1168860
doi
10.5281/zenodo.1168860
oai:zenodo.org:1168860
PyFraME: Python tools for Fragment-based Multiscale Embedding
Olsen, Jógvan Magnus Haugaard
University of Southern Denmark
url:https://gitlab.com/FraME-projects/PyFraME
info:eu-repo/semantics/openAccess
GNU General Public License v2.0 only
https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
Computational Chemistry
Quantum Chemistry
Multiscale Modeling
Polarizable Embedding
QM/MM
<p>This archive contains the source of PyFraME. Project is hosted on GitLab (https://gitlab.com/FraME-projects/PyFraME).</p>
<p>PyFraME is a Python package that provides tools for setting up and running fragment-based multiscale embedding calculations. The aim is to provide tools that can automatize the workflow of such calculations in a flexible manner.</p>
<p>The typical workflow is as follows:</p>
<ol>
<li> a part of the total molecular system is chosen as the core region which is typically treated a high level of theory</li>
<li>the remainder is split into a number of regions each of which can be treated at different levels of theory</li>
<li>each region (except the core) is divided into fragments that consist of either small molecules or parts of larger molecules that have been fragmented into smaller computationally manageable fragments</li>
<li>a calculation is run on each fragment to obtain fragment parameters (if necessary)</li>
<li>all fragment parameters of all regions are assembled and constitute the embedding potential</li>
<li>a final calculation is run on the core region using the embedding potential to model the effect from the remainder of the molecular system</li>
</ol>
Zenodo
2018-02-08
info:eu-repo/semantics/other
775113
0.1.1
1623068352.09306
693405
md5:743c1160610a348c47d23a82994421c4
https://zenodo.org/records/1168860/files/PyFraME-0.1.1.tar.gz
44988
md5:8ae0a1b44c2fa451a402e0b8a79392de
https://zenodo.org/records/1168860/files/PyFraME-v0.1.0.tar.gz
public
https://gitlab.com/FraME-projects/PyFraME
Is supplement to
url
10.5281/zenodo.775113
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doi