Merge pull request #445 from PrincetonUniversity/issue-411

Issue 411 -- Follow-up example/cookbook fixes
PrincetonUniversity · Feb 4, 2025 · 396427c · 396427c
2 parents 8f747da + 7ddb4a1
commit 396427c
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diff --git a/docs/api/assembly/receivers/receiver.rst → docs/api/assembly/receivers/receivers.rst b/docs/api/assembly/receivers/receiver.rst → docs/api/assembly/receivers/receivers.rst
diff --git a/docs/api/assembly/sources/source.rst → docs/api/assembly/sources/sources.rst b/docs/api/assembly/sources/source.rst → docs/api/assembly/sources/sources.rst
diff --git a/docs/api/mesh/boundaries/index.rst b/docs/api/mesh/boundaries/index.rst
@@ -6,3 +6,9 @@ Boundaries
 
 .. doxygenstruct:: specfem::mesh::boundaries
     :members:
+
+.. toctree::
+    :maxdepth: 1
+
+    absorbing_boundaries
+    acoustic_free_surface
diff --git a/docs/api/mesh/index.rst b/docs/api/mesh/index.rst
@@ -6,3 +6,13 @@ SPECFEM++ Mesh
 
 .. doxygenstruct:: specfem::mesh::mesh
     :members:
+
+
+.. toctree::
+    :maxdepth: 1
+
+    boundaries/index
+    control_nodes/index
+    coupled_interfaces/index
+    materials/index
+    tags/index
diff --git a/docs/cookbooks/dim2/anisotropic-crystal/index.rst b/docs/cookbooks/dim2/anisotropic-crystal/index.rst
@@ -1,4 +1,4 @@
-Wave propagration through anistoropic zinc crystal
+Wave propagration through anisotropic zinc crystal
 ==================================================
 
 In this `example

diff --git a/docs/cookbooks/dim2/anisotropic-crystal/plot.py b/docs/cookbooks/dim2/anisotropic-crystal/plot.py
@@ -2,9 +2,6 @@
 import os
 import numpy as np
 import obspy
-import matplotlib
-
-matplotlib.use("agg")
 
 
 def get_traces(directory):
@@ -16,19 +13,15 @@ def get_traces(directory):
         "S0040",
         "S0050",
     ]
-    files = [
-        glob.glob(directory + f"/{stationname}*.sem*")[0]
-        for stationname in station_name
-    ]
+    files = []
+    for station in station_name:
+        files += glob.glob(directory + f"/??.{station}.S2.BX?.semd")
 
     ## iterate over all seismograms
     for filename in files:
         station_id = os.path.splitext(filename)[0]
         station_id = station_id.split("/")[-1]
-        network = station_id[5:7]
-        station = station_id[0:5]
-        location = "00"
-        component = station_id[7:10]
+        network, station, location, channel = station_id.split(".")[:4]
         trace = np.loadtxt(filename, delimiter=" ")
         starttime = trace[0, 0]
         dt = trace[1, 0] - trace[0, 0]
@@ -39,7 +32,7 @@ def get_traces(directory):
                     "network": network,
                     "station": station,
                     "location": location,
-                    "channel": component,
+                    "channel": channel,
                     "starttime": starttime,
                     "delta": dt,
                 },
@@ -52,4 +45,5 @@ def get_traces(directory):
 
 
 stream = get_traces("OUTPUT_FILES/results")
-stream.plot(size=(800, 1000))
+stream.select(component="X").plot(size=(1000, 750))
+stream.select(component="Z").plot(size=(1000, 750))
diff --git a/docs/cookbooks/dim2/fluid-solid-interface/index.rst b/docs/cookbooks/dim2/fluid-solid-interface/index.rst
@@ -151,3 +151,31 @@ With the configuration file in place, we can run the solver using the following
 .. code:: bash
 
     specfem2d -p specfem_config.yaml
+
+
+Visualizing the results
+-----------------------
+
+The simulation generates seismograms at the stations defined in the
+``specfem_config.yaml`` file. You can visualize the seismograms using the
+following python script.
+
+.. literalinclude:: plot.py
+    :language: python
+    :caption: plot.py
+
+
+.. figure:: seismograms_X.svg
+   :alt: X-component seismograms
+   :width: 800
+   :align: center
+
+   X-component seismograms
+
+
+.. figure:: seismograms_Z.svg
+    :alt: Z-component seismograms
+    :width: 800
+    :align: center
+
+    Z-component seismograms
diff --git a/docs/cookbooks/dim2/fluid-solid-interface/plot.py b/docs/cookbooks/dim2/fluid-solid-interface/plot.py
@@ -0,0 +1,42 @@
+import glob
+import os
+import numpy as np
+import obspy
+
+
+def get_traces(directory):
+    traces = []
+
+    files = glob.glob(directory + "/AA.S00??.S2.BX?.semd")
+    files.sort()
+
+    ## iterate over all seismograms
+    for filename in files:
+        station_id = os.path.splitext(filename)[0]
+        station_id = station_id.split("/")[-1]
+        network, station, location, channel = station_id.split(".")[:4]
+        trace = np.loadtxt(filename, delimiter=" ")
+        starttime = trace[0, 0]
+        dt = trace[1, 0] - trace[0, 0]
+        traces.append(
+            obspy.Trace(
+                trace[:, 1],
+                {
+                    "network": network,
+                    "station": station,
+                    "location": location,
+                    "channel": channel,
+                    "starttime": starttime,
+                    "delta": dt,
+                },
+            )
+        )
+
+    stream = obspy.Stream(traces)
+
+    return stream
+
+
+stream = get_traces("OUTPUT_FILES/seismograms")
+stream.select(component="X").plot(size=(1000, 750))
+stream.select(component="Z").plot(size=(1000, 750))