updates for TG problem

Examples/TaylorGreen3D.py

@@ -4,6 +4,7 @@
 import parmepy as pp
 from parmepy.f2py import fftw2py
 import numpy as np
+from parmepy.mpi.topology import Cartesian
 from parmepy.operator.advection import Advection
 from parmepy.operator.stretching import Stretching
 from parmepy.operator.poisson import Poisson
@@ -11,8 +12,8 @@ from parmepy.operator.diffusion import Diffusion
 from parmepy.operator.redistribute import Redistribute
 from parmepy.problem.navier_stokes import NSProblem
 from parmepy.operator.monitors.energy_enstrophy import Energy_enstrophy
-from dataTG import dim, nb, pi, ADVECTION_METHOD, VISCOSITY, WITH_PROJ,\
-    OUTPUT_FREQ, FILENAME, simu
+from dataTG import dim, nb, pi, NBGHOSTS, ADVECTION_METHOD, VISCOSITY, \
+    WITH_PROJ, OUTPUT_FREQ, FILENAME, simu
 
 
 ## ----------- A 3d problem -----------
@@ -46,6 +47,11 @@ velo = pp.Field(domain=box, formula=computeVel,
 vorti = pp.Field(domain=box, formula=computeVort,
                  name='Vorticity', isVector=True)
 
+## Usual Cartesian topology definition
+ghosts = np.ones((box.dimension)) * NBGHOSTS
+topo = Cartesian(box, box.dimension, nbElem,
+                 ghosts=ghosts)
+
 ## Operators
 advec = Advection(velo, vorti,
                   resolutions={velo: nbElem,
@@ -55,7 +61,8 @@ advec = Advection(velo, vorti,
 
 stretch = Stretching(velo, vorti,
                      resolutions={velo: nbElem,
-                                  vorti: nbElem}
+                                  vorti: nbElem},
+                     topo=topo
                      )
 
 diffusion = Diffusion(vorti,
@@ -69,24 +76,27 @@ poisson = Poisson(velo, vorti,
                   projection=WITH_PROJ)
 
 ## Diagnostics related to the problem
+
 energy = Energy_enstrophy(velo, vorti,
-                          resolutions={velo: nbElem,
-                                       vorti: nbElem},
+                          topo=topo,
                           viscosity=VISCOSITY,
                           frequency=OUTPUT_FREQ,
                           prefix=FILENAME)
 
 distrAdvStr = Redistribute([vorti, velo], advec, stretch)
 distrStrPoiss = Redistribute([vorti], stretch, poisson)
+distrPoissStretch = Redistribute([vorti, velo], poisson, stretch)
 
 ## Define the problem to solve
 pb = NSProblem(operators=[advec, distrAdvStr, stretch, distrStrPoiss,
-                          diffusion, poisson],
+                          diffusion, poisson, distrPoissStretch],
                simulation=simu, monitors=[energy])
 
 ## Setting solver to Problem
 pb.setUp()
 
+print 'all topologies', box.topologies
+
 
 ## Solve problem
 #poisson.apply(simu)

Examples/dataTG.py

@@ -3,10 +3,12 @@
 # problem dimension
 dim = 3
 # resolution
-nb = 33
+nb = 129
 # pi constant
 import math
 pi = math.pi
+# number of ghosts in usual cartesian topo
+NBGHOSTS = 2
 # Advection method
 ADVECTION_METHOD = 'scales_p_M6'
 #

HySoP/hysop/operator/energy_enstrophy.py

@@ -66,8 +66,8 @@ class Energy_enstrophy(Monitoring):
 
         self._isUpToDate = True
 
-        spaceStep = [self.topovel.mesh.spaceStep,
-                     self.topovort.mesh.spaceStep]
+        spaceStep = [self.topovel.mesh.space_step,
+                     self.topovort.mesh.space_step]
 
         length = self.topo.domain.length
         self.coeffEnergy = 0.5 * (np.prod(spaceStep[0]) /
@@ -103,22 +103,19 @@ class Energy_enstrophy(Monitoring):
                                                   for i in xrange(nbc)])
         # Collective communications
 
-        topovelo = self.velo.topology
-        energy = topovelo.comm.reduce(energy, PARMES_MPI_REAL,
-                                      op=MPI.SUM, root=0)
-        energyBuff1 = topovelo.comm.reduce(self.buffer_1, PARMES_MPI_REAL,
-                                           op=MPI.SUM, root=0)
-        energyBuff2 = topovelo.comm.reduce(self.buffer_2, PARMES_MPI_REAL,
-                                           op=MPI.SUM, root=0)
-
-        topovort = self.vort.topology
-        enstrophy = topovort.comm.reduce(enstrophy, PARMES_MPI_REAL,
-                                         op=MPI.SUM, root=0)
+        energy = self.topovel.comm.reduce(energy, PARMES_MPI_REAL,
+                                          op=MPI.SUM, root=0)
+        energyBuff1 = self.topovel.comm.reduce(self._buffer_1, PARMES_MPI_REAL,
+                                               op=MPI.SUM, root=0)
+        energyBuff2 = self.topovel.comm.reduce(self._buffer_2, PARMES_MPI_REAL,
+                                               op=MPI.SUM, root=0)
+        enstrophy = self.topovort.comm.reduce(enstrophy, PARMES_MPI_REAL,
+                                              op=MPI.SUM, root=0)
 
         # Update buffers
 
-        self.buffer_2 = self.buffer_1
-        self.buffer_1 = energy
+        self._buffer_2 = self._buffer_1
+        self._buffer_1 = energy
 
         # Effective viscosity computation
 

HySoP/hysop/operator/multiphase.py

@@ -5,11 +5,11 @@
 MultiPhase Rot Grad P
 """
 from parmepy.operator.continuous import Operator
-from parmepy.operator.discrete.multiphase import Pressure_d
+from parmepy.operator.discrete.multiphase import Baroclinic_d
 from parmepy.constants import debug
 
 
-class Pressure(Operator):
+class Baroclinic(Operator):
     """
     Pressure operator representation
     """