src/gromacs/math/do_fit.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "do_fit.h"
  40
  41 #include <stdio.h>
  42
  43 #include <cmath>
  44
  45 #include "gromacs/linearalgebra/nrjac.h"
  46 #include "gromacs/math/functions.h"
  47 #include "gromacs/math/utilities.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/utility/fatalerror.h"
  50 #include "gromacs/utility/smalloc.h"
  51
  52 real calc_similar_ind(gmx_bool bRho, int nind, int *index, real mass[],
  53                       rvec x[], rvec xp[])
  54 {
  55     int  i, j, d;
  56     real m, tm, xs, xd, rs, rd;
  57
  58     tm = 0;
  59     rs = 0;
  60     rd = 0;
  61     for (j = 0; j < nind; j++)
  62     {
  63         if (index)
  64         {
  65             i = index[j];
  66         }
  67         else
  68         {
  69             i = j;
  70         }
  71         m   = mass[i];
  72         tm += m;
  73         for (d = 0; d < DIM; d++)
  74         {
  75             xd  = x[i][d] - xp[i][d];
  76             rd += m * gmx::square(xd);
  77             if (bRho)
  78             {
  79                 xs  = x[i][d] + xp[i][d];
  80                 rs += m * gmx::square(xs);
  81             }
  82         }
  83     }
  84     if (bRho)
  85     {
  86         return 2*std::sqrt(rd/rs);
  87     }
  88     else
  89     {
  90         return std::sqrt(rd/tm);
  91     }
  92 }
  93
  94 real rmsdev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[])
  95 {
  96     return calc_similar_ind(FALSE, nind, index, mass, x, xp);
  97 }
  98
  99 real rmsdev(int natoms, real mass[], rvec x[], rvec xp[])
 100 {
 101     return calc_similar_ind(FALSE, natoms, nullptr, mass, x, xp);
 102 }
 103
 104 real rhodev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[])
 105 {
 106     return calc_similar_ind(TRUE, nind, index, mass, x, xp);
 107 }
 108
 109 real rhodev(int natoms, real mass[], rvec x[], rvec xp[])
 110 {
 111     return calc_similar_ind(TRUE, natoms, nullptr, mass, x, xp);
 112 }
 113
 114 void calc_fit_R(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x, matrix R)
 115 {
 116     int      c, r, n, j, i, irot, s;
 117     double **omega, **om;
 118     double   d[2*DIM], xnr, xpc;
 119     matrix   vh, vk, u;
 120     real     mn;
 121     int      index;
 122     real     max_d;
 123
 124     if (ndim != 3 && ndim != 2)
 125     {
 126         gmx_fatal(FARGS, "calc_fit_R called with ndim=%d instead of 3 or 2", ndim);
 127     }
 128
 129     snew(omega, 2*ndim);
 130     snew(om, 2*ndim);
 131     for (i = 0; i < 2*ndim; i++)
 132     {
 133         snew(omega[i], 2*ndim);
 134         snew(om[i], 2*ndim);
 135     }
 136
 137     for (i = 0; i < 2*ndim; i++)
 138     {
 139         d[i] = 0;
 140         for (j = 0; j < 2*ndim; j++)
 141         {
 142             omega[i][j] = 0;
 143             om[i][j]    = 0;
 144         }
 145     }
 146
 147     /*calculate the matrix U*/
 148     clear_mat(u);
 149     for (n = 0; (n < natoms); n++)
 150     {
 151         if ((mn = w_rls[n]) != 0.0)
 152         {
 153             for (c = 0; (c < ndim); c++)
 154             {
 155                 xpc = xp[n][c];
 156                 for (r = 0; (r < ndim); r++)
 157                 {
 158                     xnr      = x[n][r];
 159                     u[c][r] += mn*xnr*xpc;
 160                 }
 161             }
 162         }
 163     }
 164
 165     /*construct omega*/
 166     /*omega is symmetric -> omega==omega' */
 167     for (r = 0; r < 2*ndim; r++)
 168     {
 169         for (c = 0; c <= r; c++)
 170         {
 171             if (r >= ndim && c < ndim)
 172             {
 173                 omega[r][c] = u[r-ndim][c];
 174                 omega[c][r] = u[r-ndim][c];
 175             }
 176             else
 177             {
 178                 omega[r][c] = 0;
 179                 omega[c][r] = 0;
 180             }
 181         }
 182     }
 183
 184     /*determine h and k*/
 185     jacobi(omega, 2*ndim, d, om, &irot);
 186     /*real   **omega = input matrix a[0..n-1][0..n-1] must be symmetric
 187      * int     natoms = number of rows and columns
 188      * real      NULL = d[0]..d[n-1] are the eigenvalues of a[][]
 189      * real       **v = v[0..n-1][0..n-1] contains the vectors in columns
 190      * int      *irot = number of jacobi rotations
 191      */
 192
 193     if (debug && irot == 0)
 194     {
 195         fprintf(debug, "IROT=0\n");
 196     }
 197
 198     index = 0; /* For the compiler only */
 199
 200     /* Copy only the first ndim-1 eigenvectors */
 201     for (j = 0; j < ndim-1; j++)
 202     {
 203         max_d = -1000;
 204         for (i = 0; i < 2*ndim; i++)
 205         {
 206             if (d[i] > max_d)
 207             {
 208                 max_d = d[i];
 209                 index = i;
 210             }
 211         }
 212         d[index] = -10000;
 213         for (i = 0; i < ndim; i++)
 214         {
 215             vh[j][i] = M_SQRT2*om[i][index];
 216             vk[j][i] = M_SQRT2*om[i+ndim][index];
 217         }
 218     }
 219     if (ndim == 3)
 220     {
 221         /* Calculate the last eigenvector as the outer-product of the first two.
 222          * This insures that the conformation is not mirrored and
 223          * prevents problems with completely flat reference structures.
 224          */
 225         cprod(vh[0], vh[1], vh[2]);
 226         cprod(vk[0], vk[1], vk[2]);
 227     }
 228     else if (ndim == 2)
 229     {
 230         /* Calculate the last eigenvector from the first one */
 231         vh[1][XX] = -vh[0][YY];
 232         vh[1][YY] =  vh[0][XX];
 233         vk[1][XX] = -vk[0][YY];
 234         vk[1][YY] =  vk[0][XX];
 235     }
 236
 237     /* determine R */
 238     clear_mat(R);
 239     for (r = 0; r < ndim; r++)
 240     {
 241         for (c = 0; c < ndim; c++)
 242         {
 243             for (s = 0; s < ndim; s++)
 244             {
 245                 R[r][c] += vk[s][r]*vh[s][c];
 246             }
 247         }
 248     }
 249     for (r = ndim; r < DIM; r++)
 250     {
 251         R[r][r] = 1;
 252     }
 253
 254     for (i = 0; i < 2*ndim; i++)
 255     {
 256         sfree(omega[i]);
 257         sfree(om[i]);
 258     }
 259     sfree(omega);
 260     sfree(om);
 261 }
 262
 263 void do_fit_ndim(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x)
 264 {
 265     int    j, m, r, c;
 266     matrix R;
 267     rvec   x_old;
 268
 269     /* Calculate the rotation matrix R */
 270     calc_fit_R(ndim, natoms, w_rls, xp, x, R);
 271
 272     /*rotate X*/
 273     for (j = 0; j < natoms; j++)
 274     {
 275         for (m = 0; m < DIM; m++)
 276         {
 277             x_old[m] = x[j][m];
 278         }
 279         for (r = 0; r < DIM; r++)
 280         {
 281             x[j][r] = 0;
 282             for (c = 0; c < DIM; c++)
 283             {
 284                 x[j][r] += R[r][c]*x_old[c];
 285             }
 286         }
 287     }
 288 }
 289
 290 void do_fit(int natoms, real *w_rls, const rvec *xp, rvec *x)
 291 {
 292     do_fit_ndim(3, natoms, w_rls, xp, x);
 293 }
 294
 295 void reset_x_ndim(int ndim, int ncm, const int *ind_cm,
 296                   int nreset, const int *ind_reset,
 297                   rvec x[], const real mass[])
 298 {
 299     int  i, m, ai;
 300     rvec xcm;
 301     real tm, mm;
 302
 303     if (ndim > DIM)
 304     {
 305         gmx_incons("More than 3 dimensions not supported.");
 306     }
 307     tm = 0.0;
 308     clear_rvec(xcm);
 309     if (ind_cm != nullptr)
 310     {
 311         for (i = 0; i < ncm; i++)
 312         {
 313             ai = ind_cm[i];
 314             mm = mass[ai];
 315             for (m = 0; m < ndim; m++)
 316             {
 317                 xcm[m] += mm*x[ai][m];
 318             }
 319             tm += mm;
 320         }
 321     }
 322     else
 323     {
 324         for (i = 0; i < ncm; i++)
 325         {
 326             mm = mass[i];
 327             for (m = 0; m < ndim; m++)
 328             {
 329                 xcm[m] += mm*x[i][m];
 330             }
 331             tm += mm;
 332         }
 333     }
 334     for (m = 0; m < ndim; m++)
 335     {
 336         xcm[m] /= tm;
 337     }
 338
 339     if (ind_reset != nullptr)
 340     {
 341         for (i = 0; i < nreset; i++)
 342         {
 343             rvec_dec(x[ind_reset[i]], xcm);
 344         }
 345     }
 346     else
 347     {
 348         for (i = 0; i < nreset; i++)
 349         {
 350             rvec_dec(x[i], xcm);
 351         }
 352     }
 353 }
 354
 355 void reset_x(int ncm, const int *ind_cm,
 356              int nreset, const int *ind_reset,
 357              rvec x[], const real mass[])
 358 {
 359     reset_x_ndim(3, ncm, ind_cm, nreset, ind_reset, x, mass);
 360 }