this_dir = os.path.dirname(os.path.realpath(__file__))
this_test = os.path.basename(this_dir)
species.allow_similarly_named_components = True
# Read in data from the CO𝘕CEPT snapshots
a = []
nprocs_list = sorted(int(dname[(dname.index('python_') + 7):])
for dname in [os.path.basename(dname)
for dname in glob('{}/output_python_*'.format(this_dir))])
components = {'cython': {n: [] for n in nprocs_list},
'python': {n: [] for n in nprocs_list}}
for cp in components.keys():
for n in nprocs_list:
for fname in sorted(glob('{}/output_{}_{}/snapshot_a=*'.format(this_dir, cp, n)),
key=lambda s: s[(s.index('=') + 1):]):
snapshot = load(fname, compare_params=False)
if cp == 'cython' and n == 1:
a.append(snapshot.params['a'])
components[cp][n].append(snapshot.components[0])
N_snapshots = len(a)
# Begin analysis
masterprint('Analyzing {} data ...'.format(this_test))
# Using the particle order of the cython snapshot as the standard, find the corresponding
# ID's in the python snapshots and order these particles accoringly.
N = components['cython'][1][0].N
D2 = zeros(N)
ID = zeros(N, dtype='int')
for i in range(N_snapshots):
for n in nprocs_list:
# Imports from the CO𝘕CEPT code
from commons import *
from snapshot import load
import species
# Absolute path and name of the directory of this file
this_dir = os.path.dirname(os.path.realpath(__file__))
this_test = os.path.basename(this_dir)
# Read in data from the CO𝘕CEPT snapshots
species.allow_similarly_named_components = True
a = []
components = []
for fname in sorted(glob(this_dir + '/output/snapshot_a=*'),
key=lambda s: s[(s.index('=') + 1):]):
snapshot = load(fname, compare_params=False)
a.append(snapshot.params['a'])
components.append(snapshot.components[0])
N_snapshots = len(a)
# Read in data from the GADGET-2 snapshots
components_gadget = []
for fname in sorted(glob(this_dir + '/Gadget2/output/snapshot_*'))[:N_snapshots]:
components_gadget.append(load(fname, compare_params=False, only_components=True)[0])
# Begin analysis
masterprint('Analysing {} data ...'.format(this_test))
# Using the particle order of CO𝘕CEPT as the standard, find the corresponding
# ID's in the GADGET-2 snapshots and order these particles accordingly.
N = components[0].N
# Imports from the CO𝘕CEPT code
from commons import *
from snapshot import load
import species
# Absolute path and name of the directory of this file
this_dir = os.path.dirname(os.path.realpath(__file__))
this_test = os.path.basename(this_dir)
# Read in data from the CO𝘕CEPT snapshots
species.allow_similarly_named_components = True
a = []
components = []
for fname in sorted(glob(this_dir + '/output/snapshot_a=*'),
key=lambda s: s[(s.index('=') + 1):]):
snapshot = load(fname, compare_params=False)
a.append(snapshot.params['a'])
components.append(snapshot.components[0])
N_snapshots = len(a)
# Read in data from the GADGET snapshots
components_gadget = []
for fname in sorted(glob(this_dir + '/output/snapshot_gadget_*'),
key=lambda s: s[(s.index('gadget_') + 7):])[:N_snapshots]:
components_gadget.append(
load(fname, compare_params=False, only_components=True)[0])
# Begin analysis
masterprint('Analyzing {} data ...'.format(this_test))
# Using the particle order of CO𝘕CEPT as the standard, find the corresponding
# The author of CO𝘕CEPT can be contacted at dakin(at)phys.au.dk
# The latest version of CO𝘕CEPT is available at
# https://github.com/jmd-dk/concept/
# This file has to be run in pure Python mode!
# Imports from the CO𝘕CEPT code
from commons import *
from snapshot import load
# Absolute path and name of the directory of this file
this_dir = os.path.dirname(os.path.realpath(__file__))
this_test = os.path.basename(this_dir)
# Read in the particles
component = load(initial_conditions, only_components=True)[0]
N = component.N
posx = component.posx
posy = component.posy
posz = component.posz
# Begin analysis
masterprint('Analyzing {} data ...'.format(this_test))
# Volume and linear size of cube with the volume of a sphere with radius R_tophat
V = 4 * π / 3 * R_tophat**3
L = cbrt(V)
# The number of complete L*L*L cubes within the box
N_cubes_lin = int(boxsize // L)
N_cubes = N_cubes_lin**3
# The number of particles in each of these cubes, if the snapshot is completely homogeneous
import snapshot
import hello_world
# First let's take a snapshot of the
# hello_world package.
path = snapshot.capture(hello_world, '/tmp/hello_world_snap/', overwrite=True)
hello_world_snap = snapshot.load(path)
print(hello_world_snap.__file__)
# The snapshot is loaded from the specified directory. The code was all copied to
# and is under the snapshot:
print("From original package code", hello_world.func1())
print("From snapshot", hello_world_snap.hello_world.func1())
# You can import from the snapshot as if it were a regular package
from hello_world_snap import hello_world
print("From snapshot, overwriting the original package code",
hello_world.func1())
from commons import *
from snapshot import load
import species
# Absolute path and name of the directory of this file
this_dir = os.path.dirname(os.path.realpath(__file__))
this_test = os.path.basename(this_dir)
# Read in data from the CO𝘕CEPT snapshots
species.allow_similarly_named_components = True
a = []
x = []
x_std = []
for fname in sorted(glob(this_dir + '/output/snapshot_a=*'),
key=lambda s: s[(s.index('=') + 1):]):
snapshot = load(fname, compare_params=False)
posx = snapshot.components[0].posx
a.append(snapshot.params['a'])
x.append(np.mean(posx))
x_std.append(np.std(posx))
N_snapshots = len(a)
# Read in data from the GADGET snapshots
x_gadget = []
x_std_gadget = []
for fname in sorted(glob(this_dir + '/output/snapshot_gadget_*'),
key=lambda s: s[(s.index('gadget_') + 7):])[:N_snapshots]:
components_gadget = load(fname, compare_params=False, only_components=True)[0]
x_gadget.append(np.mean(components_gadget.posx))
x_std_gadget.append(np.std(components_gadget.posx))
def load_results(subtest):
ncomponents_values = set()
nprocs_values = set()
subtiling_values = set()
directory_pattern = get_directory(
subtest,
'*',
'*',
subtiling={
'domain': None,
'tile': '*'
}[subtest],
)
for directory in glob(directory_pattern):
match = re.search(directory_pattern.replace('*', '(.+)'), directory)
ncomponents_values.add(int(match.group(1)))
nprocs_values.add(int(match.group(2)))
if subtest == 'tile':
subtiling_values.add(int(match.group(3)))
ncomponents_values = sorted(ncomponents_values)
nprocs_values = sorted(nprocs_values)
if subtest == 'domain':
subtiling_values = [None]
elif subtest == 'tile':
subtiling_values = sorted(subtiling_values)
pos = {}
times = set()
lattice_sites = None
for ncomponents in ncomponents_values:
for nprocs in nprocs_values:
for subtiling in subtiling_values:
directory = get_directory(subtest, ncomponents, nprocs,
subtiling)
for fname in sorted(glob(f'{directory}/snapshot_t=*')):
if not fname.endswith('.hdf5'):
continue
t = float(re.search(rf't=(.+){unit_time}', fname).group(1))
times.add(t)
snapshot = load(fname)
if subtest == 'domain':
posx, posy, posz, = [], [], []
elif subtest == 'tile':
if lattice_sites is None:
N = sum([
component.N
for component in snapshot.components
])
N_lin = int(round(cbrt(N)))
distance = boxsize / N_lin
lattice_sites = []
for i in range(N_lin):
x = (0.5 + i) * distance
for j in range(N_lin):
y = (0.5 + j) * distance
for k in range(N_lin):
z = (0.5 + k) * distance
lattice_sites.append((x, y, z))
lattice_sites = asarray(lattice_sites)
posx = empty(N_lin**3, dtype=float)
posy = empty(N_lin**3, dtype=float)
posz = empty(N_lin**3, dtype=float)
indices_all = []
for component in snapshot.components:
if component.N == 0:
continue
if subtest == 'domain':
posx += list(component.posx)
posy += list(component.posy)
posz += list(component.posz)
elif subtest == 'tile':
# Sort particles according to the lattice
indices = []
for x, y, z in zip(component.posx, component.posy,
component.posz):
orders = np.argsort(
sum((asarray(
(x, y, z)) - lattice_sites)**2, 1))
for order in orders:
if order not in indices_all:
indices.append(order)
indices_all.append(order)
break
indices = asarray(indices)
posx[indices] = component.posx
posy[indices] = component.posy
posz[indices] = component.posz
if subtest == 'tile':
key = (ncomponents, nprocs, subtiling, t)
elif subtest == 'domain':
key = (ncomponents, nprocs, t)
pos[key] = [asarray(posx), asarray(posy), asarray(posz)]
times = sorted(times)
softening_length = is_selected(component, select_softening_length)
return ncomponents_values, nprocs_values, subtiling_values, times, pos, softening_length
# https://github.com/jmd-dk/concept/
# This file has to be run in pure Python mode!
# Imports from the CO𝘕CEPT code
from commons import *
from snapshot import load
# Absolute path and name of the directory of this file
this_dir = os.path.dirname(os.path.realpath(__file__))
this_test = os.path.basename(this_dir)
# Read in the particles
component = load(initial_conditions, only_components=True)[0]
N = component.N
posx = component.posx
posy = component.posy
posz = component.posz
# Begin analysis
masterprint('Analyzing {} data ...'.format(this_test))
# Volume and linear size of cube with the volume of a sphere with radius R_tophat
V = 4*π/3*R_tophat**3
L = cbrt(V)
# The number of complete L*L*L cubes within the box
N_cubes_lin = int(boxsize//L)
N_cubes = N_cubes_lin**3
# The number of particles in each of these cubes, if the snapshot is completely homogeneous