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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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CMMDE/bin/cmmdepost.py

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#!/usr/bin/env python3
import os
import sys
import argparse
import re
from matplotlib import colors
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from prettytable import PrettyTable
matplotlib.use('PS')
#matplotlib.rc('text', usetex=True)
#matplotlib.use('Qt5agg')
from cmmde_msd_com import msd_com, msd_fit
from cmmde_rdf import rdf
from cmmde_dock import checkopt
parser = argparse.ArgumentParser(description='Program Analisis Hasil Perhitungan Dalam MOWS CMMD 2021')
parser.add_argument('-j','--job',type=str,default='None',help='Jenis perhitungan yang dilakukan. Pilihan: sp, opt, thermo, ir, reax, msd_com, msd, msd_fit rdf, td.')
parser.add_argument('-m', '--method', type=str, default='XTB2', help='Metode yang digunakan dalam perhitungan.')
parser.add_argument('-i','--input',type=str,default='geom.xyz',help='Koordinat awal dalam format .xyz (hanya diperlukan untuk program DCDFTBMD) saat optimasi geometri.')
parser.add_argument('-s', '--software', type=str, default='orca',help='Jenis software yang digunakan. Pilihan: orca, dcdftb, dftb+.')
parser.add_argument('-irx','--inputreaction',type=str, default='None', help='Input reaksi kimia')
parser.add_argument('-t','--temp',type=float,default=298.15, help='Suhu yang digunakan dalam perhitungan frekuensi dan termokimia')
parser.add_argument('-traj','--traject',type=str,default='traject.xyz',help='File trayektori dinamika molekul dalam format .xyz')
parser.add_argument('-l', '--latt', type=str, default='cmmd.in', help='Ukuran rusuk sel satuan.')
parser.add_argument('-start', '--start', type=int, default=0, help='Titik acuan dalam bilangan bulat. Default = 0.')
parser.add_argument('-end','--end', type=int, default=-1, help='Titik ahir pembacaan trayektori')
parser.add_argument('-msd','--msd',type=str, default='msd.out', help='File berisikan MSD keluaran cmmdepost.py -j msdcom.')
parser.add_argument('-dt','--dt',type=float,default=0.5, help='Time step yang didefinisikan selama simulasi berlangsung.')
parser.add_argument('-n', '--noheader', action="store_true",help='Mendefinisikan apakah file mengandung header atau tidak. Default file msd.out mengandung header berupa #.')
parser.add_argument('-g', '--groups', type=str, help='Molekul didefinisikan dengan Nama*JumlahAtom*JumlahMolekul. Contoh NAP*1*2:DMF*1*20.')
parser.add_argument('-r', '--range', default=10.0, type=float,help='Jarak terjauh pengukuran RDF')
parser.add_argument('-p', '--pair', type=str, help='Pasangan atom, misalnya "O-O" untuk pasangan atom O-O')
parser.add_argument('-res','--resolution',default=0.01, type=float, help='Resolusi untuk plot histogram atau RDF')
# Metadinamika
parser.add_argument('-metafreq','--metafreq',type=int,default=100, help='Dalam berapa step sekali potensial Gaussian ditambahkan?')
parser.add_argument('-fesstart','--fesstart',type=float,default=0, help='Titik minimum CV. Default = 0.')
parser.add_argument('-fesend','--fesend',type=float,default=1, help='Titik maksimum CV. Default = 1.')
parser.add_argument('-fesbin','--fesbin',type=float,default=0.01,help='Selang CV. Default = 0.01')
parser.add_argument('-cv','--cvtype',type=str,default='coordnum',help='Pilihan collective variable (CV) yang digunakan. Pilihan: coordnum, distance, angle, dihedral, distancediff, distanceadd, meandistance, pointplanedistance.')
parser.add_argument('-ngaus','--ngaus',type=int,help='Jumlah Gaussian yang didepositkan')
parser.add_argument('-nlig','--nligands',type=int,help='Jumlah ligan yang akan didocking.')
parser.add_argument('-nr','--nroots',type=int,default=5,help='Jumlah keadaan tereksitasi.')
parser.add_argument('-pts','--points',type=int,default=300,help='Jumlah titik untuk plot UV.')
# Analisis DOS
parser.add_argument('-pdos','--pdos',type=str,help='File DOS parsial hasil perhitungan DFTB+')
parser.add_argument('-xlabel','--xlabel',type=str,default='x',help='Label sumbu-x dalam sebuah plot')
parser.add_argument('-ylabel','--ylabel',type=str,default='y',help='Label sumbu-y dalam sebuah plot')
parser.add_argument('-file','--file',type=str,help='Nama file yang akan diplot')
parser.add_argument('-np','--nproc',type=int,default=1,help='Jumlah prosesor yang digunakan.')
parser.add_argument('-grid','--grid',type=str,default='FINE',help='Jenis grid yang akan dibangun untuk perhitungan NCI. Pilihan: FINE (default), COARSE, dan ULTRAFINE.')
# Analisis terkait perhitungan Quantum Espresso
parser.add_argument('-outdir','--outdir',type=str,default='./out',help='Folder tempat menyimpan output.')
parser.add_argument('-emin','--emin',type=float,default=-9.0,help='Batas minimum nilai keadaan elektronik pada DOS.')
parser.add_argument('-emax','--emax',type=float,default=16.0,help='Batas maksimum nilai keadaan elektronik pada DOS.')
opt = parser.parse_args(sys.argv[1:])
# Berbagai faktor konversi
Ha2kcal = 627.5096080305927
ev2kcal = 23.060541945329334
Ha2kj = 2625.5
ev2kj = 96
# Analisis Output
method = opt.method
if opt.job == 'sp' and opt.software == 'orca' and not (opt.method == 'XTB' or opt.method == 'XTB2'):
if os.path.isfile('cmmd.out'):
with open('cmmd.out','r') as f:
for line in f:
if "Total Energy" in line:
arr= line.split()
Energy = float(arr[3])
print('Energi total molekul: {} Hartree = {:.2f} kJ/mol'.format(Energy,Energy*Ha2kj))
else:
print("Mohon menunggu hingga perhitungan anda selesai.")
exit
elif opt.job == 'sp' and opt.software == 'orca':
if os.path.isfile('cmmd.out'):
with open('cmmd.out','r') as f:
for line in f:
if "TOTAL ENERGY" in line:
arr= line.split()
Energy = float(arr[3])
if "GRADIENT NORM" in line:
arr = line.split()
Gradient = float(arr[3])
if "HOMO-LUMO GAP" in line:
arr = line.split()
Egap = float(arr[3])
print('Energi total molekul: {} Hartree = {:.2f} kJ/mol'.format(Energy,Energy*Ha2kj))
print('Norm Gradien: {} Hartree/a0 = {:.2f} kJ/mol/a0'.format(Gradient,Gradient*Ha2kj))
print('HOMO-LUMO gap: {:.2f} eV = {:.2f} kJ/mol'.format(Egap,Egap*ev2kj))
else:
print("Mohon menunggu hingga perhitungan anda selesai.")
exit
if opt.job == 'opt' and opt.software == 'orca':
Energy = []
Gradient = []
TotalEnergy = []
if os.path.isfile('cmmd.out'):
with open('cmmd.out','r') as f:
for line in f:
if "Current Energy" in line:
arr = line.split()
Energy.append(float(arr[3]))
if "Current gradient" in line:
arr = line.split()
Gradient.append(float(arr[4]))
if "FINAL SINGLE POINT ENERGY" in line:
arr = line.split()
TotalEnergy.append(float(arr[4]))
Optstep = range(0,len(Energy))
print("Total energi elektronik = {} Hartree = {} kJ/mol".format(TotalEnergy[-1],TotalEnergy[-1]*Ha2kj))
if method != "XTB1" and method != "xtb1" and method != "XTB2" and method != "xtb2" and method != "XTB" and method != "xtb":
with open('cmmd.out','r') as f:
lines = f.readlines()
occ = []
energy = []
for index,line in enumerate(lines):
if 'Basis Dimension' in line:
arr = line.split()
NBas = int(arr[4])
if 'ORBITAL ENERGIES' in line:
for i in range(NBas):
arr = lines[index+i+4].split()
occ.append(arr[1])
energy.append(float(arr[3]))
Eocc = []
Evir = []
for energy in energy:
if energy > 0:
Evir.append(energy)
if energy < 0:
Eocc.append(energy)
E_HOMO = max(Eocc)
E_LUMO = min(Evir)
print('######INFORMASI ENERGI HOMO & LUMO######')
print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
else:
Gaps = []
with open("cmmd.out", 'r') as f:
print('######INFORMASI ENERGI HOMO & LUMO######')
for line in f:
if "GAP" in line:
arr = line.split()
Gaps.append(float(arr[3]))
print("Gap HOMO-LUMO = {:.2f} eV".format(Gaps[-1]))
with open('optimized.dat','w') as fout:
print("#Step Energy Gradient", file=fout)
for optstep,energy,gradient in zip(Optstep,Energy,Gradient):
print("{} {} {}".format(optstep,energy,gradient),file=fout)
## Plotting
with open('optimized.gp','w') as fout:
print("""set terminal pdf
set output "optimized.pdf"
set title "Energy Vs. Optimization Step"
set xlabel "Optimization Step"
set xtics 1
set ylabel "Energy [Hartree]"
set style line 1 \\
linecolor rgb '#0060ad' \\
linetype 1 linewidth 2 \\
pointtype 7 pointsize 1.5
plot 'optimized.dat' using 1:2 notitle with linespoints linestyle 1""",file=fout)
os.system('gnuplot optimized.gp')
else:
print("Mohon menunggu hingga perhitungan anda selesai.")
exit
if opt.job == 'ir' and opt.software == 'orca':
def gaussband(x,band,strength,stdev):
bandshape=1.3062974e8 * (strength / (1e7/stdev)) * np.exp(-(((1.0/x)-(1.0/band))/(1.0/stdev))**2)
return bandshape
Freq = []
Int = []
NFreq = 0
if os.path.isfile('cmmd.out'):
with open('cmmd.out','r') as f:
lines = f.readlines()
for index,line in enumerate(lines):
if "The total number of vibrations considered is" in line:
arr = line.split()
NFreq += int(arr[7])
for index,line in enumerate(lines):
if "Total enthalpy" in line:
arr = line.split()
Enthalpy = float(arr[3])
if "Final Gibbs free energy" in line:
arr = line.split()
Gibbs = float(arr[5])
# if "Total entropy" in line:
# arr = line.split()
# Entropy = float(arr[4])
if "IR SPECTRUM" in line:
for i in range(NFreq):
arr = lines[index+6+i].split()
Freq.append(float(arr[1]))
Int.append(float(arr[2]))
x = np.linspace(500,4000,5000)
composite = 0
for count,peak in enumerate(Freq):
thispeak = gaussband(x,peak,Int[count],1e5)
composite+=thispeak
fig,ax = plt.subplots()
ax.plot(x,composite,color='blue')
ax.tick_params(direction='in')
plt.grid(linestyle=':')
plt.xlim(500,4000)
plt.ylim(0,)
plt.xlabel('Wavenumbers [cm$^{-1}$]')
plt.ylabel('Absorbance')
plt.savefig('IR.pdf',dpi=1200,format='pdf')
with open('IR_fit.dat','w') as fout:
for x,y in zip(x,composite):
print(x,y,file=fout)
else:
print("Mohon menunggu hingga perhitungan anda selesai.")
exit
if opt.job == 'thermo' and opt.software == 'orca':
if os.path.isfile('cmmd.out'):
with open('cmmd.out','r') as f:
for line in f:
if "Total enthalpy" in line:
arr = line.split()
Enthalpy = float(arr[3])
if "Final Gibbs free energy" in line:
arr = line.split()
Gibbs = float(arr[5])
# if "Total entropy" in line:
# arr = line.split()
# Entropy = float(arr[4])
if "Non-thermal (ZPE)" in line:
arr = line.split()
ZPE = float(arr[3])
if "Electronic energy" in line:
arr = line.split()
E_elec = float(arr[3])
if "Thermal vibrational correction" in line:
arr = line.split()
Evib = float(arr[4])
if "Thermal rotational correction" in line:
arr = line.split()
Erot = float(arr[4])
if "Thermal translational correction" in line:
arr = line.split()
Etrans = float(arr[4])
if opt.method == 'XTB2' or opt.method == 'XTB':
E_HOMO = 0
E_LUMO = 0
with open('cmmd.out','r') as f:
for line in f:
if '(HOMO)' in line:
arr = line.split()
E_HOMO += float(arr[3])
if "(LUMO)" in line:
arr = line.split()
E_LUMO += float(arr[2])
print('######INFORMASI ENERGI HOMO & LUMO######')
print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
print('')
else:
with open('cmmd.out','r') as f:
lines = f.readlines()
occ = []
energy = []
for index,line in enumerate(lines):
if 'Basis Dimension' in line:
arr = line.split()
NBas = int(arr[4])
if 'ORBITAL ENERGIES' in line:
for i in range(NBas):
arr = lines[index+i+4].split()
occ.append(arr[1])
energy.append(float(arr[3]))
Eocc = []
Evir = []
for energy in energy:
if energy > 0:
Evir.append(energy)
if energy < 0:
Eocc.append(energy)
E_HOMO = max(Eocc)
E_LUMO = min(Evir)
print('######INFORMASI ENERGI HOMO & LUMO######')
print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
print('')
print('######INFORMASI ENERGI ELEKTRONIK & KOREKSI TERMAL######')
print("Energi elektronik = {} Hartree = {} kJ/mol".format(E_elec,E_elec*Ha2kj))
print("Zero point energy (ZPE) = {} Hartree = {} kJ/mol".format(ZPE,ZPE*Ha2kj))
print("Koreksi termal vibrasi = {} Hartree = {} kJ/mol".format(Evib,Evib*Ha2kj))
print("Koreksi termal rotasi = {} Hartree = {} kJ/mol".format(Erot,Erot*Ha2kj))
print("Koreksi termal translasi = {} Hartree = {} kJ/mol".format(Etrans,Etrans*Ha2kj))
print('Total koreksi termal = {} Hartree = {} kJ/mol'.format(Etrans+Evib+Erot,(Etrans+Evib+Erot)*Ha2kj))
print('')
print('######INFORMASI BESARAN TERMOKIMIA######')
print("Entalpi (H) = {} Hartree = {} kj/mol".format(Enthalpy,Enthalpy*Ha2kj))
# print("Entropi (S) = {} Hartree/K = {} J/(mol K)".format(Entropy/Temperature,Entropy*Ha2kj/Temperature*1000))
print("Energi bebas Gibbs (G) = {} Hartree = {} kJ/mol".format(Gibbs,Gibbs*Ha2kj))
else:
print("Mohon menunggu hingga perhitungan anda selesai.")
exit
### Opsi untuk print hanya HOMO-LUMO energi
if opt.job == 'gap' and ('XTB' not in opt.method and 'XTB2' not in opt.method) and opt.software == 'orca':
with open('cmmd.out','r') as f:
lines = f.readlines()
occ = []
energy = []
for index,line in enumerate(lines):
if 'Basis Dimension' in line:
arr = line.split()
NBas = int(arr[4])
if 'ORBITAL ENERGIES' in line:
for i in range(NBas):
arr = lines[index+i+4].split()
occ.append(arr[1])
energy.append(float(arr[3]))
Eocc = []
Evir = []
for energy in energy:
if energy > 0:
Evir.append(energy)
if energy < 0:
Eocc.append(energy)
E_HOMO = max(Eocc)
E_LUMO = min(Evir)
print('######INFORMASI ENERGI HOMO & LUMO######')
print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
if opt.job == 'gap' and ('XTB' in opt.method or 'XTB2' in opt.method) and opt.software == 'orca':
E_HOMO = []
E_LUMO = []
with open('cmmd.out','r') as f:
for line in f:
if '(HOMO)' in line:
arr = line.split()
E_HOMO.append(float(arr[3]))
if '(LUMO)' in line:
arr = line.split()
E_LUMO.append(float(arr[2]))
E_gap = E_LUMO[-1] - E_HOMO[-1]
print('######INFORMASI ENERGI HOMO & LUMO######')
print('Energi HOMO = {:.2f} eV'.format(E_HOMO[-1]))
print('Energi LUMO = {:.2f} eV'.format(E_LUMO[-1]))
print('Gap HOMO-LUMO = {:.2f} eV'.format(E_gap))
if opt.job == 'td' and opt.software == 'orca':
with open('cmmd.out','r') as f:
lines = f.readlines()
occ = []
energy = []
for index,line in enumerate(lines):
if 'Basis Dimension' in line:
arr = line.split()
NBas = int(arr[4])
if 'ORBITAL ENERGIES' in line:
for i in range(NBas):
arr = lines[index+i+4].split()
occ.append(arr[1])
energy.append(float(arr[3]))
Eocc = []
Evir = []
for energy in energy:
if energy > 0:
Evir.append(energy)
if energy < 0:
Eocc.append(energy)
E_HOMO = max(Eocc)
E_LUMO = min(Evir)
print('######INFORMASI ENERGI HOMO & LUMO######')
print('Energi HOMO = {:.2f} eV'.format(E_HOMO))
print('Energi LUMO = {:.2f} eV'.format(E_LUMO))
print('Gap HOMO-LUMO = {:.2f} eV'.format(E_LUMO-E_HOMO))
# A sqrt(2) * standard deviation of 0.4 eV is 3099.6 nm. 0.1 eV is 12398.4 nm. 0.2 eV is 6199.2 nm.
stdev = 4132.806433333334
# For Lorentzians, gamma is half bandwidth at half peak height (nm)
gamma = 12.5
# Excitation energies dalam nm
#bands = [330,328,328,308,290,290,288,283,276,270,268]
bands = []
fosc = []
with open("cmmd.out", 'r') as f:
for line in f:
if 'ABSORPTION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS' in line:
next(f)
next(f)
next(f)
next(f)
for i in range(opt.nroots):
arr = next(f).split()
bands.append(float(arr[2]))
fosc.append(float(arr[3]))
#f = [7.90e-7,0.00,7.16e-4,1.02e-2,1.38e-6,2.94e-7,0.00,8.86e-4,1.54e-5,1.25e-2,9.31e-3]
if len(bands) != len(fosc):
print('Jumlah panjang gelombang tidak sama dengan jumlah oscillator strength')
sys.exit()
def KurvaGaussian(x, band, strength, stdev):
"Memproduksi kurva Gaussian"
bandshape = 1.3062974e8 * (strength / (1e7/stdev)) * np.exp(-(((1.0/x)-(1.0/band))/(1.0/stdev))**2)
# Definisi di atas diambil dari P. J. Stephens, N. Harada, Chirality 22, 229 (2010)
return bandshape
def lorentzBand(x, band, strength, stdev, gamma):
"Memproduksi kurva Lorentzian"
bandshape= 1.3062974e8 * (strength / (1e7/stdev)) * ((gamma**2)/((x - band)**2 + gamma**2))
return bandshape
x = np.linspace(opt.start, opt.end, opt.points)
composite = 0
for count, peak in enumerate(bands):
PuncakIni = KurvaGaussian(x, peak, fosc[count], stdev)
composite += PuncakIni
composite = np.array(composite)
fig,ax = plt.subplots()
ax.plot(x, composite,color='blue')
plt.xlim(opt.start,opt.end)
plt.xlabel('$\lambda$ [nm]')
plt.ylabel('$\epsilon$ [L mol$^{-1}$cm$^{-1}$]')
# plt.ticklabel_format(style="sci",scilimits=(0,0))
plt.savefig('plot_uv.pdf')
if opt.job == 'td' and opt.software == 'dcdftb':
nroots = 0
with open('cmmd.out','r') as f:
for line in f:
if 'Excitation Energy' in line:
arr = line.split()
print("Gap HOMO-LUMO = {:.2f} eV".format(float(arr[3])*27.2114))
from scipy.constants import h, c
wavelength = h*c/(float(arr[3])*4.35974e-18)*1e9
print("Panjang gelombang serapan = {:.0f} nm".format(wavelength))
if 'Number of states' in line:
arr = line.split()
nroots+=int(arr[4])
print('Jumlah keadaan tereksitasi = {}'.format(nroots))
# A sqrt(2) * standard deviation of 0.4 eV is 3099.6 nm. 0.1 eV is 12398.4 nm. 0.2 eV is 6199.2 nm.
stdev = 4132.806433333334
# For Lorentzians, gamma is half bandwidth at half peak height (nm)
gamma = 12.5
# Excitation energies dalam nm
#bands = [330,328,328,308,290,290,288,283,276,270,268]
bands = []
fosc = []
with open("cmmd.out", 'r') as f:
for line in f:
if 'Energies' in line:
next(f)
next(f)
next(f)
for i in range(nroots):
arr = next(f).split()
bands.append(float(arr[1]))
if 'Strength' in line:
next(f)
for i in range(nroots):
arr = next(f).split()
fosc.append(float(arr[1]))
#f = [7.90e-7,0.00,7.16e-4,1.02e-2,1.38e-6,2.94e-7,0.00,8.86e-4,1.54e-5,1.25e-2,9.31e-3]
eVtoJoule = 1.60218e-19
bands = np.array(bands)
from scipy.constants import h,c
bands = h*c/(bands*eVtoJoule)*1e9
if len(bands) != len(fosc):
print('Jumlah panjang gelombang tidak sama dengan jumlah oscillator strength')
sys.exit()
def KurvaGaussian(x, band, strength, stdev):
"Memproduksi kurva Gaussian"
bandshape = 1.3062974e8 * (strength / (1e7/stdev)) * np.exp(-(((1.0/x)-(1.0/band))/(1.0/stdev))**2)
# Definisi di atas diambil dari P. J. Stephens, N. Harada, Chirality 22, 229 (2010)
return bandshape
def lorentzBand(x, band, strength, stdev, gamma):
"Memproduksi kurva Lorentzian"
bandshape= 1.3062974e8 * (strength / (1e7/stdev)) * ((gamma**2)/((x - band)**2 + gamma**2))
return bandshape
x = np.linspace(opt.start, opt.end, opt.points)
composite = 0
for count, peak in enumerate(bands):
PuncakIni = KurvaGaussian(x, peak, fosc[count], stdev)
composite += PuncakIni
composite = np.array(composite)
with open("uv.dat",'w') as f:
for i, j in zip(x,composite):
print(i,j,file=f)
fig,ax = plt.subplots()
ax.plot(x, composite,color='blue')
plt.xlim(opt.start,opt.end)
plt.ylim(0,)
plt.xlabel('$\lambda$ [nm]')
plt.ylabel('$\epsilon$ [L mol$^{-1}$cm$^{-1}$]')
plt.ticklabel_format(style="sci",scilimits=(0,3))
plt.savefig('plot_uv.pdf')
if opt.job == 'msdcom':
msd_com(opt.groups,opt.traject,opt.start,opt.latt,opt.dt)
if opt.job == 'msdfit':
msd_fit(opt.msd, opt.noheader,opt.start)
if opt.job == 'reax' or opt.inputreaction != 'None':
Input = opt.inputreaction
Reaksi = Input.split('->')
Reaktan = Reaksi[0]
Reaktan = Reaktan.split('+')
KoefisienReaktan = []
reak = []
for i in Reaktan:
coeff = re.split(r"(\d+)", i)
KoefisienReaktan.append(coeff[1])
reak.append("".join(coeff[2:]))
KoefisienReaktan = [-int(i) for i in KoefisienReaktan]
Reaktan = reak
Produk = Reaksi[1]
Produk = Produk.split('+')
KoefisienProduk = []
prod = []
for i in Produk:
coeff = re.split(r"(\d+)", i)
KoefisienProduk.append(coeff[1])
prod.append("".join(coeff[2:]))
KoefisienProduk = [int(i) for i in KoefisienProduk]
Produk = prod
E_reaktan = []
zpe_reaktan = []
E_cor_reaktan = []
H_cor_reaktan = []
G_cor_reaktan = []
E_produk = []
zpe_produk = []
E_cor_produk = []
H_cor_produk = []
G_cor_produk = []
H_reaktan = []
G_reaktan = []
H_produk = []
G_produk = []
for i in Reaktan:
with open('{}/cmmd.out'.format(i),'r') as f:
if opt.software == 'orca':
for line in f:
if "Total enthalpy" in line:
arr = line.split()
H_reaktan.append(float(arr[3]))
if "Final Gibbs free energy" in line:
arr = line.split()
G_reaktan.append(float(arr[5]))
if "Total thermal energy" in line:
arr = line.split()
E_reaktan.append(float(arr[3]))
if opt.software == 'dcdftb':
temp_ener = []
for line in f:
if "Final" in line and "Energy" in line:
arr = line.split()
temp_ener.append(float(arr[4]))
if "Zero" in line:
arr = line.split()
zpe_reaktan.append(float(arr[4]))
if "Thermal correction to energy" in line:
arr = line.split()
E_cor_reaktan.append(float(arr[5]))
if "Thermal correction to enthalpy" in line:
arr = line.split()
H_cor_reaktan.append(float(arr[5]))
if "Thermal correction to Gibbs free energy" in line:
arr = line.split()
G_cor_reaktan.append(float(arr[7]))
E_reaktan.append(temp_ener[-1])
for i in Produk:
with open('{}/cmmd.out'.format(i),'r') as f:
if opt.software == 'orca':
for line in f:
if "Total enthalpy" in line:
arr = line.split()
H_produk.append(float(arr[3]))
if "Final Gibbs free energy" in line:
arr = line.split()
G_produk.append(float(arr[5]))
if "Total thermal energy" in line:
arr = line.split()
E_produk.append(float(arr[3]))
if opt.software == 'dcdftb':
temp_ener = []
for line in f:
if "Final" in line and "Energy" in line:
arr = line.split()
temp_ener.append(float(arr[4]))
if "Zero" in line:
arr = line.split()
zpe_produk.append(float(arr[4]))
if "Thermal correction to energy" in line:
arr = line.split()
E_cor_produk.append(float(arr[5]))
if "Thermal correction to enthalpy" in line:
arr = line.split()
H_cor_produk.append(float(arr[5]))
if "Thermal correction to Gibbs free energy" in line:
arr = line.split()
G_cor_produk.append(float(arr[7]))
E_produk.append(temp_ener[-1])
Koefisien = KoefisienReaktan + KoefisienProduk
Koefisien = np.array(Koefisien,dtype=int)
if opt.software == 'orca':
H = H_reaktan + H_produk
H = np.array(H,dtype=float)
delta_H = (np.dot(H,Koefisien))*Ha2kj
E = E_reaktan + E_produk
E = np.array(E,dtype=float)
delta_E = (np.dot(E,Koefisien))*Ha2kj
print('Delta_E = {:.2f} kJ/mol'.format(delta_E))
print('Delta_H = {:.2f} kJ/mol'.format(delta_H))
G = G_reaktan + G_produk
G = np.array(G,dtype=float)
delta_G = (np.dot(G,Koefisien))*Ha2kj
print('Delta_G = {:.2f} kJ/mol'.format(delta_G))
delta_S = (delta_H - delta_G)/opt.temp*1000
print('Delta_S = {:.2f} J/(mol K)'.format(delta_S))
if opt.software == 'dcdftb':
E = np.array(E_reaktan + E_produk, dtype=float)
E_cor = np.array(E_cor_reaktan + E_cor_produk, dtype=float)
H_cor = np.array(H_cor_reaktan + H_cor_produk, dtype=float)
G_cor = np.array(G_cor_reaktan + G_cor_produk, dtype=float)
zpe = np.array(zpe_reaktan + zpe_produk, dtype=float)
delta_zpe = (np.dot(zpe,Koefisien))*Ha2kj
delta_El = (np.dot(E,Koefisien))*Ha2kj
delta_Ecor = (np.dot(E_cor,Koefisien))*Ha2kj
delta_Hcor = (np.dot(H_cor,Koefisien))*Ha2kj
delta_Gcor = (np.dot(G_cor,Koefisien))*Ha2kj
delta_E = delta_El + delta_zpe + delta_Ecor
delta_H = delta_El + delta_zpe + delta_Hcor
delta_G = delta_El + delta_zpe + delta_Gcor
print('Delta_E = {:.2f} kJ/mol'.format(delta_E))
print('Delta_H = {:.2f} kJ/mol'.format(delta_H))
print('Delta_G = {:.2f} kJ/mol'.format(delta_G))
delta_S = (delta_H - delta_G)/opt.temp*1000
print('Delta_S = {:.2f} J/(mol K)'.format(delta_S))
if opt.job == 'ts' and opt.software == 'orca':
Input = opt.inputreaction
Reaksi = Input.split('->')
Reaktan = Reaksi[0]
Reaktan = Reaktan.split('+')
KoefisienReaktan = [i[0] for i in Reaktan]
KoefisienReaktan = [-int(i) for i in KoefisienReaktan]
Reaktan = [i[1:] for i in Reaktan]
TS = Reaksi[1]
TS = TS.split('+')
KoefisienTS = [i[0] for i in TS]
KoefisienTS = [int(i) for i in KoefisienTS]
TS = [i[1:] for i in TS]
Produk = Reaksi[2]
Produk = Produk.split('+')
KoefisienProduk = [i[0] for i in Produk]
KoefisienProduk = [-int(i) for i in KoefisienProduk]
Produk = [i[1:] for i in Produk]
H_reaktan = []
H_TS = []
H_produk = []
G_reaktan = []
G_TS = []
G_produk = []
E_reaktan = []
E_TS = []
E_produk = []
for i in Reaktan:
with open('{}/cmmd.out'.format(i),'r') as f:
for line in f:
if "Total enthalpy" in line:
arr = line.split()
H_reaktan.append(float(arr[3]))
if "Final Gibbs free energy" in line:
arr = line.split()
G_reaktan.append(float(arr[5]))
if "Total thermal energy" in line:
arr = line.split()
E_reaktan.append(float(arr[3]))
for i in TS:
with open('{}/cmmd.out'.format(i),'r') as f:
for line in f:
if "Total enthalpy" in line:
arr = line.split()
H_TS.append(float(arr[3]))
if "Final Gibbs free energy" in line:
arr = line.split()
G_TS.append(float(arr[5]))
if "Total thermal energy" in line:
arr = line.split()
E_TS.append(float(arr[3]))
for i in Produk:
with open('{}/cmmd.out'.format(i),'r') as f:
for line in f:
if "Total enthalpy" in line:
arr = line.split()
H_produk.append(float(arr[3]))
if "Final Gibbs free energy" in line:
arr = line.split()
G_produk.append(float(arr[5]))
if "Total thermal energy" in line:
arr = line.split()
E_produk.append(float(arr[3]))
Koefisien_forward = KoefisienReaktan + KoefisienTS
Koefisien_forward = np.array(Koefisien_forward,dtype=int)
Koefisien_backward = KoefisienProduk + KoefisienTS
Koefisien_backward = np.array(Koefisien_backward,dtype=int)
E_forward = E_reaktan + E_TS
E_forward = np.array(E_forward,dtype=float)
E_backward = E_produk + E_TS
E_backward = np.array(E_backward,dtype=float)
delta_E_forward = (np.dot(E_forward,Koefisien_forward))*Ha2kj
delta_E_backward = (np.dot(E_backward,Koefisien_backward))*Ha2kj
print('Ea_forward* = {:.2f} kJ/mol'.format(delta_E_forward))
print('Ea_backward* = {:.2f} kJ/mol'.format(delta_E_backward))
H_forward = H_reaktan + H_TS
H_forward = np.array(H_forward,dtype=float)
H_backward = H_produk + H_TS
H_backward = np.array(H_backward,dtype=float)
delta_H_forward = (np.dot(H_forward,Koefisien_forward))*Ha2kj
delta_H_backward = (np.dot(H_backward,Koefisien_backward))*Ha2kj
print('Delta_H_forward* = {:.2f} kJ/mol'.format(delta_H_forward))
print('Delta_H_backward* = {:.2f} kJ/mol'.format(delta_H_backward))
G_forward = G_reaktan + G_TS
G_forward = np.array(G_forward,dtype=float)
G_backward = G_produk + G_TS
G_backward = np.array(G_backward,dtype=float)
delta_G_forward = (np.dot(G_forward,Koefisien_forward))*Ha2kj
delta_G_backward = (np.dot(G_backward,Koefisien_backward))*Ha2kj
print('Delta_G_forward* = {:.2f} kJ/mol'.format(delta_G_forward))
print('Delta_G_backward* = {:.2f} kJ/mol'.format(delta_G_backward))
delta_S_forward = (delta_H_forward - delta_G_forward)/opt.temp*1000
delta_S_backward = (delta_H_backward - delta_G_backward)/opt.temp*1000
print('Delta_S_forward* = {:.2f} J/(mol K)'.format(delta_S_forward))
print('Delta_S_backward* = {:.2f} J/(mol K)'.format(delta_S_backward))
if opt.job == 'force' and opt.software == 'orca':
with open('cmmd.xyz') as f:
x = int(f.readlines()[0])
x = round(x*3/4)
with open('cmmd.opt') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if "$gradients" in line:
data = lines[i+2:i+x+2]
data = [x.strip("\n").strip(" ") for x in data]
data_clean = []
for i in data:
x = i.split(" ")
for i in x:
data_clean.append(i.strip(""))
# data_clean = [float(x) for x in data_clean]
data = []
for i in data_clean:
if i != '':
data.append(float(i))
j = 0
for j in range(int(len(data)/3)):
if j < (len(data) - 2):
print(data[j],data[j+1],data[j+2])
j += 3
# data = [x.strip(" ") for x in data]
# data = [x.strip(",") for x in data]
if opt.job == 'opt' and opt.software == 'dcdftb':
Energy = []
Gradient = []
if os.path.isfile('cmmd.out'):
with open(opt.input,'r') as f:
Natom = int(next(f))
with open('cmmd.out', 'r') as f:
koord = []
lines = f.readlines()
for i,line in enumerate(lines):
if 'Final molecular coordinate [Angstrom]' in line:
for j in range(Natom):
koord.append(lines[i+5+j].strip('\n'))
with open('cmmd.xyz', 'w') as fout:
print(Natom,file=fout)
print('File generated by CMMDE output parser',file=fout)
for atom in koord:
print(atom, file=fout)
else:
print("Mohon menunggu hingga perhitungan anda selesai.")
exit
if opt.job == 'rdf':
rdf(opt.traject,opt.latt,opt.pair,opt.range,opt.resolution)
if opt.job == 'cv' and opt.software == 'dcdftb':
time = []
cv = []
gaus = []
with open('biaspot','r') as f:
for line in f:
if "THIS RUN'S STEP NO.=" in line:
arr = line.split()
time.append(int(arr[9])/1000.)
if "GAUSSIAN BIAS POTENTIAL:" in line:
arr = line.split()
gaus.append(arr[3])
if "Coordinate" in line:
arr = line.split()
cv.append(float(arr[2]))
with open('cv.dat','w') as f:
for i,j in zip(time,cv):
print(i,j,file=f)
time = np.array(time)
# Plot Collective Variable
fig,ax = plt.subplots()
ax2 = ax.twiny()
ax.plot(time,cv,color='blue')
ax.tick_params(direction='in')
ax2.tick_params(direction='in')
def tick_func(metafreq,step):
gauss = step/metafreq
return [int(x)-1 for x in gauss]
ax.set_xlim(time[0],time[-1])
ax2.set_xlim(ax.get_xlim())
newtics = np.arange(min(time),max(time),time[-1]/10)
ax2.set_xticks(newtics)
ax2.set_xticklabels(tick_func(opt.metafreq,newtics*1000))
ax2.set_xlabel('Number of deposited Gaussian')
plt.grid(linestyle=':')
plt.yticks(np.arange(min(cv),max(cv),0.1))
ax.set_xlabel('Time [ps]')
if opt.cvtype == 'coordnum':
ax.set_ylabel('Coordination Number')
if opt.cvtype == 'distance':
ax.set_ylabel('Distance [Angstroms]')
if opt.cvtype == 'angle':
ax.set_ylabel('Angle [degree]')
if opt.cvtype == 'dihedral':
ax.set_ylabel('Dihedral [degree]')
if opt.cvtype == 'distancediff':
ax.set_ylabel('Distance diff. [Angstroms]')
if opt.cvtype == 'distanceadd':
ax.set_ylabel('Distance add. [Angstroms]')
if opt.cvtype == 'meandistance':
ax.set_ylabel('Mean distance [Angstroms]')
if opt.cvtype == 'pointplanedistance':
ax.set_ylabel('Point plane distance [Angstroms]')
plt.savefig('cv.pdf',dpi=1200,format='pdf')
if opt.job == 'fes' and opt.software == 'dcdftb':
fesdata = []
with open('fes.dat','r') as f:
lines = f.readlines()
for index,line in enumerate(lines):
if 'FREE ENERGY SURFACE CONSISTING OF {} GAUSSIANS'.format(opt.ngaus) in line:
for i in range(int((opt.fesend-opt.fesstart)/opt.fesbin)+1):
fesdata.append(lines[index+1+i].strip())
with open('fes_{}.dat'.format(opt.ngaus),'w') as f:
for i in fesdata:
print(i,file=f)
with open('fes_{}.dat'.format(opt.ngaus),'r') as f:
cv = []
fes = []
for line in f:
arr = line.split()
cv.append(float(arr[0]))
fes.append(float(arr[1]))
fes = np.array(fes)
# Plot free energy surface
fig,ax = plt.subplots()
ax.plot(cv,fes*2625.5-min(fes*2625.5),color='blue')
ax.tick_params(direction='in')
ax.set_xlim(cv[0],cv[-1])
plt.grid(linestyle=':')
plt.ylabel('Free energy [kJ/mol]')
if opt.cvtype == 'coordnum':
plt.xlabel('Coordination Number')
if opt.cvtype == 'distance':
plt.xlabel('Distance [Angstroms]')
if opt.cvtype == 'angle':
plt.xlabel('Angle [degree]')
if opt.cvtype == 'dihedral':
plt.xlabel('Dihedral [degree]')
if opt.cvtype == 'distancediff':
plt.xlabel('Distance diff. [Angstroms]')
if opt.cvtype == 'distanceadd':
plt.xlabel('Distance add. [Angstroms]')
if opt.cvtype == 'meandistance':
plt.xlabel('Mean distance [Angstroms]')
if opt.cvtype == 'pointplanedistance':
plt.xlabel('Point plane distance [Angstroms]')
plt.savefig('fes.pdf',dpi=1200,format='pdf')
if opt.job == 'barrier' and opt.software == 'dcdftb':
from scipy.signal import argrelextrema
kJ2eV = 1.0364e-2
x = []
y = []
with open('fes_{}.dat'.format(opt.ngaus),'r') as f:
for line in f:
arr = line.split()
x.append(float(arr[0]))
y.append(float(arr[1]))
x = np.array(x)
y = np.array(y)
sortid = np.argsort(x)
x = x[sortid]
y = y[sortid]
maxm = argrelextrema(y, np.greater)
minm = argrelextrema(y, np.less)
maxval = [float(i) for i in y[maxm]]
minval = [float(i) for i in y[minm]]
# print('Minimum absis: {}'.format(x[minm]))
# print('Maximum absis: {}'.format(x[maxm]))
# print('Minimum ordinate: {}'.format(y[minm]))
# print('Maximum ordinate: {}'.format(y[maxm]))
###Activation barrier for forward and backward reactions
if (len(minval) == 3):
# If exists two transition states
Ef1 = (maxval[1]-minval[2])*2625.5 # in kJ/mol
Ef2 = (maxval[0]-minval[1])*2625.5
Eb1 = (maxval[0]-minval[0])*2625.5
Eb2 = (maxval[1]-minval[1])*2625.5
##Now calculating delta G
deltaG = (minval[-1]-minval[0])*2625.5 # in kJ/mol
print('delta_G: {:.2f} kJ/mol ({:.2f} eV)'.format(deltaG, deltaG*kJ2eV))
print('delta_G*(backward1): {:.2f} kJ/mol ({:.2f} eV)'.format(Ef1, Ef1*kJ2eV))
print('delta_G*(backward2): {:.2f} kJ/mol ({:.2f} eV)'.format(Ef2, Ef2*kJ2eV))
print('delta_G*(forward1): {:.2f} kJ/mol ({:.2f} eV)'.format(Eb1, Eb1*kJ2eV))
print('delta_G*(forward2): {:.2f} kJ/mol ({:.2f} eV)'.format(Eb2, Eb2*kJ2eV))
elif (len(minval) == 1):
Ef1 = (maxval[0]-minval[0])*2625.5
Eb1 = (maxval[0]-y[0])*2625.5
print('delta_G*(forward): {:.2f} kJ/mol ({:.2f} eV)'.format(Ef1, Ef1*kJ2eV))
print('delta_G*(backward): {:.2f} kJ/mol ({:.2f} eV)'.format(Eb1, Eb1*kJ2eV))
deltaG = (y[0]-minval[0])*2625.5
print('delta_G: {:.2f} kJ/mol ({:.2f} eV)'.format(deltaG, deltaG*kJ2eV))
else:
Ef1 = (maxval[0]-minval[1])*2625.5 # in kJ/mol
Ef2 = 0
Eb1 = (maxval[0]-minval[0])*2625.5
Eb2 = 0
##Now calculating delta G
deltaG = (minval[-1]-minval[0])*2625.5 # in kJ/mol
print('delta_G: {:.2f} kJ/mol ({:.2f} eV)'.format(deltaG, deltaG*kJ2eV))
print('delta_G*(backward1): {:.2f} kJ/mol ({:.2f} eV)'.format(Ef1, Ef1*kJ2eV))
print('delta_G*(backward2): {:.2f} kJ/mol ({:.2f} eV)'.format(Ef2, Ef2*kJ2eV))
print('delta_G*(forward1): {:.2f} kJ/mol ({:.2f} eV)'.format(Eb1, Eb1*kJ2eV))
print('delta_G*(forward2): {:.2f} kJ/mol ({:.2f} eV)'.format(Eb2, Eb2*kJ2eV))
if opt.job == 'rigiddock':
path = './'
files = []
ligands = []
scores = []
vdw = []
es = []
rep = []
rmsd = []
mw = []
for i in os.listdir(path):
if os.path.isdir(os.path.join(path,i)) and 'RigidDock' in i:
files.append(i)
for i in files:
ligands.append(i.split("RigidDock_")[1])
with open('{}/rigid_scored.mol2'.format(i),'r') as f:
for line in f:
if 'Grid_Score:' in line:
arr = line.split()
scores.append(round(float(arr[2]),2))
if 'Grid_vdw_energy:' in line:
arr = line.split()
vdw.append(round(float(arr[2]),2))
if 'Grid_es_energy:' in line:
arr = line.split()
es.append(round(float(arr[2]),2))
if 'Internal_energy_repulsive:' in line:
arr = line.split()
rep.append(round(float(arr[2]),2))
if 'HA_RMSDh' in line:
arr = line.split()
rmsd.append(round(float(arr[2]),2))
if 'Molecular_Weight' in line:
arr = line.split()
mw.append(round(float(arr[2]),2))
if len(scores) < 20:
t = PrettyTable()
t.add_column("Ligands",ligands)
# t.add_column("Mw [g/mol]",mw)
t.add_column("Scores [kJ/mol]",scores)
t.add_column("VDW [kJ/mol]",vdw)
t.add_column("Elec. [kJ/mol]",es)
# t.add_column("Rep. [kJ/mol]",rep)
if len(rmsd) > 0:
t.add_column("RMSD [Angs.]",rmsd)
print(t.get_string(sortby="Scores [kJ/mol]"))
else:
with open('DockTable.dat','w') as f:
t = PrettyTable()
t.add_column("Ligands",ligands)
# t.add_column("Mw [g/mol]",mw)
t.add_column("Scores [kJ/mol]",scores)
t.add_column("VDW [kJ/mol]",vdw)
t.add_column("Elec. [kJ/mol]",es)
# t.add_column("Rep. [kJ/mol]",rep)
if len(rmsd) > 0:
t.add_column("RMSD [Angs.]",rmsd)
print(t.get_string(sortby="Scores [kJ/mol]"),file=f)
if opt.job == 'flexdock':
path = './'
files = []
ligands = []
scores = []
vdw = []
es = []
rep = []
mw = []
rmsd = []
for i in os.listdir(path):
if os.path.isdir(os.path.join(path,i)) and 'FlexDock' in i:
if os.path.exists('{}/flex_scored.mol2'.format(i)):
if os.stat('{}/flex_scored.mol2'.format(i)).st_size !=0:
files.append(i)
for i in files:
ligands.append(i.split("FlexDock_")[1])
with open('{}/flex_scored.mol2'.format(i),'r') as f:
for line in f:
if 'Grid_Score:' in line:
arr = line.split()
scores.append(round(float(arr[2]),2))
if 'Grid_vdw_energy:' in line:
arr = line.split()
vdw.append(round(float(arr[2]),2))
if 'Grid_es_energy:' in line:
arr = line.split()
es.append(round(float(arr[2]),2))
if 'Internal_energy_repulsive:' in line:
arr = line.split()
rep.append(round(float(arr[2]),2))
if 'HA_RMSDh' in line:
arr = line.split()
rmsd.append(round(float(arr[2]),2))
if 'Molecular_Weight' in line:
arr = line.split()
mw.append(round(float(arr[2]),2))
if len(scores) < 20:
t = PrettyTable()
t.add_column("Ligands",ligands)
# t.add_column("Mw [g/mol]",mw)
t.add_column("Scores [kJ/mol]",scores)
t.add_column("VDW [kJ/mol]",vdw)
t.add_column("Elec. [kJ/mol]",es)
# t.add_column("Rep. [kJ/mol]",rep)
if len(rmsd) > 0:
t.add_column("RMSD [Angs.]",rmsd)
print(t.get_string(sortby="Scores [kJ/mol]"))
else:
with open('DockTable.dat','w') as f:
t = PrettyTable()
t.add_column("Ligands",ligands)
# t.add_column("Mw [g/mol]",mw)
t.add_column("Scores [kJ/mol]",scores)
t.add_column("VDW [kJ/mol]",vdw)
t.add_column("Elec. [kJ/mol]",es)
# t.add_column("Rep. [kJ/mol]",rep)
if len(rmsd) > 0:
t.add_column("RMSD [Angs.]",rmsd)
print(t.get_string(sortby="Scores [kJ/mol]"),file=f)
if opt.job == 'checkopt' and opt.software == 'dock':
checkopt(opt.nligands)
# Rescoring docking atau perhitungan lainnya yang melibatkan perhitungan satu titik menggunakan DCDFTB
if opt.job == 'dock' and opt.software == 'dcdftb':
Input = opt.inputreaction
Reaksi = Input.split('->')
Reaktan = Reaksi[0]
Reaktan = Reaktan.split('+')
KoefisienReaktan = [i[0] for i in Reaktan]
KoefisienReaktan = [-int(i) for i in KoefisienReaktan]
Reaktan = [i[1:] for i in Reaktan]
Produk = Reaksi[1]
Produk = Produk.split('+')
KoefisienProduk = [i[0] for i in Produk]
KoefisienProduk = [int(i) for i in KoefisienProduk]
Produk = [i[1:] for i in Produk]
E_reaktan = []
E_produk = []
for i in Reaktan:
with open('{}/cmmd.out'.format(i),'r') as f:
for line in f:
if "Final DC-DFTB-3rd Energy"in line:
arr = line.split()
E_reaktan.append(float(arr[4]))
elif "Final DFTB-3rd Energy" in line:
arr = line.split()
E_reaktan.append(float(arr[4]))
elif "Final SCC-DFTB Energy" in line:
arr = line.split()
E_reaktan.append(float(arr[4]))
for i in Produk:
with open('{}/cmmd.out'.format(i),'r') as f:
for line in f:
if "Final DC-DFTB-3rd Energy" in line:
arr = line.split()
E_produk.append(float(arr[4]))
elif "Final DFTB-3rd Energy" in line:
arr = line.split()
E_produk.append(float(arr[4]))
elif "Final SCC-DFTB Energy" in line:
arr = line.split()
E_produk.append(float(arr[4]))
Koefisien = KoefisienReaktan + KoefisienProduk
Koefisien = np.array(Koefisien,dtype=int)
E = E_reaktan + E_produk
E = np.array(E,dtype=float)
delta_E = (np.dot(E,Koefisien))*Ha2kj
print('Delta_E = {:.2f} kJ/mol'.format(delta_E))
if opt.job == 'opt' and opt.software == 'dftb':
os.system('cmmde_gen2poscar.py cmmd.gen > cmmd.vasp')
if opt.job == 'reax' and opt.software == 'dftb':
Input = opt.inputreaction
Reaksi = Input.split('->')
Reaktan = Reaksi[0]
Reaktan = Reaktan.split('+')
KoefisienReaktan = [i[0] for i in Reaktan]
KoefisienReaktan = [-int(i) for i in KoefisienReaktan]
Reaktan = [i[1:] for i in Reaktan]
Produk = Reaksi[1]
Produk = Produk.split('+')
KoefisienProduk = [i[0] for i in Produk]
KoefisienProduk = [int(i) for i in KoefisienProduk]
Produk = [i[1:] for i in Produk]
E_reaktan = []
E_produk = []
for i in Reaktan:
with open('{}/detailed.out'.format(i),'r') as f:
for line in f:
if "Total energy:"in line:
arr = line.split()
E_reaktan.append(float(arr[2]))
for i in Produk:
with open('{}/detailed.out'.format(i),'r') as f:
for line in f:
if "Total energy:" in line:
arr = line.split()
E_produk.append(float(arr[2]))
Koefisien = KoefisienReaktan + KoefisienProduk
Koefisien = np.array(Koefisien,dtype=int)
E = E_reaktan + E_produk
E = np.array(E,dtype=float)
delta_E = (np.dot(E,Koefisien))*Ha2kj
print('Delta_E = {:.2f} kJ/mol'.format(delta_E))
if opt.job == 'cell':
os.system('aflow --data < {}'.format(opt.input)) # Untuk menggunakan fitur ini, install aflow, wget http://aflow.org/install-aflow/install-aflow.sh
if opt.job == 'dos' and opt.software == 'dftb':
os.system('$DPTOOLS_DIR/dp_dos band.out dos_total.dat')
if opt.job == 'pdos' and opt.software == 'dftb':
filename = opt.pdos.split('.out')[0]
os.system('$DPTOOLS_DIR/dp_dos -w {} {}.dat'.format(opt.pdos,filename))
# Plot file x y sembarang dengan ekstensi .dat
if opt.job == 'plot':
x = []
y = []
with open(opt.file, 'r') as f:
for line in f:
arr = line.split()
x.append(float(arr[0]))
y.append(float(arr[1]))
x = np.array(x)
y = np.array(y)
fig,ax = plt.subplots()
ax.plot(x,y,color='blue')
ax.tick_params(direction='in')
# fig,ax = plt.subplots()
plt.grid(linestyle=':')
plt.ylim(0,max(y))
# plt.xticks(np.arange(0,len(x)+1,25))
# plt.yticks(np.arange(0,max(y),2))
# ax.tick_params(direction='in')
# ax.set_xlim(min(x),max(x))
# ax.set_ylim(min(y),max(y))
plt.ylabel(opt.ylabel)
plt.xlabel(opt.xlabel)
filename = opt.file.split('.dat')[0]
plt.savefig('{}.pdf'.format(filename),dpi=300,format='pdf')
if opt.job == 'nci2d':
with open('cmmd.nci','w') as f:
print("""1
cmmd.wfn
{}
RADIUS 0. 0. 0. 2.
RANGE 3
-0.5 -0.02
-0.02 0.02
0.02 0.5""".format(opt.grid),file=f)
with open('run_nci.sh','w') as f:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$NCI_COMMAND cmmd.nci""".format(opt.nproc),file = f)
os.system('sbatch run_nci.sh')
if opt.job == 'nciplot':
with open('cmmd.gp','w') as f:
print("""set terminal pngcairo size 1000,1000 enhanced font 'Helvetica,20'
set encoding iso_8859_1
set output 'nci.png'
set key
set ylabel 's(a.u.)' font "Helvetica, 30"
set xlabel 'sign({/Symbol l}_2){/Symbol r}(a.u.)' font "Helvetica, 30"
set pm3d map
# Define a color gradient palette used by pm3d
set palette defined (-0.04 "blue",0.00 "green", 0.04 "red")
set format y "% .2f"
set format x "% .2f"
set format cb "% -.2f"
set border lw 4
set xtic -0.06,0.01,0.06 nomirror rotate font "Helvetica"
set ytic 0.0,0.25,1.0 nomirror font "Helvetica"
# set the color bar tics
set cbtic -0.06,0.01,0.06 nomirror font "Helvetica"
set xrange [-0.06:0.06]
set yrange [0.0:1.0]
# set the range of values which are colored using the current palette
set cbrange [-0.06:0.06]
plot 'cmmd.dat' u 1:2:1 w p lw 6 palette t '' """,file = f)
os.system('gnuplot cmmd.gp')
if 'dos' in opt.job and opt.software == 'qe':
with open('cmmd.in','w') as f:
print("""DOS
prefix = 'cmmd_dos',
outdir = {},
fildos = 'cmmd.dos',
emin = {},
emax = {},
/""".format(opt.outdir,opt.emin,opt.emax),file=f)
os.system("$QE_DOS_COMMAND < cmmd.in > cmmd.out") # Hasil perhitungan berupa cmmd.dos
if 'charge' in opt.job and opt.software == 'qe':
with open("cmmd.in",'w') as f:
print("""&INPUTPP
outdir = {},
prefix = 'cmmd_charge',
plot_num = 0,
/
&PLOT
iflag = 3,
output_format = 6,
fileout = 'cmmd_rho.cube',
nx = 64, ny = 64, nz = 64,
/""".format(opt.outdir),file=f)
with open('run.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
export OMP_NUM_THREADS=1
cd $PWD
$QE_PP_COMMAND < cmmd.in > cmmd.out""",file=fout)
os.system('sbatch run.sh')
if opt.job == 'opt' and opt.software == 'qe':
with open('cmmd.out', 'r') as f:
lines = f.readlines()
for i,line in enumerate(lines):
if "ATOMIC_POSITIONS" in line:
print(lines[i+1])