src/gromacs/mdlib/tests/constrtestdata.h

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  35 /*! \internal \file
  36  * \brief SHAKE and LINCS tests header.
  37  *
  38  * Contains description and constructor for the test data accumulating object,
  39  * declares CPU- and GPU-based functions used to apply SHAKE or LINCS on the
  40  * test data.
  41  *
  42  * \author Artem Zhmurov <zhmurov@gmail.com>
  43  * \ingroup module_mdlib
  44  */
  45
  46 #ifndef GMX_MDLIB_TESTS_CONSTRTESTDATA_H
  47 #define GMX_MDLIB_TESTS_CONSTRTESTDATA_H
  48
  49 #include <vector>
  50
  51 #include "gromacs/gmxlib/nrnb.h"
  52 #include "gromacs/gpu_utils/gpu_testutils.h"
  53 #include "gromacs/math/paddedvector.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/math/vectypes.h"
  56 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  57 #include "gromacs/mdlib/lincs.h"
  58 #include "gromacs/mdlib/shake.h"
  59 #include "gromacs/mdrunutility/multisim.h"
  60 #include "gromacs/mdtypes/commrec.h"
  61 #include "gromacs/mdtypes/inputrec.h"
  62 #include "gromacs/mdtypes/mdatom.h"
  63 #include "gromacs/pbcutil/pbc.h"
  64 #include "gromacs/topology/idef.h"
  65 #include "gromacs/topology/ifunc.h"
  66 #include "gromacs/topology/topology.h"
  67
  68 namespace gmx
  69 {
  70 namespace test
  71 {
  72
  73 /* \brief
  74  * Constraints test data structure.
  75  *
  76  * Structure to collect all the necessary data, including system coordinates and topology,
  77  * constraints information, etc. The structure can be reset and reused.
  78  */
  79 class ConstraintsTestData
  80 {
  81     public:
  82         //! Human-friendly name for a system
  83         std::string           title_;
  84         //! Number of atoms
  85         int                   numAtoms_;
  86         //! Topology
  87         gmx_mtop_t            mtop_;
  88         //! Masses
  89         std::vector<real>     masses_;
  90         //! Inverse masses
  91         std::vector<real>     invmass_;
  92         //! Communication record
  93         t_commrec             cr_;
  94         //! Input record (info that usually in .mdp file)
  95         t_inputrec            ir_;
  96         //! Local topology
  97         t_idef                idef_;
  98         //! MD atoms
  99         t_mdatoms             md_;
 100         //! Multisim data
 101         gmx_multisim_t        ms_;
 102         //! Computational time array (normally used to benchmark performance)
 103         t_nrnb                nrnb_;
 104
 105         //! Inverse timestep
 106         real                  invdt_;
 107         //! Number of flexible constraints
 108         int                   nflexcon_   = 0;
 109         //! Whether the virial should be computed
 110         bool                  computeVirial_;
 111         //! Scaled virial
 112         tensor                virialScaled_;
 113         //! Scaled virial (reference values)
 114         tensor                virialScaledRef_;
 115         //! If the free energy is computed
 116         bool                  compute_dHdLambda_;
 117         //! For free energy computation
 118         real                  dHdLambda_;
 119         //! For free energy computation (reference value)
 120         real                  dHdLambdaRef_;
 121
 122         //! Coordinates before the timestep
 123         PaddedVector<RVec>    x_;
 124         //! Coordinates after timestep, output for the constraints
 125         PaddedVector<RVec>    xPrime_;
 126         //! Backup for coordinates (for reset)
 127         PaddedVector<RVec>    xPrime0_;
 128         //! Intermediate set of coordinates (normally used for projection correction)
 129         PaddedVector<RVec>    xPrime2_;
 130         //! Velocities
 131         PaddedVector<RVec>    v_;
 132         //! Backup for velocities (for reset)
 133         PaddedVector<RVec>    v0_;
 134
 135         //! Constraints data (type1-i1-j1-type2-i2-j2-...)
 136         std::vector<int>      constraints_;
 137         //! Target lengths for all constraint types
 138         std::vector<real>     constraintsR0_;
 139
 140         /*! \brief
 141          * Constructor for the object with all parameters and variables needed by constraints algorithms.
 142          *
 143          * This constructor assembles stubs for all the data structures, required to initialize
 144          * and apply LINCS and SHAKE constraints. The coordinates and velocities before constraining
 145          * are saved to allow for reset. The constraints data are stored for testing after constraints
 146          * were applied.
 147          *
 148          * \param[in]  title                Human-friendly name of the system.
 149          * \param[in]  numAtoms             Number of atoms in the system.
 150          * \param[in]  masses               Atom masses. Size of this vector should be equal to numAtoms.
 151          * \param[in]  constraints          List of constraints, organized in triples of integers.
 152          *                                  First integer is the index of type for a constraint, second
 153          *                                  and third are the indices of constrained atoms. The types
 154          *                                  of constraints should be sequential but not necessarily
 155          *                                  start from zero (which is the way they normally are in
 156          *                                  GROMACS).
 157          * \param[in]  constraintsR0        Target values for bond lengths for bonds of each type. The
 158          *                                  size of this vector should be equal to the total number of
 159          *                                  unique types in constraints vector.
 160          * \param[in]  computeVirial        Whether the virial should be computed.
 161          * \param[in]  virialScaledRef      Reference values for scaled virial tensor.
 162          * \param[in]  compute_dHdLambda    Whether free energy should be computed.
 163          * \param[in]  dHdLambdaRef         Reference value for dHdLambda.
 164          * \param[in]  initialTime          Initial time.
 165          * \param[in]  timestep             Timestep.
 166          * \param[in]  x                    Coordinates before integration step.
 167          * \param[in]  xPrime               Coordinates after integration step, but before constraining.
 168          * \param[in]  v                    Velocities before constraining.
 169          * \param[in]  shakeTolerance       Target tolerance for SHAKE.
 170          * \param[in]  shakeUseSOR          Use successive over-relaxation method for SHAKE iterations.
 171          *                                  The general formula is:
 172          *                                     x_n+1 = (1-omega)*x_n + omega*f(x_n),
 173          *                                  where omega = 1 if SOR is off and may be < 1 if SOR is on.
 174          * \param[in]  lincsNumIterations   Number of iterations used to compute the inverse matrix.
 175          * \param[in]  lincsExpansionOrder  The order for algorithm that adjusts the direction of the
 176          *                                  bond after constraints are applied.
 177          * \param[in]  lincsWarnAngle       The threshold value for the change in bond angle. When
 178          *                                  exceeded the program will issue a warning.
 179          *
 180          */
 181         ConstraintsTestData(const std::string &title,
 182                             int numAtoms, std::vector<real> masses,
 183                             std::vector<int> constraints, std::vector<real> constraintsR0,
 184                             bool computeVirial, tensor virialScaledRef,
 185                             bool compute_dHdLambda, float dHdLambdaRef,
 186                             real initialTime, real timestep,
 187                             const std::vector<RVec> &x, const std::vector<RVec> &xPrime, const std::vector<RVec> &v,
 188                             real shakeTolerance, gmx_bool shakeUseSOR,
 189                             int lincsNumIterations, int lincsExpansionOrder, real lincsWarnAngle);
 190
 191         /*! \brief
 192          * Reset the data structure so it can be reused.
 193          *
 194          * Set the coordinates and velocities back to their values before
 195          * constraining. The scaled virial tensor and dHdLambda are zeroed.
 196          *
 197          */
 198         void reset();
 199
 200         /*! \brief
 201          * Cleaning up the memory.
 202          */
 203         ~ConstraintsTestData();
 204 };
 205
 206 }      // namespace test
 207 }      // namespace gmx
 208
 209 #endif // GMX_MDLIB_TESTS_CONSTRTESTDATA_H