def readsnapshot(snapshot, PATH='snapshotdata/snapdir_'):
""" A program to read in gadget-2 snapshot data with filename 62.5_dm_XXX.k .
:param snapshot: The number of the snapshot as a string (e.g. '001').
:param PATH: The filepath to the snapshot data directory.
:return: A list for each variable in the snapshot data no longer split
into files, along with the relevant header data.
"""
# Read in the header data and assign to variables
head = readheader(PATH + snapshot + '/62.5_dm_' + snapshot, 'header')
npart = head.get('npartTotal')[1] # number of particles in snapshot
z = head.get('redshift') # redshift of snapshot
t = head.get('time') # time of snapshot (age)
h = head.get('h')
boxsize = head.get('boxsize') # size of simulation box
rhocrit = head.get('rhocrit') # critical density at time t
# Read in the snapshot data and assign to variable for returning
pos = readsnap(PATH + snapshot + '/62.5_dm_' + snapshot, 'pos', 1)
vel = readsnap(PATH + snapshot + '/62.5_dm_' + snapshot, 'vel', 1)
pid = readsnap(PATH + snapshot + '/62.5_dm_' + snapshot, 'pid', 1)
pmass = readsnap(PATH + snapshot + '/62.5_dm_' + snapshot, 'mass', 1)[0]
return pid, pos, vel, npart, z, t, boxsize, rhocrit, pmass, h
def snapHeader(basePath, snapNum, chunkNum=None):
"""
Return snapshot header
"""
if chunkNum is None:
chunkNum = 0
fname = snapPath(basePath, snapNum, chunkNum)
header = pyg.readheader(fname, 'header')
return header
def down_sample(outpath, dmpath, DSF):
#Create the directories to put the down-sampling output
os.system("mkdir -p %s" % outpath + "/down_sampled_dm/")
print "Down sampling on file: %s" % dmpath
print "\tDSF = %d" % DSF
Ndm = pgr.readheader(dmpath, "dmcount")
Nds = Ndm / DSF
DSpath = outpath + "/down_sampled_dm/down_sampled_dm_DSF%d" % DSF
if os.path.exists(DSpath): print "Down sampled DM catalog already exists."
else:
def get_starsnhalos(pathname,hnum,res,ver,snap_ind,xcen,ycen,zcen,rvir): #Simple function to get 2D scatter plots of star particles with circles to denote rvir of halos at z=0
global conv
for i in np.arange(8):
fname = '/nobackup/afitts/Gadget-2.0.7/production/mfm%s%s_giz%s_raw_output/snapdir_184/snapshot_184.%d.hdf5'%(hnum,res,ver,i)
bsize = pg.readheader(fname, 'boxsize')
if bsize > 25: #mfm007 is in kpc while everything else (even gizdm007) is in Mpc. This standardizes all that.
kfix = 1
else:
kfix = 1000
a = h5py.File(fname,'r')
if i == 0:
pos = a['PartType4']['Coordinates']
masstot = a['PartType4']['Masses']
else:
pos = np.vstack((pos,a['PartType4']['Coordinates']))
masstot = np.concatenate((masstot,a['PartType4']['Masses']),0)
xtot = pos[:,0]/h* kfix
ytot = pos[:,1]/h* kfix
ztot = pos[:,2]/h* kfix
for w in np.arange(16):
temph = glob.glob(pathname+'analysis/ahf_snap%03d/ahf.snap_%03d.%04d.z*.*.AHF_halos'%(snap_ind,snap_ind,w))
temph = str(temph).strip('[]').replace("'","")
halo = np.loadtxt(temph,usecols=(0,3,5,6,7,11,64,63))
for k in np.arange(len(halo)):
halodiff = np.sqrt((xcen-halo[k,2]/h)**2+(ycen-halo[k,3]/h)**2+(zcen-halo[k,4]/h)**2)
try:
if halo[k,5] > 5 and halo[k,7]>10 and halodiff>20 and halodiff<100 or halodiff==0:# and halodiff<rvir or halodiff==0:
ans = np.vstack((ans,(halo[k,1],halo[k,6])))
x = np.append(x,halo[k,2]/h)
y = np.append(y,halo[k,3]/h)
z = np.append(z,halo[k,4]/h)
rad = np.append(rad,halo[k,5]/h)
bobob += halo[k,6]
print halo[k,0], halo[k,1],halo[k,6]
except:
if halo[k,5] > 5 and halo[k,7]>10 and halodiff>20 and halodiff<100 or halodiff==0:#and halodiff<rvir or halodiff ==0:
ans = np.array([[halo[k,1],halo[k,6]]])
x = np.array([halo[k,2]])/h
y = np.array([halo[k,3]])/h
z = np.array([halo[k,4]])/h
rad = np.array([halo[k,5]])/h
bobob = halo[k,6]
print halo[k,0], halo[k,1],halo[k,6]
return xtot,ytot,ztot,x,y,z,rad
def stellar_age(pathname,snum,main_part): #Add stellar creation time
h0 = 71
om_l = 0.734
om_m = 0.266
conv = 3.085677581e+19
age = pg.readsnap(pathname+'snapdir_%03d/snapshot_%03d'%(snum,snum),'age','star')
test = pg.readheader(pathname+'snapdir_%03d/snapshot_%03d'%(snum,snum),'time')
print age[age>test]
for i in np.arange(len(age)):
age[i] = scipy.integrate.quad(_a_dot_recip, 0,age[i], (h0, om_m, om_l))[0]*conv
test = scipy.integrate.quad(_a_dot_recip, 0,test, (h0, om_m, om_l))[0]*conv
#age = np.array([age]) #So that we can easily take the transpose of age to concatenate with mass_progen
pid = pg.readsnap(pathname+'snapdir_%03d/snapshot_%03d'%(snum,snum),'pid','star')
bob = age[np.in1d(pid, main_part[:,0].astype('int'))]
main_part[np.argsort(main_part[:,0].astype('int')),11] = bob[np.argsort(pid[np.in1d(pid, main_part[:,0].astype('int'))])]/3600/24/365/1e9
#print main_part[np.argsort(main_part[:,0].astype('int')),0],main_part[np.argsort(main_part[:,0].astype('int')),11]
#main_part[np.argsort(main_part[np.in1d(main_part[:,0].astype('int'),bob[:,0].astype('int')),0])= bob[np.argsort(bob[np.in1d(bob[:,0].astype('int'),bob[:,0].astype('int')),0])
return main_part
def find_simulation_properties(self):
"""
This finds the attributes of the simulation such as
side length, number of DM paticles, number of DM JK files,
the redshift, the hubble constant.
TODO: figure out the cosmology.
"""
print "Reading the snapshot header."
import pygadgetreader as pgr
header = pgr.readheader(self.dm_files,"header")
self.pgrheader = header
self.particle_mass = max(header['massTable'])
self.side_length = header['boxsize']
self.dm_count = header['ndm']
self.ndm_jks = header['nfiles']
self.ndm_ndivs = int(round(self.ndm_jks**(1./3.)))
self.redshift = header['redshift']
self.hubble_const = header['h']
print "\tSnapshot header read. Simulation properties saved."
return
import numpy as np
from matplotlib import rc
import pylab as plt
import sys
import struct
import pygadgetreader as pg
import random
def getRad(array):
return pow(pow(array[0], 2) + pow(array[1], 2) + pow(array[2], 2), 0.5)
filename = "original_nfw"
nparts = pg.readheader(filename, "dmcount")
dmmass = pg.readsnap(filename, "mass", 'dm')[0]
bins = [0 + i / 5.0 for i in range(20)]
pos = pg.readsnap(filename, "pos", "dm")
vel = pg.readsnap(filename, "vel", "dm")
radii = []
vels = []
for i in range(nparts):
radii.append(getRad(pos[i]))
vels.append(getRad(vel[i]))
M = [0.0 for i in range(len(bins))]
N = [0 for i in range(len(bins))]
import sys
import struct
import pygadgetreader as pg
import random
import math
infile = 'icsBIG_random'
outfile = 'cone_BIG'
with open(infile, mode='rb') as file:
filecontent = file.read()
file.close()
f=0
rbump=372.448
Mmove=8.2
N=pg.readheader(infile,"dmcount")
M=struct.unpack("dddddd",filecontent[28:28+8*6])[1]
Nmove=int(Mmove/M)
PPos=[]
PVel=[]
PID=[]
PMass=[]
for i in range(N):
#Read Everything
#The positions start at byte 268 (264-268 is an int 12*N)
position=struct.unpack("fff",filecontent[268+12*i:268+12*i+12])
PPos.append([p-1000.0 for p in position])
#The velocities start at byte 276+12*N (8 previous bytes are 12*N, repeated twice)
PVel.append(filecontent[276+12*N+12*i:276+12*N+12*i+12])
#The particle IDs start at byte 284+24*N (8 previous bytes are 12*N then 4*N)
PID.append(filecontent[284+24*N+4*i:284+24*N+4*i+4])
def create_df(pathname,hist,hnum,dm):
h0 = 71
om_l = 0.734
om_m = 0.266
conv = 3.085677581e+19
numcores = 16
numsnaps = 185
massp = 1.67262178e-24 #in grams
gamma = 5./3.
kb = 1.3806e-26 #in km^2*g/s^2
for i in np.arange(len(hist)):
print i
if hist[184-i,1] != 0:
switch = 0
for j in np.arange(numcores): #Bring together all the AHF files for the snapshot
temph = glob.glob(pathname+'analysis/ahf_snap%03d/ahf.snap_%03d.%04d.z*.*.AHF_halos'%(i,i,j))
temph = str(temph).strip('[]').replace("'","")
h = np.genfromtxt(temph)
temppr = glob.glob(pathname+'analysis/ahf_snap%03d/ahf.snap_%03d.%04d.z*.*.AHF_profiles'%(i,i,j))
temppr = str(temppr).strip('[]').replace("'","")
p = np.genfromtxt(temppr)
if switch == 0 and len(h) >0:
halo = h
switch = 1
if switch == 1:
try:
halo = np.vstack((halo,h))
except:
print "nothing there"
for j in np.arange(len(halo)): #Find our halo from all the halos of the snapshot
try:
if halo[j,0] == hist[184-i,1]:
mvir = halo[j,3]/.71
vmax = halo[j,16]
xcen = halo[j,5]/1000. #Grab relevant data (can always add more later)
ycen = halo[j,6]/1000.
zcen = halo[j,7]/1000.
rvir = halo[j,11]/1000./.71
rmax = halo[j,12]/1000./.71
rhalf = 0
sname = "%ssnapdir_%03d/snapshot_%03d"%(pathname,i,i)
bsize = pg.readheader(sname, 'boxsize')
if bsize > 25: #mfm007 is in kpc while everything else (even gizdm007) is in Mpc. This standardizes all that.
kfix = 1000
else:
kfix = 1
red = pg.readheader(sname, 'redshift')
a = pg.readheader(sname, 'time')
yr = scipy.integrate.quad(_a_dot_recip, 0,a, (h0, om_m, om_l))[0]*conv/(60*60*24*365*1e9)
dpid = pg.readsnap(sname, 'pid', 'dm')
dmass = pg.readsnap(sname, 'mass', 'dm')*1.e10/.71
dpos = pg.readsnap(sname, 'pos', 'dm')/kfix
dvel = pg.readsnap(sname, 'vel', 'dm')
ddiff = np.sqrt((dpos[:,0]-xcen)**2+(dpos[:,1]-ycen)**2+(dpos[:,2]-zcen)**2)/.71
dpos = dpos[ddiff<rvir]
dvel = dvel[ddiff<rvir]
dmass = dmass[ddiff<rvir]
dpid = dpid[ddiff<rvir]
ddiff = ddiff[ddiff<rvir]
rhalf = 0
hdf = pd.HDFStore('%sanalysis/dataframes/halo%s%s_giz%s_snap%03d.h5'%(pathname,hnum,res,ver,i))
hdf.put('particles/dm',pd.DataFrame(np.hstack((dpos,np.matrix(ddiff).T,np.matrix(dmass).T)), index = dpid, columns = (['x','y','z','r','mass'])))
if dm == 0:
mstar = halo[j,64]/.71
zarray = pg.readsnap(sname, 'zarray', 'gas')
he_mf = zarray[:,1] #Helium mass fraction
y_he = he_mf/(4*(1-he_mf))
ne = pg.readsnap(sname, 'ne', 'gas') #Electron Abundance
mu = (1+4*y_he)/(1+y_he+ne)
mmw = mu*massp #mean molecular weight
u = pg.readsnap(sname,'u','gas') #specific internal energy in km^2/s^2
temp = mmw * (gamma-1.)*u/kb #temperature of gas
gpid = pg.readsnap(sname, 'pid', 'gas')
spid = pg.readsnap(sname, 'pid', 'star')
gmass = pg.readsnap(sname, 'mass', 'gas')*1.e10/.71
smass = pg.readsnap(sname, 'mass', 'star')*1.e10/.71
gpos = pg.readsnap(sname, 'pos', 'gas')/kfix
spos = pg.readsnap(sname, 'pos', 'star')/kfix
gvel = pg.readsnap(sname, 'vel', 'gas')/kfix
svel = pg.readsnap(sname, 'vel', 'star')/kfix
sfr = pg.readsnap(sname, 'sfr', 'gas')
sft = pg.readsnap(sname, 'age', 'star')
tmp = np.array([0,0])
gdiff = np.sqrt((gpos[:,0]-xcen)**2+(gpos[:,1]-ycen)**2+(gpos[:,2]-zcen)**2)/.71
sdiff = np.sqrt((spos[:,0]-xcen)**2+(spos[:,1]-ycen)**2+(spos[:,2]-zcen)**2)/.71
gpos = gpos[gdiff<rvir]
gvel = gvel[gdiff<rvir]
gmass = gmass[gdiff<rvir]
temp = temp[gdiff<rvir]
sfr = sfr[gdiff<rvir]
gpid = gpid[gdiff<rvir]
gdiff = gdiff[gdiff<rvir]
spos = spos[sdiff<rvir]
svel = svel[sdiff<rvir]
smass = smass[sdiff<rvir]
sft = sft[sdiff<rvir]
spid = spid[sdiff<rvir]
sdiff = sdiff[sdiff<rvir]
sortsdiff = sdiff[np.argsort(sdiff)]
cumsmass = np.cumsum(smass[np.argsort(sdiff)])
q = 0
print len(sortsdiff), mstar, max(cumsmass)
while (cumsmass[q]<=mstar/2):
rhalf = sortsdiff[q]
q = q+1
hdf.put('particles/gas',pd.DataFrame(np.hstack((gpos,np.matrix(gdiff).T,np.matrix(gmass).T,np.matrix(temp).T,np.matrix(sfr).T)), index = gpid, columns = (['x','y','z','r','mass','temp','sfr'])))
hdf.put('particles/star',pd.DataFrame(np.hstack((spos,np.matrix(sdiff).T,np.matrix(smass).T,np.matrix(sft).T)), index = spid, columns = (['x','y','z','r','mass','sft'])))
props = np.array([[xcen,ycen,zcen,rvir,rhalf,rmax,vmax,red,yr]])
hdf.put('props',pd.DataFrame(props,index = [halo[j,0]], columns = (['halox','haloy','haloz','rvir','rhalf','rmax','vmax','redshift','time'])))
hdf.close()
except Exception,f:
print f
props = np.array([[xcen,ycen,zcen,rvir,rhalf,rmax,vmax,red,yr]])
print halo[j,0], props
hdf = pd.HDFStore('%sanalysis/dataframes/halo%s%s_giz%s_snap%03d.h5'%(pathname,hnum,res,ver,i))
hdf.put('props',pd.DataFrame(props,index = [halo[j,0]], columns = (['halox','haloy','haloz','rvir','rhalf','rmax','vmax','redshift','time'])))
hdf.close()
print "MISS"
def radpro(pathname,sname,hist,dmo,rhalf,rmax):
global i, grain, clr, count,conv
numcores = 16
massp = 1.67262178e-24 #in grams
gamma = 5./3.
kb = 1.3806e-26 #in km^2*g/s^2
G = 4.3e-6 #in kpc/M_sun (km/s)^2
switch = 0
for j in np.arange(numcores): #Bring together all the AHF files for the snapshot
temph = glob.glob(pathname+'ahf_snap%03d/ahf.snap_%03d.%04d.z*.*.AHF_halos'%(i,i,j))
temph = str(temph).strip('[]').replace("'","")
h = np.genfromtxt(temph)
temppr = glob.glob(pathname+'ahf_snap%03d/ahf.snap_%03d.%04d.z*.*.AHF_profiles'%(i,i,j))
temppr = str(temppr).strip('[]').replace("'","")
p = np.genfromtxt(temppr)
if switch == 0:
halo = h
switch = 1
if switch == 1:
try:
halo = np.vstack((halo,h))
except:
print "nothing there"
for j in np.arange(len(halo)): #Find our halo from all the halos of the snapshot
if halo[j,0] == hist[184-i,1]:
mstar = halo[j,64]
mvir = halo[j,3]
vmax = halo[j,16]
xcen = halo[j,5] #Grab relevant data (can always add more later)
ycen = halo[j,6]
zcen = halo[j,7]
rvir = halo[j,11]/.71
bsize = pg.readheader(sname, 'boxsize')
if bsize > 25: #mfm007 is in kpc while everything else (even gizdm007) is in Mpc. This standardizes all that.
kfix = 1
else:
kfix = 1000
mass = pg.readsnap(sname, 'mass', 'dm')*1.e10/.71
pos = pg.readsnap(sname, 'pos', 'dm')*kfix
tmp = np.array([0,0])
diff = np.sqrt((pos[:,0]-xcen)**2+(pos[:,1]-ycen)**2+(pos[:,2]-zcen)**2)/.71
mass = mass[diff<=rvir]
diff = diff[diff<=rvir]
cum = np.cumsum(mass[np.argsort(diff)])
print xcen,ycen,zcen, rvir,pos
binz = np.logspace(np.log10(.06),np.log10(rvir),grain)
massall, bin_edge = np.histogram( diff,bins=binz, weights =mass)
x = 10**(np.log10(binz[1:])-np.log10(binz[1]/binz[0])/2)
if dmo == 0:
rmax = halo[j,12]/.71
gmass = pg.readsnap(sname, 'mass', 'gas')*1.e10/.71
smass = pg.readsnap(sname, 'mass', 'star')*1.e10/.71
gpos = pg.readsnap(sname, 'pos', 'gas')*kfix
spos = pg.readsnap(sname, 'pos', 'star')*kfix
sdiff = np.sqrt((spos[:,0]-xcen)**2+(spos[:,1]-ycen)**2+(spos[:,2]-zcen)**2)/.71
gdiff = np.sqrt((gpos[:,0]-xcen)**2+(gpos[:,1]-ycen)**2+(gpos[:,2]-zcen)**2)/.71
smass = smass[sdiff<=rvir]
gmass = gmass[gdiff<=rvir]
sdiff = sdiff[sdiff<=rvir]
gdiff = gdiff[gdiff<=rvir]
scum = np.cumsum(smass[np.argsort(sdiff)])
gcum = np.cumsum(gmass[np.argsort(gdiff)])
totdiff = np.append(np.append(diff,sdiff),gdiff)
totmass = np.append(np.append(mass,smass),gmass)
totcum = np.cumsum(totmass[np.argsort(totdiff)])
irhalf = abs(scum-sum(smass)/2).argmin()
rhalf = sdiff[np.argsort(sdiff)][irhalf]
itotrhalf = abs(np.sort(totdiff)-rhalf).argmin()
print 'rhalf is %f'%rhalf
irmax = np.sqrt(G*totcum/np.sort(totdiff)).argmax()
rmax = totdiff[np.argsort(totdiff)][irmax]
print 'rmax is %f'%rmax
#print len(sdiff), binz, len(smass)
gmassall, bin_edge = np.histogram( gdiff,bins=binz, weights =gmass)
smassall, bin_edge = np.histogram( sdiff,bins=binz, weights =smass)
#irhalf = (abs(bin_edge-max(bin_edge[np.cumsum(smassall)<=sum(smassall)/2]))).argmin()
#print bin_edge[np.cumsum(smassall)<=sum(smassall)/2],rvir,sum(smassall)#sum(smassall), np.cumsum(smassall) #x[irhalf],np.sqrt(G*sum(massall[:irhalf+1])/x[irhalf])
ax1.scatter(rhalf,np.sqrt(G*totcum[itotrhalf]/rhalf),marker='s',s = 80,color='%s'%clr[count],label='%s'%(hnum[w]))
#ax1.scatter(rmax,np.sqrt(G*totcum[irmax]/rmax),marker='D',s = 80,color='%s'%clr[count],label='%s Rmax'%(hnum))
return massall, gmassall, smassall, x, rhalf,rmax
else:
massall = 0.83120300751*massall
irhalf = (abs(np.sort(diff)-rhalf)).argmin()
irmax = (abs(np.sort(diff)-rmax)).argmin()
print np.sqrt(G*cum[irhalf]/rhalf), np.sqrt(G*cum[irmax]/rmax)
ax1.scatter(rhalf,np.sqrt(G*cum[irhalf]/rhalf),marker='^',s = 80,color='%s'%clr[count],label='%s DMO'%(hnum[w]))
#ax1.scatter(rmax,np.sqrt(G*cum[irmax]/rmax),marker='v',s = 80,color='%s'%clr[count],label='%s DMO Rmax'%(hnum))
count +=1
return massall, x
def gather_particles(main_progen,pathname,snum,hnum,fnum): #Use progenitors array to gather all their star particles in AHF particle files into the main particle array (now we have each particles' ID, position, velocity and whether they were part of the main progenitor or from a merger)
global switch
h0 = 71
om_l = 0.734
om_m = 0.266
conv = 3.085677581e+19
fix = 1
mainhaloid, mainprogenid, progen = gather_progen(pathname,snum,hnum)
my_cols = ['id', 'type', 'x', 'y', 'z', 'vx', 'vy', 'vz']
for i in np.arange(fnum):
temp = glob.glob(pathname+'analysis/ahf_snap%03d/ahf.snap_%03d.%04d.z*.*.AHF_particles'%(snum-1,snum-1,i))
temp = str(temp).strip('[]').replace("'","")
prev_particles = pd.read_csv(temp, names=my_cols, sep='\t')
prev_particles['main'] = pd.Series(2*np.ones(len(prev_particles)),index=prev_particles.index) # append a new column that denotes whether the particle is in the main halo (1), is from a merger(0) or is undetermined (2).
prev_particles['r_form'] = pd.Series(np.zeros(len(prev_particles)),index=prev_particles.index)
prev_particles['atime'] = pd.Series(np.zeros(len(prev_particles)),index=prev_particles.index)
prev_particles['ctime'] = pd.Series(np.zeros(len(prev_particles)),index=prev_particles.index)
prev_particles['mass'] = pd.Series(np.zeros(len(prev_particles)),index=prev_particles.index)
for j,e in enumerate(prev_particles['id']): # Search through particle file to find instances where the first column contains two numbers (acts as a header for each halo).
if type(e)==types.StringType and len(e.split())==2 and (int(e.split()[1]) in progen)==True: # Make sure the halo id is in the progenitor array
haloid = int(e.split()[1])# e.split()[0] is the number of particles, [1] is the halo ID
numpart = int(e.split()[0])
halostars =np.array(prev_particles.ix[j+1:j+numpart][prev_particles.ix[j+1:j+numpart,'type']==4])
if len(halostars>0):
try:
if haloid == mainprogenid: #Main progenitor?
if switch == 0:
halostars[:,8] = 1
halostars = formation_radius(pathname,snum,i,mainprogenid,halostars)
switch = 1
else:
halostars[np.logical_not(np.in1d(halostars[:,0].astype('int'),main_progen[:,0].astype('int'))),8] = 3 #Mark particles in halostars that arent in main_progen as 3.
main_progen[np.logical_not(np.in1d(main_progen[:,0].astype('int'),halostars[:,0].astype('int'))),8] = 3 # Mark particles in main_progen that arent in halostars as 3. This is just in case the main progenitor did not contribute ALL of its particles to the daughter.
hstar_und = halostars[:,8]==2 #Undetermined particles remaining in the halostars array (need their flags from main_progen) <---this might be overkill but its good to have regardless
main_need = main_progen[:,8]!=3 #Cuts out all the particles that did not participate in merger
halostars[np.argsort(halostars[hstar_und,0].astype('int')),8] = main_progen[np.argsort(main_progen[main_need,0].astype('int')),8]
halostars[np.argsort(halostars[hstar_und,0].astype('int')),9] = main_progen[np.argsort(main_progen[main_need,0].astype('int')),9]
halostars[np.argsort(halostars[hstar_und,0].astype('int')),10] = main_progen[np.argsort(main_progen[main_need,0].astype('int')),10]
halostars[np.argsort(halostars[hstar_und,0].astype('int')),11] = main_progen[np.argsort(main_progen[main_need,0].astype('int')),11]
halostars[np.argsort(halostars[hstar_und,0].astype('int')),12] = main_progen[np.argsort(main_progen[main_need,0].astype('int')),12]
else:# Then Merger.
halostars[:,8] = 0 #Now the last column becomes a zero to denote that the particle came from a merger MAY NEED TO EDIT THIS. CLEARLY THE COLUMNS ARE BEING PUT IN OUT OF ORDER.
atime = pg.readheader(pathname+'snapdir_%03d/snapshot_%03d'%(snum,snum),'time')
atime = scipy.integrate.quad(_a_dot_recip, 0,atime, (h0, om_m, om_l))[0]*conv/3600/24/365/1e9
halostars[:,10] = atime# SET EQUAL TO ACCRETION TIME. ALTER C TIME TO 11 AND MASS FOR 12!!!!!
progen_part = np.vstack((progen_part, halostars)) #Add the id of particle, the type (only allow stars at this point), position, velocity and main or merger flag.
except Exception,f:
print f
if haloid == mainprogenid:
if switch == 0:
halostars[:,8] = 1
halostars = formation_radius(pathname,snum,i,mainprogenid,halostars)
switch = 1
else:
halostars[np.logical_not(np.in1d(halostars[:,0].astype('int'),main_progen[:,0].astype('int'))),8] = 3
main_progen[np.logical_not(np.in1d(main_progen[:,0].astype('int'),halostars[:,0].astype('int'))),8] = 3
hstar_und = halostars[:,8]==2 #Undetermined particles remaining in the halostars array (need their flags from main_progen) <---this might be overkill but its good to have regardless
main_need = main_progen[:,8]!=3 #Cuts out all the particles that did not participate in merger
if len(halostars[hstar_und])>0:
halostars[np.argsort(halostars[hstar_und,0].astype('int')),8] = main_progen[np.argsort(main_progen[main_need,0].astype('int')),8]
else:
halostars[:,8] = 0
progen_part = halostars
import numpy as np
from matplotlib import rc
import pylab as plt
import sys
import struct
import pygadgetreader as pg
import random
original='icsMED'
outfile='icsMED_random'
with open(original, mode='rb') as file:
filecontent = file.read()
file.close()
N=pg.readheader(original,"dmcount")
print N
print struct.unpack("dddddd",filecontent[28:28+8*6])
head=filecontent[0:268]
PPos=[]
PVel=[]
PID=[]
PMass=[]
for i in range(N):
#Read Everything
#The positions start at byte 268 (264-268 is an int 12*N)
PPos.append(filecontent[268+12*i:268+12*i+12])
#The positions start at byte 276+12*N (8 previous bytes are 12*N, repeated twice)
PVel.append(filecontent[276+12*N+12*i:276+12*N+12*i+12])
#The particle IDs start at byte 284+24*N (8 previous bytes are 12*N then 4*N)
PID.append(filecontent[284+24*N+4*i:284+24*N+4*i+4])
import numpy as np
from matplotlib import rc
import pylab as plt
import sys
import struct
import pygadgetreader as pg
import random
with open('cube1e12', mode='rb') as file:
filecontent = file.read()
file.close()
f = 0
N = pg.readheader('cube1e12', "dmcount")
PPos = []
PVel = []
PID = []
PMass = []
for i in range(N):
#Read Everything
#The positions start at byte 268 (264-268 is an int 12*N)
PPos.append(filecontent[268 + 12 * i:268 + 12 * i + 12])
#The velocities start at byte 276+12*N (8 previous bytes are 12*N, repeated twice)
PVel.append(filecontent[276 + 12 * N + 12 * i:276 + 12 * N + 12 * i + 12])
#The particle IDs start at byte 284+24*N (8 previous bytes are 12*N then 4*N)
PID.append(filecontent[284 + 24 * N + 4 * i:284 + 24 * N + 4 * i + 4])
#This is followed by 4 bytes, 4*N. The particle mass array is not present in the file.
#PMass.append(filecontent[280+28*N+4*i:280+28*N+4*i+4])
PPos2 = ''
PVel2 = ''
#add it to the lists
#A key point to note is that the format of the file differs a bit from what's in the documentation. Each block (Header, Pos, Vel, Id) is bracketed by a 4-byte integer before and after equal to the number of bytes in that block. So the header, for example, does not go from 0-256, but rather 4-260, with 0-4 and 260-264 both being the integer 256. I can't find mention of this in the documentation.
#The positions start at byte 268 (264-268 is an int 12*N)
PPos = PPos + filecontent[268 + 12 * n:268 + 12 * n + 12]
#The positions start at byte 276+12*N (8 previous bytes are 12*N, repeated twice)
PVel = PVel + filecontent[276 + 12 * N[1] + 12 * n:276 + 12 * N[1] +
12 * n + 12]
#The particle IDs start at byte 284+24*N (8 previous bytes are 12*N then 4*N)
PID = PID + filecontent[284 + 24 * N[1] + 4 * n:284 + 24 * N[1] +
4 * n + 4]
#This is followed by 4 bytes, 4*N. The particle mass array is not present in the file.
#PMass = PMass+filecontent[280+28*N[1]+4*n:280+28*N[1]+4*n+4]
#Create the new file, packing up and concatenating all the data
filecontentnew = filecontent[:4] + packN + packM + filecontent[
76:100] + packN + filecontent[124:264] + struct.pack(
'i', Ndm * 12) + PPos + struct.pack('i', Ndm * 12) + struct.pack(
'i',
Ndm * 12) + PVel + struct.pack('i', Ndm * 12) + struct.pack(
'i', Ndm * 4) + PID + struct.pack('i', Ndm * 4)
with open('output', mode='wb') as file:
file.write(filecontentnew)
file.close()
#This just checks to make sure the file completed correctly
filename = 'output'
print pg.readheader(filename, "dmcount")
print pg.readheader(filename, "starcount")
print pg.readsnap(filename, "mass", 'dm')[0]
with open(infile, mode='rb') as file:
filecontent = file.read()
file.close()
#f is the SIDM fraction, Ndm is the total number of particles you want. This script takes the random NFW profile (as input) and makes half the dark matter particles non-interacting. It then adjusts the masses so as to give the desired SIDM fraction (by mass).
f = float(sys.argv[1])
Ndm = -1 #-1 for default (leave total number of particles unchanged). This removes the random sampling.
#This array lists the number of particles of each species
N = struct.unpack("iiiiii", filecontent[4:28])
print N
if (Ndm == -1):
#This leaves the number of particles unchanged, and therefore we don't rely on the random sampling.
Ndm = N[1]
packN = struct.pack('iiiiii', 0, int(Ndm * 0.5), 0, 0,
Ndm - int(Ndm * 0.5), 0)
M = struct.unpack("dddddd", filecontent[28:28 + 8 * 6])
print M
packM = struct.pack('dddddd', 0, 2 * f * M[1], 0, 0, 2 * (1 - f) * M[1], 0)
filecontentnew = filecontent[:4] + packN + packM + filecontent[
76:100] + packN + filecontent[124:]
with open(outfile, mode='wb') as file:
file.write(filecontentnew)
file.close()
#This just checks to make sure the file completed correctly
print pg.readheader(outfile, "dmcount")
print pg.readheader(outfile, "starcount")
print pg.readsnap(outfile, "mass", 'dm')[0]