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# 4.1. Source files

The source files of the LAMMPS code are found in two directories of the distribution: `src` and `lib`. Most of the code is written in C++ but there are small a number of files in several other languages like C, Fortran, Shell script, or Python.

The core of the code is located in the `src` folder and its subdirectories. A sizable number of these files are in the `src` directory itself, but there are plenty of packages, which can be included or excluded when LAMMPS is built. See the Include packages in build section of the manual for more information about that part of the build process. LAMMPS currently supports building with conventional makefiles and through CMake. Those procedures differ in how packages are enabled or disabled for inclusion into a LAMMPS binary, so they cannot be mixed. The source files for each package are in all-uppercase subdirectories of the `src` folder, for example `src/MOLECULE` or `src/EXTRA-MOLECULE`. The `src/STUBS` subdirectory is not a package but contains a dummy MPI library, that is used when building a serial version of the code. The `src/MAKE` directory and its subdirectories contain makefiles with settings and flags for a variety of configuration and machines for the build process with traditional makefiles.

The `lib` directory contains the source code for several supporting libraries or files with configuration settings to use globally installed libraries, that are required by some optional packages. They may include python scripts that can transparently download additional source code on request. Each subdirectory, like `lib/colvars` or `lib/gpu`, contains the source files, some of which are in different languages such as Fortran or CUDA. These libraries included in the LAMMPS build, if the corresponding package is installed.

LAMMPS C++ source files almost always come in pairs, such as `src/run.cpp` (implementation file) and `src/run.h` (header file). Each pair of files defines a C++ class, for example the `LAMMPS_NS::Run` class, which contains the code invoked by the run command in a LAMMPS input script. As this example illustrates, source file and class names often have a one-to-one correspondence with a command used in a LAMMPS input script. Some source files and classes do not have a corresponding input script command, for example `src/force.cpp` and the `LAMMPS_NS::Force` class. They are discussed in the next section.

The names of all source files are in lower case and may use the underscore character ‘_’ to separate words. Apart from bundled, externally maintained libraries, which may have different conventions, all C and C++ header files have a `.h` extension, all C++ files have a `.cpp` extension, and C files a `.c` extension. A few C++ classes and utility functions are implemented with only a `.h` file. Examples are the Pointers and Commands classes or the MathVec functions.

# 4.2. Class topology

Though LAMMPS has a lot of source files and classes, its class topology is not very deep, which can be seen from the LAMMPS class topology figure. In that figure, each name refers to a class and has a pair of associated source files in the `src` folder, for example the class `LAMMPS_NS::Memory` corresponds to the files `memory.cpp` and `memory.h`, or the class `LAMMPS_NS::AtomVec` corresponds to the files `atom_vec.cpp` and `atom_vec.h`. Full lines in the figure represent compositing: that is, the class at the base of the arrow holds a pointer to an instance of the class at the tip. Dashed lines instead represent inheritance: the class at the tip of the arrow is derived from the class at the base. Classes with a red boundary are not instantiated directly, but they represent the base classes for “styles”. Those “styles” make up the bulk of the LAMMPS code and only a few representative examples are included in the figure, so it remains readable.

LAMMPS class topology

> This figure shows relations of base classes of the LAMMPS simulation package. Full lines indicate that a class holds an instance of the class it is pointing to; dashed lines point to derived classes that are given as examples of what classes may be instantiated during a LAMMPS run based on the input commands and accessed through the API define by their respective base classes. At the core is the `LAMMPS` class, which holds pointers to class instances with specific purposes. Those may hold instances of other classes, sometimes directly, or only temporarily, sometimes as derived classes or derived classes of derived classes, which may also hold instances of other classes.

The `LAMMPS_NS::LAMMPS` class is the topmost class and represents what is generally referred to as an “instance of LAMMPS”. It is a composite holding pointers to instances of other core classes providing the core functionality of the MD engine in LAMMPS and through them abstractions of the required operations. The constructor of the LAMMPS class will instantiate those instances, process the command-line flags, initialize MPI (if not already done) and set up file pointers for input and output. The destructor will shut everything down and free all associated memory. Thus code for the standalone LAMMPS executable in `main.cpp` simply initializes MPI, instantiates a single instance of LAMMPS while passing it the command-line flags and input script. It deletes the LAMMPS instance after the method reading the input returns and shuts down the MPI environment before it exits the executable.

The `LAMMPS_NS::Pointers` class is not shown in the LAMMPS class topology figure for clarity. It holds references to many of the members of the LAMMPS_NS::LAMMPS, so that all classes derived from `LAMMPS_NS::Pointers` have direct access to those references. From the class topology all classes with blue boundary are referenced in the Pointers class and all classes in the second and third columns, that are not listed as derived classes, are instead derived from `LAMMPS_NS::Pointers`. To initialize the pointer references in Pointers, a pointer to the LAMMPS class instance needs to be passed to the constructor. All constructors for classes derived from it, must do so and thus pass that pointer to the constructor for `LAMMPS_NS::Pointers`. The default constructor for `LAMMPS_NS::Pointers` is disabled to enforce this.

Since all storage is supposed to be encapsulated (there are a few exceptions), the LAMMPS class can also be instantiated multiple times by a calling code. Outside the aforementioned exceptions, those LAMMPS instances can be used alternately. As of the time of this writing (early 2023) LAMMPS is not yet sufficiently thread-safe for concurrent execution. When running in parallel with MPI, care has to be taken, that suitable copies of communicators are used to not create conflicts between different instances.

The LAMMPS class currently holds instances of 19 classes representing the core functionality. There are a handful of virtual parent classes in LAMMPS that define what LAMMPS calls `styles`. These are shaded red in the LAMMPS class topology figure. Each of these are parents of a number of child classes that implement the interface defined by the parent class. There are two main categories of these `styles`: some may only have one instance active at a time (e.g. atom, pair, bond, angle, dihedral, improper, kspace, comm) and there is a dedicated pointer variable for each of them in the corresponding composite class. Setups that require a mix of different such styles have to use a hybrid class instance that acts as a proxy, and manages and forwards calls to the corresponding sub-style class instances for the designated subset of atoms or data. The composite class may also have lists of class instances, e.g. `Modify` handles lists of compute and fix styles, while `Output` handles a list of dump class instances.

The exception to this scheme are the `command` style classes. These implement specific commands that can be invoked before, after, or in between runs. For these an instance of the class is created, its command() method called and then, after completion, the class instance deleted. Examples for this are the create_box, create_atoms, minimize, run, set, or velocity command styles.

For all those `styles`, certain naming conventions are employed: for the fix nve command the class is called FixNVE and the source files are `fix_nve.h` and `fix_nve.cpp`. Similarly, for fix ave/time we have FixAveTime and `fix_ave_time.h` and `fix_ave_time.cpp`. Style names are lower case and without spaces or special characters. A suffix or words are appended with a forward slash ‘/’ which denotes a variant of the corresponding class without the suffix. To connect the style name and the class name, LAMMPS uses macros like: `AtomStyle()`, `PairStyle()`, `BondStyle()`, `RegionStyle()`, and so on in the corresponding header file. During configuration or compilation, files with the pattern `style_<name>.h` are created that consist of a list of include statements including all headers of all styles of a given type that are currently enabled (or “installed”).

More details on individual classes in the LAMMPS class topology are as follows:

- The Memory class handles allocation of all large vectors and arrays.

- The Error class prints all (terminal) error and warning messages.

- The Universe class sets up one or more partitions of processors so that one or multiple simulations can be run, on the processors allocated for a run, e.g. by the mpirun command.

- The Input class reads and processes input (strings and files), stores variables, and invokes commands.

- Command style classes are derived from the Command class. They provide input script commands that perform one-time operations before/after/between simulations or which invoke a simulation. They are usually instantiated from within the Input class, its `command` method invoked, and then immediately destructed.

- The Finish class is instantiated to print statistics to the screen after a simulation is performed, by commands like run and minimize.

- The Special class walks the bond topology of a molecular system to find first, second, third neighbors of each atom. It is invoked by several commands, like read_data, read_restart, or replicate.

- The Atom class stores per-atom properties associated with atom styles. More precisely, they are allocated and managed by a class derived from the AtomVec class, and the Atom class simply stores pointers to them. The classes derived from AtomVec represent the different atom styles, and they are instantiated through the atom_style command.

- The Update class holds instances of an integrator and a minimizer class. The Integrate class is a parent style for the Verlet and r-RESPA time integrators, as defined by the run_style command. The Min class is a parent style for various energy minimizers.

- The Neighbor class builds and stores neighbor lists. The NeighList class stores a single list (for all atoms). A NeighRequest class instance is created by pair, fix, or compute styles when they need a particular kind of neighbor list and use the NeighRequest properties to select the neighbor list settings for the given request. There can be multiple instances of the NeighRequest class. The Neighbor class will try to optimize how the requests are processed. Depending on the NeighRequest properties, neighbor lists are constructed from scratch, aliased, or constructed by post-processing an existing list into sub-lists.

- The Comm class performs inter-processor communication, typically of ghost atom information. This usually involves MPI message exchanges with 6 neighboring processors in the 3d logical grid of processors mapped to the simulation box. There are two communication styles, enabling different ways to perform the domain decomposition.

- The Irregular class is used, when atoms may migrate to arbitrary processors.

- The Domain class stores the simulation box geometry, as well as geometric Regions and any user definition of a Lattice. The latter are defined by the region and lattice commands in an input script.

- The Force class computes various forces between atoms. The Pair parent class is for non-bonded or pairwise forces, which in LAMMPS also includes many-body forces such as the Tersoff 3-body potential if those are computed by walking pairwise neighbor lists. The Bond, Angle, Dihedral, Improper parent classes are styles for bonded interactions within a static molecular topology. The KSpace parent class is for computing long-range Coulombic interactions. One of its child classes, PPPM, uses the FFT3D and Remap classes to redistribute and communicate grid-based information across the parallel processors.

- The Modify class stores lists of class instances derived from the Fix and Compute base classes.

- The Group class manipulates groups that atoms are assigned to via the group command. It also has functions to compute various attributes of groups of atoms.

- The Output class is used to generate 3 kinds of output from a LAMMPS simulation: thermodynamic information printed to the screen and log file, dump file snapshots, and restart files. These correspond to the Thermo, Dump, and WriteRestart classes respectively. The Dump class is a base class, with several derived classes implementing various dump style variants.

- The Timer class logs timing information, output at the end of a run.