/*
* ***************************************************************************
* Routine: Vcom_dtor
*
* Purpose: Destroy the communications object
*
* Author: Nathan Baker and Michael Holst
* ***************************************************************************
*/
VPUBLIC void Vcom_dtor(Vcom **thee)
{
if ((*thee) != VNULL) {
Vcom_dtor2(*thee);
Vmem_free( VNULL, 1, sizeof(Vcom_core), (void**)&((*thee)->core) );
Vmem_free( VNULL, 1, sizeof(Vcom), (void**)thee );
}
}
/*
* ***************************************************************************
* Routine: Mat_killStructureLN
*
* Purpose: Kill the nonzero structure and structure information.
*
* Notes: This routine does the reverse of Mat_initStructureLN
* (or Mat_copyStructureLN). It leaves only the information
* about the number of blocks, number of rows, and number of
* columns per block. I.e., what is left is only what was
* present after the initial call to Mat_ctor.
*
* Author: Stephen Bond and Michael Holst
* ***************************************************************************
*/
VPUBLIC void Mat_killStructureLN(Mat *thee)
{
if (thee != VNULL) {
if (thee->state != NULL_STATE) {
/* Format-dependent destruction */
switch (thee->format) {
case RLN_FORMAT:
if (thee->lnkU != VNULL) {
Vset_dtor( &(thee->lnkU) );
}
break;
case CLN_FORMAT:
if (thee->lnkL != VNULL) {
Vset_dtor( &(thee->lnkL) );
}
break;
case XLN_FORMAT:
if (thee->lnkU != VNULL)
Vset_dtor( &(thee->lnkU) );
if (thee->xln != VNULL) {
if ( Mat_sym(thee) == ISNOT_SYM ) {
Vmem_free( thee->vmem, thee->numA, sizeof(LinkRC*),
(void**)&(thee->xln));
} else {
Vmem_free( thee->vmem, thee->numA, sizeof(LinkRCS),
(void**)&(thee->xln));
}
}
thee->numA = 0;
break;
default:
VASSERT(0);
break;
}
/* initialize the state */
thee->state = NULL_STATE;
}
}
}
VPUBLIC void Vgreen_dtor(Vgreen **thee) {
if ((*thee) != VNULL) {
Vgreen_dtor2(*thee);
Vmem_free(VNULL, 1, sizeof(Vgreen), (void **)thee);
(*thee) = VNULL;
}
}
/*
* ***************************************************************************
* Routine: Bmat_dtor
*
* Purpose: The block sparse matrix destructor.
*
* Notes: This destructor does the reverse of Bmat_ctor, and if
* necessary first reverses Bmat_initStructure
* (or Bmat_copyStructure). I.e., if necessary,
* it first frees the large integer and real arrays created by
* Bmat_initStructure or Bmat_copyStructure, and then frees the
* Bmat object itself at the last moment.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Bmat_dtor(Bmat **thee)
{
int p, q;
/* VASSERT( (*thee) != VNULL ); */
if ((*thee) != VNULL) {
/* first free any coarse guy */
if ( (*thee)->coarse != VNULL ) {
Bmat_dtor( &((*thee)->coarse) );
}
/* next free the large integer and real nonzero structure */
Bmat_killStructure(*thee);
/* kill the submatrices themselves */
Mat_dtor( &((*thee)->AG) );
for (p=0; p<(*thee)->numB; p++) {
for (q=0; q<(*thee)->numB; q++) {
if ( !(*thee)->mirror[p][q] ) {
Mat_dtor( &((*thee)->AD[p][q]) );
}
}
}
/* now kill the object itself */
VDEBUGIO("Bmat_dtor: DESTROYING object..");
if ((*thee)->iMadeVmem) Vmem_dtor( &((*thee)->vmem) );
Vmem_free( VNULL, 1, sizeof(Bmat), (void**)thee );
VDEBUGIO("..done.\n");
(*thee) = VNULL;
}
}
VPUBLIC void BEMparm_dtor(BEMparm **thee) {
if ((*thee) != VNULL) {
BEMparm_dtor2(*thee);
Vmem_free(VNULL, 1, sizeof(BEMparm), (void **)thee);
(*thee) = VNULL;
}
}
VPUBLIC void Vcsm_dtor(Vcsm **thee) {
if ((*thee) != VNULL) {
Vcsm_dtor2(*thee);
Vmem_free(VNULL, 1, sizeof(Vcsm), (void **)thee);
(*thee) = VNULL;
}
}
/*
* ***************************************************************************
* Routine: Gem_dtor
*
* Purpose: Geometry manager destructor.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Gem_dtor(Gem **thee)
{
int i;
VASSERT( (*thee) != VNULL );
if ((*thee) != VNULL) {
if ((*thee)->iMadePDE) {
PDE_dtor_default( &((*thee)->pde) );
}
Vset_dtor( &((*thee)->vertices) );
Vset_dtor( &((*thee)->edges) );
Vset_dtor( &((*thee)->simplices) );
for (i=0; i<VMAXSQ; i++) {
Vset_dtor( &((*thee)->sQueM[i]) );
}
VDEBUGIO("Gem_dtor: DESTROYING object..");
if ((*thee)->iMadeVmem) Vmem_dtor( &((*thee)->vmem) );
Vmem_free( VNULL, 1, sizeof(Gem), (void**)thee );
VDEBUGIO("..done.\n");
(*thee) = VNULL;
}
}
/* Main (stub) destructor */
VPUBLIC void VclistCell_dtor2(VclistCell *thee) {
if (thee->natoms > 0) {
Vmem_free(VNULL, thee->natoms, sizeof(Vatom *),
(void **)&(thee->atoms));
}
}
/*
* ***************************************************************************
* Routine: Vmem_realloc
*
* Purpose: A logged version of realloc (using this is usually a bad idea).
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void *Vmem_realloc(Vmem *thee, size_t num, size_t size, void **ram,
size_t newNum)
{
void *tee = Vmem_malloc(thee, newNum, size);
memcpy(tee, (*ram), size*VMIN2(num,newNum));
Vmem_free(thee, num, size, ram);
return tee;
}
/* ///////////////////////////////////////////////////////////////////////////
// Routine: Vopot_dtor
// Author: Nathan Baker
/////////////////////////////////////////////////////////////////////////// */
VPUBLIC void Vopot_dtor(Vopot **thee) {
if ((*thee) != VNULL) {
Vopot_dtor2(*thee);
Vmem_free(VNULL, 1, sizeof(Vopot), (void **)thee);
(*thee) = VNULL;
}
}
VPUBLIC void VclistCell_dtor(VclistCell **thee) {
if ((*thee) != VNULL) {
VclistCell_dtor2(*thee);
Vmem_free(VNULL, 1, sizeof(VclistCell), (void **)thee);
(*thee) = VNULL;
}
}
/* ///////////////////////////////////////////////////////////////////////////
// Routine: Vpee_dtor
//
// Author: Nathan Baker
/////////////////////////////////////////////////////////////////////////// */
VPUBLIC void Vpee_dtor(Vpee **thee) {
if ((*thee) != VNULL) {
Vpee_dtor2(*thee);
Vmem_free(VNULL, 1, sizeof(Vpee), (void **)thee);
(*thee) = VNULL;
}
}
/*
* ***************************************************************************
* Routine: PDE_dtor_default
*
* Purpose: Destroy a fake differential equation object.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void PDE_dtor_default(PDE **thee)
{
VASSERT( (*thee) != VNULL );
if ((*thee) != VNULL) {
Vmem_free( VNULL, 1, sizeof(PDE), (void**)thee );
(*thee) = VNULL;
}
}
VPRIVATE int treecleanup(Vgreen *thee) {
#ifdef HAVE_TREE
Vmem_free(thee->vmem, thee->np, sizeof(double), (void **)&(thee->xp));
Vmem_free(thee->vmem, thee->np, sizeof(double), (void **)&(thee->yp));
Vmem_free(thee->vmem, thee->np, sizeof(double), (void **)&(thee->zp));
Vmem_free(thee->vmem, thee->np, sizeof(double), (void **)&(thee->qp));
F77CLEANUP();
return 1;
#else /* ifdef HAVE_TREE */
Vnm_print(2, "treecleanup: Error! APBS not linked with treecode!\n");
return 0;
#endif /* ifdef HAVE_TREE */
}
/*
* ***************************************************************************
* Routine: Vmpi_dtor
*
* Purpose: The Vmpi destructor.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Vmpi_dtor(Vmpi **thee)
{
VDEBUGIO("Vmpi_dtor: DESTROYING object..");
Vmem_free( VNULL, 1, sizeof(Vmpi), (void**)thee );
#if defined(HAVE_MPI_H)
#if 0
VASSERT( MPI_SUCCESS == MPI_Finalize() );
#endif
#endif
VDEBUGIO("..done.\n");
}
/*
* ***************************************************************************
* Routine: Vcom_ctor
*
* Purpose: Construct the communications object
*
* Notes: This routine sets up data members of class and initializes MPI.
*
* Author: Nathan Baker and Michael Holst
* ***************************************************************************
*/
VPUBLIC Vcom* Vcom_ctor(int commtype)
{
int rc;
Vcom *thee = VNULL;
/* Set up the structure */
thee = Vmem_malloc( VNULL, 1, sizeof(Vcom) );
thee->core = Vmem_malloc( VNULL, 1, sizeof(Vcom_core) );
/* Call the real constructor */
rc = Vcom_ctor2(thee, commtype);
/* Destroy the guy if something went wrong */
if (rc == 0) {
Vmem_free( VNULL, 1, sizeof(Vcom_core), (void**)&(thee->core) );
Vmem_free( VNULL, 1, sizeof(Vcom), (void**)&thee );
}
return thee;
}
/* ///////////////////////////////////////////////////////////////////////////
// Routine: PDE_dtor
//
// Purpose: Destroy the differential equation object.
//
// Speed: This function is called by MC one time during shutdown,
// and does not have to be particularly fast.
//
// Author: Michael Holst
/////////////////////////////////////////////////////////////////////////// */
VPUBLIC void myPDE_dtor(PDE **thee)
{
VASSERT( (*thee) != VNULL );
if ((*thee) != VNULL) {
PDE_killDyn( *thee );
Vmem_free( VNULL, 1, sizeof(PDE), (void**)thee );
(*thee) = VNULL;
}
}
VPUBLIC void Vcsm_dtor2(Vcsm *thee) {
int i;
if ((thee != VNULL) && thee->initFlag) {
for (i=0; i<thee->msimp; i++) {
if (thee->nsqm[i] > 0) Vmem_free(thee->vmem, thee->nsqm[i],
sizeof(int), (void **)&(thee->sqm[i]));
}
for (i=0; i<thee->natom; i++) {
if (thee->nqsm[i] > 0) Vmem_free(thee->vmem, thee->nqsm[i],
sizeof(int), (void **)&(thee->qsm[i]));
}
Vmem_free(thee->vmem, thee->msimp, sizeof(int *),
(void **)&(thee->sqm));
Vmem_free(thee->vmem, thee->msimp, sizeof(int),
(void **)&(thee->nsqm));
Vmem_free(thee->vmem, thee->natom, sizeof(int *),
(void **)&(thee->qsm));
Vmem_free(thee->vmem, thee->natom, sizeof(int),
(void **)&(thee->nqsm));
}
Vmem_dtor(&(thee->vmem));
}
VPUBLIC int Vgreen_coulomb(Vgreen *thee, int npos, double *x, double *y,
double *z, double *val) {
Vatom *atom;
double *apos, charge, dist, dx, dy, dz, scale;
double *q, qtemp, fx, fy, fz;
int iatom, ipos;
if (thee == VNULL) {
Vnm_print(2, "Vgreen_coulomb: Got NULL thee!\n");
return 0;
}
for (ipos=0; ipos<npos; ipos++) val[ipos] = 0.0;
#ifdef HAVE_TREE
/* Allocate charge array (if necessary) */
if (Valist_getNumberAtoms(thee->alist) > 1) {
if (npos > 1) {
q = VNULL;
q = Vmem_malloc(thee->vmem, npos, sizeof(double));
if (q == VNULL) {
Vnm_print(2, "Vgreen_coulomb: Error allocating charge array!\n");
return 0;
}
} else {
q = &(qtemp);
}
for (ipos=0; ipos<npos; ipos++) q[ipos] = 1.0;
/* Calculate */
treecalc(thee, x, y, z, q, npos, val, thee->xp, thee->yp, thee->zp,
thee->qp, thee->np, &fx, &fy, &fz, 1, 1, thee->np);
} else return Vgreen_coulomb_direct(thee, npos, x, y, z, val);
/* De-allocate charge array (if necessary) */
if (npos > 1) Vmem_free(thee->vmem, npos, sizeof(double), (void **)&q);
scale = Vunit_ec/(4*Vunit_pi*Vunit_eps0*1.0e-10);
for (ipos=0; ipos<npos; ipos++) val[ipos] = val[ipos]*scale;
return 1;
#else /* ifdef HAVE_TREE */
return Vgreen_coulomb_direct(thee, npos, x, y, z, val);
#endif
}
/* Main (stub) destructor */
VPUBLIC void Vclist_dtor2(Vclist *thee) {
VclistCell *cell;
int i;
for (i=0; i<thee->n; i++) {
cell = &(thee->cells[i]);
VclistCell_dtor2(cell);
}
Vmem_free(thee->vmem, thee->n, sizeof(VclistCell),
(void **)&(thee->cells));
Vmem_dtor(&(thee->vmem));
}
/*
* ***************************************************************************
* Routine: MCsh_dtor
*
* Purpose: The MCsh destructor.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void MCsh_dtor(MCsh **thee)
{
VASSERT( (*thee) != VNULL );
if ((*thee) != VNULL) {
AM_dtor( &((*thee)->am) );
Aprx_dtor( &((*thee)->aprx) );
Gem_dtor( &((*thee)->gm) );
Vsh_dtor( &((*thee)->vsh) );
VDEBUGIO("MCsh_dtor: DESTROYING object..");
Vmem_dtor( &((*thee)->vmem) );
Vmem_free( VNULL, 1, sizeof(MCsh), (void**)thee );
VDEBUGIO("..done.\n");
(*thee) = VNULL;
}
}
/*
* ***************************************************************************
* Routine: Bnode_dtor
*
* Purpose: The Block node destructor.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Bnode_dtor(Bnode **thee)
{
int i;
/* VASSERT( (*thee) != VNULL ); */
if ((*thee) != VNULL) {
for (i=0; i<(*thee)->numB; i++) {
Node_dtor( (&(*thee)->ND[i]) );
}
VDEBUGIO("Bnode_dtor: DESTROYING object..");
if ((*thee)->iMadeVmem) Vmem_dtor( &((*thee)->vmem) );
Vmem_free( VNULL, 1, sizeof(Bnode), (void**)thee );
VDEBUGIO("..done.\n");
(*thee) = VNULL;
}
}
/*
* ***************************************************************************
* Routine: Slu_dtor
*
* Purpose: The Slu destructor.
*
* Author: Michael Holst and Stephen Bond
* ***************************************************************************
*/
VPUBLIC void Slu_dtor(Slu **thee)
{
VASSERT( (*thee) != VNULL );
if ((*thee) != VNULL) {
/* destroy the factorization */
if( (*thee)->statLU == 1 ) {
umfpack_di_free_numeric( &((*thee)->work) );
(*thee)->statLU = 0;
}
/* finally destroy this container */
VDEBUGIO("Slu_dtor: DESTROYING object..");
if ((*thee)->iMadeVmem) Vmem_dtor( &((*thee)->vmem) );
Vmem_free( VNULL, 1, sizeof(Slu), (void**)thee );
VDEBUGIO("..done.\n");
(*thee) = VNULL;
}
}
VPUBLIC int Vgreen_coulombD(Vgreen *thee, int npos, double *x, double *y,
double *z, double *pot, double *gradx, double *grady, double *gradz) {
Vatom *atom;
double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale;
double *q, qtemp;
int iatom, ipos;
if (thee == VNULL) {
Vnm_print(2, "Vgreen_coulombD: Got VNULL thee!\n");
return 0;
}
for (ipos=0; ipos<npos; ipos++) {
pot[ipos] = 0.0;
gradx[ipos] = 0.0;
grady[ipos] = 0.0;
gradz[ipos] = 0.0;
}
#ifdef HAVE_TREE
if (Valist_getNumberAtoms(thee->alist) > 1) {
if (npos > 1) {
q = VNULL;
q = Vmem_malloc(thee->vmem, npos, sizeof(double));
if (q == VNULL) {
Vnm_print(2, "Vgreen_coulomb: Error allocating charge array!\n");
return 0;
}
} else {
q = &(qtemp);
}
for (ipos=0; ipos<npos; ipos++) q[ipos] = 1.0;
/* Calculate */
treecalc(thee, x, y, z, q, npos, pot, thee->xp, thee->yp, thee->zp,
thee->qp, thee->np, gradx, grady, gradz, 2, npos, thee->np);
/* De-allocate charge array (if necessary) */
if (npos > 1) Vmem_free(thee->vmem, npos, sizeof(double), (void **)&q);
} else return Vgreen_coulombD_direct(thee, npos, x, y, z, pot,
gradx, grady, gradz);
scale = Vunit_ec/(4*VPI*Vunit_eps0*(1.0e-10));
for (ipos=0; ipos<npos; ipos++) {
gradx[ipos] = gradx[ipos]*scale;
grady[ipos] = grady[ipos]*scale;
gradz[ipos] = gradz[ipos]*scale;
pot[ipos] = pot[ipos]*scale;
}
return 1;
#else /* ifdef HAVE_TREE */
return Vgreen_coulombD_direct(thee, npos, x, y, z, pot,
gradx, grady, gradz);
#endif
}
/*
* ***************************************************************************
* Routine: Vmem_dtor
*
* Purpose: Destruct the dynamic memory allocation logging object.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Vmem_dtor(Vmem **thee)
{
Vmem_free( VNULL, 1, sizeof(Vmem), (void**)thee );
}
/*
* ***************************************************************************
* Routine: Aprx_partOne
*
* Purpose: Do a single bisection step.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC int Aprx_partOne(Aprx *thee, int pkey, int pwht, int pcolor, int poff)
{
int i, j, k, ii, dim, rc, numC, numS, sCount1, sCount2, cutOff;
int *pord, *ford, *rord;
double tm, cm[3], *evec, eCount1, eCount2, ecutOff, ePart;
simHelper *simH;
SS *sm;
Vnm_print(0,"Aprx_partOne: [pcolor=%d] partitioning:\n", pcolor);
/* dimensions */
dim = Gem_dim(thee->gm);
numS = Gem_numSS(thee->gm);
/* how many guys of this color */
numC = 0;
for (i=0; i<numS; i++) {
sm = Gem_SS(thee->gm,i);
if ((int)SS_chart(sm) == pcolor) numC++;
}
/* grab some temporary storage */
pord = Vmem_malloc( thee->vmem, numC, sizeof(int) );
ford = Vmem_malloc( thee->vmem, numC, sizeof(int) );
rord = Vmem_malloc( thee->vmem, numS, sizeof(int) );
evec = Vmem_malloc( thee->vmem, numC, sizeof(double) );
simH = Vmem_malloc( thee->vmem, numC, sizeof(simHelper) );
/* build the simplex helper vector and forward/reverse ordering arrays */
ePart = 0.;
tm = 0.;
for (i=0; i<3; i++) cm[i] = 0.;
i = 0;
for (ii=0; ii<Gem_numSS(thee->gm); ii++) {
sm = Gem_SS(thee->gm,ii);
if ((int)SS_chart(sm) == pcolor) {
/* initialization */
pord[i] = i;
ford[i] = ii;
rord[ii] = i;
evec[i] = 0.;
simH[i].color = SS_chart(sm);
simH[i].diag = 0;
simH[i].mass = 1.;
simH[i].error = Bvec_valB( thee->wev, 0, ii );
for (j=0; j<4; j++) {
simH[i].faceId[j] = -1;
}
/* accumulate error into total for this partition */
ePart += simH[i].error;
/* baricenter of this simplex and center of mass of all */
tm += simH[i].mass;
for (j=0; j<3; j++) {
simH[i].bc[j] = 0.;
for (k=0; k<dim+1; k++) {
simH[i].bc[j] += VV_coord(SS_vertex(sm,k),j);
}
simH[i].bc[j] /= (dim+1.);
cm[j] += (simH[i].mass * simH[i].bc[j]);
}
i++;
} else {
rord[ii] = -1;
}
}
VASSERT( i == numC );
for (i=0; i<3; i++) cm[i] /= tm;
/* translate coordinate systems so center of mass is at origin */
for (i=0; i<numC; i++) {
for (j=0; j<3; j++) {
simH[i].bc[j] -= cm[j];
}
}
/* okay partition it */
if (pkey == 0) {
rc = Aprx_partInert(thee, pcolor, numC, evec, simH);
} else if (pkey == 1) {
rc = Aprx_partSpect(thee, pcolor, numC, evec, simH, ford, rord, 0);
} else if (pkey == 2) {
rc = Aprx_partSpect(thee, pcolor, numC, evec, simH, ford, rord, 1);
} else if (pkey == 3) {
rc = Aprx_partInert(thee, pcolor, numC, evec, simH);
rc = Aprx_partSpect(thee, pcolor, numC, evec, simH, ford, rord, 0);
} else {
Vnm_print(2,"Aprx_partOne: illegal pkey value of <%d>\n", pkey);
rc = -1;
}
/* sort the values small-to-big; allows us to have equi-size submeshes */
Vnm_dqsortOrd(evec, pord, numC);
/* color the mesh using the ordering given by the eigenvector */
sCount1 = 0;
sCount2 = 0;
eCount1 = 0.;
eCount2 = 0.;
if (rc >= 0) {
/* weighted partitioning; divides into two sets of equal error */
if (pwht == 1) {
ecutOff = ( ePart / 2. );
for (i=0; i<numC; i++) {
sm = Gem_SS(thee->gm,ford[pord[i]]);
if (eCount1 < ecutOff) {
SS_setChart( sm, pcolor );
sCount1++;
eCount1 += Bvec_valB( thee->wev, 0, ford[pord[i]] );
} else {
SS_setChart( sm, pcolor+poff );
sCount2++;
eCount2 += Bvec_valB( thee->wev, 0, ford[pord[i]] );
}
}
/* unweighted partitioning; divides into two sets of equal number */
} else {
cutOff = numC / 2;
for (i=0; i<numC; i++) {
sm = Gem_SS(thee->gm,ford[pord[i]]);
if (sCount1 < cutOff) {
SS_setChart( sm, pcolor );
sCount1++;
eCount1 += Bvec_valB( thee->wev, 0, ford[pord[i]] );
} else {
SS_setChart( sm, pcolor+poff );
sCount2++;
eCount2 += Bvec_valB( thee->wev, 0, ford[pord[i]] );
}
}
}
}
/* free the temporary storage */
Vmem_free( thee->vmem, numC, sizeof(int), (void**)&pord );
Vmem_free( thee->vmem, numC, sizeof(int), (void**)&ford );
Vmem_free( thee->vmem, numS, sizeof(int), (void**)&rord );
Vmem_free( thee->vmem, numC, sizeof(double), (void**)&evec );
Vmem_free( thee->vmem, numC, sizeof(simHelper), (void**)&simH );
Vnm_print(0,"Aprx_partOne: done.");
Vnm_print(0," [c1=%d,c2=%d,e1=%8.2e,e2=%8.2e,eT=%8.2e]\n",
sCount1, sCount2, eCount1, eCount2, (eCount1+eCount2));
if (sCount1 == 0) {
Vnm_print(2,"Aprx_partOne: ERROR: first partition has NO SIMPLICES!\n");
}
if (sCount2 == 0) {
Vnm_print(2,"Aprx_partOne: ERROR: second partition has NO SIMPLICES!\n");
}
return rc;
}
VPUBLIC int Vcsm_update(Vcsm *thee, SS **simps, int num) {
/* Counters */
int isimp, jsimp, iatom, jatom, atomID, simpID;
int nsimps, gotMem;
/* Object info */
Vatom *atom;
SS *simplex;
double *position;
/* Lists */
int *qParent, nqParent;
int **sqmNew, *nsqmNew;
int *affAtoms, nAffAtoms;
int *dnqsm, *nqsmNew, **qsmNew;
VASSERT(thee != VNULL);
VASSERT(thee->initFlag);
/* If we don't have enough memory to accommodate the new entries,
* add more by doubling the existing amount */
isimp = thee->nsimp + num - 1;
gotMem = 0;
while (!gotMem) {
if (isimp > thee->msimp) {
isimp = 2 * isimp;
thee->nsqm = Vmem_realloc(thee->vmem, thee->msimp, sizeof(int),
(void **)&(thee->nsqm), isimp);
VASSERT(thee->nsqm != VNULL);
thee->sqm = Vmem_realloc(thee->vmem, thee->msimp, sizeof(int *),
(void **)&(thee->sqm), isimp);
VASSERT(thee->sqm != VNULL);
thee->msimp = isimp;
} else gotMem = 1;
}
/* Initialize the nsqm entires we just allocated */
for (isimp = thee->nsimp; isimp<thee->nsimp+num-1 ; isimp++) {
thee->nsqm[isimp] = 0;
}
thee->nsimp = thee->nsimp + num - 1;
/* There's a simple case to deal with: if simps[0] didn't have a
* charge in the first place */
isimp = SS_id(simps[0]);
if (thee->nsqm[isimp] == 0) {
for (isimp=1; isimp<num; isimp++) {
thee->nsqm[SS_id(simps[isimp])] = 0;
}
return 1;
}
/* The more complicated case has occured; the parent simplex had one or
* more charges. First, generate the list of affected charges. */
isimp = SS_id(simps[0]);
nqParent = thee->nsqm[isimp];
qParent = thee->sqm[isimp];
sqmNew = Vmem_malloc(thee->vmem, num, sizeof(int *));
VASSERT(sqmNew != VNULL);
nsqmNew = Vmem_malloc(thee->vmem, num, sizeof(int));
VASSERT(nsqmNew != VNULL);
for (isimp=0; isimp<num; isimp++) nsqmNew[isimp] = 0;
/* Loop throught the affected atoms to determine how many atoms each
* simplex will get. */
for (iatom=0; iatom<nqParent; iatom++) {
atomID = qParent[iatom];
atom = Valist_getAtom(thee->alist, atomID);
position = Vatom_getPosition(atom);
nsimps = 0;
jsimp = 0;
for (isimp=0; isimp<num; isimp++) {
simplex = simps[isimp];
if (Gem_pointInSimplex(thee->gm, simplex, position)) {
nsqmNew[isimp]++;
jsimp = 1;
}
}
VASSERT(jsimp != 0);
}
/* Sanity check that we didn't lose any atoms... */
iatom = 0;
for (isimp=0; isimp<num; isimp++) iatom += nsqmNew[isimp];
if (iatom < nqParent) {
Vnm_print(2,"Vcsm_update: Lost %d (of %d) atoms!\n",
nqParent - iatom, nqParent);
VASSERT(0);
}
/* Allocate the storage */
for (isimp=0; isimp<num; isimp++) {
if (nsqmNew[isimp] > 0) {
sqmNew[isimp] = Vmem_malloc(thee->vmem, nsqmNew[isimp],
sizeof(int));
VASSERT(sqmNew[isimp] != VNULL);
}
}
/* Assign charges to simplices */
for (isimp=0; isimp<num; isimp++) {
jsimp = 0;
simplex = simps[isimp];
/* Loop over the atoms associated with the parent simplex */
for (iatom=0; iatom<nqParent; iatom++) {
atomID = qParent[iatom];
atom = Valist_getAtom(thee->alist, atomID);
position = Vatom_getPosition(atom);
if (Gem_pointInSimplex(thee->gm, simplex, position)) {
sqmNew[isimp][jsimp] = atomID;
jsimp++;
}
}
}
/* Update the QSM map using the old and new SQM lists */
/* The affected atoms are those contained in the parent simplex; i.e.
* thee->sqm[SS_id(simps[0])] */
affAtoms = thee->sqm[SS_id(simps[0])];
nAffAtoms = thee->nsqm[SS_id(simps[0])];
/* Each of these atoms will go somewhere else; i.e., the entries in
* thee->qsm are never destroyed and thee->nqsm never decreases.
* However, it is possible that a subdivision could cause an atom to be
* shared by two child simplices. Here we record the change, if any,
* in the number of simplices associated with each atom. */
dnqsm = Vmem_malloc(thee->vmem, nAffAtoms, sizeof(int));
VASSERT(dnqsm != VNULL);
nqsmNew = Vmem_malloc(thee->vmem, nAffAtoms, sizeof(int));
VASSERT(nqsmNew != VNULL);
qsmNew = Vmem_malloc(thee->vmem, nAffAtoms, sizeof(int*));
VASSERT(qsmNew != VNULL);
for (iatom=0; iatom<nAffAtoms; iatom++) {
dnqsm[iatom] = -1;
atomID = affAtoms[iatom];
for (isimp=0; isimp<num; isimp++) {
for (jatom=0; jatom<nsqmNew[isimp]; jatom++) {
if (sqmNew[isimp][jatom] == atomID) dnqsm[iatom]++;
}
}
VASSERT(dnqsm[iatom] > -1);
}
/* Setup the new entries in the array */
for (iatom=0;iatom<nAffAtoms; iatom++) {
atomID = affAtoms[iatom];
qsmNew[iatom] = Vmem_malloc(thee->vmem,
(dnqsm[iatom] + thee->nqsm[atomID]),
sizeof(int));
nqsmNew[iatom] = 0;
VASSERT(qsmNew[iatom] != VNULL);
}
/* Fill the new entries in the array */
/* First, do the modified entries */
for (isimp=0; isimp<num; isimp++) {
simpID = SS_id(simps[isimp]);
for (iatom=0; iatom<nsqmNew[isimp]; iatom++) {
atomID = sqmNew[isimp][iatom];
for (jatom=0; jatom<nAffAtoms; jatom++) {
if (atomID == affAtoms[jatom]) break;
}
if (jatom < nAffAtoms) {
qsmNew[jatom][nqsmNew[jatom]] = simpID;
nqsmNew[jatom]++;
}
}
}
/* Now do the unmodified entries */
for (iatom=0; iatom<nAffAtoms; iatom++) {
atomID = affAtoms[iatom];
for (isimp=0; isimp<thee->nqsm[atomID]; isimp++) {
for (jsimp=0; jsimp<num; jsimp++) {
simpID = SS_id(simps[jsimp]);
if (thee->qsm[atomID][isimp] == simpID) break;
}
if (jsimp == num) {
qsmNew[iatom][nqsmNew[iatom]] = thee->qsm[atomID][isimp];
nqsmNew[iatom]++;
}
}
}
/* Replace the existing entries in the table. Do the QSM entires
* first, since they require affAtoms = thee->sqm[simps[0]] */
for (iatom=0; iatom<nAffAtoms; iatom++) {
atomID = affAtoms[iatom];
Vmem_free(thee->vmem, thee->nqsm[atomID], sizeof(int),
(void **)&(thee->qsm[atomID]));
thee->qsm[atomID] = qsmNew[iatom];
thee->nqsm[atomID] = nqsmNew[iatom];
}
for (isimp=0; isimp<num; isimp++) {
simpID = SS_id(simps[isimp]);
if (thee->nsqm[simpID] > 0) Vmem_free(thee->vmem, thee->nsqm[simpID],
sizeof(int), (void **)&(thee->sqm[simpID]));
thee->sqm[simpID] = sqmNew[isimp];
thee->nsqm[simpID] = nsqmNew[isimp];
}
Vmem_free(thee->vmem, num, sizeof(int *), (void **)&sqmNew);
Vmem_free(thee->vmem, num, sizeof(int), (void **)&nsqmNew);
Vmem_free(thee->vmem, nAffAtoms, sizeof(int *), (void **)&qsmNew);
Vmem_free(thee->vmem, nAffAtoms, sizeof(int), (void **)&nqsmNew);
Vmem_free(thee->vmem, nAffAtoms, sizeof(int), (void **)&dnqsm);
return 1;
}
/*
* ***************************************************************************
* Routine: Gem_speedChk
*
* Purpose: Calculate the cost to traverse the various structures.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Gem_speedChk(Gem *thee)
{
const int N = 100000;
const int loop = 1000;
int i, j, itotal;
double rtotal;
double *d0;
int *i0;
VV *v0, *vx;
Vnm_print(0,"Gem_speedChk: Creating normal double vec...\n");
Vnm_tstart(90, "double vec creation");
d0 = Vmem_malloc( thee->vmem, N, sizeof(double) );
Vnm_tstop(90, "double vec creation");
Vnm_print(0,"Gem_speedChk: Creating normal int vec...\n");
Vnm_tstart(90, "int vec creation");
i0 = Vmem_malloc( thee->vmem, N, sizeof(int) );
Vnm_tstop(90, "int vec creation");
Vnm_print(0,"Gem_speedChk: Creating normal VV vec...\n");
Vnm_tstart(90, "VV vec creation");
v0 = Vmem_malloc( thee->vmem, N, sizeof(VV) );
Vnm_tstop(90, "VV vec creation");
Vnm_print(0,"Gem_speedChk: Creating Vset VV vec...\n");
Vnm_tstart(90, "VV Vset creation");
for (i=0; i<N; i++)
vx = Gem_createAndInitVV(thee);
Vnm_tstop(90, "VV Vset creation");
Vnm_print(0,"Gem_speedChk: Looping over double vec...\n");
Vnm_print(0,"Gem_speedChk: N, loop = %d, %d\n", N, loop);
Vnm_tstart(90, "double vec loop");
rtotal = 0.0;
for (j=0; j<loop; j++)
for (i=0; i<N; i++)
rtotal += ( j * d0[i] * (j+d0[i]) );
Vnm_tstop(90, "double vec loop");
Vnm_print(0,"Gem_speedChk: Looping over int vec...\n");
Vnm_print(0,"Gem_speedChk: N, loop = %d, %d\n", N, loop);
Vnm_tstart(90, "int vec loop");
itotal = 0;
for (j=0; j<loop; j++)
for (i=0; i<N; i++)
itotal += ( j * i0[i] * (j+i0[i]) );
Vnm_tstop(90, "int vec loop");
Vnm_print(0,"Gem_speedChk: Looping over VV vec...\n");
Vnm_print(0,"Gem_speedChk: N, loop = %d, %d\n", N, loop);
Vnm_tstart(90, "VV vec loop");
itotal = 0;
for (j=0; j<loop; j++)
for (i=0; i<N; i++)
itotal += ( j * VV_id(&v0[i]) * (j+VV_id(&v0[i])) );
Vnm_tstop(90, "VV vec loop");
Vnm_print(0,"Gem_speedChk: Looping (index) over Vset VV vec...\n");
Vnm_print(0,"Gem_speedChk: N, loop = %d, %d\n", N, loop);
Vnm_tstart(90, "VV Vset loop");
itotal = 0;
for (j=0; j<loop; j++)
for (i=0; i<N; i++)
itotal += ( j * VV_id(Gem_VV(thee,i))
* (j + VV_id(Gem_VV(thee,i)) ) );
Vnm_tstop(90, "VV Vset loop");
Vnm_print(0,"Gem_speedChk: Looping (iterator) over Vset VV vec...\n");
Vnm_print(0,"Gem_speedChk: N, loop = %d, %d\n", N, loop);
Vnm_tstart(90, "VV Vset loop");
itotal = 0;
for (j=0; j<loop; j++)
for (vx=Gem_firstVV(thee);vx!=VNULL;vx=Gem_nextVV(thee))
itotal += ( j * VV_id(vx) * (j + VV_id(vx)) );
Vnm_tstop(90, "VV Vset loop");
Vnm_print(0,"Gem_speedChk: Freeing normal double vec...\n");
Vnm_tstart(90, "Free double vec");
Vmem_free( thee->vmem, N, sizeof(double), (void**)&d0 );
Vnm_tstop(90, "Free double vec");
Vnm_print(0,"Gem_speedChk: Freeing normal int vec...\n");
Vnm_tstart(90, "Free int vec");
Vmem_free( thee->vmem, N, sizeof(int), (void**)&i0 );
Vnm_tstop(90, "Free int vec");
Vnm_print(0,"Gem_speedChk: Freeing normal VV vec...\n");
Vnm_tstart(90, "Free VV vec");
Vmem_free( thee->vmem, N, sizeof(VV), (void**)&v0 );
Vnm_tstop(90, "Free VV vec");
Vnm_print(0,"Gem_speedChk: Freeing Vset VV vec...\n");
Vnm_tstart(90, "Free VV Vset");
for (i=0; i<N; i++)
Gem_destroyVV(thee);
Vnm_tstop(90, "Free VV Vset");
}