Commit 0dc16751 authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Merge branch 'gizmo_fix' into 'master'

Cleaned up GIZMO code, added SineWavePotential tests.

The GIZMO code should now be clean enough to merge with `master`, and to be used in scaling tests.

I have added 1-3D versions of a new SineWavePotential test, which tests gravitational hydrostatic equilibrium in an unphysical but convenient 1D periodic sine wave potential. This allows testing gravity + GIZMO hydro without running into boundary condition problems. Unfortunately, the non conservative form of the potential makes it impossible to test energy conservation in these tests. GIZMO can keep all three set ups stable with both an isothermal and an ideal gas equation of state. I have currently only tested with the exact Riemann solver, but the approximate solvers should work as well.

The code is still not stable enough to cope with the hydrostatic and disc patch tests; these are next on my list.

See merge request !317
parents 0b3df5fe ebbae198
......@@ -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])
;;
......
###############################################################################
# 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()
###############################################################################
# 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]))
#!/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
# 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.
###############################################################################
# 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()
###############################################################################
# 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]))
#!/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
# 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.
###############################################################################
# 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')