"Fossies" - the Fresh Open Source Software Archive  

Source code changes report for "gromacs" between the packages
gromacs-2020.tar.gz and gromacs-2020.1.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 1.1% and now consists of 5667 regular files (+106), 3 symbolic links and 353 directories.

Related Informations:

See docs/gmxapi/changelog.rst (gromacs 2020.1).

Changes In Files (According File Type):

File TypeTotalAddedRemovedChanged
Header file 1227 0 0 21
C program 252 0 0 2
C++ program 1430 1 0 43
Patch 2 0 0 0
Fortran program 1 0 0 0
Perl program 5 0 0 0
Python program 104 0 0 1
Shell program 31 2 1 0
Awk program 1 0 0 0
Python compiled program 1 0 0 1
Automake file 7 0 0 0
CMake file 240 2 0 8
Configuration file 1 0 0 0
Initialization file 3 1 0 0
JSON file 5 0 0 0
Lex program 1 0 0 0
Makefile 2 0 0 0
Man page 100 100 0 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 194 1 0 9
TeX document 4 0 0 0
XML style sheet 10 0 0 0
YAML file 24 1 1 5
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 361 8 8 0
Change log 3 0 0 0
Information file 7 1 0 0
License 8 0 0 1
Readme file 29 0 0 0
Text file 521 8 9 3
Other 22 0 0 0
Total Files60421251994



Header Files (21 of 1227):

NameStatusDeltaVisual Diff
src/gromacs/domdec/domdec_setup.h changed 6.5% diff
src/gromacs/fileio/checkpoint.h changed 4.5% diff
src/gromacs/gmxlib/network.h changed 3.7% diff
src/gromacs/hardware/gpu_hw_info.h changed 10.4% diff
src/gromacs/mdlib/forcerec.h changed 8.9% diff
src/gromacs/mdlib/md_support.h changed 2.8% diff
src/gromacs/mdlib/mdoutf.h changed 5.0% diff
src/gromacs/mdlib/vsite.h changed 1.3% diff
src/gromacs/mdrunutility/multisim.h changed 3.3% diff
src/gromacs/modularsimulator/constraintelement.h changed 2.6% diff
src/gromacs/modularsimulator/modularsimulator.h changed 3.2% diff
src/gromacs/modularsimulator/parrinellorahmanbarostat.h changed 2.3% diff
src/gromacs/modularsimulator/shellfcelement.h changed 3.0% diff
src/gromacs/modularsimulator/trajectoryelement.h changed 2.4% diff
src/gromacs/nbnxm/kernels_reference/kernel_ref.h changed 13.0% diff
src/gromacs/nbnxm/nbnxm_geometry.h changed 5.0% diff
src/gromacs/simd/impl_reference/impl_reference_definitions.h changed 1.3% diff
src/gromacs/taskassignment/decidegpuusage.h changed 19.1% diff
src/gromacs/taskassignment/reportgpuusage.h changed 13.2% diff
src/gromacs/taskassignment/taskassignment.h changed 8.5% diff
src/gromacs/topology/mtop_util.h changed 2.3% diff

C Programs (2 of 252):

NameStatusDeltaVisual Diff
src/gromacs/gpu_utils/cudautils.cu changed 2.1% diff
src/gromacs/gpu_utils/gpu_utils.cu changed 11.9% diff

C++ Programs (44 of 1430):

NameStatusDeltaVisual Diff
src/api/cpp/tests/stopsignaler.cpp changed 28.8% diff
src/gromacs/domdec/domdec.cpp changed 0.5% diff
src/gromacs/domdec/domdec_setup.cpp changed 1.8% diff
src/gromacs/domdec/domdec_topology.cpp changed 0.6% diff
src/gromacs/ewald/pme.cpp changed 0.4% diff
src/gromacs/ewald/pme_gpu_internal.cpp changed 0.2% diff
src/gromacs/ewald/pme_load_balancing.cpp changed 2.4% diff
src/gromacs/ewald/pme_redistribute.cpp changed 3.8% diff
src/gromacs/fileio/checkpoint.cpp changed 1.0% diff
src/gromacs/gmxana/gmx_disre.cpp changed 3.7% diff
src/gromacs/gmxlib/network.cpp changed 1.5% diff
src/gromacs/gmxpreprocess/grompp.cpp changed 0.3% diff
src/gromacs/gmxpreprocess/readir.cpp changed 2.7% diff
src/gromacs/hardware/gpu_hw_info.cpp changed 10.4% diff
src/gromacs/listed_forces/orires.cpp changed 0.6% diff
src/gromacs/mdlib/dispersioncorrection.cpp changed 1.6% diff
src/gromacs/mdlib/forcerec.cpp changed 6.5% diff
src/gromacs/mdlib/md_support.cpp changed 1.5% diff
src/gromacs/mdlib/mdoutf.cpp changed 6.6% diff
src/gromacs/mdlib/sim_util.cpp changed 3.0% diff
src/gromacs/mdlib/vsite.cpp changed 0.1% diff
src/gromacs/mdrun/md.cpp changed 3.3% diff
src/gromacs/mdrun/mimic.cpp changed 1.7% diff
src/gromacs/mdrun/minimize.cpp changed 1.4% diff
src/gromacs/mdrun/rerun.cpp changed 1.7% diff
src/gromacs/mdrun/runner.cpp changed 3.8% diff
src/gromacs/mdrun/shellfc.cpp changed 3.6% diff
src/gromacs/mdrunutility/multisim.cpp changed 2.5% diff
src/gromacs/modularsimulator/constraintelement.cpp changed 12.7% diff
src/gromacs/modularsimulator/domdechelper.cpp changed 3.7% diff
src/gromacs/modularsimulator/forceelement.cpp changed 7.2% diff
src/gromacs/modularsimulator/modularsimulator.cpp changed 5.5% diff
src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp changed 19.0% diff
src/gromacs/modularsimulator/shellfcelement.cpp changed 16.9% diff
src/gromacs/modularsimulator/topologyholder.cpp changed 8.6% diff
src/gromacs/modularsimulator/trajectoryelement.cpp changed 9.3% diff
src/gromacs/pulling/pullutil.cpp changed 0.8% diff
src/gromacs/taskassignment/decidegpuusage.cpp changed 15.9% diff
src/gromacs/taskassignment/reportgpuusage.cpp changed 6.6% diff
src/gromacs/taskassignment/taskassignment.cpp changed 7.5% diff
src/gromacs/topology/mtop_util.cpp changed 1.6% diff
src/gromacs/utility/coolstuff.cpp changed 0.2% diff
src/programs/mdrun/tests/exactcontinuation.cpp changed 6.0% diff
src/programs/mdrun/tests/orires.cpp added

Python Programs (1 of 104):

NameStatusDeltaVisual Diff
admin/builds/gromacs.py changed 2.3% diff

Shell Programs (3 of 31):

NameStatusDeltaVisual Diff
admin/dockerfiles/build.sh removed
admin/dockerfiles/buildall.sh added
src/programs/completion/gmx-completion.bash added

Python Compiled Programs (all 1):

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

CMake Files (10 of 240):

NameStatusDeltaVisual Diff
cmake/gmxCPackUtilities.cmake changed 3.1% diff
cmake/gmxGenerateVersionInfoRelease.cmake added
cmake/gmxManageFFTLibraries.cmake changed 2.9% diff
cmake/gmxManageMPI.cmake changed 2.3% diff
cmake/gmxTestICCNextGen.cmake added
cmake/gmxTestMPI_IN_PLACE.cmake changed 12.0% diff
cmake/gmxVersionInfo.cmake changed 14.7% diff
docs/CMakeLists.txt changed 0.5% diff
scripts/GMXRC.csh.cmakein changed 2.0% diff
src/programs/mdrun/tests/CMakeLists.txt changed 2.2% diff

Initialization Files (1 of 3):

NameStatusDeltaVisual Diff
src/testutils/simulationdatabase/orires_1lvz.top added

Man Pages (all 100):

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

RST Files (10 of 194):

NameStatusDeltaVisual Diff
docs/dev-manual/jenkins.rst changed 3.3% diff
docs/dev-manual/known-issues.rst changed 36.8% diff
docs/dev-manual/releng/index.rst changed 19.6% diff
docs/gmxapi/userguide-stub/pythonreference.rst changed 10.6% diff
docs/gmxapi/userguide/install.rst changed 0.6% diff
docs/release-notes/2019/2019.6.rst changed 100.0% diff
docs/release-notes/2020/2020.1.rst added
docs/release-notes/index.rst changed 2.7% diff
docs/user-guide/mdp-options.rst changed 0.1% diff
docs/user-guide/mdrun-performance.rst changed 3.6% diff

YAML Files (7 of 24):

NameStatusDeltaVisual Diff
admin/ci-templates/.build-docs-template.yml changed 3.5% diff
admin/ci-templates/.build-template.yml changed 6.9% diff
admin/ci-templates/.cuda-gcc-build-template.yml renamed 80.8% diff
admin/ci-templates/.cuda-template.yml
admin/ci-templates/.image-templates.yml changed 15.4% diff
admin/ci-templates/.include-template.yml changed 5.2% diff
admin/ci-templates/.variables-template.yml changed 36.2% diff

Directories (16 of 361):

NameStatus
admin/dockerfiles/base added
admin/dockerfiles/ci-clang-6 renamed
admin/dockerfiles/ci-clang
admin/dockerfiles/ci-clang-7 removed
admin/dockerfiles/ci-clang-8 removed
admin/dockerfiles/ci-docs renamed
admin/dockerfiles/ci-docs-gcc
admin/dockerfiles/ci-docs-clang added
admin/dockerfiles/ci-gcc-5 renamed
admin/dockerfiles/ci-gcc
admin/dockerfiles/ci-gcc-6 removed
admin/dockerfiles/ci-gcc-7 removed
admin/dockerfiles/ci-gcc-8 renamed
admin/dockerfiles/ci-gcc-8-cuda-10.2
docs/man added
src/programs/completion added

Information Files (1 of 7):

NameStatusDeltaVisual Diff
INSTALL added

Licenses (1 of 8):

NameStatusDeltaVisual Diff
admin/copyright.py changed 0.9% diff

Text Files (20 of 521):

NameStatusDeltaVisual Diff
admin/builds/gpubufferops-matrix.txt removed
admin/builds/gpucomm-matrix.txt changed 24.2% diff
admin/builds/gpuupdate-matrix.txt changed 42.0% diff
admin/dockerfiles/base/Dockerfile added
admin/dockerfiles/ci-clang-6/Dockerfile removed
admin/dockerfiles/ci-clang-7/Dockerfile removed
admin/dockerfiles/ci-clang-8/Dockerfile removed
admin/dockerfiles/ci-clang/Dockerfile added
admin/dockerfiles/ci-docs-clang/Dockerfile added
admin/dockerfiles/ci-docs-gcc/Dockerfile added
admin/dockerfiles/ci-docs/Dockerfile removed
admin/dockerfiles/ci-gcc-5/Dockerfile removed
admin/dockerfiles/ci-gcc-6/Dockerfile removed
admin/dockerfiles/ci-gcc-7/Dockerfile removed
admin/dockerfiles/ci-gcc-8-cuda-10.2/Dockerfile added
admin/dockerfiles/ci-gcc-8/Dockerfile removed
admin/dockerfiles/ci-gcc/Dockerfile added
src/reference_checksum changed 100.0% diff
src/testutils/simulationdatabase/orires_1lvz.gro added
src/testutils/simulationdatabase/orires_1lvz.ndx added

Packages Compared:

gromacs-2020.tar.gz
gromacs-2020.1.tar.gz


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