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reorganize example, potentials, logfiles

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This commit is contained in:
Axel Kohlmeyer
2024-09-10 21:14:52 -04:00
parent 2b03a1ce17
commit 6488fd2a48
7 changed files with 18267 additions and 18058 deletions
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4
examples/ctip/NiO.ctip
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# CTIP potential parameters for Ni-O
# X (eV) J (eV) gamma (1/ang) zeta (1/ang) Z (e) qmin qmax omega
Ni -5.840000 14.157390 0.549290 0.000000 0.000000 0.000000 2.000000 100.000
O 0.000000 15.655862 1.428571 0.000000 0.000000 -2.000000 0.000000 100.000

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examples/ctip/NiO.ctip Symbolic link
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../../potentials/NiO.ctip

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examples/ctip/NiO.eam.fs
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examples/ctip/NiO.eam.fs Symbolic link
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../../potentials/NiO.eam.fs

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examples/ctip/log.10Sep24.ctip.g++.1 Normal file
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-115-g2b03a1ce17-modified)
using 1 OpenMP thread(s) per MPI task
#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
#Initialize
units metal
atom_style charge
dimension 3
boundary p p p
#Create Structure
read_data data.ctip
Reading data file ...
orthogonal box = (0 0 0) to (24.719478 24.719478 24.719478)
1 by 1 by 1 MPI processor grid
reading atoms ...
1728 atoms
read_data CPU = 0.003 seconds
#Define Charges
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
864 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
#Define Potential
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
Reading eam/fs potential file NiO.eam.fs with DATE: 2024-04-29
pair_coeff * * coul/ctip NiO.ctip Ni O
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
#Setup
timestep 0.001
thermo 100
thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
#Minimization
fix relax all box/relax iso 0
minimize 1e-10 1e-10 100000 100000
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
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair eam/fs, perpetual, trim from (2)
attributes: half, newton on, cut 8
pair build: trim
stencil: none
bin: none
(2) pair coul/ctip, perpetual, half/full from (3)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(3) fix qeq/ctip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
(src/min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 55.22 | 55.22 | 55.22 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 0 -9633.183 24.719478 24.719478 24.719478 -1482.4422 -1482.4422 -1482.4422 1.2374584 -1.2374584
6 0 -9633.1929 24.707584 24.707584 24.707584 -0.41006619 -0.41006619 -0.41006619 1.2410585 -1.2410585
Loop time of 1.50809 on 1 procs for 6 steps with 1728 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9633.18301864113 -9633.19294374889 -9633.19294376207
Force two-norm initial, final = 41.928235 0.011586833
Force max component initial, final = 41.928235 0.011586832
Final line search alpha, max atom move = 0.0017273131 2.0014087e-05
Iterations, force evaluations = 6 12
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4921 | 0.4921 | 0.4921 | 0.0 | 32.63
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00054887 | 0.00054887 | 0.00054887 | 0.0 | 0.04
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 1.0134 | 1.0134 | 1.0134 | 0.0 | 67.20
Other | | 0.002055 | | | 0.14
Nlocal: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13897 ave 13897 max 13897 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 216000 ave 216000 max 216000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.34317e+06 ave 2.34317e+06 max 2.34317e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2343168
Ave neighs/atom = 1356
Neighbor list builds = 0
Dangerous builds = 0
unfix relax
#Dynamics
reset_timestep 0
variable T equal 1000
variable rnd equal round(random(0,999,${T}))
variable rnd equal round(random(0,999,1000))
velocity all create ${T} ${rnd} mom yes rot yes
velocity all create 1000 ${rnd} mom yes rot yes
velocity all create 1000 233 mom yes rot yes
fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 1000 0.1 iso 0 0 1
run 1000
Per MPI rank memory allocation (min/avg/max) = 54.35 | 54.35 | 54.35 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 1000 -9633.1929 24.707584 24.707584 24.707584 15934.422 15754.221 15735.035 1.2410585 -1.2410585
100 600.77742 -9528.0586 24.816528 24.816528 24.816528 -16706.733 -15440.638 -17748.278 1.2181933 -1.2181933
200 578.84892 -9490.9798 24.812599 24.812599 24.812599 -5869.8414 -4841.5113 -6712.1711 1.2254412 -1.2254412
300 694.79572 -9478.5505 24.764328 24.764328 24.764328 14631.006 13819.424 13758.131 1.2372038 -1.2372038
400 803.94267 -9462.254 24.866658 24.866658 24.866658 -4649.4599 -6022.0633 -7748.7857 1.2086114 -1.2086114
500 893.70618 -9441.0062 24.891744 24.891744 24.891744 -5778.5831 -8212.0502 -4180.8669 1.2001224 -1.2001224
600 947.22132 -9416.7533 24.86364 24.86364 24.86364 11263.568 12949.819 11329.619 1.2115051 -1.2115051
700 1040.4865 -9409.8379 24.933876 24.933876 24.933876 -6572.21 -8530.9018 -3289.7496 1.1902748 -1.1902748
800 1037.9463 -9398.4839 24.935133 24.935133 24.935133 -4681.3294 -2573.8745 -7152.1217 1.1880295 -1.1880295
900 1049.4497 -9411.1235 24.899756 24.899756 24.899756 3245.0554 8109.3022 5937.385 1.202401 -1.202401
1000 964.21894 -9412.4498 24.926456 24.926456 24.926456 -7644.4098 -5151.7326 -8343.9454 1.1908842 -1.1908842
Loop time of 170.213 on 1 procs for 1000 steps with 1728 atoms
Performance: 0.508 ns/day, 47.281 hours/ns, 5.875 timesteps/s, 10.152 katom-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 | 35.178 | 35.178 | 35.178 | 0.0 | 20.67
Neigh | 0.22537 | 0.22537 | 0.22537 | 0.0 | 0.13
Comm | 0.04471 | 0.04471 | 0.04471 | 0.0 | 0.03
Output | 0.00055646 | 0.00055646 | 0.00055646 | 0.0 | 0.00
Modify | 134.75 | 134.75 | 134.75 | 0.0 | 79.17
Other | | 0.0133 | | | 0.01
Nlocal: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13901 ave 13901 max 13901 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 210392 ave 210392 max 210392 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.23448e+06 ave 2.23448e+06 max 2.23448e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2234478
Ave neighs/atom = 1293.1007
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:02:52

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examples/ctip/log.ctip → examples/ctip/log.10Sep24.ctip.g++.4
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-185-ge2e17b1326)
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-115-g2b03a1ce17-modified)
using 1 OpenMP thread(s) per MPI task
#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
@ -12,10 +13,10 @@ boundary p p p
read_data data.ctip
Reading data file ...
orthogonal box = (0 0 0) to (24.719478 24.719478 24.719478)
5 by 2 by 2 MPI processor grid
1 by 2 by 2 MPI processor grid
reading atoms ...
1728 atoms
read_data CPU = 0.411 seconds
read_data CPU = 0.007 seconds
#Define Charges
group type1 type 1
@ -30,6 +31,7 @@ compute q2 type2 reduce ave c_charge2
#Define Potential
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
Reading eam/fs potential file NiO.eam.fs with DATE: 2024-04-29
pair_coeff * * coul/ctip NiO.ctip Ni O
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
@ -41,6 +43,25 @@ thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
#Minimization
fix relax all box/relax iso 0
minimize 1e-10 1e-10 100000 100000
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
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
@ -64,42 +85,42 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
(../min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 10.02 | 10.44 | 11.08 Mbytes
(src/min.cpp:219)
Per MPI rank memory allocation (min/avg/max) = 19.71 | 19.71 | 19.71 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 0 -9633.183 24.719478 24.719478 24.719478 -1482.4422 -1482.4422 -1482.4422 1.2374584 -1.2374584
6 0 -9633.1929 24.70758 24.70758 24.70758 0.0058029496 0.0058029495 0.0058029496 1.2410596 -1.2410596
Loop time of 0.141029 on 20 procs for 6 steps with 1728 atoms
6 0 -9633.1929 24.70758 24.70758 24.70758 0.0058029359 0.0058029361 0.0058029362 1.2410596 -1.2410596
Loop time of 0.401983 on 4 procs for 6 steps with 1728 atoms
99.0% CPU use with 20 MPI tasks x no OpenMP threads
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9633.18301863317 -9633.19294375406 -9633.19294375059
Force two-norm initial, final = 41.928235 0.00016400809
Force max component initial, final = 41.928235 0.00016396812
Final line search alpha, max atom move = 0.0069092778 1.1329013e-06
-9633.18301863957 -9633.19294375212 -9633.19294375325
Force two-norm initial, final = 41.928235 0.00016399002
Force max component initial, final = 41.928235 0.00016396774
Final line search alpha, max atom move = 0.0069092828 1.1328995e-06
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035558 | 0.041786 | 0.051032 | 3.7 | 29.63
Pair | 0.13767 | 0.13917 | 0.14066 | 0.3 | 34.62
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00095936 | 0.010188 | 0.0164 | 7.4 | 7.22
Comm | 0.0032823 | 0.004768 | 0.0062486 | 1.5 | 1.19
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.087686 | 0.087716 | 0.087736 | 0.0 | 62.20
Other | | 0.001339 | | | 0.95
Modify | 0.2568 | 0.25681 | 0.25682 | 0.0 | 63.89
Other | | 0.001238 | | | 0.31
Nlocal: 86.4 ave 108 max 72 min
Histogram: 12 0 0 0 0 0 0 0 0 8
Nghost: 5617.4 ave 5704 max 5307 min
Histogram: 4 0 0 0 0 0 0 0 0 16
Neighs: 10800 ave 13500 max 9000 min
Histogram: 12 0 0 0 0 0 0 0 0 8
FullNghs: 117158 ave 146448 max 97632 min
Histogram: 12 0 0 0 0 0 0 0 0 8
Nlocal: 432 ave 432 max 432 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 8593 ave 8593 max 8593 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 54000 ave 54000 max 54000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 585792 ave 585792 max 585792 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2343168
Ave neighs/atom = 1356
@ -119,44 +140,45 @@ fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 ${T} 0.1 iso 0 0 1
fix npt all npt temp 1000 1000 0.1 iso 0 0 1
run 1000
Per MPI rank memory allocation (min/avg/max) = 9.149 | 9.566 | 10.2 Mbytes
Per MPI rank memory allocation (min/avg/max) = 18.83 | 18.83 | 18.83 Mbytes
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
0 1000 -9633.1929 24.70758 24.70758 24.70758 15934.845 15754.643 15735.458 1.2410596 -1.2410596
100 600.77735 -9528.0587 24.816528 24.816528 24.816528 -16706.896 -15440.795 -17748.438 1.2181931 -1.2181931
200 578.84855 -9490.9798 24.812601 24.812601 24.812601 -5870.3683 -4842.0362 -6712.6896 1.2254406 -1.2254406
300 694.79571 -9478.5506 24.764327 24.764327 24.764327 14631.481 13819.893 13758.612 1.2372043 -1.2372043
400 803.94245 -9462.254 24.866657 24.866657 24.866657 -4649.2497 -6021.9034 -7748.6267 1.2086116 -1.2086116
400 803.94245 -9462.254 24.866657 24.866657 24.866657 -4649.2498 -6021.9034 -7748.6268 1.2086116 -1.2086116
500 893.70588 -9441.0062 24.891745 24.891745 24.891745 -5778.8391 -8212.3527 -4181.1625 1.2001221 -1.2001221
600 947.22119 -9416.7533 24.863639 24.863639 24.863639 11263.656 12950.02 11329.777 1.2115052 -1.2115052
700 1040.4867 -9409.838 24.933876 24.933876 24.933876 -6572.1906 -8531.0436 -3289.5795 1.1902748 -1.1902748
800 1037.9461 -9398.4839 24.935134 24.935134 24.935134 -4681.5289 -2573.9057 -7152.37 1.1880294 -1.1880294
900 1049.4492 -9411.1233 24.899755 24.899755 24.899755 3245.1762 8109.7345 5937.7248 1.2024012 -1.2024012
1000 964.21897 -9412.4497 24.926456 24.926456 24.926456 -7644.82 -5151.3661 -8344.385 1.1908843 -1.1908843
Loop time of 22.2998 on 20 procs for 1000 steps with 1728 atoms
700 1040.4867 -9409.838 24.933876 24.933876 24.933876 -6572.1906 -8531.0436 -3289.5796 1.1902748 -1.1902748
800 1037.9461 -9398.4839 24.935134 24.935134 24.935134 -4681.529 -2573.9058 -7152.3701 1.1880294 -1.1880294
900 1049.4492 -9411.1233 24.899755 24.899755 24.899755 3245.1763 8109.7341 5937.7247 1.2024012 -1.2024012
1000 964.21897 -9412.4497 24.926456 24.926456 24.926456 -7644.8199 -5151.3658 -8344.3846 1.1908843 -1.1908843
Loop time of 69.128 on 4 procs for 1000 steps with 1728 atoms
Performance: 3.874 ns/day, 6.194 hours/ns, 44.843 timesteps/s, 77.489 katom-step/s
99.7% CPU use with 20 MPI tasks x no OpenMP threads
Performance: 1.250 ns/day, 19.202 hours/ns, 14.466 timesteps/s, 24.997 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0411 | 4.7454 | 5.7909 | 34.0 | 21.28
Neigh | 0.014489 | 0.017484 | 0.022231 | 1.9 | 0.08
Comm | 0.1939 | 1.2368 | 1.9393 | 66.5 | 5.55
Output | 0.00054344 | 0.00056061 | 0.00086343 | 0.0 | 0.00
Modify | 16.272 | 16.28 | 16.286 | 0.1 | 73.01
Other | | 0.01926 | | | 0.09
Pair | 14.249 | 14.363 | 14.46 | 2.5 | 20.78
Neigh | 0.087801 | 0.088947 | 0.08999 | 0.3 | 0.13
Comm | 0.40947 | 0.50585 | 0.62043 | 13.5 | 0.73
Output | 0.00041542 | 0.00043801 | 0.00050525 | 0.0 | 0.00
Modify | 54.157 | 54.158 | 54.159 | 0.0 | 78.34
Other | | 0.01134 | | | 0.02
Nlocal: 86.4 ave 113 max 67 min
Histogram: 4 3 1 3 0 3 1 1 3 1
Nghost: 5641.65 ave 5713 max 5446 min
Histogram: 4 0 0 0 0 0 0 1 7 8
Neighs: 10519.6 ave 13753 max 8190 min
Histogram: 4 3 0 4 0 3 1 1 3 1
FullNghs: 111724 ave 146057 max 86634 min
Histogram: 4 3 1 3 0 3 1 1 3 1
Nlocal: 432 ave 446 max 421 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 8594.5 ave 8608 max 8579 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 52598 ave 54464 max 51211 min
Histogram: 1 0 1 0 1 0 0 0 0 1
FullNghs: 558619 ave 576963 max 544131 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 2234476
Ave neighs/atom = 1293.0995
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:01:09