The D3 dispersion model

A simple drop-in replacement for dftd3.

This program provides a small and easy to use implementation of the DFT-D3 dispersion correction (see JCP 132, 154104 (2010) and JCC 32, 1456 (2011) for details).

It is mostly based on the dftd4 program and borrows one or two ideas from the implementation in ased3.

Installation

Conda package

This project is packaged for the conda package manager and available on the conda-forge channel. To install the conda package manager we recommend the miniforge installer. If the conda-forge channel is not yet enabled, add it to your channels with

conda config --add channels conda-forge

Once the conda-forge channel has been enabled, this project can be installed with:

conda install simple-dftd3

If you want to enable the Python API as well install

conda install dftd3-python

It is possible to list all of the versions available on your platform with:

conda search simple-dftd3 --channel conda-forge

Now you are ready to use s-dftd3.

Building from Source

To build this project from the source code in this repository you need to have a Fortran compiler supporting Fortran 2008 and one of the supported build systems:

• meson version 0.55 or newer, with a build-system backend, i.e. ninja version 1.7 or newer
• cmake version 3.14 or newer, with a build-system backend, i.e. ninja version 1.10 or newer
• fpm version 0.3.0 or newer

Meson is the primary build system and provides feature-complete functionality of this project. CMake and fpm support is available but the functionality of the project is limited. This project is currently tested with GCC 9 on Ubuntu, MacOS and Windows as well as Intel Fortran on Ubuntu.

Building with meson

Optional dependencies are

• BLAS (enabled with -Dblas=netlib)
• asciidoctor to build the manual page
• FORD to build the developer documentation
• Python 3.6 or newer with the CFFI package installed to build the Python API

Setup a build with

meson setup _build

You can select the Fortran compiler by the FC environment variable. To compile and run the projects testsuite use

meson test -C _build --print-errorlogs

If the testsuite passes you can install with

meson configure _build --prefix=/path/to/install
meson install -C _build

This might require administrator access depending on the chosen install prefix.

To include s-dftd3 in your project add the following wrap file to your subprojects directory:

[wrap-git]
directory = s-dftd3
url = https://github.com/awvwgk/simple-dftd3
revision = head

You can retrieve the dependency from the wrap fallback with

sdftd3_dep = dependency('s-dftd3', fallback: ['s-dftd3', 'sdftd3_dep'])

and add it as dependency to your targets.

Building with CMake

Alternatively, this project can be build with CMake (in this case ninja 1.10 or newer is required):

cmake -B _build -G Ninja

To compile the project with CMake run

cmake --build _build

You can run the project testsuite with

pushd _build && ctest && popd

To include s-dftd3 in your CMake project retrieve it using the FetchContent module:

if(NOT TARGET s-dftd3)
  set("s-dftd3-url" "https://github.com/awvwgk/simple-dftd3")
  message(STATUS "Retrieving s-dftd3 from ${s-dftd3-url}")
  include(FetchContent)
  FetchContent_Declare(
    "s-dftd3"
    GIT_REPOSITORY "${s-dftd3-url}"
    GIT_TAG "HEAD"
  )
  FetchContent_MakeAvailable("s-dftd3")
endif()

And link against the "s-dftd3" interface library.

target_link_libraries("${PROJECT_NAME}-lib" PUBLIC "s-dftd3")

Building with fpm

Invoke fpm in the project root with

fpm build

To run the testsuite use

fpm test

You can access the s-dftd3 program using the run subcommand

fpm run -- --help

To use s-dftd3 for testing include it as dependency in your package manifest

[dependencies]
s-dftd3.git = "https://github.com/awvwgk/simple-dftd3"

Usage

DFT-D3 calculations can be performed with the s-dftd3 executable. To calculate the dispersion correction for PBE0-D3(BJ)-ATM run:

s-dftd3 --bj pbe0 --atm coord

In case you want to access the DFT-D3 results from other programs, dump the results to JSON with (the --noedisp flag prevents the .EDISP file generation):

s-dftd3 --bj pbe0 --atm --json --noedisp --grad struct.xyz

Dispersion related properties can be calculated as well:

s-dftd3 --property geo.gen

For an overview over all command line arguments use the --help argument or checkout the s-dftd3(1) manpage.

API access

This DFT-D3 implementation provides first class API support Fortran, C and Python. Other programming languages should try to interface via one of those three APIs. To provide first class API support for a new language the interface specification should be available as meson build files.

Fortran API

The recommended way to access the Fortran module API is by using dftd3 as a meson subproject. Alternatively, the project is accessible by the Fortran package manager (fpm) or as CMake subproject as explained above.

The complete API is available from dftd3 module, the individual modules are available to the user as well but are not part of the public API and therefore not guaranteed to remain stable. API compatibility is only guaranteed for the same minor version, while ABI compatibility cannot be guaranteed in a pre 1.0 stage.

The communication with the Fortran API uses the error_type and structure_type of the modular computation tool chain library (mctc-lib) to handle errors and represent geometries, respectively.

C API

The C API provides access to the basic Fortran objects and their most important methods to interact with them. All Fortran objects are available as opaque void* in C and can only be manipulated with the correct API calls. To evaluate a dispersion correction in C four objects are available:

1. the error handler:

   Simple error handler to carry runtime exceptions created by the library. Exceptions can be handled and/or transfered to the downstream error handling system by this means.

2. the molecular structure data:

   Provides a representation of the molecular structure with immutable number of atoms, atomic species, total charge and boundary conditions. The object provides a way to update coordinates and lattice parameters, to update immutable quantities the object has to be recreated.

3. the dispersion model:

   Instantiated for a given molecular structure type, it carries no information on the geometry but relies on the atomic species of the structure object. Recreating a structure object requires to recreate the dispersion model as well.

4. the damping parameters:

   Damping parameter object determining the short-range behaviour of the dispersion correction. Standard damping parameters like the rational damping are independent of the molecular structure and can easily be reused for several structures or easily exchanged.

The user is responsible for creating and deleting the objects to avoid memory leaks.

Python API

The Python API is disabled by default and can be built in-tree or out-of-tree. The in-tree build is mainly meant for end users and packages. To build the Python API with the normal project set the python option in the configuration step with

meson setup _build -Dpython=true -Dpython_version=$(which python3)

The Python version can be used to select a different Python version, it defaults to 'python3'. Python 2 is not supported with this project, the Python version key is meant to select between several local Python 3 versions.

Proceed with the build as described before and install the projects to make the Python API available in the selected prefix.

For the out-of-tree build see the instructions in the python directory.

Contributing

This is a volunteer open source projects and contributions are always welcome. Please, take a moment to read the contributing guidelines.

License

This project is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This project is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU Lesser General Public License for more details.

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project by you, as defined in the GNU Lesser General Public license, shall be licensed as above, without any additional terms or conditions.