src/gromacs/pulling/pull.h

   1 /*
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  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/fileio/filenm.h"
  56 #include "gromacs/math/vectypes.h"
  57 #include "gromacs/utility/real.h"
  58
  59 #ifdef __cplusplus
  60 extern "C" {
  61 #endif
  62
  63 struct gmx_mtop_t;
  64 struct gmx_output_env_t;
  65 struct pull_params_t;
  66 struct t_inputrec;
  67 struct t_mdatoms;
  68 struct t_pbc;
  69
  70
  71 /*! \brief Get the value for pull coord coord_ind.
  72  *
  73  * \param[in,out] pull      The pull struct.
  74  * \param[in]     coord_ind Number of the pull coordinate.
  75  * \param[in]     pbc       Information structure about periodicity.
  76  * \param[out]    value     The value of the pull coordinate.
  77  */
  78 void get_pull_coord_value(struct pull_t      *pull,
  79                           int                 coord_ind,
  80                           const struct t_pbc *pbc,
  81                           double             *value);
  82
  83
  84 /*! \brief Set the reference value for a pull coord with rate!=0 to value_ref.
  85  *
  86  * This modifies the reference value. For potential (non-constraint) pulling,
  87  * a modification of the reference value at time t will lead to a different
  88  * force over t-dt/2 to t and over t to t+dt/2. To take this into account,
  89  * bUpdateForce=TRUE will update the force when this function is called
  90  * after calling pull_potential.
  91  * Note: can not be called for a pull coord with rate!=0.
  92  *
  93  * \param[in,out] pull         The pull struct.
  94  * \param[in]     coord_ind    The pull coordinate index to set.
  95  * \param[in]     value_ref    The reference value.
  96  * \param[in]     pbc          Information structure about periodicity.
  97  * \param[in]     md           Atom properties.
  98  * \param[in]     lambda       The value of lambda in FEP calculations.
  99  * \param[in]     bUpdateForce Update the force for the new reference value.
 100  * \param[in,out] f            The forces.
 101  * \param[in,out] vir          The virial, can be NULL.
 102  */
 103 void set_pull_coord_reference_value(struct pull_t *pull,
 104                                     int coord_ind, real value_ref,
 105                                     const struct t_pbc *pbc,
 106                                     const t_mdatoms *md,
 107                                     real lambda,
 108                                     gmx_bool bUpdateForce, rvec *f, tensor vir);
 109
 110
 111 /*! \brief Set the all the pull forces to zero.
 112  *
 113  * \param pull              The pull group.
 114  */
 115 void clear_pull_forces(struct pull_t *pull);
 116
 117
 118 /*! \brief Determine the COM pull forces and add them to f, return the potential
 119  *
 120  * \param[in,out] pull   The pull struct.
 121  * \param[in]     md     All atoms.
 122  * \param[in]     pbc    Information struct about periodicity.
 123  * \param[in]     cr     Struct for communication info.
 124  * \param[in]     t      Time.
 125  * \param[in]     lambda The value of lambda in FEP calculations.
 126  * \param[in]     x      Positions.
 127  * \param[in]     f      Forces.
 128  * \param[in,out] vir    The virial, which, if != NULL, gets a pull correction.
 129  * \param[out] dvdlambda Pull contribution to dV/d(lambda).
 130  *
 131  * \returns The pull potential energy.
 132  */
 133 real pull_potential(struct pull_t *pull, t_mdatoms *md, struct t_pbc *pbc,
 134                     t_commrec *cr, double t, real lambda,
 135                     rvec *x, rvec *f, tensor vir, real *dvdlambda);
 136
 137
 138 /*! \brief Constrain the coordinates xp in the directions in x
 139  * and also constrain v when v != NULL.
 140  *
 141  * \param[in,out] pull   The pull data.
 142  * \param[in]     md     All atoms.
 143  * \param[in]     pbc    Information struct about periodicity.
 144  * \param[in]     cr     Struct for communication info.
 145  * \param[in]     dt     The time step length.
 146  * \param[in]     t      The time.
 147  * \param[in]     x      Positions.
 148  * \param[in,out] xp     Updated x, can be NULL.
 149  * \param[in,out] v      Velocities, which may get a pull correction.
 150  * \param[in,out] vir    The virial, which, if != NULL, gets a pull correction.
 151  */
 152 void pull_constraint(struct pull_t *pull, t_mdatoms *md, struct t_pbc *pbc,
 153                      t_commrec *cr, double dt, double t,
 154                      rvec *x, rvec *xp, rvec *v, tensor vir);
 155
 156
 157 /*! \brief Make a selection of the home atoms for all pull groups.
 158  * Should be called at every domain decomposition.
 159  *
 160  * \param cr             Structure for communication info.
 161  * \param pull           The pull group.
 162  * \param md             All atoms.
 163  */
 164 void dd_make_local_pull_groups(t_commrec *cr,
 165                                struct pull_t *pull, t_mdatoms *md);
 166
 167
 168 /*! \brief Allocate, initialize and return a pull work struct.
 169  *
 170  * \param fplog       General output file, normally md.log.
 171  * \param pull_params The pull input parameters containing all pull settings.
 172  * \param ir          The inputrec.
 173  * \param nfile       Number of files.
 174  * \param fnm         Standard filename struct.
 175  * \param mtop        The topology of the whole system.
 176  * \param cr          Struct for communication info.
 177  * \param oenv        Output options.
 178  * \param lambda      FEP lambda.
 179  * \param bOutFile    Open output files?
 180  * \param Flags       Flags passed over from main, used to determine
 181  *                    whether or not we are appending.
 182  */
 183 struct pull_t *init_pull(FILE                   *fplog,
 184                          const pull_params_t    *pull_params,
 185                          const t_inputrec       *ir,
 186                          int                     nfile,
 187                          const t_filenm          fnm[],
 188                          gmx_mtop_t             *mtop,
 189                          t_commrec             * cr,
 190                          const gmx_output_env_t *oenv,
 191                          real                    lambda,
 192                          gmx_bool                bOutFile,
 193                          unsigned long           Flags);
 194
 195
 196 /*! \brief Close the pull output files.
 197  *
 198  * \param pull       The pull group.
 199  */
 200 void finish_pull(struct pull_t *pull);
 201
 202
 203 /*! \brief Print the pull output (x and/or f)
 204  *
 205  * \param pull     The pull data structure.
 206  * \param step     Time step number.
 207  * \param time     Time.
 208  */
 209 void pull_print_output(struct pull_t *pull, gmx_int64_t step, double time);
 210
 211
 212 /*! \brief Calculates centers of mass all pull groups.
 213  *
 214  * \param[in] cr       Struct for communication info.
 215  * \param[in] pull     The pull data structure.
 216  * \param[in] md       All atoms.
 217  * \param[in] pbc      Information struct about periodicity.
 218  * \param[in] t        Time, only used for cylinder ref.
 219  * \param[in] x        The local positions.
 220  * \param[in,out] xp   Updated x, can be NULL.
 221  *
 222  */
 223 void pull_calc_coms(t_commrec        *cr,
 224                     struct pull_t    *pull,
 225                     t_mdatoms        *md,
 226                     struct t_pbc     *pbc,
 227                     double            t,
 228                     rvec              x[],
 229                     rvec             *xp);
 230
 231
 232 /*! \brief Returns if we have pull coordinates with potential pulling.
 233  *
 234  * \param[in] pull     The pull data structure.
 235  */
 236 gmx_bool pull_have_potential(const struct pull_t *pull);
 237
 238
 239 /*! \brief Returns if we have pull coordinates with constraint pulling.
 240  *
 241  * \param[in] pull     The pull data structure.
 242  */
 243 gmx_bool pull_have_constraint(const struct pull_t *pull);
 244
 245 #ifdef __cplusplus
 246 }
 247 #endif
 248
 249 #endif