Resolve merge conflicts

examples/mliap/README

@@ -0,0 +1,103 @@
+This directory contains multiple examples of 
+machine-learning potentials defined using the 
+MLIAP package in LAMMPS. The input files
+are described below.
+
+in.mliap.snap.Ta06A
+-------------------
+Run linear SNAP, equivalent to examples/snap/in.snap.Ta06A
+
+in.mliap.snap.WBe.PRB2019
+-------------------------
+Run linear SNAP, equivalent to examples/snap/in.snap.WBe.PRB2019
+
+in.mliap.snap.quadratic
+-----------------------
+Run quadratic SNAP
+
+in.mliap.snap.chem
+------------------
+Run EME-SNAP, equivalent to examples/snap/in.snap.InP.JCPA2020
+
+in.mliap.snap.compute
+---------------------
+Generate the A matrix, the gradients (w.r.t. coefficients) 
+of total potential energy, forces, and stress tensor for 
+linear SNAP, equivalent to in.snap.compute
+
+in.mliap.quadratic.compute
+--------------------------
+Generate the A matrix, the gradients (w.r.t. coefficients) 
+of total potential energy, forces, and stress tensor for 
+for quadratic SNAP, equivalent to in.snap.compute.quadratic
+
+in.mliap.pytorch.Ta06A
+-----------------------
+This reproduces the output of in.mliap.snap.Ta06A above,
+but using the Python coupling to PyTorch.
+
+This example can be run in two different ways:
+
+1: Running a LAMMPS executable: in.mliap.pytorch.Ta06A
+
+First run ``python convert_mliap_Ta06A.py``. It creates
+a PyTorch energy model that replicates the 
+SNAP Ta06A potential and saves it in the file 
+"Ta06A.mliap.pytorch.model.pt".
+
+You can then run the example as follows
+
+`lmp -in in.mliap.pytorch.Ta06A -echo both`
+
+The resultant log.lammps output should be identical to that generated
+by in.mliap.snap.Ta06A.
+
+If this fails, see the instructions for building the MLIAP package
+with Python support enabled. Also, confirm that the
+LAMMPS Python embedded Python interpreter is
+working by running ../examples/in.python.
+
+2: Running a Python script: mliap_pytorch_Ta06A.py
+
+Before testing this, ensure that the previous method
+(running a LAMMPS executable) works.
+
+You can run the example in serial: 
+
+`python mliap_pytorch_Ta06A.py`
+
+or in parallel:
+
+`mpirun -np 4 python mliap_pytorch_Ta06A.py`
+
+The resultant log.lammps output should be identical to that generated
+by in.mliap.snap.Ta06A and in.mliap.pytorch.Ta06A.
+
+Not all Python installations support this mode of operation.
+It requires that the Python interpreter be initialized. If not,
+the script will exit with an error message.
+
+in.mliap.pytorch.relu1hidden
+----------------------------
+This example demonstrates a simple neural network potential
+using PyTorch and SNAP descriptors. 
+
+`lmp -in in.mliap.pytorch.relu1hidden -echo both`
+
+It was trained on just the energy component (no forces) of 
+the data used in the original SNAP Ta06A potential for 
+tantalum (Thompson, Swiler, Trott, Foiles, Tucker, 
+J Comp Phys, 285, 316 (2015).). Because of the very small amount
+of energy training data, it uses just 1 hidden layer with 
+a ReLU activation function. It is not expected to be 
+very accurate for forces. 
+
+NOTE: Unlike the previous example, this example uses 
+a pre-built PyTorch file `Ta06A.mliap.pytorch.model.pt`. 
+It is read using `torch.load`,
+which implicitly uses the Python `pickle` module.
+This is known to be insecure. It is possible to construct malicious 
+pickle data that will execute arbitrary code during unpickling. Never 
+load data that could have come from an untrusted source, or that 
+could have been tampered with. Only load data you trust.
+

examples/mliap/Ta06A.mliap.pytorch

@@ -0,0 +1,18 @@
+# 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
+ 
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} &
+mliap model mliappy Ta06A.mliap.pytorch.model.pt &
+descriptor sna Ta06A.mliap.descriptor
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff * * mliap Ta
+

examples/mliap/convert_mliap_Ta06A.py

@@ -0,0 +1,26 @@
+import sys
+import numpy as np
+import torch
+
+# torch.nn.modules useful for defining a MLIAPPY model.
+from lammps.mliap.pytorch import TorchWrapper, IgnoreElems
+
+# Read coefficients
+coeffs = np.genfromtxt("Ta06A.mliap.model",skip_header=6)
+
+# Write coefficients to a pytorch linear model
+bias = coeffs[0]
+weights = coeffs[1:]
+lin = torch.nn.Linear(weights.shape[0],1)
+lin.to(torch.float64)
+with torch.autograd.no_grad():
+    lin.weight.set_(torch.from_numpy(weights).unsqueeze(0))
+    lin.bias.set_(torch.as_tensor(bias,dtype=torch.float64).unsqueeze(0))
+
+# Wrap the pytorch model for usage with mliappy coupling.
+model = IgnoreElems(lin) # The linear module does not use the types.
+n_descriptors = lin.weight.shape[1]
+n_elements = 1
+linked_model = TorchWrapper(model,n_descriptors=n_descriptors,n_elements=n_elements)
+
+torch.save(linked_model,"Ta06A.mliap.pytorch.model.pt")

examples/mliap/in.mliap.pytorch.Ta06A

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+# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.mliap.pytorch
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/mliap/in.mliap.pytorch.relu1hidden

@@ -0,0 +1,53 @@
+# Demonstrate MLIAP interface to linear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+
+mass 1 180.88
+
+# choose potential
+
+include relu1hidden.mliap.pytorch
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/mliap/in.mliap.snap.Ta06A

@@ -1,4 +1,4 @@
-# Demonstrate MLIAP interface to kinear SNAP potential
+# Demonstrate MLIAP interface to linear SNAP potential
 
 # Initialize simulation
 

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

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+LAMMPS (30 Nov 2020)
+  using 48 OpenMP thread(s) per MPI task
+# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.316
+Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
+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 = (0.0000000 0.0000000 0.0000000) to (13.264000 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
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.mliap.pytorch
+# 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
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+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
+Loading python model complete.
+Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 1 
+SNAP keyword elems Ta 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 0 
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * mliap Ta
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      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
+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 
+      20    284.53666   -11.849587   -11.849587   -11.813095    2289.1527   -2289.1527 
+      30    266.51577   -11.847275   -11.847275   -11.813095    1851.7131   -1851.7131 
+      40    243.05007   -11.844266   -11.844266   -11.813095     1570.684    -1570.684 
+      50    215.51032   -11.840734   -11.840734   -11.813094    1468.1899   -1468.1899 
+      60    185.48331   -11.836883   -11.836883   -11.813094    1524.8757   -1524.8757 
+      70     154.6736   -11.832931   -11.832931   -11.813094    1698.3351   -1698.3351 
+      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
+
+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
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.9998     | 1.9998     | 1.9998     |   0.0 | 99.87
+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
+
+Nlocal:        128.000 ave         128 max         128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        727.000 ave         727 max         727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        3712.00 ave        3712 max        3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:      7424.00 ave        7424 max        7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58.000000
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03

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

@@ -0,0 +1,157 @@
+LAMMPS (30 Nov 2020)
+  using 48 OpenMP thread(s) per MPI task
+# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.316
+Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
+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 = (0.0000000 0.0000000 0.0000000) to (13.264000 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
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.mliap.pytorch
+# 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
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+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
+Loading python model complete.
+Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 1 
+SNAP keyword elems Ta 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 0 
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * mliap Ta
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      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
+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 
+      20    284.53666   -11.849587   -11.849587   -11.813095    2289.1527   -2289.1527 
+      30    266.51577   -11.847275   -11.847275   -11.813095    1851.7131   -1851.7131 
+      40    243.05007   -11.844266   -11.844266   -11.813095     1570.684    -1570.684 
+      50    215.51032   -11.840734   -11.840734   -11.813094    1468.1899   -1468.1899 
+      60    185.48331   -11.836883   -11.836883   -11.813094    1524.8757   -1524.8757 
+      70     154.6736   -11.832931   -11.832931   -11.813094    1698.3351   -1698.3351 
+      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
+
+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
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.53583    | 0.54622    | 0.55401    |   0.9 | 97.05
+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
+
+Nlocal:        32.0000 ave          32 max          32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:        431.000 ave         431 max         431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:        928.000 ave         928 max         928 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:      1856.00 ave        1856 max        1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58.000000
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:02

examples/mliap/mliap_pytorch_Ta06A.py

@@ -0,0 +1,104 @@
+# Demonstrate how to load a model from the python side.
+# This is essentially the same as in.mliap.pytorch.Ta06A
+# except that python is the driving program, and lammps
+# is in library mode.
+
+before_loading =\
+"""# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+
+mass 1 180.88
+
+# choose potential
+
+# 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
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} &
+mliap model mliappy LATER &
+descriptor sna Ta06A.mliap.descriptor
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff * * mliap Ta
+"""
+after_loading =\
+"""
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+"""
+
+import lammps
+
+lmp = lammps.lammps(cmdargs=['-echo','both'])
+
+# Before defining the pair style, one must do the following:
+import lammps.mliap
+lammps.mliap.activate_mliappy(lmp)
+# Otherwise, when running lammps in library mode,
+# you will get an error:
+# "ERROR: Loading MLIAPPY coupling module failure."
+
+# Setup the simulation and declare an empty model
+# by specifying model filename as "LATER"
+lmp.commands_string(before_loading)
+
+# Define the model however you like. In this example
+# we load it from disk:
+import torch
+model = torch.load('Ta06A.mliap.pytorch.model.pt')
+
+# Connect the PyTorch model to the mliap pair style.
+lammps.mliap.load_model(model)
+  
+# run the simulation with the mliap pair style
+lmp.commands_string(after_loading)

examples/mliap/relu1hidden.mliap.pytorch

@@ -0,0 +1,18 @@
+# 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
+ 
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} &
+mliap model mliappy relu1hidden.mliap.pytorch.model.pt &
+descriptor sna Ta06A.mliap.descriptor
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff * * mliap Ta
+