//! Constructor
explicit popbase(
const uint_t &initial_gamete_count,
typename gamete_t::mutation_container::size_type reserve_size
= 100)
: // No muts in the population
mutations(mcont_t()), mcounts(mcount_t()),
mcounts_from_preserved_nodes(mcount_t()),
gametes(gcont(1, gamete_t(initial_gamete_count))),
neutral(typename gamete_t::mutation_container()),
selected(typename gamete_t::mutation_container()),
mut_lookup(lookup_table_type()), fixations(mvector()),
fixation_times(ftvector())
{
// This is a good number for reserving,
// allowing for extra allocations when recycling is doing its
// thing
gametes.reserve(2 * initial_gamete_count);
// Reserve memory
neutral.reserve(reserve_size);
selected.reserve(reserve_size);
}
void Tri_setup_iprodlap()
{
int qa = QGmax;
int qb;
if(LZero) // use extra points if have Legendre zeros in 'b' direction
qb = QGmax;
else
qb = QGmax-1;
int qc = 0;
int L = LGmax;
// Set up dummy element with maximum quadrature/edge order
Coord X;
X.x = dvector(0,NTri_verts-1);
X.y = dvector(0,NTri_verts-1);
X.x[0] = 0.0;
X.x[1] = 1.0;
X.x[2] = 0.0;
X.y[0] = 0.0;
X.y[1] = 0.0;
X.y[2] = 1.0;
Tri *T = (Tri*) new Tri(0,'T', L, qa, qb, qc, &X);
free(X.x);
free(X.y);
int i,j,k,n;
int facs = Tri_DIM*Tri_DIM;
Tri_ipmodes = T->Nmodes;
Tri_iplap = (double***) calloc(facs,sizeof(double**));
for(i = 0; i < facs; ++i)
{
Tri_iplap[i] = dmatrix(0, T->Nmodes-1, 0, T->Nmodes-1);
dzero(T->Nmodes*T->Nmodes, Tri_iplap[i][0], 1);
}
// Set up gradient basis
Basis *B,*DB;
Mode *w,*m,*m1,*md,*md1,**gb,**gb1,*fac;
double *z;
B = T->getbasis();
DB = T->derbasis();
fac = B->vert;
w = mvector(0,0);
gb = (Mode **) malloc(T->Nmodes*sizeof(Mode *));
gb[0] = mvecset(0,Tri_DIM*T->Nmodes,qa, qb, qc);
gb1 = (Mode **) malloc(T->Nmodes*sizeof(Mode *));
gb1[0] = mvecset(0,Tri_DIM*T->Nmodes,qa, qb, qc);
for(i = 1; i < T->Nmodes; ++i)
gb[i] = gb[i-1]+Tri_DIM;
for(i = 1; i < T->Nmodes; ++i)
gb1[i] = gb1[i-1]+Tri_DIM;
getzw(qa,&z,&w[0].a,'a');
getzw(qb,&z,&w[0].b,'b');
/* fill gb with basis info for laplacian calculation */
// vertex modes
m = B->vert;
md = DB->vert;
for(i = 0,n=0; i < T->Nverts; ++i,++n)
T->fill_gradbase(gb[n],m+i,md+i,fac);
// edge modes
for(i = 0; i < T->Nedges; ++i)
{
m1 = B ->edge[i];
md1 = DB->edge[i];
for(j = 0; j < T->edge[i].l; ++j,++n)
T->fill_gradbase(gb[n],m1+j,md1+j,fac);
}
// face modes
for(i = 0; i < T->Nfaces; ++i)
for(j = 0; j < T->face[0].l; ++j)
{
m1 = B ->face[i][j];
md1 = DB->face[i][j];
for(k = 0; k < T->face[0].l-j; ++k,++n)
T->fill_gradbase(gb[n],m1+k,md1+k,fac);
}
/* multiply by weights */
for(i = 0; i < T->Nmodes; ++i)
{
Tri_mvmul2d(qa,qb,qc,gb[i] ,w,gb1[i]);
Tri_mvmul2d(qa,qb,qc,gb[i]+1,w,gb1[i]+1);
}
// Calculate Laplacian inner products
double s1, s2, s3, s4, s5, s6, s7, s8;
double *tmp = dvector(0, QGmax-1);
fac = B->vert+1;
for(i = 0; i < T->Nmodes; ++i)
for(j = 0; j < T->Nmodes; ++j)
{
s1 = ddot(qa,gb[i][0].a,1,gb1[j][0].a,1);
s1 *= ddot(qb,gb[i][0].b,1,gb1[j][0].b,1);
dvmul(qa, fac->a, 1, gb[i][0].a, 1, tmp, 1);
s2 = ddot(qa, tmp,1,gb1[j][0].a,1);
s2 *= ddot(qb,gb[i][0].b,1,gb1[j][0].b,1);
s3 = ddot(qa, tmp,1,gb1[j][1].a,1);
s3 *= ddot(qb,gb[i][0].b,1,gb1[j][1].b,1);
dvmul(qa, fac->a, 1, tmp, 1, tmp, 1);
s4 = ddot(qa, tmp,1,gb1[j][0].a,1);
s4 *= ddot(qb,gb[i][0].b,1,gb1[j][0].b,1);
s5 = ddot(qa,gb[i][0].a,1,gb1[j][1].a,1);
s5 *= ddot(qb,gb[i][0].b,1,gb1[j][1].b,1);
s6 = ddot(qa,gb[i][1].a,1,gb1[j][0].a,1);
s6 *= ddot(qb,gb[i][1].b,1,gb1[j][0].b,1);
dvmul(qa, fac->a, 1, gb[i][1].a, 1, tmp, 1);
s7 = ddot(qa, tmp,1,gb1[j][0].a,1);
s7 *= ddot(qb,gb[i][1].b,1,gb1[j][0].b,1);
s8 = ddot(qa,gb[i][1].a,1,gb1[j][1].a,1);
s8 *= ddot(qb,gb[i][1].b,1,gb1[j][1].b,1);
Tri_iplap[0][i][j] = s1;
Tri_iplap[1][i][j] = s5 + 2*s2 + s6;
Tri_iplap[2][i][j] = s3 + s4 + s7 + s8;
}
/* fill gb with basis info for mass matrix calculation */
// vertex modes
m = B->vert;
for(i = 0,n=0; i < T->Nverts; ++i,++n)
{
dcopy(qa, m[i].a, 1, gb[n]->a, 1);
dcopy(qb, m[i].b, 1, gb[n]->b, 1);
}
// edge modes
for(i = 0; i < T->Nedges; ++i)
{
m1 = B ->edge[i];
for(j = 0; j < T->edge[i].l; ++j,++n)
{
dcopy(qa, m1[j].a, 1, gb[n]->a, 1);
dcopy(qb, m1[j].b, 1, gb[n]->b, 1);
}
}
// face modes
for(i = 0; i < T->Nfaces; ++i)
for(j = 0; j < T->face[i].l; ++j)
{
m1 = B ->face[i][j];
for(k = 0; k < T->face[i].l-j; ++k,++n)
{
dcopy(qa, m1[k].a, 1, gb[n]->a, 1);
dcopy(qb, m1[k].b, 1, gb[n]->b, 1);
}
}
/* multiply by weights */
for(i = 0; i < T->Nmodes; ++i)
Tri_mvmul2d(qa,qb,qc,gb[i] ,w,gb1[i]);
for(i = 0; i < T->Nmodes; ++i)
for(j = 0; j < T->Nmodes; ++j)
{
s1 = ddot(qa,gb[i][0].a,1,gb1[j][0].a,1);
s1 *= ddot(qb,gb[i][0].b,1,gb1[j][0].b,1);
Tri_iplap[3][i][j] = s1;
}
free_mvec(gb[0]) ;
free((char *) gb);
free_mvec(gb1[0]);
free((char *) gb1);
free((char*)w);
free(tmp);
delete (T);
}