Naming conventions

The conventions here should be applied to all new code, and with common sense when modifying existing code. For example, renaming a widely used, existing function to follow these conventions may not be justified unless the whole code is getting a rework.

Currently, this only documents the present state of the code: no particular attempt has been made to consolidate the naming.

Files

• C++ source files have a .cpp extension, C source files .c, and headers for both use .h.

• For source file file.c/file.cpp, declarations that are visible outside the source file should go into a correspondingly named header: file.h. Some code may deviate from this rule to improve readability and/or usability of the API, but this should then be clearly documented.

  There can also be a file_impl.h file that declares classes or functions that are not accessible outside the module. If the whole file only declares symbols internal to the module, then the _impl.h suffix is omitted.

  In most cases, declarations that are not used outside a single source file are in the source file.

• Use suffix -doc.h for files that contain only Doxygen documentation for some module or such, for cases where there is no natural single header for putting the documentation.

• For C++ files, prefer naming the file the same as the (main) class it contains. Currently all file names are all-lowercase, even though class names contain capital letters. It is OK to use commonly known abbreviations, and/or omit the name of the containing directory if that would cause unnecessary repetition (e.g., as a common prefix to every file name in the directory) and the remaining part of the name is unique enough.

• Avoid having multiple files with the same name in different places within the same library. In addition to making things harder to find, C++ source files with the same name can cause obscure problems with some compilers. Currently, unit tests are an exception to the rule (there is only one particular compiler that had problems with this, and a workaround is possible if/when that starts to affect more than a few of the test files).

Common guidelines for C and C++ code

• Preprocessor macros should be all upper-case. Do not use leading underscores, as all such names are reserved according to the C/C++ standard.
• Name include guards like GMX_DIRNAME_HEADERNAME_H.
• Avoid abbreviations that are not obvious to a general reader.
• If you use acronyms (e.g., PME, DD) in names, follow the Microsoft policy on casing: two letters is uppercase (DD), three or more is lowercase (Pme). If the first letter would be lowercase in the context where it is used (e.g., at the beginning of a function name, or anywhere in a C function name), it is clearest to use all-lowercase acronym.

C code

• All function and variable names are lowercase, with underscores as word separators where needed for clarity.
• All functions that are part of the public API should start with gmx_. Preferably, other functions should as well. Some parts of the code use a _gmx_ prefix for internal functions, but strictly speaking, these are reserved names, so, e.g., a trailing underscore would be better.
• Old C code and changes to it can still use the hungarian notation for booleans and enumerated variable names, as well as enum values, where they are prefixed with b and e respectively, or you can gradually move to the C++ practice below. Whatever you choose, avoid complex abbreviations.

C++ code

• Use CamelCase for all names. Start types (such as classes, structs, typedefs and enum values) with a capital letter, other names (functions, variables) with a lowercase letter. You may use an all-lowercase name with underscores if your class closely resembles an external construct (e.g., a standard library construct) named that way.
• C++ interfaces are named with an I prefix, such as in ICommandLineModule. This keeps interfaces identifiable, without introducing too much clutter (as the interface is typically used quite widely, spelling out Interface would make many of the names unnecessarily long).
• Abstract base classes are typically named with an Abstract prefix.
• Member variables are named with a trailing underscore.
• Accessors for a variable foo_ are named foo() and setFoo().
• Global variables are named with a g_ prefix.
• Static class variables are named with a s_ prefix.
• Global constants are often named with a c_ prefix.
• If the main responsibility of a file is to implement a particular class, then the name of the file should match that class, except for possible abbreviations to avoid repetition in file names (e.g., if all classes within a module start with the module name, omitting or abbreviating the module name is OK). Currently, all source file names are lowercase, but this casing difference should be the only difference.
• For new C++ code, avoid using the hungarian notation that is a descendant from the C code (i.e., the practice of using a b prefix for boolean variables and an e prefix for enumerated variables and/or values). Instead, make the names long with a good description of what they control, typically including a verb for boolean variables, like foundAtom.
• Prefer class enums over regular ones, so that unexpected conversions to int do not happen.
• When using a non-class enum, prefer to include the name of the enumeration type as a base in the name of enum values, e.g., HelpOutputFormat_Console, in particular for settings exposed to other modules.
• Prefer to use enumerated types and values instead of booleans as control parameters to functions. It is reasonably easy to understand what the argument HelpOutputFormat_Console is controlling, while it is almost impossible to decipher TRUE in the same place without checking the documentation for the role of the parameter.

The rationale for the trailing underscore and the global/static prefixes is that it is immediately clear whether a variable referenced in a method is local to the function or has wider scope, improving the readability of the code.

Code for GPUs

Rationale: on GPUs, using the right memory space is often performance critical.

• In CUDA device code sm_, gm_, and cm_ prefixes are used for shared, global and constant memory. The absence of a prefix indicates register space. Same prefixes are used in OpenCL code, where sm_ indicates local memory and no prefixes are added to variables in private address space.
• Data transferred to and from host has to live in both CPU and GPU memory spaces. Therefore it is typical to have a pointer or container (in CUDA), or memory buffer (in OpenCL) in host memory that has a device-based counterpart. To easily distinguish these, the variables names for such objects are prefixed h_ and d_ and have identical names otherwise. Example: h_masses, and d_masses.
• In all other cases, pointers to host memory are not required to have the prefix h_ (even in parts of the host code, where both host and device pointers are present). The device pointers should always have the prefix d_ or gm_.
• In case GPU kernel arguments are combined into a structure, it is preferred that all device memory pointers within the structure have the prefix d_ (i.e. kernelArgs.d_data is preferred to d_kernelArgs.data, whereas both d_kernelArgs.d_data and kernelArgs.data are not acceptable).
• Note that the same pointer can have the prefix d_ in the host code, and gm_ in the device code. For example, if d_data is passed to the kernel as an argument, it should be aliased to gm_data in the kernel arguments list. In case a device pointer is a field of a passed structure, it can be used directly or aliased to a pointer with gm_ prefix (i.e. kernelArgs.d_data can be used as is or aliased to gm_data inside the kernel).
• Avoid using uninformative names for CUDA warp, thread, block indexes and their OpenCL analogs (i.e. threadIndex is preferred to i or atomIndex).

Unit tests

• Test fixtures (the first parameter to TEST/TEST_F) are named with a Test suffix.
• Classes meant as base classes for test fixtures (or as names to be typedefed to be fixtures) are named with a TestBase or Fixture suffix.
• The CTest test is named with CamelCase, ending with Tests (e.g., OptionsUnitTests).
• The test binary is named with the name of the module and a -test suffix.