pymolpro (version 1.15.5)

pymolpro is a Python library that provides support for working with the Molpro quantum chemistry package.

The principal feature is the Project() class that provides access to a complete Molpro job, including input and output files together with metadata such as job status information. The project is stored as a bundle implemented as a directory in the file system. The class is a Python binding of the sjef library with additional Molpro-specific customisation, and the project bundle can be accessed also through a command-line interface and the gmolpro graphical user interface.

For technical reasons, Project() invokes the submodular class pymolpro.project.Project(). Normally all that is required to instantiate a class, on either a new or existing bundle, is to pass a single argument which is the path of the bundle, with or without the compulsory suffix .molpro. Simply running Molpro and inspecting the output can be achieved as:

from pymolpro import Project
p=Project("Neon")
p.write_input("""
geometry={Ne}
rhf
ccsd(t)
""")
p.run()
print(p.out)

Normally, pymolpro.project.Project.run() launches the job in the background, potentially on a remote machine via a suitably configured backend, and its status is available through the pymolpro.project.Project.status attribute. Additionally, the job launching request is ignored if the project has already run the job successfully using the same input; this introduces the convenience of being able to re-run an entire workflow, for example in a Jupyter notebook, without needless recomputation.

Molpro produces an xml file that contains all the essential results, marked up using the molpro-output schema. The pymolpro Project class contains functions that interpret that output, and at the lowest level this can be achieved through a suitable XPath search. For extracting calculated properties, including energies, convenience functions pymolpro.project.Project.properties(), pymolpro.project.Project.energies(), that wrap suitable XPath searches, are provided. These functions can return either a Python dictionary containing all information about the property, or just its value. The following is a simple example where a job is created, run and analysed.:

from pymolpro import Project
p = Project("Neon")
p.write_input("geometry={Ne}; rhf; ccsd(t)")
p.run(wait=True)
assert p.status == 'completed' and not p.errors()
energies = {}
for node in p.xpath("//property[@name='Energy' or @name='total energy']"):
  energies[node.xpath("@method")[0]] = float(node.xpath("@value")[0])
energy_values = p.energies()
all_principal_properties_dict = p.properties(principal=True, dict=True)
final_energy = p.energy(method='CCSD(T)')

Installation

pymolpro is on conda forge and can be installed on most systems using conda install -c conda-forge pymolpro. On Microsoft Windows, you need to also install msys2, and then, in an msys command window, pacman -S rsync openssh.

For a complete set-up of pymolpro within Jupyter notebooks driven from the comand line on linux or macOS,

Install Molpro
Install Miniconda. On macOS with homebrew, this can be done with brew install miniconda. You may need to then type conda init and restart the shell.
Create a conda environment to contain at least these packages; of course you can add any others you need, e.g. matplotlib: conda create -n pymolpro-jupyter -c conda-forge pymolpro jupyter nb_conda_kernels.
If you intend to run Molpro jobs on a remote machine, set up password-free ssh access to it, using the following or otherwise: ssh-keygen; ssh-copy-id user@host. Then edit the file ~/.sjef/molpro/backends.xml to specify the backend.
Activate the environment: conda activate pymolpro-jupyter. To create a new notebook, jupyter notebook; to open an existing notebook jupyter notebook existing_file.ipynb

For a complete set-up of pymolpro within Jupyter notebooks on Windows,

Install Molpro, and msys2 as described above.
Install Anaconda3
Open Anaconda Navigator
Select the Environments tab and press the Create button. Give your new conda environment a name, e.g. pymolpro-jupyter.
With the Channels button, add the conda-forge channel, and then select Not installed and search for, and install pymolpro, jupyter, nb_conda_kernels, as well as any other packages you might want, such as matplotlib.
If you intend to run Molpro jobs on a remote machine, from the command menu run MSYS2, and (a) create a password-free ssh key by running ssh-keygen; (b) authorize that key for login on the desired remote machine: ssh-copy-id user@host; (c) edit the file .sjef\molpro\backends.xml (relative to your Windows home directory) to specify the backend.
Select the Home tab and run the Jupyter Notebook application, ensuring that the selected environment is pymolpro-jupyter.

Contents:

JSON schema for simplified Molpro input

https://www.molpro.net/molpro-input.json
Structured input for Molpro that covers the case of a single ansatz, with a given basis set at a given geometry. All fields are optional, with reasonable defaults, although at least geometry, method and basis will normally be specified
type	object
properties
geometry	The geometry, in any form that Molpro will accept. If the value is the name of a readable file, that file will be the source of the geometry specification; otherwise, the value will be interpreted directly, with or without enclosing {}.
	type	string
	default	He
job_type	The job type - single point, optimisation, frequencies etc.
	default	SP
	anyOf	Single point
		Calculate at a single geometry
		default
		const	SP
		Geometry optimisation
		Optimise the geometry
		const	OPT
		Hessian
		Calculate harmonic force constants and normal modes
		const	FREQ
		Optimise + vib frequencies
		Optimise the geometry and then calculate normal modes
		const	OPT+FREQ
		Non-covalent complex

		const	INTERACT
method	default	hf
	oneOf	type	string
		type	array
		items	type	string
hamiltonian	The Hamiltonian to be used - Schrödinger all-electron, pseudopotential or scalar-relativistic.
	enum	AE, PP, DK, DK3
	default	PP
basis	Specification of the orbital basis set
	type	object
	properties
	default	type	string
		default	cc-pVTZ-PP
	elements	type	object
		additionalProperties	type	string
	additionalProperties	False
core_correlation	Specification of core correlation
	type	string
properties	type	array
	items	type	string
	uniqueItems	True
orbitals	Types of localised orbitals to be calculated.
	type	array
	items	enum	ibo, pipek, nbo, boys
	uniqueItems	True
variables	Variables to be defined at the start of the job
	type	object
parameter	Items for gparam in Molpro input
	type	object
threshold	Items for gthresh in Molpro input
	type	object
print	Items for gprint in Molpro input
	type	object
job_type_commands	Commands for the job_type drivers
	type	object
angstrom	Whether geometry is expressed in Ångstrom instead of Bohr.
	type	boolean
orientation	Weighting of geometry to define centroid and principal axes.
	enum	mass, charge, none
	default	mass
symmetry	Whether to use molecular symmetry.
	enum	automatic, none
	default	automatic
density_fitting	Whether density fitting algorithms are to be used where possible.
	type	boolean
	default	False
prologue	Arbitrary Molpro commands to appear at the start of the job
	oneOf	type	string
		type	array
		items	type	string
epilogue	Arbitrary Molpro commands to appear at the end of the job
	oneOf	type	string
		type	array
		items	type	string
additionalProperties	False

pymolpro (version 1.15.5)

Installation

JSON schema for simplified Molpro input

Indices and tables