commit a383ae33f19e6bf8ec03dcf6b89242a7a42f779d
parent 2e900236529d1155f5c7a0a51a756b91d62a1907
Author: Fabian Wermelinger <fabianw@mavt.ethz.ch>
Date: Wed, 30 Nov 2016 12:38:40 +0100
added non-uniform marching cube mesh
Diffstat:
4 files changed, 165 insertions(+), 79 deletions(-)
diff --git a/src/Interpolator.h b/src/Interpolator.h
@@ -32,45 +32,50 @@ public:
Interpolator(ArgumentParser& p) :
m_extent(p("extent").asDouble(1.0))
{
- // cell centered or nodal values?
- if (p("data").asString("cell") == "cell") _getH = [](const Real e, const int N) { return e/static_cast<Real>(N); };
- else if (p("data").asString("cell") == "node") _getH = [](const Real e, const int N) { return e/static_cast<Real>(N-1); };
+ // load the data
+ if (p("load").asString("h5") == "h5") _load_h5(p);
+ else if (p("load").asString("h5") == "wavelet") _load_wavelet(p);
else
{
- std::cerr << "ERROR: Interpolator: Unknown data attribute \"" << p("data").asString() << "\"" << std::endl;
+ std::cerr << "ERROR: Interpolator: Undefined loader \"" << p("load").asString() << "\"" << std::endl;
abort();
}
- // load the data
- if (p("load").asString("h5") == "h5") _load_h5(p);
- else if (p("load").asString("h5") == "wavelet") _load_wavelet(p);
+ // cell centered or nodal values?
+ if (p("data").asString("cell") == "cell") _nCells = [](const int N) { return N; };
+ else if (p("data").asString("cell") == "node") _nCells = [](const int N) { return N-1; };
else
{
- std::cerr << "ERROR: Interpolator: Undefined loader \"" << p("load").asString() << "\"" << std::endl;
+ std::cerr << "ERROR: Interpolator: Unknown data attribute \"" << p("data").asString() << "\"" << std::endl;
abort();
}
const int Nmax = std::max(m_data.Nx(), std::max(m_data.Ny(), m_data.Nz()));
assert(Nmax > 1);
- m_h = _getH(m_extent, Nmax);
+ m_h = m_extent/_nCells(Nmax);
m_invh = 1.0/m_h;
+ m_extentX = m_h*_nCells(m_data.Nx());
+ m_extentY = m_h*_nCells(m_data.Ny());
+ m_extentZ = m_h*_nCells(m_data.Nz());
// init coordinate transform
- m_origin_off = 0.0;
+ _physicalDataPos = [this](const int i) { return i*this->m_h; };
+ m_origin_off = {0.0, 0.0, 0.0};
m_isNodal = 1;
if (p("data").asString("cell") == "cell")
{
+ _physicalDataPos = [this](const int i) { return (0.5+i)*this->m_h; };
+ m_origin_off = {0.5*m_h, 0.5*m_h, 0.5*m_h};
m_isNodal = 0;
- m_origin_off += 0.5*m_h;
}
}
virtual ~Interpolator() {}
Real operator()(const Real x, const Real y, const Real z) const
{
- const Real xo = x - m_origin_off;
- const Real yo = y - m_origin_off;
- const Real zo = z - m_origin_off;
+ const Real xo = x - m_origin_off[0];
+ const Real yo = y - m_origin_off[1];
+ const Real zo = z - m_origin_off[2];
const int ix0 = _idx(xo);
const int iy0 = _idx(yo);
@@ -94,6 +99,11 @@ public:
inline Real getH() const { return m_h; }
inline Real getExtent() const { return m_extent; }
+ inline Real getExtentX() const { return m_extentX; }
+ inline Real getExtentY() const { return m_extentY; }
+ inline Real getExtentZ() const { return m_extentZ; }
+ inline Real getDataPos(const int i) const { return _physicalDataPos(i); }
+ inline void setOrigin(const Real o[3]) { for (int i=0; i<3; ++i) m_origin_off[i] = o[i]; }
inline int getNx() const { return m_data.Nx(); }
inline int getNy() const { return m_data.Ny(); }
inline int getNz() const { return m_data.Nz(); }
@@ -101,7 +111,10 @@ public:
protected:
Real m_extent;
- Real m_origin_off;
+ Real m_extentX;
+ Real m_extentY;
+ Real m_extentZ;
+ Real m_origin_off[3];
Real m_h, m_invh;
int m_isNodal;
@@ -109,7 +122,8 @@ protected:
TKernel m_kernel;
// helper
- std::function<Real(const Real, const int)> _getH;
+ std::function<int(const int)> _nCells;
+ std::function<Real(const int)> _physicalDataPos;
inline int _idx(const Real x) const { return std::floor(x*m_invh); }
inline Real _pos(const int i) const { return i*m_h; }
diff --git a/src/InterpolatorMPI.h b/src/InterpolatorMPI.h
@@ -8,6 +8,7 @@
#include <cassert>
#include <vector>
+#include <cmath>
#include <mpi.h>
#include "Interpolator.h"
@@ -80,23 +81,23 @@ public:
MPI_Cart_coords(cartcomm, myrank, 3, m_myPEIndex);
m_isroot = (0 == myrank);
- // cell centered or nodal values?
- if (p("data").asString("cell") == "cell") this->_getH = [](const Real e, const int N) { return e/static_cast<Real>(N); };
- else if (p("data").asString("cell") == "node") this->_getH = [](const Real e, const int N) { return e/static_cast<Real>(N-1); };
+ // load the data
+ if (p("load").asString("h5") == "h5") this->_load_h5_MPI(p);
+ else if (p("load").asString("h5") == "wavelet") this->_load_wavelet_MPI(p);
else
{
if (m_isroot)
- std::cerr << "ERROR: InterpolatorMPI: Unknown data attribute \"" << p("data").asString() << "\"" << std::endl;
+ std::cerr << "ERROR: InterpolatorMPI: Undefined loader \"" << p("load").asString() << "\"" << std::endl;
abort();
}
- // load the data
- if (p("load").asString("h5") == "h5") this->_load_h5_MPI(p);
- else if (p("load").asString("h5") == "wavelet") this->_load_wavelet_MPI(p);
+ // cell centered or nodal values?
+ if (p("data").asString("cell") == "cell") this->_nCells = [](const int N) { return N; };
+ else if (p("data").asString("cell") == "node") this->_nCells = [](const int N) { return N-1; };
else
{
if (m_isroot)
- std::cerr << "ERROR: InterpolatorMPI: Undefined loader \"" << p("load").asString() << "\"" << std::endl;
+ std::cerr << "ERROR: InterpolatorMPI: Unknown data attribute \"" << p("data").asString() << "\"" << std::endl;
abort();
}
@@ -105,17 +106,32 @@ public:
const int Nz = m_PESize[2]*this->m_data.Nz();
const int Nmax = std::max(Nx, std::max(Ny, Nz));
assert(Nmax > 1);
- this->m_h = this->_getH(this->m_extent, Nmax);
+ this->m_h = this->m_extent/this->_nCells(Nmax);
this->m_invh = 1.0/this->m_h;
+ this->m_extentX = this->m_h*this->_nCells(Nx);
+ this->m_extentY = this->m_h*this->_nCells(Ny);
+ this->m_extentZ = this->m_h*this->_nCells(Nz);
// init coordinate transform
- this->m_origin_off = 0.0;
+ this->_physicalDataPos = [this](const int i) { return i*this->m_h; };
this->m_isNodal = 1;
if (p("data").asString("cell") == "cell")
{
+ this->_physicalDataPos = [this](const int i) { return (0.5+i)*this->m_h; };
this->m_isNodal = 0;
- this->m_origin_off += 0.5*this->m_h;
}
+ const Real Ox = (this->m_extentX / m_PESize[0]) * m_myPEIndex[0];
+ const Real Oy = (this->m_extentY / m_PESize[1]) * m_myPEIndex[1];
+ const Real Oz = (this->m_extentZ / m_PESize[2]) * m_myPEIndex[2];
+ Real origin[3];
+ origin[0] = this->_physicalDataPos(ceil(Ox*this->m_invh)) - Ox;
+ origin[1] = this->_physicalDataPos(ceil(Oy*this->m_invh)) - Oy;
+ origin[2] = this->_physicalDataPos(ceil(Oz*this->m_invh)) - Oz;
+ assert(origin[0] >= 0.0);
+ assert(origin[1] >= 0.0);
+ assert(origin[2] >= 0.0);
+ for (int i = 0; i < 3; ++i)
+ this->m_origin_off[i] = origin[i];
// fetch halos cells
_fetch_halo(cartcomm);
@@ -174,7 +190,8 @@ void InterpolatorMPI<Tinterp>::_load_h5_MPI(ArgumentParser& parser)
const std::string filename = parser("file").asString("");
if (filename == "")
{
- std::cerr << "ERROR: Interpolator: -file is not specified. No input file given" << std::endl;
+ if (m_isroot)
+ std::cerr << "ERROR: InterpolatorMPI: -file is not specified. No input file given" << std::endl;
abort();
}
@@ -201,9 +218,24 @@ void InterpolatorMPI<Tinterp>::_load_h5_MPI(ArgumentParser& parser)
MPI_Bcast(maxDim, 4, MPI_INT, 0, m_comm);
NCH = maxDim[3];
- assert(maxDim[0] % m_PESize[0] == 0);
- assert(maxDim[1] % m_PESize[1] == 0);
- assert(maxDim[2] % m_PESize[2] == 0);
+ if (maxDim[0] % m_PESize[0] != 0)
+ {
+ if (m_isroot)
+ std::cerr << "ERROR: InterpolatorMPI: Number of processes in x-direction is not an integer multiple of available data." << std::endl;
+ abort();
+ }
+ if (maxDim[1] % m_PESize[1] != 0)
+ {
+ if (m_isroot)
+ std::cerr << "ERROR: InterpolatorMPI: Number of processes in y-direction is not an integer multiple of available data." << std::endl;
+ abort();
+ }
+ if (maxDim[2] % m_PESize[2] != 0)
+ {
+ if (m_isroot)
+ std::cerr << "ERROR: InterpolatorMPI: Number of processes in z-direction is not an integer multiple of available data." << std::endl;
+ abort();
+ }
const size_t NX = maxDim[0]/m_PESize[0];
const size_t NY = maxDim[1]/m_PESize[1];
const size_t NZ = maxDim[2]/m_PESize[2];
diff --git a/src/IsoExtractor.h b/src/IsoExtractor.h
@@ -383,12 +383,14 @@ public:
const int Nx = static_cast<Real>(m_interp.getNx()) / cscale;
const int Ny = static_cast<Real>(m_interp.getNy()) / cscale;
const int Nz = static_cast<Real>(m_interp.getNz()) / cscale;
- assert(Nx > 1);
- assert(Ny > 1);
- assert(Nz > 1);
- const Real ch = m_interp.getExtent() / (std::max(Nx, std::max(Ny, Nz)) - m_interp.isNodal());
+ assert(Nx > 0);
+ assert(Ny > 0);
+ assert(Nz > 0);
+ const Real chx = m_interp.getExtentX() / Nx;
+ const Real chy = m_interp.getExtentY() / Ny;
+ const Real chz = m_interp.getExtentZ() / Nz;
- _extractIso(isoval, Nx, Ny, Nz, ch);
+ _extractIso(isoval, Nx, Ny, Nz, chx, chy, chz);
_writePLY(fout, m_triList);
}
@@ -411,10 +413,23 @@ protected:
return (t - v0)/dv;
}
- inline void _extractIso(const Real isoval, const int Nx, const int Ny, const int Nz, const Real ch, const Real Ox=0.0, const Real Oy=0.0, const Real Oz=0.0, const bool verbose=true);
- inline void _marchCube(const Real x, const Real y, const Real z, const Real h, const Real target, const Real Ox, const Real Oy, const Real Oz);
- inline void _marchTetrahedron(const Real x, const Real y, const Real z, const Real h, const Real target, const Real Ox, const Real Oy, const Real Oz);
- inline void _evalTetrahedron(const Real coords[4][3], const Real val[4], const Real target);
+ inline void _extractIso(const Real isoval,
+ const int Nx, const int Ny, const int Nz,
+ const Real chx, const Real chy, const Real chz,
+ const Real Ox=0.0, const Real Oy=0.0, const Real Oz=0.0,
+ const bool verbose=true);
+
+ inline void _marchCube(const Real isoval,
+ const Real x, const Real y, const Real z,
+ const Real hx, const Real hy, const Real hz,
+ const Real Ox, const Real Oy, const Real Oz);
+
+ inline void _marchTetrahedron(const Real isoval,
+ const Real x, const Real y, const Real z,
+ const Real hx, const Real hy, const Real hz,
+ const Real Ox, const Real Oy, const Real Oz);
+
+ inline void _evalTetrahedron(const Real coords[4][3], const Real val[4], const Real isoval);
void _writePLY(const std::string basename, const std::vector<Triangle>& tList)
{
@@ -496,7 +511,10 @@ protected:
template <typename Tkernel, template<typename> class Tinterpolator>
-void IsoExtractor<Tkernel,Tinterpolator>::_extractIso(const Real isoval, const int Nx, const int Ny, const int Nz, const Real ch, const Real Ox, const Real Oy, const Real Oz, const bool verbose)
+void IsoExtractor<Tkernel,Tinterpolator>::_extractIso(const Real isoval,
+ const int Nx, const int Ny, const int Nz,
+ const Real chx, const Real chy, const Real chz,
+ const Real Ox, const Real Oy, const Real Oz, const bool verbose)
{
const int speculate = m_parser("speculate_triangle").asInt(10000);
m_triList.clear();
@@ -507,10 +525,10 @@ void IsoExtractor<Tkernel,Tinterpolator>::_extractIso(const Real isoval, const i
for (int j = 0; j < Ny; ++j)
for (int i = 0; i < Nx; ++i)
{
- const Real x = i*ch;
- const Real y = j*ch;
- const Real z = k*ch;
- _marchCube(x, y, z, ch, isoval, Ox, Oy, Oz);
+ const Real x = i*chx;
+ const Real y = j*chy;
+ const Real z = k*chz;
+ _marchCube(isoval, x, y, z, chx, chy, chz, Ox, Oy, Oz);
}
}
else if (m_parser("march").asString("cube") == "tetrahedron")
@@ -519,10 +537,10 @@ void IsoExtractor<Tkernel,Tinterpolator>::_extractIso(const Real isoval, const i
for (int j = 0; j < Ny; ++j)
for (int i = 0; i < Nx; ++i)
{
- const Real x = i*ch;
- const Real y = j*ch;
- const Real z = k*ch;
- _marchTetrahedron(x, y, z, ch, isoval, Ox, Oy, Oz);
+ const Real x = i*chx;
+ const Real y = j*chy;
+ const Real z = k*chz;
+ _marchTetrahedron(isoval, x, y, z, chx, chy, chz, Ox, Oy, Oz);
}
}
else
@@ -535,7 +553,10 @@ void IsoExtractor<Tkernel,Tinterpolator>::_extractIso(const Real isoval, const i
template <typename Tkernel, template<typename> class Tinterpolator>
-void IsoExtractor<Tkernel,Tinterpolator>::_marchCube(const Real x, const Real y, const Real z, const Real h, const Real target, const Real Ox, const Real Oy, const Real Oz)
+void IsoExtractor<Tkernel,Tinterpolator>::_marchCube(const Real isoval,
+ const Real x, const Real y, const Real z,
+ const Real hx, const Real hy, const Real hz,
+ const Real Ox, const Real Oy, const Real Oz)
{
Real valCubeVerts[8];
Real coordEdgeVert[12][3];
@@ -543,15 +564,15 @@ void IsoExtractor<Tkernel,Tinterpolator>::_marchCube(const Real x, const Real y,
// compute cube vertex values
for (int i = 0; i < 8; ++i)
valCubeVerts[i] = m_interp(
- x + h*gVertexOffset[i][0],
- y + h*gVertexOffset[i][1],
- z + h*gVertexOffset[i][2]);
+ x + hx*gVertexOffset[i][0],
+ y + hy*gVertexOffset[i][1],
+ z + hz*gVertexOffset[i][2]);
// find if there are vertices inside and outside the target value
int flagVert = 0;
for (int i = 0; i < 8; ++i)
{
- if (valCubeVerts[i] <= target) flagVert |= 1 << i;
+ if (valCubeVerts[i] <= isoval) flagVert |= 1 << i;
}
// indentify the edge intersections
@@ -567,10 +588,10 @@ void IsoExtractor<Tkernel,Tinterpolator>::_marchCube(const Real x, const Real y,
if (flagEdge & (1 << i))
{
// linear interpolation
- const Real frac = _getEdgeFrac(valCubeVerts[gEdgeConnection[i][0]], valCubeVerts[gEdgeConnection[i][1]], target);
- coordEdgeVert[i][0] = x + h*(gVertexOffset[gEdgeConnection[i][0]][0] + frac*gEdgeDirection[i][0]) + m_x0 + Ox;
- coordEdgeVert[i][1] = y + h*(gVertexOffset[gEdgeConnection[i][0]][1] + frac*gEdgeDirection[i][1]) + m_y0 + Oy;
- coordEdgeVert[i][2] = z + h*(gVertexOffset[gEdgeConnection[i][0]][2] + frac*gEdgeDirection[i][2]) + m_z0 + Oz;
+ const Real frac = _getEdgeFrac(valCubeVerts[gEdgeConnection[i][0]], valCubeVerts[gEdgeConnection[i][1]], isoval);
+ coordEdgeVert[i][0] = x + hx*(gVertexOffset[gEdgeConnection[i][0]][0] + frac*gEdgeDirection[i][0]) + m_x0 + Ox;
+ coordEdgeVert[i][1] = y + hy*(gVertexOffset[gEdgeConnection[i][0]][1] + frac*gEdgeDirection[i][1]) + m_y0 + Oy;
+ coordEdgeVert[i][2] = z + hz*(gVertexOffset[gEdgeConnection[i][0]][2] + frac*gEdgeDirection[i][2]) + m_z0 + Oz;
}
}
@@ -593,7 +614,10 @@ void IsoExtractor<Tkernel,Tinterpolator>::_marchCube(const Real x, const Real y,
template <typename Tkernel, template<typename> class Tinterpolator>
-void IsoExtractor<Tkernel,Tinterpolator>::_marchTetrahedron(const Real x, const Real y, const Real z, const Real h, const Real target, const Real Ox, const Real Oy, const Real Oz)
+void IsoExtractor<Tkernel,Tinterpolator>::_marchTetrahedron(const Real isoval,
+ const Real x, const Real y, const Real z,
+ const Real hx, const Real hy, const Real hz,
+ const Real Ox, const Real Oy, const Real Oz)
{
Real valCubeVerts[8];
Real coordCubeVerts[8][3];
@@ -603,9 +627,9 @@ void IsoExtractor<Tkernel,Tinterpolator>::_marchTetrahedron(const Real x, const
// compute cube vertex coordinates
for (int i = 0; i < 8; ++i)
{
- coordCubeVerts[i][0] = x + h*gVertexOffset[i][0];
- coordCubeVerts[i][1] = y + h*gVertexOffset[i][1];
- coordCubeVerts[i][2] = z + h*gVertexOffset[i][2];
+ coordCubeVerts[i][0] = x + hx*gVertexOffset[i][0];
+ coordCubeVerts[i][1] = y + hy*gVertexOffset[i][1];
+ coordCubeVerts[i][2] = z + hz*gVertexOffset[i][2];
}
// compute cube vertex values
@@ -630,13 +654,13 @@ void IsoExtractor<Tkernel,Tinterpolator>::_marchTetrahedron(const Real x, const
coordTetraVerts[j][2] = coordCubeVerts[vertID][2];
valTetraVerts[j] = valCubeVerts[vertID];
}
- _evalTetrahedron(coordTetraVerts, valTetraVerts, target);
+ _evalTetrahedron(coordTetraVerts, valTetraVerts, isoval);
}
}
template <typename Tkernel, template<typename> class Tinterpolator>
-void IsoExtractor<Tkernel,Tinterpolator>::_evalTetrahedron(const Real coords[4][3], const Real val[4], const Real target)
+void IsoExtractor<Tkernel,Tinterpolator>::_evalTetrahedron(const Real coords[4][3], const Real val[4], const Real isoval)
{
Real coordEdgeVert[6][3];
@@ -644,7 +668,7 @@ void IsoExtractor<Tkernel,Tinterpolator>::_evalTetrahedron(const Real coords[4][
int flagVert = 0;
for (int i = 0; i < 4; ++i)
{
- if (val[i] <= target) flagVert |= 1 << i;
+ if (val[i] <= isoval) flagVert |= 1 << i;
}
// indentify the edge intersections
@@ -663,7 +687,7 @@ void IsoExtractor<Tkernel,Tinterpolator>::_evalTetrahedron(const Real coords[4][
const int vert1 = gTetrahedronEdgeConnection[i][1];
// linear interpolation
- const Real frac = _getEdgeFrac(val[vert0], val[vert1], target);
+ const Real frac = _getEdgeFrac(val[vert0], val[vert1], isoval);
const Real ifrac= 1.0 - frac;
coordEdgeVert[i][0] = ifrac*coords[vert0][0] + frac*coords[vert1][0];
diff --git a/src/IsoExtractorMPI.h b/src/IsoExtractorMPI.h
@@ -21,24 +21,40 @@ public:
{
const Real cscale = this->m_parser("cube_scale").asDouble(1.0);
assert(cscale > 0.0);
- const int Nx = static_cast<Real>(this->m_interp.getLocalNx()) / cscale;
- const int Ny = static_cast<Real>(this->m_interp.getLocalNy()) / cscale;
- const int Nz = static_cast<Real>(this->m_interp.getLocalNz()) / cscale;
- assert(Nx > 1);
- assert(Ny > 1);
- assert(Nz > 1);
+ int gNx = static_cast<Real>(this->m_interp.getNx()) / cscale;
+ int gNy = static_cast<Real>(this->m_interp.getNy()) / cscale;
+ int gNz = static_cast<Real>(this->m_interp.getNz()) / cscale;
int pesize[3];
this->m_interp.getPESize(pesize);
- // TODO: (fabianw@mavt.ethz.ch; Tue Nov 29 23:51:01 2016) need better
- // grid def here
- const Real ch = this->m_interp.getExtent() / (std::max(pesize[0]*Nx, std::max(pesize[1]*Ny, pesize[2]*Nz)) - this->m_interp.isNodal());
+ gNx += (gNx % pesize[0]);
+ gNy += (gNy % pesize[1]);
+ gNz += (gNz % pesize[2]);
+ const int Nx = gNx/pesize[0];
+ const int Ny = gNy/pesize[1];
+ const int Nz = gNz/pesize[2];
+ assert(Nx > 0);
+ assert(Ny > 0);
+ assert(Nz > 0);
+ const Real chx = this->m_interp.getExtentX() / gNx;
+ const Real chy = this->m_interp.getExtentY() / gNy;
+ const Real chz = this->m_interp.getExtentZ() / gNz;
int peidx[3];
this->m_interp.getPEIndex(peidx);
- const Real Ox = ch*Nx*peidx[0];
- const Real Oy = ch*Ny*peidx[1];
- const Real Oz = ch*Nz*peidx[2];
- this->_extractIso(isoval, Nx, Ny, Nz, ch, Ox, Oy, Oz, this->m_interp.isroot());
+ const Real Ox = (this->m_interp.getExtentX()/pesize[0])*peidx[0];
+ const Real Oy = (this->m_interp.getExtentY()/pesize[1])*peidx[1];
+ const Real Oz = (this->m_interp.getExtentZ()/pesize[2])*peidx[2];
+ const Real data_invh = 1.0 / this->m_interp.getH();
+ Real origin[3];
+ origin[0] = this->m_interp.getDataPos(ceil(Ox*data_invh)) - Ox;
+ origin[1] = this->m_interp.getDataPos(ceil(Oy*data_invh)) - Oy;
+ origin[2] = this->m_interp.getDataPos(ceil(Oz*data_invh)) - Oz;
+ assert(origin[0] >= 0.0);
+ assert(origin[1] >= 0.0);
+ assert(origin[2] >= 0.0);
+ this->m_interp.setOrigin(origin);
+
+ this->_extractIso(isoval, Nx, Ny, Nz, chx, chy, chz, Ox, Oy, Oz, this->m_interp.isroot());
_writePLY_MPI(fout, this->m_triList);
}
