- Author:
- Soroush Safaei <ssaf006@aucklanduni.ac.nz>
- Date:
- 2017-02-07 18:49:53+13:00
- Desc:
- adding diffusion modules
- Permanent Source URI:
- https://models.cellml.org/workspace/297/rawfile/0794c63dd492251fd095f8308b59d84f63b930b2/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="mol_per_m3" units_ref="mol_per_m3"/>
<units name="mol_per_m3_s" units_ref="mol_per_m3_s"/>
<units name="per_m" units_ref="per_m"/>
<units name="per_s" units_ref="per_s"/>
<units name="m_per_s" units_ref="m_per_s"/>
<units name="m3_per_mol" units_ref="m3_per_mol"/>
<units name="J_per_mol_K" units_ref="J_per_mol_K"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
</import>
<import xlink:href="Diffusion_module.cellml">
<component component_ref="module" name="CO2_Diffusion"/>
</import>
<import xlink:href="Diffusion_module.cellml">
<component component_ref="module" name="NH3_Diffusion"/>
</import>
<component name="AcidBase">
<variable initial_value="1.0" name="q_CO2_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0.0" name="q_CO2_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="1.0" name="q_HCO3_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0.0" name="q_HCO3_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="1" name="q_NH4_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_NH4_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="1" name="q_NH3_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_NH3_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="3.98e-5" name="q_H_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="1.99e-5" name="q_H_o" public_interface="out" units="mol_per_m3"/>
<variable name="v_Re_1" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_2" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_3" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_4" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_5" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_6" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_7" public_interface="in" units="mol_per_m3_s"/>
<variable initial_value="6e-5" name="K_Re_1" public_interface="out" units="m_per_s"/>
<variable initial_value="25152" name="K_Re_2" public_interface="out" units="mol_per_m3_s"/>
<variable initial_value="5e-9" name="K_Re_3" public_interface="out" units="m_per_s"/>
<variable initial_value="1e-6" name="K_Re_4" public_interface="out" units="m_per_s"/>
<variable initial_value="28057.8" name="K_Re_5" public_interface="out" units="mol_per_m3_s"/>
<variable initial_value="6e-5" name="K_Re_6" public_interface="out" units="m_per_s"/>
<variable initial_value="100" name="K_Re_7" public_interface="out" units="m_per_s"/>
<variable initial_value="8000" name="rho" public_interface="out" units="per_m"/>
<variable name="pH_o" units="dimensionless"/>
<variable name="pH_i" units="dimensionless"/>
<variable name="t" public_interface="out" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_CO2_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_CO2_i</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_1</ci>
<ci>v_Re_2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_HCO3_i</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_2</ci>
<ci>v_Re_3</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_HCO3_o</ci>
</apply>
<ci>v_Re_3</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH4_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_4</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH4_i</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_4</ci>
<ci>v_Re_5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH3_i</ci>
</apply>
<apply>
<plus/>
<ci>v_Re_5</ci>
<ci>v_Re_6</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH3_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_6</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_i</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v_Re_2</ci>
<ci>v_Re_5</ci>
</apply>
<ci>v_Re_7</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_o</ci>
</apply>
<ci>v_Re_7</ci>
</apply>
<apply>
<eq/>
<ci>pH_o</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="dimensionless" type="e-notation">1<sep/>-3</cn>
<ci>q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_i</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="dimensionless" type="e-notation">1<sep/>-3</cn>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="module">
<variable initial_value="0.00000006" name="u_E" units="J_per_C"/>
<variable name="q_CO2_o" public_interface="in" units="mol_per_m3"/>
<variable name="q_CO2_i" public_interface="in" units="mol_per_m3"/>
<variable name="q_HCO3_i" public_interface="in" units="mol_per_m3"/>
<variable name="q_HCO3_o" public_interface="in" units="mol_per_m3"/>
<variable name="q_NH4_o" public_interface="in" units="mol_per_m3"/>
<variable name="q_NH4_i" public_interface="in" units="mol_per_m3"/>
<variable name="q_NH3_i" public_interface="in" units="mol_per_m3"/>
<variable name="q_NH3_o" public_interface="in" units="mol_per_m3"/>
<variable name="q_H_i" public_interface="in" units="mol_per_m3"/>
<variable name="q_H_o" public_interface="in" units="mol_per_m3"/>
<variable name="v_Re_2" public_interface="out" units="mol_per_m3_s"/>
<variable name="v_Re_3" public_interface="out" units="mol_per_m3_s"/>
<variable name="v_Re_4" public_interface="out" units="mol_per_m3_s"/>
<variable name="v_Re_5" public_interface="out" units="mol_per_m3_s"/>
<variable name="v_Re_7" public_interface="out" units="mol_per_m3_s"/>
<variable initial_value="1" name="K_CO2_o" units="m3_per_mol"/>
<variable initial_value="0.0003976" name="K_CO2_i" units="m3_per_mol"/>
<variable initial_value="0.0025152" name="K_HCO3_i" units="m3_per_mol"/>
<variable initial_value="1" name="K_HCO3_o" units="m3_per_mol"/>
<variable initial_value="1" name="K_NH4_o" units="m3_per_mol"/>
<variable initial_value="0.0000356" name="K_NH4_i" units="m3_per_mol"/>
<variable initial_value="0.0280578" name="K_NH3_i" units="m3_per_mol"/>
<variable initial_value="1" name="K_NH3_o" units="m3_per_mol"/>
<variable initial_value="0.07057" name="K_H_i" units="m3_per_mol"/>
<variable initial_value="0.001" name="K_H_o" units="m3_per_mol"/>
<variable name="K_Re_2" public_interface="in" units="mol_per_m3_s"/>
<variable name="K_Re_3" public_interface="in" units="m_per_s"/>
<variable name="K_Re_4" public_interface="in" units="m_per_s"/>
<variable name="K_Re_5" public_interface="in" units="mol_per_m3_s"/>
<variable name="K_Re_7" public_interface="in" units="m_per_s"/>
<variable name="rho" public_interface="in" units="per_m"/>
<variable initial_value="96485" name="F" units="C_per_mol"/>
<variable initial_value="8.314" name="R" units="J_per_mol_K"/>
<variable initial_value="300" name="T" units="kelvin"/>
<variable name="e1" units="dimensionless"/>
<variable name="t" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>e1</ci>
<apply>
<times/>
<apply>
<divide/>
<ci>u_E</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_2</ci>
<apply>
<times/>
<ci>K_Re_2</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_CO2_i</ci>
<ci>q_CO2_i</ci>
</apply>
<apply>
<times/>
<ci>K_HCO3_i</ci>
<ci>q_HCO3_i</ci>
<ci>K_H_i</ci>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_3</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Re_3</ci>
<ci>rho</ci>
<ci>e1</ci>
<apply>
<minus/>
<ci>q_HCO3_i</ci>
<apply>
<times/>
<ci>q_HCO3_o</ci>
<apply>
<exp/>
<apply>
<minus/>
<ci>e1</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<exp/>
<apply>
<minus/>
<ci>e1</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_4</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Re_4</ci>
<ci>rho</ci>
<ci>e1</ci>
<apply>
<minus/>
<ci>q_NH4_o</ci>
<apply>
<times/>
<ci>q_NH4_i</ci>
<apply>
<exp/>
<apply>
<minus/>
<ci>e1</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<exp/>
<apply>
<minus/>
<ci>e1</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_5</ci>
<apply>
<times/>
<ci>K_Re_5</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_NH4_i</ci>
<ci>q_NH4_i</ci>
</apply>
<apply>
<times/>
<ci>K_NH3_i</ci>
<ci>q_NH3_i</ci>
<ci>K_H_i</ci>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_7</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>K_Re_7</ci>
<ci>rho</ci>
<ci>e1</ci>
<apply>
<minus/>
<ci>q_H_i</ci>
<apply>
<times/>
<ci>q_H_o</ci>
<apply>
<exp/>
<apply>
<minus/>
<ci>e1</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<exp/>
<apply>
<minus/>
<ci>e1</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="AcidBase" component_2="module"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="q_CO2_o" variable_2="q_CO2_o"/>
<map_variables variable_1="q_CO2_i" variable_2="q_CO2_i"/>
<map_variables variable_1="q_HCO3_i" variable_2="q_HCO3_i"/>
<map_variables variable_1="q_HCO3_o" variable_2="q_HCO3_o"/>
<map_variables variable_1="q_NH4_o" variable_2="q_NH4_o"/>
<map_variables variable_1="q_NH4_i" variable_2="q_NH4_i"/>
<map_variables variable_1="q_NH3_i" variable_2="q_NH3_i"/>
<map_variables variable_1="q_NH3_o" variable_2="q_NH3_o"/>
<map_variables variable_1="q_H_i" variable_2="q_H_i"/>
<map_variables variable_1="q_H_o" variable_2="q_H_o"/>
<map_variables variable_1="v_Re_2" variable_2="v_Re_2"/>
<map_variables variable_1="v_Re_3" variable_2="v_Re_3"/>
<map_variables variable_1="v_Re_4" variable_2="v_Re_4"/>
<map_variables variable_1="v_Re_5" variable_2="v_Re_5"/>
<map_variables variable_1="v_Re_7" variable_2="v_Re_7"/>
<map_variables variable_1="K_Re_2" variable_2="K_Re_2"/>
<map_variables variable_1="K_Re_3" variable_2="K_Re_3"/>
<map_variables variable_1="K_Re_4" variable_2="K_Re_4"/>
<map_variables variable_1="K_Re_5" variable_2="K_Re_5"/>
<map_variables variable_1="K_Re_7" variable_2="K_Re_7"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="CO2_Diffusion" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="q_o" variable_2="q_CO2_o"/>
<map_variables variable_1="q_i" variable_2="q_CO2_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_1"/>
<map_variables variable_1="K_Re" variable_2="K_Re_1"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="NH3_Diffusion" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="q_o" variable_2="q_NH3_o"/>
<map_variables variable_1="q_i" variable_2="q_NH3_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_6"/>
<map_variables variable_1="K_Re" variable_2="K_Re_6"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
</model>