Removed ideal gas specific SineWavePotential scripts and incorporated them in...

Removed ideal gas specific SineWavePotential scripts and incorporated them in the isothermal script. Ideal gas now seems to work.

examples/SineWavePotential_1D/makeIC.py

@@ -38,7 +38,7 @@ 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)
+u = np.zeros(numPart) + uconst
 ids = np.arange(numPart, dtype = 'L')
 rho = np.zeros(numPart)
 

examples/SineWavePotential_1D/makeIC_ideal.py

-###############################################################################
-# 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)
-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+0.5)/numPart
-
-V = 1./numPart
-for i in range(numPart):
-  rho[i] = 1000.
-  u[i] = 1.5*(-0.5*A/np.pi*np.cos(2.*np.pi*coords[i,0]) + 2.*A)
-  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()

examples/SineWavePotential_1D/plotSolution_ideal.py

-###############################################################################
-# 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"])
-
-P = 2.*rho*u/3.
-
-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][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]))

examples/SineWavePotential_1D/run_ideal.sh

-#!/bin/bash
-
-if [ ! -e sineWavePotential.hdf5 ]
-then
-  echo "Generating initial conditions for the 1D SineWavePotential example..."
-  python makeIC_ideal.py
-fi
-
-../swift -g -s -t 2 sineWavePotential.yml 2>&1 | tee output.log
-
-for f in sineWavePotential_*.hdf5
-do
-  python plotSolution_ideal.py $f
-done