diff --git a/HySoP/hysop/__init__.py.in b/HySoP/hysop/__init__.py.in
index b639d037d376f4965af8db22736552d7ca7c5109..b243b260e625b62926f7a536543ac434a61a5267 100755
--- a/HySoP/hysop/__init__.py.in
+++ b/HySoP/hysop/__init__.py.in
@@ -31,13 +31,14 @@ CartesianGrid = grid.CartesianGrid
## Fields
-#import fields.discrete
-#import fields.continuous
-#import fields.analytical
-#ScalarField = fields.discrete.ScalarField
-#VectorField = fields.discrete.VectorField
-#ContinuousField = fields.continuous.ContinuousField
-#AnalyticalField = fields.analytical.AnalyticalField
+import fields.discrete
+import fields.continuous
+import fields.analytical
+ScalarField = fields.discrete.ScalarField
+VectorField = fields.discrete.VectorField
+ContinuousField = fields.continuous.ContinuousField
+AnalyticalField = fields.analytical.AnalyticalField
+
## Obstacle
## import obstacle.obstacle
@@ -46,25 +47,25 @@ CartesianGrid = grid.CartesianGrid
## Obstacle_d = obstacle.obstacle_d.Obstacle_d
## Operators
-### import operator.advec_scales
+## import operator.advec_scales
### import operator.diffusion
## import operator.penalization
## ### import operator.poisson
-## import operator.stretching
+import operator.stretching
## import operator.transport
## import operator.velocity
## # Advec_scales = operator.advec_scales.Advec_scales
## # Diffusion = operator.diffusion.Diffusion
## Penalization = operator.penalization.Penalization
## # Poisson = operator.poisson.Poisson
-## Stretching = operator.stretching.Stretching
+Stretching = operator.stretching.Stretching
## Transport = operator.transport.Transport
## Velocity = operator.velocity.Velocity
## ## Problem
-## import problem.problem
-## Problem = problem.problem.Problem
+import problem.problem
+Problem = problem.problem.Problem
## ## Forces
@@ -72,9 +73,9 @@ CartesianGrid = grid.CartesianGrid
## Compute_forces = physics.compute_forces.Compute_forces
## ## Solver
-## # import particular_solvers.basic
+import particular_solvers.basic
## #import particular_solvers.gpu
-## # ParticleSolver = particular_solvers.basic.ParticleSolver
+ParticleSolver = particular_solvers.basic.ParticleSolver
## #GPUParticleSolver = particular_solvers.gpu.GPUParticleSolver
## ## Tools
diff --git a/HySoP/hysop/integrator/__init__.py b/HySoP/hysop/integrator/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..4a661fed99196f000dc6530c4bf4f53868907bc4
--- /dev/null
+++ b/HySoP/hysop/integrator/__init__.py
@@ -0,0 +1,15 @@
+"""
+@package parmepy.particular_solvers.integrator
+
+Everything concerning time integration.
+
+"""
+import runge_kutta2
+import runge_kutta3
+import runge_kutta4
+RK2 = runge_kutta2.RK2
+RK3 = runge_kutta3.RK3
+RK4 = runge_kutta4.RK4
+
+import euler
+euler = euler.Euler
diff --git a/HySoP/hysop/particular_solvers/integrator/euler.py b/HySoP/hysop/integrator/euler.py
similarity index 73%
rename from HySoP/hysop/particular_solvers/integrator/euler.py
rename to HySoP/hysop/integrator/euler.py
index 819c94712b6720acafad7c229a7bd90191f74d54..4e58120343b3b186580401e4214e7d38f3a9ef36 100755
--- a/HySoP/hysop/particular_solvers/integrator/euler.py
+++ b/HySoP/hysop/integrator/euler.py
@@ -1,18 +1,18 @@
# -*- coding: utf-8 -*-
"""
-@package Utils
+@package parmepy.ode_solver.Euler
+
Forward Euler method.
"""
-from .integrator import ODESolver
+from ode_solver import ODESolver
import numpy as np
-
-
-#providedClass = "Euler"
+from parmepy.constants import PARMES_REAL, ORDER
class Euler(ODESolver):
"""
- ODESolver implementation for solving an equation system with forward Euler method.
+ ODESolver implementation for solving an equation system
+ with forward Euler method.
y'(t) = f(t,y)
y(t_{n+1}) = y(t_n) + dt*f(y(t_n))
@@ -38,10 +38,9 @@ class Euler(ODESolver):
@param t : current time.
@param dt : time step.
# """
- result = y + dt * np.asarray(f(t,y))
+ result = y + dt * np.asarray(f(t, y), dtype=PARMES_REAL, order=ORDER)
return result
-
def __str__(self):
"""ToString method"""
return "Euler Method"
@@ -49,5 +48,5 @@ class Euler(ODESolver):
if __name__ == "__main__":
print __doc__
- print "- Provided class : " + providedClass
- print eval(providedClass).__doc__
+ print "- Provided class : Euler"
+ print Euler.__doc__
diff --git a/HySoP/hysop/particular_solvers/integrator/integrator.py b/HySoP/hysop/integrator/ode_solver.py
similarity index 62%
rename from HySoP/hysop/particular_solvers/integrator/integrator.py
rename to HySoP/hysop/integrator/ode_solver.py
index f418635a0904bc31df6df26b7c5e3aaced35d7e0..33125ba11320c8b9262ba16cca4ceebe3c796999 100644
--- a/HySoP/hysop/particular_solvers/integrator/integrator.py
+++ b/HySoP/hysop/integrator/ode_solver.py
@@ -1,18 +1,25 @@
# -*- coding: utf-8 -*-
"""
-@package Utils
-ODESolver interface.
+@package parmepy.integrator.ode_solver
+
+Classes to describe (time) integrators.
"""
-from ...constants import *
+from abc import ABCMeta, abstractmethod
import numpy as np
+
class ODESolver:
"""
- ODESolver interface for solving an equation system :
+ Abstract description for ODE solvers.
+ Solve the system :
y'(t) = f(t,y)
By default, f = 0.
"""
+
+ __metaclass__ = ABCMeta
+
+ @abstractmethod
def __init__(self, f=None):
"""
Constructor.
@@ -20,11 +27,13 @@ class ODESolver:
@param f function f(t,y) : Right hand side of the equation to solve.
"""
## RHS.
- if f != None:
+ if f is not None:
self.f = f
else:
- self.f = lambda t, y: np.vectorize(f)(t,y)# [0. for x in y]
+ #[0. for x in y]
+ self.f = lambda t, y: np.vectorize(f)(t, y)
+ @abstractmethod
def integrate(self, y, t, dt):
"""
Abstract method, apply operaton on a variable.
@@ -35,9 +44,8 @@ class ODESolver:
@param dt : time step.
@return y at t+dt.
"""
- raise NotImplementedError("Need to override method in a subclass of " + providedClass)
if __name__ == "__main__":
print __doc__
- print "- Provided class : ODESolver"
+ print "- Provided class : ODESolver (abstract)"
print ODESolver.__doc__
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta2.py b/HySoP/hysop/integrator/runge_kutta2.py
similarity index 66%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta2.py
rename to HySoP/hysop/integrator/runge_kutta2.py
index 6bff109502efb91c1a665bc4be1e7a326c1fc8fa..f6612e7a139800a666ef0f2ac061b277017a62c3 100755
--- a/HySoP/hysop/particular_solvers/integrator/runge_kutta2.py
+++ b/HySoP/hysop/integrator/runge_kutta2.py
@@ -1,9 +1,10 @@
# -*- coding: utf-8 -*-
"""
-@package Utils
+@package ode_solver.runge_kutta2
+
RK2 method interface.
"""
-from .integrator import ODESolver
+from ode_solver import ODESolver
import numpy as np
@@ -24,21 +25,22 @@ class RK2(ODESolver):
"""
ODESolver.__init__(self, f)
- def integrate(self, f, t , dt , y):
+ def integrate(self, f, t, dt, y):
"""
Integration step for RK2 Method.
- up = f[t, Y(t,x,y,z)].
+ up = f[t, Y(t,space)].
- @param y : function of position at time t.
- @param f : function of function of position at time t.
+ @param f : right-hand side.
@param t : current time.
@param dt : time step.
+ @param y : function Y(t,space)
"""
-#K1 = dt *f[t,y(t,x,y,z)]
- K1 = dt * np.asarray(f(t,y))
-#result = y(t,x,y,z)] + dt *f[t + dt/2 , y(t,x,y,z) + k1/2.]
- result = y + dt *np.asarray(f(t+dt/2.,y + K1/2.))
+
+ # K1 = dt *f[t,y(t,x,y,z)]
+ K1 = dt * np.asarray(f(t, y))
+ # result = y(t,x,y,z)] + dt *f[t + dt/2 , y(t,x,y,z) + k1/2.]
+ result = y + dt * np.asarray(f(t + dt / 2., y + K1 / 2.))
return result
def __str__(self):
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta3.py b/HySoP/hysop/integrator/runge_kutta3.py
similarity index 57%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta3.py
rename to HySoP/hysop/integrator/runge_kutta3.py
index dc1d95beab3c67826455acd1df6eae5348c12224..bf51ab41f4124639a78b32d2f18e6d8cf603f82e 100755
--- a/HySoP/hysop/particular_solvers/integrator/runge_kutta3.py
+++ b/HySoP/hysop/integrator/runge_kutta3.py
@@ -1,9 +1,11 @@
# -*- coding: utf-8 -*-
"""
-@package Utils
+@package ode_solver.runge_kutta3
+
RK3 method interface.
"""
-from .integrator import ODESolver
+
+from ode_solver import ODESolver
import numpy as np
@@ -25,25 +27,23 @@ class RK3(ODESolver):
"""
ODESolver.__init__(self, f)
-
- def integrate(self, f, t , dt , y):
-
+ def integrate(self, f, t, dt, y):
"""
- Integration step for RK3 Method.
- up = f[t, Y(t,x,y,z)].
+ Integration step for RK2 Method.
+ up = f[t, Y(t,space)].
- @param y : function of position at time t.
- @param f : function of function of position at time t.
+ @param f : right-hand side.
@param t : current time.
@param dt : time step.
+ @param y : function Y(t,space)
"""
-#K1 = dt *f[t,y(t,x,y,z)]
- K1 = dt * np.asarray(f(t,y))
-#result = y(t,x,y,z)] + dt *f[t + dt/2 , y(t,x,y,z) + k1/2.]
- K2 = dt *np.asarray(f(t+dt/3.,y + K1[:,:,:,:]/3.))
- K3 = dt *np.asarray(f(t+dt*2./3.,y + K2[:,:,:,:]*2./3.))
-#result = y(t,x,y,z)] + 1/4 [ k1 + 3 k3]
- result = y + 1./4.*(K1+3.*K3)
+ # K1 = dt *f[t,y(t,x,y,z)]
+ K1 = dt * np.asarray(f(t, y))
+ # result = y(t,x,y,z)] + dt *f[t + dt/2 , y(t,x,y,z) + k1/2.]
+ K2 = dt * np.asarray(f(t + dt / 3., y + K1[:, :, :, :] / 3.))
+ K3 = dt * np.asarray(f(t + dt * 2. / 3., y + K2[:, :, :, :] * 2. / 3.))
+ # result = y(t,x,y,z)] + 1/4 [ k1 + 3 k3]
+ result = y + 1. / 4. * (K1 + 3. * K3)
return result
def __str__(self):
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta4.py b/HySoP/hysop/integrator/runge_kutta4.py
similarity index 53%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta4.py
rename to HySoP/hysop/integrator/runge_kutta4.py
index 26bdba75037540614967e3da5b7ba0085143d90f..0debd1c1a44b1fadca7cb4b4bb7917e8e99d8f91 100755
--- a/HySoP/hysop/particular_solvers/integrator/runge_kutta4.py
+++ b/HySoP/hysop/integrator/runge_kutta4.py
@@ -1,9 +1,11 @@
# -*- coding: utf-8 -*-
"""
-@package Utils
+@package ode_solver.runge_kutta2
+
RK4 method interface.
"""
-from .integrator import ODESolver
+
+from ode_solver import ODESolver
import numpy as np
@@ -26,23 +28,25 @@ class RK4(ODESolver):
ODESolver.__init__(self, f)
- def integrate(self, f, t , dt , y):
+ def integrate(self, f, t, dt, y):
"""
- Integration step for RK4 Method.
- up = f[t, Y(t,x,y,z)].
+ Integration step for RK2 Method.
+ up = f[t, Y(t,space)].
- @param y : function of position at time t.
- @param f : function of function of position at time t.
+ @param f : right-hand side.
@param t : current time.
@param dt : time step.
+ @param y : function Y(t,space)
"""
-#K1 = dt *f[t,y(t,x,y,z)]
- K1 = dt * np.asarray(f(t,y))
- K2 = dt *np.asarray(f(t+dt/2.,y + K1[:,:,:,:]/2.))
- K3 = dt *np.asarray(f(t+dt/2.,y + K2[:,:,:,:]/2.))
- K4 = dt *np.asarray(f(t+dt,y + K3[:,:,:,:]))
-#result = y(t,x,y,z)] + dt *f[t + dt/2 , y(t,x,y,z) + k1/2.]
- result = y + 1./6. * (K1[:,:,:,:] + 2.*K2[:,:,:,:] + 2.*K3[:,:,:,:]+ K4[:,:,:,:])
+
+ # K1 = dt *f[t, y(t, x, y, z)]
+ K1 = dt * np.asarray(f(t, y))
+ K2 = dt * np.asarray(f(t + dt / 2., y + K1[:, :, :, :] / 2.))
+ K3 = dt * np.asarray(f(t + dt / 2., y + K2[:, :, :, :] / 2.))
+ K4 = dt * np.asarray(f(t + dt, y + K3[:, :, :, :]))
+ # result = y(t, x, y, z)] + dt *f[t + dt/2 , y(t, x, y, z) + k1/2.]
+ result = y + 1. / 6. * (K1[:, :, :, :] + 2. * K2[:, :, :, :] +
+ 2. * K3[:, :, :, :] + K4[:, :, :, :])
return result
def __str__(self):
diff --git a/HySoP/hysop/mpi/tests/test_topology.py b/HySoP/hysop/mpi/tests/test_topology.py
index 46ffd526251e2a314ffed564689e51eb42c367a3..b805313e1be7cd9c346c0ef38b5f296518b06106 100644
--- a/HySoP/hysop/mpi/tests/test_topology.py
+++ b/HySoP/hysop/mpi/tests/test_topology.py
@@ -1,6 +1,14 @@
import parmepy as pp
+## @pytest.fixture
+## def topology():
+## import parmepy.mpi.topology as pptopo
+## import parmepy as pp
+## #dom = pp.Box()
+## return resolTopo
+
+
def test_create_topology1D():
dom = pp.Box()
resolTopo = [33, 33, 17]
@@ -9,7 +17,6 @@ def test_create_topology1D():
assert topo.domain == dom
assert topo.dim == 1
assert topo.size == pp.mpi.main_size
-
print topo
@@ -44,3 +51,12 @@ def test_create_topology_with_dims():
assert topo.size == pp.mpi.main_size
testList = topo.dims == topoDims
assert testList.all()
+
+
+if __name__ == "__main__":
+
+ #test_create_topology1D()
+ #pp.mpi.main_comm.barrier()
+
+ test_create_topology2D()
+ pp.mpi.main_comm.barrier()
diff --git a/HySoP/hysop/mpi/topology.py b/HySoP/hysop/mpi/topology.py
index b51e6fe0c951f49497106b923ac737edce406af4..27df9147b5547e35733323ea62925926a08c45c7 100644
--- a/HySoP/hysop/mpi/topology.py
+++ b/HySoP/hysop/mpi/topology.py
@@ -136,7 +136,7 @@ class Cartesian(object):
"""
## Counter of topology.Cartesian instances to set idTopo.
- _ids = count(0)
+ __ids = count(0)
def __init__(self, domain, dim, globalMeshResolution,
comm=main_comm, periods=None, ghosts=None, cutdir=None):
@@ -144,7 +144,7 @@ class Cartesian(object):
## Associated domain
self.domain = domain
## An id for the topology
- self.idTopo = self._ids.next()
+ self.idTopo = self.__ids.next()
## Topology dimension
self.dim = dim
## Communicator used to build the topology
@@ -222,7 +222,7 @@ class Cartesian(object):
## Global Mesh Resolution
self.globalMeshResolution = np.asarray(globalMeshResolution,
dtype=PARMES_INTEGER)
-
+
# set cutdir if required (i.e. not set by withResolution constructor).
if cutdir is None: # not hasattr(self, '__cutdir'):
self.__cutdir = np.zeros((domain.dimension), dtype=bool)
@@ -231,7 +231,7 @@ class Cartesian(object):
self.__cutdir[:] = self.__cutdir[::-1]
else:
self.__cutdir = np.asarray(cutdir, dtype=bool)
-
+
# Number of "computed" points (i.e. excluding ghosts/boundaries).
pts_noghost = np.zeros((self.dim), dtype=PARMES_INTEGER)
# Warning FP : we should test boundary conditions type here
diff --git a/HySoP/hysop/particular_solvers/basic.py b/HySoP/hysop/particular_solvers/basic.py
index 7f47c6d99730f37d2cffc703585d40891324a191..c18d9bc62331e5e0f2092fa27d46be57aaef6f55 100644
--- a/HySoP/hysop/particular_solvers/basic.py
+++ b/HySoP/hysop/particular_solvers/basic.py
@@ -15,7 +15,7 @@ from parmepy.operator.poisson import Poisson
from parmepy.operator.splitting import Splitting
from parmepy.tools.timer import Timer
from parmepy.tools.printer import Printer
-
+from parmepy.integrator import RK3
class ParticleSolver(Solver):
"""
diff --git a/HySoP/hysop/particular_solvers/integrator/__init__.py b/HySoP/hysop/particular_solvers/integrator/__init__.py
deleted file mode 100644
index 48c83c107ba4b8011ac4d47b2f8275f204530750..0000000000000000000000000000000000000000
--- a/HySoP/hysop/particular_solvers/integrator/__init__.py
+++ /dev/null
@@ -1,6 +0,0 @@
-"""
-@package parmepy.particular_solvers.integrator
-
-Everything concerning time integration.
-
-"""
diff --git a/HySoP/hysop/problem/problem.py b/HySoP/hysop/problem/problem.py
index fce59388f3b7326dee9ce3c4511c1e46ce3a6681..b6109a1d9f5de0b06aa995f52c8c3151f25daeaf 100644
--- a/HySoP/hysop/problem/problem.py
+++ b/HySoP/hysop/problem/problem.py
@@ -3,8 +3,8 @@
Problem representation.
"""
-from ..particular_solvers.basic import ParticleSolver
-from ..particular_solvers.gpu import GPUParticleSolver
+from parmepy.particular_solvers.basic import ParticleSolver
+from parmepy.particular_solvers.gpu import GPUParticleSolver
class Problem():
diff --git a/HySoP/hysop/particular_solvers/integrator/forward_euler.py b/HySoP/hysop/unusedOrObsolet/forward_euler.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/integrator/forward_euler.py
rename to HySoP/hysop/unusedOrObsolet/forward_euler.py
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta.py b/HySoP/hysop/unusedOrObsolet/runge_kutta.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta.py
rename to HySoP/hysop/unusedOrObsolet/runge_kutta.py
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta2stretching.py b/HySoP/hysop/unusedOrObsolet/runge_kutta2stretching.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta2stretching.py
rename to HySoP/hysop/unusedOrObsolet/runge_kutta2stretching.py
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta3stretching.py b/HySoP/hysop/unusedOrObsolet/runge_kutta3stretching.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta3stretching.py
rename to HySoP/hysop/unusedOrObsolet/runge_kutta3stretching.py
diff --git a/HySoP/hysop/particular_solvers/integrator/runge_kutta4stretching.py b/HySoP/hysop/unusedOrObsolet/runge_kutta4stretching.py
similarity index 100%
rename from HySoP/hysop/particular_solvers/integrator/runge_kutta4stretching.py
rename to HySoP/hysop/unusedOrObsolet/runge_kutta4stretching.py