Daniel Wheeler
Daniel Wheeler
``` Python 3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 08:20:52) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import fipy /home/wd15/git/fipy/fipy/variables/variable.py:649:...
As [pointed out](https://www.mail-archive.com/[email protected]/msg04335.html) on the mailing list, there's a factor of dt missing in the consumption term in the adsorbing surfaction equation [at this line](https://github.com/usnistgov/fipy/blob/9da3ef84d8d3464fc8d332623cdfcaf17f020d0d/examples/levelSet/electroChem/adsorbingSurfactantEquation.py#L289).
See https://www.mail-archive.com/[email protected]/msg02746.html ~~http://thread.gmane.org/gmane.comp.python.fipy/3172~~ The thread above has an example where multiple terms of the same type are combined in an equation which breaks version 3.0.1, but works with version 2.1.3....
FiPy's sparse matrix classes should be cast to numpy arrays with numerix.array(...) rather than using the numpyArray attribute. _Imported from trac ticket [#344](http://www.ctcms.nist.gov/cgi-bin/redirectLegacyMatforge.py?url=http://matforge.org/fipy/ticket/344), created by wd15 on 05-16-2011 at 10:54,...
The issue was raised [here](https://www.mail-archive.com/[email protected]/msg04108.html). Further notes on the issue are [here](https://gist.github.com/wd15/fc34ccb2e57602fc6f9bea96d8160f4a#file-untitled-ipynb) including the correct discretization. Essentially, the cylindrical faces are ignored, which introduces a $\phi / r$ consistent error...
The following breaks with on multiple nodes ``` python import fipy as fp geoFile = 'tmsh3d.geo' mesh = fp.Gmsh3D(geoFile) mx,my,mz = mesh.getCellCenters() ``` run using ``` $ mpirun -machinefile machinefile...
C. Simon, E. Vaughan, W. Bement, and L. Edelstein-Keshet. (2013) Pattern formation of Rho GTPases in single cell wound healing. Molecular Biology of the Cell. 24 (3). http://www.molbiolcell.org/content/24/3/421.full _Imported from...
The convergence report should include measurable quantities about the mesh and solver iterations including - [ ] mesh skewness - [ ] mesh offset - [ ] matrix symmetry -...
See http://thread.gmane.org/gmane.comp.python.fipy/3126. _Imported from trac ticket [#647](http://www.ctcms.nist.gov/cgi-bin/redirectLegacyMatforge.py?url=http://matforge.org/fipy/ticket/647), created by wd15 on 07-11-2013 at 17:13, last modified: 07-11-2013 at 17:13_
**Snakemake version** 7.12.0 **Describe the bug** `snakemake --export-cwl workflow.cwl` fails with `FileNotFoundError`. **Logs** ``` Traceback (most recent call last): File "/nix/store/wlvg4adricj130jxpiyly53q767kxf66-snakemake-7.12.0/lib/python3.9/site-packages/snakemake/__init__.py", line 730, in snakemake success = workflow.execute( File "/nix/store/wlvg4adricj130jxpiyly53q767kxf66-snakemake-7.12.0/lib/python3.9/site-packages/snakemake/workflow.py",...