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anonymous_namespace{bonded.cpp} Namespace Reference

Typedefs

using BondedFunction = real(*)(int nbonds, const t_iatom iatoms[], const t_iparams iparams[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *ddgatindex)
 Type of CPU function to compute a bonded interaction.
 

Functions

int pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
 Compute dx = xi - xj, modulo PBC if non-NULL. More...
 
template<BondedKernelFlavor flavor>
void spreadBondForces (const real bondForce, const rvec dx, const int ai, const int aj, rvec4 *f, int shiftIndex, const t_graph *g, rvec *fshift)
 Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed. More...
 
template<BondedKernelFlavor flavor>
real morse_bonds (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index)
 Morse potential bond. More...
 
int cmap_setup_grid_index (int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
 Mysterious undocumented function.
 

Variables

const int cmap_coeff_matrix []
 Mysterious CMAP coefficient matrix. More...
 

Function Documentation

template<BondedKernelFlavor flavor>
real anonymous_namespace{bonded.cpp}::morse_bonds ( int  nbonds,
const t_iatom  forceatoms[],
const t_iparams  forceparams[],
const rvec  x[],
rvec4  f[],
rvec  fshift[],
const t_pbc pbc,
const t_graph *  g,
real  lambda,
real dvdlambda,
const t_mdatoms md,
t_fcdata *  fcd,
int *  global_atom_index 
)

Morse potential bond.

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)) cb = well depth in kJ/mol

Note: the potential is referenced to be +cb at infinite separation and zero at the equilibrium distance!

int anonymous_namespace{bonded.cpp}::pbc_rvec_sub ( const t_pbc pbc,
const rvec  xi,
const rvec  xj,
rvec  dx 
)

Compute dx = xi - xj, modulo PBC if non-NULL.

Todo:
This kind of code appears in many places. Consolidate it
template<BondedKernelFlavor flavor>
void anonymous_namespace{bonded.cpp}::spreadBondForces ( const real  bondForce,
const rvec  dx,
const int  ai,
const int  aj,
rvec4 *  f,
int  shiftIndex,
const t_graph *  g,
rvec *  fshift 
)
inline

Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed.

When g==nullptr, shiftIndex is used as the periodic shift. When g!=nullptr, the graph is used to compute the periodic shift.

Variable Documentation

const int anonymous_namespace{bonded.cpp}::cmap_coeff_matrix[]
Initial value:
= {
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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -6, 0, 0, -6, 4,
0, 0, 3, -2, 0, 0, 0, 0, 0, 0, -9, 6, 0, 0, 6, -4, 0, 0, 0, 0, 1, 0, -3, 2,
-2, 0, 6, -4, 1, 0, -3, 2, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 3, -2, 1, 0, -3, 2,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 2, 0, 0, 3, -2, 0, 0, 0, 0, 0, 0, 3, -2,
0, 0, -6, 4, 0, 0, 3, -2, 0, 1, -2, 1, 0, 0, 0, 0, 0, -3, 6, -3, 0, 2, -4, 2,
0, 0, 0, 0, 0, 0, 0, 0, 0, 3, -6, 3, 0, -2, 4, -2, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, -3, 3, 0, 0, 2, -2, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 3, -3, 0, 0, -2, 2,
0, 0, 0, 0, 0, 1, -2, 1, 0, -2, 4, -2, 0, 1, -2, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, -1, 2, -1, 0, 1, -2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, -1, 1,
0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 2, -2, 0, 0, -1, 1
}

Mysterious CMAP coefficient matrix.