src/gromacs/gmxana/eigio.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   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, 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.
  10  *
  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.
  15  *
  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.
  20  *
  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.
  25  *
  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.
  33  *
  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.
  36  */
  37
  38 #ifndef _eigio_h
  39 #define _eigio_h
  40
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43 #include "gromacs/utility/real.h"
  44
  45 #ifdef __cplusplus
  46 extern "C"
  47 {
  48 #endif
  49
  50 enum {
  51     eWXR_NO, eWXR_YES, eWXR_NOFIT
  52 };
  53
  54 extern void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
  55                               rvec **xref, gmx_bool *bDMR,
  56                               rvec **xav, gmx_bool *bDMA,
  57                               int *nvec, int **eignr, rvec ***eigvec, real **eigval);
  58 /* Read eigenvectors from file into eigvec, the eigenvector numbers   */
  59 /* are stored in eignr.                                               */
  60 /* When bFit=FALSE no fitting was used in the covariance analysis.    */
  61 /* xref is the reference structure, can be NULL if not present.       */
  62 /* bDMR indicates mass weighted fit.                                  */
  63 /* xav is the average/minimum structure is written (t=0).             */
  64 /* bDMA indicates mass weighted analysis/eigenvectors.                */
  65
  66 extern void write_eigenvectors(const char *trrname, int natoms, const real mat[],
  67                                gmx_bool bReverse, int begin, int end,
  68                                int WriteXref, const rvec *xref, gmx_bool bDMR,
  69                                const rvec xav[], gmx_bool bDMA, const real *eigval);
  70 /* Write eigenvectors in mat to a TRR file.                           */
  71 /* The reference structure is written (t=-1) when WriteXref=eWXR_YES. */
  72 /* When WriteXref==eWXR_NOFIT a zero frame is written (t=-1),         */
  73 /* with lambda=-1.                                                    */
  74 /* bDMR indicates mass weighted fit.                                  */
  75 /* The average/minimum structure is written (t=0).                    */
  76 /* bDMA indicates mass weighted analysis/eigenvectors.                */
  77 /* eigenvectors with begin <= num <= end are written (num is base-1), */
  78 /* the timestamp of eigenvector num is num.                           */
  79 /* If bReverse==TRUE, num=1 is the last vector in mat.                */
  80
  81
  82 /* Read up to nmax eigenvalues from file fn, store the values in eigval[],
  83  * and the corresponding indices (start counting on 0) in eigvalnr[].
  84  * Returns the number of values read.
  85  */
  86 int read_eigval  (const char *          fn,
  87                   int                   nmax,
  88                   int                   eigvalnr[],
  89                   real                  eigval[]);
  90
  91 #ifdef __cplusplus
  92 }
  93 #endif
  94
  95 #endif