>>> import thermosteam as tmo
>>> thermo_data = tmo.ThermoData.from_yaml(file_path) # A from_json method would also be available
>>> thermo_data.create_chemicals() 
CompiledChemicals([Water, Ethanol, O2, Cellulose])
>>> # Or alternatively, just load a few
>>>  thermo_data.create_chemicals(['Water', 'Cellulose']) 
CompiledChemicals([Water, Cellulose])

import thermosteam as tmo
chemicals = tmo.Chemicals(['Water', 'Ethanol', 'O2'])
Cellulose = Chemical.blank('Cellulose', phase='s', formula='C6H10O5', Hf=-975708.8)
Cellulose.default()
chemicals.append(Cellulose)
chemicals.O2.at_state('g')
chemicals.compile()
chemicals.set_synonym('Water', 'H2O')

>>> # To start creating streams; we need to set the thermo package
>>> tmo.settings.set_thermo(chemicals)
>>> # Now we can create all the streams
>>> streams = thermo_data.create_streams()
>>> streams
[<Stream: process_water>, <Stream: gasoline>]
>>> # Alternatively, choose to create the streams we want
>>> gasoline = thermo_data.create_streams('gasoline')
>>> gasoline.show(flow='kg/hr')
Stream: gasoline
 phase: 'l', T: 298.15 K, P: 101325 Pa
 flow (kg/hr): Octane  400

import thermosteam as tmo

chems = tmo.Chemicals(['Water', 'Ethanol', 'CH4', 'HMF', 'Furfural'])
tmo.settings.set_thermo(chems)

chems.HMF.Hfus = 19.8
chems.Furfural.Hfus = 14370
chems.HMF.copy_missing_slots_from(chems.Furfural)

ms_no_HMF = tmo.Stream('ms_no_HMF', units='kmol/hr', T=300, P=101325,
                       Water=4.649e+04, Ethanol=50, CH4=800, Furfural=0.5)
ms_with_HMF = tmo.Stream('ms_with_HMF', units='kmol/hr', T=300, P=101325,
                         Water=4.649e+04, Ethanol=50, CH4=800, Furfural=0.5,
                         HMF=0.5)

print('No HMF: '+str(ms_no_HMF.H))
print('With HMF: '+str(ms_with_HMF.H))

for chem in chems:
    print(str(chem.ID)+': '+str(chem.Hfus))

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Aug 23 12:11:15 2020

Modified from the cornstover biorefinery constructed in Cortes-Peña et al., 2020,
with modification of fermentation system for 2,3-Butanediol instead of the original ethanol

[1] Cortes-Peña et al., BioSTEAM: A Fast and Flexible Platform for the Design, 
    Simulation, and Techno-Economic Analysis of Biorefineries under Uncertainty. 
    ACS Sustainable Chem. Eng. 2020, 8 (8), 3302–3310. 
    https://doi.org/10.1021/acssuschemeng.9b07040.

All units are explicitly defined here for transparency and easy reference

@author: sarangbhagwat
"""

# %%  

# =============================================================================
# Setup
# =============================================================================

import thermosteam as tmo
from thermosteam import functional as fn

__all__ = ('TAL_chemicals', 'chemical_groups', 'soluble_organics', 'combustibles')

# chems is the object containing all chemicals used in this biorefinery
chems = TAL_chemicals = tmo.Chemicals([])

# To keep track of which chemicals are available in the database and which
# are created from scratch
database_chemicals_dict = {}
copied_chemicals_dict = {}
defined_chemicals_dict = {}

def chemical_database(ID, phase=None, **kwargs):
    chemical = tmo.Chemical(ID, **kwargs)
    if phase:
        chemical.at_state(phase)
        chemical.phase_ref = phase
    chems.append(chemical)
    database_chemicals_dict[ID] = f'{ID}: {chemical.formula}/{chemical.MW}'
    return chemical

def chemical_copied(ID, ref_chemical, **data):
    chemical = ref_chemical.copy(ID)
    chems.append(chemical)
    for i, j in data.items(): setattr(chemical, i, j)
    copied_chemicals_dict[ID] = f'{ID}: {chemical.formula}/{chemical.MW}'
    return chemical

def chemical_defined(ID, **kwargs):
    chemical = tmo.Chemical.blank(ID, **kwargs)
    chems.append(chemical)
    defined_chemicals_dict[ID] = f'{ID}: {chemical.formula}/{chemical.MW}'
    return chemical

_cal2joule = 4.184


# %% 

# =============================================================================
# Create chemical objects available in database
# Some common names might not be pointing to the correct chemical,
# therefore more accurate ones were used (e.g. NitricOxide was used instead of NO),
# data from Humbird et al. unless otherwise noted
# =============================================================================

H2O = chemical_database('H2O')

# =============================================================================
# Gases
# =============================================================================

O2 = chemical_database('O2', phase='g', Hf=0)
N2 = chemical_database('N2', phase='g', Hf=0)
H2 = chemical_database('H2', phase='g')
CH4 = chemical_database('CH4', phase='g')
CarbonMonoxide = chemical_database('CarbonMonoxide', phase='g', 
                                        Hf=-26400*_cal2joule)
CO2 = chemical_database('CO2', phase='g')
NH3 = chemical_database('NH3', phase='g', Hf=-10963*_cal2joule)
NitricOxide = chemical_database('NitricOxide', phase='g')
NO2 = chemical_database('NO2', phase='g')
H2S = chemical_database('H2S', phase='g', Hf=-4927*_cal2joule)
SO2 = chemical_database('SO2', phase='g')

# =============================================================================
# Soluble inorganics
# =============================================================================

H2SO4 = chemical_database('H2SO4', phase='l')
HCl = chemical_copied('HCl', H2SO4) # HCl giving errors; doesn't change things much for TAL SA biorefinery
HNO3 = chemical_database('HNO3', phase='l', Hf=-41406*_cal2joule)
NaOH = chemical_database('NaOH', phase='l')
KOH = chemical_database('KOH', phase = 's')

KCl = chemical_database('KCl', phase = 's')
# Arggone National Lab active thermochemical tables, accessed 04/07/2020
# https://atct.anl.gov/Thermochemical%20Data/version%201.118/species/?species_number=928
AmmoniumHydroxide = chemical_database('AmmoniumHydroxide', phase='l', Hf=-336.719e3)
CalciumDihydroxide = chemical_database('CalciumDihydroxide',
                                        phase='s', Hf=-235522*_cal2joule)
AmmoniumSulfate = chemical_database('AmmoniumSulfate', phase='l',
                                    Hf=-288994*_cal2joule)
NaNO3 = chemical_database('NaNO3', phase='l', Hf=-118756*_cal2joule)
# NIST https://webbook.nist.gov/cgi/cbook.cgi?ID=C7757826&Mask=2, accessed 04/07/2020
Na2SO4 = chemical_database('Na2SO4', phase='l', Hf=-1356.38e3)
# CaSO4 = chemical_database('CaSO4', phase='s', Hf=-342531*_cal2joule)
# The default Perry 151 model has a crazy value, use another model instead
# CaSO4.Cn.move_up_model_priority('Constant', 0)
# 

# =============================================================================
# Soluble organic salts
# =============================================================================

Ethanol = chemical_database('Ethanol')
Acetate = chemical_database('Acetate', phase='l', Hf=-108992*_cal2joule)
AmmoniumAcetate = chemical_database('AmmoniumAcetate', phase='l', 
                                         Hf=-154701*_cal2joule)

# Hf from a Ph.D. dissertation (Lactic Acid Production from Agribusiness Waste Starch
# Fermentation with Lactobacillus Amylophilus and Its Cradle-To-Gate Life 
# Cycle Assessment as A Precursor to Poly-L-Lactide, by Andréanne Harbec)
# The dissertation cited Cable, P., & Sitnai, O. (1971). The Manufacture of 
# Lactic Acid by the Fermentation of Whey: a Design and Cost Study. 
# Commonwealth Scientific and Industrial Research Organization, Australia, 
# which was also cited by other studies, but the origianl source cannot be found online
CalciumLactate = chemical_database('CalciumLactate', phase='l',
                                   Hf=-1686.1e3)
# Hf from Lange's Handbook of Chemistry, 15th edn., Table 6.3, PDF page 631
CalciumAcetate = chemical_database('CalciumAcetate', phase='l', Hf=-1514.73e3)

# Solubility of CalciumSuccinate is 3.2 g/L in water as Ca2+ based on 
# Burgess and Drasdo, Polyhedron 1993, 12 (24), 2905–2911, which is 12.5 g/L as CaSA
# Baseline CalciumSuccinate is ~14 g/L in fermentation broth, thus assumes all 
# CalciumSuccinate in liquid phase
CalciumSuccinate = chemical_database('CalciumSuccinate', phase='l')

# =============================================================================
# Soluble organics
# =============================================================================

AceticAcid = chemical_database('AceticAcid')
Glucose = chemical_database('Glucose', phase = 'l')

# TAL = chemical_database('Triacetic acid lactone')

# SA = chemical_database('Sorbic acid')
# KSA = chemical_database('Potassium sorbate')
# BSA = chemical_database('Butyl sorbate')

IBA = chemical_database('Isobutyraldehyde')
DPHP = chemical_database('Dipotassium hydrogen phosphate', phase = 'l')

# This one is more consistent with others
# try: Glucose.Cn.l.move_up_model_priority('Dadgostar and Shaw (2011)', 0)
# except: Glucose.Cn.move_up_model_priority('Dadgostar and Shaw (2011)', 0)
GlucoseOligomer = chemical_defined('GlucoseOligomer', phase='l', formula='C6H10O5',
                                   Hf=-233200*_cal2joule)
GlucoseOligomer.copy_models_from(Glucose, ['Hvap', 'Psat', 'Cn', 'mu', 'kappa'])
Extract = chemical_copied('Extract', Glucose)

Xylose = chemical_database('Xylose')
Xylose.copy_models_from(Glucose, ['Hvap', 'Psat', 'mu'])
XyloseOligomer = chemical_defined('XyloseOligomer', phase='l', formula='C5H8O4',
                                  Hf=-182100*_cal2joule)
XyloseOligomer.copy_models_from(Xylose, ['Hvap', 'Psat', 'Cn', 'mu'])

Sucrose = chemical_database('Sucrose', phase='l')
Sucrose.Cn.move_up_model_priority('Dadgostar and Shaw (2011)', 0)
Cellobiose = chemical_database('Cellobiose', phase='l', Hf=-480900*_cal2joule)

Mannose = chemical_database('Mannose', phase='l', Hf=Glucose.Hf)
Mannose.copy_models_from(Glucose, ['Hvap', 'Psat', 'Cn', 'mu'])
MannoseOligomer = chemical_copied('MannoseOligomer', GlucoseOligomer)

Galactose = chemical_database('Galactose', phase='l', Hf=Glucose.Hf)
Galactose.copy_models_from(Glucose, ['Hvap', 'Psat', 'Cn','mu'])
GalactoseOligomer = chemical_copied('GalactoseOligomer', GlucoseOligomer)

Arabinose = chemical_database('Arabinose', phase='l', Hf=Xylose.Hf)
Arabinose.copy_models_from(Xylose, ['Hvap', 'Psat', 'mu'])
ArabinoseOligomer = chemical_copied('ArabinoseOligomer', XyloseOligomer)

SolubleLignin = chemical_database('SolubleLignin', search_ID='Vanillin', 
                                  phase='l', Hf=-108248*_cal2joule)
Protein = chemical_defined('Protein', phase='l', 
                           formula='CH1.57O0.31N0.29S0.007', 
                           Hf=-17618*_cal2joule)
Enzyme = chemical_defined('Enzyme', phase='l', 
                           formula='CH1.59O0.42N0.24S0.01', 
                           Hf=-17618*_cal2joule)
# Properties of fermentation microbes copied from Z_mobilis as in Humbird et al.
FermMicrobe = chemical_defined('FermMicrobe', phase='l',
                      formula='CH1.8O0.5N0.2', Hf=-31169.39*_cal2joule)
WWTsludge = chemical_defined('WWTsludge', phase='s', 
                             formula='CH1.64O0.39N0.23S0.0035', 
                             Hf=-23200.01*_cal2joule)

Furfural = chemical_database('Furfural')


Acetoin = chemical_database('3-Hydroxybutanone', phase = None, Hvap = 44.56*1000) # , V = 89.5e-6
Acetoin.copy_models_from(Furfural, ['Psat', 'Cn', 'mu', 'kappa', 'V'])
Acetoin.Tb = 145.4 + 273.15


Hexanol = chemical_database('Hexanol')
Heptane = chemical_database('Heptane')
Toluene = chemical_database('Toluene')
# Tb from chemspider(chemenu database)
# http://www.chemspider.com/Chemical-Structure.207215.html, accessed 04/07/2020
# https://www.chemenu.com/products/CM196167, accessed 04/07/2020
# Using Millipore Sigma's Pressure-Temperature Nomograph Interactive Tool at
# https://www.sigmaaldrich.com/chemistry/solvents/learning-center/nomograph.html,
# will give ~300°C at 760 mmHg if using the 115°C Tb at 1 mmHg (accessed 04/07/2020)
# Hfus from NIST, accessed 04/24/2020
# https://webbook.nist.gov/cgi/cbook.cgi?ID=C67470&Mask=4
HMF = chemical_database('HMF', Hf=-99677*_cal2joule, Tb=291.5+273.15, Hfus=19800)
HMF.copy_models_from(Furfural, ['V', 'Hvap', 'Psat', 'mu', 'kappa'])
HMF.Dortmund.update(chems.Furfural.Dortmund)

# TAL = chemical_copied('Triacetic acid lactone', HMF)
# SA = chemical_copied('Sorbic acid', HMF)
# KSA = chemical_copied('Potassium sorbate', HMF)
# BSA = chemical_copied('Butyl sorbate', HMF)

TAL = Triaceticacidlactone = chemical_database('Triacetic acid lactone')
TAL.copy_models_from(Furfural, ['Psat', 'Hvap'])
SA = Sorbicacid =  chemical_database('Sorbic acid')
KSA = Potassiumsorbate = chemical_database('Potassium sorbate')
BSA = Butylsorbate = chemical_database('Butyl sorbate')
HMTHP = chemical_copied('HMTHP', TAL)

TAL.Tm = KSA.Tm = 185 + 273.15
TAL.Tb = KSA.Tb =  239.1 + 273.15

# https://pubchem.ncbi.nlm.nih.gov/compound/Sorbic-acid#section=Stability-Shelf-Life
SA.Tb = 228 + 273.15

BSA.Tm = 130 + 273.15
BSA.Tb = 226.5 + 273.15

VitaminA = chemical_database('VitaminA')
VitaminD2 = chemical_database('VitaminD2')
# Hfus from NIST, condensed phase, accessed 04/07/2020
# https://webbook.nist.gov/cgi/cbook.cgi?ID=C87990&Mask=4
Xylitol = chemical_database('Xylitol', phase='l', Hf=-243145*_cal2joule, Hfus=-1118.6e3)

# Hfus from NIST, accessed 04/07/2020
# https://webbook.nist.gov/cgi/cbook.cgi?ID=C50215&Mask=4
# LacticAcid = chemical_database('LacticAcid', Hfus=11.34e3)
LacticAcid = chemical_database('LacticAcid')
LacticAcid.Hfus = 11.34e3

SuccinicAcid = chemical_database('SuccinicAcid', phase_ref='s')

EthylAcetate = chemical_database('EthylAcetate')
# Hf from DIPPR value in Table 3 of Vatani et al., Int J Mol Sci 2007, 8 (5), 407–432
EthylLactate = chemical_database('EthylLactate', Hf=-695.08e3)

EthylSuccinate = chemical_database('EthylSuccinate')
# Cannot find data on Hf of CalciumSuccinate, estimate here assuming
# Hrxn for Ca(OH)2 and SA and Ca(OH)2 and LA are the same 
CalciumSuccinate.Hf = CalciumLactate.Hf + (SuccinicAcid.Hf-2*LacticAcid.Hf)


# =============================================================================
# Insoluble organics
# =============================================================================

Glucan = chemical_defined('Glucan', phase='s', formula='C6H10O5', Hf=-233200*_cal2joule)
Glucan.copy_models_from(Glucose, ['Cn'])
Mannan = chemical_copied('Mannan', Glucan)
Galactan = chemical_copied('Galactan', Glucan)

Xylan = chemical_defined('Xylan', phase='s', formula='C5H8O4', Hf=-182100*_cal2joule)
Xylan.copy_models_from(Xylose, ['Cn'])
Arabinan = chemical_copied('Arabinan', Xylan)

Lignin = chemical_database('Lignin', phase='s')
# Hf scaled based on vanillin
Lignin.Hf = -108248*_cal2joule/tmo.Chemical('Vanillin').MW*Lignin.MW

# =============================================================================
# Insoluble inorganics
# =============================================================================

# Holmes, Trans. Faraday Soc. 1962, 58 (0), 1916–1925, abstract
# This is for auto-population of combustion reactions
P4O10 = chemical_database('P4O10', phase='s', Hf=-713.2*_cal2joule)
Ash = chemical_database('Ash', search_ID='CaO', phase='s', Hf=-151688*_cal2joule,
                        HHV=0, LHV=0)
# This is to copy the solid state of Xylose,
# cannot directly use Xylose as Xylose is locked at liquid state now
Tar = chemical_copied('Tar', Xylose, phase_ref='s')

# =============================================================================
# Mixtures
# =============================================================================

# CSL is modeled as 50% water, 25% protein, and 25% lactic acid in Humbird et al.,
# did not model separately as only one price is given
CSL = chemical_defined('CSL', phase='l', formula='CH2.8925O1.3275N0.0725S0.00175', 
                      Hf=Protein.Hf/4+H2O.Hf/2+LacticAcid.Hf/4)

# Boiler chemicals includes amine, ammonia, and phosphate,
# did not model separately as composition unavailable and only one price is given
BoilerChems = chemical_database('BoilerChems', search_ID='DiammoniumPhosphate',
                                phase='l', Hf=0, HHV=0, LHV=0)

# =============================================================================
# Filler
# =============================================================================

BaghouseBag = chemical_defined('BaghouseBag', phase='s', MW=1, Hf=0, HHV=0, LHV=0)
BaghouseBag.Cn.add_model(0)
CoolingTowerChems = chemical_copied('CoolingTowerChems', BaghouseBag)

# =============================================================================
# Not currently in use
# =============================================================================

DAP = chemical_database('DAP', search_ID='DiammoniumPhosphate',
                             phase='l', Hf= -283996*_cal2joule)
Methanol = chemical_database('Methanol')
MethylAcetate = chemical_database('MethylAcetate')
Denaturant = chemical_database('Denaturant', search_ID='n-Heptane')
DenaturedEnzyme = chemical_copied('DenaturedEnzyme', Enzyme)

# Hf from DIPPR value in Table 3 of Vatani et al., Int J Mol Sci 2007, 8 (5), 407–432
MethylLactate = chemical_database('MethylLactate', Hf=-643.1e3)
FermMicrobeXyl = chemical_copied('FermMicrobeXyl', FermMicrobe)


# %% 

# =============================================================================
# Group chemicals
# =============================================================================

#!!! Sarang please review and update this dict, it affects simulation
chemical_groups = dict(
    OtherSugars = ('Arabinose', 'Mannose', 'Galactose', 'Cellobiose', 'Sucrose'),
    SugarOligomers = ('GlucoseOligomer', 'XyloseOligomer', 'GalactoseOligomer',
                      'ArabinoseOligomer', 'MannoseOligomer'),
    OrganicSolubleSolids = ('AmmoniumAcetate', 'SolubleLignin', 'Extract', 'CSL',
                            # 'Triacetic acid lactone',
                            'Sorbic acid', 'HMTHP',
                            'Potassium sorbate', 'Butyl sorbate', 'VitaminA', 'VitaminD2'),
                            # 'LacticAcid', 'CalciumLactate', 'CalciumAcetate',
                            # 'EthylLactate', 'EthylAcetate', 'SuccinicAcid',
                            # 'CalciumSuccinate', 'EthylSuccinate', 
                            # 'Methanol', 'MethylLactate', 'MethylAcetate'),
    InorganicSolubleSolids = ('AmmoniumSulfate', 'NaOH', 'HNO3', 'NaNO3',
                              # 'DAP',
                              'BoilerChems', 'Na2SO4', 'AmmoniumHydroxide'),
    Furfurals = ('Furfural', 'HMF'),
    #!!! I suspect you want to add some chemicals here
    OtherOrganics = ('Denaturant', 'Xylitol'),
    COSOxNOxH2S = ('NitricOxide', 'NO2', 'SO2', 'CarbonMonoxide', 'H2S'),
    Proteins = ('Protein', 'Enzyme', 'DenaturedEnzyme'),
    CellMass = ('WWTsludge', 'FermMicrobe'),
                # 'FermMicrobeXyl'),
    # Theoretically P4O10 should be soluble, but it's the product of the
    # auto-populated combusion reactions so should in solid phase, however no
    # P4O10 will be generated in the system as no P-containing chemicals 
    # are included in "combustibles"
    OtherInsolubleSolids = ('Tar', 'Ash', 'CalciumDihydroxide', 'P4O10',
                            'BaghouseBag', 'CoolingTowerChems'),
    OtherStructuralCarbohydrates = ('Glucan', 'Xylan', 'Lignin', 'Arabinan', 
                                    'Mannan', 'Galactan'),
    SeparatelyListedOrganics = ('Ethanol', 'Glucose', 'Xylose', 'AceticAcid',
                                'Acetate', 'Lignin'),
    SpearatedlyListedOthers = ('H2O', 'NH3', 'H2SO4', 'CO2', 'CH4', 'O2', 'N2')
    )

# This group is needed in the system.py module
soluble_groups = ('OtherSugars', 'SugarOligomers', 'OrganicSolubleSolids',
                  'Furfurals', 'OtherOrganics', 'Proteins', 'CellMass',
                  'SeparatelyListedOrganics')
soluble_organics = list(sum([chemical_groups[i] for i in soluble_groups], ()))
soluble_organics.remove('WWTsludge')

solubles = tuple(soluble_organics) + chemical_groups['InorganicSolubleSolids'] + ('H2SO4',)

insoluble_groups = ('OtherInsolubleSolids', 'OtherStructuralCarbohydrates')
insolubles = sum([chemical_groups[i] for i in insoluble_groups], ('WWTsludge',))

# This group is needed in the system.py module
combustibles = soluble_organics + list(chemical_groups['OtherStructuralCarbohydrates'])
# combustibles.remove('CalciumLactate')
# combustibles.remove('CalciumAcetate')
combustibles.extend(['WWTsludge','NH3', 'NitricOxide', 'CarbonMonoxide', 'H2S', 'CH4'])

# Chemicals that will be modeled in Distallation/Flash units,
# list is in ascending order of Tb,
# Xylitol is not included due to high Tm and Tb thus will stay in liquid phase


# phase_change_chemicals = ['Methanol', 'Ethanol', 'H2O', 'EthylAcetate', 'Denaturant',
#                           'AceticAcid', 'MethylAcetate', 'MethylLactate',
#                           'EthylLactate', 'Furfural', 'SuccinicAcid', 'LacticAcid', 'HMF']

#!!! Sarang please review and update this, I'm not sure what chemicals are used
# in the biorefinery, getting rid of unused chemicals (i.e., exclude them from chems)
# should help reduce simulation time
phase_change_chemicals = ['Methanol', 'Ethanol', 'H2O', 'EthylAcetate', 'Denaturant',
                          'AceticAcid', 'MethylAcetate', 'MethylLactate',
                          'EthylLactate', 'Furfural', 'EthylSuccinate',
                          'SuccinicAcid', 'LacticAcid', 'HMF']

for chem in chems:
    if chem.ID in phase_change_chemicals: pass
    elif chem.locked_state: pass
    else: 
        # Set phase_ref to avoid missing model errors
        if chem.phase_ref == 'g':
            chem.at_state('g')
        if chem.ID in solubles:
            chem.phase_ref = 'l'
            chem.at_state('l')
        if chem.ID in insolubles:
            chem.phase_ref = 's'
            chem.at_state('s')


# %% 

# =============================================================================
# Set assumptions/estimations for missing properties
# =============================================================================

# Set chemical heat capacity
# Cp of biomass (1.25 J/g/K) from Leow et al., Green Chemistry 2015, 17 (6), 3584–3599
for chemical in (CSL, Protein, Enzyme, WWTsludge, 
                 DenaturedEnzyme, FermMicrobe, FermMicrobeXyl):
    chemical.Cn.add_model(1.25*chemical.MW)

# Set chemical molar volume following assumptions in lipidcane biorefinery,
# assume densities for solulables and insolubles to be 1e5 and 1540 kg/m3, respectively
# !!! This has significant impacts on results, need to double-check accuracy
def set_rho(chemical, rho):       
    V = fn.rho_to_V(rho, chemical.MW)
    chemical.V.add_model(V, top_priority=True)

for chemical in chems:
    if chemical.ID in phase_change_chemicals: pass
    elif chemical.ID in solubles: set_rho(chemical, 1e5)
    elif chemical.ID in insolubles: set_rho(chemical, 1540)

# The Lakshmi Prasad model gives negative kappa values for some chemicals
for chemical in chems:
    if chemical.locked_state:
        try: chemical.kappa.move_up_model_priority('Lakshmi Prasad', -1)
        except: pass
        
# Default missing properties of chemicals to those of water,
for chemical in chems: chemical.default()


# %%

# Though set_thermo will first compile the Chemicals object,
# compile beforehand is easier to debug because of the helpful error message
chems.compile()
tmo.settings.set_thermo(chems)
chems.set_synonym('CalciumDihydroxide', 'Lime')
chems.set_synonym('3-Hydroxybutanone', 'Acetoin')
chems.set_synonym('Triacetic acid lactone', 'TAL')
chems.set_synonym('Triacetic acid lactone', 'Triaceticacidlactone')
chems.set_synonym('Sorbic acid', 'SA')
chems.set_synonym('Sorbic acid', 'Sorbicacid')
chems.set_synonym('Potassium sorbate', 'KSA')
chems.set_synonym('Potassium sorbate', 'Potassiumsorbate')
chems.set_synonym('Butyl sorbate', 'BSA')
chems.set_synonym('Butyl sorbate', 'Butylsorbate')
chems.set_synonym('Dipotassium hydrogen phosphate', 'DPHP')
chems.set_synonym('H2O', 'Water')
chems.set_synonym('H2SO4', 'SulfuricAcid')
chems.set_synonym('NH3', 'Ammonia')
chems.set_synonym('AmmoniumSulfate', 'NH4SO4')
chems.set_synonym('Denaturant', 'Octane')
chems.set_synonym('CO2', 'CarbonDioxide')
chems.set_synonym('CarbonMonoxide', 'CO')
chems.set_synonym('NitricOxide', 'NO')
# chems.set_synonym('CaSO4', 'Gypsum')
chems.set_synonym('P4O10', 'PhosphorusPentoxide')
chems.set_synonym('Na2SO4', 'SodiumSulfate')
chems.set_synonym('AmmoniumHydroxide', 'NH4OH')
chems.set_synonym('Isobutyraldehyde', 'IBA')

# %%

# from TAL.utils import get_chemical_properties	
# get_chemical_properties(chems, 400, 101325, output=True)

>>> from thermosteam import indexer, equilibrium, settings
>>> imol = indexer.MolarFlowIndexer(l=[('Triacetic acid lactone', 304), ('Water', 30)], phases=('s', 'l'))
>>> sle = equilibrium.SLE(imol)
>>> sle('Triacetic acid lactone', T=300)
>>> sle
  File "<ipython-input-3-fa0329f2a71f>", line 4, in <module>
    sle('Triacetic acid lactone', T=300)

  File "C:\Users\saran\Documents\Academia\Spring 2020\BioSTEAM\thermosteam\thermosteam\equilibrium\sle.py", line 136, in __call__
    x = self._solve_x(T)

  File "C:\Users\saran\Documents\Academia\Spring 2020\BioSTEAM\thermosteam\thermosteam\equilibrium\sle.py", line 164, in _solve_x
    return flx.wegstein(self._x_iter, x, xtol=1e-6, args=args)

  File "C:\Users\saran\Anaconda3\envs\bioenv\lib\site-packages\flexsolve\iterative_solvers.py", line 66, in wegstein
    x1 = g0 = f(x0, *args)

  File "C:\Users\saran\Documents\Academia\Spring 2020\BioSTEAM\thermosteam\thermosteam\equilibrium\sle.py", line 172, in _x_iter
    return solubility_eutectic(T, Tm, Hm, Cpl, Cps, gamma[self._solute_index])

IndexError: index 56 is out of bounds for axis 0 with size 2

long_description=open('README.rst', encoding='utf-8').read(),

from thermosteam import Chemical, indexer, equilibrium, settings
settings.set_thermo(['Water', 'KOH'], cache=True)
imol = indexer.MolarFlowIndexer(l=[('Water', 10), ('KOH', 3)], phases=('s', 'l'))
sle = equilibrium.SLE(imol)
sle('KOH', T=298.15, P=1e5)

sle.mixture.xH(imol, *sle.thermal_condition)
sle.mixture.xmu(imol, *sle.thermal_condition)
sle.mixture.xV(imol, *sle.thermal_condition)
sle.mixture.xS(imol, *sle.thermal_condition)

import thermosteam as tmo
from thermosteam import reaction as rxn

chemicals = tmo.Chemicals(['Water', 'Methane', 'CO2', 'O2', 'Glucose', 'Ethanol'])
tmo.settings.set_thermo(chemicals)
combustion = rxn.Reaction('Methane + 2O2 -> 2Water + CO2', reactant='Methane', X=1)

heat_of_combustion = combustion.dH / chemicals['Methane'].MW

feed = tmo.Stream(Methane=1, O2=2, T=373.15, phase='g')
print('BEFORE REACTION')
feed.show(N=100)

# React feed molar flow rate
combustion(feed)

print('AFTER REACTION')
feed.show(N=100)
print('This result is zero, if the state of the fluids is not considered in the heat of reaction:')
print(heat_of_combustion - combustion.dH / chemicals['Methane'].MW)

import thermosteam as tmo
import numpy as np

for fluid in ['Water', 'Ethanol', 'Methane', 'CO2', 'R134a']:
    fluid_data = tmo.Chemical(fluid)
    print('#' * 50)
    print('Properties of ' + fluid)
    print('#' * 50)
    for sometemperature in np.linspace(50, 1000, 20):
        print('*' * 25)
        print('Evaluation at T=' + str(sometemperature) + ' K')
        print('*' * 25)
        print('Saturation pressure')
        print('*' * 25)
        for model in fluid_data.Psat:
            try:
                print('Methematical model:', model.name)
                print('Temperature limits (min, max):', model.Tmin, model.Tmax)
                print('Saturation pressure at T=' + str(sometemperature) + ' K:', model(T=sometemperature))
                if sometemperature < model.Tmin:
                    print('There is no warning for minimum temperature!')
                elif sometemperature > model.Tmax:
                    print('There is no warning for maximum temperature!')
            except (ValueError, FloatingPointError, OverflowError) as e:
                print('ERROR: ' + str(e))

        print('*' * 25)
        print('Sufrace tension')
        print('*' * 25)
        for model in fluid_data.sigma:
            try:
                print('Methematical model:', model.name)
                print('Temperature limits (min, max):', model.Tmin, model.Tmax)
                print('Surface tension at T=' + str(sometemperature) + ' K:', model(T=sometemperature))
                if sometemperature < model.Tmin:
                    print('There is no warning for minimum temperature!')
                elif sometemperature > model.Tmax:
                    print('There is no warning for maximum temperature!')
            except (ValueError, FloatingPointError, OverflowError) as e:
                print('ERROR: ' + str(e))

from thermosteam import MultiStream, settings

settings.set_thermo(['Water', 'KOH', 'H2', 'O2'], cache=True)

s1 = MultiStream(ID='s1', l=[('Water', 1), ('KOH', 2)], g=[('H2', 3)], units='g/s')
s1.show(flow='kg/s')

import thermosteam as tmo
water, glycerol = tmo.Chemicals(['Water', 'Glycerol'])
water.show()
glycerol.show()

import thermosteam as tmo
HMF = tmo.Chemical('HMF')
HMF.Tm = 564.65

import thermosteam as tmo

def append_new_single_phase_chemical(ID, chems, *sources, **data):
    chemical = tmo.Chemical.blank(ID, **data)
    chemical.copy_missing_slots_from(*sources)
    try: chemical.at_state(phase=chemical.phase_ref)
    except: pass
    chems.append(chemical)

chems_1 = tmo.Chemicals([])
append_new_single_phase_chemical('chemical_1', chems=chems_1)
chems_1.chemical_1.MW = 1
chems_1.chemical_1.phase_ref = 's'
tmo.settings.set_thermo(chems_1)

chems_2 = tmo.Chemicals([])
append_new_single_phase_chemical('chemical_2', chems=chems_2, MW=1, phase_ref='s')
tmo.settings.set_thermo(chems_2)

for i in (
    VolumeLiquid.ranked_methods,
    VolumeLiquid.ranked_methods_P,
    VolumeGas.ranked_methods_P
        ):
    if 'EOS' in i:
        i.remove('EOS')

>>> from biorefineries import corn as cn
>>> chems = cn.create_chemicals()
>>> chems.Cellulose.aliases
{'C6H10O5'}
>>> chems.Starch.aliases
{'C6H10O5'}

import thermosteam as tmo
chems = tmo.Chemicals([tmo.Chemical('H2O'), tmo.Chemical('Ethanol')])
chems.compile()
chems.refresh_constants()

import thermosteam as tmo

chemicals = tmo.Chemicals(['Water', 'Ethanol'])
thermo = tmo.Thermo(chemicals)
tmo.settings.set_thermo(thermo)
s3 = tmo.Stream('s3', T=300, P=1e5, Water=10, units='kg/hr')
s4 = tmo.Stream('s4', phase='g', T=400, P=1e5, Water=10, units='kg/hr')
s_eq = tmo.Stream('s34_mixture')
s_eq.mix_from([s3, s4])

print('MultiStream with enthalpy added by mix_from')
s_eq.vle(H=s_eq.H, P=1e5)
s_eq.show(composition=True)
print('Absolute deviation in enthalpy:', s_eq.H - (s3.H + s4.H))

print('MultiStream with Enthalpy summed individually')
s_eq.vle(H=s3.H + s4.H, P=1e5)
s_eq.show(composition=True)

from biorefineries.cornstover.system import H301
stream = H301.outs[0]
print('Temperature of H301 output is ' + str(stream.T) + ' K \n')

stream_density_kgL = round(stream.F_mass/(stream.F_vol*1000), 3)
print('Density of H301 output at ' + str(stream.T) + ' K is ' + str(stream_density_kgL) + ' kg/L \n')
stream.show(N=100, composition=True, flow='kg/hr')

import thermosteam as tmo
thermo = tmo.Chemicals(['Water'])
tmo.settings.set_thermo(thermo)
s1 = tmo.Stream('s1', Water=1000, units='kg/hr', T=298.15)
s2 = s1.copy()
s2.T = 321.15

s1_density_kgL = round(s1.F_mass/(s1.F_vol*1000), 3)
s2_density_kgL = round(s2.F_mass/(s2.F_vol*1000), 3)
print('\n')
print('Density of water at ' + str(s1.T) + ' K is ' + str(s1_density_kgL) + ' kg/L \n')
print('Density of water at ' + str(s2.T) + ' K is ' + str(s2_density_kgL) + ' kg/L')

import thermosteam as tmo
from thermosteam import reaction as rxn

chemicals = tmo.Chemicals(['Water', 'Methane', 'CO2', 'O2'])
tmo.settings.set_thermo(chemicals)
combustion = rxn.Reaction('Methane + O2 -> Water + CO2',
                                   reactant='Methane', X=1,
                                   correct_atomic_balance=True)

    try:
        vol = self._data_cache['vol'][TP]
    except:
        chemicals = self.chemicals
        mol = self.data
        vol = np.zeros_like(mol, dtype=object)
        for i, chem in enumerate(chemicals):
            vol[i] = VolumetricFlowProperty(chem.ID, mol, i, chem.V,
                                            TP, None, self._phase)
        self._data_cache['vol'] = {}
        self._data_cache['vol'][TP] = \
        vol = ChemicalVolumetricFlowIndexer.from_data(property_array(vol),
                                                      self._phase, chemicals,
                                                      False)