GridforceGrid Class Reference

#include <GridForceGrid.h>

Inheritance diagram for GridforceGrid:

Public Types
enum	GridforceGridType { GridforceGridTypeUndefined = 0, GridforceGridTypeFull, GridforceGridTypeLite }

Public Member Functions
virtual	~GridforceGrid ()
virtual void	initialize (char *potfilename, SimParameters *simParams, MGridforceParams *mgridParams)=0
virtual void	reinitialize (SimParameters *simParams, MGridforceParams *mgridParams)=0
virtual Position	get_center (void) const =0
virtual Position	get_origin (void) const =0
virtual Tensor	get_e (void) const =0
virtual Tensor	get_inv (void) const =0
virtual Vector	get_scale (void) const =0
virtual Bool	get_checksize (void) const =0
virtual int	get_k0 (void) const =0
virtual int	get_k1 (void) const =0
virtual int	get_k2 (void) const =0
virtual int	get_total_grids (void) const =0
virtual long int	get_all_gridvals (float **all_gridvals) const =0
virtual void	set_all_gridvals (float *all_gridvals, long int sz)=0
virtual void	set_scale (Vector s)=0
Position	wrap_position (const Position &pos, const Lattice &lattice)
bool	fits_lattice (const Lattice &lattice)
virtual int	compute_VdV (Position pos, float &V, Vector &dV) const =0
GridforceGridType	get_grid_type (void)

Static Public Member Functions
static GridforceGrid *	new_grid (int gridnum, char *potfilename, SimParameters *simParams, MGridforceParams *mgridParams)
static void	pack_grid (GridforceGrid *grid, MOStream *msg)
static GridforceGrid *	unpack_grid (int gridnum, MIStream *msg)

Protected Member Functions
virtual void	pack (MOStream *msg) const =0
virtual void	unpack (MIStream *msg)=0
Position	get_corner (int idx)
	GridforceGrid ()

Protected Attributes
GridforceGridType	type
int	mygridnum

Detailed Description

Definition at line 27 of file GridForceGrid.h.

Member Enumeration Documentation

GridforceGridType

enum GridforceGrid::GridforceGridType

Enumerator
GridforceGridTypeUndefined
GridforceGridTypeFull
GridforceGridTypeLite

Definition at line 58 of file GridForceGrid.h.

                 {
        GridforceGridTypeUndefined = 0,
        GridforceGridTypeFull,
        GridforceGridTypeLite
    } GridforceGridType;

Constructor & Destructor Documentation

~GridforceGrid()

GridforceGrid::~GridforceGrid ( )

virtual

Definition at line 48 of file GridForceGrid.C.

{ ; }

GridforceGrid()

GridforceGrid::GridforceGrid ( )

inlineprotected

Definition at line 72 of file GridForceGrid.h.

References GridforceGridTypeUndefined, and type.

{ type = GridforceGridTypeUndefined; }

Member Function Documentation

compute_VdV()

virtual int GridforceGrid::compute_VdV ( Position  pos, float &  V, Vector &  dV  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

fits_lattice()

bool GridforceGrid::fits_lattice

(

const Lattice &

lattice

)

Definition at line 84 of file GridForceGrid.C.

References DebugM, endi(), get_center(), get_corner(), and wrap_position().

Referenced by ComputeGridForce::doForce(), and GridforceFullMainGrid::initialize().

{
    // Idea: Go through each grid corner and wrap it to the grid center;
    // if the position moves, then the grid is too big and we return false
    DebugM(4, "Checking whether grid fits periodic cell\n");
    Position center = get_center();
    for (int i = 0; i < 8; i++) {
        Position pos = get_corner(i);
        Position pos_wrapped = wrap_position(pos, lattice);
        if ((pos - pos_wrapped).length() > 1.) {
            DebugM(5, "(" << pos << ") != (" << pos_wrapped << ")\n" << endi);
            return false;
        }
    }
    return true;
}

get_all_gridvals()

virtual long int GridforceGrid::get_all_gridvals ( float **  all_gridvals ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

get_center()

virtual Position GridforceGrid::get_center ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by ComputeGridForce::doForce(), fits_lattice(), and wrap_position().

get_checksize()

virtual Bool GridforceGrid::get_checksize ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by ComputeGridForce::doForce().

get_corner()

Position GridforceGrid::get_corner ( int  idx )

protected

Definition at line 101 of file GridForceGrid.C.

References DebugM, endi(), get_e(), get_k0(), get_k1(), get_k2(), and get_origin().

Referenced by fits_lattice().

{
    // idx -> (x,y,z) (cell basis coordinates)
    // 0 -> (0,0,0)
    // 1 -> (1,0,0)
    // 2 -> (0,1,0)
    // 3 -> (1,1,0)
    // 4 -> (0,0,1)
    // 5 -> (1,0,1)
    // 6 -> (0,1,1)
    // 7 -> (1,1,1)
    Position pos;
    if (idx >= 8 || idx < 0) {
        // invalid index
        pos = Vector(); // default value of Vector() is strange enough to be a decent "undefined" value (-99999, -99999, -999999)
    } else if (corners[idx] != Vector()) {
        // use cached value if possible
        pos = corners[idx];
    } else {
        // must calculate
        Tensor e = get_e();
        pos = get_origin();
        if (idx & (1 << 0)) pos += e * Vector(get_k0()-1, 0, 0);
        if (idx & (1 << 1)) pos += e * Vector(0, get_k1()-1, 0);
        if (idx & (1 << 2)) pos += e * Vector(0, 0, get_k2()-1);
        corners[idx] = pos;     // cache for future use
        DebugM(4, "corner " << idx << " = " << pos << "\n" << endi);
    }
    return pos;
}

get_e()

virtual Tensor GridforceGrid::get_e ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by ComputeGridForce::doForce(), and get_corner().

get_grid_type()

GridforceGridType GridforceGrid::get_grid_type ( void  )

inline

Definition at line 64 of file GridForceGrid.h.

References type.

Referenced by colvarproxy_namd::compute_volmap(), ComputeGridForce::doForce(), and pack_grid().

{ return type; }

get_inv()

virtual Tensor GridforceGrid::get_inv ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

get_k0()

virtual int GridforceGrid::get_k0 ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by get_corner().

get_k1()

virtual int GridforceGrid::get_k1 ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by get_corner().

get_k2()

virtual int GridforceGrid::get_k2 ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by get_corner().

get_origin()

virtual Position GridforceGrid::get_origin ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by get_corner().

get_scale()

virtual Vector GridforceGrid::get_scale ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by ComputeGridForce::doForce(), and colvarproxy_namd::init_volmap_by_name().

get_total_grids()

virtual int GridforceGrid::get_total_grids ( void  ) const

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

initialize()

virtual void GridforceGrid::initialize ( char *  potfilename, SimParameters *  simParams, MGridforceParams *  mgridParams  )

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by new_grid().

new_grid()

GridforceGrid * GridforceGrid::new_grid ( int  gridnum, char *  potfilename, SimParameters *  simParams, MGridforceParams *  mgridParams  )

static

Definition at line 34 of file GridForceGrid.C.

References MGridforceParams::gridforceLite, initialize(), and simParams.

Referenced by Molecule::build_gridforce_params().

{
    GridforceGrid *grid = NULL;
    if (mgridParams->gridforceLite) {
        grid = new GridforceLiteGrid(gridnum);
    } else {
        grid = new GridforceFullMainGrid(gridnum);
    }
    
    grid->initialize(potfilename, simParams, mgridParams);
    
    return grid;
}

pack()

virtual void GridforceGrid::pack ( MOStream *  msg ) const

protectedpure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by pack_grid().

pack_grid()

void GridforceGrid::pack_grid ( GridforceGrid *  grid, MOStream *  msg  )

static

Definition at line 50 of file GridForceGrid.C.

References get_grid_type(), pack(), and MOStream::put().

Referenced by Node::reloadGridforceGrid(), and Molecule::send_Molecule().

{
    // Abstract interface for packing a grid into a message.  This
    // could easily be a non-static function as it was before, but is
    // static to make it similar to unpack_grid below, which does need
    // to be static since it creates a GridforceGrid object.
    msg->put(grid->get_grid_type());
    grid->pack(msg);
}

reinitialize()

virtual void GridforceGrid::reinitialize ( SimParameters *  simParams, MGridforceParams *  mgridParams  )

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by Node::reloadGridforceGrid().

set_all_gridvals()

virtual void GridforceGrid::set_all_gridvals ( float *  all_gridvals, long int  sz  )

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

set_scale()

virtual void GridforceGrid::set_scale ( Vector  s )

pure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by Node::updateGridScale().

unpack()

virtual void GridforceGrid::unpack ( MIStream *  msg )

protectedpure virtual

Implemented in GridforceLiteGrid, and GridforceFullMainGrid.

Referenced by unpack_grid().

unpack_grid()

GridforceGrid * GridforceGrid::unpack_grid ( int  gridnum, MIStream *  msg  )

static

Definition at line 60 of file GridForceGrid.C.

References MIStream::get(), GridforceGridTypeFull, GridforceGridTypeLite, NAMD_bug(), type, and unpack().

Referenced by Molecule::receive_Molecule(), and Node::reloadGridforceGrid().

{
    // Abstract interface for unpacking a grid from a message.
    GridforceGrid *grid = NULL;
    int type;
    
    msg->get(type);
    
    switch (type) {
    case GridforceGridTypeFull:
        grid = new GridforceFullMainGrid(gridnum);
        break;
    case GridforceGridTypeLite:
        grid = new GridforceLiteGrid(gridnum);
        break;
    default:
        NAMD_bug("GridforceGrid::unpack_grid called with unknown grid type!");
    }
    
    grid->unpack(msg);
    
    return grid;
}

wrap_position()

Position GridforceGrid::wrap_position ( const Position &  pos, const Lattice &  lattice  )

inline

Definition at line 463 of file GridForceGrid.inl.

References get_center(), Lattice::origin(), and Lattice::wrap_delta().

Referenced by fits_lattice().

{
    // Wrap 'pos' about grid center, using periodic cell information in 'lattice'
    // Position pos_wrapped = pos;
    // Position center = get_center();
    // pos_wrapped += lattice.wrap_delta(pos);
    // pos_wrapped += lattice.delta(pos_wrapped, center) - (pos_wrapped - center);
    
    Position pos_wrapped = pos + lattice.wrap_delta(pos - get_center() + lattice.origin());
    
    return pos_wrapped;
}

Member Data Documentation

mygridnum

int GridforceGrid::mygridnum

protected

Definition at line 74 of file GridForceGrid.h.

Referenced by GridforceFullMainGrid::GridforceFullMainGrid(), GridforceLiteGrid::GridforceLiteGrid(), GridforceFullMainGrid::initialize(), GridforceLiteGrid::initialize(), GridforceFullMainGrid::pack(), and GridforceFullMainGrid::unpack().

type

GridforceGridType GridforceGrid::type

protected

Definition at line 73 of file GridForceGrid.h.

Referenced by get_grid_type(), GridforceFullMainGrid::GridforceFullMainGrid(), GridforceGrid(), GridforceLiteGrid::GridforceLiteGrid(), and unpack_grid().

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

• GridForceGrid.h
• GridForceGrid.C
• GridForceGrid.inl