MRMD

MRMD - **M**ulti **R**esolution **M**olecular **D**ynamics

MRMD is a stand-alone, open-source C++ package implementing the (Hamiltonian) adaptive resolution simulation ((H-)AdResS) method, which concurrently couples regions of different resolution — e.g. atomistic Lennard-Jones and ideal gas — to simulate open molecular systems that exchange particles and energy with a reservoir.

The software exposes all of its algorithms as composable building blocks, facilitating both running AdResS simulations and developing the method itself.

How to Build

Requirements

Infrastructure

• A C++ compiler with C++20 support
• CMake >= 3.25

Libraries

Integrated libraries

These are fetched and built automatically by CMake:

• CLI11
• yaml-cpp
• Kokkos — specify flags for your target architecture and backend
• Cabana
• googletest

Optional libraries

• HDF5 — required for H5MD I/O support

CMake configuration options

MRMD specific options

Flag	Description	Default
MRMD_BUILD_DOCS	Build the Doxygen documentation (docs)	OFF
MRMD_ENABLE_COVERAGE	Enable code coverage (clang only)	OFF
MRMD_ENABLE_HDF5	Enable HDF5 / H5MD support	OFF
MRMD_ENABLE_TESTING	Build tests and add them to ctest	ON
MRMD_USE_SHARED_SPACE	Use shared space for Kokkos.	OFF
MRMD_VEC_REPORT	Enable reporting of loop vectorization	OFF
MRMD_VERBOSE_ASSERTS	Verbose asserts (CPU only)	OFF
MRMD_WERROR	Treat warnings as errors	OFF

Kokkos specific options

Flag	Description	Options
Kokkos_ENABLE_*	Enable Kokkos backends	SERIAL, OPENMP, CUDA, ...
Kokkos_ARCH_*	Select target architecture	AMPERE80, NATIVE, ...

Build Instructions

git clone https://github.com/XzzX/mrmd
cmake -S mrmd \
      -B mrmd-build \
      -DCMAKE_BUILD_TYPE=Release \
      -DKokkos_ENABLE_SERIAL=ON \
      -DKokkos_ENABLE_OPENMP=ON \
      -DKokkos_ARCH_NATIVE=ON
cmake --build mrmd-build --parallel 8
cd mrmd-build/examples/00_IdealGas_NVE
./00_IdealGas_NVE

Running the Tests

cd mrmd-build
ctest --parallel 4 --output-on-failure

Installing the Library

MRMD can be installed and consumed as a library from other CMake projects:

cmake --install mrmd-build --prefix /path/to/install

Downstream projects locate it with find_package and link against the mrmd::mrmd target:

find_package(mrmd REQUIRED)
 
add_executable(my_app main.cpp)
target_link_libraries(my_app PRIVATE mrmd::mrmd)

When configuring the downstream project, point CMake at the install location:

cmake -S . -B build -DCMAKE_PREFIX_PATH=/path/to/install

Building the Documentation

The API documentation is published at https://xzzx.github.io/mrmd/. To build it locally, install Doxygen (and optionally Graphviz for diagrams) and run:

cmake -S mrmd -B mrmd-build -DMRMD_BUILD_DOCS=ON
cmake --build mrmd-build --target docs

The HTML output is written to mrmd-build/docs/html/index.html.

Tutorial

The [examples](examples) directory contains a series of self-contained simulations that build on each other, from a minimal, non-interacting system up to a full multi-resolution production workflow. Each example is built as its own executable in mrmd-build/examples/<name>. Work through them in order to get familiar with MRMD.

Example	Description
00_IdealGas_NVE	Minimal ideal gas (non-interacting particles) simulation in the NVE (microcanonical) ensemble. Introduces the simulation domain, ghost layer, and the velocity-Verlet integrator.
01_IdealGas_NVT	Same ideal gas setup as above, but run in the NVT (canonical) ensemble using a Langevin thermostat.
02_LennardJones_NVT	Lennard-Jones fluid in the NVT ensemble with a Langevin thermostat, neighbor lists, and analysis of kinetic energy, pressure, and system momentum. Writes a .gro configuration file used by later examples.
03_LennardJones_NVE	Lennard-Jones fluid in the NVE ensemble, restoring the initial configuration from the .gro file produced by 02_LennardJones_NVT and writing H5MD output.
04_LennardJones_IdealGas_LocalCap	Relaxes a randomly placed, ideal-gas-like starting configuration into a Lennard-Jones fluid using a locally capped force during equilibration to avoid instabilities from overlapping atoms.
05_LennardJones_Equilibration	Two-stage equilibration workflow: first with a Berendsen thermostat, then a follow-up run with a Langevin thermostat, producing H5MD checkpoints for production runs.
06_LennardJones_ProductionAtomistic	Atomistic production simulation restoring from an equilibrated H5MD checkpoint, with configurable thermostat and force-capping options.
07_LennardJones_ThermoForce	Computes the thermodynamic force field iteratively for adaptive-resolution coupling; includes a variant that starts from a precomputed initial guess to speed up convergence.
08_LennardJones_ProductionTracer	Production run with tracer particles using the converged thermodynamic force field from 07_LennardJones_ThermoForce.

Contributing

Contributions are welcome! Please open an issue to discuss a bug or feature request before submitting a pull request. When contributing code, follow the existing code style (enforced via .clang-format) and ensure all tests pass.

Quality-of-life tooling: automatic formatting

format.sh formats all tracked C++ sources (*.cpp, *.hpp) in place according to .clang-format. It is also wired up as a pre-commit hook in .pre-commit-config.yaml, so formatting happens automatically on every commit.

Run it manually from the repository root:

./format.sh

Enable the commit hook once per clone:

pip install pre-commit
pre-commit install

Hard dependencies of the script:

• clang-format-18 — exactly this versioned binary name must be on your PATH; a plain clang-format or a different version will not be picked up

The pre-commit hook additionally requires pre-commit itself.

Citation

If you use MRMD in your research, please cite it using the metadata in CITATION.cff or the following:

‍Sebastian Eibl and Julian Friedrich Hille. Multi Resolution Molecular Dynamics (MRMD). doi:10.5281/zenodo.17698862

Authors

• Sebastian Eibl (@XzzX) — ORCID
• Julian Friedrich Hille (@J-Hizzle) — ORCID

License

MRMD is licensed under the Apache License 2.0. See [LICENSE](LICENSE) for details.