diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt index 9489dee160..ed6a233a2d 100644 --- a/doc/src/Section_accelerate.txt +++ b/doc/src/Section_accelerate.txt @@ -157,11 +157,11 @@ 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 with CUDA and OpenCL support for Nvidia GPUs and others :h5 +"USER-INTEL Package"_accelerate_intel.html for Intel CPUs and Intel Xeon Phi :h5 +"KOKKOS Package"_accelerate_kokkos.html for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading :h5 +"USER-OMP Package "_accelerate_omp.html for OpenMP threading and generic CPU optimizations :h5 +"OPT Package"_accelerate_opt.html generic CPU optimizations :h5 Inverting this list, LAMMPS currently has acceleration support for three kinds of hardware, via the listed packages: @@ -192,7 +192,7 @@ 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..f466680069 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: 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..e0dca629bc 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 @@ -352,7 +352,7 @@ following packages: "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..2639fd3dab 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -42,7 +42,7 @@ 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 @@ -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 diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 32bd5dae3c..a97793b89d 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -690,7 +690,7 @@ 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 @@ -795,7 +795,7 @@ libraries. Many of them are provided with LAMMPS, in which case they must be compiled first, before LAMMPS is built, if you wish to include that package. If you get a LAMMPS build error about a missing library, this is likely the reason. See the -"Section_packages"_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 @@ -1055,7 +1055,7 @@ 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 @@ -1135,8 +1135,8 @@ src/library.cpp and src/library.h. See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS thru its library interface. There are other examples as well in the COUPLE directory which are -discussed in "Section_howto 10"_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. @@ -1257,7 +1257,7 @@ 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 +1473,7 @@ 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 +1539,7 @@ 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 +1863,7 @@ 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/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/atom_style.txt b/doc/src/atom_style.txt index 95038b74fb..74b5f0b152 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -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/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/boundary.txt b/doc/src/boundary.txt index e832a74d24..c3724bdd47 100644 --- a/doc/src/boundary.txt +++ b/doc/src/boundary.txt @@ -74,7 +74,7 @@ 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/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_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_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index 9b56c264c9..82d33c0038 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -104,7 +104,7 @@ 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. -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_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_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_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_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_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_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_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_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_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_cs.txt b/doc/src/compute_temp_cs.txt index 9cdb3a9ba7..7170ef951e 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 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_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index 7d14dab2ac..334152b041 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -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/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_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_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_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/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_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_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_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_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_neb.txt b/doc/src/fix_neb.txt index c84b46a422..b80cbae0ed 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. 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_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_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_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_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_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/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/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/neb.txt b/doc/src/neb.txt index bd6956e576..fa147d08ab 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -48,7 +48,7 @@ follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1, 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 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..752ef71f98 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -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 be6608d57b..f4e411180b 100755 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -174,7 +174,7 @@ 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. @@ -189,7 +189,7 @@ 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..4711f6b185 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -206,7 +206,7 @@ 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 +221,7 @@ 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..7b0063c545 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. @@ -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 24951b1df1..2c1ed7a242 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -154,7 +154,7 @@ 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. @@ -169,7 +169,7 @@ 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/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/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/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.