src/gmxlib/do_fit.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include "maths.h"
  41 #include "sysstuff.h"
  42 #include "typedefs.h"
  43 #include "nrjac.h"
  44 #include "vec.h"
  45 #include "txtdump.h"
  46 #include "smalloc.h"
  47 #include "do_fit.h"
  48
  49 #define EPS 1.0e-09
  50
  51 real calc_similar_ind(gmx_bool bRho,int nind,atom_id *index,real mass[],
  52                       rvec x[],rvec xp[])
  53 {
  54   int i, j, d;
  55   real m, tm, xs, xd, rs, rd;
  56
  57   tm=0;
  58   rs=0;
  59   rd=0;
  60   for(j=0; j<nind; j++) {
  61     if (index)
  62       i = index[j];
  63     else
  64       i = j;
  65     m = mass[i];
  66     tm += m;
  67     for(d=0 ; d<DIM; d++) {
  68       xd = x[i][d] - xp[i][d];
  69       rd += m * sqr(xd);
  70       if (bRho) {
  71         xs = x[i][d] + xp[i][d];
  72         rs += m * sqr(xs);
  73       }
  74     }
  75   }
  76   if (bRho)
  77     return 2*sqrt(rd/rs);
  78   else
  79     return sqrt(rd/tm);
  80 }
  81
  82 real rmsdev_ind(int nind,atom_id index[],real mass[],rvec x[],rvec xp[])
  83 {
  84   return calc_similar_ind(FALSE, nind, index, mass, x, xp);
  85 }
  86
  87 real rmsdev(int natoms,real mass[],rvec x[],rvec xp[])
  88 {
  89   return calc_similar_ind(FALSE, natoms, NULL, mass, x, xp);
  90 }
  91
  92 real rhodev_ind(int nind,atom_id index[],real mass[],rvec x[],rvec xp[])
  93 {
  94   return calc_similar_ind(TRUE, nind, index, mass, x, xp);
  95 }
  96
  97 real rhodev(int natoms,real mass[],rvec x[],rvec xp[])
  98 {
  99   return calc_similar_ind(TRUE, natoms, NULL, mass, x, xp);
 100 }
 101
 102 void calc_fit_R(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x,matrix R)
 103 {
 104   int    c,r,n,j,m,i,irot,s;
 105   double **omega,**om;
 106   double d[2*DIM],xnr,xpc;
 107   matrix vh,vk,u;
 108   real   mn;
 109   int    index;
 110   real   max_d;
 111
 112   if (ndim != 3 && ndim != 2)
 113     gmx_fatal(FARGS,"calc_fit_R called with ndim=%d instead of 3 or 2",ndim);
 114
 115   snew(omega,2*ndim);
 116   snew(om,2*ndim);
 117   for(i=0; i<2*ndim; i++) {
 118     snew(omega[i],2*ndim);
 119     snew(om[i],2*ndim);
 120   }
 121
 122   for(i=0; i<2*ndim; i++) {
 123     d[i]=0;
 124     for(j=0; j<2*ndim; j++) {
 125       omega[i][j]=0;
 126       om[i][j]=0;
 127     }
 128   }
 129
 130   /*calculate the matrix U*/
 131   clear_mat(u);
 132   for(n=0;(n<natoms);n++)
 133     if ((mn = w_rls[n]) != 0.0)
 134       for(c=0; (c<ndim); c++) {
 135         xpc=xp[n][c];
 136         for(r=0; (r<ndim); r++) {
 137           xnr=x[n][r];
 138           u[c][r]+=mn*xnr*xpc;
 139         }
 140       }
 141
 142   /*construct omega*/
 143   /*omega is symmetric -> omega==omega' */
 144   for(r=0; r<2*ndim; r++)
 145     for(c=0; c<=r; c++)
 146       if (r>=ndim && c<ndim) {
 147         omega[r][c]=u[r-ndim][c];
 148         omega[c][r]=u[r-ndim][c];
 149       } else {
 150         omega[r][c]=0;
 151         omega[c][r]=0;
 152       }
 153
 154   /*determine h and k*/
 155   jacobi(omega,2*ndim,d,om,&irot);
 156   /*real   **omega = input matrix a[0..n-1][0..n-1] must be symmetric
 157    *int     natoms = number of rows and columns
 158    *real      NULL = d[0]..d[n-1] are the eigenvalues of a[][]
 159    *real       **v = v[0..n-1][0..n-1] contains the vectors in columns
 160    *int      *irot = number of jacobi rotations
 161    */
 162
 163   if (debug && irot==0) fprintf(debug,"IROT=0\n");
 164
 165   index=0; /* For the compiler only */
 166
 167   /* Copy only the first ndim-1 eigenvectors */
 168   for(j=0; j<ndim-1; j++) {
 169     max_d=-1000;
 170     for(i=0; i<2*ndim; i++)
 171       if (d[i]>max_d) {
 172         max_d=d[i];
 173         index=i;
 174       }
 175     d[index]=-10000;
 176     for(i=0; i<ndim; i++) {
 177       vh[j][i]=M_SQRT2*om[i][index];
 178       vk[j][i]=M_SQRT2*om[i+ndim][index];
 179     }
 180   }
 181   if (ndim == 3) {
 182     /* Calculate the last eigenvector as the outer-product of the first two.
 183      * This insures that the conformation is not mirrored and
 184      * prevents problems with completely flat reference structures.
 185      */
 186     cprod(vh[0],vh[1],vh[2]);
 187     cprod(vk[0],vk[1],vk[2]);
 188   } else if (ndim == 2) {
 189     /* Calculate the last eigenvector from the first one */
 190     vh[1][XX] = -vh[0][YY];
 191     vh[1][YY] =  vh[0][XX];
 192     vk[1][XX] = -vk[0][YY];
 193     vk[1][YY] =  vk[0][XX];
 194   }
 195
 196   /* determine R */
 197   clear_mat(R);
 198   for(r=0; r<ndim; r++)
 199     for(c=0; c<ndim; c++)
 200       for(s=0; s<ndim; s++)
 201         R[r][c] += vk[s][r]*vh[s][c];
 202   for(r=ndim; r<DIM; r++)
 203     R[r][r] = 1;
 204
 205   for(i=0; i<2*ndim; i++) {
 206     sfree(omega[i]);
 207     sfree(om[i]);
 208   }
 209   sfree(omega);
 210   sfree(om);
 211 }
 212
 213 void do_fit_ndim(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x)
 214 {
 215   int    i,j,m,r,c;
 216   matrix R;
 217   rvec   x_old;
 218
 219   /* Calculate the rotation matrix R */
 220   calc_fit_R(ndim,natoms,w_rls,xp,x,R);
 221
 222   /*rotate X*/
 223   for(j=0; j<natoms; j++) {
 224     for(m=0; m<DIM; m++)
 225       x_old[m]=x[j][m];
 226     for(r=0; r<DIM; r++) {
 227       x[j][r]=0;
 228       for(c=0; c<DIM; c++)
 229         x[j][r]+=R[r][c]*x_old[c];
 230     }
 231   }
 232 }
 233
 234 void do_fit(int natoms,real *w_rls,rvec *xp,rvec *x)
 235 {
 236   do_fit_ndim(3,natoms,w_rls,xp,x);
 237 }
 238
 239 void reset_x_ndim(int ndim,int ncm,const atom_id *ind_cm,
 240                   int nreset,const atom_id *ind_reset,
 241                   rvec x[],const real mass[])
 242 {
 243     int  i,m,ai;
 244     rvec xcm;
 245     real tm,mm;
 246
 247     tm = 0.0;
 248     clear_rvec(xcm);
 249     if (ind_cm != NULL)
 250     {
 251         for(i=0; i<ncm; i++)
 252         {
 253             ai = ind_cm[i];
 254             mm = mass[ai];
 255             for(m=0; m<ndim; m++)
 256             {
 257                 xcm[m] += mm*x[ai][m];
 258             }
 259             tm += mm;
 260         }
 261     }
 262     else
 263     {
 264         for(i=0; i<ncm; i++)
 265         {
 266             mm = mass[i];
 267             for(m=0; m<ndim; m++)
 268             {
 269                 xcm[m] += mm*x[i][m];
 270             }
 271             tm += mm;
 272         }
 273     }
 274     for(m=0; m<ndim; m++)
 275     {
 276         xcm[m] /= tm;
 277     }
 278
 279     if (ind_reset != NULL)
 280     {
 281         for(i=0; i<nreset; i++)
 282         {
 283             rvec_dec(x[ind_reset[i]],xcm);
 284         }
 285     }
 286     else
 287     {
 288         for(i=0; i<nreset; i++)
 289         {
 290             rvec_dec(x[i],xcm);
 291         }
 292     }
 293 }
 294
 295 void reset_x(int ncm,const atom_id *ind_cm,
 296              int nreset,const atom_id *ind_reset,
 297              rvec x[],const real mass[])
 298 {
 299     reset_x_ndim(3,ncm,ind_cm,nreset,ind_reset,x,mass);
 300 }