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Author SHA1 Message Date
Aditya Wibawa Sakti d577c73c60 update and bug fix 5 months ago
Aditya Wibawa Sakti 5b3599bb9a update 8 months ago
Aditya Wibawa Sakti 53b3d378c4 update 8 months ago
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@ -14,17 +14,17 @@ import time
parser = argparse.ArgumentParser(description='Computational Molecular & Material Design Interface')
# Input Geometri, tanpa ini perhitungan tidak akan berjalan.
# Geometry input file, without this, your calculation won't proceed.
parser.add_argument('-i','--input',type=str,default='geom.xyz',help='Input geometri dalam koordinat Cartesian')
parser.add_argument('-cons','--constraints',type=str,default='None',help='Membekukan ikatan, sudut ikatan, dan sebagainya selama proses optimasi geometri. Periksa manual Orca 5.0 lebih lanjut mengenai ini.')
# Informasi muatan dan multiplisitas spin molekul.
# Charge and spin multiplicity of the molecule.
parser.add_argument('-c','--charge',type=int,default=0, help='Muatan molekul')
parser.add_argument('-mult','--mult',type=int,default=1, help='Multiplisitas molekul')
# Input yang berkaitan dengan software, metode, dan jenis pekerjaan
# Inputs about the software, type of job, and computational methods.
parser.add_argument('-s','--software',type=str,default='orca',help='Software yang digunakan. Pilihan: orca, dcdftb, gromacs')
parser.add_argument('-j','--job',type=str,default='sp',help='Jenis perhitungan yang dilakukan. Pilihan: sp, opt, freq, md, mtd, td, dock.')
parser.add_argument('-m','--method',type=str,default='XTB2',help='Metode yang digunakan dalam perhitungan. Pilihan: XTB, XTB2, DFTB, DFTB2, DFTB3-diag, dan sebagainya.')
# Input yang berkaitan dengan perhitungan frekuensi menggunakan software Orca
# Inputs about the frequency calculations in Orca.
parser.add_argument('-sfreq','--scalefreq',type=float,default=1, help='Faktor skala frekuensi yang digunakan.')
# Input yang berkaitan dengan perhitungan menggunakan software DCDFTBMD
parser.add_argument('-disp','--dispersion',type=str,default='None', help='Model koreksi dispersi jika menggunakan software DCDFTB. Pilihan: None, D3, D3BJ, D3H5.')

@ -788,6 +788,44 @@ if opt.job == 'ts' and opt.software == 'orca':
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 = []

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@ -24,7 +24,8 @@ def azimuth(element):
'Co' : '3',
'Ti' : '3',
'C' : '2',
'Si': '3'
'Si': '3',
'Zr': '3',
}
return azimuth[element]

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