Updated ICs for the Gresho-Chan vortex test-case

examples/GreshoVortex/makeIC.py

@@ -21,93 +21,83 @@
 import h5py
 import random
 from numpy import *
+import sys
 
 # Generates a swift IC file for the Gresho Vortex in a periodic box
 
 # Parameters
+inputFile = "glass_256.hdf5"
 periodic= 1      # 1 For periodic box
-factor = 3
-boxSize = [ 1.0 , 1.0, 1.0/factor ]
-L = 120           # Number of particles along one axis
 gamma = 5./3.     # Gas adiabatic index
-eta = 1.2349      # 48 ngbs with cubic spline kernel
 rho = 1           # Gas density
 P0 = 0.           # Constant additional pressure (should have no impact on the dynamics)
-fileName = "greshoVortex.hdf5" 
-vol = boxSize[0] * boxSize[1] * boxSize[2]
+fileOutputName = "greshoVortex.hdf5" 
 
 
 #---------------------------------------------------
-
-numPart = L**3 / factor
-mass = boxSize[0]*boxSize[1]*boxSize[2] * rho / numPart
-
-#Generate particles
-coords = zeros((numPart, 3))
-v      = zeros((numPart, 3))
-m      = zeros((numPart, 1))
-h      = zeros((numPart, 1))
-u      = zeros((numPart, 1))
-ids    = zeros((numPart, 1), dtype='L')
-
-partId=0
-for i in range(L):
-    for j in range(L):
-        for k in range(L/factor):
-            index = i*L*L/factor + j*L/factor + k
-            x = i * boxSize[0] / L + boxSize[0] / (2*L)
-            y = j * boxSize[0] / L + boxSize[0] / (2*L)
-            z = k * boxSize[0] / L + boxSize[0] / (2*L)
-            r2 = (x - boxSize[0] / 2)**2 + (y - boxSize[1] / 2)**2
-            r = sqrt(r2)
-            coords[index,0] = x
-            coords[index,1] = y
-            coords[index,2] = z
-            v_phi = 0.
-            if r < 0.2:
-                v_phi = 5.*r
-            elif r < 0.4:
-                v_phi = 2. - 5.*r
-            else:
-                v_phi = 0.
-            v[index,0] = -v_phi * (y - boxSize[0] / 2) / r
-            v[index,1] =  v_phi * (x - boxSize[0] / 2) / r
-            v[index,2] = 0.
-            m[index] = mass
-            h[index] = eta * boxSize[0] / L
-            P = P0
-            if r < 0.2:
-                P = P + 5. + 12.5*r2
-            elif r < 0.4:
-                P = P + 9. + 12.5*r2 - 20.*r + 4.*log(r/0.2)
-            else:
-                P = P + 3. + 4.*log(2.)
-            u[index] = P / ((gamma - 1.)*rho)
-            ids[index] = partId + 1
-            partId = partId + 1
-
+fileInput = h5py.File(inputFile, "r")
+header = fileInput["/Header"]
+boxSize = header.attrs["BoxSize"][0]
+coords = fileInput["/PartType0/Coordinates"][:,:]
+h = fileInput["/PartType0/SmoothingLength"][:]
+ids = fileInput["/PartType0/ParticleIDs"][:]
+numPart = size(ids)
+
+m = ones(shape(ids)) * boxSize**2 / numPart
+u = zeros(shape(m))
+v = zeros(shape(coords))
+
+
+for i in range(numPart):
+    x = coords[i,0]
+    y = coords[i,1]
+    z = coords[i,2]
+
+    r2 = (x - boxSize / 2)**2 + (y - boxSize / 2)**2
+    r = sqrt(r2)
+
+    v_phi = 0.
+    if r < 0.2:
+        v_phi = 5.*r
+    elif r < 0.4:
+        v_phi = 2. - 5.*r
+    else:
+        v_phi = 0.
+    v[i,0] = -v_phi * (y - boxSize / 2) / r
+    v[i,1] =  v_phi * (x - boxSize / 2) / r
+    v[i,2] = 0.
+
+    P = P0
+    if r < 0.2:
+        P = P + 5. + 12.5*r2
+    elif r < 0.4:
+        P = P + 9. + 12.5*r2 - 20.*r + 4.*log(r/0.2)
+    else:
+        P = P + 3. + 4.*log(2.)
+    u[i] = P / ((gamma - 1.)*rho)
+    
 
 
 #File
-file = h5py.File(fileName, 'w')
+fileOutput = h5py.File(fileOutputName, 'w')
 
 # Header
-grp = file.create_group("/Header")
+grp = fileOutput.create_group("/Header")
 grp.attrs["BoxSize"] = boxSize
 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["NumFileOutputsPerSnapshot"] = 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 = file.create_group("/RuntimePars")
+grp = fileOutput.create_group("/RuntimePars")
 grp.attrs["PeriodicBoundariesOn"] = periodic
 
 #Units
-grp = file.create_group("/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.
@@ -115,20 +105,20 @@ grp.attrs["Unit current in cgs (U_I)"] = 1.
 grp.attrs["Unit temperature in cgs (U_T)"] = 1.
 
 #Particle group
-grp = file.create_group("/PartType0")
+grp = fileOutput.create_group("/PartType0")
 ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
 ds[()] = coords
 ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
 ds[()] = v
-ds = grp.create_dataset('Masses', (numPart,1), 'f')
-ds[()] = m
+ds = grp.create_dataset('Masses', (numPart, 1), 'f')
+ds[()] = m.reshape((numPart,1))
 ds = grp.create_dataset('SmoothingLength', (numPart,1), 'f')
-ds[()] = h
+ds[()] = h.reshape((numPart,1))
 ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
-ds[()] = u
+ds[()] = u.reshape((numPart,1))
 ds = grp.create_dataset('ParticleIDs', (numPart,1), 'L')
-ds[()] = ids[:]
+ds[()] = ids.reshape((numPart,1))
 
-file.close()
+fileOutput.close()
 
 

examples/PerturbedPlane/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
+import sys
+import random
+from numpy import *
+
+# Generates a swift IC file containing a perturbed 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
+rho = 1.             # Density
+P = 1.               # Pressure
+gamma = 5./3.        # Gas adiabatic index
+pert = 0.1          # Perturbation scale (in units of the interparticle separation)
+fileName = "perturbedPlane.hdf5" 
+
+
+#---------------------------------------------------
+numPart = L**2
+mass = boxSize**2 * rho / numPart
+internalEnergy = P / ((gamma - 1.)*rho)
+
+#Generate particles
+coords = zeros((numPart, 3))
+v      = zeros((numPart, 3))
+m      = zeros((numPart, 1))
+h      = zeros((numPart, 1))
+u      = zeros((numPart, 1))
+ids    = zeros((numPart, 1), dtype='L')
+
+for i in range(L):
+    for j in range(L):
+        index = i*L + j
+        x = i * boxSize / L + boxSize / (2*L) + random.random() * pert * boxSize/(2.*L)
+        y = j * boxSize / L + boxSize / (2*L) + random.random() * pert * boxSize/(2.*L)
+        z = 0
+        coords[index,0] = x
+        coords[index,1] = y
+        coords[index,2] = z
+        v[index,0] = 0.
+        v[index,1] = 0.
+        v[index,2] = 0.
+        m[index] = mass
+        h[index] = 1.23485 * boxSize / L
+        u[index] = internalEnergy
+        ids[index] = index
+            
+            
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+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]
+grp.attrs["NumPart_Total"] = numPart
+
+#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("/PartType0")
+ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
+ds[()] = coords
+ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
+ds[()] = v
+ds = grp.create_dataset('Masses', (numPart,1), 'f')
+ds[()] = m
+ds = grp.create_dataset('SmoothingLength', (numPart,1), 'f')
+ds[()] = h
+ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
+ds[()] = u
+ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
+ds[()] = ids + 1
+
+file.close()

examples/PerturbedPlane/perturbedPlane.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:   10.   # 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:            perturbedPlane # 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-3 # 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:  0.1      # 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:  ./perturbedPlane.hdf5     # The file to read

src/const.h

@@ -37,8 +37,8 @@
 #define const_max_u_change 0.1f
 
 /* Dimensionality of the problem */
-#define HYDRO_DIMENSION_3D
-//#define HYDRO_DIMENSION_2D
+//#define HYDRO_DIMENSION_3D
+#define HYDRO_DIMENSION_2D
 //#define HYDRO_DIMENSION_1D
 
 /* Hydrodynamical adiabatic index. */