[lammps] branch master updated (79b0d94 -> 81dc578)

Anton Gladky gladk at moszumanska.debian.org
Fri Feb 14 05:23:35 UTC 2014


This is an automated email from the git hooks/post-receive script.

gladk pushed a change to branch master
in repository lammps.

      from  79b0d94   Update changelog.
      adds  5127b33   Imported Upstream version 0~20140212.git32a5cd0
       new  83b0d1b   Merge tag 'upstream/0_20140212.git32a5cd0'
       new  9c47579   Refresh patch.
       new  b21f32c   Set Standards-Version: 3.9.5. No changes.
       new  249a3f2   Set canonical VCS-fields.
       new  85cb066   Add autotests.
       new  bf2b96e   Remove executable bit in examples.
       new  2138df2   Update changelog.
       new  81dc578   Fix file permissions in examples.

The 8 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/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 +
 bench/log.30Jul13.chain.fixed.linux.1              |     59 -
 bench/log.30Jul13.chain.fixed.linux.4              |     59 -
 bench/log.30Jul13.chain.scaled.linux.4             |     75 -
 bench/log.30Jul13.chute.fixed.linux.1              |     63 -
 bench/log.30Jul13.chute.fixed.linux.4              |     63 -
 bench/log.30Jul13.chute.scaled.linux.4             |     73 -
 bench/log.30Jul13.eam.fixed.linux.1                |     67 -
 bench/log.30Jul13.eam.fixed.linux.4                |     67 -
 bench/log.30Jul13.eam.scaled.linux.4               |     67 -
 bench/log.30Jul13.lj.fixed.linux.1                 |     64 -
 bench/log.30Jul13.lj.fixed.linux.4                 |     64 -
 bench/log.30Jul13.lj.scaled.linux.4                |     64 -
 bench/log.30Jul13.rhodo.fixed.linux.1              |     99 -
 bench/log.30Jul13.rhodo.fixed.linux.4              |     99 -
 bench/log.30Jul13.rhodo.scaled.linux.4             |    120 -
 debian/changelog                                   |     11 +
 debian/control                                     |      7 +-
 debian/patches/set_configure_flags.patch           |      9 +-
 debian/rules                                       |      6 +-
 debian/tests/control                               |      2 +
 debian/tests/crack                                 |      4 +
 debian/tests/in.crack                              |     77 +
 doc/Eqs/pair_comb1.jpg                             |    Bin 19008 -> 18596 bytes
 doc/Eqs/pair_comb2.jpg                             |    Bin 40980 -> 39601 bytes
 doc/Eqs/pair_comb2.tex                             |     27 +-
 doc/Manual.html                                    |      4 +-
 doc/Manual.pdf                                     |    Bin 7311778 -> 8139800 bytes
 doc/Manual.txt                                     |      4 +-
 doc/PDF/PDLammps_EPS.pdf                           |    Bin 0 -> 164229 bytes
 doc/PDF/PDLammps_overview.pdf                      |    Bin 0 -> 254253 bytes
 doc/PDF/colvars-refman-lammps.pdf                  |    Bin 599768 -> 592707 bytes
 doc/Section_accelerate.html                        |      9 +-
 doc/Section_accelerate.txt                         |      9 +-
 doc/Section_commands.html                          |    114 +-
 doc/Section_commands.txt                           |     41 +-
 doc/Section_errors.html                            |   1616 +-
 doc/Section_errors.txt                             |   1616 +-
 doc/Section_howto.html                             |     37 +-
 doc/Section_howto.txt                              |     37 +-
 doc/Section_modify.html                            |     10 +-
 doc/Section_modify.txt                             |      6 +-
 doc/Section_start.html                             |    197 +-
 doc/Section_start.txt                              |    198 +-
 doc/Section_tools.html                             |     49 +-
 doc/Section_tools.txt                              |     49 +-
 doc/angle_class2.html                              |      8 +-
 doc/angle_class2.txt                               |      8 +-
 doc/atom_modify.html                               |     89 +-
 doc/atom_modify.txt                                |     87 +-
 doc/atom_style.html                                |     57 +-
 doc/atom_style.txt                                 |     56 +-
 doc/clear.html                                     |      6 +-
 doc/clear.txt                                      |      6 +-
 doc/compute.html                                   |     18 +-
 doc/compute.txt                                    |     18 +-
 doc/compute_atom_molecule.html                     |      2 +-
 doc/compute_atom_molecule.txt                      |      2 +-
 doc/compute_damage_atom.html                       |     22 +-
 doc/compute_damage_atom.txt                        |     22 +-
 doc/compute_dilatation_atom.html                   |     71 +
 doc/compute_dilatation_atom.txt                    |     66 +
 doc/compute_plasticity_atom.html                   |     73 +
 doc/compute_plasticity_atom.txt                    |     67 +
 doc/compute_pressure.html                          |     26 +-
 doc/compute_pressure.txt                           |     28 +-
 doc/compute_property_local.html                    |      8 +
 doc/compute_property_local.txt                     |      8 +
 doc/compute_reduce.html                            |      4 +-
 doc/compute_reduce.txt                             |      4 +-
 doc/compute_stress_atom.html                       |     57 +-
 doc/compute_stress_atom.txt                        |     55 +-
 doc/compute_vacf.html                              |     76 +
 doc/compute_vacf.txt                               |     71 +
 doc/create_atoms.html                              |    212 +-
 doc/create_atoms.txt                               |    208 +-
 doc/create_box.html                                |     55 +-
 doc/create_box.txt                                 |     54 +-
 doc/dump.html                                      |     71 +-
 doc/dump.txt                                       |     69 +-
 doc/dump_image.html                                |     12 +-
 doc/dump_image.txt                                 |     12 +-
 doc/dump_modify.html                               |     94 +-
 doc/dump_modify.txt                                |     92 +-
 doc/fix.html                                       |     40 +-
 doc/fix.txt                                        |     39 +-
 doc/fix_ave_spatial.html                           |      4 +
 doc/fix_ave_spatial.txt                            |      4 +
 doc/fix_ave_time.html                              |     21 +-
 doc/fix_ave_time.txt                               |     21 +-
 doc/fix_bond_break.html                            |     10 +-
 doc/fix_bond_break.txt                             |     10 +-
 doc/fix_bond_create.html                           |     10 +-
 doc/fix_bond_create.txt                            |     10 +-
 doc/fix_box_relax.html                             |     14 +
 doc/fix_box_relax.txt                              |     13 +-
 doc/fix_deposit.html                               |    199 +-
 doc/fix_deposit.txt                                |    196 +-
 doc/fix_planeforce.html                            |      2 +-
 doc/fix_planeforce.txt                             |      2 +-
 doc/fix_pour.html                                  |     94 +-
 doc/fix_pour.txt                                   |     94 +-
 doc/fix_property_atom.html                         |     35 +-
 doc/fix_property_atom.txt                          |     35 +-
 doc/fix_rigid.html                                 |     51 +-
 doc/fix_rigid.txt                                  |     51 +-
 doc/fix_shake.html                                 |     50 +-
 doc/fix_shake.txt                                  |     47 +-
 doc/fix_vector.html                                |    159 +
 doc/fix_vector.txt                                 |    148 +
 doc/group.html                                     |     81 +-
 doc/group.txt                                      |     82 +-
 doc/if.html                                        |     37 +-
 doc/if.txt                                         |     39 +-
 doc/jump.html                                      |     17 +-
 doc/jump.txt                                       |     18 +-
 doc/kspace_modify.html                             |     54 +-
 doc/kspace_modify.txt                              |     51 +-
 doc/kspace_style.html                              |     22 +-
 doc/kspace_style.txt                               |     21 +-
 doc/min_style.html                                 |      5 +
 doc/min_style.txt                                  |      5 +
 doc/minimize.html                                  |     16 +-
 doc/minimize.txt                                   |     16 +-
 doc/molecule.html                                  |    399 +
 doc/molecule.txt                                   |    394 +
 doc/neb.html                                       |     10 +-
 doc/neb.txt                                        |     10 +-
 doc/next.html                                      |     22 +-
 doc/next.txt                                       |     20 +-
 doc/pair_coeff.html                                |    118 +-
 doc/pair_coeff.txt                                 |    118 +-
 doc/pair_comb.html                                 |      9 +-
 doc/pair_comb.txt                                  |      9 +-
 doc/pair_gromacs.html                              |      2 +
 doc/pair_gromacs.txt                               |      1 +
 doc/pair_hybrid.html                               |     10 +-
 doc/pair_hybrid.txt                                |     10 +-
 doc/pair_modify.html                               |     40 +-
 doc/pair_modify.txt                                |     38 +-
 doc/pair_peri.html                                 |     80 +-
 doc/pair_peri.txt                                  |     76 +-
 doc/pair_style.html                                |     39 +-
 doc/pair_style.txt                                 |     39 +-
 doc/pair_sw.html                                   |      2 -
 doc/pair_sw.txt                                    |      2 -
 doc/read_data.html                                 |    117 +-
 doc/read_data.txt                                  |    115 +-
 doc/read_dump.html                                 |      6 +-
 doc/read_dump.txt                                  |      6 +-
 doc/read_restart.html                              |     62 +-
 doc/read_restart.txt                               |     62 +-
 doc/restart.html                                   |     83 +-
 doc/restart.txt                                    |     80 +-
 doc/special_bonds.html                             |     32 +-
 doc/special_bonds.txt                              |     33 +-
 doc/tad.html                                       |     31 +-
 doc/tad.txt                                        |     33 +-
 doc/thermo_modify.html                             |     13 +-
 doc/thermo_modify.txt                              |     13 +-
 doc/variable.html                                  |     99 +-
 doc/variable.txt                                   |     99 +-
 doc/velocity.html                                  |      4 +-
 doc/velocity.txt                                   |      4 +-
 doc/write_data.html                                |      5 +-
 doc/write_data.txt                                 |      5 +-
 doc/write_restart.html                             |     71 +-
 doc/write_restart.txt                              |     69 +-
 examples/ASPHERE/box/log.box.10Sep13               |    289 -
 examples/ASPHERE/box/log.box.1Feb14                |    290 +
 examples/ASPHERE/box/log.box.mp.10Sep13            |    290 -
 examples/ASPHERE/box/log.box.mp.1Feb14             |    291 +
 examples/ASPHERE/dimer/log.dimer.10Sep13           |    285 -
 examples/ASPHERE/dimer/log.dimer.1Feb14            |    286 +
 examples/ASPHERE/dimer/log.dimer.mp.10Sep13        |    236 -
 examples/ASPHERE/dimer/log.dimer.mp.1Feb14         |    237 +
 examples/ASPHERE/ellipsoid/log.ellipsoid.10Sep13   |    296 -
 examples/ASPHERE/ellipsoid/log.ellipsoid.1Feb14    |    190 +
 .../ASPHERE/ellipsoid/log.ellipsoid.mp.10Sep13     |    247 -
 examples/ASPHERE/ellipsoid/log.ellipsoid.mp.1Feb14 |    247 +
 examples/ASPHERE/line/log.line.10Sep13             |    212 -
 examples/ASPHERE/line/log.line.1Feb14              |    213 +
 examples/ASPHERE/line/log.line.srd.10Sep13         |    243 -
 examples/ASPHERE/line/log.line.srd.1Feb14          |    244 +
 examples/ASPHERE/poly/log.poly.10Sep13             |    288 -
 examples/ASPHERE/poly/log.poly.1Feb14              |    288 +
 examples/ASPHERE/poly/log.poly.mp.10Sep13          |    239 -
 examples/ASPHERE/poly/log.poly.mp.1Feb14           |    239 +
 examples/ASPHERE/star/log.star.10Sep13             |    289 -
 examples/ASPHERE/star/log.star.1Feb14              |    290 +
 examples/ASPHERE/star/log.star.mp.10Sep13          |    290 -
 examples/ASPHERE/star/log.star.mp.1Feb14           |    291 +
 examples/ASPHERE/tri/log.tri.srd.10Sep13           |    242 -
 examples/ASPHERE/tri/log.tri.srd.1Feb14            |    243 +
 examples/DIFFUSE/README                            |     61 +
 examples/DIFFUSE/in.msd.2d                         |     62 +
 examples/DIFFUSE/in.vacf.2d                        |     63 +
 examples/DIFFUSE/log.msd.2d.1Feb14                 |    223 +
 examples/DIFFUSE/log.vacf.2d.1Feb14                |    224 +
 examples/KAPPA/in.heat                             |      2 +-
 examples/KAPPA/in.heatflux                         |      2 +-
 examples/KAPPA/log.heat.12Sep13                    |    195 -
 examples/KAPPA/log.heat.1Feb14                     |    208 +
 examples/KAPPA/log.heatflux.12Sep13                |    208 -
 examples/KAPPA/log.heatflux.1Feb14                 |    208 +
 examples/KAPPA/log.langevin.12Sep13                |    215 -
 examples/KAPPA/log.langevin.1Feb14                 |    215 +
 examples/KAPPA/log.mp.12Sep13                      |    200 -
 examples/KAPPA/log.mp.1Feb14                       |    200 +
 examples/KAPPA/profile.heat.12Sep13                |    423 -
 ...rofile.heatflux.12Sep13 => profile.heat.1Feb14} |      0
 ...le.heatflux.12Sep13 => profile.heatflux.1Feb14} |      0
 examples/KAPPA/profile.langevin.12Sep13            |    423 -
 examples/KAPPA/profile.langevin.1Feb14             |    423 +
 .../{profile.mp.12Sep13 => profile.mp.1Feb14}      |      0
 examples/README                                    |     25 +-
 examples/VISCOSITY/in.mp.2d                        |      4 +-
 examples/VISCOSITY/in.nemd.2d                      |      4 +-
 examples/VISCOSITY/in.wall.2d                      |      4 +-
 examples/VISCOSITY/log.gk.2d.12Sep13               |    386 -
 examples/VISCOSITY/log.gk.2d.1Feb14                |    386 +
 examples/VISCOSITY/log.mp.2d.12Sep13               |    231 -
 examples/VISCOSITY/log.mp.2d.1Feb14                |    230 +
 examples/VISCOSITY/log.nemd.2d.12Sep13             |    264 -
 examples/VISCOSITY/log.nemd.2d.1Feb14              |    271 +
 examples/VISCOSITY/log.wall.2d.12Sep13             |    216 -
 examples/VISCOSITY/log.wall.2d.1Feb14              |    221 +
 examples/VISCOSITY/profile.gk.2d.12Sep13           | 100654 ------------------
 examples/VISCOSITY/profile.gk.2d.1Feb14            | 100654 ++++++++++++++++++
 examples/VISCOSITY/profile.mp.2d.12Sep13           |   1473 -
 examples/VISCOSITY/profile.mp.2d.1Feb14            |   1473 +
 examples/VISCOSITY/profile.nemd.2d.12Sep13         |    318 -
 examples/VISCOSITY/profile.nemd.2d.1Feb14          |    423 +
 examples/VISCOSITY/profile.wall.2d.12Sep13         |     66 -
 examples/VISCOSITY/profile.wall.2d.1Feb14          |    150 +
 examples/body/in.body                              |      2 +-
 examples/body/log.body.18Feb13.linux.1             |     70 -
 examples/body/log.body.18Feb13.linux.4             |     70 -
 examples/body/log.body.1Feb14.linux.1              |     71 +
 examples/body/log.body.1Feb14.linux.4              |     71 +
 examples/colloid/in.colloid                        |      8 +-
 examples/colloid/log.colloid.18Feb13.linux.1       |    125 -
 examples/colloid/log.colloid.18Feb13.linux.4       |    125 -
 examples/colloid/log.colloid.1Feb14.linux.1        |    131 +
 examples/colloid/log.colloid.1Feb14.linux.4        |    131 +
 examples/comb/data.comb3-OHCCu                     |   1380 +-
 examples/comb/in.comb.Cu                           |      8 +-
 examples/comb/in.comb.HfO2                         |     14 +-
 examples/comb/in.comb.Si                           |      8 +-
 examples/comb/in.comb3                             |      6 +-
 examples/comb/log.comb.Cu.18Feb13.linux.1          |     73 -
 examples/comb/log.comb.Cu.18Feb13.linux.4          |     73 -
 examples/comb/log.comb.Cu.1Feb14.linux.1           |     76 +
 examples/comb/log.comb.Cu.1Feb14.linux.4           |     76 +
 .../comb/log.comb.Cu2O.elastic.18Feb13.linux.1     |    315 -
 .../comb/log.comb.Cu2O.elastic.18Feb13.linux.4     |    315 -
 examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 |    316 +
 examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 |    316 +
 examples/comb/log.comb.HfO2.18Feb13.linux.1        |    259 -
 examples/comb/log.comb.HfO2.18Feb13.linux.4        |    259 -
 examples/comb/log.comb.HfO2.1Feb14.linux.1         |    185 +
 examples/comb/log.comb.HfO2.1Feb14.linux.4         |    185 +
 examples/comb/log.comb.Si.18Feb13.linux.1          |     73 -
 examples/comb/log.comb.Si.18Feb13.linux.4          |     73 -
 examples/comb/log.comb.Si.1Feb14.linux.1           |     76 +
 examples/comb/log.comb.Si.1Feb14.linux.4           |     76 +
 examples/comb/log.comb.Si.elastic.18Feb13.linux.1  |    274 -
 examples/comb/log.comb.Si.elastic.18Feb13.linux.4  |    274 -
 examples/comb/log.comb.Si.elastic.1Feb14.linux.1   |    274 +
 examples/comb/log.comb.Si.elastic.1Feb14.linux.4   |    274 +
 examples/comb/log.comb3.1Feb14.linux.1             |     73 +
 examples/comb/log.comb3.1Feb14.linux.4             |     73 +
 examples/comb/log.comb3.4Nov13.linux.1             |     72 -
 examples/comb/log.comb3.4Nov13.linux.4             |     72 -
 examples/crack/in.crack                            |      8 +-
 examples/crack/log.crack.18Feb13.linux.1           |    135 -
 examples/crack/log.crack.18Feb13.linux.4           |    135 -
 examples/crack/log.crack.1Feb14.linux.1            |    138 +
 examples/crack/log.crack.1Feb14.linux.4            |    138 +
 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/log.dipole.18Feb13.linux.1         |     89 -
 examples/dipole/log.dipole.18Feb13.linux.4         |     89 -
 examples/dipole/log.dipole.1Feb14.linux.1          |     89 +
 examples/dipole/log.dipole.1Feb14.linux.4          |     89 +
 examples/dreiding/data.dreiding                    |      3 -
 examples/dreiding/log.dreiding.18Feb13.linux.1     |     98 -
 examples/dreiding/log.dreiding.18Feb13.linux.4     |     98 -
 examples/dreiding/log.dreiding.1Feb14.linux.1      |    106 +
 examples/dreiding/log.dreiding.1Feb14.linux.4      |    106 +
 examples/eim/in.eim                                |      8 +-
 examples/eim/log.eim.18Feb13.linux.1               |     67 -
 examples/eim/log.eim.18Feb13.linux.4               |     67 -
 examples/eim/log.eim.1Feb14.linux.1                |     72 +
 examples/eim/log.eim.1Feb14.linux.4                |     72 +
 examples/ellipse/in.ellipse.gayberne               |     12 +-
 examples/ellipse/in.ellipse.resquared              |      8 +-
 .../ellipse/log.ellipse.gayberne.18Feb13.linux.1   |    157 -
 .../ellipse/log.ellipse.gayberne.18Feb13.linux.4   |    157 -
 .../ellipse/log.ellipse.gayberne.1Feb14.linux.1    |    163 +
 .../ellipse/log.ellipse.gayberne.1Feb14.linux.4    |    163 +
 .../ellipse/log.ellipse.resquared.18Feb13.linux.1  |    157 -
 .../ellipse/log.ellipse.resquared.18Feb13.linux.4  |    157 -
 .../ellipse/log.ellipse.resquared.1Feb14.linux.1   |    160 +
 .../ellipse/log.ellipse.resquared.1Feb14.linux.4   |    160 +
 examples/flow/in.flow.couette                      |      8 +-
 examples/flow/in.flow.pois                         |      8 +-
 examples/flow/log.flow.couette.18Feb13.linux.1     |    127 -
 examples/flow/log.flow.couette.18Feb13.linux.4     |    127 -
 examples/flow/log.flow.couette.1Feb14.linux.1      |    130 +
 examples/flow/log.flow.couette.1Feb14.linux.4      |    130 +
 examples/flow/log.flow.pois.18Feb13.linux.1        |    127 -
 examples/flow/log.flow.pois.18Feb13.linux.4        |    127 -
 examples/flow/log.flow.pois.1Feb14.linux.1         |    130 +
 examples/flow/log.flow.pois.1Feb14.linux.4         |    130 +
 examples/friction/in.friction                      |      8 +-
 examples/friction/log.friction.18Feb13.linux.1     |    145 -
 examples/friction/log.friction.18Feb13.linux.4     |    145 -
 examples/friction/log.friction.1Feb14.linux.1      |    149 +
 examples/friction/log.friction.1Feb14.linux.4      |    149 +
 examples/gpu/log.gpu.melt.2.5.18Feb13.linux.1      |     77 -
 examples/gpu/log.gpu.melt.2.5.18Feb13.linux.4      |     77 -
 examples/gpu/log.gpu.melt.2.5.1Feb14.linux.1       |     80 +
 examples/gpu/log.gpu.melt.2.5.1Feb14.linux.4       |     80 +
 examples/gpu/log.gpu.melt.5.0.18Feb13.linux.1      |     77 -
 examples/gpu/log.gpu.melt.5.0.18Feb13.linux.4      |     77 -
 examples/gpu/log.gpu.melt.5.0.1Feb14.linux.1       |     80 +
 examples/gpu/log.gpu.melt.5.0.1Feb14.linux.4       |     80 +
 examples/gpu/log.gpu.phosphate.18Feb13.linux.1     |     75 -
 examples/gpu/log.gpu.phosphate.18Feb13.linux.4     |     75 -
 examples/gpu/log.gpu.phosphate.1Feb14.linux.1      |     80 +
 examples/gpu/log.gpu.phosphate.1Feb14.linux.4      |     80 +
 examples/gpu/log.gpu.rhodo.18Feb13.linux.1         |    122 -
 examples/gpu/log.gpu.rhodo.18Feb13.linux.4         |    122 -
 examples/gpu/log.gpu.rhodo.1Feb14.linux.1          |    135 +
 examples/gpu/log.gpu.rhodo.1Feb14.linux.4          |    135 +
 examples/hugoniostat/in.hugoniostat                |      8 +-
 .../hugoniostat/log.hugoniostat.18Feb13.linux.1    |     90 -
 .../hugoniostat/log.hugoniostat.18Feb13.linux.4    |     90 -
 .../hugoniostat/log.hugoniostat.1Feb14.linux.1     |     90 +
 .../hugoniostat/log.hugoniostat.1Feb14.linux.4     |     90 +
 examples/indent/in.indent                          |      8 +-
 examples/indent/in.indent.min                      |      8 +-
 examples/indent/log.indent.18Feb13.linux.1         |    176 -
 examples/indent/log.indent.18Feb13.linux.4         |    176 -
 examples/indent/log.indent.1Feb14.linux.1          |    179 +
 examples/indent/log.indent.1Feb14.linux.4          |    179 +
 examples/indent/log.indent.min.18Feb13.linux.1     |    386 -
 examples/indent/log.indent.min.18Feb13.linux.4     |    383 -
 examples/indent/log.indent.min.1Feb14.linux.1      |    404 +
 examples/indent/log.indent.min.1Feb14.linux.4      |    405 +
 examples/kim/log.kim.lj.26Jul13.mac_mpi.1          |     29 -
 examples/kim/log.kim.lj.26Jul13.mac_mpi.4          |     29 -
 examples/kim/log.kim.lj.lmp.26Jul13.mac_mpi.1      |     29 -
 examples/kim/log.kim.lj.lmp.26Jul13.mac_mpi.4      |     29 -
 examples/meam/in.meam                              |      8 +-
 examples/meam/in.meam.shear                        |      8 +-
 examples/meam/log.meam.18Feb13.linux.1             |     63 -
 examples/meam/log.meam.18Feb13.linux.4             |     63 -
 examples/meam/log.meam.1Feb14.linux.1              |     67 +
 examples/meam/log.meam.1Feb14.linux.4              |     67 +
 examples/meam/log.meam.shear.18Feb13.linux.1       |    169 -
 examples/meam/log.meam.shear.18Feb13.linux.4       |    169 -
 examples/meam/log.meam.shear.1Feb14.linux.1        |    172 +
 examples/meam/log.meam.shear.1Feb14.linux.4        |    172 +
 examples/melt/in.melt                              |      8 +-
 examples/melt/log.melt.18Feb13.linux.1             |     60 -
 examples/melt/log.melt.18Feb13.linux.4             |     60 -
 examples/melt/log.melt.1Feb14.linux.1              |     63 +
 examples/melt/log.melt.1Feb14.linux.4              |     63 +
 examples/micelle/in.micelle                        |      7 +-
 examples/micelle/log.micelle.18Feb13.linux.1       |    209 -
 examples/micelle/log.micelle.18Feb13.linux.4       |    209 -
 examples/micelle/log.micelle.1Feb14.linux.1        |    215 +
 examples/micelle/log.micelle.1Feb14.linux.4        |    215 +
 examples/min/in.min                                |      8 +-
 examples/min/in.min.box                            |      8 +-
 examples/min/log.min.18Feb13.linux.1               |    115 -
 examples/min/log.min.18Feb13.linux.4               |    115 -
 examples/min/log.min.1Feb14.linux.1                |    118 +
 examples/min/log.min.1Feb14.linux.4                |    118 +
 examples/min/log.min.box.18Feb13.linux.1           |    353 -
 examples/min/log.min.box.18Feb13.linux.4           |    353 -
 examples/min/log.min.box.1Feb14.linux.1            |    356 +
 examples/min/log.min.box.1Feb14.linux.4            |    356 +
 examples/msst/in.msst                              |      8 +-
 examples/msst/log.msst.18Feb13.linux.1             |    135 -
 examples/msst/log.msst.18Feb13.linux.4             |    135 -
 examples/msst/log.msst.1Feb14.linux.1              |    138 +
 examples/msst/log.msst.1Feb14.linux.4              |    138 +
 examples/neb/README                                |      1 +
 {bench/POTENTIALS => examples/neb}/Si.sw           |      0
 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.hop1.18Feb13.linux.4          |     11 -
 examples/neb/log.neb.hop1.1Feb14.linux.4           |     10 +
 examples/neb/log.neb.hop2.18Feb13.linux.4          |     19 -
 examples/neb/log.neb.hop2.1Feb14.linux.4           |     17 +
 examples/neb/log.neb.sivac.1Feb14.linux.3          |     13 +
 examples/nemd/in.nemd                              |      7 +-
 examples/nemd/log.nemd.18Feb13.linux.1             |    112 -
 examples/nemd/log.nemd.18Feb13.linux.4             |    112 -
 examples/nemd/log.nemd.1Feb14.linux.1              |    115 +
 examples/nemd/log.nemd.1Feb14.linux.4              |    115 +
 examples/obstacle/in.obstacle                      |      8 +-
 examples/obstacle/log.obstacle.18Feb13.linux.1     |    137 -
 examples/obstacle/log.obstacle.18Feb13.linux.4     |    137 -
 examples/obstacle/log.obstacle.1Feb14.linux.1      |    140 +
 examples/obstacle/log.obstacle.1Feb14.linux.4      |    140 +
 examples/peptide/in.peptide                        |      8 +-
 examples/peptide/log.peptide.18Feb13.linux.1       |    164 -
 examples/peptide/log.peptide.18Feb13.linux.4       |    164 -
 examples/peptide/log.peptide.1Feb14.linux.1        |    177 +
 examples/peptide/log.peptide.1Feb14.linux.4        |    177 +
 examples/peri/in.peri                              |      8 +-
 examples/peri/log.peri.18Feb13.linux.1             |     84 -
 examples/peri/log.peri.18Feb13.linux.4             |     84 -
 examples/peri/log.peri.1Feb14.linux.1              |     90 +
 examples/peri/log.peri.1Feb14.linux.4              |     90 +
 examples/pour/in.pour                              |      8 +-
 examples/pour/in.pour.2d                           |      8 +-
 examples/pour/in.pour.2d.molecule                  |     69 +
 examples/pour/log.pour.18Feb13.linux.1             |    144 -
 examples/pour/log.pour.18Feb13.linux.4             |    144 -
 examples/pour/log.pour.1Feb14.linux.1              |    147 +
 examples/pour/log.pour.1Feb14.linux.4              |    147 +
 examples/pour/log.pour.2d.18Feb13.linux.1          |     97 -
 examples/pour/log.pour.2d.18Feb13.linux.4          |     97 -
 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/pour/molecule.vshape                      |     35 +
 examples/prd/log.prd.0.18Feb13.linux.4             |    631 -
 examples/prd/log.prd.0.1Feb14.linux.4              |    631 +
 examples/prd/log.prd.1.18Feb13.linux.4             |    631 -
 examples/prd/log.prd.1.1Feb14.linux.4              |    631 +
 examples/prd/log.prd.18Feb13.linux.4               |     12 -
 examples/prd/log.prd.1Feb14.linux.4                |     12 +
 examples/prd/log.prd.2.18Feb13.linux.4             |    631 -
 examples/prd/log.prd.2.1Feb14.linux.4              |    631 +
 examples/prd/log.prd.3.18Feb13.linux.4             |    631 -
 examples/prd/log.prd.3.1Feb14.linux.4              |    631 +
 examples/reax/AB/in.AB                             |      2 +-
 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/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 +++
 .../reax/{Fluorographene => FC}/ffield.reax.FC     |      0
 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/Fluorographene/README                |     13 -
 examples/reax/Fluorographene/data.FC               |  17296 ---
 examples/reax/Fluorographene/dumpnpt.xyz           |  17282 ---
 examples/reax/Fluorographene/in.FC                 |     32 -
 examples/reax/Fluorographene/log.FC                |    290 -
 examples/reax/RDX/in.RDX                           |      2 +-
 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/{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                         |      8 +-
 examples/reax/in.reaxc.tatb                        |     10 +-
 examples/reax/log.reax.rdx.18Feb13.linux.1         |     81 -
 examples/reax/log.reax.rdx.18Feb13.linux.4         |     81 -
 examples/reax/log.reax.rdx.1Feb14.linux.1          |     85 +
 examples/reax/log.reax.rdx.1Feb14.linux.4          |     85 +
 examples/reax/log.reax.tatb.18Feb13.linux.1        |     77 -
 examples/reax/log.reax.tatb.18Feb13.linux.4        |     77 -
 examples/reax/log.reax.tatb.1Feb14.linux.1         |     81 +
 examples/reax/log.reax.tatb.1Feb14.linux.4         |     81 +
 examples/reax/log.reaxc.rdx.18Feb13.linux.1        |     81 -
 examples/reax/log.reaxc.rdx.18Feb13.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.18Feb13.linux.1       |     79 -
 examples/reax/log.reaxc.tatb.18Feb13.linux.4       |     79 -
 examples/reax/log.reaxc.tatb.1Feb14.linux.1        |     86 +
 examples/reax/log.reaxc.tatb.1Feb14.linux.4        |     86 +
 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.18Feb13.linux.1           |    310 -
 examples/rigid/log.rigid.18Feb13.linux.4           |    310 -
 examples/rigid/log.rigid.1Feb14.linux.1            |    314 +
 examples/rigid/log.rigid.1Feb14.linux.4            |    314 +
 examples/rigid/log.rigid.poems.18Feb13.linux.1     |    310 -
 examples/rigid/log.rigid.poems.18Feb13.linux.4     |    310 -
 examples/rigid/log.rigid.poems.1Feb14.linux.1      |    317 +
 examples/rigid/log.rigid.poems.1Feb14.linux.4      |    317 +
 examples/rigid/log.rigid.poems2.18Feb13.linux.1    |    314 -
 examples/rigid/log.rigid.poems2.18Feb13.linux.4    |    314 -
 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/in.shear                            |      8 +-
 examples/shear/in.shear.void                       |      8 +-
 examples/shear/log.shear.18Feb13.linux.1           |    165 -
 examples/shear/log.shear.18Feb13.linux.4           |    165 -
 examples/shear/log.shear.1Feb14.linux.1            |    168 +
 examples/shear/log.shear.1Feb14.linux.4            |    168 +
 examples/shear/log.shear.void.18Feb13.linux.1      |    166 -
 examples/shear/log.shear.void.18Feb13.linux.4      |    166 -
 examples/shear/log.shear.void.1Feb14.linux.1       |    169 +
 examples/shear/log.shear.void.1Feb14.linux.4       |    169 +
 examples/srd/in.srd.mixture                        |      7 +-
 examples/srd/in.srd.pure                           |      7 +-
 examples/srd/log.srd.mixture.18Feb13.linux.1       |    142 -
 examples/srd/log.srd.mixture.18Feb13.linux.4       |    142 -
 examples/srd/log.srd.mixture.1Feb14.linux.1        |    232 +
 examples/srd/log.srd.mixture.1Feb14.linux.4        |    232 +
 examples/srd/log.srd.pure.18Feb13.linux.1          |    592 -
 examples/srd/log.srd.pure.18Feb13.linux.4          |    592 -
 examples/srd/log.srd.pure.1Feb14.linux.1           |    148 +
 examples/srd/log.srd.pure.1Feb14.linux.4           |    148 +
 examples/tad/in.tad                                |      6 +-
 examples/tad/log.tad.0.18Feb13.linux.3             |  12877 ---
 examples/tad/log.tad.0.1Feb14.linux.3              |  12325 +++
 examples/tad/log.tad.1.18Feb13.linux.3             |   7814 --
 examples/tad/log.tad.1.1Feb14.linux.3              |   7262 ++
 examples/tad/log.tad.18Feb13.linux.3               |    114 -
 examples/tad/log.tad.1Feb14.linux.3                |    114 +
 examples/tad/log.tad.2.18Feb13.linux.3             |   7814 --
 examples/tad/log.tad.2.1Feb14.linux.3              |   7262 ++
 examples/tad/log.tad.neb.18Feb13.linux.3           |   1423 -
 examples/tad/log.tad.neb.1Feb14.linux.3            |   1160 +
 examples/voronoi/log.voronoi.4Aug13.macos.1        |    368 -
 examples/voronoi/log.voronoi.4Aug13.macos.4        |    368 -
 lib/colvars/colvar.cpp                             |     77 +-
 lib/colvars/colvarbias.cpp                         |      2 +-
 lib/colvars/colvarbias_meta.cpp                    |      3 +-
 lib/colvars/colvargrid.h                           |      2 +-
 lib/colvars/colvarmodule.cpp                       |      2 +-
 lib/colvars/colvarmodule.h                         |      2 +-
 lib/colvars/colvartypes.h                          |      2 +-
 lib/gpu/Makefile.linux                             |     17 +-
 lib/gpu/Makefile.linux.double                      |     11 +
 lib/gpu/Makefile.linux_opencl                      |     10 +-
 lib/gpu/Nvidia.makefile                            |     18 +-
 lib/gpu/Opencl.makefile                            |     15 +-
 lib/gpu/README                                     |     64 +-
 lib/gpu/lal_answer.cpp                             |     35 +-
 lib/gpu/lal_atom.h                                 |      2 +-
 lib/gpu/lal_base_atomic.cpp                        |      8 +-
 lib/gpu/lal_base_atomic.h                          |     12 +-
 lib/gpu/lal_base_charge.cpp                        |      8 +-
 lib/gpu/lal_base_charge.h                          |      8 +-
 lib/gpu/lal_base_dipole.cpp                        |      8 +-
 lib/gpu/lal_base_dipole.h                          |      8 +-
 lib/gpu/lal_base_ellipsoid.cpp                     |      8 +-
 lib/gpu/lal_base_ellipsoid.h                       |      8 +-
 lib/gpu/lal_base_three.cpp                         |      8 +-
 lib/gpu/lal_base_three.h                           |     12 +-
 lib/gpu/lal_beck_ext.cpp                           |      4 +-
 lib/gpu/lal_born_coul_long_ext.cpp                 |      4 +-
 lib/gpu/lal_born_coul_wolf_ext.cpp                 |      4 +-
 lib/gpu/lal_born_ext.cpp                           |      4 +-
 lib/gpu/lal_buck_coul_ext.cpp                      |      4 +-
 lib/gpu/lal_buck_coul_long.cpp                     |      1 +
 lib/gpu/lal_buck_coul_long_ext.cpp                 |      4 +-
 lib/gpu/lal_buck_ext.cpp                           |      4 +-
 lib/gpu/lal_cg_cmm_ext.cpp                         |      4 +-
 lib/gpu/lal_cg_cmm_long_ext.cpp                    |      4 +-
 lib/gpu/lal_charmm_long_ext.cpp                    |      4 +-
 lib/gpu/lal_colloid_ext.cpp                        |      4 +-
 lib/gpu/lal_coul_dsf.cpp                           |      2 +-
 lib/gpu/lal_coul_dsf.h                             |      2 +-
 lib/gpu/lal_coul_dsf_ext.cpp                       |      4 +-
 lib/gpu/lal_coul_long_ext.cpp                      |      4 +-
 lib/gpu/lal_device.cpp                             |      2 +-
 lib/gpu/lal_dipole_lj_ext.cpp                      |      4 +-
 lib/gpu/lal_dipole_lj_sf_ext.cpp                   |      4 +-
 lib/gpu/lal_eam.cpp                                |      2 +-
 lib/gpu/lal_eam.h                                  |      4 +-
 lib/gpu/lal_eam_ext.cpp                            |      4 +-
 lib/gpu/lal_gauss_ext.cpp                          |      4 +-
 lib/gpu/lal_gayberne_ext.cpp                       |      8 +-
 lib/gpu/lal_lj96_ext.cpp                           |      4 +-
 lib/gpu/lal_lj_class2_long_ext.cpp                 |      4 +-
 lib/gpu/lal_lj_coul_debye_ext.cpp                  |      4 +-
 lib/gpu/lal_lj_coul_ext.cpp                        |      4 +-
 lib/gpu/lal_lj_coul_long_ext.cpp                   |      4 +-
 lib/gpu/lal_lj_coul_msm_ext.cpp                    |      4 +-
 lib/gpu/lal_lj_dsf_ext.cpp                         |      4 +-
 lib/gpu/lal_lj_expand_ext.cpp                      |      4 +-
 lib/gpu/lal_lj_ext.cpp                             |      4 +-
 lib/gpu/lal_lj_gromacs.cpp                         |    164 +
 lib/gpu/lal_lj_gromacs.cu                          |    233 +
 lib/gpu/lal_lj_gromacs.h                           |     84 +
 lib/gpu/lal_lj_gromacs_ext.cpp                     |    126 +
 lib/gpu/lal_mie_ext.cpp                            |      4 +-
 lib/gpu/lal_morse_ext.cpp                          |      4 +-
 lib/gpu/lal_neighbor.cpp                           |      9 +-
 lib/gpu/lal_neighbor.h                             |      4 +-
 lib/gpu/lal_neighbor_gpu.cu                        |     33 +-
 lib/gpu/lal_precision.h                            |     18 +
 lib/gpu/lal_preprocessor.h                         |      4 +
 lib/gpu/lal_re_squared_ext.cpp                     |      6 +-
 lib/gpu/lal_soft_ext.cpp                           |      4 +-
 lib/gpu/lal_sw.cpp                                 |    172 +-
 lib/gpu/lal_sw.cu                                  |    309 +-
 lib/gpu/lal_sw.h                                   |     32 +-
 lib/gpu/lal_sw_ext.cpp                             |     31 +-
 lib/gpu/lal_table_ext.cpp                          |      4 +-
 lib/gpu/lal_yukawa_colloid.cpp                     |      4 +-
 lib/gpu/lal_yukawa_colloid.h                       |      4 +-
 lib/gpu/lal_yukawa_colloid_ext.cpp                 |      4 +-
 lib/gpu/lal_yukawa_ext.cpp                         |      4 +-
 potentials/ffield.comb3                            |    865 +-
 potentials/lib.comb3                               |   4103 +-
 python/examples/in.simple                          |      2 +
 python/examples/simple.py                          |      6 +
 src/.gitignore                                     |     14 +
 src/ASPHERE/pair_gayberne.cpp                      |     32 +-
 src/ASPHERE/pair_gayberne.h                        |      2 +
 src/BODY/body_nparticle.h                          |      8 +-
 src/CLASS2/dihedral_class2.cpp                     |      4 +-
 src/CLASS2/improper_class2.cpp                     |      5 +-
 src/COLLOID/pair_colloid.cpp                       |     27 +-
 src/COLLOID/pair_colloid.h                         |      2 +
 src/COLLOID/pair_yukawa_colloid.cpp                |      5 +-
 src/DIPOLE/atom_vec_dipole.cpp                     |    109 +-
 src/DIPOLE/atom_vec_dipole.h                       |     13 +-
 src/DIPOLE/pair_lj_cut_dipole_long.h               |      6 +-
 src/DIPOLE/pair_lj_long_dipole_long.cpp            |      2 +-
 src/DIPOLE/pair_lj_long_dipole_long.h              |     21 +-
 src/Depend.sh                                      |      1 -
 src/FLD/pair_lubricateU.cpp                        |      1 -
 src/GPU/Install.sh                                 |      2 +
 src/GPU/fix_gpu.cpp                                |     13 +-
 src/GPU/fix_gpu.h                                  |     17 +-
 src/GPU/gpu_extra.h                                |     11 +-
 src/GPU/pair_beck_gpu.cpp                          |     10 +-
 src/GPU/pair_born_coul_long_gpu.cpp                |     10 +-
 src/GPU/pair_born_coul_wolf_gpu.cpp                |     10 +-
 src/GPU/pair_born_gpu.cpp                          |      8 +-
 src/GPU/pair_buck_coul_cut_gpu.cpp                 |      8 +-
 src/GPU/pair_buck_coul_long_gpu.cpp                |      8 +-
 src/GPU/pair_buck_gpu.cpp                          |      8 +-
 src/GPU/pair_colloid_gpu.cpp                       |      8 +-
 src/GPU/pair_coul_dsf_gpu.cpp                      |     23 +-
 src/GPU/pair_coul_long_gpu.cpp                     |      8 +-
 src/GPU/pair_eam_gpu.cpp                           |      6 +-
 src/GPU/pair_gauss_gpu.cpp                         |      8 +-
 src/GPU/pair_gayberne_gpu.cpp                      |      6 +-
 src/GPU/pair_lj96_cut_gpu.cpp                      |      8 +-
 src/GPU/pair_lj_charmm_coul_long_gpu.cpp           |      8 +-
 src/GPU/pair_lj_class2_coul_long_gpu.cpp           |      8 +-
 src/GPU/pair_lj_class2_gpu.cpp                     |      8 +-
 src/GPU/pair_lj_cut_coul_cut_gpu.cpp               |      8 +-
 src/GPU/pair_lj_cut_coul_debye_gpu.cpp             |      8 +-
 src/GPU/pair_lj_cut_coul_dsf_gpu.cpp               |     23 +-
 src/GPU/pair_lj_cut_coul_long_gpu.cpp              |      8 +-
 src/GPU/pair_lj_cut_coul_msm_gpu.cpp               |      8 +-
 src/GPU/pair_lj_cut_dipole_cut_gpu.cpp             |      8 +-
 src/GPU/pair_lj_cut_gpu.cpp                        |      8 +-
 src/GPU/pair_lj_expand_gpu.cpp                     |      8 +-
 src/GPU/pair_lj_gromacs_gpu.cpp                    |    246 +
 src/GPU/pair_lj_gromacs_gpu.h                      |     59 +
 src/GPU/pair_lj_sdk_coul_long_gpu.cpp              |      8 +-
 src/GPU/pair_lj_sdk_gpu.cpp                        |      7 +-
 src/GPU/pair_lj_sf_dipole_sf_gpu.cpp               |      8 +-
 src/GPU/pair_mie_cut_gpu.cpp                       |      8 +-
 src/GPU/pair_morse_gpu.cpp                         |      8 +-
 src/GPU/pair_resquared_gpu.cpp                     |      6 +-
 src/GPU/pair_soft_gpu.cpp                          |      8 +-
 src/GPU/pair_sw_gpu.cpp                            |     83 +-
 src/GPU/pair_sw_gpu.h                              |     15 +-
 src/GPU/pair_table_gpu.cpp                         |      8 +-
 src/GPU/pair_yukawa_colloid_gpu.cpp                |      8 +-
 src/GPU/pair_yukawa_gpu.cpp                        |      8 +-
 src/GRANULAR/fix_pour.cpp                          |    745 +-
 src/GRANULAR/fix_pour.h                            |    138 +-
 src/GRANULAR/pair_gran_hooke_history.cpp           |     55 +-
 src/KIM/pair_kim.cpp                               |     10 +-
 src/KIM/pair_kim.h                                 |     11 +-
 src/KSPACE/ewald.h                                 |      3 +-
 src/KSPACE/ewald_disp.cpp                          |     21 +
 src/KSPACE/ewald_disp.h                            |      5 +-
 src/KSPACE/fix_tune_kspace.h                       |      4 +-
 src/KSPACE/msm.cpp                                 |      3 +-
 src/KSPACE/msm.h                                   |     12 +-
 src/KSPACE/pair_born_coul_long.cpp                 |     24 +
 src/KSPACE/pair_born_coul_long.h                   |      2 +
 src/KSPACE/pair_buck_coul_long.cpp                 |     23 +
 src/KSPACE/pair_buck_coul_long.h                   |      2 +
 src/KSPACE/pair_buck_long_coul_long.cpp            |    102 +-
 src/KSPACE/pair_buck_long_coul_long.h              |      7 +-
 src/KSPACE/pair_lj_cut_tip4p_long.cpp              |     10 +-
 src/KSPACE/pair_lj_long_coul_long.cpp              |     98 +-
 src/KSPACE/pair_lj_long_coul_long.h                |     23 +-
 src/KSPACE/pair_lj_long_tip4p_long.cpp             |     36 +-
 src/KSPACE/pair_tip4p_long.cpp                     |      9 +-
 src/KSPACE/pppm.h                                  |      3 +-
 src/KSPACE/pppm_disp.cpp                           |   2055 +-
 src/KSPACE/pppm_disp.h                             |    241 +-
 src/KSPACE/pppm_old.h                              |     64 +-
 src/MAKE/Makefile.mingw32-cross                    |    117 +
 src/MAKE/Makefile.mingw32-cross-mpi                |    117 +
 src/MAKE/Makefile.mingw64-cross                    |    117 +
 src/MAKE/Makefile.mingw64-cross-mpi                |    117 +
 src/MAKE/Makefile.openmpi                          |      2 +-
 src/MANYBODY/fix_qeq_comb.cpp                      |      1 -
 src/MANYBODY/fix_qeq_comb.h                        |      2 +-
 src/MANYBODY/pair_airebo.cpp                       |     15 +-
 src/MANYBODY/pair_airebo.h                         |      6 +-
 src/MANYBODY/pair_bop.cpp                          |     29 +-
 src/MANYBODY/pair_comb.cpp                         |     22 +-
 src/MANYBODY/pair_comb.h                           |      6 +
 src/MANYBODY/pair_comb3.cpp                        |    257 +-
 src/MANYBODY/pair_comb3.h                          |     12 +-
 src/MANYBODY/pair_lcbop.cpp                        |     12 +-
 src/MANYBODY/pair_lcbop.h                          |      8 +-
 src/MANYBODY/pair_nb3b_harmonic.cpp                |     17 +-
 src/MANYBODY/pair_nb3b_harmonic.h                  |     51 +
 src/MANYBODY/pair_sw.cpp                           |      5 +-
 src/MANYBODY/pair_tersoff.cpp                      |      5 +-
 src/MANYBODY/pair_tersoff.h                        |      4 +-
 src/MANYBODY/pair_tersoff_mod.cpp                  |      2 +-
 src/MANYBODY/pair_tersoff_mod.h                    |     30 +-
 src/MANYBODY/pair_tersoff_zbl.h                    |      4 +-
 src/MC/fix_bond_break.cpp                          |     27 +-
 src/MC/fix_bond_break.h                            |      5 +-
 src/MC/fix_bond_create.cpp                         |     51 +-
 src/MC/fix_bond_create.h                           |      5 +-
 src/MC/fix_bond_swap.cpp                           |     27 +-
 src/MC/fix_bond_swap.h                             |      5 +
 src/MC/fix_gcmc.cpp                                |    161 +-
 src/MC/fix_gcmc.h                                  |     22 +-
 src/MEAM/pair_meam.cpp                             |      4 +-
 src/MISC/compute_msd_nongauss.cpp                  |      2 +-
 src/MISC/fix_deposit.cpp                           |    720 +
 src/MISC/fix_deposit.h                             |    178 +
 src/MISC/fix_efield.cpp                            |      2 +-
 src/MISC/fix_efield.h                              |     22 +-
 src/MISC/fix_evaporate.cpp                         |     83 +-
 src/MISC/fix_gld.cpp                               |     18 +-
 src/MISC/fix_gld.h                                 |     32 +
 src/MISC/fix_orient_fcc.cpp                        |     15 +-
 src/MISC/fix_orient_fcc.h                          |      4 +-
 src/MISC/fix_ttm.h                                 |      3 +-
 src/MISC/pair_nm_cut.h                             |     19 +
 src/MISC/pair_nm_cut_coul_cut.h                    |      5 +
 src/MISC/pair_nm_cut_coul_long.h                   |      5 +
 src/MOLECULE/angle_cosine_periodic.cpp             |      6 +-
 src/MOLECULE/angle_table.h                         |      3 +-
 src/MOLECULE/atom_vec_angle.cpp                    |    223 +-
 src/MOLECULE/atom_vec_angle.h                      |     21 +-
 src/MOLECULE/atom_vec_bond.cpp                     |    183 +-
 src/MOLECULE/atom_vec_bond.h                       |     19 +-
 src/MOLECULE/atom_vec_full.cpp                     |    319 +-
 src/MOLECULE/atom_vec_full.h                       |     25 +-
 src/MOLECULE/atom_vec_molecular.cpp                |    320 +-
 src/MOLECULE/atom_vec_molecular.h                  |     25 +-
 src/MOLECULE/atom_vec_template.cpp                 |    873 +
 src/MOLECULE/atom_vec_template.h                   |    114 +
 src/MOLECULE/bond_fene.cpp                         |      3 +-
 src/MOLECULE/bond_fene_expand.cpp                  |      3 +-
 src/MOLECULE/bond_quartic.cpp                      |     12 +-
 src/MOLECULE/bond_quartic.h                        |      5 +
 src/MOLECULE/bond_table.h                          |      3 +-
 src/MOLECULE/dihedral_charmm.cpp                   |      4 +-
 src/MOLECULE/dihedral_harmonic.cpp                 |      4 +-
 src/MOLECULE/dihedral_helix.cpp                    |      4 +-
 src/MOLECULE/dihedral_multi_harmonic.cpp           |      4 +-
 src/MOLECULE/dihedral_opls.cpp                     |      4 +-
 src/MOLECULE/improper_cvff.cpp                     |      5 +-
 src/MOLECULE/improper_harmonic.cpp                 |      5 +-
 src/MOLECULE/improper_umbrella.cpp                 |      5 +-
 src/MOLECULE/pair_hbond_dreiding_lj.cpp            |     57 +-
 src/MOLECULE/pair_hbond_dreiding_morse.cpp         |     57 +-
 src/MOLECULE/pair_lj_charmm_coul_charmm.cpp        |      2 +-
 src/MOLECULE/pair_lj_cut_tip4p_cut.cpp             |     31 +-
 src/MOLECULE/pair_lj_cut_tip4p_cut.h               |     30 +-
 src/MOLECULE/pair_tip4p_cut.cpp                    |      9 +-
 src/MOLECULE/pair_tip4p_cut.h                      |     24 +-
 src/MPIIO/Install.sh                               |     51 +
 src/MPIIO/dump_atom_mpiio.cpp                      |    724 +
 src/MPIIO/dump_atom_mpiio.h                        |     89 +
 src/MPIIO/dump_custom_mpiio.cpp                    |    662 +
 src/MPIIO/dump_custom_mpiio.h                      |    108 +
 src/MPIIO/dump_xyz_mpiio.cpp                       |    396 +
 src/MPIIO/dump_xyz_mpiio.h                         |     76 +
 src/MPIIO/restart_mpiio.cpp                        |    194 +
 src/MPIIO/restart_mpiio.h                          |     74 +
 src/Make.sh                                        |      2 +-
 src/Makefile                                       |     38 +-
 src/Makefile.lib                                   |      4 +-
 src/Makefile.shlib                                 |      4 +-
 src/OPT/pair_lj_cut_tip4p_long_opt.cpp             |      9 +-
 src/PERI/atom_vec_peri.cpp                         |    108 +-
 src/PERI/atom_vec_peri.h                           |     13 +-
 src/PERI/compute_damage_atom.cpp                   |     17 +-
 src/PERI/compute_dilatation_atom.cpp               |    127 +
 src/PERI/compute_dilatation_atom.h                 |     48 +
 src/PERI/compute_plasticity_atom.cpp               |    111 +
 src/PERI/compute_plasticity_atom.h                 |     44 +
 src/PERI/fix_peri_neigh.cpp                        |     65 +-
 src/PERI/fix_peri_neigh.h                          |     16 +-
 src/PERI/pair_peri_eps.cpp                         |    843 +
 src/PERI/pair_peri_eps.h                           |    111 +
 src/PERI/pair_peri_lps.cpp                         |      7 +-
 src/PERI/pair_peri_lps.h                           |      9 +-
 src/PERI/pair_peri_pmb.cpp                         |      4 +-
 src/PERI/pair_peri_pmb.h                           |      4 -
 src/PERI/pair_peri_ves.cpp                         |      6 +-
 src/PERI/pair_peri_ves.h                           |      7 +-
 src/POEMS/fix_poems.cpp                            |     76 +-
 src/POEMS/fix_poems.h                              |      8 +-
 src/Package.sh                                     |      4 +-
 src/Purge.list                                     |      2 +
 src/REAX/fix_reax_bonds.cpp                        |      4 +
 src/REPLICA/compute_event_displace.cpp             |      2 +-
 src/REPLICA/fix_event.cpp                          |     12 +-
 src/REPLICA/neb.cpp                                |     10 +-
 src/REPLICA/neb.h                                  |     19 +-
 src/REPLICA/prd.cpp                                |      4 +-
 src/REPLICA/prd.h                                  |      5 +-
 src/REPLICA/tad.cpp                                |     60 +-
 src/REPLICA/tad.h                                  |      2 +-
 src/REPLICA/verlet_split.cpp                       |      3 +-
 src/REPLICA/verlet_split.h                         |      4 +
 src/RIGID/compute_erotate_rigid.cpp                |      4 +-
 src/RIGID/compute_erotate_rigid.h                  |      6 +-
 src/RIGID/compute_ke_rigid.cpp                     |      2 +
 src/RIGID/compute_ke_rigid.h                       |      8 +
 src/RIGID/fix_rigid.cpp                            |     38 +-
 src/RIGID/fix_rigid.h                              |     20 +-
 src/RIGID/fix_rigid_nh.cpp                         |      2 +-
 src/RIGID/fix_rigid_small.cpp                      |    224 +-
 src/RIGID/fix_rigid_small.h                        |     69 +-
 src/RIGID/fix_shake.cpp                            |   2655 +
 src/RIGID/fix_shake.h                              |    255 +
 src/SHOCK/fix_append_atoms.cpp                     |     20 +-
 src/SHOCK/fix_append_atoms.h                       |      8 +-
 src/SHOCK/fix_wall_piston.h                        |      4 -
 src/SRD/fix_srd.cpp                                |    178 +-
 src/SRD/fix_srd.h                                  |      9 +-
 src/SRD/fix_wall_srd.h                             |      5 -
 src/STUBS/mpi.c                                    |    187 +-
 src/STUBS/mpi.h                                    |     30 +-
 src/USER-ATC/fix_atc.cpp                           |      3 +-
 src/USER-AWPMD/atom_vec_wavepacket.cpp             |    190 +-
 src/USER-AWPMD/atom_vec_wavepacket.h               |      7 +-
 src/USER-CG-CMM/Install.sh                         |     12 -
 src/USER-CG-CMM/angle_cg_cmm.cpp                   |    433 -
 src/USER-CG-CMM/angle_cg_cmm.h                     |     55 -
 src/USER-CG-CMM/cg_cmm_parms.cpp                   |     43 -
 src/USER-CG-CMM/cg_cmm_parms.h                     |     43 -
 src/USER-CG-CMM/pair_cg_cmm.cpp                    |    174 -
 src/USER-CG-CMM/pair_cg_cmm.h                      |     51 -
 src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp           |    241 -
 src/USER-CG-CMM/pair_cg_cmm_coul_cut.h             |     53 -
 src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp          |    279 -
 src/USER-CG-CMM/pair_cg_cmm_coul_long.h            |     54 -
 src/USER-CG-CMM/pair_cmm_common.cpp                |    479 -
 src/USER-CG-CMM/pair_cmm_common.h                  |    692 -
 src/USER-COLVARS/README                            |      2 +-
 src/USER-COLVARS/colvarproxy_lammps.cpp            |      1 -
 src/USER-COLVARS/fix_colvars.cpp                   |     37 +-
 src/USER-COLVARS/fix_colvars.h                     |      2 +-
 src/USER-COLVARS/group_ndx.cpp                     |     22 +-
 src/USER-CUDA/comm_cuda.cpp                        |      4 +
 src/USER-EFF/atom_vec_electron.cpp                 |    146 +-
 src/USER-EFF/atom_vec_electron.h                   |      7 +-
 src/USER-EFF/pair_eff_cut.cpp                      |      2 -
 src/USER-LB/fix_lb_fluid.cpp                       |      4 +-
 src/USER-LB/fix_lb_rigid_pc_sphere.cpp             |     59 +-
 src/USER-LB/fix_lb_rigid_pc_sphere.h               |      2 +-
 src/USER-MISC/angle_cosine_shift_exp.cpp           |      1 -
 src/USER-MISC/angle_quartic.cpp                    |      4 +-
 src/USER-MISC/bond_harmonic_shift.cpp              |     14 +
 src/USER-MISC/bond_harmonic_shift.h                |      1 +
 src/USER-MISC/bond_harmonic_shift_cut.cpp          |     15 +
 src/USER-MISC/bond_harmonic_shift_cut.h            |      1 +
 src/USER-MISC/compute_temp_rotate.cpp              |      4 +-
 src/USER-MISC/dihedral_cosine_shift_exp.cpp        |      4 +-
 src/USER-MISC/dihedral_fourier.cpp                 |      4 +-
 src/USER-MISC/dihedral_nharmonic.cpp               |      4 +-
 src/USER-MISC/dihedral_quadratic.cpp               |      6 +-
 src/USER-MISC/fix_addtorque.cpp                    |      2 +-
 src/USER-MISC/fix_imd.cpp                          |    169 +-
 src/USER-MISC/fix_imd.h                            |      2 +-
 src/USER-MISC/fix_ti_spring.cpp                    |      4 +-
 src/USER-MISC/improper_cossq.cpp                   |      8 +-
 src/USER-MISC/improper_fourier.cpp                 |      5 +-
 src/USER-MISC/pair_edip.cpp                        |      2 -
 src/USER-MISC/pair_list.cpp                        |      8 +-
 src/USER-MISC/pair_list.h                          |      2 +-
 src/USER-MISC/pair_tersoff_table.cpp               |      6 +-
 src/USER-MISC/pair_tersoff_table.h                 |      4 +-
 src/USER-MOLFILE/dump_molfile.cpp                  |      6 +-
 src/USER-MOLFILE/dump_molfile.h                    |      2 +-
 src/USER-OMP/Install.sh                            |      2 +-
 src/USER-OMP/angle_quartic_omp.cpp                 |      2 +-
 src/USER-OMP/bond_fene_expand_omp.cpp              |      3 +-
 src/USER-OMP/bond_fene_omp.cpp                     |      3 +-
 src/USER-OMP/dihedral_charmm_omp.cpp               |      4 +-
 src/USER-OMP/dihedral_class2_omp.cpp               |      4 +-
 src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp     |      4 +-
 src/USER-OMP/dihedral_fourier_omp.cpp              |      4 +-
 src/USER-OMP/dihedral_harmonic_omp.cpp             |      4 +-
 src/USER-OMP/dihedral_helix_omp.cpp                |      4 +-
 src/USER-OMP/dihedral_multi_harmonic_omp.cpp       |      4 +-
 src/USER-OMP/dihedral_nharmonic_omp.cpp            |      4 +-
 src/USER-OMP/dihedral_opls_omp.cpp                 |      4 +-
 src/USER-OMP/dihedral_quadratic_omp.cpp            |      4 +-
 src/USER-OMP/domain_omp.cpp                        |      4 +-
 src/USER-OMP/fix_omp.cpp                           |      6 +
 src/USER-OMP/fix_rigid_nh_omp.cpp                  |      6 +-
 src/USER-OMP/fix_rigid_omp.cpp                     |      6 +-
 src/USER-OMP/fix_rigid_small_omp.cpp               |      6 +-
 src/USER-OMP/fix_shear_history_omp.cpp             |      4 +-
 src/USER-OMP/improper_class2_omp.cpp               |      5 +-
 src/USER-OMP/improper_cossq_omp.cpp                |      4 +-
 src/USER-OMP/improper_cvff_omp.cpp                 |      5 +-
 src/USER-OMP/improper_fourier_omp.cpp              |      4 +-
 src/USER-OMP/improper_harmonic_omp.cpp             |      4 +-
 src/USER-OMP/improper_umbrella_omp.cpp             |      4 +-
 src/USER-OMP/neigh_full_omp.cpp                    |    160 +-
 src/USER-OMP/neigh_gran_omp.cpp                    |     22 +-
 src/USER-OMP/neigh_half_bin_omp.cpp                |    146 +-
 src/USER-OMP/neigh_half_multi_omp.cpp              |    106 +-
 src/USER-OMP/neigh_half_nsq_omp.cpp                |     99 +-
 src/USER-OMP/neigh_respa_omp.cpp                   |    172 +-
 src/USER-OMP/pair_airebo_omp.cpp                   |     15 +-
 src/USER-OMP/pair_comb_omp.cpp                     |     11 +-
 src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp        |     37 +-
 src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp     |     36 +-
 src/USER-OMP/pair_nb3b_harmonic_omp.cpp            |      5 +-
 src/USER-OMP/pair_peri_lps_omp.cpp                 |      4 +-
 src/USER-OMP/pair_peri_pmb_omp.cpp                 |      2 +-
 src/USER-OMP/pair_sw_omp.cpp                       |      5 +-
 src/USER-OMP/pair_tersoff_mod_omp.cpp              |      5 +-
 src/USER-OMP/pair_tersoff_omp.cpp                  |      5 +-
 src/USER-OMP/respa_omp.cpp                         |     19 +-
 src/USER-PHONON/fix_phonon.cpp                     |     45 +-
 src/USER-PHONON/fix_phonon.h                       |      6 +-
 src/USER-REAXC/fix_qeq_reax.cpp                    |     12 +-
 src/USER-REAXC/fix_reaxc_bonds.cpp                 |     27 +-
 src/USER-REAXC/fix_reaxc_bonds.h                   |      3 +-
 src/USER-REAXC/fix_reaxc_species.h                 |      1 -
 src/USER-REAXC/pair_reax_c.cpp                     |      5 +-
 src/USER-REAXC/reaxc_basic_comm.cpp                |      2 +-
 src/USER-REAXC/reaxc_ffield.cpp                    |      2 +-
 src/USER-REAXC/reaxc_io_tools.cpp                  |     80 +-
 src/USER-REAXC/reaxc_io_tools.h                    |      4 -
 src/USER-REAXC/reaxc_nonbonded.cpp                 |      6 +-
 src/USER-REAXC/reaxc_tool_box.cpp                  |      8 +-
 src/USER-REAXC/reaxc_tool_box.h                    |      6 +-
 src/USER-REAXC/reaxc_types.h                       |     19 +-
 src/USER-SPH/atom_vec_meso.cpp                     |    168 +-
 src/USER-SPH/atom_vec_meso.h                       |      7 +-
 src/VORONOI/compute_voronoi_atom.cpp               |     28 +-
 src/VORONOI/compute_voronoi_atom.h                 |     13 +-
 src/WINDOWS/LAMMPS.sln                             |     36 -
 src/WINDOWS/LAMMPS.vcproj                          |   2957 -
 src/WINDOWS/LAMMPS.vsmacros                        |    Bin 182784 -> 0 bytes
 src/WINDOWS/README.txt                             |     78 -
 src/WINDOWS/STUBS.vcproj                           |    156 -
 src/WINDOWS/extra/dirent.h                         |    372 -
 src/WINDOWS/extra/erf.h                            |     19 -
 src/WINDOWS/extra/erf_namd.c                       |    345 -
 src/WINDOWS/extra/fftw2/FFTW2dll.dll               |    Bin 263168 -> 0 bytes
 src/WINDOWS/extra/fftw2/FFTW2dll.lib               |    Bin 22998 -> 0 bytes
 src/WINDOWS/extra/fftw2/FFTW2st.lib                |    Bin 404572 -> 0 bytes
 src/WINDOWS/extra/fftw2/RFFTW2dll.dll              |    Bin 481792 -> 0 bytes
 src/WINDOWS/extra/fftw2/RFFTW2dll.lib              |    Bin 35830 -> 0 bytes
 src/WINDOWS/extra/fftw2/RFFTW2st.lib               |    Bin 337962 -> 0 bytes
 src/WINDOWS/extra/fftw2/fftw.h                     |    421 -
 src/WINDOWS/extra/inttypes.h                       |    305 -
 src/WINDOWS/extra/sleep.cpp                        |     10 -
 src/WINDOWS/extra/sleep.h                          |      1 -
 src/WINDOWS/extra/stdint.h                         |    247 -
 src/WINDOWS/extra/sys/time.h                       |     28 -
 src/WINDOWS/extra/unistd.h                         |      1 -
 src/WINDOWS/settings/style_angle.h                 |      9 -
 src/WINDOWS/settings/style_atom.h                  |     12 -
 src/WINDOWS/settings/style_bond.h                  |      9 -
 src/WINDOWS/settings/style_command.h               |     16 -
 src/WINDOWS/settings/style_compute.h               |     44 -
 src/WINDOWS/settings/style_dihedral.h              |      7 -
 src/WINDOWS/settings/style_dump.h                  |      8 -
 src/WINDOWS/settings/style_fix.h                   |     69 -
 src/WINDOWS/settings/style_improper.h              |      5 -
 src/WINDOWS/settings/style_integrate.h             |      3 -
 src/WINDOWS/settings/style_kspace.h                |      5 -
 src/WINDOWS/settings/style_minimize.h              |      6 -
 src/WINDOWS/settings/style_pair.h                  |     49 -
 src/WINDOWS/settings/style_region.h                |      9 -
 src/XTC/dump_xtc.cpp                               |      6 +-
 src/XTC/dump_xtc.h                                 |      2 +-
 src/XTC/xdr_compat.h                               |      5 +-
 src/accelerator_kokkos.h                           |     70 +
 src/accelerator_omp.h                              |      3 +-
 src/atom.cpp                                       |    679 +-
 src/atom.h                                         |    160 +-
 src/atom_map.cpp                                   |    156 +-
 src/atom_masks.h                                   |     62 +-
 src/atom_vec.cpp                                   |    114 +-
 src/atom_vec.h                                     |     53 +-
 src/atom_vec_atomic.cpp                            |    105 +-
 src/atom_vec_atomic.h                              |     11 +-
 src/atom_vec_body.cpp                              |    272 +-
 src/atom_vec_body.h                                |     21 +-
 src/atom_vec_charge.cpp                            |    106 +-
 src/atom_vec_charge.h                              |     11 +-
 src/atom_vec_ellipsoid.cpp                         |    166 +-
 src/atom_vec_ellipsoid.h                           |     11 +-
 src/atom_vec_hybrid.cpp                            |     99 +-
 src/atom_vec_hybrid.h                              |     19 +-
 src/atom_vec_line.cpp                              |    204 +-
 src/atom_vec_line.h                                |     13 +-
 src/atom_vec_sphere.cpp                            |    116 +-
 src/atom_vec_sphere.h                              |     11 +-
 src/atom_vec_tri.cpp                               |    201 +-
 src/atom_vec_tri.h                                 |     13 +-
 src/balance.cpp                                    |    110 -
 src/balance.h                                      |      1 -
 src/body.h                                         |      8 +-
 src/change_box.cpp                                 |      2 +-
 src/change_box.h                                   |      5 -
 src/citeme.cpp                                     |      2 +-
 src/citeme.h                                       |      6 +
 src/compute.cpp                                    |     20 +-
 src/compute.h                                      |      6 +-
 src/compute_angle_local.cpp                        |     53 +-
 src/compute_atom_molecule.cpp                      |     12 +-
 src/compute_atom_molecule.h                        |      2 +-
 src/compute_bond_local.cpp                         |     41 +-
 src/compute_cluster_atom.cpp                       |      2 +-
 src/compute_com_molecule.cpp                       |     22 +-
 src/compute_com_molecule.h                         |      2 +-
 src/compute_dihedral_local.cpp                     |     48 +-
 src/compute_displace_atom.cpp                      |      4 +-
 src/compute_gyration.cpp                           |      2 +-
 src/compute_gyration_molecule.cpp                  |     48 +-
 src/compute_gyration_molecule.h                    |      2 +-
 src/compute_improper_local.cpp                     |     48 +-
 src/compute_inertia_molecule.cpp                   |     21 +-
 src/compute_inertia_molecule.h                     |      2 +-
 src/compute_msd.cpp                                |      4 +-
 src/compute_msd_molecule.cpp                       |     28 +-
 src/compute_msd_molecule.h                         |      2 +-
 src/compute_pressure.cpp                           |     41 +-
 src/compute_property_atom.cpp                      |     22 +-
 src/compute_property_atom.h                        |     10 +
 src/compute_property_local.cpp                     |     68 +-
 src/compute_property_local.h                       |      4 +
 src/compute_property_molecule.cpp                  |     12 +-
 src/compute_property_molecule.h                    |      2 +-
 src/compute_stress_atom.cpp                        |    127 +-
 src/compute_stress_atom.h                          |      7 +-
 src/compute_temp_ramp.h                            |      5 -
 src/compute_vacf.h                                 |      2 +-
 src/create_atoms.cpp                               |    320 +-
 src/create_atoms.h                                 |     50 +-
 src/create_box.cpp                                 |     63 +-
 src/create_box.h                                   |     21 +-
 src/delete_atoms.cpp                               |     22 +-
 src/delete_atoms.h                                 |      2 +-
 src/delete_bonds.cpp                               |      3 +-
 src/displace_atoms.cpp                             |      2 +-
 src/displace_atoms.h                               |      5 -
 src/domain.cpp                                     |    136 +-
 src/domain.h                                       |     22 +-
 src/dump.cpp                                       |    174 +-
 src/dump.h                                         |     48 +-
 src/dump_atom.cpp                                  |    124 +-
 src/dump_atom.h                                    |     35 +-
 src/dump_cfg.cpp                                   |    147 +-
 src/dump_cfg.h                                     |     10 +-
 src/dump_custom.cpp                                |    152 +-
 src/dump_custom.h                                  |     22 +-
 src/dump_dcd.cpp                                   |      6 +-
 src/dump_dcd.h                                     |      4 +-
 src/dump_image.cpp                                 |     39 +-
 src/dump_image.h                                   |      5 +
 src/dump_local.cpp                                 |     57 +-
 src/dump_local.h                                   |     10 +-
 src/dump_movie.cpp                                 |      2 +-
 src/dump_movie.h                                   |     20 +-
 src/dump_xyz.cpp                                   |     55 +-
 src/dump_xyz.h                                     |     16 +-
 src/finish.cpp                                     |     22 +-
 src/fix.cpp                                        |      6 +-
 src/fix.h                                          |     22 +
 src/fix_adapt.cpp                                  |     12 +-
 src/fix_addforce.cpp                               |      2 +-
 src/fix_ave_spatial.cpp                            |     22 +-
 src/fix_ave_spatial.h                              |     13 +-
 src/fix_ave_time.cpp                               |      2 +-
 src/fix_deform.cpp                                 |      2 +-
 src/fix_deform.h                                   |      4 -
 src/fix_deposit.cpp                                |    508 -
 src/fix_deposit.h                                  |    100 -
 src/fix_dt_reset.h                                 |      5 -
 src/fix_external.h                                 |      2 +-
 src/fix_group.cpp                                  |    207 +
 src/fix_group.h                                    |     53 +
 src/fix_heat.cpp                                   |      1 -
 src/fix_indent.h                                   |      5 -
 src/fix_langevin.cpp                               |      1 -
 src/fix_momentum.cpp                               |      2 +-
 src/fix_move.cpp                                   |      4 +-
 src/fix_move.h                                     |      5 -
 src/fix_nh.cpp                                     |      2 +-
 src/fix_nve_limit.h                                |      6 +-
 src/fix_property_atom.cpp                          |    154 +-
 src/fix_property_atom.h                            |     45 +-
 src/fix_recenter.h                                 |      5 -
 src/fix_restrain.cpp                               |      4 +-
 src/fix_shake.cpp                                  |   2481 -
 src/fix_shake.h                                    |    235 -
 src/fix_shear_history.cpp                          |     12 +-
 src/fix_shear_history.h                            |     12 +-
 src/fix_spring_rg.cpp                              |      2 +-
 src/fix_spring_self.cpp                            |      4 +-
 src/fix_store.h                                    |      4 +-
 src/fix_store_state.cpp                            |     22 +-
 src/fix_temp_rescale.cpp                           |      2 +-
 src/fix_tmd.cpp                                    |     14 +-
 src/fix_vector.cpp                                 |    315 +
 src/fix_vector.h                                   |     55 +
 src/fix_wall.h                                     |      5 -
 src/fix_wall_harmonic.h                            |      5 +-
 src/fix_wall_reflect.h                             |      5 -
 src/force.cpp                                      |     58 +
 src/force.h                                        |     10 +-
 src/group.cpp                                      |    210 +-
 src/group.h                                        |      1 +
 src/image.cpp                                      |     40 +-
 src/image.h                                        |      4 -
 src/input.cpp                                      |     16 +-
 src/input.h                                        |     15 +-
 src/kspace.cpp                                     |     28 +
 src/kspace.h                                       |     20 +-
 src/lammps.cpp                                     |    282 +-
 src/lammps.h                                       |     20 +-
 src/library.cpp                                    |      4 +-
 src/lmptype.h                                      |     22 +-
 src/lmpwindows.h                                   |      7 +
 src/main.cpp                                       |      2 +
 src/memory.h                                       |    729 +-
 src/min_fire.cpp                                   |      8 +-
 src/min_quickmin.cpp                               |      8 +-
 src/modify.h                                       |     43 +-
 src/molecule.cpp                                   |   1424 +
 src/molecule.h                                     |    310 +
 src/mpiio.h                                        |     51 +
 src/my_pool_chunk.h                                |      1 +
 src/neigh_bond.cpp                                 |    638 +-
 src/neigh_bond.h                                   |     27 +
 src/neigh_full.cpp                                 |    167 +-
 src/neigh_gran.cpp                                 |     22 +-
 src/neigh_half_bin.cpp                             |    152 +-
 src/neigh_half_multi.cpp                           |    121 +-
 src/neigh_half_nsq.cpp                             |    105 +-
 src/neigh_request.cpp                              |     24 +-
 src/neigh_request.h                                |      9 +
 src/neigh_respa.cpp                                |    194 +-
 src/neighbor.cpp                                   |     30 +-
 src/neighbor.h                                     |     10 +-
 src/output.cpp                                     |     40 +-
 src/output.h                                       |      8 +
 src/pair.h                                         |      6 +-
 src/pair_born.cpp                                  |     28 +-
 src/pair_born.h                                    |      2 +
 src/pair_born_coul_wolf.cpp                        |     29 +-
 src/pair_born_coul_wolf.h                          |      2 +
 src/pair_buck.cpp                                  |     27 +-
 src/pair_buck.h                                    |      2 +
 src/pair_buck_coul_cut.cpp                         |     30 +-
 src/pair_buck_coul_cut.h                           |      2 +
 src/pair_coul_dsf.cpp                              |     36 +-
 src/pair_coul_wolf.cpp                             |      2 +-
 src/pair_dpd.cpp                                   |     22 +
 src/pair_dpd.h                                     |      6 +-
 src/pair_dpd_tstat.cpp                             |     68 +
 src/pair_dpd_tstat.h                               |      4 +
 src/pair_hybrid.cpp                                |     34 +-
 src/pair_lj96_cut.cpp                              |     22 +
 src/pair_lj96_cut.h                                |      2 +
 src/pair_lj_cut_coul_dsf.cpp                       |     15 +-
 src/pair_lj_gromacs.cpp                            |     27 +-
 src/pair_lj_gromacs.h                              |      2 +
 src/pair_lj_gromacs_coul_gromacs.cpp               |     29 +-
 src/pair_lj_gromacs_coul_gromacs.h                 |      2 +
 src/pair_lj_smooth.cpp                             |     27 +-
 src/pair_lj_smooth.h                               |      2 +
 src/pair_morse.cpp                                 |     27 +-
 src/pair_morse.h                                   |      2 +
 src/pair_soft.cpp                                  |     26 +-
 src/pair_soft.h                                    |      2 +
 src/pair_table.cpp                                 |      2 +-
 src/pair_table.h                                   |      3 +-
 src/pair_yukawa.cpp                                |     26 +-
 src/pair_yukawa.h                                  |      2 +
 src/read_data.cpp                                  |   1516 +-
 src/read_data.h                                    |    148 +-
 src/read_dump.cpp                                  |     38 +-
 src/read_dump.h                                    |      6 +-
 src/read_restart.cpp                               |    689 +-
 src/read_restart.h                                 |     96 +-
 src/region.h                                       |      5 -
 src/region_intersect.h                             |      5 +
 src/replicate.cpp                                  |    131 +-
 src/replicate.h                                    |      5 +-
 src/respa.cpp                                      |     19 +-
 src/respa.h                                        |      9 -
 src/set.cpp                                        |     27 +-
 src/set.h                                          |     47 +-
 src/special.cpp                                    |     85 +-
 src/special.h                                      |      2 +-
 src/thermo.cpp                                     |     12 +-
 src/thermo.h                                       |     14 +-
 src/variable.cpp                                   |    311 +-
 src/variable.h                                     |     33 +-
 src/velocity.cpp                                   |      3 +-
 src/velocity.h                                     |     14 +-
 src/verlet.h                                       |      2 +-
 src/version.h                                      |      2 +-
 src/write_data.cpp                                 |    114 +-
 src/write_data.h                                   |     12 +-
 src/write_dump.h                                   |      9 +-
 src/write_restart.cpp                              |    466 +-
 src/write_restart.h                                |     42 +-
 tools/Makefile                                     |      3 -
 tools/README                                       |      4 +-
 tools/colvars/Makefile                             |     24 +
 tools/colvars/abf_data.cpp                         |    341 +
 tools/colvars/abf_data.h                           |     94 +
 tools/colvars/abf_integrate.cpp                    |    343 +
 tools/moltemplate/common/amber/amberparm2lt.sh     |     18 +-
 .../common/amber/amberparm_pair_to_lt.py           |     13 +-
 tools/moltemplate/common/gaff.lt                   |    162 +-
 .../calc_table/calc_CGLipidTableINTvsINT.py        |      5 -
 .../CG_biomolecules/membrane+protein/run.in.npt    |     11 +-
 .../CG_biomolecules/membrane+protein/run.in.nvt    |     38 +-
 .../moltemplate_files/calc_table/calc_table.py     |      5 -
 .../1beadProtSci2010/moltemplate_files/system.lt   |     13 -
 .../calc_table/calc_CGLipidTableINTvsINT.py        |      5 -
 .../packmol_files/README.sh                        |     13 +-
 .../vesicle_Brannigan2005+Bellesia2010/run.in.min  |      9 +-
 .../vesicle_Brannigan2005+Bellesia2010/run.in.nvt  |     15 +-
 .../examples/CG_misc/translocation/run.in.nvt      |      6 +
 .../CG_solvent/cyclododecane+watMW/run.in.npt      |      9 +-
 .../CG_solvent/cyclododecane+watMW/run.in.nvt      |     37 +-
 .../AMBER_force_field_examples/WARNING.TXT         |     72 +
 .../hexadecane/README.TXT                          |     44 +
 .../README_run.sh                                  |      0
 .../hexadecane/README_setup.sh                     |     74 +
 .../hexadecane}/README_visualize.txt               |      0
 .../hexadecane/WARNING.TXT                         |     16 +
 .../images/hexadecane_12x12x2_t=0_LR.jpg           |    Bin 0 -> 27017 bytes
 .../images/hexadecane_12x12x2_t=10ps_npt_LR.jpg    |    Bin 0 -> 36181 bytes
 .../hexadecane/images/hexadecane_LR.jpg            |    Bin 0 -> 5237 bytes
 .../hexadecane/moltemplate_files/ch2group.lt       |     49 +
 .../hexadecane/moltemplate_files/ch3group.lt       |     52 +
 .../hexadecane/moltemplate_files/hexadecane.lt     |     84 +
 .../hexadecane/moltemplate_files/system.lt         |     18 +
 .../hexadecane/run.in.npt                          |     85 +
 .../hexadecane/run.in.nvt                          |     42 +
 .../waterTIP3P+isobutane/README_setup.sh           |     27 +
 .../moltemplate_files/system.lt                    |      1 +
 .../waterTIP3P+isobutane/run.in.npt                |     14 +-
 .../waterTIP3P+isobutane/run.in.nvt                |     48 +-
 .../convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt  |    779 +
 .../all_atom_examples/hexadecane/README.TXT        |     38 +
 .../README_run.sh                                  |      0
 .../all_atom_examples/hexadecane/README_setup.sh   |     25 +
 .../hexadecane}/README_visualize.txt               |      0
 .../all_atom_examples/hexadecane/WARNING.TXT       |     16 +
 .../images/hexadecane_12x12x2_t=0_LR.jpg           |    Bin 0 -> 27017 bytes
 .../images/hexadecane_12x12x2_t=10ps_npt_LR.jpg    |    Bin 0 -> 36181 bytes
 .../hexadecane/images/hexadecane_LR.jpg            |    Bin 0 -> 5237 bytes
 .../hexadecane/moltemplate_files/alkanes.lt        |     84 +
 .../hexadecane/moltemplate_files/ch2group.lt       |     44 +
 .../hexadecane/moltemplate_files/ch3group.lt       |     44 +
 .../hexadecane/moltemplate_files/hexadecane.lt     |     84 +
 .../hexadecane/moltemplate_files/system.lt         |     18 +
 .../all_atom_examples/hexadecane/run.in.npt        |     85 +
 .../all_atom_examples/hexadecane/run.in.nvt        |     42 +
 .../nanotube+water/moltemplate_files/nanotube.lt   |     72 +
 .../all_atom_examples/nanotube+water/run.in.npt    |      6 +-
 .../all_atom_examples/nanotube+water/run.in.nvt    |     10 +-
 .../waterSPCE_from_PDBfile/run.in.npt              |     42 +-
 .../waterSPCE_from_PDBfile/run.in.nvt              |     63 +-
 .../all_atom_examples/waterSPCE+Na+Cl/run.in.npt   |     14 +-
 .../all_atom_examples/waterSPCE+Na+Cl/run.in.nvt   |     33 +-
 tools/moltemplate/src/dump2data.py                 |     13 +-
 tools/moltemplate/src/lttree.py                    |      4 +-
 tools/moltemplate/src/lttree_check.py              |      4 +-
 tools/moltemplate/src/moltemplate.sh               |     18 +-
 tools/moltemplate/src/nbody_by_type.py             |      4 +-
 tools/moltemplate/src/nbody_by_type_lib_old.py     |    312 -
 tools/moltemplate/src/postprocess_input_script.py  |      9 +-
 tools/moltemplate/src/raw2data.py                  |      3 -
 tools/moltemplate/src/ttree.py                     |      4 +-
 tools/restart2data.cpp                             |   4309 -
 1374 files changed, 218387 insertions(+), 223872 deletions(-)
 create mode 100644 bench/log.1Feb14.chain.fixed.linux.1
 create mode 100644 bench/log.1Feb14.chain.fixed.linux.4
 create mode 100644 bench/log.1Feb14.chain.scaled.linux.4
 create mode 100644 bench/log.1Feb14.chute.fixed.linux.1
 create mode 100644 bench/log.1Feb14.chute.fixed.linux.4
 create mode 100644 bench/log.1Feb14.chute.scaled.linux.4
 create mode 100644 bench/log.1Feb14.eam.fixed.linux.1
 create mode 100644 bench/log.1Feb14.eam.fixed.linux.4
 create mode 100644 bench/log.1Feb14.eam.scaled.linux.4
 create mode 100644 bench/log.1Feb14.lj.fixed.linux.1
 create mode 100644 bench/log.1Feb14.lj.fixed.linux.4
 create mode 100644 bench/log.1Feb14.lj.scaled.linux.4
 create mode 100644 bench/log.1Feb14.rhodo.fixed.linux.1
 create mode 100644 bench/log.1Feb14.rhodo.fixed.linux.4
 create mode 100644 bench/log.1Feb14.rhodo.scaled.linux.4
 delete mode 100644 bench/log.30Jul13.chain.fixed.linux.1
 delete mode 100644 bench/log.30Jul13.chain.fixed.linux.4
 delete mode 100644 bench/log.30Jul13.chain.scaled.linux.4
 delete mode 100644 bench/log.30Jul13.chute.fixed.linux.1
 delete mode 100644 bench/log.30Jul13.chute.fixed.linux.4
 delete mode 100644 bench/log.30Jul13.chute.scaled.linux.4
 delete mode 100644 bench/log.30Jul13.eam.fixed.linux.1
 delete mode 100644 bench/log.30Jul13.eam.fixed.linux.4
 delete mode 100644 bench/log.30Jul13.eam.scaled.linux.4
 delete mode 100644 bench/log.30Jul13.lj.fixed.linux.1
 delete mode 100644 bench/log.30Jul13.lj.fixed.linux.4
 delete mode 100644 bench/log.30Jul13.lj.scaled.linux.4
 delete mode 100644 bench/log.30Jul13.rhodo.fixed.linux.1
 delete mode 100644 bench/log.30Jul13.rhodo.fixed.linux.4
 delete mode 100644 bench/log.30Jul13.rhodo.scaled.linux.4
 create mode 100644 debian/tests/control
 create mode 100644 debian/tests/crack
 create mode 100644 debian/tests/in.crack
 create mode 100644 doc/PDF/PDLammps_EPS.pdf
 create mode 100644 doc/PDF/PDLammps_overview.pdf
 create mode 100644 doc/compute_dilatation_atom.html
 create mode 100644 doc/compute_dilatation_atom.txt
 create mode 100644 doc/compute_plasticity_atom.html
 create mode 100644 doc/compute_plasticity_atom.txt
 create mode 100644 doc/compute_vacf.html
 create mode 100644 doc/compute_vacf.txt
 create mode 100644 doc/fix_vector.html
 create mode 100644 doc/fix_vector.txt
 create mode 100644 doc/molecule.html
 create mode 100644 doc/molecule.txt
 delete mode 100644 examples/ASPHERE/box/log.box.10Sep13
 create mode 100644 examples/ASPHERE/box/log.box.1Feb14
 delete mode 100644 examples/ASPHERE/box/log.box.mp.10Sep13
 create mode 100644 examples/ASPHERE/box/log.box.mp.1Feb14
 delete mode 100644 examples/ASPHERE/dimer/log.dimer.10Sep13
 create mode 100644 examples/ASPHERE/dimer/log.dimer.1Feb14
 delete mode 100644 examples/ASPHERE/dimer/log.dimer.mp.10Sep13
 create mode 100644 examples/ASPHERE/dimer/log.dimer.mp.1Feb14
 delete mode 100644 examples/ASPHERE/ellipsoid/log.ellipsoid.10Sep13
 create mode 100644 examples/ASPHERE/ellipsoid/log.ellipsoid.1Feb14
 delete mode 100644 examples/ASPHERE/ellipsoid/log.ellipsoid.mp.10Sep13
 create mode 100644 examples/ASPHERE/ellipsoid/log.ellipsoid.mp.1Feb14
 delete mode 100644 examples/ASPHERE/line/log.line.10Sep13
 create mode 100644 examples/ASPHERE/line/log.line.1Feb14
 delete mode 100644 examples/ASPHERE/line/log.line.srd.10Sep13
 create mode 100644 examples/ASPHERE/line/log.line.srd.1Feb14
 delete mode 100644 examples/ASPHERE/poly/log.poly.10Sep13
 create mode 100644 examples/ASPHERE/poly/log.poly.1Feb14
 delete mode 100644 examples/ASPHERE/poly/log.poly.mp.10Sep13
 create mode 100644 examples/ASPHERE/poly/log.poly.mp.1Feb14
 delete mode 100644 examples/ASPHERE/star/log.star.10Sep13
 create mode 100644 examples/ASPHERE/star/log.star.1Feb14
 delete mode 100644 examples/ASPHERE/star/log.star.mp.10Sep13
 create mode 100644 examples/ASPHERE/star/log.star.mp.1Feb14
 delete mode 100644 examples/ASPHERE/tri/log.tri.srd.10Sep13
 create mode 100644 examples/ASPHERE/tri/log.tri.srd.1Feb14
 create mode 100644 examples/DIFFUSE/README
 create mode 100644 examples/DIFFUSE/in.msd.2d
 create mode 100644 examples/DIFFUSE/in.vacf.2d
 create mode 100644 examples/DIFFUSE/log.msd.2d.1Feb14
 create mode 100644 examples/DIFFUSE/log.vacf.2d.1Feb14
 delete mode 100644 examples/KAPPA/log.heat.12Sep13
 create mode 100644 examples/KAPPA/log.heat.1Feb14
 delete mode 100644 examples/KAPPA/log.heatflux.12Sep13
 create mode 100644 examples/KAPPA/log.heatflux.1Feb14
 delete mode 100644 examples/KAPPA/log.langevin.12Sep13
 create mode 100644 examples/KAPPA/log.langevin.1Feb14
 delete mode 100644 examples/KAPPA/log.mp.12Sep13
 create mode 100644 examples/KAPPA/log.mp.1Feb14
 delete mode 100644 examples/KAPPA/profile.heat.12Sep13
 copy examples/KAPPA/{profile.heatflux.12Sep13 => profile.heat.1Feb14} (100%)
 rename examples/KAPPA/{profile.heatflux.12Sep13 => profile.heatflux.1Feb14} (100%)
 delete mode 100644 examples/KAPPA/profile.langevin.12Sep13
 create mode 100644 examples/KAPPA/profile.langevin.1Feb14
 rename examples/KAPPA/{profile.mp.12Sep13 => profile.mp.1Feb14} (100%)
 delete mode 100644 examples/VISCOSITY/log.gk.2d.12Sep13
 create mode 100644 examples/VISCOSITY/log.gk.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/log.mp.2d.12Sep13
 create mode 100644 examples/VISCOSITY/log.mp.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/log.nemd.2d.12Sep13
 create mode 100644 examples/VISCOSITY/log.nemd.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/log.wall.2d.12Sep13
 create mode 100644 examples/VISCOSITY/log.wall.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/profile.gk.2d.12Sep13
 create mode 100644 examples/VISCOSITY/profile.gk.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/profile.mp.2d.12Sep13
 create mode 100644 examples/VISCOSITY/profile.mp.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/profile.nemd.2d.12Sep13
 create mode 100644 examples/VISCOSITY/profile.nemd.2d.1Feb14
 delete mode 100644 examples/VISCOSITY/profile.wall.2d.12Sep13
 create mode 100644 examples/VISCOSITY/profile.wall.2d.1Feb14
 delete mode 100644 examples/body/log.body.18Feb13.linux.1
 delete mode 100644 examples/body/log.body.18Feb13.linux.4
 create mode 100644 examples/body/log.body.1Feb14.linux.1
 create mode 100644 examples/body/log.body.1Feb14.linux.4
 delete mode 100644 examples/colloid/log.colloid.18Feb13.linux.1
 delete mode 100644 examples/colloid/log.colloid.18Feb13.linux.4
 create mode 100644 examples/colloid/log.colloid.1Feb14.linux.1
 create mode 100644 examples/colloid/log.colloid.1Feb14.linux.4
 delete mode 100644 examples/comb/log.comb.Cu.18Feb13.linux.1
 delete mode 100644 examples/comb/log.comb.Cu.18Feb13.linux.4
 create mode 100644 examples/comb/log.comb.Cu.1Feb14.linux.1
 create mode 100644 examples/comb/log.comb.Cu.1Feb14.linux.4
 delete mode 100644 examples/comb/log.comb.Cu2O.elastic.18Feb13.linux.1
 delete mode 100644 examples/comb/log.comb.Cu2O.elastic.18Feb13.linux.4
 create mode 100644 examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1
 create mode 100644 examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4
 delete mode 100644 examples/comb/log.comb.HfO2.18Feb13.linux.1
 delete mode 100644 examples/comb/log.comb.HfO2.18Feb13.linux.4
 create mode 100644 examples/comb/log.comb.HfO2.1Feb14.linux.1
 create mode 100644 examples/comb/log.comb.HfO2.1Feb14.linux.4
 delete mode 100644 examples/comb/log.comb.Si.18Feb13.linux.1
 delete mode 100644 examples/comb/log.comb.Si.18Feb13.linux.4
 create mode 100644 examples/comb/log.comb.Si.1Feb14.linux.1
 create mode 100644 examples/comb/log.comb.Si.1Feb14.linux.4
 delete mode 100644 examples/comb/log.comb.Si.elastic.18Feb13.linux.1
 delete mode 100644 examples/comb/log.comb.Si.elastic.18Feb13.linux.4
 create mode 100644 examples/comb/log.comb.Si.elastic.1Feb14.linux.1
 create mode 100644 examples/comb/log.comb.Si.elastic.1Feb14.linux.4
 create mode 100644 examples/comb/log.comb3.1Feb14.linux.1
 create mode 100644 examples/comb/log.comb3.1Feb14.linux.4
 delete mode 100644 examples/comb/log.comb3.4Nov13.linux.1
 delete mode 100644 examples/comb/log.comb3.4Nov13.linux.4
 delete mode 100644 examples/crack/log.crack.18Feb13.linux.1
 delete mode 100644 examples/crack/log.crack.18Feb13.linux.4
 create mode 100644 examples/crack/log.crack.1Feb14.linux.1
 create mode 100644 examples/crack/log.crack.1Feb14.linux.4
 create mode 100644 examples/deposit/in.deposit.atom
 create mode 100644 examples/deposit/in.deposit.molecule
 create mode 100644 examples/deposit/in.deposit.molecule.shake
 create mode 100644 examples/deposit/molecule.dimer
 create mode 100644 examples/deposit/molecule.dimer.shake
 delete mode 100644 examples/dipole/log.dipole.18Feb13.linux.1
 delete mode 100644 examples/dipole/log.dipole.18Feb13.linux.4
 create mode 100644 examples/dipole/log.dipole.1Feb14.linux.1
 create mode 100644 examples/dipole/log.dipole.1Feb14.linux.4
 delete mode 100644 examples/dreiding/log.dreiding.18Feb13.linux.1
 delete mode 100644 examples/dreiding/log.dreiding.18Feb13.linux.4
 create mode 100644 examples/dreiding/log.dreiding.1Feb14.linux.1
 create mode 100644 examples/dreiding/log.dreiding.1Feb14.linux.4
 delete mode 100644 examples/eim/log.eim.18Feb13.linux.1
 delete mode 100644 examples/eim/log.eim.18Feb13.linux.4
 create mode 100644 examples/eim/log.eim.1Feb14.linux.1
 create mode 100644 examples/eim/log.eim.1Feb14.linux.4
 delete mode 100644 examples/ellipse/log.ellipse.gayberne.18Feb13.linux.1
 delete mode 100644 examples/ellipse/log.ellipse.gayberne.18Feb13.linux.4
 create mode 100644 examples/ellipse/log.ellipse.gayberne.1Feb14.linux.1
 create mode 100644 examples/ellipse/log.ellipse.gayberne.1Feb14.linux.4
 delete mode 100644 examples/ellipse/log.ellipse.resquared.18Feb13.linux.1
 delete mode 100644 examples/ellipse/log.ellipse.resquared.18Feb13.linux.4
 create mode 100644 examples/ellipse/log.ellipse.resquared.1Feb14.linux.1
 create mode 100644 examples/ellipse/log.ellipse.resquared.1Feb14.linux.4
 delete mode 100644 examples/flow/log.flow.couette.18Feb13.linux.1
 delete mode 100644 examples/flow/log.flow.couette.18Feb13.linux.4
 create mode 100644 examples/flow/log.flow.couette.1Feb14.linux.1
 create mode 100644 examples/flow/log.flow.couette.1Feb14.linux.4
 delete mode 100644 examples/flow/log.flow.pois.18Feb13.linux.1
 delete mode 100644 examples/flow/log.flow.pois.18Feb13.linux.4
 create mode 100644 examples/flow/log.flow.pois.1Feb14.linux.1
 create mode 100644 examples/flow/log.flow.pois.1Feb14.linux.4
 delete mode 100644 examples/friction/log.friction.18Feb13.linux.1
 delete mode 100644 examples/friction/log.friction.18Feb13.linux.4
 create mode 100644 examples/friction/log.friction.1Feb14.linux.1
 create mode 100644 examples/friction/log.friction.1Feb14.linux.4
 delete mode 100644 examples/gpu/log.gpu.melt.2.5.18Feb13.linux.1
 delete mode 100644 examples/gpu/log.gpu.melt.2.5.18Feb13.linux.4
 create mode 100644 examples/gpu/log.gpu.melt.2.5.1Feb14.linux.1
 create mode 100644 examples/gpu/log.gpu.melt.2.5.1Feb14.linux.4
 delete mode 100644 examples/gpu/log.gpu.melt.5.0.18Feb13.linux.1
 delete mode 100644 examples/gpu/log.gpu.melt.5.0.18Feb13.linux.4
 create mode 100644 examples/gpu/log.gpu.melt.5.0.1Feb14.linux.1
 create mode 100644 examples/gpu/log.gpu.melt.5.0.1Feb14.linux.4
 delete mode 100644 examples/gpu/log.gpu.phosphate.18Feb13.linux.1
 delete mode 100644 examples/gpu/log.gpu.phosphate.18Feb13.linux.4
 create mode 100644 examples/gpu/log.gpu.phosphate.1Feb14.linux.1
 create mode 100644 examples/gpu/log.gpu.phosphate.1Feb14.linux.4
 delete mode 100644 examples/gpu/log.gpu.rhodo.18Feb13.linux.1
 delete mode 100644 examples/gpu/log.gpu.rhodo.18Feb13.linux.4
 create mode 100644 examples/gpu/log.gpu.rhodo.1Feb14.linux.1
 create mode 100644 examples/gpu/log.gpu.rhodo.1Feb14.linux.4
 delete mode 100644 examples/hugoniostat/log.hugoniostat.18Feb13.linux.1
 delete mode 100644 examples/hugoniostat/log.hugoniostat.18Feb13.linux.4
 create mode 100644 examples/hugoniostat/log.hugoniostat.1Feb14.linux.1
 create mode 100644 examples/hugoniostat/log.hugoniostat.1Feb14.linux.4
 delete mode 100644 examples/indent/log.indent.18Feb13.linux.1
 delete mode 100644 examples/indent/log.indent.18Feb13.linux.4
 create mode 100644 examples/indent/log.indent.1Feb14.linux.1
 create mode 100644 examples/indent/log.indent.1Feb14.linux.4
 delete mode 100644 examples/indent/log.indent.min.18Feb13.linux.1
 delete mode 100644 examples/indent/log.indent.min.18Feb13.linux.4
 create mode 100644 examples/indent/log.indent.min.1Feb14.linux.1
 create mode 100644 examples/indent/log.indent.min.1Feb14.linux.4
 delete mode 100644 examples/kim/log.kim.lj.26Jul13.mac_mpi.1
 delete mode 100644 examples/kim/log.kim.lj.26Jul13.mac_mpi.4
 delete mode 100644 examples/kim/log.kim.lj.lmp.26Jul13.mac_mpi.1
 delete mode 100644 examples/kim/log.kim.lj.lmp.26Jul13.mac_mpi.4
 delete mode 100644 examples/meam/log.meam.18Feb13.linux.1
 delete mode 100644 examples/meam/log.meam.18Feb13.linux.4
 create mode 100644 examples/meam/log.meam.1Feb14.linux.1
 create mode 100644 examples/meam/log.meam.1Feb14.linux.4
 delete mode 100644 examples/meam/log.meam.shear.18Feb13.linux.1
 delete mode 100644 examples/meam/log.meam.shear.18Feb13.linux.4
 create mode 100644 examples/meam/log.meam.shear.1Feb14.linux.1
 create mode 100644 examples/meam/log.meam.shear.1Feb14.linux.4
 delete mode 100644 examples/melt/log.melt.18Feb13.linux.1
 delete mode 100644 examples/melt/log.melt.18Feb13.linux.4
 create mode 100644 examples/melt/log.melt.1Feb14.linux.1
 create mode 100644 examples/melt/log.melt.1Feb14.linux.4
 delete mode 100644 examples/micelle/log.micelle.18Feb13.linux.1
 delete mode 100644 examples/micelle/log.micelle.18Feb13.linux.4
 create mode 100644 examples/micelle/log.micelle.1Feb14.linux.1
 create mode 100644 examples/micelle/log.micelle.1Feb14.linux.4
 delete mode 100644 examples/min/log.min.18Feb13.linux.1
 delete mode 100644 examples/min/log.min.18Feb13.linux.4
 create mode 100644 examples/min/log.min.1Feb14.linux.1
 create mode 100644 examples/min/log.min.1Feb14.linux.4
 delete mode 100644 examples/min/log.min.box.18Feb13.linux.1
 delete mode 100644 examples/min/log.min.box.18Feb13.linux.4
 create mode 100644 examples/min/log.min.box.1Feb14.linux.1
 create mode 100644 examples/min/log.min.box.1Feb14.linux.4
 delete mode 100644 examples/msst/log.msst.18Feb13.linux.1
 delete mode 100644 examples/msst/log.msst.18Feb13.linux.4
 create mode 100644 examples/msst/log.msst.1Feb14.linux.1
 create mode 100644 examples/msst/log.msst.1Feb14.linux.4
 copy {bench/POTENTIALS => examples/neb}/Si.sw (100%)
 create mode 100644 examples/neb/final.sivac
 create mode 100644 examples/neb/in.neb.sivac
 delete mode 100644 examples/neb/log.neb.hop1.18Feb13.linux.4
 create mode 100644 examples/neb/log.neb.hop1.1Feb14.linux.4
 delete mode 100644 examples/neb/log.neb.hop2.18Feb13.linux.4
 create mode 100644 examples/neb/log.neb.hop2.1Feb14.linux.4
 create mode 100644 examples/neb/log.neb.sivac.1Feb14.linux.3
 delete mode 100644 examples/nemd/log.nemd.18Feb13.linux.1
 delete mode 100644 examples/nemd/log.nemd.18Feb13.linux.4
 create mode 100644 examples/nemd/log.nemd.1Feb14.linux.1
 create mode 100644 examples/nemd/log.nemd.1Feb14.linux.4
 delete mode 100644 examples/obstacle/log.obstacle.18Feb13.linux.1
 delete mode 100644 examples/obstacle/log.obstacle.18Feb13.linux.4
 create mode 100644 examples/obstacle/log.obstacle.1Feb14.linux.1
 create mode 100644 examples/obstacle/log.obstacle.1Feb14.linux.4
 delete mode 100644 examples/peptide/log.peptide.18Feb13.linux.1
 delete mode 100644 examples/peptide/log.peptide.18Feb13.linux.4
 create mode 100644 examples/peptide/log.peptide.1Feb14.linux.1
 create mode 100644 examples/peptide/log.peptide.1Feb14.linux.4
 delete mode 100644 examples/peri/log.peri.18Feb13.linux.1
 delete mode 100644 examples/peri/log.peri.18Feb13.linux.4
 create mode 100644 examples/peri/log.peri.1Feb14.linux.1
 create mode 100644 examples/peri/log.peri.1Feb14.linux.4
 create mode 100644 examples/pour/in.pour.2d.molecule
 delete mode 100644 examples/pour/log.pour.18Feb13.linux.1
 delete mode 100644 examples/pour/log.pour.18Feb13.linux.4
 create mode 100644 examples/pour/log.pour.1Feb14.linux.1
 create mode 100644 examples/pour/log.pour.1Feb14.linux.4
 delete mode 100644 examples/pour/log.pour.2d.18Feb13.linux.1
 delete mode 100644 examples/pour/log.pour.2d.18Feb13.linux.4
 create mode 100644 examples/pour/log.pour.2d.1Feb14.linux.1
 create mode 100644 examples/pour/log.pour.2d.1Feb14.linux.4
 create mode 100644 examples/pour/log.pour.2d.molecule.1Feb14.linux.1
 create mode 100644 examples/pour/log.pour.2d.molecule.1Feb14.linux.4
 create mode 100644 examples/pour/molecule.vshape
 delete mode 100644 examples/prd/log.prd.0.18Feb13.linux.4
 create mode 100644 examples/prd/log.prd.0.1Feb14.linux.4
 delete mode 100644 examples/prd/log.prd.1.18Feb13.linux.4
 create mode 100644 examples/prd/log.prd.1.1Feb14.linux.4
 delete mode 100644 examples/prd/log.prd.18Feb13.linux.4
 create mode 100644 examples/prd/log.prd.1Feb14.linux.4
 delete mode 100644 examples/prd/log.prd.2.18Feb13.linux.4
 create mode 100644 examples/prd/log.prd.2.1Feb14.linux.4
 delete mode 100644 examples/prd/log.prd.3.18Feb13.linux.4
 create mode 100644 examples/prd/log.prd.3.1Feb14.linux.4
 create mode 100644 examples/reax/AB/log.reaxc.AB.1Feb14.linux.1
 create mode 100644 examples/reax/AB/log.reaxc.AB.1Feb14.linux.4
 delete mode 100644 examples/reax/AB/log.reaxc.ab.18Feb11.linux.1
 delete mode 100644 examples/reax/AB/log.reaxc.ab.18Feb11.linux.4
 rename examples/reax/{Au_O => AuO}/README (100%)
 rename examples/reax/{Au_O => AuO}/data.AuO (100%)
 rename examples/reax/{Au_O => AuO}/ffield.reax.AuO (100%)
 create mode 100644 examples/reax/AuO/in.AuO
 rename examples/reax/{Au_O => AuO}/lmp_control (100%)
 create mode 100644 examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.1
 create mode 100644 examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.4
 rename examples/reax/{Au_O => AuO}/param.qeq (100%)
 delete mode 100644 examples/reax/Au_O/in.AuO
 delete mode 100644 examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.1
 delete mode 100644 examples/reax/Au_O/log.reaxc.auo.18Feb11.linux.4
 create mode 100644 examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.1
 create mode 100644 examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.4
 delete mode 100644 examples/reax/CHO/log.reaxc.cho.18Feb11.linux.1
 delete mode 100644 examples/reax/CHO/log.reaxc.cho.18Feb11.linux.4
 create mode 100644 examples/reax/FC/README
 create mode 100644 examples/reax/FC/data.FC
 rename examples/reax/{Fluorographene => FC}/ffield.reax.FC (100%)
 create mode 100644 examples/reax/FC/in.FC
 create mode 100644 examples/reax/FC/log.reaxc.FC.1Feb14.linux.1
 create mode 100644 examples/reax/FC/log.reaxc.FC.1Feb14.linux.4
 rename examples/reax/{Fe_O_H => FeOH3}/README (100%)
 rename examples/reax/{Fe_O_H => FeOH3}/data.FeOH3 (100%)
 rename examples/reax/{Fe_O_H => FeOH3}/ffield.reax.Fe_O_C_H (100%)
 create mode 100644 examples/reax/FeOH3/in.FeOH3
 rename examples/reax/{Fe_O_H => FeOH3}/lmp_control (100%)
 create mode 100644 examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.1
 create mode 100644 examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.4
 rename examples/reax/{Fe_O_H => FeOH3}/param.qeq (100%)
 delete mode 100644 examples/reax/Fe_O_H/in.FeOH3
 delete mode 100644 examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.1
 delete mode 100644 examples/reax/Fe_O_H/log.reaxc.feoh.18Feb11.linux.4
 delete mode 100644 examples/reax/Fluorographene/README
 delete mode 100644 examples/reax/Fluorographene/data.FC
 delete mode 100644 examples/reax/Fluorographene/dumpnpt.xyz
 delete mode 100644 examples/reax/Fluorographene/in.FC
 delete mode 100644 examples/reax/Fluorographene/log.FC
 create mode 100644 examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.1
 create mode 100644 examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.4
 delete mode 100644 examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.1
 delete mode 100644 examples/reax/RDX/log.reaxc.rdx.18Feb11.linux.4
 rename examples/reax/{V_O_H => VOH}/README (100%)
 rename examples/reax/{V_O_H => VOH}/data.VOH (100%)
 rename examples/reax/{V_O_H => VOH}/ffield.reax.V_O_C_H (100%)
 create mode 100644 examples/reax/VOH/in.VOH
 rename examples/reax/{V_O_H => VOH}/lmp_control (100%)
 create mode 100644 examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.1
 create mode 100644 examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.4
 rename examples/reax/{V_O_H => VOH}/param.qeq (100%)
 delete mode 100644 examples/reax/V_O_H/in.VOH
 delete mode 100644 examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.1
 delete mode 100644 examples/reax/V_O_H/log.reaxc.voh.18Feb11.linux.4
 rename examples/reax/{Zn_O_H => ZnOH2}/README (100%)
 rename examples/reax/{Zn_O_H => ZnOH2}/data.ZnOH2 (100%)
 rename examples/reax/{Zn_O_H => ZnOH2}/ffield.reax.ZnOH (100%)
 create mode 100644 examples/reax/ZnOH2/in.ZnOH2
 rename examples/reax/{Zn_O_H => ZnOH2}/lmp_control (100%)
 create mode 100644 examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.1
 create mode 100644 examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.4
 rename examples/reax/{Zn_O_H => ZnOH2}/param.qeq (100%)
 delete mode 100644 examples/reax/Zn_O_H/in.ZnOH2
 delete mode 100644 examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.1
 delete mode 100644 examples/reax/Zn_O_H/log.reaxc.znoh.18Feb11.linux.4
 delete mode 100644 examples/reax/log.reax.rdx.18Feb13.linux.1
 delete mode 100644 examples/reax/log.reax.rdx.18Feb13.linux.4
 create mode 100644 examples/reax/log.reax.rdx.1Feb14.linux.1
 create mode 100644 examples/reax/log.reax.rdx.1Feb14.linux.4
 delete mode 100644 examples/reax/log.reax.tatb.18Feb13.linux.1
 delete mode 100644 examples/reax/log.reax.tatb.18Feb13.linux.4
 create mode 100644 examples/reax/log.reax.tatb.1Feb14.linux.1
 create mode 100644 examples/reax/log.reax.tatb.1Feb14.linux.4
 delete mode 100644 examples/reax/log.reaxc.rdx.18Feb13.linux.1
 delete mode 100644 examples/reax/log.reaxc.rdx.18Feb13.linux.4
 create mode 100644 examples/reax/log.reaxc.rdx.1Feb14.linux.1
 create mode 100644 examples/reax/log.reaxc.rdx.1Feb14.linux.4
 delete mode 100644 examples/reax/log.reaxc.tatb.18Feb13.linux.1
 delete mode 100644 examples/reax/log.reaxc.tatb.18Feb13.linux.4
 create mode 100644 examples/reax/log.reaxc.tatb.1Feb14.linux.1
 create mode 100644 examples/reax/log.reaxc.tatb.1Feb14.linux.4
 delete mode 100644 examples/rigid/log.rigid.18Feb13.linux.1
 delete mode 100644 examples/rigid/log.rigid.18Feb13.linux.4
 create mode 100644 examples/rigid/log.rigid.1Feb14.linux.1
 create mode 100644 examples/rigid/log.rigid.1Feb14.linux.4
 delete mode 100644 examples/rigid/log.rigid.poems.18Feb13.linux.1
 delete mode 100644 examples/rigid/log.rigid.poems.18Feb13.linux.4
 create mode 100644 examples/rigid/log.rigid.poems.1Feb14.linux.1
 create mode 100644 examples/rigid/log.rigid.poems.1Feb14.linux.4
 delete mode 100644 examples/rigid/log.rigid.poems2.18Feb13.linux.1
 delete mode 100644 examples/rigid/log.rigid.poems2.18Feb13.linux.4
 create mode 100644 examples/rigid/log.rigid.poems2.1Feb14.linux.1
 create mode 100644 examples/rigid/log.rigid.poems2.1Feb14.linux.4
 create mode 100644 examples/rigid/log.rigid.tnr.1Feb14.linux.1
 create mode 100644 examples/rigid/log.rigid.tnr.1Feb14.linux.4
 delete mode 100644 examples/shear/log.shear.18Feb13.linux.1
 delete mode 100644 examples/shear/log.shear.18Feb13.linux.4
 create mode 100644 examples/shear/log.shear.1Feb14.linux.1
 create mode 100644 examples/shear/log.shear.1Feb14.linux.4
 delete mode 100644 examples/shear/log.shear.void.18Feb13.linux.1
 delete mode 100644 examples/shear/log.shear.void.18Feb13.linux.4
 create mode 100644 examples/shear/log.shear.void.1Feb14.linux.1
 create mode 100644 examples/shear/log.shear.void.1Feb14.linux.4
 delete mode 100644 examples/srd/log.srd.mixture.18Feb13.linux.1
 delete mode 100644 examples/srd/log.srd.mixture.18Feb13.linux.4
 create mode 100644 examples/srd/log.srd.mixture.1Feb14.linux.1
 create mode 100644 examples/srd/log.srd.mixture.1Feb14.linux.4
 delete mode 100644 examples/srd/log.srd.pure.18Feb13.linux.1
 delete mode 100644 examples/srd/log.srd.pure.18Feb13.linux.4
 create mode 100644 examples/srd/log.srd.pure.1Feb14.linux.1
 create mode 100644 examples/srd/log.srd.pure.1Feb14.linux.4
 delete mode 100644 examples/tad/log.tad.0.18Feb13.linux.3
 create mode 100644 examples/tad/log.tad.0.1Feb14.linux.3
 delete mode 100644 examples/tad/log.tad.1.18Feb13.linux.3
 create mode 100644 examples/tad/log.tad.1.1Feb14.linux.3
 delete mode 100644 examples/tad/log.tad.18Feb13.linux.3
 create mode 100644 examples/tad/log.tad.1Feb14.linux.3
 delete mode 100644 examples/tad/log.tad.2.18Feb13.linux.3
 create mode 100644 examples/tad/log.tad.2.1Feb14.linux.3
 delete mode 100644 examples/tad/log.tad.neb.18Feb13.linux.3
 create mode 100644 examples/tad/log.tad.neb.1Feb14.linux.3
 delete mode 100644 examples/voronoi/log.voronoi.4Aug13.macos.1
 delete mode 100644 examples/voronoi/log.voronoi.4Aug13.macos.4
 create mode 100644 lib/gpu/lal_lj_gromacs.cpp
 create mode 100644 lib/gpu/lal_lj_gromacs.cu
 create mode 100644 lib/gpu/lal_lj_gromacs.h
 create mode 100644 lib/gpu/lal_lj_gromacs_ext.cpp
 create mode 100644 src/.gitignore
 create mode 100644 src/GPU/pair_lj_gromacs_gpu.cpp
 create mode 100644 src/GPU/pair_lj_gromacs_gpu.h
 create mode 100644 src/MAKE/Makefile.mingw32-cross
 create mode 100644 src/MAKE/Makefile.mingw32-cross-mpi
 create mode 100644 src/MAKE/Makefile.mingw64-cross
 create mode 100644 src/MAKE/Makefile.mingw64-cross-mpi
 create mode 100644 src/MISC/fix_deposit.cpp
 create mode 100644 src/MISC/fix_deposit.h
 create mode 100644 src/MOLECULE/atom_vec_template.cpp
 create mode 100644 src/MOLECULE/atom_vec_template.h
 create mode 100644 src/MPIIO/Install.sh
 create mode 100644 src/MPIIO/dump_atom_mpiio.cpp
 create mode 100644 src/MPIIO/dump_atom_mpiio.h
 create mode 100644 src/MPIIO/dump_custom_mpiio.cpp
 create mode 100644 src/MPIIO/dump_custom_mpiio.h
 create mode 100644 src/MPIIO/dump_xyz_mpiio.cpp
 create mode 100644 src/MPIIO/dump_xyz_mpiio.h
 create mode 100644 src/MPIIO/restart_mpiio.cpp
 create mode 100644 src/MPIIO/restart_mpiio.h
 create mode 100644 src/PERI/compute_dilatation_atom.cpp
 create mode 100644 src/PERI/compute_dilatation_atom.h
 create mode 100644 src/PERI/compute_plasticity_atom.cpp
 create mode 100644 src/PERI/compute_plasticity_atom.h
 create mode 100644 src/PERI/pair_peri_eps.cpp
 create mode 100644 src/PERI/pair_peri_eps.h
 create mode 100644 src/RIGID/fix_shake.cpp
 create mode 100644 src/RIGID/fix_shake.h
 delete mode 100644 src/USER-CG-CMM/angle_cg_cmm.cpp
 delete mode 100644 src/USER-CG-CMM/angle_cg_cmm.h
 delete mode 100644 src/USER-CG-CMM/cg_cmm_parms.cpp
 delete mode 100644 src/USER-CG-CMM/cg_cmm_parms.h
 delete mode 100644 src/USER-CG-CMM/pair_cg_cmm.cpp
 delete mode 100644 src/USER-CG-CMM/pair_cg_cmm.h
 delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp
 delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_cut.h
 delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
 delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_long.h
 delete mode 100644 src/USER-CG-CMM/pair_cmm_common.cpp
 delete mode 100644 src/USER-CG-CMM/pair_cmm_common.h
 delete mode 100644 src/WINDOWS/LAMMPS.sln
 delete mode 100644 src/WINDOWS/LAMMPS.vcproj
 delete mode 100644 src/WINDOWS/LAMMPS.vsmacros
 delete mode 100644 src/WINDOWS/README.txt
 delete mode 100644 src/WINDOWS/STUBS.vcproj
 delete mode 100644 src/WINDOWS/extra/dirent.h
 delete mode 100644 src/WINDOWS/extra/erf.h
 delete mode 100644 src/WINDOWS/extra/erf_namd.c
 delete mode 100644 src/WINDOWS/extra/fftw2/FFTW2dll.dll
 delete mode 100644 src/WINDOWS/extra/fftw2/FFTW2dll.lib
 delete mode 100644 src/WINDOWS/extra/fftw2/FFTW2st.lib
 delete mode 100644 src/WINDOWS/extra/fftw2/RFFTW2dll.dll
 delete mode 100644 src/WINDOWS/extra/fftw2/RFFTW2dll.lib
 delete mode 100644 src/WINDOWS/extra/fftw2/RFFTW2st.lib
 delete mode 100644 src/WINDOWS/extra/fftw2/fftw.h
 delete mode 100644 src/WINDOWS/extra/inttypes.h
 delete mode 100644 src/WINDOWS/extra/sleep.cpp
 delete mode 100644 src/WINDOWS/extra/sleep.h
 delete mode 100644 src/WINDOWS/extra/stdint.h
 delete mode 100644 src/WINDOWS/extra/sys/time.h
 delete mode 100644 src/WINDOWS/extra/unistd.h
 delete mode 100644 src/WINDOWS/settings/style_angle.h
 delete mode 100644 src/WINDOWS/settings/style_atom.h
 delete mode 100644 src/WINDOWS/settings/style_bond.h
 delete mode 100644 src/WINDOWS/settings/style_command.h
 delete mode 100644 src/WINDOWS/settings/style_compute.h
 delete mode 100644 src/WINDOWS/settings/style_dihedral.h
 delete mode 100644 src/WINDOWS/settings/style_dump.h
 delete mode 100644 src/WINDOWS/settings/style_fix.h
 delete mode 100644 src/WINDOWS/settings/style_improper.h
 delete mode 100644 src/WINDOWS/settings/style_integrate.h
 delete mode 100644 src/WINDOWS/settings/style_kspace.h
 delete mode 100644 src/WINDOWS/settings/style_minimize.h
 delete mode 100644 src/WINDOWS/settings/style_pair.h
 delete mode 100644 src/WINDOWS/settings/style_region.h
 create mode 100644 src/accelerator_kokkos.h
 delete mode 100644 src/fix_deposit.cpp
 delete mode 100644 src/fix_deposit.h
 create mode 100644 src/fix_group.cpp
 create mode 100644 src/fix_group.h
 delete mode 100644 src/fix_shake.cpp
 delete mode 100644 src/fix_shake.h
 create mode 100644 src/fix_vector.cpp
 create mode 100644 src/fix_vector.h
 create mode 100644 src/molecule.cpp
 create mode 100644 src/molecule.h
 create mode 100644 src/mpiio.h
 create mode 100644 tools/colvars/Makefile
 create mode 100644 tools/colvars/abf_data.cpp
 create mode 100644 tools/colvars/abf_data.h
 create mode 100644 tools/colvars/abf_integrate.cpp
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT
 copy tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/{waterTIP3P+isobutane => hexadecane}/README_run.sh (100%)
 create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh
 copy tools/moltemplate/examples/{CG_biomolecules/membrane+protein => all_atom_examples/AMBER_force_field_examples/hexadecane}/README_visualize.txt (100%)
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT
 copy tools/moltemplate/examples/all_atom_examples/{AMBER_force_field_examples/waterTIP3P+isobutane => hexadecane}/README_run.sh (100%)
 create mode 100755 tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh
 copy tools/moltemplate/examples/{CG_biomolecules/membrane+protein => all_atom_examples/hexadecane}/README_visualize.txt (100%)
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt
 create mode 100644 tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt
 delete mode 100644 tools/moltemplate/src/nbody_by_type_lib_old.py
 delete mode 100644 tools/restart2data.cpp

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/lammps.git



More information about the debian-science-commits mailing list