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OpenMD::CollectiveDipoleDisplacement Class Reference
Calculates the collective dipole displacement function. More...
#include <CollectiveDipoleDisplacement.hpp>
Inheritance diagram for OpenMD::CollectiveDipoleDisplacement:
Public Member Functions | |
| CollectiveDipoleDisplacement (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2) | |
| Public Member Functions inherited from OpenMD::SystemACF< Vector3d > | |
| SystemACF (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2) | |
| Public Member Functions inherited from OpenMD::AutoCorrFunc< Vector3d > | |
| AutoCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2) | |
| Public Member Functions inherited from OpenMD::TimeCorrFunc< Vector3d > | |
| TimeCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2) | |
| virtual void | doCorrelate () |
| const std::string & | getCorrFuncType () const |
| void | setCorrFuncType (const std::string &type) |
| void | setParameterString (const std::string ¶ms) |
| void | setLabelString (const std::string &label) |
| void | setWindowingParameters (RealType tcorr_fs, int nStart, RealType tsep_fs) |
| Public Member Functions inherited from OpenMD::DynamicProperty | |
| void | setOutputName (const std::string &filename) |
| const std::string & | getOutputFileName () const |
| void | setSelectionModeRestart () |
Additional Inherited Members | |
| Protected Member Functions inherited from OpenMD::SystemACF< Vector3d > | |
| virtual void | computeProperty2 (int) |
| Protected Member Functions inherited from OpenMD::TimeCorrFunc< Vector3d > | |
| void | writeCorrelate () |
| void | writeCorrelate () |
| void | writeCorrelate () |
| void | writeCorrelate () |
| virtual void | preCorrelate () |
| virtual void | correlation () |
| virtual void | postCorrelate () |
| virtual void | computeFrame (int frame) |
| virtual void | validateSelection (SelectionManager &seleMan) |
| virtual void | correlateFrames (int frame1, int frame2, int timeBin) |
| Protected Attributes inherited from OpenMD::TimeCorrFunc< Vector3d > | |
| RealType | deltaTime_ |
| unsigned int | nTimeBins_ |
| int | nFrames_ |
| std::vector< Vector3d > | histogram_ |
| std::vector< int > | count_ |
| std::vector< RealType > | times_ |
| RealType | dtMean_ |
| RealType | dtSigma_ |
| SimInfo * | info_ |
| DumpReader * | reader_ |
| std::string | dumpFilename_ |
| SelectionManager | seleMan1_ |
| SelectionManager | seleMan2_ |
| Snapshot * | currentSnapshot_ |
| std::string | selectionScript1_ |
| std::string | selectionScript2_ |
| SelectionEvaluator | evaluator1_ |
| SelectionEvaluator | evaluator2_ |
| bool | uniqueSelections_ |
| bool | autoCorrFunc_ |
| bool | doSystemProperties_ |
| bool | doMolecularProperties_ |
| bool | doObjectProperties_ |
| bool | doAtomicProperties_ |
| bool | doBondProperties_ |
| bool | allowTimeFuzz_ |
| std::string | corrFuncType_ |
| std::string | paramString_ |
| std::string | labelString_ |
| std::vector< std::vector< int > > | sele1ToIndex_ |
| std::vector< std::vector< int > > | sele2ToIndex_ |
| ProgressBarPtr | progressBar_ |
| std::vector< std::vector< int > > | GIDtoSele1_ |
| std::vector< std::vector< int > > | GIDtoSele2_ |
| std::vector< std::vector< int > > | selection1StartFrame_ |
| std::vector< std::vector< int > > | selection2StartFrame_ |
| int | nStart_ |
| int | nSep_ |
| int | nStride_ |
| int | navg_ |
| bool | useWindowing_ |
| Protected Attributes inherited from OpenMD::DynamicProperty | |
| std::string | outputFilename_ |
| bool | selectionModeRestart_ |
Detailed Description
Calculates the collective dipole displacement function.
This time correlation function is the Helfand moment conjugate to the current density. Helfand moments are used to calculate the Einstein-Helfand relations for transport that are formally equivalent to Green-Kubo expressions using a related flux. In this case, the flux,
\[ \mathbf{J}(t) = \sum_{i=1}^{N} q_i \mathbf{v}_{\mathrm{cm},i}(t) \]
is normally used to calculate an ionic conductivity,
\[ \sigma = \frac{1}{3V k_b T} \int_0^\infty \left< \mathbf{J}(0) \cdot \mathbf{J}(t) \right> dt \]
The cm subscript denotes center of mass locations for all molecules.
This class computes the collective translational dipole moment,
\[ \mathbf{M}_\mathrm{trans}(t) = \sum_{i=1}^{N} q_i \mathbf{r}_{\mathrm{cm},i}(t) \]
as well as total contributions to the system's net dipole moment
\[ \mathbf{M}_\mathrm{tot}(t) = \sum_{i=1}^{N} \sum_{a} q_{ia} \mathbf{r}_{ia}(t) = \sum_{i=1}^{N} q_i \mathbf{r}_{\mathrm{cq},i}(t) \]
where cq denotes the molecular center of charge. It also calculates the rotational contribution,
\[ \mathbf{M}_\mathrm{rot}(t) = \sum_{i=1}^{N} q_i \left[ \mathbf{r}_{\mathrm{cq},i}(t) - \mathbf{r}_{\mathrm{cm},i}(t) \right] \]
The correlation functions are the displacements of these terms from their values at an earlier time,
\[ \left< \left| \mathbf{M}_\mathrm{trans}(t) - \mathbf{M}_\mathrm{trans}(0) \right|^2 \right> \]
and identical quantities for the total and rotational contributions.
Definition at line 95 of file CollectiveDipoleDisplacement.hpp.
Constructor & Destructor Documentation
◆ CollectiveDipoleDisplacement()
| OpenMD::CollectiveDipoleDisplacement::CollectiveDipoleDisplacement | ( | SimInfo * | info, |
| const std::string & | filename, | ||
| const std::string & | sele1, | ||
| const std::string & | sele2 ) |
Definition at line 56 of file CollectiveDipoleDisplacement.cpp.
The documentation for this class was generated from the following files:
- applications/dynamicProps/CollectiveDipoleDisplacement.hpp
- applications/dynamicProps/CollectiveDipoleDisplacement.cpp
