Gromacs
2024.4
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Collect density fitting parameters only available during simulation setup.
To build the density fitting force provider during simulation setup, the DensityFitting class needs access to parameters that become available only during simulation setup.
This class collects these parameters via MDModulesNotifiers in the simulation setup phase and provides a check if all necessary parameters have been provided.
Public Member Functions | |
void | setLocalAtomSet (const LocalAtomSet &localAtomSet) |
Set the local atom set for the density fitting. More... | |
const LocalAtomSet & | localAtomSet () const |
Return local atom set for density fitting. More... | |
const TranslateAndScale & | transformationToDensityLattice () const |
Return transformation into density lattice. More... | |
basic_mdspan< const float, dynamicExtents3D > | referenceDensity () const |
Return reference density. More... | |
void | readReferenceDensityFromFile (const std::string &referenceDensityFileName) |
Reads the reference density from file. More... | |
void | normalizeReferenceDensity () |
Normalize the reference density so that the sum over all voxels is unity. | |
void | setPeriodicBoundaryConditionType (const PbcType &pbcType) |
Set the periodic boundary condition via MDModuleNotifier. More... | |
PbcType | periodicBoundaryConditionType () |
Get the periodic boundary conditions. | |
void | setSimulationTimeStep (double timeStep) |
Set the simulation time step. | |
double | simulationTimeStep () const |
Return the simulation time step. | |
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Return local atom set for density fitting.
InternalError | if local atom set is not set |
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Reads the reference density from file.
Reads and check file, then set and communicate the internal parameters related to the reference density with the file data.
FileIOError | if reading from file was not successful |
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Return reference density.
InternalError | if reference density is not set |
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Set the local atom set for the density fitting.
[in] | localAtomSet | of atoms to be fitted |
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Set the periodic boundary condition via MDModuleNotifier.
The pbc type is wrapped in PeriodicBoundaryConditionType to allow the MDModuleNotifier to statically distinguish the callback function type from other 'int' function callbacks.
[in] | pbcType | enumerates the periodic boundary condition. |
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Return transformation into density lattice.
InternalError | if transformation into density lattice is not set |