Merge pull request #1242 from akohlmey/collected-post-stable-patches

	@echo "  clean-all  reset the entire build environment"

	@echo "  txt2html   build txt2html tool"

	@echo "  anchor_check  scan for duplicate anchor labels"

	@echo "  spelling   spell-check the manual"

# ------------------------------------------

tools, but do not set policies, so it is up to the developers to come to

an agreement as to how to define and interpret policies. This document

is likely to change as our experiences and needs change and we try to

adapt accordingly. Last change 2018-11-15.

adapt accordingly. Last change 2018-12-19.

## Table of Contents

    * stdlib.h -> cstdlib

    * string.h -> cstring

    * time.h -> ctime

  Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.

    * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.

  * Code should follow the C++-98 standard. C++-11 is only accepted

  in individual special purpose packages

  * indentation is two spaces per level

  * there should be no tabs and no trailing whitespace

  * indentation is 2 spaces per level

  * there should be NO tabs and no trailing whitespace

  * header files, especially of new styles, should not include any

  other headers, except the header with the base class or cstdio.

  Forward declarations should be used instead when possible.

  * iostreams should be avoided. LAMMPS uses stdio from the C-library.

  * use of STL in headers and class definitions should be avoided.

  * there MUST NOT be any "using namespace XXX;" statements in headers.

  * static class members should be avoided at all cost.

  * anything storing atom IDs should be using `tagint` and not `int`.

  This can be flagged by the compiler only for pointers and only when

input with an error message (for instance, when an integer is required,

but a floating-point number 1.0 is provided):

ERROR: Expected integer parameter in input script or data file :pre

ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre

Some commands allow for using variable references in place of numeric

constants so that the value can be evaluated and may change over the

NOTE: Using a variable reference (i.e. {v_name}) is only allowed if

the documentation of the corresponding command explicitly says it is.

Otherwise, you will receive an error message of this kind:

ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre

Generally, LAMMPS will print a message to the screen and logfile and

exit gracefully when it encounters a fatal error.  Sometimes it will

Specifically, LAMMPS was not conceived and designed for:

being run thru a GUI

build molecular systems, or building molecular topologies

building molecular systems, or building molecular topologies

assign force-field coefficients automagically

perform sophisticated analysis of your MD simulation

visualize your MD simulation interactively

Although over the years these limitations have been somewhat

reduced through features added to LAMMPS or external tools

that either interface with LAMMPS or extend LAMMPS.

that either closely interface with LAMMPS or extend LAMMPS.

Here are suggestions on how to perform these tasks:

GUI: LAMMPS can be built as a library and a Python wrapper that wraps

[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps

the library interface is provided.  Thus, GUI interfaces can be

written in Python (or C or C++ if desired) that run LAMMPS and

visualize or plot its output.  Examples of this are provided in the

python directory and described on the "Python"_Python_head.html doc

page.  Also, there are several external wrappers or GUI front ends. :ulb,l

Builder: Several pre-processing tools are packaged with LAMMPS.  Some

[Builder:] Several pre-processing tools are packaged with LAMMPS.  Some

of them convert input files in formats produced by other MD codes such

as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of them

are simple programs that will build simple molecular systems, such as

LAMMPS.  The "Pre/post processing

page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website

describes a variety of 3rd party tools for this task.  Furthermore,

some LAMMPS internal commands to reconstruct topology, as well as

the option to insert molecule templates instead of atoms.:l

some LAMMPS internal commands allow to reconstruct, or selectively add

topology information, as well as provide the option to insert molecule

templates instead of atoms for building bulk molecular systems. :l

Force-field assignment: The conversion tools described in the previous

[Force-field assignment:] The conversion tools described in the previous

bullet for CHARMM, AMBER, and Insight will also assign force field

coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,

or BIOVIA (formerly Accelrys) force field files. :l

or BIOVIA (formerly Accelrys) force field files. The tools

"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and

"InterMol"_https://github.com/shirtsgroup/InterMol are particularly

powerful and flexible in converting force field and topology data

between various MD simulation programs.  :l

Simulation analysis: If you want to perform analysis on-the-fly as

[Simulation analysis:] If you want to perform analysis on-the-fly as

your simulation runs, see the "compute"_compute.html and

"fix"_fix.html doc pages, which list commands that can be used in a

LAMMPS input script.  Also see the "Modify"_Modify.html doc page for

make it easier to import into other programs.  See the

"Tools"_Tools.html doc page for details on these various options. :l

Visualization: LAMMPS can produce JPG or PNG snapshot images

[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images

on-the-fly via its "dump image"_dump_image.html command and pass

them to an external program FFmpeg to generate movies from them.  For

high-quality, interactive visualization there are many excellent and

free tools available.  See the "Other Codes

them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate

movies from them.  For high-quality, interactive visualization there are

many excellent and free tools available.  See the "Other Codes

page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for

visualization packages that can use LAMMPS output data. :l

Plotting: See the next bullet about Pizza.py as well as the

[Plotting:] See the next bullet about Pizza.py as well as the

"Python"_Python_head.html doc page for examples of plotting LAMMPS

output.  Scripts provided with the {python} tool in the tools

directory will extract and massage data in log and dump files to make

it easier to analyze and plot.  See the "Tools"_Tools.html doc page

for more discussion of the various tools. :l

Pizza.py: Our group has also written a separate toolkit called

[Pizza.py:] Our group has also written a separate toolkit called

"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of

setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS

simulations.  It thus provides some functionality for several of the