Merge branch 'python_scripts' into 'master'

Made all python scripts numpy 1.8.2 compatible, and fixed some bugs while doing it.

Title says it all. This should close #272.

See merge request !319

examples/BigCosmoVolume/makeIC.py

@@ -107,7 +107,7 @@ if n_copy > 1:
     for i in range(n_copy):
         for j in range(n_copy):
             for k in range(n_copy):
-                coords = np.append(coords, coords_tile + np.array([ i * boxSize, j * boxSize, k * boxSize ]), axis=0)
+                coords = np.append(coords, coords_tile + np.array([ i * boxSize[0], j * boxSize[1], k * boxSize[2] ]), axis=0)
                 v = np.append(v, v_tile, axis=0)
                 m = np.append(m, m_tile)
                 h = np.append(h, h_tile)

examples/CoolingHalo/makeIC.py

@@ -227,7 +227,7 @@ ds[()] = u
 u = np.zeros(1)
 
 # Particle IDs
-ids = 1 + np.linspace(0, N, N, endpoint=False, dtype='L')
+ids = 1 + np.linspace(0, N, N, endpoint=False)
 ds = grp.create_dataset('ParticleIDs', (N, ), 'L')
 ds[()] = ids
 

examples/CoolingHaloWithSpin/makeIC.py

@@ -233,7 +233,7 @@ ds[()] = u
 u = np.zeros(1)
 
 # Particle IDs
-ids = 1 + np.linspace(0, N, N, endpoint=False, dtype='L')
+ids = 1 + np.linspace(0, N, N, endpoint=False)
 ds = grp.create_dataset('ParticleIDs', (N, ), 'L')
 ds[()] = ids
 

examples/DiscPatch/GravityOnly/makeIC.py

@@ -150,7 +150,7 @@ ds[()] = m
 m = numpy.zeros(1)
 
 
-ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False, dtype='L')
+ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False)
 ds = grp1.create_dataset('ParticleIDs', (numPart, ), 'L')
 ds[()] = ids
 

examples/DiscPatch/HydroStatic/makeIC.py

@@ -205,7 +205,7 @@ if (entropy_flag == 1):
 else:
     ds[()] = u    
 
-ids = 1 + numpy.linspace(0, numGas, numGas, endpoint=False, dtype='L')
+ids = 1 + numpy.linspace(0, numGas, numGas, endpoint=False)
 ds = grp0.create_dataset('ParticleIDs', (numGas, ), 'L')
 ds[()] = ids
 

examples/HydrostaticHalo/density_profile.py

@@ -28,7 +28,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
 unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
 unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
 unit_time_cgs = unit_length_cgs / unit_velocity_cgs
-v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
+v_c = float(params.attrs["IsothermalPotential:vrot"])
 v_c_cgs = v_c * unit_velocity_cgs
 #lambda_cgs = float(params.attrs["LambdaCooling:lambda_cgs"])
 #X_H = float(params.attrs["LambdaCooling:hydrogen_mass_abundance"])

examples/HydrostaticHalo/internal_energy_profile.py

@@ -46,7 +46,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
 unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
 unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
 unit_time_cgs = unit_length_cgs / unit_velocity_cgs
-v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
+v_c = float(params.attrs["IsothermalPotential:vrot"])
 v_c_cgs = v_c * unit_velocity_cgs
 #lambda_cgs = float(params.attrs["LambdaCooling:lambda_cgs"])
 #X_H = float(params.attrs["LambdaCooling:hydrogen_mass_abundance"])

examples/HydrostaticHalo/makeIC.py

@@ -227,7 +227,7 @@ ds[()] = u
 u = np.zeros(1)
 
 # Particle IDs
-ids = 1 + np.linspace(0, N, N, endpoint=False, dtype='L')
+ids = 1 + np.linspace(0, N, N, endpoint=False)
 ds = grp.create_dataset('ParticleIDs', (N, ), 'L')
 ds[()] = ids
 

examples/HydrostaticHalo/velocity_profile.py

@@ -46,7 +46,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
 unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
 unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
 unit_time_cgs = unit_length_cgs / unit_velocity_cgs
-v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
+v_c = float(params.attrs["IsothermalPotential:vrot"])
 v_c_cgs = v_c * unit_velocity_cgs
 header = f["Header"]
 N = header.attrs["NumPart_Total"][0]

examples/IsothermalPotential/makeIC.py

@@ -138,7 +138,7 @@ ds = grp1.create_dataset('Masses', (numPart,), 'f')
 ds[()] = m
 m = numpy.zeros(1)
 
-ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False, dtype='L')
+ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False)
 ds = grp1.create_dataset('ParticleIDs', (numPart, ), 'L')
 ds[()] = ids
 

examples/Noh_3D/makeIC.py

@@ -35,8 +35,8 @@ glass = h5py.File("glassCube_64.hdf5", "r")
 
 vol = 8.
 
-pos = glass["/PartType0/Coordinates"][:,:] * cbrt(vol)
-h = glass["/PartType0/SmoothingLength"][:] * cbrt(vol)
+pos = glass["/PartType0/Coordinates"][:,:] * vol**(1./3.)
+h = glass["/PartType0/SmoothingLength"][:] * vol**(1./3.)
 numPart = size(h)
 
 # Generate extra arrays
@@ -65,7 +65,7 @@ file = h5py.File(fileName, 'w')
 
 # Header
 grp = file.create_group("/Header")
-grp.attrs["BoxSize"] = [cbrt(vol), cbrt(vol), cbrt(vol)]
+grp.attrs["BoxSize"] = [vol**(1./3.), vol**(1./3.), vol**(1./3.)]
 grp.attrs["NumPart_Total"] =  [numPart, 0, 0, 0, 0, 0]
 grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]

examples/SineWavePotential_3D/plotSolution.py

@@ -55,7 +55,7 @@ rho_x = 1000.*np.exp(-0.5*A/np.pi/cs2*np.cos(2.*np.pi*x))
 
 P = cs2*rho
 
-n1D = int(np.cbrt(len(P)))
+n1D = np.ceil(len(P)**(1./3.))
 gradP = np.zeros(P.shape)
 for i in range(len(P)):
   iself = int(ids[i]/n1D/n1D)