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a/src/trexio_tools/converters/convert_from.py +++ b/src/trexio_tools/converters/convert_from.py @@ -8,6 +8,7 @@ from trexio_tools.group_tools import determinant as trexio_det from .pyscf_to_trexio import pyscf_to_trexio as run_pyscf +from .orca_to_trexio import orca_to_trexio as run_orca try: import trexio @@ -767,6 +768,9 @@ def run(trexio_filename, filename, filetype, back_end, motype=None): elif filetype.lower() == "pyscf": back_end_str = "text" if back_end==trexio.TREXIO_TEXT else "hdf5" run_pyscf(trexio_filename=trexio_filename, pyscf_checkfile=filename, back_end=back_end_str) + elif filetype.lower() == "orca": + back_end_str = "text" if back_end==trexio.TREXIO_TEXT else "hdf5" + run_orca(filename=trexio_filename, orca_json=filename, back_end=back_end_str) elif filetype.lower() == "fcidump": raise NotImplementedError(f"Conversion from {filetype} to TREXIO is not supported.") #run_fcidump(trexio_file, filename) diff --git a/src/trexio_tools/converters/orca_to_trexio.py b/src/trexio_tools/converters/orca_to_trexio.py new file mode 100644 index 0000000..254d374 --- /dev/null +++ b/src/trexio_tools/converters/orca_to_trexio.py @@ -0,0 +1,616 @@ +def orca_to_trexio( + orca_json: str = "orca.json", + filename: str = "trexio.hdf5", + back_end: str = "hdf5" +): + # load python packages + import os + import json + import numpy as np + import scipy.special + + # ## ORCA -> TREX-IO + # - how to install trexio + # - pip install trexio + + # import trexio + import trexio + + # Logger + from logging import getLogger + logger = getLogger("orca-trexio").getChild(__name__) + + logger.info(f"orca_json = {orca_json}") + logger.info(f"trexio_filename = {filename}") + logger.info("Conversion starts...") + + + with open(orca_json, 'r') as f: + data = json.load(f) + + import os + try: + os.remove(filename) + except: + print(f"File {filename} does not exist.") + + trexio_file = trexio.File(filename, mode='w', back_end=trexio.TREXIO_HDF5) + + natoms = len(data["Molecule"]["Atoms"]) + #print(f"Natoms={natoms}") + coord = [] + chemical_symbol_list = [] + atom_charges_list = [] + ecp_charge_list = [] + ecp_charge = 0 + elec_num = 0 + total_charge = data["Molecule"]["Charge"] + multiplicity = data["Molecule"]["Multiplicity"] + orbital_labels = data["Molecule"]["MolecularOrbitals"]["OrbitalLabels"] + has_ecp = [] + for i in range(natoms): + atom = data["Molecule"]["Atoms"][i] + coord.append(atom["Coords"]) + chemical_symbol_list.append(atom["ElementLabel"]) + elec_num += atom["NuclearCharge"] + try: + atom["ECPs"] + has_ecp.append(True) + N_core = atom["ECPs"]["N_core"] + ecp_charge_list.append(N_core) + ecp_charge += N_core + except: + has_ecp.append(False) + atom_charges_list.append(atom["NuclearCharge"]) + elec_num = elec_num - total_charge - ecp_charge + + # Check coordinate type + coord_type = data["Molecule"]["CoordinateUnits"] + coord = np.array(coord) + if coord_type == "Angs": + # Convert to Bohrs + for i in range(natoms): + coord[i] = 1.8897259886 * coord[i] + + # Assuming multiplicity = (elec_up - elec_dn) + 1 + electron_up_num = int((elec_num + multiplicity - 1)//2) + electron_dn_num = int(elec_num - electron_up_num) + + ########################################## + # Structure info + ########################################## + trexio.write_electron_up_num(trexio_file, electron_up_num) + trexio.write_electron_dn_num(trexio_file, electron_dn_num) + trexio.write_nucleus_num(trexio_file, len(coord)) + trexio.write_nucleus_coord(trexio_file, coord) + trexio.write_nucleus_charge(trexio_file, atom_charges_list) + trexio.write_nucleus_label(trexio_file, chemical_symbol_list) + ########################################## + # basis set info + ########################################## + # check the orders of the spherical atomic basis in orca!! + # L, ml + # pz, px, py = (0,+1,-1) + # dz2, dxz, dyz, dx2y2, dxy = (0,+1,-1,+2,-2) + # gto.spheric_labels(mol, fmt="%d, %s, %s, %s") + # ORCA ordering -- TREXIO ordering + # ----------------------------------------------------- + # for s -> s -- trexio: (0) + # for p -> pz, px, py -- trexio: (-1,0,1) + # for d -> dz2, dxz, dyz, dx2y2, dxy -- trexio: (-2, -1, 0, 1, 2) + # for l -> m=(0 -1 +1 -2 +2 ... -l +l) -- (-l, ..., 0, ..., +l) + nucleus_num = natoms + atom_nshells = [] + atom_shell_ids = [] + bas_angular = [] + bas_nprim = [] + bas_ctr_coeff = [] + bas_exp = [] + basis_shell_num = 0 + for i in range(nucleus_num): + atom = data["Molecule"]["Atoms"][i] + nshells = len(atom["Basis"]) + atom_nshells.append(nshells) + shell_ids = [] + for k in range(nshells): + shell_ids.append(i) + bas_angular.append(atom["Basis"][k]["Shell"]) + bas_nprim.append(len(atom["Basis"][k]["Exponents"])) + bas_exp.append(atom["Basis"][k]["Exponents"]) + bas_ctr_coeff.append(atom["Basis"][k]["Coefficients"]) + atom_shell_ids.append(shell_ids) + + try: + S_matrix = np.array(data["Molecule"]["S-Matrix"]) + T_matrix = np.array(data["Molecule"]["T-Matrix"]) + H_matrix = np.array(data["Molecule"]["H-Matrix"]) + readS = True + except: + readS = False + dict_ang_mom = dict() + dict_ang_mom['s'] = 0 + dict_ang_mom['p'] = 1 + dict_ang_mom['d'] = 2 + dict_ang_mom['f'] = 3 + dict_ang_mom['g'] = 4 + dict_ang_mom['h'] = 5 + dict_ang_mom['i'] = 6 + + basis_type = "Gaussian" # thanks anthony! + basis_shell_num = int(np.sum([atom_nshells[i] for i in range(nucleus_num)])) + nucleus_index = [] + for i in range(nucleus_num): + for _ in range(len(atom_shell_ids[i])): + nucleus_index.append(i) + shell_ang_mom = [dict_ang_mom[bas_angular[i]] for i in range(basis_shell_num)] + basis_prim_num = int(np.sum([bas_nprim[i] for i in range(basis_shell_num)])) + + basis_exponent = [] + basis_coefficient = [] + for i in range(basis_shell_num): + for bas_exp_i in bas_exp[i]: + basis_exponent.append(float(bas_exp_i)) + for bas_ctr_coeff_i in bas_ctr_coeff[i]: + basis_coefficient.append(float(bas_ctr_coeff_i)) + + basis_shell_index = [] + for i in range(basis_shell_num): + for _ in range(len(bas_exp[i])): + basis_shell_index.append(i) + + # normalization factors + basis_shell_factor = [1.0 for _ in range(basis_shell_num)] # 1.0 in ORCA + + def gto_norm(alpha, ax, ay, az): + val = ((alpha + alpha)/np.pi)**(3/4)*((4*alpha)**((ax + ay + az)/2))/((scipy.special.factorial2(2*ax - 1) * \ + scipy.special.factorial2(2*ay - 1) * \ + scipy.special.factorial2(2*az - 1)**(1/2))) + return(val) + + # gto_norm(l, expnt) => l is angmom, expnt is exponent + # Note!! Here, the normalization factor of the spherical part + # are not included. The normalization factor is computed according + # to Eq.8 of the following paper + # H.B.S and M.J.F, Int. J. Quant. Chem., 54(1995), 83-87. + basis_prim_factor = [] + for prim_i in range(basis_prim_num): + coeff = basis_coefficient[prim_i] + expnt = basis_exponent[prim_i] + l_num = shell_ang_mom[basis_shell_index[prim_i]] + basis_prim_factor.append( + gto_norm(expnt, l_num, 0, 0) + ) + + ########################################## + # basis set info + ########################################## + trexio.write_basis_type(trexio_file, basis_type) # + trexio.write_basis_shell_num(trexio_file, basis_shell_num) # + trexio.write_basis_prim_num(trexio_file, basis_prim_num) # + trexio.write_basis_nucleus_index(trexio_file, nucleus_index) # + trexio.write_basis_shell_ang_mom(trexio_file, shell_ang_mom) # + trexio.write_basis_shell_factor(trexio_file, basis_shell_factor) # + trexio.write_basis_shell_index(trexio_file, basis_shell_index) # + trexio.write_basis_exponent(trexio_file, basis_exponent) # + trexio.write_basis_coefficient(trexio_file, basis_coefficient) # + trexio.write_basis_prim_factor(trexio_file, basis_prim_factor) # + ########################################## + # ao info + ########################################## + # to be fixed!! for Victor case mol.cart is false, but the basis seems cartesian... + cart = False + if cart: + ao_cartesian = 1 + else: + ao_cartesian = 0 # spherical basis representation + ao_shell = [] + for i, ang_mom in enumerate(shell_ang_mom): + for _ in range(2 * ang_mom + 1): + ao_shell.append(i) + ao_num = len(ao_shell) + + # 1.0 in pyscf (because spherical) + ao_normalization = [1.0 for _ in range(ao_num)] + + ########################################## + # ao info + ########################################## + trexio.write_ao_cartesian(trexio_file, ao_cartesian) # + trexio.write_ao_num(trexio_file, ao_num) # + trexio.write_ao_shell(trexio_file, ao_shell) # + trexio.write_ao_normalization(trexio_file, ao_normalization) # + if readS: + trexio.write_ao_1e_int_overlap(trexio_file, S_matrix) + trexio.write_ao_1e_int_kinetic(trexio_file, T_matrix) + trexio.write_ao_1e_int_potential_n_e(trexio_file, H_matrix) + + ########################################## + # mo info + ########################################## + mo_type = "MO" + + mo_occupation_read = [] + mo_energy_read = [] + mo_coeff_read = [] + for k in data['Molecule']['MolecularOrbitals']['MOs']: + mo_occupation_read.append(k['Occupancy']) + mo_coeff_read.append(k['MOCoefficients']) + mo_energy_read.append(k['OrbitalEnergy']) + + # check if the pySCF calculation is Restricted or Unrestricted + # Restricted -> RHF,RKS,ROHF,OROKS + # Unrestricted -> UHF,UKS + + if len(mo_energy_read) == 2: + if isinstance(mo_energy_read[0], float): + spin_restricted = True + else: + spin_restricted = False + else: + spin_restricted = True + + # the followins are given to TREXIO file lager if spin_restricted == False, + mo_coefficient_all = [] + mo_occupation_all = [] + mo_energy_all = [] + mo_spin_all = [] + + # mo read part starts both for alpha and beta spins + for ns, spin in enumerate([0, 1]): + + if spin_restricted: + mo_occupation = mo_occupation_read + mo_energy = mo_energy_read + mo_coeff = mo_coeff_read + if spin == 1: # 0 is alpha(up), 1 is beta(dn) + logger.info("This is spin-restricted calculation.") + logger.info("Skip the MO conversion step for beta MOs.") + break + else: + logger.info( + f"MO conversion step for {spin}-spin MOs. 0 is alpha(up), 1 is beta(dn)." + ) + mo_occupation = mo_occupation_read[ns] + mo_energy = mo_energy_read[ns] + mo_coeff = mo_coeff_read[ns] + + mo_num = len(mo_coeff[0]) + + mo_spin_all += [spin for _ in range(mo_num)] + + + logger.debug(mo_num) + logger.debug(len(mo_coeff)) + logger.debug(mo_occupation) + logger.debug(mo_energy) + # logger.info(mo_coeff) + + # check if MOs are descending order with respect to "mo occ" + # this is usually true, but not always true for + # RO (restricted open-shell) calculations. + order_bool = all( + [ + True if mo_occupation[i] >= mo_occupation[i + 1] else False + for i in range(len(mo_occupation) - 1) + ] + ) + logger.info(f"MO occupations are in the descending order ? -> {order_bool}") + if not order_bool: + logger.warning("MO occupations are not in the descending order!!") + logger.warning("RO (restricted open-shell) calculations?") + logger.warning("Reordering MOs...") + # reordering MOs. + # descending order (mo occ) + reo_moocc_index = np.argsort(mo_occupation)[::-1] + mo_occupation_o = [mo_occupation[l_num] for l_num in reo_moocc_index] + mo_energy_o = [mo_energy[l_num] for l_num in reo_moocc_index] + mo_coeff_o = [mo_coeff[l_num] for l_num in reo_moocc_index] + # descending order (mo energy) + mo_coeff = [] + mo_occupation = [] + mo_energy = [] + set_mo_occupation = sorted(list(set(mo_occupation_o)), reverse=True) + for mo_occ in set_mo_occupation: + mo_re_index = [ + i for i, mo in enumerate(mo_occupation_o) if mo == mo_occ + ] + mo_occupation_t = [mo_occupation_o[l_num] for l_num in mo_re_index] + mo_energy_t = [mo_energy_o[l_num] for l_num in mo_re_index] + mo_coeff_t = [mo_coeff_o[l_num] for l_num in mo_re_index] + reo_ene_index = np.argsort(mo_energy_t) + mo_occupation += [mo_occupation_t[l_num] for l_num in reo_ene_index] + mo_energy += [mo_energy_t[l_num] for l_num in reo_ene_index] + mo_coeff += [mo_coeff_t[l_num] for l_num in reo_ene_index] + + logger.debug("--mo_num--") + logger.debug(mo_num) + logger.debug("--len(mo_coeff)--") + logger.debug(len(mo_coeff)) + logger.debug("--mo_occupation--") + logger.debug(mo_occupation) + logger.debug("--mo_energy--") + logger.debug(mo_energy) + # logger.debug(mo_coeff) + + # saved mo_occ and mo_energy + mo_occupation_all += list(mo_occupation) + mo_energy_all += list(mo_energy) + + # permutation_matrix = [] # for ao and mo swaps, used later + + # molecular coefficient reordering + # TREX-IO employs (m=-l,..., 0, ..., +l) for spherical basis + mo_coefficient = [] + + for mo_i in range(mo_num): + mo = mo_coeff[mo_i] + mo_coeff_buffer = [] + + perm_list = [] + perm_n = 0 + for ao_i, ao_c in enumerate(mo): + + # initialization + if ao_i == 0: + mo_coeff_for_reord = [] + current_ang_mom = -1 + + # read ang_mom (i.e., angular momentum of the shell) + bas_i = ao_shell[ao_i] + ang_mom = shell_ang_mom[bas_i] + + previous_ang_mom = current_ang_mom + current_ang_mom = ang_mom + + # set multiplicity + multiplicity = 2 * ang_mom + 1 + # print(f"multiplicity = {multiplicity}") + + # check if the buffer is null, when ang_mom changes + if previous_ang_mom != current_ang_mom: + assert len(mo_coeff_for_reord) == 0 + + if current_ang_mom == 0: # s shell + # print("s shell/no permutation is needed.") + # print("(pyscf notation): s(l=0)") + # print("(trexio notation): s(l=0)") + reorder_index = [0] + + elif current_ang_mom == 1: # p shell + + # print("p shell/permutation is needed.") + # print("(pyscf notation): px(l=+1), py(l=-1), pz(l=0)") + # print("(trexio notation): pz(l=0), px(l=+1), py(l=-1)") + reorder_index = [2, 0, 1] + + elif current_ang_mom >= 2: # > d shell + + # print("> d shell/permutation is needed.") + # print( + # "(pyscf) e.g., f3,-3(l=-3), f3,-2(l=-2), f3,-1(l=-1), \ + # f3,0(l=0), f3,+1(l=+1), f3,+2(l=+2), f3,+3(l=+3)" + # ) + # print( + # "(trexio) e.g, f3,0(l=0), f3,+1(l=+1), f3,-1(l=-1), \ + # f3,+2(l=+2), f3,-2(l=-2), f3,+3(l=+3), f3,-3(l=-3)" + # ) + l0_index = int((multiplicity - 1) / 2) + reorder_index = [l0_index] + for i in range(1, int((multiplicity - 1) / 2) + 1): + reorder_index.append(l0_index + i) + reorder_index.append(l0_index - i) + + else: + raise ValueError("A wrong value was set to current_ang_mom.") + + mo_coeff_for_reord.append(ao_c) + + # write MOs!! + if len(mo_coeff_for_reord) == multiplicity: + # print("--write MOs!!--") + mo_coeff_buffer += [ + mo_coeff_for_reord[i] for i in reorder_index + ] + + # reset buffer + mo_coeff_for_reord = [] + + # print("--write perm_list") + perm_list += list(np.array(reorder_index) + perm_n) + perm_n = perm_n + len(reorder_index) + + mo_coefficient.append(mo) + # permutation_matrix.append(perm_list) + + mo_coefficient_all += mo_coefficient + + # MOs read part end both for alpha and beta spins[l] + logger.debug("len(mo_coefficient_all)") + logger.debug(len(mo_coefficient_all)) + logger.debug("len(mo_occupation_all)") + logger.debug(len(mo_occupation_all)) + logger.debug("len(mo_spin_all)") + logger.debug(len(mo_spin_all)) + + # Conversion from Python complex -> real, complex separately. + # force WF complex + force_wf_complex = False + if force_wf_complex: + complex_flag = True + # check if the MOs have imag.! + else: + imag_flags = [] + for mo in mo_coefficient_all: + imag_flags += list(np.isreal(list(np.real_if_close(mo, tol=100)))) + # print(imag_flags) + if all(imag_flags): + complex_flag = False + else: + complex_flag = True + + if complex_flag: + logger.info("The WF is complex") + mo_coefficient_real = [] + mo_coefficient_imag = [] + + for mo__ in mo_coefficient_all: + mo_real_b = [] + mo_imag_b = [] + for coeff in mo__: + mo_real_b.append(coeff.real) + mo_imag_b.append(coeff.imag) + mo_coefficient_real.append(mo_real_b) + mo_coefficient_imag.append(mo_imag_b) + + else: + logger.info("The WF is real") + mo_coefficient_real = [list(np.array(mo).real) for mo in mo_coefficient_all] + + logger.debug("--MOs Done--") + ########################################## + # mo info + ########################################## + trexio.write_mo_type(trexio_file, mo_type) # + + if complex_flag: + trexio.write_mo_num(trexio_file, len(mo_coefficient_real)) # + trexio.write_mo_coefficient(trexio_file, mo_coefficient_real) # + trexio.write_mo_coefficient_im(trexio_file, mo_coefficient_imag) # + else: + trexio.write_mo_num(trexio_file, len(mo_coefficient_real)) # + trexio.write_mo_coefficient(trexio_file, mo_coefficient_real) # + + trexio.write_mo_occupation(trexio_file, mo_occupation_all) # + + trexio.write_mo_spin(trexio_file, mo_spin_all) # + ########################################## + # ECP + ########################################## + # internal format of ORCA + # See Manual 5.0.4 pg : 497 + """ + ------------- + atom: + nelec (number of core electrons) + lmax (max. angular momentum for Ul to indicate |l>