From 6fd60f50ad7d42daf18d1ec2a675090c7aa378d5 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 16 Sep 2016 16:20:06 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/Manual.txt | 24 ++- doc/src/Section_accelerate.txt | 26 ++- doc/src/Section_commands.txt | 3 +- doc/src/Section_errors.txt | 2 +- doc/src/Section_history.txt | 28 ++- doc/src/Section_howto.txt | 16 +- doc/src/Section_intro.txt | 20 +- doc/src/Section_modify.txt | 2 +- doc/src/Section_packages.txt | 24 +-- doc/src/Section_python.txt | 20 +- doc/src/Section_start.txt | 194 ++++++++++-------- doc/src/Section_tools.txt | 9 +- doc/src/accelerate_gpu.txt | 4 +- doc/src/accelerate_intel.txt | 2 +- doc/src/accelerate_kokkos.txt | 2 +- doc/src/accelerate_omp.txt | 2 +- doc/src/accelerate_opt.txt | 2 +- doc/src/angle_charmm.txt | 4 +- doc/src/angle_class2.txt | 4 +- doc/src/angle_cosine.txt | 4 +- doc/src/angle_cosine_delta.txt | 4 +- doc/src/angle_cosine_periodic.txt | 4 +- doc/src/angle_cosine_shift.txt | 4 +- doc/src/angle_cosine_shift_exp.txt | 4 +- doc/src/angle_cosine_squared.txt | 4 +- doc/src/angle_dipole.txt | 4 +- doc/src/angle_fourier.txt | 4 +- doc/src/angle_fourier_simple.txt | 4 +- doc/src/angle_harmonic.txt | 4 +- doc/src/angle_quartic.txt | 4 +- doc/src/angle_table.txt | 4 +- doc/src/angles.txt | 27 +++ doc/src/atom_style.txt | 8 +- doc/src/balance.txt | 3 +- doc/src/body.txt | 10 +- doc/src/bond_class2.txt | 4 +- doc/src/bond_fene.txt | 4 +- doc/src/bond_fene_expand.txt | 4 +- doc/src/bond_harmonic.txt | 4 +- doc/src/bond_harmonic_shift.txt | 4 +- doc/src/bond_harmonic_shift_cut.txt | 4 +- doc/src/bond_morse.txt | 4 +- doc/src/bond_nonlinear.txt | 4 +- doc/src/bond_quartic.txt | 4 +- doc/src/bond_table.txt | 4 +- doc/src/bonds.txt | 22 ++ doc/src/boundary.txt | 2 +- doc/src/change_box.txt | 2 +- doc/src/commands.txt | 109 ++++++++++ doc/src/compute_ackland_atom.txt | 2 +- doc/src/compute_angmom_chunk.txt | 8 +- doc/src/compute_basal_atom.txt | 4 +- doc/src/compute_body_local.txt | 2 +- doc/src/compute_centro_atom.txt | 4 +- doc/src/compute_chunk_atom.txt | 8 +- doc/src/compute_cluster_atom.txt | 2 +- doc/src/compute_cna_atom.txt | 2 +- doc/src/compute_com_chunk.txt | 8 +- doc/src/compute_contact_atom.txt | 2 +- doc/src/compute_coord_atom.txt | 4 +- doc/src/compute_damage_atom.txt | 2 +- doc/src/compute_dipole_chunk.txt | 8 +- doc/src/compute_displace_atom.txt | 4 +- doc/src/compute_dpd_atom.txt | 2 +- doc/src/compute_erotate_asphere.txt | 2 +- doc/src/compute_erotate_rigid.txt | 2 +- doc/src/compute_erotate_sphere.txt | 2 +- doc/src/compute_erotate_sphere_atom.txt | 2 +- doc/src/compute_event_displace.txt | 2 +- doc/src/compute_fep.txt | 4 +- doc/src/compute_gyration.txt | 4 +- doc/src/compute_gyration_chunk.txt | 4 +- doc/src/compute_hexorder_atom.txt | 4 +- doc/src/compute_inertia_chunk.txt | 8 +- doc/src/compute_ke.txt | 2 +- doc/src/compute_ke_atom.txt | 2 +- doc/src/compute_ke_atom_eff.txt | 2 +- doc/src/compute_ke_eff.txt | 2 +- doc/src/compute_ke_rigid.txt | 4 +- doc/src/compute_meso_e_atom.txt | 2 +- doc/src/compute_meso_rho_atom.txt | 2 +- doc/src/compute_meso_t_atom.txt | 2 +- doc/src/compute_msd_chunk.txt | 4 +- doc/src/compute_omega_chunk.txt | 8 +- doc/src/compute_orientorder_atom.txt | 4 +- doc/src/compute_pe.txt | 4 +- doc/src/compute_pe_atom.txt | 2 +- doc/src/compute_pressure.txt | 4 +- doc/src/compute_property_chunk.txt | 4 +- doc/src/compute_rdf.txt | 2 +- doc/src/compute_reduce.txt | 2 +- doc/src/compute_smd_contact_radius.txt | 2 +- .../compute_smd_triangle_mesh_vertices.txt | 12 +- doc/src/compute_smd_ulsph_num_neighs.txt | 2 +- doc/src/compute_smd_ulsph_strain.txt | 2 +- doc/src/compute_smd_ulsph_strain_rate.txt | 4 +- doc/src/compute_smd_ulsph_stress.txt | 4 +- doc/src/compute_sna_atom.txt | 4 +- doc/src/compute_stress_atom.txt | 4 +- doc/src/compute_temp.txt | 4 +- doc/src/compute_temp_chunk.txt | 8 +- doc/src/compute_temp_cs.txt | 6 +- doc/src/compute_temp_partial.txt | 4 +- doc/src/compute_ti.txt | 4 +- doc/src/compute_torque_chunk.txt | 6 +- doc/src/compute_vcm_chunk.txt | 8 +- doc/src/compute_voronoi_atom.txt | 4 +- doc/src/compute_xrd.txt | 86 ++++---- doc/src/computes.txt | 120 +++++++++++ doc/src/create_box.txt | 2 +- doc/src/dihedral_charmm.txt | 4 +- doc/src/dihedral_class2.txt | 4 +- doc/src/dihedral_coeff.txt | 2 - doc/src/dihedral_cosine_shift_exp.txt | 4 +- doc/src/dihedral_fourier.txt | 6 +- doc/src/dihedral_harmonic.txt | 4 +- doc/src/dihedral_helix.txt | 4 +- doc/src/dihedral_multi_harmonic.txt | 4 +- doc/src/dihedral_nharmonic.txt | 4 +- doc/src/dihedral_opls.txt | 4 +- doc/src/dihedral_quadratic.txt | 4 +- doc/src/dihedral_spherical.txt | 2 +- doc/src/dihedral_table.txt | 4 +- doc/src/dihedrals.txt | 39 ++++ doc/src/dimension.txt | 2 +- doc/src/dump.txt | 2 +- doc/src/dump_custom_vtk.txt | 2 +- doc/src/dump_image.txt | 2 +- doc/src/fix_addforce.txt | 4 +- doc/src/fix_ave_chunk.txt | 4 +- doc/src/fix_aveforce.txt | 4 +- doc/src/fix_balance.txt | 3 +- doc/src/fix_deform.txt | 4 +- doc/src/fix_enforce2d.txt | 4 +- doc/src/fix_freeze.txt | 4 +- doc/src/fix_gle.txt | 14 +- doc/src/fix_gravity.txt | 4 +- doc/src/fix_ipi.txt | 4 +- doc/src/fix_langevin.txt | 4 +- doc/src/fix_lb_rigid_pc_sphere.txt | 2 +- doc/src/fix_neb.txt | 8 +- doc/src/fix_nh.txt | 4 +- doc/src/fix_nph_asphere.txt | 4 +- doc/src/fix_nph_body.txt | 4 +- doc/src/fix_nph_sphere.txt | 4 +- doc/src/fix_nphug.txt | 4 +- doc/src/fix_npt_asphere.txt | 4 +- doc/src/fix_npt_body.txt | 4 +- doc/src/fix_npt_sphere.txt | 4 +- doc/src/fix_nve.txt | 4 +- doc/src/fix_nve_asphere.txt | 4 +- doc/src/fix_nve_body.txt | 4 +- doc/src/fix_nve_line.txt | 4 +- doc/src/fix_nve_manifold_rattle.txt | 4 +- doc/src/fix_nve_sphere.txt | 4 +- doc/src/fix_nve_tri.txt | 8 +- doc/src/fix_nvt_asphere.txt | 4 +- doc/src/fix_nvt_body.txt | 4 +- doc/src/fix_nvt_manifold_rattle.txt | 4 +- doc/src/fix_nvt_sllod.txt | 4 +- doc/src/fix_nvt_sphere.txt | 4 +- doc/src/fix_qeq_comb.txt | 4 +- doc/src/fix_qeq_reax.txt | 4 +- doc/src/fix_rigid.txt | 4 +- doc/src/fix_rx.txt | 2 +- doc/src/fix_setforce.txt | 4 +- doc/src/fix_shake.txt | 4 +- doc/src/fix_shardlow.txt | 10 +- .../fix_smd_tlsph_reference_configuration.txt | 0 doc/src/fix_ti_spring.txt | 2 +- doc/src/fix_tune_kspace.txt | 2 - doc/src/fix_viscosity.txt | 4 +- doc/src/fix_wall_reflect.txt | 4 +- doc/src/fixes.txt | 156 ++++++++++++++ doc/src/group.txt | 2 +- doc/src/if.txt | 2 +- doc/src/improper_class2.txt | 4 +- doc/src/improper_cossq.txt | 4 +- doc/src/improper_cvff.txt | 4 +- doc/src/improper_fourier.txt | 4 +- doc/src/improper_harmonic.txt | 4 +- doc/src/improper_ring.txt | 4 +- doc/src/improper_umbrella.txt | 4 +- doc/src/impropers.txt | 20 ++ doc/src/kspace_style.txt | 6 +- doc/src/log.txt | 2 +- doc/src/manifolds.txt | 32 +-- doc/src/molecule.txt | 1 - doc/src/neb.txt | 23 +-- doc/src/pair_adp.txt | 4 +- doc/src/pair_airebo.txt | 4 +- doc/src/pair_beck.txt | 4 +- doc/src/pair_body.txt | 2 +- doc/src/pair_born.txt | 4 +- doc/src/pair_buck.txt | 4 +- doc/src/pair_buck_long.txt | 6 +- doc/src/pair_charmm.txt | 4 +- doc/src/pair_class2.txt | 4 +- doc/src/pair_colloid.txt | 4 +- doc/src/pair_comb.txt | 4 +- doc/src/pair_coul.txt | 4 +- doc/src/pair_cs.txt | 2 +- doc/src/pair_dipole.txt | 4 +- doc/src/pair_dpd.txt | 4 +- doc/src/pair_eam.txt | 4 +- doc/src/pair_edip.txt | 4 +- doc/src/pair_eim.txt | 4 +- doc/src/pair_gauss.txt | 4 +- doc/src/pair_gayberne.txt | 4 +- doc/src/pair_gran.txt | 4 +- doc/src/pair_gromacs.txt | 4 +- doc/src/pair_hbond_dreiding.txt | 4 +- doc/src/pair_hybrid.txt | 4 +- doc/src/pair_lj.txt | 4 +- doc/src/pair_lj96.txt | 4 +- doc/src/pair_lj_cubic.txt | 4 +- doc/src/pair_lj_expand.txt | 4 +- doc/src/pair_lj_long.txt | 4 +- doc/src/pair_lj_sf.txt | 4 +- doc/src/pair_lj_smooth.txt | 4 +- doc/src/pair_lj_smooth_linear.txt | 4 +- doc/src/pair_lj_soft.txt | 7 +- doc/src/pair_meam_spline.txt | 4 +- doc/src/pair_morse.txt | 4 +- doc/src/pair_nb3b_harmonic.txt | 4 +- doc/src/pair_nm.txt | 4 +- doc/src/pair_peri.txt | 4 +- doc/src/pair_reax_c.txt | 12 +- doc/src/pair_resquared.txt | 4 +- doc/src/pair_sdk.txt | 4 +- doc/src/pair_soft.txt | 4 +- doc/src/pair_sw.txt | 4 +- doc/src/pair_table.txt | 4 +- doc/src/pair_tersoff.txt | 4 +- doc/src/pair_tersoff_mod.txt | 4 +- doc/src/pair_tersoff_zbl.txt | 4 +- doc/src/pair_thole.txt | 4 +- doc/src/pair_vashishta.txt | 4 +- doc/src/pair_yukawa.txt | 4 +- doc/src/pair_yukawa_colloid.txt | 4 +- doc/src/pair_zbl.txt | 4 +- doc/src/pairs.txt | 102 +++++++++ doc/src/partition.txt | 2 +- doc/src/prd.txt | 4 +- doc/src/read_data.txt | 2 +- doc/src/read_restart.txt | 2 - doc/src/region.txt | 6 +- doc/src/run_style.txt | 12 +- doc/src/tad.txt | 4 +- doc/src/temper.txt | 2 +- doc/src/thermo_style.txt | 8 +- doc/src/tutorials.txt | 13 ++ 252 files changed, 1343 insertions(+), 684 deletions(-) create mode 100644 doc/src/angles.txt create mode 100644 doc/src/bonds.txt create mode 100644 doc/src/commands.txt create mode 100644 doc/src/computes.txt create mode 100644 doc/src/dihedrals.txt delete mode 100644 doc/src/fix_smd_tlsph_reference_configuration.txt create mode 100644 doc/src/fixes.txt create mode 100644 doc/src/impropers.txt create mode 100644 doc/src/pairs.txt create mode 100644 doc/src/tutorials.txt diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index b8b681d017..f4cbb840f9 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -69,7 +69,7 @@ Labs and Temple University: Aidan Thompson, athomps at sandia.gov :l Stan Moore, stamoore at sandia.gov :l "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l -:ulb +:ule Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. The [LAMMPS home page] at @@ -77,6 +77,11 @@ all at Sandia. The [LAMMPS home page] at 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."_https://github.com/lammps/lammps +The lammps.org domain, currently hosting "public continuous integration +testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux +RPM and Windows installer packages"_http://rpm.lammps.org is located +at Temple University and managed by Richard Berger, +richard.berger at temple.edu. :link(bug,http://lammps.sandia.gov/bug.html) :link(sjp,http://www.sandia.gov/~sjplimp) @@ -101,6 +106,9 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 :numbered: + :caption: User Documentation + :name: userdoc + :includehidden: Section_intro Section_start @@ -116,6 +124,20 @@ it gives quick access to documentation for all LAMMPS commands. Section_errors Section_history +.. toctree:: + :caption: Index + :name: index + :hidden: + + tutorials + commands + fixes + computes + pairs + bonds + angles + dihedrals + impropers Indices and tables ================== diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt index 9489dee160..fcdcb2d41c 100644 --- a/doc/src/Section_accelerate.txt +++ b/doc/src/Section_accelerate.txt @@ -157,11 +157,25 @@ packages"_Section_packages.html. These are the accelerator packages currently in LAMMPS, either as standard or user packages: -"GPU"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support -"USER-INTEL"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi -"KOKKOS"_accelerate_kokkos.html : for GPUs, Intel Xeon Phi, and OpenMP threading -"USER-OMP"_accelerate_omp.html : for OpenMP threading -"OPT"_accelerate_opt.html : generic CPU optimizations :tb(s=:) +"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support +"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi +"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading +"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations +"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:) + + Inverting this list, LAMMPS currently has acceleration support for three kinds of hardware, via the listed packages: @@ -192,7 +206,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html: "pair_style lj/cut/opt"_pair_lj.html :ul To see what accelerate styles are currently available, see -"Section_commands 5"_Section_commands.html#cmd_5 of the manual. The +"Section 3.5"_Section_commands.html#cmd_5 of the manual. The doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list any accelerated variants available for that style. diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 2b9df3f9a6..bbca4c49b3 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -195,7 +195,7 @@ 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"_Section_example.html, and animated on the "LAMMPS +"Section 7"_Section_example.html, and animated on the "LAMMPS WWW Site"_lws. A LAMMPS input script typically has 4 parts: @@ -660,7 +660,6 @@ package"_Section_start.html#start_3. "smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, "smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, "smd/setvel"_fix_smd_setvel.html, -"smd/tlsph/reference/configuration"_fix_smd_tlsph_reference_configuration.html, "smd/wall/surface"_fix_smd_wall_surface.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, "ti/rs"_fix_ti_rs.html, diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index 6a18b1bbdb..1b72f7003f 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -11579,7 +11579,7 @@ This may not be what you intended. :dd 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. :dd {One or more respa levels compute no forces} :dt diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt index 2c65825370..a73be9c3b6 100644 --- a/doc/src/Section_history.txt +++ b/doc/src/Section_history.txt @@ -22,15 +22,27 @@ dynamics codes our group has distributed. 13.1 Coming attractions :h4,link(hist_1) -The "Wish list link"_http://lammps.sandia.gov/future.html 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. +As of summer 2016 we are using the "LAMMPS project issue tracker +on GitHub"_https://github.com/lammps/lammps/issues 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. -You can also send "email to the -developers"_http://lammps.sandia.gov/authors.html if you want to add -your wish to the list. +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"_http://lammps.sandia.gov/authors.html or send +an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html +if you want to have your suggestion added to the list. :line diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 576c80f11f..f63892d515 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -39,7 +39,7 @@ This section describes how to perform common tasks using LAMMPS. 6.27 "Drude induced dipoles"_#howto_27 :all(b) The example input scripts included in the LAMMPS distribution and -highlighted in "Section_example"_Section_example.html also show how to +highlighted in "Section 7"_Section_example.html also show how to setup and run various kinds of simulations. :line @@ -180,7 +180,7 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the "read_data"_read_data.html command or in the input script with commands like "pair_coeff"_pair_coeff.html or -"bond_coeff"_bond_coeff.html. See "Section_tools"_Section_tools.html +"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html for additional tools that can use CHARMM or AMBER to assign force field coefficients and convert their output into LAMMPS input. @@ -673,7 +673,7 @@ 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"_Section_modify.html of the documentation for how +See "Section 10"_Section_modify.html 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 @@ -709,12 +709,12 @@ 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"_Section_python.html of the manual for a description +"Section 11"_Section_python.html 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"_Section_howto.html#howto_19 of the +to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the manual for a description of the interface and how to extend it for your needs. @@ -746,7 +746,7 @@ and atom trajectories. Several programs included with LAMMPS as auxiliary tools can convert native LAMMPS dump files to other formats. See the -"Section_tools"_Section_tools.html doc page for details. The first is +"Section 9"_Section_tools.html doc page for details. The first is the "ch2lmp tool"_Section_tools.html#charmm, which contains a lammps2pdb Perl script which converts LAMMPS dump files into PDB files. The second is the "lmp2arc tool"_Section_tools.html#arc which @@ -1840,7 +1840,7 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda 6.19 Library interface to LAMMPS :link(howto_19),h4 -As described in "Section_start 5"_Section_start.html#start_5, LAMMPS +As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can be built as a library, so that it can be called by another code, used in a "coupled manner"_Section_howto.html#howto_10 with other codes, or driven through a "Python interface"_Section_python.html. @@ -2212,7 +2212,7 @@ Note that this compute allows the per-atom output of other "variables"_variable.html 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"_Section_modify.html of the documentation for how to +"Section 10"_Section_modify.html of the documentation for how to do this. You can also define a "per-atom variable"_variable.html in the input script that uses a formula to generate a chunk ID for each atom. diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index 1a015a4edf..848e5155c7 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -41,7 +41,7 @@ parallel machines and Beowulf-style clusters. :link(mpi,http://www-unix.mcs.anl.gov/mpi) LAMMPS can model systems with only a few particles up to millions or -billions. See "Section_perf"_Section_perf.html for information on +billions. See "Section 8"_Section_perf.html for information on LAMMPS performance and scalability, or the Benchmarks section of the "LAMMPS WWW Site"_lws. @@ -54,12 +54,12 @@ brief discussion of the open-source philosophy. LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See "Section_modify"_Section_modify.html +conditions, or diagnostics. See "Section 10"_Section_modify.html for more details. The current version of LAMMPS is written in C++. Earlier versions were written in F77 and F90. See -"Section_history"_Section_history.html for more information on +"Section 13"_Section_history.html for more information on different versions. All versions can be downloaded from the "LAMMPS WWW Site"_lws. @@ -94,7 +94,7 @@ LAMMPS are listed in "this section"_#intro_5. This section highlights LAMMPS features, with pointers to specific commands which give more details. If LAMMPS doesn't have your favorite interatomic potential, boundary condition, or atom type, see -"Section_modify"_Section_modify.html, which describes how you can add +"Section 10"_Section_modify.html, which describes how you can add it to LAMMPS. General features :h5 @@ -330,7 +330,7 @@ Similarly, LAMMPS creates output files in a simple format. Most users post-process these files with their own analysis tools or re-format them for input into other programs, including visualization packages. If you are convinced you need to compute something on-the-fly as -LAMMPS runs, see "Section_modify"_Section_modify.html for a discussion +LAMMPS runs, see "Section 10"_Section_modify.html for a discussion of how you can use the "dump"_dump.html and "compute"_compute.html and "fix"_fix.html commands to print out data of your choosing. Keep in mind that complicated computations can slow down the molecular @@ -347,12 +347,12 @@ following packages: "VMD"_http://www.ks.uiuc.edu/Research/vmd "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A -"PyMol"_http://pymol.sourceforge.net +"PyMol"_http://www.pymol.org "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html "RasMol"_http://www.openrasmol.org :ul Other features that LAMMPS does not yet (and may never) support are -discussed in "Section_history"_Section_history.html. +discussed in "Section 13"_Section_history.html. Finally, these are freely-available molecular dynamics codes, most of them parallel, which may be well-suited to the problems you want to @@ -427,7 +427,7 @@ Site"_lws, or have a suggestion for something to clarify or include, send an email to the "developers"_http://lammps.sandia.gov/authors.html. :l -If you find a bug, "Section_errors 2"_Section_errors.html#err_2 +If you find a bug, "Section 12.2"_Section_errors.html#err_2 describes how to report it. :l If you publish a paper using LAMMPS results, send the citation (and @@ -440,7 +440,7 @@ directory. :l 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"_Section_tools.html. If you write +details are given in "Section 9"_Section_tools.html. If you write a new tool that users will find useful, it can be added to the LAMMPS distribution. :l @@ -531,7 +531,7 @@ Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for gran 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 :ul -As discussed in "Section_history"_Section_history.html, LAMMPS +As discussed in "Section 13"_Section_history.html, 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/src/Section_modify.txt b/doc/src/Section_modify.txt index 67b38d6936..228c7199fd 100644 --- a/doc/src/Section_modify.txt +++ b/doc/src/Section_modify.txt @@ -528,7 +528,7 @@ Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -See "Section_howto 14"_Section_howto.html#howto_14 of the manual for +See "Section 6.14"_Section_howto.html#howto_14 of the manual for an overview of using body particles and the "body"_body.html 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/src/Section_packages.txt b/doc/src/Section_packages.txt index 38afb98de1..525729a1bb 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -23,7 +23,7 @@ packages. 4.1 "Standard packages"_#pkg_1 4.2 "User packages"_#pkg_2 :all(b) -"Section_start 3"_Section_start.html#start_3 of the manual describes +"Section 2.3"_Section_start.html#start_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 @@ -64,28 +64,28 @@ The current list of standard packages is as follows. Each package name links to a sub-section below with more details. Package, Description, Author(s), Doc page, Example, Library -"ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, - +"ASPHERE"_#ASPHERE, aspherical particles, -, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, - "BODY"_#BODY, body-style particles, -, "body"_body.html, body, - "CLASS2"_#CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, - "COLLOID"_#COLLOID, colloidal particles, Kumar (1), "atom_style colloid"_atom_style.html, colloid, - "COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, - -"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, - +"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - "DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, - "GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu -"GRANULAR"_#GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, - +"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, - "KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM -"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos +"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos "KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, - "MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, - "MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam "MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, - -"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, - +"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - "OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, - "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, - "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python "REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax -"REPLICA"_#REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, - +"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, - "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, - "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, - "SNAP"_#SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, - @@ -112,7 +112,7 @@ 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"_Section_howto.html of the manual, or an input script +"Section 6"_Section_howto.html of the manual, or an input script command implemented as part of the package, or to additional documentation provided within the package. @@ -1198,7 +1198,7 @@ Mattox (Engility), and John Brennan (ARL). Daniel Queteschiner (DCS Computing). The "Doc page" column links to either a sub-section of the -"Section_howto"_Section_howto.html of the manual, or an input script +"Section 6"_Section_howto.html of the manual, or an input script command implemented as part of the package, or to additional documentation provided within the package. @@ -1440,7 +1440,7 @@ Phi-enabled styles. Supporting info: examples/accelerate, src/USER-INTEL/TEST -"Section_accelerate"_Section_accelerate.html#acc_3 +"Section 5"_Section_accelerate.html#acc_3 Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact him directly if you have questions. @@ -1532,7 +1532,7 @@ 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_commands.html#cmd_5 +"Section 3"_Section_commands.html#cmd_5 User-contributed features are listed at the bottom of the fix, compute, pair, etc sections. @@ -1609,7 +1609,7 @@ styles, and fix styles. See this section of the manual to get started: -"Section_accelerate"_Section_accelerate.html#acc_3 +"Section 5"_Section_accelerate.html#acc_3 The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index b9049d87f7..1475daa945 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -42,10 +42,10 @@ 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"_Section_howto.html#howto_10 of the manual and +See "Section 6.10"_Section_howto.html#howto_10 of the manual and the couple directory of the distribution for more ideas about coupling -LAMMPS to other codes. See "Section_howto -19"_Section_howto.html#howto_19 for a description of the LAMMPS +LAMMPS to other codes. See "Section +6.19"_Section_howto.html#howto_19 for a description of the LAMMPS library interface provided in src/library.cpp and src/library.h, and how to extend it for your needs. As described below, that interface is what is exposed to Python either when calling LAMMPS from Python or @@ -179,7 +179,7 @@ file and the shared library. 11.3 Building LAMMPS as a shared library :link(py_3),h4 Instructions on how to build LAMMPS as a shared library are given in -"Section_start 5"_Section_start.html#start_5. A shared library is one +"Section 2.5"_Section_start.html#start_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". @@ -198,7 +198,7 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other 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"_Section_start.html#start_5 for more details. +"Section 2.5"_Section_start.html#start_5 for more details. :line @@ -419,8 +419,8 @@ first importing from the lammps.py file: >>> from ctypes import CDLL >>> CDLL("liblammps.so") :pre -If an error occurs, carefully go thru the steps in "Section_start -5"_Section_start.html#start_5 and above about building a shared +If an error occurs, carefully go thru the steps in "Section +2.5"_Section_start.html#start_5 and above about building a shared library and about insuring Python can find the necessary two files it needs. @@ -656,7 +656,7 @@ 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"_Section_howto.html#howto_15 of the manual for a +See "Section 6.15"_Section_howto.html#howto_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"_compute.html and "fixes"_fix.html for a description of what @@ -790,13 +790,13 @@ capability needed by these Python scripts. Note that for PyMol, you need to have built and installed the open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages "here"_pymol or +from a Python script. See the PyMol WWW pages "here"_pymolhome or "here"_pymolopen for more details: http://www.pymol.org http://sourceforge.net/scm/?type=svn&group_id=4546 :pre -:link(pymol,http://www.pymol.org) +:link(pymolhome,http://www.pymol.org) :link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) The latter link is to the open-source version. diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 32bd5dae3c..d2202679c0 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -30,8 +30,7 @@ When you download a LAMMPS tarball you will need to unzip and untar the downloaded file with the following commands, after placing the tarball in an appropriate directory. -gunzip lammps*.tar.gz -tar xvf lammps*.tar :pre +tar -xzvf lammps*.tar.gz :pre This will create a LAMMPS directory containing two files and several sub-directories: @@ -46,16 +45,17 @@ src: source files tools: pre- and post-processing tools :tb(s=:) Note that the "download page"_download also has links to download -Windows exectubles and installers, as well as pre-built executables -for a few specific Linux distributions. It also has instructions for -how to download/install LAMMPS for Macs (via Homebrew), and to +pre-build Windows installers, as well as pre-built packages for +several widely used Linux distributions. It also has instructions +for how to download/install LAMMPS for Macs (via Homebrew), and to download and update LAMMPS from SVN and Git repositories, which gives -you the same files that are in the download tarball. +you access to the up-to-date sources that are used by the LAMMPS +core developers. :link(download,http://lammps.sandia.gov/download.html) -The Windows and Linux executables for serial or parallel only include -certain packages and bug-fixes/upgrades listed on "this +The Windows and Linux packages for serial or parallel include +only selected packages and bug-fixes/upgrades listed on "this page"_http://lammps.sandia.gov/bug.html up to a certain date, as stated on the download page. If you want an executable with non-included packages or that is more current, then you'll need to @@ -79,7 +79,7 @@ This section has the following sub-sections: :line -[{Read this first:}] :link(start_2_1) +Read this first :h5,link(start_2_1) If you want to avoid building LAMMPS yourself, read the preceeding section about options available for downloading and installing @@ -148,9 +148,9 @@ include it in the LAMMPS distribution. :line -[{Steps to build a LAMMPS executable:}] :link(start_2_2) +Steps to build a LAMMPS executable :h5,link(start_2_2) -[Step 0] +Step 0 :h6 The src directory contains the C++ source and header files for LAMMPS. It also contains a top-level Makefile and a MAKE sub-directory with @@ -172,10 +172,12 @@ a list of available choices from src/MAKE and all of its sub-directories. If one of those has the options you want or is the machine you want, you can type a command like: -make mpi +make mpi :pre or -make serial_icc + +make serial :pre or + gmake mac :pre Note that the corresponding Makefile.machine can exist in src/MAKE or @@ -189,14 +191,14 @@ Note that on a multi-processor or multi-core platform you can launch a parallel make, by using the "-j" switch with the make command, which will build LAMMPS more quickly. -If you get no errors and an executable like lmp_mpi or lmp_g++_serial -or lmp_mac is produced, then you're done; it's your lucky day. +If you get no errors and an executable like [lmp_mpi] or [lmp_serial] +or [lmp_mac] is produced, then you're done; it's your lucky day. Note that by default only a few of LAMMPS optional packages are installed. To build LAMMPS with optional packages, see "this section"_#start_3 below. -[Step 1] +Step 1 :h6 If Step 0 did not work, you will need to create a low-level Makefile for your machine, like Makefile.foo. You should make a copy of an @@ -207,13 +209,13 @@ the first line, the "compiler/linker settings" section, and the file in src/MAKE/MINE and it will not be altered by any future LAMMPS updates. -[Step 2] +Step 2 :h6 Change the first line of Makefile.foo to list the word "foo" after the "#", and whatever other options it will set. This is the line you will see if you just type "make". -[Step 3] +Step 3 :h6 The "compiler/linker settings" section lists compiler and linker settings for your C++ compiler, including optimization flags. You can @@ -242,7 +244,7 @@ first time on a new platform, a long list of *.d files will be printed out rapidly. This is not an error; it is the Makefile doing its normal creation of dependencies. -[Step 4] +Step 4 :h6 The "system-specific settings" section has several parts. Note that if you change any -D setting in this section, you should do a full @@ -349,7 +351,7 @@ platforms. The -DPACK_ARRAY setting is the default. See the "kspace_style"_kspace_style.html command for info about PPPM. See Step 6 below for info about building LAMMPS with an FFT library. -[Step 5] +Step 5 :h6 The 3 MPI variables are used to specify an MPI library to build LAMMPS with. Note that you do not need to set these if you use the MPI @@ -405,7 +407,7 @@ Note that the ANSI-standard function clock() rolls over after an hour or so, and is therefore insufficient for timing long LAMMPS simulations. -[Step 6] +Step 6 :h6 The 3 FFT variables allow you to specify an FFT library which LAMMPS uses (for performing 1d FFTs) when running the particle-particle @@ -458,7 +460,7 @@ accuracy for reduced memory use and parallel communication costs for transposing 3d FFT data. Note that single precision FFTs have only been tested with the FFTW3, FFTW2, MKL, and KISS FFT options. -[Step 7] +Step 7 :h6 The 3 JPG variables allow you to specify a JPEG and/or PNG library which LAMMPS uses when writing out JPEG or PNG files via the "dump @@ -481,13 +483,13 @@ find it. As before, if these header and library files are in the usual place on your machine, you may not need to set these variables. -[Step 8] +Step 8 :h6 Note that by default only a few of LAMMPS optional packages are installed. To build LAMMPS with optional packages, see "this section"_#start_3 below, before proceeding to Step 9. -[Step 9] +Step 9 :h6 That's it. Once you have a correct Makefile.foo, and you have pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need @@ -506,7 +508,7 @@ You should get the executable lmp_foo when the build is complete. :line -[{Errors that can occur when making LAMMPS:}] :link(start_2_3) +Errors that can occur when making LAMMPS: h5 :link(start_2_3) NOTE: If an error occurs when building LAMMPS, the compiler or linker will state very explicitly what the problem is. The error message @@ -543,22 +545,22 @@ above in Step 4. :line -[{Additional build tips:}] :link(start_2_4) +Additional build tips :h5,link(start_2_4) -(1) Building LAMMPS for multiple platforms. +Building LAMMPS for multiple platforms. :h6 You can make LAMMPS for multiple platforms from the same src directory. Each target creates its own object sub-directory called Obj_target where it stores the system-specific *.o files. -(2) Cleaning up. +Cleaning up. :h6 Typing "make clean-all" or "make clean-machine" will delete *.o object files created when LAMMPS is built, for either all builds or for a particular machine. -(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or --DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL + Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or +-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6 As explained above, any of these 3 settings can be specified on the LMP_INC line in your low-level src/MAKE/Makefile.foo. @@ -608,39 +610,43 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep. :line -[{Building for a Mac:}] :link(start_2_5) +Building for a Mac :h5,link(start_2_5) OS X is BSD Unix, so it should just work. See the src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files. :line -[{Building for Windows:}] :link(start_2_6) +Building for Windows :h5,link(start_2_6) -The LAMMPS download page has an option to download both a serial and -parallel pre-built Windows executable. See the "Running -LAMMPS"_#start_6 section for instructions on running these executables -on a Windows box. +If you want to build a Windows version of LAMMPS, you can build it +yourself, but it may require some effort. LAMMPS expects a Unix-like +build environment for the default build procedure. This can be done +using either Cygwin or MinGW; the latter also exists as a ready-to-use +Linux-to-Windows cross-compiler in several Linux distributions. In +these cases, you can do the installation after installing several +unix-style commands like make, grep, sed and bash with some shell +utilities. -The pre-built executables hosted on the "LAMMPS download -page"_http://lammps.sandia.gov/download.html are built with a subset -of the available packages; see the download page for the list. These -are single executable files. No examples or documentation in -included. You will need to download the full source code package to -obtain those. +For Cygwin and the MinGW cross-compilers, suitable makefiles are +provided in src/MAKE/MACHINES. When using other compilers, like +Visual C++ or Intel compilers for Windows, you may have to implement +your own build system. Since none of the current LAMMPS core developers +has significant experience building executables on Windows, we are +happy to distribute contributed instructions and modifications, but +we cannot provide support for those. + +With the so-called "Anniversary Update" to Windows 10, there is a +Ubuntu subsystem available for Windows, that can be installed and +then it can be used to compile/install LAMMPS as if you are running +on a Ubuntu Linux system. As an alternative, you can download "daily builds" (and some older versions) of the installer packages from "rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html. These executables are built with most optional packages and the -download includes documentation, some tools and most examples. - -If you want a Windows version with specific packages included and -excluded, you can build it yourself. - -One way to do this is install and use cygwin to build LAMMPS with a -standard unix style make program, just as you would on a Linux box; -see src/MAKE/MACHINES/Makefile.cygwin. +download includes documentation, potential files, some tools and +many examples, but no source code. :line @@ -660,7 +666,7 @@ Makefile.machine to add settings needed by some packages. :line -[{Package basics:}] :link(start_3_1) +Package basics: :h5,link(start_3_1) The source code for LAMMPS is structured as a set of core files which are always included, plus optional packages. Packages are groups of @@ -690,7 +696,7 @@ 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"_Section_packages.html of the manual. The +given in "Section 4"_Section_packages.html of the manual. The difference between standard and user packages is as follows: Standard packages, such as molecule or kspace, are supported by the @@ -714,7 +720,7 @@ files or either a standard or user-contributed package are given in :line -[{Including/excluding packages:}] :link(start_3_2) +Including/excluding packages :h5,link(start_3_2) To use (or not use) a package you must include it (or exclude it) before building LAMMPS. From the src directory, this is typically as @@ -788,14 +794,14 @@ package-related make options. :line -[{Packages that require extra libraries:}] :link(start_3_3) +Packages that require extra libraries :h5,link(start_3_3) A few of the standard and user packages require additional auxiliary 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"_Section_packages.html doc page for a list of +"Section 4"_Section_packages.html 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 @@ -873,7 +879,7 @@ the LAMMPS build will typically fail. :line -[{Packages that require Makefile.machine settings}] :link(start_3_4) +Packages that require Makefile.machine settings :h5,link(start_3_4) A few packages require specific settings in Makefile.machine, to either build or use the package effectively. These are the @@ -1033,7 +1039,7 @@ then be called from another application or a scripting language. See LAMMPS to other codes. See "this section"_Section_python.html for more info on wrapping and running LAMMPS from Python. -[Static library:] :h5 +Static library :h5 To build LAMMPS as a static library (*.a file on Linux), type @@ -1047,7 +1053,7 @@ will create the file liblammps_foo.a which another application can link to. It will also create a soft link liblammps.a, which will point to the most recently built static library. -[Shared library:] :h5 +Shared library :h5 To build LAMMPS as a shared library (*.so file on Linux), which can be dynamically loaded, e.g. from Python, type @@ -1055,7 +1061,7 @@ dynamically loaded, e.g. from Python, type make foo mode=shlib :pre where foo is the machine name. This kind of library is required when -wrapping LAMMPS with Python; see "Section_python"_Section_python.html +wrapping LAMMPS with Python; see "Section 11"_Section_python.html 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 @@ -1119,7 +1125,7 @@ For the csh or tcsh shells, you would add something like this to your setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre -[Calling the LAMMPS library:] :h5 +Calling the LAMMPS library :h5 Either flavor of library (static or shared) allows one or more LAMMPS objects to be instantiated from the calling program. @@ -1135,14 +1141,14 @@ 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"_Section_howto.html#howto_10 of the -manual. See "Section_python"_Section_python.html of the manual for a +discussed in "Section 6.10"_Section_howto.html#howto_10 of the +manual. See "Section 11"_Section_python.html 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 -using LAMMPS as a library. See "Section_howto -19"_Section_howto.html#howto_19 of the manual for a description of the +using LAMMPS as a library. See "Section +6.19"_Section_howto.html#howto_19 of the manual for a description of the interface and how to extend it for your needs. :line @@ -1191,23 +1197,17 @@ LAMMPS to be built with one or more of its optional packages. :line On a Windows box, you can skip making LAMMPS and simply download an -executable, as described above, though the pre-packaged executables -include only certain packages. +installer package from "here"_http://rpm.lammps.org/windows.html -To run a LAMMPS executable on a Windows machine, first decide whether -you want to download the non-MPI (serial) or the MPI (parallel) -version of the executable. Download and save the version you have -chosen. - -For the non-MPI version, follow these steps: +For running the non-MPI executable, follow these steps: Get a command prompt by going to Start->Run... , then typing "cmd". :ulb,l -Move to the directory where you have saved lmp_win_no-mpi.exe -(e.g. by typing: cd "Documents"). :l +Move to the directory where you have your input, e.g. a copy of +the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l -At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj +At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj] with the name of your LAMMPS input script. :l :ule @@ -1218,27 +1218,39 @@ Download and install "MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads for Windows. :ulb,l -You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 -package. Put them in same directory (or path) as the LAMMPS Windows -executable. :l +The LAMMPS Windows installer packages will automatically adjust your +path for the default location of this MPI package. After the installation +of the MPICH software, it needs to be integrated into the system. +For this you need to start a Command Prompt in {Administrator Mode} +(right click on the icon and select it). Change into the MPICH2 +installation directory, then into the subdirectory [bin] and execute +[smpd.exe -install]. Exit the command window. -Get a command prompt by going to Start->Run... , +Get a new, regular command prompt by going to Start->Run... , then typing "cmd". :l -Move to the directory where you have saved lmp_win_mpi.exe +Move to the directory where you have your input file (e.g. by typing: cd "Documents"). :l -Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in -in.lj", replacing in.lj with the name of your LAMMPS input script. :l +Then type something like this: -Note that you may need to provide smpd with a passphrase (it doesn't -matter what you type). :l +mpiexec -localonly 4 lmp_mpi -in in.lj :pre +or + +mpiexec -np 4 lmp_mpi -in in.lj :pre + +replacing in.lj with the name of your LAMMPS input script. For the latter +case, you may be prompted to enter your password. :l In this mode, output may not immediately show up on the screen, so if your input script takes a long time to execute, you may need to be -patient before the output shows up. :l Alternatively, you can still -use this executable to run on a single processor by typing something -like: "lmp_win_mpi -in in.lj". :l +patient before the output shows up. :l + +The parallel executable can also run on a single processor by typing +something like: + +lmp_mpi -in in.lj :pre + :ule :line @@ -1257,7 +1269,7 @@ 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"_Section_errors.html for a +message and continue. See "Section 12"_Section_errors.html 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. @@ -1473,7 +1485,7 @@ 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"_Section_howto.html#howto_4 +multiple partitions, see "Section 6.4"_Section_howto.html#howto_4 of the manual. World- and universe-style "variables"_variable.html are useful in this context. @@ -1539,7 +1551,7 @@ cores within each node are ranked in a desired order. Or when using the "run_style verlet/split"_run_style.html 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"_Section_accelerate.html doc pages for +See the "Section 5"_Section_accelerate.html doc pages for more details. If the keyword {nth} is used with a setting {N}, then it means every @@ -1863,7 +1875,7 @@ communication, roughly 75% in the example above. 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"_Section_history.html. The F90 and F77 versions +in "Section 13"_Section_history.html. The F90 and F77 versions (2001 and 99) are also freely distributed as open-source codes; check the "LAMMPS WWW Site"_lws for distribution information if you prefer those versions. The 99 and 2001 versions are no longer under active diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt index 189bc1e35c..3527d228de 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Section_tools.txt @@ -330,7 +330,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn. matlab tool :h4,link(matlab) -The matlab sub-directory contains several "MATLAB"_matlab scripts for +The matlab sub-directory contains several "MATLAB"_matlabhome scripts for post-processing LAMMPS output. The scripts include readers for log and dump files, a reader for EAM potential files, and a converter that reads LAMMPS dump files and produces CFG files that can be visualized @@ -342,7 +342,7 @@ See the README.pdf file for more information. These scripts were written by Arun Subramaniyan at Purdue Univ (asubrama at purdue.edu). -:link(matlab,http://www.mathworks.com) +:link(matlabhome,http://www.mathworks.com) :line @@ -427,9 +427,10 @@ pymol_asphere tool :h4,link(pymol) The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal particles into an input file for the "PyMol visualization -package"_pymol. +package"_pymolhome or its "open source variant"_pymolopen. -:link(pymol,http://pymol.sourceforge.net) +:link(pymolhome,http://www.pymol.org) +:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) Specifically, the tool triangulates the ellipsoids so they can be viewed as true ellipsoidal particles within PyMol. See the README and diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt index 6b4cddf8be..2ac7d62f6c 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/accelerate_gpu.txt @@ -9,7 +9,7 @@ "Return to Section accelerate overview"_Section_accelerate.html -5.3.1 GPU package :h4 +5.3.1 GPU package :h5 The GPU package was developed by Mike Brown at ORNL and his collaborators, particularly Trung Nguyen (ORNL). It provides GPU @@ -26,7 +26,7 @@ between the CPU(s) and GPU every timestep. :l Neighbor lists can be built on the CPU or on the GPU :l -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. :l diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index e1b715e587..43771e101a 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -9,7 +9,7 @@ "Return to Section accelerate overview"_Section_accelerate.html -5.3.2 USER-INTEL package :h4 +5.3.2 USER-INTEL package :h5 The USER-INTEL package is maintained by Mike Brown at Intel Corporation. It provides two methods for accelerating simulations, diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index c33e591712..f49c60857a 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -9,7 +9,7 @@ "Return to Section accelerate overview"_Section_accelerate.html -5.3.3 KOKKOS package :h4 +5.3.3 KOKKOS package :h5 The KOKKOS package was developed primarily by Christian Trott (Sandia) with contributions of various styles by others, including Sikandar diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt index f31bbc42a3..74a3c82381 100644 --- a/doc/src/accelerate_omp.txt +++ b/doc/src/accelerate_omp.txt @@ -9,7 +9,7 @@ "Return to Section accelerate overview"_Section_accelerate.html -5.3.4 USER-OMP package :h4 +5.3.4 USER-OMP package :h5 The USER-OMP package was developed by Axel Kohlmeyer at Temple University. It provides multi-threaded versions of most pair styles, diff --git a/doc/src/accelerate_opt.txt b/doc/src/accelerate_opt.txt index 32ea20af98..704321ca07 100644 --- a/doc/src/accelerate_opt.txt +++ b/doc/src/accelerate_opt.txt @@ -9,7 +9,7 @@ "Return to Section accelerate overview"_Section_accelerate.html -5.3.5 OPT package :h4 +5.3.5 OPT package :h5 The OPT package was developed by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt index e12602ab11..e8217d6556 100644 --- a/doc/src/angle_charmm.txt +++ b/doc/src/angle_charmm.txt @@ -51,7 +51,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -66,7 +66,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index 9977f62417..a29f1a6796 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -81,7 +81,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -96,7 +96,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt index 4f7a0820e7..50b9c9dbb6 100644 --- a/doc/src/angle_cosine.txt +++ b/doc/src/angle_cosine.txt @@ -38,7 +38,7 @@ K (energy) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -53,7 +53,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt index 4a11aadf22..c4e634ad3a 100644 --- a/doc/src/angle_cosine_delta.txt +++ b/doc/src/angle_cosine_delta.txt @@ -43,7 +43,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -58,7 +58,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt index cfd1c3e484..6e62ba56c3 100644 --- a/doc/src/angle_cosine_periodic.txt +++ b/doc/src/angle_cosine_periodic.txt @@ -51,7 +51,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -66,7 +66,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 03b0d947c3..dc1a29a86b 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -41,7 +41,7 @@ theta (angle) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -56,7 +56,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt index 0d23a621b8..48af5ba76a 100644 --- a/doc/src/angle_cosine_shift_exp.txt +++ b/doc/src/angle_cosine_shift_exp.txt @@ -53,7 +53,7 @@ A (real number) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -68,7 +68,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt index a7264087af..e06c0208bf 100644 --- a/doc/src/angle_cosine_squared.txt +++ b/doc/src/angle_cosine_squared.txt @@ -43,7 +43,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -58,7 +58,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt index 18eb57d82f..51072c7d2e 100644 --- a/doc/src/angle_dipole.txt +++ b/doc/src/angle_dipole.txt @@ -71,7 +71,7 @@ gamma0 (degrees) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -86,7 +86,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt index 367b313e58..0afaf0493e 100644 --- a/doc/src/angle_fourier.txt +++ b/doc/src/angle_fourier.txt @@ -39,7 +39,7 @@ C2 (real) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -54,7 +54,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt index 86806b4170..44ebf4268a 100644 --- a/doc/src/angle_fourier_simple.txt +++ b/doc/src/angle_fourier_simple.txt @@ -38,7 +38,7 @@ n (real) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -53,7 +53,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt index a615972d00..f7c5550733 100644 --- a/doc/src/angle_harmonic.txt +++ b/doc/src/angle_harmonic.txt @@ -45,7 +45,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -60,7 +60,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt index c203fd3c7c..b8ce3971b2 100644 --- a/doc/src/angle_quartic.txt +++ b/doc/src/angle_quartic.txt @@ -45,7 +45,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -60,7 +60,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index 759b29f319..70f4746ec7 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -124,7 +124,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -139,7 +139,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angles.txt b/doc/src/angles.txt new file mode 100644 index 0000000000..ff1f68d45a --- /dev/null +++ b/doc/src/angles.txt @@ -0,0 +1,27 @@ +Angle Styles :h1 + + diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 95038b74fb..7e2803abdb 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -98,8 +98,8 @@ output the custom values. All of the above styles define point particles, except the {sphere}, {ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and -{body} styles, which define finite-size particles. See "Section_howto -14"_Section_howto.html#howto_14 for an overview of using finite-size +{body} styles, which define finite-size particles. See "Section +6.14"_Section_howto.html#howto_14 for an overview of using finite-size particle models with LAMMPS. All of the point-particle styles assign mass to particles on a @@ -233,7 +233,7 @@ styles; see "this section"_Section_modify.html. 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -250,7 +250,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/balance.txt b/doc/src/balance.txt index 3f3ad13406..f375efe604 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -140,7 +140,8 @@ partitioning of the simulation box across processors (one sub-box for each of 16 processors); the middle diagram is after a "grid" method has been applied. -:c,image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg) +:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg) +:c The {rcb} style is a "tiling" method which does not produce a logical 3d grid of processors. Rather it tiles the simulation domain with diff --git a/doc/src/body.txt b/doc/src/body.txt index 96debf8f81..7acc297740 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -17,9 +17,9 @@ 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"_Section_howto.html#howto_14 for a general overview of all these -particle types. +simpler entities that body particles. See "Section +6.14"_Section_howto.html#howto_14 for a general overview of all +these particle types. Body particles are used via the "atom_style body"_atom_style.html command. It takes a body style as an argument. The current body @@ -38,8 +38,8 @@ style are described below. NOTE: 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"_Section_modify.html#mod_12 for details on how to add a new body +We hope to add more styles in the future. See "Section +10.12"_Section_modify.html#mod_12 for details on how to add a new body style to the code. :line diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt index 89a8f10e82..e804b5f0f0 100644 --- a/doc/src/bond_class2.txt +++ b/doc/src/bond_class2.txt @@ -43,7 +43,7 @@ K4 (energy/distance^4) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -58,7 +58,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index a60bc9fed3..d7ab09c48f 100644 --- a/doc/src/bond_fene.txt +++ b/doc/src/bond_fene.txt @@ -47,7 +47,7 @@ sigma (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -62,7 +62,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt index 88c0651292..4342231d20 100644 --- a/doc/src/bond_fene_expand.txt +++ b/doc/src/bond_fene_expand.txt @@ -50,7 +50,7 @@ delta (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -65,7 +65,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt index 16d8b59ba3..dbcc83ccc4 100644 --- a/doc/src/bond_harmonic.txt +++ b/doc/src/bond_harmonic.txt @@ -42,7 +42,7 @@ r0 (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -57,7 +57,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt index 4f317fd59c..8cb2d2ce7d 100644 --- a/doc/src/bond_harmonic_shift.txt +++ b/doc/src/bond_harmonic_shift.txt @@ -43,7 +43,7 @@ rc (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -58,7 +58,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt index 36ac210596..836d6afda4 100644 --- a/doc/src/bond_harmonic_shift_cut.txt +++ b/doc/src/bond_harmonic_shift_cut.txt @@ -43,7 +43,7 @@ rc (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -58,7 +58,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt index d42b35a487..0572555c07 100644 --- a/doc/src/bond_morse.txt +++ b/doc/src/bond_morse.txt @@ -41,7 +41,7 @@ r0 (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -56,7 +56,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt index d61694efb2..5830eb229d 100644 --- a/doc/src/bond_nonlinear.txt +++ b/doc/src/bond_nonlinear.txt @@ -41,7 +41,7 @@ lamda (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -56,7 +56,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt index 5c4a7638a0..86d9ed0836 100644 --- a/doc/src/bond_quartic.txt +++ b/doc/src/bond_quartic.txt @@ -76,7 +76,7 @@ delete_bonds all bond 0 remove :pre 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -91,7 +91,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index 3da2706640..aa0e3c8249 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -121,7 +121,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -136,7 +136,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt new file mode 100644 index 0000000000..a900fdf611 --- /dev/null +++ b/doc/src/bonds.txt @@ -0,0 +1,22 @@ +Bond Styles :h1 + + diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt index 91096589a7..ce638f11b3 100644 --- a/doc/src/boundary.txt +++ b/doc/src/boundary.txt @@ -82,7 +82,7 @@ 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"_Section_howto.html#howto_12 of the doc pages +See "Section 6.12"_Section_howto.html#howto_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/src/change_box.txt b/doc/src/change_box.txt index 15111fec08..553f19f504 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -75,7 +75,7 @@ The "create_box"_create_box.html, "read data"_read_data.html, and simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. -See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages +See "Section 6.12"_Section_howto.html#howto_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/src/commands.txt b/doc/src/commands.txt new file mode 100644 index 0000000000..958a6f34f4 --- /dev/null +++ b/doc/src/commands.txt @@ -0,0 +1,109 @@ +Commands :h1 + + diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index 62fa812822..b75d100112 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -50,7 +50,7 @@ which computes this quantity.- 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 97722c935d..439ff5192c 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -73,8 +73,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular momentum 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"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index af0185e37d..b59a3fd4c8 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -46,8 +46,8 @@ in examples/USER/misc/basal. This compute calculates a per-atom array with 3 columns, which can be accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values are unitless since the 3 columns represent diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt index 21f8d63ed1..12ce218853 100644 --- a/doc/src/compute_body_local.txt +++ b/doc/src/compute_body_local.txt @@ -32,7 +32,7 @@ Define a computation that calculates properties of individual body 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"_Section_howto.html#howto_14 +explained below. See "Section 6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html doc page for more details on using body particles. diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index 17403d71e9..2a3ae15aaf 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a By default, this compute calculates the centrosymmetry value for each atom as 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"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. If the {axes} keyword setting is {yes}, then a per-atom array is diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index 9b56c264c9..2778be4f6b 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -101,10 +101,10 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix ave/chunk"_fix_ave_chunk.html command to sum and time average a variety of per-atom properties over the atoms in each chunk. Or they can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed in "Section_howto -15"_Section_howto.html#howto_15. +compute as input, as discussed in "Section +6.15"_Section_howto.html#howto_15. -See "Section_howto 23"_Section_howto.html#howto_23 for an overview of +See "Section 6.23"_Section_howto.html#howto_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 @@ -624,7 +624,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values are unitless chunk IDs, ranging from 1 to diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt index b9137c2491..3ebf1e600e 100644 --- a/doc/src/compute_cluster_atom.txt +++ b/doc/src/compute_cluster_atom.txt @@ -59,7 +59,7 @@ the neighbor list. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_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/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 7aafcaf807..206398fbbd 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be a number from 0 to 5, as explained diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt index b7b367e01a..d497585cb0 100644 --- a/doc/src/compute_com_chunk.txt +++ b/doc/src/compute_com_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -71,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass coordinates of each chunk. These values can be accessed by any command that uses global array values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt index 0b8b31a298..f0bd62f4e8 100644 --- a/doc/src/compute_contact_atom.txt +++ b/doc/src/compute_contact_atom.txt @@ -36,7 +36,7 @@ specified compute group. 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"_Section_howto.html#howto_15 for an +input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 123feaf7dc..012a87a9a7 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -76,8 +76,8 @@ If single {type1} keyword is specified (or if none are specified), this compute calculates a per-atom vector. If multiple {typeN} keywords are specified, this compute calculates a per-atom array, with N columns. These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector or array values will be a number >= 0.0, as diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index ab76cf82de..94f49492d1 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -44,7 +44,7 @@ group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values are unitlesss numbers (damage) >= 0.0. diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt index 0d2a8011e2..7dfddfd6a1 100644 --- a/doc/src/compute_dipole_chunk.txt +++ b/doc/src/compute_dipole_chunk.txt @@ -32,8 +32,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -76,8 +76,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 4 for the x,y,z dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global -array values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +array values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 7420dffef0..566dcfc0a0 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -53,8 +53,8 @@ correctly with time=0 atom coordinates from the restart file. This compute calculates a per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom array values will be in distance "units"_units.html. diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index 0ce40f66f4..f586e0f092 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -36,7 +36,7 @@ particles. This compute calculates a per-particle array with 4 columns (u_cond, u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See -"Section_howto15"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-particle array values will be in energy (u_cond, u_mech, u_chem) diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt index 7d21c55796..b9a486c32e 100644 --- a/doc/src/compute_erotate_asphere.txt +++ b/doc/src/compute_erotate_asphere.txt @@ -40,7 +40,7 @@ will be the same as in 3d. 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"_Section_howto.html#howto_15 for an +input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt index 58f511a624..dec0939a43 100644 --- a/doc/src/compute_erotate_rigid.txt +++ b/doc/src/compute_erotate_rigid.txt @@ -42,7 +42,7 @@ 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt index b8207da8a3..41e80b0154 100644 --- a/doc/src/compute_erotate_sphere.txt +++ b/doc/src/compute_erotate_sphere.txt @@ -35,7 +35,7 @@ as in 3d. 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"_Section_howto.html#howto_15 for an +input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt index d444381fb3..a0081ff6a8 100644 --- a/doc/src/compute_erotate_sphere_atom.txt +++ b/doc/src/compute_erotate_sphere_atom.txt @@ -39,7 +39,7 @@ in the specified compute group or for point particles with a radius = 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index 4d638c74f3..d836cac17f 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -43,7 +43,7 @@ local atom displacements and may generate "false postives." 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"_Section_howto.html#howto_15 for an +input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index c5fb2f0b70..f4325f620f 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these are used in the simulation. These output results can be used by any command that uses a global -scalar or vector from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +scalar or vector from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. For example, the computed values can be averaged using "fix ave/time"_fix_ave_time.html. diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index dc03234dee..dd71431527 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -55,8 +55,8 @@ using the "set image"_set.html command. This compute calculates a global scalar (Rg) and a global vector of length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt index 53b35213b0..3beecce58f 100644 --- a/doc/src/compute_gyration_chunk.txt +++ b/doc/src/compute_gyration_chunk.txt @@ -35,8 +35,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt index bbcab832b0..c6f111a6cc 100644 --- a/doc/src/compute_hexorder_atom.txt +++ b/doc/src/compute_hexorder_atom.txt @@ -96,8 +96,8 @@ real and imaginary parts {qn}, a complex number restricted to the unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 . These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index 6f28ed0aa5..215f3c1a8a 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -72,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses global array values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt index 330306f11e..caee897162 100644 --- a/doc/src/compute_ke.txt +++ b/doc/src/compute_ke.txt @@ -44,7 +44,7 @@ include different degrees of freedom (translational, rotational, etc). 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"_Section_howto.html#howto_15 +compute as input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt index 66abf81a59..f5431f0569 100644 --- a/doc/src/compute_ke_atom.txt +++ b/doc/src/compute_ke_atom.txt @@ -34,7 +34,7 @@ specified compute group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt index 8d85043e3a..c2bc90b253 100644 --- a/doc/src/compute_ke_atom_eff.txt +++ b/doc/src/compute_ke_atom_eff.txt @@ -58,7 +58,7 @@ electrons) not in the specified compute group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt index 61c46d3377..14fc887c3c 100644 --- a/doc/src/compute_ke_eff.txt +++ b/doc/src/compute_ke_eff.txt @@ -61,7 +61,7 @@ See "compute temp/eff"_compute_temp_eff.html. 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"_Section_howto.html#howto_15 for an +input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt index 4e65cae72e..f79696a77a 100644 --- a/doc/src/compute_ke_rigid.txt +++ b/doc/src/compute_ke_rigid.txt @@ -40,8 +40,8 @@ calculation. This compute calculates a global scalar (the summed KE 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"_Section_howto.html#howto_15 for an overview of LAMMPS output +global scalar value from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt index 82a3f1db90..4e621b4301 100644 --- a/doc/src/compute_meso_e_atom.txt +++ b/doc/src/compute_meso_e_atom.txt @@ -38,7 +38,7 @@ specified compute group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt index e3aa513180..a017424dd0 100644 --- a/doc/src/compute_meso_rho_atom.txt +++ b/doc/src/compute_meso_rho_atom.txt @@ -38,7 +38,7 @@ specified compute group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in mass/volume "units"_units.html. diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt index 002aae7980..9e81b038f4 100644 --- a/doc/src/compute_meso_t_atom.txt +++ b/doc/src/compute_meso_t_atom.txt @@ -40,7 +40,7 @@ specified compute group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in temperature "units"_units.html. diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 8d3ba07857..7382ca87de 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt index 8c09cecfce..46c72d3dcb 100644 --- a/doc/src/compute_omega_chunk.txt +++ b/doc/src/compute_omega_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -73,8 +73,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular velocity 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"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 11579fe627..3b6c58c826 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -99,8 +99,8 @@ This compute calculates a per-atom array with {nlvalues} columns, giving the {Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1. These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt index 2e3f5d8beb..15f27a8eff 100644 --- a/doc/src/compute_pe.txt +++ b/doc/src/compute_pe.txt @@ -64,8 +64,8 @@ See the "thermo_style" command for more details. This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index 937e680926..78c0b8e1e6 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -80,7 +80,7 @@ those are global contributions to the system energy. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index d22b9b8aa7..06b22b19a2 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -98,7 +98,7 @@ where "thermo_temp" is the ID of a similarly defined compute of style 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -113,7 +113,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index c10fe56455..578a6df343 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -36,8 +36,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index 88fe2bd005..73d147c361 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -121,7 +121,7 @@ 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index b28f94d969..a0afc8d2c3 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -192,7 +192,7 @@ This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a -compute as input. See "Section_howto 15"_Section_howto.html#howto_15 +compute as input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt index 914357ed76..a2cb378be0 100644 --- a/doc/src/compute_smd_contact_radius.txt +++ b/doc/src/compute_smd_contact_radius.txt @@ -37,7 +37,7 @@ specified compute group. 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"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-particle vector values will be in distance "units"_units.html. diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt index 7d0b4d0dbc..1cec0090b5 100644 --- a/doc/src/compute_smd_triangle_mesh_vertices.txt +++ b/doc/src/compute_smd_triangle_mesh_vertices.txt @@ -4,8 +4,6 @@ :link(ld,Manual.html) :link(lc,Section_commands.html#comm) -:link(ls,fix_smd_wall_surface.html) - :line compute smd/triangle/mesh/vertices :h3 @@ -25,7 +23,7 @@ compute 1 all smd/triangle/mesh/vertices :pre 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. +smd/wall_surface"_fix_smd_wall_surface.html. See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. @@ -42,10 +40,10 @@ The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and 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"_fix_smd_wall_surface.html 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 +generate a VTK representation of the smd/wall_surface mesh for visualization purposes. The values will be given in "units"_units.html of distance. @@ -58,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"compute smd/move/tri/surf"_fix_smd_move_triangulated_surface.html, -"compute smd/wall/surface"_ls +"fix smd/move/tri/surf"_fix_smd_move_triangulated_surface.html, +"fix smd/wall_surface"_fix_smd_wall_surface.html [Default:] none diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt index 29eb32d5b1..1e08e0cca4 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.txt +++ b/doc/src/compute_smd_ulsph_num_neighs.txt @@ -32,7 +32,7 @@ Mach Dynamics in LAMMPS. 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"_Section_howto.html#howto_15 for an overview of +See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-particle values will be given dimentionless, see "units"_units.html. diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt index 5a36515e84..1eb6bc7c2b 100644 --- a/doc/src/compute_smd_ulsph_strain.txt +++ b/doc/src/compute_smd_ulsph_strain.txt @@ -31,7 +31,7 @@ Mach Dynamics in LAMMPS. 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"_Section_howto.html#howto_15 for an overview of +See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-particle vector has 6 entries, corresponding to the xx, yy, diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt index 3f32e43912..eb9318e072 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.txt +++ b/doc/src/compute_smd_ulsph_strain_rate.txt @@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The values will be given in "units"_units.html of one over time. diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt index 4d1994e37c..115a4d14bb 100644 --- a/doc/src/compute_smd_ulsph_stress.txt +++ b/doc/src/compute_smd_ulsph_stress.txt @@ -30,8 +30,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index b8e3f9b732..7f10fdbcce 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -205,8 +205,8 @@ notation. Each of these sub-blocks contains one column for each bispectrum component, the same as for compute {sna/atom} These values can be accessed by any command that uses per-atom values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 35e586068b..2749478439 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -137,8 +137,8 @@ thermo_style custom step temp etotal press v_press :pre This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom array values will be in pressure*volume diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt index 07be3c46ac..0bd2d4b121 100644 --- a/doc/src/compute_temp.txt +++ b/doc/src/compute_temp.txt @@ -67,7 +67,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -82,7 +82,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index 826d0f6e00..d565c95134 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -52,8 +52,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -210,8 +210,8 @@ of the optional values are specified. The number of rows in the array "compute chunk/atom"_compute_chunk_atom.html command. The number of columns is the number of specifed values (1 or more). These values can be accessed by any command that uses global array values from a -compute as input. Again, see "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +compute as input. Again, see "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 9cdb3a9ba7..46846d6ee5 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -28,7 +28,7 @@ Define a computation that calculates the temperature of a system based 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)"_#MitchellFinchham. See -"Section_howto 25"_Section_howto.html#howto_25 of the manual for an +"Section 6.25"_Section_howto.html#howto_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 @@ -83,8 +83,8 @@ langevin"_fix_langevin.html. The internal energy of core/shell pairs can be calculated by the "compute temp/chunk"_compute_temp_chunk.html command, if chunks are -defined as core/shell pairs. See "Section_howto -25"_Section_howto.html#howto_25 for more discussion on how to do this. +defined as core/shell pairs. See "Section +6.25"_Section_howto.html#howto_25 for more discussion on how to do this. [Output info:] diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt index 798d3a270b..163a00af52 100644 --- a/doc/src/compute_temp_partial.txt +++ b/doc/src/compute_temp_partial.txt @@ -74,7 +74,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -89,7 +89,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index 1fbbb592f2..71b62281dc 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -111,8 +111,8 @@ du/dl can be found in the paper by "Eike"_#Eike. This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index 7d14dab2ac..b9f832dd03 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -72,7 +72,7 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html 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"_Section_howto.html#howto_15 +compute as input. See "Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt index 0b9154713f..de02c586bf 100644 --- a/doc/src/compute_vcm_chunk.txt +++ b/doc/src/compute_vcm_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -63,8 +63,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index 3dcdffacb1..899fc84388 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -186,8 +186,8 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the {occupation} keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. If the {peratom} keyword is set to "no", the per-atom array is still created, but it is not accessible. diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt index 826970ffd9..dc0eff03da 100644 --- a/doc/src/compute_xrd.txt +++ b/doc/src/compute_xrd.txt @@ -40,8 +40,6 @@ compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre -:pre - [Description:] Define a computation that calculates x-ray diffraction intensity as described @@ -107,48 +105,48 @@ Coefficients parameterized by "(Peng)"_#Peng are assigned for each atom type designating the chemical symbol and charge of each atom type. Valid chemical symbols for compute xrd are: - H: He1-: He: Li: Li1+: - Be: Be2+: B: C: Cval: - N: O: O1-: F: F1-: - Ne: Na: Na1+: Mg: Mg2+: - Al: Al3+: Si: Sival: Si4+: - P: S: Cl: Cl1-: Ar: - K: Ca: Ca2+: Sc: Sc3+: - Ti: Ti2+: Ti3+: Ti4+: V: - V2+: V3+: V5+: Cr: Cr2+: - Cr3+: Mn: Mn2+: Mn3+: Mn4+: - Fe: Fe2+: Fe3+: Co: Co2+: - Co: Ni: Ni2+: Ni3+: Cu: - Cu1+: Cu2+: Zn: Zn2+: Ga: - Ga3+: Ge: Ge4+: As: Se: - Br: Br1-: Kr: Rb: Rb1+: - Sr: Sr2+: Y: Y3+: Zr: - Zr4+: Nb: Nb3+: Nb5+: Mo: - Mo3+: Mo5+: Mo6+: Tc: Ru: - Ru3+: Ru4+: Rh: Rh3+: Rh4+: - Pd: Pd2+: Pd4+: Ag: Ag1+: - Ag2+: Cd: Cd2+: In: In3+: - Sn: Sn2+: Sn4+: Sb: Sb3+: - Sb5+: Te: I: I1-: Xe: - Cs: Cs1+: Ba: Ba2+: La: - La3+: Ce: Ce3+: Ce4+: Pr: - Pr3+: Pr4+: Nd: Nd3+: Pm: - Pm3+: Sm: Sm3+: Eu: Eu2+: - Eu3+: Gd: Gd3+: Tb: Tb3+: - Dy: Dy3+: Ho: Ho3+: Er: - Er3+: Tm: Tm3+: Yb: Yb2+: - Yb3+: Lu: Lu3+: Hf: Hf4+: - Ta: Ta5+: W: W6+: Re: - Os: Os4+: Ir: Ir3+: Ir4+: - Pt: Pt2+: Pt4+: Au: Au1+: - Au3+: Hg: Hg1+: Hg2+: Tl: - Tl1+: Tl3+: Pb: Pb2+: Pb4+: - Bi: Bi3+: Bi5+: Po: At: - Rn: Fr: Ra: Ra2+: Ac: - Ac3+: Th: Th4+: Pa: U: - U3+: U4+: U6+: Np: Np3+: - Np4+: Np6+: Pu: Pu3+: Pu4+: - Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:) + H| He1-| He| Li| Li1+| + Be| Be2+| B| C| Cval| + N| O| O1-| F| F1-| + Ne| Na| Na1+| Mg| Mg2+| + Al| Al3+| Si| Sival| Si4+| + P| S| Cl| Cl1-| Ar| + K| Ca| Ca2+| Sc| Sc3+| + Ti| Ti2+| Ti3+| Ti4+| V| + V2+| V3+| V5+| Cr| Cr2+| + Cr3+| Mn| Mn2+| Mn3+| Mn4+| + Fe| Fe2+| Fe3+| Co| Co2+| + Co| Ni| Ni2+| Ni3+| Cu| + Cu1+| Cu2+| Zn| Zn2+| Ga| + Ga3+| Ge| Ge4+| As| Se| + Br| Br1-| Kr| Rb| Rb1+| + Sr| Sr2+| Y| Y3+| Zr| + Zr4+| Nb| Nb3+| Nb5+| Mo| + Mo3+| Mo5+| Mo6+| Tc| Ru| + Ru3+| Ru4+| Rh| Rh3+| Rh4+| + Pd| Pd2+| Pd4+| Ag| Ag1+| + Ag2+| Cd| Cd2+| In| In3+| + Sn| Sn2+| Sn4+| Sb| Sb3+| + Sb5+| Te| I| I1-| Xe| + Cs| Cs1+| Ba| Ba2+| La| + La3+| Ce| Ce3+| Ce4+| Pr| + Pr3+| Pr4+| Nd| Nd3+| Pm| + Pm3+| Sm| Sm3+| Eu| Eu2+| + Eu3+| Gd| Gd3+| Tb| Tb3+| + Dy| Dy3+| Ho| Ho3+| Er| + Er3+| Tm| Tm3+| Yb| Yb2+| + Yb3+| Lu| Lu3+| Hf| Hf4+| + Ta| Ta5+| W| W6+| Re| + Os| Os4+| Ir| Ir3+| Ir4+| + Pt| Pt2+| Pt4+| Au| Au1+| + Au3+| Hg| Hg1+| Hg2+| Tl| + Tl1+| Tl3+| Pb| Pb2+| Pb4+| + Bi| Bi3+| Bi5+| Po| At| + Rn| Fr| Ra| Ra2+| Ac| + Ac3+| Th| Th4+| Pa| U| + U3+| U4+| U6+| Np| Np3+| + Np4+| Np6+| Pu| Pu3+| Pu4+| + Pu6+| Am| Cm| Bk| Cf :tb(c=5,s=|) If the {echo} keyword is specified, compute xrd will provide extra reporting information to the screen. diff --git a/doc/src/computes.txt b/doc/src/computes.txt new file mode 100644 index 0000000000..e7e54a6b3b --- /dev/null +++ b/doc/src/computes.txt @@ -0,0 +1,120 @@ +Computes :h1 + + diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt index f0cabdba22..f4ef13654c 100644 --- a/doc/src/create_box.txt +++ b/doc/src/create_box.txt @@ -73,7 +73,7 @@ factors that exceed these limits, you can use the "box tilt"_box.html command, with a setting of {large}; a setting of {small} is the default. -See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages +See "Section 6.12"_Section_howto.html#howto_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/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 7fbdd40296..d0a3ae6b38 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -86,7 +86,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -101,7 +101,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt index e5431f5557..3c92eb0faf 100644 --- a/doc/src/dihedral_class2.txt +++ b/doc/src/dihedral_class2.txt @@ -140,7 +140,7 @@ r3 (distance) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -155,7 +155,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt index cfdac4ca79..5b43cbbe7f 100644 --- a/doc/src/dihedral_coeff.txt +++ b/doc/src/dihedral_coeff.txt @@ -23,8 +23,6 @@ dihedral_coeff 2* 80.0 1 3 0.5 :pre [Description:] -:line - Specify the dihedral force field coefficients for one or more dihedral types. The number and meaning of the coefficients depends on the dihedral style. Dihedral coefficients can also be set in the data file read by the diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt index b4c8351d6d..89614a3fdb 100644 --- a/doc/src/dihedral_cosine_shift_exp.txt +++ b/doc/src/dihedral_cosine_shift_exp.txt @@ -52,7 +52,7 @@ A (real number) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -67,7 +67,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt index 5cda91fe48..0a7a28c6e8 100644 --- a/doc/src/dihedral_fourier.txt +++ b/doc/src/dihedral_fourier.txt @@ -33,7 +33,7 @@ m (integer >=1) K1 (energy) n1 (integer >= 0) d1 (degrees) -.... +\[...\] Km (energy) nm (integer >= 0) dm (degrees) :ul @@ -43,7 +43,7 @@ dm (degrees) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -58,7 +58,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index 1de4370a46..2bff254705 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -53,7 +53,7 @@ Some force fields let {n} be positive or negative which corresponds 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -68,7 +68,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt index 573d9f14d4..59bc1407a4 100644 --- a/doc/src/dihedral_helix.txt +++ b/doc/src/dihedral_helix.txt @@ -46,7 +46,7 @@ C (energy) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -61,7 +61,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt index c2de676a96..8504bdc0ae 100644 --- a/doc/src/dihedral_multi_harmonic.txt +++ b/doc/src/dihedral_multi_harmonic.txt @@ -40,7 +40,7 @@ A5 (energy) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -55,7 +55,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt index cd614ae907..8c66c30fc1 100644 --- a/doc/src/dihedral_nharmonic.txt +++ b/doc/src/dihedral_nharmonic.txt @@ -40,7 +40,7 @@ An (energy) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -55,7 +55,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt index b5e8da93a8..ac1ab70682 100644 --- a/doc/src/dihedral_opls.txt +++ b/doc/src/dihedral_opls.txt @@ -48,7 +48,7 @@ K4 (energy) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -63,7 +63,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt index ce018e2b0e..4ab5eadf2f 100644 --- a/doc/src/dihedral_quadratic.txt +++ b/doc/src/dihedral_quadratic.txt @@ -41,7 +41,7 @@ phi0 (degrees) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -56,7 +56,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 3386c774ff..86d22977f4 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -59,7 +59,7 @@ v1 (typically 0.0 or 1.0) 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/src/dihedral_table.txt b/doc/src/dihedral_table.txt index bad6ad2c0d..f34b22f435 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -174,7 +174,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/dihedrals.txt b/doc/src/dihedrals.txt new file mode 100644 index 0000000000..500a6a52bf --- /dev/null +++ b/doc/src/dihedrals.txt @@ -0,0 +1,39 @@ +Dihedral Styles :h1 + + diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt index 4f1ee68a9c..0531e92acf 100644 --- a/doc/src/dimension.txt +++ b/doc/src/dimension.txt @@ -26,7 +26,7 @@ prior to setting up a simulation box via the "create_box"_create_box.html or "read_data"_read_data.html commands. Restart files also store this setting. -See the discussion in "Section_howto"_Section_howto.html for +See the discussion in "Section 6"_Section_howto.html for additional instructions on how to run 2d simulations. NOTE: Some models in LAMMPS treat particles as finite-size spheres or diff --git a/doc/src/dump.txt b/doc/src/dump.txt index ffeef1b0f6..694295699b 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -626,7 +626,7 @@ 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"_fix_property_atom.html. -See "Section_modify"_Section_modify.html of the manual for information +See "Section 10"_Section_modify.html 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/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt index c2408bab90..7c577d4351 100644 --- a/doc/src/dump_custom_vtk.txt +++ b/doc/src/dump_custom_vtk.txt @@ -306,7 +306,7 @@ 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"_Section_modify.html of the manual for information +See "Section 10"_Section_modify.html 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/src/dump_image.txt b/doc/src/dump_image.txt index 09afe1ae9d..b2491721ec 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -606,7 +606,7 @@ supported. :l :line -See "Section_modify"_Section_modify.html of the manual for information +See "Section 10"_Section_modify.html 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/src/fix_addforce.txt b/doc/src/fix_addforce.txt index 8bed79ebe4..da9f98a6da 100644 --- a/doc/src/fix_addforce.txt +++ b/doc/src/fix_addforce.txt @@ -106,7 +106,7 @@ 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -120,7 +120,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index d02fa17e10..3ed91c8612 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -94,8 +94,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt index 9d450c7d69..d980e9a211 100644 --- a/doc/src/fix_aveforce.txt +++ b/doc/src/fix_aveforce.txt @@ -66,7 +66,7 @@ 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -80,7 +80,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index b836869607..c997b7c27e 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -111,7 +111,8 @@ the simulation box across processors (one sub-box for each of 16 processors); the middle diagram is after a "grid" method has been applied. -:c,image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg) +:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg) +:c The {rcb} style is a "tiling" method which does not produce a logical 3d grid of processors. Rather it tiles the simulation domain with diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 6b3118b74f..01884803ab 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -545,7 +545,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -560,7 +560,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt index 5550fe72ce..1dce620033 100644 --- a/doc/src/fix_enforce2d.txt +++ b/doc/src/fix_enforce2d.txt @@ -30,7 +30,7 @@ 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -44,7 +44,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt index 14bd1afb8c..6a4f6c2fcf 100644 --- a/doc/src/fix_freeze.txt +++ b/doc/src/fix_freeze.txt @@ -34,7 +34,7 @@ using "fix setforce"_fix_setforce.html. 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -48,7 +48,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index 9b047563f1..22019e7442 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -19,17 +19,17 @@ Tstart, Tstop = temperature ramp during the run :l Amatrix = file to read the drift matrix A from :l seed = random number seed to use for generating noise (positive integer) :l zero or more keyword/value pairs may be appended :l -keyword = {noneq} and/or {every} - {noneq} Cmatrix = file to read the non-equilibrium covariance matrix from - {every} stride = apply the GLE once every time steps. Reduces the accuracy - of the integration of the GLE, but has *no effect* on the accuracy of equilibrium - sampling. It might change sampling properties when used together with {noneq}. + keyword = {noneq} or {every} + {noneq} Cmatrix = file to read the non-equilibrium covariance matrix from + {every} stride = apply the GLE once every time steps. Reduces the accuracy + of the integration of the GLE, but has *no effect* on the accuracy of equilibrium + sampling. It might change sampling properties when used together with {noneq}. :pre :ule [Examples:] fix 3 boundary gle 6 300 300 31415 smart.A -fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C +fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C :pre [Description:] @@ -48,7 +48,7 @@ with Ns additional degrees of freedom s, and the equations of motion become dq/dt=p/m -d(p,s)/dt=(F,0) - A(p,s) + B dW/dt +d(p,s)/dt=(F,0) - A(p,s) + B dW/dt :pre where F is the physical force, A is the drift matrix (that generalizes the friction in Langevin dynamics), B is the diffusion term and dW/dt diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index 242eb7d942..d2f15c195c 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -90,7 +90,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -105,7 +105,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index c429869580..4f27d481a8 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -26,7 +26,7 @@ fix 1 all ipi mysocket 666 unix [Description:] This fix enables LAMMPS to be run as a client for the i-PI Python -wrapper "(IPI)"_#IPI for performing a path integral molecular dynamics +wrapper "(IPI)"_#ipihome for performing a path integral molecular dynamics (PIMD) simulation. The philosophy behind i-PI is described in the following publication "(IPI-CPC)"_#IPICPC. @@ -86,6 +86,6 @@ environment. [(IPI-CPC)] Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014). -:link(IPI) +:link(ipihome) [(IPI)] "http://epfl-cosmo.github.io/gle4md/index.html?page=ipi"_http://epfl-cosmo.github.io/gle4md/index.html?page=ipi diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 8d0011d8ff..a1d3f97f04 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -264,7 +264,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -279,7 +279,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt index 89474d8052..bd42978c27 100755 --- a/doc/src/fix_lb_rigid_pc_sphere.txt +++ b/doc/src/fix_lb_rigid_pc_sphere.txt @@ -18,7 +18,7 @@ bodystyle = {single} or {molecule} or {group} :l {single} args = none {molecule} args = none {group} args = N groupID1 groupID2 ... - N = # of groups + N = # of groups :pre zero or more keyword/value pairs may be appended :l keyword = {force} or {torque} or {innerNodes} :l {force} values = M xflag yflag zflag diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index c84b46a422..c632ec63db 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -26,7 +26,7 @@ Add inter-replica forces to atoms in the group for a multi-replica simulation run via the "neb"_neb.html command to perform a nudged elastic band (NEB) calculation for transition state finding. Hi-level explanations of NEB are given with the "neb"_neb.html command and in -"Section_howto 5"_Section_howto.html#howto_5 of the manual. The fix +"Section 6.5"_Section_howto.html#howto_5 of the manual. The fix neb command must be used with the "neb" command to define how inter-replica forces are computed. @@ -37,7 +37,7 @@ NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting on the atoms of each intermediate replica I is altered, as described in the "(Henkelman1)"_#Henkelman1 paper, to become: -Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That :pre +Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its neighbor replicas. That (t with a hat over it) is @@ -98,9 +98,9 @@ for more info on packages. [Default:] none -:link(Henkelman) +:link(Henkelman1) [(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). -:link(Henkelman) +:link(Henkelman2) [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 36c00d8e37..192f88b8f3 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -490,7 +490,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -505,7 +505,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt index 8977962402..059498a843 100755 --- a/doc/src/fix_nph_asphere.txt +++ b/doc/src/fix_nph_asphere.txt @@ -81,7 +81,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -96,7 +96,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt index 71dd4c607c..ad5ffd8026 100755 --- a/doc/src/fix_nph_body.txt +++ b/doc/src/fix_nph_body.txt @@ -80,7 +80,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -95,7 +95,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt index 85df2ee7aa..e2ce458539 100755 --- a/doc/src/fix_nph_sphere.txt +++ b/doc/src/fix_nph_sphere.txt @@ -81,7 +81,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -96,7 +96,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nphug.txt b/doc/src/fix_nphug.txt index 7b499b8b3c..50003142d9 100644 --- a/doc/src/fix_nphug.txt +++ b/doc/src/fix_nphug.txt @@ -140,7 +140,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -155,7 +155,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt index 4c39a5ccd5..3705c8cc59 100755 --- a/doc/src/fix_npt_asphere.txt +++ b/doc/src/fix_npt_asphere.txt @@ -105,7 +105,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -120,7 +120,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt index db5052fa8a..54501ca765 100755 --- a/doc/src/fix_npt_body.txt +++ b/doc/src/fix_npt_body.txt @@ -104,7 +104,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -119,7 +119,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt index 447e51fc4d..be6e085c26 100755 --- a/doc/src/fix_npt_sphere.txt +++ b/doc/src/fix_npt_sphere.txt @@ -104,7 +104,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -119,7 +119,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nve.txt b/doc/src/fix_nve.txt index 3dda010e78..7ad8301877 100644 --- a/doc/src/fix_nve.txt +++ b/doc/src/fix_nve.txt @@ -34,7 +34,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -49,7 +49,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt index f43ff23d04..1a6febe764 100755 --- a/doc/src/fix_nve_asphere.txt +++ b/doc/src/fix_nve_asphere.txt @@ -45,7 +45,7 @@ This fix is not invoked during "energy minimization"_minimize.html. 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -60,7 +60,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt index 77d0a5e909..0f80d3aa7a 100755 --- a/doc/src/fix_nve_body.txt +++ b/doc/src/fix_nve_body.txt @@ -24,8 +24,8 @@ fix 1 all nve/body :pre Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body 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"_Section_howto.html#howto_14 of the manual and the "body"_body.html +consistent with the microcanonical ensemble. See "Section +6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html doc page for more details on using body particles. This fix differs from the "fix nve"_fix_nve.html command, which diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt index 5ae29434fb..cef1d91cca 100755 --- a/doc/src/fix_nve_line.txt +++ b/doc/src/fix_nve_line.txt @@ -25,8 +25,8 @@ Perform constant NVE integration to update position, velocity, 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"_Section_howto.html of the manual for an overview of -using line segment particles. +"Section 6.14"_Section_howto.html#howto_14 of the manual for an +overview of using line segment particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt index 7bc2a78553..f294615a56 100644 --- a/doc/src/fix_nve_manifold_rattle.txt +++ b/doc/src/fix_nve_manifold_rattle.txt @@ -35,7 +35,7 @@ Perform constant NVE integration to update position and velocity for atoms constrained to a curved surface (manifold) in the group each timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen written out for the special case of single-particle constraints as -explained in "(Paquay)"_#Paquay. V is volume; E is energy. This way, +explained in "(Paquay)"_#Paquay2. V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates Brownian motion of particles constrained to a curved @@ -95,7 +95,7 @@ manifoldforce"_fix_manifoldforce.html :link(Andersen) [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). -:link(Paquay) +:link(Paquay2) [(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index e49ca463dd..f5a303ca03 100755 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -57,7 +57,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -72,7 +72,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt index e8ee78609a..47ecc69e9a 100755 --- a/doc/src/fix_nve_tri.txt +++ b/doc/src/fix_nve_tri.txt @@ -23,10 +23,10 @@ fix 1 all nve/tri :pre 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"_Section_howto.html 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"_Section_howto.html#howto_14 of the manual for an +overview of using triangular particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt index 316320a0e2..eaf6ef83aa 100755 --- a/doc/src/fix_nvt_asphere.txt +++ b/doc/src/fix_nvt_asphere.txt @@ -86,7 +86,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -101,7 +101,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt index de570d0a22..3941425177 100755 --- a/doc/src/fix_nvt_body.txt +++ b/doc/src/fix_nvt_body.txt @@ -85,7 +85,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -100,7 +100,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt index 42a06d4ed7..a1a2a855de 100644 --- a/doc/src/fix_nvt_manifold_rattle.txt +++ b/doc/src/fix_nvt_manifold_rattle.txt @@ -37,7 +37,7 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0 [Description:] -This fix combines the RATTLE-based "(Andersen)"_#Andersen time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay with a Nose-Hoover-chain thermostat to sample the +This fix combines the RATTLE-based "(Andersen)"_#Andersen time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 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"_manifolds.html @@ -75,7 +75,7 @@ section for more info. :link(Andersen) [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). -:link(Paquay) +:link(Paquay3) [(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index edd58f0ed5..7a5ae027f8 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -109,7 +109,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -124,7 +124,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt index 99effb9211..d1594354fb 100755 --- a/doc/src/fix_nvt_sphere.txt +++ b/doc/src/fix_nvt_sphere.txt @@ -86,7 +86,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -101,7 +101,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 7c71aab1d7..05a7e2c5ad 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -62,7 +62,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -77,7 +77,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index e2c3d5d02a..e1ed027676 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -74,7 +74,7 @@ This fix is invoked during "energy minimization"_minimize.html. 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -89,7 +89,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index fb6f0e29cb..4548c3817b 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -642,7 +642,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -657,7 +657,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index 97ffd89c65..e32fbc608b 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -75,7 +75,7 @@ but no more than max_steps will be taken. If max_steps is reached, an error warn is printed and the simulation is stopped. After each ODE step, the solution error {e} is tested and weighted using the absTol -and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol) +and relTol values. The error vector is weighted as {e} / (relTol * | {u} | + absTol) where {u} is the solution vector. If the norm of the error is <= 1, the solution is accepted, {h} is increased by a proportional amount, and the next ODE step is begun. Otherwise, {h} is shrunk and the ODE step is repeated. diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index 072c09a293..90766fc5bc 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -68,7 +68,7 @@ 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -85,7 +85,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 2c99705a79..b084eff839 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -148,7 +148,7 @@ 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -162,7 +162,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 21de9a9e0b..4952127f86 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -30,7 +30,7 @@ nve"_fix_nve.html or "fix nph"_fix_nh.html). The stochastic integration of the dissipative and random forces is performed prior to the deterministic integration of the conservative force. Further details regarding the method are provided in "(Lisal)"_#Lisal and -"(Larentzos)"_#Larentzos. +"(Larentzos1)"_#Larentzos1. The fix {shardlow} must be used with the "pair_style dpd/fdt"_pair_style.html or "pair_style @@ -83,14 +83,14 @@ particle dynamics as isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", J. Chem. Phys., 135, 204105 (2011). -:link(Larentzos) -[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and +:link(Larentzos1) +[(Larentzos1)] J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). -:link(Larentzos) -[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and +:link(Larentzos2) +[(Larentzos2)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/src/fix_smd_tlsph_reference_configuration.txt b/doc/src/fix_smd_tlsph_reference_configuration.txt deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index b6c9b4950d..2fdc352d50 100755 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -86,7 +86,7 @@ NOTE: It is importante to keep the center of mass fixed during the thermodynamic integration, a non-zero total velocity will result in divergencies during the integration due to the fact that the atoms are 'attatched' to its equilibrium positions by the Einstein -crystal. Check the option {zero} of "fix langevin"_fix_langevin_html +crystal. Check the option {zero} of "fix langevin"_fix_langevin.html and "velocity"_velocity.html. The use of the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is NOT recommended due to its well documented issues with the canonical sampling of harmonic degrees of freedom diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt index 8159e1f5bb..d7fe49255f 100644 --- a/doc/src/fix_tune_kspace.txt +++ b/doc/src/fix_tune_kspace.txt @@ -98,5 +98,3 @@ lj/long/coul/long"_pair_lj_long.html, [Default:] -:line - diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 744197256d..a5e8b41560 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -100,8 +100,8 @@ accurately infer a viscosity and should try increasing the Nevery parameter. An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in "Section_howto -13"_Section_howto.html#howto_13 of the manual. NEMD simulations +simulation, as described in "Section +6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations deform the simmulation box via the "fix deform"_fix_deform.html command. Thus they cannot be run on a charged system using a "PPPM solver"_kspace_style.html since PPPM does not currently support diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt index d87326f4b8..84b8b21cb4 100644 --- a/doc/src/fix_wall_reflect.txt +++ b/doc/src/fix_wall_reflect.txt @@ -130,7 +130,7 @@ position = c0 + A (1 - cos(omega*delta)) :pre 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -145,7 +145,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt new file mode 100644 index 0000000000..f1a481fc3b --- /dev/null +++ b/doc/src/fixes.txt @@ -0,0 +1,156 @@ +Fixes :h1 + + diff --git a/doc/src/group.txt b/doc/src/group.txt index 56a5e50936..a72efebb89 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -221,7 +221,7 @@ The assignment of atoms to a dynamic group is done at the beginning of 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"_minimize.html 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 diff --git a/doc/src/if.txt b/doc/src/if.txt index 2b1728be8a..2e97d90037 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -65,7 +65,7 @@ above. NOTE: If a command itself requires a quoted argument (e.g. a "print"_print.html 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"_Section_commands.html#cmd_2 of the manual for +See "Section 3.2"_Section_commands.html#cmd_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/src/improper_class2.txt b/doc/src/improper_class2.txt index 249beaf219..7dbc4071d8 100644 --- a/doc/src/improper_class2.txt +++ b/doc/src/improper_class2.txt @@ -86,7 +86,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -101,7 +101,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt index 551e137fd8..e6f855adf1 100644 --- a/doc/src/improper_cossq.txt +++ b/doc/src/improper_cossq.txt @@ -56,7 +56,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -71,7 +71,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt index 4f82d90e7d..98be3129ae 100644 --- a/doc/src/improper_cvff.txt +++ b/doc/src/improper_cvff.txt @@ -54,7 +54,7 @@ n (0,1,2,3,4,6) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -69,7 +69,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt index a5a42647f8..a14feab3ba 100644 --- a/doc/src/improper_fourier.txt +++ b/doc/src/improper_fourier.txt @@ -48,7 +48,7 @@ all (integer >= 0) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -63,7 +63,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt index 7aa3829280..175feb4243 100644 --- a/doc/src/improper_harmonic.txt +++ b/doc/src/improper_harmonic.txt @@ -58,7 +58,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -73,7 +73,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index a9399802e9..d1eca6d5d9 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -60,7 +60,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -75,7 +75,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt index dbb6c3f237..e8616ef01c 100644 --- a/doc/src/improper_umbrella.txt +++ b/doc/src/improper_umbrella.txt @@ -51,7 +51,7 @@ omega0 (degrees) :ul 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -66,7 +66,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/impropers.txt b/doc/src/impropers.txt new file mode 100644 index 0000000000..ced6128879 --- /dev/null +++ b/doc/src/impropers.txt @@ -0,0 +1,20 @@ +Improper Styles :h1 + + diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index c8375c5daa..48f0489f24 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -142,7 +142,7 @@ 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_accelerate.html. +"Section 5"_Section_accelerate.html. NOTE: Using {pppm/stagger} may not give the same increase in the accuracy of energy and pressure as it does in forces, so some caution @@ -258,7 +258,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -282,7 +282,7 @@ KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/log.txt b/doc/src/log.txt index 29c4bd1bc5..460482ea1e 100644 --- a/doc/src/log.txt +++ b/doc/src/log.txt @@ -34,7 +34,7 @@ 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"_Section_start.html#start_7 for +switch -log. See "Section 2.7"_Section_start.html#start_7 for details. [Restrictions:] none diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index dc2b0e3fa9..9f0082d5dc 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -6,7 +6,7 @@ :line -Manifolds (surfacse) :h3 +Manifolds (surfaces) :h3 [Overview:] @@ -21,20 +21,20 @@ package, their parameters and a short description of them. The parameters listed here are in the same order as they should be passed to the relevant fixes. -{manifold} || {parameters} || {equation} || {description} -cylinder || R || x^2 + y^2 - R^2 = 0 || Cylinder along z-axis, axis going through (0,0,0) -cylinder_dent || R l a || x^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 -dumbbell || a A B c || -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 || A dumbbell || -ellipsoid || a b c || (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 || An ellipsoid -plane || a b c x0 y0 z0 || a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 || A plane with normal (a,b,c) going through point (x0,y0,z0) -plane_wiggle || a w || z - a*sin(w*x) = 0 || A plane with a sinusoidal modulation on z along x. -sphere || R || x^2 + y^2 + z^2 - R^2 = 0 || A sphere of radius R -supersphere || R q || |x|^q + |y|^q + |z|^q - R^q = 0 || A supersphere of hyperradius R -spine || a, A, B, B2, c || -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise || An approximation to a dendtritic spine -spine_two || a, A, B, B2, c || -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise || Another approximation to a dendtritic spine -thylakoid || wB LB lB || Various, see "(Paquay)"_#Paquay || A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB -torus || R r || (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 || A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=||) +{manifold} @ {parameters} @ {equation} @ {description} +cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0) +cylinder_dent @ R l a @ x^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 +dumbbell @ a A B c @ -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell @ +ellipsoid @ a b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid +plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0) +plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x. +sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R +supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R +spine @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine +spine_two @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine +thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB +torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@) -:link(Paquay) -[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published, +:link(Paquay1) +[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index 7b8c14fdad..f1311a3801 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -44,7 +44,6 @@ molecule CO2 co2.txt boff 3 aoff 2 molecule 1 mymol.txt offset 6 9 18 23 14 molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3 :pre -:pre [Description:] diff --git a/doc/src/neb.txt b/doc/src/neb.txt index bd6956e576..0d5838b78a 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -43,12 +43,12 @@ NEB is a method for finding both the atomic configurations and height of the energy barrier associated with a transition state, e.g. for an atom to perform a diffusive hop from one energy basin to another in a coordinated fashion with its neighbors. The implementation in LAMMPS -follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1, -"(Henkelman2)"_#Henkelman2, and "(Nakano)"_#Nakano. +follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA, +"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#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"_Section_start.html#start_7 of the +switch; see "Section 2.7"_Section_start.html#start_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 @@ -235,7 +235,7 @@ In the second stage of NEB, the replica with the highest energy is selected and the inter-replica forces on it are converted to a force that drives its atom coordinates to the top or saddle point of the barrier, via the barrier-climbing calculation described in -"(Henkelman2)"_#Henkelman2. As before, the other replicas rearrange +"(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced. When both stages are complete, if the NEB calculation was successful, @@ -319,10 +319,9 @@ this case), the print-out to the screen and master log.lammps file contains a line of output, printed once every {Nevery} timesteps. It contains the timestep, the maximum force per replica, the maximum force per atom (in any replica), potential gradients in the initial, - final, and climbing replicas, -the forward and backward energy barriers, -the total reaction coordinate (RDT), and -the normalized reaction coordinate and potential energy of each replica. +final, and climbing replicas, the forward and backward energy barriers, +the total reaction coordinate (RDT), and the normalized reaction +coordinate and potential energy of each replica. The "maximum force per replica" is the two-norm of the 3N-length force vector for the atoms in each @@ -415,11 +414,11 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html :line -:link(Henkelman1) -[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). +:link(HenkelmanA) +[(HenkelmanA)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). -:link(Henkelman2) -[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, +:link(HenkelmanB) +[(HenkelmanB)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). :link(Nakano) diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index f9cf0940d6..b8902e0196 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -125,7 +125,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -140,7 +140,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index be7c575218..527563bae8 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -166,7 +166,7 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index 0c1b1f67f2..6e2792a9c1 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -51,7 +51,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -66,7 +66,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_body.txt b/doc/src/pair_body.txt index 132d277def..622cc88f88 100644 --- a/doc/src/pair_body.txt +++ b/doc/src/pair_body.txt @@ -24,7 +24,7 @@ pair_coeff 1 1 1.0 1.5 2.5 :pre 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"_Section_howto.html#howto_14 +point-particles. See "Section 6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html doc page for more details on using body particles. diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index 265571e15f..06a2f5c94f 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -125,7 +125,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -140,7 +140,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index 8967e64c4c..1cad05870d 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -138,7 +138,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -153,7 +153,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 50aee51dd3..ba18738e4d 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -48,7 +48,7 @@ and Coulombic terms respectively. The purpose of this pair style is to capture long-range interactions resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r interactions. This is done by use of the {flag_buck} and {flag_coul} -settings. The ""Ismail"_#Ismail paper has more details on when it is +settings. The "Ismail"_#Ismail paper has more details on when it is appropriate to include long-range 1/r^6 interactions, using this potential. @@ -102,7 +102,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -117,7 +117,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 05baa9c026..3a1daf6c03 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -120,7 +120,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -135,7 +135,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt index 1c84b35960..23b90aae2d 100644 --- a/doc/src/pair_class2.txt +++ b/doc/src/pair_class2.txt @@ -102,7 +102,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -117,7 +117,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt index cb43ec5c6e..4b78206f12 100644 --- a/doc/src/pair_colloid.txt +++ b/doc/src/pair_colloid.txt @@ -127,7 +127,7 @@ commands for efficiency: "neighbor multi"_neighbor.html and 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -142,7 +142,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index 423d2830d5..7f073204fc 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -112,7 +112,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -127,7 +127,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index 8261e10f8d..c7f0b97df9 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -262,7 +262,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 9b9d78e17f..5351e2f852 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -36,7 +36,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre These pair styles are designed to be used with the adiabatic core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See -"Section_howto 25"_Section_howto.html#howto_25 of the manual for an +"Section 6.25"_Section_howto.html#howto_25 of the manual for an overview of the model as implemented in LAMMPS. These pair styles are identical to the "pair_style diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index b3eefa63f2..c72eb9e17d 100755 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -178,7 +178,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index a9061f710a..7072b1702d 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -109,7 +109,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -124,7 +124,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index 9373f326fb..6f56d92902 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -368,7 +368,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -383,7 +383,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accerlate"_Section_accelerate.html of the manual for more +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index 33784afa33..46b6bf2502 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -104,7 +104,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -119,7 +119,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 7fb757ab9a..7acc7e316b 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -136,7 +136,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -151,7 +151,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index b5bab5374d..40f449e98b 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -82,7 +82,7 @@ The global cutoff (r_c) 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -97,7 +97,7 @@ by including their suffix, or you can use the "-suffix command-line switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index 037e5c47e5..e60ca78182 100755 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -133,7 +133,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -148,7 +148,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index baa1154fa5..d4530d37dd 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -179,7 +179,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -194,7 +194,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt index 47620cd044..fef62397cf 100644 --- a/doc/src/pair_gromacs.txt +++ b/doc/src/pair_gromacs.txt @@ -91,7 +91,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -106,7 +106,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index ce82e1c808..52e21d43c3 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -166,7 +166,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index a5d316d25f..9eefcefd00 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -308,7 +308,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. Since the {hybrid} and {hybrid/overlay} styles delegate computation to @@ -327,7 +327,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 3f97c0b8cc..4ae2bb3d99 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -241,7 +241,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -256,7 +256,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt index 42a670107a..6e7c3cbaec 100644 --- a/doc/src/pair_lj96.txt +++ b/doc/src/pair_lj96.txt @@ -49,7 +49,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -64,7 +64,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt index f420b5ca87..30e98fa3c1 100644 --- a/doc/src/pair_lj_cubic.txt +++ b/doc/src/pair_lj_cubic.txt @@ -63,7 +63,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -78,7 +78,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index aa0adad943..c5f0c88a75 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -53,7 +53,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -68,7 +68,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index dbb49e9afb..a4fb3f0274 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -155,7 +155,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -170,7 +170,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_sf.txt b/doc/src/pair_lj_sf.txt index f0e37fcbc4..65e28b6f51 100644 --- a/doc/src/pair_lj_sf.txt +++ b/doc/src/pair_lj_sf.txt @@ -47,7 +47,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -62,7 +62,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index e26e5650d2..edec8bcf45 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -62,7 +62,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -77,7 +77,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index 63fb3ca163..7ad72b38cb 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -49,7 +49,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -64,7 +64,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index dc211c6be4..784f1f7f52 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -134,7 +134,8 @@ coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are appropriate choices. Plots of the LJ and Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. -:c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg) +:image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg) +:c For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, the following coefficients must be defined for each pair of atoms @@ -206,7 +207,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -221,7 +222,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index c7aa5fbbc3..ba46a135a2 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -82,7 +82,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -97,7 +97,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 8b4edfe673..b7cac26746 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -100,7 +100,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -115,7 +115,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 51686e9064..e147c85bc1 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -90,7 +90,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -105,7 +105,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt index 472247e7b2..87be445f84 100644 --- a/doc/src/pair_nm.txt +++ b/doc/src/pair_nm.txt @@ -133,7 +133,7 @@ the "run_style respa"_run_style.html command. They do not support the 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -148,7 +148,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index 3701dc9a30..7f19afbf09 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -139,7 +139,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -154,7 +154,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_reax_c.txt b/doc/src/pair_reax_c.txt index e4cc922220..c7f62aedff 100644 --- a/doc/src/pair_reax_c.txt +++ b/doc/src/pair_reax_c.txt @@ -46,7 +46,7 @@ the "(Aktulga)"_#Aktulga paper. 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"_Section_packages.html#kokkos and "Section_accelerate"_accelerate_kokkos.html. +see "Section 4"_Section_packages.html#kokkos and "Section 5.3.3"_accelerate_kokkos.html. 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"_package.html command. @@ -165,7 +165,7 @@ headings) the following commands could be included in an input script: compute reax all pair reax/c variable eb equal c_reax\[1\] variable ea equal c_reax\[2\] -... +\[...\] variable eqeq equal c_reax\[14\] thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre @@ -237,8 +237,8 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms) regarding the bonded interactions. (default value = 5.0) hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen -bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen - bonds) +bond interactions.(default value = 7.5. Value of 0.0 turns off +hydrogen bonds) bond_graph_cutoff: is the threshold used in determining what is a physical bond, what is not. Bonds and angles reported in the @@ -288,7 +288,7 @@ This pair style can only be used via the {pair} keyword of the 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -303,7 +303,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index f945aef9c2..f30bdcdf64 100755 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -145,7 +145,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -160,7 +160,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 56cd78f797..f816d3a4b5 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -85,7 +85,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -100,7 +100,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index c8e8179ac8..f240779050 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -82,7 +82,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -97,7 +97,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index 4c62d76a4a..2a23bb3015 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -144,7 +144,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -164,7 +164,7 @@ 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"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index 560ff43590..6504edb2a5 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -217,7 +217,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 466772373f..ffd395ff2a 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -179,7 +179,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -194,7 +194,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index ad4f10686a..fe5e8b541a 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -117,7 +117,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -132,7 +132,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index 0230be3ab6..95c031455d 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -189,7 +189,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index ab3b832ad6..a441efa2e3 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -130,7 +130,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -145,7 +145,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. [Mixing]: diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index 65d4b270cd..c35894eb46 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -169,7 +169,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html 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 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt index 621952d70b..26acdb2ccb 100644 --- a/doc/src/pair_yukawa.txt +++ b/doc/src/pair_yukawa.txt @@ -48,7 +48,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -63,7 +63,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt index 03a0dbf1f4..3d5294bbdb 100644 --- a/doc/src/pair_yukawa_colloid.txt +++ b/doc/src/pair_yukawa_colloid.txt @@ -80,7 +80,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -95,7 +95,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt index 741aa4514f..14e52f4c6e 100644 --- a/doc/src/pair_zbl.txt +++ b/doc/src/pair_zbl.txt @@ -70,7 +70,7 @@ 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"_Section_accelerate.html +hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -85,7 +85,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt new file mode 100644 index 0000000000..77f4fba807 --- /dev/null +++ b/doc/src/pairs.txt @@ -0,0 +1,102 @@ +Pair Styles :h1 + + diff --git a/doc/src/partition.txt b/doc/src/partition.txt index ab62135c83..ccef359050 100644 --- a/doc/src/partition.txt +++ b/doc/src/partition.txt @@ -27,7 +27,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre 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"_Section_start.html#start_7 +command-line switch. See "Section 2.6"_Section_start.html#start_7 for an explanation of the switch. Normally, every input script command in your script is invoked by diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 484e36004c..a7c148cd09 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -63,13 +63,13 @@ event to occur. 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"_Section_start.html#start_7 of the +switch; see "Section 2.7"_Section_start.html#start_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"_Section_howto.html#howto_5 of the manual for further +"Section 6.5"_Section_howto.html#howto_5 of the manual for further discussion. When a PRD simulation is performed, it is assumed that each replica is diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index bcdc7ac434..ce617d5d0d 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -310,7 +310,7 @@ with tilt factors that exceed these limits, you can use the "box tilt"_box.html command, with a setting of {large}; a setting of {small} is the default. -See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages +See "Section 6.12"_Section_howto.html#howto_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/src/read_restart.txt b/doc/src/read_restart.txt index 6acc0ad4a7..0e50b4028c 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -23,8 +23,6 @@ read_restart restart.* read_restart restart.*.mpiio read_restart poly.*.% remap :pre -:pre - [Description:] Read in a previously saved system configuration from a restart file. diff --git a/doc/src/region.txt b/doc/src/region.txt index 0bc578c07e..2dd7ff975a 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -181,7 +181,7 @@ functions, and include "thermo_style"_thermo_style.html 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"_Section_howto.html#howto_12 of the doc pages +See "Section 6.12"_Section_howto.html#howto_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. @@ -306,7 +306,7 @@ 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"_Section_accelerate.html of the manual. The +"Section 5"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -323,7 +323,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index cc38f7ed25..04cce536d7 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -69,7 +69,7 @@ The {verlet} style is a standard velocity-Verlet integrator. 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"_Section_start.html#start_7 for an +processors. See "Section 2.7"_Section_start.html#start_7 for an explanation of the -partition command-line switch. Specifically, this style performs all computation except the @@ -115,17 +115,17 @@ 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 +switches"_Section_start.html#start_7 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"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html 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"_processors.html command has options to support this, and strategies are discussed in -"Section_accelerate"_Section_accelerate.html of the manual. +"Section 5"_Section_accelerate.html of the manual. :line @@ -254,7 +254,7 @@ The {respa/omp} styles is a variant of {respa} adapted for use with 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"_Section_accelerate.html of the manual. +see the "Section 5"_Section_accelerate.html of the manual. Accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -263,7 +263,7 @@ you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 8e93b93c3b..8a0bd31c74 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -92,8 +92,8 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the "neb"_neb.html command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See "Section_howto -5"_Section_howto.html#howto_5 of the manual for further discussion of +partitions remain idle. See "Section +6.5"_Section_howto.html#howto_5 of the manual for further discussion of multi-replica simulations. A TAD run has several stages, which are repeated each time an event is diff --git a/doc/src/temper.txt b/doc/src/temper.txt index ef09bbab53..22c82c4195 100644 --- a/doc/src/temper.txt +++ b/doc/src/temper.txt @@ -32,7 +32,7 @@ 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"_Section_start.html#start_7 of the +switch; see "Section 2.7"_Section_start.html#start_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/src/thermo_style.txt b/doc/src/thermo_style.txt index c19134f338..3ee4fc8330 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -110,7 +110,7 @@ thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to "computes"_compute.html, "fixes"_fix.html, and equal-style "variables"_variable.html" 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"_Section_modify.html +have added to LAMMPS (see the "Section 10"_Section_modify.html section of the documentation). Thus the {custom} style provides a flexible means of outputting essentially any desired quantity as a simulation proceeds. @@ -254,9 +254,9 @@ 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"_variable.html to append to -a filename for output specific to this partition. See "Section_start -7"_Section_start.html#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"_Section_start.html#start_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"_timer.html command. diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt new file mode 100644 index 0000000000..98c748f3af --- /dev/null +++ b/doc/src/tutorials.txt @@ -0,0 +1,13 @@ +Tutorials :h1 + +