Move structs to struct.py, init default values.

- __init__ in RPacket and StorageModel resemble the
  same init methods in test_cmontecarlo.c

- The way arguments are passed in paramterization is
  changed from individual params to a dict for better
  aesthetic sense.

tardis/montecarlo/struct.py

@@ -0,0 +1,190 @@
+import os
+from ctypes import *
+
+import numpy as np
+from tardis import __path__ as path
+
+test_path = os.path.join(path[0], 'montecarlo', 'test_montecarlo.so')
+tests = CDLL(test_path)
+
+cmontecarlo_filepath = os.path.join(path[0], 'montecarlo', 'montecarlo.so')
+cmontecarlo_methods = CDLL(cmontecarlo_filepath)
+
+
+class RPacket(Structure):
+    _fields_ = [
+        ('nu', c_double),
+        ('mu', c_double),
+        ('energy', c_double),
+        ('r', c_double),
+        ('tau_event', c_double),
+        ('nu_line', c_double),
+        ('current_shell_id', c_int64),
+        ('next_line_id', c_int64),
+        ('last_line', c_int64),
+        ('close_line', c_int64),
+        ('recently_crossed_boundary', c_int64),
+        ('current_continuum_id', c_int64),
+        ('virtual_packet_flag', c_int64),
+        ('virtual_packet', c_int64),
+        ('d_line', c_double),
+        ('d_electron', c_double),
+        ('d_boundary', c_double),
+        ('d_cont', c_double),
+        ('next_shell_id', c_int64),
+        ('status', c_int),
+        ('id', c_int64),
+        ('chi_th', c_double),
+        ('chi_cont', c_double),
+        ('chi_ff', c_double),
+        ('chi_bf', c_double)
+    ]
+
+    def __init__(self, **kwargs):
+        super(RPacket, self).__init__()
+        self.nu = 0.4
+        self.mu = 0.3
+        self.energy = 0.9
+        self.r = 7.5e14
+        self.tau_event = 2.9e13
+        self.nu_line = 0.2
+        self.current_shell_id = 0
+        self.next_line_id = 1
+        self.last_line = 0
+        self.close_line = 0
+        self.recently_crossed_boundary = 1
+        self.current_continuum_id = 1
+        self.virtual_packet_flag = 1
+        self.virtual_packet = 0
+        self.status = 0
+        self.id = 0
+
+        for key, value in kwargs.iteritems():
+            setattr(self, key, value)
+
+
+class StorageModel(Structure):
+    _fields_ = [
+        ('packet_nus', POINTER(c_double)),
+        ('packet_mus', POINTER(c_double)),
+        ('packet_energies', POINTER(c_double)),
+        ('output_nus', POINTER(c_double)),
+        ('output_energies', POINTER(c_double)),
+        ('last_interaction_in_nu', POINTER(c_double)),
+        ('last_line_interaction_in_id', POINTER(c_int64)),
+        ('last_line_interaction_out_id', POINTER(c_int64)),
+        ('last_line_interaction_shell_id', POINTER(c_int64)),
+        ('last_line_interaction_type', POINTER(c_int64)),
+        ('no_of_packets', c_int64),
+        ('no_of_shells', c_int64),
+        ('r_inner', POINTER(c_double)),
+        ('r_outer', POINTER(c_double)),
+        ('v_inner', POINTER(c_double)),
+        ('time_explosion', c_double),
+        ('inverse_time_explosion', c_double),
+        ('electron_densities', POINTER(c_double)),
+        ('inverse_electron_densities', POINTER(c_double)),
+        ('line_list_nu', POINTER(c_double)),
+        ('continuum_list_nu', POINTER(c_double)),
+        ('line_lists_tau_sobolevs', POINTER(c_double)),
+        ('line_lists_tau_sobolevs_nd', c_int64),
+        ('line_lists_j_blues', POINTER(c_double)),
+        ('line_lists_j_blues_nd', c_int64),
+        ('no_of_lines', c_int64),
+        ('no_of_edges', c_int64),
+        ('line_interaction_id', c_int64),
+        ('transition_probabilities', POINTER(c_double)),
+        ('transition_probabilities_nd', c_int64),
+        ('line2macro_level_upper', POINTER(c_int64)),
+        ('macro_block_references', POINTER(c_int64)),
+        ('transition_type', POINTER(c_int64)),
+        ('destination_level_id', POINTER(c_int64)),
+        ('transition_line_id', POINTER(c_int64)),
+        ('js', POINTER(c_double)),
+        ('nubars', POINTER(c_double)),
+        ('spectrum_start_nu', c_double),
+        ('spectrum_delta_nu', c_double),
+        ('spectrum_end_nu', c_double),
+        ('spectrum_virt_start_nu', c_double),
+        ('spectrum_virt_end_nu', c_double),
+        ('spectrum_virt_nu', POINTER(c_double)),
+        ('sigma_thomson', c_double),
+        ('inverse_sigma_thomson', c_double),
+        ('inner_boundary_albedo', c_double),
+        ('reflective_inner_boundary', c_int64),
+        ('current_packet_id', c_int64),
+        ('chi_bf_tmp_partial', POINTER(c_double)),
+        ('t_electrons', POINTER(c_double)),
+        ('l_pop', POINTER(c_double)),
+        ('l_pop_r', POINTER(c_double)),
+        ('cont_status', c_int),
+        ('virt_packet_nus', POINTER(c_double)),
+        ('virt_packet_energies', POINTER(c_double)),
+        ('virt_packet_last_interaction_in_nu', POINTER(c_double)),
+        ('virt_packet_last_interaction_type', POINTER(c_int64)),
+        ('virt_packet_last_line_interaction_in_id', POINTER(c_int64)),
+        ('virt_packet_last_line_interaction_out_id', POINTER(c_int64)),
+        ('virt_packet_count', c_int64),
+        ('virt_array_size', c_int64)
+    ]
+
+    def __init__(self, **kwargs):
+        super(StorageModel, self).__init__()
+
+        self.last_line_interaction_in_id = np.ctypeslib.as_ctypes(np.array([0] * 2))
+        self.last_line_interaction_shell_id = np.ctypeslib.as_ctypes(np.array([0] * 2))
+        self.last_line_interaction_type = np.ctypeslib.as_ctypes(np.array([2]))
+
+        self.no_of_shells = 2
+
+        self.r_inner = np.ctypeslib.as_ctypes(np.array([6.912e14, 8.64e14]))
+        self.r_outer = np.ctypeslib.as_ctypes(np.array([8.64e14, 1.0368e15]))
+
+        self.time_explosion = 5.2e7
+        self.inverse_time_explosion = 1 / 5.2e7
+
+        # self.electron_densities = np.ctypeslib.as_ctypes(np.array([1.0e9] * 2))
+        # self.inverse_electron_densities = np.ctypeslib.as_ctypes(np.array([1.0e-9] * 2))
+
+        self.line_list_nu = np.ctypeslib.as_ctypes(np.array([1.26318289e+16, 1.26318289e+16,
+                                                             1.23357675e+16, 1.23357675e+16,
+                                                             1.16961598e+16]))
+
+        self.continuum_list_nu = np.ctypeslib.as_ctypes(np.array([1.e13] * 20000))
+
+        self.line_lists_tau_sobolevs = np.ctypeslib.as_ctypes(np.array([1.e-5] * 1000))
+        # self.line_lists_j_blues = np.ctypeslib.as_ctypes(np.array([1.e-10] * 2))
+        self.line_lists_j_blues_nd = 0
+
+        self.no_of_lines = 2
+        self.no_of_edges = 100
+
+        self.line_interaction_id = 0
+        # self.line2macro_level_upper = np.ctypeslib.as_ctypes(np.array([0] * 2))
+
+        # self.js = np.ctypeslib.as_ctypes(np.array([0.0] * 2))
+        # self.nubars = np.ctypeslib.as_ctypes(np.array([0.0] * 2))
+
+        self.spectrum_start_nu = 1.e14
+        self.spectrum_delta_nu = 293796608840.0
+        self.spectrum_end_nu = 6.e15
+
+        self.spectrum_virt_start_nu = 1e14
+        self.spectrum_virt_end_nu = 6e15
+        self.spectrum_virt_nu = np.ctypeslib.as_ctypes(np.array([0.0] * 20000))
+
+        self.sigma_thomson = 6.652486e-25
+        self.inverse_sigma_thomson = 1 / self.sigma_thomson
+
+        self.inner_boundary_albedo = 0.0
+        self.reflective_inner_boundary = 0
+
+        self.chi_bf_tmp_partial = np.ctypeslib.as_ctypes(np.array([160.0] * 20000))
+        # self.t_electrons = np.ctypeslib.as_ctypes(np.array([0.0] * 2))
+
+        self.l_pop = np.ctypeslib.as_ctypes(np.array([2.0] * 20000))
+        self.l_pop_r = np.ctypeslib.as_ctypes(np.array([3.0] * 20000))
+
+        for key, value in kwargs.iteritems():
+            setattr(self, key, value)
+