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4.3. Code design¶
This section explains some code design choices in LAMMPS with the goal of helping developers write new code similar to the existing code. Please see the section on Requirements for contributed code for more specific recommendations and guidelines. While that section is organized more in the form of a checklist for code contributors, the focus here is on overall code design strategy, choices made between possible alternatives, and discussing some relevant C++ programming language constructs.
Historically, the basic design philosophy of the LAMMPS C++ code was a “C with classes” style. The motivation was to make it easy to modify LAMMPS for people without significant training in C++ programming. Data structures and code constructs were used that resemble the previous implementation(s) in Fortran. A contributing factor to this choice was that at the time, C++ compilers were often not mature and some advanced features contained bugs or did not function as the standard required. There were also disagreements between compiler vendors as to how to interpret the C++ standard documents.
However, C++ compilers and the C++ programming language have advanced significantly. In 2020, the LAMMPS developers decided to require the C++11 standard as the minimum C++ language standard for LAMMPS. Since then, we have begun to replace C-style constructs with equivalent C++ functionality. This was taken either from the C++ standard library or implemented as custom classes or functions. The goal is to improve readability of the code and to increase code reuse through abstraction of commonly used functionality.
Note
Please note that as of spring 2023 there is still a sizable chunk of
legacy code in LAMMPS that has not yet been refactored to reflect
these style conventions in full. LAMMPS has a large code base and
many contributors. There is also a hierarchy of precedence in which
the code is adapted. Highest priority has been the code in the
src folder, followed by code in packages in order of their
popularity and complexity (simpler code gets adapted sooner), followed
by code in the lib folder. Source code that is downloaded from
external packages or libraries during compilation is not subject to
the conventions discussed here.
4.3.1. Object-oriented code¶
LAMMPS is designed to be an object-oriented code. Each simulation is
represented by an instance of the LAMMPS class. When running in
parallel, each MPI process creates such an instance. This can be seen
in the main.cpp file where the core steps of running a LAMMPS
simulation are the following 3 lines of code:
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
lammps->input->file();
delete lammps;
The first line creates a LAMMPS class instance and passes the command line arguments and the global communicator to its constructor. The second line triggers the LAMMPS instance to process the input (either from standard input or a provided input file) until the simulation ends. The third line deletes the LAMMPS instance. The remainder of the main.cpp file has code for error handling, MPI configuration, and other special features.
The basic LAMMPS class hierarchy which is created by the LAMMPS class constructor is shown in LAMMPS class topology. When input commands are processed, additional class instances are created, or deleted, or replaced. Likewise, specific member functions of specific classes are called to trigger actions such creating atoms, computing forces, computing properties, time-propagating the system, or writing output.
Compositing and Inheritance¶
LAMMPS makes extensive use of the object-oriented programming (OOP)
principles of compositing and inheritance. Classes like the
LAMMPS class are a composite containing pointers to instances
of other classes like Atom, Comm, Force, Neighbor,
Modify, and so on. Each of these classes implements certain
functionality by storing and manipulating data related to the
simulation and providing member functions that trigger certain
actions. Some of those classes like Force are themselves
composites, containing instances of classes describing different force
interactions. Similarly, the Modify class contains a list of
Fix and Compute classes. If the input commands that
correspond to these classes include the word style, then LAMMPS
stores only a single instance of that class. E.g. atom_style,
comm_style, pair_style, bond_style. If the input command does
not include the word style, then there may be many instances of
that class defined, for example region, fix, compute, dump.
Inheritance enables creation of derived classes that can share common functionality in their base class while providing a consistent interface. The derived classes replace (dummy or pure) functions in the base class. The higher level classes can then call those methods of the instantiated classes without having to know which specific derived class variant was instantiated. In LAMMPS these derived classes are often referred to as “styles”, e.g. pair styles, fix styles, atom styles and so on.
This is the origin of the flexibility of LAMMPS. For example, pair styles implement a variety of different non-bonded interatomic potentials functions. All details for the implementation of a potential are stored and executed in a single class.
As mentioned above, there can be multiple instances of classes derived
from the Fix or Compute base classes. They represent a
different facet of LAMMPS’ flexibility, as they provide methods which
can be called at different points within a timestep, as explained in
Developer_flow. This allows the input script to tailor how a specific
simulation is run, what diagnostic computations are performed, and how
the output of those computations is further processed or output.
Additional code sharing is possible by creating derived classes from the derived classes (e.g., to implement an accelerated version of a pair style) where only a subset of the derived class methods are replaced with accelerated versions.
Polymorphism¶
Polymorphism and dynamic dispatch are another OOP feature that play an
important role in how LAMMPS selects what code to execute. In a
nutshell, this is a mechanism where the decision of which member
function to call from a class is determined at runtime and not when
the code is compiled. To enable it, the function has to be declared
as virtual and all corresponding functions in derived classes
should use the override property. Below is a brief example.
class Base {
public:
virtual ~Base() = default;
void call();
void normal();
virtual void poly();
};
void Base::call() {
normal();
poly();
}
class Derived : public Base {
public:
~Derived() override = default;
void normal();
void poly() override;
};
// [....]
Base *base1 = new Base();
Base *base2 = new Derived();
base1->call();
base2->call();
The difference in behavior of the normal() and the poly() member
functions is which of the two member functions is called when executing
base1->call() versus base2->call(). Without polymorphism, a
function within the base class can only call member functions within the
same scope: that is, Base::call() will always call
Base::normal(). But for the base2->call() case, the call of the
virtual member function will be dispatched to Derived::poly()
instead. This mechanism results in calling functions that are within
the scope of the class that was used to create the instance, even if
they are assigned to a pointer for their base class. This is the
desired behavior, and this way LAMMPS can even use styles that are loaded
at runtime from a shared object file with the plugin command.
A special case of virtual functions are so-called pure functions. These are virtual functions that are initialized to 0 in the class declaration (see example below).
class Base {
public:
virtual void pure() = 0;
};
This has the effect that an instance of the base class cannot be created and that derived classes must implement these functions. Many of the functions listed with the various class styles in the section Modifying & extending LAMMPS are pure functions. The motivation for this is to define the interface or API of the functions, but defer their implementation to the derived classes.
However, there are downsides to this. For example, calls to virtual
functions from within a constructor, will not be in the scope of the
derived class, and thus it is good practice to either avoid calling them
or to provide an explicit scope such as Base::poly() or
Derived::poly(). Furthermore, any destructors in classes containing
virtual functions should be declared virtual too, so they will be
processed in the expected order before types are removed from dynamic
dispatch.
Important Notes
In order to be able to detect incompatibilities at compile time and
to avoid unexpected behavior, it is crucial that all member functions
that are intended to replace a virtual or pure function use the
override property keyword. For the same reason, the use of
overloads or default arguments for virtual functions should be
avoided, as they lead to confusion over which function is supposed to
override which, and which arguments need to be declared.
Style Factories¶
In order to create class instances for different styles, LAMMPS often
uses a programming pattern called Factory. Those are functions that
create an instance of a specific derived class, say PairLJCut and
return a pointer to the type of the common base class of that style,
Pair in this case. To associate the factory function with the
style keyword, a std::map class is used with function pointers
indexed by their keyword (for example “lj/cut” for PairLJCut and
“morse” for PairMorse). A couple of typedefs help keep the code
readable, and a template function is used to implement the actual
factory functions for the individual classes. Below is an example
of such a factory function from the Force class as declared in
force.h and implemented in force.cpp. The file style_pair.h
is generated during compilation and includes all main header files
(i.e. those starting with pair_) of pair styles and then the
macro PairStyle() will associate the style name “lj/cut”
with a factory function creating an instance of the PairLJCut
class.
// from force.h
typedef Pair *(*PairCreator)(LAMMPS *);
typedef std::map<std::string, PairCreator> PairCreatorMap;
PairCreatorMap *pair_map;
// from force.cpp
template <typename S, typename T> static S *style_creator(LAMMPS *lmp)
{
return new T(lmp);
}
// [...]
pair_map = new PairCreatorMap();
#define PAIR_CLASS
#define PairStyle(key, Class) (*pair_map)[#key] = &style_creator<Pair, Class>;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_CLASS
// from pair_lj_cut.h
#ifdef PAIR_CLASS
PairStyle(lj/cut,PairLJCut);
#else
// [...]
Similar code constructs are present in other files like modify.cpp and
modify.h or neighbor.cpp and neighbor.h. Those contain
similar macros and include style_*.h files for creating class instances
of styles they manage.
4.3.2. I/O and output formatting¶
C-style stdio versus C++ style iostreams¶
LAMMPS uses the “stdio” library of the standard C library for reading from and writing to files and console instead of C++ “iostreams”. This is mainly motivated by better performance, better control over formatting, and less effort to achieve specific formatting.
Since mixing “stdio” and “iostreams” can lead to unexpected behavior,
use of the latter is strongly discouraged. Output to the screen should
not use the predefined stdout FILE pointer, but rather the
screen and logfile FILE pointers managed by the LAMMPS class.
Furthermore, output should generally only be done by MPI rank 0
(comm->me == 0). Output that is sent to both screen and
logfile should use the utils::logmesg() convenience
function.
We discourage the use of stringstreams because the bundled {fmt} library and the customized tokenizer classes provide the same functionality in a cleaner way with better performance. This also helps maintain a consistent programming syntax with code from many different contributors.
Formatting with the {fmt} library¶
The LAMMPS source code includes a copy of the {fmt} library, which is preferred over formatting with the
“printf()” family of functions. The primary reason is that it allows
a typesafe default format for any type of supported data. This is
particularly useful for formatting integers of a given size (32-bit or
64-bit) which may require different format strings depending on
compile time settings or compilers/operating systems. Furthermore,
{fmt} gives better performance, has more functionality, a familiar
formatting syntax that has similarities to format() in Python, and
provides a facility that can be used to integrate format strings and a
variable number of arguments into custom functions in a much simpler
way than the varargs mechanism of the C library. Finally, {fmt} has
been included into the C++20 language standard, so changes to adopt it
are future-proof.
Formatted strings are frequently created by calling the
fmt::format() function, which will return a string as a
std::string class instance. In contrast to the % placeholder in
printf(), the {fmt} library uses {} to embed format descriptors.
In the simplest case, no additional characters are needed, as {fmt} will
choose the default format based on the data type of the argument.
Otherwise, the fmt::print() function may be used instead of
printf() or fprintf(). In addition, several LAMMPS output
functions, that originally accepted a single string as argument have
been overloaded to accept a format string with optional arguments as
well (e.g., Error::all(), Error::one(), utils::logmesg()).
Summary of the {fmt} format syntax¶
The syntax of the format string is “{[<argument id>][:<format spec>]}”, where either the argument id or the format spec (separated by a colon ‘:’) is optional. The argument id is usually a number starting from 0 that is the index to the arguments following the format string. By default, these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.). The most common case for using argument id would be to use the same argument in multiple places in the format string without having to provide it as an argument multiple times. The argument id is rarely used in the LAMMPS source code.
More common is the use of a format specifier, which starts with a colon. This may optionally be followed by a fill character (default is ‘ ‘). If provided, the fill character must be followed by an alignment character (‘<’, ‘^’, ‘>’ for left, centered, or right alignment (default)). The alignment character may be used without a fill character. The next important format parameter would be the minimum width, which may be followed by a dot ‘.’ and a precision for floating point numbers. The final character in the format string would be an indicator for the “presentation”, i.e. ‘d’ for decimal presentation of integers, ‘x’ for hexadecimal, ‘o’ for octal, ‘c’ for character etc. This mostly follows the “printf()” scheme, but without requiring an additional length parameter to distinguish between different integer widths. The {fmt} library will detect those and adapt the formatting accordingly. For floating point numbers there are correspondingly, ‘g’ for generic presentation, ‘e’ for exponential presentation, and ‘f’ for fixed point presentation.
The format string “{:8}” would thus represent any type argument and be replaced by at least 8 characters; “{:<8}” would do this as left aligned, “{:^8}” as centered, “{:>8}” as right aligned. If a specific presentation is selected, the argument type must be compatible or else the {fmt} formatting code will throw an exception. Some format string examples are given below:
auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
label, time_min, time, time_max, time_sq, tmp);
utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall);
utils::logmesg(lmp,"Lattice spacing in x,y,z = {:.8} {:.8} {:.8}\n",
xlattice,ylattice,zlattice);
which will create the following output lines:
CPU time: 0:02:16
Pair | 2.0133 | 2.0133 | 2.0133 | 0.0 | 84.21
4 = max # of 1-2 neighbors
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Finally, a special feature of the {fmt} library is that format parameters like the width or the precision may be also provided as arguments. In that case a nested format is used where a pair of curly braces (with an optional argument id) “{}” are used instead of the value, for example “{:{}d}” will consume two integer arguments, the first will be the value shown and the second the minimum width.
For more details and examples, please consult the {fmt} syntax documentation website.
4.3.3. Memory management¶
Dynamical allocation of small data and objects can be done with the C++
commands “new” and “delete/delete[]”. Large data should use the member
functions of the Memory class, most commonly, Memory::create(),
Memory::grow(), and Memory::destroy(), which provide variants
for vectors, 2d arrays, 3d arrays, etc. These can also be used for
small data.
The use of malloc(), calloc(), realloc() and free()
directly is strongly discouraged. To simplify adapting legacy code
into the LAMMPS code base the member functions Memory::smalloc(),
Memory::srealloc(), and Memory::sfree() are available, which
perform additional error checks for safety.
Use of these custom memory allocation functions is motivated by the following considerations:
Memory allocation failures on any MPI rank during a parallel run will trigger an immediate abort of the entire parallel calculation.
A failing “new” will trigger an exception, which is also captured by LAMMPS and triggers a global abort.
Allocation of multidimensional arrays will be done in a C compatible fashion, but such that the storage of the actual data is stored in one large contiguous block. Thus, when MPI communication is needed, the data can be communicated directly (similar to Fortran arrays).
The “destroy()” and “sfree()” functions may safely be called on NULL pointers.
The “destroy()” functions will nullify the pointer variables, thus making “use after free” errors easy to detect.
It is possible to use a larger than default memory alignment (not on all operating systems, since the allocated storage pointers must be compatible with
free()for technical reasons).
In the practical implementation of code this means, that any pointer
variables, that are class members should be initialized to a nullptr
value in their respective constructors. That way, it is safe to call
Memory::destroy() or delete[] on them before any allocation
outside the constructor. This helps prevent memory leaks.