src/gromacs/pulling/pull_internal.h

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  37
  38 /*! \internal \file
  39  *
  40  *
  41  * \brief
  42  * This file contains datatypes and function declarations for internal
  43    use in the pull code.
  44  *
  45  * \author Berk Hess
  46  */
  47
  48 #ifndef GMX_PULLING_PULL_INTERNAL_H
  49 #define GMX_PULLING_PULL_INTERNAL_H
  50
  51 #include "config.h"
  52
  53 #include <memory>
  54 #include <vector>
  55
  56 #include "gromacs/domdec/localatomset.h"
  57 #include "gromacs/mdtypes/pull-params.h"
  58 #include "gromacs/utility/gmxmpi.h"
  59
  60 /*! \brief Determines up to what local atom count a pull group gets processed single-threaded.
  61  *
  62  * We set this limit to 1 with debug to catch bugs.
  63  * On Haswell with GCC 5 the cross-over point is around 400 atoms,
  64  * independent of thread count and hyper-threading.
  65  */
  66 #ifdef NDEBUG
  67 static const int c_pullMaxNumLocalAtomsSingleThreaded = 100;
  68 #else
  69 static const int c_pullMaxNumLocalAtomsSingleThreaded = 1;
  70 #endif
  71
  72 class PullHistory;
  73
  74 enum {
  75     epgrppbcNONE, epgrppbcREFAT, epgrppbcCOS, epgrppbcPREVSTEPCOM
  76 };
  77
  78 /*! \internal
  79  * \brief Pull group data used during pulling
  80  */
  81 struct pull_group_work_t
  82 {
  83     /*! \brief Constructor
  84      *
  85      * \param[in] params                  The group parameters set by the user
  86      * \param[in] atomSet                 The global to local atom set manager
  87      * \param[in] setPbcRefToPrevStepCOM Does this pull group use the COM from the previous step as reference position?
  88      */
  89     pull_group_work_t(const t_pull_group &params,
  90                       gmx::LocalAtomSet   atomSet,
  91                       bool                setPbcRefToPrevStepCOM);
  92
  93     /* Data only modified at initialization */
  94     const t_pull_group params;        /**< The pull group parameters */
  95     const int          epgrppbc;      /**< The type of pbc for this pull group, see enum above */
  96     bool               needToCalcCom; /**< Do we need to calculate the COM? (Not for group 0 or if only used as cylinder group) */
  97     std::vector<real>  globalWeights; /**< Weights per atom set by the user and/or mass/friction coefficients, if empty all weights are equal */
  98
  99     /* Data modified only at init or at domain decomposition */
 100     gmx::LocalAtomSet                  atomSet;       /**< Global to local atom set mapper */
 101     std::vector<real>                  localWeights;  /**< Weights for the local atoms */
 102     std::unique_ptr<gmx::LocalAtomSet> pbcAtomSet;    /**< Keeps index of the pbc reference atom.
 103                                                            The stored LocalAtomSet consists of exactly one atom when pbc reference atom is required.
 104                                                            When no pbc refence atom is used, this pointer shall be null. */
 105
 106     /* Data, potentially, changed at every pull call */
 107     real                                  mwscale;     /**< mass*weight scaling factor 1/sum w m */
 108     real                                  wscale;      /**< scaling factor for the weights: sum w m/sum w w m */
 109     real                                  invtm;       /**< inverse total mass of the group: 1/wscale sum w m */
 110     std::vector < gmx::BasicVector < double>> mdw;     /**< mass*gradient(weight) for atoms */
 111     std::vector<double>                   dv;          /**< distance to the other group(s) along vec */
 112     dvec                                  x;           /**< COM before update */
 113     dvec                                  xp;          /**< COM after update before constraining */
 114     dvec                                  x_prev_step; /**< center of mass of the previous step */
 115 };
 116
 117 /* Struct describing the instantaneous spatial layout of a pull coordinate */
 118 struct PullCoordSpatialData
 119 {
 120     dvec          dr01;       /* The direction vector of group 1 relative to group 0 */
 121     dvec          dr23;       /* The direction vector of group 3 relative to group 2 */
 122     dvec          dr45;       /* The direction vector of group 5 relative to group 4 */
 123     dvec          vec;        /* The pull direction */
 124     double        vec_len;    /* Length of vec for direction-relative */
 125     dvec          ffrad;      /* conversion factor from vec to radial force */
 126     double        cyl_dev;    /* The deviation from the reference position */
 127     dvec          planevec_m; /* Normal of plane for groups 0, 1, 2, 3 for geometry dihedral */
 128     dvec          planevec_n; /* Normal of plane for groups 2, 3, 4, 5 for geometry dihedral */
 129
 130     double        value;      /* The current value of the coordinate, units of nm or rad */
 131 };
 132
 133 /* Struct with parameters and force evaluation local data for a pull coordinate */
 134 struct pull_coord_work_t
 135 {
 136     /* Constructor */
 137     pull_coord_work_t(const t_pull_coord &params) :
 138         params(params),
 139         value_ref(0),
 140         spatialData(),
 141         scalarForce(0),
 142         bExternalPotentialProviderHasBeenRegistered(false)
 143     {
 144     }
 145
 146     const t_pull_coord    params;      /* Pull coordinate parameters */
 147
 148     double                value_ref;   /* The reference value, usually init+rate*t, units of nm or rad */
 149
 150     PullCoordSpatialData  spatialData; /* Data defining the current geometry */
 151
 152     double                scalarForce; /* Scalar force for this cooordinate */
 153
 154     /* For external-potential coordinates only, for checking if a provider has been registered */
 155     bool          bExternalPotentialProviderHasBeenRegistered;
 156 };
 157
 158 /* Struct for storing vectorial forces for a pull coordinate */
 159 struct PullCoordVectorForces
 160 {
 161     dvec force01; /* Force due to the pulling/constraining for groups 0, 1 */
 162     dvec force23; /* Force for groups 2 and 3 */
 163     dvec force45; /* Force for groups 4 and 5 */
 164 };
 165
 166 /* Struct for sums over (local) atoms in a pull group */
 167 struct ComSums
 168 {
 169     /* For normal weighting */
 170     double sum_wm;    /* Sum of weight*mass        */
 171     double sum_wwm;   /* Sum of weight*weight*mass */
 172     dvec   sum_wmx;   /* Sum of weight*mass*x      */
 173     dvec   sum_wmxp;  /* Sum of weight*mass*xp     */
 174
 175     /* For cosine weighting */
 176     double sum_cm;    /* Sum of cos(x)*mass          */
 177     double sum_sm;    /* Sum of sin(x)*mass          */
 178     double sum_ccm;   /* Sum of cos(x)*cos(x)*mass   */
 179     double sum_csm;   /* Sum of cos(x)*sin(x)*mass   */
 180     double sum_ssm;   /* Sum of sin(x)*sin(x)*mass   */
 181     double sum_cmp;   /* Sum of cos(xp)*sin(xp)*mass */
 182     double sum_smp;   /* Sum of sin(xp)*sin(xp)*mass */
 183
 184     /* Dummy data to ensure adjacent elements in an array are separated
 185      * by a cache line size, max 128 bytes.
 186      * TODO: Replace this by some automated mechanism.
 187      */
 188     int    dummy[32];
 189 };
 190
 191 /*! \brief The normal COM buffer needs 3 elements per group */
 192 static constexpr int c_comBufferStride = 3;
 193
 194 /*! \brief The cylinder buffer needs 9 elements per group */
 195 static constexpr int c_cylinderBufferStride = 9;
 196
 197 struct pull_comm_t
 198 {
 199     gmx_bool    bParticipateAll; /* Do all ranks always participate in pulling? */
 200     gmx_bool    bParticipate;    /* Does our rank participate in pulling? */
 201 #if GMX_MPI
 202     MPI_Comm    mpi_comm_com;    /* Communicator for pulling */
 203 #endif
 204     int         nparticipate;    /* The number of ranks participating */
 205     bool        isMasterRank;    /* Tells whether our rank is the master rank and thus should add the pull virial */
 206
 207     int64_t     setup_count;     /* The number of decomposition calls */
 208     int64_t     must_count;      /* The last count our rank needed to be part */
 209
 210     /* Buffers for parallel reductions */
 211     std::vector<gmx::RVec>                pbcAtomBuffer;  /* COM calculation buffer */
 212     std::vector < gmx::BasicVector < double>> comBuffer;  /* COM calculation buffer */
 213     std::vector<double>                   cylinderBuffer; /* cylinder ref. groups calculation buffer */
 214 };
 215
 216 struct pull_t
 217 {
 218     /* Global parameters */
 219     pull_params_t      params;       /* The pull parameters, from inputrec */
 220
 221     gmx_bool           bPotential;   /* Are there coordinates with potential? */
 222     gmx_bool           bConstraint;  /* Are there constrained coordinates? */
 223     gmx_bool           bAngle;       /* Are there angle geometry coordinates? */
 224
 225     int                ePBC;         /* the boundary conditions */
 226     int                npbcdim;      /* do pbc in dims 0 <= dim < npbcdim */
 227     gmx_bool           bRefAt;       /* do we need reference atoms for a group COM ? */
 228     int                cosdim;       /* dimension for cosine weighting, -1 if none */
 229     gmx_bool           bCylinder;    /* Is group 0 a cylinder group? */
 230
 231     /* Parameters + dynamic data for groups */
 232     std::vector<pull_group_work_t>  group;  /* The pull group param and work data */
 233     std::vector<pull_group_work_t>  dyna;   /* Dynamic groups for geom=cylinder */
 234
 235     /* Parameters + dynamic data for coordinates */
 236     std::vector<pull_coord_work_t> coord;  /* The pull group param and work data */
 237
 238     /* Global dynamic data */
 239     gmx_bool             bSetPBCatoms;      /* Do we need to set x_pbc for the groups? */
 240
 241     int                  nthreads;          /* Number of threads used by the pull code */
 242     std::vector<ComSums> comSums;           /* Work array for summing for COM, 1 entry per thread */
 243
 244     pull_comm_t          comm;              /* Communication parameters, communicator and buffers */
 245
 246     FILE                *out_x;             /* Output file for pull data */
 247     FILE                *out_f;             /* Output file for pull data */
 248
 249     bool                 bXOutAverage;      /* Output average pull coordinates */
 250     bool                 bFOutAverage;      /* Output average pull forces */
 251
 252     PullHistory         *coordForceHistory; /* Pull coordinate and force history */
 253
 254     /* The number of coordinates using an external potential */
 255     int                numCoordinatesWithExternalPotential;
 256     /* Counter for checking external potential registration */
 257     int                numUnregisteredExternalPotentials;
 258     /* */
 259     int                numExternalPotentialsStillToBeAppliedThisStep;
 260 };
 261
 262 /*! \brief Copies the pull group COM of the previous step from the checkpoint state to the pull state
 263  *
 264  * \param[in]   pull  The COM pull force calculation data structure
 265  * \param[in]   state The global state container
 266  */
 267 void setPrevStepPullComFromState(struct pull_t *pull, const t_state *state);
 268
 269 /*! \brief Resizes the vector, in the state container, containing the COMs from the previous step
 270  *
 271  * \param[in]   state The global state container
 272  * \param[in]   pull  The COM pull force calculation data structure
 273  */
 274 void allocStatePrevStepPullCom(t_state *state, pull_t *pull);
 275
 276
 277 #endif