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 <memory>
  50 #include <vector>
  51
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/gpu_utils/gpu_testutils.h"
  54 #include "gromacs/math/paddedvector.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/math/vectypes.h"
  57 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  58 #include "gromacs/mdlib/lincs.h"
  59 #include "gromacs/mdlib/shake.h"
  60 #include "gromacs/mdtypes/inputrec.h"
  61 #include "gromacs/pbcutil/pbc.h"
  62 #include "gromacs/topology/idef.h"
  63 #include "gromacs/topology/ifunc.h"
  64 #include "gromacs/topology/topology.h"
  65
  66 namespace gmx
  67 {
  68 namespace test
  69 {
  70
  71 /* \brief
  72  * Constraints test data structure.
  73  *
  74  * Structure to collect all the necessary data, including system coordinates and topology,
  75  * constraints information, etc. The structure can be reset and reused.
  76  */
  77 class ConstraintsTestData
  78 {
  79 public:
  80     //! Human-friendly name for a system
  81     std::string title_;
  82     //! Number of atoms
  83     int numAtoms_;
  84     //! Topology
  85     gmx_mtop_t mtop_;
  86     //! Masses
  87     std::vector<real> masses_;
  88     //! Inverse masses
  89     std::vector<real> invmass_;
  90     //! Input record (info that usually in .mdp file)
  91     t_inputrec ir_;
  92     //! Local topology
  93     std::unique_ptr<InteractionDefinitions> idef_;
  94     //! Computational time array (normally used to benchmark performance)
  95     t_nrnb nrnb_;
  96
  97     //! Inverse timestep
  98     real invdt_;
  99     //! Number of flexible constraints
 100     int nflexcon_ = 0;
 101     //! Whether the virial should be computed
 102     bool computeVirial_;
 103     //! Scaled virial
 104     tensor virialScaled_;
 105     //! Scaled virial (reference values)
 106     tensor virialScaledRef_;
 107     //! If the free energy is computed
 108     bool compute_dHdLambda_;
 109     //! If there are atoms with perturbed mass
 110     bool hasMassPerturbed_ = false;
 111     //! Lambda value
 112     real lambda_ = 0.0;
 113     //! For free energy computation
 114     real dHdLambda_;
 115     //! For free energy computation (reference value)
 116     real dHdLambdaRef_;
 117
 118     //! Coordinates before the timestep
 119     PaddedVector<RVec> x_;
 120     //! Coordinates after timestep, output for the constraints
 121     PaddedVector<RVec> xPrime_;
 122     //! Backup for coordinates (for reset)
 123     PaddedVector<RVec> xPrime0_;
 124     //! Intermediate set of coordinates (normally used for projection correction)
 125     PaddedVector<RVec> xPrime2_;
 126     //! Velocities
 127     PaddedVector<RVec> v_;
 128     //! Backup for velocities (for reset)
 129     PaddedVector<RVec> v0_;
 130
 131     //! Constraints data (type1-i1-j1-type2-i2-j2-...)
 132     std::vector<int> constraints_;
 133     //! Target lengths for all constraint types
 134     std::vector<real> constraintsR0_;
 135
 136     /*! \brief
 137      * Constructor for the object with all parameters and variables needed by constraints algorithms.
 138      *
 139      * This constructor assembles stubs for all the data structures, required to initialize
 140      * and apply LINCS and SHAKE constraints. The coordinates and velocities before constraining
 141      * are saved to allow for reset. The constraints data are stored for testing after constraints
 142      * were applied.
 143      *
 144      * \param[in]  title                Human-friendly name of the system.
 145      * \param[in]  numAtoms             Number of atoms in the system.
 146      * \param[in]  masses               Atom masses. Size of this vector should be equal to numAtoms.
 147      * \param[in]  constraints          List of constraints, organized in triples of integers.
 148      *                                  First integer is the index of type for a constraint, second
 149      *                                  and third are the indices of constrained atoms. The types
 150      *                                  of constraints should be sequential but not necessarily
 151      *                                  start from zero (which is the way they normally are in
 152      *                                  GROMACS).
 153      * \param[in]  constraintsR0        Target values for bond lengths for bonds of each type. The
 154      *                                  size of this vector should be equal to the total number of
 155      *                                  unique types in constraints vector.
 156      * \param[in]  computeVirial        Whether the virial should be computed.
 157      * \param[in]  virialScaledRef      Reference values for scaled virial tensor.
 158      * \param[in]  compute_dHdLambda    Whether free energy should be computed.
 159      * \param[in]  dHdLambdaRef         Reference value for dHdLambda.
 160      * \param[in]  initialTime          Initial time.
 161      * \param[in]  timestep             Timestep.
 162      * \param[in]  x                    Coordinates before integration step.
 163      * \param[in]  xPrime               Coordinates after integration step, but before constraining.
 164      * \param[in]  v                    Velocities before constraining.
 165      * \param[in]  shakeTolerance       Target tolerance for SHAKE.
 166      * \param[in]  shakeUseSOR          Use successive over-relaxation method for SHAKE iterations.
 167      *                                  The general formula is:
 168      *                                     x_n+1 = (1-omega)*x_n + omega*f(x_n),
 169      *                                  where omega = 1 if SOR is off and may be < 1 if SOR is on.
 170      * \param[in]  lincsNumIterations   Number of iterations used to compute the inverse matrix.
 171      * \param[in]  lincsExpansionOrder  The order for algorithm that adjusts the direction of the
 172      *                                  bond after constraints are applied.
 173      * \param[in]  lincsWarnAngle       The threshold value for the change in bond angle. When
 174      *                                  exceeded the program will issue a warning.
 175      *
 176      */
 177     ConstraintsTestData(const std::string&       title,
 178                         int                      numAtoms,
 179                         std::vector<real>        masses,
 180                         std::vector<int>         constraints,
 181                         std::vector<real>        constraintsR0,
 182                         bool                     computeVirial,
 183                         tensor                   virialScaledRef,
 184                         bool                     compute_dHdLambda,
 185                         float                    dHdLambdaRef,
 186                         real                     initialTime,
 187                         real                     timestep,
 188                         const std::vector<RVec>& x,
 189                         const std::vector<RVec>& xPrime,
 190                         const std::vector<RVec>& v,
 191                         real                     shakeTolerance,
 192                         gmx_bool                 shakeUseSOR,
 193                         int                      lincsNumIterations,
 194                         int                      lincsExpansionOrder,
 195                         real                     lincsWarnAngle);
 196
 197     /*! \brief
 198      * Reset the data structure so it can be reused.
 199      *
 200      * Set the coordinates and velocities back to their values before
 201      * constraining. The scaled virial tensor and dHdLambda are zeroed.
 202      *
 203      */
 204     void reset();
 205 };
 206
 207 } // namespace test
 208 } // namespace gmx
 209
 210 #endif // GMX_MDLIB_TESTS_CONSTRTESTDATA_H