Commit c1731c24 authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Documentation fixes

parent d3ab083d
...@@ -763,7 +763,7 @@ INPUT = @top_srcdir@ @top_srcdir@/src @top_srcdir@/tests @top_ ...@@ -763,7 +763,7 @@ INPUT = @top_srcdir@ @top_srcdir@/src @top_srcdir@/tests @top_
INPUT += @top_srcdir@/src/hydro/Minimal INPUT += @top_srcdir@/src/hydro/Minimal
INPUT += @top_srcdir@/src/gravity/Default INPUT += @top_srcdir@/src/gravity/Default
INPUT += @top_srcdir@/src/riemann INPUT += @top_srcdir@/src/riemann
INPUT += @top_srcdir@/src/cooling/const INPUT += @top_srcdir@/src/cooling/const_lambda
# This tag can be used to specify the character encoding of the source files # This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
......
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@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
N = int(sys.argv[2]) # Write N particles at a time to avoid requiring a lot of RAM
rho = 2. # Density
P = 1. # Pressure
gamma = 5./3. # Gas adiabatic index
eta = 1.2349 # 48 ngbs with cubic spline kernel
fileName = "uniformBox_%d.hdf5"%L
#---------------------------------------------------
numPart = L**3
mass = boxSize**3 * rho / numPart
internalEnergy = P / ((gamma - 1.)*rho)
#---------------------------------------------------
n_iterations = numPart / N
remainder = numPart % N
print "Writing", numPart, "in", n_iterations, "iterations of size", N, "and a remainder of", remainder
#---------------------------------------------------
#File
file = h5py.File(fileName, 'w')
# Header
grp = file.create_group("/Header")
grp.attrs["BoxSize"] = boxSize
grp.attrs["NumPart_Total"] = [numPart % (long(1)<<32), 0, 0, 0, 0, 0]
grp.attrs["NumPart_Total_HighWord"] = [numPart / (long(1)<<32), 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")
# First create the arrays in the file
ds_v = grp.create_dataset('Velocities', (numPart, 3), 'f', chunks=True, compression="gzip")
ds_m = grp.create_dataset('Masses', (numPart,1), 'f', chunks=True, compression="gzip")
ds_h = grp.create_dataset('SmoothingLength', (numPart,1), 'f', chunks=True, compression="gzip")
ds_u = grp.create_dataset('InternalEnergy', (numPart,1), 'f', chunks=True, compression="gzip")
ds_id = grp.create_dataset('ParticleIDs', (numPart, 1), 'L', chunks=True, compression="gzip")
ds_x = grp.create_dataset('Coordinates', (numPart, 3), 'd', chunks=True, compression="gzip")
# Now loop and create parts of the dataset
offset = 0
for n in range(n_iterations):
v = zeros((N, 3))
ds_v[offset:offset+N,:] = v
v = zeros(1)
m = full((N, 1), mass)
ds_m[offset:offset+N] = m
m = zeros(1)
h = full((N, 1), eta * boxSize / L)
ds_h[offset:offset+N] = h
h = zeros(1)
u = full((N, 1), internalEnergy)
ds_u[offset:offset+N] = u
u = zeros(1)
ids = linspace(offset, offset+N, N, endpoint=False).reshape((N,1))
ds_id[offset:offset+N] = ids + 1
x = ids % L;
y = ((ids - x) / L) % L;
z = (ids - x - L * y) / L**2;
ids = zeros(1)
coords = zeros((N, 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_x[offset:offset+N,:] = coords
coords = zeros((1,3))
offset += N
print "Done", offset,"/", numPart, "(%.1f %%)"%(100*(float)(offset)/numPart)
# And now, the remainder
v = zeros((remainder, 3))
ds_v[offset:offset+remainder,:] = v
v = zeros(1)
m = full((remainder, 1), mass)
ds_m[offset:offset+remainder] = m
m = zeros(1)
h = full((remainder, 1), eta * boxSize / L)
ds_h[offset:offset+remainder] = h
h = zeros(1)
u = full((remainder, 1), internalEnergy)
ds_u[offset:offset+remainder] = u
u = zeros(1)
ids = linspace(offset, offset+remainder, remainder, endpoint=False).reshape((remainder,1))
ds_id[offset:offset+remainder] = ids + 1
x = ids % L;
y = ((ids - x) / L) % L;
z = (ids - x - L * y) / L**2;
coords = zeros((remainder, 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)
ods_x[offset:offset+remainder,:] = coords
print "Done", offset+remainder,"/", numPart
file.close()
...@@ -142,7 +142,7 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part( ...@@ -142,7 +142,7 @@ __attribute__((always_inline)) INLINE static void cooling_cool_part(
* @param cooling The #cooling_data used in the run. * @param cooling The #cooling_data used in the run.
* @param phys_const The physical constants in internal units. * @param phys_const The physical constants in internal units.
* @param us The internal system of units. * @param us The internal system of units.
* @param Pointer to the particle data. * @param p Pointer to the particle data.
*/ */
__attribute__((always_inline)) INLINE static float cooling_timestep( __attribute__((always_inline)) INLINE static float cooling_timestep(
const struct cooling_data* cooling, const struct cooling_data* cooling,
......
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