[liggghts] 01/04: Merge.
Anton Gladky
gladk at moszumanska.debian.org
Thu Mar 6 19:43:41 UTC 2014
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gladk pushed a commit to branch master
in repository liggghts.
commit 32191e2c758a03520c7ca52a3a054793a5e05df7
Merge: 19039b2 76193e3
Author: Anton Gladky <gladk at debian.org>
Date: Tue Mar 4 22:23:23 2014 +0100
Merge.
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.../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 +
.../LAMMPS/USER/atc/drift_diffusion/in.finite_well | 75 +
.../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/LAMMPS/USER/atc/elastic/Ar_CauchyBorn.mat | 8 +
.../USER/atc/elastic/Ar_CauchyBornLinear.mat | 9 +
examples/LAMMPS/USER/atc/elastic/Ar_damped.mat | 37 +
examples/LAMMPS/USER/atc/elastic/Ar_elastic.mat | 29 +
.../LAMMPS/USER/atc/elastic/Ar_thermo_elastic.mat | 11 +
examples/LAMMPS/USER/atc/elastic/Au_elastic.mat | 18 +
examples/LAMMPS/USER/atc/elastic/CNT.mat | 1315 +
.../LAMMPS/USER/atc/elastic/CNT_electrostatic.mat | 18 +
.../LAMMPS/USER/atc/elastic/CNT_electrostatic2.mat | 21 +
examples/LAMMPS/USER/atc/elastic/CNT_id.mat | 11 +
examples/LAMMPS/USER/atc/elastic/bar1d.screen | 270 +
.../LAMMPS/USER/atc/elastic/bar1d_damped.screen | 385 +
examples/LAMMPS/USER/atc/elastic/bar1d_flux.screen | 281 +
.../LAMMPS/USER/atc/elastic/bar1d_frac_step.screen | 228 +
.../USER/atc/elastic/bar1d_ghost_flux.screen | 211 +
.../USER/atc/elastic/bar1d_thermo_elastic.screen | 113 +
.../USER/atc/elastic/cnt_electrostatic.screen | 1213 +
.../USER/atc/elastic/cnt_electrostatic2.screen | 215 +
.../USER/atc/elastic/cnt_fixed_charge.screen | 351 +
examples/LAMMPS/USER/atc/elastic/eam_energy.screen | 335 +
.../USER/atc/elastic/electron_density.screen | 267 +
.../USER/atc/elastic/electrostatic_bending.screen | 846 +
.../atc/elastic/electrostatic_bending_dos.screen | 633 +
examples/LAMMPS/USER/atc/elastic/in.bar1d | 91 +
examples/LAMMPS/USER/atc/elastic/in.bar1d_damped | 116 +
examples/LAMMPS/USER/atc/elastic/in.bar1d_flux | 98 +
.../LAMMPS/USER/atc/elastic/in.bar1d_frac_step | 99 +
.../LAMMPS/USER/atc/elastic/in.bar1d_ghost_flux | 101 +
.../USER/atc/elastic/in.bar1d_thermo_elastic | 139 +
.../LAMMPS/USER/atc/elastic/in.cnt_electrostatic | 107 +
.../LAMMPS/USER/atc/elastic/in.cnt_electrostatic2 | 118 +
.../LAMMPS/USER/atc/elastic/in.cnt_fixed_charge | 145 +
examples/LAMMPS/USER/atc/elastic/in.eam_energy | 80 +
.../LAMMPS/USER/atc/elastic/in.electron_density | 74 +
.../USER/atc/elastic/in.electrostatic_bending | 186 +
.../USER/atc/elastic/in.electrostatic_bending_dos | 164 +
examples/LAMMPS/USER/atc/elastic/in.no_atoms | 42 +
examples/LAMMPS/USER/atc/elastic/in.no_atoms_cb | 43 +
.../LAMMPS/USER/atc/elastic/in.no_atoms_cb_linear | 42 +
examples/LAMMPS/USER/atc/elastic/no_atoms.screen | 75 +
.../LAMMPS/USER/atc/elastic/no_atoms_cb.screen | 78 +
.../USER/atc/elastic/no_atoms_cb_linear.screen | 79 +
examples/LAMMPS/USER/atc/fluids/Ar_elastic.mat | 8 +
.../LAMMPS/USER/atc/fluids/Ar_electrostatic.mat | 8 +
examples/LAMMPS/USER/atc/fluids/Ar_liquid.mat | 8 +
examples/LAMMPS/USER/atc/fluids/Ar_species.mat | 5 +
examples/LAMMPS/USER/atc/fluids/Ar_species_dl.mat | 8 +
examples/LAMMPS/USER/atc/fluids/Ar_thermal.mat | 9 +
.../LAMMPS/USER/atc/fluids/Ar_visc_no_atoms.mat | 6 +
examples/LAMMPS/USER/atc/fluids/Ar_viscosity.mat | 9 +
.../LAMMPS/USER/atc/fluids/bar1d_fluids.screen | 263 +
.../LAMMPS/USER/atc/fluids/concentration.screen | 169 +
.../USER/atc/fluids/conducting_interface.screen | 184 +
examples/LAMMPS/USER/atc/fluids/dielectric.mat | 15 +
.../USER/atc/fluids/dielectric_interface.screen | 184 +
.../LAMMPS/USER/atc/fluids/double_layer.screen | 203 +
examples/LAMMPS/USER/atc/fluids/in.bar1d_fluids | 98 +
examples/LAMMPS/USER/atc/fluids/in.concentration | 172 +
.../LAMMPS/USER/atc/fluids/in.conducting_interface | 111 +
.../LAMMPS/USER/atc/fluids/in.dielectric_interface | 106 +
examples/LAMMPS/USER/atc/fluids/in.double_layer | 100 +
.../LAMMPS/USER/atc/fluids/in.liquid_electrostatic | 63 +
examples/LAMMPS/USER/atc/fluids/in.opp_force | 70 +
examples/LAMMPS/USER/atc/fluids/in.poisson | 69 +
examples/LAMMPS/USER/atc/fluids/in.shear_flow | 84 +
examples/LAMMPS/USER/atc/fluids/in.shear_no_atoms | 32 +
.../USER/atc/fluids/liquid_electrostatic.screen | 143 +
examples/LAMMPS/USER/atc/fluids/opp_force.screen | 146 +
examples/LAMMPS/USER/atc/fluids/poisson.screen | 260 +
examples/LAMMPS/USER/atc/fluids/shear_flow.screen | 65 +
.../LAMMPS/USER/atc/fluids/shear_no_atoms.screen | 91 +
examples/LAMMPS/USER/atc/hardy/consistency.screen | 898 +-
.../USER/atc/hardy/eam_kernel_convergence.screen | 3334 +-
.../USER/atc/hardy/eam_unistrain_cell.screen | 83 +-
.../USER/atc/hardy/eam_unistrain_mesh.screen | 122 +-
.../USER/atc/hardy/eam_unistrain_qcylinder.screen | 80 +-
.../USER/atc/hardy/eam_unistrain_qsphere.screen | 80 +-
.../USER/atc/hardy/eam_unistrain_step.screen | 122 +-
.../USER/atc/hardy/eam_volume_stretch.screen | 143 +-
.../LAMMPS/USER/atc/hardy/eshelby_static.screen | 1273 +
examples/LAMMPS/USER/atc/hardy/in.consistency | 37 +-
.../USER/atc/hardy/in.eam_kernel_convergence | 35 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_cell | 43 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_mesh | 45 +-
.../USER/atc/hardy/in.eam_unistrain_qcylinder | 44 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_qsphere | 45 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_step | 45 +-
.../LAMMPS/USER/atc/hardy/in.eam_volume_stretch | 46 +-
examples/LAMMPS/USER/atc/hardy/in.eshelby_static | 132 +
examples/LAMMPS/USER/atc/hardy/in.nvt | 44 +-
examples/LAMMPS/USER/atc/hardy/nvt.data | 1020 +
examples/LAMMPS/USER/atc/hardy/nvt.screen | 92 +
examples/LAMMPS/USER/atc/mesh/Ar_ttm.mat | 35 +
examples/LAMMPS/USER/atc/mesh/Si.mat | 9 +
.../LAMMPS/USER/atc/mesh/gaussianIC1d_hex.screen | 108 +
.../LAMMPS/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 +
.../LAMMPS/USER/atc/mesh/gaussianIC2d_tet.screen | 102 +
examples/LAMMPS/USER/atc/mesh/in.gaussianIC1d_hex | 56 +
examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_hex | 69 +
.../USER/atc/mesh/in.gaussianIC2d_hex20_uniform | 37 +
.../USER/atc/mesh/in.gaussianIC2d_hex27_uniform | 37 +
examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_tet | 40 +
examples/LAMMPS/USER/atc/mesh/in.kernel2d_hex | 32 +
examples/LAMMPS/USER/atc/mesh/in.kernel2d_tet | 28 +
examples/LAMMPS/USER/atc/mesh/in.mesh2d_tet | 29 +
examples/LAMMPS/USER/atc/mesh/in.semicircle | 101 +
examples/LAMMPS/USER/atc/mesh/kernel2d_hex.screen | 81 +
examples/LAMMPS/USER/atc/mesh/kernel2d_tet.screen | 77 +
examples/LAMMPS/USER/atc/mesh/mesh2d_tet.screen | 78 +
examples/LAMMPS/USER/atc/mesh/semicircle.screen | 205 +
.../LAMMPS/USER/atc/molecule/harmonic_bonds.screen | 123 +
.../LAMMPS/USER/atc/molecule/in.harmonic_bonds | 55 +
examples/LAMMPS/USER/atc/molecule/in.polarize | 120 +
examples/LAMMPS/USER/atc/molecule/in.quartic_bonds | 60 +
examples/LAMMPS/USER/atc/molecule/in.water | 96 +
examples/LAMMPS/USER/atc/molecule/polarize.screen | 316 +
.../LAMMPS/USER/atc/molecule/quartic_bonds.screen | 116 +
examples/LAMMPS/USER/atc/molecule/water.mat | 5 +
examples/LAMMPS/USER/atc/molecule/water.screen | 100 +
examples/LAMMPS/USER/atc/thermal/Ar_thermal.mat | 14 +
examples/LAMMPS/USER/atc/thermal/bar1d.screen | 374 +
.../LAMMPS/USER/atc/thermal/bar1d_all_atoms.screen | 103 +
.../LAMMPS/USER/atc/thermal/bar1d_combined.screen | 165 +
examples/LAMMPS/USER/atc/thermal/bar1d_flux.screen | 252 +
.../LAMMPS/USER/atc/thermal/bar1d_frac_step.screen | 177 +
.../LAMMPS/USER/atc/thermal/bar1d_hoover.screen | 130 +
.../USER/atc/thermal/bar1d_interpolate.screen | 207 +
.../LAMMPS/USER/atc/thermal/bar1d_lumped.screen | 295 +
examples/LAMMPS/USER/atc/thermal/in.bar1d | 79 +
.../LAMMPS/USER/atc/thermal/in.bar1d_all_atoms | 101 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_combined | 87 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_flux | 79 +
.../LAMMPS/USER/atc/thermal/in.bar1d_frac_step | 80 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_hoover | 138 +
.../LAMMPS/USER/atc/thermal/in.bar1d_interpolate | 80 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_lumped | 85 +
examples/LAMMPS/USER/atc/thermal/in.no_atoms | 56 +
examples/LAMMPS/USER/atc/thermal/no_atoms.screen | 351 +
.../LAMMPS/USER/atc/two_temperature/Ar_ttm.mat | 35 +
.../LAMMPS/USER/atc/two_temperature/Cu_ttm.mat | 17 +
.../USER/atc/two_temperature/bar1d_ttm.screen | 447 +
.../LAMMPS/USER/atc/two_temperature/cutout.screen | 279 +
.../USER/atc/two_temperature/gaussianIC_ttm.screen | 169 +
.../LAMMPS/USER/atc/two_temperature/in.bar1d_ttm | 86 +
examples/LAMMPS/USER/atc/two_temperature/in.cutout | 87 +
.../USER/atc/two_temperature/in.gaussianIC_ttm | 94 +
.../LAMMPS/USER/atc/two_temperature/in.no_atoms | 61 +
.../LAMMPS/USER/atc/two_temperature/in.restart | 117 +
.../USER/atc/two_temperature/in.uniform_exchange | 66 +
.../USER/atc/two_temperature/in.uniform_heating | 53 +
.../USER/atc/two_temperature/no_atoms.screen | 203 +
.../LAMMPS/USER/atc/two_temperature/restart.screen | 160 +
.../atc/two_temperature/uniform_exchange.screen | 618 +
.../atc/two_temperature/uniform_heating.screen | 134 +
examples/LAMMPS/USER/colvars/data.peptide | 6531 ++
examples/LAMMPS/USER/colvars/in.peptide-colvars | 48 +
examples/LAMMPS/USER/colvars/in.peptide-colvars2 | 40 +
examples/LAMMPS/USER/colvars/log.peptide-colvars-1 | 516 +
examples/LAMMPS/USER/colvars/log.peptide-colvars-4 | 516 +
.../LAMMPS/USER/colvars/log.peptide-colvars2-1 | 182 +
.../LAMMPS/USER/colvars/log.peptide-colvars2-4 | 182 +
examples/LAMMPS/USER/colvars/out.colvars.state | 22 +
examples/LAMMPS/USER/colvars/out.colvars.traj | 102 +
examples/LAMMPS/USER/colvars/out2.colvars.state | 22 +
examples/LAMMPS/USER/colvars/out2.colvars.traj | 102 +
examples/LAMMPS/USER/colvars/peptide.colvars | 39 +
examples/LAMMPS/USER/colvars/peptide.colvars2 | 26 +
examples/LAMMPS/USER/colvars/peptide.psf | 126 +
.../LAMMPS/USER/colvars/peptide2.colvars.state | 17 +
examples/LAMMPS/USER/colvars/peptide2.colvars.traj | 102 +
.../eff/Auger-Adamantane/in.adamantane_ionized.nve | 2 +-
examples/LAMMPS/USER/eff/Be-solid/in.Be-solid.spe | 2 +-
examples/LAMMPS/USER/eff/ECP/Si2H6/data.Si2H6 | 2 +-
examples/LAMMPS/USER/eff/ECP/Si2H6/in.Si2H6 | 2 +-
examples/LAMMPS/USER/eff/ECP/SiC/bulk/data.SiC | 5018 +
examples/LAMMPS/USER/eff/ECP/SiC/bulk/in.SiC | 41 +
examples/LAMMPS/USER/eff/ECP/SiH4/data.SiH4 | 2 +-
examples/LAMMPS/USER/eff/ECP/SiH4/in.SiH4 | 2 +-
examples/LAMMPS/USER/eff/ECP/SiH4/in.SiH4.ang | 2 +-
examples/LAMMPS/USER/eff/H/in.h_atom.spe.ang | 2 +-
examples/LAMMPS/USER/eff/H/in.h_atom.spe.bohr | 2 +-
examples/LAMMPS/USER/eff/H2/in.h2 | 2 +-
examples/LAMMPS/USER/eff/H_plasma/in.h2bulk.npt | 2 +-
examples/LAMMPS/USER/eff/H_plasma/in.h2bulk.nve | 2 +-
.../LAMMPS/USER/eff/H_plasma/in.h2bulk.nve.ang | 2 +-
.../USER/eff/Li-dendritic/in.Li-dendritic.min | 2 +-
.../USER/eff/Li-dendritic/in.Li-dendritic.nvt | 2 +-
examples/LAMMPS/USER/eff/Li-solid/in.Li.ang | 6 +-
examples/LAMMPS/USER/eff/Li-solid/in.Li.bohr | 2 +-
.../LAMMPS/USER/eff/fixed-core/CH4/in.CH4fc.ang | 2 +-
.../LAMMPS/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 2 +-
.../USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 2 +-
.../USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr | 2 +-
.../USER/lb/confined_colloid/in.confined_colloids | 108 +
.../LAMMPS/USER/lb/confined_colloid/results64.out | 41 +
.../LAMMPS/USER/lb/dragforce/data.one_radius16d2 | 330 +
.../LAMMPS/USER/lb/dragforce/defaultgamma_drag.out | 10035 ++
.../LAMMPS/USER/lb/dragforce/in.defaultgamma_drag | 80 +
examples/LAMMPS/USER/lb/dragforce/in.setgamma_drag | 68 +
.../LAMMPS/USER/lb/dragforce/setgamma13d0_drag.out | 10035 ++
examples/LAMMPS/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/LAMMPS/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 +++++++++
.../LAMMPS/USER/lb/planewall/data.one_radius16d2 | 330 +
.../USER/lb/planewall/in.planewall_default_gamma | 99 +
.../USER/lb/planewall/in.planewall_set_gamma | 92 +
.../LAMMPS/USER/lb/planewall/wall_defaultgamma.out | 20031 ++++
.../LAMMPS/USER/lb/planewall/wall_setgamma.out | 20031 ++++
examples/LAMMPS/USER/lb/polymer/data.polymer | 1040 +
examples/LAMMPS/USER/lb/polymer/in.polymer | 105 +
examples/LAMMPS/USER/lb/polymer/out.polymer | 19 +
examples/LAMMPS/USER/misc/basal/almg.liu | 708 +
examples/LAMMPS/USER/misc/basal/in.basal | 163 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/bcc.in | 33 +
.../USER/misc/meam_sw_spline/Si/bcc_relax.in | 37 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/dc.in | 34 +
.../LAMMPS/USER/misc/meam_sw_spline/Si/dc_relax.in | 38 +
.../Si/energy_conservation.meam.sw.in | 45 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/fcc.in | 34 +
.../USER/misc/meam_sw_spline/Si/fcc_relax.in | 38 +
.../USER/misc/meam_sw_spline/Si/hcp_relax.in | 40 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/sc.in | 34 +
.../LAMMPS/USER/misc/meam_sw_spline/Si/sc_relax.in | 38 +
.../USER/misc/meam_sw_spline/Si/single_atom.in | 27 +
.../LAMMPS/USER/misc/meam_sw_spline/Ti/alpha.in | 27 +
.../misc/meam_sw_spline/Ti/alpha_relaxation.in | 38 +
.../LAMMPS/USER/misc/meam_sw_spline/Ti/beta.in | 27 +
.../Ti/energy_conservation.meam.sw.in | 74 +
examples/LAMMPS/USER/misc/meam_sw_spline/Ti/fcc.in | 28 +
.../USER/misc/meam_sw_spline/Ti/hexagonal.in | 28 +
.../LAMMPS/USER/misc/meam_sw_spline/Ti/omega.in | 27 +
.../USER/misc/meam_sw_spline/Ti/single_atom.in | 27 +
examples/LAMMPS/USER/misc/ti/in.ti_rs | 64 +
examples/LAMMPS/USER/misc/ti/in.ti_spring | 64 +
examples/LAMMPS/USER/phonon/1-1D-mono/README | 39 +
examples/LAMMPS/USER/phonon/1-1D-mono/data.pos | 57 +
examples/LAMMPS/USER/phonon/1-1D-mono/disp.dat | 19 +
examples/LAMMPS/USER/phonon/1-1D-mono/in.Ana | 50 +
examples/LAMMPS/USER/phonon/1-1D-mono/in.disp | 9 +
.../USER/phonon/1-1D-mono/log.lammps.example | 146 +
examples/LAMMPS/USER/phonon/1-1D-mono/map.in | 18 +
examples/LAMMPS/USER/phonon/1-1D-mono/pdisp.eps | 776 +
.../USER/phonon/1-1D-mono/phonon.bin.2000000 | Bin 0 -> 384 bytes
examples/LAMMPS/USER/phonon/1-1D-mono/phonon.log | 110 +
examples/LAMMPS/USER/phonon/1-1D-mono/plot.disp | 20 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/README | 37 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/data.pos | 154 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/disp.dat | 35 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/in.Ana | 46 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/in.disp | 9 +
.../USER/phonon/2-1D-diatomic/log.lammps.example | 113 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/map.in | 66 +
.../LAMMPS/USER/phonon/2-1D-diatomic/pdisp.eps | 924 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/pdos.dat | 203 +
.../USER/phonon/2-1D-diatomic/phonon.bin.2000000 | Bin 0 -> 2196 bytes
.../LAMMPS/USER/phonon/2-1D-diatomic/phonon.log | 206 +
.../LAMMPS/USER/phonon/2-1D-diatomic/plot.disp | 25 +
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 | Bin 0 -> 73872 bytes
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.log.example | 1575 +
examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/README | 47 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam | 305 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/data.pos | 524 +
.../USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat | 83 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat | 86 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat | 47 +
.../USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat | 164 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat | 101 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat | 102 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D | 40 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.disp | 21 +
examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.dos | 11 +
.../USER/phonon/3-3D-FCC-Cu-EAM/log.lammps.example | 107 +
examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/map.in | 514 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps | 1207 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps | 985 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp | 18 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos | 13 +
.../USER/sph/water_collapse/water_collapse.lmp | 4 +-
examples/LAMMPS/VISCOSITY/README | 80 +
examples/LAMMPS/VISCOSITY/in.gk.2d | 65 +
examples/LAMMPS/VISCOSITY/in.mp.2d | 76 +
examples/LAMMPS/VISCOSITY/in.nemd.2d | 83 +
examples/LAMMPS/VISCOSITY/in.wall.2d | 83 +
examples/LAMMPS/VISCOSITY/log.gk.2d.12Sep13 | 386 +
examples/LAMMPS/VISCOSITY/log.mp.2d.12Sep13 | 231 +
examples/LAMMPS/VISCOSITY/log.nemd.2d.12Sep13 | 264 +
examples/LAMMPS/VISCOSITY/log.wall.2d.12Sep13 | 216 +
examples/LAMMPS/VISCOSITY/profile.gk.2d.12Sep13 | 100654 ++++++++++++++++++
examples/LAMMPS/VISCOSITY/profile.mp.2d.12Sep13 | 1473 +
examples/LAMMPS/VISCOSITY/profile.nemd.2d.12Sep13 | 318 +
examples/LAMMPS/VISCOSITY/profile.wall.2d.12Sep13 | 66 +
examples/LAMMPS/body/data.body | 549 +
examples/LAMMPS/body/in.body | 23 +
examples/LAMMPS/body/log.body.18Feb13.linux.1 | 70 +
examples/LAMMPS/body/log.body.18Feb13.linux.4 | 70 +
.../LAMMPS/colloid/log.colloid.18Feb13.linux.1 | 125 +
.../LAMMPS/colloid/log.colloid.18Feb13.linux.4 | 125 +
examples/LAMMPS/colloid/log.colloid.9Jan12.linux.1 | 122 -
examples/LAMMPS/colloid/log.colloid.9Jan12.linux.4 | 122 -
examples/LAMMPS/comb/data.comb3-OHCCu | 695 +
examples/LAMMPS/comb/ffield.comb3 | 349 +
examples/LAMMPS/comb/in.comb.Si.elastic | 2 +-
examples/LAMMPS/comb/in.comb3 | 34 +
examples/LAMMPS/comb/lib.comb3 | 24303 +++++
examples/LAMMPS/comb/log.comb.Cu.18Feb13.linux.1 | 73 +
examples/LAMMPS/comb/log.comb.Cu.18Feb13.linux.4 | 73 +
examples/LAMMPS/comb/log.comb.Cu.9Jan12.linux.1 | 69 -
examples/LAMMPS/comb/log.comb.Cu.9Jan12.linux.4 | 69 -
.../comb/log.comb.Cu2O.elastic.18Feb13.linux.1 | 315 +
.../comb/log.comb.Cu2O.elastic.18Feb13.linux.4 | 315 +
.../comb/log.comb.Cu2O.elastic.9Jan12.linux.1 | 340 -
.../comb/log.comb.Cu2O.elastic.9Jan12.linux.4 | 342 -
examples/LAMMPS/comb/log.comb.CuaS.9Jan12.linux.1 | 41 -
examples/LAMMPS/comb/log.comb.CuaS.9Jan12.linux.4 | 41 -
examples/LAMMPS/comb/log.comb.HfO2.18Feb13.linux.1 | 259 +
examples/LAMMPS/comb/log.comb.HfO2.18Feb13.linux.4 | 259 +
examples/LAMMPS/comb/log.comb.HfO2.9Jan12.linux.1 | 193 -
examples/LAMMPS/comb/log.comb.HfO2.9Jan12.linux.4 | 291 -
examples/LAMMPS/comb/log.comb.Si.18Feb13.linux.1 | 73 +
examples/LAMMPS/comb/log.comb.Si.18Feb13.linux.4 | 73 +
examples/LAMMPS/comb/log.comb.Si.9Jan12.linux.1 | 69 -
examples/LAMMPS/comb/log.comb.Si.9Jan12.linux.4 | 69 -
.../comb/log.comb.Si.elastic.18Feb13.linux.1 | 274 +
.../comb/log.comb.Si.elastic.18Feb13.linux.4 | 274 +
.../LAMMPS/comb/log.comb.Si.elastic.9Jan12.linux.1 | 296 -
.../LAMMPS/comb/log.comb.Si.elastic.9Jan12.linux.4 | 296 -
examples/LAMMPS/comb/log.comb3.4Nov13.linux.1 | 72 +
examples/LAMMPS/comb/log.comb3.4Nov13.linux.4 | 72 +
examples/LAMMPS/crack/log.crack.18Feb13.linux.1 | 135 +
examples/LAMMPS/crack/log.crack.18Feb13.linux.4 | 135 +
examples/LAMMPS/crack/log.crack.9Jan12.linux.1 | 130 -
examples/LAMMPS/crack/log.crack.9Jan12.linux.4 | 130 -
examples/LAMMPS/dipole/in.dipole | 2 +-
examples/LAMMPS/dipole/log.dipole.18Feb13.linux.1 | 89 +
examples/LAMMPS/dipole/log.dipole.18Feb13.linux.4 | 89 +
examples/LAMMPS/dipole/log.dipole.9Jan12.linux.1 | 86 -
examples/LAMMPS/dipole/log.dipole.9Jan12.linux.4 | 86 -
.../LAMMPS/dreiding/log.dreiding.18Feb13.linux.1 | 98 +
.../LAMMPS/dreiding/log.dreiding.18Feb13.linux.4 | 98 +
.../LAMMPS/dreiding/log.dreiding.9Jan12.linux.1 | 97 -
.../LAMMPS/dreiding/log.dreiding.9Jan12.linux.4 | 121 -
examples/LAMMPS/eim/log.eim.18Feb13.linux.1 | 67 +
examples/LAMMPS/eim/log.eim.18Feb13.linux.4 | 67 +
examples/LAMMPS/eim/log.eim.9Jan12.linux.1 | 54 -
examples/LAMMPS/eim/log.eim.9Jan12.linux.4 | 54 -
examples/LAMMPS/ellipse/in.ellipse.gayberne | 4 +-
.../ellipse/log.ellipse.gayberne.18Feb13.linux.1 | 157 +
.../ellipse/log.ellipse.gayberne.18Feb13.linux.4 | 157 +
.../ellipse/log.ellipse.gayberne.9Jan12.linux.1 | 161 -
.../ellipse/log.ellipse.gayberne.9Jan12.linux.4 | 161 -
.../ellipse/log.ellipse.resquared.18Feb13.linux.1 | 157 +
.../ellipse/log.ellipse.resquared.18Feb13.linux.4 | 157 +
.../ellipse/log.ellipse.resquared.9Jan12.linux.1 | 161 -
.../ellipse/log.ellipse.resquared.9Jan12.linux.4 | 161 -
.../LAMMPS/flow/log.flow.couette.18Feb13.linux.1 | 127 +
.../LAMMPS/flow/log.flow.couette.18Feb13.linux.4 | 127 +
.../LAMMPS/flow/log.flow.couette.9Jan12.linux.1 | 123 -
.../LAMMPS/flow/log.flow.couette.9Jan12.linux.4 | 123 -
examples/LAMMPS/flow/log.flow.pois.18Feb13.linux.1 | 127 +
examples/LAMMPS/flow/log.flow.pois.18Feb13.linux.4 | 127 +
examples/LAMMPS/flow/log.flow.pois.9Jan12.linux.1 | 123 -
examples/LAMMPS/flow/log.flow.pois.9Jan12.linux.4 | 123 -
examples/LAMMPS/friction/in.friction | 1 +
.../LAMMPS/friction/log.friction.18Feb13.linux.1 | 145 +
.../LAMMPS/friction/log.friction.18Feb13.linux.4 | 145 +
.../LAMMPS/friction/log.friction.9Jan12.linux.1 | 141 -
.../LAMMPS/friction/log.friction.9Jan12.linux.4 | 141 -
.../LAMMPS/gpu/log.gpu.melt.2.5.18Feb13.linux.1 | 77 +
.../LAMMPS/gpu/log.gpu.melt.2.5.18Feb13.linux.4 | 77 +
.../LAMMPS/gpu/log.gpu.melt.2.5.9Jan12.linux.1 | 77 -
.../LAMMPS/gpu/log.gpu.melt.2.5.9Jan12.linux.4 | 77 -
.../LAMMPS/gpu/log.gpu.melt.5.0.18Feb13.linux.1 | 77 +
.../LAMMPS/gpu/log.gpu.melt.5.0.18Feb13.linux.4 | 77 +
.../LAMMPS/gpu/log.gpu.melt.5.0.9Jan12.linux.1 | 77 -
.../LAMMPS/gpu/log.gpu.melt.5.0.9Jan12.linux.4 | 77 -
.../LAMMPS/gpu/log.gpu.phosphate.18Feb13.linux.1 | 75 +
.../LAMMPS/gpu/log.gpu.phosphate.18Feb13.linux.4 | 75 +
.../LAMMPS/gpu/log.gpu.phosphate.9Jan12.linux.1 | 74 -
.../LAMMPS/gpu/log.gpu.phosphate.9Jan12.linux.4 | 74 -
examples/LAMMPS/gpu/log.gpu.rhodo.18Feb13.linux.1 | 122 +
examples/LAMMPS/gpu/log.gpu.rhodo.18Feb13.linux.4 | 122 +
examples/LAMMPS/gpu/log.gpu.rhodo.9Jan12.linux.1 | 121 -
examples/LAMMPS/gpu/log.gpu.rhodo.9Jan12.linux.4 | 121 -
.../hugoniostat/log.hugoniostat.18Feb13.linux.1 | 90 +
.../hugoniostat/log.hugoniostat.18Feb13.linux.4 | 90 +
.../hugoniostat/log.hugoniostat.9Jan12.linux.1 | 90 -
.../hugoniostat/log.hugoniostat.9Jan12.linux.4 | 90 -
examples/LAMMPS/indent/log.indent.18Feb13.linux.1 | 176 +
examples/LAMMPS/indent/log.indent.18Feb13.linux.4 | 176 +
examples/LAMMPS/indent/log.indent.9Jan12.linux.1 | 172 -
examples/LAMMPS/indent/log.indent.9Jan12.linux.4 | 172 -
.../LAMMPS/indent/log.indent.min.18Feb13.linux.1 | 386 +
.../LAMMPS/indent/log.indent.min.18Feb13.linux.4 | 383 +
.../LAMMPS/indent/log.indent.min.9Jan12.linux.1 | 404 -
.../LAMMPS/indent/log.indent.min.9Jan12.linux.4 | 386 -
examples/LAMMPS/kim/in.kim.lj | 4 +-
examples/LAMMPS/kim/in.kim.lj.lmp | 4 +-
examples/LAMMPS/kim/log.kim.lj.26Jul13.mac_mpi.1 | 29 +
examples/LAMMPS/kim/log.kim.lj.26Jul13.mac_mpi.4 | 29 +
examples/LAMMPS/kim/log.kim.lj.9Jan12.linux.1 | 71 -
examples/LAMMPS/kim/log.kim.lj.9Jan12.linux.4 | 71 -
.../LAMMPS/kim/log.kim.lj.lmp.26Jul13.mac_mpi.1 | 29 +
.../LAMMPS/kim/log.kim.lj.lmp.26Jul13.mac_mpi.4 | 29 +
examples/LAMMPS/kim/log.kim.lj.lmp.9Jan12.linux.1 | 71 -
examples/LAMMPS/kim/log.kim.lj.lmp.9Jan12.linux.4 | 71 -
examples/LAMMPS/meam/log.meam.18Feb13.linux.1 | 63 +
examples/LAMMPS/meam/log.meam.18Feb13.linux.4 | 63 +
examples/LAMMPS/meam/log.meam.9Jan12.linux.1 | 60 -
examples/LAMMPS/meam/log.meam.9Jan12.linux.4 | 60 -
.../LAMMPS/meam/log.meam.shear.18Feb13.linux.1 | 169 +
.../LAMMPS/meam/log.meam.shear.18Feb13.linux.4 | 169 +
examples/LAMMPS/meam/log.meam.shear.9Jan12.linux.1 | 165 -
examples/LAMMPS/meam/log.meam.shear.9Jan12.linux.4 | 165 -
examples/LAMMPS/melt/log.melt.18Feb13.linux.1 | 60 +
examples/LAMMPS/melt/log.melt.18Feb13.linux.4 | 60 +
examples/LAMMPS/melt/log.melt.9Jan12.linux.1 | 57 -
examples/LAMMPS/melt/log.melt.9Jan12.linux.4 | 57 -
.../LAMMPS/micelle/log.micelle.18Feb13.linux.1 | 209 +
.../LAMMPS/micelle/log.micelle.18Feb13.linux.4 | 209 +
examples/LAMMPS/micelle/log.micelle.9Jan12.linux.1 | 205 -
examples/LAMMPS/micelle/log.micelle.9Jan12.linux.4 | 205 -
examples/LAMMPS/min/log.min.18Feb13.linux.1 | 115 +
examples/LAMMPS/min/log.min.18Feb13.linux.4 | 115 +
examples/LAMMPS/min/log.min.9Jan12.linux.1 | 111 -
examples/LAMMPS/min/log.min.9Jan12.linux.4 | 111 -
examples/LAMMPS/min/log.min.box.18Feb13.linux.1 | 353 +
examples/LAMMPS/min/log.min.box.18Feb13.linux.4 | 353 +
examples/LAMMPS/min/log.min.box.9Jan12.linux.1 | 352 -
examples/LAMMPS/min/log.min.box.9Jan12.linux.4 | 352 -
examples/LAMMPS/msst/log.msst.18Feb13.linux.1 | 135 +
examples/LAMMPS/msst/log.msst.18Feb13.linux.4 | 135 +
examples/LAMMPS/msst/log.msst.9Jan12.linux.1 | 130 -
examples/LAMMPS/msst/log.msst.9Jan12.linux.4 | 130 -
examples/LAMMPS/neb/final.hop1 | 1 +
examples/LAMMPS/neb/final.hop2 | 1 +
examples/LAMMPS/neb/log.neb.hop1.18Feb13.linux.4 | 11 +
examples/LAMMPS/neb/log.neb.hop1.9Jan12.linux.4 | 11 -
examples/LAMMPS/neb/log.neb.hop2.18Feb13.linux.4 | 19 +
examples/LAMMPS/neb/log.neb.hop2.9Jan12.linux.4 | 19 -
examples/LAMMPS/nemd/in.nemd | 2 +-
examples/LAMMPS/nemd/log.nemd.18Feb13.linux.1 | 112 +
examples/LAMMPS/nemd/log.nemd.18Feb13.linux.4 | 112 +
examples/LAMMPS/nemd/log.nemd.9Jan12.linux.1 | 109 -
examples/LAMMPS/nemd/log.nemd.9Jan12.linux.4 | 109 -
.../LAMMPS/obstacle/log.obstacle.18Feb13.linux.1 | 137 +
.../LAMMPS/obstacle/log.obstacle.18Feb13.linux.4 | 137 +
.../LAMMPS/obstacle/log.obstacle.9Jan12.linux.1 | 135 -
.../LAMMPS/obstacle/log.obstacle.9Jan12.linux.4 | 135 -
examples/LAMMPS/peptide/in.peptide | 2 +-
.../LAMMPS/peptide/log.peptide.18Feb13.linux.1 | 164 +
.../LAMMPS/peptide/log.peptide.18Feb13.linux.4 | 164 +
examples/LAMMPS/peptide/log.peptide.9Jan12.linux.1 | 159 -
examples/LAMMPS/peptide/log.peptide.9Jan12.linux.4 | 159 -
examples/LAMMPS/peri/log.peri.18Feb13.linux.1 | 84 +
examples/LAMMPS/peri/log.peri.18Feb13.linux.4 | 84 +
examples/LAMMPS/peri/log.peri.9Jan12.linux.1 | 81 -
examples/LAMMPS/peri/log.peri.9Jan12.linux.4 | 81 -
examples/LAMMPS/prd/log.prd.0.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.0.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.1.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.1.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.18Feb13.linux.4 | 12 +
examples/LAMMPS/prd/log.prd.2.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.2.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.3.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.3.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.9Jan12.linux.4 | 12 -
examples/LAMMPS/reax/AB/in.AB | 2 +-
examples/LAMMPS/reax/Au_O/in.AuO | 2 +-
examples/LAMMPS/reax/CHO/in.CHO | 2 +-
examples/LAMMPS/reax/Fe_O_H/in.FeOH3 | 2 +-
examples/LAMMPS/reax/Fluorographene/README | 13 +
examples/LAMMPS/reax/Fluorographene/data.FC | 17296 +++
examples/LAMMPS/reax/Fluorographene/dumpnpt.xyz | 17282 +++
examples/LAMMPS/reax/Fluorographene/ffield.reax.FC | 361 +
examples/LAMMPS/reax/Fluorographene/in.FC | 32 +
examples/LAMMPS/reax/Fluorographene/log.FC | 290 +
examples/LAMMPS/reax/RDX/in.RDX | 2 +-
examples/LAMMPS/reax/README | 49 +-
examples/LAMMPS/reax/V_O_H/in.VOH | 2 +-
examples/LAMMPS/reax/Zn_O_H/ffield.reax.ZnOH | 2 +-
examples/LAMMPS/reax/Zn_O_H/in.ZnOH2 | 2 +-
examples/LAMMPS/reax/in.reaxc.rdx | 2 +-
examples/LAMMPS/reax/in.reaxc.tatb | 6 +-
examples/LAMMPS/reax/log.reax.rdx.18Feb13.linux.1 | 81 +
examples/LAMMPS/reax/log.reax.rdx.18Feb13.linux.4 | 81 +
examples/LAMMPS/reax/log.reax.rdx.9Jan12.linux.1 | 170 -
examples/LAMMPS/reax/log.reax.rdx.9Jan12.linux.4 | 170 -
examples/LAMMPS/reax/log.reax.tatb.18Feb13.linux.1 | 77 +
examples/LAMMPS/reax/log.reax.tatb.18Feb13.linux.4 | 77 +
examples/LAMMPS/reax/log.reax.tatb.9Jan12.linux.1 | 97 -
examples/LAMMPS/reax/log.reax.tatb.9Jan12.linux.4 | 97 -
examples/LAMMPS/reax/log.reaxc.rdx.18Feb13.linux.1 | 81 +
examples/LAMMPS/reax/log.reaxc.rdx.18Feb13.linux.4 | 81 +
examples/LAMMPS/reax/log.reaxc.rdx.9Jan12.linux.1 | 78 -
examples/LAMMPS/reax/log.reaxc.rdx.9Jan12.linux.4 | 78 -
.../LAMMPS/reax/log.reaxc.tatb.18Feb13.linux.1 | 79 +
.../LAMMPS/reax/log.reaxc.tatb.18Feb13.linux.4 | 79 +
examples/LAMMPS/reax/log.reaxc.tatb.9Jan12.linux.1 | 95 -
examples/LAMMPS/reax/log.reaxc.tatb.9Jan12.linux.4 | 95 -
examples/LAMMPS/rigid/data.rigid.tnr | 7220 ++
examples/LAMMPS/rigid/in.rigid.tnr | 89 +
examples/LAMMPS/rigid/log.rigid.18Feb13.linux.1 | 310 +
examples/LAMMPS/rigid/log.rigid.18Feb13.linux.4 | 310 +
examples/LAMMPS/rigid/log.rigid.9Jan12.linux.1 | 306 -
examples/LAMMPS/rigid/log.rigid.9Jan12.linux.4 | 306 -
.../LAMMPS/rigid/log.rigid.poems.18Feb13.linux.1 | 310 +
.../LAMMPS/rigid/log.rigid.poems.18Feb13.linux.4 | 310 +
.../LAMMPS/rigid/log.rigid.poems.9Jan12.linux.1 | 306 -
.../LAMMPS/rigid/log.rigid.poems.9Jan12.linux.4 | 306 -
.../LAMMPS/rigid/log.rigid.poems2.18Feb13.linux.1 | 314 +
.../LAMMPS/rigid/log.rigid.poems2.18Feb13.linux.4 | 314 +
.../LAMMPS/rigid/log.rigid.poems2.9Jan12.linux.1 | 310 -
.../LAMMPS/rigid/log.rigid.poems2.9Jan12.linux.4 | 310 -
examples/LAMMPS/shear/log.shear.18Feb13.linux.1 | 165 +
examples/LAMMPS/shear/log.shear.18Feb13.linux.4 | 165 +
examples/LAMMPS/shear/log.shear.9Jan12.linux.1 | 161 -
examples/LAMMPS/shear/log.shear.9Jan12.linux.4 | 161 -
.../LAMMPS/shear/log.shear.void.18Feb13.linux.1 | 166 +
.../LAMMPS/shear/log.shear.void.18Feb13.linux.4 | 166 +
.../LAMMPS/shear/log.shear.void.9Jan12.linux.1 | 162 -
.../LAMMPS/shear/log.shear.void.9Jan12.linux.4 | 162 -
examples/LAMMPS/srd/in.srd.mixture | 1 -
.../LAMMPS/srd/log.srd.mixture.18Feb13.linux.1 | 142 +
.../LAMMPS/srd/log.srd.mixture.18Feb13.linux.4 | 142 +
examples/LAMMPS/srd/log.srd.mixture.9Jan12.linux.1 | 223 -
examples/LAMMPS/srd/log.srd.mixture.9Jan12.linux.4 | 223 -
examples/LAMMPS/srd/log.srd.pure.18Feb13.linux.1 | 592 +
examples/LAMMPS/srd/log.srd.pure.18Feb13.linux.4 | 592 +
examples/LAMMPS/srd/log.srd.pure.9Jan12.linux.1 | 138 -
examples/LAMMPS/srd/log.srd.pure.9Jan12.linux.4 | 138 -
examples/LAMMPS/tad/log.tad.0.18Feb13.linux.3 | 12877 +++
examples/LAMMPS/tad/log.tad.0.9Jan12.linux.3 | 7530 --
examples/LAMMPS/tad/log.tad.1.18Feb13.linux.3 | 7814 ++
examples/LAMMPS/tad/log.tad.1.9Jan12.linux.3 | 2868 -
examples/LAMMPS/tad/log.tad.18Feb13.linux.3 | 114 +
examples/LAMMPS/tad/log.tad.2.18Feb13.linux.3 | 7814 ++
examples/LAMMPS/tad/log.tad.2.9Jan12.linux.3 | 2868 -
examples/LAMMPS/tad/log.tad.9Jan12.linux.3 | 39 -
examples/LAMMPS/tad/log.tad.neb.18Feb13.linux.3 | 1423 +
examples/LAMMPS/tad/log.tad.neb.9Jan12.linux.3 | 487 -
examples/LAMMPS/voronoi/in.voronoi | 154 +
examples/LAMMPS/voronoi/log.voronoi.4Aug13.macos.1 | 368 +
examples/LAMMPS/voronoi/log.voronoi.4Aug13.macos.4 | 368 +
.../Tutorials_public/chute_wear/in.chute_wear | 8 +-
.../chute_wear/{ => meshes}/insertion_face.stl | 0
.../chute_wear/{ => meshes}/simple_chute.stl | 0
.../post/dummy => chute_wear/post/.gitignore} | 0
.../Tutorials_public/chute_wear/post/dummy | 1 -
.../Tutorials_public/chute_wear/postscript | 2 +-
.../Tutorials_public/chute_wear/run.config | 9 +
.../LIGGGHTS/Tutorials_public/cohesion/in.cohesion | 8 +-
.../Tutorials_public/cohesion/in.noCohesion | 8 +-
.../post/dummy => cohesion/post/.gitignore} | 0
.../LIGGGHTS/Tutorials_public/cohesion/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/cohesion/run.config | 14 +
.../Tutorials_public/contactModels/in.newModels | 8 +-
.../Tutorials_public/contactModels/in.oldModels | 2 +-
.../post/dummy => contactModels/post/.gitignore} | 0
.../Tutorials_public/contactModels/post/dummy | 1 -
.../Tutorials_public/contactModels/run.config | 9 +
.../LIGGGHTS/Tutorials_public/conveyor/in.conveyor | 10 +-
.../Tutorials_public/conveyor/{ => meshes}/box.stl | 0
.../conveyor/{ => meshes}/conveyor.stl | 0
.../conveyor/{ => meshes}/insertion_face.stl | 0
.../post/dummy => conveyor/post/.gitignore} | 0
.../LIGGGHTS/Tutorials_public/conveyor/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/conveyor/run.config | 9 +
.../Tutorials_public/heatTransfer_1/in.heatGran | 8 +-
.../post/dummy => heatTransfer_1/post/.gitignore} | 0
.../Tutorials_public/heatTransfer_1/post/dummy | 1 -
.../Tutorials_public/heatTransfer_1/run.config | 9 +
.../LIGGGHTS/Tutorials_public/heatTransfer_2/LOG | 896 -
.../Tutorials_public/heatTransfer_2/in.heatGran | 8 +-
.../post/dummy => heatTransfer_2/post/.gitignore} | 0
.../Tutorials_public/heatTransfer_2/post/dummy | 1 -
.../Tutorials_public/heatTransfer_2/run.config | 9 +
.../Tutorials_public/hysteresis/in.hysteresis | 8 +-
.../Tutorials_public/hysteresis/in.noHysteresis | 8 +-
.../post/dummy => hysteresis/post/.gitignore} | 0
.../Tutorials_public/hysteresis/post/dummy | 1 -
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tools/restart2data.cpp | 0
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 +
4864 files changed, 1021821 insertions(+), 219583 deletions(-)
diff --cc doc/neigh_modify.html
index 3565337,c738c29..6afaca9
--- a/doc/neigh_modify.html
+++ b/doc/neigh_modify.html
@@@ -43,8 -46,8 +46,13 @@@
N = number of pairs stored in a single neighbor page
<I>one</I> value = N
N = max number of neighbors of one atom
++<<<<<<< HEAD
+ <I>contactHistoryDistanceFactor</I> value = N
+ N = contact history distance factor used to keep contact history of non-contacting particles (must be > 1).
++=======
+ <I>contact_distance_factor</I> value = N
+ N = contact distance factor used to extend the range of granular neighbor lists (must be > 1).
++>>>>>>> upstream/3.0.0
<I>binsize</I> value = size
size = bin size for neighbor list construction (distance units)
</PRE>
@@@ -57,7 -60,7 +65,11 @@@ neigh_modify exclude type 2
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
neigh_modify exclude molecule rigid
++<<<<<<< HEAD
+neigh_modify delay 0 contactHistoryDistanceFactor 2.0
++=======
+ neigh_modify delay 0 contact_distance_factor 1.5
++>>>>>>> upstream/3.0.0
</PRE>
<P><B>Description:</B>
</P>
@@@ -83,10 -86,28 +95,31 @@@ lists should be rebuilt
<P>When the rRESPA integrator is used (see the <A HREF = "run_style.html">run_style</A>
command), the <I>every</I> and <I>delay</I> parameters refer to the longest
(outermost) timestep.
+The <I>contactHistoryDistanceFactor</I> setting has to be used while using fix liquid transfer.
+This factor must be either 1 or greater than 1, to ensure that the extra contact history values are not lost
+when the neighbor lists are rebuilt.
</P>
+ <P>The <I>contact_distance_factor</I> setting can be used to increase the range
+ of granular neighbor lists. When <I>contact_distance_factor</I> > 1.0,
+ instead of the standard criterion ri+rj+skin < distance, LIGGGHTS is
+ checking for <I>contact_distance_factor</I> *(ri+rj)+skin < distance to
+ decided if a pair of granular particles goes into a neighbor list.
+ </P>
+ <P>The <I>cluster</I> option does a sanity test every time neighbor lists are
+ built for bond, angle, dihedral, and improper interactions, to check
+ that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It
+ does this by computing the distance between pairs of atoms in the
+ interaction and insuring they are not further apart than half the
+ periodic box length. If they are, an error is generated, since the
+ interaction would be computed between far-away atoms instead of their
+ nearby periodic images. The only way this should happen is if the
+ pairwise cutoff is so short that atoms that are part of the same
+ interaction are not communicated as ghost atoms. This is an unusual
+ model (e.g. no pair interactions at all) and the problem can be fixed
+ by use of the <A HREF = "communicate.html">communicate cutoff</A> command. Note
+ that to save time, the default <I>cluster</I> setting is <I>no</I>, so that this
+ check is not performed.
+ </P>
<P>The <I>include</I> option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful for models where a
large portion of the simulation is particles that do not interact with
diff --cc doc/neigh_modify.txt
index 0bf8511,d0773dc..cb0ebe3
--- a/doc/neigh_modify.txt
+++ b/doc/neigh_modify.txt
@@@ -39,8 -42,8 +42,13 @@@ keyword = {delay} or {every} or {check
N = number of pairs stored in a single neighbor page
{one} value = N
N = max number of neighbors of one atom
++<<<<<<< HEAD
+ {contactHistoryDistanceFactor} value = N
+ N = contact history distance factor used to keep contact history of non-contacting particles (must be > 1).
++=======
+ {contact_distance_factor} value = N
+ N = contact distance factor used to extend the range of granular neighbor lists (must be > 1).
++>>>>>>> upstream/3.0.0
{binsize} value = size
size = bin size for neighbor list construction (distance units) :pre
:ule
@@@ -52,7 -55,7 +60,11 @@@ neigh_modify exclude type 2
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
neigh_modify exclude molecule rigid
++<<<<<<< HEAD
+neigh_modify delay 0 contactHistoryDistanceFactor 2.0 :pre
++=======
+ neigh_modify delay 0 contact_distance_factor 1.5 :pre
++>>>>>>> upstream/3.0.0
[Description:]
@@@ -78,10 -81,28 +90,31 @@@ lists should be rebuilt
When the rRESPA integrator is used (see the "run_style"_run_style.html
command), the {every} and {delay} parameters refer to the longest
(outermost) timestep.
+The {contactHistoryDistanceFactor} setting has to be used while using fix liquid transfer.
+This factor must be either 1 or greater than 1, to ensure that the extra contact history values are not lost
+when the neighbor lists are rebuilt.
+ The {contact_distance_factor} setting can be used to increase the range
+ of granular neighbor lists. When {contact_distance_factor} > 1.0,
+ instead of the standard criterion ri+rj+skin < distance, LIGGGHTS is
+ checking for {contact_distance_factor} *(ri+rj)+skin < distance to
+ decided if a pair of granular particles goes into a neighbor list.
+
+ The {cluster} option does a sanity test every time neighbor lists are
+ built for bond, angle, dihedral, and improper interactions, to check
+ that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It
+ does this by computing the distance between pairs of atoms in the
+ interaction and insuring they are not further apart than half the
+ periodic box length. If they are, an error is generated, since the
+ interaction would be computed between far-away atoms instead of their
+ nearby periodic images. The only way this should happen is if the
+ pairwise cutoff is so short that atoms that are part of the same
+ interaction are not communicated as ghost atoms. This is an unusual
+ model (e.g. no pair interactions at all) and the problem can be fixed
+ by use of the "communicate cutoff"_communicate.html command. Note
+ that to save time, the default {cluster} setting is {no}, so that this
+ check is not performed.
+
The {include} option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful for models where a
large portion of the simulation is particles that do not interact with
diff --cc doc/set.html
index 34a9b49,edb7b4b..da8bcba
--- a/doc/set.html
+++ b/doc/set.html
@@@ -66,8 -80,11 +80,14 @@@
<I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
<I>improper</I> value = improper type for all impropers between selected atoms
<I>meso_e</I> value = energy of SPH particles (need units)
+ value can be an atom-style variable (see below)
<I>meso_cv</I> value = heat capacity of SPH particles (need units)
+ value can be an atom-style variable (see below)
<I>meso_rho</I> value = density of SPH particles (need units)
++<<<<<<< HEAD
++=======
+ value can be an atom-style variable (see below)
++>>>>>>> upstream/3.0.0
<I>add</I> value = yes no
yes = add per-atom quantities to a region or a group
<I>until</I> value = final timestep
diff --cc doc/set.txt
index 0bcc0ff,993f3d8..6079702
--- a/doc/set.txt
+++ b/doc/set.txt
@@@ -62,8 -76,11 +76,14 @@@ keyword = {type} or {type/fraction} or
{dihedral} value = dihedral type for all dihedrals between selected atoms
{improper} value = improper type for all impropers between selected atoms
{meso_e} value = energy of SPH particles (need units)
+ value can be an atom-style variable (see below)
{meso_cv} value = heat capacity of SPH particles (need units)
+ value can be an atom-style variable (see below)
{meso_rho} value = density of SPH particles (need units)
++<<<<<<< HEAD
++=======
+ value can be an atom-style variable (see below)
++>>>>>>> upstream/3.0.0
{add} value = yes no
yes = add per-atom quantities to a region or a group
{until} value = final timestep
diff --cc src/atom_vec_ellipsoid.cpp
index 9dae26b,dae8f39..cfc1517
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@@ -650,14 -656,14 +656,20 @@@ int AtomVecEllipsoid::pack_border_vel(i
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
- if (ellipsoid[j] < 0) buf[m++] = 0;
+ buf[m++] = ubuf(tag[j]).d;
+ buf[m++] = ubuf(type[j]).d;
+ buf[m++] = ubuf(mask[j]).d;
+ if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
else {
++<<<<<<< HEAD
+ buf[m++] = 1;
+ shape = bonus[ellipsoid[j]].shape;
+ quat = bonus[ellipsoid[j]].quat;
++=======
+ buf[m++] = ubuf(1).d;
+ shape = bonus[ellipsoid[j]].shape;
+ quat = bonus[ellipsoid[j]].quat;
++>>>>>>> upstream/3.0.0
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
diff --cc src/comm.cpp
index 94cae84,3e81fb2..f38d982
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@@ -561,10 -586,10 +586,17 @@@ void Comm::setup(
dw_->n2(nright);
dw_->center(c);
double cutghmax = MathExtraLiggghts::max(cutghost[0],cutghost[1],cutghost[2]);
++<<<<<<< HEAD
+ pleft[0] = c[0] - nleft[0] * (atom->radius ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
+ pleft[1] = c[1] - nleft[1] * (atom->radius ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
+ pright[0] = c[0] - nright[0] * (atom->radius ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
+ pright[1] = c[1] - nright[1] * (atom->radius ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
++=======
+ pleft[0] = c[0] - nleft[0] * (use_gran_opt() ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
+ pleft[1] = c[1] - nleft[1] * (use_gran_opt() ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
+ pright[0] = c[0] - nright[0] * (use_gran_opt() ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
+ pright[1] = c[1] - nright[1] * (use_gran_opt() ? (cutghmax / 2. + neighbor->skin/2.) : cutghmax);
++>>>>>>> upstream/3.0.0
}
@@@ -608,7 -633,7 +640,11 @@@
if (style == SINGLE) {
if (ineed < 2) slablo[iswap] = -BIG;
else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
++<<<<<<< HEAD
+ slabhi[iswap] = sublo[dim] + (atom->radius ? (cutghost[dim] / 2. + neighbor->skin/2.) : cutghost[dim]);
++=======
+ slabhi[iswap] = sublo[dim] + (use_gran_opt() ? (cutghost[dim] / 2. + neighbor->skin/2.) : cutghost[dim]);
++>>>>>>> upstream/3.0.0
} else {
for (i = 1; i <= ntypes; i++) {
if (ineed < 2) multilo[iswap][i] = -BIG;
@@@ -629,7 -654,7 +665,11 @@@
sendproc[iswap] = procneigh[dim][1];
recvproc[iswap] = procneigh[dim][0];
if (style == SINGLE) {
++<<<<<<< HEAD
+ slablo[iswap] = subhi[dim] - (atom->radius ? (cutghost[dim] / 2. + neighbor->skin/2.) : cutghost[dim]);
++=======
+ slablo[iswap] = subhi[dim] - (use_gran_opt() ? (cutghost[dim] / 2. + neighbor->skin/2.) : cutghost[dim]);
++>>>>>>> upstream/3.0.0
if (ineed < 2) slabhi[iswap] = BIG;
else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
} else {
diff --cc src/comm.h
index 88759e5,e4b974d..b834d2d
--- a/src/comm.h
+++ b/src/comm.h
@@@ -131,6 -144,7 +144,10 @@@ class Comm : protected Pointers
virtual void free_swap(); // free swap arrays
virtual void free_multi(); // free multi arrays
++<<<<<<< HEAD
++=======
+ bool use_gran_opt();
++>>>>>>> upstream/3.0.0
bool decide(int i,int dim,double lo,double hi,int ineed);
bool decide_wedge(int i,int dim,double lo,double hi,int ineed);
diff --cc src/comm_I.h
index 45afbd8,273a01d..49c9c99
--- a/src/comm_I.h
+++ b/src/comm_I.h
@@@ -28,6 -28,17 +28,20 @@@
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
++<<<<<<< HEAD
++=======
+ decide if use comm optimizations for granular systems
+ don't use for triclinic (current implementation not valid for triclinic,
+ would have to translate radius into triclinic coordinates)
+ ------------------------------------------------------------------------- */
+
+ inline bool Comm::use_gran_opt()
+ {
+ return (0 == domain->triclinic && atom->radius);
+ }
+
+ /* ----------------------------------------------------------------------
++>>>>>>> upstream/3.0.0
decide if border element, optimization for granular
------------------------------------------------------------------------- */
@@@ -36,8 -47,8 +50,13 @@@ inline bool Comm::decide(int i,int dim,
double **x = atom->x;
double *radius = atom->radius;
++<<<<<<< HEAD
+ if( ((ineed % 2 == 0) && x[i][dim] >= lo && x[i][dim] <= (hi + (radius? (radius[i]) : 0.)) ) ||
+ ((ineed % 2 == 1) && x[i][dim] >= (lo - (radius? radius[i] : 0.)) && x[i][dim] <= hi ) )
++=======
+ if( ((ineed % 2 == 0) && x[i][dim] >= lo && x[i][dim] <= (hi + (use_gran_opt()? (radius[i]) : 0.)) ) ||
+ ((ineed % 2 == 1) && x[i][dim] >= (lo - (use_gran_opt()? radius[i] : 0.)) && x[i][dim] <= hi ) )
++>>>>>>> upstream/3.0.0
return true;
return false;
@@@ -58,7 -69,7 +77,11 @@@ inline bool Comm::decide_wedge(int i,in
if (ineed % 2 == 0)
{
vectorSubtract2D(coo,pleft,d);
++<<<<<<< HEAD
+ if(vectorDot2D(d,nleft) >= -(radius? radius[i] : 0.))
++=======
+ if(vectorDot2D(d,nleft) >= -(use_gran_opt()? radius[i] : 0.))
++>>>>>>> upstream/3.0.0
{
return true;
@@@ -68,7 -79,7 +91,11 @@@
else if (ineed % 2 == 1)
{
vectorSubtract2D(coo,pright,d);
++<<<<<<< HEAD
+ if(vectorDot2D(d,nright) >= -(radius? radius[i] : 0.))
++=======
+ if(vectorDot2D(d,nright) >= -(use_gran_opt()? radius[i] : 0.))
++>>>>>>> upstream/3.0.0
{
return true;
diff --cc src/compute_erotate_sphere.cpp
index 20e9a09,b245fc7..b3bb9e3
--- a/src/compute_erotate_sphere.cpp
+++ b/src/compute_erotate_sphere.cpp
@@@ -50,6 -60,7 +60,10 @@@ ComputeERotateSphere::ComputeERotateSph
void ComputeERotateSphere::init()
{
pfactor = 0.5 * force->mvv2e * INERTIA;
++<<<<<<< HEAD
++=======
+
++>>>>>>> upstream/3.0.0
fix_ms = static_cast<FixMultisphere*>(modify->find_fix_style("multisphere",0));
}
diff --cc src/container_base.cpp
index 4ce62a0,4f9c343..969da4e
--- a/src/container_base.cpp
+++ b/src/container_base.cpp
@@@ -45,21 -45,21 +45,39 @@@ using namespace LAMMPS_NS
{
}
++<<<<<<< HEAD
+ ContainerBase::ContainerBase(char *_id)
+ : id_(0),
+ communicationType_(COMM_TYPE_MANUAL),
+ refFrame_(REF_FRAME_UNDEFINED),
+ restartType_(RESTART_TYPE_UNDEFINED),
+ scalePower_(-1)
+ {
+ id_ = new char[strlen(_id)+1];
+ strcpy(id_,_id);
+ }
+
+ ContainerBase::ContainerBase(char *_id, char* _comm, char* _ref, char *_restart,int _scalePower)
+ : id_(0),
+ communicationType_(COMM_TYPE_MANUAL),
+ refFrame_(REF_FRAME_UNDEFINED),
++=======
+ ContainerBase::ContainerBase(const char *_id)
+ : id_(0),
+ communicationType_(COMM_TYPE_MANUAL),
+ refFrame_(REF_FRAME_UNDEFINED),
+ restartType_(RESTART_TYPE_UNDEFINED),
+ scalePower_(-1)
+ {
+ id_ = new char[strlen(_id)+1];
+ strcpy(id_,_id);
+ }
+
+ ContainerBase::ContainerBase(const char *_id, const char* _comm, const char* _ref, const char *_restart,int _scalePower)
+ : id_(0),
+ communicationType_(COMM_TYPE_MANUAL),
+ refFrame_(REF_FRAME_UNDEFINED),
++>>>>>>> upstream/3.0.0
restartType_(RESTART_TYPE_UNDEFINED),
scalePower_(-1)
{
diff --cc src/container_base.h
index bed638f,2597f95..d5421e0
--- a/src/container_base.h
+++ b/src/container_base.h
@@@ -45,7 -45,7 +45,11 @@@ namespace LAMMPS_N
{
public:
++<<<<<<< HEAD
+ ContainerBase(char *_id);
++=======
+ ContainerBase(const char *_id);
++>>>>>>> upstream/3.0.0
virtual ~ContainerBase();
@@@ -107,7 -107,7 +111,11 @@@
protected:
++<<<<<<< HEAD
+ ContainerBase(char *_id, char* _comm, char* _ref, char *_restart,int _scalePower);
++=======
+ ContainerBase(const char *_id, const char* _comm, const char* _ref, const char *_restart,int _scalePower);
++>>>>>>> upstream/3.0.0
ContainerBase(ContainerBase const &orig);
inline bool isScaleInvariant();
diff --cc src/domain.cpp
index d73e79f,e0d8d06..fbaa1d0
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@@ -1416,4 -1641,3 +1641,7 @@@ void Domain::box_corners(
corners[7][0] = 1.0; corners[7][1] = 1.0; corners[7][2] = 1.0;
lamda2x(corners[7],corners[7]);
}
++<<<<<<< HEAD
+
++=======
++>>>>>>> upstream/3.0.0
diff --cc src/domain.h
index fb4f37d,0588e11..b296f12
--- a/src/domain.h
+++ b/src/domain.h
@@@ -126,7 -135,9 +135,12 @@@ class Domain : protected Pointers
void delete_region(int, char **);
int find_region(char *);
virtual void set_boundary(int, char **, int);
++<<<<<<< HEAD
++=======
+ void set_box(int, char **);
++>>>>>>> upstream/3.0.0
virtual void print_box(const char *);
+ void boundary_string(char *);
virtual void lamda2x(int);
virtual void x2lamda(int);
@@@ -136,25 -147,36 +150,58 @@@
void bbox(double *, double *, double *, double *);
void box_corners();
++<<<<<<< HEAD
+ int is_in_domain(double* pos);
+ int is_in_subdomain(double* pos);
+ int is_in_extended_subdomain(double* pos);
+ double dist_subbox_borders(double* pos);
+ int is_periodic_ghost(int i);
+ bool is_owned_or_first_ghost(int i);
+
+ virtual int is_in_domain_wedge(double* pos) {return 0;}
+ virtual int is_in_subdomain_wedge(double* pos) {return 0;}
+ virtual int is_in_extended_subdomain_wedge(double* pos) {return 0;}
+ virtual double dist_subbox_borders_wedge(double* pos) {return 0.;}
+ virtual int is_periodic_ghost_wedge(int i) {return 0;}
+
+ bool is_wedge;
+
+ private:
+ double small[3]; // fractions of box lengths
+};
+
++=======
+ // minimum image convention check
+ // return 1 if any distance > 1/2 of box size
+ // inline since called from neighbor build inner loop
+
+ inline int minimum_image_check(double dx, double dy, double dz) {
+ if (xperiodic && fabs(dx) > xprd_half) return 1;
+ if (yperiodic && fabs(dy) > yprd_half) return 1;
+ if (zperiodic && fabs(dz) > zprd_half) return 1;
+ return 0;
+ }
+
+ int is_in_domain(double* pos);
+ int is_in_subdomain(double* pos);
+ int is_in_extended_subdomain(double* pos);
+ double dist_subbox_borders(double* pos);
+ int is_periodic_ghost(int i);
+ bool is_owned_or_first_ghost(int i);
+
+ virtual int is_in_domain_wedge(double* pos) { UNUSED(pos); return 0; }
+ virtual int is_in_subdomain_wedge(double* pos) { UNUSED(pos); return 0; }
+ virtual int is_in_extended_subdomain_wedge(double* pos) { UNUSED(pos); return 0; }
+ virtual double dist_subbox_borders_wedge(double* pos) { UNUSED(pos); return 0.; }
+ virtual int is_periodic_ghost_wedge(int i) { UNUSED(i); return 0;}
+
+ bool is_wedge;
+
+ private:
+ double small[3]; // fractions of box lengths
+ };
+
++>>>>>>> upstream/3.0.0
#include "domain_I.h"
}
diff --cc src/fix_ave_spatial.cpp
index 734cfa9,e3e2b03..562e22c
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@@ -332,22 -321,9 +321,26 @@@ FixAveSpatial::FixAveSpatial(LAMMPS *lm
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+3*ndim+i]);
fprintf(fp,"\n");
}
+ filepos = ftell(fp);
}
++<<<<<<< HEAD
+ if (fp2 && me == 0) {
+ fprintf(fp2,"# Spatial-averaged data for fix %s and group %s\n",
+ id,arg[1]);
+ fprintf(fp2,"# Mean and standard deviation for all bins including between N1=%i and N2=%i particles\n",lowerLimit,upperLimit);
+ fprintf(fp2,"# Timestep Natoms Nbins MaxAtomsPerBin NbinsEmpty Nbins<N1 Nbins>N2 Nsamples NatomsPerSample ");
+
+ for (int i = 0; i < nvalues; i++) {
+ fprintf(fp2,"{%s: trueMean samplesMean Std} ",arg[6+3*ndim+i]);
+ }
+ fprintf(fp2,"\n");
+ }
+
+ fflush(fp2);
+
++=======
++>>>>>>> upstream/3.0.0
delete [] title1;
delete [] title2;
delete [] title3;
@@@ -851,82 -825,10 +842,73 @@@ void FixAveSpatial::end_of_step(
}
fflush(fp);
++<<<<<<< HEAD
+ }
+
+ // calculate mean and standard deviation
+
+ if (calcStd != 0) {
+ int n_samples = 0;
+ int n_empty = 0;
+ int n_lower = 0;
+ int n_higher = 0;
+ double *true_mean, *samples_mean, *std;
+ double diff, count_sum, count_samples, samples_average, count_max;
+
+ memory->create(true_mean,nvalues,"ave/spatial:true_mean");
+ memory->create(samples_mean,nvalues,"ave/spatial:samples_mean");
+ memory->create(std,nvalues,"ave/spatial:std");
+
+ count_sum = 0;
+ count_samples = 0;
+ samples_average = 0;
+ count_max = 0;
+
+ for (i = 0; i < nvalues; i++) {
+ true_mean[i] = 0;
+
+ for (m = 0; m < nbins; m++) {
+ true_mean[i] += values_total[m][i] * count_total[m];
+ if (i == 0) count_sum += count_total[m];
+ }
+
+ if (count_sum != 0) true_mean[i] /= count_sum;
+
+ samples_mean[i] = 0;
+ std[i] = 0;
+ }
+
+ for (m = 0; m < nbins; m++) {
+ if (count_total[m] > count_max) count_max = count_total[m];
+ if (count_total[m] == 0) n_empty += 1;
+ else if (count_total[m] < lowerLimit) n_lower += 1;
+ else if (count_total[m] > upperLimit) n_higher += 1;
+ else {
+ n_samples += 1;
+ count_samples += count_total[m];
+ for (i = 0; i < nvalues; i++) {
+ samples_mean[i] += values_total[m][i];
+ diff = values_total[m][i] - true_mean[i];
+ std[i] += diff * diff;
+ }
+ }
+ }
+
+ if (n_samples != 0) {
+ for (i = 0; i < nvalues; i++) {
+ samples_average = count_samples / n_samples; // average # particles per sample
+ samples_mean[i] /= n_samples;
+ std[i] /= n_samples; // not(n_sample-1) since true_mean is the true Average
+ std[i] = sqrt(std[i]);
+ samples_mean[i] /= norm;
+ std[i] /= norm;
+ }
++=======
+ if (overwrite) {
+ long fileend = ftell(fp);
+ ftruncate(fileno(fp),fileend);
++>>>>>>> upstream/3.0.0
}
-
- // output to file
- if (fp2 && me == 0) {
- fprintf(fp2,BIGINT_FORMAT " %g %d %g %d %d %d %d %g",
- ntimestep,count_sum,nbins,count_max,n_empty,n_lower,n_higher,n_samples,samples_average);
- for (i = 0; i < nvalues; i++) {
- fprintf(fp2," %g %g %g",true_mean[i],samples_mean[i],std[i]); //;
- }
- fprintf(fp2,"\n");
- fflush(fp2);
- }
-
- memory->destroy(true_mean);
- memory->destroy(samples_mean);
- memory->destroy(std);
}
}
diff --cc src/fix_cfd_coupling_force_implicit.cpp
index 1384f4f,f082a3e..a7b5ac2
--- a/src/fix_cfd_coupling_force_implicit.cpp
+++ b/src/fix_cfd_coupling_force_implicit.cpp
@@@ -47,9 -47,8 +47,13 @@@ FixCfdCouplingForceImplicit::FixCfdCoup
fix_Ksl_(0),
fix_uf_(0)
{
+ int iarg = 3;
++<<<<<<< HEAD
+ int iarg = 3;
+
++=======
++>>>>>>> upstream/3.0.0
bool hasargs = true;
while(iarg < narg && hasargs)
{
@@@ -68,7 -67,6 +72,10 @@@
}
nevery = 1;
++<<<<<<< HEAD
+
++=======
++>>>>>>> upstream/3.0.0
}
/* ---------------------------------------------------------------------- */
@@@ -97,7 -95,7 +104,11 @@@ void FixCfdCouplingForceImplicit::post_
// register Ksl
if(!fix_Ksl_)
{
++<<<<<<< HEAD
+ char* fixarg[9];
++=======
+ const char* fixarg[9];
++>>>>>>> upstream/3.0.0
fixarg[0]="Ksl";
fixarg[1]="all";
fixarg[2]="property/atom";
@@@ -195,6 -193,6 +206,27 @@@ void FixCfdCouplingForceImplicit::post_
void FixCfdCouplingForceImplicit::end_of_step()
{
++<<<<<<< HEAD
++
++ if(!useCN_) return; //return if CN not used
++
++ double **x = atom->x;
++ double **v = atom->v;
++ double **f = atom->f;
++ double *rmass = atom->rmass;
++ double *mass = atom->mass;
++ int *type = atom->type;
++
++ int *mask = atom->mask;
++ int nlocal = atom->nlocal;
++ double *Ksl = fix_Ksl_->vector_atom;
++ double **uf = fix_uf_->array_atom;
++ double **dragforce = fix_dragforce_->array_atom;
++ double KslMDeltaT, deltaU;
++ double vN32[3];
++ double frc[3];
++
++=======
if(!useCN_) return; //return if CN not used
@@@ -214,6 -212,6 +246,7 @@@
double vN32[3];
double frc[3];
++>>>>>>> upstream/3.0.0
vectorZeroize3D(dragforce_total);
// add dragforce to force vector
diff --cc src/fix_contact_history.cpp
index 301f2f9,193e372..291be18
--- a/src/fix_contact_history.cpp
+++ b/src/fix_contact_history.cpp
@@@ -41,94 -42,75 +42,95 @@@ using namespace FixConst
/* ---------------------------------------------------------------------- */
FixContactHistory::FixContactHistory(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
+ Fix(lmp, narg, arg),
+ newtonflag_(0),
+ history_id_(0),
+ index_decide_noncontacting_(-1),
+ npartner_(0),
+ partner_(0),
+ contacthistory_(0),
+ maxtouch_(0),
+ pair_gran_(0),
+ computeflag_(0),
+ pgsize_(0),
+ oneatom_(0),
+ ipage_(0),
+ dpage_(0)
{
- //parse args
- if(narg < 6)
- error->fix_error(FLERR,this,"not enough parameters");
+ restart_global = 1;
+ restart_peratom = 1;
+ create_attribute = 1;
- int iarg = 3;
+ // perform initial allocation of atom-based arrays
+ // register with atom class
- if(strcmp(arg[iarg],"pair") == 0)
- is_pair = true;
- else if(strcmp(arg[iarg],"mesh") == 0)
- is_pair = false;
- else
- error->fix_error(FLERR,this,"expecting keyword 'pair' or 'mesh'");
- iarg++;
+ grow_arrays(atom->nmax);
+ atom->add_callback(0);
+ atom->add_callback(1);
- // for mesh style, read mesh
- if(!is_pair)
- {
- Fix *f = modify->find_fix_id(arg[iarg++]);
- if(!f || strncmp(f->style,"mesh/surface",12) )
- error->fix_error(FLERR,this,"wrong ID for fix mesh/surface");
- mesh_ = (static_cast<FixMeshSurface*>(f))->triMesh();
- }
+ // initialize npartner to 0 so neighbor list creation is OK the 1st time
++<<<<<<< HEAD
+ //read dnum
+ dnum = atoi(arg[iarg++]);
+
+ index_decide_noncontacting = -1;
+
+ if(dnum < 0)
+ error->all(FLERR,"dnum must be >=0 in fix contacthistory");
+ if(dnum > 10)
+ error->warning(FLERR,"dnum >10 in fix contacthistory - are you really sure you intend this?");
+
+ newtonflag = NULL;
+ history_id = NULL;
+ if(is_pair && dnum > 0)
+ {
+ //read newtonflag
+ if(narg-iarg < 2*dnum)
+ error->all(FLERR,"Illegal fix contacthistory command - not enough parameters (need to specify an id and a newtonflag for each dnum)");
++=======
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) npartner_[i] = 0;
++>>>>>>> upstream/3.0.0
- newtonflag = new int[dnum];
- //history_id = new char*[dnum];
- history_id = (char**) memory->smalloc((dnum)*sizeof(char*),"FixContactHistory:history_id");
+ //=====================
+ // parse args
+ //=====================
- for(int i = 0 ; i < dnum; i++)
- {
-
- history_id[i] = new char[strlen(arg[iarg])+1];
- strcpy(history_id[i],arg[iarg++]);
- newtonflag[i] = atoi(arg[iarg++]);
- if(newtonflag[i] != 0 && newtonflag[i] != 1)
- error->all(FLERR,"Illegal fix history command - newtonflag must be either 0 or 1");
- }
- }
+ if(narg < 4)
+ error->fix_error(FLERR,this,"not enough parameters");
- // perform initial allocation of atom-based arrays
- // register with atom class
+ iarg_ = 3;
- restart_peratom = 1;
- restart_global = 1;
- create_attribute = 1;
+ // read dnum
+ dnum_ = atoi(arg[iarg_++]);
+
+ if(dnum_ < 0)
+ error->fix_error(FLERR,this,"dnum must be >=0");
- atom->add_callback(0);
- atom->add_callback(1);
+ // do not proceed for derived classes
+ if(strcmp(style,"contacthistory"))
+ return;
+
+ // parse args
+ if(narg < 6)
+ error->fix_error(FLERR,this,"not enough parameters");
- if(is_pair)
- maxtouch = DELTA_MAXTOUCH_PAIR;
- else
- maxtouch = DELTA_MAXTOUCH_MESH;
+ // read newtonflag
+ if(narg-iarg_ < 2*dnum_)
+ error->fix_error(FLERR,this,"not enough parameters: need to specify an id and a newtonflag for each dnum");
- npartner = NULL;
- partner = NULL;
- contacthistory = NULL;
- delflag = NULL;
- pair_gran = NULL;
+ newtonflag_ = new int[dnum_];
+ history_id_ = (char**) memory->smalloc((dnum_)*sizeof(char*),"FixContactHistory:history_id");
- // initialize npartner to 0 so neighbor list creation is OK the 1st time
- if(atom->nmax > 0)
+ for(int i = 0 ; i < dnum_; i++)
{
- grow_arrays(atom->nmax);
- int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) npartner[i] = 0;
+
+ history_id_[i] = new char[strlen(arg[iarg_])+1];
+ strcpy(history_id_[i],arg[iarg_++]);
+ newtonflag_[i] = atoi(arg[iarg_++]);
+ if(newtonflag_[i] != 0 && newtonflag_[i] != 1)
+ error->fix_error(FLERR,this,"newtonflag must be either 0 or 1");
}
}
@@@ -181,31 -153,54 +173,70 @@@ int FixContactHistory::setmask(
/* ---------------------------------------------------------------------- */
- void FixContactHistory::initial_integrate(int dummy)
+ void FixContactHistory::init()
{
-
+ if (atom->tag_enable == 0)
+ error->all(FLERR,
+ "Contact history requires atoms have IDs");
+
+ // if (-1 == index_decide_noncontacting && 1. < neighbor->contactHistoryDistanceFactor)
+ // error->fix_error(FLERR,this,"have to call set_index_decide_noncontacting() function");
+
+ if(0 == strcmp(style,"contacthistory"))
+ {
+ if(!force->pair_match("gran", 0))
+ error->fix_error(FLERR,this,"Please use a granular pair style for fix contacthistory");
+ pair_gran_ = static_cast<PairGran*>(force->pair_match("gran", 0));
+
+ int dim;
+ computeflag_ = (int *) pair_gran_->extract("computeflag",dim);
+ }
+
+ allocate_pages();
}
- /* ---------------------------------------------------------------------- */
+ /* ----------------------------------------------------------------------
+ create pages if first time or if neighbor pgsize/oneatom has changed
+ note that latter could cause shear history info to be discarded
+ ------------------------------------------------------------------------- */
- void FixContactHistory::init()
+ void FixContactHistory::allocate_pages()
{
++<<<<<<< HEAD
+ if (atom->tag_enable == 0)
+ error->fix_error(FLERR,this,"using contact history requires atoms have IDs");
+
+ if (-1 == index_decide_noncontacting && 1. < neighbor->contactHistoryDistanceFactor)
+ error->fix_error(FLERR,this,"have to call set_index_decide_noncontacting() function");
+
+ if(is_pair)
+ {
+ if(!force->pair_match("gran", 0))
+ error->fix_error(FLERR,this,"Please use a granular pair style for fix contacthistory");
+ pair_gran = static_cast<PairGran*>(force->pair_match("gran", 0));
+ int dim;
+ computeflag = (int *) pair_gran->extract("computeflag",dim);
++=======
+ int create = 0;
+ if (ipage_ == NULL) create = 1;
+ if (pgsize_ != neighbor->pgsize) create = 1;
+ if (oneatom_ != neighbor->oneatom) create = 1;
+
+ if (create) {
+ delete [] ipage_;
+ delete [] dpage_;
+
+ pgsize_ = neighbor->pgsize;
+ oneatom_ = neighbor->oneatom;
+ int nmypage = comm->nthreads;
+ ipage_ = new MyPage<int>[nmypage];
+ dpage_ = new MyPage<double>[nmypage];
+ for (int i = 0; i < nmypage; i++) {
+ ipage_[i].init(oneatom_,pgsize_);
+ dpage_[i].init(oneatom_,pgsize_);
++>>>>>>> upstream/3.0.0
}
- else if(!mesh_)
- error->fix_error(FLERR,this,"illegal");
+ }
}
/* ----------------------------------------------------------------------
@@@ -258,50 -235,38 +271,49 @@@ void FixContactHistory::setup_pre_excha
void FixContactHistory::pre_exchange()
{
-
- if(is_pair)
- pre_exchange_pair();
-
- check_grow();
- }
-
- /* ----------------------------------------------------------------------
- copy shear partner info from neighbor lists to atom arrays
- so can be exchanged with atoms
- ------------------------------------------------------------------------- */
-
- void FixContactHistory::pre_exchange_pair()
- {
- int i,j,ii,jj,m,inum,jnum,d;
+ int i,j,ii,jj,m,n,inum,jnum;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
- double contactHistDistanceFactor;
- bool considerNonContactingParticles = false;
- bool haveNonContactingParticlesInRange = false;
double *hist,*allhist,**firsthist;
- double delx, dely, delz, rPartner, radSum, rsq;
- double xPartner[3];
-
- // zero npartners for all current atoms
+
+ // nlocal may include atoms added since last neigh build
int nlocal = atom->nlocal;
- for (i = 0; i < nlocal; i++) npartner[i] = 0;
- // copy contact info from neighbor list atoms to atom arrays
+ // zero npartner for all current atoms
+ // clear 2 page data structures
++<<<<<<< HEAD
+ int *tag = atom->tag;
+ double **x = atom->x;
+ double *radius = atom->radius;
++=======
+ for (i = 0; i < nlocal; i++) npartner_[i] = 0;
- NeighList *list = pair_gran->list;
+ ipage_->reset();
+ dpage_->reset();
+
+ // 1st loop over neighbor list
+ // calculate npartner for each owned atom
+ // nlocal_neigh = nlocal when neigh list was built, may be smaller than nlocal
++>>>>>>> upstream/3.0.0
+
+ int *tag = atom->tag;
+ NeighList *list = pair_gran_->list;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
firsttouch = list->listgranhistory->firstneigh;
firsthist = list->listgranhistory->firstdouble;
++<<<<<<< HEAD
+ contactHistDistanceFactor = neighbor->contactHistoryDistanceFactor;
+ if(contactHistDistanceFactor> 1.0) considerNonContactingParticles = true;
++=======
+
+ int nlocal_neigh = 0;
+ if (inum) nlocal_neigh = ilist[inum-1] + 1;
++>>>>>>> upstream/3.0.0
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@@ -315,40 -275,64 +322,87 @@@
touch = firsttouch[i];
for (jj = 0; jj < jnum; jj++) {
+ if (touch[jj]) {
+ npartner_[i]++;
j = jlist[jj];
j &= NEIGHMASK;
++<<<<<<< HEAD
+
+ //Check if considerNonContactingParticles are within range
+ haveNonContactingParticlesInRange = false;
+
+ if(considerNonContactingParticles)
+ {
+ hist = &allhist[dnum*jj];
+ if( hist[index_decide_noncontacting]>0.0 ) //check if particles are close enough to keep contact history
+ haveNonContactingParticlesInRange = true;
+ }
+
+ if ( (touch[jj] ) || haveNonContactingParticlesInRange)
+ {
+ hist = &allhist[dnum*jj];
+
+ if (npartner[i] >= maxtouch) grow_arrays_maxtouch(atom->nmax);
+ m = npartner[i];
+ partner[i][m] = tag[j];
+ for (d = 0; d < dnum; d++) {
+ contacthistory[i][m][d] = hist[d];
++=======
+ if (j < nlocal_neigh) npartner_[j]++;
+ }
+ }
+ }
+
+ // get page chunks to store atom IDs and shear history for my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ n = npartner_[i];
+ partner_[i] = ipage_->get(n);
+ contacthistory_[i] = dpage_->get(dnum_*n);
+
+ if (partner_[i] == NULL || contacthistory_[i] == NULL)
+ error->one(FLERR,"Contact history overflow, boost neigh_modify one");
+ }
+
+ // 2nd loop over neighbor list
+ // store atom IDs and shear history for my atoms
+ // re-zero npartner to use as counter for all my atoms
+
+ for (i = 0; i < nlocal; i++) npartner_[i] = 0;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ jlist = firstneigh[i];
+ allhist = firsthist[i];
+ jnum = numneigh[i];
+ touch = firsttouch[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ if (touch[jj]) {
+ hist = &allhist[dnum_*jj];
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ m = npartner_[i];
+ partner_[i][m] = tag[j];
+
+ for (int d = 0; d < dnum_; d++) {
+ contacthistory_[i][m*dnum_+d] = hist[d];
++>>>>>>> upstream/3.0.0
}
- npartner[i]++;
- if (j < nlocal) {
- if (npartner[j] >= maxtouch) grow_arrays_maxtouch(atom->nmax);
-
- m = npartner[j];
- partner[j][m] = tag[i];
- for (d = 0; d < dnum; d++) {
- if(newtonflag[d]) contacthistory[j][m][d] = -hist[d];
- else contacthistory[j][m][d] = hist[d];
- }
- npartner[j]++;
+
+ npartner_[i]++;
+ if (j < nlocal_neigh) {
+ m = npartner_[j];
+ partner_[j][m] = tag[i];
+ for (int d = 0; d < dnum_; d++) {
+ if(newtonflag_[d])
+ contacthistory_[j][m*dnum_+d] = -hist[d];
+ else
+ contacthistory_[j][m*dnum_+d] = hist[d];
+ }
+
+ npartner_[j]++;
}
}
}
diff --cc src/fix_contact_history.h
index b8bf57c,abd62e4..d64c161
--- a/src/fix_contact_history.h
+++ b/src/fix_contact_history.h
@@@ -41,95 -40,52 +40,87 @@@ class FixContactHistory : public Fix
friend class PairGran;
public:
-
FixContactHistory(class LAMMPS *, int, char **);
~FixContactHistory();
-
- // inherited from Fix
-
- void post_create();
- int setmask();
- void init();
- void initial_integrate(int dummy);
- void setup_pre_exchange();
+ virtual int setmask();
+ virtual void init();
+ virtual void setup_pre_exchange();
virtual void pre_exchange();
- void min_setup_pre_exchange();
+ virtual void min_setup_pre_exchange();
void min_pre_exchange();
- double memory_usage();
- void grow_arrays(int);
- void copy_arrays(int, int);
+ virtual double memory_usage();
+ virtual void grow_arrays(int);
+ virtual void copy_arrays(int, int, int);
void set_arrays(int);
int pack_exchange(int, double *);
- int unpack_exchange(int, double *);
+ virtual int unpack_exchange(int, double *);
+ virtual void write_restart(FILE *fp);
+ void restart(char *buf);
int pack_restart(int, double *);
- void unpack_restart(int, int);
+ virtual void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
- void write_restart(FILE *);
- void restart(char *);
-
- // spefific interface for mesh
-
- bool handleContact(int iPart, int idTri, double *&history);
- void markAllContacts();
- void cleanUpContacts();
-
- void reset_history(int dnum_wall);
-
- // return # of contacts
- int n_contacts();
- int n_contacts(int contact_groupbit);
++<<<<<<< HEAD
+ void set_index_decide_noncontacting(int index)
+ { index_decide_noncontacting = index; };
+
+ int get_dnum()
+ { return dnum; }
++=======
+ protected:
++>>>>>>> upstream/3.0.0
- private:
+ int iarg_;
- // functions specific for pair
+ int dnum_;
+ int *newtonflag_;
+ char **history_id_;
+ int index_decide_noncontacting_;
- void pre_exchange_pair();
+ int *npartner_; // # of touching partners of each atom
+ int **partner_; // tags for the partners
+ double **contacthistory_; // contact history values with the partner
+ int maxtouch_; // max # of touching partners for my atoms
- // functions specific for mesh - contact management
+ class Pair *pair_gran_;
+ int *computeflag_; // computeflag in PairGranHookeHistory
- bool haveContact(int indexPart, int idTri, double *&history);
- bool coplanarContactAlready(int indexPart, int idTri);
- void checkCoplanarContactHistory(int indexPart, int idTri, double *&history);
- void addNewTriContactToExistingParticle(int indexPart, int idTri, double *&history);
+ int pgsize_,oneatom_; // copy of settings in Neighbor
+ MyPage<int> *ipage_; // pages of partner atom IDs
+ MyPage<double> *dpage_; // pages of shear history with partners
++<<<<<<< HEAD
+ // mem management
+ void check_grow();
+
+ // data members
+
+ int *npartner; // # of touching partners of each atom
+ int **partner; // tags for the partners
+ double ***contacthistory; // history values with the partner
+ int maxtouch; // max number of partners per atom
+ void grow_arrays_maxtouch(int);
+
+ bool **delflag;
+
+ bool is_pair;
+ class PairGran *pair_gran;
+ int *computeflag; // computeflag in PairGranHookeHistory
+ class TriMesh *mesh_;
+
+ int dnum;
+ int *newtonflag;
+ char **history_id;
+
+ //
+ int index_decide_noncontacting;
++=======
+ virtual void allocate_pages();
++>>>>>>> upstream/3.0.0
};
- // *************************************
- #include "fix_contact_history_I.h"
- // *************************************
-
}
#endif
diff --cc src/fix_massflow_mesh.cpp
index 83c0443,b97df48..8a79339
--- a/src/fix_massflow_mesh.cpp
+++ b/src/fix_massflow_mesh.cpp
@@@ -372,7 -372,9 +372,13 @@@ void FixMassflowMesh::post_integrate(
mass_this += rmass[iPart];
nparticles_this ++;
if(delete_atoms_)
++<<<<<<< HEAD
++ atom_tags_delete_.push_back(atom->tag[iPart]);
++=======
+ {
atom_tags_delete_.push_back(atom->tag[iPart]);
+ }
++>>>>>>> upstream/3.0.0
if (screenflag_ && screen)
fprintf(screen," %d %4.4g %4.4g %4.4g %4.4g %4.4g %4.4g %4.4g \n ",
@@@ -419,8 -421,6 +425,11 @@@ void FixMassflowMesh::pre_exchange(
int iPart;
double *counter = fix_counter_->vector_atom;
++<<<<<<< HEAD
+ if (update->ntimestep != next_reneighbor) return;
+
++=======
++>>>>>>> upstream/3.0.0
if (delete_atoms_)
{
double mass_deleted_this_ = 0.;
diff --cc src/fix_mesh_surface_stress_servo.cpp
index 648564c,17ca65d..2bc1030
--- a/src/fix_mesh_surface_stress_servo.cpp
+++ b/src/fix_mesh_surface_stress_servo.cpp
@@@ -56,155 -56,158 +56,247 @@@ enum{NONE,CONSTANT,EQUAL,FORCE,TORQUE}
/* ---------------------------------------------------------------------- */
FixMeshSurfaceStressServo::FixMeshSurfaceStressServo(LAMMPS *lmp, int narg, char **arg) :
- FixMeshSurfaceStress(lmp, narg, arg),
- dim_( -1),
- totalPhi_( 0.),
- xcm_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("xcm","comm_none","frame_invariant","restart_yes",3)),
- vcm_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("vcm","comm_none","frame_invariant","restart_yes",1)),
- omegacm_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("torquecm","comm_none","frame_invariant","restart_yes",1)),
- xcm_orig_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("xcm_orig","comm_none","frame_invariant","restart_yes",3)),
- mode_flag_(false),
- vel_max_( 0.),
- vel_min_( 0.),
- set_point_(0.),
- set_point_inv_(0.),
- ctrl_output_max_(0.),
- ctrl_output_min_(0.),
- ratio_(0.),
- sp_str_( NULL),
- sp_var_( -1),
- sp_style_( NONE),
- control_output_( 0),
- process_value_( 0),
- pv_flag_(NONE),
- err_( 0.),
- sum_err_( 0.),
- old_process_value_(0.),
- kp_( 0.01),
- ki_( 0.),
- kd_( 0.),
- int_flag_( true),
- nodes_( mesh()->nodePtr()),
- v_( *mesh()->prop().addElementProperty< MultiVectorContainer<double,3,3> > ("v","comm_exchange_borders","frame_invariant","restart_no",1)),
- mod_andrew_(new ModifiedAndrew(lmp))
+ FixMeshSurfaceStress(lmp, narg, arg),
+ xcm_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("xcm","comm_none","frame_invariant","restart_yes",3)),
+ vcm_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("vcm","comm_none","frame_invariant","restart_yes",1)),
+ omegacm_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("torquecm","comm_none","frame_invariant","restart_yes",1)),
+ xcm_orig_( *mesh()->prop().addGlobalProperty< VectorContainer<double,3> > ("xcm_orig","comm_none","frame_invariant","restart_yes",3)),
+
+ nodes_( mesh()->nodePtr()),
+ v_( *mesh()->prop().addElementProperty< MultiVectorContainer<double,3,3> > ("v","comm_exchange_borders","frame_invariant","restart_no",1)),
+
+ totalPhi_( 0.),
+ ctrl_op_( 0),
+ pv_vec_( 0),
+
+ vel_max_( 0.),
+ vel_min_( 0.),
+ ctrl_op_max_(0.),
+ ctrl_op_min_(0.),
+ ratio_(0.),
+
+ sp_mag_(0.),
+ sp_mag_inv_(0.),
+ pv_mag_(0.),
+ old_pv_mag_(0.),
+
+ err_( 0.),
+ sum_err_( 0.),
+ kp_( 0.01),
+ ki_( 0.),
+ kd_( 0.),
+
+ sp_var_( -1),
+ sp_style_( NONE),
+ sp_str_( NULL),
+
+ int_flag_( true),
+ mode_flag_(false),
+ ctrl_style_(NONE),
+ mod_andrew_(new ModifiedAndrew(lmp))
{
- if(!trackStress())
- error->fix_error(FLERR,this,"stress = 'on' required");
+ if(!trackStress())
+ error->fix_error(FLERR,this,"stress = 'on' required");
- if(verbose() && manipulated())
- error->warning(FLERR,"Mesh has been scaled, moved, or rotated.\n"
- "Please note that values for 'com', 'vel' refer to the scaled, moved, or rotated configuration");
+ if(verbose() && manipulated())
+ error->warning(FLERR,"Mesh has been scaled, moved, or rotated.\n"
+ "Please note that values for 'com', 'vel' refer to the scaled, moved, or rotated configuration");
- // override default from base
- size_vector = 9;
- time_depend = 1;
+ // override default from base
+ size_vector = 9;
+ time_depend = 1;
- // set defaults
+ // set defaults
- init_defaults();
+ init_defaults();
- // parse further args
+ // parse further args
++<<<<<<< HEAD
+ bool hasargs = true;
+ while(iarg_ < narg && hasargs)
+ {
+ hasargs = false;
+ if(strcmp(arg[iarg_],"com") == 0) {
+ if (narg < iarg_+4) error->fix_error(FLERR,this,"not enough arguments for 'com'");
+ iarg_++;
+ double _com[3];
+ _com[0] = force->numeric(arg[iarg_++]);
+ _com[1] = force->numeric(arg[iarg_++]);
+ _com[2] = force->numeric(arg[iarg_++]);
+ xcm_.add(_com);
+ set_p_ref(xcm_(0));
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"ctrlPV") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'ctrlPV'");
+ if (strcmp(arg[iarg_+1],"force") == 0) pv_flag_ = FORCE;
+ else if (strcmp(arg[iarg_+1],"torque") == 0) pv_flag_ = TORQUE;
+ else error->fix_error(FLERR,this,"only 'force', 'torque' are valid arguments for ctrlPV");
+ iarg_ = iarg_ + 2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"vel_max") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'vel'");
+ iarg_++;
+ vel_max_ = force->numeric(arg[iarg_++]);
+ if(vel_max_ <= 0.)
+ error->fix_error(FLERR,this,"vel_max > 0 required");
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"target_val") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'target_val'");
+ iarg_++;
+ if (strstr(arg[iarg_],"v_") == arg[iarg_]) {
+ int n = strlen(&arg[iarg_][2]) + 1;
+ sp_str_ = new char[n];
+ strcpy(sp_str_,&arg[iarg_][2]);
+ } else {
+ set_point_ = -force->numeric(arg[iarg_]); // the resultant force/torque/shear acts in opposite direction --> negative value
+ if (set_point_ == 0.) error->fix_error(FLERR,this,"'target_val' (desired force/torque) has to be != 0.0");
+ set_point_inv_ = 1./fabs(set_point_);
+ sp_style_ = CONSTANT;
+ }
+ iarg_++;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"dim") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'forceflags'");
+ iarg_++;
+ if (strcmp("x",arg[iarg_]) == 0) dim_ = 0;
+ else if(strcmp("y",arg[iarg_]) == 0) dim_ = 1;
+ else if(strcmp("z",arg[iarg_]) == 0) dim_ = 2;
+ else error->fix_error(FLERR,this,"'x', 'y' or 'z' expected after keyword 'dim'");
+ axis_[dim_] = 1.0;
+ iarg_++;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"kp") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ kp_ = force->numeric(arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"ki") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ ki_ = force->numeric(arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"kd") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ kd_ = force->numeric(arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"mode") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ iarg_++;
+ if (strcmp("auto",arg[iarg_]) == 0) {
+ mode_flag_ = true;
+ } else error->fix_error(FLERR,this,"mode supports only auto");
+ iarg_++;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"ratio") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ ratio_ = force->numeric(arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(style,"mesh/surface/stress/servo") == 0) {
+ char *errmsg = new char[strlen(arg[iarg_])+30];
+ sprintf(errmsg,"unknown keyword or wrong keyword order: %s", arg[iarg_]);
+ error->fix_error(FLERR,this,errmsg);
+ delete []errmsg;
++=======
+ bool hasargs = true;
+ while(iarg_ < narg && hasargs)
+ {
+ hasargs = false;
+ if(strcmp(arg[iarg_],"com") == 0) {
+ if (narg < iarg_+4) error->fix_error(FLERR,this,"not enough arguments for 'com'");
+ iarg_++;
+ double _com[3];
+ _com[0] = force->numeric(FLERR,arg[iarg_++]);
+ _com[1] = force->numeric(FLERR,arg[iarg_++]);
+ _com[2] = force->numeric(FLERR,arg[iarg_++]);
+ xcm_.add(_com);
+ set_p_ref(xcm_(0));
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"ctrlPV") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'ctrlPV'");
+ if (strcmp(arg[iarg_+1],"force") == 0) ctrl_style_ = FORCE;
+ else if (strcmp(arg[iarg_+1],"torque") == 0) ctrl_style_ = TORQUE;
+ else error->fix_error(FLERR,this,"only 'force', 'torque' are valid arguments for ctrlPV");
+ iarg_ = iarg_ + 2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"vel_max") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'vel'");
+ iarg_++;
+ vel_max_ = force->numeric(FLERR,arg[iarg_++]);
+ if(vel_max_ <= 0.)
+ error->fix_error(FLERR,this,"vel_max > 0 required");
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"target_val") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments for 'target_val'");
+ iarg_++;
+ if (strstr(arg[iarg_],"v_") == arg[iarg_]) {
+ int n = strlen(&arg[iarg_][2]) + 1;
+ sp_str_ = new char[n];
+ strcpy(sp_str_,&arg[iarg_][2]);
+ sp_style_ = EQUAL;
+ } else {
+ sp_mag_ = -force->numeric(FLERR,arg[iarg_]); // the resultant force/torque/shear acts in opposite direction --> negative value
+ if (sp_mag_ == 0.) error->fix_error(FLERR,this,"'target_val' (desired force/torque) has to be != 0.0");
+ sp_mag_inv_ = 1./fabs(sp_mag_);
+ sp_style_ = CONSTANT;
++>>>>>>> upstream/3.0.0
}
+ iarg_++;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"axis") == 0) {
+ if (narg < iarg_+4) error->fix_error(FLERR,this,"not enough arguments for 'axis'");
+ axis_[0] = force->numeric(FLERR,arg[iarg_+1]);
+ axis_[1] = force->numeric(FLERR,arg[iarg_+2]);
+ axis_[2] = force->numeric(FLERR,arg[iarg_+3]);
+ iarg_ = iarg_+4;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"kp") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ kp_ = force->numeric(FLERR,arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"ki") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ ki_ = force->numeric(FLERR,arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"kd") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ kd_ = force->numeric(FLERR,arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"mode") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ iarg_++;
+ if (strcmp("auto",arg[iarg_]) == 0) {
+ mode_flag_ = true;
+ } else error->fix_error(FLERR,this,"mode supports only auto");
+ iarg_++;
+ hasargs = true;
+ } else if(strcmp(arg[iarg_],"ratio") == 0) {
+ if (narg < iarg_+2) error->fix_error(FLERR,this,"not enough arguments");
+ ratio_ = force->numeric(FLERR,arg[iarg_+1]);
+ iarg_ = iarg_+2;
+ hasargs = true;
+ } else if(strcmp(style,"mesh/surface/stress/servo") == 0) {
+ char *errmsg = new char[strlen(arg[iarg_])+30];
+ sprintf(errmsg,"unknown keyword or wrong keyword order: %s", arg[iarg_]);
+ error->fix_error(FLERR,this,errmsg);
+ delete []errmsg;
}
+ }
- error_checks();
-
- // store original position
- xcm_orig_.add(xcm_(0));
+ // store original position
+ xcm_orig_.add(xcm_(0));
- if (pv_flag_ == FORCE)
- mesh()->registerMove(false,true,false);
- else if(pv_flag_ == TORQUE)
- mesh()->registerMove(false,true,true);
- else
- error->fix_error(FLERR,this,"Bad registration of upcoming move.");
+ if (ctrl_style_ == FORCE)
+ mesh()->registerMove(false,true,false);
+ else if(ctrl_style_ == TORQUE)
+ mesh()->registerMove(false,false,true);
+ else
+ error->fix_error(FLERR,this,"Bad registration of upcoming move.");
}
@@@ -416,24 -423,25 +512,33 @@@ void FixMeshSurfaceStressServo::final_i
// only if the wall should move
if (int_flag_) {
- // auto mode
-
- if (mode_flag_) {
+ // variable force, wrap with clear/add
+ if (sp_style_ == EQUAL) {
- // variable force, wrap with clear/add
- if (sp_style_ == EQUAL) {
+ modify->clearstep_compute();
- modify->clearstep_compute();
+ sp_mag_ = -input->variable->compute_equal(sp_var_);
+ if (sp_mag_ == 0.) error->fix_error(FLERR,this,"Set point (desired force/torque/shear) has to be != 0.0");
+ sp_mag_inv_ = 1./fabs(sp_mag_);
+
+ modify->addstep_compute(update->ntimestep + 1);
++<<<<<<< HEAD
+ set_point_ = -input->variable->compute_equal(sp_var_);
+ if (set_point_ == 0.) error->fix_error(FLERR,this,"Set point (desired force/torque/shear) has to be != 0.0");
+ set_point_inv_ = 1./fabs(set_point_);
+
+ modify->addstep_compute(update->ntimestep + 1);
++=======
+ }
++>>>>>>> upstream/3.0.0
- }
+ // auto mode
+
+ if (mode_flag_) {
- err_ = (set_point_ - *process_value_) * set_point_inv_;
+ pv_mag_ = vectorDot3D(pv_vec_,axis_);
+ err_ = (sp_mag_ - pv_mag_) * sp_mag_inv_;
// TODO: Valid or trash?
// Hard coded test for piecewise controller
@@@ -447,14 -455,14 +552,23 @@@
if (totNumContacts == 0) {
// cruise mode
- test_output = ctrl_output_max_;
+ ctrl_kp = ctrl_op_max_;
} else {
++<<<<<<< HEAD
+ if (fabs(err_) <= e_low) {
+ test_output = tmp_scale*ctrl_output_min_;
+ } else if(fabs(err_) >= e_high) {
+ test_output = ctrl_output_min_;
+ } else { // linear interpolation
+ test_output = tmp_scale*ctrl_output_min_ + ((1-tmp_scale)*ctrl_output_min_) * (fabs(err_)-e_low)/(e_high-e_low);
++=======
+ if (fabs(err_) <= err_low) {
+ ctrl_kp = ctrl_scale*ctrl_op_min_;
+ } else if(fabs(err_) >= err_high) {
+ ctrl_kp = ctrl_op_min_;
+ } else { // linear interpolation
+ ctrl_kp = ctrl_scale*ctrl_op_min_ + ((1-ctrl_scale)*ctrl_op_min_) * (fabs(err_)-err_low)/(err_high-err_low);
++>>>>>>> upstream/3.0.0
}
}
@@@ -462,19 -470,6 +576,22 @@@
} else {
++<<<<<<< HEAD
+ // variable force, wrap with clear/add
+ if (sp_style_ == EQUAL) {
+
+ modify->clearstep_compute();
+
+ set_point_ = -input->variable->compute_equal(sp_var_);
+ if (set_point_ == 0.) error->fix_error(FLERR,this,"Set point (desired force/torque/shear) has to be != 0.0");
+ set_point_inv_ = 1./fabs(set_point_);
+
+ modify->addstep_compute(update->ntimestep + 1);
+
+ }
+
++=======
++>>>>>>> upstream/3.0.0
// simple PID-controller
// calc error and sum of the errors
@@@ -513,8 -509,8 +631,13 @@@
void FixMeshSurfaceStressServo::limit_vel()
{
++<<<<<<< HEAD
+ double vmag, factor, maxOutput;
+ vmag = fabs(*control_output_);
++=======
+ double maxOutput;
+ const double vmag = vectorMag3D(ctrl_op_);
++>>>>>>> upstream/3.0.0
// saturation of the velocity
int totNumContacts = fix_mesh_neighlist_->getTotalNumContacts();
@@@ -605,14 -664,10 +791,16 @@@ int FixMeshSurfaceStressServo::modify_p
else error->fix_error(FLERR,this,"Variable is invalid style");
}
- if (sp_style_ == ATOM)
- error->fix_error(FLERR,this,"Control variable of style ATOM does not make any sense for a wall");
-
} else {
++<<<<<<< HEAD
+ set_point_ = -force->numeric(arg[1]); // the resultant force/torque/shear acts in opposite direction --> negative value
+ if (set_point_ == 0.) error->fix_error(FLERR,this,"'target_val' (desired force/torque) has to be != 0.0");
+ set_point_inv_ = 1./fabs(set_point_);
++=======
+ sp_mag_ = -force->numeric(FLERR,arg[1]); // the resultant force/torque/shear acts in opposite direction --> negative value
+ if (sp_mag_ == 0.) error->fix_error(FLERR,this,"'target_val' (desired force/torque) has to be != 0.0");
+ sp_mag_inv_ = 1./fabs(sp_mag_);
++>>>>>>> upstream/3.0.0
sp_style_ = CONSTANT;
}
diff --cc src/fix_neighlist_mesh.cpp
index be4735b,5eaa028..85e79ab
--- a/src/fix_neighlist_mesh.cpp
+++ b/src/fix_neighlist_mesh.cpp
@@@ -43,10 -47,23 +47,28 @@@ using namespace FixConst
FixNeighlistMesh::FixNeighlistMesh(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp,narg,arg),
++<<<<<<< HEAD
+ contactList("contactList"),
+ numContacts("numContacts"),
++=======
+ fix_nneighs_(0),
+ fix_nneighs_name_(0),
++>>>>>>> upstream/3.0.0
buildNeighList(false),
- movingMesh(false)
+ numAllContacts_(0),
+ mbinx(0),
+ mbiny(0),
+ mbinz(0),
+ maxhead(0),
+ bins(NULL),
+ binhead(NULL),
+ skin(0.0),
+ distmax(0.0),
+ x(NULL),
+ r(NULL),
+ changingMesh(false),
+ changingDomain(false),
+ last_bin_update(-1)
{
if(!modify->find_fix_id(arg[3]) || !dynamic_cast<FixMeshSurface*>(modify->find_fix_id(arg[3])))
error->fix_error(FLERR,this,"illegal caller");
diff --cc src/fix_property_atom_tracer.cpp
index 7ac92f7,bd627d8..2d0fb69
--- a/src/fix_property_atom_tracer.cpp
+++ b/src/fix_property_atom_tracer.cpp
@@@ -95,8 -95,11 +95,16 @@@ FixPropertyAtomTracer::FixPropertyAtomT
error->fix_error(FLERR,this,"not enough arguments for 'mark_step'");
iarg_++;
step_ = atoi(arg[iarg_++]);
++<<<<<<< HEAD
+ if(step_ < 0 || step_ < update->ntimestep)
+ error->fix_error(FLERR,this,"mark_step > 0 required, mark_step must not be before current time-step");
++=======
+ if(step_ < 0)
+ error->fix_error(FLERR,this,"mark_step > 0 required");
+
+ if(step_ < update->ntimestep)
+ first_mark_ = false;
++>>>>>>> upstream/3.0.0
hasargs = true;
} else if(strcmp(arg[iarg_],"marker_style") == 0) {
if(narg < iarg_+2)
diff --cc src/general_container.h
index 65d1e2f,41d1496..4343172
--- a/src/general_container.h
+++ b/src/general_container.h
@@@ -132,8 -132,8 +132,13 @@@ namespace LAMMPS_N
protected:
++<<<<<<< HEAD
+ GeneralContainer(char *_id);
+ GeneralContainer(char *_id, char *_comm, char *_ref, char *_restart, int _scalePower = 1);
++=======
+ GeneralContainer(const char *_id);
+ GeneralContainer(const char *_id, const char *_comm, const char *_ref, const char *_restart, int _scalePower = 1);
++>>>>>>> upstream/3.0.0
GeneralContainer(GeneralContainer<T,NUM_VEC,LEN_VEC> const &orig);
virtual ~GeneralContainer();
diff --cc src/general_container_I.h
index 6eb36b8,5452367..5a83516
--- a/src/general_container_I.h
+++ b/src/general_container_I.h
@@@ -33,7 -33,7 +33,11 @@@
------------------------------------------------------------------------- */
template<typename T, int NUM_VEC, int LEN_VEC>
++<<<<<<< HEAD
+ GeneralContainer<T,NUM_VEC,LEN_VEC>::GeneralContainer(char *_id)
++=======
+ GeneralContainer<T,NUM_VEC,LEN_VEC>::GeneralContainer(const char *_id)
++>>>>>>> upstream/3.0.0
: ContainerBase(_id),
numElem_(0),
maxElem_(GROW)
diff --cc src/lammps.cpp
index e8500e2,3baa9a1..594f216
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@@ -483,10 -550,30 +550,36 @@@ void LAMMPS::create(
if (cuda) comm = new CommCuda(this);
else comm = new Comm(this);
+ if (cuda) neighbor = new NeighborCuda(this);
+ else neighbor = new Neighbor(this);
+
if (cuda) domain = new DomainCuda(this);
++<<<<<<< HEAD
+ else if (wedgeflag) domain = new DomainWedge(this);
+ else domain = new Domain(this);
+ domain->is_wedge = wedgeflag;
++=======
+ #ifdef LMP_USER_OMP
+ else
+ {
+ domain = new DomainOMP(this);
+ if (wedgeflag) error->all(FLERR,"Domain wedge and OMP are not comaptible");
+ }
+ #else
+ else
+ {
+ if (wedgeflag) domain = new DomainWedge(this);
+ else domain = new Domain(this);
+ }
+ #endif
+
+ domain->is_wedge = wedgeflag;
+ if(wedgeflag && cuda)
+ error->all(FLERR,"Domain wedge and cude are not comaptible");
+
+ atom = new Atom(this);
+ atom->create_avec("atomic",0,NULL,suffix);
++>>>>>>> upstream/3.0.0
group = new Group(this);
force = new Force(this); // must be after group, to create temperature
diff --cc src/modify_liggghts.cpp
index 4b014c6,25c9eb2..54b980a
--- a/src/modify_liggghts.cpp
+++ b/src/modify_liggghts.cpp
@@@ -142,26 -142,23 +142,40 @@@ int Modify::n_fixes_style(const char *s
}
int Modify::n_computes_style(const char *style)
++<<<<<<< HEAD
+{
+ int n_computes,len;
+
+ n_computes = 0;
+ len = strlen(style);
+
+ for(int icompute = 0; icompute < ncompute; icompute++)
+ if(strncmp(compute[icompute]->style,style,len) == 0)
+ n_computes++;
+
+ return n_computes;
+}
+
+int Modify::n_fixes_style_strict(const char *style)
++=======
++>>>>>>> upstream/3.0.0
{
- int n_fixes,len;
+ int n_computes,len;
- n_fixes = 0;
+ n_computes = 0;
len = strlen(style);
+ for(int icompute = 0; icompute < ncompute; icompute++)
+ if(strncmp(compute[icompute]->style,style,len) == 0)
+ n_computes++;
+
+ return n_computes;
+ }
+
+ int Modify::n_fixes_style_strict(const char *style)
+ {
+ int n_fixes = 0;
+
for(int ifix = 0; ifix < nfix; ifix++)
if(strcmp(fix[ifix]->style,style) == 0)
n_fixes++;
diff --cc src/multi_vector_container.h
index 11b7338,f164020..e62bb1c
--- a/src/multi_vector_container.h
+++ b/src/multi_vector_container.h
@@@ -35,8 -35,8 +35,13 @@@ namespace LAMMPS_NS
class MultiVectorContainer : public GeneralContainer <T, NUM_VEC, LEN_VEC>
{
public:
++<<<<<<< HEAD
+ MultiVectorContainer(char *_id);
+ MultiVectorContainer(char *_id, char *_comm, char *_ref, char *_restart, int _scalePower = 1);
++=======
+ MultiVectorContainer(const char *_id);
+ MultiVectorContainer(const char *_id, const char *_comm, const char *_ref, const char *_restart, int _scalePower = 1);
++>>>>>>> upstream/3.0.0
MultiVectorContainer(MultiVectorContainer<T,NUM_VEC,LEN_VEC> const &orig);
virtual ~MultiVectorContainer();
};
@@@ -46,7 -46,7 +51,11 @@@
------------------------------------------------------------------------- */
template<typename T, int NUM_VEC, int LEN_VEC>
++<<<<<<< HEAD
+ MultiVectorContainer<T,NUM_VEC,LEN_VEC>::MultiVectorContainer(char *_id)
++=======
+ MultiVectorContainer<T,NUM_VEC,LEN_VEC>::MultiVectorContainer(const char *_id)
++>>>>>>> upstream/3.0.0
: GeneralContainer<T,NUM_VEC,LEN_VEC>(_id)
{
diff --cc src/neigh_gran.cpp
index 8de54ae,59fa02c..1ad523e
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@@ -71,15 -71,13 +71,15 @@@ void Neighbor::granular_nsq_no_newton(N
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
- int **pages = list->pages;
+ MyPage<int> *ipage = list->ipage;
+ double contactHistoryDistanceFactorSqr = contactHistoryDistanceFactor*contactHistoryDistanceFactor;
+
FixContactHistory *fix_history = list->fix_history;
if (fix_history) {
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- contacthistory = fix_history->contacthistory;
+ npartner = fix_history->npartner_;
+ partner = fix_history->partner_;
+ contacthistory = fix_history->contacthistory_;
listgranhistory = list->listgranhistory;
firsttouch = listgranhistory->firstneigh;
firstshear = listgranhistory->firstdouble;
@@@ -136,7 -124,7 +126,11 @@@
neighptr[n] = j;
if (fix_history) {
++<<<<<<< HEAD
+ if (rsq < radsum*radsum*contactHistoryDistanceFactorSqr)
++=======
+ if (rsq < radsum*radsum)
++>>>>>>> upstream/3.0.0
{
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == tag[j]) break;
@@@ -295,15 -278,13 +284,15 @@@ void Neighbor::granular_bin_no_newton(N
NeighList *listgranhistory;
int *npartner,**partner;
- double ***contacthistory;
+ double **contacthistory;
int **firsttouch;
double **firstshear;
- int **pages_touch;
- double **pages_shear;
+ MyPage<int> *ipage_touch;
+ MyPage<double> *dpage_shear;
int dnum;
+ double contactHistoryDistanceFactorSqr = contactHistoryDistanceFactor*contactHistoryDistanceFactor;
+
// bin local & ghost atoms
bin_atoms();
@@@ -392,7 -363,7 +371,11 @@@
neighptr[n] = j;
if (fix_history) {
++<<<<<<< HEAD
+ if (rsq < radsum*radsum*contactHistoryDistanceFactorSqr)
++=======
+ if (rsq < radsum*radsum)
++>>>>>>> upstream/3.0.0
{
for (m = 0; m < npartner[i]; m++)
if (partner[i][m] == tag[j]) break;
diff --cc src/neighbor.cpp
index 8fd321c,e471bfb..54a4f7b
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@@ -1682,14 -1814,14 +1814,22 @@@ void Neighbor::modify_params(int narg,
iarg += 2;
} else if (strcmp(arg[iarg],"delay") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
- delay = atoi(arg[iarg+1]);
+ delay = force->inumeric(FLERR,arg[iarg+1]);
if (delay < 0) error->all(FLERR,"Illegal neigh_modify command");
iarg += 2;
++<<<<<<< HEAD
+ } else if (strcmp(arg[iarg],"contactHistoryDistanceFactor") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
+ contactHistoryDistanceFactor = atof(arg[iarg+1]);
+ if (contactHistoryDistanceFactor < 1.0) error->all(FLERR,"Illegal neigh_modify command. Please set contactHistoryDistanceFactor value >=1");
+ iarg +=2;
++=======
+ } else if (strcmp(arg[iarg],"contact_distance_factor") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
+ contactDistanceFactor = atof(arg[iarg+1]);
+ if (contactDistanceFactor < 1.0) error->all(FLERR,"Illegal neigh_modify command. Please set contact_distance_factor value >=1");
+ iarg +=2;
++>>>>>>> upstream/3.0.0
} else if (strcmp(arg[iarg],"check") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) dist_check = 1;
diff --cc src/pair_hybrid.cpp
index 5ae4f2f,3aff45e..dd58b3d
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@@ -251,18 -253,21 +253,31 @@@ void PairHybrid::settings(int narg, cha
if (count == 1) multiple[i] = 0;
}
+ // set pair flags from sub-style flags
+
+ flags();
+ }
+
+ /* ----------------------------------------------------------------------
+ set top-level pair flags from sub-style flags
+ ------------------------------------------------------------------------- */
+
+ void PairHybrid::flags()
+ {
+ int m;
+
// set comm_forward, comm_reverse, comm_reverse_off to max of any sub-style
+ flags();
+}
+
+/* ----------------------------------------------------------------------
+ set top-level pair flags from sub-style flags - new from patch 19Jan2013
+------------------------------------------------------------------------- */
+
+void PairHybrid::flags() //- new from patch 19Jan2013
+{
+ int m;
for (m = 0; m < nstyles; m++) {
if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward);
if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
@@@ -609,10 -621,12 +631,13 @@@ void PairHybrid::read_restart(FILE *fp
if (me == 0) fread(&nstyles,sizeof(int),1,fp);
MPI_Bcast(&nstyles,1,MPI_INT,0,world);
+ // allocate list of sub-styles
+
styles = new Pair*[nstyles];
keywords = new char*[nstyles];
+ multiple = new int[nstyles];
+ multiple = new int[nstyles]; // - new from patch 17May2012
// each sub-style is created via new_pair()
// each reads its settings, but no coeff info
@@@ -623,9 -637,12 +648,15 @@@
keywords[m] = new char[n];
if (me == 0) fread(keywords[m],sizeof(char),n,fp);
MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
- styles[m] = force->new_pair(keywords[m],lmp->suffix,dummy);
+ styles[m] = force->new_pair_from_restart(fp, keywords[m],lmp->suffix,dummy);
styles[m]->read_restart_settings(fp);
}
++<<<<<<< HEAD
++=======
+
+ // multiple[i] = 1 to M if sub-style used multiple times, else 0
+
++>>>>>>> upstream/3.0.0
for (int i = 0; i < nstyles; i++) {
int count = 0;
for (int j = 0; j < nstyles; j++) {
@@@ -633,9 -650,9 +664,15 @@@
if (j == i) multiple[i] = count;
}
if (count == 1) multiple[i] = 0;
++<<<<<<< HEAD
+ } //- new from patch 17May2012
+
+ // set pair flags from sub-style flags // - new from patch 19Jan2013
++=======
+ }
+
+ // set pair flags from sub-style flags
++>>>>>>> upstream/3.0.0
flags();
}
diff --cc src/pair_sph.cpp
index e788ad3,24d03fa..5593f0d
--- a/src/pair_sph.cpp
+++ b/src/pair_sph.cpp
@@@ -75,7 -75,7 +75,11 @@@ PairSph::PairSph(LAMMPS *lmp) : Pair(lm
char **fixarg;
fixarg=new char*[11];
for (int kk=0;kk<11;kk++) fixarg[kk]=new char[30];
++<<<<<<< HEAD
+
++=======
+
++>>>>>>> upstream/3.0.0
strcpy(fixarg[0],"fgradP");
fixarg[1]="all";
fixarg[2]="property/atom";
@@@ -107,7 -107,7 +111,11 @@@ PairSph::~PairSph(
if(kernel_style) delete []kernel_style;
if(fppaSl) modify->delete_fix("sl");
// if(fppaSlType) modify->delete_fix("sl");
++<<<<<<< HEAD
+
++=======
+
++>>>>>>> upstream/3.0.0
if(fix_fgradP_) modify->delete_fix(fix_fgradP_->id);
}
diff --cc src/read_data.cpp
index 4b6eaec,b9e02c5..d7cf941
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@@ -526,7 -620,7 +620,11 @@@ void ReadData::header(int flag, int add
atom->nangles < 0 || atom->nangles > MAXBIGINT ||
atom->ndihedrals < 0 || atom->ndihedrals > MAXBIGINT ||
atom->nimpropers < 0 || atom->nimpropers > MAXBIGINT) {
++<<<<<<< HEAD
+ if (me == 0) error->one(FLERR,"System in data file is too big"); //- new from patch 17May2012
++=======
+ if (me == 0) error->one(FLERR,"System in data file is too big");
++>>>>>>> upstream/3.0.0
}
// check that exiting string is a valid section keyword
@@@ -534,34 -628,34 +632,63 @@@
parse_keyword(1,flag);
for (n = 0; n < NSECTIONS; n++)
if (strcmp(keyword,section_keywords[n]) == 0) break;
++<<<<<<< HEAD
+ if (n == NSECTIONS && me == 0) { //- new from patch 17May2012
+ char str[128];
+ sprintf(str,"Unknown identifier in data file: %s",keyword);
+ error->one(FLERR,str); //- new from patch 17May2012
++=======
+ if (n == NSECTIONS && me == 0) {
+ char str[128];
+ sprintf(str,"Unknown identifier in data file: %s",keyword);
+ error->one(FLERR,str);
++>>>>>>> upstream/3.0.0
}
// error check on consistency of header values
if ((atom->nbonds || atom->nbondtypes) &&
++<<<<<<< HEAD
+ atom->avec->bonds_allow == 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"No bonds allowed with this atom style");
+ if ((atom->nangles || atom->nangletypes) &&
+ atom->avec->angles_allow == 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"No angles allowed with this atom style");
+ if ((atom->ndihedrals || atom->ndihedraltypes) &&
+ atom->avec->dihedrals_allow == 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"No dihedrals allowed with this atom style");
+ if ((atom->nimpropers || atom->nimpropertypes) &&
+ atom->avec->impropers_allow == 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"No impropers allowed with this atom style");
+
+ if (atom->nbonds > 0 && atom->nbondtypes <= 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"Bonds defined but no bond types");
+ if (atom->nangles > 0 && atom->nangletypes <= 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"Angles defined but no angle types");
+ if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0 && me == 0) //- new from patch 17May2012
+ error->one(FLERR,"Dihedrals defined but no dihedral types");
+ if (atom->nimpropers > 0 && atom->nimpropertypes <= 0 && me == 0) //- new from patch 17May2012
++=======
+ atom->avec->bonds_allow == 0 && me == 0)
+ error->one(FLERR,"No bonds allowed with this atom style");
+ if ((atom->nangles || atom->nangletypes) &&
+ atom->avec->angles_allow == 0 && me == 0)
+ error->one(FLERR,"No angles allowed with this atom style");
+ if ((atom->ndihedrals || atom->ndihedraltypes) &&
+ atom->avec->dihedrals_allow == 0 && me == 0)
+ error->one(FLERR,"No dihedrals allowed with this atom style");
+ if ((atom->nimpropers || atom->nimpropertypes) &&
+ atom->avec->impropers_allow == 0 && me == 0)
+ error->one(FLERR,"No impropers allowed with this atom style");
+
+ if (atom->nbonds > 0 && atom->nbondtypes <= 0 && me == 0)
+ error->one(FLERR,"Bonds defined but no bond types");
+ if (atom->nangles > 0 && atom->nangletypes <= 0 && me == 0)
+ error->one(FLERR,"Angles defined but no angle types");
+ if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0 && me == 0)
+ error->one(FLERR,"Dihedrals defined but no dihedral types");
+ if (atom->nimpropers > 0 && atom->nimpropertypes <= 0 && me == 0)
++>>>>>>> upstream/3.0.0
error->one(FLERR,"Impropers defined but no improper types");
}
@@@ -1193,6 -1279,21 +1312,24 @@@ void ReadData::scan(int &bond_per_atom
memory->create(count,cmax,"read_data:count");
while (strlen(keyword)) {
++<<<<<<< HEAD
++=======
+
+ // allow special fixes first chance to match and process the section
+ // if fix matches, continue to next section
+
+ if (nfix) {
+ for (i = 0; i < nfix; i++) {
+ if (strcmp(keyword,fix_section[i]) == 0) {
+ int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
+ skip_lines(n);
+ parse_keyword(0,0);
+ break;
+ }
+ }
+ if (i < nfix) continue;
+ }
++>>>>>>> upstream/3.0.0
if (strcmp(keyword,"Masses") == 0) skip_lines(atom->ntypes);
else if (strcmp(keyword,"Atoms") == 0) skip_lines(add_to_existing?natoms_add:natoms);
diff --cc src/scalar_container.h
index 78f3d69,1d4a33f..cf95de5
--- a/src/scalar_container.h
+++ b/src/scalar_container.h
@@@ -38,8 -38,8 +38,13 @@@ namespace LAMMPS_N
class ScalarContainer : public GeneralContainer <T, 1, 1>
{
public:
++<<<<<<< HEAD
+ ScalarContainer(char *_id);
+ ScalarContainer(char *_id, char *_comm, char *_ref, char *_restart, int _scalePower = 1);
++=======
+ ScalarContainer(const char *_id);
+ ScalarContainer(const char *_id, const char *_comm, const char *_ref, const char *_restart, int _scalePower = 1);
++>>>>>>> upstream/3.0.0
ScalarContainer(ScalarContainer<T> const &orig);
virtual ~ScalarContainer();
@@@ -60,7 -60,7 +65,11 @@@
------------------------------------------------------------------------- */
template<typename T>
++<<<<<<< HEAD
+ ScalarContainer<T>::ScalarContainer(char *_id)
++=======
+ ScalarContainer<T>::ScalarContainer(const char *_id)
++>>>>>>> upstream/3.0.0
: GeneralContainer<T,1,1>(_id)
{
diff --cc src/set.cpp
index 2001070,c2473ce..0beb2f2
--- a/src/set.cpp
+++ b/src/set.cpp
@@@ -83,6 -86,8 +86,11 @@@ void Set::command(int narg, char **arg
id = new char[n];
strcpy(id,arg[1]);
select = NULL;
++<<<<<<< HEAD
++=======
+ selection(atom->nlocal);
+
++>>>>>>> upstream/3.0.0
add = 0;
until = 1;
@@@ -378,20 -438,42 +441,56 @@@
error->all(FLERR,"Cannot set meso_rho for this atom style");
set(MESO_RHO);
iarg += 2;
++<<<<<<< HEAD
+ } else if (strcmp(arg[iarg],"add") == 0){
+ if (iarg+1 > narg)
+ error->all(FLERR,"Illegal set command for add");
+ if(strcmp(arg[iarg+1],"yes") == 0)
+ add = 1;
+ else if(strcmp(arg[iarg+1],"no") == 0)
+ add = 0;
++=======
+
+ } else if (strstr(arg[iarg],"i_") == arg[iarg]) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
+ if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
+ else ivalue = force->inumeric(FLERR,arg[iarg+1]);
+ int flag;
+ index_custom = atom->find_custom(&arg[iarg][2],flag);
+ if (index_custom < 0 || flag != 0)
+ error->all(FLERR,"Set command integer vector does not exist");
+ set(INAME);
+ iarg += 2;
+
+ } else if (strstr(arg[iarg],"d_") == arg[iarg]) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
+ if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
+ else dvalue = force->numeric(FLERR,arg[iarg+1]);
+ int flag;
+ index_custom = atom->find_custom(&arg[iarg][2],flag);
+ if (index_custom < 0 || flag != 1)
+ error->all(FLERR,"Set command floating point vector does not exist");
+ set(DNAME);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"add") == 0){
+ if (iarg+1 > narg)
+ error->all(FLERR,"Illegal set command for add");
+ if(strcmp(arg[iarg+1],"yes") == 0)
+ add = 1;
+ else if(strcmp(arg[iarg+1],"no") == 0)
+ add = 0;
++>>>>>>> upstream/3.0.0
else error->all(FLERR,"Illegal 'add' option called");
iarg +=2;
} else if (strcmp(arg[iarg],"until") == 0){
if (iarg+1 > narg)
error->all(FLERR,"Illegal set command for until");
until = atof(arg[iarg+1]);
++<<<<<<< HEAD
+ if (until <= 0.0)
++=======
+ if (until <= 0.0)
++>>>>>>> upstream/3.0.0
error->all(FLERR,"Illegal 'until' option called. Please set keyword value >0");
iarg +=2;
} else if (strncmp(arg[iarg],"property/atom",13) == 0) {
@@@ -596,8 -738,8 +755,13 @@@ void Set::set(int keyword
else
{
currentTimestep = update->ntimestep;
++<<<<<<< HEAD
+ if (currentTimestep < until)
+ {
++=======
+ if (currentTimestep < until)
+ {
++>>>>>>> upstream/3.0.0
if (updFix->data_style) for (int m = 0; m < nUpdValues; m++)
updFix->array_atom[i][m] = updValues[m];
else updFix->vector_atom[i]=updValues[0];
diff --cc src/set.h
index 2358369,daa9879..aa98855
--- a/src/set.h
+++ b/src/set.h
@@@ -57,7 -61,7 +61,11 @@@ class Set : protected Pointers
void set(int);
void setrandom(int);
void topology(int);
++<<<<<<< HEAD
+
++=======
+ void varparse(char *, int);
++>>>>>>> upstream/3.0.0
};
}
diff --cc src/vector_container.h
index 7927e91,628af59..71bb0e2
--- a/src/vector_container.h
+++ b/src/vector_container.h
@@@ -37,8 -37,8 +37,13 @@@ namespace LAMMPS_N
class VectorContainer : public GeneralContainer <T, 1, LEN_VEC>
{
public:
++<<<<<<< HEAD
+ VectorContainer(char *_id);
+ VectorContainer(char *_id, char *_comm, char *_ref, char *_restart, int _scalePower = 1);
++=======
+ VectorContainer(const char *_id);
+ VectorContainer(const char *_id, const char *_comm, const char *_ref, const char *_restart, int _scalePower = 1);
++>>>>>>> upstream/3.0.0
VectorContainer(VectorContainer<T,LEN_VEC> const &orig);
virtual ~VectorContainer();
@@@ -62,7 -62,7 +67,11 @@@
------------------------------------------------------------------------- */
template<typename T, int LEN_VEC>
++<<<<<<< HEAD
+ VectorContainer<T,LEN_VEC>::VectorContainer(char *_id)
++=======
+ VectorContainer<T,LEN_VEC>::VectorContainer(const char *_id)
++>>>>>>> upstream/3.0.0
: GeneralContainer<T,1,LEN_VEC>(_id)
{
diff --cc src/version_liggghts.h
index 53eb557,80c3724..c99122e
--- a/src/version_liggghts.h
+++ b/src/version_liggghts.h
@@@ -1,1 -1,1 +1,5 @@@
++<<<<<<< HEAD
+#define LIGGGHTS_VERSION "LIGGGHTS-PUBLIC 2.3.8, compiled 2013-10-10-16:13:21 by ckloss"
++=======
+ #define LIGGGHTS_VERSION "LIGGGHTS-PUBLIC 3.0.0, compiled 2014-01-23-20:37:17 by kloss"
++>>>>>>> upstream/3.0.0
diff --cc src/version_liggghts.txt
index bc4abe8,4a36342..46c82a8
--- a/src/version_liggghts.txt
+++ b/src/version_liggghts.txt
@@@ -1,1 -1,1 +1,5 @@@
++<<<<<<< HEAD
+2.3.8
++=======
+ 3.0.0
++>>>>>>> upstream/3.0.0
--
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