[lammps] branch master updated (e8f6b56 -> 18e8d04)
Anton Gladky
gladk at moszumanska.debian.org
Sat Nov 12 07:00:50 UTC 2016
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch master
in repository lammps.
from e8f6b56 Update changelog.
new 7c868a1 Update get-script to clean it from VCS and other support-files.
adds 7328d32 New upstream version 0~20161109.git9806da6
new 2c045a1 Merge tag 'upstream/0_20161109.git9806da6'
new 1c61fdb Refresh patch.
new f13ed88 Generate docs during build.
new 0bf08ca Apply cme fix dpkg.
new 18e8d04 Update changelog.
The 6 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/POTENTIALS/ffield.comb | 196 +-
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.6Oct16.chain.fixed.icc.1 | 78 +
bench/log.6Oct16.chain.fixed.icc.4 | 78 +
bench/log.6Oct16.chain.scaled.icc.4 | 94 +
bench/log.6Oct16.chute.fixed.icc.1 | 80 +
bench/log.6Oct16.chute.fixed.icc.4 | 80 +
bench/log.6Oct16.chute.scaled.icc.4 | 90 +
bench/log.6Oct16.eam.fixed.icc.1 | 83 +
bench/log.6Oct16.eam.fixed.icc.4 | 83 +
bench/log.6Oct16.eam.scaled.icc.4 | 83 +
bench/log.6Oct16.lj.fixed.icc.1 | 79 +
bench/log.6Oct16.lj.fixed.icc.4 | 79 +
bench/log.6Oct16.lj.scaled.icc.4 | 79 +
bench/log.6Oct16.rhodo.fixed.icc.1 | 122 +
bench/log.6Oct16.rhodo.fixed.icc.4 | 122 +
bench/log.6Oct16.rhodo.scaled.icc.4 | 143 +
debian/changelog | 10 +
debian/control | 5 +-
debian/copyright | 8 +-
debian/lammps-doc.doc-base | 6 +-
debian/lammps-doc.docs | 3 +-
debian/patches/10_set_configure_flags.patch | 10 +-
debian/rules | 5 +-
debian/scripts/get_orig_src.sh | 2 +
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doc/Eqs/improper_umbrella.tex | 13 -
doc/Eqs/pair_comb1.tex | 7 -
doc/Eqs/pair_comb2.tex | 23 -
doc/Makefile | 145 +
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doc/Manual.html.html | 318 -
doc/Manual.pdf | Bin 10368659 -> 0 bytes
doc/Manual.txt | 304 -
doc/PDF/colvars-refman-lammps.pdf | 8124 --
doc/README | 115 +
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examples/USER/dpd/dpde-shardlow/data.dpde | 2018 +
examples/USER/dpd/dpde-shardlow/in.dpde-shardlow | 31 +
.../dpd/dpde-shardlow/log.dpde-shardlow.reference | 177 +
examples/USER/dpd/dpde-vv/data.dpd | 20266 +++
examples/USER/dpd/dpde-vv/in.dpde-vv | 33 +
examples/USER/dpd/dpde-vv/log.dpde-vv.reference | 173 +
examples/USER/dpd/dpdh-shardlow/data.dpdh | 20266 +++
examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow | 31 +
.../dpd/dpdh-shardlow/log.dpdh-shardlow.reference | 175 +
examples/USER/dpd/dpdp-shardlow/data.dpd | 2018 +
examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow | 27 +
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examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow | 59 +
examples/USER/dpd/dpdrx-shardlow/kinetics.dpdrx | 12 +
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examples/USER/dpd/dpdrx-shardlow/params.exp6 | 16 +
examples/USER/dpd/dpdrx-shardlow/table.eos | 4006 +
examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx | 17 +
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examples/USER/dpd/multi-lucy/in.multi-lucy | 40 +
.../USER/dpd/multi-lucy/log.multi-lucy.reference | 192 +
examples/USER/dpd/multi-lucy/table.multibody | 74928 ++++++++++
examples/USER/eff/Auger-Adamantane/data.adamantane | 238 +-
.../eff/Auger-Adamantane/data.adamantane_ionized | 236 +-
examples/USER/eff/Li-dendritic/data.Li-dendritic | 6944 +-
examples/USER/flow_gauss/README | 45 +
examples/USER/flow_gauss/in.GD | 258 +
examples/USER/lb/polymer/data.polymer | 2080 +-
examples/USER/lb/polymer/in.polymer_default_gamma | 214 +-
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examples/USER/manifold/diffusion/README | 1 +
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examples/USER/manifold/virus/vir.in | 75 +
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examples/USER/{ => misc}/gauss-diel/log.gauss-diel | 0
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examples/USER/{ => misc}/gle/in.h2o-quantum | 0
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examples/USER/{ => misc}/gle/qt-300k.A | 0
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examples/USER/{ => misc}/gle/smart.A | 0
examples/USER/{ => misc}/i-pi/C.opt.tersoff | 0
examples/USER/{ => misc}/i-pi/README | 0
examples/USER/{ => misc}/i-pi/data.graphene | 0
examples/USER/{ => misc}/i-pi/i-pi_input.xml | 0
examples/USER/{ => misc}/i-pi/i-pi_positions.xyz | 0
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examples/USER/{ => misc}/imd/README | 0
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examples/USER/{ => misc}/imd/bucky_cnt_imd.vmd | 0
examples/USER/{ => misc}/imd/data.bucky-plus-cnt | 0
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examples/USER/{ => misc}/imd/deca-ala-solv.psf | 0
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examples/USER/{ => misc}/imd/falcon.tcl | 0
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examples/USER/{ => misc}/imd/melt.psf | 0
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examples/USER/{ => misc}/pimd/para-h2/run.sh | 0
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examples/USER/{ => misc}/pimd/prot-hairpin/run.sh | 0
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examples/USER/{ => misc}/srp/data.chain | 0
examples/USER/misc/srp/in.srp | 41 +
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examples/USER/misc/ti/in.ti_spring | 85 +-
examples/USER/phonon/1-1D-mono/README | 7 +-
examples/USER/phonon/1-1D-mono/disp.dat | 34 +-
examples/USER/phonon/1-1D-mono/in.disp | 1 +
examples/USER/phonon/1-1D-mono/log.lammps | 20090 +++
examples/USER/phonon/1-1D-mono/log.lammps.example | 146 -
examples/USER/phonon/1-1D-mono/pdisp.eps | 99 +-
examples/USER/phonon/1-1D-mono/pdisp.gnuplot | 16 +
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examples/USER/phonon/1-1D-mono/phonon.log | 96 +-
examples/USER/phonon/2-1D-diatomic/README | 7 +-
examples/USER/phonon/2-1D-diatomic/disp.dat | 2 +-
examples/USER/phonon/2-1D-diatomic/in.Ana | 2 +-
examples/USER/phonon/2-1D-diatomic/in.disp | 1 +
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examples/USER/phonon/2-1D-diatomic/pdisp.eps | 4 +-
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examples/USER/phonon/2-1D-diatomic/phonon.log | 2 +-
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examples/USER/phonon/3-3D-FCC-Cu-EAM/README | 11 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat | 266 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp | 1 +
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examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps | 1398 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot | 18 +
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examples/USER/phonon/4-Graphene/README | 35 +
examples/USER/phonon/4-Graphene/SiC.tersoff | 39 +
examples/USER/phonon/4-Graphene/data.pos | 211 +
examples/USER/phonon/4-Graphene/in.disp | 16 +
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examples/USER/phonon/4-Graphene/map.in | 202 +
examples/USER/phonon/4-Graphene/pdisp.dat | 55 +
examples/USER/phonon/4-Graphene/pdisp.eps | 1350 +
examples/USER/phonon/4-Graphene/pdisp.gnuplot | 21 +
examples/USER/phonon/4-Graphene/plot.disp | 17 +
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examples/USER/smd/funnel_flow/boundary.stl | 132612 +++++++++---------
examples/USER/smd/funnel_flow/funnel_flow.lmp | 4 +-
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examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1 | 436 +
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examples/VISCOSITY/log.13Oct16.mp.2d.g++.1 | 260 +
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examples/VISCOSITY/log.gk.2d.1Feb14 | 386 -
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examples/VISCOSITY/profile.13Oct16.gk.2d.g++.1 | 100654 +++++++++++++
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examples/VISCOSITY/profile.gk.2d.1Feb14 | 100654 -------------
examples/VISCOSITY/profile.mp.2d.1Feb14 | 1473 -
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examples/balance/in.balance.bond.fast | 2 +-
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examples/comb/log.5Oct16.comb.Cu.g++.1 | 92 +
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examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.1 | 409 +
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examples/comb/log.5Oct16.comb.HfO2.g++.1 | 235 +
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examples/controller/in.controller | 44 +
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examples/friction/log.5Oct16.friction.g++.1 | 164 +
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...15.ubuntu.1 => log.28Jun15.kim.lj.lmp.ubuntu.1} | 0
...15.ubuntu.4 => log.28Jun15.kim.lj.lmp.ubuntu.4} | 0
...8jun15.ubuntu.1 => log.28Jun15.kim.lj.ubuntu.1} | 0
...8jun15.ubuntu.4 => log.28Jun15.kim.lj.ubuntu.4} | 0
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.5Oct16.meam.icc.1 | 84 +
examples/meam/log.5Oct16.meam.icc.4 | 84 +
examples/meam/log.5Oct16.meam.shear.icc.1 | 196 +
examples/meam/log.5Oct16.meam.shear.icc.4 | 196 +
examples/melt/log.15May15.melt.g++.1 | 67 -
examples/melt/log.15May15.melt.g++.4 | 67 -
examples/melt/log.5Oct16.melt.g++.1 | 78 +
examples/melt/log.5Oct16.melt.g++.4 | 78 +
examples/micelle/log.15May15.micelle.g++.1 | 223 -
examples/micelle/log.15May15.micelle.g++.4 | 223 -
examples/micelle/log.5Oct16.micelle.g++.1 | 244 +
examples/micelle/log.5Oct16.micelle.g++.4 | 244 +
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.5Oct16.min.box.g++.1 | 553 +
examples/min/log.5Oct16.min.box.g++.4 | 542 +
examples/min/log.5Oct16.min.g++.1 | 141 +
examples/min/log.5Oct16.min.g++.4 | 137 +
examples/msst/log.15May15.msst.g++.1 | 142 -
examples/msst/log.15May15.msst.g++.4 | 142 -
examples/msst/log.5Oct16.msst.g++.1 | 160 +
examples/msst/log.5Oct16.msst.g++.4 | 160 +
examples/nb3b/MOH.nb3b.harmonic | 27 +-
examples/nb3b/log.15May15.nb3b.g++.1 | 152 -
examples/nb3b/log.15May15.nb3b.g++.4 | 152 -
examples/nb3b/log.5Oct16.nb3b.g++.1 | 173 +
examples/nb3b/log.5Oct16.nb3b.g++.4 | 173 +
examples/neb/README | 18 +-
examples/neb/in.neb.hop1 | 9 +-
examples/neb/in.neb.hop2 | 11 +-
examples/neb/in.neb.sivac | 18 +-
examples/neb/initial.hop1 | 860 +
examples/neb/initial.hop2 | 862 +
examples/neb/initial.sivac | 1042 +
examples/neb/log.5Oct16.neb.hop1.g++.4 | 10 +
examples/neb/log.5Oct16.neb.hop1.g++.8 | 10 +
examples/neb/log.5Oct16.neb.hop2.g++.4 | 18 +
examples/neb/log.5Oct16.neb.hop2.g++.8 | 18 +
examples/neb/log.5Oct16.neb.sivac.g++.3 | 14 +
examples/neb/log.5Oct16.neb.sivac.g++.6 | 14 +
examples/neb/log.5Oct16.neb.sivac.g++.9 | 14 +
examples/neb/log.neb.hop1.1Feb14.linux.4 | 10 -
examples/neb/log.neb.hop2.1Feb14.linux.4 | 17 -
examples/neb/log.neb.sivac.1Feb14.linux.3 | 13 -
examples/nemd/log.15May15.nemd.g++.1 | 119 -
examples/nemd/log.15May15.nemd.g++.4 | 119 -
examples/nemd/log.5Oct16.nemd.g++.1 | 130 +
examples/nemd/log.5Oct16.nemd.g++.4 | 130 +
examples/obstacle/log.15May15.obstacle.g++.1 | 144 -
examples/obstacle/log.15May15.obstacle.g++.4 | 144 -
examples/obstacle/log.5Oct16.obstacle.g++.1 | 155 +
examples/obstacle/log.5Oct16.obstacle.g++.4 | 155 +
examples/peptide/log.15May15.peptide.g++.1 | 178 -
examples/peptide/log.15May15.peptide.g++.4 | 178 -
examples/peptide/log.5Oct16.peptide.g++.1 | 190 +
examples/peptide/log.5Oct16.peptide.g++.4 | 190 +
examples/peri/log.15May15.peri.g++.1 | 94 -
examples/peri/log.15May15.peri.g++.4 | 94 -
examples/peri/log.5Oct16.peri.g++.1 | 104 +
examples/peri/log.5Oct16.peri.g++.4 | 104 +
examples/pour/in.pour | 2 +-
examples/pour/in.pour.2d | 4 +-
examples/pour/in.pour.2d.molecule | 4 +-
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.5Oct16.pour.2d.g++.1 | 115 +
examples/pour/log.5Oct16.pour.2d.g++.4 | 115 +
examples/pour/log.5Oct16.pour.2d.molecule.g++.1 | 136 +
examples/pour/log.5Oct16.pour.2d.molecule.g++.4 | 136 +
examples/pour/log.5Oct16.pour.g++.1 | 169 +
examples/pour/log.5Oct16.pour.g++.4 | 169 +
examples/prd/README | 3 +-
examples/prd/log.5Oct16.prd.g++.4 | 22 +
examples/prd/log.5Oct16.prd.g++.8 | 22 +
examples/prd/log.prd.0.1Feb14.linux.4 | 631 -
examples/prd/log.prd.1.1Feb14.linux.4 | 631 -
examples/prd/log.prd.1Feb14.linux.4 | 12 -
examples/prd/log.prd.2.1Feb14.linux.4 | 631 -
examples/prd/log.prd.3.1Feb14.linux.4 | 631 -
examples/prd/screen.5Oct16.prd.g++.4.0 | 2328 +
examples/prd/screen.5Oct16.prd.g++.4.1 | 2204 +
examples/prd/screen.5Oct16.prd.g++.4.2 | 2349 +
examples/prd/screen.5Oct16.prd.g++.4.3 | 2183 +
examples/prd/screen.5Oct16.prd.g++.8.0 | 2328 +
examples/prd/screen.5Oct16.prd.g++.8.1 | 2204 +
examples/prd/screen.5Oct16.prd.g++.8.2 | 2349 +
examples/prd/screen.5Oct16.prd.g++.8.3 | 2183 +
examples/python/log.5Oct16.python.g++.1 | 396 +
examples/python/log.5Oct16.python.g++.4 | 396 +
examples/python/log.python.17Mar15.linux.1 | 315 -
examples/python/log.python.17Mar15.linux.4 | 315 -
examples/qeq/in.qeq.buck | 16 +-
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.5Oct16.qeq.buck.g++.1 | 106 +
examples/qeq/log.5Oct16.qeq.buck.g++.4 | 106 +
examples/qeq/log.5Oct16.qeq.reaxc.g++.1 | 105 +
examples/qeq/log.5Oct16.qeq.reaxc.g++.4 | 105 +
examples/reax/AB/log.5Oct16.AB.g++.1 | 70 +
examples/reax/AB/log.5Oct16.AB.g++.4 | 70 +
examples/reax/AB/log.reaxc.AB.1Feb14.linux.1 | 54 -
examples/reax/AB/log.reaxc.AB.1Feb14.linux.4 | 54 -
examples/reax/AuO/log.5Oct16.AuO.g++.1 | 70 +
examples/reax/AuO/log.5Oct16.AuO.g++.4 | 70 +
examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.1 | 54 -
examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.4 | 54 -
examples/reax/CHO/log.5Oct16.CHO.g++.1 | 70 +
examples/reax/CHO/log.5Oct16.CHO.g++.4 | 70 +
examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.1 | 54 -
examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.4 | 54 -
examples/reax/FC/log.5Oct16.FC.g++.1 | 130 +
examples/reax/FC/log.5Oct16.FC.g++.4 | 130 +
examples/reax/FC/log.reaxc.FC.1Feb14.linux.1 | 107 -
examples/reax/FC/log.reaxc.FC.1Feb14.linux.4 | 107 -
examples/reax/FeOH3/log.5Oct16.FeOH3.g++.1 | 70 +
examples/reax/FeOH3/log.5Oct16.FeOH3.g++.4 | 70 +
examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.1 | 54 -
examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.4 | 54 -
examples/reax/RDX/log.5Oct16.RDX.g++.1 | 70 +
examples/reax/RDX/log.5Oct16.RDX.g++.4 | 70 +
examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.1 | 54 -
examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.4 | 54 -
examples/reax/VOH/log.5Oct16.VOH.g++.1 | 70 +
examples/reax/VOH/log.5Oct16.VOH.g++.4 | 70 +
examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.1 | 54 -
examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.4 | 54 -
examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 | 70 +
examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 | 70 +
examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.1 | 54 -
examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.4 | 54 -
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.5Oct16.reax.rdx.g++.1 | 101 +
examples/reax/log.5Oct16.reax.rdx.g++.4 | 101 +
examples/reax/log.5Oct16.reax.tatb.g++.1 | 97 +
examples/reax/log.5Oct16.reax.tatb.g++.4 | 97 +
examples/reax/log.5Oct16.reaxc.rdx.g++.1 | 104 +
examples/reax/log.5Oct16.reaxc.rdx.g++.4 | 104 +
examples/reax/log.5Oct16.reaxc.tatb.g++.1 | 102 +
examples/reax/log.5Oct16.reaxc.tatb.g++.4 | 102 +
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.5Oct16.rigid.g++.1 | 329 +
examples/rigid/log.5Oct16.rigid.g++.4 | 329 +
examples/rigid/log.5Oct16.rigid.poems.g++.1 | 332 +
examples/rigid/log.5Oct16.rigid.poems.g++.4 | 332 +
examples/rigid/log.5Oct16.rigid.poems2.g++.1 | 336 +
examples/rigid/log.5Oct16.rigid.poems2.g++.4 | 336 +
examples/rigid/log.5Oct16.rigid.tnr.g++.1 | 452 +
examples/rigid/log.5Oct16.rigid.tnr.g++.4 | 452 +
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.5Oct16.shear.g++.1 | 191 +
examples/shear/log.5Oct16.shear.g++.4 | 191 +
examples/shear/log.5Oct16.shear.void.g++.1 | 192 +
examples/shear/log.5Oct16.shear.void.g++.4 | 192 +
examples/snap/Ta06A_pot.snap | 6 +-
examples/snap/log.15May15.snap.g++.1 | 120 -
examples/snap/log.15May15.snap.g++.4 | 120 -
examples/snap/log.5Oct16.snap.g++.1 | 136 +
examples/snap/log.5Oct16.snap.g++.4 | 136 +
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.5Oct16.srd.mixture.g++.1 | 269 +
examples/srd/log.5Oct16.srd.mixture.g++.4 | 269 +
examples/srd/log.5Oct16.srd.pure.g++.1 | 163 +
examples/srd/log.5Oct16.srd.pure.g++.4 | 163 +
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.5Oct16.streitz.ewald.g++.1 | 119 +
examples/streitz/log.5Oct16.streitz.ewald.g++.4 | 119 +
examples/streitz/log.5Oct16.streitz.wolf.g++.1 | 111 +
examples/streitz/log.5Oct16.streitz.wolf.g++.4 | 111 +
examples/tad/README | 2 +-
examples/tad/log.5Oct16.tad.g++.3 | 39 +
examples/tad/log.tad.0.1Feb14.linux.3 | 12325 --
examples/tad/log.tad.1.1Feb14.linux.3 | 7262 -
examples/tad/log.tad.1Feb14.linux.3 | 114 -
examples/tad/log.tad.2.1Feb14.linux.3 | 7262 -
examples/tad/log.tad.neb.1Feb14.linux.3 | 1160 -
{potentials => examples/threebody}/BNC.tersoff | 0
examples/threebody/CdTeZnSeHgS0.sw | 233 +
examples/{vashishta => threebody}/InP.vashishta | 0
examples/{ELASTIC => threebody}/Si.sw | 0
examples/threebody/in.threebody | 116 +
examples/vashishta/InP.vashishta | 0
examples/vashishta/SiO.1990.vashishta | 0
.../{in.indiumphosphide => in.vashishta.inp} | 0
examples/vashishta/{in.sio2 => in.vashishta.sio2} | 0
examples/vashishta/in.vashishta.table.inp | 75 +
examples/vashishta/in.vashishta.table.sio2 | 30 +
.../vashishta/log.5Oct16.indiumphosphide.g++.1 | 5276 +
.../vashishta/log.5Oct16.indiumphosphide.g++.4 | 128 +
examples/vashishta/log.5Oct16.sio2.g++.1 | 86 +
examples/vashishta/log.5Oct16.sio2.g++.4 | 86 +
examples/vashishta/log.5Oct16.vashishta.inp.g++.1 | 5276 +
examples/vashishta/log.5Oct16.vashishta.inp.g++.4 | 5276 +
examples/vashishta/log.5Oct16.vashishta.sio2.g++.1 | 86 +
examples/vashishta/log.5Oct16.vashishta.sio2.g++.4 | 86 +
.../vashishta/log.5Oct16.vashishta.table.inp.g++.1 | 5276 +
.../vashishta/log.5Oct16.vashishta.table.inp.g++.4 | 5276 +
.../log.5Oct16.vashishta.table.sio2.g++.1 | 89 +
.../log.5Oct16.vashishta.table.sio2.g++.4 | 89 +
examples/voronoi/in.voronoi.2d | 52 +
examples/voronoi/in.voronoi.data | 88 +
examples/voronoi/log.15May15.voronoi.g++.1 | 542 -
examples/voronoi/log.15May15.voronoi.g++.4 | 542 -
examples/voronoi/log.5Oct16.voronoi.2d.g++.1 | 130 +
examples/voronoi/log.5Oct16.voronoi.2d.g++.4 | 130 +
examples/voronoi/log.5Oct16.voronoi.data.g++.1 | 163 +
examples/voronoi/log.5Oct16.voronoi.data.g++.4 | 163 +
examples/voronoi/log.5Oct16.voronoi.g++.1 | 619 +
examples/voronoi/log.5Oct16.voronoi.g++.4 | 619 +
lib/README | 4 +-
lib/atc/LammpsInterface.cpp | 1 +
lib/atc/Makefile.icc | 2 +-
lib/atc/Makefile.mingw32-cross | 2 +-
lib/atc/Makefile.mingw32-cross-mpi | 2 +-
lib/atc/Makefile.mingw64-cross | 2 +-
lib/atc/Makefile.mingw64-cross-mpi | 2 +-
lib/atc/Makefile.mpic++ | 2 +-
lib/atc/Makefile.serial | 2 +-
lib/atc/ParDiagonalMatrix.cpp | 4 +
lib/atc/Utility.h | 4 +-
lib/atc/Vector.h | 4 +-
lib/awpmd/Makefile.mingw32-cross | 2 +-
lib/awpmd/Makefile.mingw64-cross | 2 +-
lib/awpmd/Makefile.mpicc | 2 +-
lib/colvars/Makefile.fermi | 66 +-
lib/colvars/Makefile.g++ | 60 +-
lib/colvars/Makefile.mingw32-cross | 66 +-
lib/colvars/Makefile.mingw32-cross-mpi | 4 +-
lib/colvars/Makefile.mingw64-cross | 66 +-
lib/colvars/Makefile.mingw64-cross-mpi | 4 +-
lib/colvars/colvar.cpp | 1389 +-
lib/colvars/colvar.h | 215 +-
lib/colvars/colvaratoms.cpp | 1166 +-
lib/colvars/colvaratoms.h | 368 +-
lib/colvars/colvarbias.cpp | 147 +-
lib/colvars/colvarbias.h | 47 +-
lib/colvars/colvarbias_abf.cpp | 297 +-
lib/colvars/colvarbias_abf.h | 40 +-
lib/colvars/colvarbias_alb.cpp | 49 +-
lib/colvars/colvarbias_alb.h | 15 +-
lib/colvars/colvarbias_histogram.cpp | 60 +-
lib/colvars/colvarbias_histogram.h | 13 +-
lib/colvars/colvarbias_meta.cpp | 137 +-
lib/colvars/colvarbias_meta.h | 28 +-
lib/colvars/colvarbias_restraint.cpp | 357 +-
lib/colvars/colvarbias_restraint.h | 94 +-
lib/colvars/colvarcomp.cpp | 277 +-
lib/colvars/colvarcomp.h | 219 +-
lib/colvars/colvarcomp_angles.cpp | 309 +-
lib/colvars/colvarcomp_coordnums.cpp | 246 +-
lib/colvars/colvarcomp_distances.cpp | 670 +-
lib/colvars/colvarcomp_protein.cpp | 16 +-
lib/colvars/colvarcomp_rotations.cpp | 115 +-
lib/colvars/colvardeps.cpp | 529 +
lib/colvars/colvardeps.h | 276 +
lib/colvars/colvargrid.cpp | 9 +-
lib/colvars/colvargrid.h | 224 +-
lib/colvars/colvarmodule.cpp | 631 +-
lib/colvars/colvarmodule.h | 147 +-
lib/colvars/colvarparse.cpp | 652 +-
lib/colvars/colvarparse.h | 204 +-
lib/colvars/colvarproxy.h | 563 +-
lib/colvars/colvarscript.cpp | 149 +-
lib/colvars/colvarscript.h | 3 +-
lib/colvars/colvartypes.cpp | 101 +-
lib/colvars/colvartypes.h | 46 +-
lib/colvars/colvarvalue.cpp | 2 +-
lib/colvars/colvarvalue.h | 2 +-
lib/cuda/Makefile | 4 -
lib/cuda/Makefile.common | 123 -
lib/cuda/Makefile.cudalib | 87 -
lib/cuda/Makefile.defaults | 19 -
lib/cuda/Makefile.lammps | 7 -
lib/cuda/README | 59 -
lib/cuda/atom_vec_angle_cuda.cu | 85 -
lib/cuda/atom_vec_angle_cuda_cu.h | 15 -
lib/cuda/atom_vec_atomic_cuda.cu | 85 -
lib/cuda/atom_vec_atomic_cuda_cu.h | 15 -
lib/cuda/atom_vec_charge_cuda.cu | 85 -
lib/cuda/atom_vec_charge_cuda_cu.h | 15 -
lib/cuda/atom_vec_cuda.cu | 628 -
lib/cuda/atom_vec_cuda_cu.h | 0
lib/cuda/atom_vec_cuda_kernel.cu | 512 -
lib/cuda/atom_vec_full_cuda.cu | 85 -
lib/cuda/atom_vec_full_cuda_cu.h | 15 -
lib/cuda/comm_cuda.cu | 539 -
lib/cuda/comm_cuda_cu.h | 35 -
lib/cuda/comm_cuda_kernel.cu | 394 -
lib/cuda/compute_temp_cuda.cu | 126 -
lib/cuda/compute_temp_cuda_cu.h | 28 -
lib/cuda/compute_temp_cuda_kernel.cu | 118 -
lib/cuda/compute_temp_partial_cuda.cu | 164 -
lib/cuda/compute_temp_partial_cuda_cu.h | 30 -
lib/cuda/compute_temp_partial_cuda_kernel.cu | 161 -
lib/cuda/crm_cuda_utils.cu | 919 -
lib/cuda/cuda.cu | 22 -
lib/cuda/cuda_common.h | 344 -
lib/cuda/cuda_cu.h | 1 -
lib/cuda/cuda_data.cu | 220 -
lib/cuda/cuda_data_cu.h | 13 -
lib/cuda/cuda_data_kernel.cu | 195 -
lib/cuda/cuda_kernel.cu | 0
lib/cuda/cuda_pair.cu | 1015 -
lib/cuda/cuda_pair_cu.h | 30 -
lib/cuda/cuda_pair_kernel.cu | 1437 -
lib/cuda/cuda_pair_virial_kernel_nc.cu | 126 -
lib/cuda/cuda_precision.h | 278 -
lib/cuda/cuda_shared.h | 370 -
lib/cuda/cuda_wrapper.cu | 337 -
lib/cuda/cuda_wrapper_cu.h | 52 -
lib/cuda/cuda_wrapper_kernel.cu | 24 -
lib/cuda/domain.cu | 202 -
lib/cuda/domain_cu.h | 29 -
lib/cuda/domain_kernel.cu | 293 -
lib/cuda/fft3d_cuda.cu | 103 -
lib/cuda/fft3d_cuda_cu.h | 30 -
lib/cuda/fft3d_cuda_kernel.cu | 46 -
lib/cuda/fix_addforce_cuda.cu | 93 -
lib/cuda/fix_addforce_cuda_cu.h | 27 -
lib/cuda/fix_addforce_cuda_kernel.cu | 90 -
lib/cuda/fix_aveforce_cuda.cu | 107 -
lib/cuda/fix_aveforce_cuda_cu.h | 28 -
lib/cuda/fix_aveforce_cuda_kernel.cu | 96 -
lib/cuda/fix_enforce2d_cuda.cu | 55 -
lib/cuda/fix_enforce2d_cuda_cu.h | 27 -
lib/cuda/fix_enforce2d_cuda_kernel.cu | 34 -
lib/cuda/fix_freeze_cuda.cu | 98 -
lib/cuda/fix_freeze_cuda_cu.h | 27 -
lib/cuda/fix_freeze_cuda_kernel.cu | 87 -
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tools/phonon/interpolate.cpp | 53 +-
tools/phonon/phonon.cpp | 515 +-
tools/phonon/phonon.h | 2 +
tools/phonon/timer.cpp | 16 +-
tools/phonon/version.h | 2 +-
tools/polybond/lmpsdata.py | 3890 +-
tools/pymol_asphere/src/cartesian.cpp | 0
tools/pymol_asphere/src/cartesian.h | 0
tools/pymol_asphere/src/colors.cpp | 0
tools/pymol_asphere/src/colors.h | 0
tools/pymol_asphere/src/commandline.cpp | 0
tools/pymol_asphere/src/commandline.h | 0
tools/pymol_asphere/src/error.cpp | 0
tools/pymol_asphere/src/error.h | 0
tools/pymol_asphere/src/glsurface.cpp | 0
tools/pymol_asphere/src/glsurface.h | 0
tools/pymol_asphere/src/m_constants.h | 0
tools/pymol_asphere/src/misc.cpp | 0
tools/pymol_asphere/src/misc.h | 0
tools/pymol_asphere/src/miscm.cpp | 0
tools/pymol_asphere/src/miscm.h | 0
tools/pymol_asphere/src/spherical.cpp | 0
tools/pymol_asphere/src/spherical.h | 0
tools/xmovie/control.c | 0
tools/xmovie/dummy.c | 0
tools/xmovie/hpsort.c | 0
tools/xmovie/read.c | 0
tools/xmovie/resource.h | 0
tools/xmovie/scene.c | 0
tools/xmovie/toascii.c | 0
tools/xmovie/tobinary.c | 0
tools/xmovie/version.c | 0
tools/xmovie/xmovie.c | 0
tools/xmovie/xmovie.h | 0
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mode change 100755 => 100644 tools/xmovie/control.c
mode change 100755 => 100644 tools/xmovie/dummy.c
mode change 100755 => 100644 tools/xmovie/hpsort.c
mode change 100755 => 100644 tools/xmovie/read.c
mode change 100755 => 100644 tools/xmovie/resource.h
mode change 100755 => 100644 tools/xmovie/scene.c
mode change 100755 => 100644 tools/xmovie/toascii.c
mode change 100755 => 100644 tools/xmovie/tobinary.c
mode change 100755 => 100644 tools/xmovie/version.c
mode change 100755 => 100644 tools/xmovie/xmovie.c
mode change 100755 => 100644 tools/xmovie/xmovie.h
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