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update SNAP package inputs and reference logs to give consistent results in serial and parallel

This commit is contained in:
Axel Kohlmeyer 2020-06-16 20:59:58 -04:00
parent 47b589bdc6
commit 1883788725
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GPG Key ID: D9B44E93BF0C375A
15 changed files with 403 additions and 409 deletions
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2
examples/snap/in.snap.Mo_Chen
View File

@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}

2
examples/snap/in.snap.Ta06A
View File

@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}

2
examples/snap/in.snap.W.2940
View File

@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}

2
examples/snap/in.snap.WBe.PRB2019
View File

@ -42,7 +42,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}

2
examples/snap/in.snap.hybrid.WSNAP.HePair
View File

@ -42,7 +42,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}

72
examples/snap/log.27Nov18.snap.Mo_Chen.g++.1 → examples/snap/log.15Jun20.snap.Mo_Chen.g++.1
View File

@ -1,13 +1,13 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Demonstrate SNAP Mo potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.160
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,21 +18,21 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.16
Lattice spacing in x,y,z = 3.16 3.16 3.16
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.00029707 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
@ -40,11 +40,11 @@ mass 1 183.84
include Mo_Chen_PRM2017.snap
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# Generated by Materials Virtual Lab
# Definition of SNAP potential.
pair_style snap
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
SNAP Element = Mo, Radius 0.5, Weight 1
Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
@ -54,7 +54,7 @@ SNAP keyword twojmax 6
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -65,7 +65,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -81,33 +81,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.335 | 3.335 | 3.335 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -22.405975 0 -22.3675 2575.7657
10 294.77555 -22.405305 0 -22.3675 2756.6894
20 279.53011 -22.40335 0 -22.3675 3285.8272
30 255.52174 -22.40027 0 -22.3675 4122.8933
40 224.7299 -22.396321 0 -22.367499 5204.3499
50 189.67529 -22.391825 0 -22.367499 6449.1308
60 153.18862 -22.387145 0 -22.367499 7765.911
70 118.14998 -22.382652 0 -22.367499 9061.1616
80 87.224916 -22.378685 0 -22.367499 10247.68
90 62.623892 -22.37553 0 -22.367498 11250.067
100 45.9103 -22.373386 0 -22.367498 12011.726
Loop time of 7.00873 on 1 procs for 100 steps with 128 atoms
10 294.8148 -22.40531 0 -22.3675 2762.0942
20 279.68628 -22.40337 0 -22.3675 3306.7656
30 255.84798 -22.400312 0 -22.3675 4168.2979
40 225.22346 -22.396384 0 -22.367499 5281.9537
50 190.25143 -22.391899 0 -22.367499 6565.6626
60 153.66642 -22.387207 0 -22.367499 7927.3186
70 118.25575 -22.382665 0 -22.367499 9271.9554
80 86.616338 -22.378607 0 -22.367499 10510.959
90 60.935787 -22.375314 0 -22.367498 11568.261
100 42.815823 -22.37299 0 -22.367498 12385.433
Loop time of 0.897752 on 1 procs for 100 steps with 128 atoms
Performance: 0.616 ns/day, 38.937 hours/ns, 14.268 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 4.812 ns/day, 4.988 hours/ns, 111.389 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.0068 | 7.0068 | 7.0068 | 0.0 | 99.97
Pair | 0.89711 | 0.89711 | 0.89711 | 0.0 | 99.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00083661 | 0.00083661 | 0.00083661 | 0.0 | 0.01
Output | 0.00025535 | 0.00025535 | 0.00025535 | 0.0 | 0.00
Modify | 0.00034285 | 0.00034285 | 0.00034285 | 0.0 | 0.00
Other | | 0.0005035 | | | 0.01
Comm | 0.0002501 | 0.0002501 | 0.0002501 | 0.0 | 0.03
Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01
Modify | 0.00010276 | 0.00010276 | 0.00010276 | 0.0 | 0.01
Other | | 0.0001559 | | | 0.02
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -123,4 +123,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07
Total wall time: 0:00:00

72
examples/snap/log.27Nov18.snap.Mo_Chen.g++.4 → examples/snap/log.15Jun20.snap.Mo_Chen.g++.4
View File

@ -1,13 +1,13 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Demonstrate SNAP Mo potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.160
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,21 +18,21 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.16
Lattice spacing in x,y,z = 3.16 3.16 3.16
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000289917 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
@ -40,11 +40,11 @@ mass 1 183.84
include Mo_Chen_PRM2017.snap
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
# Generated by Materials Virtual Lab
# Definition of SNAP potential.
pair_style snap
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
SNAP Element = Mo, Radius 0.5, Weight 1
Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
@ -54,7 +54,7 @@ SNAP keyword twojmax 6
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -65,7 +65,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -81,33 +81,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.271 | 3.271 | 3.271 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -22.405975 0 -22.3675 2575.7657
10 294.63153 -22.405286 0 -22.3675 2753.4662
20 278.98535 -22.40328 0 -22.3675 3272.416
30 254.38916 -22.400125 0 -22.3675 4091.8933
40 222.91191 -22.396088 0 -22.367499 5148.5505
50 187.16984 -22.391504 0 -22.367499 6362.2454
60 150.08253 -22.386747 0 -22.367499 7643.2732
70 114.60307 -22.382197 0 -22.367499 8900.2448
80 83.449257 -22.378201 0 -22.367499 10047.619
90 58.862643 -22.375048 0 -22.367498 11012.233
100 42.41931 -22.372939 0 -22.367498 11740.641
Loop time of 2.15419 on 4 procs for 100 steps with 128 atoms
10 294.8148 -22.40531 0 -22.3675 2762.0942
20 279.68628 -22.40337 0 -22.3675 3306.7656
30 255.84798 -22.400312 0 -22.3675 4168.2979
40 225.22346 -22.396384 0 -22.367499 5281.9537
50 190.25143 -22.391899 0 -22.367499 6565.6626
60 153.66642 -22.387207 0 -22.367499 7927.3186
70 118.25575 -22.382665 0 -22.367499 9271.9554
80 86.616338 -22.378607 0 -22.367499 10510.959
90 60.935787 -22.375314 0 -22.367498 11568.261
100 42.815823 -22.37299 0 -22.367498 12385.433
Loop time of 0.260783 on 4 procs for 100 steps with 128 atoms
Performance: 2.005 ns/day, 11.968 hours/ns, 46.421 timesteps/s
92.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 16.566 ns/day, 1.449 hours/ns, 383.461 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7677 | 1.9028 | 1.9897 | 6.2 | 88.33
Pair | 0.23045 | 0.23744 | 0.24455 | 1.2 | 91.05
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.15367 | 0.24295 | 0.38029 | 17.6 | 11.28
Output | 0.00034404 | 0.0012512 | 0.0017219 | 1.6 | 0.06
Modify | 0.00018859 | 0.00021273 | 0.00023699 | 0.0 | 0.01
Other | | 0.007011 | | | 0.33
Comm | 0.014524 | 0.021267 | 0.027713 | 3.7 | 8.15
Output | 0.00014997 | 0.00040495 | 0.0011623 | 0.0 | 0.16
Modify | 4.2439e-05 | 4.6909e-05 | 5.0068e-05 | 0.0 | 0.02
Other | | 0.00162 | | | 0.62
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -123,4 +123,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:00

71
examples/snap/log.27Nov18.snap.Ta06A.g++.1 → examples/snap/log.15Jun20.snap.Ta06A.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
@ -7,7 +7,7 @@ LAMMPS (27 Nov 2018)
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,28 +18,28 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.316
Lattice spacing in x,y,z = 3.316 3.316 3.316
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000350714 secs
create_atoms CPU = 0.000 seconds
mass 1 180.88
# choose potential
include Ta06A.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
@ -56,7 +56,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
@ -64,14 +64,13 @@ SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -82,7 +81,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -103,33 +102,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.967 | 3.967 | 3.967 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.96579 -11.851053 0 -11.813095 2696.1559
20 284.32535 -11.84956 0 -11.813095 2301.3713
30 266.04602 -11.847215 0 -11.813095 1832.1745
40 242.2862 -11.844168 0 -11.813095 1492.6765
50 214.48968 -11.840603 0 -11.813094 1312.8908
60 184.32523 -11.836734 0 -11.813094 1284.582
70 153.58055 -11.832791 0 -11.813094 1374.4457
80 124.04276 -11.829003 0 -11.813094 1537.703
90 97.37622 -11.825582 0 -11.813094 1734.9662
100 75.007873 -11.822714 0 -11.813094 1930.8005
Loop time of 5.03244 on 1 procs for 100 steps with 128 atoms
10 296.01467 -11.851059 0 -11.813095 2697.4796
20 284.53666 -11.849587 0 -11.813095 2289.1527
30 266.51577 -11.847275 0 -11.813095 1851.7131
40 243.05007 -11.844266 0 -11.813095 1570.684
50 215.51032 -11.840734 0 -11.813094 1468.1899
60 185.48331 -11.836883 0 -11.813094 1524.8757
70 154.6736 -11.832931 0 -11.813094 1698.3351
80 124.79303 -11.829099 0 -11.813094 1947.0715
90 97.448054 -11.825592 0 -11.813094 2231.9563
100 74.035418 -11.822589 0 -11.813094 2515.8526
Loop time of 0.702618 on 1 procs for 100 steps with 128 atoms
Performance: 0.858 ns/day, 27.958 hours/ns, 19.871 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 6.148 ns/day, 3.903 hours/ns, 142.325 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 | 5.0308 | 5.0308 | 5.0308 | 0.0 | 99.97
Pair | 0.70188 | 0.70188 | 0.70188 | 0.0 | 99.90
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00070858 | 0.00070858 | 0.00070858 | 0.0 | 0.01
Output | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.00
Modify | 0.0002749 | 0.0002749 | 0.0002749 | 0.0 | 0.01
Other | | 0.0004299 | | | 0.01
Comm | 0.00025487 | 0.00025487 | 0.00025487 | 0.0 | 0.04
Output | 0.00015402 | 0.00015402 | 0.00015402 | 0.0 | 0.02
Modify | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.02
Other | | 0.000217 | | | 0.03
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -145,4 +144,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:00

71
examples/snap/log.27Nov18.snap.Ta06A.g++.4 → examples/snap/log.15Jun20.snap.Ta06A.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
@ -7,7 +7,7 @@ LAMMPS (27 Nov 2018)
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,28 +18,28 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.316
Lattice spacing in x,y,z = 3.316 3.316 3.316
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000299692 secs
create_atoms CPU = 0.000 seconds
mass 1 180.88
# choose potential
include Ta06A.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
@ -56,7 +56,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
@ -64,14 +64,13 @@ SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -82,7 +81,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -103,33 +102,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.903 | 3.903 | 3.903 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.8664 -11.85104 0 -11.813095 2702.935
20 283.95868 -11.849513 0 -11.813095 2301.3242
30 265.29535 -11.847119 0 -11.813095 1870.3173
40 241.09337 -11.844015 0 -11.813095 1568.1549
50 212.86732 -11.840395 0 -11.813094 1409.2092
60 182.35256 -11.836481 0 -11.813094 1389.0527
70 151.38968 -11.83251 0 -11.813094 1474.9232
80 121.80051 -11.828715 0 -11.813094 1627.6911
90 95.262635 -11.825311 0 -11.813094 1812.9327
100 73.194645 -11.822481 0 -11.813094 1995.2199
Loop time of 1.4959 on 4 procs for 100 steps with 128 atoms
10 296.01467 -11.851059 0 -11.813095 2697.4796
20 284.53666 -11.849587 0 -11.813095 2289.1527
30 266.51577 -11.847275 0 -11.813095 1851.7131
40 243.05007 -11.844266 0 -11.813095 1570.684
50 215.51032 -11.840734 0 -11.813094 1468.1899
60 185.48331 -11.836883 0 -11.813094 1524.8757
70 154.6736 -11.832931 0 -11.813094 1698.3351
80 124.79303 -11.829099 0 -11.813094 1947.0715
90 97.448054 -11.825592 0 -11.813094 2231.9563
100 74.035418 -11.822589 0 -11.813094 2515.8526
Loop time of 0.230164 on 4 procs for 100 steps with 128 atoms
Performance: 2.888 ns/day, 8.311 hours/ns, 66.850 timesteps/s
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 18.769 ns/day, 1.279 hours/ns, 434.473 timesteps/s
93.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2973 | 1.3263 | 1.3444 | 1.6 | 88.66
Pair | 0.1824 | 0.19154 | 0.21822 | 3.5 | 83.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.14155 | 0.16475 | 0.19518 | 5.0 | 11.01
Output | 0.00055361 | 0.0006234 | 0.00078511 | 0.0 | 0.04
Modify | 0.00016427 | 0.00020635 | 0.00032949 | 0.0 | 0.01
Other | | 0.004009 | | | 0.27
Comm | 0.010843 | 0.037176 | 0.046129 | 7.9 | 16.15
Output | 0.00014973 | 0.00028926 | 0.00070024 | 0.0 | 0.13
Modify | 5.3883e-05 | 5.6803e-05 | 6.1989e-05 | 0.0 | 0.02
Other | | 0.001104 | | | 0.48
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -145,4 +144,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01
Total wall time: 0:00:00

73
examples/snap/log.27Nov18.snap.W.2940.g++.1 → examples/snap/log.15Jun20.snap.W.2940.g++.1
View File

@ -1,13 +1,13 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Demonstrate SNAP W potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,28 +18,28 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000316143 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
# choose potential
include W_2940_2017_2.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
@ -54,7 +54,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 74 ${zblz}
pair_coeff 1 1 zbl 74 74
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@ -62,7 +62,6 @@ SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
@ -70,7 +69,7 @@ SNAP keyword quadraticflag 0
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -81,7 +80,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -102,33 +101,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.40666 -11.027479 0 -10.989849 3246.0559
20 274.27375 -11.025025 0 -10.989849 3927.9497
30 244.50457 -11.021207 0 -10.989849 4983.5484
40 207.0784 -11.016407 0 -10.989849 6299.9473
50 165.74442 -11.011105 0 -10.989848 7736.5123
60 124.62181 -11.005831 0 -10.989848 9140.8587
70 87.744792 -11.001101 0 -10.989848 10366.489
80 58.605244 -10.997364 0 -10.989848 11289.914
90 39.754503 -10.994946 0 -10.989848 11824.945
100 32.524085 -10.994019 0 -10.989848 11932.118
Loop time of 18.7678 on 1 procs for 100 steps with 128 atoms
10 293.10848 -11.027441 0 -10.989849 3259.9445
20 273.14727 -11.024881 0 -10.989849 3979.8968
30 242.20285 -11.020912 0 -10.989849 5089.0797
40 203.51992 -11.01595 0 -10.989849 6462.9419
50 161.14556 -11.010515 0 -10.989848 7948.1798
60 119.47232 -11.00517 0 -10.989848 9380.8543
70 82.729175 -11.000458 0 -10.989848 10606.025
80 54.483648 -10.996835 0 -10.989848 11496.424
90 37.225263 -10.994622 0 -10.989847 11967.579
100 32.094224 -10.993964 0 -10.989847 11987.181
Loop time of 2.29953 on 1 procs for 100 steps with 128 atoms
Performance: 0.230 ns/day, 104.265 hours/ns, 5.328 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.879 ns/day, 12.775 hours/ns, 43.487 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 | 18.766 | 18.766 | 18.766 | 0.0 | 99.99
Pair | 2.2988 | 2.2988 | 2.2988 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00081968 | 0.00081968 | 0.00081968 | 0.0 | 0.00
Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00
Modify | 0.0003283 | 0.0003283 | 0.0003283 | 0.0 | 0.00
Other | | 0.0005233 | | | 0.00
Comm | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.01
Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.01
Modify | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
Other | | 0.0001643 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -144,4 +143,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:18
Total wall time: 0:00:02

73
examples/snap/log.27Nov18.snap.W.2940.g++.4 → examples/snap/log.15Jun20.snap.W.2940.g++.4
View File

@ -1,13 +1,13 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Demonstrate SNAP W potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,28 +18,28 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000297546 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
# choose potential
include W_2940_2017_2.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
@ -54,7 +54,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 74 ${zblz}
pair_coeff 1 1 zbl 74 74
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@ -62,7 +62,6 @@ SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
@ -70,7 +69,7 @@ SNAP keyword quadraticflag 0
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -81,7 +80,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -102,33 +101,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.22504 -11.027456 0 -10.989849 3258.275
20 273.60084 -11.024939 0 -10.989849 3973.9038
30 243.15327 -11.021034 0 -10.989849 5077.9172
40 205.01905 -11.016142 0 -10.989849 6448.4941
50 163.10914 -11.010767 0 -10.989848 7935.6835
60 121.67854 -11.005453 0 -10.989848 9378.9959
70 84.846972 -11.000729 0 -10.989848 10626.301
80 56.127265 -10.997046 0 -10.989848 11551.687
90 38.025013 -10.994724 0 -10.989847 12069.936
100 31.768127 -10.993922 0 -10.989847 12145.648
Loop time of 5.38055 on 4 procs for 100 steps with 128 atoms
10 293.10848 -11.027441 0 -10.989849 3259.9445
20 273.14727 -11.024881 0 -10.989849 3979.8968
30 242.20285 -11.020912 0 -10.989849 5089.0797
40 203.51992 -11.01595 0 -10.989849 6462.9419
50 161.14556 -11.010515 0 -10.989848 7948.1798
60 119.47232 -11.00517 0 -10.989848 9380.8543
70 82.729175 -11.000458 0 -10.989848 10606.025
80 54.483648 -10.996835 0 -10.989848 11496.424
90 37.225263 -10.994622 0 -10.989847 11967.579
100 32.094224 -10.993964 0 -10.989847 11987.181
Loop time of 0.700403 on 4 procs for 100 steps with 128 atoms
Performance: 0.803 ns/day, 29.892 hours/ns, 18.585 timesteps/s
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 6.168 ns/day, 3.891 hours/ns, 142.775 timesteps/s
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8254 | 5.0245 | 5.2817 | 7.7 | 93.38
Pair | 0.59296 | 0.62019 | 0.6504 | 2.8 | 88.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.093845 | 0.34915 | 0.5466 | 29.1 | 6.49
Output | 0.00032616 | 0.0011846 | 0.0037167 | 4.2 | 0.02
Modify | 0.00022507 | 0.00025326 | 0.0002687 | 0.0 | 0.00
Other | | 0.005432 | | | 0.10
Comm | 0.048731 | 0.078938 | 0.10647 | 7.8 | 11.27
Output | 0.00015879 | 0.00024194 | 0.00048518 | 0.0 | 0.03
Modify | 6.4373e-05 | 6.9439e-05 | 7.7963e-05 | 0.0 | 0.01
Other | | 0.0009654 | | | 0.14
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -144,4 +143,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:00

85
examples/snap/log.18Sep19.snap.WBeSNAP.g++.1 → examples/snap/log.15Jun20.snap.WBe.PRB2019.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (7 Aug 2019)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP W-Be potential
# Initialize simulation
@ -6,7 +7,7 @@ LAMMPS (7 Aug 2019)
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -17,33 +18,33 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000234842 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
mass 2 9.012182
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fractiongroup tungsten type 1
123 atoms in group tungsten
group beryllium type 2
group beryllium type 2
5 atoms in group beryllium
# choose potential
include WBe_Wood_PRB2019.snap
# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
@ -77,7 +78,7 @@ SNAP keyword quadraticflag 0
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -88,7 +89,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -112,43 +113,43 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -8.5980876 0 -8.5596125 -35284.855
10 299.29029 -8.5979965 0 -8.5596125 -35299.259
20 288.99334 -8.5966759 0 -8.5596124 -35004.093
30 269.91027 -8.5942284 0 -8.5596123 -34447.077
40 243.57361 -8.5908505 0 -8.5596121 -33687.105
50 212.21385 -8.5868284 0 -8.5596119 -32821.864
60 178.77144 -8.5825391 0 -8.5596116 -31971.17
70 146.71854 -8.578428 0 -8.5596113 -31245.51
80 119.50956 -8.5749383 0 -8.5596111 -30724.137
90 99.872785 -8.5724197 0 -8.559611 -30440.244
100 89.604584 -8.5711027 0 -8.5596109 -30392.805
Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms
10 296.32664 -8.5976164 0 -8.5596124 -35188.339
20 282.41417 -8.595832 0 -8.5596123 -34782.293
30 259.69014 -8.5929175 0 -8.5596121 -34113.316
40 230.50415 -8.5891741 0 -8.5596119 -33260.777
50 197.88816 -8.5849908 0 -8.5596116 -32309.975
60 165.27259 -8.5808076 0 -8.5596113 -31365.766
70 136.15697 -8.5770733 0 -8.5596111 -30542.657
80 113.58947 -8.5741788 0 -8.5596109 -29939.23
90 99.477916 -8.572369 0 -8.5596109 -29619.939
100 94.121939 -8.5716822 0 -8.559611 -29598.002
Loop time of 2.26616 on 1 procs for 100 steps with 128 atoms
Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
199.5% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1.906 ns/day, 12.590 hours/ns, 44.128 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1672 | 3.1672 | 3.1672 | 0.0 | 99.97
Neigh | 0.00030208 | 0.00030208 | 0.00030208 | 0.0 | 0.01
Comm | 0.00029612 | 0.00029612 | 0.00029612 | 0.0 | 0.01
Output | 0.00019813 | 0.00019813 | 0.00019813 | 0.0 | 0.01
Modify | 0.00014448 | 0.00014448 | 0.00014448 | 0.0 | 0.00
Other | | 0.0001433 | | | 0.00
Pair | 2.2531 | 2.2531 | 2.2531 | 0.0 | 99.42
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.01
Output | 0.012544 | 0.012544 | 0.012544 | 0.0 | 0.55
Modify | 0.00010347 | 0.00010347 | 0.00010347 | 0.0 | 0.00
Other | | 0.0001583 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3710 ave 3710 max 3710 min
Neighs: 3712 ave 3712 max 3712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 7420 ave 7420 max 7420 min
FullNghs: 7424 ave 7424 max 7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7420
Ave neighs/atom = 57.9688
Neighbor list builds = 1
Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:02

95
examples/snap/log.18Sep19.snap.WBeSNAP.g++.4 → examples/snap/log.15Jun20.snap.WBe.PRB2019.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (7 Aug 2019)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP W-Be potential
# Initialize simulation
@ -6,7 +7,7 @@ LAMMPS (7 Aug 2019)
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -17,33 +18,33 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000317097 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
mass 2 9.012182
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fractiongroup tungsten type 1
123 atoms in group tungsten
group beryllium type 2
group beryllium type 2
5 atoms in group beryllium
# choose potential
include WBe_Wood_PRB2019.snap
# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
@ -77,7 +78,7 @@ SNAP keyword quadraticflag 0
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -88,7 +89,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -112,43 +113,43 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -8.5980876 0 -8.5596125 -35284.855
10 296.24946 -8.5976065 0 -8.5596124 -35140.29
20 282.27904 -8.5958147 0 -8.5596123 -34710.3
30 259.54978 -8.5928995 0 -8.5596121 -34060.43
40 230.41412 -8.5891626 0 -8.5596119 -33258.275
50 197.85135 -8.5849861 0 -8.5596116 -32389.527
60 165.21732 -8.5808005 0 -8.5596113 -31550.426
70 135.94024 -8.5770455 0 -8.5596111 -30839.006
80 113.06617 -8.5741117 0 -8.5596109 -30339.177
90 98.542347 -8.572249 0 -8.5596109 -30094.29
100 92.524343 -8.5714774 0 -8.5596111 -30091.988
Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms
10 296.32664 -8.5976164 0 -8.5596124 -35188.339
20 282.41417 -8.595832 0 -8.5596123 -34782.293
30 259.69014 -8.5929175 0 -8.5596121 -34113.316
40 230.50415 -8.5891741 0 -8.5596119 -33260.777
50 197.88816 -8.5849908 0 -8.5596116 -32309.975
60 165.27259 -8.5808076 0 -8.5596113 -31365.766
70 136.15697 -8.5770733 0 -8.5596111 -30542.657
80 113.58947 -8.5741788 0 -8.5596109 -29939.23
90 99.477916 -8.572369 0 -8.5596109 -29619.939
100 94.121939 -8.5716822 0 -8.559611 -29598.002
Loop time of 0.668977 on 4 procs for 100 steps with 128 atoms
Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 6.458 ns/day, 3.717 hours/ns, 149.482 timesteps/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.79079 | 0.79788 | 0.80888 | 0.8 | 98.06
Neigh | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 | 0.0 | 0.01
Comm | 0.0041246 | 0.01515 | 0.022235 | 5.5 | 1.86
Output | 0.000144 | 0.00017095 | 0.00024796 | 0.0 | 0.02
Modify | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 | 0.0 | 0.01
Other | | 0.000338 | | | 0.04
Pair | 0.57811 | 0.60637 | 0.63609 | 2.6 | 90.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.031571 | 0.061612 | 0.090021 | 8.3 | 9.21
Output | 0.00015521 | 0.00021636 | 0.00038552 | 0.0 | 0.03
Modify | 5.4836e-05 | 6.1393e-05 | 7.2956e-05 | 0.0 | 0.01
Other | | 0.0007139 | | | 0.11
Nlocal: 32 ave 37 max 28 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 431 ave 435 max 426 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 927 ave 1071 max 821 min
Histogram: 1 0 1 0 1 0 0 0 0 1
FullNghs: 1854 ave 2144 max 1624 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1856 ave 1856 max 1856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7416
Ave neighs/atom = 57.9375
Neighbor list builds = 1
Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

86
examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.1 → examples/snap/log.15Jun20.snap.hybrid.WSNAP.HePair.g++.1
View File

@ -1,13 +1,13 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,34 +18,33 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000426054 secs
create_atoms CPU = 0.001 seconds
mass 1 183.84
mass 2 4.0026
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fractiongroup tungsten type 1
123 atoms in group tungsten
group helium type 2
group helium type 2
5 atoms in group helium
# choose potential
include W_2940_2017_2_He_JW2013.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
@ -60,7 +59,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 74 ${zblz}
pair_coeff 1 1 zbl 74 74
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@ -68,24 +67,23 @@ SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:467)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:467)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -96,7 +94,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -137,33 +135,33 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.789 | 6.789 | 6.789 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 290.48923 -10.436885 0 -10.399629 -5646.4813
20 271.18868 -10.434409 0 -10.399629 -5654.4646
30 246.2601 -10.431212 0 -10.399629 -5281.8873
40 218.69918 -10.427677 0 -10.399629 -4343.3636
50 189.12519 -10.423885 0 -10.399629 -2903.1138
60 155.55701 -10.419579 0 -10.399629 -1402.2278
70 118.83581 -10.414869 0 -10.399629 -146.36141
80 85.903126 -10.410645 0 -10.399628 857.74986
90 65.223651 -10.407993 0 -10.399628 1494.2746
100 59.833542 -10.407302 0 -10.399628 1938.9164
Loop time of 17.6435 on 1 procs for 100 steps with 128 atoms
10 292.90716 -10.437195 0 -10.39963 -5400.8323
20 275.59696 -10.434975 0 -10.399629 -5055.199
30 250.28699 -10.431729 0 -10.399629 -4317.4619
40 218.58148 -10.427662 0 -10.399629 -3069.0256
50 182.80754 -10.423074 0 -10.399629 -1514.9501
60 144.77789 -10.418197 0 -10.399629 134.6083
70 108.06164 -10.413487 0 -10.399628 1747.8913
80 79.630821 -10.409841 0 -10.399628 2913.2733
90 62.795831 -10.407682 0 -10.399628 3646.2528
100 57.450965 -10.406996 0 -10.399628 4022.2665
Loop time of 2.15336 on 1 procs for 100 steps with 128 atoms
Performance: 0.245 ns/day, 98.019 hours/ns, 5.668 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 2.006 ns/day, 11.963 hours/ns, 46.439 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.641 | 17.641 | 17.641 | 0.0 | 99.99
Neigh | 0.00054359 | 0.00054359 | 0.00054359 | 0.0 | 0.00
Comm | 0.00080729 | 0.00080729 | 0.00080729 | 0.0 | 0.00
Output | 0.00026512 | 0.00026512 | 0.00026512 | 0.0 | 0.00
Modify | 0.00033879 | 0.00033879 | 0.00033879 | 0.0 | 0.00
Other | | 0.0005448 | | | 0.00
Pair | 2.1524 | 2.1524 | 2.1524 | 0.0 | 99.96
Neigh | 0.00030732 | 0.00030732 | 0.00030732 | 0.0 | 0.01
Comm | 0.00026202 | 0.00026202 | 0.00026202 | 0.0 | 0.01
Output | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.01
Modify | 0.00010085 | 0.00010085 | 0.00010085 | 0.0 | 0.00
Other | | 0.0001643 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -179,4 +177,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:17
Total wall time: 0:00:02

104
examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.4 → examples/snap/log.15Jun20.snap.hybrid.WSNAP.HePair.g++.4
View File

@ -1,13 +1,13 @@
LAMMPS (27 Nov 2018)
LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units metal
units metal
# generate the box and atom positions using a BCC lattice
@ -18,34 +18,33 @@ variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
boundary p p p
lattice bcc $a
lattice bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
create_atoms 1 box
Created 128 atoms
Time spent = 0.000303984 secs
create_atoms CPU = 0.000 seconds
mass 1 183.84
mass 2 4.0026
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fraction
group tungsten type 1
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
5 settings made for type/fractiongroup tungsten type 1
123 atoms in group tungsten
group helium type 2
group helium type 2
5 atoms in group helium
# choose potential
include W_2940_2017_2_He_JW2013.snap
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
@ -60,7 +59,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 74 ${zblz}
pair_coeff 1 1 zbl 74 74
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@ -68,24 +67,23 @@ SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:467)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:467)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
# Setup output
thermo 10
thermo 10
thermo_modify norm yes
# Set up NVE run
@ -96,7 +94,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
@ -137,46 +135,46 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.687 | 6.69 | 6.692 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 292.13979 -10.437097 0 -10.39963 -5516.3963
20 272.55728 -10.434585 0 -10.399629 -5460.4268
30 245.06559 -10.431059 0 -10.399629 -5016.6351
40 212.79459 -10.42692 0 -10.399629 -3924.2175
50 178.03903 -10.422462 0 -10.399629 -2354.5485
60 141.62155 -10.417791 0 -10.399628 -595.41345
70 107.24843 -10.413383 0 -10.399628 1138.4107
80 79.985938 -10.409886 0 -10.399628 2392.1106
90 62.568933 -10.407652 0 -10.399628 3141.7027
100 56.697933 -10.406899 0 -10.399628 3583.9538
Loop time of 4.7853 on 4 procs for 100 steps with 128 atoms
10 292.90716 -10.437195 0 -10.39963 -5400.8323
20 275.59696 -10.434975 0 -10.399629 -5055.199
30 250.28699 -10.431729 0 -10.399629 -4317.4619
40 218.58148 -10.427662 0 -10.399629 -3069.0256
50 182.80754 -10.423074 0 -10.399629 -1514.9501
60 144.77789 -10.418197 0 -10.399629 134.6083
70 108.06164 -10.413487 0 -10.399628 1747.8913
80 79.630821 -10.409841 0 -10.399628 2913.2733
90 62.795831 -10.407682 0 -10.399628 3646.2528
100 57.450965 -10.406996 0 -10.399628 4022.2665
Loop time of 0.652565 on 4 procs for 100 steps with 128 atoms
Performance: 0.903 ns/day, 26.585 hours/ns, 20.897 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 6.620 ns/day, 3.625 hours/ns, 153.241 timesteps/s
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.394 | 4.5813 | 4.7463 | 5.9 | 95.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.035261 | 0.19515 | 0.38629 | 28.5 | 4.08
Output | 0.00031662 | 0.00060844 | 0.0014563 | 0.0 | 0.01
Modify | 0.00018692 | 0.0001924 | 0.00020123 | 0.0 | 0.00
Other | | 0.008012 | | | 0.17
Pair | 0.5462 | 0.57357 | 0.59096 | 2.3 | 87.89
Neigh | 8.2016e-05 | 8.3506e-05 | 8.4877e-05 | 0.0 | 0.01
Comm | 0.060158 | 0.07569 | 0.10482 | 6.5 | 11.60
Output | 0.00015974 | 0.00035232 | 0.00092149 | 0.0 | 0.05
Modify | 5.6982e-05 | 6.777e-05 | 7.3671e-05 | 0.0 | 0.01
Other | | 0.002799 | | | 0.43
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 856.25 ave 885 max 818 min
Histogram: 1 0 0 0 1 0 0 0 1 1
FullNghs: 1712.5 ave 1738 max 1658 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nlocal: 32 ave 33 max 31 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 431 ave 432 max 430 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 856.25 ave 949 max 794 min
Histogram: 1 1 0 0 0 1 0 0 0 1
FullNghs: 1712.5 ave 1854 max 1604 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 6850
Ave neighs/atom = 53.5156
Neighbor list builds = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:04
Total wall time: 0:00:00