apbs

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Investigate using the numpy.dot function to calculate the Euclidean distance.

5

**Describe the bug** Numpy may be a better way to implement the Euclidean distance .

intendo

Linking issue with using pre-compiled binaries

4

**Describe the bug** I want to use the pre-compiled binary on osx and ubuntu **To Reproduce** I downloaded the APBS-3.0.0 release APBS-3.0.0_Linux.zip and APBS-3.0.0_OSX-Darwin.zip However, in the ubuntu platform, I...

xiki-tempula

Replace SWIG with something from the last decade

8

Priority is to replace IO functionality (eg NOSH) first and work towards the more substantial kernels as needed.

sobolevnrm

* Convert YAML or JSON * Start with files in https://github.com/Electrostatics/apbs/tree/master/tools/conversion

sobolevnrm

**Is your feature request related to a problem? Please describe.** Please convert the tools/* to Python3 **Describe the solution you'd like** Replace as much C code with Python as possible

intendo

Per discussion with @intendo consider replacing NOsh with a formal workflow management system (e.g., https://www.commonwl.org/) or at least a modern input syntax that can be easily parsed in Python. Ideally,...

sobolevnrm

Very slow boundary element execution

3

Hi @lwwilson1 -- Could you please help @intendo and me with a performance issue in BEM? The details follow. ------------ From the output below you can see that the bem-pKa...

sobolevnrm

Hello, I think there is still ambiguity in APBS 3.0.0 (that does not output energy units in the geoflow computation) and the definition of the keywords on the website. Are...

sobolevnrm

Do we fork and maintain independently?

sobolevnrm

Need better integration with build/test/maintain framework

sobolevnrm