mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-22 19:43:32 +01:00
558 lines
18 KiB
Python
Executable File
558 lines
18 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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convert TREXIO file to EZFIO
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Usage:
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qp_import_trexio [-o EZFIO_DIR] FILE
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Options:
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-o --output=EZFIO_DIR Produced directory
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by default is FILE.ezfio
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"""
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import sys
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import os
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import numpy as np
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import subprocess
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import tempfile
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from functools import reduce
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from ezfio import ezfio
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from docopt import docopt
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import qp_bitmasks
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try:
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import trexio
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except ImportError:
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print("Error: trexio python module is not found. Try python3 -m pip install trexio")
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sys.exit(1)
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try:
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QP_ROOT = os.environ["QP_ROOT"]
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QP_EZFIO = os.environ["QP_EZFIO"]
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except KeyError:
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print("Error: QP_ROOT environment variable not found.")
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sys.exit(1)
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else:
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sys.path = [QP_EZFIO + "/Python",
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QP_ROOT + "/install/resultsFile",
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QP_ROOT + "/install",
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QP_ROOT + "/scripts"] + sys.path
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def uint64_to_int64(u):
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# Check if the most significant bit is set
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if u & (1 << 63):
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# Calculate the two's complement
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result = -int(np.bitwise_not(np.uint64(u))+1)
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else:
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# The number is already positive
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result = u
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return result
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def generate_xyz(l):
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def create_z(x,y,z):
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return (x, y, l-(x+y))
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def create_y(accu,x,y,z):
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if y == 0:
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result = [create_z(x,y,z)] + accu
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else:
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result = create_y([create_z(x,y,z)] + accu , x, y-1, z)
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return result
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def create_x(accu,x,y,z):
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if x == 0:
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result = create_y([], x,y,z) + accu
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else:
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xnew = x-1
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ynew = l-xnew
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result = create_x(create_y([],x,y,z) + accu , xnew, ynew, z)
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return result
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result = create_x([], l, 0, 0)
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result.reverse()
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return result
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def write_ezfio(trexio_filename, filename):
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warnings = []
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trexio_file = trexio.File(trexio_filename,mode='r',back_end=trexio.TREXIO_AUTO)
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ezfio.set_file(filename)
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ezfio.set_trexio_trexio_file(trexio_filename)
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print("Nuclei\t\t...\t", end=' ')
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charge = [0.]
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if trexio.has_nucleus(trexio_file):
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charge = trexio.read_nucleus_charge(trexio_file)
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ezfio.set_nuclei_nucl_num(len(charge))
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ezfio.set_nuclei_nucl_charge(charge)
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coord = trexio.read_nucleus_coord(trexio_file)
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coord = np.transpose(coord)
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ezfio.set_nuclei_nucl_coord(coord)
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label = trexio.read_nucleus_label(trexio_file)
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nucl_num = trexio.read_nucleus_num(trexio_file)
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# Transformt H1 into H
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import re
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p = re.compile(r'(\d*)$')
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label = [p.sub("", x).capitalize() for x in label]
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ezfio.set_nuclei_nucl_label(label)
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print("OK")
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else:
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ezfio.set_nuclei_nucl_num(1)
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ezfio.set_nuclei_nucl_charge([0.])
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ezfio.set_nuclei_nucl_coord([0.,0.,0.])
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ezfio.set_nuclei_nucl_label(["X"])
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print("None")
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warnings.append("No geometry found in the TREXIO file")
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print("Electrons\t...\t", end=' ')
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try:
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num_beta = trexio.read_electron_dn_num(trexio_file)
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except:
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num_beta = int(sum(charge))//2
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try:
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num_alpha = trexio.read_electron_up_num(trexio_file)
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except:
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num_alpha = int(sum(charge)) - num_beta
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if num_alpha == 0:
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print("\n\nError: There are zero electrons in the TREXIO file.\n\n")
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sys.exit(1)
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ezfio.set_electrons_elec_alpha_num(num_alpha)
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ezfio.set_electrons_elec_beta_num(num_beta)
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print(f"{num_alpha} {num_beta}")
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print("Basis\t\t...\t", end=' ')
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shell_num = 0
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try:
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basis_type = trexio.read_basis_type(trexio_file)
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if basis_type.lower() in ["gaussian", "slater"]:
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shell_num = trexio.read_basis_shell_num(trexio_file)
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prim_num = trexio.read_basis_prim_num(trexio_file)
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ang_mom = trexio.read_basis_shell_ang_mom(trexio_file)
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nucl_index = trexio.read_basis_nucleus_index(trexio_file)
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exponent = trexio.read_basis_exponent(trexio_file)
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coefficient = trexio.read_basis_coefficient(trexio_file)
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shell_index = trexio.read_basis_shell_index(trexio_file)
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ao_shell = trexio.read_ao_shell(trexio_file)
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ezfio.set_basis_basis("Read from TREXIO")
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ezfio.set_ao_basis_ao_basis("Read from TREXIO")
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ezfio.set_basis_shell_num(shell_num)
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ezfio.set_basis_prim_num(prim_num)
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ezfio.set_basis_shell_ang_mom(ang_mom)
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ezfio.set_basis_basis_nucleus_index([ x+1 for x in nucl_index ])
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ezfio.set_basis_prim_expo(exponent)
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nucl_shell_num = []
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prev = None
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m = 0
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for i in ao_shell:
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if i != prev:
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m += 1
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if prev is None or nucl_index[i] != nucl_index[prev]:
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nucl_shell_num.append(m)
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m = 0
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prev = i
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assert (len(nucl_shell_num) == nucl_num)
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shell_prim_num = []
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prev = shell_index[0]
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count = 0
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for i in shell_index:
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if i != prev:
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shell_prim_num.append(count)
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count = 0
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count += 1
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prev = i
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shell_prim_num.append(count)
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assert (len(shell_prim_num) == shell_num)
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ezfio.set_basis_shell_prim_num(shell_prim_num)
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ezfio.set_basis_shell_index([x+1 for x in shell_index])
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ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
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shell_factor = trexio.read_basis_shell_factor(trexio_file)
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prim_factor = trexio.read_basis_prim_factor(trexio_file)
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for i,p in enumerate(prim_factor):
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coefficient[i] *= prim_factor[i]
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ezfio.set_ao_basis_primitives_normalized(False)
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ezfio.set_basis_prim_coef(coefficient)
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elif basis_type.lower() == "numerical":
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shell_num = trexio.read_basis_shell_num(trexio_file)
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prim_num = shell_num
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ang_mom = trexio.read_basis_shell_ang_mom(trexio_file)
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nucl_index = trexio.read_basis_nucleus_index(trexio_file)
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exponent = [1.]*prim_num
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coefficient = [1.]*prim_num
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shell_index = [i for i in range(shell_num)]
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ao_shell = trexio.read_ao_shell(trexio_file)
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ezfio.set_basis_basis("None")
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ezfio.set_ao_basis_ao_basis("None")
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ezfio.set_basis_shell_num(shell_num)
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ezfio.set_basis_prim_num(prim_num)
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ezfio.set_basis_shell_ang_mom(ang_mom)
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ezfio.set_basis_basis_nucleus_index([ x+1 for x in nucl_index ])
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ezfio.set_basis_prim_expo(exponent)
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ezfio.set_basis_prim_coef(coefficient)
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nucl_shell_num = []
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prev = None
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m = 0
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for i in ao_shell:
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if i != prev:
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m += 1
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if prev is None or nucl_index[i] != nucl_index[prev]:
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nucl_shell_num.append(m)
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m = 0
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prev = i
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assert (len(nucl_shell_num) == nucl_num)
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shell_prim_num = []
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prev = shell_index[0]
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count = 0
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for i in shell_index:
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if i != prev:
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shell_prim_num.append(count)
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count = 0
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count += 1
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prev = i
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shell_prim_num.append(count)
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assert (len(shell_prim_num) == shell_num)
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ezfio.set_basis_shell_prim_num(shell_prim_num)
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ezfio.set_basis_shell_index([x+1 for x in shell_index])
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ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
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shell_factor = trexio.read_basis_shell_factor(trexio_file)
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else:
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raise TypeError
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print(basis_type)
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except:
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raise
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print("None")
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ezfio.set_ao_basis_ao_cartesian(True)
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print("AOS\t\t...\t", end=' ')
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try:
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cartesian = trexio.read_ao_cartesian(trexio_file)
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except:
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cartesian = True
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ao_num = trexio.read_ao_num(trexio_file)
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ezfio.set_ao_basis_ao_num(ao_num)
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trexio_file_cart = trexio_file
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if basis_type.lower() == "gaussian" and not cartesian:
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try:
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import trexio_tools
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fd, tmp = tempfile.mkstemp()
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os.close(fd)
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retcode = subprocess.call(["trexio", "convert-to", "-t", "cartesian", "-o", tmp, trexio_filename])
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trexio_file_cart = trexio.File(tmp,mode='r',back_end=trexio.TREXIO_AUTO)
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cartesian = trexio.read_ao_cartesian(trexio_file_cart)
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os.unlink(tmp)
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except:
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pass
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if cartesian and basis_type.lower() == "gaussian" and shell_num > 0:
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ao_shell = trexio.read_ao_shell(trexio_file)
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at = [ nucl_index[i]+1 for i in ao_shell ]
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ezfio.set_ao_basis_ao_nucl(at)
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num_prim0 = [ 0 for i in range(shell_num) ]
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for i in shell_index:
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num_prim0[i] += 1
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coef = {}
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expo = {}
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for i,c in enumerate(coefficient):
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idx = shell_index[i]
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if idx in coef:
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coef[idx].append(c)
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expo[idx].append(exponent[i])
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else:
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coef[idx] = [c]
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expo[idx] = [exponent[i]]
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coefficient = []
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exponent = []
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power_x = []
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power_y = []
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power_z = []
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num_prim = []
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for i in range(shell_num):
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for x,y,z in generate_xyz(ang_mom[i]):
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power_x.append(x)
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power_y.append(y)
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power_z.append(z)
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coefficient.append(coef[i])
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exponent.append(expo[i])
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num_prim.append(num_prim0[i])
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assert (len(coefficient) == ao_num)
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ezfio.set_ao_basis_ao_power(power_x + power_y + power_z)
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ezfio.set_ao_basis_ao_prim_num(num_prim)
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prim_num_max = max( [ len(x) for x in coefficient ] )
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for i in range(ao_num):
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coefficient[i] += [0. for j in range(len(coefficient[i]), prim_num_max)]
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exponent [i] += [0. for j in range(len(exponent[i]), prim_num_max)]
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coefficient = reduce(lambda x, y: x + y, coefficient, [])
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exponent = reduce(lambda x, y: x + y, exponent , [])
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coef = []
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expo = []
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for i in range(prim_num_max):
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for j in range(i, len(coefficient), prim_num_max):
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coef.append(coefficient[j])
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expo.append(exponent[j])
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# ezfio.set_ao_basis_ao_prim_num_max(prim_num_max)
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ezfio.set_ao_basis_ao_coef(coef)
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ezfio.set_ao_basis_ao_expo(expo)
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print("OK")
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else:
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if basis_type.lower() == "gaussian" and not cartesian:
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warnings.append(f"Spherical AOs not handled by QP. Convert the TREXIO file using trexio_tools:\n trexio convert-to -t cartesian -o cartesian_{trexio_filename} {trexio_filename}")
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warnings.append("Integrals should be imported using:\n qp run import_trexio_integrals")
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print("None")
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# _
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# |\/| _ _ |_) _. _ o _
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# | | (_) _> |_) (_| _> | _>
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#
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print("MOS\t\t...\t", end=' ')
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labels = { "Canonical" : "Canonical",
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"RHF" : "Canonical",
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"BOYS" : "Localized",
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"ROHF" : "Canonical",
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"UHF" : "Canonical",
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"Natural": "Natural" }
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try:
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label = labels[trexio.read_mo_type(trexio_file)]
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except:
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label = "None"
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ezfio.set_mo_basis_mo_label(label)
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ezfio.set_determinants_mo_label(label)
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try:
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clss = trexio.read_mo_class(trexio_file)
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core = [ i for i in clss if i.lower() == "core" ]
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inactive = [ i for i in clss if i.lower() == "inactive" ]
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active = [ i for i in clss if i.lower() == "active" ]
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virtual = [ i for i in clss if i.lower() == "virtual" ]
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deleted = [ i for i in clss if i.lower() == "deleted" ]
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except trexio.Error:
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pass
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try:
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mo_num = trexio.read_mo_num(trexio_file)
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ezfio.set_mo_basis_mo_num(mo_num)
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# Read coefs from temporary cartesian file created in the AO section
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MoMatrix = trexio.read_mo_coefficient(trexio_file_cart)
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# Renormalize MO coefs if needed
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if trexio.has_ao_normalization(trexio_file_cart):
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ezfio.set_ao_basis_ao_normalized(False)
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norm = trexio.read_ao_normalization(trexio_file_cart)
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# for j in range(mo_num):
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# for i,f in enumerate(norm):
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# MoMatrix[i,j] *= f
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ezfio.set_mo_basis_mo_coef(MoMatrix)
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mo_occ = [ 0. for i in range(mo_num) ]
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for i in range(num_alpha):
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mo_occ[i] += 1.
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for i in range(num_beta):
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mo_occ[i] += 1.
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ezfio.set_mo_basis_mo_occ(mo_occ)
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print("OK")
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except:
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print("None")
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print("Pseudos\t\t...\t", end=' ')
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ezfio.set_pseudo_do_pseudo(False)
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if trexio.has_ecp_ang_mom(trexio_file):
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ezfio.set_pseudo_do_pseudo(True)
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max_ang_mom_plus_1 = trexio.read_ecp_max_ang_mom_plus_1(trexio_file)
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z_core = trexio.read_ecp_z_core(trexio_file)
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ang_mom = trexio.read_ecp_ang_mom(trexio_file)
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nucleus_index = trexio.read_ecp_nucleus_index(trexio_file)
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exponent = trexio.read_ecp_exponent(trexio_file)
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coefficient = trexio.read_ecp_coefficient(trexio_file)
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power = trexio.read_ecp_power(trexio_file)
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lmax = max( max_ang_mom_plus_1 ) - 1
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ezfio.set_pseudo_pseudo_lmax(lmax)
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ezfio.set_pseudo_nucl_charge_remove(z_core)
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prev_center = None
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ecp = {}
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for i in range(len(ang_mom)):
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center = nucleus_index[i]
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if center != prev_center:
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ecp[center] = { "lmax": max_ang_mom_plus_1[center],
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"zcore": z_core[center],
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"contr": {} }
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for j in range(max_ang_mom_plus_1[center]+1):
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ecp[center]["contr"][j] = []
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ecp[center]["contr"][ang_mom[i]].append( (coefficient[i], power[i], exponent[i]) )
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prev_center = center
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ecp_loc = {}
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ecp_nl = {}
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kmax = 0
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klocmax = 0
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for center in ecp:
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ecp_nl [center] = {}
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for k in ecp[center]["contr"]:
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if k == ecp[center]["lmax"]:
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ecp_loc[center] = ecp[center]["contr"][k]
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klocmax = max(len(ecp_loc[center]), klocmax)
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else:
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ecp_nl [center][k] = ecp[center]["contr"][k]
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kmax = max(len(ecp_nl [center][k]), kmax)
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ezfio.set_pseudo_pseudo_klocmax(klocmax)
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ezfio.set_pseudo_pseudo_kmax(kmax)
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pseudo_n_k = [[0 for _ in range(nucl_num)] for _ in range(klocmax)]
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pseudo_v_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
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pseudo_dz_k = [[0. for _ in range(nucl_num)] for _ in range(klocmax)]
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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 center in ecp_loc:
|
|
for k in range( len(ecp_loc[center]) ):
|
|
v, n, dz = ecp_loc[center][k]
|
|
pseudo_n_k[k][center] = n
|
|
pseudo_v_k[k][center] = v
|
|
pseudo_dz_k[k][center] = dz
|
|
|
|
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)
|
|
|
|
for center in ecp_nl:
|
|
for l in range( len(ecp_nl[center]) ):
|
|
for k in range( len(ecp_nl[center][l]) ):
|
|
v, n, dz = ecp_nl[center][l][k]
|
|
pseudo_n_kl[l][k][center] = n
|
|
pseudo_v_kl[l][k][center] = v
|
|
pseudo_dz_kl[l][k][center] = dz
|
|
|
|
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)
|
|
print("OK")
|
|
|
|
else:
|
|
print("None")
|
|
|
|
print("Determinant\t...\t", end=' ')
|
|
alpha = [ i for i in range(num_alpha) ]
|
|
beta = [ i for i in range(num_beta) ]
|
|
if trexio.has_mo_spin(trexio_file):
|
|
spin = trexio.read_mo_spin(trexio_file)
|
|
if max(spin) == 1:
|
|
tmp = [ i for i in range(len(spin)) if spin[i] == 0 ]
|
|
alpha = [ tmp[i] for i in range(num_alpha) ]
|
|
tmp = [ i for i in range(len(spin)) if spin[i] == 1 ]
|
|
beta = [ tmp[i] for i in range(num_beta) ]
|
|
warnings.append("UHF orbitals orbitals read", end=' ')
|
|
alpha_s = ['0']*mo_num
|
|
beta_s = ['0']*mo_num
|
|
for i in alpha:
|
|
alpha_s[i] = '1'
|
|
for i in beta:
|
|
beta_s[i] = '1'
|
|
alpha_s = ''.join(alpha_s)[::-1]
|
|
beta_s = ''.join(beta_s)[::-1]
|
|
def conv(i):
|
|
try:
|
|
result = np.int64(i)
|
|
except:
|
|
result = np.int64(i-2**63-1)
|
|
return result
|
|
|
|
alpha = [ uint64_to_int64(int(i,2)) for i in qp_bitmasks.string_to_bitmask(alpha_s) ][::-1]
|
|
beta = [ uint64_to_int64(int(i,2)) for i in qp_bitmasks.string_to_bitmask(beta_s ) ][::-1]
|
|
ezfio.set_determinants_bit_kind(8)
|
|
ezfio.set_determinants_n_int(1+mo_num//64)
|
|
ezfio.set_determinants_n_det(1)
|
|
ezfio.set_determinants_n_states(1)
|
|
ezfio.set_determinants_psi_det(alpha+beta)
|
|
ezfio.set_determinants_psi_coef([[1.0]])
|
|
print("OK")
|
|
|
|
|
|
for w in warnings:
|
|
s = "-------------"
|
|
print (s)
|
|
print (w)
|
|
|
|
|
|
|
|
|
|
def get_full_path(file_path):
|
|
file_path = os.path.expanduser(file_path)
|
|
file_path = os.path.expandvars(file_path)
|
|
return file_path
|
|
|
|
|
|
if __name__ == '__main__':
|
|
ARGUMENTS = docopt(__doc__)
|
|
|
|
FILE = get_full_path(ARGUMENTS['FILE'])
|
|
trexio_filename = FILE
|
|
|
|
if ARGUMENTS["--output"]:
|
|
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
|
|
else:
|
|
EZFIO_FILE = "{0}.ezfio".format(FILE)
|
|
|
|
write_ezfio(trexio_filename, EZFIO_FILE)
|
|
sys.stdout.flush()
|
|
|