src/gromacs/gmxlib/conformation_utilities.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "conformation_utilities.h"
  41
  42 #include <cmath>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/math/functions.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/pbcutil/pbc.h"
  49
  50 static void low_rotate_conf(int natom, rvec* x, real alfa, real beta, real gamma)
  51 {
  52     int  i;
  53     rvec x_old;
  54
  55     for (i = 0; i < natom; i++)
  56     {
  57         copy_rvec(x[i], x_old);
  58         /*calculate new x[i] by rotation alfa around the x-axis*/
  59         x[i][XX] = x_old[XX];
  60         x[i][YY] = cos(alfa) * x_old[YY] - sin(alfa) * x_old[ZZ];
  61         x[i][ZZ] = sin(alfa) * x_old[YY] + cos(alfa) * x_old[ZZ];
  62         copy_rvec(x[i], x_old);
  63         /*calculate new x[i] by rotation beta around the y-axis*/
  64         x[i][XX] = cos(beta) * x_old[XX] + sin(beta) * x_old[ZZ];
  65         x[i][YY] = x_old[YY];
  66         x[i][ZZ] = -sin(beta) * x_old[XX] + cos(beta) * x_old[ZZ];
  67         copy_rvec(x[i], x_old);
  68         /*calculate new x[i] by rotation gamma around the z-axis*/
  69         x[i][XX] = x_old[XX] * cos(gamma) - x_old[YY] * sin(gamma);
  70         x[i][YY] = x_old[XX] * sin(gamma) + x_old[YY] * cos(gamma);
  71         x[i][ZZ] = x_old[ZZ];
  72     }
  73 }
  74
  75 void rotate_conf(int natom, rvec* x, rvec* v, real alfa, real beta, real gamma)
  76 {
  77     if (x)
  78     {
  79         low_rotate_conf(natom, x, alfa, beta, gamma);
  80     }
  81     if (v)
  82     {
  83         low_rotate_conf(natom, v, alfa, beta, gamma);
  84     }
  85 }
  86
  87 /* Make a new box around a configuration*/
  88 void make_new_box(int natoms, rvec* x, matrix box, const rvec box_space, gmx_bool bCenter)
  89 {
  90     int  i, m;
  91     rvec xmin, xmax;
  92
  93     /*calculate minimum and maximum x[0..DIM-1]*/
  94     for (m = 0; (m < DIM); m++)
  95     {
  96         xmin[m] = xmax[m] = x[0][m];
  97     }
  98     for (i = 1; (i < natoms); i++)
  99     {
 100         for (m = 0; m < DIM; m++)
 101         {
 102             xmin[m] = std::min(xmin[m], x[i][m]);
 103             xmax[m] = std::max(xmax[m], x[i][m]);
 104         }
 105     }
 106
 107     /*calculate the new box sizes for cubic and octahedral ...*/
 108     for (m = 0; (m < DIM); m++)
 109     {
 110         box[m][m] = xmax[m] - xmin[m] + 2 * box_space[m];
 111     }
 112
 113     /*move the molecule to the center of the box*/
 114     if (bCenter)
 115     {
 116         for (i = 0; (i < natoms); i++)
 117         {
 118             for (m = 0; (m < DIM); m++)
 119             {
 120                 x[i][m] += 0.5 * (box[m][m] - xmin[m] - xmax[m]);
 121             }
 122         }
 123     }
 124 }