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Merge pull request #20 from davidkastner/fixESPcalc
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Removed Charge calculation dependence in Efield Calculation
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@mane292
mane292 committed Feb 11, 2024
2 parents 644dfe3 + f7641f7 commit 06d24d4
Showing 1 changed file with 53 additions and 71 deletions.
124 changes: 53 additions & 71 deletions pyef/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,14 @@ def getmultipoles(multipole_name):
sections = re.split(r'\n\s*[*]+\s*', text)

# Define a pattern to extract the index, element name, and atomic dipole and quadrupole moment values
pattern = r'Atomic multipole moments of\s+(\d+)\s*\(([^)]+)\s*\).*?X=\s*([-+]?\d+\.\d+)\s+Y=\s*([-+]?\d+\.\d+)\s+Z=\s*([-+]?\d+\.\d+).*?XX=\s*([-+]?\d+\.\d+)\s+XY=\s*([-+]?\d+\.\d+)\s+XZ=\s*([-+]?\d+\.\d+).*?YX=\s*([-+]?\d+\.\d+)\s+YY=\s*([-+]?\d+\.\d+)\s+YZ=\s*([-+]?\d+\.\d+).*?ZX=\s*([-+]?\d+\.\d+)\s+ZY=\s*([-+]?\d+\.\d+)\s+ZZ=\s*([-+]?\d+\.\d+)'
#pattern = r'Atomic multipole moments of\s+(\d+)\s*\(([^)]+)\s*\).*?X=\s*([-+]?\d+\.\d+)\s+Y=\s*([-+]?\d+\.\d+)\s+Z=\s*([-+]?\d+\.\d+).*?XX=\s*([-+]?\d+\.\d+)\s+XY=\s*([-+]?\d+\.\d+)\s+XZ=\s*([-+]?\d+\.\d+).*?YX=\s*([-+]?\d+\.\d+)\s+YY=\s*([-+]?\d+\.\d+)\s+YZ=\s*([-+]?\d+\.\d+).*?ZX=\s*([-+]?\d+\.\d+)\s+ZY=\s*([-+]?\d+\.\d+)\s+ZZ=\s*([-+]?\d+\.\d+)'
pattern = (r'Atomic multipole moments of\s+(\d+)\s*\(([^)]+)\s*\).*?'
r'Atomic monopole moment \(electron\):\s*([-+]?\d+\.\d+)\s+Atomic charge:\s*([-+]?\d+\.\d+).*?'
r'X=\s*([-+]?\d+\.\d+)\s+Y=\s*([-+]?\d+\.\d+)\s+Z=\s*([-+]?\d+\.\d+).*?'
r'XX=\s*([-+]?\d+\.\d+)\s+XY=\s*([-+]?\d+\.\d+)\s+XZ=\s*([-+]?\d+\.\d+).*?'
r'YX=\s*([-+]?\d+\.\d+)\s+YY=\s*([-+]?\d+\.\d+)\s+YZ=\s*([-+]?\d+\.\d+).*?'
r'ZX=\s*([-+]?\d+\.\d+)\s+ZY=\s*([-+]?\d+\.\d+)\s+ZZ=\s*([-+]?\d+\.\d+)'
)
atomicDicts = []

# Iterate through sections and extract the information
Expand All @@ -219,29 +226,30 @@ def getmultipoles(multipole_name):
if match:
index = match.group(1)
element = match.group(2)
x_value = match.group(3)
y_value = match.group(4)
z_value = match.group(5)
monopole_moment = float(match.group(3))
atomic_charge = float(match.group(4))
x_value = match.group(5)
y_value = match.group(6)
z_value = match.group(7)
dipole_moment = [float(x_value), float(y_value), float(z_value)]

xx_value = match.group(6)
xy_value = match.group(7)
xz_value = match.group(8)
yx_value = match.group(9)
yy_value = match.group(10)
yz_value = match.group(11)
zx_value = match.group(12)
zy_value = match.group(13)
zz_value = match.group(14)

xx_value = match.group(8)
xy_value = match.group(9)
xz_value = match.group(10)
yx_value = match.group(11)
yy_value = match.group(12)
yz_value = match.group(13)
zx_value = match.group(14)
zy_value = match.group(15)
zz_value = match.group(16)
# Create a 3x3 matrix for the quadrupole moment
quadrupole_moment = np.array([
[float(xx_value), float(xy_value), float(xz_value)],
[float(yx_value), float(yy_value), float(yz_value)],
[float(zx_value), float(zy_value), float(zz_value)]
])

atomDict = {"Index": index, "Element": element, 'Dipole_Moment': dipole_moment, 'Quadrupole_Moment': quadrupole_moment}
atomDict = {"Index": index, "Element": element, "Atom_Charge": atomic_charge, 'Dipole_Moment': dipole_moment, 'Quadrupole_Moment': quadrupole_moment}
atomicDicts.append(atomDict)
return atomicDicts

Expand Down Expand Up @@ -404,25 +412,22 @@ def calc_firstTermE(espatom_idx, charge_range, charge_file):
E_vec = [Ex, Ey, Ez]
return [E_vec, position_vec, df['Atom'][idx_atom]]

def calc_fullE(espatom_idx, charge_range, charge_file, atom_multipole_file):
df = pd.read_csv(charge_file, sep='\s+', names=["Atom",'x', 'y', 'z', "charge"])
def calc_fullE(self, idx_atom, charge_range, xyz_file, atom_multipole_file):

df = self.getGeomInfo(xyz_file)
#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)

# Convert each column to list for quicker indexing
atoms = df['Atom']
charges = df['charge']
xs = df['x']
ys = df['y']
zs = df['z']

# Pick the index of the atom at which the esp should be calculated
idx_atom = espatom_idx
xs = df['X']
ys = df['Y']
zs = df['Z']

# Determine position and charge of the target atom
xo = xs[idx_atom]
yo = ys[idx_atom]
zo = zs[idx_atom]
chargeo = charges[idx_atom]
position_vec = [xo, yo, zo]
Ex = 0
Ey = 0
Expand All @@ -448,43 +453,37 @@ def calc_fullE(espatom_idx, charge_range, charge_file, atom_multipole_file):
else:
# Units of dipole_vec:
dipole_vec = atom_dict["Dipole_Moment"]
inv_dist_vec = np.array([1/(xs[idx] - xo),1/(ys[idx] - yo), 1/(zs[idx] - zo)])
dist_vec = np.array([(xs[idx] - xo), (ys[idx] - yo), (zs[idx] - zo)])
dist_arr = np.outer(dist_vec, dist_vec)
quadrupole_arr = atom_dict['Quadrupole_Moment']
# r_2A = ((xs[idx] - xo))**2 + ((ys[idx] - yo))**2 + ((zs[idx] - zo))**2
# Shaik_E = Shaik_E + inv_eps*k*C_e*charges[idx]*(1/r_2A)*dist_vec

# Calculate esp and convert to units (A to m); Calc E-field stenth in kJ/mol*e*m
r = (((xs[idx] - xo)*A_to_m)**2 + ((ys[idx] - yo)*A_to_m)**2 + ((zs[idx] - zo)*A_to_m)**2)**(0.5)
Shaik_E = Shaik_E + A_to_m*inv_eps*k*C_e*charges[idx]*(1/(r**2))*dist_vec/la.norm(dist_vec)
# Ex = Ex + inv_eps*k*C_e*(1/(r**3))*((xs[idx] - xo))*(-charges[idx]*(A_to_m**2) + (1/r**2)*A_to_m*np.dot(dipole_vec, dist_vec))
# Ey = Ey + inv_eps*k*C_e*(1/(r**3))*((ys[idx] - yo))*(-charges[idx]*(A_to_m**2) + (1/r**2)*A_to_m*np.dot(dipole_vec, dist_vec))
# Ez = Ez + inv_eps*k*C_e*(1/(r**3))*((zs[idx] - zo))*(-charges[idx]*(A_to_m**2) + (1/r**2)*A_to_m*np.dot(dipole_vec, dist_vec))
Shaik_E = Shaik_E + A_to_m*inv_eps*k*C_e*atom_dict["Atom_Charge"]*(1/(r**2))*dist_vec/la.norm(dist_vec)
Ex_quad = inv_eps*k*C_e*(1/(r**3))*((xs[idx] - xo))*(A_to_m**6)*(1/r**4)*dist_arr[1:, 1:]*quadrupole_arr[1:,1:]
Ey_quad = inv_eps*k*C_e*(1/(r**3))*((ys[idx] - yo))*(A_to_m**6)*(1/r**4)*dist_arr[0:2:3, 0:2:3]*quadrupole_arr[0:2:3,0:2:3]
Ez_quad = inv_eps*k*C_e*(1/(r**3))*((zs[idx] - zo))*(A_to_m**6)*(1/r**4)*dist_arr[0:2, 0:2]*quadrupole_arr[0:2,0:2]

Ex = Ex + inv_eps*k*C_e*(1/(r**3))*((xs[idx] - xo))*(-charges[idx]*(A_to_m**2) + (A_to_m**4)*(1/r**2)*np.dot(dipole_vec[1:], dist_vec[1:]))-(1/3)*Ex_quad.sum()
Ey = Ey + inv_eps*k*C_e*(1/(r**3))*((ys[idx] - yo))*(-charges[idx]*(A_to_m**2) + (A_to_m**4)*(1/r**2)*np.dot(dipole_vec[0:2:3], dist_vec[0:2:3])) -(1/3)*Ey_quad.sum()
Ez = Ez + inv_eps*k*C_e*(1/(r**3))*((zs[idx] - zo))*(-charges[idx]*(A_to_m**2) + (A_to_m**4)*(1/r**2)*np.dot(dipole_vec[0:2], dist_vec[0:2])) -(1/3)*Ez_quad.sum()
Ex = Ex + inv_eps*k*C_e*(1/(r**3))*((xs[idx] - xo))*(-atom_dict["Atom_Charge"]*(A_to_m**2) + (A_to_m**4)*(1/r**2)*np.dot(dipole_vec[1:], dist_vec[1:]))-(1/3)*Ex_quad.sum()
Ey = Ey + inv_eps*k*C_e*(1/(r**3))*((ys[idx] - yo))*(-atom_dict["Atom_Charge"]*(A_to_m**2) + (A_to_m**4)*(1/r**2)*np.dot(dipole_vec[0:2:3], dist_vec[0:2:3])) -(1/3)*Ey_quad.sum()
Ez = Ez + inv_eps*k*C_e*(1/(r**3))*((zs[idx] - zo))*(-atom_dict["Atom_Charge"]*(A_to_m**2) + (A_to_m**4)*(1/r**2)*np.dot(dipole_vec[0:2], dist_vec[0:2])) -(1/3)*Ez_quad.sum()
E_vec = [Ex, Ey, Ez]
return [E_vec, position_vec, df['Atom'][idx_atom], Shaik_E]


# Bond_indices is a list of tuples where each tuple contains the zero-indexed values of location of the atoms of interest
def E_proj_bondIndices(bond_indices, charge_file, atom_multipole_file):
def E_proj_bondIndices(self, bond_indices, xyz_filepath, atom_multipole_file):
bonded_atoms = []
E_projected = []
E_shaik_proj = []
bonded_positions = []
total_lines = Electrostatics.mapcount(charge_file)
all_lines = range(0, total_lines)
total_lines = Electrostatics.mapcount(xyz_filepath)
all_lines = range(0, total_lines - 2)
# Determine the Efield vector at point of central metal stom
bond_lens = []
for atomidxA, atomidxB in bond_indices:
print('Starting iteration at 401: atomindxA: ' + str(atomidxA))
[A_bonded_E, A_bonded_position, A_bonded_atom, A_Shaik_E_bonded] = Electrostatics.calc_fullE(atomidxA, all_lines, charge_file, atom_multipole_file)
[B_bonded_E, B_bonded_position, B_bonded_atom, B_Shaik_E_bonded] = Electrostatics.calc_fullE(atomidxB, all_lines, charge_file, atom_multipole_file)
[A_bonded_E, A_bonded_position, A_bonded_atom, A_Shaik_E_bonded] = self.calc_fullE(atomidxA, all_lines, xyz_filepath, atom_multipole_file)
[B_bonded_E, B_bonded_position, B_bonded_atom, B_Shaik_E_bonded] = self.calc_fullE(atomidxB, all_lines, xyz_filepath, atom_multipole_file)
bond_vec_unnorm = np.subtract(np.array(A_bonded_position), np.array(B_bonded_position))
bond_len = np.linalg.norm(bond_vec_unnorm)
bond_vec = bond_vec_unnorm/(bond_len)
Expand All @@ -501,20 +500,20 @@ def E_proj_bondIndices(bond_indices, charge_file, atom_multipole_file):
return [E_projected, bonded_atoms, bond_indices, bond_lens]


def E_proj_first_coord(self, metal_idx, xyz_file_path, charge_file, atom_multipole_file):
def E_proj_first_coord(self, metal_idx, xyz_file_path, atom_multipole_file):
bonded_atoms = []
E_projected = []
E_shaik_proj = []
bonded_positions = []
total_lines = Electrostatics.mapcount(charge_file)
all_lines = range(0, total_lines)
total_lines = Electrostatics.mapcount(xyz_file_path)
all_lines = range(0, total_lines - 2)
# Determine the Efield vector at point of central metal stom
[center_E, center_position, center_atom, Shaik_E_center] = Electrostatics.calc_fullE(metal_idx, all_lines, charge_file, atom_multipole_file)
[center_E, center_position, center_atom, Shaik_E_center] = self.calc_fullE(metal_idx, all_lines, xyz_file_path, atom_multipole_file)
lst_bonded_atoms = self.getBondedAtoms(xyz_file_path, metal_idx)

bond_lens = []
for bonded_atom_idx in lst_bonded_atoms:
[bonded_E, bonded_position, bonded_atom, Shaik_E_bonded] = Electrostatics.calc_fullE(bonded_atom_idx, all_lines, charge_file, atom_multipole_file)
[bonded_E, bonded_position, bonded_atom, Shaik_E_bonded] = self.calc_fullE(bonded_atom_idx, all_lines, xyz_file_path, atom_multipole_file)
bond_vec_unnorm = np.subtract(np.array(center_position), np.array(bonded_position))
bond_len = np.linalg.norm(bond_vec_unnorm)
bond_vec = bond_vec_unnorm/(bond_len)
Expand Down Expand Up @@ -811,37 +810,20 @@ def getEFieldData(self, Efield_data_filename, input_bond_indices=[]):
output = proc.communicate("\n".join(polarization_commands).encode())

try:
full_file_path = os.getcwd() +'/' + 'final_optim_Hirshfeld_I.txt'
atmrad_src = "/opt/Multiwfn_3.7_bin_Linux_noGUI/examples/atmrad"
copy_tree(atmrad_src, results_dir + 'atmrad/')
# If bond_indices is longer then one, default to manually entry mode
if bool_manual_mode:
file_bond_indices = input_bond_indices[counter]
[proj_Efields, bondedAs, bonded_idx, bond_lens] = Electrostatics.E_proj_bondIndices(file_bond_indices, full_file_path, path_to_pol)
[proj_Efields, bondedAs, bonded_idx, bond_lens] = self.E_proj_bondIndices(file_bond_indices,xyz_file_path, path_to_pol)
# Otherwise, automatically sense atoms bonded to metal and output E-fields of those
else:
[proj_Efields, bondedAs, bonded_idx, bond_lens] = self.E_proj_first_coord(atom_idx,xyz_file_path, full_file_path, path_to_pol)

[proj_Efields, bondedAs, bonded_idx, bond_lens] = self.E_proj_first_coord(atom_idx,xyz_file_path, path_to_pol)
results_dict['Max Eproj'] = max(abs(np.array(proj_Efields)))
results_dict['Projected_Efields V/Angstrom'] = proj_Efields
results_dict['Bonded Atoms'] = bondedAs
results_dict['Bonded Indices'] = bonded_idx
results_dict['Bond Lengths']= bond_lens
except Exception as e:
proc = subprocess.Popen(command_A, stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
calc_command = self.dict_of_calcs['Hirshfeld_I']
commands = ['7', calc_command, '1', 'y', '0', 'q'] # For atomic charge type corresponding to dict key
output = proc.communicate("\n".join(commands).encode())
new_name = 'final_optim_Hirshfeld_I.txt'
os.rename('final_optim.chg', new_name)
if bool_manual_mode:
file_bond_indices = input_bond_indices[counter]
[proj_Efields, bondedAs, bonded_idx, bond_lens] = Electrostatics.E_proj_bondIndices(file_bond_indices, full_file_path, path_to_pol)
# Otherwise, automatically sense atoms bonded to metal and output E-fields of those
else:
[proj_Efields, bondedAs, bonded_idx, bond_lens] = self.E_proj_first_coord(atom_idx, xyz_file_path, full_file_path, path_to_pol)
# Will ned to add additional params here for E-field data

results_dict['Max Eproj'] = max(abs(np.array(proj_Efields)))
results_dict['Projected_Efields V/Angstrom'] = proj_Efields
results_dict['Bonded Atoms'] = bondedAs
results_dict['Bonded Indices'] = bonded_idx
results_dict['Bond Lengths']= bond_lens
print(repr(e))

counter = counter + 1

Expand Down

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