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38 #ifndef GMX_MDTYPES_TYPES_FORCEREC_H
39 #define GMX_MDTYPES_TYPES_FORCEREC_H
45 #include "gromacs/math/vectypes.h"
46 #include "gromacs/mdtypes/md_enums.h"
47 #include "gromacs/pbcutil/ishift.h"
48 #include "gromacs/pbcutil/pbc.h"
49 #include "gromacs/utility/arrayref.h"
50 #include "gromacs/utility/real.h"
54 /* Abstract type for PME that is defined only in the routine that use them. */
56 struct nonbonded_verlet_t;
57 struct bonded_threading_t;
59 class DispersionCorrection;
63 struct interaction_const_t;
67 class DeviceStreamManager;
68 class ListedForcesGpu;
69 class GpuForceReduction;
71 class StatePropagatorDataGpu;
73 class WholeMoleculeTransform;
76 /* macros for the cginfo data in forcerec
78 * Since the tpx format support max 256 energy groups, we do the same here.
79 * Note that we thus have bits 8-14 still unused.
81 * The maximum cg size in cginfo is 63
82 * because we only have space for 6 bits in cginfo,
83 * this cg size entry is actually only read with domain decomposition.
85 #define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
86 #define GET_CGINFO_GID(cgi) ((cgi)&255)
87 #define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1 << 15))
88 #define GET_CGINFO_FEP(cgi) ((cgi) & (1 << 15))
89 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1 << 17))
90 #define GET_CGINFO_EXCL_INTER(cgi) ((cgi) & (1 << 17))
91 #define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1 << 20))
92 #define GET_CGINFO_CONSTR(cgi) ((cgi) & (1 << 20))
93 #define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1 << 21))
94 #define GET_CGINFO_SETTLE(cgi) ((cgi) & (1 << 21))
95 /* This bit is only used with bBondComm in the domain decomposition */
96 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1 << 22))
97 #define GET_CGINFO_BOND_INTER(cgi) ((cgi) & (1 << 22))
98 #define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1 << 23))
99 #define GET_CGINFO_HAS_VDW(cgi) ((cgi) & (1 << 23))
100 #define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1 << 24))
101 #define GET_CGINFO_HAS_Q(cgi) ((cgi) & (1 << 24))
104 /* Value to be used in mdrun for an infinite cut-off.
105 * Since we need to compare with the cut-off squared,
106 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
108 #define GMX_CUTOFF_INF 1E+18
109 //! Check the cuttoff
110 real cutoff_inf(real cutoff);
117 std::vector<int> cginfo;
121 /* Forward declaration of type for managing Ewald tables */
122 struct gmx_ewald_tab_t;
124 struct ewald_corr_thread_t;
126 /*! \brief Helper force buffers for ForceOutputs
128 * This class stores intermediate force buffers that are used
129 * internally in the force calculation and which are reduced into
130 * the output force buffer passed to the force calculation.
132 class ForceHelperBuffers
135 /*! \brief Constructs helper buffers
137 * When the forces that will be accumulated with help of these buffers
138 * have direct virial contributions, set the parameter to true, so
139 * an extra force buffer is available for these forces to enable
140 * correct virial computation.
142 ForceHelperBuffers(bool haveDirectVirialContributions);
144 //! Returns whether we have a direct virial contribution force buffer
145 bool haveDirectVirialContributions() const { return haveDirectVirialContributions_; }
147 //! Returns the buffer for direct virial contributions
148 gmx::ArrayRef<gmx::RVec> forceBufferForDirectVirialContributions()
150 GMX_ASSERT(haveDirectVirialContributions_, "Buffer can only be requested when present");
151 return forceBufferForDirectVirialContributions_;
154 //! Returns the buffer for shift forces, size c_numShiftVectors
155 gmx::ArrayRef<gmx::RVec> shiftForces() { return shiftForces_; }
157 //! Resizes the direct virial contribution buffer, when present
158 void resize(int numAtoms);
161 //! True when we have contributions that are directly added to the virial
162 bool haveDirectVirialContributions_ = false;
163 //! Force buffer for force computation with direct virial contributions
164 std::vector<gmx::RVec> forceBufferForDirectVirialContributions_;
165 //! Shift force array for computing the virial, size c_numShiftVectors
166 std::vector<gmx::RVec> shiftForces_;
168 // NOLINTNEXTLINE (clang-analyzer-optin.performance.Padding)
171 // Declare an explicit constructor and destructor, so they can be
172 // implemented in a single source file, so that not every source
173 // file that includes this one needs to understand how to find the
174 // destructors of the objects pointed to by unique_ptr members.
178 std::unique_ptr<interaction_const_t> ic;
181 PbcType pbcType = PbcType::Xyz;
182 //! Tells whether atoms inside a molecule can be in different periodic images,
183 // i.e. whether we need to take into account PBC when computing distances inside molecules.
184 // This determines whether PBC must be considered for e.g. bonded interactions.
185 bool bMolPBC = false;
186 RefCoordScaling rc_scaling = RefCoordScaling::No;
187 gmx::RVec posres_com = { 0, 0, 0 };
188 gmx::RVec posres_comB = { 0, 0, 0 };
190 bool use_simd_kernels = false;
192 /* Interaction for calculated in kernels. In many cases this is similar to
193 * the electrostatics settings in the inputrecord, but the difference is that
194 * these variables always specify the actual interaction in the kernel - if
195 * we are tabulating reaction-field the inputrec will say reaction-field, but
196 * the kernel interaction will say cubic-spline-table. To be safe we also
197 * have a kernel-specific setting for the modifiers - if the interaction is
198 * tabulated we already included the inputrec modification there, so the kernel
199 * modification setting will say 'none' in that case.
201 NbkernelElecType nbkernel_elec_interaction = NbkernelElecType::None;
202 NbkernelVdwType nbkernel_vdw_interaction = NbkernelVdwType::None;
203 InteractionModifiers nbkernel_elec_modifier = InteractionModifiers::None;
204 InteractionModifiers nbkernel_vdw_modifier = InteractionModifiers::None;
207 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
211 /* Charge sum for topology A/B ([0]/[1]) for Ewald corrections */
212 std::array<double, 2> qsum = { 0 };
213 std::array<double, 2> q2sum = { 0 };
214 std::array<double, 2> c6sum = { 0 };
216 /* Dispersion correction stuff */
217 std::unique_ptr<DispersionCorrection> dispersionCorrection;
222 std::unique_ptr<t_forcetable> pairsTable; /* for 1-4 interactions, [pairs] and [pairs_nb] */
225 FreeEnergyPerturbationType efep = FreeEnergyPerturbationType::No;
227 /* Information about atom properties for the molecule blocks in the system */
228 std::vector<cginfo_mb_t> cginfo_mb;
229 /* Information about atom properties for local and non-local atoms */
230 std::vector<int> cginfo;
232 std::vector<gmx::RVec> shift_vec;
234 std::unique_ptr<gmx::WholeMoleculeTransform> wholeMoleculeTransform;
236 /* The Nbnxm Verlet non-bonded machinery */
237 std::unique_ptr<nonbonded_verlet_t> nbv;
239 /* The wall tables (if used) */
241 std::vector<std::vector<std::unique_ptr<t_forcetable>>> wall_tab;
243 /* The number of atoms participating in do_force_lowlevel */
244 int natoms_force = 0;
245 /* The number of atoms participating in force calculation and constraints */
246 int natoms_force_constr = 0;
248 /* List of helper buffers for ForceOutputs, one for each time step with MTS */
249 std::vector<ForceHelperBuffers> forceHelperBuffers;
251 /* Data for PPPM/PME/Ewald */
252 gmx_pme_t* pmedata = nullptr;
253 LongRangeVdW ljpme_combination_rule = LongRangeVdW::Geom;
255 /* PME/Ewald stuff */
256 std::unique_ptr<gmx_ewald_tab_t> ewald_table;
258 /* Non bonded Parameter lists */
259 int ntype = 0; /* Number of atom types */
260 bool haveBuckingham = false;
261 std::vector<real> nbfp;
262 std::vector<real> ljpme_c6grid; /* C6-values used on grid in LJPME */
264 /* Energy group pair flags */
265 int* egp_flags = nullptr;
267 /* Shell molecular dynamics flexible constraints */
268 real fc_stepsize = 0;
270 /* If > 0 signals Test Particle Insertion,
271 * the value is the number of atoms of the molecule to insert
272 * Only the energy difference due to the addition of the last molecule
273 * should be calculated.
277 /* Limit for printing large forces, negative is don't print */
278 real print_force = 0;
280 /* User determined parameters, copied from the inputrec */
290 /* Tells whether we use multiple time stepping, computing some forces less frequently */
293 /* Data for special listed force calculations */
294 std::unique_ptr<t_fcdata> fcdata;
296 // The listed forces calculation data, 1 entry or multiple entries with multiple time stepping
297 std::vector<ListedForces> listedForces;
299 /* TODO: Replace the pointer by an object once we got rid of C */
300 gmx::ListedForcesGpu* listedForcesGpu = nullptr;
302 /* Ewald correction thread local virial and energy data */
304 std::vector<ewald_corr_thread_t> ewc_t;
306 gmx::ForceProviders* forceProviders = nullptr;
308 // The stateGpu object is created in runner, forcerec just keeps the copy of the pointer.
309 // TODO: This is not supposed to be here. StatePropagatorDataGpu should be a part of
310 // general StatePropagatorData object that is passed around
311 gmx::StatePropagatorDataGpu* stateGpu = nullptr;
312 // TODO: Should not be here. This is here only to pass the pointer around.
313 gmx::DeviceStreamManager* deviceStreamManager = nullptr;
315 //! GPU device context
316 DeviceContext* deviceContext = nullptr;
318 /* For PME-PP GPU communication */
319 std::unique_ptr<gmx::PmePpCommGpu> pmePpCommGpu;
321 /* For GPU force reduction (on both local and non-local atoms) */
322 gmx::EnumerationArray<gmx::AtomLocality, std::unique_ptr<gmx::GpuForceReduction>> gpuForceReduction;
325 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
326 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
327 * in the code, but beware if you are using these macros externally.
329 #define C6(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj))]
330 #define C12(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj)) + 1]
331 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj))]
332 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 1]
333 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 2]