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talinke
2025-04-14 11:33:02 -07:00
parent 09d3ac0a1b
commit e4c3b0c05e
8 changed files with 354 additions and 234 deletions
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20
examples/gjf/README
View File

@ -13,33 +13,35 @@ mpirun -np $NP lmp_mpi -in.gjf.vhalf
Compared to other thermostats, the GJ thermostat allows for larger timesteps
with the correct Boltzmann statistics. A comparison using averaged properties
from this example's input file is shown below. 'X' denotes a failed simulation.
The theoretical value for KE is 1.1168 eV.
KINETIC ENERGY (eV)
| Δt || 0.01 | 0.05 | 0.10 | 0.11 | 0.12 | 0.13 | 0.14 |
|==============||========|========|========|========|========|========|========|
| langevin/gjf || 1.112 | 1.108 | 1.114 | 1.118 | 1.111 | 1.133 | 1.168 |
| langevin || 1.113 | 1.125 | 1.121 | 1.135 | 1.152 | X | X |
| nvt || 1.094 | 1.114 | 1.117 | 1.113 | 1.121 | X | X |
| gjf half || 1.117 | 1.116 | 1.119 | 1.119 | 1.123 | 1.136 | 1.170 |
| gjf full || 1.116 | 1.071 | 0.938 | 0.898 | 0.858 | 0.817 | 0.780 |
| langevin || 1.110 | 1.113 | 1.121 | 1.129 | 1.157 | X | X |
| nvt || 1.083 | 1.109 | 1.112 | 1.113 | 1.114 | X | X |
|--------------||--------|--------|--------|--------|--------|--------|--------|
POTENTIAL ENERGY (eV)
| Δt || 0.01 | 0.05 | 0.10 | 0.11 | 0.12 | 0.13 | 0.14 |
|==============||========|========|========|========|========|========|========|
| langevin/gjf || -55.16 | -55.16 | -55.15 | -55.15 | -55.15 | -55.14 | -55.12 |
| langevin || -55.16 | -55.12 | -54.93 | -54.85 | -54.71 | X | X |
| nvt || -55.17 | -55.10 | -54.95 | -54.88 | -54.82 | X | X |
| gjf half || -55.11 | -55.11 | -55.11 | -55.11 | -55.11 | -55.10 | -55.07 |
| gjf full || -55.11 | -55.11 | -55.11 | -55.11 | -55.11 | -55.10 | -55.07 |
| langevin || -55.11 | -55.07 | -54.87 | -54.79 | -54.65 | X | X |
| nvt || -55.14 | -55.07 | -54.90 | -54.84 | -54.76 | X | X |
|--------------||--------|--------|--------|--------|--------|--------|--------|
Script Commands:
--
fix lang all langevin/gjf 10 10 1 26488
vs
--
fix lang all langevin/gjf 10 10 1 26488 vel vfull
--
fix nve all nve
fix lang all langevin 10 10 1 26488
--
vs
--
fix noho all nvt temp 10 10 1
--

11
examples/gjf/in.gjf.vfull
View File

@ -5,18 +5,21 @@ atom_style full
boundary p p p
read_data argon.lmp
include ff-argon.lmp
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin/gjf 10 10 1 26488 vel vfull method 4
compute myKE all ke
compute myPE all pe
thermo 200
fix lang all langevin/gjf 10 10 1 26488 vel vfull method 1
thermo 2000
run 5000
fix energies all ave/time 1 20000 20000 c_myKE c_myPE file ave.out
run 35000

9
examples/gjf/in.gjf.vhalf
View File

@ -5,18 +5,21 @@ atom_style full
boundary p p p
read_data argon.lmp
include ff-argon.lmp
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all langevin/gjf 10 10 1 26488
thermo 200
run 5000
fix energies all ave/time 1 20000 20000 c_myKE c_myPE file ave.out
thermo 2000
run 35000

137
examples/gjf/log.2Apr25.gjf.vfull.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (2 Apr 2025 - Development - 4dd8c66390-modified)
LAMMPS (2 Apr 2025 - Development - 09d3ac0a1b-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
@ -22,7 +22,6 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
@ -47,33 +46,33 @@ pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin/gjf 10 10 1 26488 vel vfull method 4
compute myKE all ke
compute myPE all pe
thermo 200
fix lang all langevin/gjf 10 10 1 26488 vel vfull method 1
thermo 2000
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Langevin GJF methods: doi:10.1007/s10955-024-03345-1
- Langevin GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech_jensen_2024,
title = {On the Definition of Velocity in Discrete-Time, Stochastic Langevin Simulations},
volume = {191},
number = {10},
url = {https://doi.org/10.1007/s10955-024-03345-1},
doi = {10.1007/s10955-024-03345-1},
urldate = {2024-10-22},
journal = {J. Stat. Phys.},
author = {Gronbech-Jensen, Niels},
year = {2024},
pages = {137}
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -94,46 +93,24 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
200 8.3566091 -55.074758 0 -54.142565 340.34804
400 8.5550582 -55.098903 0 -54.144573 333.63174
600 8.7873675 -55.044559 0 -54.064315 350.7384
800 8.7258741 -55.149735 0 -54.17635 318.83613
1000 8.3748307 -55.059754 0 -54.125529 343.7989
1200 8.6082188 -55.156326 0 -54.196066 316.8728
1400 8.9291902 -55.11836 0 -54.122295 328.12488
1600 8.3386383 -55.119788 0 -54.189601 325.81369
1800 8.0698034 -55.076285 0 -54.176086 338.69767
2000 8.5103978 -55.084479 0 -54.135131 338.12197
2200 8.3201517 -55.104858 0 -54.176733 329.95905
2400 8.7070407 -55.120649 0 -54.149366 328.06488
2600 8.4244379 -55.147583 0 -54.207824 321.45013
2800 8.7911907 -55.127309 0 -54.146638 325.76049
3000 8.250829 -55.1039 0 -54.183508 332.05048
3200 8.693979 -55.155552 0 -54.185726 318.29736
3400 8.9806023 -55.127303 0 -54.125504 327.48861
3600 8.8313967 -55.081076 0 -54.09592 339.16793
3800 8.8008688 -55.176748 0 -54.194998 313.08151
4000 8.1780418 -55.105368 0 -54.193096 330.04164
4200 8.3772045 -55.128813 0 -54.194323 324.29069
4400 8.3580983 -55.086979 0 -54.154621 335.63911
4600 8.1493124 -55.096648 0 -54.18758 332.51502
4800 9.0189389 -55.126828 0 -54.120752 326.36041
5000 8.7587383 -55.084993 0 -54.107943 337.17399
Loop time of 2.34344 on 1 procs for 5000 steps with 864 atoms
2000 8.5329244 -55.06102 0 -54.10916 343.01505
4000 7.8165794 -55.128803 0 -54.256851 322.07344
5000 8.4535562 -55.150518 0 -54.207511 318.20862
Loop time of 2.26625 on 1 procs for 5000 steps with 864 atoms
Performance: 18434.456 ns/day, 0.001 hours/ns, 2133.618 timesteps/s, 1.843 Matom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 19062.331 ns/day, 0.001 hours/ns, 2206.288 timesteps/s, 1.906 Matom-step/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3044 | 1.3044 | 1.3044 | 0.0 | 55.66
Bond | 0.00055276 | 0.00055276 | 0.00055276 | 0.0 | 0.02
Neigh | 0.27376 | 0.27376 | 0.27376 | 0.0 | 11.68
Comm | 0.055077 | 0.055077 | 0.055077 | 0.0 | 2.35
Output | 0.00055401 | 0.00055401 | 0.00055401 | 0.0 | 0.02
Modify | 0.68502 | 0.68502 | 0.68502 | 0.0 | 29.23
Other | | 0.02412 | | | 1.03
Pair | 1.2907 | 1.2907 | 1.2907 | 0.0 | 56.95
Bond | 0.00032498 | 0.00032498 | 0.00032498 | 0.0 | 0.01
Neigh | 0.28343 | 0.28343 | 0.28343 | 0.0 | 12.51
Comm | 0.055491 | 0.055491 | 0.055491 | 0.0 | 2.45
Output | 8.5614e-05 | 8.5614e-05 | 8.5614e-05 | 0.0 | 0.00
Modify | 0.61129 | 0.61129 | 0.61129 | 0.0 | 26.97
Other | | 0.02497 | | | 1.10
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -145,8 +122,60 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 257
Neighbor list builds = 258
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE file ave.out
Total wall time: 0:00:02
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 8.4535562 -55.150518 0 -54.207511 318.20862
6000 8.4899401 -55.108242 0 -54.161176 331.10703
8000 8.3618893 -55.092171 0 -54.15939 334.11831
10000 8.8684311 -55.100316 0 -54.111029 334.09931
12000 8.4339192 -55.07343 0 -54.132614 340.00487
14000 8.072393 -55.115121 0 -54.214633 327.98965
16000 8.3420289 -55.077813 0 -54.147247 337.74926
18000 8.3803911 -55.12201 0 -54.187164 326.10485
20000 8.4676985 -55.176339 0 -54.231754 311.57092
22000 8.8560138 -55.110505 0 -54.122603 330.66179
24000 8.3187826 -55.120592 0 -54.192619 327.01148
26000 8.0327666 -55.116664 0 -54.220596 326.25179
28000 8.3672169 -55.130413 0 -54.197037 324.2368
30000 8.1669275 -55.057678 0 -54.146645 344.9168
32000 8.3819314 -55.08989 0 -54.154873 335.45317
34000 8.109088 -55.17222 0 -54.267639 310.83717
36000 8.3048574 -55.079475 0 -54.153056 338.04291
38000 8.8708544 -55.108991 0 -54.119434 330.70097
40000 8.4012779 -55.080817 0 -54.143642 338.54326
Loop time of 19.3814 on 1 procs for 35000 steps with 864 atoms
Performance: 15602.554 ns/day, 0.002 hours/ns, 1805.851 timesteps/s, 1.560 Matom-step/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.065 | 12.065 | 12.065 | 0.0 | 62.25
Bond | 0.0021494 | 0.0021494 | 0.0021494 | 0.0 | 0.01
Neigh | 2.3755 | 2.3755 | 2.3755 | 0.0 | 12.26
Comm | 0.40916 | 0.40916 | 0.40916 | 0.0 | 2.11
Output | 0.0004907 | 0.0004907 | 0.0004907 | 0.0 | 0.00
Modify | 4.3528 | 4.3528 | 4.3528 | 0.0 | 22.46
Other | | 0.1765 | | | 0.91
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1592 ave 1592 max 1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18144 ave 18144 max 18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21

147
examples/gjf/log.2Apr25.gjf.vfull.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (2 Apr 2025 - Development - 4dd8c66390-modified)
LAMMPS (2 Apr 2025 - Development - 09d3ac0a1b-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
@ -22,7 +22,6 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.014 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
@ -47,33 +46,33 @@ pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin/gjf 10 10 1 26488 vel vfull method 4
compute myKE all ke
compute myPE all pe
thermo 200
fix lang all langevin/gjf 10 10 1 26488 vel vfull method 1
thermo 2000
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Langevin GJF methods: doi:10.1007/s10955-024-03345-1
- Langevin GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech_jensen_2024,
title = {On the Definition of Velocity in Discrete-Time, Stochastic Langevin Simulations},
volume = {191},
number = {10},
url = {https://doi.org/10.1007/s10955-024-03345-1},
doi = {10.1007/s10955-024-03345-1},
urldate = {2024-10-22},
journal = {J. Stat. Phys.},
author = {Gronbech-Jensen, Niels},
year = {2024},
pages = {137}
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -94,59 +93,89 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
200 8.3950866 -55.088994 0 -54.15251 334.90536
400 8.6408464 -55.090811 0 -54.126912 335.23135
600 8.3101447 -55.121286 0 -54.194277 325.43222
800 8.5045003 -55.090513 0 -54.141824 335.05857
1000 8.7236378 -55.101455 0 -54.12832 331.96596
1200 8.7063561 -55.109371 0 -54.138164 331.62683
1400 8.7935957 -55.089763 0 -54.108824 336.89842
1600 8.454418 -55.105207 0 -54.162104 330.18927
1800 8.7989267 -55.142078 0 -54.160544 322.47021
2000 8.7823094 -55.153625 0 -54.173945 318.95028
2200 8.6201117 -55.11511 0 -54.153524 329.13488
2400 9.1165215 -55.161069 0 -54.144107 318.48524
2600 8.7636341 -55.142401 0 -54.164805 322.46493
2800 8.4876731 -55.111528 0 -54.164715 329.66127
3000 8.7005957 -55.149445 0 -54.178881 319.92878
3200 8.1711364 -55.137611 0 -54.226108 322.83713
3400 8.7172512 -55.143449 0 -54.171026 322.68918
3600 8.6262526 -55.1002 0 -54.137928 333.02737
3800 8.1680259 -55.166423 0 -54.255267 313.66684
4000 8.8340067 -55.121759 0 -54.136312 328.58235
4200 8.427926 -55.126903 0 -54.186755 324.95528
4400 8.6352614 -55.193826 0 -54.23055 307.14392
4600 8.7381405 -55.120503 0 -54.14575 327.73985
4800 8.3857194 -55.081944 0 -54.146505 337.38629
5000 8.1179517 -55.162247 0 -54.256677 314.50176
Loop time of 2.08834 on 4 procs for 5000 steps with 864 atoms
2000 8.63533 -55.154093 0 -54.190809 317.34773
4000 8.2482881 -55.091551 0 -54.171442 333.83766
5000 7.946377 -55.076514 0 -54.190084 337.31999
Loop time of 2.06641 on 4 procs for 5000 steps with 864 atoms
Performance: 20686.324 ns/day, 0.001 hours/ns, 2394.250 timesteps/s, 2.069 Matom-step/s
63.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 20905.811 ns/day, 0.001 hours/ns, 2419.654 timesteps/s, 2.091 Matom-step/s
62.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53532 | 0.5439 | 0.54781 | 0.7 | 26.04
Bond | 0.0006347 | 0.00066042 | 0.00068198 | 0.0 | 0.03
Neigh | 0.10879 | 0.11194 | 0.118 | 1.1 | 5.36
Comm | 0.94935 | 0.96017 | 0.97155 | 0.8 | 45.98
Output | 0.0060135 | 0.006061 | 0.0061217 | 0.1 | 0.29
Modify | 0.2483 | 0.24911 | 0.25049 | 0.2 | 11.93
Other | | 0.2165 | | | 10.37
Pair | 0.53593 | 0.54393 | 0.55031 | 0.7 | 26.32
Bond | 0.0004435 | 0.00052388 | 0.000586 | 0.0 | 0.03
Neigh | 0.10844 | 0.11152 | 0.11687 | 1.0 | 5.40
Comm | 0.94337 | 0.94742 | 0.94979 | 0.3 | 45.85
Output | 0.00076423 | 0.00077499 | 0.00078949 | 0.0 | 0.04
Modify | 0.24993 | 0.25116 | 0.25286 | 0.2 | 12.15
Other | | 0.2111 | | | 10.21
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 884.25 ave 892 max 875 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.5 ave 4737 max 4333 min
Nghost: 884.75 ave 885 max 884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18142
Ave neighs/atom = 20.997685
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 280
Neighbor list builds = 273
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE file ave.out
Total wall time: 0:00:02
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 7.946377 -55.076514 0 -54.190084 337.31999
6000 8.2565866 -55.129244 0 -54.208209 324.57967
8000 7.9942397 -55.101417 0 -54.209648 331.24127
10000 8.5413968 -55.083292 0 -54.130486 337.82599
12000 8.3682078 -55.090905 0 -54.157419 335.08066
14000 8.5082065 -55.085051 0 -54.135948 336.2765
16000 8.1944037 -55.090733 0 -54.176635 334.03786
18000 8.2607106 -55.030131 0 -54.108637 352.49892
20000 8.1154691 -55.104072 0 -54.198779 330.14203
22000 8.5592601 -55.152019 0 -54.197221 318.03507
24000 8.3182914 -55.115242 0 -54.187324 328.46084
26000 8.3691375 -55.125275 0 -54.191685 325.43673
28000 8.531632 -55.107097 0 -54.155381 331.42771
30000 8.1102222 -55.099011 0 -54.194304 332.04678
32000 8.5558571 -55.077016 0 -54.122598 339.87746
34000 8.4213946 -55.097068 0 -54.157649 333.34935
36000 8.0936615 -55.152202 0 -54.249342 316.20169
38000 7.999652 -55.048407 0 -54.156034 345.07945
40000 8.6699753 -55.087634 0 -54.120485 337.23709
Loop time of 17.4329 on 4 procs for 35000 steps with 864 atoms
Performance: 17346.528 ns/day, 0.001 hours/ns, 2007.700 timesteps/s, 1.735 Matom-step/s
65.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.1129 | 5.1423 | 5.1581 | 0.8 | 29.50
Bond | 0.0029266 | 0.0034929 | 0.0038279 | 0.6 | 0.02
Neigh | 0.85004 | 0.87543 | 0.90992 | 2.4 | 5.02
Comm | 6.6875 | 6.6993 | 6.7123 | 0.4 | 38.43
Output | 0.0043725 | 0.0045522 | 0.005017 | 0.4 | 0.03
Modify | 3.2524 | 3.2579 | 3.2677 | 0.3 | 18.69
Other | | 1.45 | | | 8.32
Nlocal: 216 ave 222 max 210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 905.5 ave 911 max 899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.75 ave 4837 max 4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:19

131
examples/gjf/log.2Apr25.gjf.vhalf.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (2 Apr 2025 - Development - 4dd8c66390-modified)
LAMMPS (2 Apr 2025 - Development - 09d3ac0a1b-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
@ -21,8 +21,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.007 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
@ -47,33 +46,32 @@ pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all langevin/gjf 10 10 1 26488
thermo 200
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Langevin GJF methods: doi:10.1007/s10955-024-03345-1
- Langevin GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech_jensen_2024,
title = {On the Definition of Velocity in Discrete-Time, Stochastic Langevin Simulations},
volume = {191},
number = {10},
url = {https://doi.org/10.1007/s10955-024-03345-1},
doi = {10.1007/s10955-024-03345-1},
urldate = {2024-10-22},
journal = {J. Stat. Phys.},
author = {Gronbech-Jensen, Niels},
year = {2024},
pages = {137}
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -94,46 +92,22 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
200 9.8808461 -55.073599 0 -53.971376 345.62224
400 9.8712816 -55.072241 0 -53.971084 345.11909
600 10.528988 -55.066736 0 -53.892211 350.60112
800 10.167171 -55.148312 0 -54.014149 324.73698
1000 10.029026 -55.125705 0 -54.006952 331.93785
1200 9.8898479 -55.086642 0 -53.983414 342.04309
1400 10.610014 -55.076793 0 -53.89323 346.34338
1600 9.9402137 -55.111688 0 -54.002842 335.04779
1800 9.8078801 -55.140475 0 -54.046391 325.88652
2000 10.472791 -55.06102 0 -53.892765 349.97306
2200 9.877248 -55.191201 0 -54.089379 312.77421
2400 9.9739487 -55.108904 0 -53.996295 335.9089
2600 10.131803 -55.149444 0 -54.019226 325.44115
2800 9.6980127 -55.118395 0 -54.036568 331.2097
3000 9.7193425 -55.149785 0 -54.065577 323.32384
3200 10.27638 -55.083302 0 -53.936957 342.56458
3400 9.9253941 -55.082368 0 -53.975175 342.28594
3600 10.665862 -55.056774 0 -53.866981 352.03551
3800 10.011077 -55.084664 0 -53.967913 341.45122
4000 9.4182671 -55.128803 0 -54.078181 327.81846
4200 10.02466 -55.106046 0 -53.98778 336.56944
4400 9.3721033 -55.146068 0 -54.100596 322.38199
4600 9.5485537 -55.118577 0 -54.053421 332.04274
4800 10.039726 -55.074068 0 -53.954122 344.76817
5000 9.7731898 -55.150518 0 -54.060304 322.94195
Loop time of 2.28614 on 1 procs for 5000 steps with 864 atoms
Loop time of 2.32188 on 1 procs for 5000 steps with 864 atoms
Performance: 18896.448 ns/day, 0.001 hours/ns, 2187.089 timesteps/s, 1.890 Matom-step/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 18605.621 ns/day, 0.001 hours/ns, 2153.428 timesteps/s, 1.861 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 | 1.2918 | 1.2918 | 1.2918 | 0.0 | 56.51
Bond | 0.00048345 | 0.00048345 | 0.00048345 | 0.0 | 0.02
Neigh | 0.2776 | 0.2776 | 0.2776 | 0.0 | 12.14
Comm | 0.055375 | 0.055375 | 0.055375 | 0.0 | 2.42
Output | 0.00054609 | 0.00054609 | 0.00054609 | 0.0 | 0.02
Modify | 0.63625 | 0.63625 | 0.63625 | 0.0 | 27.83
Other | | 0.02408 | | | 1.05
Pair | 1.3154 | 1.3154 | 1.3154 | 0.0 | 56.65
Bond | 0.00030719 | 0.00030719 | 0.00030719 | 0.0 | 0.01
Neigh | 0.28939 | 0.28939 | 0.28939 | 0.0 | 12.46
Comm | 0.055279 | 0.055279 | 0.055279 | 0.0 | 2.38
Output | 4.3714e-05 | 4.3714e-05 | 4.3714e-05 | 0.0 | 0.00
Modify | 0.63675 | 0.63675 | 0.63675 | 0.0 | 27.42
Other | | 0.02471 | | | 1.06
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -148,5 +122,58 @@ Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE file ave.out
Total wall time: 0:00:02
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 9.7731898 -55.150518 0 -54.060304 322.94195
6000 10.024842 -55.108242 0 -53.989956 336.6125
8000 10.118994 -55.092171 0 -53.963382 340.42078
10000 10.541359 -55.100316 0 -53.924412 340.09986
12000 10.023234 -55.07343 0 -53.955323 345.70551
14000 9.5912018 -55.115121 0 -54.045208 333.43739
16000 9.9450498 -55.077813 0 -53.968428 343.49906
18000 10.113744 -55.12201 0 -53.993806 332.32214
20000 9.9345204 -55.176339 0 -54.068128 316.83219
22000 10.585719 -55.110505 0 -53.929652 336.86599
24000 10.024757 -55.120592 0 -54.002315 333.13056
26000 9.7787474 -55.116664 0 -54.02583 332.51437
28000 9.6092087 -55.130413 0 -54.058491 328.69165
30000 9.8245787 -55.057678 0 -53.961731 350.86255
32000 10.066994 -55.08989 0 -53.966902 341.49724
34000 9.5677059 -55.17222 0 -54.104928 316.06902
36000 9.7252627 -55.079475 0 -53.994608 343.13769
38000 10.438984 -55.108991 0 -53.944506 336.32562
40000 10.238268 -55.080817 0 -53.938723 345.13228
Loop time of 19.5673 on 1 procs for 35000 steps with 864 atoms
Performance: 15454.339 ns/day, 0.002 hours/ns, 1788.697 timesteps/s, 1.545 Matom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.065 | 12.065 | 12.065 | 0.0 | 61.66
Bond | 0.002157 | 0.002157 | 0.002157 | 0.0 | 0.01
Neigh | 2.384 | 2.384 | 2.384 | 0.0 | 12.18
Comm | 0.40912 | 0.40912 | 0.40912 | 0.0 | 2.09
Output | 0.00050573 | 0.00050573 | 0.00050573 | 0.0 | 0.00
Modify | 4.5321 | 4.5321 | 4.5321 | 0.0 | 23.16
Other | | 0.1749 | | | 0.89
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1592 ave 1592 max 1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18144 ave 18144 max 18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21

129
examples/gjf/log.2Apr25.gjf.vhalf.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (2 Apr 2025 - Development - 4dd8c66390-modified)
LAMMPS (2 Apr 2025 - Development - 09d3ac0a1b-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
@ -22,7 +22,6 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.014 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
@ -47,33 +46,32 @@ pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all langevin/gjf 10 10 1 26488
thermo 200
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Langevin GJF methods: doi:10.1007/s10955-024-03345-1
- Langevin GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech_jensen_2024,
title = {On the Definition of Velocity in Discrete-Time, Stochastic Langevin Simulations},
volume = {191},
number = {10},
url = {https://doi.org/10.1007/s10955-024-03345-1},
doi = {10.1007/s10955-024-03345-1},
urldate = {2024-10-22},
journal = {J. Stat. Phys.},
author = {Gronbech-Jensen, Niels},
year = {2024},
pages = {137}
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -94,46 +92,22 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
200 9.8046819 -55.12733 0 -54.033603 329.70683
400 10.174622 -55.092357 0 -53.957363 340.4935
600 9.6157634 -55.174205 0 -54.101552 316.68047
800 9.9617862 -55.097525 0 -53.986273 339.257
1000 10.373198 -55.116484 0 -53.959338 335.09796
1200 10.064779 -55.17366 0 -54.050919 318.66487
1400 10.562182 -55.067856 0 -53.889628 349.23452
1600 9.7696935 -55.081542 0 -53.991718 342.92593
1800 10.454466 -55.130637 0 -53.964426 330.88658
2000 10.253701 -55.154093 0 -54.010277 323.15259
2200 9.6688957 -55.143479 0 -54.064899 325.16815
2400 10.059787 -55.134941 0 -54.012756 329.83534
2600 9.9050905 -55.096231 0 -53.991303 338.94947
2800 9.663551 -55.130202 0 -54.052218 328.77571
3000 9.950484 -55.123447 0 -54.013455 332.00143
3200 9.7210637 -55.120005 0 -54.035606 331.39812
3400 9.6457139 -55.080953 0 -54.004959 341.95838
3600 10.42249 -55.102379 0 -53.939734 339.66808
3800 10.276893 -55.126271 0 -53.979868 332.40943
4000 10.135481 -55.091551 0 -53.960922 340.60675
4200 10.129209 -55.084189 0 -53.95426 343.39315
4400 10.006953 -55.120704 0 -54.004413 331.57121
4600 10.497483 -55.144898 0 -53.973888 327.22996
4800 9.9230954 -55.126028 0 -54.019091 330.70489
5000 9.3726166 -55.076514 0 -54.030985 342.43571
Loop time of 2.0887 on 4 procs for 5000 steps with 864 atoms
Loop time of 2.09273 on 4 procs for 5000 steps with 864 atoms
Performance: 20682.713 ns/day, 0.001 hours/ns, 2393.833 timesteps/s, 2.068 Matom-step/s
62.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 20642.908 ns/day, 0.001 hours/ns, 2389.226 timesteps/s, 2.064 Matom-step/s
62.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53905 | 0.54518 | 0.5484 | 0.5 | 26.10
Bond | 0.00062355 | 0.00066183 | 0.0007207 | 0.0 | 0.03
Neigh | 0.10715 | 0.10937 | 0.11212 | 0.5 | 5.24
Comm | 0.94637 | 0.95041 | 0.95905 | 0.5 | 45.50
Output | 0.0061059 | 0.0061286 | 0.0061661 | 0.0 | 0.29
Modify | 0.26086 | 0.26355 | 0.26979 | 0.7 | 12.62
Other | | 0.2134 | | | 10.22
Pair | 0.53092 | 0.54173 | 0.55017 | 1.0 | 25.89
Bond | 0.00049283 | 0.00052862 | 0.00057217 | 0.0 | 0.03
Neigh | 0.10693 | 0.11084 | 0.1158 | 1.0 | 5.30
Comm | 0.95622 | 0.96088 | 0.96553 | 0.4 | 45.92
Output | 0.00027302 | 0.00027645 | 0.00028114 | 0.0 | 0.01
Modify | 0.2615 | 0.26289 | 0.2635 | 0.2 | 12.56
Other | | 0.2156 | | | 10.30
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -148,5 +122,58 @@ Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE file ave.out
Total wall time: 0:00:02
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 9.3726166 -55.076514 0 -54.030985 342.43571
6000 9.6911866 -55.129244 0 -54.048177 329.72537
8000 9.7296551 -55.101417 0 -54.016059 337.46595
10000 10.098808 -55.083292 0 -53.956755 343.4122
12000 10.114344 -55.090905 0 -53.962635 341.3438
14000 10.230012 -55.085051 0 -53.943878 342.45237
16000 9.5989709 -55.090733 0 -54.019954 339.07584
18000 10.016071 -55.030131 0 -53.912824 358.79514
20000 9.7197057 -55.104072 0 -54.019824 335.89619
22000 9.959647 -55.152019 0 -54.041005 323.05805
24000 10.075138 -55.115242 0 -53.991345 334.76239
26000 10.227192 -55.125275 0 -53.984416 332.10131
28000 10.177109 -55.107097 0 -53.971825 337.32979
30000 9.521036 -55.099011 0 -54.036925 337.10716
32000 10.265633 -55.077016 0 -53.93187 346.01018
34000 10.173978 -55.097068 0 -53.962146 339.63562
36000 9.6032778 -55.152202 0 -54.080942 321.61646
38000 9.8802995 -55.048407 0 -53.946245 351.82506
40000 10.372288 -55.087634 0 -53.93059 343.34304
Loop time of 17.6209 on 4 procs for 35000 steps with 864 atoms
Performance: 17161.415 ns/day, 0.001 hours/ns, 1986.275 timesteps/s, 1.716 Matom-step/s
64.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0439 | 5.1029 | 5.1534 | 2.0 | 28.96
Bond | 0.0031373 | 0.0034925 | 0.0038794 | 0.5 | 0.02
Neigh | 0.84082 | 0.87558 | 0.91665 | 3.0 | 4.97
Comm | 6.7337 | 6.7936 | 6.8487 | 1.6 | 38.55
Output | 0.0044073 | 0.004559 | 0.0049773 | 0.4 | 0.03
Modify | 3.3556 | 3.3647 | 3.3722 | 0.3 | 19.10
Other | | 1.476 | | | 8.38
Nlocal: 216 ave 222 max 210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 905.5 ave 911 max 899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.75 ave 4837 max 4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:19