src/gromacs/pbcutil/pbc_aiuc.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 /*! \file
  36  *
  37  * \brief Structure and basic routines to handle periodic boundary conditions.
  38  *
  39  * This file contains CPU
  40  *
  41  * \todo CPU, GPU and SIMD routines essentially do the same operations on
  42  *       different data-types. Currently this leads to code duplication,
  43  *       which has to be resolved. For details, see Redmine task #2863
  44  *       https://redmine.gromacs.org/issues/2863
  45  *
  46  * \author Mark Abraham <mark.j.abraham@gmail.com>
  47  * \author Berk Hess <hess@kth.se>
  48  * \author Artem Zhmurov <zhmurov@gmail.com>
  49  *
  50  * \inlibraryapi
  51  * \ingroup module_pbcutil
  52  */
  53 #ifndef GMX_PBCUTIL_PBC_AIUC_H
  54 #define GMX_PBCUTIL_PBC_AIUC_H
  55
  56 #include "gromacs/pbcutil/ishift.h"
  57
  58 /*! \brief Compact and ordered version of the PBC matrix.
  59  *
  60  * The structure contains all the dimensions of the periodic box,
  61  * arranged so that the memory access pattern is more efficient.
  62  * This duplicates the information, stored in PBC 'box' matrix object,
  63  * but without duplicating off-diagonal members of the matrix.
  64  * The structure can be set by setPbcAiuc( ... ) routine below.
  65  */
  66 struct PbcAiuc
  67 {
  68     //! 1/box[ZZ][ZZ]
  69     float invBoxDiagZ;
  70     //! box[ZZ][XX]
  71     float boxZX;
  72     //! box[ZZ][YY]
  73     float boxZY;
  74     //! box[ZZ][ZZ]
  75     float boxZZ;
  76     //! 1/box[YY][YY]
  77     float invBoxDiagY;
  78     //! box[YY][XX]
  79     float boxYX;
  80     //! box[YY][YY]
  81     float boxYY;
  82     //! 1/box[XX][XX]
  83     float invBoxDiagX;
  84     //! box[XX][XX]
  85     float boxXX;
  86 };
  87
  88 /*! \brief Set the PBC data-structure.
  89  *
  90  * \param[in]   numPbcDim   Number of periodic dimensions:
  91  *                          0 - no periodicity.
  92  *                          1 - periodicity along X-axis.
  93  *                          2 - periodicity in XY plane.
  94  *                          3 - periodicity along all dimensions.
  95  * \param[in]   box         Matrix, describing the periodic cell.
  96  * \param[out]  pbcAiuc     Pointer to PbcAiuc structure to be initialized.
  97  *
  98  */
  99 static inline
 100 void setPbcAiuc(int           numPbcDim,
 101                 const matrix  box,
 102                 PbcAiuc      *pbcAiuc)
 103 {
 104
 105     pbcAiuc->invBoxDiagZ = 0.0f;
 106     pbcAiuc->boxZX       = 0.0f;
 107     pbcAiuc->boxZY       = 0.0f;
 108     pbcAiuc->boxZZ       = 0.0f;
 109     pbcAiuc->invBoxDiagY = 0.0f;
 110     pbcAiuc->boxYX       = 0.0f;
 111     pbcAiuc->boxYY       = 0.0f;
 112     pbcAiuc->invBoxDiagX = 0.0f;
 113     pbcAiuc->boxXX       = 0.0f;
 114
 115     if (numPbcDim > ZZ)
 116     {
 117         pbcAiuc->invBoxDiagZ = 1.0f/box[ZZ][ZZ];
 118         pbcAiuc->boxZX       = box[ZZ][XX];
 119         pbcAiuc->boxZY       = box[ZZ][YY];
 120         pbcAiuc->boxZZ       = box[ZZ][ZZ];
 121     }
 122     if (numPbcDim > YY)
 123     {
 124         pbcAiuc->invBoxDiagY = 1.0f/box[YY][YY];
 125         pbcAiuc->boxYX       = box[YY][XX];
 126         pbcAiuc->boxYY       = box[YY][YY];
 127     }
 128     if (numPbcDim > XX)
 129     {
 130         pbcAiuc->invBoxDiagX = 1.0f/box[XX][XX];
 131         pbcAiuc->boxXX       = box[XX][XX];
 132     }
 133 }
 134
 135 /*! \brief Computes the vector between two points taking PBC into account.
 136  *
 137  * Computes the vector dr between points r2 and r1, taking into account the
 138  * periodic boundary conditions, described in pbcAiuc object. Note that this
 139  * routine always does the PBC arithmetic for all directions, multiplying the
 140  * displacements by zeroes if the corresponding direction is not periodic.
 141  * For triclinic boxes only distances up to half the smallest box diagonal
 142  * element are guaranteed to be the shortest. This means that distances from
 143  * 0.5/sqrt(2) times a box vector length (e.g. for a rhombic dodecahedron)
 144  * can use a more distant periodic image.
 145  *
 146  * \todo This routine operates on rvec types and uses PbcAiuc to define
 147  *       periodic box, but essentially does the same thing as SIMD and GPU
 148  *       version. These will have to be unified in future to avoid code
 149  *       duplication. See Redmine task #2863:
 150  *       https://redmine.gromacs.org/issues/2863
 151  *
 152  * \param[in]  pbcAiuc  PBC object.
 153  * \param[in]  r1       Coordinates of the first point.
 154  * \param[in]  r2       Coordinates of the second point.
 155  * \param[out] dr       Resulting distance.
 156  */
 157 static inline
 158 void pbcDxAiuc(const PbcAiuc  &pbcAiuc,
 159                const rvec     &r1,
 160                const rvec     &r2,
 161                rvec            dr)
 162 {
 163     dr[XX] = r1[XX] - r2[XX];
 164     dr[YY] = r1[YY] - r2[YY];
 165     dr[ZZ] = r1[ZZ] - r2[ZZ];
 166
 167     float shz  = rintf(dr[ZZ]*pbcAiuc.invBoxDiagZ);
 168     dr[XX]    -= shz*pbcAiuc.boxZX;
 169     dr[YY]    -= shz*pbcAiuc.boxZY;
 170     dr[ZZ]    -= shz*pbcAiuc.boxZZ;
 171
 172     float shy  = rintf(dr[YY]*pbcAiuc.invBoxDiagY);
 173     dr[XX]    -= shy*pbcAiuc.boxYX;
 174     dr[YY]    -= shy*pbcAiuc.boxYY;
 175
 176     float shx  = rintf(dr[XX]*pbcAiuc.invBoxDiagX);
 177     dr[XX]    -= shx*pbcAiuc.boxXX;
 178 }
 179
 180
 181 #endif //GMX_PBCUTIL_PBC_AIUC_H