```#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
***********************************************************************************
tutorial_dealii_6.py
DAE Tools: pyDAE module, www.daetools.com
***********************************************************************************
DAE Tools is free software; you can redistribute it and/or modify it under the
Foundation. DAE Tools is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with the
DAE Tools software; if not, see <http://www.gnu.org/licenses/>.
************************************************************************************
"""
__doc__ = """
A simple steady-state diffusion and first-order reaction in an irregular catalyst shape
(Proc. 6th Int. Conf. on Mathematical Modelling, Math. Comput. Modelling, Vol. 11, 375-319, 1988)
applying Dirichlet and Robin type of boundary conditions.

.. code-block:: none

D_eA * nabla^2(C_A) - k_r * C_A = 0 in Omega
D_eA * nabla(C_A) = k_m * (C_A - C_Ab) on dOmega1
C_A = C_Ab on dOmega2

The catalyst pellet mesh:

.. image:: _static/ssdr.png
:width: 400 px

The concentration plot:

.. image:: _static/tutorial_dealii_6-results1.png
:width: 500 px

The concentration plot for Ca=Cab on all boundaries:

.. image:: _static/tutorial_dealii_6-results2.png
:width: 500 px
"""

import os, sys, numpy, json, tempfile, random
from time import localtime, strftime
from daetools.pyDAE import *
from daetools.solvers.deal_II import *
from daetools.solvers.superlu import pySuperLU

# Standard variable types are defined in variable_types.py
from pyUnits import m, kg, s, K, Pa, mol, J, W

class modTutorial(daeModel):
def __init__(self, Name, Parent = None, Description = ""):
daeModel.__init__(self, Name, Parent, Description)

dofs = [dealiiFiniteElementDOF_2D(name='Ca',
description='Concentration',
fe = FE_Q_2D(1),
multiplicity=1)]

meshes_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'meshes')
mesh_file  = os.path.join(meshes_dir, 'ssdr.msh')

# Store the object so it does not go out of scope while still in use by daetools
self.fe_system = dealiiFiniteElementSystem_2D(meshFilename    = mesh_file,     # path to mesh
dofs            = dofs)          # degrees of freedom

self.fe_model = daeFiniteElementModel('DiffusionReaction', self, 'Diffusion-reaction in a catalyst', self.fe_system)

def DeclareEquations(self):
daeModel.DeclareEquations(self)

De  = 0.1 # Diffusivity, m**2/s
km  = 0.1 # Mass transfer coefficient, mol
kr  = 1.0 # First-order reaction rate constant
Cab = 1.0 # Boundary concentration

# Create some auxiliary objects for readability
phi_i  =  phi_2D('Ca', fe_i, fe_q)
phi_j  =  phi_2D('Ca', fe_j, fe_q)
dphi_i = dphi_2D('Ca', fe_i, fe_q)
dphi_j = dphi_2D('Ca', fe_j, fe_q)
normal = normal_2D(fe_q)
xyz    = xyz_2D(fe_q)
JxW    = JxW_2D(fe_q)

dirichletBC = {}

# FE weak form terms
diffusion    = -(dphi_i * dphi_j) * De * JxW
reaction     = -kr * phi_i * phi_j * JxW
accumulation = 0.0 * JxW
rhs          = 0.0 * JxW
# Robin type BC's:
faceAij = {
2: km * phi_i * phi_j * JxW
}
faceFi  = {
2: km * Cab * phi_i * JxW
}

weakForm = dealiiFiniteElementWeakForm_2D(Aij = diffusion + reaction,
Mij = accumulation,
Fi  = rhs,
boundaryFaceAij = faceAij,
boundaryFaceFi  = faceFi,
functionsDirichletBC = dirichletBC)

self.fe_system.WeakForm = weakForm

class simTutorial(daeSimulation):
def __init__(self):
daeSimulation.__init__(self)
self.m = modTutorial("tutorial_dealii_6")
self.m.Description = __doc__
self.m.fe_model.Description = __doc__

def SetUpParametersAndDomains(self):
pass

def SetUpVariables(self):
pass

def run(**kwargs):
guiRun = kwargs.get('guiRun', False)

simulation = simTutorial()

# Create SuperLU LA solver
lasolver = pySuperLU.daeCreateSuperLUSolver()

# Create and setup two data reporters:
datareporter = daeDelegateDataReporter()
simName = simulation.m.Name + strftime(" [%d.%m.%Y %H:%M:%S]", localtime())
if guiRun:
results_folder = tempfile.mkdtemp(suffix = '-results', prefix = 'tutorial_deal_II_6-')
daeQtMessage("deal.II", "The simulation results will be located in: %s" % results_folder)
else:
results_folder = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'tutorial_deal_II_6-results')
print("The simulation results will be located in: %s" % results_folder)

# 1. deal.II (exports only FE DOFs in .vtk format to the specified directory)
feDataReporter = simulation.m.fe_system.CreateDataReporter()
if not feDataReporter.Connect(results_folder, simName):
sys.exit()

# 2. TCP/IP
tcpipDataReporter = daeTCPIPDataReporter()