[lammps] branch experimental updated (4f12b37 -> 9378dd8)
Anton Gladky
gladk at moszumanska.debian.org
Sun Mar 15 21:56:02 UTC 2015
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch experimental
in repository lammps.
from 4f12b37 Update changelog.
adds 4a7ac95 Imported Upstream version 0~20130503.gitd2adfba
adds 9eb17eb Merge tag 'upstream/0_20130503.gitd2adfba'
adds 2f578c3 Minor description update.
adds fdb3192 Use parallel build.
adds afade40 Add doc-base file.
adds 023c448 Update changelog.
adds e65b919 Imported Upstream version 0~20131119.git7162cf0
adds b41848c Merge tag 'upstream/0_20131119.git7162cf0'
adds f7bddd4 Fix some problems, introduced by upstream recently.
adds 3616dfc Use wrap-and-sort script.
adds 7e92030 Ignore quilt dir
adds 79b0d94 Update changelog.
adds 5127b33 Imported Upstream version 0~20140212.git32a5cd0
adds 83b0d1b Merge tag 'upstream/0_20140212.git32a5cd0'
adds 9c47579 Refresh patch.
adds b21f32c Set Standards-Version: 3.9.5. No changes.
adds 249a3f2 Set canonical VCS-fields.
adds 85cb066 Add autotests.
adds bf2b96e Remove executable bit in examples.
adds 2138df2 Update changelog.
adds 81dc578 Fix file permissions in examples.
adds 9fad448 Fix FTBFS on arch-only builds.
adds 77913a1 Update changelog.
adds 842e614 Fix autotest.
adds 45e21de Fix autotest.
adds 570f0e1 Update changelog.
adds db83dbb Fix autotest (MPI error).
adds eb5d230 Update changelog.
adds f2930e3 Imported Upstream version 0~20140415.git42bb280
adds 0f0d35a Merge tag 'upstream/0_20140415.git42bb280'
adds b05b302 Remove patch, applied by upstream.
adds 12f95b6 Fix autotest.
adds cca8000 Replace deprecated MPI-flag in debian/rules.
adds 261b490 Update changelog.
adds eff3471 Update/fix autopkgtest.
adds eb0d0ab Update changelog.
adds 4c132dc Grab source from GitHub page.
adds 7811c49 Move mpi-default-bin to Depends.
adds 4bd2ecb Imported Upstream version 0~20140523.gite5e877d
adds 7653943 Merge tag 'upstream/0_20140523.gite5e877d'
adds 7f4e9a8 Remove colloid autopkgtest.
adds 32b9d4b Update changelog.
adds aad2273 Imported Upstream version 0~20150313.gitfa668e1
new e205743 Merge tag 'upstream/0_20150313.gitfa668e1' into experimental
new 820b5c5 Refresh patches. Remove applied by upstream.
new b303847 Update d/copyright.
new 5dc10e0 Minor fix in d/rules.
new b833c3c Set Standards-Version: 3.9.6. No changes.
new 0e947fe Enable C++11.
new 9378dd8 Update changelog.
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 1 +
bench/FERMI/README | 103 +
bench/{GPU/in.eam.cpu => FERMI/in.eam} | 0
bench/FERMI/in.eam.titan | 37 +
bench/{GPU/in.lj.cpu => FERMI/in.lj} | 0
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bench/{GPU/in.rhodo.cpu => FERMI/in.rhodo} | 0
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bench/FERMI/in.rhodo.split.titan | 42 +
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bench/KEPLER/Makefile.gpu.double | 50 +
bench/KEPLER/Makefile.gpu.mixed | 50 +
bench/KEPLER/Makefile.gpu.single | 50 +
bench/KEPLER/Makefile.intel.cpu | 109 +
bench/KEPLER/Makefile.kokkos.cuda | 113 +
bench/KEPLER/Makefile.kokkos.omp | 110 +
bench/KEPLER/Makefile.omp | 108 +
bench/KEPLER/Makefile.opt | 108 +
bench/KEPLER/README | 68 +
bench/KEPLER/build.py | 187 +
bench/{GPU/in.lj.cpu => KEPLER/in.lj} | 0
bench/KEPLER/run_cpu.sh | 29 +
bench/KEPLER/run_cuda.sh | 20 +
bench/KEPLER/run_gpu.sh | 155 +
bench/KEPLER/run_intel_cpu.sh | 83 +
bench/KEPLER/run_kokkos_cuda.sh | 74 +
bench/KEPLER/run_kokkos_omp.sh | 17 +
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bench/KEPLER/run_opt.sh | 29 +
bench/KEPLER/run_strong.sh | 20 +
bench/KEPLER/run_weak.sh | 20 +
bench/README | 68 +-
bench/in.chute | 2 +-
bench/log.1Feb14.chain.fixed.linux.1 | 63 +
bench/log.1Feb14.chain.fixed.linux.4 | 63 +
bench/log.1Feb14.chain.scaled.linux.4 | 79 +
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bench/log.1Feb14.eam.fixed.linux.1 | 67 +
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bench/log.1Feb14.eam.scaled.linux.4 | 67 +
bench/log.1Feb14.lj.fixed.linux.1 | 64 +
bench/log.1Feb14.lj.fixed.linux.4 | 64 +
bench/log.1Feb14.lj.scaled.linux.4 | 64 +
bench/log.1Feb14.rhodo.fixed.linux.1 | 109 +
bench/log.1Feb14.rhodo.fixed.linux.4 | 109 +
bench/log.1Feb14.rhodo.scaled.linux.4 | 130 +
bench/log.9Jan12.chain.fixed.linux.1 | 59 -
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bench/log.9Jan12.rhodo.fixed.linux.4 | 98 -
bench/log.9Jan12.rhodo.scaled.linux.4 | 119 -
debian/changelog | 82 +
debian/control | 59 +-
debian/copyright | 70 +-
debian/lammps-doc.doc-base | 12 +
debian/lammps.1 | 2 +-
debian/patches/10_set_configure_flags.patch | 56 +
debian/patches/series | 2 +-
debian/patches/set_configure_flags.patch | 52 -
debian/rules | 15 +-
debian/scripts/get_orig_src.sh | 2 +-
debian/tests/control | 2 +
debian/tests/crack | 97 +
debian/tests/dipole | 61 +
debian/tests/ellipse | 86 +
debian/tests/flow | 98 +
debian/tests/friction | 110 +
debian/tests/hugo | 201 +
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doc/Scripts/correlate.py | 2 +-
doc/Section_accelerate.html | 727 +-
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doc/Section_example.html | 11 +-
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examples/USER/fep/CC-CO/fdti01/fdti01.lmp | 22 +
examples/USER/fep/CC-CO/fdti01/in.fdti01.lmp | 142 +
examples/USER/fep/CC-CO/fdti01/log.lammps | 6321 +
examples/USER/fep/CC-CO/fdti10/fdti10.lmp | 22 +
examples/USER/fep/CC-CO/fdti10/in.fdti10.lmp | 142 +
examples/USER/fep/CC-CO/fdti10/log.lammps | 6321 +
examples/USER/fep/CC-CO/fep01/data.0.lmp | 2275 +
examples/USER/fep/CC-CO/fep01/fep01.lmp | 22 +
examples/USER/fep/CC-CO/fep01/in.fep01 | 143 +
examples/USER/fep/CC-CO/fep01/in.fep01.lmp | 142 +
examples/USER/fep/CC-CO/fep01/log.lammps | 6321 +
examples/USER/fep/CC-CO/fep01/log.reference | 285 +
examples/USER/fep/CC-CO/fep01/log.reference-omp | 287 +
examples/USER/fep/CC-CO/fep10/fep10.lmp | 22 +
examples/USER/fep/CC-CO/fep10/in.fep10.lmp | 142 +
examples/USER/fep/CC-CO/fep10/log.lammps | 6321 +
examples/USER/fep/CC-CO/mols/CC-CO.ff | 49 +
examples/USER/fep/CC-CO/mols/CC-CO.zmat | 14 +
examples/USER/fep/CC-CO/mols/CO-CC.zmat | 14 +
examples/USER/fep/CC-CO/mols/README | 15 +
examples/USER/fep/CC-CO/mols/data.0.lmp | 2275 +
examples/USER/fep/CC-CO/mols/data.1.lmp | 2275 +
examples/USER/fep/CC-CO/mols/spce.ff | 14 +
examples/USER/fep/CC-CO/mols/spce.zmat | 7 +
examples/USER/fep/CH4-CF4/README | 57 +
examples/USER/fep/CH4-CF4/bar01/bar01.lmp | 5003 +
examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp | 89 +
examples/USER/fep/CH4-CF4/bar01/log.lammps | 6514 +
examples/USER/fep/CH4-CF4/bar10/bar10.lmp | 5003 +
examples/USER/fep/CH4-CF4/bar10/in.bar10.lmp | 89 +
examples/USER/fep/CH4-CF4/bar10/log.lammps | 6514 +
examples/USER/fep/CH4-CF4/mols/CF4-CH4.zmat | 16 +
examples/USER/fep/CH4-CF4/mols/CH4-CF4.ff | 28 +
examples/USER/fep/CH4-CF4/mols/CH4-CF4.zmat | 16 +
examples/USER/fep/CH4-CF4/mols/data.0.lmp | 2249 +
examples/USER/fep/CH4-CF4/mols/data.1.lmp | 2249 +
examples/USER/fep/CH4-CF4/mols/spce.ff | 14 +
examples/USER/fep/CH4-CF4/mols/spce.zmat | 7 +
examples/USER/fep/CH4hyd/README | 59 +
examples/USER/fep/CH4hyd/fdti01/fdti01.lmp | 22 +
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp | 80 +
examples/USER/fep/CH4hyd/fdti01/log.lammps | 5156 +
examples/USER/fep/CH4hyd/fdti10/fdti10.lmp | 22 +
examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp | 80 +
examples/USER/fep/CH4hyd/fdti10/log.lammps | 5156 +
examples/USER/fep/CH4hyd/fep01/fep01.lmp | 22 +
examples/USER/fep/CH4hyd/fep01/in.fep01.lmp | 80 +
examples/USER/fep/CH4hyd/fep01/log.lammps | 5156 +
examples/USER/fep/CH4hyd/fep10/fep10.lmp | 22 +
examples/USER/fep/CH4hyd/fep10/in.fep10.lmp | 80 +
examples/USER/fep/CH4hyd/fep10/log.lammps | 5156 +
examples/USER/fep/CH4hyd/mols/data.lmp | 2215 +
examples/USER/fep/CH4hyd/mols/methane.zmat | 9 +
examples/USER/fep/CH4hyd/mols/oplsaa.ff | 85 +
examples/USER/fep/CH4hyd/mols/tip4pew.ff | 14 +
examples/USER/fep/CH4hyd/mols/tip4pew.zmat | 7 +
examples/USER/fep/README | 11 +
examples/USER/gle/data.h2o-quantum | 413 +
examples/USER/gle/data.h2o-smart | 413 +
examples/USER/gle/in.h2o-quantum | 41 +
examples/USER/gle/in.h2o-smart | 41 +
examples/USER/gle/log.h2o-quantum | 201 +
examples/USER/gle/log.h2o-smart | 200 +
examples/USER/gle/qt-300k.A | 7 +
examples/USER/gle/qt-300k.C | 7 +
examples/USER/gle/smart.A | 7 +
examples/USER/i-pi/C.opt.tersoff | 66 +
examples/USER/i-pi/README | 46 +
examples/USER/i-pi/data.graphene | 1939 +
examples/USER/i-pi/i-pi_input.xml | 31 +
examples/USER/i-pi/i-pi_positions.xyz | 962 +
examples/USER/i-pi/in.graphene | 34 +
.../USER/lb/confined_colloid/in.confined_colloids | 108 +
examples/USER/lb/confined_colloid/results64.out | 41 +
examples/USER/lb/dragforce/data.one_radius16d2 | 330 +
examples/USER/lb/dragforce/defaultgamma_drag.out | 10035 +
examples/USER/lb/dragforce/in.defaultgamma_drag | 80 +
examples/USER/lb/dragforce/in.setgamma_drag | 68 +
examples/USER/lb/dragforce/setgamma13d0_drag.out | 10035 +
examples/USER/lb/fourspheres/data.four | 1290 +
.../fourspheres_velocity0d0001_defaultgamma.out | 15039 ++
.../fourspheres_velocity0d0001_setgamma.out | 15039 ++
.../lb/fourspheres/in.fourspheres_default_gamma | 84 +
.../USER/lb/fourspheres/in.fourspheres_set_gamma | 76 +
examples/USER/lb/microrheology/data.two | 492 +
.../microrheology/in.microrheology_default_gamma | 119 +
.../lb/microrheology/in.microrheology_set_gamma | 113 +
.../microrheology/microrheology_defaultgamma.out | 50000 +++++
.../lb/microrheology/microrheology_setgamma.out | 50000 +++++
examples/USER/lb/planewall/data.one_radius16d2 | 330 +
.../USER/lb/planewall/in.planewall_default_gamma | 99 +
examples/USER/lb/planewall/in.planewall_set_gamma | 92 +
examples/USER/lb/planewall/wall_defaultgamma.out | 20031 ++
examples/USER/lb/planewall/wall_setgamma.out | 20031 ++
examples/USER/lb/polymer/data.polymer | 1040 +
examples/USER/lb/polymer/in.polymer | 105 +
examples/USER/lb/polymer/out.polymer | 19 +
examples/USER/misc/basal/almg.liu | 708 +
examples/USER/misc/basal/in.basal | 163 +
examples/USER/misc/ti/in.ti_rs | 64 +
examples/USER/misc/ti/in.ti_spring | 64 +
examples/USER/phonon/1-1D-mono/README | 39 +
examples/USER/phonon/1-1D-mono/data.pos | 57 +
examples/USER/phonon/1-1D-mono/disp.dat | 19 +
examples/USER/phonon/1-1D-mono/in.Ana | 50 +
examples/USER/phonon/1-1D-mono/in.disp | 9 +
examples/USER/phonon/1-1D-mono/log.lammps.example | 146 +
examples/USER/phonon/1-1D-mono/map.in | 18 +
examples/USER/phonon/1-1D-mono/pdisp.eps | 776 +
examples/USER/phonon/1-1D-mono/phonon.bin.2000000 | Bin 0 -> 384 bytes
examples/USER/phonon/1-1D-mono/phonon.log | 110 +
examples/USER/phonon/1-1D-mono/plot.disp | 20 +
examples/USER/phonon/2-1D-diatomic/README | 37 +
examples/USER/phonon/2-1D-diatomic/data.pos | 154 +
examples/USER/phonon/2-1D-diatomic/disp.dat | 35 +
examples/USER/phonon/2-1D-diatomic/in.Ana | 46 +
examples/USER/phonon/2-1D-diatomic/in.disp | 9 +
.../USER/phonon/2-1D-diatomic/log.lammps.example | 113 +
examples/USER/phonon/2-1D-diatomic/map.in | 66 +
examples/USER/phonon/2-1D-diatomic/pdisp.eps | 924 +
examples/USER/phonon/2-1D-diatomic/pdos.dat | 203 +
.../USER/phonon/2-1D-diatomic/phonon.bin.2000000 | Bin 0 -> 2196 bytes
examples/USER/phonon/2-1D-diatomic/phonon.log | 206 +
examples/USER/phonon/2-1D-diatomic/plot.disp | 25 +
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 | Bin 0 -> 73872 bytes
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.log.example | 1575 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/README | 47 +
.../USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam | 0
examples/USER/phonon/3-3D-FCC-Cu-EAM/data.pos | 524 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat | 83 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat | 86 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat | 47 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat | 164 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat | 101 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat | 102 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D | 40 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp | 21 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.dos | 11 +
.../USER/phonon/3-3D-FCC-Cu-EAM/log.lammps.example | 107 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/map.in | 514 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps | 1207 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps | 985 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp | 18 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos | 13 +
examples/USER/pimd/para-h2/H2.data | 196 +
examples/USER/pimd/para-h2/H2.xyz | 182 +
examples/USER/pimd/para-h2/NM.info | 21 +
examples/USER/pimd/para-h2/in.scp | 29 +
examples/USER/pimd/para-h2/pair.table | 18003 ++
examples/USER/pimd/para-h2/run.sh | 1 +
examples/USER/pimd/para-h2/vmd.src | 94 +
examples/USER/pimd/prot-hairpin/in.scp | 31 +
examples/USER/pimd/prot-hairpin/run.sh | 1 +
examples/USER/pimd/prot-hairpin/system.data | 27593 +++
examples/USER/quip/data_gap | 78 +
examples/USER/quip/data_sw | 22 +
examples/USER/quip/gap_example.xml | 707 +
examples/USER/quip/gap_example_sparse.dat | 25500 +++
examples/USER/quip/in.gap | 23 +
examples/USER/quip/in.sw | 23 +
examples/USER/quip/sw_example.xml | 46 +
.../USER/sph/water_collapse/water_collapse.lmp | 4 +-
examples/USER/srp/data.chain | 8724 +
examples/USER/srp/in.srp | 37 +
examples/VISCOSITY/README | 80 +
examples/VISCOSITY/in.gk.2d | 76 +
examples/VISCOSITY/in.mp.2d | 76 +
examples/VISCOSITY/in.nemd.2d | 83 +
examples/VISCOSITY/in.wall.2d | 83 +
examples/VISCOSITY/log.gk.2d.1Feb14 | 386 +
examples/VISCOSITY/log.mp.2d.1Feb14 | 230 +
examples/VISCOSITY/log.nemd.2d.1Feb14 | 271 +
examples/VISCOSITY/log.wall.2d.1Feb14 | 221 +
examples/VISCOSITY/profile.gk.2d.1Feb14 | 100654 +++++++++
examples/VISCOSITY/profile.mp.2d.1Feb14 | 1473 +
examples/VISCOSITY/profile.nemd.2d.1Feb14 | 423 +
examples/VISCOSITY/profile.wall.2d.1Feb14 | 150 +
examples/accelerate/Make.list | 41 +
examples/accelerate/README | 158 +
examples/{USER/cuda => accelerate}/data.phosphate | 0
examples/accelerate/in.lc | 57 +
examples/accelerate/in.lj | 33 +
examples/accelerate/in.lj.5.0 | 33 +
examples/accelerate/in.phosphate | 33 +
examples/accelerate/in.rhodo | 34 +
examples/accelerate/log.lj.1Feb14.gpu.1 | 80 +
examples/accelerate/log.lj.1Feb14.gpu.4 | 80 +
examples/accelerate/log.lj.1Feb14.kokkos.cuda.1 | 68 +
examples/accelerate/log.lj.1Feb14.kokkos.cuda.2 | 68 +
examples/accelerate/log.lj.1Feb14.kokkos.omp.1 | 68 +
examples/accelerate/log.lj.1Feb14.kokkos.omp.4 | 68 +
examples/accelerate/log.lj.5.0.1Feb14.gpu.1 | 80 +
examples/accelerate/log.lj.5.0.1Feb14.gpu.4 | 80 +
examples/accelerate/log.phosphate.1Feb14.gpu.1 | 80 +
examples/accelerate/log.phosphate.1Feb14.gpu.4 | 80 +
examples/accelerate/log.rhodo.1Feb14.gpu.1 | 135 +
examples/accelerate/log.rhodo.1Feb14.gpu.4 | 135 +
examples/balance/in.balance | 54 +
examples/balance/in.balance.bond.fast | 63 +
examples/balance/in.balance.bond.slow | 62 +
examples/balance/log.balance.8Aug14.linux.1 | 187 +
examples/balance/log.balance.8Aug14.linux.4 | 187 +
.../balance/log.balance.bond.fast.21Jan15.linux.1 | 203 +
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.../balance/log.balance.bond.slow.21Jan15.linux.1 | 502 +
.../balance/log.balance.bond.slow.21Jan15.linux.4 | 502 +
examples/body/in.body | 2 +-
examples/body/log.body.1Feb13.linux.1 | 70 -
examples/body/log.body.1Feb13.linux.4 | 70 -
examples/body/log.body.1Feb14.linux.1 | 71 +
examples/body/log.body.1Feb14.linux.4 | 71 +
examples/colloid/in.colloid | 10 +-
examples/colloid/log.colloid.1Feb14.linux.1 | 131 +
examples/colloid/log.colloid.1Feb14.linux.4 | 131 +
examples/colloid/log.colloid.9Jan12.linux.1 | 122 -
examples/colloid/log.colloid.9Jan12.linux.4 | 122 -
examples/comb/data.comb3-OHCCu | 695 +
examples/comb/elastic.f90 | 384 +-
examples/comb/ffield.comb3 | 349 +
examples/comb/in.comb.Cu | 8 +-
examples/comb/in.comb.Cu2O.elastic | 8 +-
examples/comb/in.comb.HfO2 | 14 +-
examples/comb/in.comb.Si | 8 +-
examples/comb/in.comb.Si.elastic | 10 +-
examples/comb/in.comb3 | 34 +
examples/comb/lib.comb3 | 24303 +++
examples/comb/log.comb.Cu.1Feb14.linux.1 | 76 +
examples/comb/log.comb.Cu.1Feb14.linux.4 | 76 +
examples/comb/log.comb.Cu.9Jan12.linux.1 | 69 -
examples/comb/log.comb.Cu.9Jan12.linux.4 | 69 -
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 | 316 +
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 | 316 +
examples/comb/log.comb.Cu2O.elastic.9Jan12.linux.1 | 340 -
examples/comb/log.comb.Cu2O.elastic.9Jan12.linux.4 | 342 -
examples/comb/log.comb.CuaS.9Jan12.linux.1 | 41 -
examples/comb/log.comb.CuaS.9Jan12.linux.4 | 41 -
examples/comb/log.comb.HfO2.1Feb14.linux.1 | 185 +
examples/comb/log.comb.HfO2.1Feb14.linux.4 | 185 +
examples/comb/log.comb.HfO2.9Jan12.linux.1 | 193 -
examples/comb/log.comb.HfO2.9Jan12.linux.4 | 291 -
examples/comb/log.comb.Si.1Feb14.linux.1 | 76 +
examples/comb/log.comb.Si.1Feb14.linux.4 | 76 +
examples/comb/log.comb.Si.9Jan12.linux.1 | 69 -
examples/comb/log.comb.Si.9Jan12.linux.4 | 69 -
examples/comb/log.comb.Si.elastic.1Feb14.linux.1 | 274 +
examples/comb/log.comb.Si.elastic.1Feb14.linux.4 | 274 +
examples/comb/log.comb.Si.elastic.9Jan12.linux.1 | 296 -
examples/comb/log.comb.Si.elastic.9Jan12.linux.4 | 296 -
examples/comb/log.comb3.1Feb14.linux.1 | 73 +
examples/comb/log.comb3.1Feb14.linux.4 | 73 +
examples/coreshell/data.coreshell | 1114 +
examples/coreshell/in.coreshell | 72 +
examples/coreshell/log.coreshell.6Mar15.linux.1 | 188 +
examples/coreshell/log.coreshell.6Mar15.linux.4 | 188 +
examples/crack/in.crack | 8 +-
examples/crack/log.crack.1Feb14.linux.1 | 138 +
examples/crack/log.crack.1Feb14.linux.4 | 138 +
examples/crack/log.crack.9Jan12.linux.1 | 130 -
examples/crack/log.crack.9Jan12.linux.4 | 130 -
examples/deposit/in.deposit.atom | 51 +
examples/deposit/in.deposit.molecule | 55 +
examples/deposit/in.deposit.molecule.shake | 56 +
examples/deposit/molecule.dimer | 28 +
examples/deposit/molecule.dimer.shake | 44 +
examples/dipole/in.dipole | 2 +-
examples/dipole/log.dipole.1Feb14.linux.1 | 89 +
examples/dipole/log.dipole.1Feb14.linux.4 | 89 +
examples/dipole/log.dipole.9Jan12.linux.1 | 86 -
examples/dipole/log.dipole.9Jan12.linux.4 | 86 -
examples/dreiding/data.dreiding | 3 -
examples/dreiding/log.dreiding.1Feb14.linux.1 | 106 +
examples/dreiding/log.dreiding.1Feb14.linux.4 | 106 +
examples/dreiding/log.dreiding.9Jan12.linux.1 | 97 -
examples/dreiding/log.dreiding.9Jan12.linux.4 | 121 -
examples/eim/in.eim | 8 +-
examples/eim/log.eim.1Feb14.linux.1 | 72 +
examples/eim/log.eim.1Feb14.linux.4 | 72 +
examples/eim/log.eim.9Jan12.linux.1 | 54 -
examples/eim/log.eim.9Jan12.linux.4 | 54 -
examples/ellipse/in.ellipse.gayberne | 12 +-
examples/ellipse/in.ellipse.resquared | 8 +-
.../ellipse/log.ellipse.gayberne.1Feb14.linux.1 | 163 +
.../ellipse/log.ellipse.gayberne.1Feb14.linux.4 | 163 +
.../ellipse/log.ellipse.gayberne.9Jan12.linux.1 | 161 -
.../ellipse/log.ellipse.gayberne.9Jan12.linux.4 | 161 -
.../ellipse/log.ellipse.resquared.1Feb14.linux.1 | 160 +
.../ellipse/log.ellipse.resquared.1Feb14.linux.4 | 160 +
.../ellipse/log.ellipse.resquared.9Jan12.linux.1 | 161 -
.../ellipse/log.ellipse.resquared.9Jan12.linux.4 | 161 -
examples/flow/in.flow.couette | 8 +-
examples/flow/in.flow.pois | 8 +-
examples/flow/log.flow.couette.1Feb14.linux.1 | 130 +
examples/flow/log.flow.couette.1Feb14.linux.4 | 130 +
examples/flow/log.flow.couette.9Jan12.linux.1 | 123 -
examples/flow/log.flow.couette.9Jan12.linux.4 | 123 -
examples/flow/log.flow.pois.1Feb14.linux.1 | 130 +
examples/flow/log.flow.pois.1Feb14.linux.4 | 130 +
examples/flow/log.flow.pois.9Jan12.linux.1 | 123 -
examples/flow/log.flow.pois.9Jan12.linux.4 | 123 -
examples/friction/in.friction | 9 +-
examples/friction/log.friction.1Feb14.linux.1 | 149 +
examples/friction/log.friction.1Feb14.linux.4 | 149 +
examples/friction/log.friction.9Jan12.linux.1 | 141 -
examples/friction/log.friction.9Jan12.linux.4 | 141 -
examples/gpu/data.phosphate | 21922 --
examples/gpu/data.rhodo | 191072 ------------------
examples/gpu/in.gpu.melt.2.5 | 34 -
examples/gpu/in.gpu.melt.5.0 | 34 -
examples/gpu/in.gpu.phosphate | 31 -
examples/gpu/in.gpu.rhodo | 36 -
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.1 | 77 -
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.4 | 77 -
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.1 | 77 -
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.4 | 77 -
examples/gpu/log.gpu.phosphate.9Jan12.linux.1 | 74 -
examples/gpu/log.gpu.phosphate.9Jan12.linux.4 | 74 -
examples/gpu/log.gpu.rhodo.9Jan12.linux.1 | 121 -
examples/gpu/log.gpu.rhodo.9Jan12.linux.4 | 121 -
examples/hugoniostat/in.hugoniostat | 8 +-
.../hugoniostat/log.hugoniostat.1Feb14.linux.1 | 90 +
.../hugoniostat/log.hugoniostat.1Feb14.linux.4 | 90 +
.../hugoniostat/log.hugoniostat.9Jan12.linux.1 | 90 -
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examples/indent/in.indent | 8 +-
examples/indent/in.indent.min | 8 +-
examples/indent/log.indent.1Feb14.linux.1 | 179 +
examples/indent/log.indent.1Feb14.linux.4 | 179 +
examples/indent/log.indent.9Jan12.linux.1 | 172 -
examples/indent/log.indent.9Jan12.linux.4 | 172 -
examples/indent/log.indent.min.1Feb14.linux.1 | 404 +
examples/indent/log.indent.min.1Feb14.linux.4 | 405 +
examples/indent/log.indent.min.9Jan12.linux.1 | 404 -
examples/indent/log.indent.min.9Jan12.linux.4 | 386 -
examples/kim/log.kim.lj.12Jul12.mac_mpi.1 | 69 -
examples/kim/log.kim.lj.12Jul12.mac_mpi.4 | 69 -
examples/kim/log.kim.lj.27Jul14.ubuntu.1 | 29 +
examples/kim/log.kim.lj.27Jul14.ubuntu.4 | 29 +
examples/kim/log.kim.lj.lmp.12Jul12.mac_mpi.1 | 69 -
examples/kim/log.kim.lj.lmp.12Jul12.mac_mpi.4 | 69 -
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.1 | 29 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.4 | 29 +
examples/meam/in.meam | 8 +-
examples/meam/in.meam.shear | 8 +-
examples/meam/log.meam.1Feb14.linux.1 | 67 +
examples/meam/log.meam.1Feb14.linux.4 | 67 +
examples/meam/log.meam.9Jan12.linux.1 | 60 -
examples/meam/log.meam.9Jan12.linux.4 | 60 -
examples/meam/log.meam.shear.1Feb14.linux.1 | 172 +
examples/meam/log.meam.shear.1Feb14.linux.4 | 172 +
examples/meam/log.meam.shear.9Jan12.linux.1 | 165 -
examples/meam/log.meam.shear.9Jan12.linux.4 | 165 -
examples/melt/in.melt | 8 +-
examples/melt/log.melt.1Feb14.linux.1 | 63 +
examples/melt/log.melt.1Feb14.linux.4 | 63 +
examples/melt/log.melt.9Jan12.linux.1 | 57 -
examples/melt/log.melt.9Jan12.linux.4 | 57 -
examples/micelle/in.micelle | 7 +-
examples/micelle/log.micelle.1Feb14.linux.1 | 215 +
examples/micelle/log.micelle.1Feb14.linux.4 | 215 +
examples/micelle/log.micelle.9Jan12.linux.1 | 205 -
examples/micelle/log.micelle.9Jan12.linux.4 | 205 -
examples/min/in.min | 8 +-
examples/min/in.min.box | 53 +-
examples/min/log.min.1Feb14.linux.1 | 118 +
examples/min/log.min.1Feb14.linux.4 | 118 +
examples/min/log.min.9Jan12.linux.1 | 111 -
examples/min/log.min.9Jan12.linux.4 | 111 -
examples/min/log.min.box.1Feb14.linux.1 | 356 +
examples/min/log.min.box.1Feb14.linux.4 | 356 +
examples/min/log.min.box.9Jan12.linux.1 | 352 -
examples/min/log.min.box.9Jan12.linux.4 | 352 -
examples/msst/in.msst | 8 +-
examples/msst/log.msst.1Feb14.linux.1 | 138 +
examples/msst/log.msst.1Feb14.linux.4 | 138 +
examples/msst/log.msst.9Jan12.linux.1 | 130 -
examples/msst/log.msst.9Jan12.linux.4 | 130 -
examples/nb3b/MOH.nb3b.harmonic | 20 +
examples/nb3b/data.nb3b | 1991 +
examples/nb3b/in.nb3b | 49 +
examples/nb3b/log.nb3b.1Feb14.linux.1 | 144 +
examples/nb3b/log.nb3b.1Feb14.linux.4 | 144 +
examples/neb/README | 1 +
{bench/POTENTIALS => examples/neb}/Si.sw | 0
examples/neb/final.hop1 | 1 +
examples/neb/final.hop2 | 1 +
examples/neb/final.sivac | 8 +
examples/neb/in.neb.hop1 | 4 +-
examples/neb/in.neb.hop2 | 5 +-
examples/neb/in.neb.sivac | 76 +
examples/neb/log.neb.hop1.1Feb14.linux.4 | 10 +
examples/neb/log.neb.hop1.9Jan12.linux.4 | 11 -
examples/neb/log.neb.hop2.1Feb14.linux.4 | 17 +
examples/neb/log.neb.hop2.9Jan12.linux.4 | 19 -
examples/neb/log.neb.sivac.1Feb14.linux.3 | 13 +
examples/nemd/in.nemd | 9 +-
examples/nemd/log.nemd.1Feb14.linux.1 | 115 +
examples/nemd/log.nemd.1Feb14.linux.4 | 115 +
examples/nemd/log.nemd.9Jan12.linux.1 | 109 -
examples/nemd/log.nemd.9Jan12.linux.4 | 109 -
examples/obstacle/in.obstacle | 8 +-
examples/obstacle/log.obstacle.1Feb14.linux.1 | 140 +
examples/obstacle/log.obstacle.1Feb14.linux.4 | 140 +
examples/obstacle/log.obstacle.9Jan12.linux.1 | 135 -
examples/obstacle/log.obstacle.9Jan12.linux.4 | 135 -
examples/peptide/in.peptide | 8 +-
examples/peptide/log.peptide.1Feb14.linux.1 | 177 +
examples/peptide/log.peptide.1Feb14.linux.4 | 177 +
examples/peptide/log.peptide.9Jan12.linux.1 | 159 -
examples/peptide/log.peptide.9Jan12.linux.4 | 159 -
examples/peri/in.peri | 8 +-
examples/peri/log.peri.1Feb14.linux.1 | 90 +
examples/peri/log.peri.1Feb14.linux.4 | 90 +
examples/peri/log.peri.9Jan12.linux.1 | 81 -
examples/peri/log.peri.9Jan12.linux.4 | 81 -
examples/pour/in.pour | 10 +-
examples/pour/in.pour.2d | 12 +-
examples/pour/in.pour.2d.molecule | 69 +
examples/pour/log.pour.1Feb14.linux.1 | 147 +
examples/pour/log.pour.1Feb14.linux.4 | 147 +
examples/pour/log.pour.2d.1Feb14.linux.1 | 100 +
examples/pour/log.pour.2d.1Feb14.linux.4 | 100 +
examples/pour/log.pour.2d.9Jan12.linux.1 | 93 -
examples/pour/log.pour.2d.9Jan12.linux.4 | 93 -
examples/pour/log.pour.2d.molecule.1Feb14.linux.1 | 113 +
examples/pour/log.pour.2d.molecule.1Feb14.linux.4 | 113 +
examples/pour/log.pour.9Jan12.linux.1 | 140 -
examples/pour/log.pour.9Jan12.linux.4 | 140 -
examples/pour/molecule.vshape | 35 +
examples/prd/in.prd | 2 +-
examples/prd/log.prd.0.1Feb14.linux.4 | 631 +
examples/prd/log.prd.0.9Jan12.linux.4 | 630 -
examples/prd/log.prd.1.1Feb14.linux.4 | 631 +
examples/prd/log.prd.1.9Jan12.linux.4 | 630 -
examples/prd/log.prd.1Feb14.linux.4 | 12 +
examples/prd/log.prd.2.1Feb14.linux.4 | 631 +
examples/prd/log.prd.2.9Jan12.linux.4 | 630 -
examples/prd/log.prd.3.1Feb14.linux.4 | 631 +
examples/prd/log.prd.3.9Jan12.linux.4 | 630 -
examples/prd/log.prd.9Jan12.linux.4 | 12 -
examples/{reax/CHO => qeq}/data.CHO | 0
examples/qeq/data.aC | 1216 +
examples/{reax/CHO => qeq}/ffield.reax.cho | 0
examples/qeq/in.qeq.buck | 39 +
examples/qeq/in.qeq.reaxc | 46 +
examples/qeq/log.qeq.buck.8Sep14.linux.1 | 85 +
examples/qeq/log.qeq.buck.8Sep14.linux.4 | 85 +
examples/qeq/log.qeq.reaxc.8Sep14.linux.1 | 89 +
examples/qeq/log.qeq.reaxc.8Sep14.linux.4 | 89 +
.../{reax/CHO/param.qeq => qeq/param.qeq.reax} | 0
examples/qeq/param.qeq1 | 3 +
examples/qeq/param.qeq2 | 2 +
examples/reax/AB/in.AB | 4 +-
examples/reax/AB/log.reaxc.AB.1Feb14.linux.1 | 54 +
examples/reax/AB/log.reaxc.AB.1Feb14.linux.4 | 54 +
examples/reax/AB/log.reaxc.ab.18Feb11.linux.1 | 50 -
examples/reax/AB/log.reaxc.ab.18Feb11.linux.4 | 50 -
examples/reax/{Au_O => AuO}/README | 0
examples/reax/{Au_O => AuO}/data.AuO | 0
examples/reax/{Au_O => AuO}/ffield.reax.AuO | 0
examples/reax/AuO/in.AuO | 23 +
examples/reax/{Au_O => AuO}/lmp_control | 0
examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.1 | 54 +
examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.4 | 54 +
examples/reax/{Au_O => AuO}/param.qeq | 0
examples/reax/Au_O/in.AuO | 23 -
examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.1 | 50 -
examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.4 | 50 -
examples/reax/CHO/in.CHO | 2 +-
examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.1 | 54 +
examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.4 | 54 +
examples/reax/CHO/log.reaxc.cho.18Feb11.linux.1 | 50 -
examples/reax/CHO/log.reaxc.cho.18Feb11.linux.4 | 50 -
examples/reax/FC/README | 13 +
examples/reax/FC/data.FC | 17296 ++
examples/reax/FC/ffield.reax.FC | 361 +
examples/reax/FC/in.FC | 35 +
examples/reax/FC/log.reaxc.FC.1Feb14.linux.1 | 107 +
examples/reax/FC/log.reaxc.FC.1Feb14.linux.4 | 107 +
examples/reax/{Fe_O_H => FeOH3}/README | 0
examples/reax/{Fe_O_H => FeOH3}/data.FeOH3 | 0
.../reax/{Fe_O_H => FeOH3}/ffield.reax.Fe_O_C_H | 0
examples/reax/FeOH3/in.FeOH3 | 23 +
examples/reax/{Fe_O_H => FeOH3}/lmp_control | 0
examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.1 | 54 +
examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.4 | 54 +
examples/reax/{Fe_O_H => FeOH3}/param.qeq | 0
examples/reax/Fe_O_H/in.FeOH3 | 23 -
.../reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.1 | 50 -
.../reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.4 | 50 -
examples/reax/RDX/in.RDX | 4 +-
examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.1 | 54 +
examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.4 | 54 +
examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.1 | 50 -
examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.4 | 50 -
examples/reax/README | 49 +-
examples/reax/{V_O_H => VOH}/README | 0
examples/reax/{V_O_H => VOH}/data.VOH | 0
examples/reax/{V_O_H => VOH}/ffield.reax.V_O_C_H | 0
examples/reax/VOH/in.VOH | 23 +
examples/reax/{V_O_H => VOH}/lmp_control | 0
examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.1 | 54 +
examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.4 | 54 +
examples/reax/{V_O_H => VOH}/param.qeq | 0
examples/reax/V_O_H/in.VOH | 23 -
examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.1 | 50 -
examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.4 | 50 -
examples/reax/{Zn_O_H => ZnOH2}/README | 0
examples/reax/{Zn_O_H => ZnOH2}/data.ZnOH2 | 0
examples/reax/{Zn_O_H => ZnOH2}/ffield.reax.ZnOH | 0
examples/reax/ZnOH2/in.ZnOH2 | 23 +
examples/reax/{Zn_O_H => ZnOH2}/lmp_control | 0
examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.1 | 54 +
examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.4 | 54 +
examples/reax/{Zn_O_H => ZnOH2}/param.qeq | 0
examples/reax/Zn_O_H/in.ZnOH2 | 23 -
.../reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.1 | 50 -
.../reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.4 | 50 -
examples/reax/in.reax.rdx | 8 +-
examples/reax/in.reax.tatb | 8 +-
examples/reax/in.reaxc.rdx | 10 +-
examples/reax/in.reaxc.tatb | 14 +-
examples/reax/log.reax.rdx.1Feb14.linux.1 | 85 +
examples/reax/log.reax.rdx.1Feb14.linux.4 | 85 +
examples/reax/log.reax.rdx.9Jan12.linux.1 | 170 -
examples/reax/log.reax.rdx.9Jan12.linux.4 | 170 -
examples/reax/log.reax.tatb.1Feb14.linux.1 | 81 +
examples/reax/log.reax.tatb.1Feb14.linux.4 | 81 +
examples/reax/log.reax.tatb.9Jan12.linux.1 | 97 -
examples/reax/log.reax.tatb.9Jan12.linux.4 | 97 -
examples/reax/log.reaxc.rdx.1Feb14.linux.1 | 88 +
examples/reax/log.reaxc.rdx.1Feb14.linux.4 | 88 +
examples/reax/log.reaxc.rdx.9Jan12.linux.1 | 78 -
examples/reax/log.reaxc.rdx.9Jan12.linux.4 | 78 -
examples/reax/log.reaxc.tatb.1Feb14.linux.1 | 86 +
examples/reax/log.reaxc.tatb.1Feb14.linux.4 | 86 +
examples/reax/log.reaxc.tatb.9Jan12.linux.1 | 95 -
examples/reax/log.reaxc.tatb.9Jan12.linux.4 | 95 -
examples/rigid/in.rigid | 8 +-
examples/rigid/in.rigid.poems | 8 +-
examples/rigid/in.rigid.poems2 | 8 +-
examples/rigid/in.rigid.tnr | 4 +-
examples/rigid/log.rigid.1Feb14.linux.1 | 314 +
examples/rigid/log.rigid.1Feb14.linux.4 | 314 +
examples/rigid/log.rigid.9Jan12.linux.1 | 306 -
examples/rigid/log.rigid.9Jan12.linux.4 | 306 -
examples/rigid/log.rigid.poems.1Feb14.linux.1 | 317 +
examples/rigid/log.rigid.poems.1Feb14.linux.4 | 317 +
examples/rigid/log.rigid.poems.9Jan12.linux.1 | 306 -
examples/rigid/log.rigid.poems.9Jan12.linux.4 | 306 -
examples/rigid/log.rigid.poems2.1Feb14.linux.1 | 321 +
examples/rigid/log.rigid.poems2.1Feb14.linux.4 | 321 +
examples/rigid/log.rigid.poems2.9Jan12.linux.1 | 310 -
examples/rigid/log.rigid.poems2.9Jan12.linux.4 | 310 -
examples/rigid/log.rigid.tnr.1Feb14.linux.1 | 401 +
examples/rigid/log.rigid.tnr.1Feb14.linux.4 | 401 +
examples/rigid/log.rigid.tnr.9Jan12.linux.1 | 54 -
examples/rigid/log.rigid.tnr.9Jan12.linux.4 | 54 -
examples/shear/in.shear | 8 +-
examples/shear/in.shear.void | 8 +-
examples/shear/log.shear.1Feb14.linux.1 | 168 +
examples/shear/log.shear.1Feb14.linux.4 | 168 +
examples/shear/log.shear.9Jan12.linux.1 | 161 -
examples/shear/log.shear.9Jan12.linux.4 | 161 -
examples/shear/log.shear.void.1Feb14.linux.1 | 169 +
examples/shear/log.shear.void.1Feb14.linux.4 | 169 +
examples/shear/log.shear.void.9Jan12.linux.1 | 162 -
examples/shear/log.shear.void.9Jan12.linux.4 | 162 -
examples/snap/Ta06A.snapcoeff | 36 +
examples/snap/Ta06A.snapparam | 12 +
examples/snap/Ta06A_pot.snap | 16 +
examples/snap/in.snap | 45 +
examples/snap/log.snap.5Sep14.linux.1 | 116 +
examples/snap/log.snap.5Sep14.linux.4 | 116 +
examples/srd/in.srd.mixture | 10 +-
examples/srd/in.srd.pure | 11 +-
examples/srd/log.srd.mixture.1Feb14.linux.1 | 232 +
examples/srd/log.srd.mixture.1Feb14.linux.4 | 232 +
examples/srd/log.srd.mixture.9Jan12.linux.1 | 223 -
examples/srd/log.srd.mixture.9Jan12.linux.4 | 223 -
examples/srd/log.srd.pure.1Feb14.linux.1 | 148 +
examples/srd/log.srd.pure.1Feb14.linux.4 | 148 +
examples/srd/log.srd.pure.9Jan12.linux.1 | 138 -
examples/srd/log.srd.pure.9Jan12.linux.4 | 138 -
examples/streitz/AlO.eam.alloy | 7007 +
examples/streitz/AlO.streitz | 8 +
examples/streitz/data.streitz | 2171 +
examples/streitz/in.streitz.ewald | 50 +
examples/streitz/in.streitz.wolf | 50 +
examples/streitz/log.streitz.ewald.19Feb15.linux.1 | 111 +
examples/streitz/log.streitz.ewald.19Feb15.linux.4 | 107 +
examples/streitz/log.streitz.wolf.19Feb15.linux.1 | 100 +
examples/streitz/log.streitz.wolf.19Feb15.linux.4 | 100 +
examples/tad/in.tad | 8 +-
examples/tad/log.tad.0.1Feb14.linux.3 | 12325 ++
examples/tad/log.tad.0.9Jan12.linux.3 | 7530 -
examples/tad/log.tad.1.1Feb14.linux.3 | 7262 +
examples/tad/log.tad.1.9Jan12.linux.3 | 2868 -
examples/tad/log.tad.1Feb14.linux.3 | 114 +
examples/tad/log.tad.2.1Feb14.linux.3 | 7262 +
examples/tad/log.tad.2.9Jan12.linux.3 | 2868 -
examples/tad/log.tad.9Jan12.linux.3 | 39 -
examples/tad/log.tad.neb.1Feb14.linux.3 | 1160 +
examples/tad/log.tad.neb.9Jan12.linux.3 | 487 -
examples/voronoi/in.voronoi | 211 +
lib/README | 32 +-
lib/atc/ATC_Coupling.cpp | 2358 +
lib/atc/ATC_Coupling.h | 500 +
lib/atc/ATC_CouplingEnergy.cpp | 412 +
lib/atc/ATC_CouplingEnergy.h | 82 +
lib/atc/ATC_CouplingMass.cpp | 285 +
lib/atc/ATC_CouplingMass.h | 88 +
lib/atc/ATC_CouplingMomentum.cpp | 453 +
lib/atc/ATC_CouplingMomentum.h | 84 +
lib/atc/ATC_CouplingMomentumEnergy.cpp | 510 +
lib/atc/ATC_CouplingMomentumEnergy.h | 83 +
lib/atc/ATC_Error.h | 43 +-
lib/atc/ATC_HardyKernel.cpp | 386 -
lib/atc/ATC_HardyKernel.h | 127 -
lib/atc/ATC_Method.cpp | 2427 +
lib/atc/ATC_Method.h | 870 +
lib/atc/ATC_Transfer.cpp | 2956 +-
lib/atc/ATC_Transfer.h | 1134 +-
lib/atc/ATC_TransferHardy.cpp | 2320 -
lib/atc/ATC_TransferHardy.h | 346 -
lib/atc/ATC_TransferKernel.cpp | 485 +
lib/atc/ATC_TransferKernel.h | 53 +
lib/atc/ATC_TransferPartitionOfUnity.cpp | 506 +
lib/atc/ATC_TransferPartitionOfUnity.h | 59 +
lib/atc/ATC_TransferThermal.cpp | 541 -
lib/atc/ATC_TransferThermal.h | 96 -
lib/atc/ATC_TransferUtility.cpp | 2221 -
lib/atc/ATC_TypeDefs.h | 626 +-
lib/atc/Array.h | 214 +-
lib/atc/Array2D.h | 26 +-
lib/atc/AtomToMoleculeTransfer.cpp | 225 +
lib/atc/AtomToMoleculeTransfer.h | 239 +
lib/atc/AtomicRegulator.cpp | 833 +-
lib/atc/AtomicRegulator.h | 418 +-
lib/atc/BodyForce.cpp | 37 +
lib/atc/BodyForce.h | 68 +
lib/atc/CBLattice.cpp | 204 +
lib/atc/CBLattice.h | 97 +
lib/atc/CG.h | 7 +-
lib/atc/CauchyBorn.cpp | 572 +
lib/atc/CauchyBorn.h | 114 +
lib/atc/CbEam.h | 209 +
lib/atc/CbLjCut.h | 62 +
lib/atc/CbLjSmoothLinear.h | 88 +
lib/atc/CbPotential.cpp | 88 +
lib/atc/CbPotential.h | 70 +
lib/atc/ChargeRegulator.cpp | 735 +
lib/atc/ChargeRegulator.h | 282 +
lib/atc/CloneVector.h | 44 +-
lib/atc/ConcentrationRegulator.cpp | 635 +
lib/atc/ConcentrationRegulator.h | 216 +
lib/atc/DenseMatrix.h | 176 +-
lib/atc/DenseVector.h | 32 +-
lib/atc/DependencyManager.h | 326 +
lib/atc/DiagonalMatrix.h | 96 +-
lib/atc/DislocationExtractor.h | 434 +
lib/atc/ElasticTimeIntegrator.cpp | 796 +-
lib/atc/ElasticTimeIntegrator.h | 420 +-
lib/atc/ElectronChargeDensity.cpp | 131 +
lib/atc/ElectronChargeDensity.h | 269 +
lib/atc/ElectronDragPower.cpp | 77 +
lib/atc/ElectronDragPower.h | 71 +
lib/atc/ElectronFlux.cpp | 51 +-
lib/atc/ElectronFlux.h | 245 +-
lib/atc/ElectronHeatCapacity.cpp | 40 +-
lib/atc/ElectronHeatCapacity.h | 209 +-
lib/atc/ElectronHeatFlux.cpp | 59 +-
lib/atc/ElectronHeatFlux.h | 184 +-
lib/atc/ElectronPhononExchange.cpp | 79 +-
lib/atc/ElectronPhononExchange.h | 107 +-
lib/atc/ExtrinsicModel.cpp | 151 +-
lib/atc/ExtrinsicModel.h | 143 +-
lib/atc/ExtrinsicModelDriftDiffusion.cpp | 601 +
lib/atc/ExtrinsicModelDriftDiffusion.h | 191 +
lib/atc/ExtrinsicModelElectrostatic.cpp | 1011 +
lib/atc/ExtrinsicModelElectrostatic.h | 187 +
lib/atc/ExtrinsicModelTwoTemperature.cpp | 96 +-
lib/atc/ExtrinsicModelTwoTemperature.h | 27 +-
lib/atc/FE_Element.cpp | 1084 +-
lib/atc/FE_Element.h | 369 +-
lib/atc/FE_Engine.cpp | 3478 +-
lib/atc/FE_Engine.h | 621 +-
lib/atc/FE_Interpolate.cpp | 993 +
lib/atc/FE_Interpolate.h | 263 +
lib/atc/FE_Mesh.cpp | 2752 +-
lib/atc/FE_Mesh.h | 619 +-
lib/atc/FE_Quadrature.h | 709 +
lib/atc/FieldEulerIntegrator.cpp | 100 +-
lib/atc/FieldEulerIntegrator.h | 57 +-
lib/atc/FieldManager.cpp | 549 +
lib/atc/FieldManager.h | 132 +
lib/atc/Function.cpp | 554 +
lib/atc/Function.h | 424 +
lib/atc/FundamentalAtomicQuantity.cpp | 152 +
lib/atc/FundamentalAtomicQuantity.h | 254 +
lib/atc/GMRES.h | 65 +-
lib/atc/GhostManager.cpp | 785 +
lib/atc/GhostManager.h | 383 +
lib/atc/ImplicitSolveOperator.cpp | 246 +-
lib/atc/ImplicitSolveOperator.h | 112 +-
lib/atc/InterscaleOperators.cpp | 666 +
lib/atc/InterscaleOperators.h | 465 +
lib/atc/KD_Tree.cpp | 169 +
lib/atc/KD_Tree.h | 89 +
lib/atc/KernelFunction.cpp | 726 +
lib/atc/KernelFunction.h | 255 +
lib/atc/KinetoThermostat.cpp | 703 +
lib/atc/KinetoThermostat.h | 798 +
lib/atc/Kinetostat.cpp | 2312 +-
lib/atc/Kinetostat.h | 692 +-
lib/atc/LammpsInterface.cpp | 1269 +-
lib/atc/LammpsInterface.h | 717 +-
lib/atc/LinearSolver.cpp | 564 +
lib/atc/LinearSolver.h | 183 +
lib/atc/MPI_Wrappers.cpp | 342 +
lib/atc/MPI_Wrappers.h | 46 +
lib/atc/Makefile.g++ | 96 +-
lib/atc/Makefile.icc | 94 +-
lib/atc/Makefile.lammps.empty | 5 +
.../{Makefile.lammps => Makefile.lammps.installed} | 0
lib/atc/Makefile.lammps.linalg | 6 +
lib/atc/Makefile.mingw32-cross | 67 +
lib/atc/Makefile.mingw32-cross-mpi | 68 +
lib/atc/Makefile.mingw64-cross | 67 +
lib/atc/Makefile.mingw64-cross-mpi | 68 +
lib/atc/Makefile.mpic++ | 39 +
lib/atc/Makefile.serial | 102 +-
lib/atc/Material.cpp | 835 +-
lib/atc/Material.h | 193 +-
lib/atc/Matrix.cpp | 183 +-
lib/atc/Matrix.h | 542 +-
lib/atc/MatrixDef.h | 78 +-
lib/atc/MatrixLibrary.h | 11 +-
lib/atc/MeshReader.cpp | 225 +
lib/atc/MeshReader.h | 51 +
lib/atc/MoleculeSet.cpp | 292 +
lib/atc/MoleculeSet.h | 158 +
lib/atc/NonLinearSolver.cpp | 114 +
lib/atc/NonLinearSolver.h | 105 +
lib/atc/OutputManager.cpp | 552 +-
lib/atc/OutputManager.h | 81 +-
lib/{poems => atc}/POEMSChain.h | 0
lib/atc/PaqAtcUtility.cpp | 89 +
lib/atc/PaqAtcUtility.h | 65 +
lib/atc/ParDenseMatrix.h | 172 +
lib/atc/ParDiagonalMatrix.cpp | 93 +
lib/atc/ParDiagonalMatrix.h | 38 +
lib/atc/ParSparseMatrix.cpp | 302 +
lib/atc/ParSparseMatrix.h | 150 +
lib/atc/PerAtomQuantity-inl.h | 801 +
lib/atc/PerAtomQuantity.h | 1469 +
lib/atc/PerAtomQuantityLibrary.cpp | 2510 +
lib/atc/PerAtomQuantityLibrary.h | 1804 +
lib/atc/PerPairQuantity.cpp | 370 +
lib/atc/PerPairQuantity.h | 425 +
lib/atc/PhysicsModel.cpp | 443 +
lib/atc/PhysicsModel.h | 383 +-
lib/atc/PhysicsModelThermal.cpp | 84 -
lib/atc/PhysicsModelThermal.h | 53 -
lib/atc/PhysicsModelTwoTemperature.cpp | 123 -
lib/atc/PhysicsModelTwoTemperature.h | 71 -
lib/atc/PoissonSolver.cpp | 218 +
lib/atc/PoissonSolver.h | 137 +
lib/atc/PolynomialSolver.cpp | 139 +
lib/atc/PolynomialSolver.h | 14 +
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create mode 100644 tools/phonon/version.h
create mode 100644 tools/polybond/Manual.pdf
create mode 100644 tools/polybond/README
create mode 100644 tools/polybond/lmpsdata.py
delete mode 100644 tools/restart2data.cpp
delete mode 100644 tools/thermo_extract.c
create mode 100644 tools/xmgrace/README
create mode 100644 tools/xmgrace/lammpsplot.cpp
create mode 100644 tools/xmgrace/lammpsplot.pdf
create mode 100644 tools/xmgrace/logplotawk.oneliner
create mode 100644 tools/xmgrace/logplotgrep.oneliner
create mode 100755 tools/xmgrace/plotthermodata.awk
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