src/gromacs/pulling/pull.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 /*! \libinternal \file
  39  *
  40  *
  41  * \brief
  42  * This file contains datatypes and function declarations necessary
  43    for mdrun to interface with the pull code.
  44  *
  45  * \author Berk Hess
  46  *
  47  * \inlibraryapi
  48  */
  49
  50 #ifndef GMX_PULLING_PULL_H
  51 #define GMX_PULLING_PULL_H
  52
  53 #include <cstdio>
  54
  55 #include "gromacs/math/vectypes.h"
  56 #include "gromacs/mdtypes/pull-params.h"
  57 #include "gromacs/pulling/pull_internal.h"
  58 #include "gromacs/utility/basedefinitions.h"
  59 #include "gromacs/utility/real.h"
  60
  61 #ifdef __cplusplus
  62 extern "C" {
  63 #endif
  64
  65 struct gmx_mtop_t;
  66 struct gmx_output_env_t;
  67 struct pull_params_t;
  68 struct t_commrec;
  69 struct t_filenm;
  70 struct t_inputrec;
  71 struct t_mdatoms;
  72 struct t_pbc;
  73
  74 /*! \brief Returns the units of the pull coordinate.
  75  *
  76  * \param[in] pcrd The pull coordinate to query the units for.
  77  * \returns a string with the units of the coordinate.
  78  */
  79 const char *pull_coordinate_units(const t_pull_coord *pcrd);
  80
  81 /*! \brief Returns the conversion factor from the pull coord init/rate unit to internal value unit.
  82  *
  83  * \param[in] pcrd The pull coordinate to get the conversion factor for.
  84  * \returns the conversion factor.
  85  */
  86 double pull_conversion_factor_userinput2internal(const t_pull_coord *pcrd);
  87
  88 /*! \brief Returns the conversion factor from the pull coord internal value unit to the init/rate unit.
  89  *
  90  * \param[in] pcrd The pull coordinate to get the conversion factor for.
  91  * \returns the conversion factor.
  92  */
  93 double pull_conversion_factor_internal2userinput(const t_pull_coord *pcrd);
  94
  95 /*! \brief Get the value for pull coord coord_ind.
  96  *
  97  * \param[in,out] pull      The pull struct.
  98  * \param[in]     coord_ind Number of the pull coordinate.
  99  * \param[in]     pbc       Information structure about periodicity.
 100  * \param[out]    value     The value of the pull coordinate.
 101  */
 102 void get_pull_coord_value(struct pull_t      *pull,
 103                           int                 coord_ind,
 104                           const struct t_pbc *pbc,
 105                           double             *value);
 106
 107
 108 /*! \brief Registers the provider of an external potential for a coordinate.
 109  *
 110  * This function is only used for checking the consistency of the pull setup.
 111  * For each pull coordinate of type external-potential, selected by the user
 112  * in the mdp file, there has to be a module that provides this potential.
 113  * The module registers itself as the provider by calling this function.
 114  * The passed \p provider string has to match the string that the user
 115  * passed with the potential-provider pull coordinate mdp option.
 116  * This function should be called after init_pull has been called and before
 117  * pull_potential is called for the first time.
 118  * This function does many consistency checks and when it returns and the
 119  * first call to do_potential passes, the pull setup is guaranteed to be
 120  * correct (unless the module doesn't call apply_external_pull_coord_force
 121  * every step or calls it with incorrect forces). This registering function
 122  * will exit with a (release) assertion failure when used incorrely or
 123  * with a fatal error when the user (mdp) input in inconsistent.
 124  *
 125  * \param[in,out] pull         The pull struct.
 126  * \param[in]     coord_index  The pull coordinate index to register the external potential for.
 127  * \param[in]     provider     Provider string, should match the potential-provider pull coordinate mdp option.
 128  */
 129 void register_external_pull_potential(struct pull_t *pull,
 130                                       int            coord_index,
 131                                       const char    *provider);
 132
 133
 134 /*! \brief Apply forces of an external potential to a pull coordinate.
 135  *
 136  * This function applies the external scalar force \p coord_force to
 137  * the pull coordinate, distributing it over the atoms in the groups
 138  * involved in the pull coordinate. The corresponding potential energy
 139  * value should be added to the pull or the module's potential energy term
 140  * separately by the module itself.
 141  * This function should be called after pull_potential has been called and,
 142  * obviously, before the coordinates are updated uses the forces.
 143  *
 144  * \param[in,out] pull           The pull struct.
 145  * \param[in]     coord_index    The pull coordinate index to set the force for.
 146  * \param[in]     coord_force    The scalar force for the pull coordinate.
 147  * \param[in]     mdatoms        Atom properties, only masses are used.
 148  * \param[in,out] force          The force buffer.
 149  * \param[in,out] virial         The virial, can be NULL.
 150  */
 151 void apply_external_pull_coord_force(struct pull_t   *pull,
 152                                      int              coord_index,
 153                                      double           coord_force,
 154                                      const t_mdatoms *mdatoms,
 155                                      rvec            *force,
 156                                      tensor           virial);
 157
 158
 159 /*! \brief Set the all the pull forces to zero.
 160  *
 161  * \param pull              The pull group.
 162  */
 163 void clear_pull_forces(struct pull_t *pull);
 164
 165
 166 /*! \brief Determine the COM pull forces and add them to f, return the potential
 167  *
 168  * \param[in,out] pull   The pull struct.
 169  * \param[in]     md     All atoms.
 170  * \param[in]     pbc    Information struct about periodicity.
 171  * \param[in]     cr     Struct for communication info.
 172  * \param[in]     t      Time.
 173  * \param[in]     lambda The value of lambda in FEP calculations.
 174  * \param[in]     x      Positions.
 175  * \param[in]     f      Forces.
 176  * \param[in,out] vir    The virial, which, if != NULL, gets a pull correction.
 177  * \param[out] dvdlambda Pull contribution to dV/d(lambda).
 178  *
 179  * \returns The pull potential energy.
 180  */
 181 real pull_potential(struct pull_t *pull, t_mdatoms *md, struct t_pbc *pbc,
 182                     t_commrec *cr, double t, real lambda,
 183                     rvec *x, rvec *f, tensor vir, real *dvdlambda);
 184
 185
 186 /*! \brief Constrain the coordinates xp in the directions in x
 187  * and also constrain v when v != NULL.
 188  *
 189  * \param[in,out] pull   The pull data.
 190  * \param[in]     md     All atoms.
 191  * \param[in]     pbc    Information struct about periodicity.
 192  * \param[in]     cr     Struct for communication info.
 193  * \param[in]     dt     The time step length.
 194  * \param[in]     t      The time.
 195  * \param[in]     x      Positions.
 196  * \param[in,out] xp     Updated x, can be NULL.
 197  * \param[in,out] v      Velocities, which may get a pull correction.
 198  * \param[in,out] vir    The virial, which, if != NULL, gets a pull correction.
 199  */
 200 void pull_constraint(struct pull_t *pull, t_mdatoms *md, struct t_pbc *pbc,
 201                      t_commrec *cr, double dt, double t,
 202                      rvec *x, rvec *xp, rvec *v, tensor vir);
 203
 204
 205 /*! \brief Make a selection of the home atoms for all pull groups.
 206  * Should be called at every domain decomposition.
 207  *
 208  * \param cr             Structure for communication info.
 209  * \param pull           The pull group.
 210  * \param md             All atoms.
 211  */
 212 void dd_make_local_pull_groups(t_commrec *cr,
 213                                struct pull_t *pull, t_mdatoms *md);
 214
 215
 216 /*! \brief Allocate, initialize and return a pull work struct.
 217  *
 218  * \param fplog       General output file, normally md.log.
 219  * \param pull_params The pull input parameters containing all pull settings.
 220  * \param ir          The inputrec.
 221  * \param nfile       Number of files.
 222  * \param fnm         Standard filename struct.
 223  * \param mtop        The topology of the whole system.
 224  * \param cr          Struct for communication info.
 225  * \param oenv        Output options.
 226  * \param lambda      FEP lambda.
 227  * \param bOutFile    Open output files?
 228  * \param Flags       Flags passed over from main, used to determine
 229  *                    whether or not we are appending.
 230  */
 231 struct pull_t *init_pull(FILE                   *fplog,
 232                          const pull_params_t    *pull_params,
 233                          const t_inputrec       *ir,
 234                          int                     nfile,
 235                          const t_filenm          fnm[],
 236                          const gmx_mtop_t       *mtop,
 237                          t_commrec             * cr,
 238                          const gmx_output_env_t *oenv,
 239                          real                    lambda,
 240                          gmx_bool                bOutFile,
 241                          unsigned long           Flags);
 242
 243
 244 /*! \brief Close the pull output files.
 245  *
 246  * \param pull       The pull group.
 247  */
 248 void finish_pull(struct pull_t *pull);
 249
 250
 251 /*! \brief Print the pull output (x and/or f)
 252  *
 253  * \param pull     The pull data structure.
 254  * \param step     Time step number.
 255  * \param time     Time.
 256  */
 257 void pull_print_output(struct pull_t *pull, gmx_int64_t step, double time);
 258
 259
 260 /*! \brief Calculates centers of mass all pull groups.
 261  *
 262  * \param[in] cr       Struct for communication info.
 263  * \param[in] pull     The pull data structure.
 264  * \param[in] md       All atoms.
 265  * \param[in] pbc      Information struct about periodicity.
 266  * \param[in] t        Time, only used for cylinder ref.
 267  * \param[in] x        The local positions.
 268  * \param[in,out] xp   Updated x, can be NULL.
 269  *
 270  */
 271 void pull_calc_coms(t_commrec        *cr,
 272                     struct pull_t    *pull,
 273                     t_mdatoms        *md,
 274                     struct t_pbc     *pbc,
 275                     double            t,
 276                     rvec              x[],
 277                     rvec             *xp);
 278
 279
 280 /*! \brief Returns if we have pull coordinates with potential pulling.
 281  *
 282  * \param[in] pull     The pull data structure.
 283  */
 284 gmx_bool pull_have_potential(const struct pull_t *pull);
 285
 286
 287 /*! \brief Returns if we have pull coordinates with constraint pulling.
 288  *
 289  * \param[in] pull     The pull data structure.
 290  */
 291 gmx_bool pull_have_constraint(const struct pull_t *pull);
 292
 293 /*! \brief Returns the maxing distance for pulling
 294  *
 295  * For distance geometries, only dimensions with pcrd->params[dim]=1
 296  * are included in the distance calculation.
 297  * For directional geometries, only dimensions with pcrd->vec[dim]!=0
 298  * are included in the distance calculation.
 299  *
 300  * \param[in] pcrd Pulling data structure
 301  * \param[in] pbc  Information on periodic boundary conditions
 302  * \returns The maximume distance
 303  */
 304 real max_pull_distance2(const pull_coord_work_t *pcrd,
 305                         const t_pbc             *pbc);
 306
 307 #ifdef __cplusplus
 308 }
 309 #endif
 310
 311 #endif