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This commit is contained in:
Dave Goodwin 2007-07-27 03:38:23 +00:00
parent a5ade5036f
commit 77a3fdbd56
6 changed files with 3961 additions and 4523 deletions
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104
Cantera/matlab/Makefile.in
View file

@ -60,86 +60,86 @@ endif
rm -f setup.m
install:
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera-demos
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@ThermoPhase/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Mixture/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Kinetics/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Transport/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Interface/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Solution
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@XML_Node/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Reactor/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@ReactorNet/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Wall/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@FlowDevice/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/@Func/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/1D
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/1D/@Domain1D/private
@INSTALL@ -d @prefix@/matlab/toolbox/cantera/cantera/1D/@Stack/private
cd cantera; @INSTALL@ *.m *.@mex_ext@ @prefix@/matlab/toolbox/cantera/cantera
cd cantera/private; @INSTALL@ *.m \
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera-demos
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@ThermoPhase/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Mixture/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Kinetics/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Transport/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Interface/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Solution
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@XML_Node/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Reactor/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@ReactorNet/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Wall/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@FlowDevice/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/@Func/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/1D
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/1D/@Domain1D/private
@INSTALL_abs@ -d @prefix@/matlab/toolbox/cantera/cantera/1D/@Stack/private
cd cantera; @INSTALL_abs@ *.m *.@mex_ext@ @prefix@/matlab/toolbox/cantera/cantera
cd cantera/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/private
cd cantera/examples; @INSTALL@ *.m @prefix@/matlab/toolbox/cantera/cantera-demos
cd cantera/@ThermoPhase; @INSTALL@ \
cd cantera/examples; @INSTALL_abs@ *.m @prefix@/matlab/toolbox/cantera/cantera-demos
cd cantera/@ThermoPhase; @INSTALL_abs@ \
*.m @prefix@/matlab/toolbox/cantera/cantera/@ThermoPhase
cd cantera/@ThermoPhase/private; @INSTALL@ *.m \
cd cantera/@ThermoPhase/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@ThermoPhase/private
cd cantera/@Kinetics; @INSTALL@ *.m \
cd cantera/@Kinetics; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Kinetics
cd cantera/@Kinetics/private; @INSTALL@ *.m \
cd cantera/@Kinetics/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Kinetics/private
cd cantera/@Solution; @INSTALL@ *.m \
cd cantera/@Solution; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Solution
cd cantera/@Transport; @INSTALL@ *.m \
cd cantera/@Transport; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Transport
cd cantera/@Transport/private; @INSTALL@ *.m \
cd cantera/@Transport/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Transport/private
cd cantera/@Interface; @INSTALL@ \
cd cantera/@Interface; @INSTALL_abs@ \
*.m @prefix@/matlab/toolbox/cantera/cantera/@Interface
cd cantera/@Interface/private; @INSTALL@ *.m \
cd cantera/@Interface/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Interface/private
cd cantera/@Mixture; @INSTALL@ \
cd cantera/@Mixture; @INSTALL_abs@ \
*.m @prefix@/matlab/toolbox/cantera/cantera/@Mixture
cd cantera/@Mixture/private; @INSTALL@ *.m \
cd cantera/@Mixture/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Mixture/private
cd cantera/@XML_Node; @INSTALL@ *.m \
cd cantera/@XML_Node; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@XML_Node
cd cantera/@Reactor; @INSTALL@ *.m \
cd cantera/@Reactor; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Reactor
cd cantera/@Reactor/private; @INSTALL@ *.m \
cd cantera/@Reactor/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Reactor/private
cd cantera/@ReactorNet; @INSTALL@ *.m \
cd cantera/@ReactorNet; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@ReactorNet
cd cantera/@ReactorNet/private; @INSTALL@ *.m \
cd cantera/@ReactorNet/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@ReactorNet/private
cd cantera/@Wall; @INSTALL@ *.m \
cd cantera/@Wall; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Wall
cd cantera/@Wall/private; @INSTALL@ *.m \
cd cantera/@Wall/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Wall/private
cd cantera/@FlowDevice; @INSTALL@ *.m \
cd cantera/@FlowDevice; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@FlowDevice
cd cantera/@FlowDevice/private; @INSTALL@ *.m \
cd cantera/@FlowDevice/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@FlowDevice/private
cd cantera/@Func; @INSTALL@ *.m \
cd cantera/@Func; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Func
cd cantera/@Func/private; @INSTALL@ *.m \
cd cantera/@Func/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/@Func/private
cd cantera/1D; @INSTALL@ *.m \
cd cantera/1D; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/1D
cd cantera/1D/@Domain1D; @INSTALL@ *.m \
cd cantera/1D/@Domain1D; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/1D/@Domain1D
cd cantera/1D/@Domain1D/private; @INSTALL@ *.m \
cd cantera/1D/@Domain1D/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/1D/@Domain1D/private
cd cantera/1D/@Stack; @INSTALL@ *.m \
cd cantera/1D/@Stack; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/1D/@Stack
cd cantera/1D/@Stack/private; @INSTALL@ *.m \
cd cantera/1D/@Stack/private; @INSTALL_abs@ *.m \
@prefix@/matlab/toolbox/cantera/cantera/1D/@Stack/private
@INSTALL@ -d @ct_demodir@/matlab
@INSTALL@ cantera/examples/*.m @ct_demodir@/matlab
@INSTALL@ -d @ct_tutdir@/matlab
@INSTALL@ cantera/tutorial/*.m @ct_tutdir@/matlab
@INSTALL_abs@ -d @ct_demodir@/matlab
@INSTALL_abs@ cantera/examples/*.m @ct_demodir@/matlab
@INSTALL_abs@ -d @ct_tutdir@/matlab
@INSTALL_abs@ cantera/tutorial/*.m @ct_tutdir@/matlab
chown -R @username@ @ct_demodir@/matlab
chown -R @username@ @ct_tutdir@/matlab

2
Cantera/src/oneD/MultiJac.cpp
View file

@ -63,7 +63,7 @@ namespace Cantera {
* Evaluate the Jacobian at x0. The array of residual values at x0
* is supplied as an input.
*/
void MultiJac::eval(doublereal* x0, doublereal* resid0, doublereal rdt)
void MultiJac::eval(doublereal* x0, doublereal* resid0, doublereal rdt)
{
m_nevals++;
clock_t t0 = clock();

4
Cantera/src/zeroD/ReactorBase.h
View file

@ -89,6 +89,10 @@ namespace CanteraZeroD {
FlowDevice& inlet(int n = 0);
FlowDevice& outlet(int n = 0);
int nInlets() { return m_inlet.size(); }
int nOutlets() { return m_outlet.size(); }
int nWalls() { return m_wall.size(); }
void addWall(Wall& w, int lr);
Wall& wall(int n);

70
Cantera/src/zeroD/ReactorNet.cpp
View file

@ -1,5 +1,7 @@
#include "ReactorNet.h"
#include "Integrator.h"
#include "FlowDevice.h"
#include "Wall.h"
using namespace std;
@ -48,6 +50,7 @@ namespace CanteraZeroD {
m_ntotpar += r->nSensParams();
m_nv += nv;
m_nreactors++;
if (m_verbose) {
sprintf(buf,"Reactor %d: %d variables.\n",n,nv);
writelog(buf);
@ -62,6 +65,35 @@ namespace CanteraZeroD {
}
}
m_connect.resize(m_nr*m_nr,0);
m_ydot.resize(m_nv,0.0);
int i, j, nin, nout, nw;
ReactorBase *r, *rj;
for (i = 0; i < m_nr; i++) {
r = m_reactors[i];
for (j = 0; j < m_nr; j++) {
if (i == j) connect(i,j);
else {
rj = m_reactors[j];
nin = rj->nInlets();
for (n = 0; n < nin; n++) {
if (&rj->inlet(n).out() == r) connect(i,j);
}
nout = rj->nOutlets();
for (n = 0; n < nout; n++) {
if (&rj->outlet(n).in() == r) connect(i,j);
}
nw = rj->nWalls();
for (n = 0; n < nw; n++) {
if (&rj->wall(n).left() == rj
&& &rj->wall(n).right() == r) connect(i,j);
else if (&rj->wall(n).left() == r
&& &rj->wall(n).right() == rj) connect(i,j);
}
}
}
}
m_atol.resize(neq());
fill(m_atol.begin(), m_atol.end(), m_atols);
m_integ->setTolerances(m_rtol, neq(), DATA_PTR(m_atol));
@ -114,6 +146,7 @@ namespace CanteraZeroD {
// }
// }
// }
void ReactorNet::eval(doublereal t, doublereal* y,
doublereal* ydot, doublereal* p) {
@ -137,6 +170,43 @@ namespace CanteraZeroD {
}
}
void ReactorNet::evalJacobian(doublereal t, doublereal* y,
doublereal* ydot, doublereal* p, Array2D* j) {
int n, m;
doublereal ysave, dy;
Array2D& jac = *j;
// use a try... catch block, since exceptions are not passed
// through CVODE, since it is C code
try {
//evaluate the unperturbed ydot
eval(t, y, ydot, p);
for (n = 0; n < m_nv; n++) {
// perturb x(n)
ysave = y[n];
dy = m_atol[n] + fabs(ysave)*m_rtol;
y[n] = ysave + dy;
dy = y[n] - ysave;
// calculate perturbed residual
eval(t, y, DATA_PTR(m_ydot), p);
// compute nth column of Jacobian
for (m = 0; m < m_nv; m++) {
jac(m,n) = (m_ydot[m] - ydot[m])/dy;
}
y[n] = ysave;
}
}
catch (...) {
showErrors();
error("Terminating execution.");
}
}
void ReactorNet::updateState(doublereal* y) {
int n;
int start = 0;

15
Cantera/src/zeroD/ReactorNet.h
View file

@ -21,6 +21,7 @@
#include "Reactor.h"
#include "FuncEval.h"
#include "Integrator.h"
#include "Array.h"
namespace CanteraZeroD {
@ -124,6 +125,9 @@ namespace CanteraZeroD {
return sensitivity(k, p);
}
void evalJacobian(doublereal t, doublereal* y,
doublereal* ydot, doublereal* p, Array2D* j);
//-----------------------------------------------------
// overloaded methods of class FuncEval
@ -136,6 +140,15 @@ namespace CanteraZeroD {
int globalComponentIndex(std::string species, int reactor=0);
void connect(int i, int j) {
m_connect[j*m_nr + i] = 1;
m_connect[i*m_nr + j] = 1;
}
bool connected(int i, int j) {
return (m_connect[m_nr*i + j] == 1);
}
protected:
std::vector<ReactorBase*> m_r;
@ -154,6 +167,8 @@ namespace CanteraZeroD {
bool m_verbose;
int m_ntotpar;
vector_int m_nparams;
vector_int m_connect;
vector_fp m_ydot;
private:

8289
configure vendored
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