mirror of
https://github.com/LCPQ/quantum_package
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Working pseudo
This commit is contained in:
TApplencourt
parent
be6cef694c
commit
90418ec728
2
configure
vendored
2
configure
vendored
@ -122,7 +122,7 @@ docopt = Info(
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default_path=join(QP_ROOT_INSTALL, "docopt"))
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resultsFile = Info(
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url='{head}/LCPQ/resultsFile/{tail}'.format(**path_github),
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url='{head}/TApplencourt/resultsFile/{tail}'.format(**path_github),
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description=' resultsFile',
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default_path=join(QP_ROOT_INSTALL, "resultsFile"))
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@ -12,26 +12,24 @@ Option:
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"""
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import sys
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import os
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from functools import reduce
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# ~#~#~#~#~#~#~#~ #
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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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sys.path = [
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QP_ROOT + "/install/EZFIO/Python", QP_ROOT + "/resultsFile", QP_ROOT +
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"/scripts"
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] + sys.path
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# ~#~#~#~#~#~ #
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# I m p o r t #
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@ -39,7 +37,6 @@ else:
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from ezfio import ezfio
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try:
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from resultsFile import *
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except:
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@ -273,7 +270,6 @@ def write_ezfio(res, filename):
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# \_| |___/\___|\__,_|\__,_|\___/
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#
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# INPUT
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# {% for lanel,zcore, l_block in l_atom $}
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# #local l_block l=0}
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@ -312,7 +308,7 @@ 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_3d.append([ [coef_n_zeta.split()[1:] for coef_n_zeta in l.split('\n')] for l in array_party[1:] ])
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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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return (matrix, array_l_max_block, array_z_remove)
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@ -321,12 +317,11 @@ def write_ezfio(res, filename):
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matrix_local_unpad = [atom[0] for atom in matrix]
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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.,0,0.]) for ll 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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return (k_loc_max, m_coef, m_n, m_zeta)
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def get_non_local_stuff(matrix):
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@ -335,14 +330,14 @@ def write_ezfio(res, filename):
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l_max_block = max(len(i) for i in matrix_unlocal_unpad)
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k_max = max([len(item) for row in matrix_unlocal_unpad for item in row])
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matrix_unlocal_semipaded =[ [pad(item,k_max,[0.,0,0.]) for item in row] for row in matrix_unlocal_unpad]
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matrix_unlocal_semipaded = [[pad(item, k_max, [0., 2, 0.]) for item in row] for row in matrix_unlocal_unpad]
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empty_row = [ [0.,0,0.] for k in range(l_max_block)]
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empty_row = [[0., 2, 0.] for k in range(l_max_block)]
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matrix_unlocal = [ pad(ll, l_max_block, empty_row) for ll in matrix_unlocal_semipaded ]
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m_coef_noloc = [ [ [ float(k[0]) for k in j ] for j in i ] for i in matrix_local ]
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m_n_noloc = [ [ [ int(k[1])-2 for k in j ] for j in i ] for i in matrix_local ]
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m_zeta_noloc = [ [ [ float(k[2]) for k in j ] for j in i ] for i in matrix_local ]
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m_coef_noloc = [[[float(k[0]) for k in j] for j in i] for i in matrix_unlocal]
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m_n_noloc = [[[int(k[1]) - 2 for k in j] for j in i] for i in matrix_unlocal]
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m_zeta_noloc = [[[float(k[2]) for k in j] for j in i] for i in matrix_unlocal]
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return (l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc)
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@ -352,20 +347,22 @@ def write_ezfio(res, filename):
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ezfio.set_pseudo_do_pseudo(False)
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else:
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ezfio.set_pseudo_do_pseudo(True)
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matrix, array_l_max_block, array_z_remove = parse(pseudo_str)
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matrix, array_l_max_block, array_z_remove = parse_str(pseudo_str)
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# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
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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 = ezfio.nuclei_nucl_charge - array_z_remove
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ezfio.nuclei_nucl_charge = [
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i - j for i, j in zip(ezfio.nuclei_nucl_charge, array_z_remove)
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]
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import math
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num_elec = sum(ezfio.nuclei_nucl_charge)
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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_beta / 2.))
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ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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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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@ -388,18 +385,24 @@ def write_ezfio(res, filename):
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# N o n _ L o c a l #
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# ~#~#~#~#~#~#~#~#~ #
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l_max_block,k_max, m_coef_noloc,m_n_noloc,m_zeta_noloc = get_non_local_stuff(matrix)
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l_max_block, k_max, m_coef_noloc, m_n_noloc, m_zeta_noloc = get_non_local_stuff(
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matrix)
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ezfio.pseudo_pseudo_lmax = l_max_block - 1
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ezfio.pseudo_pseudo_kmax = k_max
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ezfio.pseudo_pseudo_v_kl = zip(*m_coef_noloc)
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ezfio.pseudo_pseudo_n_kl = zip(*m_n_noloc)
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ezfio.pseudo_pseudo_dz_kl = zip(*m_zeta_noloc)
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def get_full_path(file_path):
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file_path = os.path.expanduser(file_path)
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file_path = os.path.expandvars(file_path)
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file_path = os.path.abspath(file_path)
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return file_path
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if __name__ == '__main__':
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arguments = docopt(__doc__)
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@ -298,6 +298,7 @@ if __name__ == '__main__':
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# Don't update if we are not in the main repository
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from is_master_repository import is_master_repository
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if not is_master_repository:
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print 'Not in the master repo'
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sys.exit()
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path = os.path.join(module_abs, ".gitignore")
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@ -4,6 +4,10 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integral, (ao_num_align,ao_num)]
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! Pseudo-potential integrals
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END_DOC
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print*, 'Hi from ao_pseudo_integral'
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print*, read_ao_one_integrals
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if (read_ao_one_integrals) then
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call read_one_e_integrals('ao_pseudo_integral', ao_pseudo_integral,&
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size(ao_pseudo_integral,1), size(ao_pseudo_integral,2))
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@ -53,13 +57,6 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integral_local, (ao_num_align,ao_nu
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call wall_time(wall_1)
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call cpu_time(cpu_1)
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!write(33,*) 'xxxLOCxxx'
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!write(33,*) 'pseudo_klocmax', pseudo_klocmax
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!write(33,*) 'pseudo_v_k_transp ', pseudo_v_k_transp
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!write(33,*) 'pseudo_n_k_transp ', pseudo_n_k_transp
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!write(33,*) 'pseudo_dz_k_transp', pseudo_dz_k_transp
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!write(33,*) 'xxxLOCxxx'
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thread_num = 0
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!$OMP PARALLEL &
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!$OMP DEFAULT (NONE) &
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@ -109,14 +106,6 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integral_local, (ao_num_align,ao_nu
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pseudo_n_k_transp (1,k), &
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pseudo_dz_k_transp(1,k), &
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A_center,power_A,alpha,B_center,power_B,beta,C_center)
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! write(33,*) i,j,k
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! write(33,*) A_center,power_A,alpha,B_center,power_B,beta,C_center, &
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! Vloc(pseudo_klocmax, &
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! pseudo_v_k_transp (1,k), &
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! pseudo_n_k_transp (1,k), &
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! pseudo_dz_k_transp(1,k), &
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! A_center,power_A,alpha,B_center,power_B,beta,C_center)
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! write(33,*)
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enddo
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ao_pseudo_integral_local(i,j) = ao_pseudo_integral_local(i,j) +&
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@ -86,4 +86,16 @@ doc: QMC grid
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interface: ezfio
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size: (ao_basis.ao_num,-pseudo.pseudo_lmax:pseudo.pseudo_lmax,0:pseudo.pseudo_lmax,nuclei.nucl_num,pseudo.pseudo_grid_size)
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[disk_access_pseudo_local_integrals]
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type: Disk_access
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doc: Read/Write the local ntegrals from/to disk [ Write | Read | None ]
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interface: ezfio,provider,ocaml
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default: None
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[disk_access_pseudo_no_local_integrals]
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type: Disk_access
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doc: Read/Write the no-local ntegrals from/to disk [ Write | Read | None ]
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interface: ezfio,provider,ocaml
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default: None
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@ -17,17 +17,22 @@ module map_module
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! should be called before getting data from the map.
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use omp_lib
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use iso_fortran_env
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integer, parameter :: integral_kind = 8
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integer, parameter :: integral_kind = 16 ! 8
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integer, parameter :: cache_key_kind = 2
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integer, parameter :: cache_map_size_kind = 4
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integer, parameter :: cache_key_kind = 4 ! 2
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integer, parameter :: cache_map_size_kind = 8 ! 4
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integer, parameter :: key_kind = 8
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integer, parameter :: map_size_kind = 8
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integer, parameter :: key_kind = 16 !8
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integer, parameter :: map_size_kind =16 ! 8
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integer, parameter :: map_shift = -15
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integer*8, parameter :: map_mask = ibset(0_8,15)-1_8
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integer, parameter :: map_shift = -31 !-15
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!integer*8, parameter :: map_mask = ibset(0_8,15)-1_8
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integer(kind=int16), parameter :: z_kind = 0
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integer(kind=int16), parameter :: o_kind = 1
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integer(kind=int16), parameter :: map_mask = ibset(z_kind,15)-o_kind
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type cache_map_type
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real(integral_kind), pointer :: value(:)
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@ -45,8 +50,13 @@ module map_module
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integer*8, pointer :: consolidated_idx(:)
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logical :: sorted
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logical :: consolidated
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integer(map_size_kind) :: map_size
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integer(map_size_kind) :: n_elements
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! integer(kind=map_size_kind) :: map_size
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! integer(kind=map_size_kind) :: n_elements
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integer(kind=int16) :: map_size
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integer(kind=int16) :: n_elements
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integer(omp_lock_kind) :: lock
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end type map_type
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@ -1,6 +1,6 @@
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3
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XYZ file: coordinates in Angstrom
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H 0.7510000000 0.1940000000 0.0000000000
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O 0.0000000000 -0.3880000000 0.0000000000
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H 0.7510000000 0.1940000000 0.0000000000
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H -0.7510000000 0.1940000000 0.0000000000
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