def save_moving_window_coordinates(path, frame):
s = "%2.2i" % frame # conversion to 2-character-long-string
file_name = "Bdenout" + s + ".bin"
matrix, x, y, z = read_ALaDyn_bin(path, file_name, "grid")
# --- axis coordinates of the moving window ---#
print "saving moving window axes"
np.savetxt(os.path.join(path, "data", "axes", ("x_" + ("%2.2i" % frame) + ".dat")), x, fmt="%15.14e")
np.savetxt(os.path.join(path, "data", "axes", ("y_" + ("%2.2i" % frame) + ".dat")), y, fmt="%15.14e")
np.savetxt(os.path.join(path, "data", "axes", ("z_" + ("%2.2i" % frame) + ".dat")), z, fmt="%15.14e")
def save_moving_window_coordinates(path,frame):
s='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Bdenout'+s+'.bin'
matrix, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#--- axis coordinates of the moving window ---#
print 'saving moving window axes'
np.savetxt( os.path.join(path,'data','Moving_window_axes',('moving_window_x_axis_'+('%2.2i'%frame)+'.dat')) ,x,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','Moving_window_axes',('moving_window_y_axis_'+('%2.2i'%frame)+'.dat')) ,y,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','Moving_window_axes',('moving_window_z_axis_'+('%2.2i'%frame)+'.dat')) ,z,fmt='%15.14e')
def save_moving_window_coordinates(path, frame):
s = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Bdenout' + s + '.bin'
matrix, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#--- axis coordinates of the moving window ---#
print('saving moving window axes')
np.savetxt(os.path.join(path, 'data', 'axes',
('x_' + ('%2.2i' % frame) + '.dat')),
x,
fmt='%15.14e')
np.savetxt(os.path.join(path, 'data', 'axes',
('y_' + ('%2.2i' % frame) + '.dat')),
y,
fmt='%15.14e')
np.savetxt(os.path.join(path, 'data', 'axes',
('z_' + ('%2.2i' % frame) + '.dat')),
z,
fmt='%15.14e')
def write_vts(path,frame,X,Y,Z,cell_cut):
# for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ):
# write_VTS(path,i)
sf='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Bdenout'+sf+'.bin'
rhobunch, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rhobunch = np.abs( rhobunch )
file_name = 'Edenout'+sf+'.bin'
rhobck, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rhobck = np.abs( rhobck )
#- matrix shaving
if cell_cut > 0:
rhobunch = rhobunch[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
rhobck = rhobck[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = rhobunch.shape
#-
#- writing vts header
f = open(os.path.join(path,'VTS_files','ALaDyn_output_'+sf+'.vts'),'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#--- ---#
#- generating vector-MESH
mesh=[]
for i in range(0,size[0]):
for j in range(0,size[1]):
for k in range(0,size[2]):
mesh.append( Y[j] )
mesh.append( Z[k] )
mesh.append( X[i] )
#- Writing MESH -#
f.write('<Points> \n')
f.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f.write( s )
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
# f.write('<CellData> \n')
#- -#
#- Writing BUNCH Density -#
f.write('<DataArray type="Float32" Name="rho_bunch" format="binary"> \n')
mesh = matrix2vector( rhobunch )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Writing Tot-Density -#
f.write('<DataArray type="Float32" Name="rho" format="binary"> \n')
mesh = matrix2vector( rhobunch+rhobck )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
rhobunch = [0.]; rhobck = [0.]
#- Writing E-field -#
#- background -#
file_name = 'Exfout'+sf+'.bin'
Ex, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eyfout'+sf+'.bin'
Ey, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezfout'+sf+'.bin'
Ez, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- bunch(es) -#
file_name = 'Exbout'+sf+'.bin'
Exb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+sf+'.bin'
Eyb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezbout'+sf+'.bin'
Ezb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Ex = Ex[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Ey = Ey[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Ez = Ez[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Exb = Exb[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Eyb = Eyb[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Ezb = Ezb[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
#-
#- E-field bunch
f.write('<DataArray type="Float32" Name="E_bunch" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Exb,Eyb,Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- E-field total
f.write('<DataArray type="Float32" Name="E" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Ex+Exb,Ey+Eyb,Ez+Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Ex=[0.];Ey=[0.];Ez=[0.];Exb=[0.];Eyb=[0.];Ezb=[0.];
#- Writing B-field -#
#- background -#
file_name = 'Bxfout'+sf+'.bin'
Bx, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Byfout'+sf+'.bin'
By, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Bzfout'+sf+'.bin'
Bz, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# #- bunch(es) -#
# file_name = 'Bxbout'+sf+'.bin'
# Bxb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bybout'+sf+'.bin'
# Byb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bzbout'+sf+'.bin'
# Bzb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Bx = Bx[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
By = By[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Bz = Bz[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
#-
#- B-field bunch
# f.write('<DataArray type="Float32" Name="B_bunch" NumberOfComponents="3" format="binary"> \n')
# mesh = matrix2vectorField(Bxb,Byb,Bzb)
# s = base64.b64encode(np.array(mesh,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# f.write('</DataArray> \n')
#- B-field total
f.write('<DataArray type="Float32" Name="B" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Bx,By,Bz)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Bx=[0.];By=[0.];Bz=[0.];#Bxb=[0.];Byb=[0.];Bzb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
# f.write('</CellData> \n')
#- -#
# frame = 0
# s='%2.2i'%frame #conversion to 2-character-long-string
# file_name = 'Bdenout'+s+'.bin'
# matrix, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# # file_name = 'Edenout'+s+'.bin'
# # matrix2, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# #- cut & sign
# matrix = np.abs( matrix )
# # matrix2 = np.abs( matrix2 )
# size = matrix.shape
#- writing vts header
# f = open('test.vts','w+')
# f.write('<?xml version="1.0"?>' + '\n')
# f.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
# f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1],0,size[0],0,size[2]) )
# f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1],0,size[0],0,size[2]) )
# f.write('<Points> \n')
# f.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
# buffer=[]
# for i in range(1,NI+2):
# for j in range(1,NJ+2):
# for k in range(1,NK+2):
# buffer.append(1./float(NJ)*(float(j)-1.))
# buffer.append(1./float(NI)*(float(i)-1.))
# buffer.append(1./float(NK)*(float(k)-1.))
#
# s = base64.b64encode(np.array(buffer,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# f.write('</DataArray> \n')
# f.write('</Points> \n')
# f.write('<PointData>\n')
# f.write('<DataArray type="Float32" Name="rhoEdge" format="binary"> \n')
# buffer=[]
# n=0
# for i in range(0,NI+1):
# for j in range(0,NJ+1):
# for k in range(0,NK+1):
# buffer.append(n*1.)
# n+=1
#
# s = base64.b64encode(np.array(buffer,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# # for item in buffer:
# # f.write(str(item)+'\n')
# f.write('</DataArray> \n')
# f.write('</PointData> \n')
# f.write('<CellData> \n')
# f.write('<DataArray type="Float32" Name="rho" format="ascii"> \n')
#
# buffer=[]
# n=0
# for i in range(0,NI):
# for j in range(0,NJ):
# for k in range(0,NK):
# buffer.append(str(n*1.))
# n+=1
#
# for item in buffer:
# f.write(str(item)+'\n')
#
# f.write('</DataArray> \n')
# f.write('</CellData> \n')
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
def write_density_vts(path,frame,X,Y,Z,cell_cut):
sf='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Bdenout'+sf+'.bin'
rhobunch, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rhobunch = np.abs( rhobunch )
file_name = 'Edenout'+sf+'.bin'
rhobck, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rhobck = np.abs( rhobck )
#- matrix shaving
if cell_cut > 0:
rhobunch = rhobunch[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
rhobck = rhobck[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = rhobunch.shape
#-
#- writing vts header
#total
f_total = open(os.path.join(path,'VTS_files','ALaDyn_rho_'+sf+'.vts'),'w+')
f_total.write('<?xml version="1.0"?>' + '\n')
f_total.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f_total.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
f_total.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#bunch(es)
f_bunch = open(os.path.join(path,'VTS_files','ALaDyn_rho_bunch_'+sf+'.vts'),'w+')
f_bunch.write('<?xml version="1.0"?>' + '\n')
f_bunch.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f_bunch.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
f_bunch.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#background
f_bck = open(os.path.join(path,'VTS_files','ALaDyn_rho_bck_'+sf+'.vts'),'w+')
f_bck.write('<?xml version="1.0"?>' + '\n')
f_bck.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f_bck.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
f_bck.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#--- ---#
#- generating vector-MESH
mesh=[]
for i in range(0,size[0]):
for j in range(0,size[1]):
for k in range(0,size[2]):
mesh.append( Y[j] )
mesh.append( Z[k] )
mesh.append( X[i] )
#- Writing MESH -#
#it's the same for the whole 3 cases
#total
f_total.write('<Points> \n')
f_total.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f_total.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f_total.write( s )
f_total.write('</DataArray> \n')
f_total.write('</Points> \n')
#bunch(es)
f_bunch.write('<Points> \n')
f_bunch.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f_bunch.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f_bunch.write( s )
f_bunch.write('</DataArray> \n')
f_bunch.write('</Points> \n')
#background
f_bck.write('<Points> \n')
f_bck.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f_bck.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f_bck.write( s )
f_bck.write('</DataArray> \n')
f_bck.write('</Points> \n')
#- -#
#- Point Data Begin-#
f_total.write('<PointData>\n')
f_bunch.write('<PointData>\n')
f_bck.write('<PointData>\n')
#- -#
#- Writing DensitIES -#
#total
f_total.write('<DataArray type="Float32" Name="rho" format="binary"> \n')
mesh = matrix2vector( rhobunch+rhobck )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f_total.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f_total.write(s)
f_total.write('</DataArray> \n')
#bunch(es)
f_bunch.write('<DataArray type="Float32" Name="rho_bunch" format="binary"> \n')
mesh = matrix2vector( rhobunch )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f_bunch.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f_bunch.write(s)
f_bunch.write('</DataArray> \n')
#background
f_bck.write('<DataArray type="Float32" Name="rho_bck" format="binary"> \n')
mesh = matrix2vector( rhobck )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f_bck.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f_bck.write(s)
f_bck.write('</DataArray> \n')
#-Deallocate memory
rhobunch = [0.]; rhobck = [0.]
#- Point Data End-#
f_total.write('</PointData> \n')
f_bunch.write('</PointData> \n')
f_bck.write('</PointData> \n')
#- -#
# --- #
f_total.write('</Piece> \n')
f_bunch.write('</Piece> \n')
f_bck.write('</Piece> \n')
f_total.write('</StructuredGrid> \n')
f_bunch.write('</StructuredGrid> \n')
f_bck.write('</StructuredGrid> \n')
f_total.write('</VTKFile>')
f_bunch.write('</VTKFile>')
f_bck.write('</VTKFile>')
def write_E_vts(path,frame,X,Y,Z,cell_cut):
# for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ):
# write_VTS(path,i)
sf='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Exfout'+sf+'.bin'
Ex, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eyfout'+sf+'.bin'
Ey, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezfout'+sf+'.bin'
Ez, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- bunch(es) -#
file_name = 'Exbout'+sf+'.bin'
Exb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+sf+'.bin'
Eyb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezbout'+sf+'.bin'
Ezb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Ex = Ex[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Ey = Ey[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Ez = Ez[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Exb = Exb[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Eyb = Eyb[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Ezb = Ezb[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = Ex.shape
#-
#- writing vts header
f = open(os.path.join(path,'VTS_files','ALaDyn_E_'+sf+'.vts'),'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#--- ---#
#- writing Ex-vts header
fEx = open(os.path.join(path,'VTS_files','ALaDyn_Ex_'+sf+'.vts'),'w+')
fEx.write('<?xml version="1.0"?>' + '\n')
fEx.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
fEx.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
fEx.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#- writing Ey-vts header
fEy = open(os.path.join(path,'VTS_files','ALaDyn_Ey_'+sf+'.vts'),'w+')
fEy.write('<?xml version="1.0"?>' + '\n')
fEy.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
fEy.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
fEy.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#- writing Ex-vts header
fEz = open(os.path.join(path,'VTS_files','ALaDyn_Ez_'+sf+'.vts'),'w+')
fEz.write('<?xml version="1.0"?>' + '\n')
fEz.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
fEz.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
fEz.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#--- ---#
#- generating vector-MESH
mesh=[]
for i in range(0,size[0]):
for j in range(0,size[1]):
for k in range(0,size[2]):
mesh.append( Y[j] )
mesh.append( Z[k] )
mesh.append( X[i] )
#- Writing MESH -#
f.write('<Points> \n')
f.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f.write( s )
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Writing ExMESH -#
fEx.write('<Points> \n')
fEx.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
fEx.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
fEx.write( s )
fEx.write('</DataArray> \n')
fEx.write('</Points> \n')
#- Writing ExMESH -#
fEy.write('<Points> \n')
fEy.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
fEy.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
fEy.write( s )
fEy.write('</DataArray> \n')
fEy.write('</Points> \n')
#- Writing ExMESH -#
fEz.write('<Points> \n')
fEz.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
fEz.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
fEz.write( s )
fEz.write('</DataArray> \n')
fEz.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
fEx.write('<PointData>\n')
fEy.write('<PointData>\n')
fEz.write('<PointData>\n')
#- -#
#- Writing E-field -#
#- E-field total
f.write('<DataArray type="Float32" Name="E" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Ex+Exb,Ey+Eyb,Ez+Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Writing Ex-field -#
fEx.write('<DataArray type="Float32" Name="Ex" NumberOfComponents="1" format="binary"> \n')
mesh = matrix2vector(Ex+Exb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
fEx.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
fEx.write(s)
fEx.write('</DataArray> \n')
#- Writing Ex-field -#
fEy.write('<DataArray type="Float32" Name="Ey" NumberOfComponents="1" format="binary"> \n')
mesh = matrix2vector(Ey+Eyb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
fEy.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
fEy.write(s)
fEy.write('</DataArray> \n')
#- Writing Ex-field -#
fEz.write('<DataArray type="Float32" Name="Ez" NumberOfComponents="1" format="binary"> \n')
mesh = matrix2vector(Ez+Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
fEz.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
fEz.write(s)
fEz.write('</DataArray> \n')
#-Deallocate memory
Ex=[0.];Ey=[0.];Ez=[0.];Exb=[0.];Eyb=[0.];Ezb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
fEx.write('</PointData> \n')
fEy.write('</PointData> \n')
fEz.write('</PointData> \n')
#- -#
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
fEx.write('</Piece> \n')
fEx.write('</StructuredGrid> \n')
fEx.write('</VTKFile>')
fEy.write('</Piece> \n')
fEy.write('</StructuredGrid> \n')
fEy.write('</VTKFile>')
fEz.write('</Piece> \n')
fEz.write('</StructuredGrid> \n')
fEz.write('</VTKFile>')
# FRAME NUMBER
frame = 6
# --- #
magnification_fig = 3.0
rho_min = 10
rho_max = 0.001
#--- *** ---#
file_name = 'Bdenout'+('%2.2i'%frame)+'.bin'
matrix, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Edenout'+('%2.2i'%frame)+'.bin'
matrix2, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#--- *** ---#
file_name = 'Exbout'+('%2.2i'%frame)+'.bin'
Ex_b, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+('%2.2i'%frame)+'.bin'
Ey_b, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezbout'+('%2.2i'%frame)+'.bin'
Ez_b, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Exfout'+('%2.2i'%frame)+'.bin'
Ex_w, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eyfout'+('%2.2i'%frame)+'.bin'
def write_vts_section_longitudinal(path, frame, X, Y, Z, cell_cut,
sliceposition_y):
sf = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Bdenout' + sf + '.bin'
rhobunch, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
rhobunch = np.abs(rhobunch)
file_name = 'Edenout' + sf + '.bin'
rhobck, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
rhobck = np.abs(rhobck)
#-original size
sizeO = rhobunch.shape
#- matrix shaving
if cell_cut > 0:
rhobunch = rhobunch[:, sizeO[1] / 2 + sliceposition_y,
cell_cut:-cell_cut]
rhobck = rhobck[:, sizeO[1] / 2 + sliceposition_y, cell_cut:-cell_cut]
Y = Y[sizeO[1] / 2 + sliceposition_y]
Z = Z[cell_cut:-cell_cut]
else:
rhobunch = rhobunch[:, sizeO[1] / 2 + sliceposition_y, :]
rhobck = rhobck[:, sizeO[1] / 2 + sliceposition_y, :]
Y = Y[sizeO[1] / 2 + sliceposition_y]
Z = Z[:]
#-
size = rhobunch.shape
#-
#- writing vts header
f = open(
os.path.join(path, 'VTS_files',
'ALaDyn_section_longitudinal_output_' + sf + '.vts'),
'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, 0, 0, size[1] - 1, 0, size[0] - 1))
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, 0, 0, size[1] - 1, 0, size[0] - 1))
#--- ---#
#- generating vector-MESH
mesh = []
for i in range(0, size[0]):
for k in range(0, size[1]):
mesh.append(Y)
mesh.append(Z[k])
mesh.append(X[i])
#- Writing MESH -#
f.write('<Points> \n')
f.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
# f.write('<CellData> \n')
#- -#
#- Writing BUNCH Density -#
f.write('<DataArray type="Float32" Name="rho_bunch" format="binary"> \n')
mesh = matrix2vector(rhobunch)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Writing Tot-Density -#
f.write('<DataArray type="Float32" Name="rho" format="binary"> \n')
mesh = matrix2vector(rhobunch + rhobck)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
rhobunch = [0.]
rhobck = [0.]
#- Writing E-field -#
#- background -#
file_name = 'Exfout' + sf + '.bin'
Ex, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Eyfout' + sf + '.bin'
Ey, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Ezfout' + sf + '.bin'
Ez, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- bunch(es) -#
file_name = 'Exbout' + sf + '.bin'
Exb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Eybout' + sf + '.bin'
Eyb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Ezbout' + sf + '.bin'
Ezb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- matrix shaving
if cell_cut > 0:
Ex = Ex[:, sizeO[1] / 2, cell_cut:-cell_cut]
Ey = Ey[:, sizeO[1] / 2, cell_cut:-cell_cut]
Ez = Ez[:, sizeO[1] / 2, cell_cut:-cell_cut]
Exb = Exb[:, sizeO[1] / 2, cell_cut:-cell_cut]
Eyb = Eyb[:, sizeO[1] / 2, cell_cut:-cell_cut]
Ezb = Ezb[:, sizeO[1] / 2, cell_cut:-cell_cut]
else:
Ex = Ex[:, sizeO[1] / 2, :]
Ey = Ey[:, sizeO[1] / 2, :]
Ez = Ez[:, sizeO[1] / 2, :]
Exb = Exb[:, sizeO[1] / 2, :]
Eyb = Eyb[:, sizeO[1] / 2, :]
Ezb = Ezb[:, sizeO[1] / 2, :]
#-
#- E-field bunch
f.write(
'<DataArray type="Float32" Name="E_bunch" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Exb, Eyb, Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- E-field total
f.write(
'<DataArray type="Float32" Name="E" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Ex + Exb, Ey + Eyb, Ez + Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Ex-total
f.write(
'<DataArray type="Float32" Name="Ex" NumberOfComponents="1" format="binary"> \n'
)
mesh = matrix2vector(Ex + Exb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Ey-total
f.write(
'<DataArray type="Float32" Name="Ey" NumberOfComponents="1" format="binary"> \n'
)
mesh = matrix2vector(Ey + Eyb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Ez-total
f.write(
'<DataArray type="Float32" Name="Ez" NumberOfComponents="1" format="binary"> \n'
)
mesh = matrix2vector(Ez + Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Ex = [0.]
Ey = [0.]
Ez = [0.]
Exb = [0.]
Eyb = [0.]
Ezb = [0.]
#- Writing B-field -#
#- background -#
file_name = 'Bxfout' + sf + '.bin'
Bx, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Byfout' + sf + '.bin'
By, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Bzfout' + sf + '.bin'
Bz, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
# #- bunch(es) -#
# file_name = 'Bxbout'+sf+'.bin'
# Bxb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bybout'+sf+'.bin'
# Byb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bzbout'+sf+'.bin'
# Bzb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Bx = Bx[:, sizeO[1] / 2, cell_cut:-cell_cut]
By = By[:, sizeO[1] / 2, cell_cut:-cell_cut]
Bz = Bz[:, sizeO[1] / 2, cell_cut:-cell_cut]
else:
Bx = Bx[:, sizeO[1] / 2, :]
By = By[:, sizeO[1] / 2, :]
Bz = Bz[:, sizeO[1] / 2, :]
#-
#- B-field bunch
# f.write('<DataArray type="Float32" Name="B_bunch" NumberOfComponents="3" format="binary"> \n')
# mesh = matrix2vectorField(Bxb,Byb,Bzb)
# s = base64.b64encode(np.array(mesh,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# f.write('</DataArray> \n')
#- B-field total
f.write(
'<DataArray type="Float32" Name="B" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Bx, By, Bz)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Bx = [0.]
By = [0.]
Bz = [0.]
#Bxb=[0.];Byb=[0.];Bzb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
# f.write('</CellData> \n')
#- -#
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
### --- ###
#--- *** ---#
path = os.getcwd()
# --- #
# FRAME NUMBER
frame = 2
# --- #
magnification_fig = 3.0
#--- *** ---#
file_name = 'Bdenout'+('%2.2i'%frame)+'.bin'
rho_b, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Edenout'+('%2.2i'%frame)+'.bin'
rho_w, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rho_b=np.abs( rho_b )
rho_w=np.abs( rho_w )
rho = rho_b+rho_w
p = rho.shape
x2=p[0]/2; y2=p[1]/2; z2=p[2]/2;
#--- *** ---#
file_name = 'Exbout'+('%2.2i'%frame)+'.bin'
Ex_b, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+('%2.2i'%frame)+'.bin'
path = os.getcwd()
#-folder output structure
generate_folder_output_structure(path,'True')
for i in range(frame_begin,frame_end+1):
print '-------------------'
s='%2.2i'%i
path_read = os.path.join(path,'%4.4i'%i)
path_write = path
print path_read
if output_exists(path_read,'rho',i) == True:
print 'n_bunch --- frame >>> ',i
n_bunch,ax1,ax2,ax3 = read_ALaDyn_bin(path_read,'Bdenout'+s+'.bin','grid')
print 'n_bck --- frame >>> ',i
n_bck,ax4,ax5,ax6 = read_ALaDyn_bin(path_read,'Edenout'+s+'.bin','grid')
print 'jx_bunch --- frame >>> ',i
jx_bunch,ax7,ax8,ax9= read_ALaDyn_bin(path_read,'Jxbout'+s+'.bin','grid')
print 'jx_bck --- frame >>> ',i
jx_bck,ax7,ax8,ax9 = read_ALaDyn_bin(path_read,'Jxfout'+s+'.bin','grid')
n = n_bunch + n_bck
jx = jx_bunch + jx_bck
#variable declaration
[nx,ny,nz]=n_bck.shape
xmin = min(ax1)
def plot_Bfield_sections(path,frame,scale_factor,sliceposition_x,sliceposition_y,sliceposition_z,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
#- background -#
file_name = 'Bxfout'+s+'.bin'
Bx, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Byfout'+s+'.bin'
By, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Bzfout'+s+'.bin'
Bz, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- bunch(es) -#
file_name = 'Bxbout'+s+'.bin'
Bxb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Bybout'+s+'.bin'
Byb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Bzbout'+s+'.bin'
Bzb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#-sum-#
Bx = Bx+Bxb
By = By+Byb
Bz = Bz+Bzb
p = Bx.shape
x2=p[0]/2; y2=p[1]/2; z2=p[2]/2;
sizeX, sizeZ = figure_dimension_inch(x,y,z,scale_factor)
#- Bx_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Bx[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Bx_XY_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- By_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,By[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'By_XY_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- Bz_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Bz[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Bz_XY_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- Bx_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Bx[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Bx_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- By_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,By[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'By_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- Bz_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Bz[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Bz_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
# #- Bx_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Bx[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Bx_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','B_field',name_output) )
# close(fig)
# #- By_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,By[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'By_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','B_field',name_output) )
# close(fig)
# #- Bz_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Bz[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Bz_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','B_field',name_output) )
# close(fig)
#- norm(B) -#
norm_B = np.power( np.power(Bx,2)+np.power(By,2)+np.power(Bz,2) , 0.5 )
#- norm_E_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,norm_B[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'B_XY_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- norm_E_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,norm_B[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'B_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
#- norm_E_YZ -#
fig = figure(1, figsize=(sizeZ, sizeZ))
contourf(y,z,norm_B[x2,:,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'B_YZ_'+s+'.png'
savefig( os.path.join(path,'plots','B_field',name_output) )
close(fig)
if (savedata == 'True'):
print 'saving E field data'
#--- saves E-sections data---#
np.savetxt( os.path.join(path,'plots','B_field',('Bx_z0_section_'+('%2.2i'%frame)+'.dat')) ,Bx[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'plots','B_field',('By_z0_section_'+('%2.2i'%frame)+'.dat')) ,By[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'plots','B_field',('Bz_z0_section_'+('%2.2i'%frame)+'.dat')) ,Bz[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'plots','B_field',('B_z0_section_'+('%2.2i'%frame)+'.dat')) ,norm_B[:,:,z2].T,fmt='%15.14e')
def plot_ionization_profile(path,frame,min_ionization_rate,max_ionzation_rate,isolines,celltocut,sliceposition_x,sliceposition_y,sliceposition_z,magnification_fig,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
# file_name = 'Elpout'+s+'.bin'
file_name = 'H1dnout'+s+'.bin'
matrix, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- cut & sign
matrix = np.abs( matrix )
#---cut edges---#
if celltocut > 0:
matrix = matrix[:,celltocut:-celltocut,celltocut:-celltocut]
y = y[celltocut:-celltocut]
z = z[celltocut:-celltocut]
p = matrix.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
sizeX, sizeZ = figure_dimension_inch(x,y,z,magnification_fig)
# levs_lin = np.linspace( rho_min , rho_max ,isolines)
# levs_lin = np.insert(levs_lin,0,np.min([np.min(matrix),np.min(matrix2)]))
# levs_lin = np.insert(levs_lin,len(levs_lin),np.min([np.max(matrix),np.max(matrix2)]))
# levs_log = np.logspace(log10(rho_min),log10(rho_max),isolines)
#--------------------#
#--- Linear plots ---#
#--------------------#
#- Plot Bdenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_XY_lin_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_XZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix2[:,:,z2].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_XY_lin_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix2[:,y2,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_XZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T + matrix2[:,:,z2].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_XY_lin_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T + matrix2[:,y2,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_XZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T - matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#--------------------#
#--- Log plots ---#
#--------------------#
#- Plot Bdenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_XY_log_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T,levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_XZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix2[:,:,z2].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_XY_log_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix2[:,y2,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_XZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T + matrix2[:,:,z2].T,levs_log , norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_XY_log_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T + matrix2[:,y2,:].T,levs_log , norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_XZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T + matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#----- Save density sections data -----#
if (savedata == 'True'):
print('saving ionization data')
ionization_map = matrix
ionization_map=np.abs( ionization_map )
p = ionization_map.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
np.savetxt( os.path.join(path,'data','ionization',('ionization_profile_'+('%2.2i'%frame)+'.dat')),ionization_map[:,:,z2].T,fmt='%15.14e')
### --- ###
sys.path.append(
os.path.join(os.path.expanduser('~'), 'Codes', 'Code_ALaDyn',
'tools-ALaDyn', 'pythons'))
from read_ALaDyn_bin import *
### --- ###
#FLAGS
plotDensitySlice = 0
plotDephasingMap = 0
plotInterferogram = 1
# - #
#LOAD FILE
bin_path = 'C:/Users/Fil/Codes/synthetic_diagnostics'
n, x, y, z = read_ALaDyn_bin(bin_path, 'Edenout10.bin', 'grid')
n_0 = 1E19 #CHIEDI ALBERTO NOME IN ALADYN
n = n * n_0
#FUNDAMENTAL CONSTANTS
c = 299792458 #[m/s]
e = 1.60219E-19 # elementary charge [C]
me = 9.1091E-31
# electron rest mass [kg]
eps0 = 8.854187817e-12
#[F/m]
#CCD
#CCD_x=659
#CCD_z=494
recording_bit = 16
def write_B_vts(path,frame,X,Y,Z,cell_cut):
# for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ):
# write_VTS(path,i)
sf='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Bxfout'+sf+'.bin'
Bx, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Byfout'+sf+'.bin'
By, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Bzfout'+sf+'.bin'
Bz, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
size = Bx.shape
#- matrix shaving
if cell_cut > 0:
Bx = Bx[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
By = By[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Bz = Bz[:,cell_cut:-cell_cut,cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = Bx.shape
#-
#- writing vts header
f = open(os.path.join(path,'VTS_files','ALaDyn_B_'+sf+'.vts'),'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1]-1,0,size[2]-1,0,size[0]-1) )
#--- ---#
#- generating vector-MESH
mesh=[]
for i in range(0,size[0]):
for j in range(0,size[1]):
for k in range(0,size[2]):
mesh.append( Y[j] )
mesh.append( Z[k] )
mesh.append( X[i] )
#- Writing MESH -#
f.write('<Points> \n')
f.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f.write( s )
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
#- -#
#- Writing B-field -#
f.write('<DataArray type="Float32" Name="B" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Bx,By,Bz)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Bx=[0.];By=[0.];Bz=[0.];#Bxb=[0.];Byb=[0.];Bzb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
#- -#
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
#--- *** ---# if __name__ == '__main__': #-path path = os.getcwd() #-folder output structure generate_folder_vts(path) # write_vts(path,2) frame =0; s='%2.2i'%frame rhobunch, X,Y,Z = read_ALaDyn_bin(path,'Bdenout'+s+'.bin','grid') print '--- Generating VTS ---' for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ): # print '--- COMPLETE vts: frame >',i # write_vts(path,i,X,Y,Z,cell_cut) print '--- write vts-section longitudinal: frame >',i write_vts_section_longitudinal(path,i,X,Y,Z,cell_cut,sliceposition_y) #- in such a way it is much longer, but it is neater to write #- plus: it has to be done only once print '--- density only vts: frame >',i write_density_vts(path,i,X,Y,Z,cell_cut) print '--- E-field only vts: frame >',i
def plot_Efield_sections(path,frame,scale_factor,sliceposition_x,sliceposition_y,sliceposition_z,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
#- background -#
file_name = 'Exfout'+s+'.bin'
Ex, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eyfout'+s+'.bin'
Ey, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezfout'+s+'.bin'
Ez, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- bunch(es) -#
file_name = 'Exbout'+s+'.bin'
Exb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+s+'.bin'
Eyb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezbout'+s+'.bin'
Ezb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#-sum-#
Ex = Ex+Exb
Ey = Ey+Eyb
Ez = Ez+Ezb
p = Ex.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
sizeX, sizeZ = figure_dimension_inch(x,y,z,scale_factor)
#- Ex_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Ex[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ex_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ey_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Ey[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ey_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ez_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Ez[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ez_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ex_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Ex[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ex_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ey_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Ey[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ey_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ez_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Ez[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ez_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
# #- Ex_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Ex[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Ex_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','E_field',name_output) )
# close(fig)
# #- Ey_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Ey[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Ey_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','E_field',name_output) )
# close(fig)
# #- Ez_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Ez[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Ez_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','E_field',name_output) )
# close(fig)
#- norm(E) -#
norm_E = np.power( np.power(Ex,2)+np.power(Ey,2)+np.power(Ez,2) , 0.5 )
#- norm_E_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,norm_E[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'E_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- norm_E_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,norm_E[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'E_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- norm_E_YZ -#
fig = figure(1, figsize=(sizeZ, sizeZ))
contourf(y,z,norm_E[x2,:,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'E_YZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
if (savedata == 'True'):
print 'saving E field data'
#--- saves E-sections ---#
np.savetxt( os.path.join(path,'data','E_field',('Ex_z0_section_'+('%2.2i'%frame)+'.dat' )),Ex[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','E_field',('Ey_z0_section_'+('%2.2i'%frame)+'.dat' )),Ey[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','E_field',('Ez_z0_section_'+('%2.2i'%frame)+'.dat' )),Ez[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','E_field',('E_z0_section_'+('%2.2i'%frame)+'.dat' )),norm_E[:,:,z2].T,fmt='%15.14e')
def plot_energy_density_sections(path,frame,Energy_density_min,Energy_density_max,isolines,celltocut,sliceposition_x,sliceposition_y,sliceposition_z,magnification_fig,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Elenout'+s+'.bin'
matrix3, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- cut & sign
matrix3 = np.abs( matrix3 )
print 'Energy_density_max >>', np.max([np.max(matrix3)])
print 'Energy_density_min >>', np.min([np.min(matrix3)])
#---cut edges---#
if celltocut > 0:
matrix3 = matrix3[:,celltocut:-celltocut,celltocut:-celltocut]
y = y[celltocut:-celltocut]
z = z[celltocut:-celltocut]
p = matrix3.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
sizeX, sizeZ = figure_dimension_inch(x,y,z,magnification_fig)
levs_lin = np.linspace( Energy_density_min , Energy_density_max ,isolines)
levs_log = np.logspace(log10(Energy_density_min),log10(Energy_density_max),isolines)
#--------------------#
#--- Linear plots ---#
#--------------------#
#- Plot Elenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix3[:,:,z2].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'Energy_density_XY_lin_'+s+'.png'
savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix3[:,y2,:].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'Energy_density_XZ_lin_'+s+'.png'
fig.savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
#--------------------#
#--- Log plots ---#
#--------------------#
#- Plot Elenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix3[:,:,z2].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'Energy_density_XY_log_'+s+'.png'
savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix3[:,y2,:].T,levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'Energy_density_XZ_log_'+s+'.png'
fig.savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#----- Save density sections data -----#
if (savedata == 'True'):
print 'saving Energy_density data'
Energy_density = matrix3
p = Energy_density.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
np.savetxt( os.path.join(path,'data','Energy_density',('Energy_Density'+('%2.2i'%frame)+'.dat')),Energy_density[:,:,z2].T,fmt='%15.14e')
def plot_Efield_sections(path,frame,scale_factor,sliceposition_x,sliceposition_y,sliceposition_z,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
#- background -#
file_name = 'Exfout'+s+'.bin'
Ex, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eyfout'+s+'.bin'
Ey, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezfout'+s+'.bin'
Ez, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- bunch(es) -#
file_name = 'Exbout'+s+'.bin'
Exb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+s+'.bin'
Eyb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezbout'+s+'.bin'
Ezb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#-sum-#
Ex = Ex+Exb
Ey = Ey+Eyb
Ez = Ez+Ezb
p = Ex.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
sizeX, sizeZ = figure_dimension_inch(x,y,z,scale_factor)
#- Ex_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Ex[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ex_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ey_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Ey[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ey_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ez_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,Ez[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ez_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ex_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Ex[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ex_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ey_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Ey[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ey_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- Ez_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,Ez[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'Ez_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
# #- Ex_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Ex[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Ex_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','E_field',name_output) )
# close(fig)
# #- Ey_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Ey[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Ey_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','E_field',name_output) )
# close(fig)
# #- Ez_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Ez[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Ez_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','E_field',name_output) )
# close(fig)
#- norm(E) -#
norm_E = np.power( np.power(Ex,2)+np.power(Ey,2)+np.power(Ez,2) , 0.5 )
#- norm_E_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,norm_E[:,:,z2].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'E_XY_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- norm_E_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,norm_E[:,y2,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'E_XZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
#- norm_E_YZ -#
fig = figure(1, figsize=(sizeZ, sizeZ))
contourf(y,z,norm_E[x2,:,:].T,100, linewidths = 0.00001)
axis('tight')
name_output = 'E_YZ_'+s+'.png'
savefig( os.path.join(path,'plots','E_field',name_output) )
close(fig)
if (savedata == 'True'):
print('saving E field data')
#--- saves E-sections ---#
np.savetxt( os.path.join(path,'data','E_field',('Ex_z0_section_'+('%2.2i'%frame)+'.dat' )),Ex[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','E_field',('Ey_z0_section_'+('%2.2i'%frame)+'.dat' )),Ey[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','E_field',('Ez_z0_section_'+('%2.2i'%frame)+'.dat' )),Ez[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','E_field',('E_z0_section_'+('%2.2i'%frame)+'.dat' )),norm_E[:,:,z2].T,fmt='%15.14e')
path = os.getcwd()
#-folder output structure
generate_folder_output_structure(path, 'True')
for i in range(frame_begin, frame_end + 1):
print '-------------------'
s = '%2.2i' % i
path_read = os.path.join(path, '%4.4i' % i)
path_write = path
print path_read
if output_exists(path_read, 'rho', i) == True:
print 'n_bunch --- frame >>> ', i
n_bunch, ax1, ax2, ax3 = read_ALaDyn_bin(path_read,
'Bdenout' + s + '.bin',
'grid')
print 'n_bck --- frame >>> ', i
n_bck, ax4, ax5, ax6 = read_ALaDyn_bin(path_read,
'Edenout' + s + '.bin', 'grid')
print 'jx_bunch --- frame >>> ', i
jx_bunch, ax7, ax8, ax9 = read_ALaDyn_bin(path_read,
'Jxbout' + s + '.bin',
'grid')
print 'jx_bck --- frame >>> ', i
jx_bck, ax7, ax8, ax9 = read_ALaDyn_bin(path_read,
'Jxfout' + s + '.bin', 'grid')
n = n_bunch + n_bck
jx = jx_bunch + jx_bck
def write_vts_section_longitudinal(path,frame,X,Y,Z,cell_cut,sliceposition_y):
sf='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Bdenout'+sf+'.bin'
rhobunch, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rhobunch = np.abs( rhobunch )
file_name = 'Edenout'+sf+'.bin'
rhobck, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
rhobck = np.abs( rhobck )
#-original size
sizeO = rhobunch.shape
#- matrix shaving
if cell_cut > 0:
rhobunch = rhobunch[:, sizeO[1]/2+sliceposition_y, cell_cut:-cell_cut]
rhobck = rhobck[:, sizeO[1]/2+sliceposition_y, cell_cut:-cell_cut]
Y = Y[ sizeO[1]/2+sliceposition_y ]
Z = Z[cell_cut:-cell_cut]
else:
rhobunch = rhobunch[:, sizeO[1]/2+sliceposition_y,:]
rhobck = rhobck[:, sizeO[1]/2+sliceposition_y,:]
Y = Y[ sizeO[1]/2+sliceposition_y ]
Z = Z[:]
#-
size = rhobunch.shape
#-
#- writing vts header
f = open(os.path.join(path,'VTS_files','ALaDyn_section_longitudinal_output_'+sf+'.vts'),'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,0,0,size[1]-1,0,size[0]-1) )
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,0,0,size[1]-1,0,size[0]-1) )
#--- ---#
#- generating vector-MESH
mesh=[]
for i in range(0,size[0]):
for k in range(0,size[1]):
mesh.append( Y )
mesh.append( Z[k] )
mesh.append( X[i] )
#- Writing MESH -#
f.write('<Points> \n')
f.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write( base64.b64encode(np.array(len(s),dtype=np.int32)) )
f.write( s )
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
# f.write('<CellData> \n')
#- -#
#- Writing BUNCH Density -#
f.write('<DataArray type="Float32" Name="rho_bunch" format="binary"> \n')
mesh = matrix2vector( rhobunch )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Writing Tot-Density -#
f.write('<DataArray type="Float32" Name="rho" format="binary"> \n')
mesh = matrix2vector( rhobunch+rhobck )
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
rhobunch = [0.]; rhobck = [0.]
#- Writing E-field -#
#- background -#
file_name = 'Exfout'+sf+'.bin'
Ex, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eyfout'+sf+'.bin'
Ey, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezfout'+sf+'.bin'
Ez, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- bunch(es) -#
file_name = 'Exbout'+sf+'.bin'
Exb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Eybout'+sf+'.bin'
Eyb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Ezbout'+sf+'.bin'
Ezb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Ex = Ex[:,sizeO[1]/2,cell_cut:-cell_cut]
Ey = Ey[:,sizeO[1]/2,cell_cut:-cell_cut]
Ez = Ez[:,sizeO[1]/2,cell_cut:-cell_cut]
Exb = Exb[:,sizeO[1]/2,cell_cut:-cell_cut]
Eyb = Eyb[:,sizeO[1]/2,cell_cut:-cell_cut]
Ezb = Ezb[:,sizeO[1]/2,cell_cut:-cell_cut]
else:
Ex = Ex[:,sizeO[1]/2,:]
Ey = Ey[:,sizeO[1]/2,:]
Ez = Ez[:,sizeO[1]/2,:]
Exb = Exb[:,sizeO[1]/2,:]
Eyb = Eyb[:,sizeO[1]/2,:]
Ezb = Ezb[:,sizeO[1]/2,:]
#-
#- E-field bunch
f.write('<DataArray type="Float32" Name="E_bunch" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Exb,Eyb,Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- E-field total
f.write('<DataArray type="Float32" Name="E" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Ex+Exb,Ey+Eyb,Ez+Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Ex-total
f.write('<DataArray type="Float32" Name="Ex" NumberOfComponents="1" format="binary"> \n')
mesh = matrix2vector(Ex+Exb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Ey-total
f.write('<DataArray type="Float32" Name="Ey" NumberOfComponents="1" format="binary"> \n')
mesh = matrix2vector(Ey+Eyb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Ez-total
f.write('<DataArray type="Float32" Name="Ez" NumberOfComponents="1" format="binary"> \n')
mesh = matrix2vector(Ez+Ezb)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Ex=[0.];Ey=[0.];Ez=[0.];Exb=[0.];Eyb=[0.];Ezb=[0.];
#- Writing B-field -#
#- background -#
file_name = 'Bxfout'+sf+'.bin'
Bx, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Byfout'+sf+'.bin'
By, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Bzfout'+sf+'.bin'
Bz, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# #- bunch(es) -#
# file_name = 'Bxbout'+sf+'.bin'
# Bxb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bybout'+sf+'.bin'
# Byb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bzbout'+sf+'.bin'
# Bzb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Bx = Bx[:,sizeO[1]/2,cell_cut:-cell_cut]
By = By[:,sizeO[1]/2,cell_cut:-cell_cut]
Bz = Bz[:,sizeO[1]/2,cell_cut:-cell_cut]
else:
Bx = Bx[:,sizeO[1]/2,:]
By = By[:,sizeO[1]/2,:]
Bz = Bz[:,sizeO[1]/2,:]
#-
#- B-field bunch
# f.write('<DataArray type="Float32" Name="B_bunch" NumberOfComponents="3" format="binary"> \n')
# mesh = matrix2vectorField(Bxb,Byb,Bzb)
# s = base64.b64encode(np.array(mesh,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# f.write('</DataArray> \n')
#- B-field total
f.write('<DataArray type="Float32" Name="B" NumberOfComponents="3" format="binary"> \n')
mesh = matrix2vectorField(Bx,By,Bz)
s = base64.b64encode(np.array(mesh,dtype=np.float32))
f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Bx=[0.];By=[0.];Bz=[0.];#Bxb=[0.];Byb=[0.];Bzb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
# f.write('</CellData> \n')
#- -#
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
def plot_Bfield_sections(path, frame, scale_factor, sliceposition_x,
sliceposition_y, sliceposition_z, savedata):
s = '%2.2i' % frame #conversion to 2-character-long-string
#- background -#
file_name = 'Bxfout' + s + '.bin'
Bx, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Byfout' + s + '.bin'
By, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Bzfout' + s + '.bin'
Bz, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- bunch(es) -#
file_name = 'Bxbout' + s + '.bin'
Bxb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Bybout' + s + '.bin'
Byb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Bzbout' + s + '.bin'
Bzb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#-sum-#
Bx = Bx + Bxb
By = By + Byb
Bz = Bz + Bzb
p = Bx.shape
x2 = p[0] / 2
y2 = p[1] / 2
z2 = p[2] / 2
sizeX, sizeZ = figure_dimension_inch(x, y, z, scale_factor)
#- Bx_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, Bx[:, :, z2].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'Bx_XY_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- By_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, By[:, :, z2].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'By_XY_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- Bz_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, Bz[:, :, z2].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'Bz_XY_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- Bx_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, Bx[:, y2, :].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'Bx_XZ_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- By_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, By[:, y2, :].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'By_XZ_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- Bz_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, Bz[:, y2, :].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'Bz_XZ_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
# #- Bx_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Bx[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Bx_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','B_field',name_output) )
# close(fig)
# #- By_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,By[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'By_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','B_field',name_output) )
# close(fig)
# #- Bz_YZ -#
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,Bz[x2,:,:].T,100, linewidths = 0.00001)
# axis('tight')
# name_output = 'Bz_YZ_'+s+'.png'
# savefig( os.path.join(path,'plots','B_field',name_output) )
# close(fig)
#- norm(B) -#
norm_B = np.power(np.power(Bx, 2) + np.power(By, 2) + np.power(Bz, 2), 0.5)
#- norm_E_XY -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, norm_B[:, :, z2].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'B_XY_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- norm_E_XZ -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, norm_B[:, y2, :].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'B_XZ_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
#- norm_E_YZ -#
fig = figure(1, figsize=(sizeZ, sizeZ))
contourf(y, z, norm_B[x2, :, :].T, 100, linewidths=0.00001)
axis('tight')
name_output = 'B_YZ_' + s + '.png'
savefig(os.path.join(path, 'plots', 'B_field', name_output))
close(fig)
if (savedata == 'True'):
print('saving E field data')
#--- saves E-sections data---#
np.savetxt(os.path.join(path, 'plots', 'B_field',
('Bx_z0_section_' +
('%2.2i' % frame) + '.dat')),
Bx[:, :, z2].T,
fmt='%15.14e')
np.savetxt(os.path.join(path, 'plots', 'B_field',
('By_z0_section_' +
('%2.2i' % frame) + '.dat')),
By[:, :, z2].T,
fmt='%15.14e')
np.savetxt(os.path.join(path, 'plots', 'B_field',
('Bz_z0_section_' +
('%2.2i' % frame) + '.dat')),
Bz[:, :, z2].T,
fmt='%15.14e')
np.savetxt(os.path.join(path, 'plots', 'B_field',
('B_z0_section_' +
('%2.2i' % frame) + '.dat')),
norm_B[:, :, z2].T,
fmt='%15.14e')
def plot_density_sections(path,frame,rho_min,rho_max,isolines,celltocut,sliceposition_x,sliceposition_y,sliceposition_z,magnification_fig,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Bdenout'+s+'.bin'
matrix, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
file_name = 'Edenout'+s+'.bin'
matrix2, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- cut & sign
matrix = np.abs( matrix )
matrix2 = np.abs( matrix2 )
print 'rho-max >>', np.max([np.max(matrix),np.max(matrix2)])
print 'rho-min >>', np.min([np.min(matrix),np.min(matrix2)])
# matrix[ (matrix<rho_min) ] = rho_min
# matrix[ (matrix>rho_max) ] = rho_max
# matrix2[ (matrix2<rho_min) ] = rho_min
# matrix2[ (matrix2>rho_max) ] = rho_max
#---cut edges---#
if celltocut > 0:
matrix = matrix[:,celltocut:-celltocut,celltocut:-celltocut]
matrix2 = matrix2[:,celltocut:-celltocut,celltocut:-celltocut]
y = y[celltocut:-celltocut]
z = z[celltocut:-celltocut]
p = matrix.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
sizeX, sizeZ = figure_dimension_inch(x,y,z,magnification_fig)
levs_lin = np.linspace( rho_min , rho_max ,isolines)
# levs_lin = np.insert(levs_lin,0,np.min([np.min(matrix),np.min(matrix2)]))
# levs_lin = np.insert(levs_lin,len(levs_lin),np.min([np.max(matrix),np.max(matrix2)]))
levs_log = np.logspace(log10(rho_min),log10(rho_max),isolines)
#--------------------#
#--- Linear plots ---#
#--------------------#
#- Plot Bdenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix[:,:,z2].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'rho_Bunch_XY_lin_'+s+'.png'
savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix[:,y2,:].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'rho_Bunch_XZ_lin_'+s+'.png'
fig.savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix2[:,:,z2].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'rho_Background_XY_lin_'+s+'.png'
savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix2[:,y2,:].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'rho_Background_XZ_lin_'+s+'.png'
fig.savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix[:,:,z2].T + matrix2[:,:,z2].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'rho_tot_XY_lin_'+s+'.png'
savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix[:,y2,:].T + matrix2[:,y2,:].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'rho_tot_XZ_lin_'+s+'.png'
fig.savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T - matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#--------------------#
#--- Log plots ---#
#--------------------#
#- Plot Bdenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix[:,:,z2].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Bunch_XY_log_'+s+'.png'
savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix[:,y2,:].T,levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Bunch_XZ_log_'+s+'.png'
fig.savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix2[:,:,z2].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Background_XY_log_'+s+'.png'
savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix2[:,y2,:].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Background_XZ_log_'+s+'.png'
fig.savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix[:,:,z2].T + matrix2[:,:,z2].T,levs_log , norm=colors.LogNorm())
axis('tight')
name_output = 'rho_tot_XY_log_'+s+'.png'
savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix[:,y2,:].T + matrix2[:,y2,:].T,levs_log , norm=colors.LogNorm())
axis('tight')
name_output = 'rho_tot_XZ_log_'+s+'.png'
fig.savefig( os.path.join(path,'plots','rho',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T + matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#----- Save density sections data -----#
if (savedata == 'True'):
print 'saving rho data'
rho_b = matrix
rho_w = matrix2
rho_b=np.abs( rho_b )
rho_w=np.abs( rho_w )
rho = rho_b+rho_w
p = rho.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
np.savetxt( os.path.join(path,'data','rho',('rho_section_'+('%2.2i'%frame)+'.dat')),rho[:,:,z2].T,fmt='%15.14e')
np.savetxt( os.path.join(path,'data','rho',('rho_bunch_section_'+('%2.2i'%frame)+'.dat')),rho_b[:,:,z2].T,fmt='%15.14e')
def write_density_vts(path, frame, X, Y, Z, cell_cut):
sf = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Bdenout' + sf + '.bin'
rhobunch, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
rhobunch = np.abs(rhobunch)
file_name = 'Edenout' + sf + '.bin'
rhobck, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
rhobck = np.abs(rhobck)
#- matrix shaving
if cell_cut > 0:
rhobunch = rhobunch[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
rhobck = rhobck[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = rhobunch.shape
#-
#- writing vts header
#total
f_total = open(
os.path.join(path, 'VTS_files', 'ALaDyn_rho_' + sf + '.vts'), 'w+')
f_total.write('<?xml version="1.0"?>' + '\n')
f_total.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f_total.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
f_total.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#bunch(es)
f_bunch = open(
os.path.join(path, 'VTS_files', 'ALaDyn_rho_bunch_' + sf + '.vts'),
'w+')
f_bunch.write('<?xml version="1.0"?>' + '\n')
f_bunch.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f_bunch.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
f_bunch.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#background
f_bck = open(
os.path.join(path, 'VTS_files', 'ALaDyn_rho_bck_' + sf + '.vts'), 'w+')
f_bck.write('<?xml version="1.0"?>' + '\n')
f_bck.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f_bck.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
f_bck.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#--- ---#
#- generating vector-MESH
mesh = []
for i in range(0, size[0]):
for j in range(0, size[1]):
for k in range(0, size[2]):
mesh.append(Y[j])
mesh.append(Z[k])
mesh.append(X[i])
#- Writing MESH -#
#it's the same for the whole 3 cases
#total
f_total.write('<Points> \n')
f_total.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f_total.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f_total.write(s)
f_total.write('</DataArray> \n')
f_total.write('</Points> \n')
#bunch(es)
f_bunch.write('<Points> \n')
f_bunch.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f_bunch.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f_bunch.write(s)
f_bunch.write('</DataArray> \n')
f_bunch.write('</Points> \n')
#background
f_bck.write('<Points> \n')
f_bck.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f_bck.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f_bck.write(s)
f_bck.write('</DataArray> \n')
f_bck.write('</Points> \n')
#- -#
#- Point Data Begin-#
f_total.write('<PointData>\n')
f_bunch.write('<PointData>\n')
f_bck.write('<PointData>\n')
#- -#
#- Writing DensitIES -#
#total
f_total.write('<DataArray type="Float32" Name="rho" format="binary"> \n')
mesh = matrix2vector(rhobunch + rhobck)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f_total.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f_total.write(s)
f_total.write('</DataArray> \n')
#bunch(es)
f_bunch.write(
'<DataArray type="Float32" Name="rho_bunch" format="binary"> \n')
mesh = matrix2vector(rhobunch)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f_bunch.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f_bunch.write(s)
f_bunch.write('</DataArray> \n')
#background
f_bck.write('<DataArray type="Float32" Name="rho_bck" format="binary"> \n')
mesh = matrix2vector(rhobck)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f_bck.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f_bck.write(s)
f_bck.write('</DataArray> \n')
#-Deallocate memory
rhobunch = [0.]
rhobck = [0.]
#- Point Data End-#
f_total.write('</PointData> \n')
f_bunch.write('</PointData> \n')
f_bck.write('</PointData> \n')
#- -#
# --- #
f_total.write('</Piece> \n')
f_bunch.write('</Piece> \n')
f_bck.write('</Piece> \n')
f_total.write('</StructuredGrid> \n')
f_bunch.write('</StructuredGrid> \n')
f_bck.write('</StructuredGrid> \n')
f_total.write('</VTKFile>')
f_bunch.write('</VTKFile>')
f_bck.write('</VTKFile>')
def plot_density_sections(path, frame, rho_min, rho_max, isolines, celltocut,
sliceposition_x, sliceposition_y, sliceposition_z,
magnification_fig, savedata):
s = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Bdenout' + s + '.bin'
matrix, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Edenout' + s + '.bin'
matrix2, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- cut & sign
matrix = np.abs(matrix)
matrix2 = np.abs(matrix2)
print('rho-max >>', np.max([np.max(matrix), np.max(matrix2)]))
print('rho-min >>', np.min([np.min(matrix), np.min(matrix2)]))
# matrix[ (matrix<rho_min) ] = rho_min
# matrix[ (matrix>rho_max) ] = rho_max
# matrix2[ (matrix2<rho_min) ] = rho_min
# matrix2[ (matrix2>rho_max) ] = rho_max
#---cut edges---#
if celltocut > 0:
matrix = matrix[:, celltocut:-celltocut, celltocut:-celltocut]
matrix2 = matrix2[:, celltocut:-celltocut, celltocut:-celltocut]
y = y[celltocut:-celltocut]
z = z[celltocut:-celltocut]
p = matrix.shape
x2 = p[0] / 2 + sliceposition_x
y2 = p[1] / 2 + sliceposition_y
z2 = p[2] / 2 + sliceposition_z
sizeX, sizeZ = figure_dimension_inch(x, y, z, magnification_fig)
levs_lin = np.linspace(rho_min, rho_max, isolines)
# levs_lin = np.insert(levs_lin,0,np.min([np.min(matrix),np.min(matrix2)]))
# levs_lin = np.insert(levs_lin,len(levs_lin),np.min([np.max(matrix),np.max(matrix2)]))
levs_log = np.logspace(log10(rho_min), log10(rho_max), isolines)
#--------------------#
#--- Linear plots ---#
#--------------------#
#- Plot Bdenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, matrix[:, :, z2].T, levs_lin, linewidths=0.00001)
axis('tight')
name_output = 'rho_Bunch_XY_lin_' + s + '.png'
savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, matrix[:, y2, :].T, levs_lin, linewidths=0.00001)
axis('tight')
name_output = 'rho_Bunch_XZ_lin_' + s + '.png'
fig.savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, matrix2[:, :, z2].T, levs_lin, linewidths=0.00001)
axis('tight')
name_output = 'rho_Background_XY_lin_' + s + '.png'
savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, matrix2[:, y2, :].T, levs_lin, linewidths=0.00001)
axis('tight')
name_output = 'rho_Background_XZ_lin_' + s + '.png'
fig.savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,
y,
matrix[:, :, z2].T + matrix2[:, :, z2].T,
levs_lin,
linewidths=0.00001)
axis('tight')
name_output = 'rho_tot_XY_lin_' + s + '.png'
savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,
z,
matrix[:, y2, :].T + matrix2[:, y2, :].T,
levs_lin,
linewidths=0.00001)
axis('tight')
name_output = 'rho_tot_XZ_lin_' + s + '.png'
fig.savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T - matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#--------------------#
#--- Log plots ---#
#--------------------#
#- Plot Bdenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, matrix[:, :, z2].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Bunch_XY_log_' + s + '.png'
savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, matrix[:, y2, :].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Bunch_XZ_log_' + s + '.png'
fig.savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, y, matrix2[:, :, z2].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Background_XY_log_' + s + '.png'
savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x, z, matrix2[:, y2, :].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'rho_Background_XZ_log_' + s + '.png'
fig.savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,
y,
matrix[:, :, z2].T + matrix2[:, :, z2].T,
levs_log,
norm=colors.LogNorm())
axis('tight')
name_output = 'rho_tot_XY_log_' + s + '.png'
savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,
z,
matrix[:, y2, :].T + matrix2[:, y2, :].T,
levs_log,
norm=colors.LogNorm())
axis('tight')
name_output = 'rho_tot_XZ_log_' + s + '.png'
fig.savefig(os.path.join(path, 'plots', 'rho', name_output))
close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T + matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#----- Save density sections data -----#
if (savedata == 'True'):
print('saving rho data')
rho_b = matrix
rho_w = matrix2
rho_b = np.abs(rho_b)
rho_w = np.abs(rho_w)
rho = rho_b + rho_w
p = rho.shape
x2 = p[0] / 2 + sliceposition_x
y2 = p[1] / 2 + sliceposition_y
z2 = p[2] / 2 + sliceposition_z
np.savetxt(os.path.join(path, 'data', 'rho',
('rho_section_' + ('%2.2i' % frame) + '.dat')),
rho[:, :, z2].T,
fmt='%15.14e')
np.savetxt(os.path.join(path, 'data', 'rho',
('rho_bunch_section_' +
('%2.2i' % frame) + '.dat')),
rho_b[:, :, z2].T,
fmt='%15.14e')
def write_E_vts(path, frame, X, Y, Z, cell_cut):
# for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ):
# write_VTS(path,i)
sf = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Exfout' + sf + '.bin'
Ex, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Eyfout' + sf + '.bin'
Ey, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Ezfout' + sf + '.bin'
Ez, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- bunch(es) -#
file_name = 'Exbout' + sf + '.bin'
Exb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Eybout' + sf + '.bin'
Eyb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Ezbout' + sf + '.bin'
Ezb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- matrix shaving
if cell_cut > 0:
Ex = Ex[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Ey = Ey[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Ez = Ez[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Exb = Exb[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Eyb = Eyb[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Ezb = Ezb[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = Ex.shape
#-
#- writing vts header
f = open(os.path.join(path, 'VTS_files', 'ALaDyn_E_' + sf + '.vts'), 'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#--- ---#
#- writing Ex-vts header
fEx = open(os.path.join(path, 'VTS_files', 'ALaDyn_Ex_' + sf + '.vts'),
'w+')
fEx.write('<?xml version="1.0"?>' + '\n')
fEx.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
fEx.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
fEx.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#- writing Ey-vts header
fEy = open(os.path.join(path, 'VTS_files', 'ALaDyn_Ey_' + sf + '.vts'),
'w+')
fEy.write('<?xml version="1.0"?>' + '\n')
fEy.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
fEy.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
fEy.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#- writing Ex-vts header
fEz = open(os.path.join(path, 'VTS_files', 'ALaDyn_Ez_' + sf + '.vts'),
'w+')
fEz.write('<?xml version="1.0"?>' + '\n')
fEz.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
fEz.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
fEz.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#--- ---#
#- generating vector-MESH
mesh = []
for i in range(0, size[0]):
for j in range(0, size[1]):
for k in range(0, size[2]):
mesh.append(Y[j])
mesh.append(Z[k])
mesh.append(X[i])
#- Writing MESH -#
f.write('<Points> \n')
f.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Writing ExMESH -#
fEx.write('<Points> \n')
fEx.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
fEx.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
fEx.write(s)
fEx.write('</DataArray> \n')
fEx.write('</Points> \n')
#- Writing ExMESH -#
fEy.write('<Points> \n')
fEy.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
fEy.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
fEy.write(s)
fEy.write('</DataArray> \n')
fEy.write('</Points> \n')
#- Writing ExMESH -#
fEz.write('<Points> \n')
fEz.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
fEz.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
fEz.write(s)
fEz.write('</DataArray> \n')
fEz.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
fEx.write('<PointData>\n')
fEy.write('<PointData>\n')
fEz.write('<PointData>\n')
#- -#
#- Writing E-field -#
#- E-field total
f.write(
'<DataArray type="Float32" Name="E" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Ex + Exb, Ey + Eyb, Ez + Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Writing Ex-field -#
fEx.write(
'<DataArray type="Float32" Name="Ex" NumberOfComponents="1" format="binary"> \n'
)
mesh = matrix2vector(Ex + Exb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
fEx.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
fEx.write(s)
fEx.write('</DataArray> \n')
#- Writing Ex-field -#
fEy.write(
'<DataArray type="Float32" Name="Ey" NumberOfComponents="1" format="binary"> \n'
)
mesh = matrix2vector(Ey + Eyb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
fEy.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
fEy.write(s)
fEy.write('</DataArray> \n')
#- Writing Ex-field -#
fEz.write(
'<DataArray type="Float32" Name="Ez" NumberOfComponents="1" format="binary"> \n'
)
mesh = matrix2vector(Ez + Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
fEz.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
fEz.write(s)
fEz.write('</DataArray> \n')
#-Deallocate memory
Ex = [0.]
Ey = [0.]
Ez = [0.]
Exb = [0.]
Eyb = [0.]
Ezb = [0.]
#- Point Data End-#
f.write('</PointData> \n')
fEx.write('</PointData> \n')
fEy.write('</PointData> \n')
fEz.write('</PointData> \n')
#- -#
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
fEx.write('</Piece> \n')
fEx.write('</StructuredGrid> \n')
fEx.write('</VTKFile>')
fEy.write('</Piece> \n')
fEy.write('</StructuredGrid> \n')
fEy.write('</VTKFile>')
fEz.write('</Piece> \n')
fEz.write('</StructuredGrid> \n')
fEz.write('</VTKFile>')
def plot_ionization_profile(path, frame, min_ionization_rate,
max_ionzation_rate, isolines, celltocut,
sliceposition_x, sliceposition_y, sliceposition_z,
magnification_fig, savedata):
s = '%2.2i' % frame #conversion to 2-character-long-string
# file_name = 'Elpout'+s+'.bin'
file_name = 'H1dnout' + s + '.bin'
matrix, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- cut & sign
matrix = np.abs(matrix)
#---cut edges---#
if celltocut > 0:
matrix = matrix[:, celltocut:-celltocut, celltocut:-celltocut]
y = y[celltocut:-celltocut]
z = z[celltocut:-celltocut]
p = matrix.shape
x2 = p[0] / 2 + sliceposition_x
y2 = p[1] / 2 + sliceposition_y
z2 = p[2] / 2 + sliceposition_z
sizeX, sizeZ = figure_dimension_inch(x, y, z, magnification_fig)
# levs_lin = np.linspace( rho_min , rho_max ,isolines)
# levs_lin = np.insert(levs_lin,0,np.min([np.min(matrix),np.min(matrix2)]))
# levs_lin = np.insert(levs_lin,len(levs_lin),np.min([np.max(matrix),np.max(matrix2)]))
# levs_log = np.logspace(log10(rho_min),log10(rho_max),isolines)
#--------------------#
#--- Linear plots ---#
#--------------------#
#- Plot Bdenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_XY_lin_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_XZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Bunch_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix2[:,:,z2].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_XY_lin_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix2[:,y2,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_XZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_Background_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T + matrix2[:,:,z2].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_XY_lin_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T + matrix2[:,y2,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_XZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T - matrix2[x2,:,:].T,levs_lin, linewidths = 0.00001)
# axis('tight')
# name_output = 'rho_tot_YZ_lin_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#--------------------#
#--- Log plots ---#
#--------------------#
#- Plot Bdenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_XY_log_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T,levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_XZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix2[:,:,z2].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_XY_log_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix2[:,y2,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_XZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Background_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#- Plot Bdenout+Edenout -#
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,y,matrix[:,:,z2].T + matrix2[:,:,z2].T,levs_log , norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_XY_log_'+s+'.png'
# savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeZ))
# contourf(x,z,matrix[:,y2,:].T + matrix2[:,y2,:].T,levs_log , norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_XZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
# fig = figure(1, figsize=(sizeX, sizeX))
# contourf(y,z,matrix[x2,:,:].T + matrix2[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_tot_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#----- Save density sections data -----#
if (savedata == 'True'):
print('saving ionization data')
ionization_map = matrix
ionization_map = np.abs(ionization_map)
p = ionization_map.shape
x2 = p[0] / 2 + sliceposition_x
y2 = p[1] / 2 + sliceposition_y
z2 = p[2] / 2 + sliceposition_z
np.savetxt(os.path.join(path, 'data', 'ionization',
('ionization_profile_' +
('%2.2i' % frame) + '.dat')),
ionization_map[:, :, z2].T,
fmt='%15.14e')
def write_vts(path, frame, X, Y, Z, cell_cut):
# for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ):
# write_VTS(path,i)
sf = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Bdenout' + sf + '.bin'
rhobunch, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
rhobunch = np.abs(rhobunch)
file_name = 'Edenout' + sf + '.bin'
rhobck, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
rhobck = np.abs(rhobck)
#- matrix shaving
if cell_cut > 0:
rhobunch = rhobunch[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
rhobck = rhobck[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = rhobunch.shape
#-
#- writing vts header
f = open(os.path.join(path, 'VTS_files', 'ALaDyn_output_' + sf + '.vts'),
'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#--- ---#
#- generating vector-MESH
mesh = []
for i in range(0, size[0]):
for j in range(0, size[1]):
for k in range(0, size[2]):
mesh.append(Y[j])
mesh.append(Z[k])
mesh.append(X[i])
#- Writing MESH -#
f.write('<Points> \n')
f.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
# f.write('<CellData> \n')
#- -#
#- Writing BUNCH Density -#
f.write('<DataArray type="Float32" Name="rho_bunch" format="binary"> \n')
mesh = matrix2vector(rhobunch)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- Writing Tot-Density -#
f.write('<DataArray type="Float32" Name="rho" format="binary"> \n')
mesh = matrix2vector(rhobunch + rhobck)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
rhobunch = [0.]
rhobck = [0.]
#- Writing E-field -#
#- background -#
file_name = 'Exfout' + sf + '.bin'
Ex, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Eyfout' + sf + '.bin'
Ey, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Ezfout' + sf + '.bin'
Ez, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- bunch(es) -#
file_name = 'Exbout' + sf + '.bin'
Exb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Eybout' + sf + '.bin'
Eyb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Ezbout' + sf + '.bin'
Ezb, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
#- matrix shaving
if cell_cut > 0:
Ex = Ex[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Ey = Ey[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Ez = Ez[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Exb = Exb[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Eyb = Eyb[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Ezb = Ezb[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
#-
#- E-field bunch
f.write(
'<DataArray type="Float32" Name="E_bunch" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Exb, Eyb, Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#- E-field total
f.write(
'<DataArray type="Float32" Name="E" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Ex + Exb, Ey + Eyb, Ez + Ezb)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Ex = [0.]
Ey = [0.]
Ez = [0.]
Exb = [0.]
Eyb = [0.]
Ezb = [0.]
#- Writing B-field -#
#- background -#
file_name = 'Bxfout' + sf + '.bin'
Bx, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Byfout' + sf + '.bin'
By, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Bzfout' + sf + '.bin'
Bz, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
# #- bunch(es) -#
# file_name = 'Bxbout'+sf+'.bin'
# Bxb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bybout'+sf+'.bin'
# Byb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# file_name = 'Bzbout'+sf+'.bin'
# Bzb, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- matrix shaving
if cell_cut > 0:
Bx = Bx[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
By = By[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Bz = Bz[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
#-
#- B-field bunch
# f.write('<DataArray type="Float32" Name="B_bunch" NumberOfComponents="3" format="binary"> \n')
# mesh = matrix2vectorField(Bxb,Byb,Bzb)
# s = base64.b64encode(np.array(mesh,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# f.write('</DataArray> \n')
#- B-field total
f.write(
'<DataArray type="Float32" Name="B" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Bx, By, Bz)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Bx = [0.]
By = [0.]
Bz = [0.]
#Bxb=[0.];Byb=[0.];Bzb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
# f.write('</CellData> \n')
#- -#
# frame = 0
# s='%2.2i'%frame #conversion to 2-character-long-string
# file_name = 'Bdenout'+s+'.bin'
# matrix, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# # file_name = 'Edenout'+s+'.bin'
# # matrix2, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
# #- cut & sign
# matrix = np.abs( matrix )
# # matrix2 = np.abs( matrix2 )
# size = matrix.shape
#- writing vts header
# f = open('test.vts','w+')
# f.write('<?xml version="1.0"?>' + '\n')
# f.write('<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">' + '\n')
# f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' % (0,size[1],0,size[0],0,size[2]) )
# f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' % (0,size[1],0,size[0],0,size[2]) )
# f.write('<Points> \n')
# f.write('<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n')
# buffer=[]
# for i in range(1,NI+2):
# for j in range(1,NJ+2):
# for k in range(1,NK+2):
# buffer.append(1./float(NJ)*(float(j)-1.))
# buffer.append(1./float(NI)*(float(i)-1.))
# buffer.append(1./float(NK)*(float(k)-1.))
#
# s = base64.b64encode(np.array(buffer,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# f.write('</DataArray> \n')
# f.write('</Points> \n')
# f.write('<PointData>\n')
# f.write('<DataArray type="Float32" Name="rhoEdge" format="binary"> \n')
# buffer=[]
# n=0
# for i in range(0,NI+1):
# for j in range(0,NJ+1):
# for k in range(0,NK+1):
# buffer.append(n*1.)
# n+=1
#
# s = base64.b64encode(np.array(buffer,dtype=np.float32))
# f.write(base64.b64encode(np.array(len(s),dtype=np.int32)))
# f.write(s)
# # for item in buffer:
# # f.write(str(item)+'\n')
# f.write('</DataArray> \n')
# f.write('</PointData> \n')
# f.write('<CellData> \n')
# f.write('<DataArray type="Float32" Name="rho" format="ascii"> \n')
#
# buffer=[]
# n=0
# for i in range(0,NI):
# for j in range(0,NJ):
# for k in range(0,NK):
# buffer.append(str(n*1.))
# n+=1
#
# for item in buffer:
# f.write(str(item)+'\n')
#
# f.write('</DataArray> \n')
# f.write('</CellData> \n')
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
def write_B_vts(path, frame, X, Y, Z, cell_cut):
# for i in range(frame_begin, min(frame_end,last_output(os.getcwd())) + 1 ):
# write_VTS(path,i)
sf = '%2.2i' % frame #conversion to 2-character-long-string
file_name = 'Bxfout' + sf + '.bin'
Bx, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Byfout' + sf + '.bin'
By, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
file_name = 'Bzfout' + sf + '.bin'
Bz, x, y, z = read_ALaDyn_bin(path, file_name, 'grid')
size = Bx.shape
#- matrix shaving
if cell_cut > 0:
Bx = Bx[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
By = By[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Bz = Bz[:, cell_cut:-cell_cut, cell_cut:-cell_cut]
Y = Y[cell_cut:-cell_cut]
Z = Z[cell_cut:-cell_cut]
#-
size = Bx.shape
#-
#- writing vts header
f = open(os.path.join(path, 'VTS_files', 'ALaDyn_B_' + sf + '.vts'), 'w+')
f.write('<?xml version="1.0"?>' + '\n')
f.write(
'<VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian">'
+ '\n')
f.write('<StructuredGrid WholeExtent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
f.write('<Piece Extent=" %d %d %d %d %d %d "> \n' %
(0, size[1] - 1, 0, size[2] - 1, 0, size[0] - 1))
#--- ---#
#- generating vector-MESH
mesh = []
for i in range(0, size[0]):
for j in range(0, size[1]):
for k in range(0, size[2]):
mesh.append(Y[j])
mesh.append(Z[k])
mesh.append(X[i])
#- Writing MESH -#
f.write('<Points> \n')
f.write(
'<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary"> \n'
)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
f.write('</Points> \n')
#- -#
#- Point Data Begin-#
f.write('<PointData>\n')
#- -#
#- Writing B-field -#
f.write(
'<DataArray type="Float32" Name="B" NumberOfComponents="3" format="binary"> \n'
)
mesh = matrix2vectorField(Bx, By, Bz)
s = base64.b64encode(np.array(mesh, dtype=np.float32))
f.write(base64.b64encode(np.array(len(s), dtype=np.int32)))
f.write(s)
f.write('</DataArray> \n')
#-Deallocate memory
Bx = [0.]
By = [0.]
Bz = [0.]
#Bxb=[0.];Byb=[0.];Bzb=[0.];
#- Point Data End-#
f.write('</PointData> \n')
#- -#
f.write('</Piece> \n')
f.write('</StructuredGrid> \n')
f.write('</VTKFile>')
def plot_energy_density_sections(path,frame,Energy_density_min,Energy_density_max,isolines,celltocut,sliceposition_x,sliceposition_y,sliceposition_z,magnification_fig,savedata):
s='%2.2i'%frame #conversion to 2-character-long-string
file_name = 'Elenout'+s+'.bin'
matrix3, x,y,z = read_ALaDyn_bin(path,file_name,'grid')
#- cut & sign
matrix3 = np.abs( matrix3 )
print('Energy_density_max >>', np.max([np.max(matrix3)]))
print('Energy_density_min >>', np.min([np.min(matrix3)]))
#---cut edges---#
if celltocut > 0:
matrix3 = matrix3[:,celltocut:-celltocut,celltocut:-celltocut]
y = y[celltocut:-celltocut]
z = z[celltocut:-celltocut]
p = matrix3.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
sizeX, sizeZ = figure_dimension_inch(x,y,z,magnification_fig)
levs_lin = np.linspace( Energy_density_min , Energy_density_max ,isolines)
levs_log = np.logspace(log10(Energy_density_min),log10(Energy_density_max),isolines)
#--------------------#
#--- Linear plots ---#
#--------------------#
#- Plot Elenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix3[:,:,z2].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'Energy_density_XY_lin_'+s+'.png'
savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix3[:,y2,:].T,levs_lin, linewidths = 0.00001)
axis('tight')
name_output = 'Energy_density_XZ_lin_'+s+'.png'
fig.savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
#--------------------#
#--- Log plots ---#
#--------------------#
#- Plot Elenout -#
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,y,matrix3[:,:,z2].T, levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'Energy_density_XY_log_'+s+'.png'
savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
fig = figure(1, figsize=(sizeX, sizeZ))
contourf(x,z,matrix3[:,y2,:].T,levs_log, norm=colors.LogNorm())
axis('tight')
name_output = 'Energy_density_XZ_log_'+s+'.png'
fig.savefig( os.path.join(path,'plots','Energy_density',name_output) )
close(fig)
# fig = figure(1, figsize=(sizeZ, sizeZ))
# contourf(y,z,matrix[x2,:,:].T, levs_log, norm=colors.LogNorm())
# axis('tight')
# name_output = 'rho_Bunch_YZ_log_'+s+'.png'
# fig.savefig( os.path.join(path,'plots','rho',name_output) )
# close(fig)
#----- Save density sections data -----#
if (savedata == 'True'):
print('saving Energy_density data')
Energy_density = matrix3
p = Energy_density.shape
x2=p[0]/2+sliceposition_x; y2=p[1]/2+sliceposition_y; z2=p[2]/2+sliceposition_z;
np.savetxt( os.path.join(path,'data','Energy_density',('Energy_Density'+('%2.2i'%frame)+'.dat')),Energy_density[:,:,z2].T,fmt='%15.14e')
