dftd4 3.6.0

Python API of the DFT-D4 project

Python interface for the generally applicable atomic-charge dependent London dispersion correction, DFT-D4. This Python project is targeted at developers who want to interface their project via Python with dftd4.

This interface provides access to the C-API of dftd4 via the CFFI module. The low-level CFFI interface is available in the dftd4.library module and only required for implementing other interfaces. A more pythonic interface is provided in the dftd4.interface module which can be used to build more specific interfaces.

>>> from dftd4.interface import DampingParam, DispersionModel
>>> import numpy as np
>>> numbers = np.array([1, 1, 6, 5, 1, 15, 8, 17, 13, 15, 5, 1, 9, 15, 1, 15])
>>> positions = np.array([  # Coordinates in Bohr
...     [+2.79274810283778, +3.82998228828316, -2.79287054959216],
...     [-1.43447454186833, +0.43418729987882, +5.53854345129809],
...     [-3.26268343665218, -2.50644032426151, -1.56631149351046],
...     [+2.14548759959147, -0.88798018953965, -2.24592534506187],
...     [-4.30233097423181, -3.93631518670031, -0.48930754109119],
...     [+0.06107643564880, -3.82467931731366, -2.22333344469482],
...     [+0.41168550401858, +0.58105573172764, +5.56854609916143],
...     [+4.41363836635653, +3.92515871809283, +2.57961724984000],
...     [+1.33707758998700, +1.40194471661647, +1.97530004949523],
...     [+3.08342709834868, +1.72520024666801, -4.42666116106828],
...     [-3.02346932078505, +0.04438199934191, -0.27636197425010],
...     [+1.11508390868455, -0.97617412809198, +6.25462847718180],
...     [+0.61938955433011, +2.17903547389232, -6.21279842416963],
...     [-2.67491681346835, +3.00175899761859, +1.05038813614845],
...     [-4.13181080289514, -2.34226739863660, -3.44356159392859],
...     [+2.85007173009739, -2.64884892757600, +0.71010806424206],
... ])
>>> model = DispersionModel(numbers, positions)
>>> res = model.get_dispersion(DampingParam(method="scan"), grad=False)
>>> res.get("energy")  # Results in atomic units
-0.005328888532435093
>>> res.update(**model.get_properties())  # also allows access to properties
>>> res.get("c6 coefficients")[0, 0]
1.5976689760849156
>>> res.get("polarizibilities")
array([ 1.97521745,  1.48512704,  7.33564674, 10.28920458,  1.99973802,
       22.85298573,  6.65877552, 15.39410319, 22.73119177, 22.86303028,
       14.56038118,  1.4815783 ,  3.91266859, 25.8236368 ,  1.93444627,
       23.02494331])

Additional features

The dftd4.parameters module becomes available if a TOML parser is available, either tomlkit or toml can be used here. The returned dict can be used to supply parameters to the constructor of the DampingParam object, only the s6, s8, s9, a1, a2 and alp entries will be used, the remaining entries are meta data describing the damping parameters.

>>> from dftd4.parameters import get_damping_param
>>> get_damping_param("b97m")
{'s6': 1.0, 's9': 1.0, 'alp': 16.0, 's8': 0.6633, 'a1': 0.4288, 'a2': 3.9935}
>>> get_damping_param("r2scan", keep_meta=True)
{'s6': 1.0, 's9': 1.0, 'alp': 16.0, 'damping': 'bj', 'mbd': 'approx-atm', 's8': 0.6018749, 'a1': 0.51559235, 'a2': 5.77342911, 'doi': '10.1063/5.0041008'}

QCSchema Integration

This Python API natively understands QCSchema and the QCArchive infrastructure. If the QCElemental package is installed the dftd4.qcschema module becomes importable and provides the run_qcschema function.

>>> from dftd4.qcschema import run_qcschema
>>> import qcelemental as qcel
>>> atomic_input = qcel.models.AtomicInput(
...     molecule = qcel.models.Molecule(
...         symbols = ["O", "H", "H"],
...         geometry = [
...             0.00000000000000,  0.00000000000000, -0.73578586109551,
...             1.44183152868459,  0.00000000000000,  0.36789293054775,
...            -1.44183152868459,  0.00000000000000,  0.36789293054775
...         ],
...     ),
...     driver = "energy",
...     model = {
...         "method": "TPSS-D4",
...     },
...     keywords = {},
... )
...
>>> atomic_result = run_qcschema(atomic_input)
>>> atomic_result.return_result
-0.0002667885779142513

ASE Integration

To integrate with ASE this interface implements an ASE Calculator. The DFTD4 calculator becomes importable if an ASE installation is available.

>>> from ase.build import molecule
>>> from dftd4.ase import DFTD4
>>> atoms = molecule('H2O')
>>> atoms.calc = DFTD4(method="TPSS")
>>> atoms.get_potential_energy()
-0.007310393443152083
>>> atoms.calc.set(method="PBE")
{'method': 'PBE'}
>>> atoms.get_potential_energy()
-0.005358475432239303
>>> atoms.get_forces()
array([[-0.        , -0.        ,  0.00296845],
       [-0.        ,  0.00119152, -0.00148423],
       [-0.        , -0.00119152, -0.00148423]])

To use the DFTD4 calculator as dispersion correction the calculator can be combined using the SumCalculator from the ase.calculators.mixing module.

>>> from ase.build import molecule
>>> from ase.calculators.mixing import SumCalculator
>>> from ase.calculators.nwchem import NWChem
>>> from dftd4.ase import DFTD4
>>> atoms = molecule('H2O')
>>> atoms.calc = SumCalculator([DFTD4(method="PBE"), NWChem(xc="PBE")])

For convenience DFTD4 allows to combine itself with another calculator by using the add_calculator method which returns a SumCalculator:

>>> from ase.build import molecule
>>> from ase.calculators.emt import EMT
>>> from dftd4.ase import DFTD4
>>> atoms = molecule("C60")
>>> atoms.calc = DFTD4(method="pbe").add_calculator(EMT())
>>> atoms.get_potential_energy()
6.348142387048062
>>> [calc.get_potential_energy() for calc in atoms.calc.calcs]
[-6.015477436263984, 12.363619823312046]

The individual contributions are available by iterating over the list of calculators in calc.calcs. Note that DFTD4 will always place itself as first calculator in the list.

PySCF support

Integration with PySCF is possible by using the dftd4.pyscf module. The module provides a DFTD4Dispersion class to construct a PySCF compatible calculator for evaluating the dispersion energy and gradients.

>>> from pyscf import gto
>>> import dftd4.pyscf as disp
>>> mol = gto.M(
...     atom="""
...          C   -0.755422531  -0.796459123  -1.023590391
...          C    0.634274834  -0.880017014  -1.075233285
...          C    1.406955202   0.199695367  -0.653144334
...          C    0.798863737   1.361204515  -0.180597909
...          C   -0.593166787   1.434312023  -0.133597923
...          C   -1.376239198   0.359205222  -0.553258516
...          I   -1.514344238   3.173268101   0.573601106
...          H    1.110906949  -1.778801728  -1.440619836
...          H    1.399172302   2.197767355   0.147412751
...          H    2.486417780   0.142466525  -0.689380574
...          H   -2.454252250   0.422581120  -0.512807958
...          H   -1.362353593  -1.630564523  -1.348743149
...          S   -3.112683203   6.289227834   1.226984439
...          H   -4.328789697   5.797771251   0.973373089
...          C   -2.689135032   6.703163830  -0.489062886
...          H   -1.684433029   7.115457372  -0.460265708
...          H   -2.683867206   5.816530502  -1.115183775
...          H   -3.365330613   7.451201412  -0.890098894
...          """
... )
>>> d4 = disp.DFTD4Dispersion(mol, xc="r2SCAN")
>>> d4.kernel()[0]
array(-0.0050011)

To make use of the dispersion correction together with other calculators, the energy method allows to apply a dispersion correction to an existing calculator.

>>> from pyscf import gto, scf
>>> import dftd4.pyscf as disp
>>> mol = gto.M(
...     atom="""
...          O  -1.65542061  -0.12330038   0.00000000
...          O   1.24621244   0.10268870   0.00000000
...          H  -0.70409026   0.03193167   0.00000000
...          H  -2.03867273   0.75372294   0.00000000
...          H   1.57598558  -0.38252146  -0.75856129
...          H   1.57598558  -0.38252146   0.75856129
...          """
... )
>>> mf = disp.energy(scf.RHF(mol)).run()
converged SCF energy = -149.939098424774
>>> grad = mf.nuc_grad_method().kernel()
--------------- DFTD4 gradients ---------------
         x                y                z
0 O     0.0172438133     0.0508406920     0.0000000000
1 O     0.0380018285    -0.0460223790    -0.0000000000
2 H    -0.0305058266    -0.0126478132    -0.0000000000
3 H     0.0069233858    -0.0382898692    -0.0000000000
4 H    -0.0158316004     0.0230596847     0.0218908543
5 H    -0.0158316004     0.0230596847    -0.0218908543
----------------------------------------------

Installing

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-python

Now you are ready to use dftd4, check if you can import it with

>>> import dftd4
>>> from dftd4.libdftd4 import get_api_version
>>> get_api_version()
'3.6.0'

Building the extension module

To perform an out-of-tree build some version of dftd4 has to be available on your system and preferably findable by pkg-config. Try to find a dftd4 installation you build against first with

pkg-config --modversion dftd4

Adjust the PKG_CONFIG_PATH environment variable to include the correct directories to find the installation if necessary.

Using pip

This project support installation with pip as an easy way to build the Python API.

• C compiler to build the C-API and compile the extension module (the compiler name should be exported in the CC environment variable)

• Python 3.6 or newer

• The following Python packages are required additionally

  • cffi

  • numpy

  • pkgconfig (setup only)

Make sure to have your C compiler set to the CC environment variable

export CC=gcc

Install the project with pip

pip install .

To install extra dependencies as well use

pip install '.[parameters,ase,qcschema]'

If you already have a dftd4 installation, e.g. from conda-forge, you can build the Python extension module directly without cloning this repository

pip install "https://github.com/dftd4/dftd4/archive/refs/heads/main#egg=dftd4-python&subdirectory=python"

Using meson

This directory contains a separate meson build file to allow the out-of-tree build of the CFFI extension module. The out-of-tree build requires

• C compiler to build the C-API and compile the extension module

• meson version 0.55 or newer

• a build-system backend, i.e. ninja version 1.7 or newer

• Python 3.6 or newer with the CFFI package installed

Setup a build with

meson setup _build -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.

Compile the project with

meson compile -C _build

The extension module is now available in _build/dftd4/_libdftd4.*.so. You can install as usual with

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