*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <config.h>
#endif
-
-#include <sysstuff.h>
-#include <string.h>
#include <math.h>
+#include <string.h>
+
#include "typedefs.h"
#include "smalloc.h"
#include "xvgr.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <typedefs.h>
+#include <math.h>
+
+#include "typedefs.h"
#include "smalloc.h"
#include "macros.h"
-#include <math.h>
#include "xvgr.h"
#include "gromacs/commandline/pargs.h"
#include "string2.h"
#include "index.h"
#include "pbc.h"
#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
#include "gstat.h"
#include "pbc.h"
#include "do_fit.h"
#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/trxio.h"
int gmx_helixorient(int argc, char *argv[])
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "thread_mpi/threads.h"
-#if ((defined(WIN32) || defined( _WIN32 ) || defined(WIN64) || defined( _WIN64 )) && !(defined (__CYGWIN__) || defined (__CYGWIN32__)))
-#include "windows.h"
+#ifdef GMX_NATIVE_WINDOWS
+#include <windows.h>
#endif
#ifdef GMX_GPU
#include <config.h>
#endif
-#include <sysstuff.h>
#include <ctype.h>
#include <errno.h>
#include <stdarg.h>
#include <string.h>
-#include "gromacs/fileio/futil.h"
+
#include "main.h"
#include "network.h"
#include "gmx_fatal.h"
#include "macros.h"
#include "string2.h"
#include "smalloc.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/legacyheaders/thread_mpi/threads.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <config.h>
#endif
-#include <gmx_random.h>
+#include "gmx_random.h"
#include <stdio.h>
#include <stdlib.h>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <limits.h>
#include "maths.h"
#ifdef HAVE__FINITE
-#include "float.h"
+#include <float.h>
#endif
int gmx_nint(real a)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <config.h>
#endif
-#include <sysstuff.h>
#include <string.h>
+
#include "typedefs.h"
#include "main.h"
#include "mvdata.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "smalloc.h"
#include "main.h"
#ifdef WITH_DMALLOC
-#include "dmalloc.h"
+#include <dmalloc.h>
#endif
#ifdef DEBUG
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <math.h>
#include <string.h>
-#include <smalloc.h>
-#include <vec.h>
+#include "smalloc.h"
+#include "vec.h"
-#include <histogram.h>
+#include "histogram.h"
/*! \internal \brief
* Stores data for a histogram.
#include <stdlib.h>
#include <string.h>
#ifdef WITH_DMALLOC
-#include "dmalloc.h"
+#include <dmalloc.h>
#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2009,2010,2012,2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \page displacements Displacement calculation routines
- *
- * Functions to calculate particle displacements as a function of time are
- * defined in displacement.h.
- * These functions allow one to easily calculate the displacement during a
- * single pass over the trajectory.
- * A new calculation is initialized with gmx_ana_displ_create().
- * For each frame, gmx_ana_displ_start_frame() needs to be called, followed by
- * a series of gmx_ana_displ_store() or a single call to
- * gmx_ana_displ_store_array(), gmx_ana_displ_store_all() or
- * gmx_ana_displ_store_pos().
- * The displacements for the current frame can then be calculated with
- * gmx_ana_displ_vector(), gmx_ana_displ_vectors() and/or
- * gmx_ana_displ_vectors_all().
- * These calculate the displacements from old positions to the ones on the
- * current frame.
- * The input frames should be evenly spaced, otherwise a fatal error is
- * reported. A time interval can be converted to a number of steps for
- * the calculation functions using gmx_ana_displ_time_to_steps().
- * When the structure is no longer required, gmx_ana_displ_free() can be used
- * to free the memory.
- *
- * The functions support calculation for dynamic selections:
- * when storing the positions, it is possible to specify whether a particle
- * is present or not.
- * This data is then accessible in the \p pout array returned by the
- * calculation functions.
- * Note that if you only call gmx_ana_displ_store() for the particles that are
- * present, use gmx_ana_displ_store_array(), or use positions calculated without
- * POS_MASKONLY for gmx_ana_displ_store_pos(), you should ensure that you
- * do not use the displacements for which \p pout is FALSE (the values cannot
- * be calculated based on the provided data, and are undefined).
- */
-/*! \internal \file
- * \brief Implementation of functions in displacement.h.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include <pbc.h>
-#include <smalloc.h>
-#include <vec.h>
-
-#include <displacement.h>
-#include <position.h>
-
-/*! \internal \brief
- * Internal structure used by the displacement calculation routines in
- * displacement.h.
- */
-typedef struct gmx_ana_displpos_t
-{
- /** Stored position vector. */
- rvec x;
- /** TRUE if there is something stored. */
- gmx_bool bPres;
-} gmx_ana_displpos_t;
-
-/*! \internal
- * \brief
- * Stores displacement calculation data and parameters.
- *
- * There data can be accessed only through the functions defined in
- * displacement.h.
- */
-struct gmx_ana_displ_t
-{
- /** Maximum number of particles for which the displacements are calculated. */
- int nmax;
- /** Maximum time for which the displacements are needed. */
- real tmax;
-
- /** TRUE if no frames have been read. */
- gmx_bool bFirst;
- /** Stores the time of the first frame. */
- real t0;
- /** Stores the time interval between frames. */
- real dt;
- /** Stores the time of the current frame. */
- real t;
- /** Stores the index in the store for the current positions. */
- int ci;
-
- /** Maximum number of positions to store for a particle. */
- int max_store;
- /** The total number of positions ever stored (can be larger than \p max_store). */
- int nstored;
- /** Two-dimensional array of stored positions, second index is the particle position. */
- gmx_ana_displpos_t **p;
- /** Pointer to the memory allocated for \p p. */
- gmx_ana_displpos_t *palloc;
-};
-
-/*!
- * \param[out] data Displacement calculation data structure pointer to
- * initialize.
- * \param[in] nmax Number of particles
- * for which displacements should be calculated.
- * \param[in] tmax Maximum interval (in same units as in the trajectory)
- * for which displacements are required.
- * \returns 0 on success.
- *
- * This function only allocates memory for the first frame;
- * gmx_ana_displ_start_frame() allocates a sufficient amount of memory for
- * storing all the required positions once it known the interval between
- * the trajectory frames.
- */
-int
-gmx_ana_displ_create(gmx_ana_displ_t **data, int nmax, real tmax)
-{
- gmx_ana_displ_t *d;
-
- snew(d, 1);
- d->nmax = nmax;
- d->tmax = tmax;
-
- d->bFirst = TRUE;
- d->t0 = 0;
- d->dt = 0;
- d->t = 0;
- d->ci = -1;
- d->nstored = 0;
-
- d->max_store = -1;
- snew(d->palloc, nmax);
- snew(d->p, 1);
- d->p[0] = d->palloc;
-
- *data = d;
- return 0;
-}
-
-/*!
- * \param[in,out] d Displacement calculation data.
- * \param[in] t Time for the new frame.
- * \returns 0 on success, -1 on failure.
- *
- * This function should be called at the beginning of each frame for which
- * atomic positions should be stored.
- * It is required that the times for which this function is called are
- * evenly spaced; otherwise, it reports a fatal error.
- */
-int
-gmx_ana_displ_start_frame(gmx_ana_displ_t *d, real t)
-{
- int i;
-
- /* Initialize times */
- if (d->bFirst)
- {
- d->t0 = t;
- }
- else if (d->dt <= 0)
- {
- d->dt = t - d->t0;
- }
- else
- {
- if (!gmx_within_tol(t - d->t, d->dt, GMX_REAL_EPS))
- {
- gmx_input("Trajectory not evenly spaced");
- return -1;
- }
- }
- d->t = t;
-
- /* Allocate memory for all the positions once it is possible */
- if (d->max_store == -1 && !d->bFirst)
- {
- d->max_store = (int)(d->tmax/d->dt + 1);
- srenew(d->palloc, d->nmax * d->max_store);
- sfree(d->p);
- snew(d->p, d->max_store);
- for (i = 0; i < d->max_store; ++i)
- {
- d->p[i] = &d->palloc[d->nmax*i];
- }
- }
-
- /* Increment the index where current positions are stored */
- d->ci++;
- if (d->ci >= d->max_store)
- {
- d->ci = 0;
- }
-
- for (i = 0; i < d->nmax; ++i)
- {
- d->p[d->ci][i].bPres = FALSE;
- }
- d->nstored++;
- d->bFirst = FALSE;
- return 0;
-}
-
-/*!
- * \param[in] d Displacement calculation data.
- * \param[in] time Time to convert to steps.
- * \param[out] steps The number of steps between the frames separated by
- * \p time, 0 if the number of steps cannot be determined.
- * \returns 0 on success (also if \p *steps is 0), -1 on error.
- *
- * \p *steps is set to zero if gmx_ana_displ_start_frame() has not yet been
- * called twice.
- * -1 is returned if \p time is not an integer multiple of the interval
- * between frames.
- */
-int
-gmx_ana_displ_time_to_steps(gmx_ana_displ_t *d, real time, int *steps)
-{
- if (d->dt <= 0)
- {
- *steps = 0;
- return 0;
- }
- if (!gmx_within_tol(fmod(time, d->dt), 0, GMX_REAL_EPS))
- {
- gmx_input("Interval not multiple of trajectory time step");
- return -1;
- }
- *steps = (int)(time / d->dt + 0.5);
- return 0;
-}
-
-/*!
- * \param[in,out] d Displacement calculation data.
- * \param[in] id Particle ID.
- * \param[in] x Particle position.
- * \param[in] bPres TRUE if the particle should be marked as present.
- * \returns 0 on success.
- */
-int
-gmx_ana_displ_store(gmx_ana_displ_t *d, atom_id id, rvec x, gmx_bool bPres)
-{
- copy_rvec(x, d->p[d->ci][id].x);
- d->p[d->ci][id].bPres = bPres;
- return 0;
-}
-
-/*!
- * \param[in,out] d Displacement calculation data.
- * \param[in] n Number of elements in the \p id and \p x arrays.
- * \param[in] id Particle IDs.
- * \param[in] x Particle positions.
- * \returns 0 on success.
- *
- * The positions of the given \p n particles are stored, and all of them
- * are marked as present.
- */
-int
-gmx_ana_displ_store_array(gmx_ana_displ_t *d, int n, atom_id id[], rvec x[])
-{
- int i;
-
- for (i = 0; i < n; ++i)
- {
- gmx_ana_displ_store(d, id[i], x[i], TRUE);
- }
- return 0;
-}
-
-/*!
- * \param[in,out] d Displacement calculation data.
- * \param[in] id Particle IDs.
- * \param[in] x Particle positions.
- * \returns 0 on success.
- *
- * Both the \p id and \p x arrays should have
- * \p nmax items, where \p nmax was provided for gmx_ana_displ_create(), and
- * the \p id[i] should be either \p i or -1.
- * If \p id[i]==-1, then that particle is marked as not present,
- * but the position is still stored.
- */
-int
-gmx_ana_displ_store_all(gmx_ana_displ_t *d, atom_id id[], rvec x[])
-{
- int i;
-
- for (i = 0; i < d->nmax; ++i)
- {
- gmx_ana_displ_store(d, i, x[i], id[i] >= 0);
- }
- return 0;
-}
-
-/*!
- * \param[in,out] d Displacement calculation data.
- * \param[in] p Particle positions.
- * \returns 0 on success.
- *
- * \p p should have at most \p nmax positions, where \p nmax was provided for
- * gmx_ana_displ_create().
- * If \p has exactly \p nmax positions, gmx_ana_displ_store_all() is called,
- * otherwise gmx_ana_displ_store_array() is used.
- */
-int
-gmx_ana_displ_store_pos(gmx_ana_displ_t *d, gmx_ana_pos_t *p)
-{
- if (p->nr == d->nmax)
- {
- gmx_ana_displ_store_all(d, p->m.refid, p->x);
- }
- else
- {
- gmx_ana_displ_store_array(d, p->nr, p->m.refid, p->x);
- }
- return 0;
-}
-
-/*! \brief
- * Finds the index in the displacement position storage array.
- *
- * \param[in] d Displacement calculation data.
- * \param[in] step Calculate the index of positions \p steps back.
- * \returns Index into the \ref gmx_ana_displ_t::p "d->p" array
- * that contains the positions \p steps back, -1 on error.
- *
- * If \p step is too large, -1 is returned.
- */
-static int
-find_store_index(gmx_ana_displ_t *d, int step)
-{
- int si;
-
- si = d->ci - step;
- if (si < 0)
- {
- si += d->max_store;
- }
- if (si < 0)
- {
- gmx_incons("Displacement requested for an interval too long");
- return -1;
- }
-
- return si;
-}
-
-/*!
- * \param[in] d Displacement calculation data.
- * \param[in] step Displacement is calculated from the location
- * \p step steps back.
- * \param[in] pbc Periodic boundary structure
- * (if NULL, PBC are not used in distance calculation).
- * \param[in] id Particle ID for which the displacement is calculated.
- * \param[in] x Current particle position.
- * \param[out] xout Displacement of the particle.
- * \param[out] pout TRUE if the old particle position was marked present.
- * If \p *pout is FALSE and the old particle position was not stored,
- * the value of \p xout is undefined.
- * Can be NULL, in which case the value is not stored.
- * \return 0 on success, -1 if less than \p step frames have been
- * stored or \p step <= 0, or EINVAL if \p step is too large.
- */
-int
-gmx_ana_displ_vector(gmx_ana_displ_t *d, int step, t_pbc *pbc,
- atom_id id, rvec x, rvec xout, gmx_bool *pout)
-{
- int si;
-
- if (step >= d->nstored || step <= 0)
- {
- return -1;
- }
- si = find_store_index(d, step);
- if (si == -1)
- {
- return EINVAL;
- }
- if (pout)
- {
- *pout = d->p[si][id].bPres;
- }
- if (pbc)
- {
- pbc_dx(pbc, x, d->p[si][id].x, xout);
- }
- else
- {
- rvec_sub(x, d->p[si][id].x, xout);
- }
- return 0;
-}
-
-/*!
- * \param[in] d Displacement calculation data.
- * \param[in] step Displacement is calculated from the location
- * \p step steps back.
- * \param[in] pbc Periodic boundary structure
- * (if NULL, PBC are not used in distance calculation).
- * \param[in] n Number of particles for which to calculate.
- * \param[in] id Particle IDs for which the displacement is calculated.
- * \param[in] x Current particle positions.
- * \param[out] xout Displacement of the particles.
- * \param[out] pout TRUE if the old particle position was marked present.
- * If \p pout[i] is FALSE and the old particle position was not stored,
- * the value of \p xout[i] is undefined.
- * Can be NULL, in which case the value is not stored.
- * \return 0 on success, -1 if less than \p step frames have been
- * stored or \p step <= 0, or EINVAL if \p step is too large.
- */
-int
-gmx_ana_displ_vectors(gmx_ana_displ_t *d, int step, t_pbc *pbc,
- int n, atom_id id[], rvec x[], rvec xout[], gmx_bool *pout)
-{
- int si, i;
-
- if (step >= d->nstored || step <= 0)
- {
- return -1;
- }
- si = find_store_index(d, step);
- if (si == -1)
- {
- return EINVAL;
- }
- for (i = 0; i < n; ++i)
- {
- if (pout)
- {
- pout[i] = d->p[si][id[i]].bPres;
- }
- if (pbc)
- {
- pbc_dx(pbc, x[i], d->p[si][id[i]].x, xout[i]);
- }
- else
- {
- rvec_sub(x[i], d->p[si][id[i]].x, xout[i]);
- }
- }
- return 0;
-}
-
-/*!
- * \param[in] d Displacement calculation data.
- * \param[in] step Displacement is calculated from the location
- * \p step steps back.
- * \param[in] pbc Periodic boundary structure
- * (if NULL, PBC are not used in distance calculation).
- * \param[in] x Current particle positions.
- * \param[out] xout Displacement of the particles.
- * \param[out] pout TRUE if the old particle position was marked present.
- * If \p pout[i] is FALSE and the old particle position was not stored,
- * the value of \p xout[i] is undefined.
- * Can be NULL, in which case the value is not stored.
- * \return 0 on success, -1 if less than \p step frames have been
- * stored or \p step <= 0, or EINVAL if \p step is too large.
- *
- * The \p x array should have \p nmax items, where \p nmax is the one provided
- * to init_displ_calc().
- */
-int
-gmx_ana_displ_vectors_all(gmx_ana_displ_t *d, int step, t_pbc *pbc,
- rvec x[], rvec xout[], gmx_bool *pout)
-{
- int si, i;
-
- if (step >= d->nstored || step <= 0)
- {
- return -1;
- }
- si = find_store_index(d, step);
- if (si == -1)
- {
- return EINVAL;
- }
- for (i = 0; i < d->nmax; ++i)
- {
- if (pout)
- {
- pout[i] = d->p[si][i].bPres;
- }
- if (pbc)
- {
- pbc_dx(pbc, x[i], d->p[si][i].x, xout[i]);
- }
- else
- {
- rvec_sub(x[i], d->p[si][i].x, xout[i]);
- }
- }
- return 0;
-}
-
-/*!
- * \param[in,out] d Displacement calculation data.
- *
- * After the call, the pointer \p d is invalid.
- */
-void
-gmx_ana_displ_free(gmx_ana_displ_t *d)
-{
- sfree(d->p);
- sfree(d->palloc);
- sfree(d);
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <config.h>
#endif
-#include <sysstuff.h>
#include <string.h>
+
#include "smalloc.h"
#include "copyrite.h"
#include "string2.h"
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2009,2010, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \file
- * \brief API for on-line calculation of displacements.
- *
- * The API is documented in more detail on a separate page:
- * \ref displacements
- *
- * The functions within this file can be used and developed independently of
- * the other parts of the library.
- * Other parts of the library do not reference these functions.
- */
-#ifndef DISPLACEMENT_H
-#define DISPLACEMENT_H
-
-#include "typedefs.h"
-
-#ifdef __cplusplus
-extern "C"
-{
-#endif
-
-/** Data structure for displacement calculation. */
-typedef struct gmx_ana_displ_t gmx_ana_displ_t;
-
-struct gmx_ana_pos_t;
-
-/** Allocates memory for displacement calculation. */
-int
-gmx_ana_displ_create(gmx_ana_displ_t **d, int nmax, real tmax);
-/** Initializes displacement calculation for a frame. */
-int
-gmx_ana_displ_start_frame(gmx_ana_displ_t *d, real t);
-/** Returns the number of steps corresponding to a given time interval. */
-int
-gmx_ana_displ_time_to_steps(gmx_ana_displ_t *d, real time, int *nsteps);
-/** Stores the position of a particle for displacement calculation. */
-int
-gmx_ana_displ_store(gmx_ana_displ_t *d, atom_id id, rvec x, gmx_bool bPres);
-/** Convenience function for storing an array of particle positions for displacement calculation. */
-int
-gmx_ana_displ_store_array(gmx_ana_displ_t *d, int n, atom_id id[], rvec x[]);
-/** Stores an array of particle positions for displacement calculation, including unselected particles. */
-int
-gmx_ana_displ_store_all(gmx_ana_displ_t *d, atom_id id[], rvec x[]);
-/** Convenience function for storing a set of positions from \c gmx_ana_pos_t. */
-int
-gmx_ana_displ_store_pos(gmx_ana_displ_t *d, struct gmx_ana_pos_t *p);
-/** Calculates the displacement vector for a particle. */
-int
-gmx_ana_displ_vector(gmx_ana_displ_t *d, int step, t_pbc *pbc,
- atom_id id, rvec x, rvec xout, gmx_bool *pout);
-/** Calculates the displacement vectors for a list of particles. */
-int
-gmx_ana_displ_vectors(gmx_ana_displ_t *d, int step, t_pbc *pbc,
- int n, atom_id id[], rvec x[],
- rvec xout[], gmx_bool *pout);
-/** Calculates the displacement vectors for all particles, including unselected. */
-int
-gmx_ana_displ_vectors_all(gmx_ana_displ_t *d, int step, t_pbc *pbc,
- rvec x[], rvec xout[], gmx_bool *pout);
-/** Frees the memory allocated for displacement calculation. */
-void
-gmx_ana_displ_free(gmx_ana_displ_t *d);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include <math.h>
#include <ctype.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
double
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include <ctype.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
float
#include <math.h>
#include <ctype.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dbdsdc,DBDSDC)(const char *uplo,
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dbdsqr,DBDSQR)(const char *uplo,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlaed6,DLAED6)(int *kniter,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
double
F77_FUNC(dlapy2,DLAPY2)(double * x, double * y)
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlarf,DLARF)(const char *side,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <ctype.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlartg,DLARTG)(double *f,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlasd2,DLASD2)(int *nl,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlasd4,DLASD4)(int *n,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlasq1,DLASQ1)(int *n,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
#ifdef _MSC_VER
#pragma warning(disable: 4723) /*division by zero - is used on purpose here*/
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlasq6,DLASQ6)(int *i0,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dlasv2,DLASV2)(double *f,
#include <ctype.h>
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dorml2,DORML2)(const char *side,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dstebz,DSTEBZ)(const char *range,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dstegr,DSTEGR)(const char *jobz,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dstein,DSTEIN)(int *n,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dsterf,DSTERF)(int *n,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(dtrtri,DTRTRI)(const char *uplo,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(sbdsdc,SBDSDC)(const char *uplo,
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(sbdsqr,SBDSQR)(const char *uplo,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slaed6,SLAED6)(int *kniter,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
float
F77_FUNC(slapy2,SLAPY2)(float * x, float * y)
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slarf,SLARF)(const char *side,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <ctype.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slartg,SLARTG)(float *f,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slasd2,SLASD2)(int *nl,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slasd4,SLASD4)(int *n,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slasq1,SLASQ1)(int *n,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
#ifdef _MSC_VER
#pragma warning(disable: 4723) /*division by zero - is used on purpose here*/
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slasq6,SLASQ6)(int *i0,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
void
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(slasv2,SLASV2)(float *f,
#include <ctype.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_lapack.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(sstebz,SSTEBZ)(const char *range,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(sstegr,SSTEGR)(const char *jobz,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(sstein,SSTEIN)(int *n,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(ssterf,SSTERF)(int *n,
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include <types/simple.h>
+#include "types/simple.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include <types/simple.h>
+#include "types/simple.h"
void
F77_FUNC(strtri,STRTRI)(const char *uplo,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <config.h>
#endif
-#include <sysstuff.h>
#include <string.h>
+
#include "typedefs.h"
#include "main.h"
#include "mvdata.h"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff