BioD PNPI Git Repos - alexxy/gromacs.git/commit - src/gromacs/gmxlib/calcgrid.cpp

biod.pnpi.spb.ru / alexxy / gromacs.git / commit

author	David van der Spoel <spoel@xray.bmc.uu.se>
	Wed, 4 Nov 2015 12:28:04 +0000 (13:28 +0100)
committer	Gerrit Code Review <gerrit@gerrit.gromacs.org>
	Tue, 10 Nov 2015 23:53:01 +0000 (00:53 +0100)
commit	2a9f03845068f94bb3859f9ba8e18d3e86585ce0
tree	94b30dc294c2dbfa4f8b3f6f01356744633eea36	tree \| snapshot
parent	6424c7bc3c6ce0f7b09f6f7cd79245c23c0149ba	commit \| diff

Removed legacyheaders/typedefs.h

More cleaning up in legacyheaders. Mostly this patch involves
shuffling around include files, and adding a couple of forward
declarations. Renames gmxlib/typedefs.* to mdtypes/state.* and
introduces new utility/int64_to_int.cpp with header.
Introduced new directory mdtypes to resolve circular dependencies.
Right now state.* and history files
are the only files living there.

Part of #1415

Change-Id: I5dc59a2ca3bd1f9c5391f4b9deb9f116b30106fc

426 files changed:

src/gromacs/CMakeLists.txt		diff \| blob \| history
src/gromacs/domdec/domdec.cpp		diff \| blob \| history
src/gromacs/domdec/domdec_box.cpp		diff \| blob \| history
src/gromacs/domdec/domdec_setup.cpp		diff \| blob \| history
src/gromacs/domdec/domdec_topology.cpp		diff \| blob \| history
src/gromacs/essentialdynamics/edsam.cpp		diff \| blob \| history
src/gromacs/essentialdynamics/edsam.h		diff \| blob \| history
src/gromacs/ewald/pme-internal.h		diff \| blob \| history
src/gromacs/ewald/pme-only.cpp		diff \| blob \| history
src/gromacs/ewald/pme-pp.cpp		diff \| blob \| history
src/gromacs/fileio/checkpoint.cpp	[moved from src/gromacs/gmxlib/checkpoint.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/fileio/checkpoint.h	[moved from src/gromacs/legacyheaders/checkpoint.h with 98% similarity]	diff \| blob \| history
src/gromacs/fileio/tpxio.cpp		diff \| blob \| history
src/gromacs/fileio/trxio.cpp		diff \| blob \| history
src/gromacs/gmxana/anadih.cpp		diff \| blob \| history
src/gromacs/gmxana/dens_filter.cpp		diff \| blob \| history
src/gromacs/gmxana/edittop.cpp		diff \| blob \| history
src/gromacs/gmxana/eigio.h		diff \| blob \| history
src/gromacs/gmxana/fitahx.h		diff \| blob \| history
src/gromacs/gmxana/gmx_anadock.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_anaeig.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_analyze.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_angle.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_bar.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_bundle.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_chi.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_cluster.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_clustsize.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_confrms.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_covar.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_current.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_density.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_densmap.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_densorder.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_dielectric.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_disre.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_do_dssp.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_dos.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_editconf.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_eneconv.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_enemat.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_energy.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_filter.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_genion.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_genpr.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_gyrate.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_h2order.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_hbond.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_helix.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_helixorient.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_hydorder.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_lie.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_make_edi.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_make_ndx.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_mdmat.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_mindist.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_mk_angndx.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_msd.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_nmeig.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_nmens.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_nmtraj.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_order.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_pme_error.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_polystat.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_potential.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_principal.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_rama.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_rms.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_rmsdist.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_rmsf.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_rotacf.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_rotmat.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_saltbr.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_sans.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_sham.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_sigeps.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_spatial.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_tcaf.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_traj.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_trjcat.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_trjconv.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_trjorder.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_tune_pme.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_vanhove.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_velacc.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_wham.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_wheel.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_xpm2ps.cpp		diff \| blob \| history
src/gromacs/gmxana/hxprops.cpp		diff \| blob \| history
src/gromacs/gmxana/hxprops.h		diff \| blob \| history
src/gromacs/gmxana/interf.h		diff \| blob \| history
src/gromacs/gmxana/powerspect.cpp		diff \| blob \| history
src/gromacs/gmxana/powerspect.h		diff \| blob \| history
src/gromacs/gmxana/pp2shift.cpp		diff \| blob \| history
src/gromacs/gmxana/princ.cpp		diff \| blob \| history
src/gromacs/gmxana/princ.h		diff \| blob \| history
src/gromacs/gmxana/sfactor.cpp		diff \| blob \| history
src/gromacs/gmxlib/calcgrid.cpp		diff \| blob \| history
src/gromacs/gmxlib/chargegroup.cpp		diff \| blob \| history
src/gromacs/gmxlib/cuda_tools/cudautils.cu		diff \| blob \| history
src/gromacs/gmxlib/disre.cpp		diff \| blob \| history
src/gromacs/gmxlib/disre.h		diff \| blob \| history
src/gromacs/gmxlib/gmx_detect_hardware.cpp		diff \| blob \| history
src/gromacs/gmxlib/gmx_omp_nthreads.cpp		diff \| blob \| history
src/gromacs/gmxlib/ifunc.cpp		diff \| blob \| history
src/gromacs/gmxlib/inputrec.cpp		diff \| blob \| history
src/gromacs/gmxlib/main.h		diff \| blob \| history
src/gromacs/gmxlib/names.cpp		diff \| blob \| history
src/gromacs/gmxlib/orires.cpp		diff \| blob \| history
src/gromacs/gmxlib/orires.h		diff \| blob \| history
src/gromacs/gmxlib/readinp.cpp		diff \| blob \| history
src/gromacs/gmxlib/sighandler.cpp		diff \| blob \| history
src/gromacs/gmxlib/thread_affinity.cpp		diff \| blob \| history
src/gromacs/gmxlib/txtdump.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/convparm.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/genhydro.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/gpp_atomtype.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/grompp.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/hizzie.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/pdb2gmx.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/readir.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/readpull.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/specbond.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/ter_db.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/tomorse.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/topio.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/topshake.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/xlate.cpp		diff \| blob \| history
src/gromacs/imd/imd.h		diff \| blob \| history
src/gromacs/legacyheaders/genborn.h		diff \| blob \| history
src/gromacs/legacyheaders/gmx_detect_hardware.h		diff \| blob \| history
src/gromacs/legacyheaders/nrnb.h		diff \| blob \| history
src/gromacs/legacyheaders/txtdump.h		diff \| blob \| history
src/gromacs/legacyheaders/types/state.h		diff \| blob \| history
src/gromacs/listed-forces/listed-forces.cpp		diff \| blob \| history
src/gromacs/listed-forces/listed-forces.h		diff \| blob \| history
src/gromacs/listed-forces/position-restraints.h		diff \| blob \| history
src/gromacs/mdlib/adress.cpp		diff \| blob \| history
src/gromacs/mdlib/adress.h		diff \| blob \| history
src/gromacs/mdlib/broadcaststructs.cpp		diff \| blob \| history
src/gromacs/mdlib/calc_verletbuf.cpp		diff \| blob \| history
src/gromacs/mdlib/calc_verletbuf.h		diff \| blob \| history
src/gromacs/mdlib/calcmu.cpp		diff \| blob \| history
src/gromacs/mdlib/compute_io.cpp		diff \| blob \| history
src/gromacs/mdlib/compute_io.h		diff \| blob \| history
src/gromacs/mdlib/constr.h		diff \| blob \| history
src/gromacs/mdlib/coupling.cpp		diff \| blob \| history
src/gromacs/mdlib/ebin.cpp		diff \| blob \| history
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src/gromacs/mdlib/force.cpp		diff \| blob \| history
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src/gromacs/mdlib/forcerec.cpp		diff \| blob \| history
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src/gromacs/mdlib/genborn.cpp		diff \| blob \| history
src/gromacs/mdlib/genborn_allvsall.cpp		diff \| blob \| history
src/gromacs/mdlib/genborn_allvsall.h		diff \| blob \| history
src/gromacs/mdlib/groupcoord.h		diff \| blob \| history
src/gromacs/mdlib/md_support.cpp		diff \| blob \| history
src/gromacs/mdlib/md_support.h		diff \| blob \| history
src/gromacs/mdlib/mdatoms.cpp		diff \| blob \| history
src/gromacs/mdlib/mdebin.cpp		diff \| blob \| history
src/gromacs/mdlib/mdebin_bar.cpp		diff \| blob \| history
src/gromacs/mdlib/mdoutf.cpp		diff \| blob \| history
src/gromacs/mdlib/mdrun.h		diff \| blob \| history
src/gromacs/mdlib/minimize.cpp		diff \| blob \| history
src/gromacs/mdlib/nbnxn_atomdata.h		diff \| blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu		diff \| blob \| history
src/gromacs/mdlib/nbnxn_grid.h		diff \| blob \| history
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src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h		diff \| blob \| history
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src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_4xn_kernel.cpp.pre		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.h.pre		diff \| blob \| history
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src/gromacs/mdlib/rbin.cpp		diff \| blob \| history
src/gromacs/mdlib/rf_util.cpp		diff \| blob \| history
src/gromacs/mdlib/shakef.cpp		diff \| blob \| history
src/gromacs/mdlib/shellfc.cpp		diff \| blob \| history
src/gromacs/mdlib/shellfc.h		diff \| blob \| history
src/gromacs/mdlib/sim_util.cpp		diff \| blob \| history
src/gromacs/mdlib/sim_util.h		diff \| blob \| history
src/gromacs/mdlib/stat.cpp		diff \| blob \| history
src/gromacs/mdlib/tgroup.cpp		diff \| blob \| history
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src/gromacs/mdlib/tpi.cpp		diff \| blob \| history
src/gromacs/mdlib/trajectory_writing.cpp		diff \| blob \| history
src/gromacs/mdlib/update.cpp		diff \| blob \| history
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src/gromacs/mdlib/vsite.cpp		diff \| blob \| history
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src/gromacs/mdlib/wall.cpp		diff \| blob \| history
src/gromacs/mdrunutility/handlerestart.cpp		diff \| blob \| history
src/gromacs/mdtypes/CMakeLists.txt	[new file with mode: 0644]	blob
src/gromacs/mdtypes/df_history.cpp	[moved from src/gromacs/gmxlib/df_history.cpp with 100% similarity]	blob \| history
src/gromacs/mdtypes/df_history.h	[moved from src/gromacs/gmxlib/df_history.h with 100% similarity]	blob \| history
src/gromacs/mdtypes/energyhistory.cpp	[moved from src/gromacs/gmxlib/energyhistory.cpp with 96% similarity]	diff \| blob \| history
src/gromacs/mdtypes/energyhistory.h	[moved from src/gromacs/gmxlib/energyhistory.h with 100% similarity]	blob \| history
src/gromacs/mdtypes/state.cpp	[moved from src/gromacs/gmxlib/typedefs.cpp with 92% similarity]	diff \| blob \| history
src/gromacs/mdtypes/state.h	[moved from src/gromacs/legacyheaders/typedefs.h with 75% similarity]	diff \| blob \| history
src/gromacs/pulling/pull.cpp		diff \| blob \| history
src/gromacs/pulling/pull.h		diff \| blob \| history
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src/gromacs/pulling/pull_rotation.h		diff \| blob \| history
src/gromacs/pulling/pullutil.cpp		diff \| blob \| history
src/gromacs/swap/swapcoords.cpp		diff \| blob \| history
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src/gromacs/tables/forcetable.cpp		diff \| blob \| history
src/gromacs/tools/convert_tpr.cpp		diff \| blob \| history
src/gromacs/tools/dump.cpp		diff \| blob \| history
src/gromacs/utility/int64_to_int.cpp	[new file with mode: 0644]	blob
src/gromacs/utility/int64_to_int.h	[new file with mode: 0644]	blob
src/programs/mdrun/md.cpp		diff \| blob \| history
src/programs/mdrun/mdrun.cpp		diff \| blob \| history
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src/programs/mdrun/repl_ex.h		diff \| blob \| history
src/programs/mdrun/resource-division.h		diff \| blob \| history
src/programs/mdrun/runner.cpp		diff \| blob \| history
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src/programs/view/xmb.cpp		diff \| blob \| history
src/programs/view/xutil.cpp		diff \| blob \| history
src/programs/view/xutil.h		diff \| blob \| history

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