Merge branch 'develop' into compute-pace-update
This commit is contained in:
Axel Kohlmeyer
@ -2,15 +2,15 @@
|
||||
dimension 2
|
||||
boundary p f p
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
units lj
|
||||
atom_style bond
|
||||
atom_modify sort 0 1.
|
||||
bond_style harmonic
|
||||
pair_style none
|
||||
communicate single cutoff 2.0
|
||||
comm_modify cutoff 2.0
|
||||
|
||||
# geometry
|
||||
read_data data.pos
|
||||
read_data data.pos
|
||||
|
||||
#
|
||||
neighbor 1.0 nsq
|
||||
@ -43,4 +43,4 @@ thermo_modify temp MyTemp
|
||||
thermo 100
|
||||
|
||||
#
|
||||
run 2000000
|
||||
run 2000000
|
||||
|
||||
@ -0,0 +1,28 @@
|
||||
variable ibead uloop 99 pad
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
boundary p p p
|
||||
pair_style lj/cut 9.5251
|
||||
read_data data.metalnpt${ibead}
|
||||
|
||||
pair_coeff * * 0.00965188 3.4
|
||||
pair_modify shift yes
|
||||
|
||||
mass 1 39.948
|
||||
|
||||
timestep 0.001
|
||||
|
||||
velocity all create 0.0 ${ibead}
|
||||
|
||||
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
|
||||
|
||||
thermo_style custom step temp f_1[*] vol press
|
||||
thermo 100
|
||||
thermo_modify norm no
|
||||
|
||||
# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
|
||||
# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
|
||||
|
||||
run 1000
|
||||
@ -16,7 +16,7 @@ timestep 0.001
|
||||
|
||||
velocity all create 0.0 ${ibead}
|
||||
|
||||
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
|
||||
fix 1 all pimd/langevin method pimd ensemble nvt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 taup 1.0 fixcom no
|
||||
|
||||
thermo_style custom step temp f_1[*] vol press
|
||||
thermo 100
|
||||
@ -1,2 +1,2 @@
|
||||
LAMMPS (28 Mar 2023)
|
||||
LAMMPS (3 Aug 2023)
|
||||
Running on 4 partitions of processors
|
||||
@ -1,5 +1,6 @@
|
||||
LAMMPS (28 Mar 2023)
|
||||
LAMMPS (3 Aug 2023)
|
||||
Processor partition = 0
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable ibead uloop 99 pad
|
||||
|
||||
@ -29,10 +30,10 @@ timestep 0.001
|
||||
velocity all create 0.0 ${ibead}
|
||||
velocity all create 0.0 01
|
||||
|
||||
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
|
||||
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
|
||||
|
||||
Initializing PIMD BZP barostat...
|
||||
The barostat mass is W = 2.3401256650800001e+01
|
||||
The barostat mass is W = 2.3401256650800001e+01
|
||||
|
||||
thermo_style custom step temp f_1[*] vol press
|
||||
thermo 100
|
||||
@ -43,14 +44,13 @@ thermo_modify norm no
|
||||
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
Initializing PI Langevin equation thermostat...
|
||||
Bead ID | omega | tau | c1 | c2
|
||||
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
|
||||
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
|
||||
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
|
||||
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
|
||||
PILE_L thermostat successfully initialized!
|
||||
Bead ID | omega | tau | c1 | c2
|
||||
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
|
||||
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
|
||||
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
|
||||
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
|
||||
PILE_L thermostat successfully initialized!
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
@ -66,31 +66,31 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
|
||||
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
|
||||
0 0 0 0 -7.3046601 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373
|
||||
100 149.95804 3.8573359 0 -7.7921375 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374
|
||||
200 245.00113 6.3021074 0 -8.2639651 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426
|
||||
300 300.57486 7.7316177 0 -8.2986331 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889
|
||||
400 368.08438 9.4681493 0 -8.4800193 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398
|
||||
500 419.32066 10.786088 0 -8.640773 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748
|
||||
600 385.4127 9.9138817 0 -8.4356035 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913
|
||||
700 360.14242 9.2638601 0 -8.2900275 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446
|
||||
800 346.92167 8.923786 0 -8.0694169 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123
|
||||
900 364.39442 9.3732334 0 -8.0415668 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868
|
||||
1000 390.77042 10.051697 0 -8.1948009 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799
|
||||
Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
|
||||
0 0 0 0 -7.3046601 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -164.47373
|
||||
100 149.95804 3.8573359 0 -7.7921375 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 -101.30374
|
||||
200 245.00113 6.3021074 0 -8.2639651 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 112.22426
|
||||
300 300.57486 7.7316177 0 -8.2986331 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 814.45889
|
||||
400 368.08438 9.4681493 0 -8.4800193 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1202.0398
|
||||
500 419.32066 10.786088 0 -8.640773 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 952.59748
|
||||
600 385.4127 9.9138817 0 -8.4356035 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 676.62913
|
||||
700 360.14242 9.2638601 0 -8.2900275 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 456.91446
|
||||
800 346.92167 8.923786 0 -8.0694169 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 454.60123
|
||||
900 364.39442 9.3732334 0 -8.0415668 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 499.75868
|
||||
1000 390.77042 10.051697 0 -8.1948009 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 572.98799
|
||||
Loop time of 0.218442 on 1 procs for 1000 steps with 200 atoms
|
||||
|
||||
Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 395.527 ns/day, 0.061 hours/ns, 4577.865 timesteps/s, 915.573 katom-step/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14541 | 0.14541 | 0.14541 | 0.0 | 58.59
|
||||
Neigh | 0.00099082 | 0.00099082 | 0.00099082 | 0.0 | 0.40
|
||||
Comm | 0.0039966 | 0.0039966 | 0.0039966 | 0.0 | 1.61
|
||||
Output | 0.00016346 | 0.00016346 | 0.00016346 | 0.0 | 0.07
|
||||
Modify | 0.096205 | 0.096205 | 0.096205 | 0.0 | 38.76
|
||||
Other | | 0.001425 | | | 0.57
|
||||
Pair | 0.11918 | 0.11918 | 0.11918 | 0.0 | 54.56
|
||||
Neigh | 0.0010314 | 0.0010314 | 0.0010314 | 0.0 | 0.47
|
||||
Comm | 0.0046197 | 0.0046197 | 0.0046197 | 0.0 | 2.11
|
||||
Output | 0.0001329 | 0.0001329 | 0.0001329 | 0.0 | 0.06
|
||||
Modify | 0.092616 | 0.092616 | 0.092616 | 0.0 | 42.40
|
||||
Other | | 0.0008616 | | | 0.39
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -1,5 +1,6 @@
|
||||
LAMMPS (28 Mar 2023)
|
||||
LAMMPS (3 Aug 2023)
|
||||
Processor partition = 1
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable ibead uloop 99 pad
|
||||
|
||||
@ -17,7 +18,7 @@ Reading data file ...
|
||||
200 atoms
|
||||
reading velocities ...
|
||||
200 velocities
|
||||
read_data CPU = 0.001 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_coeff * * 0.00965188 3.4
|
||||
pair_modify shift yes
|
||||
@ -29,10 +30,7 @@ timestep 0.001
|
||||
velocity all create 0.0 ${ibead}
|
||||
velocity all create 0.0 02
|
||||
|
||||
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
|
||||
|
||||
Initializing PIMD BZP barostat...
|
||||
The barostat mass is W = 2.3401256650800001e+01
|
||||
fix 1 all pimd/langevin method nmpimd ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
|
||||
|
||||
thermo_style custom step temp f_1[*] vol press
|
||||
thermo 100
|
||||
@ -43,15 +41,6 @@ thermo_modify norm no
|
||||
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
Initializing PI Langevin equation thermostat...
|
||||
Bead ID | omega | tau | c1 | c2
|
||||
0 0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
|
||||
1 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
|
||||
2 1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
|
||||
3 8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
|
||||
PILE_L thermostat successfully initialized!
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -66,31 +55,31 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
|
||||
Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] f_1[11] f_1[12] f_1[13] f_1[14] f_1[15] Volume Press
|
||||
0 0 0 11.920908 -7.3063682 4.3005229 -21.877018 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544
|
||||
100 483.61933 12.440028 11.405863 -7.7749671 42.886648 -23.396327 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668
|
||||
200 452.03836 11.627678 11.47094 -8.2534927 41.690123 -22.521598 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476
|
||||
300 470.25997 12.096389 11.739306 -8.3750153 43.180131 -21.755813 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851
|
||||
400 459.46597 11.818737 12.502421 -8.5240576 49.109699 -24.824142 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251
|
||||
500 442.73121 11.388273 11.19396 -8.6488583 45.427771 -22.825143 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119
|
||||
600 493.47034 12.693424 11.91335 -8.4625706 47.783726 -22.456104 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944
|
||||
700 470.04548 12.090871 10.348757 -8.278182 42.626187 -20.571698 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796
|
||||
800 458.04928 11.782296 11.152029 -8.0926613 45.160336 -21.885719 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261
|
||||
900 468.60547 12.05383 10.937315 -8.0319335 45.604542 -21.816625 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377
|
||||
1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 -22.833545 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311
|
||||
Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
|
||||
0 0 0 11.920908 -7.3063682 4.3005229 3.3062167 -8.7249482 2.9571502 -1743.5332 -698.49808 -172.07477 0 0 0.033460054 -0.37064378 4.216227 13402.228 -167.65544
|
||||
100 483.61933 12.440028 11.405863 -7.7749671 42.886648 2.9263894 -1.980193 2.954003 -1888.0547 -1648.7118 -332.0298 -0.099139345 0.11500091 0.033044702 -0.3701566 42.83112 13235.861 606.14668
|
||||
200 452.03836 11.627678 11.47094 -8.2534927 41.690123 3.1450717 -4.273021 2.9600599 -1906.2904 -1609.02 -265.94404 -0.20527926 0.49305948 0.031504957 -0.36829556 41.729191 12619.125 583.5476
|
||||
300 470.25997 12.096389 11.739306 -8.3750153 43.180131 3.336518 -7.7032433 2.9714114 -1968.7685 290.49656 251.72564 -0.21935745 0.56300721 0.029467915 -0.36568855 43.236828 11803.2 1152.6851
|
||||
400 459.46597 11.818737 12.502421 -8.5240576 49.109699 2.5694358 2.9744597 2.9794185 -2335.993 1368.7398 570.03286 -0.028366234 0.0094148316 0.028338146 -0.36416383 49.028096 11350.678 1381.0251
|
||||
500 442.73121 11.388273 11.19396 -8.6488583 45.427771 3.0691855 16.22356 2.9684828 -2113.91 -272.84753 185.53392 0.091614289 0.098205455 0.028793585 -0.36478567 45.368325 11533.101 1000.6119
|
||||
600 493.47034 12.693424 11.91335 -8.4625706 47.783726 3.1614452 6.837575 2.967236 -2023.8117 -918.27943 -2.4106994 0.093360761 0.10198539 0.029589188 -0.36584873 47.725157 11851.775 904.52944
|
||||
700 470.04548 12.090871 10.348757 -8.278182 42.626187 3.6325468 -5.7252564 2.9560528 -1806.9448 -1418.2247 -148.41657 0.075011202 0.065835696 0.030359455 -0.36685105 42.558523 12160.301 715.22796
|
||||
800 458.04928 11.782296 11.152029 -8.0926613 45.160336 3.3040415 -6.7745694 2.9575472 -1894.3641 -1329.3179 -136.42193 0.011114896 0.0014455064 0.030808183 -0.3674233 45.076543 12340.037 678.21261
|
||||
900 468.60547 12.05383 10.937315 -8.0319335 45.604542 3.321315 5.586068 2.9578604 -1890.4653 -1271.1107 -111.89061 -0.020285587 0.0048148677 0.030774258 -0.36738033 45.521594 12326.448 735.24377
|
||||
1000 427.44192 10.99499 11.916587 -8.2229199 45.264242 3.0670849 6.9260573 2.960122 -2007.6188 -1179.7125 -70.907567 -0.062733519 0.046047757 0.030329191 -0.36681215 45.191633 12148.179 637.98311
|
||||
Loop time of 0.218435 on 1 procs for 1000 steps with 200 atoms
|
||||
|
||||
Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 395.541 ns/day, 0.061 hours/ns, 4578.021 timesteps/s, 915.604 katom-step/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14654 | 0.14654 | 0.14654 | 0.0 | 59.04
|
||||
Neigh | 0.00099986 | 0.00099986 | 0.00099986 | 0.0 | 0.40
|
||||
Comm | 0.0041628 | 0.0041628 | 0.0041628 | 0.0 | 1.68
|
||||
Output | 0.00018019 | 0.00018019 | 0.00018019 | 0.0 | 0.07
|
||||
Modify | 0.094878 | 0.094878 | 0.094878 | 0.0 | 38.23
|
||||
Other | | 0.001424 | | | 0.57
|
||||
Pair | 0.11791 | 0.11791 | 0.11791 | 0.0 | 53.98
|
||||
Neigh | 0.0010247 | 0.0010247 | 0.0010247 | 0.0 | 0.47
|
||||
Comm | 0.0035577 | 0.0035577 | 0.0035577 | 0.0 | 1.63
|
||||
Output | 0.00011003 | 0.00011003 | 0.00011003 | 0.0 | 0.05
|
||||
Modify | 0.09496 | 0.09496 | 0.09496 | 0.0 | 43.47
|
||||
Other | | 0.0008711 | | | 0.40
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -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
|
||||
|
||||
|
||||
33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
Normal file
33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
Normal file
@ -0,0 +1,33 @@
|
||||
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
||||
#The default system size may take a while to run you can change to a smaller size
|
||||
variable x_rep equal 5 #x-direction replication number
|
||||
variable y_rep equal 5 #y-direction replication number
|
||||
variable z_rep equal 10 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
||||
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
||||
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
||||
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
include methane_qtb.mod
|
||||
|
||||
|
||||
##Shock compression with quantum nuclear corrections
|
||||
reset_timestep 0
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 20
|
||||
timestep ${delta_t}
|
||||
#restart 1000 restart
|
||||
run 500
|
||||
@ -0,0 +1,280 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
||||
#The default system size may take a while to run you can change to a smaller size
|
||||
variable x_rep equal 5 #x-direction replication number
|
||||
variable y_rep equal 5 #y-direction replication number
|
||||
variable z_rep equal 10 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
||||
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
||||
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
||||
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
include methane_qtb.mod
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 5 ${y_rep} ${z_rep}
|
||||
replicate 5 5 ${z_rep}
|
||||
replicate 5 5 10
|
||||
Replication is creating a 5x5x10 = 250 times larger system...
|
||||
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
1250 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 20
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 500 #500 fs
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 4 4 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 201.3 | 201.3 | 201.3 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15717.706 -110869.31 15741.751
|
||||
20 133.92166 8773.5364 -110569.51 15741.751
|
||||
40 184.43244 -12136.835 -110378.92 15741.751
|
||||
60 203.58164 6527.2188 -110190.9 15741.751
|
||||
80 183.0518 -9667.6163 -110095.24 15741.751
|
||||
100 236.07378 4393.5089 -109905.8 15741.751
|
||||
120 226.94599 -5612.6845 -109708.46 15741.751
|
||||
140 249.34156 988.50573 -109631.88 15741.751
|
||||
160 255.08331 -1397.98 -109469.09 15741.751
|
||||
180 281.64743 -1682.598 -109285.53 15741.751
|
||||
200 303.76929 2594.8345 -109206.84 15741.751
|
||||
220 311.6547 -4566.4307 -109053.21 15741.751
|
||||
240 350.68316 5132.0272 -108918.26 15741.751
|
||||
260 347.11102 -6078.5078 -108828.31 15741.751
|
||||
280 366.56298 6373.2426 -108694.64 15741.751
|
||||
300 393.62524 -6438.9321 -108521.5 15741.751
|
||||
320 403.64821 5946.6873 -108487.83 15741.751
|
||||
340 406.12883 -5053.5592 -108331.25 15741.751
|
||||
360 450.60139 4323.0942 -108185.06 15741.751
|
||||
380 429.46056 -3317.8604 -108146.84 15741.751
|
||||
400 448.11876 3264.6165 -108048.01 15741.751
|
||||
420 485.98657 -3047.3542 -107882.88 15741.751
|
||||
440 463.23761 3088.3325 -107853.09 15741.751
|
||||
460 504.27223 -1966.5888 -107689.56 15741.751
|
||||
480 515.66783 2915.6322 -107550.83 15741.751
|
||||
500 516.26369 -1733.2701 -107498.06 15741.751
|
||||
Loop time of 41.4818 on 1 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.260 ns/day, 92.182 hours/ns, 12.053 timesteps/s, 15.067 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 | 30.707 | 30.707 | 30.707 | 0.0 | 74.03
|
||||
Neigh | 2.2815 | 2.2815 | 2.2815 | 0.0 | 5.50
|
||||
Comm | 0.023963 | 0.023963 | 0.023963 | 0.0 | 0.06
|
||||
Output | 0.00073327 | 0.00073327 | 0.00073327 | 0.0 | 0.00
|
||||
Modify | 8.4653 | 8.4653 | 8.4653 | 0.0 | 20.41
|
||||
Other | | 0.00334 | | | 0.01
|
||||
|
||||
Nlocal: 1250 ave 1250 max 1250 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8444 ave 8444 max 8444 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 601915 ave 601915 max 601915 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 601915
|
||||
Ave neighs/atom = 481.532
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
##Shock compression with quantum nuclear corrections
|
||||
reset_timestep 0
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
|
||||
Shock velocity = 1.22000e-01
|
||||
Artificial viscosity (units of mass/length/time) = 9.00000e-01
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 20
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
#restart 1000 restart
|
||||
run 500
|
||||
Fix QBMSST v0 = 1.57418e+04
|
||||
Fix QBMSST p0 = -3.03801e+03
|
||||
Fix QBMSST e0 = to be -1.07498e+05
|
||||
Fix QBMSST initial strain rate of -1.02043e-04 established by reducing temperature by factor of 1.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 201.4 | 201.4 | 201.4 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 110 -1789.091 -107498.06 15741.751 19.891812 19.891812 39.783624 -3095.1546 1.9543098e-12 -57.148468 0 0
|
||||
20 110 313.41128 -107231.57 15733.908 19.891812 19.891812 39.763803 1026.815 -35.805172 3755.1834 6.0783853e-05 -0.60983919
|
||||
40 110 1248.5771 -107106.23 15726.494 19.891812 19.891812 39.745066 -277.53233 -52.672766 2158.1479 0.00011824041 -1.219383
|
||||
60 110 -944.55947 -107017.75 15719.482 19.891812 19.891812 39.727345 1006.8843 -64.550247 3165.7346 0.00017258388 -1.8286479
|
||||
80 110 2164.646 -107053.82 15712.848 19.891812 19.891812 39.710579 686.99949 -59.728513 2583.9345 0.00022399951 -2.4376489
|
||||
100 110 -332.40946 -106996.04 15706.579 19.891812 19.891812 39.694734 1555.274 -67.472889 3204.6947 0.00027258815 -3.0464001
|
||||
120 110 2556.8172 -106828.33 15700.655 19.891812 19.891812 39.679765 -1406.2492 -90.123866 9.330762 0.00031849257 -3.6549157
|
||||
140 110 -649.1633 -106851.95 15695.029 19.891812 19.891812 39.665545 3704.8784 -86.742267 4898.3193 0.00036209988 -4.2632077
|
||||
160 110 2301.4774 -106787.04 15689.738 19.891812 19.891812 39.652174 -893.31294 -95.690383 91.247096 0.00040310452 -4.8712886
|
||||
180 110 -701.59672 -106639.61 15684.711 19.891812 19.891812 39.63947 3211.2065 -115.27944 3997.3199 0.00044206086 -5.47917
|
||||
200 110 3857.6228 -106696.51 15679.975 19.891812 19.891812 39.627501 -1722.9124 -107.93584 -1123.778 0.00047876602 -6.0868625
|
||||
220 110 -1057.1346 -106590.95 15675.462 19.891812 19.891812 39.616094 3285.0876 -121.80821 3706.0326 0.00051374575 -6.6943761
|
||||
240 110 2748.5299 -106428.9 15671.216 19.891812 19.891812 39.605364 172.15717 -143.78629 425.48974 0.00054664912 -7.3017201
|
||||
260 110 64.99143 -106442.23 15667.188 19.891812 19.891812 39.595183 981.21139 -141.94851 1075.4979 0.00057787086 -7.9089043
|
||||
280 110 1612.9607 -106412.77 15663.362 19.891812 19.891812 39.585514 662.48897 -145.93658 605.73218 0.00060752164 -8.5159364
|
||||
300 110 1435.9566 -106307.06 15659.725 19.891812 19.891812 39.576323 759.46794 -160.13403 559.12791 0.00063570794 -9.1228243
|
||||
320 110 -890.72712 -106332.6 15656.258 19.891812 19.891812 39.56756 234.14376 -156.75496 -103.07714 0.00066257852 -9.7295747
|
||||
340 110 4270.0983 -106252.72 15652.976 19.891812 19.891812 39.559265 5411.2268 -167.0427 4944.423 0.00068801647 -10.336194
|
||||
360 110 -2801.0763 -106105.96 15649.905 19.891812 19.891812 39.551504 -3276.3824 -187.5258 -3864.4213 0.00071181569 -10.942691
|
||||
380 110 5566.9116 -106139.88 15646.926 19.891812 19.891812 39.543977 2737.1121 -182.43141 2031.4929 0.00073489745 -11.549071
|
||||
400 110 -4432.9416 -106074.79 15644.09 19.891812 19.891812 39.536808 -4946.1908 -191.90759 -5763.8068 0.00075688314 -12.155339
|
||||
420 52.599535 5582.8126 -105959.96 15641.311 19.891812 19.891812 39.529786 7869.5301 -206.09135 6942.2136 0.00077841805 -12.761497
|
||||
440 52.599535 -2861.6332 -106017.66 15638.758 19.891812 19.891812 39.523335 -1820.4742 -199.30721 -2848.5648 0.00079820063 -13.367553
|
||||
460 52.599535 3942.7505 -105984.45 15636.294 19.891812 19.891812 39.517106 3327.0393 -203.24794 2201.6559 0.00081729985 -13.973511
|
||||
480 52.599535 419.18442 -105827.32 15633.955 19.891812 19.891812 39.511194 -1910.6109 -224.9021 -3128.3482 0.00083542949 -14.579377
|
||||
500 52.599535 117.60016 -105904.83 15631.655 19.891812 19.891812 39.505383 -603.40365 -214.36236 -1911.9203 0.00085325005 -15.185153
|
||||
Loop time of 41.8312 on 1 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.258 ns/day, 92.958 hours/ns, 11.953 timesteps/s, 14.941 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 | 31.016 | 31.016 | 31.016 | 0.0 | 74.15
|
||||
Neigh | 2.2849 | 2.2849 | 2.2849 | 0.0 | 5.46
|
||||
Comm | 0.020391 | 0.020391 | 0.020391 | 0.0 | 0.05
|
||||
Output | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.00
|
||||
Modify | 8.505 | 8.505 | 8.505 | 0.0 | 20.33
|
||||
Other | | 0.003238 | | | 0.01
|
||||
|
||||
Nlocal: 1250 ave 1250 max 1250 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8489 ave 8489 max 8489 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 606382 ave 606382 max 606382 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 606382
|
||||
Ave neighs/atom = 485.1056
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:01:23
|
||||
@ -0,0 +1,280 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
||||
#The default system size may take a while to run you can change to a smaller size
|
||||
variable x_rep equal 5 #x-direction replication number
|
||||
variable y_rep equal 5 #y-direction replication number
|
||||
variable z_rep equal 10 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
||||
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
||||
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
||||
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
include methane_qtb.mod
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 5 ${y_rep} ${z_rep}
|
||||
replicate 5 5 ${z_rep}
|
||||
replicate 5 5 10
|
||||
Replication is creating a 5x5x10 = 250 times larger system...
|
||||
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
1250 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 20
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 500 #500 fs
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 4 4 7
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 125.2 | 125.3 | 125.4 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15717.706 -110869.31 15741.751
|
||||
20 133.92621 9503.0083 -110548.47 15741.751
|
||||
40 188.1524 -13687.131 -110344.93 15741.751
|
||||
60 205.85747 8421.3906 -110165.58 15741.751
|
||||
80 185.08989 -11337.006 -110026.24 15741.751
|
||||
100 245.36524 5805.0694 -109841.66 15741.751
|
||||
120 218.83661 -7740.8838 -109674.15 15741.751
|
||||
140 254.6075 3396.3936 -109589.89 15741.751
|
||||
160 262.20963 -3574.2575 -109413.81 15741.751
|
||||
180 297.89271 917.40867 -109204.79 15741.751
|
||||
200 315.54026 -371.17448 -109129.45 15741.751
|
||||
220 323.90745 -2811.4367 -108988.12 15741.751
|
||||
240 358.28478 3972.8358 -108848.95 15741.751
|
||||
260 359.12673 -6289.689 -108788.08 15741.751
|
||||
280 376.47656 6851.3186 -108664.07 15741.751
|
||||
300 404.30975 -7805.7238 -108482.75 15741.751
|
||||
320 410.9097 7696.2518 -108421.87 15741.751
|
||||
340 406.19092 -8175.1703 -108311.84 15741.751
|
||||
360 460.37085 7630.6182 -108139.6 15741.751
|
||||
380 413.96355 -7515.2307 -108150.73 15741.751
|
||||
400 452.17428 7148.0954 -108027.39 15741.751
|
||||
420 467.1725 -6662.4113 -107842.71 15741.751
|
||||
440 481.03775 6117.6862 -107759.03 15741.751
|
||||
460 509.03937 -4095.0215 -107648.46 15741.751
|
||||
480 533.22373 2211.9169 -107481.89 15741.751
|
||||
500 517.71195 -214.23969 -107489.48 15741.751
|
||||
Loop time of 22.2711 on 4 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.485 ns/day, 49.491 hours/ns, 22.451 timesteps/s, 28.063 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.689 | 15.195 | 16.732 | 27.7 | 68.23
|
||||
Neigh | 1.5325 | 1.5496 | 1.5658 | 1.0 | 6.96
|
||||
Comm | 0.073366 | 1.6105 | 3.116 | 85.1 | 7.23
|
||||
Output | 0.00052192 | 0.00057642 | 0.00073657 | 0.0 | 0.00
|
||||
Modify | 3.896 | 3.9129 | 3.9306 | 0.6 | 17.57
|
||||
Other | | 0.00241 | | | 0.01
|
||||
|
||||
Nlocal: 312.5 ave 317 max 308 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 4982 ave 4995 max 4967 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 172509 ave 174182 max 170676 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 690037
|
||||
Ave neighs/atom = 552.0296
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
|
||||
##Shock compression with quantum nuclear corrections
|
||||
reset_timestep 0
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
|
||||
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
|
||||
QBMSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
|
||||
Shock velocity = 1.22000e-01
|
||||
Artificial viscosity (units of mass/length/time) = 9.00000e-01
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 20
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
#restart 1000 restart
|
||||
run 500
|
||||
Fix QBMSST v0 = 1.57418e+04
|
||||
Fix QBMSST p0 = -5.88788e+01
|
||||
Fix QBMSST e0 = to be -1.07489e+05
|
||||
Fix QBMSST initial strain rate of -1.02186e-04 established by reducing temperature by factor of 1.00000e-02
|
||||
Per MPI rank memory allocation (min/avg/max) = 126.1 | 126.1 | 126.1 Mbytes
|
||||
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
0 110 -270.21489 -107489.48 15741.751 19.891812 19.891812 39.783624 -118.93551 0 -60.056661 0 0
|
||||
20 110 -2180.5877 -107208.2 15733.847 19.891812 19.891812 39.763648 223.47326 -37.773571 -29.703539 6.1258507e-05 -0.60983836
|
||||
40 110 5004.864 -107109.95 15726.306 19.891812 19.891812 39.744592 3335.6341 -50.920246 2784.77 0.00011969641 -1.2193771
|
||||
60 110 -4549.1199 -106949.22 15719.136 19.891812 19.891812 39.72647 -4461.4212 -72.656651 -5295.3675 0.00017526726 -1.8286321
|
||||
80 110 6695.6833 -106942.12 15712.214 19.891812 19.891812 39.708976 5333.2741 -73.356417 4226.043 0.00022891479 -2.4376137
|
||||
100 110 -5337.7671 -106930.78 15705.644 19.891812 19.891812 39.692373 -2682.4224 -75.129348 -4049.0157 0.00027982924 -3.0463347
|
||||
120 110 6526.5587 -106736.15 15699.334 19.891812 19.891812 39.676424 7038.2375 -100.8809 5422.5046 0.00032873694 -3.6548061
|
||||
140 110 -3284.0472 -106761.36 15693.36 19.891812 19.891812 39.661329 -3999.8116 -97.977739 -5851.3636 0.00037502973 -4.2630401
|
||||
160 110 4792.0537 -106662.24 15687.56 19.891812 19.891812 39.64667 4484.6905 -110.86184 2404.1579 0.00041998006 -4.8710464
|
||||
180 110 -1253.5849 -106532.38 15682.037 19.891812 19.891812 39.632711 -723.78287 -128.58314 -3022.3825 0.00046278801 -5.4788331
|
||||
200 110 3276.2225 -106488.13 15676.725 19.891812 19.891812 39.619286 5117.4749 -134.15782 2609.1518 0.00050395806 -6.0864105
|
||||
220 110 -553.17982 -106421.17 15671.675 19.891812 19.891812 39.606524 -1360.8796 -143.56979 -4068.5641 0.00054309397 -6.6937871
|
||||
240 110 1329.8793 -106309.56 15666.794 19.891812 19.891812 39.594187 775.35326 -158.40869 -2125.0508 0.00058092605 -7.300972
|
||||
260 110 1809.8974 -106360.42 15662.075 19.891812 19.891812 39.582262 3075.2725 -151.39659 -11.4097 0.00061749364 -7.9079706
|
||||
280 110 24.534819 -106310.46 15657.56 19.891812 19.891812 39.570852 1043.8352 -158.25965 -2221.0935 0.00065248454 -8.5147908
|
||||
300 110 2854.2862 -106150.2 15653.217 19.891812 19.891812 39.559874 3727.6844 -179.54521 291.27132 0.00068614803 -9.1214393
|
||||
320 110 -776.61228 -106199.04 15649.041 19.891812 19.891812 39.549322 -1285.3999 -173.42703 -4886.655 0.00071850756 -9.7279234
|
||||
340 110 3778.2238 -106201.03 15644.958 19.891812 19.891812 39.539001 3694.462 -172.6926 -68.017561 0.00075015694 -10.334247
|
||||
360 110 -1505.9413 -106025.15 15641.031 19.891812 19.891812 39.529078 -1491.3768 -196.81063 -5408.8787 0.00078058882 -10.940416
|
||||
380 110 3414.9599 -106071.49 15637.176 19.891812 19.891812 39.519335 4956.6752 -189.93327 886.98409 0.00081046454 -11.546435
|
||||
400 110 -947.2273 -106003.34 15633.49 19.891812 19.891812 39.510021 726.91825 -199.51619 -3488.2795 0.0008390284 -12.152307
|
||||
420 46.681884 1610.2414 -105884.37 15629.905 19.891812 19.891812 39.500961 -1377.8364 -215.72223 -5734.5653 0.00086681188 -12.758039
|
||||
440 46.681884 2290.4653 -105923.83 15626.371 19.891812 19.891812 39.492029 6296.7177 -209.55961 1800.4591 0.00089420243 -13.363632
|
||||
460 46.681884 -2068.0472 -105879.44 15622.969 19.891812 19.891812 39.483432 -5629.8405 -216.88862 -10260.4 0.00092056659 -13.969092
|
||||
480 46.681884 5011.06 -105748.92 15619.556 19.891812 19.891812 39.474805 8649.5097 -232.72756 3884.1859 0.00094702163 -14.574419
|
||||
500 46.681884 -3314.8335 -105829.23 15616.305 19.891812 19.891812 39.46659 -5120.4784 -223.60669 -10014.132 0.00097221364 -15.179618
|
||||
Loop time of 26.5748 on 4 procs for 500 steps with 1250 atoms
|
||||
|
||||
Performance: 0.406 ns/day, 59.055 hours/ns, 18.815 timesteps/s, 23.519 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.259 | 18.109 | 19.999 | 31.1 | 68.14
|
||||
Neigh | 1.8265 | 1.8477 | 1.8638 | 1.0 | 6.95
|
||||
Comm | 0.045073 | 1.9349 | 3.7845 | 95.1 | 7.28
|
||||
Output | 0.0019058 | 0.0019666 | 0.0021202 | 0.2 | 0.01
|
||||
Modify | 4.6619 | 4.6782 | 4.699 | 0.6 | 17.60
|
||||
Other | | 0.002774 | | | 0.01
|
||||
|
||||
Nlocal: 312.5 ave 318 max 307 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 5059 ave 5080 max 5039 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 173854 ave 176807 max 170839 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 695414
|
||||
Ave neighs/atom = 556.3312
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:49
|
||||
@ -1,33 +0,0 @@
|
||||
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
|
||||
#The default system size may take a while to run you can change to a smaller size
|
||||
variable x_rep equal 5 #x-direction replication number
|
||||
variable y_rep equal 5 #y-direction replication number
|
||||
variable z_rep equal 10 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
|
||||
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
|
||||
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
|
||||
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
|
||||
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
|
||||
|
||||
|
||||
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
include methane_qtb.mod
|
||||
|
||||
|
||||
##Shock compression with quantum nuclear corrections
|
||||
reset_timestep 0
|
||||
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
|
||||
fix_modify shock energy yes
|
||||
variable dhug equal f_shock[1]
|
||||
variable dray equal f_shock[2]
|
||||
variable lgr_vel equal f_shock[3]
|
||||
variable lgr_pos equal f_shock[4]
|
||||
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
|
||||
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
|
||||
thermo 100
|
||||
timestep ${delta_t}
|
||||
restart 1000 restart
|
||||
run 5000
|
||||
@ -3,62 +3,62 @@
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 100
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 20
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 2000 #500 fs
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 500 #500 fs
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
|
||||
70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
Normal file
70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
Normal file
@ -0,0 +1,70 @@
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 50
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 1000
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
Normal file
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
Normal file
@ -0,0 +1,174 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 2 ${z_rep}
|
||||
replicate 2 2 2
|
||||
Replication is creating a 2x2x2 = 8 times larger system...
|
||||
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
40 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 50
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 2 2 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 82.45 | 82.45 | 82.45 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15746.508 -3548.1354 503.73603
|
||||
50 191.27715 -7523.7503 -3530.4179 503.73603
|
||||
100 214.09982 12016.892 -3517.4544 503.73603
|
||||
150 317.38272 3098.2254 -3499.5793 503.73603
|
||||
200 338.76362 -4484.9241 -3490.3649 503.73603
|
||||
250 402.05826 3973.0488 -3474.81 503.73603
|
||||
300 340.80076 11193.4 -3470.8029 503.73603
|
||||
350 556.19747 8086.3266 -3451.5937 503.73603
|
||||
400 566.8737 5499.5505 -3439.2335 503.73603
|
||||
450 643.2883 -8270.5736 -3426.0767 503.73603
|
||||
500 613.09742 -12406.229 -3419.8547 503.73603
|
||||
550 669.28891 -9757.601 -3410.7281 503.73603
|
||||
600 600.66922 10407.403 -3408.3776 503.73603
|
||||
650 573.1485 30971.977 -3405.0744 503.73603
|
||||
700 726.22146 29573.798 -3386.3167 503.73603
|
||||
750 777.22659 13265.88 -3378.8462 503.73603
|
||||
800 652.46476 -9231.9331 -3388.7229 503.73603
|
||||
850 679.18414 -19802.254 -3384.6321 503.73603
|
||||
900 711.60594 -18792.396 -3373.2944 503.73603
|
||||
950 865.79013 -2837.6042 -3363.2971 503.73603
|
||||
1000 884.14995 6160.4875 -3360.6295 503.73603
|
||||
Loop time of 7.87 on 1 procs for 1000 steps with 40 atoms
|
||||
|
||||
Performance: 2.745 ns/day, 8.744 hours/ns, 127.065 timesteps/s, 5.083 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.3662 | 6.3662 | 6.3662 | 0.0 | 80.89
|
||||
Neigh | 0.97757 | 0.97757 | 0.97757 | 0.0 | 12.42
|
||||
Comm | 0.013653 | 0.013653 | 0.013653 | 0.0 | 0.17
|
||||
Output | 0.00042319 | 0.00042319 | 0.00042319 | 0.0 | 0.01
|
||||
Modify | 0.50971 | 0.50971 | 0.50971 | 0.0 | 6.48
|
||||
Other | | 0.00248 | | | 0.03
|
||||
|
||||
Nlocal: 40 ave 40 max 40 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2552 ave 2552 max 2552 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 25110 ave 25110 max 25110 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 25110
|
||||
Ave neighs/atom = 627.75
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:07
|
||||
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
Normal file
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
Normal file
@ -0,0 +1,174 @@
|
||||
LAMMPS (21 Nov 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
|
||||
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
|
||||
Created 5 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
replicate 2 ${y_rep} ${z_rep}
|
||||
replicate 2 2 ${z_rep}
|
||||
replicate 2 2 2
|
||||
Replication is creating a 2x2x2 = 8 times larger system...
|
||||
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
40 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reaxff NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 50
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
|
||||
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
|
||||
timestep ${delta_t}
|
||||
timestep 0.25
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
number = {4--5},
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
||||
|
||||
@Article{Aktulga12,
|
||||
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
||||
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
||||
journal = {Parallel Computing},
|
||||
year = 2012,
|
||||
volume = 38,
|
||||
pages = {245--259}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 2 2 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair reaxff, perpetual
|
||||
attributes: half, newton off, ghost
|
||||
pair build: half/bin/newtoff/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) fix qeq/reax, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 72.47 | 72.47 | 72.47 Mbytes
|
||||
Step Temp Press TotEng Volume
|
||||
0 110 -15746.508 -3548.1354 503.73603
|
||||
50 183.74482 -917.59204 -3534.8518 503.73603
|
||||
100 200.96363 16464.403 -3517.1456 503.73603
|
||||
150 255.33305 14801.963 -3507.7299 503.73603
|
||||
200 328.11626 5119.3618 -3498.0388 503.73603
|
||||
250 356.88626 -11306.151 -3485.1746 503.73603
|
||||
300 284.7363 -25276.091 -3479.4732 503.73603
|
||||
350 434.79382 -23326.29 -3471.7491 503.73603
|
||||
400 414.69602 2800.9047 -3465.7225 503.73603
|
||||
450 464.61242 20775.398 -3449.1675 503.73603
|
||||
500 671.43369 15272.581 -3433.9453 503.73603
|
||||
550 534.01157 -8545.4173 -3427.6672 503.73603
|
||||
600 512.69648 -15904.052 -3417.8071 503.73603
|
||||
650 604.62051 -1777.9242 -3419.4324 503.73603
|
||||
700 650.2196 20108.199 -3415.8902 503.73603
|
||||
750 677.45644 21721.335 -3409.1253 503.73603
|
||||
800 707.98295 171.53756 -3413.4048 503.73603
|
||||
850 740.68522 -23846.627 -3384.7024 503.73603
|
||||
900 739.55514 -22742.841 -3377.091 503.73603
|
||||
950 769.44821 -7060.9388 -3389.817 503.73603
|
||||
1000 987.6246 -0.47618437 -3373.9263 503.73603
|
||||
Loop time of 6.80367 on 4 procs for 1000 steps with 40 atoms
|
||||
|
||||
Performance: 3.175 ns/day, 7.560 hours/ns, 146.980 timesteps/s, 5.879 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1801 | 5.3491 | 5.5417 | 6.1 | 78.62
|
||||
Neigh | 0.76934 | 0.77281 | 0.77567 | 0.3 | 11.36
|
||||
Comm | 0.072213 | 0.26492 | 0.4339 | 27.2 | 3.89
|
||||
Output | 0.00032365 | 0.00035547 | 0.00044739 | 0.0 | 0.01
|
||||
Modify | 0.41139 | 0.41424 | 0.4179 | 0.4 | 6.09
|
||||
Other | | 0.00226 | | | 0.03
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1950 ave 1950 max 1950 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6434.5 ave 6447 max 6427 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 25738
|
||||
Ave neighs/atom = 643.45
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
Total wall time: 0:00:06
|
||||
@ -1,70 +0,0 @@
|
||||
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
|
||||
variable x_rep equal 2 #x-direction replication number
|
||||
variable y_rep equal 2 #y-direction replication number
|
||||
variable z_rep equal 2 #z-direction replication number
|
||||
variable temperature equal 110.0 #Target quantum temperature (K in real units)
|
||||
variable delta_t equal 0.25 #MD timestep length (fs in real units)
|
||||
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
|
||||
|
||||
|
||||
## This part defines units, methane structure, and atomic information
|
||||
#General
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
#Lattice
|
||||
lattice custom 1.0 &
|
||||
a1 3.9783624 0 0 &
|
||||
a2 0 3.9783624 0 &
|
||||
a3 0 0 3.9783624 &
|
||||
&
|
||||
basis 0.5 0.5 0.5 &
|
||||
basis 0.663 0.663 0.663 &
|
||||
basis 0.337 0.337 0.663 &
|
||||
basis 0.663 0.337 0.337 &
|
||||
basis 0.337 0.663 0.337
|
||||
|
||||
#Computational Cell
|
||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||
create_box 2 simbox
|
||||
create_atoms 1 box &
|
||||
basis 1 1 &
|
||||
basis 2 2 &
|
||||
basis 3 2 &
|
||||
basis 4 2 &
|
||||
basis 5 2
|
||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||
|
||||
#Atomic Information
|
||||
mass 1 12.011150
|
||||
mass 2 1.007970
|
||||
|
||||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
thermo_style custom step temp press etotal vol
|
||||
thermo 100
|
||||
|
||||
#Colored thermal bath
|
||||
fix scapegoat_qtb all nve #NVE does the time integration
|
||||
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
|
||||
timestep ${delta_t}
|
||||
run 3000 #750 fs
|
||||
unfix methane_qtb
|
||||
unfix scapegoat_qtb
|
||||
Reference in New Issue
Block a user