[NewKid]

I got a Segmentation fault message while having alternateSteadyReactingFoam running on an cantera example.
Can somebody give me some suggestions?

[NewKid]

I use cantera input file-mix.cti with 9 species and 27 reactions including 6 duplicate reactions.
If somebody knows something about it, contact me, I can show you all the files.

[NewKid]

Now I give the complete content of mix.cti-cantera input file:


units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol")
#ideal_gas(name = "hydrogen_oxygen",
ideal_gas(name = "mix",
elements = " O H Ar ",
species = " H2 H O O2 OH H2O HO2 H2O2 AR",
#New added line
transport="Mix",
reactions = "all",
#The beneath is changed
initial_state=state(temperature=300,pressure=OneAt m,mole_fractions='O2:0.026, H2:0.009')
#The beneath means no validation of input,just a try!
#options = ("no_validation")
)
#-------------------------------------------------------------------------------
# Species data
#-------------------------------------------------------------------------------
species(name = "H2",
atoms = " H:2 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 2.344331120E+00, 7.980520750E-03,
-1.947815100E-05, 2.015720940E-08, -7.376117610E-12,
-9.179351730E+02, 6.830102380E-01] ),
NASA( [ 1000.00, 3500.00], [ 3.337279200E+00, -4.940247310E-05,
4.994567780E-07, -1.795663940E-10, 2.002553760E-14,
-9.501589220E+02, -3.205023310E+00] )
),
transport = gas_transport(
geom = "linear",
diam = 2.92,
well_depth = 38.00,
polar = 0.79,
rot_relax = 280.00)
)

species(name = "H",
atoms = " H:1 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 2.500000000E+00, 7.053328190E-13,
-1.995919640E-15, 2.300816320E-18, -9.277323320E-22,
2.547365990E+04, -4.466828530E-01] ),
NASA( [ 1000.00, 3500.00], [ 2.500000010E+00, -2.308429730E-11,
1.615619480E-14, -4.735152350E-18, 4.981973570E-22,
2.547365990E+04, -4.466829140E-01] )
),
transport = gas_transport(
geom = "atom",
diam = 2.05,
well_depth = 145.00)
)

species(name = "O",
atoms = " O:1 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 3.168267100E+00, -3.279318840E-03,
6.643063960E-06, -6.128066240E-09, 2.112659710E-12,
2.912225920E+04, 2.051933460E+00] ),
NASA( [ 1000.00, 3500.00], [ 2.569420780E+00, -8.597411370E-05,
4.194845890E-08, -1.001777990E-11, 1.228336910E-15,
2.921757910E+04, 4.784338640E+00] )
),
transport = gas_transport(
geom = "atom",
diam = 2.75,
well_depth = 80.00)
)

species(name = "O2",
atoms = " O:2 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 3.782456360E+00, -2.996734160E-03,
9.847302010E-06, -9.681295090E-09, 3.243728370E-12,
-1.063943560E+03, 3.657675730E+00] ),
NASA( [ 1000.00, 3500.00], [ 3.282537840E+00, 1.483087540E-03,
-7.579666690E-07, 2.094705550E-10, -2.167177940E-14,
-1.088457720E+03, 5.453231290E+00] )
),
transport = gas_transport(
geom = "linear",
diam = 3.46,
well_depth = 107.40,
polar = 1.60,
rot_relax = 3.80)
)

species(name = "OH",
atoms = " O:1 H:1 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 3.992015430E+00, -2.401317520E-03,
4.617938410E-06, -3.881133330E-09, 1.364114700E-12,
3.615080560E+03, -1.039254580E-01] ),
NASA( [ 1000.00, 3500.00], [ 3.092887670E+00, 5.484297160E-04,
1.265052280E-07, -8.794615560E-11, 1.174123760E-14,
3.858657000E+03, 4.476696100E+00] )
),
transport = gas_transport(
geom = "linear",
diam = 2.75,
well_depth = 80.00)
)

species(name = "H2O",
atoms = " H:2 O:1 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 4.198640560E+00, -2.036434100E-03,
6.520402110E-06, -5.487970620E-09, 1.771978170E-12,
-3.029372670E+04, -8.490322080E-01] ),
NASA( [ 1000.00, 3500.00], [ 3.033992490E+00, 2.176918040E-03,
-1.640725180E-07, -9.704198700E-11, 1.682009920E-14,
-3.000429710E+04, 4.966770100E+00] )
),
transport = gas_transport(
geom = "nonlinear",
diam = 2.60,
well_depth = 572.40,
dipole = 1.84,
rot_relax = 4.00)
)

species(name = "HO2",
atoms = " H:1 O:2 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 4.301798010E+00, -4.749120510E-03,
2.115828910E-05, -2.427638940E-08, 9.292251240E-12,
2.948080400E+02, 3.716662450E+00] ),
NASA( [ 1000.00, 3500.00], [ 4.017210900E+00, 2.239820130E-03,
-6.336581500E-07, 1.142463700E-10, -1.079085350E-14,
1.118567130E+02, 3.785102150E+00] )
),
transport = gas_transport(
geom = "nonlinear",
diam = 3.46,
well_depth = 107.40,
rot_relax = 1.00)
)

species(name = "H2O2",
atoms = " H:2 O:2 ",
thermo = (
NASA( [ 200.00, 1000.00], [ 4.276112690E+00, -5.428224170E-04,
1.673357010E-05, -2.157708130E-08, 8.624543630E-12,
-1.770258210E+04, 3.435050740E+00] ),
NASA( [ 1000.00, 3500.00], [ 4.165002850E+00, 4.908316940E-03,
-1.901392250E-06, 3.711859860E-10, -2.879083050E-14,
-1.786178770E+04, 2.916156620E+00] )
),
transport = gas_transport(
geom = "nonlinear",
diam = 3.46,
well_depth = 107.40,
rot_relax = 3.80)
)

species(name = "AR",
atoms = " Ar:1 ",
thermo = (
NASA( [ 300.00, 1000.00], [ 2.500000000E+00, 0.000000000E+00,
0.000000000E+00, 0.000000000E+00, 0.000000000E+00,
-7.453750000E+02, 4.366000000E+00] ),
NASA( [ 1000.00, 5000.00], [ 2.500000000E+00, 0.000000000E+00,
0.000000000E+00, 0.000000000E+00, 0.000000000E+00,
-7.453750000E+02, 4.366000000E+00] )
),
transport = gas_transport(
geom = "atom",
diam = 3.33,
well_depth = 136.50)
)
#-------------------------------------------------------------------------------
# Reaction data
#-------------------------------------------------------------------------------
# Reaction 1
three_body_reaction( "2 O + M <=> O2 + M", [1.20000E+17, -1, 0],
efficiencies = " AR:0.83 H2:2.4 H2O:15.4 ")

# Reaction 2
three_body_reaction( "O + H + M <=> OH + M", [5.00000E+17, -1, 0],
efficiencies = " AR:0.7 H2:2 H2O:6 ")

# Reaction 3
reaction( "O + H2 <=> H + OH", [3.87000E+04, 2.7, 6260])

# Reaction 4
reaction( "O + HO2 <=> OH + O2", [2.00000E+13, 0, 0])

# Reaction 5
reaction( "O + H2O2 <=> OH + HO2", [9.63000E+06, 2, 4000])

# Reaction 6
reaction( "H + 2 O2 <=> HO2 + O2", [2.08000E+19, -1.24, 0])

# Reaction 7
reaction( "H + O2 + H2O <=> HO2 + H2O", [1.12600E+19, -0.76, 0])

# Reaction 8
reaction( "H + O2 + AR <=> HO2 + AR", [7.00000E+17, -0.8, 0])

# Reaction 9
reaction( "H + O2 <=> O + OH", [2.65000E+16, -0.6707, 17041])

# Reaction 10
three_body_reaction( "2 H + M <=> H2 + M", [1.00000E+18, -1, 0],
efficiencies = " AR:0.63 H2:0 H2O:0 ")

# Reaction 11
reaction( "2 H + H2 <=> 2 H2", [9.00000E+16, -0.6, 0])

# Reaction 12
reaction( "2 H + H2O <=> H2 + H2O", [6.00000E+19, -1.25, 0])

# Reaction 13
three_body_reaction( "H + OH + M <=> H2O + M", [2.20000E+22, -2, 0],
efficiencies = " AR:0.38 H2:0.73 H2O:3.65 ")

# Reaction 14
reaction( "H + HO2 <=> O + H2O", [3.97000E+12, 0, 671])

# Reaction 15
reaction( "H + HO2 <=> O2 + H2", [4.48000E+13, 0, 1068])

# Reaction 16
reaction( "H + HO2 <=> 2 OH", [8.40000E+13, 0, 635])

# Reaction 17
reaction( "H + H2O2 <=> HO2 + H2", [1.21000E+07, 2, 5200])

# Reaction 18
reaction( "H + H2O2 <=> OH + H2O", [1.00000E+13, 0, 3600])

# Reaction 19
reaction( "OH + H2 <=> H + H2O", [2.16000E+08, 1.51, 3430])

# Reaction 20
falloff_reaction( "2 OH (+ M) <=> H2O2 (+ M)",
#rate_coeff_inf = [7.40000E+13, -0.37, 0],
kf=[7.40000E+13, -0.37, 0],
#rate_coeff_0 = [2.30000E+18, -0.9, -1700],
kf0=[2.30000E+18, -0.9, -1700],
falloff = Troe(A = 0.7346, T3 = 94, T1 = 1756, T2 = 5182),
efficiencies = " AR:0.7 H2:2 H2O:6 ")

# Reaction 21
reaction( "2 OH <=> O + H2O", [3.57000E+04, 2.4, -2110])

# Reaction 22
reaction( "OH + HO2 <=> O2 + H2O", [1.45000E+13, 0, -500],options=("duplicate"))

# Reaction 23
reaction( "OH + H2O2 <=> HO2 + H2O", [2.00000E+12, 0, 427],options=("duplicate"))

# Reaction 24
reaction( "OH + H2O2 <=> HO2 + H2O", [1.70000E+18, 0, 29410],options=("duplicate"))

# Reaction 25
reaction( "2 HO2 <=> O2 + H2O2", [1.30000E+11, 0, -1630],options=("duplicate"))

# Reaction 26
reaction( "2 HO2 <=> O2 + H2O2", [4.20000E+14, 0, 12000],options=("duplicate"))

# Reaction 27
reaction( "OH + HO2 <=> O2 + H2O", [5.00000E+15, 0, 17330],options=("duplicate"))

[NewKid]

And I still have those files:
blockmeshDict
gasThermo
chemistryProperties
environmentalProperties
gasReactions
RASProperties
thermophysicalProperties
controlDict
fvSchemes
fvSolution

Any experienced one needs the content of any file above, please let me know.

PS: This is a steady issue with solver alternateSteatReactingFoam.

[gschaider]

Originally Posted by NewKid

And I still have those files:
blockmeshDict
gasThermo
chemistryProperties
environmentalProperties
gasReactions
RASProperties
thermophysicalProperties
controlDict
fvSchemes
fvSolution

Any experienced one needs the content of any file above, please let me know.

PS: This is a steady issue with solver alternateSteatReactingFoam.

The crucial question is: WHEN did this segmentation fault occur? Output and a stack-trace would be helpful.

The most common reason for segmentation faults with the Cantera-libray is that the gasId specified in thermophysicalProperties doesn't fit the name given in the CTI-file. But that is only a guess

Bernhard

[NewKid]

Thanks, Bernhard.
I'll check this as soon as possible.

[NewKid]

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.2-devel |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/

// FoamX Case Dictionary.

FoamFile
{
version 2.0;
format ascii;

root "/Werner/bgschaid/bgschaid-foamStuff/Solver/Spray";
case "dualInjector2D";
instance "constant";
local "";

class dictionary;
object thermophysicalProperties;
}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

thermoType hMixtureThermo<canteraMixture>;
// thermoType hMixtureThermo<reactingMixture>;

chemistryReader foamChemistryReader;
// chemistryReader chemkinReader;

foamChemistryThermoFile "$FOAM_CASE/constant/gasThermo";
foamChemistryFile "$FOAM_CASE/constant/gasReactions";

// CHEMKINFile "$FOAM_CASE/constant/gri30.inp";
// CHEMKINThermoFile "$FOAM_CASE/constant/...";

inertSpecie N2;

cantera {
gasFile "$FOAM_CASE/constant/mix.cti"; //Bernhard, here? Is it right?
gasId mix; //or here? I have no ideals about gasId.
standinThermoFile "$FOAM_CASE/constant/gasThermo";
//standinThermoFile $foamChemistryThermoFile;
}

// ************************************************** *********************** //

[NewKid]

The attachment is the running info file with 1600k.
When the content of file is over, 'Segmentation fault' occurs.

[NewKid]

The attachment is the running info file with 300k.
When the content of file is over, 'Segmentation fault' occurs.

[gschaider]

Originally Posted by NewKid

The attachment is the running info file with 300k.
When the content of file is over, 'Segmentation fault' occurs.

No idea. Look like perfect OK runs. At least the gasID is alright (see my comment above) otherwise it wouldn't have come that far

Before running say

export FOAM_ABORT=1

to provoke a stack-trace

[NewKid]

Thank you!
I'll try very soon!

[NewKid]

And I wonder any relationship among the initial conditions exist?

[NewKid]

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5-dev |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Exec : alternateSteadyReactingFoam
Date : Dec 28 2010
Time : 09:42:34
Host : slax
PID : 9423
Case : /OpenFOAM/OpenFOAM-1.5-dev/applications/solvers/AlternateChemistry/Steady/firstSample
nProcs : 1

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

--> FOAM Warning :
From function dlLibraryTable:pen(const fileName& functionLibName)
in file db/dlLibraryTable/dlLibraryTable.C at line 86
could not load libcompressibleFluxBCs.so: cannot open shared object file: No such file or directory
Create mesh for time = 0

Reading chemistry properties


Reading environmentalProperties

Reading thermophysicalProperties
Selecting thermodynamics package hMixtureThermo<canteraMixture>
Reading from Cantera-File "/OpenFOAM/OpenFOAM-1.5-dev/applications/solvers/AlternateChemistry/Steady/firstSample/constant/mix.cti" the mixture mix
Reading from Cantera-File "/OpenFOAM/OpenFOAM-1.5-dev/applications/solvers/AlternateChemistry/Steady/firstSample/constant/mix.cti" the mixture mix
Reading field U

Reading/calculating face flux field phi

Creating turbulence model.

Selecting RAS turbulence model kEpsilon
kEpsilonCoeffs
{
Cmu 0.09;
C1 1.44;
C2 1.92;
C3 -0.33;
alphah 1;
alphak 1;
alphaEps 0.76923;
}

Constructing chemical mechanism
Choosing the chemistry engine
Selecting chemistry engine canteraLocalTimeChemistryModel
with STEADY chemistry model

Starting time loop

Time = 1

Solving chemistry
Characteristic time of chemistry: 0.1
smoothSolver: Solving for Ux, Initial residual = 1, Final residual = 0.000958722, No Iterations 2
smoothSolver: Solving for Uy, Initial residual = 1, Final residual = 0.000662575, No Iterations 2
PBiCG: Solving for H2, Initial residual = 0.999962, Final residual = 0.00552089, No Iterations 1
PBiCG: Solving for H, Initial residual = 0.999987, Final residual = 0.00256162, No Iterations 1
PBiCG: Solving for O, Initial residual = 0.999985, Final residual = 0.00256161, No Iterations 1
PBiCG: Solving for O2, Initial residual = 1, Final residual = 0.00552054, No Iterations 1
PBiCG: Solving for OH, Initial residual = 0.999987, Final residual = 0.00256162, No Iterations 1
PBiCG: Solving for H2O, Initial residual = 0.999994, Final residual = 0.00256163, No Iterations 1
PBiCG: Solving for HO2, Initial residual = 1, Final residual = 0.00256165, No Iterations 1
PBiCG: Solving for H2O2, Initial residual = 0.346973, Final residual = 0.000888823, No Iterations 1
PBiCG: Solving for AR, Initial residual = 1.7173e-11, Final residual = 1.7173e-11, No Iterations 0
Max summe Yi = max((0*H2)) [0 0 0 0 0 0 0] 0.035 Min summe Yi = min((0*H2)) [0 0 0 0 0 0 0] 0.035
Fixed kappa in 0 cells due to large deltaY

#0 Foam::error:rintStack(Foam::Ostream&) in "/OpenFOAM/OpenFOAM-1.5-dev/lib/linuxGccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/OpenFOAM/OpenFOAM-1.5-dev/lib/linuxGccDPOpt/libOpenFOAM.so"
#2 Uninterpreted:
#3 Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>:perator=(Foam::tmp<Foam::Geometri cField<double, Foam::fvPatchField, Foam::volMesh> > const&) in "/home/slax/OpenFOAM/slax-1.5-dev/applications/bin/linuxGccDPOpt/alternateSteadyReactingFoam"
#4 main in "/home/slax/OpenFOAM/slax-1.5-dev/applications/bin/linuxGccDPOpt/alternateSteadyReactingFoam"
#5 __libc_start_main in "/lib/libc.so.6"
#6 _start in "/home/slax/OpenFOAM/slax-1.5-dev/applications/bin/linuxGccDPOpt/alternateSteadyReactingFoam"

[NewKid]

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5-dev |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Exec : alternateSteadyReactingFoam
Date : Dec 28 2010
Time : 09:42:34
Host : slax
PID : 9423
Case : /OpenFOAM/OpenFOAM-1.5-dev/applications/solvers/AlternateChemistry/Steady/firstSample
nProcs : 1

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

--> FOAM Warning :
From function dlLibraryTable::open(const fileName& functionLibName)
in file db/dlLibraryTable/dlLibraryTable.C at line 86
could not load libcompressibleFluxBCs.so: cannot open shared object file: No such file or directory
Create mesh for time = 0

Reading chemistry properties


Reading environmentalProperties

Reading thermophysicalProperties
Selecting thermodynamics package hMixtureThermo<canteraMixture>
Reading from Cantera-File "/OpenFOAM/OpenFOAM-1.5-dev/applications/solvers/AlternateChemistry/Steady/firstSample/constant/mix.cti" the mixture mix
Reading from Cantera-File "/OpenFOAM/OpenFOAM-1.5-dev/applications/solvers/AlternateChemistry/Steady/firstSample/constant/mix.cti" the mixture mix
Reading field U

Reading/calculating face flux field phi

Creating turbulence model.

Selecting RAS turbulence model kEpsilon
kEpsilonCoeffs
{
Cmu 0.09;
C1 1.44;
C2 1.92;
C3 -0.33;
alphah 1;
alphak 1;
alphaEps 0.76923;
}

Constructing chemical mechanism
Choosing the chemistry engine
Selecting chemistry engine canteraLocalTimeChemistryModel
with STEADY chemistry model

Starting time loop

Time = 1

Solving chemistry
Characteristic time of chemistry: 0.1
smoothSolver: Solving for Ux, Initial residual = 1, Final residual = 0.000958722, No Iterations 2
smoothSolver: Solving for Uy, Initial residual = 1, Final residual = 0.000662575, No Iterations 2
PBiCG: Solving for H2, Initial residual = 0.999962, Final residual = 0.00552089, No Iterations 1
PBiCG: Solving for H, Initial residual = 0.999987, Final residual = 0.00256162, No Iterations 1
PBiCG: Solving for O, Initial residual = 0.999985, Final residual = 0.00256161, No Iterations 1
PBiCG: Solving for O2, Initial residual = 1, Final residual = 0.00552054, No Iterations 1
PBiCG: Solving for OH, Initial residual = 0.999987, Final residual = 0.00256162, No Iterations 1
PBiCG: Solving for H2O, Initial residual = 0.999994, Final residual = 0.00256163, No Iterations 1
PBiCG: Solving for HO2, Initial residual = 1, Final residual = 0.00256165, No Iterations 1
PBiCG: Solving for H2O2, Initial residual = 0.346973, Final residual = 0.000888823, No Iterations 1
PBiCG: Solving for AR, Initial residual = 1.7173e-11, Final residual = 1.7173e-11, No Iterations 0
Max summe Yi = max((0*H2)) [0 0 0 0 0 0 0] 0.035 Min summe Yi = min((0*H2)) [0 0 0 0 0 0 0] 0.035
Fixed kappa in 0 cells due to large deltaY

#0 Foam::error::printStack(Foam::Ostream&) in "/OpenFOAM/OpenFOAM-1.5-dev/lib/linuxGccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/OpenFOAM/OpenFOAM-1.5-dev/lib/linuxGccDPOpt/libOpenFOAM.so"
#2 Uninterpreted:
#3 Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::operator=(Foam::tmp<Foam::Geometri cField<double, Foam::fvPatchField, Foam::volMesh> > const&) in "/home/slax/OpenFOAM/slax-1.5-dev/applications/bin/linuxGccDPOpt/alternateSteadyReactingFoam"
#4 main in "/home/slax/OpenFOAM/slax-1.5-dev/applications/bin/linuxGccDPOpt/alternateSteadyReactingFoam"
#5 __libc_start_main in "/lib/libc.so.6"
#6 _start in "/home/slax/OpenFOAM/slax-1.5-dev/applications/bin/linuxGccDPOpt/alternateSteadyReactingFoam"

[gschaider]

Look at your conf-files. You specified a inert specie that is not part of the gas mix. When the solver tries to normalize for that it tries to access a field that isn't there and produces a segFault.

Surprised that the solver doesn't check for that, but obviously it doesn't

Bernhard

[NewKid]

Thank you.
I modified the source of cantera, I'll fix it ASAP.

[NewKid]

Bernhard, I've got your point, those species in mix.cti file are not in gasThermo file, right? Cantera needs the content of gasThermo file to complete computation.
Now I wonder what the content of gasThermo file means, and where can I get those right numbers?
In the thermophysicalProperties file, there are two places related to gasThermo file, what's the difference?

[NewKid]

I've got it running, but the temperature is too high

[N. A.]

Hello Folks,

I was wondering if any one can confirm following:
Q1. what are the units of pre-exponential factor (A) and activation energy (E) that is given in input file foam.inp for foamchemistry reader.
Q2. what are the units of coefficient that are given in foam.dat (file that has thermo data of the species).

I am asking this as I want to modify the existing foam.inp and foam.dat from coalchemistryfoam for one of cases for my gas phase chemistry.

thanks in advance.

cheers,
Nir