MPI-AMRVAC  2.0
The MPI - Adaptive Mesh Refinement - Versatile Advection Code
Code style guide

Table of Contents

Introduction

Below we present some guidelines for new code contributed to MPI-AMRVAC. The goal of these guidelines is to make it easier to understand, modify and maintain MPI-AMRVAC. Although some of the guidelines are simply a matter of preference and convention, sticking to these preferences and conventions is still valuable. The guide below has been inspired by a number of other Fortran style guides: 1 2 3 4

Standards and language features

Code should conform to a reasonably modern Fortran standard (e.g., Fortran 90, 95, 2003). Only make use of the latest language features if you really need them, since this can cause problems for users with different compilers.

Do not use deprecated features:

Deprecated feature solution
common block use a module
implicit typing explicit typing
statement functions define a real function
double precision :: x real(kind) :: x
real*N :: x real(kind) :: x
integer*N :: x integer(kind) :: x
character*N :: x character(len=N) :: x

Naming conventions

Use self-explanatory names when possible. Only variables that are locally defined and have a simple meaning, such as loop indices, can have short names such as i or ix. The farther away the definition of a variable is, the more important it becomes that is has a self-explanatory name.

Here are some examples, inspired by looking at the current version of MPI-AMRVAC:

Description Too short Better
Time variable t time
Iteration counter it iteration
Maximum refinement level mxnest max_refinement_level
Subroutine to update AMR grid resettree update_amr_grid

A list of further naming guidelines:

Code style conventions

Comments

Write comments such that a reasonably experienced programmer can understand your code as quickly as possible. In practice, this could mean writing the following comments:

When in doubt, you should probably add a comment: it will help the reader to confirm his/her understanding. Do not write comments around trivial statements, such as i = i + 1.

The documentation page explains how to write Doxygen comments, which show up in the documentation of MPI-AMRVAC.

Modules and programs

A source file should contain either a module or a program. Try to use modules in the following way:

module mod_name
! Selectively import when needed in the whole module
use mod_first, only: ...
implicit none ! Don't allow implicit types
private ! Entities are private by default
public :: ... ! Explicitly state public entities
contains ! Place subroutines and functions below
subroutine test()
use mod_second, only: ... ! Use local imports
...
end subroutine test
end module mod_name

The selective imports with use ..., only: help the reader with figuring out where things come from. However, when you need a lot of functionality from another module, it makes more sense to simply include everything with use module.

Functions and subroutines

All functions and subroutines should at least have a brief comment describing their functionality, as stated in Comments.

Side-effects

Functions should not have side-effects, meaning that they do not change the state of the program. Functions without such side-effects can be marked with pure. Functions should also not change their arguments. Consider making pure functions operating on scalars elemental, so that you can also use them on arrays.

The result of a function should not be directly used in a print or write statement, unless you are sure the function itself does no IO (input/output). The reason for this is that recursive IO can lead to hard to debug hangs / crashes.

Subroutines are ideally also pure (without side-effects), but they can change their arguments.

Arguments

All arguments should have their intent declared, using one of intent(in,out,inout).

Ideally, functions and subroutines get their information from their arguments. If that requires a lot of arguments, perhaps the functions and subroutines can be split in smaller pieces. Sometimes it can also help to define types with the relevant information. There should not be more than about 4 or 5 arguments.

Global and module variables

Don't use global variables. Instead place variables inside modules, and include them where needed. In cases where this is not possible, gather the global variables in a module and give them a recognizable prefix such as GLOBAL_.

To ensure that variables defined in a module are not accidentally changed, you can use the Fortran 2003 protected attribute:

integer, protected :: my_age

Such variables can only be changed from inside the defining module.

Numbers

Floating point

The usage of double precision is deprecated. Instead use the kind-parameter dp to declare double precision numbers:

real(dp) :: x ! good
double precision :: x ! deprecated

In MPI-AMRVAC dp is defined in ...

Todo:
Include a parameter dp

Write floating point constants using the _dp suffix:

x = x * 1.1_dp ! good
x = x * 1.1 ! bad: single precision constant

Integers are automatically converted to real numbers when they are mixed, without a loss of precision. However, be careful with expressions such as:

x = 0.5_dp * 5 / 6   ! Bad: is this (0.5_dp * 5)/6 or 0.5_dp * (5/6)?
x = (0.5_dp * 5) / 6 ! Good

Integers

Use the default integer type, unless there is a specific reason to use a larger type. Be aware of the different ways of converting a real number x to an integer:

Named constants vs magic numbers

Use named constants instead of magic numbers:

real(dp), parameter :: pi = 3.14_dp
x = sin(pi * x) ! good
x = sin(3.14_dp * x) ! bad: magic number

However, don't use named constants for simple numbers such as 0, or 0.5:

x = 1.0_dp/pi ! good
x = one/pi ! bad: what is one?

Arrays

Correct order for loops

Always loop over arrays in the correct order, meaning that the loop indices are ordered from right to left (opposite to loops in e.g., C or C++):

do j = 1, n
do i = 1, n
array(i, j) = 1
end do
end do

Because Fortran stores arrays in column-major order, the loop then follows the 'natural' memory order of the array. For the same reason, it pays off to think about the ordering of your arrays, for example:

array(:, i, j) = 1 ! Fast
array(i, j, :) = 1 ! slower

Allocatable arrays

Use allocatable arrays when:

Allocatable arrays are automatically deallocated, so you cannot create memory leaks. They are also automatically reallocated on assignment (with gfortran, for ifort you have to enable this behavior).

Passing arrays as arguments

Use assumed-shape arrays when performance is not critical, for example:

subroutine square(values, squares)
integer, intent(in) :: values(:)
integer, intent(out) :: squares(:)
...
end subroutine square

The advantage of assumed-shape arrays is that they allow for run-time bounds checking. When performance is critical, you can use explicit-shape arrays:

subroutine square(values, squares, n_values)
integer, intent(in) :: n_values
integer, intent(in) :: values(n_values)
integer, intent(out) :: squares(n_values)
...
end subroutine square

Another option is to embed the array in a type, and pass the type as argument. See this guide by Intel for more information about the performance differences.

Array constants

In new code, use the [...] syntax to define array constants:

x = [1, 2, 3] ! Fortran 2003 and later
x = (/1, 2, 3/) ! old style

Indentation and whitespace

Indent with spaces, using the following indentations:

Construct number of spaces
program, module, subroutine, function, associate 2
type, interface 3
do, if, select case, where, forall 3

Include empty lines to visually separate blocks of code. Include a newline between functions and subroutines, after and before do loops, around if blocks, after the variable declarations, etc.

Warnings and runtime checks

Enable all normal warnings during compilation, ideally using different compilers. Fix all warnings, except those that are incorrect, and those for which the fix does more harm than good.

Run the code with different inputs, perhaps using a different number of processors, to detect the most obvious bugs. Enable all sensible run-time checks to catch errors. Try to use a tool like valgrind to detect memory problems.

Useful Gfortran flags

Flag meaning
-Wall Enable all standard warnings
-Wextra Enable additional warnings
-Wimplicit-interface Warn about procedures with implicit interfaces
-fcheck=all Enable all run-time checks
-ffpe-trap=... Enable floating point traps. Recommended: invalid, zero, overflow
-finit-real=snan Initialize real values with a signalling NaN
-finit-integer=-2147483648 Initialize integers with this value
-g Include debugging info into the executable
-pg Enable support for profiling with a tool like gprof
-O0 Disable optimizations (when debugging)
-fimplicit-none Do not allow implicit types
-std=... Set the Fortran standard to use (f95, f2003, etc.)

Useful ifort flags

Flag meaning
-traceback Generate a backtrace after a run-time error
-ftrapuv Initialize stack variables to unlikely values
-warn all Enable all standard warnings
-check all Enable all run-time checks
-check ... Useful are: bounds, uninit
-fpe[0,1,3] Lower values enable more floating point exceptions
-g Include debugging info into the executable
-pg Enable support for profiling with a tool like gprof
-O0 Disable optimizations (when debugging)
-implicitnone Do not allow implicit types
-stand ... Set the Fortran standard to use (f95, f2003, etc.)