* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief This file defines functions necessary for mdrun and tools to
+ * compute energies and forces for bonded interactions.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
#include "gmxpre.h"
#include "bonded.h"
#include <algorithm>
-#include "gromacs/bonded/restcbt.h"
#include "gromacs/legacyheaders/disre.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-/* Find a better place for this? */
+#include "restcbt.h"
+
+/*! \brief Mysterious CMAP coefficient matrix */
const int cmap_coeff_matrix[] = {
1, 0, -3, 2, 0, 0, 0, 0, -3, 0, 9, -6, 2, 0, -6, 4,
0, 0, 0, 0, 0, 0, 0, 0, 3, 0, -9, 6, -2, 0, 6, -4,
return atnr;
}
-/* TODO This kind of code appears in many places. Consolidate it */
+/*! \brief Compute dx = xi - xj, modulo PBC if non-NULL
+ *
+ * \todo This kind of code appears in many places. Consolidate it */
static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
{
if (pbc)
gmx_simd_real_t bxx;
} pbc_simd_t;
-/* Set the SIMD pbc data from a normal t_pbc struct */
+/*! \brief Set the SIMD pbc data from a normal t_pbc struct */
static void set_pbc_simd(const t_pbc *pbc, pbc_simd_t *pbc_simd)
{
rvec inv_bdiag;
}
}
-/* Correct distance vector *dx,*dy,*dz for PBC using SIMD */
+/*! \brief Correct distance vector *dx,*dy,*dz for PBC using SIMD */
static gmx_inline void
pbc_dx_simd(gmx_simd_real_t *dx, gmx_simd_real_t *dy, gmx_simd_real_t *dz,
const pbc_simd_t *pbc)
#endif /* GMX_SIMD_HAVE_REAL */
-/*
- * Morse potential bond by Frank Everdij
+/*! \brief Morse potential bond
*
- * Three parameters needed:
+ * By Frank Everdij. Three parameters needed:
*
* b0 = equilibrium distance in nm
* be = beta in nm^-1 (actually, it's nu_e*Sqrt(2*pi*pi*mu/D_e))
* Note: the potential is referenced to be +cb at infinite separation
* and zero at the equilibrium distance!
*/
-
real morse_bonds(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
return vtot;
}
+//! \cond
real cubic_bonds(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
return vtot;
}
-int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
+//! \endcond
+
+/*! \brief Mysterious undocumented function */
+static int
+cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
{
int im1, ip1, ip2;
}
-real cmap_dihs(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const gmx_cmap_t *cmap_grid,
- const rvec x[], rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g,
- real gmx_unused lambda, real gmx_unused *dvdlambda,
- const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
- int gmx_unused *global_atom_index)
+/*! \brief Compute CMAP dihedral energies and forces */
+static real
+cmap_dihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const gmx_cmap_t *cmap_grid,
+ const rvec x[], rvec f[], rvec fshift[],
+ const t_pbc *pbc, const t_graph *g,
+ real gmx_unused lambda, real gmx_unused *dvdlambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
{
int i, j, k, n, idx;
int ai, aj, ak, al, am;
}
-
+//! \cond
/***********************************************************
*
* G R O M O S 9 6 F U N C T I O N S
return vtot;
}
-/* TODO This function could go away when idef is not a big bucket of
- everything. */
-gmx_bool ftype_is_bonded_potential(int ftype)
+//! \endcond
+
+gmx_bool
+ftype_is_bonded_potential(int ftype)
{
return
(interaction_function[ftype].flags & IF_BOND) &&
(ftype < F_GB12 || ftype > F_GB14);
}
+/*! \brief Zero thread-local force-output buffers */
static void zero_thread_forces(f_thread_t *f_t, int n,
int nblock, int blocksize)
{
}
}
+/*! \brief The max thread number is arbitrary, we used a fixed number
+ * to avoid memory management. Using more than 16 threads is probably
+ * never useful performance wise. */
+#define MAX_BONDED_THREADS 256
+
+/*! \brief Reduce thread-local force buffers */
static void reduce_thread_force_buffer(int n, rvec *f,
int nthreads, f_thread_t *f_t,
int nblock, int block_size)
{
- /* The max thread number is arbitrary,
- * we used a fixed number to avoid memory management.
- * Using more than 16 threads is probably never useful performance wise.
- */
-#define MAX_BONDED_THREADS 256
int b;
if (nthreads > MAX_BONDED_THREADS)
}
}
+/*! \brief Reduce thread-local forces */
static void reduce_thread_forces(int n, rvec *f, rvec *fshift,
real *ener, gmx_grppairener_t *grpp, real *dvdl,
int nthreads, f_thread_t *f_t,
}
}
+/*! \brief Calculate one element of the list of bonded interactions
+ for this thread */
static real calc_one_bond(int thread,
int ftype, const t_idef *idef,
const rvec x[], rvec f[], rvec fshift[],
const t_idef *idef,
const rvec x[], history_t *hist,
rvec f[], t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
+ const struct t_pbc *pbc, const struct t_graph *g,
gmx_enerdata_t *enerd, t_nrnb *nrnb,
real *lambda,
const t_mdatoms *md,
void calc_bonds_lambda(const t_idef *idef,
const rvec x[],
t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
+ const struct t_pbc *pbc, const struct t_graph *g,
gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
real *lambda,
const t_mdatoms *md,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff