src/gromacs/mdtypes/forcerec.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_MDTYPES_TYPES_FORCEREC_H
  38 #define GMX_MDTYPES_TYPES_FORCEREC_H
  39
  40 #include <array>
  41 #include <memory>
  42 #include <vector>
  43
  44 #include "gromacs/math/vectypes.h"
  45 #include "gromacs/mdtypes/interaction_const.h"
  46 #include "gromacs/mdtypes/md_enums.h"
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49
  50 /* Abstract type for PME that is defined only in the routine that use them. */
  51 struct gmx_ns_t;
  52 struct gmx_pme_t;
  53 struct nonbonded_verlet_t;
  54 struct bonded_threading_t;
  55 class DispersionCorrection;
  56 struct t_forcetable;
  57 struct t_QMMMrec;
  58
  59 namespace gmx
  60 {
  61 class GpuBonded;
  62 class ForceProviders;
  63 class StatePropagatorDataGpu;
  64 class PmePpCommGpu;
  65 } // namespace gmx
  66
  67 /* macros for the cginfo data in forcerec
  68  *
  69  * Since the tpx format support max 256 energy groups, we do the same here.
  70  * Note that we thus have bits 8-14 still unused.
  71  *
  72  * The maximum cg size in cginfo is 63
  73  * because we only have space for 6 bits in cginfo,
  74  * this cg size entry is actually only read with domain decomposition.
  75  */
  76 #define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
  77 #define GET_CGINFO_GID(cgi) ((cgi)&255)
  78 #define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1 << 15))
  79 #define GET_CGINFO_FEP(cgi) ((cgi) & (1 << 15))
  80 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1 << 17))
  81 #define GET_CGINFO_EXCL_INTER(cgi) ((cgi) & (1 << 17))
  82 #define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1 << 20))
  83 #define GET_CGINFO_CONSTR(cgi) ((cgi) & (1 << 20))
  84 #define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1 << 21))
  85 #define GET_CGINFO_SETTLE(cgi) ((cgi) & (1 << 21))
  86 /* This bit is only used with bBondComm in the domain decomposition */
  87 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1 << 22))
  88 #define GET_CGINFO_BOND_INTER(cgi) ((cgi) & (1 << 22))
  89 #define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1 << 23))
  90 #define GET_CGINFO_HAS_VDW(cgi) ((cgi) & (1 << 23))
  91 #define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1 << 24))
  92 #define GET_CGINFO_HAS_Q(cgi) ((cgi) & (1 << 24))
  93
  94
  95 /* Value to be used in mdrun for an infinite cut-off.
  96  * Since we need to compare with the cut-off squared,
  97  * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
  98  */
  99 #define GMX_CUTOFF_INF 1E+18
 100
 101 /* enums for the neighborlist type */
 102 enum
 103 {
 104     enbvdwNONE,
 105     enbvdwLJ,
 106     enbvdwBHAM,
 107     enbvdwTAB,
 108     enbvdwNR
 109 };
 110
 111 struct cginfo_mb_t
 112 {
 113     int              cg_start = 0;
 114     int              cg_end   = 0;
 115     int              cg_mod   = 0;
 116     std::vector<int> cginfo;
 117 };
 118
 119
 120 /* Forward declaration of type for managing Ewald tables */
 121 struct gmx_ewald_tab_t;
 122
 123 struct ewald_corr_thread_t;
 124
 125 struct t_forcerec
 126 { // NOLINT (clang-analyzer-optin.performance.Padding)
 127     // Declare an explicit constructor and destructor, so they can be
 128     // implemented in a single source file, so that not every source
 129     // file that includes this one needs to understand how to find the
 130     // destructors of the objects pointed to by unique_ptr members.
 131     t_forcerec();
 132     ~t_forcerec();
 133
 134     struct interaction_const_t* ic = nullptr;
 135
 136     /* PBC stuff */
 137     int ePBC = 0;
 138     //! Tells whether atoms inside a molecule can be in different periodic images,
 139     //  i.e. whether we need to take into account PBC when computing distances inside molecules.
 140     //  This determines whether PBC must be considered for e.g. bonded interactions.
 141     gmx_bool bMolPBC     = FALSE;
 142     int      rc_scaling  = 0;
 143     rvec     posres_com  = { 0 };
 144     rvec     posres_comB = { 0 };
 145
 146     gmx_bool use_simd_kernels = FALSE;
 147
 148     /* Interaction for calculated in kernels. In many cases this is similar to
 149      * the electrostatics settings in the inputrecord, but the difference is that
 150      * these variables always specify the actual interaction in the kernel - if
 151      * we are tabulating reaction-field the inputrec will say reaction-field, but
 152      * the kernel interaction will say cubic-spline-table. To be safe we also
 153      * have a kernel-specific setting for the modifiers - if the interaction is
 154      * tabulated we already included the inputrec modification there, so the kernel
 155      * modification setting will say 'none' in that case.
 156      */
 157     int nbkernel_elec_interaction = 0;
 158     int nbkernel_vdw_interaction  = 0;
 159     int nbkernel_elec_modifier    = 0;
 160     int nbkernel_vdw_modifier     = 0;
 161
 162     /* Cut-Off stuff.
 163      * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
 164      */
 165     real rlist = 0;
 166
 167     /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
 168     double qsum[2]   = { 0 };
 169     double q2sum[2]  = { 0 };
 170     double c6sum[2]  = { 0 };
 171     rvec   mu_tot[2] = { { 0 } };
 172
 173     /* Dispersion correction stuff */
 174     std::unique_ptr<DispersionCorrection> dispersionCorrection;
 175
 176     /* Fudge factors */
 177     real fudgeQQ = 0;
 178
 179     /* Table stuff */
 180     gmx_bool bcoultab = FALSE;
 181     gmx_bool bvdwtab  = FALSE;
 182
 183     t_forcetable* pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
 184
 185     /* Free energy */
 186     int  efep          = 0;
 187     real sc_alphavdw   = 0;
 188     real sc_alphacoul  = 0;
 189     int  sc_power      = 0;
 190     real sc_r_power    = 0;
 191     real sc_sigma6_def = 0;
 192     real sc_sigma6_min = 0;
 193
 194     /* Information about atom properties for the molecule blocks in the system */
 195     std::vector<cginfo_mb_t> cginfo_mb;
 196     /* Information about atom properties for local and non-local atoms */
 197     std::vector<int> cginfo;
 198
 199     rvec* shift_vec = nullptr;
 200
 201     int      cutoff_scheme = 0;     /* group- or Verlet-style cutoff */
 202     gmx_bool bNonbonded    = FALSE; /* true if nonbonded calculations are *not* turned off */
 203
 204     /* The Nbnxm Verlet non-bonded machinery */
 205     std::unique_ptr<nonbonded_verlet_t> nbv;
 206
 207     /* The wall tables (if used) */
 208     int             nwall    = 0;
 209     t_forcetable*** wall_tab = nullptr;
 210
 211     /* The number of atoms participating in do_force_lowlevel */
 212     int natoms_force = 0;
 213     /* The number of atoms participating in force and constraints */
 214     int natoms_force_constr = 0;
 215     /* The allocation size of vectors of size natoms_force */
 216     int nalloc_force = 0;
 217
 218     /* Forces that should not enter into the coord x force virial summation:
 219      * PPPM/PME/Ewald/posres/ForceProviders
 220      */
 221     /* True when we have contributions that are directly added to the virial */
 222     bool haveDirectVirialContributions = false;
 223     /* Force buffer for force computation with direct virial contributions */
 224     std::vector<gmx::RVec> forceBufferForDirectVirialContributions;
 225
 226     /* Data for PPPM/PME/Ewald */
 227     struct gmx_pme_t* pmedata                = nullptr;
 228     int               ljpme_combination_rule = 0;
 229
 230     /* PME/Ewald stuff */
 231     struct gmx_ewald_tab_t* ewald_table = nullptr;
 232
 233     /* Shift force array for computing the virial, size SHIFTS */
 234     std::vector<gmx::RVec> shiftForces;
 235
 236     /* Non bonded Parameter lists */
 237     int               ntype = 0; /* Number of atom types */
 238     gmx_bool          bBHAM = FALSE;
 239     std::vector<real> nbfp;
 240     real*             ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
 241
 242     /* Energy group pair flags */
 243     int* egp_flags = nullptr;
 244
 245     /* Shell molecular dynamics flexible constraints */
 246     real fc_stepsize = 0;
 247
 248     /* If > 0 signals Test Particle Insertion,
 249      * the value is the number of atoms of the molecule to insert
 250      * Only the energy difference due to the addition of the last molecule
 251      * should be calculated.
 252      */
 253     int n_tpi = 0;
 254
 255     /* QMMM stuff */
 256     gmx_bool          bQMMM = FALSE;
 257     struct t_QMMMrec* qr    = nullptr;
 258
 259     /* QM-MM neighborlists */
 260     struct t_nblist* QMMMlist = nullptr;
 261
 262     /* Limit for printing large forces, negative is don't print */
 263     real print_force = 0;
 264
 265     /* User determined parameters, copied from the inputrec */
 266     int  userint1  = 0;
 267     int  userint2  = 0;
 268     int  userint3  = 0;
 269     int  userint4  = 0;
 270     real userreal1 = 0;
 271     real userreal2 = 0;
 272     real userreal3 = 0;
 273     real userreal4 = 0;
 274
 275     /* Pointer to struct for managing threading of bonded force calculation */
 276     struct bonded_threading_t* bondedThreading = nullptr;
 277
 278     /* TODO: Replace the pointer by an object once we got rid of C */
 279     gmx::GpuBonded* gpuBonded = nullptr;
 280
 281     /* Ewald correction thread local virial and energy data */
 282     int                         nthread_ewc = 0;
 283     struct ewald_corr_thread_t* ewc_t       = nullptr;
 284
 285     gmx::ForceProviders* forceProviders = nullptr;
 286
 287     // The stateGpu object is created in runner, forcerec just keeps the copy of the pointer.
 288     // TODO: This is not supposed to be here. StatePropagatorDataGpu should be a part of
 289     //       general StatePropagatorData object that is passed around
 290     gmx::StatePropagatorDataGpu* stateGpu = nullptr;
 291
 292     /* For PME-PP GPU communication */
 293     std::unique_ptr<gmx::PmePpCommGpu> pmePpCommGpu;
 294 };
 295
 296 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
 297  * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
 298  * in the code, but beware if you are using these macros externally.
 299  */
 300 #define C6(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj))]
 301 #define C12(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj)) + 1]
 302 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj))]
 303 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 1]
 304 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 2]
 305
 306 #endif