get_dispersion_api not public in module dftd4_api

DFT-D4 project

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

Installing

A statically linked binary distribution for Linux platforms is available at the latest release tag. Bleeding edge releases of the latest source from this repository are available on the continuous release tag.

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 dftd4

If you want to enable the Python API as well install

conda install dftd4-python

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

conda search dftd4 --channel conda-forge

Now you are ready to use dftd4.

Spack package

This project is available with spack in its develop version. You can install and load dftd4 with

spack install dftd4
spack load dftd4

The Python API can be enabled by adding +python to the command.

FreeBSD Port

A port for FreeBSD is available and can be installed using

pkg install science/dftd4

In case no package is available build the port using

cd /usr/ports/science/dftd4
make install clean

For more information see the dftd4 port details.

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 0.2.0 or newer

Currently this project supports GCC and Intel compilers.

Building with meson

To compile this version of DFT-D4 with meson the following programs are needed (the number in parentheses specifies the tested versions).

To build this project from the source code in this repository you need to have

a Fortran compiler supporting Fortran 2008
meson version 0.55 or newer
a build-system backend, i.e. ninja version 1.7 or newer
a LAPACK / BLAS provider, like MKL or OpenBLAS

Optional dependencies are

asciidoctor to build the manual page
FORD to build the developer documentation
C compiler to test the C-API and compile the Python extension module
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.

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 -DCMAKE_INSTALL_PREFIX=$HOME/.local

To compile the project with CMake run

cmake --build _build

You can run the project testsuite with

ctest --test-dir _build --parallel --output-on-failure

Finally, you can install the project to the selected prefix

cmake --install _build

Note that the CMake build does not support to build the Python extension module as part of the main build.

Building with fpm

This project support the Fortran package manager (fpm). Invoke fpm in the project root with

fpm build

To run the testsuite use

fpm test

You can access the dftd4 program using the run subcommand

fpm run -- --help

To use dftd4 for testing include it as dependency in your package manifest

[dependencies]
dftd4.git = "https://github.com/dftd4/dftd4"

Note that the fpm build does not support exporting the C-API, it only provides access to the standalone binary.

Usage

DFT-D4 calculations can be performed with the dftd4 executable. To calculate the dispersion correction for PBE0-D4 run:

dftd4 --func pbe0 coord

In case you want to access the DFT-D4 results from other programs, dump the results to JSON with (the --noedisp flag prevents the .EDISP file generation):

dftd4 --func pbe0 --json --grad --noedisp struct.xyz

Dispersion related properties can be calculated as well:

dftd4 --property geo.gen

To evaluate pairwise resolved dispersion energies use

dftd4 --pair-resolved mol.xyz

For an overview over all command line arguments use the --help argument or checkout the dftd4(1) manpage.

Parameters

DFT-D4 is parametrized for plenty of density functionals. The available parameters are listed in the parameters.toml file or with the following command.

dftd4 param --list

While the functionals can be selected with their common names (e.g., PBE), the libxc names can also be used (e.g., GGA_X_PBE:GGA_C_PBE).

dftd4 --func PBE coord
dftd4 --func GGA_X_PBE:GGA_C_PBE coord

The exchange and correlation functional must be separated by a colon. All names are case-insensitive.

You can add new functionals using to the TOML file by adding a new subtable

[parameter.name]
reference.doi = ["<functional reference>"]
d4.bj-eeq-atm = { s8=1.0, a1=0.4, a2=5.0, doi="<parameter reference>" }

Those parameters are currently only used as reference and not yet usable in the library or executable.

API access

The DFT-D4 project provides first class API support Fortran, C and Python. Other programming languages should try to interface with to DFT-D4 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 dftd4 binary provides with the --json option access to all quantities available from the APIs as well.

Fortran API

The recommended way to access the Fortran module API is by using dftd4 as a meson subproject. Alternatively, the project is accessible by the Fortran package manager (fpm).

The complete API is available from dftd4 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. ABI compatibility is only guaranteed for the same minor version.

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.

Building Vasp with support for D4

To use dftd4 in Vasp the compatibility layer for the 2.5.x API has to be enable with -Dapi_v2=true (meson) or -DWITH_API_V2=ON (CMake). It is important to build dftd4 with the same Fortran compiler you build Vasp with.

After you completed the installation of dftd4, make sure it is findable by pkg-config, you can check by running:

pkg-config --modversion dftd4

If your dftd4 installation is not findable, you have to update your environment variables. One option is to provide a module file for your dftd4 installation. The example module file below can be placed in your MODULEPATH to provide access to an installation in ~/opt/dftd4/3.6.0. Retry the above comment after loading the dftd4 module and adjust the module file until pkg-config finds your installation.

-- dftd4/3.6.0.lua
local name = "dftd4"
local version = "3.6.0"
local prefix = pathJoin(os.getenv("HOME"), "opt", name, version)
local libdir = "lib"  -- or lib64

whatis("Name        : " .. name)
whatis("Version     : " .. version)
whatis("Description : Generally applicable charge dependent London dispersion correction")
whatis("URL         : https://github.com/dftd4/dftd4")

prepend_path("PATH", pathJoin(prefix, "bin"))
prepend_path("MANPATH", pathJoin(prefix, "share", "man"))
prepend_path("CPATH", pathJoin(prefix, "include"))
prepend_path("LIBRARY_PATH", pathJoin(prefix, libdir))
prepend_path("LD_LIBRARY_PATH", pathJoin(prefix, libdir))
prepend_path("PKG_CONFIG_PATH", pathJoin(prefix, libdir, "pkgconfig"))

To enable support for D4 in Vasp add the following lines to the Makefile:

CPP_OPTIONS += -DDFTD4
LLIBS       += $(shell pkg-config --libs dftd4)
INCS        += $(shell pkg-config --cflags dftd4)

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:

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. For convenience the type-generic macro dftd4_delete is available to free any memory allocation made in the library.

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.

Citation

Always cite:

Eike Caldeweyher, Christoph Bannwarth and Stefan Grimme, J. Chem. Phys., 2017, 147, 034112. DOI: 10.1063/1.4993215

Eike Caldeweyher, Sebastian Ehlert, Andreas Hansen, Hagen Neugebauer, Sebastian Spicher, Christoph Bannwarth and Stefan Grimme, J. Chem Phys, 2019, 150, 154122. DOI: 10.1063/1.5090222 chemrxiv: 10.26434/chemrxiv.7430216

Eike Caldeweyher, Jan-Michael Mewes, Sebastian Ehlert and Stefan Grimme, Phys. Chem. Chem. Phys., 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A chemrxiv: 10.26434/chemrxiv.10299428

License

This project is free software: you can redistribute it and/or modify it under the terms of the Lesser GNU 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 Lesser GNU 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 Lesser GNU General Public license, shall be licensed as above, without any additional terms or conditions.

	! ------------------------------------------------------------------------
	! command line arguments
	! ------------------------------------------------------------------------
	call read_commandline_arguments(env,set)
	call env%checkpoint

	! ------------------------------------------------------------------------
	! get molecular geometry
	! ------------------------------------------------------------------------
	call read_geometry(set%fname,mol,env)
	call env%checkpoint
	call generate_wsc(mol,mol%wsc)
	if (set%inchrg) mol%chrg = set%chrg

	def __init__(self, , method=None, *kwargs):
	"""Create new damping parameter from method name or explicit data"""

	if method is not None:
	_method = _ffi.new("char[]", method.encode())
	self._param = load_rational_damping(
	_method,
	kwargs.get("s9", 1.0) > 0.0,
	)
	else:
	try:
	self._param = new_rational_damping(
	kwargs.get("s6", 1.0),
	kwargs["s8"],
	kwargs.get("s9", 1.0),
	kwargs["a1"],
	kwargs["a2"],
	kwargs.get("alp", 16.0),
	)
	except KeyError as e:
	raise RuntimeError("Constructor requires argument for " + str(e))

dftd4 / dftd4 Goto Github PK

dftd4's Introduction

DFT-D4 project

Installing

Conda package

Spack package

FreeBSD Port

Building from Source

Building with meson

Building with CMake

Building with fpm

Usage

Parameters

API access

Fortran API

Building Vasp with support for D4

C API

Python API

Citation

License

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dftd4's Issues

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Expected behaviour:

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