Update readme and dockerfile

.docker/hymd/Dockerfile

@@ -0,0 +1,27 @@
+FROM ubuntu:20.04
+
+# Fix for tzdata installation from
+# https://rtfm.co.ua/en/docker-configure-tzdata-and-timezone-during-build/
+ENV TZ=Europe/Oslo
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+RUN apt-get update && apt-get install -y     \
+    libopenmpi-dev                           \
+    libhdf5-openmpi-dev                      \
+    pkg-config                               \
+    curl                                     \
+    python3.8                                \
+    python3-pip                              \
+    python3-mpi4py                           \
+    python3-numpy
+
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install --no-cache-dir cython numpy mpi4py cython && \
+    python3 -m pip install networkx sympy pytest pytest-mpi mpsort pfft-python pmesh tomli
+
+ENV CC=mpicc
+ENV HDF5_MPI="ON"
+RUN python3 -m pip install --no-cache-dir --no-binary=h5py h5py
+
+COPY . /app
+WORKDIR /app

README.md

@@ -1,37 +1,79 @@
-HyMD testing and development · [![License: GPL v3](https://img.shields.io/badge/License-LGPLv3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.html) ![build](https://github.com/Cascella-Group-UiO/HyMD-2021/workflows/build/badge.svg)
+<img src="docs/img/hymd_logo_text_black.png" width="500" title="HylleraasMD">
+
+[![License: GPL v3](https://img.shields.io/badge/License-LGPLv3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.html) ![build](https://github.com/Cascella-Group-UiO/HyMD-2021/workflows/build/badge.svg) [![docs_pages](https://github.com/Cascella-Group-UiO/HyMD/actions/workflows/docs_pages.yml/badge.svg?branch=docs_setup)](https://github.com/Cascella-Group-UiO/HyMD/actions/workflows/docs_pages.yml) [![codecov](https://codecov.io/gh/Cascella-Group-UiO/HyMD/branch/main/graph/badge.svg?token=BXZ7B9RXV9)](https://codecov.io/gh/Cascella-Group-UiO/HyMD)
+
 ---------
-HyMD is a software that can run coarse-grained molecular dynamics simulations
-using the hybrid-particle field model approach, introduced initially in [1].
-In HyMD we implement the formulation presented in [2].
+**HylleraasMD** (HyMD) is a massively parallel Python package for hybrid particle-field molecular dynamics (hPF-MD) simulations of coarse-grained bio- and soft-matter systems.
+
+HyMD can run canonical hPF-MD simulations [[1]](#1), or filtered density Hamiltonian hPF (HhPF-MD) simulations [[2]](#2), with or without explicit PME electrostatic interactions [[3]](#3). It includes all standard intramolecular interactions, including stretching, bending, torsional, and combined bending-dihedral potentials. Additionally, topological reconstruction of permanent peptide chain backbone dipoles is possible for accurate recreation of protein conformational dynamics [[4]](#4). Martini style elastic networks (ElNeDyn) [[5]](#5) are also supported.
+
+HyMD uses the [pmesh](github.com/rainwoodman/pmesh) library for particle-mesh operations, with the PPFT [[6]](#6) backend for FFTs through the [pfft-python bindings](github.com/rainwoodman/pfft-python). File IO is done via HDF5 formats to allow MPI parallel reads.
+
+## User Guide
+Detailed installation and user guide, together with comprehensive example simulations are located in the [HylleraasMD documentation](https://cascella-group-uio.github.io/HyMD/index.html).
+
+Run simulations by
+```bash
+python3 -m hymd [CONFIGURATION_FILE] [TOPOLOGY_FILE]
+```
 
-## Setup
-First compile the FORTRAN modules:
+## Installation
+Install HyMD with `pip` by
+```bash
+python3 -m pip install hymd
+```
+#### Install dependencies
+HyMD installation **requires** a working MPI compiler. It is highly recommended to have *MPI-enabled* HDF5 and [h5py](https://docs.h5py.org/en/stable/mpi.html) for running parallel simulations with HyMD. Install both on Ubuntu with
 ```bash
-> cd hymd/
-> make clean
-> make
-> cd ..
+sudo apt-get update -y
+sudo apt-get install -y curl pkg-config python3-pip python3-mpi4py libhdf5-mpi-dev
+export CC=mpicc
+export HDF5_MPI="ON"
+python3 -m pip install --no-binary=h5py h5py
 ```
 
-Check out all the available options with
+#### Run in docker
+Alternatively, an up-to-date docker image is available from [docker hub](https://hub.docker.com/repository/docker/mortele/hymd)
 ```bash
-> python3 hymd/main.py --help
+docker pull mortele/hymd
+docker run -it mortele/hymd
+/app# apt-get install -y git
+/app# git clone https://github.com/Cascella-Group-UiO/HyMD.git hymd
+/app# cd hymd/
+/app/hymd# pip3 install .
+/app/hymd# pytest 
 ```
 
-Start a simple example simulation with:
+## Run tests
+Clone the repository and run tests with [pytest](https://docs.pytest.org/en/latest)
 ```bash
-> mpirun -n 4 python3 hymd/main.py peptide.toml peptide.h5 -v
+git clone https://github.com/Cascella-Group-UiO/HyMD.git hymd
+cd hymd
+pytest
 ```
+Running MPI enabled pytest tests is simplified with a convenient script
+```bash
+chmod +x pytest-mpi
+pytest-mpi -oo -n 2 -ns
+```
+
+---------
 
-## References
-[1] Milano, G. & Kawakatsu, T. Hybrid particle-field molecular dynamics
-simulations for dense polymer systems Journal of Chemical Physics, American
-Institute of Physics, 2009, 130, 214106 
+### References
+<a id="1">[1]</a>
+Milano, G.; Kawakatsu, T. Hybrid particle-field molecular dynamics simulations for densepolymer systems. J. Chem. Phys. **2009**, 130, 214106.
 
-[2] Bore, S. L. & Cascella, M. Hamiltonian and alias-free hybrid
-particle--field molecular dynamics The Journal of Chemical Physics, AIP
-Publishing LLC, 2020, 153, 094106 
+<a id="2">[2]</a>
+Bore, S. L.; Cascella, M. Hamiltonian and alias-free hybrid particle–field molecular dynam-ics. J. Chem. Phys. **2020**, 153, 094106.
 
+<a id="3">[3]</a>
+Kolli, H. B.; De Nicola, A.; Bore, S. L.; Schäfer, K.; Diezemann, G.; Gauss, J.; Kawakatsu, T.;Lu, Z.-Y.; Zhu, Y.-L.; Milano, G.; Cascella, M. Hybrid Particle-Field Molecular DynamicsSimulations of Charged Amphiphiles in an Aqueous Environment. J. Chem. Theory Comput. **2018**, 14, 4928–4937.
 
+<a id="4">[4]</a>
+Bore, S. L.; Milano, G.; Cascella, M. Hybrid Particle-Field Model for Conformational Dy-namics of Peptide Chains. J. Chem. Theory Comput. **2018**, 14, 1120–1130.
 
+<a id="5">[5]</a>
+Periole, X.; Cavalli, M.; Marrink, S. J.; Ceruso, M. A. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition. J. Chem. Theory Comput. **2009**, 5.9, 2531-2543.
 
+<a id="6">[6]</a>
+Pippig, M. PFFT: An extension of FFTW to massively parallel architectures. SIAM J. Sci. Comput. **2013**, 35, C213–C236.

hymd/version.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

setup.py

@@ -41,6 +41,18 @@ def find_version(path):
     packages=["hymd"],
     version=find_version("hymd/version.py"),
     ext_modules=[force_kernels],
+    install_requires=[
+        "cython",
+        "h5py",
+        "mpi4py",
+        "mpsort",
+        "networkx",
+        "numpy",
+        "pfft-python",
+        "pmesh",
+        "sympy",
+        "tomli",
+    ],
     python_requires=">=3.6",
     classifiers=[
         "Development Status :: 5 - Production/Stable",