schrodinger.application.mopac.results2012 module

This module parses and stores the results of a MOPAC2012 calculation. A MopacResults2012 class is populated with data from the MOPAC2012 output files using a text parser.

exception schrodinger.application.mopac.results2012.MopacPropertyError

Bases: Exception

exception schrodinger.application.mopac.results2012.MopacNumericalError

Bases: Exception

exception schrodinger.application.mopac.results2012.MopacBasisError1

Bases: Exception

exception schrodinger.application.mopac.results2012.MopacBasisError2

Bases: Exception

exception schrodinger.application.mopac.results2012.MopacBasisError3

Bases: Exception

exception schrodinger.application.mopac.results2012.MopacBasisError4

Bases: Exception

exception schrodinger.application.mopac.results2012.MopacBasisError5

Bases: Exception

class schrodinger.application.mopac.results2012.Mopac2012TextParser(file_iter)

Bases: object

Parser for the MOPAC2012 .out and .aux files. Using decorators, the callback() function below populates the “callbacks” dictionary in this class with key-value pairs of the form (regex,func) where “regex” is a regular expression to catch patterns in the output file, and “func” is the callback function which is triggered when the regex is matched.

In this way, each specific callback is triggered by a given pattern such as ‘HOMO LUMO ENERGIES (EV) =’, and the callback function processes the matched lines.

Note that multiple regex’s can be associated with a given callback function by associating it with two or more decorators. In this way, the same callback can be triggered multiple times. e.g. for both the .aux and .out files, perhaps for consistency checking etc.

Typically, however, only one regex is associated with each callback so that data for a given property is grepped from either the .out file OR the .aux file, but not both.

callbacks = OrderedDict([(re.compile('HEAT_OF_FORMATION:KCAL/MOL=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('FINAL HEAT OF FORMATION\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('\\s+(.*)\\s+CALCULATION RESULTS'), <function func>), (re.compile('IONIZATION_POTENTIAL:EV=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('HOMO LUMO ENERGIES \\(EV\\) =(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('ALPHA SOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('ALPHA HOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('BETA\\s+SOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('BETA\\s+HOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('Parr & Pople absolute hardness:(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('Mulliken electronegativity:(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('DIPOLE:DEBYE=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('DIP_VEC:DEBYE\\[3\\]=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('DIPOLE MOMENT EVALUATED FROM THE POINT CHARGES'), <function func>), (re.compile('ATOM_X:ANGSTROMS\\[(\\d+)\\]='), <function func>), (re.compile('ATOM_X_OPT:ANGSTROMS\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('^ MULLIKEN_ATOM_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('^ ELECTOSTATIC_POTENTIAL_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('a\\s+n\\s+Dn\\(r\\)\\s+De\\(r\\)\\s+q\\(r\\) - Z\\(r\\)'), <function func>), (re.compile('a\\s+n\\s+piS\\(r\\)'), <function func>), (re.compile('^ ATOM_EL\\[(\\d+)\\]='), <function func>), (re.compile('^ NUM_ELECTRONS=(\\d+)'), <function func>), (re.compile('^ AO_ATOMINDEX\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_SYMTYPE\\[(\\d+)\\]='), <function func>), (re.compile('^ AO_ZETA\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_PQN\\[(\\d+)\\]='), <function func>), (re.compile('^ EIGENVALUES\\[(\\d+)\\]='), <function func>), (re.compile('^ MOLECULAR_ORBITAL_OCCUPANCIES\\[(\\d+)\\]='), <function func>), (re.compile('^ OVERLAP_MATRIX\\[(\\d+)\\]='), <function func>), (re.compile('^ EIGENVECTORS\\[(\\d+)\\]='), <function func>)])

parse()

Loop over self.file_iter and trigger the callbacks.

schrodinger.application.mopac.results2012.fortfloat(val)

Convert a floating point number in Fortran notation to a regular float.

schrodinger.application.mopac.results2012.check_memory_use(nvals, name)

Check memory requirment for a long list of floats. Print message if size exceeds MEMORY_WARNING.

schrodinger.application.mopac.results2012.update_props(props, key, value, precision=5)

Update the props dictionary with the key-value pair, performing consistency checks if the key already exists.

schrodinger.application.mopac.results2012.callback(regex)

This decorator is just a convenient way to populate the callbacks dictionary in the Mopac2012TextParser. The associated functions themselves are not actually decorated.

schrodinger.application.mopac.results2012.func(props, match, it)

class schrodinger.application.mopac.results2012.MopacResults2012

Bases: schrodinger.application.mopac.mopac_results.MopacResults

A class to parse and store the results of a MOPAC2012 calculation.

structure

A Schrodinger Structure object which is populated with output data.

method

Type:str

name of semi-empirical method (i.e. a MOPAC keyword)

output_file

Type:str

name of output file generated by MOPAC.

set_method(value)

set_status(value)

set_output_file(value)

statusOk()

Needed to be consistent with legacy code

get_error_text()

Needed to be consistent with legacy code

populate_from_file(filename)

Parse “filename” containing MOPAC2012 output data.

set_final_structure(structure, filename)

Compile parsed results into the structure.properties dictionary.

write_vis_files(jobname, nplot, gridres, gridext)

This function will call the Fortran routines to generate the 3D data and .vis files for plotting surfaces.

Parameters:nplot (int) – number of MOs to plot around HOMO/LUMO gap.