from sys import argv
from sys import stdout
from sys import stderr
import logging
from nbodykit.utils.pluginargparse import PluginArgumentParser
from nbodykit import plugins
import h5py
parser = PluginArgumentParser(None,
loader=plugins.load,
description=
"""
Finding subhalos from FOF groups. This is a variant of FOF6D.
""",
epilog=
"""
This script is written by Yu Feng, as part of `nbodykit'.
"""
)
parser.add_argument("datasource", type=plugins.DataSource.open,
help='Data source')
parser.add_argument("halolabel",
help='basename of the halo label files, only nbodykit format is supported in this script')
parser.add_argument("linklength", type=float,
help='Linking length of subhalos, in units of mean particle seperation')
parser.add_argument("vfactor", type=float, default=0.368,
help='velocity linking length in units of 1d velocity dispersion.')
from sys import argv
from sys import stdout
from sys import stderr
import logging
from nbodykit.utils.pluginargparse import PluginArgumentParser
from nbodykit import plugins
import numpy
import h5py
parser = PluginArgumentParser(
None,
loader=plugins.load,
description="""
Find friend of friend groups from a Nbody simulation snapshot
""",
epilog="""
This script is written by Yu Feng, as part of `nbodykit'.
""",
)
h = "Data source to read particle position:\n\n"
parser.add_argument("datasource", type=plugins.DataSource.open, help=h + plugins.DataSource.format_help())
parser.add_argument("LinkingLength", type=float, help="LinkingLength in mean separation (0.2)")
parser.add_argument("output", help="output file; output.grp.N and output.halo are written")
parser.add_argument("--nmin", type=float, default=32, help="minimum number of particles in a halo")
ns = parser.parse_args()
logging.basicConfig(level=logging.DEBUG)
from mpi4py import MPI
from sys import argv
from sys import stdout
from sys import stderr
import logging
from nbodykit.utils.pluginargparse import PluginArgumentParser
from nbodykit import plugins
import h5py
parser = PluginArgumentParser(None,
loader=plugins.load,
description=
"""This script trace particles in halo at datasource_tf by ID
find their positions datasource_ti, then compute FOF group
properties at datasource_ti and save it to a file.
""",
epilog=
"""
This script is written by Yu Feng, as part of `nbodykit'.
"""
)
parser.add_argument("datasource_ti", type=plugins.DataSource.open,
help=plugins.DataSource.format_help())
parser.add_argument("datasource_tf", type=plugins.DataSource.open,
help=plugins.DataSource.format_help())
parser.add_argument("halolabel",
help='basename of the halo label files, only nbodykit format is supported in this script')
parser.add_argument("output", help='write output to this file (hdf5 is appended)')
ns = parser.parse_args()
def initialize_power_parser(**kwargs):
"""
Initialize the command-line parser for ``power.py``,
optionally providing``args`` to be passed to the
initializing (for, i.e., the case when this is called
not from the command line)
Parameters
----------
kwargs :
keyword arguments to pass to the `PluginArgumentParser` class
"""
parser = PluginArgumentParser("Parallel Power Spectrum Calculator",
loader=plugins.load,
description=
"""Calculating matter power spectrum from RunPB input files.
Output is written to stdout, in Mpc/h units.
PowerSpectrum is the true one, without (2 pi) ** 3 factor. (differ from Gadget/NGenIC internal)
This script moves all particles to the halo center.
""",
epilog=
"""
This script is written by Yu Feng, as part of `nbodykit'.
Other contributors are: Nick Hand, Man-yat Chu
The author would like thank Marcel Schmittfull for the explanation on cic, shotnoise, and k==0 plane errors.
""",
**kwargs
)
# add the positional arguments
parser.add_argument("mode", choices=["2d", "1d"])
parser.add_argument("Nmesh", type=int, help='size of calculation mesh, recommend 2 * Ngrid')
parser.add_argument("output", help='write power to this file. set as `-` for stdout')
# add the input field types
h = "one or two input fields, specified as:\n\n"
parser.add_argument("inputs", nargs="+", type=plugins.DataSource.open,
help=h+plugins.DataSource.format_help())
# add the optional arguments
parser.add_argument("--bunchsize", type=int, default=1024*1024*4,
help='Number of particles to read per rank. A larger number usually means faster IO, but less memory for the FFT mesh. This is not respected by some data sources.')
parser.add_argument("--binshift", type=float, default=0.0,
help='Shift the bin center by this fraction of the bin width. Default is 0.0. Marcel uses 0.5. this shall rarely be changed.' )
parser.add_argument("--remove-cic", default='anisotropic', choices=["anisotropic","isotropic", "none"],
help='deconvolve cic, anisotropic is the proper way, see http://www.personal.psu.edu/duj13/dissertation/djeong_diss.pdf')
parser.add_argument("--remove-shotnoise", action='store_true', default=False,
help='Remove shotnoise')
parser.add_argument("--Nmu", type=int, default=5,
help='the number of mu bins to use; if `mode = 1d`, then `Nmu` is set to 1' )
parser.add_argument("--los", choices="xyz", default='z',
help="the line-of-sight direction, which the angle `mu` is defined with respect to")
parser.add_argument("--dk", type=float,
help='the spacing of k bins to use; if not provided, the fundamental mode of the box is used')
parser.add_argument("--kmin", type=float, default=0,
help='the edge of the first bin to use; default is 0')
parser.add_argument('-q', '--quiet', help="silence the logging output",
action="store_const", dest="log_level", const=logging.ERROR, default=logging.DEBUG)
parser.add_argument('--poles', type=lambda s: map(int, s.split()), default=[],
help='if specified, compute these multipoles from P(k,mu), saving to `pole_output`')
parser.add_argument('--pole_output', type=str, help='the name of the output file for multipoles')
return parser