dlpoly-py 0.2.0

dlpoly4 python module for file manipulation

dlpoly-py package contains tools to read input and output for DL_POLY it can also produce inputs and be mixed with other python packages like ASE, MDAnalysis, MDAnse or pymatgen

install

You need Python 3.6 or later to run dlpoly-py. You can have multiple Python versions (2.x and 3.x) installed on the same system without problems.

To install Python 3 for different Linux flavors, macOS and Windows, packages are available at https://www.python.org/getit

Using pip

pip is the most popular tool for installing Python packages, and the one included with modern versions of Python.

dlpoly-py can be installed with pip

pip install dlpoly-py

Note:

Depending on your Python installation, you may need to use pip3 instead of pip.

pip3 install dlpoly-py

Depending on your configuration, you may have to run pip like this:

python3 -m pip install dlpoly-py

Using pip (GIT Support)

pip currently supports cloning over git

pip install git+https://gitlab.com/drFaustroll/dlpoly-py.git

For more information and examples, see the pip install reference.

Using a virtual environment

# create virtual env
virtualenv3 venv/dlpoly
source venv/dlpoly/bin/activate
pip3 install dlpoly-py

Using conda

conda is the package management tool for Anaconda Python installations.

Installing dlpoly-py from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge

Once the conda-forge channel has been enabled, dlpoly-py can be installed with:

conda install dlpoly-py

It is possible to list all of the versions of dlpoly-py available on your platform with:

conda search dlpoly-py --channel conda-forge

usage

Examples can be found in https://gitlab.com/drFaustroll/dlpoly-py/-/tree/devel/examples

sime run using Ar data from above folder.

from dlpoly import DLPoly

dlp="/home/drFaustroll/playground/dlpoly/dl-poly-alin/build-yaml/bin/DLPOLY.Z"

dlPoly = DLPoly(control="Ar.control", config="Ar.config",
                field="Ar.field", workdir="argon")
dlPoly.run(executable=dlp,numProcs = 4)

# change temperature and rerun, from previous termination
dlPoly = DLPoly(control="Ar.control", config="argon/REVCON", destconfig="Ar.config",
             field="Ar.field", workdir="argon-T310")
dlPoly.control.temp = 310.0
dlPoly.run(executable=dlp,numProcs = 4)

alternatively you can set the environment variable DLP_EXE to point to DL_POLY_4 executable and remove the executable parameter from run.

export DLP_EXE="/home/drFaustroll/playground/dlpoly/dl-poly-alin/build-yaml/bin/DLPOLY.Z"

from dlpoly import DLPoly

dlPoly = DLPoly(control="Ar.control", config="Ar.config",
                field="Ar.field", workdir="argon")
dlPoly.run(numProcs = 4)

# change temperature and rerun, from previous termination
dlPoly = DLPoly(control="Ar.control", config="argon/REVCON", destconfig="Ar.config",
             field="Ar.field", workdir="argon-T310")
dlPoly.control.temp = 310.0
dlPoly.run(numProcs = 4)

authors

• Alin M Elena, Daresbury Laboratory, UK

• Jacob Wilkins, University of Oxford, UK

contact

• please report issues in the gitlab tracker

• available in the matrix room