Problem of github checkout command

MehdiBgh · October 12, 2022, 9:11am

I am trying to make a feature branch from the updated branch for the feature I want to work on. But faced error as bellow:
$ git checkout -b new-pair-style-ylz upstream/develop
error: The following untracked working tree files would be overwritten by checkout:
LICENSE
README
bench/Cu_u3.eam
bench/POTENTIALS/CH.airebo
bench/POTENTIALS/CH.rebo
bench/POTENTIALS/CdTe.bop.table
bench/POTENTIALS/Cu_u3.eam
bench/POTENTIALS/Ni.adp
bench/POTENTIALS/Ni.meam
bench/POTENTIALS/README
bench/POTENTIALS/Si.sw
bench/POTENTIALS/Si.tersoff
bench/POTENTIALS/data.airebo
bench/POTENTIALS/data.comb
bench/POTENTIALS/data.eff
bench/POTENTIALS/data.eim
bench/POTENTIALS/data.fene
bench/POTENTIALS/data.gb
bench/POTENTIALS/data.granular
bench/POTENTIALS/data.protein
bench/POTENTIALS/data.reax
bench/POTENTIALS/data.rebo
bench/POTENTIALS/data.spce
bench/POTENTIALS/ffield.comb
bench/POTENTIALS/ffield.eim
bench/POTENTIALS/ffield.reax
bench/POTENTIALS/in.adp
bench/POTENTIALS/in.airebo
bench/POTENTIALS/in.bop
bench/POTENTIALS/in.comb
bench/POTENTIALS/in.dpd
bench/POTENTIALS/in.eam
bench/POTENTIALS/in.eff
bench/POTENTIALS/in.eim
bench/POTENTIALS/in.fene
bench/POTENTIALS/in.gb
bench/POTENTIALS/in.granular
bench/POTENTIALS/in.lj
bench/POTENTIALS/in.meam
bench/POTENTIALS/in.peri
bench/POTENTIALS/in.protein
bench/POTENTIALS/in.reaxc
bench/POTENTIALS/in.rebo
bench/POTENTIALS/in.spce
bench/POTENTIALS/in.sw
bench/POTENTIALS/in.tersoff
bench/POTENTIALS/library.meam
bench/POTENTIALS/log.9Oct20.adp.1
bench/POTENTIALS/log.9Oct20.adp.4
bench/POTENTIALS/log.9Oct20.airebo.1
bench/POTENTIALS/log.9Oct20.airebo.4
bench/POTENTIALS/log.9Oct20.bop.1
bench/POTENTIALS/log.9Oct20.bop.4
bench/POTENTIALS/log.9Oct20.comb.1
bench/POTENTIALS/log.9Oct20.comb.4
bench/POTENTIALS/log.9Oct20.dpd.1
bench/POTENTIALS/log.9Oct20.dpd.4
bench/POTENTIALS/log.9Oct20.eam.1
bench/POTENTIALS/log.9Oct20.eam.4
bench/POTENTIALS/log.9Oct20.eff.1
bench/POTENTIALS/log.9Oct20.eff.4
bench/POTENTIALS/log.9Oct20.eim.1
bench/POTENTIALS/log.9Oct20.eim.4
bench/POTENTIALS/log.9Oct20.fene.1
bench/POTENTIALS/log.9Oct20.fene.4
bench/POTENTIALS/log.9Oct20.gb.1
bench/POTENTIALS/log.9Oct20.gb.4
bench/POTENTIALS/log.9Oct20.granular.1
bench/POTENTIALS/log.9Oct20.granular.4
bench/POTENTIALS/log.9Oct20.lj.1
bench/POTENTIALS/log.9Oct20.lj.4
bench/POTENTIALS/log.9Oct20.meam.1
bench/POTENTIALS/log.9Oct20.meam.4
bench/POTENTIALS/log.9Oct20.peri.1
bench/POTENTIALS/log.9Oct20.peri.4
bench/POTENTIALS/log.9Oct20.protein.1
bench/POTENTIALS/log.9Oct20.protein.4
bench/POTENTIALS/log.9Oct20.reaxc.1
bench/POTENTIALS/log.9Oct20.reaxc.4
bench/POTENTIALS/log.9Oct20.rebo.1
bench/POTENTIALS/log.9Oct20.rebo.4
bench/POTENTIALS/log.9Oct20.spce.1
bench/POTENTIALS/log.9Oct20.spce.4
bench/POTENTIALS/log.9Oct20.sw.1
bench/POTENTIALS/log.9Oct20.sw.4
bench/POTENTIALS/log.9Oct20.tersoff.1
bench/POTENTIALS/log.9Oct20.tersoff.4
bench/README
bench/data.chain
bench/data.chute
bench/data.rhodo
bench/in.chain
bench/in.chain.scaled
bench/in.chute
bench/in.chute.scaled
bench/in.eam
bench/in.lj
bench/in.rhodo
bench/in.rhodo.scaled
bench/log.6Oct16.chain.fixed.icc.1
bench/log.6Oct16.chain.fixed.icc.4
bench/log.6Oct16.chain.scaled.icc.4
bench/log.6Oct16.chute.fixed.icc.1
bench/log.6Oct16.chute.fixed.icc.4
bench/log.6Oct16.chute.scaled.icc.4
bench/log.6Oct16.eam.fixed.icc.1
bench/log.6Oct16.eam.fixed.icc.4
bench/log.6Oct16.eam.scaled.icc.4
bench/log.6Oct16.lj.fixed.icc.1
bench/log.6Oct16.lj.fixed.icc.4
bench/log.6Oct16.lj.scaled.icc.4
bench/log.6Oct16.rhodo.fixed.icc.1
bench/log.6Oct16.rhodo.fixed.icc.4
bench/log.6Oct16.rhodo.scaled.icc.4
cmake/.coveragerc.in
cmake/CMakeLists.jpeg
cmake/CMakeLists.png
cmake/CMakeLists.txt
cmake/CMakeLists.zlib
cmake/CMakeSettings.json
cmake/LAMMPSConfig.cmake.in
cmake/Modules/CheckGeneratorSupport.cmake
cmake/Modules/CodeCoverage.cmake
cmake/Modules/CodingStandard.cmake
cmake/Modules/Documentation.cmake
cmake/Modules/ExternalCMakeProject.cmake
cmake/Modules/FindCUB.cmake
cmake/Modules/FindClangFormat.cmake
cmake/Modules/FindCythonize.cmake
cmake/Modules/FindFFTW3.cmake
cmake/Modules/FindFFTW3F.cmake
cmake/Modules/FindMKL.cmake
cmake/Modules/FindMSCG.cmake
cmake/Modules/
Aborting

What is the problem and how I can fix it?

Germain · October 12, 2022, 9:57am

Hi @MehdiBgh ,

This clearly is a git problem and not directly related to LAMMPS. Your tree structure seems to be set in a wrong way and apparently changes were commited that would erase the listed files that are not currently tracked by Git. This is not normal since the bench and cmake directories as well as the LICENSE and README are supposed to be tracked by git if you use the provided .gitignore files. Be sure to check that the branch you’re using as a remote and your local branch do not have conflicts in git tracking behaviour.

If you do not care about the version you have of this files and want them to be erased by the branch you are using checkout on AND ONLY IN THIS CASE you can force the checkout with the -f flag. Else you have to verify your .gitignore and git setup carefully.

Good luck.

stamoor · October 17, 2022, 3:21pm

If you don’t care about the files, can also use git clean -fd ., but again this will DELETE the “untracked” files and allow the checkout to proceed.

MehdiBgh · October 18, 2022, 4:48am

Thanks for comments. The problem is solved.