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examples/GravityTests/HydrostaticHalo/makeIC.py
+109
-97
109 additions, 97 deletions
examples/GravityTests/HydrostaticHalo/makeIC.py
examples/GravityTests/HydrostaticHalo/run.sh
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examples/GravityTests/HydrostaticHalo/run.sh
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examples/GravityTests/HydrostaticHalo/makeIC.py
View file @
9c17498b
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2016 Stefan Arridge (stefan.arridge@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/>.
#
##############################################################################
# This file is part of SWIFT.
# Copyright (c) 2016 Stefan Arridge (stefan.arridge@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
...
...
@@ -24,71 +24,79 @@ import math
import
random
# Generates N particles in a spherically symmetric distribution with density profile ~r^(-2)
# usage: python makeIC.py 1000: generate 1000 particles
# usage: python
3
makeIC.py 1000: generate 1000 particles
# Some constants
OMEGA
=
0.3
# Cosmological matter fraction at z = 0
OMEGA
=
0.3
# Cosmological matter fraction at z = 0
PARSEC_IN_CGS
=
3.0856776e18
KM_PER_SEC_IN_CGS
=
1.0e5
CONST_G_CGS
=
6.672e-8
h
=
0.67777
# hubble parameter
gamma
=
5.
/
3.
h
=
0.67777
# hubble parameter
gamma
=
5.
0
/
3.
0
eta
=
1.2349
# First set unit velocity and then the circular velocity parameter for the isothermal potential
const_unit_velocity_in_cgs
=
1.e5
#kms^-1
const_unit_velocity_in_cgs
=
1.
0
e5
#
kms^-1
v_c
=
200.
v_c
=
200.
0
v_c_cgs
=
v_c
*
const_unit_velocity_in_cgs
# Now we use this to get the virial mass and virial radius, which we will set to be the unit mass and radius
# Find H_0, the inverse Hubble time, in cgs
H_0_cgs
=
100.
*
h
*
KM_PER_SEC_IN_CGS
/
(
1.0e6
*
PARSEC_IN_CGS
)
H_0_cgs
=
100.
0
*
h
*
KM_PER_SEC_IN_CGS
/
(
1.0e6
*
PARSEC_IN_CGS
)
# From this we can find the virial radius, the radius within which the average density of the halo is
# 200. * the mean matter density
r_vir_cgs
=
v_c_cgs
/
(
10.
*
H_0_cgs
*
np
.
sqrt
(
OMEGA
))
r_vir_cgs
=
v_c_cgs
/
(
10.
0
*
H_0_cgs
*
np
.
sqrt
(
OMEGA
))
# Now get the virial mass
M_vir_cgs
=
r_vir_cgs
*
v_c_cgs
**
2
/
CONST_G_CGS
M_vir_cgs
=
r_vir_cgs
*
v_c_cgs
**
2
/
CONST_G_CGS
# Now set the unit length and mass
const_unit_mass_in_cgs
=
M_vir_cgs
const_unit_length_in_cgs
=
r_vir_cgs
print
(
"
UnitMass_in_cgs:
"
,
const_unit_mass_in_cgs
)
print
(
"
UnitMass_in_cgs:
"
,
const_unit_mass_in_cgs
)
print
(
"
UnitLength_in_cgs:
"
,
const_unit_length_in_cgs
)
print
(
"
UnitVelocity_in_cgs:
"
,
const_unit_velocity_in_cgs
)
#derived quantities
const_unit_time_in_cgs
=
(
const_unit_length_in_cgs
/
const_unit_velocity_in_cgs
)
#
derived quantities
const_unit_time_in_cgs
=
const_unit_length_in_cgs
/
const_unit_velocity_in_cgs
print
(
"
UnitTime_in_cgs:
"
,
const_unit_time_in_cgs
)
const_G
=
((
CONST_G_CGS
*
const_unit_mass_in_cgs
*
const_unit_time_in_cgs
*
const_unit_time_in_cgs
/
(
const_unit_length_in_cgs
*
const_unit_length_in_cgs
*
const_unit_length_in_cgs
)))
print
(
'
G=
'
,
const_G
)
const_G
=
(
CONST_G_CGS
*
const_unit_mass_in_cgs
*
const_unit_time_in_cgs
*
const_unit_time_in_cgs
/
(
const_unit_length_in_cgs
*
const_unit_length_in_cgs
*
const_unit_length_in_cgs
)
)
print
(
"
G=
"
,
const_G
)
# Parameters
periodic
=
1
# 1 For periodic box
boxSize
=
4.
G
=
const_G
N
=
int
(
sys
.
argv
[
1
])
# Number of particles
periodic
=
1
# 1 For periodic box
boxSize
=
4.
0
G
=
const_G
N
=
int
(
sys
.
argv
[
1
])
# Number of particles
# Create the file
filename
=
"
Hydrostatic.hdf5
"
file
=
h5py
.
File
(
filename
,
'
w
'
)
file
=
h5py
.
File
(
filename
,
"
w
"
)
#Units
#
Units
grp
=
file
.
create_group
(
"
/Units
"
)
grp
.
attrs
[
"
Unit length in cgs (U_L)
"
]
=
const_unit_length_in_cgs
grp
.
attrs
[
"
Unit mass in cgs (U_M)
"
]
=
const_unit_mass_in_cgs
grp
.
attrs
[
"
Unit time in cgs (U_t)
"
]
=
const_unit_length_in_cgs
/
const_unit_velocity_in_cgs
grp
.
attrs
[
"
Unit current in cgs (U_I)
"
]
=
1.
grp
.
attrs
[
"
Unit temperature in cgs (U_T)
"
]
=
1.
grp
.
attrs
[
"
Unit mass in cgs (U_M)
"
]
=
const_unit_mass_in_cgs
grp
.
attrs
[
"
Unit time in cgs (U_t)
"
]
=
(
const_unit_length_in_cgs
/
const_unit_velocity_in_cgs
)
grp
.
attrs
[
"
Unit current in cgs (U_I)
"
]
=
1.0
grp
.
attrs
[
"
Unit temperature in cgs (U_T)
"
]
=
1.0
# set seed for random number
...
...
@@ -97,37 +105,39 @@ np.random.seed(1234)
# Positions
# r^(-2) distribution corresponds to uniform distribution in radius
radius
=
boxSize
*
np
.
sqrt
(
3.
)
/
2.
*
np
.
random
.
rand
(
N
)
#the diagonal extent of the cube
ctheta
=
-
1.
+
2
*
np
.
random
.
rand
(
N
)
stheta
=
np
.
sqrt
(
1.
-
ctheta
**
2
)
phi
=
2
*
math
.
pi
*
np
.
random
.
rand
(
N
)
coords
=
np
.
zeros
((
N
,
3
))
coords
[:,
0
]
=
radius
*
stheta
*
np
.
cos
(
phi
)
coords
[:,
1
]
=
radius
*
stheta
*
np
.
sin
(
phi
)
coords
[:,
2
]
=
radius
*
ctheta
#shift to centre of box
coords
+=
np
.
full
((
N
,
3
),
boxSize
/
2.
)
print
(
"
x range = (%f,%f)
"
%
(
np
.
min
(
coords
[:,
0
]),
np
.
max
(
coords
[:,
0
])))
print
(
"
y range = (%f,%f)
"
%
(
np
.
min
(
coords
[:,
1
]),
np
.
max
(
coords
[:,
1
])))
print
(
"
z range = (%f,%f)
"
%
(
np
.
min
(
coords
[:,
2
]),
np
.
max
(
coords
[:,
2
])))
#print np.mean(coords[:,0])
#print np.mean(coords[:,1])
#print np.mean(coords[:,2])
#now find the particles which are within the box
x_coords
=
coords
[:,
0
]
y_coords
=
coords
[:,
1
]
z_coords
=
coords
[:,
2
]
radius
=
(
boxSize
*
np
.
sqrt
(
3.0
)
/
2.0
*
np
.
random
.
rand
(
N
)
)
# the diagonal extent of the cube
ctheta
=
-
1.0
+
2
*
np
.
random
.
rand
(
N
)
stheta
=
np
.
sqrt
(
1.0
-
ctheta
**
2
)
phi
=
2
*
math
.
pi
*
np
.
random
.
rand
(
N
)
coords
=
np
.
zeros
((
N
,
3
))
coords
[:,
0
]
=
radius
*
stheta
*
np
.
cos
(
phi
)
coords
[:,
1
]
=
radius
*
stheta
*
np
.
sin
(
phi
)
coords
[:,
2
]
=
radius
*
ctheta
# shift to centre of box
coords
+=
np
.
full
((
N
,
3
),
boxSize
/
2.0
)
print
(
"
x range = (%f,%f)
"
%
(
np
.
min
(
coords
[:,
0
]),
np
.
max
(
coords
[:,
0
])))
print
(
"
y range = (%f,%f)
"
%
(
np
.
min
(
coords
[:,
1
]),
np
.
max
(
coords
[:,
1
])))
print
(
"
z range = (%f,%f)
"
%
(
np
.
min
(
coords
[:,
2
]),
np
.
max
(
coords
[:,
2
])))
# print np.mean(coords[:,0])
# print np.mean(coords[:,1])
# print np.mean(coords[:,2])
# now find the particles which are within the box
x_coords
=
coords
[:,
0
]
y_coords
=
coords
[:,
1
]
z_coords
=
coords
[:,
2
]
ind
=
np
.
where
(
x_coords
<
boxSize
)[
0
]
x_coords
=
x_coords
[
ind
]
y_coords
=
y_coords
[
ind
]
z_coords
=
z_coords
[
ind
]
ind
=
np
.
where
(
x_coords
>
0.
)[
0
]
ind
=
np
.
where
(
x_coords
>
0.
0
)[
0
]
x_coords
=
x_coords
[
ind
]
y_coords
=
y_coords
[
ind
]
z_coords
=
z_coords
[
ind
]
...
...
@@ -137,7 +147,7 @@ x_coords = x_coords[ind]
y_coords
=
y_coords
[
ind
]
z_coords
=
z_coords
[
ind
]
ind
=
np
.
where
(
y_coords
>
0.
)[
0
]
ind
=
np
.
where
(
y_coords
>
0.
0
)[
0
]
x_coords
=
x_coords
[
ind
]
y_coords
=
y_coords
[
ind
]
z_coords
=
z_coords
[
ind
]
...
...
@@ -147,39 +157,39 @@ x_coords = x_coords[ind]
y_coords
=
y_coords
[
ind
]
z_coords
=
z_coords
[
ind
]
ind
=
np
.
where
(
z_coords
>
0.
)[
0
]
ind
=
np
.
where
(
z_coords
>
0.
0
)[
0
]
x_coords
=
x_coords
[
ind
]
y_coords
=
y_coords
[
ind
]
z_coords
=
z_coords
[
ind
]
#count number of particles
#
count number of particles
N
=
x_coords
.
size
print
(
"
Number of particles in the box =
"
,
N
)
print
(
"
Number of particles in the box =
"
,
N
)
#make the coords and radius arrays again
coords_2
=
np
.
zeros
((
N
,
3
))
coords_2
[:,
0
]
=
x_coords
coords_2
[:,
1
]
=
y_coords
coords_2
[:,
2
]
=
z_coords
#
make the coords and radius arrays again
coords_2
=
np
.
zeros
((
N
,
3
))
coords_2
[:,
0
]
=
x_coords
coords_2
[:,
1
]
=
y_coords
coords_2
[:,
2
]
=
z_coords
radius
=
np
.
sqrt
(
coords_2
[:,
0
]
**
2
+
coords_2
[:,
1
]
**
2
+
coords_2
[:,
2
]
**
2
)
radius
=
np
.
sqrt
(
coords_2
[:,
0
]
**
2
+
coords_2
[:,
1
]
**
2
+
coords_2
[:,
2
]
**
2
)
#test we've done it right
#
test we've done it right
print
(
"
x range = (%f,%f)
"
%
(
np
.
min
(
coords_2
[:,
0
]),
np
.
max
(
coords_2
[:,
0
])))
print
(
"
y range = (%f,%f)
"
%
(
np
.
min
(
coords_2
[:,
1
]),
np
.
max
(
coords_2
[:,
1
])))
print
(
"
z range = (%f,%f)
"
%
(
np
.
min
(
coords_2
[:,
2
]),
np
.
max
(
coords_2
[:,
2
])))
print
(
"
x range = (%f,%f)
"
%
(
np
.
min
(
coords_2
[:,
0
]),
np
.
max
(
coords_2
[:,
0
])))
print
(
"
y range = (%f,%f)
"
%
(
np
.
min
(
coords_2
[:,
1
]),
np
.
max
(
coords_2
[:,
1
])))
print
(
"
z range = (%f,%f)
"
%
(
np
.
min
(
coords_2
[:,
2
]),
np
.
max
(
coords_2
[:,
2
])))
print
(
np
.
mean
(
coords_2
[:,
0
]))
print
(
np
.
mean
(
coords_2
[:,
1
]))
print
(
np
.
mean
(
coords_2
[:,
2
]))
print
(
np
.
mean
(
coords_2
[:,
0
]))
print
(
np
.
mean
(
coords_2
[:,
1
]))
print
(
np
.
mean
(
coords_2
[:,
2
]))
# Header
grp
=
file
.
create_group
(
"
/Header
"
)
grp
.
attrs
[
"
BoxSize
"
]
=
boxSize
grp
.
attrs
[
"
NumPart_Total
"
]
=
[
N
,
0
,
0
,
0
,
0
,
0
]
grp
.
attrs
[
"
NumPart_Total
"
]
=
[
N
,
0
,
0
,
0
,
0
,
0
]
grp
.
attrs
[
"
NumPart_Total_HighWord
"
]
=
[
0
,
0
,
0
,
0
,
0
,
0
]
grp
.
attrs
[
"
NumPart_ThisFile
"
]
=
[
N
,
0
,
0
,
0
,
0
,
0
]
grp
.
attrs
[
"
Time
"
]
=
0.0
...
...
@@ -191,40 +201,42 @@ grp.attrs["Dimension"] = 3
# Particle group
grp
=
file
.
create_group
(
"
/PartType0
"
)
ds
=
grp
.
create_dataset
(
'
Coordinates
'
,
(
N
,
3
),
'
d
'
)
ds
=
grp
.
create_dataset
(
"
Coordinates
"
,
(
N
,
3
),
"
d
"
)
ds
[()]
=
coords_2
coords_2
=
np
.
zeros
(
1
)
# All velocities set to zero
v
=
np
.
zeros
((
N
,
3
))
ds
=
grp
.
create_dataset
(
'
Velocities
'
,
(
N
,
3
),
'
f
'
)
v
=
np
.
zeros
((
N
,
3
))
ds
=
grp
.
create_dataset
(
"
Velocities
"
,
(
N
,
3
),
"
f
"
)
ds
[()]
=
v
v
=
np
.
zeros
(
1
)
# All particles of equal mass
mass
=
1.
/
N
m
=
np
.
full
((
N
,),
mass
)
ds
=
grp
.
create_dataset
(
'
Masses
'
,
(
N
,
),
'
f
'
)
mass
=
1.
0
/
N
m
=
np
.
full
((
N
,),
mass
)
ds
=
grp
.
create_dataset
(
"
Masses
"
,
(
N
,),
"
f
"
)
ds
[()]
=
m
m
=
np
.
zeros
(
1
)
# Smoothing lengths
l
=
(
4.
*
np
.
pi
*
radius
**
2
/
N
)
**
(
1.
/
3.
)
#local mean inter-particle separation
h
=
np
.
full
((
N
,
),
eta
*
l
)
ds
=
grp
.
create_dataset
(
'
SmoothingLength
'
,
(
N
,),
'
f
'
)
l
=
(
4.0
*
np
.
pi
*
radius
**
2
/
N
)
**
(
1.0
/
3.0
)
# local mean inter-particle separation
h
=
np
.
full
((
N
,),
eta
*
l
)
ds
=
grp
.
create_dataset
(
"
SmoothingLength
"
,
(
N
,),
"
f
"
)
ds
[()]
=
h
h
=
np
.
zeros
(
1
)
# Internal energies
u
=
v_c
**
2
/
(
2.
*
(
gamma
-
1.
))
u
=
np
.
full
((
N
,
),
u
)
ds
=
grp
.
create_dataset
(
'
InternalEnergy
'
,
(
N
,),
'
f
'
)
u
=
v_c
**
2
/
(
2.
0
*
(
gamma
-
1.
0
))
u
=
np
.
full
((
N
,),
u
)
ds
=
grp
.
create_dataset
(
"
InternalEnergy
"
,
(
N
,),
"
f
"
)
ds
[()]
=
u
u
=
np
.
zeros
(
1
)
# Particle IDs
ids
=
1
+
np
.
linspace
(
0
,
N
,
N
,
endpoint
=
False
)
ds
=
grp
.
create_dataset
(
'
ParticleIDs
'
,
(
N
,
),
'
L
'
)
ds
=
grp
.
create_dataset
(
"
ParticleIDs
"
,
(
N
,),
"
L
"
)
ds
[()]
=
ids
file
.
close
()
This diff is collapsed.
Click to expand it.
examples/GravityTests/HydrostaticHalo/run.sh
View file @
9c17498b
...
...
@@ -4,24 +4,24 @@
if
[
!
-e
Hydrostatic.hdf5
]
then
echo
"Generating initial conditions for the isothermal potential box example..."
python makeIC.py 100000
python
3
makeIC.py 100000
fi
# Run for 10 dynamical times
../../swift
--external-gravity
--hydro
--threads
=
1 hydrostatic.yml 2>&1 |
tee
output.log
../../
../
swift
--external-gravity
--hydro
--threads
=
1 hydrostatic.yml 2>&1 |
tee
output.log
echo
"Plotting density profiles"
mkdir
plots
mkdir
plots/density_profile
python density_profile.py 2. 200 300
python
3
density_profile.py 2. 200 300
echo
"Plotting internal energy profiles"
mkdir
plots/internal_energy
python internal_energy_profile.py 2. 200 300
python
3
internal_energy_profile.py 2. 200 300
echo
"Plotting radial velocity profiles"
mkdir
plots/radial_velocity_profile
python velocity_profile.py 2. 200 300
python
3
velocity_profile.py 2. 200 300
echo
"Plotting energy as a function of time"
python test_energy_conservation.py 300
python
3
test_energy_conservation.py 300
This diff is collapsed.
Click to expand it.
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