#include <MsmMap.h>

Inheritance diagram for msm::Grid< T >:

Public Member Functions
	Grid ()

void	init (const IndexRange &n)

void	set (int pia, int pni, int pja, int pnj, int pka, int pnk)

void	setbounds (int pia, int pib, int pja, int pjb, int pka, int pkb)

void	resize (int n)

const T &	operator() (int i, int j, int k) const

const T &	operator() (const Ivec &n) const

const T &	elem (int i, int j, int k) const

T &	operator() (int i, int j, int k)

T &	operator() (const Ivec &n)

T &	elem (int i, int j, int k)

int	flatindex (int i, int j, int k) const

const Array< T > &	data () const

Array< T > &	data ()

void	reset (const T &t)

void	updateLower (const Ivec &n)

Grid< T > &	operator+= (const Grid< T > &g)

void	extract (Grid< T > &g)

template<int N>
Grid< T > &	operator+= (const GridFixed< T, N > &g)

template<int N>
void	extract (GridFixed< T, N > &g)

Public Member Functions inherited from msm::IndexRange
	IndexRange ()

void	set (int pia, int pni, int pja, int pnj, int pka, int pnk)

void	setbounds (int pia, int pib, int pja, int pjb, int pka, int pkb)

int	ia () const

int	ib () const

int	ja () const

int	jb () const

int	ka () const

int	kb () const

int	ni () const

int	nj () const

int	nk () const

int	nn () const

Ivec	lower () const

Ivec	extent () const

int	operator<= (const IndexRange &n)

Additional Inherited Members
Protected Attributes inherited from msm::IndexRange
Ivec	nlower

Ivec	nextent

Detailed Description

template<class T>
class msm::Grid< T >

Definition at line 464 of file MsmMap.h.

Constructor & Destructor Documentation

◆ Grid()

template<class T>

msm::Grid< T >::Grid ( )

inline

Definition at line 602 of file MsmMap.h.

602 { }

Member Function Documentation

◆ data() [1/2]

template<class T>

const Array<T>& msm::Grid< T >::data ( ) const

inline

Definition at line 666 of file MsmMap.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), MsmGridCutoffKernel< Float, Float >::compute(), MsmGridCutoff::compute(), MsmC1HermiteGridCutoff::compute(), MsmC1HermiteGridCutoff::compute_specialized(), MsmBlock::gridCutoff(), MsmC1HermiteBlock::gridCutoff(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), GridMsg::put(), msm::PatchData::sendCharge(), msm::PatchData::sendChargeC1Hermite(), MsmBlock::sumReducedPotential(), and MsmC1HermiteBlock::sumReducedPotential().

666 { return gdata; }

◆ data() [2/2]

template<class T>

Array<T>& msm::Grid< T >::data ( )

inline

Definition at line 667 of file MsmMap.h.

667 { return gdata; }

◆ elem() [1/2]

template<class T>

const T& msm::Grid< T >::elem	(	int	i,
		int	j,
		int	k
	)		const

inline

Definition at line 629 of file MsmMap.h.

Referenced by msm::Grid< Vtype >::operator()().

                                                {
         if (i<ia() || i>ib() || j<ja() || j>jb() || k<ka() || k>kb()) {
           char msg[200];
           snprintf(msg, sizeof(msg), "Grid indexing:\n"
               "ia=%d, ib=%d, i=%d\n"
               "ja=%d, jb=%d, j=%d\n"
               "ka=%d, kb=%d, k=%d\n",
               ia(), ib(), i, ja(), jb(), j, ka(), kb(), k);
           NAMD_die(msg);
         }
         return gdata[flatindex(i,j,k)];
       }

◆ elem() [2/2]

template<class T>

T& msm::Grid< T >::elem	(	int	i,
		int	j,
		int	k
	)

inline

Definition at line 651 of file MsmMap.h.

                                    {
         if (i<ia() || i>ib() || j<ja() || j>jb() || k<ka() || k>kb()) {
           char msg[200];
           snprintf(msg, sizeof(msg), "Grid indexing:\n"
               "ia=%d, ib=%d, i=%d\n"
               "ja=%d, jb=%d, j=%d\n"
               "ka=%d, kb=%d, k=%d\n",
               ia(), ib(), i, ja(), jb(), j, ka(), kb(), k);
           NAMD_die(msg);
         }
         return gdata[flatindex(i,j,k)];
       }

◆ extract() [1/2]

template<class T>

void msm::Grid< T >::extract ( Grid< T > & g )

inline

Definition at line 748 of file MsmMap.h.

Referenced by msm::PatchData::sendCharge(), msm::PatchData::sendChargeC1Hermite(), MsmBlock::sendDownPotential(), MsmC1HermiteBlock::sendDownPotential(), MsmBlock::sendPatch(), MsmC1HermiteBlock::sendPatch(), MsmBlock::sendUpCharge(), and MsmC1HermiteBlock::sendUpCharge().

                                {
         ASSERT(IndexRange(g) <= IndexRange(*this));
         int gni = g.nextent.i;
         int gnj = g.nextent.j;
         int gnk = g.nextent.k;
         int index = 0;
         int ni = nextent.i;
         int nij = nextent.i * nextent.j;
         int koff = (g.nlower.k - nlower.k) * nij
           + (g.nlower.j - nlower.j) * ni + (g.nlower.i - nlower.i);
         T *gbuf = g.gdata.buffer();
         const T *buf = gdata.buffer();
         for (int k = 0;  k < gnk;  k++) {
           int jkoff = k * nij + koff;
           for (int j = 0;  j < gnj;  j++) {
             int ijkoff = j * ni + jkoff;
             for (int i = 0;  i < gni;  i++, index++) {
               gbuf[index] = buf[i + ijkoff];
             }
           }
         }
       }

◆ extract() [2/2]

template<class T>

template<int N>

void msm::Grid< T >::extract ( GridFixed< T, N > & g )

inline

Definition at line 801 of file MsmMap.h.

                                       {
         ASSERT(IndexRange(g) <= IndexRange(*this));
         int gni = g.nextent.i;
         int gnj = g.nextent.j;
         int gnk = g.nextent.k;
         int index = 0;
         int ni = nextent.i;
         int nij = nextent.i * nextent.j;
         int koff = (g.nlower.k - nlower.k) * nij
           + (g.nlower.j - nlower.j) * ni + (g.nlower.i - nlower.i);
         T *gbuf = g.buffer();
         const T *buf = gdata.buffer();
         for (int k = 0;  k < gnk;  k++) {
           int jkoff = k * nij + koff;
           for (int j = 0;  j < gnj;  j++) {
             int ijkoff = j * ni + jkoff;
             for (int i = 0;  i < gni;  i++, index++) {
               gbuf[index] = buf[i + ijkoff];
             }
           }
         }
       }

◆ flatindex()

template<class T>

int msm::Grid< T >::flatindex	(	int	i,
		int	j,
		int	k
	)		const

inline

Definition at line 663 of file MsmMap.h.

Referenced by msm::Grid< Vtype >::elem(), and msm::Grid< Vtype >::operator()().

                                                {
         return ((k-ka())*nj() + (j-ja()))*ni() + (i-ia());
       }

◆ init()

template<class T>

void msm::Grid< T >::init ( const IndexRange & n )

inline

Definition at line 603 of file MsmMap.h.

Referenced by MsmGridCutoffKernel< Float, Float >::compute(), MsmC1HermiteGridCutoff::compute_specialized(), MsmBlockKernel< Float, Float >::MsmBlockKernel(), msm::PatchData::PatchData(), msm::PatchData::sendCharge(), msm::PatchData::sendChargeC1Hermite(), MsmBlock::sendDownPotential(), MsmC1HermiteBlock::sendDownPotential(), MsmBlock::sendPatch(), MsmC1HermiteBlock::sendPatch(), MsmBlock::sendUpCharge(), MsmC1HermiteBlock::sendUpCharge(), MsmGridCutoffKernel< Float, Float >::setup(), MsmGridCutoff::setup(), MsmC1HermiteGridCutoff::setup(), MsmBlock::sumReducedPotential(), and MsmC1HermiteBlock::sumReducedPotential().

                                      {
         nlower = n.lower();
         nextent = n.extent();
         gdata.resize(nn());
       }

◆ operator()() [1/4]

template<class T>

const T& msm::Grid< T >::operator()	(	int	i,
		int	j,
		int	k
	)		const

inline

Definition at line 619 of file MsmMap.h.

Referenced by msm::Grid< Vtype >::operator()().

                                                      {
 #ifdef DEBUG_MSM
         return elem(i,j,k);
 #else
         return gdata[flatindex(i,j,k)];
 #endif
       }

◆ operator()() [2/4]

template<class T>

const T& msm::Grid< T >::operator() ( const Ivec & n ) const

inline

Definition at line 626 of file MsmMap.h.

                                                {
         return this->operator()(n.i, n.j, n.k);
       }

◆ operator()() [3/4]

template<class T>

T& msm::Grid< T >::operator()	(	int	i,
		int	j,
		int	k
	)

inline

Definition at line 641 of file MsmMap.h.

                                          {
 #ifdef DEBUG_MSM
         return elem(i,j,k);
 #else
         return gdata[flatindex(i,j,k)];
 #endif
       }

◆ operator()() [4/4]

template<class T>

T& msm::Grid< T >::operator() ( const Ivec & n )

inline

Definition at line 648 of file MsmMap.h.

                                    {
         return this->operator()(n.i, n.j, n.k);
       }

◆ operator+=() [1/2]

template<class T>

Grid<T>& msm::Grid< T >::operator+= ( const Grid< T > & g )

inline

Definition at line 681 of file MsmMap.h.

                                             {
 #if 1
         ASSERT(IndexRange(g) <= IndexRange(*this));
 #else
         if ( ! (IndexRange(g) <= IndexRange(*this)) ) {
           Grid<T> tmp = *this;
           // expand myself to hold sum
           int ia = nlower.i;
           if (ia > g.nlower.i) ia = g.nlower.i;
           int ja = nlower.j;
           if (ja > g.nlower.j) ja = g.nlower.j;
           int ka = nlower.k;
           if (ka > g.nlower.k) ka = g.nlower.k;
           int ib1 = nlower.i + nextent.i;
           int gib1 = g.nlower.i + g.nextent.i;
           if (ib1 < gib1) ib1 = gib1;
           int jb1 = nlower.j + nextent.j;
           int gjb1 = g.nlower.j + g.nextent.j;
           if (jb1 < gjb1) jb1 = gjb1;
           int kb1 = nlower.k + nextent.k;
           int gkb1 = g.nlower.k + g.nextent.k;
           if (kb1 < gkb1) kb1 = gkb1;
           setbounds(ia, ib1-1, ja, jb1-1, ka, kb1-1);
           reset(0);  // make sure constructor for T accepts "0" as its zero
           // now copy "tmp" grid elements into my expanded self
           int index = 0;
           int ni = nextent.i;
           int nij = nextent.i * nextent.j;
           int koff = (tmp.nlower.k - nlower.k) * nij
             + (tmp.nlower.j - nlower.j) * ni + (tmp.nlower.i - nlower.i);
           const T *gbuf = tmp.gdata.buffer();
           T *buf = gdata.buffer();
           for (int k = 0;  k < tmp.nextent.k;  k++) {
             int jkoff = k * nij + koff;
             for (int j = 0;  j < tmp.nextent.j;  j++) {
               int ijkoff = j * ni + jkoff;
               for (int i = 0;  i < tmp.nextent.i;  i++, index++) {
                 buf[i + ijkoff] = gbuf[index];
               }
             }
           }
         }
 #endif
         int gni = g.nextent.i;
         int gnj = g.nextent.j;
         int gnk = g.nextent.k;
         int index = 0;
         int ni = nextent.i;
         int nij = nextent.i * nextent.j;
         int koff = (g.nlower.k - nlower.k) * nij
           + (g.nlower.j - nlower.j) * ni + (g.nlower.i - nlower.i);
         const T *gbuf = g.gdata.buffer();
         T *buf = gdata.buffer();
         for (int k = 0;  k < gnk;  k++) {
           int jkoff = k * nij + koff;
           for (int j = 0;  j < gnj;  j++) {
             int ijkoff = j * ni + jkoff;
             for (int i = 0;  i < gni;  i++, index++) {
               buf[i + ijkoff] += gbuf[index];
             }
           }
         }
         return(*this);
       }

◆ operator+=() [2/2]

template<class T>

template<int N>

Grid<T>& msm::Grid< T >::operator+= ( const GridFixed< T, N > & g )

inline

Definition at line 774 of file MsmMap.h.

                                                    {
         ASSERT(IndexRange(g) <= IndexRange(*this));
         int gni = g.nextent.i;
         int gnj = g.nextent.j;
         int gnk = g.nextent.k;
         int index = 0;
         int ni = nextent.i;
         int nij = nextent.i * nextent.j;
         int koff = (g.nlower.k - nlower.k) * nij
           + (g.nlower.j - nlower.j) * ni + (g.nlower.i - nlower.i);
         const T *gbuf = g.buffer();
         T *buf = gdata.buffer();
         for (int k = 0;  k < gnk;  k++) {
           int jkoff = k * nij + koff;
           for (int j = 0;  j < gnj;  j++) {
             int ijkoff = j * ni + jkoff;
             for (int i = 0;  i < gni;  i++, index++) {
               buf[i + ijkoff] += gbuf[index];
             }
           }
         }
         return(*this);
       }

◆ reset()

template<class T>

void msm::Grid< T >::reset ( const T & t )

inline

Definition at line 670 of file MsmMap.h.

Referenced by MsmGridCutoffKernel< Float, Float >::compute(), MsmGridCutoff::compute(), MsmC1HermiteGridCutoff::compute(), MsmC1HermiteGridCutoff::compute_specialized(), msm::PatchData::init(), MsmBlockKernel< Float, Float >::init(), ComputeMsmMgr::initialize(), ComputeMsmMgr::initVirialContrib(), and msm::Grid< Vtype >::operator+=().

                              {
         T *buf = gdata.buffer();
         int len = nn();
         for (int n = 0;  n < len;  n++) { buf[n] = t; }
       }

◆ resize()

template<class T>

void msm::Grid< T >::resize ( int n )

inline

Definition at line 616 of file MsmMap.h.

Referenced by msm::PatchData::PatchData().

                          { // reserve space but don't set grid indexing
         gdata.resize(n);
       }

◆ set()

template<class T>

void msm::Grid< T >::set	(	int	pia,
		int	pni,
		int	pja,
		int	pnj,
		int	pka,
		int	pnk
	)

inline

Definition at line 608 of file MsmMap.h.

Referenced by MsmGridCutoffKernel< Float, Float >::compute(), MsmC1HermiteGridCutoff::compute_specialized(), and ComputeMsmMgr::initialize().

                                                                      {
         IndexRange::set(pia, pni, pja, pnj, pka, pnk);
         gdata.resize(nn());
       }

◆ setbounds()

template<class T>

void msm::Grid< T >::setbounds	(	int	pia,
		int	pib,
		int	pja,
		int	pjb,
		int	pka,
		int	pkb
	)

inline

Definition at line 612 of file MsmMap.h.

Referenced by ComputeMsmMgr::initialize(), and msm::Grid< Vtype >::operator+=().

                                                                            {
         IndexRange::setbounds(pia, pib, pja, pjb, pka, pkb);
         gdata.resize(nn());
       }

◆ updateLower()

template<class T>

void msm::Grid< T >::updateLower ( const Ivec & n )

inline

Definition at line 677 of file MsmMap.h.

Referenced by MsmGridCutoffKernel< Float, Float >::compute(), MsmC1HermiteGridCutoff::compute_specialized(), msm::PatchData::sendCharge(), msm::PatchData::sendChargeC1Hermite(), MsmBlock::sendDownPotential(), MsmC1HermiteBlock::sendDownPotential(), MsmBlock::sendPatch(), MsmC1HermiteBlock::sendPatch(), MsmBlock::sendUpCharge(), and MsmC1HermiteBlock::sendUpCharge().

677 { nlower = n; }

msm::IndexRange::nlower

Ivec nlower

Definition: MsmMap.h:458

The documentation for this class was generated from the following file:

MsmMap.h

Public Member Functions

Additional Inherited Members

Detailed Description

template<class T> class msm::Grid< T >

Constructor & Destructor Documentation

◆ Grid()

Member Function Documentation

◆ data() [1/2]

◆ data() [2/2]

◆ elem() [1/2]

◆ elem() [2/2]

◆ extract() [1/2]

◆ extract() [2/2]

◆ flatindex()

◆ init()

◆ operator()() [1/4]

◆ operator()() [2/4]

◆ operator()() [3/4]

◆ operator()() [4/4]

◆ operator+=() [1/2]

◆ operator+=() [2/2]

◆ reset()

◆ resize()

◆ set()

◆ setbounds()

◆ updateLower()

template<class T>
class msm::Grid< T >