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from fipy import CellVariable, Grid1D,Viewer, TransientTerm, DiffusionTerm, ImplicitSourceTerm
from fipy.tools import numerix

size, dl, q = 100, 3e-6, 14.1
Ds, Ks = 1e-4, 5.8e-4
order = 2
dt = dl ** 2 / (2 * Ds)

mesh = Grid1D(dx=dl, nx=size)
phi_s = CellVariable(name='substrate', mesh=mesh)

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$ gmsh test2D.geo -3 -nopopup -format msh -o teset2D.msh
Info    : Running 'gmsh test2D.geo -3 -nopopup -format msh -o teset2D.msh' [Gmsh 3.0.6, 1 node, max. 1 thread]
Info    : Started on Tue May 28 14:08:46 2019
Info    : Reading 'test2D.geo'...
Info    : Done reading 'test2D.geo'
Info    : Finalized high order topology of periodic connections
Info    : Meshing 1D...
Info    : Meshing curve 5 (Line)
Info    : Meshing curve 6 (Line)
Info    : Meshing curve 7 (Line)

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# -*- coding: utf-8 -*-
"""
Created on Tue Apr  2 15:14:40 2019

@author: ddesantis
"""

from fipy import *
import numpy as np
import matplotlib.pyplot as plt

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from fipy import *

g = 0.66
L = 10.
nx = 1000
mu1 = 1.
mu2 = 1.
K = 1.
D1 = 1.
D2 = 1.

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$ nix-shell --pure
warning: dumping very large path (> 256 MiB); this may run out of memory
these derivations will be built:
  /nix/store/yfyl2cq05lswwb47vj71h5fbzwpj5rk4-scikit-fmm-0.0.9.tar.gz.drv
  /nix/store/2ykvqyvfp41rc1hq2vk4ys66c4msyl07-python2.7-scikit-fmm-0.0.9.drv
  /nix/store/ap25cv9l4gig0sw0vxh3a4vbh967n90w-gmsh-3.0.6.drv
  /nix/store/hmzya72gq1j92fj60zn2labci3ww2mlb-python2.7-tkinter-2.7.14.drv
  /nix/store/mmyaxmp7zcsxnkzpiinp1q5xmfaka8is-pysparse-1.1.1-dev.tar.gz.drv
  /nix/store/y86g8gr18ajb2frcis2dv474jaa1dpi3-python2.7-pysparse-1.1.1-dev.drv
  /nix/store/p0kriliyjc5cgygyr4j2r1gx42qw1v17-fipy.drv

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DEBUG conda.gateways.logging:set_verbosity(148): verbosity set to 3
TRACE conda.gateways.disk.test:file_path_is_writable(23): checking path is writable /data/guyer/miniconda2/pkgs/urls.txt
DEBUG conda.core.package_cache_data:_check_writable(236): package cache directory '/data/guyer/miniconda2/pkgs' writable: True
Solving environment: ...working... DEBUG conda.core.solve:solve_final_state(141): solving prefix /data/guyer/miniconda2/envs/fipy12
  specs_to_remove: frozenset([])
  specs_to_add: frozenset([MatchSpec(name=LowerStrMatch('scipy')), MatchSpec(name=LowerStrMatch('gmsh')), MatchSpec(name=LowerStrMatch('mpi4py')), MatchSpec(name=LowerStrMatch('python')), MatchSpec(name=LowerStrMatch('mayavi')), MatchSpec(name=LowerStrMatch('matplotlib')), MatchSpec(name=LowerStrMatch('trilinos')), MatchSpec(name=LowerStrMatch('pysparse')), MatchSpec(name=LowerStrMatch('numpy')), MatchSpec(name=LowerStrMatch('nomkl'))])
  prune: False
TRACE conda.gateways.disk.test:file_path_is_writable(23): checking path is writable /us

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#! ${PYTHON_EXECUTABLE}
# -*- python -*-

# @HEADER
# ***********************************************************************
#
#          PyTrilinos: Python Interfaces to Trilinos Packages
#                 Copyright (2014) Sandia Corporation
#
# Under the terms of Contract DE-AC04-94AL85000 with Sandia

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