howto.txt

conda create -n genome
conda activate genome
conda install -c conda-forge pymatgen
conda install -c psi4 -c conda-forge psi4

###################### test
#python
#>>> import pymatgen.io.gaussian
#>>> gau=pymatgen.io.gaussian.GaussianInput.from_file('1.com')
#>>> gau.basis_set
#'DEF2TZVP'
#>>> gau.charge
#-1
#>>> gau.spin_multiplicity
#1
#>>> gau.functional
#'PBEPBE'
#
#mol=pymatgen.core.Molecule(gau.molecule.species,gau.molecule.cart_coords)
#import pymatgen.io.xyz
#xyz=pymatgen.io.xyz.XYZ(mol)
#xyz.write_file("gau.xyz")
##########################
#
#def readXYZ(file):
#    f = open(file, "r")
#    lines = f.readlines()
#    filelength = len(lines)
#    progress = 0
#    geomcount = 0
#    geom = []
#    while progress < filelength:
#        tmpgeom = ""
#        length = int(lines[progress])+2
#        rangestart = progress
#        rangeend = progress + length
#        for i in range(rangestart, rangeend):
#            tmpgeom = tmpgeom + lines[i]
#        geom = geom + [tmpgeom]
#        geomcount = geomcount + 1
#        progress = progress + length
#    f.close()
#    return(''.join((geom)))
#
#
#geom = readXYZ("gau.xyz")
#psi4geom = psi4.geometry(geom)
#psi4.set_memory('1024 MB')
#psi4.set_options({'basis':gau.basis_set})
#psi4.set_options({'pcm': 'true'})
#psi4geom.set_molecular_charge(gau.charge)
#psi4geom.set_multiplicity(gau.spin_multiplicity)
#psi4.set_options({'basis': gau.basis_set,
#                   'scf_type': 'pk',
#                   'e_convergence': 1e-8,
#                   'd_convergence': 1e-8})
#e=psi4.energy('pbe')
#print(e)
#################################