QuantumPackage/bin/qp_convert_output_to_ezfio

#!/usr/bin/env python3
"""
convert output of GAMESS/GAU$$IAN to ezfio

Usage:
    qp_convert_output_to_ezfio [-o EZFIO_DIR] FILE

Options:
    -o --output=EZFIO_DIR    Produced directory
                             by default is FILE.ezfio

"""

import sys
import os
from functools import reduce
from ezfio import ezfio
from docopt import docopt


try:
    QP_ROOT = os.environ["QP_ROOT"]
    QP_EZFIO = os.environ["QP_EZFIO"]
except KeyError:
    print("Error: QP_ROOT environment variable not found.")
    sys.exit(1)
else:
    sys.path = [QP_EZFIO + "/Python",
                QP_ROOT + "/install/resultsFile",
                QP_ROOT + "/install",
                QP_ROOT + "/scripts"] + sys.path

from resultsFile import *
try:
    from resultsFile import *
except:
    print("Error: resultsFile Python library not installed")
    sys.exit(1)




def write_ezfio(res, filename):

    res.clean_uncontractions()
    ezfio.set_file(filename)

    #  _
    # |_ |  _   _ _|_ ._ _  ._   _
    # |_ | (/_ (_  |_ | (_) | | _>
    #
    print("Electrons\t...\t", end=' ')
    ezfio.set_electrons_elec_alpha_num(res.num_alpha)
    ezfio.set_electrons_elec_beta_num(res.num_beta)
    print("OK")

    #
    # |\ |      _ |  _  o
    # | \| |_| (_ | (/_ |
    #

    print("Nuclei\t\t...\t", end=' ')
    # ~#~#~#~ #
    # I n i t #
    # ~#~#~#~ #

    charge = []
    coord_x = []
    coord_y = []
    coord_z = []

    # ~#~#~#~#~#~#~ #
    # P a r s i n g #
    # ~#~#~#~#~#~#~ #

    for a in res.geometry:
        charge.append(a.charge)
        if res.units == 'BOHR':
            coord_x.append(a.coord[0])
            coord_y.append(a.coord[1])
            coord_z.append(a.coord[2])
        else:
            coord_x.append(a.coord[0] / a0)
            coord_y.append(a.coord[1] / a0)
            coord_z.append(a.coord[2] / a0)


    # ~#~#~#~#~ #
    # W r i t e #
    # ~#~#~#~#~ #

    ezfio.set_nuclei_nucl_num(len(res.geometry))
    ezfio.set_nuclei_nucl_charge(charge)

    # Transformt H1 into H
    import re
    p = re.compile(r'(\d*)$')
    label = [p.sub("", x.name).capitalize() for x in res.geometry]
    ezfio.set_nuclei_nucl_label(label)

    ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
    print("OK")

    #                 _
    #   /\   _   _   |_)  _.  _ o  _
    #  /--\ (_) _>   |_) (_| _> | _>
    #

    print("AOS\t\t...\t", end=' ')
    # ~#~#~#~ #
    # I n i t #
    # ~#~#~#~ #

    at = []
    num_prim = []
    power_x = []
    power_y = []
    power_z = []
    coefficient = []
    exponent = []

    res.convert_to_cartesian()

    # ~#~#~#~#~#~#~ #
    # P a r s i n g #
    # ~#~#~#~#~#~#~ #

    for b in res.basis:
        c = b.center
        for i, atom in enumerate(res.geometry):
            if atom.coord == c:
                at.append(i + 1)
        num_prim.append(len(b.prim))
        s = b.sym
        power_x.append(str.count(s, "x"))
        power_y.append(str.count(s, "y"))
        power_z.append(str.count(s, "z"))
        coefficient.append(b.coef)
        exponent.append([p.expo for p in b.prim])

    # ~#~#~#~#~ #
    # W r i t e #
    # ~#~#~#~#~ #

    ezfio.set_ao_basis_ao_num(len(res.basis))
    ezfio.set_ao_basis_ao_nucl(at)
    ezfio.set_ao_basis_ao_prim_num(num_prim)
    ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)

    # ~#~#~#~#~#~#~ #
    # P a r s i n g #
    # ~#~#~#~#~#~#~ #

    prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()

    for i in range(len(res.basis)):
        coefficient[
            i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
        exponent[i] += [0. for j in range(len(exponent[i]), prim_num_max)]

    coefficient = reduce(lambda x, y: x + y, coefficient, [])
    exponent = reduce(lambda x, y: x + y, exponent, [])

    coef = []
    expo = []
    for i in range(prim_num_max):
        for j in range(i, len(coefficient), prim_num_max):
            coef.append(coefficient[j])
            expo.append(exponent[j])

    # ~#~#~#~#~ #
    # W r i t e #
    # ~#~#~#~#~ #

    ezfio.set_ao_basis_ao_coef(coef)
    ezfio.set_ao_basis_ao_expo(expo)
    ezfio.set_ao_basis_ao_basis("Read by resultsFile")

    print("OK")

    #   _
    #  |_)  _.  _ o  _
    #  |_) (_| _> | _>
    #

    print("Basis\t\t...\t", end=' ')
    # ~#~#~#~ #
    # I n i t #
    # ~#~#~#~ #

    coefficient = []
    exponent = []

    # ~#~#~#~#~#~#~ #
    # P a r s i n g #
    # ~#~#~#~#~#~#~ #

    nbasis = 0
    nucl_center = []
    curr_center = -1
    nucl_shell_num = []
    ang_mom = []
    nshell = 0
    shell_prim_index = [1]
    shell_prim_num = []
    for b in res.basis:
        s = b.sym
        if str.count(s, "y") + str.count(s, "x") == 0:
          c = b.center
          nshell += 1
          if c != curr_center:
             curr_center = c
             nucl_center.append(nbasis+1)
             nucl_shell_num.append(nshell)
             nshell = 0
          nbasis += 1
          coefficient += b.coef[:len(b.prim)]
          exponent += [p.expo for p in b.prim]
          ang_mom.append(str.count(s, "z"))
          shell_prim_index.append(len(exponent)+1)
          shell_prim_num.append(len(b.prim))

    nucl_shell_num.append(nshell+1)
    nucl_shell_num = nucl_shell_num[1:]

    # ~#~#~#~#~ #
    # W r i t e #
    # ~#~#~#~#~ #

    ezfio.set_basis_basis("Read from ResultsFile")
    ezfio.set_basis_basis_nucleus_index(nucl_center)
    ezfio.set_basis_prim_num(len(coefficient))
    ezfio.set_basis_shell_num(len(ang_mom))
    ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
    ezfio.set_basis_prim_coef(coefficient)
    ezfio.set_basis_prim_expo(exponent)
    ezfio.set_basis_shell_ang_mom(ang_mom)
    ezfio.set_basis_shell_prim_num(shell_prim_num)
    ezfio.set_basis_shell_prim_index(shell_prim_index)

    print("OK")

    #                _
    # |\/|  _   _   |_)  _.  _ o  _
    # |  | (_) _>   |_) (_| _> | _>
    #

    print("MOS\t\t...\t", end=' ')
    # ~#~#~#~ #
    # I n i t #
    # ~#~#~#~ #

    MoTag = res.determinants_mo_type
    ezfio.set_mo_basis_mo_label('Orthonormalized')
    MO_type = MoTag
    allMOs = res.mo_sets[MO_type]

    # ~#~#~#~#~#~#~ #
    # P a r s i n g #
    # ~#~#~#~#~#~#~ #

    try:
        closed = [(allMOs[i].eigenvalue, i) for i in res.closed_mos]
        active = [(allMOs[i].eigenvalue, i) for i in res.active_mos]
        virtual = [(allMOs[i].eigenvalue, i) for i in res.virtual_mos]
    except:
        closed = []
        virtual = []
        active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]

    closed = [x[1] for x in closed]
    active = [x[1] for x in active]
    virtual = [x[1] for x in virtual]
    MOindices = closed + active + virtual

    MOs = []
    for i in MOindices:
        MOs.append(allMOs[i])

    mo_num = len(MOs)
    while len(MOindices) < mo_num:
        MOindices.append(len(MOindices))

    MOmap = list(MOindices)
    for i in range(len(MOindices)):
        MOmap[i] = MOindices.index(i)

    energies = []
    for i in range(mo_num):
        energies.append(MOs[i].eigenvalue)

    OccNum = []
    if res.occ_num is not None:
        for i in MOindices:
            OccNum.append(res.occ_num[MO_type][i])
    else:
        for i in range(res.num_beta):
            OccNum.append(2.)
        for i in range(res.num_beta,res.num_alpha):
            OccNum.append(1.)

    while len(OccNum) < mo_num:
            OccNum.append(0.)

    MoMatrix = []
    sym0 = [i.sym for i in res.mo_sets[MO_type]]
    sym = [i.sym for i in res.mo_sets[MO_type]]
    for i in range(len(sym)):
        sym[MOmap[i]] = sym0[i]

    MoMatrix = []
    for i in range(len(MOs)):
        m = MOs[i]
        for coef in m.vector:
            MoMatrix.append(coef)

    while len(MoMatrix) < len(MOs[0].vector)**2:
        MoMatrix.append(0.)

    # ~#~#~#~#~ #
    # W r i t e #
    # ~#~#~#~#~ #

    ezfio.set_mo_basis_mo_num(mo_num)
    ezfio.set_mo_basis_mo_coef(MoMatrix)
    ezfio.set_mo_basis_mo_occ(OccNum)

    print("OK")


    print("Pseudos\t\t...\t", end=' ')
    try:
        lmax = 0
        nucl_charge_remove = []
        klocmax = 0
        kmax = 0
        nucl_num = len(res.geometry)
        for ecp in res.pseudo:
            lmax_local = ecp['lmax']
            lmax = max(lmax_local, lmax)
            nucl_charge_remove.append(ecp['zcore'])
            klocmax = max(klocmax, len(ecp[str(lmax_local)]))
            for l in range(lmax_local):
                kmax = max(kmax, len(ecp[str(l)]))
        lmax = lmax-1
        ezfio.set_pseudo_pseudo_lmax(lmax)
        ezfio.set_pseudo_nucl_charge_remove(nucl_charge_remove)
        ezfio.set_pseudo_pseudo_klocmax(klocmax)
        ezfio.set_pseudo_pseudo_kmax(kmax)
        pseudo_n_k = [[0  for _ in range(nucl_num)] for _ in range(klocmax)]
        pseudo_v_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
        pseudo_dz_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
        pseudo_n_kl = [[[0  for _ in range(nucl_num)] for _ in range(kmax)] for _ in range(lmax+1)]
        pseudo_v_kl = [[[0. for _ in range(nucl_num)] for _ in range(kmax)] for _ in range(lmax+1)]
        pseudo_dz_kl = [[[0. for _ in range(nucl_num)] for _ in range(kmax)] for _ in range(lmax+1)]
        for ecp in res.pseudo:
            lmax_local = ecp['lmax']
            klocmax = len(ecp[str(lmax_local)])
            atom = ecp['atom']-1
            for kloc in range(klocmax):
                try:
                    v, n, dz = ecp[str(lmax_local)][kloc]
                    pseudo_n_k[kloc][atom] = n-2
                    pseudo_v_k[kloc][atom] = v
                    pseudo_dz_k[kloc][atom] = dz
                except:
                    pass
            for l in range(lmax_local):
                for k in range(kmax):
                    try:
                        v, n, dz = ecp[str(l)][k]
                        pseudo_n_kl[l][k][atom] = n-2
                        pseudo_v_kl[l][k][atom] = v
                        pseudo_dz_kl[l][k][atom] = dz
                    except:
                        pass
        ezfio.set_pseudo_pseudo_n_k(pseudo_n_k)
        ezfio.set_pseudo_pseudo_v_k(pseudo_v_k)
        ezfio.set_pseudo_pseudo_dz_k(pseudo_dz_k)
        ezfio.set_pseudo_pseudo_n_kl(pseudo_n_kl)
        ezfio.set_pseudo_pseudo_v_kl(pseudo_v_kl)
        ezfio.set_pseudo_pseudo_dz_kl(pseudo_dz_kl)

        n_alpha = res.num_alpha
        n_beta = res.num_beta
        for i in range(nucl_num):
            charge[i] -= nucl_charge_remove[i]
            n_alpha -= nucl_charge_remove[i]/2
            n_beta -= nucl_charge_remove[i]/2
        ezfio.set_nuclei_nucl_charge(charge)
        ezfio.set_electrons_elec_alpha_num(n_alpha)
        ezfio.set_electrons_elec_beta_num(n_beta)

    except:
        ezfio.set_pseudo_do_pseudo(False)
    else:
        ezfio.set_pseudo_do_pseudo(True)

    print("OK")




def get_full_path(file_path):
    file_path = os.path.expanduser(file_path)
    file_path = os.path.expandvars(file_path)
#    file_path = os.path.abspath(file_path)
    return file_path


if __name__ == '__main__':
    ARGUMENTS = docopt(__doc__)

    FILE = get_full_path(ARGUMENTS['FILE'])

    if ARGUMENTS["--output"]:
        EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
    else:
        EZFIO_FILE = "{0}.ezfio".format(FILE)

    try:
        RES_FILE = getFile(FILE)
    except:
        raise
    else:
        print(FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0])

    write_ezfio(RES_FILE, EZFIO_FILE)
    sys.stdout.flush()
    if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
        print("""Warning: You need to run

         qp run save_ortho_mos

to be sure your MOs will be orthogonal, which is not the case when
the MOs are read from output files (not enough precision in output).""")