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This commit is contained in:
Dave Goodwin 2003-08-08 21:03:00 +00:00
parent 918ee4a588
commit c471052ef8
5 changed files with 121 additions and 46 deletions
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55
Cantera/python/Cantera/ctml_writer.py
View file

@ -19,16 +19,18 @@ SPECIES_SET = 20
COLLECTION = 30
THERMO = 40
ALL = 10
SKIP_UNDECLARED_ELEMENTS = 20
SKIP_UNDECLARED_SPECIES = 30
STOP = 0
#ALL = 10
#SKIP_UNDECLARED_ELEMENTS = 20
#SKIP_UNDECLARED_SPECIES = 30
#STOP = 0
_EXCEPT = 10
_WARN = 2
_SKIP = 1
_handle_undeclared_element = _EXCEPT
_handle_undeclared_species = _EXCEPT
#_EXCEPT = 10
#_WARN = 2
#_SKIP = 1
_handle_error = {}
#_handle_undeclared_element = _EXCEPT
#_handle_undeclared_species = _EXCEPT
#_handle_neg_A = _EXCEPT
# default units
_ulen = 'm'
@ -71,13 +73,17 @@ def standard_pressure(p0):
global _pref
_pref = p0
def on_error(undeclared_element = '', undeclared_species = ''):
global _handle_undeclared_species
global _handle_undeclared_element
def on_error(undeclared_element = '',
undeclared_species = '',
negative_A = ''):
global _handle_error
_handle_undeclared_species = undeclared_species
_handle_undeclared_element = undeclared_element
if undeclared_element:
_handle_error['undeclared_element'] = undeclared_element
if undeclared_species:
_handle_error['undeclared_species'] = undeclared_species
if negative_A:
_handle_error['negative_A'] = negative_A
def get_atomic_wts():
@ -324,8 +330,9 @@ class NASA(thermo):
class const_cp(thermo):
"""Constant specific heat."""
def __init__(self, tmax = -1.0, tmin = -1.0,
t0 = 298.15, cp0 = 0.0, h0 = 0.0, s0 = 0.0):
def __init__(self,
t0 = 298.15, cp0 = 0.0, h0 = 0.0, s0 = 0.0,
tmax = -1.0, tmin = -1.0):
self._t = [tmin, tmax]
self._c = [t0, h0, s0, cp0]
@ -373,6 +380,16 @@ class Arrhenius(writer):
self._c = [A, n, E]
def build(self, p, units = '', gas_species = [], name = ''):
if self._c[0] < 0.0:
e = _handle_error['negative_A']
if e == 'skip': return
elif e == 'warn':
print 'Warning: negative pre-exponential: A = ',self._c[0]
elif e == 'continue':
pass
else:
raise CanteraError('negative pre-exponential: A = '+`self._c[0]`)
a = p.addChild('Arrhenius')
if name: a['name'] = name
if isnum(self._c[0]):
@ -809,7 +826,7 @@ class phase(writer):
datasrc = r[0]
ra = p.addChild('reactionArray')
ra['datasrc'] = datasrc+'#reaction_data'
if _handle_undeclared_species == 'skip':
if _handle_error['undeclared_species'] == 'skip':
rk = ra.addChild('skip')
rk['species'] = 'undeclared'
@ -836,7 +853,7 @@ class phase(writer):
sa = ph.addChild('speciesArray',names)
sa['datasrc'] = datasrc+'#species_data'
if _handle_undeclared_element == 'skip':
if _handle_error['undeclared_element'] == 'skip':
sk = sa.addChild('skip')
sk['element'] = 'undeclared'

89
Cantera/src/ImplicitSurfChem.cpp
View file

@ -21,15 +21,50 @@
namespace Cantera {
ImplicitSurfChem::ImplicitSurfChem(InterfaceKinetics& kin)
: FuncEval(), m_kin(&kin), m_integ(0),
// ImplicitSurfChem::ImplicitSurfChem(InterfaceKinetics& kin)
// : FuncEval(), m_kin(&kin), m_integ(0),
// m_atol(1.e-14), m_rtol(1.e-7), m_maxstep(0.0)
// {
// m_integ = new CVodeInt;
// m_surfindex = kin.surfacePhaseIndex();
// if (m_surfindex < 0)
// throw CanteraError("ImplicitSurfChem","kinetics manager contains no surface phase");
// m_surf = (SurfPhase*)&kin.thermo(m_surfindex);;
// // use backward differencing, with a full Jacobian computed
// // numerically, and use a Newton linear iterator
// m_integ->setMethod(BDF_Method);
// m_integ->setProblemType(DENSE + NOJAC);
// m_integ->setIterator(Newton_Iter);
// m_nsp = m_surf->nSpecies();
// m_work.resize(m_kin->nTotalSpecies());
// }
ImplicitSurfChem::ImplicitSurfChem(vector<InterfaceKinetics*> k)
: FuncEval(), m_nv(0), m_integ(0),
m_atol(1.e-14), m_rtol(1.e-7), m_maxstep(0.0)
{
m_nsurf = k.size();
int ns;
int nt, ntmax = 0;
for (int n = 0; n < m_nsurf; n++) {
m_kin.push_back(k[n]);
ns = k[n]->surfacePhaseIndex();
if (ns < 0)
throw CanteraError("ImplicitSurfChem",
"kinetics manager contains no surface phase");
m_surfindex.push_back(ns);
m_surf.push_back((SurfPhase*)&k[n]->thermo(ns));
m_nsp.push_back(m_surf.back()->nSpecies());
m_nv += m_nsp.back();
nt = k[n]->nTotalSpecies();
if (nt > ntmax) ntmax = nt;
}
m_integ = new CVodeInt;
m_surfindex = kin.surfacePhaseIndex();
if (m_surfindex < 0)
throw CanteraError("ImplicitSurfChem","kinetics manager contains no surface phase");
m_surf = (SurfPhase*)&kin.thermo(m_surfindex);;
//m_surfindex = kin.surfacePhaseIndex();
//m_surf = (SurfPhase*)&kin.thermo(m_surfindex);;
// use backward differencing, with a full Jacobian computed
// numerically, and use a Newton linear iterator
@ -37,8 +72,8 @@ namespace Cantera {
m_integ->setMethod(BDF_Method);
m_integ->setProblemType(DENSE + NOJAC);
m_integ->setIterator(Newton_Iter);
m_nsp = m_surf->nSpecies();
m_work.resize(m_kin->nTotalSpecies());
//m_nsp = m_surf->nSpecies();
m_work.resize(ntmax);
}
@ -47,7 +82,11 @@ namespace Cantera {
void ImplicitSurfChem::getInitialConditions(double t0, size_t lenc,
double* c)
{
m_surf->getCoverages(c);
int loc = 0;
for (int n = 0; n < m_nsurf; n++) {
m_surf[n]->getCoverages(c + loc);
loc += m_nsp[n];
}
}
@ -61,7 +100,11 @@ namespace Cantera {
void ImplicitSurfChem::updateState(doublereal* c) {
m_surf->setCoverages(c);
int loc = 0;
for (int n = 0; n < m_nsurf; n++) {
m_surf[n]->setCoverages(c + loc);
loc += m_nsp[n];
}
}
@ -71,18 +114,22 @@ namespace Cantera {
void ImplicitSurfChem::eval(doublereal time, doublereal* y,
doublereal* ydot)
{
updateState(y); // synchronize the surface state with y
doublereal rs0 = 1.0/m_surf->siteDensity();
m_kin->getNetProductionRates(m_work.begin());
int k;
int kstart = m_kin->start(m_surfindex);
doublereal sum = 0.0;
for (k = 1; k < m_nsp; k++) {
ydot[k] = m_work[kstart + k] * rs0 * m_surf->size(k);
sum -= ydot[k];
updateState(y); // synchronize the surface state(s) with y
doublereal rs0, sum;
int loc, k, kstart;
for (int n = 0; n < m_nsurf; n++) {
rs0 = 1.0/m_surf[n]->siteDensity();
m_kin[n]->getNetProductionRates(m_work.begin());
kstart = m_kin[n]->start(m_surfindex[n]);
sum = 0.0;
loc = 0;
for (k = 1; k < m_nsp[n]; k++) {
ydot[k + loc] = m_work[kstart + k] * rs0 * m_surf[n]->size(k);
sum -= ydot[k];
}
ydot[loc] = sum;
loc += m_nsp[n];
}
//if (sum < 0.0) sum = 0.0;
ydot[0] = sum;
}
}

18
Cantera/src/ImplicitSurfChem.h
View file

@ -38,8 +38,12 @@ namespace Cantera {
/**
* Constructor.
*/
ImplicitSurfChem(InterfaceKinetics& kin);
//ImplicitSurfChem(InterfaceKinetics& kin);
/**
* Constructor for multiple surfaces.
*/
ImplicitSurfChem(vector<InterfaceKinetics*> k);
/**
* Destructor. Deletes the integrator.
@ -77,7 +81,7 @@ namespace Cantera {
}
// overloaded methods of class FuncEval
virtual int neq() { return m_nsp; }
virtual int neq() { return m_nv; }
virtual void eval(doublereal t, doublereal* y, doublereal* ydot);
virtual void getInitialConditions(doublereal t0,
size_t leny, doublereal* y);
@ -91,9 +95,13 @@ namespace Cantera {
*/
void updateState(doublereal* y);
SurfPhase* m_surf;
InterfaceKinetics* m_kin;
int m_nsp, m_surfindex;
vector<SurfPhase*> m_surf;
vector<InterfaceKinetics*> m_kin;
vector_int m_nsp;
vector_int m_surfindex;
int m_nsurf;
int m_nv;
//int m_nsp, m_surfindex;
Integrator* m_integ; // pointer to integrator
doublereal m_atol, m_rtol; // tolerances
doublereal m_maxstep; // max step size

4
Cantera/src/InterfaceKinetics.cpp
View file

@ -608,7 +608,9 @@ namespace Cantera {
void InterfaceKinetics::
advanceCoverages(doublereal tstep) {
if (m_integrator == 0) {
m_integrator = new ImplicitSurfChem(*this);
vector<InterfaceKinetics*> k;
k.push_back(this);
m_integrator = new ImplicitSurfChem(k);
m_integrator->initialize();
}
m_integrator->integrate(0.0, tstep);

1
Cantera/src/InterfaceKinetics.h
View file

@ -166,6 +166,7 @@ namespace Cantera {
void advanceCoverages(doublereal tstep);
protected:
int m_kk;