BioD PNPI Git Repos - alexxy/gromacs.git/commit - src/gromacs/listed

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

author	Roland Schulz <roland.schulz@intel.com>
	Tue, 22 Jan 2019 19:45:01 +0000 (11:45 -0800)
committer	David van der Spoel <spoel@xray.bmc.uu.se>
	Sat, 2 Feb 2019 16:05:11 +0000 (17:05 +0100)
commit	7c1764b2c763c8f0483d43f919f12e1218c9f004
tree	aa353509160a49a13e3e7ae0bfd69fb36cdc1482	tree \| snapshot
parent	03eb4a196b7b0a79f6ec38e14eec0b081f89ab88	commit \| diff

Renamed listed-forces to listed_forces

There should be consistency in naming. _ is used in almost
all cases (2744 to 122 in src/gromacs not counting files
changed here). Follow up changes will change the remaining
files.

Change-Id: Iea57accfd94d7ede180b9becd7d607425a8df7f6

113 files changed:

docs/doxygen/cycle-suppressions.txt		diff \| blob \| history
src/gromacs/CMakeLists.txt		diff \| blob \| history
src/gromacs/domdec/domdec.cpp		diff \| blob \| history
src/gromacs/gmxana/anadih.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_dipoles.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_disre.cpp		diff \| blob \| history
src/gromacs/gmxana/gmx_eneconv.cpp		diff \| blob \| history
src/gromacs/gmxana/hxprops.cpp		diff \| blob \| history
src/gromacs/gmxana/nrama.cpp		diff \| blob \| history
src/gromacs/gmxlib/nonbonded/nonbonded.cpp		diff \| blob \| history
src/gromacs/gmxpreprocess/x2top.cpp		diff \| blob \| history
src/gromacs/listed_forces/CMakeLists.txt	[moved from src/gromacs/listed-forces/CMakeLists.txt with 95% similarity]	diff \| blob \| history
src/gromacs/listed_forces/bonded.cpp	[moved from src/gromacs/listed-forces/bonded.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/bonded.h	[moved from src/gromacs/listed-forces/bonded.h with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/disre.cpp	[moved from src/gromacs/listed-forces/disre.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/disre.h	[moved from src/gromacs/listed-forces/disre.h with 96% similarity]	diff \| blob \| history
src/gromacs/listed_forces/gpubonded-impl.cpp	[moved from src/gromacs/listed-forces/gpubonded-impl.cpp with 97% similarity]	diff \| blob \| history
src/gromacs/listed_forces/gpubonded-impl.cu	[moved from src/gromacs/listed-forces/gpubonded-impl.cu with 98% similarity]	diff \| blob \| history
src/gromacs/listed_forces/gpubonded-impl.h	[moved from src/gromacs/listed-forces/gpubonded-impl.h with 98% similarity]	diff \| blob \| history
src/gromacs/listed_forces/gpubonded.h	[moved from src/gromacs/listed-forces/gpubonded.h with 97% similarity]	diff \| blob \| history
src/gromacs/listed_forces/gpubondedkernels.cu	[moved from src/gromacs/listed-forces/gpubondedkernels.cu with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/listed-internal.cpp	[moved from src/gromacs/listed-forces/listed-internal.cpp with 94% similarity]	diff \| blob \| history
src/gromacs/listed_forces/listed-internal.h	[moved from src/gromacs/listed-forces/listed-internal.h with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/listed_forces.cpp	[moved from src/gromacs/listed-forces/listed-forces.cpp with 98% similarity]	diff \| blob \| history
src/gromacs/listed_forces/listed_forces.h	[moved from src/gromacs/listed-forces/listed-forces.h with 97% similarity]	diff \| blob \| history
src/gromacs/listed_forces/manage-threading.cpp	[moved from src/gromacs/listed-forces/manage-threading.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/manage-threading.h	[moved from src/gromacs/listed-forces/manage-threading.h with 96% similarity]	diff \| blob \| history
src/gromacs/listed_forces/orires.cpp	[moved from src/gromacs/listed-forces/orires.cpp with 100% similarity]	blob \| history
src/gromacs/listed_forces/orires.h	[moved from src/gromacs/listed-forces/orires.h with 97% similarity]	diff \| blob \| history
src/gromacs/listed_forces/pairs.cpp	[moved from src/gromacs/listed-forces/pairs.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/pairs.h	[moved from src/gromacs/listed-forces/pairs.h with 95% similarity]	diff \| blob \| history
src/gromacs/listed_forces/position-restraints.cpp	[moved from src/gromacs/listed-forces/position-restraints.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/position-restraints.h	[moved from src/gromacs/listed-forces/position-restraints.h with 96% similarity]	diff \| blob \| history
src/gromacs/listed_forces/restcbt.cpp	[moved from src/gromacs/listed-forces/restcbt.cpp with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/restcbt.h	[moved from src/gromacs/listed-forces/restcbt.h with 99% similarity]	diff \| blob \| history
src/gromacs/listed_forces/tests/CMakeLists.txt	[moved from src/gromacs/listed-forces/tests/CMakeLists.txt with 93% similarity]	diff \| blob \| history
src/gromacs/listed_forces/tests/bonded.cpp	[moved from src/gromacs/listed-forces/tests/bonded.cpp with 98% similarity]	diff \| blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_BondAngle_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_DihedralAngle_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncAngles_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncBonds_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedralsFEP_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncImproperDihedrals_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_0.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_0.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_1.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_1.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_2.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_2.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_3.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_3.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_4.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_4.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_5.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_6.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_7.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml	[moved from src/gromacs/listed-forces/tests/refdata/ForPbcValues_BondedTest_IfuncProperDihedrals_8.xml with 100% similarity]	blob \| history
src/gromacs/listed_forces/utilities.h	[moved from src/gromacs/listed-forces/utilities.h with 95% similarity]	diff \| blob \| history
src/gromacs/mdlib/expanded.cpp		diff \| blob \| history
src/gromacs/mdlib/force.cpp		diff \| blob \| history
src/gromacs/mdlib/forcerec.cpp		diff \| blob \| history
src/gromacs/mdlib/mdebin.cpp		diff \| blob \| history
src/gromacs/mdlib/mdsetup.cpp		diff \| blob \| history
src/gromacs/mdlib/sim_util.cpp		diff \| blob \| history
src/gromacs/mdlib/update.cpp		diff \| blob \| history
src/gromacs/mdrun/md.cpp		diff \| blob \| history
src/gromacs/mdrun/mimic.cpp		diff \| blob \| history
src/gromacs/mdrun/minimize.cpp		diff \| blob \| history
src/gromacs/mdrun/rerun.cpp		diff \| blob \| history
src/gromacs/mdrun/runner.cpp		diff \| blob \| history

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