Added 'C' cooling flag as an option

examples/IsothermalPotential/GravityOnly/isothermal.yml

@@ -9,7 +9,7 @@ InternalUnitSystem:
 # Parameters governing the time integration
 TimeIntegration:
   time_begin: 0.    # The starting time of the simulation (in internal units).
-  time_end:   8.    # The end time of the simulation (in internal units).
+  time_end:   10.    # The end time of the simulation (in internal units).
   dt_min:     1e-7  # The minimal time-step size of the simulation (in internal units).
   dt_max:     1e-1  # The maximal time-step size of the simulation (in internal units).
 
@@ -21,7 +21,7 @@ Statistics:
 Snapshots:
   basename:            Isothermal # Common part of the name of output files
   time_first:          0.         # Time of the first output (in internal units)
-  delta_time:          0.02       # Time difference between consecutive outputs (in internal units)
+  delta_time:          0.1       # Time difference between consecutive outputs (in internal units)
 
 # Parameters for the hydrodynamics scheme
 SPH:
@@ -33,15 +33,15 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Isothermal.hdf5       # The file to read
-  shift_x:    100.                  # A shift to apply to all particles read from the ICs (in internal units).
-  shift_y:    100.
-  shift_z:    100.
+  shift_x:    200.                  # A shift to apply to all particles read from the ICs (in internal units).
+  shift_y:    200.
+  shift_z:    200.
  
 # External potential parameters
 IsothermalPotential:
-  position_x:      100.     # location of centre of isothermal potential in internal units
-  position_y:      100.
-  position_z:      100.	
+  position_x:      200.     # location of centre of isothermal potential in internal units
+  position_y:      200.
+  position_z:      200.	
   vrot:            200.     # rotation speed of isothermal potential in internal units
   timestep_mult:   0.03     # controls time step
 

examples/IsothermalPotential/GravityOnly/makeIC.py

@@ -25,8 +25,8 @@ import math
 import random
 
 # Generates N particles in a spherical distribution centred on [0,0,0], to be moved in an isothermal potential
-# usage: python makeIC.py 1000 0 : generate 1000 particles on circular orbits
-#        python makeIC.py 1000 1 : generate 1000 particles with Lz/L uniform in [0,1]
+# usage: python makeIC.py 1000 0 1: generate 1000 particles on circular orbits
+#        python makeIC.py 1000 1 1: generate 1000 particles with Lz/L uniform in [0,1]
 # all particles move in the xy plane, and start at y=0
 
 # physical constants in cgs
@@ -64,6 +64,7 @@ G       = const_G
 
 N       = int(sys.argv[1])  # Number of particles
 icirc   = int(sys.argv[2])  # if = 0, all particles are on circular orbits, if = 1, Lz/Lcirc uniform in ]0,1[
+three_d = int(sys.argv[3])  # if = 0, particles distributed in 3 dimensions, if 1, all along one straight line
 L       = N**(1./3.)
 
 # these are not used but necessary for I/O
@@ -119,23 +120,44 @@ ctheta = -1. + 2 * numpy.random.rand(N)
 stheta = numpy.sqrt(1.-ctheta**2)
 phi    =  2 * math.pi * numpy.random.rand(N)
 r      = numpy.zeros((numPart, 3))
-#r[:,0] = radius * stheta * numpy.cos(phi)
-#r[:,1] = radius * stheta * numpy.sin(phi)
-#r[:,2] = radius * ctheta
-r[:,0] = radius
+
+if (three_d == 0):
+    r[:,0] = radius * stheta * numpy.cos(phi)
+    r[:,1] = radius * stheta * numpy.sin(phi)
+    r[:,2] = radius * ctheta
+else:
+    r[:,0] = radius
 #
+
 speed  = vrot
 v      = numpy.zeros((numPart, 3))
-omega  = speed / radius
-period = 2.*math.pi/omega
-print 'period = minimum = ',min(period), ' maximum = ',max(period)
-
-omegav = omega
-if (icirc != 0):
-    omegav = omega * numpy.random.rand(N)
 
-v[:,0] = -omegav * r[:,1]
-v[:,1] =  omegav * r[:,0]
+if(three_d == 0):
+    #make N random angular momentum vectors
+    omega = numpy.random.rand(N,3)
+    #cross with r to get velocities perpendicular to displacement vector
+    v = numpy.cross(omega,r)
+    #rescale v
+    mag_v = numpy.zeros(N)
+    for i in range(N):
+        mag_v[i] = numpy.sqrt(v[i,0]**2 + v[i,1]**2 + v[i,2]**2)
+        v[i,:] /= mag_v[i]
+    v *= speed
+    if (icirc != 0):
+        for i in range(N):
+            v[i,:] *= numpy.random.rand()
+    
+else:
+    omega  = speed / radius
+    period = 2.*math.pi/omega
+    print 'period = minimum = ',min(period), ' maximum = ',max(period)
+
+    omegav = omega
+    if (icirc != 0):
+        omegav = omega * numpy.random.rand(N)
+        
+    v[:,0] = -omegav * r[:,1]
+    v[:,1] =  omegav * r[:,0]
 
 ds = grp1.create_dataset('Velocities', (numPart, 3), 'f')
 ds[()] = v

examples/IsothermalPotential/GravityOnly/plots/energy_plot.py

+import numpy as np
+import matplotlib.pyplot as plt
+import h5py as h5
+
+n_snaps = 102
+directory = '../'
+snap_name_base = "Isothermal_"
+plot_dir = "random_orbits_1d"
+plot_filename_base = "snap"
+
+v_rot = 200.
+r_0 = 100.
+
+e_kin_array = []
+e_pot_array = []
+e_total_array = []
+snap_numbers = np.linspace(0,n_snaps)
+for i in range(n_snaps):
+    snap_number = "%03d" %i
+    filename = directory + snap_name_base + snap_number + ".hdf5"
+    f = h5.File(filename)
+
+    header = f["Header"]
+    n_parts = header.attrs["NumPart_ThisFile"][1]
+    pos = np.array(f["PartType1/Coordinates"])
+    x = pos[:,0]
+    y = pos[:,1]
+    z = pos[:,2]
+    r = np.sqrt(x**2 + y**2 + z**2)
+    e_pot_particles = v_rot**2 * np.log(r/r_0)
+    e_pot_total = np.sum(e_pot_particles)
+    e_pot_array = np.append(e_pot_array,e_pot_total)
+    v = np.array(f["PartType1/Velocities"])
+    e_kin_particles = 0.5*v**2
+    e_kin_total = np.sum(e_kin_particles)
+    e_kin_array = np.append(e_kin_array,e_kin_total)
+    e_total_array = np.append(e_total_array,e_kin_total+e_pot_total)
+
+print snap_numbers.shape
+print e_kin_array.shape
+plt.plot(e_kin_array,label = "Kinetic Energy")
+plt.plot(e_pot_array,label = "Potential Energy")
+plt.plot(e_total_array,label = "Total Energy")
+plt.legend(loc = "upper right")    
+plot_filename = "%s/energy_plot.png" %plot_dir
+plt.savefig(plot_filename,format = "png")
+plt.close()

examples/IsothermalPotential/GravityOnly/plots/plot_particle_positions.py

+import h5py as h5
+import numpy as np
+import matplotlib.pyplot as plt
+
+n_snaps = 102
+directory = '../'
+snap_name_base = "Isothermal_"
+plot_directory = "random_orbits_3d"
+plot_filename_base = "snap"
+for i in range(n_snaps):
+    snap_number = "%03d" %i
+    filename = directory + snap_name_base + snap_number + ".hdf5"
+    f = h5.File(filename)
+    #find the box size
+
+    header = f["Header"]
+    box_size = header.attrs["BoxSize"][0]
+    pos = np.array(f["PartType1/Coordinates"])
+    x = pos[:,0]
+    y = pos[:,1]
+    z = pos[:,2]
+
+    #x_projection
+    plt.plot(y,z,'bo')
+    plt.xlabel("y")
+    plt.ylabel("z")
+    plt.xlim((0.0,box_size))
+    plt.ylim((0.0,box_size))
+    plot_dir = "%s/projection_x" %plot_directory
+    plot_filename = "%s/%s_%03d.png" %(plot_dir,plot_filename_base,i)
+    plt.savefig(plot_filename,format = "png")
+    plt.close()
+
+    #y_projection
+    plt.plot(x,z,'bo')
+    plt.xlabel("x")
+    plt.ylabel("z")
+    plt.xlim((0.0,box_size))
+    plt.ylim((0.0,box_size))
+    plot_dir = "%s/projection_y" %plot_directory
+    plot_filename = "%s/%s_%03d.png" %(plot_dir,plot_filename_base,i)
+    plt.savefig(plot_filename,format = "png")
+    plt.close()
+
+    #x_projection
+    plt.plot(x,y,'bo')
+    plt.xlabel("x")
+    plt.ylabel("y")
+    plt.xlim((0.0,box_size))
+    plt.ylim((0.0,box_size))
+    plot_dir = "%s/projection_z" %plot_directory
+    plot_filename = "%s/%s_%03d.png" %(plot_dir,plot_filename_base,i)
+    plt.savefig(plot_filename,format = "png")
+    plt.close()
+    
+

examples/IsothermalPotential/GravityOnly/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e Isothermal.hdf5 ]
 then
     echo "Generating initial conditions for the isothermal potential box example..."
-    python makeIC.py 1000 1
+    python makeIC.py 10000 1 1
 fi
 
 ../../swift -g -t 2 isothermal.yml

examples/UniformBox/plots/energy_plot.py

+import numpy as np
+import matplotlib.pyplot as plt
+import h5py as h5
+
+n_snaps = 102
+directory = '../'
+snap_name_base = "Isothermal_"
+plot_dir = "random_orbits_1d"
+plot_filename_base = "snap"
+
+v_rot = 200.
+r_0 = 100.
+
+e_kin_array = []
+e_pot_array = []
+e_total_array = []
+snap_numbers = np.linspace(0,n_snaps)
+for i in range(n_snaps):
+    snap_number = "%03d" %i
+    filename = directory + snap_name_base + snap_number + ".hdf5"
+    f = h5.File(filename)
+
+    header = f["Header"]
+    n_parts = header.attrs["NumPart_ThisFile"][1]
+    pos = np.array(f["PartType1/Coordinates"])
+    x = pos[:,0]
+    y = pos[:,1]
+    z = pos[:,2]
+    r = np.sqrt(x**2 + y**2 + z**2)
+    e_pot_particles = v_rot**2 * np.log(r/r_0)
+    e_pot_total = np.sum(e_pot_particles)
+    e_pot_array = np.append(e_pot_array,e_pot_total)
+    v = np.array(f["PartType1/Velocities"])
+    e_kin_particles = 0.5*v**2
+    e_kin_total = np.sum(e_kin_particles)
+    e_kin_array = np.append(e_kin_array,e_kin_total)
+    e_total_array = np.append(e_total_array,e_kin_total+e_pot_total)
+
+print snap_numbers.shape
+print e_kin_array.shape
+plt.plot(e_kin_array,label = "Kinetic Energy")
+plt.plot(e_pot_array,label = "Potential Energy")
+plt.plot(e_total_array,label = "Total Energy")
+plt.legend(loc = "upper right")    
+plot_filename = "%s/energy_plot.png" %plot_dir
+plt.savefig(plot_filename,format = "png")
+plt.close()

examples/UniformBox/plots/plot_particle_positions.py

+import h5py as h5
+import numpy as np
+import matplotlib.pyplot as plt
+
+n_snaps = 100
+directory = '../'
+snap_name_base = "uniformBox_"
+plot_directory = "./"
+plot_filename_base = "snap"
+for i in range(n_snaps):
+    snap_number = "%03d" %i
+    filename = directory + snap_name_base + snap_number + ".hdf5"
+    f = h5.File(filename)
+    #find the box size
+
+    header = f["Header"]
+    box_size = header.attrs["BoxSize"][0]
+    pos = np.array(f["PartType0/Coordinates"])
+    x = pos[:,0]
+    y = pos[:,1]
+    z = pos[:,2]
+
+    #x_projection
+    plt.plot(y,z,'bo')
+    plt.xlabel("y")
+    plt.ylabel("z")
+    plt.xlim((0.0,box_size))
+    plt.ylim((0.0,box_size))
+    plot_dir = "%s/projection_x" %plot_directory
+    plot_filename = "%s/%s_%03d.png" %(plot_dir,plot_filename_base,i)
+    plt.savefig(plot_filename,format = "png")
+    plt.close()
+
+    #y_projection
+    plt.plot(x,z,'bo')
+    plt.xlabel("x")
+    plt.ylabel("z")
+    plt.xlim((0.0,box_size))
+    plt.ylim((0.0,box_size))
+    plot_dir = "%s/projection_y" %plot_directory
+    plot_filename = "%s/%s_%03d.png" %(plot_dir,plot_filename_base,i)
+    plt.savefig(plot_filename,format = "png")
+    plt.close()
+
+    #x_projection
+    plt.plot(x,y,'bo')
+    plt.xlabel("x")
+    plt.ylabel("y")
+    plt.xlim((0.0,box_size))
+    plt.ylim((0.0,box_size))
+    plot_dir = "%s/projection_z" %plot_directory
+    plot_filename = "%s/%s_%03d.png" %(plot_dir,plot_filename_base,i)
+    plt.savefig(plot_filename,format = "png")
+    plt.close()
+    
+

examples/UniformBox/run.sh

@@ -7,4 +7,4 @@ then
     python makeIC.py 100
 fi
 
-../swift -s -t 16 uniformBox.yml
+../swift -s -C -t 16 uniformBox.yml

examples/main.c

@@ -58,6 +58,7 @@ void print_help_message() {
   printf("Valid options are:\n");
   printf("  %2s %8s %s\n", "-a", "", "Pin runners using processor affinity");
   printf("  %2s %8s %s\n", "-c", "", "Run with cosmological time integration");
+  printf("  %2s %8s %s\n", "-C", "", "Run with cooling");
   printf(
       "  %2s %8s %s\n", "-d", "",
       "Dry run. Read the parameter file, allocate memory but does not read ");
@@ -154,7 +155,7 @@ int main(int argc, char *argv[]) {
 
   /* Parse the parameters */
   int c;
-  while ((c = getopt(argc, argv, "acdef:gGhn:st:v:y:")) != -1) switch (c) {
+  while ((c = getopt(argc, argv, "acCdef:gGhn:st:v:y:")) != -1) switch (c) {
       case 'a':
         with_aff = 1;
         break;