Updated isothermal test-case to python scripts.

examples/Feedback/feedback.pro

-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

examples/Feedback/feedback.yml

-# 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)

examples/Feedback/makeIC.py

-###############################################################################
- # 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()

examples/IsothermalPotential/energy_plot.py

+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)
+
+

examples/IsothermalPotential/isothermal.yml

@@ -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

examples/IsothermalPotential/makeIC.py

@@ -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

examples/IsothermalPotential/run.sh

@@ -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

examples/IsothermalPotential/test.pro

-;
-;  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
-
-