src/gromacs/gmxana/cmat.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "cmat.h"
  40
  41 #include <algorithm>
  42
  43 #include "gromacs/fileio/matio.h"
  44 #include "gromacs/fileio/xvgr.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/utility/futil.h"
  47 #include "gromacs/utility/smalloc.h"
  48
  49 t_mat *init_mat(int n1, gmx_bool b1D)
  50 {
  51     t_mat *m;
  52
  53     snew(m, 1);
  54     m->n1     = n1;
  55     m->nn     = 0;
  56     m->b1D    = b1D;
  57     m->maxrms = 0;
  58     m->minrms = 1e20;
  59     m->sumrms = 0;
  60     m->mat    = mk_matrix(n1, n1, b1D);
  61
  62     snew(m->erow, n1);
  63     snew(m->m_ind, n1);
  64     reset_index(m);
  65
  66     return m;
  67 }
  68
  69 void copy_t_mat(t_mat *dst, t_mat *src)
  70 {
  71     int i, j;
  72
  73     if (dst->nn != src->nn)
  74     {
  75         fprintf(stderr, "t_mat structures not identical in size dst %d src %d\n", dst->nn, src->nn);
  76         return;
  77     }
  78     dst->maxrms = src->maxrms;
  79     dst->minrms = src->minrms;
  80     dst->sumrms = src->sumrms;
  81     for (i = 0; (i < src->nn); i++)
  82     {
  83         for (j = 0; (j < src->nn); j++)
  84         {
  85             dst->mat[i][j] = src->mat[i][j];
  86         }
  87         dst->erow[i]  = src->erow[i];
  88         dst->m_ind[i] = src->m_ind[i];
  89     }
  90 }
  91
  92 void enlarge_mat(t_mat *m, int deltan)
  93 {
  94     int i, j;
  95
  96     srenew(m->erow, m->nn+deltan);
  97     srenew(m->m_ind, m->nn+deltan);
  98     srenew(m->mat, m->nn+deltan);
  99
 100     /* Reallocate existing rows in the matrix, and set them to zero */
 101     for (i = 0; (i < m->nn); i++)
 102     {
 103         srenew(m->mat[i], m->nn+deltan);
 104         for (j = m->nn; (j < m->nn+deltan); j++)
 105         {
 106             m->mat[i][j] = 0;
 107         }
 108     }
 109     /* Allocate new rows of the matrix, set energies to zero */
 110     for (i = m->nn; (i < m->nn+deltan); i++)
 111     {
 112         m->erow[i]  = 0;
 113         snew(m->mat[i], m->nn+deltan);
 114     }
 115     m->nn += deltan;
 116 }
 117
 118 void reset_index(t_mat *m)
 119 {
 120     int i;
 121
 122     for (i = 0; (i < m->n1); i++)
 123     {
 124         m->m_ind[i] = i;
 125     }
 126 }
 127
 128 void set_mat_entry(t_mat *m, int i, int j, real val)
 129 {
 130     m->mat[i][j] = m->mat[j][i] = val;
 131     m->maxrms    = std::max(m->maxrms, val);
 132     if (j != i)
 133     {
 134         m->minrms  = std::min(m->minrms, val);
 135     }
 136     m->sumrms   += val;
 137     m->nn        = std::max(m->nn, std::max(j+1, i+1));
 138 }
 139
 140 void done_mat(t_mat **m)
 141 {
 142     done_matrix((*m)->n1, &((*m)->mat));
 143     sfree((*m)->m_ind);
 144     sfree((*m)->erow);
 145     sfree(*m);
 146     *m = NULL;
 147 }
 148
 149 real mat_energy(t_mat *m)
 150 {
 151     int  j;
 152     real emat = 0;
 153
 154     for (j = 0; (j < m->nn-1); j++)
 155     {
 156         emat += sqr(m->mat[j][j+1]);
 157     }
 158     return emat;
 159 }
 160
 161 void swap_rows(t_mat *m, int iswap, int jswap)
 162 {
 163     real *tmp, ttt;
 164     int   i, itmp;
 165
 166     /* Swap indices */
 167     itmp            = m->m_ind[iswap];
 168     m->m_ind[iswap] = m->m_ind[jswap];
 169     m->m_ind[jswap] = itmp;
 170
 171     /* Swap rows (since the matrix is an array of pointers) */
 172     tmp           = m->mat[iswap];
 173     m->mat[iswap] = m->mat[jswap];
 174     m->mat[jswap] = tmp;
 175
 176     /* Swap columns */
 177     for (i = 0; (i < m->nn); i++)
 178     {
 179         ttt              = m->mat[i][iswap];
 180         m->mat[i][iswap] = m->mat[i][jswap];
 181         m->mat[i][jswap] = ttt;
 182     }
 183 }
 184
 185 void swap_mat(t_mat *m)
 186 {
 187     t_mat *tmp;
 188     int    i, j;
 189
 190     tmp = init_mat(m->nn, FALSE);
 191     for (i = 0; (i < m->nn); i++)
 192     {
 193         for (j = 0; (j < m->nn); j++)
 194         {
 195             tmp->mat[m->m_ind[i]][m->m_ind[j]] = m->mat[i][j];
 196         }
 197     }
 198     /*tmp->mat[i][j] =  m->mat[m->m_ind[i]][m->m_ind[j]]; */
 199     for (i = 0; (i < m->nn); i++)
 200     {
 201         for (j = 0; (j < m->nn); j++)
 202         {
 203             m->mat[i][j] = tmp->mat[i][j];
 204         }
 205     }
 206     done_mat(&tmp);
 207 }
 208
 209 void low_rmsd_dist(const char *fn, real maxrms, int nn, real **mat,
 210                    const gmx_output_env_t *oenv)
 211 {
 212     FILE   *fp;
 213     int     i, j, *histo, x;
 214     real    fac;
 215
 216     fac = 100/maxrms;
 217     snew(histo, 101);
 218     for (i = 0; i < nn; i++)
 219     {
 220         for (j = i+1; j < nn; j++)
 221         {
 222             x = static_cast<int>(fac*mat[i][j]+0.5);
 223             if (x <= 100)
 224             {
 225                 histo[x]++;
 226             }
 227         }
 228     }
 229
 230     fp = xvgropen(fn, "RMS Distribution", "RMS (nm)", "a.u.", oenv);
 231     for (i = 0; (i < 101); i++)
 232     {
 233         fprintf(fp, "%10g  %10d\n", i/fac, histo[i]);
 234     }
 235     xvgrclose(fp);
 236     sfree(histo);
 237 }
 238
 239 void rmsd_distribution(const char *fn, t_mat *rms, const gmx_output_env_t *oenv)
 240 {
 241     low_rmsd_dist(fn, rms->maxrms, rms->nn, rms->mat, oenv);
 242 }
 243
 244 t_clustid *new_clustid(int n1)
 245 {
 246     t_clustid *c;
 247     int        i;
 248
 249     snew(c, n1);
 250     for (i = 0; (i < n1); i++)
 251     {
 252         c[i].conf  = i;
 253         c[i].clust = i;
 254     }
 255     return c;
 256 }