pymolpro package

Module contents

class pymolpro.Orbital(node)

Bases: object

Container for an orbital (usually molecular).

property ID
attribute(key)
property axes

The coordinate system for the orbital. The \(z\) axis is the normalised vector \(\vec e_{z}\) that is the eigenvector of the second-moment tensor of largest eigenvalue, similarly for \(\vec e_y, \vec e_x\). The phase of each axis is chosen such that the largest of the coefficients specifying the axis in the global coordinate system is positive.

Returns:

The axes, with the first index labelling the component in the base coordinate system, and the second index specifying which orbital axis.

Return type:

np.array(3,3)

centroid

Centroid of the orbital

evaluate(points, values=False)

Evaluate orbital on a grid of points

Parameters:

  • points – List of geometries specified as 3-list of values in bohr

  • values

Returns:

array of dictionaries giving the occupation and values on the grid, or if ID is specified, a single dictionary, or if values==True, a numpy array

grid(npt, method='erfinv', scale=1.0, grid_parameters=[], spherical_average=False)

Generate a grid centred on the orbital.

Parameters:

  • npt – Number of desired points in each coordinate.

  • method – Algorithm for grid generation.

  • scale – Scale the grid by this factor.

Returns:

points and weights (numpy array [npt,4])

property kinetic_energy

Kinetic energy expectation value for the orbital.

property local_second_moments
occupation

Occupation of the orbital

second_moment_eigenvalues

Eigenvalues of the orbital second-moment tensor (origin at centre of charge) in ascending order

class pymolpro.Pair(node)

Bases: Tuple

Container for a pair of orbitals

property axes

The coordinate system for the pair of orbitals. The \(z\) axis is the vector \(\vec e_{z,10}=(\vec r_1-\vec r_0)/|\vec r_1-\vec r_0|\) from orbital 0 to orbital 1. The \(x\) axis is the along the vector \(\vec e_{x,10} = \vec e_{z,10} \times \vec e_z\) (or \(\vec e_y\) if necessary), normalised. Then \(\vec e_{y,10}=\vec e_{z,10}\times\vec e_{x,10}\). If \(|\vec r_1-\vec r_0|\) is small, the global coordinate axes are adopted.

Returns:

The axes, with the first index labelling the component in the base coordinate system, and the second index specifying which pair axis.

Return type:

np.array(3,3)

property local_orbital_axes

The coordinate axes of the orbitals expressed in the basis of the pair coordinate system.

Returns:

Return type:

list(np.array(3,3))

pymolpro.Project(name='', suffix=None, **kwargs)

This is a project factory. Based on filename suffix it decides which Project to create.

Extensions of pysjef which define a new project should add theirs to the PROJECT_FACTORY. The key is the suffix specifying the backend.

Project(‘a’) # creates a.sjef Project(‘a.molpro’) # creates a.molpro and sets suffix to .molpro Project(‘a.sjef`, suffix=’molpro’) # creates a.sjef.molpro and sets suffix to .molpro

Parameters:

  • name – name of the file

  • suffix – suffix indicating which program to use

Returns:

class pymolpro.Single(node)

Bases: Tuple

Container for a single orbital

class pymolpro.Tuple(node)

Bases: object

Container for a tuple of orbitals

Parameters:

node (lxml.etree.Element) – Node holding a correlation single or pair descriptor

energy

Correlation energy contribution from a Single or Pair

orbitals

Orbital objects forming the tuple

spins

1(alpha) or -1(beta) for each orbital

pymolpro.element_to_dict(node, attributes=True)

Convert an lxml.etree node tree into a dict.

Parameters:

  • node (lxml.etree.ElementTree) – A node in an lxml tree

  • attributes (bool, optional) – whether to include attributes in the result

Returns:

A dictionary representing the tree

Return type:

dict

pymolpro.no_errors(projects, ignore_warning=True)

Checks that none of the projects have any errors. Projects can by running.

Parameters:

  • projects – list of projects to check for errors

  • ignore_warning – Whether to count warnings as well as errors.

Returns:

True/False whether any projects have errors

pymolpro.xyz_to_zmat(xyz: str, algorithm='chemcoord')

Converts from xyz to z-matrix coordinates.

Parameters:

  • xyz – xyz-file

  • algorithm – algorithm to choose, default is the chemcoord algorithm

Returns:

The Z matrix as a string, or None in case of unknown algorithm,

Return type:

str

Submodules

pymolpro.project module

class pymolpro.project.Project(name=None, geometry=None, method='hf', basis='cc-pVTZ', func='energy', extrapolate='', symm=True, ansatz=None, geometry_method=None, geometry_basis=None, preamble=None, postamble=None, initial=None, charge=None, spin=None, **kwargs)

Bases: Project

A Project holds all the data associated with a single Molpro job. This includes input, output, any auxiliary files, and information about the state of the job. Project acts as a reference to a sjef Project with some added functionality. All of the data is stored in the project bundle on the file system, with the consequence that it is safe to construct and recreate multiple Project objects all mapping the same underlying project.

The underlying functionality of sjef includes job submission and monitoring on local or remote machines, and structured searching of Molpro’s xml output stream. This class provides additional convenience operations:

  • Preparation of simple Molpro input from provided geometry, method, basis set and other options.

  • Molpro-specific error checking.

  • Computed properties, energies and geometries.

  • Computed orbitals, including their evaluation on a grid.

  • Values of Molpro variables.

Parameters:

  • name (str) – The base filename of the filesystem bundle carrying the project. If the bundle does not yet exist, it is created.

  • geometry (str) – The geometry. If specified, the input for the job will be constructed, without the need for a subsequent call to write_input(). Any format recognised by Molpro can be used. This includes xyz, with or without the two header lines, or Z matrix, and lines can be separated either with newline or ;. The geometry can be specified either as a string, or a filename or url reference, in which case the contents of the reference are resolved now.

  • method (str) – The computational method for constructed input. Anything accepted as Molpro input, including parameters and directives, can be given. If the method needs a preceding Hartree-Fock calculation, this is prepended automatically.

  • basis (str) – The orbital basis set for constructed input. Anything that can appear after basis= in Molpro input is accepted.

  • ansatz (str) – String of the form method/basis//geometry_method/geometry_basis or method/basis which is parsed to give the same effect as the

method and basis parameters. If geometry_method/geometry_basis is specified, the calculation will be preceded by a geometry optimisation at that level of theory. :param str func: This should be one of

  • energy for a single geometry

  • opt for a geometry optimisation

Parameters:

  • extrapolate (str) – If specified, carry out basis-set extrapolation. Anything that can appear after extrapolate,basis= in Molpro input is accepted.

  • spin (int) – The spin multiplicity minus one

  • charge (int) – Electrical charge of molecule

backend_get(backend, key)

Obtain the value of a field in the backend :param backend: :param key: :return:

backend_names()

Get the names of all the backend objects associated with the object.

backend_parameter_default(backend, param)

Returns default value for backend parameter

Parameters:

  • backend – name of the backend

  • param – name of parameter

backend_parameter_delete(backend, param)

Delete backend parameter from property file.

Parameters:

  • backend – name of the backend

  • param – name of parameter

backend_parameter_documentation(backend, param)

Returns documentation for backend parameter

Parameters:

  • backend – name of the backend

  • param – name of parameter

backend_parameter_get(backend, param)

Gets backend parameter from property file.

Parameters:

  • backend – name of the backend

  • param – name of parameter

backend_parameter_set(backend, param, value)

Sets backend parameter in property file. The parameter will be used by the backend when interacting with the current jobs.

Parameters:

  • backend – name of the backend

  • param – name of parameter

  • value – parameter value to set

backend_parameters(backend, doc=False)

Get all of the parameters referenced in the run_command of a backend

Parameters:

  • backend – The name of the backend

  • doc – Whether to return documentation instead of default values

Returns:

A dictionary where the keys are the parameter names, and the values the defaults.

basis_registry()

Get the basis registry from the Molpro pointed to in the local backend

Returns:

Return type:

dict

builtins = <module 'builtins' (built-in)>
child(*attributes, nodename='', **kwargs_and_callables)

Utility wrapper over select routine to do a 1 level search of children and select a single one. If more than one child is selected, RuntimeError is thrown.

Arguments are translated into selectors by attribute name ( see select). Key word arguements are translated into selectors by attribute name ( see select).

Example:

out = p.select(‘container[location, name=directory, exists(location)]’,

exists=os.path.exists)

is equivalent to

out = p.child(‘location’, nodename=’container’, name=’directory’, ‘exists(location)’,

exists=os.path.exists)

Parameters:

  • nodename – selector for name of the node class

  • attributes – list of attributes for defining selectors by name, [attribute] and callable selectors [func(attr1, attr2)] ( see select)

  • kwargs_and_callables – dictionary of other kwargs defining attribute selectors key = value and callable functions for callable selectors func = function_name

Returns:

clean(keep_run_directories=1)

Remove run directories from the project

commandify_method(method)
completed()
Returns:

True if status is completed

copy(name, location=None, force=False, keep_hash=False, keep_run_directories=1000000)

Make a copy of the project and its directory to a new path.

Parameters:

  • name – name of the new project

  • location – path to the parent of the project, by default parent directory stays the same

  • force – whether to first remove anything already existing at the new location

  • keep_hash – whether to clone the project_hash, or allow a fresh one to be generated

  • keep_run_directories – how many run directories to retain in the copy

Returns:

copied project

copy_node()

Returns a copy of itself

energies(*args, **kwargs)

Wrapper for properties() that restricts to energy values

Parameters:

  • args

  • kwargs

Returns:

energy(*args, **kwargs)

Wrapper for energies() that returns a single value as a scalar. An exception is thrown if more than one value is found.

Parameters:

  • args

  • kwargs

Returns:

erase(path=None)

Delete the project under path with its directory and all files.

Parameters:

path – path to the project, defaults to current project

Todo:

what should happend to attributes and children?

errors(ignore_warning=True)

Return all error nodes

Returns:

list of error nodes

Return type:

lxml.etree

evaluateOrbitals(points, instance=-1, minocc=1e-10, ID=None, values=False)

Evaluate molecular orbitals on a grid of points

Parameters:

  • points – List of geometries specified as 3-list of values in bohr, or numpy [:,3] array

  • instance – Which set of orbitals

  • minocc – Only orbitals with at least this occupation will be returned

  • ID – Only the orbital whose ID attribute matches this will be selected

  • values

Returns:

array of dictionaries giving the occupation and values on the grid, or if ID is specified, a single dictionary, or if values==True, a numpy array

export_file(filename, location, overwrite)

Export one or more files from the project.

Parameters:

  • filename – name of the file in the project

  • location – The relative or absolute path to the destination directory

  • overwrite – Whether to overwrite an existing file.

filename(suffix='', name='', run=0)

Get the file name of the bundle, or a primary file of particular type, or a general file in the bundle

Parameters:

  • suffix – If present without name, look for a primary file with that type. If absent, the file name of the bundle is instead selected

  • name – If present, look for a file of this name, appended with .suffix if that is non-blank

  • run –

    • 0: the currently focussed run directory

    • other: the specified run directory

Returns:

the fully-qualified name of the file

findall(search_pattern)
geometries(preamble='//')

Obtain all geometries from the job output

Parameters:

preamble – Prepend this to the xpath search expression to locate the geometry

Returns:

list of dictionaries holding the geometry. Coordinates are in bohr

geometry(preamble='//', instance=-1)

Obtain the geometry from the job output

Parameters:

  • preamble – Prepend this to the xpath search expression to locate the geometry

  • instance – In the case of multiple geometries in the output stream, which occurence

Returns:

dictionary holding the geometry. Coordinates are in bohr

import_file(location, overwrite=True)

Import file at path location into the project.

Parameters:

  • location – path to file

  • overwrite – if corresponding file already exists in the project, flags that it should be overwritten

import_input(fpath)

Copy file into the project as input file, or write string to input file :param fpath: path to input file

property input_file_path
input_from_output(instance=-1)

Return a list of all defined input in the output stream

Parameters:

instance – index of occurence of input node in output

Returns:

kill()

Kill the job started by run()

list_files()

Return a list of files in the project directory

property local_molpro_root

Get the directory of the Molpro installation in the local backend :return: directory :rtype: pathlib.Path

property location

Local path to the project directory

move(name=None, location=None, force=False)

Move the project bundle to a new location

Parameters:

  • name – new name of the project

  • location – path to the directory where project should be moved. Defaults to same directory as current project.

  • force – whether to first remove anything already existing at the new location

property name

Name of the project

orbitals(instance=-1, minocc=1.0, ID=None)

Obtain some or all of the orbitals in the job output

Parameters:

  • instance – Which set of orbitals

  • minocc – Only orbitals with at least this occupation will be returned

  • ID – Only the orbital whose ID attribute matches this will be selected

Returns:

a list of Orbital objects

property out
property output
Returns:

node with Molpro’s output

property output_file_path
pairs(instance=-1)

Obtain some or all of the correlation pairs in the job output

Parameters:

instance – Which set of pairs

Returns:

a list of Pair objects

parse(force=False, **options)

Parse the output file and save resultant node as a child :param force: reparse the output

parse_ansatz(ansatz)
procedures_registry()

Get the procedures registry from the Molpro pointed to in the local backend

Returns:

Return type:

dict

properties(*args, **kwargs)

Obtain selected properties from the job output

Parameters:

  • args – any trailing XPath qualifier, for example '[@StateSymmetry = "1" or @StateSymmetry = "4"]'. For restrictions that should be combined with and, it’s simpler to instead use a kwarg argument, eg StateSymmetry=1

  • kwargs – any attribute selectors for the select function, including the following

  • name – name of property

  • principal – restrict to principal property

  • preamble – XPath expression to prepend the search for the property node

  • command – restrict to properties contained in a jobstep with this command

  • dict – return property value, scalar float or list of floats as appropriate, if False or omitted. Otherwise, a dictionary containing all the data in the property node is returned

Returns:

list of properties

properties_old(name='Energy', principal=True, *, value=False, **kwargs)

Obtain selected properties from the job output

Parameters:

  • name – name of property

  • principal – principal property

  • value – return by value

  • kwargs – any other attribute selectors for the select function

Returns:

list of properties

Shorthand for p.select(‘//properties[name= {}, principal ={}, … ]’)

property(*args, **kwargs)

Wrapper for properties() that returns a single value as a scalar. An exception is thrown if more than one value is found.

Parameters:

  • args

  • kwargs

Returns:

property_delete(*properties)

Delete properties

property_get(*properties)

Return a dictionary of property, value pairs

property_names()

Return names of all assigned properties

property_set(properties)

Set the value of a project property

recent_find(location)
refresh_backends()

Reload the backends from the configuration file :return:

registry(set=None)

Access the registry belonging to Molpro in the local backend.

Parameters:

set – If present, obtain as a dictionary the specified registry set. If absent, obtain a list of all sets

Returns:

run(backend=None, verbosity=0, force=False, wait=False, options='')

Start a sjef job :param backend: name of the backend :param verbosity: If >0, show underlying processing :param force: whether to force submission of job even if run_needed() reports that it’s unnecessary :param wait: whether to wait until the job completes instead of returning after launchin it :param options: command-line options

run_local_molpro(options: list)
run_needed(verbosity=0)

Check weather the job has changed since the previous run and needs to be rerun :return: True/False

select(selection_string, **options_and_callables)

Specialization of pysjef.select() which applies selection to the parsed output

Returns:

list of nodes that pass selection criteria

singles(instance=-1)

Obtain some or all of the correlation singles in the job output

Parameters:

instance – Which set of singles

Returns:

a list of Single objects

property status

String status of the project. Can be one of: unknown, running, waiting, completed, unevaluated, killed, or failed.

trash()

Move the project bundle to the trash

tree_view(**options)

Build tree view from this node

variable(name, instance=-1, list=False, dict=False)

Return the value of a variable in the output xml stream

Parameters:

  • name – The name of the variable

  • instance – index of occurence in output

  • list – Whether to force returning a list. If true, a list is always returned; otherwise if the result is a scalar, a scalar is returned, and if no match is found, None is returned

  • dict – return property value, scalar float or list of floats as appropriate, if False or omitted. Otherwise, a dictionary containing all the data in the property node is returned

Returns:

variables(instance=-1)

Return a list of all defined variables

Parameters:

instance – index of occurence of variables node in output

Returns:

view_input()

Opens the input file in editor as specified by ‘$EDITOR’ environment variable. Should by called from an interactive session

view_output()

Opens the input file in editor as specified by ‘$EDITOR’ environment variable. Should by called from an interactive session

wait(max_epoch=0.005)

Wait unconditionally for status() to return neither ‘waiting’ nor ‘running’ :param max_epoch: maximum time to wait between checking status (seconds)

write_file(filename, content, overwrite=True)

Creates a file in the project with specified content

Parameters:

  • filename – name of the file to create in the project

  • content – string content to write in the file

  • overwrite – if corresponding file already exists in the project, flags that it should be overwritten

Returns:

True if file was created or overwritten, otherwise False

write_input(content)

Create an input file with content specified as a string :param content: string with content for the input file

property xml
xpath(query, element=None)

Run xpath search on an element in the job xml, with support for default namespace

Parameters:

  • query – Any xpath search expression supported by lxml.etree.Element

  • element – The root element for the search, defaulting to the job xml root element

Returns:

list of etree.Element objects or of strings, depending on whether the xpath expression results in an attribute

Simple XPath search on the xml document. For each matching node found, return a string that contains the value of a specified attribute, or if the attribute is omitted, the node contents.

Parameters:

  • xpath_query

  • attribute

  • run

xyz(preamble='//', instance=-1, title='')

Obtain a geometry in xyz file format

Parameters:

  • instance – In the case of multiple geometries in the output stream, which occurence

  • preamble – Prepend this to the xpath search expression to locate the geometry

  • title – A title to be injected into the second line

Returns:

A string containing the xyz representation of the geometry

xyzs(preamble='//', title='')

Obtain a set of geometries in xyz file format

Parameters:

  • preamble – Prepend this to the xpath search expression to locate the geometry

  • title – A title to be injected into the second line

Returns:

A list of strings containing the xyz representation of the geometry

pymolpro.project.element_to_dict(node, attributes=True)

Convert an lxml.etree node tree into a dict.

Parameters:

  • node (lxml.etree.ElementTree) – A node in an lxml tree

  • attributes (bool, optional) – whether to include attributes in the result

Returns:

A dictionary representing the tree

Return type:

dict

pymolpro.project.method_from_commands(commands)
pymolpro.project.no_errors(projects, ignore_warning=True)

Checks that none of the projects have any errors. Projects can by running.

Parameters:

  • projects – list of projects to check for errors

  • ignore_warning – Whether to count warnings as well as errors.

Returns:

True/False whether any projects have errors

pymolpro.project.resolve_geometry(geometry)

pymolpro.database module

class pymolpro.database.Database(molecules={}, reactions={}, description=None, method=None, basis=None, options=None, project_directory=None)

Bases: object

Database of molecular structures and reactions. The class contains and supports the following data.

  • Descriptions of molecules: geometry, charge, spin state.

  • Descriptions of reactions between the molecules: stochiometric factors.

  • Optionally, computed data: energies of molecules and/or reactions,s the parameters used to obtain them, and references to persistent data that can be used to further query or restart.

  • Description and external URLs that serve to further define the provenance of the data.

  • Specification of recommended subsets of the reactions

Parameters:

  • molecules (list) – Initial molecules to be added with default options to add_molecule().

  • reactions (list) – Initial reactions to be added with default options to add_reaction().

  • description (str) – Text describing the database

  • method (str) – A string specifying the ansatz that was used to compute the energies. In the Molpro context, this will be a valid fragment of Molpro input.

  • basis (str) – A string specifying the orbital basis set that was used to compute the energies.

  • options (str) – A string specifying any additional options used to compute energies.

  • project_directory (str) – The path of the directory where support files that were generated in calculating energies can be found.

add_molecule(name, geometry, energy=None, description=None, InChI=None, SMILES=None, spin=None, charge=None, preamble=None)

Add a molecule to the database. The minimal information that is stored is the geometry, but information from each of the optional arguments, if given, is also stored in the molecules dictionary.

Parameters:

  • name (str) – The key for the molecule in molecules.

  • geometry (str) – The geometry. Any format recognised by Molpro can be used. This includes xyz, with or without the two header lines, or Z matrix, and lines can be separated either with newline or ;. The geometry can be specified either as a string, or a filename or url reference, in which case the contents of the reference are resolved now.

  • energy (float) – The reference value for the energy of the molecule in Hartree units

  • description (str) – Descriptive text

  • InChI (str) – InChI string describing the molecule

  • SMILES (str) – SMILES string describing the molecule

  • spin (int) – The spin multiplicity minus one

  • charge (int) – Electrical charge of molecule

  • preamble (str) – Additional Molpro input to be added before geometry

Returns:

The added molecule

Return type:

dict

add_reaction(name, stoichiometry, energy=None, description=None)

Add a reaction to the database. The minimal information that is stored is the stoichiometry, which references existing molecules in the database, but information from each of the optional arguments, if given, is also stored in the reactions dictionary.

Parameters:

  • name – The key for the reaction in reactions.

  • stoichiometry – A dictionary describing the stoichiometry of the reaction. Each key should be a key in molecules, and the value is an integer giving the number of equivalents of the molecule in the reaction, with the sign convention of positive for products, negative for reactants.

  • energy – The reference value for the energy change of the reaction in Hartree units. If not given, and if all molecules in the reaction have an energy, it will be computed.

  • description – Descriptive text

Returns:

The added reaction

Return type:

dict

add_reference(key, url)
add_subset(subset_name, subset)
basis

A string specifying the orbital basis-set used to compute the energies.

calculate_reaction_energies(check=False)
copy()
description

Text describing the database

dump(filename=None)

Dump the database in json format.

Parameters:

filename (str) – If specified, the destination of the result

Returns:

If filename is not specified, the json is returned as a string

Return type:

str

failed

Subset of projects corresponding to jobs that did not complete successfully.

load(source)

Load the database from a json dump in either the library, a file or a string

Parameters:

source (str) – Source of dump

Returns:

The database

Return type:

Database

method

A string specifying the ansatz used to compute the energies. In the Molpro context, this will be a valid fragment of Molpro input.

molecule_energies

A dictionary with molecule keys giving the molecular energy/Hartree reference values associated with the Database. The dictionary could be empty or only partly filled.

molecules

Dictionary of molecules

options

Any additional options used to compute reference values.

preamble

any Molpro commands that should be executed before geometry specification. Typically angstrom could be specified if the geometry specification is in Z-matrix format with numerical values that would, by default, be interpreted as Bohr.

project_directory

A string giving the path of the directory where support files generated in calculating energies can be found.

projects

A dictionary with molecule handles pointing to filesystem project bundles for each Molpro job that has been run.

reaction_energies

A dictionary with reaction keys giving the reaction energy/Hartree reference values associated with the Database. The dictionary could be empty or only partly filled. A database might have either, both or none of molecule_energies or reaction_energies.

reactions

Dictionary of reactions involving the molecules together with stoichiometric factors

references

A dictionary of external references to the data. The keys should be a short-form string that you want printed, eg author, year, and the values URLs that lead to the resource.

subset(subset=None, open_shell=True, max_atoms=None, max_electrons=None)

Extract a subset of this database as a new database

Parameters:

  • subset – Either a key in the subsets or a list of keys in reactions. If not given, all the reactions in the database

  • open_shell – Whether to include reactions involving open-shell molecules, or prune to closed-shell only

  • max_atoms – Exclude reactions with one or more molecules with more than this number of atoms

  • max_electrons – Exclude reactions with one or more molecules with more than this number of electrons

Returns:

The subset

Return type:

Database

subsets

A dictionary defining named subsets of the database reactions

pymolpro.database.analyse(databases, reference_database=None, unit=None, **kwargs)

Analyse and format the results in one or more databases

Parameters:

  • databases (list(Database)|Database)

  • reference_database (Database)

  • unit – Either a string or a float specifying desired units for the output. In the case of a string, it should match (case insensitive) one of the keys of units; if an explicit value is given, it should be the value of the desired units in atomic units, ie the results will be divided by the value.

Returns:

A dictionary with keys, where possible,

  • molecule energies

  • molecule energy deviations

  • molecule statistics

  • molecule violin

  • reaction energies

  • reaction energy deviations

  • reaction statistics

  • reaction violin

The energy deviations are, for each molecule or reaction, the difference between the energies in each element of databases and the value in reference_database. The values are pandas Dataframe objects, whose columns correspond to the elements of databases. In the case of the molecule or reaction energies or energy deviations, the rows correspond to the individual molecule or reaction. In the case of statistics, the rows are

  • MSD: the mean of the deviations

  • STDEVD: the standard deviation of the deviations

  • MAD: the mean of the absolute value of the deviations

  • MAXD: the maximum absolute value of the deviations

  • RMSD: the root mean square deviation

Return type:

dict

pymolpro.database.basis_extrapolate(results, hf_results, x=None)
pymolpro.database.load(source)

Construct a Database from a json dump in either the library, a file or a string

Parameters:

source (str) – Source of dump

Returns:

The database

Return type:

Database

pymolpro.database.run(db, ansatz=None, method='hf', basis='cc-pVTZ', location='.', parallel=None, backend='local', clean=False, initial='', check=False, check_energy=True, **kwargs)

Construct and run a Molpro job for each molecule in a Database, and compute reaction energies.

Parameters:

  • db (Database) – The database that defines molecules and reactions.

  • method (str) – The computational method for constructed input. Anything accepted as Molpro input, including parameters and directives, can be given. If the method needs a preceding Hartree-Fock calculation, this is prepended automatically.

  • basis (str) – The orbital basis set for constructed input. Anything that can appear after basis= in Molpro input is accepted.

  • ansatz (str) – String of the form method/basis//geometry_method/geometry_basis or method/basis which is parsed to give the same effect as the

method and basis parameters. If geometry_method/geometry_basis is specified, the calculation will be preceded by a geometry optimisation at that level of theory. :param str func: This should be one of

  • energy for a single geometry

  • opt for a geometry optimisation

Parameters:

  • extrapolate (str) – If specified, carry out basis-set extrapolation. Anything that can appear after extrapolate,basis= in Molpro input is accepted.

  • location (str) – The filesystem directory in which projects will be constructed.

  • parallel (int) – The number of simultaneous jobs to be launched. The default is the number of cores on the local machine.

  • backend (str) – The sjef backend to be used for running jobs.

  • clean (bool) – Whether to destroy the project bundles on successful completion. This should not normally be done, since later invocations of run() will use cached results when possible. If there are errors, this parameter is ignored.

  • initial (str) – Any valid molpro input to be placed before the geometry specification.

  • check (bool) – Whether to check for status of jobs instead of running them.

  • check_energy (bool) – Whether to throw an exception if any job did not set the Molpro ENERGY variable

  • kwargs – Any other options to pass to project.Project.run(), including func, extrapolate, preamble, postamble.

Returns:

A new database which is a copy of db but with the new results overwriting any old ones

Return type:

Database

pymolpro.database.units = <pymolpro.database.Units object>

dictionary of units, giving their values in atomic units

pymolpro.grid module

pymolpro.grid.cubical_grid(points1d, weights1d)

Take a one-dimensional grid, and construct a 3-dimensional outer-product cubical grid

Parameters:

  • points1d

  • weights1d

Returns:

points and weights (numpy array [npt,4])

pymolpro.grid.evaluateBasis(molecule, points)

Evaluate the orbital basis set on a grid

Parameters:

  • molecule – lxml.etree.Element holding the molecule

  • points – numpy :,3 array

Returns:

numpy :,: array, first index basis function, second index brid point

pymolpro.grid.evaluateOrbitals(molecule, points, minocc=1e-10, ID=None, values=False)

Evaluate the molecular orbitals on a grid

Parameters:

  • molecule – lxml.etree.Element holding the molecule

  • points – numpy :,3 array

  • minocc – Only orbitals with at least this occupation will be returned

  • ID – Only the orbital whose ID attribute matches this will be selected

  • values

Returns:

array of dictionaries giving the occupation and values on the grid, or if ID is specified, a single dictionary, or if values==True, a numpy array

pymolpro.grid.spherical_grid(radial_points, radial_weights, l: int)

Take a one-dimensional grid, and use it for radial integration, together with a Lebedev grid of specified order, to generate a 3-dimensional grid (cartesian coordinates, weights) for quadrature.

Parameters:

  • radial_points

  • radial_weights

  • l – Largest rank of spherical harmonic for which exact quadrature is wanted.

Returns:

points and weights (numpy array [npt,4])

pymolpro.node_xml module

class pymolpro.node_xml.AxesXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:axes Children: [list of doubles]

class pymolpro.node_xml.BasisSetXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:basisSet - Container for a basis set Children: basisGroup, association Attributes: str id, str type, str angular, int groups, str primitives, int length, int cartesianLength

class pymolpro.node_xml.CmlAtomXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

cml:atom - Output about a single atom

class pymolpro.node_xml.CmlMoleculeXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

cml:molecule - Output about a single molecule Children: cml:atomarry, cml:symmetry

class pymolpro.node_xml.CubeXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:cube - Metadata for a cube dataset Children: field, dimensions, origin, axes, step Attributes: str method

class pymolpro.node_xml.DateXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:date - The time of the calculation. Children: [string datetime] Attributes: int year, int month, int day, int hour, int minute, int second

class pymolpro.node_xml.DiagnosticsXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:diagnostics - Diagnostic info from the job Attributes: int warnings

class pymolpro.node_xml.DimensionsXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:dimensions Children: [list of doubles]

class pymolpro.node_xml.FieldXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:field Attributes: str quantity, str type, str number, str symmetry, double occupancy, double energy, str file

class pymolpro.node_xml.InputXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:input - Molpro input dataset Children: p, include

class pymolpro.node_xml.JobstepXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:jobstep - Output from a single job step Children: error, gradient, opt, property, cube, time, storage, vibrations, jobstep, cml:molecule, variables, instanton Attributes: str command, str commandset, bool displaced

class pymolpro.node_xml.LicenceXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:licence Attributes: str id

class pymolpro.node_xml.MachineXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:machine Attributes: str hostname

class pymolpro.node_xml.MoleculeXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:molecule - Summary output about the job Children: cml:molecule, basisSet, vibrations, orbitals, stm:metadataList, platform Attributes: str id, str index, str InChI, str InChIKey, str SMILES, str title, str method, str basis, str geometryMethod, str geometryBasis, double energy

class pymolpro.node_xml.NormalCoordinateXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:normalCoordinate - A normal vibrational coordinate Children: [list of doubles] Attributes: double wavenumber, str units, double IRintensity, str IRintensityunits, str symmetry, str real_zero_imag

class pymolpro.node_xml.OrbitalXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:orbital - A Molpro molecular orbital Children: [string] Attributes: str symmetryID, double energy, double occupation

class pymolpro.node_xml.OrbitalsXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:orbitals - Container for Molpro internal orbitals Children: orbital Attributes: str basis, str angular, str spin, str method

class pymolpro.node_xml.OriginXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:origin Children: [list of doubles]

class pymolpro.node_xml.ParallelXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:parallel Attributes: int processes, int nodes, int all_processes, int openmp

class pymolpro.node_xml.PlatformXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:platform - Container for metadata about the platform Children: version, licence, parallel, machine, dimensions

class pymolpro.node_xml.PlotXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:plot - Metadata for plot from a Molpro table Attributes: str table, str plot, str type Also attributes from http://www.w3.org/1999/xlink

class pymolpro.node_xml.PropertyXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:property - Output about a single property of a single molecule Attributes: str name, any value

class pymolpro.node_xml.StepXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:step Children: [list of doubles]

class pymolpro.node_xml.VariableXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

TODO Doc

class pymolpro.node_xml.VariablesXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:variables - Container for Molpro internal variables Children: variable

class pymolpro.node_xml.VersionXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:version Children: [string], date Attributes: int major, int minor, str SHA, int integer_bits, str parallelism

class pymolpro.node_xml.VibrationsXml(filename=None, xml=None, parent=None, suffix=None, **options)

Bases: RootXml

molpro-output:vibrations - Container for info on molecular vibrations Children: normalCoordinate Attributes: str name, str type, str units, int length

pymolpro.node_xml.tag_to_name(tag)

Takes XML tag with namespace, outputs raw node name.