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197 lines
7.3 KiB
197 lines
7.3 KiB
#!/usr/bin/env python3 |
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import os |
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import argparse |
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import sys |
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from cmmde_dftb import xyz2gen |
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import numpy as np |
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from cmmde_surface import surface |
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from cmmde_formats import read, write |
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from cmmde_dftb import xyz2gen |
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from cmmde_tools import sort |
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from cmmde_decahedron import Decahedron |
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from cmmde_icosahedron import Icosahedron |
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from cmmde_tetrahedron import Tetrahedron |
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from cmmde_cubic import FaceCenteredCubic, SimpleCubic, BodyCenteredCubic |
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import pymatgen.analysis.adsorption as pa |
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import pymatgen.core.structure as st |
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from pymatgen.core import Structure |
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import argparse |
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import sys |
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import warnings |
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warnings.filterwarnings("ignore") |
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parser = argparse.ArgumentParser(description='CMMDEPRE: Program untuk modifikasi input file') |
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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.') |
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parser.add_argument('-j','--job', type=str, default='sp',help='Jenis pekerjaan yang dilakukan.') |
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parser.add_argument('-s','--size',type=str,help='Ukuran supersel yang ingin dibuat.') |
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parser.add_argument('-hkl','--hkl',type=str,help='Indeks Miller (hkl) permukaan yang akan dibuat.') |
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parser.add_argument('-v', '--vacuum', type=float, default=20, help='Tebal lapisan vakum yang dibuat (dalam angstrom). Default: 20 Angstrom.') |
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parser.add_argument('-n', '--layer', type=int, help='Jumlah lapisan permukaan atau klaster yang akan dibuat.') |
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parser.add_argument('-ads','--ads',type=str, help='File koordinat Cartesian berisikan molekul adsorbat') |
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parser.add_argument('-d','--distance',type=float,default=1.5,help='Jarak adsorbat dari lapisan teratas permukaan (Angstrom). Default: 1.5 Angstrom.') |
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parser.add_argument('-height','--height',type=float,default=2.0, help='Tebal lapisan sisi aktif (Angstrom). Default: 2.0.') |
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parser.add_argument('-dyn','--dyn',type=float,default=3.0, help='Tebal lapisan bawah permukaan yang dibuat kaku (Angstrom). Default: 3.0.') |
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parser.add_argument('-e', '--element', type=str, help='Unsur yang akan dibuat klaster' ) |
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parser.add_argument('-t', '--type', type=str, help='Tipe klaster yang akan dibuat. Pilihan: decahedron dan icosahedron') |
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parser.add_argument('-lc', '--lc', type=float, help='Panjang sel satuan kristal ruah jika dianggap kubus.' ) |
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# Setup untuk klaster decahedron |
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parser.add_argument('-npar', '--parallel', type=int, help='Jumlah atom pada sisi sejajar dengan ekuatorial.' ) |
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parser.add_argument('-nper', '--perpendicular', type=int, help='Jumlah atom pada sisi tegak lurus dengan ekuatorial.' ) |
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opt = parser.parse_args(sys.argv[1:]) |
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opt = parser.parse_args(sys.argv[1:]) |
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if opt.job == 'smi2xyz': |
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os.system("echo '{}' > geom.smi".format(opt.input)) |
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with open('run_babel.sh', 'w') as fout: |
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print("""#!/bin/bash |
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#SBATCH --nodes=1 |
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#SBATCH --ntasks=1 |
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#SBATCH --cpus-per-task=1 |
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#SBATCH --time=168:0:0 |
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export OMP_NUM_THREADS=1 |
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cd $PWD |
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obabel geom.smi -O geom.xyz --gen3d""",file=fout) |
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os.system('sbatch run_babel.sh') |
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if opt.job == 'mol2xyz' or opt.job == 'pdb2xyz': |
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with open('run_babel.sh', 'w') as fout: |
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print("""#!/bin/bash |
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#SBATCH --nodes=1 |
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#SBATCH --ntasks=1 |
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#SBATCH --cpus-per-task=1 |
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#SBATCH --time=168:0:0 |
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export OMP_NUM_THREADS=1 |
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cd $PWD |
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obabel {} -O geom.xyz""".format(opt.input),file=fout) |
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os.system('sbatch run_babel.sh') |
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if opt.job == 'gen2poscar': |
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from cmmde_gen2poscar import gen2poscar |
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gen2poscar(opt.input) |
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if '.mol2' in opt.input and 'charge' in opt.job: |
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charges = [] |
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with open(opt.input,'r') as f: |
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lines = f.readlines() |
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Natom = int(lines[2].split()[0]) |
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for i in range(1,Natom+1): |
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charges.append(float(lines[7+i].split()[8])) |
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charges = np.array(charges) |
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print("Muatan total = {}".format(round(sum(charges)))) |
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if opt.job == 'combinexyz': |
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xyz = opt.input.split(' ') |
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natom = 0 |
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coord = [] |
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for i in xyz: |
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with open(i, '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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coord.append(line.strip()) |
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with open('geom.xyz','w') as f: |
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print(natom,file=f) |
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print('Complex file generated by CMMDE',file=f) |
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for i in coord: |
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print(i,file=f) |
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if opt.job == 'supercell': |
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cell = opt.size.split('x') |
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filename = opt.input.split('.')[0] |
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os.system('aflow --supercell={},{},{} < {} > {}_{}{}{}.vasp'.format(cell[0],cell[1],cell[2],opt.input,filename,cell[0],cell[1],cell[2])) |
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if opt.job == 'surface': |
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hkl = [int(x) for x in str(opt.hkl)] |
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bulk = read(opt.input) |
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slab = surface(bulk, (hkl[0],hkl[1],hkl[2]), opt.layer, vacuum=opt.vacuum) |
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size = opt.size.split('x') |
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superslab = slab*(int(size[0]),int(size[1]),1) |
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superslab_sorted = sort(superslab) |
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write('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]), superslab_sorted) |
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# write('slab.vasp', slab*(int(size[0]),int(size[1]),1)) |
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x = [] |
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y = [] |
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z = [] |
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sym = [] |
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a1 = 0 |
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b1 = 0 |
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c1 = 0 |
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a2 = 0 |
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b2 = 0 |
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c2 = 0 |
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a3 = 0 |
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b3 = 0 |
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c3 = 0 |
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with open('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),'r') as f: |
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Natoms = int(next(f)) |
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lat = next(f).split('Lattice=')[1].split() |
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a1+=float(lat[0].strip('"')) |
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a2+=float(lat[1]) |
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a3+=float(lat[2]) |
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b1+=float(lat[3]) |
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b2+=float(lat[4]) |
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b3+=float(lat[5]) |
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c1+=float(lat[6]) |
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c2+=float(lat[7]) |
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c3+=float(lat[8].strip('"')) |
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xyz2gen('slab_{}{}{}.xyz'.format(hkl[0],hkl[1],hkl[2]),a1,a2,a3,b1,b2,b3,c1,c2,c3) |
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from cmmde_gen2poscar import gen2poscar |
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gen2poscar("in.gen") |
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os.system("mv in.vasp slab_{}{}{}.vasp".format(hkl[0],hkl[1],hkl[2])) |
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if opt.job == 'adsorb': |
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os.system('cmmde_adsorbate.py -s {} -ad {} -all true -dyn {} -height {} -d {}'.format(opt.input,opt.ads,opt.dyn, opt.height, opt.distance)) |
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if opt.job == 'clusadsorb': |
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os.system('cmmde_xyz2poscar.rb {} > POSCAR'.format(opt.input)) |
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os.system('cmmde_adsorbate.py -s POSCAR -ad {} -all true -dyn {} -height {} -d {}'.format(opt.ads,opt.dyn, opt.height, opt.distance)) |
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if opt.job == 'poscar2xyz': |
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os.system('cmmde_poscar2gen.rb {} > in.gen'.format(opt.input)) |
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filename = opt.input.split('.')[0] |
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os.system('cmmde_gen2xyz.rb in.gen > {}.xyz'.format(filename)) |
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if opt.job == 'surfinfo': |
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moveatoms = [] |
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frozen = [] |
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index = 0 |
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with open(opt.input, 'r') as f: |
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next(f) |
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next(f) |
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next(f) |
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next(f) |
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next(f) |
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next(f) |
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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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index += 1 |
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if (arr[3] == "T" and arr[4] == "T" and arr[5] == "T"): |
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moveatoms.append(index) |
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else: |
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frozen.append(index) |
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print('Serial Atom-atom beku:') |
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for i in frozen: |
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print(i, end=' ') |
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print('') |
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print('Serial Atom-atom aktif:') |
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for i in moveatoms: |
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print(i, end=' ') |
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print('') |
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if opt.job == 'cluster': |
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if (opt.type == "icosahedron"): |
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struct = Icosahedron(opt.element,opt.layer, opt.lc) |
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struct.write("{}_{}_{}.xyz".format(opt.element,opt.type,opt.layer)) |
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if (opt.type == "decahedron"): |
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struct = Decahedron(opt.element,opt.perpendicular,opt.parallel,0,opt.lc) |
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struct.write("{}_{}_{}_{}.xyz".format(opt.element,opt.type,opt.parallel,opt.perpendicular)) |
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if (opt.type == "tetrahedron"): |
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struct = Tetrahedron(opt.element)
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