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move and update ctip example

This commit is contained in:
Axel Kohlmeyer 2024-09-12 00:17:21 -04:00
parent 5a12c762f3
commit 58272bca00
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GPG Key ID: D9B44E93BF0C375A
7 changed files with 78 additions and 74 deletions
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0
examples/ctip/NiO.ctip → examples/streitz/NiO.ctip
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examples/ctip/NiO.eam.fs → examples/streitz/NiO.eam.fs
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examples/ctip/data.ctip → examples/streitz/data.ctip
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examples/ctip/in.ctip → examples/streitz/in.ctip
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78
examples/ctip/log.10Sep24.ctip.g++.1 → examples/streitz/log.11Sep24.ctip.g++.1
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@ -1,4 +1,5 @@
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-115-g2b03a1ce17-modified)
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-269-g5a12c762f3-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
@ -16,7 +17,7 @@ Reading data file ...
1 by 1 by 1 MPI processor grid
reading atoms ...
1728 atoms
read_data CPU = 0.003 seconds
read_data CPU = 0.004 seconds
#Define Charges
group type1 type 1
@ -33,6 +34,7 @@ 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
Reading coul/ctip potential file NiO.ctip with DATE: 2024-09-11
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
#Setup
@ -88,30 +90,30 @@ WARNING: Energy due to 1 extra global DOFs will be included in minimizer energie
(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
0 0 -9633.183 24.719478 24.719478 24.719478 -1491.273 -1491.273 -1491.273 1.2374666 -1.2374666
6 0 -9633.1929 24.707505 24.707505 24.707505 0.0050470506 0.0050470504 0.0050470502 1.2410908 -1.2410908
Loop time of 1.04745 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
-9633.18301850704 -9633.19294329023 -9633.19294333485
Force two-norm initial, final = 42.177998 0.00014264694
Force max component initial, final = 42.177998 0.00014260857
Final line search alpha, max atom move = 0.0079490417 1.1336014e-06
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4921 | 0.4921 | 0.4921 | 0.0 | 32.63
Pair | 0.3534 | 0.3534 | 0.3534 | 0.0 | 33.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00054887 | 0.00054887 | 0.00054887 | 0.0 | 0.04
Comm | 0.0004205 | 0.0004205 | 0.0004205 | 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
Modify | 0.69216 | 0.69216 | 0.69216 | 0.0 | 66.08
Other | | 0.001461 | | | 0.14
Nlocal: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -142,43 +144,43 @@ 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
0 1000 -9633.1929 24.707505 24.707505 24.707505 15934.991 15754.787 15735.602 1.2410908 -1.2410908
100 600.77874 -9528.0602 24.816519 24.816519 24.816519 -16709.313 -15443.072 -17750.832 1.2181988 -1.2181988
200 578.84295 -9490.9794 24.812627 24.812627 24.812627 -5879.8769 -4851.4601 -6722.107 1.2254363 -1.2254363
300 694.7973 -9478.5512 24.764285 24.764285 24.764285 14639.415 13827.989 13766.766 1.2372201 -1.2372201
400 803.93731 -9462.2542 24.866629 24.866629 24.866629 -4644.2854 -6017.2884 -7744.2567 1.2086229 -1.2086229
500 893.70492 -9441.0072 24.891756 24.891756 24.891756 -5784.2232 -8219.1644 -4187.392 1.2001224 -1.2001224
600 947.21728 -9416.7532 24.863623 24.863623 24.863623 11265.076 12952.469 11331.883 1.2115124 -1.2115124
700 1040.4874 -9409.8397 24.933859 24.933859 24.933859 -6570.5927 -8532.7457 -3284.7317 1.1902794 -1.1902794
800 1037.9366 -9398.4828 24.935138 24.935138 24.935138 -4681.8676 -2576.4998 -7160.562 1.1880324 -1.1880324
900 1049.4211 -9411.115 24.899733 24.899733 24.899733 3250.2695 8121.9271 5945.0542 1.2024086 -1.2024086
1000 964.18789 -9412.4405 24.926442 24.926442 24.926442 -7652.603 -5142.9259 -8351.8835 1.1908935 -1.1908935
Loop time of 183.932 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
Performance: 0.470 ns/day, 51.092 hours/ns, 5.437 timesteps/s, 9.395 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 | 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
Pair | 37.347 | 37.347 | 37.347 | 0.0 | 20.30
Neigh | 0.22667 | 0.22667 | 0.22667 | 0.0 | 0.12
Comm | 0.052514 | 0.052514 | 0.052514 | 0.0 | 0.03
Output | 0.00053967 | 0.00053967 | 0.00053967 | 0.0 | 0.00
Modify | 146.29 | 146.29 | 146.29 | 0.0 | 79.53
Other | | 0.01552 | | | 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
Neighs: 210388 ave 210388 max 210388 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
Total # of neighbors = 2234476
Ave neighs/atom = 1293.0995
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:02:52
Total wall time: 0:03:05

72
examples/ctip/log.10Sep24.ctip.g++.4 → examples/streitz/log.11Sep24.ctip.g++.4
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@ -1,4 +1,5 @@
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-115-g2b03a1ce17-modified)
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-269-g5a12c762f3-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
#CTIP potential for NiO
#Contributing author: Gabriel Plummer (NASA)
@ -33,6 +34,7 @@ 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
Reading coul/ctip potential file NiO.ctip with DATE: 2024-09-11
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
#Setup
@ -88,30 +90,30 @@ WARNING: Energy due to 1 extra global DOFs will be included in minimizer energie
(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 0.0058029359 0.0058029361 0.0058029362 1.2410596 -1.2410596
Loop time of 0.401983 on 4 procs for 6 steps with 1728 atoms
0 0 -9633.183 24.719478 24.719478 24.719478 -1491.273 -1491.273 -1491.273 1.2374666 -1.2374666
6 0 -9633.1929 24.707505 24.707505 24.707505 0.0050498849 0.0050498856 0.0050498855 1.2410908 -1.2410908
Loop time of 0.288818 on 4 procs for 6 steps with 1728 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-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
-9633.18301849946 -9633.19294329957 -9633.19294333066
Force two-norm initial, final = 42.177998 0.00014286398
Force max component initial, final = 42.177998 0.00014268867
Final line search alpha, max atom move = 0.0079490643 1.1342414e-06
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13767 | 0.13917 | 0.14066 | 0.3 | 34.62
Pair | 0.09401 | 0.095886 | 0.097631 | 0.4 | 33.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0032823 | 0.004768 | 0.0062486 | 1.5 | 1.19
Comm | 0.0024298 | 0.004185 | 0.0060676 | 2.1 | 1.45
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.2568 | 0.25681 | 0.25682 | 0.0 | 63.89
Other | | 0.001238 | | | 0.31
Modify | 0.18779 | 0.1878 | 0.18781 | 0.0 | 65.02
Other | | 0.000945 | | | 0.33
Nlocal: 432 ave 432 max 432 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -142,43 +144,43 @@ fix npt all npt temp 1000 1000 0.1 iso 0 0 1
run 1000
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 -4649.2498 -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 -3289.5796 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
0 1000 -9633.1929 24.707505 24.707505 24.707505 15934.991 15754.787 15735.602 1.2410908 -1.2410908
100 600.77874 -9528.0602 24.816519 24.816519 24.816519 -16709.313 -15443.072 -17750.832 1.2181988 -1.2181988
200 578.84295 -9490.9794 24.812627 24.812627 24.812627 -5879.8769 -4851.4601 -6722.107 1.2254363 -1.2254363
300 694.7973 -9478.5512 24.764285 24.764285 24.764285 14639.415 13827.989 13766.766 1.2372201 -1.2372201
400 803.93731 -9462.2542 24.866629 24.866629 24.866629 -4644.2853 -6017.2884 -7744.2567 1.2086229 -1.2086229
500 893.70492 -9441.0072 24.891756 24.891756 24.891756 -5784.2232 -8219.1644 -4187.392 1.2001224 -1.2001224
600 947.21728 -9416.7532 24.863623 24.863623 24.863623 11265.076 12952.469 11331.883 1.2115124 -1.2115124
700 1040.4874 -9409.8397 24.933859 24.933859 24.933859 -6570.5926 -8532.7456 -3284.7317 1.1902794 -1.1902794
800 1037.9366 -9398.4828 24.935138 24.935138 24.935138 -4681.8675 -2576.5001 -7160.5622 1.1880324 -1.1880324
900 1049.4211 -9411.115 24.899733 24.899733 24.899733 3250.2695 8121.9274 5945.0541 1.2024086 -1.2024086
1000 964.18789 -9412.4405 24.926442 24.926442 24.926442 -7652.603 -5142.926 -8351.8839 1.1908935 -1.1908935
Loop time of 63.5378 on 4 procs for 1000 steps with 1728 atoms
Performance: 1.250 ns/day, 19.202 hours/ns, 14.466 timesteps/s, 24.997 katom-step/s
Performance: 1.360 ns/day, 17.649 hours/ns, 15.739 timesteps/s, 27.196 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 | 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
Pair | 12.737 | 12.782 | 12.839 | 1.1 | 20.12
Neigh | 0.082989 | 0.083627 | 0.084898 | 0.3 | 0.13
Comm | 0.39773 | 0.45431 | 0.49896 | 5.5 | 0.72
Output | 0.00038299 | 0.0004067 | 0.00047658 | 0.0 | 0.00
Modify | 50.207 | 50.207 | 50.208 | 0.0 | 79.02
Other | | 0.01047 | | | 0.02
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
Neighs: 52597 ave 54466 max 51209 min
Histogram: 1 0 1 0 1 0 0 0 0 1
FullNghs: 558619 ave 576963 max 544131 min
FullNghs: 558619 ave 576961 max 544134 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
Total wall time: 0:01:04

2
potentials/NiO.ctip
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@ -1,4 +1,4 @@
# CTIP potential parameters for Ni-O
# CTIP potential parameters for Ni-O UNITS: metal DATE: 2024-09-11 CONTRIBUTOR: Gabriel Plummer gabriel.w.plummer@nasa.gov
# 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