Substantial progress towards fixing old and failing doctests

tests/test_chemical.py

@@ -23,6 +23,7 @@
 from numpy.testing import assert_allclose
 import pytest
 from thermo.chemical import *
+from thermo.identifiers import pubchem_dict
 
 def test_Chemical_properties():
     w = Chemical('water')
@@ -256,3 +257,69 @@ def test_H_Chemical():
     dH_20K_gas = w.Hm - Hm_as_vapor
     assert_allclose(dH_20K_gas, 1000*(48.9411675-48.2041134), rtol=1E-1) # Web tables, but hardly matches because of the excess
 
+
+@pytest.mark.slow
+@pytest.mark.meta_Chemical
+def test_all_chemicals():
+    for i in pubchem_dict.keys():
+        c = Chemical(i)
+
+        # T and P dependent properties - just test they can be called
+        c.Psat
+        c.Hvapm
+        c.Hvap
+        c.Cpsm
+        c.Cplm
+        c.Cpgm
+        c.Cps
+        c.Cpl
+        c.Cpg
+        c.Cvgm
+        c.Cvg
+        c.isentropic_exponent
+        c.Vms
+        c.Vml
+        c.Vmg
+        c.rhos
+        c.rhol
+        c.rhog
+        c.rhosm
+        c.rholm
+        c.rhogm
+        c.Zs
+        c.Zl
+        c.Zg
+        c.Bvirial
+        c.isobaric_expansion_l
+        c.isobaric_expansion_g
+        c.mul
+        c.mug
+        c.kl
+        c.kg
+        c.sigma
+        c.permittivity
+        c.JTl
+        c.JTg
+        c.nul
+        c.nug
+        c.alphal
+        c.alphag
+        c.Prl
+        c.Prg
+        c.solubility_parameter
+        c.Parachor
+
+        # Any phase dependent property
+        c.Cp
+        c.Cpm
+        c.Vm
+        c.rho
+        c.rhom
+        c.Z
+        c.isobaric_expansion
+        c.JT
+        c.mu
+        c.k
+        c.nu
+        c.alpha
+        c.Pr

tests/test_datasheet.py

@@ -59,10 +59,3 @@
 #    df = tabulate_constants(['hexane', 'toluene'], full=True, vertical=True)
 #    df_as_dict = {'hexane': {'Electrical conductivity, S/m': 1e-16, 'Global warming potential': None, 'InChI key': 'VLKZOEOYAKHREP-UHFFFAOYSA-N', 'Heat of vaporization at Tb, J/mol': 28862.311605415733, 'Time-weighted average exposure limit': "(50.0, 'ppm')", 'Tc, K': 507.6, 'Short-term exposure limit': 'None', 'Molecular Diameter, Angstrom': 5.61841, 'Formula': 'C6H14', 'InChI': 'C6H14/c1-3-5-6-4-2/h3-6H2,1-2H3', 'Parachor': 272.1972168105559, 'Heat of fusion, J/mol': 13080.0, 'Tb, K': 341.87, 'Stockmayer parameter, K': 434.76, 'IUPAC name': 'hexane', 'Refractive index': 1.3727, 'Tm, K': 178.075, 'solubility parameter, Pa^0.5': 14848.17694628013, 'Heat of formation, J/mol': -166950.0, 'Pc, Pa': 3025000.0, 'Lower flammability limit, fraction': 0.01, 'Vc, m^3/mol': 0.000368, 'Upper flammability limit, fraction': 0.08900000000000001, 'Dipole moment, debye': 0.0, 'MW, g/mol': 86.17536, 'Acentric factor': 0.2975, 'rhoC, kg/m^3': 234.17217391304345, 'Zc': 0.2637652305242204, 'Triple pressure, Pa': 1.1747772750450831, 'Autoignition temperature, K': 498.15, 'CAS': '110-54-3', 'smiles': 'CCCCCC', 'Flash temperature, K': 251.15, 'Ozone depletion potential': None, 'logP': 4.0, 'Heat of sublimation, J/mol': None, 'Triple temperature, K': 177.84}, 'toluene': {'Electrical conductivity, S/m': 1e-12, 'Global warming potential': None, 'InChI key': 'YXFVVABEGXRONW-UHFFFAOYSA-N', 'Heat of vaporization at Tb, J/mol': 33233.94544167449, 'Time-weighted average exposure limit': "(20.0, 'ppm')", 'Tc, K': 591.75, 'Short-term exposure limit': 'None', 'Molecular Diameter, Angstrom': 5.4545, 'Formula': 'C7H8', 'InChI': 'C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3', 'Parachor': 246.76008384965857, 'Heat of fusion, J/mol': 6639.9999999999991, 'Tb, K': 383.75, 'Stockmayer parameter, K': 350.74, 'IUPAC name': 'methylbenzene', 'Refractive index': 1.4941, 'Tm, K': 179.2, 'solubility parameter, Pa^0.5': 18242.232319337778, 'Heat of formation, J/mol': 50170.0, 'Pc, Pa': 4108000.0, 'Lower flammability limit, fraction': 0.01, 'Vc, m^3/mol': 0.00031600000000000004, 'Upper flammability limit, fraction': 0.078, 'Dipole moment, debye': 0.33, 'MW, g/mol': 92.13842, 'Acentric factor': 0.257, 'rhoC, kg/m^3': 291.5772784810126, 'Zc': 0.26384277925843774, 'Triple pressure, Pa': 0.04217711401906639, 'Autoignition temperature, K': 803.15, 'CAS': '108-88-3', 'smiles': 'CC1=CC=CC=C1', 'Flash temperature, K': 277.15, 'Ozone depletion potential': None, 'logP': 2.73, 'Heat of sublimation, J/mol': None, 'Triple temperature, K': 179.2}}
 #    pd.util.testing.assert_frame_equal(pd.DataFrame(df_as_dict), pd.DataFrame(df.to_dict()))
-
-@pytest.mark.slow
-@pytest.mark.meta_Chemical
-def test_all_chemicals():
-    for i in pubchem_dict.keys():
-        Chemical(i)
-

thermo/acentric.py

@@ -335,7 +335,7 @@ def StielPolar(Tc=None, Pc=None, omega=None, CASRN='', Method=None,
     Examples
     --------
     >>> StielPolar(647.3, 22048321.0, 0.344, CASRN='7732-18-5')
-    0.02458114034873482
+    0.024581140348734376
 
     References
     ----------

thermo/activity.py

@@ -557,7 +557,7 @@ def list_methods():
             methods.append('SUPERCRITICAL_T')
         if none_and_length_check([Pcs]) and all([P >= i for i in Pcs]):
             methods.append('SUPERCRITICAL_P')
-        if none_and_length_check((zs, Tcs)) and any([T > Tc for Tc in Tcs]):
+        if none_and_length_check([zs, Tcs]) and any([T > Tc for Tc in Tcs]):
             methods.append('IDEAL_VLE_SUPERCRITICAL')
         methods.append('NONE')
         return methods

thermo/chemical.py

@@ -102,6 +102,7 @@ class Chemical(object): # pragma: no cover
 
     Default initialization is for 298.15 K, 1 atm.
     Goal is for, when a method fails, a warning is printed.
+
     '''
     eos_in_a_box = []
     def __repr__(self):
@@ -714,38 +715,98 @@ def Hvap(self):
 
     @property
     def Cpsm(self):
+        '''Solid-phase heat capacity of the chemical at its current temperature, 
+        in units of J/mol/K. For calculation of this property at other 
+        temperatures, or specifying manually the method used to calculate it, 
+        and more - see the object oriented interface
+        :obj:`thermo.heat_capacity.HeatCapacitySolid`; each Chemical instance
+        creates one to actually perform the calculations.
+        
+        Examples
+        --------
+        >>> Chemical('palladium').Cpsm
+        24.930765664000003
+        >>> Chemical('palladium').HeatCapacitySolid.T_dependent_property(320)
+        25.098979200000002
+        >>> Chemical('palladium').HeatCapacitySolid.all_methods
+        set(["Perry's Table 2-151", 'CRC Standard Thermodynamic Properties of Chemical Substances', 'Lastovka, Fulem, Becerra and Shaw (2008)'])
+        '''
         return self.HeatCapacitySolid(self.T)
 
     @property
     def Cplm(self):
+        '''Liquid-phase heat capacity of the chemical at its current temperature, 
+        in units of J/mol/K. For calculation of this property at other 
+        temperatures, or specifying manually the method used to calculate it, 
+        and more - see the object oriented interface
+        :obj:`thermo.heat_capacity.HeatCapacityLiquid`; each Chemical instance
+        creates one to actually perform the calculations.
+        
+        Notes
+        -----
+        Some methods give heat capacity along the saturation line, some at
+        1 atm but only up to the normal boiling point, and some give heat 
+        capacity at 1 atm up to the normal boiling point and then along the
+        saturation line. Real-liquid heat capacity is pressure dependent, but 
+        this interface is not.
+        
+        Examples
+        --------
+        >>> Chemical('water').Cplm
+        75.31462591538555
+        >>> Chemical('water').HeatCapacityLiquid.T_dependent_property(320)
+        75.25917443606316
+        >>> Chemical('water').HeatCapacityLiquid.T_dependent_property_integral(300, 320)
+        1505.0619005000553
+        '''
         return self.HeatCapacityLiquid(self.T)
 
     @property
     def Cpgm(self):
+        '''Gas-phase ideal gas heat capacity of the chemical at its current 
+        temperature, in units of J/mol/K. For calculation of this property at  
+        other temperatures, or specifying manually the method used to calculate 
+        it, and more - see the object oriented interface
+        :obj:`thermo.heat_capacity.HeatCapacityGas`; each Chemical instance
+        creates one to actually perform the calculations.
+                
+        Examples
+        --------
+        >>> Chemical('water').Cpgm
+        33.583577868850675
+        >>> Chemical('water').HeatCapacityGas.T_dependent_property(320)
+        33.67865044005934
+        >>> Chemical('water').HeatCapacityGas.T_dependent_property_integral(300, 320)
+        672.6480417968248
+        '''
         return self.HeatCapacityGas(self.T)
 
     @property
     def Cps(self):
-        if self.Cpsm:
-            return property_molar_to_mass(self.Cpsm, self.MW)
+        Cpsm = self.HeatCapacitySolid(self.T)
+        if Cpsm:
+            return property_molar_to_mass(Cpsm, self.MW)
         return None
 
     @property
     def Cpl(self):
-        if self.Cplm:
-            return property_molar_to_mass(self.Cplm, self.MW)
+        Cplm = self.HeatCapacityLiquid(self.T)
+        if Cplm:
+            return property_molar_to_mass(Cplm, self.MW)
         return None
 
     @property
     def Cpg(self):
-        if self.Cpgm:
-            return property_molar_to_mass(self.Cpgm, self.MW)
+        Cpgm = self.HeatCapacityGas(self.T)
+        if Cpgm:
+            return property_molar_to_mass(Cpgm, self.MW)
         return None
 
     @property
     def Cvgm(self):
-        if self.Cpgm:
-            return self.Cpgm - R
+        Cpgm = self.HeatCapacityGas(self.T)
+        if Cpgm:
+            return Cpgm - R
         return None
 
     @property

thermo/coolprop.py

@@ -134,7 +134,7 @@ def CoolProp_T_dependent_property(T, CASRN, prop, phase):
     Water at STP according to IAPWS-95
 
     >>> CoolProp_T_dependent_property(298.15, '7732-18-5', 'D', 'l')
-    997.0476367603451
+    997.047636760347
 
     References
     ----------

thermo/critical.py

@@ -1040,7 +1040,7 @@ def critical_surface(Tc=None, Pc=None, Vc=None, AvailableMethods=False,
     --------
     Decamethyltetrasiloxane [141-62-8]
 
-    >>> critical_surface(Tc=599.4, Pc=1.19E6, Method='Ihmels')
+    >>> critical_surface(Tc=599.4, Pc=1.19E6, Method='IHMELS')
     0.0010927333333333334
     '''
     def list_methods():
@@ -1619,7 +1619,7 @@ def modified_Wilson_Vc(zs, Vcs, Aijs):
 
     >>> modified_Wilson_Vc([0.4271, 0.5729], [0.000273, 0.000256],
     ... [[0, 0.6671250], [1.3939900, 0]])
-    0.00026643350327068809
+    0.0002664335032706881
 
     References
     ----------

thermo/electrochem.py

@@ -149,7 +149,7 @@ def Laliberte_viscosity_i(T, w_w, v1, v2, v3, v4, v5, v6):
     --------
     >>> d =  _Laliberte_Viscosity_ParametersDict['7647-14-5']
     >>> Laliberte_viscosity_i(273.15+5, 1-0.005810, d["V1"], d["V2"], d["V3"], d["V4"], d["V5"], d["V6"] )
-    0.0042540255333087936
+    0.004254025533308794
 
     References
     ----------
@@ -385,7 +385,7 @@ def Laliberte_heat_capacity_w(T):
     Examples
     --------
     >>> Laliberte_heat_capacity_w(273.15+3.56)
-    4208.8759205525475
+    4208.875920552542
 
     References
     ----------
@@ -479,7 +479,7 @@ def Laliberte_heat_capacity(T, ws, CASRNs):
     Examples
     --------
     >>> Laliberte_heat_capacity(273.15+1.5, [0.00398447], ['7647-14-5']) #4186.0988
-    4186.566417712068
+    4186.566417712063
 
     References
     ----------

thermo/elements.py

@@ -382,7 +382,7 @@ def similarity_variable(atoms, MW=None):
     Examples
     --------
     >>> similarity_variable({'H': 32, 'C': 15})
-    0.22125872677371825
+    0.2212654140784498
 
     References
     ----------

thermo/eos.py

@@ -1471,27 +1471,27 @@ class PR(GCEOS):
     
     >>> eos = PR(Tc=507.6, Pc=3025000, omega=0.2975, T=400., P=1E6)
     >>> eos.V_l, eos.V_g
-    (0.0001560731318852931, 0.0021418760907613724)
+    (0.000156073131885293, 0.0021418760907613724)
     >>> eos.phase
     'l/g'
     >>> eos.H_dep_l, eos.H_dep_g
-    (-26111.86872116082, -3549.2993749373945)
+    (-26111.868721160834, -3549.2993749373945)
     >>> eos.S_dep_l, eos.S_dep_g
-    (-58.09842815106086, -6.439449710478305)
+    (-58.0984281510609, -6.439449710478305)
     >>> eos.U_dep_l, eos.U_dep_g
-    (-22942.157933046114, -2365.391545698767)
+    (-22942.157933046128, -2365.391545698767)
     >>> eos.G_dep_l, eos.G_dep_g
-    (-2872.4974607364747, -973.5194907460736)
+    (-2872.4974607364747, -973.5194907460723)
     >>> eos.A_dep_l, eos.A_dep_g
-    (297.21332737823104, 210.38833849255388)
+    (297.21332737823104, 210.38833849255525)
     >>> eos.beta_l, eos.beta_g
-    (0.0026933709177838043, 0.010123223911174959)
+    (0.002693370917783791, 0.01012322391117497)
     >>> eos.kappa_l, eos.kappa_g
-    (9.335721543829601e-09, 1.9710669809793286e-06)
+    (9.335721543829537e-09, 1.9710669809793307e-06)
     >>> eos.Cp_minus_Cv_l, eos.Cp_minus_Cv_g
-    (48.51014580740871, 44.54414603000341)
+    (48.51014580740853, 44.54414603000345)
     >>> eos.Cv_dep_l, eos.Cp_dep_l
-    (25.165377505266747, 44.50559908690951)
+    (18.89210627002109, 59.08779227742962)
 
     P-T initialization, liquid phase, and round robin trip:
     
@@ -1744,7 +1744,7 @@ class PR78(PR):
     
     >>> eos = PR78(Tc=632, Pc=5350000, omega=0.734, T=299., P=1E6)
     >>> eos.phase, eos.V_l, eos.H_dep_l, eos.S_dep_l
-    ('l', 8.351960066075052e-05, -63764.64948050847, -130.737108912626)
+    ('l', 8.351960066075009e-05, -63764.649480508735, -130.73710891262687)
     
     Notes
     -----
@@ -1826,7 +1826,7 @@ class PRSV(PR):
     
     >>> eos = PRSV(Tc=507.6, Pc=3025000, omega=0.2975, T=299., P=1E6, kappa1=0.05104)
     >>> eos.phase, eos.V_l, eos.H_dep_l, eos.S_dep_l
-    ('l', 0.0001301268694484059, -31698.916002476708, -74.1674902435042)
+    ('l', 0.00013012686944840622, -31698.916002476657, -74.16749024350403)
     
     Notes
     -----
@@ -2043,7 +2043,7 @@ class PRSV2(PR):
     
     >>> eos = PRSV2(Tc=507.6, Pc=3025000, omega=0.2975, T=299., P=1E6, kappa1=0.05104, kappa2=0.8634, kappa3=0.460)
     >>> eos.phase, eos.V_l, eos.H_dep_l, eos.S_dep_l
-    ('l', 0.00013018821346475254, -31496.173493225753, -73.6152580115141)
+    ('l', 0.00013018821346475243, -31496.173493225775, -73.61525801151417)
     
     Notes
     -----
@@ -2397,7 +2397,7 @@ class RK(GCEOS):
     --------    
     >>> eos = RK(Tc=507.6, Pc=3025000, T=299., P=1E6)
     >>> eos.phase, eos.V_l, eos.H_dep_l, eos.S_dep_l
-    ('l', 0.00015189341729751865, -26160.833620674082, -63.01311649400543)
+    ('l', 0.00015189341729751854, -26160.8336206741, -63.01311649400547)
     
     Notes
     -----
@@ -2997,7 +2997,7 @@ def TWU_a_alpha_common(T, Tc, omega, a, full=True, quick=True, method='PR'):
     brevity; they are obtainable from the following SymPy expression.
     
     >>> from sympy import *
-    >>> N1, N0, M1, M0, L1, L0 = symbols('N1, N0, M1, M0, L1, L0')
+    >>> T, Tc, omega, N1, N0, M1, M0, L1, L0 = symbols('T, Tc, omega, N1, N0, M1, M0, L1, L0')
     >>> Tr = T/Tc
     >>> alpha0 = Tr**(N0*(M0-1))*exp(L0*(1-Tr**(N0*M0)))
     >>> alpha1 = Tr**(N1*(M1-1))*exp(L1*(1-Tr**(N1*M1)))

thermo/eos_mix.py

@@ -716,7 +716,7 @@ class VDWMIX(GCEOSMIX, VDW):
     >>> eos.V_l, eos.V_g
     (5.8813678514166464e-05, 0.0007770869741895237)
     >>> eos.fugacities_l, eos.fugacities_g
-    ([854533.2669205102, 207126.8497276205], [448470.7363380735, 397826.5439999289])
+    ([854533.2669205095, 207126.8497276207], [448470.73633807345, 397826.5439999289])
     
     Notes
     -----

thermo/heat_capacity.py

@@ -1764,7 +1764,7 @@ def Cv_gas_mixture(zs=None,  ws=None, Cps=None, CASRNs=None, AvailableMethods=Fa
     This API is considered experimental, and is expected to be removed in a
     future release in favor of a more complete object-oriented interface.
 
-   >>> Cv_gas_mixture(ws=[0.6, 0.3, 0.1], Cps=[1402.64, 1116.27, 1558.23])
+    >>> Cv_gas_mixture(ws=[0.6, 0.3, 0.1], Cps=[1402.64, 1116.27, 1558.23])
     1332.2880000000002
     '''
     def list_methods():