Apply re-formatting to C++ in src/ tree.
authorM. Eric Irrgang <ericirrgang@gmail.com>
Wed, 16 Dec 2020 17:45:40 +0000 (20:45 +0300)
committerM. Eric Irrgang <ericirrgang@gmail.com>
Wed, 16 Dec 2020 17:47:48 +0000 (20:47 +0300)
commitfdfc58342a6911b18a3d2916f3c07f45b9a204a2
tree5afb4c3604bebc2d8a9643d94184eb45be290a2f
parent182ae679c676a35a3cc7de3a969eb167aa9b166b
Apply re-formatting to C++ in src/ tree.

Apply formatting changes in bulk to reduce noise in subsequent
functional changes.

Will likely need to be repeated if clang-format version is updated
per #3708.

The formatting is sensitive to differences even between llvm tools
versions 7.1.0.2 and 8.0.1.3. Here, I used 7.1.

Refs #3833
637 files changed:
api/gmxapi/cpp/context.cpp
api/gmxapi/cpp/mdsignals.cpp
api/gmxapi/cpp/session.cpp
api/gmxapi/cpp/tpr.cpp
api/legacy/include/gromacs/utility/gmxassert.h
api/legacy/include/gromacs/utility/listoflists.h
api/nblib/gmxcalculator.cpp
api/nblib/gmxsetup.cpp
api/nblib/interactions.cpp
api/nblib/listed_forces/gmxcalculator.cpp
api/nblib/listed_forces/tests/bondtypes.cpp
api/nblib/listed_forces/tests/calculator.cpp
api/nblib/listed_forces/tests/helpers.cpp
api/nblib/molecules.cpp
api/nblib/molecules.h
api/nblib/ppmap.h
api/nblib/samples/argon-forces-integration.cpp
api/nblib/tests/integrator.cpp
api/nblib/tests/interactions.cpp
api/nblib/tests/nbkernelsystem.cpp
api/nblib/tests/testsystems.cpp
api/nblib/tests/topology.cpp
api/nblib/topology.cpp
api/nblib/topologyhelpers.cpp
api/nblib/util/user.cpp
python_packaging/src/gmxapi/export_context.cpp
python_packaging/src/gmxapi/export_exceptions.cpp
python_packaging/src/gmxapi/export_system.cpp
python_packaging/src/gmxapi/export_tprfile.cpp
python_packaging/src/gmxapi/module.cpp
src/api/cpp/tests/testingconfiguration.h
src/gromacs/analysisdata/arraydata.cpp
src/gromacs/analysisdata/datastorage.cpp
src/gromacs/analysisdata/modules/lifetime.cpp
src/gromacs/analysisdata/modules/plot.cpp
src/gromacs/analysisdata/tests/datatest.cpp
src/gromacs/analysisdata/tests/mock_datamodule.cpp
src/gromacs/applied_forces/awh/awh.cpp
src/gromacs/applied_forces/awh/bias.cpp
src/gromacs/applied_forces/awh/bias.h
src/gromacs/applied_forces/awh/biasgrid.cpp
src/gromacs/applied_forces/awh/biasgrid.h
src/gromacs/applied_forces/awh/biasstate.cpp
src/gromacs/applied_forces/awh/coordstate.cpp
src/gromacs/applied_forces/awh/correlationhistory.cpp
src/gromacs/applied_forces/awh/histogramsize.cpp
src/gromacs/applied_forces/awh/read_params.cpp
src/gromacs/applied_forces/awh/tests/bias.cpp
src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp
src/gromacs/applied_forces/awh/tests/biasstate.cpp
src/gromacs/applied_forces/densityfitting/densityfitting.cpp
src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp
src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp
src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp
src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp
src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp
src/gromacs/applied_forces/electricfield.cpp
src/gromacs/commandline/cmdlinehelpmodule.cpp
src/gromacs/commandline/cmdlinehelpwriter.cpp
src/gromacs/commandline/pargs.cpp
src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
src/gromacs/commandline/tests/pargs.cpp
src/gromacs/coordinateio/coordinatefile.cpp
src/gromacs/coordinateio/outputadaptercontainer.cpp
src/gromacs/coordinateio/tests/coordinate_test.h
src/gromacs/coordinateio/tests/outputadapters.h
src/gromacs/correlationfunctions/autocorr.cpp
src/gromacs/correlationfunctions/expfit.cpp
src/gromacs/correlationfunctions/gmx_lmcurve.cpp
src/gromacs/correlationfunctions/manyautocorrelation.cpp
src/gromacs/correlationfunctions/tests/autocorr.cpp
src/gromacs/correlationfunctions/tests/expfit.cpp
src/gromacs/domdec/box.cpp
src/gromacs/domdec/cellsizes.cpp
src/gromacs/domdec/collect.cpp
src/gromacs/domdec/distribute.cpp
src/gromacs/domdec/domdec.cpp
src/gromacs/domdec/domdec_constraints.cpp
src/gromacs/domdec/domdec_network.cpp
src/gromacs/domdec/domdec_setup.cpp
src/gromacs/domdec/domdec_specatomcomm.cpp
src/gromacs/domdec/domdec_topology.cpp
src/gromacs/domdec/domdec_vsite.cpp
src/gromacs/domdec/dump.cpp
src/gromacs/domdec/gpuhaloexchange_impl.cu
src/gromacs/domdec/mdsetup.cpp
src/gromacs/domdec/partition.cpp
src/gromacs/domdec/redistribute.cpp
src/gromacs/domdec/tests/haloexchange_mpi.cpp
src/gromacs/essentialdynamics/edsam.cpp
src/gromacs/ewald/long_range_correction.cpp
src/gromacs/ewald/pme.cpp
src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cu
src/gromacs/ewald/pme_gather.clh
src/gromacs/ewald/pme_gather.cu
src/gromacs/ewald/pme_gpu.cpp
src/gromacs/ewald/pme_gpu_3dfft.cu
src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp
src/gromacs/ewald/pme_gpu_calculate_splines.cuh
src/gromacs/ewald/pme_gpu_internal.cpp
src/gromacs/ewald/pme_gpu_program_impl_ocl.cpp
src/gromacs/ewald/pme_grid.cpp
src/gromacs/ewald/pme_load_balancing.cpp
src/gromacs/ewald/pme_only.cpp
src/gromacs/ewald/pme_pp.cpp
src/gromacs/ewald/pme_pp_comm_gpu_impl.cu
src/gromacs/ewald/pme_redistribute.cpp
src/gromacs/ewald/pme_solve.cpp
src/gromacs/ewald/pme_spread.clh
src/gromacs/ewald/pme_spread.cpp
src/gromacs/ewald/pme_spread.cu
src/gromacs/ewald/tests/pmebsplinetest.cpp
src/gromacs/ewald/tests/pmegathertest.cpp
src/gromacs/ewald/tests/pmesolvetest.cpp
src/gromacs/ewald/tests/pmesplinespreadtest.cpp
src/gromacs/ewald/tests/pmetestcommon.cpp
src/gromacs/fft/calcgrid.cpp
src/gromacs/fft/fft5d.cpp
src/gromacs/fft/fft_fftw3.cpp
src/gromacs/fft/parallel_3dfft.cpp
src/gromacs/fft/tests/fft.cpp
src/gromacs/fileio/checkpoint.cpp
src/gromacs/fileio/confio.cpp
src/gromacs/fileio/enxio.cpp
src/gromacs/fileio/espio.cpp
src/gromacs/fileio/filetypes.cpp
src/gromacs/fileio/g96io.cpp
src/gromacs/fileio/gmxfio_xdr.cpp
src/gromacs/fileio/groio.cpp
src/gromacs/fileio/libxdrf.cpp
src/gromacs/fileio/matio.cpp
src/gromacs/fileio/mrcdensitymap.cpp
src/gromacs/fileio/mrcdensitymapheader.cpp
src/gromacs/fileio/mtxio.cpp
src/gromacs/fileio/pdbio.cpp
src/gromacs/fileio/readinp.cpp
src/gromacs/fileio/tests/confio.cpp
src/gromacs/fileio/tests/mrcdensitymap.cpp
src/gromacs/fileio/tngio.cpp
src/gromacs/fileio/tpxio.cpp
src/gromacs/fileio/trrio.cpp
src/gromacs/fileio/trxio.cpp
src/gromacs/fileio/vmdio.cpp
src/gromacs/fileio/warninp.cpp
src/gromacs/fileio/writeps.cpp
src/gromacs/fileio/xtcio.cpp
src/gromacs/fileio/xvgr.cpp
src/gromacs/gmxana/anadih.cpp
src/gromacs/gmxana/dlist.cpp
src/gromacs/gmxana/eigio.cpp
src/gromacs/gmxana/fitahx.cpp
src/gromacs/gmxana/gmx_anaeig.cpp
src/gromacs/gmxana/gmx_analyze.cpp
src/gromacs/gmxana/gmx_angle.cpp
src/gromacs/gmxana/gmx_awh.cpp
src/gromacs/gmxana/gmx_bar.cpp
src/gromacs/gmxana/gmx_bundle.cpp
src/gromacs/gmxana/gmx_chi.cpp
src/gromacs/gmxana/gmx_cluster.cpp
src/gromacs/gmxana/gmx_clustsize.cpp
src/gromacs/gmxana/gmx_confrms.cpp
src/gromacs/gmxana/gmx_covar.cpp
src/gromacs/gmxana/gmx_current.cpp
src/gromacs/gmxana/gmx_density.cpp
src/gromacs/gmxana/gmx_densmap.cpp
src/gromacs/gmxana/gmx_densorder.cpp
src/gromacs/gmxana/gmx_dielectric.cpp
src/gromacs/gmxana/gmx_dipoles.cpp
src/gromacs/gmxana/gmx_disre.cpp
src/gromacs/gmxana/gmx_do_dssp.cpp
src/gromacs/gmxana/gmx_dos.cpp
src/gromacs/gmxana/gmx_dyecoupl.cpp
src/gromacs/gmxana/gmx_enemat.cpp
src/gromacs/gmxana/gmx_energy.cpp
src/gromacs/gmxana/gmx_filter.cpp
src/gromacs/gmxana/gmx_gyrate.cpp
src/gromacs/gmxana/gmx_h2order.cpp
src/gromacs/gmxana/gmx_hbond.cpp
src/gromacs/gmxana/gmx_helix.cpp
src/gromacs/gmxana/gmx_helixorient.cpp
src/gromacs/gmxana/gmx_hydorder.cpp
src/gromacs/gmxana/gmx_lie.cpp
src/gromacs/gmxana/gmx_make_edi.cpp
src/gromacs/gmxana/gmx_mdmat.cpp
src/gromacs/gmxana/gmx_mindist.cpp
src/gromacs/gmxana/gmx_msd.cpp
src/gromacs/gmxana/gmx_nmeig.cpp
src/gromacs/gmxana/gmx_nmens.cpp
src/gromacs/gmxana/gmx_nmr.cpp
src/gromacs/gmxana/gmx_nmtraj.cpp
src/gromacs/gmxana/gmx_order.cpp
src/gromacs/gmxana/gmx_polystat.cpp
src/gromacs/gmxana/gmx_potential.cpp
src/gromacs/gmxana/gmx_principal.cpp
src/gromacs/gmxana/gmx_rama.cpp
src/gromacs/gmxana/gmx_rms.cpp
src/gromacs/gmxana/gmx_rmsdist.cpp
src/gromacs/gmxana/gmx_rmsf.cpp
src/gromacs/gmxana/gmx_rotacf.cpp
src/gromacs/gmxana/gmx_rotmat.cpp
src/gromacs/gmxana/gmx_saltbr.cpp
src/gromacs/gmxana/gmx_sans.cpp
src/gromacs/gmxana/gmx_saxs.cpp
src/gromacs/gmxana/gmx_sham.cpp
src/gromacs/gmxana/gmx_sigeps.cpp
src/gromacs/gmxana/gmx_sorient.cpp
src/gromacs/gmxana/gmx_spatial.cpp
src/gromacs/gmxana/gmx_spol.cpp
src/gromacs/gmxana/gmx_tcaf.cpp
src/gromacs/gmxana/gmx_traj.cpp
src/gromacs/gmxana/gmx_trjorder.cpp
src/gromacs/gmxana/gmx_vanhove.cpp
src/gromacs/gmxana/gmx_velacc.cpp
src/gromacs/gmxana/gmx_wham.cpp
src/gromacs/gmxana/gmx_xpm2ps.cpp
src/gromacs/gmxana/hxprops.cpp
src/gromacs/gmxana/nrama.cpp
src/gromacs/gmxana/pp2shift.cpp
src/gromacs/gmxana/princ.cpp
src/gromacs/gmxana/sfactor.cpp
src/gromacs/gmxana/thermochemistry.cpp
src/gromacs/gmxlib/network.cpp
src/gromacs/gmxlib/nrnb.cpp
src/gromacs/gmxpreprocess/add_par.cpp
src/gromacs/gmxpreprocess/convparm.cpp
src/gromacs/gmxpreprocess/editconf.cpp
src/gromacs/gmxpreprocess/fflibutil.cpp
src/gromacs/gmxpreprocess/gen_ad.cpp
src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
src/gromacs/gmxpreprocess/gen_vsite.cpp
src/gromacs/gmxpreprocess/genconf.cpp
src/gromacs/gmxpreprocess/genhydro.cpp
src/gromacs/gmxpreprocess/genion.cpp
src/gromacs/gmxpreprocess/genrestr.cpp
src/gromacs/gmxpreprocess/gmxcpp.cpp
src/gromacs/gmxpreprocess/gpp_atomtype.cpp
src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/gmxpreprocess/h_db.cpp
src/gromacs/gmxpreprocess/insert_molecules.cpp
src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
src/gromacs/gmxpreprocess/nm2type.cpp
src/gromacs/gmxpreprocess/pdb2gmx.cpp
src/gromacs/gmxpreprocess/pdb2top.cpp
src/gromacs/gmxpreprocess/pgutil.cpp
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/gmxpreprocess/readpull.cpp
src/gromacs/gmxpreprocess/readrot.cpp
src/gromacs/gmxpreprocess/resall.cpp
src/gromacs/gmxpreprocess/solvate.cpp
src/gromacs/gmxpreprocess/specbond.cpp
src/gromacs/gmxpreprocess/ter_db.cpp
src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
src/gromacs/gmxpreprocess/tests/readir.cpp
src/gromacs/gmxpreprocess/tomorse.cpp
src/gromacs/gmxpreprocess/topdirs.cpp
src/gromacs/gmxpreprocess/topio.cpp
src/gromacs/gmxpreprocess/toppush.cpp
src/gromacs/gmxpreprocess/topshake.cpp
src/gromacs/gmxpreprocess/toputil.cpp
src/gromacs/gmxpreprocess/vsite_parm.cpp
src/gromacs/gmxpreprocess/x2top.cpp
src/gromacs/gmxpreprocess/xlate.cpp
src/gromacs/gpu_utils/cudautils.cuh
src/gromacs/gpu_utils/device_context_ocl.cpp
src/gromacs/gpu_utils/device_stream_ocl.cpp
src/gromacs/gpu_utils/devicebuffer.cuh
src/gromacs/gpu_utils/devicebuffer_ocl.h
src/gromacs/gpu_utils/gpu_utils.cu
src/gromacs/gpu_utils/gpuregiontimer_ocl.h
src/gromacs/gpu_utils/ocl_caching.cpp
src/gromacs/gpu_utils/ocl_compiler.cpp
src/gromacs/gpu_utils/oclutils.h
src/gromacs/gpu_utils/tests/device_buffer.cpp
src/gromacs/gpu_utils/tests/device_stream_manager.cpp
src/gromacs/gpu_utils/tests/devicetransfers_ocl.cpp
src/gromacs/gpu_utils/tests/typecasts_runner.cu
src/gromacs/hardware/cpuinfo.cpp
src/gromacs/hardware/detecthardware.cpp
src/gromacs/hardware/device_information.h
src/gromacs/hardware/device_management.cu
src/gromacs/hardware/device_management_common.cpp
src/gromacs/hardware/device_management_ocl.cpp
src/gromacs/hardware/device_management_sycl.cpp
src/gromacs/hardware/hardwaretopology.cpp
src/gromacs/hardware/identifyavx512fmaunits.cpp
src/gromacs/hardware/printhardware.cpp
src/gromacs/hardware/tests/hardwaretopology.cpp
src/gromacs/imd/imd.cpp
src/gromacs/linearalgebra/eigensolver.cpp
src/gromacs/linearalgebra/gmx_arpack.cpp
src/gromacs/listed_forces/bonded.cpp
src/gromacs/listed_forces/disre.cpp
src/gromacs/listed_forces/gpubonded_impl.cu
src/gromacs/listed_forces/gpubondedkernels.cu
src/gromacs/listed_forces/listed_forces.cpp
src/gromacs/listed_forces/manage_threading.cpp
src/gromacs/listed_forces/orires.cpp
src/gromacs/listed_forces/pairs.cpp
src/gromacs/listed_forces/position_restraints.cpp
src/gromacs/listed_forces/tests/bonded.cpp
src/gromacs/math/densityfit.cpp
src/gromacs/math/densityfittingforce.cpp
src/gromacs/math/gausstransform.cpp
src/gromacs/math/matrix.cpp
src/gromacs/math/neldermead.cpp
src/gromacs/math/optimization.cpp
src/gromacs/math/tests/arrayrefwithpadding.cpp
src/gromacs/math/tests/coordinatetransformation.cpp
src/gromacs/math/tests/densityfit.cpp
src/gromacs/math/tests/dofit.cpp
src/gromacs/math/tests/gausstransform.cpp
src/gromacs/math/veccompare.cpp
src/gromacs/math/vecdump.cpp
src/gromacs/mdlib/calc_verletbuf.cpp
src/gromacs/mdlib/calcvir.cpp
src/gromacs/mdlib/constr.cpp
src/gromacs/mdlib/constraintrange.cpp
src/gromacs/mdlib/coupling.cpp
src/gromacs/mdlib/dispersioncorrection.cpp
src/gromacs/mdlib/ebin.cpp
src/gromacs/mdlib/enerdata_utils.cpp
src/gromacs/mdlib/energydrifttracker.cpp
src/gromacs/mdlib/energyoutput.cpp
src/gromacs/mdlib/expanded.cpp
src/gromacs/mdlib/force.cpp
src/gromacs/mdlib/forcerec.cpp
src/gromacs/mdlib/freeenergyparameters.cpp
src/gromacs/mdlib/gmx_omp_nthreads.cpp
src/gromacs/mdlib/gpuforcereduction_impl.cu
src/gromacs/mdlib/leapfrog_gpu.cu
src/gromacs/mdlib/leapfrog_gpu_sycl.cpp
src/gromacs/mdlib/lincs.cpp
src/gromacs/mdlib/lincs_gpu.cu
src/gromacs/mdlib/md_support.cpp
src/gromacs/mdlib/mdatoms.cpp
src/gromacs/mdlib/mdebin_bar.cpp
src/gromacs/mdlib/mdoutf.cpp
src/gromacs/mdlib/membed.cpp
src/gromacs/mdlib/nsgrid.cpp
src/gromacs/mdlib/perf_est.cpp
src/gromacs/mdlib/resethandler.h
src/gromacs/mdlib/rf_util.cpp
src/gromacs/mdlib/settle.cpp
src/gromacs/mdlib/settle_gpu.cu
src/gromacs/mdlib/shake.cpp
src/gromacs/mdlib/sighandler.cpp
src/gromacs/mdlib/sim_util.cpp
src/gromacs/mdlib/simulationsignal.cpp
src/gromacs/mdlib/splitter.cpp
src/gromacs/mdlib/stat.cpp
src/gromacs/mdlib/stophandler.cpp
src/gromacs/mdlib/tests/constr.cpp
src/gromacs/mdlib/tests/constrtestrunners.cpp
src/gromacs/mdlib/tests/constrtestrunners.cu
src/gromacs/mdlib/tests/energyoutput.cpp
src/gromacs/mdlib/tests/leapfrog.cpp
src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp
src/gromacs/mdlib/tests/settle.cpp
src/gromacs/mdlib/tests/settletestrunners.cpp
src/gromacs/mdlib/tests/settletestrunners.cu
src/gromacs/mdlib/tests/shake.cpp
src/gromacs/mdlib/trajectory_writing.cpp
src/gromacs/mdlib/update.cpp
src/gromacs/mdlib/update_constrain_gpu_impl.cu
src/gromacs/mdlib/update_vv.cpp
src/gromacs/mdlib/updategroups.cpp
src/gromacs/mdlib/vcm.cpp
src/gromacs/mdlib/vsite.cpp
src/gromacs/mdlib/wall.cpp
src/gromacs/mdrun/legacymdrunoptions.cpp
src/gromacs/mdrun/legacymdrunoptions.h
src/gromacs/mdrun/md.cpp
src/gromacs/mdrun/mimic.cpp
src/gromacs/mdrun/minimize.cpp
src/gromacs/mdrun/replicaexchange.cpp
src/gromacs/mdrun/rerun.cpp
src/gromacs/mdrun/runner.cpp
src/gromacs/mdrun/shellfc.cpp
src/gromacs/mdrun/simulationinput.cpp
src/gromacs/mdrun/tpi.cpp
src/gromacs/mdrunutility/handlerestart.cpp
src/gromacs/mdrunutility/multisim.cpp
src/gromacs/mdrunutility/printtime.cpp
src/gromacs/mdrunutility/tests/threadaffinitytest.h
src/gromacs/mdrunutility/threadaffinity.cpp
src/gromacs/mdspan/extensions.h
src/gromacs/mdspan/tests/mdspan.cpp
src/gromacs/mdtypes/checkpointdata.h
src/gromacs/mdtypes/forcebuffers.cpp
src/gromacs/mdtypes/inputrec.cpp
src/gromacs/mdtypes/md_enums.cpp
src/gromacs/mdtypes/multipletimestepping.cpp
src/gromacs/mdtypes/state.cpp
src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp
src/gromacs/modularsimulator/checkpointhelper.cpp
src/gromacs/modularsimulator/checkpointhelper.h
src/gromacs/modularsimulator/computeglobalselement.cpp
src/gromacs/modularsimulator/constraintelement.cpp
src/gromacs/modularsimulator/domdechelper.cpp
src/gromacs/modularsimulator/energydata.cpp
src/gromacs/modularsimulator/forceelement.cpp
src/gromacs/modularsimulator/freeenergyperturbationdata.cpp
src/gromacs/modularsimulator/modularsimulator.cpp
src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
src/gromacs/modularsimulator/propagator.cpp
src/gromacs/modularsimulator/signallers.h
src/gromacs/modularsimulator/simulatoralgorithm.cpp
src/gromacs/modularsimulator/simulatoralgorithm.h
src/gromacs/modularsimulator/statepropagatordata.cpp
src/gromacs/modularsimulator/topologyholder.cpp
src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp
src/gromacs/nbnxm/atomdata.cpp
src/gromacs/nbnxm/benchmark/bench_setup.cpp
src/gromacs/nbnxm/benchmark/bench_system.cpp
src/gromacs/nbnxm/clusterdistancekerneltype.h
src/gromacs/nbnxm/cuda/nbnxm_cuda.cu
src/gromacs/nbnxm/cuda/nbnxm_cuda_data_mgmt.cu
src/gromacs/nbnxm/cuda/nbnxm_cuda_kernel.cuh
src/gromacs/nbnxm/gpu_common.h
src/gromacs/nbnxm/grid.cpp
src/gromacs/nbnxm/gridset.cpp
src/gromacs/nbnxm/kerneldispatch.cpp
src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
src/gromacs/nbnxm/kernels_reference/kernel_ref.h
src/gromacs/nbnxm/kernels_simd_2xmm/kernel_common.h
src/gromacs/nbnxm/kernels_simd_2xmm/kernel_inner.h
src/gromacs/nbnxm/kernels_simd_4xm/kernel_inner.h
src/gromacs/nbnxm/nbnxm.cpp
src/gromacs/nbnxm/nbnxm_geometry.h
src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
src/gromacs/nbnxm/nbnxm_setup.cpp
src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp
src/gromacs/nbnxm/opencl/nbnxm_ocl_data_mgmt.cpp
src/gromacs/nbnxm/opencl/nbnxm_ocl_jit_support.cpp
src/gromacs/nbnxm/opencl/nbnxm_ocl_kernel.clh
src/gromacs/nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
src/gromacs/nbnxm/pairlist.cpp
src/gromacs/nbnxm/pairlist_tuning.cpp
src/gromacs/nbnxm/pairsearch.cpp
src/gromacs/nbnxm/pairsearch.h
src/gromacs/nbnxm/prunekerneldispatch.cpp
src/gromacs/onlinehelp/helpmanager.cpp
src/gromacs/onlinehelp/helpwritercontext.cpp
src/gromacs/options/basicoptions.h
src/gromacs/options/filenameoption.cpp
src/gromacs/options/filenameoptionmanager.cpp
src/gromacs/options/timeunitmanager.cpp
src/gromacs/options/treesupport.cpp
src/gromacs/pbcutil/mshift.cpp
src/gromacs/pbcutil/pbc.cpp
src/gromacs/pbcutil/pbcmethods.cpp
src/gromacs/pbcutil/rmpbc.cpp
src/gromacs/pbcutil/tests/com.cpp
src/gromacs/pulling/output.cpp
src/gromacs/pulling/pull.cpp
src/gromacs/pulling/pull_rotation.cpp
src/gromacs/pulling/pullutil.cpp
src/gromacs/pulling/tests/pull.cpp
src/gromacs/random/tests/threefry.cpp
src/gromacs/selection/compiler.cpp
src/gromacs/selection/evaluate.cpp
src/gromacs/selection/indexutil.cpp
src/gromacs/selection/nbsearch.cpp
src/gromacs/selection/params.cpp
src/gromacs/selection/parsetree.cpp
src/gromacs/selection/poscalc.cpp
src/gromacs/selection/selection.cpp
src/gromacs/selection/selectioncollection.cpp
src/gromacs/selection/selectionoptionmanager.cpp
src/gromacs/selection/selelem.cpp
src/gromacs/selection/selmethod.cpp
src/gromacs/selection/sm_insolidangle.cpp
src/gromacs/selection/sm_merge.cpp
src/gromacs/selection/sm_permute.cpp
src/gromacs/selection/tests/indexutil.cpp
src/gromacs/selection/tests/nbsearch.cpp
src/gromacs/selection/tests/poscalc.cpp
src/gromacs/selection/tests/selectioncollection.cpp
src/gromacs/selection/tests/toputils.cpp
src/gromacs/simd/impl_arm_sve/impl_arm_sve_simd4_double.h
src/gromacs/simd/impl_arm_sve/impl_arm_sve_simd_double.h
src/gromacs/simd/impl_arm_sve/impl_arm_sve_simd_float.h
src/gromacs/simd/impl_arm_sve/impl_arm_sve_util_double.h
src/gromacs/simd/impl_ibm_vmx/impl_ibm_vmx_simd4_float.h
src/gromacs/simd/impl_ibm_vmx/impl_ibm_vmx_simd_float.h
src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_double.h
src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_simd_double.h
src/gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_util_float.h
src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_simd4_double.h
src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_simd4_float.h
src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_simd_double.h
src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_simd_float.h
src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_double.h
src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h
src/gromacs/simd/impl_x86_mic/impl_x86_mic_simd4_double.h
src/gromacs/simd/impl_x86_mic/impl_x86_mic_simd4_float.h
src/gromacs/simd/impl_x86_mic/impl_x86_mic_simd_double.h
src/gromacs/simd/impl_x86_mic/impl_x86_mic_simd_float.h
src/gromacs/simd/impl_x86_mic/impl_x86_mic_util_double.h
src/gromacs/simd/impl_x86_mic/impl_x86_mic_util_float.h
src/gromacs/simd/support.cpp
src/gromacs/simd/tests/simd4_vector_operations.cpp
src/gromacs/simd/tests/simd_floatingpoint.cpp
src/gromacs/simd/tests/simd_math.cpp
src/gromacs/simd/tests/simd_vector_operations.cpp
src/gromacs/statistics/statistics.cpp
src/gromacs/swap/swapcoords.cpp
src/gromacs/tables/cubicsplinetable.cpp
src/gromacs/tables/cubicsplinetable.h
src/gromacs/tables/forcetable.cpp
src/gromacs/tables/quadraticsplinetable.cpp
src/gromacs/tables/quadraticsplinetable.h
src/gromacs/tables/splineutil.cpp
src/gromacs/tables/tests/splinetable.cpp
src/gromacs/taskassignment/findallgputasks.cpp
src/gromacs/taskassignment/reportgpuusage.cpp
src/gromacs/taskassignment/resourcedivision.cpp
src/gromacs/taskassignment/taskassignment.cpp
src/gromacs/taskassignment/usergpuids.cpp
src/gromacs/timing/wallcycle.cpp
src/gromacs/tools/check.cpp
src/gromacs/tools/convert_tpr.cpp
src/gromacs/tools/dump.cpp
src/gromacs/tools/eneconv.cpp
src/gromacs/tools/mk_angndx.cpp
src/gromacs/tools/pme_error.cpp
src/gromacs/tools/report_methods.cpp
src/gromacs/tools/tests/dump.cpp
src/gromacs/tools/tests/report_methods.cpp
src/gromacs/tools/trjcat.cpp
src/gromacs/tools/trjconv.cpp
src/gromacs/tools/tune_pme.cpp
src/gromacs/topology/atomprop.cpp
src/gromacs/topology/atoms.cpp
src/gromacs/topology/block.cpp
src/gromacs/topology/forcefieldparameters.cpp
src/gromacs/topology/idef.cpp
src/gromacs/topology/ifunc.cpp
src/gromacs/topology/index.cpp
src/gromacs/topology/invblock.cpp
src/gromacs/topology/mtop_lookup.h
src/gromacs/topology/mtop_util.cpp
src/gromacs/topology/residuetypes.cpp
src/gromacs/topology/symtab.cpp
src/gromacs/topology/topology.cpp
src/gromacs/topology/topsort.cpp
src/gromacs/trajectory/energyframe.cpp
src/gromacs/trajectoryanalysis/modules/angle.cpp
src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
src/gromacs/trajectoryanalysis/modules/distance.cpp
src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
src/gromacs/trajectoryanalysis/modules/freevolume.cpp
src/gromacs/trajectoryanalysis/modules/pairdist.cpp
src/gromacs/trajectoryanalysis/modules/sasa.cpp
src/gromacs/trajectoryanalysis/modules/select.cpp
src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
src/gromacs/trajectoryanalysis/runnercommon.cpp
src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
src/gromacs/trajectoryanalysis/tests/moduletest.cpp
src/gromacs/trajectoryanalysis/tests/rdf.cpp
src/gromacs/trajectoryanalysis/tests/select.cpp
src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
src/gromacs/trajectoryanalysis/tests/test_selection.cpp
src/gromacs/utility/binaryinformation.cpp
src/gromacs/utility/coolstuff.cpp
src/gromacs/utility/cstringutil.cpp
src/gromacs/utility/directoryenumerator.cpp
src/gromacs/utility/exceptions.cpp
src/gromacs/utility/fatalerror.cpp
src/gromacs/utility/filestream.cpp
src/gromacs/utility/futil.cpp
src/gromacs/utility/gmxomp.cpp
src/gromacs/utility/keyvaluetree.cpp
src/gromacs/utility/path.cpp
src/gromacs/utility/pleasecite.cpp
src/gromacs/utility/smalloc.cpp
src/gromacs/utility/strconvert.h
src/gromacs/utility/strdb.cpp
src/gromacs/utility/stringutil.cpp
src/gromacs/utility/tests/inmemoryserializer.cpp
src/gromacs/utility/tests/keyvaluetreetransform.cpp
src/gromacs/utility/tests/path.cpp
src/gromacs/utility/tests/stringutil.cpp
src/gromacs/utility/tests/template_mp.cpp
src/programs/legacymodules.cpp
src/programs/mdrun/mdrun.cpp
src/programs/mdrun/tests/energycomparison.cpp
src/programs/mdrun/tests/ewaldsurfaceterm.cpp
src/programs/mdrun/tests/exactcontinuation.cpp
src/programs/mdrun/tests/freeenergy.cpp
src/programs/mdrun/tests/initialconstraints.cpp
src/programs/mdrun/tests/minimize.cpp
src/programs/mdrun/tests/moduletest.cpp
src/programs/mdrun/tests/multiple_time_stepping.cpp
src/programs/mdrun/tests/multisimtest.cpp
src/programs/mdrun/tests/nonbonded_bench.cpp
src/programs/mdrun/tests/normalmodes.cpp
src/programs/mdrun/tests/outputfiles.cpp
src/programs/mdrun/tests/periodicactions.cpp
src/programs/mdrun/tests/rerun.cpp
src/programs/mdrun/tests/simple_mdrun.cpp
src/programs/mdrun/tests/simulator.cpp
src/programs/mdrun/tests/termination.cpp
src/programs/mdrun/tests/tpitest.cpp
src/programs/mdrun/tests/trajectorycomparison.cpp
src/programs/mdrun/tests/trajectoryreader.cpp
src/programs/mdrun_main.cpp
src/programs/view/buttons.cpp
src/programs/view/dialogs.cpp
src/programs/view/fgrid.cpp
src/programs/view/filter.cpp
src/programs/view/logo.cpp
src/programs/view/manager.cpp
src/programs/view/molps.cpp
src/programs/view/nmol.cpp
src/programs/view/popup.cpp
src/programs/view/pulldown.cpp
src/programs/view/view.cpp
src/programs/view/x11.cpp
src/programs/view/xdlg.cpp
src/programs/view/xdlghi.cpp
src/programs/view/xdlgitem.cpp
src/programs/view/xmb.cpp
src/programs/view/xutil.cpp
src/testutils/cmdlinetest.cpp
src/testutils/include/testutils/testasserts.h
src/testutils/refdata.cpp
src/testutils/simulationdatabase.cpp
src/testutils/testasserts.cpp
src/testutils/testinit.cpp
src/testutils/tests/xvgtest_tests.cpp
src/testutils/unittest_main.cpp