From 242f77fce93fd054e28b462ee0cad0baf1f6b84f Mon Sep 17 00:00:00 2001 From: Ofir Blumer Date: Tue, 11 Mar 2025 10:56:07 +0200 Subject: [PATCH] Changed the names of fix pimdb/* commands to pimd/*/bosonic; Changed file names accordingly. --- .../PACKAGES/{pimdb => pimd_bosonic}/README | 6 ++--- .../harmonic_trap_langevin/in.lmp | 2 +- .../harmonic_trap_langevin/log.lammps.0 | 22 ++++++++--------- .../harmonic_trap_langevin/log.lammps.1 | 22 ++++++++--------- .../harmonic_trap_langevin/log.lammps.2 | 22 ++++++++--------- .../harmonic_trap_langevin/log.lammps.3 | 22 ++++++++--------- .../harmonic_trap_langevin/run.sh | 0 .../harmonic_trap_nvt/in.lmp | 2 +- .../harmonic_trap_nvt/log.lammps.0 | 24 +++++++++---------- .../harmonic_trap_nvt/log.lammps.1 | 24 +++++++++---------- .../harmonic_trap_nvt/log.lammps.2 | 24 +++++++++---------- .../harmonic_trap_nvt/log.lammps.3 | 22 ++++++++--------- .../harmonic_trap_nvt/run.sh | 0 ...evin.cpp => fix_pimd_langevin_bosonic.cpp} | 2 +- ...langevin.h => fix_pimd_langevin_bosonic.h} | 2 +- ...pimdb_nvt.cpp => fix_pimd_nvt_bosonic.cpp} | 2 +- ...fix_pimdb_nvt.h => fix_pimd_nvt_bosonic.h} | 2 +- 17 files changed, 100 insertions(+), 100 deletions(-) rename examples/PACKAGES/{pimdb => pimd_bosonic}/README (64%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_langevin/in.lmp (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_langevin/log.lammps.0 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_langevin/log.lammps.1 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_langevin/log.lammps.2 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_langevin/log.lammps.3 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_langevin/run.sh (100%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_nvt/in.lmp (94%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_nvt/log.lammps.0 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_nvt/log.lammps.1 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_nvt/log.lammps.2 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_nvt/log.lammps.3 (92%) rename examples/PACKAGES/{pimdb => pimd_bosonic}/harmonic_trap_nvt/run.sh (100%) rename src/REPLICA/{fix_pimdb_langevin.cpp => fix_pimd_langevin_bosonic.cpp} (99%) rename src/REPLICA/{fix_pimdb_langevin.h => fix_pimd_langevin_bosonic.h} (96%) rename src/REPLICA/{fix_pimdb_nvt.cpp => fix_pimd_nvt_bosonic.cpp} (98%) rename src/REPLICA/{fix_pimdb_nvt.h => fix_pimd_nvt_bosonic.h} (96%) diff --git a/examples/PACKAGES/pimdb/README b/examples/PACKAGES/pimd_bosonic/README similarity index 64% rename from examples/PACKAGES/pimdb/README rename to examples/PACKAGES/pimd_bosonic/README index 2d77f6a767..9e8e3cf527 100644 --- a/examples/PACKAGES/pimdb/README +++ b/examples/PACKAGES/pimd_bosonic/README @@ -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 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 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. -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. -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. diff --git a/examples/PACKAGES/pimdb/harmonic_trap_langevin/in.lmp b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_langevin/in.lmp rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp index 83978af20f..f5d984eed4 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_langevin/in.lmp +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp @@ -45,7 +45,7 @@ fix harm all spring/self ${k} fix_modify harm energy yes # 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 variable prim_kinetic equal f_pimdb[5] diff --git a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.0 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.0 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 index 4d6999af13..2e5f1b0225 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.0 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 @@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/langevin 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 ${Temp} 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 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 99 9.5058078e-06 1.8141862e-05 0.00082913227 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 -96.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 35144210.362 fs/day, 0.000 hours/fs, 813.523 timesteps/s, 2.441 katom-step/s +70.1% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 4.265e-05 | 4.265e-05 | 4.265e-05 | 0.0 | 0.51 -Comm | 0.00031198 | 0.00031198 | 0.00031198 | 0.0 | 3.75 -Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 12.48 -Modify | 0.0063106 | 0.0063106 | 0.0063106 | 0.0 | 75.93 -Other | | 0.000609 | | | 7.33 +Neigh | 1.1593e-05 | 1.1593e-05 | 1.1593e-05 | 0.0 | 0.01 +Comm | 9.2183e-05 | 9.2183e-05 | 9.2183e-05 | 0.0 | 0.07 +Output | 0.023243 | 0.023243 | 0.023243 | 0.0 | 18.91 +Modify | 0.099386 | 0.099386 | 0.099386 | 0.0 | 80.85 +Other | | 0.0001896 | | | 0.15 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.1 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.1 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 index f3b7281d9b..a00ac90be8 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.1 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 @@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/langevin 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 ${Temp} 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 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 99 2.624134e-05 1.8141862e-05 0.00082913227 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 -88.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 35156789.883 fs/day, 0.000 hours/fs, 813.815 timesteps/s, 2.441 katom-step/s +46.7% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 4.9248e-05 | 4.9248e-05 | 4.9248e-05 | 0.0 | 0.59 -Comm | 0.00027661 | 0.00027661 | 0.00027661 | 0.0 | 3.34 -Output | 0.00095948 | 0.00095948 | 0.00095948 | 0.0 | 11.58 -Modify | 0.0064815 | 0.0064815 | 0.0064815 | 0.0 | 78.26 -Other | | 0.0005157 | | | 6.23 +Neigh | 1.9787e-05 | 1.9787e-05 | 1.9787e-05 | 0.0 | 0.02 +Comm | 9.2033e-05 | 9.2033e-05 | 9.2033e-05 | 0.0 | 0.07 +Output | 0.0022584 | 0.0022584 | 0.0022584 | 0.0 | 1.84 +Modify | 0.12033 | 0.12033 | 0.12033 | 0.0 | 97.93 +Other | | 0.0001755 | | | 0.14 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.2 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.2 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 index 9dd335cce4..9cc0033c8a 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.2 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 @@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/langevin 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 ${Temp} 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 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 99 1.9188379e-05 1.8141862e-05 0.00082913227 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 -79.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 38570373.396 fs/day, 0.000 hours/fs, 892.833 timesteps/s, 2.678 katom-step/s +52.7% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 4.6257e-05 | 4.6257e-05 | 4.6257e-05 | 0.0 | 0.56 -Comm | 0.00029611 | 0.00029611 | 0.00029611 | 0.0 | 3.57 -Output | 0.00096988 | 0.00096988 | 0.00096988 | 0.0 | 11.69 -Modify | 0.0064529 | 0.0064529 | 0.0064529 | 0.0 | 77.76 -Other | | 0.0005331 | | | 6.42 +Neigh | 1.4356e-05 | 1.4356e-05 | 1.4356e-05 | 0.0 | 0.01 +Comm | 9.7936e-05 | 9.7936e-05 | 9.7936e-05 | 0.0 | 0.09 +Output | 0.0017373 | 0.0017373 | 0.0017373 | 0.0 | 1.55 +Modify | 0.10997 | 0.10997 | 0.10997 | 0.0 | 98.19 +Other | | 0.0001804 | | | 0.16 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.3 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.3 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 index b472b76a2d..941334c25c 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.3 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 @@ -51,7 +51,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/langevin 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 ${Temp} 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 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 99 2.5384836e-05 1.8141862e-05 0.00082913227 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 -97.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 35144393.915 fs/day, 0.000 hours/fs, 813.528 timesteps/s, 2.441 katom-step/s +88.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 5.2767e-05 | 5.2767e-05 | 5.2767e-05 | 0.0 | 0.64 -Comm | 0.00029534 | 0.00029534 | 0.00029534 | 0.0 | 3.56 -Output | 0.001037 | 0.001037 | 0.001037 | 0.0 | 12.51 -Modify | 0.0063429 | 0.0063429 | 0.0063429 | 0.0 | 76.54 -Other | | 0.0005594 | | | 6.75 +Neigh | 1.5885e-05 | 1.5885e-05 | 1.5885e-05 | 0.0 | 0.01 +Comm | 9.4707e-05 | 9.4707e-05 | 9.4707e-05 | 0.0 | 0.08 +Output | 0.0027076 | 0.0027076 | 0.0027076 | 0.0 | 2.20 +Modify | 0.11993 | 0.11993 | 0.11993 | 0.0 | 97.57 +Other | | 0.0001738 | | | 0.14 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_langevin/run.sh b/examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/run.sh similarity index 100% rename from examples/PACKAGES/pimdb/harmonic_trap_langevin/run.sh rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/run.sh diff --git a/examples/PACKAGES/pimdb/harmonic_trap_nvt/in.lmp b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp similarity index 94% rename from examples/PACKAGES/pimdb/harmonic_trap_nvt/in.lmp rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp index bd1c28b7fc..56d6d3932a 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_nvt/in.lmp +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/in.lmp @@ -48,7 +48,7 @@ fix harm all spring/self ${k} fix_modify harm energy yes # 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 variable virial equal f_pimdb[3] diff --git a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.0 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.0 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 index 28e8fe3e3b..bf46982da6 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.0 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 @@ -54,7 +54,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} -fix pimdb all pimdb/nvt 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 ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 # Outputs 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 99 7.622805e-06 1.9289045e-06 0.00023466684 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 -80.6% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 459208566.791 fs/day, 0.000 hours/fs, 10629.828 timesteps/s, 31.889 katom-step/s +90.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 3.3682e-05 | 3.3682e-05 | 3.3682e-05 | 0.0 | 0.67 -Comm | 0.00029392 | 0.00029392 | 0.00029392 | 0.0 | 5.84 -Output | 0.00092846 | 0.00092846 | 0.00092846 | 0.0 | 18.46 -Modify | 0.0031767 | 0.0031767 | 0.0031767 | 0.0 | 63.17 -Other | | 0.0005963 | | | 11.86 +Neigh | 8.466e-06 | 8.466e-06 | 8.466e-06 | 0.0 | 0.09 +Comm | 7.8365e-05 | 7.8365e-05 | 7.8365e-05 | 0.0 | 0.83 +Output | 0.0012482 | 0.0012482 | 0.0012482 | 0.0 | 13.27 +Modify | 0.0079193 | 0.0079193 | 0.0079193 | 0.0 | 84.18 +Other | | 0.0001532 | | | 1.63 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.1 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.1 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 index 0a61186d68..f129f10c09 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.1 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 @@ -54,7 +54,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} -fix pimdb all pimdb/nvt 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 ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 # Outputs 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 99 7.4315008e-06 1.88617e-06 0.00024137268 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 -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 458913876.206 fs/day, 0.000 hours/fs, 10623.006 timesteps/s, 31.869 katom-step/s +50.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 2.3358e-05 | 2.3358e-05 | 2.3358e-05 | 0.0 | 0.46 -Comm | 0.00022527 | 0.00022527 | 0.00022527 | 0.0 | 4.42 -Output | 0.00078435 | 0.00078435 | 0.00078435 | 0.0 | 15.39 -Modify | 0.0036209 | 0.0036209 | 0.0036209 | 0.0 | 71.06 -Other | | 0.0004416 | | | 8.67 +Neigh | 8.215e-06 | 8.215e-06 | 8.215e-06 | 0.0 | 0.09 +Comm | 7.7692e-05 | 7.7692e-05 | 7.7692e-05 | 0.0 | 0.83 +Output | 0.0047662 | 0.0047662 | 0.0047662 | 0.0 | 50.63 +Modify | 0.004407 | 0.004407 | 0.004407 | 0.0 | 46.82 +Other | | 0.0001545 | | | 1.64 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.2 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.2 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 index 36c299b110..074acc9d50 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.2 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 @@ -54,7 +54,7 @@ create_atoms 1 single -14 9 ${z1} create_atoms 1 single -14 9 2 Created 1 atoms 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 jump SELF loop 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 # PIMD command -fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} -fix pimdb all pimdb/nvt 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 ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 # Outputs 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 99 7.2605738e-06 1.7643404e-06 0.00022943234 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 -98.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 458904516.311 fs/day, 0.000 hours/fs, 10622.790 timesteps/s, 31.868 katom-step/s +24.7% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 3.1029e-05 | 3.1029e-05 | 3.1029e-05 | 0.0 | 0.61 -Comm | 0.00027821 | 0.00027821 | 0.00027821 | 0.0 | 5.48 -Output | 0.001016 | 0.001016 | 0.001016 | 0.0 | 20.00 -Modify | 0.0032013 | 0.0032013 | 0.0032013 | 0.0 | 63.02 -Other | | 0.0005529 | | | 10.89 +Neigh | 8.785e-06 | 8.785e-06 | 8.785e-06 | 0.0 | 0.09 +Comm | 7.9921e-05 | 7.9921e-05 | 7.9921e-05 | 0.0 | 0.85 +Output | 0.0071119 | 0.0071119 | 0.0071119 | 0.0 | 75.55 +Modify | 0.0020558 | 0.0020558 | 0.0020558 | 0.0 | 21.84 +Other | | 0.0001572 | | | 1.67 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.3 b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 similarity index 92% rename from examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.3 rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 index 6afd6536bf..edebd7096c 100644 --- a/examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.3 +++ b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 @@ -87,9 +87,9 @@ fix harm all spring/self 1.215461412e-08 fix_modify harm energy yes # PIMD command -fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc} -fix pimdb all pimdb/nvt 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 ${Temp} nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc} +fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4 # Outputs 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 99 7.4250201e-06 1.8736806e-06 0.00023685186 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 -79.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 459771778.655 fs/day, 0.000 hours/fs, 10642.865 timesteps/s, 31.929 katom-step/s +25.2% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 1.5273e-05 | 1.5273e-05 | 1.5273e-05 | 0.0 | 0.30 -Comm | 0.00013505 | 0.00013505 | 0.00013505 | 0.0 | 2.65 -Output | 0.00046743 | 0.00046743 | 0.00046743 | 0.0 | 9.16 -Modify | 0.0042111 | 0.0042111 | 0.0042111 | 0.0 | 82.53 -Other | | 0.0002734 | | | 5.36 +Neigh | 8.404e-06 | 8.404e-06 | 8.404e-06 | 0.0 | 0.09 +Comm | 8.6872e-05 | 8.6872e-05 | 8.6872e-05 | 0.0 | 0.92 +Output | 0.0071309 | 0.0071309 | 0.0071309 | 0.0 | 75.89 +Modify | 0.0020085 | 0.0020085 | 0.0020085 | 0.0 | 21.38 +Other | | 0.0001612 | | | 1.72 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pimdb/harmonic_trap_nvt/run.sh b/examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh similarity index 100% rename from examples/PACKAGES/pimdb/harmonic_trap_nvt/run.sh rename to examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh diff --git a/src/REPLICA/fix_pimdb_langevin.cpp b/src/REPLICA/fix_pimd_langevin_bosonic.cpp similarity index 99% rename from src/REPLICA/fix_pimdb_langevin.cpp rename to src/REPLICA/fix_pimd_langevin_bosonic.cpp index 1ce661e777..140dd1afc5 100644 --- a/src/REPLICA/fix_pimdb_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin_bosonic.cpp @@ -22,7 +22,7 @@ Version 1.0 ------------------------------------------------------------------------- */ -#include "fix_pimdb_langevin.h" +#include "fix_pimd_langevin_bosonic.h" #include "bosonic_exchange.h" diff --git a/src/REPLICA/fix_pimdb_langevin.h b/src/REPLICA/fix_pimd_langevin_bosonic.h similarity index 96% rename from src/REPLICA/fix_pimdb_langevin.h rename to src/REPLICA/fix_pimd_langevin_bosonic.h index a1efe94e5f..fb1f7e7af9 100644 --- a/src/REPLICA/fix_pimdb_langevin.h +++ b/src/REPLICA/fix_pimd_langevin_bosonic.h @@ -13,7 +13,7 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(pimdb/langevin, FixPIMDBLangevin); +FixStyle(pimd/langevin/bosonic, FixPIMDBLangevin); // clang-format on #else diff --git a/src/REPLICA/fix_pimdb_nvt.cpp b/src/REPLICA/fix_pimd_nvt_bosonic.cpp similarity index 98% rename from src/REPLICA/fix_pimdb_nvt.cpp rename to src/REPLICA/fix_pimd_nvt_bosonic.cpp index 7f91f88c18..1458a4b72f 100644 --- a/src/REPLICA/fix_pimdb_nvt.cpp +++ b/src/REPLICA/fix_pimd_nvt_bosonic.cpp @@ -21,7 +21,7 @@ Version 1.0 ------------------------------------------------------------------------- */ -#include "fix_pimdb_nvt.h" +#include "fix_pimd_nvt_bosonic.h" #include "bosonic_exchange.h" diff --git a/src/REPLICA/fix_pimdb_nvt.h b/src/REPLICA/fix_pimd_nvt_bosonic.h similarity index 96% rename from src/REPLICA/fix_pimdb_nvt.h rename to src/REPLICA/fix_pimd_nvt_bosonic.h index 72db4cbe7f..3d4adb2a7d 100644 --- a/src/REPLICA/fix_pimdb_nvt.h +++ b/src/REPLICA/fix_pimd_nvt_bosonic.h @@ -13,7 +13,7 @@ #ifdef FIX_CLASS // clang-format off -FixStyle(pimdb/nvt,FixPIMDBNVT); +FixStyle(pimd/nvt/bosonic,FixPIMDBNVT); // clang-format on #else