schrodinger.application.mopac.results71 module

A module to parse and store the results of a MOPAC7.1 calculation. It interfaces directly with the Fortran code to populate the output variables from memory.

class schrodinger.application.mopac.results71.MopacResults71(mopfile)

Bases: object

A class to parse and store the results of a MOPAC7.1 calculation.

MULLIK = 'MULLIK'

ESP = 'ESP'

SUPER = 'SUPER'

UHF = 'UHF'

PLOTESP = 'PLOTESP'

PLOTALIE = 'PLOTALIE'

PLOTALEA = 'PLOTALEA'

scf_OK = 1

scf_FAIL = 2

exit_status_OK = 0

exit_status_FATAL = -1

exit_status_BAD_INPUT = 1

energy_prop = 'r_NDDO_NDDO_Heat_of_Formation'

method_prop = 's_NDDO_SemiEmpirical_Method'

homo_prop = 'r_NDDO_HOMO_Energy'

lumo_prop = 'r_NDDO_LUMO_Energy'

ahomo_prop = 'r_NDDO_Alpha_HOMO_Energy'

alumo_prop = 'r_NDDO_Alpha_LUMO_Energy'

bhomo_prop = 'r_NDDO_Beta_HOMO_Energy'

blumo_prop = 'r_NDDO_Beta_LUMO_Energy'

hardness_prop = 'r_NDDO_Molecular_Hardness'

eneg_prop = 'r_NDDO_Molecular_Electronegativity'

se_tot_prop = 'r_NDDO_Total_Electrophilic_Superdelocalizability'

sn_tot_prop = 'r_NDDO_Total_Nucleophilic_Superdelocalizability'

sr_tot_prop = 'r_NDDO_Total_Radical_Superdelocalizability'

asp_tot_prop = 'r_NDDO_Total_Atom_Self_Polarizability'

dipole_prop = 'r_NDDO_Dipole'

dipole_x_prop = 'r_NDDO_Dipole_X'

dipole_y_prop = 'r_NDDO_Dipole_Y'

dipole_z_prop = 'r_NDDO_Dipole_Z'

dipole_esp_prop = 'r_NDDO_Dipole_ESP'

dipole_esp_x_prop = 'r_NDDO_Dipole_ESP_X'

dipole_esp_y_prop = 'r_NDDO_Dipole_ESP_Y'

dipole_esp_z_prop = 'r_NDDO_Dipole_ESP_Z'

min_esp_prop = 'r_NDDO_Min_ESP_On_Mol_Surface'

max_esp_prop = 'r_NDDO_Max_ESP_On_Mol_Surface'

mean_esp_prop = 'r_NDDO_Mean_ESP_On_Mol_Surface'

mean_pos_esp_prop = 'r_NDDO_Mean_Pos_ESP_On_Mol_Surface'

mean_neg_esp_prop = 'r_NDDO_Mean_Neg_ESP_On_Mol_Surface'

sig_pos_esp_prop = 'r_NDDO_Pos_ESP_Variance_On_Mol_Surface'

sig_neg_esp_prop = 'r_NDDO_Neg_ESP_Variance_On_Mol_Surface'

sig_tot_esp_prop = 'r_NDDO_Tot_ESP_Variance_On_Mol_Surface'

balance_esp_prop = 'r_NDDO_ESP_Balance_On_Mol_Surface'

local_pol_esp_prop = 'r_NDDO_Avg_Abs_Dev_from_Mean_ESP_On_Mol_Surface'

min_alie_prop = 'r_NDDO_Min_ALIE_On_Mol_Surface'

max_alie_prop = 'r_NDDO_Max_ALIE_On_Mol_Surface'

mean_alie_prop = 'r_NDDO_Mean_ALIE_On_Mol_Surface'

mean_pos_alie_prop = 'r_NDDO_Mean_Pos_ALIE_On_Mol_Surface'

mean_neg_alie_prop = 'r_NDDO_Mean_Neg_ALIE_On_Mol_Surface'

sig_pos_alie_prop = 'r_NDDO_Pos_ALIE_Variance_On_Mol_Surface'

sig_neg_alie_prop = 'r_NDDO_Neg_ALIE_Variance_On_Mol_Surface'

sig_tot_alie_prop = 'r_NDDO_Tot_ALIE_Variance_On_Mol_Surface'

balance_alie_prop = 'r_NDDO_ALIE_Balance_On_Mol_Surface'

local_pol_alie_prop = 'r_NDDO_Avg_Abs_Dev_from_Mean_ALIE_On_Mol_Surface'

min_alea_prop = 'r_NDDO_Min_ALEA_On_Mol_Surface'

max_alea_prop = 'r_NDDO_Max_ALEA_On_Mol_Surface'

mean_alea_prop = 'r_NDDO_Mean_ALEA_On_Mol_Surface'

mean_pos_alea_prop = 'r_NDDO_Mean_Pos_ALEA_On_Mol_Surface'

mean_neg_alea_prop = 'r_NDDO_Mean_Neg_ALEA_On_Mol_Surface'

sig_pos_alea_prop = 'r_NDDO_Pos_ALEA_Variance_On_Mol_Surface'

sig_neg_alea_prop = 'r_NDDO_Neg_ALEA_Variance_On_Mol_Surface'

sig_tot_alea_prop = 'r_NDDO_Tot_ALEA_Variance_On_Mol_Surface'

balance_alea_prop = 'r_NDDO_ALEA_Balance_On_Mol_Surface'

local_pol_alea_prop = 'r_NDDO_Avg_Abs_Dev_from_Mean_ALEA_On_Mol_Surface'

mulliken_charge_prop = 'r_NDDO_Mulliken_Charge'

atomic_charge_prop = 'r_NDDO_NDDO_Charge'

esp_charge_prop = 'r_NDDO_ESP_Charge'

fe_prop = 'r_NDDO_Electrophilic_Frontier_Electron_Density'

fn_prop = 'r_NDDO_Nucleophilic_Frontier_Electron_Density'

se_prop = 'r_NDDO_Electrophilic_Superdelocalizability'

sn_prop = 'r_NDDO_Nucleophilic_Superdelocalizability'

sr_prop = 'r_NDDO_Radical_Superdelocalizability'

asp_prop = 'r_NDDO_Atom_Self_Polarizability'

maxat_esp_prop = 'r_NDDO_Max_surface_ESP'

minat_esp_prop = 'r_NDDO_Min_surface_ESP'

maxat_alie_prop = 'r_NDDO_Max_surface_ALIE'

minat_alie_prop = 'r_NDDO_Min_surface_ALIE'

maxat_alea_prop = 'r_NDDO_Max_surface_ALEA'

minat_alea_prop = 'r_NDDO_Min_surface_ALEA'

__init__(mopfile)

property structure

property method

property output_file

property statusOk

Check the summary status of the job, looking at SCF status and return code of the main routine.

Return True if all is ok, False if not.

set_method(value)

set_output_file(value)

set_return_code(value)

set_count(value)

populate_from_memory()

Populate data derived from the f2py wrapped code.

check_key(keyword)

If the given keyword was set in the job specification, return True, otherwise return False.

set_final_structure(structure)

Set the final structure and update the coordinates to match the final geometry.

get_error_text()

Get the error text set during the main MOPAC calculation. If there is no error text, returns the empty string.

write_vis_files()

This function is not needed in this API

populate_from_outfile(structures)

Parse a MOPAC .out file for a limited set of properties and populate an associated Structure instance with the parsed values.

Currently only “semi-empirical method” (e.g. AM1, PM3) and “Final Heat of Formation” are supported. We consider a subjob to have failed for a given structure if any of these properties fail to be populated from the output file. i.e. we expect any type of MOPAC job will generate these properties.

This method should be used when running a multi-structure MOPAC input file when the f2py interface cannot be used to get results.

Parameters

structures (list) – list of Structure objects

Returns

list of bools denoting job status of each subjob