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42 #include "gromacs/utility/smalloc.h"
43 #include "gromacs/legacyheaders/macros.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/fileio/xvgr.h"
46 #include "gromacs/fileio/matio.h"
47 #include "gromacs/utility/futil.h"
49 t_mat *init_mat(int n1, gmx_bool b1D)
60 m->mat = mk_matrix(n1, n1, b1D);
69 void copy_t_mat(t_mat *dst, t_mat *src)
73 if (dst->nn != src->nn)
75 fprintf(stderr, "t_mat structures not identical in size dst %d src %d\n", dst->nn, src->nn);
78 dst->maxrms = src->maxrms;
79 dst->minrms = src->minrms;
80 dst->sumrms = src->sumrms;
81 for (i = 0; (i < src->nn); i++)
83 for (j = 0; (j < src->nn); j++)
85 dst->mat[i][j] = src->mat[i][j];
87 dst->erow[i] = src->erow[i];
88 dst->m_ind[i] = src->m_ind[i];
92 void enlarge_mat(t_mat *m, int deltan)
96 srenew(m->erow, m->nn+deltan);
97 srenew(m->m_ind, m->nn+deltan);
98 srenew(m->mat, m->nn+deltan);
100 /* Reallocate existing rows in the matrix, and set them to zero */
101 for (i = 0; (i < m->nn); i++)
103 srenew(m->mat[i], m->nn+deltan);
104 for (j = m->nn; (j < m->nn+deltan); j++)
109 /* Allocate new rows of the matrix, set energies to zero */
110 for (i = m->nn; (i < m->nn+deltan); i++)
113 snew(m->mat[i], m->nn+deltan);
118 void reset_index(t_mat *m)
122 for (i = 0; (i < m->n1); i++)
128 void set_mat_entry(t_mat *m, int i, int j, real val)
130 m->mat[i][j] = m->mat[j][i] = val;
131 m->maxrms = max(m->maxrms, val);
134 m->minrms = min(m->minrms, val);
137 m->nn = max(m->nn, max(j+1, i+1));
140 void done_mat(t_mat **m)
142 done_matrix((*m)->n1, &((*m)->mat));
149 real mat_energy(t_mat *m)
154 for (j = 0; (j < m->nn-1); j++)
156 emat += sqr(m->mat[j][j+1]);
161 void swap_rows(t_mat *m, int iswap, int jswap)
167 itmp = m->m_ind[iswap];
168 m->m_ind[iswap] = m->m_ind[jswap];
169 m->m_ind[jswap] = itmp;
171 /* Swap rows (since the matrix is an array of pointers) */
173 m->mat[iswap] = m->mat[jswap];
177 for (i = 0; (i < m->nn); i++)
179 ttt = m->mat[i][iswap];
180 m->mat[i][iswap] = m->mat[i][jswap];
181 m->mat[i][jswap] = ttt;
185 void swap_mat(t_mat *m)
190 tmp = init_mat(m->nn, FALSE);
191 for (i = 0; (i < m->nn); i++)
193 for (j = 0; (j < m->nn); j++)
195 tmp->mat[m->m_ind[i]][m->m_ind[j]] = m->mat[i][j];
198 /*tmp->mat[i][j] = m->mat[m->m_ind[i]][m->m_ind[j]]; */
199 for (i = 0; (i < m->nn); i++)
201 for (j = 0; (j < m->nn); j++)
203 m->mat[i][j] = tmp->mat[i][j];
209 void low_rmsd_dist(const char *fn, real maxrms, int nn, real **mat,
210 const output_env_t oenv)
218 for (i = 0; i < nn; i++)
220 for (j = i+1; j < nn; j++)
222 x = (int)(fac*mat[i][j]+0.5);
230 fp = xvgropen(fn, "RMS Distribution", "RMS (nm)", "a.u.", oenv);
231 for (i = 0; (i < 101); i++)
233 fprintf(fp, "%10g %10d\n", i/fac, histo[i]);
239 void rmsd_distribution(const char *fn, t_mat *rms, const output_env_t oenv)
241 low_rmsd_dist(fn, rms->maxrms, rms->nn, rms->mat, oenv);
244 t_clustid *new_clustid(int n1)
250 for (i = 0; (i < n1); i++)