def test_paramfile():
#Create an empty gadget snapshot
snap = Gadget2Snapshot()
#Generate random positions and velocities
NumPart = 32**3
x = np.random.normal(loc=7.0,scale=5.0,size=(NumPart,3)) * Mpc
v = np.zeros((NumPart,3)) * m / s
#Put the particles in the snapshot
snap.setPositions(x)
snap.setVelocities(v)
#Generate minimal header
snap.setHeaderInfo()
#Split the particles between two files
snap.write("gadget_sphere",files=2)
#Generate the parameter file that will determine the evolution
snap.writeParameterFile("gadget_sphere.param")
#Generate a file with the scale factor of the output snapshots
z = np.arange(90.0,0.0,-10.0)
a = 1.0 / (1 + z)
np.savetxt("outputs.txt",a)
def ihalo_ID_position_fcn(snap_fn): '''snap_fn is the gadget snapshot file''' print 'GADGET', snap_fn snaps_gadget = Gadget2Snapshot.open(snap_fn) ID_gadget = snaps_gadget.getID() idx = where(in1d (ID_gadget, ID_amiga, assume_unique=1) == True)[0] ID_HaloParticles = ID_gadget[idx] Positions_HaloParticles = snaps_gadget.getPositions()[idx] return ID_HaloParticles, Positions_HaloParticles
def halo_particles(IDsnap_id):
'''
input:
ID = e.g. 'Om0.300_Ol0.700|512b240|ic1'
snap_id = N, where N runs from 0 to total number of snapshots
i = n, where n is one of the 16 split files for each snapshots
'''
ID, snap_id = IDsnap_id
cosmo_id,geometry_id, ic_id = ID.split("|")
new_snap_fn = os.path.join(storage, cosmo_id, geometry_id, ic_id, 'snapshots_amiga/snapshot_%03d'%(snap_id))
print new_snap_fn
if len(glob.glob(new_snap_fn+'.*'))<16:
print 'file doesnt exist:', new_snap_fn
#### file names for gadget snap and AHF particles
amiga_dir = os.path.join(storage, cosmo_id, geometry_id, ic_id, 'amiga')
os.system('mkdir -p %s'%(os.path.join(storage, cosmo_id, geometry_id, ic_id, 'snapshots_amiga')))
halo_fn_arr = glob.glob(amiga_dir+'/snap%i.*.z*.AHF_particle*'%(snap_id))
snap_fn_arr = glob.glob(os.path.join(storage, cosmo_id, geometry_id, ic_id, 'snapshots_gadget/snapshot_%03d.*'%(snap_id)))
##### test on laptop #####
#halo_fn_arr = glob.glob("*particles")
#snap_fn_arr = glob.glob('snapshot_060.*')
##### read all the amiga particle files #########
txt_amiga = concatenate(array(map(genamigatxt, halo_fn_arr)), axis = 0).T
ID_amiga = txt_amiga[0][txt_amiga[1]==1]
##### find all the halo particles in gadget ########
def ihalo_ID_position_fcn(snap_fn):
'''snap_fn is the gadget snapshot file'''
print 'GADGET', snap_fn
snaps_gadget = Gadget2Snapshot.open(snap_fn)
ID_gadget = snaps_gadget.getID()
idx = where(in1d (ID_gadget, ID_amiga, assume_unique=1) == True)[0]
ID_HaloParticles = ID_gadget[idx]
Positions_HaloParticles = snaps_gadget.getPositions()[idx]
return ID_HaloParticles, Positions_HaloParticles
halo_ID_position = map(ihalo_ID_position_fcn, snap_fn_arr)
halo_ID = concatenate([halo_ID_position[i][0] for i in range(len(halo_ID_position))])
halo_position = concatenate([halo_ID_position[i][1] for i in range(len(halo_ID_position))], axis=0)
###### create new gadget snapshot ############
halo_snap = Gadget2Snapshot()
hg = Gadget2Snapshot.open(snap_fn_arr[0]).header #header_gadget
halo_snap.setPositions(array(halo_position)*halo_ID_position[0][1].unit)
halo_snap.setHeaderInfo(Om0=hg['Om0'], Ode0=hg['Ode0'], w0=hg['w0'], wa=hg['wa'], h=hg['h'], redshift=hg['redshift'], box_size=hg['box_size'])
###### write the new snapshot to file ##########
halo_snap.write(new_snap_fn, files = len(snap_fn_arr))
print "WROTE", new_snap_fn
def reorganize_snaps (IDsnap_id):
ID, snap_id = IDsnap_id
cosmo_id,geometry_id, ic_id = ID.split("|")
new_snap_fn = os.path.join(storage, cosmo_id, geometry_id, ic_id, 'snapshots_amiga/snapshot_%03d'%(snap_id))
os.system('mkdir -p %s'%(os.path.join(storage, cosmo_id, geometry_id, ic_id, 'snapshots_amiga')))
amiga8_arr = glob.glob(os.path.join(storage, cosmo_id, geometry_id, ic_id, 'snapshots_amiga8/snapshot_%03d.*'%(snap_id)))
halo_position = concatenate(array(map(snapposition, amiga8_arr)),axis=0)
halo_snap = Gadget2Snapshot()
hg = Gadget2Snapshot.open(amiga8_arr[0]).header
halo_snap.setPositions(array(halo_position)*Mpc)
halo_snap.setHeaderInfo(Om0=hg['Om0'], Ode0=hg['Ode0'], w0=hg['w0'], wa=hg['wa'], h=hg['h'], redshift=hg['redshift'], box_size=hg['box_size'])
halo_snap.write(new_snap_fn, files = 16)
def test_read():
#Open the gadget snapshot
snapshot = Gadget2Snapshot.open("Data/gadget/snapshot_001")
#Get the particles positions and play with the indices
pospart = snapshot.getPositions(first=500,last=1000)
pos = snapshot.getPositions()
assert np.all(pospart==pos[500:1000])
#Visualize the snapshot
snapshot.visualize(s=1)
#Save the visualization
snapshot.ax.set_title(r"${0}^3$ particles".format(snapshot.header["num_particles_total_side"]))
snapshot.savefig("gadget_snapshot.png")
#Close the snapshot
snapshot.close()
def test_write():
#Create an empty gadget snapshot
snap = Gadget2Snapshot()
#Generate random positions and velocities
NumPart = 32**3
x = np.random.normal(loc=7.0,scale=5.0,size=(NumPart,3)) * Mpc
v = np.random.uniform(-1,1,size=(NumPart,3)) * m / s
#Put the particles in the snapshot
snap.setPositions(x)
snap.setVelocities(v)
#Generate minimal header
snap.setHeaderInfo()
#Visualize
snap.visualize(s=1)
snap.savefig("gadget_initial_condition.png")
#Write the snapshot
snap.write("gadget_ic")
from scipy.ndimage import filters
from mayavi import mlab
# Initialize MPIWhirlPool
try:
pool = MPIWhirlPool()
except:
pool = None
if pool is None:
print("Processing ICs in series...")
# If we run on one core only the snapshots need to be processed in series
snap = Gadget2Snapshot.open("Data/gadget/ic1.0")
n1, r = snap.numberDensity(resolution=64, left_corner=np.array([0.0, 0.0, 0.0]) * snap.Mpc_over_h)
snap.close()
snap = Gadget2Snapshot.open("Data/gadget/ic1.1")
n2, r = snap.numberDensity(resolution=64, left_corner=np.array([0.0, 0.0, 0.0]) * snap.Mpc_over_h)
snap.close()
n = n1 + n2
ns = filters.gaussian_filter(n, 2)
scene = mlab.pipeline.volume(mlab.pipeline.scalar_field(ns))
else:
if pool.is_master():
print("Processing ICs in parallel on {0} cores".format(pool.size + 1))
from scipy.ndimage import filters
from mayavi import mlab
#Initialize MPIWhirlPool
try:
pool = MPIWhirlPool()
except:
pool = None
if pool is None:
print("Processing ICs in series...")
#If we run on one core only the snapshots need to be processed in series
snap = Gadget2Snapshot.open("Data/gadget/ic1.0")
n1,r = snap.numberDensity(resolution=64,left_corner=np.array([0.0,0.0,0.0])*snap.Mpc_over_h)
snap.close()
snap = Gadget2Snapshot.open("Data/gadget/ic1.1")
n2,r = snap.numberDensity(resolution=64,left_corner=np.array([0.0,0.0,0.0])*snap.Mpc_over_h)
snap.close()
n = n1+n2
ns = filters.gaussian_filter(n,2)
scene = mlab.pipeline.volume(mlab.pipeline.scalar_field(ns))
else:
if pool.is_master():
print("Processing ICs in parallel on {0} cores".format(pool.size+1))
import sys
sys.path.append("..")
from lenstools.simulations import Gadget2Snapshot
import numpy as np
from mayavi import mlab
snap = Gadget2Snapshot.open("Data/gadget/snapshot_001")
plane,res,NumPart = snap.cutLens(normal=2,center=7.0*snap.Mpc_over_h,thickness=0.5*snap.Mpc_over_h,plane_size=snap.lensMaxSize(),plane_resolution=128,thickness_resolution=8,smooth=2,tomography=True)
scene = mlab.pipeline.volume(mlab.pipeline.scalar_field(plane))
snap.close()
import sys
sys.path.append("..")
from lenstools.simulations import Gadget2Snapshot
import numpy as np
from mayavi import mlab
snap = Gadget2Snapshot.open("Data/gadget/snapshot_001")
plane, res, NumPart = snap.cutLens(normal=2,
center=7.0 * snap.Mpc_over_h,
thickness=0.5 * snap.Mpc_over_h,
plane_size=snap.lensMaxSize(),
plane_resolution=128,
thickness_resolution=8,
smooth=2,
tomography=True)
scene = mlab.pipeline.volume(mlab.pipeline.scalar_field(plane))
snap.close()
def snapposition (fn): snap = Gadget2Snapshot.open(fn) return snap.getPositions()
from lenstools.simulations import Gadget2Snapshot
import numpy as np
import matplotlib.pyplot as plt
from astropy.units import Mpc, m, s
########################Write#################################
#Create an empty gadget snapshot
snap = Gadget2Snapshot()
#Generate random positions and velocities
NumPart = 32**3
x = np.random.normal(loc=7.0, scale=5.0, size=(NumPart, 3)) * Mpc
v = np.random.uniform(-1, 1, size=(NumPart, 3)) * m / s
#Put the particles in the snapshot
snap.setPositions(x)
snap.setVelocities(v)
#Generate minimal header
snap.setHeaderInfo()
#Write the snapshot
snap.write("gadget_ic")
######################Read and visualize#########################
#Open the snapshot
snap = Gadget2Snapshot.open("gadget_ic")
