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surfchem - modified ck,py, production.py, utilities.py and converter.py #486

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937fea0
modified ck.py, production.py, converter.py
jAnirudh Mar 1, 2024
018ebd4
Modifed cksyme_str and cksyms_str methods in ck.py
jAnirudh Mar 6, 2024
3b4556d
Wrote utility functions and simplified elements list representation
jAnirudh Mar 8, 2024
c0adc01
Moved utility functions to utilities.py
jAnirudh Mar 14, 2024
f16d526
Conformed to black formatting
jAnirudh Mar 14, 2024
6e33900
created functions that return one value
jAnirudh Mar 23, 2024
22115bf
Regenerated non-qss mechanism files
jAnirudh Mar 23, 2024
8ed92aa
Ran isort for imports
jAnirudh Mar 23, 2024
047aa13
Merge branch 'development' into anirudh/surfchem
jAnirudh Mar 23, 2024
71e6917
Merge branch 'development' into anirudh/surfchem
jrood-nrel Apr 24, 2024
4119832
Update qss mechs
marchdf Apr 29, 2024
3ee65bf
Merge branch 'AMReX-Combustion:development' into anirudh/surfchem
jAnirudh Apr 29, 2024
f4add8e
Changed NUM_QSSA_GAS_SPECIES to NUM_GAS_SPECIES in ceptr/production.py
jAnirudh Apr 29, 2024
da30940
update qss mechs
marchdf Apr 29, 2024
6da8827
Merge branch 'development' into anirudh/surfchem
jAnirudh May 10, 2024
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1 change: 1 addition & 0 deletions Mechanisms/Aromatic_KrNara/mechanism.H
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,7 @@
#define NUM_GAS_ELEMENTS 5 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 158 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 1049 // Reactions in the homogeneous phase
#define NUM_QSS_GAS_SPECIES 0 // QSS species in the homogeneous phase

#define SITE_DENSITY 0.000000E+00 // mol/cm^2

Expand Down
18 changes: 9 additions & 9 deletions Mechanisms/Aromatic_KrNara/mechanism.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -877,7 +877,7 @@ CKINU(const int i, int& nspec, int ki[], int nu[])
}
}

// Returns the progress rates of each reactions
// Returns the progress rates of each reaction
// Given P, T, and mole fractions
void
CKKFKR(
Expand All @@ -887,20 +887,20 @@ CKKFKR(
amrex::Real q_f[],
amrex::Real q_r[])
{
amrex::Real c[158]; // temporary storage
amrex::Real c[NUM_SPECIES]; // temporary storage
amrex::Real PORT =
1e6 * P / (8.31446261815324e+07 * T); // 1e6 * P/RT so c goes to SI units
1e6 * P / (8.31446261815324e+07 * T); // convert to SI (mol/cm^3 to mol/m^3)

// Compute conversion, see Eq 10
for (int id = 0; id < 158; ++id) {
for (int id = 0; id < NUM_GAS_SPECIES; ++id) {
c[id] = x[id] * PORT;
}

// convert to chemkin units
progressRateFR(q_f, q_r, c, T);

// convert to chemkin units
for (int id = 0; id < 1049; ++id) {
for (int id = 0; id < NUM_GAS_REACTIONS; ++id) {
q_f[id] *= 1.0e-6;
q_r[id] *= 1.0e-6;
}
Expand All @@ -915,7 +915,7 @@ progressRateFR(
const amrex::Real invT = 1.0 / T;
const amrex::Real logT = log(T);
// compute the Gibbs free energy
amrex::Real g_RT[158];
amrex::Real g_RT[NUM_SPECIES];
gibbs(g_RT, T);

amrex::Real sc_qss[1];
Expand Down Expand Up @@ -947,7 +947,7 @@ CKNCF(int* ncf)
{
int kd = 5;
// Zero ncf
for (int id = 0; id < kd * 158; ++id) {
for (int id = 0; id < kd * NUM_GAS_SPECIES; ++id) {
ncf[id] = 0;
}

Expand Down Expand Up @@ -1627,7 +1627,7 @@ CKNCF(int* ncf)
void
CKSYME_STR(amrex::Vector<std::string>& ename)
{
ename.resize(5);
ename.resize(NUM_ELEMENTS);
ename[0] = "N";
ename[1] = "H";
ename[2] = "O";
Expand All @@ -1639,7 +1639,7 @@ CKSYME_STR(amrex::Vector<std::string>& ename)
void
CKSYMS_STR(amrex::Vector<std::string>& kname)
{
kname.resize(158);
kname.resize(NUM_SPECIES);
kname[0] = "H";
kname[1] = "O2";
kname[2] = "O";
Expand Down
7 changes: 4 additions & 3 deletions Mechanisms/BurkeDryer/mechanism.H
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,10 @@
#define CO_ID 11
#define CO2_ID 12

#define NUM_GAS_ELEMENTS 6 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 13 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 27 // Reactions in the homogeneous phase
#define NUM_GAS_ELEMENTS 6 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 13 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 27 // Reactions in the homogeneous phase
#define NUM_QSS_GAS_SPECIES 0 // QSS species in the homogeneous phase

#define SITE_DENSITY 0.000000E+00 // mol/cm^2

Expand Down
18 changes: 9 additions & 9 deletions Mechanisms/BurkeDryer/mechanism.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ CKINU(const int i, int& nspec, int ki[], int nu[])
}
}

// Returns the progress rates of each reactions
// Returns the progress rates of each reaction
// Given P, T, and mole fractions
void
CKKFKR(
Expand All @@ -58,20 +58,20 @@ CKKFKR(
amrex::Real q_f[],
amrex::Real q_r[])
{
amrex::Real c[13]; // temporary storage
amrex::Real c[NUM_SPECIES]; // temporary storage
amrex::Real PORT =
1e6 * P / (8.31446261815324e+07 * T); // 1e6 * P/RT so c goes to SI units
1e6 * P / (8.31446261815324e+07 * T); // convert to SI (mol/cm^3 to mol/m^3)

// Compute conversion, see Eq 10
for (int id = 0; id < 13; ++id) {
for (int id = 0; id < NUM_GAS_SPECIES; ++id) {
c[id] = x[id] * PORT;
}

// convert to chemkin units
progressRateFR(q_f, q_r, c, T);

// convert to chemkin units
for (int id = 0; id < 27; ++id) {
for (int id = 0; id < NUM_GAS_REACTIONS; ++id) {
q_f[id] *= 1.0e-6;
q_r[id] *= 1.0e-6;
}
Expand All @@ -86,7 +86,7 @@ progressRateFR(
const amrex::Real invT = 1.0 / T;
const amrex::Real logT = log(T);
// compute the Gibbs free energy
amrex::Real g_RT[13];
amrex::Real g_RT[NUM_SPECIES];
gibbs(g_RT, T);

amrex::Real sc_qss[1];
Expand Down Expand Up @@ -119,7 +119,7 @@ CKNCF(int* ncf)
{
int kd = 6;
// Zero ncf
for (int id = 0; id < kd * 13; ++id) {
for (int id = 0; id < kd * NUM_GAS_SPECIES; ++id) {
ncf[id] = 0;
}

Expand Down Expand Up @@ -173,7 +173,7 @@ CKNCF(int* ncf)
void
CKSYME_STR(amrex::Vector<std::string>& ename)
{
ename.resize(6);
ename.resize(NUM_ELEMENTS);
ename[0] = "H";
ename[1] = "O";
ename[2] = "N";
Expand All @@ -186,7 +186,7 @@ CKSYME_STR(amrex::Vector<std::string>& ename)
void
CKSYMS_STR(amrex::Vector<std::string>& kname)
{
kname.resize(13);
kname.resize(NUM_SPECIES);
kname[0] = "H";
kname[1] = "H2";
kname[2] = "O";
Expand Down
1 change: 1 addition & 0 deletions Mechanisms/C1-C2-NO/mechanism.H
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@
#define NUM_GAS_ELEMENTS 5 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 44 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 269 // Reactions in the homogeneous phase
#define NUM_QSS_GAS_SPECIES 0 // QSS species in the homogeneous phase

#define SITE_DENSITY 0.000000E+00 // mol/cm^2

Expand Down
18 changes: 9 additions & 9 deletions Mechanisms/C1-C2-NO/mechanism.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,7 @@ CKINU(const int i, int& nspec, int ki[], int nu[])
}
}

// Returns the progress rates of each reactions
// Returns the progress rates of each reaction
// Given P, T, and mole fractions
void
CKKFKR(
Expand All @@ -209,20 +209,20 @@ CKKFKR(
amrex::Real q_f[],
amrex::Real q_r[])
{
amrex::Real c[44]; // temporary storage
amrex::Real c[NUM_SPECIES]; // temporary storage
amrex::Real PORT =
1e6 * P / (8.31446261815324e+07 * T); // 1e6 * P/RT so c goes to SI units
1e6 * P / (8.31446261815324e+07 * T); // convert to SI (mol/cm^3 to mol/m^3)

// Compute conversion, see Eq 10
for (int id = 0; id < 44; ++id) {
for (int id = 0; id < NUM_GAS_SPECIES; ++id) {
c[id] = x[id] * PORT;
}

// convert to chemkin units
progressRateFR(q_f, q_r, c, T);

// convert to chemkin units
for (int id = 0; id < 269; ++id) {
for (int id = 0; id < NUM_GAS_REACTIONS; ++id) {
q_f[id] *= 1.0e-6;
q_r[id] *= 1.0e-6;
}
Expand All @@ -237,7 +237,7 @@ progressRateFR(
const amrex::Real invT = 1.0 / T;
const amrex::Real logT = log(T);
// compute the Gibbs free energy
amrex::Real g_RT[44];
amrex::Real g_RT[NUM_SPECIES];
gibbs(g_RT, T);

amrex::Real sc_qss[1];
Expand Down Expand Up @@ -269,7 +269,7 @@ CKNCF(int* ncf)
{
int kd = 5;
// Zero ncf
for (int id = 0; id < kd * 44; ++id) {
for (int id = 0; id < kd * NUM_GAS_SPECIES; ++id) {
ncf[id] = 0;
}

Expand Down Expand Up @@ -460,7 +460,7 @@ CKNCF(int* ncf)
void
CKSYME_STR(amrex::Vector<std::string>& ename)
{
ename.resize(5);
ename.resize(NUM_ELEMENTS);
ename[0] = "O";
ename[1] = "H";
ename[2] = "C";
Expand All @@ -472,7 +472,7 @@ CKSYME_STR(amrex::Vector<std::string>& ename)
void
CKSYMS_STR(amrex::Vector<std::string>& kname)
{
kname.resize(44);
kname.resize(NUM_SPECIES);
kname[0] = "AR";
kname[1] = "N2";
kname[2] = "H";
Expand Down
9 changes: 5 additions & 4 deletions Mechanisms/C1-C2-NO_qss/mechanism.H
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Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,10 @@
#define NCO_ID 37
#define CH3O2_ID 38

#define NUM_GAS_ELEMENTS 5 // Elements in the homogeneous phase
#define NUM_QSSA_GAS_SPECIES 39 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 269 // Reactions in the homogeneous phase
#define NUM_GAS_ELEMENTS 5 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 39 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 269 // Reactions in the homogeneous phase
#define NUM_QSS_GAS_SPECIES 5 // QSS species in the homogeneous phase

#define SITE_DENSITY 0.000000E+00 // mol/cm^2

Expand All @@ -64,7 +65,7 @@
#define NUM_SURFACE_REACTIONS 0 // Reactions in the heterogeneous phase

#define NUM_ELEMENTS (NUM_GAS_ELEMENTS + NUM_SURFACE_ELEMENTS)
#define NUM_SPECIES (NUM_QSSA_GAS_SPECIES + NUM_SURFACE_SPECIES)
#define NUM_SPECIES (NUM_GAS_SPECIES + NUM_SURFACE_SPECIES)
#define NUM_REACTIONS (NUM_GAS_REACTIONS + NUM_SURFACE_REACTIONS)

#define NUM_IONS 0
Expand Down
20 changes: 10 additions & 10 deletions Mechanisms/C1-C2-NO_qss/mechanism.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,7 @@ CKINU(const int i, int& nspec, int ki[], int nu[])
}
}

// Returns the progress rates of each reactions
// Returns the progress rates of each reaction
// Given P, T, and mole fractions
void
CKKFKR(
Expand All @@ -209,20 +209,20 @@ CKKFKR(
amrex::Real q_f[],
amrex::Real q_r[])
{
amrex::Real c[39]; // temporary storage
amrex::Real c[NUM_SPECIES]; // temporary storage
amrex::Real PORT =
1e6 * P / (8.31446261815324e+07 * T); // 1e6 * P/RT so c goes to SI units
1e6 * P / (8.31446261815324e+07 * T); // convert to SI (mol/cm^3 to mol/m^3)

// Compute conversion, see Eq 10
for (int id = 0; id < 39; ++id) {
for (int id = 0; id < NUM_GAS_SPECIES; ++id) {
c[id] = x[id] * PORT;
}

// convert to chemkin units
progressRateFR(q_f, q_r, c, T);

// convert to chemkin units
for (int id = 0; id < 269; ++id) {
for (int id = 0; id < NUM_GAS_REACTIONS; ++id) {
q_f[id] *= 1.0e-6;
q_r[id] *= 1.0e-6;
}
Expand All @@ -237,9 +237,9 @@ progressRateFR(
const amrex::Real invT = 1.0 / T;
const amrex::Real logT = log(T);
// compute the Gibbs free energy
amrex::Real g_RT[39];
amrex::Real g_RT[NUM_SPECIES];
gibbs(g_RT, T);
amrex::Real g_RT_qss[5];
amrex::Real g_RT_qss[NUM_GAS_SPECIES];
gibbs_qss(g_RT_qss, T);

amrex::Real sc_qss[5];
Expand Down Expand Up @@ -276,7 +276,7 @@ CKNCF(int* ncf)
{
int kd = 5;
// Zero ncf
for (int id = 0; id < kd * 39; ++id) {
for (int id = 0; id < kd * NUM_GAS_SPECIES; ++id) {
ncf[id] = 0;
}

Expand Down Expand Up @@ -448,7 +448,7 @@ CKNCF(int* ncf)
void
CKSYME_STR(amrex::Vector<std::string>& ename)
{
ename.resize(5);
ename.resize(NUM_ELEMENTS);
ename[0] = "Ar";
ename[1] = "N";
ename[2] = "H";
Expand All @@ -460,7 +460,7 @@ CKSYME_STR(amrex::Vector<std::string>& ename)
void
CKSYMS_STR(amrex::Vector<std::string>& kname)
{
kname.resize(39);
kname.resize(NUM_SPECIES);
kname[0] = "AR";
kname[1] = "N2";
kname[2] = "H";
Expand Down
7 changes: 4 additions & 3 deletions Mechanisms/CH4_lean/mechanism.H
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Original file line number Diff line number Diff line change
Expand Up @@ -31,9 +31,10 @@
#define CH2OH_ID 15
#define N2_ID 16

#define NUM_GAS_ELEMENTS 5 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 17 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 73 // Reactions in the homogeneous phase
#define NUM_GAS_ELEMENTS 5 // Elements in the homogeneous phase
#define NUM_GAS_SPECIES 17 // Species in the homogeneous phase
#define NUM_GAS_REACTIONS 73 // Reactions in the homogeneous phase
#define NUM_QSS_GAS_SPECIES 0 // QSS species in the homogeneous phase

#define SITE_DENSITY 0.000000E+00 // mol/cm^2

Expand Down
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