2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2008, The GROMACS development team.
6 * Copyright (c) 2013,2014, 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.
38 /*! \libinternal \file
41 * Declares functions to enforce rotational motion upon a group of particles.
43 * \author Carsten Kutzner <ckutzne@gwdg.de>
48 #ifndef GMX_PULLING_PULL_ROTATION_H
49 #define GMX_PULLING_PULL_ROTATION_H
51 #include "gromacs/legacyheaders/typedefs.h"
52 #include "gromacs/timing/wallcycle.h"
53 #include "../fileio/filenm.h"
61 /*! \brief Initializes the enforced rotation groups.
63 * This routine does the memory allocation for various helper arrays, opens
64 * the output files etc.
66 * \param fplog General output file, normally md.log.
67 * \param ir Struct containing MD input parameters, among those
68 * also the enforced rotation parameters.
69 * \param nfile Number of entries in the fnm structure.
70 * \param fnm The filenames struct containing also the names
71 * of the rotation output files.
72 * \param cr Pointer to MPI communication data.
73 * \param x The positions of all MD particles.
74 * \param box The simulation box.
75 * \param mtop Molecular topology.
76 * \param oenv Needed to open the rotation output xvgr file.
77 * \param bVerbose Whether to print extra status information.
78 * \param Flags Flags passed over from main, used to determine
79 * whether or not we are doing a rerun.
81 extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
82 t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
83 gmx_bool bVerbose, unsigned long Flags);
86 /*! \brief Make a selection of the home atoms for all enforced rotation groups.
88 * This routine is similar to \ref dd_make_local_pull_groups, but works only with
89 * domain decomposition. It should be called at every domain decomposition.
91 * \param dd Structure containing domain decomposition data.
92 * \param rot Pointer to all the enforced rotation data.
94 extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot);
97 /*! \brief Calculates the enforced rotation potential(s).
99 * This is the main enforced rotation module which is called during every time
100 * step. Here the rotation potential as well as the resulting forces are
103 * \param cr Pointer to MPI communication data.
104 * \param ir Struct containing MD input parameters, among those
105 * \param box Simulation box, needed to make group whole.
106 * \param x The positions of all the local particles.
108 * \param step The time step.
109 * \param wcycle During the potential calculation the wallcycles are
110 * counted. Later they enter the dynamic load balancing.
111 * \param bNS After domain decomposition / neighbor searching several
112 * local arrays have to be updated (masses, shifts)
114 extern void do_rotation(t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
115 gmx_int64_t step, gmx_wallcycle_t wcycle, gmx_bool bNS);
118 /*! \brief Add the enforced rotation forces to the official force array.
120 * Adds the forces from enforced rotation potential to the local forces and
121 * sums up the contributions to the rotation potential from all the nodes. Since
122 * this needs communication, this routine should be called after the short range
123 * forces have been evaluated (in order not to spoil cycle counts).
124 * This routine also outputs data to the rotation output files (e.g.
125 * the potential, the angle of the group(s), and torques).
127 * \param rot Pointer to all the enforced rotation data.
128 * \param f The local forces to which the rotational forces have
130 * \param cr Pointer to MPI communication data.
131 * \param step The time step, used for output.
132 * \param t Time, used for output.
133 * \returns The potential energy of the rotation potentials.
135 extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_int64_t step, real t);
138 /*! \brief Close the enforced rotation output files.
140 * \param rot Pointer to all the enforced rotation data.
142 extern void finish_rot(t_rot *rot);