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https://github.com/LCPQ/quantum_package
synced 2024-12-22 12:23:48 +01:00
Fixed pseudos
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70d52c126a
commit
20e7a23ef7
@ -38,7 +38,7 @@ subroutine run_wf
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do
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call wait_for_states(states,zmq_state,3)
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call wait_for_states(states,zmq_state,4)
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if(trim(zmq_state) == 'Stopped') then
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@ -3,7 +3,7 @@
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convert output of gamess/GAU$$IAN to ezfio
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Usage:
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qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
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qp_convert_output_to_ezfio.py <file.out> [--ezfio=<ezfio_directory>]
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Option:
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file.out is the file to check (like gamess.out)
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@ -20,18 +20,17 @@ from functools import reduce
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# Add to the path #
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# ~#~#~#~#~#~#~#~ #
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try:
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QP_ROOT = os.environ["QP_ROOT"]
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except:
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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_ROOT + "/install/EZFIO/Python",
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QP_ROOT + "/resultsFile",
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QP_ROOT + "/scripts"] + sys.path
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# ~#~#~#~#~#~ #
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# I m p o r t #
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# ~#~#~#~#~#~ #
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@ -280,12 +279,13 @@ def write_ezfio(res, filename):
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# {% for coef,n,zeta for l_param}
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# {coef,n, zeta}
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# OUTPUT
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# Local are 1 array padded by max(n_max_block) when l == 0 (output:k_loc_max)
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# v_k[n-2][atom] = value
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#No Local are 2 array padded with max of lmax_block when l!=0 (output:lmax+1) and max(n_max_block)whem l !=0 (kmax)
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#Non Local are 2 array padded with max of lmax_block when l!=0 (output:lmax+1) and max(n_max_block)whem l !=0 (kmax)
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# v_kl[l][n-2][atom] = value
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def pad(array, size, value=0):
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@ -309,8 +309,16 @@ def write_ezfio(res, filename):
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array_l_max_block.append(l_max_block)
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array_z_remove.append(z_remove)
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matrix.append([[coef_n_zeta.split()[1:] for coef_n_zeta in l.split('\n')] for l in array_party[1:]])
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x = [[coef_n_zeta.split() for coef_n_zeta in l.split('\n')] \
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for l in array_party[1:] ]
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x = []
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for l in array_party[1:]:
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y = []
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for coef_n_zeta in l.split('\n'):
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z = coef_n_zeta.split()
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if z : y.append(z)
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x.append(y)
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matrix.append(x)
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return (matrix, array_l_max_block, array_z_remove)
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def get_local_stuff(matrix):
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@ -319,7 +327,6 @@ def write_ezfio(res, filename):
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k_loc_max = max(len(i) for i in matrix_local_unpad)
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matrix_local = [ pad(ll, k_loc_max, [0., 2, 0.]) for ll in matrix_local_unpad]
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m_coef = [[float(i[0]) for i in atom] for atom in matrix_local]
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m_n = [[int(i[1]) - 2 for i in atom] for atom in matrix_local]
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m_zeta = [[float(i[2]) for i in atom] for atom in matrix_local]
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@ -343,9 +350,21 @@ def write_ezfio(res, filename):
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return (l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc)
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try:
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pseudo_str = res_file.get_pseudo()
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matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
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pseudo_str = []
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label = ezfio.get_nuclei_nucl_label()
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for ecp in res.pseudo:
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pseudo_str += [ "%(label)s GEN %(zcore)d %(lmax)d" % { "label": label[ ecp["atom"]-1 ],
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"zcore": ecp["zcore"], "lmax": ecp["lmax"] } ]
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lmax = ecp["lmax"]
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for l in [lmax] + list(range(0,lmax)):
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pseudo_str += [ "%d"%len(ecp[str(l)]) ]
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for t in ecp[str(l)]:
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pseudo_str += [ "%f %d %f"%t ]
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pseudo_str += [""]
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pseudo_str = "\n".join(pseudo_str)
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matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
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array_z_remove = map(float,array_z_remove)
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except:
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ezfio.set_pseudo_do_pseudo(False)
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else:
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@ -355,14 +374,18 @@ def write_ezfio(res, filename):
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# Z _ e f f , a l p h a / b e t a _ e l e c #
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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ezfio.pseudo_charge_remove = array_z_remove
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ezfio.nuclei_nucl_charge = [i - j for i, j in zip(ezfio.nuclei_nucl_charge, array_z_remove)]
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ezfio.set_pseudo_nucl_charge_remove(array_z_remove)
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charge = ezfio.get_nuclei_nucl_charge()
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charge = [ i - j for i, j in zip(charge, array_z_remove) ]
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ezfio.set_nuclei_nucl_charge (charge)
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import math
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num_elec = sum(ezfio.nuclei_nucl_charge)
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num_elec_diff = sum(array_z_remove)/2
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nalpha = ezfio.get_electrons_elec_alpha_num() - num_elec_diff
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nbeta = ezfio.get_electrons_elec_beta_num() - num_elec_diff
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ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
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ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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ezfio.set_electrons_elec_alpha_num(nalpha)
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ezfio.set_electrons_elec_beta_num( nbeta )
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# Change all the array 'cause EZFIO
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# v_kl (v, l) => v_kl(l,v)
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@ -421,3 +444,4 @@ if __name__ == '__main__':
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print file_, 'recognized as', str(res_file).split('.')[-1].split()[0]
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write_ezfio(res_file, ezfio_file)
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os.system("qp_run save_ortho_mos "+ezfio_file)
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