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added: support for XML based input files

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git-svn-id: http://svn.sintef.no/trondheim/IFEM/trunk@1341 e10b68d5-8a6e-419e-a041-bce267b0401d
This commit is contained in:
akva 2011-12-08 16:23:42 +00:00 committed by Knut Morten Okstad
parent 25f4b2ecf3
commit 5ea84f25c9
14 changed files with 1005 additions and 1 deletions
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49
src/LinAlg/LinSolParams.C
View File

@ -18,6 +18,8 @@
#include "petscmg.h"
#endif
#include "tinyxml.h"
void LinSolParams::setDefault ()
{
@ -147,6 +149,53 @@ bool LinSolParams::read (std::istream& is, int nparam)
return true;
}
static bool IsOK(const TiXmlElement* child, const char* value)
{
return !strcasecmp(child->Value(),value) &&
child->FirstChild() && child->FirstChild()->Value();
}
bool LinSolParams::read (const TiXmlElement* elem)
{
const TiXmlElement *child = elem->FirstChildElement();
while (child) {
#ifdef HAS_PETSC
if (IsOK(child,"type")) {
method = child->FirstChild()->Value();
} else if (IsOK(child,"pc")) {
prec = child->FirstChild()->Value();
} else if (IsOK(child,"hypretype")) {
hypretype = child->FirstChild()->Value();
} else if (IsOK(child,"package")) {
package = child->FirstChild()->Value();
} else if (IsOK(child,"levels")) {
levels = atoi(child->FirstChild()->Value());
} else if (IsOK(child,"overlap")) {
overlap = atoi(child->FirstChild()->Value());
} else if (IsOK(child,"atol")) {
atol = atof(child->FirstChild()->Value());
} else if (IsOK(child,"rtol")) {
rtol = atof(child->FirstChild()->Value());
} else if (IsOK(child,"dtol")) {
dtol = atof(child->FirstChild()->Value());
} else if (IsOK(child,"maxits")) {
maxIts = atoi(child->FirstChild()->Value());
} else if (IsOK(child,"nullspace")) {
if (!strcasecmp(child->FirstChild()->Value(),"constant"))
nullspc = CONSTANT;
else if (!strcasecmp(child->FirstChild()->Value(),"rigid_body"))
nullspc = RIGID_BODY;
}
else {
std::cerr <<" *** LinSolParams::read: Unknown keyword: "
<< child->Value() << std::endl;
}
#endif
child = child->NextSiblingElement();
}
return true;
}
bool LinSolParams::read (const char* filename)
{

6
src/LinAlg/LinSolParams.h
View File

@ -23,6 +23,9 @@
#endif
class TiXmlElement;
//! \brief Null-space for matrix operator
enum NullSpace { NONE, CONSTANT, RIGID_BODY };
@ -49,6 +52,9 @@ public:
//! \brief Read linear solver parameters from stream.
virtual bool read(std::istream& is, int nparams = 10);
//! \brief Read linear solver parameters from XML document.
virtual bool read(const TiXmlElement* elem);
//! \brief Read linear solver parameters from file.
virtual bool read(const char* filename);

61
src/SIM/NonLinSIM.C
View File

@ -17,6 +17,8 @@
#include "Utilities.h"
#include <sstream>
#include "tinyxml.h"
NonLinSIM::NonLinSIM (SIMbase* sim) : model(sim), nBlock(0)
{
@ -111,6 +113,65 @@ void NonLinSIM::initSystem (SystemMatrix::Type mType, size_t nGauss)
}
bool NonLinSIM::parse (const TiXmlElement* elem)
{
if (strcasecmp(elem->Value(),"nonlinearsolver"))
return model->parse(elem);
const TiXmlElement* child = elem->FirstChildElement();
while (child) {
if (!strcasecmp(child->Value(),"timestepping")) {
const TiXmlElement* step = child->FirstChildElement("step");
steps.clear();
while (step) {
double dt;
std::pair<std::vector<double>,double> tstep;
double start, end;
if (step->Attribute("start"))
start = atof(step->Attribute("start"));
if (step->Attribute("end"))
end = atof(step->Attribute("end"));
if (steps.empty())
startTime = start;
if (step->FirstChild() && step->FirstChild()->Value()) {
std::istringstream cline(child->FirstChild()->Value());
cline >> dt;
if (dt > 1.0 && ceil(dt) == dt) { // number of steps specified
dt = (end-steps.empty()?start:steps.back().second)/dt;
tstep.first.push_back(dt);
} else while (!cline.fail() && !cline.bad()) { // steps specified
tstep.first.push_back(dt);
cline >> dt;
}
tstep.second = end;
steps.push_back(tstep);
}
}
stopTime = steps.back().second;
} else if (!strcasecmp(child->Value(),"maxits")) {
if (child->FirstChild() && child->FirstChild()->Value())
maxit = atoi(child->FirstChild()->Value());
} else if (!strcasecmp(child->Value(),"nupdate")) {
if (child->FirstChild() && child->FirstChild()->Value())
nupdat = atoi(child->FirstChild()->Value());
} else if (!strcasecmp(child->Value(),"rtol")) {
if (child->FirstChild() && child->FirstChild()->Value())
convTol = atof(child->FirstChild()->Value());
} else if (!strcasecmp(child->Value(),"dtol")) {
if (child->FirstChild() && child->FirstChild()->Value())
divgLim = atof(child->FirstChild()->Value());
} else if (!strcasecmp(child->Value(),"eta")) {
if (child->FirstChild() && child->FirstChild()->Value())
eta = atof(child->FirstChild()->Value());
}
child = child->NextSiblingElement();
}
return true;
}
void NonLinSIM::init (SolvePrm& param, const RealArray& initVal)
{
param.initTime(startTime,stopTime,steps);

5
src/SIM/NonLinSIM.h
View File

@ -171,6 +171,11 @@ public:
//! \param is The file stream to read from
virtual bool parse(char* keyWord, std::istream& is);
//! \brief Parses a data section from an input stream.
//! \param[in] keyWord Keyword of current data section to read
//! \param is The file stream to read from
virtual bool parse(const TiXmlElement* elem);
private:
SIMbase* model; //!< The isogeometric FE model

158
src/SIM/SIM1D.C
View File

@ -21,6 +21,8 @@
#include <stdlib.h>
#include <ctype.h>
#include "tinyxml.h"
SIM1D::SIM1D (unsigned char n_f)
{
@ -218,6 +220,162 @@ bool SIM1D::parse (char* keyWord, std::istream& is)
}
bool SIM1D::parseGeometryTag(const TiXmlElement* elem)
{
// The remaining keywords are retained for backward compatibility with the
// prototype version. They enable direct specification of topology and
// properties as well as grid refinement without using the GPM module.
if (!strcasecmp(elem->Value(),"refine")) {
ASMs1D* pch = 0;
bool uniform=true;
if (elem->Attribute("type") && !strcasecmp(elem->Attribute("type"),"nonuniform"))
uniform = false;
size_t lowpatch = 1, uppatch = 2;
if (elem->Attribute("patch"))
lowpatch = uppatch = atoi(elem->Attribute("patch"));
if (elem->Attribute("lowerpatch")) {
lowpatch = atoi(elem->Attribute("lowerpatch"));
uppatch = myModel.size();
}
if (elem->Attribute("upperpatch"))
uppatch = atoi(elem->Attribute("upperpatch"));
if (lowpatch < 1 || uppatch > myModel.size())
{
std::cerr <<" *** SIM1D::parse: Invalid patch index "
<< "lower: " << lowpatch << " upper: " << uppatch << std::endl;
return false;
}
if (uniform)
{
int addu=0;
if (elem->Attribute("u"))
addu = atoi(elem->Attribute("u"));
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASMs1D*>(myModel[j]))) {
std::cout <<"\tRefining P"<< j+1
<<" "<< addu << std::endl;
pch->uniformRefine(addu);
}
}
} else {
char* cline2 = strdup(elem->FirstChildElement()->Value());
char* cline = cline2;
strtok(cline," ");
RealArray xi;
while (cline) {
xi.push_back(atof(cline));
cline = strtok(NULL," ");
}
free(cline2);
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASMs1D*>(myModel[j])))
{
std::cout <<"\tRefining P"<< j+1;
for (size_t i = 0; i < xi.size(); i++)
std::cout <<" "<< xi[i];
std::cout << std::endl;
pch->refine(xi);
}
}
}
} else if (!strcasecmp(elem->Value(),"raiseorder")) {
size_t lowpatch = 1, uppatch = 2;
if (elem->Attribute("patch"))
lowpatch = uppatch = atoi(elem->Attribute("patch"));
if (elem->Attribute("lowerpatch")) {
lowpatch = atoi(elem->Attribute("lowerpatch"));
uppatch = myModel.size();
}
if (elem->Attribute("upperpatch"))
uppatch = atoi(elem->Attribute("upperpatch"));
if (lowpatch < 1 || uppatch > myModel.size())
{
std::cerr <<" *** SIM2D::parse: Invalid patch index "
<< "lower: " << lowpatch << " upper: " << uppatch << std::endl;
return false;
}
int addu=0;
if (elem->Attribute("u"))
addu = atoi(elem->Attribute("u"));
ASMs1D* pch;
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASMs1D*>(myModel[j]))) {
std::cout <<"\tRaising order of P"<< j+1 <<" "<< addu << std::endl;
pch->raiseOrder(addu);
}
}
}
else if (!strcasecmp(elem->Value(),"topology")) {
if (createFEMmodel()) return false;
const TiXmlElement* child = elem->FirstChildElement("connection");
while (child) {
int master=0, slave=0, mVert=0, sVert=0;
if (child->Attribute("master"))
master = atoi(child->Attribute("master"));
if (child->Attribute("mvert"))
mVert = atoi(child->Attribute("mvert"));
if (child->Attribute("slave"))
slave = atoi(child->Attribute("slave"));
if (child->Attribute("svert"))
sVert = atoi(child->Attribute("svert"));
if (master == slave ||
master < 1 || master > (int)myModel.size() ||
slave < 1 || slave > (int)myModel.size())
{
std::cerr <<" *** SIM1D::parse: Invalid patch indices "
<< master <<" "<< slave << std::endl;
return false;
}
std::cout <<"\tConnecting P"<< slave <<" V"<< sVert
<<" to P"<< master <<" E"<< mVert << std::endl;
ASMs1D* spch = static_cast<ASMs1D*>(myModel[slave-1]);
ASMs1D* mpch = static_cast<ASMs1D*>(myModel[master-1]);
if (!spch->connectPatch(sVert,*mpch,mVert))
return false;
child = child->NextSiblingElement();
}
} else if (!strcasecmp(elem->Value(),"periodic")) {
if (createFEMmodel()) return false;
int patch=0;
if (elem->Attribute("patch"))
patch = atoi(elem->Attribute("patch"));
if (patch < 1 || patch > (int)myModel.size()) {
std::cerr <<" *** SIM1D::parse: Invalid patch index "
<< patch << std::endl;
return false;
}
std::cout <<"\tPeriodic P" << patch << std::endl;
static_cast<ASMs1D*>(myModel[patch-1])->closeEnds();
}
// TODO: constraints? fixpoints?
return true;
}
bool SIM1D::parse(const TiXmlElement* elem)
{
bool result=SIMbase::parse(elem);
const TiXmlElement* child = elem->FirstChildElement();
while (child) {
if (!strcasecmp(elem->Value(),"geometry"))
result &= parseGeometryTag(child);
child = child->NextSiblingElement();
}
return result;
}
/*!
\brief Local-scope convenience function for error message generation.
*/

7
src/SIM/SIM1D.h
View File

@ -48,6 +48,10 @@ protected:
//! \param[in] pchInd 0-based index of the patch to read
virtual bool readPatch(std::istream& isp, int pchInd);
//! \brief Parses a data section from an XML document.
//! \param[in] elem The XML element to parse
virtual bool parse(const TiXmlElement* elem);
//! \brief Preprocesses a user-defined Dirichlet boundary property.
//! \param[in] patch 1-based index of the patch to receive the property
//! \param[in] lndx Local index of the boundary item to receive the property
@ -59,6 +63,9 @@ protected:
protected:
unsigned char nf; //!< Number of scalar fields
private:
//! \brief Parse subtags of the <geometry> block from the input file
bool parseGeometryTag(const TiXmlElement* elem);
};
#endif

210
src/SIM/SIM2D.C
View File

@ -19,6 +19,8 @@
#include <stdlib.h>
#include <ctype.h>
#include "tinyxml.h"
/*!
A struct defining a patch interface for C1-continuous models.
@ -48,6 +50,179 @@ SIM2D::SIM2D (unsigned char n1, unsigned char n2) : isRefined(false)
}
bool SIM2D::parseGeometryTag(const TiXmlElement* elem)
{
// The remaining keywords are retained for backward compatibility with the
// prototype version. They enable direct specification of topology and
// properties as well as grid refinement without using the GPM module.
if (!strcasecmp(elem->Value(),"refine") && !isRefined) {
ASM2D* pch = 0;
bool uniform=true;
if (elem->Attribute("type") && !strcasecmp(elem->Attribute("type"),"nonuniform"))
uniform = false;
size_t lowpatch = 1, uppatch = 2;
if (elem->Attribute("patch"))
lowpatch = uppatch = atoi(elem->Attribute("patch"));
if (elem->Attribute("lowerpatch")) {
lowpatch = atoi(elem->Attribute("lowerpatch"));
uppatch = myModel.size();
}
if (elem->Attribute("upperpatch"))
uppatch = atoi(elem->Attribute("upperpatch"));
if (lowpatch < 1 || uppatch > myModel.size())
{
std::cerr <<" *** SIM2D::parse: Invalid patch index "
<< "lower: " << lowpatch << " upper: " << uppatch << std::endl;
return false;
}
if (uniform)
{
int addu=0, addv = 0;
if (elem->Attribute("u"))
addu = atoi(elem->Attribute("u"));
if (elem->Attribute("v"))
addv = atoi(elem->Attribute("v"));
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASM2D*>(myModel[j]))) {
std::cout <<"\tRefining P"<< j+1
<<" "<< addu <<" "<< addv << std::endl;
pch->uniformRefine(0,addu);
pch->uniformRefine(1,addv);
}
}
} else {
int dir=1;
if (elem->Attribute("dir"))
dir = atoi(elem->Attribute("dir"));
char* cline2 = strdup(elem->FirstChildElement()->Value());
char* cline = cline2;
strtok(cline," ");
RealArray xi;
while (cline) {
xi.push_back(atof(cline));
cline = strtok(NULL," ");
}
free(cline2);
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASM2D*>(myModel[j])))
{
std::cout <<"\tRefining P"<< j+1 <<" dir="<< dir;
for (size_t i = 0; i < xi.size(); i++)
std::cout <<" "<< xi[i];
std::cout << std::endl;
pch->refine(dir-1,xi);
}
}
}
} else if (!strcasecmp(elem->Value(),"raiseorder") && !isRefined) {
size_t lowpatch = 1, uppatch = 2;
if (elem->Attribute("patch"))
lowpatch = uppatch = atoi(elem->Attribute("patch"));
if (elem->Attribute("lowerpatch")) {
lowpatch = atoi(elem->Attribute("lowerpatch"));
uppatch = myModel.size();
}
if (elem->Attribute("upperpatch"))
uppatch = atoi(elem->Attribute("upperpatch"));
if (lowpatch < 1 || uppatch > myModel.size())
{
std::cerr <<" *** SIM2D::parse: Invalid patch index "
<< "lower: " << lowpatch << " upper: " << uppatch << std::endl;
return false;
}
int addu=0, addv = 0;
if (elem->Attribute("u"))
addu = atoi(elem->Attribute("u"));
if (elem->Attribute("v"))
addv = atoi(elem->Attribute("v"));
ASM2D* pch;
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASM2D*>(myModel[j]))) {
std::cout <<"\tRaising order of P"<< j+1
<<" "<< addu <<" "<< addv << std::endl;
pch->raiseOrder(addu,addv);
}
}
}
else if (!strcasecmp(elem->Value(),"topology")) {
if (createFEMmodel()) return false;
const TiXmlElement* child = elem->FirstChildElement("connection");
while (child) {
int master=0, slave=0, mEdge=0, sEdge=0;
if (child->Attribute("master"))
master = atoi(child->Attribute("master"));
if (child->Attribute("medge"))
mEdge = atoi(child->Attribute("medge"));
if (child->Attribute("slave"))
slave = atoi(child->Attribute("slave"));
if (child->Attribute("sedge"))
sEdge = atoi(child->Attribute("sedge"));
bool rever=false;
if (child->Attribute("reverse") && !strcasecmp(child->Attribute("reverse"),"true"))
rever = true;
if (master == slave ||
master < 1 || master > (int)myModel.size() ||
slave < 1 || slave > (int)myModel.size())
{
std::cerr <<" *** SIM2D::parse: Invalid patch indices "
<< master <<" "<< slave << std::endl;
return false;
}
std::cout <<"\tConnecting P"<< slave <<" E"<< sEdge
<<" to P"<< master <<" E"<< mEdge
<<" reversed? "<< rever << std::endl;
ASMs2D* spch = static_cast<ASMs2D*>(myModel[slave-1]);
ASMs2D* mpch = static_cast<ASMs2D*>(myModel[master-1]);
if (!spch->connectPatch(sEdge,*mpch,mEdge,rever))
return false;
child = child->NextSiblingElement();
}
} else if (!strcasecmp(elem->Value(),"periodic")) {
if (createFEMmodel()) return false;
int patch=0, pedir=1;
if (elem->Attribute("patch"))
patch = atoi(elem->Attribute("patch"));
if (elem->Attribute("dir"))
pedir = atoi(elem->Attribute("dir"));
if (patch < 1 || patch > (int)myModel.size()) {
std::cerr <<" *** SIM2D::parse: Invalid patch index "
<< patch << std::endl;
return false;
}
std::cout <<"\tPeriodic "<< char('H'+pedir) <<"-direction P"<< patch
<< std::endl;
static_cast<ASMs2D*>(myModel[patch-1])->closeEdges(pedir);
}
// TODO: constraints? fixpoints?
return true;
}
bool SIM2D::parse(const TiXmlElement* elem)
{
bool result=SIMbase::parse(elem);
const TiXmlElement* child = elem->FirstChildElement();
while (child) {
if (!strcasecmp(elem->Value(),"geometry"))
result &= parseGeometryTag(child);
child = child->NextSiblingElement();
}
return result;
}
bool SIM2D::parse (char* keyWord, std::istream& is)
{
char* cline = 0;
@ -431,6 +606,41 @@ void SIM2D::clonePatches (const FEModelVec& patches,
}
void SIM2D::readNodes (std::istream& isn)
{
while (isn.good()) {
int patch = 0;
isn >> patch;
++patch;
int pid = getLocalPatchIndex(patch);
if (pid < 0)
return;
ASMs2D::BlockNodes n;
for (size_t i = 0; i < 4 && isn.good(); i++)
isn >> n.ibnod[i];
for (size_t i = 0; i < 4 && isn.good(); i++)
isn >> n.edges[i].icnod >> n.edges[i].incr;
isn >> n.iinod;
// We always require the node numbers to be 1-based
for (size_t i = 0; i < 4; i++)
++n.ibnod[i];
for (size_t i = 0; i < 4; i++)
++n.edges[i].icnod;
++n.iinod;
if (isn.good() && pid > 0) {
if (!static_cast<ASMs2D*>(myModel[pid-1])->assignNodeNumbers(n)) {
std::cerr <<" *** SIM2D::readNodes: Failed to assign node numbers"
<<" for patch "<< patch << std::endl;
return;
}
}
}
}
bool SIM2D::refine (const std::vector<int>& elements,
const std::vector<int>& options, const char* fName)
{

10
src/SIM/SIM2D.h
View File

@ -48,6 +48,10 @@ protected:
//! \param is The file stream to read from
virtual bool parse(char* keyWord, std::istream& is);
//! \brief Parses a data section from an XML document.
//! \param[in] elem The XML element to parse
virtual bool parse(const TiXmlElement* elem);
//! \brief Reads patches from given input stream.
//! \param[in] isp The input stream to read from
virtual bool readPatches(std::istream& isp);
@ -64,6 +68,10 @@ protected:
virtual bool readNodes(std::istream& isn, int pchInd, int basis = 0,
bool oneBased = false);
//! \brief Reads node numbers from given input stream.
//! \param[in] isn The file stream to read from
void readNodes(std::istream& isn);
//! \brief Refines a list of elements.
//! \param[in] elements 1-based indices of the elements to refine
//! \param[in] options Input options to refinement algorithm
@ -83,6 +91,8 @@ protected:
private:
bool isRefined; //!< If \e true, the model has been adaptively refined
//! \brief Parse subtags of the <geometry> block from the input file
bool parseGeometryTag(const TiXmlElement* elem);
protected:
unsigned char nf[2]; //!< Number of scalar fields

183
src/SIM/SIM3D.C
View File

@ -22,6 +22,8 @@
#include <stdlib.h>
#include <ctype.h>
#include "tinyxml.h"
SIM3D::SIM3D (bool checkRHS, unsigned char n1, unsigned char n2)
{
@ -292,6 +294,148 @@ bool SIM3D::parse (char* keyWord, std::istream& is)
}
bool SIM3D::parseGeometryTag(const TiXmlElement* elem)
{
// The remaining keywords are retained for backward compatibility with the
// prototype version. They enable direct specification of topology and
// properties as well as grid refinement without using the GPM module.
if (!strcasecmp(elem->Value(),"refine")) {
bool uniform=true;
if (elem->Attribute("type") && !strcasecmp(elem->Attribute("type"),"nonuniform"))
uniform = false;
size_t lowpatch = 1, uppatch = 2;
if (elem->Attribute("patch"))
lowpatch = uppatch = atoi(elem->Attribute("patch"));
if (elem->Attribute("lowerpatch")) {
lowpatch = atoi(elem->Attribute("lowerpatch"));
uppatch = myModel.size();
}
if (elem->Attribute("upperpatch"))
uppatch = atoi(elem->Attribute("upperpatch"));
if (lowpatch < 1 || uppatch > myModel.size())
{
std::cerr <<" *** SIM3D::parse: Invalid patch index "
<< "lower: " << lowpatch << " upper: " << uppatch << std::endl;
return false;
}
if (uniform)
{
int addu=0, addv = 0, addw = 0;
if (elem->Attribute("u"))
addu = atoi(elem->Attribute("u"));
if (elem->Attribute("v"))
addv = atoi(elem->Attribute("v"));
if (elem->Attribute("w"))
addw = atoi(elem->Attribute("w"));
for (size_t j = lowpatch-1; j < uppatch; j++) {
std::cout <<"\tRefining P"<< j+1
<<" "<< addu <<" "<< addv <<" "<< addw << std::endl;
ASMs3D* pch = static_cast<ASMs3D*>(myModel[j]);
pch->uniformRefine(0,addu);
pch->uniformRefine(1,addv);
pch->uniformRefine(2,addw);
}
} else {
int dir=1;
if (elem->Attribute("dir"))
dir = atoi(elem->Attribute("dir"));
char* cline2 = strdup(elem->FirstChildElement()->Value());
char* cline = cline2;
strtok(cline," ");
RealArray xi;
while (cline) {
xi.push_back(atof(cline));
cline = strtok(NULL," ");
}
free(cline2);
ASMs3D* pch;
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASMs3D*>(myModel[j])))
{
std::cout <<"\tRefining P"<< j+1 <<" dir="<< dir;
for (size_t i = 0; i < xi.size(); i++)
std::cout <<" "<< xi[i];
std::cout << std::endl;
pch->refine(dir-1,xi);
}
}
}
} else if (!strcasecmp(elem->Value(),"raiseorder")) {
size_t lowpatch = 1, uppatch = 2;
if (elem->Attribute("patch"))
lowpatch = uppatch = atoi(elem->Attribute("patch"));
if (elem->Attribute("lowerpatch")) {
lowpatch = atoi(elem->Attribute("lowerpatch"));
uppatch = myModel.size();
}
if (elem->Attribute("upperpatch"))
uppatch = atoi(elem->Attribute("upperpatch"));
if (lowpatch < 1 || uppatch > myModel.size())
{
std::cerr <<" *** SIM3D::parse: Invalid patch index "
<< "lower: " << lowpatch << " upper: " << uppatch << std::endl;
return false;
}
int addu=0, addv = 0, addw = 0;
if (elem->Attribute("u"))
addu = atoi(elem->Attribute("u"));
if (elem->Attribute("v"))
addv = atoi(elem->Attribute("v"));
if (elem->Attribute("w"))
addw = atoi(elem->Attribute("w"));
ASMs3D* pch;
for (size_t j = lowpatch-1; j < uppatch; j++) {
if ((pch = dynamic_cast<ASMs3D*>(myModel[j]))) {
std::cout <<"\tRaising order of P"<< j+1
<<" "<< addu <<" "<< addv <<" " << addw << std::endl;
pch->raiseOrder(addu,addv,addw);
}
}
}
else if (!strcasecmp(elem->Value(),"topology")) { // TODO?
assert(0);
} else if (!strcasecmp(elem->Value(),"periodic")) {
if (createFEMmodel()) return false;
int patch=0, pfdir=1;
if (elem->Attribute("patch"))
patch = atoi(elem->Attribute("patch"));
if (elem->Attribute("dir"))
pfdir = atoi(elem->Attribute("dir"));
if (patch < 1 || patch > (int)myModel.size()) {
std::cerr <<" *** SIM3D::parse: Invalid patch index "
<< patch << std::endl;
return false;
}
std::cout <<"\tPeriodic "<< char('H'+pfdir) <<"-direction P"<< patch
<< std::endl;
static_cast<ASMs3D*>(myModel[patch-1])->closeFaces(pfdir);
}
// TODO: topology? constraints? fixpoints?
return true;
}
bool SIM3D::parse(const TiXmlElement* elem)
{
bool result=SIMbase::parse(elem);
const TiXmlElement* child = elem->FirstChildElement();
while (child) {
if (!strcasecmp(elem->Value(),"geometry"))
result &= parseGeometryTag(child);
child = child->NextSiblingElement();
}
return result;
}
/*!
\brief Local-scope convenience function for error message generation.
*/
@ -528,3 +672,42 @@ bool SIM3D::readNodes (std::istream& isn, int pchInd, int basis, bool oneBased)
return static_cast<ASMs3D*>(myModel[pchInd])->assignNodeNumbers(n,basis);
}
void SIM3D::readNodes (std::istream& isn)
{
while (isn.good()) {
int patch = 0;
isn >> patch;
++patch;
int pid = getLocalPatchIndex(patch);
if (pid < 0)
return;
ASMs3D::BlockNodes n;
for (size_t i = 0; i < 8 && isn.good(); i++)
isn >> n.ibnod[i];
for (size_t i = 0; i < 12 && isn.good(); i++)
isn >> n.edges[i].icnod >> n.edges[i].incr;
for (size_t i = 0; i < 6 && isn.good(); i++)
isn >> n.faces[i].isnod >> n.faces[i].incrI >> n.faces[i].incrJ;
isn >> n.iinod;
// We always require the node numbers to be 1-based
for (size_t i = 0; i < 8; i++)
++n.ibnod[i];
for (size_t i = 0; i < 12; i++)
++n.edges[i].icnod;
for (size_t i = 0; i < 6; i++)
++n.faces[i].isnod;
++n.iinod;
if (isn.good() && pid > 0) {
if (!static_cast<ASMs3D*>(myModel[pid-1])->assignNodeNumbers(n)) {
std::cerr <<" *** SIM3D::readNodes: Failed to assign node numbers"
<<" for patch "<< patch << std::endl;
return;
}
}
}
}

12
src/SIM/SIM3D.h
View File

@ -38,6 +38,10 @@ public:
//! \param[in] ng Number of Gauss points in each parameter direction
virtual void setQuadratureRule(size_t ng);
//! \brief Reads node numbers from given input stream.
//! \param[in] isn The file stream to read from
void readNodes(std::istream& isn);
protected:
//! \brief Parses a data section from an input stream.
//! \param[in] keyWord Keyword of current data section to read
@ -60,6 +64,11 @@ protected:
virtual bool readNodes(std::istream& isn, int pchInd, int basis = 0,
bool oneBased = false);
//! \brief Parses a data section from an XML element
//! \param[in] elem The XML element to parse
////! \param is The file stream to read from
virtual bool parse(const TiXmlElement* elem);
//! \brief Preprocesses a user-defined Dirichlet boundary property.
//! \param[in] patch 1-based index of the patch to receive the property
//! \param[in] lndx Local index of the boundary item to receive the property
@ -81,6 +90,9 @@ protected:
unsigned char nf[2]; //!< Number of scalar fields
bool checkRHSys; //!< Check if all patches are in a right-hand system
private:
//! \brief Parse subtags of the <geometry> block from the input file
bool parseGeometryTag(const TiXmlElement* elem);
};
#endif

204
src/SIM/SIMbase.C
View File

@ -28,6 +28,7 @@
#include "Tensor.h"
#include "Vec3Oper.h"
#include "EigSolver.h"
#include "Functions.h"
#include "Profiler.h"
#include "ElementBlock.h"
#include "VTF.h"
@ -38,6 +39,9 @@
#include <iomanip>
#include <ctype.h>
#include <stdio.h>
#include <fstream>
#include "tinyxml.h"
ASM::Discretization SIMbase::discretization = ASM::Spline;
@ -114,6 +118,197 @@ void SIMbase::clearProperties ()
}
bool SIMbase::parseGeometryTag(const TiXmlElement* elem)
{
if (!strcasecmp(elem->Value(),"patchfile")) {
if (myModel.empty()) {
std::string file = elem->FirstChild()->Value();
std::cout <<"\nReading data file "<< file << std::endl;
std::ifstream isp(file.c_str());
readPatches(isp);
if (myModel.empty()) {
std::cerr <<" *** SIMbase::parse: No patches read"<< std::endl;
return false;
}
}
} else if (!strcasecmp(elem->Value(),"nodefile")) {
if (!createFEMmodel())
return false;
std::string file = elem->FirstChild()->Value();
std::ifstream isn(file.c_str());
if (isn) {
std::cout <<"\nReading data file "<< file << std::endl;
} else {
std::cerr <<" *** SIMbase::read: Failure opening input file "
<< file << std::endl;
return false;
}
readNodes(isn);
} else if (!strcasecmp(elem->Value(),"partitioning")) {
if (!elem->Attribute("procs") || atoi(elem->Attribute("procs")) != nProc)
return false;
if (myPid == 0)
std::cout <<"\nNumber of partitions: "<< nProc << std::endl;
const TiXmlElement* part = elem->FirstChildElement("part");
while (part) {
if (part->Attribute("proc") && atoi(part->Attribute("proc")) == myPid) {
int first=-2, last=-2;
if (part->Attribute("lower"))
first = atoi(part->Attribute("upper"));
if (part->Attribute("upper"))
last = atoi(part->Attribute("upper"));
if (last > nGlPatches) nGlPatches = last;
myPatches.reserve(last-first+1);
for (int j = first; j <= last && j > -1; j++)
myPatches.push_back(j);
}
part = part->NextSiblingElement("part");
}
}
return true;
}
bool SIMbase::parseOutputTag(const TiXmlElement* elem)
{
if (!strcasecmp(elem->Value(),"resultpoints")) {
const TiXmlElement* point = elem->FirstChildElement("point");
int i=0;
while (point) {
ResultPoint thePoint;
if (point->Attribute("patch"))
thePoint.patch = atoi(point->Attribute("patch"));
if (myPid == 0)
std::cout <<"\n\tPoint "<< i+1 <<": P"<< thePoint.patch <<" xi =";
if (point->Attribute("u")) {
thePoint.par[0] = atof(point->Attribute("u"));
if (myPid == 0)
std::cout << ' ' << thePoint.par[0];
}
if (point->Attribute("v")) {
thePoint.par[1] = atof(point->Attribute("v"));
if (myPid == 0)
std::cout << ' ' << thePoint.par[1];
}
if (point->Attribute("w")) {
thePoint.par[2] = atoi(point->Attribute("w"));
if (myPid == 0)
std::cout << ' ' << thePoint.par[2];
}
myPoints.push_back(thePoint);
i++;
point = point->NextSiblingElement();
}
if (myPid == 0)
std::cout << std::endl;
} else if (!strcasecmp(elem->Value(),"vtfformat")) {
if (elem->FirstChild()->Value() &&
!strcasecmp(elem->FirstChild()->Value(),"ascii"))
format = 0;
else if (elem->FirstChild()->Value() &&
!strcasecmp(elem->FirstChild()->Value(),"binary"))
format = 1;
} else if (!strcasecmp(elem->Value(),"stride")) {
if (elem->FirstChild()->Value())
vizIncr = atoi(elem->FirstChild()->Value());
}
return true;
}
bool SIMbase::parseBCTag(const TiXmlElement* elem)
{
if (!strcasecmp(elem->Value(),"propertycodes")) {
const TiXmlElement* code = elem->FirstChildElement("code");
while (code) {
int icode=0;
if (code->Attribute("value"))
icode = atoi(code->Attribute("value"));
const TiXmlElement* patch = code->FirstChildElement("patch");
while (patch) {
Property p;
p.pindx = icode;
// TODO WTF is the only read number if lindex < 2 ?
if (patch->Attribute("face")) {
p.lindx = atoi(patch->Attribute("face"));
p.ldim = 2;
}
if (patch->Attribute("edge")) {
p.lindx = atoi(patch->Attribute("edge"));
p.ldim = 1;
}
if (patch->Attribute("vertex")) {
p.lindx = atoi(patch->Attribute("vertex"));
p.ldim = 0;
}
if (patch->Attribute("index"))
p.patch = getLocalPatchIndex(atoi(patch->Attribute("index")));
if (p.patch > 0)
myProps.push_back(p);
patch = patch->NextSiblingElement("patch");
}
code = code->NextSiblingElement();
}
} else if (!strcasecmp(elem->Value(),"dirichlet")) {
if (ignoreDirichlet) // ignore all boundary conditions
return true;
int code=0;
if (elem->Attribute("code"))
code = atoi(elem->Attribute("code"));
double val=0.f;
if (elem->FirstChild() && elem->FirstChild()->Value())
val = atof(elem->FirstChild()->Value());
if (val == 0.f) {
setPropertyType(code,Property::DIRICHLET);
} else {
setPropertyType(code,Property::DIRICHLET_INHOM);
char* func=NULL;
if (elem->Attribute("function"))
func = strdup(elem->Attribute("function"));
if (func) {
char* func2 = func;
func = strtok(func," ");
myScalars[code] = const_cast<RealFunc*>(utl::parseRealFunc(const_cast<char*>(func),val));
free(func2);
} else
myScalars[code] = new ConstFunc(val);
}
}
return true;
}
bool SIMbase::parse (const TiXmlElement* elem)
{
if (!strcasecmp(elem->Value(),"linearsolver"))
readLinSolParams(elem);
else {
const TiXmlElement* child = elem->FirstChildElement();
bool result = true;
while (child) {
if (!strcasecmp(elem->Value(),"geometry"))
result &= parseGeometryTag(child);
else if (!strcasecmp(elem->Value(),"resultoutput"))
result &= parseOutputTag(child);
else if (!strcasecmp(elem->Value(),"boundaryconditions"))
result &= parseBCTag(child);
child = child->NextSiblingElement();
}
return result;
}
return true;
}
bool SIMbase::parse (char* keyWord, std::istream& is)
{
char* cline = 0;
@ -358,6 +553,15 @@ void SIMbase::readLinSolParams (std::istream& is, int npar)
}
void SIMbase::readLinSolParams (const TiXmlElement* elem)
{
if (!mySolParams)
mySolParams = new LinSolParams();
mySolParams->read(elem);
}
bool SIMbase::createFEMmodel ()
{
for (size_t i = 0; i < myModel.size(); i++)

19
src/SIM/SIMbase.h
View File

@ -97,6 +97,10 @@ public:
//! \param is The file stream to read from
virtual bool parse(char* keyWord, std::istream& is);
//! \brief Parses a data section from an xml document.
//! \param[in] elem The XML element to parse
virtual bool parse(const TiXmlElement* elem);
//! \brief Refines a list of elements.
virtual bool refine(const std::vector<int>&, const std::vector<int>&,
const char* = 0) { return false; }
@ -484,6 +488,9 @@ protected:
//! \brief Creates the computational FEM model from the spline patches.
bool createFEMmodel();
//! \brief Reads node numbers from given input stream.
//! \param[in] isp The file stream to read from
virtual void readNodes(std::istream& isp) {}
public:
//! \brief Returns the local patch index for the given global patch number.
//! \details For serial applications this is an identity mapping only, whereas
@ -554,6 +561,10 @@ protected:
//! \details This method helps with encapsulating PETSc in libIFEM.
void readLinSolParams(std::istream& is, int npar);
//! \brief Reads a LinSolParams object from the given XML element
//! \details This method helps with encapsulating PETSc in libIFEM.
void readLinSolParams(const TiXmlElement* elem);
//! \brief Finalizes the global equation system assembly.
virtual bool finalizeAssembly(bool newLHSmatrix = true);
@ -603,6 +614,14 @@ protected:
AlgEqSystem* myEqSys; //!< The actual linear equation system
SAMpatch* mySam; //!< Auxiliary data for FE assembly management
LinSolParams* mySolParams; //!< Input parameters for PETSc
private:
//! \brief Parses a subelement of the <geometry> tag from input file
//! \param[in] elem The XML element to parse
bool parseGeometryTag(const TiXmlElement* elem);
//! \brief Parses a subelement of the <resultoutput> tag from input file
//! \param[in] elem The XML element to parse
bool parseOutputTag(const TiXmlElement* elem);
bool parseBCTag(const TiXmlElement* elem);
};
#endif

66
src/SIM/SIMinput.C
View File

@ -18,6 +18,8 @@
#endif
#include <fstream>
#include "tinyxml.h"
int SIMinput::msgLevel = 2;
@ -34,7 +36,16 @@ SIMinput::SIMinput ()
}
bool SIMinput::read (const char* fileName)
bool SIMinput::read(const char* fileName)
{
if (strcasestr(fileName,".xinp"))
return readXML(fileName);
return readFlat(fileName);
}
bool SIMinput::readFlat (const char* fileName)
{
std::ifstream is(fileName);
if (is)
@ -58,3 +69,56 @@ bool SIMinput::read (const char* fileName)
std::cout <<"\nReading input file succeeded."<< std::endl;
return true;
}
bool SIMinput::readXML (const char* fileName)
{
TiXmlDocument doc;
if (!doc.LoadFile(fileName)) {
std::cerr << __PRETTY_FUNCTION__ << ": Failed to load " << fileName << std::endl;
std::cerr << "\t Error at line " << doc.ErrorRow() << ": " << doc.ErrorDesc() << std::endl;
return false;
}
if (!doc.RootElement() ||
strcmp(doc.RootElement()->Value(),"simulation")) {
std::cerr << __PRETTY_FUNCTION__ << ": Malformatted input file " << fileName << std::endl;
return false;
}
std::vector<const TiXmlElement*> parsed = handlePriorityTags(doc.RootElement());
// now parse the rest
TiXmlElement* elem = doc.RootElement()->FirstChildElement();
while (elem) {
if (find(parsed.begin(),parsed.end(),elem) == parsed.end()) {
if (!parse(elem)) {
std::cerr <<" *** SIMinput::read: Failure occured while parsing \""
<< elem->Value() <<"\""<< std::endl;
return false;
}
}
elem = elem->NextSiblingElement();
}
return true;
}
std::vector<const TiXmlElement*> SIMinput::handlePriorityTags(const TiXmlElement* base)
{
// add particular keywords to this list. these will be parsed first,
// in the order specified in the list
const char* special[] = {"geometry","boundaryconditions"};
std::vector<const TiXmlElement*> parsed;
for (size_t i=0;i<sizeof(special)/sizeof(char*);++i) {
const TiXmlElement* elem = base->FirstChildElement(special[i]);
if (elem) {
if (!parse(elem)) {
std::cerr <<" *** SIMinput::read: Failure occured while parsing \""
<< elem->Value() <<"\""<< std::endl;
}
parsed.push_back(elem);
}
}
return parsed;
}

16
src/SIM/SIMinput.h
View File

@ -15,12 +15,15 @@
#define _SIM_INPUT_H
#include <iostream>
#include <vector>
/*!
\brief Base class for NURBS-based FEM simulators with input file parsing.
*/
class TiXmlElement;
class SIMinput
{
protected:
@ -33,14 +36,27 @@ public:
//! \brief Reads model data from the specified input file \a *fileName.
virtual bool read(const char* fileName);
//! \brief Reads a flat text input file
virtual bool readFlat(const char* fileName);
//! \brief Reads an XML input file
bool readXML(const char* fileName);
//! \brief Parses a data section from an input stream.
virtual bool parse(char* keyWord, std::istream& is) = 0;
//! \brief Parses a data section from an XML element.
virtual bool parse(const TiXmlElement* elem) { return false; }
static int msgLevel; //!< Controls the amount of console output during solving
protected:
int myPid; //!< Processor ID in parallel simulations
int nProc; //!< Number of processors in parallel simulations
//! \brief Certain tags needs to be parsed before others. This function takes care of this
//! \param[in] base The base tag containing the elements to be prioritized
//! \returns A vector with elements that was handled
//! \details This function needs to be called in the app specific SIM classes
// prior parsing its app specific block.
std::vector<const TiXmlElement*> handlePriorityTags(const TiXmlElement* base);
};
#endif