Merge pull request #13 from davidkastner/fixradii

Fixed Atomic radii andmmap issues
davidkastner · Jan 18, 2024 · 7066b9b · 7066b9b
2 parents d7c1fec + 7008daf
commit 7066b9b
Showing 1 changed file with 19 additions and 17 deletions.
diff --git a/pyef/analysis.py b/pyef/analysis.py
@@ -1,3 +1,4 @@
+import mmap
 import re
 import os
 import glob
@@ -39,6 +40,8 @@ def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCag
 
         #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
+        #some covalent radii updated with 2008 updated values from webelements.com accessed 1/18/24 
         self.amassdict = {'X': (1.0, 0, 0.77, 0), 'H': (1.0079, 1, 0.37, 1),
              'D': (2.0141, 1, 0.37, 1), 'He': (4.002602, 2, 0.46, 2),
              'Li': (6.94, 3, 1.33, 1), 'Be': (9.0121831, 4, 1.02, 2), 'B': (10.83, 5, 0.85, 3),
@@ -47,34 +50,33 @@ def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCag
              'Mg': (24.30, 12, 1.39, 2), 'Al': (26.98, 13, 1.26, 3), 'Si': (28.08, 14, 1.16, 4),
              'P': (30.9738, 15, 1.06, 5), 'S': (32.065, 16, 1.02, 6), 'Cl': (35.453, 17, 0.99, 7),
              'Ar': (39.948, 18, 0.96, 8), 'K': (39.10, 19, 1.96, 1), 'Ca': (40.08, 20, 1.71, 2),
-             'Sc': (44.96, 21, 1.7, 3), 'Ti': (47.867, 22, 1.36, 4), 'V': (50.94, 23, 1.22, 5),
-             'Cr': (51.9961, 24, 1.27, 6), 'Mn': (54.938, 25, 1.39, 7), 'Fe': (55.84526, 26, 1.25, 8),
-             'Co': (58.9332, 27, 1.26, 9), 'Ni': (58.4934, 28, 1.21, 10), 'Cu': (63.546, 29, 1.38, 11),
-             'Zn': (65.39, 30, 1.31, 12), 'Ga': (69.72, 31, 1.24, 3), 'Ge': (72.63, 32, 1.21, 4),
+             'Sc': (44.96, 21, 1.7, 3), 'Ti': (47.867, 22, 1.36, 4), 'V': (50.94, 23, 1.34, 5),
+             'Cr': (51.9961, 24, 1.27, 6), 'Mn': (54.938, 25, 1.39, 7), 'Fe': (55.84526, 26, 1.32, 8),
+             'Co': (58.9332, 27, 1.26, 9), 'Ni': (58.4934, 28, 1.24, 10), 'Cu': (63.546, 29, 1.38, 11),
+             'Zn': (65.39, 30, 1.31, 12), 'Ga': (69.72, 31, 1.26, 3), 'Ge': (72.63, 32, 1.22, 4),
              'As': (74.92, 33, 1.21, 5), 'Se': (78.96, 34, 1.16, 6), 'Br': (79.904, 35, 1.14, 7),
              'Kr': (83.798, 36, 1.17, 8), 'Rb': (85.47, 37, 2.10, 1), 'Sr': (87.62, 38, 1.85, 2),
-             'Y': (88.91, 39, 1.63, 3), 'Zr': (91.22, 40, 1.54, 4), 'Nb': (92.91, 41, 1.47, 5),
-             'Mo': (95.96, 42, 1.38, 6), 'Tc': (98.9, 43, 1.56, 7), 'Ru': (101.1, 44, 1.25, 8),
-             'Rh': (102.9, 45, 1.25, 9), 'Pd': (106.4, 46, 1.39, 10), 'Ag': (107.9, 47, 1.28, 11),
-             'Cd': (112.4, 48, 1.48, 12), 'In': (111.818, 49, 1.42, 3), 'Sn': (118.710, 50, 1.40, 4),
+             'Y': (88.91, 39, 1.63, 3), 'Zr': (91.22, 40, 1.48, 4), 'Nb': (92.91, 41, 1.47, 5),
+             'Mo': (95.96, 42, 1.45, 6), 'Tc': (98.9, 43, 1.56, 7), 'Ru': (101.1, 44, 1.25, 8),
+             'Rh': (102.9, 45, 1.35, 9), 'Pd': (106.4, 46, 1.38, 10), 'Ag': (107.9, 47, 1.45, 11),
+             'Cd': (112.4, 48, 1.48, 12), 'In': (111.818, 49, 1.42, 3), 'Sn': (118.710, 50, 1.41, 4),
              'Sb': (121.760, 51, 1.40, 5), 'Te': (127.60, 52, 1.99, 6), 'I': (126.90447, 53, 1.40, 7),
-             'Xe': (131.293, 54, 1.31, 8), 'Cs': (132.9055, 55, 2.32, 1), 'Ba': (137.327, 56, 1.96, 2),
+             'Xe': (131.293, 54, 1.31, 8), 'Cs': (132.9055, 55, 2.44, 1), 'Ba': (137.327, 56, 1.96, 2),
              'La': (138.9, 57, 1.69, 3), 'Ce': (140.116, 58, 1.63, 4), 'Pr': (140.90766, 59, 1.76, 5),
              'Nd': (144.242, 60, 1.74, 6), 'Pm': (145, 61, 1.73, 7), 'Sm': (150.36, 62, 1.72, 8),
              'Eu': (151.964, 63, 1.68, 9), 'Gd': (157.25, 64, 1.69, 10), 'Tb': (158.92535, 65, 1.68, 11),
              'Dy': (162.500, 66, 1.67, 12), 'Ho': (164.93033, 67, 1.66, 13), 'Er': (167.259, 68, 1.65, 14),
              'Tm': (168.93422, 69, 1.64, 15), 'Yb': (173.045, 70, 1.70, 16), 'Lu': (174.9668, 71, 1.62, 3),
              'Hf': (178.5, 72, 1.50, 8), 'Ta': (180.9, 73, 1.38, 5), 'W': (183.8, 74, 1.46, 6),
              'Re': (186.2, 75, 1.59, 7), 'Os': (190.2, 76, 1.28, 8), 'Ir': (192.2, 77, 1.37, 9),
-             'Pt': (195.1, 78, 1.23, 10), 'Au': (197.0, 79, 1.24, 11), 'Hg': (200.6, 80, 1.49, 2),
-             'Tl': (204.38, 81, 1.44, 3), 'Pb': (207.2, 82, 1.44, 4), 'Bi': (208.9804, 83, 1.51, 5),
+             'Pt': (195.1, 78, 1.36, 10), 'Au': (197.0, 79, 1.44, 11), 'Hg': (200.6, 80, 1.49, 2),
+             'Tl': (204.38, 81, 1.44, 3), 'Pb': (207.2, 82, 1.47, 4), 'Bi': (208.9804, 83, 1.51, 5),
              'Po': (208.98, 84, 1.90, 6), 'At': (209.99, 85, 2.00, 7), 'Rn': (222.6, 86, 142, 4),
              'Fr': (223.02, 87, 3.48, 8), 'Ra': (226.03, 88, 2.01, 2), 'Ac': (277, 89, 1.86, 3),
              'Th': (232.0377, 90, 1.75, 4), 'Pa': (231.04, 91, 2.00, 5), 'U': (238.02891, 92, 1.70, 6),
              '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)}
+             'Cm': (247.07, 96, 1.69, 10), 'Bk': (247.07, 97, 1.68, 11), 'Cf': (251.08, 98, 1.68, 12)}        
         self.prepData()
-
 
     def fix_ECPmolden(self):
         """Prepares output terachem data for analysis, mainly isolating final .xyz frame and naming .molden file appropriotely"""
@@ -121,10 +123,10 @@ def prepData(self):
                     num_lines = num_atoms + 2
                     head = [next(full_traj) for _ in range(num_lines)]
 
-                with open(os.path.join(folder_path, 'initial_' + os.path.basename(optim_file_path)), 'w') as initxyz:
-                    initxyz.writelines(head)
-                with open(final_optim_xyz, 'w') as finalxyz:
-                    finalxyz.writelines(deque(full_traj, num_lines))
+                    with open(os.path.join(folder_path, 'initial_' + os.path.basename(optim_file_path)), 'w') as initxyz:
+                        initxyz.writelines(head)
+                    with open(final_optim_xyz, 'w') as finalxyz:
+                        finalxyz.writelines(deque(full_traj, num_lines))
             except Exception as e:
                 backup_file = os.path.join(folder_path, 'xyz.xyz')
                 if os.path.exists(backup_file):