"Fossies" - the Fresh Open Source Software Archive  

Source code changes report for "gromacs" between the packages
gromacs-2020.1.tar.gz and gromacs-2020.2.tar.gz

About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules but used also for e.g. polymers). Release of 2020 series.

Summary:

The "gromacs" source code changed by about 0.1% and now consists of 5655 regular files (-12), 3 symbolic links and 355 directories (+2).

Related Informations:

See docs/gmxapi/changelog.rst (gromacs 2020.2).

Changes In Files (According File Type):

File TypeTotalAddedRemovedChanged
Header file 1227 0 0 16
C program 252 0 0 0
C++ program 1430 0 0 23
Patch 2 0 0 0
Fortran program 1 0 0 0
Perl program 5 0 0 0
Python program 106 2 0 0
Shell program 36 6 0 2
Awk program 1 0 0 0
Python compiled program 1 0 0 1
Automake file 7 0 0 0
CMake file 240 0 0 11
Configuration file 1 0 0 0
Initialization file 3 0 0 0
JSON file 5 0 0 0
Lex program 1 0 0 0
Makefile 2 0 0 0
Man page 100 0 0 100
Pkg-config file 1 0 0 0
Symbolic link 3 0 0 0
XML document 1161 0 0 0
Yacc program 1 0 0 0
DOS Batch file 2 0 0 0
Doxygen file 12 0 0 0
DTD file 1 0 0 0
MS office document 15 0 0 0
RST file 196 2 0 1
TeX document 4 0 0 0
XML style sheet 10 0 0 0
YAML file 23 0 22 0
Data file 56 0 0 0
Image file 9 0 0 0
PDF file 75 0 0 0
Vector Image file 110 0 0 0
Directory 356 3 1 0
Change log 3 0 0 0
Information file 7 0 0 1
License 8 0 0 0
Readme file 29 0 0 0
Text file 512 0 0 5
Other 22 0 0 0
Total Files60361323160



Header Files (16 of 1227):

NameStatusDeltaVisual Diff
src/api/cpp/tests/testingconfiguration.h changed 11.9% diff
src/gromacs/coordinateio/tests/outputadapters.h changed 3.6% diff
src/gromacs/mdrun/isimulator.h changed 1.3% diff
src/gromacs/mdtypes/interaction_const.h changed 4.2% diff
src/gromacs/nbnxm/grid.h changed 0.8% diff
src/gromacs/nbnxm/pairlist.h changed 2.8% diff
src/gromacs/options/optionstoragetemplate.h changed 0.5% diff
src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256_simd_float.h changed 2.6% diff
src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_simd4_double.h changed 3.1% diff
src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_simd4_float.h changed 3.5% diff
src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_simd_double.h changed 2.9% diff
src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_simd_float.h changed 3.0% diff
src/gromacs/simd/simd.h changed 0.5% diff
src/gromacs/topology/block.h changed 3.2% diff
src/gromacs/utility/basedefinitions.h changed 10.5% diff
src/testutils/testasserts.h changed 3.8% diff

C++ Programs (23 of 1430):

NameStatusDeltaVisual Diff
src/gromacs/compat/tests/pointers.cpp changed 5.4% diff
src/gromacs/coordinateio/tests/outputadapters.cpp changed 1.8% diff
src/gromacs/domdec/domdec.cpp changed 0.1% diff
src/gromacs/ewald/pme_only.cpp changed 0.6% diff
src/gromacs/fft/fft5d.cpp changed 0.4% diff
src/gromacs/fileio/checkpoint.cpp changed 1.1% diff
src/gromacs/fileio/matio.cpp changed 0.6% diff
src/gromacs/fileio/oenv.cpp changed 4.2% diff
src/gromacs/gmxana/gmx_do_dssp.cpp changed 0.5% diff
src/gromacs/gmxana/nrama.cpp changed 4.5% diff
src/gromacs/gmxlib/network.cpp changed 2.9% diff
src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp changed 3.7% diff
src/gromacs/gmxpreprocess/tests/readir.cpp changed 8.9% diff
src/gromacs/listed_forces/bonded.cpp changed 0.4% diff
src/gromacs/mdlib/forcerec.cpp changed 1.4% diff
src/gromacs/mdlib/sim_util.cpp changed 0.1% diff
src/gromacs/mdrun/md.cpp changed 0.6% diff
src/gromacs/mdrunutility/multisim.cpp changed 3.1% diff
src/gromacs/nbnxm/nbnxm_setup.cpp changed 1.4% diff
src/gromacs/taskassignment/reportgpuusage.cpp changed 1.6% diff
src/gromacs/utility/binaryinformation.cpp changed 3.2% diff
src/gromacs/utility/tests/enumerationhelpers.cpp changed 15.7% diff
src/programs/mdrun/tests/densityfittingmodule.cpp changed 2.9% diff

Python Programs (2 of 106):

NameStatusDeltaVisual Diff
admin/containers/scripted_gmx_docker_builds.py added
admin/containers/utility.py added

Shell Programs (8 of 36):

NameStatusDeltaVisual Diff
admin/ci-scripts/build-and-test-py-gmxapi-0.1.sh added
admin/ci-scripts/build-and-test-py-gmxapi-0.2.sh added
admin/ci-scripts/build-and-test-sample_restraint-2020.sh added
admin/ci-scripts/build-and-test-sample_restraint-2021.sh added
admin/clang-format.sh changed 1.7% diff
admin/clang-tidy.sh added
admin/containers/buildall.sh added
admin/dockerfiles/buildall.sh changed 49.5% diff

Python Compiled Programs (all 1):

NameStatusDeltaVisual Diff
docs/__pycache__/gmxsphinx.cpython-36.pyc changed 0.1%

CMake Files (11 of 240):

NameStatusDeltaVisual Diff
cmake/gmxGenerateVersionInfoRelease.cmake changed 4.1% diff
cmake/gmxManageSimd.cmake changed 2.6% diff
cmake/gmxVersionInfo.cmake changed 3.0% diff
docs/CMakeLists.txt changed 0.1% diff
scripts/CMakeLists.txt changed 6.8% diff
src/api/cpp/CMakeLists.txt changed 2.1% diff
src/buildinfo.h.cmakein changed 12.2% diff
src/CMakeLists.txt changed 15.8% diff
src/gromacs/CMakeLists.txt changed 3.2% diff
src/gromacs/selection/CMakeLists.txt changed 7.5% diff
src/testutils/TestMacros.cmake changed 11.5% diff

Man Pages (all 100):

NameStatusDeltaVisual Diff
docs/man/gmx-anaeig.1 changed 1.4% diff
docs/man/gmx-analyze.1 changed 1.2% diff
docs/man/gmx-angle.1 changed 2.3% diff
docs/man/gmx-awh.1 changed 5.0% diff
docs/man/gmx-bar.1 changed 1.6% diff
docs/man/gmx-bundle.1 changed 3.1% diff
docs/man/gmx-check.1 changed 2.7% diff
docs/man/gmx-chi.1 changed 1.2% diff
docs/man/gmx-cluster.1 changed 1.2% diff
docs/man/gmx-clustsize.1 changed 2.6% diff
docs/man/gmx-confrms.1 changed 4.1% diff
docs/man/gmx-convert-tpr.1 changed 18.0% diff
docs/man/gmx-convert-trj.1 changed 2.8% diff
docs/man/gmx-covar.1 changed 2.6% diff
docs/man/gmx-current.1 changed 2.0% diff
docs/man/gmx-density.1 changed 1.8% diff
docs/man/gmx-densmap.1 changed 2.5% diff
docs/man/gmx-densorder.1 changed 3.6% diff
docs/man/gmx-dielectric.1 changed 2.8% diff
docs/man/gmx-dipoles.1 changed 1.4% diff
docs/man/gmx-disre.1 changed 3.1% diff
docs/man/gmx-distance.1 changed 2.4% diff
docs/man/gmx-do_dssp.1 changed 2.5% diff
docs/man/gmx-dos.1 changed 2.8% diff
docs/man/gmx-dump.1 changed 4.9% diff
docs/man/gmx-dyecoupl.1 changed 3.6% diff
docs/man/gmx-editconf.1 changed 1.3% diff
docs/man/gmx-eneconv.1 changed 4.6% diff
docs/man/gmx-enemat.1 changed 2.7% diff
docs/man/gmx-energy.1 changed 1.2% diff
docs/man/gmx-extract-cluster.1 changed 2.7% diff
docs/man/gmx-filter.1 changed 3.5% diff
docs/man/gmx-freevolume.1 changed 2.6% diff
docs/man/gmx-gangle.1 changed 1.9% diff
docs/man/gmx-genconf.1 changed 4.9% diff
docs/man/gmx-genion.1 changed 3.4% diff
docs/man/gmx-genrestr.1 changed 2.8% diff
docs/man/gmx-grompp.1 changed 1.5% diff
docs/man/gmx-gyrate.1 changed 3.1% diff
docs/man/gmx-h2order.1 changed 4.1% diff
docs/man/gmx-hbond.1 changed 1.3% diff
docs/man/gmx-helix.1 changed 3.1% diff
docs/man/gmx-helixorient.1 changed 3.2% diff
docs/man/gmx-help.1 changed 26.7% diff
docs/man/gmx-hydorder.1 changed 4.0% diff
docs/man/gmx-insert-molecules.1 changed 2.2% diff
docs/man/gmx-lie.1 changed 4.7% diff
docs/man/gmx-make_edi.1 changed 1.0% diff
docs/man/gmx-make_ndx.1 changed 4.8% diff
docs/man/gmx-mdmat.1 changed 4.6% diff
docs/man/gmx-mdrun.1 changed 0.7% diff
docs/man/gmx-mindist.1 changed 2.6% diff
docs/man/gmx-mk_angndx.1 changed 8.7% diff
docs/man/gmx-msd.1 changed 2.2% diff
docs/man/gmx-nmeig.1 changed 2.2% diff
docs/man/gmx-nmens.1 changed 5.2% diff
docs/man/gmx-nmr.1 changed 2.8% diff
docs/man/gmx-nmtraj.1 changed 4.1% diff
docs/man/gmx-nonbonded-benchmark.1 changed 1.7% diff
docs/man/gmx-order.1 changed 2.6% diff
docs/man/gmx-pairdist.1 changed 2.1% diff
docs/man/gmx-pdb2gmx.1 changed 1.0% diff
docs/man/gmx-pme_error.1 changed 5.4% diff
docs/man/gmx-polystat.1 changed 3.3% diff
docs/man/gmx-potential.1 changed 3.5% diff
docs/man/gmx-principal.1 changed 4.7% diff
docs/man/gmx-rama.1 changed 7.1% diff
docs/man/gmx-rdf.1 changed 1.9% diff
docs/man/gmx-report-methods.1 changed 8.6% diff
docs/man/gmx-rms.1 changed 2.0% diff
docs/man/gmx-rmsdist.1 changed 2.8% diff
docs/man/gmx-rmsf.1 changed 2.7% diff
docs/man/gmx-rotacf.1 changed 3.3% diff
docs/man/gmx-rotmat.1 changed 3.7% diff
docs/man/gmx-saltbr.1 changed 6.0% diff
docs/man/gmx-sans.1 changed 3.1% diff
docs/man/gmx-sasa.1 changed 2.1% diff
docs/man/gmx-saxs.1 changed 5.5% diff
docs/man/gmx-select.1 changed 1.5% diff
docs/man/gmx-sham.1 changed 1.8% diff
docs/man/gmx-sigeps.1 changed 5.9% diff
docs/man/gmx-solvate.1 changed 2.3% diff
docs/man/gmx-sorient.1 changed 3.0% diff
docs/man/gmx-spatial.1 changed 2.3% diff
docs/man/gmx-spol.1 changed 3.5% diff
docs/man/gmx-tcaf.1 changed 2.3% diff
docs/man/gmx-traj.1 changed 2.0% diff
docs/man/gmx-trajectory.1 changed 3.0% diff
docs/man/gmx-trjcat.1 changed 3.3% diff
docs/man/gmx-trjconv.1 changed 1.0% diff
docs/man/gmx-trjorder.1 changed 3.3% diff
docs/man/gmx-tune_pme.1 changed 0.9% diff
docs/man/gmx-vanhove.1 changed 2.7% diff
docs/man/gmx-velacc.1 changed 3.3% diff
docs/man/gmx-view.1 changed 5.4% diff
docs/man/gmx-wham.1 changed 0.9% diff
docs/man/gmx-wheel.1 changed 8.0% diff
docs/man/gmx-x2top.1 changed 2.9% diff
docs/man/gmx-xpm2ps.1 changed 2.1% diff
docs/man/gmx.1 changed 1.0% diff

RST Files (3 of 196):

NameStatusDeltaVisual Diff
docs/dev-manual/containers.rst added
docs/release-notes/2020/2020.2.rst added
docs/release-notes/index.rst changed 0.5% diff

YAML Files (22 of 23):

NameStatusDeltaVisual Diff
admin/ci-templates/.build-cache-template.yml removed
admin/ci-templates/.build-docs-template.yml removed
admin/ci-templates/.build-gmxapi-template.yml removed
admin/ci-templates/.build-mpi-template.yml removed
admin/ci-templates/.build-template.yml removed
admin/ci-templates/.clang-before-script.yml removed
admin/ci-templates/.clang-build-template.yml removed
admin/ci-templates/.clang-test-template.yml removed
admin/ci-templates/.cuda-template.yml removed
admin/ci-templates/.documentation-before-script.yml removed
admin/ci-templates/.gcc-before-script.yml removed
admin/ci-templates/.gcc-build-template.yml removed
admin/ci-templates/.gcc-test-template.yml removed
admin/ci-templates/.image-templates.yml removed
admin/ci-templates/.include-template.yml removed
admin/ci-templates/.pull-cache-template.yml removed
admin/ci-templates/.regressiontest-template.yml removed
admin/ci-templates/.release-template.yml removed
admin/ci-templates/.tags-template.yml removed
admin/ci-templates/.test-runner-template.yml removed
admin/ci-templates/.test-script-template.yml removed
admin/ci-templates/.variables-template.yml removed

Directories (4 of 356):

NameStatus
admin/ci-scripts added
admin/ci-templates removed
admin/containers added
admin/gitlab-ci added

Information Files (1 of 7):

NameStatusDeltaVisual Diff
INSTALL changed 0.5% diff

Text Files (5 of 512):

NameStatusDeltaVisual Diff
admin/dockerfiles/ci-clang/Dockerfile changed 1.9% diff
admin/dockerfiles/ci-docs-clang/Dockerfile changed 2.4% diff
admin/dockerfiles/ci-docs-gcc/Dockerfile changed 2.3% diff
admin/dockerfiles/ci-gcc/Dockerfile changed 7.2% diff
src/reference_checksum changed 100.0% diff

Packages Compared:

gromacs-2020.1.tar.gz
gromacs-2020.2.tar.gz


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