From 9c81ad1ab6e30dd010158ccf4df2257bc8f1b7b0 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 25 Oct 2016 09:45:55 -0600 Subject: [PATCH] doc page changes --- doc/src/Section_commands.txt | 2 +- doc/src/Section_errors.txt | 30 +++++++++++++++--------------- doc/src/Section_packages.txt | 24 ++++++++++++++++++++++++ doc/src/Section_start.txt | 6 +++--- doc/src/accelerate_intel.txt | 4 ++-- doc/src/atom_style.txt | 2 +- doc/src/bond_fene.txt | 2 +- doc/src/bond_fene_expand.txt | 2 +- doc/src/compute_fep.txt | 2 +- doc/src/compute_property_local.txt | 2 +- doc/src/fix_phonon.txt | 2 +- doc/src/fix_property_atom.txt | 2 +- doc/src/fix_rigid.txt | 2 +- doc/src/fix_ti_spring.txt | 2 +- doc/src/neb.txt | 6 +++--- doc/src/pair_hbond_dreiding.txt | 4 ++-- doc/src/pair_line_lj.txt | 4 ++-- doc/src/pair_lubricateU.txt | 2 +- doc/src/pair_thole.txt | 2 +- doc/src/read_data.txt | 4 ++-- doc/src/read_dump.txt | 3 +++ doc/src/read_restart.txt | 4 ++-- doc/src/thermo_style.txt | 2 +- doc/src/write_dump.txt | 2 +- 24 files changed, 72 insertions(+), 45 deletions(-) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index f44f61362d..4f949648f0 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -106,7 +106,7 @@ the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and "x". How the variable is converted to a text string depends on what style -of variable it is; see the "variable"_variable doc page for details. +of variable it is; see the "variable"_variable.html doc page for details. It can be a variable that stores multiple text strings, and return one of them. The returned text string can be multiple "words" (space separated) which will then be interpreted as multiple arguments in the diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index c7ea5844b5..d3ae9d94b7 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -8116,11 +8116,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the -"neigh_modify"_neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. :dd +"neigh_modify"_neigh_modify.html command. The safest settings are +"delay 0 every 1 check yes". Second, it may mean that an atom has +moved far outside a processor's sub-domain or even the entire +simulation box. This indicates bad physics, e.g. due to highly +overlapping atoms, too large a timestep, etc. :dd {Out of range atoms - cannot compute PPPM} :dt @@ -8132,11 +8132,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the -"neigh_modify"_neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. :dd +"neigh_modify"_neigh_modify.html command. The safest settings are +"delay 0 every 1 check yes". Second, it may mean that an atom has +moved far outside a processor's sub-domain or even the entire +simulation box. This indicates bad physics, e.g. due to highly +overlapping atoms, too large a timestep, etc. :dd {Out of range atoms - cannot compute PPPMDisp} :dt @@ -8148,11 +8148,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the -"neigh_modify"_neigh_modify command. The safest settings are "delay 0 -every 1 check yes". Second, it may mean that an atom has moved far -outside a processor's sub-domain or even the entire simulation box. -This indicates bad physics, e.g. due to highly overlapping atoms, too -large a timestep, etc. :dd +"neigh_modify"_neigh_modify.html command. The safest settings are +"delay 0 every 1 check yes". Second, it may mean that an atom has +moved far outside a processor's sub-domain or even the entire +simulation box. This indicates bad physics, e.g. due to highly +overlapping atoms, too large a timestep, etc. :dd {Overflow of allocated fix vector storage} :dt diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 27ab64d50b..341483d7a7 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -1153,6 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, - "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE +"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, - "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, - "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm @@ -1598,6 +1599,29 @@ The person who created this package is Axel Kohlmeyer at Temple U :line +USER-NC-DUMP package :link(USER-NC-DUMP),h5 + +Contents: Dump styles for writing NetCDF format files. NetCDF is a binary, +portable, self-describing file format on top of HDF5. The file format +contents follow the AMBER NetCDF trajectory conventions +(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this +convention. This package implements a "dump nc"_dump_nc.html command +and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots +in this format. See src/USER-NC-DUMP/README for more details. + +NetCDF files can be directly visualized with the following tools: +Ovito (http://www.ovito.org/). Ovito supports the AMBER convention + and all of the above extensions. :ulb,l +VMD (http://www.ks.uiuc.edu/Research/vmd/) :l +AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains + a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule + +The person who created these files is Lars Pastewka at +Karlsruhe Institute of Technology (lars.pastewka at kit.edu). +Contact him directly if you have questions. + +:line + USER-OMP package :link(USER-OMP),h5 Supporting info: diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 4d46ce82ae..a0cc792455 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1601,9 +1601,9 @@ implementations, either by environment variables that specify how to order physical processors, or by config files that specify what physical processors to assign to each MPI rank. The -reorder switch simply gives you a portable way to do this without relying on MPI -itself. See the "processors out"_processors command for how to output -info on the final assignment of physical processors to the LAMMPS -simulation domain. +itself. See the "processors out"_processors.html command for how +to output info on the final assignment of physical processors to +the LAMMPS simulation domain. -screen file :pre diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index cda5a80c4e..3e94e7762a 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or +USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or "KOKKOS package"_accelerate_kokkos.html. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% @@ -343,7 +343,7 @@ when using offload. Not all styles are supported in the USER-INTEL package. You can mix the USER-INTEL package with styles from the "OPT"_accelerate_opt.html -package or the "USER-OMP package"_accelerate_omp.html". Of course, +package or the "USER-OMP package"_accelerate_omp.html. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index e632d0018d..9ba817a663 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -166,7 +166,7 @@ stores a per-particle mass and size and orientation (i.e. the corner points of the triangle). The {template} style allows molecular topolgy (bonds,angles,etc) to be -defined via a molecule template using the "molecule"_molecule.txt +defined via a molecule template using the "molecule"_molecule.html command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms only store a template index and template atom to identify which diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index d7ab09c48f..a4dd393d8d 100644 --- a/doc/src/bond_fene.txt +++ b/doc/src/bond_fene.txt @@ -73,7 +73,7 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package (which it is by default). See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. -You typically should specify "special_bonds fene"_special_bonds.html" +You typically should specify "special_bonds fene"_special_bonds.html or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond style. LAMMPS will issue a warning it that's not the case. diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt index 4342231d20..6ddd6d4876 100644 --- a/doc/src/bond_fene_expand.txt +++ b/doc/src/bond_fene_expand.txt @@ -76,7 +76,7 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package (which it is by default). See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. -You typically should specify "special_bonds fene"_special_bonds.html" +You typically should specify "special_bonds fene"_special_bonds.html or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond style. LAMMPS will issue a warning it that's not the case. diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index 1db74fef06..9bbae7b20f 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -236,7 +236,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html, -"pair_lj_soft_coul_soft"_pair_lj_soft_coul_soft.txt +"pair_style lj/soft/coul/soft"_pair_lj_soft.html [Default:] diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt index bc2ecca466..f7851e864b 100644 --- a/doc/src/compute_property_local.txt +++ b/doc/src/compute_property_local.txt @@ -78,7 +78,7 @@ defined by the "pair_style"_pair_style.html command for the types of the two atoms is used. For the {radius} setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are -overlapping, as computed by "granular pair styles"_pair_gran.txt. +overlapping, as computed by "granular pair styles"_pair_gran.html. If the inputs are bond, angle, etc attributes, the local data is generated by looping over all the atoms owned on a processor and diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 254cf47408..10a0c95c80 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -184,7 +184,7 @@ This fix requires LAMMPS be built with an FFT library. See the [Default:] The option defaults are sysdim = the same dimemsion as specified by -the "dimension"_dimension command, and nasr = 20. +the "dimension"_dimension.html command, and nasr = 20. :line diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 10dd08738f..8c9164c25d 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -177,7 +177,7 @@ their values. This means that the values can be output via the "dump custom"_dump.html command, accessed by fixes like "fix ave/atom"_fix_ave_atom.html, accessed by other computes like "compute reduce"_compute_reduce.html, or used in "atom-style -variables"_variables. +variables"_variable.html. For example, these commands will output two new properties to a custom dump file: diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 685e2694d3..a38948e560 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -620,7 +620,7 @@ rigid styles for the rigid bodies. :l Use "fix press/berendsen"_fix_press_berendsen.html to compute the pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT -rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.thml (or any +rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.html (or any other thermostat) for the non-rigid particles. :l :ule diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index 64ffe2fc8a..40e595e21e 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -104,7 +104,7 @@ the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT} recommended due to its well documented issues with the canonical sampling of harmonic degrees of freedom (notice that the {chain} option will {NOT} solve this problem). The Langevin thermostat ("fix -langevin"_fix_langevin.html") correctly thermostats the system and we +langevin"_fix_langevin.html) correctly thermostats the system and we advise its usage with ti/spring command. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/neb.txt b/doc/src/neb.txt index a2f8161ee7..17bd8544b7 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -83,9 +83,9 @@ replica. Conceptually, the non-NEB atoms provide a background force field for the NEB atoms. They can be allowed to move during the NEB minimiation procedure (which will typically induce different coordinates for non-NEB atoms in different replicas), or held fixed -using other LAMMPS commands such as "fix setforce"_fix_setforce. Note -that the "partition"_partition.html command can be used to invoke a -command on a subset of the replicas, e.g. if you wish to hold NEB or +using other LAMMPS commands such as "fix setforce"_fix_setforce.html. +Note that the "partition"_partition.html command can be used to invoke +a command on a subset of the replicas, e.g. if you wish to hold NEB or non-NEB atoms fixed in only the end-point replicas. The initial atomic configuration for each of the replicas can be diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index caaa715a7b..b3c9b5b5d5 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -138,8 +138,8 @@ angle cutoff (degrees) :ul A single hydrogen atom type K can be specified, or a wild-card asterisk can be used in place of or in conjunction with the K arguments to select multiple types as hydrogens. This takes the form -"*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff command -doc page for details. +"*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff.html +command doc page for details. If the donor flag is {i}, then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor. If the donor diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index 6a72e296a6..bb1146b64e 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -60,8 +60,8 @@ pair_style command or overridden with an optional argument in the pair_coeff command for a type pair as discussed below. The distance between the centers of 2 line segments, or the center of a line segment and a point particle, must be less than this distance (plus -the neighbor skin; see the "neighbor"_neighbor command), for the pair -of particles to be included in the neighbor list. +the neighbor skin; see the "neighbor"_neighbor.html command), for +the pair of particles to be included in the neighbor list. NOTE: This means that a too-short value for the {cutoff} setting can exclude a pair of particles from the neighbor list even if pairs of diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt index fb1ce8d89b..52e63ac350 100644 --- a/doc/src/pair_lubricateU.txt +++ b/doc/src/pair_lubricateU.txt @@ -119,7 +119,7 @@ of walls (whether moving or stationary) will affect the volume fraction available to colloidal particles. This is currently accounted for with the following types of walls: "wall/lj93"_fix_wall.html, "wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and -"wall/harmonic_fix_wall.html". For these wall styles, the correct +"wall/harmonic"_fix_wall.html. For these wall styles, the correct volume fraction will be used when walls do not coincide with the box boundary, as well as when walls move and thereby cause a change in the volume fraction. To use these wall styles with pair_style {lubricateU} diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index cf43e69673..923485eaa7 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -180,7 +180,7 @@ package. langevin/drude"_fix_langevin_drude.html, "fix drude/transform"_fix_drude_transform.html, "compute temp/drude"_compute_temp_drude.html -"pair_style lj/cut/coul/long"_pair_lj_cut_coul_long +"pair_style lj/cut/coul/long"_pair_lj.html [Default:] none diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index ce617d5d0d..9ddc9d8921 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -431,8 +431,8 @@ Atoms # sphere Pair Coeffs # lj/cut :pre will check if the currently-defined "atom_style"_atom_style.html is -{sphere}, and the current "pair_style"_pair_style is {lj/cut}. If -not, LAMMPS will issue a warning to indicate that the data file +{sphere}, and the current "pair_style"_pair_style.html is {lj/cut}. +If not, LAMMPS will issue a warning to indicate that the data file section likely does not contain the correct number or type of parameters expected for the currently-defined style. diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index 30345fd6cd..f6424f6529 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -322,3 +322,6 @@ They are only enabled if LAMMPS was built with that packages. See the The option defaults are box = yes, replace = yes, purge = no, trim = no, add = no, scaled = no, wrapped = yes, and format = native. + +:link(vmd,http://www.ks.uiuc.edu/Research/vmd) + diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index c79ca4460d..d59b5313fd 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -141,11 +141,11 @@ these settings after the restart file is read. "units"_units.html "newton bond"_newton.html (see discussion of newton command below) "atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort -"comm style"_comm_style.html and "comm_modify"_comm_modify settings mode, cutoff, vel +"comm style"_comm_style.html and "comm_modify"_comm_modify.html settings mode, cutoff, vel "timestep"_timestep.html simulation box size and shape and "boundary"_boundary.html settings atom "group"_group.html definitions -per-type atom settings such as "mass"_mass.thml +per-type atom settings such as "mass"_mass.html per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc) force field styles ("pair"_pair_style.html, "bond"_bond_style.html, "angle"_angle_style.html, etc) force field coefficients ("pair"_pair_coeff.html, "bond"_bond_coeff.html, "angle"_angle_coeff.html, etc) in some cases (see below) diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 5e662e85b9..6cdb8a3cc8 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -108,7 +108,7 @@ Style {custom} is the most general setting and allows you to specify which of the keywords listed above you want printed on each 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 +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 10"_Section_modify.html section of the documentation). Thus the {custom} style provides a diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index cf8302121c..ae32a94e84 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -26,7 +26,7 @@ write_dump all atom dump.atom write_dump subgroup atom dump.run.bin write_dump all custom dump.myforce.* id type x y vx fx write_dump flow custom dump.%.myforce id type c_myF\[3\] v_ke modify sort id -write_dump all xyz system.xyz modify sort id elements O H +write_dump all xyz system.xyz modify sort id element O H write_dump all image snap*.jpg type type size 960 960 modify backcolor white write_dump all image snap*.jpg element element & bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600 &