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