src/gromacs/pbcutil/boxutilities.cpp

   1 /*
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  35 /*! \internal \file
  36  * \brief
  37  * Implements routines in boxutilities.h.
  38  *
  39  * Utility functions for handling boxes.
  40  */
  41 #include "gmxpre.h"
  42
  43 #include "boxutilities.h"
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/math/utilities.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/math/vectypes.h"
  50
  51 void do_box_rel(int ndim, const matrix deform, matrix box_rel,
  52                 matrix b, bool bInit)
  53 {
  54     for (int d = YY; d <= ZZ; ++d)
  55     {
  56         for (int d2 = XX; d2 < ndim; ++d2)
  57         {
  58             /* We need to check if this box component is deformed
  59              * or if deformation of another component might cause
  60              * changes in this component due to box corrections.
  61              */
  62             if (deform[d][d2] == 0 &&
  63                 !(d == ZZ && d2 == XX && deform[d][YY] != 0 &&
  64                   (b[YY][d2] != 0 || deform[YY][d2] != 0)))
  65             {
  66                 if (bInit)
  67                 {
  68                     box_rel[d][d2] = b[d][d2]/b[XX][XX];
  69                 }
  70                 else
  71                 {
  72                     b[d][d2] = b[XX][XX]*box_rel[d][d2];
  73                 }
  74             }
  75         }
  76     }
  77 }
  78
  79 namespace gmx
  80 {
  81
  82 namespace
  83 {
  84
  85 //! Whether two box elements are equal (with a tolerance).
  86 bool boxElementEqual(real element1, real element2)
  87 {
  88     // Compare with a relative tolerance (for big boxes) and with
  89     // an absolute tolerance (small boxes are generally not specified with very
  90     // high number of decimals).
  91     return gmx_within_tol(element1, element2, 10*GMX_REAL_EPS)
  92            || std::fabs(element1 - element2) < 1e-3;
  93 }
  94
  95 }   // namespace
  96
  97 bool boxesAreEqual(const matrix box1, const matrix box2)
  98 {
  99     return boxElementEqual(box1[XX][XX], box2[XX][XX])
 100            && boxElementEqual(box1[YY][XX], box2[YY][XX])
 101            && boxElementEqual(box1[YY][YY], box2[YY][YY])
 102            && boxElementEqual(box1[ZZ][XX], box2[ZZ][XX])
 103            && boxElementEqual(box1[ZZ][YY], box2[ZZ][YY])
 104            && boxElementEqual(box1[ZZ][ZZ], box2[ZZ][ZZ]);
 105 }
 106
 107 bool boxIsZero(const matrix box)
 108 {
 109     return boxElementEqual(box[XX][XX], 0.0)
 110            && boxElementEqual(box[YY][XX], 0.0)
 111            && boxElementEqual(box[YY][YY], 0.0)
 112            && boxElementEqual(box[ZZ][XX], 0.0)
 113            && boxElementEqual(box[ZZ][YY], 0.0)
 114            && boxElementEqual(box[ZZ][ZZ], 0.0);
 115 }
 116
 117 } // namespace gmx