Merge branch 'big_ICs' into 'master'

New script for very large ICs

This just adds a new script to generate a very large uniform box ICs. 

I wanted to test the code with a very large number of particles on cosma-5 so needed a script robust enough and that did not need to keep all the data in memory before writing to a file.  

See merge request !97

examples/UniformBox/makeICbig.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ # 
+ # 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 Lesser General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ # 
+ ##############################################################################
+
+import h5py
+import sys
+from numpy import *
+
+# Generates a swift IC file containing a cartesian distribution of particles
+# at a constant density and pressure in a cubic box
+
+# Parameters
+periodic= 1           # 1 For periodic box
+boxSize = 1.
+L = int(sys.argv[1])  # Number of particles along one axis
+N = int(sys.argv[2])  # Write N particles at a time to avoid requiring a lot of RAM
+rho = 2.              # Density
+P = 1.                # Pressure
+gamma = 5./3.         # Gas adiabatic index
+fileName = "uniformBox_%d.hdf5"%L
+
+#---------------------------------------------------
+numPart = L**3
+mass = boxSize**3 * rho / numPart
+internalEnergy = P / ((gamma - 1.)*rho)
+
+#---------------------------------------------------
+
+n_iterations = numPart / N
+remainder = numPart % N
+
+print "Writing", numPart, "in", n_iterations, "iterations of size", N, "and a remainder of", remainder
+
+#---------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+grp.attrs["NumPart_Total"] =  [numPart % (long(1)<<32), 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [numPart / (long(1)<<32), 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = periodic
+
+#Particle group
+grp = file.create_group("/PartType0")
+
+# First create the arrays in the file
+ds_v = grp.create_dataset('Velocities', (numPart, 3), 'f', chunks=True, compression="gzip")
+ds_m = grp.create_dataset('Masses', (numPart,1), 'f', chunks=True, compression="gzip")
+ds_h = grp.create_dataset('SmoothingLength', (numPart,1), 'f', chunks=True, compression="gzip")
+ds_u = grp.create_dataset('InternalEnergy', (numPart,1), 'f', chunks=True, compression="gzip")
+ds_id = grp.create_dataset('ParticleIDs', (numPart, 1), 'L', chunks=True, compression="gzip")
+ds_x = grp.create_dataset('Coordinates', (numPart, 3), 'd', chunks=True, compression="gzip")
+
+# Now loop and create parts of the dataset
+offset = 0
+for n in range(n_iterations):
+    v  = zeros((N, 3))
+    ds_v[offset:offset+N,:] = v
+    v = zeros(1)
+
+    m = full((N, 1), mass)
+    ds_m[offset:offset+N] = m
+    m = zeros(1)
+
+    h = full((N, 1), 1.1255 * boxSize / L)
+    ds_h[offset:offset+N] = h
+    h = zeros(1)
+
+    u = full((N, 1), internalEnergy)
+    ds_u[offset:offset+N] = u
+    u = zeros(1)
+
+    ids = linspace(offset, offset+N, N, endpoint=False).reshape((N,1))
+    ds_id[offset:offset+N] = ids
+    x      = ids % L;
+    y      = ((ids - x) / L) % L;
+    z      = (ids - x - L * y) / L**2;
+    ids    = zeros(1)
+    coords = zeros((N, 3))
+    coords[:,0] = z[:,0] * boxSize / L + boxSize / (2*L)
+    coords[:,1] = y[:,0] * boxSize / L + boxSize / (2*L)
+    coords[:,2] = x[:,0] * boxSize / L + boxSize / (2*L)
+    ds_x[offset:offset+N,:] = coords
+    coords  = zeros((1,3))
+
+    offset += N
+    print "Done", offset,"/", numPart, "(%.1f %%)"%(100*(float)(offset)/numPart)
+
+# And now, the remainder
+v  = zeros((remainder, 3))
+ds_v[offset:offset+remainder,:] = v
+v = zeros(1)
+
+m = full((remainder, 1), mass)
+ds_m[offset:offset+remainder] = m
+m = zeros(1)
+
+h = full((remainder, 1), 1.1255 * boxSize / L)
+ds_h[offset:offset+remainder] = h
+h = zeros(1)
+
+u = full((remainder, 1), internalEnergy)
+ds_u[offset:offset+remainder] = u
+u = zeros(1)
+
+print "Done", offset+remainder,"/", numPart
+
+ids = linspace(offset, offset+remainder, remainder, endpoint=False).reshape((remainder,1))
+ds_id[offset:offset+remainder] = ids
+x      = ids % L;
+y      = ((ids - x) / L) % L;
+z      = (ids - x - L * y) / L**2;
+coords = zeros((remainder, 3))
+coords[:,0] = z[:,0] * boxSize / L + boxSize / (2*L)
+coords[:,1] = y[:,0] * boxSize / L + boxSize / (2*L)
+coords[:,2] = x[:,0] * boxSize / L + boxSize / (2*L)
+ds_x[offset:offset+remainder,:] = coords
+
+
+
+
+
+file.close()