diff --git a/LICENSE b/LICENSE
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+++ b/LICENSE
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+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ PySwiftsim
+ Copyright (C) 2017 Loic Hausammann
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU 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 General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ PySwiftsim Copyright (C) 2017 Loic Hausammann
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/pyswiftsim/__init__.py b/pyswiftsim/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..50a5cb6cd4d2eec05cc57e8c426c001cd68b2db3
--- /dev/null
+++ b/pyswiftsim/__init__.py
@@ -0,0 +1,2 @@
+
+from pyswiftsim import *
diff --git a/pyswiftsim/structure.py b/pyswiftsim/structure.py
new file mode 100644
index 0000000000000000000000000000000000000000..6197a2241d1dfa038cbc64d5836fe261b1618dc5
--- /dev/null
+++ b/pyswiftsim/structure.py
@@ -0,0 +1,441 @@
+from pyswiftsim import wrapper
+
+import struct
+import numpy
+from ctypes import *
+
+PARSER_MAX_LINE_SIZE = 256
+PARSER_MAX_NO_OF_PARAMS = 256
+PARSER_MAX_NO_OF_SECTIONS = 64
+
+######################################################################
+# #
+# SwiftStruct #
+# #
+######################################################################
+class SwiftStruct(struct.Struct):
+ """
+ Abstract class constructing a wrapper around a C structure
+
+ Parameters
+ ----------
+
+ struct_format: str
+ Text defining the data type in the structure (see struct module for
+ more informations)
+
+ data: str, list
+ Bytes string containing all the data of a structure or
+ dictionary of attribute (all the attribute should be present)
+
+ parent: :class:`SwiftStruct`
+ Parent containing the data (usefull for :class:`ArrayStruct`)
+ """
+ def __init__(self, struct_format, data, parent):
+ super().__init__(struct_format)
+ self.parent = parent # parent for ArrayStruct
+
+ if isinstance(data, bytes):
+ self.data = data # bytes string data
+ elif isinstance(data, dict):
+ tmp = []
+ for i in self.struct_name:
+ tmp.append(data[i])
+
+ self.data = self.pack(*tmp)
+ else:
+ raise ValueError("Data should be either bytes or dict, "
+ "received ", type(data))
+
+ @property
+ def struct_name(self):
+ """
+ List of the structure attribute names.
+
+ Should be implemented for each sub class
+ """
+ return self.__class__._name
+
+ @property
+ def struct_format(self):
+ """
+ String containing the data type of each attribute
+ """
+ return self.__class__._format
+
+ @property
+ def struct_substruct(self):
+ """
+ Dictionary containing the class of each substructure.
+ See for example SwiftParams
+ """
+ return {}
+
+
+ def _getInfoFromName(self, name):
+ """
+ Compute index, format and size from an attribute name.
+
+ Parameters
+ ----------
+
+ name: str
+ Name of an attribute
+
+ Returns
+ -------
+
+ i: int, slice
+ index of the attribute
+
+ form: char
+ data type (see module struct for more information)
+
+ n: int
+ number of element in attribute
+ """
+ struct_size, form = self.struct_size_format
+ i = self.struct_name.index(name)
+ form = form[i]
+ n = struct_size[i]
+ i = sum(struct_size[:i])
+
+ if n > 1:
+ i = slice(i, i+n)
+
+ return i, form, n
+
+
+ @property
+ def struct_size_format(self):
+ """
+ Compute size and format for each field
+
+ Returns
+ -------
+
+ out_nber: list
+ number of element for each attribute
+
+ out_form: list
+ format for each attribute
+ """
+ out_nber = []
+ out_form = []
+ form = self.struct_format
+
+ N = len(form)
+ ii = 0
+ while ii < N:
+ v = form[ii]
+ count = ""
+ while v.isdigit():
+ count += v
+ ii += 1
+ v = form[ii]
+
+ if count == "":
+ count = 1
+
+ if v == "s":
+ count = 1
+
+ count = int(count)
+ out_nber.append(count)
+ out_form.append(v)
+ ii += 1
+
+ return out_nber, out_form
+
+
+ def __str__(self):
+ tab = ""
+ parent = self.parent
+ while parent is not None:
+ tab += "\t"
+ parent = parent.parent
+
+ txt = tab + "%s:\n" % type(self)
+ for name in self.struct_name:
+ d = getattr(self, name)
+ txt += tab + "\t%s: %s\n" % (name, d)
+ return txt
+
+ def __getattr__(self, name):
+ # case where the attribute is not in the structure
+ if name not in self.struct_name:
+ return object.__getattribute__(self, name)
+
+ # case where the attribute is in the structure
+ else:
+ i, form, n = self._getInfoFromName(name)
+
+ data = self.unpack(self.data)
+ if n == 1:
+ # if substruct
+ if name in self.struct_substruct:
+ d = self.struct_substruct[name]
+ cl = d["class"]
+ tmp = []
+ size = struct.calcsize(cl._format)
+ for j in range(d["size"]):
+ data_tmp = data[i][size*j:(j+1)*size]
+ tmp.append(cl(data_tmp, parent=self))
+ return tmp
+ # other case => array
+ else:
+ return data[i]
+
+ else:
+ # transform scalar -> vector
+ nform = str(n) + form
+ i = slice(i.start, i.start+n)
+ data = data[i]
+
+ # compress data and create return struct
+ data = struct.pack(nform, *data)
+ return ArrayStruct(nform, data, self, name)
+
+
+ def __setattr__(self, name, value):
+ # case where the attribute is not in the structure
+ if name not in self.struct_name:
+ object.__setattr__(self, name, value)
+ # case where the attribute is in the structure
+ else:
+ data = list(self.unpack(self.data))
+
+ i, form, n = self._getInfoFromName(name)
+
+ if isinstance(value, ArrayStruct):
+ value = value.getArray()
+
+ data[i] = value
+ self.data = self.pack(*data)
+
+
+######################################################################
+# #
+# ArrayStruct #
+# #
+######################################################################
+class ArrayStruct(SwiftStruct):
+ _name = [
+ "array_data"
+ ]
+
+ def __init__(self, struct_format, data, parent, name):
+ super().__init__(struct_format, data, parent)
+ self._format = struct_format
+ self._name = name
+
+ def __getitem__(self, ii):
+ data = self.unpack(self.data)
+ data = self._clean(data)
+ return data[ii]
+
+ def __setitem__(self, ii, value):
+ data = list(self.unpack(self.data))
+ data[ii] = value
+ setattr(self.parent, self._name, data)
+
+ def _clean(self, data):
+ if self._format[-1] == "c":
+ data = b"".join(data)
+ # find end of txt character
+ n = data.index(b"\x00")
+ data = data[:n].decode("utf-8")
+
+ return data
+
+ def __str__(self):
+ data = self.unpack(self.data)
+ data = self._clean(data)
+ return str(data)
+
+
+ def getArray(self):
+ return self.unpack(self.data)
+
+ @property
+ def struct_format(self):
+ return self._format
+
+
+######################################################################
+# #
+# UnitSystem #
+# #
+######################################################################
+class UnitSystem(SwiftStruct):
+ _format = "ddddd"
+ _name = [
+ "UnitMass_in_cgs",
+ "UnitLength_in_cgs",
+ "UnitTime_in_cgs",
+ "UnitCurrent_in_cgs",
+ "UnitTemperature_in_cgs",
+ ]
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
+
+
+######################################################################
+# #
+# Part #
+# #
+######################################################################
+class Part(SwiftStruct):
+ _format = "qP3d3f3ffffffN7f4c"
+ _name = [
+ "id",
+ "gpart",
+ "pos",
+ "vel",
+ "a_hydro",
+ "h",
+ "mass",
+ "rho",
+ "entropy",
+ "entropy_dt",
+ "last_offset",
+ "density",
+ "time_bin"
+ ]
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
+ print("ERROR, need to fix density/time_bin")
+
+
+######################################################################
+# #
+# Parameter #
+# #
+######################################################################
+class Parameter(SwiftStruct):
+ _format = "{line_size}c{line_size}c".format(
+ line_size=PARSER_MAX_LINE_SIZE
+ )
+
+ _name = [
+ "name",
+ "value"
+ ]
+
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
+
+######################################################################
+# #
+# Section #
+# #
+######################################################################
+class Section(SwiftStruct):
+ _format = "{line_size}c".format(
+ line_size=PARSER_MAX_LINE_SIZE
+ )
+ _name = [
+ "name"
+ ]
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
+
+######################################################################
+# #
+# SwiftParams #
+# #
+######################################################################
+class SwiftParams(SwiftStruct):
+ _format = "{sec}s{data}sii{line_size}c".format(
+ sec=struct.calcsize(Section._format)*PARSER_MAX_NO_OF_SECTIONS,
+ data=struct.calcsize(Parameter._format)*PARSER_MAX_NO_OF_PARAMS,
+ line_size=PARSER_MAX_LINE_SIZE
+ )
+
+ _name = [
+ "section",
+ "data_params",
+ "sectionCount",
+ "paramCount",
+ "filename"
+ ]
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
+
+ @property
+ def struct_substruct(self):
+ sec = {
+ "class": Section,
+ "size": PARSER_MAX_NO_OF_SECTIONS
+ }
+
+ param = {
+ "class": Parameter,
+ "size": PARSER_MAX_NO_OF_PARAMS
+ }
+ return {
+ "section": sec,
+ "data_params": param
+ }
+
+######################################################################
+# #
+# PhysConst #
+# #
+######################################################################
+class PhysConst(SwiftStruct):
+ _format = "dddddddddddddddd"
+ _name = [
+ "const_newton_G",
+ "const_speed_light_c",
+ "const_planck_h",
+ "const_planck_hbar",
+ "const_boltzmann_k",
+ "const_thomson_cross_section",
+ "const_electron_charge",
+ "const_electron_volt",
+ "const_electron_mass",
+ "const_proton_mass",
+ "const_year",
+ "const_astronomical_unit",
+ "const_parsec",
+ "const_light_year",
+ "const_solar_mass",
+ "const_earth_mass",
+ ]
+
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
+
+
+class CoolingFunctionData(SwiftStruct):
+ cooling_type = wrapper.configGetCooling()
+ if cooling_type == "const_lambda":
+ _format = "dffff"
+ _name = [
+ "lambda",
+ "hydrogen_mass_abundance",
+ "mean_molecular_weight",
+ "min_energy",
+ "cooling_tstep_mult"
+ ]
+ elif cooling_type == "grackle":
+ _format = "200cidd"
+ _name = [
+ "GrackleCloudyTable",
+ "UVbackground",
+ "GrackleRedshift",
+ "GrackleHSShieldingDensityThreshold"
+ ]
+ else:
+ raise ValueError(
+ "Cooling Type %s not implemented" % cooling_type)
+
+ def __init__(self, data, parent=None):
+ super().__init__(self.struct_format, data, parent)
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..3efb6897a93e83a649044df5aab442b22b33769d
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python3
+
+descr = """
+Wrapper around the SPH cosmological simulation code SWIFT
+"""
+
+from setuptools import setup, find_packages, Extension
+import sys
+import os
+from glob import glob
+import numpy
+
+os.environ["CC"] = "mpicc"
+
+# deal with arguments
+def parseCmdLine(arg, store=False):
+ ret = False
+ if arg in sys.argv:
+ if store:
+ i = sys.argv.index(arg)
+ ret = sys.argv[i+1]
+ sys.argv.remove(ret)
+ else:
+ ret = True
+
+ sys.argv.remove(arg)
+
+ return ret
+
+swift_path = parseCmdLine("--with-swift", store=True)
+
+# python lib dependency
+install_requires=["numpy"]
+
+
+def getValueFromMakefile(swift_root, value):
+ makefile = swift_root + "/src/Makefile"
+ N = len(value)
+
+ with open(makefile, "r") as f:
+ for line in f.readlines():
+ if value == line[:N]:
+ return line[N:-1] # remove \n
+
+ raise ValueError("Value %s not found in Makefile" % value)
+
+
+if swift_path:
+ hdf5_root = getValueFromMakefile(swift_path, "H5CC = ")
+
+# link to non pypi dependencies
+dependency_links = []
+
+# C includes
+include = [numpy.get_include()]
+
+if swift_path:
+ # swift
+ include.extend([
+ swift_path + "/src",
+ swift_path
+ ])
+
+ # hdf5
+ include.append(hdf5_root + "/include")
+
+ # grackle
+ grackle_inc = getValueFromMakefile(swift_path, "GRACKLE_INCS = -I")
+ include.append(grackle_inc)
+
+# C libraries
+lib = ["m",
+ "swiftsim",
+ "hdf5",
+]
+
+lib_dir = []
+
+if swift_path:
+ lib_dir.append(swift_path + "/src/.libs")
+ lib_dir.append(hdf5_root + "/lib")
+
+# src files
+c_src = []
+
+# data files
+data_files = []
+
+
+##############
+## C ext
+##############
+
+c_src = glob("src/*.c")
+ext_modules = Extension("pyswiftsim.wrapper",
+ c_src,
+ include_dirs=include,
+ libraries=lib,
+ library_dirs=lib_dir)
+
+ext_modules = [ext_modules]
+
+##############
+## data
+##############
+
+data_files = []
+
+##############
+## scripts
+##############
+
+list_scripts = []
+
+##############
+## Setup
+##############
+
+setup(
+ name = "pyswiftsim",
+ version = "0.1",
+ author = "Hausammann Loic",
+ author_email = "loic.hausammann@epfl.ch",
+ description = descr,
+ license = "GPLv3",
+ keywords = "nbody sph simulation hpc",
+ url = "",
+
+ packages = find_packages(),
+
+ data_files = data_files,
+
+ scripts = list_scripts,
+
+ install_requires = install_requires,
+
+ dependency_links = dependency_links,
+
+ ext_modules = ext_modules,
+)
diff --git a/src/config_wrapper.h b/src/config_wrapper.h
new file mode 100644
index 0000000000000000000000000000000000000000..bc84738cd80c204ab003f74da0539bd6a19156c6
--- /dev/null
+++ b/src/config_wrapper.h
@@ -0,0 +1,24 @@
+#ifndef __PYSWIFTSIM_CONFIG_H__
+#define __PYSWIFTSIM_CONFIG_H__
+
+#include "pyswiftsim_tools.h"
+
+#include <config.h>
+
+/**
+ * @brief give the cooling type name
+ *
+ * @return Cooling name (PyUnicode)
+ */
+PyObject* config_get_cooling() {
+ char *cooling_name;
+#ifdef COOLING_CONST_LAMBDA
+ cooling_name = "const_lambda";
+#elif defined(COOLING_GRACKLE)
+ cooling_name = "grackle";
+#endif
+ return PyUnicode_FromString(cooling_name);
+};
+
+
+#endif // __PYSWIFTSIM_CONFIG_H__
diff --git a/src/cooling_wrapper.c b/src/cooling_wrapper.c
new file mode 100644
index 0000000000000000000000000000000000000000..49d6592c4cb9d4f63a61633e21f8dbedbc7379e8
--- /dev/null
+++ b/src/cooling_wrapper.c
@@ -0,0 +1,124 @@
+#include "pyswiftsim_tools.h"
+#include "cooling_wrapper.h"
+
+#include <cooling.h>
+#include <cooling_struct.h>
+#include <equation_of_state.h>
+
+
+#include <numpy/arrayobject.h>
+
+
+PyObject* pycooling_init(PyObject* self, PyObject* args) {
+ PyObject *pyparams;
+ PyObject *pyus;
+ PyObject *pypconst;
+
+ /* parse arguments */
+ if (!PyArg_ParseTuple(args, "OOO", &pyparams, &pyus, &pypconst))
+ return NULL;
+
+ struct swift_params *params = (struct swift_params*) pytools_construct(pyparams, class_swift_params);
+ if (params == NULL)
+ return NULL;
+
+ struct unit_system *us = (struct unit_system*) pytools_construct(pyus, class_unit_system);
+ if (us == NULL)
+ return NULL;
+
+ struct phys_const *pconst = (struct phys_const*) pytools_construct(pypconst, class_phys_const);
+ if (pconst == NULL)
+ return NULL;
+
+
+ struct cooling_function_data cooling;
+
+ /* init cooling */
+ cooling_init_backend(params, us, pconst, &cooling);
+
+ /* construct python object */
+ PyObject *pycooling = pytools_return(&cooling, class_cooling_function_data);
+
+ return pycooling;
+}
+
+PyArrayObject* pycooling_rate(PyObject* self, PyObject* args) {
+ IMPORT_ARRAY();
+
+ PyObject *pycooling;
+ PyObject *pyus;
+ PyObject *pypconst;
+
+ PyArrayObject *rho;
+ PyArrayObject *energy;
+
+ float dt = 1e-3;
+
+ /* parse argument */
+ if (!PyArg_ParseTuple(args,
+ "OOOOO|f",
+ &pypconst,
+ &pyus,
+ &pycooling,
+ &rho,
+ &energy,
+ &dt))
+ return NULL;
+
+ /* check numpy array */
+ if (pytools_check_array(energy, 1, NPY_FLOAT) != SUCCESS)
+ {
+ return NULL;
+ }
+
+ if (pytools_check_array(rho, 1, NPY_FLOAT) != SUCCESS)
+ {
+ return NULL;
+ }
+
+ if (PyArray_DIM(energy, 0) != PyArray_DIM(rho, 0))
+ {
+ pyerror("Density and energy should have the same dimension");
+ }
+
+ size_t N = PyArray_DIM(energy, 0);
+
+ /* transform PyObject to C struct */
+
+ struct cooling_function_data *cooling = (struct cooling_function_data*) pytools_construct(pycooling, class_cooling_function_data);
+ if (cooling == NULL)
+ return NULL;
+
+ struct unit_system *us = (struct unit_system*) pytools_construct(pyus, class_unit_system);
+ if (us == NULL)
+ return NULL;
+
+ struct phys_const *pconst = (struct phys_const*) pytools_construct(pypconst, class_phys_const);
+ if (pconst == NULL)
+ return NULL;
+
+ struct part p;
+
+ /* return object */
+ PyArrayObject *rate = PyArray_NewLikeArray(energy, NPY_ANYORDER, NULL, 1);
+
+ /* loop over all particles */
+ for(size_t i = 0; i < N; i++)
+ {
+ /* set particle data */
+ p.rho = *(float*) PyArray_GETPTR1(rho, i);
+ float u = *(float*) PyArray_GETPTR1(energy, i);
+ p.entropy = gas_entropy_from_internal_energy(p.rho, u);
+
+ /* compute cooling rate */
+ float *tmp = PyArray_GETPTR1(rate, i);
+#ifdef COOLING_GRACKLE
+ *tmp = cooling_rate(pconst, us, cooling, &p, dt);
+#else
+ *tmp = cooling_rate(pconst, us, cooling, &p);
+#endif
+ }
+
+ return rate;
+
+}
diff --git a/src/cooling_wrapper.h b/src/cooling_wrapper.h
new file mode 100644
index 0000000000000000000000000000000000000000..4fbdd8abbc746d5d42aa4e32baa707c7770aa602
--- /dev/null
+++ b/src/cooling_wrapper.h
@@ -0,0 +1,33 @@
+#ifndef __PYSWIFTSIM_COOLING_H__
+#define __PYSWIFTSIM_COOLING_H__
+
+#include "pyswiftsim_tools.h"
+
+/**
+ * @brief Initialize the cooling
+ *
+ * args is expecting pyswiftsim classes in the following order:
+ * SwiftParams, UnitSystem and PhysConst.
+ *
+ * @param self calling object
+ * @param args arguments
+ * @return CoolingFunctionData
+ */
+PyObject* pycooling_init(PyObject* self, PyObject* args);
+
+/**
+ * @brief Compute cooling rate
+ *
+ * args is expecting pyswiftsim classes in the following order:
+ * PhysConst, UnitSystem and CoolingFunctionData.
+ * Then two numpy arrays (density and specific energy) and an optional
+ * float for the time step
+ *
+ * @param self calling object
+ * @param args arguments
+ * @return cooling rate
+ */
+PyArrayObject* pycooling_rate(PyObject* self, PyObject* args);
+
+#endif // __PYSWIFTSIM_COOLING_H__
+
diff --git a/src/parser_wrapper.c b/src/parser_wrapper.c
new file mode 100644
index 0000000000000000000000000000000000000000..ef164f58389ef5d3d2ecbce0de2e4aec081b2736
--- /dev/null
+++ b/src/parser_wrapper.c
@@ -0,0 +1,24 @@
+#include "parser_wrapper.h"
+#include "pyswiftsim_tools.h"
+
+#include <parser.h>
+
+PyObject* pyparser_read_file(PyObject *self, PyObject *args)
+{
+
+ char *filename;
+
+ /* parse argument */
+ if (!PyArg_ParseTuple(args, "s", &filename))
+ return NULL;
+
+ struct swift_params params;
+
+ /* parse file */
+ parser_read_file(filename, ¶ms);
+
+ /* create return python object */
+ PyObject* obj = pytools_return(¶ms, class_swift_params);
+
+ return obj;
+}
diff --git a/src/parser_wrapper.h b/src/parser_wrapper.h
new file mode 100644
index 0000000000000000000000000000000000000000..529d352a7698f9180688033ca913efd870ddd272
--- /dev/null
+++ b/src/parser_wrapper.h
@@ -0,0 +1,18 @@
+#ifndef __PYSWIFTSIM_PARSER_H__
+#define __PYSWIFTSIM_PARSER_H__
+
+#include <Python.h>
+
+/**
+ * @brief Read swift parameters
+ *
+ * args is expecting a string.
+ *
+ * @param self calling object
+ * @param args arguments
+ * @return SwiftParams
+ */
+PyObject* pyparser_read_file(PyObject *self, PyObject *args);
+
+
+#endif // __PYSWIFTSIM_PARSER_H__
diff --git a/src/part_wrapper.c b/src/part_wrapper.c
new file mode 100644
index 0000000000000000000000000000000000000000..a4765eecae376cd000fb4c4850bee4b420cd8b0a
--- /dev/null
+++ b/src/part_wrapper.c
@@ -0,0 +1,40 @@
+#include "pyswiftsim_tools.h"
+
+#include <part.h>
+#include <hydro.h>
+
+#include <Python.h>
+#include <stdlib.h>
+#include <string.h>
+
+PyObject* pypart_test_struct(PyObject *self, PyObject *args)
+{
+
+ size_t N = sizeof(struct part);
+
+ /* initialize particle */
+ struct part *p = malloc(N);
+ p->id = 0;
+ for(size_t k = 0; k < DIM; k++)
+ {
+ p->x[k] = 1. + k;
+ p->v[k] = 4. + k;
+ p->a_hydro[k] = 7. + k;
+ }
+
+ p->h = 10;
+ p->mass = 11.;
+ p->rho = 12.;
+ p->entropy = 13;
+ p->entropy_dt = 14;
+
+ hydro_init_part(p, NULL);
+
+ /* create python object */
+ PyObject *object = pytools_return(p, class_part);
+
+ free(p);
+
+ return object;
+}
+
diff --git a/src/part_wrapper.h b/src/part_wrapper.h
new file mode 100644
index 0000000000000000000000000000000000000000..58a426fa48a57c6c88dc591df01754ffe8ea8e91
--- /dev/null
+++ b/src/part_wrapper.h
@@ -0,0 +1,18 @@
+#ifndef __PYSWIFTSIM_PART_H__
+#define __PYSWIFTSIM_PART_H__
+
+#include <Python.h>
+#include <part.h>
+
+/**
+ * @brief Test function for the struct
+ *
+ * args is expecting no argument.
+ *
+ * @param self calling object
+ * @param args arguments
+ * @return Part
+ */
+PyObject* pypart_test_struct(PyObject *self, PyObject *args);
+
+#endif // __PYSWIFTSIM_PART_H__
diff --git a/src/pyswiftsim_tools.c b/src/pyswiftsim_tools.c
new file mode 100644
index 0000000000000000000000000000000000000000..41814598be72886abeb35ca6a750fb59b3748a1e
--- /dev/null
+++ b/src/pyswiftsim_tools.c
@@ -0,0 +1,207 @@
+#include "pyswiftsim_tools.h"
+
+/* include swift */
+#include <part.h>
+#include <units.h>
+#include <parser.h>
+#include <physical_constants.h>
+#include <cooling_struct.h>
+
+#include <Python.h>
+#include <numpy/arrayobject.h>
+
+
+const size_t class_size[class_count] = {
+ sizeof(struct unit_system),
+ sizeof(struct part),
+ sizeof(struct swift_params),
+ sizeof(struct phys_const),
+ sizeof(struct cooling_function_data)
+};
+
+const char *class_name[class_count] = {
+ "UnitSystem",
+ "Part",
+ "SwiftParams",
+ "PhysConst",
+ "CoolingFunctionData"
+};
+
+
+PyObject* pytools_import(char* module_name, char* object_name)
+{
+ /* load module */
+ PyObject *module;
+
+ module = PyImport_ImportModule(module_name);
+
+ if (module == NULL)
+ {
+ pyerror("Failed to import module '%s'.", module_name);
+ }
+
+ /* get module dictionary */
+ PyObject *dict;
+
+ dict = PyModule_GetDict(module);
+ Py_DECREF(module);
+
+ if (dict == NULL)
+ {
+ pyerror("Failed to get module '%s' dictionary", module_name);
+ }
+
+ /* get right object */
+ PyObject *python_obj = PyDict_GetItemString(dict, object_name);
+ Py_DECREF(dict);
+
+ if (python_obj == NULL)
+ pyerror("Object %s does not exist in module %s", object_name, module_name);
+
+ return python_obj;
+}
+
+
+PyObject* pytools_return(void *p, int class)
+{
+
+ PyObject *python_class;
+ size_t nber_bytes;
+
+ char module_name[STRING_SIZE] = "pyswiftsim.structure";
+ char *class_pyname;
+
+ /* check class */
+ if (class >= class_count)
+ pyerror("Class %i does not exists", class);
+
+ /* get class information */
+ nber_bytes = class_size[class];
+ class_pyname = class_name[class];
+
+ /* import python class */
+ python_class = pytools_import(module_name, class_pyname);
+
+ if (python_class == NULL)
+ return NULL;
+
+ if (!PyCallable_Check(python_class))
+ {
+ Py_DECREF(python_class);
+ pyerror("Unable to import class %s from %s", class_pyname, module_name);
+ }
+
+ /* create object */
+ PyObject *object, *args;
+
+ args = PyTuple_Pack(1, PyBytes_FromStringAndSize((char *) p, nber_bytes));
+
+ object = PyObject_CallObject(python_class, args);
+
+ Py_DECREF(args);
+ Py_DECREF(python_class);
+
+ return object;
+
+}
+
+char* pytools_get_type_name(PyObject *obj)
+{
+ /* get object type */
+ PyObject *type = PyObject_Type(obj);
+ if (type == NULL)
+ {
+ Py_DECREF(type);
+ pyerror("Unable to get type");
+ }
+
+ /* get object name */
+ PyObject* recv = PyObject_Str(type);
+ Py_DECREF(type);
+
+ if (recv == NULL)
+ {
+ Py_DECREF(recv);
+ pyerror("Unable to get string representation");
+ }
+
+ /* transform to C */
+ size_t size;
+ char *name = PyUnicode_AsUTF8AndSize(recv, size);
+ Py_DECREF(recv);
+
+ if (name == NULL)
+ {
+ pyerror("Unable to convert string to char");
+ }
+
+ return name;
+}
+
+
+char* pytools_construct(PyObject* obj, int class)
+{
+ char *module_name = "pyswiftsim.structure";
+ char *class_pyname;
+
+ /* check python class */
+ if (class >= class_count)
+ pyerror("Class %i does not exists", class);
+
+ /* get class information */
+ class_pyname = class_name[class];
+
+ /* import class */
+ PyObject *pyclass = pytools_import(module_name, class_pyname);
+
+ /* check if classes correspond */
+ int test = !PyObject_IsInstance(obj, pyclass);
+ Py_DECREF(pyclass);
+ if (test)
+ {
+ char *recv = pytools_get_type_name(obj);
+ if (recv == NULL)
+ return NULL;
+ pyerror("Expecting class %s, received %s", class_pyname, recv);
+ }
+
+
+ /* copy python class' data to C */
+ PyObject* data = PyObject_GetAttrString(obj, "data");
+
+ if (data == NULL)
+ pyerror("Unable to get the attribute 'data'");
+
+ char *ret = PyBytes_AsString(data);
+
+ Py_DECREF(data);
+ return ret;
+}
+
+
+int pytools_check_array(PyArrayObject *obj, int dim, int type)
+{
+ /* ensure to have numpy arrays */
+ IMPORT_ARRAY();
+
+ /* check if array */
+ if (!PyArray_Check(obj))
+ {
+ pyerror("Expecting a numpy array");
+ }
+
+ /* check if required dim */
+ if (PyArray_NDIM(obj) != dim)
+ {
+ pyerror("Array should be a %i dimensional object", dim);
+ }
+
+ /* check data type */
+ if (PyArray_TYPE(obj) != type)
+ {
+ pyerror("Wrong array type");
+ }
+
+ return SUCCESS;
+
+}
diff --git a/src/pyswiftsim_tools.h b/src/pyswiftsim_tools.h
new file mode 100644
index 0000000000000000000000000000000000000000..9d03af9f77ade6f241bcf93c2252464fc9ae0e10
--- /dev/null
+++ b/src/pyswiftsim_tools.h
@@ -0,0 +1,107 @@
+#ifndef __PYSWIFTSIM_TOOLS_H__
+#define __PYSWIFTSIM_TOOLS_H__
+
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+
+#include <Python.h>
+#include <numpy/arrayobject.h>
+
+#define DIM 3
+#define STRING_SIZE 200
+
+/* Check if arrays are imported and if not import them */
+#define IMPORT_ARRAY() \
+ ({ \
+ if (PyArray_API == NULL) \
+ { \
+ import_array(); \
+ } \
+ })
+
+/* Set the error message for python (still need to return NULL) */
+#define pyerror(s, ...) \
+ ({ \
+ char error_msg[STRING_SIZE]; \
+ PyErr_Print(); \
+ sprintf(error_msg, "\n%s:%s():%i: " s, __FILE__, \
+ __FUNCTION__, __LINE__, ##__VA_ARGS__); \
+ PyErr_SetString(PyExc_RuntimeError, error_msg); \
+ return FAIL; \
+ })
+
+/* debugging function */
+#define pydebug(s, ...) \
+ ({ \
+ PyErr_Print(); \
+ fprintf(stderr, "\n%s:%s():%i: Test " s "\n", __FILE__, \
+ __FUNCTION__, __LINE__, ##__VA_ARGS__); \
+ })
+
+/* Enum swift classes */
+enum swift_class {
+ class_unit_system,
+ class_part,
+ class_swift_params,
+ class_phys_const,
+ class_cooling_function_data,
+ class_count /* should always be last! */
+};
+
+/* size of each structure in enum swift_class */
+extern const size_t class_size[];
+/* name of each Python class representing a swift class */
+extern const char *class_name[];
+
+/* error code in pyswiftsim */
+enum error_code {
+ FAIL = 0, // ensure NULL == FAIL
+ SUCCESS,
+};
+
+
+/**
+ * @brief Construct a python object from a C struct
+ *
+ * @param p pointer to the C struct
+ * @param class #swift_class of the pointer
+ * @return PyObject of the required class
+ */
+PyObject* pytools_return(void* p, int class);
+
+/**
+ * @brief Construct a C struct from a python object
+ *
+ * @param obj pointer to the python object
+ * @param class #swift_class of the pointer
+ * @return pointer to the required struct
+ */
+char* pytools_construct(PyObject* obj, int class);
+
+/**
+ * @brief Import a python library/function
+ *
+ * @param module Module name
+ * @param object_name object to import from module
+ * @return (PyObject) imported object
+ */
+PyObject* pytools_import(char* module, char* object_name);
+
+/**
+ * @brief get type name in C
+ *
+ * @param obj PyObject from which to get the name0
+ * @return type name
+ */
+char* pytools_get_type_name(PyObject *obj);
+
+/**
+ * @brief Check if object is the expected PyArray type
+ *
+ * @param obj PyArray to check
+ * @param dim required dimension
+ * @param int required type
+ * @return #error_code result of the test
+ */
+int pytools_check_array(PyArrayObject *obj, int dim, int type);
+
+#endif // __PYSWIFTSIM_TOOLS_H__
diff --git a/src/units_wrapper.c b/src/units_wrapper.c
new file mode 100644
index 0000000000000000000000000000000000000000..aeda170ac6f6e74e55ce10e0c11c637ae3621778
--- /dev/null
+++ b/src/units_wrapper.c
@@ -0,0 +1,66 @@
+#include "pyswiftsim_tools.h"
+
+#include <units.h>
+#include <parser.h>
+#include <physical_constants.h>
+
+#include <Python.h>
+#include <stdlib.h>
+#include <string.h>
+
+PyObject* pyunit_system_test_struct(PyObject *self, PyObject *args)
+{
+
+ size_t N = sizeof(struct unit_system);
+
+ /* initialize array */
+ struct unit_system *us = malloc(N);
+ us->UnitMass_in_cgs = 1.;
+ us->UnitLength_in_cgs = 2.;
+ us->UnitTime_in_cgs = 3.;
+ us->UnitCurrent_in_cgs = 4.;
+ us->UnitTemperature_in_cgs = 5.;
+
+ /* construct python object */
+ PyObject *object = pytools_return(us, class_unit_system);
+ free(us);
+ if (object == NULL)
+ return NULL;
+
+ return object;
+}
+
+PyObject* pyunit_system_init(PyObject *self, PyObject *args)
+{
+ PyObject* parser;
+
+ /* parse arguement */
+ if (!PyArg_ParseTuple(args, "O", &parser))
+ return NULL;
+
+ struct swift_params *params = pytools_construct(parser, class_swift_params);
+
+ if (params == NULL)
+ return NULL;
+
+ /* initialize units */
+ struct unit_system us;
+ units_init(&us, params, "InternalUnitSystem");
+
+ /* initialize phys_const */
+ struct phys_const pconst;
+ phys_const_init(&us, &pconst);
+
+ /* create python object to return */
+ PyObject *pyus = pytools_return(&us, class_unit_system);
+ if (pyus == NULL)
+ return NULL;
+
+ PyObject *pypconst = pytools_return(&pconst, class_phys_const);
+ if (pypconst == NULL)
+ return NULL;
+
+ return PyTuple_Pack(2, pyus, pypconst);
+}
+
+
diff --git a/src/units_wrapper.h b/src/units_wrapper.h
new file mode 100644
index 0000000000000000000000000000000000000000..867e055863d24203dbfb41213ef6fd837252a28e
--- /dev/null
+++ b/src/units_wrapper.h
@@ -0,0 +1,28 @@
+#ifndef __PYSWIFTSIM_UNITS_H__
+#define __PYSWIFTSIM_UNITS_H__
+
+#include <Python.h>
+
+/**
+ * @brief Test function for the struct
+ *
+ * args is expecting no argument.
+ *
+ * @param self calling object
+ * @param args arguments
+ * @return UnitSystem
+ */
+PyObject* pyunit_system_test_struct(PyObject *self, PyObject *args);
+
+/**
+ * @brief Initialize the unit system
+ *
+ * args is expecting a pyswift SwiftParms object.
+ *
+ * @param self calling object
+ * @param args arguments
+ * @return UnitSystem
+ */
+PyObject* pyunit_system_init(PyObject *self, PyObject *args);
+
+#endif // __PYSWIFTSIM_UNITS_H__
diff --git a/src/wrapper.c b/src/wrapper.c
new file mode 100644
index 0000000000000000000000000000000000000000..27fc59183559641a6b0d3fbfa1e59011b16eae92
--- /dev/null
+++ b/src/wrapper.c
@@ -0,0 +1,68 @@
+#include "units_wrapper.h"
+#include "part_wrapper.h"
+#include "parser_wrapper.h"
+#include "cooling_wrapper.h"
+#include "pyswiftsim_tools.h"
+#include "config_wrapper.h"
+
+
+#include <Python.h>
+#include <math.h>
+#include <numpy/arrayobject.h>
+
+
+/* definition of the method table */
+
+static PyMethodDef wrapper_methods[] = {
+
+ {"partTestStruct", pypart_test_struct, METH_VARARGS,
+ "Construct a part object and return it."},
+
+ {"unitSystemTestStruct", pyunit_system_test_struct, METH_VARARGS,
+ "Construct a unit_system object and return it."},
+
+ {"parserReadFile", pyparser_read_file, METH_VARARGS,
+ "Read a swift params file."},
+
+ {"unitSystemInit", pyunit_system_init, METH_VARARGS,
+ "Construct a unit_system object and return it."},
+
+ {"coolingInit", pycooling_init, METH_VARARGS,
+ "Initialize cooling."},
+
+ {"coolingRate", pycooling_rate, METH_VARARGS,
+ "Compute the cooling rate."},
+
+ {"configGetCooling", config_get_cooling, METH_VARARGS,
+ "Get the cooling type."},
+
+ {NULL, NULL, 0, NULL} /* Sentinel */
+};
+
+
+
+static struct PyModuleDef wrapper_cmodule = {
+ PyModuleDef_HEAD_INIT,
+ "wrapper",
+ "Wrapper around the SPH cosmological simulation code SWIFT",
+ -1,
+ wrapper_methods
+};
+
+
+PyMODINIT_FUNC PyInit_wrapper(void)
+{
+ PyObject *m;
+
+ /* set time for swift */
+ clocks_set_cpufreq(0);
+
+ import_array();
+ Py_Initialize();
+ m = PyModule_Create(&wrapper_cmodule);
+
+ if (m == NULL)
+ return NULL;
+
+ return m;
+}
diff --git a/test/cooling.yml b/test/cooling.yml
new file mode 100644
index 0000000000000000000000000000000000000000..96555e68c238897b81b856a624468385f0f9af90
--- /dev/null
+++ b/test/cooling.yml
@@ -0,0 +1,51 @@
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1.989e43 # Grams
+ UnitLength_in_cgs: 3.085e21 # Centimeters
+ UnitVelocity_in_cgs: 20725573.785998672 # 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: sedov # 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
+ tasks_per_cell: 1000
+
+# 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).
+ CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./sedov.hdf5 # The file to read
+ h_scaling: 3.33
+
+
+# Cooling with Grackle 2.0
+GrackleCooling:
+ GrackleCloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table
+ UVbackground: 1 # Enable or not the UV background
+ GrackleRedshift: 0 # Redshift to use (-1 means time based redshift)
+ GrackleHSShieldingDensityThreshold: 1.1708e-26 # self shielding threshold in internal system of units
+
+Gravity:
+ eta: 0.025 # Constant dimensionless multiplier for time integration.
+ theta: 0.7 # Opening angle (Multipole acceptance criterion)
+ epsilon: 0.1 # Softening length (in internal units).
+ a_smooth: 1.25 # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
+ r_cut_max: 4.5 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
+ r_cut_min: 0.1 # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
diff --git a/test/test_cooling.py b/test/test_cooling.py
new file mode 100644
index 0000000000000000000000000000000000000000..43148ce9a7e875bf9a747afc8e7847d605a3c845
--- /dev/null
+++ b/test/test_cooling.py
@@ -0,0 +1,136 @@
+#!/usr/bin/env python3
+
+from pyswiftsim import wrapper
+from pyswiftsim import structure
+
+from copy import deepcopy
+import numpy as np
+import matplotlib.pyplot as plt
+from astropy import units
+
+#
+# parameters
+#
+
+# adiabatic index
+gamma = 5. / 3.
+
+# swift params filename
+filename = "test/cooling.yml"
+
+# number of points
+N_rho = 300
+N_T = 300
+
+# density in atom / cm3
+if N_rho == 1:
+ rho = np.array([1.])
+else:
+ #rho = np.array([1.])
+ rho = np.logspace(-6, 4, N_rho)
+
+# temperature in K
+T = np.logspace(1, 9, N_T)
+
+# time step
+dt = units.Myr * 1e-5
+dt = dt.to("s") / units.s
+
+
+
+# generate grid
+rho, T = np.meshgrid(rho, T)
+shape = rho.shape
+rho = deepcopy(rho.reshape(-1))
+T = T.reshape(-1)
+
+#
+# swift init
+#
+
+# parse swift params
+params = wrapper.parserReadFile(filename)
+# init units
+us, pconst = wrapper.unitSystemInit(params)
+# init cooling
+cooling = wrapper.coolingInit(params, us, pconst)
+
+
+#
+# Deal with units
+#
+
+# change units of rho and T
+# rho
+rho *= us.UnitLength_in_cgs**3 * pconst.const_proton_mass
+# specific energy
+energy = pconst.const_boltzmann_k * T / us.UnitTemperature_in_cgs
+energy /= (gamma - 1.) * pconst.const_proton_mass
+# time step
+dt /= us.UnitTime_in_cgs
+
+#
+# compute rate
+#
+
+# du / dt
+rate = wrapper.coolingRate(pconst, us, cooling,
+ rho.astype(np.float32),
+ energy.astype(np.float32),
+ dt)
+
+#
+# plot
+#
+
+
+# change units => cgs
+energy *= us.UnitLength_in_cgs**2 / us.UnitTime_in_cgs**2
+
+rate *= us.UnitLength_in_cgs**2 / us.UnitTime_in_cgs**3
+
+if N_rho == 1 or N_T == 1:
+ plt.figure()
+ n = rho / (pconst.const_proton_mass * us.UnitLength_in_cgs**3)
+ proton_mass_in_cgs = pconst.const_proton_mass * us.UnitMass_in_cgs
+ lambda_ = rate * proton_mass_in_cgs / (n)
+
+ if N_rho == 1:
+ plt.loglog(T, np.abs(lambda_))
+ plt.xlabel("Temperature [K]")
+ else:
+ plt.loglog(rho, np.abs(lambda_))
+ plt.xlabel("Density [atom / cm3]")
+ plt.ylabel("Rate")
+
+else:
+ cooling_time = energy / rate
+ cooling_length = np.sqrt(gamma * (gamma-1.) * energy) * cooling_time
+
+ cooling_length = np.log10(np.abs(cooling_length) / units.kpc.to('cm'))
+
+ # reshape
+ rho = rho.reshape(shape)
+ T = T.reshape(shape)
+ energy = energy.reshape(shape)
+ cooling_length = cooling_length.reshape(shape)
+
+ _min = -7
+ _max = 7
+ N_levels = 100
+ levels = np.linspace(_min, _max, N_levels)
+ plt.figure()
+ plt.contourf(rho, T, cooling_length, levels)
+ plt.xlabel("Density [atom/cm3]")
+ plt.ylabel("Temperature [K]")
+
+ ax = plt.gca()
+ ax.set_xscale("log")
+ ax.set_yscale("log")
+
+ cbar = plt.colorbar()
+ tc = np.arange(_min, _max, 1.5)
+ cbar.set_ticks(tc)
+ cbar.set_ticklabels(tc)
+
+plt.show()
diff --git a/test/test_struct.py b/test/test_struct.py
new file mode 100644
index 0000000000000000000000000000000000000000..7c228d849979d2229cfd9d741862f54535f63744
--- /dev/null
+++ b/test/test_struct.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+from pyswiftsim import wrapper
+from pyswiftsim import structure
+
+us = wrapper.unitSystemTestStruct()
+
+print(us)
+
+part = wrapper.partTestStruct()
+
+print(part)
+
+#us = structure.Units(t)
+
+#print(type(us), us.struct_name)
+#print(us.struct_size_format)
+
+#for i in us.struct_name:
+# print(i, getattr(us, i))
+
+"""
+print(us.pos)
+us.pos = [12., 16., 11.]
+#us.pos[0] = 10.
+
+print(us)
+print(us.pos)
+
+print("setitem")
+us.pos[2] = 20.
+
+print(us.pos)
+print(us)
+
+d = {}
+d["UnitMass_in_cgs"] = 1.
+d["UnitLength_in_cgs"] = 2.
+d["UnitTime_in_cgs"] = 3.
+d["UnitCurrent_in_cgs"] = 4.
+d["UnitTemperature_in_cgs"] = 5.
+
+us = structure.UnitSystem(d)
+
+print(us)
+"""