api docs

docs/source/api.rst

@@ -1,51 +1,101 @@
-.. _commands:
+.. _api:
 
 *******************
 API
 *******************
 
-gprMax can be also be run using its API in additional to input file commands. For instance,
+Introduction
+==================
+In additional to input file command interface gprMax can also be run using its API. The usage of the API differs from the use of the Python blocks syntax as follows. In the API gprMax functionality is called directly from any Python file via the gprMax module. Using the Python blocks syntax the Python code is executed within an embedded interpreter. The API has the advantage that it can be included within any Python file and can be included within any Python script.
+
+There are several advantages to using API. Firstly, users can take advantage of the Python language. For instance, the structural elements of Python can be utilised more easily. gprMax objects can be used directly within functions, classes, modules and packages. In this way collections of components can be defined, reused and modified. For example, multiple SMA type connectors can be imported as a module and combined with an antenna from another module.
+
+The API also allows gprMax to interface with other Python libraries. For example, the API could be used to create a parametric antenna and the external library Scipy could then be used to optimise its parameters. Although, this is possible using Python blocks syntax, the script file can also be debugged.
+
+The syntax of the API is generally more verbose than the input file command syntax. However, for input file commands where there are an undefined number of parameters, such as adding dispersive properties, the user may find the API more manageable.
+
+Example
+==================
+
+The following example is used to give an introduction to the gprMax API. the example file is found in
+``user_models/antenna_wire_dipole_fs.py``.
+
+First, import the gprMax module.
 
 .. code-block:: python
 
   import gprMax
 
-  # Make simulation objects
+Next, simulation objects for the simulation are created from the gprMax module. Each input file command is available as an object. Simulation objects are created by passing the object parameters as key=value option arguments. The following example shows the creation of simulation objects and also their equivalent input file command for clarity.
 
-  #title: GSSI 400MHz 'like' antenna in free-space
-  #domain: 0.380 0.380 0.360
+.. code-block:: python
+
+  #title: Wire antenna - half-wavelength dipole in free-space
+  title = gprMax.Title(name="Wire antenna - half-wavelength dipole in free-space")
+  #domain: 0.050 0.050 0.200
+  domain = gprMax.Domain(p1=(0.050, 0.050, 0.200))
   #dx_dy_dz: 0.001 0.001 0.001
-  #time_window: 12e-9
+  dxdydz = gprMax.Discretisation(p1=(0.001, 0.001, 0.001))
+  #time_window: 60e-9
+  time_window = gprMax.TimeWindow(time=10e-9)
+  #waveform: gaussian 1 1e9 mypulse
+  waveform = gprMax.Waveform(wave_type='gaussian', amp=1, freq=1e9, id='mypulse')
+  #transmission_line: z 0.025 0.025 0.100 73 mypulse
+  transmission_line = gprMax.TransmissionLine(polarisation='z',
+                                              p1=(0.025, 0.025, 0.100),
+                                              resistance=73,
+                                              waveform_id='mypulse')
+  ## 150mm length
+  #edge: 0.025 0.025 0.025 0.025 0.025 0.175 pec
+  e1 = gprMax.Edge(p1=(0.025, 0.025, 0.025),
+                   p2=(0.025, 0.025, 0.175),
+                   material_id='pec')
 
-  # equivalent to 'title: API example'
-  title = gprMax.Title(name='API example')
-  # equivalent to 'dx_dy_dz: 1e-3 1e-3 1e-3'
-  dxdydz = gprMax.Discretisation(p1=(1e-3, 1e-3, 1e-3))
-  # equivalent to 'time_window: 6e-9'
-  tw = gprMax.TimeWindow(time=6e-9)
-  # equivalent to 'domain: 0.15 0.15 0.15'
-  domain = gprMax.Domain(p1=(0.15, 0.15, 0.15))
+  ## 1mm gap at centre of dipole
+  #edge: 0.025 0.025 0.100 0.025 0.025 0.101 free_space
+  e2 = gprMax.Edge(p1=(0.025, 0.025, 0.100),
+                   p2=(0.025, 0.025, 0.100),
+                   material_id='free_space')
 
-  # equivalent to #waveform: ricker 1 1.5e9 myricker
-  waveform = gprMax.Waveform(wave_type='ricker', amp=1, freq=1.5e9, id='my_ricker')
-  # equivalent to 'hertzian_dipole: y 0.045 0.075 0.085 my_ricker'
-  dipole = gprMax.HertzianDipole(p1=(0.045, 0.075, 0.085), polarisation='y', waveform_id='my_ricker')
-  # equivalent to 'rx: 0.045, 0.075 + 10e-3, 0.085'
-  rx = gprMax.Rx(p1=(0.045, 0.075 + 10e-3, 0.085))
+  #geometry_view: 0.020 0.020 0.020 0.030 0.030 0.180 0.001 0.001 0.001 antenna_wire_dipole_fs f
+  gv = gprMax.GeometryView(p1=(0.020, 0.020, 0.020),
+                           p2=(0.030, 0.030, 0.180),
+                           dl=(0.001, 0.001, 0.001),
+                           filename='antenna_wire_dipole_fs',
+                           output_type='n')
 
-  # make a container for the simulation
+
+Next a :class:`gprMax.scene.Scene` object is created. The scene is a container for all the objects required in a simulation. The objects are added to the scene as follows:
+
+.. code-block:: python
+
+  # Create a scene
   scene = gprMax.Scene()
-  # add the objects to the container
-  scene.add(dxdydz)
-  scene.add(tw)
-  scene.add(domain)
+  # Add the simulation objects to the scene
   scene.add(title)
+  scene.add(domain)
+  scene.add(dxdydz)
+  scene.add(time_window)
   scene.add(waveform)
-  scene.add(dipole)
+  scene.add(transmission_line)
+  scene.add(e1)
+  scene.add(e2)
+  scene.add(gv)
+
+
+Once the simulation objects have been added to the scene the simulation is run as follows:
+
+.. code-block:: python
 
   # run the simulation
-  gprMax.run(scenes=[scene], n=1, geometry_only=False, outputfile='mysimulation')
+  gprMax.run(scenes=[scene], n=1, outputfile='mysimulation')
 
+The run function arguments are similar to the flags in the CLI. The most notable difference is that a file path for the data output must be provided.
+
+Multiple simulation can be specified by providing multiple scene objects to the run function. Each scene must contain the essential commands and each user object required for that particular model.
+
+Reference
+=========
 
 The commands have been grouped into six categories:
 
@@ -105,11 +155,87 @@ Number of Model Runs
 
 Material
 ========
+
+Material
+--------
+.. autoclass:: gprMax.cmds_multiple.Material
+
+Debye Dispersion
+----------------
+.. autoclass:: gprMax.cmds_multiple.AddDebyeDispersion
+
+Lorentz Dispersion
+------------------
+.. autoclass:: gprMax.cmds_multiple.AddLorentzDispersion
+
+Drude Dispersion
+----------------
+.. autoclass:: gprMax.cmds_multiple.AddDrudeDispersion
+
+Soil Peplinski
+--------------
+.. autoclass:: gprMax.cmds_multiple.SoilPeplinski
+
+
 Object Construction
 ===================
+
+Object construction commands are processed in the order they appear in the scene. Therefore space in the model allocated to a specific material using for example the :class:`gprMax.cmds_geometry.box.Box` command can be reallocated to another material using the same or any other object construction command. Space in the model can be regarded as a canvas in which objects are introduced and one can be overlaid on top of the other overwriting its properties in order to produce the desired geometry. The object construction commands can therefore be used to create complex shapes and configurations.
+
+Box
+---
+.. autoclass:: gprMax.cmds_geometry.box.Box
+
+Cylinder
+--------
+.. autoclass:: gprMax.cmds_geometry.cylinder.Cylinder
+
+Cylindrical Sector
+------------------
+.. autoclass:: gprMax.cmds_geometry.cylindrical_sector.CylindricalSector
+
+Edge
+----
+.. autoclass:: gprMax.cmds_geometry.edge.Edge
+
+Plate
+-----
+.. autoclass:: gprMax.cmds_geometry.plate.Plate
+
+Triangle
+-----
+.. autoclass:: gprMax.cmds_geometry.triangle.Triangle
+
+Sphere
+-----
+.. autoclass:: gprMax.cmds_geometry.sphere.Sphere
+
+Fractal Box
+-----
+.. autoclass:: gprMax.cmds_geometry.fractal_box.FractalBox
+
+Add Grass
+---------
+.. autoclass:: gprMax.cmds_geometry.add_grass.AddGrass
+
+Add Surface Roughness
+---------------------
+.. autoclass:: gprMax.cmds_geometry.add_surface_roughness.AddSurfaceRoughness
+
+Add Surface Water
+-----------------
+.. autoclass:: gprMax.cmds_geometry.add_surface_water.AddSurfaceWater
+
+Geometry View
+-------------
+.. autoclass:: gprMax.cmds_multiple.GeometryView
+
+Geometry Objects Write
+----------------------
+.. autoclass:: gprMax.cmds_multiple.GeometryObjectsWrite
+
 Source and Output
 =================
-
 Waveform
 --------
 .. autoclass:: gprMax.cmds_multiple.Waveform
@@ -150,8 +276,28 @@ Rx Steps
 ------------
 .. autoclass:: gprMax.cmds_single_use.RxSteps
 
+Snapshot
+--------
+.. autoclass:: gprMax.cmds_multiple.Snapshot
+
 PML
 ===
+
+The default behaviour for the absorbing boundary conditions (ABC) is first order Complex Frequency Shifted (CFS) Perfectly Matched Layers (PML), with thicknesses of 10 cells on each of the six sides of the model domain. This can be altered by using the following command
+
 PML Cells
 --------------------------
 .. autoclass:: gprMax.cmds_single_use.PMLCells
+
+PML CFS
+--------------------------
+.. autoclass:: gprMax.cmds_multiple.PMLCFS
+
+
+Additional API objects
+======================
+
+Function to run the simulation
+------------------------------
+.. autofunction:: gprMax.gprMax.run
+.. autoclass:: gprMax.scene.Scene

gprMax/__init__.py

@@ -52,7 +52,7 @@ from .cmds_geometry.add_surface_water import AddSurfaceWater
 from .cmds_geometry.add_grass import AddGrass
 
 from .scene import Scene
-from .gprMax import api as run
+from .gprMax import run as run
 
 import gprMax.config as config
 

gprMax/gprMax.py

@@ -22,9 +22,8 @@ from .solvers import create_solver
 
 import argparse
 
-def api(
+def run(
     scenes=None,
-    id=None,
     inputfile=None,
     outputfile=None,
     n=1,
@@ -40,8 +39,36 @@ def api(
     geometry_fixed=False,
     write_processed=False,
 ):
-    """If installed as a module this is the entry point."""
+    """Run the simulation for the given list of scenes.
 
+    :param scenes: List of the scenes to run the model. Multiple scene objects can given in order to run multiple simulation runs. Each scene must contain the essential simulation objects
+    :type scenes: list, optional
+    :param inputfile:  Input file path. Can also run simulation by providing an input file.
+    :type inputfile: str, optional
+    :param outputfile: File path to the output data file.
+    :type outputfile: str, non-optional
+    :param n: Number of required simulation runs.
+    :type n: int, non-optional
+    :param task: task identifier (model number) when running simulation as a job array on open grid scheduler/grid engine. for further details see the parallel performance section of the user guide
+    :type task: int, optional
+    :param restart: model number to start/restart simulation from. It would typically be used to restart a series of models from a specific model number, with the n argument, e.g. to restart from A-scan 45 when creating a B-scan with 60 traces
+    :type restart: int, optional
+    :param mpi: number of Message Passing Interface (MPI) tasks, i.e. master + workers, for MPI task farm. This option is most usefully combined with n to allow individual models to be farmed out using a MPI task farm, e.g. to create a B-scan with 60 traces and use MPI to farm out each trace1. For further details see the parallel performance section of the User Guide
+    :type mpi: int, optional
+    :param mpi_no_spawn: use MPI task farm without spawn mechanism. For further details see the parallel performance section of the User Guide.
+    :type mpi_no_spawn: bool, optional
+    :param gpu: Flag to use NVIDIA GPU or list of NVIDIA GPU device ID(s) for specific GPU card(s)
+    :type gpu: list or bool, optional
+    :param subgrid: Use sub-gridding.
+    :type subgrid: bool, optional
+    :param benchmark: Switch on benchmarking mode. This can be used to benchmark the threading (parallel) performance of gprMax on different hardware. For further details see the benchmarking section of the User Guide
+    :type benchmark: bool, optional
+    :param geometry_only: build a model and produce any geometry views but do not run the simulation.
+    :type geometry_only: bool, optional
+    :param geometry_fixed: build a model and produce any geometry views but do not run the simulation.
+    :type geometry_fixed: bool, optional
+
+    """
     class ImportArguments:
         pass
 

gprMax/scene.py

@@ -13,11 +13,10 @@ from .utilities import human_size
 
 
 class Scene:
-
-    """Scene stores all of the user created objects
-    """
+    """Scene stores all of the user created objects."""
 
     def __init__(self):
+        """Constructor"""
         self.multiple_cmds = []
         self.single_cmds = []
         self.geometry_cmds = []
@@ -28,12 +27,17 @@ class Scene:
         fbb = FractalBoxBuilder()
         self.add(fbb)
 
-    def add(self, node):
-        if isinstance(node, UserObjectMulti):
-            self.multiple_cmds.append(node)
-        elif isinstance(node, UserObjectGeometry):
-            self.geometry_cmds.append(node)
-        elif isinstance(node, UserObjectSingle):
+    def add(self, user_object):
+        """Add the user object to the scene.
+
+        :param user_object: User object to add to the scene. For example, :class:`gprMax.cmds_single_use.Domain`
+        :type user_object: UserObjectMulti/UserObjectGeometry/UserObjectSingle
+        """
+        if isinstance(user_object, UserObjectMulti):
+            self.multiple_cmds.append(user_object)
+        elif isinstance(user_object, UserObjectGeometry):
+            self.geometry_cmds.append(user_object)
+        elif isinstance(user_object, UserObjectSingle):
             self.single_cmds.append(node)
         else:
             raise Exception('This Object is Unknown to gprMax')

user_models/antenna_wire_dipole_fs.py

@@ -1,8 +1,6 @@
 # import the gprMax module
 import gprMax
 
-
-
 # Create simulation objects. The equivalent input commands are given.
 
 #title: Wire antenna - half-wavelength dipole in free-space