"Fossies" - the Fresh Open Source Software Archive  

Source code changes report for "gromacs" between the packages
gromacs-2020-rc1.tar.gz and gromacs-2020.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 1.0% and now consists of 5561 regular files (-68), 3 symbolic links and 353 directories (+9).

Related Informations:

See docs/gmxapi/changelog.rst (gromacs 2020).

Changes In Files (According File Type):

File TypeTotalAddedRemovedChanged
Header file 1227 1 0 4
C program 252 0 0 1
C++ program 1429 2 0 17
Patch 2 0 0 0
Fortran program 1 0 0 0
Perl program 5 0 0 0
Python program 104 0 0 9
Shell program 32 1 3 0
Awk program 1 0 0 0
Python compiled program 2 1 1 0
Automake file 7 0 0 0
CMake file 238 0 0 5
Configuration file 1 0 0 0
Initialization file 2 0 0 0
JSON file 5 0 0 0
Lex program 1 0 0 0
Makefile 2 0 0 0
Man page 100 0 100 0
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 193 1 0 23
TeX document 4 0 0 0
XML style sheet 10 1 0 0
YAML file 23 22 0 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 355 11 2 0
Change log 3 0 0 0
Information file 7 0 1 0
License 8 0 0 0
Readme file 29 0 0 0
Text file 513 8 0 2
Other 22 0 0 0
Total Files60244810761



Header Files (5 of 1227):

NameStatusDeltaVisual Diff
src/gromacs/fileio/gmxfio_xdr.h changed 4.8% diff
src/gromacs/gmxana/angle_correction.h added
src/gromacs/taskassignment/decidegpuusage.h changed 13.7% diff
src/gromacs/utility/inmemoryserializer.h changed 14.0% diff
src/gromacs/utility/iserializer.h changed 15.5% diff

C Programs (1 of 252):

NameStatusDeltaVisual Diff
src/gromacs/mdlib/lincs_cuda.cu changed 6.1% diff

C++ Programs (19 of 1429):

NameStatusDeltaVisual Diff
python_packaging/src/gmxapi/export_tprfile.cpp changed 6.5% diff
src/gromacs/fileio/gmxfio_xdr.cpp changed 15.0% diff
src/gromacs/fileio/mrcdensitymap.cpp changed 2.1% diff
src/gromacs/fileio/pdbio.cpp changed 0.4% diff
src/gromacs/fileio/tests/fileioxdrserializer.cpp added
src/gromacs/fileio/tpxio.cpp changed 1.7% diff
src/gromacs/gmxana/anadih.cpp changed 2.6% diff
src/gromacs/gmxana/angle_correction.cpp added
src/gromacs/gmxana/cmat.cpp changed 1.1% diff
src/gromacs/gmxana/gmx_angle.cpp changed 6.9% diff
src/gromacs/gmxpreprocess/topio.cpp changed 1.1% diff
src/gromacs/listed_forces/bonded.cpp changed 0.02% diff
src/gromacs/mdlib/forcerec.cpp changed 0.1% diff
src/gromacs/mdlib/sim_util.cpp changed 0.1% diff
src/gromacs/mdrun/runner.cpp changed 1.0% diff
src/gromacs/taskassignment/decidegpuusage.cpp changed 12.8% diff
src/gromacs/utility/inmemoryserializer.cpp changed 22.2% diff
src/gromacs/utility/tests/inmemoryserializer.cpp changed 15.7% diff
src/gromacs/utility/tests/keyvaluetreeserializer.cpp changed 1.9% diff

Python Programs (9 of 104):

NameStatusDeltaVisual Diff
admin/builds/gromacs.py changed 1.0% diff
docs/conf.py changed 0.5% diff
python_packaging/documentation/conf.py changed 41.4% diff
python_packaging/src/gmxapi/_logging.py changed 3.2% diff
python_packaging/src/gmxapi/commandline.py changed 5.7% diff
python_packaging/src/gmxapi/datamodel.py changed 13.4% diff
python_packaging/src/gmxapi/operation.py changed 0.2% diff
python_packaging/src/gmxapi/version.py changed 4.7% diff
python_packaging/src/setup.py changed 11.0% diff

Shell Programs (4 of 32):

NameStatusDeltaVisual Diff
admin/ccache-wrapper-c.in removed
admin/ccache-wrapper-cxx.in removed
admin/dockerfiles/build.sh added
src/programs/completion/gmx-completion.bash removed

Python Compiled Programs (all 2):

NameStatusDeltaVisual Diff
docs/__pycache__/gmxsphinx.cpython-36.pyc added
docs/gmxsphinx.pyc removed

CMake Files (5 of 238):

NameStatusDeltaVisual Diff
cmake/gmxCPackUtilities.cmake changed 3.5% diff
cmake/gmxVersionInfo.cmake changed 1.6% diff
docs/CMakeLists.txt changed 0.1% diff
scripts/CMakeLists.txt changed 7.0% diff
src/gromacs/fileio/tests/CMakeLists.txt changed 1.5% diff

Man Pages (all 100):

NameStatusDeltaVisual Diff
docs/man/gmx-anaeig.1 removed
docs/man/gmx-analyze.1 removed
docs/man/gmx-angle.1 removed
docs/man/gmx-awh.1 removed
docs/man/gmx-bar.1 removed
docs/man/gmx-bundle.1 removed
docs/man/gmx-check.1 removed
docs/man/gmx-chi.1 removed
docs/man/gmx-cluster.1 removed
docs/man/gmx-clustsize.1 removed
docs/man/gmx-confrms.1 removed
docs/man/gmx-convert-tpr.1 removed
docs/man/gmx-convert-trj.1 removed
docs/man/gmx-covar.1 removed
docs/man/gmx-current.1 removed
docs/man/gmx-density.1 removed
docs/man/gmx-densmap.1 removed
docs/man/gmx-densorder.1 removed
docs/man/gmx-dielectric.1 removed
docs/man/gmx-dipoles.1 removed
docs/man/gmx-disre.1 removed
docs/man/gmx-distance.1 removed
docs/man/gmx-do_dssp.1 removed
docs/man/gmx-dos.1 removed
docs/man/gmx-dump.1 removed
docs/man/gmx-dyecoupl.1 removed
docs/man/gmx-editconf.1 removed
docs/man/gmx-eneconv.1 removed
docs/man/gmx-enemat.1 removed
docs/man/gmx-energy.1 removed
docs/man/gmx-extract-cluster.1 removed
docs/man/gmx-filter.1 removed
docs/man/gmx-freevolume.1 removed
docs/man/gmx-gangle.1 removed
docs/man/gmx-genconf.1 removed
docs/man/gmx-genion.1 removed
docs/man/gmx-genrestr.1 removed
docs/man/gmx-grompp.1 removed
docs/man/gmx-gyrate.1 removed
docs/man/gmx-h2order.1 removed
docs/man/gmx-hbond.1 removed
docs/man/gmx-helix.1 removed
docs/man/gmx-helixorient.1 removed
docs/man/gmx-help.1 removed
docs/man/gmx-hydorder.1 removed
docs/man/gmx-insert-molecules.1 removed
docs/man/gmx-lie.1 removed
docs/man/gmx-make_edi.1 removed
docs/man/gmx-make_ndx.1 removed
docs/man/gmx-mdmat.1 removed
docs/man/gmx-mdrun.1 removed
docs/man/gmx-mindist.1 removed
docs/man/gmx-mk_angndx.1 removed
docs/man/gmx-msd.1 removed
docs/man/gmx-nmeig.1 removed
docs/man/gmx-nmens.1 removed
docs/man/gmx-nmr.1 removed
docs/man/gmx-nmtraj.1 removed
docs/man/gmx-nonbonded-benchmark.1 removed
docs/man/gmx-order.1 removed
docs/man/gmx-pairdist.1 removed
docs/man/gmx-pdb2gmx.1 removed
docs/man/gmx-pme_error.1 removed
docs/man/gmx-polystat.1 removed
docs/man/gmx-potential.1 removed
docs/man/gmx-principal.1 removed
docs/man/gmx-rama.1 removed
docs/man/gmx-rdf.1 removed
docs/man/gmx-report-methods.1 removed
docs/man/gmx-rms.1 removed
docs/man/gmx-rmsdist.1 removed
docs/man/gmx-rmsf.1 removed
docs/man/gmx-rotacf.1 removed
docs/man/gmx-rotmat.1 removed
docs/man/gmx-saltbr.1 removed
docs/man/gmx-sans.1 removed
docs/man/gmx-sasa.1 removed
docs/man/gmx-saxs.1 removed
docs/man/gmx-select.1 removed
docs/man/gmx-sham.1 removed
docs/man/gmx-sigeps.1 removed
docs/man/gmx-solvate.1 removed
docs/man/gmx-sorient.1 removed
docs/man/gmx-spatial.1 removed
docs/man/gmx-spol.1 removed
docs/man/gmx-tcaf.1 removed
docs/man/gmx-traj.1 removed
docs/man/gmx-trajectory.1 removed
docs/man/gmx-trjcat.1 removed
docs/man/gmx-trjconv.1 removed
docs/man/gmx-trjorder.1 removed
docs/man/gmx-tune_pme.1 removed
docs/man/gmx-vanhove.1 removed
docs/man/gmx-velacc.1 removed
docs/man/gmx-view.1 removed
docs/man/gmx-wham.1 removed
docs/man/gmx-wheel.1 removed
docs/man/gmx-x2top.1 removed
docs/man/gmx-xpm2ps.1 removed
docs/man/gmx.1 removed

RST Files (24 of 193):

NameStatusDeltaVisual Diff
docs/dev-manual/releng/index.rst changed 100.0% diff
docs/dev-manual/testutils.rst changed 0.5% diff
docs/gmxapi/userguide/install.rst changed 0.9% diff
docs/reference-manual/algorithms/energy-minimization.rst changed 1.8% diff
docs/reference-manual/algorithms/molecular-dynamics.rst changed 0.1% diff
docs/reference-manual/analysis/rmsd.rst changed 3.9% diff
docs/reference-manual/averages.rst changed 1.0% diff
docs/reference-manual/functions/interaction-methods.rst changed 0.4% diff
docs/reference-manual/special/density-guided-simulation.rst changed 4.0% diff
docs/reference-manual/special/remove-fast-dgf.rst changed 0.4% diff
docs/reference-manual/special/viscosity-calculation.rst changed 6.2% diff
docs/reference-manual/topologies/particle-type.rst changed 3.4% diff
docs/release-notes/2018/2018.2.rst changed 0.7% diff
docs/release-notes/2019/2019.5.rst changed 35.3% diff
docs/release-notes/2019/2019.6.rst added
docs/release-notes/2020/major/deprecated-functionality.rst changed 11.3% diff
docs/release-notes/2020/major/highlights.rst changed 17.7% diff
docs/release-notes/2020/major/miscellaneous.rst changed 2.8% diff
docs/release-notes/2020/major/performance.rst changed 3.4% diff
docs/release-notes/index.rst changed 3.0% diff
docs/user-guide/environment-variables.rst changed 6.3% diff
docs/user-guide/mdp-options.rst changed 0.7% diff
docs/user-guide/mdrun-features.rst changed 44.0% diff
docs/user-guide/mdrun-performance.rst changed 2.9% diff

XML Style Sheets (1 of 10):

NameStatusDeltaVisual Diff
scripts/CTest2JUnit.xsl added

YAML Files (22 of 23):

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

Directories (13 of 355):

NameStatus
admin/ci-templates added
admin/dockerfiles added
admin/dockerfiles/ci-clang-6 added
admin/dockerfiles/ci-clang-7 added
admin/dockerfiles/ci-clang-8 added
admin/dockerfiles/ci-docs added
admin/dockerfiles/ci-gcc-5 added
admin/dockerfiles/ci-gcc-6 added
admin/dockerfiles/ci-gcc-7 added
admin/dockerfiles/ci-gcc-8 added
docs/__pycache__ added
docs/man removed
src/programs/completion removed

Information Files (1 of 7):

NameStatusDeltaVisual Diff
INSTALL removed

Text Files (10 of 513):

NameStatusDeltaVisual Diff
admin/dockerfiles/ci-clang-6/Dockerfile added
admin/dockerfiles/ci-clang-7/Dockerfile added
admin/dockerfiles/ci-clang-8/Dockerfile added
admin/dockerfiles/ci-docs/Dockerfile added
admin/dockerfiles/ci-gcc-5/Dockerfile added
admin/dockerfiles/ci-gcc-6/Dockerfile added
admin/dockerfiles/ci-gcc-7/Dockerfile added
admin/dockerfiles/ci-gcc-8/Dockerfile added
python_packaging/src/requirements.txt changed 18.1% diff
src/reference_checksum changed 100.0% diff

Packages Compared:

gromacs-2020-rc1.tar.gz
gromacs-2020.tar.gz


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