if __name__ == "__main__": args= docopt(__doc__) rcut= float(args['--cutoff']) pmddir= args['--pmddir'] execname= args['--exec'] infname= args['PMDFILE'] plot= args['--plot'] #print(args) sys0= NAPSystem() sys0.read_pmd(infname) sys0.write_POSCAR() print(' POSCAR was written.') natm0= sys0.num_atoms() h0=np.zeros((3,3)) h0[0]= sys0.a1 *sys0.alc h0[1]= sys0.a2 *sys0.alc h0[2]= sys0.a3 *sys0.alc n1,n2,n3= calc_extention_ratio(h0,rcut) print("n1,n2,n3 = {0:d} {1:d} {2:d}".format(n1,n2,n3)) # Make displaced POSCARS via phonopy os.system("phonopy -d --dim=\"{0:d} {1:d} {2:d}\"".format(n1,n2,n3)) with open('disp.yaml','r') as f: disp= yaml.load(f) # Make directories for the calculation of those POSCARS poscars= glob.glob("POSCAR-[0-9]??")
help="path to the pmd executable.") (options, args) = parser.parse_args() displace = options.displace print ' displacement = ', displace, ' Ang.' rcut = options.rcut print ' rcut = ', rcut, ' Ang.' pmdexec = options.pmdexec infname = args[0] sys0 = NAPSystem() sys0.read_pmd(infname) sys0.write_POSCAR() print ' POSCAR was written.' natm0 = sys0.num_atoms() h0 = np.zeros((3, 3)) h0[0] = sys0.a1 * sys0.alc h0[1] = sys0.a2 * sys0.alc h0[2] = sys0.a3 * sys0.alc n1, n2, n3 = calc_extention_ratio(h0, rcut) r1 = 2 * n1 + 1 r2 = 2 * n2 + 1 r3 = 2 * n3 + 1 print ' num of cells in each axis=', r1, r2, r3 print ' num of atoms in extended system=', natm0 * r1 * r2 * r3 sysext = NAPSystem() sysext.set_lattice(sys0.alc, np.multiply(sys0.a1, r1),
help="path to the pmd executable.") (options,args)= parser.parse_args() displace= options.displace print ' displacement = ',displace,' Ang.' rcut= options.rcut print ' rcut = ',rcut,' Ang.' pmdexec= options.pmdexec infname= args[0] sys0= NAPSystem() sys0.read_pmd(infname) sys0.write_POSCAR() print ' POSCAR was written.' natm0= sys0.num_atoms() h0=np.zeros((3,3)) h0[0]= sys0.a1 *sys0.alc h0[1]= sys0.a2 *sys0.alc h0[2]= sys0.a3 *sys0.alc n1,n2,n3= calc_extention_ratio(h0,rcut) r1= 2*n1+1 r2= 2*n2+1 r3= 2*n3+1 print ' num of cells in each axis=',r1,r2,r3 print ' num of atoms in extended system=',natm0*r1*r2*r3 sysext= NAPSystem() sysext.set_lattice( sys0.alc