settle.cpp File Reference

#include "gmxpre.h"
#include "settle.h"
#include <cassert>
#include <cmath>
#include <cstdio>
#include <algorithm>
#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_simd.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"

Include dependency graph for settle.cpp:

Description

Defines SETTLE code.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

Functions
static void	gmx::initializeProjectionMatrix (const real invmO, const real invmH, const real dOH, const real dHH, matrix inverseCouplingMatrix)
	Initializes a projection matrix. More...
SettleParameters	gmx::settleParameters (real mO, real mH, real dOH, real invmO, real invmH, real dHH)
	Computes and returns settle parameters. More...
void	gmx::settle_proj (const SettleData &settled, ConstraintVariable econq, int nsettle, const int iatoms[], const t_pbc *pbc,ArrayRef< const RVec > x, ArrayRef< RVec > der, ArrayRef< RVec > derp, int CalcVirAtomEnd, tensor vir_r_m_dder)
	Analytical algorithm to subtract the components of derivatives of coordinates working on settle type constraint.
template<typename T , typename TypeBool , int packSize, typename TypePbc , bool bCorrectVelocity, bool bCalcVirial>
static void	gmx::settleTemplate (const SettleData &settled, int settleStart, int settleEnd, const TypePbc pbc, const real *x, real *xprime, real invdt, real *gmx_restrict v, tensor vir_r_m_dr, bool *bErrorHasOccurred)
	The actual settle code, templated for real/SimdReal and for optimization.
template<typename T , typename TypeBool , int packSize, typename TypePbc >
static void	gmx::settleTemplateWrapper (const SettleData &settled, int nthread, int thread, TypePbc pbc, const real x[], real xprime[], real invdt, real *v, bool bCalcVirial, tensor vir_r_m_dr, bool *bErrorHasOccurred)
	Wrapper template function that divides the settles over threads and instantiates the core template with instantiated booleans.
void	gmx::csettle (const SettleData &settled,int nthread,int thread,const t_pbc *pbc,ArrayRefWithPadding< const RVec > x,ArrayRefWithPadding< RVec > xprime,real invdt,ArrayRefWithPadding< RVec > v,bool bCalcVirial,tensor vir_r_m_dr,bool *bErrorHasOccurred)
	Constrain coordinates using SETTLE. Can be called on any number of threads.