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add log files for fix pimd/langevin

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This commit is contained in:
Axel Kohlmeyer
2023-06-14 14:53:06 -04:00
parent 82f664acd4
commit 4faebaf4ed
18 changed files with 628 additions and 6 deletions
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0
examples/PACKAGES/pimd/lj/data.metalnpt01 → examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt01
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examples/PACKAGES/pimd/lj/data.metalnpt02 → examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt02
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examples/PACKAGES/pimd/lj/data.metalnpt03 → examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt03
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examples/PACKAGES/pimd/lj/data.metalnpt04 → examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt04
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6
examples/PACKAGES/pimd/lj/in.lmp → examples/PACKAGES/pimd/langevin_metal_units/in.lmp
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@ -20,9 +20,9 @@ fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
thermo_modify norm no
dump dcd all custom 100 ${ibead}.xyz 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"
# 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

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examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ Normal file
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LAMMPS (28 Mar 2023)
Running on 4 partitions of processors

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examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 Normal file
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LAMMPS (28 Mar 2023)
Processor partition = 0
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 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
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 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
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] 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
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
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
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1342 ave 1342 max 1342 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 10325 ave 10325 max 10325 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10325
Ave neighs/atom = 51.625
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

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examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 Normal file
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@ -0,0 +1,106 @@
LAMMPS (28 Mar 2023)
Processor partition = 1
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 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
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 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
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] 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
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
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
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1346 ave 1346 max 1346 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 10328 ave 10328 max 10328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10328
Ave neighs/atom = 51.64
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

106
examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 Normal file
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@ -0,0 +1,106 @@
LAMMPS (28 Mar 2023)
Processor partition = 2
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 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
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 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
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] 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
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
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
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1346 ave 1346 max 1346 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 10313 ave 10313 max 10313 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10313
Ave neighs/atom = 51.565
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (28 Mar 2023)
Processor partition = 3
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 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
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 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
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] 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
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
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
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1346 ave 1346 max 1346 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 10332 ave 10332 max 10332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 10332
Ave neighs/atom = 51.66
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

0
examples/PACKAGES/pimd/lj/run.sh → examples/PACKAGES/pimd/langevin_metal_units/run.sh
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0
examples/PACKAGES/pimd/lj_reduced_units/data.lj01 → examples/PACKAGES/pimd/langevin_reduced_units/data.lj01
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0
examples/PACKAGES/pimd/lj_reduced_units/data.lj02 → examples/PACKAGES/pimd/langevin_reduced_units/data.lj02
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6
examples/PACKAGES/pimd/lj_reduced_units/in.lmp → examples/PACKAGES/pimd/langevin_reduced_units/in.lmp
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@ -18,9 +18,9 @@ fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
thermo_modify norm no
dump dcd all custom 1 ${ibead}.xyz id type x y z 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"
#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z 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

2
examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++ Normal file
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@ -0,0 +1,2 @@
LAMMPS (28 Mar 2023)
Running on 2 partitions of processors

97
examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.0 Normal file
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@ -0,0 +1,97 @@
LAMMPS (28 Mar 2023)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 32 pad
units lj
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 2.8015
read_data data.lj${ibead}
read_data data.lj01
Reading data file ...
orthogonal box = (-3.4945131 -3.4945131 -3.4945131) to (3.4945131 3.4945131 3.4945131)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.001 seconds
pair_coeff * * 1.0 1.0
pair_modify shift yes
mass 1 1.0
timestep 0.00044905847
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L 01
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z 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 0.00000000e+00 1.00000000e+00 9.99775496e-01 2.11886210e-02
1 1.31777963e+02 3.79426112e-03 9.42540858e-01 3.34090903e-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
master list distance cutoff = 3.1015
ghost atom cutoff = 3.1015
binsize = 1.55075, 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) = 3.117 | 3.117 | 3.117 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 0 -875.67022 841866.06 -843041.14 253.30998 382.47517 -1646.2945 -1.9663356 -0.82731217 341.38937 -1.3810467
100 14.815998 4422.5753 0 -534.91485 5336.9805 -409.03828 7790.9787 306.80845 -0.79877176 13.250868 8.3263811 341.38937 12.561531
200 13.762526 4108.114 0 -535.07896 4177.1707 63.548813 -8225.489 308.68383 0.1240984 12.723365 8.0800159 341.38937 12.1757
300 12.566448 3751.0847 0 -493.13907 3999.3337 -31.433066 8675.7059 309.21599 -0.061382631 14.105486 8.6052841 341.38937 12.245009
400 11.843976 3535.4267 0 -515.14836 3784.077 -23.971605 -81.467506 309.02093 -0.046811856 13.638064 8.2470184 341.38937 11.61585
500 11.100239 3313.4214 0 -521.49831 3555.6926 -56.076799 648.94757 309.45936 -0.10950702 12.805213 7.7261445 341.38937 10.991018
600 9.9616183 2973.5431 0 -462.72888 3219.061 41.992567 3171.6576 309.48724 0.082003271 13.759365 8.0375919 341.38937 11.071546
700 9.3388468 2787.6458 0 -501.33865 2901.4483 81.033913 2000.5159 309.02619 0.15824338 12.744135 7.4580508 341.38937 10.129991
800 8.9069211 2658.716 0 -523.1858 2864.6773 -29.435005 2329.1521 308.67617 -0.057480808 11.604242 6.8135454 341.38937 9.3513467
900 8.5046965 2538.6519 0 -543.75602 2597.5491 50.752591 601.47078 308.62547 0.099109884 10.497389 6.2142574 341.38937 8.6389792
1000 8.0725601 2409.6592 0 -571.72872 2533.47 -23.431499 -1267.4683 308.58765 -0.045757135 9.421094 5.5928021 341.38937 7.8375753
Loop time of 0.201181 on 1 procs for 1000 steps with 200 atoms
Performance: 192854.150 tau/day, 4970.640 timesteps/s, 994.128 katom-step/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11949 | 0.11949 | 0.11949 | 0.0 | 59.39
Neigh | 0.011868 | 0.011868 | 0.011868 | 0.0 | 5.90
Comm | 0.0041169 | 0.0041169 | 0.0041169 | 0.0 | 2.05
Output | 0.00011916 | 0.00011916 | 0.00011916 | 0.0 | 0.06
Modify | 0.064249 | 0.064249 | 0.064249 | 0.0 | 31.94
Other | | 0.00134 | | | 0.67
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1117 ave 1117 max 1117 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7492 ave 7492 max 7492 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7492
Ave neighs/atom = 37.46
Neighbor list builds = 55
Dangerous builds = 0
Total wall time: 0:00:00

97
examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.1 Normal file
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@ -0,0 +1,97 @@
LAMMPS (28 Mar 2023)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
variable ibead uloop 32 pad
units lj
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 2.8015
read_data data.lj${ibead}
read_data data.lj02
Reading data file ...
orthogonal box = (-3.4945131 -3.4945131 -3.4945131) to (3.4945131 3.4945131 3.4945131)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.001 seconds
pair_coeff * * 1.0 1.0
pair_modify shift yes
mass 1 1.0
timestep 0.00044905847
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L 02
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no
#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z 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 0.00000000e+00 1.00000000e+00 9.99775496e-01 2.11886210e-02
1 1.31777963e+02 3.79426112e-03 9.42540858e-01 3.34090903e-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
master list distance cutoff = 3.1015
ghost atom cutoff = 3.1015
binsize = 1.55075, 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) = 3.117 | 3.117 | 3.117 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 843646.47 -904.74343 841866.06 -843041.14 253.30998 382.47517 -1646.2945 -1.9663356 -0.82731217 341.38937 -0.58528882
100 3.1994696 955.04167 1014.3663 -520.08788 5336.9805 -409.03828 7790.9787 306.80845 -0.79877176 13.250868 8.3263811 341.38937 5.9400539
200 2.0518234 612.46927 541.77919 -550.11284 4177.1707 63.548813 -8225.489 308.68383 0.1240984 12.723365 8.0800159 341.38937 5.1568532
300 2.0005565 597.16612 636.76107 -492.53916 3999.3337 -31.433066 8675.7059 309.21599 -0.061382631 14.105486 8.6052841 341.38937 6.1061183
400 2.1301774 635.85796 629.2996 -501.35894 3784.077 -23.971605 -81.467506 309.02093 -0.046811856 13.638064 8.2470184 341.38937 6.0950651
500 2.1090509 629.55171 661.4048 -527.18699 3555.6926 -56.076799 648.94757 309.45936 -0.10950702 12.805213 7.7261445 341.38937 5.6641225
600 2.1073653 629.04855 563.33543 -484.13719 3219.061 41.992567 3171.6576 309.48724 0.082003271 13.759365 8.0375919 341.38937 6.2053973
700 1.9719777 588.63535 524.29409 -497.78822 2901.4483 81.033913 2000.5159 309.02619 0.15824338 12.744135 7.4580508 341.38937 5.9107525
800 2.0469949 611.02799 634.76301 -516.64387 2864.6773 -29.435005 2329.1521 308.67617 -0.057480808 11.604242 6.8135454 341.38937 5.445481
900 1.9587942 584.70008 554.57541 -536.62232 2597.5491 50.752591 601.47078 308.62547 0.099109884 10.497389 6.2142574 341.38937 4.9080572
1000 2.0978185 626.19882 628.7595 -559.41879 2533.47 -23.431499 -1267.4683 308.58765 -0.045757135 9.421094 5.5928021 341.38937 4.5477372
Loop time of 0.20118 on 1 procs for 1000 steps with 200 atoms
Performance: 192855.450 tau/day, 4970.674 timesteps/s, 994.135 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12009 | 0.12009 | 0.12009 | 0.0 | 59.69
Neigh | 0.012807 | 0.012807 | 0.012807 | 0.0 | 6.37
Comm | 0.0040331 | 0.0040331 | 0.0040331 | 0.0 | 2.00
Output | 0.00012271 | 0.00012271 | 0.00012271 | 0.0 | 0.06
Modify | 0.062764 | 0.062764 | 0.062764 | 0.0 | 31.20
Other | | 0.001361 | | | 0.68
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1117 ave 1117 max 1117 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7460 ave 7460 max 7460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7460
Ave neighs/atom = 37.3
Neighbor list builds = 57
Dangerous builds = 0
Total wall time: 0:00:00

0
examples/PACKAGES/pimd/lj_reduced_units/run.sh → examples/PACKAGES/pimd/langevin_reduced_units/run.sh
View File