Ecosyste.ms: Issues

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GitHub / Probe-Particle/ppafm issues and pull requests

#315 - Put back the "fit-density" option

Issue - State: open - Opened by mondracek 9 days ago
Labels: enhancement

#314 - Unify the storage for examples

Issue - State: open - Opened by ondrejkrejci 9 days ago - 4 comments
Labels: question

#313 - Add density cutoff option to fix FDBM for all-electron densities.

Pull Request - State: open - Opened by NikoOinonen 27 days ago - 3 comments

#312 - FDBM (Full-density based method) broken by recent changes

Issue - State: open - Opened by mondracek about 1 month ago - 3 comments
Labels: bug

#311 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 month ago

#310 - Pydantic deprecation warning

Issue - State: open - Opened by NikoOinonen about 1 month ago
Labels: chore

#309 - Fix spline interpolation segfaults.

Pull Request - State: closed - Opened by NikoOinonen about 1 month ago - 7 comments

#308 - Problems with spline interpolation code.

Issue - State: closed - Opened by NikoOinonen about 1 month ago - 4 comments
Labels: bug

#307 - Invalid command option in Wiki

Issue - State: closed - Opened by huangchieh about 2 months ago - 1 comment
Labels: documentation

#306 - Fix typos and formatting in example of PTCDA_Hartree

Pull Request - State: closed - Opened by huangchieh about 2 months ago

#305 - Fix API docs

Pull Request - State: closed - Opened by NikoOinonen about 2 months ago

#304 - Sphinx docs failing

Issue - State: closed - Opened by NikoOinonen about 2 months ago
Labels: bug

#303 - fix comment handling

Pull Request - State: closed - Opened by LauriKurki about 2 months ago

#302 - comments in params.ini not recognised

Issue - State: closed - Opened by LauriKurki about 2 months ago

#301 - Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago
Labels: dependencies

#300 - Remove the `tex` files from the documentation folder

Issue - State: open - Opened by yakutovicha 3 months ago
Labels: documentation

#299 - End support for Python 3.7

Pull Request - State: closed - Opened by yakutovicha 3 months ago - 3 comments

#298 - Fix some typos in examples.

Pull Request - State: closed - Opened by huangchieh 3 months ago

#297 - Update README.md

Pull Request - State: closed - Opened by yakutovicha 3 months ago

#296 - Update README.md

Pull Request - State: closed - Opened by ondrejkrejci 3 months ago - 1 comment

#295 - Automatic tests failed:

Issue - State: closed - Opened by ondrejkrejci 3 months ago - 2 comments
Labels: possibly_bug

#294 - updating references - readme and paper_figure

Pull Request - State: closed - Opened by ondrejkrejci 3 months ago - 1 comment

#293 - Update links to the new paper

Issue - State: closed - Opened by NikoOinonen 3 months ago - 7 comments
Labels: documentation, chore

#292 - Fix automated builds for MacOS.

Pull Request - State: closed - Opened by NikoOinonen 3 months ago

#291 - Default values in the "atomtypes.ini" file

Issue - State: closed - Opened by prometeus3 4 months ago - 5 comments
Labels: help wanted

#290 - Fix reading atom_frac from geometry.in

Pull Request - State: closed - Opened by mondracek 4 months ago - 2 comments

#289 - Reading geometry.in with fractional coordinates incorrect

Issue - State: closed - Opened by mondracek 4 months ago
Labels: bug

#288 - MacOS github runner deprecated

Issue - State: open - Opened by NikoOinonen 4 months ago - 2 comments
Labels: bug

#287 - Compatibility with NumPy 2.0

Pull Request - State: closed - Opened by NikoOinonen 4 months ago - 1 comment

#286 - Compatibility with Numpy 2.0

Issue - State: closed - Opened by NikoOinonen 5 months ago - 3 comments
Labels: bug, chore

#285 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#284 - Mismatch between GPU and CPU simulations "pyridineDensOverlap" example

Issue - State: open - Opened by prometeus3 5 months ago - 2 comments
Labels: help wanted

#283 - Addressing point 1 of the reviewer.

Issue - State: closed - Opened by ondrejkrejci 6 months ago - 5 comments
Labels: documentation

#282 - Code benchmark

Issue - State: closed - Opened by NikoOinonen 6 months ago - 29 comments
Labels: enhancement, documentation

#281 - Make scanner work when scan_dim is passed as a non-tuple array

Pull Request - State: closed - Opened by NikoOinonen 6 months ago

#280 - Temporarily disable one of the CI tests.

Pull Request - State: closed - Opened by NikoOinonen 6 months ago

#279 - Continuous-integration tests keep failing, blocking any new pull request

Issue - State: closed - Opened by mondracek 6 months ago - 10 comments
Labels: bug, help wanted

#278 - LCPD for general ranges of bias, amplitudes, tip charge and cantilever stiffness

Pull Request - State: closed - Opened by mondracek 6 months ago - 9 comments

#277 - Figure out electrostatics in FDBM

Issue - State: open - Opened by mondracek 6 months ago

#276 - Fixing FHI-aims electron densities for FDBM

Issue - State: open - Opened by NikoOinonen 7 months ago - 8 comments
Labels: enhancement

#275 - Implement `PpafmParameters` class based on `pydantic.BaseModel`

Pull Request - State: closed - Opened by yakutovicha 7 months ago - 7 comments

#274 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 1 comment

#274 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 1 comment

#274 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 1 comment

#273 - Generator update

Pull Request - State: closed - Opened by NikoOinonen 8 months ago - 2 comments

#273 - Generator update

Pull Request - State: closed - Opened by NikoOinonen 8 months ago - 2 comments

#273 - Generator update

Pull Request - State: closed - Opened by NikoOinonen 8 months ago - 2 comments

#271 - updated naming in README and addding the arxiv manuscript

Pull Request - State: closed - Opened by ondrejkrejci 8 months ago - 4 comments

#271 - updated naming in README and addding the arxiv manuscript

Pull Request - State: closed - Opened by ondrejkrejci 8 months ago - 4 comments

#270 - KPFM examples

Pull Request - State: closed - Opened by mondracek 8 months ago - 8 comments

#269 - Python API GPU tutorial

Pull Request - State: closed - Opened by NikoOinonen 9 months ago - 5 comments

#268 - Add tutorial for the AFMulator

Issue - State: closed - Opened by NikoOinonen 9 months ago
Labels: documentation

#267 - Tutorials for using the GPU-accelerated Python API

Issue - State: open - Opened by NikoOinonen 9 months ago
Labels: documentation

#266 - Too many names

Issue - State: closed - Opened by yakutovicha 9 months ago - 4 comments

#265 - API docs update

Pull Request - State: closed - Opened by NikoOinonen 9 months ago - 3 comments

#264 - Clean-up the API doc pages

Issue - State: closed - Opened by NikoOinonen 9 months ago
Labels: documentation

#263 - Windows wheel build failing

Issue - State: closed - Opened by NikoOinonen 9 months ago - 2 comments
Labels: bug

#262 - Adding the FePc_Au-IETS example

Pull Request - State: closed - Opened by ondrejkrejci 9 months ago - 5 comments

#261 - new version, of PPAFM released and added to Zenodo description

Issue - State: closed - Opened by ondrejkrejci 9 months ago - 4 comments
Labels: enhancement

#260 - Adding a beter description for the Zenodo database of images

Issue - State: closed - Opened by ondrejkrejci 9 months ago - 17 comments
Labels: documentation

#259 - Adding the FePc example to the examples

Issue - State: closed - Opened by ondrejkrejci 9 months ago
Labels: documentation

#258 - Proper documentation for the FDBM (full denity based method) is missing

Issue - State: closed - Opened by mondracek 10 months ago - 12 comments
Labels: documentation

#257 - DFT-D3 van der Waals does not work correctly with hydroxyl (-OH) groups

Issue - State: closed - Opened by mondracek 10 months ago - 22 comments
Labels: documentation, possibly_bug

#256 - The "tip" option in params.ini does not work

Issue - State: open - Opened by mondracek 10 months ago - 1 comment
Labels: bug

#255 - Add the FFPB_KPFM example

Pull Request - State: closed - Opened by mondracek 10 months ago - 2 comments

#254 - Add labels to color bars

Pull Request - State: closed - Opened by mondracek 10 months ago - 1 comment

#253 - Labels need to be added to the color bar in PNG images

Issue - State: open - Opened by mondracek 10 months ago - 3 comments
Labels: enhancement

#252 - Too large color bar makes png figures ugly

Issue - State: closed - Opened by mondracek 10 months ago - 3 comments
Labels: enhancement

#251 - Correct sign of densities and potentials in KPFM

Pull Request - State: closed - Opened by mondracek 10 months ago - 2 comments
Labels: bug

#250 - KPFM is wrong because of sign issues

Issue - State: closed - Opened by mondracek 10 months ago
Labels: bug

#249 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago - 1 comment

#248 - Paper figure

Pull Request - State: closed - Opened by NikoOinonen 11 months ago - 2 comments

#247 - Figure out the open access policy of the journal we submit to

Issue - State: closed - Opened by yakutovicha 11 months ago - 2 comments
Labels: question

#246 - Add example that plots the main figure of the new paper

Issue - State: closed - Opened by NikoOinonen 11 months ago
Labels: enhancement

#245 - Make KPAFM work with general bias voltage

Issue - State: closed - Opened by yakutovicha 11 months ago - 1 comment
Labels: enhancement

#244 - Write a wiki page about KPFM

Issue - State: open - Opened by yakutovicha 11 months ago
Labels: documentation

#243 - KPAFM: check that all examples working fine

Issue - State: closed - Opened by yakutovicha 11 months ago - 4 comments
Labels: enhancement

#242 - Add badges to the readme

Pull Request - State: closed - Opened by yakutovicha 11 months ago - 2 comments

#241 - Fix codecov report

Issue - State: closed - Opened by yakutovicha 11 months ago - 2 comments
Labels: bug, chore

#240 - Corrected IETS

Pull Request - State: closed - Opened by ProkopHapala 11 months ago - 5 comments

#239 - Electric field scaling corrected for non-zero grid origin

Pull Request - State: closed - Opened by mondracek 12 months ago - 7 comments

#237 - repair in plot_results.py for IETS (still not fully working).

Pull Request - State: closed - Opened by ondrejkrejci almost 1 year ago - 5 comments

#236 - nPBC z parameter should be 0 ?

Issue - State: open - Opened by ondrejkrejci almost 1 year ago - 1 comment
Labels: enhancement

#235 - `ci.yml`: add codecov and update checkout action

Pull Request - State: closed - Opened by yakutovicha about 1 year ago - 2 comments

#233 - Update the default parameters in `common.py`

Issue - State: open - Opened by ondrejkrejci about 1 year ago - 3 comments
Labels: enhancement, documentation

#232 - Create a class to manage simulation inputs

Issue - State: closed - Opened by yakutovicha about 1 year ago
Labels: enhancement

#231 - Removes the directory examples/_bak

Pull Request - State: closed - Opened by mondracek about 1 year ago - 1 comment

#230 - Default scanning region

Issue - State: open - Opened by mondracek about 1 year ago - 1 comment
Labels: enhancement

#229 - Consider non-zero origin of the grid cell

Pull Request - State: closed - Opened by mondracek about 1 year ago

#228 - Run PTCDA_single example with pytest

Pull Request - State: closed - Opened by yakutovicha about 1 year ago - 5 comments

#227 - Fix OpenCL compilation not working during CI tests

Pull Request - State: closed - Opened by NikoOinonen about 1 year ago

#226 - CI tests failing on OpenCL compile

Issue - State: closed - Opened by NikoOinonen about 1 year ago
Labels: bug

#225 - 224 add openmp acceleration

Pull Request - State: closed - Opened by ProkopHapala about 1 year ago - 26 comments

#224 - add OpenMP acceleration?

Issue - State: closed - Opened by ProkopHapala about 1 year ago - 2 comments
Labels: enhancement