https://github.com/geodynamics/citcoms
Tip revision: 60c9538a11a48ae533f752115f5456df3c302303 authored by Eh Tan on 16 January 2012, 21:25:08 UTC
Merged r18932, r19073, and r19192 from trunk to v3.1 branch
Merged r18932, r19073, and r19192 from trunk to v3.1 branch
Tip revision: 60c9538
CitcomInterpolator.cc
// -*- C++ -*-
//
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
//
//<LicenseText>
//
// CitcomS.py by Eh Tan, Eun-seo Choi, and Pururav Thoutireddy.
// Copyright (C) 2002-2005, California Institute of Technology.
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
//</LicenseText>
//
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
//
#include "config.h"
#include <algorithm>
#include <stdexcept>
#include <cmath>
#include "global_bbox.h"
#include "global_defs.h"
#include "journal/diagnostics.h"
#include "Exchanger/BoundedBox.h"
#include "Exchanger/BoundedMesh.h"
#include "CitcomInterpolator.h"
using Exchanger::Array2D;
using Exchanger::BoundedBox;
using Exchanger::BoundedMesh;
using Exchanger::DIM;
using Exchanger::NODES_PER_ELEMENT;
using Exchanger::STRESS_DIM;
CitcomInterpolator::CitcomInterpolator(const BoundedMesh& boundedMesh,
Array2D<int,1>& meshNode,
const All_variables* e) :
Exchanger::Interpolator(),
E(e)
{
journal::debug_t debug("CitcomS-Exchanger");
debug << journal::at(__HERE__) << journal::endl;
// for each node in boundedMesh, find whether it is inside this
// processor, if yes, find which element it is inside and
// calculate the shape functions
init(boundedMesh, meshNode);
// testing the shape functions
selfTest(boundedMesh, meshNode);
elem_.print("CitcomS-CitcomInterpolator-elem");
shape_.print("CitcomS-CitcomInterpolator-shape");
}
CitcomInterpolator::~CitcomInterpolator()
{}
void CitcomInterpolator::interpolatePressure(Array2D<double,1>& P)
{
P.assign(size(), 0);
const int mm = 1;
for(int i=0; i<size(); i++) {
int n1 = elem_[0][i];
for(int k=0; k<NODES_PER_ELEMENT; k++) {
int node = E->ien[mm][n1].node[k+1];
P[0][i] += shape_[k][i] * E->NP[mm][node];
}
}
}
void CitcomInterpolator::interpolateStress(Array2D<double,STRESS_DIM>& S)
{
S.assign(size(), 0);
const int mm = 1;
for(int i=0; i<size(); i++) {
int n1 = elem_[0][i];
for(int k=0; k<NODES_PER_ELEMENT; k++) {
int node = E->ien[mm][n1].node[k+1] - 1;
for(int d=0; d<STRESS_DIM; d++)
S[d][i] += shape_[k][i] * E->gstress[mm][node*STRESS_DIM+d+1];
}
}
}
void CitcomInterpolator::interpolateTemperature(Array2D<double,1>& T)
{
T.assign(size(), 0);
const int mm = 1;
for(int i=0; i<size(); i++) {
int n1 = elem_[0][i];
for(int k=0; k<NODES_PER_ELEMENT; k++) {
int node = E->ien[mm][n1].node[k+1];
T[0][i] += shape_[k][i] * E->T[mm][node];
}
}
}
void CitcomInterpolator::interpolateVelocity(Array2D<double,DIM>& V)
{
V.assign(size(), 0);
const int mm = 1;
for(int i=0; i<size(); i++) {
int n1 = elem_[0][i];
for(int k=0; k<NODES_PER_ELEMENT; k++) {
int node = E->ien[mm][n1].node[k+1];
for(int d=0; d<DIM; d++)
V[d][i] += shape_[k][i] * E->sphere.cap[mm].V[d+1][node];
}
}
}
// private functions
void CitcomInterpolator::init(const BoundedMesh& boundedMesh,
Array2D<int,1>& meshNode)
{
journal::debug_t debug("CitcomS-Exchanger");
debug << journal::at(__HERE__) << journal::endl;
const int mm = 1;
elem_.reserve(boundedMesh.size());
shape_.reserve(boundedMesh.size());
Array2D<double,DIM*DIM> etaAxes; // axes of eta coord.
Array2D<double,DIM> inv_length_sq; // reciprocal of (length of etaAxes)^2
computeElementGeometry(etaAxes, inv_length_sq);
// get remote BoundedBox
BoundedBox remoteBBox(boundedMesh.tightBBox());
// get local BoundedBox
BoundedBox bbox(DIM);
if(E->parallel.nprocxy == 12) {
// for CitcomS Full
fullGlobalBoundedBox(bbox, E);
}
else {
// for CitcomS Regional
regionalGlobalBoundedBox(bbox, E);
}
// z is the range of depth in current processor
std::vector<double> z(E->lmesh.noz);
for(size_t i=0; i<z.size(); ++i)
z[i] = E->sx[mm][DIM][i+1];
for(int n=0; n<boundedMesh.size(); ++n) {
std::vector<double> x(DIM);
for(int d=0; d<DIM; ++d)
x[d] = boundedMesh.X(d,n);
// sometimes after coordinate conversion, surface nodes of different
// solvers won't line up, need this special treatment --
// if x is a little bit above my top surface, move it back to surface
if(x[DIM-1] == remoteBBox[1][DIM-1]) {
double offtop = x[DIM-1]/bbox[1][DIM-1] - 1.0;
if(offtop < 1e-5 && offtop > 0)
x[DIM-1] = bbox[1][DIM-1];
}
// skip if x is not inside bbox
if(!isInside(x, bbox)) continue;
#if 1
// skip if x is not in the range of depth
if(x.back() < z.front() || x.back() > z.back()) continue;
int elz = bisectInsertPoint(x.back(), z);
// Since the mesh of CitcomS is structural and regular
// we only need to loop over elements in a constant depth
for(int el=elz; el<E->lmesh.nel; el+=E->lmesh.elz) {
#else
// If the mesh is not regular, loop over all elements
for(int el=0; el<E->lmesh.nel; ++el) {
#endif
std::vector<double> elmShape(NODES_PER_ELEMENT);
double accuracy = E->control.accuracy * E->control.accuracy
* E->eco[mm][el+1].area;
bool found = elementInverseMapping(elmShape, x,
etaAxes, inv_length_sq,
el, accuracy);
if(found) {
meshNode.push_back(n);
elem_.push_back(el+1);
shape_.push_back(elmShape);
break;
}
}
}
}
void CitcomInterpolator::computeElementGeometry(Array2D<double,DIM*DIM>& etaAxes,
Array2D<double,DIM>& inv_length_sq) const
{
etaAxes.resize(E->lmesh.nel);
inv_length_sq.resize(E->lmesh.nel);
const int mm = 1;
const int surfnodes = 4; // # of nodes on element's face
// node 1, 2, 5, 6 are in the face that is on positive x axis
// node 2, 3, 6, 7 are in the face that is on positive y axis
// node 4, 5, 6, 7 are in the face that is on positive z axis
// node 0, 3, 4, 7 are in the face that is on negative x axis
// node 0, 1, 4, 5 are in the face that is on negative y axis
// node 0, 1, 2, 3 are in the face that is on negative z axis
// see comment of getShapeFunction() for the ordering of nodes
const int high[] = {1, 2, 5, 6,
2, 3, 6, 7,
4, 5, 6, 7};
const int low[] = {0, 3, 4, 7,
0, 1, 4, 5,
0, 1, 2, 3};
std::vector<int> node(NODES_PER_ELEMENT);
for(int element=0; element<E->lmesh.nel; ++element) {
for(int k=0; k<NODES_PER_ELEMENT; ++k)
node[k] = E->ien[mm][element+1].node[k+1];
for(int n=0; n<DIM; ++n) {
int k = n * surfnodes;
for(int d=0; d<DIM; ++d) {
double lowmean = 0;
double highmean = 0;
for(int i=0; i<surfnodes; ++i) {
highmean += E->sx[mm][d+1][node[high[k+i]]];
lowmean += E->sx[mm][d+1][node[low[k+i]]];
}
etaAxes[n*DIM+d][element] = 0.5 * (highmean - lowmean)
/ surfnodes;
}
}
}
for(int element=0; element<E->lmesh.nel; ++element)
for(int n=0; n<DIM; ++n) {
double lengthsq = 0;
for(int d=0; d<DIM; ++d)
lengthsq += etaAxes[n*DIM+d][element]
* etaAxes[n*DIM+d][element];
inv_length_sq[n][element] = 1 / lengthsq;
}
etaAxes.print("CitcomS-CitcomInterpolator-etaAxes");
inv_length_sq.print("CitcomS-CitcomInterpolator-inv-length-sq");
}
int CitcomInterpolator::bisectInsertPoint(double x,
const std::vector<double>& v) const
{
int low = 0;
int high = v.size();
int insert_point = (low + high) / 2;
while(low < high) {
if(x < v[insert_point])
high = insert_point;
else if(x > v[insert_point+1])
low = insert_point;
else
break;
insert_point = (low + high) / 2;
}
return insert_point;
}
bool CitcomInterpolator::elementInverseMapping(std::vector<double>& elmShape,
const std::vector<double>& x,
const Array2D<double,DIM*DIM>& etaAxes,
const Array2D<double,DIM>& inv_length_sq,
int element,
double accuracy)
{
const int mm = 1;
bool found = false;
int count = 0;
std::vector<double> eta(DIM); // initial eta = (0,0,0)
while (1) {
getShapeFunction(elmShape, eta);
std::vector<double> xx(DIM);
for(int k=0; k<NODES_PER_ELEMENT; ++k) {
int node = E->ien[mm][element+1].node[k+1];
for(int d=0; d<DIM; ++d)
xx[d] += E->sx[mm][d+1][node] * elmShape[k];
}
std::vector<double> dx(DIM);
double distancesq = 0;
for(int d=0; d<DIM; ++d) {
dx[d] = x[d] - xx[d];
distancesq += dx[d] * dx[d];
}
// correction of eta
std::vector<double> deta(DIM);
for(int d=0; d<DIM; ++d) {
for(int i=0; i<DIM; ++i)
deta[d] += dx[i] * etaAxes[d*DIM+i][element];
deta[d] *= inv_length_sq[d][element];
}
if(count == 0)
for(int d=0; d<DIM; ++d)
eta[d] += deta[d];
else // Damping
for(int d=0; d<DIM; ++d)
eta[d] += 0.9 * deta[d];
// if x is inside this element, -1 < eta[d] < 1, d = 0 ... DIM
bool outside = false;
for(int d=0; d<DIM; ++d)
outside = outside || (std::abs(eta[d]) > 1.5);
// iterate at least twice
found = (distancesq < accuracy) && (count > 0);
if (outside || found || (count > 100))
break;
++count;
/* Only need to iterate if this is marginal. If eta > distortion of
an individual element then almost certainly x is in a
different element ... or the mesh is terrible ! */
}
return found;
}
void CitcomInterpolator::getShapeFunction(std::vector<double>& shape,
const std::vector<double>& eta) const
{
// the ordering of nodes in an element
// node #: eta coordinate
// node 0: (-1, -1, -1)
// node 1: ( 1, -1, -1)
// node 2: ( 1, 1, -1)
// node 3: (-1, 1, -1)
// node 4: (-1, -1, 1)
// node 5: ( 1, -1, 1)
// node 6: ( 1, 1, 1)
// node 7: (-1, 1, 1)
shape[0] = 0.125 * (1.0-eta[0]) * (1.0-eta[1]) * (1.0-eta[2]);
shape[1] = 0.125 * (1.0+eta[0]) * (1.0-eta[1]) * (1.0-eta[2]);
shape[2] = 0.125 * (1.0+eta[0]) * (1.0+eta[1]) * (1.0-eta[2]);
shape[3] = 0.125 * (1.0-eta[0]) * (1.0+eta[1]) * (1.0-eta[2]);
shape[4] = 0.125 * (1.0-eta[0]) * (1.0-eta[1]) * (1.0+eta[2]);
shape[5] = 0.125 * (1.0+eta[0]) * (1.0-eta[1]) * (1.0+eta[2]);
shape[6] = 0.125 * (1.0+eta[0]) * (1.0+eta[1]) * (1.0+eta[2]);
shape[7] = 0.125 * (1.0-eta[0]) * (1.0+eta[1]) * (1.0+eta[2]);
}
void CitcomInterpolator::selfTest(const BoundedMesh& boundedMesh,
const Array2D<int,1>& meshNode) const
{
journal::debug_t debug("CitcomS-Exchanger");
debug << journal::at(__HERE__) << journal::endl;
for(int i=0; i<size(); i++) {
// xt is the node that we like to interpolate to
std::vector<double> xt(DIM);
for(int j=0; j<DIM; j++)
xt[j] = boundedMesh.X(j, meshNode[0][i]);
// xi is the result of interpolation
std::vector<double> xi(DIM);
int n1 = elem_[0][i];
for(int j=0; j<NODES_PER_ELEMENT; j++) {
int node = E->ien[1][n1].node[j+1];
for(int k=0; k<DIM; k++)
xi[k] += E->sx[1][k+1][node] * shape_[j][i];
}
// if xi and xt are not coincide, the interpolation is wrong
double norm = 0.0;
for(int k=0; k<DIM; k++)
norm += (xt[k]-xi[k]) * (xt[k]-xi[k]);
if(norm > E->control.accuracy * E->control.accuracy) {
double tshape = 0.0;
for(int j=0; j<NODES_PER_ELEMENT; j++)
tshape += shape_[j][i];
journal::firewall_t firewall("CitcomS-CitcomInterpolator");
firewall << journal::at(__HERE__)
<< "node #" << i << " tshape = " << tshape
<< journal::newline
<< xi[0] << " " << xt[0] << " "
<< xi[1] << " " << xt[1] << " "
<< xi[2] << " " << xt[2] << " "
<< " norm = " << norm << journal::newline
<< "elem interpolation functions are wrong"
<< journal::endl;
throw std::domain_error("CitcomInterpolator");
}
}
}
// version
// $Id$
// End of file