tmp
<
GeometricField
<
typename outerProduct<vector,Type>::type, fvPatchField, volMesh
>
>
grad
(
const tmp<GeometricField<Type, fvsPatchField, surfaceMesh> >& tssf
)
{
typedef typename outerProduct<vector, Type>::type GradType;
tmp<GeometricField<GradType, fvPatchField, volMesh> > Grad
(
fvc::grad(tssf())
);
tssf.clear();
return Grad;
}
//*****************************************************************************
//
//
// *
//=============================================================================
float SJCNoise::
Eval(const float x, const float y, const float z)
//=============================================================================
{
int ix = (int)floor(x);
float dx = x - ix;
int iy = (int)floor(y);
float dy = y - iy;
int iz = (int)floor(z);
float dz = z - iz;
ix &= ( PERM_SIZE - 1 );
iy &= ( PERM_SIZE - 1 );
iz &= ( PERM_SIZE - 1 );
float w000 = Grad(ix, iy, iz, dx, dy, dz);
float w010 = Grad(ix, iy+1, iz, dx, dy-1.0f, dz);
float w100 = Grad(ix+1, iy, iz, dx-1.0f, dy, dz);
float w110 = Grad(ix+1, iy+1, iz, dx-1.0f, dy-1.0f, dz);
float w001 = Grad(ix, iy, iz+1, dx, dy, dz-1.0f);
float w011 = Grad(ix, iy+1, iz+1, dx, dy-1.0f, dz-1.0f);
float w101 = Grad(ix+1, iy, iz+1, dx-1.0f, dy, dz-1.0f);
float w111 = Grad(ix+1, iy+1, iz+1, dx-1.0f, dy-1.0f, dz-1.0f);
float ux = NoiseWeight(dx);
float uy = NoiseWeight(dy);
float uz = NoiseWeight(dz);
float x00 = ( 1 - ux ) * w000 + ux * w100;
float x10 = ( 1 - ux ) * w010 + ux * w110;
float x01 = ( 1 - ux ) * w001 + ux * w101;
float x11 = ( 1 - ux ) * w011 + ux * w111;
float y0 = ( 1 - uy ) * x00 + uy * x10;
float y1 = ( 1 - uy ) * x01 + uy * x11;
return ( 1 - uz ) * y0 + uz * y1;
}
PreconditionerAS<space_type,coef_space_type>::PreconditionerAS( std::string t,
space_ptrtype Xh,
coef_space_ptrtype Mh,
BoundaryConditions bcFlags,
std::string const& p,
sparse_matrix_ptrtype Pm,
double k )
:
M_type( AS ),
M_Xh( Xh ),
M_Vh(Xh->template functionSpace<0>() ),
M_Qh(Xh->template functionSpace<1>() ),
M_Mh( Mh ),
M_Vh_indices( M_Vh->nLocalDofWithGhost() ),
M_Qh_indices( M_Qh->nLocalDofWithGhost() ),
M_Qh3_indices( Dim ),
A(backend()->newVector(M_Vh)),
B(backend()->newVector(M_Vh)),
C(backend()->newVector(M_Vh)),
M_r(backend()->newVector(M_Vh)),
M_r_t(backend()->newVector(M_Vh)),
M_uout(backend()->newVector(M_Vh)),
M_diagPm(backend()->newVector(M_Vh)),
//M_t(backend()->newVector(M_Vh)),
U( M_Vh, "U" ),
M_mu(M_Mh, "mu"),
M_er(M_Mh, "er"),
M_bcFlags( bcFlags ),
M_prefix( p ),
M_k(k),
M_g(1.-k*k)
{
tic();
LOG(INFO) << "[PreconditionerAS] setup starts";
this->setMatrix( Pm ); // Needed only if worldComm > 1
// QH3 : Lagrange vectorial space type
M_Qh3 = lag_v_space_type::New(Xh->mesh());
M_qh3_elt = M_Qh3->element();
M_qh_elt = M_Qh->element();
M_vh_elt = M_Vh->element();
// Block 11.1
M_s = backend()->newVector(M_Qh3);
M_y = backend()->newVector(M_Qh3);
// Block 11.2
M_z = backend()->newVector(M_Qh);
M_t = backend()->newVector(M_Qh);
// Create the interpolation and keep only the matrix
auto pi_curl = I(_domainSpace=M_Qh3, _imageSpace=M_Vh);
auto Igrad = Grad( _domainSpace=M_Qh, _imageSpace=M_Vh);
M_P = pi_curl.matPtr();
M_C = Igrad.matPtr();
M_Pt = backend()->newMatrix(M_Qh3,M_Vh);
M_Ct = backend()->newMatrix(M_Qh3,M_Vh);
M_P->transpose(M_Pt,MATRIX_TRANSPOSE_UNASSEMBLED);
M_C->transpose(M_Ct,MATRIX_TRANSPOSE_UNASSEMBLED);
LOG(INFO) << "size of M_C = " << M_C->size1() << ", " << M_C->size2() << std::endl;
LOG(INFO) << "size of M_P = " << M_P->size1() << ", " << M_P->size2() << std::endl;
// Create vector of indices to create subvectors/matrices
std::iota( M_Vh_indices.begin(), M_Vh_indices.end(), 0 ); // Vh indices in Xh
std::iota( M_Qh_indices.begin(), M_Qh_indices.end(), M_Vh->nLocalDofWithGhost() ); // Qh indices in Xh
// "Components" of Qh3
auto Qh3_dof_begin = M_Qh3->dof()->dofPointBegin();
auto Qh3_dof_end = M_Qh3->dof()->dofPointEnd();
int dof_comp, dof_idx;
for( auto it = Qh3_dof_begin; it!= Qh3_dof_end; it++ )
{
dof_comp = it->template get<2>(); //Component
dof_idx = it->template get<1>(); //Global index
M_Qh3_indices[dof_comp].push_back( dof_idx );
}
// Subvectors for M_y (per component)
M_y1 = M_y->createSubVector(M_Qh3_indices[0], true);
M_y2 = M_y->createSubVector(M_Qh3_indices[1], true);
#if FEELPP_DIM == 3
M_y3 = M_y->createSubVector(M_Qh3_indices[2], true);
#endif
// Subvectors for M_s (per component)
M_s1 = M_y->createSubVector(M_Qh3_indices[0], true);
M_s2 = M_y->createSubVector(M_Qh3_indices[1], true);
#if FEELPP_DIM == 3
M_s3 = M_y->createSubVector(M_Qh3_indices[2], true);
#endif
this->setType ( t );
toc( "[PreconditionerAS] setup done ", FLAGS_v > 0 );
}
void Problem::CheckGradHessian(const Variable *xin) const
{
UseGrad = true;
UseHess = true;
integer length;
double normxi;
double t, fx, fy;
double *X, *Y;
Vector *etax;
Variable *x = xin->ConstructEmpty();
xin->CopyTo(x);
if (Domain->GetIsIntrinsic())
etax = Domain->GetEMPTYINTR()->ConstructEmpty();
else
etax = Domain->GetEMPTYEXTR()->ConstructEmpty();
etax->RandUnform();
Vector *xi = etax->ConstructEmpty();
Vector *gfx = etax->ConstructEmpty();
Vector *Hv = etax->ConstructEmpty();
Variable *y = x->ConstructEmpty();
fx = f(x);
Grad(x, gfx);
gfx->CopyTo(etax);//--
//double *etaxTV = etax->ObtainWriteEntireData();///---
//integer nnn = etax->Getlength();
//for (integer i = 0; i < nnn; i++)//--
//{
// etaxTV[i] = sin(static_cast<double> (i) / (etax->Getlength() - 1) / 2);
//}
//for (integer i = 0; i < 5; i++)//---
// etaxTV[nnn - 1 - i] = 0;//--
//etax->Print("etax:");//--
Domain->Projection(x, etax, xi);
normxi = sqrt(Domain->Metric(x, xi, xi));
Domain->ScaleTimesVector(x, 100.0 / normxi, xi, xi); // initial length of xi is 100
//xi->Print("xi:");//---
// the length of xi variances from 100 to 100*2^(-35) approx 6e-9
t = 1;
length = 35;
X = new double [length * 2];
Y = X + length;
for (integer i = 0; i < length; i++)
{
Domain->Retraction(x, xi, y);
fy = f(y);
HessianEta(x, xi, Hv);
Y[i] = log(fabs(fy - fx - Domain->Metric(x, gfx, xi) - 0.5 * Domain->Metric(x, xi, Hv)));
X[i] = 0.5 * log(Domain->Metric(x, xi, xi));
Rprintf("i:%d,|eta|:%.3e,(fy-fx)/<gfx,eta>:%.3e,(fy-fx-<gfx,eta>)/<0.5 eta, Hessian eta>:%.3e\n", i,
sqrt(Domain->Metric(x, xi, xi)), (fy-fx)/Domain->Metric(x, gfx, xi),
(fy - fx - Domain->Metric(x, gfx, xi)) / (0.5 * Domain->Metric(x, xi, Hv)));
Domain->ScaleTimesVector(x, 0.5, xi, xi);
}
Rcpp::Rcout << "CHECK GRADIENT:" << std::endl;
Rcpp::Rcout << "\tSuppose the point is not a critical point." << std::endl;
Rcpp::Rcout << "\tIf there exists an interval of |eta| such that (fy - fx) / <gfx, eta>" << std::endl;
Rcpp::Rcout << "\tapproximates ONE, then the gradient is probably correct!" << std::endl;
Rcpp::Rcout << "CHECK THE ACTION OF THE HESSIAN (PRESUME GRADIENT IS CORRECT):" << std::endl;
Rcpp::Rcout << "\tSuppose the retraction is second order or the point is a critical point." << std::endl;
Rcpp::Rcout << "\tIf there exists an interval of |eta| such that (fy-fx-<gfx,eta>)/<0.5 eta, Hessian eta>" << std::endl;
Rcpp::Rcout << "\tapproximates ONE, then the action of Hessian is probably correct." << std::endl;
////TEST IDEA2:
//for (integer i = 1; i < length - 1; i++)
// Rprintf("log(|eta|):%.3e, slope:%.3e\n", X[i], (Y[i + 1] - Y[i - 1]) / (X[i + 1] - X[i - 1]));
//Rcpp::Rcout << "CHECK GRADIENT:" << std::endl;
//Rcpp::Rcout << "\tIf there exists an interval of |eta| such that the slopes " << std::endl;
//Rcpp::Rcout << "\tapproximate TWO, then the gradient is probably correct!" << std::endl;
//Rcpp::Rcout << "CHECK THE ACTION OF THE HESSIAN (PRESUME GRADIENT IS CORRECT AND" << std::endl;
//Rcpp::Rcout << "THE COST FUNCTION IS NOT ONLY QUADRATIC):" << std::endl;
//Rcpp::Rcout << "\tIf there exists an interval of |eta| such that the slopes" << std::endl;
//Rcpp::Rcout << "\tapproximate THREE, then the action of Hessian is probably correct." << std::endl;
//x->Print("1, x:", false);//---
delete xi;
//x->Print("2, x:", false);//---
//gfx->Print("2, gfx:", false);//---
delete gfx;
//x->Print("3, x:", false);//---
delete y;
//x->Print("4, x:", false);//---
delete Hv;
//x->Print("5, x:", false);//---
delete[] X;
delete etax;
//x->Print("x:", false);//---
delete x;
};
CFlightVisualiser::CFlightVisualiser(QWidget *parent) :
CFlightVisualiser(parent, Point3D(100, 100, 100), Point2D(100, 250), Point3D(500, 500, 500), Vector3D(Grad(0), Grad(0)))
{
}
namespace XLEMath
{
class Grad
{
public:
float x, y, z, w;
Grad(float ix, float iy, float iz)
{ x = ix; y = iy; z = iz; }
Grad(float ix, float iy, float iz, float iw)
{ x = ix; y = iy; z = iz; w = iw; }
};
Grad grad3[] =
{
Grad(1,1,0), Grad(-1,1,0), Grad(1,-1,0), Grad(-1,-1,0),
Grad(1,0,1), Grad(-1,0,1), Grad(1,0,-1), Grad(-1,0,-1),
Grad(0,1,1), Grad(0,-1,1), Grad(0,1,-1), Grad(0,-1,-1)
};
Grad grad4[]=
{
Grad(0,1,1,1), Grad(0,1,1,-1), Grad(0,1,-1,1), Grad(0,1,-1,-1),
Grad(0,-1,1,1), Grad(0,-1,1,-1), Grad(0,-1,-1,1), Grad(0,-1,-1,-1),
Grad(1,0,1,1), Grad(1,0,1,-1), Grad(1,0,-1,1), Grad(1,0,-1,-1),
Grad(-1,0,1,1), Grad(-1,0,1,-1), Grad(-1,0,-1,1), Grad(-1,0,-1,-1),
Grad(1,1,0,1), Grad(1,1,0,-1), Grad(1,-1,0,1), Grad(1,-1,0,-1),
Grad(-1,1,0,1), Grad(-1,1,0,-1), Grad(-1,-1,0,1), Grad(-1,-1,0,-1),
Grad(1,1,1,0), Grad(1,1,-1,0), Grad(1,-1,1,0), Grad(1,-1,-1,0),
Grad(-1,1,1,0), Grad(-1,1,-1,0), Grad(-1,-1,1,0), Grad(-1,-1,-1,0)
};
short p[] = {
151,160,137,91,90,15,
131,13,201,95,96,53,194,233,7,225,140,36,103,30,69,142,8,99,37,240,21,10,23,
190, 6,148,247,120,234,75,0,26,197,62,94,252,219,203,117,35,11,32,57,177,33,
88,237,149,56,87,174,20,125,136,171,168, 68,175,74,165,71,134,139,48,27,166,
77,146,158,231,83,111,229,122,60,211,133,230,220,105,92,41,55,46,245,40,244,
102,143,54, 65,25,63,161, 1,216,80,73,209,76,132,187,208, 89,18,169,200,196,
135,130,116,188,159,86,164,100,109,198,173,186, 3,64,52,217,226,250,124,123,
5,202,38,147,118,126,255,82,85,212,207,206,59,227,47,16,58,17,182,189,28,42,
223,183,170,213,119,248,152, 2,44,154,163, 70,221,153,101,155,167, 43,172,9,
129,22,39,253, 19,98,108,110,79,113,224,232,178,185, 112,104,218,246,97,228,
251,34,242,193,238,210,144,12,191,179,162,241, 81,51,145,235,249,14,239,107,
49,192,214, 31,181,199,106,157,184, 84,204,176,115,121,50,45,127, 4,150,254,
138,236,205,93,222,114,67,29,24,72,243,141,128,195,78,66,215,61,156,180};
// To remove the need for index wrapping, float the permutation table length
static short perm[512];
static short permMod12[512];
static bool permDoneInit = false;
static void InitPerm()
{
if (permDoneInit) return;
permDoneInit = true;
for(int i=0; i<512; i++)
{
perm[i]=p[i & 255];
permMod12[i] = (short)(perm[i] % 12);
}
}
// Skewing and unskewing factors for 2, 3, and 4 dimensions
static float F2 = 0.5f*(XlSqrt(3.0f)-1.0f);
static float G2 = (3.0f-XlSqrt(3.0f))/6.0f;
static float F3 = 1.0f/3.0f;
static float G3 = 1.0f/6.0f;
static float F4 = (XlSqrt(5.0f)-1.0f)/4.0f;
static float G4 = (5.0f-XlSqrt(5.0f))/20.0f;
static int fastfloor(float x) {
// this method was built for Java... Maybe it's not the best option for C++?
int xi = (int)x;
return x<xi ? xi-1 : xi;
}
static float dot(Grad g, float x, float y) { return g.x*x + g.y*y; }
static float dot(Grad g, float x, float y, float z) { return g.x*x + g.y*y + g.z*z; }
static float dot(Grad g, float x, float y, float z, float w) { return g.x*x + g.y*y + g.z*z + g.w*w; }
// 2D simplex noise
float SimplexNoise(Float2 input)
{
float xin = input[0], yin = input[1];
InitPerm();
float n0, n1, n2; // Noise contributions from the three corners
// Skew the input space to determine which simplex cell we're in
float s = (xin+yin)*F2; // Hairy factor for 2D
int i = fastfloor(xin+s);
int j = fastfloor(yin+s);
float t = (i+j)*G2;
float X0 = i-t; // Unskew the cell origin back to (x,y) space
float Y0 = j-t;
float x0 = xin-X0; // The x,y distances from the cell origin
float y0 = yin-Y0;
// For the 2D case, the simplex shape is an equilateral triangle.
// Determine which simplex we are in.
int i1, j1; // Offsets for second (middle) corner of simplex in (i,j) coords
if(x0>y0) { i1=1; j1=0; } // lower triangle, XY order: (0,0)->(1,0)->(1,1)
else { i1=0; j1=1; } // upper triangle, YX order: (0,0)->(0,1)->(1,1)
// A step of (1,0) in (i,j) means a step of (1-c,-c) in (x,y), and
// a step of (0,1) in (i,j) means a step of (-c,1-c) in (x,y), where
// c = (3-sqrt(3))/6
float x1 = x0 - i1 + G2; // Offsets for middle corner in (x,y) unskewed coords
float y1 = y0 - j1 + G2;
float x2 = x0 - 1.f + 2.f * G2; // Offsets for last corner in (x,y) unskewed coords
float y2 = y0 - 1.f + 2.f * G2;
// Work out the hashed gradient indices of the three simplex corners
int ii = i & 255;
int jj = j & 255;
int gi0 = permMod12[ii+perm[jj]];
int gi1 = permMod12[ii+i1+perm[jj+j1]];
int gi2 = permMod12[ii+1+perm[jj+1]];
// Calculate the contribution from the three corners
float t0 = 0.5f - x0*x0-y0*y0;
if(t0<0) n0 = 0.f;
else {
t0 *= t0;
n0 = t0 * t0 * dot(grad3[gi0], x0, y0); // (x,y) of grad3 used for 2D gradient
}
float t1 = 0.5f - x1*x1-y1*y1;
if(t1<0) n1 = 0.f;
else {
t1 *= t1;
n1 = t1 * t1 * dot(grad3[gi1], x1, y1);
}
float t2 = 0.5f - x2*x2-y2*y2;
if(t2<0) n2 = 0.f;
else {
t2 *= t2;
n2 = t2 * t2 * dot(grad3[gi2], x2, y2);
}
// Add contributions from each corner to get the final noise value.
// The result is scaled to return values in the interval [-1,1].
return 70.f * (n0 + n1 + n2);
}
// 3D simplex noise
float SimplexNoise(Float3 input)
{
float xin = input[0], yin = input[1], zin = input[2];
InitPerm();
float n0, n1, n2, n3; // Noise contributions from the four corners
// Skew the input space to determine which simplex cell we're in
float s = (xin+yin+zin)*F3; // Very nice and simple skew factor for 3D
int i = fastfloor(xin+s);
int j = fastfloor(yin+s);
int k = fastfloor(zin+s);
float t = (i+j+k)*G3;
float X0 = i-t; // Unskew the cell origin back to (x,y,z) space
float Y0 = j-t;
float Z0 = k-t;
float x0 = xin-X0; // The x,y,z distances from the cell origin
float y0 = yin-Y0;
float z0 = zin-Z0;
// For the 3D case, the simplex shape is a slightly irregular tetrahedron.
// Determine which simplex we are in.
int i1, j1, k1; // Offsets for second corner of simplex in (i,j,k) coords
int i2, j2, k2; // Offsets for third corner of simplex in (i,j,k) coords
if(x0>=y0) {
if(y0>=z0) { i1=1; j1=0; k1=0; i2=1; j2=1; k2=0; } // X Y Z order
else if(x0>=z0) { i1=1; j1=0; k1=0; i2=1; j2=0; k2=1; } // X Z Y order
else { i1=0; j1=0; k1=1; i2=1; j2=0; k2=1; } // Z X Y order
} else { // x0<y0
if(y0<z0) { i1=0; j1=0; k1=1; i2=0; j2=1; k2=1; } // Z Y X order
else if(x0<z0) { i1=0; j1=1; k1=0; i2=0; j2=1; k2=1; } // Y Z X order
else { i1=0; j1=1; k1=0; i2=1; j2=1; k2=0; } // Y X Z order
}
// A step of (1,0,0) in (i,j,k) means a step of (1-c,-c,-c) in (x,y,z),
// a step of (0,1,0) in (i,j,k) means a step of (-c,1-c,-c) in (x,y,z), and
// a step of (0,0,1) in (i,j,k) means a step of (-c,-c,1-c) in (x,y,z), where
// c = 1/6.
float x1 = x0 - i1 + G3; // Offsets for second corner in (x,y,z) coords
float y1 = y0 - j1 + G3;
float z1 = z0 - k1 + G3;
float x2 = x0 - i2 + 2.f*G3; // Offsets for third corner in (x,y,z) coords
float y2 = y0 - j2 + 2.f*G3;
float z2 = z0 - k2 + 2.f*G3;
float x3 = x0 - 1.f + 3.f*G3; // Offsets for last corner in (x,y,z) coords
float y3 = y0 - 1.f + 3.f*G3;
float z3 = z0 - 1.f + 3.f*G3;
// Work out the hashed gradient indices of the four simplex corners
int ii = i & 255;
int jj = j & 255;
int kk = k & 255;
int gi0 = permMod12[ii+perm[jj+perm[kk]]];
int gi1 = permMod12[ii+i1+perm[jj+j1+perm[kk+k1]]];
int gi2 = permMod12[ii+i2+perm[jj+j2+perm[kk+k2]]];
int gi3 = permMod12[ii+1+perm[jj+1+perm[kk+1]]];
// Calculate the contribution from the four corners
float t0 = 0.6f - x0*x0 - y0*y0 - z0*z0;
if(t0<0) n0 = 0.f;
else {
t0 *= t0;
n0 = t0 * t0 * dot(grad3[gi0], x0, y0, z0);
}
float t1 = 0.6f - x1*x1 - y1*y1 - z1*z1;
if(t1<0) n1 = 0.f;
else {
t1 *= t1;
n1 = t1 * t1 * dot(grad3[gi1], x1, y1, z1);
}
float t2 = 0.6f - x2*x2 - y2*y2 - z2*z2;
if(t2<0) n2 = 0.f;
else {
t2 *= t2;
n2 = t2 * t2 * dot(grad3[gi2], x2, y2, z2);
}
float t3 = 0.6f - x3*x3 - y3*y3 - z3*z3;
if(t3<0) n3 = 0.f;
else {
t3 *= t3;
n3 = t3 * t3 * dot(grad3[gi3], x3, y3, z3);
}
// Add contributions from each corner to get the final noise value.
// The result is scaled to stay just inside [-1,1]
return 32.f*(n0 + n1 + n2 + n3);
}
#if 1
// 4D simplex noise, better simplex rank ordering method 2012-03-09
float SimplexNoise(Float4 input)
{
float x = input[0], y = input[1], z = input[2], w = input[3];
InitPerm();
float n0, n1, n2, n3, n4; // Noise contributions from the five corners
// Skew the (x,y,z,w) space to determine which cell of 24 simplices we're in
float s = (x + y + z + w) * F4; // Factor for 4D skewing
int i = fastfloor(x + s);
int j = fastfloor(y + s);
int k = fastfloor(z + s);
int l = fastfloor(w + s);
float t = (i + j + k + l) * G4; // Factor for 4D unskewing
float X0 = i - t; // Unskew the cell origin back to (x,y,z,w) space
float Y0 = j - t;
float Z0 = k - t;
float W0 = l - t;
float x0 = x - X0; // The x,y,z,w distances from the cell origin
float y0 = y - Y0;
float z0 = z - Z0;
float w0 = w - W0;
// For the 4D case, the simplex is a 4D shape I won't even try to describe.
// To find out which of the 24 possible simplices we're in, we need to
// determine the magnitude ordering of x0, y0, z0 and w0.
// Six pair-wise comparisons are performed between each possible pair
// of the four coordinates, and the results are used to rank the numbers.
int rankx = 0;
int ranky = 0;
int rankz = 0;
int rankw = 0;
if(x0 > y0) rankx++; else ranky++;
if(x0 > z0) rankx++; else rankz++;
if(x0 > w0) rankx++; else rankw++;
if(y0 > z0) ranky++; else rankz++;
if(y0 > w0) ranky++; else rankw++;
if(z0 > w0) rankz++; else rankw++;
int i1, j1, k1, l1; // The integer offsets for the second simplex corner
int i2, j2, k2, l2; // The integer offsets for the third simplex corner
int i3, j3, k3, l3; // The integer offsets for the fourth simplex corner
// simplex[c] is a 4-vector with the numbers 0, 1, 2 and 3 in some order.
// Many values of c will never occur, since e.g. x>y>z>w makes x<z, y<w and x<w
// impossible. Only the 24 indices which have non-zero entries make any sense.
// We use a thresholding to set the coordinates in turn from the largest magnitude.
// Rank 3 denotes the largest coordinate.
i1 = rankx >= 3 ? 1 : 0;
j1 = ranky >= 3 ? 1 : 0;
k1 = rankz >= 3 ? 1 : 0;
l1 = rankw >= 3 ? 1 : 0;
// Rank 2 denotes the second largest coordinate.
i2 = rankx >= 2 ? 1 : 0;
j2 = ranky >= 2 ? 1 : 0;
k2 = rankz >= 2 ? 1 : 0;
l2 = rankw >= 2 ? 1 : 0;
// Rank 1 denotes the second smallest coordinate.
i3 = rankx >= 1 ? 1 : 0;
j3 = ranky >= 1 ? 1 : 0;
k3 = rankz >= 1 ? 1 : 0;
l3 = rankw >= 1 ? 1 : 0;
// The fifth corner has all coordinate offsets = 1, so no need to compute that.
float x1 = x0 - i1 + G4; // Offsets for second corner in (x,y,z,w) coords
float y1 = y0 - j1 + G4;
float z1 = z0 - k1 + G4;
float w1 = w0 - l1 + G4;
float x2 = x0 - i2 + 2.0f*G4; // Offsets for third corner in (x,y,z,w) coords
float y2 = y0 - j2 + 2.0f*G4;
float z2 = z0 - k2 + 2.0f*G4;
float w2 = w0 - l2 + 2.0f*G4;
float x3 = x0 - i3 + 3.0f*G4; // Offsets for fourth corner in (x,y,z,w) coords
float y3 = y0 - j3 + 3.0f*G4;
float z3 = z0 - k3 + 3.0f*G4;
float w3 = w0 - l3 + 3.0f*G4;
float x4 = x0 - 1.0f + 4.0f*G4; // Offsets for last corner in (x,y,z,w) coords
float y4 = y0 - 1.0f + 4.0f*G4;
float z4 = z0 - 1.0f + 4.0f*G4;
float w4 = w0 - 1.0f + 4.0f*G4;
// Work out the hashed gradient indices of the five simplex corners
int ii = i & 255;
int jj = j & 255;
int kk = k & 255;
int ll = l & 255;
int gi0 = perm[ii+perm[jj+perm[kk+perm[ll]]]] % 32;
int gi1 = perm[ii+i1+perm[jj+j1+perm[kk+k1+perm[ll+l1]]]] % 32;
int gi2 = perm[ii+i2+perm[jj+j2+perm[kk+k2+perm[ll+l2]]]] % 32;
int gi3 = perm[ii+i3+perm[jj+j3+perm[kk+k3+perm[ll+l3]]]] % 32;
int gi4 = perm[ii+1+perm[jj+1+perm[kk+1+perm[ll+1]]]] % 32;
// Calculate the contribution from the five corners
float t0 = 0.6f - x0*x0 - y0*y0 - z0*z0 - w0*w0;
if(t0<0) n0 = 0.0f;
else {
t0 *= t0;
n0 = t0 * t0 * dot(grad4[gi0], x0, y0, z0, w0);
}
float t1 = 0.6f - x1*x1 - y1*y1 - z1*z1 - w1*w1;
if(t1<0) n1 = 0.0f;
else {
t1 *= t1;
n1 = t1 * t1 * dot(grad4[gi1], x1, y1, z1, w1);
}
float t2 = 0.6f - x2*x2 - y2*y2 - z2*z2 - w2*w2;
if(t2<0) n2 = 0.0f;
else {
t2 *= t2;
n2 = t2 * t2 * dot(grad4[gi2], x2, y2, z2, w2);
}
float t3 = 0.6f - x3*x3 - y3*y3 - z3*z3 - w3*w3;
if(t3<0) n3 = 0.0f;
else {
t3 *= t3;
n3 = t3 * t3 * dot(grad4[gi3], x3, y3, z3, w3);
}
float t4 = 0.6f - x4*x4 - y4*y4 - z4*z4 - w4*w4;
if(t4<0) n4 = 0.0f;
else {
t4 *= t4;
n4 = t4 * t4 * dot(grad4[gi4], x4, y4, z4, w4);
}
// Sum up and scale the result to cover the range [-1,1]
return 27.0f * (n0 + n1 + n2 + n3 + n4);
}
#endif
template<typename Type>
float SimplexFBM(Type pos, float hgrid, float gain, float lacunarity, int octaves)
{
float total = 0.0f;
float frequency = 1.0f/(float)hgrid;
float amplitude = 1.f;
for (int i = 0; i < octaves; ++i) {
total += SimplexNoise(Type(pos * frequency)) * amplitude;
frequency *= lacunarity;
amplitude *= gain;
}
return total;
}
template float SimplexFBM(Float2, float, float, float, int);
template float SimplexFBM(Float3, float, float, float, int);
template float SimplexFBM(Float4, float, float, float, int);
}
float bePerlinNoise2D::Get(float x, float y)
{
float xi, xf, yi, yf;
xf = modf(x, &xi);
yf = modf(y, &yi);
constexpr float zf = 0.5f;
if (xf < 0.0)
{
xi -= 1.0;
xf += 1.0;
}
if (yf < 0.0)
{
yi -= 1.0;
yf += 1.0;
}
int x0 = (int)xi;
int y0 = (int)yi;
const int maxX = 255;
const int maxY = 255;
x0 = ((x0 % maxX) + maxX) % maxX; // [0, maxX)
y0 = ((y0 % maxY) + maxY) % maxY; // [0, maxX)
const int x1 = (x0 + 1) % maxX; // [0, maxX)
const int y1 = (y0 + 1) % maxY; // [0, maxX)
const float u = beMath::SmootherStep(xf);
const float v = beMath::SmootherStep(yf);
constexpr float w = beMath::SmootherStep(zf);
u8* p = m_hashTable.data();
const int z0 = 0;
const int z1 = 1;
#pragma warning(push)
#pragma warning(disable:26481) // pointer arithmetic
int aaa, aba, aab, abb, baa, bba, bab, bbb;
aaa = p[p[p[x0]+y0]+z0];
aba = p[p[p[x0]+y1]+z0];
aab = p[p[p[x0]+y0]+z1];
abb = p[p[p[x0]+y1]+z1];
baa = p[p[p[x1]+y0]+z0];
bba = p[p[p[x1]+y1]+z0];
bab = p[p[p[x1]+y0]+z1];
bbb = p[p[p[x1]+y1]+z1];
#pragma warning(pop)
// The gradient function calculates the dot product between a pseudorandom
// gradient vector and the vector from the input coordinate to the 8
// surrounding points in its unit cube.
// This is all then lerped together as a sort of weighted average based on the faded (u,v,w)
// values we made earlier.
float X1, X2, Y1, Y2;
X1 = Lerp(Grad(aaa, xf, yf , zf) , Grad(baa, xf-1.f, yf , zf) , u);
X2 = Lerp(Grad(aba, xf, yf-1.f, zf) , Grad(bba, xf-1.f, yf-1.f, zf) , u);
Y1 = Lerp(X1, X2, v);
X1 = Lerp(Grad(aab, xf, yf , zf-1.f), Grad(bab, xf-1.f, yf , zf-1.f), u);
X2 = Lerp(Grad(abb, xf, yf-1.f, zf-1.f), Grad(bbb, xf-1.f, yf-1.f, zf-1.f), u);
Y2 = Lerp(X1, X2, v);
// Change (-1,1) => (0, 1)
const float result = (Lerp(Y1, Y2, w)+1.f) * 0.5f;
//LOG("X,Y,Z {%3.1f, %3.1f, %3.1f}\t = %3.3f", x, y, zf, result);
return result;
}
void OptimizeGeometry(string type) {
// Initialize geometry opt parameters
int opt_cycle = 1;
double dE = 1000, Gnorm = 1000; //nonsense initial values
double econv = 1.0e-6;
double gconv = 3.0e-4;
double stepsize = 0.25;
bool reset; // for resetting CG algorithm
// Initialize some empty vectors with same dimensions as the Gradient
Vector StepDir(Cluster::cluster().GetHMBIGradient(),false);
Vector Grad_current(Cluster::cluster().GetHMBIGradient(),false);
Vector StepDir_old(Cluster::cluster().GetHMBIGradient(),false);
Vector Grad_old(Cluster::cluster().GetHMBIGradient(),false);
if (type == "SteepestDescent") {
while (opt_cycle <= Params::Parameters().GetMaxOptCycles() &&
(fabs(dE) > econv || fabs(Gnorm) > gconv ) ) {
//printf("XXX\nXXX Starting next opt cycle\n");
// before the step
double E_current = Cluster::cluster().GetHMBIEnergy();
Grad_current = Cluster::cluster().GetHMBIGradient();
Vector Coords_current = Cluster::cluster().GetCurrentCoordinates();
//printf("XXX Current Gradient: %12.6f\n",Grad_current.Norm());
// If this is the first cycle, do some special printing
if (opt_cycle == 1) {
printf("Cycle %d: Energy = %15.9f |Grad| = %12.6f\n",
0, E_current, Grad_current.Max(true));
printf("Cycle %d: dE = %15.9f |dGrad| = %12.6f\n",
0, 0.0, 0.0);
Cluster::cluster().UpdateTrajectoryFile(0,true);
}
// use Gradient printer to show coords
if (Params::Parameters().PrintLevel() > 0 )
Cluster::cluster().PrintGradient("Original coordinates",Coords_current);
// Create empty coords array with proper size
Vector Coords_new(Coords_current, false);
// Take optimization step
//Grad_current.Scale(-1.0);
SteepestDescent(Coords_new, Coords_current, Grad_current, stepsize);
// use Gradient printer to show coords
if (Params::Parameters().PrintLevel() > 0 )
Cluster::cluster().PrintGradient("New coordinates",Coords_new);
// Update the coordinates in the cluster object
Cluster::cluster().SetNewCoordinates(Coords_new);
// Create the new jobs, run them, and get the HMBI energy
Cluster::cluster().RunJobsAndComputeEnergy();
// Print output
double E = Cluster::cluster().GetHMBIEnergy();
Vector Grad( Cluster::cluster().GetHMBIGradient() );
//printf("XXX New Gradient: %12.6f\n",Grad.Max(true));
Gnorm = Grad.Max(true);
printf("Cycle %d: Energy = %15.9f |Grad| = %10.6f\n",opt_cycle,
E,Gnorm);
dE = E - E_current;
Vector dGrad(Grad);
dGrad -= Grad_current;
double dG = dGrad.Max(true);
printf("Cycle %d: dE = %15.9f |dGrad| = %10.6f step = %8.3f\n",
opt_cycle, dE, dG, stepsize);
Cluster::cluster().UpdateTrajectoryFile(opt_cycle);
// Save a copy of the new geometry in a new input file.
FILE *input;
string input_file = "new_geom.in";
if ((input = fopen(input_file.c_str(),"w"))==NULL) {
printf("OptimizeGeometry() : Cannot open file '%s'\n",input_file.c_str());
exit(1);
}
Cluster::cluster().PrintInputFile(input);
printf("\nNew input file written to '%s'\n",input_file.c_str());
fclose(input);
// Adjust step size
if (opt_cycle > 1) {
// if stepped too far, backup and shrink stepsize
if (dE > 0.0) {
printf("Cycle Back-up. Decreasing step size for next cycle.\n");
stepsize /= 1.5;
// Back up
Cluster::cluster().SetNewCoordinates(Coords_current);
Cluster::cluster().RunJobsAndComputeEnergy();
Grad_current = Grad_old;
}
else {
printf("Cycle Increasing step size for next cycle.\n");
stepsize *= 1.2;
}
if (stepsize > 2.0)
stepsize = 2.0;
}
//stepsize = 0.5;
opt_cycle++;
}
}
else if (type == "ConjugateGradients") {
// Start optimization cycles
while (opt_cycle <= Params::Parameters().GetMaxOptCycles() &&
(fabs(dE) > econv || fabs(Gnorm) > gconv ) ) {
reset = false;
//printf("XXX\nXXX Starting next opt cycle\n");
// For CG optimizer, need to save previous gradient
if (opt_cycle > 1) {
Grad_old = Grad_current;
StepDir_old = StepDir;
//printf("Backing up Gradient and StepDir\n");
//printf("XXX |Grad_old| = %12.6f, |StepDir_old| = %12.6f\n",
//Grad_old.Norm(),StepDir_old.Norm());
}
// Grab Energy, Gradient, and XYZ coordinates for geometry
// before the step
double E_current = Cluster::cluster().GetHMBIEnergy();
Grad_current = Cluster::cluster().GetHMBIGradient();
Vector Coords_current = Cluster::cluster().GetCurrentCoordinates();
//printf("XXX Current Gradient: %12.6f\n",Grad_current.Norm());
// If this is the first cycle, do some special printing
if (opt_cycle == 1) {
printf("Cycle %d: Energy = %15.9f |Grad| = %12.6f\n",
0, E_current, Grad_current.Max(true));
printf("Cycle %d: dE = %15.9f |dGrad| = %12.6f\n",
0, 0.0, 0.0);
Cluster::cluster().UpdateTrajectoryFile(0,true);
}
// use Gradient printer to show coords
if (Params::Parameters().PrintLevel() > 0 )
Cluster::cluster().PrintGradient("Original coordinates",Coords_current);
// Create empty coords array with proper size
Vector Coords_new(Coords_current, false);
if (opt_cycle % 20 == 0) {
reset = true;
//if (stepsize > 0.5)
stepsize = 0.25;
}
// Take optimization step
if (opt_cycle==1) {
// Use steepest descent for first step, sets StepDir
Grad_current.Scale(-1.0);
SteepestDescent(Coords_new, Coords_current, Grad_current, stepsize);
StepDir = Grad_current;
StepDir.Scale(-1.0);
}
else
ConjugateGradients(Coords_new, StepDir, Coords_current, Grad_current,
Grad_old, StepDir_old,stepsize, reset);
// use Gradient printer to show coords
if (Params::Parameters().PrintLevel() > 0 )
Cluster::cluster().PrintGradient("New coordinates",Coords_new);
// Update the coordinates in the cluster object
Cluster::cluster().SetNewCoordinates(Coords_new);
// Create the new jobs, run them, and get the HMBI energy
Cluster::cluster().RunJobsAndComputeEnergy();
// Print output
double E = Cluster::cluster().GetHMBIEnergy();
Vector Grad( Cluster::cluster().GetHMBIGradient() );
//printf("XXX New Gradient: %12.6f\n",Grad.Max(true));
Gnorm = Grad.Max(true);
printf("Cycle %d: Energy = %15.9f |Grad| = %10.6f\n",opt_cycle,
E,Gnorm);
dE = E - E_current;
Vector dGrad(Grad);
dGrad -= Grad_current;
double dG = dGrad.Max(true);
printf("Cycle %d: dE = %15.9f |dGrad| = %10.6f step = %8.3f\n",
opt_cycle, dE, dG, stepsize);
Cluster::cluster().UpdateTrajectoryFile(opt_cycle);
// Save a copy of the new geometry in a new input file.
FILE *input;
string input_file = "new_geom.in";
if ((input = fopen(input_file.c_str(),"w"))==NULL) {
printf("OptimizeGeometry() : Cannot open file '%s'\n",input_file.c_str());
exit(1);
}
Cluster::cluster().PrintInputFile(input);
printf("\nNew input file written to '%s'\n",input_file.c_str());
fclose(input);
// Adjust step size
if (opt_cycle > 1) {
// if stepped too far, backup and shrink stepsize
if (dE > 0.0) {
printf("Cycle Back-up. Decreasing step size for next cycle.\n");
stepsize /= 1.5;
// Back up
Cluster::cluster().SetNewCoordinates(Coords_current);
Cluster::cluster().RunJobsAndComputeEnergy();
Grad_current = Grad_old;
StepDir = StepDir_old;
}
else {
printf("Cycle Increasing step size for next cycle.\n");
stepsize *= 1.2;
}
if (stepsize > 2.0)
stepsize = 2.0;
}
//stepsize = 0.5;
opt_cycle++;
}
}
printf("Cycle %d: Opt completed. dE = %15.9f, |Grad| = %10.6f\n",opt_cycle-1,
dE,Gnorm);
Cluster::cluster().ComputeDistanceMatrix();
// Save a copy of the new geometry in a new input file.
FILE *input;
string input_file = "new_geom.in";
if ((input = fopen(input_file.c_str(),"w"))==NULL) {
printf("OptimizeGeometry() : Cannot open file '%s'\n",input_file.c_str());
exit(1);
}
Cluster::cluster().PrintInputFile(input);
printf("\nNew input file written to '%s'\n",input_file.c_str());
fclose(input);
}
PreconditionerBlockMS<space_type>::PreconditionerBlockMS(space_ptrtype Xh, // (u)x(p)
ModelProperties model, // model
std::string const& p, // prefix
sparse_matrix_ptrtype AA ) // The matrix
:
M_backend(backend()), // the backend associated to the PC
M_Xh( Xh ),
M_Vh( Xh->template functionSpace<0>() ), // Potential
M_Qh( Xh->template functionSpace<1>() ), // Lagrange
M_Vh_indices( M_Vh->nLocalDofWithGhost() ),
M_Qh_indices( M_Qh->nLocalDofWithGhost() ),
M_uin( M_backend->newVector( M_Vh ) ),
M_uout( M_backend->newVector( M_Vh ) ),
M_pin( M_backend->newVector( M_Qh ) ),
M_pout( M_backend->newVector( M_Qh ) ),
U( M_Xh, "U" ),
M_mass(M_backend->newMatrix(M_Vh,M_Vh)),
M_L(M_backend->newMatrix(M_Qh,M_Qh)),
M_er( 1. ),
M_model( model ),
M_prefix( p ),
M_prefix_11( p+".11" ),
M_prefix_22( p+".22" ),
u(M_Vh, "u"),
ozz(M_Vh, "ozz"),
zoz(M_Vh, "zoz"),
zzo(M_Vh, "zzo"),
M_ozz(M_backend->newVector( M_Vh )),
M_zoz(M_backend->newVector( M_Vh )),
M_zzo(M_backend->newVector( M_Vh )),
X(M_Qh, "X"),
Y(M_Qh, "Y"),
Z(M_Qh, "Z"),
M_X(M_backend->newVector( M_Qh )),
M_Y(M_backend->newVector( M_Qh )),
M_Z(M_backend->newVector( M_Qh )),
phi(M_Qh, "phi")
{
tic();
LOG(INFO) << "[PreconditionerBlockMS] setup starts";
this->setMatrix( AA );
this->setName(M_prefix);
/* Indices are need to extract sub matrix */
std::iota( M_Vh_indices.begin(), M_Vh_indices.end(), 0 );
std::iota( M_Qh_indices.begin(), M_Qh_indices.end(), M_Vh->nLocalDofWithGhost() );
M_11 = AA->createSubMatrix( M_Vh_indices, M_Vh_indices, true, true);
/* Boundary conditions */
BoundaryConditions M_bc = M_model.boundaryConditions();
map_vector_field<FEELPP_DIM,1,2> m_dirichlet_u { M_bc.getVectorFields<FEELPP_DIM> ( "u", "Dirichlet" ) };
map_scalar_field<2> m_dirichlet_p { M_bc.getScalarFields<2> ( "phi", "Dirichlet" ) };
/* Compute the mass matrix (needed in first block, constant) */
auto f2A = form2(_test=M_Vh, _trial=M_Vh, _matrix=M_mass);
auto f1A = form1(_test=M_Vh);
f2A = integrate(_range=elements(M_Vh->mesh()), _expr=inner(idt(u),id(u))); // M
for(auto const & it : m_dirichlet_u )
{
LOG(INFO) << "Applying " << it.second << " on " << it.first << " for "<<M_prefix_11<<"\n";
f2A += on(_range=markedfaces(M_Vh->mesh(),it.first), _expr=it.second,_rhs=f1A, _element=u, _type="elimination_symmetric");
}
/* Compute the L (= er * grad grad) matrix (the second block) */
auto f2L = form2(_test=M_Qh,_trial=M_Qh, _matrix=M_L);
for(auto it : M_model.materials() )
{
f2L += integrate(_range=markedelements(M_Qh->mesh(),marker(it)), _expr=M_er*inner(gradt(phi), grad(phi)));
}
auto f1LQ = form1(_test=M_Qh);
for(auto const & it : m_dirichlet_p)
{
LOG(INFO) << "Applying " << it.second << " on " << it.first << " for "<<M_prefix_22<<"\n";
f2L += on(_range=markedfaces(M_Qh->mesh(),it.first),_element=phi, _expr=it.second, _rhs=f1LQ, _type="elimination_symmetric");
}
if(soption(_name="pc-type", _prefix=M_prefix_11) == "ams")
#if FEELPP_DIM == 3
{
M_grad = Grad( _domainSpace=M_Qh, _imageSpace=M_Vh);
// This preconditioner is linked to that backend : the backend will
// automatically use the preconditioner.
auto prec = preconditioner(_pc=pcTypeConvertStrToEnum(soption(M_prefix_11+".pc-type")),
_backend=backend(_name=M_prefix_11),
_prefix=M_prefix_11,
_matrix=M_11
);
prec->setMatrix(M_11);
prec->attachAuxiliarySparseMatrix("G",M_grad.matPtr());
if(boption(M_prefix_11+".useEdge"))
{
LOG(INFO) << "[ AMS ] : using SetConstantEdgeVector \n";
ozz.on(_range=elements(M_Vh->mesh()),_expr=vec(cst(1),cst(0),cst(0)));
zoz.on(_range=elements(M_Vh->mesh()),_expr=vec(cst(0),cst(1),cst(0)));
zzo.on(_range=elements(M_Vh->mesh()),_expr=vec(cst(0),cst(0),cst(1)));
*M_ozz = ozz; M_ozz->close();
*M_zoz = zoz; M_zoz->close();
*M_zzo = zzo; M_zzo->close();
prec->attachAuxiliaryVector("Px",M_ozz);
prec->attachAuxiliaryVector("Py",M_zoz);
prec->attachAuxiliaryVector("Pz",M_zzo);
}
else
{
LOG(INFO) << "[ AMS ] : using SetCoordinates \n";
X.on(_range=elements(M_Vh->mesh()),_expr=Px());
Y.on(_range=elements(M_Vh->mesh()),_expr=Py());
Z.on(_range=elements(M_Vh->mesh()),_expr=Pz());
*M_X = X; M_X->close();
*M_Y = Y; M_Y->close();
*M_Z = Z; M_Z->close();
prec->attachAuxiliaryVector("X",M_X);
prec->attachAuxiliaryVector("Y",M_Y);
prec->attachAuxiliaryVector("Z",M_Z);
}
}
#else
std::cerr << "ams preconditioner is not interfaced in two dimensions\n";
#endif
toc( "[PreconditionerBlockMS] setup done ", FLAGS_v > 0 );
}
