A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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from cmmde_hubbard import hubbard, azimuth
def xyz2gen(geom,a1,a2,a3,b1,b2,b3,c1,c2,c3):
sym = []
x = []
y = []
z = []
elements = []
with open(geom,'r') as f:
Natom = int(next(f))
next(f)
for line in f:
arr = line.split()
sym.append(arr[0])
x.append(float(arr[1]))
y.append(float(arr[2]))
z.append(float(arr[3]))
for index,element in enumerate(sym):
if sym[index] != sym[index-1]:
elements.append(element)
with open("in.gen", 'w') as f:
types = ""
if a1 != 0:
types += "S"
else:
types += "C"
print("{} {}".format(Natom,types),file=f)
for i in elements:
print(i, end=' ',file=f)
print("",file=f)
indx = 1
sindx = 0
sym_indx = []
for i,symbol in enumerate(sym):
if sym[i] != sym[i-1]:
sindx+=1
sym_indx.append(sindx)
else:
sindx+=0
sym_indx.append(sindx)
for sym_indx,i,j,k in zip(sym_indx,x,y,z):
print(indx,sym_indx,i,j,k,file=f)
indx+=1
if 'S' in types:
print("0 0 0",file=f)
print("{} {} {}".format(a1,a2,a3),file=f)
print("{} {} {}".format(b1,b2,b3),file=f)
print("{} {} {}".format(c1,c2,c3),file=f)
def poscar2gen(geom):
sym = []
a = []
b = []
c = []
x = []
y = []
z = []
coord_type = []
with open(geom, 'r') as f:
next(f)
next(f)
acell = next(f).split()
bcell = next(f).split()
ccell = next(f).split()
a.append(acell)
b.append(bcell)
c.append(ccell)
next(f)
next(f)
if 'direct' in next(f):
coord_type.append("F")
else:
coord_type.append("S")
for line in f:
arr = line.split()
x.append(arr[0])
y.append(arr[1])
z.append(arr[2])
sym.append(arr[3])
with open('in.gen','w') as f:
elements = []
print("{} {}".format(len(sym),coord_type[-1]),file=f)
for index,element in enumerate(sym):
if sym[index] != sym[index-1]:
elements.append(element)
for i in elements:
print(i, end=' ',file=f)
print("",file=f)
indx = 1
sindx = 0
sym_indx = []
for i,symbol in enumerate(sym):
if sym[i] != sym[i-1]:
sindx+=1
sym_indx.append(sindx)
else:
sindx+=0
sym_indx.append(sindx)
for sym_indx,i,j,k in zip(sym_indx,x,y,z):
print(indx,sym_indx,i,j,k,file=f)
indx+=1
if 'S' or 'F' in coord_type:
print("0 0 0",file=f)
print("{} {} {}".format(a[0][0],a[0][1],a[0][2]),file=f)
print("{} {} {}".format(b[0][0],b[0][1],b[0][2]),file=f)
print("{} {} {}".format(c[0][0],c[0][1],c[0][2]),file=f)
def vasp2gen(geom):
sym = []
a = []
b = []
c = []
x = []
y = []
z = []
coord_type = []
with open(geom, 'r') as f:
next(f)
next(f)
acell = next(f).split()
bcell = next(f).split()
ccell = next(f).split()
a.append(acell)
b.append(bcell)
c.append(ccell)
next(f)
next(f)
next(f)
if 'direct' in next(f):
coord_type.append("F")
else:
coord_type.append("S")
for line in f:
arr = line.split()
x.append(arr[0])
y.append(arr[1])
z.append(arr[2])
sym.append(arr[-1])
with open('in.gen','w') as f:
elements = []
print("{} {}".format(len(sym),coord_type[-1]),file=f)
for index,element in enumerate(sym):
if sym[index] != sym[index-1]:
elements.append(element)
for i in elements:
print(i, end=' ',file=f)
print("",file=f)
indx = 1
sindx = 0
sym_indx = []
for i,symbol in enumerate(sym):
if sym[i] != sym[i-1]:
sindx+=1
sym_indx.append(sindx)
else:
sindx+=0
sym_indx.append(sindx)
for sym_indx,i,j,k in zip(sym_indx,x,y,z):
print(indx,sym_indx,i,j,k,file=f)
indx+=1
if 'S' or 'F' in coord_type:
print("0 0 0",file=f)
print("{} {} {}".format(a[0][0],a[0][1],a[0][2]),file=f)
print("{} {} {}".format(b[0][0],b[0][1],b[0][2]),file=f)
print("{} {} {}".format(c[0][0],c[0][1],c[0][2]),file=f)
def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr):
elements = ""
coord_type = ""
if '.gen' in geom:
with open(geom,'r') as f:
arr = next(f).split()
coord_type+=arr[1]
elements+=next(f)
elements = elements.split()
if '.xyz' in geom:
sym = []
elements = []
with open(geom,'r') as f:
next(f)
next(f)
for line in f:
arr = line.split()
sym.append(arr[0])
for i in set(sym):
elements.append(i)
with open ("cmmd.in",'w') as f:
if '.gen' in geom:
print("""Geometry = GenFormat {{
<<< {}
}}""".format(geom),file=f)
if '.xyz' in geom:
print("""Geometry = xyzFormat {{
<<< {}
}}""".format(geom),file=f)
if job == 'opt':
print("""Driver = ConjugateGradient {{
MovedAtoms = {}
MaxForceComponent = 1e-4
MaxSteps = 1000
OutputPrefix = "cmmd"
""".format(activeatoms),file=f)
print('}',file=f)
if job == 'optcell':
print("""Driver = ConjugateGradient {{
MovedAtoms = {}
MaxForceComponent = 1e-4
MaxSteps = 1000
LatticeOpt = Yes
OutputPrefix = "cmmd"
""".format(activeatoms),file=f)
print('}',file=f)
if method == 'XTB1':
kpts = kpts.split('x')
shift = 0
if int(kpts[0])%2 == 0:
shift+=0.5
else:
shift +=0
print("""Hamiltonian = xTB {{
Method = "GFN1-xTB"
kPointsAndWeights = SuperCellFolding{{
{} 0 0
0 {} 0
0 0 {}
{} {} {}
}}
}}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f)
else:
print("Hamiltonian = DFTB {",file=f)
if method == 'DFTB2':
print("scc = Yes",file=f)
print("MaxSCCIterations = 1000",file=f)
if method == 'DFTB3diag':
print("""scc = Yes
ThirdOrder = Yes
MaxSCCIterations = 1000
""",file=f)
if method == 'DFTB3':
print("""scc = Yes
ThirdOrderFull = Yes
""",file=f)
## Koreksi ikatan hidrogen
hdamp = {
'DFTB3': '4.0',
'DFTB3diag': '4.95',
'DFTB2': '4.5'
}
if hcorr == 'hdamp':
print("""HCorrection = Damping {{
Exponent = {}
}}""".format(hdamp[method]),file=f)
if hcorr == 'H5':
print("""HCorrection = H5{ }""",file=f)
if dispersion == 'D3':
print("""Dispersion = DftD3 {
Damping = ZeroDamping {
sr6 = 0.7461
alpha6 = 14.0
}
s6 = 1.0
s8 = 3.209
}""",file=f)
if dispersion == 'D3BJ':
print("""Dispersion = DftD3 {
Damping = BeckeJohnson {
a1 = 0.5719
a2 = 3.6017
}
s6 = 1.0
s8 = 0.5883
}""",file=f)
if dispersion == 'D3H5':
print("""Dispersion = DftD3{
Damping = ZeroDamping{
sr6 = 1.25
alpha6 = 29.61
}
s6 = 1.0
s8 = 0.49
HHRepulsion = Yes
}""",file=f)
print("""SlaterKosterFiles = Type2FileNames {{
Prefix = {}/
Separator = "-"
Suffix = ".skf" """.format(parapath),file=f)
print('}',file=f)
# Mapping bilangan kuantum azimuth ke penamaan orbital
azi2orb = {'1':'s','2':'p','3':'d','4':'f'}
print("MaxAngularMomentum {",file=f)
for element in elements:
print("""{} = "{}" """.format(element,azi2orb[azimuth(element)]),file=f)
print("}",file=f)
if method == 'DFTB3':
print("HubbardDerivs {",file=f)
for element in elements:
print("""{} = {}""".format(element,hubbard(element)),file=f)
print("}",file=f)
# Informasi K-points
kpts = kpts.split('x')
shift = 0
if int(kpts[0])%2 == 0:
shift+=0.5
else:
shift +=0
# if 'F' or 'S' in coord_type:
if '.gen' in geom:
print("""KPointsAndWeights = SuperCellFolding {{
{} 0 0
0 {} 0
0 0 {}
{} {} {}
}}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f)
print("}", file=f)
if job == 'dos':
print("Analysis {",file=f)
print(" ProjectStates {",file=f)
for element in elements:
print("""Region {{
Atoms = {}
ShellResolved = Yes
Label = "dos_{}"
}}""".format(element,element),file=f)
print(" }",file=f)
print("}",file=f)
print("""ParserOptions {
ParserVersion = 7
}""",file=f)