Probe-Particle/ppafm issues and pull requests

#223 - Atoms with negative coordinates in non-periodic systems invisible (in the CPU version)

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

#222 - Apply `pre-commit` for the whole repository

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

#221 - Add multipole tip to CLI arguments

Issue - State: open - Opened by NikoOinonen about 1 year ago

#220 - formating

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

#219 - Formatting

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

#218 - Wrong note on the *.xyz input format on Wiki

Issue - State: open - Opened by mondracek about 1 year ago - 2 comments
Labels: documentation

#217 - Enable loading XSF files from FHI-AIMS

Issue - State: open - Opened by mondracek about 1 year ago - 5 comments
Labels: enhancement

#216 - Generate automatic lattice vectors in loadGeometry

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

#215 - Work on cli tools

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

#214 - Replace print statements with logging tools

Issue - State: open - Opened by yakutovicha about 1 year ago
Labels: chore

#213 - Automatic lattice vectors

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

#212 - Add Python 3.12 to CI tests.

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

#211 - GUI: visual manipulation of atom positions

Issue - State: open - Opened by NikoOinonen about 1 year ago - 2 comments
Labels: enhancement

#210 - Protocol for dealing with formatting changes needed

Issue - State: closed - Opened by mondracek about 1 year ago - 2 comments
Labels: question

#209 - Fixed incorrect loading of aims .in and poscar files.

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

#208 - The examples in examples/_bak do not work

Issue - State: closed - Opened by mondracek about 1 year ago - 4 comments
Labels: chore

#207 - Sign of atomic forces in the C++ version

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

#206 - Fitting directory needs update

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

#205 - Test examples with pytest

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

#204 - Dockerfile: switch to extended-support image.

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

#203 - Merging of new pull requests is blocked by automatic checks

Issue - State: closed - Opened by mondracek about 1 year ago - 1 comment
Labels: bug, help wanted

#202 - Improve Fz2df conversion

Pull Request - State: closed - Opened by mondracek about 1 year ago - 5 comments
Labels: bug, enhancement

#201 - ppafm.io.loadGeometry returns wrong properties with FHI-aims format input

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

#200 - ppafm-plot-results --atoms requires input_plot.xyz

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

#199 - Wrong height of the scanned region in df.xsf

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

#198 - Suggest cleanup of geometry handling in the CPU version

Issue - State: open - Opened by mondracek about 1 year ago - 26 comments

#197 - Create automatic lattice vectors if none are specified in the input

Pull Request - State: closed - Opened by mondracek about 1 year ago - 10 comments

#196 - Apply black to the `ml` package.

Pull Request - State: closed - Opened by yakutovicha about 1 year ago - 18 comments

#195 - GitHub Copilot for organization ?

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

#194 - Adding double electrostatics to the new version of the code

Issue - State: open - Opened by ondrejkrejci about 1 year ago
Labels: dev/WIP

#193 - Making KPFM work

Pull Request - State: closed - Opened by mondracek about 1 year ago - 3 comments

#192 - Add ppafm-conv-rho and ppafm-generate-dftd3. Closes #186

Pull Request - State: closed - Opened by mondracek over 1 year ago - 4 comments

#191 - Example of organometallic complex not working

Issue - State: closed - Opened by ELpolloGUAPO over 1 year ago - 4 comments

#190 - Enable full input from Cube files, including densities

Issue - State: open - Opened by mondracek over 1 year ago - 4 comments
Labels: enhancement, blocked

#189 - Implement FDBM in the GUI.

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 11 comments

#188 - Merge relaxed_scan_PVE.py to relaxed_scan.py.

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 2 comments

#187 - Temporarily disable flake8 pre-commit hook.

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

#186 - Merge `relaxed_scan_PVE.py` into `relaxed_scan.py`?

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 8 comments
Labels: enhancement

#185 - Overhaul of CLI arguments

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 5 comments

#184 - About CI and tests on the wiki

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 3 comments
Labels: documentation

#183 - Update README

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

#182 - Adding fit size script to Utilities

Pull Request - State: closed - Opened by ondrejkrejci over 1 year ago

#181 - Update the docker container.

Pull Request - State: closed - Opened by yakutovicha over 1 year ago - 9 comments

#180 - Fixed API docs for AFMulator.

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

#179 - Fixes #39

Pull Request - State: closed - Opened by mondracek over 1 year ago - 6 comments

#178 - CI wheels build

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

#177 - Return .in as an accepted geometry file type for generating force fields

Issue - State: closed - Opened by LauriKurki over 1 year ago - 3 comments

#176 - Release schedule?

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 6 comments
Labels: question, documentation

#175 - Update README.md

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

#174 - Replaced origin='image' with origin='lower' in PPPlot.py

Pull Request - State: closed - Opened by LauriKurki over 1 year ago

#173 - Temporary disable wheel build.

Pull Request - State: closed - Opened by yakutovicha over 1 year ago - 1 comment

#172 - Improve the `README.md` file

Pull Request - State: closed - Opened by yakutovicha over 1 year ago - 1 comment

#171 - Automate release with bumpver

Pull Request - State: closed - Opened by yakutovicha over 1 year ago - 1 comment

#170 - Release automatically on PyPi

Pull Request - State: closed - Opened by yakutovicha over 1 year ago

#169 - Option to draw atom positions onto the AFM image in GUI

Issue - State: open - Opened by NikoOinonen over 1 year ago
Labels: enhancement

#168 - Set fixed locale during array read.

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

#167 - Locale problem resurfaced

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

#166 - Implemented DFT-D3 in the CPU code.

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

#165 - Implement DFT-D3 in the CPU code as well

Issue - State: closed - Opened by NikoOinonen over 1 year ago
Labels: enhancement

#164 - Set maximum for initial scan size in GUI.

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

#163 - Add Grimme-D3 calculation

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 6 comments

#162 - Added g++ and make to readthedocs build requirements.

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 2 comments

#161 - Readthedocs builds are failing

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

#160 - set atomic number of Cl to 17

Pull Request - State: closed - Opened by alexriss over 1 year ago

#159 - Fix sign of electrostatic force in density overlap.

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

#158 - Fix vdW in the density overlap model

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 9 comments

#157 - Fix the sign issue on the ES force in FDBM

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

#156 - Test Density Overlap Properly

Issue - State: open - Opened by ProkopHapala over 1 year ago - 40 comments
Labels: question, possibly_bug

#155 - Delete `dev` folder from the `ppafm` directory.

Issue - State: open - Opened by yakutovicha over 1 year ago - 7 comments

#154 - Fixing issue with saving numpy format

Pull Request - State: closed - Opened by ondrejkrejci over 1 year ago - 2 comments

#153 - Replace `params.ini` input with a more standard format

Issue - State: open - Opened by yakutovicha over 1 year ago - 3 comments

#152 - Chore: move `dev/fitPPM` to `ppafm/cli/fitting`

Pull Request - State: closed - Opened by yakutovicha over 1 year ago

#151 - Fix to OpenCL compilation paths.

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

#150 - Solve electrostatic potential from electron density

Issue - State: open - Opened by NikoOinonen over 1 year ago
Labels: enhancement

#149 - Odd sign convention in force calculation

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 12 comments

#148 - Inconsistent parameter loading from script arguments

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 6 comments
Labels: bug

#147 - Implement tip density resampling.

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

#146 - Proper documentation of the new executable scripts

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 11 comments
Labels: documentation

#145 - Fix coordinate offset in OpenCL force field interpolation.

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 4 comments

#144 - Try tri-cubic interpolation of just Energy rather than tri-linear interpolation of Force

Issue - State: open - Opened by ProkopHapala over 1 year ago - 19 comments
Labels: enhancement

#143 - Implemented normalization to power raising method for DataGrid.

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

#142 - Differences in probe relaxation between the C++ and OpenCL code

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 10 comments
Labels: bug, question

#141 - Removed locale change in ReadNumsUpTo that was causing trouble.

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

#140 - Added clarity for changing values of GUI widgets.

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

#139 - Parameter saving/loading from params.ini for AFMulator and the GUI

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

#138 - Tip electron density resampling in FDBM in OpenCL

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 2 comments
Labels: enhancement

#137 - Add FDBM support to the GUI

Issue - State: closed - Opened by NikoOinonen over 1 year ago
Labels: enhancement

#136 - Proper handling of negative values in FDBM electron densities in OpenCL

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 3 comments
Labels: bug

#135 - Cannot install ppafm after code reorganization

Issue - State: closed - Opened by ProkopHapala over 1 year ago - 14 comments

#134 - Better explanations for all of the keywords

Issue - State: closed - Opened by NikoOinonen over 1 year ago - 16 comments
Labels: enhancement, documentation

#133 - Application for KPFM

Issue - State: closed - Opened by Aimannor over 1 year ago - 12 comments
Labels: question, documentation

#132 - Rename basUtils to io also in sphinx docs.

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

#131 - Remove remaining sys.path manipulation.

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

#130 - Full-density based model in OpenCL

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 3 comments

#129 - Test(s) for plot_results?

Issue - State: closed - Opened by mondracek over 1 year ago - 2 comments
Labels: question

#128 - ppafm-plot-results fails because of missing load_scal_field in GridUtils

Issue - State: closed - Opened by mondracek over 1 year ago - 1 comment
Labels: bug

#127 - Completes renaming "basUtils" to "io"

Pull Request - State: closed - Opened by mondracek over 1 year ago - 2 comments
Labels: bug

#126 - ppafm-plot-results fails, missing basUtils

Issue - State: closed - Opened by mondracek over 1 year ago - 1 comment
Labels: bug

#125 - Fix CI tests

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 2 comments

#124 - Fix for sign issues in electrostatics and Pauli calculations.

Pull Request - State: closed - Opened by NikoOinonen over 1 year ago - 15 comments

GitHub / Probe-Particle/ppafm issues and pull requests