ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #4481 from akohlmey/collected-small-fixes

Browse Source 
Collected small fixes and changes
This commit is contained in:
Axel Kohlmeyer
2025-03-14 18:10:14 -04:00
committed by GitHub
parent 55eeaca69c 4e0d37ecc2
commit 3aba21f6e2
126 changed files with 3796 additions and 9645 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ Normal file
View File

@ -0,0 +1,2 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Running on 4 partitions of processors

24
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.0 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -103,8 +104,8 @@ Initializing PI Langevin equation thermostat...
3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
PILE_L thermostat successfully initialized!
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
@ -208,20 +209,20 @@ 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 0.122922 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms
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
Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s
89.8% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.292e-06 | 1.292e-06 | 1.292e-06 | 0.0 | 0.11
Comm | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 | 0.0 | 1.06
Output | 0.00018105 | 0.00018105 | 0.00018105 | 0.0 | 15.55
Modify | 0.00090255 | 0.00090255 | 0.00090255 | 0.0 | 77.54
Other | | 6.68e-05 | | | 5.74
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -234,3 +235,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 33
Dangerous builds = 0
Total wall time: 0:00:00

24
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.1 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
@ -200,20 +201,20 @@ 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 0.122878 on 1 procs for 100 steps with 3 atoms
Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms
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
Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s
88.4% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.773e-06 | 1.773e-06 | 1.773e-06 | 0.0 | 0.15
Comm | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 | 0.0 | 1.27
Output | 0.00021888 | 0.00021888 | 0.00021888 | 0.0 | 18.58
Modify | 0.00086503 | 0.00086503 | 0.00086503 | 0.0 | 73.42
Other | | 7.754e-05 | | | 6.58
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -226,3 +227,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:00

24
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.2 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 2
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
@ -200,20 +201,20 @@ 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 0.112003 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms
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
Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s
89.6% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.582e-06 | 1.582e-06 | 1.582e-06 | 0.0 | 0.14
Comm | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 | 0.0 | 1.15
Output | 0.00017996 | 0.00017996 | 0.00017996 | 0.0 | 15.49
Modify | 0.00090771 | 0.00090771 | 0.00090771 | 0.0 | 78.14
Other | | 5.907e-05 | | | 5.09
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -226,3 +227,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 41
Dangerous builds = 0
Total wall time: 0:00:00

24
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.lammps.3 → examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 3
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
@ -200,20 +201,20 @@ 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 0.122921 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms
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
Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s
88.3% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.441e-06 | 1.441e-06 | 1.441e-06 | 0.0 | 0.12
Comm | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 | 0.0 | 1.04
Output | 0.00018148 | 0.00018148 | 0.00018148 | 0.0 | 15.64
Modify | 0.0009054 | 0.0009054 | 0.0009054 | 0.0 | 78.01
Other | | 6.023e-05 | | | 5.19
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -226,3 +227,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 42
Dangerous builds = 0
Total wall time: 0:00:00

2
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++ Normal file
View File

@ -0,0 +1,2 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Running on 4 partitions of processors

25
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.0 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -99,11 +100,11 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024794798
@ -207,20 +208,20 @@ 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 0.00940749 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms
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
Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s
36.5% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.454e-06 | 1.454e-06 | 1.454e-06 | 0.0 | 0.08
Comm | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 | 0.0 | 1.19
Output | 0.00030824 | 0.00030824 | 0.00030824 | 0.0 | 15.96
Modify | 0.001541 | 0.001541 | 0.001541 | 0.0 | 79.79
Other | | 5.754e-05 | | | 2.98
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0

25
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.1 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024796164
@ -205,20 +206,20 @@ 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 0.00941353 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms
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
Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s
0.0% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 2.774e-06 | 2.774e-06 | 2.774e-06 | 0.0 | 0.15
Comm | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 | 0.0 | 1.22
Output | 0.00042246 | 0.00042246 | 0.00042246 | 0.0 | 22.13
Modify | 0.0013744 | 0.0013744 | 0.0013744 | 0.0 | 72.00
Other | | 8.601e-05 | | | 4.51
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0

25
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.2 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 2
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024796164
@ -205,20 +206,20 @@ 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 0.00941372 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms
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
Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s
39.2% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.602e-06 | 1.602e-06 | 1.602e-06 | 0.0 | 0.08
Comm | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 | 0.0 | 0.87
Output | 0.00032627 | 0.00032627 | 0.00032627 | 0.0 | 16.66
Modify | 0.0015486 | 0.0015486 | 0.0015486 | 0.0 | 79.07
Other | | 6.514e-05 | | | 3.33
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0

25
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.lammps.3 → examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3
View File

@ -1,5 +1,6 @@
LAMMPS (4 Feb 2025)
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 3
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024796164
@ -205,20 +206,20 @@ 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 0.00939597 on 1 procs for 100 steps with 3 atoms
Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms
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
Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s
37.5% 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 | 0 | 0 | 0.0 | 0.00
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
Neigh | 1.652e-06 | 1.652e-06 | 1.652e-06 | 0.0 | 0.08
Comm | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 | 0.0 | 0.91
Output | 0.00036011 | 0.00036011 | 0.00036011 | 0.0 | 18.27
Modify | 0.0015231 | 0.0015231 | 0.0015231 | 0.0 | 77.28
Other | | 6.806e-05 | | | 3.45
Nlocal: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0