openpnm 1.0.0__zip

OpenPNM-1.1/OpenPNM/Physics/models/generic_source_term.py

@@ -0,0 +1,564 @@
+r"""
+===============================================================================
+Submodule -- generic_source_term
+===============================================================================
+
+"""
+
+import scipy as _sp
+
+def linear(physics,
+           phase,
+           A1='',
+           A2='',
+           x='',
+           return_rate=True,
+           **kwargs):
+    r"""
+    For the following source term:
+        .. math::
+            r = A_{1}   x  +  A_{2} 
+    If return_rate is True, it returns the value of source term for the provided x in each pore. 
+    If return_rate is False, it calculates the slope and intercept for the following linear form :                 
+        .. math::            
+            r = S_{1}   x  +  S_{2}               
+
+    Parameters
+    ----------
+    A1 , A2 : string
+        The property name of the coefficients in the source term model. With A2 set to zero
+        this equation takes on the familiar for of r=kx.  
+    x : string or float/int or array/list
+        The property name or numerical value or array for the main quantity
+    Notes
+    -----    
+    Because this source term is linear in concentration (x) is it not necessary
+    to iterate during the solver step.  Thus, when using the 
+    ``set_source_term`` method for an algorithm, it is recommended to set the ``maxiter`` 
+    argument to 0.  This will save 1 unncessary solution of the system, since
+    the solution would coverge after the first pass anyway.  
+    
+    """
+    if x=='':   
+        X = _sp.ones(physics.Np)*_sp.nan
+    else:
+        if type(x)==str:
+            x = 'pore.'+x.split('.')[-1]
+            try:    X = physics[x]
+            except: raise Exception(physics.name+' does not have the pore property :'+x+'!')
+        else:
+            X = _sp.array(x)      
+
+    length_X = _sp.size(X)
+    if length_X!=physics.Np:
+        if length_X==1:
+            X = X*_sp.ones(physics.Np) 
+        elif length_X>=phase.Np:
+            X = X[physics.map_pores()] 
+        else:   raise Exception('Wrong size for the numerical array of x!')     
+
+    if A1 == '':    a1 = 0
+    else:
+        if type(A1)==str:
+            A1 = 'pore.'+A1.split('.')[-1]
+            try:    a1 = physics[A1]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A1+'!')
+        else:  raise Exception('A1 can be only string!')
+
+    if A2 == '':    a2 = 0
+    else:
+        if type(A2)==str:
+            A2 = 'pore.'+A2.split('.')[-1]
+            try:    a2 = physics[A2]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A2+'!')
+        else:  raise Exception('A2 can be only string!')
+
+    if return_rate:
+        return(a1*X**a2)
+    else:
+        S1 = a1
+        S2 = a2
+        return(_sp.vstack((S1,S2)).T)   
+
+def power_law(physics,
+            phase,
+            A1='',
+            A2='',
+            A3='',
+            x='',
+            return_rate=True,
+            **kwargs):
+    r"""
+    For the following source term:
+        .. math::
+            r = A_{1}   x^{A_{2}}  +  A_{3}
+    If return_rate is True, it returns the value of source term for the provided x in each pore. 
+    If return_rate is False, it calculates the slope and intercept for the following linear form :                 
+        .. math::            
+            r = S_{1}   x  +  S_{2} 
+    
+    Parameters
+    ----------
+    A1 -> A3 : string
+        The property name of the coefficients in the source term model
+    x : string or float/int or array/list
+        The property name or numerical value or array for the main quantity
+    Notes
+    -----
+    
+    """
+    if x=='':   
+        X = _sp.ones(physics.Np)*_sp.nan
+#        length_X = _sp.size(x)
+    else:
+        if type(x)==str:
+            x = 'pore.'+x.split('.')[-1]
+            try:    X = physics[x]
+            except: raise Exception(physics.name+' does not have the pore property :'+x+'!')
+        else:
+            X = _sp.array(x)      
+
+    length_X = _sp.size(X)
+    if length_X!=physics.Np:
+        if length_X==1:
+            X = X*_sp.ones(physics.Np) 
+        elif length_X>=phase.Np:
+            X = X[physics.map_pores()] 
+        else:   raise Exception('Wrong size for the numerical array of x!')     
+
+    if A1 == '':    a1 = 0
+    else:
+        if type(A1)==str:
+            A1 = 'pore.'+A1.split('.')[-1]
+            try:    a1 = physics[A1]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A1+'!')
+        else:  raise Exception('A1 can be only string!')
+
+    if A2 == '':    a2 = 0
+    else:
+        if type(A2)==str:
+            A2 = 'pore.'+A2.split('.')[-1]
+            try:    a2 = physics[A2]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A2+'!')
+        else:  raise Exception('A2 can be only string!')
+
+    if A3 == '':    a3 = 0
+    else:
+        if type(A3)==str:
+            A3 = 'pore.'+A3.split('.')[-1]
+            try:    a3 = physics[A3]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A3+'!')
+        else:  raise Exception('A3 can be only string!')
+
+    if return_rate:
+        return(a1*X**a2 +a3)
+    else:
+        S1 = a1*a2*X**(a2-1)
+        S2 = a1*X**a2*(1-a2)+a3
+        return(_sp.vstack((S1,S2)).T)    
+
+
+def exponential(physics,
+            phase,
+            A1='',
+            A2='',
+            A3='',
+            A4='',
+            A5='',
+            A6='',
+            x='',
+            return_rate=True,
+            **kwargs):
+    r"""
+    For the following source term:
+        .. math::
+            r =  A_{1} A_{2}^{( A_{3} x^{ A_{4} } + A_{5})} + A_{6} 
+    If return_rate is True, it returns the value of source term for the provided x in each pore. 
+    If return_rate is False, it calculates the slope and intercept for the following linear form :                 
+        .. math::            
+            r = S_{1}   x  +  S_{2} 
+    
+    Parameters
+    ----------
+    A1 -> A6 : string
+        The property name of the coefficients in the source term model
+    x : string or float/int or array/list
+        The property name or numerical value or array for the main quantity
+    Notes
+    -----
+    
+    """
+    if x=='':   
+        X = _sp.ones(physics.Np)*_sp.nan
+#        length_X = _sp.size(x)
+    else:
+        if type(x)==str:
+            x = 'pore.'+x.split('.')[-1]
+            try:    X = physics[x]
+            except: raise Exception(physics.name+' does not have the pore property :'+x+'!')
+        else:
+            X = _sp.array(x)      
+
+    length_X = _sp.size(X)
+    if length_X!=physics.Np:
+        if length_X==1:
+            X = X*_sp.ones(physics.Np) 
+        elif length_X>=phase.Np:
+            X = X[physics.map_pores()] 
+        else:   raise Exception('Wrong size for the numerical array of x!')     
+
+    if A1 == '':    a1 = 1
+    else:
+        if type(A1)==str:
+            A1 = 'pore.'+A1.split('.')[-1]
+            try:    a1 = physics[A1]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A1+'!')
+        else:  raise Exception('A1 can be only string!')
+
+    if A2 == '':    a2 = 0
+    else:
+        if type(A2)==str:
+            A2 = 'pore.'+A2.split('.')[-1]
+            try:    a2 = physics[A2]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A2+'!')
+        else:  raise Exception('A2 can be only string!')
+
+    if A3 == '':    a3 = 0
+    else:
+        if type(A3)==str:
+            A3 = 'pore.'+A3.split('.')[-1]
+            try:    a3 = physics[A3]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A3+'!')
+        else:  raise Exception('A3 can be only string!')
+
+
+    if A4 == '':    a4 = 0
+    else:
+        if type(A4)==str:
+            A4 = 'pore.'+A4.split('.')[-1]
+            try:    a4 = physics[A4]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A4+'!')
+        else:  raise Exception('A4 can be only string!')
+
+    if A5 == '':    a5 = 0
+    else:
+        if type(A5)==str:
+            A5 = 'pore.'+A5.split('.')[-1]
+            try:    a5 = physics[A5]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A5+'!')
+        else:  raise Exception('A5 can be only string!')
+
+    if A6 == '':    a6 = 0
+    else:
+        if type(A6)==str:
+            A6 = 'pore.'+A6.split('.')[-1]
+            try:    a6 = physics[A6]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A6+'!')
+        else:  raise Exception('A6 can be only string!')
+
+    if return_rate:
+        return(a1*a2**(a3*X**a4 +a5)+a6)
+    else:
+        S1 = a1*a3*a4*_sp.log(a2)*a2**(a3*X**a4+a5)*X**(a4-1)
+        S2 = a1*a2**(a3*X**a4+a5)*(1-a3*a4*_sp.log(a2)*X**a4)+a6
+        return(_sp.vstack((S1,S2)).T) 
+
+
+def natural_exponential(physics,
+                        phase,
+                        A1='',
+                        A2='',
+                        A3='',
+                        A4='',
+                        A5='',
+                        x='',
+                        return_rate=True,
+                        **kwargs):
+    r"""
+    For the following source term:
+        .. math::
+            r =   A_{1} exp( A_{2}  x^{ A_{3} } + A_{4} )+ A_{5} 
+    If return_rate is True, it returns the value of source term for the provided x in each pore. 
+    If return_rate is False, it calculates the slope and intercept for the following linear form :                 
+        .. math::            
+            r = S_{1}   x  +  S_{2} 
+    
+    Parameters
+    ----------
+    A1 -> A5 : string
+        The property name of the coefficients in the source term model
+    x : string or float/int or array/list
+        The property name or numerical value or array for the main quantity
+    Notes
+    -----
+    
+    """
+    if x=='':   
+        X = _sp.ones(physics.Np)*_sp.nan
+#        length_X = _sp.size(x)
+    else:
+        if type(x)==str:
+            x = 'pore.'+x.split('.')[-1]
+            try:    X = physics[x]
+            except: raise Exception(physics.name+' does not have the pore property :'+x+'!')
+        else:
+            X = _sp.array(x)      
+
+    length_X = _sp.size(X)
+    if length_X!=physics.Np:
+        if length_X==1:
+            X = X*_sp.ones(physics.Np) 
+        elif length_X>=phase.Np:
+            X = X[physics.map_pores()] 
+        else:   raise Exception('Wrong size for the numerical array of x!')     
+
+    if A1 == '':    a1 = 1
+    else:
+        if type(A1)==str:
+            A1 = 'pore.'+A1.split('.')[-1]
+            try:    a1 = physics[A1]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A1+'!')
+        else:  raise Exception('A1 can be only string!')
+
+    if A2 == '':    a2 = 0
+    else:
+        if type(A2)==str:
+            A2 = 'pore.'+A2.split('.')[-1]
+            try:    a2 = physics[A2]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A2+'!')
+        else:  raise Exception('A2 can be only string!')
+
+    if A3 == '':    a3 = 0
+    else:
+        if type(A3)==str:
+            A3 = 'pore.'+A3.split('.')[-1]
+            try:    a3 = physics[A3]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A3+'!')
+        else:  raise Exception('A3 can be only string!')
+
+
+    if A4 == '':    a4 = 0
+    else:
+        if type(A4)==str:
+            A4 = 'pore.'+A4.split('.')[-1]
+            try:    a4 = physics[A4]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A4+'!')
+        else:  raise Exception('A4 can be only string!')
+
+    if A5 == '':    a5 = 0
+    else:
+        if type(A5)==str:
+            A5 = 'pore.'+A5.split('.')[-1]
+            try:    a5 = physics[A5]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A5+'!')
+        else:  raise Exception('A5 can be only string!')
+
+    if return_rate:
+        return(a1*_sp.exp(a2*X**a3+a4) +a5)
+    else:
+        S1 = a1*a2*a3*X**(a3-1)*_sp.exp(a2*X**a3+a4)
+        S2 = a1*_sp.exp(a2*X**a3+a4)*(1-a2*a3*X**a3)+a5
+        return(_sp.vstack((S1,S2)).T) 
+
+def logarithm(physics,
+            phase,
+            A1='',
+            A2='',
+            A3='',
+            A4='',
+            A5='',
+            A6='',
+            x='',
+            return_rate=True,
+            **kwargs):
+    r"""
+    For the following source term:
+        .. math::
+            r =  A_{1}   Log_{ A_{2} }( A_{3} x^{ A_{4} }+ A_{5})+ A_{6}  
+    If return_rate is True, it returns the value of source term for the provided x in each pore. 
+    If return_rate is False, it calculates the slope and intercept for the following linear form :                 
+        .. math::            
+            r = S_{1}   x  +  S_{2} 
+    
+    Parameters
+    ----------
+    A1 -> A6 : string
+        The property name of the coefficients in the source term model
+    x : string or float/int or array/list
+        The property name or numerical value or array for the main quantity
+    Notes
+    -----
+    
+    """
+    if x=='':   
+        X = _sp.ones(physics.Np)*_sp.nan
+#        length_X = _sp.size(x)
+    else:
+        if type(x)==str:
+            x = 'pore.'+x.split('.')[-1]
+            try:    X = physics[x]
+            except: raise Exception(physics.name+' does not have the pore property :'+x+'!')
+        else:
+            X = _sp.array(x)      
+
+    length_X = _sp.size(X)
+    if length_X!=physics.Np:
+        if length_X==1:
+            X = X*_sp.ones(physics.Np) 
+        elif length_X>=phase.Np:
+            X = X[physics.map_pores()] 
+        else:   raise Exception('Wrong size for the numerical array of x!')     
+
+    if A1 == '':    a1 = 1
+    else:
+        if type(A1)==str:
+            A1 = 'pore.'+A1.split('.')[-1]
+            try:    a1 = physics[A1]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A1+'!')
+        else:  raise Exception('A1 can be only string!')
+
+    if A2 == '':    a2 = 0
+    else:
+        if type(A2)==str:
+            A2 = 'pore.'+A2.split('.')[-1]
+            try:    a2 = physics[A2]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A2+'!')
+        else:  raise Exception('A2 can be only string!')
+
+    if A3 == '':    a3 = 0
+    else:
+        if type(A3)==str:
+            A3 = 'pore.'+A3.split('.')[-1]
+            try:    a3 = physics[A3]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A3+'!')
+        else:  raise Exception('A3 can be only string!')
+
+
+    if A4 == '':    a4 = 0
+    else:
+        if type(A4)==str:
+            A4 = 'pore.'+A4.split('.')[-1]
+            try:    a4 = physics[A4]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A4+'!')
+        else:  raise Exception('A4 can be only string!')
+
+    if A5 == '':    a5 = 0
+    else:
+        if type(A5)==str:
+            A5 = 'pore.'+A5.split('.')[-1]
+            try:    a5 = physics[A5]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A5+'!')
+        else:  raise Exception('A5 can be only string!')
+
+    if A6 == '':    a6 = 0
+    else:
+        if type(A6)==str:
+            A6 = 'pore.'+A6.split('.')[-1]
+            try:    a6 = physics[A6]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A6+'!')
+        else:  raise Exception('A6 can be only string!')
+
+    if return_rate:
+        return(a1*_sp.log(a3*X**a4 +a5)/_sp.log(a2)+a6)
+    else:
+        S1 = a1*a3*a4*X**(a4-1)/(_sp.log(a2)*(a3*X**a4+a5))
+        S2 = a1*_sp.log(a3*X**a4+a5)/_sp.log(a2)+a6-a1*a3*a4*X**a4/(_sp.log(a2)*(a3*X**a4+a5))
+        return(_sp.vstack((S1,S2)).T) 
+        
+
+def natural_logarithm(physics,
+                      phase,
+                      A1='',
+                      A2='',
+                      A3='',
+                      A4='',
+                      A5='',
+                      x='',
+                      return_rate=True,
+                      **kwargs):
+    r"""
+    For the following source term:
+        .. math::
+            r =   A_{1}  Ln( A_{2} x^{ A_{3} }+ A_{4})+ A_{5}    
+    If return_rate is True, it returns the value of source term for the provided x in each pore. 
+    If return_rate is False, it calculates the slope and intercept for the following linear form :                 
+        .. math::            
+            r = S_{1}   x  +  S_{2} 
+    
+    Parameters
+    ----------
+    A1 -> A5 : string
+        The property name of the coefficients in the source term model
+    x : string or float/int or array/list
+        The property name or numerical value or array for the main quantity
+    Notes
+    -----
+    
+    """
+    if x=='':   
+        X = _sp.ones(physics.Np)*_sp.nan
+#        length_X = _sp.size(x)
+    else:
+        if type(x)==str:
+            x = 'pore.'+x.split('.')[-1]
+            try:    X = physics[x]
+            except: raise Exception(physics.name+' does not have the pore property :'+x+'!')
+        else:
+            X = _sp.array(x)      
+
+    length_X = _sp.size(X)
+    if length_X!=physics.Np:
+        if length_X==1:
+            X = X*_sp.ones(physics.Np) 
+        elif length_X>=phase.Np:
+            X = X[physics.map_pores()] 
+        else:   raise Exception('Wrong size for the numerical array of x!')     
+
+    if A1 == '':    a1 = 1
+    else:
+        if type(A1)==str:
+            A1 = 'pore.'+A1.split('.')[-1]
+            try:    a1 = physics[A1]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A1+'!')
+        else:  raise Exception('A1 can be only string!')
+
+    if A2 == '':    a2 = 0
+    else:
+        if type(A2)==str:
+            A2 = 'pore.'+A2.split('.')[-1]
+            try:    a2 = physics[A2]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A2+'!')
+        else:  raise Exception('A2 can be only string!')
+
+    if A3 == '':    a3 = 0
+    else:
+        if type(A3)==str:
+            A3 = 'pore.'+A3.split('.')[-1]
+            try:    a3 = physics[A3]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A3+'!')
+        else:  raise Exception('A3 can be only string!')
+
+
+    if A4 == '':    a4 = 0
+    else:
+        if type(A4)==str:
+            A4 = 'pore.'+A4.split('.')[-1]
+            try:    a4 = physics[A4]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A4+'!')
+        else:  raise Exception('A4 can be only string!')
+
+    if A5 == '':    a5 = 0
+    else:
+        if type(A5)==str:
+            A5 = 'pore.'+A5.split('.')[-1]
+            try:    a5 = physics[A5]
+            except: raise Exception(physics.name+'/'+phase.name+' does not have the pore property :'+A5+'!')
+        else:  raise Exception('A5 can be only string!')
+
+
+    if return_rate:
+        return(a1*_sp.log(a2*X**a3 +a4)+a5)
+    else:
+        S1 = a1*a2*a3*X**(a3-1)/(a2*X**a3+a4)
+        S2 = a1*_sp.log(a2*X**a3+a4)+a5-a1*a2*a3*X**a3/(a2*X**a3+a4)
+        return(_sp.vstack((S1,S2)).T)         

OpenPNM-1.1/OpenPNM/Physics/models/hydraulic_conductance.py

@@ -0,0 +1,76 @@
+r"""
+===============================================================================
+Submodule -- hydraulic_conductance
+===============================================================================
+
+"""
+
+import scipy as _sp
+import OpenPNM.Utilities.misc as misc
+
+def hagen_poiseuille(physics,
+                     phase,
+                     network,
+                     pore_diameter='pore.diameter',
+                     pore_viscosity='pore.viscosity',
+                     throat_length='throat.length',
+                     throat_diameter='throat.diameter',
+                     calc_pore_len=True,
+                     **kwargs):
+    r"""
+    Calculates the hydraulic conductivity of throat assuming cylindrical 
+    geometry using the Hagen-Poiseuille model
+
+    Parameters
+    ----------
+    network : OpenPNM Network Object
+
+    phase : OpenPNM Phase Object
+    
+    Notes
+    -----
+    (1) This function requires that all the necessary phase properties already 
+    be calculated.
+    
+    (2) This function calculates the specified property for the *entire* 
+    network then extracts the values for the appropriate throats at the end.
+    
+    """    
+    #Get Nt-by-2 list of pores connected to each throat
+    Ps = network['throat.conns']
+    #Get properties in every pore in the network
+    mup = phase[pore_viscosity]
+    mut = phase.interpolate_data(mup)
+    pdia = network[pore_diameter]
+    if calc_pore_len:
+        lengths = misc.conduit_lengths(network,mode='centroid')
+        plen1 = lengths[:,0]
+        plen2 = lengths[:,2]
+    else:        
+        plen1 = (0.5*pdia[Ps[:,0]])
+        plen2 = (0.5*pdia[Ps[:,1]]) 
+    #remove any non-positive lengths    
+    plen1[plen1<=0]=1e-12
+    plen2[plen2<=0]=1e-12
+    #Find g for half of pore 1
+    gp1 = _sp.pi*(pdia[Ps[:,0]])**4/(128*plen1*mut)
+    gp1[_sp.isnan(gp1)] = _sp.inf
+    gp1[~(gp1>0)] = _sp.inf #Set 0 conductance pores (boundaries) to inf
+    
+    #Find g for half of pore 2
+    #gp2 = 2.28*(pdia[pores[:,1]]/2)**4/(pdia[pores[:,1]]*mut)
+    gp2 = _sp.pi*(pdia[Ps[:,1]])**4/(128*plen2*mut)
+    gp2[_sp.isnan(gp2)] = _sp.inf
+    gp2[~(gp2>0)] = _sp.inf #Set 0 conductance pores (boundaries) to inf
+    #Find g for full throat
+    tdia = network[throat_diameter]
+    tlen = network[throat_length]
+    #remove any non-positive lengths
+    tlen[tlen<=0] = 1e-12
+    gt = _sp.pi*(tdia)**4/(128*tlen*mut)
+    gt[~(gt>0)] = _sp.inf #Set 0 conductance pores (boundaries) to inf
+    value = (1/gt + 1/gp1 + 1/gp2)**(-1)
+    value = value[phase.throats(physics.name)]
+    return value
+
+