#ifndef GMX_MDTYPES_FCDATA_H
#define GMX_MDTYPES_FCDATA_H
+#include <memory>
#include <vector>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/idef.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
enum class DistanceRestraintWeighting : int;
+struct gmx_mtop_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
typedef real rvec5[5];
};
/* Orientation restraining stuff */
-typedef struct t_oriresdata
+struct t_oriresdata
{
- real fc; /* Force constant for the restraints */
- real edt; /* Multiplication factor for time averaging */
- real edt_1; /* 1 - edt */
- real exp_min_t_tau; /* Factor for slowly switching on the force */
- int nr; /* The number of orientation restraints */
- int nex; /* The number of experiments */
- int typeMin; /* The minimum iparam type index for restraints */
- int nref; /* The number of atoms for the fit */
- real* mref; /* The masses of the reference atoms */
- rvec* xref; /* The reference coordinates for the fit (nref) */
- rvec* xtmp; /* Temporary array for fitting (nref) */
- matrix R; /* Rotation matrix to rotate to the reference coor. */
- tensor* S; /* Array of order tensors for each experiment (nexp) */
- rvec5* Dinsl; /* The order matrix D for all restraints (nr x 5) */
- rvec5* Dins; /* The ensemble averaged D (nr x 5) */
- rvec5* Dtav; /* The time and ensemble averaged D (nr x 5) */
- real* oinsl; /* The calculated instantaneous orientations */
- real* oins; /* The calculated emsemble averaged orientations */
- real* otav; /* The calculated time and ensemble averaged orient. */
- real rmsdev; /* The weighted (using kfac) RMS deviation */
- OriresMatEq* tmpEq; /* An temporary array of matrix + rhs */
- real* eig; /* Eigenvalues/vectors, for output only (nex x 12) */
-
- /* variables for diagonalization with diagonalize_orires_tensors()*/
- double** M;
- double* eig_diag;
- double** v;
-} t_oriresdata;
+ /*! Constructor
+ *
+ * \param[in] fplog Log file, can be nullptr
+ * \param[in] mtop The global topology
+ * \param[in] ir The input record
+ * \param[in] cr The commrec, can be nullptr when not running in parallel
+ * \param[in] ms The multisim communicator, pass nullptr to avoid ensemble averaging
+ * \param[in,out] globalState The global state, orientation restraint entires are added
+ *
+ * \throws InvalidInputError when there is domain decomposition, fewer than 5 restraints,
+ * periodic molecules or more than 1 molecule for a moleculetype with restraints.
+ */
+ t_oriresdata(FILE* fplog,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
+ const t_commrec* cr,
+ const gmx_multisim_t* ms,
+ t_state* globalState);
+
+ //! Destructor
+ ~t_oriresdata();
+
+ //! Force constant for the restraints
+ real fc;
+ //! Multiplication factor for time averaging
+ real edt;
+ //! 1 - edt
+ real edt_1;
+ //! Factor for slowly switching on the force
+ real exp_min_t_tau;
+ //! The number of orientation restraints
+ const int numRestraints;
+ //! The number of experiments
+ int numExperiments;
+ //! The minimum iparam type index for restraints
+ int typeMin;
+ //! The number of atoms for the fit
+ int numReferenceAtoms;
+ //! The masses of the reference atoms
+ std::vector<real> mref;
+ //! The reference coordinates for the fit
+ std::vector<gmx::RVec> xref;
+ //! Temporary array for fitting
+ std::vector<gmx::RVec> xtmp;
+ //! Rotation matrix to rotate to the reference coordinates
+ matrix rotationMatrix;
+ //! Array of order tensors, one for each experiment
+ tensor* orderTensors = nullptr;
+ //! The order tensor D for all restraints
+ rvec5* DTensors = nullptr;
+ //! The ensemble averaged D for all restraints
+ rvec5* DTensorsEnsembleAv = nullptr;
+ //! The time and ensemble averaged D restraints
+ rvec5* DTensorsTimeAndEnsembleAv = nullptr;
+ //! The calculated instantaneous orientations
+ std::vector<real> orientations;
+ //! The calculated emsemble averaged orientations
+ gmx::ArrayRef<real> orientationsEnsembleAv;
+ //! Buffer for the calculated emsemble averaged orientations, only used with ensemble averaging
+ std::vector<real> orientationsEnsembleAvBuffer;
+ //! The calculated time and ensemble averaged orientations
+ gmx::ArrayRef<real> orientationsTimeAndEnsembleAv;
+ //! The weighted (using kfac) RMS deviation
+ std::vector<real> orientationsTimeAndEnsembleAvBuffer;
+ //! Buffer for the weighted (using kfac) RMS deviation, only used with time averaging
+ real rmsdev;
+ //! An temporary array of matrix + rhs
+ std::vector<OriresMatEq> tmpEq;
+ //! The number of eigenvalues + eigenvectors per experiment
+ static constexpr int c_numEigenRealsPerExperiment = 12;
+ //! Eigenvalues/vectors, for output only (numExperiments x 12)
+ std::vector<real> eigenOutput;
+
+ // variables for diagonalization with diagonalize_orires_tensors()
+ //! Tensor to diagonalize
+ std::array<gmx::DVec, DIM> M;
+ //! Eigenvalues
+ std::array<double, DIM> eig_diag;
+ //! Eigenvectors
+ std::array<gmx::DVec, DIM> v;
+
+ // Default copy and assign would be incorrect and manual versions are not yet implemented.
+ GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata);
+};
/* Cubic spline table for tabulated bonded interactions */
struct bondedtable_t
std::vector<bondedtable_t> dihtab;
// TODO: Convert to C++ and unique_ptr (currently this data is not freed)
- t_disresdata* disres = nullptr;
- t_oriresdata* orires = nullptr;
+ t_disresdata* disres = nullptr;
+ std::unique_ptr<t_oriresdata> orires;
};
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff