Parallel processing works in principle

mala/descriptors/bispectrum.py

@@ -171,11 +171,17 @@ def __calculate_lammps(self, outdir, **kwargs):
             if self.parameters._configuration["mpi"]:
                 if self.parameters.use_z_splitting:
                     self.parameters.lammps_compute_file = os.path.join(
-                        filepath, "in.bgridlocal.python"
+                        filepath,
+                        "in.bgridlocal_n{0}.python".format(
+                            len(set(self.atoms.numbers))
+                        ),
                     )
                 else:
                     self.parameters.lammps_compute_file = os.path.join(
-                        filepath, "in.bgridlocal_defaultproc.python"
+                        filepath,
+                        "in.bgridlocal_defaultproc_n{0}.python".format(
+                            len(set(self.atoms.numbers))
+                        ),
                     )
             else:
                 self.parameters.lammps_compute_file = os.path.join(
@@ -184,7 +190,6 @@ def __calculate_lammps(self, outdir, **kwargs):
                         len(set(self.atoms.numbers))
                     ),
                 )
-
         # Do the LAMMPS calculation and clean up.
         lmp.file(self.parameters.lammps_compute_file)
 

mala/descriptors/in.bgridlocal_defaultproc_n2.python

@@ -0,0 +1,41 @@
+# Calculate bispectrum descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, twojmax, rcutfac, atom_config_fname
+# using command-line -var option
+
+# Initialize simulation
+
+units		metal
+
+read_data ${atom_config_fname}
+
+mass * 1.0
+
+# define grid compute and atom compute
+
+group 		snapgroup type 1
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	wj1 equal 1
+variable 	wj2 equal 1
+variable 	wj1local equal ${wj1}-1.0e-15 # inject a bit of fuzz
+variable 	wj2local equal ${wj2}-1.0e-15 # inject a bit of fuzz
+variable 	radelem1 equal 0.5
+variable 	radelem2 equal 0.5
+variable 	bzero equal 0
+variable 	quadratic equal 0
+
+compute bgridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1local} ${wj2local}  rmin0 ${rmin0} bzeroflag ${bzero} quadraticflag ${quadratic} switchflag ${switch}
+
+# is this important? or does it just need to be big enough?
+
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# define output
+
+thermo_modify norm yes
+
+run 0

mala/descriptors/in.bgridlocal_n2.python

@@ -0,0 +1,46 @@
+# Calculate bispectrum descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, twojmax, rcutfac, atom_config_fname 
+# using command-line -var option
+
+# set up processor grid to match QE
+${lammps_procs}
+
+# Initialize simulation
+
+units		metal
+
+read_data ${atom_config_fname}
+
+mass * 1.0
+
+# is this important? or does it just need to be big enough?
+
+variable 	radelem1 equal 0.5
+variable 	radelem2 equal 0.5
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# set up plane cutoff values to evenly distribute grid points
+
+${zbal}
+
+# define grid compute and atom compute
+
+group 		snapgroup type 1 2
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	wj1 equal 1
+variable 	wj2 equal 1
+variable 	wj1local equal ${wj1}-1.0e-15 # inject a bit of fuzz
+variable 	wj2local equal ${wj2}-1.0e-15 # inject a bit of fuzz
+variable 	bzero equal 0
+variable 	quadratic equal 0
+
+compute bgridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1local} ${wj2local} rmin0 ${rmin0} bzeroflag ${bzero} quadraticflag ${quadratic} switchflag ${switch}
+
+thermo_modify norm yes
+
+run 0