doc page changes

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

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
 

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:

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
 

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"

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

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.
 

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.
 

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:]
 

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

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
 

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:

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
 

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:]

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

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

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

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}

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
 

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.
 

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)
+

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)

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

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  &