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guyer / multipass_beer_lambert.py
Created June 8, 2012 13:40 — forked from danieljfarrell/multipass_beer_lambert.py
Fipy: Beer-Lambert law with multiple reflections
# http://matforge.org/wd15/blog
from __future__ import division
from fipy import *
# Grid things
N = 1000
D = 1
dx = D / N
m = Grid1D(nx=N+1, dx=dx) + [[-dx/2.]]
I_right = CellVariable(mesh=m, value=1., name='I_right') # Intensity along the positive direction
@guyer
guyer / config.log
Created February 14, 2013 18:13
log file generated by `./configure --disable-tecplot --enable-tecio --with-netcdf=old --with-exodus=old --with-nemesis=old`
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by libmesh configure 0.9.1pre, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --disable-tecplot --enable-tecio --with-netcdf=old --with-exodus=old --with-nemesis=old
## --------- ##
## Platform. ##
@guyer
guyer / ammended stderr & stdout
Last active December 17, 2015 13:39
homebrew-science/vtk failure information
This file has been truncated, but you can view the full file.
$ HOMEBREW_MAKE_JOBS=1 VERBOSE=1 brew install --qt vtk
dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/sudo) is setuid or setgid
==> Downloading http://www.vtk.org/files/release/5.10/vtk-5.10.1.tar.gz
Already downloaded: /Library/Caches/Homebrew/vtk-5.10.1.tar.gz
tar xf /Library/Caches/Homebrew/vtk-5.10.1.tar.gz
==> Patching
/usr/bin/patch -f -p1 -i 000-homebrew.diff
patching file Wrapping/Python/setup_install_paths.py
==> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/vtk/5.10.1 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DVTK_REQUIRED_OBJCXX_FLAGS='' -DVTK_USE_CARBON=OFF -DVTK_USE_TK=OFF -DBUILD_TESTING=OFF -DBUILD_SHARED_LIBS=ON -DIOKit:FILEPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/System/Library/Frameworks/IOKit.framework -DCMAKE_INSTALL_RPATH:STRING='/usr/local/Cellar/vtk/5.10.1/lib/vtk-5.10' -DCMAKE_INSTALL_NAME_DIR:STRING='/usr/local/Cellar/vtk/5.10.1/lib/vtk-5.10' -DBUILD_EXAMPLES=OFF -DVT
@guyer
guyer / gist:5796578
Last active December 18, 2015 14:19
make output culminating in PyTrilinos link failure
/usr/local/Cellar/cmake/2.8.11/bin/cmake -H/Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source -B/Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source/TEST1 --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/Cellar/cmake/2.8.11/bin/cmake -E cmake_progress_start /Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source/TEST1/CMakeFiles /Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source/TEST1/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make -f packages/teuchos/src/CMakeFiles/teuchos.dir/build.make packages/teuchos/src/CMakeFiles/teuchos.dir/depend
cd /Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source/TEST1 && /usr/local/Cellar/cmake/2.8.11/bin/cmake -E cmake_depends "Unix Makefiles" /Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source /Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source/packages/teuchos/src /Users/guyer/.virtualenvs/trilinos/build/trilinos-11.0.3-Source/TEST1 /Users/guyer/.virtualenvs/trilinos/bu
@guyer
guyer / gist:5796687
Created June 17, 2013 13:01
make output culminating in syntax errors in EpetraExt
Scanning dependencies of target teuchos
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_ArrayView.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_BLAS.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_CTimeMonitor.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_CommandLineProcessor.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_CompObject.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_CWrapperSupport.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_Describable.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_Dependency.cpp.o
[ 0%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_DependencySheet.cpp.o
@guyer
guyer / gist:090e6314d4425fddb769
Last active August 29, 2015 14:15
conda build debug-weirdness
BUILD START: weirdness-1.2.3-py27_1
Fetching package metadata: ......
Solving package specifications: .
The following NEW packages will be INSTALLED:
openssl: 1.0.1k-0
python: 2.7.9-1
readline: 6.2-2
sqlite: 3.8.4.1-0
tk: 8.5.15-0
@guyer
guyer / fipy-ibm2_test_forum.py
Last active August 26, 2015 18:37
FiPy script for Fokker-Planck with attractor and clustered signals
from fipy import *
#numerix.random.seed(13)
from scipy import interpolate
import matplotlib.pyplot as plt
import matplotlib.mlab as ml
import time
fig = plt.figure(figsize=(15,6))
ax1 = plt.subplot((121))
ax2 = plt.subplot((122))
@guyer
guyer / internal_conductor.ipynb
Created October 22, 2015 13:43
IPython notebook demonstrating setting an internal boundary condition in FiPy
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@guyer
guyer / internal_conductor2.ipynb
Created October 28, 2015 15:17
IPython notebook demonstrating setting a conducting region in FiPy
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@guyer
guyer / solverscaling.py
Created November 19, 2015 21:37
FiPy script to test time scaling with dimension
from fipy import *
import time
# Spatial parameters
nx = 27000 # bins
dx = 1.
L = nx * dx
# Diffusion and time step
D = 1.