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