def redefineFileds(self):
# Create tuples for species
speciesTuples = (('time', F.Quantity('Time', default=(1, 's'))), )
datasetColumns = ['t']
for itSpecies in self.species:
X = itSpecies[0] #species variable
speciesTuple = (('%s' % X,
F.Quantity('Bio_MolarConcentration',
default=(1, 'M'))), )
speciesTuples += speciesTuple
datasetColumns.append('%s' % X)
# Redefine Fields
redefinedStorage = F.HdfStorage(
hdfFile='BioReactors_SimulationResults.h5',
hdfGroup='/BiochemicalReactions',
datasetColumns=datasetColumns)
self.redefineField('storage', 'storageVG', redefinedStorage)
redefinedPlot = F.PlotView(speciesTuples,
label='Plot',
options={
'ylabel': 'concentration',
'title': ''
},
useHdfStorage=True,
storage='storage')
self.redefineField('plot', 'resultsVG', redefinedPlot)
redefinedTable = F.TableView(
speciesTuples,
label='Table',
options={'formats': ['0.000', '0.000', '0.000', '0.000']},
useHdfStorage=True,
storage='storage')
self.redefineField('table', 'resultsVG', redefinedTable)
class ADM1H2CH4Bioreactors(NumericalModel):
label = "(H2,CH4) Bioreactors"
description = F.ModelDescription(
"A model of the process of hydrogen and methane production by anaerobic digestion of organic wastes in a cascade of two continuously stirred bioreactors.",
show=True)
figure = F.ModelFigure(
src="BioReactors/img/ModuleImages/ADM1H2CH4Bioreactors.png", show=True)
async = True
progressOptions = {'suffix': 'day', 'fractionOutput': True}
#1. ############ Inputs ###############
#1.1 Fields - Input values
parametersRH2 = F.SubModelGroup(H2Bioreactor,
'parametersSG',
label='Parameters (R-H2)')
concentrationsRH2 = F.SubModelGroup(H2Bioreactor,
'concentrationsSG',
label='Concentrations (R-H2)')
parametersRCH4 = F.SubModelGroup(CH4Bioreactor,
'parametersSG',
label='Parameters (R-CH4)')
concentrationsRCH4 = F.SubModelGroup(CH4Bioreactor,
'concentrationsSG',
label='Concentrations (R-CH4)')
#1.3 Fields - Settings
solverSettings = F.SubModelGroup(SolverSettings,
'FG',
label='H2 & CH4 - Bioreactors')
settingsSG = F.SuperGroup([solverSettings], label='Solver settings')
#1.4 Model view
exampleAction = A.ServerAction(
"loadEg",
label="Examples",
options=(
#('exampleDef', 'Reset to default values'),
('exampleADM1', 'Reset to ADM1 values'), ))
inputView = F.ModelView(
ioType="input",
superGroups=[
parametersRH2, concentrationsRH2, parametersRCH4,
concentrationsRCH4, settingsSG
],
autoFetch=True,
actionBar=A.ActionBar([exampleAction]),
)
#2. ############ Results ###############
storage = F.HdfStorage(hdfFile=DM.dataStorageFilePath,
hdfGroup=DM.dataStorageDatasetPath)
varTuples = (
('time', F.Quantity('Bio_Time', default=(1, 'day'))), #0
('S_su_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #1
('S_aa_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #2
('S_fa_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #3
('S_ac_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #4
('X_c_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #5
('X_ch_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #6
('X_pr_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #7
('X_li_RH2', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #8
('X_suaa_RH2', F.Quantity('Bio_MassConcentration',
default=(1, 'g/L'))), #9
('X_fa_RH2', F.Quantity('Bio_MassConcentration',
default=(1, 'g/L'))), #10
('intQ_h2_RH2',
F.Quantity('Bio_CODConcentration', default=(1, 'gCOD/L'))), #11
('S_ac_RCH4', F.Quantity('Bio_CODConcentration',
default=(1, 'gCOD/L'))), #12
('X_ac_RCH4', F.Quantity('Bio_MassConcentration',
default=(1, 'g/L'))), #13
('intQ_ch4_RCH4',
F.Quantity('Bio_CODConcentration', default=(1, 'gCOD/L'))), #14
('Q_h2_RH2',
F.Quantity('Bio_CODConcentrationFlowRate',
default=(1, 'gCOD/L/day'))), #15
('Q_ch4_RCH4',
F.Quantity('Bio_CODConcentrationFlowRate',
default=(1, 'gCOD/L/day'))), #16
('D_RH2', F.Quantity('Bio_TimeRate', default=(1, '1/day'))), #17
('D_RCH4', F.Quantity('Bio_TimeRate', default=(1, '1/day'))), #18
)
plot1RH2 = F.PlotView(
varTuples,
label='R-H2 (S<sub>su</sub>, S<sub>aa</sub>, S<sub>fa</sub>)',
options={'ylabel': None},
visibleColumns=[0, 1, 2, 3],
useHdfStorage=True,
storage='storage',
)
plot2RH2 = F.PlotView(
varTuples,
label='R-H2 (X<sub>ch</sub>, X<sub>pr</sub>, X<sub>li</sub>)',
options={'ylabel': None},
visibleColumns=[0, 6, 7, 8],
useHdfStorage=True,
storage='storage',
)
plot3RH2 = F.PlotView(
varTuples,
label='R-H2 (X<sub>su-aa</sub>,X<sub>fa</sub>)',
options={'ylabel': None},
visibleColumns=[0, 9, 10],
useHdfStorage=True,
storage='storage',
)
plot4RH2 = F.PlotView(
varTuples,
label='R-H2 (H<sub>2</sub>)',
options={'ylabel': None},
visibleColumns=[0, 11, 15],
useHdfStorage=True,
storage='storage',
)
plot1RCH4 = F.PlotView(
varTuples,
label='R-CH4 (S<sub>ac</sub>, X<sub>ac</sub>)',
options={'ylabel': None},
visibleColumns=[0, 12, 13],
useHdfStorage=True,
storage='storage',
)
plot2RCH4 = F.PlotView(
varTuples,
label='R-CH4 (CH<sub>4</sub>)',
options={'ylabel': None},
visibleColumns=[0, 14, 16],
useHdfStorage=True,
storage='storage',
)
plotD = F.PlotView(
varTuples,
label='(D<sub>RH2</sub>, D<sub>RCH4</sub>)',
options={'ylabel': None},
visibleColumns=[0, 17, 18],
useHdfStorage=True,
storage='storage',
)
table = F.TableView(
varTuples,
label='Table',
options={
'title': 'Bioreactors',
'formats': ['0.000']
},
useHdfStorage=True,
storage='storage',
)
storageVG = F.ViewGroup([storage], show="false")
resultsVG = F.ViewGroup([
plot1RH2, plot2RH2, plot3RH2, plot4RH2, plot1RCH4, plot2RCH4, plotD,
table
])
resultsSG = F.SuperGroup([resultsVG, storageVG], label='Results')
#2.1 Model view
resultView = F.ModelView(ioType="output", superGroups=[resultsSG])
############# Page structure ########
modelBlocks = [inputView, resultView]
############# Methods ###############
def __init__(self):
self.exampleADM1()
def exampleDef(self):
############# H2 Bioreactor ###############
#Stoichiometric parameter values
self.parametersRH2.f_ch_xc = 0.5 #-
self.parametersRH2.f_pr_xc = 0.15 #-
self.parametersRH2.f_li_xc = 0.15 #-
self.parametersRH2.f_su_li = 0.05 #-
self.parametersRH2.f_fa_li = 0.9 #-
self.parametersRH2.f_ac_su = 0.41 #-
self.parametersRH2.f_ac_aa = 0.4 #-
self.parametersRH2.Y_suaa = 0.1 #-
self.parametersRH2.Y_fa = 0.06 #-
#Biochemical parameter values
self.parametersRH2.k_dis = (0.5, '1/day')
self.parametersRH2.k_hyd_ch = (10.0, '1/day')
self.parametersRH2.k_hyd_pr = (10.0, '1/day')
self.parametersRH2.k_hyd_li = (10.0, '1/day')
self.parametersRH2.k_m_suaa = (30.0, '1/day')
self.parametersRH2.K_S_suaa = (0.5, 'g/L')
self.parametersRH2.k_m_fa = (6.0, '1/day')
self.parametersRH2.K_S_fa = (0.4, 'g/L')
# Physiochemical parameter values
self.parametersRH2.Y_h2_su = 1.0 #-
self.parametersRH2.Y_h2_aa = 1.0 #-
self.parametersRH2.Y_h2_fa = 1.0 #-
# Volumetric flow rate values
self.parametersRH2.D_liq_arr[0] = (10.0, 0.0) #(day, 1/day)
self.parametersRH2.D_liq_arr[1] = (10.0, 0.1) #(day, 1/day)
self.parametersRH2.D_liq_arr[2] = (10.0, 0.05) #(day, 1/day)
self.parametersRH2.D_liq_arr[3] = (10.0, 0.15) #(day, 1/day)
# Input concentrations
self.concentrationsRH2.S_su_in = (0.0, 'gCOD/L')
self.concentrationsRH2.S_aa_in = (0.0, 'gCOD/L')
self.concentrationsRH2.S_fa_in = (0.0, 'gCOD/L')
self.concentrationsRH2.S_ac_in = (0.0, 'gCOD/L')
self.concentrationsRH2.X_c_in = (2.0, 'gCOD/L')
self.concentrationsRH2.X_ch_in = (0.0, 'gCOD/L')
self.concentrationsRH2.X_pr_in = (0.0, 'gCOD/L')
self.concentrationsRH2.X_li_in = (0.0, 'gCOD/L')
self.concentrationsRH2.X_suaa_in = (0.0, 'g/L')
self.concentrationsRH2.X_fa_in = (0.0, 'g/L')
# Initial values of state variables
self.concentrationsRH2.S_su_0 = (0.012, 'gCOD/L')
self.concentrationsRH2.S_aa_0 = (0.005, 'gCOD/L')
self.concentrationsRH2.S_fa_0 = (0.099, 'gCOD/L')
self.concentrationsRH2.S_ac_0 = (0.20, 'gCOD/L')
self.concentrationsRH2.X_c_0 = (30.0, 'gCOD/L')
self.concentrationsRH2.X_ch_0 = (0.028, 'gCOD/L')
self.concentrationsRH2.X_pr_0 = (0.10, 'gCOD/L')
self.concentrationsRH2.X_li_0 = (0.03, 'gCOD/L')
self.concentrationsRH2.X_suaa_0 = (0.42, 'g/L')
self.concentrationsRH2.X_fa_0 = (0.24, 'g/L')
############# CH4 Bioreactor ###############
#Stoichiometric parameter values
self.parametersRCH4.Y_ac = 0.5 #-
#Biochemical parameter values
self.parametersRCH4.k_m_ac = (8.0, '1/day')
self.parametersRCH4.K_S_ac = (0.15, 'g/L')
# Physiochemical parameter values
self.parametersRCH4.Y_ch4_ac = 1.0 #-
# Physical parameter values
self.parametersRCH4.V_liq_RCH4_del_V_liq_RH2 = (50.0, '-') #L/L
# Input concentrations
self.concentrationsRCH4.X_ac_in = (0.0, 'g/L')
# Initial values of state variables
self.concentrationsRCH4.S_ac_0 = (0.0, 'gCOD/L')
self.concentrationsRCH4.X_ac_0 = (2.0, 'g/L')
############# Solver settings ###############
self.solverSettings.tFinal = (50.0, 'day')
self.solverSettings.tPrint = (0.1, 'day')
self.solverSettings.absTol = (1e-9, 'day')
self.solverSettings.relTol = (1e-7, 'day')
def exampleADM1(self):
############# H2 Bioreactor ###############
#Stoichiometric parameter values
self.parametersRH2.f_ch_xc = 0.2 #-
self.parametersRH2.f_pr_xc = 0.2 #-
self.parametersRH2.f_li_xc = 0.3 #-
self.parametersRH2.f_su_li = 0.05 #-
self.parametersRH2.f_fa_li = 0.95 #-
self.parametersRH2.f_ac_su = 0.41 #-
self.parametersRH2.f_ac_aa = 0.4 #-
self.parametersRH2.Y_suaa = 0.1 #-
self.parametersRH2.Y_fa = 0.06 #-
#Biochemical parameter values
self.parametersRH2.k_dis = (0.5, '1/day')
self.parametersRH2.k_hyd_ch = (10.0, '1/day')
self.parametersRH2.k_hyd_pr = (10.0, '1/day')
self.parametersRH2.k_hyd_li = (10.0, '1/day')
self.parametersRH2.k_m_suaa = (30.0, '1/day')
self.parametersRH2.K_S_suaa = (0.5, 'g/L')
self.parametersRH2.k_m_fa = (6.0, '1/day')
self.parametersRH2.K_S_fa = (0.4, 'g/L')
# Physiochemical parameter values
self.parametersRH2.Y_h2_su = 1.0 #-
self.parametersRH2.Y_h2_aa = 1.0 #-
self.parametersRH2.Y_h2_fa = 1.0 #-
# Volumetric flow rate values
self.parametersRH2.D_liq_arr[0] = (10.0, 0.0) #(day, 1/day)
self.parametersRH2.D_liq_arr[1] = (10.0, 0.1) #(day, 1/day)
self.parametersRH2.D_liq_arr[2] = (10.0, 0.05) #(day, 1/day)
self.parametersRH2.D_liq_arr[3] = (10.0, 0.15) #(day, 1/day)
# Input concentrations
self.concentrationsRH2.S_su_in = (0.01, 'gCOD/L')
self.concentrationsRH2.S_aa_in = (0.001, 'gCOD/L')
self.concentrationsRH2.S_fa_in = (0.001, 'gCOD/L')
self.concentrationsRH2.S_ac_in = (0.001, 'gCOD/L')
self.concentrationsRH2.X_c_in = (2.0, 'gCOD/L')
self.concentrationsRH2.X_ch_in = (5.0, 'gCOD/L')
self.concentrationsRH2.X_pr_in = (20.0, 'gCOD/L')
self.concentrationsRH2.X_li_in = (5.0, 'gCOD/L')
self.concentrationsRH2.X_suaa_in = (0.0, 'g/L')
self.concentrationsRH2.X_fa_in = (0.01, 'g/L')
# Initial values of state variables
self.concentrationsRH2.S_su_0 = (0.012, 'gCOD/L')
self.concentrationsRH2.S_aa_0 = (0.005, 'gCOD/L')
self.concentrationsRH2.S_fa_0 = (0.099, 'gCOD/L')
self.concentrationsRH2.S_ac_0 = (0.20, 'gCOD/L')
self.concentrationsRH2.X_c_0 = (0.31, 'gCOD/L')
self.concentrationsRH2.X_ch_0 = (0.028, 'gCOD/L')
self.concentrationsRH2.X_pr_0 = (0.10, 'gCOD/L')
self.concentrationsRH2.X_li_0 = (0.03, 'gCOD/L')
self.concentrationsRH2.X_suaa_0 = (0.42, 'g/L')
self.concentrationsRH2.X_fa_0 = (0.24, 'g/L')
############# CH4 Bioreactor ###############
#Stoichiometric parameter values
self.parametersRCH4.Y_ac = 0.05 #-
#Biochemical parameter values
self.parametersRCH4.k_m_ac = (8.0, '1/day')
self.parametersRCH4.K_S_ac = (0.15, 'g/L')
# Physiochemical parameter values
self.parametersRCH4.Y_ch4_ac = 1.0 #-
# Physical parameter values
self.parametersRCH4.V_liq_RCH4_del_V_liq_RH2 = (50.0, '-') #L/L
# Input concentrations
self.concentrationsRCH4.X_ac_in = (0.0, 'g/L')
# Initial values of state variables
self.concentrationsRCH4.S_ac_0 = (0.0, 'gCOD/L')
self.concentrationsRCH4.X_ac_0 = (0.76, 'g/L')
############# Solver settings ###############
self.solverSettings.tFinal = (50.0, 'day')
self.solverSettings.tPrint = (0.1, 'day')
self.solverSettings.absTol = (1e-12, 'day')
self.solverSettings.relTol = (1e-10, 'day')
def computeAsync(self):
# Simulate RH2 and RCH4 Bioreactors
bioreactor = DM.ADM1H2CH4Bioreactors(self, self.parametersRH2,
self.concentrationsRH2,
self.parametersRCH4,
self.concentrationsRCH4)
bioreactor.prepareSimulation(self.solverSettings)
bioreactor.run(self.solverSettings)
# Show results
self.storage = bioreactor.resultStorage.simulationName
class ThermodynamicalCycle(NumericalModel):
abstract = True
#================ Inputs ================#
# Cycle diagram
cycleDiagram = F.SubModelGroup(TC.CycleDiagram,
'inputs',
label='Diagram settings')
# Solver settings
solver = F.SubModelGroup(CycleIterator, 'solverSettings', label='Solver')
#================ Results ================#
#---------------- Fields ----------------#
cycleStatesTable = F.TableView(
(('T', F.Quantity('Temperature', default=(1, 'degC'))),
('p', F.Quantity('Pressure', default=(1, 'bar'))),
('rho', F.Quantity('Density', default=(1, 'kg/m**3'))),
('h', F.Quantity('SpecificEnthalpy', default=(1, 'kJ/kg'))),
('s', F.Quantity('SpecificEntropy', default=(1, 'kJ/kg-K'))),
('q', F.Quantity()),
('dT', F.Quantity('TemperatureDifference', default=(1, 'degC'))),
('mDot', F.Quantity('MassFlowRate', default=(1, 'kg/min'))),
('b', F.Quantity('SpecificEnergy', default=(1, 'kJ/kg')))),
label="Cycle states")
cycleStates = F.ViewGroup([cycleStatesTable], label="States")
resultStates = F.SuperGroup([cycleStates], label="States")
#---------------- Cycle diagram -----------#
phDiagram = F.Image(default='')
cycleDiagramVG = F.ViewGroup([phDiagram], label="P-H Diagram")
resultDiagrams = F.SuperGroup([cycleDiagramVG], label="Diagrams")
#---------------- Convergence parameters -----------#
residualPlot = F.PlotView((('iteration #', F.Quantity('Dimensionless')),
('h change', F.Quantity('SpecificEnthalpy'))),
label='Residual (plot)',
ylog=True)
iterationTable = F.TableView((
('h1', F.Quantity('SpecificEnthalpy')),
('h2', F.Quantity('SpecificEnthalpy')),
('h3', F.Quantity('SpecificEnthalpy')),
('h4', F.Quantity('SpecificEnthalpy')),
('h5', F.Quantity('SpecificEnthalpy')),
('h6', F.Quantity('SpecificEnthalpy')),
('h7', F.Quantity('SpecificEnthalpy')),
('h8', F.Quantity('SpecificEnthalpy')),
('h9', F.Quantity('SpecificEnthalpy')),
('h10', F.Quantity('SpecificEnthalpy')),
('h11', F.Quantity('SpecificEnthalpy')),
('h12', F.Quantity('SpecificEnthalpy')),
('h13', F.Quantity('SpecificEnthalpy')),
('h14', F.Quantity('SpecificEnthalpy')),
('h15', F.Quantity('SpecificEnthalpy')),
('h16', F.Quantity('SpecificEnthalpy')),
('h17', F.Quantity('SpecificEnthalpy')),
('h18', F.Quantity('SpecificEnthalpy')),
('h19', F.Quantity('SpecificEnthalpy')),
('h20', F.Quantity('SpecificEnthalpy')),
),
label='Residual (table)',
options={'formats': (['0.0000E0'] * 20)})
residualGroup = F.ViewGroup([residualPlot, iterationTable],
label='Iterations')
solverStats = F.SuperGroup([residualGroup], label='Convergence')
# Info fields
cycleTranscritical = F.Boolean(default=False)
cycleSupercritical = F.Boolean(default=False)
def initCompute(self, fluid):
# Create fluid points
self.fluid = Fluid(fluid)
self.fp = [] #[FluidState(fluid) for _ in range(numPoints)]
self.flows = []
self.solver.cycle = self
def connectPorts(self, port1, port2, fluid=None):
if fluid == None:
fluid = self.fluid
fp = FluidState(fluid)
flow = P.FluidFlow()
self.fp.append(fp)
self.flows.append(flow)
port1.state = fp
port2.state = fp
port1.flow = flow
port2.flow = flow
def solve(self):
self.solver.run()
self.residualPlot.resize(len(self.solver.change_hHistory))
for i in range(len(self.solver.change_hHistory)):
self.residualPlot[i] = (i + 1, self.solver.change_hHistory[i])
self.iterationTable.resize(len(self.solver.hHistory))
v = self.iterationTable.view(dtype=np.float).reshape(
-1, len(self.iterationTable.dtype))
numCols = len(self.solver.hHistory[0])
for i in range(len(self.solver.hHistory)):
v[i, :numCols] = self.solver.hHistory[i]
# print self.iterationTable
# iterRecord = np.zeros(1, dtype = self.iterationTable.dtype)
# numCols = len(self.solver.hHistory[0])
# for i in range(len(self.solver.hHistory)):
# for j in range(numCols):
# iterRecord[j] = self.solver.hHistory[i][j]
# self.iterationTable[i] = iterRecord
def postProcess(self, TAmbient):
## State diagram
if (self.cycleDiagram.enable):
self.createStateDiagram()
## Table of states
self.cycleStatesTable.resize(len(self.fp))
for i in range(len(self.fp)):
fp = self.fp[i]
self.cycleStatesTable[i] = (fp.T, fp.p, fp.rho, fp.h, fp.s, fp.q,
fp.dT, self.flows[i].mDot,
fp.b(TAmbient))
# Select the zero for the exergy scale
fp = FluidState(self.fluid)
fp.update_Tp(TAmbient, 1e5)
b0 = fp.b(TAmbient)
self.cycleStatesTable['b'] -= b0
def createStateDiagram(self):
ncp = len(self.fp)
fluidLines = []
for i in range(ncp):
fluidLines.append((self.fp[i], self.fp[(i + 1) % ncp]))
self.phDiagram = self.cycleDiagram.draw(self.fluid, self.fp,
fluidLines)
def setPLow(self, p):
if (self.fluid.tripple['p'] < p < self.fluid.critical['p']):
self.pLow = p
sat = self.fluid.saturation_p(p)
self.TEvaporation = sat['TsatL']
elif (p > self.fluid.critical['p']):
self.pLow = p
self.cycleSupercritical = True
else:
raise ValueError(
'PLow ({} bar) must be between {} bar and {} bar'.format(
p / 1e5, self.fluid.tripple['p'] / 1e5,
self.fluid.critical['p'] / 1e5))
def setPHigh(self, p):
if (self.fluid.tripple['p'] < p < self.fluid.critical['p']):
self.pHigh = p
sat = self.fluid.saturation_p(p)
self.TCondensation = sat['TsatL']
elif (p > self.fluid.critical['p']):
self.pHigh = p
self.cycleTranscritical = True
else:
raise ValueError(
'PHigh ({} bar) must be between {} bar and {} bar'.format(
p / 1e5, self.fluid.tripple['p'] / 1e5,
self.fluid.critical['p'] / 1e5))
class ChemostatDDE2_ESA(NumericalModel):
label = "DDE Chemostat (Example 2 - ESA)"
description = F.ModelDescription(
"Chemostat model with delay differential equations (DDE) and extremum seeking algorithm (ESA) - Example 2",
show=True)
figure = F.ModelFigure(
src="BioReactors/img/ModuleImages/SimpleChemostat.png", show=False)
#1. ############ Inputs ###############
#1.1 Fields - Input values
# Parameters
k1 = F.Quantity(
default=0,
minValue=0,
maxValue=1e6,
label='k<sub>1</sub>',
description=
'yield coefficient related to substrate-1 consumption from bacteria-1')
k2 = F.Quantity(
default=0,
minValue=0,
maxValue=1e6,
label='k<sub>2</sub>',
description=
'yield coefficient related to substrate-2 production from bacteria-1')
k3 = F.Quantity(
default=0,
minValue=0,
maxValue=1e6,
label='k<sub>3</sub>',
description=
'yield coefficient related to substrate-2 consumption from bacteria-2')
k4 = F.Quantity(
default=0,
minValue=0,
maxValue=1e6,
label='k<sub>4</sub>',
description=
'yield coefficient of methane (biogas) on bacteria-2 and substrate-2')
s1_in = F.Quantity('Bio_MassConcentration',
default=(0, 'g/L'),
label='s<sub>1</sub><sup>in</sub>',
description='input substrate-1 concentration')
s2_in = F.Quantity('Bio_MassConcentration',
default=(0, 'g/L'),
label='s<sub>2</sub><sup>in</sub>',
description='input substrate-2 concentration')
a = F.Quantity(
'Fraction',
default=(0, '-'),
label='α',
description=
'proportion of organisms that are affected by the dilution rate D')
D = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0, '1/day'),
label='D',
description='dilution rate')
parametersFG = F.FieldGroup([s1_in, s2_in, k1, k2, k3, k4, a, D],
label='Parameters')
# Parameters - specific growth rates
m1 = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0, '1/day'),
label='m<sub>1</sub>',
description='maximum specific growth rate of bacteria-1')
m2 = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0, '1/day'),
label='m<sub>2</sub>',
description='maximum specific growth rate of bacteria-2')
k_s1 = F.Quantity('Bio_MassConcentration',
default=(0, 'g/L'),
label='k<sub>s1</sub>',
description='half saturation constant of bacteria-1')
k_s2 = F.Quantity('Bio_MassConcentration',
default=(0, 'g/L'),
label='k<sub>s2</sub>',
description='half saturation constant of bacteria-2')
k_I = F.Quantity('Dimensionless',
default=(0, '-'),
label='k<sub>I</sub>',
description='constant in unit: [ sqrt( g/L ) ]')
parametersMuFG = F.FieldGroup([m1, m2, k_s1, k_s2, k_I],
label='Parameters - specific growth rates')
# Parameters - time delays
tau1 = F.Quantity(
'Bio_Time',
default=(0, 'day'),
minValue=(0, 'day'),
label='τ<sub>1</sub>',
description=
'time delay in conversion of the substrate-1 to viable biomass for bacteria-1'
)
tau2 = F.Quantity(
'Bio_Time',
default=(0, 'day'),
minValue=(0, 'day'),
label='τ<sub>2</sub>',
description=
'time delay in conversion of the substrate-2 to viable biomass for bacteria-2'
)
parametersTauFG = F.FieldGroup([tau1, tau2],
label='Parameters - time delay')
# historical initial conditions
s1_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(0, 'g/L'),
label='s<sub>1</sub><sup>[-τ<sub>1</sub>, 0]</sup>',
description='historical initial condition for substrate-1 concentration'
)
x1_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(0, 'g/L'),
label='x<sub>1</sub><sup>[-τ<sub>1</sub>, 0]</sup>',
description='historical initial condition for bacteria-1 concentration'
)
s2_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(0, 'g/L'),
label='s<sub>2</sub><sup>[-τ<sub>2</sub>, 0]</sup>',
description='historical initial condition for substrate-2 concentration'
)
x2_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(0, 'g/L'),
label='x<sub>2</sub><sup>[-τ<sub>2</sub>, 0]</sup>',
description='historical initial condition for bacteria-2 concentration'
)
parametersHistFG = F.FieldGroup(
[s1_hist_vals, x1_hist_vals, s2_hist_vals, x2_hist_vals],
label='Historical initial conditions')
inputValuesSG = F.SuperGroup(
[parametersMuFG, parametersFG, parametersTauFG, parametersHistFG],
label="Input values")
#1.2 Fields - Settings
ESA_enable = F.Boolean(
default=False,
label='enable',
description=
'find the the maximum methane flow rate (i.e. run extremum seeking algorithm)'
)
ESA_DMin = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0.0, '1/day'),
label='D<sub>min</sub>',
description='minimum dilution rate',
show='self.ESA_enable')
ESA_DMax = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0.0, '1/day'),
label='D<sub>max</sub>',
description='maximum dilution rate',
show='self.ESA_enable')
ESA_eps = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(1e-9, '1/day'),
maxValue=(1.0, '1/day'),
label='ε*',
description='D max tolerance',
show='self.ESA_enable')
ESA_h = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(1e-8, '1/day'),
maxValue=(1.0, '1/day'),
label='h*',
description='seeking step of D max',
show='self.ESA_enable')
ESA_eps_z = F.Quantity('Bio_MassConcentration',
default=(0, 'g/L'),
minValue=(1e-9, 'g/L'),
maxValue=(1.0, 'g/L'),
label='ε<sub>z</sub>*',
description='equilibrium point tolerance',
show='self.ESA_enable')
ESA_FG = F.FieldGroup(
[ESA_enable, ESA_DMin, ESA_DMax, ESA_eps, ESA_h, ESA_eps_z],
label='Extremum Seeking Algorithm (ESA)')
DsQs_DMin = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0, '1/day'),
label='D<sub>min</sub>',
description='minimum dilution rate')
DsQs_DMax = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(0, '1/day'),
label='D<sub>max</sub>',
description='maximum dilution rate')
DsQs_Step = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
minValue=(1e-4, '1/day'),
maxValue=(1.0, '1/day'),
label='D<sub>step</sub>',
description='step of dilution rate')
DsQs_FG = F.FieldGroup([DsQs_DMin, DsQs_DMax, DsQs_Step],
label='Chart (Ds, Qs)')
tFinal = F.Quantity('Bio_Time',
default=(100, 'day'),
minValue=(0, 'day'),
maxValue=(5000, 'day'),
label='simulation time')
tPrint = F.Quantity('Bio_Time',
default=(0.1, 'day'),
minValue=(1e-5, 'day'),
maxValue=(100, 'day'),
label='print interval*')
mainSimStep = F.Quantity('Bio_Time',
default=(10., 'day'),
minValue=(0.25, 'day'),
maxValue=(1e3, 'day'),
label='main simulation step*')
absTol = F.Quantity('Bio_Time',
default=(1e-12, 'day'),
minValue=(1e-16, 'day'),
maxValue=(1e-5, 'day'),
label='absolute tolerance*')
relTol = F.Quantity('Bio_Time',
default=(1e-12, 'day'),
minValue=(1e-16, 'day'),
maxValue=(1e-3, 'day'),
label='relative tolerance*')
solverFG = F.FieldGroup([tFinal, tPrint, mainSimStep, absTol, relTol],
label='Solver')
settingsSG = F.SuperGroup([solverFG, DsQs_FG, ESA_FG], label='Settings')
#1.4 Model view
inputView = F.ModelView(ioType="input",
superGroups=[inputValuesSG, settingsSG],
autoFetch=True)
#2. ############ Results ###############
# 2.1. Results
dataSeries = (
('time', F.Quantity('Bio_Time', default=(1, 'day'))),
('s1', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('x1', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('s2', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('x2', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('D', F.Quantity('Bio_TimeRate', default=(1, '1/day'))),
('Q',
F.Quantity('Bio_MassConcentrationFlowRate', default=(1, 'g/L/day'))),
)
plot = F.PlotView(
dataSeries,
label='Plot',
options={
'ylabel': None,
'title': 'Chemostat (DDE)'
},
)
table = F.TableView(dataSeries,
label='Table',
options={
'title':
'Title',
'formats': [
'0.0000', '0.0000', '0.0000', '0.0000',
'0.0000', '0.0000', '0.0000'
]
})
chartS1S2 = F.MPLPlot(label='Chart (s<sub>1</sub>, s<sub>2</sub>)')
chartX1X2 = F.MPLPlot(label='Chart (x<sub>1</sub>, x<sub>2</sub>)')
chartS1X1 = F.MPLPlot(label='Chart (s<sub>1</sub>, x<sub>1</sub>)')
chartS2X2 = F.MPLPlot(label='Chart (s<sub>2</sub>, x<sub>2</sub>)')
chartS2X2 = F.MPLPlot(label='Chart (s<sub>2</sub>, x<sub>2</sub>)')
chartDQ = F.MPLPlot(label='Chart (D, Q)')
chartDsQs = F.MPLPlot(label='Chart (Ds, Qs)')
resultsVG = F.ViewGroup([
plot, table, chartS1S2, chartX1X2, chartS1X1, chartS2X2, chartDQ,
chartDsQs
],
label='Results')
resultsSG = F.SuperGroup([resultsVG], label="Results")
# 2.2 Equilibrium point
s1_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='s<sub>1</sub><sup>*</sup>',
description='substrate-1 concentration at the equilibrium point')
x1_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='x<sub>1</sub><sup>*</sup>',
description='bacteria-1 concentration at the equilibrium point')
s2_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='s<sub>2</sub><sup>*</sup>',
description='substrate-2 concentration at the equilibrium point')
x2_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='x<sub>2</sub><sup>*</sup>',
description='bacteria-1 concentration at the equilibrium point')
equilibriumPointFG = F.FieldGroup([s1_eqpnt, x1_eqpnt, s2_eqpnt, x2_eqpnt],
label='Equilibrium point')
equilibriumPointSG = F.SuperGroup([equilibriumPointFG],
label='Equilibrium point')
# 2.3 ESA Results
resESA_QMaxIsFound = F.Boolean(label='Q<sub>max</sub> is found')
resESA_DMax = F.Quantity('Bio_TimeRate',
default=(0, '1/day'),
label='D<sub>max</sub>',
description='maximum dilution rate')
resESA_QMax = F.Quantity('Bio_MassConcentrationFlowRate',
default=(0, 'g/L/day'),
label='Q<sub>max</sub>',
description='maximum methane (biogas) flow rate')
resESA_FG = F.FieldGroup([resESA_QMaxIsFound, resESA_DMax, resESA_QMax],
label='Results (ESA)')
resESA_SG = F.SuperGroup([resESA_FG], label='Results (ESA)')
#2.1 Model view
resultView = F.ModelView(
ioType="output",
superGroups=[resultsSG, resESA_SG, equilibriumPointSG])
############# Page structure ########
modelBlocks = [inputView, resultView]
def __init__(self):
self.k1 = (10.53, '-')
self.k2 = (28.6, '-')
self.k3 = (1074, '-')
self.k4 = (100, '-')
self.s1_in = (7.5, 'g/L')
self.s2_in = (75, 'g/L')
self.a = (0.5, '-')
self.m1 = (1.2, '1/day')
self.m2 = (0.74, '1/day')
self.k_s1 = (7.1, 'g/L')
self.k_s2 = (9.28, 'g/L')
self.k_I = (16, '-')
self.D = (0.25, '1/day')
self.tau1 = (2, 'day')
self.tau2 = (7, 'day')
self.s1_hist_vals = (2, 'g/L')
self.x1_hist_vals = (0.1, 'g/L')
self.s2_hist_vals = (10, 'g/L')
self.x2_hist_vals = (0.05, 'g/L')
self.DsQs_DMin = (0.0, '1/day')
self.DsQs_DMax = (1.0, '1/day')
self.DsQs_Step = (0.01, '1/day')
self.tFinal = (2000, 'day')
self.tPrint = (1.0, 'day')
self.mainSimStep = (10., 'day')
self.absTol = (1e-12, 'day')
self.relTol = (1e-12, 'day')
self.ESA_enable = True
self.ESA_DMin = (0.01, '1/day')
self.ESA_DMax = (0.33, '1/day')
self.ESA_eps = (0.01, '1/day')
self.ESA_h = (0.025, '1/day')
self.ESA_eps_z = (0.01, 'g/L')
def compute(self):
chemostatDDE = DM.ChemostatDDE2_ESA(self)
if self.ESA_enable:
chemostatDDE.runESA(self)
else:
chemostatDDE.run(self)
resESA = chemostatDDE.getResultsESA()
self.resESA_QMaxIsFound = resESA['QMaxIsFound']
self.resESA_DMax = (resESA['DMax'], '1/day')
self.resESA_QMax = (resESA['QMax'], 'kg/m**3/day')
res = chemostatDDE.getResults()
results = np.array([
res['t'], res['s1'], res['x1'], res['s2'], res['x2'], res['D'],
res['Q']
]).transpose()
self.plot = results
self.table = results
chemostatDDE.plotS1S2(self.chartS1S2)
chemostatDDE.plotX1X2(self.chartX1X2)
chemostatDDE.plotS1X1(self.chartS1X1)
chemostatDDE.plotS2X2(self.chartS2X2)
chemostatDDE.plotDQ(self.chartDQ)
chemostatDDE.plotDsQs(self.chartDsQs)
self.s1_eqpnt = (chemostatDDE.equilibriumPoint[0], 'kg/m**3')
self.x1_eqpnt = (chemostatDDE.equilibriumPoint[1], 'kg/m**3')
self.s2_eqpnt = (chemostatDDE.equilibriumPoint[2], 'kg/m**3')
self.x2_eqpnt = (chemostatDDE.equilibriumPoint[3], 'kg/m**3')
class ChemostatDDE1(NumericalModel):
label = "DDE Chemostat (Example 1)"
description = F.ModelDescription(
"Chemostat model with delay differential equations (DDE) - Example 1",
show=True)
figure = F.ModelFigure(
src="BioReactors/img/ModuleImages/SimpleChemostat.png", show=False)
#1. ############ Inputs ###############
#1.1 Fields - Input values
# Parameters
k1 = F.Quantity(
default=10.53,
minValue=0,
maxValue=1e6,
label='k<sub>1</sub>',
description=
'yield coefficient related to substrate-1 consumption from bacteria-1')
k2 = F.Quantity(
default=28.6,
minValue=0,
maxValue=1e6,
label='k<sub>2</sub>',
description=
'yield coefficient related to substrate-2 production from bacteria-1')
k3 = F.Quantity(
default=1074.,
minValue=0,
maxValue=1e6,
label='k<sub>3</sub>',
description=
'yield coefficient related to substrate-2 consumption from bacteria-2')
s1_in = F.Quantity('Bio_MassConcentration',
default=(7.5, 'g/L'),
label='s<sub>1</sub><sup>in</sub>',
description='input substrate-1 concentration')
s2_in = F.Quantity('Bio_MassConcentration',
default=(75., 'g/L'),
label='s<sub>2</sub><sup>in</sub>',
description='input substrate-2 concentration')
a = F.Quantity(
'Fraction',
default=(0.5, '-'),
label='α',
description=
'proportion of organisms that are affected by the dilution rate D')
D = F.Quantity('Bio_TimeRate',
default=(0.89, '1/day'),
minValue=(0, '1/day'),
label='D',
description='dilution rate')
parametersFG = F.FieldGroup([s1_in, s2_in, k1, k2, k3, a, D],
label='Parameters')
# Parameters - specific growth rates
m1 = F.Quantity('Bio_TimeRate',
default=(1.20, '1/day'),
minValue=(0, '1/day'),
label='m<sub>1</sub>',
description='maximum specific growth rate of bacteria-1')
m2 = F.Quantity('Bio_TimeRate',
default=(0.74, '1/day'),
minValue=(0, '1/day'),
label='m<sub>2</sub>',
description='maximum specific growth rate of bacteria-2')
k_s1 = F.Quantity('Bio_MassConcentration',
default=(7.1, 'g/L'),
label='k<sub>s1</sub>',
description='half saturation constant of bacteria-1')
k_s2 = F.Quantity('Bio_MassConcentration',
default=(9.28, 'g/L'),
label='k<sub>s2</sub>',
description='half saturation constant of bacteria-2')
k_I = F.Quantity('Dimensionless',
default=(16., '-'),
label='k<sub>I</sub>',
description='constant in unit: [ sqrt( g/L ) ]')
parametersMuFG = F.FieldGroup([m1, m2, k_s1, k_s2, k_I],
label='Parameters - specific growth rates')
# Parameters - time delays
tau1 = F.Quantity(
'Bio_Time',
default=(10.1, 'day'),
minValue=(0, 'day'),
label='τ<sub>1</sub>',
description=
'time delay in conversion of the substrate-1 to viable biomass for bacteria-1'
)
tau2 = F.Quantity(
'Bio_Time',
default=(5.7, 'day'),
minValue=(0, 'day'),
label='τ<sub>2</sub>',
description=
'time delay in conversion of the substrate-2 to viable biomass for bacteria-2'
)
parametersTauFG = F.FieldGroup([tau1, tau2],
label='Parameters - time delay')
# historical initial conditions
s1_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(3., 'g/L'),
label='s<sub>1</sub><sup>[-τ<sub>1</sub>, 0]</sup>',
description='historical initial condition for substrate-1 concentration'
)
x1_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(0.5, 'g/L'),
label='x<sub>1</sub><sup>[-τ<sub>1</sub>, 0]</sup>',
description='historical initial condition for bacteria-1 concentration'
)
s2_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(15., 'g/L'),
label='s<sub>2</sub><sup>[-τ<sub>2</sub>, 0]</sup>',
description='historical initial condition for substrate-2 concentration'
)
x2_hist_vals = F.Quantity(
'Bio_MassConcentration',
default=(0.1, 'g/L'),
label='x<sub>2</sub><sup>[-τ<sub>2</sub>, 0]</sup>',
description='historical initial condition for bacteria-2 concentration'
)
parametersHistFG = F.FieldGroup(
[s1_hist_vals, x1_hist_vals, s2_hist_vals, x2_hist_vals],
label='Historical initial conditions')
inputValuesSG = F.SuperGroup(
[parametersMuFG, parametersFG, parametersTauFG, parametersHistFG],
label="Input values")
#1.2 Fields - Settings
tFinal = F.Quantity('Bio_Time',
default=(100, 'day'),
minValue=(0, 'day'),
maxValue=(1000, 'day'),
label='simulation time')
tPrint = F.Quantity('Bio_Time',
default=(0.1, 'day'),
minValue=(1e-5, 'day'),
maxValue=(100, 'day'),
label='print interval')
absTol = F.Quantity('Bio_Time',
default=(1e-12, 'day'),
minValue=(1e-16, 'day'),
maxValue=(1e-5, 'day'),
label='absolute tolerance')
relTol = F.Quantity('Bio_Time',
default=(1e-12, 'day'),
minValue=(1e-16, 'day'),
maxValue=(1e-3, 'day'),
label='relative tolerance')
solverFG = F.FieldGroup([tFinal, tPrint, absTol, relTol], label='Solver')
settingsSG = F.SuperGroup([solverFG], label='Settings')
#1.4 Model view
inputView = F.ModelView(ioType="input",
superGroups=[inputValuesSG, settingsSG],
autoFetch=True)
#2. ############ Results ###############
dataSeries = (
('time', F.Quantity('Bio_Time', default=(1, 'day'))),
('s1', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('x1', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('s2', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
('x2', F.Quantity('Bio_MassConcentration', default=(1, 'g/L'))),
)
plot = F.PlotView(
dataSeries,
label='Plot',
options={
'ylabel': None,
'title': 'Chemostat (DDE)'
},
)
table = F.TableView(dataSeries,
label='Table',
options={
'title':
'Title',
'formats':
['0.0000', '0.0000', '0.0000', '0.0000', '0.0000']
})
chartS1S2 = F.MPLPlot(label='Chart (s<sub>1</sub>, s<sub>2</sub>)')
chartX1X2 = F.MPLPlot(label='Chart (x<sub>1</sub>, x<sub>2</sub>)')
chartS1X1 = F.MPLPlot(label='Chart (s<sub>1</sub>, x<sub>1</sub>)')
chartS2X2 = F.MPLPlot(label='Chart (s<sub>2</sub>, x<sub>2</sub>)')
resultsVG = F.ViewGroup(
[plot, table, chartS1S2, chartX1X2, chartS1X1, chartS2X2],
label='Results')
resultsSG = F.SuperGroup([resultsVG], label="Results")
# 2.2 Equilibrium point
s1_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='s<sub>1</sub><sup>*</sup>',
description='substrate-1 concentration at the equilibrium point')
x1_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='x<sub>1</sub><sup>*</sup>',
description='bacteria-1 concentration at the equilibrium point')
s2_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='s<sub>2</sub><sup>*</sup>',
description='substrate-2 concentration at the equilibrium point')
x2_eqpnt = F.Quantity(
'Bio_MassConcentration',
default=(0., 'g/L'),
label='x<sub>2</sub><sup>*</sup>',
description='bacteria-1 concentration at the equilibrium point')
equilibriumPointFG = F.FieldGroup([s1_eqpnt, x1_eqpnt, s2_eqpnt, x2_eqpnt],
label='Equilibrium point')
equilibriumPointSG = F.SuperGroup([equilibriumPointFG],
label='Equilibrium point')
#2.1 Model view
resultView = F.ModelView(ioType="output",
superGroups=[resultsSG, equilibriumPointSG])
############# Page structure ########
modelBlocks = [inputView, resultView]
def __init__(self):
self.k1 = 10.53
self.k2 = 28.6
self.k3 = 1074
self.s1_in = 7.5
self.s2_in = 75
self.a = 0.5
self.m1 = 1.2
self.m2 = 0.74
self.k_s1 = 7.1
self.k_s2 = 9.28
self.k_I = 16
self.D = 0.85
self.tau1 = 2
self.tau2 = 7
self.s1_hist_vals = 2
self.x1_hist_vals = 0.1
self.s2_hist_vals = 10
self.x2_hist_vals = 0.05
def compute(self):
chemostatDDE = DM.ChemostatDDE1(self)
chemostatDDE.run(self)
res = chemostatDDE.getResults()
results = np.array(
[res['t'], res['s1'], res['x1'], res['s2'],
res['x2']]).transpose()
self.plot = results
self.table = results
chemostatDDE.plotS1S2(self.chartS1S2)
chemostatDDE.plotX1X2(self.chartX1X2)
chemostatDDE.plotS1X1(self.chartS1X1)
chemostatDDE.plotS2X2(self.chartS2X2)
self.s1_eqpnt = (chemostatDDE.equilibriumPoint[0], 'kg/m**3')
self.x1_eqpnt = (chemostatDDE.equilibriumPoint[1], 'kg/m**3')
self.s2_eqpnt = (chemostatDDE.equilibriumPoint[2], 'kg/m**3')
self.x2_eqpnt = (chemostatDDE.equilibriumPoint[3], 'kg/m**3')
class BiochemicalReactions(NumericalModel):
label = "Biochemical reactions"
description = F.ModelDescription(
"Solver for elementary biochemical reactions", show=True)
figure = F.ModelFigure(
src="BioReactors/img/ModuleImages/BiochemicalReactions.png",
show=False)
async = True
progressOptions = {'suffix': 's', 'fractionOutput': True}
#1. ############ Inputs ###############
#1.1 Fields - Input values
reactions = F.RecordArray(
(
('reactionEquation',
F.String('E + S <-> ES', label='Equation', inputBoxWidth=160)),
('rateConstnats',
F.String('0.0, 0.0', label='Rate constants', inputBoxWidth=100)),
('reactionName',
F.String('enzyme binding to a substrate',
label='Name',
inputBoxWidth=400,
showTooltip=True)),
),
toggle=False,
label='Reactions',
numRows=2,
description='Biochemical reactions',
)
reactionsFG = F.FieldGroup([reactions],
hideContainer=True,
label="Reactions")
reactionsSG = F.SuperGroup([reactionsFG], label="Reactions")
species = F.RecordArray(
(
('speciesVariable',
F.String('E', label='Variable', inputBoxWidth=70)),
('initialValue',
F.Quantity('Bio_MolarConcentration',
default=(1, 'M'),
minValue=(0, 'M'),
label='Initial value',
inputBoxWidth=75)),
('speciesName', F.String('enzyme', label='Name',
inputBoxWidth=270)),
),
toggle=False,
label='species',
numRows=4,
description='Species of the reactions',
)
speciesFG = F.FieldGroup([species], hideContainer=True, label="Species")
speciesSG = F.SuperGroup([speciesFG], label="Species")
#1.2 Fields - Settings
tFinal = F.Quantity('Time',
default=(0.0, 's'),
minValue=(0, 's'),
maxValue=(1000, 's'),
label='simulation time')
tPrint = F.Quantity('Time',
default=(0.0, 's'),
minValue=(1e-3, 's'),
maxValue=(100, 's'),
label='print interval')
solverFG = F.FieldGroup([tFinal, tPrint], label='Solver')
settingsSG = F.SuperGroup([solverFG], label='Settings')
#1.4 Model view
exampleAction = A.ServerAction(
"loadEg",
label="Examples",
options=(
('exampleMMK', 'Michaelis-Menten kinetics'),
('exampleMMKI', 'Michaelis-Menten kinetics with inhibition'),
))
inputView = F.ModelView(
ioType="input",
superGroups=[reactionsSG, speciesSG, settingsSG],
autoFetch=True,
actionBar=A.ActionBar([exampleAction]),
)
#2. ############ Results ###############
storage = F.HdfStorage(hdfFile=DM.dataStorageFilePath,
hdfGroup=DM.dataStorageDatasetPath)
dataSeries = (
('time', F.Quantity('Time', default=(1, 's'))),
('E', F.Quantity('Bio_MolarConcentration', default=(1, 'M'))),
)
plot = F.PlotView(dataSeries,
label='Plot',
useHdfStorage=True,
storage='storage')
table = F.TableView(
dataSeries,
label='Table',
options={'formats': ['0.000', '0.000', '0.000', '0.000']},
useHdfStorage=True,
storage='storage')
storageVG = F.ViewGroup([storage], show="false")
resultsVG = F.ViewGroup([plot, table], label='Results')
resultsSG = F.SuperGroup([resultsVG, storageVG], label='Results')
# 2.2 ODEs plot
odesPlot = F.MPLPlot(label='ODEs')
odesVG = F.ViewGroup([odesPlot], label='Ordinary differential equations')
odesSG = F.SuperGroup([odesVG], label='ODEs')
# 2.3 Results plot
chartPlot = F.MPLPlot(label='Chart')
chartPlotVG = F.ViewGroup([chartPlot], label='Chart')
chartPlotSG = F.SuperGroup([chartPlotVG], label='Chart')
#2.1 Model view
resultView = F.ModelView(ioType="output",
superGroups=[resultsSG, odesSG, chartPlotSG],
keepDefaultDefs=True)
############# Page structure ########
modelBlocks = [inputView, resultView]
def __init__(self):
self.exampleMMK()
def exampleMMK(self):
self.species[0] = ('E', 4.0, 'enzyme')
self.species[1] = ('S', 8.0, 'substrate')
self.species[2] = ('ES', 0.0, 'complex')
self.species[3] = ('P', 0.0, 'product')
self.reactions[0] = (
'E + S <=> ES', '2.0, 1.0',
'an enzyme binding to a substrate form an enzyme-substrate complex (reversible process)'
)
self.reactions[1] = (
'ES -> E + P', '1.5',
'an enzyme-substrate complex decomposition to a product and the enzyme'
)
self.tFinal = 20.0
self.tPrint = 0.01
def exampleMMKI(self):
self.species.resize(6)
self.species[0] = ('E', 4.0, 'enzyme')
self.species[1] = ('S', 8.0, 'substrate')
self.species[2] = ('ES', 0.0, 'enzyme-substrate complex')
self.species[3] = ('P', 0.0, 'product')
self.species[4] = ('I', 5.0, 'inhibitor')
self.species[5] = ('EI', 0.0, 'inactive enzyme-inhibitor complex')
self.reactions.resize(3)
self.reactions[0] = (
'E + S <=> ES', '2.0, 1.0',
'an enzyme binding to a substrate form an enzyme-substrate complex (reversible process)'
)
self.reactions[1] = (
'ES -> E + P', '1.5',
'an enzyme-substrate complex decomposition to a product and an enzyme'
)
self.reactions[2] = (
'E + I <=> EI', '2.0, 0.5',
'an inhibitor binding to the active site of an enzyme form an inactive enzyme-inhibitor complex (reversible processes)'
)
self.tFinal = 20.0
self.tPrint = 0.01
def computeAsync(self):
# Redefine some fields
self.redefineFileds()
# Create the model
model = DM.BiochemicalReactions(self)
# Tun simulation
model.prepareSimulation()
model.run(self)
# Show results
self.storage = model.resultStorage.simulationName
# Plot results
model.plotODEsTxt(self.odesPlot)
model.plotHDFResults(self.chartPlot)
def redefineFileds(self):
# Create tuples for species
speciesTuples = (('time', F.Quantity('Time', default=(1, 's'))), )
datasetColumns = ['t']
for itSpecies in self.species:
X = itSpecies[0] #species variable
speciesTuple = (('%s' % X,
F.Quantity('Bio_MolarConcentration',
default=(1, 'M'))), )
speciesTuples += speciesTuple
datasetColumns.append('%s' % X)
# Redefine Fields
redefinedStorage = F.HdfStorage(
hdfFile='BioReactors_SimulationResults.h5',
hdfGroup='/BiochemicalReactions',
datasetColumns=datasetColumns)
self.redefineField('storage', 'storageVG', redefinedStorage)
redefinedPlot = F.PlotView(speciesTuples,
label='Plot',
options={
'ylabel': 'concentration',
'title': ''
},
useHdfStorage=True,
storage='storage')
self.redefineField('plot', 'resultsVG', redefinedPlot)
redefinedTable = F.TableView(
speciesTuples,
label='Table',
options={'formats': ['0.000', '0.000', '0.000', '0.000']},
useHdfStorage=True,
storage='storage')
self.redefineField('table', 'resultsVG', redefinedTable)
class CylindricalBlockHeatExchanger(NumericalModel):
label = "Cylindrical heat exchanger"
figure = F.ModelFigure(
src="ThermoFluids/img/ModuleImages/HeatExchangerDesign.png",
show=False)
description = F.ModelDescription(
"""Model of heat exchanger made out of a solid cylindrical block, with
central channels for one of the fluids and a spiraling
channel around the block for the other fluid
""")
async = True
progressOptions = {'suffix': '%', 'fractionOutput': False}
#================ Inputs ================#
#---------------- Fields ----------------#
# Fields: geometry
blockGeom = F.SubModelGroup(BlockGeometry, 'FG', 'Geometry')
blockProps = F.SubModelGroup(BlockProperties, 'FG', 'Properties')
blockSG = F.SuperGroup([blockGeom, blockProps], label='Block')
# Fields: internal channels
primaryChannelsGeom = F.SubModelGroup(ChannelGroupGeometry,
'FG',
label='Primary channels')
secondaryChannelsGeom = F.SubModelGroup(ChannelGroupGeometry,
'FG',
label='Secondary channels')
primaryFlowIn = F.SubModelGroup(FluidFlowInput,
'FG',
label='Primary flow inlet')
secondaryFlowIn = F.SubModelGroup(FluidFlowInput,
'FG',
label='Secondary flow inlet')
internalChannelSG = F.SuperGroup([
primaryChannelsGeom, secondaryChannelsGeom, primaryFlowIn,
secondaryFlowIn
],
label='Channels')
# Fields: external channel
externalChannelGeom = F.SubModelGroup(ExternalChannelGeometry,
'FG',
label='Geometry')
externalFlowIn = F.SubModelGroup(IncompressibleSolutionFlowInput,
'incomSolFG',
label='Inlet flow')
externalChannelSG = F.SuperGroup([externalChannelGeom, externalFlowIn],
label='External channel')
# Fields: settings
fvSolverSettings = F.SubModelGroup(FiniteVolumeSolverSettings,
'FG',
label='Finite volume solver')
sectionResultsSettings = F.SubModelGroup(SectionResultsSettings,
'FG',
label='Section results plots')
settingsSG = F.SuperGroup([fvSolverSettings, sectionResultsSettings],
label='Settings')
#--------------- Model view ---------------#
inputView = F.ModelView(ioType="input",
superGroups=[
blockSG, internalChannelSG, externalChannelSG,
settingsSG
],
autoFetch=True)
#================ Results ================#
meshView = F.MPLPlot(label='Cross-section mesh')
crossSectionProfileView = F.MPLPlot(label='Cross-section profile')
longitudinalProfileView = F.MPLPlot(label='Longitudinal profile')
primaryChannelProfileView = F.MPLPlot(label='Primary channel profile')
secondaryChannelProfileView = F.MPLPlot(label='Secondary channel profile')
geometryVG = F.ViewGroup([
meshView, crossSectionProfileView, longitudinalProfileView,
primaryChannelProfileView, secondaryChannelProfileView
],
label='Geometry/Mesh')
geometrySG = F.SuperGroup([geometryVG], label='Geometry/mesh')
primaryFlowOut = F.SubModelGroup(FluidFlowOutput,
'FG',
label='Primary flow outlet')
secondaryFlowOut = F.SubModelGroup(FluidFlowOutput,
'FG',
label='Secondary flow outlet')
externalFlowOut = F.SubModelGroup(FluidFlowOutput,
'FG',
label='External flow outlet')
QDotChannels = F.SubModelGroup(HeatFlowChannels, 'FG', label='Heat flow')
resultSG = F.SuperGroup(
[primaryFlowOut, secondaryFlowOut, externalFlowOut, QDotChannels],
label='Results')
resultTable = F.TableView((
('xStart', F.Quantity('Length', default=(1, 'm'))),
('xEnd', F.Quantity('Length', default=(1, 'm'))),
('TPrimFluid', F.Quantity('Temperature', default=(1, 'degC'))),
('TPrimWall', F.Quantity('Temperature', default=(1, 'degC'))),
('RePrim', F.Quantity()),
('hConvPrim',
F.Quantity('HeatTransferCoefficient', default=(1, 'W/m**2-K'))),
('QDotPrim', F.Quantity('HeatFlowRate', default=(1, 'W'))),
('TSecFluid', F.Quantity('Temperature', default=(1, 'degC'))),
('TSecWall', F.Quantity('Temperature', default=(1, 'degC'))),
('ReSec', F.Quantity()),
('hConvSec',
F.Quantity('HeatTransferCoefficient', default=(1, 'W/m**2-K'))),
('QDotSec', F.Quantity('HeatFlowRate', default=(1, 'W'))),
('TExtFluid', F.Quantity('Temperature', default=(1, 'degC'))),
('TExtWall', F.Quantity('Temperature', default=(1, 'degC'))),
('ReExt', F.Quantity()),
('hConvExt',
F.Quantity('HeatTransferCoefficient', default=(1, 'W/m**2-K'))),
('QDotExt', F.Quantity('HeatFlowRate', default=(1, 'W'))),
),
label='Detailed results')
resultTPlot = F.PlotView((
('x', F.Quantity('Length', default=(1, 'm'))),
('TPrimFluid', F.Quantity('Temperature', default=(1, 'degC'))),
('TPrimWall', F.Quantity('Temperature', default=(1, 'degC'))),
('TSecFluid', F.Quantity('Temperature', default=(1, 'degC'))),
('TSecWall', F.Quantity('Temperature', default=(1, 'degC'))),
('TExtFluid', F.Quantity('Temperature', default=(1, 'degC'))),
('TExtWall', F.Quantity('Temperature', default=(1, 'degC'))),
),
label='Temperature plots')
resultQPlot = F.PlotView((
('x', F.Quantity('Length', default=(1, 'm'))),
('QDotPrim', F.Quantity('HeatFlowRate', default=(1, 'W'))),
('QDotSec', F.Quantity('HeatFlowRate', default=(1, 'W'))),
('QDotExt', F.Quantity('HeatFlowRate', default=(1, 'W'))),
),
label='Heat flow plots')
detailedResultVG = F.ViewGroup([resultTable, resultTPlot, resultQPlot],
label='Detailed results')
detailedResultSG = F.SuperGroup([detailedResultVG],
label='Detailed results')
sectionPlot1 = F.MPLPlot(label='Section 1')
sectionPlot2 = F.MPLPlot(label='Section 2')
sectionPlot3 = F.MPLPlot(label='Section 3')
sectionPlot4 = F.MPLPlot(label='Section 4')
sectionPlot5 = F.MPLPlot(label='Section 5')
sectionResultsVG = F.ViewGroup(
[sectionPlot1, sectionPlot2, sectionPlot3, sectionPlot4, sectionPlot5],
label='Section temperatures')
sectionResultsSG = F.SuperGroup([sectionResultsVG],
label='Section results')
resultView = F.ModelView(
ioType="output",
superGroups=[geometrySG, resultSG, detailedResultSG, sectionResultsSG])
############# Page structure ########
modelBlocks = [inputView, resultView]
############# Methods ###############
def __init__Internal(self):
self.blockGeom.diameter = (58.0, 'mm')
self.blockGeom.length = (0.8, 'm')
self.blockProps.divisionStep = (0.1, 'm')
self.blockProps.material = 'Aluminium6061'
self.primaryChannelsGeom.number = 3
self.primaryChannelsGeom.radialPosition = (7, 'mm')
self.primaryChannelsGeom.startingAngle = (0, 'deg')
self.primaryChannelsGeom.meshFineness = 4
self.primaryChannelsGeom.channelName = "PrimaryChannel"
self.primaryChannelsGeom.externalDiameter = (7.5, 'mm')
self.primaryChannelsGeom.sections[0] = (0.002, 0.2)
self.primaryChannelsGeom.sections[1] = (0.004, 0.1)
self.primaryChannelsGeom.sections[2] = (0.006, 0.1)
self.primaryChannelsGeom.sections[3] = (0.0065, 0.1)
self.primaryChannelsGeom.sections[4] = (0.007, 0.3)
self.secondaryChannelsGeom.number = 3
self.secondaryChannelsGeom.radialPosition = (17.5, 'mm')
self.secondaryChannelsGeom.startingAngle = (60, 'deg')
self.secondaryChannelsGeom.meshFineness = 4
self.secondaryChannelsGeom.channelName = "SecondaryChannel"
self.secondaryChannelsGeom.externalDiameter = (7.5, 'mm')
self.secondaryChannelsGeom.sections[0] = (0.002, 0.2)
self.secondaryChannelsGeom.sections[1] = (0.004, 0.1)
self.secondaryChannelsGeom.sections[2] = (0.006, 0.1)
self.secondaryChannelsGeom.sections[3] = (0.0065, 0.1)
self.secondaryChannelsGeom.sections[4] = (0.007, 0.3)
self.primaryFlowIn.fluidName = 'ParaHydrogen'
self.primaryFlowIn.flowRateChoice = 'm'
self.primaryFlowIn.mDot = (1, 'kg/h')
self.primaryFlowIn.T = (100, 'K')
self.primaryFlowIn.p = (1, 'bar')
self.secondaryFlowIn.fluidName = 'ParaHydrogen'
self.secondaryFlowIn.flowRateChoice = 'm'
self.secondaryFlowIn.mDot = (1, 'kg/h')
self.secondaryFlowIn.T = (100, 'K')
self.secondaryFlowIn.p = (1, 'bar')
self.externalFlowIn.solName = 'MEG'
self.externalFlowIn.solMassFraction = (50, '%')
self.externalFlowIn.flowRateChoice = 'V'
self.externalFlowIn.VDot = (3, 'm**3/h')
self.externalFlowIn.T = (80, 'degC')
self.externalFlowIn.p = (1, 'bar')
self.externalChannelGeom.widthAxial = (30, 'mm')
self.externalChannelGeom.heightRadial = (12, 'mm')
self.externalChannelGeom.coilPitch = (32, 'mm')
self.externalChannelGeom.meshFineness = 4
self.sectionResultsSettings.setTRange = False
self.sectionResultsSettings.Tmin = (100, 'K')
self.sectionResultsSettings.Tmax = (380, 'K')
def __init__(self):
self.blockGeom.diameter = (60.0, 'mm')
self.blockGeom.length = (1.0, 'm')
self.blockProps.divisionStep = (0.1, 'm')
self.blockProps.material = 'Aluminium6061'
self.primaryChannelsGeom.number = 4
self.primaryChannelsGeom.radialPosition = (10, 'mm')
self.primaryChannelsGeom.startingAngle = (0, 'deg')
self.primaryChannelsGeom.meshFineness = 3
self.primaryChannelsGeom.channelName = "PrimaryChannel"
self.primaryChannelsGeom.externalDiameter = (10, 'mm')
self.primaryChannelsGeom.sections[0] = (0.000, 0.2)
self.primaryChannelsGeom.sections[1] = (0.002, 0.2)
self.primaryChannelsGeom.sections[2] = (0.004, 0.2)
self.primaryChannelsGeom.sections[3] = (0.006, 0.2)
self.primaryChannelsGeom.sections[4] = (0.008, 0.2)
self.secondaryChannelsGeom.number = 6
self.secondaryChannelsGeom.radialPosition = (22.5, 'mm')
self.secondaryChannelsGeom.startingAngle = (60, 'deg')
self.secondaryChannelsGeom.meshFineness = 3
self.secondaryChannelsGeom.channelName = "SecondaryChannel"
self.secondaryChannelsGeom.externalDiameter = (7, 'mm')
self.secondaryChannelsGeom.sections[0] = (0.002, 0.2)
self.secondaryChannelsGeom.sections[1] = (0.003, 0.2)
self.secondaryChannelsGeom.sections[2] = (0.004, 0.2)
self.secondaryChannelsGeom.sections[3] = (0.005, 0.2)
self.secondaryChannelsGeom.sections[4] = (0.006, 0.2)
self.primaryFlowIn.fluidName = 'Ammonia'
self.primaryFlowIn.flowRateChoice = 'm'
self.primaryFlowIn.mDot = (50, 'kg/h')
self.primaryFlowIn.T = (400, 'K')
self.primaryFlowIn.p = (20, 'bar')
self.secondaryFlowIn.fluidName = 'Ammonia'
self.secondaryFlowIn.flowRateChoice = 'm'
self.secondaryFlowIn.mDot = (50, 'kg/h')
self.secondaryFlowIn.T = (400, 'K')
self.secondaryFlowIn.p = (20, 'bar')
self.externalFlowIn.solName = 'MPG'
self.externalFlowIn.solMassFraction = (50, '%')
self.externalFlowIn.flowRateChoice = 'V'
self.externalFlowIn.VDot = (0.5, 'm**3/h')
self.externalFlowIn.T = (20, 'degC')
self.externalFlowIn.p = (1, 'bar')
self.externalChannelGeom.widthAxial = (40, 'mm')
self.externalChannelGeom.heightRadial = (10, 'mm')
self.externalChannelGeom.coilPitch = (43, 'mm')
self.externalChannelGeom.meshFineness = 3
self.sectionResultsSettings.setTRange = False
self.sectionResultsSettings.Tmin = (200, 'K')
self.sectionResultsSettings.Tmax = (350, 'K')
def computeAsync(self):
# PreComputation
self.externalChannelGeom.compute(self.blockGeom.diameter)
self.primaryChannelsGeom.compute()
self.secondaryChannelsGeom.compute()
self.primaryFlowIn.compute()
self.secondaryFlowIn.compute()
self.externalFlowIn.compute()
# Validation
self.validateInputs()
# Create the mesh
mesher = HeatExchangerMesher()
mesher.create(self)
# Create channel calculator objects
solver = HeatExchangerSolver(self, mesher)
solver.createChannelCalculators(self)
# Produce geometry/mesh drawings
self.drawGeometry(mesher, solver)
solver.solve(self)
# Produce results
self.postProcess(mesher, solver)
def drawGeometry(self, mesher, solver):
# Draw the mesh
vertexCoords = mesher.mesh.vertexCoords
vertexIDs = mesher.mesh._orderedCellVertexIDs
triPlotMesh = tri.Triangulation(vertexCoords[0], vertexCoords[1],
np.transpose(vertexIDs))
self.meshView.triplot(triPlotMesh)
self.meshView.set_aspect('equal')
self.meshView.set_title('%d elements' %
len(mesher.mesh.cellCenters[0]))
# Draw the channels profiles
ticks = ticker.FuncFormatter(lambda x, pos: '{0:g}'.format(x * 1e3))
solver.primChannelCalc.plotGeometry(self.primaryChannelProfileView)
self.primaryChannelProfileView.set_xlabel('[m]')
self.primaryChannelProfileView.set_ylabel('[mm]')
self.primaryChannelProfileView.yaxis.set_major_formatter(ticks)
solver.secChannelCalc.plotGeometry(self.secondaryChannelProfileView)
self.secondaryChannelProfileView.set_xlabel('[m]')
self.secondaryChannelProfileView.set_ylabel('[mm]')
self.secondaryChannelProfileView.yaxis.set_major_formatter(ticks)
#Draw the cross-section profile
crossSectionProfile = HeatExchangerCrossSectionProfile()
crossSectionProfile.addBlock(self.blockGeom)
crossSectionProfile.addChannels(self.primaryChannelsGeom)
crossSectionProfile.addChannels(self.secondaryChannelsGeom)
crossSectionProfile.plotGeometry(self.crossSectionProfileView)
self.crossSectionProfileView.set_xlabel('[mm]')
self.crossSectionProfileView.set_ylabel('[mm]')
self.crossSectionProfileView.xaxis.set_major_formatter(ticks)
self.crossSectionProfileView.yaxis.set_major_formatter(ticks)
#Draw the longitudinal profile
longitudinalProfile = HeatExchangerLongitudinalProfile()
longitudinalProfile.addBlock(self.blockGeom)
longitudinalProfile.addExternalChannel(self.externalChannelGeom)
longitudinalProfile.plotGeometry(self.longitudinalProfileView)
self.longitudinalProfileView.set_xlabel('[mm]')
self.longitudinalProfileView.set_ylabel('[mm]')
self.longitudinalProfileView.xaxis.set_major_formatter(ticks)
self.longitudinalProfileView.yaxis.set_major_formatter(ticks)
def postProcess(self, mesher, solver):
# Get the value for the outlet conditions
self.primaryFlowOut.compute(fState=solver.primChannelStateOut,
mDot=self.primaryFlowIn.mDot)
self.secondaryFlowOut.compute(fState=solver.secChannelStateOut,
mDot=self.secondaryFlowIn.mDot)
self.externalFlowOut.compute(fState=solver.extChannelStateOut,
mDot=self.externalFlowIn.mDot)
self.QDotChannels.QDotPrimaryChannels = self.primaryFlowIn.mDot * \
abs(self.primaryFlowOut.fState.h - self.primaryFlowIn.fState.h)
self.QDotChannels.QDotSecondaryChannels = self.secondaryFlowIn.mDot * \
abs(self.secondaryFlowOut.fState.h - self.secondaryFlowIn.fState.h)
self.QDotChannels.QDotExternalChannel = self.externalFlowIn.mDot * \
abs(self.externalFlowOut.fState.h - self.externalFlowIn.fState.h)
# Fill the table with values
self.resultTable.resize(solver.numSectionSteps)
self.resultTPlot.resize(solver.numSectionSteps)
self.resultQPlot.resize(solver.numSectionSteps)
for i in range(solver.numSectionSteps):
self.resultTable[i] = (
solver.primChannelCalc.sections[i].xStart,
solver.primChannelCalc.sections[i].xEnd,
solver.primChannelCalc.sections[i].fState.T,
solver.primChannelCalc.sections[i].TWall,
solver.primChannelCalc.sections[i].Re,
solver.primChannelCalc.sections[i].hConv,
abs(solver.primChannelCalc.sections[i].QDotWall),
solver.secChannelCalc.sections[i].fState.T,
solver.secChannelCalc.sections[i].TWall,
solver.secChannelCalc.sections[i].Re,
solver.secChannelCalc.sections[i].hConv,
abs(solver.secChannelCalc.sections[i].QDotWall),
solver.extChannelCalc.sections[i].fState.T,
solver.extChannelCalc.sections[i].TWall,
solver.extChannelCalc.sections[i].Re,
solver.extChannelCalc.sections[i].hConv,
abs(solver.extChannelCalc.sections[i].QDotWall),
)
self.resultTPlot[i] = (
(solver.primChannelCalc.sections[i].xStart +
solver.primChannelCalc.sections[i].xEnd) / 2,
solver.primChannelCalc.sections[i].fState.T,
solver.primChannelCalc.sections[i].TWall,
solver.secChannelCalc.sections[i].fState.T,
solver.secChannelCalc.sections[i].TWall,
solver.extChannelCalc.sections[i].fState.T,
solver.extChannelCalc.sections[i].TWall,
)
self.resultQPlot[i] = (
(solver.primChannelCalc.sections[i].xStart +
solver.primChannelCalc.sections[i].xEnd) / 2,
abs(solver.primChannelCalc.sections[i].QDotWall),
abs(solver.secChannelCalc.sections[i].QDotWall),
abs(solver.extChannelCalc.sections[i].QDotWall),
)
def validateInputs(self):
self.validateChannels(self.primaryChannelsGeom, "primary")
self.validateChannels(self.secondaryChannelsGeom, "secondary")
if self.externalChannelGeom.widthAxial > self.externalChannelGeom.coilPitch:
raise ValueError(
'The coil pitch of the external channel is less than the axial width.'
)
def validateChannels(self, channelsGeom, channelsName):
if self.blockGeom.diameter <= channelsGeom.externalDiameter:
raise ValueError(
'The block diameter is less than the external diameter of the {0} channels.'
.format(channelsName))
if self.blockGeom.diameter / 2. <= (
channelsGeom.radialPosition +
channelsGeom.externalDiameter / 2.):
raise ValueError(
'The radial position of the {0} channels is too big (the channels are outside of the block).'
.format(channelsName))
if self.blockGeom.length != channelsGeom.length:
raise ValueError(
'The length of the block is different from the length of the {0} channels.'
.format(channelsName))
i = 0
for section in channelsGeom.sections:
if (section['length'] < self.blockProps.divisionStep):
raise ValueError(
'The axial division step of the block is greater than the {0}-th section of the {1} channels'
.format(i, channelsName))
if self.isDividedExactly(section['length'],
self.blockProps.divisionStep) == False:
raise ValueError(
'The axial division step of the block does not divide the {0}-th section of the {1} channels in equal parts.'
.format(i, channelsName))
i += 1
def isDividedExactly(self, a, b):
bigE = 1e6
return int(a * bigE) % int(b * bigE) == 0
class ChemostatSimple(NumericalModel):
label = "Simple Chemostat"
description = F.ModelDescription(
"Simple chemostat model with ordinary differential equations (ODE)",
show=True)
figure = F.ModelFigure(
src="BioReactors/img/ModuleImages/SimpleChemostat.png", show=False)
async = True
progressOptions = {'suffix': 'day', 'fractionOutput': True}
#1. ############ Inputs ###############
#1.1 Fields - Input values
S_in = F.Quantity('Bio_MassConcentration',
default=(5, 'g/L'),
minValue=(0, 'g/L'),
label='S<sub>in</sub>',
description='input substrate concentration')
X_in = F.Quantity('Bio_MassConcentration',
default=(0.0, 'g/L'),
minValue=(0, 'g/L'),
label='X<sub>in</sub>',
description='input microorganisms concentration')
m = F.Quantity(
'Bio_TimeRate',
default=(3, '1/day'),
minValue=(0, '1/day'),
label='m',
description='maximum specific growth rate of the microorganisms')
K = F.Quantity('Bio_MassConcentration',
default=(3.7, 'g/L'),
minValue=(0, 'g/L'),
label='K',
description='half saturation constant')
gamma = F.Quantity(default=0.6,
minValue=0,
maxValue=1.0,
label='γ',
description='yield coefficient of microorganisms')
D_vals = F.RecordArray((
('time',
F.Quantity('Bio_Time',
default=(20, 'day'),
minValue=(0, 'day'),
label='Duration')),
('D',
F.Quantity('Bio_TimeRate',
default=(1, '1/day'),
minValue=(0, '1/day'),
label='D')),
),
label='D',
description='dilution (or washout) rate')
parametersFG = F.FieldGroup([S_in, X_in, m, K, gamma, D_vals],
label="Parameters")
S0 = F.Quantity('Bio_MassConcentration',
default=(0, 'g/L'),
minValue=0,
label='S<sub>0</sub>',
description='initial substrate concentration')
X0 = F.Quantity('Bio_MassConcentration',
default=(0.5, 'g/L'),
minValue=0,
label='X<sub>0</sub>',
description='initial microorganisms concentration')
initialValuesFG = F.FieldGroup([S0, X0], label="Initial values")
inputValuesSG = F.SuperGroup([parametersFG, initialValuesFG],
label="Input values")
#1.2 Fields - Settings
tFinal = F.Quantity('Bio_Time',
default=(100, 'day'),
minValue=(0, 'day'),
maxValue=(1000, 'day'),
label='simulation time')
tPrint = F.Quantity('Bio_Time',
default=(0.1, 'day'),
minValue=(1e-5, 'day'),
maxValue=(100, 'day'),
label='print interval')
solverFG = F.FieldGroup([tFinal, tPrint], label='Solver')
settingsSG = F.SuperGroup([solverFG], label='Settings')
#1.4 Model view
inputView = F.ModelView(ioType="input",
superGroups=[inputValuesSG, settingsSG],
autoFetch=True)
#2. ############ Results ###############
storage = F.HdfStorage(hdfFile=DM.dataStorageFilePath,
hdfGroup=DM.dataStorageDatasetPath)
dataSeries = (('time', F.Quantity('Bio_Time', default=(1, 'day'))),
('S', F.Quantity('Bio_MassConcentration',
default=(1, 'g/L'))),
('X', F.Quantity('Bio_MassConcentration',
default=(1, 'g/L'))),
('D', F.Quantity('Bio_TimeRate', default=(1, '1/day'))))
plot = F.PlotView(dataSeries,
label='Plot',
options={'ylabel': None},
useHdfStorage=True,
storage='storage')
table = F.TableView(dataSeries,
label='Table',
options={
'title': 'Simple Chemostat',
'formats': ['0.000', '0.000', '0.000', '0.000']
},
useHdfStorage=True,
storage='storage')
resultsVG = F.ViewGroup([plot, table], label='Results')
storageVG = F.ViewGroup([storage], show="false")
resultsSG = F.SuperGroup([resultsVG, storageVG])
#2.1 Model view
resultView = F.ModelView(ioType="output", superGroups=[resultsSG])
############# Page structure ########
modelBlocks = [inputView, resultView]
def computeAsync(self):
# Create the model
chemostat = DM.ChemostatSimple(self)
# Run simulation
chemostat.prepareSimulation()
chemostat.run(self)
# Show results
self.storage = chemostat.resultStorage.simulationName