Removed d'Alembert force and chaned halo model to NFW

three_components.py

@@ -15,8 +15,8 @@ file_name = 'data/subhalo_411321.hdf5'
 # centers_file_name = 'data/centers_411321.hdf5'
 
 ### Snapshot parameters ###
-snapshot = 99
-a        = 1.0 # Should read this value from somewhere!
+snapshot = 25
+a        = 0.2494928434225328 # Should read this value from somewhere!
 
 # Read the centre from separate file
 # DISABLED: we calculate on our own.
@@ -32,6 +32,48 @@ particle_types['dm']    = '1'
 particle_types['stars'] = '4'
 particle_types['bhs']   = '5'
 
+# Read DM
+particle_type = 'dm'
+with h5py.File(file_name, 'r') as f:
+    m = f[str(snapshot)][particle_types[particle_type]]['Masses'][...]
+    X = f[str(snapshot)][particle_types[particle_type]]['Coordinates'][...] * a / h0
+    V = f[str(snapshot)][particle_types[particle_type]]['Velocities'][...] * sqrt(a)
+M_tot = sum(m)
+
+# Calculate density centre and shift appropriately
+X_center_new, V_center_new = def_dc(m, X, V)
+X -= X_center_new
+V -= V_center_new
+
+r = linalg.norm(X, axis=1)
+
+i = r.argsort()
+rr = r[i]
+m_cumulative = cumsum(m[i])/sum(m)
+
+nfw_cumulative_mass = lambda rho_0, b, r: 4*pi*rho_0*b**3*(log(1+r/b) - r/(b+r))
+cost = lambda args: sum((nfw_cumulative_mass(*args, rr) - m_cumulative)**2)
+res = scipy.optimize.minimize(cost, [0.001, 30.], method='Nelder-Mead')
+print(res)
+rho_0_nfw, b_nfw = res.x
+
+
+plot(rr, m_cumulative*sum(m))
+plot(rr, nfw_cumulative_mass(*res.x, rr)*sum(m))
+
+figure()
+counts, bin_edges = histogram(r, logspace(-2, 2, 65))
+volumes = 4*pi/3*(bin_edges[1:]**3 - bin_edges[:-1]**3)
+means = lambda arr: 0.5*(arr[:-1]+arr[1:])
+bins = means(bin_edges)
+density = counts*m[0]/volumes
+loglog(bins, density)
+nfw_density = lambda rho_0, b, r: rho_0/((r/b) * (1 + r/b)**2)
+loglog(bins, nfw_density(*res.x, bins)*sum(m))
+
+show()
+raise SystemExit
+
 # Read stars
 particle_type = 'stars'
 with h5py.File(file_name, 'r') as f: