From be6cef694c2658d457019d80281565198c230684 Mon Sep 17 00:00:00 2001 From: TApplencourt Date: Tue, 8 Nov 2016 11:40:55 -0600 Subject: [PATCH] Add pseudo to qp_convert --- .../qp_convert_output_to_ezfio.py | 120 +++++++++++++++++- 1 file changed, 119 insertions(+), 1 deletion(-) diff --git a/scripts/ezfio_interface/qp_convert_output_to_ezfio.py b/scripts/ezfio_interface/qp_convert_output_to_ezfio.py index ff7ad225..87743686 100755 --- a/scripts/ezfio_interface/qp_convert_output_to_ezfio.py +++ b/scripts/ezfio_interface/qp_convert_output_to_ezfio.py @@ -273,8 +273,126 @@ def write_ezfio(res, filename): # \_| |___/\___|\__,_|\__,_|\___/ # - ezfio.set_pseudo_do_pseudo(False) + # INPUT + # {% for lanel,zcore, l_block in l_atom $} + # #local l_block l=0} + # {label} GEN {zcore} {len(l_block)-1 #lmax_block} + # {% for l_param in l_block%} + # {len(l_param) # list of parameter aka n_max_bock_max(n)} + # {% for coef,n,zeta for l_param} + # {coef,n, zeta} + + # OUTPUT + + # Local are 1 array padded by max(n_max_block) when l == 0 (output:k_loc_max) + # v_k[n-2][atom] = value + + #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) + # v_kl[l][n-2][atom] = value + + def pad(array, size, value=0): + new_array= array + for add in xrange(len(array), size): + new_array.append(value) + + return new_array + + def parse_str(pseudo_str): + '''Return 4d array atom,l,n, attribute (attribute is coef, n, zeta)''' + matrix = [] + array_l_max_block = [] + array_z_remove = [] + + for block in [b for b in pseudo_str.split('\n\n') if b]: + #First element is header, the rest are l_param + array_party = [i for i in re.split(r"\n\d+\n",block) if i] + + z_remove, l_max_block = map(int,array_party[0].split()[-2:]) + array_l_max_block.append(l_max_block) + array_z_remove.append(z_remove) + + matrix_3d.append([ [coef_n_zeta.split()[1:] for coef_n_zeta in l.split('\n')] for l in array_party[1:] ]) + + return (matrix, array_l_max_block, array_z_remove) + + def get_local_stuff(matrix): + + matrix_local_unpad = [atom[0] for atom in matrix] + k_loc_max = max(len(i) for i in matrix_local_unpad) + + matrix_local = [pad(ll,k_loc_max,[0.,0,0.]) for ll in matrix_local_unpad] + + m_coef =[ [float(i[0]) for i in atom] for atom in matrix_local] + m_n = [ [int(i[1])-2 for i in atom] for atom in matrix_local] + m_zeta = [ [float(i[2]) for i in atom] for atom in matrix_local] + + return (k_loc_max, m_coef,m_n,m_zeta) + + def get_non_local_stuff(matrix): + + matrix_unlocal_unpad = [atom[1:] for atom in matrix] + l_max_block = max(len(i) for i in matrix_unlocal_unpad) + k_max = max( [len(item) for row in matrix_unlocal_unpad for item in row ] ) + + matrix_unlocal_semipaded =[ [pad(item,k_max,[0.,0,0.]) for item in row] for row in matrix_unlocal_unpad] + + empty_row = [ [0.,0,0.] for k in range(l_max_block)] + matrix_unlocal = [pad(ll,l_max_block,empty_row) for ll in matrix_unlocal_semipaded] + + m_coef_noloc = [ [ [ float(k[0]) for k in j ] for j in i ] for i in matrix_local ] + m_n_noloc = [ [ [ int(k[1])-2 for k in j ] for j in i ] for i in matrix_local ] + m_zeta_noloc = [ [ [ float(k[2]) for k in j ] for j in i ] for i in matrix_local ] + + return (l_max_block,k_max, m_coef_noloc,m_n_noloc,m_zeta_noloc) + + try: + pseudo_str = res_file.get_pseudo() + except: + ezfio.set_pseudo_do_pseudo(False) + else: + ezfio.set_pseudo_do_pseudo(True) + matrix, array_l_max_block, array_z_remove = parse(pseudo_str) + + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + # Z _ e f f , a l p h a / b e t a _ e l e c # + # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ # + + ezfio.pseudo_charge_remove = array_z_remove + ezfio.nuclei_nucl_charge = ezfio.nuclei_nucl_charge - array_z_remove + + import math + num_elec = sum(ezfio.nuclei_nucl_charge) + + ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.)) + ezfio.electrons_elec_beta_num = int(math.floor(num_beta / 2.)) + + # Change all the array 'cause EZFIO + # v_kl (v, l) => v_kl(l,v) + # v_kl => zip(*_v_kl) + # [[7.0, 79.74474797, -49.45159098], [1.0, 5.41040609, -4.60151975]] + # [(7.0, 1.0), (79.74474797, 5.41040609), (-49.45159098, -4.60151975)] + + # ~#~#~#~#~ # + # L o c a l # + # ~#~#~#~#~ # + + klocmax, m_coef,m_n,m_zeta = get_local_stuff(matrix) + ezfio.pseudo_pseudo_klocmax = klocmax + + ezfio.pseudo_pseudo_v_k = zip(*m_coef) + ezfio.pseudo_pseudo_n_k = zip(*m_n) + ezfio.pseudo_pseudo_dz_k = zip(*m_zeta) + + # ~#~#~#~#~#~#~#~#~ # + # N o n _ L o c a l # + # ~#~#~#~#~#~#~#~#~ # + + l_max_block,k_max, m_coef_noloc,m_n_noloc,m_zeta_noloc = get_non_local_stuff(matrix) + + ezfio.pseudo_pseudo_v_kl = zip(*m_coef_noloc) + ezfio.pseudo_pseudo_n_kl = zip(*m_n_noloc) + ezfio.pseudo_pseudo_dz_kl = zip(*m_zeta_noloc) def get_full_path(file_path): file_path = os.path.expanduser(file_path)