QCElemental
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MolSSI
Periodic table, physical constants, and molecule parsing for quantum chemistry.
Hello, We are using Psi4 within ChemCompute at the latest MolSSI workshop in Texas. We can visualize geometries with NGLViewer using the `show` method of the `qc.models.Molecule` class. Currently, we...
## Description Add a `Molecule.to_string(..., use=masses=True)` toggle to transmit masses info. Only for NWChem. Not used anywhere; I worked it out for debugging. ## Status - [x] Code base linted...
2 tests always fail and the message about py3Dmol is printed: ``` ==================================================================================== test session starts ===================================================================================== platform freebsd13 -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0 rootdir: /disk-samsung/freebsd-ports/science/py-qcelemental/work-py38/qcelemental-0.25.0 plugins: forked-1.4.0, hypothesis-6.47.0, xdist-2.5.0,...
See description and purpose and proposed tests at #288. This is a separate implementation of the parsing. ## Status - [x] Code base linted - [x] Ready to go
## Description This PR just updates the TDKeywords model to be consistent with the qcfractal model as converting between the two causes issues currently. ## Changelog description `TDKeywords` now accepts...
## Description GDB .xyz files cannot be opened because they contain a 5th column (mulliken charges) and data after the usual xyz coordinates. This PR adds a catch-all to the...
**Is your feature request related to a problem? Please describe.** As I've worked through compute implementations of single point calculations and the optimization procedures in `qcengine` I've found some redundancies...
**Is your feature request related to a problem? Please describe.** I would like to cite QCElemental (and related packages) as software I am using, but there seems to be no...
## Description - Adds serialization/deserialization support for YAML to [ProtoModel](https://github.com/MolSSI/QCElemental/tree/master/qcelemental/models/basemodels.py) and the [serialization](https://github.com/MolSSI/QCElemental/blob/serial/qcelemental/util/serialization.py) module. - Modifies `to_file` method in [Molecule](https://github.com/MolSSI/QCElemental/tree/master/qcelemental/models/molecule.py) for passing serialization arguments. The general idea is to be...
**Describe the bug** The `Molecule.align()` method for atom mapping could not successfully map some (relatively simple?) examples. The problem seems to be in mapping H atoms. ## Example 1: ```...
