src/gromacs/gmxana/princ.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "princ.h"
  41
  42 #include <cmath>
  43
  44 #include "gromacs/linearalgebra/nrjac.h"
  45 #include "gromacs/math/functions.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/topology/topology.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 #define NDIM 4
  51
  52 #ifdef DEBUG
  53 static void m_op(matrix mat, rvec x)
  54 {
  55     rvec xp;
  56     int  m;
  57
  58     for (m = 0; (m < DIM); m++)
  59     {
  60         xp[m] = mat[m][XX]*x[XX]+mat[m][YY]*x[YY]+mat[m][ZZ]*x[ZZ];
  61     }
  62     fprintf(stderr, "x    %8.3f  %8.3f  %8.3f\n", x[XX], x[YY], x[ZZ]);
  63     fprintf(stderr, "xp   %8.3f  %8.3f  %8.3f\n", xp[XX], xp[YY], xp[ZZ]);
  64     fprintf(stderr, "fac  %8.3f  %8.3f  %8.3f\n", xp[XX]/x[XX], xp[YY]/x[YY],
  65             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",
  79                 s, x, y, z, 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[],
 100                     matrix trans, rvec d)
 101 {
 102     int      i, j, ai, m, nrot;
 103     real     mm, rx, ry, rz;
 104     double **inten, dd[NDIM], tvec[NDIM], **ev;
 105 #ifdef DEBUG
 106     real     e[NDIM];
 107 #endif
 108     real     temp;
 109
 110     snew(inten, NDIM);
 111     snew(ev, NDIM);
 112     for (i = 0; (i < NDIM); i++)
 113     {
 114         snew(inten[i], NDIM);
 115         snew(ev[i], NDIM);
 116         dd[i] = 0.0;
 117 #ifdef DEBUG
 118         e[i] = 0.0;
 119 #endif
 120     }
 121
 122     for (i = 0; (i < NDIM); i++)
 123     {
 124         for (m = 0; (m < NDIM); m++)
 125         {
 126             inten[i][m] = 0;
 127         }
 128     }
 129     for (i = 0; (i < n); i++)
 130     {
 131         ai           = index[i];
 132         mm           = atom[ai].m;
 133         rx           = x[ai][XX];
 134         ry           = x[ai][YY];
 135         rz           = x[ai][ZZ];
 136         inten[0][0] += mm*(gmx::square(ry)+gmx::square(rz));
 137         inten[1][1] += mm*(gmx::square(rx)+gmx::square(rz));
 138         inten[2][2] += mm*(gmx::square(rx)+gmx::square(ry));
 139         inten[1][0] -= mm*(ry*rx);
 140         inten[2][0] -= mm*(rx*rz);
 141         inten[2][1] -= mm*(rz*ry);
 142     }
 143     inten[0][1] = inten[1][0];
 144     inten[0][2] = inten[2][0];
 145     inten[1][2] = inten[2][1];
 146 #ifdef DEBUG
 147     ptrans("initial", inten, dd, e);
 148 #endif
 149
 150     for (i = 0; (i < DIM); i++)
 151     {
 152         for (m = 0; (m < DIM); m++)
 153         {
 154             trans[i][m] = inten[i][m];
 155         }
 156     }
 157
 158     /* Call numerical recipe routines */
 159     jacobi(inten, 3, dd, ev, &nrot);
 160 #ifdef DEBUG
 161     ptrans("jacobi", ev, dd, e);
 162 #endif
 163
 164     /* Sort eigenvalues in ascending order */
 165 #define SWAPPER(i)          \
 166     if (std::abs(dd[(i)+1]) < std::abs(dd[i])) {    \
 167         temp = dd[i];         \
 168         for (j = 0; (j < NDIM); j++) { tvec[j] = ev[j][i]; } \
 169         dd[i] = dd[(i)+1];          \
 170         for (j = 0; (j < NDIM); j++) { ev[j][i] = ev[j][(i)+1]; }        \
 171         dd[(i)+1] = temp;           \
 172         for (j = 0; (j < NDIM); j++) { ev[j][(i)+1] = tvec[j]; }         \
 173     }
 174     SWAPPER(0)
 175     SWAPPER(1)
 176     SWAPPER(0)
 177 #ifdef DEBUG
 178     ptrans("swap", ev, dd, e);
 179     t_trans(trans, dd, ev);
 180 #endif
 181
 182     for (i = 0; (i < DIM); i++)
 183     {
 184         d[i] = dd[i];
 185         for (m = 0; (m < DIM); m++)
 186         {
 187             trans[i][m] = ev[m][i];
 188         }
 189     }
 190
 191     for (i = 0; (i < NDIM); i++)
 192     {
 193         sfree(inten[i]);
 194         sfree(ev[i]);
 195     }
 196     sfree(inten);
 197     sfree(ev);
 198 }
 199
 200 void rotate_atoms(int gnx, const int *index, rvec x[], matrix trans)
 201 {
 202     real   xt, yt, zt;
 203     int    i, ii;
 204
 205     for (i = 0; (i < gnx); i++)
 206     {
 207         ii        = index ? index[i] : i;
 208         xt        = x[ii][XX];
 209         yt        = x[ii][YY];
 210         zt        = x[ii][ZZ];
 211         x[ii][XX] = trans[XX][XX]*xt+trans[XX][YY]*yt+trans[XX][ZZ]*zt;
 212         x[ii][YY] = trans[YY][XX]*xt+trans[YY][YY]*yt+trans[YY][ZZ]*zt;
 213         x[ii][ZZ] = trans[ZZ][XX]*xt+trans[ZZ][YY]*yt+trans[ZZ][ZZ]*zt;
 214     }
 215 }
 216
 217 real calc_xcm(const rvec x[], int gnx, const int *index, const t_atom *atom, rvec xcm,
 218               gmx_bool bQ)
 219 {
 220     int  i, ii, m;
 221     real m0, tm;
 222
 223     clear_rvec(xcm);
 224     tm = 0;
 225     for (i = 0; (i < gnx); i++)
 226     {
 227         ii = index ? index[i] : i;
 228         if (atom)
 229         {
 230             if (bQ)
 231             {
 232                 m0 = std::abs(atom[ii].q);
 233             }
 234             else
 235             {
 236                 m0 = atom[ii].m;
 237             }
 238         }
 239         else
 240         {
 241             m0 = 1;
 242         }
 243         tm += m0;
 244         for (m = 0; (m < DIM); m++)
 245         {
 246             xcm[m] += m0*x[ii][m];
 247         }
 248     }
 249     for (m = 0; (m < DIM); m++)
 250     {
 251         xcm[m] /= tm;
 252     }
 253
 254     return tm;
 255 }
 256
 257 real sub_xcm(rvec x[], int gnx, const int *index, const t_atom atom[], rvec xcm,
 258              gmx_bool bQ)
 259 {
 260     int  i, ii;
 261     real tm;
 262
 263     tm = calc_xcm(x, gnx, index, atom, xcm, bQ);
 264     for (i = 0; (i < gnx); i++)
 265     {
 266         ii = index ? index[i] : i;
 267         rvec_dec(x[ii], xcm);
 268     }
 269     return tm;
 270 }
 271
 272 void add_xcm(rvec x[], int gnx, const int *index, rvec xcm)
 273 {
 274     int  i, ii;
 275
 276     for (i = 0; (i < gnx); i++)
 277     {
 278         ii = index ? index[i] : i;
 279         rvec_inc(x[ii], xcm);
 280     }
 281 }
 282
 283 void orient_princ(const t_atoms *atoms, int isize, const int *index,
 284                   int natoms, rvec x[], rvec *v, rvec d)
 285 {
 286     int     i, m;
 287     rvec    xcm, prcomp;
 288     matrix  trans;
 289
 290     calc_xcm(x, isize, index, atoms->atom, xcm, FALSE);
 291     for (i = 0; i < natoms; i++)
 292     {
 293         rvec_dec(x[i], xcm);
 294     }
 295     principal_comp(isize, index, atoms->atom, x, trans, prcomp);
 296     if (d)
 297     {
 298         copy_rvec(prcomp, d);
 299     }
 300
 301     /* Check whether this trans matrix mirrors the molecule */
 302     if (det(trans) < 0)
 303     {
 304         for (m = 0; (m < DIM); m++)
 305         {
 306             trans[ZZ][m] = -trans[ZZ][m];
 307         }
 308     }
 309     rotate_atoms(natoms, nullptr, x, trans);
 310     if (v)
 311     {
 312         rotate_atoms(natoms, nullptr, v, trans);
 313     }
 314
 315     for (i = 0; i < natoms; i++)
 316     {
 317         rvec_inc(x[i], xcm);
 318     }
 319 }