class ForceProviders;
class StatePropagatorDataGpu;
class PmePpCommGpu;
-}
+} // namespace gmx
/* macros for the cginfo data in forcerec
*
* because we only have space for 6 bits in cginfo,
* this cg size entry is actually only read with domain decomposition.
*/
-#define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
-#define GET_CGINFO_GID(cgi) ( (cgi) & 255)
-#define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1<<15))
-#define GET_CGINFO_FEP(cgi) ( (cgi) & (1<<15))
-#define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
-#define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
-#define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1<<20))
-#define GET_CGINFO_CONSTR(cgi) ( (cgi) & (1<<20))
-#define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1<<21))
-#define GET_CGINFO_SETTLE(cgi) ( (cgi) & (1<<21))
+#define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
+#define GET_CGINFO_GID(cgi) ((cgi)&255)
+#define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1 << 15))
+#define GET_CGINFO_FEP(cgi) ((cgi) & (1 << 15))
+#define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1 << 17))
+#define GET_CGINFO_EXCL_INTER(cgi) ((cgi) & (1 << 17))
+#define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1 << 20))
+#define GET_CGINFO_CONSTR(cgi) ((cgi) & (1 << 20))
+#define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1 << 21))
+#define GET_CGINFO_SETTLE(cgi) ((cgi) & (1 << 21))
/* This bit is only used with bBondComm in the domain decomposition */
-#define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
-#define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
-#define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1<<23))
-#define GET_CGINFO_HAS_VDW(cgi) ( (cgi) & (1<<23))
-#define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1<<24))
-#define GET_CGINFO_HAS_Q(cgi) ( (cgi) & (1<<24))
+#define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1 << 22))
+#define GET_CGINFO_BOND_INTER(cgi) ((cgi) & (1 << 22))
+#define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1 << 23))
+#define GET_CGINFO_HAS_VDW(cgi) ((cgi) & (1 << 23))
+#define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1 << 24))
+#define GET_CGINFO_HAS_Q(cgi) ((cgi) & (1 << 24))
/* Value to be used in mdrun for an infinite cut-off.
#define GMX_CUTOFF_INF 1E+18
/* enums for the neighborlist type */
-enum {
- enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
+enum
+{
+ enbvdwNONE,
+ enbvdwLJ,
+ enbvdwBHAM,
+ enbvdwTAB,
+ enbvdwNR
};
struct cginfo_mb_t
int cg_start;
int cg_end;
int cg_mod;
- int *cginfo;
+ int* cginfo;
};
struct ewald_corr_thread_t;
-struct t_forcerec { // NOLINT (clang-analyzer-optin.performance.Padding)
+struct t_forcerec
+{ // NOLINT (clang-analyzer-optin.performance.Padding)
// Declare an explicit constructor and destructor, so they can be
// implemented in a single source file, so that not every source
// file that includes this one needs to understand how to find the
t_forcerec();
~t_forcerec();
- struct interaction_const_t *ic = nullptr;
+ struct interaction_const_t* ic = nullptr;
/* PBC stuff */
- int ePBC = 0;
+ int ePBC = 0;
//! Tells whether atoms inside a molecule can be in different periodic images,
// i.e. whether we need to take into account PBC when computing distances inside molecules.
// This determines whether PBC must be considered for e.g. bonded interactions.
- gmx_bool bMolPBC = FALSE;
- int rc_scaling = 0;
- rvec posres_com = { 0 };
- rvec posres_comB = { 0 };
+ gmx_bool bMolPBC = FALSE;
+ int rc_scaling = 0;
+ rvec posres_com = { 0 };
+ rvec posres_comB = { 0 };
- gmx_bool use_simd_kernels = FALSE;
+ gmx_bool use_simd_kernels = FALSE;
/* Interaction for calculated in kernels. In many cases this is similar to
* the electrostatics settings in the inputrecord, but the difference is that
real fudgeQQ = 0;
/* Table stuff */
- gmx_bool bcoultab = FALSE;
- gmx_bool bvdwtab = FALSE;
+ gmx_bool bcoultab = FALSE;
+ gmx_bool bvdwtab = FALSE;
- t_forcetable *pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
+ t_forcetable* pairsTable = nullptr; /* for 1-4 interactions, [pairs] and [pairs_nb] */
/* Free energy */
- int efep = 0;
- real sc_alphavdw = 0;
- real sc_alphacoul = 0;
- int sc_power = 0;
- real sc_r_power = 0;
- real sc_sigma6_def = 0;
- real sc_sigma6_min = 0;
+ int efep = 0;
+ real sc_alphavdw = 0;
+ real sc_alphacoul = 0;
+ int sc_power = 0;
+ real sc_r_power = 0;
+ real sc_sigma6_def = 0;
+ real sc_sigma6_min = 0;
/* Information about atom properties for the molecule blocks in the system */
- struct cginfo_mb_t *cginfo_mb = nullptr;
+ struct cginfo_mb_t* cginfo_mb = nullptr;
/* Information about atom properties for local and non-local atoms */
- std::vector<int> cginfo;
+ std::vector<int> cginfo;
- rvec *shift_vec = nullptr;
+ rvec* shift_vec = nullptr;
- int cutoff_scheme = 0; /* group- or Verlet-style cutoff */
- gmx_bool bNonbonded = FALSE; /* true if nonbonded calculations are *not* turned off */
+ int cutoff_scheme = 0; /* group- or Verlet-style cutoff */
+ gmx_bool bNonbonded = FALSE; /* true if nonbonded calculations are *not* turned off */
/* The Nbnxm Verlet non-bonded machinery */
std::unique_ptr<nonbonded_verlet_t> nbv;
/* The wall tables (if used) */
- int nwall = 0;
- t_forcetable ***wall_tab = nullptr;
+ int nwall = 0;
+ t_forcetable*** wall_tab = nullptr;
/* The number of atoms participating in do_force_lowlevel */
int natoms_force = 0;
* PPPM/PME/Ewald/posres/ForceProviders
*/
/* True when we have contributions that are directly added to the virial */
- bool haveDirectVirialContributions = false;
+ bool haveDirectVirialContributions = false;
/* Force buffer for force computation with direct virial contributions */
std::vector<gmx::RVec> forceBufferForDirectVirialContributions;
/* Data for PPPM/PME/Ewald */
- struct gmx_pme_t *pmedata = nullptr;
+ struct gmx_pme_t* pmedata = nullptr;
int ljpme_combination_rule = 0;
/* PME/Ewald stuff */
- struct gmx_ewald_tab_t *ewald_table = nullptr;
+ struct gmx_ewald_tab_t* ewald_table = nullptr;
/* Shift force array for computing the virial, size SHIFTS */
std::vector<gmx::RVec> shiftForces;
/* Non bonded Parameter lists */
int ntype = 0; /* Number of atom types */
gmx_bool bBHAM = FALSE;
- real *nbfp = nullptr;
- real *ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
+ real* nbfp = nullptr;
+ real* ljpme_c6grid = nullptr; /* C6-values used on grid in LJPME */
/* Energy group pair flags */
- int *egp_flags = nullptr;
+ int* egp_flags = nullptr;
/* Shell molecular dynamics flexible constraints */
real fc_stepsize = 0;
/* QMMM stuff */
gmx_bool bQMMM = FALSE;
- struct t_QMMMrec *qr = nullptr;
+ struct t_QMMMrec* qr = nullptr;
/* QM-MM neighborlists */
- struct t_nblist *QMMMlist = nullptr;
+ struct t_nblist* QMMMlist = nullptr;
/* Limit for printing large forces, negative is don't print */
real print_force = 0;
real userreal4 = 0;
/* Pointer to struct for managing threading of bonded force calculation */
- struct bonded_threading_t *bondedThreading = nullptr;
+ struct bonded_threading_t* bondedThreading = nullptr;
/* TODO: Replace the pointer by an object once we got rid of C */
- gmx::GpuBonded *gpuBonded = nullptr;
+ gmx::GpuBonded* gpuBonded = nullptr;
/* Ewald correction thread local virial and energy data */
int nthread_ewc = 0;
- struct ewald_corr_thread_t *ewc_t = nullptr;
+ struct ewald_corr_thread_t* ewc_t = nullptr;
- gmx::ForceProviders *forceProviders = nullptr;
+ gmx::ForceProviders* forceProviders = nullptr;
// The stateGpu object is created in runner, forcerec just keeps the copy of the pointer.
// TODO: This is not supposed to be here. StatePropagatorDataGpu should be a part of
// general StatePropagatorData object that is passed around
- gmx::StatePropagatorDataGpu *stateGpu = nullptr;
+ gmx::StatePropagatorDataGpu* stateGpu = nullptr;
/* For PME-PP GPU communication */
std::unique_ptr<gmx::PmePpCommGpu> pmePpCommGpu;
* been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
* in the code, but beware if you are using these macros externally.
*/
-#define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
-#define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
-#define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
-#define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
-#define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]
+#define C6(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj))]
+#define C12(nbfp, ntp, ai, aj) (nbfp)[2 * ((ntp) * (ai) + (aj)) + 1]
+#define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj))]
+#define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 1]
+#define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3 * ((ntp) * (ai) + (aj)) + 2]
#endif
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