Hi everyone, I am experiencing /troubles /with the *fipy.Gmsh2D function
with* *string*-wise script *input* in the /circle diffusion example/.
Please find the script in attachment (and note that I applied a little
trick <http://comments.gmane.org/gmane.comp.python.fipy/3725> to
circumvent the Gmsh version error). Running it gives me this error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"C:\Programs\Anaconda\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
line 685, in runfile
execfile(filename, namespace)
File
"C:\Programs\Anaconda\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py",
line 71, in execfile
exec(compile(scripttext, filename, 'exec'), glob, loc)
File
"C:/Users/Michael/Desktop/wuirkspees/fipybug/circular_diffusion_gmsh2DProb.py",
line 25, in <module>
mesh = fipy.Gmsh2D(mesh_string)
File
"C:\Programs\Anaconda\lib\site-packages\fipy\meshes\gmshMesh.py", line
1578, in __init__
background=background)
File
"C:\Programs\Anaconda\lib\site-packages\fipy\meshes\gmshMesh.py", line
228, in openMSHFile
stdout=PIPE)
File "C:\Programs\Anaconda\lib\subprocess.py", line 710, in __init__
errread, errwrite)
File "C:\Programs\Anaconda\lib\subprocess.py", line 958, in
_execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
It seems something goes wrong in the /temporary file creation/ in the
*openMSHFile*()-function in *gmshMesh*.*py *since it /can not find the
file/ with *Popen*() at *line 227.
*If anyone could assist me with this it would be really great.
Thank you in advance!
Michael_*
*_**
--
---
ir. Michael Ghijs
PhD Researcher
BIOMATH - Model based bioprocess analysis and optimisation
LFPAT - Laboratory of Pharmaceutical Process Analytical Technology
Ghent University
Faculty of Bioscience Engineering
Coupure Links 653, B-9000 Gent, Belgium
Phone: +32 (0)473 84.92.81
import fipy
fipy.meshes.gmshMesh._gmshVersion = lambda **kwargs : 2.0
#preferred edge length of each mesh element
cellSize = 0.05
#radius of circular mesh domain
radius = 1.
#create mesh with Gmsh (part of FiPy)
mesh_string = '''
cellSize = %(cellSize)g;
radius = %(radius)g;
Point(1) = {0, 0, 0, cellSize};
Point(2) = {-radius, 0, 0, cellSize};
Point(3) = {0, radius, 0, cellSize};
Point(4) = {radius, 0, 0, cellSize};
Point(5) = {0, -radius, 0, cellSize};
Circle(6) = {2, 1, 3};
Circle(7) = {3, 1, 4};
Circle(8) = {4, 1, 5};
Circle(9) = {5, 1, 2};
Line Loop(10) = {6, 7, 8, 9};
Plane Surface(11) = {10};
''' % locals()
mesh = fipy.Gmsh2D(mesh_string) Windows 7 Professional
64-bit OS
C:\Programs\Anaconda>conda list
# packages in environment at C:\Programs\Anaconda:
#
_license 1.1 py27_0 <unknown>
alabaster 0.7.3 py27_0 defaults
anaconda 2.2.0 np19py27_0 <unknown>
argcomplete 0.8.4 py27_0 <unknown>
astropy 1.0.1 np19py27_0 <unknown>
babel 2.1.1 py27_0 defaults
bcolz 0.8.1 np19py27_0 <unknown>
beautiful-soup 4.3.2 py27_1 <unknown>
binstar 0.10.1 py27_3 <unknown>
bitarray 0.8.1 py27_1 <unknown>
blaze-core 0.7.3 np19py27_0 <unknown>
blz 0.6.2 np19py27_0 <unknown>
bokeh 0.8.1 np19py27_1 <unknown>
boto 2.36.0 py27_0 <unknown>
cdecimal 2.3 py27_1 <unknown>
certifi 14.05.14 py27_0 <unknown>
cffi 0.9.2 py27_0 <unknown>
clyent 0.3.4 py27_0 <unknown>
colorama 0.3.3 py27_0 <unknown>
conda 3.19.3 py27_0 defaults
conda-build 1.11.0 py27_0 <unknown>
conda-env 2.4.5 py27_0 defaults
configobj 5.0.6 py27_0 <unknown>
cryptography 0.8 py27_1 <unknown>
cython 0.22 py27_0 <unknown>
cytoolz 0.7.2 py27_0 <unknown>
datashape 0.4.4 np19py27_1 <unknown>
decorator 4.0.9 py27_0 defaults
docutils 0.12 py27_1 <unknown>
dynd-python 0.6.5 np19py27_0 <unknown>
enum34 1.0.4 py27_0 <unknown>
fastcache 1.0.2 py27_0 <unknown>
flask 0.10.1 py27_1 <unknown>
funcsigs 0.4 py27_0 <unknown>
futures 2.2.0 py27_0 <unknown>
gevent 1.0.1 py27_0 <unknown>
gevent-websocket 0.9.3 py27_0 <unknown>
greenlet 0.4.5 py27_0 <unknown>
grin 1.2.1 py27_2 <unknown>
h5py 2.4.0 np19py27_0 <unknown>
ipykernel 4.1.0 py27_0 defaults
ipython 4.1.1 py27_0 defaults
ipython-notebook 3.0.0 py27_2 <unknown>
ipython-qtconsole 3.0.0 py27_1 <unknown>
ipython_genutils 0.1.0 py27_0 defaults
itsdangerous 0.24 py27_0 <unknown>
jdcal 1.0 py27_0 <unknown>
jedi 0.9.0 py27_0 defaults
jinja2 2.8 py27_0 defaults
jsonschema 2.4.0 py27_0 <unknown>
jupyter_client 4.1.1 py27_0 defaults
jupyter_core 4.0.6 py27_0 defaults
launcher 1.0.0 1 <unknown>
llvmlite 0.2.2 py27_1 <unknown>
lxml 3.4.2 py27_0 <unknown>
markupsafe 0.23 py27_0 <unknown>
matplotlib 1.4.3 np19py27_1 <unknown>
menuinst 1.3.2 py27_0 defaults
mistune 0.7.1 py27_0 defaults
mock 1.0.1 py27_0 <unknown>
msvc_runtime 1.0.1 vc9_0 [vc9] defa
multipledispatch 0.4.7 py27_0 <unknown>
nbconvert 4.0.0 py27_0 defaults
nbformat 4.0.1 py27_0 defaults
networkx 1.9.1 py27_0 <unknown>
nltk 3.0.2 np19py27_0 <unknown>
node-webkit 0.10.1 0 <unknown>
nose 1.3.4 py27_1 <unknown>
numba 0.17.0 np19py27_0 <unknown>
numexpr 2.3.1 np19py27_0 <unknown>
numpy 1.10.1 py27_0 defaults
odo 0.3.1 np19py27_0 <unknown>
openpyxl 1.8.5 py27_0 <unknown>
pandas 0.17.0 np110py27_0 defaults
path.py 8.1.2 py27_1 defaults
patsy 0.3.0 np19py27_0 <unknown>
pep8 1.6.2 py27_0 <unknown>
pickleshare 0.5 py27_0 defaults
pillow 2.7.0 py27_0 <unknown>
pip 8.0.3 py27_0 defaults
ply 3.4 py27_0 <unknown>
psutil 3.2.2 py27_0 defaults
py 1.4.26 py27_0 <unknown>
pyasn1 0.1.7 py27_0 <unknown>
pycosat 0.6.1 py27_0 <unknown>
pycparser 2.10 py27_0 <unknown>
pycrypto 2.6.1 py27_3 <unknown>
pyflakes 1.0.0 py27_0 defaults
pygments 2.0.2 py27_0 <unknown>
pyopenssl 0.14 py27_0 <unknown>
pyparsing 2.0.3 py27_0 <unknown>
pyqt 4.10.4 py27_1 <unknown>
pyreadline 2.1 py27_0 defaults
pytables 3.1.1 np19py27_1 <unknown>
pytest 2.6.4 py27_0 <unknown>
python 2.7.11 2 defaults
python-dateutil 2.4.2 py27_0 defaults
pytz 2015.6 py27_0 defaults
pywin32 219 py27_0 <unknown>
pyyaml 3.11 py27_2 defaults
pyzmq 14.7.0 py27_0 defaults
qtconsole 4.1.0 py27_0 defaults
requests 2.9.1 py27_0 defaults
rope 0.9.4 py27_1 <unknown>
runipy 0.1.3 py27_0 <unknown>
scikit-image 0.11.2 np19py27_0 <unknown>
scikit-learn 0.15.2 np19py27_0 <unknown>
scipy 0.15.1 np19py27_0 <unknown>
setuptools 20.1.1 py27_0 defaults
simplegeneric 0.8.1 py27_0 defaults
six 1.10.0 py27_0 defaults
snowballstemmer 1.2.0 py27_0 defaults
sockjs-tornado 1.0.1 py27_0 <unknown>
sphinx 1.3.1 py27_0 defaults
sphinx_rtd_theme 0.1.7 py27_0 defaults
spyder 2.3.7 py27_1 defaults
spyder-app 2.3.4 py27_0 <unknown>
sqlalchemy 0.9.9 py27_0 <unknown>
ssl_match_hostname 3.4.0.2 py27_0 <unknown>
statsmodels 0.6.1 np19py27_0 <unknown>
sympy 0.7.6 py27_0 <unknown>
toolz 0.7.1 py27_0 <unknown>
tornado 4.1 py27_0 <unknown>
traitlets 4.1.0 py27_0 defaults
ujson 1.33 py27_0 <unknown>
unicodecsv 0.9.4 py27_0 <unknown>
werkzeug 0.10.1 py27_0 <unknown>
wheel 0.29.0 py27_0 defaults
xlrd 0.9.3 py27_0 <unknown>
xlsxwriter 0.6.7 py27_0 <unknown>
xlwings 0.3.4 py27_0 <unknown>
xlwt 0.7.5 py27_0 <unknown>
_______________________________________________
fipy mailing list
fipy@nist.gov
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
