fix a bunch of typos and broken links as detected by ebook-convert

real physical system.  To do that, the "compute

temp/cs"_compute_temp_cs.html command can be used, in conjunction with

any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix

langevin"_fix_langevin.  This compute uses the center-of-mass velocity

langevin"_fix_langevin.html.  This compute uses the center-of-mass velocity

of the core/shell pairs to calculate a temperature, and insures that

velocity is what is rescaled for thermostatting purposes.  This

compute also works for a system with both core/shell pairs and

LAMMPS convention by "treating the cores and shells as individual

particles"_#MitchellFincham2. For the thermo output of the pressure

as well as for the application of a barostat, it is necessary to

use an additional "pressure"_compute_pressure compute based on the

default "temperature"_compute_temp and specifying it as a second

argument in "fix modify"_fix_modify.html and

use an additional "pressure"_compute_pressure.html compute based on

the default "temperature"_compute_temp.html and specifying it as a

second argument in "fix modify"_fix_modify.html and

"thermo_modify"_thermo_modify.html resulting in:

(...)

NOTE: By default, for 2d systems, granular particles are still modeled

as 3d spheres, not 2d discs (circles), meaning their moment of inertia

will be the same as in 3d.  If you wish to model granular particles in

2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d

2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d.html

doc page, where 2d simulations are discussed.

[Running on GPUs:]

Use the "-k" "command-line switch"_Run_options.thml to

Use the "-k" "command-line switch"_Run_options.html to

specify the number of GPUs per node. Typically the -np setting of the

mpirun command should set the number of MPI tasks/node to be equal to

the number of physical GPUs on the node.  You can assign multiple MPI

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.  Note that if a granular model defines atom

styles"_pair_gran.html.  Note that if a granular model defines atom

types such that all particles of a specific type are monodisperse

(same diameter), then the two settings are effectively identical.

The {single/angle} style creates a single angle of type {atype}

between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}.  The

ordering of the atoms is the same as in the {Angles} section of a data

file read by the "read_data"_read_data command.  I.e. the 3 atoms are

file read by the "read_data"_read_data.html command.  I.e. the 3 atoms are

ordered linearly within the angle; the central atom is {aatom2}.

{Atype} must be a value between 1 and the number of angle types

defined.

The {single/dihedral} style creates a single dihedral of type {btype}

between two atoms with IDs {batom1} and {batom2}.  The ordering of the

atoms is the same as in the {Dihedrals} section of a data file read by

the "read_data"_read_data command.  I.e. the 4 atoms are ordered

the "read_data"_read_data.html command.  I.e. the 4 atoms are ordered

linearly within the dihedral.  {Dtype} must be a value between 1 and

the number of dihedral types defined.