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.
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.
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.
Optional dependencies are
- 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/dftd3/simple-dftd3
revision = headYou 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.
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/dftd3/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")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/dftd3/simple-dftd3"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.
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.
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.
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:
-
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.
-
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.
-
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.
-
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.
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.
This is a volunteer open source projects and contributions are always welcome. Please, take a moment to read the contributing guidelines.
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.
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent