From 862a5ad2b64fcbf05a7716c0048a2cccaa8163ce Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 3 Mar 2021 12:07:45 -0700 Subject: [PATCH] Cleaned up names of PyTorch files --- examples/mliap/Ta06A.pytorch.mliap | 1 + examples/mliap/in.mliap.pytorch.Ta06A | 2 +- .../log.04Dec20.mliap.pytorch.Ta06A.g++.1 | 32 ++++++++--------- .../log.04Dec20.mliap.pytorch.Ta06A.g++.4 | 34 +++++++++---------- potentials/README | 3 ++ ...a06A.mliap.pytorch => Ta06A.pytorch.mliap} | 0 6 files changed, 38 insertions(+), 34 deletions(-) create mode 120000 examples/mliap/Ta06A.pytorch.mliap rename potentials/{Ta06A.mliap.pytorch => Ta06A.pytorch.mliap} (100%) diff --git a/examples/mliap/Ta06A.pytorch.mliap b/examples/mliap/Ta06A.pytorch.mliap new file mode 120000 index 0000000000..22bb47850e --- /dev/null +++ b/examples/mliap/Ta06A.pytorch.mliap @@ -0,0 +1 @@ +../../potentials/Ta06A.pytorch.mliap \ No newline at end of file diff --git a/examples/mliap/in.mliap.pytorch.Ta06A b/examples/mliap/in.mliap.pytorch.Ta06A index 59cdcc8c81..e346c8a864 100644 --- a/examples/mliap/in.mliap.pytorch.Ta06A +++ b/examples/mliap/in.mliap.pytorch.Ta06A @@ -24,7 +24,7 @@ mass 1 180.88 # choose potential -include Ta06A.mliap.pytorch +include Ta06A.pytorch.mliap # Setup output diff --git a/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.1 b/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.1 index f56a79650e..0527e40757 100644 --- a/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.1 +++ b/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.1 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) - using 48 OpenMP thread(s) per MPI task +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task # Demonstrate MLIAP/PyTorch interface to linear SNAP potential # 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 create_atoms 1 box Created 128 atoms - create_atoms CPU = 0.002 seconds + create_atoms CPU = 0.000 seconds mass 1 180.88 # 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) # Definition of SNAP potential Ta_Cand06A @@ -50,9 +50,9 @@ variable zblz equal 73 # 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 4 ${zblcutouter} 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.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.pt 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. Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 @@ -112,7 +112,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d 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 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 @@ -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 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 -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 -288.8% CPU use with 1 MPI tasks x 48 OpenMP threads +Performance: 2.110 ns/day, 11.373 hours/ns, 48.847 timesteps/s +100.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: 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 -Comm | 0.0011814 | 0.0011814 | 0.0011814 | 0.0 | 0.06 -Output | 0.00059724 | 0.00059724 | 0.00059724 | 0.0 | 0.03 -Modify | 0.00047352 | 0.00047352 | 0.00047352 | 0.0 | 0.02 -Other | | 0.0003468 | | | 0.02 +Comm | 0.001157 | 0.001157 | 0.001157 | 0.0 | 0.06 +Output | 0.00080857 | 0.00080857 | 0.00080857 | 0.0 | 0.04 +Modify | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.03 +Other | | 0.0004304 | | | 0.02 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.4 b/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.4 index 7f1bc818d1..3c5bf24bf2 100644 --- a/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.4 +++ b/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.4 @@ -1,5 +1,5 @@ -LAMMPS (30 Nov 2020) - using 48 OpenMP thread(s) per MPI task +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task # Demonstrate MLIAP/PyTorch interface to linear SNAP potential # 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 create_atoms 1 box Created 128 atoms - create_atoms CPU = 0.002 seconds + create_atoms CPU = 0.000 seconds mass 1 180.88 # 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) # Definition of SNAP potential Ta_Cand06A @@ -50,9 +50,9 @@ variable zblz equal 73 # 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 4 ${zblcutouter} 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.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.pt 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. Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 @@ -112,7 +112,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d 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 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 @@ -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 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 -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 -99.7% CPU use with 4 MPI tasks x 48 OpenMP threads +Performance: 7.548 ns/day, 3.180 hours/ns, 174.720 timesteps/s +100.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.53583 | 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 -Comm | 0.0071442 | 0.01491 | 0.025289 | 5.4 | 2.65 -Output | 0.00092525 | 0.00095771 | 0.0010166 | 0.0 | 0.17 -Modify | 0.00014479 | 0.00015043 | 0.00015893 | 0.0 | 0.03 -Other | | 0.0005624 | | | 0.10 +Comm | 0.0044844 | 0.030393 | 0.052464 | 10.2 | 5.31 +Output | 0.001 | 0.0010351 | 0.0011083 | 0.1 | 0.18 +Modify | 0.0001468 | 0.00016417 | 0.00017977 | 0.0 | 0.03 +Other | | 0.0006567 | | | 0.11 Nlocal: 32.0000 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -154,4 +154,4 @@ Ave neighs/atom = 58.000000 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:05 diff --git a/potentials/README b/potentials/README index 63b32b6f4a..fbc49f8613 100644 --- a/potentials/README +++ b/potentials/README @@ -100,6 +100,9 @@ meam.spline modified EAM (MEAM) spline potential meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential mesocnt mesoscopic carbon nanotube (CNT) 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 poly polymorphic 3-body potential reax ReaxFF potential (see README.reax for more info) diff --git a/potentials/Ta06A.mliap.pytorch b/potentials/Ta06A.pytorch.mliap similarity index 100% rename from potentials/Ta06A.mliap.pytorch rename to potentials/Ta06A.pytorch.mliap