Added a new example: A small cosmological volume with some cooling on.

examples/SmallCosmoVolume/small_cosmo_volume.yml

@@ -56,8 +56,3 @@ InitialConditions:
   cleanup_velocity_factors:    1  
   generate_gas_in_ics: 1            # Generate gas particles from the DM-only ICs
   cleanup_smoothing_lengths: 1      # Since we generate gas, make use of the (expensive) cleaning-up procedure.
-
-# Constant lambda cooling function
-LambdaCooling:
-  lambda_cgs:                  1e-22 # Cooling rate (in cgs units)
-  cooling_tstep_mult:          1.0   # Dimensionless pre-factor for the time-step condition

examples/SmallCosmoVolume_cooling/README

+Small LCDM cosmological simulation generated by C. Power. Cosmology
+is WMAP9 and the box is 100Mpc/h in size with 64^3 particles.
+We use a softening length of 1/25th of the mean inter-particle separation.
+
+The ICs have been generated to run with Gadget-2 so we need to switch
+on the options to cancel the h-factors and a-factors at reading time.
+We generate gas from the ICs using SWIFT's internal mechanism and set the
+temperature to the expected gas temperature at this redshift.
+
+The 'plotTempEvolution.py' plots the temperature evolution of the gas
+in the simulated volume.
+
+MD5 checksum of the ICs:
+08736c3101fd738e22f5159f78e6022b  small_cosmo_volume.hdf5

examples/SmallCosmoVolume_cooling/getIC.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/small_cosmo_volume.hdf5
+

examples/SmallCosmoVolume_cooling/plotTempEvolution.py

+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 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/>.
+#
+################################################################################
+
+# Computes the temperature evolution of the gas in a cosmological box
+
+# Physical constants needed for internal energy to temperature conversion
+k_in_J_K = 1.38064852e-23
+mH_in_kg = 1.6737236e-27
+
+# Number of snapshots generated
+n_snapshots = 160
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+import h5py
+import os.path
+
+# Plot parameters
+params = {'axes.labelsize': 10,
+'axes.titlesize': 10,
+'font.size': 9,
+'legend.fontsize': 9,
+'xtick.labelsize': 10,
+'ytick.labelsize': 10,
+'text.usetex': True,
+ 'figure.figsize' : (3.15,3.15),
+'figure.subplot.left'    : 0.14,
+'figure.subplot.right'   : 0.99,
+'figure.subplot.bottom'  : 0.12,
+'figure.subplot.top'     : 0.99,
+'figure.subplot.wspace'  : 0.15,
+'figure.subplot.hspace'  : 0.12,
+'lines.markersize' : 6,
+'lines.linewidth' : 2.,
+'text.latex.unicode': True
+}
+rcParams.update(params)
+rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the simulation data
+sim = h5py.File("snap_0000.hdf5", "r")
+boxSize = sim["/Header"].attrs["BoxSize"][0]
+time = sim["/Header"].attrs["Time"][0]
+scheme = sim["/HydroScheme"].attrs["Scheme"][0]
+kernel = sim["/HydroScheme"].attrs["Kernel function"][0]
+neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = sim["/HydroScheme"].attrs["Kernel eta"][0]
+alpha = sim["/HydroScheme"].attrs["Alpha viscosity"][0]
+H_mass_fraction = sim["/HydroScheme"].attrs["Hydrogen mass fraction"][0]
+H_transition_temp = sim["/HydroScheme"].attrs["Hydrogen ionization transition temperature"][0]
+T_initial = sim["/HydroScheme"].attrs["Initial temperature"][0]
+T_minimal = sim["/HydroScheme"].attrs["Minimal temperature"][0]
+git = sim["Code"].attrs["Git Revision"]
+cooling_model = sim["/SubgridScheme"].attrs["Cooling Model"]
+
+if cooling_model == "Constant Lambda":
+    Lambda = sim["/SubgridScheme"].attrs["Lambda [cgs]"][0]
+    
+# Cosmological parameters
+H_0 = sim["/Cosmology"].attrs["H0 [internal units]"][0]
+gas_gamma = sim["/HydroScheme"].attrs["Adiabatic index"][0]
+
+unit_length_in_cgs = sim["/Units"].attrs["Unit length in cgs (U_L)"]
+unit_mass_in_cgs = sim["/Units"].attrs["Unit mass in cgs (U_M)"]
+unit_time_in_cgs = sim["/Units"].attrs["Unit time in cgs (U_t)"]
+
+unit_length_in_si = 0.01 * unit_length_in_cgs
+unit_mass_in_si = 0.001 * unit_mass_in_cgs
+unit_time_in_si = unit_time_in_cgs
+
+# Primoridal ean molecular weight as a function of temperature
+def mu(T, H_frac=H_mass_fraction, T_trans=H_transition_temp):
+    if T > T_trans:
+        return 4. / (8. - 5. * (1. - H_frac))
+    else:
+        return 4. / (1. + 3. * H_frac)
+    
+# Temperature of some primoridal gas with a given internal energy
+def T(u, H_frac=H_mass_fraction, T_trans=H_transition_temp):
+    T_over_mu = (gas_gamma - 1.) * u * mH_in_kg / k_in_J_K
+    ret = np.ones(np.size(u)) * T_trans
+
+    # Enough energy to be ionized?
+    mask_ionized = (T_over_mu > (T_trans+1) / mu(T_trans+1, H_frac, T_trans))
+    if np.sum(mask_ionized)  > 0:
+        ret[mask_ionized] = T_over_mu[mask_ionized] * mu(T_trans*10, H_frac, T_trans)
+
+    # Neutral gas?
+    mask_neutral = (T_over_mu < (T_trans-1) / mu((T_trans-1), H_frac, T_trans))
+    if np.sum(mask_neutral)  > 0:
+        ret[mask_neutral] = T_over_mu[mask_neutral] * mu(0, H_frac, T_trans)
+        
+    return ret
+
+
+z = np.zeros(n_snapshots)
+a = np.zeros(n_snapshots)
+T_mean = np.zeros(n_snapshots)
+T_std = np.zeros(n_snapshots)
+T_log_mean = np.zeros(n_snapshots)
+T_log_std = np.zeros(n_snapshots)
+T_median = np.zeros(n_snapshots)
+T_min = np.zeros(n_snapshots)
+T_max = np.zeros(n_snapshots)
+
+# Loop over all the snapshots
+for i in range(n_snapshots):
+    sim = h5py.File("snap_%04d.hdf5"%i, "r")
+
+    z[i] = sim["/Cosmology"].attrs["Redshift"][0]
+    a[i] = sim["/Cosmology"].attrs["Scale-factor"][0]
+
+    u = sim["/PartType0/InternalEnergy"][:]
+
+    # Compute the temperature
+    u *= (unit_length_in_si**2 / unit_time_in_si**2)
+    u /= a[i]**(3 * (gas_gamma - 1.))
+    Temp = T(u)
+
+    # Gather statistics
+    T_median[i] = np.median(Temp)
+    T_mean[i] = Temp.mean()
+    T_std[i] = Temp.std()
+    T_log_mean[i] = np.log10(Temp).mean()
+    T_log_std[i] = np.log10(Temp).std()
+    T_min[i] = Temp.min()
+    T_max[i] = Temp.max()
+
+# CMB evolution
+a_evol = np.logspace(-3, 0, 60)
+T_cmb = (1. / a_evol)**2 * 2.72
+
+# Plot the interesting quantities
+figure()
+subplot(111, xscale="log", yscale="log")
+
+fill_between(a, T_mean-T_std, T_mean+T_std, color='C0', alpha=0.1)
+plot(a, T_max, ls='-.', color='C0', lw=1., label="${\\rm max}~T$")
+plot(a, T_min, ls=':', color='C0', lw=1., label="${\\rm min}~T$")
+plot(a, T_mean, color='C0', label="${\\rm mean}~T$", lw=1.5)
+fill_between(a, 10**(T_log_mean-T_log_std), 10**(T_log_mean+T_log_std), color='C1', alpha=0.1)
+plot(a, 10**T_log_mean, color='C1', label="${\\rm mean}~{\\rm log} T$", lw=1.5)
+plot(a, T_median, color='C2', label="${\\rm median}~T$", lw=1.5)
+
+legend(loc="upper left", frameon=False, handlelength=1.5)
+
+# Cooling model
+if cooling_model == "Constant Lambda":
+    text(1e-2, 6e4, "$\Lambda_{\\rm const} = %.1f\\times10^{%d}~[\\rm{cgs}]$"%(Lambda/10.**(int(log10(Lambda))), log10(Lambda)), fontsize=8)
+else:
+    text(1e-2, 6e4, "No cooling")
+    
+# Expected lines
+plot([1e-10, 1e10], [H_transition_temp, H_transition_temp], 'k--', lw=0.5, alpha=0.7)
+text(2.5e-2, H_transition_temp*1.07, "$T_{\\rm HII\\rightarrow HI}$", va="bottom", alpha=0.7, fontsize=8)
+plot([1e-10, 1e10], [T_minimal, T_minimal], 'k--', lw=0.5, alpha=0.7)
+text(1e-2, T_minimal*0.8, "$T_{\\rm min}$", va="top", alpha=0.7, fontsize=8)
+plot(a_evol, T_cmb, 'k--', lw=0.5, alpha=0.7)
+text(a_evol[20], T_cmb[20]*0.55, "$(1+z)^2\\times T_{\\rm CMB,0}$", rotation=-34, alpha=0.7, fontsize=8, va="top", bbox=dict(facecolor='w', edgecolor='none', pad=1.0, alpha=0.9))
+
+
+redshift_ticks = np.array([0., 1., 2., 5., 10., 20., 50., 100.])
+redshift_labels = ["$0$", "$1$", "$2$", "$5$", "$10$", "$20$", "$50$", "$100$"]
+a_ticks = 1. / (redshift_ticks + 1.)
+
+xticks(a_ticks, redshift_labels)
+minorticks_off()
+
+xlabel("${\\rm Redshift}~z$", labelpad=0)
+ylabel("${\\rm Temperature}~T~[{\\rm K}]$", labelpad=0)
+xlim(9e-3, 1.1)
+ylim(20, 2.5e7)
+
+savefig("Temperature_evolution.png", dpi=200)
+

examples/SmallCosmoVolume_cooling/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e small_cosmo_volume.hdf5 ]
+then
+    echo "Fetching initial conditions for the small cosmological volume example..."
+    ./getIC.sh
+fi
+
+# Run SWIFT
+../swift -c -s -G -C -t 8 small_cosmo_volume.yml 2>&1 | tee output.log
+
+# Plot the temperature evolution
+python plotTempEvolution.py

examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun
+  UnitLength_in_cgs:   3.08567758e24 # 1 Mpc
+  UnitVelocity_in_cgs: 1e5           # 1 km/s
+  UnitCurrent_in_cgs:  1             # Amperes
+  UnitTemp_in_cgs:     1             # Kelvin
+
+Cosmology:                      # WMAP9 cosmology
+  Omega_m:        0.276
+  Omega_lambda:   0.724
+  Omega_b:        0.0455
+  h:              0.703
+  a_begin:        0.019607843	# z_ini = 50.
+  a_end:          1.0		# z_end = 0.
+
+# Parameters governing the time integration
+TimeIntegration:
+  dt_min:     1e-6 
+  dt_max:     1e-2 
+
+# Parameters for the self-gravity scheme
+Gravity:
+  eta:          0.025         
+  theta:        0.3           
+  comoving_softening:     0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  max_physical_softening: 0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
+  mesh_side_length:       64
+
+# Parameters of the hydro scheme
+SPH:
+  resolution_eta:      1.2348   # "48 Ngb" with the cubic spline kernel
+  CFL_condition:       0.1
+  initial_temperature: 7075.    # (1 + z_ini)^2 * 2.72K
+  minimal_temperature: 100.
+
+# Parameters governing the snapshots
+Snapshots:
+  basename:            snap
+  delta_time:          1.02
+  scale_factor_first:  0.02
+  
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          1.02
+  scale_factor_first:  0.02
+  
+Scheduler:
+  max_top_level_cells: 8
+  cell_split_size:     50
+  
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  small_cosmo_volume.hdf5
+  cleanup_h_factors:           1    
+  cleanup_velocity_factors:    1  
+  generate_gas_in_ics: 1            # Generate gas particles from the DM-only ICs
+  cleanup_smoothing_lengths: 1      # Since we generate gas, make use of the (expensive) cleaning-up procedure.
+
+# Constant lambda cooling function
+LambdaCooling:
+  lambda_cgs:                  1e-30 # Cooling rate (in cgs units)
+  cooling_tstep_mult:          1.0   # Dimensionless pre-factor for the time-step condition

src/cooling/const_lambda/cooling_io.h

@@ -35,9 +35,10 @@
  * @param h_grpsph The HDF5 group in which to write
  */
 __attribute__((always_inline)) INLINE static void cooling_write_flavour(
-    hid_t h_grpsph) {
+    hid_t h_grp, const struct cooling_function_data* cooling) {
 
-  io_write_attribute_s(h_grpsph, "Cooling Model", "Constant Lambda");
+  io_write_attribute_s(h_grp, "Cooling Model", "Constant Lambda");
+  io_write_attribute_d(h_grp, "Lambda [cgs]", cooling->lambda_cgs);
 }
 #endif
 

src/parallel_io.c

@@ -1020,7 +1020,7 @@ void prepare_file(struct engine* e, const char* baseName, long long N_total[6],
   h_grp = H5Gcreate(h_file, "/SubgridScheme", H5P_DEFAULT, H5P_DEFAULT,
                     H5P_DEFAULT);
   if (h_grp < 0) error("Error while creating subgrid group");
-  cooling_write_flavour(h_grp);
+  cooling_write_flavour(h_grp, e->cooling_func);
   chemistry_write_flavour(h_grp);
   H5Gclose(h_grp);
 

src/serial_io.c

@@ -870,7 +870,7 @@ void write_output_serial(struct engine* e, const char* baseName,
     h_grp = H5Gcreate(h_file, "/SubgridScheme", H5P_DEFAULT, H5P_DEFAULT,
                       H5P_DEFAULT);
     if (h_grp < 0) error("Error while creating subgrid group");
-    cooling_write_flavour(h_grp);
+    cooling_write_flavour(h_grp, e->cooling_func);
     chemistry_write_flavour(h_grp);
     H5Gclose(h_grp);
 

src/single_io.c

@@ -720,7 +720,7 @@ void write_output_single(struct engine* e, const char* baseName,
   h_grp = H5Gcreate(h_file, "/SubgridScheme", H5P_DEFAULT, H5P_DEFAULT,
                     H5P_DEFAULT);
   if (h_grp < 0) error("Error while creating subgrid group");
-  cooling_write_flavour(h_grp);
+  cooling_write_flavour(h_grp, e->cooling_func);
   chemistry_write_flavour(h_grp);
   H5Gclose(h_grp);