src/gromacs/domdec/utility.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 /*! \internal \file
  36  *
  37  * \brief Declares utility functions used in the domain decomposition module.
  38  *
  39  * \author Berk Hess <hess@kth.se>
  40  * \ingroup module_domdec
  41  */
  42
  43 #include "gmxpre.h"
  44
  45 #include "utility.h"
  46
  47 #include "gromacs/mdtypes/state.h"
  48 #include "gromacs/utility/fatalerror.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 #include "domdec_internal.h"
  52
  53 char dim2char(int dim)
  54 {
  55     char c = '?';
  56
  57     switch (dim)
  58     {
  59         case XX: c = 'X'; break;
  60         case YY: c = 'Y'; break;
  61         case ZZ: c = 'Z'; break;
  62         default: gmx_fatal(FARGS, "Unknown dim %d", dim);
  63     }
  64
  65     return c;
  66 }
  67
  68 void make_tric_corr_matrix(int npbcdim, const matrix box, matrix tcm)
  69 {
  70     if (YY < npbcdim)
  71     {
  72         tcm[YY][XX] = -box[YY][XX] / box[YY][YY];
  73     }
  74     else
  75     {
  76         tcm[YY][XX] = 0;
  77     }
  78     if (ZZ < npbcdim)
  79     {
  80         tcm[ZZ][XX] = -(box[ZZ][YY] * tcm[YY][XX] + box[ZZ][XX]) / box[ZZ][ZZ];
  81         tcm[ZZ][YY] = -box[ZZ][YY] / box[ZZ][ZZ];
  82     }
  83     else
  84     {
  85         tcm[ZZ][XX] = 0;
  86         tcm[ZZ][YY] = 0;
  87     }
  88 }
  89
  90 void check_screw_box(const matrix box)
  91 {
  92     /* Mathematical limitation */
  93     if (box[YY][XX] != 0 || box[ZZ][XX] != 0)
  94     {
  95         gmx_fatal(FARGS,
  96                   "With screw pbc the unit cell can not have non-zero off-diagonal x-components");
  97     }
  98
  99     /* Limitation due to the asymmetry of the eighth shell method */
 100     if (box[ZZ][YY] != 0)
 101     {
 102         gmx_fatal(FARGS, "pbc=screw with non-zero box_zy is not supported");
 103     }
 104 }
 105 /*! \brief Resize the state and f*/
 106 void dd_resize_state(t_state* state, PaddedHostVector<gmx::RVec>* f, int natoms)
 107 {
 108     if (debug)
 109     {
 110         fprintf(debug, "Resizing state: currently %d, required %d\n", state->natoms, natoms);
 111     }
 112
 113     state_change_natoms(state, natoms);
 114
 115     if (f != nullptr)
 116     {
 117         /* We need to allocate one element extra, since we might use
 118          * (unaligned) 4-wide SIMD loads to access rvec entries.
 119          */
 120         f->resizeWithPadding(natoms);
 121     }
 122 }
 123
 124 /*! \brief Ensure fr, state and f, if != nullptr, can hold numChargeGroups
 125  *         atoms for the Verlet scheme and charge groups for the group scheme.
 126  *
 127  * todo refactor this now that group scheme is removed
 128  */
 129 void dd_check_alloc_ncg(t_forcerec* fr, t_state* state, PaddedHostVector<gmx::RVec>* f, int numChargeGroups)
 130 {
 131     fr->cginfo.resize(numChargeGroups);
 132
 133     /* We use x during the setup of the atom communication */
 134     dd_resize_state(state, f, numChargeGroups);
 135 }