proteindf_tools.pdfparam_object module¶

class proteindf_tools.pdfparam_object.PdfParamObject(rhs=None)[source]¶

Bases: object

ProteinDF parameter object

property CDAM_tau¶

property CD_epsilon¶

property TEs¶

property comment¶

compare_energy(rhs, threshold=1e-05)[source]¶

compare_grad(rhs)[source]¶

compare_info(rhs)[source]¶

compare_pop(rhs)[source]¶

property convergence_threshold¶

property convergence_threshold_energy¶

property convergence_type¶

property counterpoise¶

property cut_value¶

digest()[source]¶

property extra_keywords¶

find_atom_index(atom)[source]¶: If the given atom is registered, return its index (0-based). If there is no match, return -1.

get_basisset(atom_label)[source]¶

get_basisset_atomlabels()[source]¶

get_basisset_gridfree(atom_label)[source]¶

get_basisset_gridfree_atomlabels()[source]¶

get_basisset_gridfree_name(atomlabel)[source]¶

get_basisset_j(atom_label)[source]¶

get_basisset_j_atomlabels()[source]¶

get_basisset_j_name(atomlabel)[source]¶

get_basisset_name(atomlabel)[source]¶

get_basisset_xc(atom_label)[source]¶

get_basisset_xc_atomlabels()[source]¶

get_basisset_xc_name(atomlabel)[source]¶

get_c_mat_path(runtype='rks', itr=-1)[source]¶: return Cmatrix path

get_clo_mat_path(runtype='rks', itr=-1)[source]¶: return localized matrix (C_lo) path

get_density_matrix_path(runtype='rks', itr=-1)[source]¶: return density matrix path

get_energy_level_path(runtype, itr)[source]¶: return energy level vector file path

get_f_mat_path(runtype='rks', itr=-1)[source]¶: return Fmatrix path

get_gradient(atom_index)[source]¶

get_gradient_matrix_path()[source]¶

get_gradient_rms()[source]¶: Return the RMS of the gradient.

get_h2_mat_path()[source]¶: return Hpq2 matrix path

get_h_mat_path()[source]¶: return Hpq matrix path

get_inputfile_contents()[source]¶: Create the contents of the ProteinDF input file (fl_Userinput).

get_mulliken_atom_population(atomindex)[source]¶

get_occ_path(runtype)[source]¶: return electron occupation information file path

get_pop_mulliken_path(run_type='rks', iteration=-1)[source]¶

get_raw_data()[source]¶

get_s_mat_path()[source]¶: return overlap matrix path

get_total_energy(iteration)[source]¶

get_x_mat_path()[source]¶: return X matrix path

get_xinv_mat_path()[source]¶: return X^-1 matrix path

property gridfree_CDAM_tau¶

property gridfree_CD_epsilon¶

property gridfree_dedicated_basis¶

property gridfree_orthogonalize_method¶

property guess¶

property iterations¶

property j_engine¶

property k_engine¶

property level_shift¶

property level_shift_start_iteration¶

property level_shift_virtual_mo¶

property lo_num_of_iterations¶

property lo_satisfied¶

property max_iterations¶

property method¶

property molecule¶

property num_of_AOs¶

property num_of_MOs¶

property num_of_atoms¶

property num_of_electrons¶

property occupation_level¶

property orbital_independence_threshold¶

property orbital_independence_threshold_canonical¶

property orbital_independence_threshold_lowdin¶

run_types()[source]¶

property scf_acceleration¶

property scf_acceleration_anderson_damping_factor¶

property scf_acceleration_anderson_start¶

property scf_acceleration_damping_damping_factor¶

property scf_acceleration_damping_damping_type¶

property scf_converged¶

set_basisset(atom_label, basisset)[source]¶

set_basisset_gridfree(atom_label, basisset)[source]¶

set_basisset_gridfree_name(atomlabel, value)[source]¶

set_basisset_j(atom_label, basisset)[source]¶

set_basisset_j_name(atomlabel, value)[source]¶

set_basisset_name(atomlabel, value)[source]¶

set_basisset_xc(atom_label, basisset)[source]¶

set_basisset_xc_name(atomlabel, value)[source]¶

set_by_raw_data(odict)[source]¶

set_gradient(atom_index, fx, fy, fz)[source]¶

set_mulliken_atom_population(atomindex, value)[source]¶

set_total_energy(iteration, total_energy)[source]¶

property step_control¶

property work_path¶

property xc_engine¶

property xc_functional¶