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.
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.
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.
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)|
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.
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.
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.
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.
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|
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.
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 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.
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).