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kSC.py
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kSC.py
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#!/usr/bin/env python
import argparse
import sys, os
import numpy as np
from tunneling import *
###########################################################################################
def read_input(f_name):
"""
Given an input file in the current working directory returns:
list of barriers, T, E_reactants, E_TS, E_products, imaginary frequency of TS, variation of free Gibbs energy from reactants to TS
The units must be K, Hartree and cm^-1 for Temperature, Energy and Frequency respectively.
For more information see advanced help (keyword '--help_adv').
"""
# Read file
f = open(f_name, "r")
data = f.read()
data = data.split("\n")
f.close()
# Process information
list_barriers = data[0].replace(",", "").split(" ") # deletes all ',' from possible cells
input_values = [[j for j in line.split(",")] for line in data[1:] if line != ""]
for i in range(len(input_values)):
for j in range(len(input_values[i])):
if input_values[i][j] == "": input_values[i][j] = "0" # solves empty cells
try:
input_values[i][j] = float(input_values[i][j])
except:
print("ERROR: Could not convert an input value to float: {}".format(input_values[i][j]))
sys.exit(0)
# Checks
DEFAULT_BARRIERS = ["classical", "squared", "parabolic", "eckart", "eckart-approx", "wigner"]
list_barriers = [i for i in list_barriers if i != ""]
for b in list_barriers:
if b not in DEFAULT_BARRIERS:
print("ERROR: '{}' is not a valid barrier. The default barriers are: ".format(b) + ", ".join(DEFAULT_BARRIERS))
sys.exit(0)
for i in range(len(input_values)):
if len(input_values[i]) != 7:
print("ERROR: Values do not follow the required 7-column CSV format:\n{}".format([line for line in data[1:] if line != ""][i]))
sys.exit(0)
# Prepare input data
input_values = np.array(input_values)
T, E_r, E_TS, E_p, freq_TS, G_r, G_TS = input_values[:,0], input_values[:,1], input_values[:,2], input_values[:,3], input_values[:,4], input_values[:,5], input_values[:,6]
AG_TS = G_TS - G_r
# Change Hartrees to eV (1 Hartree = 27.211386245988 eV, https://en.wikipedia.org/wiki/Hartree)
factor = 27.211386245988 # ev * Hartree^-1
E_r, E_TS, E_p, AG_TS = E_r*factor, E_TS*factor, E_p*factor, AG_TS*factor
return list_barriers, T, E_r, E_TS, E_p, freq_TS, AG_TS
def gaussian2input(f_reactant, f_TS, f_product, f_output):
# REACTANT
f = open(f_reactant, "r")
data = {}
for line in f:
if "Temperature " in line:
T = float(line.replace("Temperature ", "").split("Kelvin")[0]) # Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
T = "{:0.2f}".format(T)
data[T] = []
if "Sum of electronic and zero-point Energies=" in line:
data[T] += [float(line.replace("Sum of electronic and zero-point Energies=", ""))] # Sum of electronic and zero-point Energies= -3046.798852
if "Sum of electronic and thermal Free Energies=" in line:
data[T] += [float(line.replace(" Sum of electronic and thermal Free Energies=", ""))] # Sum of electronic and thermal Free Energies= -3046.839950
f.close()
# TRANSITION STATE
f = open(f_TS, "r")
freq_TS = 0 # will only select the first frequency
for line in f:
if ("Frequencies --" in line) and (freq_TS == 0):
freq_TS = float(line.split("Frequencies --")[1].split(" ")[0]) # Frequencies -- -1272.9599 86.8910 109.8062
if freq_TS > 0:
print("WARNING: No imaginary frequency found in TS")
if "Temperature " in line:
T = float(line.replace("Temperature ", "").split("Kelvin")[0])
T = "{:0.2f}".format(T)
if T not in data: print("ERROR: No T={} (from TS) found in Reactants".format(T)); sys.exit(0)
data[T] += [freq_TS]
if "Sum of electronic and zero-point Energies=" in line:
data[T] += [float(line.replace("Sum of electronic and zero-point Energies=", ""))]
if "Sum of electronic and thermal Free Energies=" in line:
data[T] += [float(line.replace(" Sum of electronic and thermal Free Energies=", ""))]
f.close()
# PRODUCT
f = open(f_product, "r")
for line in f:
if "Temperature " in line:
T = float(line.replace("Temperature ", "").split("Kelvin")[0])
T = "{:0.2f}".format(T)
if T not in data: print("ERROR: No T={} (from Products) found in Reactants".format(T)); sys.exit(0)
if "Sum of electronic and zero-point Energies=" in line:
data[T] += [float(line.replace("Sum of electronic and zero-point Energies=", ""))]
f.close()
# PREPARE INPUT
f = open(f_output, "w")
f.write("classical squared parabolic eckart eckart-approx wigner\n")
for T in data.keys():
E_r, G_r, freq_TS, E_TS, G_TS, E_p = data[T]
# T, E_reactants, E_TS, E_products, imaginary frequency of TS, G_reactants, G_TS
f.write("{},{},{},{},{},{},{}\n".format(T, E_r, E_TS, E_p, freq_TS, G_r, G_TS))
f.close()
return
def general_k(barrier, T, E_r, E_TS, E_p, freq_TS, AG_TS, PRINT=False):
"""
Returns rate constant from the specified values.
The energies must be in eV, temperatures in K and frequencies in cm^-1.
"""
k = 0
if "classical" == barrier:
k = k_classical(T, AG_TS)
if "squared" == barrier:
k = kSC_squared(T, [E_r, E_TS, E_p, freq_TS, AG_TS], PRINT=PRINT)
if "parabolic" == barrier:
k = kSC_parabolic(T, [E_r, E_TS, E_p, freq_TS, AG_TS])
if "eckart" == barrier:
k = kSC_eckart(T, [E_r, E_TS, E_p, freq_TS, AG_TS], PRINT=PRINT)
if "eckart-approx" == barrier:
k = kSC_eckart_approx(T, [E_r, E_TS, E_p, freq_TS, AG_TS], PRINT=PRINT)
if "wigner" == barrier:
k = kSC_wigner(T, [E_r, E_TS, E_p, freq_TS, AG_TS], PRINT=PRINT)
return k
def general_coeff(barrier, T, E_r, E_TS, E_p, freq_TS, PRINT=False):
"""
Returns tunneling coefficient from the specified values.
The energies must be in eV, temperatures in K and frequencies in cm^-1.
"""
kappa = 0
if "classical" == barrier:
kappa = coeff_classical(T)
if "squared" == barrier:
kappa = coeff_squared(T, [E_r, E_TS, E_p, freq_TS], PRINT=PRINT)
if "parabolic" == barrier:
kappa = coeff_parabolic(T, [E_r, E_TS, E_p, freq_TS])
if "eckart" == barrier:
kappa = coeff_eckart(T, [E_r, E_TS, E_p, freq_TS], PRINT=PRINT)
if "eckart-approx" == barrier:
kappa = coeff_eckart_approx(T, [E_r, E_TS, E_p, freq_TS], PRINT=PRINT)
if "wigner" == barrier:
kappa = coeff_wigner(T, [E_r, E_TS, E_p, freq_TS], PRINT=PRINT)
return kappa
def general_prob(barrier, E, E_r, E_TS, E_p, freq_TS):
"""
Returns tunneling probability from the specified values.
The energies must be in eV and frequencies in cm^-1.
"""
prob = 0
if "classical" == barrier:
prob = prob_classical(E, E_TS)
if "squared" == barrier:
prob = prob_squared(E, [E_r, E_TS, E_p, freq_TS])
if "eckart" == barrier:
prob = coeff_eckart(E, [E_r, E_TS, E_p, freq_TS])
return prob
###########################################################################################
help_info = \
"""
========================
RATE CONSTANT CALCULATOR
========================
Script that calculates the semi-classical rate constant, tunneling coefficient and tunneling probability for a given reaction.
All the barriers included are described in 'TYPES OF BARRIERS'.
INPUT FILE
=============
The input file must be in the same directory as this script is executed.
It is a txt or csv file with the following format:
* First line: names of the type of barriers to calculate separated by spaces (see 'TYPES OF BARRIERS' for the options)
* Next lines: values of T, E_reactants, E_TS, E_products, imaginary frequency of TS, G_reactants, G_TS in the CSV format
INPUT ENERGY
=============
Energies must include the Zero Point Energy:
E(input) = E + ZPE
This applies to the energy and free Gibbs energy of: reactants, transition state, products.
All energies must have the same origin of energies.
UNITS
=============
Input:
Temperature in [K]
Energy in [Hartree]
Free Gibbs Energy in [Hartree]
Frequency in [cm^-1]
Output:
Rate constant in [s^-1]
Tunneling coefficient does not have units
Tunneling probability does not have units
TYPES OF BARRIERS
=============
Description of the included barriers:
classical : no tunelling considered
squared : squared barrier
parabolic : parabolic barrier
eckart : Eckart barrier
eckart-approx : Eckart barrier with high barrier approximation
wigner : Eckart barrier with high barrier and high temperature approximation
For further information read each function's description in the repository:
https://github.com/MarcSerraPeralta/k_tunneling
"""
input_file = \
"""%nprocs=8
%chk=/users/....chk
%mem=20Gb
#p
freq=noraman temperature=
B3LYP/6-311G(d,p)
guess=read geom=checkpoint
NAME
0 1
"""
###########################################################################################
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--help_adv', action='store_true', help="Full explanation of the script")
parser.add_argument('-n', type=str, default=None, help="Name of the input file")
parser.add_argument('-o', type=str, default=None, help="Name of the output file")
parser.add_argument('-log', action='store_true', help="Saves data as: ln(k) and 1/T")
parser.add_argument('-verbose', action='store_true', help="Prints additional information of the calculation")
parser.add_argument('-Tx', action='store_true', help="Prints crossover temperature")
parser.add_argument('-gaussian', type=str, nargs='+', default=None, help="Name of the input gaussian files (reactants, TS and products)")
parser.add_argument('-gaussian_T', type=str, default=None, help="Name of the input gaussian files for multiple themochemical calculations")
parser.add_argument('-T', type=float, nargs='+', default=None, help="With -gaussian_T, specifies Tmin, Tmax and DeltaT")
parser.add_argument('-prob', action='store_true', help="Calculates tunneling probability")
parser.add_argument('-coeff', action='store_true', help="Calculates tunneling coefficient")
args = parser.parse_args()
# NO ARGS PARSED
if (args.n is None) and (not args.Tx) and (args.gaussian is None) and (args.gaussian_T is None) and (not args.prob) and (not args.coeff):
print(help_info); sys.exit(0)
# HELP
if args.help_adv: print(help_info); sys.exit(0)
# CORSSOVER TEMPERATURE
if args.Tx:
# check
if args.n is None: print("ERROR: Specify input file (-n)"); sys.exit(0)
if args.n not in os.listdir(): print("ERROR: '{}' not in working directory".format(args.n)); sys.exit(0)
list_barriers, T, E_r, E_TS, E_p, freq_TS, AG_TS = read_input(args.n)
for i in range(len(T)):
print("Tx = {0:0.2f}".format(Tx(E_TS[i] - E_r[i], freq_TS[i])))
sys.exit(0)
# CREATE INPUT CSV FROM GAUSSIAN OUTPUT FILES
if args.gaussian is not None:
# check
if len(args.gaussian) != 3: print("ERROR: Specify 3 output gaussian files (reactants, TS and products) (-gaussian)"); sys.exit(0)
for name in args.gaussian:
if name not in os.listdir(): print("ERROR: '{}' not in working directory".format(name)); sys.exit(0)
if args.o is None: print("ERROR: Specify name of the input file for kSC.py (-o)"); sys.exit(0)
gaussian2input(*args.gaussian, args.o)
sys.exit(0)
# CREATE GAUSSIAN INPUT FILE FOR MULTIPLE GAUSSIAN THERMOCHEMICAL CALCULATIONS
if args.gaussian_T is not None:
# check
if len(args.T) != 3: print("ERROR: Specify 3 values in -T (Tmin, Tmax, DeltaT)"); sys.exit(0)
if (args.T[1] - args.T[0])*args.T[2] <= 0: print("ERROR: Step increment and Tmin and Tmax are not compatible"); sys.exit(0)
Ti, Tf, AT = args.T
list_T = np.arange(Ti, Tf + AT, AT)
f_output = open(args.gaussian_T, "w")
f_output.write(input_file.replace("temperature=", "temperature={}".format(list_T[0])) + "\n\n")
for T in list_T[1:]:
f_output.write("--link1--\n" + input_file.replace("temperature=", "temperature={}".format(T)) + "\n\n")
f_output.close()
sys.exit(0)
# PERFORM CALCULATIONS
# checks
if args.n is None: print("ERROR: Specify input file (-n)"); sys.exit(0)
if args.n not in os.listdir(): print("ERROR: Input file not in working directory"); sys.exit(0)
if args.o is None: args.o = (args.n).replace(".csv", "_output.csv")
if ".csv" not in args.o: print("ERROR: Input file must have CSV extension"); sys.exit(0)
# PROBABILITY CALCULATION
if args.prob:
possible_barriers = ["classical", "squared", "eckart"]
list_barriers, E, E_r, E_TS, E_p, freq_TS, AG_TS = read_input(args.n)
list_barriers = [b for b in list_barriers if b in possible_barriers] # deletes not possible barriers
# change units of E from Hartree to eV as all the others are in eV (1 Hartree = 27.211386245988 eV, https://en.wikipedia.org/wiki/Hartree)
factor = 27.211386245988 # ev * Hartree^-1
E = E*factor
f_output = open(args.o, "w")
if not args.log: # save data as prob vs E
f_output.write(",".join(["E"] + ["prob " + i for i in list_barriers]) + "\n")
for i in range(len(E)):
f_output.write("{},".format(E[i]))
prob_all = []
for barrier in list_barriers:
prob_all += [general_prob(barrier, E[i], E_r[i], E_TS[i], E_p[i], freq_TS[i])]
f_output.write(",".join(["{:0.9e}".format(k) for k in prob_all]))
f_output.write("\n")
if args.log: # save data as ln(k) vs E
f_output.write(",".join(["E"] + ["ln(prob) " + i for i in list_barriers]) + "\n")
for i in range(len(E)):
f_output.write("{},".format(E[i]))
prob_all = []
for barrier in list_barriers:
prob_all += [general_prob(barrier, E[i], E_r[i], E_TS[i], E_p[i], freq_TS[i])]
f_output.write(",".join(["{:0.9e}".format(np.log(k)) for k in prob_all]))
f_output.write("\n")
f_output.close()
sys.exit(0)
# COEFFICIENT CALCULATION
if args.coeff:
possible_barriers = ["classical", "squared", "parabolic", "eckart", "eckart-approx", "wigner"]
list_barriers, T, E_r, E_TS, E_p, freq_TS, AG_TS = read_input(args.n)
list_barriers = [b for b in list_barriers if b in possible_barriers] # deletes not possible barriers
f_output = open(args.o, "w")
if not args.log: # save data as coeff vs T
f_output.write(",".join(["T"] + ["coeff " + i for i in list_barriers]) + "\n")
for i in range(len(T)):
f_output.write("{},".format(T[i]))
coeff_all = []
for barrier in list_barriers:
coeff_all += [general_coeff(barrier, T[i], E_r[i], E_TS[i], E_p[i], freq_TS[i], PRINT=args.verbose)]
f_output.write(",".join(["{:0.9e}".format(k) for k in coeff_all]))
f_output.write("\n")
if args.log: # save data as ln(k) vs 1/T
f_output.write(",".join(["1/T"] + ["ln(coeff) " + i for i in list_barriers]) + "\n")
for i in range(len(T)):
f_output.write("{},".format(1/T[i]))
coeff_all = []
for barrier in list_barriers:
coeff_all += [general_coeff(barrier, T[i], E_r[i], E_TS[i], E_p[i], freq_TS[i], PRINT=args.verbose)]
f_output.write(",".join(["{:0.9e}".format(np.log(k)) for k in coeff_all]))
f_output.write("\n")
f_output.close()
sys.exit(0)
# RATE CONSTANT
possible_barriers = ["classical", "squared", "parabolic", "eckart", "eckart-approx", "wigner"]
list_barriers, T, E_r, E_TS, E_p, freq_TS, AG_TS = read_input(args.n)
list_barriers = [b for b in list_barriers if b in possible_barriers] # deletes not possible barriers
f_output = open(args.o, "w")
if not args.log: # save data as k vs T
f_output.write(",".join(["T"] + ["k " + i for i in list_barriers]) + "\n")
for i in range(len(T)):
f_output.write("{},".format(T[i]))
k_all = []
for barrier in list_barriers:
k_all += [general_k(barrier, T[i], E_r[i], E_TS[i], E_p[i], freq_TS[i], AG_TS[i], PRINT=args.verbose)]
f_output.write(",".join(["{:0.9e}".format(k) for k in k_all]))
f_output.write("\n")
if args.log: # save data as ln(k) vs 1/T
f_output.write(",".join(["1/T"] + ["ln(k) " + i for i in list_barriers]) + "\n")
for i in range(len(T)):
f_output.write("{},".format(1/T[i]))
k_all = []
for barrier in list_barriers:
k_all += [general_k(barrier, T[i], E_r[i], E_TS[i], E_p[i], freq_TS[i], AG_TS[i], PRINT=args.verbose)]
f_output.write(",".join(["{:0.9e}".format(np.log(k)) for k in k_all]))
f_output.write("\n")
f_output.close()