CMMDE/bin/cmmdepre.py

#!/usr/bin/env python3
import os
import argparse
import sys
from cmmde_dftb import xyz2gen
import numpy as np
from cmmde_surface import surface
from cmmde_formats import read, write
from cmmde_dftb import xyz2gen
from cmmde_tools import sort
from cmmde_decahedron import Decahedron
from cmmde_icosahedron import Icosahedron
from cmmde_tetrahedron import Tetrahedron
from cmmde_cubic import FaceCenteredCubic, SimpleCubic, BodyCenteredCubic
import pymatgen.analysis.adsorption as pa
import pymatgen.core.structure as st
from pymatgen.core import Structure
import argparse
import sys
import warnings
warnings.filterwarnings("ignore")

parser = argparse.ArgumentParser(description='CMMDEPRE: Program untuk modifikasi input file')
parser.add_argument('-i','--input', type=str, default='',help='Input geometri dalam berbagai format. Format yang didukung: .smi, .mol2, dan semua format yang didukung oleh openbabel.')
parser.add_argument('-j','--job', type=str, default='sp',help='Jenis pekerjaan yang dilakukan.')
parser.add_argument('-s','--size',type=str,help='Ukuran supersel yang ingin dibuat.')
parser.add_argument('-hkl','--hkl',type=str,help='Indeks Miller (hkl) permukaan yang akan dibuat.')
parser.add_argument('-v', '--vacuum', type=float, default=20, help='Tebal lapisan vakum yang dibuat (dalam angstrom). Default: 20 Angstrom.')
parser.add_argument('-n', '--layer', type=int, help='Jumlah lapisan permukaan atau klaster yang akan dibuat.')
parser.add_argument('-ads','--ads',type=str, help='File koordinat Cartesian berisikan molekul adsorbat')
parser.add_argument('-d','--distance',type=float,default=1.5,help='Jarak adsorbat dari lapisan teratas permukaan (Angstrom). Default: 1.5 Angstrom.')
parser.add_argument('-height','--height',type=float,default=2.0, help='Tebal lapisan sisi aktif (Angstrom). Default: 2.0.')
parser.add_argument('-dyn','--dyn',type=float,default=3.0, help='Tebal lapisan bawah permukaan yang dibuat kaku (Angstrom). Default: 3.0.')
parser.add_argument('-e', '--element', type=str, help='Unsur yang akan dibuat klaster' )
parser.add_argument('-t', '--type', type=str, help='Tipe klaster yang akan dibuat. Pilihan: decahedron dan icosahedron')
parser.add_argument('-lc', '--lc', type=float, help='Panjang sel satuan kristal ruah jika dianggap kubus.' )
# Setup untuk klaster decahedron
parser.add_argument('-npar', '--parallel', type=int, help='Jumlah atom pada sisi sejajar dengan ekuatorial.' )
parser.add_argument('-nper', '--perpendicular', type=int, help='Jumlah atom pada sisi tegak lurus dengan ekuatorial.' )
opt = parser.parse_args(sys.argv[1:])


opt = parser.parse_args(sys.argv[1:])


if opt.job == 'smi2xyz':
    os.system("echo '{}' > geom.smi".format(opt.input))
    with open('run_babel.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
obabel geom.smi -O geom.xyz --gen3d""",file=fout)
    os.system('sbatch run_babel.sh')
if opt.job == 'mol2xyz' or opt.job == 'pdb2xyz':
    with open('run_babel.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
obabel {} -O geom.xyz""".format(opt.input),file=fout)
        os.system('sbatch run_babel.sh')
if opt.job == 'gen2poscar':
    from cmmde_gen2poscar import gen2poscar
    gen2poscar(opt.input)

if '.mol2' in opt.input and 'charge' in opt.job:
    charges = []
    with open(opt.input,'r') as f:
        lines = f.readlines()
        Natom = int(lines[2].split()[0])
        for i in range(1,Natom+1):
            charges.append(float(lines[7+i].split()[8]))
    charges = np.array(charges)
    print("Muatan total = {}".format(round(sum(charges))))

if opt.job == 'combinexyz':
    xyz = opt.input.split(' ')
    natom = 0
    coord = []
    for i in xyz:
        with open(i, 'r') as f:
            natom+=int(next(f))
            next(f)
            for line in f:
                coord.append(line.strip())
    with open('geom.xyz','w') as f:
        print(natom,file=f)
        print('Complex file generated by CMMDE',file=f)
        for i in coord:
            print(i,file=f)

if opt.job == 'supercell':
    cell = opt.size.split('x')
    filename = opt.input.split('.')[0]
    os.system('aflow --supercell={},{},{} < {} > {}_{}{}{}.vasp'.format(cell[0],cell[1],cell[2],opt.input,filename,cell[0],cell[1],cell[2]))

if opt.job == 'surface':
    hkl = [int(x) for x in str(opt.hkl)]

    bulk = read(opt.input)

    slab = surface(bulk, (hkl[0],hkl[1],hkl[2]), opt.layer, vacuum=opt.vacuum)
    size = opt.size.split('x')
    superslab = slab*(int(size[0]),int(size[1]),1)
    superslab_sorted = sort(superslab)

    write('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]), superslab_sorted)
    # write('slab.vasp', slab*(int(size[0]),int(size[1]),1))
    x = []
    y = []
    z = []
    sym = []
    a1 = 0
    b1 = 0
    c1 = 0
    a2 = 0
    b2 = 0
    c2 = 0
    a3 = 0
    b3 = 0
    c3 = 0
    with open('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),'r') as f:
        Natoms = int(next(f))
        lat = next(f).split('Lattice=')[1].split()
        a1+=float(lat[0].strip('"'))
        a2+=float(lat[1])
        a3+=float(lat[2])
        b1+=float(lat[3])
        b2+=float(lat[4])
        b3+=float(lat[5])
        c1+=float(lat[6])
        c2+=float(lat[7])
        c3+=float(lat[8].strip('"'))
    xyz2gen('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),a1,a2,a3,b1,b2,b3,c1,c2,c3)
    from cmmde_gen2poscar import gen2poscar
    gen2poscar("in.gen")
    os.system("mv in.vasp slab_{}{}{}.vasp".format(hkl[0],hkl[1],hkl[2]))
    

if opt.job == 'adsorb':
    os.system('cmmde_adsorbate.py -s {} -ad {} -all true -dyn {} -height {} -d {}'.format(opt.input,opt.ads,opt.dyn, opt.height, opt.distance))

if opt.job == 'clusadsorb':
    os.system('cmmde_xyz2poscar.rb {} > POSCAR'.format(opt.input))
    os.system('cmmde_adsorbate.py -s POSCAR -ad {} -all true -dyn {} -height {} -d {}'.format(opt.ads,opt.dyn, opt.height, opt.distance))

if opt.job == 'poscar2xyz':
    os.system('cmmde_poscar2gen.rb {} > in.gen'.format(opt.input))
    filename = opt.input.split('.')[0]
    os.system('cmmde_gen2xyz.rb in.gen > {}.xyz'.format(filename))

if opt.job == 'surfinfo':
    moveatoms = []
    frozen = []
    index = 0
    with open(opt.input, 'r') as f:
        next(f)
        next(f)
        next(f)
        next(f)
        next(f)
        next(f)
        next(f)
        next(f)
        next(f)
        for line in f:
            arr = line.split()
            index += 1
            if (arr[3] == "T" and arr[4] == "T" and arr[5] == "T"):
                moveatoms.append(index)
            else:
                frozen.append(index)
    print('Serial Atom-atom beku:')
    for i in frozen:
        print(i, end=' ')
    print('')
    print('Serial Atom-atom aktif:')
    for i in moveatoms:
        print(i, end=' ')
    print('')

if opt.job == 'cluster':
    if (opt.type == "icosahedron"):
        struct = Icosahedron(opt.element,opt.layer, opt.lc)
        struct.write("{}_{}_{}.xyz".format(opt.element,opt.type,opt.layer))
    if (opt.type == "decahedron"):
        struct = Decahedron(opt.element,opt.perpendicular,opt.parallel,0,opt.lc)
        struct.write("{}_{}_{}_{}.xyz".format(opt.element,opt.type,opt.parallel,opt.perpendicular))
    if (opt.type == "tetrahedron"):
        struct = Tetrahedron(opt.element)