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Gromacs
2024.3
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#include <gromacs/nbnxm/atomdata.h>
Collaboration diagram for nbnxn_atomdata_t:Struct that stores atom related data for the nbnxn module.
Note: performance would improve slightly when all std::vector containers in this struct would not initialize during resize().
Classes | |
| struct | Params |
| The actual atom data parameter values. More... | |
| struct | SimdMasks |
| Diagonal and topology exclusion helper data for all SIMD kernels. More... | |
Public Member Functions | |
| nbnxn_atomdata_t (gmx::PinningPolicy pinningPolicy, const gmx::MDLogger &mdlog, Nbnxm::KernelType kernelType, int enbnxninitcombrule, int ntype, gmx::ArrayRef< const real > nbfp, int n_energygroups, int nout) | |
| Constructor. More... | |
| const Params & | params () const |
| Returns a const reference to the parameters. | |
| Params & | paramsDeprecated () |
| Returns a non-const reference to the parameters. | |
| int | numAtoms () const |
| Returns the current total number of atoms stored. | |
| gmx::ArrayRef< const real > | x () const |
| Return the coordinate buffer, and q with xFormat==nbatXYZQ. | |
| gmx::ArrayRef< real > | x () |
| Return the coordinate buffer, and q with xFormat==nbatXYZQ. | |
| void | resizeCoordinateBuffer (int numAtoms) |
| Resizes the coordinate buffer and sets the number of atoms. | |
| void | resizeForceBuffers () |
| Resizes the force buffers for the current number of atoms. | |
Public Attributes | |
| int | natoms_local |
| Number of local atoms. | |
| int | XFormat |
| The format of x (and q), enum. | |
| int | FFormat |
| The format of f, enum. | |
| bool | bDynamicBox |
| Do we need to update shift_vec every step? | |
| gmx::HostVector< gmx::RVec > | shift_vec |
| Shift vectors, copied from t_forcerec. | |
| int | xstride |
| stride for a coordinate in x (usually 3 or 4) | |
| int | fstride |
| stride for a coordinate in f (usually 3 or 4) | |
| const SimdMasks | simdMasks |
| Masks for handling exclusions in the SIMD kernels. | |
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std::vector < nbnxn_atomdata_output_t > | out |
| Output data structures, 1 per thread. | |
| bool | bUseBufferFlags |
| Reduction related dataUse the flags or operate on all atoms. | |
| std::vector< gmx_bitmask_t > | buffer_flags |
| Flags for buffer zeroing+reduc. | |
| nbnxn_atomdata_t::nbnxn_atomdata_t | ( | gmx::PinningPolicy | pinningPolicy, |
| const gmx::MDLogger & | mdlog, | ||
| Nbnxm::KernelType | kernelType, | ||
| int | enbnxninitcombrule, | ||
| int | ntype, | ||
| gmx::ArrayRef< const real > | nbfp, | ||
| int | n_energygroups, | ||
| int | nout | ||
| ) |
Constructor.
| [in] | pinningPolicy | Sets the pinning policy for all data that might be transferred to a GPU |
| [in] | mdlog | The logger |
| [in] | kernelType | Nonbonded NxN kernel type |
| [in] | enbnxninitcombrule | LJ combination rule |
| [in] | ntype | Number of atom types |
| [in] | nbfp | Non-bonded force parameters |
| [in] | n_energygroups | Number of energy groups |
| [in] | nout | Number of output data structures |
1.8.5