lj/cut 9.5251
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read_data data.metalnpt${ibead}
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pair_coeff * * 0.00965188 3.4
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pair_modify shift yes
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mass 1 39.948
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timestep 0.001
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velocity all create 0.0 ${ibead}
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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
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thermo_style custom step temp f_1[*] vol press
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thermo 100
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thermo_modify norm no
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# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
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# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
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run 1000
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@ -16,7 +16,7 @@ timestep 0.001
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velocity all create 0.0 ${ibead}
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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
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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
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thermo_style custom step temp f_1[*] vol press
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thermo 100
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@ -1,2 +1,2 @@
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LAMMPS (28 Mar 2023)
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LAMMPS (3 Aug 2023)
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Running on 4 partitions of processors
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@ -1,5 +1,6 @@
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LAMMPS (28 Mar 2023)
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LAMMPS (3 Aug 2023)
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Processor partition = 0
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 99 pad
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@ -29,10 +30,10 @@ timestep 0.001
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velocity all create 0.0 ${ibead}
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velocity all create 0.0 01
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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
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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
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Initializing PIMD BZP barostat...
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The barostat mass is W = 2.3401256650800001e+01
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The barostat mass is W = 2.3401256650800001e+01
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thermo_style custom step temp f_1[*] vol press
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thermo 100
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@ -43,14 +44,13 @@ thermo_modify norm no
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run 1000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Initializing PI Langevin equation thermostat...
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Bead ID | omega | tau | c1 | c2
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0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
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1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
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2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
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3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
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PILE_L thermostat successfully initialized!
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Bead ID | omega | tau | c1 | c2
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0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
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1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
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2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
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3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
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PILE_L thermostat successfully initialized!
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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@ -66,31 +66,31 @@ Neighbor list info ...
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Loop time of 0.218442 on 1 procs for 1000 steps with 200 atoms
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Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 395.527 ns/day, 0.061 hours/ns, 4577.865 timesteps/s, 915.573 katom-step/s
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98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.14541 | 0.14541 | 0.14541 | 0.0 | 58.59
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Neigh | 0.00099082 | 0.00099082 | 0.00099082 | 0.0 | 0.40
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Comm | 0.0039966 | 0.0039966 | 0.0039966 | 0.0 | 1.61
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Output | 0.00016346 | 0.00016346 | 0.00016346 | 0.0 | 0.07
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Modify | 0.096205 | 0.096205 | 0.096205 | 0.0 | 38.76
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Other | | 0.001425 | | | 0.57
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Pair | 0.11918 | 0.11918 | 0.11918 | 0.0 | 54.56
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Neigh | 0.0010314 | 0.0010314 | 0.0010314 | 0.0 | 0.47
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Comm | 0.0046197 | 0.0046197 | 0.0046197 | 0.0 | 2.11
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Output | 0.0001329 | 0.0001329 | 0.0001329 | 0.0 | 0.06
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Modify | 0.092616 | 0.092616 | 0.092616 | 0.0 | 42.40
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Other | | 0.0008616 | | | 0.39
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Nlocal: 200 ave 200 max 200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,5 +1,6 @@
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LAMMPS (28 Mar 2023)
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LAMMPS (3 Aug 2023)
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Processor partition = 1
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 99 pad
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@ -17,7 +18,7 @@ Reading data file ...
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200 atoms
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reading velocities ...
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200 velocities
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read_data CPU = 0.001 seconds
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read_data CPU = 0.002 seconds
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pair_coeff * * 0.00965188 3.4
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pair_modify shift yes
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@ -29,10 +30,7 @@ timestep 0.001
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velocity all create 0.0 ${ibead}
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velocity all create 0.0 02
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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
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Initializing PIMD BZP barostat...
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The barostat mass is W = 2.3401256650800001e+01
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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
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thermo_style custom step temp f_1[*] vol press
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thermo 100
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@ -43,15 +41,6 @@ thermo_modify norm no
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run 1000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Initializing PI Langevin equation thermostat...
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Bead ID | omega | tau | c1 | c2
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0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
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1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
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2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
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3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
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PILE_L thermostat successfully initialized!
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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@ -66,31 +55,31 @@ Neighbor list info ...
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
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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
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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
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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
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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
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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
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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
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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
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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
|
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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
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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
|
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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
|
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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
|
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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
|
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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
|
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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
|
||||
@ -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
|
||||
@ -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
|
||||
@ -0,0 +1,2 @@
|
||||
LAMMPS (3 Aug 2023)
|
||||
Running on 4 partitions of processors
|
||||
@ -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
|
||||
@ -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
|
||||
@ -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
|
||||
@ -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
|
||||
@ -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
|
||||
|
||||
|
||||
@ -98,7 +98,7 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro
|
||||
|
||||
// creates socket
|
||||
sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
|
||||
if (sockfd < 0) error->one(FLERR, "Error opening socket");
|
||||
if (sockfd < 0) error->one(FLERR, "Error creating socket for fix ipi");
|
||||
|
||||
// makes connection
|
||||
if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0)
|
||||
@ -116,6 +116,7 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro
|
||||
|
||||
// creates the socket
|
||||
sockfd = socket(AF_UNIX, SOCK_STREAM, 0);
|
||||
if (sockfd < 0) error->one(FLERR, "Error creating socket for fix ipi");
|
||||
|
||||
// connects
|
||||
if (connect(sockfd, (struct sockaddr *) &serv_addr, sizeof(serv_addr)) < 0)
|
||||
|
||||
@ -419,10 +419,10 @@ int FixPIMDLangevin::setmask()
|
||||
void FixPIMDLangevin::init()
|
||||
{
|
||||
if (atom->map_style == Atom::MAP_NONE)
|
||||
error->all(FLERR, "fix pimd/langevin requires an atom map, see atom_modify");
|
||||
error->all(FLERR, "Fix pimd/langevin requires an atom map, see atom_modify");
|
||||
|
||||
if (universe->me == 0 && universe->uscreen)
|
||||
fprintf(universe->uscreen, "fix pimd/langevin initializing Path-Integral ...\n");
|
||||
fprintf(universe->uscreen, "Fix pimd/langevin: initializing Path-Integral ...\n");
|
||||
|
||||
// prepare the constants
|
||||
|
||||
@ -446,7 +446,7 @@ void FixPIMDLangevin::init()
|
||||
|
||||
if ((universe->me == 0) && (universe->uscreen))
|
||||
fprintf(universe->uscreen,
|
||||
"fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
|
||||
"Fix pimd/langevin: -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
|
||||
|
||||
if (integrator == OBABO) {
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
@ -904,8 +904,8 @@ void FixPIMDLangevin::baro_init()
|
||||
}
|
||||
Vcoeff = 1.0;
|
||||
std::string out = fmt::format("\nInitializing PIMD {:s} barostat...\n", Barostats[barostat]);
|
||||
out += fmt::format("The barostat mass is W = {:.16e}\n", W);
|
||||
utils::logmesg(lmp, out);
|
||||
out += fmt::format(" The barostat mass is W = {:.16e}\n", W);
|
||||
if (universe->me == 0) utils::logmesg(lmp, out);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -1022,8 +1022,8 @@ void FixPIMDLangevin::langevin_init()
|
||||
c2 = sqrt(1.0 - c1 * c1); // note that c1 and c2 here only works for the centroid mode.
|
||||
|
||||
if (thermostat == PILE_L) {
|
||||
std::string out = "\nInitializing PI Langevin equation thermostat...\n";
|
||||
out += "Bead ID | omega | tau | c1 | c2\n";
|
||||
std::string out = "Initializing PI Langevin equation thermostat...\n";
|
||||
out += " Bead ID | omega | tau | c1 | c2\n";
|
||||
if (method == NMPIMD) {
|
||||
tau_k = new double[np];
|
||||
c1_k = new double[np];
|
||||
@ -1044,18 +1044,18 @@ void FixPIMDLangevin::langevin_init()
|
||||
c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]);
|
||||
}
|
||||
for (int i = 0; i < np; i++) {
|
||||
out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_k[i], tau_k[i],
|
||||
c1_k[i], c2_k[i]);
|
||||
out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i,
|
||||
_omega_k[i], tau_k[i], c1_k[i], c2_k[i]);
|
||||
}
|
||||
} else if (method == PIMD) {
|
||||
for (int i = 0; i < np; i++) {
|
||||
out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_np / sqrt(fmass),
|
||||
tau, c1, c2);
|
||||
out += fmt::format(" {:d} {:.8e} {:.8e} {:.8e} {:.8e}\n", i,
|
||||
_omega_np / sqrt(fmass), tau, c1, c2);
|
||||
}
|
||||
}
|
||||
if (thermostat == PILE_L) out += "PILE_L thermostat successfully initialized!\n";
|
||||
if (thermostat == PILE_L) out += " PILE_L thermostat successfully initialized!\n";
|
||||
out += "\n";
|
||||
utils::logmesg(lmp, out);
|
||||
if (universe->me == 0) utils::logmesg(lmp, out);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -61,7 +61,7 @@ const T& first(const T& value, const Tail&...) {
|
||||
return value;
|
||||
}
|
||||
|
||||
#if defined(__cpp_if_constexpr) && defined(__cpp_return_type_deduction)
|
||||
#if defined(__cpp_if_constexpr) && defined(__cpp_return_type_deduction) && (FMT_CPLUSPLUS >= 201703L) && !FMT_ICC_VERSION
|
||||
template <typename... Args> struct type_list {};
|
||||
|
||||
// Returns a reference to the argument at index N from [first, rest...].
|
||||
|
||||
@ -1499,9 +1499,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
||||
}
|
||||
}
|
||||
|
||||
// equal-style variable is being evaluated
|
||||
// equal-style or immediate variable is being evaluated
|
||||
|
||||
if (style[ivar] == EQUAL) {
|
||||
if ((style[ivar] == EQUAL) || (ivar < 0)) {
|
||||
|
||||
// c_ID = scalar from global scalar
|
||||
|
||||
@ -1767,9 +1767,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
|
||||
}
|
||||
}
|
||||
|
||||
// equal-style variable is being evaluated
|
||||
// equal-style or immediate variable is being evaluated
|
||||
|
||||
if (style[ivar] == EQUAL) {
|
||||
if ((style[ivar] == EQUAL) || (ivar < 0)) {
|
||||
|
||||
// f_ID = scalar from global scalar
|
||||
|
||||
|
||||
@ -282,6 +282,13 @@ TEST_F(VariableTest, AtomicSystem)
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("v_rgsum"), 3.75);
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("v_sum[1]"), 1.25);
|
||||
|
||||
// check handling of immediate variables
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("f_press[1]"), 0.0);
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("c_press"), 0.0);
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("c_press[2]"), 0.0);
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("1.5+3.25"), 4.75);
|
||||
ASSERT_DOUBLE_EQ(variable->compute_equal("-2.5*1.5"), -3.75);
|
||||
|
||||
TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*",
|
||||
command("variable one atom x"););
|
||||
TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*",
|
||||
@ -294,6 +301,8 @@ TEST_F(VariableTest, AtomicSystem)
|
||||
variable->compute_equal("v_self"););
|
||||
TEST_FAILURE(".*ERROR: Variable sum2: Inconsistent lengths in vector-style variable.*",
|
||||
variable->compute_equal("max(v_sum2)"););
|
||||
TEST_FAILURE("ERROR: Mismatched fix in variable formula.*",
|
||||
variable->compute_equal("f_press"););
|
||||
}
|
||||
|
||||
TEST_F(VariableTest, Expressions)
|
||||
|
||||
@ -26,6 +26,7 @@
|
||||
#include "angle.h"
|
||||
#include "atom.h"
|
||||
#include "compute.h"
|
||||
#include "exceptions.h"
|
||||
#include "fmt/format.h"
|
||||
#include "force.h"
|
||||
#include "info.h"
|
||||
@ -59,7 +60,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
delete lmp;
|
||||
}
|
||||
|
||||
LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newton = true)
|
||||
LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton = true)
|
||||
{
|
||||
LAMMPS *lmp;
|
||||
|
||||
@ -90,7 +91,21 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newto
|
||||
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string &line) {
|
||||
lmp->input->one(line);
|
||||
try {
|
||||
lmp->input->one(line);
|
||||
} catch (LAMMPSAbortException &ae) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", ae.what());
|
||||
exit(2);
|
||||
} catch (LAMMPSException &e) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", e.what());
|
||||
exit(3);
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
exit(4);
|
||||
} catch (std::exception &e) {
|
||||
fprintf(stderr, "General exception: %s\n", e.what());
|
||||
exit(5);
|
||||
}
|
||||
};
|
||||
auto parse_input_script = [&](const std::string &filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
|
||||
@ -26,6 +26,7 @@
|
||||
#include "atom.h"
|
||||
#include "bond.h"
|
||||
#include "compute.h"
|
||||
#include "exceptions.h"
|
||||
#include "fmt/format.h"
|
||||
#include "force.h"
|
||||
#include "info.h"
|
||||
@ -59,7 +60,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
delete lmp;
|
||||
}
|
||||
|
||||
LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newton = true)
|
||||
LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton = true)
|
||||
{
|
||||
LAMMPS *lmp;
|
||||
|
||||
@ -90,7 +91,21 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newto
|
||||
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string &line) {
|
||||
lmp->input->one(line);
|
||||
try {
|
||||
lmp->input->one(line);
|
||||
} catch (LAMMPSAbortException &ae) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", ae.what());
|
||||
exit(2);
|
||||
} catch (LAMMPSException &e) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", e.what());
|
||||
exit(3);
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
exit(4);
|
||||
} catch (std::exception &e) {
|
||||
fprintf(stderr, "General exception: %s\n", e.what());
|
||||
exit(5);
|
||||
}
|
||||
};
|
||||
auto parse_input_script = [&](const std::string &filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
|
||||
@ -26,6 +26,7 @@
|
||||
#include "atom.h"
|
||||
#include "compute.h"
|
||||
#include "dihedral.h"
|
||||
#include "exceptions.h"
|
||||
#include "fmt/format.h"
|
||||
#include "force.h"
|
||||
#include "info.h"
|
||||
@ -59,7 +60,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
delete lmp;
|
||||
}
|
||||
|
||||
LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newton = true)
|
||||
LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton = true)
|
||||
{
|
||||
LAMMPS *lmp = new LAMMPS(args, MPI_COMM_WORLD);
|
||||
|
||||
@ -88,7 +89,21 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newto
|
||||
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string &line) {
|
||||
lmp->input->one(line);
|
||||
try {
|
||||
lmp->input->one(line);
|
||||
} catch (LAMMPSAbortException &ae) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", ae.what());
|
||||
exit(2);
|
||||
} catch (LAMMPSException &e) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", e.what());
|
||||
exit(3);
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
exit(4);
|
||||
} catch (std::exception &e) {
|
||||
fprintf(stderr, "General exception: %s\n", e.what());
|
||||
exit(5);
|
||||
}
|
||||
};
|
||||
auto parse_input_script = [&](const std::string &filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
|
||||
@ -25,6 +25,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "compute.h"
|
||||
#include "exceptions.h"
|
||||
#include "fmt/format.h"
|
||||
#include "force.h"
|
||||
#include "improper.h"
|
||||
@ -59,7 +60,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
delete lmp;
|
||||
}
|
||||
|
||||
LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newton = true)
|
||||
LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton = true)
|
||||
{
|
||||
LAMMPS *lmp;
|
||||
|
||||
@ -90,7 +91,21 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newto
|
||||
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string &line) {
|
||||
lmp->input->one(line);
|
||||
try {
|
||||
lmp->input->one(line);
|
||||
} catch (LAMMPSAbortException &ae) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", ae.what());
|
||||
exit(2);
|
||||
} catch (LAMMPSException &e) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", e.what());
|
||||
exit(3);
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
exit(4);
|
||||
} catch (std::exception &e) {
|
||||
fprintf(stderr, "General exception: %s\n", e.what());
|
||||
exit(5);
|
||||
}
|
||||
};
|
||||
auto parse_input_script = [&](const std::string &filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
|
||||
@ -26,6 +26,7 @@
|
||||
#include "atom.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "exceptions.h"
|
||||
#include "force.h"
|
||||
#include "info.h"
|
||||
#include "input.h"
|
||||
@ -61,7 +62,7 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
delete lmp;
|
||||
}
|
||||
|
||||
LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newton = true)
|
||||
LAMMPS *init_lammps(LAMMPS::argv &args, const TestConfig &cfg, const bool newton = true)
|
||||
{
|
||||
LAMMPS *lmp;
|
||||
|
||||
@ -92,8 +93,23 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool newto
|
||||
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string &line) {
|
||||
lmp->input->one(line);
|
||||
try {
|
||||
lmp->input->one(line);
|
||||
} catch (LAMMPSAbortException &ae) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", ae.what());
|
||||
exit(2);
|
||||
} catch (LAMMPSException &e) {
|
||||
fprintf(stderr, "LAMMPS Error: %s\n", e.what());
|
||||
exit(3);
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
exit(4);
|
||||
} catch (std::exception &e) {
|
||||
fprintf(stderr, "General exception: %s\n", e.what());
|
||||
exit(5);
|
||||
}
|
||||
};
|
||||
|
||||
auto parse_input_script = [&](const std::string &filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
};
|
||||
@ -760,7 +776,7 @@ TEST(PairStyle, gpu)
|
||||
"screen", "-nocite", "-sf", "gpu"};
|
||||
LAMMPS::argv args_noneigh = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", "-sf",
|
||||
"gpu", "-pk", "gpu", "0", "neigh", "no"};
|
||||
LAMMPS::argv args = args_neigh;
|
||||
LAMMPS::argv args = args_neigh;
|
||||
|
||||
// cannot use GPU neighbor list with hybrid pair style (yet)
|
||||
if (test_config.pair_style.substr(0, 6) == "hybrid") {
|
||||
|
||||
Reference in New Issue
Block a user