apbs

apbs copied to clipboard

**Describe the bug** The merging of PR #232 should have triggered the Release workflow, which then should have created a tag that would trigger the Build workflow on that tag....

nsoblath

Multithreaded Build

1

* Cross-platform multithreaded build * Based on build improvements in #163 * Using existing OpenMP support

nsoblath

python2->3 bug in psize.py

8

At line 175, a list is compared to an integer. This is ok to do in python2, but not 3:  To fix the issue, consider replacing line 175 with:...

itaneja2

Broken example - TABI-PB (Boundary Element Method)

1

I was trying to run the example of the TABI-PB (Boundary Element Method) - [link](https://github.com/Electrostatics/apbs/tree/main/examples/bem). Running the following command: `apbs 1a63_NanoShaper_SES.in` gave the following error:  I didn't change the...

tomer196

Closes #198

nsoblath

Hello -- `srfm mol` and `srfm smol` will generate surface contributions from zero-radius atoms. They probably shouldn't do that but that's a low-priority bug to fix. What are you trying...

sobolevnrm

Please strip share/apbs/tools/bin/* executables

6

``` ====> Running Q/A tests (stage-qa) Warning: 'share/apbs/tools/bin/uhbd_asc2bin' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'share/apbs/tools/bin/dx2mol' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'share/apbs/tools/bin/dx2uhbd'...

yurivict

Hi @rwxayheee -- The [Debye length](https://en.wikipedia.org/wiki/Debye_length) isn't defined at zero ionic strength so I just had the output report "0". This should probably be "infinite" or "undefined" instead. In general,...

sobolevnrm

Calculation of electric field

2

Dear, I have a very simple system of highly charged sphere in ionic solution (1M). I would like to write out the gradient of the electrostatic potential (electric field) for...

ESgit2021

There's plenty of documentation (e.g., https://github.com/Electrostatics/apbs/blob/master/apbs/input_file/read.py) but ReadTheDocs isn't building it (https://apbs.readthedocs.io/en/latest/api/index.html#module-apbs). The documentation builds fine locally in Sphinx.

sobolevnrm