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qp_import_trexio.py

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This commit is contained in:
Anthony Scemama 2024-11-01 10:30:54 +01:00
parent 1d4dbad7e5
commit b68cc4ef9a
1 changed files with 30 additions and 9 deletions
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39
scripts/qp_import_trexio.py
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@ -14,6 +14,8 @@ Options:
import sys
import os
import numpy as np
import subprocess
import tempfile
from functools import reduce
from ezfio import ezfio
from docopt import docopt
@ -77,10 +79,8 @@ def generate_xyz(l):
def write_ezfio(trexio_filename, filename):
try:
trexio_file = trexio.File(trexio_filename,mode='r',back_end=trexio.TREXIO_TEXT)
except:
trexio_file = trexio.File(trexio_filename,mode='r',back_end=trexio.TREXIO_HDF5)
warnings = []
trexio_file = trexio.File(trexio_filename,mode='r',back_end=trexio.TREXIO_AUTO)
ezfio.set_file(filename)
ezfio.set_trexio_trexio_file(trexio_filename)
@ -113,6 +113,7 @@ def write_ezfio(trexio_filename, filename):
ezfio.set_nuclei_nucl_coord([0.,0.,0.])
ezfio.set_nuclei_nucl_label(["X"])
print("None")
warnings.append("No geometry found in the TREXIO file")
@ -142,7 +143,6 @@ def write_ezfio(trexio_filename, filename):
try:
basis_type = trexio.read_basis_type(trexio_file)
print ("BASIS TYPE: ", basis_type.lower())
if basis_type.lower() in ["gaussian", "slater"]:
shell_num = trexio.read_basis_shell_num(trexio_file)
prim_num = trexio.read_basis_prim_num(trexio_file)
@ -251,6 +251,7 @@ def write_ezfio(trexio_filename, filename):
print(basis_type)
except:
raise
print("None")
ezfio.set_ao_basis_ao_cartesian(True)
@ -264,7 +265,20 @@ def write_ezfio(trexio_filename, filename):
ao_num = trexio.read_ao_num(trexio_file)
ezfio.set_ao_basis_ao_num(ao_num)
if cartesian and shell_num > 0:
trexio_file_cart = trexio_file
if basis_type.lower() == "gaussian" and not cartesian:
try:
import trexio_tools
fd, tmp = tempfile.mkstemp()
os.close(fd)
retcode = subprocess.call(["trexio", "convert-to", "-t", "cartesian", "-o", tmp, trexio_filename])
trexio_file_cart = trexio.File(tmp,mode='r',back_end=trexio.TREXIO_AUTO)
cartesian = trexio.read_ao_cartesian(trexio_file_cart)
os.unlink(tmp)
except:
pass
if cartesian and basis_type.lower() == "gaussian" and shell_num > 0:
ao_shell = trexio.read_ao_shell(trexio_file)
at = [ nucl_index[i]+1 for i in ao_shell ]
ezfio.set_ao_basis_ao_nucl(at)
@ -327,7 +341,9 @@ def write_ezfio(trexio_filename, filename):
print("OK")
else:
print("None: integrals should be also imported using qp run import_trexio_integrals")
warnings.append("Integrals should be imported using `qp run import_trexio_integrals`")
print("None")
# _
@ -364,7 +380,8 @@ def write_ezfio(trexio_filename, filename):
mo_num = trexio.read_mo_num(trexio_file)
ezfio.set_mo_basis_mo_num(mo_num)
MoMatrix = trexio.read_mo_coefficient(trexio_file)
# Read coefs from temporary cartesian file created in the AO section
MoMatrix = trexio.read_mo_coefficient(trexio_file_cart)
ezfio.set_mo_basis_mo_coef(MoMatrix)
mo_occ = [ 0. for i in range(mo_num) ]
@ -471,7 +488,7 @@ def write_ezfio(trexio_filename, filename):
alpha = [ alpha[i] for i in range(num_alpha) ]
beta = [ i for i in range(len(spin)) if spin[i] == 1 ]
beta = [ beta[i] for i in range(num_beta) ]
print("Warning -- UHF orbitals --", end=' ')
warnings.append("UHF orbitals orbitals read", end=' ')
alpha_s = ['0']*mo_num
beta_s = ['0']*mo_num
for i in alpha:
@ -498,6 +515,10 @@ def write_ezfio(trexio_filename, filename):
print("OK")
for w in warnings:
print(w)
def get_full_path(file_path):