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update USER-RANN example to run faster and provide reference logs

This commit is contained in:
Axel Kohlmeyer 2021-06-22 12:27:05 -04:00
parent f4de4902e2
commit 8f60a54656
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GPG Key ID: D9B44E93BF0C375A
5 changed files with 332 additions and 45 deletions
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examples/USER/rann/in.lammps
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units metal
dimension 3
boundary p p p
atom_style atomic
lattice hcp 2.9962594
region whole block 0 10 0 10 0 10 units lattice
create_box 2 whole
create_atoms 2 box
timestep 0.001
set group all type 1
set group all type/fraction 2 0.10 486
pair_style rann
pair_coeff * * TiZr_2.nn Ti Zr
compute peratom all pe/atom
shell mkdir ovito_files2
dump 1 all custom 10 ovito_files2/dump.*.gz id type x y z c_peratom
dump_modify 1 element Ti Zr
thermo 1
thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp
variable etol equal 1.0e-32
variable ftol equal 1.0e-32
variable maxiter equal 1.0e+9
variable maxeval equal 1.0e+9
variable dmax equal 1.0e-2
fix 1 all box/relax aniso 0.0
min_style cg
minimize ${etol} ${ftol} ${maxiter} ${maxeval}
unfix 1
write_restart TiZr.min
#-------------------------EQUILIBRATION--------------------------------
velocity all create 300 12345 mom yes rot no
fix 1 all npt temp 300 300 0.1 aniso 0 0 1
run 100
unfix 1

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units metal
dimension 3
boundary p p p
atom_style atomic
lattice hcp 2.995 origin 0.5 0.5 0.5
region whole block 0 4 0 2 0 1.94 units lattice
create_box 2 whole
create_atoms 2 box
timestep 0.001
set group all type 1
set group all type/fraction 2 0.10 486
pair_style rann
pair_coeff * * TiZr_2.rann Ti Zr
velocity all create 300 12345 mom yes rot no loop geom
compute peratom all pe/atom
#dump 1 all custom 10 rann.dump id type x y z c_peratom
#dump_modify 1 element Ti Zr
thermo 25
thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp
fix 1 all box/relax aniso 0.0
min_style cg
minimize 1.0e-10 1.0e-10 250 1000
unfix 1
#write_restart TiZr.min
#-------------------------EQUILIBRATION--------------------------------
fix 1 all npt temp 300 300 0.1 aniso 0 0 1
run 250
unfix 1

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examples/USER/rann/log.22Jun21.rann.g++.1 Normal file
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LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
units metal
dimension 3
boundary p p p
atom_style atomic
lattice hcp 2.995 origin 0.5 0.5 0.5
Lattice spacing in x,y,z = 2.9950000 5.1874922 4.8908145
region whole block 0 4 0 2 0 1.94 units lattice
create_box 2 whole
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (11.980000 10.374984 9.4881802)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 64 atoms
create_atoms CPU = 0.001 seconds
timestep 0.001
set group all type 1
Setting atom values ...
64 settings made for type
set group all type/fraction 2 0.10 486
Setting atom values ...
3 settings made for type/fraction
pair_style rann
pair_coeff * * TiZr_2.rann Ti Zr
velocity all create 300 12345 mom yes rot no loop geom
compute peratom all pe/atom
#dump 1 all custom 10 rann.dump id type x y z c_peratom
#dump_modify 1 element Ti Zr
thermo 25
thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp
fix 1 all box/relax aniso 0.0
min_style cg
minimize 1.0e-10 1.0e-10 250 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 3 3 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rann, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.731 | 4.731 | 4.731 Mbytes
Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp
0 11.98 10.374984 9.4881802 -29375.303 -28706.895 -32525.995 -26893.017 -405.95229 150.93453 -694.91972 -103433.05 300
25 11.950182 10.349549 9.4684279 -21452.379 -23337.292 -22794.542 -18225.304 -134.67238 18.687575 99.672896 -103433.82 300
50 11.920232 10.32424 9.4496837 -14826.163 -16604.987 -16114.802 -11758.699 -137.29961 19.192625 98.496407 -103433.93 300
75 11.890282 10.299105 9.4325798 -8241.3799 -9829.5396 -9413.8421 -5480.758 -139.61723 19.753871 96.739255 -103434.01 300
100 11.860332 10.274334 9.4188725 -1918.2777 -3140.1632 -2843.6796 229.00961 -141.67556 20.337591 93.803319 -103434.06 300
125 11.833362 10.25385 9.4174816 2267.7814 2244.5712 2225.4032 2333.3697 -145.79432 20.426911 85.921454 -103434.27 300
150 11.845047 10.264313 9.3943614 2154.2266 2077.795 2064.0012 2320.8837 -166.59541 20.457485 86.593349 -103434.98 300
175 11.851749 10.270526 9.3807742 2356.6765 2258.3767 2245.2877 2566.3649 -198.93901 21.826088 87.211907 -103435.42 300
200 11.85791 10.276284 9.3740248 2116.088 2014.9253 2000.9373 2332.4013 -239.79555 23.069264 88.211395 -103435.71 300
225 11.86067 10.279084 9.3688089 2380.6783 2266.3876 2253.624 2622.0232 -284.70218 23.782436 89.32664 -103435.9 300
250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300
Loop time of 5.54687 on 1 procs for 250 steps with 64 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-103433.047620681 -103436.028362733 -103436.034678926
Force two-norm initial, final = 40.834083 2.1923162
Force max component initial, final = 25.471215 0.42479025
Final line search alpha, max atom move = 0.0013092641 0.00055616263
Iterations, force evaluations = 250 250
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.535 | 5.535 | 5.535 | 0.0 | 99.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0021643 | 0.0021643 | 0.0021643 | 0.0 | 0.04
Output | 0.00040175 | 0.00040175 | 0.00040175 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009261 | | | 0.17
Nlocal: 64.0000 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1508.00 ave 1508 max 1508 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15136.0 ave 15136 max 15136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15136
Ave neighs/atom = 236.50000
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
#write_restart TiZr.min
#-------------------------EQUILIBRATION--------------------------------
fix 1 all npt temp 300 300 0.1 aniso 0 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 3.606 | 3.606 | 3.606 Mbytes
Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp
250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300
275 11.868972 10.287532 9.3712492 5459.6466 3913.9919 6041.4929 6423.455 1860.057 -169.89698 -163.71384 -103435.08 182.98209
300 11.883725 10.306821 9.3893899 821.53461 -1023.4738 2711.5668 776.51078 2816.8806 446.29412 -732.33785 -103434.5 116.94541
325 11.894878 10.332706 9.4085094 -7099.8438 -7329.3175 -4694.3612 -9275.8528 2957.9222 1086.6737 -1549.5101 -103434.96 192.09731
350 11.885259 10.347441 9.4071117 -6402.0644 -5181.1103 -5986.8957 -8038.1873 3057.1547 867.09919 -1625.3988 -103434.62 168.81926
375 11.860011 10.346166 9.3858556 -2508.1672 766.71963 -4549.8268 -3741.3944 1666.1095 224.37185 -926.42628 -103434.73 195.28196
400 11.837235 10.332927 9.3557562 3324.0157 7044.0305 -512.01476 3440.0314 -1246.2047 -108.13943 -18.443174 -103434.99 245.22981
425 11.835641 10.318434 9.3346884 8707.7341 9660.2158 4055.4863 12407.5 -2772.2282 -243.25933 619.5127 -103434.58 215.25674
450 11.862626 10.313654 9.3420741 6651.6061 5159.117 3236.6007 11559.101 -2538.4591 -179.54384 998.92807 -103434.53 225.2827
475 11.905198 10.317019 9.3767687 -823.32707 -3847.0367 -1183.0257 2560.0812 -2415.4604 -135.15481 1006.8549 -103434.64 259.05599
500 11.936602 10.317134 9.4184969 -7923.5224 -11138.312 -5701.3928 -6930.8623 -2175.4452 878.30934 737.79497 -103434.28 240.16605
Loop time of 5.28008 on 1 procs for 250 steps with 64 atoms
Performance: 4.091 ns/day, 5.867 hours/ns, 47.348 timesteps/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 | 5.2728 | 5.2728 | 5.2728 | 0.0 | 99.86
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0021591 | 0.0021591 | 0.0021591 | 0.0 | 0.04
Output | 0.00040452 | 0.00040452 | 0.00040452 | 0.0 | 0.01
Modify | 0.0040597 | 0.0040597 | 0.0040597 | 0.0 | 0.08
Other | | 0.0006859 | | | 0.01
Nlocal: 64.0000 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1508.00 ave 1508 max 1508 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15320.0 ave 15320 max 15320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15320
Ave neighs/atom = 239.37500
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
Total wall time: 0:00:10

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LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
units metal
dimension 3
boundary p p p
atom_style atomic
lattice hcp 2.995 origin 0.5 0.5 0.5
Lattice spacing in x,y,z = 2.9950000 5.1874922 4.8908145
region whole block 0 4 0 2 0 1.94 units lattice
create_box 2 whole
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (11.980000 10.374984 9.4881802)
2 by 2 by 1 MPI processor grid
create_atoms 2 box
Created 64 atoms
create_atoms CPU = 0.000 seconds
timestep 0.001
set group all type 1
Setting atom values ...
64 settings made for type
set group all type/fraction 2 0.10 486
Setting atom values ...
3 settings made for type/fraction
pair_style rann
pair_coeff * * TiZr_2.rann Ti Zr
velocity all create 300 12345 mom yes rot no loop geom
compute peratom all pe/atom
#dump 1 all custom 10 rann.dump id type x y z c_peratom
#dump_modify 1 element Ti Zr
thermo 25
thermo_style custom step lx ly lz press pxx pyy pzz pxy pxz pyz pe temp
fix 1 all box/relax aniso 0.0
min_style cg
minimize 1.0e-10 1.0e-10 250 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 3 3 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rann, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes
Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp
0 11.98 10.374984 9.4881802 -29375.303 -28706.895 -32525.995 -26893.017 -405.95229 150.93453 -694.91972 -103433.05 300
25 11.950182 10.349549 9.4684279 -21452.379 -23337.292 -22794.542 -18225.304 -134.67238 18.687575 99.672896 -103433.82 300
50 11.920232 10.32424 9.4496837 -14826.163 -16604.987 -16114.802 -11758.699 -137.29961 19.192625 98.496407 -103433.93 300
75 11.890282 10.299105 9.4325798 -8241.3799 -9829.5396 -9413.8421 -5480.758 -139.61723 19.753871 96.739255 -103434.01 300
100 11.860332 10.274334 9.4188725 -1918.2777 -3140.1632 -2843.6796 229.00961 -141.67556 20.337591 93.803319 -103434.06 300
125 11.833362 10.25385 9.4174816 2267.7814 2244.5712 2225.4032 2333.3697 -145.79432 20.426911 85.921454 -103434.27 300
150 11.845047 10.264313 9.3943614 2154.2266 2077.795 2064.0012 2320.8837 -166.59541 20.457485 86.593349 -103434.98 300
175 11.851749 10.270526 9.3807742 2356.6765 2258.3767 2245.2877 2566.3649 -198.93901 21.826088 87.211907 -103435.42 300
200 11.85791 10.276284 9.3740248 2116.088 2014.9253 2000.9373 2332.4013 -239.79555 23.069264 88.211395 -103435.71 300
225 11.86067 10.279084 9.3688089 2380.6783 2266.3876 2253.624 2622.0232 -284.70218 23.782436 89.32664 -103435.9 300
250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300
Loop time of 2.4811 on 4 procs for 250 steps with 64 atoms
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-103433.047620681 -103436.028362733 -103436.034678926
Force two-norm initial, final = 40.834083 2.1923162
Force max component initial, final = 25.471215 0.42479025
Final line search alpha, max atom move = 0.0013092641 0.00055616263
Iterations, force evaluations = 250 250
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3295 | 2.3474 | 2.3627 | 0.9 | 94.61
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.089974 | 0.10466 | 0.12186 | 4.0 | 4.22
Output | 0.00048351 | 0.0010692 | 0.0028254 | 3.1 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02802 | | | 1.13
Nlocal: 16.0000 ave 16 max 16 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1035.00 ave 1035 max 1035 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3784.00 ave 3784 max 3784 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15136
Ave neighs/atom = 236.50000
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
#write_restart TiZr.min
#-------------------------EQUILIBRATION--------------------------------
fix 1 all npt temp 300 300 0.1 aniso 0 0 1
run 250
Per MPI rank memory allocation (min/avg/max) = 3.353 | 3.353 | 3.353 Mbytes
Step Lx Ly Lz Press Pxx Pyy Pzz Pxy Pxz Pyz PotEng Temp
250 11.86457 10.282908 9.3667795 2093.631 1983.7868 1969.8563 2327.2499 -334.45392 23.717921 90.543955 -103436.03 300
275 11.868972 10.287532 9.3712492 5459.6466 3913.9919 6041.4929 6423.455 1860.057 -169.89698 -163.71384 -103435.08 182.98209
300 11.883725 10.306821 9.3893899 821.53461 -1023.4738 2711.5668 776.51078 2816.8806 446.29412 -732.33785 -103434.5 116.94541
325 11.894878 10.332706 9.4085094 -7099.8438 -7329.3175 -4694.3612 -9275.8528 2957.9222 1086.6737 -1549.5101 -103434.96 192.09731
350 11.885259 10.347441 9.4071117 -6402.0644 -5181.1103 -5986.8957 -8038.1873 3057.1547 867.09919 -1625.3988 -103434.62 168.81926
375 11.860011 10.346166 9.3858556 -2508.1672 766.71963 -4549.8268 -3741.3944 1666.1095 224.37185 -926.42628 -103434.73 195.28196
400 11.837235 10.332927 9.3557562 3324.0157 7044.0305 -512.01476 3440.0314 -1246.2047 -108.13943 -18.443174 -103434.99 245.22981
425 11.835641 10.318434 9.3346884 8707.7341 9660.2158 4055.4863 12407.5 -2772.2282 -243.25933 619.5127 -103434.58 215.25674
450 11.862626 10.313654 9.3420741 6651.6061 5159.117 3236.6007 11559.101 -2538.4591 -179.54384 998.92807 -103434.53 225.2827
475 11.905198 10.317019 9.3767687 -823.32707 -3847.0367 -1183.0257 2560.0812 -2415.4604 -135.15481 1006.8549 -103434.64 259.05599
500 11.936602 10.317134 9.4184969 -7923.5224 -11138.312 -5701.3928 -6930.8623 -2175.4452 878.30934 737.79497 -103434.28 240.16605
Loop time of 2.55414 on 4 procs for 250 steps with 64 atoms
Performance: 8.457 ns/day, 2.838 hours/ns, 97.880 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5174 | 2.1911 | 2.5037 | 26.7 | 85.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.035032 | 0.34713 | 1.0204 | 67.1 | 13.59
Output | 0.00048485 | 0.0010827 | 0.0028745 | 3.1 | 0.04
Modify | 0.01054 | 0.012633 | 0.013719 | 1.1 | 0.49
Other | | 0.002167 | | | 0.08
Nlocal: 16.0000 ave 18 max 11 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Nghost: 1035.00 ave 1040 max 1033 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3830.00 ave 4316 max 2636 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 15320
Ave neighs/atom = 239.37500
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
Total wall time: 0:00:05

0
examples/USER/rann/TiZr_2.nn → potentials/TiZr_2.rann
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