src/gromacs/gmxana/princ.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "princ.h"
  42
  43 #include <cmath>
  44
  45 #include "gromacs/linearalgebra/nrjac.h"
  46 #include "gromacs/math/functions.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/topology/topology.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 #define NDIM 4
  52
  53 #ifdef DEBUG
  54 static void m_op(matrix mat, rvec x)
  55 {
  56     rvec xp;
  57     int  m;
  58
  59     for (m = 0; (m < DIM); m++)
  60     {
  61         xp[m] = mat[m][XX] * x[XX] + mat[m][YY] * x[YY] + mat[m][ZZ] * x[ZZ];
  62     }
  63     fprintf(stderr, "x    %8.3f  %8.3f  %8.3f\n", x[XX], x[YY], x[ZZ]);
  64     fprintf(stderr, "xp   %8.3f  %8.3f  %8.3f\n", xp[XX], xp[YY], xp[ZZ]);
  65     fprintf(stderr, "fac  %8.3f  %8.3f  %8.3f\n", xp[XX] / x[XX], xp[YY] / x[YY], xp[ZZ] / x[ZZ]);
  66 }
  67
  68 static void ptrans(char* s, real** inten, real d[], real e[])
  69 {
  70     int  m;
  71     real n, x, y, z;
  72     for (m = 1; (m < NDIM); m++)
  73     {
  74         x = inten[m][1];
  75         y = inten[m][2];
  76         z = inten[m][3];
  77         n = x * x + y * y + z * z;
  78         fprintf(stderr, "%8s %8.3f %8.3f %8.3f, norm:%8.3f, d:%8.3f, e:%8.3f\n", s, x, y, z,
  79                 std::sqrt(n), d[m], e[m]);
  80     }
  81     fprintf(stderr, "\n");
  82 }
  83
  84 void t_trans(matrix trans, real d[], real** ev)
  85 {
  86     rvec x;
  87     int  j;
  88     for (j = 0; (j < DIM); j++)
  89     {
  90         x[XX] = ev[1][j + 1];
  91         x[YY] = ev[2][j + 1];
  92         x[ZZ] = ev[3][j + 1];
  93         m_op(trans, x);
  94         fprintf(stderr, "d[%d]=%g\n", j, d[j + 1]);
  95     }
  96 }
  97 #endif
  98
  99 void principal_comp(int n, const int index[], t_atom atom[], rvec x[], matrix trans, rvec d)
 100 {
 101     int      i, j, ai, m, nrot;
 102     real     mm, rx, ry, rz;
 103     double **inten, dd[NDIM], tvec[NDIM], **ev;
 104 #ifdef DEBUG
 105     real e[NDIM];
 106 #endif
 107     real temp;
 108
 109     snew(inten, NDIM);
 110     snew(ev, NDIM);
 111     for (i = 0; (i < NDIM); i++)
 112     {
 113         snew(inten[i], NDIM);
 114         snew(ev[i], NDIM);
 115         dd[i] = 0.0;
 116 #ifdef DEBUG
 117         e[i] = 0.0;
 118 #endif
 119     }
 120
 121     for (i = 0; (i < NDIM); i++)
 122     {
 123         for (m = 0; (m < NDIM); m++)
 124         {
 125             inten[i][m] = 0;
 126         }
 127     }
 128     for (i = 0; (i < n); i++)
 129     {
 130         ai = index[i];
 131         mm = atom[ai].m;
 132         rx = x[ai][XX];
 133         ry = x[ai][YY];
 134         rz = x[ai][ZZ];
 135         inten[0][0] += mm * (gmx::square(ry) + gmx::square(rz));
 136         inten[1][1] += mm * (gmx::square(rx) + gmx::square(rz));
 137         inten[2][2] += mm * (gmx::square(rx) + gmx::square(ry));
 138         inten[1][0] -= mm * (ry * rx);
 139         inten[2][0] -= mm * (rx * rz);
 140         inten[2][1] -= mm * (rz * ry);
 141     }
 142     inten[0][1] = inten[1][0];
 143     inten[0][2] = inten[2][0];
 144     inten[1][2] = inten[2][1];
 145 #ifdef DEBUG
 146     ptrans("initial", inten, dd, e);
 147 #endif
 148
 149     for (i = 0; (i < DIM); i++)
 150     {
 151         for (m = 0; (m < DIM); m++)
 152         {
 153             trans[i][m] = inten[i][m];
 154         }
 155     }
 156
 157     /* Call numerical recipe routines */
 158     jacobi(inten, 3, dd, ev, &nrot);
 159 #ifdef DEBUG
 160     ptrans("jacobi", ev, dd, e);
 161 #endif
 162
 163     /* Sort eigenvalues in ascending order */
 164 #define SWAPPER(i)                               \
 165     if (std::abs(dd[(i) + 1]) < std::abs(dd[i])) \
 166     {                                            \
 167         temp = dd[i];                            \
 168         for (j = 0; (j < NDIM); j++)             \
 169         {                                        \
 170             tvec[j] = ev[j][i];                  \
 171         }                                        \
 172         dd[i] = dd[(i) + 1];                     \
 173         for (j = 0; (j < NDIM); j++)             \
 174         {                                        \
 175             ev[j][i] = ev[j][(i) + 1];           \
 176         }                                        \
 177         dd[(i) + 1] = temp;                      \
 178         for (j = 0; (j < NDIM); j++)             \
 179         {                                        \
 180             ev[j][(i) + 1] = tvec[j];            \
 181         }                                        \
 182     }
 183     SWAPPER(0)
 184     SWAPPER(1)
 185     SWAPPER(0)
 186 #ifdef DEBUG
 187     ptrans("swap", ev, dd, e);
 188     t_trans(trans, dd, ev);
 189 #endif
 190
 191     for (i = 0; (i < DIM); i++)
 192     {
 193         d[i] = dd[i];
 194         for (m = 0; (m < DIM); m++)
 195         {
 196             trans[i][m] = ev[m][i];
 197         }
 198     }
 199
 200     for (i = 0; (i < NDIM); i++)
 201     {
 202         sfree(inten[i]);
 203         sfree(ev[i]);
 204     }
 205     sfree(inten);
 206     sfree(ev);
 207 }
 208
 209 void rotate_atoms(int gnx, const int* index, rvec x[], matrix trans)
 210 {
 211     real xt, yt, zt;
 212     int  i, ii;
 213
 214     for (i = 0; (i < gnx); i++)
 215     {
 216         ii        = index ? index[i] : i;
 217         xt        = x[ii][XX];
 218         yt        = x[ii][YY];
 219         zt        = x[ii][ZZ];
 220         x[ii][XX] = trans[XX][XX] * xt + trans[XX][YY] * yt + trans[XX][ZZ] * zt;
 221         x[ii][YY] = trans[YY][XX] * xt + trans[YY][YY] * yt + trans[YY][ZZ] * zt;
 222         x[ii][ZZ] = trans[ZZ][XX] * xt + trans[ZZ][YY] * yt + trans[ZZ][ZZ] * zt;
 223     }
 224 }
 225
 226 real calc_xcm(const rvec x[], int gnx, const int* index, const t_atom* atom, rvec xcm, gmx_bool bQ)
 227 {
 228     int  i, ii, m;
 229     real m0, tm;
 230
 231     clear_rvec(xcm);
 232     tm = 0;
 233     for (i = 0; (i < gnx); i++)
 234     {
 235         ii = index ? index[i] : i;
 236         if (atom)
 237         {
 238             if (bQ)
 239             {
 240                 m0 = std::abs(atom[ii].q);
 241             }
 242             else
 243             {
 244                 m0 = atom[ii].m;
 245             }
 246         }
 247         else
 248         {
 249             m0 = 1;
 250         }
 251         tm += m0;
 252         for (m = 0; (m < DIM); m++)
 253         {
 254             xcm[m] += m0 * x[ii][m];
 255         }
 256     }
 257     for (m = 0; (m < DIM); m++)
 258     {
 259         xcm[m] /= tm;
 260     }
 261
 262     return tm;
 263 }
 264
 265 real sub_xcm(rvec x[], int gnx, const int* index, const t_atom atom[], rvec xcm, gmx_bool bQ)
 266 {
 267     int  i, ii;
 268     real tm;
 269
 270     tm = calc_xcm(x, gnx, index, atom, xcm, bQ);
 271     for (i = 0; (i < gnx); i++)
 272     {
 273         ii = index ? index[i] : i;
 274         rvec_dec(x[ii], xcm);
 275     }
 276     return tm;
 277 }
 278
 279 void add_xcm(rvec x[], int gnx, const int* index, rvec xcm)
 280 {
 281     int i, ii;
 282
 283     for (i = 0; (i < gnx); i++)
 284     {
 285         ii = index ? index[i] : i;
 286         rvec_inc(x[ii], xcm);
 287     }
 288 }
 289
 290 void orient_princ(const t_atoms* atoms, int isize, const int* index, int natoms, rvec x[], rvec* v, rvec d)
 291 {
 292     int    i, m;
 293     rvec   xcm, prcomp;
 294     matrix trans;
 295
 296     calc_xcm(x, isize, index, atoms->atom, xcm, FALSE);
 297     for (i = 0; i < natoms; i++)
 298     {
 299         rvec_dec(x[i], xcm);
 300     }
 301     principal_comp(isize, index, atoms->atom, x, trans, prcomp);
 302     if (d)
 303     {
 304         copy_rvec(prcomp, d);
 305     }
 306
 307     /* Check whether this trans matrix mirrors the molecule */
 308     if (det(trans) < 0)
 309     {
 310         for (m = 0; (m < DIM); m++)
 311         {
 312             trans[ZZ][m] = -trans[ZZ][m];
 313         }
 314     }
 315     rotate_atoms(natoms, nullptr, x, trans);
 316     if (v)
 317     {
 318         rotate_atoms(natoms, nullptr, v, trans);
 319     }
 320
 321     for (i = 0; i < natoms; i++)
 322     {
 323         rvec_inc(x[i], xcm);
 324     }
 325 }