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150 lines
3.6 KiB
150 lines
3.6 KiB
2 years ago
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from cmmde_mass import mass
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def qe(geom,job,mode,pseudo,outdir,bravais,unit,ecutwfc,ecutrho,mixing,conv_thr,dftfunc,extpseudo,kpts,optalgo,press,press_conv_thr,nband,occ):
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# Mapping istilah job pada CMMDE dengan istilah job di Quantum Espresso
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jobmap = {
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'sp':'scf',
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'opt':'relax',
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'optcell':'vc-relax',
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'md':'md',
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'band':'bands',
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'mdnpt':'vc-md'
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}
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x = []
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y = []
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z = []
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symb = []
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v1 = []
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v2 = []
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v3 = []
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k_points = kpts.split("x")
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shift = []
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for k in k_points:
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if int(k)%2 == 0:
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shift.append(1)
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else:
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shift.append(0)
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if 'POSCAR' in geom or 'CONTCAR' in geom:
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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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v1.append(next(f).split())
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v2.append(next(f).split())
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v3.append(next(f).split())
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next(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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x.append(arr[0])
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y.append(arr[1])
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z.append(arr[2])
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symb.append(arr[3])
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if '.xyz' in geom:
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with open(geom,'r') as f:
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N_Atom = next(f)
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for line in f:
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arr = line.split()
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symb.append(arr[0])
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x.append(arr[1])
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y.append(arr[2])
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z.append(arr[3])
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with open("cmmd.in",'w') as f:
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# CONTROL card in input file
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print("""&CONTROL
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calculation = {},
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restart_mode = {},
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prefix = 'cmmd',
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pseudo_dir = {},
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outdir = {},
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/
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&SYSTEM
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ibrav = {},
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nat = {},
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ntyp = {},
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ecutwfc = {},
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ecutrho = {},
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occupations = {},
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/
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&ELECTRONS
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mixing_beta = {},
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conv_thr = {},
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/
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""".format(jobmap[job],mode,pseudo,outdir,bravais,len(symb),len(set(symb)),ecutwfc,ecutrho,occ,mixing,conv_thr),file=f)
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if 'opt' in job:
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print("""&IONS
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ion_dynamics = {},
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/""".format(optalgo),file=f)
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if 'optcell' in job:
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print("""&CELL
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cell_dynamics = {},
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press = {},
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press_conv_thr = {},
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/""".format(optalgo,press,press_conv_thr),file=f)
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print("ATOMIC_SPECIES",file=f)
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for i in set(symb):
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print("{} {} {}.{}.{}".format(i,mass(i),i,dftfunc,extpseudo),file=f)
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if bravais == 0:
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print("""CELL_PARAMETERS ({})
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{} {} {}
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{} {} {}
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{} {} {}""".format(unit,v1[0][0],v1[0][1],v1[0][2] ,v2[0][0],v2[0][1],v2[0][2] ,v3[0][0],v3[0][1],v3[0][2] ),file=f)
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print("ATOMIC_POSITIONS ({})".format(unit),file=f)
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for i,x,y,z in zip(symb,x,y,z):
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print("{} {} {} {}".format(i,x,y,z),file=f)
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print("K_POINTS automatic",file=f)
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print("{} {} {} {} {} {}".format(k_points[0],k_points[1],k_points[2],shift[0],shift[1],shift[2]),file=f)
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if 'charge' in job:
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with open("cmmd.in",'w') as f:
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print("""&INPUTPP
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outdir = {},
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prefix = 'cmmd',
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plot_num = 0,
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/
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&PLOT
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iflag = 3,
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output_format = 6,
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fileout = 'cmmd_rho.cube',
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nx = 64, ny = 64, nz = 64,
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/""".format(outdir),file=f)
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if 'nscf' in job:
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with open('cmmd.in', 'w') as f:
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print("""&CONTROL
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calculation = 'nscf',
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restart_mode = {},
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prefix = 'cmmd',
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pseudo_dir = {},
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outdir = {},
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/
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&SYSTEM
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ibrav = {},
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nat = {},
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ntyp = {},
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ecutwfc = {},
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ecutrho = {},
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nbnd = {},
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occupations = {},
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/
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&ELECTRONS
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mixing_beta = {},
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conv_thr = {},
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/""".format(mode,pseudo,outdir,bravais,len(symb),len(set(symb)),ecutwfc,ecutrho,nband,occ,mixing,conv_thr),file=f)
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print("ATOMIC_SPECIES",file=f)
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for i in set(symb):
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print("{} {} {}.{}.{}".format(i,mass(i),i,dftfunc,extpseudo),file=f)
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if bravais == 0:
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print("""CELL_PARAMETERS ({})
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{} {} {}
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{} {} {}
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{} {} {}""".format(unit,v1[0][0],v1[0][1],v1[0][2] ,v2[0][0],v2[0][1],v2[0][2] ,v3[0][0],v3[0][1],v3[0][2] ),file=f)
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print("ATOMIC_POSITIONS crystal",file=f)
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for i,x,y,z in zip(symb,x,y,z):
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print("{} {} {} {}".format(i,x,y,z),file=f)
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print("K_POINTS automatic",file=f)
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print("{} {} {} {} {} {}".format(k_points[0],k_points[1],k_points[2],shift[0],shift[1],shift[2]),file=f)
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