2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017,2019, 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.
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.
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.
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.
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.
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.
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,
59 gmx_trr_header_t head;
61 struct t_fileio* status;
68 /* read (reference (t=-1) and) average (t=0) structure */
69 status = gmx_trr_open(file, "r");
70 gmx_trr_read_frame_header(status, &head, &bOK);
71 *natoms = head.natoms;
73 gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
75 if ((head.t >= -1.1) && (head.t <= -0.9))
78 for (i = 0; i < *natoms; i++)
80 copy_rvec((*xav)[i], (*xref)[i]);
82 *bDMR = (head.lambda > 0.5);
83 *bFit = (head.lambda > -0.5);
86 fprintf(stderr, "Read %smass weighted reference structure with %d atoms from %s\n",
87 *bDMR ? "" : "non ", *natoms, file);
91 fprintf(stderr, "Eigenvectors in %s were determined without fitting\n", file);
95 gmx_trr_read_frame_header(status, &head, &bOK);
96 gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
103 *bDMA = (head.lambda > 0.5);
104 if ((head.t <= -0.01) || (head.t >= 0.01))
107 "WARNING: %s does not start with t=0, which should be the "
108 "average structure. This might not be a eigenvector file. "
109 "Some things might go wrong.\n",
114 fprintf(stderr, "Read %smass weighted average/minimum structure with %d atoms from %s\n",
115 *bDMA ? "" : "non ", *natoms, file);
120 snew(*eignr, snew_size);
121 snew(*eigval, snew_size);
122 snew(*eigvec, snew_size);
125 while (gmx_trr_read_frame_header(status, &head, &bOK))
127 gmx_trr_read_frame_data(status, &head, box, x, nullptr, nullptr);
128 if (*nvec >= snew_size)
131 srenew(*eignr, snew_size);
132 srenew(*eigval, snew_size);
133 srenew(*eigvec, snew_size);
136 (*eigval)[*nvec] = head.t;
137 (*eignr)[*nvec] = i - 1;
138 snew((*eigvec)[*nvec], *natoms);
139 for (i = 0; i < *natoms; i++)
141 copy_rvec(x[i], (*eigvec)[*nvec][i]);
146 gmx_trr_close(status);
147 fprintf(stderr, "Read %d eigenvectors (for %d atoms)\n\n", *nvec, *natoms);
151 void write_eigenvectors(const char* trrname,
164 struct t_fileio* trrout;
165 int ndim, i, j, d, vec;
173 fprintf(stderr, "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
174 (WriteXref == eWXR_YES) ? "reference, " : "", begin, end, trrname);
176 trrout = gmx_trr_open(trrname, "w");
177 if (WriteXref == eWXR_YES)
179 /* misuse lambda: 0/1 mass weighted fit no/yes */
180 gmx_trr_write_frame(trrout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, nullptr, nullptr);
182 else if (WriteXref == eWXR_NOFIT)
184 /* misuse lambda: -1 no fit */
185 gmx_trr_write_frame(trrout, -1, -1, -1.0, zerobox, natoms, x, nullptr, nullptr);
188 /* misuse lambda: 0/1 mass weighted analysis no/yes */
189 gmx_trr_write_frame(trrout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, nullptr, nullptr);
191 for (i = 0; i <= (end - begin); i++)
203 for (j = 0; j < natoms; j++)
205 for (d = 0; d < DIM; d++)
207 x[j][d] = mat[vec * ndim + DIM * j + d];
211 /* Store the eigenvalue in the time field */
212 gmx_trr_write_frame(trrout, begin + i, eigval[vec], 0, zerobox, natoms, x, nullptr, nullptr);
214 gmx_trr_close(trrout);