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vaspsol

New VASPsol ++

VASPsol is a community driven code implementing implicit solvents described by continuum models. A new version VASPsol++, has been released.This page will be maintained, however, all updates to VASPsol's code will now feature at this new repository : https://github.com/VASPsol/VASPsol/

VAPSsol ++ Paper : https://pubs.aip.org/aip/jcp/article-abstract/159/23/234117/2930317/An-implicit-electrolyte-model-for-plane-wave?redirectedFrom=fulltext

VASPsol (2014)

We have implemented an implicit solvation model that describes the effect of electrostatics, cavitation, and dispersion on the interaction between a solute and solvent into the plane-wave DFT code VASP. Our implementation provides a computationally efficient means to calculate the effects of solvation on molecules and crystal surfaces as well as reaction barriers. The strength of our solvation model implementation is its capability to handle large periodic systems such as metal and semiconductor surfaces and its interoperability with standard ultrasoft pseudopotential and projector-augmented wave potential libraries.

Prerequisites

VASP versions 5.2.12 or 5.3.3 or 5.3.5 or >=5.4.1.

Compiler and library requirements are the same as that of VASP ([vasp wiki] (http://cms.mpi.univie.ac.at/wiki/index.php/Installing_VASP))

Installation

For VASP versions = 5.2.12 or 5.3.3 or 5.3.5:

Note:

  • Apply the appropriate interface patch to the original VASP source code. There are 3 interface_patch files available in the VASPsol/patches folder, one for each supported versions of VASP.
    cd <VASP src directory>
    patch -p1 < <path to the interface patch file>
  • After applying the patch, copy VASPsol/src/solvation.F file to the VASP source directory:
  • In the original VASP Makefile, put solvation.o object file name before pot.o in that order.
  • make clean
  • make

Note:

The file VASPsol/src/solvation.F combines all the modules defined in the files in the folder VASPsol/src/modules so as to conform with the new builtin interface for solvation in vasp(versions >= 5.4.1). The files in the VASPsol/src/modules folder do not play any role in the installation procedure.

For VASP versions >= 5.4.1:

These versions of VASP support solvation calculations out of the box. The only thing that the user needs to do is to update the solvation routines by copying the VASPsol/src/solvation.F file to the src/ folder in the original VASP folder, vasp.5.4.X/src/ and follow the install instructions for the compilation of the original VASP.

Note on versions >=5.4.4:

It seems like the complementary error function definition has been refactored a bit in the newer versions. Inorder to ensure the solvation module's compatibility with the newer versions of vasp please add -Dsol_compat option to the list of precompiler options(CPP_OPTIONS) in the makefile.

Note on binaries:

VASP.5.4.1 by default compiles all the three binaries: standard one(vasp_std), gamma version(vasp_gamma) and the one for noncollinear calculations(vasp_ncl). Some users have reported in the past that the version 5.4.1 compilation fails after updating the solvation related files. This was due to the fact that the solvation modules were written and tested using the real to complex FFTs(same as vasp_std and vasp_gamma) whereas the non-collinear compilation uses complex to complex FFTs. The issue has been fixed and all three binaries will compile fine without any errors.

Note on running Poisson-Boltzmann solver with 5.4.1:

To compute the FERMI_SHIFT as mentioned in the documentation in version 5.4.1, minor modification is required to the pot.F file. This can be done by applying the patch file pbz_patch_541 provided in the src/patches folder as follows.

    cd vasp.5.4.1
    patch src/pot.F < <path to the pbz_patch_541 patch file>

For VASP6 versions >= 6.1.0:

For VASP versions > 6.1.0 there is currently a patch in /VASPsol/patches/VASPsol6.patch. This patch applies the FERMI_SHIFT patch to the pot.F as well as providing additional subroutines. This patch was developed by user shk11 in Issue #43.

  • copy solvation.F from path_to_VASPsol/src/solvation.F to path_to_VASP6_install/src/
  • Navigate to path_to_VASP6_install/src/ and modify the .objects file by ensuring that “solvation.o” appears before “pot.o”
  • Set the CPP option "-Dsol_compat" in the VASP makefile.include file.
  • Compile the code as described in the instructions on the VASP wiki.
    cd vasp.6.1.0
    patch -p0 < <path to the pbz_patch_610 patch file>

Usage

Please see the file USAGE.md in the docs folder for instructions and the examples folder for some sample calculations.

License

VASPSol is released under the terms of Apache version 2.0 license:

Copyright 2013-2015 Kiran Mathew and Richard Hennig

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

For discussions and feedback

Join our mailing list: https://groups.google.com/forum/#!forum/vaspsol

Contributing

Please contact Dr. Richard Hennig (rhennig[at]mse.ufl.edu)

Authors

Kiran Mathew

Dr. Richard Hennig

How to cite

DOI for the VASPsol Github repository:

DOI

If you use the VASPsol package in your research, please cite the following papers:

  • Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways. K. Mathew, R. Sundararaman, K. Letchworth-Weaver, T. A. Arias, and R. G. Hennig, J. Chem. Phys. 140, 084106 (2014), [doi:10.1063/1.4865107] (https://doi.org/10.1063/1.4865107).

  • Implicit self-consistent electrolyte model in plane-wave density-functional theory. K. Mathew, V. S. C. Kolluru, S. Mula, S. N. Steinmann, and R. G. Hennig, J. Chem. Phys. 151, 234101 (2019), [doi:10.1063/1.5132354] (https://doi.org/10.1063/1.5132354).

BibTex entry for the Github repository and the publications::

   @misc{VASPsol-Software,
     title        = {VASPsol: Implicit solvation and electrolyte model for density-functional theory},
     author       = {K. Mathew and V. S. Chaitanya Kolluru and R. G. Hennig},
     year         = 2018,
     publisher    = {GitHub},
     journal      = {GitHub repository},
     howpublished = {\url{https://github.com/henniggroup/VASPsol}},
     url          = {https://github.com/henniggroup/VASPsol},
     doi          = {10.5281/zenodo.2555053}
   }
   
   @article{VASPsol2014-Dielectric,
     title        = {Implicit solvation model for density-functional study of nanocrystal surfaces
                     and reaction pathways.},
     author       = {K. Mathew and R. Sundararaman and K. Letchworth-Weaver and T. A. Arias and
                     R. G. Hennig},
     year         = 2014,
     journal      = {J. Chem. Phys.},
     volume       = 140,
     pages        = {084106},
     doi          = {10.1063/1.4865107}
   }
   
   @article{VASPsol2019-Electrolyte,
     title        = {Implicit self-consistent electrolyte model in plane-wave density-functional theory.},
     author       = {K. Mathew and V. S. C. Kolluru and S. Mula and S. N. Steinmann and R. G. Hennig},
     year         = 2019,
     journal      = {J. Chem. Phys.},
     volume       = 151,
     pages        = {234101},
     doi          = {10.1063/1.5132354}
   }