[lammps] branch master updated (32b9d4b -> ff7d03f)
Anton Gladky
gladk at moszumanska.debian.org
Wed Apr 29 22:14:23 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 32b9d4b Update changelog.
adds aad2273 Imported Upstream version 0~20150313.gitfa668e1
adds e205743 Merge tag 'upstream/0_20150313.gitfa668e1' into experimental
adds 820b5c5 Refresh patches. Remove applied by upstream.
adds b303847 Update d/copyright.
adds 5dc10e0 Minor fix in d/rules.
adds b833c3c Set Standards-Version: 3.9.6. No changes.
adds 0e947fe Enable C++11.
adds 9378dd8 Update changelog.
new ff7d03f Update changelog.
The 1 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/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
bench/FERMI/in.lj.titan | 35 +
bench/{GPU/in.rhodo.cpu => FERMI/in.rhodo} | 0
bench/FERMI/in.rhodo.scaled.titan | 39 +
bench/FERMI/in.rhodo.split.titan | 42 +
bench/GPU/README | 60 -
bench/GPU/in.eam.cuda | 29 -
bench/GPU/in.eam.gpu | 31 -
bench/GPU/in.lj.cuda | 27 -
bench/GPU/in.lj.gpu | 29 -
bench/GPU/in.rhodo.cuda | 35 -
bench/GPU/in.rhodo.gpu | 37 -
bench/KEPLER/Makefile.cpu | 108 +
bench/KEPLER/Makefile.cuda | 108 +
bench/KEPLER/Makefile.gpu | 108 +
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 +
bench/KEPLER/run_omp.sh | 17 +
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 +-
debian/changelog | 17 +
debian/control | 2 +-
debian/copyright | 10 +-
debian/patches/10_set_configure_flags.patch | 56 +
debian/patches/fix_format_not_a_string.patch | 17 -
debian/patches/series | 3 +-
debian/patches/set_configure_flags.patch | 55 -
debian/rules | 4 +-
doc/Eqs/compute_sna_atom1.jpg | Bin 0 -> 19001 bytes
doc/Eqs/compute_sna_atom1.tex | 11 +
doc/Eqs/compute_sna_atom2.jpg | Bin 0 -> 17114 bytes
doc/Eqs/compute_sna_atom2.tex | 11 +
doc/Eqs/compute_sna_atom3.jpg | Bin 0 -> 19644 bytes
doc/Eqs/compute_sna_atom3.tex | 16 +
doc/Eqs/compute_sna_atom4.jpg | Bin 0 -> 35933 bytes
doc/Eqs/compute_sna_atom4.tex | 14 +
doc/Eqs/compute_sna_atom5.jpg | Bin 0 -> 14734 bytes
doc/Eqs/compute_sna_atom5.tex | 12 +
doc/Eqs/compute_sna_atom6.jpg | Bin 0 -> 17274 bytes
doc/Eqs/compute_sna_atom6.tex | 12 +
doc/Eqs/fix_pimd.jpg | Bin 0 -> 14569 bytes
doc/Eqs/fix_pimd.tex | 17 +
doc/Eqs/fix_rattle_constraints.jpg | Bin 0 -> 4556 bytes
doc/Eqs/fix_rattle_constraints.tex | 9 +
doc/Eqs/fix_rattle_rij.jpg | Bin 0 -> 1812 bytes
doc/Eqs/fix_rattle_rij.tex | 8 +
doc/Eqs/fix_ttm_blast.jpg | Bin 0 -> 4449 bytes
doc/Eqs/fix_ttm_blast.tex | 13 +
doc/Eqs/fix_ttm_blast1.jpg | Bin 0 -> 8657 bytes
doc/Eqs/fix_ttm_blast1.tex | 13 +
doc/Eqs/fix_ttm_ce.jpg | Bin 0 -> 7446 bytes
doc/Eqs/fix_ttm_ce.tex | 13 +
doc/Eqs/fix_ttm_mod.jpg | Bin 0 -> 10179 bytes
doc/Eqs/fix_ttm_mod.tex | 15 +
doc/Eqs/pair_cs.jpg | Bin 0 -> 3500 bytes
doc/Eqs/pair_cs.tex | 9 +
doc/Eqs/pair_snap.jpg | Bin 0 -> 32505 bytes
doc/Eqs/pair_snap.tex | 9 +
doc/Eqs/pair_srp1.jpg | Bin 0 -> 3537 bytes
doc/Eqs/pair_srp1.tex | 9 +
doc/Eqs/pair_srp2.jpg | Bin 0 -> 5648 bytes
doc/Eqs/pair_srp2.tex | 10 +
doc/JPG/balance.jpg | Bin 34031 -> 0 bytes
doc/JPG/balance_nonuniform.jpg | Bin 0 -> 78857 bytes
doc/JPG/balance_nonuniform_small.jpg | Bin 0 -> 16588 bytes
doc/JPG/balance_rcb.jpg | Bin 0 -> 72941 bytes
doc/JPG/balance_rcb_small.jpg | Bin 0 -> 15571 bytes
doc/JPG/balance_uniform.jpg | Bin 0 -> 79281 bytes
doc/JPG/balance_uniform_small.jpg | Bin 0 -> 17279 bytes
doc/JPG/pimd.jpg | Bin 0 -> 29560 bytes
doc/JPG/sinusoid.jpg | Bin 0 -> 128596 bytes
doc/JPG/sinusoid_small.jpg | Bin 0 -> 29397 bytes
doc/Manual.html | 36 +-
doc/Manual.pdf | Bin 8139800 -> 9325726 bytes
doc/Manual.txt | 30 +-
doc/PDF/PDLammps_EPS.pdf | Bin 164229 -> 79021 bytes
doc/PDF/PDLammps_VES.pdf | Bin 65659 -> 74846 bytes
doc/PDF/colvars-refman-lammps.pdf | Bin 601866 -> 528423 bytes
doc/Section_accelerate.html | 690 +-
doc/Section_accelerate.txt | 691 +-
doc/Section_commands.html | 402 +-
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doc/Section_howto.txt | 505 +-
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doc/Section_intro.txt | 12 +-
doc/Section_modify.html | 12 +-
doc/Section_modify.txt | 12 +-
doc/Section_packages.html | 45 +-
doc/Section_packages.txt | 45 +-
doc/Section_python.html | 6 +-
doc/Section_python.txt | 4 +-
doc/Section_start.html | 911 +-
doc/Section_start.txt | 899 +-
doc/Section_tools.html | 20 +-
doc/Section_tools.txt | 20 +-
doc/accelerate_cuda.html | 228 +
doc/accelerate_cuda.txt | 223 +
doc/accelerate_gpu.html | 257 +
doc/accelerate_gpu.txt | 252 +
doc/accelerate_intel.html | 352 +
doc/accelerate_intel.txt | 347 +
doc/accelerate_kokkos.html | 514 +
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doc/accelerate_omp.html | 206 +
doc/accelerate_omp.txt | 201 +
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doc/angle_cosine_shift.html | 21 +-
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doc/angle_cosine_shift_exp.html | 23 +-
doc/angle_cosine_shift_exp.txt | 23 +-
doc/angle_cosine_squared.html | 25 +-
doc/angle_cosine_squared.txt | 25 +-
doc/angle_dipole.html | 23 +-
doc/angle_dipole.txt | 23 +-
doc/angle_fourier.html | 21 +-
doc/angle_fourier.txt | 23 +-
doc/angle_fourier_simple.html | 21 +-
doc/angle_fourier_simple.txt | 23 +-
doc/angle_harmonic.html | 25 +-
doc/angle_harmonic.txt | 25 +-
doc/angle_hybrid.html | 2 +-
doc/angle_hybrid.txt | 2 +-
doc/angle_quartic.html | 23 +-
doc/angle_quartic.txt | 23 +-
doc/angle_style.html | 2 +-
doc/angle_style.txt | 2 +-
doc/angle_table.html | 25 +-
doc/angle_table.txt | 25 +-
doc/atom_style.html | 35 +-
doc/atom_style.txt | 34 +-
doc/balance.html | 191 +-
doc/balance.txt | 192 +-
doc/bond_class2.html | 23 +-
doc/bond_class2.txt | 23 +-
doc/bond_fene.html | 25 +-
doc/bond_fene.txt | 25 +-
doc/bond_fene_expand.html | 25 +-
doc/bond_fene_expand.txt | 25 +-
doc/bond_harmonic.html | 23 +-
doc/bond_harmonic.txt | 25 +-
doc/bond_harmonic_shift.html | 21 +-
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doc/bond_harmonic_shift_cut.html | 21 +-
doc/bond_harmonic_shift_cut.txt | 23 +-
doc/bond_hybrid.html | 2 +-
doc/bond_hybrid.txt | 2 +-
doc/bond_morse.html | 23 +-
doc/bond_morse.txt | 25 +-
doc/bond_nonlinear.html | 25 +-
doc/bond_nonlinear.txt | 25 +-
doc/bond_quartic.html | 25 +-
doc/bond_quartic.txt | 25 +-
doc/bond_style.html | 2 +-
doc/bond_style.txt | 2 +-
doc/bond_table.html | 25 +-
doc/bond_table.txt | 25 +-
doc/change_box.html | 15 +
doc/change_box.txt | 15 +
doc/comm_modify.html | 8 +-
doc/comm_modify.txt | 8 +-
doc/comm_style.html | 2 -
doc/comm_style.txt | 2 -
doc/compute.html | 17 +-
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doc/compute_chunk_atom.html | 568 +
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doc/compute_com.html | 8 -
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doc/compute_com_chunk.html | 92 +
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doc/compute_com_molecule.html | 81 -
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doc/compute_displace_atom.html | 14 +-
doc/compute_displace_atom.txt | 14 +-
doc/compute_fep.html | 21 +-
doc/compute_fep.txt | 19 +-
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doc/compute_gyration_molecule.html | 102 -
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doc/compute_heat_flux.html | 2 +-
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doc/compute_inertia_chunk.html | 93 +
doc/compute_inertia_chunk.txt | 88 +
doc/compute_inertia_molecule.html | 83 -
doc/compute_inertia_molecule.txt | 78 -
doc/compute_msd.html | 16 +-
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doc/compute_msd_chunk.html | 125 +
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doc/compute_msd_molecule.html | 99 -
doc/compute_msd_molecule.txt | 94 -
doc/compute_pair_local.html | 9 +-
doc/compute_pair_local.txt | 9 +-
doc/compute_pressure.html | 12 +-
doc/compute_pressure.txt | 11 +-
doc/compute_property_atom.html | 43 +-
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doc/compute_property_molecule.html | 77 -
doc/compute_property_molecule.txt | 68 -
doc/compute_sna_atom.html | 262 +
doc/compute_sna_atom.txt | 241 +
doc/compute_stress_atom.html | 16 +
doc/compute_stress_atom.txt | 15 +
doc/compute_temp_asphere.html | 10 +-
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doc/compute_temp_chunk.txt | 234 +
doc/compute_temp_cs.html | 117 +
doc/compute_temp_cs.txt | 111 +
doc/compute_temp_region.html | 13 +-
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doc/compute_temp_sphere.html | 10 +-
doc/compute_temp_sphere.txt | 10 +-
doc/compute_torque_chunk.html | 92 +
doc/compute_torque_chunk.txt | 87 +
doc/compute_vacf.html | 6 +-
doc/compute_vacf.txt | 6 +-
doc/compute_vcm_chunk.html | 82 +
doc/compute_vcm_chunk.txt | 77 +
doc/create_atoms.html | 68 +-
doc/create_atoms.txt | 70 +-
doc/create_bonds.html | 114 +
doc/create_bonds.txt | 109 +
doc/create_box.html | 39 +-
doc/create_box.txt | 39 +-
doc/delete_atoms.html | 54 +-
doc/delete_atoms.txt | 54 +-
doc/delete_bonds.html | 40 +-
doc/delete_bonds.txt | 40 +-
doc/dihedral_charmm.html | 25 +-
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doc/dihedral_cosine_shift_exp.html | 23 +-
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doc/dihedral_fourier.html | 21 +-
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doc/dihedral_harmonic.html | 23 +-
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examples/ASPHERE/box/in.box | 2 +-
examples/ASPHERE/box/in.box.mp | 2 +-
examples/ASPHERE/dimer/in.dimer | 2 +-
examples/ASPHERE/dimer/in.dimer.mp | 2 +-
examples/ASPHERE/ellipsoid/in.ellipsoid | 2 +-
examples/ASPHERE/ellipsoid/in.ellipsoid.mp | 2 +-
examples/ASPHERE/line/in.line.srd | 2 +-
examples/ASPHERE/poly/in.poly | 2 +-
examples/ASPHERE/poly/in.poly.mp | 2 +-
examples/ASPHERE/star/in.star | 2 +-
examples/ASPHERE/star/in.star.mp | 2 +-
examples/ASPHERE/tri/in.tri.srd | 2 +-
examples/COUPLE/lammps_quest/lmpqst.cpp | 10 +-
examples/COUPLE/simple/README | 9 +-
examples/COUPLE/simple/in.lj | 3 -
examples/COUPLE/simple/simple.c | 4 +-
examples/COUPLE/simple/simple.cpp | 4 +-
examples/COUPLE/simple/simple.f90 | 4 +-
examples/KAPPA/README | 2 +
examples/MC/README | 30 +
examples/MC/in.mc | 119 +
examples/MC/log.mc.6Jun14 | 106235 ++++++++++
examples/README | 33 +-
examples/USER/atc/hardy/consistency.screen | 850 +-
.../USER/atc/hardy/eam_kernel_convergence.screen | 2462 +-
examples/USER/atc/hardy/eam_unistrain_cell.screen | 78 +-
examples/USER/atc/hardy/eam_unistrain_mesh.screen | 118 +-
.../USER/atc/hardy/eam_unistrain_qcylinder.screen | 75 +-
.../USER/atc/hardy/eam_unistrain_qsphere.screen | 75 +-
examples/USER/atc/hardy/eam_unistrain_step.screen | 117 +-
examples/USER/atc/hardy/eam_volume_stretch.screen | 121 +-
examples/USER/atc/hardy/eshelby_static.screen | 1280 +-
examples/USER/atc/hardy/nvt.screen | 99 +-
examples/USER/cuda/data.rhodo | 191072 ------------------
examples/USER/cuda/in.melt_2.5.cuda | 34 -
examples/USER/cuda/in.melt_5.0.cuda | 34 -
examples/USER/cuda/in.phosphate.cuda | 32 -
examples/USER/cuda/in.rhodo.cuda | 34 -
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examples/USER/eff/Be-solid/in.Be-solid.spe | 5 +-
examples/USER/eff/CH4/in.ch4.dynamics | 7 +-
examples/USER/eff/CH4/in.ch4.min | 5 +-
examples/USER/eff/CH4/in.ch4_ionized.dynamics | 5 +-
examples/USER/eff/ECP/Si2H6/in.Si2H6 | 5 +-
examples/USER/eff/ECP/Si2H6/in.Si2H6.ang | 7 +-
examples/USER/eff/ECP/SiC/bulk/in.SiC | 7 +-
examples/USER/eff/ECP/SiH4/in.SiH4 | 5 +-
examples/USER/eff/ECP/SiH4/in.SiH4.ang | 5 +-
examples/USER/eff/H/in.h_atom.spe.ang | 3 +-
examples/USER/eff/H/in.h_atom.spe.bohr | 2 +-
examples/USER/eff/H2/in.h2 | 5 +-
examples/USER/eff/H_plasma/in.h2bulk.npt | 5 +-
examples/USER/eff/H_plasma/in.h2bulk.nve | 5 +-
examples/USER/eff/H_plasma/in.h2bulk.nve.ang | 5 +-
examples/USER/eff/Li-dendritic/in.Li-dendritic.min | 5 +-
examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt | 8 +-
examples/USER/eff/Li-solid/in.Li.ang | 5 +-
examples/USER/eff/Li-solid/in.Li.bohr | 7 +-
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang | 9 +-
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr | 11 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.ang | 7 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 7 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 3 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr | 2 +-
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 +
examples/USER/misc/basal/in.basal | 2 +-
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 +
examples/USER/srp/data.chain | 8724 +
examples/USER/srp/in.srp | 37 +
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 +
.../log.lj.1Feb14.gpu.1} | 0
.../log.lj.1Feb14.gpu.4} | 0
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 +
.../log.lj.5.0.1Feb14.gpu.1} | 0
.../log.lj.5.0.1Feb14.gpu.4} | 0
.../log.phosphate.1Feb14.gpu.1} | 0
.../log.phosphate.1Feb14.gpu.4} | 0
.../log.rhodo.1Feb14.gpu.1} | 0
.../log.rhodo.1Feb14.gpu.4} | 0
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 +
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examples/comb/elastic.f90 | 384 +-
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/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/kim/log.kim.lj.27Jul14.ubuntu.1 | 29 +
examples/kim/log.kim.lj.27Jul14.ubuntu.4 | 29 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.1 | 29 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.4 | 29 +
examples/min/in.min.box | 45 +-
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/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/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 +
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lib/atc/ATC_Coupling.cpp | 242 +-
lib/atc/ATC_Coupling.h | 50 +-
lib/atc/ATC_CouplingEnergy.cpp | 16 +-
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lib/atc/ATC_Method.cpp | 141 +-
lib/atc/ATC_Method.h | 9 +-
lib/atc/ATC_TypeDefs.h | 8 +-
lib/atc/AtomicRegulator.cpp | 23 +-
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lib/atc/CauchyBorn.h | 3 +-
lib/atc/ChargeRegulator.cpp | 4 +-
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lib/atc/DenseVector.h | 6 +-
lib/atc/DependencyManager.h | 2 +-
lib/atc/DiagonalMatrix.h | 8 +-
lib/atc/ElectronDragPower.cpp | 4 +-
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lib/atc/ExtrinsicModelDriftDiffusion.cpp | 133 +-
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lib/atc/ExtrinsicModelTwoTemperature.cpp | 35 +-
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lib/atc/Matrix.h | 49 +-
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lib/atc/OutputManager.cpp | 9 +-
lib/atc/OutputManager.h | 2 +
lib/{poems => atc}/POEMSChain.h | 0
lib/atc/PerAtomQuantity.h | 2 +-
lib/atc/PerAtomQuantityLibrary.cpp | 153 +-
lib/atc/PerAtomQuantityLibrary.h | 85 +-
lib/atc/PoissonSolver.cpp | 7 +-
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lib/atc/PrescribedDataManager.h | 26 +-
lib/atc/SchrodingerSolver.cpp | 560 +-
lib/atc/SchrodingerSolver.h | 106 +-
lib/atc/SparseMatrix-inl.h | 4 +-
lib/{poems => atc}/SystemProcessor.h | 0
lib/atc/Thermostat.cpp | 840 +-
lib/atc/Thermostat.h | 284 +-
lib/atc/TimeIntegrator.h | 4 +-
lib/atc/TransferLibrary.cpp | 2 +-
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lib/atc/Utility.h | 61 +-
lib/atc/Vector.h | 30 +-
lib/atc/WeakEquationElectronContinuity.cpp | 1 +
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lib/atc/WeakEquationElectronMomentum.cpp | 1 +
lib/atc/WeakEquationElectronTemperature.cpp | 15 +-
lib/atc/WeakEquationElectronTemperature.h | 2 +-
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lib/colvars/colvarcomp_distances.cpp | 697 +-
lib/colvars/colvarcomp_protein.cpp | 167 +-
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lib/colvars/colvargrid.h | 919 +-
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lib/colvars/colvarvalue.h | 975 +-
lib/cuda/Makefile.defaults | 4 +-
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lib/cuda/atom_vec_cuda.cu | 56 +-
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