diff --git a/pyef/analysis.py b/pyef/analysis.py index 375daac..e61971a 100644 --- a/pyef/analysis.py +++ b/pyef/analysis.py @@ -41,7 +41,7 @@ def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCag self.dielectric = 1 #To avoid over-estimating screening from bound atoms, set dielectric to 1 for primary bound atoms in ESP calv - self.changeDielectBoundBool = True + self.changeDielectBoundBool = False # Dictionary is originally from molsimplify, # Data from http://www.webelements.com/ (last accessed May 13th 2015) # Palladium covalent radius seemed to be under-estimated in original implementation, so changed to 1.39 per https://webelements.com/palladium/atom_sizes.html # Dictionary from molsimplify, https://molsimplify.readthedocs.io/en/latest/_modules/molSimplify/Classes/globalvars.html @@ -81,8 +81,13 @@ def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCag 'Np': (237.05, 93, 1.90, 7), 'Pu': (244.06, 94, 1.75, 8), 'Am': (243.06, 95, 1.80, 9), 'Cm': (247.07, 96, 1.69, 10), 'Bk': (247.07, 97, 1.68, 11), 'Cf': (251.08, 98, 1.68, 12)} self.prepData() + + def minDielecBonds(self, bool_bonds): + self.changeDielectBoundBool = bool_bonds + def changeDielectric(self, dlc): self.dielectric = dlc + def fix_ECPmolden(self): """Prepares output terachem data for analysis, mainly isolating final .xyz frame and naming .molden file appropriotely"""