Package: tad-dftd4
Implementation of the DFT-D4 dispersion model in PyTorch.
This module allows to process a single structure or a batch of structures for the calculation of atom-resolved dispersion energies.For details on the D4 dispersion model, seeE. Caldeweyher, C. Bannwarth and S. Grimme,J. Chem. Phys.,2017,147, 034112. DOI:10.1063/1.4993215E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, C. Bannwarth and S. Grimme,J. Chem. Phys.,2019,150, 154122. DOI:10.1063/1.5090222E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme,Phys. Chem. Chem. Phys.,2020,22, 8499-8512. DOI:10.1039/D0CP00502AFor alternative implementations, also check outdftd4:Implementation of the DFT-D4 dispersion model in Fortran with Python bindings.cpp-d4:Implementation of the DFT-D4 dispersion model in C++.Installationpiptad-dftd4can easily be installed withpip.pip install tad-dftd4From sourceThis project is hosted on GitHub atdftd4/tad-dftd4.
Obtain the source by cloning the repository withgit clone https://github.com/dftd4/tad-dftd4
cd tad-dftd4We recommend using acondaenvironment to install the package.
You can setup the environment manager using amambaforgeinstaller.
Install the required dependencies from the conda-forge channel.mamba env create -n torch -f environment.yaml
mamba activate torchInstall this project withpipin the environmentpip install .The following dependencies are requirednumpytorchpytest(tests only)DevelopmentFor development, additionally install the following tools in your environment.mamba install black covdefaults coverage mypy pre-commit pylint toxWith pip, add the option-efor installing in development mode, and add[dev]for the development dependenciespip install -e .[dev]The pre-commit hooks are initialized by running the following command in the root of the repository.pre-commit installFor testing all Python environments, simply runtox.toxNote that this randomizes the order of tests but skips “large” tests. To modify this behavior,toxhas to skip the optionalposargs.tox -- testExamplesThe following example shows how to calculate the DFT-D4 dispersion energy for a single structure.importtorchimporttad_dftd4asd4numbers=d4.utils.to_number(symbols="C C C C N C S H H H H H".split())# coordinates in Bohrpositions=torch.tensor([[-2.56745685564671,-0.02509985979910,0.00000000000000],[-1.39177582455797,+2.27696188880014,0.00000000000000],[+1.27784995624894,+2.45107479759386,0.00000000000000],[+2.62801937615793,+0.25927727028120,0.00000000000000],[+1.41097033661123,-1.99890996077412,0.00000000000000],[-1.17186102298849,-2.34220576284180,0.00000000000000],[-2.39505990368378,-5.22635838332362,0.00000000000000],[+2.41961980455457,-3.62158019253045,0.00000000000000],[-2.51744374846065,+3.98181713686746,0.00000000000000],[+2.24269048384775,+4.24389473203647,0.00000000000000],[+4.66488984573956,+0.17907568006409,0.00000000000000],[-4.60044244782237,-0.17794734637413,0.00000000000000],])# total charge of the systemcharge=torch.tensor(0.0)# TPSS0-D4-ATM parametersparam={"s6":positions.new_tensor(1.0),"s8":positions.new_tensor(1.85897750),"s9":positions.new_tensor(1.0),"a1":positions.new_tensor(0.44286966),"a2":positions.new_tensor(4.60230534),}energy=d4.dftd4(numbers,positions,charge,param)torch.set_printoptions(precision=10)print(energy)# tensor([-0.0020841344, -0.0018971195, -0.0018107513, -0.0018305695,#         -0.0021737693, -0.0019484236, -0.0022788253, -0.0004080658,#         -0.0004261866, -0.0004199839, -0.0004280768, -0.0005108935])The next example shows the calculation of dispersion energies for a batch of structures.importtorchimporttad_dftd4asd4# S22 system 4: formamide dimernumbers=d4.utils.pack((d4.utils.to_number("C C N N H H H H H H O O".split()),d4.utils.to_number("C O N H H H".split()),))# coordinates in Bohrpositions=d4.utils.pack((torch.tensor([[-3.81469488143921,+0.09993441402912,0.00000000000000],[+3.81469488143921,-0.09993441402912,0.00000000000000],[-2.66030049324036,-2.15898251533508,0.00000000000000],[+2.66030049324036,+2.15898251533508,0.00000000000000],[-0.73178529739380,-2.28237795829773,0.00000000000000],[-5.89039325714111,-0.02589114569128,0.00000000000000],[-3.71254944801331,-3.73605775833130,0.00000000000000],[+3.71254944801331,+3.73605775833130,0.00000000000000],[+0.73178529739380,+2.28237795829773,0.00000000000000],[+5.89039325714111,+0.02589114569128,0.00000000000000],[-2.74426102638245,+2.16115570068359,0.00000000000000],[+2.74426102638245,-2.16115570068359,0.00000000000000],]),torch.tensor([[-0.55569743203406,+1.09030425468557,0.00000000000000],[+0.51473634678469,+3.15152550263611,0.00000000000000],[+0.59869690244446,-1.16861263789477,0.00000000000000],[-0.45355203669134,-2.74568780438064,0.00000000000000],[+2.52721209544999,-1.29200800956867,0.00000000000000],[-2.63139587595376,+0.96447869452240,0.00000000000000],]),))# total charge of both systemcharge=torch.tensor([0.0,0.0])# TPSS0-D4-ATM parametersparam={"s6":positions.new_tensor(1.0),"s8":positions.new_tensor(1.85897750),"s9":positions.new_tensor(1.0),"a1":positions.new_tensor(0.44286966),"a2":positions.new_tensor(4.60230534),}# calculate dispersion energy in Hartreeenergy=torch.sum(d4.dftd4(numbers,positions,charge,param),-1)torch.set_printoptions(precision=10)print(energy)# tensor([-0.0088341432, -0.0027013607])print(energy[0]-2*energy[1])# tensor(-0.0034314217)ContributingThis is a volunteer open source projects and contributions are always welcome.
Please, take a moment to read thecontributing guidelines.LicenseThis 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.