Commit 7fb703af authored by James Willis's avatar James Willis
Browse files

Merge branch 'master' into dopair-vectorisation

parents d896e167 3b974424
......@@ -143,6 +143,8 @@ before you can build it.
- DOXYGEN: the doxygen library is required to create the SWIFT API
documentation.
- python: Examples and solution script use python and rely on the
numpy library version 1.8.2 or higher.
SWIFT Coding style
......
......@@ -200,6 +200,20 @@ if test "$enable_debugging_checks" = "yes"; then
AC_DEFINE([SWIFT_DEBUG_CHECKS],1,[Enable expensive debugging])
fi
# Check if gravity force checks are on for some particles.
AC_ARG_ENABLE([gravity-force-checks],
[AS_HELP_STRING([--enable-gravity-force-checks],
[Activate expensive brute-force gravity checks for a fraction 1/N of all particles @<:@N@:>@]
)],
[gravity_force_checks="$enableval"],
[gravity_force_checks="no"]
)
if test "$gravity_force_checks" == "yes"; then
AC_MSG_ERROR(Need to specify the fraction of particles to check when using --enable-gravity-force-checks!)
elif test "$gravity_force_checks" != "no"; then
AC_DEFINE_UNQUOTED([SWIFT_GRAVITY_FORCE_CHECKS], [$enableval] ,[Enable gravity brute-force checks])
fi
# Define HAVE_POSIX_MEMALIGN if it works.
AX_FUNC_POSIX_MEMALIGN
......@@ -637,13 +651,13 @@ AC_ARG_WITH([hydro-dimension],
)
case "$with_dimension" in
1)
AC_DEFINE([HYDRO_DIMENSION_1D], [1], [1D analysis])
AC_DEFINE([HYDRO_DIMENSION_1D], [1], [1D solver])
;;
2)
AC_DEFINE([HYDRO_DIMENSION_2D], [2], [2D analysis])
AC_DEFINE([HYDRO_DIMENSION_2D], [2], [2D solver])
;;
3)
AC_DEFINE([HYDRO_DIMENSION_3D], [3], [3D analysis])
AC_DEFINE([HYDRO_DIMENSION_3D], [3], [3D solver])
;;
*)
AC_MSG_ERROR([Dimensionality must be 1, 2 or 3])
......@@ -751,7 +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="$withval"],
[with_potential="none"]
......@@ -769,6 +783,9 @@ case "$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])
;;
......@@ -821,8 +838,10 @@ AC_MSG_RESULT([
Riemann solver : $with_riemann
Cooling function : $with_cooling
External potential : $with_potential
Task debugging : $enable_task_debugging
Debugging checks : $enable_debugging_checks
Gravity checks : $gravity_force_checks
])
# Make sure the latest git revision string gets included
......
......@@ -107,7 +107,7 @@ if n_copy > 1:
for i in range(n_copy):
for j in range(n_copy):
for k in range(n_copy):
coords = np.append(coords, coords_tile + np.array([ i * boxSize, j * boxSize, k * boxSize ]), axis=0)
coords = np.append(coords, coords_tile + np.array([ i * boxSize[0], j * boxSize[1], k * boxSize[2] ]), axis=0)
v = np.append(v, v_tile, axis=0)
m = np.append(m, m_tile)
h = np.append(h, h_tile)
......
......@@ -227,7 +227,7 @@ ds[()] = u
u = np.zeros(1)
# Particle IDs
ids = 1 + np.linspace(0, N, N, endpoint=False, dtype='L')
ids = 1 + np.linspace(0, N, N, endpoint=False)
ds = grp.create_dataset('ParticleIDs', (N, ), 'L')
ds[()] = ids
......
......@@ -233,7 +233,7 @@ ds[()] = u
u = np.zeros(1)
# Particle IDs
ids = 1 + np.linspace(0, N, N, endpoint=False, dtype='L')
ids = 1 + np.linspace(0, N, N, endpoint=False)
ds = grp.create_dataset('ParticleIDs', (N, ), 'L')
ds[()] = ids
......
......@@ -150,7 +150,7 @@ ds[()] = m
m = numpy.zeros(1)
ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False, dtype='L')
ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False)
ds = grp1.create_dataset('ParticleIDs', (numPart, ), 'L')
ds[()] = ids
......
......@@ -205,7 +205,7 @@ if (entropy_flag == 1):
else:
ds[()] = u
ids = 1 + numpy.linspace(0, numGas, numGas, endpoint=False, dtype='L')
ids = 1 + numpy.linspace(0, numGas, numGas, endpoint=False)
ds = grp0.create_dataset('ParticleIDs', (numGas, ), 'L')
ds[()] = ids
......
......@@ -28,7 +28,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
unit_time_cgs = unit_length_cgs / unit_velocity_cgs
v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
v_c = float(params.attrs["IsothermalPotential:vrot"])
v_c_cgs = v_c * unit_velocity_cgs
#lambda_cgs = float(params.attrs["LambdaCooling:lambda_cgs"])
#X_H = float(params.attrs["LambdaCooling:hydrogen_mass_abundance"])
......
......@@ -46,7 +46,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
unit_time_cgs = unit_length_cgs / unit_velocity_cgs
v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
v_c = float(params.attrs["IsothermalPotential:vrot"])
v_c_cgs = v_c * unit_velocity_cgs
#lambda_cgs = float(params.attrs["LambdaCooling:lambda_cgs"])
#X_H = float(params.attrs["LambdaCooling:hydrogen_mass_abundance"])
......
......@@ -227,7 +227,7 @@ ds[()] = u
u = np.zeros(1)
# Particle IDs
ids = 1 + np.linspace(0, N, N, endpoint=False, dtype='L')
ids = 1 + np.linspace(0, N, N, endpoint=False)
ds = grp.create_dataset('ParticleIDs', (N, ), 'L')
ds[()] = ids
......
......@@ -46,7 +46,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
unit_time_cgs = unit_length_cgs / unit_velocity_cgs
v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
v_c = float(params.attrs["IsothermalPotential:vrot"])
v_c_cgs = v_c * unit_velocity_cgs
header = f["Header"]
N = header.attrs["NumPart_Total"][0]
......
......@@ -138,7 +138,7 @@ ds = grp1.create_dataset('Masses', (numPart,), 'f')
ds[()] = m
m = numpy.zeros(1)
ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False, dtype='L')
ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False)
ds = grp1.create_dataset('ParticleIDs', (numPart, ), 'L')
ds[()] = ids
......
......@@ -35,8 +35,8 @@ glass = h5py.File("glassCube_64.hdf5", "r")
vol = 8.
pos = glass["/PartType0/Coordinates"][:,:] * cbrt(vol)
h = glass["/PartType0/SmoothingLength"][:] * cbrt(vol)
pos = glass["/PartType0/Coordinates"][:,:] * vol**(1./3.)
h = glass["/PartType0/SmoothingLength"][:] * vol**(1./3.)
numPart = size(h)
# Generate extra arrays
......@@ -65,7 +65,7 @@ file = h5py.File(fileName, 'w')
# Header
grp = file.create_group("/Header")
grp.attrs["BoxSize"] = [cbrt(vol), cbrt(vol), cbrt(vol)]
grp.attrs["BoxSize"] = [vol**(1./3.), vol**(1./3.), vol**(1./3.)]
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]
......
###############################################################################
# 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: