getting tighter now

Author: jgostick

.gitignore

@@ -159,3 +159,4 @@ openpnm/core/.DS_Store
 */.DS_Store
 *.DS_Store
 *.nblink
+.idea

openpnm/core/_base2.py

@@ -188,9 +188,11 @@ def __getitem__(self, key):
         # meant for exploring the idea of putting phase values in the
         # network dict, like pn['pore.temperature.air'], but we're not doing
         # that now.
-        if '*' in key:
+        if key.startswith('*'):
             d = {}
-            key = key[1:]
+            key = key[1:]  # Remove astrisk
+            if key.startswith('.'):  # Remove leading dot if *. was given
+                key = key[1:]
             for k, v in self.items():
                 if k.endswith(key):
                     d[k[:-len(key)-1]] = super().__getitem__(k)

openpnm/models/collections/phase/__init__.py

@@ -2,4 +2,4 @@
 from .water import water
 from .mercury import mercury
 from .liquid_mixture import liquid_mixture
-from .gas_mixture import gas_mixture
+from .gas_mixture import binary_gas_mixture, gas_mixture

openpnm/models/collections/phase/gas_mixture.py

@@ -2,13 +2,13 @@
 from openpnm.utils import get_model_collection
 
 
-def gas_mixture(regen_mode=None, domain=None):
-    return get_model_collection(collection=_gas_mixture,
+def binary_gas_mixture(regen_mode=None, domain=None):
+    return get_model_collection(collection=_binary_gas_mixture,
                                 regen_mode=regen_mode,
                                 domain=domain)
 
 
-_gas_mixture = {
+_binary_gas_mixture = {
     'pore.molecular_weight': {
         'model': mods.mixtures.mixture_molecular_weight,
     },
@@ -34,3 +34,25 @@ def gas_mixture(regen_mode=None, domain=None):
         'model': mods.diffusivity.gas_mixture_diffusivity,
     },
 }
+
+
+def gas_mixture(regen_mode=None, domain=None):
+    return get_model_collection(collection=_gas_mixture,
+                                regen_mode=regen_mode,
+                                domain=domain)
+
+
+_gas_mixture = {
+    'pore.molecular_weight': {
+        'model': mods.mixtures.mixture_molecular_weight,
+    },
+    'pore.viscosity': {
+        'model': mods.viscosity.gas_mixture_viscosity,
+    },
+    'pore.thermal_conductivity': {
+        'model': mods.thermal_conductivity.gas_mixture_thermal_conductivity,
+    },
+    'pore.heat_capacity': {
+        'model': mods.heat_capacity.mixture_heat_capacity,
+    },
+}

openpnm/models/phase/diffusivity/_funcs.py

@@ -212,6 +212,7 @@ def gas_mixture_LJ_epsilon(target):
     Calculates the effective molecular diameter for a binary mixture
     """
     es = [c['param.lennard_jones_epsilon'] for c in target.components.values()]
+    assert len(es) == 2
     eAB = np.sqrt(np.prod(es))
     return eAB
 
@@ -344,13 +345,13 @@ class MixDict(dict):
         only two components of a mixture that has several.  This is necessary for
         use of the fuller model for calculating binary diffusivities.
         """
+
         def __init__(self, target, components):
             super().__init__(target)
             self.components = {}
             for item in components:
                 self.components.update({item.name: item})
 
-
     comps = list(target.components.values())
     values = {}
     for i in range(len(comps)):
@@ -361,10 +362,10 @@ def __init__(self, target, components):
                 B = comps[j]
                 temp = MixDict(target=target, components=(A, B))
                 D = fuller_mixture(target=temp,
-                                       molecular_weight=molecular_weight,
-                                       molar_diffusion_volume=molar_diffusion_volume,
-                                       temperature=temperature,
-                                       pressure=pressure)
+                                   molecular_weight=molecular_weight,
+                                   molar_diffusion_volume=molar_diffusion_volume,
+                                   temperature=temperature,
+                                   pressure=pressure)
                 yB = target['pore.mole_fraction.' + B.name]
                 denom += yB/D
         yA = target['pore.mole_fraction.' + A.name]

openpnm/phase/_mixture.py

@@ -1,10 +1,10 @@
 import numpy as np
 import logging
-from copy import deepcopy
 from openpnm.phase import Phase
-from openpnm.models.collections.phase import liquid_mixture, gas_mixture
+from openpnm.models.collections.phase import liquid_mixture
+from openpnm.models.collections.phase import gas_mixture, binary_gas_mixture
 from openpnm.models.phase.mixtures import mole_summation
-from openpnm.utils import HealthDict, PrintableList, SubDict
+from openpnm.utils import HealthDict
 from openpnm.utils import Docorator, Workspace
 
 
@@ -15,22 +15,14 @@
 
 __all__ = [
     'Mixture',
-    'GasMixture',
+    'BinaryGasMixture',
+    'MultiGasMixture',
     'LiquidMixture',
 ]
 
 
 class MixtureSettings:
-    r"""
-    The following settings are specific to Mixture objects
-
-    Parameters
-    ----------
-    components : list of strings
-        The names of each pure component object that constitute the mixture
-
-    """
-    components = []
+    ...
 
 
 @docstr.get_sections(base='Mixture', sections=['Parameters'])
@@ -64,10 +56,21 @@ def __getitem__(self, key):
             if key.split('.')[-1] in self.components.keys():
                 comp = self.project[key.split('.')[-1]]
                 vals = comp[key.rsplit('.', maxsplit=1)[0]]
+            elif key.endswith('*'):
+                key = key[:-1]
+                if key.endswith('.'):
+                    key = key[:-1]
+                vals = self._get_comp_vals(key)
             else:
                 raise KeyError(key)
         return vals
 
+    def _get_comp_vals(self, propname):
+        vals = {}
+        for comp in self.components.keys():
+            vals[comp] = self[propname + '.' + comp]
+        return vals
+
     def __str__(self):
         horizontal_rule = '―' * 78
         temp = super().__str__().split(horizontal_rule)
@@ -101,8 +104,13 @@ def _set_comps(self, components):
     def add_comp(self, component, mole_fraction=0.0):
         self['pore.mole_fraction.' + component.name] = mole_fraction
 
-    def remove_comp(self, compname):
-        del self['pore.mole_fraction.' + compname]
+    def remove_comp(self, component):
+        if hasattr(component, 'name'):
+            component = component.name
+        try:
+            del self['pore.mole_fraction.' + component]
+        except KeyError:
+            pass
 
     def check_mixture_health(self):
         r"""
@@ -133,6 +141,7 @@ def check_mixture_health(self):
 
 
 class LiquidMixture(Mixture):
+
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self.models.update(liquid_mixture())
@@ -171,10 +180,6 @@ def x(self, compname=None, x=None):
 
 
 class GasMixture(Mixture):
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
-        self.models.update(gas_mixture())
-        self.regenerate_models()
 
     def y(self, compname=None, y=None):
         r"""
@@ -208,13 +213,80 @@ def y(self, compname=None, y=None):
             self['pore.mole_fraction.' + compname] = y
 
 
+class MultiGasMixture(GasMixture):
+
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+        self.models.clear()
+        self.models.update(gas_mixture())
+        self.regenerate_models()
+
+class BinaryGasMixture(GasMixture):
+
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+        self.models.clear()
+        self.models.update(binary_gas_mixture())
+        self.regenerate_models()
+
+    def add_comp(self, component, mole_fraction=0.0):
+        if len(self['pore.mole_fraction'].keys()) >= 2:
+            raise Exception("Binary mixtures cannot have more than 2 components"
+                            + ", remove one first")
+        super().add_component(component=component, mole_fraction=mole_fraction)
+
+
 if __name__ == '__main__':
     import openpnm as op
     pn = op.network.Demo()
     o2 = op.phase.GasByName(network=pn, species='o2', name='pure_O2')
     n2 = op.phase.GasByName(network=pn, species='n2', name='pure_N2')
-    air = op.phase.GasMixture(network=pn, components=[o2, n2])
+    air = op.phase.BinaryGasMixture(network=pn, components=[o2, n2], name='air')
     air.y(o2.name, 0.21)
     air['pore.mole_fraction.pure_N2'] = 0.79
     air.regenerate_models()
     print(air)
+
+    ch4 = op.phase.GasByName(network=pn, species='ch4', name='methane')
+    h2 = op.phase.GasByName(network=pn, species='h2', name='hydrogen')
+    h2o = op.phase.GasByName(network=pn, species='h2o', name='water')
+    co2 = op.phase.GasByName(network=pn, species='co2', name='co2')
+    syngas = op.phase.MultiGasMixture(network=pn, components=[ch4, h2, h2o, co2],
+                                      name='syngas')
+    syngas.y(h2.name, 0.25)
+    syngas.y(ch4.name, 0.25)
+    syngas.y(h2o.name, 0.25)
+    syngas.y(co2.name, 0.25)
+    syngas.regenerate_models()
+    print(syngas)
+
+
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+

openpnm/phase/_species.py

@@ -38,6 +38,7 @@ def mixture(self):
                 for comp in item.components.values():
                     if self is comp:
                         return item
+        logger.warn("No mixture phase found for this species")
 
 
 class SpeciesByName(Species):
@@ -61,22 +62,25 @@ class SpeciesByName(Species):
     """
 
     def __init__(self, species, **kwargs):
-        super().__init__(**kwargs)
+        # Create temp first to ensure all look-ups pass before initializing obj
+        temp = {}
         CAS = chem.CAS_from_any(species)
-        self['param.CAS'] = CAS
+        temp['param.CAS'] = CAS
         a = chem.identifiers.search_chemical(CAS)
-        self['param.common_name'] = a.common_name
-        self['param.molecular_weight'] = a.MW/1000  # Convert to kg/mol
-        self['param.critical_temperature'] = chem.critical.Tc(CAS)
-        self['param.critical_pressure'] = chem.critical.Pc(CAS)
-        self['param.critical_volume'] = chem.critical.Vc(CAS)
-        self['param.critical_compressibilty_factor'] = chem.critical.Zc(CAS)
-        self['param.boiling_temperature'] = chem.Tb(CAS)
-        self['param.melting_temperature'] = chem.Tm(CAS)
-        self['param.acentric_factor'] = chem.acentric.omega(CAS)
-        self['param.dipole_moment'] = chem.dipole.dipole_moment(CAS)
-        self['param.lennard_jones_epsilon'] = k*chem.lennard_jones.Stockmayer(CAS)
-        self['param.lennard_jones_sigma'] = chem.lennard_jones.molecular_diameter(CAS)
+        temp['param.common_name'] = a.common_name
+        temp['param.molecular_weight'] = a.MW/1000  # Convert to kg/mol
+        temp['param.critical_temperature'] = chem.critical.Tc(CAS)
+        temp['param.critical_pressure'] = chem.critical.Pc(CAS)
+        temp['param.critical_volume'] = chem.critical.Vc(CAS)
+        temp['param.critical_compressibilty_factor'] = chem.critical.Zc(CAS)
+        temp['param.boiling_temperature'] = chem.Tb(CAS)
+        temp['param.melting_temperature'] = chem.Tm(CAS)
+        temp['param.acentric_factor'] = chem.acentric.omega(CAS)
+        temp['param.dipole_moment'] = chem.dipole.dipole_moment(CAS)
+        temp['param.lennard_jones_epsilon'] = k*chem.lennard_jones.Stockmayer(CAS)
+        temp['param.lennard_jones_sigma'] = chem.lennard_jones.molecular_diameter(CAS)
+        super().__init__(**kwargs)
+        self._params.update(temp)
 
 
 class GasByName(SpeciesByName):

tests/unit/phase/MixtureTest.py

@@ -31,14 +31,13 @@ def test_set_component_by_property(self):
         del self.air['pore.mole_fraction.pure_CO2']
         assert len(self.air.components) == 2
 
-    def test_set_component_method(self):
+    def test_add_and_remove_component_method(self):
         net = op.network.Demo()
         o2 = op.phase.GasByName(network=net, species='o2', name='pure_O2')
         n2 = op.phase.GasByName(network=net, species='n2', name='pure_N2')
-        air = op.phase.GasMixture(network=net)
-        air.y(o2.name, 0.21)
-        air['pore.mole_fraction.pure_N2'] = 0.79
-        air.regenerate_models()
+        air = op.phase.GasMixture(network=net, components=[n2, o2])
+        air.remove_comp(n2)
+        air.remove_component(o2)
 
     def test_check_health(self):
         self.air['pore.mole_fraction.pure_N2'] = 0.79