VOTCA has 3 major parts, the Coarse-graining toolkit (VOTCA-CSG), the Charge Transport toolkit (VOTCA-CTP) and the Excitation Transport Toolkit (VOTCA-XTP). All of them are based on the VOTCA Tools library, which implements shared procedures.
Coarse-graining toolkit (VOTCA-CSG)edit
VOTCA-CSG[4] supports a variety of different coarse-graining methods, incl. (iterative) Boltzmann Inversion, Inverse Monte Carlo, Force Matching (also known as the multiscale coarse-graining method) and the Relative entropy[5] method and hybrid combinations of those as well as optimization-driven approaches, like simplex and CMA. To gather statistics VOTCA-CSG can use multiple molecular dynamics package incl. GROMACS, DL_POLY, ESPResSo, ESPResSo++, LAMMPS and HOOMD-blue for sampling.
Charge Transport toolkit (VOTCA-CTP)edit
VOTCA-CTP[6] is a module, which does molecular orbital overlap calculations and can evaluate energetic disorder and electronic couplings needed to estimate charge transport properties.
Excitation Transport toolkit (VOTCA-XTP)edit
VOTCA-XTP is an extension to VOTCA-CTP, allowing to simulate excitation transport and properties.[7] Therefore, it provides its own implementation of GW-BSE and a basic DFT implementation, employing localized basissets. Polarized QM/MM calculations for excited states are provided in the Thole framework. It features an interface to the Quantum Chemistry package ORCA for large scale production runs.
Release namesedit
Major releases have names assigned to them:
1.1 SuperAnn
1.2 SuperDoris
1.3 SuperUzma
1.4 SuperKurt - in occasion of Kurt Kremer's 60th birthday[8]
1.5 SuperVictor - named after Victor Rühle, one of the original core developers[9]
^ abVictor Rühle, Christoph Junghans, Alexander Lukyanov, Kurt Kremer and Denis Andrienko. "Versatile Object-oriented Toolkit for Coarse-graining Applications" Journal of Chemical Theory and Computation 5 (2009): 3201. doi:10.1021/ct900369w
^Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin; Aluru, N. R.; Rühle, Victor; Junghans, Christoph (2015-07-20). "Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA". PLOS ONE. 10 (7): e0131754. Bibcode:2015PLoSO..1031754M. doi:10.1371/journal.pone.0131754. ISSN 1932-6203. PMC4507862. PMID 26192992.
^Victor Rühle, Alexander Lukyanov, Falk May, Manuel Schrader, Thorsten Vehoff, James Kirkpatrick, Bjoern Baumeier, Denis Andrienko . "Microscopic simulations of charge transport in disordered organic semiconductors" Journal of Chemical Theory and Computation, 7 (2011): 3335. doi:10.1021/ct200388s
^Jens Wehner, Lothar Brombacher, Joshua Brown, Christoph Junghans, Onur Çaylak, Yuriy Khalak, Pranav Madhikar, Gianluca Tirimbò, and Björn Baumeier. "Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP" Journal of Chemical Theory and Computation. doi:10.1021/acs.jctc.8b00617
votca, versatile, object, oriented, toolkit, coarse, graining, applications, coarse, grained, modeling, package, which, focuses, analysis, molecular, dynamics, data, development, systematic, coarse, graining, techniques, well, methods, used, simulating, micros. Versatile Object oriented Toolkit for Coarse graining Applications VOTCA is a Coarse grained modeling package which focuses on the analysis of molecular dynamics data the development of systematic coarse graining techniques as well as methods used for simulating microscopic charge and exciton transport in disordered semiconductors It was originally developed at the Max Planck Institute for Polymer Research and is now maintained by developers at the Max Planck Institute for Polymer Research Los Alamos National Laboratory Eindhoven University of Technology and the Beckman Institute for Advanced Science and Technology with contributions from researcher worldwide 4 VOTCAOriginal author s Victor Ruhle Christoph Junghans Alexander Lukyanov Kurt Kremer Denis AndrienkoDeveloper s Max Planck Institute for Polymer ResearchLos Alamos National LaboratoryBeckman Institute for Advanced Science and TechnologyEindhoven University of Technology 1 Initial release2008 16 years ago 2008 Stable release1 6 4 12 January 2021 3 years ago 2021 01 12 2 Preview release2021 rc 1 15 January 2021 3 years ago 2021 01 15 3 Repositorygithub wbr com wbr votcaWritten inC Perl BashOperating systemLinux macOS Windows any other Unix varietyPlatformx86 x86 64Available inEnglishTypeCoarse grained modelingLicenseApache License 2 0Websitewww wbr votca wbr org Contents 1 Features 1 1 Coarse graining toolkit VOTCA CSG 1 2 Charge Transport toolkit VOTCA CTP 1 3 Excitation Transport toolkit VOTCA XTP 2 Release names 3 See also 4 ReferencesFeatures editVOTCA has 3 major parts the Coarse graining toolkit VOTCA CSG the Charge Transport toolkit VOTCA CTP and the Excitation Transport Toolkit VOTCA XTP All of them are based on the VOTCA Tools library which implements shared procedures Coarse graining toolkit VOTCA CSG edit VOTCA CSG 4 supports a variety of different coarse graining methods incl iterative Boltzmann Inversion Inverse Monte Carlo Force Matching also known as the multiscale coarse graining method and the Relative entropy 5 method and hybrid combinations of those as well as optimization driven approaches like simplex and CMA To gather statistics VOTCA CSG can use multiple molecular dynamics package incl GROMACS DL POLY ESPResSo ESPResSo LAMMPS and HOOMD blue for sampling Charge Transport toolkit VOTCA CTP edit VOTCA CTP 6 is a module which does molecular orbital overlap calculations and can evaluate energetic disorder and electronic couplings needed to estimate charge transport properties Excitation Transport toolkit VOTCA XTP edit VOTCA XTP is an extension to VOTCA CTP allowing to simulate excitation transport and properties 7 Therefore it provides its own implementation of GW BSE and a basic DFT implementation employing localized basissets Polarized QM MM calculations for excited states are provided in the Thole framework It features an interface to the Quantum Chemistry package ORCA for large scale production runs Release names editMajor releases have names assigned to them 1 1 SuperAnn 1 2 SuperDoris 1 3 SuperUzma 1 4 SuperKurt in occasion of Kurt Kremer s 60th birthday 8 1 5 SuperVictor named after Victor Ruhle one of the original core developers 9 1 6 SuperPelagia 1 6 2 SuperGittaSee also editGROMACS MARTINI OpenMMReferences edit VOTCA Development page VOTCA Releases on Github VOTCA Releases on Github a b Victor Ruhle Christoph Junghans Alexander Lukyanov Kurt Kremer and Denis Andrienko Versatile Object oriented Toolkit for Coarse graining Applications Journal of Chemical Theory and Computation 5 2009 3201 doi 10 1021 ct900369w Mashayak S Y Jochum Mara N Koschke Konstantin Aluru N R Ruhle Victor Junghans Christoph 2015 07 20 Relative Entropy and Optimization Driven Coarse Graining Methods in VOTCA PLOS ONE 10 7 e0131754 Bibcode 2015PLoSO 1031754M doi 10 1371 journal pone 0131754 ISSN 1932 6203 PMC 4507862 PMID 26192992 Victor Ruhle Alexander Lukyanov Falk May Manuel Schrader Thorsten Vehoff James Kirkpatrick Bjoern Baumeier Denis Andrienko Microscopic simulations of charge transport in disordered organic semiconductors Journal of Chemical Theory and Computation 7 2011 3335 doi 10 1021 ct200388s Jens Wehner Lothar Brombacher Joshua Brown Christoph Junghans Onur Caylak Yuriy Khalak Pranav Madhikar Gianluca Tirimbo and Bjorn Baumeier Electronic Excitations in Complex Molecular Environments Many Body Green s Functions Theory in VOTCA XTP Journal of Chemical Theory and Computation doi 10 1021 acs jctc 8b00617 Votca 1 4 released Votca 1 5 released Retrieved from https en wikipedia org w index php title VOTCA amp oldid 1150889637, wikipedia, wiki, book, books, library,
