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41 #include "gromacs/utility/smalloc.h"
44 #include "gromacs/fileio/trnio.h"
45 #include "gromacs/fileio/tpxio.h"
46 #include "gromacs/fileio/futil.h"
48 void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
49 rvec **xref, gmx_bool *bDMR,
50 rvec **xav, gmx_bool *bDMA,
51 int *nvec, int **eignr,
52 rvec ***eigvec, real **eigval)
63 /* read (reference (t=-1) and) average (t=0) structure */
64 status = open_trn(file, "r");
65 fread_trnheader(status, &head, &bOK);
66 *natoms = head.natoms;
68 fread_htrn(status, &head, box, *xav, NULL, NULL);
70 if ((head.t >= -1.1) && (head.t <= -0.9))
73 for (i = 0; i < *natoms; i++)
75 copy_rvec((*xav)[i], (*xref)[i]);
77 *bDMR = (head.lambda > 0.5);
78 *bFit = (head.lambda > -0.5);
81 fprintf(stderr, "Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ", *natoms, file);
85 fprintf(stderr, "Eigenvectors in %s were determined without fitting\n", file);
89 fread_trnheader(status, &head, &bOK);
90 fread_htrn(status, &head, box, *xav, NULL, NULL);
97 *bDMA = (head.lambda > 0.5);
98 if ((head.t <= -0.01) || (head.t >= 0.01))
100 fprintf(stderr, "WARNING: %s does not start with t=0, which should be the "
101 "average structure. This might not be a eigenvector file. "
102 "Some things might go wrong.\n",
108 "Read %smass weighted average/minimum structure with %d atoms from %s\n",
109 *bDMA ? "" : "non ", *natoms, file);
114 snew(*eignr, snew_size);
115 snew(*eigval, snew_size);
116 snew(*eigvec, snew_size);
119 while (fread_trnheader(status, &head, &bOK))
121 fread_htrn(status, &head, box, x, NULL, NULL);
122 if (*nvec >= snew_size)
125 srenew(*eignr, snew_size);
126 srenew(*eigval, snew_size);
127 srenew(*eigvec, snew_size);
130 (*eigval)[*nvec] = head.t;
131 (*eignr)[*nvec] = i-1;
132 snew((*eigvec)[*nvec], *natoms);
133 for (i = 0; i < *natoms; i++)
135 copy_rvec(x[i], (*eigvec)[*nvec][i]);
140 fprintf(stderr, "Read %d eigenvectors (for %d atoms)\n\n", *nvec, *natoms);
144 void write_eigenvectors(const char *trnname, int natoms, real mat[],
145 gmx_bool bReverse, int begin, int end,
146 int WriteXref, rvec *xref, gmx_bool bDMR,
147 rvec xav[], gmx_bool bDMA, real eigval[])
150 int ndim, i, j, d, vec;
159 "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
160 (WriteXref == eWXR_YES) ? "reference, " : "",
161 begin, end, trnname);
163 trnout = open_tpx(trnname, "w");
164 if (WriteXref == eWXR_YES)
166 /* misuse lambda: 0/1 mass weighted fit no/yes */
167 fwrite_trn(trnout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, NULL, NULL);
169 else if (WriteXref == eWXR_NOFIT)
171 /* misuse lambda: -1 no fit */
172 fwrite_trn(trnout, -1, -1, -1.0, zerobox, natoms, x, NULL, NULL);
175 /* misuse lambda: 0/1 mass weighted analysis no/yes */
176 fwrite_trn(trnout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, NULL, NULL);
178 for (i = 0; i <= (end-begin); i++)
190 for (j = 0; j < natoms; j++)
192 for (d = 0; d < DIM; d++)
194 x[j][d] = mat[vec*ndim+DIM*j+d];
198 /* Store the eigenvalue in the time field */
199 fwrite_trn(trnout, begin+i, eigval[vec], 0, zerobox, natoms, x, NULL, NULL);