Generate ICs for FOF test. Uniform DM box with each particle position perturbed by a random amount.

examples/fof_test/makeIC.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
+ #                    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 *
+import numpy as np
+
+# Generates a swift IC file containing a cartesian distribution of DM particles
+# with a density of 1
+
+# Parameters
+periodic= 1           # 1 For periodic box
+boxSize = 1.
+rho = 1.
+L = int(sys.argv[1])  # Number of particles along one axis
+fileName = "uniformDMBox_%d.hdf5"%L 
+
+#---------------------------------------------------
+numPart = L**3
+mass = boxSize**3 * rho / numPart
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+grp.attrs["NumPart_Total"] =  [0, numPart, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [0, numPart, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, mass, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = periodic
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+
+#Particle group
+grp = file.create_group("/PartType1")
+
+v  = zeros((numPart, 3))
+ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
+ds[()] = v
+v = zeros(1)
+
+m = full((numPart, 1), mass)
+ds = grp.create_dataset('Masses', (numPart,1), 'f')
+ds[()] = m
+m = zeros(1)
+
+ids = linspace(0, numPart, numPart, endpoint=False).reshape((numPart,1))
+ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
+ds[()] = ids + 1
+
+# set seed for random number
+np.random.seed(1234)
+
+x_pert = 1.2 * (np.random.rand(numPart, 1) - 0.5)
+z_pert = 1.2 * (np.random.rand(numPart, 1) - 0.5)
+y_pert = 1.2 * (np.random.rand(numPart, 1) - 0.5)
+
+#x_pert = zeros((numPart, 1))
+#y_pert = zeros((numPart, 1))
+#z_pert = zeros((numPart, 1))
+
+x      = (ids + x_pert) % L;
+y      = ((ids - x) / L + y_pert) % L;
+z      = (ids - x - L * y + z_pert) / L**2;
+coords = zeros((numPart, 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 = grp.create_dataset('Coordinates', (numPart, 3), 'd')
+ds[()] = coords
+
+file.close()

examples/fof_test/uniformBox.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1   # Grams
+  UnitLength_in_cgs:   1   # Centimeters
+  UnitVelocity_in_cgs: 1   # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   100.    # The end time of the simulation (in internal units).
+  dt_min:     1e-6  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1.  # The maximal time-step size of the simulation (in internal units).
+
+Scheduler:
+  max_top_level_cells: 8
+  cell_split_size:     50
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:            uniformDMBox # Common part of the name of output files
+  time_first:          0.           # Time of the first output (in internal units)
+  delta_time:          10.         # Time difference between consecutive outputs (in internal units)
+
+# Parameters for the self-gravity scheme
+Gravity:
+  eta:                    0.025    # Constant dimensionless multiplier for time integration.
+  theta:                  0.85     # Opening angle (Multipole acceptance criterion)
+  comoving_softening:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
+  
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100      # (internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          5. # Time between statistics output
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./uniformDMBox_100.hdf5     # The file to read