Add replacements for pbc enumerations
[gromacs.git] / src / gromacs / gmxana / eigio.cpp
blob416b9b4ca23c86ed4b9f11b3b367ae62321500d3
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37 #include "gmxpre.h"
39 #include "eigio.h"
41 #include "gromacs/fileio/tpxio.h"
42 #include "gromacs/fileio/trrio.h"
43 #include "gromacs/math/vec.h"
44 #include "gromacs/utility/futil.h"
45 #include "gromacs/utility/smalloc.h"
47 void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
48 rvec **xref, gmx_bool *bDMR,
49 rvec **xav, gmx_bool *bDMA,
50 int *nvec, int **eignr,
51 rvec ***eigvec, real **eigval)
53 gmx_trr_header_t head;
54 int i, snew_size;
55 struct t_fileio *status;
56 rvec *x;
57 matrix box;
58 gmx_bool bOK;
60 *bDMR = FALSE;
62 /* read (reference (t=-1) and) average (t=0) structure */
63 status = gmx_trr_open(file, "r");
64 gmx_trr_read_frame_header(status, &head, &bOK);
65 *natoms = head.natoms;
66 snew(*xav, *natoms);
67 gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
69 if ((head.t >= -1.1) && (head.t <= -0.9))
71 snew(*xref, *natoms);
72 for (i = 0; i < *natoms; i++)
74 copy_rvec((*xav)[i], (*xref)[i]);
76 *bDMR = (head.lambda > 0.5);
77 *bFit = (head.lambda > -0.5);
78 if (*bFit)
80 fprintf(stderr, "Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ", *natoms, file);
82 else
84 fprintf(stderr, "Eigenvectors in %s were determined without fitting\n", file);
85 sfree(*xref);
86 *xref = nullptr;
88 gmx_trr_read_frame_header(status, &head, &bOK);
89 gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
91 else
93 *bFit = TRUE;
94 *xref = nullptr;
96 *bDMA = (head.lambda > 0.5);
97 if ((head.t <= -0.01) || (head.t >= 0.01))
99 fprintf(stderr, "WARNING: %s does not start with t=0, which should be the "
100 "average structure. This might not be a eigenvector file. "
101 "Some things might go wrong.\n",
102 file);
104 else
106 fprintf(stderr,
107 "Read %smass weighted average/minimum structure with %d atoms from %s\n",
108 *bDMA ? "" : "non ", *natoms, file);
111 snew(x, *natoms);
112 snew_size = 10;
113 snew(*eignr, snew_size);
114 snew(*eigval, snew_size);
115 snew(*eigvec, snew_size);
117 *nvec = 0;
118 while (gmx_trr_read_frame_header(status, &head, &bOK))
120 gmx_trr_read_frame_data(status, &head, box, x, nullptr, nullptr);
121 if (*nvec >= snew_size)
123 snew_size += 10;
124 srenew(*eignr, snew_size);
125 srenew(*eigval, snew_size);
126 srenew(*eigvec, snew_size);
128 i = head.step;
129 (*eigval)[*nvec] = head.t;
130 (*eignr)[*nvec] = i-1;
131 snew((*eigvec)[*nvec], *natoms);
132 for (i = 0; i < *natoms; i++)
134 copy_rvec(x[i], (*eigvec)[*nvec][i]);
136 (*nvec)++;
138 sfree(x);
139 gmx_trr_close(status);
140 fprintf(stderr, "Read %d eigenvectors (for %d atoms)\n\n", *nvec, *natoms);
144 void write_eigenvectors(const char *trrname, int natoms, const real mat[],
145 gmx_bool bReverse, int begin, int end,
146 int WriteXref, const rvec *xref, gmx_bool bDMR,
147 const rvec xav[], gmx_bool bDMA, const real eigval[])
149 struct t_fileio *trrout;
150 int ndim, i, j, d, vec;
151 matrix zerobox;
152 rvec *x;
154 ndim = natoms*DIM;
155 clear_mat(zerobox);
156 snew(x, natoms);
158 fprintf (stderr,
159 "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
160 (WriteXref == eWXR_YES) ? "reference, " : "",
161 begin, end, trrname);
163 trrout = gmx_trr_open(trrname, "w");
164 if (WriteXref == eWXR_YES)
166 /* misuse lambda: 0/1 mass weighted fit no/yes */
167 gmx_trr_write_frame(trrout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, nullptr, nullptr);
169 else if (WriteXref == eWXR_NOFIT)
171 /* misuse lambda: -1 no fit */
172 gmx_trr_write_frame(trrout, -1, -1, -1.0, zerobox, natoms, x, nullptr, nullptr);
175 /* misuse lambda: 0/1 mass weighted analysis no/yes */
176 gmx_trr_write_frame(trrout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, nullptr, nullptr);
178 for (i = 0; i <= (end-begin); i++)
181 if (!bReverse)
183 vec = i;
185 else
187 vec = ndim-i-1;
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 gmx_trr_write_frame(trrout, begin+i, eigval[vec], 0, zerobox, natoms, x, nullptr, nullptr);
201 gmx_trr_close(trrout);
203 sfree(x);