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Check out http://www.gromacs.org. 37 */ 38 #ifndef GMX_MDTYPES_TYPES_FORCEREC_H 39 #define GMX_MDTYPES_TYPES_FORCEREC_H 40 41 #include <array> 42 #include <memory> 43 #include <vector> 44 45 #include "gromacs/math/vectypes.h" 46 #include "gromacs/mdtypes/md_enums.h" 47 #include "gromacs/pbcutil/pbc.h" 48 #include "gromacs/utility/arrayref.h" 49 #include "gromacs/utility/basedefinitions.h" 50 #include "gromacs/utility/real.h" 51 52 #include "locality.h" 53 54 /* Abstract type for PME that is defined only in the routine that use them. */ 55 struct gmx_pme_t; 56 struct nonbonded_verlet_t; 57 struct bonded_threading_t; 58 class DeviceContext; 59 class DispersionCorrection; 60 class ListedForces; 61 struct t_fcdata; 62 struct t_forcetable; 63 struct t_QMMMrec; 64 65 namespace gmx 66 { 67 class DeviceStreamManager; 68 class GpuBonded; 69 class GpuForceReduction; 70 class ForceProviders; 71 class StatePropagatorDataGpu; 72 class PmePpCommGpu; 73 class WholeMoleculeTransform; 74 } // namespace gmx 75 76 /* macros for the cginfo data in forcerec 77 * 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. 80 * 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. 84 */ 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)) 102 103 104 /* 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). 107 */ 108 #define GMX_CUTOFF_INF 1E+18 109 110 /* enums for the neighborlist type */ 111 enum 112 { 113 enbvdwNONE, 114 enbvdwLJ, 115 enbvdwBHAM, 116 enbvdwTAB, 117 enbvdwNR 118 }; 119 120 struct cginfo_mb_t 121 { 122 int cg_start = 0; 123 int cg_end = 0; 124 int cg_mod = 0; 125 std::vector<int> cginfo; 126 }; 127 128 129 /* Forward declaration of type for managing Ewald tables */ 130 struct gmx_ewald_tab_t; 131 132 struct ewald_corr_thread_t; 133 134 /*! \brief Helper force buffers for ForceOutputs 135 * 136 * This class stores intermediate force buffers that are used 137 * internally in the force calculation and which are reduced into 138 * the output force buffer passed to the force calculation. 139 */ 140 class ForceHelperBuffers 141 { 142 public: 143 /*! \brief Constructs helper buffers 144 * 145 * When the forces that will be accumulated with help of these buffers 146 * have direct virial contributions, set the parameter to true, so 147 * an extra force buffer is available for these forces to enable 148 * correct virial computation. 149 */ 150 ForceHelperBuffers(bool haveDirectVirialContributions); 151 152 //! Returns whether we have a direct virial contribution force buffer haveDirectVirialContributions()153 bool haveDirectVirialContributions() const { return haveDirectVirialContributions_; } 154 155 //! Returns the buffer for direct virial contributions forceBufferForDirectVirialContributions()156 gmx::ArrayRef<gmx::RVec> forceBufferForDirectVirialContributions() 157 { 158 GMX_ASSERT(haveDirectVirialContributions_, "Buffer can only be requested when present"); 159 return forceBufferForDirectVirialContributions_; 160 } 161 162 //! Returns the buffer for shift forces, size SHIFTS shiftForces()163 gmx::ArrayRef<gmx::RVec> shiftForces() { return shiftForces_; } 164 165 //! Resizes the direct virial contribution buffer, when present 166 void resize(int numAtoms); 167 168 private: 169 //! True when we have contributions that are directly added to the virial 170 bool haveDirectVirialContributions_ = false; 171 //! Force buffer for force computation with direct virial contributions 172 std::vector<gmx::RVec> forceBufferForDirectVirialContributions_; 173 //! Shift force array for computing the virial, size SHIFTS 174 std::vector<gmx::RVec> shiftForces_; 175 }; 176 177 struct t_forcerec 178 { // NOLINT (clang-analyzer-optin.performance.Padding) 179 // Declare an explicit constructor and destructor, so they can be 180 // implemented in a single source file, so that not every source 181 // file that includes this one needs to understand how to find the 182 // destructors of the objects pointed to by unique_ptr members. 183 t_forcerec(); 184 ~t_forcerec(); 185 186 struct interaction_const_t* ic = nullptr; 187 188 /* PBC stuff */ 189 PbcType pbcType = PbcType::Xyz; 190 //! Tells whether atoms inside a molecule can be in different periodic images, 191 // i.e. whether we need to take into account PBC when computing distances inside molecules. 192 // This determines whether PBC must be considered for e.g. bonded interactions. 193 gmx_bool bMolPBC = FALSE; 194 int rc_scaling = 0; 195 rvec posres_com = { 0 }; 196 rvec posres_comB = { 0 }; 197 198 gmx_bool use_simd_kernels = FALSE; 199 200 /* Interaction for calculated in kernels. In many cases this is similar to 201 * the electrostatics settings in the inputrecord, but the difference is that 202 * these variables always specify the actual interaction in the kernel - if 203 * we are tabulating reaction-field the inputrec will say reaction-field, but 204 * the kernel interaction will say cubic-spline-table. To be safe we also 205 * have a kernel-specific setting for the modifiers - if the interaction is 206 * tabulated we already included the inputrec modification there, so the kernel 207 * modification setting will say 'none' in that case. 208 */ 209 int nbkernel_elec_interaction = 0; 210 int nbkernel_vdw_interaction = 0; 211 int nbkernel_elec_modifier = 0; 212 int nbkernel_vdw_modifier = 0; 213 214 /* Cut-Off stuff. 215 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0). 216 */ 217 real rlist = 0; 218 219 /* Charge sum for topology A/B ([0]/[1]) for Ewald corrections */ 220 double qsum[2] = { 0 }; 221 double q2sum[2] = { 0 }; 222 double c6sum[2] = { 0 }; 223 224 /* Dispersion correction stuff */ 225 std::unique_ptr<DispersionCorrection> dispersionCorrection; 226 227 /* Fudge factors */ 228 real fudgeQQ = 0; 229 230 /* Table stuff */ 231 gmx_bool bcoultab = FALSE; 232 gmx_bool bvdwtab = FALSE; 233 234 t_forcetable* pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */ 235 236 /* Free energy */ 237 int efep = 0; 238 239 /* Information about atom properties for the molecule blocks in the system */ 240 std::vector<cginfo_mb_t> cginfo_mb; 241 /* Information about atom properties for local and non-local atoms */ 242 std::vector<int> cginfo; 243 244 rvec* shift_vec = nullptr; 245 246 std::unique_ptr<gmx::WholeMoleculeTransform> wholeMoleculeTransform; 247 248 /* The Nbnxm Verlet non-bonded machinery */ 249 std::unique_ptr<nonbonded_verlet_t> nbv; 250 251 /* The wall tables (if used) */ 252 int nwall = 0; 253 t_forcetable*** wall_tab = nullptr; 254 255 /* The number of atoms participating in do_force_lowlevel */ 256 int natoms_force = 0; 257 /* The number of atoms participating in force calculation and constraints */ 258 int natoms_force_constr = 0; 259 260 /* List of helper buffers for ForceOutputs, one for each time step with MTS */ 261 std::vector<ForceHelperBuffers> forceHelperBuffers; 262 263 /* Data for PPPM/PME/Ewald */ 264 struct gmx_pme_t* pmedata = nullptr; 265 int ljpme_combination_rule = 0; 266 267 /* PME/Ewald stuff */ 268 struct gmx_ewald_tab_t* ewald_table = nullptr; 269 270 /* Non bonded Parameter lists */ 271 int ntype = 0; /* Number of atom types */ 272 gmx_bool bBHAM = FALSE; 273 std::vector<real> nbfp; 274 real* ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */ 275 276 /* Energy group pair flags */ 277 int* egp_flags = nullptr; 278 279 /* Shell molecular dynamics flexible constraints */ 280 real fc_stepsize = 0; 281 282 /* If > 0 signals Test Particle Insertion, 283 * the value is the number of atoms of the molecule to insert 284 * Only the energy difference due to the addition of the last molecule 285 * should be calculated. 286 */ 287 int n_tpi = 0; 288 289 /* Limit for printing large forces, negative is don't print */ 290 real print_force = 0; 291 292 /* User determined parameters, copied from the inputrec */ 293 int userint1 = 0; 294 int userint2 = 0; 295 int userint3 = 0; 296 int userint4 = 0; 297 real userreal1 = 0; 298 real userreal2 = 0; 299 real userreal3 = 0; 300 real userreal4 = 0; 301 302 /* Tells whether we use multiple time stepping, computing some forces less frequently */ 303 bool useMts = false; 304 305 /* Data for special listed force calculations */ 306 std::unique_ptr<t_fcdata> fcdata; 307 308 // The listed forces calculation data, 1 entry or multiple entries with multiple time stepping 309 std::vector<ListedForces> listedForces; 310 311 /* TODO: Replace the pointer by an object once we got rid of C */ 312 gmx::GpuBonded* gpuBonded = nullptr; 313 314 /* Ewald correction thread local virial and energy data */ 315 int nthread_ewc = 0; 316 struct ewald_corr_thread_t* ewc_t = nullptr; 317 318 gmx::ForceProviders* forceProviders = nullptr; 319 320 // The stateGpu object is created in runner, forcerec just keeps the copy of the pointer. 321 // TODO: This is not supposed to be here. StatePropagatorDataGpu should be a part of 322 // general StatePropagatorData object that is passed around 323 gmx::StatePropagatorDataGpu* stateGpu = nullptr; 324 // TODO: Should not be here. This is here only to pass the pointer around. 325 gmx::DeviceStreamManager* deviceStreamManager = nullptr; 326 327 //! GPU device context 328 DeviceContext* deviceContext = nullptr; 329 330 /* For PME-PP GPU communication */ 331 std::unique_ptr<gmx::PmePpCommGpu> pmePpCommGpu; 332 333 /* For GPU force reduction (on both local and non-local atoms) */ 334 gmx::EnumerationArray<gmx::AtomLocality, std::unique_ptr<gmx::GpuForceReduction>> gpuForceReduction; 335 }; 336 337 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have 338 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere 339 * in the code, but beware if you are using these macros externally. 340 */ 341 #define C6(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj))] 342 #define C12(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj)) + 1] 343 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj))] 344 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 1] 345 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 2] 346 347 #endif 348