[lammps] 01/05: Merge tag 'upstream/0_20131119.git7162cf0'
Anton Gladky
gladk at moszumanska.debian.org
Wed Nov 20 22:20:15 UTC 2013
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository lammps.
commit b41848cb177f9ea19ed5106cc479067af445cdb7
Merge: 023c448 e65b919
Author: Anton Gladky <gladk at debian.org>
Date: Wed Nov 20 22:36:46 2013 +0100
Merge tag 'upstream/0_20131119.git7162cf0'
Upstream version 0~20131119.git7162cf0
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examples/ASPHERE/star/log.star.mp.10Sep13 | 290 +
examples/ASPHERE/star/star.py | 11 +
examples/ASPHERE/tri/data.tri.srd | 3013 +
examples/ASPHERE/tri/in.tri.srd | 105 +
examples/ASPHERE/tri/log.tri.srd.10Sep13 | 242 +
examples/ASPHERE/tri/tri.srd.py | 14 +
examples/ASPHERE/tri/tri.srd.viz.py | 18 +
examples/COUPLE/fortran2/LAMMPS.F90 | 1883 +-
examples/COUPLE/simple/README | 21 +-
examples/COUPLE/simple/in.lj | 2 +
examples/COUPLE/simple/simple.c | 4 +-
examples/ELASTIC/displace.mod | 24 +-
examples/ELASTIC/displace_restart.mod | 24 +-
examples/ELASTIC/displace_reverse.mod | 48 +-
examples/KAPPA/README | 89 +
examples/KAPPA/in.heat | 76 +
examples/KAPPA/in.heatflux | 79 +
examples/KAPPA/in.langevin | 88 +
examples/KAPPA/in.mp | 71 +
examples/KAPPA/log.heat.12Sep13 | 195 +
examples/KAPPA/log.heatflux.12Sep13 | 208 +
examples/KAPPA/log.langevin.12Sep13 | 215 +
examples/KAPPA/log.mp.12Sep13 | 200 +
examples/KAPPA/profile.heat.12Sep13 | 423 +
examples/KAPPA/profile.heatflux.12Sep13 |10254 ++
examples/KAPPA/profile.langevin.12Sep13 | 423 +
examples/KAPPA/profile.mp.12Sep13 | 843 +
examples/README | 11 +
examples/USER/atc/README | 255 +-
examples/USER/atc/bar1d_thermal/Ar_thermal.mat | 11 -
examples/USER/atc/bar1d_thermal/bar1d.log | 286 -
examples/USER/atc/bar1d_thermal/bar1d_flux.log | 334 -
examples/USER/atc/bar1d_thermal/in.bar1d | 100 -
examples/USER/atc/bar1d_thermal/in.bar1d_flux | 103 -
examples/USER/atc/bar1d_thermal/in.bar1d_frac_step | 112 -
examples/USER/atc/bar1d_thermal/temp.init | 2903 -
examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat | 35 -
examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat | 17 -
.../USER/atc/bar1d_two_temperature/bar1d_ttm.log | 537 -
.../atc/bar1d_two_temperature/gaussianIC_ttm.log | 168 -
.../USER/atc/bar1d_two_temperature/in.bar1d_ttm | 105 -
.../atc/bar1d_two_temperature/in.gaussianIC_ttm | 97 -
.../USER/atc/bar1d_two_temperature/in.no_atoms | 57 -
.../atc/bar1d_two_temperature/in.uniform_exchange | 67 -
.../atc/bar1d_two_temperature/in.uniform_heating | 74 -
.../USER/atc/bar1d_two_temperature/no_atoms.log | 190 -
examples/USER/atc/bar1d_two_temperature/temp.init | 6935 --
.../atc/bar1d_two_temperature/uniform_exchange.log | 672 -
.../uniform_exchange_init.data | 6935 --
.../atc/bar1d_two_temperature/uniform_heating.log | 91 -
.../uniform_heating_init.data | 4631 -
examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat | 7 +
.../USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat | 7 +
examples/USER/atc/cauchy_born/Au_CauchyBorn.mat | 6 +
.../USER/atc/cauchy_born/Au_CauchyBorn_linear.mat | 6 +
examples/USER/atc/cauchy_born/Au_eam.mat | 5 +
examples/USER/atc/cauchy_born/Au_eam_linear.mat | 6 +
examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat | 5 +
examples/USER/atc/cauchy_born/cb_biaxial.screen | 402 +
examples/USER/atc/cauchy_born/cb_shear.screen | 386 +
examples/USER/atc/cauchy_born/cb_unistrain.screen | 124 +
.../USER/atc/cauchy_born/cb_unistrain_eam.screen | 146 +
.../atc/cauchy_born/cb_unistrain_eam_linear.screen | 160 +
.../atc/cauchy_born/cb_unistrain_linear.screen | 163 +
examples/USER/atc/cauchy_born/cb_volumetric.screen | 391 +
examples/USER/atc/cauchy_born/flying_cube.screen | 569 +
examples/USER/atc/cauchy_born/ftcb_constV.screen | 302 +
examples/USER/atc/cauchy_born/in.cb_biaxial | 54 +
examples/USER/atc/cauchy_born/in.cb_shear | 55 +
examples/USER/atc/cauchy_born/in.cb_unistrain | 46 +
examples/USER/atc/cauchy_born/in.cb_unistrain_eam | 51 +
.../atc/cauchy_born/in.cb_unistrain_eam_linear | 51 +
.../USER/atc/cauchy_born/in.cb_unistrain_linear | 54 +
examples/USER/atc/cauchy_born/in.cb_volumetric | 49 +
examples/USER/atc/cauchy_born/in.flying_cube | 61 +
examples/USER/atc/cauchy_born/in.ftcb_constV | 74 +
examples/USER/atc/cauchy_born/in.read_xref | 37 +
examples/USER/atc/cauchy_born/read_xref.screen | 84 +
examples/USER/atc/drift_diffusion/Ar_ddm.mat | 37 +
examples/USER/atc/drift_diffusion/CNT_ddm.mat | 41 +
examples/USER/atc/drift_diffusion/Cu_cddm.mat | 45 +
.../atc/drift_diffusion/SiGe_ddm_schrodinger.mat | 86 +
.../drift_diffusion/SiVacuum_cddm_schrodinger.mat | 64 +
.../drift_diffusion/SiVacuum_ddm_schrodinger.mat | 52 +
examples/USER/atc/drift_diffusion/Si_ddm.mat | 35 +
examples/USER/atc/drift_diffusion/Si_ddm_eq.mat | 44 +
.../atc/drift_diffusion/Si_ddm_schrodinger.mat | 41 +
.../atc/drift_diffusion/Si_ddm_thermopower.mat | 36 +
.../atc/drift_diffusion/convective_pulse.screen | 145 +
.../atc/drift_diffusion/ddm_schrodinger.screen | 79 +
.../USER/atc/drift_diffusion/finite_well.screen | 106 +
.../USER/atc/drift_diffusion/in.convective_pulse | 72 +
.../USER/atc/drift_diffusion/in.ddm_schrodinger | 66 +
examples/USER/atc/drift_diffusion/in.finite_well | 75 +
examples/USER/atc/drift_diffusion/in.no_atoms_ddm | 65 +
.../USER/atc/drift_diffusion/in.null_material_ddm | 79 +
.../USER/atc/drift_diffusion/in.poisson1d_noatoms | 41 +
.../USER/atc/drift_diffusion/in.poisson2d_noatoms | 73 +
.../in.schrodinger-poisson2d_Jconstraint | 138 +
.../in.schrodinger-poisson2d_convective | 150 +
.../in.schrodinger-poisson2d_noatoms | 124 +
.../USER/atc/drift_diffusion/no_atoms_ddm.screen | 143 +
.../atc/drift_diffusion/null_material_ddm.screen | 159 +
.../atc/drift_diffusion/poisson1d_noatoms.screen | 42 +
.../atc/drift_diffusion/poisson2d_noatoms.screen | 110 +
.../schrodinger-poisson2d_Jconstraint.screen | 163 +
.../schrodinger-poisson2d_convective.screen | 220 +
.../schrodinger-poisson2d_noatoms.screen | 192 +
examples/USER/atc/elastic/Ar_CauchyBorn.mat | 8 +
examples/USER/atc/elastic/Ar_CauchyBornLinear.mat | 9 +
examples/USER/atc/elastic/Ar_damped.mat | 37 +
examples/USER/atc/elastic/Ar_elastic.mat | 29 +
examples/USER/atc/elastic/Ar_thermo_elastic.mat | 11 +
examples/USER/atc/elastic/Au_elastic.mat | 18 +
examples/USER/atc/elastic/CNT.mat | 1315 +
examples/USER/atc/elastic/CNT_electrostatic.mat | 18 +
examples/USER/atc/elastic/CNT_electrostatic2.mat | 21 +
examples/USER/atc/elastic/CNT_id.mat | 11 +
examples/USER/atc/elastic/bar1d.screen | 270 +
examples/USER/atc/elastic/bar1d_damped.screen | 385 +
examples/USER/atc/elastic/bar1d_flux.screen | 281 +
examples/USER/atc/elastic/bar1d_frac_step.screen | 228 +
examples/USER/atc/elastic/bar1d_ghost_flux.screen | 211 +
.../USER/atc/elastic/bar1d_thermo_elastic.screen | 113 +
examples/USER/atc/elastic/cnt_electrostatic.screen | 1213 +
.../USER/atc/elastic/cnt_electrostatic2.screen | 215 +
examples/USER/atc/elastic/cnt_fixed_charge.screen | 351 +
examples/USER/atc/elastic/eam_energy.screen | 335 +
examples/USER/atc/elastic/electron_density.screen | 267 +
.../USER/atc/elastic/electrostatic_bending.screen | 846 +
.../atc/elastic/electrostatic_bending_dos.screen | 633 +
examples/USER/atc/elastic/in.bar1d | 91 +
examples/USER/atc/elastic/in.bar1d_damped | 116 +
examples/USER/atc/elastic/in.bar1d_flux | 98 +
examples/USER/atc/elastic/in.bar1d_frac_step | 99 +
examples/USER/atc/elastic/in.bar1d_ghost_flux | 101 +
examples/USER/atc/elastic/in.bar1d_thermo_elastic | 139 +
examples/USER/atc/elastic/in.cnt_electrostatic | 107 +
examples/USER/atc/elastic/in.cnt_electrostatic2 | 118 +
examples/USER/atc/elastic/in.cnt_fixed_charge | 145 +
examples/USER/atc/elastic/in.eam_energy | 80 +
examples/USER/atc/elastic/in.electron_density | 74 +
examples/USER/atc/elastic/in.electrostatic_bending | 186 +
.../USER/atc/elastic/in.electrostatic_bending_dos | 164 +
examples/USER/atc/elastic/in.no_atoms | 42 +
examples/USER/atc/elastic/in.no_atoms_cb | 43 +
examples/USER/atc/elastic/in.no_atoms_cb_linear | 42 +
examples/USER/atc/elastic/no_atoms.screen | 75 +
examples/USER/atc/elastic/no_atoms_cb.screen | 78 +
.../USER/atc/elastic/no_atoms_cb_linear.screen | 79 +
examples/USER/atc/fluids/Ar_elastic.mat | 8 +
examples/USER/atc/fluids/Ar_electrostatic.mat | 8 +
examples/USER/atc/fluids/Ar_liquid.mat | 8 +
examples/USER/atc/fluids/Ar_species.mat | 5 +
examples/USER/atc/fluids/Ar_species_dl.mat | 8 +
examples/USER/atc/fluids/Ar_thermal.mat | 9 +
examples/USER/atc/fluids/Ar_visc_no_atoms.mat | 6 +
examples/USER/atc/fluids/Ar_viscosity.mat | 9 +
examples/USER/atc/fluids/bar1d_fluids.screen | 263 +
examples/USER/atc/fluids/concentration.screen | 169 +
.../USER/atc/fluids/conducting_interface.screen | 184 +
examples/USER/atc/fluids/dielectric.mat | 15 +
.../USER/atc/fluids/dielectric_interface.screen | 184 +
examples/USER/atc/fluids/double_layer.screen | 203 +
examples/USER/atc/fluids/in.bar1d_fluids | 98 +
examples/USER/atc/fluids/in.concentration | 172 +
examples/USER/atc/fluids/in.conducting_interface | 111 +
examples/USER/atc/fluids/in.dielectric_interface | 106 +
examples/USER/atc/fluids/in.double_layer | 100 +
examples/USER/atc/fluids/in.liquid_electrostatic | 63 +
examples/USER/atc/fluids/in.opp_force | 70 +
examples/USER/atc/fluids/in.poisson | 69 +
examples/USER/atc/fluids/in.shear_flow | 84 +
examples/USER/atc/fluids/in.shear_no_atoms | 32 +
.../USER/atc/fluids/liquid_electrostatic.screen | 143 +
examples/USER/atc/fluids/opp_force.screen | 146 +
examples/USER/atc/fluids/poisson.screen | 260 +
examples/USER/atc/fluids/shear_flow.screen | 65 +
examples/USER/atc/fluids/shear_no_atoms.screen | 91 +
examples/USER/atc/hardy/consistency.screen | 825 +-
.../USER/atc/hardy/eam_kernel_convergence.screen | 2755 +-
examples/USER/atc/hardy/eam_unistrain_cell.screen | 82 +-
examples/USER/atc/hardy/eam_unistrain_mesh.screen | 121 +-
.../USER/atc/hardy/eam_unistrain_qcylinder.screen | 79 +-
.../USER/atc/hardy/eam_unistrain_qsphere.screen | 79 +-
examples/USER/atc/hardy/eam_unistrain_step.screen | 121 +-
examples/USER/atc/hardy/eam_volume_stretch.screen | 128 +-
examples/USER/atc/hardy/eshelby_static.screen | 1688 +-
examples/USER/atc/hardy/in.consistency | 35 +-
examples/USER/atc/hardy/in.eam_kernel_convergence | 46 +-
examples/USER/atc/hardy/in.eam_unistrain_cell | 44 +-
examples/USER/atc/hardy/in.eam_unistrain_mesh | 46 +-
examples/USER/atc/hardy/in.eam_unistrain_qcylinder | 45 +-
examples/USER/atc/hardy/in.eam_unistrain_qsphere | 46 +-
examples/USER/atc/hardy/in.eam_unistrain_step | 46 +-
examples/USER/atc/hardy/in.eam_volume_stretch | 45 +-
examples/USER/atc/hardy/in.eshelby_static | 122 +-
examples/USER/atc/hardy/in.nvt | 53 +-
examples/USER/atc/hardy/nvt.screen | 132 +-
examples/USER/atc/mesh/Ar_ttm.mat | 35 +
examples/USER/atc/mesh/Si.mat | 9 +
examples/USER/atc/mesh/gaussianIC1d_hex.screen | 108 +
examples/USER/atc/mesh/gaussianIC2d_hex.screen | 287 +
.../atc/mesh/gaussianIC2d_hex20_uniform.screen | 107 +
.../atc/mesh/gaussianIC2d_hex27_uniform.screen | 99 +
.../USER/atc/mesh/gaussianIC2d_hex_uniform.screen | 126 +
examples/USER/atc/mesh/gaussianIC2d_tet.screen | 102 +
examples/USER/atc/mesh/in.gaussianIC1d_hex | 56 +
examples/USER/atc/mesh/in.gaussianIC2d_hex | 69 +
.../USER/atc/mesh/in.gaussianIC2d_hex20_uniform | 37 +
.../USER/atc/mesh/in.gaussianIC2d_hex27_uniform | 37 +
examples/USER/atc/mesh/in.gaussianIC2d_tet | 40 +
examples/USER/atc/mesh/in.kernel2d_hex | 32 +
examples/USER/atc/mesh/in.kernel2d_tet | 28 +
examples/USER/atc/mesh/in.mesh2d_tet | 29 +
examples/USER/atc/mesh/in.semicircle | 101 +
examples/USER/atc/mesh/kernel2d_hex.screen | 81 +
examples/USER/atc/mesh/kernel2d_tet.screen | 77 +
examples/USER/atc/mesh/mesh2d_tet.screen | 78 +
examples/USER/atc/mesh/semicircle.screen | 205 +
examples/USER/atc/molecule/harmonic_bonds.screen | 123 +
examples/USER/atc/molecule/in.harmonic_bonds | 55 +
examples/USER/atc/molecule/in.polarize | 120 +
examples/USER/atc/molecule/in.quartic_bonds | 60 +
examples/USER/atc/molecule/in.water | 96 +
examples/USER/atc/molecule/polarize.screen | 316 +
examples/USER/atc/molecule/quartic_bonds.screen | 116 +
examples/USER/atc/molecule/water.mat | 5 +
examples/USER/atc/molecule/water.screen | 100 +
examples/USER/atc/thermal/Ar_thermal.mat | 14 +
examples/USER/atc/thermal/bar1d.screen | 374 +
examples/USER/atc/thermal/bar1d_all_atoms.screen | 103 +
examples/USER/atc/thermal/bar1d_combined.screen | 165 +
examples/USER/atc/thermal/bar1d_flux.screen | 252 +
examples/USER/atc/thermal/bar1d_frac_step.screen | 177 +
examples/USER/atc/thermal/bar1d_hoover.screen | 130 +
examples/USER/atc/thermal/bar1d_interpolate.screen | 207 +
examples/USER/atc/thermal/bar1d_lumped.screen | 295 +
examples/USER/atc/thermal/in.bar1d | 79 +
examples/USER/atc/thermal/in.bar1d_all_atoms | 101 +
examples/USER/atc/thermal/in.bar1d_combined | 87 +
examples/USER/atc/thermal/in.bar1d_flux | 79 +
examples/USER/atc/thermal/in.bar1d_frac_step | 80 +
examples/USER/atc/thermal/in.bar1d_hoover | 138 +
examples/USER/atc/thermal/in.bar1d_interpolate | 80 +
examples/USER/atc/thermal/in.bar1d_lumped | 85 +
examples/USER/atc/thermal/in.no_atoms | 56 +
examples/USER/atc/thermal/no_atoms.screen | 351 +
examples/USER/atc/two_temperature/Ar_ttm.mat | 35 +
examples/USER/atc/two_temperature/Cu_ttm.mat | 17 +
examples/USER/atc/two_temperature/bar1d_ttm.screen | 447 +
examples/USER/atc/two_temperature/cutout.screen | 279 +
.../USER/atc/two_temperature/gaussianIC_ttm.screen | 169 +
examples/USER/atc/two_temperature/in.bar1d_ttm | 86 +
examples/USER/atc/two_temperature/in.cutout | 87 +
.../USER/atc/two_temperature/in.gaussianIC_ttm | 94 +
examples/USER/atc/two_temperature/in.no_atoms | 61 +
examples/USER/atc/two_temperature/in.restart | 117 +
.../USER/atc/two_temperature/in.uniform_exchange | 66 +
.../USER/atc/two_temperature/in.uniform_heating | 53 +
examples/USER/atc/two_temperature/no_atoms.screen | 203 +
examples/USER/atc/two_temperature/restart.screen | 160 +
.../atc/two_temperature/uniform_exchange.screen | 618 +
.../atc/two_temperature/uniform_heating.screen | 134 +
.../USER/lb/confined_colloid/in.confined_colloids | 108 +
examples/USER/lb/confined_colloid/results64.out | 41 +
examples/USER/lb/dragforce/data.one_radius16d2 | 330 +
examples/USER/lb/dragforce/defaultgamma_drag.out |10035 ++
examples/USER/lb/dragforce/in.defaultgamma_drag | 80 +
examples/USER/lb/dragforce/in.setgamma_drag | 68 +
examples/USER/lb/dragforce/setgamma13d0_drag.out |10035 ++
examples/USER/lb/fourspheres/data.four | 1290 +
.../fourspheres_velocity0d0001_defaultgamma.out |15039 +++
.../fourspheres_velocity0d0001_setgamma.out |15039 +++
.../lb/fourspheres/in.fourspheres_default_gamma | 84 +
.../USER/lb/fourspheres/in.fourspheres_set_gamma | 76 +
examples/USER/lb/microrheology/data.two | 492 +
.../microrheology/in.microrheology_default_gamma | 119 +
.../lb/microrheology/in.microrheology_set_gamma | 113 +
.../microrheology/microrheology_defaultgamma.out |50000 ++++++++++
.../lb/microrheology/microrheology_setgamma.out |50000 ++++++++++
examples/USER/lb/planewall/data.one_radius16d2 | 330 +
.../USER/lb/planewall/in.planewall_default_gamma | 99 +
examples/USER/lb/planewall/in.planewall_set_gamma | 92 +
examples/USER/lb/planewall/wall_defaultgamma.out |20031 ++++
examples/USER/lb/planewall/wall_setgamma.out |20031 ++++
examples/USER/lb/polymer/data.polymer | 1040 +
examples/USER/lb/polymer/in.polymer | 105 +
examples/USER/lb/polymer/out.polymer | 19 +
examples/USER/misc/basal/almg.liu | 708 +
examples/USER/misc/basal/in.basal | 163 +
examples/USER/misc/ti/in.ti_rs | 64 +
examples/USER/misc/ti/in.ti_spring | 64 +
.../USER/sph/water_collapse/water_collapse.lmp | 4 +-
examples/VISCOSITY/README | 80 +
examples/VISCOSITY/in.gk.2d | 65 +
examples/VISCOSITY/in.mp.2d | 76 +
examples/VISCOSITY/in.nemd.2d | 83 +
examples/VISCOSITY/in.wall.2d | 83 +
examples/VISCOSITY/log.gk.2d.12Sep13 | 386 +
examples/VISCOSITY/log.mp.2d.12Sep13 | 231 +
examples/VISCOSITY/log.nemd.2d.12Sep13 | 264 +
examples/VISCOSITY/log.wall.2d.12Sep13 | 216 +
examples/VISCOSITY/profile.gk.2d.12Sep13 |100654 ++++++++++++++++++++
examples/VISCOSITY/profile.mp.2d.12Sep13 | 1473 +
examples/VISCOSITY/profile.nemd.2d.12Sep13 | 318 +
examples/VISCOSITY/profile.wall.2d.12Sep13 | 66 +
examples/comb/data.comb3-OHCCu | 695 +
examples/comb/ffield.comb3 | 349 +
examples/comb/in.comb3 | 34 +
examples/comb/lib.comb3 |24303 +++++
examples/comb/log.comb3.4Nov13.linux.1 | 72 +
examples/comb/log.comb3.4Nov13.linux.4 | 72 +
examples/dipole/in.dipole | 2 +-
examples/friction/in.friction | 1 +
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/neb/final.hop1 | 1 +
examples/neb/final.hop2 | 1 +
examples/nemd/in.nemd | 2 +-
examples/pour/in.pour.2d | 2 +-
examples/reax/Fluorographene/README | 13 +
examples/reax/Fluorographene/data.FC |17296 ++++
examples/reax/Fluorographene/dumpnpt.xyz |17282 ++++
examples/reax/Fluorographene/ffield.reax.FC | 361 +
examples/reax/Fluorographene/in.FC | 32 +
examples/reax/Fluorographene/log.FC | 290 +
examples/reax/README | 49 +-
examples/srd/in.srd.mixture | 1 -
examples/voronoi/in.voronoi | 154 +
examples/voronoi/log.voronoi.4Aug13.macos.1 | 368 +
examples/voronoi/log.voronoi.4Aug13.macos.4 | 368 +
lib/atc/ATC_Coupling.cpp | 2215 +
lib/atc/ATC_Coupling.h | 456 +
lib/atc/ATC_CouplingEnergy.cpp | 412 +
lib/atc/ATC_CouplingEnergy.h | 82 +
lib/atc/ATC_CouplingMass.cpp | 285 +
lib/atc/ATC_CouplingMass.h | 88 +
lib/atc/ATC_CouplingMomentum.cpp | 453 +
lib/atc/ATC_CouplingMomentum.h | 84 +
lib/atc/ATC_CouplingMomentumEnergy.cpp | 508 +
lib/atc/ATC_CouplingMomentumEnergy.h | 83 +
lib/atc/ATC_Error.h | 44 +-
lib/atc/ATC_HardyKernel.cpp | 386 -
lib/atc/ATC_HardyKernel.h | 127 -
lib/atc/ATC_Method.cpp | 2310 +
lib/atc/ATC_Method.h | 863 +
lib/atc/ATC_Transfer.cpp | 2956 +-
lib/atc/ATC_Transfer.h | 1134 +-
lib/atc/ATC_TransferHardy.cpp | 2320 -
lib/atc/ATC_TransferHardy.h | 346 -
lib/atc/ATC_TransferKernel.cpp | 485 +
lib/atc/ATC_TransferKernel.h | 53 +
lib/atc/ATC_TransferPartitionOfUnity.cpp | 506 +
lib/atc/ATC_TransferPartitionOfUnity.h | 59 +
lib/atc/ATC_TransferThermal.cpp | 541 -
lib/atc/ATC_TransferThermal.h | 96 -
lib/atc/ATC_TransferUtility.cpp | 2221 -
lib/atc/ATC_TypeDefs.h | 621 +-
lib/atc/Array.h | 214 +-
lib/atc/Array2D.h | 26 +-
lib/atc/AtomToMoleculeTransfer.cpp | 225 +
lib/atc/AtomToMoleculeTransfer.h | 239 +
lib/atc/AtomicRegulator.cpp | 830 +-
lib/atc/AtomicRegulator.h | 411 +-
lib/atc/BodyForce.cpp | 37 +
lib/atc/BodyForce.h | 68 +
lib/atc/CBLattice.cpp | 204 +
lib/atc/CBLattice.h | 97 +
lib/atc/CG.h | 7 +-
lib/atc/CauchyBorn.cpp | 572 +
lib/atc/CauchyBorn.h | 113 +
lib/atc/CbEam.h | 209 +
lib/atc/CbLjCut.h | 62 +
lib/atc/CbLjSmoothLinear.h | 88 +
lib/atc/CbPotential.cpp | 88 +
lib/atc/CbPotential.h | 70 +
lib/atc/ChargeRegulator.cpp | 735 +
lib/atc/ChargeRegulator.h | 282 +
lib/atc/CloneVector.h | 44 +-
lib/atc/ConcentrationRegulator.cpp | 635 +
lib/atc/ConcentrationRegulator.h | 216 +
lib/atc/DenseMatrix.h | 146 +-
lib/atc/DenseVector.h | 28 +-
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tools/msi2lmp/test/in.h2-h2o-class2b | 13 +
tools/msi2lmp/test/in.hap_crystal-class1 | 13 +
tools/msi2lmp/test/in.hap_crystal-class2b | 14 +
tools/msi2lmp/test/in.hydrogen-class1 | 12 +
tools/msi2lmp/test/in.hydrogen-class2a | 12 +
tools/msi2lmp/test/in.naphthalene-class1 | 15 +
tools/msi2lmp/test/in.naphthalene-class2a | 15 +
tools/msi2lmp/test/in.naphthalene-class2b | 15 +
tools/msi2lmp/test/in.nylon-class1 | 16 +
tools/msi2lmp/test/in.phen3_cff97-class1 | 16 +
tools/msi2lmp/test/in.water-class1 | 13 +
tools/msi2lmp/test/in.water-class2b | 13 +
tools/msi2lmp/test/naphthalene-class1.car | 25 +
tools/msi2lmp/test/naphthalene-class1.mdf | 46 +
tools/msi2lmp/test/naphthalene-class2a.car | 25 +
tools/msi2lmp/test/naphthalene-class2a.mdf | 46 +
tools/msi2lmp/test/naphthalene-class2b.car | 25 +
tools/msi2lmp/test/naphthalene-class2b.mdf | 46 +
tools/msi2lmp/test/{nylon.car => nylon-class1.car} | 0
tools/msi2lmp/test/{nylon.mdf => nylon-class1.mdf} | 0
.../{phen3_cff97.car => phen3_cff97-class1.car} | 0
.../{phen3_cff97.mdf => phen3_cff97-class1.mdf} | 0
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 1450 +
.../msi2lmp/test/reference/PyAC_bulk-clayff.data2 | 2728 +
tools/msi2lmp/test/reference/benzene-class1.data | 135 +
tools/msi2lmp/test/reference/benzene-class1.data2 | 148 +
tools/msi2lmp/test/reference/benzene-class1.data3 | 135 +
tools/msi2lmp/test/reference/benzene-class2a.data | 179 +
tools/msi2lmp/test/reference/benzene-class2a.data2 | 192 +
tools/msi2lmp/test/reference/benzene-class2b.data | 179 +
tools/msi2lmp/test/reference/benzene-class2b.data2 | 192 +
tools/msi2lmp/test/reference/crambin-class1.data | 4727 +
tools/msi2lmp/test/reference/crambin-class1.data2 | 5370 ++
tools/msi2lmp/test/reference/ethane-class1.data | 89 +
tools/msi2lmp/test/reference/ethane-class1.data2 | 97 +
tools/msi2lmp/test/reference/ethane-class2a.data | 141 +
tools/msi2lmp/test/reference/ethane-class2a.data2 | 150 +
tools/msi2lmp/test/reference/ethane-class2b.data | 141 +
tools/msi2lmp/test/reference/ethane-class2b.data2 | 150 +
tools/msi2lmp/test/reference/ethane-oplsaa.data | 89 +
tools/msi2lmp/test/reference/ethane-oplsaa.data2 | 97 +
tools/msi2lmp/test/reference/h2-h2o-class1.data | 55 +
tools/msi2lmp/test/reference/h2-h2o-class1.data2 | 59 +
tools/msi2lmp/test/reference/h2-h2o-class2b.data | 63 +
tools/msi2lmp/test/reference/h2-h2o-class2b.data2 | 67 +
.../msi2lmp/test/reference/hap_crystal-class1.data | 260 +
.../test/reference/hap_crystal-class1.data2 | 347 +
.../test/reference/hap_crystal-class2b.data | 328 +
.../test/reference/hap_crystal-class2b.data2 | 416 +
tools/msi2lmp/test/reference/hydrogen-class1.data | 36 +
tools/msi2lmp/test/reference/hydrogen-class1.data2 | 36 +
tools/msi2lmp/test/reference/hydrogen-class2a.data | 36 +
.../msi2lmp/test/reference/hydrogen-class2a.data2 | 36 +
.../msi2lmp/test/reference/naphthalene-class1.data | 185 +
.../test/reference/naphthalene-class1.data2 | 204 +
.../test/reference/naphthalene-class2a.data | 230 +
.../test/reference/naphthalene-class2a.data2 | 249 +
.../test/reference/naphthalene-class2b.data | 230 +
.../test/reference/naphthalene-class2b.data2 | 249 +
tools/msi2lmp/test/reference/nylon-class1.data | 898 +
tools/msi2lmp/test/reference/nylon-class1.data2 | 1016 +
.../msi2lmp/test/reference/phen3_cff97-class1.data | 258 +
.../test/reference/phen3_cff97-class1.data2 | 282 +
tools/msi2lmp/test/reference/water-class1.data | 49 +
tools/msi2lmp/test/reference/water-class1.data2 | 51 +
tools/msi2lmp/test/reference/water-class2b.data | 57 +
tools/msi2lmp/test/reference/water-class2b.data2 | 59 +
tools/msi2lmp/test/runtests.sh | 158 +
tools/msi2lmp/test/water-class1.car | 10 +
tools/msi2lmp/test/water-class1.mdf | 31 +
tools/msi2lmp/test/water-class2b.car | 10 +
tools/msi2lmp/test/water-class2b.mdf | 31 +
tools/polybond/Manual.pdf | Bin 0 -> 92552 bytes
tools/polybond/README | 12 +
tools/polybond/lmpsdata.py | 1945 +
tools/pymol_asphere/src/Makefile | 2 +-
tools/python/dump2cfg.py | 2 +-
tools/python/dump2pdb.py | 2 +-
tools/python/dump2xyz.py | 2 +-
tools/python/dumpsort.py | 2 +-
tools/python/log2txt.py | 2 +-
tools/python/logplot.py | 2 +-
tools/python/neb_combine.py | 2 +-
tools/python/neb_final.py | 2 +-
tools/restart2data.cpp | 43 +-
tools/thermo_extract.c | 238 -
tools/xmgrace/README | 16 +
tools/xmgrace/lammpsplot.cpp | 830 +
tools/xmgrace/lammpsplot.pdf | Bin 0 -> 71715 bytes
tools/xmgrace/logplotawk.oneliner | 7 +
tools/xmgrace/logplotgrep.oneliner | 6 +
tools/xmgrace/plotthermodata.awk | 18 +
2707 files changed, 662047 insertions(+), 104545 deletions(-)
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