Minor cosmetic changes

Author: ibackus

ICgen_utils.py

@@ -177,7 +177,7 @@ def delistify(in_list):
 
         return in_list
 
-def est_eps(smoothlength_file):
+def est_eps(smoothlength_file, nstar=1):
     """
     Estimate gravitational softening length (eps) from a ChaNGa output .smoothlength
     file.  eps is estimated as 1/2 the mean smoothing length
@@ -186,6 +186,8 @@ def est_eps(smoothlength_file):
     
     smoothlength_file : str
         Filename of the .smoothlength file
+    nstar : int
+        Number of star particles present
         
     **RETURNS**
     
@@ -204,7 +206,7 @@ def est_eps(smoothlength_file):
         smoothlength[i] = float(line.strip())
 
     # Calculate eps, ignoring star particle
-    mean_smooth = (smoothlength.sum() - smoothlength[-1])/(nParticles-1)
+    mean_smooth = (smoothlength.sum() - smoothlength[-nstar])/(nParticles-nstar)
     eps = mean_smooth/2
 
     return eps

calc_rho.py

@@ -301,6 +301,7 @@ def erf_res(scale_size):
 
     return SimArray(rho0,'Msol au**-3'), SimArray(z,'au')
 
+
 def cdfinv_z(z,rho):
     """
     Calculates the inverse of the cumulative distribution function for
@@ -359,60 +360,3 @@ def finv(m):
 
     return finv
 
-#def cdfinv_z(z,rho):
-#    """
-#    Calculates the inverse of the cumulative distribution function for
-#    probability as a function of z for a given r
-#    
-#    *** Arguments ***
-#    
-#    * z *   z positions to calculate over.  1D array
-#            
-#    * rho *     Density as a function of z.  Treated as an un-normalized
-#    probability.  1D array
-#    
-#    IF Z doesn't have units, units of 'au' are assumed
-#    
-#    *** Returns ***
-#        
-#    Returns the inverse normalized CDF as 1D spline interpolation
-#    """
-#    # Check for units
-#    if pynbody.units.has_units(z):
-#        
-#        zunit = z.units
-#        
-#    else:
-#        
-#        zunit = pynbody.units.au
-#        
-#    # Calculate the CDF from prob
-#    nz = len(z)
-#    f = np.zeros(nz)
-#    f[1:] = nInt.cumtrapz(rho,z)
-#    if f.max() <= 0.0:
-#        # The density (rho) is zero here for all z or neg or something.
-#        # Make all particles go to z = 0.0
-#        def finv(m_in):
-#            return m_in*0.0
-#        return finv
-#    f /= f.max()
-#    # Calculate the inverse CDF.
-#    # Assume CDF is approximately monotonic and sort to force it to be
-#    ind = f.argsort()
-#    f = f[ind]
-#    z = z[ind]
-#    # Drop values where CDF is constant (ie, prob = 0)
-#    mask = np.ones(nz,dtype='bool')
-#    for n in range(1,nz):
-#        if f[n] == f[n-1]:
-#            mask[n] = False
-#    f = f[mask]
-#    z = z[mask]
-#    finv_spline = interp1d(f,z,kind='linear')
-#    
-#    def finv(m):
-#        
-#        return SimArray(finv_spline(m), zunit)
-#        
-#    return finv

calc_rho_zr.py

@@ -95,6 +95,7 @@ def rho_zr(ICobj):
     # Calculate rho using multiprocessing
     pool = Pool(n_proc)
     results = pool.map(multirun_rho, arg_list)
+    pool.close()
 
     # Extract results
     for i in range(nr):

make_snapshot.py

@@ -83,7 +83,7 @@ def snapshot_gen(ICobj):
     star_metals = metals
 
     # -------------------------------------------------
-    # Generate snapshot
+    # Initialize snapshot
     # -------------------------------------------------
     # Note that empty pos, vel, and mass arrays are created in the snapshot
     snapshot = pynbody.new(star=1,gas=nParticles)