Index based connectivity

.coveragerc

@@ -0,0 +1,10 @@
+[run]
+omit =
+    setup.py
+    conf.py
+    test/*
+    benchmarks/*
+    examples/*
+    docs/*
+    utils/*
+    hymd/__init__.py

.docker/hpf/Dockerfile

@@ -0,0 +1,42 @@
+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=4.0.3-0ubuntu1 \
+    libhdf5-openmpi-dev=1.10.4+repack-11ubuntu1 \
+    pkg-config=0.29.1-0ubuntu4 \
+    curl=7.68.0-1ubuntu2.2 \
+    python3.8 \
+    python3-pip
+
+RUN pip3 install --upgrade pip && \
+    pip3 install --no-cache-dir cython==0.29.21 && \
+    pip3 install --no-cache-dir numpy==1.19.1 && \
+    pip3 install --no-cache-dir mpi4py==3.0.3 && \
+    pip3 install --no-cache-dir cython==0.29.21 && \
+    pip3 install --no-cache-dir networkx==2.5 && \
+    pip3 install --no-cache-dir sympy==1.6.2 && \
+    pip3 install --no-cache-dir pytest==6.0.1 && \
+    pip3 install --no-cache-dir pytest-mpi==0.4 && \
+    pip3 install --no-cache-dir mpsort==0.1.17 && \
+    pip3 install --no-cache-dir pfft-python==0.1.21 && \
+    pip3 install --no-cache-dir pmesh==0.1.56 && \
+    pip3 install --no-cache-dir numba==0.51.2
+
+COPY . /app
+WORKDIR /app
+
+# Compile h5py with MPI support from source. The h5py install script does not
+# like to be told where MPI includes are, so first we just put them where
+# configure.py expects them to be.
+RUN ln -s /usr/lib/x86_64-linux-gnu/openmpi/include/ /usr/include/openmpi
+
+RUN curl -L -o h5py.tar.gz \
+    https://github.com/h5py/h5py/archive/6f4c578f78321b857da31eee0ce8d9b1ba291888.tar.gz
+RUN tar -xzf h5py.tar.gz && rm h5py.tar.gz && \
+  mv h5py-6f4c578f78321b857da31eee0ce8d9b1ba291888 h5py
+RUN cd h5py && HDF5_MPI="ON" pip3 install -v . && cd ..

.gitattributes

@@ -0,0 +1,13 @@
+*.1 linguist-generated
+*.2 linguist-generated
+*.3 linguist-generated
+*.4 linguist-generated
+*.5 linguist-generated
+*.6 linguist-generated
+*.7 linguist-generated
+*.8 linguist-generated
+*.9 linguist-generated
+*.10 linguist-generated
+*.11 linguist-generated
+*.h5 linguist-generated
+*.hdf5 linguist-generated

.github/workflows/ci.yml

@@ -0,0 +1,49 @@
+name: build
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+          ${{ runner.os }}-
+    - name: Install dependencies
+      run: |
+        sudo apt-get install libhdf5-openmpi-dev libfftw3-3 libfftw3-dev
+        python -m pip install --upgrade pip
+        pip install wheel
+        pip install pytest pytest-cov pytest-mpi coverage
+        pip install --upgrade numpy mpi4py cython
+        pip install -r requirements.txt
+    - name: Compile fortran modules
+      run: |
+        cd hymd/
+        make clean
+        make
+        cd ..
+    - name: Test with pytest
+      run: |
+        pytest -v --cov=./ --cov-report=
+        #### NPROCS=6
+        #### chmod +x pytest-mpi
+        #### ./pytest-mpi --nprocs ${NPROCS} --order-output --verbose
+        #### mpirun -n ${NPROCS} utils/mute_all_ranks_except.sh 0 pytest -v --only-mpi --cov=./ --cov-append --cov-report=
+    - name: Coverage report
+      run: |
+        coverage report

.gitignore

@@ -0,0 +1,16 @@
+_build
+_static
+_templates
+hymd.egg-info
+*.hypothesis
+*.mypy_cache
+*.pytest_cache
+*.eggs
+*.coverage
+hymd/__pycache__
+test/__pycache__
+coverage.xml
+*.DS_Store
+__pycache__
+RUN/
+*.so

LICENSE.txt

@@ -0,0 +1,165 @@
+GNU LESSER GENERAL PUBLIC LICENSE
+    Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+
+
+This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+0. Additional Definitions.
+
+As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+"The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
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+A "Combined Work" is a work produced by combining or linking an
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+1. Exception to Section 3 of the GNU GPL.
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+You may convey a covered work under sections 3 and 4 of this License
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README.md

@@ -1,12 +1,18 @@
-# Hamiltonian and Alias-Free Hybrid Particle-Field Molecular Dynamics MPI VERSION
-This depository contains a simple python-code implementation of hybrid particle-field molecular dynamics (hPF-MD) that allows one to conserve energy and reduce aliasing by refinement of grid. The code supports monoatom particles of any amount of types and interactions.
+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)
+---------
+Compile FORTRAN modules:
+```bash
+> cd hymd/
+> make clean
+> make
+> cd ..
+```
 
-The code is contained in main.py and input files are created with make_input.py from CONF.py. To convert results to unitless units the units.py module is provided.
+Run a simple example simulation with
+```bash
+> mpirun -n 4 python3 hymd/main.py config.toml dppc.h5 --verbose -logfile log.txt
+```
 
-To try out the code, simply:
-   python make_input.py CONF.py 
-   mpirun python main.py CONF.py input.hdf5
-
-Note that to run the code, the following may need to be installed:
-pip3 install pmesh
-pip3 install pfft-python
+Notes:
+- Changed numpy data types (Float32, Int32 -> float32, int32) to run in local computer
+- TODO: Fix for running monoatomic (or non molecular) systems