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switch to Chemical 1.4.1
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@MarekMatejak
MarekMatejak committed Nov 23, 2023
1 parent 15dd529 commit 6433127
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Showing 3 changed files with 37 additions and 18 deletions.
2 changes: 1 addition & 1 deletion Chemical
Submodule Chemical updated 4 files
+2 −2 Chemical/libraryinfo.mos
+38 −28 Chemical/package.mo
+1 −1 LICENSE
+3 −3 README.md
51 changes: 35 additions & 16 deletions Physiolibrary/Media.mo
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Original file line number Diff line number Diff line change
Expand Up @@ -313,8 +313,8 @@ package Media "Models of physiological fluids"

aH2O_P = aH2O_E "osmolarity";

aH2O_P = state.X[i("H2O_P")]*Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule((state.X[i("H2O_P")]/pct)*1,x_P*1,Substances.Water,T,p,v) / (pct*x_P);
aH2O_E = state.X[i("H2O_E")]*Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule((state.X[i("H2O_E")]/hct)*1,x_E*1,Substances.Water,T,p,v) / (hct*x_E);
aH2O_P = state.X[i("H2O_P")]*Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(Substances.Water,T,p,v,0,(state.X[i("H2O_P")]/pct)*1,x_P*1) / (pct*x_P);
aH2O_E = state.X[i("H2O_E")]*Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(Substances.Water,T,p,v,0,(state.X[i("H2O_E")]/hct)*1,x_E*1) / (hct*x_E);

pct = plasmaMassFraction(state);
hct = formedElementsMassFraction(state);
Expand Down Expand Up @@ -499,10 +499,10 @@ package Media "Models of physiological fluids"
nSolution_E = x_E;


state.X[i("H2O_P")] = aH2O_P*pct*x_P/Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(massH2O_P,nSolution_P,Substances.Water,T,p,v);
state.X[i("H2O_E")] = aH2O_E*hct*x_E/Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(massH2O_E,nSolution_E,Substances.Water,T,p,v);
state.X[i("H2O_P")] = aH2O_P*pct*x_P/Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(Substances.Water,T,p,v,0,massH2O_P,nSolution_P);
state.X[i("H2O_E")] = aH2O_E*hct*x_E/Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(Substances.Water,T,p,v,0,massH2O_E,nSolution_E);
H2O_Ery2Plasma = KC_H2O*(Modelica.Constants.R*T*log(aH2O_E/aH2O_P)) "Osmolarity equilibration rate";
expected_XH2O_E = aH2O_P*hct*x_E/Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(massH2O_E,nSolution_E,Substances.Water,T,p,v) "Debug of osmolarity equilibration";
expected_XH2O_E = aH2O_P*hct*x_E/Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(Substances.Water,T,p,v,0,massH2O_E,nSolution_E) "Debug of osmolarity equilibration";


x_P =plasmaSpecificAmountOfParticles(state);
Expand Down Expand Up @@ -581,7 +581,7 @@ package Media "Models of physiological fluids"
pK_WaterSelfIonization = -log10(exp((Chemical.Interfaces.Incompressible.electroChemicalPotentialPure(
Substances.Water, T, p, v)
+ Modelica.Constants.R*T*log(
(Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(massH2O_P,nSolution_P,Substances.Water, T, p, v)
(Chemical.Interfaces.Incompressible.specificAmountOfFreeBaseMolecule(Substances.Water, T, p, v, 0, massH2O_P, nSolution_P)
* massH2O_P)/nSolution_P)
- Chemical.Interfaces.Incompressible.electroChemicalPotentialPure(Substances.OH, T, p, v)
- Chemical.Interfaces.Incompressible.electroChemicalPotentialPure(Substances.H, T, p, v))/(Modelica.Constants.R*T)))
Expand Down Expand Up @@ -843,6 +843,8 @@ package Media "Models of physiological fluids"
"inorganic phosphates concentration in blood plasma";
input Types.Concentration _cDPG=cDPG(state) "DPG concentration in blood plasma";
input Types.Concentration _SID=SID(state) "strong ion difference of blood";
input Types.Concentration _SID_P=plasmaSID(state) "strong ion difference of blood plasma";
input Types.Concentration _SID_E=formedElementsSID(state) "strong ion difference of blood formed elements";

constant Physiolibrary.Types.Temperature T0=273.15 + 37 "normal temperature";
constant Physiolibrary.Types.pH pH0=7.4 "normal pH";
Expand All @@ -853,7 +855,7 @@ package Media "Models of physiological fluids"
Physiolibrary.Types.Concentration NSIDP;
Physiolibrary.Types.Concentration NSIDE;
Physiolibrary.Types.Concentration NSID;
Physiolibrary.Types.Concentration BEox;
Physiolibrary.Types.Concentration BEox, BEox_P, BEox_E;
Physiolibrary.Types.Concentration cdCO2;

Physiolibrary.Types.pH pH_ery;
Expand Down Expand Up @@ -1007,12 +1009,11 @@ package Media "Models of physiological fluids"
"Bohr's protons = number of protons released during deoxygenation of one hemoglobin subunit";
dTH = sO2*dH + sCO2D*(1+1/(1+10^(pH-pKzD)))
"Total titration shift with Bohr protons and carbamination";
/*
sHO =
"H+ saturation of oxy-hemoglobin";
sHD =
"H+ saturation of deoxy-hemoglobin";
*/

BEox_P = _SID_P - NSIDP;
BEox_E = _SID_E + dTH*ceHb - NSIDE;


annotation (Icon(coordinateSystem(preserveAspectRatio=false)), Diagram(
coordinateSystem(preserveAspectRatio=false)),
Documentation(info="<html>
Expand Down Expand Up @@ -1628,6 +1629,24 @@ package Media "Models of physiological fluids"
end plasmaMassFractionWithoutOther;


replaceable function plasmaSID "Strong ion difference of blood plasma"
extends GetConcentration;
algorithm
C := plasmaDensity(state) * (
state.X[i("Na_P")]/Na.MolarWeight +
state.X[i("K_P")]/K.MolarWeight -
state.X[i("Cl_P")]/Cl.MolarWeight -
SO4.z*state.X[i("SO4_P")]/SO4.MolarWeight) / plasmacrit(state);
end plasmaSID;

replaceable function formedElementsSID "Strong ion difference of blood formed elements"
extends GetConcentration;
algorithm
C := density(state) * (
state.X[i("Na_E")]/Na.MolarWeight +
state.X[i("K_E")]/K.MolarWeight -
state.X[i("Cl_E")]/Cl.MolarWeight) / hematocrit(state);
end formedElementsSID;
annotation (Documentation(info="<html>
<p>Adding new substance to blood model:</p>
<p><br>- add to Blood.substanceNames</p>
Expand Down Expand Up @@ -1886,7 +1905,7 @@ Modelica source.

NpM = stateOfMatter.specificAmountOfParticles(substanceData,T=T,p=p);

x_baseMolecule = X.*stateOfMatter.specificAmountOfFreeBaseMolecule(0,0,substanceData,T=T,p=p)./(X*NpM);
x_baseMolecule = X.*stateOfMatter.specificAmountOfFreeBaseMolecule(substanceData,T=T,p=p)./(X*NpM);

T = stateOfMatter.solution_temperature(
substanceData,
Expand Down Expand Up @@ -2156,8 +2175,8 @@ Modelica source.
equation
NpM = stateOfMatter.specificAmountOfParticles(substanceData,T=T,p=p);

nSolution = X*NpM;
x_baseMolecule = X.*stateOfMatter.specificAmountOfFreeBaseMolecule(X,nSolution,substanceData,T=T,p=p)./(X*NpM);
nSolution = X*NpM*1;
x_baseMolecule = X.*stateOfMatter.specificAmountOfFreeBaseMolecule(substanceData,T=T,p=p,v=0,I=0,massH2O=X,nSolution=nSolution)./(X*NpM);

T = stateOfMatter.solution_temperature(
substanceData,
Expand Down
2 changes: 1 addition & 1 deletion Physiolibrary/package.mo
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ package Physiolibrary "System biology, integrative physiology and pathophysiolog
versionDate = "2023-10-10",
dateModified = "2023-10-10 1:00:00Z",
uses(Modelica(version = "4.0.0"), Complex(version = "4.0.0"),
Chemical(version="1.5.0-alpha")),
Chemical(version="1.4.1")),
conversion(
from(version = "BioChem-1.0.1", script = "modelica://Physiolibrary/Resources/Scripts/Dymola/ConvertBioChem_1.0.1_to_Physiolibrary_2.3.mos", to = "3.0.0"),
from(version = "0.4980", script = "modelica://Physiolibrary/Resources/Scripts/Dymola/ConvertPhysiolibrary_from_0.4980_to_2.3.mos", to = "3.0.0"),
Expand Down

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