Added runfiles for multielement Gaussian grid

mala/descriptors/atomic_density.py

@@ -150,9 +150,16 @@ def __calculate_lammps(self, outdir, **kwargs):
 
         # Create LAMMPS instance.
         lammps_dict = {
-            "sigma": self.parameters.atomic_density_sigma,
             "rcutfac": self.parameters.atomic_density_cutoff,
         }
+        if len(set(self._atoms.numbers)) == 1:
+            lammps_dict["sigma"] = self.parameters.atomic_density_sigma
+        else:
+            for i in range(len(set(self._atoms.numbers))):
+                lammps_dict["sigma" + str(i + 1)] = (
+                    self.parameters.atomic_density_sigma
+                )
+
         lmp = self._setup_lammps(nx, ny, nz, lammps_dict)
 
         # For now the file is chosen automatically, because this is used
@@ -161,15 +168,24 @@ 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.ggrid.python"
+                    filepath,
+                    "in.ggrid_n{0}.python".format(
+                        len(set(self._atoms.numbers))
+                    ),
                 )
             else:
                 self.parameters.lammps_compute_file = os.path.join(
-                    filepath, "in.ggrid_defaultproc.python"
+                    filepath,
+                    "in.ggrid_defaultproc_n{0}.python".format(
+                        len(set(self._atoms.numbers))
+                    ),
                 )
         else:
             self.parameters.lammps_compute_file = os.path.join(
-                filepath, "in.ggrid_defaultproc.python"
+                filepath,
+                "in.ggrid_defaultproc_n{0}.python".format(
+                    len(set(self._atoms.numbers))
+                ),
             )
 
         # Do the LAMMPS calculation and clean up.

mala/descriptors/in.ggrid_defaultproc_n2.python

@@ -0,0 +1,25 @@
+# Calculate Gaussian atomic density descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, sigma, atom_config_fname
+# using command-line -var option
+
+# 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 * *
+
+compute ggrid all gaussian/grid/local  grid ${ngridx} ${ngridy} ${ngridz}  ${rcutfac}  ${radelem1}  ${radelem2}  ${sigma1} ${sigma2}
+
+thermo_modify norm yes
+
+run 0

mala/descriptors/in.ggrid_n1.python

@@ -0,0 +1,32 @@
+# Calculate Gaussian atomic density descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, sigma, 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}
+
+
+compute ggrid all gaussian/grid/local  grid ${ngridx} ${ngridy} ${ngridz}  ${rcutfac}  ${radelem1}  ${radelem2}  ${sigma1} ${sigma2}
+
+thermo_modify norm yes
+
+run 0

mala/descriptors/in.ggrid.python → mala/descriptors/in.ggrid_n2.python

@@ -14,7 +14,8 @@ mass * 1.0
 
 
 # is this important? or does it just need to be big enough?
-variable	radelem equal 0.5
+variable	radelem1 equal 0.5
+variable	radelem2 equal 0.5
 variable rcutneigh equal 2.0*${rcutfac}*${radelem}
 
 pair_style zero ${rcutneigh}
@@ -24,7 +25,7 @@ pair_coeff * *
 ${zbal}
 
 
-compute ggrid all gaussian/grid/local  grid ${ngridx} ${ngridy} ${ngridz}  ${rcutfac}  ${radelem}  ${sigma}
+compute ggrid all gaussian/grid/local  grid ${ngridx} ${ngridy} ${ngridz}  ${rcutfac}  ${radelem1}  ${radelem2}  ${sigma1} ${sigma2}
 
 thermo_modify norm yes