Python class linked with fortran module#
%load_ext fortranmagic
%%fortran
module particles_f90
implicit none
real(8), dimension(:), allocatable :: positions
real(8), dimension(:), allocatable :: velocities
contains
subroutine init_particles( n )
integer, intent(in) :: n
integer :: i
if (.not. allocated(positions)) then
allocate(positions(n))
end if
positions = [(i, i = 1, n, 1)]
if (.not. allocated(velocities)) then
allocate(velocities(n))
end if
velocities = 1.0
end subroutine init_particles
subroutine push_particles( dt )
real(8), intent(in) :: dt
positions = positions + dt * velocities
end subroutine push_particles
end module particles_f90
Traceback (most recent call last):
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/f2py/__main__.py", line 5, in <module>
main()
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/f2py/f2py2e.py", line 770, in main
run_compile()
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/f2py/f2py2e.py", line 594, in run_compile
build_backend = f2py_build_generator(backend_key)
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/f2py/_backends/__init__.py", line 6, in f2py_build_generator
from ._distutils import DistutilsBackend
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/f2py/_backends/_distutils.py", line 3, in <module>
from numpy.distutils.core import setup, Extension
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/distutils/core.py", line 24, in <module>
from numpy.distutils.command import config, config_compiler, \
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/distutils/command/config.py", line 19, in <module>
from numpy.distutils.mingw32ccompiler import generate_manifest
File "/usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/numpy/distutils/mingw32ccompiler.py", line 27, in <module>
from distutils.msvccompiler import get_build_version as get_build_msvc_version
ModuleNotFoundError: No module named 'distutils.msvccompiler'
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[2], line 1
----> 1 get_ipython().run_cell_magic('fortran', '', 'module particles_f90\n\n implicit none\n \n real(8), dimension(:), allocatable :: positions\n real(8), dimension(:), allocatable :: velocities\n \ncontains\n subroutine init_particles( n )\n \n integer, intent(in) :: n\n \n integer :: i\n \n if (.not. allocated(positions)) then\n allocate(positions(n))\n end if\n positions = [(i, i = 1, n, 1)]\n if (.not. allocated(velocities)) then\n allocate(velocities(n))\n end if\n velocities = 1.0\n\n end subroutine init_particles\n \n subroutine push_particles( dt )\n \n real(8), intent(in) :: dt\n \n positions = positions + dt * velocities\n \n end subroutine push_particles\nend module particles_f90\n')
File /usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2517, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
2515 with self.builtin_trap:
2516 args = (magic_arg_s, cell)
-> 2517 result = fn(*args, **kwargs)
2519 # The code below prevents the output from being displayed
2520 # when using magics with decorator @output_can_be_silenced
2521 # when the last Python token in the expression is a ';'.
2522 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
File /usr/share/miniconda/envs/python-fortran/lib/python3.9/site-packages/fortranmagic.py:516, in FortranMagics.fortran(self, line, cell)
511 res = self._run_f2py(f2py_args + ['-m', module_name, '-c',
512 f_f90_file],
513 verbosity=args.verbosity,
514 fflags=fflags)
515 if res != 0:
--> 516 raise RuntimeError("f2py failed, see output")
518 self._code_cache[key] = module_name
519 module = _imp_load_dynamic(module_name, module_path)
RuntimeError: f2py failed, see output
The Python class#
class Particles(object):
def __init__(self, n):
self.index = 0
self.numberof = n
particles_f90.init_particles( n)
self.positions = particles_f90.positions
self.velocities = particles_f90.velocities
@property
def position(self):
return self.positions[self.index]
@property
def velocity(self):
return self.velocities[self.index]
Access to Fortran data from Python#
particles = Particles(10)
particles.velocities
array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1.])
particles.positions
array([ 1., 2., 3., 4., 5., 6., 7., 8., 9., 10.])
particles.index = 0
particles.position
np.float64(1.0)
particles.index = 1
particles.position
np.float64(2.0)
Create an Iterator class#
class ParticleArray(object):
def __init__(self, particles):
self.particles = particles
self.numberof = particles.numberof
def __getitem__(self, index):
self.particles.index = index
return self.particles
def __len__(self):
return self.numberof
def __iter__(self):
for i in range(self.numberof):
self.particles.index = i
yield self.particles
particle_array = ParticleArray(particles)
particle_array[0].position
np.float64(1.0)
for p in particle_array:
print(p.position)
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0
10.0
Fortran derived type#
%%fortran
module mesh
implicit none
type :: geometry
real(8) :: xmin, xmax, dx ! coordinates of origin and grid size
integer :: nx ! number of grid points
real(8), dimension(:), pointer :: x ! coordinates of points
end type geometry
contains
subroutine create(geom, xmin, xmax, nx)
!f2py integer(8), intent(out) :: geom
type(geometry), pointer :: geom
real(8), intent(in) :: xmin, xmax
integer, intent(in) :: nx
real(8) :: dx
integer :: i
allocate(geom)
geom%xmin = xmin
geom%xmax = xmax
geom%dx = ( xmax - xmin ) / (nx-1)
geom%nx = nx
allocate(geom%x(nx))
do i=1,nx
geom%x(i)=geom%xmin+(i-1)*geom%dx
end do
end subroutine create
subroutine view(geom)
!f2py integer(8), intent(in) :: geom
type(geometry), pointer :: geom
print*, 'nx = ', geom%nx
print*, geom%xmin, geom%xmax
print*, geom%x(:)
end subroutine view
subroutine get_size(geom, nx)
!f2py integer(8), intent(in) :: geom
type(geometry), pointer :: geom
integer, intent(out) :: nx
nx = geom%nx
end subroutine get_size
end module mesh
geom = mesh.create(0.0, 1.0, 10)
mesh.get_size(geom)
10
type(geom)
int
f2py with C code#
Signature file is mandatory
intent(c)must be used for all variables and can be set globally.Function name is declared with
intent(c)
%rm -rf cfuncts*
%%file cfuncts.c
void push_particles(double* positions, double* velocities, double dt, int n){
for (int i=0; i<n; i++){
positions[i] = positions[i] + dt * velocities[i];
}
}
Writing cfuncts.c
%%file cfuncts.pyf
python module cfuncts
interface
subroutine push_particles(positions, velocities, dt, n)
intent(c):: push_particles
intent(c)
integer, optional, depend(velocities) :: n = len(velocities)
real(8), dimension(n), intent(inplace) :: positions
real(8), dimension(n), intent(in) :: velocities
real(8), intent(in) :: dt
end subroutine push_particles
end interface
end python module cfuncts
Writing cfuncts.pyf
import sys
!{sys.executable} -m numpy.f2py --quiet -c cfuncts.c cfuncts.pyf -m cfuncts
/home/pnavaro/.julia/conda/3/x86_64/envs/f2py/lib/python3.11/site-packages/numpy/f2py/f2py2e.py:723: VisibleDeprecationWarning:
distutils has been deprecated since NumPy 1.26.x
Use the Meson backend instead, or generate wrappers without -c and use a custom build script
builder = build_backend(
WARN: Could not locate executable armflang
Removing build directory /tmp/tmpksoj2o88
import numpy as np
import cfuncts
print(cfuncts.push_particles.__doc__)
push_particles(positions,velocities,dt,[n])
Wrapper for ``push_particles``.
Parameters
----------
positions : rank-1 array('d') with bounds (n)
velocities : input rank-1 array('d') with bounds (n)
dt : input float
Other Parameters
----------------
n : input int, optional
Default: len(velocities)
n = 10
dt = 0.1
x = np.arange(n, dtype="d")
v = np.ones(n, dtype="d")
cfuncts.push_particles( x, v, dt)
x
array([0.1, 1.1, 2.1, 3.1, 4.1, 5.1, 6.1, 7.1, 8.1, 9.1])
References#
f2py documentation https://docs.scipy.org/doc/numpy/f2py/
Transparents E. Sonnendrucker http://calcul.math.cnrs.fr/Documents/Journees/dec2006/python-fortran.pdf
Documentation Sagemath http://doc.sagemath.org/html/en/thematic_tutorials/numerical_sage/f2py.html
Hans Petter Langtangen : Python Scripting for Computational Science.