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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15588 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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doc/src/Section_howto.txt
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@ -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.