mfsjmenger/pysurf

A Framework for Database Accelerated Quantum Chemistry

PySurf: A Framework for Database Accelerated Quantum Chemistry

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Requirements

• pycolt >=0.2
• qctools

Both can be installed by:

pip install pycolt qctools

Additionally:

• netcdf4
• numpy
• matplotlib

• Free software: Apache License 2.0

General Aim:

• Fast prototyping
• Easily extensible
• Light-weight
• Developer/user friendly

Credits

This work was supported by the Innovational Research Incentives Scheme Vidi 2017 with project number 016.Vidi.189.044, (partly) funded by the Dutch Research Council (NWO).

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

pysurf's Issues

Atom masses twice implemented

• pysurf version:
• Python version:
• Operating System:

Description

I have just noticed that we have twice the atom information implemented. Once in utils/chemutils (used by the SPP) and once in atominfo.py (used by the wigner sampling)

They should be combined to one

Load Plugins

• pysurf version: 0.1.0
• Python version: 3.9
• Operating System: Linux

Suggestion

Change default behaviour for plugins from loading all to loading specific files

COORD and CRD

Description

For the initial conditions CRD is used as variable for coordinates. In the SPP and the output databases coord is used. We agreed to use crd everywhere so it has to be changed wherever coord is used.

Pysurf_plugins select foldername

• pysurf version: 0.1.0
• Python version: 3.9
• Operating System: Linux

Wish

Change pysurf_plugins foldername

Suggested Solution:

add environmental variable for Pysurf Plugins

Distance measurement in Database

Description

the measure for the distance of two geometries in the database has to be investigated. Maybe it should be changed to a standard euclidean norm.
The distance measurement has to be in a separate class so that it can be used from everywhere.
At the moment a simple dummy class is in analysis/combine_dbs.py which has to be moved to the dbinter.py