diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index 4b3b3446a4..1fe9224652 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -1344,9 +1344,9 @@ to output and the kind of data they operate on and produce:

  • Scalar/vector/array data
  • Thermodynamic output
  • Dump file output
    • -
  • Fixes that write output files
    • +
  • Fixes that write output files
  • Computes that process output quantities
    • -
  • Fixes that process output quantities
    • +
  • Fixes that process output quantities
  • Computes that generate values to output
  • Fixes that generate values to output
  • Variables that generate values to output
    • @@ -1372,7 +1372,7 @@ per-atom vector.

    When a quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket notation, where ID in this case is the ID of a compute. The leading -“c_” would be replaced by “f_” for a fix, or “v_” for a variable:

    +“c_” would be replaced by “f_” for a fix, or “v_” for a variable:

    @@ -1509,7 +1509,7 @@ are produced as output values which can be used as input to other output commands.

    -

    6.15.7. Fixes that process output quantities

    +

    6.15.7. Fixes that process output quantities

    The fix vector command can create global vectors as output from global scalars as input, accumulating them one element at a time.

    @@ -2274,7 +2274,7 @@ fix produces a global array as output with one row of values per chunk.

    -

    6.23.3. Compute */chunk commands:

    +

    6.23.3. Compute */chunk commands:

    Currently the following computes operate on chunks of atoms to produce per-chunk values.

    diff --git a/doc/html/angle_cosine_shift_exp.html b/doc/html/angle_cosine_shift_exp.html index 739fdcecd5..f4233d2d99 100644 --- a/doc/html/angle_cosine_shift_exp.html +++ b/doc/html/angle_cosine_shift_exp.html @@ -194,8 +194,8 @@ section for more info on packages.

    diff --git a/doc/html/angle_dipole.html b/doc/html/angle_dipole.html index 866c08afd5..66cc040b11 100644 --- a/doc/html/angle_dipole.html +++ b/doc/html/angle_dipole.html @@ -198,7 +198,7 @@ more instructions on how to use the accelerated styles effectively.

    Restrictions

    This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the Making LAMMPS +USER-MISC package. See the Making LAMMPS section for more info on packages.

    Note

    diff --git a/doc/html/bond_harmonic_shift_cut.html b/doc/html/bond_harmonic_shift_cut.html index b68ba4435f..68d9152ff6 100644 --- a/doc/html/bond_harmonic_shift_cut.html +++ b/doc/html/bond_harmonic_shift_cut.html @@ -187,7 +187,7 @@ section for more info on packages.

    Related commands

    bond_coeff, delete_bonds, bond_harmonic, -bond_harmonicshift

    +bond_harmonic_shift

    Default: none

    diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html index 6c34a7c4e8..9bc19a1095 100644 --- a/doc/html/dihedral_cosine_shift_exp.html +++ b/doc/html/dihedral_cosine_shift_exp.html @@ -193,7 +193,7 @@ section for more info on packages.

    diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index 03cc2f6720..51eefacda2 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -341,7 +341,7 @@ N timesteps.

    If the keyword trilinear is used, the trilinear stencil is used to interpolate the particle nodes onto the fluid mesh. By default, the immersed boundary method, Peskin stencil is used. Both of these -interpolation methods are described in Mackay et al..

    +interpolation methods are described in Mackay et al..

    If the keyword D3Q19 is used, the 19 velocity (D3Q19) lattice is used by the lattice-Boltzmann algorithm. By default, the 15 velocity (D3Q15) lattice is used.

    @@ -384,7 +384,7 @@ binary restart files, if requested, independent of the main LAMMPS is written to the main LAMMPS binary restart files.

    None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various output commands. No +access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

    diff --git a/doc/html/fix_ti_rs.html b/doc/html/fix_ti_rs.html index 74300f5dd1..311cabb702 100644 --- a/doc/html/fix_ti_rs.html +++ b/doc/html/fix_ti_rs.html @@ -152,7 +152,7 @@

    Description

    This fix allows you to compute the free energy temperature dependence by performing a thermodynamic integration procedure known as -Reversible Scaling (de Koning99, de Koning00a). The thermodynamic integration is performed +Reversible Scaling (de Koning99, de Koning00a). The thermodynamic integration is performed using the nonequilibrium method of Adiabatic Switching (Watanabe, de Koning96).

    The forces on the atoms are dynamically scaled during the simulation, diff --git a/doc/html/neb.html b/doc/html/neb.html index a96fa16817..d820af07c5 100644 --- a/doc/html/neb.html +++ b/doc/html/neb.html @@ -346,7 +346,7 @@ due to the inter-replica spring force added by the (Henkelman2). As before, the other replicas rearrange +(Henkelman2). As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced.

    When both stages are complete, if the NEB calculation was successful, one of the replicas should be an atomic configuration at the top or diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html index d0af86ccdd..5f4df83aa4 100644 --- a/doc/html/pair_body.html +++ b/doc/html/pair_body.html @@ -212,7 +212,7 @@ shift, table, and tail options.

    Restrictions

    This style is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the Making LAMMPS section for more info.

    +was built with that package. See the Making LAMMPS section for more info.

    Defining particles to be bodies so they participate in body/body or body/particle interactions requires the use of the atom_style body command.

    diff --git a/doc/html/pair_bop.html b/doc/html/pair_bop.html index 1b07d82d76..1c1d5e2ce7 100644 --- a/doc/html/pair_bop.html +++ b/doc/html/pair_bop.html @@ -156,8 +156,8 @@ quantum mechanical theory incorporating both sigma and pi bondings. By analytically deriving the BOP from quantum mechanical theory its transferability to different phases can approach that of quantum mechanical methods. This potential is similar to the original BOP -developed by Pettifor (Pettifor_1, -Pettifor_2, Pettifor_3) and later updated +developed by Pettifor (Pettifor_1, +Pettifor_2, Pettifor_3) and later updated by Murdick, Zhou, and Ward (Murdick, Ward). Currently, BOP potential files for these systems are provided with LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with @@ -195,7 +195,7 @@ simulations, the derived BOP only takes (and retains) the first two levels of the recursive representations for both the sigma and the pi bond-orders. Bond-order terms can be understood in terms of molecular orbital hopping paths based upon the Cyrot-Lackmann theorem -(Pettifor_1). The sigma bond-order with a half-full +(Pettifor_1). The sigma bond-order with a half-full valence shell is used to interpolate the bond-order expressiont that incorporated explicite valance band filling. This pi bond-order expression also contains also contains a three-member ring term that @@ -213,7 +213,7 @@ the mass potentials with hydrogen, you will likely want to set the mass of H atoms to be 10x or 20x larger to avoid having to use a tiny timestep. You can do this by using the mass command after using the -pair_coeff command to read the BOP potential +pair_coeff command to read the BOP potential file.

    One option can be specified as a keyword with the pair_style command.

    @@ -483,11 +483,11 @@ appropriate units if your simulation does not use “metal” units.

    Default

    non-tabulated potential file, a_0 is non-zero.

    -

    (Pettifor_1) D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 +

    (Pettifor_1) D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 (1999).

    -

    (Pettifor_2) D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, +

    (Pettifor_2) D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, 4124 (2000).

    -

    (Pettifor_3) D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 +

    (Pettifor_3) D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).

    (Murdick) D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R. Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).

    diff --git a/doc/html/pair_coul_diel.html b/doc/html/pair_coul_diel.html index e97c0ccf16..1f7d3e04af 100644 --- a/doc/html/pair_coul_diel.html +++ b/doc/html/pair_coul_diel.html @@ -198,7 +198,7 @@ pressure.

    Restrictions

    This style is part of the “user-misc” package. It is only enabled -if LAMMPS was built with that package. See the Making LAMMPS section for more info.

    +if LAMMPS was built with that package. See the Making LAMMPS section for more info.