Commit f772cc7a authored by Matthieu Schaller's avatar Matthieu Schaller

Updated isothermal test-case to python scripts.

parent 5b56fc26
base = 'Feedback'
inf = 'Feedback_005.hdf5'
blast = [5.650488e-01, 5.004371e-01, 5.010494e-01] ; location of blast
pos = h5rd(inf,'PartType0/Coordinates')
vel = h5rd(inf,'PartType0/Velocities')
rho = h5rd(inf,'PartType0/Density')
utherm = h5rd(inf,'PartType0/InternalEnergy')
; shift to centre
for ic=0,2 do pos[ic,*] = pos[ic,*] - blast[ic]
;; distance from centre
dist = fltarr(n_elements(rho))
for ic=0,2 do dist = dist + pos[ic,*]^2
dist = sqrt(dist)
; radial velocity
vr = fltarr(n_elements(rho))
for ic=0,2 do vr = vr + pos[ic,*]*vel[ic,*]
vr = vr / dist
;
end
# Define the system of units to use internally.
InternalUnitSystem:
UnitMass_in_cgs: 1 # Grams
UnitLength_in_cgs: 1 # Centimeters
UnitVelocity_in_cgs: 1 # Centimeters per second
UnitCurrent_in_cgs: 1 # Amperes
UnitTemp_in_cgs: 1 # Kelvin
# Parameters governing the time integration
TimeIntegration:
time_begin: 0. # The starting time of the simulation (in internal units).
time_end: 5e-2 # The end time of the simulation (in internal units).
dt_min: 1e-7 # The minimal time-step size of the simulation (in internal units).
dt_max: 1e-4 # The maximal time-step size of the simulation (in internal units).
# Parameters governing the snapshots
Snapshots:
basename: Feedback # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 1e-2 # Time difference between consecutive outputs (in internal units)
# Parameters governing the conserved quantities statistics
Statistics:
delta_time: 1e-3 # Time between statistics output
# Parameters for the hydrodynamics scheme
SPH:
resolution_eta: 1.2348 # Target smoothing length in units of the mean inter-particle separation (1.2348 == 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: ./Feedback.hdf5 # The file to read
# Parameters for feedback
SN:
time: 0.001 # time the SN explodes (internal units)
energy: 1.0 # energy of the explosion (internal units)
x: 0.5 # x-position of explostion (internal units)
y: 0.5 # y-position of explostion (internal units)
z: 0.5 # z-position of explostion (internal units)
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
# Matthieu Schaller (matthieu.schaller@durham.ac.uk)
# 2016 Tom Theuns (tom.theuns@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
from numpy import *
# Generates a swift IC file containing a cartesian distribution of particles
# at a constant density and pressure in a cubic box
# Parameters
periodic= 1 # 1 For periodic box
boxSize = 1.
L = int(sys.argv[1]) # Number of particles along one axis
rho = 1. # Density
P = 1.e-6 # Pressure
gamma = 5./3. # Gas adiabatic index
eta = 1.2349 # 48 ngbs with cubic spline kernel
fileName = "Feedback.hdf5"
#---------------------------------------------------
numPart = L**3
mass = boxSize**3 * rho / numPart
internalEnergy = P / ((gamma - 1.)*rho)
#--------------------------------------------------
#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
#Runtime parameters
grp = file.create_group("/RuntimePars")
grp.attrs["PeriodicBoundariesOn"] = periodic
#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")
v = zeros((numPart, 3))
ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
ds[()] = v
v = zeros(1)
m = full((numPart, 1), mass)
ds = grp.create_dataset('Masses', (numPart,1), 'f')
ds[()] = m
m = zeros(1)
h = full((numPart, 1), eta * boxSize / L)
ds = grp.create_dataset('SmoothingLength', (numPart,1), 'f')
ds[()] = h
h = zeros(1)
u = full((numPart, 1), internalEnergy)
ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
ds[()] = u
u = zeros(1)
ids = linspace(0, numPart, numPart, endpoint=False).reshape((numPart,1))
ds = grp.create_dataset('ParticleIDs', (numPart, 1), 'L')
ds[()] = ids + 1
x = ids % L;
y = ((ids - x) / L) % L;
z = (ids - x - L * y) / L**2;
coords = zeros((numPart, 3))
coords[:,0] = z[:,0] * boxSize / L + boxSize / (2*L)
coords[:,1] = y[:,0] * boxSize / L + boxSize / (2*L)
coords[:,2] = x[:,0] * boxSize / L + boxSize / (2*L)
ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
ds[()] = coords
file.close()
import matplotlib
matplotlib.use("Agg")
from pylab import *
import h5py
# Plot parameters
params = {'axes.labelsize': 10,
'axes.titlesize': 10,
'font.size': 12,
'legend.fontsize': 12,
'xtick.labelsize': 10,
'ytick.labelsize': 10,
'text.usetex': True,
'figure.figsize' : (3.15,3.15),
'figure.subplot.left' : 0.145,
'figure.subplot.right' : 0.99,
'figure.subplot.bottom' : 0.11,
'figure.subplot.top' : 0.99,
'figure.subplot.wspace' : 0.15,
'figure.subplot.hspace' : 0.12,
'lines.markersize' : 6,
'lines.linewidth' : 3.,
'text.latex.unicode': True
}
rcParams.update(params)
rc('font',**{'family':'sans-serif','sans-serif':['Times']})
import numpy as np
import h5py as h5
import sys
# File containing the total energy
stats_filename = "./energy.txt"
# First snapshot
snap_filename = "Isothermal_000.hdf5"
f = h5.File(snap_filename,'r')
# Read the units parameters from the snapshot
units = f["InternalCodeUnits"]
unit_mass = units.attrs["Unit mass in cgs (U_M)"]
unit_length = units.attrs["Unit length in cgs (U_L)"]
unit_time = units.attrs["Unit time in cgs (U_t)"]
# Read the header
header = f["Header"]
box_size = float(header.attrs["BoxSize"][0])
# Read the properties of the potential
parameters = f["Parameters"]
R200 = 100
Vrot = float(parameters.attrs["IsothermalPotential:vrot"])
centre = [box_size/2, box_size/2, box_size/2]
f.close()
# Read the statistics summary
file_energy = np.loadtxt("energy.txt")
time_stats = file_energy[:,0]
E_kin_stats = file_energy[:,3]
E_pot_stats = file_energy[:,5]
E_tot_stats = E_kin_stats + E_pot_stats
# Read the snapshots
time_snap = np.zeros(402)
E_kin_snap = np.zeros(402)
E_pot_snap = np.zeros(402)
E_tot_snap = np.zeros(402)
Lz_snap = np.zeros(402)
# Read all the particles from the snapshots
for i in range(402):
snap_filename = "Isothermal_%0.3d.hdf5"%i
f = h5.File(snap_filename,'r')
pos_x = f["PartType1/Coordinates"][:,0]
pos_y = f["PartType1/Coordinates"][:,1]
pos_z = f["PartType1/Coordinates"][:,2]
vel_x = f["PartType1/Velocities"][:,0]
vel_y = f["PartType1/Velocities"][:,1]
vel_z = f["PartType1/Velocities"][:,2]
mass = f["/PartType1/Masses"][:]
r = np.sqrt((pos_x[:] - centre[0])**2 + (pos_y[:] - centre[1])**2 + (pos_z[:] - centre[2])**2)
Lz = (pos_x[:] - centre[0]) * vel_y[:] - (pos_y[:] - centre[1]) * vel_x[:]
time_snap[i] = f["Header"].attrs["Time"]
E_kin_snap[i] = np.sum(0.5 * mass * (vel_x[:]**2 + vel_y[:]**2 + vel_z[:]**2))
E_pot_snap[i] = np.sum(-mass * Vrot**2 * log(r))
E_tot_snap[i] = E_kin_snap[i] + E_pot_snap[i]
Lz_snap[i] = np.sum(Lz)
# Plot energy evolution
figure()
plot(time_stats, E_kin_stats, "r-", lw=0.5, label="Kinetic energy")
plot(time_stats, E_pot_stats, "g-", lw=0.5, label="Potential energy")
plot(time_stats, E_tot_stats, "k-", lw=0.5, label="Total energy")
plot(time_snap[::10], E_kin_snap[::10], "rD", lw=0.5, ms=2)
plot(time_snap[::10], E_pot_snap[::10], "gD", lw=0.5, ms=2)
plot(time_snap[::10], E_tot_snap[::10], "kD", lw=0.5, ms=2)
legend(loc="center right", fontsize=8, frameon=False, handlelength=3, ncol=1)
xlabel("${\\rm{Time}}$", labelpad=0)
ylabel("${\\rm{Energy}}$",labelpad=0)
xlim(0, 8)
savefig("energy.png", dpi=200)
# Plot angular momentum evolution
figure()
plot(time_snap, Lz_snap, "k-", lw=0.5, ms=2)
xlabel("${\\rm{Time}}$", labelpad=0)
ylabel("${\\rm{Angular~momentum}}$",labelpad=0)
xlim(0, 8)
savefig("angular_momentum.png", dpi=200)
......@@ -15,7 +15,7 @@ TimeIntegration:
# Parameters governing the conserved quantities statistics
Statistics:
delta_time: 1e-2 # Time between statistics output
delta_time: 1e-3 # Time between statistics output
# Parameters governing the snapshots
Snapshots:
......@@ -23,25 +23,18 @@ Snapshots:
time_first: 0. # Time of the first output (in internal units)
delta_time: 0.02 # 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: 1. # The tolerance for the targetted number of neighbours.
CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
max_smoothing_length: 40. # Maximal smoothing length allowed (in internal units).
# Parameters related to the initial conditions
InitialConditions:
file_name: Isothermal.hdf5 # The file to read
shift_x: 100. # A shift to apply to all particles read from the ICs (in internal units).
shift_y: 100.
shift_z: 100.
shift_x: 200. # Shift all particles to be in the potential
shift_y: 200.
shift_z: 200.
# External potential parameters
IsothermalPotential:
position_x: 100. # location of centre of isothermal potential in internal units
position_y: 100.
position_z: 100.
position_x: 0. # location of centre of isothermal potential in internal units
position_y: 0.
position_z: 0.
vrot: 200. # rotation speed of isothermal potential in internal units
timestep_mult: 0.03 # controls time step
timestep_mult: 0.01 # controls time step
epsilon: 0. # No softening at the centre of the halo
......@@ -30,10 +30,10 @@ import random
# all particles move in the xy plane, and start at y=0
# physical constants in cgs
NEWTON_GRAVITY_CGS = 6.672e-8
NEWTON_GRAVITY_CGS = 6.67408e-8
SOLAR_MASS_IN_CGS = 1.9885e33
PARSEC_IN_CGS = 3.0856776e18
PROTON_MASS_IN_CGS = 1.6726231e24
PROTON_MASS_IN_CGS = 1.672621898e24
YEAR_IN_CGS = 3.154e+7
# choice of units
......@@ -66,17 +66,12 @@ N = int(sys.argv[1]) # Number of particles
icirc = int(sys.argv[2]) # if = 0, all particles are on circular orbits, if = 1, Lz/Lcirc uniform in ]0,1[
L = N**(1./3.)
# these are not used but necessary for I/O
rho = 2. # Density
P = 1. # Pressure
gamma = 5./3. # Gas adiabatic index
fileName = "Isothermal.hdf5"
#---------------------------------------------------
numPart = N
mass = 1
internalEnergy = P / ((gamma - 1.)*rho)
#--------------------------------------------------
......@@ -111,7 +106,6 @@ grp.attrs["PeriodicBoundariesOn"] = periodic
numpy.random.seed(1234)
#Particle group
#grp0 = file.create_group("/PartType0")
grp1 = file.create_group("/PartType1")
#generate particle positions
radius = Radius * (numpy.random.rand(N))**(1./3.)
......@@ -119,10 +113,8 @@ ctheta = -1. + 2 * numpy.random.rand(N)
stheta = numpy.sqrt(1.-ctheta**2)
phi = 2 * math.pi * numpy.random.rand(N)
r = numpy.zeros((numPart, 3))
#r[:,0] = radius * stheta * numpy.cos(phi)
#r[:,1] = radius * stheta * numpy.sin(phi)
#r[:,2] = radius * ctheta
r[:,0] = radius
#
speed = vrot
v = numpy.zeros((numPart, 3))
......@@ -146,17 +138,6 @@ ds = grp1.create_dataset('Masses', (numPart,), 'f')
ds[()] = m
m = numpy.zeros(1)
h = numpy.full((numPart, ), 1.1255 * boxSize / L, dtype='f')
ds = grp1.create_dataset('SmoothingLength', (numPart,), 'f')
ds[()] = h
h = numpy.zeros(1)
u = numpy.full((numPart, ), internalEnergy, dtype='f')
ds = grp1.create_dataset('InternalEnergy', (numPart,), 'f')
ds[()] = u
u = numpy.zeros(1)
ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False, dtype='L')
ds = grp1.create_dataset('ParticleIDs', (numPart, ), 'L')
ds[()] = ids
......
......@@ -7,4 +7,7 @@ then
python makeIC.py 1000 1
fi
rm -rf Isothermal_*.hdf5
../swift -g -t 1 isothermal.yml 2>&1 | tee output.log
python energy_plot.py
;
; test energy / angular momentum conservation of test problem
;
iplot = 1 ; if iplot = 1, make plot of E/Lz conservation, else, simply compare final and initial energy
; set physical constants
@physunits
indir = './'
basefile = 'Isothermal_'
; set properties of potential
uL = 1e3 * phys.pc ; unit of length
uM = phys.msun ; unit of mass
uV = 1d5 ; unit of velocity
vrot = 200. ; km/s
r200 = 100. ; virial radius
; derived units
constG = 10.^(alog10(phys.g)+alog10(uM)-2d0*alog10(uV)-alog10(uL)) ;
pcentre = [100.,100.,100.] * 1d3 * pc / uL
;
infile = indir + basefile + '*'
spawn,'ls -1 '+infile,res
nfiles = n_elements(res)
; choose: calculate change of energy and Lz, comparing first and last
; snapshots for all particles, or do so for a subset
; compare all
ifile = 0
inf = indir + basefile + strtrim(string(ifile,'(i3.3)'),1) + '.hdf5'
id = h5rd(inf,'PartType1/ParticleIDs')
nfollow = n_elements(id)
; follow a subset
nfollow = 500 ; number of particles to follow
;
if (iplot eq 1) then begin
nskip = 1
nsave = nfiles
endif else begin
nskip = nfiles - 2
nsave = 2
endelse
;
lout = fltarr(nfollow, nsave) ; Lz
xout = fltarr(nfollow, nsave) ; x
yout = fltarr(nfollow, nsave) ; y
zout = fltarr(nfollow, nsave) ; z
eout = fltarr(nfollow, nsave) ; energies
ekin = fltarr(nfollow, nsave)
epot = fltarr(nfollow, nsave)
tout = fltarr(nsave)
ifile = 0
isave = 0
for ifile=0,nfiles-1,nskip do begin
inf = indir + basefile + strtrim(string(ifile,'(i3.3)'),1) + '.hdf5'
time = h5ra(inf, 'Header','Time')
p = h5rd(inf,'PartType1/Coordinates')
v = h5rd(inf,'PartType1/Velocities')
id = h5rd(inf,'PartType1/ParticleIDs')
indx = sort(id)
;
id = id[indx]
for ic=0,2 do begin
tmp = reform(p[ic,*]) & p[ic,*] = tmp[indx]
tmp = reform(v[ic,*]) & v[ic,*] = tmp[indx]
endfor
; calculate energy
dd = size(p,/dimen) & npart = dd[1]
ener = fltarr(npart)
dr = fltarr(npart) & dv = dr
for ic=0,2 do dr[*] = dr[*] + (p[ic,*]-pcentre[ic])^2
for ic=0,2 do dv[*] = dv[*] + v[ic,*]^2
xout[*,isave] = p[0,0:nfollow-1]-pcentre[0]
yout[*,isave] = p[1,0:nfollow-1]-pcentre[1]
zout[*,isave] = p[2,0:nfollow-1]-pcentre[2]
Lz = (p[0,*]-pcentre[0]) * v[1,*] - (p[1,*]-pcentre[1]) * v[0,*]
dr = sqrt(dr)
; print,'time = ',time,p[0,0],v[0,0],id[0]
ek = 0.5 * dv
; ep = - constG * mextern / dr
ep = -vrot*vrot * (1 + alog(r200/dr))
ener = ek + ep
tout(isave) = time
lout[*,isave] = lz[0:nfollow-1]
eout(*,isave) = ener[0:nfollow-1]
ekin(*,isave) = ek[0:nfollow-1]
epot(*,isave) = ep[0:nfollow-1]
; write some output
; print,' time= ',time,' e= ',eout[0],' Lz= ',lz[0],format='(%a %f %a
; %f)'
print,format='('' time= '',f7.1,'' E= '',f9.2,'' Lz= '',e9.2)', time,eout[0],lz[0]
isave = isave + 1
endfor
x0 = reform(xout[0,*])
y0 = reform(xout[1,*])
z0 = reform(xout[2,*])
; calculate relative energy change
de = 0.0 * eout
dl = 0.0 * lout
nsave = isave
for ifile=1, nsave-1 do de[*,ifile] = (eout[*,ifile]-eout[*,0])/eout[*,0]
for ifile=1, nsave-1 do dl[*,ifile] = (lout[*,ifile] - lout[*,0])/lout[*,0]
; calculate statistics of energy changes
print,' relatve energy change: (per cent) ',minmax(de) * 100.
print,' relative Lz change: (per cent) ',minmax(dl) * 100.
; plot enery and Lz conservation for some particles
if(iplot eq 1) then begin
; plot results on energy conservation for some particles
nplot = min(10, nfollow)
win,0
xr = [min(tout), max(tout)]
yr = [-2,2]*1d-2 ; in percent
plot,[0],[0],xr=xr,yr=yr,/xs,/ys,/nodata,xtitle='time',ytitle='dE/E, dL/L (%)'
for i=0,nplot-1 do oplot,tout,de[i,*]
for i=0,nplot-1 do oplot,tout,dl[i,*],color=red
legend,['dE/E','dL/L'],linestyle=[0,0],color=[black,red],box=0,/bottom,/left
screen_to_png,'e-time.png'
; plot orbits of those particles
win,2
xr = [-100,100]
yr = xr
plot,[0],[0],xr=xr,yr=yr,/xs,/ys,/iso,/nodata,xtitle='x',ytitle='y'
color = floor(findgen(nplot)*255/float(nplot))
for i=0,nplot-1 do oplot,xout[i,*],yout[i,*],color=color(i)
screen_to_png,'orbit.png'
; plot radial position of these particles
win,4
xr = [min(tout), max(tout)]
yr = [0,80]
plot,[0],[0],xr=xr,yr=yr,/xs,/ys,/nodata,xtitle='t',ytitle='r'
color = floor(findgen(nplot)*255/float(nplot))
for i=0,nplot-1 do begin dr = sqrt(reform(xout[i,*])^2 + reform(yout[i,*])^2) & oplot,tout,dr,color=color[i] & endfor
screen_to_png,'r-time.png'
; make histogram of energy changes at end
win,6
ohist,de,x,y,-0.05,0.05,0.001
plot,x,y,psym=10,xtitle='de (%)'
screen_to_png,'de-hist.png'
endif
end
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