Merge branch 'correct_ICs' into 'master'

Corrected the IC generation scripts

IC generation scripts now create files that can be read without problems with the MPI parallel version of the HDF5 library.

Solves bug #23.

See merge request !11


Former-commit-id: 46c7cc9be9046ce69958a4f1a55fdef7ee628b43

examples/SedovBlast/makeIC.py

@@ -48,10 +48,10 @@ if L%2 == 0:
 #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')
+m      = zeros(numPart)
+h      = zeros(numPart)
+u      = zeros(numPart)
+ids    = zeros(numPart, dtype='L')
 
 for i in range(L):
     for j in range(L):
@@ -100,17 +100,11 @@ grp.attrs["PeriodicBoundariesOn"] = periodic
 
 #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
+grp.create_dataset('Coordinates', data=coords, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
 
 file.close()

examples/SedovBlast/makeIC_fcc.py

@@ -50,10 +50,10 @@ hbox = boxSize / L
 #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')
+m      = zeros(numPart)
+h      = zeros(numPart)
+u      = zeros(numPart)
+ids    = zeros(numPart, dtype='L')
 
 for i in range(L):
     for j in range(L):
@@ -103,17 +103,11 @@ grp.attrs["PeriodicBoundariesOn"] = periodic
 
 #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
+grp.create_dataset('Coordinates', data=coords, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
 
 file.close()

examples/SodShock/makeIC.py

@@ -61,9 +61,9 @@ coord1 = append(coord1, coord1 + [0.25, 0, 0], 0)
 # coord1 = append(coord1, pos1 + [0, 0.5, 0.5], 0)
 N1 = size(coord1)/3
 v1 = zeros((N1, 3))
-h1 = ones((N1, 1)) * 2.251 * 0.5 * vol / (size(pos1)/3)**(1./3.)
-u1 = ones((N1, 1)) * P1 / ((gamma - 1.) * rho1)
-m1 = ones((N1, 1)) * vol * 0.5 * rho1 / N1
+h1 = ones(N1) * 2.251 * 0.5 * vol / (size(pos1)/3)**(1./3.)
+u1 = ones(N1) * P1 / ((gamma - 1.) * rho1)
+m1 = ones(N1) * vol * 0.5 * rho1 / N1
 
 #Generate low density region
 rho2 = 0.25
@@ -74,9 +74,9 @@ coord2 = append(coord2, coord2 + [0.25, 0, 0], 0)
 # coord2 = append(coord2, pos2 + [0, 0.5, 0.5], 0)
 N2 = size(coord2)/3
 v2 = zeros((N2, 3))
-h2 = ones((N2, 1)) * 2.251 * 0.5 * vol / (size(pos2)/3)**(1./3.)
-u2 = ones((N2, 1)) * P2 / ((gamma - 1.) * rho2)
-m2 = ones((N2, 1)) * vol * 0.5 * rho2 / N2
+h2 = ones(N2) * 2.251 * 0.5 * vol / (size(pos2)/3)**(1./3.)
+u2 = ones(N2) * P2 / ((gamma - 1.) * rho2)
+m2 = ones(N2) * vol * 0.5 * rho2 / N2
 
 #Merge arrays
 numPart = N1 + N2
@@ -85,10 +85,13 @@ v = append(v1, v2,0)
 h = append(h1, h2,0)
 u = append(u1, u2,0)
 m = append(m1, m2,0)
-ids = zeros((numPart, 1), dtype='L')
+ids = zeros(numPart, dtype='L')
 for i in range(numPart):
     ids[i] = i
 
+#Final operations
+h /= 2
+
 #File
 file = h5py.File(fileName, 'w')
 
@@ -109,18 +112,13 @@ grp.attrs["PeriodicBoundariesOn"] = periodic
 
 #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 / 2
-ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
-ds[()] = u
-ds = grp.create_dataset('ParticleIDs', (numPart,1), 'L')
-ds[()] = ids[:]
+grp.create_dataset('Coordinates', data=coords, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
 
 file.close()
 

examples/runs.sh

@@ -44,11 +44,11 @@ do
     # Sedov blast
     if [ ! -e SedovBlast_mindt_${cpu}.dump ]
     then
-        ./test_mindt -c 0.2 -t $cpu -f SedovBlast/sedov.hdf5 -m 0.1 -w 5000 -d 1e-10 > SedovBlast_${cpu}.dump
+        ./test_mindt -c 0.2 -t $cpu -f SedovBlast/sedov.hdf5 -m 0.02 -w 5000 -d 1e-10 > SedovBlast_${cpu}.dump
     fi
     if [ ! -e SedovBlast_fixed_${cpu}.dump ]
     then
-        ./test_fixdt -r 4096 -t $cpu -f SedovBlast/sedov.hdf5 -m 0.1 -w 5000 -d 5e-5 > SedovBlast_fixed_${cpu}.dump
+        ./test_fixdt -r 4096 -t $cpu -f SedovBlast/sedov.hdf5 -m 0.02 -w 5000 -d 5e-5 > SedovBlast_fixed_${cpu}.dump
     fi
     
     # Cosmological volume