Added blessed log files

examples/mliap/README.pytorch

@@ -1,6 +1,7 @@
 README for the PyTorch energy model example
 
-These examples run the Ta06 example from the MLIAP package, but using the python coupling.
+These two examples run the Ta06 example from the MLIAP package, but using the python coupling.
+The differ only in how the coupling is constructed.
 
 1: Running models using LAMMPS executable: in.mliap.pytorch.Ta06A
 
@@ -13,14 +14,22 @@ creating or unpicking a PyTorch energy model.
 
 From that point you can run the example lmp -in in.mliap.pytorch.Ta06A -echo both
 
-2: Running models from python with LAMMPS in library mode: load_external.py
+2: Running models from python with LAMMPS in library mode: mliap_pytorch_Ta06A.py
 
 Before testing this, ensure that the first example (using LAMMPS executable) works.
+Also, not all python installations support this mode of operation. 
+It requires that the Python interpreter be initialized. 
+To check this for your Python library,
+run the Py_IsInitialized() method.
+If the return value is True, you should be able to run the example,
+as follows:
 
-Not all python installations support this mode of operation. 
+`python mliap_pytorch_Ta06A.py`
-Too test if your interpreter supports this, run:
+
-`python test_pylibs.py`
+or
- and examine the output.
+
+`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
 
-If this succeeds, you should be able to run:
-`python load_external.py`

examples/mliap/mliap.pytorch.Ta06A.py

@@ -1,106 +0,0 @@
-# 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'])
-
-# this commmand must be run before the MLIAP object is declared in lammps.
-
-lmp.mliappy.activate()
-
-# setup the simulation and declare an empty model
-# by specifying model filename as "LATER"
-
-lmp.commands_string(before_loading)
-
-# define the PyTorch model by loading a pkl file.
-# this could also be done in other ways.
-
-import pickle
-with open('Ta06A.mliap.pytorch.model.pkl','rb') as pfile:
-  model = pickle.load(pfile)
-  
-# connect the PyTorch model to the mliap pair style
-
-lmp.mliappy.load_model(model)
-
-# run the simulation with the mliap pair style
-
-lmp.commands_string(after_loading)

examples/mliap/mliap_pytorch_Ta06A.py

@@ -0,0 +1,106 @@
+# 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'])
+
+# this commmand must be run before the MLIAP object is declared in lammps.
+
+lmp.mliappy.activate()
+
+# setup the simulation and declare an empty model
+# by specifying model filename as "LATER"
+
+lmp.commands_string(before_loading)
+
+# define the PyTorch model by loading a pkl file.
+# this could also be done in other ways.
+
+import pickle
+with open('Ta06A.mliap.pytorch.model.pkl','rb') as pfile:
+  model = pickle.load(pfile)
+  
+# connect the PyTorch model to the mliap pair style
+
+lmp.mliappy.load_model(model)
+
+# run the simulation with the mliap pair style
+
+lmp.commands_string(after_loading)