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simplify and shorten charmmfsw example. add reference logs.

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This commit is contained in:
Axel Kohlmeyer
2024-07-26 19:34:23 -04:00
parent e7d338573f
commit 2a99b9957d
3 changed files with 448 additions and 6 deletions
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12
examples/charmmfsw/in.charmmfsw
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@ -25,13 +25,13 @@ fix_modify cmap energy yes
read_data data.charmmfsw.gz fix cmap crossterm CMAP
neighbor 2 bin
neigh_modify delay 5 every 1
neigh_modify delay 2 every 1
fix 1 all shake 1e-6 500 0 m 1.008 a 142
fix 2 all npt temp 303.15 303.15 100.0 iso 0.9869233 0.9869233 1000 couple xyz mtk no pchain 0
fix 1 all shake 1e-6 100 100 m 1.008 a 142
fix 2 all nvt temp 303.15 303.15 100.0
thermo 100
thermo_style custom step time spcpu cpuremain etotal evdwl ecoul elong edihed pe ke temp press vol
thermo 10
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
run 1000
run 100

221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1 Normal file
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@ -0,0 +1,221 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# charmmfsw example generated by https://charmm-gui.org/
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
#
# Dependencies: packages MOLECULE / KSPACE / RIGID
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
pair_modify mix arithmetic
kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
special_bonds charmm
improper_style harmonic
timestep 2
fix cmap all cmap charmmff.cmap
Reading CMAP parameters from: charmmff.cmap
Read in CMAP data for 2 crossterm types
fix_modify cmap energy yes
read_data data.charmmfsw.gz fix cmap crossterm CMAP
Reading data file ...
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
reading atoms ...
10245 atoms
reading velocities ...
10245 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
15 = max angles/atom
scanning dihedrals ...
48 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
reading bonds ...
6973 bonds
reading angles ...
4057 angles
reading dihedrals ...
1363 dihedrals
reading impropers ...
70 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.072 seconds
neighbor 2 bin
neigh_modify delay 2 every 1
fix 1 all shake 1e-6 100 100 m 1.008 a 142
Finding SHAKE clusters ...
75 = # of size 2 clusters
47 = # of size 3 clusters
9 = # of size 4 clusters
3265 = # of frozen angles
find clusters CPU = 0.003 seconds
fix 2 all nvt temp 303.15 303.15 100.0
thermo 10
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.27938162
grid = 54 54 54
stencil order = 5
estimated absolute RMS force accuracy = 0.00036407395
estimated relative force accuracy = 1.0963718e-06
using double precision FFTW3
3d grid and FFT values/proc = 226981 157464
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 2 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmmfsw/coul/long, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: full/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 16 1.09 1.38032e-07 6
Bond: 18 1.09 1.00046e-07 3
Bond: 34 1.111 1.11388e-06 10
Bond: 39 1.111 4.83041e-08 5
Bond: 43 1.111 1.97842e-07 10
Bond: 44 1.111 1.71815e-06 10
Bond: 59 1.111 8.42509e-08 2
Bond: 62 1.111 2.84854e-08 2
Bond: 63 1.111 2.14153e-07 46
Bond: 64 1.111 1.59305e-07 18
Bond: 65 1.08 5.67061e-07 16
Bond: 66 1.08 1.43965e-06 4
Bond: 67 1 1.81926e-07 10
Bond: 68 1.01 0 1
Bond: 69 1.08 1.34571e-07 5
Bond: 70 1.09 0 1
Bond: 71 1.083 0 1
Bond: 72 0.9572 2.71955e-07 6530
Bond: 75 1 1.46045e-07 10
Bond: 79 0.997 5.24499e-07 17
Bond: 81 1 1.32984e-07 4
Bond: 84 1.04 7.65389e-07 9
Bond: 87 1 0 1
Bond: 95 0.96 5.75241e-07 2
Bond: 97 1.325 4.3613e-08 3
Angle: 142 104.52 2.67611e-05 3265
Per MPI rank memory allocation (min/avg/max) = 143.6 | 143.6 | 143.6 Mbytes
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2031
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
SHAKE stats (type/ave/delta/count) on step 100
Bond: 16 1.09 3.78281e-07 6
Bond: 18 1.09 1.12288e-07 3
Bond: 34 1.111 7.60709e-07 10
Bond: 39 1.111 2.37855e-07 5
Bond: 43 1.111 6.00872e-07 10
Bond: 44 1.111 3.75324e-07 10
Bond: 59 1.111 1.12311e-07 2
Bond: 62 1.111 2.99471e-07 2
Bond: 63 1.111 6.10589e-07 46
Bond: 64 1.111 4.50733e-07 18
Bond: 65 1.08 2.90668e-07 16
Bond: 66 1.08 1.61592e-07 4
Bond: 67 1 5.4508e-07 10
Bond: 68 1.01 0 1
Bond: 69 1.08 4.1398e-07 5
Bond: 70 1.09 0 1
Bond: 71 1.083 0 1
Bond: 72 0.9572 1.76706e-06 6530
Bond: 75 1 3.96686e-07 10
Bond: 79 0.997 7.72922e-07 17
Bond: 81 1 1.30673e-07 4
Bond: 84 1.04 1.44551e-07 9
Bond: 87 1 0 1
Bond: 95 0.96 1.03526e-07 2
Bond: 97 1.325 3.64689e-08 3
Angle: 142 104.52 0.000130126 3265
100 -27913.241 3159.0677 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
Loop time of 11.5304 on 1 procs for 100 steps with 10245 atoms
Performance: 1.499 ns/day, 16.014 hours/ns, 8.673 timesteps/s, 88.852 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.6772 | 8.6772 | 8.6772 | 0.0 | 75.25
Bond | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.11
Kspace | 1.2286 | 1.2286 | 1.2286 | 0.0 | 10.66
Neigh | 1.5276 | 1.5276 | 1.5276 | 0.0 | 13.25
Comm | 0.010441 | 0.010441 | 0.010441 | 0.0 | 0.09
Output | 0.00055001 | 0.00055001 | 0.00055001 | 0.0 | 0.00
Modify | 0.07101 | 0.07101 | 0.07101 | 0.0 | 0.62
Other | | 0.002628 | | | 0.02
Nlocal: 10245 ave 10245 max 10245 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 30479 ave 30479 max 30479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7.05928e+06 ave 7.05928e+06 max 7.05928e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7059275
Ave neighs/atom = 689.04588
Ave special neighs/atom = 2.3664226
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:11

221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4 Normal file
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@ -0,0 +1,221 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# charmmfsw example generated by https://charmm-gui.org/
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
#
# Dependencies: packages MOLECULE / KSPACE / RIGID
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
pair_modify mix arithmetic
kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
special_bonds charmm
improper_style harmonic
timestep 2
fix cmap all cmap charmmff.cmap
Reading CMAP parameters from: charmmff.cmap
Read in CMAP data for 2 crossterm types
fix_modify cmap energy yes
read_data data.charmmfsw.gz fix cmap crossterm CMAP
Reading data file ...
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
reading atoms ...
10245 atoms
reading velocities ...
10245 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
15 = max angles/atom
scanning dihedrals ...
48 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
reading bonds ...
6973 bonds
reading angles ...
4057 angles
reading dihedrals ...
1363 dihedrals
reading impropers ...
70 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.068 seconds
neighbor 2 bin
neigh_modify delay 2 every 1
fix 1 all shake 1e-6 100 100 m 1.008 a 142
Finding SHAKE clusters ...
75 = # of size 2 clusters
47 = # of size 3 clusters
9 = # of size 4 clusters
3265 = # of frozen angles
find clusters CPU = 0.001 seconds
fix 2 all nvt temp 303.15 303.15 100.0
thermo 10
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.27938162
grid = 54 54 54
stencil order = 5
estimated absolute RMS force accuracy = 0.00036407395
estimated relative force accuracy = 1.0963718e-06
using double precision FFTW3
3d grid and FFT values/proc = 70516 40824
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 2 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmmfsw/coul/long, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: full/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 16 1.09 1.38032e-07 6
Bond: 18 1.09 1.00046e-07 3
Bond: 34 1.111 1.11388e-06 10
Bond: 39 1.111 4.83041e-08 5
Bond: 43 1.111 1.97842e-07 10
Bond: 44 1.111 1.71815e-06 10
Bond: 59 1.111 8.42509e-08 2
Bond: 62 1.111 2.84854e-08 2
Bond: 63 1.111 2.14153e-07 46
Bond: 64 1.111 1.59305e-07 18
Bond: 65 1.08 5.67061e-07 16
Bond: 66 1.08 1.43965e-06 4
Bond: 67 1 1.81926e-07 10
Bond: 68 1.01 0 1
Bond: 69 1.08 1.34571e-07 5
Bond: 70 1.09 0 1
Bond: 71 1.083 0 1
Bond: 72 0.9572 2.71955e-07 6530
Bond: 75 1 1.46045e-07 10
Bond: 79 0.997 5.24499e-07 17
Bond: 81 1 1.32984e-07 4
Bond: 84 1.04 7.65389e-07 9
Bond: 87 1 0 1
Bond: 95 0.96 5.75241e-07 2
Bond: 97 1.325 4.3613e-08 3
Angle: 142 104.52 2.67611e-05 3265
Per MPI rank memory allocation (min/avg/max) = 76.88 | 77.06 | 77.25 Mbytes
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2032
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
SHAKE stats (type/ave/delta/count) on step 100
Bond: 16 1.09 3.78281e-07 6
Bond: 18 1.09 1.12288e-07 3
Bond: 34 1.111 7.60709e-07 10
Bond: 39 1.111 2.37855e-07 5
Bond: 43 1.111 6.00872e-07 10
Bond: 44 1.111 3.75324e-07 10
Bond: 59 1.111 1.12311e-07 2
Bond: 62 1.111 2.99471e-07 2
Bond: 63 1.111 6.10589e-07 46
Bond: 64 1.111 4.50733e-07 18
Bond: 65 1.08 2.90668e-07 16
Bond: 66 1.08 1.61592e-07 4
Bond: 67 1 5.4508e-07 10
Bond: 68 1.01 0 1
Bond: 69 1.08 4.1398e-07 5
Bond: 70 1.09 0 1
Bond: 71 1.083 0 1
Bond: 72 0.9572 1.76706e-06 6530
Bond: 75 1 3.96686e-07 10
Bond: 79 0.997 7.72922e-07 17
Bond: 81 1 1.30673e-07 4
Bond: 84 1.04 1.44551e-07 9
Bond: 87 1 0 1
Bond: 95 0.96 1.03526e-07 2
Bond: 97 1.325 3.64689e-08 3
Angle: 142 104.52 0.000130126 3265
100 -27913.241 3159.0676 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
Loop time of 3.49837 on 4 procs for 100 steps with 10245 atoms
Performance: 4.939 ns/day, 4.859 hours/ns, 28.585 timesteps/s, 292.851 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4572 | 2.5133 | 2.5634 | 2.6 | 71.84
Bond | 0.0040264 | 0.0050718 | 0.0069286 | 1.6 | 0.14
Kspace | 0.45979 | 0.50903 | 0.56364 | 5.6 | 14.55
Neigh | 0.42029 | 0.42034 | 0.42036 | 0.0 | 12.02
Comm | 0.013207 | 0.013292 | 0.013404 | 0.1 | 0.38
Output | 0.00026525 | 0.00029549 | 0.00038249 | 0.0 | 0.01
Modify | 0.035024 | 0.035546 | 0.03621 | 0.3 | 1.02
Other | | 0.001504 | | | 0.04
Nlocal: 2561.25 ave 2599 max 2520 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 16491.5 ave 16541 max 16442 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.99855e+06 ave 2.04035e+06 max 1.95468e+06 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 7994217
Ave neighs/atom = 780.30425
Ave special neighs/atom = 2.3664226
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:03