def __init__(self, res, vel, snapnum):
#self.res = res
#self.vel = vel
#self.snapnum = snapnum
if res == "1.12Mpc":
s_res = '112Mpc'
elif res == "1.4Mpc":
s_res = '14Mpc'
if vel == "Sig0":
s_vel = "Sig0"
elif vel == "11.8kms":
s_vel = '118kms'
snapnum = int(snapnum)
filename = "/n/hernquistfs3/mvogelsberger/GlobularClusters/InterfaceWArepo_All_" + res + '_' + vel + "/output/"
filename2 = filename + "GasOnly_FOF" #Used for readsubfHDF5
########## CHANGED FILENAME3 TO GROUPORDERED IN GAS ONLY
filename3 = filename2 + "/snap-groupordered_" + str(snapnum).zfill(
3) #Used for hdf5lib, snapHDF5
#### Not sure if this works with change but don't care about 2.8
if res == '2.8Mpc':
filename3 = filename + "snapdir_" + str(snapnum).zfill(
3) + "/snap_" + str(snapnum).zfill(3)
#Units
GRAVITY_cgs = 6.672e-8
UnitLength_in_cm = 3.085678e21 # code length unit in cm/h
UnitMass_in_g = 1.989e43 # code length unit in g/h
UnitVelocity_in_cm_per_s = 1.0e5
UnitTime_in_s = UnitLength_in_cm / UnitVelocity_in_cm_per_s
UnitDensity_in_cgs = UnitMass_in_g / np.power(UnitLength_in_cm, 3)
UnitPressure_in_cgs = UnitMass_in_g / UnitLength_in_cm / np.power(
UnitTime_in_s, 2)
UnitEnergy_in_cgs = UnitMass_in_g * np.power(
UnitLength_in_cm, 2) / np.power(UnitTime_in_s, 2)
GCONST = GRAVITY_cgs / np.power(
UnitLength_in_cm, 3) * UnitMass_in_g * np.power(UnitTime_in_s, 2)
critical_density = 3.0 * .1 * .1 / 8.0 / np.pi / GCONST #.1 is for 1/Mpc to 1/kpc, also in units of h^2
header = snap.snapshot_header(filename3)
if res == "2.8Mpc":
fs = hdf5lib.OpenFile(filename3 + ".0.hdf5")
else:
fs = hdf5lib.OpenFile(filename3 + ".hdf5")
red = hdf5lib.GetAttr(fs, "Header", "Redshift")
atime = hdf5lib.GetAttr(fs, "Header", "Time")
boxSize = hdf5lib.GetAttr(fs, "Header", "BoxSize")
boxSize *= atime #convert from ckpc/h to kpc/h
Omega0 = hdf5lib.GetAttr(fs, "Header", "Omega0")
OmegaLambda = hdf5lib.GetAttr(fs, "Header", "OmegaLambda")
fs.close()
cat = readsubfHDF5.subfind_catalog(filename2, snapnum)
Omega_a = Omega0 / (Omega0 + OmegaLambda * atime * atime * atime)
critical_density *= (Omega0 / Omega_a)
r200 = cat.Group_R_Crit200
r200 *= atime #convert from ckpc/h to kpc/h
m200 = cat.Group_M_Crit200
haloCMvel = cat.GroupVel
haloCMvel *= 1. / atime #convert from km/s/a to km/s
haloPos = cat.GroupPos
haloPos *= atime #convert from ckpc/h to kpc/h
#Read in particles
#read in all simulation masses to calculate cosmic baryon fraction
massgassim = snap.read_block(filename + "snap_" +
str(snapnum).zfill(3),
"MASS",
parttype=0)
massdmsim = snap.read_block(filename + "snap_" + str(snapnum).zfill(3),
"MASS",
parttype=1)
massgas = snap.read_block(filename3, "MASS", parttype=0)
massdm = snap.read_block(filename3, "MASS", parttype=1)
posgas = snap.read_block(filename3, "POS ", parttype=0)
posdm = snap.read_block(filename3, "POS ", parttype=1)
velgas = snap.read_block(filename3, "VEL ", parttype=0)
veldm = snap.read_block(filename3, "VEL ", parttype=1)
#redefine position units from ckpc/h to kpc/h
posgas *= atime
posdm *= atime
#redefine velocity units from kmsqrt(a)/s to km/s
velgas *= np.sqrt(atime)
veldm *= np.sqrt(atime)
fb = massgassim.sum(dtype="float64") / (
massgassim.sum(dtype="float64") + massdmsim.sum(dtype="float64"))
gaslimit = .4 # Set the limit for gas fraction in plots
#boxSize hubble flow correction for halo CM velocity subtraction
boxSizeVel = boxSize * .1 * UnitLength_in_cm / UnitVelocity_in_cm_per_s * np.sqrt(
Omega0 / atime / atime / atime + OmegaLambda)
#load particle indices
pGas = snap.read_block(filename3, "POS ", parttype=0)
mGas = snap.read_block(filename3, "MASS", parttype=0)
pDM = snap.read_block(filename3, "POS ", parttype=1)
halo100_indices = np.where(cat.GroupLenType[:, 0] > 100)[0]
startAllGas = []
endAllGas = []
for i in halo100_indices:
startAllGas += [np.sum(cat.GroupLenType[:i, 0])]
endAllGas += [startAllGas[-1] + cat.GroupLenType[i, 0]]
#Initialize arrays
spinparam = np.zeros(np.size(halo100_indices))
jsptotspinparam = np.zeros(np.size(halo100_indices))
jspgasspinparam = np.zeros(np.size(halo100_indices))
jspdmspinparam = np.zeros(np.size(halo100_indices))
gasfrac = np.zeros(np.size(halo100_indices))
costheta = np.zeros(np.size(halo100_indices)) #misalignment angle
v200 = np.zeros(np.size(halo100_indices))
velgasall = np.zeros(np.size(halo100_indices))
veldmall = np.zeros(np.size(halo100_indices))
virialratio = np.zeros(np.size(halo100_indices))
numGas = np.zeros(np.size(halo100_indices))
numDM = np.zeros(np.size(halo100_indices))
j200gas = np.zeros(np.size(halo100_indices))
j200dm = np.zeros(np.size(halo100_indices))
j200 = np.zeros(np.size(halo100_indices))
totmass = np.zeros(np.size(halo100_indices))
gasmass = np.zeros(np.size(halo100_indices))
DMmass = np.zeros(np.size(halo100_indices))
rmax = np.zeros(np.size(halo100_indices))
rmin = np.zeros(np.size(halo100_indices))
j200gasNoNorm = np.zeros(np.size(halo100_indices))
closestm200 = np.zeros(np.size(halo100_indices))
#some radii are errors and negative, will have a value of 1 to be excluded
negradii = np.zeros(np.size(halo100_indices))
#Indexing for global variable works because halos are ordered from largest to smallest so <100 particles are at the end and not counted.
for i in halo100_indices:
exec("cm = cm_%s_%s_%d[0][i]" % (s_res, s_vel, snapnum))
exec("rotation = rotation_%s_%s_%d[0][i]" %
(s_res, s_vel, snapnum))
exec("radii = radii_%s_%s_%d[0][i]" % (s_res, s_vel, snapnum))
#some radii are errors and negative, will have a value of 1 to be excluded
if radii[0] < 0.:
negradii[i] = 1.
else:
maxrad = radii[2]
maxrad *= atime #convert from ckpc to kpc
exec("mDM=mDM_%s_%s_%d[0][i]" % (s_res, s_vel, snapnum))
exec("DMinEll=DMindices_%s_%s_%d[0][i]" %
(s_res, s_vel, snapnum))
exec("m200dm = M200dm_%s_%s[snapnum-10][i]" % (s_res, s_vel))
#Check if CM is buggy
if np.sum(cm == np.array([0., 0., 0.])) == 3:
# it's probbaly an error; recompute com
totalGas = np.sum(mGas[startAllGas[i]:endAllGas[i]])
cm = np.array([
np.sum(pGas[startAllGas[i]:endAllGas[i], j] *
mGas[startAllGas[i]:endAllGas[i]]) / totalGas
for j in range(3)
])
# Get positions of gas particles
P = pGas[startAllGas[i]:endAllGas[i]]
# Shift coordinate system to center on the center of the ellipsoid
Precentered = dx_wrap(P - cm, boxSize / atime)
# Rotate coordinated to the the axes point along x,y,z directions:
Precentered = np.array(
[np.dot(pp, rotation.T) for pp in Precentered])
# Figure out which particles are inside the ellipsoid
inEll = (Precentered[:, 0]**2. / radii[0]**2. +
Precentered[:, 1]**2. / radii[1]**2 +
Precentered[:, 2]**2. / radii[2]**2) <= 1.
#remove halo CM velocity
tempvelgas = dx_wrap(
velgas[startAllGas[i]:endAllGas[i]][inEll] - haloCMvel[i],
boxSizeVel)
tempveldm = dx_wrap(veldm[DMinEll] - haloCMvel[i], boxSizeVel)
#redefine positions wrt COM
tempposgas = dx_wrap(
posgas[startAllGas[i]:endAllGas[i]][inEll] - haloPos[i],
boxSize)
tempposdm = dx_wrap(posdm[DMinEll] - haloPos[i], boxSize)
numDM[i] = np.size(tempposdm)
numGas[i] = np.size(tempposgas)
#Calculating j200
#j200 of all particles
j200vecgas = np.sum(
np.cross(tempposgas, tempvelgas) *
massgas[startAllGas[i]:endAllGas[i]][inEll][:, np.newaxis],
axis=0)
j200vecdm = np.sum(np.cross(tempposdm, tempveldm) *
massdm[DMinEll][:, np.newaxis],
axis=0)
#if np.size(tempveldm)!=0: #can be no dm particles!
# costheta[i] = np.dot(j200vecgas,j200vecdm)/np.linalg.norm(j200vecgas)/np.linalg.norm(j200vecdm)
j200vec = j200vecgas + j200vecdm
j200[i] = np.linalg.norm(j200vec)
j200dm[i] = np.linalg.norm(j200vecdm)
j200gas[i] = np.linalg.norm(j200vecgas)
j200gasNoNorm[i] = np.linalg.norm(j200vecgas)
gasmass[i] = np.sum(
massgas[startAllGas[i]:endAllGas[i]][inEll])
totmass[i] = gasmass[i] + mDM
DMmass[i] = mDM
rmax[i] = radii[2]
rmin[i] = radii[0]
closestm200[i] = m200dm
#using fudicial m200~6mgas
#get r200 from analytic formula in Barkana,Loeb 01 review
if gasmass[i] != 0.: #Some ellpsoids fit nothing
m200fid = 6. * gasmass[i]
omgz = .27 * atime**(-3.) / (.27 * atime**(-3.) + .73)
dfact = omgz - 1.
delc = 18. * np.pi**2. + 82 * dfact - 39. * dfact**2.
r200fid = .784 * (m200fid * 100.)**(1. / 3.) * (
.27 / omgz * delc / 18. / np.pi**2)**(-1. /
3.) * 10 * atime
v200fid = np.sqrt(GCONST * (m200fid) / r200fid)
j200gas[i] *= 1. / np.sqrt(2) / (
gasmass[i]) / v200fid / r200fid
j200[i] *= 1. / np.sqrt(2) / (
totmass[i]) / v200fid / r200fid
if mDM != 0.:
j200dm[i] *= 1. / np.sqrt(2) / mDM / v200fid / r200fid
gasfrac[i] = gasmass[i] / totmass[i]
#Reindex to account for shrunken ellipsoids with gas particles >100
goodidx, = np.where(np.logical_and(numGas > 100, negradii == 0.))
self.j200gas = j200gas[goodidx]
self.j200dm = j200dm[goodidx]
self.j200 = j200[goodidx]
self.j200gasNoNorm = j200gasNoNorm[goodidx]
self.gasfrac = gasfrac[goodidx]
self.totmass = totmass[goodidx]
self.totmass *= 10**10
#costheta = costheta[goodidx]
self.rmax = rmax[goodidx]
self.rmin = rmin[goodidx]
#thetadeg = np.arccos(costheta)*180./np.pi
self.gasmass = gasmass[goodidx]
self.closestm200 = closestm200[goodidx]
#Reindex the Rmin, R200_DM params
exec("self.rclosest = Rmin_%s_%s[snapnum-10][goodidx]" %
(s_res, s_vel))
exec("self.R200dm = R200dm_%s_%s[snapnum-10][goodidx]" %
(s_res, s_vel))
fp_result = open(
'/home/nakazatoyr/arepo-c/Analysis/ArepoPostProcessing-H/snapnum_ID_matching_'
+ res + '_' + vel + '_' + species + '.dat', 'w')
SIGO_data = np.loadtxt(
'/home/nakazatoyr/arepo-c/Analysis/ArepoPostProcessing-H/SIGOs_info_' +
res + '_' + vel + '_' + species + '.dat')
ID_posi = np.loadtxt(
'/home/nakazatoyr/arepo-c/Analysis/ArepoPostProcessing-H/SIGO_IDinfo_' +
res + '_' + vel + '_' + species + '.dat')
filename = "/xc-work/chiakign/arepo-c/" + res + vel + species + "/"
filename2 = filename + "GasOnly_FOF" #Used for readsubfHDF5
#filename3_032 = filename2 + "/snap-groupordered_" + str(32).zfill(3) #Used for snapHDF5
filename3_030 = filename2 + "/snap-groupordered_" + str(30).zfill(
3) #Used for snapHDF5
print(filename3_030)
iGas = snapHDF5.read_block(filename3_030, "ID ",
parttype=0) #load particle indices and catalogs
print('loading data done!')
#get unique ID
#for i in range(ID_posi.shape[0]):
for i in [0]:
if i > 10:
break
else:
idx = int(ID_posi[i, 0]) #SIGO_idx
startidx = int(ID_posi[i, 1]) #startAllGas
endidx = int(ID_posi[i, 2]) #endAllGas
ID = iGas[startidx:endidx]
fp_result = open(
'/home/nakazatoyr/arepo-c/Analysis/ArepoPostProcessing-H/halo' +
str(i) + '_ID_matching_' + res + '_' + vel + '_' + species +
#Read header information header = snapHDF5.snapshot_header(filename3) red = header.redshift atime = header.time boxSize = header.boxsize Omega0 = header.omega0 OmegaLambda = header.omegaL massDMParticle = header.massarr[1] #all DM particles have same mass #redshift evolution of critical_density critical_density *= Omega0 + atime**3 * OmegaLambda critical_density_gas = critical_density * baryonfraction #load particle indices and catalogs pGas= snapHDF5.read_block(filename3,"POS ", parttype=0) mGas= snapHDF5.read_block(filename3,"MASS", parttype=0) pDM = snapHDF5.read_block(filename3,"POS ", parttype=1) cat = readsubfHDF5.subfind_catalog(filename2, snapnum) halo100_indices= np.where(cat.GroupLenType[:,0] >100)[0] startAllGas = [] endAllGas = [] for i in halo100_indices: startAllGas += [np.sum(cat.GroupLenType[:i,0])] endAllGas += [startAllGas[-1] + cat.GroupLenType[i,0]] SIGOidx = [] #Load shrinker and match data
dir = "/media/ethan/Watson/research/data/metaldiff/res880/"
# num = 500 # 132
# snap_name = "snapshot_"
# fname = Base_dir + sim_name + "/" + snap_name + "%03d" % (num)
fname = dir + "snapshot_600"
## Example: get info from header:
# header = snap.snapshot_header(fname)
# Ngas = header.nall[0]
# print("Num of gas=%s" % Ngas)
# ##----
# ## Example, read gas density:
# rho = snap.read_block(fname,"RHO ",parttype=0)
## Example, read stellar positions and mass:
pos_str = snap.read_block(
fname, "POS ",
parttype=4) #NOTE: get the 4-char flag "POS ", from the snappHDF5.py list
# mass_str = snap.read_block(fname,"MASS",parttype=4)
plt.plot(pos_str[:, 0], pos_str[:, 2], ',', alpha=0.2)
plt.title("x-z")
plt.show()
pdb.set_trace()
def readhalo(base,
snapbase,
num,
block_name,
parttype,
fof_num,
sub_num,
long_ids=False,
double_output=False,
verbose=False):
global FlagRead, cat, GroupOffset, HaloOffset, multiple, filename, Parttype, FileTypeNumbers, FileNum
if (FlagRead == False) | ((parttype in Parttype) == False):
if verbose:
print("READHALO: INITIAL READ")
#add parttype to list
Parttype.append(parttype)
if verbose:
print(("READHALO: Parttype = ", Parttype))
#read in catalog
cat = readsubfHDF5.subfind_catalog(base,
num,
long_ids=long_ids,
double_output=double_output,
keysel=[
"GroupLenType", "GroupNsubs",
"GroupFirstSub",
"SubhaloLenType",
"SubhaloMassType"
])
if (cat.ngroups == 0):
if verbose:
print("READHALO: no groups in catalog... returning")
return
if (FlagRead == False):
GroupOffset = np.zeros([cat.ngroups, 6], dtype="int64")
HaloOffset = np.zeros([cat.nsubs, 6], dtype="int64")
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
multiple = False
if (os.path.exists(filename + ".hdf5") == False):
filename = base + "/snapdir_" + str(num).zfill(
3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(
0)
multiple = True
if (os.path.exists(filename + ".hdf5") == False):
print(("READHALO: [error] file not found : ", filename))
sys.exit()
FlagRead = True
#construct offset tables
k = 0
for i in range(0, cat.ngroups):
if (i > 0):
GroupOffset[i, parttype] = GroupOffset[
i - 1, parttype] + cat.GroupLenType[i - 1, parttype]
if (cat.GroupNsubs[i] > 0):
HaloOffset[k, parttype] = GroupOffset[i, parttype]
k += 1
for j in range(1, cat.GroupNsubs[i]):
HaloOffset[k, parttype] = HaloOffset[
k - 1, parttype] + cat.SubhaloLenType[k - 1, parttype]
k += 1
if (k != cat.nsubs):
print(("READHALO: problem with offset table", k, cat.nsubs))
sys.exit()
#construct file tables
if (multiple):
filename = base + "/snapdir_" + str(num).zfill(
3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(0)
else:
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
head = snapHDF5.snapshot_header(filename)
FileNum = head.filenum
FileTypeNumbers = np.zeros([FileNum, 6], dtype="int64")
cumcount = np.zeros(6, dtype="int64")
for fnr in range(0, FileNum - 1):
if (multiple):
filename = base + "/snapdir_" + str(num).zfill(
3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(
fnr)
else:
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
if verbose:
print(("READHALO: initial reading file :", filename))
head = snapHDF5.snapshot_header(filename)
cumcount[:] += head.npart[:]
FileTypeNumbers[fnr + 1, :] = cumcount[:]
if (sub_num >= 0) & (fof_num < 0):
off = HaloOffset[sub_num, parttype]
left = cat.SubhaloLenType[sub_num, parttype]
if verbose:
print(("READHALO: nr / particle # / mass :", sub_num,
cat.SubhaloLenType[sub_num, parttype],
cat.SubhaloMassType[sub_num, parttype].astype("float64")))
if (fof_num >= 0) & (sub_num < 0):
off = GroupOffset[fof_num, parttype]
left = cat.GroupLenType[fof_num, parttype]
if verbose:
print(("READHALO: nr / particle # / mass :", fof_num,
cat.GroupLenType[fof_num, parttype],
cat.GroupMassType[fof_num, parttype].astype("float64")))
if (sub_num >= 0) & (fof_num >= 0):
real_sub_num = sub_num + cat.GroupFirstSub[fof_num]
off = HaloOffset[real_sub_num, parttype]
left = cat.SubhaloLenType[real_sub_num, parttype]
if verbose:
print(("READHALO: nr / particle # / mass :", real_sub_num,
cat.SubhaloLenType[real_sub_num, parttype],
cat.SubhaloMassType[real_sub_num,
parttype].astype("float64")))
if (left == 0):
if verbose:
print("READHALO: no particles of type... returning")
return
#get first file that contains particles of required halo/fof/etc
findex = np.argmax(FileTypeNumbers[:, parttype] > off) - 1
#in case we reached the end argmax returns 0
if (findex == -1):
findex = FileNum - 1
if verbose:
print(("READHALO: first file that contains particles =", findex))
for fnr in range(0, findex):
off -= FileTypeNumbers[fnr + 1, parttype] - FileTypeNumbers[fnr,
parttype]
#read data from file
first = True
for fnr in range(findex, FileNum):
if (multiple):
filename = base + "/snapdir_" + str(num).zfill(
3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(fnr)
else:
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
if verbose:
print(("READHALO: reading file :", filename))
head = snapHDF5.snapshot_header(filename)
nloc = head.npart[parttype]
if (nloc > off):
if verbose:
print("READHALO: data")
start = off
if (nloc - off > left):
count = left
else:
count = nloc - off
if (first == True):
data = snapHDF5.read_block(filename,
block_name,
parttype,
slab_start=start,
slab_len=count)
first = False
else:
data = np.append(data,
snapHDF5.read_block(filename,
block_name,
parttype,
slab_start=start,
slab_len=count),
axis=0)
left -= count
off += count
if (left == 0):
break
off -= nloc
return data
Example to read snapshot from FIRE simulation Author: Pouria A. Mistani email: [email protected] """ import numpy as np import matplotlib.pyplot as plt import snapHDF5 as snap import pdb import PySmoother as PyS import matplotlib.pyplot as plt filename = '../../../snapshot_440' filename = '../m12qq_hr_Dec16_2013/snapshot_440' ## -- read stellar components --- pos = snap.read_block( filename, "POS ", parttype=4 ) #Notice that to read POS and VEL of gas and DM, only change parttype=0 or 1, respectively print 'pase pos' vel = snap.read_block(filename, "VEL ", parttype=4) print 'pase vel' mass = snap.read_block(filename, "MASS", parttype=4) print 'pase mass' ''' age = snap.read_block(filename, "AGE ", parttype=4) print 'pase age' metal = snap.read_block(filename, "Z ", parttype=4) print 'pase metal' ## -- read some gas-exclusive info ----- ## sfr = snap.read_block(filename, "SFR ", parttype=0) print 'pase sfr' '''
#Read halo catalog
cat = readsubfHDF5.subfind_catalog(filename2, snapnum)
r200 = cat.Group_R_Crit200
haloPos = cat.GroupPos
#indices of haloes >300 dm particles and r200 not 0
over300idx, = np.where(
np.logical_and(np.greater(cat.GroupLenType[:, 1], 300),
np.not_equal(r200, 0.)))
#Initialize gas/DM indices for all haloes
allgasindex = np.empty(np.size(r200), dtype=list)
alldmindex = np.empty(np.size(r200), dtype=list)
#Read in particles
posgas = snapHDF5.read_block(filename3, "POS ", parttype=0)
posdm = snapHDF5.read_block(filename3, "POS ", parttype=1)
for j in over300idx:
#Calculate indices of particles within r200
indgas, = np.where(
dist2(posgas[:, 0] - haloPos[j][0], posgas[:, 1] -
haloPos[j][1], posgas[:, 2] -
haloPos[j][2], boxSize) < r200[j]**2)
allgasindex[j] = indgas
inddm, = np.where(
dist2(posdm[:, 0] - haloPos[j][0], posdm[:, 1] -
haloPos[j][1], posdm[:, 2] -
haloPos[j][2], boxSize) < r200[j]**2)
alldmindex[j] = inddm
def readhalo(
base, snapbase, num, block_name, parttype, fof_num, sub_num, long_ids=False, double_output=False, verbose=False
):
global FlagRead, cat, GroupOffset, HaloOffset, multiple, filename, Parttype, FileTypeNumbers, FileNum
if (FlagRead == False) | ((parttype in Parttype) == False):
if verbose:
print "READHALO: INITIAL READ"
# add parttype to list
Parttype.append(parttype)
if verbose:
print "READHALO: Parttype = ", Parttype
# read in catalog
cat = readsubfHDF5.subfind_catalog(
base,
num,
long_ids=long_ids,
double_output=double_output,
keysel=["GroupLenType", "GroupNsubs", "GroupFirstSub", "SubhaloLenType", "SubhaloMassType"],
)
if cat.ngroups == 0:
if verbose:
print "READHALO: no groups in catalog... returning"
return
if FlagRead == False:
GroupOffset = np.zeros([cat.ngroups, 6], dtype="int64")
HaloOffset = np.zeros([cat.nsubs, 6], dtype="int64")
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
multiple = False
if os.path.exists(filename + ".hdf5") == False:
filename = (
base + "/snapdir_" + str(num).zfill(3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(0)
)
multiple = True
if os.path.exists(filename + ".hdf5") == False:
print "READHALO: [error] file not found : ", filename
sys.exit()
FlagRead = True
# construct offset tables
k = 0
for i in range(0, cat.ngroups):
if i > 0:
GroupOffset[i, parttype] = GroupOffset[i - 1, parttype] + cat.GroupLenType[i - 1, parttype]
if cat.GroupNsubs[i] > 0:
HaloOffset[k, parttype] = GroupOffset[i, parttype]
k += 1
for j in range(1, cat.GroupNsubs[i]):
HaloOffset[k, parttype] = HaloOffset[k - 1, parttype] + cat.SubhaloLenType[k - 1, parttype]
k += 1
if k != cat.nsubs:
print "READHALO: problem with offset table", k, cat.nsubs
sys.exit()
# construct file tables
if multiple:
filename = base + "/snapdir_" + str(num).zfill(3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(0)
else:
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
head = snapHDF5.snapshot_header(filename)
FileNum = head.filenum
FileTypeNumbers = np.zeros([FileNum, 6], dtype="int64")
cumcount = np.zeros(6, dtype="int64")
for fnr in range(0, FileNum - 1):
if multiple:
filename = (
base + "/snapdir_" + str(num).zfill(3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(fnr)
)
else:
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
if verbose:
print "READHALO: initial reading file :", filename
head = snapHDF5.snapshot_header(filename)
cumcount[:] += head.npart[:]
FileTypeNumbers[fnr + 1, :] = cumcount[:]
if (sub_num >= 0) & (fof_num < 0):
off = HaloOffset[sub_num, parttype]
left = cat.SubhaloLenType[sub_num, parttype]
if verbose:
print "READHALO: nr / particle # / mass :", sub_num, cat.SubhaloLenType[
sub_num, parttype
], cat.SubhaloMassType[sub_num, parttype].astype("float64")
if (fof_num >= 0) & (sub_num < 0):
off = GroupOffset[fof_num, parttype]
left = cat.GroupLenType[fof_num, parttype]
if verbose:
print "READHALO: nr / particle # / mass :", fof_num, cat.GroupLenType[fof_num, parttype], cat.GroupMassType[
fof_num, parttype
].astype("float64")
if (sub_num >= 0) & (fof_num >= 0):
real_sub_num = sub_num + cat.GroupFirstSub[fof_num]
off = HaloOffset[real_sub_num, parttype]
left = cat.SubhaloLenType[real_sub_num, parttype]
if verbose:
print "READHALO: nr / particle # / mass :", real_sub_num, cat.SubhaloLenType[
real_sub_num, parttype
], cat.SubhaloMassType[real_sub_num, parttype].astype("float64")
if left == 0:
if verbose:
print "READHALO: no particles of type... returning"
return
# get first file that contains particles of required halo/fof/etc
findex = np.argmax(FileTypeNumbers[:, parttype] > off) - 1
# in case we reached the end argmax returns 0
if findex == -1:
findex = FileNum - 1
if verbose:
print "READHALO: first file that contains particles =", findex
for fnr in range(0, findex):
off -= FileTypeNumbers[fnr + 1, parttype] - FileTypeNumbers[fnr, parttype]
# read data from file
first = True
for fnr in range(findex, FileNum):
if multiple:
filename = (
base + "/snapdir_" + str(num).zfill(3) + "/" + snapbase + "_" + str(num).zfill(3) + "." + str(fnr)
)
else:
filename = base + "/" + snapbase + "_" + str(num).zfill(3)
if verbose:
print "READHALO: reading file :", filename
head = snapHDF5.snapshot_header(filename)
nloc = head.npart[parttype]
if nloc > off:
if verbose:
print "READHALO: data"
start = off
if nloc - off > left:
count = left
else:
count = nloc - off
if first == True:
data = snapHDF5.read_block(filename, block_name, parttype, slab_start=start, slab_len=count)
first = False
else:
data = np.append(
data, snapHDF5.read_block(filename, block_name, parttype, slab_start=start, slab_len=count), axis=0
)
left -= count
off += count
if left == 0:
break
off -= nloc
return data
#Read header information header = snapHDF5.snapshot_header(filename3) red = header.redshift atime = header.time boxSize = header.boxsize Omega0 = header.omega0 OmegaLambda = header.omegaL massDMParticle = header.massarr[1] #all DM particles have same mass #redshift evolution of critical_density critical_density *= Omega0 + atime**3 * OmegaLambda critical_density_gas = critical_density * baryonfraction #load particle indices and catalogs pGas = snapHDF5.read_block(filename3,"POS ", parttype=0) mGas = snapHDF5.read_block(filename3,"MASS", parttype=0) vGas = snapHDF5.read_block(filename3,"VEL ", parttype=0) rGas = snapHDF5.read_block(filename3,"RHO ",parttype=0) uGas = snapHDF5.read_block(filename3,"U ",parttype=0) pDM = snapHDF5.read_block(filename3,"POS ",parttype=1) catGas = readsubfHDF5.subfind_catalog(filename2, snapnum) halo100_indices= np.where(catGas.GroupLenType[:,0] >100)[0] startAllGas = [] endAllGas = [] for i in halo100_indices: startAllGas += [np.sum(catGas.GroupLenType[:i,0])] endAllGas += [startAllGas[-1] + catGas.GroupLenType[i,0]]
header = snapHDF5.snapshot_header(filename3)
red = header.redshift
atime = header.time
boxSize = header.boxsize
Omega0 = header.omega0
OmegaLambda = header.omegaL
massDMParticle = header.massarr[1] #all DM particles have same mass
print('reading header information done')
#redshift evolution of critical density
critical_density *= Omega0 + atime**3 * OmegaLambda
critical_density_gas = critical_density * baryonfraction
print(filename3)
#load particle indices and catalogs
pGas = snapHDF5.read_block(filename3, "POS ", parttype=0)
iGas = snapHDF5.read_block(filename3, "ID ", parttype=0)
mGas = snapHDF5.read_block(filename3, "MASS", parttype=0)
eGas = snapHDF5.read_block(filename3, "U ", parttype=0)
dGas = snapHDF5.read_block(filename3, "RHO ", parttype=0)
xHI = snapHDF5.read_block(filename3, "HI ", parttype=0)
if str(species) == 'H2':
xH2I = snapHDF5.read_block(filename3, "H2I ", parttype=0)
pDM = snapHDF5.read_block(filename3, "POS ", parttype=1)
cat = readsubfHDF5.subfind_catalog(filename2, snapnum)
#Read in particles
'''
posgas = snapHDF5.read_block(filename4, "POS ", parttype=0)
posdm = snapHDF5.read_block(filename4, "POS ", parttype=1)
idxdm = snapHDF5.read_block(filename4, "ID ", parttype=1)
idxgas = snapHDF5.read_block(filename4, "ID ", parttype=0)
'''
mass = snap.read_block(filename, "MASS", parttype=4)
print 'pase mass'
age = snap.read_block(filename, "AGE ", parttype=4)
print 'pase age'
metal = snap.read_block(filename, "Z ", parttype=4)
print 'pase metal'
## -- read some gas-exclusive info ----- ##
sfr = snap.read_block(filename, "SFR ", parttype=0)
print 'pase sfr'
'''
print '1e10'
pos = snap.read_block(
filename1, "POS ", parttype=1
) #Notice that to read POS and VEL of gas and DM, only change parttype=0 or 1, respectively
print 'pase pos'
vel = snap.read_block(filename1, "VEL ", parttype=1)
print 'pase vel'
print 'done reading', pos.shape
X = pos[:, 0]
Y = pos[:, 1]
Z = pos[:, 2]
Vx = vel[:, 0]
Vy = vel[:, 1]
Vz = vel[:, 2]
mass = np.ones(len(X))
image = PyS.PyS(X, Y, Z, mass, Vx, Vy, Vz, r=2, w=1000, h=1000, offset=50)
M_Vir = image.Virial_Cut(45)
#SIGO_data = np.loadtxt('/home/nakazatoyr/arepo-c/Analysis/output/'+res+vel+species+'/SIGOs_info_'+res+'_'+vel+'_'+species+'.dat')
ID_posi = np.loadtxt('/home/nakazatoyr/arepo-c/Analysis/output/' + res +
vel + species + '/SIGO_IDinfo_' + res + '_' + vel +
'_' + species + '.dat')
filename = "/xc-work/nakazatoyr/arepo-c/" + res + vel + species + "_refine/"
if str(ref) == 'OFF':
#SIGO_data = np.loadtxt('/home/nakazatoyr/arepo-c/Analysis/output/'+res+vel+species+'_nonref/SIGOs_info_'+res+'_'+vel+'_'+species+'.dat')
ID_posi = np.loadtxt('/home/nakazatoyr/arepo-c/Analysis/output/' + res +
vel + species + '_nonref/SIGO_IDinfo_' + res + '_' +
vel + '_' + species + '.dat')
filename = "/xc-work/nakazatoyr/arepo-c/" + res + vel + species + "_nonref/"
filename2 = filename + "GasOnly_FOF" #Used for readsubfHDF5
filename3_032 = filename2 + "/snap-groupordered_" + str(32).zfill(
3) #Used for snapHDF5
print(filename3_032)
iGas = snapHDF5.read_block(filename3_032, "ID ",
parttype=0) #load particle indices and catalogs
print('loading data done!')
#get unique ID
#for i in range(ID_posi.shape[0]):
for i in [0]:
if i > 10:
break
else:
idx = int(ID_posi[i, 0]) #SIGO_idx
startidx = int(ID_posi[i, 1]) #startAllGas
endidx = int(ID_posi[i, 2]) #endAllGas
ID = iGas[startidx:endidx]
print("halo" + str(idx) + ", startidx is" + str(startidx) +
", endidx is" + str(endidx))
print("the number of IDs is" + str(len(ID)))
def __init__(self, res, vel, snapnum):
self.vel = vel
self.res = res
self.snapnum = int(snapnum)
self.s_vel = vel.replace(".","")
self.s_res = res.replace(".","")
#File paths
filename = "/n/hernquistfs3/mvogelsberger/GlobularClusters/InterfaceWArepo_All_" + self.res + '_' + self.vel + "/output/"
filename2 = filename + "DM_FOF" #Used for readsubfHDF5
filename3 = filename + "snap_" + str(self.snapnum).zfill(3) #Used for hdf5lib, snapHDF5
#Read header information
header = snapHDF5.snapshot_header(filename3)
with hdf5lib.OpenFile(filename3 + ".hdf5") as fs:
red = hdf5lib.GetAttr(fs, "Header", "Redshift")
atime = hdf5lib.GetAttr(fs, "Header", "Time")
boxSize = hdf5lib.GetAttr(fs, "Header", "BoxSize")
boxSize *= atime / hubbleparam #convert from ckpc/h to kpc
Omega0 = hdf5lib.GetAttr(fs, "Header", "Omega0")
OmegaLambda = hdf5lib.GetAttr(fs, "Header", "OmegaLambda")
#Read halo catalog
cat = readsubfHDF5.subfind_catalog(filename2, self.snapnum)
#critical_density *= 1. / (Omega0 + OmegaLambda * atime * atime * atime) #redshift correction
r200 = cat.Group_R_Crit200
r200 *= atime / hubbleparam #convert from ckpc/h to kpc
m200 = cat.Group_M_Crit200
m200 *= 1. / hubbleparam #convert to 10^10 M_sun
haloCMvel = cat.GroupVel
haloCMvel *= 1. / atime #convert from km/s/a to km/s
haloPos = cat.GroupPos
haloPos *= atime / hubbleparam #convert from ckpc/h to kpc
#Initialize arrays
spinparamTotal = np.zeros(np.size(r200))
spinparamGas = np.zeros(np.size(r200))
spinparamDM = np.zeros(np.size(r200))
gasfrac = np.zeros(np.size(r200))
costheta = np.zeros(np.size(r200)) #misalignment angle
v200 = np.zeros(np.size(r200))
numGas = np.zeros(np.size(r200))
numDM = np.zeros(np.size(r200))
#Read in particles
massgas = snapHDF5.read_block(filename3, "MASS", parttype=0)
massdm = snapHDF5.read_block(filename3, "MASS", parttype=1)
posgas = snapHDF5.read_block(filename3, "POS ", parttype=0)
posdm = snapHDF5.read_block(filename3, "POS ", parttype=1)
velgas = snapHDF5.read_block(filename3, "VEL ", parttype=0)
veldm = snapHDF5.read_block(filename3, "VEL ", parttype=1)
#redefine position units from ckpc/h to kpc
posgas *= atime / hubbleparam
posdm *= atime / hubbleparam
#redefine velocity units from kmsqrt(a)/s to km/s
velgas *= np.sqrt(atime)
veldm *= np.sqrt(atime)
#boxSize hubble flow correction for halo CM velocity subtraction
boxSizeVel = boxSize * hubbleparam * .1 * np.sqrt(Omega0/atime/atime/atime + OmegaLambda)
#load particle indices
over300idx, indgas, inddm = np.load('particleindex_' + self.res + '_' + self.vel + '_' + str(self.snapnum) + '.npy')
over300idx = over300idx.astype(int)
over1 = []
for i,j in enumerate(over300idx):
#remove halo CM velocity
tempvelgas = dx_wrap(velgas[indgas[i]] - haloCMvel[j],boxSizeVel)
tempveldm = dx_wrap(veldm[inddm[i]] - haloCMvel[j],boxSizeVel)
#redefine positions wrt COM
tempposgas = dx_wrap(posgas[indgas[i]] - haloPos[j],boxSize)
tempposdm = dx_wrap(posdm[inddm[i]] - haloPos[j],boxSize)
numDM[j] = np.size(tempposdm)
numGas[j] = np.size(tempposgas)
#Calculating j200
#j200 of all particles
j200vecgas = np.sum(np.cross(tempposgas,tempvelgas)*massgas[indgas[i]][:, np.newaxis],axis=0)
j200vecdm = np.sum(np.cross(tempposdm,tempveldm)*massdm[inddm[i]][:, np.newaxis],axis=0)
if np.size(tempvelgas)!=0: #can be no gas particles!
costheta[j] = np.dot(j200vecgas,j200vecdm)/np.linalg.norm(j200vecgas)/np.linalg.norm(j200vecdm)
j200vec = j200vecgas + j200vecdm
j200 = np.linalg.norm(j200vec)
j200gas = np.linalg.norm(j200vecgas)
j200dm = np.linalg.norm(j200vecdm)
v200[j] = np.sqrt(GCONST*m200[j]/r200[j])
#Bullock spin parameter
totalmass = massgas[indgas[i]].sum(dtype='float64') + massdm[inddm[i]].sum(dtype='float64')
spinparamTotal[j] = j200/np.sqrt(2)/v200[j]/r200[j]/totalmass
if np.size(tempveldm)!=0: #tempveldm can be empty no dm particles!
spinparamDM[j] = j200dm/np.sqrt(2)/v200[j]/r200[j]/massdm[inddm[i]].sum(dtype='float64')
if np.size(tempvelgas)!=0: #tempvelgas can be empty no gas particles!
spinparamGas[j] = j200gas/np.sqrt(2)/v200[j]/r200[j]/massgas[indgas[i]].sum(dtype='float64')
gasfrac[j] = massgas[indgas[i]].sum(dtype='float64') / (massgas[indgas[i]].sum(dtype='float64') + massdm[inddm[i]].sum(dtype='float64'))
#Reindex over300idx to account for SO halos with DM particles >300
over300idx2 = over300idx[numDM[over300idx] > 300]
#Plotting
#Redfine in terms of over300idx2
self.spinparamTotal = spinparamTotal[over300idx2]
self.spinparamGas = spinparamGas[over300idx2]
self.spinparamDM = spinparamDM[over300idx2]
self.gasfrac = gasfrac[over300idx2]
self.m200 = m200[over300idx2]
self.m200 *= 10**10 #Convert to solar mass.
self.costheta = costheta[over300idx2]
self.gasfracCosTheta = self.gasfrac[self.costheta!=0.]
self.m2002 = self.m200[self.costheta!=0.]
self.costheta = self.costheta[self.costheta!=0.] #take out the 0 gas components
self.thetadeg = np.arccos(self.costheta)*180./np.pi
