Style Guide
Introduction
The CASTEP code has been designed from conception to achieve various goals - including efficiency and maintainability. The following are some simple guidelines on writing code for inclusion within CASTEP. These are intended to enable the writing of correct, efficient code, and to ensure a consistent style for multiple authors throughout the code that is straightforward for others to maintain in the future. Fortran 2003 has been chosen as the language that all the code will be written in, as it has many modern features which enable the writing of clean, modular code without compromising efficiency and portability.
In this document, there is a template for writing modules, and for writing subprograms within a module. These templates are designed to enforce good programming practice and documentation of routine function and side-effects. It is important that all routines be written with these templates. The general guidelines about style addressed here, the use of module templates, the completeness of the documentation, etc. all help to make writing new code and maintaining the existing code a simple task.
It is also the programmer's responsibility to ensure that each routine is coded as efficiently as possible. Whilst it is tempting to use some of the new built-in features of Fortran 2003, experience has shown that discretion is required in their usage so as not to compromise efficiency. Therefore, guidelines on the use of such features has also been included.
CASTEP linter
The CASTEP linter is a Python tool which checks your CASTEP build for any issues related to the CASTEP style. It should be used after making any major modifications.
Note
The linter is also run on the CASTEP CI system and will warn you if any new issues arise from your modifications. Should any new issues be in your PR, it may not be accepted.
Using the CASTEP linter
The linter is available on PyPI and
can be installed on your system using pip:
Following the install, it should be possible to run the linter by running:
e.g.
For further information, type
It is also possible to use the CASTEP linter in
emacs through a flycheck
extension. To
use this you must install the flycheck package which can be done through the
MELPA emacs package repository.
Writing to the Specification Document
"It does exactly what it says on the tin"
Obviously, it is of paramount importance to make sure that any routine that you are responsible for does exactly what the specification says that it should do, particularly with regard to exit conditions, side-effects, etc.
Routines and variables that are covered by the specification are public whilst
other routines and variables are private. The specification says nothing about
the rôle or meaning of private routines. Private routines and variables are
only accessible within the module in which they occur.
Do not assume anything that is not written in the specification document
If the specification does not say that a particular routine will preserve the input values on exit, then you cannot presume that whoever coded it will do likewise! Even if that routine was written by you...
Similarly, it may seem obvious that a particular variable has a particular meaning, but if it is not defined in the specification, then it cannot be presumed. Future revisions of the code may change non-specified routines freely. If all code sticks to the specification at all times, then maintaining the code is much simpler.
Note that the specification does not say anything about private routines or variables in any module. For this reason, great care must be taken when using such routines. The subprogram template is there to remind you to document all side-effects of each routine!
Code robustly for errors
That is, the user should never see a Fortran run-time error message - your code
should check for possible error conditions, and either correct the error or
print a nice, meaningful error message and do a graceful exit via io_abort.
Conditions on execution
Conditions given in the specification must be true for correct execution of each
routine. Obviously, these should be tested for to ensure correctness, but this
may introduce a considerable performance penalty, particularly for Utility or
Fundamental routines. For this reason, it is recommended to use a single
#ifdef debug block at the start of each routine to test these conditions where
appropriate and call io_abort as necessary. The code can then be compiled
either with or without full error checking as appropriate.
Errors and Warnings
Use stderr from any node
Unlike normal messages, any node can write an error or warning message. Any
such message is to be written to stderr from the relevant node. The
routine shall then call io_abort to terminate the program neatly.
Use iprint consistently
Normal output, including warning messages and debugging information, should
only by written to stdout by the root node. The level of detail is
controlled by the iprint variable:
-
0- Minimal output - just the basic parameters controlling the run and the answers! -
1- Default output - breakdown of energies and forces into components, etc. but no debugging output. -
2- Minimal debugging - values of all significant parameters, etc. Not printing all the arrays. -
3- Maximal debugging - the works!
Efficiency Issues
Libraries
The use of BLAS and LAPACK libraries are recommended, as these are freely available libraries and often come in vendor-optimised versions for each platform. For efficiency, it is also recommended that you do not use BLAS "level 0 routines" as there are little efficiency gains to be made, and the equivalent fortran is often much neater and easier to read.
Fortran array intrinsics
Beware the use of fortran array intrinsics - they can be inefficient and may cause
memory problems, e.g. result=matmul(a,matmul(b,c)) requires an implicit
dynamic memory allocation. Wherever practical use BLAS instead. Some intrinsics
may also impede compiler optimisation, particularly on a vector
machine. Similarly, do not use functions such as transfer or mold - these
can be very inefficient.
Passing arrays to subprograms
This is a tricky subject, which can easily lead to confusion and inefficient code. The main problem is that there are multiple ways of passing arrays, and these are not in general equivalent!
The best practice is to always pass the whole array together with its size, such as:
call foo(int_array, N1, N2)
...
subroutine foo(int_array, N1, N2)
implicit none
integer, intent(in) :: N1, N2
integer, dimension(1:N1, 1:N2) :: int_array
...
as this does not cause any copying of the array and allows the compiler to do bound-checking etc.
The use of assumed-shape arrays, such as int_array(:, :) is less efficient
as this has an explicit rank, but an implicit shape. This requires the use of
functions such as size(int_array,1) and may prevent certain compiler
optimisations. However, it does allow the compiler to do bound-checking.
Care must be taken in passing the array though. If an array section is to be passed then it is much better to use assumed-size arrays (i.e. the old fashioned way), that is
call foo2(int_array(1, N))
...
subroutine foo2(int_array)
implicit none
integer, dimension(*) :: int_array
...
than to pass int_array(:, N) and receive int_array(:) as this will create a
copy of the array on the stack which will rapidly lead to "out of memory"
errors.
The use of assumed-size arrays, such as int_array(*) is useful if you want to
write a general purpose routine that will work with any size and/or rank
array. Note however, that it will not in general work with scalars, nor does it
allow bounds-checking. However, it does not cause the creation of any copies of
the array.
Machine-Specific Code
Avoid!
Write in standard fortran without vendor extensions and without using any system
routines wherever possible, for maximum portability. The one exception that is
allowed to this is in the Utility modules, where all the low-level
input/output and communications are handled.
Test thoroughly to prevent
Always test your routines on several different platforms and with several different compilers to be sure that you have not inadvertently relied upon some default behaviour of one specific compiler. The CI system will handle compilation for all supported compilers once submitted as a merge request into the Bitbucket repository, but these should be performed beforehand to minimise the effort in bugfixing.
File handling
One obvious area of machine dependency is that of file handling. For this reason,
the io module should be used to handle the opening of all files. The programmer
is responsible for reading / writing the data and closing the file. Files are
not to be kept open for any longer than strictly necessary.
Compiler/preprocessor directives
These should be avoided wherever possible as they hinder portability. They
should only be used in the Utility modules for machine specific code. All
module filenames should be given the extension .f90, with the exception of
Utility modules, where .F90 is permitted, but generally only if
preproccesing is used.
Fortran90 Features
Use of dynamic arrays
Each routine is responsible for allocating/using/deallocating its own workspace.
We recommend that such allocate/deallocates only occur once in a routine -
never inside a loop as this will produce a significant performance penalty. You
must ensure that you always deallocate local work arrays on termination of the
routine. Obviously, care needs to be taken if there are multiple exit points
from a routine.
Pointers
Always accept passed arrays in subprograms as arrays and not as pointers. This will force automatic dereferencing of the array and enable better optimisations by the compiler.
Flow of control
Use of constructs such as select case and do ... end do, with labelling of
"do loops", etc. is recommended for clarity. Use of cycle and exit is OK -
but only use to move a maximum of one level of nesting where possible. Do NOT
use goto.
Functions
A function subprogram should be "pure", i.e. generate no side-effects through modification of variables in argument list or module variables through "use association". Avoid recursion.
Use of use
Use modules with an only clause if only a small number of variables
required. Put appropriate use statements into each subroutine required, NOT
into the module header, in order to keep track of module variable modification.
Line numbers
Avoid where possible. Line numbers are only to be used for format statements,
and end= or err= in file handling. Do not use continue.
General features
Avoid multiple statement lines unless trivially simple.
Modules
General
All code is to be contained within modules.
Usage
Each module described in the specification is to be one source file. All routines given in the specification for this module are to be in this file.
Auxiliary modules
CASTEP also encourages the use of the more recent (Fortran 2008)
submodules. Submodules allow the programmatic subdivision of a module enabling
the compiler to precompile interfaces, reduce required compilation if only the
submodule has changed and allowing the developer to more effectively control
scope of module internals.
For clarity, and to keep the module from being excessively long, the module may also use auxiliary modules, which can be in separate files (again with one file per module). Any auxiliary modules must be used in only one specified module, i.e. no auxiliary code reuse in other specified modules as the auxiliary routines are not specified!
The naming convention of any auxiliary modules is to be inherited from the
specified module to make it clear where the auxiliary routines are to be used,
e.g. if the specified module is called me.F90 with routines called me_sub,
etc. then an auxiliary module would be me_extra.F90 with routines called
me_extra_sub, etc.
Note
Rather than using full auxilliary modules in modern CASTEP, submodules are
encouraged.
Style and Layout
Use the module template
The module template gives the recommended layout for a module and
for a subprogram. This is available in the CASTEP source at
Source/template.f90. In particular, note the layout and contents of the
comment header, and the order of declarations. Everything is to be private
unless explicitly specified as public! This also makes it simple to check the
code against the specification.
Layout
All code is to use indentation as generated by GNU-Emacs f90-mode. Use any editor you like to create the code, but please ensure that whatever goes into the Bitbucket repository has been passed through Emacs f90-mode indentation at the finished stage. To assist in Emacs usage, the module template contains Emacs directives to set f90-mode, etc.
Case
Use lower case for keywords and use capitalisation as given in the specification
for all routines and variables mentioned therein. For private routines and variables
use lower case in general. However, you may use upper case to differentiate
words within a name, e.g. userInputData - as long as you are consistent
throughout the module.
Use upper case, with stripped spaces, for the value of string variables that are
passed between routines, e.g. run_type='MOLECULARDYNAMICS' not
'MolecularDynamics' or 'molecular dynamics' etc. to simplify string
comparisons.
Names
For clarity, don't change variable name on passing to a different routine
wherever possible. Avoid short (1 or 2 letter) variable names except for simple
loop counters. Use new form end subroutine name etc. not older form
end subroutine.
Types
Do NOT use implicit typing. Similarly, you do not have to stick to the old rules
for implicit typing - you can have integer names beginning with "c" etc! Do
not give type as double precision - use real(kind=dp) instead, as dp is a
constant in the Constants module and this will make porting to other
architectures (e.g. Cray) much simpler. Remember that all machine-specific code
stays in the Utility routines. Similarly, when declaring a constant, use
1.234_dp NOT 1.234d0.
Free format
Use free-format f90, with a maximum line length of 132 characters.
Spaces
Use spaces between keywords e.g. end if not endif.
Code cleanly
Obviously, to ensure correctness and make it easier for others to maintain the code. If the obvious way to code a routine is inefficient, whilst the efficient way is obscure, then this is allowed as long as the routine is well documented internally, with a discussion as to the design decisions made.
Be aware of vectorisation
When coding, be aware that the code is almost always executed upon vector
architectures. Therefore code with a style that enables good vectorisation -
e.g. don't put if statements inside nested loops wherever possible.
Documentation
Internal
Each module, based upon the module template, is to have a header block describing its overall purpose and function.
Each routine, written to the template, is to have a header block describing its function, the variables required and how modified, the necessary conditions for correct operation, etc. These comments should be clear and easy to understand.
Each routine is also to contain lots of comments within the code. Comments are to be either on the same line(s) as the feature being comment upon, or in a block of lines above the feature.
Comment density should be comparable to code density.
All comments are to be in English and obey standard rules of English grammar.
External
A module (or any modifications) is only considered complete when additional documentation has been supplied for inclusion. Documentation must be provided in the appropriate module and function header blocks, explaining the function of the module and each routine, the physics behind the code, the algorithms used, the key variables and data structures, and appropriate references to the literature.
Testing
Test Program
Each module shall be tested for correctness before being added to the Bitbucket repository. To this end a set of tests shall be provided, which must compile and execute correctly in the CI system. The purpose of these tests is to verify the correct operation of every specified routine in the module.
CASTEP uses the testcode testing
platform which allows automated generation of benchmark data from a set of valid
CASTEP input files.
Please see Testing for more information on how to do this.
Reference data
The module test program shall come with both appropriate input datafiles and reference output results. Correct operation of the test shall be verified by comparing the actual output against the reference output results.
Module Template
General
Note particularly the order of declaration, use of implicit none and
private, and the standard comment header, for internal documentation. All
lines in comment headers are to be 80 characters wide. Not all sections of the
header will be relevant to all subprograms and so can be deleted. It is very
important that the header is kept up-to-date and as complete as possible.
Use of public and private
Each module uses an initial private statement to force all entities
in the module to be private by default. Then have explicit public statements
to expose those datatypes, variables and (overloaded) routine names, as listed
in the specification document. This makes it easy to compare the code to the
specification document.
Template
! -*- mode: F90 ; mode: font-lock ; column-number-mode: true ; vc-back-end: git -*-
!=============================================================================!
! D U M M Y !
!=============================================================================!
! Overall explanation of purpose and function of module. !
! !
!-----------------------------------------------------------------------------!
! Written from "Module Specification for New Plane Wave Code", M. Segall, !
! P. Lindan, M. Probert, C. Pickard, P. Hasnip, S. Clark and M. Payne !
! Copyright 1999/2000 !
!-----------------------------------------------------------------------------!
! Written by author, version, date !
!-----------------------------------------------------------------------------!
! !
! !
!=============================================================================!
module dummy
use constants, only : dp !Minimal useage where practical
implicit none !Impose strong typing
private !Everything is private ...
!---------------------------------------------------------------------------!
! P u b l i c R o u t i n e s !
!---------------------------------------------------------------------------!
public :: routine_name ... !... unless exposed here.
interface routine_name !Overloaded routines, etc.
... !(specific names are private)
end interface
!---------------------------------------------------------------------------!
! P u b l i c V a r i a b l e s !
!---------------------------------------------------------------------------!
public datatypes ...
public variables ...
!---------------------------------------------------------------------------!
! P r i v a t e R o u t i n e s !
!---------------------------------------------------------------------------!
!---------------------------------------------------------------------------!
! P r i v a t e V a r i a b l e s !
!---------------------------------------------------------------------------!
datatypes ... !Private data for all routines
variables .. !in this module ...
...
contains
subroutine public1(var1,var2,...)
!=========================================================================!
! Explanation of purpose of routine !
! ... !
!-------------------------------------------------------------------------!
! Arguments: !
! var1, intent, meaning !
! ... (in order of call list) !
!-------------------------------------------------------------------------!
! Parent module variables used: !
! globalvar1, meaning !
! ... !
!-------------------------------------------------------------------------!
! Modules used: !
! other_module used, !
! other_vars, meanings, changes !
! ... !
!-------------------------------------------------------------------------!
! Key Internal Variables: !
! intvar1, meaning !
! ... !
!-------------------------------------------------------------------------!
! Necessary conditions: !
! ... !
!-------------------------------------------------------------------------!
! Written by author, version, date !
!=========================================================================!
use my_module, only : some_other_function
use other_module, only : other_var1
implicit none
integer, intent(in), dimension(:,:) :: var1 !Variables in call order
real(kind=dp), intent(in), parameter :: var2
... (other variables in call list)
real(kind=dp) :: my_var1=2.7182818_dp !base of natural logs
complex(kind=dp), allocatable, dimension(:) :: my_work1
... (other internal variables)
... (condition checks)
... (actual code)
return
end subroutine public1
... (other public subroutines)
subroutine private1(....)
!=========================================================================!
! Explanation of purpose of routine !
! ... !
! (etc, as for public routines) !
!=========================================================================!
....
end subroutine private1
end module dummy