Added the 'Square test' in 2D.

examples/GreshoVortex_2D/gresho.yml

@@ -27,7 +27,7 @@ Statistics:
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
-  max_smoothing_length:  0.1      # Maximal smoothing length allowed (in internal units).
+  max_smoothing_length:  0.02     # Maximal smoothing length allowed (in internal units).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
   
 # Parameters related to the initial conditions

examples/GreshoVortex_2D/makeIC.py

@@ -19,7 +19,6 @@
 
 import h5py
 from numpy import *
-import sys
 
 # Generates a swift IC file for the Gresho-Chan vortex in a periodic box
 
@@ -80,7 +79,7 @@ fileOutput = h5py.File(fileOutputName, 'w')
 
 # Header
 grp = fileOutput.create_group("/Header")
-grp.attrs["BoxSize"] = boxSize
+grp.attrs["BoxSize"] = [boxSize, boxSize, 0.2]
 grp.attrs["NumPart_Total"] =  [numPart, 0, 0, 0, 0, 0]
 grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]

examples/SquareTest_2D/makeIC.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
+from numpy import *
+
+# Generates a swift IC file for the Square test in a periodic box
+
+# Parameters
+L = 64            # Number of particles on the side 
+gamma = 5./3.     # Gas adiabatic index
+rho0 = 4          # Gas central density
+rho1 = 1          # Gas outskirt density
+P0 = 2.5          # Gas central pressure
+P1 = 2.5          # Gas central pressure
+vx = 142.3        # Random velocity for all particles 
+vy = -31.4
+fileOutputName = "square.hdf5"
+#---------------------------------------------------
+
+vol = 1.
+
+numPart_out = L * L
+numPart_in = L * L * rho0 / rho1 / 4
+
+L_out = int(sqrt(numPart_out))
+L_in = int(sqrt(numPart_in))
+
+pos_out = zeros((numPart_out, 3))
+for i in range(L_out):
+    for j in range(L_out):
+        index = i * L_out + j
+        pos_out[index, 0] =  i / (float(L_out)) + 1./(2. * L_out)
+        pos_out[index, 1] =  j / (float(L_out)) + 1./(2. * L_out)
+h_out = ones(numPart_out) * (1. / L_out) * 1.2348
+m_out = ones(numPart_out) * vol  * rho1 / numPart_out
+u_out = ones(numPart_out) * P1 / (rho1 * (gamma - 1.))
+
+pos_in = zeros((numPart_in, 3))
+for i in range(L_in):
+    for j in range(L_in):
+        index = i * L_in + j
+        pos_in[index, 0] =  0.25 + i / float(2. * L_in) + 1./(2. * 2. * L_in)
+        pos_in[index, 1] =  0.25 + j / float(2. * L_in) + 1./(2. * 2. * L_in)
+h_in = ones(numPart_in) * (1. / L_in) * 1.2348
+m_in = ones(numPart_in) * 0.25 * vol * rho0 / numPart_in
+u_in = ones(numPart_in) * P0 / (rho0 * (gamma - 1.))
+
+# Remove the central particles 
+select_out = logical_or(logical_or(pos_out[:,0] < 0.25 , pos_out[:,0] > 0.75), logical_or(pos_out[:,1] < 0.25, pos_out[:,1] > 0.75))
+pos_out = pos_out[select_out, :]
+h_out = h_out[select_out]
+u_out = u_out[select_out]
+m_out = m_out[select_out]
+
+# Add the central region
+pos = append(pos_out, pos_in, axis=0)
+h = append(h_out, h_in, axis=0)
+u = append(u_out, u_in)
+m = append(m_out, m_in)
+numPart = size(h)
+ids = linspace(1, numPart, numPart)
+vel = zeros((numPart, 3))
+vel[:,0] = vx
+vel[:,1] = vy
+        
+
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [vol, vol, 0.2]
+grp.attrs["NumPart_Total"] =  [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 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, 0, 0, 0, 0, 0]
+
+#Runtime parameters
+grp = fileOutput.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = fileOutput.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 = fileOutput.create_group("/PartType0")
+ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
+ds[()] = pos
+ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
+ds[()] = vel
+ds = grp.create_dataset('Masses', (numPart, 1), 'f')
+ds[()] = m.reshape((numPart,1))
+ds = grp.create_dataset('SmoothingLength', (numPart,1), 'f')
+ds[()] = h.reshape((numPart,1))
+ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
+ds[()] = u.reshape((numPart,1))
+ds = grp.create_dataset('ParticleIDs', (numPart,1), 'L')
+ds[()] = ids.reshape((numPart,1))
+
+fileOutput.close()
+
+

examples/SquareTest_2D/plotSolution.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/>.
+ # 
+ ##############################################################################
+
+# Computes the analytical solution of the square test
+
+# Parameters
+gas_gamma = 5./3.     # Gas adiabatic index
+gamma = 5./3.     # Gas adiabatic index
+rho0 = 4          # Gas central density
+rho1 = 1          # Gas outskirt density
+P0 = 2.5          # Gas central pressure
+P1 = 2.5          # Gas central pressure
+vx = 142.3        # Random velocity for all particles 
+vy = -31.4
+
+# ---------------------------------------------------------------
+# Don't touch anything after this.
+# ---------------------------------------------------------------
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+import h5py
+
+# Plot parameters
+params = {'axes.labelsize': 10,
+'axes.titlesize': 10,
+'font.size': 12,
+'legend.fontsize': 12,
+'xtick.labelsize': 10,
+'ytick.labelsize': 10,
+'text.usetex': True,
+ 'figure.figsize' : (9.90,6.45),
+'figure.subplot.left'    : 0.045,
+'figure.subplot.right'   : 0.99,
+'figure.subplot.bottom'  : 0.05,
+'figure.subplot.top'     : 0.99,
+'figure.subplot.wspace'  : 0.15,
+'figure.subplot.hspace'  : 0.12,
+'lines.markersize' : 6,
+'lines.linewidth' : 3.,
+'text.latex.unicode': True
+}
+rcParams.update(params)
+rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+snap = int(sys.argv[1])
+
+# Read the simulation data
+sim = h5py.File("square_%03d.hdf5"%snap, "r")
+boxSize = sim["/Header"].attrs["BoxSize"][0]
+time = sim["/Header"].attrs["Time"][0]
+scheme = sim["/HydroScheme"].attrs["Scheme"]
+kernel = sim["/HydroScheme"].attrs["Kernel function"]
+neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"]
+eta = sim["/HydroScheme"].attrs["Kernel eta"]
+git = sim["Code"].attrs["Git Revision"]
+
+# Analytical soltion
+centre_x = 0.5 + time * vx
+centre_y = 0.5 + time * vy
+
+while centre_x > 1.:
+    centre_x -= 1.
+while centre_x < 0.:
+    centre_x += 1.
+while centre_y > 1.:
+    centre_y -= 1.
+while centre_y < 0.:
+    centre_y += 1.
+
+pos = sim["/PartType0/Coordinates"][:,:]
+vel = sim["/PartType0/Velocities"][:,:]
+v_norm = sqrt(vel[:,0]**2 + vel[:,1]**2)
+rho = sim["/PartType0/Density"][:]
+u = sim["/PartType0/InternalEnergy"][:]
+S = sim["/PartType0/Entropy"][:]
+P = sim["/PartType0/Pressure"][:]
+x = pos[:,0] - centre_x
+y = pos[:,1] - centre_y
+
+# Box wrapping
+x[x>0.5] -= 1.
+x[x<-0.5] += 1.
+y[y>0.5] -= 1.
+y[y<-0.5] += 1.
+
+# Azimuthal velocity profile -----------------------------
+subplot(231)
+scatter(x, y, c=v_norm, cmap="PuBu", edgecolors='face', s=4, vmin=-1., vmax=1.)
+text(0.47, 0.47, "${\\rm{Velocity~norm}}$", ha="right", va="top", backgroundcolor="w")
+plot([-0.25, 0.25], [0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, 0.25], [-0.25, -0.25], '--', color='k', alpha=0.8, lw=2)
+plot([0.25, 0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, -0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=-7)
+xlim(-0.5, 0.5)
+ylim(-0.5, 0.5)
+
+# Radial density profile --------------------------------
+subplot(232)
+scatter(x, y, c=rho, cmap="PuBu", edgecolors='face', s=4, vmin=0., vmax=4.)
+text(0.47, 0.47, "${\\rm{Density}}$", ha="right", va="top", backgroundcolor="w")
+plot([-0.25, 0.25], [0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, 0.25], [-0.25, -0.25], '--', color='k', alpha=0.8, lw=2)
+plot([0.25, 0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, -0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=-7)
+xlim(-0.5, 0.5)
+ylim(-0.5, 0.5)
+
+# Radial pressure profile --------------------------------
+subplot(233)
+scatter(x, y, c=P, cmap="PuBu", edgecolors='face', s=4, vmin=2, vmax=4)
+text(0.47, 0.47, "${\\rm{Pressure}}$", ha="right", va="top", backgroundcolor="w")
+plot([-0.25, 0.25], [0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, 0.25], [-0.25, -0.25], '--', color='k', alpha=0.8, lw=2)
+plot([0.25, 0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, -0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=-7)
+xlim(-0.5, 0.5)
+ylim(-0.5, 0.5)
+
+# Internal energy profile --------------------------------
+subplot(234)
+scatter(x, y, c=u, cmap="PuBu", edgecolors='face', s=4, vmin=0.5, vmax=4.)
+text(0.47, 0.47, "${\\rm{Internal~energy}}$", ha="right", va="top", backgroundcolor="w")
+plot([-0.25, 0.25], [0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, 0.25], [-0.25, -0.25], '--', color='k', alpha=0.8, lw=2)
+plot([0.25, 0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, -0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=-7)
+xlim(-0.5, 0.5)
+ylim(-0.5, 0.5)
+
+# Radial entropy profile --------------------------------
+subplot(235)
+scatter(x, y, c=S, cmap="PuBu", edgecolors='face', s=4, vmin=0., vmax=3.)
+text(0.47, 0.47, "${\\rm{Entropy}}$", ha="right", va="top", backgroundcolor="w")
+plot([-0.25, 0.25], [0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, 0.25], [-0.25, -0.25], '--', color='k', alpha=0.8, lw=2)
+plot([0.25, 0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+plot([-0.25, -0.25], [-0.25, 0.25], '--', color='k', alpha=0.8, lw=2)
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=-7)
+xlim(-0.5, 0.5)
+ylim(-0.5, 0.5)
+
+
+# Information -------------------------------------
+subplot(236, frameon=False)
+
+text(-0.49, 0.9, "Square test with $\\gamma=%.3f$ at $t=%.2f$"%(gas_gamma,time), fontsize=10)
+text(-0.49, 0.8, "Centre:~~~ $(P, \\rho) = (%.3f, %.3f)$"%(P0, rho0), fontsize=10)
+text(-0.49, 0.7, "Outskirts: $(P, \\rho) = (%.3f, %.3f)$"%(P1, rho1), fontsize=10)
+plot([-0.49, 0.1], [0.62, 0.62], 'k-', lw=1)
+text(-0.49, 0.5, "$\\textsc{Swift}$ %s"%git, fontsize=10)
+text(-0.49, 0.4, scheme, fontsize=10)
+text(-0.49, 0.3, kernel, fontsize=10)
+text(-0.49, 0.2, "$%.2f$ neighbours ($\\eta=%.3f$)"%(neighbours, eta), fontsize=10)
+xlim(-0.5, 0.5)
+ylim(0, 1)
+xticks([])
+yticks([])
+
+savefig("SquareTest.png", dpi=200)

examples/SquareTest_2D/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e square.hdf5 ]
+then
+    echo "Generating initial conditions for the square test ..."
+    python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 square.yml
+
+# Plot the solution
+python plotSolution.py 40

examples/SquareTest_2D/square.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:   4.   # 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:     1e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+  basename:            square # Common part of the name of output files
+  time_first:          0.     # Time of the first output (in internal units)
+  delta_time:          1e-1   # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+
+# 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).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  max_smoothing_length:  0.02     # Maximal smoothing length allowed (in internal units).
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./square.hdf5     # The file to read