From 4f941abdfd2a2be852c91e14c4e943a0951505c6 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 20 Sep 2016 16:19:25 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15601 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Section_commands.html | 2 +- doc/html/Section_example.html | 2 +- doc/html/Section_perf.html | 2 +- doc/html/_images/fix_ti_spring_force.jpg | Bin 3627 -> 2673 bytes doc/html/_images/fix_ti_spring_function_1.jpg | Bin 1040 -> 1173 bytes doc/html/_images/fix_ti_spring_function_2.jpg | Bin 5753 -> 5662 bytes doc/html/angle_coeff.html | 2 +- doc/html/angle_hybrid.html | 2 +- doc/html/angle_none.html | 2 +- doc/html/angle_style.html | 2 +- doc/html/angle_zero.html | 2 +- doc/html/atom_modify.html | 2 +- doc/html/bond_coeff.html | 2 +- doc/html/bond_hybrid.html | 6 +- doc/html/bond_none.html | 6 +- doc/html/bond_style.html | 2 +- doc/html/bond_write.html | 2 +- doc/html/bond_zero.html | 6 +- doc/html/box.html | 2 +- doc/html/clear.html | 2 +- doc/html/comm_modify.html | 2 +- doc/html/comm_style.html | 2 +- doc/html/compute.html | 2 +- doc/html/compute_angle.html | 2 +- doc/html/compute_angle_local.html | 2 +- doc/html/compute_bond.html | 2 +- doc/html/compute_bond_local.html | 2 +- doc/html/compute_com.html | 2 +- doc/html/compute_dihedral.html | 2 +- doc/html/compute_dihedral_local.html | 2 +- doc/html/compute_dilatation_atom.html | 2 +- doc/html/compute_group_group.html | 2 +- doc/html/compute_improper.html | 2 +- doc/html/compute_improper_local.html | 2 +- doc/html/compute_modify.html | 2 +- doc/html/compute_msd.html | 2 +- doc/html/compute_msd_nongauss.html | 16 +- doc/html/compute_pair.html | 2 +- doc/html/compute_pair_local.html | 2 +- doc/html/compute_plasticity_atom.html | 2 +- doc/html/compute_property_atom.html | 2 +- doc/html/compute_property_local.html | 2 +- doc/html/compute_rigid_local.html | 2 +- doc/html/compute_saed.html | 22 ++- doc/html/compute_slice.html | 2 +- doc/html/compute_smd_damage.html | 2 +- doc/html/compute_smd_hourglass_error.html | 2 +- doc/html/compute_smd_internal_energy.html | 2 +- doc/html/compute_smd_plastic_strain.html | 2 +- doc/html/compute_smd_plastic_strain_rate.html | 2 +- doc/html/compute_smd_rho.html | 2 +- doc/html/compute_smd_tlsph_defgrad.html | 2 +- doc/html/compute_smd_tlsph_dt.html | 2 +- doc/html/compute_smd_tlsph_num_neighs.html | 2 +- doc/html/compute_smd_tlsph_shape.html | 2 +- doc/html/compute_smd_tlsph_strain.html | 2 +- doc/html/compute_smd_tlsph_strain_rate.html | 2 +- doc/html/compute_smd_tlsph_stress.html | 2 +- doc/html/compute_smd_vol.html | 2 +- doc/html/compute_tally.html | 2 +- doc/html/compute_temp_asphere.html | 2 +- doc/html/compute_temp_body.html | 2 +- doc/html/compute_temp_com.html | 2 +- doc/html/compute_temp_deform.html | 2 +- doc/html/compute_temp_deform_eff.html | 2 +- doc/html/compute_temp_drude.html | 2 +- doc/html/compute_temp_eff.html | 2 +- doc/html/compute_temp_profile.html | 2 +- doc/html/compute_temp_ramp.html | 2 +- doc/html/compute_temp_region.html | 2 +- doc/html/compute_temp_region_eff.html | 2 +- doc/html/compute_temp_rotate.html | 2 +- doc/html/compute_temp_sphere.html | 2 +- doc/html/compute_vacf.html | 2 +- doc/html/create_atoms.html | 18 ++- doc/html/create_bonds.html | 2 +- doc/html/delete_atoms.html | 2 +- doc/html/delete_bonds.html | 2 +- doc/html/dielectric.html | 2 +- doc/html/dihedral_hybrid.html | 2 +- doc/html/dihedral_none.html | 2 +- doc/html/dihedral_zero.html | 2 +- doc/html/displace_atoms.html | 2 +- doc/html/dump_h5md.html | 2 +- doc/html/dump_modify.html | 2 +- doc/html/dump_molfile.html | 2 +- doc/html/echo.html | 2 +- doc/html/fix.html | 2 +- doc/html/fix_adapt.html | 3 +- doc/html/fix_adapt_fep.html | 3 +- doc/html/fix_addforce.html | 1 - doc/html/fix_addtorque.html | 3 +- doc/html/fix_append_atoms.html | 3 +- doc/html/fix_atc.html | 1 - doc/html/fix_atom_swap.html | 3 +- doc/html/fix_ave_atom.html | 3 +- doc/html/fix_ave_chunk.html | 1 - doc/html/fix_ave_correlate.html | 3 +- doc/html/fix_ave_correlate_long.html | 3 +- doc/html/fix_ave_histo.html | 3 +- doc/html/fix_ave_time.html | 3 +- doc/html/fix_aveforce.html | 1 - doc/html/fix_balance.html | 1 - doc/html/fix_bond_break.html | 3 +- doc/html/fix_bond_create.html | 3 +- doc/html/fix_bond_swap.html | 1 - doc/html/fix_box_relax.html | 11 +- doc/html/fix_colvars.html | 3 +- doc/html/fix_controller.html | 35 +++-- doc/html/fix_deform.html | 1 - doc/html/fix_deposit.html | 3 +- doc/html/fix_drag.html | 3 +- doc/html/fix_drude.html | 3 +- doc/html/fix_drude_transform.html | 3 +- doc/html/fix_dt_reset.html | 3 +- doc/html/fix_efield.html | 3 +- doc/html/fix_ehex.html | 23 +-- doc/html/fix_enforce2d.html | 1 - doc/html/fix_eos_cv.html | 1 - doc/html/fix_eos_table.html | 3 +- doc/html/fix_eos_table_rx.html | 1 - doc/html/fix_evaporate.html | 3 +- doc/html/fix_external.html | 3 +- doc/html/fix_flow_gauss.html | 3 +- doc/html/fix_freeze.html | 1 - doc/html/fix_gcmc.html | 5 +- doc/html/fix_gld.html | 32 ++-- doc/html/fix_gle.html | 1 - doc/html/fix_gravity.html | 1 - doc/html/fix_heat.html | 3 +- doc/html/fix_imd.html | 3 +- doc/html/fix_indent.html | 3 +- doc/html/fix_ipi.html | 1 - doc/html/fix_langevin.html | 5 +- doc/html/fix_langevin_drude.html | 3 +- doc/html/fix_langevin_eff.html | 3 +- doc/html/fix_lb_fluid.html | 31 ++-- doc/html/fix_lb_momentum.html | 3 +- doc/html/fix_lb_pc.html | 3 +- doc/html/fix_lb_rigid_pc_sphere.html | 3 +- doc/html/fix_lb_viscous.html | 3 +- doc/html/fix_lineforce.html | 3 +- doc/html/fix_manifoldforce.html | 3 +- doc/html/fix_meso.html | 3 +- doc/html/fix_meso_stationary.html | 3 +- doc/html/fix_modify.html | 2 +- doc/html/fix_momentum.html | 3 +- doc/html/fix_move.html | 3 +- doc/html/fix_msst.html | 3 +- doc/html/fix_neb.html | 1 - doc/html/fix_nh.html | 1 - doc/html/fix_nh_eff.html | 3 +- doc/html/fix_nph_asphere.html | 1 - doc/html/fix_nph_body.html | 1 - doc/html/fix_nph_sphere.html | 1 - doc/html/fix_nphug.html | 1 - doc/html/fix_npt_asphere.html | 1 - doc/html/fix_npt_body.html | 1 - doc/html/fix_npt_sphere.html | 1 - doc/html/fix_nve.html | 1 - doc/html/fix_nve_asphere.html | 1 - doc/html/fix_nve_asphere_noforce.html | 3 +- doc/html/fix_nve_body.html | 1 - doc/html/fix_nve_eff.html | 3 +- doc/html/fix_nve_limit.html | 3 +- doc/html/fix_nve_line.html | 1 - doc/html/fix_nve_manifold_rattle.html | 1 - doc/html/fix_nve_noforce.html | 3 +- doc/html/fix_nve_sphere.html | 1 - doc/html/fix_nve_tri.html | 1 - doc/html/fix_nvt_asphere.html | 1 - doc/html/fix_nvt_body.html | 1 - doc/html/fix_nvt_manifold_rattle.html | 1 - doc/html/fix_nvt_sllod.html | 1 - doc/html/fix_nvt_sllod_eff.html | 3 +- doc/html/fix_nvt_sphere.html | 1 - doc/html/fix_oneway.html | 3 +- doc/html/fix_orient.html | 1 - doc/html/fix_phonon.html | 3 +- doc/html/fix_pimd.html | 17 ++- doc/html/fix_planeforce.html | 3 +- doc/html/fix_poems.html | 3 +- doc/html/fix_pour.html | 3 +- doc/html/fix_press_berendsen.html | 3 +- doc/html/fix_print.html | 3 +- doc/html/fix_property_atom.html | 3 +- doc/html/fix_qbmsst.html | 23 +-- doc/html/fix_qeq.html | 3 +- doc/html/fix_qeq_comb.html | 1 - doc/html/fix_qeq_reax.html | 1 - doc/html/fix_qmmm.html | 3 +- doc/html/fix_qtb.html | 3 +- doc/html/fix_reax_bonds.html | 3 +- doc/html/fix_reaxc_species.html | 3 +- doc/html/fix_recenter.html | 3 +- doc/html/fix_restrain.html | 17 ++- doc/html/fix_rigid.html | 1 - doc/html/fix_rx.html | 1 - doc/html/fix_saed_vtk.html | 3 +- doc/html/fix_setforce.html | 1 - doc/html/fix_shake.html | 1 - doc/html/fix_shardlow.html | 1 - doc/html/fix_smd.html | 3 +- doc/html/fix_smd_adjust_dt.html | 3 +- doc/html/fix_smd_integrate_tlsph.html | 3 +- doc/html/fix_smd_integrate_ulsph.html | 3 +- .../fix_smd_move_triangulated_surface.html | 3 +- doc/html/fix_smd_setvel.html | 3 +- doc/html/fix_smd_wall_surface.html | 3 +- doc/html/fix_spring.html | 3 +- doc/html/fix_spring_chunk.html | 3 +- doc/html/fix_spring_rg.html | 1 - doc/html/fix_spring_self.html | 3 +- doc/html/fix_srd.html | 3 +- doc/html/fix_store_force.html | 3 +- doc/html/fix_store_state.html | 3 +- doc/html/fix_temp_berendsen.html | 3 +- doc/html/fix_temp_csvr.html | 3 +- doc/html/fix_temp_rescale.html | 3 +- doc/html/fix_temp_rescale_eff.html | 3 +- doc/html/fix_tfmc.html | 3 +- doc/html/fix_thermal_conductivity.html | 9 +- doc/html/fix_ti_spring.html | 141 ++++++++++-------- doc/html/fix_tmd.html | 3 +- doc/html/fix_ttm.html | 22 +-- doc/html/fix_tune_kspace.html | 1 - doc/html/fix_vector.html | 3 +- doc/html/fix_viscosity.html | 1 - doc/html/fix_viscous.html | 3 +- doc/html/fix_wall.html | 25 ++-- doc/html/fix_wall_gran.html | 1 - doc/html/fix_wall_piston.html | 3 +- doc/html/fix_wall_reflect.html | 1 - doc/html/fix_wall_region.html | 1 - doc/html/fix_wall_srd.html | 3 +- doc/html/fixes.html | 2 - doc/html/genindex.html | 8 +- doc/html/group2ndx.html | 2 +- doc/html/improper_coeff.html | 2 +- doc/html/improper_hybrid.html | 2 +- doc/html/improper_none.html | 2 +- doc/html/improper_style.html | 2 +- doc/html/improper_zero.html | 2 +- doc/html/include.html | 2 +- doc/html/info.html | 2 +- doc/html/jump.html | 2 +- doc/html/kspace_modify.html | 2 +- doc/html/label.html | 2 +- doc/html/lattice.html | 2 +- doc/html/mass.html | 2 +- doc/html/min_modify.html | 2 +- doc/html/min_style.html | 2 +- doc/html/neigh_modify.html | 2 +- doc/html/neighbor.html | 2 +- doc/html/newton.html | 2 +- doc/html/next.html | 2 +- doc/html/package.html | 2 +- doc/html/pair_awpmd.html | 2 +- doc/html/pair_brownian.html | 2 +- doc/html/pair_coeff.html | 2 +- doc/html/pair_dsmc.html | 2 +- doc/html/pair_eff.html | 10 +- doc/html/pair_kim.html | 2 +- doc/html/pair_lcbop.html | 2 +- doc/html/pair_line_lj.html | 2 +- doc/html/pair_list.html | 16 +- doc/html/pair_mdf.html | 10 +- doc/html/pair_modify.html | 2 +- doc/html/pair_none.html | 2 +- doc/html/pair_quip.html | 2 +- doc/html/pair_reax.html | 2 +- doc/html/pair_smd_hertz.html | 2 +- doc/html/pair_smd_tlsph.html | 2 +- doc/html/pair_smd_triangulated_surface.html | 2 +- doc/html/pair_smd_ulsph.html | 2 +- doc/html/pair_smtbq.html | 2 +- doc/html/pair_sph_heatconduction.html | 2 +- doc/html/pair_sph_lj.html | 2 +- doc/html/pair_sph_rhosum.html | 2 +- doc/html/pair_srp.html | 19 ++- doc/html/pair_style.html | 2 +- doc/html/pair_table.html | 2 +- doc/html/pair_table_rx.html | 2 +- doc/html/pair_thole.html | 4 +- doc/html/pair_tri_lj.html | 2 +- doc/html/pair_write.html | 2 +- doc/html/pair_zero.html | 8 +- doc/html/print.html | 2 +- doc/html/processors.html | 2 +- doc/html/python.html | 2 +- doc/html/quit.html | 2 +- doc/html/read_dump.html | 2 +- doc/html/region.html | 55 ++++++- doc/html/replicate.html | 2 +- doc/html/rerun.html | 2 +- doc/html/reset_timestep.html | 2 +- doc/html/restart.html | 2 +- doc/html/run.html | 2 +- doc/html/set.html | 2 +- doc/html/shell.html | 2 +- doc/html/special_bonds.html | 2 +- doc/html/suffix.html | 2 +- doc/html/thermo.html | 2 +- doc/html/thermo_modify.html | 2 +- doc/html/timer.html | 2 +- doc/html/timestep.html | 2 +- doc/html/tutorial_drude.html | 4 +- doc/html/uncompute.html | 2 +- doc/html/undump.html | 2 +- doc/html/unfix.html | 2 +- doc/html/units.html | 2 +- doc/html/variable.html | 2 +- doc/html/velocity.html | 2 +- doc/html/write_coeff.html | 2 +- doc/html/write_data.html | 2 +- doc/html/write_dump.html | 2 +- doc/html/write_restart.html | 2 +- doc/src/Section_commands.txt | 1 - 318 files changed, 597 insertions(+), 612 deletions(-) diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 950cea475c..a9d08d0cbd 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -858,9 +858,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

smd/setvel smd/wall/surface temp/rescale/eff -ti/rs ti/spring ttm/mod +  diff --git a/doc/html/Section_example.html b/doc/html/Section_example.html index ba1649a09d..593de3184a 100644 --- a/doc/html/Section_example.html +++ b/doc/html/Section_example.html @@ -100,7 +100,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/Section_perf.html b/doc/html/Section_perf.html index 99337aaaac..9562cb166c 100644 --- a/doc/html/Section_perf.html +++ b/doc/html/Section_perf.html @@ -96,7 +96,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
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z!@NJhYvGN7DRii751eLCk_;lewY=2&q}56 zVjgoF5u>_LJl|AA2!sR-cb=D=b@bpk4l1)FmF}34a+Yyc>J`GJ26qGE+&xK`eHaa( z>wMq@E@@X>`j<6YiQa9`Y6-chiIN(}cbPVcv7bD`ab<6{2sawXGv}-$F^iJ)Q&oe- zl|XlP3xt&_nf7032RYPb?guBe#M}ui+EobKFixes

  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/angle_hybrid.html b/doc/html/angle_hybrid.html index db4e3b9c8f..7c1b3a0aad 100644 --- a/doc/html/angle_hybrid.html +++ b/doc/html/angle_hybrid.html @@ -97,7 +97,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_msd_nongauss.html b/doc/html/compute_msd_nongauss.html index 004f670e98..2b6544efcc 100644 --- a/doc/html/compute_msd_nongauss.html +++ b/doc/html/compute_msd_nongauss.html @@ -287,15 +287,19 @@ 
    compute ID group-ID msd/nongauss keyword values ...
    -
      -
    • ID, group-ID are documented in compute command
      • -
    • msd/nongauss = style name of this compute command
      • -
    • zero or more keyword/value pairs may be appended
      • -
    • keyword = com
      • -
    +
      +

    • ID, group-ID are documented in compute command

      +
      • +

    • msd/nongauss = style name of this compute command

      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = com

       com value = yes or no
      +
      • +

    Examples

    diff --git a/doc/html/compute_pair.html b/doc/html/compute_pair.html index c318802cc1..295b837530 100644 --- a/doc/html/compute_pair.html +++ b/doc/html/compute_pair.html @@ -226,7 +226,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_pair_local.html b/doc/html/compute_pair_local.html index ff6ed23713..df948bad92 100644 --- a/doc/html/compute_pair_local.html +++ b/doc/html/compute_pair_local.html @@ -226,7 +226,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_plasticity_atom.html b/doc/html/compute_plasticity_atom.html index 761215a62f..6fc6e432e8 100644 --- a/doc/html/compute_plasticity_atom.html +++ b/doc/html/compute_plasticity_atom.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html index 27623e0526..d92de591ca 100644 --- a/doc/html/compute_property_atom.html +++ b/doc/html/compute_property_atom.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_property_local.html b/doc/html/compute_property_local.html index 49512210b1..c30c9eb685 100644 --- a/doc/html/compute_property_local.html +++ b/doc/html/compute_property_local.html @@ -226,7 +226,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_rigid_local.html b/doc/html/compute_rigid_local.html index a252c51f39..b42c9f81cf 100644 --- a/doc/html/compute_rigid_local.html +++ b/doc/html/compute_rigid_local.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_saed.html b/doc/html/compute_saed.html index 5a46875ada..d9f4118168 100644 --- a/doc/html/compute_saed.html +++ b/doc/html/compute_saed.html @@ -287,14 +287,18 @@ 
    compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...
    -
      -
    • ID, group-ID are documented in compute command
      • -
    • saed = style name of this compute command
      • -
    • lambda = wavelength of incident radiation (length units)
      • -
    • type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
      • -
    • zero or more keyword/value pairs may be appended
      • -
    • keyword = Kmax or Zone or dR_Ewald or c or manual or echo
      • -
    +
      +

    • ID, group-ID are documented in compute command

      +
      • +

    • saed = style name of this compute command

      +
      • +

    • lambda = wavelength of incident radiation (length units)

      +
      • +

    • type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)

      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = Kmax or Zone or dR_Ewald or c or manual or echo

       Kmax value = Maximum distance explored from reciprocal space origin
                (inverse length units)
@@ -310,6 +314,8 @@
            based on the values of the c parameters
 echo = flag to provide extra output for debugging purposes
      +
      • +

    Examples

    diff --git a/doc/html/compute_slice.html b/doc/html/compute_slice.html index e0c9e9cacc..bc736d8708 100644 --- a/doc/html/compute_slice.html +++ b/doc/html/compute_slice.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_damage.html b/doc/html/compute_smd_damage.html index 2a3200e33e..6882ddac84 100644 --- a/doc/html/compute_smd_damage.html +++ b/doc/html/compute_smd_damage.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_hourglass_error.html b/doc/html/compute_smd_hourglass_error.html index f43932ebcb..519aba68bb 100644 --- a/doc/html/compute_smd_hourglass_error.html +++ b/doc/html/compute_smd_hourglass_error.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_internal_energy.html b/doc/html/compute_smd_internal_energy.html index c0dd671fb3..2a4a521fba 100644 --- a/doc/html/compute_smd_internal_energy.html +++ b/doc/html/compute_smd_internal_energy.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_plastic_strain.html b/doc/html/compute_smd_plastic_strain.html index 438cb54d9f..3692543c88 100644 --- a/doc/html/compute_smd_plastic_strain.html +++ b/doc/html/compute_smd_plastic_strain.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_plastic_strain_rate.html b/doc/html/compute_smd_plastic_strain_rate.html index bf78e17185..9b7313c4f6 100644 --- a/doc/html/compute_smd_plastic_strain_rate.html +++ b/doc/html/compute_smd_plastic_strain_rate.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_rho.html b/doc/html/compute_smd_rho.html index 5d38c4a63b..d300bdd36a 100644 --- a/doc/html/compute_smd_rho.html +++ b/doc/html/compute_smd_rho.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_defgrad.html b/doc/html/compute_smd_tlsph_defgrad.html index 0497619058..19dedeed7a 100644 --- a/doc/html/compute_smd_tlsph_defgrad.html +++ b/doc/html/compute_smd_tlsph_defgrad.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_dt.html b/doc/html/compute_smd_tlsph_dt.html index 6817f32e2b..05e858151d 100644 --- a/doc/html/compute_smd_tlsph_dt.html +++ b/doc/html/compute_smd_tlsph_dt.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_num_neighs.html b/doc/html/compute_smd_tlsph_num_neighs.html index 2b4fff05ac..b2659f3db7 100644 --- a/doc/html/compute_smd_tlsph_num_neighs.html +++ b/doc/html/compute_smd_tlsph_num_neighs.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_shape.html b/doc/html/compute_smd_tlsph_shape.html index 3882f20d1d..6d5f8a736f 100644 --- a/doc/html/compute_smd_tlsph_shape.html +++ b/doc/html/compute_smd_tlsph_shape.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_strain.html b/doc/html/compute_smd_tlsph_strain.html index 178e98cfd6..bc74e3949c 100644 --- a/doc/html/compute_smd_tlsph_strain.html +++ b/doc/html/compute_smd_tlsph_strain.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_strain_rate.html b/doc/html/compute_smd_tlsph_strain_rate.html index 232e7f2078..b7284eee25 100644 --- a/doc/html/compute_smd_tlsph_strain_rate.html +++ b/doc/html/compute_smd_tlsph_strain_rate.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_tlsph_stress.html b/doc/html/compute_smd_tlsph_stress.html index 43189db431..dfa34d326f 100644 --- a/doc/html/compute_smd_tlsph_stress.html +++ b/doc/html/compute_smd_tlsph_stress.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_smd_vol.html b/doc/html/compute_smd_vol.html index a502129e34..754ab7e73e 100644 --- a/doc/html/compute_smd_vol.html +++ b/doc/html/compute_smd_vol.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_tally.html b/doc/html/compute_tally.html index dbdf0b256c..b45bfc4858 100644 --- a/doc/html/compute_tally.html +++ b/doc/html/compute_tally.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_asphere.html b/doc/html/compute_temp_asphere.html index 116dbd071a..2b7e60a395 100644 --- a/doc/html/compute_temp_asphere.html +++ b/doc/html/compute_temp_asphere.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_body.html b/doc/html/compute_temp_body.html index d52146adf0..2d957b35f2 100644 --- a/doc/html/compute_temp_body.html +++ b/doc/html/compute_temp_body.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_com.html b/doc/html/compute_temp_com.html index 52ca99d536..66d568b7fb 100644 --- a/doc/html/compute_temp_com.html +++ b/doc/html/compute_temp_com.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_deform.html b/doc/html/compute_temp_deform.html index d1b1ad4084..ab6b870c21 100644 --- a/doc/html/compute_temp_deform.html +++ b/doc/html/compute_temp_deform.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_deform_eff.html b/doc/html/compute_temp_deform_eff.html index 67ac367805..716787c70c 100644 --- a/doc/html/compute_temp_deform_eff.html +++ b/doc/html/compute_temp_deform_eff.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_drude.html b/doc/html/compute_temp_drude.html index 9da9895636..e2f8c9bcc6 100644 --- a/doc/html/compute_temp_drude.html +++ b/doc/html/compute_temp_drude.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_eff.html b/doc/html/compute_temp_eff.html index 4f457ec164..3b653ec6d4 100644 --- a/doc/html/compute_temp_eff.html +++ b/doc/html/compute_temp_eff.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_profile.html b/doc/html/compute_temp_profile.html index 0d080701ea..8406c83f21 100644 --- a/doc/html/compute_temp_profile.html +++ b/doc/html/compute_temp_profile.html @@ -226,7 +226,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_ramp.html b/doc/html/compute_temp_ramp.html index ab6cbe6eef..5af9de4707 100644 --- a/doc/html/compute_temp_ramp.html +++ b/doc/html/compute_temp_ramp.html @@ -226,7 +226,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_region.html b/doc/html/compute_temp_region.html index b2022a8657..79733cbed8 100644 --- a/doc/html/compute_temp_region.html +++ b/doc/html/compute_temp_region.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_region_eff.html b/doc/html/compute_temp_region_eff.html index 2a10c2d4dd..644c9e701b 100644 --- a/doc/html/compute_temp_region_eff.html +++ b/doc/html/compute_temp_region_eff.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_rotate.html b/doc/html/compute_temp_rotate.html index f657bba0cc..a93904e01c 100644 --- a/doc/html/compute_temp_rotate.html +++ b/doc/html/compute_temp_rotate.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_temp_sphere.html b/doc/html/compute_temp_sphere.html index c5ad097c3e..1e9ba089ac 100644 --- a/doc/html/compute_temp_sphere.html +++ b/doc/html/compute_temp_sphere.html @@ -226,7 +226,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/compute_vacf.html b/doc/html/compute_vacf.html index 36d1c94cbd..0adf5c2700 100644 --- a/doc/html/compute_vacf.html +++ b/doc/html/compute_vacf.html @@ -225,7 +225,7 @@
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/create_atoms.html b/doc/html/create_atoms.html index c3c6d15fa4..fdf3abf182 100644 --- a/doc/html/create_atoms.html +++ b/doc/html/create_atoms.html @@ -275,10 +275,10 @@ 
     create_atoms type style args keyword values ...
    -
      -
    • type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
      • -
    • style = box or region or single or random
      • -
    +
      +

    • type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)

      +
      • +

    • style = box or region or single or random

       box args = none
 region args = region-ID
@@ -290,10 +290,10 @@ create_atoms type style args keyword values ...
   seed = random # seed (positive integer)
   region-ID = create atoms within this region, use NULL for entire simulation box
      -
        -
      • zero or more keyword/value pairs may be appended
        • -
      • keyword = mol or basis or remap or var or set or units
        • -
      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = mol or basis or remap or var or set or units

       mol value = template-ID seed
   template-ID = ID of molecule template specified in a separate molecule command
@@ -313,6 +313,8 @@ create_atoms type style args keyword values ...
   lattice = the geometry is defined in lattice units
   box = the geometry is defined in simulation box units
      +
      • +

    Examples

    diff --git a/doc/html/create_bonds.html b/doc/html/create_bonds.html index 9db231ef15..081c62263d 100644 --- a/doc/html/create_bonds.html +++ b/doc/html/create_bonds.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/delete_atoms.html b/doc/html/delete_atoms.html index 87e2d932fd..3d65d88ba1 100644 --- a/doc/html/delete_atoms.html +++ b/doc/html/delete_atoms.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/delete_bonds.html b/doc/html/delete_bonds.html index 982390386d..ccde1b7d72 100644 --- a/doc/html/delete_bonds.html +++ b/doc/html/delete_bonds.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/dielectric.html b/doc/html/dielectric.html index f4983c1c96..9da01d0ba8 100644 --- a/doc/html/dielectric.html +++ b/doc/html/dielectric.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/dihedral_hybrid.html b/doc/html/dihedral_hybrid.html index f7c4497e9a..c89446e40b 100644 --- a/doc/html/dihedral_hybrid.html +++ b/doc/html/dihedral_hybrid.html @@ -97,7 +97,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles

    • Examples

    diff --git a/doc/html/fix_colvars.html b/doc/html/fix_colvars.html index 4498435e1d..13aac43bc7 100644 --- a/doc/html/fix_colvars.html +++ b/doc/html/fix_colvars.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_controller.html b/doc/html/fix_controller.html index 9f95b3228b..7717a59faf 100644 --- a/doc/html/fix_controller.html +++ b/doc/html/fix_controller.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -371,16 +370,22 @@ 
    fix ID group-ID controller Nevery alpha Kp Ki Kd pvar setpoint cvar
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • controller = style name of this fix command
      • -
    • Nevery = invoke controller every this many timesteps
      • -
    • alpha = coupling constant for PID equation (see units discussion below)
      • -
    • Kp = proportional gain in PID equation (unitless)
      • -
    • Ki = integral gain in PID equation (unitless)
      • -
    • Kd = derivative gain in PID equation (unitless)
      • -
    • pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • controller = style name of this fix command

      +
      • +

    • Nevery = invoke controller every this many timesteps

      +
      • +

    • alpha = coupling constant for PID equation (see units discussion below)

      +
      • +

    • Kp = proportional gain in PID equation (unitless)

      +
      • +

    • Ki = integral gain in PID equation (unitless)

      +
      • +

    • Kd = derivative gain in PID equation (unitless)

      +
      • +

    • pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name

       c_ID = global scalar calculated by a compute with ID
 c_ID[I] = Ith component of global vector calculated by a compute with ID
@@ -388,9 +393,11 @@ f_ID = global scalar calculated by a fix with ID
 f_ID[I] = Ith component of global vector calculated by a fix with ID
 v_name = value calculated by an equal-style variable with name
      -
        -
      • setpoint = desired value of process variable (same units as process variable)
        • -
      • cvar = name of control variable
        • + +

      • setpoint = desired value of process variable (same units as process variable)

        +
        • +

      • cvar = name of control variable

        +
    diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html index 259cf7c2af..4e3d278009 100644 --- a/doc/html/fix_deform.html +++ b/doc/html/fix_deform.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html index ae097c4fd2..d793c89378 100644 --- a/doc/html/fix_deposit.html +++ b/doc/html/fix_deposit.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_drag.html b/doc/html/fix_drag.html index e4b8741360..fbb3802a72 100644 --- a/doc/html/fix_drag.html +++ b/doc/html/fix_drag.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_drude.html b/doc/html/fix_drude.html index a41598cdf6..31ccad00c1 100644 --- a/doc/html/fix_drude.html +++ b/doc/html/fix_drude.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_drude_transform.html b/doc/html/fix_drude_transform.html index 1dcd8ca41d..708009e787 100644 --- a/doc/html/fix_drude_transform.html +++ b/doc/html/fix_drude_transform.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_dt_reset.html b/doc/html/fix_dt_reset.html index f26f8aab03..5cce091cd5 100644 --- a/doc/html/fix_dt_reset.html +++ b/doc/html/fix_dt_reset.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_efield.html b/doc/html/fix_efield.html index 520ec6c8a6..92edf2cecb 100644 --- a/doc/html/fix_efield.html +++ b/doc/html/fix_efield.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_ehex.html b/doc/html/fix_ehex.html index 20d2d29394..5f381712a8 100644 --- a/doc/html/fix_ehex.html +++ b/doc/html/fix_ehex.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -371,14 +370,18 @@ 
    fix ID group-ID ehex nevery F keyword value
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • ehex = style name of this fix command
      • -
    • nevery = add/subtract heat every this many timesteps
      • -
    • F = energy flux into the reservoir (energy/time units)
      • -
    • zero or more keyword/value pairs may be appended to args
      • -
    • keyword = region or constrain or com or hex
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • ehex = style name of this fix command

      +
      • +

    • nevery = add/subtract heat every this many timesteps

      +
      • +

    • F = energy flux into the reservoir (energy/time units)

      +
      • +

    • zero or more keyword/value pairs may be appended to args

      +
      • +

    • keyword = region or constrain or com or hex

       region value = region-ID
   region-ID = ID of region (reservoir) atoms must be in for added thermostatting force
@@ -389,6 +392,8 @@
 hex value = none
   omit the coordinate correction to recover the HEX algorithm
      +
      • +

    Examples

    diff --git a/doc/html/fix_enforce2d.html b/doc/html/fix_enforce2d.html index f08d9bf34e..67aa205fcf 100644 --- a/doc/html/fix_enforce2d.html +++ b/doc/html/fix_enforce2d.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_eos_cv.html b/doc/html/fix_eos_cv.html index 4e77d1a50d..2cef2e5105 100644 --- a/doc/html/fix_eos_cv.html +++ b/doc/html/fix_eos_cv.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_eos_table.html b/doc/html/fix_eos_table.html index ca7e48c67b..7ebf758664 100644 --- a/doc/html/fix_eos_table.html +++ b/doc/html/fix_eos_table.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_eos_table_rx.html b/doc/html/fix_eos_table_rx.html index e1f7bfd710..8a2e0e2336 100644 --- a/doc/html/fix_eos_table_rx.html +++ b/doc/html/fix_eos_table_rx.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_evaporate.html b/doc/html/fix_evaporate.html index 6401874be7..d2911e918d 100644 --- a/doc/html/fix_evaporate.html +++ b/doc/html/fix_evaporate.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html index 5755473611..46071be299 100644 --- a/doc/html/fix_external.html +++ b/doc/html/fix_external.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -309,7 +308,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_flow_gauss.html b/doc/html/fix_flow_gauss.html index 20e7ca930e..ab0158d5f4 100644 --- a/doc/html/fix_flow_gauss.html +++ b/doc/html/fix_flow_gauss.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_freeze.html b/doc/html/fix_freeze.html index 4fb5942bbd..8072bfdf04 100644 --- a/doc/html/fix_freeze.html +++ b/doc/html/fix_freeze.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_gcmc.html b/doc/html/fix_gcmc.html index e353610972..502c60d59f 100644 --- a/doc/html/fix_gcmc.html +++ b/doc/html/fix_gcmc.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • @@ -431,7 +430,7 @@ fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk

    This fix performs grand canonical Monte Carlo (GCMC) exchanges of atoms or molecules of the given type with an imaginary ideal gas reservoir at the specified T and chemical potential (mu) as discussed in -(Frenkel). If used with the fix nvt command, +(Frenkel). If used with the fix nvt command, simulations in the grand canonical ensemble (muVT, constant chemical potential, constant volume, and constant temperature) can be performed. Specific uses include computing isotherms in microporous diff --git a/doc/html/fix_gld.html b/doc/html/fix_gld.html index dec00607b0..9255a8fd02 100644 --- a/doc/html/fix_gld.html +++ b/doc/html/fix_gld.html @@ -287,7 +287,6 @@

  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -372,17 +371,24 @@ 
     fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • gld = style name of this fix command
      • -
    • Tstart,Tstop = desired temperature at start/end of run (temperature units)
      • -
    • N_k = number of terms in the Prony series representation of the memory kernel
      • -
    • seed = random number seed to use for white noise (positive integer)
      • -
    • series = pprony is presently the only available option
      • -
    • c_k = the weight of the kth term in the Prony series (mass per time units)
      • -
    • tau_k = the time constant of the kth term in the Prony series (time units)
      • -
    • zero or more keyword/value pairs may be appended
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • gld = style name of this fix command

      +
      • +

    • Tstart,Tstop = desired temperature at start/end of run (temperature units)

      +
      • +

    • N_k = number of terms in the Prony series representation of the memory kernel

      +
      • +

    • seed = random number seed to use for white noise (positive integer)

      +
      • +

    • series = pprony is presently the only available option

      +
      • +

    • c_k = the weight of the kth term in the Prony series (mass per time units)

      +
      • +

    • tau_k = the time constant of the kth term in the Prony series (time units)

      +
      • +

    • zero or more keyword/value pairs may be appended

       keyword = frozen or zero
   frozen value = no or yes
@@ -392,6 +398,8 @@ keyword = frozen or zero
     no = do not set total random force to zero
     yes = set total random force to zero
      +
      • +

    Examples

    diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html index 728f7085ef..79ae5c3a8a 100644 --- a/doc/html/fix_gle.html +++ b/doc/html/fix_gle.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html index d8ebafc779..a3b1b365a0 100644 --- a/doc/html/fix_gravity.html +++ b/doc/html/fix_gravity.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html index 2411f2b5a8..6d4c98d780 100644 --- a/doc/html/fix_heat.html +++ b/doc/html/fix_heat.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_imd.html b/doc/html/fix_imd.html index 60ffb0e6a3..5778a61d4b 100644 --- a/doc/html/fix_imd.html +++ b/doc/html/fix_imd.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -309,7 +308,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_indent.html b/doc/html/fix_indent.html index 2b7d4491c0..6bb13ed99f 100644 --- a/doc/html/fix_indent.html +++ b/doc/html/fix_indent.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html index ba69231085..7e49767d86 100644 --- a/doc/html/fix_ipi.html +++ b/doc/html/fix_ipi.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html index 32196c9651..44e52eba06 100644 --- a/doc/html/fix_langevin.html +++ b/doc/html/fix_langevin.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -424,7 +423,7 @@

    Description

    -

    Apply a Langevin thermostat as described in (Schneider) +

    Apply a Langevin thermostat as described in (Schneider) to a group of atoms which models an interaction with a background implicit solvent. Used with fix nve, this command performs Brownian dynamics (BD), since the total force on each atom @@ -452,7 +451,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as described in -(Dunweg), where a uniform random number is used (instead of +(Dunweg), where a uniform random number is used (instead of a Gaussian random number) for speed.

    Note that unless you use the omega or angmom keywords, the thermostat effect of this fix is applied to only the translational diff --git a/doc/html/fix_langevin_drude.html b/doc/html/fix_langevin_drude.html index efc3d01574..c57b9c4da5 100644 --- a/doc/html/fix_langevin_drude.html +++ b/doc/html/fix_langevin_drude.html @@ -287,7 +287,6 @@

  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_langevin_eff.html b/doc/html/fix_langevin_eff.html index 1350637ebd..ef279a754c 100644 --- a/doc/html/fix_langevin_eff.html +++ b/doc/html/fix_langevin_eff.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index cb6d92d48b..11e364e0fb 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -372,17 +371,23 @@ 
    fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ...
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • lb/fluid = style name of this fix command
      • -
    • nevery = update the lattice-Boltzmann fluid every this many timesteps
      • -
    • LBtype = 1 to use the standard finite difference LB integrator, -2 to use the LB integrator of Ollila et al.
      • -
    • viscosity = the fluid viscosity (units of mass/(time*length)).
      • -
    • density = the fluid density.
      • -
    • zero or more keyword/value pairs may be appended
      • -
    • keyword = setArea or setGamma or scaleGamma or dx or dm or a0 or noise or calcforce or trilinear or D3Q19 or read_restart or write_restart or zwall_velocity or bodyforce or printfluid
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • lb/fluid = style name of this fix command

      +
      • +

    • nevery = update the lattice-Boltzmann fluid every this many timesteps

      +
      • +

    • LBtype = 1 to use the standard finite difference LB integrator, +2 to use the LB integrator of Ollila et al.

      +
      • +

    • viscosity = the fluid viscosity (units of mass/(time*length)).

      +
      • +

    • density = the fluid density.

      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = setArea or setGamma or scaleGamma or dx or dm or a0 or noise or calcforce or trilinear or D3Q19 or read_restart or write_restart or zwall_velocity or bodyforce or printfluid

       setArea values = type node_area
     type = atom type (1-N)
@@ -409,6 +414,8 @@
 bodyforce values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
 printfluid values = N = print the fluid density and velocity at each grid point every N timesteps.
      +
      • +

    Examples

    diff --git a/doc/html/fix_lb_momentum.html b/doc/html/fix_lb_momentum.html index 3b514b0865..8784ca5cd9 100644 --- a/doc/html/fix_lb_momentum.html +++ b/doc/html/fix_lb_momentum.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html index cf656a5f8b..b25f51c767 100644 --- a/doc/html/fix_lb_pc.html +++ b/doc/html/fix_lb_pc.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html index c41a4b0b20..7f054909ac 100644 --- a/doc/html/fix_lb_rigid_pc_sphere.html +++ b/doc/html/fix_lb_rigid_pc_sphere.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -414,7 +413,7 @@ created to be used in place of that fix, to integrate the equations of motion of spherical rigid bodies when a lattice-Boltzmann fluid is present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of +The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of a set of spherical rigid bodies experiencing velocity dependent hydrodynamic forces. The spherical bodies are assumed to rotate as solid, uniform density spheres, with moments of inertia calculated diff --git a/doc/html/fix_lb_viscous.html b/doc/html/fix_lb_viscous.html index 4cd85462f8..1fcf7f0e0e 100644 --- a/doc/html/fix_lb_viscous.html +++ b/doc/html/fix_lb_viscous.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_lineforce.html b/doc/html/fix_lineforce.html index d37f896efa..1e2152aaca 100644 --- a/doc/html/fix_lineforce.html +++ b/doc/html/fix_lineforce.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_manifoldforce.html b/doc/html/fix_manifoldforce.html index fd2a796feb..458eaa4204 100644 --- a/doc/html/fix_manifoldforce.html +++ b/doc/html/fix_manifoldforce.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_meso.html b/doc/html/fix_meso.html index 5ba2d473e6..3bbdfb82c1 100644 --- a/doc/html/fix_meso.html +++ b/doc/html/fix_meso.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_meso_stationary.html b/doc/html/fix_meso_stationary.html index aa984e285a..de04247e5a 100644 --- a/doc/html/fix_meso_stationary.html +++ b/doc/html/fix_meso_stationary.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_modify.html b/doc/html/fix_modify.html index c04c310ec3..c2cc6a795d 100644 --- a/doc/html/fix_modify.html +++ b/doc/html/fix_modify.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_momentum.html b/doc/html/fix_momentum.html index d5e0a95ddf..4ba88e416a 100644 --- a/doc/html/fix_momentum.html +++ b/doc/html/fix_momentum.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html index 11ccb6b6d7..702ed64d8c 100644 --- a/doc/html/fix_move.html +++ b/doc/html/fix_move.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_msst.html b/doc/html/fix_msst.html index ec7156e5d9..dbe4ef677e 100644 --- a/doc/html/fix_msst.html +++ b/doc/html/fix_msst.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html index 43b68f730c..7517fa8c67 100644 --- a/doc/html/fix_neb.html +++ b/doc/html/fix_neb.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index c466ff6143..89f94fac3d 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html index c01ecebe3e..259021784f 100644 --- a/doc/html/fix_nh_eff.html +++ b/doc/html/fix_nh_eff.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html index 7322a3de41..563dda3ab5 100644 --- a/doc/html/fix_nph_asphere.html +++ b/doc/html/fix_nph_asphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nph_body.html b/doc/html/fix_nph_body.html index 58339d4e79..7a37ccea77 100644 --- a/doc/html/fix_nph_body.html +++ b/doc/html/fix_nph_body.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html index 4a2a90e364..26075d70f6 100644 --- a/doc/html/fix_nph_sphere.html +++ b/doc/html/fix_nph_sphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html index d164455776..01be6266da 100644 --- a/doc/html/fix_nphug.html +++ b/doc/html/fix_nphug.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html index 9e2b3a9b5b..825f49bf83 100644 --- a/doc/html/fix_npt_asphere.html +++ b/doc/html/fix_npt_asphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html index dd1e4800d5..9a1f9cafe1 100644 --- a/doc/html/fix_npt_body.html +++ b/doc/html/fix_npt_body.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html index 5346be62ff..7b856db766 100644 --- a/doc/html/fix_npt_sphere.html +++ b/doc/html/fix_npt_sphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve.html b/doc/html/fix_nve.html index fe48732a77..9e1e8f872b 100644 --- a/doc/html/fix_nve.html +++ b/doc/html/fix_nve.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html index 23079d9571..c78ac5e36a 100644 --- a/doc/html/fix_nve_asphere.html +++ b/doc/html/fix_nve_asphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve_asphere_noforce.html b/doc/html/fix_nve_asphere_noforce.html index a5b2b19af9..9375c873bf 100644 --- a/doc/html/fix_nve_asphere_noforce.html +++ b/doc/html/fix_nve_asphere_noforce.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html index 07ab60e08c..b2b57fe67b 100644 --- a/doc/html/fix_nve_body.html +++ b/doc/html/fix_nve_body.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve_eff.html b/doc/html/fix_nve_eff.html index 4e04fb5965..a1f7b8d893 100644 --- a/doc/html/fix_nve_eff.html +++ b/doc/html/fix_nve_eff.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_nve_limit.html b/doc/html/fix_nve_limit.html index 8ec3d0cfda..78be195355 100644 --- a/doc/html/fix_nve_limit.html +++ b/doc/html/fix_nve_limit.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html index 689bcc938c..c33df0a338 100644 --- a/doc/html/fix_nve_line.html +++ b/doc/html/fix_nve_line.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html index 5c90a38e16..19909a419c 100644 --- a/doc/html/fix_nve_manifold_rattle.html +++ b/doc/html/fix_nve_manifold_rattle.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve_noforce.html b/doc/html/fix_nve_noforce.html index 03a96faef8..c1a4d50933 100644 --- a/doc/html/fix_nve_noforce.html +++ b/doc/html/fix_nve_noforce.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html index 4e8b3232cf..396253a750 100644 --- a/doc/html/fix_nve_sphere.html +++ b/doc/html/fix_nve_sphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html index 60323b496f..bf98546955 100644 --- a/doc/html/fix_nve_tri.html +++ b/doc/html/fix_nve_tri.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html index d73154c32a..c9e94409b9 100644 --- a/doc/html/fix_nvt_asphere.html +++ b/doc/html/fix_nvt_asphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html index f9ecc9f59f..e7b2439208 100644 --- a/doc/html/fix_nvt_body.html +++ b/doc/html/fix_nvt_body.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html index 004433fc7a..6289374902 100644 --- a/doc/html/fix_nvt_manifold_rattle.html +++ b/doc/html/fix_nvt_manifold_rattle.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html index 1e1b27f252..6307c235cb 100644 --- a/doc/html/fix_nvt_sllod.html +++ b/doc/html/fix_nvt_sllod.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_nvt_sllod_eff.html b/doc/html/fix_nvt_sllod_eff.html index 3711572e2b..1d33b10f24 100644 --- a/doc/html/fix_nvt_sllod_eff.html +++ b/doc/html/fix_nvt_sllod_eff.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html index 93d9a96dca..4682296178 100644 --- a/doc/html/fix_nvt_sphere.html +++ b/doc/html/fix_nvt_sphere.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_oneway.html b/doc/html/fix_oneway.html index 48e68681f2..67aea3fb04 100644 --- a/doc/html/fix_oneway.html +++ b/doc/html/fix_oneway.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html index d9096b12d3..dacf84ae98 100644 --- a/doc/html/fix_orient.html +++ b/doc/html/fix_orient.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html index 3df24b4202..88d87036db 100644 --- a/doc/html/fix_phonon.html +++ b/doc/html/fix_phonon.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html index 23a356eea3..c9e2545927 100644 --- a/doc/html/fix_pimd.html +++ b/doc/html/fix_pimd.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -371,12 +370,14 @@ 
    fix ID group-ID pimd keyword value ...
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • pimd = style name of this fix command
      • -
    • zero or more keyword/value pairs may be appended
      • -
    • keyword = method or fmass or sp or temp or nhc
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • pimd = style name of this fix command

      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = method or fmass or sp or temp or nhc

       method value = pimd or nmpimd or cmd
 fmass value = scaling factor on mass
@@ -384,6 +385,8 @@
 temp value = temperature (temperarate units)
 nhc value = Nc = number of chains in Nose-Hoover thermostat
      +
      • +

    Examples

    diff --git a/doc/html/fix_planeforce.html b/doc/html/fix_planeforce.html index 6755b4931c..49ed32568d 100644 --- a/doc/html/fix_planeforce.html +++ b/doc/html/fix_planeforce.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_poems.html b/doc/html/fix_poems.html index 072446aa6c..682556382d 100644 --- a/doc/html/fix_poems.html +++ b/doc/html/fix_poems.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -309,7 +308,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_pour.html b/doc/html/fix_pour.html index a776cf0b4c..f5ca90d384 100644 --- a/doc/html/fix_pour.html +++ b/doc/html/fix_pour.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_press_berendsen.html b/doc/html/fix_press_berendsen.html index 44cf747d20..d17e43d7ee 100644 --- a/doc/html/fix_press_berendsen.html +++ b/doc/html/fix_press_berendsen.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_print.html b/doc/html/fix_print.html index 35600e587e..a38d3643f6 100644 --- a/doc/html/fix_print.html +++ b/doc/html/fix_print.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_property_atom.html b/doc/html/fix_property_atom.html index e101f82290..af0d3ac984 100644 --- a/doc/html/fix_property_atom.html +++ b/doc/html/fix_property_atom.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_qbmsst.html b/doc/html/fix_qbmsst.html index df4948ae6e..104047e88c 100644 --- a/doc/html/fix_qbmsst.html +++ b/doc/html/fix_qbmsst.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -372,14 +371,18 @@ 
    fix ID group-ID qbmsst dir shockvel keyword value ...
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • qbmsst = style name of this fix
      • -
    • dir = x or y or z
      • -
    • shockvel = shock velocity (strictly positive, velocity units)
      • -
    • zero or more keyword/value pairs may be appended
      • -
    • keyword = q or mu or p0 or v0 or e0 or tscale or damp or seedor f_max or N_f or eta or beta or T_init
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • qbmsst = style name of this fix

      +
      • +

    • dir = x or y or z

      +
      • +

    • shockvel = shock velocity (strictly positive, velocity units)

      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = q or mu or p0 or v0 or e0 or tscale or damp or seedor f_max or N_f or eta or beta or T_init

       q value = cell mass-like parameter (mass^2/distance^4 units)
 mu value = artificial viscosity (mass/distance/time units)
@@ -395,6 +398,8 @@
 beta value = the quantum temperature is updated every beta time steps (positive integer)
 T_init value = quantum temperature for the initial state (temperature units)
      +
      • +

    Examples

    diff --git a/doc/html/fix_qeq.html b/doc/html/fix_qeq.html index 979261442d..ddbcfc7b1b 100644 --- a/doc/html/fix_qeq.html +++ b/doc/html/fix_qeq.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html index 72716d5d6e..f1f857e227 100644 --- a/doc/html/fix_qeq_comb.html +++ b/doc/html/fix_qeq_comb.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html index 2129c28069..1bd5f29ed4 100644 --- a/doc/html/fix_qeq_reax.html +++ b/doc/html/fix_qeq_reax.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_qmmm.html b/doc/html/fix_qmmm.html index e0278a4022..74ede34075 100644 --- a/doc/html/fix_qmmm.html +++ b/doc/html/fix_qmmm.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -309,7 +308,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_qtb.html b/doc/html/fix_qtb.html index ea05b6486e..bc14d4fbac 100644 --- a/doc/html/fix_qtb.html +++ b/doc/html/fix_qtb.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_reax_bonds.html b/doc/html/fix_reax_bonds.html index aabf418202..e4e3b9f47d 100644 --- a/doc/html/fix_reax_bonds.html +++ b/doc/html/fix_reax_bonds.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_reaxc_species.html b/doc/html/fix_reaxc_species.html index 7bb4c8c250..5d266da490 100644 --- a/doc/html/fix_reaxc_species.html +++ b/doc/html/fix_reaxc_species.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_recenter.html b/doc/html/fix_recenter.html index a990f2df12..2f0e7f0c38 100644 --- a/doc/html/fix_recenter.html +++ b/doc/html/fix_recenter.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_restrain.html b/doc/html/fix_restrain.html index 8239ffa95d..086800aed9 100644 --- a/doc/html/fix_restrain.html +++ b/doc/html/fix_restrain.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -370,12 +369,14 @@ 
    fix ID group-ID restrain keyword args ...
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • restrain = style name of this fix command
      • -
    • one or more keyword/arg pairs may be appended
      • -
    • keyword = bond or angle or dihedral
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • restrain = style name of this fix command

      +
      • +

    • one or more keyword/arg pairs may be appended

      +
      • +

    • keyword = bond or angle or dihedral

       bond args = atom1 atom2 Kstart Kstop r0
   atom1,atom2 = IDs of 2 atoms in bond
@@ -390,6 +391,8 @@
   Kstart,Kstop = restraint coefficients at start/end of run (energy units)
   phi0 = equilibrium dihedral angle phi (degrees)
      +
      • +

    Examples

    diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html index fb239375f3..b9750c0658 100644 --- a/doc/html/fix_rigid.html +++ b/doc/html/fix_rigid.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html index a92b79a705..f14294aaa8 100644 --- a/doc/html/fix_rx.html +++ b/doc/html/fix_rx.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_saed_vtk.html b/doc/html/fix_saed_vtk.html index 44c767a97c..91c53635c7 100644 --- a/doc/html/fix_saed_vtk.html +++ b/doc/html/fix_saed_vtk.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_setforce.html b/doc/html/fix_setforce.html index f4eab36cb2..85cca4a765 100644 --- a/doc/html/fix_setforce.html +++ b/doc/html/fix_setforce.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html index 4233578699..fcdae0fa46 100644 --- a/doc/html/fix_shake.html +++ b/doc/html/fix_shake.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_shardlow.html b/doc/html/fix_shardlow.html index 252f298bcc..cfc53785ad 100644 --- a/doc/html/fix_shardlow.html +++ b/doc/html/fix_shardlow.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html index e5fcbec095..ab2bf6a825 100644 --- a/doc/html/fix_smd.html +++ b/doc/html/fix_smd.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_smd_adjust_dt.html b/doc/html/fix_smd_adjust_dt.html index 8604e3cf63..da4c19eeb7 100644 --- a/doc/html/fix_smd_adjust_dt.html +++ b/doc/html/fix_smd_adjust_dt.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_smd_integrate_tlsph.html b/doc/html/fix_smd_integrate_tlsph.html index 8a670b41c4..7746114268 100644 --- a/doc/html/fix_smd_integrate_tlsph.html +++ b/doc/html/fix_smd_integrate_tlsph.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_smd_integrate_ulsph.html b/doc/html/fix_smd_integrate_ulsph.html index 1283604524..4f6d9cff5b 100644 --- a/doc/html/fix_smd_integrate_ulsph.html +++ b/doc/html/fix_smd_integrate_ulsph.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_smd_move_triangulated_surface.html b/doc/html/fix_smd_move_triangulated_surface.html index 17be63d9be..5ada7a6e6c 100644 --- a/doc/html/fix_smd_move_triangulated_surface.html +++ b/doc/html/fix_smd_move_triangulated_surface.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_smd_setvel.html b/doc/html/fix_smd_setvel.html index 0a18a671c2..ba29891595 100644 --- a/doc/html/fix_smd_setvel.html +++ b/doc/html/fix_smd_setvel.html @@ -285,7 +285,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -309,7 +308,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_smd_wall_surface.html b/doc/html/fix_smd_wall_surface.html index d2a04553c4..2000ee48d1 100644 --- a/doc/html/fix_smd_wall_surface.html +++ b/doc/html/fix_smd_wall_surface.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_spring.html b/doc/html/fix_spring.html index 7b4827f36c..3793799c65 100644 --- a/doc/html/fix_spring.html +++ b/doc/html/fix_spring.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_spring_chunk.html b/doc/html/fix_spring_chunk.html index 84db5448df..b676d1829f 100644 --- a/doc/html/fix_spring_chunk.html +++ b/doc/html/fix_spring_chunk.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_spring_rg.html b/doc/html/fix_spring_rg.html index b29e97e656..c2de33b35f 100644 --- a/doc/html/fix_spring_rg.html +++ b/doc/html/fix_spring_rg.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_spring_self.html b/doc/html/fix_spring_self.html index e83902727e..5cbd5a17a6 100644 --- a/doc/html/fix_spring_self.html +++ b/doc/html/fix_spring_self.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_srd.html b/doc/html/fix_srd.html index 451d227bcd..6f6b55af03 100644 --- a/doc/html/fix_srd.html +++ b/doc/html/fix_srd.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_store_force.html b/doc/html/fix_store_force.html index 04e1e63eb3..834250d4ae 100644 --- a/doc/html/fix_store_force.html +++ b/doc/html/fix_store_force.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_store_state.html b/doc/html/fix_store_state.html index 4a66a07f54..e2052991d9 100644 --- a/doc/html/fix_store_state.html +++ b/doc/html/fix_store_state.html @@ -287,7 +287,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_temp_berendsen.html b/doc/html/fix_temp_berendsen.html index 2edc0200b4..9f95d8837b 100644 --- a/doc/html/fix_temp_berendsen.html +++ b/doc/html/fix_temp_berendsen.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_temp_csvr.html b/doc/html/fix_temp_csvr.html index 4a12c1ecb2..bf19a7354f 100644 --- a/doc/html/fix_temp_csvr.html +++ b/doc/html/fix_temp_csvr.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_temp_rescale.html b/doc/html/fix_temp_rescale.html index add43295b1..af0f375a77 100644 --- a/doc/html/fix_temp_rescale.html +++ b/doc/html/fix_temp_rescale.html @@ -286,7 +286,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_temp_rescale_eff.html b/doc/html/fix_temp_rescale_eff.html index 9b15bdb74d..86754f432c 100644 --- a/doc/html/fix_temp_rescale_eff.html +++ b/doc/html/fix_temp_rescale_eff.html @@ -286,7 +286,6 @@
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_tfmc.html b/doc/html/fix_tfmc.html index f421647d8c..8d8b5fa991 100644 --- a/doc/html/fix_tfmc.html +++ b/doc/html/fix_tfmc.html @@ -287,7 +287,6 @@
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html index 2b839b3d5e..06e94c1644 100644 --- a/doc/html/fix_thermal_conductivity.html +++ b/doc/html/fix_thermal_conductivity.html @@ -34,7 +34,7 @@ - + @@ -287,7 +287,6 @@
  • Default
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • @@ -354,7 +353,7 @@ diff --git a/doc/html/fix_tmd.html b/doc/html/fix_tmd.html index 0abaf5d4f6..d580b26b55 100644 --- a/doc/html/fix_tmd.html +++ b/doc/html/fix_tmd.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
    • Syntax
      • @@ -309,7 +308,7 @@
    • Computes
    • Pair Styles
      • -
    • Bonds
      • +
    • Bond Styles
    • Angle Styles
    • Dihedral Styles
    • Improper Styles
      • diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html index ed0b6da5fc..25425bc2a0 100644 --- a/doc/html/fix_ttm.html +++ b/doc/html/fix_ttm.html @@ -279,7 +279,6 @@
    • fix temp/rescale/eff command
    • fix tfmc command
    • fix thermal/conductivity command
      • -
    • fix ti/rs command
    • fix ti/spring command
    • fix tmd command
    • fix ttm command
      • @@ -375,12 +374,14 @@ fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile -
        -
      • ID, group-ID are documented in fix command
        • -
      • style = ttm or ttm_mod
        • -
      • seed = random number seed to use for white noise (positive integer)
        • -
      • remaining arguments for fix ttm:
        • -
      +
        +

      • ID, group-ID are documented in fix command

        +
        • +

      • style = ttm or ttm_mod

        +
        • +

      • seed = random number seed to use for white noise (positive integer)

        +
        • +

      • remaining arguments for fix ttm:

         C_e  = electronic specific heat (energy/(electron*temperature) units)
 rho_e = electronic density (electrons/volume units)
@@ -395,9 +396,8 @@ T_infile = filename to read initial electronic temperature from
 N = dump TTM temperatures every this many timesteps, 0 = no dump
 T_outfile = filename to write TTM temperatures to (only needed if N > 0)
        -
          -
        • remaining arguments for fix ttm/mod:
          • -
        +
        • +

      • remaining arguments for fix ttm/mod:

         init_file = file with the parameters to TTM
 Nx = number of thermal solve grid points in the x-direction (positive integer)
@@ -407,6 +407,8 @@ T_infile = filename to read initial electronic temperature from
 N = dump TTM temperatures every this many timesteps, 0 = no dump
 T_outfile = filename to write TTM temperatures to (only needed if N > 0)
        +
        • +

    • Examples

    diff --git a/doc/html/fix_tune_kspace.html b/doc/html/fix_tune_kspace.html index 444123ff8f..5e778d31a8 100644 --- a/doc/html/fix_tune_kspace.html +++ b/doc/html/fix_tune_kspace.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_vector.html b/doc/html/fix_vector.html index 25be269057..0f147e6381 100644 --- a/doc/html/fix_vector.html +++ b/doc/html/fix_vector.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html index c44115552e..d822a755cb 100644 --- a/doc/html/fix_viscosity.html +++ b/doc/html/fix_viscosity.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html index 05bdd1e5e2..aaacf5e155 100644 --- a/doc/html/fix_viscous.html +++ b/doc/html/fix_viscous.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html index b0acb6ad2e..d092bf203f 100644 --- a/doc/html/fix_wall.html +++ b/doc/html/fix_wall.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -384,12 +383,14 @@ 
    fix ID group-ID style face args ... keyword value ...
    -
      -
    • ID, group-ID are documented in fix command
      • -
    • style = wall/lj93 or wall/lj126 or wall/lj1043 or wall/colloid or wall/harmonic
      • -
    • one or more face/arg pairs may be appended
      • -
    • face = xlo or xhi or ylo or yhi or zlo or zhi
      • -
    +
      +

    • ID, group-ID are documented in fix command

      +
      • +

    • style = wall/lj93 or wall/lj126 or wall/lj1043 or wall/colloid or wall/harmonic

      +
      • +

    • one or more face/arg pairs may be appended

      +
      • +

    • face = xlo or xhi or ylo or yhi or zlo or zhi

       args = coord epsilon sigma cutoff
   coord = position of wall = EDGE or constant or variable
@@ -402,10 +403,10 @@ args = coord epsilon sigma cutoff
     sigma can be a variable (see below)
   cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
      -
        -
      • zero or more keyword/value pairs may be appended
        • -
      • keyword = units or fld
        • -
      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = units or fld

       units value = lattice or box
   lattice = the wall position is defined in lattice units
@@ -417,6 +418,8 @@ args = coord epsilon sigma cutoff
   yes = allow periodic boundary in a wall dimension
   no = require non-perioidic boundaries in any wall dimension
      +
      • +

    Examples

    diff --git a/doc/html/fix_wall_gran.html b/doc/html/fix_wall_gran.html index 147f852bef..8c83ff97fe 100644 --- a/doc/html/fix_wall_gran.html +++ b/doc/html/fix_wall_gran.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html index 0f441736ea..abad7b8e82 100644 --- a/doc/html/fix_wall_piston.html +++ b/doc/html/fix_wall_piston.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -311,7 +310,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html index b34251a0b0..67c356b241 100644 --- a/doc/html/fix_wall_reflect.html +++ b/doc/html/fix_wall_reflect.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_wall_region.html b/doc/html/fix_wall_region.html index dd2eb051d0..e28a722315 100644 --- a/doc/html/fix_wall_region.html +++ b/doc/html/fix_wall_region.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/fix_wall_srd.html b/doc/html/fix_wall_srd.html index a43ce5e4b7..fef5e3b877 100644 --- a/doc/html/fix_wall_srd.html +++ b/doc/html/fix_wall_srd.html @@ -279,7 +279,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -310,7 +309,7 @@
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/fixes.html b/doc/html/fixes.html index 4c2b19e026..049f82365c 100644 --- a/doc/html/fixes.html +++ b/doc/html/fixes.html @@ -278,7 +278,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • @@ -542,7 +541,6 @@
  • fix temp/rescale/eff command
  • fix tfmc command
  • fix thermal/conductivity command
    • -
  • fix ti/rs command
  • fix ti/spring command
  • fix tmd command
  • fix ttm command
    • diff --git a/doc/html/genindex.html b/doc/html/genindex.html index e12b6894db..716c0e3496 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -1497,10 +1497,6 @@ -
    fix ti/rs -
    - -
    fix ti/spring
    @@ -1533,6 +1529,10 @@ +
    fix wall/gran/region +
    + +
    fix wall/lj93
    diff --git a/doc/html/group2ndx.html b/doc/html/group2ndx.html index f693217530..06e3c1644e 100644 --- a/doc/html/group2ndx.html +++ b/doc/html/group2ndx.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/improper_coeff.html b/doc/html/improper_coeff.html index 9e2afcbb2c..46640cb3f0 100644 --- a/doc/html/improper_coeff.html +++ b/doc/html/improper_coeff.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/improper_hybrid.html b/doc/html/improper_hybrid.html index b1b6f7dfd4..195941b226 100644 --- a/doc/html/improper_hybrid.html +++ b/doc/html/improper_hybrid.html @@ -97,7 +97,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_eff.html b/doc/html/pair_eff.html index 9fc10aa28c..73bb76a8b3 100644 --- a/doc/html/pair_eff.html +++ b/doc/html/pair_eff.html @@ -529,10 +529,10 @@ 
     pair_style eff/cut cutoff keyword args ...
    -
      -
    • cutoff = global cutoff for Coulombic interactions
      • -
    • zero or more keyword/value pairs may be appended
      • -
    +
      +

    • cutoff = global cutoff for Coulombic interactions

      +
      • +

    • zero or more keyword/value pairs may be appended

       keyword = limit/eradius or pressure/evirials or ecp
   limit/eradius args = none
@@ -541,6 +541,8 @@ keyword = limit/eradius or pressure/evirials or ecp
     type = LAMMPS atom type (1 to Ntypes)
     element = element symbol (e.g. H, Si)
      +
      • +

    Examples

    diff --git a/doc/html/pair_kim.html b/doc/html/pair_kim.html index fb81c086ce..6167f06913 100644 --- a/doc/html/pair_kim.html +++ b/doc/html/pair_kim.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_lcbop.html b/doc/html/pair_lcbop.html index 7e18e7d2b4..5da5259ded 100644 --- a/doc/html/pair_lcbop.html +++ b/doc/html/pair_lcbop.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html index 3efa81dc1b..de1a8282a0 100644 --- a/doc/html/pair_line_lj.html +++ b/doc/html/pair_line_lj.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_list.html b/doc/html/pair_list.html index 997155343e..7029f7a656 100644 --- a/doc/html/pair_list.html +++ b/doc/html/pair_list.html @@ -560,12 +560,14 @@ an additional interaction within the hybrid/overlay pair style. It currently supports three interaction styles: a 12-6 Lennard-Jones, a Morse and a harmonic potential.

    The format of the list file is as follows:

    -
      -
    • one line per pair of atoms
      • -
    • empty lines will be ignored
      • -
    • comment text starts with a ‘#’ character
      • -
    • line syntax: ID1 ID2 style coeffs cutoff
      • -
    +
      +

    • one line per pair of atoms

      +
      • +

    • empty lines will be ignored

      +
      • +

    • comment text starts with a ‘#’ character

      +
      • +

    • line syntax: ID1 ID2 style coeffs cutoff

      ID1 = atom ID of first atom
 ID2 = atom ID of second atom
 style = style of interaction
@@ -573,6 +575,8 @@ Morse and a harmonic potential.
      
 cutoff = cutoff for interaction (optional)
      +
      • +

    The cutoff parameter is optional. If not specified, the global cutoff is used.

    Here is an example file:

    diff --git a/doc/html/pair_mdf.html b/doc/html/pair_mdf.html index d725697c9a..76ca3c09a7 100644 --- a/doc/html/pair_mdf.html +++ b/doc/html/pair_mdf.html @@ -534,10 +534,10 @@ 
     pair_style style args
    -
      -
    • style = lj/mdf or buck/mdf or lennard/mdf
      • -
    • args = list of arguments for a particular style
      • -
    +
      +

    • style = lj/mdf or buck/mdf or lennard/mdf

      +
      • +

    • args = list of arguments for a particular style

       lj/mdf args = cutoff1 cutoff2
   cutoff1 = inner cutoff for the start of the tapering function
@@ -549,6 +549,8 @@ pair_style style args
   cutoff1 = inner cutoff for the start of the tapering function
   cutoff1 = out cutoff for the end of the tapering function
      +
      • +

    Examples

    diff --git a/doc/html/pair_modify.html b/doc/html/pair_modify.html index d61bcf26a6..5afdd40ee4 100644 --- a/doc/html/pair_modify.html +++ b/doc/html/pair_modify.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_none.html b/doc/html/pair_none.html index 4d3413863e..d31dd4806a 100644 --- a/doc/html/pair_none.html +++ b/doc/html/pair_none.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html index c312f448eb..6bbae4136a 100644 --- a/doc/html/pair_quip.html +++ b/doc/html/pair_quip.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html index af2524764e..b1c820beca 100644 --- a/doc/html/pair_reax.html +++ b/doc/html/pair_reax.html @@ -468,7 +468,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_smd_hertz.html b/doc/html/pair_smd_hertz.html index aa2f95e84d..1fd2e6e0ab 100644 --- a/doc/html/pair_smd_hertz.html +++ b/doc/html/pair_smd_hertz.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_smd_tlsph.html b/doc/html/pair_smd_tlsph.html index a907df674a..758b115da8 100644 --- a/doc/html/pair_smd_tlsph.html +++ b/doc/html/pair_smd_tlsph.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_smd_triangulated_surface.html b/doc/html/pair_smd_triangulated_surface.html index 24131ce45f..e1b4f16b3d 100644 --- a/doc/html/pair_smd_triangulated_surface.html +++ b/doc/html/pair_smd_triangulated_surface.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_smd_ulsph.html b/doc/html/pair_smd_ulsph.html index aac8a0d37a..0333ae1e1b 100644 --- a/doc/html/pair_smd_ulsph.html +++ b/doc/html/pair_smd_ulsph.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_smtbq.html b/doc/html/pair_smtbq.html index 1994f51c81..59afe9a188 100644 --- a/doc/html/pair_smtbq.html +++ b/doc/html/pair_smtbq.html @@ -703,7 +703,7 @@ quotation marks (‘’).

  • Mode for the electronegativity equalization (Qeq)
      • -
    • Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
      • +
    • Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
    • Parameter if necessary
    • Divided line
    diff --git a/doc/html/pair_sph_heatconduction.html b/doc/html/pair_sph_heatconduction.html index 659c98cf15..192f5027e0 100644 --- a/doc/html/pair_sph_heatconduction.html +++ b/doc/html/pair_sph_heatconduction.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_sph_lj.html b/doc/html/pair_sph_lj.html index 2cd9121255..c4644364a2 100644 --- a/doc/html/pair_sph_lj.html +++ b/doc/html/pair_sph_lj.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_sph_rhosum.html b/doc/html/pair_sph_rhosum.html index 6bccf6ae75..8405cb8e67 100644 --- a/doc/html/pair_sph_rhosum.html +++ b/doc/html/pair_sph_rhosum.html @@ -467,7 +467,7 @@
  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_srp.html b/doc/html/pair_srp.html index f3c6b30634..78795c2729 100644 --- a/doc/html/pair_srp.html +++ b/doc/html/pair_srp.html @@ -527,17 +527,22 @@

    Syntax

    pair_style srp cutoff btype dist keyword value ...

    -
      -
    • cutoff = global cutoff for SRP interactions (distance units)
      • -
    • btype = bond type to apply SRP interactions to (can be wildcard, see below)
      • -
    • distance = min or mid
      • -
    • zero or more keyword/value pairs may be appended
      • -
    • keyword = exclude
      • -
    +
      +

    • cutoff = global cutoff for SRP interactions (distance units)

      +
      • +

    • btype = bond type to apply SRP interactions to (can be wildcard, see below)

      +
      • +

    • distance = min or mid

      +
      • +

    • zero or more keyword/value pairs may be appended

      +
      • +

    • keyword = exclude

       bptype value = atom type for bond particles
 exclude value = yes or no
      +
      • +

    Examples

    diff --git a/doc/html/pair_style.html b/doc/html/pair_style.html index 5d72eff1a5..ed64289d8d 100644 --- a/doc/html/pair_style.html +++ b/doc/html/pair_style.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_table.html b/doc/html/pair_table.html index fbf113efe7..d1ee64bef7 100644 --- a/doc/html/pair_table.html +++ b/doc/html/pair_table.html @@ -585,7 +585,7 @@ computes the energy or force.

    For the bitmap style, the specified N is used to create interpolation tables that are 2^N in length. The distance R is used to index into the table via a fast bit-mapping technique due to -(Wolff), and a linear interpolation is performed between +(Wolff), and a linear interpolation is performed between adjacent table values.

    The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples diff --git a/doc/html/pair_table_rx.html b/doc/html/pair_table_rx.html index a4fcc0fce5..2f4bd592c8 100644 --- a/doc/html/pair_table_rx.html +++ b/doc/html/pair_table_rx.html @@ -467,7 +467,7 @@

  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html index 9aa9b491e1..2b13301e76 100644 --- a/doc/html/pair_thole.html +++ b/doc/html/pair_thole.html @@ -586,8 +586,8 @@ short distances by a function

    \frac{s_{ij} r_{ij} }{2} \right) \exp \left( - s_{ij} r_{ij} \right) \end{equation}\]

    This function results from an adaptation to point charges -(Noskov) of the dipole screening scheme originally proposed -by Thole. The scaling coefficient \(s_{ij}\) is determined +(Noskov) of the dipole screening scheme originally proposed +by Thole. The scaling coefficient \(s_{ij}\) is determined by the polarizability of the atoms, \(\alpha_i\), and by a Thole damping parameter \(a\). This Thole damping parameter usually takes a value of 2.6, but in certain force fields the value can depend upon diff --git a/doc/html/pair_tri_lj.html b/doc/html/pair_tri_lj.html index 094d285f24..8bf81d1b8c 100644 --- a/doc/html/pair_tri_lj.html +++ b/doc/html/pair_tri_lj.html @@ -467,7 +467,7 @@

  • pair_style zero command
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_write.html b/doc/html/pair_write.html index 9e0dcb8554..c878482cf3 100644 --- a/doc/html/pair_write.html +++ b/doc/html/pair_write.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/pair_zero.html b/doc/html/pair_zero.html index 38f90060ad..b288e86d21 100644 --- a/doc/html/pair_zero.html +++ b/doc/html/pair_zero.html @@ -34,7 +34,7 @@ - + @@ -467,7 +467,7 @@ -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • @@ -510,7 +510,7 @@
    diff --git a/doc/html/replicate.html b/doc/html/replicate.html index e3733cec2d..e8fb2f55a1 100644 --- a/doc/html/replicate.html +++ b/doc/html/replicate.html @@ -212,7 +212,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/rerun.html b/doc/html/rerun.html index 8695c605a2..a0a0e37ebb 100644 --- a/doc/html/rerun.html +++ b/doc/html/rerun.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/reset_timestep.html b/doc/html/reset_timestep.html index a2712f0d03..a8a9701f5d 100644 --- a/doc/html/reset_timestep.html +++ b/doc/html/reset_timestep.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/restart.html b/doc/html/restart.html index 4c323c745e..0ca000eb6d 100644 --- a/doc/html/restart.html +++ b/doc/html/restart.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/run.html b/doc/html/run.html index 4a8db201e5..b5da31116b 100644 --- a/doc/html/run.html +++ b/doc/html/run.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/set.html b/doc/html/set.html index a1c44a1be3..936e37d3f9 100644 --- a/doc/html/set.html +++ b/doc/html/set.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/shell.html b/doc/html/shell.html index a103e18f42..52d65d6f1d 100644 --- a/doc/html/shell.html +++ b/doc/html/shell.html @@ -212,7 +212,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/special_bonds.html b/doc/html/special_bonds.html index 7b77398e1c..8b5715d825 100644 --- a/doc/html/special_bonds.html +++ b/doc/html/special_bonds.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/suffix.html b/doc/html/suffix.html index 6aa90ebf6c..d38c952122 100644 --- a/doc/html/suffix.html +++ b/doc/html/suffix.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/thermo.html b/doc/html/thermo.html index 0496493cc7..c062bfe969 100644 --- a/doc/html/thermo.html +++ b/doc/html/thermo.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/thermo_modify.html b/doc/html/thermo_modify.html index 23ea71a08e..57f590db01 100644 --- a/doc/html/thermo_modify.html +++ b/doc/html/thermo_modify.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/timer.html b/doc/html/timer.html index 9ea3aeb769..a083f68d22 100644 --- a/doc/html/timer.html +++ b/doc/html/timer.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/timestep.html b/doc/html/timestep.html index 7db6eaa179..b78460ed8a 100644 --- a/doc/html/timestep.html +++ b/doc/html/timestep.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/tutorial_drude.html b/doc/html/tutorial_drude.html index 4467b2f3a9..65821735a6 100644 --- a/doc/html/tutorial_drude.html +++ b/doc/html/tutorial_drude.html @@ -96,14 +96,14 @@
  • Tutorial for Thermalized Drude oscillators in LAMMPS
  • LAMMPS GitHub tutorial
  • Body particles
    • -
  • Manifolds (surfacse)
    • +
  • Manifolds (surfaces)
  • Commands
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/uncompute.html b/doc/html/uncompute.html index eabaf83b69..c743659a0c 100644 --- a/doc/html/uncompute.html +++ b/doc/html/uncompute.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/undump.html b/doc/html/undump.html index 95e08ef636..9c86545b19 100644 --- a/doc/html/undump.html +++ b/doc/html/undump.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/unfix.html b/doc/html/unfix.html index 8d42009950..2d63448853 100644 --- a/doc/html/unfix.html +++ b/doc/html/unfix.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/units.html b/doc/html/units.html index 428181998e..78a1b9dd83 100644 --- a/doc/html/units.html +++ b/doc/html/units.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/variable.html b/doc/html/variable.html index e6e9cd59a8..c8d52a71e1 100644 --- a/doc/html/variable.html +++ b/doc/html/variable.html @@ -225,7 +225,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/velocity.html b/doc/html/velocity.html index a9cd5c25c0..8a50f40767 100644 --- a/doc/html/velocity.html +++ b/doc/html/velocity.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/write_coeff.html b/doc/html/write_coeff.html index 4e1ad65a72..d7e180653f 100644 --- a/doc/html/write_coeff.html +++ b/doc/html/write_coeff.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/write_data.html b/doc/html/write_data.html index 9770687417..ccf4998678 100644 --- a/doc/html/write_data.html +++ b/doc/html/write_data.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/write_dump.html b/doc/html/write_dump.html index 956253096c..aaa58d3767 100644 --- a/doc/html/write_dump.html +++ b/doc/html/write_dump.html @@ -214,7 +214,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/html/write_restart.html b/doc/html/write_restart.html index 9565f1d22c..b6bf3470f9 100644 --- a/doc/html/write_restart.html +++ b/doc/html/write_restart.html @@ -213,7 +213,7 @@
  • Fixes
  • Computes
  • Pair Styles
    • -
  • Bonds
    • +
  • Bond Styles
  • Angle Styles
  • Dihedral Styles
  • Improper Styles
    • diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index bbca4c49b3..3e18037a83 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -662,7 +662,6 @@ package"_Section_start.html#start_3. "smd/setvel"_fix_smd_setvel.html, "smd/wall/surface"_fix_smd_wall_surface.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, -"ti/rs"_fix_ti_rs.html, "ti/spring"_fix_ti_spring.html, "ttm/mod"_fix_ttm.html :tb(c=6,ea=c)