├── .clang-format ├── .dockerignore ├── .gitattributes ├── .github └── ISSUE_TEMPLATE │ └── issue-template.md ├── .gitignore ├── .gitlab-ci.yml ├── .travis.yml ├── AUTHORS ├── CMakeLists.txt ├── COPYING ├── CPackInit.cmake ├── CTestConfig.cmake ├── INSTALL-dev ├── README ├── README.md ├── admin ├── .isreposource ├── InstallInfo.txt ├── InstallWelcome.txt ├── ccache-wrapper-c.in ├── ccache-wrapper-cxx.in ├── ci-scripts │ ├── build-and-test-py-gmxapi-0.1.sh │ ├── build-and-test-py-gmxapi-0.2.sh │ ├── build-and-test-sample_restraint-2020.sh │ └── build-and-test-sample_restraint-2021.sh ├── clang-format.sh ├── clang-tidy.sh ├── containers │ ├── buildall.sh │ ├── scripted_gmx_docker_builds.py │ └── utility.py ├── copyright.py ├── copyright.sh ├── createFileHash.py ├── git-pre-commit ├── gitlab-ci │ ├── archive.gitlab-ci.yml │ ├── documentation.gitlab-ci.yml │ ├── global.gitlab-ci.yml │ ├── gromacs.gitlab-ci.yml │ ├── lint.gitlab-ci.yml │ ├── python-gmxapi.gitlab-ci.yml │ ├── rules.gitlab-ci.yml │ ├── sample_restraint-regression.gitlab-ci.yml │ └── sample_restraint.gitlab-ci.yml ├── iwyu.imp ├── iwyu.sh ├── lsan-suppressions.txt ├── reformat_all.sh ├── split_copyright_years.sh └── ubsan-suppressions.txt ├── api ├── CMakeLists.txt ├── gmxapi │ ├── CMakeLists.txt │ ├── cpp │ │ ├── CMakeLists.txt │ │ ├── cmake │ │ │ └── gmxapi-config.cmake.in │ │ ├── context.cpp │ │ ├── context_impl.h │ │ ├── createsession.h │ │ ├── exceptions.cpp │ │ ├── gmxapi.cpp │ │ ├── md.cpp │ │ ├── md_impl.h │ │ ├── mdmodule.cpp │ │ ├── mdsignals.cpp │ │ ├── mdsignals.h │ │ ├── resourceassignment.cpp │ │ ├── session.cpp │ │ ├── session_impl.h │ │ ├── sessionresources.h │ │ ├── status.cpp │ │ ├── system.cpp │ │ ├── system_impl.h │ │ ├── tpr.cpp │ │ ├── version.cpp │ │ ├── workflow.cpp │ │ ├── workflow.h │ │ └── workflow_impl.h │ └── include │ │ ├── gmxapi │ │ ├── compat │ │ │ ├── mdparams.h │ │ │ └── tpr.h │ │ ├── context.h │ │ ├── exceptions.h │ │ ├── gmxapi.h │ │ ├── gmxapicompat.h │ │ ├── gromacsfwd.h │ │ ├── md.h │ │ ├── md │ │ │ ├── mdmodule.h │ │ │ └── mdsignals.h │ │ ├── mpi │ │ │ └── gmxapi_mpi.h │ │ ├── session.h │ │ ├── session │ │ │ └── resources.h │ │ ├── status.h │ │ └── system.h │ │ ├── gmxapiversion.h.in │ │ └── resourceassignment.cmakein.h └── nblib │ ├── CMakeLists.txt │ ├── basicdefinitions.h │ ├── box.cpp │ ├── box.h │ ├── exception.h │ ├── forcecalculator.cpp │ ├── forcecalculator.h │ ├── gmxcalculator.cpp │ ├── gmxcalculator.h │ ├── gmxsetup.cpp │ ├── gmxsetup.h │ ├── integrator.cpp │ ├── integrator.h │ ├── interactions.cpp │ ├── interactions.h │ ├── kerneloptions.h │ ├── molecules.cpp │ ├── molecules.h │ ├── nblib.h │ ├── particletype.cpp │ ├── particletype.h │ ├── samples │ ├── CMakeLists.txt │ ├── argon-forces-integration.cpp │ └── tests │ │ ├── CMakeLists.txt │ │ └── samples.cpp │ ├── simulationstate.cpp │ ├── simulationstate.h │ ├── simulationstateimpl.h │ ├── tests │ ├── CMakeLists.txt │ ├── box.cpp │ ├── gmxcalculator.cpp │ ├── integrator.cpp │ ├── interactions.cpp │ ├── molecules.cpp │ ├── nbkernelsystem.cpp │ ├── nbnxnsetup.cpp │ ├── particletype.cpp │ ├── refdata │ │ ├── NBlibTest_ArgonForcesAreCorrect.xml │ │ └── NBlibTest_SpcMethanolForcesAreCorrect.xml │ ├── simstate.cpp │ ├── testhelpers.cpp │ ├── testhelpers.h │ ├── testsystems.cpp │ ├── testsystems.h │ └── topology.cpp │ ├── topology.cpp │ ├── topology.h │ ├── topologyhelpers.cpp │ ├── topologyhelpers.h │ ├── util │ ├── CMakeLists.txt │ ├── internal.h │ ├── tests │ │ ├── CMakeLists.txt │ │ ├── refdata │ │ │ └── NBlibTest_GeneratedVelocitiesAreCorrect.xml │ │ └── user.cpp │ ├── user.cpp │ └── user.h │ └── vector.h ├── ci_scripts ├── install_gromacs_2019.sh ├── install_gromacs_2020.sh ├── install_gromacs_devel.sh ├── prepare_python.sh ├── pygmx.sh ├── sample_restraint.sh ├── set_compilers ├── set_python └── test_installers.sh ├── cmake ├── FindEXTRAE.cmake ├── FindFFTW.cmake ├── FindHWLOC.cmake ├── FindLibStdCpp.cmake ├── FindLmfit.cmake ├── FindMuparser.cmake ├── FindPythonModule.cmake ├── FindSphinx.cmake ├── FindTinyXML-2.cmake ├── FindVMD.cmake ├── FindclFFT.cmake ├── Platform │ ├── Linux-Intel-C-XeonPhi.cmake │ ├── Linux-Intel-CXX-XeonPhi.cmake │ ├── Toolchain-Fujitsu-Sparc64-mpi.cmake │ ├── Toolchain-Fujitsu-Sparc64.cmake │ └── XeonPhi.cmake ├── TestCUDA.cu ├── TestFileOffsetBits.cpp ├── TestFujitsuSparc64.cpp ├── TestGlibcVersion.cpp ├── TestImageMagickConvert.pdf ├── TestInlineASM_gcc_x86.cpp ├── TestLargeFiles.c.cmakein ├── TestMIC.cpp ├── TestMMMalloc.cpp ├── TestMPI.cpp ├── TestPipes.cpp ├── TestSIGUSR1.cpp ├── TestSchedAffinity.cmake ├── TestVMD.cpp ├── TestWinProcNum.cpp ├── TestWindowsFSeek.cpp ├── TestX86.cpp ├── TestXDR.cpp ├── ThreadMPI.cmake ├── VersionInfo.cmake.cmakein ├── cmake_uninstall.cmake.in ├── gmxBuildTreeInfo.cmake ├── gmxBuildTypeASAN.cmake ├── gmxBuildTypeMSAN.cmake ├── gmxBuildTypeProfile.cmake ├── gmxBuildTypeReference.cmake ├── gmxBuildTypeReleaseWithAssert.cmake ├── gmxBuildTypeTSAN.cmake ├── gmxBuildTypeUBSAN.cmake ├── gmxCFlags.cmake ├── gmxCPackUtilities.cmake ├── gmxCTestUtilities.cmake ├── gmxClangCudaUtils.cmake ├── gmxConfigureVersionInfo.cmake ├── gmxCustomCommandUtilities.cmake ├── gmxDetectAvx512FmaUnits.cmake ├── gmxDetectCpu.cmake ├── gmxDetectSimd.cmake ├── gmxDetectTargetArchitecture.cmake ├── gmxFindFlagsForSource.cmake ├── gmxGenerateVersionInfo.cmake ├── gmxGenerateVersionInfoRelease.cmake ├── gmxManageCcache.cmake ├── gmxManageClangCudaConfig.cmake ├── gmxManageCuda.cmake ├── gmxManageFFTLibraries.cmake ├── gmxManageFujitsuSparc64.cmake ├── gmxManageLinearAlgebraLibraries.cmake ├── gmxManageLmfit.cmake ├── gmxManageMPI.cmake ├── gmxManageMimic.cmake ├── gmxManageMuparser.cmake ├── gmxManageNvccConfig.cmake ├── gmxManageOpenCL.cmake ├── gmxManageOpenMP.cmake ├── gmxManagePluginSupport.cmake ├── gmxManageSYCL.cmake ├── gmxManageSharedLibraries.cmake ├── gmxManageSimd.cmake ├── gmxManageSuffixes.cmake ├── gmxManageTNG.cmake ├── gmxOptionUtilities.cmake ├── gmxPythonDiscovery.cmake ├── gmxSetBuildInformation.cmake ├── gmxSimdFlags.cmake ├── gmxTestCompilerProblems.cmake ├── gmxTestICCNextGen.cmake ├── gmxTestImageMagick.cmake ├── gmxTestInlineASM.cmake ├── gmxTestLargeFiles.cmake ├── gmxTestLibXml2.cmake ├── gmxTestMMMalloc.cmake ├── gmxTestMPI_IN_PLACE.cmake ├── gmxTestPipes.cmake ├── gmxTestSignal.cmake ├── gmxTestXDR.cmake ├── gmxTestZLib.cmake ├── gmxTestdlopen.cmake ├── gmxVersionInfo.cmake ├── legacy_and_external.supp └── with_asan_opts.sh ├── docs ├── .gitattributes ├── CMakeLists.txt ├── OpenCLTODOList.txt ├── SphinxMacros.cmake ├── conf.cmakein.py ├── dev-manual │ ├── build-system.rst │ ├── change-management.rst │ ├── code-formatting.rst │ ├── commitstyle.rst │ ├── containers.rst │ ├── contribute.rst │ ├── documentation-generation.rst │ ├── doxygen.rst │ ├── error-handling.rst │ ├── formatting.rst │ ├── gitlab.rst │ ├── gmxtree.rst │ ├── includestyle.rst │ ├── index.rst │ ├── infrastructure.rst │ ├── jenkins.rst │ ├── known-issues.rst │ ├── language-features.rst │ ├── naming.rst │ ├── overview.rst │ ├── physical_validation.rst │ ├── redmine-states.png │ ├── releng │ │ ├── index.rst │ │ ├── jenkins-howto.rst │ │ └── jenkins-ui.rst │ ├── relocatable-binaries.rst │ ├── reportstyle.rst │ ├── style.rst │ ├── testutils.rst │ └── tools.rst ├── download.rst ├── doxygen │ ├── .gitignore │ ├── CMakeLists.txt │ ├── Doxyfile-common.cmakein │ ├── Doxyfile-compact │ ├── Doxyfile-dev.cmakein │ ├── Doxyfile-full.cmakein │ ├── Doxyfile-lib.cmakein │ ├── Doxyfile-user.cmakein │ ├── Doxyfile-version.cmakein │ ├── Doxyfile-xml.cmakein │ ├── DoxygenLayout.xml │ ├── RunDoxygen.cmake.cmakein │ ├── check-source.py │ ├── cycle-suppressions.txt │ ├── directories.cpp │ ├── doxygenxml.py │ ├── generateGraphs.cmake │ ├── gmxtree.py │ ├── graphbuilder.py │ ├── includesorter.py │ ├── lib │ │ ├── awh.md │ │ ├── logging.md │ │ ├── mdmodules.md │ │ ├── modularsimulator.md │ │ ├── modulegraph.md │ │ ├── nbnxm.md │ │ ├── refdata.md │ │ ├── simd.md │ │ └── wrapperbinary.md │ ├── misc.cpp │ ├── reporter.py │ ├── suppressions.txt │ └── user │ │ ├── analysisdata.md │ │ ├── analysisframework.md │ │ ├── analysisnbsearch.md │ │ ├── analysistemplate.md │ │ ├── mainpage.md │ │ ├── onlinehelp.md │ │ ├── selections.md │ │ └── usinglibrary.md ├── fragments │ └── doxygen-links.rst ├── gmxapi │ ├── README.md │ ├── changelog.rst │ ├── index.rst │ ├── reference │ │ ├── contributing.rst │ │ ├── datamodel.rst │ │ ├── executionmodel.rst │ │ ├── extending.rst │ │ ├── projectstructure.rst │ │ └── reference.rst │ ├── userguide-stub │ │ └── pythonreference.rst │ └── userguide │ │ ├── install.rst │ │ ├── pythonreference.rst │ │ ├── usage.rst │ │ └── userguide.rst ├── gmxsphinx.py ├── how-to │ ├── beginners.rst │ ├── index.rst │ ├── special.rst │ ├── topology.rst │ └── visualize.rst ├── index.rst ├── install-guide │ └── index.rst ├── linkcheckerrc ├── links.dat ├── manual │ ├── CMakeLists.txt │ ├── README │ ├── UseLATEX.cmake │ ├── fancy.sty │ ├── here.sty │ ├── hfill.ist │ ├── picins.sty │ ├── subindex │ └── underscore.sty ├── nblib │ ├── guide-to-writing-MD-programs.rst │ └── index.rst ├── reference-manual │ ├── algorithms.rst │ ├── algorithms │ │ ├── brownian-dynamics.rst │ │ ├── constraint-algorithms.rst │ │ ├── energy-minimization.rst │ │ ├── essential-dynamics.rst │ │ ├── expanded-ensemble.rst │ │ ├── free-energy-calculations.rst │ │ ├── group-concept.rst │ │ ├── molecular-dynamics.rst │ │ ├── normal-mode-analysis.rst │ │ ├── parallelization-domain-decomp.rst │ │ ├── periodic-boundary-conditions.rst │ │ ├── plots │ │ │ ├── dd-cells.fig │ │ │ ├── dd-cells.pdf │ │ │ ├── dd-cells.svg │ │ │ ├── dd-tric.fig │ │ │ ├── dd-tric.pdf │ │ │ ├── dd-tric.svg │ │ │ ├── flowchart.pdf │ │ │ ├── flowchart.svg │ │ │ ├── free1.fig │ │ │ ├── free1.pdf │ │ │ ├── free1.svg │ │ │ ├── free2.fig │ │ │ ├── free2.pdf │ │ │ ├── free2.svg │ │ │ ├── leapfrog.pdf │ │ │ ├── leapfrog.svg │ │ │ ├── lincs.pdf │ │ │ ├── lincs.svg │ │ │ ├── maxwell.pdf │ │ │ ├── maxwell.svg │ │ │ ├── maxwell.xvg │ │ │ ├── mpmd-pme.fig │ │ │ ├── mpmd-pme.pdf │ │ │ ├── mpmd-pme.svg │ │ │ ├── nstric.fig │ │ │ ├── nstric.pdf │ │ │ ├── nstric.svg │ │ │ ├── par-lincs2.fig │ │ │ ├── par-lincs2.pdf │ │ │ ├── par-lincs2.svg │ │ │ ├── pbctric.fig │ │ │ ├── pbctric.pdf │ │ │ ├── pbctric.svg │ │ │ ├── rhododec.ogl │ │ │ ├── rhododec.pdf │ │ │ ├── rhododec.svg │ │ │ ├── truncoct.ogl │ │ │ ├── truncoct.pdf │ │ │ ├── truncoct.svg │ │ │ ├── verlet-drift.pdf │ │ │ ├── verlet-drift.svg │ │ │ └── verlet-drift.xvg │ │ ├── replica-exchange.rst │ │ ├── shell-molecular-dynamics.rst │ │ ├── simulated-annealing.rst │ │ └── stochastic-dynamics.rst │ ├── analysis.rst │ ├── analysis │ │ ├── bond-angle-dihedral.rst │ │ ├── correlation-function.rst │ │ ├── covariance-analysis.rst │ │ ├── curve-fitting.rst │ │ ├── dihedral-pca.rst │ │ ├── general-properties.rst │ │ ├── hydrogen-bonds.rst │ │ ├── interface-related.rst │ │ ├── looking-at-trajectory.rst │ │ ├── mean-square-displacement.rst │ │ ├── plots │ │ │ ├── dih-def.fig │ │ │ ├── dih-def.pdf │ │ │ ├── dih-def.svg │ │ │ ├── distm.pdf │ │ │ ├── distm.svg │ │ │ ├── dssp.pdf │ │ │ ├── dssp.svg │ │ │ ├── hbond-insert.fig │ │ │ ├── hbond-insert.pdf │ │ │ ├── hbond-insert.svg │ │ │ ├── hbond.fig │ │ │ ├── hbond.pdf │ │ │ ├── hbond.svg │ │ │ ├── hpr-wheel.pdf │ │ │ ├── hpr-wheel.svg │ │ │ ├── msdwater.pdf │ │ │ ├── msdwater.svg │ │ │ ├── msdwater.xvg │ │ │ ├── ngmxdump.pdf │ │ │ ├── ngmxdump.svg │ │ │ ├── phipsi.fig │ │ │ ├── phipsi.pdf │ │ │ ├── phipsi.svg │ │ │ ├── rama.pdf │ │ │ ├── rama.svg │ │ │ ├── rama.xvg │ │ │ ├── rdf.fig │ │ │ ├── rdf.pdf │ │ │ ├── rdf.svg │ │ │ ├── rdfO-O.pdf │ │ │ ├── rdfO-O.svg │ │ │ ├── rdfO-O.xvg │ │ │ ├── sgangle.pdf │ │ │ └── sgangle.svg │ │ ├── protein-related.rst │ │ ├── radial-distribution-function.rst │ │ ├── radius-of-gyration.rst │ │ ├── rmsd.rst │ │ └── using-groups.rst │ ├── averages.rst │ ├── definitions.rst │ ├── details.rst │ ├── file-formats.rst │ ├── functions.rst │ ├── functions │ │ ├── bonded-interactions.rst │ │ ├── force-field.rst │ │ ├── free-energy-interactions.rst │ │ ├── interaction-methods.rst │ │ ├── long-range-electrostatics.rst │ │ ├── long-range-vdw.rst │ │ ├── nonbonded-interactions.rst │ │ ├── plots │ │ │ ├── angle.fig │ │ │ ├── angle.pdf │ │ │ ├── angle.svg │ │ │ ├── bstretch.fig │ │ │ ├── bstretch.pdf │ │ │ ├── bstretch.svg │ │ │ ├── chain.fig │ │ │ ├── chain.pdf │ │ │ ├── chain.svg │ │ │ ├── dummies.fig │ │ │ ├── dummies.pdf │ │ │ ├── dummies.svg │ │ │ ├── f-bham.pdf │ │ │ ├── f-bham.svg │ │ │ ├── f-bham.xvg │ │ │ ├── f-dih.pdf │ │ │ ├── f-dih.svg │ │ │ ├── f-dih.xvg │ │ │ ├── f-dr.pdf │ │ │ ├── f-dr.svg │ │ │ ├── f-dr.xvg │ │ │ ├── f-imps.pdf │ │ │ ├── f-imps.xvg │ │ │ ├── f-lj.pdf │ │ │ ├── f-lj.svg │ │ │ ├── f-lj.xvg │ │ │ ├── f-morse.pdf │ │ │ ├── f-morse.svg │ │ │ ├── f-morse.xvg │ │ │ ├── f-pr.pdf │ │ │ ├── f-pr.svg │ │ │ ├── f-pr.xvg │ │ │ ├── f-rbs.pdf │ │ │ ├── f-rbs.svg │ │ │ ├── f-rbs.xvg │ │ │ ├── fbposres.pdf │ │ │ ├── fbposres.svg │ │ │ ├── fbposres.xvg │ │ │ ├── fig-02.pdf │ │ │ ├── fig-02.svg │ │ │ ├── fig-04.pdf │ │ │ ├── fig-04.svg │ │ │ ├── ring-imp.fig │ │ │ ├── ring-imp.pdf │ │ │ ├── ring-imp.svg │ │ │ ├── softcore.pdf │ │ │ ├── softcore.svg │ │ │ ├── softcore.xvg │ │ │ ├── subst-im.fig │ │ │ ├── subst-im.pdf │ │ │ ├── subst-im.svg │ │ │ ├── tetra-im.fig │ │ │ ├── tetra-im.pdf │ │ │ ├── tetra-im.svg │ │ │ ├── vcrf.pdf │ │ │ ├── vcrf.svg │ │ │ ├── vcrf.xvg │ │ │ ├── vsite-4fdn.pdf │ │ │ └── vsite-4fdn.svg │ │ ├── polarization.rst │ │ └── restraints.rst │ ├── index.rst │ ├── introduction.rst │ ├── plots │ │ ├── adress.png │ │ ├── decomp.fig │ │ ├── decomp.pdf │ │ ├── decomp.svg │ │ ├── dih.fig │ │ ├── dih.pdf │ │ ├── dih.svg │ │ ├── drift-all.pdf │ │ ├── drift-all.svg │ │ ├── drift-all.xvg │ │ ├── f-angle.pdf │ │ ├── f-angle.svg │ │ ├── f-angle.xvg │ │ ├── f-bond.pdf │ │ ├── f-bond.svg │ │ ├── f-bond.xvg │ │ ├── fp-highres.jpg │ │ ├── fp-highres.pdf │ │ ├── fp-highres.svg │ │ ├── int-mat.pdf │ │ ├── int-mat.svg │ │ ├── mdpar.pdf │ │ ├── mdpar.svg │ │ ├── myvi │ │ ├── parsort.fig │ │ ├── parsort.pdf │ │ ├── parsort.svg │ │ ├── peregrine.jpg │ │ ├── peregrine.png │ │ ├── plotje.png │ │ ├── ring.pdf │ │ ├── ring.svg │ │ ├── shiftf.pdf │ │ ├── shiftf.svg │ │ └── xvgr.png │ ├── preface.rst │ ├── references.rst │ ├── run-parameters.rst │ ├── special.rst │ ├── special │ │ ├── awh.rst │ │ ├── comp-electrophys.rst │ │ ├── density-guided-simulation.rst │ │ ├── electric-fields.rst │ │ ├── enforced-rotation.rst │ │ ├── free-energy-implementation.rst │ │ ├── free-energy-pmf.rst │ │ ├── membrane-embedding.rst │ │ ├── mimic-qmmm.rst │ │ ├── plots │ │ │ ├── awh-invN.pdf │ │ │ ├── awh-invN.svg │ │ │ ├── awh-pmfs.pdf │ │ │ ├── awh-pmfs.svg │ │ │ ├── awh-sampleweights.pdf │ │ │ ├── awh-sampleweights.svg │ │ │ ├── awh-traj.pdf │ │ │ ├── awh-traj.svg │ │ │ ├── compelsetup.pdf │ │ │ ├── dumaro.fig │ │ │ ├── dumaro.pdf │ │ │ ├── dumaro.svg │ │ │ ├── dumtypes.fig │ │ │ ├── dumtypes.pdf │ │ │ ├── dumtypes.svg │ │ │ ├── equipotential.pdf │ │ │ ├── field.pdf │ │ │ ├── field.svg │ │ │ ├── field.xvg │ │ │ ├── gaussians.pdf │ │ │ ├── pull.pdf │ │ │ ├── pull.svg │ │ │ ├── pulldirrel.fig │ │ │ ├── pulldirrel.pdf │ │ │ ├── pulldirrel.svg │ │ │ ├── pullref.pdf │ │ │ ├── pullref.svg │ │ │ └── rotation.pdf │ │ ├── pulling.rst │ │ ├── qmmm.rst │ │ ├── remove-fast-dgf.rst │ │ ├── tabulated-interaction-functions.rst │ │ ├── viscosity-calculation.rst │ │ └── vmd-imd.rst │ ├── topologies.rst │ └── topologies │ │ ├── constraint-algorithm-section.rst │ │ ├── force-field-organization.rst │ │ ├── molecule-definition.rst │ │ ├── parameter-files.rst │ │ ├── particle-type.rst │ │ ├── pdb2gmx-input-files.rst │ │ └── topology-file-formats.rst ├── release-notes │ ├── 2016 │ │ ├── 2016.1.rst │ │ ├── 2016.2.rst │ │ ├── 2016.3.rst │ │ ├── 2016.4.rst │ │ ├── 2016.5.rst │ │ └── major │ │ │ ├── bugs-fixed.rst │ │ │ ├── highlights.rst │ │ │ ├── miscellaneous.rst │ │ │ ├── new-features.rst │ │ │ ├── performance.rst │ │ │ ├── removed-features.rst │ │ │ └── tools.rst │ ├── 2018 │ │ ├── 2018.1.rst │ │ ├── 2018.2.rst │ │ ├── 2018.3.rst │ │ ├── 2018.4.rst │ │ ├── 2018.5.rst │ │ ├── 2018.6.rst │ │ ├── 2018.7.rst │ │ └── major │ │ │ ├── bugs-fixed.rst │ │ │ ├── features.rst │ │ │ ├── highlights.rst │ │ │ ├── miscellaneous.rst │ │ │ ├── performance.rst │ │ │ ├── portability.rst │ │ │ ├── removed-features.rst │ │ │ └── tools.rst │ ├── 2019 │ │ ├── 2019.1.rst │ │ ├── 2019.2.rst │ │ ├── 2019.3.rst │ │ ├── 2019.4.rst │ │ ├── 2019.5.rst │ │ ├── 2019.6.rst │ │ └── major │ │ │ ├── bugs-fixed.rst │ │ │ ├── deprecated-functionality.rst │ │ │ ├── features.rst │ │ │ ├── highlights.rst │ │ │ ├── miscellaneous.rst │ │ │ ├── performance.rst │ │ │ ├── portability.rst │ │ │ ├── removed-functionality.rst │ │ │ └── tools.rst │ ├── 2020 │ │ ├── 2020.1.rst │ │ ├── 2020.2.rst │ │ ├── 2020.3.rst │ │ ├── 2020.4.rst │ │ ├── 2020.5.rst │ │ └── major │ │ │ ├── bugs-fixed.rst │ │ │ ├── deprecated-functionality.rst │ │ │ ├── features.rst │ │ │ ├── highlights.rst │ │ │ ├── miscellaneous.rst │ │ │ ├── performance.rst │ │ │ ├── portability.rst │ │ │ ├── removed-functionality.rst │ │ │ └── tools.rst │ ├── 2021 │ │ └── major │ │ │ ├── bugs-fixed.rst │ │ │ ├── deprecated-functionality.rst │ │ │ ├── features.rst │ │ │ ├── highlights.rst │ │ │ ├── miscellaneous.rst │ │ │ ├── performance.rst │ │ │ ├── portability.rst │ │ │ ├── removed-functionality.rst │ │ │ └── tools.rst │ ├── index.rst │ └── older │ │ └── index.rst └── user-guide │ ├── cmdline.rst │ ├── deprecation-policy.rst │ ├── environment-variables.rst │ ├── faq.rst │ ├── floating-point.rst │ ├── flow.rst │ ├── force-fields.rst │ ├── getting-started.rst │ ├── index.rst │ ├── managing-simulations.rst │ ├── mdp-options.rst │ ├── mdrun-features.rst │ ├── mdrun-performance.rst │ ├── plotje.gif │ ├── run-time-errors.rst │ ├── security.rst │ ├── system-preparation.rst │ ├── terminology.rst │ └── xvgr.gif ├── python_packaging ├── .dockerignore ├── .gitignore ├── CMakeLists.txt ├── README.md ├── ci_scripts │ ├── README.md │ └── gitrefs ├── docker │ ├── README.md │ ├── ci.dockerfile │ ├── docs.dockerfile │ ├── entrypoint.sh │ ├── gromacs-dependencies.dockerfile │ ├── gromacs.dockerfile │ ├── notebook │ └── notebook.dockerfile ├── documentation │ ├── conf.py │ └── reference │ │ ├── diagrams │ │ ├── graphSequence.pu │ │ ├── launchSequence.pu │ │ ├── operationFactory.pu │ │ └── outputAccessSequence.pu │ │ └── workspec_schema_0_2.rst ├── examples │ ├── README.md │ ├── analysis.py │ ├── brer.py │ ├── restrained_ensemble.py │ ├── restrained_md_analysis.py │ ├── rmsf.py │ └── run_adaptive_msm.py ├── naming.rst ├── requirements-docs.txt ├── requirements-test.txt ├── roadmap.rst ├── sample_restraint │ ├── .gitattributes │ ├── .gitignore │ ├── .travis.yml │ ├── CMakeLists.pybind.in │ ├── CMakeLists.txt │ ├── Dockerfile │ ├── README.md │ ├── ci_scripts │ │ ├── install_gromacs_2019.sh │ │ ├── install_gromacs_devel.sh │ │ ├── pygmx_0_0_7.sh │ │ ├── pygmx_devel.sh │ │ ├── sample_restraint.sh │ │ └── set_compilers │ ├── cmake │ │ └── FindGROMACS.cmake │ ├── docs │ │ ├── CMakeLists.txt │ │ └── Doxyfile.in │ ├── examples │ │ ├── example.ipynb │ │ ├── job.sh │ │ ├── restrained-ensemble.py │ │ └── strip_notebook.py │ ├── src │ │ ├── CMakeLists.txt │ │ ├── cpp │ │ │ ├── CMakeLists.txt │ │ │ ├── ensemblepotential.cpp │ │ │ ├── ensemblepotential.h │ │ │ ├── restraint.h │ │ │ ├── sessionresources.cpp │ │ │ └── sessionresources.h │ │ └── pythonmodule │ │ │ ├── CMakeLists.txt │ │ │ ├── export_plugin.cpp │ │ │ └── export_plugin.h │ └── tests │ │ ├── .gitignore │ │ ├── CMakeGROMACS.txt │ │ ├── CMakeLists.gtest.in │ │ ├── CMakeLists.txt │ │ ├── conftest.py │ │ ├── pytest.ini │ │ ├── test_binding.cpp │ │ ├── test_binding.py │ │ ├── test_bounding_restraint.cpp │ │ ├── test_histogram.cpp │ │ ├── testdata.json │ │ └── testingconfiguration.in.h ├── scripts │ ├── README.md │ ├── run_acceptance_test │ ├── run_flake8 │ ├── run_full │ ├── run_full_mpi │ ├── run_gmxapi_unittest │ └── run_sample_test ├── src │ ├── .gitignore │ ├── CMakeLists.txt │ ├── external │ │ ├── .gitattributes │ │ ├── README.md │ │ └── pybind │ │ │ ├── CMakeLists.txt │ │ │ ├── LICENSE │ │ │ ├── include │ │ │ └── pybind11 │ │ │ │ ├── attr.h │ │ │ │ ├── buffer_info.h │ │ │ │ ├── cast.h │ │ │ │ ├── chrono.h │ │ │ │ ├── common.h │ │ │ │ ├── complex.h │ │ │ │ ├── detail │ │ │ │ ├── class.h │ │ │ │ ├── common.h │ │ │ │ ├── descr.h │ │ │ │ ├── init.h │ │ │ │ ├── internals.h │ │ │ │ └── typeid.h │ │ │ │ ├── eigen.h │ │ │ │ ├── embed.h │ │ │ │ ├── eval.h │ │ │ │ ├── functional.h │ │ │ │ ├── iostream.h │ │ │ │ ├── numpy.h │ │ │ │ ├── operators.h │ │ │ │ ├── options.h │ │ │ │ ├── pybind11.h │ │ │ │ ├── pytypes.h │ │ │ │ ├── stl.h │ │ │ │ └── stl_bind.h │ │ │ └── tools │ │ │ ├── FindCatch.cmake │ │ │ ├── FindEigen3.cmake │ │ │ ├── FindPythonLibsNew.cmake │ │ │ ├── check-style.sh │ │ │ ├── libsize.py │ │ │ ├── mkdoc.py │ │ │ ├── pybind11Config.cmake.in │ │ │ └── pybind11Tools.cmake │ ├── gmxapi │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── _logging.py │ │ ├── abc.py │ │ ├── commandline.py │ │ ├── data.py │ │ ├── datamodel.py │ │ ├── exceptions.py │ │ ├── export_context.cpp │ │ ├── export_exceptions.cpp │ │ ├── export_system.cpp │ │ ├── export_tprfile.cpp │ │ ├── fileio.py │ │ ├── gmxconfig.json.in │ │ ├── module.cpp │ │ ├── module.h │ │ ├── operation.py │ │ ├── pycontext.cpp │ │ ├── pycontext.h │ │ ├── pysystem.cpp │ │ ├── pysystem.h │ │ ├── simulation │ │ │ ├── .gitattributes │ │ │ ├── __init__.py │ │ │ ├── abc.py │ │ │ ├── context.py │ │ │ ├── fileio.py │ │ │ ├── mdrun.py │ │ │ ├── modify_input.py │ │ │ ├── read_tpr.py │ │ │ └── workflow.py │ │ ├── testsupport.py │ │ ├── typing.py │ │ └── version.py │ ├── pyproject.toml │ ├── requirements.txt │ ├── setup.py │ └── test │ │ ├── CMakeLists.txt │ │ ├── conftest.py │ │ ├── pytest.ini │ │ ├── test_commandline.py │ │ ├── test_data.py │ │ ├── test_exceptions.py │ │ ├── test_fileio.py │ │ ├── test_mdrun.py │ │ ├── test_operation.py │ │ ├── test_subgraph.py │ │ └── testdata.json └── test │ ├── README.md │ ├── conftest.py │ ├── pytest.ini │ ├── pytesthelpers.py │ ├── test_fr01.py │ ├── test_fr03.py │ ├── test_fr04.py │ ├── test_fr05.py │ ├── test_fr07.py │ ├── test_fr08.py │ ├── test_fr09.py │ ├── test_fr10.py │ ├── test_fr11.py │ ├── test_fr12.py │ ├── test_fr13.py │ ├── test_fr14.py │ ├── test_fr15.py │ ├── test_fr16.py │ ├── test_fr17.py │ ├── test_fr18.py │ ├── test_fr19.py │ ├── test_fr20.py │ ├── test_fr21.py │ ├── test_fr22.py │ ├── test_fr23.py │ └── testdata.json ├── scripts ├── .gitignore ├── CMakeLists.txt ├── CTest2JUnit.xsl ├── GMXRC.bash.cmakein ├── GMXRC.cmakein ├── GMXRC.csh.cmakein ├── GMXRC.zsh.cmakein ├── checkheaders.sh ├── demux.pl ├── grompplog2top ├── make_gromos_bon.pl ├── make_gromos_nb.pl ├── make_gromos_rtp.pl ├── make_gromos_rtp.py └── xplor2gmx.pl ├── share ├── CMakeLists.txt ├── README.tutor ├── README_FreeEnergyModifications.txt ├── template │ ├── CMakeLists.txt │ ├── CMakeLists.txt.template │ ├── Makefile.pkg │ ├── README.cmakein │ ├── cmake │ │ └── FindGROMACS.cmake │ └── template.cpp └── top │ ├── README │ ├── amber03.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── amber94.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── amber96.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── amber99.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── amber99sb-ildn.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── amber99sb.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── amberGS.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dna.arn │ ├── dna.hdb │ ├── dna.r2b │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── rna.arn │ ├── rna.hdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── urea.itp │ └── watermodels.dat │ ├── atom_nom.tbl │ ├── atommass.dat │ ├── bonds.dlg │ ├── ca-shift.dat │ ├── cb-shift.dat │ ├── charmm27.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── cmap.itp │ ├── dna.arn │ ├── dna.c.tdb │ ├── dna.hdb │ ├── dna.n.tdb │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnabonded.itp │ ├── ffnanonbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── lipids.hdb │ ├── lipids.rtp │ ├── rna.arn │ ├── rna.c.tdb │ ├── rna.hdb │ ├── rna.n.tdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip5p.itp │ ├── tips3p.itp │ └── watermodels.dat │ ├── co-shift.dat │ ├── defselection.dat │ ├── dgsolv.dat │ ├── edissoc.dat │ ├── electroneg.dat │ ├── elements.dat │ ├── export.dlg │ ├── ffG43a1.itp │ ├── ffG43a2.itp │ ├── ffG45a3.itp │ ├── ffG53a5.itp │ ├── ffG53a6.itp │ ├── ffoplsaa-n.tst │ ├── ffoplsaa.itp │ ├── flexspc.itp │ ├── flexspce.itp │ ├── flexwat-ferguson.itp │ ├── gromos43a1.ff │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── methanol.itp │ ├── methanol216.gro │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat │ ├── gromos43a2.ff │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat │ ├── gromos45a3.ff │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat │ ├── gromos53a5.ff │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomname2type.n2t │ ├── atomtypes.atp │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat │ ├── gromos53a6.ff │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat │ ├── gromos54a7.ff │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── dppc.itp │ ├── ff_dum.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── popc.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tmcl.itp │ └── watermodels.dat │ ├── ha-shift.dat │ ├── ions.itp │ ├── nsfactor.dat │ ├── oplsaa.ff │ ├── 1propanol.itp │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomname2type.n2t │ ├── atomtypes.atp │ ├── ethanol.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── ions.itp │ ├── methanol.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── tip5pe.itp │ └── watermodels.dat │ ├── phbres.dat │ ├── ps.m2p │ ├── random.dat │ ├── refi_aa.dat │ ├── residues.dtd │ ├── residues.xml │ ├── residuetypes.dat │ ├── sfactor.dat │ ├── spc.itp │ ├── spc216.gro │ ├── spce.itp │ ├── specbond.dat │ ├── ss.map │ ├── surface.dat │ ├── sw.itp │ ├── table6-10.xvg │ ├── table6-11.xvg │ ├── table6-12.xvg │ ├── table6-8.xvg │ ├── table6-9.xvg │ ├── tip3p.itp │ ├── tip4p.gro │ ├── tip4p.itp │ ├── tip5p.gro │ ├── vdw-msms.dat │ ├── vdwradii.dat │ └── xlateat.dat ├── src ├── .clang-tidy ├── .clang-tidy.new.code ├── .gitignore ├── CMakeLists.txt ├── GetCompilerInfo.cmake ├── api │ ├── CMakeLists.txt │ ├── cpp │ │ ├── CMakeLists.txt │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── context.cpp │ │ │ ├── restraint.cpp │ │ │ ├── runner.cpp │ │ │ ├── status.cpp │ │ │ ├── stopsignaler.cpp │ │ │ ├── system.cpp │ │ │ ├── testingconfiguration.h │ │ │ └── version.cpp │ │ └── workflow │ │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ └── workflow.cpp │ └── docs │ │ ├── CMakeLists.txt │ │ ├── Doxyfile-dev.in │ │ └── Doxyfile.in ├── buildinfo.h.cmakein ├── compilerflaginfo.h.cmakein ├── config.h.cmakein ├── external │ ├── .clang-tidy │ ├── .gitattributes │ ├── CMakeLists.txt │ ├── boost │ │ ├── CMakeLists.txt │ │ ├── README │ │ └── stl_interfaces │ │ │ ├── fwd.hpp │ │ │ └── iterator_interface.hpp │ ├── build-fftw │ │ ├── .gitattributes │ │ └── CMakeLists.txt │ ├── clFFT │ │ ├── LICENSE │ │ ├── NOTICE │ │ ├── README.Gromacs │ │ ├── ReleaseNotes.txt │ │ └── src │ │ │ ├── CMakeLists.txt │ │ │ ├── clFFTConfig.cmake.in │ │ │ ├── clFFTConfigVersion.cmake.in │ │ │ ├── include │ │ │ ├── clAmdFft.h │ │ │ ├── clAmdFft.version.h │ │ │ ├── clFFT.h │ │ │ ├── clFFT.version.h │ │ │ ├── clFFT.version.h.in │ │ │ ├── convenienceFunctions.h │ │ │ ├── sharedLibrary.h │ │ │ ├── stdafx.h │ │ │ ├── targetver.h │ │ │ └── unicode.compatibility.h │ │ │ ├── library │ │ │ ├── CMakeLists.txt │ │ │ ├── ReadMe.txt │ │ │ ├── accessors.cpp │ │ │ ├── action.h │ │ │ ├── action.transpose.cpp │ │ │ ├── action.transpose.h │ │ │ ├── clFFT.pc.in │ │ │ ├── dllmain.cpp │ │ │ ├── enqueue.cpp │ │ │ ├── fft_binary_lookup.cpp │ │ │ ├── fft_binary_lookup.h │ │ │ ├── generator.copy.cpp │ │ │ ├── generator.h │ │ │ ├── generator.stockham.cpp │ │ │ ├── generator.stockham.h │ │ │ ├── generator.transpose.cpp │ │ │ ├── generator.transpose.gcn.cpp │ │ │ ├── generator.transpose.gcn.h │ │ │ ├── generator.transpose.h │ │ │ ├── lifetime.cpp │ │ │ ├── lock.h │ │ │ ├── mainpage.h │ │ │ ├── md5sum.cpp │ │ │ ├── md5sum.h │ │ │ ├── plan.cpp │ │ │ ├── plan.h │ │ │ ├── private.h │ │ │ ├── repo.cpp │ │ │ ├── repo.h │ │ │ ├── stdafx.cpp │ │ │ └── transform.cpp │ │ │ └── statTimer │ │ │ ├── CMakeLists.txt │ │ │ ├── ReadMe.txt │ │ │ ├── dllmain.cpp │ │ │ ├── statisticalTimer.CPU.cpp │ │ │ ├── statisticalTimer.CPU.h │ │ │ ├── statisticalTimer.GPU.cpp │ │ │ ├── statisticalTimer.GPU.h │ │ │ ├── statisticalTimer.extern.cpp │ │ │ ├── statisticalTimer.extern.h │ │ │ ├── statisticalTimer.h │ │ │ ├── stdafx.cpp │ │ │ ├── stdafx.h │ │ │ └── targetver.h │ ├── fftpack │ │ ├── README │ │ ├── fftpack.cpp │ │ └── fftpack.h │ ├── googletest │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── README.Gromacs │ │ ├── README.md │ │ ├── googlemock │ │ │ ├── CHANGES │ │ │ ├── CMakeLists.txt │ │ │ ├── CONTRIBUTORS │ │ │ ├── LICENSE │ │ │ ├── README.md │ │ │ ├── docs │ │ │ │ ├── CheatSheet.md │ │ │ │ ├── CookBook.md │ │ │ │ ├── DesignDoc.md │ │ │ │ ├── Documentation.md │ │ │ │ ├── ForDummies.md │ │ │ │ ├── FrequentlyAskedQuestions.md │ │ │ │ └── KnownIssues.md │ │ │ ├── include │ │ │ │ └── gmock │ │ │ │ │ ├── gmock-actions.h │ │ │ │ │ ├── gmock-cardinalities.h │ │ │ │ │ ├── gmock-generated-actions.h │ │ │ │ │ ├── gmock-generated-function-mockers.h │ │ │ │ │ ├── gmock-generated-matchers.h │ │ │ │ │ ├── gmock-generated-nice-strict.h │ │ │ │ │ ├── gmock-matchers.h │ │ │ │ │ ├── gmock-more-actions.h │ │ │ │ │ ├── gmock-more-matchers.h │ │ │ │ │ ├── gmock-spec-builders.h │ │ │ │ │ ├── gmock.h │ │ │ │ │ └── internal │ │ │ │ │ ├── custom │ │ │ │ │ ├── gmock-generated-actions.h │ │ │ │ │ ├── gmock-matchers.h │ │ │ │ │ └── gmock-port.h │ │ │ │ │ ├── gmock-generated-internal-utils.h │ │ │ │ │ ├── gmock-internal-utils.h │ │ │ │ │ └── gmock-port.h │ │ │ └── src │ │ │ │ ├── gmock-all.cc │ │ │ │ ├── gmock-cardinalities.cc │ │ │ │ ├── gmock-internal-utils.cc │ │ │ │ ├── gmock-matchers.cc │ │ │ │ ├── gmock-spec-builders.cc │ │ │ │ ├── gmock.cc │ │ │ │ └── gmock_main.cc │ │ └── googletest │ │ │ ├── .gitignore │ │ │ ├── CHANGES │ │ │ ├── CMakeLists.txt │ │ │ ├── CONTRIBUTORS │ │ │ ├── LICENSE │ │ │ ├── README.md │ │ │ ├── cmake │ │ │ ├── Config.cmake.in │ │ │ ├── gtest.pc.in │ │ │ ├── gtest_main.pc.in │ │ │ └── internal_utils.cmake │ │ │ ├── docs │ │ │ ├── Pkgconfig.md │ │ │ ├── PumpManual.md │ │ │ ├── XcodeGuide.md │ │ │ ├── advanced.md │ │ │ ├── faq.md │ │ │ ├── primer.md │ │ │ └── samples.md │ │ │ ├── include │ │ │ └── gtest │ │ │ │ ├── gtest-death-test.h │ │ │ │ ├── gtest-message.h │ │ │ │ ├── gtest-param-test.h │ │ │ │ ├── gtest-printers.h │ │ │ │ ├── gtest-spi.h │ │ │ │ ├── gtest-test-part.h │ │ │ │ ├── gtest-typed-test.h │ │ │ │ ├── gtest.h │ │ │ │ ├── gtest_pred_impl.h │ │ │ │ ├── gtest_prod.h │ │ │ │ └── internal │ │ │ │ ├── custom │ │ │ │ ├── README.md │ │ │ │ ├── gtest-port.h │ │ │ │ ├── gtest-printers.h │ │ │ │ └── gtest.h │ │ │ │ ├── gtest-death-test-internal.h │ │ │ │ ├── gtest-filepath.h │ │ │ │ ├── gtest-internal.h │ │ │ │ ├── gtest-linked_ptr.h │ │ │ │ ├── gtest-param-util-generated.h │ │ │ │ ├── gtest-param-util.h │ │ │ │ ├── gtest-port-arch.h │ │ │ │ ├── gtest-port.h │ │ │ │ ├── gtest-string.h │ │ │ │ ├── gtest-tuple.h │ │ │ │ └── gtest-type-util.h │ │ │ └── src │ │ │ ├── gtest-all.cc │ │ │ ├── gtest-death-test.cc │ │ │ ├── gtest-filepath.cc │ │ │ ├── gtest-internal-inl.h │ │ │ ├── gtest-port.cc │ │ │ ├── gtest-printers.cc │ │ │ ├── gtest-test-part.cc │ │ │ ├── gtest-typed-test.cc │ │ │ ├── gtest.cc │ │ │ └── gtest_main.cc │ ├── lmfit │ │ ├── README │ │ ├── lmmin.cpp │ │ ├── lmmin.h │ │ └── lmstruct.h │ ├── muparser │ │ ├── README │ │ ├── muParser.cpp │ │ ├── muParser.h │ │ ├── muParserBase.cpp │ │ ├── muParserBase.h │ │ ├── muParserBytecode.cpp │ │ ├── muParserBytecode.h │ │ ├── muParserCallback.cpp │ │ ├── muParserCallback.h │ │ ├── muParserDLL.cpp │ │ ├── muParserDLL.h │ │ ├── muParserDef.h │ │ ├── muParserError.cpp │ │ ├── muParserError.h │ │ ├── muParserFixes.h │ │ ├── muParserInt.cpp │ │ ├── muParserInt.h │ │ ├── muParserTemplateMagic.h │ │ ├── muParserTest.cpp │ │ ├── muParserTest.h │ │ ├── muParserToken.h │ │ ├── muParserTokenReader.cpp │ │ └── muParserTokenReader.h │ ├── thread_mpi │ │ ├── include │ │ │ ├── thread_mpi.h │ │ │ ├── thread_mpi │ │ │ │ ├── atomic.h │ │ │ │ ├── atomic │ │ │ │ │ ├── cce.h │ │ │ │ │ ├── cce_intrinsics.h │ │ │ │ │ ├── cce_spinlock.h │ │ │ │ │ ├── cycles.h │ │ │ │ │ ├── derived.h │ │ │ │ │ ├── fujitsu_sparc64.h │ │ │ │ │ ├── gcc.h │ │ │ │ │ ├── gcc_ia64.h │ │ │ │ │ ├── gcc_intrinsics.h │ │ │ │ │ ├── gcc_ppc.h │ │ │ │ │ ├── gcc_spinlock.h │ │ │ │ │ ├── gcc_x86.h │ │ │ │ │ ├── msvc.h │ │ │ │ │ ├── suncc-sparc.h │ │ │ │ │ └── xlc_ppc.h │ │ │ │ ├── barrier.h │ │ │ │ ├── collective.h │ │ │ │ ├── event.h │ │ │ │ ├── hwinfo.h │ │ │ │ ├── list.h │ │ │ │ ├── lock.h │ │ │ │ ├── mpi_bindings.h │ │ │ │ ├── mutex.h │ │ │ │ ├── numa_malloc.h │ │ │ │ ├── system_error.h │ │ │ │ ├── threads.h │ │ │ │ ├── tmpi.h │ │ │ │ ├── visibility.h │ │ │ │ └── wait.h │ │ │ └── tmpi.h │ │ └── src │ │ │ ├── alltoall.cpp │ │ │ ├── atomic.cpp │ │ │ ├── barrier.cpp │ │ │ ├── bcast.cpp │ │ │ ├── collective.cpp │ │ │ ├── collective.h │ │ │ ├── comm.cpp │ │ │ ├── errhandler.cpp │ │ │ ├── event.cpp │ │ │ ├── gather.cpp │ │ │ ├── group.cpp │ │ │ ├── impl.h │ │ │ ├── list.cpp │ │ │ ├── lock.cpp │ │ │ ├── numa_malloc.cpp │ │ │ ├── once.cpp │ │ │ ├── p2p.h │ │ │ ├── p2p_buffer.cpp │ │ │ ├── p2p_protocol.cpp │ │ │ ├── p2p_send_recv.cpp │ │ │ ├── p2p_wait.cpp │ │ │ ├── profile.cpp │ │ │ ├── profile.h │ │ │ ├── pthreads.cpp │ │ │ ├── pthreads.h │ │ │ ├── reduce.cpp │ │ │ ├── reduce_fast.cpp │ │ │ ├── scan.cpp │ │ │ ├── scatter.cpp │ │ │ ├── settings.h │ │ │ ├── system_error.cpp │ │ │ ├── tmpi_init.cpp │ │ │ ├── tmpi_malloc.cpp │ │ │ ├── tmpi_ops.h │ │ │ ├── topology.cpp │ │ │ ├── type.cpp │ │ │ ├── unused.h │ │ │ ├── winthreads.cpp │ │ │ └── winthreads.h │ ├── tinyxml2 │ │ ├── README │ │ ├── tinyxml2.cpp │ │ └── tinyxml2.h │ ├── tng_io │ │ ├── AUTHORS │ │ ├── BuildTNG.cmake │ │ ├── CMakeLists.txt │ │ ├── COPYING │ │ ├── Doxyfile.in │ │ ├── INSTALL │ │ ├── README.gromacs │ │ ├── Trajectoryformatspecification.mk │ │ ├── example_files │ │ │ └── tng_example.tng │ │ ├── external │ │ │ ├── README │ │ │ └── zlib │ │ │ │ ├── README │ │ │ │ ├── adler32.c │ │ │ │ ├── compress.c │ │ │ │ ├── crc32.c │ │ │ │ ├── crc32.h │ │ │ │ ├── deflate.c │ │ │ │ ├── deflate.h │ │ │ │ ├── inffast.c │ │ │ │ ├── inffast.h │ │ │ │ ├── inffixed.h │ │ │ │ ├── inflate.c │ │ │ │ ├── inflate.h │ │ │ │ ├── inftrees.c │ │ │ │ ├── inftrees.h │ │ │ │ ├── trees.c │ │ │ │ ├── trees.h │ │ │ │ ├── uncompr.c │ │ │ │ ├── zconf.h │ │ │ │ ├── zlib.h │ │ │ │ ├── zutil.c │ │ │ │ └── zutil.h │ │ ├── include │ │ │ ├── compression │ │ │ │ ├── bwlzh.h │ │ │ │ ├── bwt.h │ │ │ │ ├── coder.h │ │ │ │ ├── dict.h │ │ │ │ ├── fixpoint.h │ │ │ │ ├── huffman.h │ │ │ │ ├── lz77.h │ │ │ │ ├── merge_sort.h │ │ │ │ ├── mtf.h │ │ │ │ ├── my64bit.h │ │ │ │ ├── rle.h │ │ │ │ ├── tng_compress.h │ │ │ │ ├── vals16.h │ │ │ │ ├── warnmalloc.h │ │ │ │ └── widemuldiv.h │ │ │ └── tng │ │ │ │ ├── md5.h │ │ │ │ ├── tng_io.h │ │ │ │ ├── tng_io.hpp │ │ │ │ ├── tng_io_fwd.h │ │ │ │ └── version.h.in │ │ └── src │ │ │ ├── CMakeLists.txt │ │ │ ├── compression │ │ │ ├── bwlzh.c │ │ │ ├── bwt.c │ │ │ ├── coder.c │ │ │ ├── dict.c │ │ │ ├── fixpoint.c │ │ │ ├── huffman.c │ │ │ ├── huffmem.c │ │ │ ├── lz77.c │ │ │ ├── merge_sort.c │ │ │ ├── mtf.c │ │ │ ├── rle.c │ │ │ ├── tng_compress.c │ │ │ ├── vals16.c │ │ │ ├── warnmalloc.c │ │ │ ├── widemuldiv.c │ │ │ ├── xtc2.c │ │ │ └── xtc3.c │ │ │ ├── lib │ │ │ ├── md5.c │ │ │ ├── tng_io-config.cmake.in │ │ │ ├── tng_io-configVersion.cmake.in │ │ │ ├── tng_io.c │ │ │ └── tng_io_fortran.c │ │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── compression │ │ │ ├── CMakeLists.txt │ │ │ ├── getfilesize.sh │ │ │ ├── test1.h │ │ │ ├── test10.h │ │ │ ├── test11.h │ │ │ ├── test12.h │ │ │ ├── test13.h │ │ │ ├── test14.h │ │ │ ├── test15.h │ │ │ ├── test16.h │ │ │ ├── test17.h │ │ │ ├── test18.h │ │ │ ├── test19.h │ │ │ ├── test2.h │ │ │ ├── test20.h │ │ │ ├── test21.h │ │ │ ├── test22.h │ │ │ ├── test23.h │ │ │ ├── test24.h │ │ │ ├── test25.h │ │ │ ├── test26.h │ │ │ ├── test27.h │ │ │ ├── test28.h │ │ │ ├── test29.h │ │ │ ├── test3.h │ │ │ ├── test30.h │ │ │ ├── test31.h │ │ │ ├── test32.h │ │ │ ├── test33.h │ │ │ ├── test34.h │ │ │ ├── test35.h │ │ │ ├── test36.h │ │ │ ├── test37.h │ │ │ ├── test38.h │ │ │ ├── test39.h │ │ │ ├── test4.h │ │ │ ├── test40.h │ │ │ ├── test41.h │ │ │ ├── test42.h │ │ │ ├── test43.h │ │ │ ├── test44.h │ │ │ ├── test45.h │ │ │ ├── test46.h │ │ │ ├── test47.h │ │ │ ├── test48.h │ │ │ ├── test49.h │ │ │ ├── test5.h │ │ │ ├── test50.h │ │ │ ├── test51.h │ │ │ ├── test52.h │ │ │ ├── test53.h │ │ │ ├── test54.h │ │ │ ├── test55.h │ │ │ ├── test56.h │ │ │ ├── test57.h │ │ │ ├── test58.h │ │ │ ├── test59.h │ │ │ ├── test6.h │ │ │ ├── test60.h │ │ │ ├── test61.h │ │ │ ├── test62.h │ │ │ ├── test63.h │ │ │ ├── test64.h │ │ │ ├── test65.h │ │ │ ├── test66.h │ │ │ ├── test67.h │ │ │ ├── test68.h │ │ │ ├── test69.h │ │ │ ├── test7.h │ │ │ ├── test70.h │ │ │ ├── test71.h │ │ │ ├── test72.h │ │ │ ├── test73.h │ │ │ ├── test74.h │ │ │ ├── test75.h │ │ │ ├── test76.h │ │ │ ├── test77.h │ │ │ ├── test78.h │ │ │ ├── test8.h │ │ │ ├── test9.h │ │ │ ├── test_tng_compress_read.bat │ │ │ ├── test_tng_compress_read.sh │ │ │ ├── test_tng_compress_write.bat │ │ │ ├── test_tng_compress_write.sh │ │ │ └── testsuite.c │ │ │ ├── md_openmp.c │ │ │ ├── md_openmp.f │ │ │ ├── md_openmp_util.c │ │ │ ├── tng_io_read_pos.c │ │ │ ├── tng_io_read_pos_util.c │ │ │ ├── tng_io_testing.c │ │ │ ├── tng_parallel_read.c │ │ │ └── using │ │ │ ├── CMakeLists.txt │ │ │ ├── dummy_zlib.c │ │ │ ├── main.c │ │ │ ├── use_tng.c │ │ │ └── use_zlib.c │ └── vmd_molfile │ │ ├── molfile_plugin.h │ │ ├── vmddlopen.cpp │ │ ├── vmddlopen.h │ │ └── vmdplugin.h ├── gmxpre-config.h.cmakein ├── gmxpre.h ├── gromacs │ ├── CMakeLists.txt │ ├── InstallLibInfo.cmake │ ├── analysisdata.h │ ├── analysisdata │ │ ├── .clang-tidy │ │ ├── CMakeLists.txt │ │ ├── abstractdata.cpp │ │ ├── abstractdata.h │ │ ├── analysisdata.cpp │ │ ├── analysisdata.h │ │ ├── arraydata.cpp │ │ ├── arraydata.h │ │ ├── dataframe.cpp │ │ ├── dataframe.h │ │ ├── datamodule.cpp │ │ ├── datamodule.h │ │ ├── datamodulemanager.cpp │ │ ├── datamodulemanager.h │ │ ├── dataproxy.cpp │ │ ├── dataproxy.h │ │ ├── datastorage.cpp │ │ ├── datastorage.h │ │ ├── framelocaldata.h │ │ ├── modules │ │ │ ├── CMakeLists.txt │ │ │ ├── average.cpp │ │ │ ├── average.h │ │ │ ├── displacement.cpp │ │ │ ├── displacement.h │ │ │ ├── frameaverager.cpp │ │ │ ├── frameaverager.h │ │ │ ├── histogram.cpp │ │ │ ├── histogram.h │ │ │ ├── lifetime.cpp │ │ │ ├── lifetime.h │ │ │ ├── plot.cpp │ │ │ └── plot.h │ │ ├── paralleloptions.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── analysisdata.cpp │ │ │ ├── arraydata.cpp │ │ │ ├── average.cpp │ │ │ ├── datatest.cpp │ │ │ ├── datatest.h │ │ │ ├── histogram.cpp │ │ │ ├── lifetime.cpp │ │ │ ├── mock_datamodule.cpp │ │ │ ├── mock_datamodule.h │ │ │ └── refdata │ │ │ ├── AbstractAverageHistogramTest_ComputesCumulativeHistogram.xml │ │ │ ├── AbstractAverageHistogramTest_ResamplesAtDoubleBinWidth.xml │ │ │ ├── AbstractAverageHistogramTest_ResamplesAtDoubleBinWidthWithIntegerBins.xml │ │ │ ├── AverageModuleTest_BasicTest.xml │ │ │ ├── AverageModuleTest_CanCustomizeNonUniformXAxis.xml │ │ │ ├── AverageModuleTest_CanCustomizeXAxis.xml │ │ │ ├── AverageModuleTest_HandlesDataSetAveraging.xml │ │ │ ├── AverageModuleTest_HandlesMultipleDataSets.xml │ │ │ ├── AverageModuleTest_HandlesMultipointData.xml │ │ │ ├── BinAverageModuleTest_ComputesCorrectly.xml │ │ │ ├── BinAverageModuleTest_ComputesCorrectlyWithAll.xml │ │ │ ├── BinAverageModuleTest_HandlesMultipleDataSets.xml │ │ │ ├── FrameAverageModuleTest_BasicTest.xml │ │ │ ├── FrameAverageModuleTest_HandlesMultipleDataSets.xml │ │ │ ├── LifetimeModuleTest_BasicTest.xml │ │ │ ├── LifetimeModuleTest_CumulativeTest.xml │ │ │ ├── LifetimeModuleTest_HandlesMultipleDataSets.xml │ │ │ ├── SimpleHistogramModuleTest_ComputesCorrectly.xml │ │ │ ├── SimpleHistogramModuleTest_ComputesCorrectlyWithAll.xml │ │ │ ├── WeightedHistogramModuleTest_ComputesCorrectly.xml │ │ │ ├── WeightedHistogramModuleTest_ComputesCorrectlyWithAll.xml │ │ │ ├── WeightedHistogramModuleTest_HandlesMultipleDataSets.xml │ │ │ ├── analysisdata-referencedata.xsl │ │ │ ├── common-referencedata.xsl │ │ │ └── referencedata.xsl │ ├── applied_forces │ │ ├── CMakeLists.txt │ │ ├── awh │ │ │ ├── CMakeLists.txt │ │ │ ├── awh.cpp │ │ │ ├── awh.h │ │ │ ├── bias.cpp │ │ │ ├── bias.h │ │ │ ├── biasgrid.cpp │ │ │ ├── biasgrid.h │ │ │ ├── biasparams.cpp │ │ │ ├── biasparams.h │ │ │ ├── biassharing.cpp │ │ │ ├── biassharing.h │ │ │ ├── biasstate.cpp │ │ │ ├── biasstate.h │ │ │ ├── biaswriter.cpp │ │ │ ├── biaswriter.h │ │ │ ├── coordstate.cpp │ │ │ ├── coordstate.h │ │ │ ├── correlationgrid.cpp │ │ │ ├── correlationgrid.h │ │ │ ├── correlationhistory.cpp │ │ │ ├── correlationhistory.h │ │ │ ├── correlationtensor.cpp │ │ │ ├── correlationtensor.h │ │ │ ├── dimparams.h │ │ │ ├── histogramsize.cpp │ │ │ ├── histogramsize.h │ │ │ ├── pointstate.cpp │ │ │ ├── pointstate.h │ │ │ ├── read_params.cpp │ │ │ ├── read_params.h │ │ │ └── tests │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── bias.cpp │ │ │ │ ├── bias_fep_lambda_state.cpp │ │ │ │ ├── biasgrid.cpp │ │ │ │ ├── biasstate.cpp │ │ │ │ ├── pmf_target_format0.xvg │ │ │ │ ├── pmf_target_format1.xvg │ │ │ │ └── refdata │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_0.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_1.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_2.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_3.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_4.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_5.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_6.xml │ │ │ │ ├── WithParameters_BiasFepLambdaStateTest_ForcesBiasPmf_7.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_0.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_1.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_2.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_3.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_4.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_5.xml │ │ │ │ ├── WithParameters_BiasTest_ForcesBiasPmf_6.xml │ │ │ │ └── WithParameters_BiasTest_ForcesBiasPmf_7.xml │ │ ├── densityfitting │ │ │ ├── CMakeLists.txt │ │ │ ├── densityfitting.cpp │ │ │ ├── densityfitting.h │ │ │ ├── densityfittingamplitudelookup.cpp │ │ │ ├── densityfittingamplitudelookup.h │ │ │ ├── densityfittingforceprovider.cpp │ │ │ ├── densityfittingforceprovider.h │ │ │ ├── densityfittingoptions.cpp │ │ │ ├── densityfittingoptions.h │ │ │ ├── densityfittingoutputprovider.cpp │ │ │ ├── densityfittingoutputprovider.h │ │ │ ├── densityfittingparameters.cpp │ │ │ ├── densityfittingparameters.h │ │ │ └── tests │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── densityfitting.cpp │ │ │ │ ├── densityfittingamplitudelookup.cpp │ │ │ │ ├── densityfittingforceprovider.cpp │ │ │ │ └── densityfittingoptions.cpp │ │ ├── electricfield.cpp │ │ ├── electricfield.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ └── electricfield.cpp │ ├── commandline.h │ ├── commandline │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── cmdlinehelpcontext.cpp │ │ ├── cmdlinehelpcontext.h │ │ ├── cmdlinehelpmodule.cpp │ │ ├── cmdlinehelpmodule.h │ │ ├── cmdlinehelpwriter.cpp │ │ ├── cmdlinehelpwriter.h │ │ ├── cmdlineinit.cpp │ │ ├── cmdlineinit.h │ │ ├── cmdlinemodule.cpp │ │ ├── cmdlinemodule.h │ │ ├── cmdlinemodulemanager.cpp │ │ ├── cmdlinemodulemanager.h │ │ ├── cmdlinemodulemanager_impl.h │ │ ├── cmdlineoptionsmodule.cpp │ │ ├── cmdlineoptionsmodule.h │ │ ├── cmdlineparser.cpp │ │ ├── cmdlineparser.h │ │ ├── cmdlineprogramcontext.cpp │ │ ├── cmdlineprogramcontext.h │ │ ├── filenm.cpp │ │ ├── filenm.h │ │ ├── pargs.cpp │ │ ├── pargs.h │ │ ├── shellcompletions.cpp │ │ ├── shellcompletions.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── cmdlinehelpmodule.cpp │ │ │ ├── cmdlinehelpwriter.cpp │ │ │ ├── cmdlinemodulemanager.cpp │ │ │ ├── cmdlinemodulemanagertest.cpp │ │ │ ├── cmdlinemodulemanagertest.h │ │ │ ├── cmdlineparser.cpp │ │ │ ├── cmdlineprogramcontext.cpp │ │ │ ├── filenm.cpp │ │ │ ├── pargs.cpp │ │ │ └── refdata │ │ │ │ ├── CommandLineHelpModuleTest_ExportsHelp.xml │ │ │ │ ├── CommandLineHelpModuleTest_PrintsGeneralHelp.xml │ │ │ │ ├── CommandLineHelpModuleTest_PrintsHelpOnTopic.xml │ │ │ │ ├── CommandLineHelpWriterTest_HandlesDefaultValuesFromVariables.xml │ │ │ │ ├── CommandLineHelpWriterTest_HandlesHelpText.xml │ │ │ │ ├── CommandLineHelpWriterTest_HandlesKnownIssues.xml │ │ │ │ ├── CommandLineHelpWriterTest_HandlesLongFileOptions.xml │ │ │ │ ├── CommandLineHelpWriterTest_HandlesLongOptions.xml │ │ │ │ ├── CommandLineHelpWriterTest_HandlesOptionGroups.xml │ │ │ │ └── CommandLineHelpWriterTest_HandlesOptionTypes.xml │ │ ├── viewit.cpp │ │ └── viewit.h │ ├── compat │ │ ├── .gitattributes │ │ ├── CMakeLists.txt │ │ ├── pointers.h │ │ ├── tests │ │ │ ├── .gitattributes │ │ │ ├── CMakeLists.txt │ │ │ └── pointers.cpp │ │ └── utility.h │ ├── coordinateio.h │ ├── coordinateio │ │ ├── CMakeLists.txt │ │ ├── coordinatefile.cpp │ │ ├── coordinatefile.h │ │ ├── enums.h │ │ ├── ioutputadapter.h │ │ ├── outputadaptercontainer.cpp │ │ ├── outputadaptercontainer.h │ │ ├── outputadapters.h │ │ ├── outputadapters │ │ │ ├── outputselector.cpp │ │ │ ├── outputselector.h │ │ │ ├── setatoms.cpp │ │ │ ├── setatoms.h │ │ │ ├── setbox.h │ │ │ ├── setforces.cpp │ │ │ ├── setforces.h │ │ │ ├── setprecision.cpp │ │ │ ├── setprecision.h │ │ │ ├── setstarttime.cpp │ │ │ ├── setstarttime.h │ │ │ ├── settimestep.cpp │ │ │ ├── settimestep.h │ │ │ ├── setvelocities.cpp │ │ │ └── setvelocities.h │ │ ├── requirements.cpp │ │ ├── requirements.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── builder.cpp │ │ │ ├── coordinate_test.h │ │ │ ├── outputadaptercontainer.cpp │ │ │ ├── outputadapters.cpp │ │ │ ├── outputadapters.h │ │ │ ├── requirements.cpp │ │ │ ├── requirements.h │ │ │ ├── setatoms.cpp │ │ │ ├── setbothtime.cpp │ │ │ ├── setstarttime.cpp │ │ │ ├── settimestep.cpp │ │ │ ├── testmodule.cpp │ │ │ └── testmodule.h │ ├── correlationfunctions │ │ ├── CMakeLists.txt │ │ ├── autocorr.cpp │ │ ├── autocorr.h │ │ ├── crosscorr.cpp │ │ ├── crosscorr.h │ │ ├── expfit.cpp │ │ ├── expfit.h │ │ ├── gmx_lmcurve.cpp │ │ ├── gmx_lmcurve.h │ │ ├── integrate.cpp │ │ ├── integrate.h │ │ ├── manyautocorrelation.cpp │ │ ├── manyautocorrelation.h │ │ ├── polynomials.cpp │ │ ├── polynomials.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── autocorr.cpp │ │ │ ├── correlationdataset.cpp │ │ │ ├── correlationdataset.h │ │ │ ├── expfit.cpp │ │ │ ├── manyautocorrelation.cpp │ │ │ ├── refdata │ │ │ ├── AutocorrTest_EacCos.xml │ │ │ ├── AutocorrTest_EacNoNormalize.xml │ │ │ ├── AutocorrTest_EacNormal.xml │ │ │ ├── AutocorrTest_EacP0.xml │ │ │ ├── AutocorrTest_EacP1.xml │ │ │ ├── AutocorrTest_EacP2.xml │ │ │ ├── AutocorrTest_EacP3.xml │ │ │ ├── AutocorrTest_EacP4.xml │ │ │ ├── AutocorrTest_EacRcross.xml │ │ │ ├── AutocorrTest_EacVector.xml │ │ │ ├── ExpfitTest_EffnERF.xml │ │ │ ├── ExpfitTest_EffnERREST.xml │ │ │ ├── ExpfitTest_EffnEXP1.xml │ │ │ ├── ExpfitTest_EffnEXP2.xml │ │ │ ├── ExpfitTest_EffnEXP5.xml │ │ │ ├── ExpfitTest_EffnEXP7.xml │ │ │ ├── ExpfitTest_EffnEXP9.xml │ │ │ ├── ExpfitTest_EffnEXPEXP.xml │ │ │ ├── ExpfitTest_EffnPRES.xml │ │ │ └── ExpfitTest_EffnVAC.xml │ │ │ ├── testCOS3.xvg │ │ │ ├── testERF.xvg │ │ │ ├── testERREST.xvg │ │ │ ├── testINVEXP.xvg │ │ │ ├── testINVEXP79.xvg │ │ │ └── testPRES.xvg │ ├── domdec │ │ ├── CMakeLists.txt │ │ ├── atomdistribution.cpp │ │ ├── atomdistribution.h │ │ ├── box.cpp │ │ ├── box.h │ │ ├── builder.h │ │ ├── cellsizes.cpp │ │ ├── cellsizes.h │ │ ├── collect.cpp │ │ ├── collect.h │ │ ├── distribute.cpp │ │ ├── distribute.h │ │ ├── dlb.cpp │ │ ├── dlb.h │ │ ├── dlbtiming.cpp │ │ ├── dlbtiming.h │ │ ├── domdec.cpp │ │ ├── domdec.h │ │ ├── domdec_constraints.cpp │ │ ├── domdec_constraints.h │ │ ├── domdec_internal.h │ │ ├── domdec_network.cpp │ │ ├── domdec_network.h │ │ ├── domdec_setup.cpp │ │ ├── domdec_setup.h │ │ ├── domdec_specatomcomm.cpp │ │ ├── domdec_specatomcomm.h │ │ ├── domdec_struct.h │ │ ├── domdec_topology.cpp │ │ ├── domdec_vsite.cpp │ │ ├── domdec_vsite.h │ │ ├── dump.cpp │ │ ├── dump.h │ │ ├── ga2la.cpp │ │ ├── ga2la.h │ │ ├── gpuhaloexchange.h │ │ ├── gpuhaloexchange_impl.cpp │ │ ├── gpuhaloexchange_impl.cu │ │ ├── gpuhaloexchange_impl.cuh │ │ ├── hashedmap.h │ │ ├── localatomset.cpp │ │ ├── localatomset.h │ │ ├── localatomsetdata.cpp │ │ ├── localatomsetdata.h │ │ ├── localatomsetmanager.cpp │ │ ├── localatomsetmanager.h │ │ ├── mdsetup.cpp │ │ ├── mdsetup.h │ │ ├── options.h │ │ ├── partition.cpp │ │ ├── partition.h │ │ ├── redistribute.cpp │ │ ├── redistribute.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── hashedmap.cpp │ │ │ └── localatomsetmanager.cpp │ │ ├── utility.cpp │ │ └── utility.h │ ├── energyanalysis │ │ ├── CMakeLists.txt │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── dhdl.edr │ │ │ ├── dhdl.tpr │ │ │ ├── ener.edr │ │ │ ├── legacyenergy.cpp │ │ │ ├── orires.edr │ │ │ ├── orires.tpr │ │ │ └── refdata │ │ │ ├── DhdlTest_ExtractDhdl.xml │ │ │ ├── EnergyTest_ExtractEnergy.xml │ │ │ ├── EnergyTest_ExtractEnergyByNumber.xml │ │ │ ├── EnergyTest_ExtractEnergyMixed.xml │ │ │ ├── OriresTest_ExtractOrires.xml │ │ │ ├── ViscosityTest_EinsteinViscosity.xml │ │ │ └── ViscosityTest_EinsteinViscosityIntegral.xml │ ├── essentialdynamics │ │ ├── CMakeLists.txt │ │ ├── edsam.cpp │ │ └── edsam.h │ ├── ewald │ │ ├── CMakeLists.txt │ │ ├── calculate_spline_moduli.cpp │ │ ├── calculate_spline_moduli.h │ │ ├── ewald.cpp │ │ ├── ewald.h │ │ ├── ewald_utils.cpp │ │ ├── ewald_utils.h │ │ ├── long_range_correction.cpp │ │ ├── long_range_correction.h │ │ ├── pme.cpp │ │ ├── pme.cuh │ │ ├── pme.h │ │ ├── pme_coordinate_receiver_gpu.h │ │ ├── pme_coordinate_receiver_gpu_impl.cpp │ │ ├── pme_coordinate_receiver_gpu_impl.cu │ │ ├── pme_coordinate_receiver_gpu_impl.h │ │ ├── pme_force_sender_gpu.h │ │ ├── pme_force_sender_gpu_impl.cpp │ │ ├── pme_force_sender_gpu_impl.cu │ │ ├── pme_force_sender_gpu_impl.h │ │ ├── pme_gather.clh │ │ ├── pme_gather.cpp │ │ ├── pme_gather.cu │ │ ├── pme_gather.h │ │ ├── pme_gpu.cpp │ │ ├── pme_gpu_3dfft.cu │ │ ├── pme_gpu_3dfft.h │ │ ├── pme_gpu_3dfft_ocl.cpp │ │ ├── pme_gpu_calculate_splines.clh │ │ ├── pme_gpu_calculate_splines.cuh │ │ ├── pme_gpu_calculate_splines.h │ │ ├── pme_gpu_constants.h │ │ ├── pme_gpu_internal.cpp │ │ ├── pme_gpu_internal.h │ │ ├── pme_gpu_program.cpp │ │ ├── pme_gpu_program.h │ │ ├── pme_gpu_program_impl.cpp │ │ ├── pme_gpu_program_impl.cu │ │ ├── pme_gpu_program_impl.h │ │ ├── pme_gpu_program_impl_ocl.cpp │ │ ├── pme_gpu_settings.h │ │ ├── pme_gpu_staging.h │ │ ├── pme_gpu_timings.cpp │ │ ├── pme_gpu_timings.h │ │ ├── pme_gpu_types.h │ │ ├── pme_gpu_types_host.h │ │ ├── pme_gpu_types_host_impl.h │ │ ├── pme_grid.cpp │ │ ├── pme_grid.h │ │ ├── pme_internal.h │ │ ├── pme_load_balancing.cpp │ │ ├── pme_load_balancing.h │ │ ├── pme_only.cpp │ │ ├── pme_only.h │ │ ├── pme_output.h │ │ ├── pme_pp.cpp │ │ ├── pme_pp.h │ │ ├── pme_pp_comm_gpu.h │ │ ├── pme_pp_comm_gpu_impl.cpp │ │ ├── pme_pp_comm_gpu_impl.cu │ │ ├── pme_pp_comm_gpu_impl.h │ │ ├── pme_pp_communication.h │ │ ├── pme_program.cl │ │ ├── pme_redistribute.cpp │ │ ├── pme_redistribute.h │ │ ├── pme_simd.h │ │ ├── pme_simd4.h │ │ ├── pme_solve.clh │ │ ├── pme_solve.cpp │ │ ├── pme_solve.cu │ │ ├── pme_solve.h │ │ ├── pme_spline_work.cpp │ │ ├── pme_spline_work.h │ │ ├── pme_spread.clh │ │ ├── pme_spread.cpp │ │ ├── pme_spread.cu │ │ ├── pme_spread.h │ │ ├── spline_vectors.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── pmebsplinetest.cpp │ │ │ ├── pmegathertest.cpp │ │ │ ├── pmesolvetest.cpp │ │ │ ├── pmesplinespreadtest.cpp │ │ │ ├── pmetestcommon.cpp │ │ │ ├── pmetestcommon.h │ │ │ └── refdata │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_0.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_1.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_10.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_11.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_12.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_13.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_14.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_15.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_2.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_3.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_4.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_5.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_6.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_7.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_8.xml │ │ │ ├── DifferentEpsilonR_PmeSolveTest_ReproducesOutputs_9.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_0.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_1.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_2.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_3.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_4.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_5.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_6.xml │ │ │ ├── DifferentEwaldCoeffLJ_PmeSolveTest_ReproducesOutputs_7.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_0.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_1.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_2.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_3.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_4.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_5.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_6.xml │ │ │ ├── DifferentEwaldCoeffQ_PmeSolveTest_ReproducesOutputs_7.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_0.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_1.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_10.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_11.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_2.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_3.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_4.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_5.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_6.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_7.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_8.xml │ │ │ ├── SaneInput13_PmeSplineAndSpreadTest_ReproducesOutputs_9.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_0.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_1.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_10.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_11.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_12.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_13.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_14.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_15.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_16.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_17.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_18.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_19.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_2.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_20.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_21.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_22.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_23.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_3.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_4.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_5.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_6.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_7.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_8.xml │ │ │ ├── SaneInput1_PmeBSplineModuliCorrectnessTest_ReproducesValues_9.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_0.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_1.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_10.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_11.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_2.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_3.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_4.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_5.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_6.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_7.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_8.xml │ │ │ ├── SaneInput1_PmeSplineAndSpreadTest_ReproducesOutputs_9.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_0.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_1.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_10.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_11.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_2.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_3.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_4.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_5.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_6.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_7.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_8.xml │ │ │ ├── SaneInput2_PmeSplineAndSpreadTest_ReproducesOutputs_9.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_0.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_1.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_10.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_11.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_12.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_13.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_14.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_15.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_16.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_17.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_18.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_19.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_2.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_20.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_21.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_22.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_23.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_24.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_25.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_26.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_27.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_28.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_29.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_3.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_30.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_31.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_32.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_33.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_34.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_35.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_36.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_37.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_38.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_39.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_4.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_40.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_41.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_42.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_43.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_44.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_45.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_46.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_47.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_48.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_49.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_5.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_50.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_51.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_52.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_53.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_54.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_55.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_56.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_57.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_58.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_59.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_6.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_60.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_61.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_62.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_63.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_64.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_65.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_66.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_67.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_68.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_69.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_7.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_70.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_71.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_8.xml │ │ │ ├── SaneInput_PmeGatherTest_ReproducesOutputs_9.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_0.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_1.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_10.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_11.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_12.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_13.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_14.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_15.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_2.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_3.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_4.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_5.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_6.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_7.xml │ │ │ ├── SaneInput_PmeSolveTest_ReproducesOutputs_8.xml │ │ │ └── SaneInput_PmeSolveTest_ReproducesOutputs_9.xml │ ├── fft │ │ ├── CMakeLists.txt │ │ ├── calcgrid.cpp │ │ ├── calcgrid.h │ │ ├── fft.cpp │ │ ├── fft.h │ │ ├── fft5d.cpp │ │ ├── fft5d.h │ │ ├── fft_fftpack.cpp │ │ ├── fft_fftw3.cpp │ │ ├── fft_mkl.cpp │ │ ├── parallel_3dfft.cpp │ │ ├── parallel_3dfft.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── fft.cpp │ │ │ └── refdata │ │ │ ├── 7_8_25_36_60_FFTTest1D_Complex_0.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Complex_1.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Complex_2.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Complex_3.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Complex_4.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Real_0.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Real_1.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Real_2.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Real_3.xml │ │ │ ├── 7_8_25_36_60_FFTTest1D_Real_4.xml │ │ │ ├── FFFTest3D_Real5_6_9.xml │ │ │ ├── FFTTest_Real2DLength18_15Test.xml │ │ │ ├── ManyFFTTest_Complex1DLength48Multi5Test.xml │ │ │ └── ManyFFTTest_Real1DLength48Multi5Test.xml │ ├── fileio │ │ ├── CMakeLists.txt │ │ ├── checkpoint.cpp │ │ ├── checkpoint.h │ │ ├── confio.cpp │ │ ├── confio.h │ │ ├── enxio.cpp │ │ ├── enxio.h │ │ ├── espio.cpp │ │ ├── espio.h │ │ ├── filetypes.cpp │ │ ├── filetypes.h │ │ ├── g96io.cpp │ │ ├── g96io.h │ │ ├── gmx_internal_xdr.cpp │ │ ├── gmx_internal_xdr.h │ │ ├── gmxfio.cpp │ │ ├── gmxfio.h │ │ ├── gmxfio_impl.h │ │ ├── gmxfio_xdr.cpp │ │ ├── gmxfio_xdr.h │ │ ├── groio.cpp │ │ ├── groio.h │ │ ├── libxdrf.cpp │ │ ├── matio.cpp │ │ ├── matio.h │ │ ├── md5.cpp │ │ ├── md5.h │ │ ├── mrcdensitymap.cpp │ │ ├── mrcdensitymap.h │ │ ├── mrcdensitymapheader.cpp │ │ ├── mrcdensitymapheader.h │ │ ├── mrcserializer.cpp │ │ ├── mrcserializer.h │ │ ├── mtxio.cpp │ │ ├── mtxio.h │ │ ├── oenv.cpp │ │ ├── oenv.h │ │ ├── pdbio.cpp │ │ ├── pdbio.h │ │ ├── readinp.cpp │ │ ├── readinp.h │ │ ├── rgb.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── checkpoint.cpp │ │ │ ├── confio.cpp │ │ │ ├── fileioxdrserializer.cpp │ │ │ ├── filemd5.cpp │ │ │ ├── mrcdensitymap.cpp │ │ │ ├── mrcdensitymapheader.cpp │ │ │ ├── mrcserializer.cpp │ │ │ ├── readinp.cpp │ │ │ ├── refdata │ │ │ │ └── MrcDensityMap_ReadsDensityDataFromFile.xml │ │ │ ├── spc2-traj.tng │ │ │ ├── tngio.cpp │ │ │ └── xvgio.cpp │ │ ├── timecontrol.cpp │ │ ├── timecontrol.h │ │ ├── tngio.cpp │ │ ├── tngio.h │ │ ├── tpxio.cpp │ │ ├── tpxio.h │ │ ├── trrio.cpp │ │ ├── trrio.h │ │ ├── trxio.cpp │ │ ├── trxio.h │ │ ├── vmdio.cpp │ │ ├── vmdio.h │ │ ├── warninp.cpp │ │ ├── warninp.h │ │ ├── writeps.cpp │ │ ├── writeps.h │ │ ├── xdr_datatype.h │ │ ├── xdrd.cpp │ │ ├── xdrf.h │ │ ├── xtcio.cpp │ │ ├── xtcio.h │ │ ├── xvgr.cpp │ │ └── xvgr.h │ ├── gmxana │ │ ├── CMakeLists.txt │ │ ├── anadih.cpp │ │ ├── angle_correction.cpp │ │ ├── angle_correction.h │ │ ├── binsearch.cpp │ │ ├── binsearch.h │ │ ├── cmat.cpp │ │ ├── cmat.h │ │ ├── dens_filter.cpp │ │ ├── dens_filter.h │ │ ├── dlist.cpp │ │ ├── eigio.cpp │ │ ├── eigio.h │ │ ├── fitahx.cpp │ │ ├── fitahx.h │ │ ├── gmx_ana.h │ │ ├── gmx_anaeig.cpp │ │ ├── gmx_analyze.cpp │ │ ├── gmx_angle.cpp │ │ ├── gmx_awh.cpp │ │ ├── gmx_bar.cpp │ │ ├── gmx_bundle.cpp │ │ ├── gmx_chi.cpp │ │ ├── gmx_cluster.cpp │ │ ├── gmx_clustsize.cpp │ │ ├── gmx_confrms.cpp │ │ ├── gmx_covar.cpp │ │ ├── gmx_current.cpp │ │ ├── gmx_density.cpp │ │ ├── gmx_densmap.cpp │ │ ├── gmx_densorder.cpp │ │ ├── gmx_dielectric.cpp │ │ ├── gmx_dipoles.cpp │ │ ├── gmx_disre.cpp │ │ ├── gmx_do_dssp.cpp │ │ ├── gmx_dos.cpp │ │ ├── gmx_dyecoupl.cpp │ │ ├── gmx_enemat.cpp │ │ ├── gmx_energy.cpp │ │ ├── gmx_filter.cpp │ │ ├── gmx_gyrate.cpp │ │ ├── gmx_h2order.cpp │ │ ├── gmx_hbond.cpp │ │ ├── gmx_helix.cpp │ │ ├── gmx_helixorient.cpp │ │ ├── gmx_hydorder.cpp │ │ ├── gmx_lie.cpp │ │ ├── gmx_make_edi.cpp │ │ ├── gmx_mdmat.cpp │ │ ├── gmx_mindist.cpp │ │ ├── gmx_msd.cpp │ │ ├── gmx_nmeig.cpp │ │ ├── gmx_nmens.cpp │ │ ├── gmx_nmr.cpp │ │ ├── gmx_nmtraj.cpp │ │ ├── gmx_order.cpp │ │ ├── gmx_polystat.cpp │ │ ├── gmx_potential.cpp │ │ ├── gmx_principal.cpp │ │ ├── gmx_rama.cpp │ │ ├── gmx_rms.cpp │ │ ├── gmx_rmsdist.cpp │ │ ├── gmx_rmsf.cpp │ │ ├── gmx_rotacf.cpp │ │ ├── gmx_rotmat.cpp │ │ ├── gmx_saltbr.cpp │ │ ├── gmx_sans.cpp │ │ ├── gmx_saxs.cpp │ │ ├── gmx_sham.cpp │ │ ├── gmx_sigeps.cpp │ │ ├── gmx_sorient.cpp │ │ ├── gmx_spatial.cpp │ │ ├── gmx_spol.cpp │ │ ├── gmx_tcaf.cpp │ │ ├── gmx_traj.cpp │ │ ├── gmx_trjorder.cpp │ │ ├── gmx_vanhove.cpp │ │ ├── gmx_velacc.cpp │ │ ├── gmx_wham.cpp │ │ ├── gmx_wheel.cpp │ │ ├── gmx_xpm2ps.cpp │ │ ├── gstat.h │ │ ├── hxprops.cpp │ │ ├── hxprops.h │ │ ├── interf.h │ │ ├── nrama.cpp │ │ ├── nrama.h │ │ ├── nsfactor.cpp │ │ ├── nsfactor.h │ │ ├── powerspect.cpp │ │ ├── powerspect.h │ │ ├── pp2shift.cpp │ │ ├── princ.cpp │ │ ├── princ.h │ │ ├── sfactor.cpp │ │ ├── sfactor.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── entropy.cpp │ │ │ ├── gmx_make_ndx.cpp │ │ │ ├── gmx_mindist.cpp │ │ │ ├── gmx_msd.cpp │ │ │ ├── gmx_traj.cpp │ │ │ ├── msd.ndx │ │ │ ├── msd_coords.gro │ │ │ ├── msd_traj.xtc │ │ │ └── refdata │ │ │ │ ├── Entropy_QuasiHarmonic_200_Linear.xml │ │ │ │ ├── Entropy_QuasiHarmonic_200_NoLinear.xml │ │ │ │ ├── Entropy_QuasiHarmonic_300_NoLinear.xml │ │ │ │ ├── Entropy_Schlitter_300_Linear.xml │ │ │ │ ├── Entropy_Schlitter_300_NoLinear.xml │ │ │ │ ├── GmxMakeNdx_WritesDefaultProteinIndexGroups.xml │ │ │ │ ├── MindistTest_groupWorks.xml │ │ │ │ ├── MindistTest_matrixWorks.xml │ │ │ │ ├── MindistTest_maxDistWorks.xml │ │ │ │ ├── MindistTest_mindistDoesNotPickUpContacts.xml │ │ │ │ ├── MindistTest_mindistPicksUpContacts.xml │ │ │ │ ├── MindistTest_mindistWorksWithMultipleAtoms.xml │ │ │ │ ├── MindistTest_mindistWorksWithSingleAtoms.xml │ │ │ │ ├── MindistTest_ngWorks.xml │ │ │ │ ├── MindistTest_noPbcWorks.xml │ │ │ │ ├── MindistTest_resPerTimeWorks.xml │ │ │ │ ├── MsdMolTest_diffMolMassWeighted.xml │ │ │ │ ├── MsdMolTest_diffMolNonMassWeighted.xml │ │ │ │ ├── MsdMolTest_diffMolSelected.xml │ │ │ │ ├── MsdTest_oneDimensionalDiffusion.xml │ │ │ │ ├── MsdTest_threeDimensionalDiffusion.xml │ │ │ │ └── MsdTest_twoDimensionalDiffusion.xml │ │ ├── thermochemistry.cpp │ │ └── thermochemistry.h │ ├── gmxlib │ │ ├── CMakeLists.txt │ │ ├── conformation_utilities.cpp │ │ ├── conformation_utilities.h │ │ ├── network.cpp │ │ ├── network.h │ │ ├── nonbonded │ │ │ ├── .clang-tidy │ │ │ ├── CMakeLists.txt │ │ │ ├── nb_free_energy.cpp │ │ │ ├── nb_free_energy.h │ │ │ ├── nb_kernel.h │ │ │ └── nonbonded.h │ │ ├── nrnb.cpp │ │ ├── nrnb.h │ │ └── tests │ │ │ └── CMakeLists.txt │ ├── gmxpreprocess │ │ ├── CMakeLists.txt │ │ ├── add_par.cpp │ │ ├── add_par.h │ │ ├── calch.cpp │ │ ├── calch.h │ │ ├── convparm.cpp │ │ ├── convparm.h │ │ ├── editconf.cpp │ │ ├── editconf.h │ │ ├── fflibutil.cpp │ │ ├── fflibutil.h │ │ ├── gen_ad.cpp │ │ ├── gen_ad.h │ │ ├── gen_maxwell_velocities.cpp │ │ ├── gen_maxwell_velocities.h │ │ ├── gen_vsite.cpp │ │ ├── gen_vsite.h │ │ ├── genconf.cpp │ │ ├── genconf.h │ │ ├── genhydro.cpp │ │ ├── genhydro.h │ │ ├── genion.cpp │ │ ├── genion.h │ │ ├── genrestr.cpp │ │ ├── genrestr.h │ │ ├── gmxcpp.cpp │ │ ├── gmxcpp.h │ │ ├── gpp_atomtype.cpp │ │ ├── gpp_atomtype.h │ │ ├── gpp_bond_atomtype.cpp │ │ ├── gpp_bond_atomtype.h │ │ ├── gpp_nextnb.cpp │ │ ├── gpp_nextnb.h │ │ ├── grompp.cpp │ │ ├── grompp.h │ │ ├── grompp_impl.h │ │ ├── h_db.cpp │ │ ├── h_db.h │ │ ├── hackblock.cpp │ │ ├── hackblock.h │ │ ├── hizzie.cpp │ │ ├── hizzie.h │ │ ├── insert_molecules.cpp │ │ ├── insert_molecules.h │ │ ├── makeexclusiondistances.cpp │ │ ├── makeexclusiondistances.h │ │ ├── nm2type.cpp │ │ ├── nm2type.h │ │ ├── notset.h │ │ ├── pdb2gmx.cpp │ │ ├── pdb2gmx.h │ │ ├── pdb2top.cpp │ │ ├── pdb2top.h │ │ ├── pgutil.cpp │ │ ├── pgutil.h │ │ ├── readir.cpp │ │ ├── readir.h │ │ ├── readpull.cpp │ │ ├── readrot.cpp │ │ ├── resall.cpp │ │ ├── resall.h │ │ ├── solvate.cpp │ │ ├── solvate.h │ │ ├── specbond.cpp │ │ ├── specbond.h │ │ ├── ter_db.cpp │ │ ├── ter_db.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── chainTer.pdb │ │ │ ├── editconf.cpp │ │ │ ├── fragment1.g96 │ │ │ ├── fragment1.gro │ │ │ ├── fragment1.ndx │ │ │ ├── fragment1.pdb │ │ │ ├── fragment2.pdb │ │ │ ├── fragment3.pdb │ │ │ ├── fragment4.pdb │ │ │ ├── genconf.cpp │ │ │ ├── genion.cpp │ │ │ ├── genrestr.cpp │ │ │ ├── gpp_atomtype.cpp │ │ │ ├── gpp_bond_atomtype.cpp │ │ │ ├── insert_molecules.cpp │ │ │ ├── mixed_solvent.gro │ │ │ ├── pdb2gmx.cpp │ │ │ ├── peptide-and-other.pdb │ │ │ ├── peptide-and-water.pdb │ │ │ ├── readir.cpp │ │ │ ├── refdata │ │ │ │ ├── ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ChainChanges_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_4.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_5.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_6.xml │ │ │ │ ├── ChainSep_Pdb2gmxTest_ProducesMatchingTopology_7.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_4.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_5.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_6.xml │ │ │ │ ├── ForAmber99sb_ildn_Pdb2gmxTest_ProducesMatchingTopology_7.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_4.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_5.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_6.xml │ │ │ │ ├── ForCharmm27_Pdb2gmxTest_ProducesMatchingTopology_7.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_10.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_11.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_12.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_13.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_14.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_15.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_4.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_5.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_6.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_7.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_8.xml │ │ │ │ ├── ForGromos43a1_Pdb2gmxTest_ProducesMatchingTopology_9.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_10.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_11.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_12.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_13.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_14.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_15.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_4.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_5.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_6.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_7.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_8.xml │ │ │ │ ├── ForGromos53a6_Pdb2gmxTest_ProducesMatchingTopology_9.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_0.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_1.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_10.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_11.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_12.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_13.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_14.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_15.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_16.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_17.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_18.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_19.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_2.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_20.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_21.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_22.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_23.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_3.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_4.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_5.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_6.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_7.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_8.xml │ │ │ │ ├── ForOplsaa_Pdb2gmxTest_ProducesMatchingTopology_9.xml │ │ │ │ ├── GenRestrTest_SimpleRestraintsGenerated.xml │ │ │ │ ├── GenconfTest_nbox_Works.xml │ │ │ │ ├── GenconfTest_nbox_dist_Works.xml │ │ │ │ ├── GenconfTest_nbox_norenumber_Works.xml │ │ │ │ ├── GenconfTest_nbox_rot_Works.xml │ │ │ │ ├── GenionTest_HighConcentrationIonPlacement.xml │ │ │ │ ├── GenionTest_NoIonPlacement.xml │ │ │ │ ├── GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment.xml │ │ │ │ ├── GetIrTest_AcceptsElectricField.xml │ │ │ │ ├── GetIrTest_AcceptsElectricFieldOscillating.xml │ │ │ │ ├── GetIrTest_AcceptsElectricFieldPulsed.xml │ │ │ │ ├── GetIrTest_AcceptsEmptyLines.xml │ │ │ │ ├── GetIrTest_AcceptsImplicitSolventNo.xml │ │ │ │ ├── GetIrTest_AcceptsKeyWithoutValue.xml │ │ │ │ ├── GetIrTest_AcceptsMimic.xml │ │ │ │ ├── GetIrTest_HandlesDifferentKindsOfMdpLines.xml │ │ │ │ ├── InsertMoleculesTest_InsertsMoleculesIntoEmptyBox.xml │ │ │ │ ├── InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox.xml │ │ │ │ ├── InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration.xml │ │ │ │ ├── InsertMoleculesTest_InsertsMoleculesIntoFixedPositions.xml │ │ │ │ ├── InsertMoleculesTest_InsertsMoleculesWithReplacement.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_0.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_1.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_2.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_3.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_4.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_5.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_6.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_7.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFileUsingIndexGroup_8.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_0.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_1.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_2.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_3.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_4.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_5.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_6.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_7.xml │ │ │ │ ├── SinglePeptideFragments_EditconfTest_ProducesMatchingOutputStructureFile_8.xml │ │ │ │ ├── SolvateTest_cs_box_Works.xml │ │ │ │ ├── SolvateTest_cs_cp_Works.xml │ │ │ │ ├── SolvateTest_cs_cp_p_Works.xml │ │ │ │ ├── SolvateTest_shell_Works.xml │ │ │ │ └── SolvateTest_update_Topology_Works.xml │ │ │ ├── simple.gro │ │ │ ├── simple.top │ │ │ ├── solvate.cpp │ │ │ ├── spc216.gro │ │ │ ├── topdirs.cpp │ │ │ ├── two-fragments.pdb │ │ │ ├── x.gro │ │ │ ├── x0.gro │ │ │ └── x2.gro │ │ ├── tomorse.cpp │ │ ├── tomorse.h │ │ ├── topdirs.cpp │ │ ├── topdirs.h │ │ ├── topio.cpp │ │ ├── topio.h │ │ ├── toppush.cpp │ │ ├── toppush.h │ │ ├── topshake.cpp │ │ ├── topshake.h │ │ ├── toputil.cpp │ │ ├── toputil.h │ │ ├── vsite_parm.cpp │ │ ├── vsite_parm.h │ │ ├── x2top.cpp │ │ ├── x2top.h │ │ ├── xlate.cpp │ │ └── xlate.h │ ├── gpu_utils │ │ ├── CMakeLists.txt │ │ ├── clfftinitializer.cpp │ │ ├── clfftinitializer.h │ │ ├── cuda_arch_utils.cuh │ │ ├── cuda_kernel_utils.cuh │ │ ├── cudautils.cu │ │ ├── cudautils.cuh │ │ ├── device_context.cpp │ │ ├── device_context.h │ │ ├── device_context_ocl.cpp │ │ ├── device_context_sycl.cpp │ │ ├── device_stream.cpp │ │ ├── device_stream.cu │ │ ├── device_stream.h │ │ ├── device_stream_manager.cpp │ │ ├── device_stream_manager.h │ │ ├── device_stream_ocl.cpp │ │ ├── device_stream_sycl.cpp │ │ ├── device_utils.clh │ │ ├── devicebuffer.cuh │ │ ├── devicebuffer.h │ │ ├── devicebuffer_datatype.h │ │ ├── devicebuffer_ocl.h │ │ ├── devicebuffer_sycl.cpp │ │ ├── devicebuffer_sycl.h │ │ ├── gmxopencl.h │ │ ├── gmxsycl.h │ │ ├── gpu_macros.h │ │ ├── gpu_utils.cpp │ │ ├── gpu_utils.cu │ │ ├── gpu_utils.h │ │ ├── gpueventsynchronizer.cuh │ │ ├── gpueventsynchronizer_ocl.h │ │ ├── gpueventsynchronizer_sycl.h │ │ ├── gpuregiontimer.cuh │ │ ├── gpuregiontimer.h │ │ ├── gpuregiontimer_ocl.h │ │ ├── gpuregiontimer_sycl.h │ │ ├── gputraits.cuh │ │ ├── gputraits.h │ │ ├── gputraits_ocl.h │ │ ├── gputraits_sycl.h │ │ ├── hostallocator.cpp │ │ ├── hostallocator.h │ │ ├── ocl_caching.cpp │ │ ├── ocl_caching.h │ │ ├── ocl_compiler.cpp │ │ ├── ocl_compiler.h │ │ ├── oclraii.h │ │ ├── oclutils.cpp │ │ ├── oclutils.h │ │ ├── pinning.cu │ │ ├── pinning.h │ │ ├── pmalloc_cuda.cu │ │ ├── pmalloc_cuda.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── clfftinitializer.cpp │ │ │ ├── device_availability.cpp │ │ │ ├── device_buffer.cpp │ │ │ ├── device_stream_manager.cpp │ │ │ ├── devicetransfers.cpp │ │ │ ├── devicetransfers.cu │ │ │ ├── devicetransfers.h │ │ │ ├── devicetransfers_ocl.cpp │ │ │ ├── devicetransfers_sycl.cpp │ │ │ ├── hostallocator.cpp │ │ │ ├── pinnedmemorychecker.cpp │ │ │ ├── typecasts.cpp │ │ │ ├── typecasts_runner.cpp │ │ │ ├── typecasts_runner.cu │ │ │ └── typecasts_runner.h │ │ ├── typecasts.cuh │ │ ├── vectype_ops.clh │ │ └── vectype_ops.cuh │ ├── gromacs-config-version.cmake.cmakein │ ├── gromacs-config.cmake.cmakein │ ├── gromacs-toolchain.cmake.cmakein │ ├── hardware │ │ ├── CMakeLists.txt │ │ ├── architecture.h │ │ ├── cpuinfo.cpp │ │ ├── cpuinfo.h │ │ ├── detecthardware.cpp │ │ ├── detecthardware.h │ │ ├── device_information.h │ │ ├── device_management.cpp │ │ ├── device_management.cu │ │ ├── device_management.h │ │ ├── device_management_common.cpp │ │ ├── device_management_ocl.cpp │ │ ├── device_management_sycl.cpp │ │ ├── hardwaretopology.cpp │ │ ├── hardwaretopology.h │ │ ├── hw_info.h │ │ ├── identifyavx512fmaunits.cpp │ │ ├── identifyavx512fmaunits.h │ │ ├── printhardware.cpp │ │ ├── printhardware.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── cpuinfo.cpp │ │ │ ├── device_management.cpp │ │ │ └── hardwaretopology.cpp │ ├── imd │ │ ├── CMakeLists.txt │ │ ├── imd.cpp │ │ ├── imd.h │ │ ├── imdsocket.cpp │ │ └── imdsocket.h │ ├── libgromacs.pc.cmakein │ ├── linearalgebra │ │ ├── .clang-tidy │ │ ├── CMakeLists.txt │ │ ├── eigensolver.cpp │ │ ├── eigensolver.h │ │ ├── gmx_arpack.cpp │ │ ├── gmx_arpack.h │ │ ├── gmx_blas.h │ │ ├── gmx_blas │ │ │ ├── blas_copyright │ │ │ ├── dasum.cpp │ │ │ ├── daxpy.cpp │ │ │ ├── dcopy.cpp │ │ │ ├── ddot.cpp │ │ │ ├── dgemm.cpp │ │ │ ├── dgemv.cpp │ │ │ ├── dger.cpp │ │ │ ├── dnrm2.cpp │ │ │ ├── drot.cpp │ │ │ ├── dscal.cpp │ │ │ ├── dswap.cpp │ │ │ ├── dsymv.cpp │ │ │ ├── dsyr2.cpp │ │ │ ├── dsyr2k.cpp │ │ │ ├── dtrmm.cpp │ │ │ ├── dtrmv.cpp │ │ │ ├── dtrsm.cpp │ │ │ ├── idamax.cpp │ │ │ ├── isamax.cpp │ │ │ ├── sasum.cpp │ │ │ ├── saxpy.cpp │ │ │ ├── scopy.cpp │ │ │ ├── sdot.cpp │ │ │ ├── sgemm.cpp │ │ │ ├── sgemv.cpp │ │ │ ├── sger.cpp │ │ │ ├── snrm2.cpp │ │ │ ├── srot.cpp │ │ │ ├── sscal.cpp │ │ │ ├── sswap.cpp │ │ │ ├── ssymv.cpp │ │ │ ├── ssyr2.cpp │ │ │ ├── ssyr2k.cpp │ │ │ ├── strmm.cpp │ │ │ ├── strmv.cpp │ │ │ └── strsm.cpp │ │ ├── gmx_lapack.h │ │ ├── gmx_lapack │ │ │ ├── dbdsdc.cpp │ │ │ ├── dbdsqr.cpp │ │ │ ├── dgebd2.cpp │ │ │ ├── dgebrd.cpp │ │ │ ├── dgelq2.cpp │ │ │ ├── dgelqf.cpp │ │ │ ├── dgeqr2.cpp │ │ │ ├── dgeqrf.cpp │ │ │ ├── dgesdd.cpp │ │ │ ├── dgetf2.cpp │ │ │ ├── dgetrf.cpp │ │ │ ├── dgetri.cpp │ │ │ ├── dgetrs.cpp │ │ │ ├── dlabrd.cpp │ │ │ ├── dlacpy.cpp │ │ │ ├── dlae2.cpp │ │ │ ├── dlaebz.cpp │ │ │ ├── dlaed6.cpp │ │ │ ├── dlaev2.cpp │ │ │ ├── dlagtf.cpp │ │ │ ├── dlagts.cpp │ │ │ ├── dlamrg.cpp │ │ │ ├── dlange.cpp │ │ │ ├── dlanst.cpp │ │ │ ├── dlansy.cpp │ │ │ ├── dlapy2.cpp │ │ │ ├── dlar1vx.cpp │ │ │ ├── dlarf.cpp │ │ │ ├── dlarfb.cpp │ │ │ ├── dlarfg.cpp │ │ │ ├── dlarft.cpp │ │ │ ├── dlarnv.cpp │ │ │ ├── dlarrbx.cpp │ │ │ ├── dlarrex.cpp │ │ │ ├── dlarrfx.cpp │ │ │ ├── dlarrvx.cpp │ │ │ ├── dlartg.cpp │ │ │ ├── dlaruv.cpp │ │ │ ├── dlas2.cpp │ │ │ ├── dlascl.cpp │ │ │ ├── dlasd0.cpp │ │ │ ├── dlasd1.cpp │ │ │ ├── dlasd2.cpp │ │ │ ├── dlasd3.cpp │ │ │ ├── dlasd4.cpp │ │ │ ├── dlasd5.cpp │ │ │ ├── dlasd6.cpp │ │ │ ├── dlasd7.cpp │ │ │ ├── dlasd8.cpp │ │ │ ├── dlasda.cpp │ │ │ ├── dlasdq.cpp │ │ │ ├── dlasdt.cpp │ │ │ ├── dlaset.cpp │ │ │ ├── dlasq1.cpp │ │ │ ├── dlasq2.cpp │ │ │ ├── dlasq3.cpp │ │ │ ├── dlasq4.cpp │ │ │ ├── dlasq5.cpp │ │ │ ├── dlasq6.cpp │ │ │ ├── dlasr.cpp │ │ │ ├── dlasrt.cpp │ │ │ ├── dlasrt2.cpp │ │ │ ├── dlassq.cpp │ │ │ ├── dlasv2.cpp │ │ │ ├── dlaswp.cpp │ │ │ ├── dlatrd.cpp │ │ │ ├── dorg2r.cpp │ │ │ ├── dorgbr.cpp │ │ │ ├── dorgl2.cpp │ │ │ ├── dorglq.cpp │ │ │ ├── dorgqr.cpp │ │ │ ├── dorm2l.cpp │ │ │ ├── dorm2r.cpp │ │ │ ├── dormbr.cpp │ │ │ ├── dorml2.cpp │ │ │ ├── dormlq.cpp │ │ │ ├── dormql.cpp │ │ │ ├── dormqr.cpp │ │ │ ├── dormtr.cpp │ │ │ ├── dstebz.cpp │ │ │ ├── dstegr.cpp │ │ │ ├── dstein.cpp │ │ │ ├── dsteqr.cpp │ │ │ ├── dsterf.cpp │ │ │ ├── dstevr.cpp │ │ │ ├── dsyevr.cpp │ │ │ ├── dsytd2.cpp │ │ │ ├── dsytrd.cpp │ │ │ ├── dtrti2.cpp │ │ │ ├── dtrtri.cpp │ │ │ ├── ilasrt2.cpp │ │ │ ├── lapack_copyright │ │ │ ├── lapack_limits.h │ │ │ ├── sbdsdc.cpp │ │ │ ├── sbdsqr.cpp │ │ │ ├── sgebd2.cpp │ │ │ ├── sgebrd.cpp │ │ │ ├── sgelq2.cpp │ │ │ ├── sgelqf.cpp │ │ │ ├── sgeqr2.cpp │ │ │ ├── sgeqrf.cpp │ │ │ ├── sgesdd.cpp │ │ │ ├── sgetf2.cpp │ │ │ ├── sgetrf.cpp │ │ │ ├── sgetri.cpp │ │ │ ├── sgetrs.cpp │ │ │ ├── slabrd.cpp │ │ │ ├── slacpy.cpp │ │ │ ├── slae2.cpp │ │ │ ├── slaebz.cpp │ │ │ ├── slaed6.cpp │ │ │ ├── slaev2.cpp │ │ │ ├── slagtf.cpp │ │ │ ├── slagts.cpp │ │ │ ├── slamrg.cpp │ │ │ ├── slange.cpp │ │ │ ├── slanst.cpp │ │ │ ├── slansy.cpp │ │ │ ├── slapy2.cpp │ │ │ ├── slar1vx.cpp │ │ │ ├── slarf.cpp │ │ │ ├── slarfb.cpp │ │ │ ├── slarfg.cpp │ │ │ ├── slarft.cpp │ │ │ ├── slarnv.cpp │ │ │ ├── slarrbx.cpp │ │ │ ├── slarrex.cpp │ │ │ ├── slarrfx.cpp │ │ │ ├── slarrvx.cpp │ │ │ ├── slartg.cpp │ │ │ ├── slaruv.cpp │ │ │ ├── slas2.cpp │ │ │ ├── slascl.cpp │ │ │ ├── slasd0.cpp │ │ │ ├── slasd1.cpp │ │ │ ├── slasd2.cpp │ │ │ ├── slasd3.cpp │ │ │ ├── slasd4.cpp │ │ │ ├── slasd5.cpp │ │ │ ├── slasd6.cpp │ │ │ ├── slasd7.cpp │ │ │ ├── slasd8.cpp │ │ │ ├── slasda.cpp │ │ │ ├── slasdq.cpp │ │ │ ├── slasdt.cpp │ │ │ ├── slaset.cpp │ │ │ ├── slasq1.cpp │ │ │ ├── slasq2.cpp │ │ │ ├── slasq3.cpp │ │ │ ├── slasq4.cpp │ │ │ ├── slasq5.cpp │ │ │ ├── slasq6.cpp │ │ │ ├── slasr.cpp │ │ │ ├── slasrt.cpp │ │ │ ├── slasrt2.cpp │ │ │ ├── slassq.cpp │ │ │ ├── slasv2.cpp │ │ │ ├── slaswp.cpp │ │ │ ├── slatrd.cpp │ │ │ ├── sorg2r.cpp │ │ │ ├── sorgbr.cpp │ │ │ ├── sorgl2.cpp │ │ │ ├── sorglq.cpp │ │ │ ├── sorgqr.cpp │ │ │ ├── sorm2l.cpp │ │ │ ├── sorm2r.cpp │ │ │ ├── sormbr.cpp │ │ │ ├── sorml2.cpp │ │ │ ├── sormlq.cpp │ │ │ ├── sormql.cpp │ │ │ ├── sormqr.cpp │ │ │ ├── sormtr.cpp │ │ │ ├── sstebz.cpp │ │ │ ├── sstegr.cpp │ │ │ ├── sstein.cpp │ │ │ ├── ssteqr.cpp │ │ │ ├── ssterf.cpp │ │ │ ├── sstevr.cpp │ │ │ ├── ssyevr.cpp │ │ │ ├── ssytd2.cpp │ │ │ ├── ssytrd.cpp │ │ │ ├── strti2.cpp │ │ │ └── strtri.cpp │ │ ├── matrix.cpp │ │ ├── matrix.h │ │ ├── nrjac.cpp │ │ ├── nrjac.h │ │ ├── sparsematrix.cpp │ │ └── sparsematrix.h │ ├── listed_forces │ │ ├── CMakeLists.txt │ │ ├── bonded.cpp │ │ ├── bonded.h │ │ ├── disre.cpp │ │ ├── disre.h │ │ ├── gpubonded.h │ │ ├── gpubonded_impl.cpp │ │ ├── gpubonded_impl.cu │ │ ├── gpubonded_impl.h │ │ ├── gpubondedkernels.cu │ │ ├── listed_forces.cpp │ │ ├── listed_forces.h │ │ ├── listed_internal.cpp │ │ ├── listed_internal.h │ │ ├── manage_threading.cpp │ │ ├── manage_threading.h │ │ ├── orires.cpp │ │ ├── orires.h │ │ ├── pairs.cpp │ │ ├── pairs.h │ │ ├── position_restraints.cpp │ │ ├── position_restraints.h │ │ ├── restcbt.cpp │ │ ├── restcbt.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── bonded.cpp │ │ │ └── refdata │ │ │ │ ├── AngleZero_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── AngleZero_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── AngleZero_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_10.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_11.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_12.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_13.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_14.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_15.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_16.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_17.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_18.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_19.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_20.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_21.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_22.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_23.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_24.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_25.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_26.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_27.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_28.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_29.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_3.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_30.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_31.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_32.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_33.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_34.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_35.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_36.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_37.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_38.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_39.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_4.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_40.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_41.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_42.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_43.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_44.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_45.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_46.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_47.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_48.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_49.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_5.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_50.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_51.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_52.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_53.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_54.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_55.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_56.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_57.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_58.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_59.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_6.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_60.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_61.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_62.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_63.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_64.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_65.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_66.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_67.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_68.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_69.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_7.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_70.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_71.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_72.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_73.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_74.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_75.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_76.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_77.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_78.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_79.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_8.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_80.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_81.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_82.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_83.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_84.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_85.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_86.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_87.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_88.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_89.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_9.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_90.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_91.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_92.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_93.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_94.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_95.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_96.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_97.xml │ │ │ │ ├── Angle_ListedForcesTest_Ifunc_98.xml │ │ │ │ ├── BondZeroLength_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── BondZeroLength_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── BondZeroLength_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_10.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_11.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_12.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_13.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_14.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_15.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_16.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_17.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_18.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_19.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_20.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_21.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_22.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_23.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_24.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_25.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_26.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_27.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_28.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_29.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_3.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_30.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_31.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_32.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_33.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_34.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_35.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_36.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_37.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_38.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_39.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_4.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_40.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_41.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_42.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_43.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_44.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_45.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_46.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_47.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_48.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_49.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_5.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_50.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_51.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_52.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_53.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_54.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_55.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_56.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_57.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_58.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_59.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_6.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_60.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_61.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_62.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_63.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_64.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_65.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_66.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_67.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_68.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_69.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_7.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_70.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_71.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_8.xml │ │ │ │ ├── Bond_ListedForcesTest_Ifunc_9.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_10.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_11.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_12.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_13.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_14.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_15.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_16.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_17.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_18.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_19.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_20.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_21.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_22.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_23.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_24.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_25.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_26.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_27.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_28.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_29.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_3.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_30.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_31.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_32.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_33.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_34.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_35.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_36.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_37.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_38.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_39.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_4.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_40.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_41.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_42.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_43.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_44.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_45.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_46.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_47.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_48.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_49.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_5.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_50.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_51.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_52.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_53.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_6.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_7.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_8.xml │ │ │ │ ├── Dihedral_ListedForcesTest_Ifunc_9.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_10.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_11.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_12.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_13.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_14.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_15.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_16.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_17.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_18.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_19.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_20.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_21.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_22.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_23.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_24.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_25.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_26.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_27.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_28.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_29.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_3.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_30.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_31.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_32.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_33.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_34.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_35.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_4.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_5.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_6.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_7.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_8.xml │ │ │ │ ├── Polarize_ListedForcesTest_Ifunc_9.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_0.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_1.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_10.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_11.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_12.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_13.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_14.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_15.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_16.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_17.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_18.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_19.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_2.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_20.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_21.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_22.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_23.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_24.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_25.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_26.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_27.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_28.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_29.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_3.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_30.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_31.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_32.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_33.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_34.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_35.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_36.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_37.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_38.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_39.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_4.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_40.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_41.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_42.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_43.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_44.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_45.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_46.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_47.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_48.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_49.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_5.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_50.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_51.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_52.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_53.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_6.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_7.xml │ │ │ │ ├── Restraints_ListedForcesTest_Ifunc_8.xml │ │ │ │ └── Restraints_ListedForcesTest_Ifunc_9.xml │ │ └── utilities.h │ ├── math │ │ ├── 3dtransforms.cpp │ │ ├── 3dtransforms.h │ │ ├── CMakeLists.txt │ │ ├── arrayrefwithpadding.h │ │ ├── coordinatetransformation.cpp │ │ ├── coordinatetransformation.h │ │ ├── densityfit.cpp │ │ ├── densityfit.h │ │ ├── densityfittingforce.cpp │ │ ├── densityfittingforce.h │ │ ├── do_fit.cpp │ │ ├── do_fit.h │ │ ├── exponentialmovingaverage.cpp │ │ ├── exponentialmovingaverage.h │ │ ├── functions.cpp │ │ ├── functions.h │ │ ├── gausstransform.cpp │ │ ├── gausstransform.h │ │ ├── gmxcomplex.h │ │ ├── invertmatrix.cpp │ │ ├── invertmatrix.h │ │ ├── matrix.cpp │ │ ├── matrix.h │ │ ├── multidimarray.h │ │ ├── neldermead.cpp │ │ ├── neldermead.h │ │ ├── optimization.cpp │ │ ├── optimization.h │ │ ├── paddedvector.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── arrayrefwithpadding.cpp │ │ │ ├── coordinatetransformation.cpp │ │ │ ├── densityfit.cpp │ │ │ ├── densityfittingforce.cpp │ │ │ ├── dofit.cpp │ │ │ ├── exponentialmovingaverage.cpp │ │ │ ├── functions.cpp │ │ │ ├── gausstransform.cpp │ │ │ ├── invertmatrix.cpp │ │ │ ├── matrix.cpp │ │ │ ├── multidimarray.cpp │ │ │ ├── neldermead.cpp │ │ │ ├── optimization.cpp │ │ │ ├── paddedvector.cpp │ │ │ ├── refdata │ │ │ │ ├── DensitySimilarityTest_CrossCorrelationGradientIsCorrect.xml │ │ │ │ ├── DensitySimilarityTest_RelativeEntropyGradientIsCorrect.xml │ │ │ │ ├── FunctionTest_ErfInvDouble.xml │ │ │ │ ├── FunctionTest_ErfInvFloat.xml │ │ │ │ ├── FunctionTest_FastsqrtDouble.xml │ │ │ │ ├── FunctionTest_FastsqrtFloat.xml │ │ │ │ ├── FunctionTest_FastsqrtInteger.xml │ │ │ │ ├── FunctionTest_InvcbrtDouble.xml │ │ │ │ ├── FunctionTest_InvcbrtFloat.xml │ │ │ │ ├── FunctionTest_InvcbrtInteger.xml │ │ │ │ ├── FunctionTest_InvsixthrootDouble.xml │ │ │ │ ├── FunctionTest_InvsixthrootFloat.xml │ │ │ │ ├── FunctionTest_InvsixthrootInteger.xml │ │ │ │ ├── FunctionTest_InvsqrtDouble.xml │ │ │ │ ├── FunctionTest_InvsqrtFloat.xml │ │ │ │ ├── FunctionTest_InvsqrtInteger.xml │ │ │ │ ├── FunctionTest_Log2I32Bit.xml │ │ │ │ ├── FunctionTest_Log2I64Bit.xml │ │ │ │ ├── FunctionTest_SixthrootDouble.xml │ │ │ │ ├── FunctionTest_SixthrootFloat.xml │ │ │ │ ├── FunctionTest_SixthrootInteger.xml │ │ │ │ └── FunctionTest_StaticLog2.xml │ │ │ ├── testarrayrefs.h │ │ │ └── vectypes.cpp │ │ ├── units.cpp │ │ ├── units.h │ │ ├── utilities.cpp │ │ ├── utilities.h │ │ ├── vec.h │ │ ├── veccompare.cpp │ │ ├── veccompare.h │ │ ├── vecdump.cpp │ │ ├── vecdump.h │ │ └── vectypes.h │ ├── mdlib │ │ ├── CMakeLists.txt │ │ ├── boxdeformation.cpp │ │ ├── boxdeformation.h │ │ ├── broadcaststructs.cpp │ │ ├── broadcaststructs.h │ │ ├── calc_verletbuf.cpp │ │ ├── calc_verletbuf.h │ │ ├── calcmu.cpp │ │ ├── calcmu.h │ │ ├── calcvir.cpp │ │ ├── calcvir.h │ │ ├── checkpointhandler.cpp │ │ ├── checkpointhandler.h │ │ ├── compute_io.cpp │ │ ├── compute_io.h │ │ ├── constr.cpp │ │ ├── constr.h │ │ ├── constraintrange.cpp │ │ ├── constraintrange.h │ │ ├── coupling.cpp │ │ ├── coupling.h │ │ ├── dispersioncorrection.cpp │ │ ├── dispersioncorrection.h │ │ ├── ebin.cpp │ │ ├── ebin.h │ │ ├── enerdata_utils.cpp │ │ ├── enerdata_utils.h │ │ ├── energyoutput.cpp │ │ ├── energyoutput.h │ │ ├── expanded.cpp │ │ ├── expanded.h │ │ ├── force.cpp │ │ ├── force.h │ │ ├── force_flags.h │ │ ├── forcerec.cpp │ │ ├── forcerec.h │ │ ├── forcerec_threading.h │ │ ├── freeenergyparameters.cpp │ │ ├── freeenergyparameters.h │ │ ├── gmx_omp_nthreads.cpp │ │ ├── gmx_omp_nthreads.h │ │ ├── gpuforcereduction.h │ │ ├── gpuforcereduction_impl.cpp │ │ ├── gpuforcereduction_impl.cu │ │ ├── gpuforcereduction_impl.cuh │ │ ├── groupcoord.cpp │ │ ├── groupcoord.h │ │ ├── leapfrog_gpu.cu │ │ ├── leapfrog_gpu.h │ │ ├── lincs.cpp │ │ ├── lincs.h │ │ ├── lincs_gpu.cu │ │ ├── lincs_gpu.cuh │ │ ├── makeconstraints.h │ │ ├── md_support.cpp │ │ ├── md_support.h │ │ ├── mdatoms.cpp │ │ ├── mdatoms.h │ │ ├── mdebin_bar.cpp │ │ ├── mdebin_bar.h │ │ ├── mdoutf.cpp │ │ ├── mdoutf.h │ │ ├── membed.cpp │ │ ├── membed.h │ │ ├── nsgrid.cpp │ │ ├── nsgrid.h │ │ ├── perf_est.cpp │ │ ├── perf_est.h │ │ ├── rbin.cpp │ │ ├── rbin.h │ │ ├── resethandler.cpp │ │ ├── resethandler.h │ │ ├── rf_util.cpp │ │ ├── rf_util.h │ │ ├── settle.cpp │ │ ├── settle.h │ │ ├── settle_gpu.cu │ │ ├── settle_gpu.cuh │ │ ├── shake.cpp │ │ ├── shake.h │ │ ├── sighandler.cpp │ │ ├── sighandler.h │ │ ├── sim_util.cpp │ │ ├── simulationsignal.cpp │ │ ├── simulationsignal.h │ │ ├── splitter.cpp │ │ ├── splitter.h │ │ ├── stat.cpp │ │ ├── stat.h │ │ ├── stophandler.cpp │ │ ├── stophandler.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── calc_verletbuf.cpp │ │ │ ├── constr.cpp │ │ │ ├── constrtestdata.cpp │ │ │ ├── constrtestdata.h │ │ │ ├── constrtestrunners.cpp │ │ │ ├── constrtestrunners.cu │ │ │ ├── constrtestrunners.h │ │ │ ├── ebin.cpp │ │ │ ├── energyoutput.cpp │ │ │ ├── freeenergyparameters.cpp │ │ │ ├── leapfrog.cpp │ │ │ ├── leapfrogtestdata.cpp │ │ │ ├── leapfrogtestdata.h │ │ │ ├── leapfrogtestrunners.cpp │ │ │ ├── leapfrogtestrunners.h │ │ │ ├── leapfrogtestrunners_gpu.cpp │ │ │ ├── refdata │ │ │ │ ├── PrEbinTest_HandlesAverages.xml │ │ │ │ ├── PrEbinTest_HandlesEmptyAverages.xml │ │ │ │ ├── UpdateGroupsCog_ComputesCogs.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_0.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_1.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_10.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_11.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_2.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_3.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_4.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_5.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_6.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_7.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_8.xml │ │ │ │ ├── WithParameters_EnergyOutputTest_CheckOutput_9.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_0.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_1.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_10.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_11.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_12.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_13.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_14.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_15.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_2.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_3.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_4.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_5.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_6.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_7.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_8.xml │ │ │ │ ├── WithParameters_LeapFrogTest_SimpleIntegration_9.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_0.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_1.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_10.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_11.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_12.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_2.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_3.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_4.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_5.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_6.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_7.xml │ │ │ │ ├── WithParameters_SettleTest_SatisfiesConstraints_8.xml │ │ │ │ └── WithParameters_SettleTest_SatisfiesConstraints_9.xml │ │ │ ├── settle.cpp │ │ │ ├── settletestdata.cpp │ │ │ ├── settletestdata.h │ │ │ ├── settletestrunners.cpp │ │ │ ├── settletestrunners.cu │ │ │ ├── settletestrunners.h │ │ │ ├── shake.cpp │ │ │ ├── simulationsignal.cpp │ │ │ ├── updategroups.cpp │ │ │ ├── updategroupscog.cpp │ │ │ └── watersystem.h │ │ ├── tgroup.cpp │ │ ├── tgroup.h │ │ ├── trajectory_writing.cpp │ │ ├── trajectory_writing.h │ │ ├── update.cpp │ │ ├── update.h │ │ ├── update_constrain_gpu.h │ │ ├── update_constrain_gpu_impl.cpp │ │ ├── update_constrain_gpu_impl.cu │ │ ├── update_constrain_gpu_impl.h │ │ ├── updategroups.cpp │ │ ├── updategroups.h │ │ ├── updategroupscog.cpp │ │ ├── updategroupscog.h │ │ ├── vcm.cpp │ │ ├── vcm.h │ │ ├── vsite.cpp │ │ ├── vsite.h │ │ ├── wall.cpp │ │ ├── wall.h │ │ ├── wholemoleculetransform.cpp │ │ └── wholemoleculetransform.h │ ├── mdrun │ │ ├── CMakeLists.txt │ │ ├── isimulator.h │ │ ├── legacymdrunoptions.cpp │ │ ├── legacymdrunoptions.h │ │ ├── legacysimulator.cpp │ │ ├── legacysimulator.h │ │ ├── md.cpp │ │ ├── mdmodules.cpp │ │ ├── mdmodules.h │ │ ├── membedholder.cpp │ │ ├── membedholder.h │ │ ├── mimic.cpp │ │ ├── minimize.cpp │ │ ├── minimize.h │ │ ├── replicaexchange.cpp │ │ ├── replicaexchange.h │ │ ├── rerun.cpp │ │ ├── runner.cpp │ │ ├── runner.h │ │ ├── shellfc.cpp │ │ ├── shellfc.h │ │ ├── simulationcontext.cpp │ │ ├── simulationcontext.h │ │ ├── simulationinput.cpp │ │ ├── simulationinput.h │ │ ├── simulationinputhandle.cpp │ │ ├── simulationinputhandle.h │ │ ├── simulatorbuilder.cpp │ │ ├── simulatorbuilder.h │ │ └── tpi.cpp │ ├── mdrunutility │ │ ├── CMakeLists.txt │ │ ├── handlerestart.cpp │ │ ├── handlerestart.h │ │ ├── logging.cpp │ │ ├── logging.h │ │ ├── multisim.cpp │ │ ├── multisim.h │ │ ├── printtime.cpp │ │ ├── printtime.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── threadaffinity.cpp │ │ │ ├── threadaffinity_mpi.cpp │ │ │ ├── threadaffinitytest.cpp │ │ │ └── threadaffinitytest.h │ │ ├── threadaffinity.cpp │ │ └── threadaffinity.h │ ├── mdspan │ │ ├── CMakeLists.txt │ │ ├── README │ │ ├── accessor_policy.h │ │ ├── extensions.h │ │ ├── extents.h │ │ ├── layouts.h │ │ ├── mdspan.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── accessor_policy.cpp │ │ │ ├── extensions.cpp │ │ │ ├── extents.cpp │ │ │ ├── layouts.cpp │ │ │ └── mdspan.cpp │ ├── mdtypes │ │ ├── CMakeLists.txt │ │ ├── awh_correlation_history.h │ │ ├── awh_history.h │ │ ├── awh_params.h │ │ ├── checkpointdata.cpp │ │ ├── checkpointdata.h │ │ ├── commrec.h │ │ ├── df_history.cpp │ │ ├── df_history.h │ │ ├── edsamhistory.h │ │ ├── enerdata.h │ │ ├── energyhistory.cpp │ │ ├── energyhistory.h │ │ ├── fcdata.h │ │ ├── forcebuffers.cpp │ │ ├── forcebuffers.h │ │ ├── forceoutput.h │ │ ├── forcerec.h │ │ ├── group.cpp │ │ ├── group.h │ │ ├── iforceprovider.cpp │ │ ├── iforceprovider.h │ │ ├── imdmodule.h │ │ ├── imdoutputprovider.h │ │ ├── imdpoptionprovider.h │ │ ├── inputrec.cpp │ │ ├── inputrec.h │ │ ├── interaction_const.cpp │ │ ├── interaction_const.h │ │ ├── locality.h │ │ ├── md_enums.cpp │ │ ├── md_enums.h │ │ ├── mdatom.h │ │ ├── mdrunoptions.h │ │ ├── multipletimestepping.cpp │ │ ├── multipletimestepping.h │ │ ├── nblist.h │ │ ├── observableshistory.cpp │ │ ├── observableshistory.h │ │ ├── pull_params.h │ │ ├── pullhistory.h │ │ ├── simulation_workload.h │ │ ├── state.cpp │ │ ├── state.h │ │ ├── state_propagator_data_gpu.h │ │ ├── state_propagator_data_gpu_impl.cpp │ │ ├── state_propagator_data_gpu_impl.h │ │ ├── state_propagator_data_gpu_impl_gpu.cpp │ │ ├── swaphistory.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── checkpointdata.cpp │ │ │ └── forcebuffers.cpp │ ├── mimic │ │ ├── CMakeLists.txt │ │ ├── communicator.cpp │ │ ├── communicator.h │ │ ├── utilities.cpp │ │ └── utilities.h │ ├── modularsimulator │ │ ├── CMakeLists.txt │ │ ├── checkpointhelper.cpp │ │ ├── checkpointhelper.h │ │ ├── compositesimulatorelement.cpp │ │ ├── compositesimulatorelement.h │ │ ├── computeglobalselement.cpp │ │ ├── computeglobalselement.h │ │ ├── constraintelement.cpp │ │ ├── constraintelement.h │ │ ├── domdechelper.cpp │ │ ├── domdechelper.h │ │ ├── energydata.cpp │ │ ├── energydata.h │ │ ├── forceelement.cpp │ │ ├── forceelement.h │ │ ├── freeenergyperturbationdata.cpp │ │ ├── freeenergyperturbationdata.h │ │ ├── modularsimulator.cpp │ │ ├── modularsimulator.h │ │ ├── modularsimulatorinterfaces.h │ │ ├── parrinellorahmanbarostat.cpp │ │ ├── parrinellorahmanbarostat.h │ │ ├── pmeloadbalancehelper.cpp │ │ ├── pmeloadbalancehelper.h │ │ ├── propagator.cpp │ │ ├── propagator.h │ │ ├── signallers.cpp │ │ ├── signallers.h │ │ ├── simulatoralgorithm.cpp │ │ ├── simulatoralgorithm.h │ │ ├── statepropagatordata.cpp │ │ ├── statepropagatordata.h │ │ ├── topologyholder.cpp │ │ ├── topologyholder.h │ │ ├── trajectoryelement.cpp │ │ ├── trajectoryelement.h │ │ ├── velocityscalingtemperaturecoupling.cpp │ │ └── velocityscalingtemperaturecoupling.h │ ├── nbnxm │ │ ├── CMakeLists.txt │ │ ├── atomdata.cpp │ │ ├── atomdata.h │ │ ├── benchmark │ │ │ ├── bench_coords.h │ │ │ ├── bench_setup.cpp │ │ │ ├── bench_setup.h │ │ │ ├── bench_system.cpp │ │ │ └── bench_system.h │ │ ├── boundingboxes.h │ │ ├── clusterdistancekerneltype.h │ │ ├── cuda │ │ │ ├── CMakeLists.txt │ │ │ ├── nbnxm_buffer_ops_kernels.cuh │ │ │ ├── nbnxm_cuda.cu │ │ │ ├── nbnxm_cuda.h │ │ │ ├── nbnxm_cuda_data_mgmt.cu │ │ │ ├── nbnxm_cuda_kernel.cuh │ │ │ ├── nbnxm_cuda_kernel_F_noprune.cu │ │ │ ├── nbnxm_cuda_kernel_F_prune.cu │ │ │ ├── nbnxm_cuda_kernel_VF_noprune.cu │ │ │ ├── nbnxm_cuda_kernel_VF_prune.cu │ │ │ ├── nbnxm_cuda_kernel_pruneonly.cu │ │ │ ├── nbnxm_cuda_kernel_pruneonly.cuh │ │ │ ├── nbnxm_cuda_kernel_utils.cuh │ │ │ ├── nbnxm_cuda_kernels.cuh │ │ │ └── nbnxm_cuda_types.h │ │ ├── gpu_common.h │ │ ├── gpu_common_utils.h │ │ ├── gpu_data_mgmt.h │ │ ├── gpu_jit_support.h │ │ ├── gpu_types_common.h │ │ ├── grid.cpp │ │ ├── grid.h │ │ ├── gridset.cpp │ │ ├── gridset.h │ │ ├── gridsetdata.h │ │ ├── kernel_common.cpp │ │ ├── kernel_common.h │ │ ├── kernel_file_generator │ │ │ ├── kernel_simd_2xmm_kernel.cpp.pre │ │ │ ├── kernel_simd_4xm_kernel.cpp.pre │ │ │ ├── kernel_simd_template.h.pre │ │ │ └── make_verlet_simd_kernel_files.py │ │ ├── kerneldispatch.cpp │ │ ├── kernels_reference │ │ │ ├── kernel_gpu_ref.cpp │ │ │ ├── kernel_gpu_ref.h │ │ │ ├── kernel_ref.cpp │ │ │ ├── kernel_ref.h │ │ │ ├── kernel_ref_includes.h │ │ │ ├── kernel_ref_inner.h │ │ │ ├── kernel_ref_outer.h │ │ │ ├── kernel_ref_prune.cpp │ │ │ └── kernel_ref_prune.h │ │ ├── kernels_simd_2xmm │ │ │ ├── CMakeLists.txt │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJ_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJ_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJ_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJ_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJ_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_common.h │ │ │ ├── kernel_inner.h │ │ │ ├── kernel_outer.h │ │ │ ├── kernel_prune.cpp │ │ │ ├── kernel_prune.h │ │ │ └── kernels.h │ │ ├── kernels_simd_4xm │ │ │ ├── CMakeLists.txt │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJ_F.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecEw_VdwLJ_F.cpp │ │ │ ├── kernel_ElecEw_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecEw_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJ_F.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJ_F.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecQSTab_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombGeom_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombGeom_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombLB_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombLB_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJCombLB_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJEwCombGeom_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJEwCombGeom_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJFSw_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJFSw_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJFSw_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJPSw_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJPSw_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJPSw_VgrpF.cpp │ │ │ ├── kernel_ElecRF_VdwLJ_F.cpp │ │ │ ├── kernel_ElecRF_VdwLJ_VF.cpp │ │ │ ├── kernel_ElecRF_VdwLJ_VgrpF.cpp │ │ │ ├── kernel_common.h │ │ │ ├── kernel_inner.h │ │ │ ├── kernel_outer.h │ │ │ ├── kernel_prune.cpp │ │ │ ├── kernel_prune.h │ │ │ └── kernels.h │ │ ├── nbnxm.cpp │ │ ├── nbnxm.h │ │ ├── nbnxm_geometry.cpp │ │ ├── nbnxm_geometry.h │ │ ├── nbnxm_gpu.h │ │ ├── nbnxm_gpu_data_mgmt.cpp │ │ ├── nbnxm_gpu_data_mgmt.h │ │ ├── nbnxm_setup.cpp │ │ ├── nbnxm_simd.h │ │ ├── opencl │ │ │ ├── CMakeLists.txt │ │ │ ├── nbnxm_ocl.cpp │ │ │ ├── nbnxm_ocl_consts.h │ │ │ ├── nbnxm_ocl_data_mgmt.cpp │ │ │ ├── nbnxm_ocl_jit_support.cpp │ │ │ ├── nbnxm_ocl_kernel.clh │ │ │ ├── nbnxm_ocl_kernel_pruneonly.clh │ │ │ ├── nbnxm_ocl_kernel_utils.clh │ │ │ ├── nbnxm_ocl_kernels.cl │ │ │ ├── nbnxm_ocl_kernels.clh │ │ │ ├── nbnxm_ocl_kernels_fastgen.clh │ │ │ ├── nbnxm_ocl_kernels_fastgen_add_twincut.clh │ │ │ └── nbnxm_ocl_types.h │ │ ├── pairlist.cpp │ │ ├── pairlist.h │ │ ├── pairlist_simd_2xmm.h │ │ ├── pairlist_simd_4xm.h │ │ ├── pairlist_tuning.cpp │ │ ├── pairlist_tuning.h │ │ ├── pairlistparams.cpp │ │ ├── pairlistparams.h │ │ ├── pairlistset.cpp │ │ ├── pairlistset.h │ │ ├── pairlistsets.h │ │ ├── pairlistwork.h │ │ ├── pairsearch.cpp │ │ ├── pairsearch.h │ │ └── prunekerneldispatch.cpp │ ├── onlinehelp │ │ ├── CMakeLists.txt │ │ ├── helpformat.cpp │ │ ├── helpformat.h │ │ ├── helpmanager.cpp │ │ ├── helpmanager.h │ │ ├── helptopic.cpp │ │ ├── helptopic.h │ │ ├── helpwritercontext.cpp │ │ ├── helpwritercontext.h │ │ ├── ihelptopic.h │ │ ├── rstparser.cpp │ │ ├── rstparser.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── helpformat.cpp │ │ │ ├── helpmanager.cpp │ │ │ ├── helpwritercontext.cpp │ │ │ ├── mock_helptopic.cpp │ │ │ ├── mock_helptopic.h │ │ │ └── refdata │ │ │ ├── HelpTopicFormattingTest_FormatsCompositeTopicWithSubTopics.xml │ │ │ ├── HelpTopicFormattingTest_FormatsSimpleTopic.xml │ │ │ ├── HelpWriterContextTest_CleansUpExtraWhitespace.xml │ │ │ ├── HelpWriterContextTest_FormatsBulletList.xml │ │ │ ├── HelpWriterContextTest_FormatsEnumeratedList.xml │ │ │ ├── HelpWriterContextTest_FormatsGridTable.xml │ │ │ ├── HelpWriterContextTest_FormatsLiteralText.xml │ │ │ ├── HelpWriterContextTest_FormatsLiteralTextAtBeginning.xml │ │ │ ├── HelpWriterContextTest_FormatsLiteralTextWithIndentation.xml │ │ │ ├── HelpWriterContextTest_FormatsParagraphs.xml │ │ │ ├── HelpWriterContextTest_FormatsRstStyleParagraphs.xml │ │ │ ├── HelpWriterContextTest_FormatsSimpleTable.xml │ │ │ ├── HelpWriterContextTest_FormatsTitles.xml │ │ │ ├── TextTableFormatterTest_HandlesBasicCase.xml │ │ │ ├── TextTableFormatterTest_HandlesEmptyColumnTitles.xml │ │ │ ├── TextTableFormatterTest_HandlesEmptyColumns.xml │ │ │ ├── TextTableFormatterTest_HandlesIndentation.xml │ │ │ ├── TextTableFormatterTest_HandlesLastColumnFolding.xml │ │ │ └── TextTableFormatterTest_HandlesOverflowingLines.xml │ ├── onlinehelp_doc.h │ ├── options.h │ ├── options │ │ ├── .clang-tidy │ │ ├── CMakeLists.txt │ │ ├── abstractoption.cpp │ │ ├── abstractoption.h │ │ ├── abstractoptionstorage.h │ │ ├── abstractsection.cpp │ │ ├── abstractsection.h │ │ ├── basicoptions.cpp │ │ ├── basicoptions.h │ │ ├── basicoptionstorage.h │ │ ├── behaviorcollection.cpp │ │ ├── behaviorcollection.h │ │ ├── filenameoption.cpp │ │ ├── filenameoption.h │ │ ├── filenameoptionmanager.cpp │ │ ├── filenameoptionmanager.h │ │ ├── filenameoptionstorage.h │ │ ├── ioptionsbehavior.h │ │ ├── ioptionscontainer.h │ │ ├── ioptionscontainerwithsections.h │ │ ├── isectionstorage.h │ │ ├── ivaluestore.h │ │ ├── optionfiletype.h │ │ ├── optionflags.h │ │ ├── optionmanagercontainer.h │ │ ├── options.cpp │ │ ├── options.h │ │ ├── options_impl.h │ │ ├── optionsassigner.cpp │ │ ├── optionsassigner.h │ │ ├── optionsection.cpp │ │ ├── optionsection.h │ │ ├── optionstoragetemplate.h │ │ ├── optionsvisitor.cpp │ │ ├── optionsvisitor.h │ │ ├── repeatingsection.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── abstractoptionstorage.cpp │ │ │ ├── filenameoption.cpp │ │ │ ├── filenameoptionmanager.cpp │ │ │ ├── option.cpp │ │ │ ├── optionsassigner.cpp │ │ │ ├── refdata │ │ │ │ ├── TreeValueSupportAdjustTest_FillsDefaultObjectValues.xml │ │ │ │ ├── TreeValueSupportAdjustTest_FillsDefaultValues.xml │ │ │ │ ├── TreeValueSupportAdjustTest_FillsDefaultVectorValues.xml │ │ │ │ ├── TreeValueSupportAdjustTest_MergesDefaultValues.xml │ │ │ │ ├── TreeValueSupportAdjustTest_NormalizesValues.xml │ │ │ │ ├── TreeValueSupportAdjustTest_OrdersValues.xml │ │ │ │ ├── TreeValueSupportTest_SupportsBooleanOption.xml │ │ │ │ ├── TreeValueSupportTest_SupportsDoubleOption.xml │ │ │ │ ├── TreeValueSupportTest_SupportsEnumOption.xml │ │ │ │ ├── TreeValueSupportTest_SupportsEnumerationArrayOption.xml │ │ │ │ ├── TreeValueSupportTest_SupportsFloatOption.xml │ │ │ │ ├── TreeValueSupportTest_SupportsInt64Option.xml │ │ │ │ ├── TreeValueSupportTest_SupportsIntegerOption.xml │ │ │ │ └── TreeValueSupportTest_SupportsStringOption.xml │ │ │ ├── repeatingsection.cpp │ │ │ ├── timeunitmanager.cpp │ │ │ └── treesupport.cpp │ │ ├── timeunitmanager.cpp │ │ ├── timeunitmanager.h │ │ ├── treesupport.cpp │ │ ├── treesupport.h │ │ ├── valueconverter.h │ │ └── valuestore.h │ ├── pbcutil │ │ ├── CMakeLists.txt │ │ ├── boxutilities.cpp │ │ ├── boxutilities.h │ │ ├── com.cpp │ │ ├── com.h │ │ ├── ishift.h │ │ ├── mshift.cpp │ │ ├── mshift.h │ │ ├── pbc.cpp │ │ ├── pbc.h │ │ ├── pbc_aiuc.h │ │ ├── pbc_aiuc_cuda.cuh │ │ ├── pbc_simd.cpp │ │ ├── pbc_simd.h │ │ ├── pbcenums.cpp │ │ ├── pbcenums.h │ │ ├── pbcmethods.cpp │ │ ├── pbcmethods.h │ │ ├── rmpbc.cpp │ │ ├── rmpbc.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── com.cpp │ │ │ ├── mshift.cpp │ │ │ ├── pbc.cpp │ │ │ ├── pbcenums.cpp │ │ │ └── refdata │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_0.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_1.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_10.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_11.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_12.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_13.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_14.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_15.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_16.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_17.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_18.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_19.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_2.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_20.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_21.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_22.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_23.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_24.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_25.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_26.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_3.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_4.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_5.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_6.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_7.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_8.xml │ │ │ ├── CorrectCoordinates_COMInPlaceTest_MatrixDefault_9.xml │ │ │ └── PbcTest_CalcShiftsWorks.xml │ ├── pulling │ │ ├── CMakeLists.txt │ │ ├── output.cpp │ │ ├── output.h │ │ ├── pull.cpp │ │ ├── pull.h │ │ ├── pull_internal.h │ │ ├── pull_rotation.cpp │ │ ├── pull_rotation.h │ │ ├── pullutil.cpp │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ └── pull.cpp │ ├── random.h │ ├── random │ │ ├── CMakeLists.txt │ │ ├── exponentialdistribution.h │ │ ├── gammadistribution.h │ │ ├── normaldistribution.h │ │ ├── seed.cpp │ │ ├── seed.h │ │ ├── tabulatednormaldistribution.cpp │ │ ├── tabulatednormaldistribution.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── exponentialdistribution.cpp │ │ │ ├── gammadistribution.cpp │ │ │ ├── normaldistribution.cpp │ │ │ ├── refdata │ │ │ │ ├── ExponentialDistributionTest_Output.xml │ │ │ │ ├── GammaDistributionTest_Output.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Default_0.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Default_1.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Default_2.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Fast_0.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Fast_1.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Fast_2.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Using40Rounds_0.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Using40Rounds_1.xml │ │ │ │ ├── KnownAnswersTest_ThreeFry2x64Test_Using40Rounds_2.xml │ │ │ │ ├── NormalDistributionTest_Output.xml │ │ │ │ ├── TabulatedNormalDistributionTest_Output14.xml │ │ │ │ ├── TabulatedNormalDistributionTest_Output16.xml │ │ │ │ ├── TabulatedNormalDistributionTest_OutputDouble14.xml │ │ │ │ ├── ThreeFry2x64Test_InternalCounterSequence.xml │ │ │ │ ├── UniformIntDistributionTest_Output.xml │ │ │ │ ├── UniformRealDistributionTest_GenerateCanonical.xml │ │ │ │ └── UniformRealDistributionTest_Output.xml │ │ │ ├── seed.cpp │ │ │ ├── tabulatednormaldistribution.cpp │ │ │ ├── threefry.cpp │ │ │ ├── uniformintdistribution.cpp │ │ │ └── uniformrealdistribution.cpp │ │ ├── threefry.h │ │ ├── uniformintdistribution.h │ │ └── uniformrealdistribution.h │ ├── restraint │ │ ├── CMakeLists.txt │ │ ├── manager.cpp │ │ ├── manager.h │ │ ├── restraintmdmodule.cpp │ │ ├── restraintmdmodule.h │ │ ├── restraintmdmodule_impl.h │ │ ├── restraintpotential.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ └── manager.cpp │ ├── selection.h │ ├── selection │ │ ├── CMakeLists.txt │ │ ├── centerofmass.cpp │ │ ├── centerofmass.h │ │ ├── compiler.cpp │ │ ├── compiler.h │ │ ├── evaluate.cpp │ │ ├── evaluate.h │ │ ├── indexutil.cpp │ │ ├── indexutil.h │ │ ├── keywords.h │ │ ├── mempool.cpp │ │ ├── mempool.h │ │ ├── nbsearch.cpp │ │ ├── nbsearch.h │ │ ├── params.cpp │ │ ├── parser.cpp │ │ ├── parser.h │ │ ├── parser.patch │ │ ├── parser.y │ │ ├── parser_internal.h │ │ ├── parsetree.cpp │ │ ├── parsetree.h │ │ ├── poscalc.cpp │ │ ├── poscalc.h │ │ ├── position.cpp │ │ ├── position.h │ │ ├── regenerate_parser.sh │ │ ├── scanner.cpp │ │ ├── scanner.h │ │ ├── scanner.l │ │ ├── scanner.patch │ │ ├── scanner_flex.h │ │ ├── scanner_internal.cpp │ │ ├── scanner_internal.h │ │ ├── selection.cpp │ │ ├── selection.h │ │ ├── selectioncollection.cpp │ │ ├── selectioncollection.h │ │ ├── selectioncollection_impl.h │ │ ├── selectionenums.h │ │ ├── selectionfileoption.h │ │ ├── selectionfileoptionstorage.h │ │ ├── selectionoption.cpp │ │ ├── selectionoption.h │ │ ├── selectionoptionbehavior.cpp │ │ ├── selectionoptionbehavior.h │ │ ├── selectionoptionmanager.cpp │ │ ├── selectionoptionmanager.h │ │ ├── selectionoptionstorage.h │ │ ├── selelem.cpp │ │ ├── selelem.h │ │ ├── selhelp.cpp │ │ ├── selhelp.h │ │ ├── selmethod.cpp │ │ ├── selmethod.h │ │ ├── selmethod_impl.h │ │ ├── selparam.h │ │ ├── selvalue.cpp │ │ ├── selvalue.h │ │ ├── sm_compare.cpp │ │ ├── sm_distance.cpp │ │ ├── sm_insolidangle.cpp │ │ ├── sm_keywords.cpp │ │ ├── sm_merge.cpp │ │ ├── sm_permute.cpp │ │ ├── sm_position.cpp │ │ ├── sm_same.cpp │ │ ├── sm_simple.cpp │ │ ├── symrec.cpp │ │ ├── symrec.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── gensphere.py │ │ │ ├── indexutil.cpp │ │ │ ├── nbsearch.cpp │ │ │ ├── poscalc.cpp │ │ │ ├── refdata │ │ │ ├── IndexBlockTest_CreatesAtomBlock.xml │ │ │ ├── IndexBlockTest_CreatesMoleculeBlock.xml │ │ │ ├── IndexBlockTest_CreatesMoleculeBlocksForComplexTopology.xml │ │ │ ├── IndexBlockTest_CreatesMoleculeBlocksForSimpleTopology.xml │ │ │ ├── IndexBlockTest_CreatesResidueBlock.xml │ │ │ ├── IndexBlockTest_CreatesResidueBlocksForComplexTopology.xml │ │ │ ├── IndexBlockTest_CreatesResidueBlocksForSimpleTopology.xml │ │ │ ├── IndexBlockTest_CreatesSingleBlock.xml │ │ │ ├── IndexBlockTest_CreatesUnknownBlock.xml │ │ │ ├── IndexMapTest_HandlesMultipleRequests.xml │ │ │ ├── IndexMapTest_InitializesAtomBlock.xml │ │ │ ├── IndexMapTest_InitializesMoleculeBlock.xml │ │ │ ├── IndexMapTest_InitializesOrgIdGroupAll.xml │ │ │ ├── IndexMapTest_InitializesOrgIdGroupAtom.xml │ │ │ ├── IndexMapTest_InitializesOrgIdGroupMolecule.xml │ │ │ ├── IndexMapTest_InitializesOrgIdGroupResidue.xml │ │ │ ├── IndexMapTest_InitializesOrgIdGroupSingle.xml │ │ │ ├── IndexMapTest_MapsResidueBlocks.xml │ │ │ ├── IndexMapTest_MapsResidueBlocksWithMask.xml │ │ │ ├── IndexMapTest_MapsSingleBlock.xml │ │ │ ├── PositionCalculationTest_ComputesAtomPositions.xml │ │ │ ├── PositionCalculationTest_ComputesGroupCOGPositions.xml │ │ │ ├── PositionCalculationTest_ComputesGroupCOMPositions.xml │ │ │ ├── PositionCalculationTest_ComputesPositionMask.xml │ │ │ ├── PositionCalculationTest_ComputesPositionsWithCompleteMax.xml │ │ │ ├── PositionCalculationTest_ComputesPositionsWithCompleteWhole.xml │ │ │ ├── PositionCalculationTest_ComputesResidueCOGPositions.xml │ │ │ ├── PositionCalculationTest_ComputesResidueCOMPositions.xml │ │ │ ├── PositionCalculationTest_HandlesFramesWithLessAtoms.xml │ │ │ ├── PositionCalculationTest_HandlesFramesWithLessAtoms2.xml │ │ │ ├── PositionCalculationTest_HandlesIdenticalStaticCalculations.xml │ │ │ ├── PositionCalculationTest_HandlesOverlappingStaticCalculations.xml │ │ │ ├── SelectionCollectionDataTest_ComputesMassesAndCharges.xml │ │ │ ├── SelectionCollectionDataTest_ComputesMassesAndChargesWithoutTopology.xml │ │ │ ├── SelectionCollectionDataTest_HandlesAllNone.xml │ │ │ ├── SelectionCollectionDataTest_HandlesAltLoc.xml │ │ │ ├── SelectionCollectionDataTest_HandlesArithmeticExpressions.xml │ │ │ ├── SelectionCollectionDataTest_HandlesAtomname.xml │ │ │ ├── SelectionCollectionDataTest_HandlesAtomnr.xml │ │ │ ├── SelectionCollectionDataTest_HandlesAtomtype.xml │ │ │ ├── SelectionCollectionDataTest_HandlesBasicBoolean.xml │ │ │ ├── SelectionCollectionDataTest_HandlesBeta.xml │ │ │ ├── SelectionCollectionDataTest_HandlesBooleanStaticAnalysis.xml │ │ │ ├── SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithMoreVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesChain.xml │ │ │ ├── SelectionCollectionDataTest_HandlesCharge.xml │ │ │ ├── SelectionCollectionDataTest_HandlesComplexNumericVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesConstantPositionInVariable.xml │ │ │ ├── SelectionCollectionDataTest_HandlesConstantPositions.xml │ │ │ ├── SelectionCollectionDataTest_HandlesConstantPositionsWithModifiers.xml │ │ │ ├── SelectionCollectionDataTest_HandlesCoordinateKeywords.xml │ │ │ ├── SelectionCollectionDataTest_HandlesDistanceKeyword.xml │ │ │ ├── SelectionCollectionDataTest_HandlesDynamicAtomValuedParameters.xml │ │ │ ├── SelectionCollectionDataTest_HandlesEmptyReferenceForSame.xml │ │ │ ├── SelectionCollectionDataTest_HandlesEmptySelectionWithUnevaluatedExpressions.xml │ │ │ ├── SelectionCollectionDataTest_HandlesForcedStringMatchingMode.xml │ │ │ ├── SelectionCollectionDataTest_HandlesFramesWithAtomSubsets.xml │ │ │ ├── SelectionCollectionDataTest_HandlesInSolidAngleKeyword.xml │ │ │ ├── SelectionCollectionDataTest_HandlesIndexGroupsInSelections.xml │ │ │ ├── SelectionCollectionDataTest_HandlesIndexGroupsInSelectionsDelayed.xml │ │ │ ├── SelectionCollectionDataTest_HandlesInsertCode.xml │ │ │ ├── SelectionCollectionDataTest_HandlesKeywordOfPositions.xml │ │ │ ├── SelectionCollectionDataTest_HandlesKeywordOfPositionsInArithmetic.xml │ │ │ ├── SelectionCollectionDataTest_HandlesMass.xml │ │ │ ├── SelectionCollectionDataTest_HandlesMergeModifier.xml │ │ │ ├── SelectionCollectionDataTest_HandlesMinDistanceKeyword.xml │ │ │ ├── SelectionCollectionDataTest_HandlesMolIndex.xml │ │ │ ├── SelectionCollectionDataTest_HandlesNumericComparisons.xml │ │ │ ├── SelectionCollectionDataTest_HandlesNumericConstantsInVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesNumericVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesOccupancy.xml │ │ │ ├── SelectionCollectionDataTest_HandlesOverlappingIntegerRanges.xml │ │ │ ├── SelectionCollectionDataTest_HandlesOverlappingRealRanges.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPdbAtomname.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPermuteModifier.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPlusModifier.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPositionKeywords.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPositionModifiersForKeywords.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPositionModifiersForMethods.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPositionVariableInModifier.xml │ │ │ ├── SelectionCollectionDataTest_HandlesPositionVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesRegexMatching.xml │ │ │ ├── SelectionCollectionDataTest_HandlesResIndex.xml │ │ │ ├── SelectionCollectionDataTest_HandlesResname.xml │ │ │ ├── SelectionCollectionDataTest_HandlesResnr.xml │ │ │ ├── SelectionCollectionDataTest_HandlesSameResidue.xml │ │ │ ├── SelectionCollectionDataTest_HandlesSameResidueName.xml │ │ │ ├── SelectionCollectionDataTest_HandlesSelectionNames.xml │ │ │ ├── SelectionCollectionDataTest_HandlesUnsortedIndexGroupsInSelections.xml │ │ │ ├── SelectionCollectionDataTest_HandlesUnsortedIndexGroupsInSelectionsDelayed.xml │ │ │ ├── SelectionCollectionDataTest_HandlesUnusedVariables.xml │ │ │ ├── SelectionCollectionDataTest_HandlesVariablesWithMixedEvaluationGroups.xml │ │ │ ├── SelectionCollectionDataTest_HandlesVariablesWithMixedEvaluationGroups2.xml │ │ │ ├── SelectionCollectionDataTest_HandlesVariablesWithStaticEvaluationGroups.xml │ │ │ ├── SelectionCollectionDataTest_HandlesWildcardMatching.xml │ │ │ ├── SelectionCollectionDataTest_HandlesWithinConstantPositions.xml │ │ │ ├── SelectionCollectionDataTest_HandlesWithinKeyword.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesBasicInput.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesContinuation.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesEmptySelections.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesMultiSelectionInputStatus.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesMultipleSelectionsOnLine.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesNoFinalNewline.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesNoninteractiveInput.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesSingleSelectionInput.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesSingleSelectionInputNoninteractively.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesSingleSelectionInputStatus.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesStatusWithExistingSelections.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesStatusWithGroups.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesTwoSelectionInput.xml │ │ │ ├── SelectionCollectionInteractiveTest_HandlesTwoSelectionInputStatus.xml │ │ │ ├── common-referencedata.xsl │ │ │ └── referencedata.xsl │ │ │ ├── selectioncollection.cpp │ │ │ ├── selectionoption.cpp │ │ │ ├── selfile.dat │ │ │ ├── simple.gro │ │ │ ├── simple.ndx │ │ │ ├── simple.pdb │ │ │ ├── sphere.gro │ │ │ ├── toputils.cpp │ │ │ └── toputils.h │ ├── simd │ │ ├── CMakeLists.txt │ │ ├── impl_arm_neon │ │ │ ├── impl_arm_neon.h │ │ │ ├── impl_arm_neon_definitions.h │ │ │ ├── impl_arm_neon_general.h │ │ │ ├── impl_arm_neon_simd4_float.h │ │ │ ├── impl_arm_neon_simd_float.h │ │ │ └── impl_arm_neon_util_float.h │ │ ├── impl_arm_neon_asimd │ │ │ ├── impl_arm_neon_asimd.h │ │ │ ├── impl_arm_neon_asimd_definitions.h │ │ │ ├── impl_arm_neon_asimd_general.h │ │ │ ├── impl_arm_neon_asimd_simd4_float.h │ │ │ ├── impl_arm_neon_asimd_simd_double.h │ │ │ ├── impl_arm_neon_asimd_simd_float.h │ │ │ ├── impl_arm_neon_asimd_util_double.h │ │ │ └── impl_arm_neon_asimd_util_float.h │ │ ├── impl_arm_sve │ │ │ ├── impl_arm_sve.h │ │ │ ├── impl_arm_sve_definitions.h │ │ │ ├── impl_arm_sve_general.h │ │ │ ├── impl_arm_sve_simd4_double.h │ │ │ ├── impl_arm_sve_simd4_float.h │ │ │ ├── impl_arm_sve_simd_double.h │ │ │ ├── impl_arm_sve_simd_float.h │ │ │ ├── impl_arm_sve_util_double.h │ │ │ └── impl_arm_sve_util_float.h │ │ ├── impl_ibm_vmx │ │ │ ├── impl_ibm_vmx.h │ │ │ ├── impl_ibm_vmx_definitions.h │ │ │ ├── impl_ibm_vmx_general.h │ │ │ ├── impl_ibm_vmx_simd4_float.h │ │ │ ├── impl_ibm_vmx_simd_float.h │ │ │ └── impl_ibm_vmx_util_float.h │ │ ├── impl_ibm_vsx │ │ │ ├── impl_ibm_vsx.h │ │ │ ├── impl_ibm_vsx_definitions.h │ │ │ ├── impl_ibm_vsx_general.h │ │ │ ├── impl_ibm_vsx_simd4_float.h │ │ │ ├── impl_ibm_vsx_simd_double.h │ │ │ ├── impl_ibm_vsx_simd_float.h │ │ │ ├── impl_ibm_vsx_util_double.h │ │ │ └── impl_ibm_vsx_util_float.h │ │ ├── impl_none │ │ │ └── impl_none.h │ │ ├── impl_reference │ │ │ ├── impl_reference.h │ │ │ ├── impl_reference_definitions.h │ │ │ ├── impl_reference_general.h │ │ │ ├── impl_reference_simd4_double.h │ │ │ ├── impl_reference_simd4_float.h │ │ │ ├── impl_reference_simd_double.h │ │ │ ├── impl_reference_simd_float.h │ │ │ ├── impl_reference_util_double.h │ │ │ └── impl_reference_util_float.h │ │ ├── impl_sparc64_hpc_ace │ │ │ ├── impl_sparc64_hpc_ace.h │ │ │ ├── impl_sparc64_hpc_ace_common.h │ │ │ ├── impl_sparc64_hpc_ace_simd_double.h │ │ │ └── impl_sparc64_hpc_ace_simd_float.h │ │ ├── impl_x86_avx2_128 │ │ │ ├── impl_x86_avx2_128.h │ │ │ ├── impl_x86_avx2_128_definitions.h │ │ │ ├── impl_x86_avx2_128_general.h │ │ │ ├── impl_x86_avx2_128_simd4_double.h │ │ │ ├── impl_x86_avx2_128_simd4_float.h │ │ │ ├── impl_x86_avx2_128_simd_double.h │ │ │ ├── impl_x86_avx2_128_simd_float.h │ │ │ ├── impl_x86_avx2_128_util_double.h │ │ │ └── impl_x86_avx2_128_util_float.h │ │ ├── impl_x86_avx2_256 │ │ │ ├── impl_x86_avx2_256.h │ │ │ ├── impl_x86_avx2_256_definitions.h │ │ │ ├── impl_x86_avx2_256_general.h │ │ │ ├── impl_x86_avx2_256_simd4_double.h │ │ │ ├── impl_x86_avx2_256_simd4_float.h │ │ │ ├── impl_x86_avx2_256_simd_double.h │ │ │ ├── impl_x86_avx2_256_simd_float.h │ │ │ ├── impl_x86_avx2_256_util_double.h │ │ │ └── impl_x86_avx2_256_util_float.h │ │ ├── impl_x86_avx_128_fma │ │ │ ├── impl_x86_avx_128_fma.h │ │ │ ├── impl_x86_avx_128_fma_definitions.h │ │ │ ├── impl_x86_avx_128_fma_general.h │ │ │ ├── impl_x86_avx_128_fma_simd4_double.h │ │ │ ├── impl_x86_avx_128_fma_simd4_float.h │ │ │ ├── impl_x86_avx_128_fma_simd_double.h │ │ │ ├── impl_x86_avx_128_fma_simd_float.h │ │ │ ├── impl_x86_avx_128_fma_util_double.h │ │ │ └── impl_x86_avx_128_fma_util_float.h │ │ ├── impl_x86_avx_256 │ │ │ ├── impl_x86_avx_256.h │ │ │ ├── impl_x86_avx_256_definitions.h │ │ │ ├── impl_x86_avx_256_general.h │ │ │ ├── impl_x86_avx_256_simd4_double.h │ │ │ ├── impl_x86_avx_256_simd4_float.h │ │ │ ├── impl_x86_avx_256_simd_double.h │ │ │ ├── impl_x86_avx_256_simd_float.h │ │ │ ├── impl_x86_avx_256_util_double.h │ │ │ └── impl_x86_avx_256_util_float.h │ │ ├── impl_x86_avx_512 │ │ │ ├── impl_x86_avx_512.h │ │ │ ├── impl_x86_avx_512_definitions.h │ │ │ ├── impl_x86_avx_512_general.h │ │ │ ├── impl_x86_avx_512_simd4_double.h │ │ │ ├── impl_x86_avx_512_simd4_float.h │ │ │ ├── impl_x86_avx_512_simd_double.h │ │ │ ├── impl_x86_avx_512_simd_float.h │ │ │ ├── impl_x86_avx_512_util_double.h │ │ │ └── impl_x86_avx_512_util_float.h │ │ ├── impl_x86_avx_512_knl │ │ │ ├── impl_x86_avx_512_knl.h │ │ │ ├── impl_x86_avx_512_knl_definitions.h │ │ │ ├── impl_x86_avx_512_knl_general.h │ │ │ ├── impl_x86_avx_512_knl_simd4_double.h │ │ │ ├── impl_x86_avx_512_knl_simd4_float.h │ │ │ ├── impl_x86_avx_512_knl_simd_double.h │ │ │ ├── impl_x86_avx_512_knl_simd_float.h │ │ │ ├── impl_x86_avx_512_knl_util_double.h │ │ │ └── impl_x86_avx_512_knl_util_float.h │ │ ├── impl_x86_mic │ │ │ ├── impl_x86_mic.h │ │ │ ├── impl_x86_mic_definitions.h │ │ │ ├── impl_x86_mic_general.h │ │ │ ├── impl_x86_mic_simd4_double.h │ │ │ ├── impl_x86_mic_simd4_float.h │ │ │ ├── impl_x86_mic_simd_double.h │ │ │ ├── impl_x86_mic_simd_float.h │ │ │ ├── impl_x86_mic_util_double.h │ │ │ └── impl_x86_mic_util_float.h │ │ ├── impl_x86_sse2 │ │ │ ├── impl_x86_sse2.h │ │ │ ├── impl_x86_sse2_definitions.h │ │ │ ├── impl_x86_sse2_general.h │ │ │ ├── impl_x86_sse2_simd4_float.h │ │ │ ├── impl_x86_sse2_simd_double.h │ │ │ ├── impl_x86_sse2_simd_float.h │ │ │ ├── impl_x86_sse2_util_double.h │ │ │ └── impl_x86_sse2_util_float.h │ │ ├── impl_x86_sse4_1 │ │ │ ├── impl_x86_sse4_1.h │ │ │ ├── impl_x86_sse4_1_definitions.h │ │ │ ├── impl_x86_sse4_1_general.h │ │ │ ├── impl_x86_sse4_1_simd4_float.h │ │ │ ├── impl_x86_sse4_1_simd_double.h │ │ │ ├── impl_x86_sse4_1_simd_float.h │ │ │ ├── impl_x86_sse4_1_util_double.h │ │ │ └── impl_x86_sse4_1_util_float.h │ │ ├── scalar │ │ │ ├── scalar.h │ │ │ ├── scalar_math.h │ │ │ └── scalar_util.h │ │ ├── simd.h │ │ ├── simd_math.h │ │ ├── simd_memory.h │ │ ├── support.cpp │ │ ├── support.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── base.cpp │ │ │ ├── base.h │ │ │ ├── bootstrap_loadstore.cpp │ │ │ ├── data.h │ │ │ ├── refdata │ │ │ │ ├── SimdMathTest_generateTestPointsDouble.xml │ │ │ │ └── SimdMathTest_generateTestPointsFloat.xml │ │ │ ├── scalar.cpp │ │ │ ├── scalar_math.cpp │ │ │ ├── scalar_util.cpp │ │ │ ├── simd.cpp │ │ │ ├── simd.h │ │ │ ├── simd4.cpp │ │ │ ├── simd4.h │ │ │ ├── simd4_floatingpoint.cpp │ │ │ ├── simd4_math.cpp │ │ │ ├── simd4_vector_operations.cpp │ │ │ ├── simd_floatingpoint.cpp │ │ │ ├── simd_floatingpoint_util.cpp │ │ │ ├── simd_integer.cpp │ │ │ ├── simd_math.cpp │ │ │ ├── simd_memory.cpp │ │ │ └── simd_vector_operations.cpp │ │ └── vector_operations.h │ ├── statistics │ │ ├── CMakeLists.txt │ │ ├── statistics.cpp │ │ └── statistics.h │ ├── swap │ │ ├── CMakeLists.txt │ │ ├── swapcoords.cpp │ │ └── swapcoords.h │ ├── tables │ │ ├── CMakeLists.txt │ │ ├── cubicsplinetable.cpp │ │ ├── cubicsplinetable.h │ │ ├── forcetable.cpp │ │ ├── forcetable.h │ │ ├── quadraticsplinetable.cpp │ │ ├── quadraticsplinetable.h │ │ ├── splineutil.cpp │ │ ├── splineutil.h │ │ ├── tableinput.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ └── splinetable.cpp │ ├── taskassignment │ │ ├── CMakeLists.txt │ │ ├── decidegpuusage.cpp │ │ ├── decidegpuusage.h │ │ ├── decidesimulationworkload.cpp │ │ ├── decidesimulationworkload.h │ │ ├── findallgputasks.cpp │ │ ├── findallgputasks.h │ │ ├── reportgpuusage.cpp │ │ ├── reportgpuusage.h │ │ ├── resourcedivision.cpp │ │ ├── resourcedivision.h │ │ ├── taskassignment.cpp │ │ ├── taskassignment.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ └── usergpuids.cpp │ │ ├── usergpuids.cpp │ │ └── usergpuids.h │ ├── timing │ │ ├── CMakeLists.txt │ │ ├── cyclecounter.cpp │ │ ├── cyclecounter.h │ │ ├── gpu_timing.h │ │ ├── wallcycle.cpp │ │ ├── wallcycle.h │ │ ├── wallcyclereporting.h │ │ ├── walltime_accounting.cpp │ │ └── walltime_accounting.h │ ├── tools │ │ ├── CMakeLists.txt │ │ ├── check.cpp │ │ ├── check.h │ │ ├── convert_tpr.cpp │ │ ├── convert_tpr.h │ │ ├── dump.cpp │ │ ├── dump.h │ │ ├── eneconv.cpp │ │ ├── eneconv.h │ │ ├── make_ndx.cpp │ │ ├── make_ndx.h │ │ ├── mk_angndx.cpp │ │ ├── mk_angndx.h │ │ ├── pme_error.cpp │ │ ├── pme_error.h │ │ ├── report_methods.cpp │ │ ├── report_methods.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── dump.cpp │ │ │ ├── helpwriting.cpp │ │ │ ├── refdata │ │ │ │ ├── HelpwritingTest_ConvertTprWritesHelp.xml │ │ │ │ ├── HelpwritingTest_DumpWritesHelp.xml │ │ │ │ └── HelpwritingTest_ReportMethodsWritesHelp.xml │ │ │ ├── report_methods.cpp │ │ │ └── trjconv.cpp │ │ ├── trjcat.cpp │ │ ├── trjcat.h │ │ ├── trjconv.cpp │ │ ├── trjconv.h │ │ ├── tune_pme.cpp │ │ └── tune_pme.h │ ├── topology │ │ ├── CMakeLists.txt │ │ ├── atomprop.cpp │ │ ├── atomprop.h │ │ ├── atoms.cpp │ │ ├── atoms.h │ │ ├── atomsbuilder.cpp │ │ ├── atomsbuilder.h │ │ ├── block.cpp │ │ ├── block.h │ │ ├── exclusionblocks.cpp │ │ ├── exclusionblocks.h │ │ ├── forcefieldparameters.cpp │ │ ├── forcefieldparameters.h │ │ ├── idef.cpp │ │ ├── idef.h │ │ ├── ifunc.cpp │ │ ├── ifunc.h │ │ ├── index.cpp │ │ ├── index.h │ │ ├── invblock.cpp │ │ ├── invblock.h │ │ ├── mtop_lookup.h │ │ ├── mtop_util.cpp │ │ ├── mtop_util.h │ │ ├── residuetypes.cpp │ │ ├── residuetypes.h │ │ ├── symtab.cpp │ │ ├── symtab.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── exclusionblocks.cpp │ │ │ ├── idef.cpp │ │ │ ├── mtop.cpp │ │ │ ├── refdata │ │ │ │ ├── LegacySymtabTest_AddLargeNumberOfEntries.xml │ │ │ │ ├── LegacySymtabTest_NoDuplicatesInLargeTable.xml │ │ │ │ ├── StringTableTest_AddLargeNumberOfEntries.xml │ │ │ │ ├── StringTableTest_AddSingleEntry.xml │ │ │ │ ├── StringTableTest_AddTwoDistinctEntries.xml │ │ │ │ ├── StringTableTest_CanAccessWithAt.xml │ │ │ │ ├── StringTableTest_CanAccessWithBracket.xml │ │ │ │ ├── StringTableTest_NoDuplicatesInLargeTable.xml │ │ │ │ ├── StringTableTest_StringCompareIsCorrect.xml │ │ │ │ ├── StringTableTest_ThrowsOutOfRange.xml │ │ │ │ └── StringTableTest_TryToAddDuplicates.xml │ │ │ └── symtab.cpp │ │ ├── topology.cpp │ │ ├── topology.h │ │ ├── topsort.cpp │ │ └── topsort.h │ ├── trajectory │ │ ├── CMakeLists.txt │ │ ├── energyframe.cpp │ │ ├── energyframe.h │ │ ├── trajectoryframe.cpp │ │ └── trajectoryframe.h │ ├── trajectoryanalysis.h │ ├── trajectoryanalysis │ │ ├── .clang-tidy │ │ ├── CMakeLists.txt │ │ ├── analysismodule.cpp │ │ ├── analysismodule.h │ │ ├── analysissettings.cpp │ │ ├── analysissettings.h │ │ ├── analysissettings_impl.h │ │ ├── cmdlinerunner.cpp │ │ ├── cmdlinerunner.h │ │ ├── modules.cpp │ │ ├── modules.h │ │ ├── modules │ │ │ ├── angle.cpp │ │ │ ├── angle.h │ │ │ ├── convert_trj.cpp │ │ │ ├── convert_trj.h │ │ │ ├── distance.cpp │ │ │ ├── distance.h │ │ │ ├── extract_cluster.cpp │ │ │ ├── extract_cluster.h │ │ │ ├── freevolume.cpp │ │ │ ├── freevolume.h │ │ │ ├── pairdist.cpp │ │ │ ├── pairdist.h │ │ │ ├── rdf.cpp │ │ │ ├── rdf.h │ │ │ ├── sasa.cpp │ │ │ ├── sasa.h │ │ │ ├── select.cpp │ │ │ ├── select.h │ │ │ ├── surfacearea.cpp │ │ │ ├── surfacearea.h │ │ │ ├── trajectory.cpp │ │ │ ├── trajectory.h │ │ │ └── unionfind.h │ │ ├── runnercommon.cpp │ │ ├── runnercommon.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── angle.cpp │ │ │ ├── angle.gro │ │ │ ├── clustsize.cpp │ │ │ ├── clustsize.ndx │ │ │ ├── clustsize.pdb │ │ │ ├── clustsize.tpr │ │ │ ├── cmdlinerunner.cpp │ │ │ ├── convert_trj.cpp │ │ │ ├── distance.cpp │ │ │ ├── extract_cluster.cpp │ │ │ ├── extract_cluster.ndx │ │ │ ├── extract_cluster.trr │ │ │ ├── freevolume.cpp │ │ │ ├── freevolume.tpr │ │ │ ├── freevolume.xtc │ │ │ ├── index.ndx │ │ │ ├── lysozyme.gro │ │ │ ├── lysozyme.pdb │ │ │ ├── lysozyme.top │ │ │ ├── moduletest.cpp │ │ │ ├── moduletest.h │ │ │ ├── pairdist.cpp │ │ │ ├── rdf.cpp │ │ │ ├── refdata │ │ │ │ ├── AngleModuleTest_ComputesDihedrals.xml │ │ │ │ ├── AngleModuleTest_ComputesMultipleAngles.xml │ │ │ │ ├── AngleModuleTest_ComputesPlaneZAxisAngles.xml │ │ │ │ ├── AngleModuleTest_ComputesSimpleAngles.xml │ │ │ │ ├── AngleModuleTest_ComputesVectorPairAngles.xml │ │ │ │ ├── AngleModuleTest_ComputesVectorPlanePairAngles.xml │ │ │ │ ├── AngleModuleTest_ComputesVectorSphereNormalZAxisAngles.xml │ │ │ │ ├── AngleModuleTest_ComputesVectorTimeZeroAngles.xml │ │ │ │ ├── AngleModuleTest_HandlesDynamicSelections.xml │ │ │ │ ├── AngleModuleTest_HandlesOneVsMultipleVectorAngles.xml │ │ │ │ ├── AngleModuleTest_HandlesOneVsMultipleVectorGroupsAngles.xml │ │ │ │ ├── ClustsizeTest_MolCSize.xml │ │ │ │ ├── ClustsizeTest_MolDefaultCutoff.xml │ │ │ │ ├── ClustsizeTest_MolShortCutoff.xml │ │ │ │ ├── ClustsizeTest_NoMolDefaultCutoff.xml │ │ │ │ ├── ClustsizeTest_NoMolShortCutoff.xml │ │ │ │ ├── ConvertTrjModuleTest_WorksWithAtomAdding.xml │ │ │ │ ├── ConvertTrjModuleTest_WorksWithAtomsAndSelection.xml │ │ │ │ ├── ConvertTrjModuleTest_WritesAtomSubset.xml │ │ │ │ ├── ConvertTrjModuleTest_WritesNormalOutput.xml │ │ │ │ ├── DistanceModuleTest_ComputesDistances.xml │ │ │ │ ├── DistanceModuleTest_ComputesMultipleDistances.xml │ │ │ │ ├── DistanceModuleTest_HandlesDynamicSelections.xml │ │ │ │ ├── ExtractClusterModuleTest_WorksWithAllAtoms.xml │ │ │ │ ├── ExtractClusterModuleTest_WorksWithAtomSubset.xml │ │ │ │ ├── FreeVolumeModuleTest_ComputesFreeVolume.xml │ │ │ │ ├── FreeVolumeModuleTest_ComputesFreeVolumeSelection.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesAllDistances.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesAllDistancesWithCutoff.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesGroupedMaxDistanceWithCutoff.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesGroupedMinDistanceWithCutoff.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesMaxDistance.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesMaxDistanceWithCutoff.xml │ │ │ │ ├── PairDistanceModuleTest_ComputesMinDistanceWithCutoff.xml │ │ │ │ ├── RdfModuleTest_BasicTest.xml │ │ │ │ ├── RdfModuleTest_CalculatesSurf.xml │ │ │ │ ├── RdfModuleTest_CalculatesXY.xml │ │ │ │ ├── RdfModuleTest_SelectionsFromBothTopologyFileAndIndexFileWork.xml │ │ │ │ ├── RdfModuleTest_SelectionsSolelyFromIndexFileWork.xml │ │ │ │ ├── SasaModuleTest_BasicTest.xml │ │ │ │ ├── SasaModuleTest_HandlesDynamicCalculationGroup.xml │ │ │ │ ├── SasaModuleTest_HandlesDynamicOutputGroup.xml │ │ │ │ ├── SasaModuleTest_HandlesSelectedResidues.xml │ │ │ │ ├── SasaModuleTest_WritesConnollySurfaceWithSolute.xml │ │ │ │ ├── SelectModuleTest_BasicTest.xml │ │ │ │ ├── SelectModuleTest_HandlesMaxPDBOutput.xml │ │ │ │ ├── SelectModuleTest_HandlesPDBOutputWithNonPDBInput.xml │ │ │ │ ├── SelectModuleTest_HandlesPDBOutputWithPDBInput.xml │ │ │ │ ├── SelectModuleTest_HandlesSelectedPDBOutput.xml │ │ │ │ ├── SelectModuleTest_NormalizesSizes.xml │ │ │ │ ├── SelectModuleTest_WritesResidueIndices.xml │ │ │ │ ├── SelectModuleTest_WritesResidueNumbers.xml │ │ │ │ ├── SurfaceAreaTest_Computes100Points.xml │ │ │ │ ├── SurfaceAreaTest_Computes100PointsWithRectangularPBC.xml │ │ │ │ ├── SurfaceAreaTest_Computes100PointsWithTriclinicPBC.xml │ │ │ │ ├── SurfaceAreaTest_SurfacePoints12.xml │ │ │ │ ├── SurfaceAreaTest_SurfacePoints122.xml │ │ │ │ ├── SurfaceAreaTest_SurfacePoints32.xml │ │ │ │ ├── SurfaceAreaTest_SurfacePoints42.xml │ │ │ │ ├── TrajectoryAnalysisCommandLineRunnerTest_WritesHelp.xml │ │ │ │ ├── TrajectoryModuleTest_BasicTest.xml │ │ │ │ ├── TrajectoryModuleTest_HandlesNoForces.xml │ │ │ │ ├── TrajectoryModuleTest_HandlesNoVelocities.xml │ │ │ │ ├── TrajectoryModuleTest_PlotsXOnly.xml │ │ │ │ ├── analysisdata-referencedata.xsl │ │ │ │ ├── common-referencedata.xsl │ │ │ │ └── referencedata.xsl │ │ │ ├── sasa.cpp │ │ │ ├── select.cpp │ │ │ ├── simple-subset.gro │ │ │ ├── simple.gro │ │ │ ├── simple.pdb │ │ │ ├── spc216.gro │ │ │ ├── surfacearea.cpp │ │ │ ├── test_selection.cpp │ │ │ ├── topologyinformation.cpp │ │ │ ├── trajectory.cpp │ │ │ └── unionfind.cpp │ │ ├── topologyinformation.cpp │ │ └── topologyinformation.h │ ├── utility.h │ ├── utility │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── alignedallocator.cpp │ │ ├── alignedallocator.h │ │ ├── allocator.h │ │ ├── any.cpp │ │ ├── any.h │ │ ├── arrayref.h │ │ ├── arraysize.h │ │ ├── basedefinitions.h │ │ ├── basenetwork.cpp │ │ ├── basenetwork.h │ │ ├── baseversion-gen.cpp.cmakein │ │ ├── baseversion.cpp │ │ ├── baseversion.h │ │ ├── baseversion_gen.h │ │ ├── binaryinformation.cpp │ │ ├── binaryinformation.h │ │ ├── bitmask.h │ │ ├── classhelpers.h │ │ ├── compare.cpp │ │ ├── compare.h │ │ ├── coolstuff.cpp │ │ ├── coolstuff.h │ │ ├── cstringutil.cpp │ │ ├── cstringutil.h │ │ ├── cuda_version_information.cu │ │ ├── cuda_version_information.h │ │ ├── current_function.h │ │ ├── datafilefinder.cpp │ │ ├── datafilefinder.h │ │ ├── defaultinitializationallocator.h │ │ ├── dir_separator.h │ │ ├── directoryenumerator.cpp │ │ ├── directoryenumerator.h │ │ ├── enumerationhelpers.h │ │ ├── errorcodes.cpp │ │ ├── errorcodes.h │ │ ├── errorformat.cpp │ │ ├── errorformat.h │ │ ├── exceptions.cpp │ │ ├── exceptions.h │ │ ├── fatalerror.cpp │ │ ├── fatalerror.h │ │ ├── fileptr.h │ │ ├── fileredirector.cpp │ │ ├── fileredirector.h │ │ ├── filestream.cpp │ │ ├── filestream.h │ │ ├── fixedcapacityvector.h │ │ ├── flags.h │ │ ├── futil.cpp │ │ ├── futil.h │ │ ├── gmxassert.cpp │ │ ├── gmxassert.h │ │ ├── gmxmpi.h │ │ ├── gmxomp.cpp │ │ ├── gmxomp.h │ │ ├── ikeyvaluetreeerror.cpp │ │ ├── ikeyvaluetreeerror.h │ │ ├── init.cpp │ │ ├── init.h │ │ ├── inmemoryserializer.cpp │ │ ├── inmemoryserializer.h │ │ ├── int64_to_int.cpp │ │ ├── int64_to_int.h │ │ ├── iserializer.h │ │ ├── keyvaluetree.cpp │ │ ├── keyvaluetree.h │ │ ├── keyvaluetreebuilder.h │ │ ├── keyvaluetreemdpwriter.cpp │ │ ├── keyvaluetreemdpwriter.h │ │ ├── keyvaluetreeserializer.cpp │ │ ├── keyvaluetreeserializer.h │ │ ├── keyvaluetreetransform.cpp │ │ ├── keyvaluetreetransform.h │ │ ├── listoflists.h │ │ ├── logger.cpp │ │ ├── logger.h │ │ ├── loggerbuilder.cpp │ │ ├── loggerbuilder.h │ │ ├── mdmodulenotification-impl.h │ │ ├── mdmodulenotification.h │ │ ├── messagestringcollector.cpp │ │ ├── messagestringcollector.h │ │ ├── mutex.h │ │ ├── niceheader.cpp │ │ ├── niceheader.h │ │ ├── nodelete.h │ │ ├── path.cpp │ │ ├── path.h │ │ ├── physicalnodecommunicator.cpp │ │ ├── physicalnodecommunicator.h │ │ ├── pleasecite.cpp │ │ ├── pleasecite.h │ │ ├── programcontext.cpp │ │ ├── programcontext.h │ │ ├── range.h │ │ ├── real.h │ │ ├── smalloc.cpp │ │ ├── smalloc.h │ │ ├── snprintf.h │ │ ├── strconvert.cpp │ │ ├── strconvert.h │ │ ├── strdb.cpp │ │ ├── strdb.h │ │ ├── stringcompare.h │ │ ├── stringstream.cpp │ │ ├── stringstream.h │ │ ├── stringutil.cpp │ │ ├── stringutil.h │ │ ├── sysinfo.cpp │ │ ├── sysinfo.h │ │ ├── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── alignedallocator.cpp │ │ │ ├── alignedallocator_impl.h │ │ │ ├── arrayref.cpp │ │ │ ├── bitmask.h │ │ │ ├── bitmask128.cpp │ │ │ ├── bitmask32.cpp │ │ │ ├── bitmask64.cpp │ │ │ ├── cstringutil.cpp │ │ │ ├── defaultinitializationallocator.cpp │ │ │ ├── enumerationhelpers.cpp │ │ │ ├── fixedcapacityvector.cpp │ │ │ ├── inmemoryserializer.cpp │ │ │ ├── keyvaluetreeserializer.cpp │ │ │ ├── keyvaluetreetransform.cpp │ │ │ ├── listoflists.cpp │ │ │ ├── logger.cpp │ │ │ ├── mdmodulenotification-impl.cpp │ │ │ ├── mutex.cpp │ │ │ ├── path.cpp │ │ │ ├── physicalnodecommunicator.cpp │ │ │ ├── physicalnodecommunicator_mpi.cpp │ │ │ ├── range.cpp │ │ │ ├── refdata │ │ │ │ ├── KeyValueTreeSerializerTest_EmptyTree.xml │ │ │ │ ├── KeyValueTreeSerializerTest_ObjectWithArrays.xml │ │ │ │ ├── KeyValueTreeSerializerTest_ObjectWithObjects.xml │ │ │ │ ├── KeyValueTreeSerializerTest_SimpleObject.xml │ │ │ │ ├── LoggerTest_LevelFilteringWorks.xml │ │ │ │ ├── LoggerTest_LogsToFile.xml │ │ │ │ ├── LoggerTest_LogsToMultipleFiles.xml │ │ │ │ ├── LoggerTest_LogsToMultipleStreams.xml │ │ │ │ ├── LoggerTest_LogsToStream.xml │ │ │ │ ├── LoggerTest_LogsToStreamAndFile.xml │ │ │ │ ├── PathTest_SearchOperationsWork.xml │ │ │ │ ├── TextLineWrapperTest_HandlesContinuationCharacter.xml │ │ │ │ ├── TextLineWrapperTest_HandlesHangingIndent.xml │ │ │ │ ├── TextLineWrapperTest_HandlesIndent.xml │ │ │ │ ├── TextLineWrapperTest_HandlesIndentWithEmptyLines.xml │ │ │ │ ├── TextLineWrapperTest_WrapsCorrectly.xml │ │ │ │ ├── TextLineWrapperTest_WrapsCorrectlyWithExistingBreaks.xml │ │ │ │ ├── TextLineWrapperTest_WrapsCorrectlyWithExtraWhitespace.xml │ │ │ │ ├── TextWriterTest_PreservesTrailingWhitespace.xml │ │ │ │ ├── TextWriterTest_TracksNewlines.xml │ │ │ │ ├── TextWriterTest_WritesLines.xml │ │ │ │ ├── TextWriterTest_WritesLinesInParts.xml │ │ │ │ ├── TextWriterTest_WritesLinesInPartsWithWrapper.xml │ │ │ │ ├── TextWriterTest_WritesWrappedLines.xml │ │ │ │ ├── TreeValueTransformTest_ObjectFromMultipleStrings.xml │ │ │ │ ├── TreeValueTransformTest_ObjectFromString.xml │ │ │ │ ├── TreeValueTransformTest_ScopedTransformRules.xml │ │ │ │ ├── TreeValueTransformTest_SimpleTransforms.xml │ │ │ │ ├── TreeValueTransformTest_SimpleTransformsCaseAndDashInsensitive.xml │ │ │ │ └── TreeValueTransformTest_SimpleTransformsToObject.xml │ │ │ ├── strconvert.cpp │ │ │ ├── stringutil.cpp │ │ │ ├── textreader.cpp │ │ │ ├── textwriter.cpp │ │ │ └── typetraits.cpp │ │ ├── textreader.cpp │ │ ├── textreader.h │ │ ├── textstream.h │ │ ├── textwriter.cpp │ │ ├── textwriter.h │ │ ├── txtdump.cpp │ │ ├── txtdump.h │ │ ├── typetraits.h │ │ └── unique_cptr.h │ └── version.h.cmakein ├── programs │ ├── .gitignore │ ├── BuildCompletions.cmake │ ├── CMakeLists.txt │ ├── gmx.cpp │ ├── legacymodules.cpp │ ├── legacymodules.h │ ├── mdrun │ │ ├── mdrun.cpp │ │ ├── mdrun_main.h │ │ ├── nonbonded_bench.cpp │ │ ├── nonbonded_bench.h │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── comparison_helpers.h │ │ │ ├── compressed_x_output.cpp │ │ │ ├── densityfittingmodule.cpp │ │ │ ├── dispersion_correction.cpp │ │ │ ├── domain_decomposition.cpp │ │ │ ├── energycomparison.cpp │ │ │ ├── energycomparison.h │ │ │ ├── energyreader.cpp │ │ │ ├── energyreader.h │ │ │ ├── ewaldsurfaceterm.cpp │ │ │ ├── exactcontinuation.cpp │ │ │ ├── freeenergy.cpp │ │ │ ├── grompp.cpp │ │ │ ├── helpwriting.cpp │ │ │ ├── initialconstraints.cpp │ │ │ ├── interactiveMD.cpp │ │ │ ├── mdruncomparison.h │ │ │ ├── mimic.cpp │ │ │ ├── minimize.cpp │ │ │ ├── moduletest.cpp │ │ │ ├── moduletest.h │ │ │ ├── multiple_time_stepping.cpp │ │ │ ├── multisim.cpp │ │ │ ├── multisimtest.cpp │ │ │ ├── multisimtest.h │ │ │ ├── nonbonded_bench.cpp │ │ │ ├── normalmodes.cpp │ │ │ ├── orires.cpp │ │ │ ├── outputfiles.cpp │ │ │ ├── periodicactions.cpp │ │ │ ├── pmetest.cpp │ │ │ ├── refdata │ │ │ ├── Angles1_SimpleMdrunTest_WithinTolerances_0.xml │ │ │ ├── Angles1_SimpleMdrunTest_WithinTolerances_1.xml │ │ │ ├── DensityFittingTest_CheckpointWorks.xml │ │ │ ├── DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.xml │ │ │ ├── DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.xml │ │ │ ├── DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.xml │ │ │ ├── DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.xml │ │ │ ├── DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.xml │ │ │ ├── EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.xml │ │ │ ├── EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_1.xml │ │ │ ├── EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d.xml │ │ │ ├── FreeEnergyCalculationsAreEquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s.xml │ │ │ ├── MdrunTest_WritesHelp.xml │ │ │ ├── MimicTest_AllQuantumMol.xml │ │ │ ├── MimicTest_BondCuts.xml │ │ │ ├── MimicTest_OneQuantumMol.xml │ │ │ ├── MimicTest_TwoQuantumMol.xml │ │ │ ├── MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.xml │ │ │ ├── MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.xml │ │ │ ├── MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.xml │ │ │ ├── MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.xml │ │ │ ├── MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.xml │ │ │ ├── MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.xml │ │ │ ├── MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.xml │ │ │ ├── MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.xml │ │ │ ├── MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.xml │ │ │ ├── MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.xml │ │ │ ├── MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.xml │ │ │ ├── MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.xml │ │ │ ├── NormalModesWorks_NormalModesTest_WithinTolerances_0.xml │ │ │ ├── NormalModesWorks_NormalModesTest_WithinTolerances_1.xml │ │ │ ├── NormalModesWorks_NormalModesTest_WithinTolerances_2.xml │ │ │ ├── NormalModesWorks_NormalModesTest_WithinTolerances_3.xml │ │ │ ├── NormalModesWorks_NormalModesTest_WithinTolerances_4.xml │ │ │ ├── PmeTest_ReproducesEnergies.xml │ │ │ ├── PmeTest_ScalesTheBox.xml │ │ │ ├── PmeTest_ScalesTheBoxWithWalls.xml │ │ │ ├── Simple_TpiTest_ReproducesOutput_0.xml │ │ │ └── Simple_TpiTest_ReproducesOutput_1.xml │ │ │ ├── replicaexchange.cpp │ │ │ ├── rerun.cpp │ │ │ ├── simple_mdrun.cpp │ │ │ ├── simulator.cpp │ │ │ ├── simulatorcomparison.cpp │ │ │ ├── simulatorcomparison.h │ │ │ ├── swapcoords.cpp │ │ │ ├── tabulated_bonded_interactions.cpp │ │ │ ├── termination.cpp │ │ │ ├── terminationhelper.cpp │ │ │ ├── terminationhelper.h │ │ │ ├── tpitest.cpp │ │ │ ├── trajectory_writing.cpp │ │ │ ├── trajectorycomparison.cpp │ │ │ ├── trajectorycomparison.h │ │ │ ├── trajectoryreader.cpp │ │ │ └── trajectoryreader.h │ ├── mdrun_main.cpp │ └── view │ │ ├── 3dview.cpp │ │ ├── 3dview.h │ │ ├── Xstuff.h │ │ ├── alert.bm │ │ ├── buttons.cpp │ │ ├── buttons.h │ │ ├── dialogs.cpp │ │ ├── dialogs.h │ │ ├── ff.bm │ │ ├── fgrid.cpp │ │ ├── fgrid.h │ │ ├── filter.cpp │ │ ├── gromacs.bm │ │ ├── info.bm │ │ ├── logo.cpp │ │ ├── logo.h │ │ ├── manager.cpp │ │ ├── manager.h │ │ ├── molps.cpp │ │ ├── molps.h │ │ ├── nleg.cpp │ │ ├── nleg.h │ │ ├── nmol.cpp │ │ ├── nmol.h │ │ ├── play.bm │ │ ├── popup.cpp │ │ ├── popup.h │ │ ├── pulldown.cpp │ │ ├── pulldown.h │ │ ├── rewind.bm │ │ ├── stop.bm │ │ ├── stop_ani.bm │ │ ├── view.cpp │ │ ├── view.h │ │ ├── x11.cpp │ │ ├── x11.h │ │ ├── xdlg.cpp │ │ ├── xdlg.h │ │ ├── xdlghi.cpp │ │ ├── xdlghi.h │ │ ├── xdlgitem.cpp │ │ ├── xdlgitem.h │ │ ├── xmb.cpp │ │ ├── xmb.h │ │ ├── xutil.cpp │ │ └── xutil.h └── testutils │ ├── CMakeLists.txt │ ├── TestMacros.cmake │ ├── cmdlinetest.cpp │ ├── cmdlinetest.h │ ├── common-referencedata.xsl │ ├── conftest.cpp │ ├── conftest.h │ ├── copy_xsl.sh │ ├── filematchers.cpp │ ├── filematchers.h │ ├── interactivetest.cpp │ ├── interactivetest.h │ ├── loggertest.cpp │ ├── loggertest.h │ ├── mpi_printer.cpp │ ├── mpi_printer.h │ ├── mpitest.cpp │ ├── mpitest.h │ ├── refdata.cpp │ ├── refdata.h │ ├── refdata_checkers.h │ ├── refdata_impl.h │ ├── refdata_xml.cpp │ ├── refdata_xml.h │ ├── setenv.h │ ├── simulationdatabase.cpp │ ├── simulationdatabase.h │ ├── simulationdatabase │ ├── 1quantum.ndx │ ├── 2quantum.ndx │ ├── 4water.gro │ ├── 4water.top │ ├── OctaneSandwich.gro │ ├── OctaneSandwich.ndx │ ├── OctaneSandwich.top │ ├── ala.gro │ ├── ala.ndx │ ├── ala.top │ ├── alanine_vsite.itp │ ├── alanine_vsite_solvated.gro │ ├── alanine_vsite_solvated.ndx │ ├── alanine_vsite_solvated.top │ ├── alanine_vsite_vacuo.gro │ ├── alanine_vsite_vacuo.ndx │ ├── alanine_vsite_vacuo.top │ ├── allquantum.ndx │ ├── angles1.gro │ ├── angles1.ndx │ ├── angles1.top │ ├── argon12.gro │ ├── argon12.ndx │ ├── argon12.top │ ├── argon5832.gro │ ├── argon5832.ndx │ ├── argon5832.top │ ├── butane1.gro │ ├── butane1.ndx │ ├── butane_a0.xvg │ ├── butane_b0.xvg │ ├── butane_d0.xvg │ ├── dipoles.gro │ ├── dipoles.ndx │ ├── dipoles.top │ ├── ellipsoid-density.mrc │ ├── freeenergy │ │ ├── README.txt │ │ ├── coulandvdwintramol │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ └── topol.top │ │ ├── coulandvdwsequential_coul │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ └── topol.top │ │ ├── coulandvdwsequential_vdw │ │ │ ├── ana.itp │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ └── topol.top │ │ ├── coulandvdwtogether │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ └── topol.top │ │ ├── expanded │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ └── topol.top │ │ ├── relative-position-restraints │ │ │ ├── README │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ ├── no-nb-gpu-support │ │ │ ├── posre.itp │ │ │ └── topol.top │ │ ├── relative │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ ├── no-nb-gpu-support │ │ │ └── topol.top │ │ ├── restraints │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ ├── no-nb-gpu-support │ │ │ └── topol.top │ │ ├── simtemp │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ ├── no-nb-gpu-support │ │ │ └── topol.top │ │ ├── transformAtoB │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ └── topol.top │ │ └── vdwalone │ │ │ ├── conf.gro │ │ │ ├── grompp.mdp │ │ │ ├── no-nb-gpu-support │ │ │ └── topol.top │ ├── glycine_no_constraints_vacuo.gro │ ├── glycine_no_constraints_vacuo.ndx │ ├── glycine_no_constraints_vacuo.top │ ├── glycine_vacuo.gro │ ├── glycine_vacuo.itp │ ├── glycine_vacuo.ndx │ ├── glycine_vacuo.top │ ├── lysozyme.pdb │ ├── lysozyme.top │ ├── mindist.ndx │ ├── mindist_coords.gro │ ├── nonanol_vacuo.gro │ ├── nonanol_vacuo.ndx │ ├── nonanol_vacuo.top │ ├── one-tip5p.g96 │ ├── one-tip5p.ndx │ ├── one-tip5p.top │ ├── orires_1lvz.gro │ ├── orires_1lvz.ndx │ ├── orires_1lvz.top │ ├── scaled-water.g96 │ ├── scaled-water.ndx │ ├── scaled-water.top │ ├── spc-and-methanol.gro │ ├── spc-and-methanol.ndx │ ├── spc-and-methanol.top │ ├── spc-dimer.g96 │ ├── spc-dimer.ndx │ ├── spc-dimer.top │ ├── spc2-traj.g96 │ ├── spc2-traj.gro │ ├── spc2-traj.pdb │ ├── spc2-traj.tng │ ├── spc2-traj.trr │ ├── spc2-traj.xtc │ ├── spc2.gro │ ├── spc2.ndx │ ├── spc2.top │ ├── spc2.trr │ ├── spc216.gro │ ├── spc216.ndx │ ├── spc216.top │ ├── spc216_with_methane.gro │ ├── spc216_with_methane.top │ ├── spc2_and_vacuum.gro │ ├── spc5.ndx │ ├── spc5.pdb │ ├── spc5.top │ ├── spc5_3.ndx │ ├── spc_and_methane.gro │ ├── spc_and_methane.ndx │ ├── spc_and_methane.top │ ├── sw-dimer.g96 │ ├── sw-dimer.ndx │ ├── sw-dimer.top │ ├── tip3p5.gro │ ├── tip3p5.ndx │ ├── tip3p5.top │ ├── villin.g96 │ ├── villin.ndx │ └── villin.top │ ├── stdiohelper.cpp │ ├── stdiohelper.h │ ├── stringtest.cpp │ ├── stringtest.h │ ├── test_device.cpp │ ├── test_device.h │ ├── test_hardware_environment.cpp │ ├── test_hardware_environment.h │ ├── testasserts.cpp │ ├── testasserts.h │ ├── testexceptions.h │ ├── testfilemanager.cpp │ ├── testfilemanager.h │ ├── testfileredirector.cpp │ ├── testfileredirector.h │ ├── testinit.cpp │ ├── testinit.h │ ├── testmatchers.cpp │ ├── testmatchers.h │ ├── testoptions.cpp │ ├── testoptions.h │ ├── tests │ ├── CMakeLists.txt │ ├── interactivetest.cpp │ ├── mpitest.cpp │ ├── refdata_tests.cpp │ ├── testasserts_tests.cpp │ └── xvgtest_tests.cpp │ ├── testutils_doc.h │ ├── textblockmatchers.cpp │ ├── textblockmatchers.h │ ├── tprfilegenerator.cpp │ ├── tprfilegenerator.h │ ├── unittest_main.cpp │ ├── xvgtest.cpp │ └── xvgtest.h └── tests ├── CMakeLists.txt ├── CheckTarget.cmake └── physicalvalidation ├── .gitattributes ├── gmx_physicalvalidation.py ├── physical_validation ├── README.md ├── __init__.py ├── data │ ├── __init__.py │ ├── ensemble_data.py │ ├── flatfile_parser.py │ ├── gromacs_parser.py │ ├── observable_data.py │ ├── parser.py │ ├── simulation_data.py │ ├── system_data.py │ ├── trajectory_data.py │ └── unit_data.py ├── ensemble.py ├── integrator.py ├── kinetic_energy.py └── util │ ├── __init__.py │ ├── ensemble.py │ ├── error.py │ ├── gromacs_interface.py │ ├── integrator.py │ ├── kinetic_energy.py │ ├── plot.py │ └── trajectory.py ├── systems.json ├── systems ├── ens_argon_md-vv_verlet_pme_nh_mttk │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_argon_md-vv_verlet_pme_vr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_argon_md_verlet_pme_vr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_argon_md_verlet_pme_vr_cr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_argon_md_verlet_pme_vr_pr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_water_md-vv_verlet_none_pme_nh_mttk │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_water_md-vv_verlet_settle_pme_vr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_water_md_verlet_settle_pme_vr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_water_md_verlet_settle_pme_vr_cr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── ens_water_md_verlet_settle_pme_vr_pr │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_argon_md-vv_verlet_pme │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_argon_md-vv_verlet_switch │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_argon_md_verlet_pme │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_argon_md_verlet_switch │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_water_md-vv_verlet_lincs_pme_pme │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_water_md-vv_verlet_lincs_pme_switch │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_water_md-vv_verlet_none_pme_pme │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── system.top ├── int_water_md-vv_verlet_none_pme_switch │ └── input │ │ ├── system.gro │ │ ├── system.mdp │ │ └── 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