Updated user_models to examples

docs/source/examples_advanced.rst

@@ -7,11 +7,11 @@ This section provides example models of some of the more advanced features of gp
 Building a heterogeneous soil
 =============================
 
-:download:`heterogeneous_soil.in <../../user_models/heterogeneous_soil.in>`
+:download:`heterogeneous_soil.in <../../examples/heterogeneous_soil.in>`
 
 This example demonstrates how to build a more realistic soil model using a stochastic distribution of dielectric properties. A mixing model for soils proposed by Peplinski (http://dx.doi.org/10.1109/36.387598) is used to define a series of dispersive material properties for the soil.
 
-.. literalinclude:: ../../user_models/heterogeneous_soil.in
+.. literalinclude:: ../../examples/heterogeneous_soil.in
     :language: none
     :linenos:
 

docs/source/examples_antennas.rst

@@ -9,11 +9,11 @@ This section provides some example models of antennas. Each example comes with a
 Wire dipole antenna model
 =========================
 
-:download:`antenna_wire_dipole_fs.in <../../user_models/antenna_wire_dipole_fs.in>`
+:download:`antenna_wire_dipole_fs.in <../../examples/antenna_wire_dipole_fs.in>`
 
 This example demonstrates a model of a half-wavelength wire dipole antenna in free space. It is a balanced antenna and it's characteristics are well known from theory [BAL2005]_. The length of the dipole is 150mm with a 1mm gap between the arms.
 
-.. literalinclude:: ../../user_models/antenna_wire_dipole_fs.in
+.. literalinclude:: ../../examples/antenna_wire_dipole_fs.in
     :language: none
     :linenos:
 
@@ -28,7 +28,7 @@ You can view the results (see :ref:`output` and :ref:`tools<plotting>` sections)
 
 .. code-block:: none
 
-    python -m tools.plot_antenna_params user_models/antenna_wire_dipole_fs.out
+    python -m tools.plot_antenna_params examples/antenna_wire_dipole_fs.out
 
 .. _antenna_wire_dipole_fs_tl_params:
 
@@ -68,11 +68,11 @@ You can view the results (see :ref:`output` and :ref:`tools<plotting>` sections)
 Bowtie antenna model
 ====================
 
-:download:`antenna_like_MALA_1200_fs.in <../../user_models/antenna_like_MALA_1200_fs.in>`
+:download:`antenna_like_MALA_1200_fs.in <../../examples/antenna_like_MALA_1200_fs.in>`
 
 This example demonstrates how to use one of the built-in antenna models in a simulation. Using a model of an antenna rather than a simple source, such as a Hertzian dipole, can improve the accuracy of the results of a simulation for many situations. It is especially important when the target is in the near-field of the antenna and there are complex interactions between the antenna and the environment. The simulation uses the model of an antenna similar to a MALA 1.2GHz antenna.
 
-.. literalinclude:: ../../user_models/antenna_like_MALA_1200_fs.in
+.. literalinclude:: ../../examples/antenna_like_MALA_1200_fs.in
     :language: none
     :linenos:
 
@@ -90,7 +90,7 @@ When the simulation is run two geometry files for the antenna are produced along
 
 .. code-block:: none
 
-    python -m tools.plot_Ascan user_models/antenna_like_MALA_1200_fs.out --outputs Ey
+    python -m tools.plot_Ascan examples/antenna_like_MALA_1200_fs.out --outputs Ey
 
 :numref:`antenna_like_MALA_1200_fs_results` shows the time history of the y-component of the electric field from the receiver bowtie of the antenna model (the antenna bowties are aligned with the y axis).
 
@@ -105,11 +105,11 @@ When the simulation is run two geometry files for the antenna are produced along
 B-scan with a bowtie antenna model
 ==================================
 
-:download:`cylinder_Bscan_GSSI_1500.in <../../user_models/cylinder_Bscan_GSSI_1500.in>`
+:download:`cylinder_Bscan_GSSI_1500.in <../../examples/cylinder_Bscan_GSSI_1500.in>`
 
 This example demonstrates how to create a B-scan with an antenna model. The scenario is purposely simple to illustrate the method. A metal cylinder of diameter 20mm is buried in a dielectric half-space which has a relative permittivity of six. The simulation uses the model of an antenna similar to a GSSI 1.5GHz antenna.
 
-.. literalinclude:: ../../user_models/cylinder_Bscan_GSSI_1500.in
+.. literalinclude:: ../../examples/cylinder_Bscan_GSSI_1500.in
     :language: none
     :linenos:
 
@@ -137,7 +137,7 @@ After merging the A-scans into a single file you can now view an image of the B-
 
 .. code-block:: none
 
-    python -m tools.plot_Bscan user_models/cylinder_Bscan_GSSI_1500_merged.out Ey
+    python -m tools.plot_Bscan examples/cylinder_Bscan_GSSI_1500_merged.out Ey
 
 :numref:`cylinder_Bscan_GSSI_1500_results` shows the B-scan (of the Ey field component). The initial part of the signal (~1-2 ns) represents the direct wave from transmitter to receiver. Then comes a hyperbolic response from the metal cylinder.
 

docs/source/examples_simple_2D.rst

@@ -9,11 +9,11 @@ This section provides some introductory example models in 2D that demonstrate ba
 A-scan from a metal cylinder
 ============================
 
-:download:`cylinder_Ascan_2D.in <../../user_models/cylinder_Ascan_2D.in>`
+:download:`cylinder_Ascan_2D.in <../../examples/cylinder_Ascan_2D.in>`
 
 This example is the GPR modelling equivalent of 'Hello World'! It demonstrates how to simulate a single trace (A-scan) from a metal cylinder buried in a dielectric half-space.
 
-.. literalinclude:: ../../user_models/cylinder_Ascan_2D.in
+.. literalinclude:: ../../examples/cylinder_Ascan_2D.in
     :language: none
     :linenos:
 
@@ -100,7 +100,7 @@ You can now run the model:
 
 .. code-block:: none
 
-    python -m gprMax user_models/cylinder_Ascan_2D.in
+    python -m gprMax examples/cylinder_Ascan_2D.in
 
 .. tip::
     * You can use the ``--geometry-only`` command line argument to build a model and produce any geometry views but not run the simulation. This option is useful for checking the geometry of the model is correct.
@@ -112,7 +112,7 @@ You should have produced an output file ``cylinder_Ascan_2D.h5``. You can view t
 
 .. code-block:: none
 
-    python -m tools.plot_Ascan user_models/cylinder_Ascan_2D.h5
+    python -m tools.plot_Ascan examples/cylinder_Ascan_2D.h5
 
 :numref:`cylinder_Ascan_results` shows the time history of the electric and magnetic field components and currents at the receiver location. The :math:`E_z` field component can be converted to voltage which represents the A-scan (trace). The initial part of the signal (~0.5-1.5 ns) represents the direct wave from transmitter to receiver. Then comes the reflected wavelet (~1.8-2.6 ns), which has opposite polarity, from the metal cylinder.
 
@@ -129,11 +129,11 @@ Check out a `video of the field propagation in this example <https://youtu.be/Bp
 B-scan from a metal cylinder
 ============================
 
-:download:`cylinder_Bscan_2D.in <../../user_models/cylinder_Bscan_2D.in>`
+:download:`cylinder_Bscan_2D.in <../../examples/cylinder_Bscan_2D.in>`
 
 This example uses the same geometry as the previous example but this time a B-scan is created. A B-scan is composed of multiple traces (A-scans) recorded as the source and receiver are moved over the target, in this case the metal cylinder.
 
-.. literalinclude:: ../../user_models/cylinder_Bscan_2D.in
+.. literalinclude:: ../../examples/cylinder_Bscan_2D.in
     :language: none
     :linenos:
 
@@ -143,7 +143,7 @@ To run the model to create a B-scan you must pass an optional argument to specif
 
 .. code-block:: none
 
-    python -m gprMax user_models/cylinder_Bscan_2D.in -n 60
+    python -m gprMax examples/cylinder_Bscan_2D.in -n 60
 
 
 Results
@@ -153,7 +153,7 @@ You should have produced 60 output files, one for each A-scan, with names ``cyli
 
 .. code-block:: none
 
-    python -m tools.outputfiles_merge user_models/cylinder_Bscan_2D
+    python -m tools.outputfiles_merge examples/cylinder_Bscan_2D
 
 You should see a combined output file ``cylinder_Bscan_2D_merged.h5``. You can add the optional argument ``--remove-files`` if you want to automatically delete the original single A-scan output files.
 
@@ -161,7 +161,7 @@ You can now view an image of the B-scan using the command:
 
 .. code-block:: none
 
-    python -m tools.plot_Bscan user_models/cylinder_Bscan_2D_merged.h5 Ez
+    python -m tools.plot_Bscan examples/cylinder_Bscan_2D_merged.h5 Ez
 
 :numref:`cylinder_Bscan_results` shows the B-scan (of the :math:`E_z` field component). Again, the initial part of the signal (~0.5-1.5 ns) represents the direct wave from transmitter to receiver. Then comes the refelected wave (~2-3 ns) from the metal cylinder which creates the hyperbolic shape.