[lammps] branch master updated (ff7d03f -> 3e569e5)
Anton Gladky
gladk at moszumanska.debian.org
Wed Nov 18 21:19:38 UTC 2015
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch master
in repository lammps.
from ff7d03f Update changelog.
adds 7ff7818 Imported Upstream version 0~20151116.git27798d4
new 0438b9c Merge tag 'upstream/0_20151116.git27798d4'
new 87826f5 Update copyright.
new 879c7b4 Add libeigen3-dev to BD.
new 50e6397 Apply cme fix dpkg-control.
new 14e7d41 Update patch.
adds a00dbfc Imported Upstream version 0~20151117.gite3c4db7
new c1ee275 Merge tag 'upstream/0_20151117.gite3c4db7'
new 8f8aa65 Update d/copyright.
new 646b4a9 Update changelog.
new 1f8fec9 Update d/copyright.
new ce58358 Update get_orig script.
new 7fe6df7 Remove embedded js-scripts.
new 3e569e5 Update changelog.
The 12 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:
bench/Cu_u3.eam | 2 +-
bench/POTENTIALS/in.dpd | 2 +-
bench/README | 2 +-
bench/in.chute.scaled | 2 +-
bench/log.15May15.chain.fixed.icc.1 | 67 +
bench/log.15May15.chain.fixed.icc.4 | 67 +
bench/log.15May15.chain.scaled.icc.4 | 83 +
bench/log.15May15.chute.fixed.icc.1 | 69 +
bench/log.15May15.chute.fixed.icc.4 | 69 +
bench/log.15May15.chute.scaled.icc.4 | 79 +
bench/log.15May15.eam.fixed.icc.1 | 71 +
bench/log.15May15.eam.fixed.icc.4 | 71 +
bench/log.15May15.eam.scaled.icc.4 | 71 +
bench/log.15May15.lj.fixed.icc.1 | 68 +
bench/log.15May15.lj.fixed.icc.4 | 68 +
bench/log.15May15.lj.scaled.icc.4 | 68 +
bench/log.15May15.rhodo.fixed.icc.1 | 110 +
bench/log.15May15.rhodo.fixed.icc.4 | 110 +
bench/log.15May15.rhodo.scaled.icc.4 | 131 +
bench/log.1Feb14.chain.fixed.linux.1 | 63 -
bench/log.1Feb14.chain.fixed.linux.4 | 63 -
bench/log.1Feb14.chain.scaled.linux.4 | 79 -
bench/log.1Feb14.chute.fixed.linux.1 | 65 -
bench/log.1Feb14.chute.fixed.linux.4 | 65 -
bench/log.1Feb14.chute.scaled.linux.4 | 75 -
bench/log.1Feb14.eam.fixed.linux.1 | 67 -
bench/log.1Feb14.eam.fixed.linux.4 | 67 -
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 -
debian/changelog | 17 +
debian/control | 39 +-
debian/copyright | 34 +
debian/lammps-doc.links | 3 +
debian/patches/10_set_configure_flags.patch | 8 +-
debian/rules | 3 +-
debian/scripts/get_orig_src.sh | 1 +
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doc/Manual.html | 850 +-
doc/Manual.html.html | 318 +
doc/Manual.pdf | Bin 9325726 -> 10368659 bytes
doc/Manual.txt | 63 +-
doc/PDF/SMD_LAMMPS_userguide.pdf | Bin 0 -> 3435420 bytes
doc/{USER/sph => PDF}/SPH_LAMMPS_userguide.pdf | Bin
doc/PDF/colvars-refman-lammps.pdf | Bin 528423 -> 632477 bytes
doc/Section_accelerate.html | 809 +-
doc/Section_accelerate.txt | 40 +-
doc/Section_commands.html | 2010 +-
doc/Section_commands.txt | 201 +-
doc/Section_errors.html | 15764 ++--
doc/Section_errors.txt | 2076 +-
doc/Section_example.html | 473 +-
doc/Section_example.txt | 11 +-
doc/Section_history.html | 394 +-
doc/Section_howto.html | 4129 +-
doc/Section_howto.txt | 259 +-
doc/Section_intro.html | 1079 +-
doc/Section_intro.txt | 38 +-
doc/Section_modify.html | 1645 +-
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doc/Section_packages.html | 1950 +-
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doc/Section_tools.html | 1123 +-
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examples/USER/drude/butane/data.butane | 21561 +++++
examples/USER/drude/butane/in.butane.lang | 58 +
examples/USER/drude/butane/in.butane.nh | 62 +
.../drude/butane/log.butane.lang.18Jul15.linux.1 | 171 +
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examples/USER/drude/ethanol/data.ethanol | 12067 +++
examples/USER/drude/ethanol/in.ethanol.lang | 80 +
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examples/USER/drude/swm4-ndp/data.swm4-ndp | 5037 ++
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examples/USER/lb/polymer/out.polymer | 19 -
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examples/USER/mgpt/Ta6.8x.mgpt.parmin | 2 +
examples/USER/mgpt/Ta6.8x.mgpt.potin | 11253 +++
examples/USER/mgpt/in.bcc0 | 68 +
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.../aluminum_strip_pull/aluminum_strip_pull.lmp | 139 +
.../fluid_structure_interaction.lmp | 156 +
examples/USER/smd/funnel_flow/boundary.stl | 66306 +++++++++++++++
examples/USER/smd/funnel_flow/funnel_flow.lmp | 130 +
.../USER/smd/rubber_rings_3d/rubber_rings_3d.lmp | 112 +
.../smd/rubber_rings_3d/washer_hex_adjusted.data | 973 +
examples/USER/smd/rubber_strip_pull/plot.gpl | 13 +
.../smd/rubber_strip_pull/rubber_strip_pull.lmp | 109 +
examples/USER/smtbq/data.Alpha | 1811 +
examples/USER/smtbq/ffield.smtbq.Al | 34 +
examples/USER/smtbq/ffield.smtbq.Al2O3 | 56 +
examples/USER/smtbq/ffield.smtbq.TiO2 | 53 +
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examples/USER/smtbq/log.smtbq.TiO2 | 255 +
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examples/colloid/log.colloid.1Feb14.linux.1 | 131 -
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examples/comb/ffield.comb | 108 +-
examples/comb/ffield.comb3 | 866 +-
examples/comb/lib.comb3 | 4104 +-
examples/comb/log.15May15.comb.Cu.g++.1 | 80 +
examples/comb/log.15May15.comb.Cu.g++.4 | 80 +
examples/comb/log.15May15.comb.Cu2O.elastic.g++.1 | 329 +
examples/comb/log.15May15.comb.Cu2O.elastic.g++.4 | 329 +
examples/comb/log.15May15.comb.HfO2.g++.1 | 197 +
examples/comb/log.15May15.comb.HfO2.g++.4 | 197 +
examples/comb/log.15May15.comb.Si.elastic.g++.1 | 284 +
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examples/comb/log.15May15.comb.Si.g++.1 | 80 +
examples/comb/log.15May15.comb.Si.g++.4 | 80 +
examples/comb/log.15May15.comb3.g++.1 | 77 +
examples/comb/log.15May15.comb3.g++.4 | 77 +
examples/comb/log.comb.Cu.1Feb14.linux.1 | 76 -
examples/comb/log.comb.Cu.1Feb14.linux.4 | 76 -
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 | 316 -
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 | 316 -
examples/comb/log.comb.HfO2.1Feb14.linux.1 | 185 -
examples/comb/log.comb.HfO2.1Feb14.linux.4 | 185 -
examples/comb/log.comb.Si.1Feb14.linux.1 | 76 -
examples/comb/log.comb.Si.1Feb14.linux.4 | 76 -
examples/comb/log.comb.Si.elastic.1Feb14.linux.1 | 274 -
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examples/comb/log.comb3.1Feb14.linux.1 | 73 -
examples/comb/log.comb3.1Feb14.linux.4 | 73 -
examples/crack/log.15May15.crack.g++.1 | 142 +
examples/crack/log.15May15.crack.g++.4 | 142 +
examples/crack/log.crack.1Feb14.linux.1 | 138 -
examples/crack/log.crack.1Feb14.linux.4 | 138 -
examples/deposit/log.15May15.deposit.atom.g++.1 | 182 +
examples/deposit/log.15May15.deposit.atom.g++.4 | 182 +
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examples/dipole/log.15May15.dipole.g++.1 | 93 +
examples/dipole/log.15May15.dipole.g++.4 | 93 +
examples/dipole/log.dipole.1Feb14.linux.1 | 89 -
examples/dipole/log.dipole.1Feb14.linux.4 | 89 -
examples/dreiding/log.15May15.dreiding.g++.1 | 107 +
examples/dreiding/log.15May15.dreiding.g++.4 | 107 +
examples/dreiding/log.dreiding.1Feb14.linux.1 | 106 -
examples/dreiding/log.dreiding.1Feb14.linux.4 | 106 -
examples/eim/ffield.eim | 2 +-
examples/eim/log.15May15.eim.g++.1 | 76 +
examples/eim/log.15May15.eim.g++.4 | 76 +
examples/eim/log.eim.1Feb14.linux.1 | 72 -
examples/eim/log.eim.1Feb14.linux.4 | 72 -
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examples/flow/log.15May15.flow.couette.g++.1 | 134 +
examples/flow/log.15May15.flow.couette.g++.4 | 134 +
examples/flow/log.15May15.flow.pois.g++.1 | 134 +
examples/flow/log.15May15.flow.pois.g++.4 | 134 +
examples/flow/log.flow.couette.1Feb14.linux.1 | 130 -
examples/flow/log.flow.couette.1Feb14.linux.4 | 130 -
examples/flow/log.flow.pois.1Feb14.linux.1 | 130 -
examples/flow/log.flow.pois.1Feb14.linux.4 | 130 -
examples/friction/log.15May15.friction.g++.1 | 153 +
examples/friction/log.15May15.friction.g++.4 | 153 +
examples/friction/log.friction.1Feb14.linux.1 | 149 -
examples/friction/log.friction.1Feb14.linux.4 | 149 -
examples/hugoniostat/log.15May15.hugoniostat.g++.1 | 98 +
examples/hugoniostat/log.15May15.hugoniostat.g++.4 | 98 +
.../hugoniostat/log.hugoniostat.1Feb14.linux.1 | 90 -
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examples/indent/log.15May15.indent.g++.1 | 183 +
examples/indent/log.15May15.indent.g++.4 | 183 +
examples/indent/log.15May15.indent.min.g++.1 | 406 +
examples/indent/log.15May15.indent.min.g++.4 | 399 +
examples/indent/log.indent.1Feb14.linux.1 | 179 -
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examples/indent/log.indent.min.1Feb14.linux.1 | 404 -
examples/indent/log.indent.min.1Feb14.linux.4 | 405 -
examples/kim/log.kim.lj.27Jul14.ubuntu.1 | 29 -
examples/kim/log.kim.lj.27Jul14.ubuntu.4 | 29 -
examples/kim/log.kim.lj.28jun15.ubuntu.1 | 33 +
examples/kim/log.kim.lj.28jun15.ubuntu.4 | 33 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.1 | 29 -
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.4 | 29 -
examples/kim/log.kim.lj.lmp.28jun15.ubuntu.1 | 33 +
examples/kim/log.kim.lj.lmp.28jun15.ubuntu.4 | 33 +
examples/meam/Ni.meam | 1 +
examples/meam/SiC.meam | 1 +
examples/meam/library.meam | 16 +
examples/meam/log.15May15.meam.icc.1 | 71 +
examples/meam/log.15May15.meam.icc.4 | 71 +
examples/meam/log.15May15.meam.shear.icc.1 | 176 +
examples/meam/log.15May15.meam.shear.icc.4 | 176 +
examples/meam/log.meam.1Feb14.linux.1 | 67 -
examples/meam/log.meam.1Feb14.linux.4 | 67 -
examples/meam/log.meam.shear.1Feb14.linux.1 | 172 -
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examples/melt/log.15May15.melt.g++.1 | 67 +
examples/melt/log.15May15.melt.g++.4 | 67 +
examples/melt/log.melt.1Feb14.linux.1 | 63 -
examples/melt/log.melt.1Feb14.linux.4 | 63 -
examples/micelle/log.15May15.micelle.g++.1 | 223 +
examples/micelle/log.15May15.micelle.g++.4 | 223 +
examples/micelle/log.micelle.1Feb14.linux.1 | 215 -
examples/micelle/log.micelle.1Feb14.linux.4 | 215 -
examples/min/log.15May15.min.box.g++.1 | 500 +
examples/min/log.15May15.min.box.g++.4 | 489 +
examples/min/log.15May15.min.g++.1 | 124 +
examples/min/log.15May15.min.g++.4 | 120 +
examples/min/log.min.1Feb14.linux.1 | 118 -
examples/min/log.min.1Feb14.linux.4 | 118 -
examples/min/log.min.box.1Feb14.linux.1 | 356 -
examples/min/log.min.box.1Feb14.linux.4 | 356 -
examples/msst/log.15May15.msst.g++.1 | 142 +
examples/msst/log.15May15.msst.g++.4 | 142 +
examples/msst/log.msst.1Feb14.linux.1 | 138 -
examples/msst/log.msst.1Feb14.linux.4 | 138 -
examples/nb3b/MOH.nb3b.harmonic | 11 +-
examples/nb3b/log.15May15.nb3b.g++.1 | 152 +
examples/nb3b/log.15May15.nb3b.g++.4 | 152 +
examples/nb3b/log.nb3b.1Feb14.linux.1 | 144 -
examples/nb3b/log.nb3b.1Feb14.linux.4 | 144 -
examples/neb/Si.sw | 1 +
examples/nemd/log.15May15.nemd.g++.1 | 119 +
examples/nemd/log.15May15.nemd.g++.4 | 119 +
examples/nemd/log.nemd.1Feb14.linux.1 | 115 -
examples/nemd/log.nemd.1Feb14.linux.4 | 115 -
examples/obstacle/log.15May15.obstacle.g++.1 | 144 +
examples/obstacle/log.15May15.obstacle.g++.4 | 144 +
examples/obstacle/log.obstacle.1Feb14.linux.1 | 140 -
examples/obstacle/log.obstacle.1Feb14.linux.4 | 140 -
examples/peptide/log.15May15.peptide.g++.1 | 178 +
examples/peptide/log.15May15.peptide.g++.4 | 178 +
examples/peptide/log.peptide.1Feb14.linux.1 | 177 -
examples/peptide/log.peptide.1Feb14.linux.4 | 177 -
examples/peri/log.15May15.peri.g++.1 | 94 +
examples/peri/log.15May15.peri.g++.4 | 94 +
examples/peri/log.peri.1Feb14.linux.1 | 90 -
examples/peri/log.peri.1Feb14.linux.4 | 90 -
examples/pour/in.pour.2d.molecule | 8 +-
examples/pour/log.15May15.pour.2d.g++.1 | 104 +
examples/pour/log.15May15.pour.2d.g++.4 | 104 +
examples/pour/log.15May15.pour.2d.molecule.g++.1 | 125 +
examples/pour/log.15May15.pour.2d.molecule.g++.4 | 125 +
examples/pour/log.15May15.pour.g++.1 | 151 +
examples/pour/log.15May15.pour.g++.4 | 151 +
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.molecule.1Feb14.linux.1 | 113 -
examples/pour/log.pour.2d.molecule.1Feb14.linux.4 | 113 -
examples/prd/Si.sw | 1 +
examples/python/funcs.py | 22 +
examples/python/in.python | 64 +
examples/python/log.python.17Mar15.linux.1 | 315 +
examples/python/log.python.17Mar15.linux.4 | 315 +
examples/qeq/ffield.reax.cho | 2 +-
examples/qeq/log.15May15.qeq.buck.g++.1 | 89 +
examples/qeq/log.15May15.qeq.buck.g++.4 | 89 +
examples/qeq/log.15May15.qeq.reaxc.g++.1 | 93 +
examples/qeq/log.15May15.qeq.reaxc.g++.4 | 93 +
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 -
examples/reax/AB/ffield.reax.AB | 2 +-
examples/reax/AuO/ffield.reax.AuO | 2 +-
examples/reax/CHO/ffield.reax.cho | 2 +-
examples/reax/FC/ffield.reax.FC | 2 +-
examples/reax/FeOH3/ffield.reax.Fe_O_C_H | 2 +-
examples/reax/RDX/ffield.reax.rdx | 2 +-
examples/reax/VOH/ffield.reax.V_O_C_H | 2 +-
examples/reax/ZnOH2/ffield.reax.ZnOH | 2 +-
examples/reax/ffield.reax | 2 +-
examples/reax/log.15May15.reax.rdx.g++.1 | 89 +
examples/reax/log.15May15.reax.rdx.g++.4 | 89 +
examples/reax/log.15May15.reax.tatb.g++.1 | 85 +
examples/reax/log.15May15.reax.tatb.g++.4 | 85 +
examples/reax/log.15May15.reaxc.rdx.g++.1 | 92 +
examples/reax/log.15May15.reaxc.rdx.g++.4 | 92 +
examples/reax/log.15May15.reaxc.tatb.g++.1 | 90 +
examples/reax/log.15May15.reaxc.tatb.g++.4 | 90 +
examples/reax/log.reax.rdx.1Feb14.linux.1 | 85 -
examples/reax/log.reax.rdx.1Feb14.linux.4 | 85 -
examples/reax/log.reax.tatb.1Feb14.linux.1 | 81 -
examples/reax/log.reax.tatb.1Feb14.linux.4 | 81 -
examples/reax/log.reaxc.rdx.1Feb14.linux.1 | 88 -
examples/reax/log.reaxc.rdx.1Feb14.linux.4 | 88 -
examples/reax/log.reaxc.tatb.1Feb14.linux.1 | 86 -
examples/reax/log.reaxc.tatb.1Feb14.linux.4 | 86 -
examples/rigid/log.15May15.rigid.g++.1 | 318 +
examples/rigid/log.15May15.rigid.g++.4 | 318 +
examples/rigid/log.15May15.rigid.poems.g++.1 | 321 +
examples/rigid/log.15May15.rigid.poems.g++.4 | 321 +
examples/rigid/log.15May15.rigid.poems2.g++.1 | 325 +
examples/rigid/log.15May15.rigid.poems2.g++.4 | 325 +
examples/rigid/log.15May15.rigid.tnr.g++.1 | 399 +
examples/rigid/log.15May15.rigid.tnr.g++.4 | 399 +
examples/rigid/log.rigid.1Feb14.linux.1 | 314 -
examples/rigid/log.rigid.1Feb14.linux.4 | 314 -
examples/rigid/log.rigid.poems.1Feb14.linux.1 | 317 -
examples/rigid/log.rigid.poems.1Feb14.linux.4 | 317 -
examples/rigid/log.rigid.poems2.1Feb14.linux.1 | 321 -
examples/rigid/log.rigid.poems2.1Feb14.linux.4 | 321 -
examples/rigid/log.rigid.tnr.1Feb14.linux.1 | 401 -
examples/rigid/log.rigid.tnr.1Feb14.linux.4 | 401 -
examples/shear/Ni_u3.eam | 2 +-
examples/shear/log.15May15.shear.g++.1 | 172 +
examples/shear/log.15May15.shear.g++.4 | 172 +
examples/shear/log.15May15.shear.void.g++.1 | 173 +
examples/shear/log.15May15.shear.void.g++.4 | 173 +
examples/shear/log.shear.1Feb14.linux.1 | 168 -
examples/shear/log.shear.1Feb14.linux.4 | 168 -
examples/shear/log.shear.void.1Feb14.linux.1 | 169 -
examples/shear/log.shear.void.1Feb14.linux.4 | 169 -
examples/snap/Ta06A.snapcoeff | 1 +
examples/snap/Ta06A.snapparam | 2 +
examples/snap/Ta06A_pot.snap | 5 +-
examples/snap/log.15May15.snap.g++.1 | 120 +
examples/snap/log.15May15.snap.g++.4 | 120 +
examples/snap/log.snap.5Sep14.linux.1 | 116 -
examples/snap/log.snap.5Sep14.linux.4 | 116 -
examples/srd/log.15May15.srd.mixture.g++.1 | 245 +
examples/srd/log.15May15.srd.mixture.g++.4 | 245 +
examples/srd/log.15May15.srd.pure.g++.1 | 152 +
examples/srd/log.15May15.srd.pure.g++.4 | 152 +
examples/srd/log.srd.mixture.1Feb14.linux.1 | 232 -
examples/srd/log.srd.mixture.1Feb14.linux.4 | 232 -
examples/srd/log.srd.pure.1Feb14.linux.1 | 148 -
examples/srd/log.srd.pure.1Feb14.linux.4 | 148 -
examples/streitz/log.15May15.streitz.ewald.g++.1 | 107 +
examples/streitz/log.15May15.streitz.ewald.g++.4 | 107 +
examples/streitz/log.15May15.streitz.wolf.g++.1 | 100 +
examples/streitz/log.15May15.streitz.wolf.g++.4 | 100 +
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/Si.sw | 1 +
examples/vashishta/InP.vashishta | 38 +
examples/vashishta/SiO.1990.vashishta | 41 +
examples/vashishta/data.quartz | 26 +
examples/vashishta/in.indiumphosphide | 75 +
examples/vashishta/in.sio2 | 28 +
examples/voronoi/log.15May15.voronoi.g++.1 | 542 +
examples/voronoi/log.15May15.voronoi.g++.4 | 542 +
lib/README | 8 +
lib/atc/ATC_Error.h | 2 +-
lib/atc/ATC_TypeDefs.h | 14 +-
lib/atc/DependencyManager.h | 2 +-
lib/atc/ExtrinsicModel.h | 2 +-
lib/atc/FE_Element.h | 2 +-
lib/atc/FE_Mesh.h | 2 +-
lib/atc/MatrixDef.h | 4 +-
lib/atc/MeshReader.h | 2 +-
lib/atc/PaqAtcUtility.h | 2 +-
lib/atc/PerPairQuantity.cpp | 2 +
lib/atc/PhysicsModel.h | 2 +-
lib/atc/TimeFilter.h | 2 +-
lib/atc/WeakEquation.h | 2 +-
lib/awpmd/ivutils/include/logexc.h | 2 +-
lib/awpmd/ivutils/include/pairhash.h | 1 -
lib/awpmd/ivutils/include/vector_3.h | 10 +-
lib/awpmd/systems/interact/TCP/wpmd_split.h | 1 +
lib/colvars/Makefile.fermi | 25 +-
lib/colvars/Makefile.g++ | 35 +-
lib/colvars/Makefile.mingw32-cross | 20 +-
lib/colvars/Makefile.mingw64-cross | 20 +-
lib/colvars/colvar.cpp | 214 +-
lib/colvars/colvar.h | 7 +-
lib/colvars/colvaratoms.cpp | 6 +-
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lib/colvars/colvarbias.cpp | 7 +
lib/colvars/colvarbias.h | 16 +-
lib/colvars/colvarbias_abf.cpp | 205 +-
lib/colvars/colvarbias_abf.h | 36 +-
lib/colvars/colvarbias_histogram.cpp | 253 +
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lib/colvars/colvarbias_meta.h | 2 +
lib/colvars/colvarbias_restraint.h | 2 +-
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lib/colvars/colvarcomp.h | 9 +-
lib/colvars/colvarcomp_distances.cpp | 37 +-
lib/colvars/colvarcomp_rotations.cpp | 4 +-
lib/colvars/colvargrid.cpp | 103 +-
lib/colvars/colvargrid.h | 135 +-
lib/colvars/colvarmodule.cpp | 65 +-
lib/colvars/colvarmodule.h | 36 +-
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lib/colvars/colvarscript.cpp | 165 +-
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lib/colvars/colvartypes.cpp | 1 -
lib/compress/Makefile.lammps | 21 +
lib/compress/README | 7 +
lib/gpu/Nvidia.makefile | 53 +-
lib/gpu/Opencl.makefile | 46 +-
lib/gpu/cudpp_mini/license.txt | 2 +-
lib/gpu/geryon/ocl_kernel.h | 8 +-
lib/gpu/lal_answer.cpp | 2 +-
lib/gpu/lal_base_three.cpp | 8 +-
lib/gpu/lal_base_three.h | 4 +-
lib/gpu/lal_coul_dsf.cu | 24 +-
lib/gpu/lal_device.cpp | 4 +-
lib/gpu/lal_eam_alloy_ext.cpp | 143 +
lib/gpu/lal_eam_fs_ext.cpp | 143 +
lib/gpu/lal_lj_cubic.cpp | 159 +
lib/gpu/lal_lj_cubic.cu | 229 +
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lib/gpu/lal_lj_cubic_ext.cpp | 124 +
lib/gpu/lal_lj_dsf.cu | 16 +-
lib/gpu/lal_sw.cu | 10 +-
lib/gpu/lal_tersoff.cpp | 451 +
lib/gpu/lal_tersoff.cu | 1090 +
lib/gpu/lal_tersoff.h | 116 +
lib/gpu/lal_tersoff_ext.cpp | 139 +
lib/gpu/lal_tersoff_extra.h | 612 +
lib/gpu/lal_zbl.cpp | 159 +
lib/gpu/lal_zbl.cu | 276 +
lib/gpu/lal_zbl.h | 84 +
lib/gpu/lal_zbl_ext.cpp | 123 +
lib/h5md/LICENSE | 25 +
lib/h5md/Makefile | 33 +
lib/h5md/Makefile.lammps.empty | 7 +
lib/h5md/README | 27 +
lib/h5md/include/ch5md.h | 74 +
lib/h5md/src/ch5md.c | 445 +
lib/kim/Makefile.lammps | 23 +-
lib/kim/README | 71 +-
lib/kim/pair-kim.release.info | 6 +
lib/kokkos/Copyright.txt | 40 +
lib/kokkos/LICENSE | 40 +
lib/kokkos/Makefile.kokkos | 377 +
lib/kokkos/Makefile.lammps | 170 -
lib/kokkos/Makefile.targets | 57 +
lib/kokkos/README | 168 +-
lib/kokkos/TPL/cmake/Dependencies.cmake | 9 -
lib/kokkos/TPL/cub/block/block_discontinuity.cuh | 587 -
lib/kokkos/TPL/cub/block/block_exchange.cuh | 918 -
lib/kokkos/TPL/cub/block/block_histogram.cuh | 414 -
lib/kokkos/TPL/cub/block/block_load.cuh | 1122 -
lib/kokkos/TPL/cub/block/block_radix_rank.cuh | 479 -
lib/kokkos/TPL/cub/block/block_radix_sort.cuh | 608 -
lib/kokkos/TPL/cub/block/block_raking_layout.cuh | 145 -
lib/kokkos/TPL/cub/block/block_reduce.cuh | 563 -
lib/kokkos/TPL/cub/block/block_scan.cuh | 2233 -
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lib/kokkos/TPL/cub/cub.cuh | 84 -
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lib/kokkos/TPL/cub/device/device_histogram.cuh | 1062 -
lib/kokkos/TPL/cub/device/device_radix_sort.cuh | 890 -
lib/kokkos/TPL/cub/device/device_reduce.cuh | 775 -
lib/kokkos/TPL/cub/device/device_reduce_by_key.cuh | 633 -
lib/kokkos/TPL/cub/device/device_reorder.cuh | 550 -
lib/kokkos/TPL/cub/device/device_scan.cuh | 812 -
lib/kokkos/TPL/cub/grid/grid_barrier.cuh | 211 -
lib/kokkos/TPL/cub/grid/grid_even_share.cuh | 197 -
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lib/smd/Makefile.lammps | 5 +
lib/smd/README | 41 +
potentials/AlCu.bop.table | 5684 ++
potentials/CCu_v2.bop.table | 6039 ++
potentials/CdTe.bop | 44 -
potentials/CdTeSe.bop.table | 9664 +++
potentials/CdTeZnSeHgS0.sw | 225 +
potentials/CdZnTe_v1.bop.table | 9664 +++
potentials/CdZnTe_v2.bop.table | 9664 +++
potentials/CuH.bop.table | 6039 ++
potentials/CuTa_eam.poly | 2830 +
potentials/GaAs.bop | 45 -
potentials/GaAs.bop.table | 2 +-
potentials/GaN_sw.poly | 6836 ++
potentials/GaN_tersoff.poly | 8430 ++
potentials/InP.vashishta | 38 +
potentials/Mo5.2.mgpt.README | 55 +
potentials/Mo5.2.mgpt.parmin | 2 +
potentials/Mo5.2.mgpt.potin | 9701 +++
potentials/README | 32 +-
potentials/Si.tersoff.mod | 54 +-
potentials/SiC.vashishta | 41 +
potentials/SiO.1990.vashishta | 41 +
potentials/SiO.1994.vashishta | 38 +
potentials/SiO.1997.vashishta | 37 +
potentials/Ta06A_pot.snap | 3 +-
potentials/Ta4.mgpt.README | 49 +
potentials/Ta4.mgpt.parmin | 2 +
potentials/Ta4.mgpt.potin | 6597 ++
potentials/Ta6.8x.mgpt.README | 57 +
potentials/Ta6.8x.mgpt.parmin | 2 +
potentials/Ta6.8x.mgpt.potin | 11253 +++
potentials/V6.1.mgpt.README | 56 +
potentials/V6.1.mgpt.parmin | 2 +
potentials/V6.1.mgpt.potin | 9701 +++
potentials/ffield.comb | 196 +-
potentials/ffield.smtbq.Al | 34 +
potentials/ffield.smtbq.Al2O3 | 56 +
potentials/ffield.smtbq.TiO2 | 53 +
potentials/lib.comb3 | 3 +-
python/README | 12 +-
python/install.py | 37 +-
python/lammps.py | 14 +-
src/ASPHERE/compute_erotate_asphere.cpp | 2 +-
src/ASPHERE/compute_temp_asphere.cpp | 21 +-
src/ASPHERE/fix_nh_asphere.cpp | 6 +-
src/ASPHERE/fix_nph_asphere.cpp | 2 +-
src/ASPHERE/fix_npt_asphere.cpp | 2 +-
src/ASPHERE/fix_nve_asphere.cpp | 6 +-
src/ASPHERE/fix_nve_asphere_noforce.cpp | 6 +-
src/ASPHERE/fix_nve_line.cpp | 6 +-
src/ASPHERE/fix_nve_tri.cpp | 6 +-
src/ASPHERE/fix_nvt_asphere.cpp | 2 +-
src/ASPHERE/pair_gayberne.cpp | 8 +-
src/ASPHERE/pair_line_lj.cpp | 8 +-
src/ASPHERE/pair_resquared.cpp | 8 +-
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src/BODY/compute_body_local.cpp | 8 +-
src/BODY/fix_nve_body.cpp | 6 +-
src/BODY/pair_body.cpp | 12 +-
src/CLASS2/angle_class2.cpp | 6 +-
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src/CLASS2/bond_class2.cpp | 4 +-
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src/CLASS2/pair_lj_class2_coul_long.cpp | 74 +-
src/CLASS2/pair_lj_class2_coul_long.h | 8 +-
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src/COLLOID/pair_yukawa_colloid.cpp | 4 +-
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src/COMPRESS/README | 13 +
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src/COMPRESS/dump_cfg_gz.cpp | 153 +
src/COMPRESS/dump_cfg_gz.h | 53 +
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src/CORESHELL/Install.sh | 4 +
src/CORESHELL/compute_temp_cs.cpp | 64 +-
src/CORESHELL/compute_temp_cs.h | 40 +-
src/CORESHELL/pair_born_coul_long_cs.cpp | 33 +-
src/CORESHELL/pair_born_coul_long_cs.h | 4 -
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src/CORESHELL/pair_coul_long_cs.cpp | 185 +
src/CORESHELL/pair_coul_long_cs.h | 58 +
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 572 +
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src/DIPOLE/atom_vec_dipole.cpp | 4 +-
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src/DIPOLE/pair_lj_long_dipole_long.h | 9 +-
src/Depend.sh | 10 +
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src/FLD/pair_brownian_poly.cpp | 10 +-
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src/FLD/pair_lubricateU_poly.cpp | 12 +-
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src/GPU/pair_born_coul_wolf_gpu.cpp | 68 +-
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src/GPU/pair_eam_alloy_gpu.cpp | 249 +-
src/GPU/pair_eam_alloy_gpu.h | 20 +-
src/GPU/pair_eam_fs_gpu.cpp | 253 +-
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src/GPU/pair_table_gpu.cpp | 8 +-
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src/GPU/pair_zbl_gpu.cpp | 242 +
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src/GPU/pppm_gpu.cpp | 18 +-
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src/GRANULAR/pair_gran_hertz_history.cpp | 8 +-
src/GRANULAR/pair_gran_hooke.cpp | 6 +-
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