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Fix typos
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tbeu committed Mar 4, 2015
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16 changes: 8 additions & 8 deletions Physiolibrary/Chemical.mo
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Expand Up @@ -3014,7 +3014,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
<pre><b>plotExpression(apply(-log10(CarbonDioxideInWater.H3O.solute)),&nbsp;false,&nbsp;&QUOT;pH&QUOT;,&nbsp;1);</b></pre>
<p><br>Please note, that OH- (and CO3^-2) can be neglected from electroneutrality calculation, because of very small concentrations (in physiological pH) anyway. </p>
<p>And if SID&GT;0 then also H3O+ can be also neglected from electroneutrality, because only bicarbonate anions HCO3- (or CO3^-2) are needed there to balance the electroneutrality.</p>
<p><br>The partial pressure of CO2 in gas are input parameter. Outputs are an amount of free disolved CO2 in liquid and an amount of HCO3-.</p>
<p><br>The partial pressure of CO2 in gas are input parameter. Outputs are an amount of free dissolved CO2 in liquid and an amount of HCO3-.</p>
<p><br>The titration slope der(pH)/der(SID)=17.5 1/(mol/L) at pH=7.4 and pCO2=40 mmHg.</p>
<p><br>Molar heat of formation (aqueous):</p>
<p>CO2: -413.5 kJ/mol (gas: -393.5 kJ/mol )</p>
Expand Down Expand Up @@ -3291,7 +3291,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
smooth=Smooth.None));
annotation ( Documentation(info="<html>
<p>Henderson-Hasselbalch equation in ideal buffered solution, where pH remains constant.</p>
<p>The partial pressure of CO2 in gas are input parameter. Outputs are an amount of free disolved CO2 in liquid and an amount of HCO3-.</p>
<p>The partial pressure of CO2 in gas are input parameter. Outputs are an amount of free dissolved CO2 in liquid and an amount of HCO3-.</p>
</html>", revisions="<html>
<p><i>2014</i></p>
<p>Marek Matejak, Charles University, Prague, Czech Republic </p>
Expand Down Expand Up @@ -3868,7 +3868,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
</tr>
<tr>
<td><p>T<sub>K</sub></p></td>
<td><p>base temperature of tabulated coeficients</p></td>
<td><p>base temperature of tabulated coefficients</p></td>
</tr>
<tr>
<td><p>&omega;</p></td>
Expand Down Expand Up @@ -4004,7 +4004,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
</tr>
<tr>
<td><p>T<sub>K</sub></p></td>
<td><p>base temperature of tabulated coeficients</p></td>
<td><p>base temperature of tabulated coefficients</p></td>
</tr>
<tr>
<td><p>&Omega;</p></td>
Expand Down Expand Up @@ -4198,7 +4198,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
extends Chemical.Interfaces.ConditionalVolume;

parameter Integer NumberOfSubunits=1
"Number of independent subunits occuring in molecule";
"Number of independent subunits occurring in molecule";

Chemical.Interfaces.ChemicalPort_a specificForm
"Specific form composed with subunits form of subunitSpiecies" annotation (Placement(
Expand Down Expand Up @@ -4237,7 +4237,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
annotation(Evaluate=true, HideResult=true, choices(__Dymola_checkBox=true),Dialog(group="External inputs/outputs",tab="Heat"));

parameter Types.MolarEnergy SubunitEnthalpies[NumberOfSubunits]=zeros(NumberOfSubunits)
"Enthalpy changes of substances (can relative to one choosen specific form of chemical substance in the system) if useEnthalpiesInput=false"
"Enthalpy changes of substances (can relative to one chosen specific form of chemical substance in the system) if useEnthalpiesInput=false"
annotation (HideResult=not useInternalHeatsInput, Dialog(enable=not useInternalHeatsInput,tab="Heat"));

Types.RealIO.EnergyInput subunitInternalHeat[NumberOfSubunits](each start=0)=internalHeatOfSubunit if useInternalHeatsInput
Expand Down Expand Up @@ -4282,7 +4282,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
<p>This block identifies one specific chemical form of one macromolecule defined by forms of its subunits (one chosen chemical species - called <i>specie</i>).</p>
<p>Only main connector called <b>species </b>is designed for inflow and outflow of macromolecule to/from <i>system</i>. The concentration in this connector is the concentration of its specific <i>specie.</i></p>
<p>Connectors <b>subunitSpecies[:] </b>represent specific forms of the macromolecule subunit types. If the subnunit type occures n-times in macromolecule, the inflow is n-time greater than the inflow of macromolecule.</p>
<p><br>Initial total concentrations of subunits must be set to be right distribution of total macromolecule concentration. So the ratios between subunit concentrations are the ratios of their occurence in macromolecule. In equilibrium are this proporties fullfiled.</p>
<p><br>Initial total concentrations of subunits must be set to be right distribution of total macromolecule concentration. So the ratios between subunit concentrations are the ratios of their occurrence in macromolecule. In equilibrium are this proporties fulfilled.</p>
<p><br>For example: If the macromolecule has four identical independent subunits and each subunit can occur in two form F1 and F2, then the concentration of macromolecule <i>specie </i>composed only from four subunits in form F1 is <b>species.conc=</b>conc*fF1^4. </p>
<p>Where:</p>
<p>conc is totat concentration of macromolecule in <i>system</i> accumulated by <b>species.q</b>,</p>
Expand Down Expand Up @@ -5104,7 +5104,7 @@ Connector with one flow signal of type Real.
end ChemicalPort_b;

partial model OnePort
"Partial transfer of solute beween two ports without its accumulation"
"Partial transfer of solute between two ports without its accumulation"

ChemicalPort_b q_out
annotation (Placement(transformation(extent={{90,-10},{110,10}})));
Expand Down
4 changes: 2 additions & 2 deletions Physiolibrary/Hydraulic.mo
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Expand Up @@ -511,7 +511,7 @@ package Hydraulic "Domain with Pressure and Volumetric Flow"
Physiolibrary.Types.RealIO.VolumeFlowRateOutput volumeflowrate
annotation (Placement(transformation(extent={{80,-10},{100,10}}),
iconTransformation(extent={{80,-10},{100,10}})));
discrete Time T0 "begining of cardiac cycle";
discrete Time T0 "beginning of cardiac cycle";
Boolean b(start=false);
discrete Time HP "duration of cardiac cycle";
parameter Frequency HR=1.2;
Expand All @@ -522,7 +522,7 @@ package Hydraulic "Domain with Pressure and Volumetric Flow"
equation
b = time - pre(T0) >= pre(HP) "true if new cardiac cycle begins";
when {initial(),b} then
T0 = time "set begining of cardiac cycle";
T0 = time "set beginning of cardiac cycle";
HP = 1/HR "update length of carciac cycle";
TD2 = TD1 + (2/5)*HP "compute end time of systole";
end when;
Expand Down
4 changes: 2 additions & 2 deletions Physiolibrary/Population.mo
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Expand Up @@ -98,7 +98,7 @@ package Population
annotation ( HideResult=true, Dialog(group="Initialization"));

parameter Types.Population NominalPopulation = 1
"Numerical scale. Default is 1, but for huge amount of cells it should be any number in the apropriate numerical order of typical amount."
"Numerical scale. Default is 1, but for huge amount of cells it should be any number in the appropriate numerical order of typical amount."
annotation ( HideResult=true, Dialog(tab="Solver",group="Numerical support of very huge populations"));
parameter Types.PopulationChange NominalPopulationChange = 1/(60*60*24)
"Numerical scale. Default change is 1 individual per day, but for much faster or much slower chnages should be different."
Expand Down Expand Up @@ -382,7 +382,7 @@ Connector with one flow signal of type Real.
end PopulationPort_b;

partial model OnePort
"Partial change of population beween two ports without its accumulation"
"Partial change of population between two ports without its accumulation"

PopulationPort_b port_b
annotation (Placement(transformation(extent={{90,-10},{110,10}})));
Expand Down
2 changes: 1 addition & 1 deletion Physiolibrary/Resources/Install/SystemModeler/README.txt
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@@ -1,4 +1,4 @@
Be carefull, this installation is not tested! It should copy the Physiolibrary files into ProgramFiles/Wolfram/SystemModeler directory.
Be careful, this installation is not tested! It should copy the Physiolibrary files into ProgramFiles/Wolfram/SystemModeler directory.

To add library WITHOUT display units to Wolfram SystemModeler 4.0 please run "install.bat".

Expand Down
4 changes: 2 additions & 2 deletions Physiolibrary/SteadyStates.mo
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Expand Up @@ -1316,7 +1316,7 @@ package SteadyStates "Dynamic Simulation / Steady State"

if Simulation <> Types.SimulationType.SteadyState then
der(state) = change;
elseif not isDependent then /*** this test and equation exclusion could be done automatically, if the solver will be so smart that it removes all this dependend equations from the total equilibrated system. The most probable form of this dependent equation in equilibrium setting is (0 = 0). ***/
elseif not isDependent then /*** this test and equation exclusion could be done automatically, if the solver will be so smart that it removes all this dependent equations from the total equilibrated system. The most probable form of this dependent equation in equilibrium setting is (0 = 0). ***/
change = 0;
end if;

Expand Down Expand Up @@ -1419,7 +1419,7 @@ package SteadyStates "Dynamic Simulation / Steady State"
der(state) = change;
else
for i in 1:n loop
if not isDependent[n] then /*** this test and equation exclusion could be done automatically, if the solver will be so smart that it removes all this dependend equations from the total equilibrated system. The most probable form of this dependent equation in equilibrium setting is (0 = 0). ***/
if not isDependent[n] then /*** this test and equation exclusion could be done automatically, if the solver will be so smart that it removes all this dependent equations from the total equilibrated system. The most probable form of this dependent equation in equilibrium setting is (0 = 0). ***/
change[i] = 0;
end if;
end for;
Expand Down
2 changes: 1 addition & 1 deletion Physiolibrary/Thermal.mo
Original file line number Diff line number Diff line change
Expand Up @@ -642,7 +642,7 @@ i.e., it defines a fixed temperature as a boundary condition.
transformation(extent={{90,-10},{110,10}}), iconTransformation(
extent={{90,-10},{110,10}})));
parameter Types.SpecificEnergy dH=0
"Enthalpy of incomming substance (i.e. enthalpy of solvation)"; // or 2428344 for water vaporization
"Enthalpy of incoming substance (i.e. enthalpy of solvation)"; // or 2428344 for water vaporization
parameter Types.SpecificHeatCapacity SpecificHeat=4186.8
"Of inflowing medium"; //default heat capacity of water is 1 kcal/(degC.kg)

Expand Down
8 changes: 4 additions & 4 deletions Physiolibrary/Types.mo
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Expand Up @@ -34,7 +34,7 @@ package Types "Physiological units with nominals"
</tr>
<tr>
<td valign=\"top\"><p>Blocks</p></td>
<td valign=\"top\"><p>Usefull blocks, that are missing in package Modelica.Blocks (MSL 3.2), cubic interpolation curves, multiplication factors.</p></td>
<td valign=\"top\"><p>Useful blocks, that are missing in package Modelica.Blocks (MSL 3.2), cubic interpolation curves, multiplication factors.</p></td>
</tr>
<tr>
<td valign=\"top\"><p>Chemical</p></td>
Expand Down Expand Up @@ -6181,7 +6181,7 @@ The Real output y is a constant signal:
extends Modelica.Icons.Function;

input String name "Name of parameter";
input String storeUnit "Prefered units to store variable value";
input String storeUnit "Preferred units to store variable value";
input UnitConversions.RealTypeRecord[:] unitConversions = UnitConversions.RealTypeDef
"Unit conversions";

Expand Down Expand Up @@ -6214,7 +6214,7 @@ The Real output y is a constant signal:

input String name "Variable name";
input Real value "Variable value";
input String storeUnit "Prefered units to store variable value";
input String storeUnit "Preferred units to store variable value";
input UnitConversions.RealTypeRecord[:] unitConversions = UnitConversions.RealTypeDef
"Unit conversions";
//algorithm
Expand Down Expand Up @@ -6248,7 +6248,7 @@ The Real output y is a constant signal:
input Real initialValue "Initial variable value[in SI units]";
input Real finalValue "Final variable value[in SI units]";

input String storeUnit "Prefered units to store variable value";
input String storeUnit "Preferred units to store variable value";
input UnitConversions.RealTypeRecord[:] unitConversions = UnitConversions.RealTypeDef
"Unit conversions";
//algorithm
Expand Down
4 changes: 2 additions & 2 deletions Physiolibrary/package.mo
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Expand Up @@ -392,7 +392,7 @@ package Physiolibrary "Modelica library for Physiology (version 2.3.0)"
annotation (Documentation(info="<html>
<p><ul>
<li>migration to GITHub https://github.com/MarekMatejak/Physiolibrary from http://patf-biokyb.lf1.cuni.cz/repos/Modelica/Physiolibrary svn repository, commit 4947 </li>
<li><font style=\"color: #333333; \">The library uses the Modelica Standard Libary (MSL) version 3.2.</font></li>
<li><font style=\"color: #333333; \">The library uses the Modelica Standard Library (MSL) version 3.2.</font></li>
<li><font style=\"color: #333333; \">Contains nice physiological icons.</font></li>
<li><font style=\"color: #333333; \">Support for physiological units: min,kcal,mmHg,ml,mEq,..</font></li>
<li><font style=\"color: #333333; \">Base blocks for chemical, hydraulical, osmotic, thermal or mixed domains</font></li>
Expand Down Expand Up @@ -486,7 +486,7 @@ package Physiolibrary "Modelica library for Physiology (version 2.3.0)"
</tr>
<tr>
<td valign=\"top\"><p><a href=\"modelica://Physiolibrary.Blocks\">Blocks</a></p></td>
<td valign=\"top\"><p>Usefull blocks, that are missing in package Modelica.Blocks (MSL 3.2), cubic interpolation curves, multiplication factors.</p></td>
<td valign=\"top\"><p>Useful blocks, that are missing in package Modelica.Blocks (MSL 3.2), cubic interpolation curves, multiplication factors.</p></td>
</tr>
</table>
</html>"));
Expand Down
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -93,7 +93,7 @@ Download [Physiolibrary 2.3.0 (2015-02-16)](../../archive/v2.3.0.zip)
* Fix: references in overview (user's guide)

* [Version v2.0.2 (2014-01-26)](../../archive/v2.0.2.zip)
* Support for steady states calculation by energy/mass conservation laws or enviroment sources
* Support for steady states calculation by energy/mass conservation laws or environment sources
* Conditional inputs for each domain blocks
* Package States renamed to SteadyStates, added SteadyStates.Components
* Removed package Mixed
Expand All @@ -114,7 +114,7 @@ Download [Physiolibrary 2.3.0 (2015-02-16)](../../archive/v2.3.0.zip)
* New examples

* [Version v1.0.1 (2013-12-11)](../../archive/v1.0.1.zip)
* The library uses the Modelica Standard Libary (MSL) version 3.2.
* The library uses the Modelica Standard Library (MSL) version 3.2.
* Contains nice physiological icons.
* Support for physiological units: min,kcal,mmHg,ml,mEq,..
* Base blocks for chemical, hydraulical, osmotic, thermal or mixed domains
Expand Down

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