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searchindex.js
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Search.setIndex({"alltitles": {"(Optional) Plot the spectrum": [[154, "(Optional)-Plot-the-spectrum"]], "AMD Processors": [[3, "amd-processors"]], "Additional tutorials": [[5, "additional-tutorials"]], "Adiabatic vs Diabatic States": [[193, "adiabatic-vs-diabatic-states"]], "Advanced pressure correction": [[36, "advanced-pressure-correction"]], "Advanced topics": [[5, "advanced-topics"], [6, "advanced-topics"]], "Advanced topology handling": [[33, "advanced-topology-handling"]], "Alternatives": [[37, "alternatives"]], "An example on non-bonded interactions": [[37, "an-example-on-non-bonded-interactions"]], "Architecture of votca-xtp": [[161, "architecture-of-votca-xtp"]], "Atomic Forces and Geometry Optimizaiton": [[159, "Atomic-Forces-and-Geometry-Optimizaiton"]], "Atomistic simulation": [[5, "atomistic-simulation"], [5, "id3"], [5, "id6"]], "Attribution": [[1, "attribution"]], "Auto": [[2, "auto"]], "Automating Formatting": [[2, "automating-formatting"]], "Bibliography": [[7, "bibliography"], [164, "bibliography"]], "Boltzmann Inversion": [[36, "boltzmann-inversion"]], "Boltzmann inversion": [[147, "boltzmann-inversion"]], "Building VOTCA": [[5, "building-votca"]], "Building the documentation and website locally": [[153, "building-the-documentation-and-website-locally"]], "CPP Coding Rules": [[2, "cpp-coding-rules"]], "CPP Coding Style Guide": [[2, "cpp-coding-style-guide"]], "CPP Comment Guide": [[2, "cpp-comment-guide"]], "CPP Resources": [[2, "cpp-resources"]], "CSG Manual": [[32, "csg-manual"]], "CSG Tutorial": [[5, "csg-tutorial"]], "CUDA support": [[3, "cuda-support"]], "Calculation of RDF": [[5, "calculation-of-rdf"]], "CentOS": [[3, "centos"]], "Changing the theme": [[153, "changing-the-theme"]], "Charge and Energy Transfer Theory": [[193, "charge-and-energy-transfer-theory"]], "Charge and Energy Transport Model": [[194, "charge-and-energy-transport-model"]], "Check the mapping": [[156, "Check-the-mapping"], [157, "Check-the-mapping"]], "Citations": [[32, "citations"], [162, "citations"]], "Classes": [[2, "classes"]], "Clipping of poorly sampled regions": [[37, "clipping-of-poorly-sampled-regions"]], "Closure and optimization method": [[36, "closure-and-optimization-method"]], "Coarse-graining of liquid hexane": [[5, "coarse-graining-of-liquid-hexane"]], "Coarse-graining of liquid methanol": [[5, "coarse-graining-of-liquid-methanol"]], "Code of Conduct": [[1, "code-of-conduct"]], "Common CMake Flags": [[3, "common-cmake-flags"]], "Compute site energy": [[156, "Compute-site-energy"], [157, "Compute-site-energy"]], "Compute the forces": [[159, "Compute-the-forces"]], "Conda-forge": [[3, "conda-forge"]], "Configure the xtp calculator": [[159, "Configure-the-xtp-calculator"], [160, "Configure-the-xtp-calculator"]], "Coordination Iterative Boltzmann Inversion": [[36, "coordination-iterative-boltzmann-inversion"]], "Copyright": [[32, "copyright"], [162, "copyright"]], "Correlation analysis": [[36, "correlation-analysis"]], "Correlation groups": [[36, "correlation-groups"]], "Coupling": [[156, "Coupling"]], "Coupling analysis": [[156, "Coupling-analysis"]], "Couplings histrogram": [[155, "Couplings-histrogram"]], "Customization": [[6, "customization"]], "DESCRIPTION": [[8, "description"], [9, "description"], [11, "description"], [12, "description"], [13, "description"], [14, "description"], [15, "description"], [16, "description"], [17, "description"], [18, "description"], [19, "description"], [20, "description"], [21, "description"], [22, "description"], [23, "description"], [24, "description"], [25, "description"], [26, "description"], [27, "description"], [27, "id3"], [27, "id6"], [27, "id9"], [27, "id12"], [27, "id15"], [27, "id18"], [27, "id21"], [27, "id24"], [27, "id28"], [27, "id31"], [27, "id35"], [27, "id38"], [27, "id42"], [27, "id47"], [27, "id50"], [27, "id53"], [27, "id56"], [27, "id59"], [27, "id62"], [27, "id66"], [27, "id69"], [27, "id72"], [27, "id75"], [27, "id78"], [27, "id81"], [27, "id86"], [27, 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"DL_POLY": [[6, "dl-poly"]], "DL_POLY interface": [[6, "dl-poly-interface"]], "Debian / Ubuntu": [[3, "debian-ubuntu"]], "Define the molecular structure": [[159, "Define-the-molecular-structure"], [160, "Define-the-molecular-structure"]], "Density-Functional Theory": [[171, "density-functional-theory"]], "Dependency Installation": [[3, "dependency-installation"]], "Developer and Contributor Guide": [[2, "developer-and-contributor-guide"]], "Development": [[32, "development"], [162, "development"]], "Development version": [[3, "development-version"]], "Directed Graphs": [[194, "directed-graphs"]], "Distribution functions and tabulated potentials": [[36, "distribution-functions-and-tabulated-potentials"]], "Docker": [[3, "docker"]], "Doxygen documentation": [[2, "doxygen-documentation"]], "ESPResSo": [[6, "espresso"]], "EXAMPLES": [[9, "examples"], [12, "examples"], [18, "examples"], [19, "examples"], [27, "examples"], [27, "id43"], [27, "id82"], [27, "id94"], [27, "id196"], [27, 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"Extrapolation": [[37, "extrapolation"]], "FM for all interactions together": [[5, "fm-for-all-interactions-together"]], "FM for non-bonded interactions only": [[5, "fm-for-non-bonded-interactions-only"]], "Failed Release Builds": [[2, "failed-release-builds"]], "Fedora": [[3, "id1"]], "Files": [[2, "files"]], "Force Matching": [[147, "force-matching"]], "Force matching": [[36, "force-matching"]], "Force matching (FM)": [[5, "force-matching-fm"], [5, "id4"]], "Force matching for SPC/E water": [[5, "force-matching-for-spc-e-water"]], "Force matching for SPC/E water with 3body SW interactions": [[5, "force-matching-for-spc-e-water-with-3body-sw-interactions"]], "Formatting code": [[2, "formatting-code"]], "FreeBSD": [[3, "freebsd"]], "Functions": [[2, "functions"]], "GCC and MKL : undefined symbol:": [[3, "gcc-and-mkl-undefined-symbol"]], "GROMACS": [[6, "gromacs"]], "General": [[2, "general"]], "General (Source) Installation Instructions": [[3, "general-source-installation-instructions"]], "General considerations": [[36, "general-considerations"], [36, "id5"], [36, "id6"]], "Generate the topology from the Gromacs file": [[156, "Generate-the-topology-from-the-Gromacs-file"], [157, "Generate-the-topology-from-the-Gromacs-file"]], "Generating a topology file for a coarse-grained run": [[37, "generating-a-topology-file-for-a-coarse-grained-run"]], "Generating exclusion lists": [[36, "generating-exclusion-lists"]], "Gentoo": [[3, "gentoo"]], "Geometry Optimization": [[189, "geometry-optimization"]], "Geometry optimization": [[159, "Geometry-optimization"]], "Gnuplot": [[6, "gnuplot"]], "Header Files": [[2, "header-files"]], "How code is executed": [[161, "how-code-is-executed"]], "How electronic structure calculations are run": [[161, "how-electronic-structure-calculations-are-run"]], "How options are parsed in xtp": [[161, "how-options-are-parsed-in-xtp"]], "How statefiles are parsed in": [[161, "how-statefiles-are-parsed-in"]], "How the cuda support works": [[161, "how-the-cuda-support-works"]], "How to start:": [[36, "how-to-start"]], "IBI for all interactions": [[5, "ibi-for-all-interactions"]], "IBI for non-bonded interactions only": [[5, "ibi-for-non-bonded-interactions-only"]], "Includes": [[2, "includes"]], "Indexing in VOTCA": [[4, "indexing-in-votca"]], "Input files": [[5, "input-files"], [33, "input-files"]], "Input preparation": [[36, "input-preparation"]], "Installation": [[3, "installation"], [5, "installation"], [189, "installation"]], "Instantiate the xtp calculator": [[160, "Instantiate-the-xtp-calculator"]], "Integration and extrapolation of .force files": [[36, "integration-and-extrapolation-of-force-files"]], "Intel Processors": [[3, "intel-processors"]], "Interacting with the XTP command line interface": [[154, "Interacting-with-the-XTP-command-line-interface"], [156, "Interacting-with-the-XTP-command-line-interface"], [157, "Interacting-with-the-XTP-command-line-interface"]], "Internal degrees of freedom": [[36, "internal-degrees-of-freedom"]], "Introduction": [[34, "introduction"], [154, "Introduction"], [198, "introduction"]], "Inverse Monte Carlo": [[36, "inverse-monte-carlo"], [147, "inverse-monte-carlo"]], "Inverse Monte Carlo (IMC) for SPC/E water": [[5, "inverse-monte-carlo-imc-for-spc-e-water"]], "Iterative Boltzmann Inversion": [[36, "iterative-boltzmann-inversion"], [147, "iterative-boltzmann-inversion"]], "Iterative Boltzmann inversion (IBI) for SPC/E water": [[5, "iterative-boltzmann-inversion-ibi-for-spc-e-water"]], "Iterative Integral Equation methods": [[36, "iterative-integral-equation-methods"], [147, "iterative-integral-equation-methods"]], "Iterative methods": [[36, "iterative-methods"], [147, "iterative-methods"]], "Iterative workflow control": [[36, "iterative-workflow-control"]], "KMC simulations of multiple holes or electrons in periodic boundary conditions": [[155, "KMC-simulations-of-multiple-holes-or-electrons-in-periodic-boundary-conditions"]], "Kinect Monte Carlo Simulations Using LAMMPS": [[155, "Kinect-Monte-Carlo-Simulations-Using-LAMMPS"]], "Kirkwood-Buff correction": [[36, "kirkwood-buff-correction"]], "LAMMPS": [[6, "lammps"]], "Linking Error: Undefined reference to": [[3, "linking-error-undefined-reference-to"]], "MD simulations": [[5, "md-simulations"]], "Making a Release": [[2, "making-a-release"]], "Many-Body Green\u2019s Functions and the Bethe-Salpeter Equation": [[171, "many-body-green-s-functions-and-the-bethe-salpeter-equation"]], "Mapping": [[147, "mapping"]], "Mapping an atomistic trajectory onto a coarse-grained trajectory": [[5, "mapping-an-atomistic-trajectory-onto-a-coarse-grained-trajectory"]], "Mapping file": [[38, "mapping-file"]], "Mapping files": [[33, "mapping-files"]], "Methods": [[36, "methods"]], "Monomer States as Approximations to Diabatic States": [[193, "monomer-states-as-approximations-to-diabatic-states"]], 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"NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "NAME", "Theoretical background", "<no title>", "Welcome to VOTCA\u2019s documentation!", "TOOLS Manual", "Reference", "NAME", "Website and Documentation", "DFT + GWBSE Energy Calculation Using CH4", "Kinect Monte Carlo Simulations Using LAMMPS", "QMMM workflow using GROMACS and VOTCA-XTP", "QMMM workflow using LAMMPS and VOTCA-XTP", "XTP Tutorials", "Atomic Forces and Geometry Optimizaiton", "Single Point Energy using <code class=\"docutils literal notranslate\"><span class=\"pre\">pyxtp</span></code>", "Architecture of votca-xtp", "XTP Manual", "<span class=\"section-number\">6.4.1.4.1. </span>apdft", "<span class=\"section-number\">8. </span>Bibliography", "<span class=\"section-number\">6.4.1.4.2. </span>coupling", "<span class=\"section-number\">6.4.1.4.3. </span>densityanalysis", "<span class=\"section-number\">6.4.1.4.4. </span>dftgwbse", "<span class=\"section-number\">6.4.1.4.5. </span>diabatization", "<span class=\"section-number\">6.3.1.4.1. </span>eanalyze", "<span class=\"section-number\">6.3.1.4.2. </span>einternal", "<span class=\"section-number\">2. </span>Electronic Structure Theories", "<span class=\"section-number\">6.2.1.4.1. </span>eqm", "<span class=\"section-number\">6.4.1.4.6. </span>excitoncoupling", "<span class=\"section-number\">6.4.1.4.7. </span>gencube", "<span class=\"section-number\">6.4.1.4.15. </span>gpu_benchmark", "<span class=\"section-number\">6.3.1.4.3. </span>ianalyze", "<span class=\"section-number\">6.2.1.4.2. </span>iexcitoncl", "<span class=\"section-number\">6.2.1.4.3. </span>iqm", "<span class=\"section-number\">6.3.1.4.4. </span>kmclifetime", "<span class=\"section-number\">6.3.1.4.5. </span>kmcmultiple", "<span class=\"section-number\">6.4.1.4.8. </span>log2mps", "<span class=\"section-number\">6.3.1.4.6. </span>mapchecker", "<span class=\"section-number\">6.4.1.4.14. </span>mol2orb", "<span class=\"section-number\">6.4.1.4.9. </span>molpol", "<span class=\"section-number\">6.3.1.4.7. </span>neighborlist", "<span class=\"section-number\">6.4.1.4.12. </span>orb2fchk", "<span class=\"section-number\">6.4.1.4.13. </span>orb2mol", "<span class=\"section-number\">6.4.1.4.10. </span>partialcharges", "<span class=\"section-number\">5. </span>XTP ASE Interface", "<span class=\"section-number\">6.2.1.4.4. </span>qmmm", "<span class=\"section-number\">7. </span>Reference", "<span class=\"section-number\">6.4.1.4.11. </span>spectrum", "<span class=\"section-number\">3. </span>Charge and Energy Transfer Theory", "<span class=\"section-number\">4. </span>Charge and Energy 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