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Changed the names of fix pimdb/* commands to pimd/*/bosonic; Changed file names accordingly.

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This commit is contained in:
Ofir Blumer
2025-03-11 10:56:07 +02:00
parent 4ed7d95bf9
commit 242f77fce9
17 changed files with 100 additions and 100 deletions
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6
examples/PACKAGES/pimdb/README → examples/PACKAGES/pimd_bosonic/README
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@ -1,11 +1,11 @@
This directory contains example input files for the pimdb/nvt and pimdb/langevin fix commands. This directory contains example input files for the pimd/nvt/bosonic and pimd/langevin/bosonic fix commands.
The demonstrated system is that of 3 non-interacting bosons in a harmonic trap. The demonstrated system is that of 3 non-interacting bosons in a harmonic trap.
The input files initiate a simulation of 100 steps using 4 beads. The expected output log files are included. The input files initiate a simulation of 100 steps using 4 beads. The expected output log files are included.
The input files can be edited to provide a physically meaningful output, by extending the simulations to a few nanoseconds The input files can be edited to provide a physically meaningful output, by extending the simulations to a few nanoseconds
and increasing the number of beads (32 beads should be enough). and increasing the number of beads (32 beads should be enough).
The total energy can be computed by summing the potential energy and either the virial or primitive kinetic energy estimator, and averaging over time. The total energy can be computed by summing the potential energy and either the virial or primitive kinetic energy estimator, and averaging over time.
Notice that for pimdb/langevin the summed value of either kinetic estimator is printed across all log files. Notice that for pimd/langevin/bosonic the summed value of either kinetic estimator is printed across all log files.
It should be taken from a single log file, with all files providing the same output. It should be taken from a single log file, with all files providing the same output.
For pimdb/nvt, one has to sum over the output of all log files. For the potential energy, summing over log files is required for both fix commands. For pimd/nvt/bosonic, one has to sum over the output of all log files. For the potential energy, summing over log files is required for both fix commands.
The obtained energy should be compared to the analytical value of 0.00058031 Hartree. The obtained energy should be compared to the analytical value of 0.00058031 Hartree.

2
examples/PACKAGES/pimdb/harmonic_trap_langevin/in.lmp → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp
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@ -45,7 +45,7 @@ fix harm all spring/self ${k}
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
# Outputs # Outputs
variable prim_kinetic equal f_pimdb[5] variable prim_kinetic equal f_pimdb[5]

22
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.0 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0
View File

@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -84,8 +84,8 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs # Outputs
variable prim_kinetic equal f_pimdb[5] variable prim_kinetic equal f_pimdb[5]
@ -208,20 +208,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
98 9.2042324e-06 1.780703e-05 0.00083221292 98 9.2042324e-06 1.780703e-05 0.00083221292
99 9.5058078e-06 1.8141862e-05 0.00082913227 99 9.5058078e-06 1.8141862e-05 0.00082913227
100 9.8087647e-06 1.8457846e-05 0.00082619877 100 9.8087647e-06 1.8457846e-05 0.00082619877
Loop time of 0.00831106 on 1 procs for 100 steps with 3 atoms Loop time of 0.122922 on 1 procs for 100 steps with 3 atoms
Performance: 519789292.822 fs/day, 0.000 hours/fs, 12032.160 timesteps/s, 36.096 katom-step/s Performance: 35144210.362 fs/day, 0.000 hours/fs, 813.523 timesteps/s, 2.441 katom-step/s
96.4% CPU use with 1 MPI tasks x no OpenMP threads 70.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 4.265e-05 | 4.265e-05 | 4.265e-05 | 0.0 | 0.51 Neigh | 1.1593e-05 | 1.1593e-05 | 1.1593e-05 | 0.0 | 0.01
Comm | 0.00031198 | 0.00031198 | 0.00031198 | 0.0 | 3.75 Comm | 9.2183e-05 | 9.2183e-05 | 9.2183e-05 | 0.0 | 0.07
Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 12.48 Output | 0.023243 | 0.023243 | 0.023243 | 0.0 | 18.91
Modify | 0.0063106 | 0.0063106 | 0.0063106 | 0.0 | 75.93 Modify | 0.099386 | 0.099386 | 0.099386 | 0.0 | 80.85
Other | | 0.000609 | | | 7.33 Other | | 0.0001896 | | | 0.15
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.1 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1
View File

@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -84,8 +84,8 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs # Outputs
variable prim_kinetic equal f_pimdb[5] variable prim_kinetic equal f_pimdb[5]
@ -200,20 +200,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
98 2.5769956e-05 1.780703e-05 0.00083221292 98 2.5769956e-05 1.780703e-05 0.00083221292
99 2.624134e-05 1.8141862e-05 0.00082913227 99 2.624134e-05 1.8141862e-05 0.00082913227
100 2.6731735e-05 1.8457846e-05 0.00082619877 100 2.6731735e-05 1.8457846e-05 0.00082619877
Loop time of 0.00828251 on 1 procs for 100 steps with 3 atoms Loop time of 0.122878 on 1 procs for 100 steps with 3 atoms
Performance: 521580766.419 fs/day, 0.000 hours/fs, 12073.629 timesteps/s, 36.221 katom-step/s Performance: 35156789.883 fs/day, 0.000 hours/fs, 813.815 timesteps/s, 2.441 katom-step/s
88.2% CPU use with 1 MPI tasks x no OpenMP threads 46.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 4.9248e-05 | 4.9248e-05 | 4.9248e-05 | 0.0 | 0.59 Neigh | 1.9787e-05 | 1.9787e-05 | 1.9787e-05 | 0.0 | 0.02
Comm | 0.00027661 | 0.00027661 | 0.00027661 | 0.0 | 3.34 Comm | 9.2033e-05 | 9.2033e-05 | 9.2033e-05 | 0.0 | 0.07
Output | 0.00095948 | 0.00095948 | 0.00095948 | 0.0 | 11.58 Output | 0.0022584 | 0.0022584 | 0.0022584 | 0.0 | 1.84
Modify | 0.0064815 | 0.0064815 | 0.0064815 | 0.0 | 78.26 Modify | 0.12033 | 0.12033 | 0.12033 | 0.0 | 97.93
Other | | 0.0005157 | | | 6.23 Other | | 0.0001755 | | | 0.14
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.2 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2
View File

@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -84,8 +84,8 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs # Outputs
variable prim_kinetic equal f_pimdb[5] variable prim_kinetic equal f_pimdb[5]
@ -200,20 +200,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
98 1.8568337e-05 1.780703e-05 0.00083221292 98 1.8568337e-05 1.780703e-05 0.00083221292
99 1.9188379e-05 1.8141862e-05 0.00082913227 99 1.9188379e-05 1.8141862e-05 0.00082913227
100 1.9789011e-05 1.8457846e-05 0.00082619877 100 1.9789011e-05 1.8457846e-05 0.00082619877
Loop time of 0.00829826 on 1 procs for 100 steps with 3 atoms Loop time of 0.112003 on 1 procs for 100 steps with 3 atoms
Performance: 520591251.874 fs/day, 0.000 hours/fs, 12050.723 timesteps/s, 36.152 katom-step/s Performance: 38570373.396 fs/day, 0.000 hours/fs, 892.833 timesteps/s, 2.678 katom-step/s
79.5% CPU use with 1 MPI tasks x no OpenMP threads 52.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 4.6257e-05 | 4.6257e-05 | 4.6257e-05 | 0.0 | 0.56 Neigh | 1.4356e-05 | 1.4356e-05 | 1.4356e-05 | 0.0 | 0.01
Comm | 0.00029611 | 0.00029611 | 0.00029611 | 0.0 | 3.57 Comm | 9.7936e-05 | 9.7936e-05 | 9.7936e-05 | 0.0 | 0.09
Output | 0.00096988 | 0.00096988 | 0.00096988 | 0.0 | 11.69 Output | 0.0017373 | 0.0017373 | 0.0017373 | 0.0 | 1.55
Modify | 0.0064529 | 0.0064529 | 0.0064529 | 0.0 | 77.76 Modify | 0.10997 | 0.10997 | 0.10997 | 0.0 | 98.19
Other | | 0.0005331 | | | 6.42 Other | | 0.0001804 | | | 0.16
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.3 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3
View File

@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -84,8 +84,8 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs # Outputs
variable prim_kinetic equal f_pimdb[5] variable prim_kinetic equal f_pimdb[5]
@ -200,20 +200,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
98 2.5288512e-05 1.780703e-05 0.00083221292 98 2.5288512e-05 1.780703e-05 0.00083221292
99 2.5384836e-05 1.8141862e-05 0.00082913227 99 2.5384836e-05 1.8141862e-05 0.00082913227
100 2.5401412e-05 1.8457846e-05 0.00082619877 100 2.5401412e-05 1.8457846e-05 0.00082619877
Loop time of 0.00828746 on 1 procs for 100 steps with 3 atoms Loop time of 0.122921 on 1 procs for 100 steps with 3 atoms
Performance: 521269232.663 fs/day, 0.000 hours/fs, 12066.417 timesteps/s, 36.199 katom-step/s Performance: 35144393.915 fs/day, 0.000 hours/fs, 813.528 timesteps/s, 2.441 katom-step/s
97.4% CPU use with 1 MPI tasks x no OpenMP threads 88.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 5.2767e-05 | 5.2767e-05 | 5.2767e-05 | 0.0 | 0.64 Neigh | 1.5885e-05 | 1.5885e-05 | 1.5885e-05 | 0.0 | 0.01
Comm | 0.00029534 | 0.00029534 | 0.00029534 | 0.0 | 3.56 Comm | 9.4707e-05 | 9.4707e-05 | 9.4707e-05 | 0.0 | 0.08
Output | 0.001037 | 0.001037 | 0.001037 | 0.0 | 12.51 Output | 0.0027076 | 0.0027076 | 0.0027076 | 0.0 | 2.20
Modify | 0.0063429 | 0.0063429 | 0.0063429 | 0.0 | 76.54 Modify | 0.11993 | 0.11993 | 0.11993 | 0.0 | 97.57
Other | | 0.0005594 | | | 6.75 Other | | 0.0001738 | | | 0.14
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

0
examples/PACKAGES/pimdb/harmonic_trap_langevin/run.sh → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/run.sh
View File

2
examples/PACKAGES/pimdb/harmonic_trap_nvt/in.lmp → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp
View File

@ -48,7 +48,7 @@ fix harm all spring/self ${k}
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
# Outputs # Outputs
variable virial equal f_pimdb[3] variable virial equal f_pimdb[3]

24
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.0 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0
View File

@ -54,7 +54,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -87,9 +87,9 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4 fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs # Outputs
variable virial equal f_pimdb[3] variable virial equal f_pimdb[3]
@ -207,20 +207,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
98 7.4842314e-06 1.8940408e-06 0.0002348915 98 7.4842314e-06 1.8940408e-06 0.0002348915
99 7.622805e-06 1.9289045e-06 0.00023466684 99 7.622805e-06 1.9289045e-06 0.00023466684
100 7.76221e-06 1.9639756e-06 0.00023444136 100 7.76221e-06 1.9639756e-06 0.00023444136
Loop time of 0.00502911 on 1 procs for 100 steps with 3 atoms Loop time of 0.00940749 on 1 procs for 100 steps with 3 atoms
Performance: 858998737.550 fs/day, 0.000 hours/fs, 19884.230 timesteps/s, 59.653 katom-step/s Performance: 459208566.791 fs/day, 0.000 hours/fs, 10629.828 timesteps/s, 31.889 katom-step/s
80.6% CPU use with 1 MPI tasks x no OpenMP threads 90.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 3.3682e-05 | 3.3682e-05 | 3.3682e-05 | 0.0 | 0.67 Neigh | 8.466e-06 | 8.466e-06 | 8.466e-06 | 0.0 | 0.09
Comm | 0.00029392 | 0.00029392 | 0.00029392 | 0.0 | 5.84 Comm | 7.8365e-05 | 7.8365e-05 | 7.8365e-05 | 0.0 | 0.83
Output | 0.00092846 | 0.00092846 | 0.00092846 | 0.0 | 18.46 Output | 0.0012482 | 0.0012482 | 0.0012482 | 0.0 | 13.27
Modify | 0.0031767 | 0.0031767 | 0.0031767 | 0.0 | 63.17 Modify | 0.0079193 | 0.0079193 | 0.0079193 | 0.0 | 84.18
Other | | 0.0005963 | | | 11.86 Other | | 0.0001532 | | | 1.63
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

24
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.1 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1
View File

@ -54,7 +54,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -87,9 +87,9 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4 fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs # Outputs
variable virial equal f_pimdb[3] variable virial equal f_pimdb[3]
@ -205,20 +205,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
98 7.3002707e-06 1.8531354e-06 0.00024148118 98 7.3002707e-06 1.8531354e-06 0.00024148118
99 7.4315008e-06 1.88617e-06 0.00024137268 99 7.4315008e-06 1.88617e-06 0.00024137268
100 7.563358e-06 1.9193596e-06 0.00024126398 100 7.563358e-06 1.9193596e-06 0.00024126398
Loop time of 0.0050955 on 1 procs for 100 steps with 3 atoms Loop time of 0.00941353 on 1 procs for 100 steps with 3 atoms
Performance: 847807054.814 fs/day, 0.000 hours/fs, 19625.163 timesteps/s, 58.875 katom-step/s Performance: 458913876.206 fs/day, 0.000 hours/fs, 10623.006 timesteps/s, 31.869 katom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 50.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 2.3358e-05 | 2.3358e-05 | 2.3358e-05 | 0.0 | 0.46 Neigh | 8.215e-06 | 8.215e-06 | 8.215e-06 | 0.0 | 0.09
Comm | 0.00022527 | 0.00022527 | 0.00022527 | 0.0 | 4.42 Comm | 7.7692e-05 | 7.7692e-05 | 7.7692e-05 | 0.0 | 0.83
Output | 0.00078435 | 0.00078435 | 0.00078435 | 0.0 | 15.39 Output | 0.0047662 | 0.0047662 | 0.0047662 | 0.0 | 50.63
Modify | 0.0036209 | 0.0036209 | 0.0036209 | 0.0 | 71.06 Modify | 0.004407 | 0.004407 | 0.004407 | 0.0 | 46.82
Other | | 0.0004416 | | | 8.67 Other | | 0.0001545 | | | 1.64
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

24
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.2 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2
View File

@ -54,7 +54,7 @@ create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2 create_atoms 1 single -14 9 2
Created 1 atoms Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500) using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
next a next a
jump SELF loop jump SELF loop
variable x1 equal -15.0+0.5*v_a variable x1 equal -15.0+0.5*v_a
@ -87,9 +87,9 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4 fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs # Outputs
variable virial equal f_pimdb[3] variable virial equal f_pimdb[3]
@ -205,20 +205,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
98 7.1356907e-06 1.7335027e-06 0.0002297417 98 7.1356907e-06 1.7335027e-06 0.0002297417
99 7.2605738e-06 1.7643404e-06 0.00022943234 99 7.2605738e-06 1.7643404e-06 0.00022943234
100 7.3859169e-06 1.7952968e-06 0.00022912226 100 7.3859169e-06 1.7952968e-06 0.00022912226
Loop time of 0.00507947 on 1 procs for 100 steps with 3 atoms Loop time of 0.00941372 on 1 procs for 100 steps with 3 atoms
Performance: 850481762.482 fs/day, 0.000 hours/fs, 19687.078 timesteps/s, 59.061 katom-step/s Performance: 458904516.311 fs/day, 0.000 hours/fs, 10622.790 timesteps/s, 31.868 katom-step/s
98.9% CPU use with 1 MPI tasks x no OpenMP threads 24.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 3.1029e-05 | 3.1029e-05 | 3.1029e-05 | 0.0 | 0.61 Neigh | 8.785e-06 | 8.785e-06 | 8.785e-06 | 0.0 | 0.09
Comm | 0.00027821 | 0.00027821 | 0.00027821 | 0.0 | 5.48 Comm | 7.9921e-05 | 7.9921e-05 | 7.9921e-05 | 0.0 | 0.85
Output | 0.001016 | 0.001016 | 0.001016 | 0.0 | 20.00 Output | 0.0071119 | 0.0071119 | 0.0071119 | 0.0 | 75.55
Modify | 0.0032013 | 0.0032013 | 0.0032013 | 0.0 | 63.02 Modify | 0.0020558 | 0.0020558 | 0.0020558 | 0.0 | 21.84
Other | | 0.0005529 | | | 10.89 Other | | 0.0001572 | | | 1.67
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

22
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.3 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3
View File

@ -87,9 +87,9 @@ fix harm all spring/self 1.215461412e-08
fix_modify harm energy yes fix_modify harm energy yes
# PIMD command # PIMD command
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc} fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4 fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs # Outputs
variable virial equal f_pimdb[3] variable virial equal f_pimdb[3]
@ -205,20 +205,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
98 7.2937187e-06 1.8407787e-06 0.00023702765 98 7.2937187e-06 1.8407787e-06 0.00023702765
99 7.4250201e-06 1.8736806e-06 0.00023685186 99 7.4250201e-06 1.8736806e-06 0.00023685186
100 7.5569619e-06 1.9067398e-06 0.00023667607 100 7.5569619e-06 1.9067398e-06 0.00023667607
Loop time of 0.00510222 on 1 procs for 100 steps with 3 atoms Loop time of 0.00939597 on 1 procs for 100 steps with 3 atoms
Performance: 846690098.292 fs/day, 0.000 hours/fs, 19599.308 timesteps/s, 58.798 katom-step/s Performance: 459771778.655 fs/day, 0.000 hours/fs, 10642.865 timesteps/s, 31.929 katom-step/s
79.1% CPU use with 1 MPI tasks x no OpenMP threads 25.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 1.5273e-05 | 1.5273e-05 | 1.5273e-05 | 0.0 | 0.30 Neigh | 8.404e-06 | 8.404e-06 | 8.404e-06 | 0.0 | 0.09
Comm | 0.00013505 | 0.00013505 | 0.00013505 | 0.0 | 2.65 Comm | 8.6872e-05 | 8.6872e-05 | 8.6872e-05 | 0.0 | 0.92
Output | 0.00046743 | 0.00046743 | 0.00046743 | 0.0 | 9.16 Output | 0.0071309 | 0.0071309 | 0.0071309 | 0.0 | 75.89
Modify | 0.0042111 | 0.0042111 | 0.0042111 | 0.0 | 82.53 Modify | 0.0020085 | 0.0020085 | 0.0020085 | 0.0 | 21.38
Other | | 0.0002734 | | | 5.36 Other | | 0.0001612 | | | 1.72
Nlocal: 3 ave 3 max 3 min Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

0
examples/PACKAGES/pimdb/harmonic_trap_nvt/run.sh → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh
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2
src/REPLICA/fix_pimdb_langevin.cpp → src/REPLICA/fix_pimd_langevin_bosonic.cpp
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@ -22,7 +22,7 @@
Version 1.0 Version 1.0
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_pimdb_langevin.h" #include "fix_pimd_langevin_bosonic.h"
#include "bosonic_exchange.h" #include "bosonic_exchange.h"

2
src/REPLICA/fix_pimdb_langevin.h → src/REPLICA/fix_pimd_langevin_bosonic.h
View File

@ -13,7 +13,7 @@
#ifdef FIX_CLASS #ifdef FIX_CLASS
// clang-format off // clang-format off
FixStyle(pimdb/langevin, FixPIMDBLangevin); FixStyle(pimd/langevin/bosonic, FixPIMDBLangevin);
// clang-format on // clang-format on
#else #else

2
src/REPLICA/fix_pimdb_nvt.cpp → src/REPLICA/fix_pimd_nvt_bosonic.cpp
View File

@ -21,7 +21,7 @@
Version 1.0 Version 1.0
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_pimdb_nvt.h" #include "fix_pimd_nvt_bosonic.h"
#include "bosonic_exchange.h" #include "bosonic_exchange.h"

2
src/REPLICA/fix_pimdb_nvt.h → src/REPLICA/fix_pimd_nvt_bosonic.h
View File

@ -13,7 +13,7 @@
#ifdef FIX_CLASS #ifdef FIX_CLASS
// clang-format off // clang-format off
FixStyle(pimdb/nvt,FixPIMDBNVT); FixStyle(pimd/nvt/bosonic,FixPIMDBNVT);
// clang-format on // clang-format on
#else #else