Merge branch 'master' into timebin_optimization

configure.ac

@@ -765,7 +765,7 @@ esac
 #  External potential
 AC_ARG_WITH([ext-potential],
    [AS_HELP_STRING([--with-ext-potential=<pot>],
-      [external potential @<:@none, point-mass, isothermal, softened-isothermal, disc-patch default: none@:>@]
+      [external potential @<:@none, point-mass, isothermal, softened-isothermal, disc-patch, sine-wave default: none@:>@]
    )],
    [with_potential="$withval"],
    [with_potential="none"]
@@ -783,6 +783,9 @@ case "$with_potential" in
    disc-patch)
       AC_DEFINE([EXTERNAL_POTENTIAL_DISC_PATCH], [1], [Disc-patch external potential])
    ;; 
+   sine-wave)
+      AC_DEFINE([EXTERNAL_POTENTIAL_SINE_WAVE], [1], [Sine wave external potential in 1D])
+   ;; 
    *)
       AC_MSG_ERROR([Unknown external potential: $with_potential])
    ;;

examples/SineWavePotential_1D/makeIC.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+# Generates a distorted 1D grid with a density profile that balances out the
+# external sine wave potential if run with an isothermal equation of state.
+
+import numpy as np
+import h5py
+
+# constant thermal energy
+# the definition below assumes the same thermal energy is defined in const.h,
+# and also that the code was configured with an adiabatic index of 5./3.
+uconst = 20.2615290634
+cs2 = 2.*uconst/3.
+A = 10.
+
+fileName = "sineWavePotential.hdf5"
+numPart = 100
+boxSize = 1.
+
+coords = np.zeros((numPart, 3))
+v = np.zeros((numPart, 3))
+m = np.zeros(numPart) + 1.
+h = np.zeros(numPart) + 2./numPart
+u = np.zeros(numPart) + uconst
+ids = np.arange(numPart, dtype = 'L')
+rho = np.zeros(numPart)
+
+# first set the positions, as we try to do a reasonable volume estimate to
+# set the masses
+for i in range(numPart):
+  coords[i,0] = (i+np.random.random())/numPart
+
+for i in range(numPart):
+  # reasonable mass estimate (actually not really good, but better than assuming
+  # a constant volume)
+  if i == 0:
+    V = 0.5*(coords[1,0]-coords[-1,0]+1.)
+  elif i == numPart-1:
+    V = 0.5*(coords[0,0]+1.-coords[-2,0])
+  else:
+    V = 0.5*(coords[i+1,0] - coords[i-1,0])
+  rho[i] = 1000.*np.exp(-0.5*A/np.pi/cs2*np.cos(2.*np.pi*coords[i,0]))
+  m[i] = rho[i]*V
+
+#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
+grp.attrs["Dimension"] = 1
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#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")
+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')
+grp.create_dataset('Density', data=rho, dtype='f')
+
+file.close()

examples/SineWavePotential_1D/plotSolution.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+# Plots some quantities for the snapshot file which is passed on as a command
+# line argument (full name)
+
+import numpy as np
+import h5py
+import sys
+import pylab as pl
+
+# these should be the same as in makeIC.py
+uconst = 20.2615290634
+cs2 = 2.*uconst/3.
+A = 10.
+
+if len(sys.argv) < 2:
+  print "Need to provide a filename argument!"
+  exit()
+
+fileName = sys.argv[1]
+
+file = h5py.File(fileName, 'r')
+coords = np.array(file["/PartType0/Coordinates"])
+rho = np.array(file["/PartType0/Density"])
+u = np.array(file["/PartType0/InternalEnergy"])
+agrav = np.array(file["/PartType0/GravAcceleration"])
+m = np.array(file["/PartType0/Masses"])
+ids = np.array(file["/PartType0/ParticleIDs"])
+
+x = np.linspace(0., 1., 1000)
+rho_x = 1000.*np.exp(-0.5*A/np.pi/cs2*np.cos(2.*np.pi*x))
+
+P = cs2*rho
+
+ids_reverse = np.argsort(ids)
+
+gradP = np.zeros(P.shape)
+for i in range(len(P)):
+  iself = int(ids[i])
+  corr = 0.
+  im1 = iself-1
+  if im1 < 0:
+    im1 = len(P)-1
+    corr = 1.
+  ip1 = iself+1
+  if ip1 == len(P):
+    ip1 = 0
+    corr = 1.
+  idxp1 = ids_reverse[ip1]
+  idxm1 = ids_reverse[im1]
+  gradP[i] = (P[idxp1]-P[idxm1])/(coords[idxp1,0]-coords[idxm1,0])
+
+fig, ax = pl.subplots(2, 2)
+
+ax[0][0].plot(coords[:,0], rho, "r.", markersize = 0.5)
+ax[0][0].plot(x, rho_x, "g-")
+ax[0][1].plot(coords[:,0], gradP/rho, "b.")
+ax[1][0].plot(coords[:,0], agrav[:,0], "g.", markersize = 0.5)
+ax[1][1].plot(coords[:,0], m, "y.")
+pl.savefig("{fileName}.png".format(fileName = fileName[:-5]))

examples/SineWavePotential_1D/run.sh

+#!/bin/bash
+
+if [ ! -e sineWavePotential.hdf5 ]
+then
+  echo "Generating initial conditions for the 1D SineWavePotential example..."
+  python makeIC.py
+fi
+
+../swift -g -s -t 2 sineWavePotential.yml 2>&1 | tee output.log
+
+for f in sineWavePotential_*.hdf5
+do
+  python plotSolution.py $f
+done

examples/SineWavePotential_1D/sineWavePotential.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.
+  UnitLength_in_cgs:   1.
+  UnitVelocity_in_cgs: 1.
+  UnitCurrent_in_cgs:  1.
+  UnitTemp_in_cgs:     1.
+
+# 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 conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:            sineWavePotential  # Common part of the name of output files
+  time_first:          0.           # Time of the first output (in internal units)
+  delta_time:          1.          # Time difference between consecutive outputs (in internal units)
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  sineWavePotential.hdf5       # The file to read
+ 
+# External potential parameters
+SineWavePotential:
+  amplitude: 10.
+  timestep_limit: 1.

examples/SineWavePotential_2D/makeIC.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+# Generates a distorted 1D grid with a density profile that balances out the
+# external sine wave potential if run with an isothermal equation of state.
+
+import numpy as np
+import h5py
+
+# constant thermal energy
+# the definition below assumes the same thermal energy is defined in const.h,
+# and also that the code was configured with an adiabatic index of 5./3.
+uconst = 20.2615290634
+cs2 = 2.*uconst/3.
+A = 10.
+
+fileName = "sineWavePotential.hdf5"
+numPart_1D = 50
+boxSize = [1., 1.]
+numPart = numPart_1D**2
+
+coords = np.zeros((numPart, 3))
+v = np.zeros((numPart, 3))
+m = np.zeros(numPart) + 1.
+h = np.zeros(numPart) + 2./numPart
+u = np.zeros(numPart) + uconst
+ids = np.arange(numPart, dtype = 'L')
+rho = np.zeros(numPart)
+
+# first set the positions, as we try to do a reasonable volume estimate to
+# set the masses
+for i in range(numPart_1D):
+  for j in range(numPart_1D):
+    coords[numPart_1D*i+j,0] = (i+0.5)/numPart_1D
+    coords[numPart_1D*i+j,1] = (j+0.5)/numPart_1D
+
+V = 1./numPart
+for i in range(numPart):
+  rho[i] = 1000.*np.exp(-0.5*A/np.pi/cs2*np.cos(2.*np.pi*coords[i,0]))
+  m[i] = rho[i]*V
+
+#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
+grp.attrs["Dimension"] = 2
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#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")
+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')
+grp.create_dataset('Density', data=rho, dtype='f')
+
+file.close()

examples/SineWavePotential_2D/plotSolution.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+# Plots some quantities for the snapshot file which is passed on as a command
+# line argument (full name)
+
+import numpy as np
+import h5py
+import sys
+import pylab as pl
+
+# these should be the same as in makeIC.py
+uconst = 20.2615290634
+cs2 = 2.*uconst/3.
+A = 10.
+
+if len(sys.argv) < 2:
+  print "Need to provide a filename argument!"
+  exit()
+
+fileName = sys.argv[1]
+
+file = h5py.File(fileName, 'r')
+coords = np.array(file["/PartType0/Coordinates"])
+rho = np.array(file["/PartType0/Density"])
+u = np.array(file["/PartType0/InternalEnergy"])
+agrav = np.array(file["/PartType0/GravAcceleration"])
+m = np.array(file["/PartType0/Masses"])
+ids = np.array(file["/PartType0/ParticleIDs"])
+
+# ids_reverse gives the index original particle 0 now has in the particle arrays
+# and so on
+# note that this will only work if the particles do not move away too much from
+# there initial positions
+ids_reverse = np.argsort(ids)
+
+x = np.linspace(0., 1., 1000)
+rho_x = 1000.*np.exp(-0.5*A/np.pi/cs2*np.cos(2.*np.pi*x))
+
+P = cs2*rho
+
+n1D = int(np.sqrt(len(P)))
+gradP = np.zeros(P.shape)
+for i in range(len(P)):
+  iself = int(ids[i]/n1D)
+  jself = int(ids[i]-n1D*iself)
+  corr = 0.
+  im1 = iself-1
+  if im1 < 0:
+    im1 = n1D-1
+    corr = 1.
+  ip1 = iself+1
+  if ip1 == n1D:
+    ip1 = 0
+    corr = 1.
+  idxp1 = ids_reverse[ip1*n1D+jself]
+  idxm1 = ids_reverse[im1*n1D+jself]
+  gradP[i] = (P[idxp1]-P[idxm1])/(coords[idxp1,0]-coords[idxm1,0]+corr)
+
+fig, ax = pl.subplots(2, 2)
+
+ax[0][0].plot(coords[:,0], rho, "r.", markersize = 0.5)
+ax[0][0].plot(x, rho_x, "g-")
+ax[0][1].plot(coords[:,0], gradP/rho, "b.")
+ax[1][0].plot(coords[:,0], agrav[:,0], "g.", markersize = 0.5)
+ax[1][1].plot(coords[:,0], m, "y.")
+pl.savefig("{fileName}.png".format(fileName = fileName[:-5]))

examples/SineWavePotential_2D/run.sh

+#!/bin/bash
+
+if [ ! -e sineWavePotential.hdf5 ]
+then
+  echo "Generating initial conditions for the 1D SineWavePotential example..."
+  python makeIC.py
+fi
+
+../swift -g -s -t 2 sineWavePotential.yml 2>&1 | tee output.log
+
+for f in sineWavePotential_*.hdf5
+do
+  python plotSolution.py $f
+done

examples/SineWavePotential_2D/sineWavePotential.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.
+  UnitLength_in_cgs:   1.
+  UnitVelocity_in_cgs: 1.
+  UnitCurrent_in_cgs:  1.
+  UnitTemp_in_cgs:     1.
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.   # 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:     1.e-2  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-2 # Time between statistics output
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:            sineWavePotential  # Common part of the name of output files
+  time_first:          0.           # Time of the first output (in internal units)
+  delta_time:          0.1          # Time difference between consecutive outputs (in internal units)
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  sineWavePotential.hdf5       # The file to read
+ 
+# External potential parameters
+SineWavePotential:
+  amplitude: 10.
+  timestep_limit: 1.

examples/SineWavePotential_3D/makeIC.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+# Generates a distorted 1D grid with a density profile that balances out the
+# external sine wave potential if run with an isothermal equation of state.
+
+import numpy as np
+import h5py
+
+# constant thermal energy
+# the definition below assumes the same thermal energy is defined in const.h,
+# and also that the code was configured with an adiabatic index of 5./3.
+uconst = 20.2615290634
+cs2 = 2.*uconst/3.
+A = 10.
+
+fileName = "sineWavePotential.hdf5"
+numPart_1D = 20
+boxSize = [1., 1.]
+numPart = numPart_1D**3
+
+coords = np.zeros((numPart, 3))
+v = np.zeros((numPart, 3))
+m = np.zeros(numPart) + 1.
+h = np.zeros(numPart) + 2./numPart
+u = np.zeros(numPart) + uconst
+ids = np.arange(numPart, dtype = 'L')
+rho = np.zeros(numPart)
+
+# first set the positions, as we try to do a reasonable volume estimate to
+# set the masses
+for i in range(numPart_1D):
+#  coords[i,0] = (i+np.random.random())/numPart
+  for j in range(numPart_1D):
+    for k in range(numPart_1D):
+      coords[numPart_1D**2*i+numPart_1D*j+k,0] = (i+0.5)/numPart_1D
+      coords[numPart_1D**2*i+numPart_1D*j+k,1] = (j+0.5)/numPart_1D
+      coords[numPart_1D**2*i+numPart_1D*j+k,2] = (k+0.5)/numPart_1D
+
+V = 1./numPart
+for i in range(numPart):
+  # reasonable mass estimate (actually not really good, but better than assuming
+  # a constant volume)
+#  if i == 0:
+#    V = 0.5*(coords[1,0]-coords[-1,0]+1.)
+#  elif i == numPart-1:
+#    V = 0.5*(coords[0,0]+1.-coords[-2,0])
+#  else:
+#    V = 0.5*(coords[i+1,0] - coords[i-1,0])
+  rho[i] = 1000.*np.exp(-0.5*A/np.pi/cs2*np.cos(2.*np.pi*coords[i,0]))
+  m[i] = rho[i]*V
+
+#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
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#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")
+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')