jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Cleaned up names of PyTorch files

This commit is contained in:
Aidan Thompson 2021-03-03 12:07:45 -07:00
parent aa5da53b8a
commit 862a5ad2b6
6 changed files with 38 additions and 34 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
examples/mliap/Ta06A.pytorch.mliap Symbolic link
View File

@ -0,0 +1 @@
../../potentials/Ta06A.pytorch.mliap

2
examples/mliap/in.mliap.pytorch.Ta06A
View File

@ -24,7 +24,7 @@ mass 1 180.88
# choose potential # choose potential
include Ta06A.mliap.pytorch include Ta06A.pytorch.mliap
# Setup output # Setup output

32
examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.1
View File

@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020) LAMMPS (10 Feb 2021)
using 48 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# Demonstrate MLIAP/PyTorch interface to linear SNAP potential # Demonstrate MLIAP/PyTorch interface to linear SNAP potential
# Initialize simulation # Initialize simulation
@ -32,13 +32,13 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 128 atoms Created 128 atoms
create_atoms CPU = 0.002 seconds create_atoms CPU = 0.000 seconds
mass 1 180.88 mass 1 180.88
# choose potential # choose potential
include Ta06A.mliap.pytorch include Ta06A.pytorch.mliap
# DATE: 2014-09-05 UNITS: metal 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 # Definition of SNAP potential Ta_Cand06A
@ -50,9 +50,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL # Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
Loading python model complete. Loading python model complete.
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637 SNAP keyword rcutfac 4.67637
@ -112,7 +112,7 @@ Neighbor list info ...
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 159.8 | 159.8 | 159.8 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes
Step Temp E_pair c_energy TotEng Press v_press Step Temp E_pair c_energy TotEng Press v_press
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796 10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
@ -125,20 +125,20 @@ Step Temp E_pair c_energy TotEng Press v_press
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 2.00236 on 48 procs for 100 steps with 128 atoms Loop time of 2.0472 on 1 procs for 100 steps with 128 atoms
Performance: 2.157 ns/day, 11.124 hours/ns, 49.941 timesteps/s Performance: 2.110 ns/day, 11.373 hours/ns, 48.847 timesteps/s
288.8% CPU use with 1 MPI tasks x 48 OpenMP threads 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.9998 | 1.9998 | 1.9998 | 0.0 | 99.87 Pair | 2.0443 | 2.0443 | 2.0443 | 0.0 | 99.86
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0011814 | 0.0011814 | 0.0011814 | 0.0 | 0.06 Comm | 0.001157 | 0.001157 | 0.001157 | 0.0 | 0.06
Output | 0.00059724 | 0.00059724 | 0.00059724 | 0.0 | 0.03 Output | 0.00080857 | 0.00080857 | 0.00080857 | 0.0 | 0.04
Modify | 0.00047352 | 0.00047352 | 0.00047352 | 0.0 | 0.02 Modify | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.03
Other | | 0.0003468 | | | 0.02 Other | | 0.0004304 | | | 0.02
Nlocal: 128.000 ave 128 max 128 min Nlocal: 128.000 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

34
examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.4
View File

@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020) LAMMPS (10 Feb 2021)
using 48 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# Demonstrate MLIAP/PyTorch interface to linear SNAP potential # Demonstrate MLIAP/PyTorch interface to linear SNAP potential
# Initialize simulation # Initialize simulation
@ -32,13 +32,13 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 128 atoms Created 128 atoms
create_atoms CPU = 0.002 seconds create_atoms CPU = 0.000 seconds
mass 1 180.88 mass 1 180.88
# choose potential # choose potential
include Ta06A.mliap.pytorch include Ta06A.pytorch.mliap
# DATE: 2014-09-05 UNITS: metal 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 # Definition of SNAP potential Ta_Cand06A
@ -50,9 +50,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL # Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
Loading python model complete. Loading python model complete.
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637 SNAP keyword rcutfac 4.67637
@ -112,7 +112,7 @@ Neighbor list info ...
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 159.7 | 159.7 | 159.7 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.06 | 18.06 | 18.06 Mbytes
Step Temp E_pair c_energy TotEng Press v_press Step Temp E_pair c_energy TotEng Press v_press
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796 10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
@ -125,20 +125,20 @@ Step Temp E_pair c_energy TotEng Press v_press
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715 80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563 90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526 100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 0.562802 on 192 procs for 100 steps with 128 atoms Loop time of 0.572344 on 4 procs for 100 steps with 128 atoms
Performance: 7.676 ns/day, 3.127 hours/ns, 177.682 timesteps/s Performance: 7.548 ns/day, 3.180 hours/ns, 174.720 timesteps/s
99.7% CPU use with 4 MPI tasks x 48 OpenMP threads 100.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.53583 | 0.54622 | 0.55401 | 0.9 | 97.05 Pair | 0.51796 | 0.5401 | 0.56608 | 2.4 | 94.37
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0071442 | 0.01491 | 0.025289 | 5.4 | 2.65 Comm | 0.0044844 | 0.030393 | 0.052464 | 10.2 | 5.31
Output | 0.00092525 | 0.00095771 | 0.0010166 | 0.0 | 0.17 Output | 0.001 | 0.0010351 | 0.0011083 | 0.1 | 0.18
Modify | 0.00014479 | 0.00015043 | 0.00015893 | 0.0 | 0.03 Modify | 0.0001468 | 0.00016417 | 0.00017977 | 0.0 | 0.03
Other | | 0.0005624 | | | 0.10 Other | | 0.0006567 | | | 0.11
Nlocal: 32.0000 ave 32 max 32 min Nlocal: 32.0000 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
@ -154,4 +154,4 @@ Ave neighs/atom = 58.000000
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:02 Total wall time: 0:00:05

3
potentials/README
View File

@ -100,6 +100,9 @@ meam.spline modified EAM (MEAM) spline potential
meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential
mesocnt mesoscopic carbon nanotube (CNT) potential mesocnt mesoscopic carbon nanotube (CNT) potential
mgpt model generalized pseudopotential theory (MGPT) potential mgpt model generalized pseudopotential theory (MGPT) potential
mliap MLIAP potential
mliap.descriptor MLIAP potential descriptor
mliap.model MLIAP potential model
nb3b.harmonic nonbonded 3-body harmonic potential nb3b.harmonic nonbonded 3-body harmonic potential
poly polymorphic 3-body potential poly polymorphic 3-body potential
reax ReaxFF potential (see README.reax for more info) reax ReaxFF potential (see README.reax for more info)

0
potentials/Ta06A.mliap.pytorch → potentials/Ta06A.pytorch.mliap
View File