From e96a8a46772cf16cbc63834bfd06de7632c8e5bb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 10 Sep 2016 21:15:44 -0400 Subject: [PATCH] regenerate html pages with the updated content from the corrections --- doc/html/Manual.html | 5 +- doc/html/Section_accelerate.html | 49 ++++++++-------- doc/html/Section_commands.html | 2 +- doc/html/Section_errors.html | 2 +- doc/html/Section_history.html | 25 +++++--- doc/html/Section_howto.html | 16 ++--- doc/html/Section_intro.html | 18 +++--- doc/html/Section_modify.html | 2 +- doc/html/Section_packages.html | 24 ++++---- doc/html/Section_python.html | 10 ++-- doc/html/Section_start.html | 18 +++--- doc/html/accelerate_gpu.html | 2 +- doc/html/accelerate_opt.html | 14 ++--- doc/html/angle_charmm.html | 4 +- doc/html/angle_class2.html | 4 +- doc/html/angle_coeff.html | 26 ++++----- doc/html/angle_cosine.html | 4 +- doc/html/angle_cosine_delta.html | 4 +- doc/html/angle_cosine_periodic.html | 4 +- doc/html/angle_cosine_shift.html | 4 +- doc/html/angle_cosine_shift_exp.html | 4 +- doc/html/angle_cosine_squared.html | 4 +- doc/html/angle_dipole.html | 4 +- doc/html/angle_fourier.html | 4 +- doc/html/angle_fourier_simple.html | 4 +- doc/html/angle_harmonic.html | 4 +- doc/html/angle_hybrid.html | 16 ++--- doc/html/angle_none.html | 12 ++-- doc/html/angle_quartic.html | 4 +- doc/html/angle_style.html | 22 +++---- doc/html/angle_table.html | 18 +++--- doc/html/angle_zero.html | 12 ++-- doc/html/atom_style.html | 4 +- doc/html/body.html | 6 +- doc/html/bond_class2.html | 4 +- doc/html/bond_coeff.html | 28 ++++----- doc/html/bond_fene.html | 4 +- doc/html/bond_fene_expand.html | 4 +- doc/html/bond_harmonic.html | 4 +- doc/html/bond_harmonic_shift.html | 4 +- doc/html/bond_harmonic_shift_cut.html | 4 +- doc/html/bond_hybrid.html | 16 ++--- doc/html/bond_morse.html | 4 +- doc/html/bond_none.html | 12 ++-- doc/html/bond_nonlinear.html | 4 +- doc/html/bond_quartic.html | 4 +- doc/html/bond_style.html | 16 ++--- doc/html/bond_table.html | 18 +++--- doc/html/bond_write.html | 14 ++--- doc/html/bond_zero.html | 12 ++-- doc/html/boundary.html | 2 +- doc/html/change_box.html | 2 +- doc/html/comm_modify.html | 22 +++---- doc/html/comm_style.html | 14 ++--- doc/html/compute_ackland_atom.html | 2 +- doc/html/compute_angle_local.html | 10 ++-- doc/html/compute_angmom_chunk.html | 10 ++-- doc/html/compute_body_local.html | 10 ++-- doc/html/compute_chunk_atom.html | 10 ++-- doc/html/compute_cluster_atom.html | 2 +- doc/html/compute_cna_atom.html | 2 +- doc/html/compute_com_chunk.html | 10 ++-- doc/html/compute_contact_atom.html | 2 +- doc/html/compute_coord_atom.html | 12 ++-- doc/html/compute_damage_atom.html | 2 +- doc/html/compute_dihedral_local.html | 10 ++-- doc/html/compute_erotate_asphere.html | 2 +- doc/html/compute_erotate_rigid.html | 2 +- doc/html/compute_erotate_sphere.html | 2 +- doc/html/compute_erotate_sphere_atom.html | 2 +- doc/html/compute_event_displace.html | 2 +- doc/html/compute_improper_local.html | 10 ++-- doc/html/compute_ke.html | 2 +- doc/html/compute_ke_atom.html | 2 +- doc/html/compute_ke_atom_eff.html | 2 +- doc/html/compute_ke_eff.html | 2 +- doc/html/compute_meso_e_atom.html | 2 +- doc/html/compute_meso_rho_atom.html | 2 +- doc/html/compute_meso_t_atom.html | 4 +- doc/html/compute_msd_chunk.html | 10 ++-- doc/html/compute_omega_chunk.html | 10 ++-- doc/html/compute_pair_local.html | 10 ++-- doc/html/compute_pe.html | 6 +- doc/html/compute_pe_atom.html | 2 +- doc/html/compute_pressure.html | 4 +- doc/html/compute_rdf.html | 26 ++++----- doc/html/compute_reduce.html | 2 +- doc/html/compute_slice.html | 28 ++++----- doc/html/compute_smd_contact_radius.html | 2 +- .../compute_smd_triangle_mesh_vertices.html | 4 +- doc/html/compute_smd_ulsph_num_neighs.html | 2 +- doc/html/compute_smd_ulsph_strain.html | 2 +- doc/html/compute_temp.html | 10 ++-- doc/html/compute_temp_chunk.html | 10 ++-- doc/html/compute_temp_cs.html | 2 +- doc/html/compute_temp_partial.html | 4 +- doc/html/compute_torque_chunk.html | 12 ++-- doc/html/compute_vacf.html | 12 ++-- doc/html/compute_vcm_chunk.html | 10 ++-- doc/html/create_bonds.html | 14 ++--- doc/html/create_box.html | 16 ++--- doc/html/delete_atoms.html | 20 +++---- doc/html/dihedral_charmm.html | 4 +- doc/html/dihedral_class2.html | 4 +- doc/html/dihedral_coeff.html | 26 ++++----- doc/html/dihedral_cosine_shift_exp.html | 4 +- doc/html/dihedral_fourier.html | 6 +- doc/html/dihedral_harmonic.html | 4 +- doc/html/dihedral_helix.html | 4 +- doc/html/dihedral_hybrid.html | 16 ++--- doc/html/dihedral_multi_harmonic.html | 4 +- doc/html/dihedral_nharmonic.html | 4 +- doc/html/dihedral_none.html | 12 ++-- doc/html/dihedral_opls.html | 4 +- doc/html/dihedral_quadratic.html | 4 +- doc/html/dihedral_spherical.html | 2 +- doc/html/dihedral_table.html | 4 +- doc/html/dihedral_zero.html | 10 ++-- doc/html/dimension.html | 2 +- doc/html/displace_atoms.html | 14 ++--- doc/html/dump.html | 2 +- doc/html/dump_custom_vtk.html | 2 +- doc/html/dump_h5md.html | 28 ++++----- doc/html/dump_image.html | 2 +- doc/html/dump_molfile.html | 10 ++-- doc/html/fix_adapt.html | 40 ++++++------- doc/html/fix_addforce.html | 18 +++--- doc/html/fix_append_atoms.html | 4 +- doc/html/fix_aveforce.html | 18 +++--- doc/html/fix_deform.html | 4 +- doc/html/fix_dt_reset.html | 4 +- doc/html/fix_enforce2d.html | 8 +-- doc/html/fix_evaporate.html | 4 +- doc/html/fix_flow_gauss.html | 4 +- doc/html/fix_freeze.html | 8 +-- doc/html/fix_gravity.html | 4 +- doc/html/fix_indent.html | 44 +++++++------- doc/html/fix_langevin.html | 4 +- doc/html/fix_manifoldforce.html | 4 +- doc/html/fix_meso.html | 4 +- doc/html/fix_meso_stationary.html | 4 +- doc/html/fix_modify.html | 16 ++--- doc/html/fix_momentum.html | 4 +- doc/html/fix_neb.html | 2 +- doc/html/fix_nh.html | 4 +- doc/html/fix_nph_asphere.html | 4 +- doc/html/fix_nph_body.html | 16 +++-- doc/html/fix_nph_sphere.html | 4 +- doc/html/fix_nphug.html | 4 +- doc/html/fix_npt_asphere.html | 4 +- doc/html/fix_npt_body.html | 4 +- doc/html/fix_npt_sphere.html | 4 +- doc/html/fix_nve.html | 8 +-- doc/html/fix_nve_asphere.html | 4 +- doc/html/fix_nve_eff.html | 4 +- doc/html/fix_nve_limit.html | 4 +- doc/html/fix_nve_line.html | 4 +- doc/html/fix_nve_manifold_rattle.html | 2 +- doc/html/fix_nve_noforce.html | 4 +- doc/html/fix_nve_sphere.html | 4 +- doc/html/fix_nve_tri.html | 8 +-- doc/html/fix_nvt_asphere.html | 4 +- doc/html/fix_nvt_body.html | 4 +- doc/html/fix_nvt_manifold_rattle.html | 4 +- doc/html/fix_nvt_sllod.html | 4 +- doc/html/fix_nvt_sphere.html | 4 +- doc/html/fix_oneway.html | 4 +- doc/html/fix_planeforce.html | 4 +- doc/html/fix_poems.html | 4 +- doc/html/fix_press_berendsen.html | 12 ++-- doc/html/fix_print.html | 4 +- doc/html/fix_property_atom.html | 50 ++++++++-------- doc/html/fix_qeq_comb.html | 4 +- doc/html/fix_qeq_reax.html | 4 +- doc/html/fix_recenter.html | 4 +- doc/html/fix_rigid.html | 4 +- doc/html/fix_setforce.html | 18 +++--- doc/html/fix_shake.html | 4 +- doc/html/fix_srd.html | 10 ++-- doc/html/fix_store_force.html | 4 +- doc/html/fix_tmd.html | 18 +++--- doc/html/fix_vector.html | 46 +++++++-------- doc/html/fix_wall_reflect.html | 4 +- doc/html/fix_wall_srd.html | 58 +++++++++---------- doc/html/group.html | 2 +- doc/html/if.html | 2 +- doc/html/improper_class2.html | 4 +- doc/html/improper_coeff.html | 26 ++++----- doc/html/improper_cossq.html | 4 +- doc/html/improper_cvff.html | 4 +- doc/html/improper_fourier.html | 4 +- doc/html/improper_harmonic.html | 4 +- doc/html/improper_hybrid.html | 16 ++--- doc/html/improper_none.html | 12 ++-- doc/html/improper_ring.html | 4 +- doc/html/improper_style.html | 22 +++---- doc/html/improper_umbrella.html | 4 +- doc/html/improper_zero.html | 10 ++-- doc/html/kspace_style.html | 6 +- doc/html/log.html | 2 +- doc/html/manifolds.html | 10 ++-- doc/html/mass.html | 12 ++-- doc/html/neb.html | 2 +- doc/html/pair_adp.html | 4 +- doc/html/pair_airebo.html | 4 +- doc/html/pair_awpmd.html | 18 +++--- doc/html/pair_beck.html | 4 +- doc/html/pair_body.html | 2 +- doc/html/pair_born.html | 4 +- doc/html/pair_buck.html | 4 +- doc/html/pair_buck_long.html | 4 +- doc/html/pair_charmm.html | 4 +- doc/html/pair_class2.html | 4 +- doc/html/pair_coeff.html | 46 +++++++-------- doc/html/pair_colloid.html | 4 +- doc/html/pair_comb.html | 4 +- doc/html/pair_coul.html | 4 +- doc/html/pair_cs.html | 2 +- doc/html/pair_dipole.html | 4 +- doc/html/pair_dpd.html | 4 +- doc/html/pair_eam.html | 4 +- doc/html/pair_edip.html | 4 +- doc/html/pair_eim.html | 4 +- doc/html/pair_gauss.html | 4 +- doc/html/pair_gayberne.html | 4 +- doc/html/pair_gran.html | 4 +- doc/html/pair_gromacs.html | 4 +- doc/html/pair_hbond_dreiding.html | 4 +- doc/html/pair_hybrid.html | 4 +- doc/html/pair_kim.html | 28 ++++----- doc/html/pair_lcbop.html | 20 +++---- doc/html/pair_lj.html | 4 +- doc/html/pair_lj96.html | 4 +- doc/html/pair_lj_cubic.html | 4 +- doc/html/pair_lj_expand.html | 4 +- doc/html/pair_lj_long.html | 4 +- doc/html/pair_lj_sf.html | 4 +- doc/html/pair_lj_smooth.html | 4 +- doc/html/pair_lj_smooth_linear.html | 4 +- doc/html/pair_lj_soft.html | 4 +- doc/html/pair_meam_spline.html | 4 +- doc/html/pair_morse.html | 4 +- doc/html/pair_nb3b_harmonic.html | 4 +- doc/html/pair_nm.html | 4 +- doc/html/pair_none.html | 12 ++-- doc/html/pair_peri.html | 4 +- doc/html/pair_reax_c.html | 6 +- doc/html/pair_resquared.html | 4 +- doc/html/pair_sdk.html | 4 +- doc/html/pair_smd_tlsph.html | 18 +++--- doc/html/pair_smd_ulsph.html | 24 ++++---- doc/html/pair_soft.html | 4 +- doc/html/pair_sph_heatconduction.html | 14 ++--- doc/html/pair_sph_lj.html | 14 ++--- doc/html/pair_sph_rhosum.html | 14 ++--- doc/html/pair_sw.html | 4 +- doc/html/pair_table.html | 4 +- doc/html/pair_tersoff.html | 4 +- doc/html/pair_tersoff_mod.html | 4 +- doc/html/pair_tersoff_zbl.html | 4 +- doc/html/pair_thole.html | 4 +- doc/html/pair_vashishta.html | 4 +- doc/html/pair_write.html | 14 ++--- doc/html/pair_yukawa.html | 4 +- doc/html/pair_yukawa_colloid.html | 4 +- doc/html/pair_zbl.html | 4 +- doc/html/pair_zero.html | 12 ++-- doc/html/partition.html | 8 +-- doc/html/prd.html | 4 +- doc/html/read_data.html | 2 +- doc/html/read_restart.html | 20 +++---- doc/html/region.html | 6 +- doc/html/reset_timestep.html | 14 ++--- doc/html/run_style.html | 13 ++--- doc/html/shell.html | 34 +++++------ doc/html/temper.html | 2 +- doc/html/thermo_modify.html | 18 +++--- doc/html/thermo_style.html | 6 +- doc/html/write_data.html | 14 ++--- doc/html/write_restart.html | 16 ++--- 280 files changed, 1154 insertions(+), 1208 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 2281f57fbd..9884247458 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -181,7 +181,10 @@ all at Sandia. The LAMMPS home page at http://lammps.sandia.gov has more information about the code and its uses. Interaction with external LAMMPS developers, bug reports and feature requests are mainly coordinated through the -LAMMPS project on GitHub.

+LAMMPS project on GitHub. +The lammps.org domain, currently hosting public continuous integration testing and precompiled Linux RPM and Windows installer packages is located +at Temple University and managed by Richard Berger, +richard.berger at temple.edu.

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for diff --git a/doc/html/Section_accelerate.html b/doc/html/Section_accelerate.html index db8d8af4bd..770d09d3bb 100644 --- a/doc/html/Section_accelerate.html +++ b/doc/html/Section_accelerate.html @@ -81,7 +81,14 @@

  • 5. Accelerating LAMMPS performance
    • @@ -274,29 +281,20 @@ coprocessors.

    overview of packages is give in Section packages.

    These are the accelerator packages currently in LAMMPS, either as standard or user packages:

    - ---- - - - - - - - - - - - - - - - - - -
    GPUfor NVIDIA GPUs as well as OpenCL support
    USER-INTELfor Intel CPUs and Intel Xeon Phi
    KOKKOSfor GPUs, Intel Xeon Phi, and OpenMP threading
    USER-OMPfor OpenMP threading
    OPTgeneric CPU optimizations
    +
    +

    5.3.1. GPU Package with CUDA and OpenCL support for Nvidia GPUs and others

    +
    +
    +

    5.3.2. USER-INTEL Package for Intel CPUs and Intel Xeon Phi

    +
    +
    +

    5.3.3. KOKKOS Package for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading

    +
    +
    +

    5.3.4. USER-OMP Package for OpenMP threading and generic CPU optimizations

    +
    +
    +

    5.3.5. OPT Package generic CPU optimizations

    Inverting this list, LAMMPS currently has acceleration support for three kinds of hardware, via the listed packages:

    @@ -336,7 +334,7 @@ Lennard-Jones pair_style lj/cut/opt

    To see what accelerate styles are currently available, see -Section_commands 5 of the manual. The +Section 3.5 of the manual. The doc pages for individual commands (e.g. pair lj/cut or fix nve) also list any accelerated variants available for that style.

    @@ -457,6 +455,7 @@ CPU.
    +

    5.4. Comparison of various accelerator packages

    diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 69c6609b6c..9c902fb9ad 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -318,7 +318,7 @@ allowed, but that should be sufficient for most use cases.

    This section describes the structure of a typical LAMMPS input script. The “examples” directory in the LAMMPS distribution contains many sample input scripts; the corresponding problems are discussed in -Section_example, and animated on the LAMMPS WWW Site.

    +Section 7, and animated on the LAMMPS WWW Site.

    A LAMMPS input script typically has 4 parts:

    1. Initialization
      2. diff --git a/doc/html/Section_errors.html b/doc/html/Section_errors.html index 680f6140be..6e37d3ef9f 100644 --- a/doc/html/Section_errors.html +++ b/doc/html/Section_errors.html @@ -6491,7 +6491,7 @@ per timestep.
      If there are other fixes that act immediately after the intitial stage of time integration within a timestep (i.e. after atoms move), then the command that sets up the dynamic group should appear after those -fixes. This will insure that dynamic group assignements are made +fixes. This will insure that dynamic group assignments are made after all atoms have moved.
      One or more respa levels compute no forces
      This is computationally inefficient.
      diff --git a/doc/html/Section_history.html b/doc/html/Section_history.html index 19d35eb60a..dbdecba683 100644 --- a/doc/html/Section_history.html +++ b/doc/html/Section_history.html @@ -148,13 +148,24 @@ dynamics codes our group has distributed.

    13.1. Coming attractions

    -

    The Wish list link on the -LAMMPS WWW page gives a list of features we are hoping to add to -LAMMPS in the future, including contact names of individuals you can -email if you are interested in contributing to the developement or -would be a future user of that feature.

    -

    You can also send email to the developers if you want to add -your wish to the list.

    +

    As of summer 2016 we are using the LAMMPS project issue tracker on GitHub for keeping +track of suggested, planned or pending new features. This includes +discussions of how to best implement them, or why they would be +useful. Especially if a planned or proposed feature is non-trivial +to add, e.g. because it requires changes to some of the core +classes of LAMMPS, people planning to contribute a new feature to +LAMMS are encouraged to submit an issue about their planned +implementation this way in order to receive feedback from the +LAMMPS core developers. They will provide suggestions about +the validity of the proposed approach and possible improvements, +pitfalls or alternatives.

    +

    Please see some of the closed issues for examples of how to +suggest code enhancements, submit proposed changes, or report +elated issues and how they are resoved.

    +

    As an alternative to using GitHub, you may e-mail the +core developers or send +an e-mail to the LAMMPS Mail list +if you want to have your suggestion added to the list.

    diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index feb6e5e5c9..8ae31c0409 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -224,7 +224,7 @@

    The example input scripts included in the LAMMPS distribution and -highlighted in Section_example also show how to +highlighted in Section 7 also show how to setup and run various kinds of simulations.

    6.1. Restarting a simulation

    @@ -360,7 +360,7 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the read_data command or in the input script with commands like pair_coeff or -bond_coeff. See Section_tools +bond_coeff. See Section 9 for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input.

    See (MacKerell) for a description of the CHARMM force @@ -805,7 +805,7 @@ made by the command (assuming your parallel machine allows one or more processors to start up another program). In the latter case the stand-alone code could communicate with LAMMPS thru files that the command writes and reads.

    -

    See Section_modify of the documentation for how +

    See Section 10 of the documentation for how to add a new command to LAMMPS.

    (3) Use LAMMPS as a library called by another code. In this case the other code is the driver and calls LAMMPS as needed. Or a wrapper @@ -833,11 +833,11 @@ example, from C++ you could create one (or more) “instances” of LAMMPS, pass it an input script to process, or execute individual commands, all by invoking the correct class methods in LAMMPS. From C or Fortran you can make function calls to do the same things. See -Section_python of the manual for a description +Section 11 of the manual for a description of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface.

    The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See Section_howto 19 of the +to LAMMPS. See Section 6.19 of the manual for a description of the interface and how to extend it for your needs.

    Note that the lammps_open() function that creates an instance of @@ -865,7 +865,7 @@ systems, and can be useful for rapid debugging of simulation geometry and atom trajectories.

    Several programs included with LAMMPS as auxiliary tools can convert native LAMMPS dump files to other formats. See the -Section_tools doc page for details. The first is +Section 9 doc page for details. The first is the ch2lmp tool, which contains a lammps2pdb Perl script which converts LAMMPS dump files into PDB files. The second is the lmp2arc tool which @@ -1898,7 +1898,7 @@ converge and requires careful post-processing

    6.19. Library interface to LAMMPS

    -

    As described in Section_start 5, LAMMPS +

    As described in Section 2.5, LAMMPS can be built as a library, so that it can be called by another code, used in a coupled manner with other codes, or driven through a Python interface.

    @@ -2254,7 +2254,7 @@ ID), or dynamic (e.g. what spatial bin an atom is in as it moves).

    variables to be used to define chunk IDs for each atom. This means you can write your own compute or fix to output a per-atom quantity to use as chunk ID. See -Section_modify of the documentation for how to +Section 10 of the documentation for how to do this. You can also define a per-atom variable in the input script that uses a formula to generate a chunk ID for each atom.

    diff --git a/doc/html/Section_intro.html b/doc/html/Section_intro.html index 3f41a6b156..9a757f7d72 100644 --- a/doc/html/Section_intro.html +++ b/doc/html/Section_intro.html @@ -183,7 +183,7 @@ parallel machine that compiles C++ and supports the Section_perf for information on +billions. See Section 8 for information on LAMMPS performance and scalability, or the Benchmarks section of the LAMMPS WWW Site.

    LAMMPS is a freely-available open-source code, distributed under the @@ -192,11 +192,11 @@ modify the code however you wish. See Section_modify +conditions, or diagnostics. See Section 10 for more details.

    The current version of LAMMPS is written in C++. Earlier versions were written in F77 and F90. See -Section_history for more information on +Section 13 for more information on different versions. All versions can be downloaded from the LAMMPS WWW Site.

    LAMMPS was originally developed under a US Department of Energy CRADA (Cooperative Research and Development Agreement) between two DOE labs @@ -225,7 +225,7 @@ LAMMPS are listed in Section_modify, which describes how you can add +Section 10, which describes how you can add it to LAMMPS.

    1.2.1. General features

    @@ -452,7 +452,7 @@ reformat the file as LAMMPS input. Some of the tools in Section_modify for a discussion +LAMMPS runs, see Section 10 for a discussion of how you can use the dump and compute and fix commands to print out data of your choosing. Keep in mind that complicated computations can slow down the molecular @@ -472,7 +472,7 @@ following packages:

  • RasMol

    • Other features that LAMMPS does not yet (and may never) support are -discussed in Section_history.

    +discussed in Section 13.

    Finally, these are freely-available molecular dynamics codes, most of them parallel, which may be well-suited to the problems you want to model. They can also be used in conjunction with LAMMPS to perform @@ -526,7 +526,7 @@ talks or link to it from your WWW site.

  • If you find an error or omission in this manual or on the LAMMPS WWW Site, or have a suggestion for something to clarify or include, send an email to the developers.
    • -
  • If you find a bug, Section_errors 2 +
  • If you find a bug, Section 12.2 describes how to report it.
  • If you publish a paper using LAMMPS results, send the citation (and any cool pictures or movies if you like) to add to the Publications, @@ -536,7 +536,7 @@ and attributions back to you.
    • directory.
  • The tools sub-directory of the LAMMPS distribution has various stand-alone codes for pre- and post-processing of LAMMPS data. More -details are given in Section_tools. If you write +details are given in Section 9. If you write a new tool that users will find useful, it can be added to the LAMMPS distribution.
  • LAMMPS is designed to be easy to extend with new code for features @@ -608,7 +608,7 @@ and efforts.

  • Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
  • Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package
    • -

    As discussed in Section_history, LAMMPS +

    As discussed in Section 13, LAMMPS originated as a cooperative project between DOE labs and industrial partners. Folks involved in the design and testing of the original version of LAMMPS were the following:

    diff --git a/doc/html/Section_modify.html b/doc/html/Section_modify.html index b760c3c002..fb9509d150 100644 --- a/doc/html/Section_modify.html +++ b/doc/html/Section_modify.html @@ -955,7 +955,7 @@ class. See region.h for details.

    Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc.

    -

    See Section_howto 14 of the manual for +

    See Section 6.14 of the manual for an overview of using body particles and the body doc page for details on the various body styles LAMMPS supports. New styles can be created to add new kinds of body particles to LAMMPS.

    diff --git a/doc/html/Section_packages.html b/doc/html/Section_packages.html index 2565c51206..1dd6871da4 100644 --- a/doc/html/Section_packages.html +++ b/doc/html/Section_packages.html @@ -215,7 +215,7 @@ packages.

    4.2 User packages

    -

    Section_start 3 of the manual describes +

    Section 2.3 of the manual describes the difference between standard packages and user packages. It also has general details on how to include/exclude specific packages as part of the LAMMPS build process, and on how to build auxiliary @@ -275,7 +275,7 @@ name links to a sub-section below with more details.

  • -
    + - + - + - + @@ -446,7 +446,7 @@ name links to a sub-section below with more details.

  • - + - +
    Section_howto 6.14Section 6.6.14 ellipse
    • @@ -337,7 +337,7 @@ name links to a sub-section below with more details.

    CORESHELL adiabatic core/shell model Hendrik Heenen (Technical U of Munich)Section_howto 6.25Section 6.6.25 coreshell
    • @@ -370,7 +370,7 @@ name links to a sub-section below with more details.

    		Section_howto 6.6Section 6.6.6 pour
    • @@ -387,7 +387,7 @@ name links to a sub-section below with more details.

    KOKKOS Kokkos-enabled styles Trott & Moore (4)Section_accelerateSection 5 kokkos lib/kokkos
    Section_howto 6.3Section 6.6.3 peptide
    • @@ -506,7 +506,7 @@ name links to a sub-section below with more details.

    		Section_howto 6.5Section 6.6.5 tad
    • @@ -598,7 +598,7 @@ and Ellad Tadmor (U Minn).

      Stan Moore (Sandia). It uses the Kokkos library which was developed by Carter Edwards, Christian Trott, and others at Sandia.

      The “Doc page” column links to either a sub-section of the -Section_howto of the manual, or an input script +Section 6 of the manual, or an input script command implemented as part of the package, or to additional documentation provided within the package.

      The “Example” column is a sub-directory in the examples directory of @@ -1951,7 +1951,7 @@ Mattox (Engility), and John Brennan (ARL).

      (6) The USER-VTK package was created by Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).

      The “Doc page” column links to either a sub-section of the -Section_howto of the manual, or an input script +Section 6 of the manual, or an input script command implemented as part of the package, or to additional documentation provided within the package.

      The “Example” column is a sub-directory in the examples directory of @@ -2144,7 +2144,7 @@ this package. Also see src/USER-INTEL/README for more details. See the KOKKOS, OPT, and USER-OMP packages, which also have CPU and Phi-enabled styles.

      Supporting info: examples/accelerate, src/USER-INTEL/TEST

      -

      Section_accelerate

      +

      Section 5

      Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact him directly if you have questions.

      For the USER-INTEL package, you have 2 choices when building. You can @@ -2216,7 +2216,7 @@ pair of files (*.cpp and *.h).

      More information about each feature can be found by reading its doc page in the LAMMPS doc directory. The doc page which lists all LAMMPS input script commands is as follows:

      -

      Section_commands

      +

      Section 3

      User-contributed features are listed at the bottom of the fix, compute, pair, etc sections.

      The list of features and author of each is given in the @@ -2273,7 +2273,7 @@ application itself.

      other optimizations of various LAMMPS pair styles, dihedral styles, and fix styles.

      See this section of the manual to get started:

      -

      Section_accelerate

      +

      Section 5

      The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions.

      For the USER-OMP package, your Makefile.machine needs additional diff --git a/doc/html/Section_python.html b/doc/html/Section_python.html index 971aeb58dc..f59ef777dc 100644 --- a/doc/html/Section_python.html +++ b/doc/html/Section_python.html @@ -182,7 +182,7 @@ drive a program through its library interface, or to hook multiple pieces of software together, such as a simulation package plus a visualization package, or to run a coupled multiscale or multiphysics model.

      -

      See Section_howto 10 of the manual and +

      See Section 6.10 of the manual and the couple directory of the distribution for more ideas about coupling LAMMPS to other codes. See Section_howto 19 for a description of the LAMMPS library interface provided in src/library.cpp and src/library.h, and @@ -302,7 +302,7 @@ file and the shared library.

      11.3. Building LAMMPS as a shared library

      Instructions on how to build LAMMPS as a shared library are given in -Section_start 5. A shared library is one +Section 2.5. A shared library is one that is dynamically loadable, which is what Python requires to wrap LAMMPS. On Linux this is a library file that ends in ”.so”, not ”.a”.

      From the src directory, type

      @@ -321,7 +321,7 @@ most recently built version.

      auxiliary libraries (used by various packages), then all of these extra libraries must also be shared libraries. If the LAMMPS shared-library build fails with an error complaining about this, see -Section_start 5 for more details.

      +Section 2.5 for more details.

      @@ -531,7 +531,7 @@ first importing from the lammps.py file:

      >>> CDLL("liblammps.so") -

      If an error occurs, carefully go thru the steps in Section_start 5 and above about building a shared +

      If an error occurs, carefully go thru the steps in Section 2.5 and above about building a shared library and about insuring Python can find the necessary two files it needs.

      @@ -762,7 +762,7 @@ subscripting. The one exception is that for a fix that calculates a global vector or array, a single double value from the vector or array is returned, indexed by I (vector) or I and J (array). I,J are zero-based indices. The I,J arguments can be left out if not needed. -See Section_howto 15 of the manual for a +See Section 6.15 of the manual for a discussion of global, per-atom, and local data, and of scalar, vector, and array data types. See the doc pages for individual computes and fixes for a description of what diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html index b3ebfd3dca..be6c738edf 100644 --- a/doc/html/Section_start.html +++ b/doc/html/Section_start.html @@ -749,7 +749,7 @@ lmp_machine -h commands known to your executable, and immediately exit.

      There are two kinds of packages in LAMMPS, standard and user packages. More information about the contents of standard and user packages is -given in Section_packages of the manual. The +given in Section 4 of the manual. The difference between standard and user packages is as follows:

      Standard packages, such as molecule or kspace, are supported by the LAMMPS developers and are written in a syntax and style consistent @@ -843,7 +843,7 @@ libraries. Many of them are provided with LAMMPS, in which case they must be compiled first, before LAMMPS is built, if you wish to include that package. If you get a LAMMPS build error about a missing library, this is likely the reason. See the -Section_packages doc page for a list of +Section 4 doc page for a list of packages that have these kinds of auxiliary libraries.

      The lib directory in the distribution has sub-directories with package names that correspond to the needed auxiliary libs, e.g. lib/gpu. @@ -1101,7 +1101,7 @@ dynamically loaded, e.g. from Python, type

      where foo is the machine name. This kind of library is required when -wrapping LAMMPS with Python; see Section_python +wrapping LAMMPS with Python; see Section 11 for details. This will use the SHFLAGS and SHLIBFLAGS settings in src/MAKE/Makefile.foo and perform the build in the directory Obj_shared_foo. This is so that each file can be compiled with the @@ -1174,8 +1174,8 @@ src/library.cpp and src/library.h.

      See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS thru its library interface. There are other examples as well in the COUPLE directory which are -discussed in Section_howto 10 of the -manual. See Section_python of the manual for a +discussed in Section 6.10 of the +manual. See Section 11 of the manual for a description of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface.

      The files src/library.cpp and library.h define the C-style API for @@ -1273,7 +1273,7 @@ files and write its output files to the executable directory, rather than your working directory, which is probably not what you want.

      If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING -message and continue. See Section_errors for a +message and continue. See Section 12 for a discussion of the various kinds of errors LAMMPS can or can’t detect, a list of all ERROR and WARNING messages, and what to do about them.

      LAMMPS can run a problem on any number of processors, including a @@ -1480,7 +1480,7 @@ replica runs on on one or a few processors. Note that with MPI installed on a machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors.

      To run multiple independent simulatoins from one input script, using -multiple partitions, see Section_howto 4 +multiple partitions, see Section 6.4 of the manual. World- and universe-style variables are useful in this context.

      -plog file
@@ -1544,7 +1544,7 @@ cores within each node are ranked in a desired order.  Or when using
 the run_style verlet/split command with 2 partitions
 to insure that a specific Kspace processor (in the 2nd partition) is
 matched up with a specific set of processors in the 1st partition.
-See the Section_accelerate doc pages for
+See the Section 5 doc pages for
 more details.
      
 
      If the keyword nth is used with a setting N, then it means every
 Nth processor will be moved to the end of the ranking.  This is useful
@@ -1849,7 +1849,7 @@ communication, roughly 75% in the example above.
      
 
      2.9. Tips for users of previous LAMMPS versions
      
 
      The current C++ began with a complete rewrite of LAMMPS 2001, which
 was written in F90.  Features of earlier versions of LAMMPS are listed
-in Section_history.  The F90 and F77 versions
+in Section 13.  The F90 and F77 versions
 (2001 and 99) are also freely distributed as open-source codes; check
 the LAMMPS WWW Site for distribution information if you prefer
 those versions.  The 99 and 2001 versions are no longer under active
diff --git a/doc/html/accelerate_gpu.html b/doc/html/accelerate_gpu.html
index 33e9cc6d76..704d13f873 100644
--- a/doc/html/accelerate_gpu.html
+++ b/doc/html/accelerate_gpu.html
@@ -139,7 +139,7 @@ e.g. within a node of a parallel machine.
 
    • Atom-based data (e.g. coordinates, forces) moves back-and-forth
 between the CPU(s) and GPU every timestep.
      • 
 
    • Neighbor lists can be built on the CPU or on the GPU
      • 
-
    • The charge assignement and force interpolation portions of PPPM can be
+
    • The charge assignment and force interpolation portions of PPPM can be
 run on the GPU.  The FFT portion, which requires MPI communication
 between processors, runs on the CPU.
      • 
 
    • Asynchronous force computations can be performed simultaneously on the
diff --git a/doc/html/accelerate_opt.html b/doc/html/accelerate_opt.html
index e75b4ee1a0..b07be6064d 100644
--- a/doc/html/accelerate_opt.html
+++ b/doc/html/accelerate_opt.html
@@ -139,10 +139,10 @@ follow.
      
 Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py
      • -
      lmp_mpi -sf opt -in in.script                # run in serial
-mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel
-
      -
      +
      +lmp_mpi -sf opt -in in.script                # run in serial
+mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel
+

      Required hardware/software:

      None.

      Building LAMMPS with the OPT package:

      @@ -159,9 +159,9 @@ The Make.py command will add this automatically.

      Or run with the OPT package by editing an input script:

      Use the suffix opt command, or you can explicitly add an “opt” suffix to individual styles in your input script, e.g.

      -
      pair_style lj/cut/opt 2.5
-
      -
      +
      +pair_style lj/cut/opt 2.5
+

      Speed-ups to expect:

      You should see a reduction in the “Pair time” value printed at the end of a run. On most machines for reasonable problem sizes, it will be a diff --git a/doc/html/angle_charmm.html b/doc/html/angle_charmm.html index 3d6bb4e8cd..051d2f01d5 100644 --- a/doc/html/angle_charmm.html +++ b/doc/html/angle_charmm.html @@ -173,7 +173,7 @@ internally; hence the units of K are in energy/radian^2.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -183,7 +183,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_class2.html b/doc/html/angle_class2.html index 1b800d6c0d..26f1f8a6b9 100644 --- a/doc/html/angle_class2.html +++ b/doc/html/angle_class2.html @@ -197,7 +197,7 @@ same value from the Ea formula.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -207,7 +207,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_coeff.html b/doc/html/angle_coeff.html index 2856575a7d..3ae8743871 100644 --- a/doc/html/angle_coeff.html +++ b/doc/html/angle_coeff.html @@ -128,9 +128,9 @@

      angle_coeff command

      Syntax

      -
      angle_coeff N args
-
      -
      +
      +angle_coeff N args
+
      • N = angle type (see asterisk form below)
      • args = coefficients for one or more angle types
        • @@ -138,11 +138,11 @@

      Examples

      -
      angle_coeff 1 300.0 107.0
-angle_coeff * 5.0
-angle_coeff 2*10 5.0
-
      -
      +
      +angle_coeff 1 300.0 107.0
+angle_coeff * 5.0
+angle_coeff 2*10 5.0
+

      Description

      @@ -153,7 +153,7 @@ Angle coefficients can also be set in the data file read by the

      N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple angle types. This takes the -form “*” or “n” or “n” or “m*n”. If N = the number of angle types, +form “*” or “*n” or “n*” or “m*n”. If N = the number of angle types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk @@ -161,10 +161,10 @@ means all types from m to n (inclusive).

      Note that using an angle_coeff command can override a previous setting for the same angle type. For example, these commands set the coeffs for all angle types, then overwrite the coeffs for just angle type 2:

      -
      angle_coeff * 200.0 107.0 1.2
-angle_coeff 2 50.0 107.0
-
      -
      +
      +angle_coeff * 200.0 107.0 1.2
+angle_coeff 2 50.0 107.0
+

      A line in a data file that specifies angle coefficients uses the exact same format as the arguments of the angle_coeff command in an input script, except that wild-card asterisks should not be used since diff --git a/doc/html/angle_cosine.html b/doc/html/angle_cosine.html index 6876620bb5..990f432ddb 100644 --- a/doc/html/angle_cosine.html +++ b/doc/html/angle_cosine.html @@ -158,7 +158,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -168,7 +168,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_cosine_delta.html b/doc/html/angle_cosine_delta.html index fda0b0a0a5..c3ef174998 100644 --- a/doc/html/angle_cosine_delta.html +++ b/doc/html/angle_cosine_delta.html @@ -162,7 +162,7 @@ internally.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -172,7 +172,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_cosine_periodic.html b/doc/html/angle_cosine_periodic.html index 9851cea9d4..713f15a2ac 100644 --- a/doc/html/angle_cosine_periodic.html +++ b/doc/html/angle_cosine_periodic.html @@ -169,7 +169,7 @@ geometry.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -179,7 +179,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_cosine_shift.html b/doc/html/angle_cosine_shift.html index 76d4b6dcb4..5a31d8f89b 100644 --- a/doc/html/angle_cosine_shift.html +++ b/doc/html/angle_cosine_shift.html @@ -161,7 +161,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -171,7 +171,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_cosine_shift_exp.html b/doc/html/angle_cosine_shift_exp.html index 2bb957b561..cadcd4b0ae 100644 --- a/doc/html/angle_cosine_shift_exp.html +++ b/doc/html/angle_cosine_shift_exp.html @@ -171,7 +171,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -181,7 +181,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_cosine_squared.html b/doc/html/angle_cosine_squared.html index e7f0d49193..ef6a278ed5 100644 --- a/doc/html/angle_cosine_squared.html +++ b/doc/html/angle_cosine_squared.html @@ -162,7 +162,7 @@ internally.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -172,7 +172,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_dipole.html b/doc/html/angle_dipole.html index 13f560db0e..b6d91300b0 100644 --- a/doc/html/angle_dipole.html +++ b/doc/html/angle_dipole.html @@ -182,7 +182,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -192,7 +192,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_fourier.html b/doc/html/angle_fourier.html index c49686daf1..9dd82b3ea4 100644 --- a/doc/html/angle_fourier.html +++ b/doc/html/angle_fourier.html @@ -158,7 +158,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -168,7 +168,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_fourier_simple.html b/doc/html/angle_fourier_simple.html index 91c3ac4eeb..7a479ec44f 100644 --- a/doc/html/angle_fourier_simple.html +++ b/doc/html/angle_fourier_simple.html @@ -157,7 +157,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -167,7 +167,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_harmonic.html b/doc/html/angle_harmonic.html index 403ca622ca..ebd1c0c4b2 100644 --- a/doc/html/angle_harmonic.html +++ b/doc/html/angle_harmonic.html @@ -168,7 +168,7 @@ internally; hence the units of K are in energy/radian^2.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -178,7 +178,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_hybrid.html b/doc/html/angle_hybrid.html index 000ae7cfd6..da8c39f9f1 100644 --- a/doc/html/angle_hybrid.html +++ b/doc/html/angle_hybrid.html @@ -128,20 +128,20 @@

      angle_style hybrid command

      Syntax

      -
      angle_style hybrid style1 style2 ...
-
      -
      +
      +angle_style hybrid style1 style2 ...
+
      • style1,style2 = list of one or more angle styles

      Examples

      -
      angle_style hybrid harmonic cosine
-angle_coeff 1 harmonic 80.0 30.0
-angle_coeff 2* cosine 50.0
-
      -
      +
      +angle_style hybrid harmonic cosine
+angle_coeff 1 harmonic 80.0 30.0
+angle_coeff 2* cosine 50.0
+

      Description

      diff --git a/doc/html/angle_none.html b/doc/html/angle_none.html index a386d3b444..51cb14149d 100644 --- a/doc/html/angle_none.html +++ b/doc/html/angle_none.html @@ -128,15 +128,15 @@

      angle_style none command

      Syntax

      -
      angle_style none
-
      -
      +
      +angle_style none
+

      Examples

      -
      angle_style none
-
      -
      +
      +angle_style none
+

      Description

      diff --git a/doc/html/angle_quartic.html b/doc/html/angle_quartic.html index 4134601496..17c89b582f 100644 --- a/doc/html/angle_quartic.html +++ b/doc/html/angle_quartic.html @@ -164,7 +164,7 @@ internally; hence the units of K are in energy/radian^2.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -174,7 +174,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_style.html b/doc/html/angle_style.html index cc152c026e..3fe225941f 100644 --- a/doc/html/angle_style.html +++ b/doc/html/angle_style.html @@ -128,20 +128,20 @@

      angle_style command

      Syntax

      -
      angle_style style
-
      -
      +
      +angle_style style
+
      • style = none or hybrid or charmm or class2 or cosine or cosine/squared or harmonic

      Examples

      -
      angle_style harmonic
-angle_style charmm
-angle_style hybrid harmonic cosine
-
      -
      +
      +angle_style harmonic
+angle_style charmm
+angle_style hybrid harmonic cosine
+

      Description

      @@ -207,9 +207,9 @@ package.

      Default

      -
      angle_style none
-
      -
      +
      +angle_style none
+
      diff --git a/doc/html/angle_table.html b/doc/html/angle_table.html index 82e77f8d7c..e734684fc8 100644 --- a/doc/html/angle_table.html +++ b/doc/html/angle_table.html @@ -131,9 +131,9 @@

      angle_style table/omp command

      Syntax

      -
      angle_style table style N
-
      -
      +
      +angle_style table style N
+
      • style = linear or spline = method of interpolation
      • N = use N values in table
        • @@ -141,10 +141,10 @@

      Examples

      -
      angle_style table linear 1000
-angle_coeff 3 file.table ENTRY1
-
      -
      +
      +angle_style table linear 1000
+angle_coeff 3 file.table ENTRY1
+

      Description

      @@ -236,7 +236,7 @@ one that matches the specified keyword.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -246,7 +246,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/angle_zero.html b/doc/html/angle_zero.html index 01fd28ed95..a22915ceea 100644 --- a/doc/html/angle_zero.html +++ b/doc/html/angle_zero.html @@ -134,12 +134,12 @@ angle_style zero nocoeff

      Examples

      -
      angle_style zero
-angle_style zero nocoeff
-angle_coeff *
-angle_coeff * 120.0
-
      -
      +
      +angle_style zero
+angle_style zero nocoeff
+angle_coeff *
+angle_coeff * 120.0
+

      Description

      diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html index a2cbd22a72..0ec90b2ce3 100644 --- a/doc/html/atom_style.html +++ b/doc/html/atom_style.html @@ -395,7 +395,7 @@ styles; see Styles with a kk suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      Note that other acceleration packages in LAMMPS, specifically the GPU, @@ -406,7 +406,7 @@ enabled if LAMMPS was built with those packages. See the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/body.html b/doc/html/body.html index 5aaa8ec563..cb9ea23363 100644 --- a/doc/html/body.html +++ b/doc/html/body.html @@ -134,8 +134,8 @@ surface meshes of discrete points, collections of sub-particles, deformable objects, etc. Note that other kinds of finite-size spherical and aspherical particles are also supported by LAMMPS, such as spheres, ellipsoids, line segments, and triangles, but they are -simpler entities that body particles. See Section_howto 14 for a general overview of all these -particle types.

      +simpler entities that body particles. See Section 6.14 for a general overview of all +these particle types.

      Body particles are used via the atom_style body command. It takes a body style as an argument. The current body styles supported by LAMMPS are as follows. The name in the first @@ -163,7 +163,7 @@ style are described below.

      The rounded/polygon style listed in the table above and described below has not yet been relesed in LAMMPS. It will be soon.

      -

      We hope to add more styles in the future. See Section_modify 12 for details on how to add a new body +

      We hope to add more styles in the future. See Section 10.12 for details on how to add a new body style to the code.

      When to use body particles:

      diff --git a/doc/html/bond_class2.html b/doc/html/bond_class2.html index dad9e1dba9..43ea0dc970 100644 --- a/doc/html/bond_class2.html +++ b/doc/html/bond_class2.html @@ -162,7 +162,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -172,7 +172,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_coeff.html b/doc/html/bond_coeff.html index feaec2ccf5..3859141ce8 100644 --- a/doc/html/bond_coeff.html +++ b/doc/html/bond_coeff.html @@ -128,9 +128,9 @@

      bond_coeff command

      Syntax

      -
      bond_coeff N args
-
      -
      +
      +bond_coeff N args
+
      • N = bond type (see asterisk form below)
      • args = coefficients for one or more bond types
        • @@ -138,12 +138,12 @@

      Examples

      -
      bond_coeff 5 80.0 1.2
-bond_coeff * 30.0 1.5 1.0 1.0
-bond_coeff 1*4 30.0 1.5 1.0 1.0
-bond_coeff 1 harmonic 200.0 1.0
-
      -
      +
      +bond_coeff 5 80.0 1.2
+bond_coeff * 30.0 1.5 1.0 1.0
+bond_coeff 1*4 30.0 1.5 1.0 1.0
+bond_coeff 1 harmonic 200.0 1.0
+

      Description

      @@ -154,7 +154,7 @@ Bond coefficients can also be set in the data file read by the

      N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple bond types. This takes the -form “*” or “n” or “n” or “m*n”. If N = the number of bond types, +form “*” or “*n” or “n*” or “m*n”. If N = the number of bond types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk @@ -162,10 +162,10 @@ means all types from m to n (inclusive).

      Note that using a bond_coeff command can override a previous setting for the same bond type. For example, these commands set the coeffs for all bond types, then overwrite the coeffs for just bond type 2:

      -
      bond_coeff * 100.0 1.2
-bond_coeff 2 200.0 1.2
-
      -
      +
      +bond_coeff * 100.0 1.2
+bond_coeff 2 200.0 1.2
+

      A line in a data file that specifies bond coefficients uses the exact same format as the arguments of the bond_coeff command in an input script, except that wild-card asterisks should not be used since diff --git a/doc/html/bond_fene.html b/doc/html/bond_fene.html index d836487156..dcf743e4c3 100644 --- a/doc/html/bond_fene.html +++ b/doc/html/bond_fene.html @@ -171,7 +171,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -181,7 +181,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_fene_expand.html b/doc/html/bond_fene_expand.html index 577a4cde04..e19aa7e23d 100644 --- a/doc/html/bond_fene_expand.html +++ b/doc/html/bond_fene_expand.html @@ -169,7 +169,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -179,7 +179,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_harmonic.html b/doc/html/bond_harmonic.html index fc22160d18..79cfa0a02d 100644 --- a/doc/html/bond_harmonic.html +++ b/doc/html/bond_harmonic.html @@ -166,7 +166,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -176,7 +176,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_harmonic_shift.html b/doc/html/bond_harmonic_shift.html index 4ab86dc316..a9b85a076a 100644 --- a/doc/html/bond_harmonic_shift.html +++ b/doc/html/bond_harmonic_shift.html @@ -163,7 +163,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -173,7 +173,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_harmonic_shift_cut.html b/doc/html/bond_harmonic_shift_cut.html index 121eda2221..e683870120 100644 --- a/doc/html/bond_harmonic_shift_cut.html +++ b/doc/html/bond_harmonic_shift_cut.html @@ -163,7 +163,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -173,7 +173,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_hybrid.html b/doc/html/bond_hybrid.html index 1db68e1169..2b7b99ece6 100644 --- a/doc/html/bond_hybrid.html +++ b/doc/html/bond_hybrid.html @@ -128,20 +128,20 @@

      bond_style hybrid command

      Syntax

      -
      bond_style hybrid style1 style2 ...
-
      -
      +
      +bond_style hybrid style1 style2 ...
+
      • style1,style2 = list of one or more bond styles

      Examples

      -
      bond_style hybrid harmonic fene
-bond_coeff 1 harmonic 80.0 1.2
-bond_coeff 2* fene 30.0 1.5 1.0 1.0
-
      -
      +
      +bond_style hybrid harmonic fene
+bond_coeff 1 harmonic 80.0 1.2
+bond_coeff 2* fene 30.0 1.5 1.0 1.0
+

      Description

      diff --git a/doc/html/bond_morse.html b/doc/html/bond_morse.html index 42794978e3..f98c9e2aa9 100644 --- a/doc/html/bond_morse.html +++ b/doc/html/bond_morse.html @@ -161,7 +161,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -171,7 +171,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_none.html b/doc/html/bond_none.html index 128019039c..a7befee4b4 100644 --- a/doc/html/bond_none.html +++ b/doc/html/bond_none.html @@ -128,15 +128,15 @@

      bond_style none command

      Syntax

      -
      bond_style none
-
      -
      +
      +bond_style none
+

      Examples

      -
      bond_style none
-
      -
      +
      +bond_style none
+

      Description

      diff --git a/doc/html/bond_nonlinear.html b/doc/html/bond_nonlinear.html index ad8a574f82..239b673671 100644 --- a/doc/html/bond_nonlinear.html +++ b/doc/html/bond_nonlinear.html @@ -161,7 +161,7 @@ or read

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -171,7 +171,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_quartic.html b/doc/html/bond_quartic.html index 290a9f8055..c645ef2966 100644 --- a/doc/html/bond_quartic.html +++ b/doc/html/bond_quartic.html @@ -192,7 +192,7 @@ delete_bonds all bond 0 remove

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -202,7 +202,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_style.html b/doc/html/bond_style.html index 45a70ff3ba..2f04d0d0e2 100644 --- a/doc/html/bond_style.html +++ b/doc/html/bond_style.html @@ -128,9 +128,9 @@

      bond_style command

      Syntax

      -
      bond_style style args
-
      -
      +
      +bond_style style args
+
      • style = none or hybrid or class2 or fene or fene/expand or harmonic or morse or nonlinear or quartic
      @@ -141,11 +141,11 @@ args = none for any style except hybrid

      Examples

      -
      bond_style harmonic
-bond_style fene
-bond_style hybrid harmonic fene
-
      -
      +
      +bond_style harmonic
+bond_style fene
+bond_style hybrid harmonic fene
+

      Description

      diff --git a/doc/html/bond_table.html b/doc/html/bond_table.html index 57b1a25deb..031d9e0998 100644 --- a/doc/html/bond_table.html +++ b/doc/html/bond_table.html @@ -131,9 +131,9 @@

      bond_style table/omp command

      Syntax

      -
      bond_style table style N
-
      -
      +
      +bond_style table style N
+
      • style = linear or spline = method of interpolation
      • N = use N values in table
        • @@ -141,10 +141,10 @@

      Examples

      -
      bond_style table linear 1000
-bond_coeff 1 file.table ENTRY1
-
      -
      +
      +bond_style table linear 1000
+bond_coeff 1 file.table ENTRY1
+

      Description

      @@ -233,7 +233,7 @@ one that matches the specified keyword.

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -243,7 +243,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      diff --git a/doc/html/bond_write.html b/doc/html/bond_write.html index 19c746e4aa..c864a7f35a 100644 --- a/doc/html/bond_write.html +++ b/doc/html/bond_write.html @@ -128,9 +128,9 @@

      bond_write command

      Syntax

      -
      bond_write btype N inner outer file keyword itype jtype
-
      -
      +
      +bond_write btype N inner outer file keyword itype jtype
+
      • btype = bond types
      • N = # of values
        • @@ -143,10 +143,10 @@

      Examples

      -
      bond_write 1 500 0.5 3.5 table.txt Harmonic_1
-bond_write 3 1000 0.1 6.0 table.txt Morse
-
      -
      +
      +bond_write 1 500 0.5 3.5 table.txt Harmonic_1
+bond_write 3 1000 0.1 6.0 table.txt Morse
+

      Description

      diff --git a/doc/html/bond_zero.html b/doc/html/bond_zero.html index 4ddeb0e8cc..2989c2f867 100644 --- a/doc/html/bond_zero.html +++ b/doc/html/bond_zero.html @@ -134,12 +134,12 @@ bond_style zero nocoeff

      Examples

      -
      bond_style zero
-bond_style zero nocoeff
-bond_coeff *
-bond_coeff * 2.14
-
      -
      +
      +bond_style zero
+bond_style zero nocoeff
+bond_coeff *
+bond_coeff * 2.14
+

      Description

      diff --git a/doc/html/boundary.html b/doc/html/boundary.html index 75b29e927c..3433026590 100644 --- a/doc/html/boundary.html +++ b/doc/html/boundary.html @@ -190,7 +190,7 @@ face, to encompass the atoms. E.g. for a positive xy tilt, the xlo and xhi faces of the box are planes tilting in the +y direction as y increases. These tilted planes are shrink-wrapped around the atoms to determine the x extent of the box.

      -

      See Section_howto 12 of the doc pages +

      See Section 6.12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.

      diff --git a/doc/html/change_box.html b/doc/html/change_box.html index 5fd817925f..742aedf702 100644 --- a/doc/html/change_box.html +++ b/doc/html/change_box.html @@ -200,7 +200,7 @@ The creat read_restart commands also determine whether the simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors.

      -

      See Section_howto 12 of the doc pages +

      See Section 6.12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.

      diff --git a/doc/html/comm_modify.html b/doc/html/comm_modify.html index 81645ca56b..5bc228cc68 100644 --- a/doc/html/comm_modify.html +++ b/doc/html/comm_modify.html @@ -128,9 +128,9 @@

      comm_modify command

      Syntax

      -
      comm_modify keyword value ...
-
      -
      +
      +comm_modify keyword value ...
+
      • zero or more keyword/value pairs may be appended
      • keyword = mode or cutoff or cutoff/multi or group or vel
        • @@ -147,14 +147,14 @@

      Examples

      -
      comm_modify mode multi
-comm_modify mode multi group solvent
-comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
-comm_modify vel yes
-comm_modify mode single cutoff 5.0 vel yes
-comm_modify cutoff/multi * 0.0
-
      -
      +
      +comm_modify mode multi
+comm_modify mode multi group solvent
+comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
+comm_modify vel yes
+comm_modify mode single cutoff 5.0 vel yes
+comm_modify cutoff/multi * 0.0
+

      Description

      diff --git a/doc/html/comm_style.html b/doc/html/comm_style.html index e39c6d896c..a3a1bfd04d 100644 --- a/doc/html/comm_style.html +++ b/doc/html/comm_style.html @@ -128,19 +128,19 @@

      comm_style command

      Syntax

      -
      comm_style style
-
      -
      +
      +comm_style style
+
      • style = brick or tiled

      Examples

      -
      comm_style brick
-comm_style tiled
-
      -
      +
      +comm_style brick
+comm_style tiled
+

      Description

      diff --git a/doc/html/compute_ackland_atom.html b/doc/html/compute_ackland_atom.html index 81a9ef4a5c..ddd2c6c8a9 100644 --- a/doc/html/compute_ackland_atom.html +++ b/doc/html/compute_ackland_atom.html @@ -168,7 +168,7 @@ which computes this quantity.-

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      diff --git a/doc/html/compute_angle_local.html b/doc/html/compute_angle_local.html index 221ec3ba67..11074e825d 100644 --- a/doc/html/compute_angle_local.html +++ b/doc/html/compute_angle_local.html @@ -174,11 +174,11 @@ For example, angle output from the dump local command in a consistent way.

      Here is an example of how to do this:

      -
      compute 1 all property/local atype aatom1 aatom2 aatom3
-compute 2 all angle/local theta eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2]
-
      -
      +
      +compute 1 all property/local atype aatom1 aatom2 aatom3
+compute 2 all angle/local theta eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2]
+

      Output info:

      This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the diff --git a/doc/html/compute_angmom_chunk.html b/doc/html/compute_angmom_chunk.html index 97dadb33c0..88bb01d89f 100644 --- a/doc/html/compute_angmom_chunk.html +++ b/doc/html/compute_angmom_chunk.html @@ -178,11 +178,11 @@ how they are set for each atom. You can reset the image flags

      The simplest way to output the results of the compute angmom/chunk calculation to a file is to use the fix ave/time command, for example:

      -
      compute cc1 all chunk/atom molecule
-compute myChunk all angmom/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      -
      +
      +compute cc1 all chunk/atom molecule
+compute myChunk all angmom/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+

      Output info:

      This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/compute_body_local.html b/doc/html/compute_body_local.html index 33119b8b46..0b394b0582 100644 --- a/doc/html/compute_body_local.html +++ b/doc/html/compute_body_local.html @@ -156,7 +156,7 @@ sub-particles. The number of datums generated, aggregated across all processors, equals the number of body sub-particles plus the number of non-body particles in the system, modified by the group parameter as -explained below. See Section_howto 14 +explained below. See Section 6.14 of the manual and the body doc page for more details on using body particles.

      The local data stored by this command is generated by looping over all @@ -183,10 +183,10 @@ details of the different styles.

      body sub-particles are x,y,z coordinates, then the dump file will be formatted similar to the output of a dump atom or custom command.

      -
      compute 1 all body/local type 1 2 3
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
-
      -
      +
      +compute 1 all body/local type 1 2 3
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
+

      Output info:

      This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the diff --git a/doc/html/compute_chunk_atom.html b/doc/html/compute_chunk_atom.html index 8319769579..817d511170 100644 --- a/doc/html/compute_chunk_atom.html +++ b/doc/html/compute_chunk_atom.html @@ -225,7 +225,7 @@ computes with “chunk” in their style name, such as Section_howto 15.

      -

      See Section_howto 23 for an overview of +

      See Section 6.23 for an overview of how this compute can be used with a variety of other commands to tabulate properties of a simulation. The howto section gives several examples of input script commands that can be used to calculate @@ -361,13 +361,13 @@ is assigned to the atom. If the integer value is > 0, it becomes the chunk ID to the atom. Nchunk is set to the largest chunk ID. Note that this excludes atoms which are not in the specified group or optional region.

      -

      If the style begins with “c_”, a compute ID must follow which has been +

      If the style begins with “c_”, a compute ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS.

      -

      If the style begins with “f_”, a fix ID must follow which has been +

      If the style begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array @@ -375,7 +375,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with the timestep on which this compute accesses the fix, else an error results. Users can also write code for their own fix styles and add them to LAMMPS.

      -

      If a value begins with “v_”, a variable name for an atom or +

      If a value begins with “v_”, a variable name for an atom or atomfile style variable must follow which has been previously defined in the input script. Variables of style atom can reference thermodynamic keywords and various per-atom attributes, or @@ -662,7 +662,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values are unitless chunk IDs, ranging from 1 to Nchunk (inclusive) for atoms assigned to chunks, and 0 for atoms not diff --git a/doc/html/compute_cluster_atom.html b/doc/html/compute_cluster_atom.html index 87b9a15594..25cd87f319 100644 --- a/doc/html/compute_cluster_atom.html +++ b/doc/html/compute_cluster_atom.html @@ -179,7 +179,7 @@ the neighbor list.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be an ID > 0, as explained above.

      diff --git a/doc/html/compute_cna_atom.html b/doc/html/compute_cna_atom.html index b395acd816..20342f2b2a 100644 --- a/doc/html/compute_cna_atom.html +++ b/doc/html/compute_cna_atom.html @@ -187,7 +187,7 @@ too frequently or to have multiple compute/dump commands, each with a

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be a number from 0 to 5, as explained above.

      diff --git a/doc/html/compute_com_chunk.html b/doc/html/compute_com_chunk.html index 6967998f69..e2bce3f872 100644 --- a/doc/html/compute_com_chunk.html +++ b/doc/html/compute_com_chunk.html @@ -176,11 +176,11 @@ and how they are set for each atom. You can reset the image flags

      The simplest way to output the results of the compute com/chunk calculation to a file is to use the fix ave/time command, for example:

      -
      compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      -
      +
      +compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+

      Output info:

      This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/compute_contact_atom.html b/doc/html/compute_contact_atom.html index 686bbd9eb5..c601f15ded 100644 --- a/doc/html/compute_contact_atom.html +++ b/doc/html/compute_contact_atom.html @@ -155,7 +155,7 @@ specified compute group.

      Output info:

      This compute calculates a per-atom vector, whose values can be accessed by any command that uses per-atom values from a compute as -input. See Section_howto 15 for an +input. See Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be a number >= 0.0, as explained above.

      diff --git a/doc/html/compute_coord_atom.html b/doc/html/compute_coord_atom.html index 8f89d6769d..67663e1ce2 100644 --- a/doc/html/compute_coord_atom.html +++ b/doc/html/compute_coord_atom.html @@ -140,11 +140,11 @@

      Examples

      -
      compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 *
-
      -
      +
      +compute 1 all coord/atom 2.0
+compute 1 all coord/atom 6.0 1 2
+compute 1 all coord/atom 6.0 2*4 5*8 *
+

      Description

      @@ -162,7 +162,7 @@ atoms of all types (same as the “*” format, see below).

      The typeN keywords can be specified in one of two ways. An explicit numeric value can be used, as in the 2nd example above. Or a wild-card asterisk can be used to specify a range of atom types. This -takes the form “*” or “n” or “n” or “m*n”. If N = the number of +takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N diff --git a/doc/html/compute_damage_atom.html b/doc/html/compute_damage_atom.html index 97a0eba0d0..b27fd7c778 100644 --- a/doc/html/compute_damage_atom.html +++ b/doc/html/compute_damage_atom.html @@ -159,7 +159,7 @@ group.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values are unitlesss numbers (damage) >= 0.0.

      diff --git a/doc/html/compute_dihedral_local.html b/doc/html/compute_dihedral_local.html index 22ac63b16f..e2e289c87d 100644 --- a/doc/html/compute_dihedral_local.html +++ b/doc/html/compute_dihedral_local.html @@ -168,11 +168,11 @@ For example, dihedral output from the dump local command in a consistent way.

      Here is an example of how to do this:

      -
      compute 1 all property/local dtype datom1 datom2 datom3 datom4
-compute 2 all dihedral/local phi
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
-
      -
      +
      +compute 1 all property/local dtype datom1 datom2 datom3 datom4
+compute 2 all dihedral/local phi
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
+

      Output info:

      This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the diff --git a/doc/html/compute_erotate_asphere.html b/doc/html/compute_erotate_asphere.html index 4af35ae60a..2cfb8230ee 100644 --- a/doc/html/compute_erotate_asphere.html +++ b/doc/html/compute_erotate_asphere.html @@ -162,7 +162,7 @@ will be the same as in 3d.

      Output info:

      This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an +input. See Section 6.15 for an overview of LAMMPS output options.

      The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.

      diff --git a/doc/html/compute_erotate_rigid.html b/doc/html/compute_erotate_rigid.html index 501319d8c8..d9a1cc238c 100644 --- a/doc/html/compute_erotate_rigid.html +++ b/doc/html/compute_erotate_rigid.html @@ -160,7 +160,7 @@ calculation.

      This compute calculates a global scalar (the summed rotational energy of all the rigid bodies). This value can be used by any command that uses a global scalar value from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.

      diff --git a/doc/html/compute_erotate_sphere.html b/doc/html/compute_erotate_sphere.html index 4785bf0a12..55be55ff6e 100644 --- a/doc/html/compute_erotate_sphere.html +++ b/doc/html/compute_erotate_sphere.html @@ -157,7 +157,7 @@ as in 3d.

      Output info:

      This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an +input. See Section 6.15 for an overview of LAMMPS output options.

      The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.

      diff --git a/doc/html/compute_erotate_sphere_atom.html b/doc/html/compute_erotate_sphere_atom.html index 0ab254c224..994d45b69f 100644 --- a/doc/html/compute_erotate_sphere_atom.html +++ b/doc/html/compute_erotate_sphere_atom.html @@ -160,7 +160,7 @@ in the specified compute group or for point particles with a radius =

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in energy units.

      diff --git a/doc/html/compute_event_displace.html b/doc/html/compute_event_displace.html index e9e283a1d9..466690ac13 100644 --- a/doc/html/compute_event_displace.html +++ b/doc/html/compute_event_displace.html @@ -165,7 +165,7 @@ local atom displacements and may generate “false postives.”

      Output info:

      This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an +input. See Section 6.15 for an overview of LAMMPS output options.

      The scalar value calculated by this compute is “intensive”. The scalar value will be a 0 or 1 as explained above.

      diff --git a/doc/html/compute_improper_local.html b/doc/html/compute_improper_local.html index d44d0c1326..e676a143c3 100644 --- a/doc/html/compute_improper_local.html +++ b/doc/html/compute_improper_local.html @@ -169,11 +169,11 @@ For example, improper output from the dump local command in a consistent way.

      Here is an example of how to do this:

      -
      compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4
-compute 2 all improper/local chi
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
-
      -
      +
      +compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4
+compute 2 all improper/local chi
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
+

      Output info:

      This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the diff --git a/doc/html/compute_ke.html b/doc/html/compute_ke.html index a3000f0f0d..eced6a5024 100644 --- a/doc/html/compute_ke.html +++ b/doc/html/compute_ke.html @@ -163,7 +163,7 @@ include different degrees of freedom (translational, rotational, etc).

      Output info:

      This compute calculates a global scalar (the summed KE). This value can be used by any command that uses a global scalar value from a -compute as input. See Section_howto 15 +compute as input. See Section 6.15 for an overview of LAMMPS output options.

      The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.

      diff --git a/doc/html/compute_ke_atom.html b/doc/html/compute_ke_atom.html index ea8c40a8bb..e79a8a2399 100644 --- a/doc/html/compute_ke_atom.html +++ b/doc/html/compute_ke_atom.html @@ -153,7 +153,7 @@ specified compute group.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in energy units.

      diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html index 6a017dc79b..c829a89d0a 100644 --- a/doc/html/compute_ke_atom_eff.html +++ b/doc/html/compute_ke_atom_eff.html @@ -178,7 +178,7 @@ electrons) not in the specified compute group.

      Output info:

      This compute calculates a scalar quantity for each atom, which can be accessed by any command that uses per-atom computes as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in energy units.

      diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html index ff0e0b4e68..615cc59776 100644 --- a/doc/html/compute_ke_eff.html +++ b/doc/html/compute_ke_eff.html @@ -178,7 +178,7 @@ thermo_modify temp effTemp

      Output info:

      This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See Section_howto 15 for an +input. See Section 6.15 for an overview of LAMMPS output options.

      The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.

      diff --git a/doc/html/compute_meso_e_atom.html b/doc/html/compute_meso_e_atom.html index 21b1e95553..7fb8d1448c 100644 --- a/doc/html/compute_meso_e_atom.html +++ b/doc/html/compute_meso_e_atom.html @@ -156,7 +156,7 @@ specified compute group.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in energy units.

      diff --git a/doc/html/compute_meso_rho_atom.html b/doc/html/compute_meso_rho_atom.html index dd832b844d..ee3f4cf940 100644 --- a/doc/html/compute_meso_rho_atom.html +++ b/doc/html/compute_meso_rho_atom.html @@ -156,7 +156,7 @@ specified compute group.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in mass/volume units.

      diff --git a/doc/html/compute_meso_t_atom.html b/doc/html/compute_meso_t_atom.html index c6111acd65..bd5fa05312 100644 --- a/doc/html/compute_meso_t_atom.html +++ b/doc/html/compute_meso_t_atom.html @@ -149,7 +149,7 @@ for each atom in a group.

      The internal temperature is the ratio of internal energy over the heat capacity associated with the internal degrees of freedom of a mesoscopic particles, e.g. a Smooth-Particle Hydrodynamics particle.

      -

      T_int = E_int / C_V, int

      +

      T_int = E_int / C_V, int

      See this PDF guide to using SPH in LAMMPS.

      The value of the internal energy will be 0.0 for atoms not in the @@ -157,7 +157,7 @@ specified compute group.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in temperature units.

      diff --git a/doc/html/compute_msd_chunk.html b/doc/html/compute_msd_chunk.html index 86215724b3..2ef599ab24 100644 --- a/doc/html/compute_msd_chunk.html +++ b/doc/html/compute_msd_chunk.html @@ -213,11 +213,11 @@ correctly with chunk reference positions from the restart file.

      The simplest way to output the results of the compute com/msd calculation to a file is to use the fix ave/time command, for example:

      -
      compute cc1 all chunk/atom molecule
-compute myChunk all com/msd cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      -
      +
      +compute cc1 all chunk/atom molecule
+compute myChunk all com/msd cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+

      Output info:

      This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/compute_omega_chunk.html b/doc/html/compute_omega_chunk.html index 7abc60a788..cb2e600901 100644 --- a/doc/html/compute_omega_chunk.html +++ b/doc/html/compute_omega_chunk.html @@ -178,11 +178,11 @@ how they are set for each atom. You can reset the image flags

      The simplest way to output the results of the compute omega/chunk calculation to a file is to use the fix ave/time command, for example:

      -
      compute cc1 all chunk/atom molecule
-compute myChunk all omega/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      -
      +
      +compute cc1 all chunk/atom molecule
+compute myChunk all omega/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+

      Output info:

      This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/compute_pair_local.html b/doc/html/compute_pair_local.html index ae12f688ba..5bcc7b6e8e 100644 --- a/doc/html/compute_pair_local.html +++ b/doc/html/compute_pair_local.html @@ -206,11 +206,11 @@ For example, pair output from the dump local command in a consistent way.

      Here is an example of how to do this:

      -
      compute 1 all property/local patom1 patom2
-compute 2 all pair/local dist eng force
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3]
-
      -
      +
      +compute 1 all property/local patom1 patom2
+compute 2 all pair/local dist eng force
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3]
+

      Note

      For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 diff --git a/doc/html/compute_pe.html b/doc/html/compute_pe.html index bf60951641..6d81108da5 100644 --- a/doc/html/compute_pe.html +++ b/doc/html/compute_pe.html @@ -173,9 +173,9 @@ specified if a fix is to contribute potential energy to this command.

      A compute of this style with the ID of “thermo_pe” is created when LAMMPS starts up, as if this command were in the input script:

      -
      compute thermo_pe all pe
-
      -
      +
      +compute thermo_pe all pe
+

      See the “thermo_style” command for more details.

      Output info:

      diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html index b5de90dfdb..4dd839ca23 100644 --- a/doc/html/compute_pe_atom.html +++ b/doc/html/compute_pe_atom.html @@ -199,7 +199,7 @@ those are global contributions to the system energy.

      Output info:

      This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The per-atom vector values will be in energy units.

      diff --git a/doc/html/compute_pressure.html b/doc/html/compute_pressure.html index 1d117a4f5e..29eec73877 100644 --- a/doc/html/compute_pressure.html +++ b/doc/html/compute_pressure.html @@ -205,7 +205,7 @@ compute thermo_press all pressure thermo_temp

      Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

      @@ -215,7 +215,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

      -

      See Section_accelerate of the manual for +

      See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

      Output info:

      diff --git a/doc/html/compute_rdf.html b/doc/html/compute_rdf.html index ef1d1d8cfc..e8125b2c35 100644 --- a/doc/html/compute_rdf.html +++ b/doc/html/compute_rdf.html @@ -141,13 +141,13 @@

      Examples

      -
      compute 1 all rdf 100
-compute 1 all rdf 100 1 1
-compute 1 all rdf 100 * 3
-compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
-compute 1 fluid rdf 500 1*3 2 5 *10
-
      -
      +
      +compute 1 all rdf 100
+compute 1 all rdf 100 1 1
+compute 1 all rdf 100 * 3
+compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
+compute 1 fluid rdf 500 1*3 2 5 *10
+

      Description

      @@ -184,7 +184,7 @@ listed, then a separate histogram is generated for each

      The itypeN and jtypeN settings can be specified in one of two ways. An explicit numeric value can be used, as in the 4th example above. Or a wild-card asterisk can be used to specify a range of atom -types. This takes the form “*” or “n” or “n” or “m*n”. If N = the +types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N @@ -226,10 +226,10 @@ atoms of type jtypeN.

      The simplest way to output the results of the compute rdf calculation to a file is to use the fix ave/time command, for example:

      -
      compute myRDF all rdf 50
-fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp.rdf mode vector
-
      -
      +
      +compute myRDF all rdf 50
+fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp.rdf mode vector
+

      Output info:

      This compute calculates a global array with the number of rows = Nbins, and the number of columns = 1 + 2*Npairs, where Npairs is the @@ -238,7 +238,7 @@ coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of itypeN versus jtypeN interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

      The array values calculated by this compute are all “intensive”.

      The first column of array values will be in distance diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html index 56a155c53a..4bd950e20b 100644 --- a/doc/html/compute_reduce.html +++ b/doc/html/compute_reduce.html @@ -300,7 +300,7 @@ values are desired, this compute can be accessed by the Section_howto 15 +compute as input. See Section 6.15 for an overview of LAMMPS output options.

      All the scalar or vector values calculated by this compute are “intensive”, except when the sum or sumsq modes are used on diff --git a/doc/html/compute_slice.html b/doc/html/compute_slice.html index 427f49ee77..768d82f2cb 100644 --- a/doc/html/compute_slice.html +++ b/doc/html/compute_slice.html @@ -139,20 +139,20 @@

    • Nskip = extract every Nskip elements from input vector(s)
    • input = c_ID, c_ID[N], f_ID, f_ID[N]
    -
    c_ID = global vector calculated by a compute with ID
-c_ID[I] = Ith column of global array calculated by a compute with ID
-f_ID = global vector calculated by a fix with ID
-f_ID[I] = Ith column of global array calculated by a fix with ID
-v_name = vector calculated by an vector-style variable with name
-
    -
    +
    +c_ID = global vector calculated by a compute with ID
+c_ID[I] = Ith column of global array calculated by a compute with ID
+f_ID = global vector calculated by a fix with ID
+f_ID[I] = Ith column of global array calculated by a fix with ID
+v_name = vector calculated by an vector-style variable with name
+

    Examples

    -
    compute 1 all slice 1 100 10 c_msdmol[4]
-compute 1 all slice 301 400 1 c_msdmol[4] v_myVec
-
    -
    +
    +compute 1 all slice 1 100 10 c_msdmol[4]
+compute 1 all slice 301 400 1 c_msdmol[4] v_myVec
+

    Description

    @@ -172,14 +172,14 @@ vector, which is typically shorter than the input vector.

    vector. Each listed input must be a global vector or column of a global array calculated by another compute or fix.

    -

    If an input value begins with “c_”, a compute ID must follow which has +

    If an input value begins with “c_”, a compute ID must follow which has been previously defined in the input script and which generates a global vector or array. See the individual compute doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script and which generates a global vector or array. See the individual fix doc page for details. Note that some fixes only produce their values on certain @@ -188,7 +188,7 @@ the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and add them to LAMMPS.

    -

    If an input value begins with “v_”, a variable name must follow which +

    If an input value begins with “v_”, a variable name must follow which has been previously defined in the input script. Only vector-style variables can be referenced. See the variable command for details. Note that variables of style vector define a formula diff --git a/doc/html/compute_smd_contact_radius.html b/doc/html/compute_smd_contact_radius.html index 0e19b35fa0..547aef952b 100644 --- a/doc/html/compute_smd_contact_radius.html +++ b/doc/html/compute_smd_contact_radius.html @@ -156,7 +156,7 @@ specified compute group.

    Output info:

    This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. See -Section_howto 15 for an overview of +Section 6.15 for an overview of LAMMPS output options.

    The per-particle vector values will be in distance units.

    diff --git a/doc/html/compute_smd_triangle_mesh_vertices.html b/doc/html/compute_smd_triangle_mesh_vertices.html index 2b4077d564..374f7f4135 100644 --- a/doc/html/compute_smd_triangle_mesh_vertices.html +++ b/doc/html/compute_smd_triangle_mesh_vertices.html @@ -145,7 +145,7 @@

    Description

    Define a computation that returns the coordinates of the vertices -corresponding to the triangle-elements of a mesh created by the `fix smd/wall_surface <ls_>`_.

    +corresponding to the triangle-elements of a mesh created by the `fix smd/wall\_surface <ls_>`_.

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    Output info:

    @@ -157,7 +157,7 @@ for an overview of LAMMPS output options.

    (x3/y3/z3) corresponding to the first, second, and third vertex of each triangle.

    It is only meaningful to use this compute for a group of particles -which is created via the `fix smd/wall_surface <ls_>`_ command.

    +which is created via the `fix smd/wall\_surface <ls_>`_ command.

    The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the smd/wall_surace mesh for visualization purposes.

    diff --git a/doc/html/compute_smd_ulsph_num_neighs.html b/doc/html/compute_smd_ulsph_num_neighs.html index 425c4b81e5..484d59499b 100644 --- a/doc/html/compute_smd_ulsph_num_neighs.html +++ b/doc/html/compute_smd_ulsph_num_neighs.html @@ -152,7 +152,7 @@ Mach Dynamics in LAMMPS.

    Output info:

    This compute returns a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See Section_howto 15 for an overview of +See Section 6.15 for an overview of LAMMPS output options.

    The per-particle values will be given dimentionless, see units.

    diff --git a/doc/html/compute_smd_ulsph_strain.html b/doc/html/compute_smd_ulsph_strain.html index 86f90ceb6a..1bc908bf45 100644 --- a/doc/html/compute_smd_ulsph_strain.html +++ b/doc/html/compute_smd_ulsph_strain.html @@ -151,7 +151,7 @@ Mach Dynamics in LAMMPS.

    Output info:

    This compute calculates a per-particle tensor, which can be accessed by any command that uses per-particle values from a compute as input. -See Section_howto 15 for an overview of +See Section 6.15 for an overview of LAMMPS output options.

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components of the symmetric strain rate tensor.

    diff --git a/doc/html/compute_temp.html b/doc/html/compute_temp.html index 59de9e2a12..ee35b3a7e9 100644 --- a/doc/html/compute_temp.html +++ b/doc/html/compute_temp.html @@ -172,9 +172,9 @@ needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    A compute of this style with the ID of “thermo_temp” is created when LAMMPS starts up, as if this command were in the input script:

    -
    compute thermo_temp all temp
-
    -
    +
    +compute thermo_temp all temp
+

    See the “thermo_style” command for more details.

    See this howto section of the manual for a discussion of different ways to compute temperature and perform @@ -183,7 +183,7 @@ thermostatting.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Output info:

    diff --git a/doc/html/compute_temp_chunk.html b/doc/html/compute_temp_chunk.html index 3d0d3eeb6d..88aba84049 100644 --- a/doc/html/compute_temp_chunk.html +++ b/doc/html/compute_temp_chunk.html @@ -254,11 +254,11 @@ IDs.

    The simplest way to output the per-chunk results of the compute temp/chunk calculation to a file is to use the fix ave/time command, for example:

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all temp/chunk cc1 temp
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
-
    -
    +
    +compute cc1 all chunk/atom molecule
+compute myChunk all temp/chunk cc1 temp
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+

    The keyword/value option pairs are used in the following ways.

    The com keyword can be used with a value of yes to subtract the diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html index 81927952be..cfa909d7f1 100644 --- a/doc/html/compute_temp_cs.html +++ b/doc/html/compute_temp_cs.html @@ -151,7 +151,7 @@ compute core_shells all temp/cs cores shells on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of (Mitchell and Finchham). See -Section_howto 25 of the manual for an +Section 6.25 of the manual for an overview of the model as implemented in LAMMPS. Specifically, this compute enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of diff --git a/doc/html/compute_temp_partial.html b/doc/html/compute_temp_partial.html index 33460f2218..8700d71d44 100644 --- a/doc/html/compute_temp_partial.html +++ b/doc/html/compute_temp_partial.html @@ -185,7 +185,7 @@ thermostatting.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -195,7 +195,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Output info:

    diff --git a/doc/html/compute_torque_chunk.html b/doc/html/compute_torque_chunk.html index 924030c28b..650ce622aa 100644 --- a/doc/html/compute_torque_chunk.html +++ b/doc/html/compute_torque_chunk.html @@ -177,17 +177,17 @@ how they are set for each atom. You can reset the image flags

    The simplest way to output the results of the compute torque/chunk calculation to a file is to use the fix ave/time command, for example:

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all torque/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
    -
    +
    +compute cc1 all chunk/atom molecule
+compute myChunk all torque/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+

    Output info:

    This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 3 for the 3 xyz components of the torque for each chunk. These values can be accessed by any command that uses global array values from a -compute as input. See Section_howto 15 +compute as input. See Section 6.15 for an overview of LAMMPS output options.

    The array values are “intensive”. The array values will be in force-distance units.

    diff --git a/doc/html/compute_vacf.html b/doc/html/compute_vacf.html index 713789bce4..d9f174a294 100644 --- a/doc/html/compute_vacf.html +++ b/doc/html/compute_vacf.html @@ -159,12 +159,12 @@ averaged over atoms in the group.

    The integral of the VACF versus time is proportional to the diffusion coefficient of the diffusing atoms. This can be computed in the following manner, using the variable trap() function:

    -
    compute         2 all vacf
-fix             5 all vector 1 c_2[4]
-variable        diff equal dt*trap(f_5)
-thermo_style    custom step v_diff
-
    -
    +
    +compute         2 all vacf
+fix             5 all vector 1 c_2[4]
+variable        diff equal dt*trap(f_5)
+thermo_style    custom step v_diff
+

    Note

    If you want the quantities calculated by this compute to be diff --git a/doc/html/compute_vcm_chunk.html b/doc/html/compute_vcm_chunk.html index 99ed48375e..c8574fa37f 100644 --- a/doc/html/compute_vcm_chunk.html +++ b/doc/html/compute_vcm_chunk.html @@ -167,11 +167,11 @@ non-zero chunk IDs.

    The simplest way to output the results of the compute vcm/chunk calculation to a file is to use the fix ave/time command, for example:

    -
    compute cc1 all chunk/atom molecule
-compute myChunk all vcm/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
    -
    +
    +compute cc1 all chunk/atom molecule
+compute myChunk all vcm/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+

    Output info:

    This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = diff --git a/doc/html/create_bonds.html b/doc/html/create_bonds.html index 3873a631f5..fe90e2311e 100644 --- a/doc/html/create_bonds.html +++ b/doc/html/create_bonds.html @@ -128,9 +128,9 @@

    create_bonds command

    Syntax

    -
    create_bonds group-ID group2-ID btype rmin rmax
-
    -
    +
    +create_bonds group-ID group2-ID btype rmin rmax
+
    • group-ID = ID of first group
    • group2-ID = ID of second group, bonds will be between atoms in the 2 groups
      • @@ -141,10 +141,10 @@

    Examples

    -
    create_bonds all all 1 1.0 1.2
-create_bonds surf solvent 3 2.0 2.4
-
    -
    +
    +create_bonds all all 1 1.0 1.2
+create_bonds surf solvent 3 2.0 2.4
+

    Description

    diff --git a/doc/html/create_box.html b/doc/html/create_box.html index 27a19a1021..ee2d222808 100644 --- a/doc/html/create_box.html +++ b/doc/html/create_box.html @@ -128,9 +128,9 @@

    create_box command

    Syntax

    -
    create_box N region-ID keyword value ...
-
    -
    +
    +create_box N region-ID keyword value ...
+
    • N = # of atom types to use in this simulation
    • region-ID = ID of region to use as simulation domain
      • @@ -151,10 +151,10 @@

    Examples

    -
    create_box 2 mybox
-create_box 2 mybox bond/types 2 extra/bond/per/atom 1
-
    -
    +
    +create_box 2 mybox
+create_box 2 mybox bond/types 2 extra/bond/per/atom 1
+

    Description

    @@ -191,7 +191,7 @@ geometrically equivalent. If you wish to define a box with tilt factors that exceed these limits, you can use the box tilt command, with a setting of large; a setting of small is the default.

    -

    See Section_howto 12 of the doc pages +

    See Section 6.12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.

    diff --git a/doc/html/delete_atoms.html b/doc/html/delete_atoms.html index 63d2667cf6..cb151917cc 100644 --- a/doc/html/delete_atoms.html +++ b/doc/html/delete_atoms.html @@ -128,9 +128,9 @@

    delete_atoms command

    Syntax

    -
    delete_atoms style args keyword value ...
-
    -
    +
    +delete_atoms style args keyword value ...
+
    • style = group or region or overlap or porosity
    @@ -158,13 +158,13 @@

    Examples

    -
    delete_atoms group edge
-delete_atoms region sphere compress no
-delete_atoms overlap 0.3 all all
-delete_atoms overlap 0.5 solvent colloid
-delete_atoms porosity cube 0.1 482793 bond yes
-
    -
    +
    +delete_atoms group edge
+delete_atoms region sphere compress no
+delete_atoms overlap 0.3 all all
+delete_atoms overlap 0.5 solvent colloid
+delete_atoms porosity cube 0.1 482793 bond yes
+

    Description

    diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html index 9794ca050e..e4ee982fa5 100644 --- a/doc/html/dihedral_charmm.html +++ b/doc/html/dihedral_charmm.html @@ -207,7 +207,7 @@ non-bonded interactions.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -217,7 +217,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html index e9556733e2..c25b90747a 100644 --- a/doc/html/dihedral_class2.html +++ b/doc/html/dihedral_class2.html @@ -255,7 +255,7 @@ listed under a “BondBond13 Coeffs” heading and you must leave out th

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -265,7 +265,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_coeff.html b/doc/html/dihedral_coeff.html index c098bed43a..1c150bd7af 100644 --- a/doc/html/dihedral_coeff.html +++ b/doc/html/dihedral_coeff.html @@ -128,9 +128,9 @@

    dihedral_coeff command

    Syntax

    -
    dihedral_coeff N args
-
    -
    +
    +dihedral_coeff N args
+
    • N = dihedral type (see asterisk form below)
    • args = coefficients for one or more dihedral types
      • @@ -138,11 +138,11 @@

    Examples

    -
    dihedral_coeff 1 80.0 1 3
-dihedral_coeff * 80.0 1 3 0.5
-dihedral_coeff 2* 80.0 1 3 0.5
-
    -
    +
    +dihedral_coeff 1 80.0 1 3
+dihedral_coeff * 80.0 1 3 0.5
+dihedral_coeff 2* 80.0 1 3 0.5
+

    Description

    @@ -154,7 +154,7 @@ Dihedral coefficients can also be set in the data file read by the

    N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple dihedral types. This takes the -form “*” or “n” or “n” or “m*n”. If N = the number of dihedral types, +form “*” or “*n” or “n*” or “m*n”. If N = the number of dihedral types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk @@ -162,10 +162,10 @@ means all types from m to n (inclusive).

    Note that using a dihedral_coeff command can override a previous setting for the same dihedral type. For example, these commands set the coeffs for all dihedral types, then overwrite the coeffs for just dihedral type 2:

    -
    dihedral_coeff * 80.0 1 3
-dihedral_coeff 2 200.0 1 3
-
    -
    +
    +dihedral_coeff * 80.0 1 3
+dihedral_coeff 2 200.0 1 3
+

    A line in a data file that specifies dihedral coefficients uses the exact same format as the arguments of the dihedral_coeff command in an input script, except that wild-card asterisks should not be used since diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html index 1cc73331be..c8af55fabc 100644 --- a/doc/html/dihedral_cosine_shift_exp.html +++ b/doc/html/dihedral_cosine_shift_exp.html @@ -170,7 +170,7 @@ commands:

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -180,7 +180,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_fourier.html b/doc/html/dihedral_fourier.html index 1470ba7346..14164b6795 100644 --- a/doc/html/dihedral_fourier.html +++ b/doc/html/dihedral_fourier.html @@ -155,7 +155,7 @@ or read
  • K1 (energy)
  • n1 (integer >= 0)
  • d1 (degrees)
    • -
  • +
  • [...]
  • Km (energy)
  • nm (integer >= 0)
  • dm (degrees)
    • @@ -164,7 +164,7 @@ or     read

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -174,7 +174,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_harmonic.html b/doc/html/dihedral_harmonic.html index 2a8ed8a6f7..384c7777ca 100644 --- a/doc/html/dihedral_harmonic.html +++ b/doc/html/dihedral_harmonic.html @@ -176,7 +176,7 @@ in some force fields trans = 0 degrees.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -186,7 +186,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_helix.html b/doc/html/dihedral_helix.html index b8d5653099..ed824fdf70 100644 --- a/doc/html/dihedral_helix.html +++ b/doc/html/dihedral_helix.html @@ -166,7 +166,7 @@ or read

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -176,7 +176,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_hybrid.html b/doc/html/dihedral_hybrid.html index 9b495bb81f..dc9383e3f2 100644 --- a/doc/html/dihedral_hybrid.html +++ b/doc/html/dihedral_hybrid.html @@ -128,20 +128,20 @@

    dihedral_style hybrid command

    Syntax

    -
    dihedral_style hybrid style1 style2 ...
-
    -
    +
    +dihedral_style hybrid style1 style2 ...
+
    • style1,style2 = list of one or more dihedral styles

    Examples

    -
    dihedral_style hybrid harmonic helix
-dihedral_coeff 1 harmonic 6.0 1 3
-dihedral_coeff 2* helix 10 10 10
-
    -
    +
    +dihedral_style hybrid harmonic helix
+dihedral_coeff 1 harmonic 6.0 1 3
+dihedral_coeff 2* helix 10 10 10
+

    Description

    diff --git a/doc/html/dihedral_multi_harmonic.html b/doc/html/dihedral_multi_harmonic.html index ec192b670e..fcb4157be5 100644 --- a/doc/html/dihedral_multi_harmonic.html +++ b/doc/html/dihedral_multi_harmonic.html @@ -161,7 +161,7 @@ or read

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -171,7 +171,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_nharmonic.html b/doc/html/dihedral_nharmonic.html index eb59b45627..e860b94d5e 100644 --- a/doc/html/dihedral_nharmonic.html +++ b/doc/html/dihedral_nharmonic.html @@ -161,7 +161,7 @@ or read

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -171,7 +171,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_none.html b/doc/html/dihedral_none.html index 84f445b4da..c30711154a 100644 --- a/doc/html/dihedral_none.html +++ b/doc/html/dihedral_none.html @@ -128,15 +128,15 @@

    dihedral_style none command

    Syntax

    -
    dihedral_style none
-
    -
    +
    +dihedral_style none
+

    Examples

    -
    dihedral_style none
-
    -
    +
    +dihedral_style none
+

    Description

    diff --git a/doc/html/dihedral_opls.html b/doc/html/dihedral_opls.html index fd7c9f1e4f..3aaf233587 100644 --- a/doc/html/dihedral_opls.html +++ b/doc/html/dihedral_opls.html @@ -171,7 +171,7 @@ or read

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -181,7 +181,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_quadratic.html b/doc/html/dihedral_quadratic.html index 3b490ae5d6..f95da06830 100644 --- a/doc/html/dihedral_quadratic.html +++ b/doc/html/dihedral_quadratic.html @@ -161,7 +161,7 @@ commands:

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -171,7 +171,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_spherical.html b/doc/html/dihedral_spherical.html index 3e38d2d8ca..4cb9e6f2f4 100644 --- a/doc/html/dihedral_spherical.html +++ b/doc/html/dihedral_spherical.html @@ -178,7 +178,7 @@ the Dihedral Coeffs section of a data file file read by the
  • M1 (typically an integer)
  • c1 (degrees, typically 0.0 or 90.0)
  • w1 (typically 0.0 or 1.0)
    • -
  • +
  • [...]
  • Cn (energy)
  • Kn (typically an integer)
  • an (degrees)
    • diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html index fe30f6ab11..9981d281c0 100644 --- a/doc/html/dihedral_table.html +++ b/doc/html/dihedral_table.html @@ -285,7 +285,7 @@ that matches the specified keyword.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -295,7 +295,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/dihedral_zero.html b/doc/html/dihedral_zero.html index 99891fae28..9ff190c609 100644 --- a/doc/html/dihedral_zero.html +++ b/doc/html/dihedral_zero.html @@ -134,11 +134,11 @@ dihedral_style zero nocoeff

    Examples

    -
    dihedral_style zero
-dihedral_style zero nocoeff
-dihedral_coeff *
-
    -
    +
    +dihedral_style zero
+dihedral_style zero nocoeff
+dihedral_coeff *
+

    Description

    diff --git a/doc/html/dimension.html b/doc/html/dimension.html index bc1cb2efb1..c46aeb1c0b 100644 --- a/doc/html/dimension.html +++ b/doc/html/dimension.html @@ -148,7 +148,7 @@ simulations. To run a 2d simulation, this command should be used prior to setting up a simulation box via the create_box or read_data commands. Restart files also store this setting.

    -

    See the discussion in Section_howto for +

    See the discussion in Section 6 for additional instructions on how to run 2d simulations.

    Note

    diff --git a/doc/html/displace_atoms.html b/doc/html/displace_atoms.html index 9208e97052..968c7345cd 100644 --- a/doc/html/displace_atoms.html +++ b/doc/html/displace_atoms.html @@ -128,9 +128,9 @@

    displace_atoms command

    Syntax

    -
    displace_atoms group-ID style args keyword value ...
-
    -
    +
    +displace_atoms group-ID style args keyword value ...
+
    • group-ID = ID of group of atoms to displace
    • style = move or ramp or random or rotate
      • @@ -162,10 +162,10 @@ keyword = units

    Examples

    -
    displace_atoms top move 0 -5 0 units box
-displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
-
    -
    +
    +displace_atoms top move 0 -5 0 units box
+displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
+

    Description

    diff --git a/doc/html/dump.html b/doc/html/dump.html index d76697dbba..5a73f86c08 100644 --- a/doc/html/dump.html +++ b/doc/html/dump.html @@ -705,7 +705,7 @@ dump file.

    The d_name and i_name attributes allow to output custom per atom floating point or integer properties that are managed by fix property/atom.

    -

    See Section_modify of the manual for information +

    See Section 10 of the manual for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files.

    diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html index b77890476a..307a25ddff 100644 --- a/doc/html/dump_custom_vtk.html +++ b/doc/html/dump_custom_vtk.html @@ -392,7 +392,7 @@ attributes, per-atom atom attributes, thermodynamic keywords, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file.

    -

    See Section_modify of the manual for information +

    See Section 10 of the manual for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files.

    diff --git a/doc/html/dump_h5md.html b/doc/html/dump_h5md.html index 5980b4368d..e883ea5695 100644 --- a/doc/html/dump_h5md.html +++ b/doc/html/dump_h5md.html @@ -156,23 +156,23 @@ author value = quoted string may specify a sub-interval to write the data only every N_element iterations of the dump (i.e. every N*N_element time steps). This is specified by the option

    -
    every N_element
-
    -
    +
    +every N_element
+

    that follows directly the element declaration.

    Examples

    -
    dump h5md1 all h5md 100 dump_h5md.h5 position image
-dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
-dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
-
    -
    +
    +dump h5md1 all h5md 100 dump_h5md.h5 position image
+dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10
+dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe"
+

    Description

    Dump a snapshot of atom coordinates every N timesteps in the -HDF5 based H5MD file format (de Buyl). +HDF5 based H5MD file format (de Buyl). HDF5 files are binary, portable and self-describing. This dump style will write only one file, on the root node.

    Several dumps may write to the same file, by using file_from and @@ -201,10 +201,10 @@ using the file_from keyword.

    Typically, the species data is fixed. The following two commands store the position data every 100 timesteps, with the image data, and store once the species data in the same file.

    -
    dump h5md1 all h5md 100 dump.h5 position image
-write_dump all h5md dump.h5 file_from h5md1 species
-
    -
    +
    +dump h5md1 all h5md 100 dump.h5 position image
+write_dump all h5md dump.h5 file_from h5md1 species
+
    @@ -217,7 +217,7 @@ a limitation of the present dump h5md command and not of H5MD itself.

    enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. It also requires (i) building the ch5md library provided with LAMMPS (See the Making LAMMPS section for more info.) and -(ii) having the HDF5 library installed (C bindings are +(ii) having the HDF5 library installed (C bindings are sufficient) on your system. The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library.

    diff --git a/doc/html/dump_image.html b/doc/html/dump_image.html index 356893b5d4..db7d5eb586 100644 --- a/doc/html/dump_image.html +++ b/doc/html/dump_image.html @@ -690,7 +690,7 @@ additional libraries, purchasing a license, or may not be supported.
    -

    See Section_modify of the manual for information +

    See Section 10 of the manual for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files.

    diff --git a/doc/html/dump_molfile.html b/doc/html/dump_molfile.html index 7986ce9562..60ee56baf7 100644 --- a/doc/html/dump_molfile.html +++ b/doc/html/dump_molfile.html @@ -143,11 +143,11 @@

    Examples

    -
    dump mf1 all molfile 10 melt1.xml hoomd
-dump mf2 all molfile 10 melt2-*.pdb pdb .
-dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
-
    -
    +
    +dump mf1 all molfile 10 melt1.xml hoomd
+dump mf2 all molfile 10 melt2-*.pdb pdb .
+dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile
+

    Description

    diff --git a/doc/html/fix_adapt.html b/doc/html/fix_adapt.html index 2f5eece4a1..32babbf737 100644 --- a/doc/html/fix_adapt.html +++ b/doc/html/fix_adapt.html @@ -165,12 +165,12 @@

    Examples

    -
    fix 1 all adapt 1 pair soft a 1 1 v_prefactor
-fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
-fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt 10 atom diameter v_size
-
    -
    +
    +fix 1 all adapt 1 pair soft a 1 1 v_prefactor
+fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
+fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+fix 1 all adapt 10 atom diameter v_size
+

    Description

    @@ -224,9 +224,9 @@ pages for individual pair styles and their energy formulas for the meaning of these parameters:

    ---+++ @@ -315,7 +315,7 @@ each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values.

    A wild-card asterisk can be used in place of or in conjunction with the I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form “*” or “n” or “n” or “m*n”. If N = the +types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N @@ -341,10 +341,10 @@ details.

    For example, these commands would change the prefactor coefficient of the pair_style soft potential from 10.0 to 30.0 in a linear fashion over the course of a simulation:

    -
    variable prefactor equal ramp(10,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor
-
    -
    +
    +variable prefactor equal ramp(10,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+

    The kspace keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is @@ -380,14 +380,12 @@ constant).

    For example, these commands would shrink the diameter of all granular particles in the “center” group from 1.0 to 0.1 in a linear fashion over the course of a 1000-step simulation:

    -
    variable size equal ramp(1.0,0.1)
-fix 1 center adapt 10 atom diameter v_size
-
    -
    - +
    +variable size equal ramp(1.0,0.1)
+fix 1 center adapt 10 atom diameter v_size
+
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_addforce.html b/doc/html/fix_addforce.html index 2e773e8d92..0d70f117d5 100644 --- a/doc/html/fix_addforce.html +++ b/doc/html/fix_addforce.html @@ -154,11 +154,11 @@

    Examples

    -
    fix kick flow addforce 1.0 0.0 0.0
-fix kick flow addforce 1.0 0.0 v_oscillate
-fix ff boundary addforce 0.0 0.0 v_push energy v_espace
-
    -
    +
    +fix kick flow addforce 1.0 0.0 0.0
+fix kick flow addforce 1.0 0.0 v_oscillate
+fix ff boundary addforce 0.0 0.0 v_push energy v_espace
+

    Description

    @@ -221,7 +221,7 @@ converge properly.

    Styles with a suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, @@ -230,12 +230,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files.

    The fix_modify energy option is supported by this fix to add the potential “energy” inferred by the added force to the diff --git a/doc/html/fix_append_atoms.html b/doc/html/fix_append_atoms.html index d53243c00f..c15d2330aa 100644 --- a/doc/html/fix_append_atoms.html +++ b/doc/html/fix_append_atoms.html @@ -197,10 +197,8 @@ A box value selects standard distance units as defined by the A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_aveforce.html b/doc/html/fix_aveforce.html index b5d312fdc6..dc0690a91d 100644 --- a/doc/html/fix_aveforce.html +++ b/doc/html/fix_aveforce.html @@ -150,11 +150,11 @@

    Examples

    -
    fix pressdown topwall aveforce 0.0 -1.0 0.0
-fix 2 bottomwall aveforce NULL -1.0 0.0 region top
-fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
-
    -
    +
    +fix pressdown topwall aveforce 0.0 -1.0 0.0
+fix 2 bottomwall aveforce NULL -1.0 0.0 region top
+fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
+

    Description

    @@ -187,7 +187,7 @@ to it.

    Styles with a suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, @@ -196,12 +196,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files.

    The fix_modify respa option is supported by this fix. This allows to set at which level of the r-RESPA diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html index d23425a85b..9bf14204bc 100644 --- a/doc/html/fix_deform.html +++ b/doc/html/fix_deform.html @@ -621,7 +621,7 @@ command if you want to include lattice spacings in a variable formula.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -631,7 +631,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options diff --git a/doc/html/fix_dt_reset.html b/doc/html/fix_dt_reset.html index 9d7eaee03a..a6e011a7ac 100644 --- a/doc/html/fix_dt_reset.html +++ b/doc/html/fix_dt_reset.html @@ -182,9 +182,7 @@ outer loop (largest) timestep, which is the same timestep that the

    Note that the cumulative simulation time (in time units), which accounts for changes in the timestep size as a simulation proceeds, can be accessed by the thermo_style time keyword.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix computes a global scalar which can be accessed by various diff --git a/doc/html/fix_enforce2d.html b/doc/html/fix_enforce2d.html index 3b70700e85..2790632437 100644 --- a/doc/html/fix_enforce2d.html +++ b/doc/html/fix_enforce2d.html @@ -151,7 +151,7 @@ not move from their initial z coordinate.

    Styles with a suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, @@ -160,12 +160,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_evaporate.html b/doc/html/fix_evaporate.html index 2f9d6f8aba..929f36c037 100644 --- a/doc/html/fix_evaporate.html +++ b/doc/html/fix_evaporate.html @@ -187,9 +187,7 @@ count is changing due to evaporation, you typically should use the compute_modify dynamic yes command for the temperature compute you are using.

    - -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix computes a global scalar, which can be accessed by various diff --git a/doc/html/fix_flow_gauss.html b/doc/html/fix_flow_gauss.html index ca10c2d38d..7c5defac59 100644 --- a/doc/html/fix_flow_gauss.html +++ b/doc/html/fix_flow_gauss.html @@ -219,10 +219,8 @@ work on the system must have fix_modify energy yes set as well. This includes thermostat fixes and any constraints that hold the positions of wall atoms fixed, such as fix spring/self.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix 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.

    No information about this fix is written to binary restart files.

    diff --git a/doc/html/fix_freeze.html b/doc/html/fix_freeze.html index 0d285a3709..36a0b3c6fa 100644 --- a/doc/html/fix_freeze.html +++ b/doc/html/fix_freeze.html @@ -155,7 +155,7 @@ using f

    Styles with a suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, @@ -164,12 +164,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix computes a global 3-vector of forces, which can be accessed diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html index f10e0f3416..84a652448b 100644 --- a/doc/html/fix_gravity.html +++ b/doc/html/fix_gravity.html @@ -208,7 +208,7 @@ field.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -218,7 +218,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_indent.html b/doc/html/fix_indent.html index 366694bd8a..92dafa1af5 100644 --- a/doc/html/fix_indent.html +++ b/doc/html/fix_indent.html @@ -163,11 +163,11 @@

    Examples

    -
    fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
-fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
-fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
-
    -
    +
    +fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
+fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
+fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box
+

    Description

    @@ -179,9 +179,9 @@ constraining wall around a simulation; see the discussion of the

    The indenter can either be spherical or cylindrical or planar. You must set one of those 3 keywords.

    A spherical indenter exerts a force of magnitude

    -
    F(r) = - K (r - R)^2
-
    -
    +
    +F(r) = - K (r - R)^2
+

    on each atom where K is the specified force constant, r is the distance from the atom to the center of the indenter, and R is the radius of the indenter. The force is repulsive and F(r) = 0 for r > @@ -226,23 +226,23 @@ fashion. For the latter, see the start and stop keywords of t then this variable definition will keep it’s center at a relative position in the simulation box, 1/4 of the way from the left edge to the right edge, even if the box size changes:

    -
    variable x equal "xlo + 0.25*lx"
-
    -
    +
    +variable x equal "xlo + 0.25*lx"
+

    Similarly, either of these variable definitions will move the indenter from an initial position at 2.5 at a constant velocity of 5:

    -
    variable x equal "2.5 + 5*elaplong*dt"
-variable x equal vdisplace(2.5,5)
-
    -
    +
    +variable x equal "2.5 + 5*elaplong*dt"
+variable x equal vdisplace(2.5,5)
+

    If a spherical indenter’s radius is specified as v_r, then these variable definitions will grow the size of the indenter at a specfied rate.

    -
    variable r0 equal 0.0
-variable rate equal 1.0
-variable r equal "v_r0 + step*dt*v_rate"
-
    -
    +
    +variable r0 equal 0.0
+variable rate equal 1.0
+variable r equal "v_r0 + step*dt*v_rate"
+

    If the side keyword is specified as out, which is the default, then particles outside the indenter are pushded away from its outer surface, as described above. This only applies to spherical or @@ -275,9 +275,7 @@ contains xlat, ylat, zlat keywords of the fix 1 all indent $k sphere ...

    - -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files.

    The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and the indenter to diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html index bf67a0e983..b9c5e56f09 100644 --- a/doc/html/fix_langevin.html +++ b/doc/html/fix_langevin.html @@ -363,7 +363,7 @@ generates an average temperature of 220 K, instead of 300 K.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -373,7 +373,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_manifoldforce.html b/doc/html/fix_manifoldforce.html index bba7854a61..fa64343002 100644 --- a/doc/html/fix_manifoldforce.html +++ b/doc/html/fix_manifoldforce.html @@ -147,10 +147,8 @@ This can be used in combination with minimize to remove overlap between particles while keeping them (roughly) constrained to the given manifold, e.g. to set up a run with fix nve/manifold/rattle. I have found that only hftn and quickmin with a very small time step perform adequately though.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_meso.html b/doc/html/fix_meso.html index a3727a2590..0ad7f8f622 100644 --- a/doc/html/fix_meso.html +++ b/doc/html/fix_meso.html @@ -150,9 +150,7 @@ needed to time-integrate mesoscopic systems where particles carry internal variables such as SPH or DPDE.

    See this PDF guide to using SPH in LAMMPS.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_meso_stationary.html b/doc/html/fix_meso_stationary.html index 42106fb5c2..b4fb2d708c 100644 --- a/doc/html/fix_meso_stationary.html +++ b/doc/html/fix_meso_stationary.html @@ -151,9 +151,7 @@ fixed boundary particles which constrain a fluid to a given region in space.

    See this PDF guide to using SPH in LAMMPS.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_modify.html b/doc/html/fix_modify.html index 7e3b41240e..2af8e6a5be 100644 --- a/doc/html/fix_modify.html +++ b/doc/html/fix_modify.html @@ -128,9 +128,9 @@

    fix_modify command

    Syntax

    -
    fix_modify fix-ID keyword value ...
-
    -
    +
    +fix_modify fix-ID keyword value ...
+
    • fix-ID = ID of the fix to modify
    • one or more keyword/value pairs may be appended
      • @@ -145,11 +145,11 @@

    Examples

    -
    fix_modify 3 temp myTemp press myPress
-fix_modify 1 energy yes
-fix_modify tether respa 2
-
    -
    +
    +fix_modify 3 temp myTemp press myPress
+fix_modify 1 energy yes
+fix_modify tether respa 2
+

    Description

    diff --git a/doc/html/fix_momentum.html b/doc/html/fix_momentum.html index 8329e21764..c5388609c5 100644 --- a/doc/html/fix_momentum.html +++ b/doc/html/fix_momentum.html @@ -175,9 +175,7 @@ thermostatting).

    of atoms by rescaling the velocities after the momentum was removed.

    Note that the velocity command can be used to create initial velocities with zero aggregate linear and/or angular momentum.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html index 1e50f393e0..77ce3e40aa 100644 --- a/doc/html/fix_neb.html +++ b/doc/html/fix_neb.html @@ -149,7 +149,7 @@ simulation run via the neb command to perform a nudged elastic band (NEB) calculation for transition state finding. Hi-level explanations of NEB are given with the neb command and in -Section_howto 5 of the manual. The fix +Section 6.5 of the manual. The fix neb command must be used with the “neb” command to define how inter-replica forces are computed.

    Only the N atoms in the fix group experience inter-replica forces. diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index 8cbee0b46f..5b4e907f36 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -594,7 +594,7 @@ the various ways to do this.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -604,7 +604,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html index 2c2d1a4d0a..f32f344a7d 100644 --- a/doc/html/fix_nph_asphere.html +++ b/doc/html/fix_nph_asphere.html @@ -195,7 +195,7 @@ It also means that changing attributes of thermo_temp or

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -205,7 +205,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart diff --git a/doc/html/fix_nph_body.html b/doc/html/fix_nph_body.html index 891af950d5..314d162346 100644 --- a/doc/html/fix_nph_body.html +++ b/doc/html/fix_nph_body.html @@ -172,10 +172,10 @@ unchanged and controlling the pressure of a surrounding fluid.

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp/body” and “pressure”, as if these commands had been issued:

    -
    compute fix-ID_temp all temp/body
-compute fix-ID_press all pressure fix-ID_temp
-
    -
    +
    +compute fix-ID_temp all temp/body
+compute fix-ID_press all pressure fix-ID_temp
+

    See the compute temp/body and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” @@ -192,7 +192,7 @@ It also means that changing attributes of thermo_temp or

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -202,11 +202,9 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html index ec7a15a0cd..ce7e1a82fc 100644 --- a/doc/html/fix_nph_sphere.html +++ b/doc/html/fix_nph_sphere.html @@ -195,7 +195,7 @@ It also means that changing attributes of thermo_temp or

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -205,7 +205,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html index 85dd234fe3..4297f3c953 100644 --- a/doc/html/fix_nphug.html +++ b/doc/html/fix_nphug.html @@ -254,7 +254,7 @@ It also means that changing attributes of thermo_temp or

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -264,7 +264,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html index 2216a34678..f0514cc211 100644 --- a/doc/html/fix_npt_asphere.html +++ b/doc/html/fix_npt_asphere.html @@ -215,7 +215,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -225,7 +225,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat and barostat diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html index b037898463..b5b4b2c806 100644 --- a/doc/html/fix_npt_body.html +++ b/doc/html/fix_npt_body.html @@ -212,7 +212,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -222,7 +222,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat and barostat diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html index f05e786221..6e17faf4a1 100644 --- a/doc/html/fix_npt_sphere.html +++ b/doc/html/fix_npt_sphere.html @@ -214,7 +214,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -224,7 +224,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat and barostat diff --git a/doc/html/fix_nve.html b/doc/html/fix_nve.html index bda99e1820..049b4aea64 100644 --- a/doc/html/fix_nve.html +++ b/doc/html/fix_nve.html @@ -161,7 +161,7 @@ ensemble.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -171,12 +171,10 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html index 88dbabd521..76b01445dc 100644 --- a/doc/html/fix_nve_asphere.html +++ b/doc/html/fix_nve_asphere.html @@ -163,7 +163,7 @@ This fix is not invoked during Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -173,7 +173,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/fix_nve_eff.html b/doc/html/fix_nve_eff.html index d7e486fe39..cb8c7c772f 100644 --- a/doc/html/fix_nve_eff.html +++ b/doc/html/fix_nve_eff.html @@ -149,9 +149,7 @@ nuclei and electrons in the group for the fix nve command, except that the radius and radial velocity of electrons are also updated.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_nve_limit.html b/doc/html/fix_nve_limit.html index ede833982c..febff4c671 100644 --- a/doc/html/fix_nve_limit.html +++ b/doc/html/fix_nve_limit.html @@ -178,9 +178,7 @@ strategy is to turn off fix shake when performing initial dynamics that need this fix, then turn fix shake on when doing normal dynamics with a fixed-size timestep.

    - -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix computes a global scalar which can be accessed by various diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html index 5b6a9bb8ab..4ace7ccd77 100644 --- a/doc/html/fix_nve_line.html +++ b/doc/html/fix_nve_line.html @@ -148,8 +148,8 @@ orientation, and angular velocity for line segment particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. See -Section_howto 14 of the manual for an overview of -using line segment particles.

    +Section 6.14 of the manual for an +overview of using line segment particles.

    This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html index 149e6de046..de2190636f 100644 --- a/doc/html/fix_nve_manifold_rattle.html +++ b/doc/html/fix_nve_manifold_rattle.html @@ -159,7 +159,7 @@ keyword = every atoms constrained to a curved surface (manifold) in the group each timestep. The constraint is handled by RATTLE (Andersen) written out for the special case of single-particle constraints as -explained in (Paquay). V is volume; E is energy. This way, +explained in (Paquay). V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be studied. If combined with fix langevin, this generates Brownian motion of particles constrained to a curved diff --git a/doc/html/fix_nve_noforce.html b/doc/html/fix_nve_noforce.html index 495a804493..ddde5961c0 100644 --- a/doc/html/fix_nve_noforce.html +++ b/doc/html/fix_nve_noforce.html @@ -155,9 +155,7 @@ command, but with fix nve/noforce, the forces on the wall atoms are unchanged, and can thus be printed by the dump command or queried with an equal-style variable that uses the fcm() group function to compute the total force on the group of atoms.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html index 2a70998598..5874f2a8e2 100644 --- a/doc/html/fix_nve_sphere.html +++ b/doc/html/fix_nve_sphere.html @@ -177,7 +177,7 @@ at only a small additional computational cost.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -187,7 +187,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html index 1462555ef2..407af506f5 100644 --- a/doc/html/fix_nve_tri.html +++ b/doc/html/fix_nve_tri.html @@ -146,10 +146,10 @@

    Description

    Perform constant NVE integration to update position, velocity, orientation, and angular momentum for triangular particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See -Section_howto 14 of the manual for an overview of -using triangular particles.

    +group each timestep. V is volume; E is energy. This creates a +system trajectory consistent with the microcanonical ensemble. See +Section 6.14 of the manual for an +overview of using triangular particles.

    This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html index 473db13d7f..ffa5445676 100644 --- a/doc/html/fix_nvt_asphere.html +++ b/doc/html/fix_nvt_asphere.html @@ -201,7 +201,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -211,7 +211,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html index 57ba66659d..0ad3a20fb6 100644 --- a/doc/html/fix_nvt_body.html +++ b/doc/html/fix_nvt_body.html @@ -198,7 +198,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -208,7 +208,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html index bcb049ebeb..d20d96a113 100644 --- a/doc/html/fix_nvt_manifold_rattle.html +++ b/doc/html/fix_nvt_manifold_rattle.html @@ -160,10 +160,8 @@ keyword = temp or tchain or every

    This fix combines the RATTLE-based (Andersen) time integrator of fix nve/manifold/rattle (Paquay) with a Nose-Hoover-chain thermostat to sample the canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt). For a list of currently supported manifolds and their parameters, see manifolds

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html index 09875bceb8..a7e91fc5f5 100644 --- a/doc/html/fix_nvt_sllod.html +++ b/doc/html/fix_nvt_sllod.html @@ -226,7 +226,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -236,7 +236,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html index 6a27b967ed..b79b7c419a 100644 --- a/doc/html/fix_nvt_sphere.html +++ b/doc/html/fix_nvt_sphere.html @@ -201,7 +201,7 @@ thermal degrees of freedom, and the bias is added back in.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -211,7 +211,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/html/fix_oneway.html b/doc/html/fix_oneway.html index 8d22f6f62f..bb5b2a052e 100644 --- a/doc/html/fix_oneway.html +++ b/doc/html/fix_oneway.html @@ -156,10 +156,8 @@ dimension. The effect is that the particle moves in one direction only.

    This can be used, for example, as a simple model of a semi-permeable membrane, or as an implementation of Maxwell’s demon.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_planeforce.html b/doc/html/fix_planeforce.html index 9adcd39dda..83c023cc9e 100644 --- a/doc/html/fix_planeforce.html +++ b/doc/html/fix_planeforce.html @@ -151,9 +151,7 @@ components of force in the plane specified by the normal vector force perpendicular to the plane.

    If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_poems.html b/doc/html/fix_poems.html index d7308971fb..f1dc2c297e 100644 --- a/doc/html/fix_poems.html +++ b/doc/html/fix_poems.html @@ -208,9 +208,7 @@ for in temperature and pressure computations. Similarly, the rigid body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_press_berendsen.html b/doc/html/fix_press_berendsen.html index ffd58394b6..5afff5a4f3 100644 --- a/doc/html/fix_press_berendsen.html +++ b/doc/html/fix_press_berendsen.html @@ -275,10 +275,10 @@ these 4 keywords:

    This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp” and “pressure”, as if these commands had been issued:

    -
    compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-
    -
    +
    +compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+

    See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is the same @@ -291,9 +291,7 @@ fix’s temperature or pressure via the or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files.

    The fix_modify temp and press options are supported by this fix. You can use them to assign a diff --git a/doc/html/fix_print.html b/doc/html/fix_print.html index 68739849fc..85cd254494 100644 --- a/doc/html/fix_print.html +++ b/doc/html/fix_print.html @@ -186,9 +186,7 @@ keyword was used. By default, the title line is as follows:

    where ID is replaced with the fix-ID.

    - -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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 parameter of this fix can diff --git a/doc/html/fix_property_atom.html b/doc/html/fix_property_atom.html index 474600ad06..81dc2b6611 100644 --- a/doc/html/fix_property_atom.html +++ b/doc/html/fix_property_atom.html @@ -153,11 +153,11 @@

    Examples

    -
    fix 1 all property/atom mol
-fix 1 all property/atom i_myflag1 i_myflag2
-fix 1 all property/atom d_sx d_sy d_sz
-
    -
    +
    +fix 1 all property/atom mol
+fix 1 all property/atom i_myflag1 i_myflag2
+fix 1 all property/atom d_sx d_sy d_sz
+

    Description

    @@ -246,10 +246,10 @@ you need to initialize them explicitly. This can be done by the read_data command, using its fix keyword and passing it the fix-ID of this fix.

    Thus these commands:

    -
    fix prop all property/atom mol d_flag
-read_data data.txt fix prop NULL Molecules
-
    -
    +
    +fix prop all property/atom mol d_flag
+read_data data.txt fix prop NULL Molecules
+

    would allow a data file to have a section like this:

    Molecules
    @@ -271,11 +271,11 @@ per-atom properties can be in any order.

    set command. For example, if you wanted molecules defined for every set of 10 atoms, based on their atom-IDs, these commands could be used:

    -
    fix prop all property/atom mol
-variable cluster atom ((id-1)/10)+1
-set id * mol v_cluster
-
    -
    +
    +fix prop all property/atom mol
+variable cluster atom ((id-1)/10)+1
+set id * mol v_cluster
+

    The atom-style variable will create values for atoms with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the set commands assigns them to the molecule ID for each atom, @@ -292,11 +292,11 @@ properties in a completely general fashion.

    their values. This means that the values can be output via the dump custom command, accessed by fixes like fix ave/atom, accessed by other computes like compute reduce, or used in atom-style variables.

    For example, these commands will output two new properties to a custom dump file:

    -
    fix prop all property/atom i_flag1 d_flag2
-compute 1 all property/atom i_flag1 d_flag2
-dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
-
    -
    +
    +fix prop all property/atom i_flag1 d_flag2
+compute 1 all property/atom i_flag1 d_flag2
+dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
+

    If you wish to add new pair styles, fixes, or computes that use the per-atom @@ -324,10 +324,10 @@ command, there will be a new section named with the fix-ID existing data file and just add this Isotopes section with one line per atom containing atom-ID and mass. Either way, the extended data file can be read back with:

    -
    fix Isotopes all property/atom rmass ghost yes
-read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
-
    -
    +
    +fix Isotopes all property/atom rmass ghost yes
+read_data tip4p-isotopes.data fix Isotopes NULL Isotopes
+

    Please note that the first Isotopes refers to the fix-ID and the second to the name of the section. The following input script code will now change the first 100 water molecules in this @@ -337,10 +337,8 @@ example to heavy water:

    set group hwat mass 2.0141018
    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    This fix writes the per-atom values it stores to binary restart files, so that the values can be restored when a simulation is restarted. See the read_restart command for info on how to re-specify a fix in an input script that diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html index 3bf7a12a5c..13a0577b28 100644 --- a/doc/html/fix_qeq_comb.html +++ b/doc/html/fix_qeq_comb.html @@ -183,7 +183,7 @@ equilibration calculation is written to the specifed file.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html index 665de2e845..a973e86218 100644 --- a/doc/html/fix_qeq_reax.html +++ b/doc/html/fix_qeq_reax.html @@ -189,7 +189,7 @@ be used with the start/stop keywords of the Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -199,7 +199,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/fix_recenter.html b/doc/html/fix_recenter.html index 6428f2b3a3..59a3c11e74 100644 --- a/doc/html/fix_recenter.html +++ b/doc/html/fix_recenter.html @@ -208,9 +208,7 @@ solvent would be cooled to compensate. A better solution for this simulation scenario is to use the fix spring command to tether the molecule in place.

    - -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix computes a global scalar which can be accessed by various diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html index 3dc4ef9053..aced61874e 100644 --- a/doc/html/fix_rigid.html +++ b/doc/html/fix_rigid.html @@ -733,7 +733,7 @@ rigid/nvt.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -743,7 +743,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_setforce.html b/doc/html/fix_setforce.html index 35b7f76194..dd03b992f6 100644 --- a/doc/html/fix_setforce.html +++ b/doc/html/fix_setforce.html @@ -149,11 +149,11 @@

    Examples

    -
    fix freeze indenter setforce 0.0 0.0 0.0
-fix 2 edge setforce NULL 0.0 0.0
-fix 2 edge setforce NULL 0.0 v_oscillate
-
    -
    +
    +fix freeze indenter setforce 0.0 0.0 0.0
+fix 2 edge setforce NULL 0.0 0.0
+fix 2 edge setforce NULL 0.0 v_oscillate
+

    Description

    @@ -187,7 +187,7 @@ to it.

    Styles with a r kk suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    The region keyword is also supported by Kokkos, but a Kokkos-enabled @@ -198,12 +198,10 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files.

    The fix_modify respa option is supported by this fix. This allows to set at which level of the r-RESPA diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html index 6c279062d0..8622c1515e 100644 --- a/doc/html/fix_shake.html +++ b/doc/html/fix_shake.html @@ -262,7 +262,7 @@ info of atoms in the molecule.

    Styles with a suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, @@ -271,7 +271,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    RATTLE:

    diff --git a/doc/html/fix_srd.html b/doc/html/fix_srd.html index 10de92548e..8ee372d9d4 100644 --- a/doc/html/fix_srd.html +++ b/doc/html/fix_srd.html @@ -207,9 +207,9 @@ rotations every N timesteps.

    SRD particles have a mass, temperature, characteristic timestep dt_SRD, and mean free path between collisions (lamda). The fundamental equation relating these 4 quantities is

    -
    lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
-
    -
    +
    +lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
+

    The mass of SRD particles is set by the mass command elsewhere in the input script. The SRD timestep dt_SRD is N times the step dt defined by the timestep command. Big @@ -419,10 +419,8 @@ epsilon or cutoff length to 0.0.

    The “delete_atoms overlap” command may be useful in setting up an SRD simulation to insure there are no initial overlaps between big and SRD particles.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix tabulates several SRD statistics which are stored in a vector diff --git a/doc/html/fix_store_force.html b/doc/html/fix_store_force.html index 30ced5f810..43d5848e79 100644 --- a/doc/html/fix_store_force.html +++ b/doc/html/fix_store_force.html @@ -168,9 +168,7 @@ i.e. before other fixes that apply constraints. However, if you wish to include certain constraints (e.g. fix shake) in the stored force, then it could be specified after some fixes and before others.

    - -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix produces a per-atom array which can be accessed by various diff --git a/doc/html/fix_tmd.html b/doc/html/fix_tmd.html index c8e628825e..a6a826dd62 100644 --- a/doc/html/fix_tmd.html +++ b/doc/html/fix_tmd.html @@ -128,9 +128,9 @@

    fix tmd command

    Syntax

    -
    fix ID group-ID tmd rho_final file1 N file2
-
    -
    +
    +fix ID group-ID tmd rho_final file1 N file2
+
    • ID, group-ID are documented in fix command
    • tmd = style name of this fix command
      • @@ -142,10 +142,10 @@

    Examples

    -
    fix 1 all nve
-fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
-
    -
    +
    +fix 1 all nve
+fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
+

    Description

    @@ -199,9 +199,7 @@ restarted runs, the name of the TMD statistics file should be changed to prevent it being overwritten.

    For more information about TMD, see (Schlitter1) and (Schlitter2).

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to 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.

    diff --git a/doc/html/fix_vector.html b/doc/html/fix_vector.html index 87d0a0ebd7..17b80b0202 100644 --- a/doc/html/fix_vector.html +++ b/doc/html/fix_vector.html @@ -138,21 +138,21 @@
  • one or more input values can be listed
  • value = c_ID, c_ID[N], f_ID, f_ID[N], 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
-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
-v_name[I] = Ith component of vector-style variable with 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
+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
+v_name[I] = Ith component of vector-style variable with name
+

    Examples

    -
    fix 1 all vector 100 c_myTemp
-fix 1 all vector 5 c_myTemp v_integral
-
    -
    +
    +fix 1 all vector 100 c_myTemp
+fix 1 all vector 5 c_myTemp v_integral
+

    Description

    @@ -166,12 +166,12 @@ rows is growing. The resulting vector or array can be used by other time-integrated using the variable trap() function. For example the velocity auto-correlation function (VACF) can be time-integrated, to yield a diffusion coefficient, as follows:

    -
    compute         2 all vacf
-fix             5 all vector 1 c_2[4]
-variable        diff equal dt*trap(f_5)
-thermo_style    custom step v_diff
-
    -
    +
    +compute         2 all vacf
+fix             5 all vector 1 c_2[4]
+variable        diff equal dt*trap(f_5)
+thermo_style    custom step v_diff
+

    The group specified with this command is ignored. However, note that specified values may represent calculations performed by computes and fixes which store their own “group” definitions.

    @@ -197,7 +197,7 @@ command with a timestep value that encompasses all the runs. This is so that the vector or array stored by this fix can be allocated to a sufficient size.

    -

    If a value begins with “c_”, a compute ID must follow which has been +

    If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of the global vector @@ -209,7 +209,7 @@ not in your input script, but by fix temp/rescale. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and add them to LAMMPS.

    -

    If a value begins with “f_”, a fix ID must follow which has been +

    If a value begins with “f_”, a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the global vector @@ -217,7 +217,7 @@ calculated by the fix is used.

    Note that some fixes only produce their values on certain timesteps, which must be compatible with Nevery, else an error will result. Users can also write code for their own fix styles and add them to LAMMPS.

    -

    If a value begins with “v_”, a variable name must follow which has +

    If a value begins with “v_”, a variable name must follow which has been previously defined in the input script. An equal-style or vector-style variable can be referenced; the latter requires a bracketed term to specify the Ith element of the vector calculated by @@ -227,10 +227,8 @@ which can reference individual atom properties or thermodynamic keywords, or they can invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of specifying quantities to be stored by fix vector.

    -
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix produces a global vector or global array which can be diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html index 9df5dfe8ef..31e0ed2501 100644 --- a/doc/html/fix_wall_reflect.html +++ b/doc/html/fix_wall_reflect.html @@ -252,7 +252,7 @@ position = c0 + A (1 - cos(omega*delta))

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -262,7 +262,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/html/fix_wall_srd.html b/doc/html/fix_wall_srd.html index c72f90b6bb..d244f4b0cb 100644 --- a/doc/html/fix_wall_srd.html +++ b/doc/html/fix_wall_srd.html @@ -159,11 +159,11 @@

    Examples

    -
    fix xwalls all wall/srd xlo EDGE xhi EDGE
-fix walls all wall/srd xlo 0.0 ylo 10.0 units box
-fix top all wall/srd zhi v_pressdown
-
    -
    +
    +fix xwalls all wall/srd xlo EDGE xhi EDGE
+fix walls all wall/srd xlo 0.0 ylo 10.0 units box
+fix top all wall/srd zhi v_pressdown
+

    Description

    @@ -249,22 +249,22 @@ define the lattice spacings.

    Here are examples of variable definitions that move the wall position in a time-dependent fashion using equal-style variables.

    -
    variable ramp equal ramp(0,10)
-fix 1 all wall/srd xlo v_ramp
-
    -
    -
    variable linear equal vdisplace(0,20)
-fix 1 all wall/srd xlo v_linear
-
    -
    -
    variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/srd xlo v_wiggle
-
    -
    -
    variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/srd xlo v_wiggle
-
    -
    +
    +variable ramp equal ramp(0,10)
+fix 1 all wall/srd xlo v_ramp
+
    +
    +variable linear equal vdisplace(0,20)
+fix 1 all wall/srd xlo v_linear
+
    +
    +variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/srd xlo v_wiggle
+
    +
    +variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/srd xlo v_wiggle
+

    The ramp(lo,hi) function adjusts the wall position linearly from lo to hi over the course of a run. The displace(c0,velocity) function does something similar using the equation position = c0 + velocity*delta, @@ -272,20 +272,18 @@ where delta is the elapsed time.

    The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period:

    -
    position = c0 + A sin(omega*delta)
-
    -
    +
    +position = c0 + A sin(omega*delta)
+

    The cwiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles:

    -
    position = c0 + A (1 - cos(omega*delta))
-
    -
    -
    +
    +position = c0 + A (1 - cos(omega*delta))
+
    -
    -

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Restart, fix_modify, output, run start/stop, minimize info:

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

    This fix computes a global array of values which can be accessed by diff --git a/doc/html/group.html b/doc/html/group.html index 009ce0deea..29c9364e48 100644 --- a/doc/html/group.html +++ b/doc/html/group.html @@ -329,7 +329,7 @@ per-atom values are 0.0, are removed from the dynamic group.

    each run and on every timestep that is a multiple of N, which is the argument for the every keyword (N = 1 is the default). For an energy minimization, via the minimize command, an -assignement is made at the beginning of the minimization, but not +assignment is made at the beginning of the minimization, but not during the iterations of the minimizer.

    The point in the timestep at which atoms are assigned to a dynamic group is after the initial stage of velocity Verlet time integration diff --git a/doc/html/if.html b/doc/html/if.html index fe0350f9d5..b6fa9347b2 100644 --- a/doc/html/if.html +++ b/doc/html/if.html @@ -186,7 +186,7 @@ above.

    If a command itself requires a quoted argument (e.g. a print command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. -See Section_commands 2 of the manual for +See Section 3.2 of the manual for more details on using quotes in arguments. Only one of level of nesting is allowed, but that should be sufficient for most use cases.

    diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html index 0d39e5935a..281b2e7a45 100644 --- a/doc/html/improper_class2.html +++ b/doc/html/improper_class2.html @@ -199,7 +199,7 @@ radians internally; hence the units of M are in energy/radian^2.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -209,7 +209,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_coeff.html b/doc/html/improper_coeff.html index bad06f5d5e..a457db6736 100644 --- a/doc/html/improper_coeff.html +++ b/doc/html/improper_coeff.html @@ -128,9 +128,9 @@

    improper_coeff command

    Syntax

    -
    improper_coeff N args
-
    -
    +
    +improper_coeff N args
+
    • N = improper type (see asterisk form below)
    • args = coefficients for one or more improper types
      • @@ -138,11 +138,11 @@

    Examples

    -
    improper_coeff 1 300.0 0.0
-improper_coeff * 80.2 -1 2
-improper_coeff *4 80.2 -1 2
-
    -
    +
    +improper_coeff 1 300.0 0.0
+improper_coeff * 80.2 -1 2
+improper_coeff *4 80.2 -1 2
+

    Description

    @@ -154,7 +154,7 @@ file.

    N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the coefficients for multiple improper types. This takes -the form “*” or “n” or “n” or “m*n”. If N = the number of improper +the form “*” or “*n” or “n*” or “m*n”. If N = the number of improper types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle @@ -163,10 +163,10 @@ asterisk means all types from m to n (inclusive).

    setting for the same improper type. For example, these commands set the coeffs for all improper types, then overwrite the coeffs for just improper type 2:

    -
    improper_coeff * 300.0 0.0
-improper_coeff 2 50.0 0.0
-
    -
    +
    +improper_coeff * 300.0 0.0
+improper_coeff 2 50.0 0.0
+

    A line in a data file that specifies improper coefficients uses the exact same format as the arguments of the improper_coeff command in an input script, except that wild-card asterisks should not be used since diff --git a/doc/html/improper_cossq.html b/doc/html/improper_cossq.html index 28c2370f09..7f477dd600 100644 --- a/doc/html/improper_cossq.html +++ b/doc/html/improper_cossq.html @@ -173,7 +173,7 @@ internally; hence the units of K are in energy/radian^2.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -183,7 +183,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_cvff.html b/doc/html/improper_cvff.html index 461f02eeab..dfc56136b6 100644 --- a/doc/html/improper_cvff.html +++ b/doc/html/improper_cvff.html @@ -174,7 +174,7 @@ commands:

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -184,7 +184,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_fourier.html b/doc/html/improper_fourier.html index be22144ccf..ea9ee9d225 100644 --- a/doc/html/improper_fourier.html +++ b/doc/html/improper_fourier.html @@ -166,7 +166,7 @@ commands:

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -176,7 +176,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_harmonic.html b/doc/html/improper_harmonic.html index 11553c0187..cc024bb0f6 100644 --- a/doc/html/improper_harmonic.html +++ b/doc/html/improper_harmonic.html @@ -179,7 +179,7 @@ internally; hence the units of K are in energy/radian^2.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -189,7 +189,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_hybrid.html b/doc/html/improper_hybrid.html index 438f01c690..742c0c785e 100644 --- a/doc/html/improper_hybrid.html +++ b/doc/html/improper_hybrid.html @@ -128,20 +128,20 @@

    improper_style hybrid command

    Syntax

    -
    improper_style hybrid style1 style2 ...
-
    -
    +
    +improper_style hybrid style1 style2 ...
+
    • style1,style2 = list of one or more improper styles

    Examples

    -
    improper_style hybrid harmonic helix
-improper_coeff 1 harmonic 120.0 30
-improper_coeff 2 cvff 20.0 -1 2
-
    -
    +
    +improper_style hybrid harmonic helix
+improper_coeff 1 harmonic 120.0 30
+improper_coeff 2 cvff 20.0 -1 2
+

    Description

    diff --git a/doc/html/improper_none.html b/doc/html/improper_none.html index 5b3ddfa062..daeabe5196 100644 --- a/doc/html/improper_none.html +++ b/doc/html/improper_none.html @@ -128,15 +128,15 @@

    improper_style none command

    Syntax

    -
    improper_style none
-
    -
    +
    +improper_style none
+

    Examples

    -
    improper_style none
-
    -
    +
    +improper_style none
+

    Description

    diff --git a/doc/html/improper_ring.html b/doc/html/improper_ring.html index 0e7e4330b0..c970326ef4 100644 --- a/doc/html/improper_ring.html +++ b/doc/html/improper_ring.html @@ -177,7 +177,7 @@ internally; hence the units of K are in energy/radian^2.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -187,7 +187,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_style.html b/doc/html/improper_style.html index b21d0199f5..cd71f9a567 100644 --- a/doc/html/improper_style.html +++ b/doc/html/improper_style.html @@ -128,20 +128,20 @@

    improper_style command

    Syntax

    -
    improper_style style
-
    -
    +
    +improper_style style
+
    • style = none or hybrid or class2 or cvff or harmonic

    Examples

    -
    improper_style harmonic
-improper_style cvff
-improper_style hybrid cvff harmonic
-
    -
    +
    +improper_style harmonic
+improper_style cvff
+improper_style hybrid cvff harmonic
+

    Description

    @@ -208,9 +208,9 @@ a package.

    Default

    -
    improper_style none
-
    -
    +
    +improper_style none
+
    diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html index de79db67ef..f8fcfb706e 100644 --- a/doc/html/improper_umbrella.html +++ b/doc/html/improper_umbrella.html @@ -168,7 +168,7 @@ commands:

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -178,7 +178,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/improper_zero.html b/doc/html/improper_zero.html index 35365943bc..8fcf52d50c 100644 --- a/doc/html/improper_zero.html +++ b/doc/html/improper_zero.html @@ -134,11 +134,11 @@ improper_style zero nocoeff

    Examples

    -
    improper_style zero
-improper_style zero nocoeff
-improper_coeff *
-
    -
    +
    +improper_style zero
+improper_style zero nocoeff
+improper_coeff *
+

    Description

    diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html index 5cecc5b41d..68a9f47895 100644 --- a/doc/html/kspace_style.html +++ b/doc/html/kspace_style.html @@ -271,7 +271,7 @@ However, for low relative accuracy, the staggered PPPM mesh size may be essentially the same as for regular PPPM, which means the method will be up to 2x slower in the KSpace time (simply 2x more expensive). For more details and timings, see -Section_accelerate.

    +Section 5.

    Note

    Using pppm/stagger may not give the same increase in the @@ -374,7 +374,7 @@ relative RMS error.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -393,7 +393,7 @@ calculated on the CPU in non-threaded mode.

    These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if LAMMPS was built with those packages. See the Making LAMMPS section for more info.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/log.html b/doc/html/log.html index d0aedd79d7..00b63cc6b8 100644 --- a/doc/html/log.html +++ b/doc/html/log.html @@ -155,7 +155,7 @@ be a variable, so that different processors do not attempt to write to the same log file.

    The file “log.lammps” is the default log file for a LAMMPS run. The name of the initial log file can also be set by the command-line -switch -log. See Section_start 6 for +switch -log. See Section 2.7 for details.

    diff --git a/doc/html/manifolds.html b/doc/html/manifolds.html index 73f57ef600..5fec3a287f 100644 --- a/doc/html/manifolds.html +++ b/doc/html/manifolds.html @@ -139,9 +139,9 @@ to the relevant fixes.

    born
    ---+++ @@ -159,7 +159,7 @@ to the relevant fixes.

    - + @@ -195,7 +195,7 @@ to the relevant fixes.

    - + diff --git a/doc/html/mass.html b/doc/html/mass.html index b52482445a..45725432bf 100644 --- a/doc/html/mass.html +++ b/doc/html/mass.html @@ -138,11 +138,11 @@

    Examples

    -
    mass 1 1.0
-mass * 62.5
-mass 2* 62.5
-
    -
    +
    +mass 1 1.0
+mass * 62.5
+mass 2* 62.5
+

    Description

    @@ -153,7 +153,7 @@ what mass units to use.

    The I index can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to set the mass for multiple atom types. This -takes the form “*” or “n” or “n” or “m*n”. If N = the number of +takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N diff --git a/doc/html/neb.html b/doc/html/neb.html index d820af07c5..38af41fdab 100644 --- a/doc/html/neb.html +++ b/doc/html/neb.html @@ -170,7 +170,7 @@ follows the discussion in these 3 papers: (Henkelman2), and (Nakano).

    Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see Section_start 7 of the +switch; see Section 2.7 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on just diff --git a/doc/html/pair_adp.html b/doc/html/pair_adp.html index 5bc88ab7d0..759795cc8b 100644 --- a/doc/html/pair_adp.html +++ b/doc/html/pair_adp.html @@ -235,7 +235,7 @@ array tabulated with a scaling by r.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -245,7 +245,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html index 6827568073..4624ba98c7 100644 --- a/doc/html/pair_airebo.html +++ b/doc/html/pair_airebo.html @@ -284,7 +284,7 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -294,7 +294,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_awpmd.html b/doc/html/pair_awpmd.html index 5fb4a74c41..4b2dc24da3 100644 --- a/doc/html/pair_awpmd.html +++ b/doc/html/pair_awpmd.html @@ -128,9 +128,9 @@

    pair_style awpmd/cut command

    Syntax

    -
    pair_style awpmd/cut Rc keyword value ...
-
    -
    +
    +pair_style awpmd/cut Rc keyword value ...
+
    • Rc = global cutoff, -1 means cutoff of half the shortest box length
    • zero or more keyword/value pairs may be appended
      • @@ -154,12 +154,12 @@

    Examples

    -
    pair_style awpmd/cut -1
-pair_style awpmd/cut 40.0 uhf free
-pair_coeff * *
-pair_coeff 2 2 20.0
-
    -
    +
    +pair_style awpmd/cut -1
+pair_style awpmd/cut 40.0 uhf free
+pair_coeff * *
+pair_coeff 2 2 20.0
+

    Description

    diff --git a/doc/html/pair_beck.html b/doc/html/pair_beck.html index baf69eecfa..e807bdb7aa 100644 --- a/doc/html/pair_beck.html +++ b/doc/html/pair_beck.html @@ -174,7 +174,7 @@ Rc is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -184,7 +184,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html index 5f623fb0b7..f71c89bec2 100644 --- a/doc/html/pair_body.html +++ b/doc/html/pair_body.html @@ -145,7 +145,7 @@ pair_coeff 1 1 1.0 1.5 2.5

    Description

    Style body is for use with body particles and calculates pairwise body/body interactions as well as interactions between body and -point-particles. See Section_howto 14 +point-particles. See Section 6.14 of the manual and the body doc page for more details on using body particles.

    This pair style is designed for use with the “nparticle” body style, diff --git a/doc/html/pair_born.html b/doc/html/pair_born.html index c73ca9761f..d3edfaaded 100644 --- a/doc/html/pair_born.html +++ b/doc/html/pair_born.html @@ -261,7 +261,7 @@ same global Coulombic cutoff specified in the pair_style command.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -271,7 +271,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_buck.html b/doc/html/pair_buck.html index fa537931bf..e24b875998 100644 --- a/doc/html/pair_buck.html +++ b/doc/html/pair_buck.html @@ -289,7 +289,7 @@ pair_style command.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -299,7 +299,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_buck_long.html b/doc/html/pair_buck_long.html index 82fc5d5641..5d8371e461 100644 --- a/doc/html/pair_buck_long.html +++ b/doc/html/pair_buck_long.html @@ -223,7 +223,7 @@ global Coulombic cutoff is allowed.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -233,7 +233,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html index 93e44709ce..8fc752ddf6 100644 --- a/doc/html/pair_charmm.html +++ b/doc/html/pair_charmm.html @@ -260,7 +260,7 @@ the pair_style command.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -270,7 +270,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html index a2dee8a442..3efdc15034 100644 --- a/doc/html/pair_class2.html +++ b/doc/html/pair_class2.html @@ -238,7 +238,7 @@ cutoff distance.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -248,7 +248,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_coeff.html b/doc/html/pair_coeff.html index 1689bf6047..c5bb770a91 100644 --- a/doc/html/pair_coeff.html +++ b/doc/html/pair_coeff.html @@ -128,9 +128,9 @@

    pair_coeff command

    Syntax

    -
    pair_coeff I J args
-
    -
    +
    +pair_coeff I J args
+
    • I,J = atom types (see asterisk form below)
    • args = coefficients for one or more pairs of atom types
      • @@ -138,15 +138,15 @@

    Examples

    -
    pair_coeff 1 2 1.0 1.0 2.5
-pair_coeff 2 * 1.0 1.0
-pair_coeff 3* 1*2 1.0 1.0 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff * * nialhjea 1 1 2
-pair_coeff * 3 morse.table ENTRY1
-pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
-
    -
    +
    +pair_coeff 1 2 1.0 1.0 2.5
+pair_coeff 2 * 1.0 1.0
+pair_coeff 3* 1*2 1.0 1.0 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff * * nialhjea 1 1 2
+pair_coeff * 3 morse.table ENTRY1
+pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
+

    Description

    @@ -160,7 +160,7 @@ required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values.

    A wildcard asterisk can be used in place of or in conjunction with the I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form “*” or “n” or “n” or “m*n”. If N = the +types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N @@ -170,10 +170,10 @@ asterisks imply type pairs where J < I, they are ignored.

    Note that a pair_coeff command can override a previous setting for the same I,J pair. For example, these commands set the coeffs for all I,J pairs, then overwrite the coeffs for just the I,J = 2,3 pair:

    -
    pair_coeff * * 1.0 1.0 2.5
-pair_coeff 2 3 2.0 1.0 1.12
-
    -
    +
    +pair_coeff * * 1.0 1.0 2.5
+pair_coeff 2 3 2.0 1.0 1.12
+

    A line in a data file that specifies pair coefficients uses the exact same format as the arguments of the pair_coeff command in an input script, with the exception of the I,J type arguments. In each line of @@ -214,13 +214,13 @@ copying them into your working directory. Environment variables are set in different ways for different shells. Here are example settings for

    csh, tcsh:

    -
    % setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
-
    -
    +
    +% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
+

    bash:

    -
    % export LAMMPS_POTENTIALS=/path/to/lammps/potentials
-
    -
    +
    +% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
+

    Windows:

     % set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"
diff --git a/doc/html/pair_colloid.html b/doc/html/pair_colloid.html
index a1520bc730..57ec62a36b 100644
--- a/doc/html/pair_colloid.html
+++ b/doc/html/pair_colloid.html
@@ -239,7 +239,7 @@ commands for efficiency: Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -249,7 +249,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html
index c0768ee36a..3fffa53753 100644
--- a/doc/html/pair_comb.html
+++ b/doc/html/pair_comb.html
@@ -230,7 +230,7 @@ nor file ffield.comb3 with style comb.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -240,7 +240,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_coul.html b/doc/html/pair_coul.html
index 98cba31724..252ace1d8a 100644
--- a/doc/html/pair_coul.html
+++ b/doc/html/pair_coul.html
@@ -415,7 +415,7 @@ command.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -425,7 +425,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_cs.html b/doc/html/pair_cs.html
index 12d0c515ef..05c7ec567b 100644
--- a/doc/html/pair_cs.html
+++ b/doc/html/pair_cs.html
@@ -164,7 +164,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
 
    Description
    
 
    These pair styles are designed to be used with the adiabatic
 core/shell model of (Mitchell and Finchham).  See
-Section_howto 25 of the manual for an
+Section 6.25 of the manual for an
 overview of the model as implemented in LAMMPS.
    
 
    These pair styles are identical to the pair_style born/coul/long and pair_style buck/coul/long styles, except they correctly treat the
 special case where the distance between two charged core and shell
diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html
index 25e82fc6e3..bedd2387db 100644
--- a/doc/html/pair_dipole.html
+++ b/doc/html/pair_dipole.html
@@ -298,7 +298,7 @@ type pair.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -308,7 +308,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_dpd.html b/doc/html/pair_dpd.html
index 1275469c41..8ae775068a 100644
--- a/doc/html/pair_dpd.html
+++ b/doc/html/pair_dpd.html
@@ -235,7 +235,7 @@ random force.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -245,7 +245,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_eam.html b/doc/html/pair_eam.html
index 62a0305a0c..06a22a2d74 100644
--- a/doc/html/pair_eam.html
+++ b/doc/html/pair_eam.html
@@ -493,7 +493,7 @@ are listed.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -503,7 +503,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accerlate of the manual for more
+
    See Section 5 of the manual for more
 instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_edip.html b/doc/html/pair_edip.html
index 54a690dde1..0be43042ec 100644
--- a/doc/html/pair_edip.html
+++ b/doc/html/pair_edip.html
@@ -216,7 +216,7 @@ the EDIP package.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -226,7 +226,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    
 
    
 
    Mixing, shift, table, tail correction, restart, rRESPA info:
    
diff --git a/doc/html/pair_eim.html b/doc/html/pair_eim.html
index 831c9f00dc..235f487b3d 100644
--- a/doc/html/pair_eim.html
+++ b/doc/html/pair_eim.html
@@ -244,7 +244,7 @@ needs.
    
 
    Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed in Section_accelerate
+hardware, as discussed in Section 5
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
    
@@ -254,7 +254,7 @@ LAMMPS was built with those packages.  See the You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
 use the suffix command in your input script.
    
-
    See Section_accelerate of the manual for
+
    See Section 5 of the manual for
 more instructions on how to use the accelerated styles effectively.
    diff --git a/doc/html/pair_gauss.html b/doc/html/pair_gauss.html index d90d449b83..086a35e74f 100644 --- a/doc/html/pair_gauss.html +++ b/doc/html/pair_gauss.html @@ -204,7 +204,7 @@ commands:

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -215,7 +215,7 @@ LAMMPS was built with those packages. See the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html index 68e46bd2d8..9a5923113e 100644 --- a/doc/html/pair_gayberne.html +++ b/doc/html/pair_gayberne.html @@ -247,7 +247,7 @@ pair_coeff sigma to 1.0 as well.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -257,7 +257,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_gran.html b/doc/html/pair_gran.html index 37946c96aa..2932d4e4bd 100644 --- a/doc/html/pair_gran.html +++ b/doc/html/pair_gran.html @@ -299,7 +299,7 @@ potential.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -309,7 +309,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_gromacs.html b/doc/html/pair_gromacs.html index a58a10912a..a8a5ce03b2 100644 --- a/doc/html/pair_gromacs.html +++ b/doc/html/pair_gromacs.html @@ -217,7 +217,7 @@ cutoff(s) specified in the pair_style command.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -227,7 +227,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html index e639ba34e8..a2b9b14aed 100644 --- a/doc/html/pair_hbond_dreiding.html +++ b/doc/html/pair_hbond_dreiding.html @@ -287,7 +287,7 @@ optional parameters.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -297,7 +297,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html index 60044d0faf..fc5db924e0 100644 --- a/doc/html/pair_hybrid.html +++ b/doc/html/pair_hybrid.html @@ -419,7 +419,7 @@ off C/C interaction, i.e. by setting the appropriate coefficients to

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual.

    Since the hybrid and hybrid/overlay styles delegate computation to the individual sub-styles, the suffix versions of the hybrid and @@ -433,7 +433,7 @@ LAMMPS was built with those packages. See the

    You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_kim.html b/doc/html/pair_kim.html index 0465abb269..b3dd8684cb 100644 --- a/doc/html/pair_kim.html +++ b/doc/html/pair_kim.html @@ -128,9 +128,9 @@

    pair_style kim command

    Syntax

    -
    pair_style kim virialmode model printflag
-
    -
    +
    +pair_style kim virialmode model printflag
+
    • virialmode = KIMvirial or LAMMPSvirial
    • model = name of KIM model (potential)
      • @@ -139,14 +139,14 @@

    Examples

    -
    pair_style kim KIMvirial model_Ar_P_Morse
-pair_coeff * * Ar Ar
-
    -
    -
    pair_style kim KIMvirial model_Ar_P_Morse 1
-pair_coeff * * Ar Ar
-
    -
    +
    +pair_style kim KIMvirial model_Ar_P_Morse
+pair_coeff * * Ar Ar
+
    +
    +pair_style kim KIMvirial model_Ar_P_Morse 1
+pair_coeff * * Ar Ar
+

    Description

    @@ -177,9 +177,9 @@ pair_coeff command, where N is the number of LAMMPS atom types:

    As an example, imagine the KIM model supports Si and C atoms. If your LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command:

    -
    pair_coeff * * Si Si Si C
-
    -
    +
    +pair_coeff * * Si Si Si C
+

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to Si as defined within KIM. The final C argument maps LAMMPS atom type 4 to C diff --git a/doc/html/pair_lcbop.html b/doc/html/pair_lcbop.html index 7e2e82ff4a..9f3f225455 100644 --- a/doc/html/pair_lcbop.html +++ b/doc/html/pair_lcbop.html @@ -128,16 +128,16 @@

    pair_style lcbop command

    Syntax

    -
    pair_style lcbop
-
    -
    +
    +pair_style lcbop
+

    Examples

    -
    pair_style lcbop
-pair_coeff * * ../potentials/C.lcbop C
-
    -
    +
    +pair_style lcbop
+pair_coeff * * ../potentials/C.lcbop C
+

    Description

    @@ -157,9 +157,9 @@ where N is the number of LAMMPS atom types:

    to specify the path for the potential file.

    As an example, if your LAMMPS simulation has 4 atom types and you want the 1st 3 to be C you would use the following pair_coeff command:

    -
    pair_coeff * * C.lcbop C C C NULL
-
    -
    +
    +pair_coeff * * C.lcbop C C C NULL
+

    The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first C argument maps LAMMPS atom type 1 to the C element in the LCBOP file. If a mapping value is specified as NULL, the mapping is diff --git a/doc/html/pair_lj.html b/doc/html/pair_lj.html index 73f9948c27..881bf9c6aa 100644 --- a/doc/html/pair_lj.html +++ b/doc/html/pair_lj.html @@ -414,7 +414,7 @@ pair_style command.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -424,7 +424,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj96.html b/doc/html/pair_lj96.html index 3f7e8fdd9b..8db501bd12 100644 --- a/doc/html/pair_lj96.html +++ b/doc/html/pair_lj96.html @@ -171,7 +171,7 @@ cutoff specified in the pair_style command is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -181,7 +181,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_cubic.html b/doc/html/pair_lj_cubic.html index 6dad5de332..32b652937a 100644 --- a/doc/html/pair_lj_cubic.html +++ b/doc/html/pair_lj_cubic.html @@ -183,7 +183,7 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma =

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_expand.html b/doc/html/pair_lj_expand.html index 69fc39c046..0202b2e153 100644 --- a/doc/html/pair_lj_expand.html +++ b/doc/html/pair_lj_expand.html @@ -175,7 +175,7 @@ optional. If not specified, the global LJ cutoff is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -185,7 +185,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_long.html b/doc/html/pair_lj_long.html index 2256d2d48e..f72aad0384 100644 --- a/doc/html/pair_lj_long.html +++ b/doc/html/pair_lj_long.html @@ -275,7 +275,7 @@ specified in the pair_style command.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -285,7 +285,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_sf.html b/doc/html/pair_lj_sf.html index b09ff7e036..ded174264c 100644 --- a/doc/html/pair_lj_sf.html +++ b/doc/html/pair_lj_sf.html @@ -168,7 +168,7 @@ LJ cutoff specified in the pair_style command is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -178,7 +178,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_smooth.html b/doc/html/pair_lj_smooth.html index 0973d95ff9..e42ea25efd 100644 --- a/doc/html/pair_lj_smooth.html +++ b/doc/html/pair_lj_smooth.html @@ -183,7 +183,7 @@ specified, the global values for Rin and Rc are used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -193,7 +193,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_smooth_linear.html b/doc/html/pair_lj_smooth_linear.html index edd6d68386..067334a27d 100644 --- a/doc/html/pair_lj_smooth_linear.html +++ b/doc/html/pair_lj_smooth_linear.html @@ -169,7 +169,7 @@ for Rc is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -179,7 +179,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_lj_soft.html b/doc/html/pair_lj_soft.html index f67e200935..26592c9f94 100644 --- a/doc/html/pair_lj_soft.html +++ b/doc/html/pair_lj_soft.html @@ -353,7 +353,7 @@ directory tree, under examples/USER/fep.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -363,7 +363,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, tail correction, restart info:

    diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html index d0f57e43cb..1d5ef40828 100644 --- a/doc/html/pair_meam_spline.html +++ b/doc/html/pair_meam_spline.html @@ -199,7 +199,7 @@ MEAM potentials. It may be extended for alloy systems in the future.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -209,7 +209,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html index bcf7271af0..f4844c2192 100644 --- a/doc/html/pair_morse.html +++ b/doc/html/pair_morse.html @@ -222,7 +222,7 @@ cutoff is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -232,7 +232,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_nb3b_harmonic.html b/doc/html/pair_nb3b_harmonic.html index a24bb092e7..a05117a647 100644 --- a/doc/html/pair_nb3b_harmonic.html +++ b/doc/html/pair_nb3b_harmonic.html @@ -202,7 +202,7 @@ simulation; LAMMPS ignores those entries.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -212,7 +212,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/pair_nm.html b/doc/html/pair_nm.html index c7759721cf..97dea100ae 100644 --- a/doc/html/pair_nm.html +++ b/doc/html/pair_nm.html @@ -250,7 +250,7 @@ the run_st

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -260,7 +260,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/pair_none.html b/doc/html/pair_none.html index 1b294a15f5..84a0e71b67 100644 --- a/doc/html/pair_none.html +++ b/doc/html/pair_none.html @@ -128,15 +128,15 @@

    pair_style none command

    Syntax

    -
    pair_style none
-
    -
    +
    +pair_style none
+

    Examples

    -
    pair_style none
-
    -
    +
    +pair_style none
+

    Description

    diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html index c2fa31cce8..14fa845a22 100644 --- a/doc/html/pair_peri.html +++ b/doc/html/pair_peri.html @@ -258,7 +258,7 @@ details please see the description in “(Mtchell2011a)”.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -268,7 +268,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html index 38e27022b9..ff0e1ee9ea 100644 --- a/doc/html/pair_reax_c.html +++ b/doc/html/pair_reax_c.html @@ -170,7 +170,7 @@ the (Akt

    The reax/c/kk style is a Kokkos version of the ReaxFF potential that is derived from the reax/c style. The Kokkos version can run on GPUs and can also use OpenMP multithreading. For more information about the Kokkos package, -see Section_packages and Section_accelerate. +see Section 4 and Section 5.3.3. One important consideration when using the reax/c/kk style is the choice of either half or full neighbor lists. This setting can be changed using the Kokkos package command.

    @@ -377,7 +377,7 @@ script that reads a restart file.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -387,7 +387,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/pair_resquared.html b/doc/html/pair_resquared.html index 70c4fd0ba0..dcba82a43e 100644 --- a/doc/html/pair_resquared.html +++ b/doc/html/pair_resquared.html @@ -247,7 +247,7 @@ specified in the pair_style command is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -257,7 +257,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_sdk.html b/doc/html/pair_sdk.html index 21a9ded1a5..67ce57044a 100644 --- a/doc/html/pair_sdk.html +++ b/doc/html/pair_sdk.html @@ -215,7 +215,7 @@ pair_style command.

    Styles with a gpu, intel, kk, omp or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -225,7 +225,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, and rRESPA info:

    diff --git a/doc/html/pair_smd_tlsph.html b/doc/html/pair_smd_tlsph.html index 69ea38dfa4..330e3c56f2 100644 --- a/doc/html/pair_smd_tlsph.html +++ b/doc/html/pair_smd_tlsph.html @@ -128,9 +128,9 @@

    pair_style smd/tlsph command

    Syntax

    -
    pair_style smd/tlsph args
-
    -
    +
    +pair_style smd/tlsph args
+

    Examples

    @@ -140,11 +140,11 @@

    Description

    The smd/tlsph style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.

    This pair style is invoked with the following command:

    -
    pair_style smd/tlsph
-pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
-               *END
-
    -
    +
    +pair_style smd/tlsph
+pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
+               *END
+

    Here, i and j denote the LAMMPS particle types for which this pair style is defined. Note that i and j must be equal, i.e., no tlsph cross interactions between different particle types are allowed. @@ -152,7 +152,7 @@ In contrast to the usual LAMMPS pair coeff definitions, which number of floats and integers, the tlsph pair coeff definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The pair coeff line must be terminated with -the **END* keyword. The use the line continuation operator & is recommended. A typical +the *END keyword. The use the line continuation operator & is recommended. A typical invocation of the tlsph for a solid body would consist of an equation of state for computing the pressure (the diagonal components of the stress tensor), and a material model to compute shear stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.

    diff --git a/doc/html/pair_smd_ulsph.html b/doc/html/pair_smd_ulsph.html index a838c63e41..1e21539e51 100644 --- a/doc/html/pair_smd_ulsph.html +++ b/doc/html/pair_smd_ulsph.html @@ -128,27 +128,27 @@

    pair_style smd/ulsph command

    Syntax

    -
    pair_style smd/ulsph args
-
    -
    +
    +pair_style smd/ulsph args
+
    • these keywords must be given
    -

    keyword = **DENSITY_SUMMATION* or **DENSITY_CONTINUITY* and **VELOCITY_GRADIENT* or **NO_VELOCITY_GRADIENT* and **GRADIENT_CORRECTION* or **NO_GRADIENT_CORRECTION*

    +

    keyword = *DENSITY_SUMMATION or *DENSITY_CONTINUITY and *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT and *GRADIENT_CORRECTION or *NO_GRADIENT_CORRECTION

    Examples

    -

    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION

    +

    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION

    Description

    The smd/ulsph style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.

    This pair style is invoked similar to the following command:

    -
    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
-pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
-               *END
-
    -
    +
    +pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
+               *END
+

    Here, i and j denote the LAMMPS particle types for which this pair style is defined. Note that i and j can be different, i.e., ulsph cross interactions between different particle types are allowed. However, i–i respectively j–j pair_coeff lines have to preceed a cross interaction. @@ -156,11 +156,11 @@ In contrast to the usual LAMMPS pair coeff definitions, which number of floats and integers, the ulsph pair coeff definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The pair coeff line must be terminated with -the **END* keyword. The use the line continuation operator & is recommended. A typical +the *END keyword. The use the line continuation operator & is recommended. A typical invocation of the ulsph for a solid body would consist of an equation of state for computing the pressure (the diagonal components of the stress tensor), and a material model to compute shear stresses (the off-diagonal components of the stress tensor).

    -

    Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.

    +

    Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.

    Please see the SMD user guide for a complete listing of the possible keywords and material models.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_soft.html b/doc/html/pair_soft.html index 3443927106..0569003710 100644 --- a/doc/html/pair_soft.html +++ b/doc/html/pair_soft.html @@ -205,7 +205,7 @@ variables.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -215,7 +215,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_sph_heatconduction.html b/doc/html/pair_sph_heatconduction.html index b864553905..d4161616a4 100644 --- a/doc/html/pair_sph_heatconduction.html +++ b/doc/html/pair_sph_heatconduction.html @@ -128,16 +128,16 @@

    pair_style sph/heatconduction command

    Syntax

    -
    pair_style sph/heatconduction
-
    -
    +
    +pair_style sph/heatconduction
+

    Examples

    -
    pair_style sph/heatconduction
-pair_coeff * * 1.0 2.4
-
    -
    +
    +pair_style sph/heatconduction
+pair_coeff * * 1.0 2.4
+

    Description

    diff --git a/doc/html/pair_sph_lj.html b/doc/html/pair_sph_lj.html index ffc548c39f..78b5ba0a20 100644 --- a/doc/html/pair_sph_lj.html +++ b/doc/html/pair_sph_lj.html @@ -128,16 +128,16 @@

    pair_style sph/lj command

    Syntax

    -
    pair_style sph/lj
-
    -
    +
    +pair_style sph/lj
+

    Examples

    -
    pair_style sph/lj
-pair_coeff * * 1.0 2.4
-
    -
    +
    +pair_style sph/lj
+pair_coeff * * 1.0 2.4
+

    Description

    diff --git a/doc/html/pair_sph_rhosum.html b/doc/html/pair_sph_rhosum.html index 77029fa778..358b99eaf7 100644 --- a/doc/html/pair_sph_rhosum.html +++ b/doc/html/pair_sph_rhosum.html @@ -128,19 +128,19 @@

    pair_style sph/rhosum command

    Syntax

    -
    pair_style sph/rhosum Nstep
-
    -
    +
    +pair_style sph/rhosum Nstep
+
    • Nstep = timestep interval

    Examples

    -
    pair_style sph/rhosum 10
-pair_coeff * * 2.4
-
    -
    +
    +pair_style sph/rhosum 10
+pair_coeff * * 2.4
+

    Description

    diff --git a/doc/html/pair_sw.html b/doc/html/pair_sw.html index 687c162b34..763585aa01 100644 --- a/doc/html/pair_sw.html +++ b/doc/html/pair_sw.html @@ -263,7 +263,7 @@ taken from the ij and ik pairs (sigma, a, gamma)

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -277,7 +277,7 @@ use the suffi additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_table.html b/doc/html/pair_table.html index 703a6081cc..7eea6f862b 100644 --- a/doc/html/pair_table.html +++ b/doc/html/pair_table.html @@ -323,7 +323,7 @@ one that matches the specified keyword.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -333,7 +333,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_tersoff.html b/doc/html/pair_tersoff.html index 8345a1c90b..596a46ff18 100644 --- a/doc/html/pair_tersoff.html +++ b/doc/html/pair_tersoff.html @@ -294,7 +294,7 @@ defined in various papers.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -304,7 +304,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_tersoff_mod.html b/doc/html/pair_tersoff_mod.html index 34a2120f67..dbd370c774 100644 --- a/doc/html/pair_tersoff_mod.html +++ b/doc/html/pair_tersoff_mod.html @@ -235,7 +235,7 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -245,7 +245,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_tersoff_zbl.html b/doc/html/pair_tersoff_zbl.html index 694938f86e..cf04608f95 100644 --- a/doc/html/pair_tersoff_zbl.html +++ b/doc/html/pair_tersoff_zbl.html @@ -297,7 +297,7 @@ providing the base ZBL implementation.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -307,7 +307,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html index 8e8f15daf2..a4537a9e02 100644 --- a/doc/html/pair_thole.html +++ b/doc/html/pair_thole.html @@ -242,7 +242,7 @@ the pair_style command line.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -252,7 +252,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing:

    The thole pair style does not support mixing. Thus, coefficients diff --git a/doc/html/pair_vashishta.html b/doc/html/pair_vashishta.html index 6dd3e02f8f..22c01edfe5 100644 --- a/doc/html/pair_vashishta.html +++ b/doc/html/pair_vashishta.html @@ -268,7 +268,7 @@ two-body parameters from the CCC and CSiSi entries.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -278,7 +278,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_write.html b/doc/html/pair_write.html index 3b82d7c51d..f9dfa7d90d 100644 --- a/doc/html/pair_write.html +++ b/doc/html/pair_write.html @@ -128,9 +128,9 @@

    pair_write command

    Syntax

    -
    pair_write itype jtype N style inner outer file keyword Qi Qj
-
    -
    +
    +pair_write itype jtype N style inner outer file keyword Qi Qj
+
    • itype,jtype = 2 atom types
    • N = # of values
      • @@ -143,10 +143,10 @@

    Examples

    -
    pair_write 1 3 500 r 1.0 10.0 table.txt LJ
-pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5
-
    -
    +
    +pair_write 1 3 500 r 1.0 10.0 table.txt LJ
+pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5
+

    Description

    diff --git a/doc/html/pair_yukawa.html b/doc/html/pair_yukawa.html index 3f0d3b3e2c..058c6e1885 100644 --- a/doc/html/pair_yukawa.html +++ b/doc/html/pair_yukawa.html @@ -170,7 +170,7 @@ cutoff is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -180,7 +180,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_yukawa_colloid.html b/doc/html/pair_yukawa_colloid.html index 0c16f65c1d..aa52328359 100644 --- a/doc/html/pair_yukawa_colloid.html +++ b/doc/html/pair_yukawa_colloid.html @@ -199,7 +199,7 @@ yukawa/colloid cutoff is used.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -209,7 +209,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_zbl.html b/doc/html/pair_zbl.html index 54ad6b5344..c76585916b 100644 --- a/doc/html/pair_zbl.html +++ b/doc/html/pair_zbl.html @@ -194,7 +194,7 @@ copper.

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in Section_accelerate +hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    @@ -204,7 +204,7 @@ LAMMPS was built with those packages. See the You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    Mixing, shift, table, tail correction, restart, rRESPA info:

    diff --git a/doc/html/pair_zero.html b/doc/html/pair_zero.html index b0605c1fce..e64a46c138 100644 --- a/doc/html/pair_zero.html +++ b/doc/html/pair_zero.html @@ -139,12 +139,12 @@ nocoeff = ignore all pair_coeff parameters (optional)

    Examples

    -
    pair_style zero 10.0
-pair_style zero 5.0 nocoeff
-pair_coeff * *
-pair_coeff 1 2*4 3.0
-
    -
    +
    +pair_style zero 10.0
+pair_style zero 5.0 nocoeff
+pair_coeff * *
+pair_coeff 1 2*4 3.0
+

    Description

    diff --git a/doc/html/partition.html b/doc/html/partition.html index 858da5aef8..89b57e9711 100644 --- a/doc/html/partition.html +++ b/doc/html/partition.html @@ -142,15 +142,15 @@ 
     partition yes 1 processors 4 10 6
 partition no 5 print "Active partition"
-partition yes 5 fix all nve
-partition yes 6 fix all nvt temp 1.0 1.0 0.1
+partition yes *5 fix all nve
+partition yes 6* fix all nvt temp 1.0 1.0 0.1

    Description

    This command invokes the specified command on a subset of the partitions of processors you have defined via the -partition -command-line switch. See Section_start 6 +command-line switch. See Section 2.6 for an explanation of the switch.

    Normally, every input script command in your script is invoked by every partition. This behavior can be modified by defining world- or @@ -171,7 +171,7 @@ partitions specified by the Section_start 6 of the +switch; see Section 2.7 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or two processors. For PRD, this makes little sense, since this offers no effective parallel speed-up in searching for infrequent events. See -Section_howto 5 of the manual for further +Section 6.5 of the manual for further discussion.

    When a PRD simulation is performed, it is assumed that each replica is running the same model, though LAMMPS does not check for this. diff --git a/doc/html/read_data.html b/doc/html/read_data.html index 0087555e4b..6b3d3cd347 100644 --- a/doc/html/read_data.html +++ b/doc/html/read_data.html @@ -406,7 +406,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent. If you wish to define a box with tilt factors that exceed these limits, you can use the box tilt command, with a setting of large; a setting of small is the default.

    -

    See Section_howto 12 of the doc pages +

    See Section 6.12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.

    diff --git a/doc/html/read_restart.html b/doc/html/read_restart.html index 5a2e8099fa..ca1284f6aa 100644 --- a/doc/html/read_restart.html +++ b/doc/html/read_restart.html @@ -128,9 +128,9 @@

    read_restart command

    Syntax

    -
    read_restart file flag
-
    -
    +
    +read_restart file flag
+
    • file = name of binary restart file to read in
    • flag = remap (optional)
      • @@ -138,13 +138,13 @@

    Examples

    -
    read_restart save.10000
-read_restart save.10000 remap
-read_restart restart.*
-read_restart restart.*.mpiio
-read_restart poly.*.% remap
-
    -
    +
    +read_restart save.10000
+read_restart save.10000 remap
+read_restart restart.*
+read_restart restart.*.mpiio
+read_restart poly.*.% remap
+

    Description

    diff --git a/doc/html/region.html b/doc/html/region.html index 8e3f0aa71b..99ba092a06 100644 --- a/doc/html/region.html +++ b/doc/html/region.html @@ -301,7 +301,7 @@ its value used to determine the radius of the region.

    functions, and include thermo_style command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent radius.

    -

    See Section_howto 12 of the doc pages +

    See Section 6.12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.

    @@ -407,7 +407,7 @@ point of the rotate keyword.

    Styles with a kk suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in -Section_accelerate of the manual. The +Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    The code using the region (such as a fix or compute) must also be supported @@ -418,7 +418,7 @@ only enabled if LAMMPS was built with that package. See the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/reset_timestep.html b/doc/html/reset_timestep.html index 9a274dfb77..b261a67791 100644 --- a/doc/html/reset_timestep.html +++ b/doc/html/reset_timestep.html @@ -128,19 +128,19 @@

    reset_timestep command

    Syntax

    -
    reset_timestep N
-
    -
    +
    +reset_timestep N
+
    • N = timestep number

    Examples

    -
    reset_timestep 0
-reset_timestep 4000000
-
    -
    +
    +reset_timestep 0
+reset_timestep 4000000
+

    Description

    diff --git a/doc/html/run_style.html b/doc/html/run_style.html index b00835c7e1..4038b3f075 100644 --- a/doc/html/run_style.html +++ b/doc/html/run_style.html @@ -192,7 +192,7 @@ simulations performed by LAMMPS.

    The verlet/split style is also a velocity-Verlet integrator, but it splits the force calculation within each timestep over 2 partitions of -processors. See Section_start 6 for an +processors. See Section 2.7 for an explanation of the -partition command-line switch.

    Specifically, this style performs all computation except the kspace_style portion of the force field on the 1st @@ -232,17 +232,16 @@ of 60 and 15 processors each:

    When you run in 2-partition mode with the verlet/split style, the thermodyanmic data for the entire simulation will be output to the log and screen file of the 1st partition, which are log.lammps.0 and -screen.0 by default; see the “-plog and -pscreen command-line -switches”Section_start.html#start_7 to change this. The log and +screen.0 by default; see the -plog and -pscreen command-line switches to change this. The log and screen file for the 2nd partition will not contain thermodynamic output beyone the 1st timestep of the run.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for performance details of the speed-up offered by the verlet/split style. One important performance consideration is the assignemnt of logical processors in the 2 partitions to the physical cores of a parallel machine. The processors command has options to support this, and strategies are discussed in -Section_accelerate of the manual.

    +Section 5 of the manual.

    The respa style implements the rRESPA multi-timescale integrator (Tuckerman) with N hierarchical levels, where level 1 is @@ -357,14 +356,14 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 pair, bond, angle, dihedral, improper, or kspace styles with an omp suffix. It is functionally equivalent to respa but performs additional operations required for managing omp styles. For more on omp styles -see the Section_accelerate of the manual. +see the Section 5 of the manual. Accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

    You can specify respa/omp explicitly in your input script, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

    -

    See Section_accelerate of the manual for +

    See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

    diff --git a/doc/html/shell.html b/doc/html/shell.html index 732af4e4f4..c4ed4806b4 100644 --- a/doc/html/shell.html +++ b/doc/html/shell.html @@ -153,17 +153,17 @@ anything else is passed as a command to the shell for direct execution

    Examples

    -
    shell cd sub1
-shell cd ..
-shell mkdir tmp1 tmp2 tmp3
-shell rmdir tmp1
-shell mv log.lammps hold/log.1
-shell rm TMP/file1 TMP/file2
-shell putenv LAMMPS_POTENTIALS=../../potentials
-shell my_setup file1 10 file2
-shell my_post_process 100 dump.out
-
    -
    +
    +shell cd sub1
+shell cd ..
+shell mkdir tmp1 tmp2 tmp3
+shell rmdir tmp1
+shell mv log.lammps hold/log.1
+shell rm TMP/file1 TMP/file2
+shell putenv LAMMPS_POTENTIALS=../../potentials
+shell my_setup file1 10 file2
+shell my_post_process 100 dump.out
+

    Description

    @@ -199,15 +199,15 @@ performed. The resulting string is then used literally.

    Any other cmd is passed as-is to the shell along with its arguments as one string, invoked by the C-library system() call. For example, these lines in your input script:

    -
    variable n equal 10
+
    +variable n equal 10
 variable foo string file2
 shell my_setup file1 $n ${foo}
-
    -
    +

    would be the same as invoking

    -
    % my_setup file1 10 file2
-
    -
    +
    +% my_setup file1 10 file2
+

    from a command-line prompt. The executable program “my_setup” is run with 3 arguments: file1 10 file2.

    diff --git a/doc/html/temper.html b/doc/html/temper.html index b8503a7268..58505e5216 100644 --- a/doc/html/temper.html +++ b/doc/html/temper.html @@ -154,7 +154,7 @@ temper 40000 100 $t tempfix 0 32285 $w replicas (ensembles) of a system. Two or more replicas must be used.

    Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see Section_start 6 of the +switch; see Section 2.7 of the manual. Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or diff --git a/doc/html/thermo_modify.html b/doc/html/thermo_modify.html index 403b94ca91..17118e5b21 100644 --- a/doc/html/thermo_modify.html +++ b/doc/html/thermo_modify.html @@ -128,9 +128,9 @@

    thermo_modify command

    Syntax

    -
    thermo_modify keyword value ...
-
    -
    +
    +thermo_modify keyword value ...
+
    • one or more keyword/value pairs may be listed
    @@ -150,12 +150,12 @@ keyword = lost or lost/bond or norm or flush

    Examples

    -
    thermo_modify lost ignore flush yes
-thermo_modify temp myTemp format 3 %15.8g
-thermo_modify temp myTemp format line "%ld %g %g %15.8g"
-thermo_modify line multi format float %g
-
    -
    +
    +thermo_modify lost ignore flush yes
+thermo_modify temp myTemp format 3 %15.8g
+thermo_modify temp myTemp format line "%ld %g %g %15.8g"
+thermo_modify line multi format float %g
+

    Description

    diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html index 4f0f68acae..fb9e327adc 100644 --- a/doc/html/thermo_style.html +++ b/doc/html/thermo_style.html @@ -231,7 +231,7 @@ thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to computes, fixes, and equal-style variables that have been defined elsewhere in the input script or can even be new styles which users -have added to LAMMPS (see the Section_modify +have added to LAMMPS (see the Section 10 section of the documentation). Thus the custom style provides a flexible means of outputting essentially any desired quantity as a simulation proceeds.

    @@ -357,8 +357,8 @@ proceed for the maximum number of allowed iterations.

    The part keyword is useful for multi-replica or multi-partition simulations to indicate which partition this output and this file corresponds to, or for use in a variable to append to -a filename for output specific to this partition. See Section_start 7 of the manual for details on running in -multi-partition mode.

    +a filename for output specific to this partition. See Section 2.7 of the manual for details on running +in multi-partition mode.

    The timeremain keyword returns the remaining seconds when a timeout has been configured via the timer timeout command. If the timeout timer is inactive, the value of this keyword is 0.0 and diff --git a/doc/html/write_data.html b/doc/html/write_data.html index d0d619bb4a..5e4286d69d 100644 --- a/doc/html/write_data.html +++ b/doc/html/write_data.html @@ -128,9 +128,9 @@

    write_data command

    Syntax

    -
    write_data file keyword value ...
-
    -
    +
    +write_data file keyword value ...
+
    • file = name of data file to write out
    • zero or more keyword/value pairs may be appended
      • @@ -145,10 +145,10 @@

    Examples

    -
    write_data data.polymer
-write_data data.*
-
    -
    +
    +write_data data.polymer
+write_data data.*
+

    Description

    diff --git a/doc/html/write_restart.html b/doc/html/write_restart.html index b3403777c6..f1a7fba6bb 100644 --- a/doc/html/write_restart.html +++ b/doc/html/write_restart.html @@ -128,9 +128,9 @@

    write_restart command

    Syntax

    -
    write_restart file keyword value ...
-
    -
    +
    +write_restart file keyword value ...
+
    • file = name of file to write restart information to
    • zero or more keyword/value pairs may be appended
      • @@ -145,11 +145,11 @@

    Examples

    -
    write_restart restart.equil
-write_restart restart.equil.mpiio
-write_restart poly.%.* nfile 10
-
    -
    +
    +write_restart restart.equil
+write_restart restart.equil.mpiio
+write_restart poly.%.* nfile 10
+

    Description

    cylinder_dent R l ax^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwisex^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise A cylinder with a dent around z = 0  
    supersphere R q|x|^q + |y|^q + |z|^q - R^q = 0|x|^q + |y|^q + |z|^q - R^q = 0 A supersphere of hyperradius R