Release/integrate gpu

Bassetti_Erskine.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

FFT_OpenBoundary.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

FFT_OpenBoundary_SquareGrid.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

FFT_PEC_Boundary_SquareGrid.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

FiniteDifferences_ShortleyWeller_SquareGrid.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

FiniteDifferences_Staircase_SquareGrid.py

@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyPIC Version 2.1.0                     
+#		           PyPIC Version 2.2.0                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

GPU/.gitignore

@@ -0,0 +1,10 @@
+*.pickle
+*.so
+*.pyc
+.project
+.pydevproject
+*.png
+norepository_*
+PyPIC.egg-info
+build
+.ipynb_checkpoints/

GPU/Makefile

@@ -0,0 +1,5 @@
+all:
+	python setup.py build_ext
+
+clean:
+	rm -r build dist PyPIC.egg-info *.so *.pyc

GPU/backwards_compatibility_1_03.py

@@ -0,0 +1,235 @@
+'''
+Module providing backwards compatibility with PyPIC 1.0.3
+How to: Add 'from backwards_compatibility_1_02 import *' to the beginning
+        of your old scripts
+Main idea: 1) Wrap the new classes with the old interface
+           2) Create new modules (via imp) with the same names as the old ones
+           3) Add them to sys.modules
+@author Stefan Hegglin
+@date 12.07.2015
+'''
+
+
+# provide a way to use modules from the parent directory
+import sys
+sys.path.append('../')
+import imp
+from scipy.constants import e, epsilon_0
+import numpy as np
+from pypic import PyPIC_Fortran_M2P_P2M
+from meshing import RectMesh2D
+from poisson_solver import FD_solver as FD
+from poisson_solver import FFT_solver as FFT
+
+
+
+
+class _Proxy_v103(object):
+    '''
+    Base Class providing the interface of PyPIC 1.0.3 solvers while
+    internally using the newer version
+    '''
+    def __init__(self, poissonsolver):
+        '''
+        Set up all members which are available in the old PyPIC classes
+        '''
+        mesh = RectMesh2D(poissonsolver.bias_x,
+                          poissonsolver.bias_y,
+                          poissonsolver.Dh, poissonsolver.Dh,
+                          poissonsolver.Nxg,
+                          poissonsolver.Nyg)
+        if getattr(poissonsolver, 'gradient', None) != None:
+            pypic = PyPIC_Fortran_M2P_P2M(mesh, poissonsolver,
+                                          poissonsolver.gradient)
+        else:
+            pypic = PyPIC_Fortran_M2P_P2M(mesh, poissonsolver)
+        self.pypic = pypic
+        self.Dh = poissonsolver.Dh
+        self.xg = poissonsolver.xg
+        self.yg = poissonsolver.yg
+        self.bias_x = poissonsolver.bias_x
+        self.bias_y = poissonsolver.bias_y
+        self.Nxg = poissonsolver.Nxg
+        self.Nyg = poissonsolver.Nyg
+
+        self.rho = np.zeros((self.Nxg, self.Nyg))
+        self.phi = np.zeros((self.Nxg, self.Nyg))
+        self.efx = np.zeros((self.Nxg, self.Nyg))
+        self.efy = np.zeros((self.Nxg, self.Nyg))
+        self.xn = getattr(poissonsolver, 'xn', None)
+        self.yn = getattr(poissonsolver, 'yn', None)
+
+    def scatter_and_solve(self, x_mp, y_mp, nel_mp, charge=-e):
+        ''' Calls scatter and solve '''
+        self.scatter(x_mp, y_mp, nel_mp, charge)
+        self.solve()
+
+    def scatter(self, x_mp, y_mp, nel_mp, charge=-e):
+        ''' Difficulties: not all entires in nel_mp are the same, however our
+        solver can only handle the same charge for all mp.
+        Solution: Call p2m seperately for all particles with different nel_mp
+                  and add the charge densities
+        '''
+        if len(x_mp) > 0:
+            nel_mp_uniques = np.unique(nel_mp)
+            mesh_charges = self.rho.T*0
+            for n_mp in nel_mp_uniques:
+                idx = np.where(np.isclose(n_mp, nel_mp))[0]
+                charge_ = charge * n_mp
+                mesh_charges += self.pypic.particles_to_mesh(x_mp[idx],
+                                                             y_mp[idx],
+                                                             charge=charge_)
+            self.rho = mesh_charges.T / self.pypic.mesh.volume_elem
+        else:
+            self.rho *= 0
+
+    def solve(self, rho=None, flag_verbose=False):
+        if rho == None:
+            rho = self.rho.T
+        else:
+            rho = rho.T
+        phi = self.pypic.poisson_solve(rho)
+        self.phi = phi.reshape((self.Nyg, self.Nxg)).T
+        mesh_e_fields = self.pypic.get_electric_fields(phi)
+        self.efx = mesh_e_fields[0].reshape(self.Nyg, self.Nxg).T
+        self.efy = mesh_e_fields[1].reshape(self.Nyg, self.Nxg).T
+        self.rho = rho.T
+
+    def gather(self, x_mp, y_mp):
+        if len(x_mp) > 0:
+            mesh_e_fields = [self.efx.T, self.efy.T]
+            mesh_e_fields_and_mp_coords = zip(list(mesh_e_fields),[x_mp, y_mp])
+            E = self.pypic.field_to_particles(*mesh_e_fields_and_mp_coords)
+            Ex_sc_n = E[0]
+            Ey_sc_n = E[1]
+        else:
+            Ex_sc_n = 0.
+            Ey_sc_n = 0.
+        return Ex_sc_n, Ey_sc_n
+
+class _PyPIC_Scatter_Gather(_Proxy_v103):
+    ''' Wrapper which can be used in the PyHEADTAIL TransverseEfield_map
+    The initializer has to take xg, yg
+    Internally Dh, x_aper and y_aper get computed and a FFT poissonsolver
+    is instantiated (which takes care of the mesh/.. creation
+    '''
+    def __init__(self, xg, yg):
+        Dh = xg[1]-xg[0]
+        x_aper = max(xg) - 5.*Dh
+        y_aper = max(yg) - 4.*Dh
+        poissonsolver = FFT.FFT_OpenBoundary_SquareGrid(x_aper, y_aper, Dh,
+                                                        fftlib='pyfftw',
+                                                        ext_boundary=True)
+        super(_PyPIC_Scatter_Gather, self).__init__(poissonsolver)
+
+
+class _FiniteDifferences_Staircase_SquareGrid(_Proxy_v103):
+    '''
+    Wrapper for the FiniteDifferences_Staircase_SquareGrid class v1.0.3
+    Provides the same functionality and interface
+    '''
+    def __init__(self, chamb, Dh, sparse_solver='scipy_slu'):
+        poissonsolver = FD.FiniteDifferences_Staircase_SquareGrid(
+                chamb=chamb, Dh=Dh, sparse_solver=sparse_solver,
+                ext_boundary=True)
+        super(_FiniteDifferences_Staircase_SquareGrid,
+                self).__init__(poissonsolver)
+
+
+class _FiniteDifferences_ShortleyWeller_SquareGrid(_Proxy_v103):
+    '''
+    Wrapper for the FiniteDifferences_ShortleyWeller_SquareGrid class v1.0.3
+    Provides the same functionality and interface
+    '''
+    def __init__(self, chamb, Dh, sparse_solver='scipy_slu'):
+        poissonsolver = FD.FiniteDifferences_ShortleyWeller_SquareGrid(
+                chamb=chamb, Dh=Dh, sparse_solver=sparse_solver,
+                ext_boundary=True)
+        super(_FiniteDifferences_ShortleyWeller_SquareGrid,
+                self).__init__(poissonsolver)
+
+
+class _FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation(_Proxy_v103):
+    '''
+    Wrapper for the FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation
+    class v1.0.3
+    Provides the same functionality and interface
+    '''
+    def __init__(self, chamb, Dh, sparse_solver='scipy_slu'):
+        poissonsolver = FD.FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation(
+                chamb=chamb, Dh=Dh, sparse_solver=sparse_solver)
+        super(_FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation,
+                self).__init__(poissonsolver)
+
+
+class _FFT_OpenBoundary_SquareGrid(_Proxy_v103):
+    '''
+    Wrapper for the FFT_OpenBoundary_SquareGrid class v1.0.3
+    Provides the same functionality and interface
+    '''
+    def __init__(self, x_aper, y_aper, Dh, fftlib='pyfftw'):
+        poissonsolver = FFT.FFT_OpenBoundary_SquareGrid(x_aper=x_aper,
+                                                        y_aper=y_aper,
+                                                        Dh=Dh,
+                                                        fftlib=fftlib,
+                                                        ext_boundary=True)
+        super(_FFT_OpenBoundary_SquareGrid, self).__init__(poissonsolver)
+        self.fgreen = poissonsolver.fgreen
+        self.fgreentr = poissonsolver.fgreentr
+        self.nx = len(self.xg)
+        self.ny = len(self.yg)
+        self.fft2 = poissonsolver.fft2
+
+class _FFT_PEC_Boundary_SquareGrid(_Proxy_v103):
+    '''
+    Wrapper for the FFT_PEC_Boundary_SquareGrid class v1.0.3
+    Provides the same functionality and interface
+    '''
+    def __init__(self, x_aper, y_aper, Dh, fftlib='pyfftw'):
+        poissonsolver = FFT.FFT_PEC_Boundary_SquareGrid(x_aper=x_aper,
+                                                        y_aper=y_aper,
+                                                        Dh=Dh,
+                                                        fftlib=fftlib,
+                                                        ext_boundary=True)
+        super(_FFT_PEC_Boundary_SquareGrid, self).__init__(poissonsolver)
+
+''' @author Stefan... '''
+# this is where the magic happens: create new modules
+PyPIC_Scatter_Gather = imp.new_module('PyPIC_Scatter_Gather')
+FFT_OpenBoundary_SquareGrid = imp.new_module('FFT_OpenBoundary_SquareGrid')
+FFT_PEC_Boundary_SquareGrid = imp.new_module('FFT_PEC_Boundary_SquareGrid')
+FiniteDifferences_ShortleyWeller_SquareGrid = imp.new_module('FiniteDifferences_Shortleyweller_SquareGrid')
+FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation = imp.new_module('FiniteDifferences_Shortleyweller_SquareGrid_extrapolation')
+FiniteDifferences_Staircase_SquareGrid = imp.new_module('FiniteDifferences_Staircase_SquareGrid')
+
+# bind the classes to the correct names inside the modules
+PyPIC_Scatter_Gather.PyPIC_Scatter_Gather = _PyPIC_Scatter_Gather
+FFT_OpenBoundary_SquareGrid.FFT_OpenBoundary_SquareGrid = _FFT_OpenBoundary_SquareGrid
+FFT_PEC_Boundary_SquareGrid.FFT_PEC_Boundary_SquareGrid = _FFT_PEC_Boundary_SquareGrid
+FiniteDifferences_ShortleyWeller_SquareGrid.FiniteDifferences_ShortleyWeller_SquareGrid = _FiniteDifferences_ShortleyWeller_SquareGrid
+FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation.FiniteDifferences_ShortleyWeller_SquareGrid = _FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation
+FiniteDifferences_Staircase_SquareGrid.FiniteDifferences_Staircase_SquareGrid = _FiniteDifferences_Staircase_SquareGrid
+
+# add the modules to sys.modules to make statements like
+# 'from FFT_PEC_Boundary_SquareGrid import FFT_PEC_Boundary_Squaregrid' valid
+sys.modules['PyPIC_Scatter_Gather'] = PyPIC_Scatter_Gather
+sys.modules['FFT_OpenBoundary_SquareGrid'] = FFT_OpenBoundary_SquareGrid
+sys.modules['FFT_PEC_Boundary_SquareGrid'] = FFT_PEC_Boundary_SquareGrid
+sys.modules['FiniteDifferences_ShortleyWeller_SquareGrid'] = FiniteDifferences_ShortleyWeller_SquareGrid
+sys.modules['FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation'] = FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation
+sys.modules['FiniteDifferences_Staircase_SquareGrid'] = FiniteDifferences_Staircase_SquareGrid
+
+# add to sys.modules to make import PyPIC.[solver] statements possible
+current_module = __import__(__name__)
+setattr(current_module,'FiniteDifferences_Staircase_SquareGrid', FiniteDifferences_Staircase_SquareGrid)
+setattr(current_module,'FiniteDifferences_ShortleyWeller_SquareGrid', FiniteDifferences_ShortleyWeller_SquareGrid)
+setattr(current_module,'FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation', FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation)
+setattr(current_module,'FFT_OpenBoundary_SquareGrid', FFT_OpenBoundary_SquareGrid)
+setattr(current_module,'FFT_PEC_Boundary_SquareGrid', FFT_PEC_Boundary_SquareGrid)
+setattr(current_module,'PyPIC_Scatter_Gather' , PyPIC_Scatter_Gather )
+sys.modules['PyPIC.FiniteDifferences_Staircase_SquareGrid'] = FiniteDifferences_Staircase_SquareGrid
+sys.modules['PyPIC.FiniteDifferences_ShortleyWeller_SquareGrid'] = FiniteDifferences_ShortleyWeller_SquareGrid
+sys.modules['PyPIC.FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation'] = FiniteDifferences_ShortleyWeller_SquareGrid_extrapolation
+sys.modules['PyPIC.FFT_OpenBoundary_SquareGrid'] = FFT_OpenBoundary_SquareGrid
+sys.modules['PyPIC.FFT_PEC_Boundary_SquareGrid'] = FFT_PEC_Boundary_SquareGrid
+sys.modules['PyPIC.PyPIC_Scatter_Gather'] = PyPIC_Scatter_Gather