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39 #include "gromacs/math/utilities.h"
41 #include "gromacs/math/vec.h"
44 #include "gromacs/linearalgebra/nrjac.h"
45 #include "gromacs/utility/fatalerror.h"
46 #include "gromacs/utility/smalloc.h"
48 real calc_similar_ind(gmx_bool bRho, int nind, atom_id *index, real mass[],
52 real m, tm, xs, xd, rs, rd;
57 for (j = 0; j < nind; j++)
69 for (d = 0; d < DIM; d++)
71 xd = x[i][d] - xp[i][d];
75 xs = x[i][d] + xp[i][d];
90 real rmsdev_ind(int nind, atom_id index[], real mass[], rvec x[], rvec xp[])
92 return calc_similar_ind(FALSE, nind, index, mass, x, xp);
95 real rmsdev(int natoms, real mass[], rvec x[], rvec xp[])
97 return calc_similar_ind(FALSE, natoms, NULL, mass, x, xp);
100 real rhodev_ind(int nind, atom_id index[], real mass[], rvec x[], rvec xp[])
102 return calc_similar_ind(TRUE, nind, index, mass, x, xp);
105 real rhodev(int natoms, real mass[], rvec x[], rvec xp[])
107 return calc_similar_ind(TRUE, natoms, NULL, mass, x, xp);
110 void calc_fit_R(int ndim, int natoms, real *w_rls, rvec *xp, rvec *x, matrix R)
112 int c, r, n, j, m, i, irot, s;
113 double **omega, **om;
114 double d[2*DIM], xnr, xpc;
120 if (ndim != 3 && ndim != 2)
122 gmx_fatal(FARGS, "calc_fit_R called with ndim=%d instead of 3 or 2", ndim);
127 for (i = 0; i < 2*ndim; i++)
129 snew(omega[i], 2*ndim);
133 for (i = 0; i < 2*ndim; i++)
136 for (j = 0; j < 2*ndim; j++)
143 /*calculate the matrix U*/
145 for (n = 0; (n < natoms); n++)
147 if ((mn = w_rls[n]) != 0.0)
149 for (c = 0; (c < ndim); c++)
152 for (r = 0; (r < ndim); r++)
155 u[c][r] += mn*xnr*xpc;
162 /*omega is symmetric -> omega==omega' */
163 for (r = 0; r < 2*ndim; r++)
165 for (c = 0; c <= r; c++)
167 if (r >= ndim && c < ndim)
169 omega[r][c] = u[r-ndim][c];
170 omega[c][r] = u[r-ndim][c];
180 /*determine h and k*/
181 jacobi(omega, 2*ndim, d, om, &irot);
182 /*real **omega = input matrix a[0..n-1][0..n-1] must be symmetric
183 * int natoms = number of rows and columns
184 * real NULL = d[0]..d[n-1] are the eigenvalues of a[][]
185 * real **v = v[0..n-1][0..n-1] contains the vectors in columns
186 * int *irot = number of jacobi rotations
189 if (debug && irot == 0)
191 fprintf(debug, "IROT=0\n");
194 index = 0; /* For the compiler only */
196 /* Copy only the first ndim-1 eigenvectors */
197 for (j = 0; j < ndim-1; j++)
200 for (i = 0; i < 2*ndim; i++)
209 for (i = 0; i < ndim; i++)
211 vh[j][i] = M_SQRT2*om[i][index];
212 vk[j][i] = M_SQRT2*om[i+ndim][index];
217 /* Calculate the last eigenvector as the outer-product of the first two.
218 * This insures that the conformation is not mirrored and
219 * prevents problems with completely flat reference structures.
221 cprod(vh[0], vh[1], vh[2]);
222 cprod(vk[0], vk[1], vk[2]);
226 /* Calculate the last eigenvector from the first one */
227 vh[1][XX] = -vh[0][YY];
228 vh[1][YY] = vh[0][XX];
229 vk[1][XX] = -vk[0][YY];
230 vk[1][YY] = vk[0][XX];
235 for (r = 0; r < ndim; r++)
237 for (c = 0; c < ndim; c++)
239 for (s = 0; s < ndim; s++)
241 R[r][c] += vk[s][r]*vh[s][c];
245 for (r = ndim; r < DIM; r++)
250 for (i = 0; i < 2*ndim; i++)
259 void do_fit_ndim(int ndim, int natoms, real *w_rls, rvec *xp, rvec *x)
265 /* Calculate the rotation matrix R */
266 calc_fit_R(ndim, natoms, w_rls, xp, x, R);
269 for (j = 0; j < natoms; j++)
271 for (m = 0; m < DIM; m++)
275 for (r = 0; r < DIM; r++)
278 for (c = 0; c < DIM; c++)
280 x[j][r] += R[r][c]*x_old[c];
286 void do_fit(int natoms, real *w_rls, rvec *xp, rvec *x)
288 do_fit_ndim(3, natoms, w_rls, xp, x);
291 void reset_x_ndim(int ndim, int ncm, const atom_id *ind_cm,
292 int nreset, const atom_id *ind_reset,
293 rvec x[], const real mass[])
301 gmx_incons("More than 3 dimensions not supported.");
307 for (i = 0; i < ncm; i++)
311 for (m = 0; m < ndim; m++)
313 xcm[m] += mm*x[ai][m];
320 for (i = 0; i < ncm; i++)
323 for (m = 0; m < ndim; m++)
325 xcm[m] += mm*x[i][m];
330 for (m = 0; m < ndim; m++)
335 if (ind_reset != NULL)
337 for (i = 0; i < nreset; i++)
339 rvec_dec(x[ind_reset[i]], xcm);
344 for (i = 0; i < nreset; i++)
351 void reset_x(int ncm, const atom_id *ind_cm,
352 int nreset, const atom_id *ind_reset,
353 rvec x[], const real mass[])
355 reset_x_ndim(3, ncm, ind_cm, nreset, ind_reset, x, mass);