MedeA-VASP includes a comprehensive graphical interface to set up, run and analyze VASP calculations. 1 (I am currently using my own multiply patched version 5. In solid-state physics, the electronic band structure (or simply band structure) of a solid describes the range of energies that. VASP comes with a library of PAW datasets, (one or more) for most elements of the periodic table:. Each individual PAW data set starts with a descriptive section, specifying amongst other things:. Parameters that were required to generate the dataset:. Number of valence electrons. Atomic mass. Default energy cutoffs. The vasp.6.1.0, vasp.6.1.1 and vasp.6.1.2 releases have a potentially serious issue related to the test suite. Please read about it here. VASP 5.4.4 and VASP 6.1.1 executables. Dedicated VASP 6 GUI enabling easy access to newly implemented functionality of VASP 6.1.1 as listed below. Space-time based approach for the calculation of polarizibility, providing essentially cubic rather than quartic scaling with system size, facilitating the study of larger systems.
News
02/08/20 - Version 1.04 Released
Bug fix for printing Bader volumes.
Introduction
Richard Bader, from McMaster University, developed an intuitive way of dividing molecules into atoms. His definition of an atom is based purely on the electronic charge density. Bader uses what are called zero flux surfaces to divide atoms. A zero flux surface is a 2-D surface on which the charge density is a minimum perpendicular to the surface. Typically in molecular systems, the charge density reaches a minimum between atoms and this is a natural place to separate atoms from each other.
Besides being an intuitive scheme for visualizing atoms in molecules, Bader's definition is often useful for charge analysis. For example, the charge enclosed within the Bader volume is a good approximation to the total electronic charge of an atom. The charge distribution can be used to determine multipole moments of interacting atoms or molecules. Bader's analysis has also been used to define the hardness of atoms, which can be used to quantify the cost of removing charge from an atom.
Program Overview
We have developed a fast algorithm for doing Bader's analysis on a charge density grid. The program (see below) can read in charge densities in the VASP CHGCAR format, or the Gaussian CUBE format. Essential visuals plugin for virtual dj crack downloads pirate bay. The program outputs the total charge associated with each atom, and the zero flux surfaces defining the Bader volumes.
Download
Select the appropriate platform to download a binary of the Bader analysis program:
- Linux x86-64 (ifort)
- Mac OS X, gfortran (ifort)
The F90 source code is also available:
- Source Code (v1.04 02/08/20)
Running the Program
The program can be run with the command
It will automatically determine if the chargefile is a VASP CHGCAR file or a Gaussian CUBE file. The only required input argument is the name of the charge density file.
Command line arguments and output files
The following options can be used when running the Bader analysis program.
To get a description of the options, run 'bader -h'.
Output files
The following output files are generated: ACF.dat, BCF.dat, AtomVolumes.dat.
ACF.dat contains the coordinates of each atom, the charge associated with it according to Bader partitioning, percentage of the whole according to Bader partitioning and the minimum distance to the surface. This distance should be compared to maximum cut-off radius for the core region if pseudo potentials have been used.
BCF.dat contains the coordinates of each Bader maxima, the charge within that volume, the nearest atom and the distance to that atom.
AtomVolumes.dat contains the number of each volume that has been assigned to each atom. These numbers correspond to the number of the BvAtxxxx.dat files.
The Bader volumes can be written using the print options.
-p none The default is to write no charge density files.
-p all_atom Combine all volumes associated with an atom and write to file. This is done for all atoms and written to files named BvAtxxxx.dat. The volumes associated with atoms are those for which the maximum in charge density within the volume is closest to the atom.
-p all_bader Write all Bader volumes (containing charge above threshold of 0.0001) to a file. The charge distribution in each volume is written to a separate file, named Bvolxxxx.dat. It will either be of a CHGCAR format or a CUBE file format, depending on the format of the initial charge density file. These files can be quite large, so this option should be used with caution.
-p sel_atom Write the selected atomic volumes, read from the subsequent list or range of volumes.
-p sel_bader Write the selected Bader volumes, read from the subsequent list or range of volumes.
-p sum_atom Write the sum of selected atomic volumes, read from the subsequent list of volumes.
-p sum_bader Write the sum of selected Bader volumes, read from the subsequent list of volumes.
You need to download Mac OS from an external trusted source. Let's get started with this tutorialStep One: Download Mac OS ISO Image file Download Mac OS Mojave Image fileAs you are on a Windows PC, you don't have access to Apple Store to download Mac OS.
-p atom_index Write the atomic volume index to a charge density file.
-p bader_index Write the Bader volume index to a charge density file.
Visualization
The Bader volumes can be written and visualized with the VASP Data Viewer, VMD, Jmol, VESTA, or a cube file viewer (such as GaussView) for Gaussian cube files.
Examples
- NaCl crystal (vasp chgcar)
- NaCl crystal including core charges (vasp chgcar)
- C2H4 molecule, orientation 1 (vasp chgcar)
- C2H4 molecule, orientation 2 (vasp chgcar)
- H2O molecule (gaussian cube)
Note for VASP users
One major issue with the charge density (CHGCAR) files from the VASPcode is that they only contain the valance charge density. The Bader analysis assumes that charge density maxima are located at atomic centers (or at pseudoatoms). Aggressive pseudopotentials remove charge from atomic centers where it is both expensive to calculate and irrelevant for the important bonding properties of atoms.
VASP contains a module (aedens) which allows forthe core charge to be written out from PAW calculations. This module is includedin vasp version 4.6.31 08Feb07 and later.By adding the LAECHG=.TRUE. to the INCAR file, the corecharge is written to AECCAR0 and the valance charge to AECCAR2. These two charge densityfiles can be summed using thechgsum.pl script:The total charge will be written to CHGCAR_sum.
The bader analysis can then be done on this total charge density file:
One finally note is that you need a fine fft grid to accurately reproduce the correcttotal core charge. It is essential to do a few calculations, increasing NG(X,Y,Z)F untilthe total charge is correct.
Note for CASTEP users
Aaron Hopkinson and Dr. Matt Probert from the University of York have provided a den2vasp.tar.gz utility to convert from the CASTEP charge density to the VASP CHGCAR format so that it can be read in by the Bader analysis program (updated 25/11/16).
Authors
This program was written byAndri Arnaldsson,Wenjie Tang,Sam Chill,Wenrui Chai, andGraeme Henkelman.
Improvements to the original algorithm were developed by Ed Sanville (Loughborough University, UK).
With contributions from: Johannes Voss (DTU), Erik McNellis (FHI), and Matthew Dyer (Liverpool)
Multipole code added by: Sebastien Lebegue, Angyan Janos, and Emmanuel Aubert (Institut Jean Barriol, Nancy-University)
References
- W. Tang, E. Sanville, and G. Henkelman A grid-based Bader analysis algorithm without lattice bias, J. Phys.: Condens. Matter21, 084204 (2009).
- E. Sanville, S. D. Kenny, R. Smith, and G. Henkelman An improved grid-based algorithm for Bader charge allocation, J. Comp. Chem.28, 899-908 (2007).
- G. Henkelman, A. Arnaldsson, and H. Jónsson, A fast and robust algorithm for Bader decomposition of charge density, Comput. Mater. Sci.36, 354-360 (2006).
- M. Yu and D. R. Trinkle, Accurate and efficient algorithm for Bader charge integration, J. Chem. Phys.134, 064111 (2011).
Translations
Abstract: Aquation free energy profiles of neutral cisplatin and cationicmonofunctional derivatives, including triaminochloroplatinum(II) andcis-diammine(pyridine)chloroplatinum(II), were computed using state of the artthermodynamic integration, for which temperature and solvent were accounted forexplicitly using density functional theory based canonical molecular dynamics(DFT-MD). For all the systems the 'inverse-hydration' where the metal centeracts as an acceptor of hydrogen bond has been observed. This has motivated toconsider the inversely bonded solvent molecule in the definition of thereaction coordinate required to initiate the constrained DFT-MD trajectories.We found that there exists little difference in free enthalpies of activations,such that these platinum-based anticancer drugs are likely to behave the sameway in aqueous media. Detailed analysis of the microsolvation structure of thesquare-planar complexes, along with the key steps of the aquation mechanism arediscussed.
Submission history
- Source Code (v1.04 02/08/20)
Running the Program
The program can be run with the command
It will automatically determine if the chargefile is a VASP CHGCAR file or a Gaussian CUBE file. The only required input argument is the name of the charge density file.
Command line arguments and output files
The following options can be used when running the Bader analysis program.
To get a description of the options, run 'bader -h'.
Output files
The following output files are generated: ACF.dat, BCF.dat, AtomVolumes.dat.
ACF.dat contains the coordinates of each atom, the charge associated with it according to Bader partitioning, percentage of the whole according to Bader partitioning and the minimum distance to the surface. This distance should be compared to maximum cut-off radius for the core region if pseudo potentials have been used.
BCF.dat contains the coordinates of each Bader maxima, the charge within that volume, the nearest atom and the distance to that atom.
AtomVolumes.dat contains the number of each volume that has been assigned to each atom. These numbers correspond to the number of the BvAtxxxx.dat files.
The Bader volumes can be written using the print options.
-p none The default is to write no charge density files.
-p all_atom Combine all volumes associated with an atom and write to file. This is done for all atoms and written to files named BvAtxxxx.dat. The volumes associated with atoms are those for which the maximum in charge density within the volume is closest to the atom.
-p all_bader Write all Bader volumes (containing charge above threshold of 0.0001) to a file. The charge distribution in each volume is written to a separate file, named Bvolxxxx.dat. It will either be of a CHGCAR format or a CUBE file format, depending on the format of the initial charge density file. These files can be quite large, so this option should be used with caution.
-p sel_atom Write the selected atomic volumes, read from the subsequent list or range of volumes.
-p sel_bader Write the selected Bader volumes, read from the subsequent list or range of volumes.
-p sum_atom Write the sum of selected atomic volumes, read from the subsequent list of volumes.
-p sum_bader Write the sum of selected Bader volumes, read from the subsequent list of volumes.
You need to download Mac OS from an external trusted source. Let's get started with this tutorialStep One: Download Mac OS ISO Image file Download Mac OS Mojave Image fileAs you are on a Windows PC, you don't have access to Apple Store to download Mac OS.
-p atom_index Write the atomic volume index to a charge density file.
-p bader_index Write the Bader volume index to a charge density file.
Visualization
The Bader volumes can be written and visualized with the VASP Data Viewer, VMD, Jmol, VESTA, or a cube file viewer (such as GaussView) for Gaussian cube files.
Examples
- NaCl crystal (vasp chgcar)
- NaCl crystal including core charges (vasp chgcar)
- C2H4 molecule, orientation 1 (vasp chgcar)
- C2H4 molecule, orientation 2 (vasp chgcar)
- H2O molecule (gaussian cube)
Note for VASP users
One major issue with the charge density (CHGCAR) files from the VASPcode is that they only contain the valance charge density. The Bader analysis assumes that charge density maxima are located at atomic centers (or at pseudoatoms). Aggressive pseudopotentials remove charge from atomic centers where it is both expensive to calculate and irrelevant for the important bonding properties of atoms.
VASP contains a module (aedens) which allows forthe core charge to be written out from PAW calculations. This module is includedin vasp version 4.6.31 08Feb07 and later.By adding the LAECHG=.TRUE. to the INCAR file, the corecharge is written to AECCAR0 and the valance charge to AECCAR2. These two charge densityfiles can be summed using thechgsum.pl script:The total charge will be written to CHGCAR_sum.
The bader analysis can then be done on this total charge density file:
One finally note is that you need a fine fft grid to accurately reproduce the correcttotal core charge. It is essential to do a few calculations, increasing NG(X,Y,Z)F untilthe total charge is correct.
Note for CASTEP users
Aaron Hopkinson and Dr. Matt Probert from the University of York have provided a den2vasp.tar.gz utility to convert from the CASTEP charge density to the VASP CHGCAR format so that it can be read in by the Bader analysis program (updated 25/11/16).
Authors
This program was written byAndri Arnaldsson,Wenjie Tang,Sam Chill,Wenrui Chai, andGraeme Henkelman.
Improvements to the original algorithm were developed by Ed Sanville (Loughborough University, UK).
With contributions from: Johannes Voss (DTU), Erik McNellis (FHI), and Matthew Dyer (Liverpool)
Multipole code added by: Sebastien Lebegue, Angyan Janos, and Emmanuel Aubert (Institut Jean Barriol, Nancy-University)
References
- W. Tang, E. Sanville, and G. Henkelman A grid-based Bader analysis algorithm without lattice bias, J. Phys.: Condens. Matter21, 084204 (2009).
- E. Sanville, S. D. Kenny, R. Smith, and G. Henkelman An improved grid-based algorithm for Bader charge allocation, J. Comp. Chem.28, 899-908 (2007).
- G. Henkelman, A. Arnaldsson, and H. Jónsson, A fast and robust algorithm for Bader decomposition of charge density, Comput. Mater. Sci.36, 354-360 (2006).
- M. Yu and D. R. Trinkle, Accurate and efficient algorithm for Bader charge integration, J. Chem. Phys.134, 064111 (2011).
Translations
Abstract: Aquation free energy profiles of neutral cisplatin and cationicmonofunctional derivatives, including triaminochloroplatinum(II) andcis-diammine(pyridine)chloroplatinum(II), were computed using state of the artthermodynamic integration, for which temperature and solvent were accounted forexplicitly using density functional theory based canonical molecular dynamics(DFT-MD). For all the systems the 'inverse-hydration' where the metal centeracts as an acceptor of hydrogen bond has been observed. This has motivated toconsider the inversely bonded solvent molecule in the definition of thereaction coordinate required to initiate the constrained DFT-MD trajectories.We found that there exists little difference in free enthalpies of activations,such that these platinum-based anticancer drugs are likely to behave the sameway in aqueous media. Detailed analysis of the microsolvation structure of thesquare-planar complexes, along with the key steps of the aquation mechanism arediscussed.
Submission history
From: Lionel Truflandier [view email]Medea Vasp Download Torrent
[v1]Tue, 3 Mar 2020 10:07:52 UTC (5,157 KB)Full-text links:
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