PrivacyScanData/truncate/new2/harmonic_fit-master/harmonic_fit_rot_phi.py

#! /usr/bin/env python 

import subprocess, re, os, time, random
#from harmonic_fit import comp_k_analytic
import sys
import csv
import numpy as np
import matplotlib.pyplot as plt
import math
#from mpl_toolkits.mplot3d import axes3d
from scipy.interpolate import interp1d, CubicSpline

plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.family'] = 'Times New Roman'
plt.rcParams['axes.edgecolor']='#333F4B'
plt.rcParams['axes.linewidth']=0.8
plt.rcParams['xtick.color']='#333F4B'
plt.rcParams['ytick.color']='#333F4B'
plt.rcParams["axes.prop_cycle"]

# Read CSV
csvFileName = sys.argv[1]
scan_var = csvFileName.split('.')[0]
pltFileName = scan_var + '.png'

csvData = []

with open(csvFileName, 'r') as csvFile:
    csvReader = csv.reader(csvFile, delimiter = ' ')
    for csvRow in csvReader:
        csvData.append(csvRow)

# Get X, Y and store in np array

csvData = np.array(csvData)
csvData = csvData.astype(np.float)
X, Y = csvData[:,0], csvData[:,1]

au_to_kJpmol = 2625.5 

# convert kJpmol to au

Y = np.array([y/au_to_kJpmol for y in Y])

def comp_k_analytic(X,Y):
    """
    Compute the analytic force constant given X, and V(X)    
    """
    N = X.size
    eq = 0
    f2 = CubicSpline(X,Y)
    k_analytic = f2(X, 2)[0]
    return k_analytic, f2

def convert_k_to_cminv_rotor(k):
    """
    Convert force constant in Hartree/Radian^2 to cm-1
    this is for h2
    """
    I = 1948.37443393238771437461228584
    nu = 1/(2*np.pi)*math.sqrt(k/I)*(1/(137*5.29*10**-9))
    return nu



#k_numeric = comp_k_numeric(X, Y)
k_analytic, f2 = comp_k_analytic(X, Y)
nu_analytic = convert_k_to_cminv_rotor(k_analytic)
zpve_analytic = nu_analytic/2


print (scan_var, "Analytic", k_analytic, nu_analytic, zpve_analytic)


#k_numeric = comp_k_numeric(X, Y)
#k_analytic, f2 = comp_k_analytic(X, Y)

#print ("Force constants for ", scan_var)
#print ("Analytic_derivative ==", k_analytic, "Hartree/Ang^2")
#print ("Numeric_derivative ==", k_numeric, "Hartree/Ang^2")

plt.plot(X, Y, 'bo')
plt.plot(X, f2(X), 'b-')
plt.plot(X, f2(X, 1), 'rx--')
plt.plot(X, f2(X, 2), 'co')

plt.legend(['Points', 'Cubic Spline', r'dV/d${\phi}$', r"d2V/d${\phi}^{2}$"], fontsize = 12)
plt.xlabel(r"$\phi$", fontsize = 16)
plt.ylabel("E(a.u) and higher derivs", fontsize = 16)

plt.savefig(pltFileName)