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36 #ifndef GROMACS_RESTRAINTMDMODULE_IMPL_H
37 #define GROMACS_RESTRAINTMDMODULE_IMPL_H
39 /*! \libinternal \file
40 * \brief Implementation details for RestraintMDModule
42 * \author M. Eric Irrgang <ericirrgang@gmail.com>
44 * \ingroup module_restraint
50 #include "gromacs/domdec/domdec_struct.h"
51 #include "gromacs/domdec/ga2la.h"
52 #include "gromacs/gmxlib/network.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/mdtypes/commrec.h"
55 #include "gromacs/mdtypes/iforceprovider.h"
56 #include "gromacs/mdtypes/imdmodule.h"
57 #include "gromacs/mdtypes/imdoutputprovider.h"
58 #include "gromacs/mdtypes/imdpoptionprovider.h"
59 #include "gromacs/mdtypes/mdatom.h"
60 #include "gromacs/pbcutil/pbc.h"
61 #include "gromacs/restraint/restraintpotential.h"
62 #include "gromacs/utility/arrayref.h"
68 * \brief Abstraction for a restraint interaction site.
70 * A restraint may operate on a single atom or some other entity, such as a selection of atoms.
71 * The Restraint implementation is very independent from how coordinates are provided or what they mean.
73 * First implementation can only represent single atoms in a global context.
75 * Ultimately, this should be replaced with a more universal facility for acting
76 * on distributed atom data or simple transformations thereof.
79 * \ingroup module_restraint
84 /*! \brief Construct from global atom indices
86 * \param globalIndex Atom index in the global state (as input to the simulation)
88 explicit Site(int globalIndex
) : index_(globalIndex
), r_(0, 0, 0) {}
91 * \brief Explicitly define copies.
93 * Implicit definition is not possible because of the mutex member,
94 * and a copy constructor is necessary to use Site in a std::vector. Really, we should make
95 * a copy point to the same implementation object to reuse its cache.
98 Site(const Site
& site
) : index_(site
.index_
), r_(site
.r_
) {}
100 /*! \brief Disallow assignment.
102 * Assignment doesn't make sense because it implies that a site's meaning is fuzzy.
103 * If the definition of a site is changing, just make a new site.
104 * There's nothing to be gained by reusing one or by creating it uninitialized.
106 Site
& operator=(const Site
&) = delete;
109 * \brief Get the global atom index of an atomic site.
111 * \return global index provided at construction.
114 int index() const { return index_
; }
117 * \brief Get the position of this site at time t.
119 * \param cr Communications record.
120 * \param nx Number of locally available atoms (size of local atom data arrays)
121 * \param x Array of locally available atom coordinates.
122 * \param t the current time.
123 * \return position vector.
126 * By providing the current time, we can cache results in order to use them once per timestep.
127 * In the long term, we would prefer to also allow client code to preregister interest in a
128 * position at a given time, or issue "futures".
130 RVec
centerOfMass(const t_commrec
& cr
, size_t nx
, ArrayRef
<const RVec
> x
, double gmx_unused t
)
132 // Center of mass to return for the site. Currently the only form of site
133 // implemented is as a global atomic coordinate.
134 gmx::RVec r
= { 0, 0, 0 };
135 if (DOMAINDECOMP(&cr
)) // Domain decomposition
137 // Get global-to-local indexing structure
138 auto crossRef
= cr
.dd
->ga2la
;
139 GMX_ASSERT(crossRef
, "Domain decomposition must provide global/local cross-reference.");
140 if (const auto localIndex
= crossRef
->findHome(index_
))
142 GMX_ASSERT(localIndex
,
143 "Expect not to reach this point if findHome does not find index_.");
144 GMX_ASSERT(*localIndex
< static_cast<decltype(*localIndex
)>(nx
),
145 "We assume that the local index cannot be larger than the number of "
147 GMX_ASSERT(*localIndex
>= 0, "localIndex is a signed type, but is assumed >0.");
148 // If atom is local, get its location
149 copy_rvec(x
[*localIndex
], r
);
153 // Nothing to contribute on this rank. Leave position == [0,0,0].
155 // AllReduce across the ranks of the simulation to get the center-of-mass
156 // of the site locally available everywhere. For single-atom sites, this
157 // is trivial: exactly one rank should have a non-zero position.
158 // For future multi-atom selections,
159 // we will receive weighted center-of-mass contributions from
160 // each rank and combine to get the global center of mass.
161 // \todo use generalized "pull group" facility when available.
162 std::array
<double, 3> buffer
{ { r
[0], r
[1], r
[2] } };
163 // This should be an all-reduce sum, which gmx_sumd appears to be.
164 gmx_sumd(3, buffer
.data(), &cr
);
165 r
[0] = static_cast<real
>(buffer
[0]);
166 r
[1] = static_cast<real
>(buffer
[1]);
167 r
[2] = static_cast<real
>(buffer
[2]);
169 } // end domain decomposition branch
172 // No DD so all atoms are local.
173 copy_rvec(x
[index_
], r
);
176 // Update cache and cache status.
184 * \brief Global index of the single-atom site.
186 * \todo This class should be a specialization of a more general Site data source.
187 * \todo use LocalAtomSet
192 * \brief Last known value of the center-of-mass.
194 * Updated with centerOfMass().
200 * \brief Provide IForceProvider for RestraintMDModuleImpl
202 * Adapter class from IForceProvider to IRestraintPotential.
203 * Objects of this type are uniquely owned by instances of RestraintMDModuleImpl. The object will
204 * dispatch calls to IForceProvider->calculateForces() to the functor managed by
205 * RestraintMDModuleImpl. \ingroup module_restraint
207 class RestraintForceProvider final
: public gmx::IForceProvider
211 * \brief Can only be constructed when initialized from a restraint.
213 RestraintForceProvider() = delete;
215 ~RestraintForceProvider() = default;
218 * \brief RAII construction with an IRestraintPotential
220 * Note, this object must outlive the pointer that will be provided to ForceProviders.
221 * \param restraint handle to an object providing restraint potential calculation
222 * \param sites List of atomic site indices
224 explicit RestraintForceProvider(std::shared_ptr
<gmx::IRestraintPotential
> restraint
,
225 const std::vector
<int>& sites
);
228 * \brief Implement the IForceProvider interface.
230 * Update the force array with restraint contribution(s) for local atoms.
232 * RestraintForceProvider is implemented with the assumption that few
233 * restraints apply to many atoms.
234 * That is, the number of restraints affecting a large number of atoms is small,
235 * though there may be several restraints that apply to few atoms each.
236 * Under this assumption, it is considered computationally inexpensive to iterate
237 * over restraints in an outer loop and iterate over atoms within each restraint.
238 * This would be an invalid assumption if, say, several restraints applied
239 * to an entire membrane or the entire solvent group.
241 * If the assumption causes performance problems, we can look for a good
242 * way to reduce from several restraints in a single pass or a very
243 * lightweight way to determine whether a given restraint applies to a given atom.
244 * There is also the notion in the pulling code of a limited number of
245 * "pull groups" used by the "pull coordinates".
246 * The right optimization will depend on how the code is being used.
248 * Call the evaluator(s) for the restraints for the configured sites.
249 * Forces are applied to atoms in the first and last site listed.
250 * Intermediate sites are used as reference coordinates when the relevant
251 * vector between sites is on the order of half a box length or otherwise
252 * ambiguous in the case of periodic boundary conditions.
254 void calculateForces(const ForceProviderInput
& forceProviderInput
,
255 ForceProviderOutput
* forceProviderOutput
) override
;
258 std::shared_ptr
<gmx::IRestraintPotential
> restraint_
;
259 std::vector
<Site
> sites_
;
263 * \brief IMDModule implementation for RestraintMDModule.
265 * Provides IMDModule interface.
267 * \ingroup module_restraint
269 class RestraintMDModuleImpl final
272 RestraintMDModuleImpl() = delete;
274 * \brief Wrap an object implementing IRestraintPotential
276 * \param restraint handle to restraint to wrap.
277 * \param sites list of sites for framework to process for restraint force calculator.
279 RestraintMDModuleImpl(std::shared_ptr
<gmx::IRestraintPotential
> restraint
,
280 const std::vector
<int>& sites
);
283 * \brief Allow moves.
287 RestraintMDModuleImpl(RestraintMDModuleImpl
&&) noexcept
= default;
288 RestraintMDModuleImpl
& operator=(RestraintMDModuleImpl
&&) noexcept
= default;
291 ~RestraintMDModuleImpl();
294 * \brief Implement IMDModule interface.
296 * \param forceProviders force module manager in the force record that will call this.
298 * The calling code must ensure that this object stays alive as long as forceProviders needs
299 * the RestraintForceProvider, since forceProviders can't. Typically that is the duration of a do_md() call.
301 void initForceProviders(ForceProviders
* forceProviders
);
303 //! handle to RestraintForceProvider implementation
304 std::unique_ptr
<RestraintForceProvider
> forceProvider_
;
307 } // end namespace gmx
309 #endif // GROMACS_RESTRAINTMDMODULE_IMPL_H