dlpoly4 python module for file manipulation
Project description
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)
contact
please report issues in the gitlab tracker
available in the matrix room
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