"Fossies" - the Fresh Open Source Software Archive  

Source code changes report for "gromacs" between the packages
gromacs-2021-rc1.tar.gz and gromacs-2021.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 7.8% and now consists of 5742 regular files (+41), 3 symbolic links and 389 directories (+1).

Related Informations:

See docs/gmxapi/changelog.rst (gromacs 2021).

Changes In Files (According File Type):

File TypeTotalAddedRemovedChanged
Header file 1305 6 4 34
C program 255 0 0 4
C++ program 1530 7 5 51
Patch 2 0 0 0
Fortran program 1 0 0 0
Perl program 5 0 0 0
Python program 93 0 0 4
Shell program 36 0 0 1
Awk program 1 0 0 0
Python compiled program 3 0 0 3
Automake file 8 0 0 0
CMake file 256 0 1 11
Initialization file 4 0 0 0
JSON file 7 0 0 0
Lex program 1 0 0 0
Makefile 3 0 0 0
Man page 100 0 0 100
Pkg-config file 3 0 0 0
Symbolic link 3 0 0 0
XML document 986 15 3 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
PostScript file 6 6 0 0
RST file 215 1 0 11
TeX document 4 0 0 0
XML style sheet 10 0 0 0
YAML file 1 0 0 0
Data file 57 0 0 0
Image file 19 10 2 0
PDF file 76 1 0 0
Vector Image file 119 9 0 0
Directory 390 2 1 0
Change log 3 0 0 0
Information file 7 0 0 1
License 8 0 0 1
Readme file 31 0 0 0
Text file 544 1 0 4
Other 27 0 0 0
Total Files61505816225



Header Files (44 of 1305):

NameStatusDeltaVisual Diff
api/nblib/box.h changed 2.6% diff
api/nblib/exception.h changed 2.3% diff
api/nblib/gmxsetup.h changed 2.3% diff
api/nblib/interactions.h changed 1.9% diff
api/nblib/kerneloptions.h changed 1.8% diff
api/nblib/listed_forces/bondtypes.h changed 4.5% diff
api/nblib/listed_forces/calculator.h changed 3.4% diff
api/nblib/listed_forces/conversions.hpp changed 14.1% diff
api/nblib/listed_forces/dataflow.hpp changed 25.5% diff
api/nblib/listed_forces/definitions.h changed 67.0% diff
api/nblib/listed_forces/gmxcalculator.h removed
api/nblib/listed_forces/helpers.hpp changed 1.9% diff
api/nblib/listed_forces/kernels.hpp changed 0.8% diff
api/nblib/listed_forces/tests/linear_chain_input.hpp changed 10.4% diff
api/nblib/listed_forces/traits.h changed 30.2% diff
api/nblib/listed_forces/transformations.h changed 18.3% diff
api/nblib/molecules.h changed 60.3% diff
api/nblib/nblib.h changed 7.7% diff
api/nblib/particlesequencer.h added
api/nblib/particletype.h changed 4.1% diff
api/nblib/pbc.hpp changed 0.7% diff
api/nblib/ppmap.h removed
api/nblib/sequencing.hpp added
api/nblib/simulationstate.h changed 3.8% diff
api/nblib/tests/testhelpers.h changed 17.4% diff
api/nblib/topology.h changed 15.1% diff
api/nblib/topologyhelpers.h changed 56.7% diff
api/nblib/util/internal.h removed
api/nblib/util/setup.h added
api/nblib/util/traits.hpp added
api/nblib/util/user.h removed
api/nblib/util/util.hpp added
api/nblib/vector.h changed 3.2% diff
src/gromacs/fileio/tpxio.h changed 2.0% diff
src/gromacs/gmxpreprocess/topdirs.h changed 3.2% diff
src/gromacs/math/paddedvector.h changed 5.3% diff
src/gromacs/math/tests/testarrayrefs.h changed 20.1% diff
src/gromacs/mdlib/expanded_internal.h added
src/gromacs/modularsimulator/signallers.h changed 3.7% diff
src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.h changed 7.7% diff
src/gromacs/simd/impl_arm_sve/impl_arm_sve_definitions.h changed 9.9% diff
src/gromacs/simd/impl_arm_sve/impl_arm_sve_simd_double.h changed 0.7% diff
src/gromacs/simd/impl_arm_sve/impl_arm_sve_util_double.h changed 6.0% diff
src/gromacs/simd/impl_arm_sve/impl_arm_sve_util_float.h changed 0.5% diff

C Programs (4 of 255):

NameStatusDeltaVisual Diff
src/gromacs/gpu_utils/cuda_arch_utils.cuh changed 6.1% diff
src/gromacs/listed_forces/gpubonded_impl.cu changed 0.5% diff
src/gromacs/listed_forces/gpubondedkernels.cu changed 0.3% diff
src/gromacs/nbnxm/cuda/nbnxm_cuda_data_mgmt.cu changed 0.7% diff

C++ Programs (63 of 1530):

NameStatusDeltaVisual Diff
api/nblib/forcecalculator.cpp changed 10.6% diff
api/nblib/gmxsetup.cpp changed 4.8% diff
api/nblib/interactions.cpp changed 1.1% diff
api/nblib/listed_forces/calculator.cpp changed 2.0% diff
api/nblib/listed_forces/gmxcalculator.cpp removed
api/nblib/listed_forces/tests/bondtypes.cpp changed 10.8% diff
api/nblib/listed_forces/tests/calculator.cpp changed 34.7% diff
api/nblib/listed_forces/tests/conversions.cpp changed 15.4% diff
api/nblib/listed_forces/tests/helpers.cpp changed 20.5% diff
api/nblib/listed_forces/tests/transformations.cpp changed 14.5% diff
api/nblib/listed_forces/tests/typetests.cpp changed 57.0% diff
api/nblib/listed_forces/transformations.cpp changed 18.2% diff
api/nblib/molecules.cpp changed 43.4% diff
api/nblib/particlesequencer.cpp added
api/nblib/samples/argon-forces-integration.cpp changed 24.0% diff
api/nblib/samples/methane-water-integration.cpp added
api/nblib/samples/tests/samples.cpp removed
api/nblib/simulationstate.cpp changed 2.0% diff
api/nblib/tests/gmxcalculator.cpp changed 3.5% diff
api/nblib/tests/integrator.cpp changed 8.6% diff
api/nblib/tests/molecules.cpp changed 11.9% diff
api/nblib/tests/nbkernelsystem.cpp changed 6.2% diff
api/nblib/tests/testsystems.cpp changed 1.0% diff
api/nblib/tests/topology.cpp changed 6.0% diff
api/nblib/topology.cpp changed 12.9% diff
api/nblib/topologyhelpers.cpp changed 75.0% diff
api/nblib/util/setup.cpp added
api/nblib/util/tests/internal.cpp removed
api/nblib/util/tests/setup.cpp added
api/nblib/util/tests/traits.cpp added
api/nblib/util/tests/user.cpp removed
api/nblib/util/user.cpp removed
src/gromacs/applied_forces/awh/biasstate.cpp changed 0.4% diff
src/gromacs/applied_forces/electricfield.cpp changed 1.7% diff
src/gromacs/fileio/checkpoint.cpp changed 0.2% diff
src/gromacs/fileio/tpxio.cpp changed 0.7% diff
src/gromacs/gmxana/gmx_msd.cpp changed 0.5% diff
src/gromacs/gmxana/gmx_xpm2ps.cpp changed 0.4% diff
src/gromacs/gmxpreprocess/pdb2gmx.cpp changed 4.3% diff
src/gromacs/gmxpreprocess/readir.cpp changed 0.8% diff
src/gromacs/gmxpreprocess/topdirs.cpp changed 6.3% diff
src/gromacs/gmxpreprocess/topio.cpp changed 0.2% diff
src/gromacs/gpu_utils/tests/devicetransfers_sycl.cpp changed 10.6% diff
src/gromacs/gpu_utils/tests/hostallocator.cpp changed 1.8% diff
src/gromacs/hardware/device_management_sycl.cpp changed 3.8% diff
src/gromacs/listed_forces/listed_forces.cpp changed 0.9% diff
src/gromacs/math/densityfit.cpp changed 2.2% diff
src/gromacs/math/tests/paddedvector.cpp changed 51.2% diff
src/gromacs/mdlib/coupling.cpp changed 0.2% diff
src/gromacs/mdlib/expanded.cpp changed 34.3% diff
src/gromacs/mdlib/expanded_internal.cpp added
src/gromacs/mdlib/tests/expanded.cpp added
src/gromacs/mdrun/md.cpp changed 0.2% diff
src/gromacs/mdrunutility/handlerestart.cpp changed 8.6% diff
src/gromacs/modularsimulator/signallers.cpp changed 3.8% diff
src/gromacs/modularsimulator/simulatoralgorithm.cpp changed 0.8% diff
src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp changed 6.6% diff
src/gromacs/nbnxm/opencl/nbnxm_ocl_data_mgmt.cpp changed 2.1% diff
src/gromacs/pulling/pull.cpp changed 1.9% diff
src/gromacs/random/seed.cpp changed 9.8% diff
src/gromacs/taskassignment/resourcedivision.cpp changed 1.9% diff
src/gromacs/topology/idef.cpp changed 0.7% diff
src/gromacs/utility/binaryinformation.cpp changed 1.3% diff

Python Programs (4 of 93):

NameStatusDeltaVisual Diff
admin/containers/utility.py changed 1.5% diff
docs/conf.cmakein.py changed 4.4% diff
python_packaging/src/gmxapi/version.py changed 0.9% diff
python_packaging/src/setup.py changed 1.3% diff

Shell Programs (1 of 36):

NameStatusDeltaVisual Diff
admin/git-pre-commit changed 10.6% diff

Python Compiled Programs (all 3):

NameStatusDeltaVisual Diff
admin/containers/__pycache__/scripted_gmx_docker_builds.cpython-36.pyc changed 0.01%
admin/containers/__pycache__/utility.cpython-36.pyc changed 0.2%
docs/__pycache__/gmxsphinx.cpython-36.pyc changed 0.1%

CMake Files (12 of 256):

NameStatusDeltaVisual Diff
api/nblib/CMakeLists.txt changed 2.6% diff
api/nblib/listed_forces/tests/CMakeLists.txt changed 2.8% diff
api/nblib/samples/CMakeLists.txt changed 28.9% diff
api/nblib/samples/tests/CMakeLists.txt removed
api/nblib/util/CMakeLists.txt changed 5.4% diff
api/nblib/util/tests/CMakeLists.txt changed 5.1% diff
cmake/gmxGenerateVersionInfoWithoutGit.cmake changed 10.6% diff
cmake/gmxVersionInfo.cmake changed 2.3% diff
CMakeLists.txt changed 0.4% diff
docs/CMakeLists.txt changed 0.6% diff
src/gromacs/mdlib/tests/CMakeLists.txt changed 4.8% diff
tests/CMakeLists.txt changed 1.1% diff

Man Pages (all 100):

NameStatusDeltaVisual Diff
docs/man/gmx-anaeig.1 changed 1.9% diff
docs/man/gmx-analyze.1 changed 1.7% diff
docs/man/gmx-angle.1 changed 3.2% diff
docs/man/gmx-awh.1 changed 6.8% diff
docs/man/gmx-bar.1 changed 2.2% diff
docs/man/gmx-bundle.1 changed 4.2% diff
docs/man/gmx-check.1 changed 3.7% diff
docs/man/gmx-chi.1 changed 1.7% diff
docs/man/gmx-cluster.1 changed 1.7% diff
docs/man/gmx-clustsize.1 changed 3.5% diff
docs/man/gmx-confrms.1 changed 5.6% diff
docs/man/gmx-convert-tpr.1 changed 7.2% diff
docs/man/gmx-convert-trj.1 changed 3.8% diff
docs/man/gmx-covar.1 changed 3.5% diff
docs/man/gmx-current.1 changed 2.7% diff
docs/man/gmx-density.1 changed 2.5% diff
docs/man/gmx-densmap.1 changed 3.4% diff
docs/man/gmx-densorder.1 changed 4.9% diff
docs/man/gmx-dielectric.1 changed 3.8% diff
docs/man/gmx-dipoles.1 changed 1.9% diff
docs/man/gmx-disre.1 changed 4.2% diff
docs/man/gmx-distance.1 changed 3.3% diff
docs/man/gmx-do_dssp.1 changed 3.4% diff
docs/man/gmx-dos.1 changed 3.8% diff
docs/man/gmx-dump.1 changed 6.7% diff
docs/man/gmx-dyecoupl.1 changed 4.9% diff
docs/man/gmx-editconf.1 changed 1.8% diff
docs/man/gmx-eneconv.1 changed 6.2% diff
docs/man/gmx-enemat.1 changed 3.6% diff
docs/man/gmx-energy.1 changed 1.6% diff
docs/man/gmx-extract-cluster.1 changed 3.7% diff
docs/man/gmx-filter.1 changed 4.7% diff
docs/man/gmx-freevolume.1 changed 3.5% diff
docs/man/gmx-gangle.1 changed 2.5% diff
docs/man/gmx-genconf.1 changed 6.6% diff
docs/man/gmx-genion.1 changed 4.7% diff
docs/man/gmx-genrestr.1 changed 3.9% diff
docs/man/gmx-grompp.1 changed 2.0% diff
docs/man/gmx-gyrate.1 changed 4.3% diff
docs/man/gmx-h2order.1 changed 5.5% diff
docs/man/gmx-hbond.1 changed 1.8% diff
docs/man/gmx-helix.1 changed 4.3% diff
docs/man/gmx-helixorient.1 changed 4.3% diff
docs/man/gmx-help.1 changed 36.0% diff
docs/man/gmx-hydorder.1 changed 5.4% diff
docs/man/gmx-insert-molecules.1 changed 2.9% diff
docs/man/gmx-lie.1 changed 6.4% diff
docs/man/gmx-make_edi.1 changed 1.4% diff
docs/man/gmx-make_ndx.1 changed 6.5% diff
docs/man/gmx-mdmat.1 changed 6.3% diff
docs/man/gmx-mdrun.1 changed 1.0% diff
docs/man/gmx-mindist.1 changed 3.6% diff
docs/man/gmx-mk_angndx.1 changed 11.7% diff
docs/man/gmx-msd.1 changed 3.0% diff
docs/man/gmx-nmeig.1 changed 3.0% diff
docs/man/gmx-nmens.1 changed 7.0% diff
docs/man/gmx-nmr.1 changed 3.8% diff
docs/man/gmx-nmtraj.1 changed 5.6% diff
docs/man/gmx-nonbonded-benchmark.1 changed 2.2% diff
docs/man/gmx-order.1 changed 3.6% diff
docs/man/gmx-pairdist.1 changed 2.8% diff
docs/man/gmx-pdb2gmx.1 changed 1.3% diff
docs/man/gmx-pme_error.1 changed 7.4% diff
docs/man/gmx-polystat.1 changed 4.5% diff
docs/man/gmx-potential.1 changed 4.7% diff
docs/man/gmx-principal.1 changed 6.3% diff
docs/man/gmx-rama.1 changed 9.6% diff
docs/man/gmx-rdf.1 changed 2.6% diff
docs/man/gmx-report-methods.1 changed 11.8% diff
docs/man/gmx-rms.1 changed 2.7% diff
docs/man/gmx-rmsdist.1 changed 3.8% diff
docs/man/gmx-rmsf.1 changed 3.7% diff
docs/man/gmx-rotacf.1 changed 4.5% diff
docs/man/gmx-rotmat.1 changed 5.0% diff
docs/man/gmx-saltbr.1 changed 8.1% diff
docs/man/gmx-sans.1 changed 4.2% diff
docs/man/gmx-sasa.1 changed 2.9% diff
docs/man/gmx-saxs.1 changed 7.5% diff
docs/man/gmx-select.1 changed 2.0% diff
docs/man/gmx-sham.1 changed 2.5% diff
docs/man/gmx-sigeps.1 changed 8.0% diff
docs/man/gmx-solvate.1 changed 3.2% diff
docs/man/gmx-sorient.1 changed 4.0% diff
docs/man/gmx-spatial.1 changed 3.1% diff
docs/man/gmx-spol.1 changed 4.8% diff
docs/man/gmx-tcaf.1 changed 3.1% diff
docs/man/gmx-traj.1 changed 2.7% diff
docs/man/gmx-trajectory.1 changed 4.1% diff
docs/man/gmx-trjcat.1 changed 4.5% diff
docs/man/gmx-trjconv.1 changed 1.3% diff
docs/man/gmx-trjorder.1 changed 4.4% diff
docs/man/gmx-tune_pme.1 changed 1.2% diff
docs/man/gmx-vanhove.1 changed 3.7% diff
docs/man/gmx-velacc.1 changed 4.5% diff
docs/man/gmx-view.1 changed 7.3% diff
docs/man/gmx-wham.1 changed 1.2% diff
docs/man/gmx-wheel.1 changed 10.8% diff
docs/man/gmx-x2top.1 changed 3.9% diff
docs/man/gmx-xpm2ps.1 changed 2.9% diff
docs/man/gmx.1 changed 1.3% diff

XML Documents (18 of 986):

NameStatusDeltaVisual Diff
api/nblib/listed_forces/tests/refdata/FourCenter_ListedForcesProperDihedralTest_CheckListed_0.xml renamed 0.0%
api/nblib/listed_forces/tests/refdata/FourCenter_ProperDihedralTest_CheckListed_0.xml
api/nblib/listed_forces/tests/refdata/FourCenter_ListedForcesProperDihedralTest_CheckListed_1.xml renamed 0.0%
api/nblib/listed_forces/tests/refdata/FourCenter_ProperDihedralTest_CheckListed_1.xml
api/nblib/listed_forces/tests/refdata/FourCenter_ListedForcesProperDihedralTest_CheckListed_2.xml renamed 0.0%
api/nblib/listed_forces/tests/refdata/FourCenter_ProperDihedralTest_CheckListed_2.xml
api/nblib/listed_forces/tests/refdata/ListedExampleData_CanReduceEnergies.xml added
api/nblib/listed_forces/tests/refdata/ListedExampleData_CanReduceForces.xml added
api/nblib/listed_forces/tests/refdata/ListedExampleData_ComputeHarmonicAngleEnergies.xml added
api/nblib/listed_forces/tests/refdata/ListedExampleData_ComputeHarmonicAngleForces.xml added
api/nblib/listed_forces/tests/refdata/ListedExampleData_ComputeHarmonicBondEnergies.xml added
api/nblib/listed_forces/tests/refdata/ListedExampleData_ComputeHarmonicBondForces.xml added
api/nblib/listed_forces/tests/refdata/ThreeCenter_HarmonicAngleTest_CheckListed_0.xml added
api/nblib/listed_forces/tests/refdata/ThreeCenter_HarmonicAngleTest_CheckListed_1.xml added
api/nblib/listed_forces/tests/refdata/ThreeCenter_HarmonicAngleTest_CheckListed_2.xml added
api/nblib/listed_forces/tests/refdata/TwoCenter_HarmonicBondTest_CheckListed_0.xml added
api/nblib/listed_forces/tests/refdata/TwoCenter_HarmonicBondTest_CheckListed_1.xml added
api/nblib/listed_forces/tests/refdata/TwoCenter_HarmonicBondTest_CheckListed_2.xml added

PostScript Files (all 6):

NameStatusDeltaVisual Diff
docs/reference-manual/plots/GMX_logos/gmx_falcon_black.eps added
docs/reference-manual/plots/GMX_logos/gmx_falcon_blue.eps added
docs/reference-manual/plots/GMX_logos/gmx_falcon_waterstamp.eps added
docs/reference-manual/plots/GMX_logos/gmx_logo_black.eps added
docs/reference-manual/plots/GMX_logos/gmx_logo_blue.eps added
docs/reference-manual/plots/GMX_logos/gmx_logo_waterstamp.eps added

RST Files (12 of 215):

NameStatusDeltaVisual Diff
docs/install-guide/index.rst changed 0.3% diff
docs/reference-manual/special/free-energy-implementation.rst changed 6.1% diff
docs/reference-manual/topologies/particle-type.rst changed 5.3% diff
docs/reference-manual/topologies/topology-file-formats.rst changed 0.7% diff
docs/release-notes/2020/2020.5.rst changed 100.0% diff
docs/release-notes/2020/2020.6.rst added
docs/release-notes/2021/major/bugs-fixed.rst changed 38.4% diff
docs/release-notes/2021/major/deprecated-functionality.rst changed 9.3% diff
docs/release-notes/2021/major/highlights.rst changed 6.2% diff
docs/release-notes/2021/major/performance.rst changed 35.7% diff
docs/release-notes/index.rst changed 0.5% diff
docs/user-guide/mdp-options.rst changed 0.3% diff

Image Files (12 of 19):

NameStatusDeltaVisual Diff
docs/reference-manual/plots/GMX_logos/gmx_falcon_black.png added
docs/reference-manual/plots/GMX_logos/gmx_falcon_blue.png added
docs/reference-manual/plots/GMX_logos/gmx_falcon_waterstamp.png added
docs/reference-manual/plots/GMX_logos/gmx_falcon_white.png added
docs/reference-manual/plots/GMX_logos/gmx_logo_black.png added
docs/reference-manual/plots/GMX_logos/gmx_logo_blue.png added
docs/reference-manual/plots/GMX_logos/gmx_logo_waterstamp.png added
docs/reference-manual/plots/GMX_logos/gmx_logo_white.png added
docs/reference-manual/plots/peregrine.jpg renamed 0.0%
docs/reference-manual/plots/peregrine-old.jpg
docs/reference-manual/plots/peregrine.png renamed 0.0%
docs/reference-manual/plots/peregrine-old.png

PDF Files (1 of 76):

NameStatusDeltaVisual Diff
docs/reference-manual/special/plots/lambda-values.pdf added

Vector Image Files (9 of 119):

NameStatusDeltaVisual Diff
docs/reference-manual/plots/GMX_logos/gmx_falcon_black.svg added
docs/reference-manual/plots/GMX_logos/gmx_falcon_blue.svg added
docs/reference-manual/plots/GMX_logos/gmx_falcon_waterstamp.svg added
docs/reference-manual/plots/GMX_logos/gmx_falcon_white.svg added
docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg added
docs/reference-manual/plots/GMX_logos/gmx_logo_blue.svg added
docs/reference-manual/plots/GMX_logos/gmx_logo_waterstamp.svg added
docs/reference-manual/plots/GMX_logos/gmx_logo_white.svg added
docs/reference-manual/special/plots/lambda-values.svg added

Directories (3 of 390):

NameStatus
admin/gitlab-ci/gromacs.matrix added
api/nblib/samples/tests removed
docs/reference-manual/plots/GMX_logos added

Information Files (1 of 7):

NameStatusDeltaVisual Diff
INSTALL changed 1.1% diff

Licenses (1 of 8):

NameStatusDeltaVisual Diff
admin/copyright.py changed 0.8% diff

Text Files (5 of 544):

NameStatusDeltaVisual Diff
python_packaging/docker/gromacs-dependencies.dockerfile changed 16.6% diff
python_packaging/docker/gromacs.dockerfile changed 18.2% diff
src/gromacs/gmxpreprocess/tests/fragment2.pdb changed 4.9% diff
src/gromacs/gmxpreprocess/tests/fragment4.pdb changed 4.9% diff
src/reference_checksum added

Packages Compared:

gromacs-2021-rc1.tar.gz
gromacs-2021.tar.gz


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