In [1]:

    

import numpy as np
import sys
import matplotlib.pyplot as plt
import os
import scipy.constants as ct
import lxml.etree as lxml
import sqlite3

from mpl_toolkits.mplot3d import Axes3D
%matplotlib inline
Ryd2eV=13.605692
epsilon=3
bohr2m=5.2917721092E-11


    

In [2]:

    

def readSqlall(sqlname):
        sqlstatement = "SELECT eSinglet FROM segments"
        con = sqlite3.connect(sqlname)
        with con:
                cur = con.cursor()
                cur.execute(sqlstatement)
                rows = cur.fetchall()

        sqlall=(np.array(rows)[:,0])
        
        return sqlall
    
def writeEnergies(sqlname,energies):
    con = sqlite3.connect(sqlname)
    with con:      
        cur = con.cursor()
        for i in range(energies.size):
            sqlstatement = "UPDATE segments SET UxXnNs={} WHERE id={}".format(energies[i],i+1)
            
            cur.execute(sqlstatement)
             
    
def readorb(filename):
    trdip=False
    energy=False
    with open(filename,"r") as f:
        lines=f.readlines()
        for line in lines:
            if "Singlet1[eV]:" in line:
                energy=float(line.split()[3])
            if "Singlet1 x y z" in line:
                #print line
                a=line.split()
                x=float(a[7])
                y=float(a[8])
                z=float(a[9])
                trdip=bohr2m*np.array([x,y,z])*np.sqrt(2)
                
        
    return trdip,energy


    

In [3]:

    

#files1=os.listdir("logfiles2")
files1=[]
files2=[]
senergies=readSqlall("system_individualmps.sql")
energies=[]
for i in range(1,1569):
    files1.append("molecule_{}.orb.log".format(i))
#files2=os.listdir("espfits")

hbar=ct.physical_constants['Planck constant over 2 pi in eV s'][0]

lifetimes=[]
for filename,sitenergy in zip(files1,senergies):
    #print filename
    trp,energy=readorb("logfiles2/"+filename)
    energies.append(energy)
    omega=(energy+sitenergy)/hbar
    lifetime=(3*ct.c**2)/(np.sqrt(epsilon)*4*ct.alpha*omega**3*np.dot(trp,trp))
    lifetimes.append(lifetime)
lifetimes=np.array(lifetimes)
energies=np.array(energies)
print np.std(energies),np.mean(energies),np.std(senergies),np.average(senergies)
print np.average(lifetimes)
print np.std(lifetimes)


    

    




0.0988749615107 2.16558397321 0.0587592182765 -0.11309557602
8.49977465134e-10
1.08802712566e-10

In [4]:

    

#writeEnergies("system_individualmps.sql",energies)


    

    




  File "<ipython-input-4-45103e01eaa3>", line 1
    8.writeEnergies("system_individualmps.sql",energies)
                  ^
SyntaxError: invalid syntax

In [5]:

    

n, bins, patches = plt.hist(lifetimes, 50,  facecolor='green')
plt.xlabel('lifetime [s]')
plt.ylabel('Counts')
plt.savefig("lifetimedistribution.svg")
plt.show()
print lifetimes.shape


    

    













    




(1568,)

In [7]:

    

root = lxml.Element("lifetimes")
for i,tau in  zip(range(1,1569),lifetimes):
    entry=lxml.Element("site",id="{}".format(i))
    entry.text="{:1.6e}".format(tau)
    root.append(entry)
with open("lifetimes.xml", 'w') as f:
    f.write(lxml.tostring(root, pretty_print=True))


    

In [6]:

    

total=energies+senergies
n=plt.hist((total-np.mean(total)),50,label="combined std={:1.2f}".format(np.std(total)))
n=plt.hist((energies-np.mean(energies)),50,label="conformational disorder std={:1.2f}".format(np.std(energies)))
n=plt.hist((senergies-np.mean(senergies)),50,label="estatic disorder std={:1.2f}".format(np.std(senergies)))
plt.ylabel('Counts')
plt.xlabel('deviation from average siteenergy [eV]')
plt.savefig("siteenergies.svg")

plt.legend()
plt.show()


    

In [ ]: