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 Type	Total	Added	Removed	Changed
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 Files	6150	58	16	225

---

Header Files (44 of 1305):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual Diff
admin/git-pre-commit	changed	10.6%	diff

Python Compiled Programs (all 3):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual 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):

Name	Status	Delta	Visual Diff
docs/reference-manual/special/plots/lambda-values.pdf	added

Vector Image Files (9 of 119):

Name	Status	Delta	Visual 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):

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

Information Files (1 of 7):

Name	Status	Delta	Visual Diff
INSTALL	changed	1.1%	diff

Licenses (1 of 8):

Name	Status	Delta	Visual Diff
admin/copyright.py	changed	0.8%	diff

Text Files (5 of 544):

Name	Status	Delta	Visual 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

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