https://github.com/pdebuyl-lab/rmpcdmd

Code to perform chemical MPCD simulations
https://github.com/pdebuyl-lab/rmpcdmd

colloids fortran hydrodynamics nanomotor openmp simulation

Last synced: about 2 months ago
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Code to perform chemical MPCD simulations

• Host: GitHub
• URL: https://github.com/pdebuyl-lab/rmpcdmd
• Owner: pdebuyl-lab
• License: bsd-3-clause
• Created: 2013-08-03T17:42:31.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2020-02-13T10:50:54.000Z (almost 5 years ago)
• Last Synced: 2024-03-27T09:27:35.967Z (10 months ago)
• Topics: colloids, fortran, hydrodynamics, nanomotor, openmp, simulation
• Language: Fortran
• Homepage: http://lab.pdebuyl.be/rmpcdmd/
• Size: 1.19 MB
• Stars: 8
• Watchers: 5
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION

Awesome Lists containing this project

README

        
RMPCDMD: Reactive MultiParticle Collision Dynamics - Molecular Dynamics

=======================================================================

**Homepage:** [RMPCDMD](http://lab.pdebuyl.be/rmpcdmd/) (includes documentation)  

**License:** BSD 3-clause, see [LICENSE](LICENSE).

[![Build Status](https://travis-ci.org/pdebuyl-lab/RMPCDMD.svg?branch=master)](https://travis-ci.org/pdebuyl-lab/RMPCDMD)

RMPCDMD is a collection of Fortran modules and programs for the

mesoscopic modeling of chemically active fluids with embedded colloids.

## Status

RMPCDMD is ready to use for chemically powered dimer nanomotor simulations.

A former version of this code, still available in the branches `trs`

and `trs_two_prod`, was used to obtain the results presented in P. de

Buyl and R. Kapral [Nanoscale 5, 1337-1344

(2013)](http://dx.doi.org/10.1039/C2NR33711H) and P. de Buyl,

A. S. Mikhailov and R. Kapral [EPL 103, 60009

(2013)](http://dx.doi.org/10.1209/0295-5075/103/60009).

The current version has been totally refactored to remove the use of global variables,

enable testing and enable OpenMP multithreaded operation.

## Citation

RMPCDMD is presented in the article *RMPCDMD: Simulations of colloids with

coarse-grained hydrodynamics, chemical reactions and external fields*, Journal

of Open Research Software (JORS) **5**, 3 (2017)

[doi](http://doi.org/10.5334/jors.142) -

[arXiv:1608.04904](https://arxiv.org/abs/1608.04904)

Please cite this paper if you use RMPCDMD in a research work. A bibtex entry is provided in

the [CITATION](CITATION) file.

## Requirements

RMPCDMD has the following requirements:

- A Fortran 2008 compiler (e.g. [gfortran](https://gcc.gnu.org/wiki/GFortran) ≥ 4.7 with support for [OpenMP](https://gcc.gnu.org/wiki/openmp) ≥ 3.1)

- A Fortran enabled [HDF5](https://www.hdfgroup.org/HDF5/) installation

- [CMake](http://cmake.org/)

- [GNU Make](https://www.gnu.org/software/make/)

- [git](http://git-scm.com/)

See the documentation for

[installation instructions](http://lab.pdebuyl.be/rmpcdmd/install.html) for Linux and OS X.

## Contact

- The contact for RMPCDMD is the main author, [Pierre de Buyl](http://pdebuyl.be/).

- Bug reports are welcome either by email or via

  [GitHub issues](https://github.com/pdebuyl-lab/RMPCDMD/issues).

## Contributors

Peter Colberg: general programming improvements, OpenMP, debugging  

Laurens Deprez: single colloid setup, gravity field and corresponding bounce-back, shake/rattle for dimers  

Mu-Jie Huang: parts of the tutorial