- Author:
- Soroush Safaei <ssaf006@aucklanduni.ac.nz>
- Date:
- 2017-01-24 18:17:17+13:00
- Desc:
- setting the parameters
- Permanent Source URI:
- https://models.cellml.org/workspace/297/rawfile/f306308900275d04fa30afb5d2e8cb97ea6d0027/BG/Acid_BG.cellml
<?xml version='1.0'?>
<model name="Acid_BG" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="Units.cellml">
<units name="per_mol" units_ref="per_mol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="mol_per_s" units_ref="mol_per_s"/>
<units name="per_C" units_ref="per_C"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="C_per_s" units_ref="C_per_s"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="per_m" units_ref="per_m"/>
<units name="m_per_s" units_ref="m_per_s"/>
<units name="mM" units_ref="mM"/>
<units name="per_mM" units_ref="per_mM"/>
<units name="mM_m_per_s" units_ref="mM_m_per_s"/>
<units name="mM_per_s" units_ref="mM_per_s"/>
</import>
<import xlink:href="StateDiagram.cellml">
<component component_ref="state" name="state"/>
</import>
<import xlink:href="Parameters.cellml">
<component component_ref="param" name="param"/>
</import>
<component name="module">
<variable name="time" private_interface="out" units="second"/>
<variable initial_value="2494.34" name="RT" private_interface="out" units="J_per_mol"/>
<variable initial_value="2" name="z" private_interface="out" units="dimensionless"/>
<variable initial_value="96485" name="F" private_interface="out" units="C_per_mol"/>
<!-- State variables-->
<variable name="q_0_CO2_o" private_interface="out" units="mM"/>
<variable initial_value="0" name="q_0_CO2_i" private_interface="out" units="mM"/>
<variable initial_value="0" name="q_0_HCO3_i" private_interface="out" units="mM"/>
<variable initial_value="0" name="q_0_HCO3_o" private_interface="out" units="mM"/>
<variable name="q_0_NH4_o" private_interface="out" units="mM"/>
<variable initial_value="0" name="q_0_NH4_i" private_interface="out" units="mM"/>
<variable initial_value="0" name="q_0_NH3_i" private_interface="out" units="mM"/>
<variable initial_value="0" name="q_0_NH3_o" private_interface="out" units="mM"/>
<variable initial_value="0.0000398" name="q_0_H_i" private_interface="out" units="mM"/>
<variable initial_value="0.0000199" name="q_0_H_o" private_interface="out" units="mM"/>
<variable name="q_CO2_o" private_interface="in" units="mM"/>
<variable name="q_CO2_i" private_interface="in" units="mM"/>
<variable name="q_HCO3_i" private_interface="in" units="mM"/>
<variable name="q_HCO3_o" private_interface="in" units="mM"/>
<variable name="q_NH4_o" private_interface="in" units="mM"/>
<variable name="q_NH4_i" private_interface="in" units="mM"/>
<variable name="q_NH3_i" private_interface="in" units="mM"/>
<variable name="q_NH3_o" private_interface="in" units="mM"/>
<variable name="q_H_i" private_interface="in" units="mM"/>
<variable name="q_H_o" private_interface="in" units="mM"/>
<variable name="v_Re1" private_interface="in" units="mM_m_per_s"/>
<variable name="v_Re2" private_interface="in" units="mM_per_s"/>
<variable name="v_Re3" private_interface="in" units="mM_m_per_s"/>
<variable name="v_Re4" private_interface="in" units="mM_m_per_s"/>
<variable name="v_Re5" private_interface="in" units="mM_per_s"/>
<variable name="v_Re6" private_interface="in" units="mM_m_per_s"/>
<variable name="v_Re7" private_interface="in" units="mM_m_per_s"/>
<variable name="i_Re1" units="C_per_s"/>
<variable name="i_Re2" units="C_per_s"/>
<variable name="i_Re3" units="C_per_s"/>
<variable name="i_Re4" units="C_per_s"/>
<variable name="i_Re5" units="C_per_s"/>
<variable name="i_Re6" units="C_per_s"/>
<variable name="i_Re7" units="C_per_s"/>
<variable name="pH_i" units="dimensionless"/>
<variable name="pH_o" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>pH_i</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="dimensionless">0.001</cn>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_o</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="dimensionless">0.001</cn>
<ci>q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re1</ci>
<apply>
<times/>
<ci>v_Re1</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re2</ci>
<apply>
<times/>
<ci>v_Re2</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re3</ci>
<apply>
<times/>
<ci>v_Re3</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re4</ci>
<apply>
<times/>
<ci>v_Re4</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re5</ci>
<apply>
<times/>
<ci>v_Re5</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re6</ci>
<apply>
<times/>
<ci>v_Re6</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>i_Re7</ci>
<apply>
<times/>
<ci>v_Re7</ci>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_0_NH4_o</ci>
<piecewise>
<piece>
<cn cellml:units="mM">10</cn>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">10</cn>
</apply>
<apply>
<leq/>
<ci>time</ci>
<cn cellml:units="second">600</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM">0.0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>q_0_CO2_o</ci>
<piecewise>
<piece>
<cn cellml:units="mM">1.1</cn>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">10</cn>
</apply>
<apply>
<leq/>
<ci>time</ci>
<cn cellml:units="second">600</cn>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<!-- Mapping to the BG state diagram-->
<connection>
<map_components component_1="module" component_2="state"/>
<map_variables variable_1="time" variable_2="t"/>
<map_variables variable_1="RT" variable_2="RT"/>
<map_variables variable_1="z" variable_2="z"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="q_0_CO2_o" variable_2="q1_init"/>
<map_variables variable_1="q_0_CO2_i" variable_2="q2_init"/>
<map_variables variable_1="q_0_HCO3_i" variable_2="q3_init"/>
<map_variables variable_1="q_0_HCO3_o" variable_2="q4_init"/>
<map_variables variable_1="q_0_NH4_o" variable_2="q5_init"/>
<map_variables variable_1="q_0_NH4_i" variable_2="q6_init"/>
<map_variables variable_1="q_0_NH3_i" variable_2="q7_init"/>
<map_variables variable_1="q_0_NH3_o" variable_2="q8_init"/>
<map_variables variable_1="q_0_H_i" variable_2="q9_init"/>
<map_variables variable_1="q_0_H_o" variable_2="q10_init"/>
<map_variables variable_1="q_CO2_o" variable_2="q1"/>
<map_variables variable_1="q_CO2_i" variable_2="q2"/>
<map_variables variable_1="q_HCO3_i" variable_2="q3"/>
<map_variables variable_1="q_HCO3_o" variable_2="q4"/>
<map_variables variable_1="q_NH4_o" variable_2="q5"/>
<map_variables variable_1="q_NH4_i" variable_2="q6"/>
<map_variables variable_1="q_NH3_i" variable_2="q7"/>
<map_variables variable_1="q_NH3_o" variable_2="q8"/>
<map_variables variable_1="q_H_i" variable_2="q9"/>
<map_variables variable_1="q_H_o" variable_2="q10"/>
<map_variables variable_1="v_Re1" variable_2="v_Re1"/>
<map_variables variable_1="v_Re2" variable_2="v_Re2"/>
<map_variables variable_1="v_Re3" variable_2="v_Re3"/>
<map_variables variable_1="v_Re4" variable_2="v_Re4"/>
<map_variables variable_1="v_Re5" variable_2="v_Re5"/>
<map_variables variable_1="v_Re6" variable_2="v_Re6"/>
<map_variables variable_1="v_Re7" variable_2="v_Re7"/>
</connection>
<!-- Mapping to the Parameters module-->
<connection>
<map_components component_1="param" component_2="state"/>
<map_variables variable_1="K_CO2_o" variable_2="K_q1"/>
<map_variables variable_1="K_CO2_i" variable_2="K_q2"/>
<map_variables variable_1="K_HCO3_i" variable_2="K_q3"/>
<map_variables variable_1="K_HCO3_o" variable_2="K_q4"/>
<map_variables variable_1="K_NH4_o" variable_2="K_q5"/>
<map_variables variable_1="K_NH4_i" variable_2="K_q6"/>
<map_variables variable_1="K_NH3_i" variable_2="K_q7"/>
<map_variables variable_1="K_NH3_o" variable_2="K_q8"/>
<map_variables variable_1="K_H_i" variable_2="K_q9"/>
<map_variables variable_1="K_H_o" variable_2="K_q10"/>
<map_variables variable_1="K_Re1" variable_2="K_Re1"/>
<map_variables variable_1="K_Re2" variable_2="K_Re2"/>
<map_variables variable_1="K_Re3" variable_2="K_Re3"/>
<map_variables variable_1="K_Re4" variable_2="K_Re4"/>
<map_variables variable_1="K_Re5" variable_2="K_Re5"/>
<map_variables variable_1="K_Re6" variable_2="K_Re6"/>
<map_variables variable_1="K_Re7" variable_2="K_Re7"/>
</connection>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="module">
<component_ref component="state"/>
<component_ref component="param"/>
</component_ref>
</group>
</model>
