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pymolresponse

Molecular frequency-dependent response properties for arbitrary operators

https://github.com/berquist/pymolresponse

Science Score: 57.0%

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    Low similarity (15.6%) to scientific vocabulary

Keywords

computational-chemistry hacktoberfest python python-chemistry quantum-chemistry
Last synced: 6 months ago · JSON representation ·

Repository

Molecular frequency-dependent response properties for arbitrary operators

Basic Info
  • Host: GitHub
  • Owner: berquist
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 9.76 MB
Statistics
  • Stars: 11
  • Watchers: 3
  • Forks: 3
  • Open Issues: 19
  • Releases: 0
Topics
computational-chemistry hacktoberfest python python-chemistry quantum-chemistry
Created almost 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

README.md

pymolresponse

Molecular frequency-dependent response properties for arbitrary operators.

build status codecov license pre-commit.ci status

For documentation, go to https://berquist.github.io/pymolresponse/.

Currently, the goal is to provide:

  1. a pedagogical example of a working molecular orbital response program as an almost direct translation from equations to code,
  2. an implementation that gives "exact" results for testing, and
  3. an example of testing and documenting scientific code using modern software development tools.

Installation

To set up a conda environment with all dependencies for running, testing, and building the documentation, look under devtools.

Requirements

  • Python >= ~~3.2 because of pyscf~~3.6 because of f-strings.
  • pyscf and its dependencies: CMake, NumPy, SciPy, HDF5 + h5py
  • Psi4

Other Python dependencies

Testing

bash make pytest

Caveats

  • RHF and UHF references only; no ROHF yet.
  • Hartree-Fock and DFT only; no post-HF methods yet.
  • Real orbitals only; no complex or generalized orbitals yet.
  • Because the dimensioning of all arrays is based around the ov/vo space, methods that have non-zero contributions from the oo space (specifically derivatives of GIAOs/London orbitals w.r.t. the B-field) are not currently possible.
  • An iterative solver exists for response properties, not transition properties, where only explicit formation and then diagonalization of the orbital Hessian is available.
  • Linear response and single residues only.
  • unrestricted diagonalization-based properties are not implemented/working

Desired features (in no specific order)

  • Non-orthogonal orbitals. Requires switch from using MO energies to full Fock matrices.
  • ROHF reference (compare against DALTON). Requires equations for the ROHF orbital Hessian.
  • Post-HF support: MP2, CCSD, and CIS. Requires constriction of a Lagrangian.
  • Support for GIAOs. Only requires re-dimensioning as long as AO matrix elements are available??
  • At least one iterative method for each property type, for example DIIS for inversion and Davidson for diagonalization. Requires matrix-vector products.
  • Quadratic response and associated single residues (needed for phosphorescence) and double residues (excited state expectation values and transition moments of linear operators). Requires permutation of linear response solution vectors.

Desired features that don't fix the caveats

References

Forthcoming...

Owner

  • Name: Eric Berquist
  • Login: berquist
  • Kind: user
  • Location: Boston, MA
  • Company: Sandia National Laboratories

full-stack quantum chemist

Citation (CITATION.cff) 

---
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: pymolresponse
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - email: eric.berquist@gmail.com
    orcid: 'https://orcid.org/0000-0001-8186-9522'
    given-names: Eric
    family-names: Berquist

GitHub Events

Total
  • Watch event: 2
  • Delete event: 36
  • Issue comment event: 3
  • Push event: 139
  • Pull request event: 91
  • Create event: 46
Last Year
  • Watch event: 2
  • Delete event: 36
  • Issue comment event: 3
  • Push event: 139
  • Pull request event: 91
  • Create event: 46

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 44
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: 3 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.05
  • Merged pull requests: 27
  • Bot issues: 1
  • Bot pull requests: 38
Past Year
  • Issues: 1
  • Pull requests: 44
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: 3 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.05
  • Merged pull requests: 27
  • Bot issues: 1
  • Bot pull requests: 38
View more stats
Top Authors
Issue Authors
  • renovate[bot] (2)
Pull Request Authors
  • renovate[bot] (41)
  • pre-commit-ci[bot] (26)
  • berquist (15)
  • dependabot[bot] (9)
Top Labels
Issue Labels
dependencies (1) pre-commit (1)
Pull Request Labels
dependencies (41) github_actions (28) pre-commit (12) continuous-integration (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 9 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: pymolresponse

Molecular frequency-dependent response properties for arbitrary operators

  • Homepage: https://github.com/berquist/pymolresponse
  • Documentation: https://berquist.github.io/pymolresponse_docs/
  • License: BSD 3-Clause License Copyright (c) 2017, Eric Berquist All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.2.0
    published about 2 years ago
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 9 Last month
Rankings
Dependent packages count: 9.8%
Average: 37.3%
Dependent repos count: 64.8%
Maintainers (1)
berquist
Last synced: 6 months ago

Dependencies

requirements-dev.txt pypi
  • mypy * development
  • numpydoc * development
  • pylint * development
  • pytest-black * development
  • pytest-cov * development
  • pytest-isort * development
  • sphinx * development
  • sphinx-rtd-theme * development
requirements.txt pypi
  • cclib *
  • deepdiff *
  • h5py *
  • periodictable *
  • pint *
  • qcelemental *
  • scipy *
setup.py pypi
  • cclib *
.github/workflows/test.yml actions
  • JamesIves/github-pages-deploy-action 4.1.5 composite
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite