This section describes how to customize LAMMPS by modifying and extending its source code.10.1 Atom styles
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.
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 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
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 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:
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.
IMPORTANT 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 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 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);
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 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)|
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)|
|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 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 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 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|
Of course, the new class can define other methods and variables as needed.
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|
|memory_usage||tally of memory usage|
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|
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|
The inner/middle/outer routines are optional.
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|
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_howto 14 of the manual for an overview of using body particles and the body 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|
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 LAMMPS; 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, y, vx, ... compute values = c_mytemp, c_thermo_press, ...
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.
We encourage users to submit new features to the developers that they add to LAMMPS, especially if you think they will be of interest to other users. If they are broadly useful we may add them as core files to LAMMPS or as part of a standard package. 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 the 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 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 of the LAMMPS WWW site), 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).
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, 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 are the 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.
Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your doc 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.
(Foo) Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).