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/functions.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/utility/futil.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 t_mat *init_mat(int n1, gmx_bool b1D)
  51 {
  52     t_mat *m;
  53
  54     snew(m, 1);
  55     m->n1     = n1;
  56     m->nn     = 0;
  57     m->b1D    = b1D;
  58     m->maxrms = 0;
  59     m->minrms = 1e20;
  60     m->sumrms = 0;
  61     m->mat    = mk_matrix(n1, n1, b1D);
  62
  63     snew(m->erow, n1);
  64     snew(m->m_ind, n1);
  65     reset_index(m);
  66
  67     return m;
  68 }
  69
  70 void copy_t_mat(t_mat *dst, t_mat *src)
  71 {
  72     int i, j;
  73
  74     if (dst->nn != src->nn)
  75     {
  76         fprintf(stderr, "t_mat structures not identical in size dst %d src %d\n", dst->nn, src->nn);
  77         return;
  78     }
  79     dst->maxrms = src->maxrms;
  80     dst->minrms = src->minrms;
  81     dst->sumrms = src->sumrms;
  82     for (i = 0; (i < src->nn); i++)
  83     {
  84         for (j = 0; (j < src->nn); j++)
  85         {
  86             dst->mat[i][j] = src->mat[i][j];
  87         }
  88         dst->erow[i]  = src->erow[i];
  89         dst->m_ind[i] = src->m_ind[i];
  90     }
  91 }
  92
  93 void enlarge_mat(t_mat *m, int deltan)
  94 {
  95     int i, j;
  96
  97     srenew(m->erow, m->nn+deltan);
  98     srenew(m->m_ind, m->nn+deltan);
  99     srenew(m->mat, m->nn+deltan);
 100
 101     /* Reallocate existing rows in the matrix, and set them to zero */
 102     for (i = 0; (i < m->nn); i++)
 103     {
 104         srenew(m->mat[i], m->nn+deltan);
 105         for (j = m->nn; (j < m->nn+deltan); j++)
 106         {
 107             m->mat[i][j] = 0;
 108         }
 109     }
 110     /* Allocate new rows of the matrix, set energies to zero */
 111     for (i = m->nn; (i < m->nn+deltan); i++)
 112     {
 113         m->erow[i]  = 0;
 114         snew(m->mat[i], m->nn+deltan);
 115     }
 116     m->nn += deltan;
 117 }
 118
 119 void reset_index(t_mat *m)
 120 {
 121     int i;
 122
 123     for (i = 0; (i < m->n1); i++)
 124     {
 125         m->m_ind[i] = i;
 126     }
 127 }
 128
 129 void set_mat_entry(t_mat *m, int i, int j, real val)
 130 {
 131     m->mat[i][j] = m->mat[j][i] = val;
 132     m->maxrms    = std::max(m->maxrms, val);
 133     if (j != i)
 134     {
 135         m->minrms  = std::min(m->minrms, val);
 136     }
 137     m->sumrms   += val;
 138     m->nn        = std::max(m->nn, std::max(j+1, i+1));
 139 }
 140
 141 void done_mat(t_mat **m)
 142 {
 143     done_matrix((*m)->n1, &((*m)->mat));
 144     sfree((*m)->m_ind);
 145     sfree((*m)->erow);
 146     sfree(*m);
 147     *m = nullptr;
 148 }
 149
 150 real mat_energy(t_mat *m)
 151 {
 152     int  j;
 153     real emat = 0;
 154
 155     for (j = 0; (j < m->nn-1); j++)
 156     {
 157         emat += gmx::square(m->mat[j][j+1]);
 158     }
 159     return emat;
 160 }
 161
 162 void swap_rows(t_mat *m, int iswap, int jswap)
 163 {
 164     real *tmp, ttt;
 165     int   i, itmp;
 166
 167     /* Swap indices */
 168     itmp            = m->m_ind[iswap];
 169     m->m_ind[iswap] = m->m_ind[jswap];
 170     m->m_ind[jswap] = itmp;
 171
 172     /* Swap rows (since the matrix is an array of pointers) */
 173     tmp           = m->mat[iswap];
 174     m->mat[iswap] = m->mat[jswap];
 175     m->mat[jswap] = tmp;
 176
 177     /* Swap columns */
 178     for (i = 0; (i < m->nn); i++)
 179     {
 180         ttt              = m->mat[i][iswap];
 181         m->mat[i][iswap] = m->mat[i][jswap];
 182         m->mat[i][jswap] = ttt;
 183     }
 184 }
 185
 186 void swap_mat(t_mat *m)
 187 {
 188     t_mat *tmp;
 189     int    i, j;
 190
 191     tmp = init_mat(m->nn, FALSE);
 192     for (i = 0; (i < m->nn); i++)
 193     {
 194         for (j = 0; (j < m->nn); j++)
 195         {
 196             tmp->mat[m->m_ind[i]][m->m_ind[j]] = m->mat[i][j];
 197         }
 198     }
 199     /*tmp->mat[i][j] =  m->mat[m->m_ind[i]][m->m_ind[j]]; */
 200     for (i = 0; (i < m->nn); i++)
 201     {
 202         for (j = 0; (j < m->nn); j++)
 203         {
 204             m->mat[i][j] = tmp->mat[i][j];
 205         }
 206     }
 207     done_mat(&tmp);
 208 }
 209
 210 void low_rmsd_dist(const char *fn, real maxrms, int nn, real **mat,
 211                    const gmx_output_env_t *oenv)
 212 {
 213     FILE   *fp;
 214     int     i, j, *histo, x;
 215     real    fac;
 216
 217     fac = 100/maxrms;
 218     snew(histo, 101);
 219     for (i = 0; i < nn; i++)
 220     {
 221         for (j = i+1; j < nn; j++)
 222         {
 223             x = gmx::roundToInt(fac*mat[i][j]);
 224             if (x <= 100)
 225             {
 226                 histo[x]++;
 227             }
 228         }
 229     }
 230
 231     fp = xvgropen(fn, "RMS Distribution", "RMS (nm)", "a.u.", oenv);
 232     for (i = 0; (i < 101); i++)
 233     {
 234         fprintf(fp, "%10g  %10d\n", i/fac, histo[i]);
 235     }
 236     xvgrclose(fp);
 237     sfree(histo);
 238 }
 239
 240 void rmsd_distribution(const char *fn, t_mat *rms, const gmx_output_env_t *oenv)
 241 {
 242     low_rmsd_dist(fn, rms->maxrms, rms->nn, rms->mat, oenv);
 243 }
 244
 245 t_clustid *new_clustid(int n1)
 246 {
 247     t_clustid *c;
 248     int        i;
 249
 250     snew(c, n1);
 251     for (i = 0; (i < n1); i++)
 252     {
 253         c[i].conf  = i;
 254         c[i].clust = i;
 255     }
 256     return c;
 257 }