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8. Modifying & extending LAMMPS :h3
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"_#package.
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.
Here is a list of the new features that can be added in this way,
along with information about how to submit your features for inclusion
in the LAMMPS distribution.
"Atom styles"_#atom
"Bond, angle, dihedral, improper potentials"_#bond
"Compute styles"_#compute
"Dump styles"_#dump
"Dump custom output options"_#dump
"Fix styles"_#fix which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
"Input script commands"_#command
"Kspace computations"_#kspace
"Minimization solvers"_#min
"Pairwise potentials"_#pair
"Region styles"_#region
"Thermodynamic output options"_#thermo
"Variable options"_#variable :ul
"Submitting new features to the developers to include in LAMMPS"_#package :ul
As illustrated by the pairwise example, these 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 in
these sections:
"Dump custom output options"_#dump_custom
"Thermodynamic output options"_#thermo
"Variable options"_#variable :ul
:line
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. :l,ule
:line
:line
Atom styles :link(atom),h4
Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
A new atom style can be created if one of the existing atom styles
does not define all the arrays 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.h for details.
grow: re-allocate atom arrays to longer lengths
copy: copy info for one atom to another atom's array locations
pack_comm: store an atom's info in a buffer communicated every timestep
pack_comm_vel: add velocity info to buffer
pack_comm_one: store extra info unique to this atom style
unpack_comm: retrieve an atom's info from the buffer
unpack_comm_vel: also retrieve velocity info
unpack_comm_one: retreive extra info unique to this atom style
pack_reverse: store an atom's info in a buffer communicating partial forces
pack_reverse_one: store extra info unique to this atom style
unpack_reverse: retrieve an atom's info from the buffer
unpack_reverse_one: retreive extra info unique to this atom style
pack_border: store an atom's info in a buffer communicated on neighbor re-builds
pack_border_vel: add velocity info to buffer
pack_border_one: store extra info unique to this atom style
unpack_border: retrieve an atom's info from the buffer
unpack_border_vel: also retrieve velocity info
unpack_border_one: retreive extra info unique to this atom style
pack_exchange: store all an atom's info to migrate to another processor
unpack_exchange: retrieve an atom's info from the buffer
size_restart: number of restart quantities associated with proc's atoms
pack_restart: pack atom quantities into a buffer
unpack_restart: unpack atom quantities from a buffer
create_atom: create an individual atom of this style
data_atom: parse an atom line from the data file
memory_usage: tally memory allocated by atom arrays :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.
:line
Bond, angle, dihedral, improper potentials :link(bond),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 methods you define in your new derived
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
details.
compute: compute the molecular interactions
coeff: set coefficients for one bond type
equilibrium_distance: length of bond, used by SHAKE
write & read_restart: writes/reads coeffs to restart files
single: force and energy of a single bond :tb(s=:)
:line
Compute styles :link(compute),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.
compute_scalar: compute a scalar quantity
compute_vector: compute a vector of quantities
compute_peratom: compute one or more quantities per atom
pack_comm: pack a buffer with items to communicate
unpack_comm: unpack the buffer
pack_reverse: pack a buffer with items to reverse communicate
unpack_reverse: unpack the buffer
memory_usage: tally memory usage :tb(s=:)
:line
Dump styles :link(dump),h4
Dump custom output options :link(dump_custom),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
Fix styles :link(fix),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
init: initialization before a run
setup: called immediately before the 1st timestep
initial_integrate: called at very beginning of each timestep
pre_exchange: called before atom exchange on re-neighboring steps
pre_neighbor: called before neighbor list build
post_force: called after pair & molecular forces are computed
final_integrate: called at end of each timestep
end_of_step: called at very end of timestep
write_restart: dumps fix info to restart file
restart: uses info from restart file to re-initialize the fix
grow_arrays: allocate memory for atom-based arrays used by fix
copy_arrays: copy atom info when an atom migrates to a new processor
memory_usage: report memory used by fix
pack_exchange: store atom's data in a buffer
unpack_exchange: retrieve atom's data from a buffer
pack_restart: store atom's data for writing to restart file
unpack_restart: retrieve atom's data from a restart file buffer
size_restart: size of atom's data
maxsize_restart: max size of atom's data
initial_integrate_respa: same as initial_integrate, but for rRESPA
post_force_respa: same as post_force, but for rRESPA
final_integrate_respa: same as final_integrate, but for rRESPA
pack_comm: pack a buffer to communicate a per-atom quantity
unpack_comm: unpack a buffer to communicate a per-atom quantity
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity
thermo: compute quantities for thermodynamic output :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
Input script commands :link(command),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
Kspace computations :link(kspace),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
Minimization solvers :link(min),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
Pairwise potentials :link(pair),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
Region styles :link(region),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.
match: determine whether a point is in the region :tb(s=:)
:line
Thermodynamic output options :link(thermo),h4
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
There are several styles defined in thermo.cpp: "one", "multi",
"granular", etc. 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
Variable options :link(variable),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], ...
Adding keywords for the "thermo_style custom"_thermo_style.html command
(which can then be accessed by variables) was discussed
"here"_Section_modify.html#thermo on this page.
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaulate() 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::evaulate() 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::evaulate() 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#compute on this page.
:line
Submitting new features to the developers to include in LAMMPS :link(package),h4
We encourage users to submit new features that they add to LAMMPS to
"the developers"_http://lammps.sandia.gov/authors.html, especially if
you think they will be useful to other users. If they are broadly
useful we may add them as core files to LAMMPS or as part of a
"standard package"_Section_start.html#2_3. Else we will add them as a
user-contributed package. Examples of user packages are in src
sub-directories that start with USER. You can see a list of the both
standard and user packages by typing "make package" in the LAMMPS src
directory.
With user packages, 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.
The previous sections of this doc page describe how to add new
features 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
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature does requires changes in
other 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.
Here is what you need to do to submit a user package for our
consideration. Following these steps will save time for both you and
us. See existing package files for examples.
Your user package will be a directory with a name like USER-FOO. In
addition to your new files, the directory should contain a README, and
Install.csh file. Send us a tarball of this USER-FOO directory.
The README text file should contain your name and contact information
and a brief description of what your new package does.
The Install.csh file enables LAMMPS to include and exclude your
package.
Your new source files need to have the LAMMPS copyright, GPL notice,
and your name at the top. They need to create a class that is inside
the LAMMPS namespace. Other than that, your files can do whatever is
necessary to implement the new features. They don't have to be
written in the same style and syntax as other LAMMPS files, thought
that would be nice.
Finally, in addition to the USER-FOO tarball, you also need to send us
a documentation file for each new command or style you are adding to
LAMMPS. These are text files which we will convert to HTML. Use one
of the *.txt files in the doc dir as a starting point for the new file
you create, since it should look similar to the doc files for existing
commands and styles. The "Restrictions" section of the doc page
should indicate that your feature is only available if LAMMPS is built
with the "user-foo" package. See other user package files for an
example of how to do this.
Note that the more clear and self-explanatory you make your doc and
README files, 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).
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