mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
Merged in python3 (pull request #5)
Port to python3, large code cleanup * Fixed command line for cosmotool * Fix path * Dump command line is log file * Fix important typo * Modify paths for example * Fix path again * Use an explicit constructor * Change file to open (python 2->3) * python3 fix for xrange in periodic_kdtree.py * Fixed index for Np, numPart, numZones, numZonesTot, partID, zoneID in catalogUtil.py
This commit is contained in:
parent
8249256508
commit
affb56ff48
392 changed files with 4092 additions and 260938 deletions
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@ -1,431 +1,450 @@
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# routines for reading headers and data blocks from Gadget snapshot files
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# usage e.g.:
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#
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# import readsnap as rs
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# header = rs.snapshot_header("snap_063.0") # reads snapshot header
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# print header.massarr
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# mass = rs.read_block("snap_063","MASS",parttype=5) # reads mass for particles of type 5, using block names should work for both format 1 and 2 snapshots
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# print "mass for", mass.size, "particles read"
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# print mass[0:10]
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#
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# before using read_block, make sure that the description (and order if using format 1 snapshot files) of the data blocks
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# is correct for your configuration of Gadget
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#
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# for mutliple file snapshots give e.g. the filename "snap_063" rather than "snap_063.0" to read_block
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# for snapshot_header the file number should be included, e.g."snap_063.0", as the headers of the files differ
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#
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# the returned data block is ordered by particle species even when read from a multiple file snapshot
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import numpy as np
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import os
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import sys
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import math
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# ----- class for snapshot header -----
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class snapshot_header:
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def __init__(self, filename):
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if os.path.exists(filename):
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curfilename = filename
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elif os.path.exists(filename+".0"):
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curfilename = filename+".0"
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else:
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print "file not found:", filename
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sys.exit()
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self.filename = filename
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f = open(curfilename,'rb')
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blocksize = np.fromfile(f,dtype=np.int32,count=1)
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if blocksize[0] == 8:
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swap = 0
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format = 2
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elif blocksize[0] == 256:
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swap = 0
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format = 1
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else:
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blocksize.byteswap(True)
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if blocksize[0] == 8:
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swap = 1
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format = 2
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elif blocksize[0] == 256:
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swap = 1
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format = 1
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else:
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print "incorrect file format encountered when reading header of", filename
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sys.exit()
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self.format = format
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self.swap = swap
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if format==2:
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f.seek(16, os.SEEK_CUR)
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self.npart = np.fromfile(f,dtype=np.int32,count=6)
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self.massarr = np.fromfile(f,dtype=np.float64,count=6)
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self.time = (np.fromfile(f,dtype=np.float64,count=1))[0]
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self.redshift = (np.fromfile(f,dtype=np.float64,count=1))[0]
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self.sfr = (np.fromfile(f,dtype=np.int32,count=1))[0]
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self.feedback = (np.fromfile(f,dtype=np.int32,count=1))[0]
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self.nall = np.fromfile(f,dtype=np.int32,count=6)
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self.cooling = (np.fromfile(f,dtype=np.int32,count=1))[0]
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self.filenum = (np.fromfile(f,dtype=np.int32,count=1))[0]
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self.boxsize = (np.fromfile(f,dtype=np.float64,count=1))[0]
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self.omega_m = (np.fromfile(f,dtype=np.float64,count=1))[0]
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self.omega_l = (np.fromfile(f,dtype=np.float64,count=1))[0]
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self.hubble = (np.fromfile(f,dtype=np.float64,count=1))[0]
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if swap:
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self.npart.byteswap(True)
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self.massarr.byteswap(True)
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self.time = self.time.byteswap()
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self.redshift = self.redshift.byteswap()
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self.sfr = self.sfr.byteswap()
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self.feedback = self.feedback.byteswap()
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self.nall.byteswap(True)
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self.cooling = self.cooling.byteswap()
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self.filenum = self.filenum.byteswap()
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self.boxsize = self.boxsize.byteswap()
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self.omega_m = self.omega_m.byteswap()
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self.omega_l = self.omega_l.byteswap()
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self.hubble = self.hubble.byteswap()
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f.close()
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# ----- find offset and size of data block -----
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def find_block(filename, format, swap, block, block_num, only_list_blocks=False):
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if (not os.path.exists(filename)):
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print "file not found:", filename
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sys.exit()
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f = open(filename,'rb')
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f.seek(0, os.SEEK_END)
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filesize = f.tell()
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f.seek(0, os.SEEK_SET)
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found = False
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curblock_num = 1
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while ((not found) and (f.tell()<filesize)):
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if format==2:
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f.seek(4, os.SEEK_CUR)
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curblock = f.read(4)
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if (block == curblock):
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found = True
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f.seek(8, os.SEEK_CUR)
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else:
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if curblock_num==block_num:
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found = True
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curblocksize = (np.fromfile(f,dtype=np.uint32,count=1))[0]
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if swap:
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curblocksize = curblocksize.byteswap()
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# - print some debug info about found data blocks -
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#if format==2:
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# print curblock, curblock_num, curblocksize
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#else:
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# print curblock_num, curblocksize
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if only_list_blocks:
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if format==2:
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print curblock_num,curblock,f.tell(),curblocksize
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else:
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print curblock_num,f.tell(),curblocksize
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found = False
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if found:
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blocksize = curblocksize
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offset = f.tell()
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else:
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f.seek(curblocksize, os.SEEK_CUR)
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blocksize_check = (np.fromfile(f,dtype=np.uint32,count=1))[0]
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if swap: blocksize_check = blocksize_check.byteswap()
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if (curblocksize != blocksize_check):
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print "something wrong"
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sys.exit()
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curblock_num += 1
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f.close()
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if ((not found) and (not only_list_blocks)):
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print "Error: block not found"
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sys.exit()
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if (not only_list_blocks):
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return offset,blocksize
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# ----- read data block -----
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#for snapshots with very very large number of particles set nall manually
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#for instance nall=np.array([0,2048**3,0,0,0,0])
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def read_block(filename, block, parttype=-1, physical_velocities=True, arepo=0, no_masses=False, verbose=False, nall=[0,0,0,0,0,0]):
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if (verbose):
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print "reading block", block
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blockadd=0
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blocksub=0
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if arepo==0:
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if (verbose):
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print "Gadget format"
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blockadd=0
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if arepo==1:
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if (verbose):
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print "Arepo format"
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blockadd=1
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if arepo==2:
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if (verbose):
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print "Arepo extended format"
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blockadd=4
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if no_masses==True:
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if (verbose):
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print "No mass block present"
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blocksub=1
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if parttype not in [-1,0,1,2,3,4,5]:
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print "wrong parttype given"
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sys.exit()
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if os.path.exists(filename):
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curfilename = filename
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elif os.path.exists(filename+".0"):
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curfilename = filename+".0"
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else:
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print "file not found:", filename
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print "and:", curfilename
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sys.exit()
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head = snapshot_header(curfilename)
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format = head.format
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print "FORMAT=", format
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swap = head.swap
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npart = head.npart
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massarr = head.massarr
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if np.all(nall==[0,0,0,0,0,0]):
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nall = head.nall
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filenum = head.filenum
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redshift = head.redshift
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time = head.time
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del head
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# - description of data blocks -
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# add or change blocks as needed for your Gadget version
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data_for_type = np.zeros(6,bool) # should be set to "True" below for the species for which data is stored in the data block #by doing this, the default value is False data_for_type=[False,False,False,False,False,False]
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dt = np.float32 # data type of the data in the block
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if block=="POS ":
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data_for_type[:] = True
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dt = np.dtype((np.float32,3))
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block_num = 2
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elif block=="VEL ":
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data_for_type[:] = True
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dt = np.dtype((np.float32,3))
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block_num = 3
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elif block=="ID ":
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data_for_type[:] = True
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dt = np.uint32
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block_num = 4
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#only used for format I, when file structure is HEAD,POS,VEL,ID,ACCE
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elif block=="ACCE": #This is only for the PIETRONI project
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data_for_type[:] = True #This is only for the PIETRONI project
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dt = np.dtype((np.float32,3)) #This is only for the PIETRONI project
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block_num = 5 #This is only for the PIETRONI project
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elif block=="MASS":
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data_for_type[np.where(massarr==0)] = True
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block_num = 5
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if parttype>=0 and massarr[parttype]>0:
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if (verbose):
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print "filling masses according to massarr"
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return np.ones(nall[parttype],dtype=dt)*massarr[parttype]
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elif block=="U ":
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data_for_type[0] = True
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block_num = 6-blocksub
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elif block=="RHO ":
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data_for_type[0] = True
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block_num = 7-blocksub
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elif block=="VOL ":
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data_for_type[0] = True
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block_num = 8-blocksub
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elif block=="CMCE":
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data_for_type[0] = True
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dt = np.dtype((np.float32,3))
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block_num = 9-blocksub
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elif block=="AREA":
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data_for_type[0] = True
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block_num = 10-blocksub
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elif block=="NFAC":
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data_for_type[0] = True
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dt = np.dtype(np.int64) #depends on code version, most recent hast int32, old MyIDType
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block_num = 11-blocksub
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elif block=="NE ":
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data_for_type[0] = True
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block_num = 8+blockadd-blocksub
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elif block=="NH ":
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data_for_type[0] = True
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block_num = 9+blockadd-blocksub
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elif block=="HSML":
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data_for_type[0] = True
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block_num = 10+blockadd-blocksub
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elif block=="SFR ":
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data_for_type[0] = True
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block_num = 11+blockadd-blocksub
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elif block=="MHI ": #This is only for the bias_HI project
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data_for_type[0] = True #This is only for the bias_HI project
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block_num = 12+blockadd-blocksub #This is only for the bias_HI project
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elif block=="TEMP": #This is only for the bias_HI project
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data_for_type[0] = True #This is only for the bias_HI project
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block_num = 13+blockadd-blocksub #This is only for the bias_HI project
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elif block=="AGE ":
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data_for_type[4] = True
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block_num = 12+blockadd-blocksub
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elif block=="Z ":
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data_for_type[0] = True
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data_for_type[4] = True
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block_num = 13+blockadd-blocksub
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elif block=="BHMA":
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data_for_type[5] = True
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block_num = 14+blockadd-blocksub
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elif block=="BHMD":
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data_for_type[5] = True
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block_num = 15+blockadd-blocksub
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else:
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print "Sorry! Block type", block, "not known!"
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sys.exit()
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# - end of block description -
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actual_data_for_type = np.copy(data_for_type)
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if parttype >= 0:
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actual_data_for_type[:] = False
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actual_data_for_type[parttype] = True
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if data_for_type[parttype]==False:
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print "Error: no data for specified particle type", parttype, "in the block", block
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sys.exit()
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elif block=="MASS":
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actual_data_for_type[:] = True
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allpartnum = np.int64(0)
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species_offset = np.zeros(6,np.int64)
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for j in range(6):
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species_offset[j] = allpartnum
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if actual_data_for_type[j]:
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allpartnum += nall[j]
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for i in range(filenum): # main loop over files
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if filenum>1:
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curfilename = filename+"."+str(i)
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if i>0:
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head = snapshot_header(curfilename)
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npart = head.npart
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del head
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curpartnum = np.int32(0)
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cur_species_offset = np.zeros(6,np.int64)
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for j in range(6):
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cur_species_offset[j] = curpartnum
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if data_for_type[j]:
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curpartnum += npart[j]
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if parttype>=0:
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actual_curpartnum = npart[parttype]
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add_offset = cur_species_offset[parttype]
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else:
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actual_curpartnum = curpartnum
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add_offset = np.int32(0)
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offset,blocksize = find_block(curfilename,format,swap,block,block_num)
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if i==0: # fix data type for ID if long IDs are used
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if block=="ID ":
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if blocksize == np.dtype(dt).itemsize*curpartnum * 2:
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dt = np.uint64
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if np.dtype(dt).itemsize*curpartnum != blocksize:
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print "something wrong with blocksize! expected =",np.dtype(dt).itemsize*curpartnum,"actual =",blocksize
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sys.exit()
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f = open(curfilename,'rb')
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f.seek(offset + add_offset*np.dtype(dt).itemsize, os.SEEK_CUR)
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curdat = np.fromfile(f,dtype=dt,count=actual_curpartnum) # read data
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f.close()
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if swap:
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curdat.byteswap(True)
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if i==0:
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data = np.empty(allpartnum,dt)
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for j in range(6):
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if actual_data_for_type[j]:
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if block=="MASS" and massarr[j]>0: # add mass block for particles for which the mass is specified in the snapshot header
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data[species_offset[j]:species_offset[j]+npart[j]] = massarr[j]
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else:
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if parttype>=0:
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data[species_offset[j]:species_offset[j]+npart[j]] = curdat
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else:
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data[species_offset[j]:species_offset[j]+npart[j]] = curdat[cur_species_offset[j]:cur_species_offset[j]+npart[j]]
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species_offset[j] += npart[j]
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del curdat
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if physical_velocities and block=="VEL " and redshift!=0:
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data *= math.sqrt(time)
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return data
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# ----- list all data blocks in a format 2 snapshot file -----
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def list_format2_blocks(filename):
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if os.path.exists(filename):
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curfilename = filename
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elif os.path.exists(filename+".0"):
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curfilename = filename+".0"
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else:
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print "file not found:", filename
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sys.exit()
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head = snapshot_header(curfilename)
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format = head.format
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swap = head.swap
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del head
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print 'GADGET FORMAT ',format
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if (format != 2):
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print "# OFFSET SIZE"
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else:
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print "# BLOCK OFFSET SIZE"
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print "-------------------------"
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find_block(curfilename, format, swap, "XXXX", 0, only_list_blocks=True)
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print "-------------------------"
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def read_gadget_header(filename):
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if os.path.exists(filename):
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curfilename = filename
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elif os.path.exists(filename+".0"):
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curfilename = filename+".0"
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else:
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print "file not found:", filename
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sys.exit()
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head=snapshot_header(curfilename)
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print 'npar=',head.npart
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print 'nall=',head.nall
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print 'a=',head.time
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print 'z=',head.redshift
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print 'masses=',head.massarr*1e10,'Msun/h'
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print 'boxsize=',head.boxsize,'kpc/h'
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print 'filenum=',head.filenum
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print 'cooling=',head.cooling
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print 'Omega_m,Omega_l=',head.omega_m,head.omega_l
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print 'h=',head.hubble,'\n'
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rhocrit=2.77536627e11 #h**2 M_sun/Mpc**3
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rhocrit=rhocrit/1e9 #h**2M_sun/kpc**3
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Omega_DM=head.nall[1]*head.massarr[1]*1e10/(head.boxsize**3*rhocrit)
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print 'DM mass=',head.massarr[1]*1e10,'Omega_DM=',Omega_DM
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if head.nall[2]>0 and head.massarr[2]>0:
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Omega_NU=head.nall[2]*head.massarr[2]*1e10/(head.boxsize**3*rhocrit)
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print 'NU mass=',head.massarr[2]*1e10,'Omega_NU=',Omega_NU
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print 'Sum of neutrino masses=',Omega_NU*head.hubble**2*94.1745,'eV'
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#+
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# VIDE -- Void IDentification and Examination -- ./python_tools/fit_hod/readsnap.py
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# Copyright (C) 2010-2014 Guilhem Lavaux
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# Copyright (C) 2011-2014 P. M. Sutter
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#
|
||||
# This program is free software; you can redistribute it and/or modify
|
||||
# it under the terms of the GNU General Public License as published by
|
||||
# the Free Software Foundation; version 2 of the License.
|
||||
#
|
||||
#
|
||||
# This program is distributed in the hope that it will be useful,
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
# GNU General Public License for more details.
|
||||
#
|
||||
# You should have received a copy of the GNU General Public License along
|
||||
# with this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#+
|
||||
# routines for reading headers and data blocks from Gadget snapshot files
|
||||
# usage e.g.:
|
||||
#
|
||||
# import readsnap as rs
|
||||
# header = rs.snapshot_header("snap_063.0") # reads snapshot header
|
||||
# print header.massarr
|
||||
# mass = rs.read_block("snap_063","MASS",parttype=5) # reads mass for particles of type 5, using block names should work for both format 1 and 2 snapshots
|
||||
# print "mass for", mass.size, "particles read"
|
||||
# print mass[0:10]
|
||||
#
|
||||
# before using read_block, make sure that the description (and order if using format 1 snapshot files) of the data blocks
|
||||
# is correct for your configuration of Gadget
|
||||
#
|
||||
# for mutliple file snapshots give e.g. the filename "snap_063" rather than "snap_063.0" to read_block
|
||||
# for snapshot_header the file number should be included, e.g."snap_063.0", as the headers of the files differ
|
||||
#
|
||||
# the returned data block is ordered by particle species even when read from a multiple file snapshot
|
||||
|
||||
import numpy as np
|
||||
import os
|
||||
import sys
|
||||
import math
|
||||
|
||||
# ----- class for snapshot header -----
|
||||
|
||||
class snapshot_header:
|
||||
def __init__(self, filename):
|
||||
|
||||
if os.path.exists(filename):
|
||||
curfilename = filename
|
||||
elif os.path.exists(filename+".0"):
|
||||
curfilename = filename+".0"
|
||||
else:
|
||||
print("file not found:", filename)
|
||||
sys.exit()
|
||||
|
||||
self.filename = filename
|
||||
f = open(curfilename,'rb')
|
||||
blocksize = np.fromfile(f,dtype=np.int32,count=1)
|
||||
if blocksize[0] == 8:
|
||||
swap = 0
|
||||
format = 2
|
||||
elif blocksize[0] == 256:
|
||||
swap = 0
|
||||
format = 1
|
||||
else:
|
||||
blocksize.byteswap(True)
|
||||
if blocksize[0] == 8:
|
||||
swap = 1
|
||||
format = 2
|
||||
elif blocksize[0] == 256:
|
||||
swap = 1
|
||||
format = 1
|
||||
else:
|
||||
print("incorrect file format encountered when reading header of", filename)
|
||||
sys.exit()
|
||||
|
||||
self.format = format
|
||||
self.swap = swap
|
||||
|
||||
if format==2:
|
||||
f.seek(16, os.SEEK_CUR)
|
||||
|
||||
self.npart = np.fromfile(f,dtype=np.int32,count=6)
|
||||
self.massarr = np.fromfile(f,dtype=np.float64,count=6)
|
||||
self.time = (np.fromfile(f,dtype=np.float64,count=1))[0]
|
||||
self.redshift = (np.fromfile(f,dtype=np.float64,count=1))[0]
|
||||
self.sfr = (np.fromfile(f,dtype=np.int32,count=1))[0]
|
||||
self.feedback = (np.fromfile(f,dtype=np.int32,count=1))[0]
|
||||
self.nall = np.fromfile(f,dtype=np.int32,count=6)
|
||||
self.cooling = (np.fromfile(f,dtype=np.int32,count=1))[0]
|
||||
self.filenum = (np.fromfile(f,dtype=np.int32,count=1))[0]
|
||||
self.boxsize = (np.fromfile(f,dtype=np.float64,count=1))[0]
|
||||
self.omega_m = (np.fromfile(f,dtype=np.float64,count=1))[0]
|
||||
self.omega_l = (np.fromfile(f,dtype=np.float64,count=1))[0]
|
||||
self.hubble = (np.fromfile(f,dtype=np.float64,count=1))[0]
|
||||
|
||||
if swap:
|
||||
self.npart.byteswap(True)
|
||||
self.massarr.byteswap(True)
|
||||
self.time = self.time.byteswap()
|
||||
self.redshift = self.redshift.byteswap()
|
||||
self.sfr = self.sfr.byteswap()
|
||||
self.feedback = self.feedback.byteswap()
|
||||
self.nall.byteswap(True)
|
||||
self.cooling = self.cooling.byteswap()
|
||||
self.filenum = self.filenum.byteswap()
|
||||
self.boxsize = self.boxsize.byteswap()
|
||||
self.omega_m = self.omega_m.byteswap()
|
||||
self.omega_l = self.omega_l.byteswap()
|
||||
self.hubble = self.hubble.byteswap()
|
||||
|
||||
f.close()
|
||||
|
||||
# ----- find offset and size of data block -----
|
||||
|
||||
def find_block(filename, format, swap, block, block_num, only_list_blocks=False):
|
||||
if (not os.path.exists(filename)):
|
||||
print("file not found:", filename)
|
||||
sys.exit()
|
||||
|
||||
f = open(filename,'rb')
|
||||
f.seek(0, os.SEEK_END)
|
||||
filesize = f.tell()
|
||||
f.seek(0, os.SEEK_SET)
|
||||
|
||||
found = False
|
||||
curblock_num = 1
|
||||
while ((not found) and (f.tell()<filesize)):
|
||||
if format==2:
|
||||
f.seek(4, os.SEEK_CUR)
|
||||
curblock = f.read(4)
|
||||
if (block == curblock):
|
||||
found = True
|
||||
f.seek(8, os.SEEK_CUR)
|
||||
else:
|
||||
if curblock_num==block_num:
|
||||
found = True
|
||||
|
||||
curblocksize = (np.fromfile(f,dtype=np.uint32,count=1))[0]
|
||||
if swap:
|
||||
curblocksize = curblocksize.byteswap()
|
||||
|
||||
# - print some debug info about found data blocks -
|
||||
#if format==2:
|
||||
# print curblock, curblock_num, curblocksize
|
||||
#else:
|
||||
# print curblock_num, curblocksize
|
||||
|
||||
if only_list_blocks:
|
||||
if format==2:
|
||||
print(curblock_num,curblock,f.tell(),curblocksize)
|
||||
else:
|
||||
print(curblock_num,f.tell(),curblocksize)
|
||||
found = False
|
||||
|
||||
|
||||
if found:
|
||||
blocksize = curblocksize
|
||||
offset = f.tell()
|
||||
else:
|
||||
f.seek(curblocksize, os.SEEK_CUR)
|
||||
blocksize_check = (np.fromfile(f,dtype=np.uint32,count=1))[0]
|
||||
if swap: blocksize_check = blocksize_check.byteswap()
|
||||
if (curblocksize != blocksize_check):
|
||||
print("something wrong")
|
||||
sys.exit()
|
||||
curblock_num += 1
|
||||
f.close()
|
||||
|
||||
if ((not found) and (not only_list_blocks)):
|
||||
print("Error: block not found")
|
||||
sys.exit()
|
||||
|
||||
if (not only_list_blocks):
|
||||
return offset,blocksize
|
||||
|
||||
# ----- read data block -----
|
||||
#for snapshots with very very large number of particles set nall manually
|
||||
#for instance nall=np.array([0,2048**3,0,0,0,0])
|
||||
def read_block(filename, block, parttype=-1, physical_velocities=True, arepo=0, no_masses=False, verbose=False, nall=[0,0,0,0,0,0]):
|
||||
if (verbose):
|
||||
print("reading block", block)
|
||||
|
||||
blockadd=0
|
||||
blocksub=0
|
||||
|
||||
if arepo==0:
|
||||
if (verbose):
|
||||
print("Gadget format")
|
||||
blockadd=0
|
||||
if arepo==1:
|
||||
if (verbose):
|
||||
print("Arepo format")
|
||||
blockadd=1
|
||||
if arepo==2:
|
||||
if (verbose):
|
||||
print("Arepo extended format")
|
||||
blockadd=4
|
||||
if no_masses==True:
|
||||
if (verbose):
|
||||
print("No mass block present")
|
||||
blocksub=1
|
||||
|
||||
if parttype not in [-1,0,1,2,3,4,5]:
|
||||
print("wrong parttype given")
|
||||
sys.exit()
|
||||
|
||||
if os.path.exists(filename):
|
||||
curfilename = filename
|
||||
elif os.path.exists(filename+".0"):
|
||||
curfilename = filename+".0"
|
||||
else:
|
||||
print("file not found:", filename)
|
||||
print("and:", curfilename)
|
||||
sys.exit()
|
||||
|
||||
head = snapshot_header(curfilename)
|
||||
format = head.format
|
||||
|
||||
print("FORMAT=", format)
|
||||
swap = head.swap
|
||||
npart = head.npart
|
||||
massarr = head.massarr
|
||||
if np.all(nall==[0,0,0,0,0,0]):
|
||||
nall = head.nall
|
||||
filenum = head.filenum
|
||||
redshift = head.redshift
|
||||
time = head.time
|
||||
del head
|
||||
|
||||
# - description of data blocks -
|
||||
# add or change blocks as needed for your Gadget version
|
||||
data_for_type = np.zeros(6,bool) # should be set to "True" below for the species for which data is stored in the data block #by doing this, the default value is False data_for_type=[False,False,False,False,False,False]
|
||||
dt = np.float32 # data type of the data in the block
|
||||
if block=="POS ":
|
||||
data_for_type[:] = True
|
||||
dt = np.dtype((np.float32,3))
|
||||
block_num = 2
|
||||
elif block=="VEL ":
|
||||
data_for_type[:] = True
|
||||
dt = np.dtype((np.float32,3))
|
||||
block_num = 3
|
||||
elif block=="ID ":
|
||||
data_for_type[:] = True
|
||||
dt = np.uint32
|
||||
block_num = 4
|
||||
#only used for format I, when file structure is HEAD,POS,VEL,ID,ACCE
|
||||
elif block=="ACCE": #This is only for the PIETRONI project
|
||||
data_for_type[:] = True #This is only for the PIETRONI project
|
||||
dt = np.dtype((np.float32,3)) #This is only for the PIETRONI project
|
||||
block_num = 5 #This is only for the PIETRONI project
|
||||
elif block=="MASS":
|
||||
data_for_type[np.where(massarr==0)] = True
|
||||
block_num = 5
|
||||
if parttype>=0 and massarr[parttype]>0:
|
||||
if (verbose):
|
||||
print("filling masses according to massarr")
|
||||
return np.ones(nall[parttype],dtype=dt)*massarr[parttype]
|
||||
elif block=="U ":
|
||||
data_for_type[0] = True
|
||||
block_num = 6-blocksub
|
||||
elif block=="RHO ":
|
||||
data_for_type[0] = True
|
||||
block_num = 7-blocksub
|
||||
elif block=="VOL ":
|
||||
data_for_type[0] = True
|
||||
block_num = 8-blocksub
|
||||
elif block=="CMCE":
|
||||
data_for_type[0] = True
|
||||
dt = np.dtype((np.float32,3))
|
||||
block_num = 9-blocksub
|
||||
elif block=="AREA":
|
||||
data_for_type[0] = True
|
||||
block_num = 10-blocksub
|
||||
elif block=="NFAC":
|
||||
data_for_type[0] = True
|
||||
dt = np.dtype(np.int64) #depends on code version, most recent hast int32, old MyIDType
|
||||
block_num = 11-blocksub
|
||||
elif block=="NE ":
|
||||
data_for_type[0] = True
|
||||
block_num = 8+blockadd-blocksub
|
||||
elif block=="NH ":
|
||||
data_for_type[0] = True
|
||||
block_num = 9+blockadd-blocksub
|
||||
elif block=="HSML":
|
||||
data_for_type[0] = True
|
||||
block_num = 10+blockadd-blocksub
|
||||
elif block=="SFR ":
|
||||
data_for_type[0] = True
|
||||
block_num = 11+blockadd-blocksub
|
||||
elif block=="MHI ": #This is only for the bias_HI project
|
||||
data_for_type[0] = True #This is only for the bias_HI project
|
||||
block_num = 12+blockadd-blocksub #This is only for the bias_HI project
|
||||
elif block=="TEMP": #This is only for the bias_HI project
|
||||
data_for_type[0] = True #This is only for the bias_HI project
|
||||
block_num = 13+blockadd-blocksub #This is only for the bias_HI project
|
||||
elif block=="AGE ":
|
||||
data_for_type[4] = True
|
||||
block_num = 12+blockadd-blocksub
|
||||
elif block=="Z ":
|
||||
data_for_type[0] = True
|
||||
data_for_type[4] = True
|
||||
block_num = 13+blockadd-blocksub
|
||||
elif block=="BHMA":
|
||||
data_for_type[5] = True
|
||||
block_num = 14+blockadd-blocksub
|
||||
elif block=="BHMD":
|
||||
data_for_type[5] = True
|
||||
block_num = 15+blockadd-blocksub
|
||||
else:
|
||||
print("Sorry! Block type", block, "not known!")
|
||||
sys.exit()
|
||||
# - end of block description -
|
||||
|
||||
actual_data_for_type = np.copy(data_for_type)
|
||||
if parttype >= 0:
|
||||
actual_data_for_type[:] = False
|
||||
actual_data_for_type[parttype] = True
|
||||
if data_for_type[parttype]==False:
|
||||
print("Error: no data for specified particle type", parttype, "in the block", block)
|
||||
sys.exit()
|
||||
elif block=="MASS":
|
||||
actual_data_for_type[:] = True
|
||||
|
||||
allpartnum = np.int64(0)
|
||||
species_offset = np.zeros(6,np.int64)
|
||||
for j in range(6):
|
||||
species_offset[j] = allpartnum
|
||||
if actual_data_for_type[j]:
|
||||
allpartnum += nall[j]
|
||||
|
||||
for i in range(filenum): # main loop over files
|
||||
if filenum>1:
|
||||
curfilename = filename+"."+str(i)
|
||||
|
||||
if i>0:
|
||||
head = snapshot_header(curfilename)
|
||||
npart = head.npart
|
||||
del head
|
||||
|
||||
curpartnum = np.int32(0)
|
||||
cur_species_offset = np.zeros(6,np.int64)
|
||||
for j in range(6):
|
||||
cur_species_offset[j] = curpartnum
|
||||
if data_for_type[j]:
|
||||
curpartnum += npart[j]
|
||||
|
||||
if parttype>=0:
|
||||
actual_curpartnum = npart[parttype]
|
||||
add_offset = cur_species_offset[parttype]
|
||||
else:
|
||||
actual_curpartnum = curpartnum
|
||||
add_offset = np.int32(0)
|
||||
|
||||
offset,blocksize = find_block(curfilename,format,swap,block,block_num)
|
||||
|
||||
if i==0: # fix data type for ID if long IDs are used
|
||||
if block=="ID ":
|
||||
if blocksize == np.dtype(dt).itemsize*curpartnum * 2:
|
||||
dt = np.uint64
|
||||
|
||||
if np.dtype(dt).itemsize*curpartnum != blocksize:
|
||||
print("something wrong with blocksize! expected =",np.dtype(dt).itemsize*curpartnum,"actual =",blocksize)
|
||||
sys.exit()
|
||||
|
||||
f = open(curfilename,'rb')
|
||||
f.seek(offset + add_offset*np.dtype(dt).itemsize, os.SEEK_CUR)
|
||||
curdat = np.fromfile(f,dtype=dt,count=actual_curpartnum) # read data
|
||||
f.close()
|
||||
if swap:
|
||||
curdat.byteswap(True)
|
||||
|
||||
if i==0:
|
||||
data = np.empty(allpartnum,dt)
|
||||
|
||||
for j in range(6):
|
||||
if actual_data_for_type[j]:
|
||||
if block=="MASS" and massarr[j]>0: # add mass block for particles for which the mass is specified in the snapshot header
|
||||
data[species_offset[j]:species_offset[j]+npart[j]] = massarr[j]
|
||||
else:
|
||||
if parttype>=0:
|
||||
data[species_offset[j]:species_offset[j]+npart[j]] = curdat
|
||||
else:
|
||||
data[species_offset[j]:species_offset[j]+npart[j]] = curdat[cur_species_offset[j]:cur_species_offset[j]+npart[j]]
|
||||
species_offset[j] += npart[j]
|
||||
|
||||
del curdat
|
||||
|
||||
if physical_velocities and block=="VEL " and redshift!=0:
|
||||
data *= math.sqrt(time)
|
||||
|
||||
return data
|
||||
|
||||
# ----- list all data blocks in a format 2 snapshot file -----
|
||||
|
||||
def list_format2_blocks(filename):
|
||||
if os.path.exists(filename):
|
||||
curfilename = filename
|
||||
elif os.path.exists(filename+".0"):
|
||||
curfilename = filename+".0"
|
||||
else:
|
||||
print("file not found:", filename)
|
||||
sys.exit()
|
||||
|
||||
head = snapshot_header(curfilename)
|
||||
format = head.format
|
||||
swap = head.swap
|
||||
del head
|
||||
|
||||
print('GADGET FORMAT ',format)
|
||||
if (format != 2):
|
||||
print("# OFFSET SIZE")
|
||||
else:
|
||||
print("# BLOCK OFFSET SIZE")
|
||||
print("-------------------------")
|
||||
|
||||
find_block(curfilename, format, swap, "XXXX", 0, only_list_blocks=True)
|
||||
|
||||
print("-------------------------")
|
||||
|
||||
def read_gadget_header(filename):
|
||||
if os.path.exists(filename):
|
||||
curfilename = filename
|
||||
elif os.path.exists(filename+".0"):
|
||||
curfilename = filename+".0"
|
||||
else:
|
||||
print("file not found:", filename)
|
||||
sys.exit()
|
||||
|
||||
head=snapshot_header(curfilename)
|
||||
print('npar=',head.npart)
|
||||
print('nall=',head.nall)
|
||||
print('a=',head.time)
|
||||
print('z=',head.redshift)
|
||||
print('masses=',head.massarr*1e10,'Msun/h')
|
||||
print('boxsize=',head.boxsize,'kpc/h')
|
||||
print('filenum=',head.filenum)
|
||||
print('cooling=',head.cooling)
|
||||
print('Omega_m,Omega_l=',head.omega_m,head.omega_l)
|
||||
print('h=',head.hubble,'\n')
|
||||
|
||||
rhocrit=2.77536627e11 #h**2 M_sun/Mpc**3
|
||||
rhocrit=rhocrit/1e9 #h**2M_sun/kpc**3
|
||||
|
||||
Omega_DM=head.nall[1]*head.massarr[1]*1e10/(head.boxsize**3*rhocrit)
|
||||
print('DM mass=',head.massarr[1]*1e10,'Omega_DM=',Omega_DM)
|
||||
if head.nall[2]>0 and head.massarr[2]>0:
|
||||
Omega_NU=head.nall[2]*head.massarr[2]*1e10/(head.boxsize**3*rhocrit)
|
||||
print('NU mass=',head.massarr[2]*1e10,'Omega_NU=',Omega_NU)
|
||||
print('Sum of neutrino masses=',Omega_NU*head.hubble**2*94.1745,'eV')
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue