https://github.com/psi4/psi4numpy

Combining Psi4 and Numpy for education and development.
https://github.com/psi4/psi4numpy

computational-chemistry numpy psi python scipy tutorial

Last synced: 4 days ago
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Combining Psi4 and Numpy for education and development.

• Host: GitHub
• URL: https://github.com/psi4/psi4numpy
• Owner: psi4
• License: bsd-3-clause
• Created: 2014-08-04T22:30:47.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2024-01-08T00:41:05.000Z (12 months ago)
• Last Synced: 2024-12-20T21:13:23.827Z (11 days ago)
• Topics: computational-chemistry, numpy, psi, python, scipy, tutorial
• Language: Jupyter Notebook
• Homepage:
• Size: 11.6 MB
• Stars: 351
• Watchers: 36
• Forks: 160
• Open Issues: 17
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        





 


 



 






 

 

 

 






---

### Overview

> What I cannot create, I do not understand. - Richard Feynman

The overall goal of the Psi4NumPy project is to provide an interactive quantum chemistry

framework for reference implementations, rapid prototyping, development, and education.

To do this, quantities relevant to quantum chemistry are computed with the

 Psi4  electronic structure package, and subsequently manipulated 

using the Numerical Python (NumPy) package.  This combination

provides an interface that is both simple to use and remains relatively fast

to execute. 

A series of short scripts demonstrating the implementation of Hartree-Fock Self-Consistent 

Field, SCF Response, Møller-Plesset Perturbation Theory, Symmetry-Adapted Perturbation Theory, 

Coupled Cluster Theory, and more are provided for the reference of the quantum chemistry

community at large to facilitate both reproducibility and low-level methodological understanding.

Additionally, the Tutorials folder above represents an interactive educational

environment containing modules discussing the theory and implementation of various

quantum and computational chemistry methods.  By leveraging the popular Jupyter Notebook

application, each tutorial is constructed as hybrid theory and programming in an easy to use

interactive environment, removing the gap between theory and implementation.

If you have comments, questions, or would like to contribute to the project

please see our [contributor guidelines](https://github.com/psi4/psi4numpy/blob/master/CONTRIBUTING.md).

### Getting Started

1. Obtain required software

    1. [Psi4NumPy](https://github.com/psi4/psi4numpy) (clone this repository; no install available)

    2. [Psi4](http://psicode.org/psi4manual/1.1/build_obtaining.html)

        * Option 1 (easiest): [Download installer](https://psicode.org/installs/latest/) based on your preferred operating system and version of Python. Proceed to follow the instructions described at the bottom of that page.  

        * Option 2 (easy): Download Conda package according to [instructions](https://psicode.org/psi4manual/master/conda.html#how-to-install-a-psi4-binary-into-an-ana-miniconda-distribution). To find the different versions available visit the [anaconda website](https://anaconda.org/psi4/psi4).

          ```

          # Have Anaconda or Miniconda (https://conda.io/miniconda.html)

          >>> conda create -n p4env psi4 -c psi4 # Create a new environment named p4env and install psi4. 

          >>> bash

          >>> source activate p4env

          ```

        * Option 3 (medium): [Clone source](https://github.com/psi4/psi4) and [compile](https://github.com/psi4/psi4/blob/master/CMakeLists.txt#L16-L143) according to [instructions](http://psicode.org/psi4manual/master/build_faq.html#configuring-building-and-installing-psifour-via-source)

          ```

          # Get Psi4 source

          >>> git clone https://github.com/psi4/psi4.git

          >>> git checkout v1.1

          >>> cmake -H. -Bobjdir -Doption=value ...

          >>> cd objdir && make -j`getconf _NPROCESSORS_ONLN`

          # Find `psi4` command at objdir/stage///.../bin/psi4; adjust path if needed

          ```

    3. [Python](https://python.org) 3.6+ (incl. w/ Psi4 Options 1 & 2)

    4. [NumPy](http://www.numpy.org) 1.7.2+ (incl. w/ Psi4 Options 1 & 2)

    5. [Scipy](https://scipy.org) 0.13.0+

2. Enable Psi4 & PsiAPI (if Psi4 was built from source)

   1. Find appropriate paths

        ```

        >>> psi4 --psiapi-path

        export PATH=/path/to/dir/of/python/interpreter/against/which/psi4/compiled:$PATH

        export PYTHONPATH=/path/to/dir/of/psi4/core-dot-so:$PYTHONPATH

        ```

    2. Export relevant paths

        ```

        >>> bash

        >>> export PATH=/path/to/dir/of/python/interpreter/against/which/psi4/compiled:$PATH

        >>> export PYTHONPATH=/path/to/dir/of/psi4/core-dot-so:$PYTHONPATH

        ```

3. Run scripts as conventional Python scripts

    * Example: Run `DF-MP2.py`

        ```

        >>> python psi4numpy/Moller-Plesset/DF-MP2.py

        ```

New users can follow the

[Tutorials](https://github.com/psi4/psi4numpy/blob/master/Tutorials/01_Psi4NumPy-Basics/) or the [PsiAPI documentation](http://psicode.org/psi4manual/master/psiapi.html) for an introduction to running Psi4 within the PsiAPI.

A tutorial that covers the basics of NumPy can be found

[here](https://education.molssi.org/python-data-analysis/01-numpy-arrays/index.html).

### Repository Organization

This repository contains

* reference implementations, which provide working Python scripts implementing

various quantum chemical methods, and

* interactive tutorials, which provide Jupyter notebooks presenting a hybrid

theory-and-implementation educational framework for learning to program quantum

chemistry methods.

Reference implementations are organized into top-level directories

corresponding to the over-arching theory upon which each method is based, i.e.,

both EOM-CCSD and TD-CCSD are contained in the

[Coupled-Cluster](https://github.com/psi4/psi4numpy/tree/master/Coupled-Cluster)

directory.  All interactive tutorials are contained in the top-level directory

[Tutorials](https://github.com/psi4/psi4numpy/tree/master/Tutorials).  These

tutorials are organized in logical order of progression, which is enumerated in

detail

[here](https://github.com/psi4/psi4numpy/tree/master/Tutorials#interactive-tutorials).

### Psi4 v1.1 (c. May 2017)

This repostitory has recently been updated to be compatible with Psi4 version 1.1.

Please see the [v0.1-beta tag](https://github.com/psi4/psi4numpy/tree/v0.1-beta) for a Psi4 v1.0 compliant Psi4NumPy version. 

### Psi4 v1.2 (c. May 2018)

This reposititory is fully compatible with the upcoming Psi4 version 1.2.

In fact (for a while), if you use v1.2, there's no need to worry if your Psi4 has

all the features to run all the reference implementations and tutorials.

### Citation

Please consider citing this repository through the Psi4NumPy paper:

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development

Daniel G. A. Smith, Lori A. Burns, Dominic A. Sirianni, Daniel R. Nascimento, Ashutosh Kumar, Andrew M. James, Jeffrey B. Schriber, Tianyuan Zhang, Boyi Zhang, Adam S. Abbott, Eric J. Berquist, Marvin H. Lechner, Leonardo A. Cunha, Alexander G. Heide, Jonathan M. Waldrop, Tyler Y. Takeshita, Asem Alenaizan, Daniel Neuhauser, Rollin A. King, Andrew C. Simmonett, Justin M. Turney, Henry F. Schaefer, Francesco A. Evangelista, A. Eugene DePrince III, T. Daniel Crawford, Konrad Patkowski, and C. David Sherrill

*Journal of Chemical Theory and Computation*, **2018**, 14 (7), 3504-3511

DOI: 10.1021/acs.jctc.8b00286