src/gromacs/mdlib/constr.h

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  38 /*! \libinternal \file
  39  * \brief Declares interface to constraint code.
  40  *
  41  * \author Berk Hess <hess@kth.se>
  42  * \author Mark Abraham <mark.j.abraham@gmail.com>
  43  * \ingroup module_mdlib
  44  * \inlibraryapi
  45  */
  46
  47 #ifndef GMX_MDLIB_CONSTR_H
  48 #define GMX_MDLIB_CONSTR_H
  49
  50 #include <cstdio>
  51
  52 #include "gromacs/math/vectypes.h"
  53 #include "gromacs/topology/idef.h"
  54 #include "gromacs/utility/arrayref.h"
  55 #include "gromacs/utility/basedefinitions.h"
  56 #include "gromacs/utility/classhelpers.h"
  57 #include "gromacs/utility/gmxassert.h"
  58 #include "gromacs/utility/real.h"
  59
  60 struct gmx_edsam;
  61 struct gmx_localtop_t;
  62 struct gmx_moltype_t;
  63 struct gmx_mtop_t;
  64 struct gmx_multisim_t;
  65 struct gmx_wallcycle;
  66 struct pull_t;
  67 struct t_commrec;
  68 struct t_ilist;
  69 struct t_inputrec;
  70 struct t_nrnb;
  71 struct t_pbc;
  72 class t_state;
  73
  74 namespace gmx
  75 {
  76 template<typename T>
  77 class ArrayRefWithPadding;
  78 template<typename>
  79 class ListOfLists;
  80
  81 //! Describes supported flavours of constrained updates.
  82 enum class ConstraintVariable : int
  83 {
  84     Positions,     /* Constrain positions (mass weighted)             */
  85     Velocities,    /* Constrain velocities (mass weighted)            */
  86     Derivative,    /* Constrain a derivative (mass weighted),         *
  87                     * for instance velocity or acceleration,          *
  88                     * constraint virial can not be calculated.        */
  89     Deriv_FlexCon, /* As Derivative, but only output flex. con.       */
  90     Force,         /* Constrain forces (non mass-weighted)            */
  91     // TODO What does this do? Improve the comment.
  92     ForceDispl /* Like Force, but free particles will have mass
  93                 * 1 and frozen particles mass 0                   */
  94 };
  95
  96 /*! \libinternal
  97  * \brief Handles constraints */
  98 class Constraints
  99 {
 100 private:
 101     /*! \brief Constructor
 102      *
 103      * Private to enforce use of makeConstraints() factory
 104      * function. */
 105     Constraints(const gmx_mtop_t&     mtop,
 106                 const t_inputrec&     ir,
 107                 pull_t*               pull_work,
 108                 FILE*                 log,
 109                 const t_commrec*      cr,
 110                 const gmx_multisim_t* ms,
 111                 t_nrnb*               nrnb,
 112                 gmx_wallcycle*        wcycle,
 113                 bool                  pbcHandlingRequired,
 114                 int                   numConstraints,
 115                 int                   numSettles);
 116
 117 public:
 118     /*! \brief This member type helps implement a factory
 119      * function, because its objects can access the private
 120      * constructor. */
 121     struct CreationHelper;
 122
 123     ~Constraints();
 124
 125     /*! \brief Returns the total number of flexible constraints in the system. */
 126     int numFlexibleConstraints() const;
 127
 128     /*! \brief Returns whether the system contains perturbed constraints */
 129     bool havePerturbedConstraints() const;
 130
 131     /*! \brief Set up all the local constraints for the domain.
 132      *
 133      * \todo Make this a callback that is called automatically
 134      * once a new domain has been made. */
 135     void setConstraints(gmx_localtop_t* top,
 136                         int             numAtoms,
 137                         int             numHomeAtoms,
 138                         real*           masses,
 139                         real*           inverseMasses,
 140                         bool            hasMassPerturbedAtoms,
 141                         real            lambda,
 142                         unsigned short* cFREEZE);
 143
 144     /*! \brief Applies constraints to coordinates.
 145      *
 146      * When econq=ConstraintVariable::Positions constrains
 147      * coordinates xprime using the directions in x, min_proj is
 148      * not used.
 149      *
 150      * When econq=ConstraintVariable::Derivative, calculates the
 151      * components xprime in the constraint directions and
 152      * subtracts these components from min_proj.  So when
 153      * min_proj=xprime, the constraint components are projected
 154      * out.
 155      *
 156      * When econq=ConstraintVariable::Deriv_FlexCon, the same is
 157      * done as with ConstraintVariable::Derivative, but only the
 158      * components of the flexible constraints are stored.
 159      *
 160      * delta_step is used for determining the constraint reference lengths
 161      * when lenA != lenB or will the pull code with a pulling rate.
 162      * step + delta_step is the step at which the final configuration
 163      * is meant to be; for update delta_step = 1.
 164      *
 165      * step_scaling can be used to update coordinates based on the time
 166      * step multiplied by this factor. Thus, normally 1.0 is passed. The
 167      * SD1 integrator uses 0.5 in one of its calls, to correct positions
 168      * for half a step of changed velocities.
 169      *
 170      * If v!=NULL also constrain v by adding the constraint corrections / dt.
 171      *
 172      * If computeVirial is true, calculate the constraint virial.
 173      *
 174      * Return whether the application of constraints succeeded without error.
 175      *
 176      * /note x is non-const, because non-local atoms need to be communicated.
 177      */
 178     bool apply(bool                      bLog,
 179                bool                      bEner,
 180                int64_t                   step,
 181                int                       delta_step,
 182                real                      step_scaling,
 183                ArrayRefWithPadding<RVec> x,
 184                ArrayRefWithPadding<RVec> xprime,
 185                ArrayRef<RVec>            min_proj,
 186                const matrix              box,
 187                real                      lambda,
 188                real*                     dvdlambda,
 189                ArrayRefWithPadding<RVec> v,
 190                bool                      computeVirial,
 191                tensor                    constraintsVirial,
 192                ConstraintVariable        econq);
 193     //! Links the essentialdynamics and constraint code.
 194     void saveEdsamPointer(gmx_edsam* ed);
 195     //! Getter for use by domain decomposition.
 196     ArrayRef<const ListOfLists<int>> atom2constraints_moltype() const;
 197     //! Getter for use by domain decomposition.
 198     ArrayRef<const std::vector<int>> atom2settle_moltype() const;
 199
 200     /*! \brief Return the data for reduction for determining
 201      * constraint RMS relative deviations, or an empty ArrayRef
 202      * when not supported for any active constraints. */
 203     ArrayRef<real> rmsdData() const;
 204     /*! \brief Return the RMSD of the constraints when available. */
 205     real rmsd() const;
 206
 207     /*! \brief Get the total number of constraints.
 208      *
 209      * \returns Total number of constraints, including SETTLE and LINCS/SHAKE constraints.
 210      */
 211     int numConstraintsTotal();
 212
 213 private:
 214     //! Implementation type.
 215     class Impl;
 216     //! Implementation object.
 217     PrivateImplPointer<Impl> impl_;
 218 };
 219
 220 /*! \brief Generate a fatal error because of too many LINCS/SETTLE warnings. */
 221 [[noreturn]] void too_many_constraint_warnings(int eConstrAlg, int warncount);
 222
 223 /*! \brief Returns whether constraint with parameter \p iparamsIndex is a flexible constraint */
 224 static inline bool isConstraintFlexible(ArrayRef<const t_iparams> iparams, int iparamsIndex)
 225 {
 226     return (iparams[iparamsIndex].constr.dA == 0 && iparams[iparamsIndex].constr.dB == 0);
 227 };
 228
 229 /* The at2con t_blocka struct returned by the routines below
 230  * contains a list of constraints per atom.
 231  * The F_CONSTRNC constraints in this structure number consecutively
 232  * after the F_CONSTR constraints.
 233  */
 234
 235 /*! \brief Tells make_at2con how to treat flexible constraints */
 236 enum class FlexibleConstraintTreatment
 237 {
 238     Include, //!< Include all flexible constraints
 239     Exclude  //!< Exclude all flexible constraints
 240 };
 241
 242 /*! \brief Returns the flexible constraint treatment depending on whether the integrator is dynamic */
 243 FlexibleConstraintTreatment flexibleConstraintTreatment(bool haveDynamicsIntegrator);
 244
 245 /*! \brief Returns a ListOfLists object to go from atoms to constraints
 246  *
 247  * The object will contain constraint indices with lower indices
 248  * directly matching the order in F_CONSTR and higher indices matching
 249  * the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.
 250  *
 251  * \param[in]  moltype   The molecule data
 252  * \param[in]  iparams   Interaction parameters, can be null when
 253  *                       \p flexibleConstraintTreatment==Include
 254  * \param[in]  flexibleConstraintTreatment  The flexible constraint treatment,
 255  *                                          see enum above
 256  *
 257  * \returns a ListOfLists object with all constraints for each atom
 258  */
 259 ListOfLists<int> make_at2con(const gmx_moltype_t&           moltype,
 260                              gmx::ArrayRef<const t_iparams> iparams,
 261                              FlexibleConstraintTreatment    flexibleConstraintTreatment);
 262
 263 /*! \brief Returns a ListOfLists object to go from atoms to constraints
 264  *
 265  * The object will contain constraint indices with lower indices
 266  * directly matching the order in F_CONSTR and higher indices matching
 267  * the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.
 268  *
 269  * \param[in]  numAtoms  The number of atoms to construct the list for
 270  * \param[in]  ilist     Interaction list, size F_NRE
 271  * \param[in]  iparams   Interaction parameters, can be null when
 272  *                       \p flexibleConstraintTreatment==Include
 273  * \param[in]  flexibleConstraintTreatment  The flexible constraint treatment,
 274  *                                          see enum above
 275  *
 276  * \returns a ListOfLists object with all constraints for each atom
 277  */
 278 ListOfLists<int> make_at2con(int                             numAtoms,
 279                              ArrayRef<const InteractionList> ilist,
 280                              ArrayRef<const t_iparams>       iparams,
 281                              FlexibleConstraintTreatment     flexibleConstraintTreatment);
 282
 283 //! Return the number of flexible constraints in the \c ilist and \c iparams.
 284 int countFlexibleConstraints(ArrayRef<const InteractionList> ilist, ArrayRef<const t_iparams> iparams);
 285
 286 /*! \brief Returns the constraint iatoms for a constraint number con
 287  * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 288  * are concatenated. */
 289 inline const int* constr_iatomptr(gmx::ArrayRef<const int> iatom_constr,
 290                                   gmx::ArrayRef<const int> iatom_constrnc,
 291                                   int                      con)
 292 {
 293     if (con * 3 < iatom_constr.ssize())
 294     {
 295         return iatom_constr.data() + con * 3;
 296     }
 297     else
 298     {
 299         return iatom_constrnc.data() + con * 3 - iatom_constr.size();
 300     }
 301 };
 302
 303 /*! \brief Returns whether there are inter charge group constraints */
 304 bool inter_charge_group_constraints(const gmx_mtop_t& mtop);
 305
 306 /*! \brief Returns whether there are inter charge group settles */
 307 bool inter_charge_group_settles(const gmx_mtop_t& mtop);
 308
 309 /*! \brief Constrain the initial coordinates and velocities */
 310 void do_constrain_first(FILE*                     log,
 311                         gmx::Constraints*         constr,
 312                         const t_inputrec*         inputrec,
 313                         int                       numAtoms,
 314                         int                       numHomeAtoms,
 315                         ArrayRefWithPadding<RVec> x,
 316                         ArrayRefWithPadding<RVec> v,
 317                         const matrix              box,
 318                         real                      lambda);
 319
 320 /* the dvdlambda contribution to be added to the bonded interactions */
 321 void constrain_velocities(gmx::Constraints* constr,
 322                           bool              do_log,
 323                           bool              do_ene,
 324                           int64_t           step,
 325                           t_state*          state,
 326                           real*             dvdlambda,
 327                           gmx_bool          computeVirial,
 328                           tensor            constraintsVirial);
 329
 330 /* the dvdlambda contribution to be added to the bonded interactions */
 331 void constrain_coordinates(gmx::Constraints*         constr,
 332                            bool                      do_log,
 333                            bool                      do_ene,
 334                            int64_t                   step,
 335                            t_state*                  state,
 336                            ArrayRefWithPadding<RVec> xp,
 337                            real*                     dvdlambda,
 338                            gmx_bool                  computeVirial,
 339                            tensor                    constraintsVirial);
 340
 341 } // namespace gmx
 342
 343 #endif