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pes2mp.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Nov 14 15:28:43 2023
@author: Apoorv Kushwaha, Pooja Chahal, Habit Tatin & Prof. T. J. Dhilip Kumar
main file for PES2MP package (to debug/modify --> refer manual)
This program:
(*) imports necessary libraries
(*) creates required folders
(*) PESGen:
(*) calculates and moves respective Rigid Rotor(s) (RR) to COM.
(*) generates PES using Psi4 internally (for rough estimation)
(*) generates input files by transforming Jacobi coordinates (R, θ_n) to XYZ
(*) auxillary scripts are provided for external calculations (Molpro/Gaussian) and collecting results
(*) PESPlot:
(*) Plots 1D/2D and 4D PES using (a) R vs E plots and (b) polar plots
(*) NNGen:
(*) Can generate NN model for augmenting PES2MP
(*) Can handle N inputs and M outputs with PES and non-PES data
(*) MPExp:
(*) Does Multipole expansion of 2D and 4D PES
(*) 2D PES is expanded using Legendre polynomials and 4D using Spherical Harmonics
(*) Also performs inverse fitting after analytical fitting to print residual errors.
(*) AnaFit:
(*) Uses analytical expressions for fitting either PES or V Lambda terms.
"""
# general libraries
import numpy as np
import pandas as pd
# importing driver.py
import pes2mp_driver as driver
import os
from tqdm import tqdm
#import re
import shutil
import sys
import importlib
from datetime import datetime
import time
import subprocess
# Start the timer.
start_time = time.time()
# uncomment the fllowing two linesto catch segmentation error!!
# import faulthandler
# faulthandler.enable()
# defining current directory for creating new directories
input_dir = os.getcwd()+'/'
# the fllowing two lines define input file for pes2mp
inputfile = sys.argv[1]
sys.path.append(input_dir)
inp = importlib.import_module(inputfile)
# original_stdout = sys.stdout # Save a reference to the original standard output
driver.varerr(inp, inp.Proj_name)
Proj_name = inp.Proj_name
out_data = input_dir + 'Projects/' + Proj_name + '/' # directory for psi4 data
if not os.path.exists(out_data):
os.makedirs(out_data)
input_files_data = out_data + 'input_files/' # directory for Gaussian/Molpro input files
if not os.path.exists(input_files_data):
os.makedirs(input_files_data)
log_filex = inp.Proj_name + '.log' # Set a project name (Important)
f = open(out_data+log_filex, 'a+')
num_bars = 60
print("#####################################################################")
print("--- Date {} ---".format(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
print("#####################################################################")
print("##################### PES2MP Initiated ########################")
print("#####################################################################")
print('Necessary files Created')
f.write("#####################################################################")
f.write("\n--- Date {} ---".format(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
f.write("\n#####################################################################")
f.write("\n##################### PES2MP Initiated ########################")
f.write("\n#####################################################################")
f.write('\n \n /data and /project folders created. \n\n')
# with open(out_data+log_filex, 'w+') as f:
# sys.stdout = f # Change the standard output to the file we created.
# print('/data/ ; /psi4_PES_data/ ; /scratch/ folders created.')
# sys.stdout = original_stdout # Reset the standard output to its original value
# The program checks for job type in the input file uses series of if-else
# commands to execute the task inside the jobtype.
try:
inp.Create_PES_input
except:
print("Create_PES_input not provided! Skipping PESGen module!")
PESGen =False
direct_plot = False
else:
PESGen = inp.Create_PES_input
###############################################################################
###############################################################################
########################## PES Generation #####################################
###############################################################################
###############################################################################
if PESGen == True:
print("#-------------------------------------------------------------------#")
print("#-------------------# Using PESGen module #-------------------#")
print("#-------------------------------------------------------------------#")
f.write("\n#-------------------------------------------------------------------#")
f.write("\n#-------------------# Using PESGen module #-------------------#")
f.write("\n#-------------------------------------------------------------------#")
f.write("\n\n")
#print("Using PESGen module!")
import psi4
coll_1D = False
coll_2D = False
coll_4D = False
# determining nature of collision (1D/2D/4D)
f.write("\nIdentifying collision type !!!: ")
if (len(inp.RR1_atoms) == 1 and len(inp.RR2_atoms) == 1):
coll_1D = True
print("\n \t atom-atom collision: Using 1D template for PES")
f.write("\n \t atom-atom collision: Using 1D template for PES")
driver.PES_handler(inp, 1)
elif (len(inp.RR1_atoms) > 1 and len(inp.RR2_atoms) == 1):
coll_2D = True
print("\n \t RR1 has >1 atoms and RR2 has 1 atom: Using 2D Template for PES")
f.write("\n \t RR1 has >1 atoms and RR2 has 1 atom: Using 2D Template for PES")
driver.PES_handler(inp, 2)
elif (len(inp.RR1_atoms) > 1 and len(inp.RR2_atoms) > 1):
coll_4D = True
print("\n \t Both RR1 and RR2 have >1 atoms: Using 4D Template for PES")
f.write("\n \t Both RR1 and RR2 have >1 atoms: Using 4D Template for PES")
driver.PES_handler(inp, 4)
else:
print("\n Something wrong with the input atoms.\n")
print("\n For 1D collision, make sure that the num of atoms in the lists: RR1 = 1 and RR2 = 1")
print("\n For 2D collision, make sure that the num of atoms in the lists: RR1 > 1 and RR2 = 1")
print("\n For 2D collision, make sure that the num of atoms in the lists: RR1 > 1 and RR2 > 1")
f.write("\n Something wrong with the input atoms.\n")
f.write("\n For 1D collision, make sure that the num of atoms in the lists: RR1 = 1 and RR2 = 1")
f.write("\n For 2D collision, make sure that the num of atoms in the lists: RR1 > 1 and RR2 = 1")
f.write("\n For 2D collision, make sure that the num of atoms in the lists: RR1 > 1 and RR2 > 1")
driver.exit_program()
R = np.empty(0)
for i in range (len(inp.R_i)):
R_1 = np.arange(inp.R_i[i], inp.R_f[i], inp.R_stp[i]) # R_1 from R_i to R_f Ang with step size R_stp Ang
R = np.concatenate((R,R_1),axis=None) # merging R columns
r_n = len(R) # saving number of R data points
print("\n The R coodinates are: \n", R)
print("\n Total number of data points in R coordinates are: ", r_n)
r4 = np.atleast_2d(R).T # Converting R from row to column vector
f.write("\n \n The R coodinates are: \n")
f.write(str(R))
f.write("\n\n Total number of data points in R coordinates are: {} \n\n".format (r_n))
if coll_1D:
np.savetxt(out_data + "1D_input_coordinates.dat", R,fmt='%.2f')
# saving input coordinates
print("Saving input coordinates in 'Projects/{}/1D_input_coordinates.dat'".format(Proj_name))
f.write("\n\nSaving input coordinates in 'Projects/{}/1D_input_coordinates.dat'".format(Proj_name))
elif coll_2D:
# creating matrix for 2D collision coordinates
ang_i= inp.theta
A_nr = np.ndarray(shape=(1,2)) # R, theta array initialization
for i_gamma in tqdm(range (ang_i[0], ang_i[1], ang_i[2])):
b = np.array([i_gamma]) # defining array with angle
c = np.tile(b,(r_n,1)) # creating angles as columns
d = np.c_[ r4, c ] # joining r and columns
A_nr = np.vstack([A_nr, d]) # repeating for different geoms and joining
A_nr = np.delete(A_nr, 0, 0) # deleting first row (empty)
# sorting coordinates by theta and then R
keys = (A_nr[:, 1], A_nr[:, 0])
# creating matrix for 2D collision coordinates
sorted_indices = np.lexsort(keys)
A = A_nr[sorted_indices]
f.write("\nCreating matrix for 2D collision coordinates")
#f.write("\nTQDM LOOP FINISHED:\n {'|' * num_bars} 100% |\n\n")
f.write(f"\nTQDM LOOP FINISHED:\n {'|' * num_bars} 100% |\n\n")
# creating matrix for 4D collision coordinates
elif coll_4D:
phi= inp.phi
th2= inp.theta2
th1 = inp.theta1
A_nr = np.ndarray(shape=(1,4)) # internal coordinates array initialization
# to include final value in python, step size is added to it.
for i_phi in tqdm(range (phi[0],phi[1],phi[2])):
for j_theta2 in range (th2[0],th2[1],th2[2]):
for k_theta1 in range (th1[0],th1[1],th1[2]):
b = np.array([i_phi,j_theta2,k_theta1]) # defining array with angle
c = np.tile(b,(r_n,1)) # creating angles as columns
d = np.c_[ r4, c ] # joining r and columns
A_nr = np.vstack([A_nr, d]) # repeating for different geoms and joining
A_nr = np.delete(A_nr, 0, 0) # deleting first row (empty)
# sorting coordinates by phi, th2, th1 and then R
keys = (A_nr[:, 3], A_nr[:, 2], A_nr[:, 1], A_nr[:, 0])
# creating matrix for 4D collision coordinates
sorted_indices = np.lexsort(keys)
A = A_nr[sorted_indices]
f.write("\nCreating matrix for 4D collision coordinates")
f.write(f"\nTQDM LOOP FINISHED:\n {'|' * num_bars} 100% |\n\n")
else:
# this condition is non viable
pass
# checking if isotopic substitution is requested!
try:
inp.Use_isotope
except:
Use_isotope = False
print('\n Not using isotopic substitution! \n')
else:
Use_isotope = inp.Use_isotope
if Use_isotope:
print('\n Using isotopic substitution! \n')
f.write('\n Using isotopic substitution! \n')
RR1_isotope_mass = inp.RR1_isotope_mass
RR2_isotope_mass = inp.RR2_isotope_mass
#RR1_isotope_G = inp.RR1_isotope_G
#RR2_isotope_G = inp.RR2_isotope_G
else:
RR1_isotope_mass = [0] * len(inp.RR1_atoms)
RR2_isotope_mass = [0] * len(inp.RR2_atoms)
#RR1_isotope_G = [0] * len(inp.RR1_atoms)
#RR2_isotope_G = [0] * len(inp.RR1_atoms)
# Printing coordinates for 2D/4D rigid rotors and extracting COM coordinates
if coll_1D:
pass
else:
# if 2D/4D collision
print('\n Input coordinates (first 5, mid and last 5)\n')
print(A[:5]) # prints first 5 coordinates of R, gamma
print('---')
half_c = int(len(A)/2)
print(A[half_c-3:half_c+2]) # prints mid coordinates of R, gamma
print('---')
print(A[-5:]) # prints last 5 coordinates of R, gamma
print("\nTotal number of input coordinates : ",len(A))
f.write('\n Input coordinates (first 5, mid and last 5)\n')
f.write('\n' + str(A[:5]) + '\n') # prints first 5 coordinates of R, gamma
f.write('---')
f.write('\n' + str(A[half_c-3:half_c+2]) + '\n' ) # prints mid coordinates of R, gamma
f.write('---')
f.write('\n' + str(A[-5:]) + '\n' ) # prints last 5 coordinates of R, gamma
f.write("\nTotal number of input coordinates : {}".format(len(A)))
# Creating rigid rotor 1 (RR1) coordinates below and extracting COM coordinates
RR1_psi4, RR1_COM_len = driver.RR_com(f, inp.RR1_atoms, inp.RR1_bond_len,
inp.Charge[0], inp.Multiplicity[0],
RR1_isotope_mass)
if coll_2D:
np.savetxt(out_data + "2D_input_coordinates.dat", A,fmt='%.2f\t%d')
# saving input coordinates
print("Saving input coordinates in 'Projects/{}/2D_input_coordinates.dat'".format(Proj_name))
f.write("\n\nSaving input coordinates in 'Projects/{}/2D_input_coordinates.dat'".format(Proj_name))
elif coll_4D:
np.savetxt(out_data + "4D_input_coordinates.dat", A,fmt='%.2f\t%d\t%d\t%d')
print("Saving input coordinates in '/{}/4D_input_coordinates.dat'".format(Proj_name))
f.write("\n\nSaving input coordinates in '/{}/4D_input_coordinates.dat'".format(Proj_name))
# Creating RR2 input file with XYZ coordinates below and extracting COM coordinates
RR2_psi4, RR2_COM_len = driver.RR_com(f, inp.RR2_atoms, inp.RR2_bond_len,
inp.Charge[1], inp.Multiplicity[1],
RR2_isotope_mass)
else:
pass
###############################################################################
#-----------------------Gaussian Input Parameters-----------------------------#
###############################################################################
try:
inp.Create_GAUSSIAN_input_files
except:
Create_GAUSSIAN_input_files = False
else:
Create_GAUSSIAN_input_files = inp.Create_GAUSSIAN_input_files
print("\nCreating Gaussian Input files!\n")
f.write("\nCreating Gaussian Input files!\n")
# creating input files for Gaussian (CP corrected) ########################
if Create_GAUSSIAN_input_files:
gaussian_data = input_files_data + 'Gaussian_CP/' # directory for Gaussian data
# creating gaussian directory
if not os.path.exists(gaussian_data):
os.makedirs(gaussian_data)
# appending gaussian template with charge spin and other info!
Gaussian_input_template = "%nprocshared={}".format(inp.proc_g)
Gaussian_input_template += "\n%mem={}".format(inp.mem_g)
Gaussian_input_template += "\n%chk={}.chk\n".format(inp.chk_g)
Gaussian_input_template += inp.cmd_g
# Creating input files by calling appropriate function in driver file.
#-------------------------------# Gaussian 1D #-------------------------------#
if coll_1D:
FxD_geom_G = driver.gaussian_files_1D(f, Gaussian_input_template,
inp.RR1_atoms, inp.RR2_atoms,
inp.Charge, inp.Multiplicity,
R, gaussian_data)
#-------------------------------# Gaussian 2D #-------------------------------#
elif coll_2D :
FxD_geom_G = driver.gaussian_files_2D(f, Gaussian_input_template,
inp.RR1_atoms, inp.RR2_atoms,
inp.Charge, inp.Multiplicity,
R, gaussian_data, RR1_COM_len,A)
#-------------------------------# Gaussian 4D #-------------------------------#
elif coll_4D:
FxD_geom_G = driver.gaussian_files_4D(f, Gaussian_input_template,
inp.RR1_atoms, inp.RR2_atoms,
inp.Charge, inp.Multiplicity,
R, gaussian_data, RR1_COM_len,
RR2_COM_len, A)
else:
print('ID: 260 --> All coll_1D, coll_2D and coll_4D are False. Check for error!')
f.write("\n---- Gaussian input file template : see Template_Gaussian_CP.dat .")
template_filex = 'Template_Gaussian_CP.log'
f2 = open(input_files_data+template_filex, 'a+')
f2.write(str(FxD_geom_G))
f2.close()
f.write(f"\n TQDM LOOP: Gaussian input files created:\n {'|' * num_bars} 100% |\n\n")
print(" \n Gaussian (CP) Input files Created! Check: 'Projects/{}/input_files/Gaussian_CP/' \n".format(Proj_name))
f.write(" \n Gaussian (CP) Input files Created! Check: 'Projects/{}/input_files/Gaussian_CP/' \n".format(Proj_name))
else:
print(" \n Create_GAUSSIAN_input_files = False : Skipping Gaussian (CP) Input! \n")
f.write('\n Create_GAUSSIAN_input_files = False : Skipping Gaussian (CP) Input! \n ')
###############################################################################
#-----------------------Molpro Input Parameters (CP)--------------------------#
###############################################################################
try:
inp.Create_MOLPRO_CP_input_files
except:
Create_MOLPRO_CP_input_files = False
else:
Create_MOLPRO_CP_input_files = inp.Create_MOLPRO_CP_input_files
print("\nCreating molpro (CP) Input files!\n")
f.write("\nCreating molpro (CP) Input files!\n")
# creating input files for Molpro (CP corrected) ########################
if Create_MOLPRO_CP_input_files:
molpro_data = input_files_data + 'Molpro_CP/' # directory for psi4 data
if not os.path.exists(molpro_data):
os.makedirs(molpro_data)
Molpro_input_template = "***,single point energies \n"
Molpro_input_template += "memory,{}\n".format(inp.mem_m)
Molpro_input_template += "basis= {}\n".format(inp.basis_cp)
Molpro_input_template += "run_method={}\n".format(inp.run_method)
# converting RR atoms with label eg. C1, C2, etc.
RR1_name = [f'{name}{ii}' for ii, name in enumerate(inp.RR1_atoms, 1)]
RR2_name = [f'{name}{iii}' for iii, name in enumerate(inp.RR2_atoms, len(inp.RR1_atoms)+1)]
#print(psi4.core.Molecule.mass(RR1_psi4))
#-----------------------------# Molpro 1D (CP) #------------------------------#
if coll_1D:
FxD_geom_M = driver.molpro_files_CP_1D(f, Molpro_input_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_data)
#-------------------------------# Molpro 2D #-------------------------------#
elif coll_2D :
FxD_geom_M = driver.molpro_files_CP_2D(f, Molpro_input_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_data,
RR1_COM_len, A)
#-------------------------------# Molpro 4D #-------------------------------#
elif coll_4D:
FxD_geom_M = driver.molpro_files_CP_4D(f, Molpro_input_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_data,
RR1_COM_len, RR2_COM_len, A)
else:
print('ID: 317 --> All coll_1D, coll_2D and coll_4D are False. Check for error!')
f.write("\n---- Molpro input file template : see Template_Molpro_CP.dat.")
template_filex = 'Template_Molpro_CP.log'
f3 = open(input_files_data+template_filex, 'a+')
f3.write(str(FxD_geom_M))
f3.close()
f.write(f"\n TQDM LOOP: Molpro (CP) input files created:\n {'|' * num_bars} 100% |\n\n")
print(" \n Molpro (CP) Input files Created! Check: 'Projects/{}/input_files/Molpro_CP/' \n".format(Proj_name))
f.write(" \n Molpro (CP) Input files Created! Check: 'Projects/{}/input_files/Molpro_CP/' \n".format(Proj_name))
else:
print(" \n Create_MOLPRO_input_files = False : Skipping Molpro (CP) Input! \n")
f.write('\n Create_MOLPRO_input_files = False : Skipping Molpro (CP) Input! \n ')
###############################################################################
#----------------------Molpro Input Parameters (CBS)--------------------------#
###############################################################################
try:
inp.Create_MOLPRO_CBS_input_files
except:
Create_MOLPRO_CBS_input_files = False
else:
Create_MOLPRO_CBS_input_files = inp.Create_MOLPRO_CBS_input_files
print("\nCreating molpro (CBS) Input files!\n")
f.write("\nCreating molpro (CBS) Input files!\n")
# creating input files for Molpro (CBS extrapolated energies) #############
if Create_MOLPRO_CBS_input_files:
molpro_cbs_data = input_files_data + 'Molpro_CBS/' # directory for psi4 data
if not os.path.exists(molpro_cbs_data):
os.makedirs(molpro_cbs_data)
Molpro_cbs_template = "***,single point energies \n"
Molpro_cbs_template += "memory,{} \n".format(inp.mem_m)
Molpro_cbs_template += "run_method={} \n".format(inp.run_method)
# converting RR atoms with label eg. C1, C2, etc.
RR1_name = [f'{name}{ii}' for ii, name in enumerate(inp.RR1_atoms, 1)]
RR2_name = [f'{name}{iii}' for iii, name in enumerate(inp.RR2_atoms, len(inp.RR1_atoms)+1)]
#-----------------------------# Molpro 1D (CBS) #------------------------------#
if coll_1D:
FxD_geom_M_cbs = driver.molpro_files_CBS_1D(f, Molpro_cbs_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_cbs_data,
inp.basis_ref,inp.basis_cbs)
#-------------------------------# Molpro 2D #-------------------------------#
elif coll_2D :
FxD_geom_M_cbs = driver.molpro_files_CBS_2D(f, Molpro_cbs_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_cbs_data,
RR1_COM_len, A, inp.basis_ref,inp.basis_cbs)
#-------------------------------# Molpro 4D #-------------------------------#
elif coll_4D:
FxD_geom_M_cbs = driver.molpro_files_CBS_4D(f, Molpro_cbs_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_cbs_data,
RR1_COM_len, RR2_COM_len, A,
inp.basis_ref,inp.basis_cbs)
else:
print('ID: 375 --> All coll_1D, coll_2D and coll_4D are False. Check for error!')
f.write("\n---- Molpro input file template : see Template_Molpro_CBS.dat.")
template_filex = 'Template_Molpro_CBS.log'
f4 = open(input_files_data+template_filex, 'a+')
f4.write(str(FxD_geom_M_cbs))
f4.close()
f.write(f"\n TQDM LOOP: Molpro(CBS) input files created:\n {'|' * num_bars} 100% |\n\n")
print(" \n Molpro (CBS) Input files Created! Check: 'Projects/{}/input_files/Molpro_CBS/' \n".format(Proj_name))
f.write(" \n Molpro (CBS) Input files Created! Check: 'Projects/{}/input_files/Molpro_CBS/' \n".format(Proj_name))
else:
print(" \n Create_MOLPRO_CBS_input_files = False : Skipping Molpro (CBS) Input! \n")
f.write('\n Create_MOLPRO_CBS_input_files = False : Skipping Molpro (CBS) Input! \n ')
###############################################################################
#----------------------Molpro Input Parameters (Custom)-----------------------#
###############################################################################
try:
inp.Create_MOLPRO_custom_input_files
except:
Create_MOLPRO_custom_input_files = False
else:
Create_MOLPRO_custom_input_files = inp.Create_MOLPRO_custom_input_files
print("\nCreating molpro (custom) Input files!\n")
f.write("\nCreating molpro (custom) Input files!\n")
# creating input files for Molpro (custom input) #############
if Create_MOLPRO_custom_input_files:
molpro_custom_data = input_files_data + 'Molpro_custom/' # directory for psi4 data
if not os.path.exists(molpro_custom_data):
os.makedirs(molpro_custom_data)
Molpro_custom_template = "***,single point energies \n"
Molpro_custom_template += "memory,{} \n".format(inp.mem_m)
# converting RR atoms with label eg. C1, C2, etc.
RR1_name = [f'{name}{ii}' for ii, name in enumerate(inp.RR1_atoms, 1)]
RR2_name = [f'{name}{iii}' for iii, name in enumerate(inp.RR2_atoms, len(inp.RR1_atoms)+1)]
#-----------------------------# Molpro 1D (CBS) #------------------------------#
if coll_1D:
FxD_geom_M_ext = driver.molpro_files_custom_1D(f, Molpro_custom_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_custom_data,
inp.molpro_ext)
#-------------------------------# Molpro 2D #-------------------------------#
elif coll_2D :
FxD_geom_M_ext = driver.molpro_files_custom_2D(f, Molpro_custom_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_custom_data,
RR1_COM_len, A, inp.molpro_ext)
#-------------------------------# Molpro 4D #-------------------------------#
elif coll_4D:
FxD_geom_M_ext = driver.molpro_files_custom_4D(f, Molpro_custom_template, RR1_name, RR2_name,
inp.Charge, inp.Multiplicity, R, molpro_custom_data,
RR1_COM_len, RR2_COM_len, A, inp.molpro_ext)
else:
print('ID: 428 --> All coll_1D, coll_2D and coll_4D are False. Check for error!')
f.write("\n---- Molpro input file template : see Template_Molpro_custom.dat.")
template_filex = 'Template_Molpro_custom.log'
f5 = open(input_files_data+template_filex, 'a+')
f5.write(str(FxD_geom_M_ext))
f5.close()
f.write(f"\n TQDM LOOP: Molpro (custom) input files created:\n {'|' * num_bars} 100% |\n\n")
print(" \n Molpro (custom) Input files Created! Check: 'Projects/{}/input_files/Molpro_custom/' \n".format(Proj_name))
f.write(" \n Molpro (custom) Input files Created! Check: 'Projects/{}/input_files/Molpro_custom/' \n".format(Proj_name))
else:
print(" \n Create_MOLPRO_custom_input_files = False : Skipping Molpro (custom) Input! \n")
f.write('\n Create_MOLPRO_custom_input_files = False : Skipping Molpro (custom) Input! \n ')
###############################################################################
#--------- Psi4 Input Parameters (Custom for external calculation) -----------#
###############################################################################
try:
inp.Create_Psi4_custom_input_files
except:
Create_Psi4_custom_input_files = False
else:
Create_Psi4_custom_input_files = inp.Create_Psi4_custom_input_files
print("\nCreating Psi4 (custom) Input files!\n")
f.write("\nCreating Psi4 (custom) Input files!\n")
# creating input files for Psi4 (Custom Template) #############
if Create_Psi4_custom_input_files:
psi4_custom_data = input_files_data + 'psi4_custom/' # directory for psi4 data
if not os.path.exists(psi4_custom_data):
os.makedirs(psi4_custom_data)
Psi4_custom_template = 'molecule {{'
#-----------------------------# Psi4 1D (Custom) #------------------------------#
if coll_1D:
FxD_geom_psi4 = driver.psi4_input_1D(inp)
Psi4_custom_template += FxD_geom_psi4
Psi4_custom_template += '}}'
Psi4_custom_template += '\nR = {:.4f}\n'
Psi4_custom_template += inp.psi4_ext
for j in tqdm(range (len(R))): # python loop to generate PES
R_ii = R[j] # radial coordinate
inp_file = open(psi4_custom_data + '{:d}.inp'.format(int(j)), "w") # open input file
inp_file.write(Psi4_custom_template.format(R_ii,R_ii)) # write string to file
inp_file.close() # close file
f.write(f"\n TQDM LOOP: Psi4 1D input files created:\n {'|' * num_bars} 100% |\n\n")
#-----------------------------# Psi4 2D (Custom) #------------------------------#
elif coll_2D :
FxD_geom_psi4 = driver.psi4_input_2D(inp,RR1_psi4)
Psi4_custom_template += FxD_geom_psi4
Psi4_custom_template += '}}'
Psi4_custom_template += '\nR = {:.4f} \nTheta = {:.4f}\n'
Psi4_custom_template += inp.psi4_ext
for j in tqdm(range (len(A))): # python loop to generate PES
R = A[j,0] # radial coordinate
gamma = A[j,1] # angular coordinate
# Rigid rotor (RR) lies on Z axis (no rotation of RR : no projection)
R_x, R_z = driver.proj2D (R, gamma)
inp_file = open(psi4_custom_data + '{:d}.inp'.format(int(j)), "w") # open input file
inp_file.write(Psi4_custom_template.format(R_x, R_z,R, gamma))
inp_file.close() # close file
f.write(f"\n TQDM LOOP: Psi4 2D input files created:\n {'|' * num_bars} 100% |\n\n")
#-----------------------------# Psi4 4D (Custom) #------------------------------#
elif coll_4D:
FxD_geom_psi4 = driver.psi4_input_4D(inp,RR1_COM_len,RR2_COM_len)
Psi4_custom_template += FxD_geom_psi4
Psi4_custom_template += '}}'
Psi4_custom_template += '\nR = {:.4f} \nPhi = {:.4f} \nTheta2 = {:.4f} \nTheta1 = {:.4f}'
Psi4_custom_template += inp.psi4_ext
for j in tqdm(range (len(A))): # python loop to generate PES
R = A[j,0] # radial coordinate
phi = A[j,1] # angular coordinate phi
theta2 = A[j,2] # angular coordinate theta2
theta1 = A[j,3] # angular coordinate theta1
RR_mat = driver.proj4D (R, phi, theta2, theta1, RR1_COM_len, RR2_COM_len) # calling 4D projection function
inp_file = open(psi4_custom_data + '{:d}.inp'.format(int(j)), "w") # open input file
inp_file.write(Psi4_custom_template.format(*RR_mat,R, phi, theta2, theta1))
inp_file.close() # close file
f.write(f"\n TQDM LOOP: Psi4 4D input files created:\n {'|' * num_bars} 100% |\n\n")
else:
print('ID: 475 --> All coll_1D, coll_2D and coll_4D are False. Check for error!')
template_filex = 'Template_psi4_custom.log'
f5 = open(input_files_data+template_filex, 'a+')
f5.write(str(Psi4_custom_template))
f5.close()
print(" \n Psi4 (custom) Input files Created! Check: 'Projects/{}/input_files/psi4_custom/' \n".format(Proj_name))
f.write("\n Psi4 (custom) Input files Created! Check: 'Projects/{}/input_files/psi4_custom/' \n".format(Proj_name))
else:
print(" \n Create_Psi4_custom_input_files = False : Skipping Psi4 (custom) Input! \n")
f.write('\n Create_Psi4_custom_input_files = False : Skipping Psi4 (custom) Input! \n ')
################################################################################
#----------------- Running Psi4 calculations internally------------------------#
################################################################################
#Important:
#Try/Except/Finally block (in Psi4 - for rough PES calculation):
#Use 'pass' to ignore failed calculations (only store data points that converge)
#Use 'raise' to show error ! --> to debug code
################################################################################
try:
inp.Run_psi4
except:
Run_psi4 = False
else:
Run_psi4 = inp.Run_psi4
if Run_psi4:
direct_plot = True
psi4_int = out_data + 'psi4_PES_data/' # directory for psi4 data
psi4_data = psi4_int + 'data/' # directory for psi4 data
if not os.path.exists(psi4_data):
os.makedirs(psi4_data)
scratch_dir = psi4_int + 'scratch/' # scratch directory for Psi4
if not os.path.exists(scratch_dir):
os.makedirs(scratch_dir)
f1 = open(psi4_int+'psi4_failed_coordinates', 'a+')
psi4_io = psi4.core.IOManager.shared_object()
psi4_io.set_default_path(scratch_dir)
psi4.set_memory(inp.psi4_mem)
psi4.set_num_threads(inp.psi4_proc)
print("Generating Psi4 PES!")
f.write("Generating Psi4 PES!")
# 1D PES calculation using psi4
if coll_1D:
# geometry specifications
ecp = {} # dictionary for energies
F1D_geom = driver.psi4_input_1D(inp)
# print(" \n Psi4 Input : \n ")
# print(F1D_geom)
f.write(" \n Psi4 Input : \n ")
f.write('-x'*30 + '\n')
f.write(str(F1D_geom))
f.write('-x'*30 + '\n')
print(F1D_geom)
for fx in os.listdir(scratch_dir): # removing any previous scratch files
os.remove(os.path.join(scratch_dir, fx))
for j in tqdm(range (len(R))): # python loop to generate PES (using try and except to suppress error)
try:
R_ii = R[j] # radial coordinate
# Rigid rotor (RR) lies on Z axis (no rotation of RR : no projection)
psi4.core.set_output_file(psi4_data+'{:.2f}.out'.format(R_ii), False) # sets output file location
F1D_mol = psi4.geometry(F1D_geom.format(R_ii))
psi4_inp = psi4.core.Molecule.create_psi4_string_from_molecule(F1D_mol)
psi4.set_options({'reference': inp.psi4_reference,'freeze_core': inp.psi4_Frozen_Core})
if inp.psi4_bsse == None:
ecp[j] = psi4.energy(inp.psi4_method_basis, molecule=F1D_mol)
else:
ecp[j] = psi4.energy(inp.psi4_method_basis, bsse_type= inp.psi4_bsse,
return_total_data=True, molecule=F1D_mol)
except:
print("\n\n")
print ("Failed coordinate : (R = %.2f) \n" % (R_ii) )
f1.write("Failed coordinate : (R = %.2f) \n" % (R_ii) )
# replace 'pass' with 'raise' to show error ! to debug code
pass
finally:
psi4.core.close_outfile()
try:
os.remove(psi4_data+'{:.2f}.log'.format(R_ii)) # removing log file (too large)
except:
pass
psi4.core.clean()
psi4.core.clean_variables()
psi4.core.clean_options()
psi4.core.clean_timers()
for fx in os.listdir(scratch_dir): # removing remaining files after psi4 clean()
os.remove(os.path.join(scratch_dir, fx))
f.write(f"\n TQDM LOOP: Psi4 1D PES created:\n {'|' * num_bars} 100% |\n\n")
#####################################################################################################################
# coordinates for calculating E_inf ( to convert energies to cm-1 )
R_inf = inp.R_inf
#####################################################################################################################
# Section 4.0.2 : Calculating E infinity (200 Angstroms) at 90 degrees (BSSE approx. 0 at infinity)
# print("\n Geometry at infinity: \n ", F1D_geom.format(R_inf))
f.write("\n Geometry at infinity: \n ")
f.write("R = {}".format(R_inf))
psi4.core.set_output_file(psi4_data+'E_Inf.out',False) # sets output file location
F1D_mol_inf = psi4.geometry(F1D_geom.format(R_inf))
psi4.set_options({'reference': inp.psi4_reference,'freeze_core': inp.psi4_Frozen_Core})
try:
if inp.psi4_bsse == None:
ecp_inf = psi4.energy(inp.psi4_method_basis, molecule=F1D_mol_inf)
else:
ecp_inf = psi4.energy(inp.psi4_method_basis, bsse_type= inp.psi4_bsse,
return_total_data=True, molecule=F1D_mol_inf)
#os.remove(psi4_data+'E_Inf.log') # removing log file
psi4.core.clean()
except:
print('E infinity convergence failed! using last converged energy')
f.write('\n E infinity convergence failed! using last converged energy \n')
ecp_inf = list(ecp.values())[-1]
print(list(ecp.values())[-1])
pass
print("\n Energy at inifinity (Hartree): ", ecp_inf)
f.write("\n Energy at inifinity (Hartree): {}" .format(ecp_inf) )
# converting ecp diectionary into dataframe
df_ecp = pd.DataFrame.from_dict([ecp]).T
df_ecp.columns = ['E'] # giving suitable name for header
# converting coordinates to dataframe with suitable names
df_A = pd.DataFrame({'R': R })
# merging coordinate and energy dataframes
# The coordinates for which calculations have failed are dropped automatically
merged_df = pd.merge(df_A, df_ecp, left_index=True, right_index=True)
# set precision of each column
merged_df['R'] = merged_df['R'].apply(lambda x: format(x,".2f"))
merged_df['E'] = merged_df['E'].apply(lambda x: round(x,12))
# saving csv file
merged_df.to_csv(psi4_int + inp.PES_filename, index=None, header=True,sep='\t')
# converting energies in cm-1 and saving file
merged_df['E'] = (merged_df['E']-ecp_inf)*219474.6
merged_df['E'] = merged_df['E'].apply(lambda x: round(x,6))
merged_df.to_csv(out_data + inp.PES_filename_cm, index=None, header=True,sep='\t')
print("All required files are saved ! Check folder --> ", out_data)
try:
shutil.rmtree(scratch_dir) # removing scratch directory (residual files)
print("Scratch Directory Removed!")
except:
print("Most probably the scratch directory is already deleted! \n To see error replace 'pass' with 'raise' in the code.")
pass
# 2D PES calculation using psi4
elif coll_2D:
# geometry specifications
ecp = {} # dictionary for energies
F2D_geom = driver.psi4_input_2D(inp, RR1_psi4)
# print(" \n Psi4 Input : \n ")
#print(F2D_geom)
f.write(" \n Psi4 Input : \n ")
f.write(str(F2D_geom))
for fx in os.listdir(scratch_dir): # removing any previous scratch files
os.remove(os.path.join(scratch_dir, fx))
for j in tqdm(range (len(A))): # python loop to generate PES (using try and except to suppress error)
try:
R = A[j,0] # radial coordinate
gamma = A[j,1] # angular coordinate
# Rigid rotor (RR) lies on Z axis (no rotation of RR : no projection)
R_x, R_z = driver.proj2D (R, gamma)
psi4.core.set_output_file(psi4_data+'{:.2f}_{:d}.out'.format(R,int(gamma)), False) # sets output file location
F2D_mol = psi4.geometry(F2D_geom.format(R_x, R_z))
psi4.set_options({'reference': inp.psi4_reference,'freeze_core': inp.psi4_Frozen_Core})
if inp.psi4_bsse == None:
ecp[j] = psi4.energy(inp.psi4_method_basis, molecule=F2D_mol)
else:
ecp[j] = psi4.energy(inp.psi4_method_basis, bsse_type= inp.psi4_bsse,
return_total_data=True, molecule=F2D_mol)
except:
print ("Failed coordinate : (R = %.2f, theta = %d ) \n" % (A[j,0], A[j,1]) )
f1.write("Failed coordinate : (R = %.2f, theta = %d ) \n" % (A[j,0], A[j,1]) )
# replace 'pass' with 'raise' to show error ! to debug code
pass
finally:
psi4.core.close_outfile()
try:
os.remove(psi4_data+'{:.2f}_{:d}.log'.format(R,int(gamma))) # removing log file
except:
pass
psi4.core.clean()
psi4.core.clean_variables()
psi4.core.clean_options()
psi4.core.clean_timers()
for fx in os.listdir(scratch_dir): # removing remaining files after psi4 clean()
os.remove(os.path.join(scratch_dir, fx))
f.write(f"\n TQDM LOOP: Psi4 2D PES created:\n {'|' * num_bars} 100% |\n\n")
#####################################################################################################################
# coordinates for calculating E_inf ( to convert energies to cm-1 )
R_inf = inp.R_inf
ang_inf = inp.theta_2D_inf
#####################################################################################################################
# Section 4.0.2 : Calculating E infinity (200 Angstroms) at 90 degrees (BSSE approx. 0 at infinity)
R_x_inf, R_z_inf = driver.proj2D (R_inf, ang_inf)
# print("\n Geometry at infinity: \n ", F2D_geom.format(R_x_inf, R_z_inf))
f.write("\n Geometry at infinity: \n ")
f.write("R = {}\n Theta = {}\n".format(R_inf,ang_inf))
psi4.core.set_output_file(psi4_data+'E_Inf.out',False) # sets output file location
F2D_mol_inf = psi4.geometry(F2D_geom.format(R_x, R_z))
psi4.set_options({'reference': inp.psi4_reference,'freeze_core': inp.psi4_Frozen_Core})
try:
if inp.psi4_bsse == None:
ecp_inf = psi4.energy(inp.psi4_method_basis, molecule=F2D_mol_inf)
else:
ecp_inf = psi4.energy(inp.psi4_method_basis, bsse_type= inp.psi4_bsse,
return_total_data=True, molecule=F2D_mol_inf)
#os.remove(psi4_data+'E_Inf.log') # removing log file
psi4.core.clean()
except:
print('E infinity convergence failed! using last converged energy')
f.write('E infinity convergence failed! using last converged energy \n ')
ecp_inf = list(ecp.values())[-1]
print(list(ecp.values())[-1])
pass
print("\n Energy at inifinity (Hartree): ", ecp_inf)
f.write("\n Energy at inifinity (Hartree): " )
f.write(str(ecp_inf))
# converting ecp diectionary into dataframe
df_ecp = pd.DataFrame.from_dict([ecp]).T
df_ecp.columns = ['E'] # giving suitable name for header
# converting coordinates to dataframe with suitable names
df_A = pd.DataFrame({'R': A[:, 0], 'Gamma': A[:, 1]})
# merging coordinate and energy dataframes
# The coordinates for which calculations have failed are dropped automatically
merged_df = pd.merge(df_A, df_ecp, left_index=True, right_index=True)
# set precision of each column
merged_df['R'] = merged_df['R'].apply(lambda x: format(x,".2f"))
merged_df['Gamma'] = merged_df['Gamma'].apply(lambda x: format(x,".0f"))
merged_df['E'] = merged_df['E'].apply(lambda x: round(x,12))
# saving csv file
merged_df.to_csv(psi4_int + inp.PES_filename, index=None, header=True,sep='\t')
# converting energies in cm-1 and saving file
merged_df['E'] = (merged_df['E']-ecp_inf)*219474.6
merged_df['E'] = merged_df['E'].apply(lambda x: round(x,6))
merged_df.to_csv(out_data + inp.PES_filename_cm, index=None, header=True,sep='\t')
print("All required files are saved ! Check folder --> ", out_data)
try:
shutil.rmtree(scratch_dir) # removing scratch directory (residual files)
print("Scratch Directory Removed!")
except:
print("Most probably the scratch directory is already deleted! \n To see error replace 'pass' with 'raise' in the code.")
pass
# 4D PES calculation using psi4
elif coll_4D:
ecp = {} # dictionary for energies
F4D_geom = driver.psi4_input_4D(inp,RR1_COM_len,RR2_COM_len)
# print(" \n Psi4 Input : \n ")
# print(F4D_geom)
f.write(" \n Psi4 Input : \n ")
f.write(str(F4D_geom))
for fx in os.listdir(scratch_dir): # removing any previous scratch files
os.remove(os.path.join(scratch_dir, fx))
for j in tqdm(range (len(A))): # python loop to generate PES (using try and except to suppress convergence error)
try:
R = A[j,0] # radial coordinate
phi = A[j,1] # angular coordinate phi
theta2 = A[j,2] # angular coordinate theta2
theta1 = A[j,3] # angular coordinate theta1
RR_mat = driver.proj4D (R, phi, theta2, theta1, RR1_COM_len, RR2_COM_len) # calling 4D projection function
psi4.core.set_output_file(psi4_data+'{:.2f}_{:d}_{:d}_{:d}.out'.format(R,int(phi),int(theta2),int(theta1)),
False) # sets output file location
F4D_mol = psi4.geometry(F4D_geom.format(*RR_mat))
psi4.set_options({'reference': inp.psi4_reference,'freeze_core': inp.psi4_Frozen_Core})
if inp.psi4_bsse == None:
ecp[j] = psi4.energy(inp.psi4_method_basis, molecule=F4D_mol)
else:
ecp[j] = psi4.energy(inp.psi4_method_basis, bsse_type= inp.psi4_bsse,
return_total_data=True, molecule=F4D_mol)
except:
print ("Failed coordinate : (R = %.2f, phi = %d, theta2= %d, theta1= %d ) \n" % (A[j,0], A[j,1], A[j,2], A[j,3]) )
f1.write("Failed coordinate : (R = %.2f, phi = %d, theta2= %d, theta1= %d ) \n" % (A[j,0], A[j,1], A[j,2], A[j,3]) )
# replace 'pass' with 'raise' to show error ! to debug code
pass
finally:
psi4.core.close_outfile()
try:
os.remove(psi4_data+'{:.2f}_{:d}_{:d}_{:d}.log'.format(R,int(phi),int(theta2),int(theta1))) # removing log file
except:
pass
psi4.core.clean()
psi4.core.clean_variables()
psi4.core.clean_options()
psi4.core.clean_timers()
for fx in os.listdir(scratch_dir): # removing remaining files after psi4 clean()
os.remove(os.path.join(scratch_dir, fx))
f.write(f"\n TQDM LOOP: Psi4 4D PES created:\n {'|' * num_bars} 100% |\n\n")
#####################################################################################################################
# coordinates for calculating E_inf ( to convert energies to cm-1 )
R_inf = inp.R_inf
phi_inf = inp.phi_4D_inf
theta2_inf = inp.theta2_4D_inf
theta1_inf = inp.theta1_4D_inf
#####################################################################################################################
# Section 4.0.2 : Calculating E infinity (200 Angstroms) at 90 degrees (BSSE approx. 0 at infinity)
RR_mat_inf = driver.proj4D ( R_inf, phi_inf, theta2_inf, theta1_inf, RR1_COM_len, RR2_COM_len) # calling 4D projection function
F4D_mol_inf = psi4.geometry(F4D_geom.format(*RR_mat_inf))
# print("\n Geometry at infinity: \n ", F4D_geom.format(*RR_mat_inf))
f.write("\n Geometry at infinity: \n ")
f.write(" R = {}\n Phi = {}\n Theta 2 = {}\n Theta 1 = {}\n".format(R_inf,phi_inf, theta2_inf, theta1_inf))
psi4.core.set_output_file(psi4_data+'E_Inf.out',False) # sets output file location
psi4.set_options({'reference': inp.psi4_reference,'freeze_core': inp.psi4_Frozen_Core})
try:
if inp.psi4_bsse == None:
ecp_inf = psi4.energy(inp.psi4_method_basis, molecule=F4D_mol_inf)
else:
ecp_inf = psi4.energy(inp.psi4_method_basis, bsse_type= inp.psi4_bsse,
return_total_data=True, molecule=F4D_mol_inf)
#os.remove(psi4_data+'E_Inf.log') # removing log file
psi4.core.clean()
except:
print('E infinity convergence failed! using last converged energy')
f.write('\n E infinity convergence failed! using last converged energy \n')
ecp_inf = list(ecp.values())[-1]
print(list(ecp.values())[-1])
pass
print("\n Energy at inifinity (Hartree): ", ecp_inf)
f.write("\n Energy at inifinity (Hartree): ")
f.write(str(ecp_inf))
#####################################################################################################################
# converting ecp diectionary into dataframe
df_ecp = pd.DataFrame.from_dict([ecp]).T
df_ecp.columns = ['E'] # giving suitable name for header
# converting coordinates to dataframe with suitable names
df_A = pd.DataFrame({'R': A[:, 0], 'phi': A[:, 1], 'theta2': A[:, 2], 'theta1': A[:, 3]})
# merging coordinate and energy dataframes
# The coordinates for which calculations have failed are dropped automatically
merged_df = pd.merge(df_A, df_ecp, left_index=True, right_index=True)
# set precision of each column
merged_df['R'] = merged_df['R'].apply(lambda x: format(x,".2f"))
merged_df['phi'] = merged_df['phi'].apply(lambda x: format(x,".0f"))
merged_df['theta2'] = merged_df['theta2'].apply(lambda x: format(x,".0f"))
merged_df['theta1'] = merged_df['theta1'].apply(lambda x: format(x,".0f"))
merged_df['E'] = merged_df['E'].apply(lambda x: round(x,12))
# saving csv file
merged_df.to_csv(psi4_int + inp.PES_filename, index=None, header=True,sep='\t')
# converting energies in cm-1 and saving file
merged_df['E'] = (merged_df['E']-ecp_inf)*219474.6
merged_df['E'] = merged_df['E'].apply(lambda x: round(x,6))
merged_df.to_csv(out_data + inp.PES_filename_cm, index=None, header=True,sep='\t')
print("All required files are saved ! \n Check folder : \n ", out_data)
try:
shutil.rmtree(scratch_dir) # removing scratch directory (along with residual files)
print("Scratch Directory Removed!")
except:
print("Most probably the scratch directory is already deleted! \n To see error replace 'pass' with 'raise' in the code.")
else:
print('ID: 235 --> All coll_1D, coll_2D and coll_4D are False. Check for error!')
print(" \n Psi4 calculations finished! \n")
f.write('\n Psi4 calculations finished! \n ')
f1.close()
else:
direct_plot = False
print(" \n Run_psi4 = False : Skipping Psi4 calculations! \n")
f.write('\n Run_psi4 = False : Skipping Psi4 calculations! \n ')
print("#-------------------------------------------------------------------#")
print("#--------------# PES Files Created Successfully #-------------#")
print("#-------------------------------------------------------------------#")
f.write("\n#-------------------------------------------------------------------#")
f.write("\n#--------------# PES Files Created Successfully #-------------#")
f.write("\n#-------------------------------------------------------------------#")
f.write("\n\n")
else:
print(" \n Create_PES_input = False : Checking input for external Plots \n")
f.write('\n Create_PES_input = False : Checking input for external Plots! \n ')
###############################################################################
###############################################################################
############################# PES Plot ########################################
###############################################################################
###############################################################################