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GridforceLiteGrid Class Reference

#include <GridForceGrid.h>

Inheritance diagram for GridforceLiteGrid:

GridforceGrid List of all members.

Public Member Functions

 GridforceLiteGrid (int gridnum)
virtual ~GridforceLiteGrid ()
void initialize (char *potfilename, SimParameters *simParams, MGridforceParams *mgridParams)
void reinitialize (SimParameters *simParams, MGridforceParams *mgridParams)
Position get_center (void) const
Position get_origin (void) const
Tensor get_e (void) const
Tensor get_inv (void) const
Vector get_scale (void) const
int get_k0 (void) const
int get_k1 (void) const
int get_k2 (void) const
int get_total_grids (void) const
float get_grid (int i0, int i1, int i2, int i3) const
double get_grid_d (int i0, int i1, int i2, int i3) const
void set_grid (int i0, int i1, int i2, int i3, float V)
int get_all_gridvals (float **all_gridvals) const
void set_all_gridvals (float *all_gridvals, int sz)
int compute_VdV (Position pos, float &V, Vector &dV) const

Protected Member Functions

void compute_derivative_grids (void)
void compute_wts (float *wts, const Vector &dg) const
int get_inds (Position pos, int *inds, Vector &dg) const
float linear_interpolate (int i0, int i1, int i2, int i3, const float *wts) const
void pack (MOStream *msg) const
void unpack (MIStream *msg)
int grid_index (int i0, int i1, int i2, int i3) const

Protected Attributes

float * grid
int k [4]
int size
int dk [4]
Position origin
Position center
Tensor e
Tensor inv
Vector scale
char filename [129]

Constructor & Destructor Documentation

GridforceLiteGrid::GridforceLiteGrid (  int  gridnum  )  [explicit]
 

Definition at line 1291 of file GridForceGrid.C.

References grid.

01292 {
01293     mygridnum = gridnum;
01294     grid = NULL;
01295     type = GridforceGridTypeLite;
01296 }

GridforceLiteGrid::~GridforceLiteGrid (   )  [virtual]
 

Definition at line 1299 of file GridForceGrid.C.

01300 {
01301     delete[] grid;
01302 }

Member Function Documentation

void GridforceLiteGrid::compute_derivative_grids (  void   )  [protected]
 

Definition at line 1355 of file GridForceGrid.C.

References DebugM, endi(), get_grid(), get_grid_d(), k, and set_grid().

Referenced by initialize().

01356 {
01357     // calculate derivative grids
01358     // separate loop so all V values have been set already
01359     for (int i0 = 0; i0 < k[0]; i0++) {
01360         for (int i1 = 0; i1 < k[1]; i1++) {
01361             for (int i2 = 0; i2 < k[2]; i2++) {
01362                 float dx, dy, dz;
01363                 if (i0 == 0 || i0 == k[0]-1 || i1 == 0 || i1 == k[1]-1 || i2 == 0 || i2 == k[2]-1) {
01364                     // on edge, set ALL derivatives to zero (make up for lack of padding)
01365                     dx = 0;
01366                     dy = 0;
01367                     dz = 0;
01368                 } else {
01369                     dx = 0.5 * (get_grid_d(i0+1,i1,i2,0) - get_grid_d(i0-1,i1,i2,0));
01370                     dy = 0.5 * (get_grid_d(i0,i1+1,i2,0) - get_grid_d(i0,i1-1,i2,0));
01371                     dz = 0.5 * (get_grid_d(i0,i1,i2+1,0) - get_grid_d(i0,i1,i2-1,0));
01372                 }
01373                 set_grid(i0, i1, i2, 1, dx);
01374                 set_grid(i0, i1, i2, 2, dy);
01375                 set_grid(i0, i1, i2, 3, dz);
01376                 DebugM(1, "dx[" << i0 << "," << i1 << "," << i2 << "] = " << get_grid(i0, i1, i2, 1) << "(" << dx << ")\n" << endi);
01377                 DebugM(1, "dy[" << i0 << "," << i1 << "," << i2 << "] = " << get_grid(i0, i1, i2, 2) << "(" << dy << ")\n" << endi);
01378                 DebugM(1, "dz[" << i0 << "," << i1 << "," << i2 << "] = " << get_grid(i0, i1, i2, 3) << "(" << dz << ")\n" << endi);
01379             }
01380         }
01381     }
01382 }

int GridforceLiteGrid::compute_VdV (  Position  pos,
float &  V,
Vector &  dV
)  const [inline]
 

Reimplemented from GridforceGrid.

Definition at line 66 of file GridForceGrid.inl.

References compute_wts(), get_inds(), linear_interpolate(), and Position.

00067 {
00068     int inds[3];
00069     Vector g, dg;
00070     
00071     int err = get_inds(pos, inds, dg);
00072     if (err) {
00073         return -1;
00074     }
00075     
00076     float wts[8];
00077     float results[4];
00078     
00079     compute_wts(wts, dg);
00080     for (int i = 0; i < 4; i++) {
00081         results[i] = linear_interpolate(inds[0], inds[1], inds[2], i, wts);
00082     }
00083     
00084     V = results[0];
00085     dV = Vector(results[1], results[2], results[3]) * inv;
00086     
00087     return 0;
00088 }

void GridforceLiteGrid::compute_wts (  float *  wts,
const Vector &  dg
)  const [inline, protected]
 

Definition at line 360 of file GridForceGrid.inl.

References DebugM, endi(), Vector::x, Vector::y, and Vector::z.

Referenced by compute_VdV().

00361 {
00362     wts[0] = (1-dg.x) * (1-dg.y) * (1-dg.z);
00363     wts[1] = (1-dg.x) * (1-dg.y) *   dg.z;
00364     wts[2] = (1-dg.x) *   dg.y   * (1-dg.z);
00365     wts[3] = (1-dg.x) *   dg.y   *   dg.z;
00366     wts[4] =   dg.x   * (1-dg.y) * (1-dg.z);
00367     wts[5] =   dg.x   * (1-dg.y) *   dg.z;
00368     wts[6] =   dg.x   *   dg.y   * (1-dg.z);
00369     wts[7] =   dg.x   *   dg.y   *   dg.z;
00370     DebugM(2, "dg = " << dg << "\n" << endi);
00371 }

int GridforceLiteGrid::get_all_gridvals (  float **  all_gridvals  )  const [virtual]
 

Implements GridforceGrid.

Definition at line 1431 of file GridForceGrid.C.

References DebugM, endi(), and grid.

01432 {
01433     // Creates a flat array of all grid values and puts it in the
01434     // value pointed to by the 'all_gridvals' argument. Returns the
01435     // resulting array size. Caller is responsible for destroying the
01436     // array via 'delete[]'
01437     
01438     DebugM(4, "GridforceLiteGrid::get_all_gridvals called\n" << endi);
01439     
01440     int sz = size;
01441     DebugM(4, "size = " << sz << "\n" << endi);
01442     
01443     float *grid_vals = new float[sz];
01444     int idx = 0;
01445     for (int i = 0; i < size; i++) {
01446         grid_vals[idx++] = grid[i];
01447     }
01448     CmiAssert(idx == sz);
01449     
01450     *all_gridvals = grid_vals;
01451     
01452     DebugM(4, "GridforceLiteGrid::get_all_gridvals finished\n" << endi);
01453     
01454     return sz;
01455 }

Position GridforceLiteGrid::get_center (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 285 of file GridForceGrid.h.

References Position.

00285 { return center; }

Tensor GridforceLiteGrid::get_e (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 287 of file GridForceGrid.h.

00287 { return e; }

float GridforceLiteGrid::get_grid (  int  i0,
int  i1,
int  i2,
int  i3
)  const [inline]
 

Definition at line 295 of file GridForceGrid.h.

References grid, and grid_index().

Referenced by compute_derivative_grids(), initialize(), and linear_interpolate().

00295                                                                 {
00296         return grid[grid_index(i0, i1, i2, i3)];
00297     }

double GridforceLiteGrid::get_grid_d (  int  i0,
int  i1,
int  i2,
int  i3
)  const [inline]
 

Definition at line 298 of file GridForceGrid.h.

References grid, and grid_index().

Referenced by compute_derivative_grids().

00298                                                                    {
00299         return double(grid[grid_index(i0, i1, i2, i3)]);
00300     }

int GridforceLiteGrid::get_inds (  Position  pos,
int *  inds,
Vector &  dg
)  const [inline, protected]
 

Definition at line 338 of file GridForceGrid.inl.

References inv, k, and Position.

Referenced by compute_VdV().

00339 {
00340     Vector p = pos - origin;
00341     Vector g;
00342     
00343     g = inv * p;
00344     
00345     for (int i = 0; i < 3; i++) {
00346         inds[i] = (int)floor(g[i]);
00347         dg[i] = g[i] - inds[i];
00348     }
00349     
00350     for (int i = 0; i < 3; i++) {
00351         if (inds[i] < 0 || inds[i] >= k[i]-1) {
00352             return -1;  // Outside potential and grid is not continuous
00353         }
00354     }
00355     
00356     return 0;
00357 }

Tensor GridforceLiteGrid::get_inv (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 288 of file GridForceGrid.h.

00288 { return inv; }

int GridforceLiteGrid::get_k0 (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 290 of file GridForceGrid.h.

References k.

00290 { return k[0]; }

int GridforceLiteGrid::get_k1 (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 291 of file GridForceGrid.h.

References k.

00291 { return k[1]; }

int GridforceLiteGrid::get_k2 (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 292 of file GridForceGrid.h.

References k.

00292 { return k[2]; }

Position GridforceLiteGrid::get_origin (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 286 of file GridForceGrid.h.

References Position.

00286 { return origin; }

Vector GridforceLiteGrid::get_scale (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 289 of file GridForceGrid.h.

00289 { return scale; }

int GridforceLiteGrid::get_total_grids (  void   )  const [inline, virtual]
 

Implements GridforceGrid.

Definition at line 293 of file GridForceGrid.h.

00293 { return 1; }

int GridforceLiteGrid::grid_index (  int  i0,
int  i1,
int  i2,
int  i3
)  const [inline, protected]
 

Definition at line 319 of file GridForceGrid.h.

References dk.

Referenced by get_grid(), get_grid_d(), and set_grid().

00319                                                                 {
00320         // 'i3' is an index for the grid itself (0=V, 1=dV/dx, 2=dV/dy, 3=dV/dz)
00321         register int inds[4] = {i0, i1, i2, i3};
00322         return inds[0]*dk[0] + inds[1]*dk[1] + inds[2]*dk[2] + inds[3]*dk[3];
00323     }

void GridforceLiteGrid::initialize (  char *  potfilename,
SimParameters *  simParams,
MGridforceParams *  mgridParams
)  [virtual]
 

Implements GridforceGrid.

Definition at line 1305 of file GridForceGrid.C.

References center, compute_derivative_grids(), DebugM, dk, e, endi(), filename, GridforceFullMainGrid::get_center(), GridforceFullMainGrid::get_e(), get_grid(), GridforceFullBaseGrid::get_grid(), GridforceFullMainGrid::get_inv(), GridforceFullMainGrid::get_k0(), GridforceFullMainGrid::get_k1(), GridforceFullMainGrid::get_k2(), GridforceFullMainGrid::get_origin(), GridforceFullMainGrid::get_scale(), GridforceFullMainGrid::get_total_grids(), grid, GridforceFullMainGrid::initialize(), inv, k, NAMD_die(), origin, scale, set_grid(), simParams, and size.

Referenced by reinitialize().

01306 {
01307     // cheat and use GridforceFullMainGrid to read the file
01308     GridforceFullMainGrid *tmp_grid = new GridforceFullMainGrid(mygridnum);
01309     tmp_grid->initialize(potfilename, simParams, mgridParams, 1);
01310     
01311     if (tmp_grid->get_total_grids() != 1) {
01312         NAMD_die("Cannot use gridforcelite option with multi-resolution grid!");
01313     }
01314     
01315     // save file name so that grid can be re-read via Tcl
01316     strcpy(filename, potfilename);
01317     
01318     // copy parameters
01319     k[0] = tmp_grid->get_k0();
01320     k[1] = tmp_grid->get_k1();
01321     k[2] = tmp_grid->get_k2();
01322     k[3] = 4;   // for V, dV/dx, dV/dy, dV/dz grids
01323     origin = tmp_grid->get_origin();
01324     center = tmp_grid->get_center();
01325     e = tmp_grid->get_e();
01326     inv = tmp_grid->get_inv();
01327     scale = tmp_grid->get_scale();
01328     
01329     // calculate rest of parameters
01330     size = k[0] * k[1] * k[2] * k[3];
01331     dk[0] = k[1] * k[2] * k[3];
01332     dk[1] = k[2] * k[3];
01333     dk[2] = k[3];
01334     dk[3] = 1;
01335     
01336     // copy the potential grid
01337     delete[] grid;
01338     grid = new float[size];
01339     for (int i0 = 0; i0 < k[0]; i0++) {
01340         for (int i1 = 0; i1 < k[1]; i1++) {
01341             for (int i2 = 0; i2 < k[2]; i2++) {
01342                 float V = tmp_grid->get_grid(i0, i1, i2);
01343                 set_grid(i0, i1, i2, 0, V);
01344                 DebugM(1, "V[" << i0 << "," << i1 << "," << i2 << "] = " << get_grid(i0, i1, i2, 0) << "(" << V << ")\n" << endi);
01345             }
01346         }
01347     }
01348     
01349     delete tmp_grid;
01350     
01351     compute_derivative_grids();
01352 }

float GridforceLiteGrid::linear_interpolate (  int  i0,
int  i1,
int  i2,
int  i3,
const float *  wts
)  const [inline, protected]
 

Definition at line 374 of file GridForceGrid.inl.

References DebugM, endi(), and get_grid().

Referenced by compute_VdV().

00375 {
00376 #ifdef DEBUGM
00377     float vals[8];
00378     vals[0] = get_grid(i0,   i1,   i2,   i3);
00379     vals[1] = get_grid(i0,   i1,   i2+1, i3);
00380     vals[2] = get_grid(i0,   i1+1, i2,   i3);
00381     vals[3] = get_grid(i0,   i1+1, i2+1, i3);
00382     vals[4] = get_grid(i0+1, i1,   i2,   i3);
00383     vals[5] = get_grid(i0+1, i1,   i2+1, i3);
00384     vals[6] = get_grid(i0+1, i1+1, i2,   i3);
00385     vals[7] = get_grid(i0+1, i1+1, i2+1, i3);
00386     
00387     switch (i3) {
00388     case 0:
00389         DebugM(2, "V\n" << endi);
00390         break;
00391     case 1:
00392         DebugM(2, "dV/dx\n" << endi);
00393         break;
00394     case 2:
00395         DebugM(2, "dV/dy\n" << endi);
00396         break;
00397     case 3:
00398         DebugM(2, "dV/dz\n" << endi);
00399         break;
00400     }
00401     
00402     for (int i = 0; i < 8; i++) {
00403         DebugM(2, "vals[" << i << "] = " << vals[i] << " wts[" << i << "] = " << wts[i] << "\n" << endi);
00404     }
00405 #endif
00406     
00407     float result =
00408         wts[0] * get_grid(i0,   i1,   i2,   i3) +
00409         wts[1] * get_grid(i0,   i1,   i2+1, i3) +
00410         wts[2] * get_grid(i0,   i1+1, i2,   i3) +
00411         wts[3] * get_grid(i0,   i1+1, i2+1, i3) +
00412         wts[4] * get_grid(i0+1, i1,   i2,   i3) +
00413         wts[5] * get_grid(i0+1, i1,   i2+1, i3) +
00414         wts[6] * get_grid(i0+1, i1+1, i2,   i3) +
00415         wts[7] * get_grid(i0+1, i1+1, i2+1, i3);
00416     
00417     DebugM(2, "result = " << result << "\n" << endi);
00418     
00419     return result;
00420 }

void GridforceLiteGrid::pack (  MOStream *  msg  )  const [protected, virtual]
 

Implements GridforceGrid.

Definition at line 1391 of file GridForceGrid.C.

References center, dk, e, filename, grid, inv, k, origin, MOStream::put(), scale, and size.

01392 {
01393     msg->put(4*sizeof(int), (char*)k);
01394     msg->put(size);
01395     msg->put(4*sizeof(int), (char*)dk);
01396     
01397     msg->put(sizeof(Vector), (char*)&origin);
01398     msg->put(sizeof(Vector), (char*)&center);
01399     msg->put(sizeof(Tensor), (char*)&e);
01400     msg->put(sizeof(Tensor), (char*)&inv);
01401     msg->put(sizeof(Vector), (char*)&scale);
01402     
01403     msg->put(129*sizeof(char), (char*)filename);
01404     
01405     msg->put(size*sizeof(float), (char*)grid);
01406 }

void GridforceLiteGrid::reinitialize (  SimParameters *  simParams,
MGridforceParams *  mgridParams
)  [virtual]
 

Implements GridforceGrid.

Definition at line 1385 of file GridForceGrid.C.

References filename, initialize(), and simParams.

01386 {
01387     initialize(filename, simParams, mgridParams);
01388 }

void GridforceLiteGrid::set_all_gridvals (  float *  all_gridvals,
int  sz
)  [virtual]
 

Implements GridforceGrid.

Definition at line 1458 of file GridForceGrid.C.

References DebugM, endi(), and grid.

01459 {
01460     DebugM(4, "GridforceLiteGrid::set_all_gridvals called\n" << endi);
01461     
01462     int sz_calc = size;
01463     CmiAssert(sz == sz_calc);
01464     
01465     int idx = 0;
01466     for (int i = 0; i < size; i++) {
01467         grid[i] = all_gridvals[idx++];
01468     }
01469     CmiAssert(idx == sz);
01470     
01471     //compute_derivative_grids();       // not needed if we're sending all 4 grids
01472     
01473     DebugM(4, "GridforceLiteGrid::set_all_gridvals finished\n" << endi);
01474 }

void GridforceLiteGrid::set_grid (  int  i0,
int  i1,
int  i2,
int  i3,
float  V
)  [inline]
 

Definition at line 301 of file GridForceGrid.h.

References grid, and grid_index().

Referenced by compute_derivative_grids(), and initialize().

00301                                                                   {
00302         grid[grid_index(i0, i1, i2, i3)] = V;
00303     }

void GridforceLiteGrid::unpack (  MIStream *  msg  )  [protected, virtual]
 

Implements GridforceGrid.

Definition at line 1409 of file GridForceGrid.C.

References center, dk, e, filename, MIStream::get(), grid, inv, k, origin, scale, and size.

01410 {
01411     msg->get(4*sizeof(int), (char*)k);
01412     msg->get(size);
01413     msg->get(4*sizeof(int), (char*)dk);
01414     
01415     msg->get(sizeof(Vector), (char*)&origin);
01416     msg->get(sizeof(Vector), (char*)&center);
01417     msg->get(sizeof(Tensor), (char*)&e);
01418     msg->get(sizeof(Tensor), (char*)&inv);
01419     msg->get(sizeof(Vector), (char*)&scale);
01420     
01421     msg->get(129*sizeof(char), (char*)filename);
01422     
01423     if (size) {
01424         delete[] grid;
01425         grid = new float[size];
01426         msg->get(size*sizeof(float), (char*)grid);
01427     }
01428 }

Member Data Documentation

Position GridforceLiteGrid::center [protected]
 

Definition at line 332 of file GridForceGrid.h.

Referenced by initialize(), pack(), and unpack().

int GridforceLiteGrid::dk[4] [protected]
 

Definition at line 329 of file GridForceGrid.h.

Referenced by grid_index(), initialize(), pack(), and unpack().

Tensor GridforceLiteGrid::e [protected]
 

Definition at line 333 of file GridForceGrid.h.

Referenced by initialize(), pack(), and unpack().

char GridforceLiteGrid::filename[129] [protected]
 

Definition at line 338 of file GridForceGrid.h.

Referenced by initialize(), pack(), reinitialize(), and unpack().

float* GridforceLiteGrid::grid [protected]
 

Definition at line 325 of file GridForceGrid.h.

Referenced by get_all_gridvals(), get_grid(), get_grid_d(), GridforceLiteGrid(), initialize(), pack(), set_all_gridvals(), set_grid(), and unpack().

Tensor GridforceLiteGrid::inv [protected]
 

Definition at line 334 of file GridForceGrid.h.

Referenced by get_inds(), initialize(), pack(), and unpack().

int GridforceLiteGrid::k[4] [protected]
 

Definition at line 327 of file GridForceGrid.h.

Referenced by compute_derivative_grids(), get_inds(), get_k0(), get_k1(), get_k2(), initialize(), pack(), and unpack().

Position GridforceLiteGrid::origin [protected]
 

Definition at line 331 of file GridForceGrid.h.

Referenced by initialize(), pack(), and unpack().

Vector GridforceLiteGrid::scale [protected]
 

Definition at line 336 of file GridForceGrid.h.

Referenced by initialize(), pack(), and unpack().

int GridforceLiteGrid::size [protected]
 

Definition at line 328 of file GridForceGrid.h.

Referenced by initialize(), pack(), and unpack().

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