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doc changes for Examples and Modify sections

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Steven J. Plimpton
2018-07-25 09:27:13 -06:00
parent 0fc789bae5
commit 22c9258b8e
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16
doc/src/Section_example.txt → doc/src/Examples.txt
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@ -1,4 +1,12 @@
"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c
"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_perf.html :c
<!-- future sequence of sections:
"Previous Section"_Speed.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Python.html :c
-->
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -6,7 +14,7 @@
:line
7. Example problems :h2
Example scripts :h3
The LAMMPS distribution includes an examples sub-directory with many
sample problems. Many are 2d models that run quickly are are
@ -46,7 +54,7 @@ Lists of both kinds of directories are given below.
:line
Lowercase directories :h3
Lowercase directories :h4
accelerate: run with various acceleration options (OpenMP, GPU, Phi)
airebo: polyethylene with AIREBO potential
@ -122,7 +130,7 @@ browser.
:line
Uppercase directories :h3
Uppercase directories :h4
ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
COUPLE: examples of how to use LAMMPS as a library

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doc/src/Manual.txt
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@ -114,10 +114,10 @@ it gives quick access to documentation for all LAMMPS commands.
Section_packages
Section_accelerate
Section_howto
Section_example
Examples
Section_perf
Tools
Section_modify
Modify
Section_python
Section_errors
Section_history
@ -208,25 +208,10 @@ END_RST -->
6.25 "Polarizable models"_howto_25 :b
6.26 "Adiabatic core/shell model"_howto_26 :b
6.27 "Drude induced dipoles"_howto_27 :ule,b
"Example problems"_Section_example.html :l
"Example scripts"_Examples.html :l
"Performance & scalability"_Section_perf.html :l
"Auxiliary tools"_Tools.html :l
"Modifying & extending LAMMPS"_Section_modify.html :l
10.1 "Atom styles"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
10.3 "Compute styles"_mod_3 :b
10.4 "Dump styles"_mod_4 :b
10.5 "Dump custom output options"_mod_5 :b
10.6 "Fix styles"_mod_6 :b
10.7 "Input script commands"_mod_7 :b
10.8 "Kspace computations"_mod_8 :b
10.9 "Minimization styles"_mod_9 :b
10.10 "Pairwise potentials"_mod_10 :b
10.11 "Region styles"_mod_11 :b
10.12 "Body styles"_mod_12 :b
10.13 "Thermodynamic output options"_mod_13 :b
10.14 "Variable options"_mod_14 :b
10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
"Modify & extend LAMMPS"_Modify.html :l
"Python interface"_Section_python.html :l
11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b
11.2 "Overview of using Python from a LAMMPS script"_py_2 :b
@ -302,22 +287,6 @@ END_RST -->
:link(howto_26,Section_howto.html#howto_26)
:link(howto_27,Section_howto.html#howto_27)
:link(mod_1,Section_modify.html#mod_1)
:link(mod_2,Section_modify.html#mod_2)
:link(mod_3,Section_modify.html#mod_3)
:link(mod_4,Section_modify.html#mod_4)
:link(mod_5,Section_modify.html#mod_5)
:link(mod_6,Section_modify.html#mod_6)
:link(mod_7,Section_modify.html#mod_7)
:link(mod_8,Section_modify.html#mod_8)
:link(mod_9,Section_modify.html#mod_9)
:link(mod_10,Section_modify.html#mod_10)
:link(mod_11,Section_modify.html#mod_11)
:link(mod_12,Section_modify.html#mod_12)
:link(mod_13,Section_modify.html#mod_13)
:link(mod_14,Section_modify.html#mod_14)
:link(mod_15,Section_modify.html#mod_15)
:link(py_1,Section_python.html#py_1)
:link(py_2,Section_python.html#py_2)
:link(py_3,Section_python.html#py_3)

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"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_python.html :c
<!-- future sequence of sections:
"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Errors.html :c
-->
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Modify & extend LAMMPS :h3
LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 95% of its source code
is add-on files. These doc pages give basic instructions on how to do
this.
If you add a new feature to LAMMPS and think it will be of interest to
general users, we encourage you to submit it for inclusion in LAMMPS
as a pull request on our "GitHub
site"_https://github.com/lammps/lammps, after reading the "Modify
contribute"_Modify_contribute.html doc page.
<!-- RST
.. toctree::
Modify_overview
Modify_contribute
Modify_atom
Modify_pair
Modify_bond
Modify_compute
Modify_fix
Modify_command
Modify_dump
Modify_kspace
Modify_min
Modify_region
Modify_body
Modify_thermo
Modify_variable
END_RST -->
<!-- HTML_ONLY -->
"Overview"_Modify_overview.html
"Submitting new features for inclusion in LAMMPS"_Modify_contribute.html :all(b)
"Atom styles"_Modify_atom.html
"Pair styles"_Modify_pair.html
"Bond, angle, dihedral, improper styles"_Modify_bond.html
"Compute styles"_Modify_compute.html
"Fix styles"_Modify_fix.html
"Input script command styles"_Modify_command.html :all(b)
"Dump styles"_Modify_dump.html
"Kspace styles"_Modify_kspace.html
"Minimization styles"_Modify_min.html
"Region styles"_Modify_region.html
"Body styles"_Modify_body.html :all(b)
"Thermodynamic output options"_Modify_thermo.html
"Variable options"_Modify_variable.html :all(b)
<!-- END_HTML_ONLY -->

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"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Atom styles :h3
Classes that define an "atom style"_atom_style.html are derived from
the AtomVec class and managed by the Atom class. The atom style
determines what attributes are associated with an atom. A new atom
style can be created if one of the existing atom styles does not
define all the attributes you need to store and communicate with
atoms.
Atom_vec_atomic.cpp is a simple example of an atom style.
Here is a brief description of methods you define in your new derived
class. See atom_vec.h for details.
init: one time setup (optional)
grow: re-allocate atom arrays to longer lengths (required)
grow_reset: make array pointers in Atom and AtomVec classes consistent (required)
copy: copy info for one atom to another atom's array locations (required)
pack_comm: store an atom's info in a buffer communicated every timestep (required)
pack_comm_vel: add velocity info to communication buffer (required)
pack_comm_hybrid: store extra info unique to this atom style (optional)
unpack_comm: retrieve an atom's info from the buffer (required)
unpack_comm_vel: also retrieve velocity info (required)
unpack_comm_hybrid: retrieve extra info unique to this atom style (optional)
pack_reverse: store an atom's info in a buffer communicating partial forces (required)
pack_reverse_hybrid: store extra info unique to this atom style (optional)
unpack_reverse: retrieve an atom's info from the buffer (required)
unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional)
pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
pack_border_vel: add velocity info to buffer (required)
pack_border_hybrid: store extra info unique to this atom style (optional)
unpack_border: retrieve an atom's info from the buffer (required)
unpack_border_vel: also retrieve velocity info (required)
unpack_border_hybrid: retrieve extra info unique to this atom style (optional)
pack_exchange: store all an atom's info to migrate to another processor (required)
unpack_exchange: retrieve an atom's info from the buffer (required)
size_restart: number of restart quantities associated with proc's atoms (required)
pack_restart: pack atom quantities into a buffer (required)
unpack_restart: unpack atom quantities from a buffer (required)
create_atom: create an individual atom of this style (required)
data_atom: parse an atom line from the data file (required)
data_atom_hybrid: parse additional atom info unique to this atom style (optional)
data_vel: parse one line of velocity information from data file (optional)
data_vel_hybrid: parse additional velocity data unique to this atom style (optional)
memory_usage: tally memory allocated by atom arrays (required) :tb(s=:)
The constructor of the derived class sets values for several variables
that you must set when defining a new atom style, which are documented
in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
the word "customize" and you will find locations you will need to
modify.
NOTE: It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the "fix
property/atom"_fix_property_atom.html doc page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
New "pair styles"_pair_style.html, "fixes"_fix.html, or
"computes"_compute.html can be added to LAMMPS, as discussed below.
The code for these classes can use the per-atom properties defined by
fix property/atom. The Atom class has a find_custom() method that is
useful in this context:
int index = atom->find_custom(char *name, int &flag); :pre
The "name" of a custom attribute, as specified in the "fix
property/atom"_fix_property_atom.html command, is checked to verify
that it exists and its index is returned. The method also sets flag =
0/1 depending on whether it is an integer or floating-point attribute.
The vector of values associated with the attribute can then be
accessed using the returned index as
int *ivector = atom->ivector\[index\];
double *dvector = atom->dvector\[index\]; :pre
Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.

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doc/src/Modify_body.txt Normal file
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@ -0,0 +1,35 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Body styles :h3
Classes that define body particles are derived from the Body class.
Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
See "Section 6.14"_Section_howto.html#howto_14 of the manual for
an overview of using body particles and the "body"_body.html doc page
for details on the various body styles LAMMPS supports. New styles
can be created to add new kinds of body particles to LAMMPS.
Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.
Here is a brief description of methods you define in your new derived
class. See body.h for details.
data_body: process a line from the Bodies section of a data file
noutrow: number of sub-particles output is generated for
noutcol: number of values per-sub-particle output is generated for
output: output values for the Mth sub-particle
pack_comm_body: body attributes to communicate every timestep
unpack_comm_body: unpacking of those attributes
pack_border_body: body attributes to communicate when reneighboring is done
unpack_border_body: unpacking of those attributes :tb(s=:)

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@ -0,0 +1,33 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Bond, angle, dihedral, improper styles :h3
Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.
Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
init: check if all coefficients are set, calls {init_style} (optional)
init_style: check if style specific conditions are met (optional)
compute: compute the molecular interactions (required)
settings: apply global settings for all types (optional)
coeff: set coefficients for one type (required)
equilibrium_distance: length of bond, used by SHAKE (required, bond only)
equilibrium_angle: opening of angle, used by SHAKE (required, angle only)
write & read_restart: writes/reads coeffs to restart files (required)
single: force and energy of a single bond or angle (required, bond or angle only)
memory_usage: tally memory allocated by the style (optional) :tb(s=:)

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"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Input script command style :h3
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on LAMMPS data structures.
The single method your new class must define is as follows:
command: operations performed by the new command :tb(s=:)
Of course, the new class can define other methods and variables as
needed.

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@ -0,0 +1,49 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Compute styles :h3
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
Here is a brief description of methods you define in your new derived
class. See compute.h for details.
init: perform one time setup (required)
init_list: neighbor list setup, if needed (optional)
compute_scalar: compute a scalar quantity (optional)
compute_vector: compute a vector of quantities (optional)
compute_peratom: compute one or more quantities per atom (optional)
compute_local: compute one or more quantities per processor (optional)
pack_comm: pack a buffer with items to communicate (optional)
unpack_comm: unpack the buffer (optional)
pack_reverse: pack a buffer with items to reverse communicate (optional)
unpack_reverse: unpack the buffer (optional)
remove_bias: remove velocity bias from one atom (optional)
remove_bias_all: remove velocity bias from all atoms in group (optional)
restore_bias: restore velocity bias for one atom after remove_bias (optional)
restore_bias_all: same as before, but for all atoms in group (optional)
pair_tally_callback: callback function for {tally}-style computes (optional).
memory_usage: tally memory usage (optional) :tb(s=:)
Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides {examples}_compute_tally.html for utilizing this mechanism.

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"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Submitting new features for inclusion in LAMMPS :h3
We encourage users to submit new features or modifications for LAMMPS
to "the core developers"_http://lammps.sandia.gov/authors.html so they
can be added to the LAMMPS distribution. The preferred way to manage
and coordinate this is as of Fall 2016 via the LAMMPS project on
"GitHub"_https://github.com/lammps/lammps. An alternative is to
contact the LAMMPS developers or the indicated developer of a package
or feature directly and send in your contribution via e-mail.
For any larger modifications or programming project, you are
encouraged to contact the LAMMPS developers ahead of time, in order to
discuss implementation strategies and coding guidelines, that will
make it easier to integrate your contribution and result in less work
for everybody involved. You are also encouraged to search through the
list of "open issues on
GitHub"_https://github.com/lammps/lammps/issues and submit a new issue
for a planned feature, so you would not duplicate the work of others
(and possibly get scooped by them) or have your work duplicated by
others.
How quickly your contribution will be integrated depends largely on
how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
typical requirements. Once you have prepared everything, see "this
tutorial"_tutorial_github.html for instructions on how to submit your
changes or new files through a GitHub pull request. If you prefer to
submit patches or full files, you should first make certain, that your
code works correctly with the latest patch-level version of LAMMPS and
contains all bugfixes from it. Then create a gzipped tar file of all
changed or added files or a corresponding patch file using 'diff -u'
or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a "standard
package"_Section_start.html#start_3. Else we will add them as a
user-contributed file or package. Examples of user packages are in
src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
simplest way to have your contribution quickly added to the LAMMPS
distribution. You can see a list of the both standard and user
packages by typing "make package" in the LAMMPS src directory.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See "Section
1.4"_Section_intro.html#intro_4 for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the "Authors page"_http://lammps.sandia.gov/authors.html
of the "LAMMPS WWW site"_lws), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
contact with new collaborators. Note that you're also implicitly
agreeing to support your code which means answer questions, fix bugs,
and maintain it if LAMMPS changes in some way that breaks it (an
unusual event).
NOTE: If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the "Offsite LAMMPS packages and
tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
"developers"_http://lammps.sandia.gov/authors.html with info about
your package and we will post it there.
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you'll need to "communicate with the
developers"_http://lammps.sandia.gov/authors.html, since we may or may
not want to make those changes. An example of a trivial change is
making a parent-class method "virtual" when you derive a new child
class from it.
Here is a checklist of steps you need to follow to submit a single file
or user package for our consideration. Following these steps will save
both you and us time. See existing files in packages in the src dir for
examples. If you are uncertain, please ask.
All source files you provide must compile with the most current
version of LAMMPS with multiple configurations. In particular you
need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG
set in addition to the default -DLAMMPS_SMALLBIG setting. Your code
will need to work correctly in serial and in parallel using MPI. :ulb,l
For consistency with the rest of LAMMPS and especially, if you want
your contribution(s) to be added to main LAMMPS code or one of its
standard packages, it needs to be written in a style compatible with
other LAMMPS source files. This means: 2-character indentation per
level, [no tabs], no lines over 80 characters. I/O is done via
the C-style stdio library, class header files should not import any
system headers outside <stdio.h>, STL containers should be avoided
in headers, and forward declarations used where possible or needed.
All added code should be placed into the LAMMPS_NS namespace or a
sub-namespace; global or static variables should be avoided, as they
conflict with the modular nature of LAMMPS and the C++ class structure.
Header files must [not] import namespaces with {using}.
This all is so the developers can more easily understand, integrate,
and maintain your contribution and reduce conflicts with other parts
of LAMMPS. This basically means that the code accesses data
structures, performs its operations, and is formatted similar to other
LAMMPS source files, including the use of the error class for error
and warning messages. :l
If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a *.cpp and *.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line
entry to add to the USER-MISC/README file in that dir, along with the
2 source files. You can do this multiple times if you wish to
contribute several individual features. :l
If you want your contribution to be added as a user-contribution and
it is several related features, it is probably best to make it a user
package directory with a name like USER-FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
description of what your new package does. If your files depend on
other LAMMPS style files also being installed (e.g. because your file
is a derived class from the other LAMMPS class), then an Install.sh
file is also needed to check for those dependencies. See other README
and Install.sh files in other USER directories as examples. Send us a
tarball of this USER-FOO directory. :l
Your new source files need to have the LAMMPS copyright, GPL notice,
and your name and email address at the top, like other
user-contributed LAMMPS source files. They need to create a class
that is inside the LAMMPS namespace. If the file is for one of the
USER packages, including USER-MISC, then we are not as picky about the
coding style (see above). I.e. the files do not need to be in the
same stylistic format and syntax as other LAMMPS files, though that
would be nice for developers as well as users who try to read your
code. :l
You [must] also create a [documentation] file for each new command or
style you are adding to LAMMPS. For simplicity and convenience, the
documentation of groups of closely related commands or styles may be
combined into a single file. This will be one file for a single-file
feature. For a package, it might be several files. These are simple
text files with a specific markup language, that are then auto-converted
to HTML and PDF. The tools for this conversion are included in the
source distribution, and the translation can be as simple as doing
"make html pdf" in the doc folder.
Thus the documentation source files must be in the same format and
style as other *.txt files in the lammps/doc/src directory for similar
commands and styles; use one or more of them as a starting point.
A description of the markup can also be found in
lammps/doc/utils/txt2html/README.html
As appropriate, the text files can include links to equations
(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
files), or figures (see doc/JPG for examples), or even additional PDF
files with further details (see doc/PDF for examples). The doc page
should also include literature citations as appropriate; see the
bottom of doc/fix_nh.txt for examples and the earlier part of the same
file for how to format the cite itself. The "Restrictions" section of
the doc page should indicate that your command is only available if
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this. The
prerequisite for building the HTML format files are Python 3.x and
virtualenv, the requirement for generating the PDF format manual
is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least
"make html" and carefully inspect and proofread the resulting HTML format
doc page before submitting your code. :l
For a new package (or even a single command) you should include one or
more example scripts demonstrating its use. These should run in no
more than a couple minutes, even on a single processor, and not require
large data files as input. See directories under examples/USER for
examples of input scripts other users provided for their packages.
These example inputs are also required for validating memory accesses
and testing for memory leaks with valgrind :l
If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the *.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the
constructor of the class. Whenever a user invokes your feature from
their input script, this will cause LAMMPS to output the citation to a
log.cite file and prompt the user to examine the file. Note that you
should only use this for a paper you or your group authored.
E.g. adding a cite in the code for a paper by Nose and Hoover if you
write a fix that implements their integrator is not the intended
usage. That kind of citation should just be in the doc page you
provide. :l
:ule
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the
easier you make it for people to get started, e.g. by providing example
scripts, the more likely it is that users will try out your new feature.

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"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Dump styles :h2
Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
DumpCustom class contained in the dump_custom.cpp file.
Dump_atom.cpp is a simple example of a derived dump class.
Here is a brief description of methods you define in your new derived
class. See dump.h for details.
write_header: write the header section of a snapshot of atoms
count: count the number of lines a processor will output
pack: pack a proc's output data into a buffer
write_data: write a proc's data to a file :tb(s=:)
See the "dump"_dump.html command and its {custom} style for a list of
keywords for atom information that can already be dumped by
DumpCustom. It includes options to dump per-atom info from Compute
classes, so adding a new derived Compute class is one way to calculate
new quantities to dump.
Note that new keywords for atom properties are not typically
added to the "dump custom"_dump.html command. Instead they are added
to the "compute property/atom"_compute_property_atom.html command.

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"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Fix styles :h3
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
neighbor list construction, and output, is a "fix". This includes
time integration (update of coordinates and velocities), force
constraints or boundary conditions (SHAKE or walls), and diagnostics
(compute a diffusion coefficient). New styles can be created to add
new options to LAMMPS.
Fix_setforce.cpp is a simple example of setting forces on atoms to
prescribed values. There are dozens of fix options already in LAMMPS;
choose one as a template that is similar to what you want to
implement.
Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
setmask: determines when the fix is called during the timestep (required)
init: initialization before a run (optional)
setup_pre_exchange: called before atom exchange in setup (optional)
setup_pre_force: called before force computation in setup (optional)
setup: called immediately before the 1st timestep and after forces are computed (optional)
min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional)
min_setup: like setup, but for minimizations instead of MD runs (optional)
initial_integrate: called at very beginning of each timestep (optional)
pre_exchange: called before atom exchange on re-neighboring steps (optional)
pre_neighbor: called before neighbor list build (optional)
pre_force: called before pair & molecular forces are computed (optional)
post_force: called after pair & molecular forces are computed and communicated (optional)
final_integrate: called at end of each timestep (optional)
end_of_step: called at very end of timestep (optional)
write_restart: dumps fix info to restart file (optional)
restart: uses info from restart file to re-initialize the fix (optional)
grow_arrays: allocate memory for atom-based arrays used by fix (optional)
copy_arrays: copy atom info when an atom migrates to a new processor (optional)
pack_exchange: store atom's data in a buffer (optional)
unpack_exchange: retrieve atom's data from a buffer (optional)
pack_restart: store atom's data for writing to restart file (optional)
unpack_restart: retrieve atom's data from a restart file buffer (optional)
size_restart: size of atom's data (optional)
maxsize_restart: max size of atom's data (optional)
setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional)
initial_integrate_respa: same as initial_integrate, but for rRESPA (optional)
post_integrate_respa: called after the first half integration step is done in rRESPA (optional)
pre_force_respa: same as pre_force, but for rRESPA (optional)
post_force_respa: same as post_force, but for rRESPA (optional)
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional)
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore: push the minimization LIFO stack one element down (optional)
min_popstore: pop the minimization LIFO stack one element up (optional)
min_clearstore: clear minimization LIFO stack (optional)
min_step: reset or move forward on line search minimization (optional)
min_dof: report number of degrees of freedom {added} by this fix in minimization (optional)
max_alpha: report maximum allowed step size during linesearch minimization (optional)
pack_comm: pack a buffer to communicate a per-atom quantity (optional)
unpack_comm: unpack a buffer to communicate a per-atom quantity (optional)
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional)
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional)
dof: report number of degrees of freedom {removed} by this fix during MD (optional)
compute_scalar: return a global scalar property that the fix computes (optional)
compute_vector: return a component of a vector property that the fix computes (optional)
compute_array: return a component of an array property that the fix computes (optional)
deform: called when the box size is changed (optional)
reset_target: called when a change of the target temperature is requested during a run (optional)
reset_dt: is called when a change of the time step is requested during a run (optional)
modify_param: called when a fix_modify request is executed (optional)
memory_usage: report memory used by fix (optional)
thermo: compute quantities for thermodynamic output (optional) :tb(s=:)
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
will be invoked during the timestep. Fixes that perform time
integration ({nve}, {nvt}, {npt}) implement initial_integrate() and
final_integrate() to perform velocity Verlet updates. Fixes that
constrain forces implement post_force().
Fixes that perform diagnostics typically implement end_of_step(). For
an end_of_step fix, one of your fix arguments must be the variable
"nevery" which is used to determine when to call the fix and you must
set this variable in the constructor of your fix. By convention, this
is the first argument the fix defines (after the ID, group-ID, style).
If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate the info
with the atoms as they move from processors to processor by
implementing the grow_arrays, copy_arrays, pack_exchange, and
unpack_exchange methods. Similarly, the pack_restart and
unpack_restart methods can be implemented to store information about
the fix in restart files. If you wish an integrator or force
constraint fix to work with rRESPA (see the "run_style"_run_style.html
command), the initial_integrate, post_force_integrate, and
final_integrate_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.

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@ -0,0 +1,25 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Kspace styles :h3
Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.
Ewald.cpp is an example of computing K-space interactions.
Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
init: initialize the calculation before a run
setup: computation before the 1st timestep of a run
compute: every-timestep computation
memory_usage: tally of memory usage :tb(s=:)

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@ -0,0 +1,23 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Minimization styles :h3
Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.
Min_cg.cpp is an example of conjugate gradient minimization.
Here is a brief description of methods you define in your new derived
class. See min.h for details.
init: initialize the minimization before a run
run: perform the minimization
memory_usage: tally of memory usage :tb(s=:)

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@ -0,0 +1,101 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Overview :h3
The best way to add a new feature to LAMMPS is to find a similar
featureand look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
Most of the new features described on the "Modify"_Modify.html doc
page require you to write a new C++ derived class (except for
exceptions described below, where you can make small edits to existing
files). Creating a new class requires 2 files, a source code file
(*.cpp) and a header file (*.h). The derived class must provide
certain methods to work as a new option. Depending on how different
your new feature is compared to existing features, you can either
derive from the base class itself, or from a derived class that
already exists. Enabling LAMMPS to invoke the new class is as simple
as putting the two source files in the src dir and re-building LAMMPS.
The advantage of C++ and its object-orientation is that all the code
and variables needed to define the new feature are in the 2 files you
write, and thus shouldn't make the rest of LAMMPS more complex or
cause side-effect bugs.
Here is a concrete example. Suppose you write 2 files pair_foo.cpp
and pair_foo.h that define a new class PairFoo that computes pairwise
potentials described in the classic 1997 "paper"_#Foo by Foo, et al.
If you wish to invoke those potentials in a LAMMPS input script with a
command like
pair_style foo 0.1 3.5 :pre
then your pair_foo.h file should be structured as follows:
#ifdef PAIR_CLASS
PairStyle(foo,PairFoo)
#else
...
(class definition for PairFoo)
...
#endif :pre
where "foo" is the style keyword in the pair_style command, and
PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
files.
When you re-build LAMMPS, your new pairwise potential becomes part of
the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
As illustrated by this pairwise example, many kinds of options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
The "Modify page"_Modify.html lists all the common styles in LAMMPS,
and discusses the header file for the base class that these styles are
derived from. Public variables in that file are ones used and set by
the derived classes which are also used by the base class. Sometimes
they are also used by the rest of LAMMPS. Virtual functions in the
base class header file which are set = 0 are ones you must define in
your new derived class to give it the functionality LAMMPS expects.
Virtual functions that are not set to 0 are functions you can
optionally define.
Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files. These are also
listed on the "Modify page"_Modify.html.
Here are additional guidelines for modifying LAMMPS and adding new
functionality:
Think about whether what you want to do would be better as a pre- or
post-processing step. Many computations are more easily and more
quickly done that way. :ulb,l
Don't do anything within the timestepping of a run that isn't
parallel. E.g. don't accumulate a bunch of data on a single processor
and analyze it. You run the risk of seriously degrading the parallel
efficiency. :l
If your new feature reads arguments or writes output, make sure you
follow the unit conventions discussed by the "units"_units.html
command. :l
:ule
:line
:link(Foo)
[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).

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@ -0,0 +1,33 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Pair styles :h3
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
Here is a brief description of the class methods in pair.h:
compute: workhorse routine that computes pairwise interactions
settings: reads the input script line with arguments you define
coeff: set coefficients for one i,j type pair
init_one: perform initialization for one i,j type pair
init_style: initialization specific to this pair style
write & read_restart: write/read i,j pair coeffs to restart files
write & read_restart_settings: write/read global settings to restart files
single: force and energy of a single pairwise interaction between 2 atoms
compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:)
The inner/middle/outer routines are optional.

25
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@ -0,0 +1,25 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Region styles :h3
Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
styles can be created to add new region shapes to LAMMPS.
Region_sphere.cpp is an example of a spherical region.
Here is a brief description of methods you define in your new derived
class. See region.h for details.
inside: determine whether a point is in the region
surface_interior: determine if a point is within a cutoff distance inside of surc
surface_exterior: determine if a point is within a cutoff distance outside of surf
shape_update : change region shape if set by time-dependent variable :tb(s=:)

35
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@ -0,0 +1,35 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Thermodynamic output options :h3
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the "thermo_style"_thermo_style.html command for a list
of defined quantities.
The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
Note that the "thermo_style custom"_thermo.html command already allows
for thermo output of quantities calculated by "fixes"_fix.html,
"computes"_compute.html, and "variables"_variable.html. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.

46
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@ -0,0 +1,46 @@
"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Variable options :h3
There is one class that computes and stores "variable"_variable.html
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
via the "print"_print.html, "fix print"_fix_print.html, or
"thermo_style custom"_thermo_style.html commands. Variables of style
"equal" can compute complex equations that involve the following types
of arguments:
thermo keywords = ke, vol, atoms, ...
other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x\[123\], y\[3\], vx\[34\], ...
compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre
Adding keywords for the "thermo_style custom"_thermo_style.html
command (which can then be accessed by variables) is discussed on the
"Modify thermo"_Modify_thermo.html doc page.
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaluate() method. Search for
the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the
Variable::evaluate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
Accessing a new atom-based vector can be done by editing one section
of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location.
Adding new "compute styles"_compute.html (whose calculated values can
then be accessed by variables) is discussed on the "Modify
compute"_Modify_compute.html doc page.

8
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@ -204,10 +204,10 @@ allowed, but that should be sufficient for most use cases.
3.3 Input script structure :h3,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
"Section 7"_Section_example.html, and animated on the "LAMMPS
WWW Site"_lws.
The examples directory in the LAMMPS distribution contains many sample
input scripts; the corresponding problems are discussed on the
"Examples"_Examples.html doc page, and animated on the "LAMMPS WWW
Site"_lws.
A LAMMPS input script typically has 4 parts:

35
doc/src/Section_howto.txt
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@ -1,4 +1,4 @@
"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c
"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Examples.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -40,7 +40,7 @@ This section describes how to perform common tasks using LAMMPS.
6.28 "Magnetic spins"_#howto_28 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "Section 7"_Section_example.html also show how to
highlighted on the "Examples"_Examples.html doc page also show how to
setup and run various kinds of simulations.
:line
@ -672,10 +672,10 @@ this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
which has been linked to LAMMPS as a library. This is the way the
"POEMS"_poems package that performs constrained rigid-body motion on
groups of atoms is hooked to LAMMPS. See the
"fix poems"_fix_poems.html command for more details. See "this
section"_Section_modify.html of the documentation for info on how to add
a new fix to LAMMPS.
groups of atoms is hooked to LAMMPS. See the "fix
poems"_fix_poems.html command for more details. See the
"Modify"_Modify.html doc page for info on how to add a new fix to
LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
@ -696,8 +696,8 @@ 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 10"_Section_modify.html of the documentation for how
to add a new command to LAMMPS.
See the "Modify"_Modify.html doc page for how to add a new command to
LAMMPS.
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
@ -1057,7 +1057,7 @@ rigid bodies composed of finite-size particles :ul
Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
"examples directory"_Section_example.html in the LAMMPS distribution.
"examples directory"_Examples.html in the LAMMPS distribution.
Atom styles :h4
@ -1302,8 +1302,8 @@ As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also "add their own computes and fixes
to LAMMPS"_Section_modify.html which can then generate values that can
then be output with these commands.
to LAMMPS"_Modify.html which can then generate values that can then be
output with these commands.
The following sub-sections discuss different LAMMPS command related
to output and the kind of data they operate on and produce:
@ -1824,8 +1824,8 @@ At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
"change_box"_change_box.html command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/elastic directory described in "this
section"_Section_example.html.
examples/elastic directory described on the "Examples"_Examples.html
doc page.
Calculating elastic constants at finite temperature is more
challenging, because it is necessary to run a simulation that perfoms
@ -2322,11 +2322,10 @@ Note that this compute allows the per-atom output of other
"computes"_compute.html, "fixes"_fix.html, and
"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 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.
per-atom quantity to use as chunk ID. See the "Modify"_Modify.html
doc page 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.
Fix ave/chunk command: :h4

17
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@ -54,8 +54,8 @@ brief discussion of the open-source philosophy.
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See "Section 10"_Section_modify.html
for more details.
conditions, or diagnostics. See the "Modify"_Modify.html doc page for
more details.
The current version of LAMMPS is written in C++. Earlier versions
were written in F77 and F90. See
@ -94,8 +94,8 @@ LAMMPS are listed in "this section"_#intro_5.
This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
favorite interatomic potential, boundary condition, or atom type, see
"Section 10"_Section_modify.html, which describes how you can add
it to LAMMPS.
the "Modify"_Modify.html doc page, which describes how you can add it
to LAMMPS.
General features :h4
@ -334,8 +334,8 @@ Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see "Section 10"_Section_modify.html for a discussion
of how you can use the "dump"_dump.html and "compute"_compute.html and
LAMMPS runs, see the "Modify"_Modify.html doc page for a discussion of
how you can use the "dump"_dump.html and "compute"_compute.html and
"fix"_fix.html commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
dynamics timestepping, particularly if the computations are not
@ -448,9 +448,8 @@ distribution. :l
LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
"This section"_Section_modify.html gives details. If you add a
feature of general interest, it can be added to the LAMMPS
distribution. :l
The "Modify"_Modify.html doc page gives details. If you add a feature
of general interest, it can be added to the LAMMPS distribution. :l
The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
performance on various platforms. The files needed to run the

827
doc/src/Section_modify.txt
View File

@ -1,827 +0,0 @@
"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_python.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
10. Modifying & extending LAMMPS :h2
This section describes how to customize LAMMPS by modifying
and extending its source code.
10.1 "Atom styles"_#mod_1
10.2 "Bond, angle, dihedral, improper potentials"_#mod_2
10.3 "Compute styles"_#mod_3
10.4 "Dump styles"_#mod_4
10.5 "Dump custom output options"_#mod_5
10.6 "Fix styles"_#mod_6 which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
10.7 "Input script commands"_#mod_7
10.8 "Kspace computations"_#mod_8
10.9 "Minimization styles"_#mod_9
10.10 "Pairwise potentials"_#mod_10
10.11 "Region styles"_#mod_11
10.12 "Body styles"_#mod_12
10.13 "Thermodynamic output options"_#mod_13
10.14 "Variable options"_#mod_14
10.15 "Submitting new features for inclusion in LAMMPS"_#mod_15 :all(b)
LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 75% of its source code
is files added in this fashion.
In this section, changes and additions users can make are listed along
with minimal instructions. If you add a new feature to LAMMPS and
think it will be of interest to general users, we encourage you to
submit it to the developers for inclusion in the released version of
LAMMPS. Information about how to do this is provided
"below"_#mod_14.
The best way to add a new feature is to find a similar feature in
LAMMPS and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
Most of the new features described in this section require you to
write a new C++ derived class (except for exceptions described below,
where you can make small edits to existing files). Creating a new
class requires 2 files, a source code file (*.cpp) and a header file
(*.h). The derived class must provide certain methods to work as a
new option. Depending on how different your new feature is compared
to existing features, you can either derive from the base class
itself, or from a derived class that already exists. Enabling LAMMPS
to invoke the new class is as simple as putting the two source
files in the src dir and re-building LAMMPS.
The advantage of C++ and its object-orientation is that all the code
and variables needed to define the new feature are in the 2 files you
write, and thus shouldn't make the rest of LAMMPS more complex or
cause side-effect bugs.
Here is a concrete example. Suppose you write 2 files pair_foo.cpp
and pair_foo.h that define a new class PairFoo that computes pairwise
potentials described in the classic 1997 "paper"_#Foo by Foo, et al.
If you wish to invoke those potentials in a LAMMPS input script with a
command like
pair_style foo 0.1 3.5 :pre
then your pair_foo.h file should be structured as follows:
#ifdef PAIR_CLASS
PairStyle(foo,PairFoo)
#else
...
(class definition for PairFoo)
...
#endif :pre
where "foo" is the style keyword in the pair_style command, and
PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
files.
When you re-build LAMMPS, your new pairwise potential becomes part of
the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
As illustrated by this pairwise example, many kinds of options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
The instructions below give the header file for the base class that
these styles are derived from. Public variables in that file are ones
used and set by the derived classes which are also used by the base
class. Sometimes they are also used by the rest of LAMMPS. Virtual
functions in the base class header file which are set = 0 are ones you
must define in your new derived class to give it the functionality
LAMMPS expects. Virtual functions that are not set to 0 are functions
you can optionally define.
Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
below.
Here are additional guidelines for modifying LAMMPS and adding new
functionality:
Think about whether what you want to do would be better as a pre- or
post-processing step. Many computations are more easily and more
quickly done that way. :ulb,l
Don't do anything within the timestepping of a run that isn't
parallel. E.g. don't accumulate a bunch of data on a single processor
and analyze it. You run the risk of seriously degrading the parallel
efficiency. :l
If your new feature reads arguments or writes output, make sure you
follow the unit conventions discussed by the "units"_units.html
command. :l
If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
"developers"_http://lammps.sandia.gov/authors.html. We might be
interested in adding it to the LAMMPS distribution. See further
details on this at the bottom of this page. :l
:ule
:line
:line
10.1 Atom styles :link(mod_1),h4
Classes that define an "atom style"_atom_style.html are derived from
the AtomVec class and managed by the Atom class. The atom style
determines what attributes are associated with an atom. A new atom
style can be created if one of the existing atom styles does not
define all the attributes you need to store and communicate with
atoms.
Atom_vec_atomic.cpp is a simple example of an atom style.
Here is a brief description of methods you define in your new derived
class. See atom_vec.h for details.
init: one time setup (optional)
grow: re-allocate atom arrays to longer lengths (required)
grow_reset: make array pointers in Atom and AtomVec classes consistent (required)
copy: copy info for one atom to another atom's array locations (required)
pack_comm: store an atom's info in a buffer communicated every timestep (required)
pack_comm_vel: add velocity info to communication buffer (required)
pack_comm_hybrid: store extra info unique to this atom style (optional)
unpack_comm: retrieve an atom's info from the buffer (required)
unpack_comm_vel: also retrieve velocity info (required)
unpack_comm_hybrid: retrieve extra info unique to this atom style (optional)
pack_reverse: store an atom's info in a buffer communicating partial forces (required)
pack_reverse_hybrid: store extra info unique to this atom style (optional)
unpack_reverse: retrieve an atom's info from the buffer (required)
unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional)
pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
pack_border_vel: add velocity info to buffer (required)
pack_border_hybrid: store extra info unique to this atom style (optional)
unpack_border: retrieve an atom's info from the buffer (required)
unpack_border_vel: also retrieve velocity info (required)
unpack_border_hybrid: retrieve extra info unique to this atom style (optional)
pack_exchange: store all an atom's info to migrate to another processor (required)
unpack_exchange: retrieve an atom's info from the buffer (required)
size_restart: number of restart quantities associated with proc's atoms (required)
pack_restart: pack atom quantities into a buffer (required)
unpack_restart: unpack atom quantities from a buffer (required)
create_atom: create an individual atom of this style (required)
data_atom: parse an atom line from the data file (required)
data_atom_hybrid: parse additional atom info unique to this atom style (optional)
data_vel: parse one line of velocity information from data file (optional)
data_vel_hybrid: parse additional velocity data unique to this atom style (optional)
memory_usage: tally memory allocated by atom arrays (required) :tb(s=:)
The constructor of the derived class sets values for several variables
that you must set when defining a new atom style, which are documented
in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
the word "customize" and you will find locations you will need to
modify.
NOTE: It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the "fix
property/atom"_fix_property_atom.html doc page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
New "pair styles"_pair_style.html, "fixes"_fix.html, or
"computes"_compute.html can be added to LAMMPS, as discussed below.
The code for these classes can use the per-atom properties defined by
fix property/atom. The Atom class has a find_custom() method that is
useful in this context:
int index = atom->find_custom(char *name, int &flag); :pre
The "name" of a custom attribute, as specified in the "fix
property/atom"_fix_property_atom.html command, is checked to verify
that it exists and its index is returned. The method also sets flag =
0/1 depending on whether it is an integer or floating-point attribute.
The vector of values associated with the attribute can then be
accessed using the returned index as
int *ivector = atom->ivector\[index\];
double *dvector = atom->dvector\[index\]; :pre
Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.
:line
10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4
Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.
Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
init: check if all coefficients are set, calls {init_style} (optional)
init_style: check if style specific conditions are met (optional)
compute: compute the molecular interactions (required)
settings: apply global settings for all types (optional)
coeff: set coefficients for one type (required)
equilibrium_distance: length of bond, used by SHAKE (required, bond only)
equilibrium_angle: opening of angle, used by SHAKE (required, angle only)
write & read_restart: writes/reads coeffs to restart files (required)
single: force and energy of a single bond or angle (required, bond or angle only)
memory_usage: tally memory allocated by the style (optional) :tb(s=:)
:line
10.3 Compute styles :link(mod_3),h4
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
Here is a brief description of methods you define in your new derived
class. See compute.h for details.
init: perform one time setup (required)
init_list: neighbor list setup, if needed (optional)
compute_scalar: compute a scalar quantity (optional)
compute_vector: compute a vector of quantities (optional)
compute_peratom: compute one or more quantities per atom (optional)
compute_local: compute one or more quantities per processor (optional)
pack_comm: pack a buffer with items to communicate (optional)
unpack_comm: unpack the buffer (optional)
pack_reverse: pack a buffer with items to reverse communicate (optional)
unpack_reverse: unpack the buffer (optional)
remove_bias: remove velocity bias from one atom (optional)
remove_bias_all: remove velocity bias from all atoms in group (optional)
restore_bias: restore velocity bias for one atom after remove_bias (optional)
restore_bias_all: same as before, but for all atoms in group (optional)
pair_tally_callback: callback function for {tally}-style computes (optional).
memory_usage: tally memory usage (optional) :tb(s=:)
Tally-style computes are a special case, as their computation is done
in two stages: the callback function is registered with the pair style
and then called from the Pair::ev_tally() function, which is called for
each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute_scalar or
compute_vector or compute_peratom methods. The USER-TALLY package
provides {examples}_compute_tally.html for utilizing this mechanism.
:line
10.4 Dump styles :link(mod_4),h4
10.5 Dump custom output options :link(mod_5),h4
Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
DumpCustom class contained in the dump_custom.cpp file.
Dump_atom.cpp is a simple example of a derived dump class.
Here is a brief description of methods you define in your new derived
class. See dump.h for details.
write_header: write the header section of a snapshot of atoms
count: count the number of lines a processor will output
pack: pack a proc's output data into a buffer
write_data: write a proc's data to a file :tb(s=:)
See the "dump"_dump.html command and its {custom} style for a list of
keywords for atom information that can already be dumped by
DumpCustom. It includes options to dump per-atom info from Compute
classes, so adding a new derived Compute class is one way to calculate
new quantities to dump.
Alternatively, you can add new keywords to the dump custom command.
Search for the word "customize" in dump_custom.cpp to see the
half-dozen or so locations where code will need to be added.
:line
10.6 Fix styles :link(mod_6),h4
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
neighbor list construction, and output, is a "fix". This includes
time integration (update of coordinates and velocities), force
constraints or boundary conditions (SHAKE or walls), and diagnostics
(compute a diffusion coefficient). New styles can be created to add
new options to LAMMPS.
Fix_setforce.cpp is a simple example of setting forces on atoms to
prescribed values. There are dozens of fix options already in LAMMPS;
choose one as a template that is similar to what you want to
implement.
Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
setmask: determines when the fix is called during the timestep (required)
init: initialization before a run (optional)
setup_pre_exchange: called before atom exchange in setup (optional)
setup_pre_force: called before force computation in setup (optional)
setup: called immediately before the 1st timestep and after forces are computed (optional)
min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional)
min_setup: like setup, but for minimizations instead of MD runs (optional)
initial_integrate: called at very beginning of each timestep (optional)
pre_exchange: called before atom exchange on re-neighboring steps (optional)
pre_neighbor: called before neighbor list build (optional)
pre_force: called before pair & molecular forces are computed (optional)
post_force: called after pair & molecular forces are computed and communicated (optional)
final_integrate: called at end of each timestep (optional)
end_of_step: called at very end of timestep (optional)
write_restart: dumps fix info to restart file (optional)
restart: uses info from restart file to re-initialize the fix (optional)
grow_arrays: allocate memory for atom-based arrays used by fix (optional)
copy_arrays: copy atom info when an atom migrates to a new processor (optional)
pack_exchange: store atom's data in a buffer (optional)
unpack_exchange: retrieve atom's data from a buffer (optional)
pack_restart: store atom's data for writing to restart file (optional)
unpack_restart: retrieve atom's data from a restart file buffer (optional)
size_restart: size of atom's data (optional)
maxsize_restart: max size of atom's data (optional)
setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional)
initial_integrate_respa: same as initial_integrate, but for rRESPA (optional)
post_integrate_respa: called after the first half integration step is done in rRESPA (optional)
pre_force_respa: same as pre_force, but for rRESPA (optional)
post_force_respa: same as post_force, but for rRESPA (optional)
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional)
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore: push the minimization LIFO stack one element down (optional)
min_popstore: pop the minimization LIFO stack one element up (optional)
min_clearstore: clear minimization LIFO stack (optional)
min_step: reset or move forward on line search minimization (optional)
min_dof: report number of degrees of freedom {added} by this fix in minimization (optional)
max_alpha: report maximum allowed step size during linesearch minimization (optional)
pack_comm: pack a buffer to communicate a per-atom quantity (optional)
unpack_comm: unpack a buffer to communicate a per-atom quantity (optional)
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional)
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional)
dof: report number of degrees of freedom {removed} by this fix during MD (optional)
compute_scalar: return a global scalar property that the fix computes (optional)
compute_vector: return a component of a vector property that the fix computes (optional)
compute_array: return a component of an array property that the fix computes (optional)
deform: called when the box size is changed (optional)
reset_target: called when a change of the target temperature is requested during a run (optional)
reset_dt: is called when a change of the time step is requested during a run (optional)
modify_param: called when a fix_modify request is executed (optional)
memory_usage: report memory used by fix (optional)
thermo: compute quantities for thermodynamic output (optional) :tb(s=:)
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
will be invoked during the timestep. Fixes that perform time
integration ({nve}, {nvt}, {npt}) implement initial_integrate() and
final_integrate() to perform velocity Verlet updates. Fixes that
constrain forces implement post_force().
Fixes that perform diagnostics typically implement end_of_step(). For
an end_of_step fix, one of your fix arguments must be the variable
"nevery" which is used to determine when to call the fix and you must
set this variable in the constructor of your fix. By convention, this
is the first argument the fix defines (after the ID, group-ID, style).
If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate the info
with the atoms as they move from processors to processor by
implementing the grow_arrays, copy_arrays, pack_exchange, and
unpack_exchange methods. Similarly, the pack_restart and
unpack_restart methods can be implemented to store information about
the fix in restart files. If you wish an integrator or force
constraint fix to work with rRESPA (see the "run_style"_run_style.html
command), the initial_integrate, post_force_integrate, and
final_integrate_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.
:line
10.7 Input script commands :link(mod_7),h4
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on LAMMPS data structures.
The single method your new class must define is as follows:
command: operations performed by the new command :tb(s=:)
Of course, the new class can define other methods and variables as
needed.
:line
10.8 Kspace computations :link(mod_8),h4
Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.
Ewald.cpp is an example of computing K-space interactions.
Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
init: initialize the calculation before a run
setup: computation before the 1st timestep of a run
compute: every-timestep computation
memory_usage: tally of memory usage :tb(s=:)
:line
10.9 Minimization styles :link(mod_9),h4
Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.
Min_cg.cpp is an example of conjugate gradient minimization.
Here is a brief description of methods you define in your new derived
class. See min.h for details.
init: initialize the minimization before a run
run: perform the minimization
memory_usage: tally of memory usage :tb(s=:)
:line
10.10 Pairwise potentials :link(mod_10),h4
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
Here is a brief description of the class methods in pair.h:
compute: workhorse routine that computes pairwise interactions
settings: reads the input script line with arguments you define
coeff: set coefficients for one i,j type pair
init_one: perform initialization for one i,j type pair
init_style: initialization specific to this pair style
write & read_restart: write/read i,j pair coeffs to restart files
write & read_restart_settings: write/read global settings to restart files
single: force and energy of a single pairwise interaction between 2 atoms
compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:)
The inner/middle/outer routines are optional.
:line
10.11 Region styles :link(mod_11),h4
Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
styles can be created to add new region shapes to LAMMPS.
Region_sphere.cpp is an example of a spherical region.
Here is a brief description of methods you define in your new derived
class. See region.h for details.
inside: determine whether a point is in the region
surface_interior: determine if a point is within a cutoff distance inside of surc
surface_exterior: determine if a point is within a cutoff distance outside of surf
shape_update : change region shape if set by time-dependent variable :tb(s=:)
:line
10.12 Body styles :link(mod_12),h4
Classes that define body particles are derived from the Body class.
Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
See "Section 6.14"_Section_howto.html#howto_14 of the manual for
an overview of using body particles and the "body"_body.html doc page
for details on the various body styles LAMMPS supports. New styles
can be created to add new kinds of body particles to LAMMPS.
Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.
Here is a brief description of methods you define in your new derived
class. See body.h for details.
data_body: process a line from the Bodies section of a data file
noutrow: number of sub-particles output is generated for
noutcol: number of values per-sub-particle output is generated for
output: output values for the Mth sub-particle
pack_comm_body: body attributes to communicate every timestep
unpack_comm_body: unpacking of those attributes
pack_border_body: body attributes to communicate when reneighboring is done
unpack_border_body: unpacking of those attributes :tb(s=:)
:line
10.13 Thermodynamic output options :link(mod_13),h4
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the "thermo_style"_thermo_style.html command for a list
of defined quantities.
The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
Note that the "thermo_style custom"_thermo.html command already allows
for thermo output of quantities calculated by "fixes"_fix.html,
"computes"_compute.html, and "variables"_variable.html. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
:line
10.14 Variable options :link(mod_14),h4
There is one class that computes and stores "variable"_variable.html
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
via the "print"_print.html, "fix print"_fix_print.html, or
"thermo_style custom"_thermo_style.html commands. Variables of style
"equal" can compute complex equations that involve the following types
of arguments:
thermo keywords = ke, vol, atoms, ...
other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x\[123\], y\[3\], vx\[34\], ...
compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre
Adding keywords for the "thermo_style custom"_thermo_style.html command
(which can then be accessed by variables) was discussed
"here"_Section_modify.html#mod_13 on this page.
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaluate() method. Search for
the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the
Variable::evaluate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
Accessing a new atom-based vector can be done by editing one section
of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location.
Adding new "compute styles"_compute.html (whose calculated values can
then be accessed by variables) was discussed
"here"_Section_modify.html#mod_3 on this page.
:line
:line
10.15 Submitting new features for inclusion in LAMMPS :link(mod_15),h4
We encourage users to submit new features or modifications for
LAMMPS to "the core developers"_http://lammps.sandia.gov/authors.html
so they can be added to the LAMMPS distribution. The preferred way to
manage and coordinate this is as of Fall 2016 via the LAMMPS project on
"GitHub"_https://github.com/lammps/lammps. An alternative is to contact
the LAMMPS developers or the indicated developer of a package or feature
directly and send in your contribution via e-mail.
For any larger modifications or programming project, you are encouraged
to contact the LAMMPS developers ahead of time, in order to discuss
implementation strategies and coding guidelines, that will make it
easier to integrate your contribution and result in less work for
everybody involved. You are also encouraged to search through the list
of "open issues on GitHub"_https://github.com/lammps/lammps/issues and
submit a new issue for a planned feature, so you would not duplicate
the work of others (and possibly get scooped by them) or have your work
duplicated by others.
How quickly your contribution will be integrated
depends largely on how much effort it will cause to integrate and test
it, how much it requires changes to the core codebase, and of how much
interest it is to the larger LAMMPS community. Please see below for a
checklist of typical requirements. Once you have prepared everything,
see "this tutorial"_tutorial_github.html for instructions on how to
submit your changes or new files through a GitHub pull request. If you
prefer to submit patches or full files, you should first make certain,
that your code works correctly with the latest patch-level version of
LAMMPS and contains all bugfixes from it. Then create a gzipped tar
file of all changed or added files or a corresponding patch file using
'diff -u' or 'diff -c' and compress it with gzip. Please only use
gzip compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a "standard
package"_Section_start.html#start_3. Else we will add them as a
user-contributed file or package. Examples of user packages are in
src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
simplest way to have your contribution quickly added to the LAMMPS
distribution. You can see a list of the both standard and user
packages by typing "make package" in the LAMMPS src directory.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See "Section
1.4"_Section_intro.html#intro_4 for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the "Authors page"_http://lammps.sandia.gov/authors.html
of the "LAMMPS WWW site"_lws), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
contact with new collaborators. Note that you're also implicitly
agreeing to support your code which means answer questions, fix bugs,
and maintain it if LAMMPS changes in some way that breaks it (an
unusual event).
NOTE: If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the "Offsite LAMMPS packages and
tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
"developers"_http://lammps.sandia.gov/authors.html with info about
your package and we will post it there.
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you'll need to "communicate with the
developers"_http://lammps.sandia.gov/authors.html, since we may or may
not want to make those changes. An example of a trivial change is
making a parent-class method "virtual" when you derive a new child
class from it.
Here is a checklist of steps you need to follow to submit a single file
or user package for our consideration. Following these steps will save
both you and us time. See existing files in packages in the src dir for
examples. If you are uncertain, please ask.
All source files you provide must compile with the most current
version of LAMMPS with multiple configurations. In particular you
need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG
set in addition to the default -DLAMMPS_SMALLBIG setting. Your code
will need to work correctly in serial and in parallel using MPI. :ulb,l
For consistency with the rest of LAMMPS and especially, if you want
your contribution(s) to be added to main LAMMPS code or one of its
standard packages, it needs to be written in a style compatible with
other LAMMPS source files. This means: 2-character indentation per
level, [no tabs], no lines over 80 characters. I/O is done via
the C-style stdio library, class header files should not import any
system headers outside <stdio.h>, STL containers should be avoided
in headers, and forward declarations used where possible or needed.
All added code should be placed into the LAMMPS_NS namespace or a
sub-namespace; global or static variables should be avoided, as they
conflict with the modular nature of LAMMPS and the C++ class structure.
Header files must [not] import namespaces with {using}.
This all is so the developers can more easily understand, integrate,
and maintain your contribution and reduce conflicts with other parts
of LAMMPS. This basically means that the code accesses data
structures, performs its operations, and is formatted similar to other
LAMMPS source files, including the use of the error class for error
and warning messages. :l
If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a *.cpp and *.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line
entry to add to the USER-MISC/README file in that dir, along with the
2 source files. You can do this multiple times if you wish to
contribute several individual features. :l
If you want your contribution to be added as a user-contribution and
it is several related features, it is probably best to make it a user
package directory with a name like USER-FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
description of what your new package does. If your files depend on
other LAMMPS style files also being installed (e.g. because your file
is a derived class from the other LAMMPS class), then an Install.sh
file is also needed to check for those dependencies. See other README
and Install.sh files in other USER directories as examples. Send us a
tarball of this USER-FOO directory. :l
Your new source files need to have the LAMMPS copyright, GPL notice,
and your name and email address at the top, like other
user-contributed LAMMPS source files. They need to create a class
that is inside the LAMMPS namespace. If the file is for one of the
USER packages, including USER-MISC, then we are not as picky about the
coding style (see above). I.e. the files do not need to be in the
same stylistic format and syntax as other LAMMPS files, though that
would be nice for developers as well as users who try to read your
code. :l
You [must] also create a [documentation] file for each new command or
style you are adding to LAMMPS. For simplicity and convenience, the
documentation of groups of closely related commands or styles may be
combined into a single file. This will be one file for a single-file
feature. For a package, it might be several files. These are simple
text files with a specific markup language, that are then auto-converted
to HTML and PDF. The tools for this conversion are included in the
source distribution, and the translation can be as simple as doing
"make html pdf" in the doc folder.
Thus the documentation source files must be in the same format and
style as other *.txt files in the lammps/doc/src directory for similar
commands and styles; use one or more of them as a starting point.
A description of the markup can also be found in
lammps/doc/utils/txt2html/README.html
As appropriate, the text files can include links to equations
(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
files), or figures (see doc/JPG for examples), or even additional PDF
files with further details (see doc/PDF for examples). The doc page
should also include literature citations as appropriate; see the
bottom of doc/fix_nh.txt for examples and the earlier part of the same
file for how to format the cite itself. The "Restrictions" section of
the doc page should indicate that your command is only available if
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this. The
prerequisite for building the HTML format files are Python 3.x and
virtualenv, the requirement for generating the PDF format manual
is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least
"make html" and carefully inspect and proofread the resulting HTML format
doc page before submitting your code. :l
For a new package (or even a single command) you should include one or
more example scripts demonstrating its use. These should run in no
more than a couple minutes, even on a single processor, and not require
large data files as input. See directories under examples/USER for
examples of input scripts other users provided for their packages.
These example inputs are also required for validating memory accesses
and testing for memory leaks with valgrind :l
If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the *.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the
constructor of the class. Whenever a user invokes your feature from
their input script, this will cause LAMMPS to output the citation to a
log.cite file and prompt the user to examine the file. Note that you
should only use this for a paper you or your group authored.
E.g. adding a cite in the code for a paper by Nose and Hoover if you
write a fix that implements their integrator is not the intended
usage. That kind of citation should just be in the doc page you
provide. :l
:ule
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the
easier you make it for people to get started, e.g. by providing example
scripts, the more likely it is that users will try out your new feature.
:line
:line
:link(Foo)
[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).

3
doc/src/Section_packages.txt
View File

@ -51,8 +51,7 @@ technical questions about compiling the package. If you have problems
using a feature provided in a user package, you may need to contact
the contributor directly to get help. Information on how to submit
additions you make to LAMMPS as single files or as a standard or user
package are given in "this section"_Section_modify.html#mod_15 of the
manual.
package are given in the "Modify contribute"_Modify.html doc page.
Following the next two tables is a sub-section for each package. It
lists authors (if applicable) and summarizes the package contents. It

6
doc/src/Section_perf.txt
View File

@ -1,6 +1,6 @@
"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Tools.html :c
"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html
:c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)

4
doc/src/Section_python.txt
View File

@ -1,4 +1,6 @@
"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c
"Previous Section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_errors.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)

4
doc/src/Tools.txt
View File

@ -1,6 +1,6 @@
"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_modify.html :c
Section"_Modify.html :c
<!-- future sequence of sections:
"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
@ -377,7 +377,7 @@ micelle2d < def.micelle2d > data.file :pre
See the def.micelle2d file in the tools directory for an example of a
definition file. This tool was used to create the system for the
"micelle example"_Section_example.html.
"micelle example"_Examples.html.
:line

2
doc/src/atom_style.txt
View File

@ -255,7 +255,7 @@ with another molecular style that stores bond,angle,etc info on a
per-atom basis.
LAMMPS can be extended with new atom styles as well as new body
styles; see "this section"_Section_modify.html.
styles; see the "Modify"_Modify.html doc page.
:line

4
doc/src/body.txt
View File

@ -36,8 +36,8 @@ thus how they can be used to compute pairwise body/body or
bond/non-body (point particle) interactions. More details of each
style are described below.
More styles may be added in the future. See "Section
10.12"_Section_modify.html#mod_12 for details on how to add a new body
More styles may be added in the future. See the "Modify
body"_Modify_body.html doc page for details on how to add a new body
style to the code.
:line

4
doc/src/compute.txt
View File

@ -153,8 +153,8 @@ via the "compute_modify"_compute_modify.html command.
Computes can be deleted with the "uncompute"_uncompute.html command.
Code for new computes can be added to LAMMPS (see "this
section"_Section_modify.html of the manual) and the results of their
Code for new computes can be added to LAMMPS; see the
"Modify"_Modify.html doc page for details. The results of their
calculations accessed in the various ways described above.
:line

4
doc/src/compute_chunk_atom.txt
View File

@ -275,7 +275,7 @@ previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and "add them to LAMMPS"_Section_modify.html.
their own compute styles and "add them to LAMMPS"_Modify.html.
If the style begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
@ -285,7 +285,7 @@ calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with the
timestep on which this compute accesses the fix, else an error
results. Users can also write code for their own fix styles and "add
them to LAMMPS"_Section_modify.html.
them to LAMMPS"_Modify.html.
If a value begins with "v_", a variable name for an {atom} or
{atomfile} style "variable"_variable.html must follow which has been

8
doc/src/compute_global_atom.txt
View File

@ -130,7 +130,7 @@ page for details. If no bracketed integer is appended, the per-atom
vector calculated by the compute is used. If a bracketed integer is
appended, the Ith column of the per-atom array calculated by the
compute is used. Users can also write code for their own compute
styles and "add them to LAMMPS"_Section_modify.html. See the
styles and "add them to LAMMPS"_Modify.html. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
@ -143,7 +143,7 @@ references the values, else an error results. If no bracketed integer
is appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the fix is used. Users can also write code for their
own fix style and "add them to LAMMPS"_Section_modify.html. See the
own fix style and "add them to LAMMPS"_Modify.html. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
@ -168,7 +168,7 @@ page for details. If no bracketed integer is appended, the vector
calculated by the compute is used. If a bracketed integer is
appended, the Ith column of the array calculated by the compute is
used. Users can also write code for their own compute styles and "add
them to LAMMPS"_Section_modify.html. See the discussion above for how
them to LAMMPS"_Modify.html. See the discussion above for how
I can be specified with a wildcard asterisk to effectively specify
multiple values.
@ -181,7 +181,7 @@ global/atom references the values, else an error results. If no
bracketed integer is appended, the vector calculated by the fix is
used. If a bracketed integer is appended, the Ith column of the array
calculated by the fix is used. Users can also write code for their
own fix style and "add them to LAMMPS"_Section_modify.html. See the
own fix style and "add them to LAMMPS"_Modify.html. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.

8
doc/src/compute_reduce.txt
View File

@ -116,7 +116,7 @@ per-atom or local quantities. See the individual
is appended, the vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the array calculated
by the compute is used. Users can also write code for their own
compute styles and "add them to LAMMPS"_Section_modify.html. See the
compute styles and "add them to LAMMPS"_Modify.html. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
@ -129,9 +129,9 @@ references the values, else an error results. If no bracketed integer
is appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
is used. Users can also write code for their own fix style and "add
them to LAMMPS"_Section_modify.html. See the discussion above for how
I can be specified with a wildcard asterisk to effectively specify
multiple values.
them to LAMMPS"_Modify.html. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. It must be an

4
doc/src/compute_slice.txt
View File

@ -58,7 +58,7 @@ page for details. If no bracketed integer is appended, the vector
calculated by the compute is used. If a bracketed integer is
appended, the Ith column of the array calculated by the compute is
used. Users can also write code for their own compute styles and "add
them to LAMMPS"_Section_modify.html.
them to LAMMPS"_Modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script and which generates a global
@ -69,7 +69,7 @@ the values, else an error results. If no bracketed integer is
appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
is used. Users can also write code for their own fix style and "add
them to LAMMPS"_Section_modify.html.
them to LAMMPS"_Modify.html.
If an input value begins with "v_", a variable name must follow which
has been previously defined in the input script. Only vector-style

6
doc/src/dump.txt
View File

@ -625,9 +625,9 @@ The {d_name} and {i_name} attributes allow to output custom per atom
floating point or integer properties that are managed by
"fix property/atom"_fix_property_atom.html.
See "Section 10"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
See the "Modify"_Modify.html doc page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities
which could then be output into dump files.
:line

6
doc/src/dump_image.txt
View File

@ -606,9 +606,9 @@ supported. :l
:line
See "Section 10"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
See the "Modify"_Modify.html doc page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities
which could then be output into dump files.
:line

6
doc/src/fix.txt
View File

@ -30,9 +30,9 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a
timestepping or minimization. Examples include updating of atom
positions and velocities due to time integration, controlling
temperature, applying constraint forces to atoms, enforcing boundary
conditions, computing diagnostics, etc. There are dozens of fixes
defined in LAMMPS and new ones can be added; see "this
section"_Section_modify.html for a discussion.
conditions, computing diagnostics, etc. There are hundredes of fixes
defined in LAMMPS and new ones can be added; see the
"Modify"_Modify.html doc page for details.
Fixes perform their operations at different stages of the timestep.
If 2 or more fixes operate at the same stage of the timestep, they are

6
doc/src/fix_ave_atom.txt
View File

@ -124,7 +124,7 @@ appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the compute is used. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html. See the discussion above for how I can
LAMMPS"_Modify.html. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
@ -136,8 +136,8 @@ the per-atom array calculated by the fix is used. Note that some
fixes only produce their values on certain timesteps, which must be
compatible with {Nevery}, else an error will result. Users can also
write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
LAMMPS"_Modify.html. See the discussion above for how I can be
specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "v_", a variable name must follow which has

4
doc/src/fix_ave_chunk.txt
View File

@ -263,7 +263,7 @@ previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and "add them to LAMMPS"_Section_modify.html.
their own compute styles and "add them to LAMMPS"_Modify.html.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
@ -274,7 +274,7 @@ bracketed integer is appended, the Ith column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
{Nevery}, else an error results. Users can also write code for their
own fix styles and "add them to LAMMPS"_Section_modify.html. See the
own fix styles and "add them to LAMMPS"_Modify.html. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.

4
doc/src/fix_ave_correlate.txt
View File

@ -176,7 +176,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
LAMMPS"_Modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
@ -189,7 +189,7 @@ values.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
LAMMPS"_Modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style or

12
doc/src/fix_ave_histo.txt
View File

@ -183,11 +183,11 @@ Note that there is a "compute reduce"_compute_reduce.html command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/histo. Or it can be a compute defined
not in your input script, but by "thermodynamic
output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and "add them
to LAMMPS"_Section_modify.html.
output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If {mode} = scalar, then if
@ -204,7 +204,7 @@ values.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
LAMMPS"_Modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. If {mode} = scalar, then

4
doc/src/fix_ave_time.txt
View File

@ -168,7 +168,7 @@ output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and "add them
to LAMMPS"_Section_modify.html.
to LAMMPS"_Modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If {mode} = scalar, then if
@ -184,7 +184,7 @@ specify multiple values.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
LAMMPS"_Modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. If {mode} = scalar, then

4
doc/src/fix_controller.txt
View File

@ -139,7 +139,7 @@ for details. If no bracketed integer is appended, the scalar
calculated by the compute is used. If a bracketed integer is
appended, the Ith value of the vector calculated by the compute is
used. Users can also write code for their own compute styles and "add
them to LAMMPS"_Section_modify.html.
them to LAMMPS"_Modify.html.
If {pvar} begins with "f_", a fix ID must follow which has been
previously defined in the input script and which generates a global
@ -150,7 +150,7 @@ references the values, or else an error results. If no bracketed integer
is appended, the scalar calculated by the fix is used. If a bracketed
integer is appended, the Ith value of the vector calculated by the fix
is used. Users can also write code for their own fix style and "add
them to LAMMPS"_Section_modify.html.
them to LAMMPS"_Modify.html.
If {pvar} begins with "v_", a variable name must follow which has been
previously defined in the input script. Only equal-style variables

6
doc/src/fix_property_atom.txt
View File

@ -194,9 +194,9 @@ dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre
If you wish to add new "pair styles"_pair_style.html,
"fixes"_fix.html, or "computes"_compute.html that use the per-atom
properties defined by this fix, see "Section
modify"_Section_modify.html#mod_1 of the manual which has some details
on how the properties can be accessed from added classes.
properties defined by this fix, see the "Modify atom"_Modify_atom.html
doc page which has details on how the properties can be accessed from
added classes.
:line

4
doc/src/fix_vector.txt
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@ -94,7 +94,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
LAMMPS"_Modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
@ -105,7 +105,7 @@ calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
LAMMPS"_Modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. An equal-style or

4
doc/src/lammps.book
View File

@ -12,10 +12,10 @@ accelerate_kokkos.html
accelerate_omp.html
accelerate_opt.html
Section_howto.html
Section_example.html
Examples.html
Section_perf.html
Tools.html
Section_modify.html
Modify.html
Section_python.html
Section_errors.html
Section_history.html

5
doc/src/run.txt
View File

@ -126,9 +126,8 @@ and interleaving commands in your input script. For example, a
be redefined, e.g. to reset a thermostat temperature. Or this could
be useful for invoking a command you have added to LAMMPS that wraps
some other code (e.g. as a library) to perform a computation
periodically during a long LAMMPS run. See "this
section"_Section_modify.html of the documentation for info about how
to add new commands to LAMMPS. See "this
periodically during a long LAMMPS run. See the "Modify"_Modify.html
doc page for info about how to add new commands to LAMMPS. See "this
section"_Section_howto.html#howto_10 of the documentation for ideas
about how to couple LAMMPS to other codes.

11
doc/src/thermo_style.txt
View File

@ -108,12 +108,11 @@ 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
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
flexible means of outputting essentially any desired quantity as a
simulation proceeds.
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 "Modify"_Modify.html doc page for details on the
latter. Thus the {custom} style provides a flexible means of
outputting essentially any desired quantity as a simulation proceeds.
All styles except {custom} have {vol} appended to their list of
outputs if the simulation box volume changes during the simulation.

4
doc/src/tutorial_github.txt
View File

@ -25,8 +25,8 @@ or improvements to LAMMPS, as it significantly reduces the amount of
work required by the LAMMPS developers. Consequently, creating a pull
request will increase your chances to have your contribution included
and will reduce the time until the integration is complete. For more
information on the requirements to have your code included into LAMMPS
please see "Section 10.15"_Section_modify.html#mod_15
information on the requirements to have your code included in LAMMPS,
see the "Modify contribute"_Modify_contribute.html doc page.
:line