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Dielectric now a parameter rather than hardcoded #25

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Apr 5, 2024
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Dielectric now a parameter rather than hardcoded #25

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33 changes: 17 additions & 16 deletions pyef/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ def __init__(self, lst_of_folders, lst_of_tmcm_idx, folder_to_file_path, inGaCag
self.folder_to_file_path = folder_to_file_path
self.dict_of_calcs = {'Hirshfeld': '1', 'Voronoi':'2', 'Mulliken': '5', 'Lowdin': '6', 'SCPA': '7', 'Becke': '10', 'ADCH': '11', 'CHELPG': '12', 'MK':'13', 'AIM': '14', 'Hirshfeld_I': '15', 'CM5':'16', 'EEM': '17', 'RESP': '18', 'PEOE': '19'}
self.inGaCageBool = inGaCage

self.dielectric = 1
# 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
Expand Down Expand Up @@ -78,7 +78,8 @@ 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 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"""

Expand Down Expand Up @@ -336,7 +337,7 @@ def calcNearestCageAtom(espatom_idx, charge_file):
total_esp = 0

# Distance to cage atoms
cage_idxs = list(np.range(0, 280))
cage_idxs = list(np.arange(0, 280))
distances_toCage = []
counter = 0

Expand All @@ -352,7 +353,7 @@ def calcNearestCageAtom(espatom_idx, charge_file):
return [NearestCageAtom]


def calcesp(espatom_idx, charge_range, charge_file):
def calcesp(espatom_idx, charge_range, charge_file, dielectric):
"""
Calculate the esp

Expand Down Expand Up @@ -399,7 +400,7 @@ def calcesp(espatom_idx, charge_range, charge_file):
r = (((xs[idx] - xo)*A_to_m)**2 + ((ys[idx] - yo)*A_to_m)**2 + ((zs[idx] - zo)*A_to_m)**2)**(0.5)
total_esp = total_esp + (charges[idx]/r)

final_esp = k*total_esp*((C_e))*cal_J*faraday # Note: cal/kcal * kJ/J gives 1
final_esp = k*total_esp*((C_e))*cal_J*faraday*(1/dielectric) # Note: cal/kcal * kJ/J gives 1
# print(str(final_esp) + ' kJ/(mol*e)')
return [final_esp, df['Atom'][idx_atom]]

Expand Down Expand Up @@ -570,7 +571,7 @@ def E_proj_first_coord(self, metal_idx, xyz_file_path, atom_multipole_file):
def esp_first_coord(self, metal_idx, charge_file, path_to_xyz):
print('The index of the metal atom is: ' + str(metal_idx))
lst_bonded_atoms = self.getBondedAtoms(path_to_xyz, metal_idx)
[First_coord_ESP, atom_type] = Electrostatics.calcesp(metal_idx, lst_bonded_atoms, charge_file)
[First_coord_ESP, atom_type] = Electrostatics.calcesp(metal_idx, lst_bonded_atoms, charge_file, self.dielectric)
return First_coord_ESP

def esp_second_coord(self, metal_idx, charge_file, path_to_xyz):
Expand All @@ -583,7 +584,7 @@ def esp_second_coord(self, metal_idx, charge_file, path_to_xyz):
set_second_coor = set(lst_first_and_second)
final_lst = list(set_second_coor)
final_lst.remove(metal_idx)
[second_coord_ESP, atom_type] = Electrostatics.calcesp(metal_idx, final_lst, charge_file)
[second_coord_ESP, atom_type] = Electrostatics.calcesp(metal_idx, final_lst, charge_file, self.dielectric)
return second_coord_ESP

# Boolean CageTrue
Expand All @@ -598,18 +599,18 @@ def charge_atom(filename, atom_idx):
partial_charge_atom = charges[atom_idx]
return [total_charge, partial_charge_atom]

def ESP_all_calcs(filename, atom_idx, cageTrue):
def ESP_all_calcs(filename, atom_idx, cageTrue, dlc):
# Get the number of lines in the txt file
total_lines =Electrostatics.mapcount(filename)
all_lines = range(0, total_lines)
[ESP_all, atom_type] = Electrostatics.calcesp(atom_idx, all_lines, filename)
[ESP_all, atom_type] = Electrostatics.calcesp(atom_idx, all_lines, filename, dlc)
if cageTrue:
cage_lines = range(0, 280)
guest_lines = range(280, total_lines)
# print('Cage indices: ' + str(cage_lines))
# print('Guest indices: ' + str(guest_lines))
ESP_just_ligand = Electrostatics.calcesp(atom_idx, guest_lines, filename)[0]
ESP_just_cage = Electrostatics.calcesp(atom_idx, cage_lines, filename)[0]
ESP_just_ligand = Electrostatics.calcesp(atom_idx, guest_lines, filename, dlc)[0]
ESP_just_cage = Electrostatics.calcesp(atom_idx, cage_lines, filename, dlc)[0]
print('ESP for all atoms: ' + str(ESP_all) + ' kJ/(mol*e)')
print('ESP just ligand: ' + str(ESP_just_ligand) + ' kJ/(mol*e)')
print('ESP just cage: ' + str(ESP_just_cage) + ' kJ/(mol*e)')
Expand All @@ -619,7 +620,7 @@ def ESP_all_calcs(filename, atom_idx, cageTrue):
return [ESP_all, atom_type]


def esp_bydistance(espatom_idx, charge_file):
def esp_bydistance(espatom_idx, charge_file, dielectric):
df = pd.read_csv(charge_file, sep='\s+', names=["Atom",'x', 'y', 'z', "charge"])
k = 8.987551*(10**9) # Coulombic constant in kg*m**3/(s**4*A**2)

Expand Down Expand Up @@ -658,7 +659,7 @@ def esp_bydistance(espatom_idx, charge_file):
else:
r = (((xs[idx] - xo)*A_to_m)**2 + ((ys[idx] - yo)*A_to_m)**2 + ((zs[idx] - zo)*A_to_m)**2)**(0.5)
distances.append(r)
esps.append(k*C_e*cal_J*faraday*charges[idx]/r)
esps.append(k*(1/dielectric)*C_e*cal_J*faraday*charges[idx]/r)
# Now we sort the distance list, and use sorted indices to sort the
dist_arr = np.array(distances)
sorted_idx = np.argsort(dist_arr)
Expand Down Expand Up @@ -743,12 +744,12 @@ def getESPData(self, charge_types, ESPdata_filename):
try:
if self.inGaCageBool:
# With newly analyzed partial charges, re-compute ESP data
[ESP_all, ESP_just_ligand, ESP_just_cage, atom_type] = Electrostatics.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool)
[ESP_all, ESP_just_ligand, ESP_just_cage, atom_type] = Electrostatics.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool, self.dielectric)
else:
[ESP_all, atom_type] = Electrostatics.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool)
[ESP_all, atom_type] = Electrostatics.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool, self.dielectric)

[total_charge,partial_charge_atom] = Electrostatics.charge_atom(full_file_path, atom_idx)
[sorted_distances, sorted_esps, cum_esps] = Electrostatics.esp_bydistance(atom_idx, full_file_path)
[sorted_distances, sorted_esps, cum_esps] = Electrostatics.esp_bydistance(atom_idx, full_file_path, self.dielectric)
ESP_fcoord = self.esp_first_coord(atom_idx, full_file_path, path_to_xyz)
ESP_scoord = self.esp_second_coord(atom_idx, full_file_path, path_to_xyz)

Expand Down
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