9. Modifying & extending LIGGGHTS(R)-PUBLIC

This section describes how to customize LIGGGHTS(R)-PUBLIC by modifying and extending its source code.

LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC. Information about how to do this is provided below.

The best way to add a new feature is to find a similar feature in LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC to invoke the new class is as simple as putting the two source files in the src dir and re-building LIGGGHTS(R)-PUBLIC.

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 LIGGGHTS(R)-PUBLIC 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 by Foo, et al. If you wish to invoke those potentials in a LIGGGHTS(R)-PUBLIC input script with a command like

pair_style foo 0.1 3.5

then your pair_foo.h file should be structured as follows:

#ifdef PAIR_CLASS
PairStyle(foo,PairFoo)
#else
...
(class definition for PairFoo)
...
#endif

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 LIGGGHTS(R)-PUBLIC, 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 LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC. 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 LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC 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.
  • 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.
  • If your new feature reads arguments or writes output, make sure you follow the unit conventions discussed by the units command.
  • If you add something you think is truly useful and doesn’t impact LIGGGHTS(R)-PUBLIC performance when it isn’t used, send an email to the developers. We might be interested in adding it to the LIGGGHTS(R)-PUBLIC distribution. See further details on this at the bottom of this page.

9.1. Atom styles

Classes that define an atom style 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 retreive 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 retreive 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 retreive 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)

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.

Warning

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 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 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, fixes, or computes can be added to LIGGGHTS(R)-PUBLIC, 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);

The “name” of a custom attribute, as specified in the fix property/atom 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];

Ivector or dvector are vectors of length Nlocal = # of owned atoms, which store the attributes of individual atoms.

9.2. Compute styles

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 LIGGGHTS(R)-PUBLIC.

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)
memory_usage tally memory usage (optional)

9.4. Dump custom output options

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

See the dump 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.

9.5. Fix styles

In LIGGGHTS(R)-PUBLIC, 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 LIGGGHTS(R)-PUBLIC.

Fix_setforce.cpp is a simple example of setting forces on atoms to prescribed values. There are dozens of fix options already in LIGGGHTS(R)-PUBLIC; 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 after 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 minmizer (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)

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 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.

9.6. Input script commands

New commands can be added to LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC input script, LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC data structures.

The single method your new class must define is as follows:

command operations performed by the new command

Of course, the new class can define other methods and variables as needed.

9.7. Pairwise potentials

Classes that compute pairwise interactions are derived from the Pair class. In LIGGGHTS(R)-PUBLIC, 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 LIGGGHTS(R)-PUBLIC.

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

The inner/middle/outer routines are optional.

9.8. Region styles

Classes that define geometric regions are derived from the Region class. Regions are used elsewhere in LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC.

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

9.9. Thermodynamic output options

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 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 command already allows for thermo output of quantities calculated by fixes, computes, and variables. 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.

9.10. Variable options

There is one class that computes and stores variable information in LIGGGHTS(R)-PUBLIC; see the file variable.cpp. The value associated with a variable can be periodically printed to the screen via the print, fix print, or thermo_style custom 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 command (which can then be accessed by variables) was discussed here 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 (whose calculated values can then be accessed by variables) was discussed here on this page.

9.11. Submitting new features for inclusion in LIGGGHTS(R)-PUBLIC

We encourage users to submit new features that they add to LIGGGHTS(R)-PUBLIC, especially if you think the features will be of interest to other users. If they are broadly useful we may add them as core files to LIGGGHTS(R)-PUBLIC.

The previous sections of this doc page describe how to add new features of various kinds to LIGGGHTS(R)-PUBLIC. Packages are simply collections of one or more new class files which are invoked as a new “style” within a LIGGGHTS(R)-PUBLIC input script. If designed correctly, these additions typically do not require changes to the main core of LIGGGHTS(R)-PUBLIC; they are simply add-on files.

Here is what you need to do to submit a user package or single file for our consideration. Following these steps will save time for both you and us. See existing package files for examples.

  • All source files you provide must compile with the most current version of LIGGGHTS(R)-PUBLIC.
  • If you want your file(s) to be added to main LIGGGHTS(R)-PUBLIC or one of its standard packages, then it needs to be written in a style compatible with other LIGGGHTS(R)-PUBLIC source files. This is so the developers can understand it and hopefully maintain it. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LIGGGHTS(R)-PUBLIC source files, including the use of the error class for error and warning messages.
  • Your new source files need to have the LIGGGHTS(R)-PUBLIC copyright, GPL notice, and your name at the top, like other LIGGGHTS(R)-PUBLIC source files. They need to create a class that is inside the LIGGGHTS(R)-PUBLIC namespace. I.e. they do not need to be in the same stylistic format and syntax as other LIGGGHTS(R)-PUBLIC files, though that would be nice.
  • Finally, you must also send a documentation file for each new command or style you are adding to LIGGGHTS(R)-PUBLIC. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files which we will convert to HTML. They must be in the same format as other *.txt files in the lammps/doc directory for similar commands and styles. The txt2html tool we use to do the conversion can be downloaded from this site, so you can perform the HTML conversion yourself to proofread your doc page.

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.

(Foo) Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).