Add molecule-species grid scaling to allow closer molecules.

README.md

@@ -194,6 +194,8 @@ inputDict = {
     "species_grid_pad":5, # How much to pad around the molecule species are being added to (in Angstroms)
     "species_gridspec":0.3, # How large of steps in R3 the grid surrounding a molecule should be
     # to which a species could be added. (in Angstroms)
+    "species_grid_rad_scale":1, # Factor to multiply molecule+species vdw by to set molecules.
+    # e.g. Reduce to allow for closer molecule-species distances.
     "species_skin":0.2, # How much buffer or "skin" should be added to around a molecule 
     # to which the species could be added. (in Angstroms)
     "species_location_method":'default', # Default attempts a basic Coulomb repulsion placement.

architector/io_arch_dock.py

@@ -197,8 +197,9 @@ def decide_new_species_location(mol, species, parameters={}):
     upper_radvect = []
     lower_radvect = []
     for z in mol.ase_atoms.get_atomic_numbers():
-        upper_radvect.append(io_ptable.rvdw[z]+spec_rad+parameters['species_skin'])
-        lower_radvect.append(io_ptable.rvdw[z]+spec_rad)
+        grid_radii = parameters.get('species_grid_rad_scale',1)*(io_ptable.rvdw[z]+spec_rad)
+        upper_radvect.append(grid_radii+parameters['species_skin'])
+        lower_radvect.append(grid_radii)
     upper_radvect = np.array(upper_radvect).reshape(-1,1)
     lower_radvect = np.array(lower_radvect).reshape(-1,1)
     upper_inds = np.where(np.any(np.less_equal(dist_grid_molecule, upper_radvect), axis=0))[0]

architector/io_process_input.py

@@ -775,6 +775,8 @@ def inparse(inputDict):
             # to which a species could be added. (in Angstroms)
             'species_skin':0.2, # How much buffer or "skin" should be added to around a molecule 
             # to which the species could be added. (in Angstroms)
+            'species_grid_rad_scale':1, # Factor to multiply molecule+species vdw by to set molecules.
+    # e.g. Reduce to allow for closer molecule-species distances
             'species_location_method':'default', # Default attempts a basic colomb repulsion placement.
             # Only other option is 'random' at the moment.
             'species_add_copies':1, # Number of species addition orientations to build