Numba montecarlo

docs/development/continuous_integration.rst

@@ -203,11 +203,7 @@ After defining the variable, one could optionally encrypt it using this lock sym
 Variables are referenced as $(variable_name), as seen in the InstallSSHKey@0 task in the hostName and sshPublicKey inputs.
 
 Azure provides a list of agent hosts that can run the pipeline on a virtual machine. In our pipelines, we
-<<<<<<< HEAD
 use the vm_Images: Ubuntu 16.04 and macOs-10.14.
-=======
-use the vm_Images: Ubuntu 16.04 and macOS-10.13.
->>>>>>> Add periods, correct capitalizations, correct typos, and shuffle commas in continuous integration page.
 
 In a job, you can list a single vm as::
 

docs/development/debug_numba.rst

@@ -0,0 +1,14 @@
+**************************
+Debugging numba_montecarlo
+**************************
+To facilitate more in-depth debugging when interfacing with the `montecarlo_numba`
+module, we provide a set of debugging configurations. PyCharm debugging
+configurations, in addition to related scripts and .yml files, are contained in
+`tardis.scripts.debug`. Currently, these include the ability to run TARDIS
+in asingle-packet mode, with the packet seed identified at debug time.
+`tardis_example_single.yml` is the configuration filethat is used to set up the
+single-packet TARDIS run; `run_numba_single.py` is thePython script that runs
+this .yml file; `run_numba_single.xml` is the PyCharmdebug configuration file
+that can be used in conjunction with the above files.
+
+

docs/development/index.rst

@@ -11,8 +11,8 @@ to the Astropy team for designing it.
 .. toctree::
     :maxdepth: 2
 
-    running_tests
     issues
+    debug_numba
 
 
 

docs/index.rst

@@ -69,6 +69,14 @@ Mission Statement
     Physics overview <physics/index>
     physics/plasma/index
 
+.. toctree::
+    :maxdepth: 2
+    :caption: Testing TARDIS
+    :hidden:
+
+    testing/automated_tests
+    testing/numba
+
 
 .. toctree::
     :maxdepth: 2

docs/running/custom_source.ipynb

@@ -52,9 +52,10 @@
     "    \n",
     "    def __init__(self, seed, truncation_wavelength):\n",
     "        super().__init__(seed)\n",
+    "        self.rng = np.random.default_rng(seed=seed)\n",
     "        self.truncation_wavelength = truncation_wavelength\n",
     "    \n",
-    "    def create_packets(self, T, no_of_packets,\n",
+    "    def create_packets(self, T, no_of_packets, rng,\n",
     "                       drawing_sample_size=None):\n",
     "        \"\"\"\n",
     "        Packet source that generates a truncated Blackbody source.\n",
@@ -70,11 +71,10 @@
     "            Only wavelengths higher than the truncation wavelength\n",
     "            will be sampled.\n",
     "        \"\"\"\n",
-    "        \n",
-    "        \n",
+    "\n",
     "        # Use mus and energies from normal blackbody source.\n",
-    "        mus = self.create_zero_limb_darkening_packet_mus(no_of_packets)\n",
-    "        energies = self.create_uniform_packet_energies(no_of_packets)\n",
+    "        mus = self.create_zero_limb_darkening_packet_mus(no_of_packets, self.rng)\n",
+    "        energies = self.create_uniform_packet_energies(no_of_packets, self.rng)\n",
     "\n",
     "        # If not specified, draw 2 times as many packets and reject any beyond no_of_packets.\n",
     "        if drawing_sample_size is None:\n",
@@ -86,15 +86,15 @@
     "        \n",
     "        # Draw nus from blackbody distribution and reject based on truncation_frequency.\n",
     "        # If more nus.shape[0] > no_of_packets use only the first no_of_packets.\n",
-    "        nus = self.create_blackbody_packet_nus(T, drawing_sample_size)\n",
+    "        nus = self.create_blackbody_packet_nus(T, drawing_sample_size, self.rng)\n",
     "        nus = nus[nus<truncation_frequency][:no_of_packets]\n",
     "        \n",
     "        \n",
     "        # Only required if the truncation wavelength is too big compared to the maximum \n",
     "        # of the blackbody distribution. Keep sampling until nus.shape[0] > no_of_packets.\n",
     "        while nus.shape[0] < no_of_packets:\n",
     "            additional_nus = self.create_blackbody_packet_nus(\n",
-    "                T, drawing_sample_size\n",
+    "                T, drawing_sample_size, self.rng\n",
     "            )\n",
     "            mask = additional_nus < truncation_frequency\n",
     "            additional_nus = additional_nus[mask][:no_of_packets]\n",
@@ -170,4 +170,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

tardis/io/schemas/montecarlo.yml

@@ -33,21 +33,17 @@ properties:
     multipleOf: 1.0
     default: 0
     description: Setting the number of virtual packets for the last iteration.
-  virtual_spectrum_range:
+  virtual_spectrum_spawn_range:
     type: object
     default: {}
     properties:
       start:
         type: quantity
-        default: 50 angstrom
-      stop:
+        default: 0 angstrom
+      end:
         type: quantity
-        default: 250000 angstrom
-      num:
-        type: number
-        multipleOf: 1.0
-        default: 1000000
-    description: Limits of virtual packet spectrum (giving maximum and minimum packet
+        default: inf angstrom
+    description: Limits of virtual packet spawn spectrum (giving maximum and minimum packet
       frequency)
   enable_reflective_inner_boundary:
     type: boolean
@@ -68,6 +64,19 @@ properties:
     default: false
     description: Enables a more complete treatment of relativitic effects. This includes
       angle aberration as well as use of the fully general Doppler formula.
+  debug_packets:
+    type: boolean
+    default: false
+    description: Decide whether to go into debugging mode.
+  logger_buffer:
+    type: number
+    default: 1
+    description: Provides option to not log every line.
+  single_packet_seed:
+    type:
+      - number
+    default: -1
+    description: If debug_packets is true, this is the seed for the only packet.
 
 required:
 - no_of_packets

tardis/io/schemas/plasma.yml

@@ -17,6 +17,11 @@ properties:
     default: false
     description: disable electron scattering process in montecarlo part - non-physical
       only for tests
+  disable_line_scattering:
+    type: boolean
+    default: false
+    description: disable line scattering process in montecarlo part - non-physical
+      only for tests
   ionization:
     type: string
     enum:

tardis/io/schemas/spectrum.yml

@@ -50,3 +50,7 @@ properties:
         default: False
         description: If True bias v-packet emission based on the electron
             scattering optical depth
+      virtual_packet_logging:
+        type: boolean
+        default: False
+        description: If True, enable virtual packet logging output

tardis/io/util.py

@@ -284,7 +284,7 @@ def get_properties(self):
     @property
     def full_hdf_properties(self):
         # If tardis was compiled --with-vpacket-logging, add vpacket properties
-        if hasattr(self, "virt_logging") and self.virt_logging == 1:
+        if hasattr(self, "virt_logging") and self.virt_logging:
             self.hdf_properties.extend(self.vpacket_hdf_properties)
 
         return self.optional_hdf_properties + self.hdf_properties

tardis/montecarlo/__init__.py

@@ -1 +1 @@
-from tardis.montecarlo.base import *
+from tardis.montecarlo.base import *