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doc pages and sync qm vs qmmm fixes

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This commit is contained in:
Steve Plimpton
2023-02-22 17:21:40 -07:00
parent 17e1ed4869
commit 8b16301e5f
12 changed files with 5308 additions and 667 deletions
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2
examples/QUANTUM/NWChem/in.water.qmmm
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@ -56,4 +56,4 @@ thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
f_2 pe etotal press
thermo 1
run 2
run 10

2
examples/QUANTUM/NWChem/in.water.qmmm.plugin
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@ -60,4 +60,4 @@ variable p equal extract_setting(world_size)
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
extra "template.water.nw water.nw log.water.pwdft.qmmm.plugin.$p" &
command "run 1"
command "run 10"

2253
examples/QUANTUM/NWChem/log.8Feb23.water.pwdft.qmmm.mpi.2
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File diff suppressed because it is too large Load Diff

2447
examples/QUANTUM/NWChem/log.8Feb23.water.pwdft.qmmm.plugin.2
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File diff suppressed because it is too large Load Diff

34
examples/QUANTUM/NWChem/log.8Feb23.water.qmmm.mpi.1
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@ -94,7 +94,7 @@ fix_modify 2 energy yes
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
thermo 1
run 2
run 10
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
@ -115,24 +115,32 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
0 0 0 0 0.95937448 -170.68735 -169.72797 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
1 1.3827511 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
2 4.3658207 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
Loop time of 4.36586 on 1 procs for 2 steps with 6 atoms
0 0 0 0 0.95937448 -170.68735 -169.72798 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
1 1.3998539 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
2 4.2727994 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
3 8.6537003 10.410148 0.15515337 0.95908482 -170.73725 -169.77816 3.2558316 0 -10627.857 -10794.38 -10794.224 -393.99
4 14.050859 18.303344 0.27279397 0.95886179 -170.78053 -169.82167 3.1495694 0 -10627.837 -10794.509 -10794.236 -408.93357
5 19.424842 28.194049 0.42020553 0.9585778 -170.83354 -169.87496 3.016716 0 -10627.813 -10794.671 -10794.251 -428.10518
6 25.315002 39.895741 0.59460812 0.95823491 -170.90236 -169.94412 2.8599973 0 -10627.779 -10794.864 -10794.269 -451.5421
7 31.945826 53.187854 0.79271445 0.95783553 -170.98485 -170.02702 2.6826348 0 -10627.739 -10795.083 -10794.29 -479.20295
8 38.843432 67.819953 1.010792 0.95738252 -171.0742 -170.11682 2.4882829 0 -10627.697 -10795.325 -10794.314 -510.99723
9 46.718156 83.516497 1.2447341 0.95687915 -171.17882 -170.22194 2.2809581 0 -10627.645 -10795.586 -10794.342 -546.9588
10 54.366233 99.982124 1.4901386 0.95632904 -171.28928 -170.33295 2.0649603 0 -10627.594 -10795.862 -10794.372 -586.9531
Loop time of 54.3663 on 1 procs for 10 steps with 6 atoms
Performance: 0.004 ns/day, 6063.691 hours/ns, 0.458 timesteps/s, 2.749 atom-step/s
Performance: 0.002 ns/day, 15101.736 hours/ns, 0.184 timesteps/s, 1.104 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.572e-06 | 7.572e-06 | 7.572e-06 | 0.0 | 0.00
Bond | 5.119e-06 | 5.119e-06 | 5.119e-06 | 0.0 | 0.00
Pair | 3.4059e-05 | 3.4059e-05 | 3.4059e-05 | 0.0 | 0.00
Bond | 1.1659e-05 | 1.1659e-05 | 1.1659e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.881e-06 | 2.881e-06 | 2.881e-06 | 0.0 | 0.00
Output | 5.439e-05 | 5.439e-05 | 5.439e-05 | 0.0 | 0.00
Modify | 4.3658 | 4.3658 | 4.3658 | 0.0 |100.00
Other | | 6.093e-06 | | | 0.00
Comm | 1.0583e-05 | 1.0583e-05 | 1.0583e-05 | 0.0 | 0.00
Output | 0.00016554 | 0.00016554 | 0.00016554 | 0.0 | 0.00
Modify | 54.366 | 54.366 | 54.366 | 0.0 |100.00
Other | | 1.567e-05 | | | 0.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -146,4 +154,4 @@ Ave neighs/atom = 2
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:11
Total wall time: 0:01:59

37
examples/QUANTUM/NWChem/log.8Feb23.water.qmmm.plugin.2
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@ -96,8 +96,8 @@ thermo 1
variable p equal extract_setting(world_size)
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.$p" command "run 1"
run 1
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" extra "template.water.nw water.nw log.water.pwdft.qmmm.plugin.$p" command "run 10"
run 10
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
@ -118,23 +118,32 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.453 | 7.453 | 7.453 Mbytes
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
0 0 0 0 0.95937448 -170.68735 -169.72797 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
1 1.2206038 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
Loop time of 1.22062 on 2 procs for 1 steps with 6 atoms
0 0 0 0 0.95937448 -170.68735 -169.72798 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
1 1.2511997 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
2 3.8385452 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
3 7.7938711 10.410148 0.15515337 0.95908482 -170.73725 -169.77816 3.2558316 0 -10627.857 -10794.38 -10794.224 -393.99
4 12.421381 18.303344 0.27279396 0.95886179 -170.78051 -169.82164 3.1495694 0 -10627.837 -10794.509 -10794.236 -408.93334
5 17.269932 28.194049 0.42020553 0.9585778 -170.83354 -169.87496 3.016716 0 -10627.813 -10794.671 -10794.251 -428.10518
6 22.792492 39.895742 0.59460814 0.95823491 -170.90235 -169.94412 2.8599973 0 -10627.779 -10794.864 -10794.269 -451.54206
7 28.768848 53.187856 0.79271447 0.95783553 -170.98485 -170.02701 2.6826348 0 -10627.739 -10795.083 -10794.29 -479.20292
8 34.74838 67.819955 1.010792 0.95738253 -171.07427 -170.11688 2.4882829 0 -10627.697 -10795.325 -10794.314 -510.99784
9 41.409904 83.516502 1.2447341 0.95687915 -171.17899 -170.22211 2.2809581 0 -10627.645 -10795.586 -10794.342 -546.96024
10 48.305399 99.982132 1.4901387 0.95632904 -171.28935 -170.33302 2.0649603 0 -10627.594 -10795.862 -10794.372 -586.95371
Loop time of 48.3054 on 2 procs for 10 steps with 6 atoms
Performance: 0.007 ns/day, 3390.614 hours/ns, 0.819 timesteps/s, 4.916 atom-step/s
88.7% CPU use with 2 MPI tasks x no OpenMP threads
Performance: 0.002 ns/day, 13418.171 hours/ns, 0.207 timesteps/s, 1.242 atom-step/s
93.0% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.563e-06 | 4.9165e-06 | 5.27e-06 | 0.0 | 0.00
Bond | 1.201e-06 | 2.0745e-06 | 2.948e-06 | 0.0 | 0.00
Pair | 4.6638e-05 | 4.8108e-05 | 4.9577e-05 | 0.0 | 0.00
Bond | 1.5399e-05 | 2.157e-05 | 2.7741e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.511e-06 | 8.0675e-06 | 8.624e-06 | 0.0 | 0.00
Output | 1.7987e-05 | 1.9748e-05 | 2.151e-05 | 0.0 | 0.00
Modify | 1.2206 | 1.2206 | 1.2206 | 0.0 |100.00
Other | | 7.148e-06 | | | 0.00
Comm | 7.9132e-05 | 8.3424e-05 | 8.7716e-05 | 0.0 | 0.00
Output | 0.0001854 | 0.00020373 | 0.00022205 | 0.0 | 0.00
Modify | 48.305 | 48.305 | 48.305 | 0.0 |100.00
Other | | 4.187e-05 | | | 0.00
Nlocal: 3 ave 4 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 1
@ -148,4 +157,4 @@ Ave neighs/atom = 2
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00
Total wall time: 0:01:45