Merge branch 'init' into 'master'

Init

See merge request !1

LICENSE

+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
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+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  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>.

pyswiftsim/__init__.py

+
+from pyswiftsim import *

pyswiftsim/structure.py

+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)

setup.py

+#!/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,
+)

src/config_wrapper.h

+#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__

src/cooling_wrapper.c

+#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;
+  
+}

src/cooling_wrapper.h

+#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__
+

src/parser_wrapper.c

+#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, &params);
+
+  /* create return python object */
+  PyObject* obj = pytools_return(&params, class_swift_params);
+
+  return obj;
+}

src/parser_wrapper.h

+#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__

src/part_wrapper.c

+#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;
+}
+

src/part_wrapper.h

+#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__

src/pyswiftsim_tools.c

+#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;
+
+}

src/pyswiftsim_tools.h

+#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__

src/units_wrapper.c

+#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);
+}
+
+

src/units_wrapper.h

+#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__

src/wrapper.c

+#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;
+}

test/cooling.yml

+# 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).

test/test_cooling.py

+#!/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()

test/test_struct.py

+#!/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)
+"""