Merge pull request #240 from PrincetonUniversity/issue-213

Issue 213

examples/Tromp_2005/CMakeFiles/Snakefile.in

@@ -229,6 +229,10 @@ rule plot_kernels:
     run:
         from plot import plot_kernels
 
+        # Set matplotlib gui off
+        import matplotlib
+        matplotlib.use("Agg")
+
         plot_kernels(input.kernels, output.plot)
 
 

examples/fluid-solid-bathymetry/.gitignore

@@ -1,2 +1,4 @@
 specfem_config.yaml
 Par_File
+line_sources.yaml
+__pycache__

examples/fluid-solid-bathymetry/CMakeFiles/specfem_config.yaml.in

@@ -9,8 +9,6 @@ parameters:
       Interfaces : Acoustic-elastic interface (1) (orientation horizontal with acoustic domain on top)
       Sources : Moment-tensor (234)
       Boundary conditions : Neumann BCs on all edges
-      Debugging comments: This tests checks coupling acoustic-elastic interface implementation.
-                          The orientation of the interface is horizontal with acoustic domain on top.
 
   simulation-setup:
     ## quadrature setup
@@ -31,7 +29,7 @@ parameters:
         writer:
           seismogram:
             format: ascii
-            directory: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/seismograms
+            directory: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/results
 
           display:
             format: PNG
@@ -44,7 +42,6 @@ parameters:
     stations-file: @CMAKE_SOURCE_DIR@/examples/fluid-solid-bathymetry/OUTPUT_FILES/STATIONS
     angle: 0.0
     seismogram-type:
-      - displacement
       - pressure
     nstep_between_samples: 10
 

examples/fluid-solid-bathymetry/README.md

@@ -0,0 +1,39 @@
+# Wave propagration through fluid-solid interface
+
+This example simulates a tele-seismic plane wave within a fluid-solid domain. This example is contributed by Sirawich Pipatprathanporn and is part of the publication [Pipatprathanporn et al. (2024)](https://doi.org/10.1093/gji/ggae238)
+
+## Running the examples
+
+To run the examples, you first need to install poetry following these [instructions](https://python-poetry.org/docs/#installation). Once you've done so, you can install the dependencies for the examples by running the following command in the current directory:
+
+```bash
+# verify poetry is installed
+poetry --version
+
+# install dependencies
+poetry install
+
+```
+
+After installing the dependencies, you can run the examples by running the following command within the example directory you want to run:
+
+```bash
+
+# run the example
+poetry run snakemake -j 1
+
+# or to run the example on a slurm cluster
+poetry run snakemake --executor slurm -j 1
+
+```
+
+## Cleaning up
+
+To clean up the example directory, you can run the following command in the directory of the example you want to clean up:
+
+```bash
+
+# clean up the example
+poetry run snakemake clean
+
+```

examples/fluid-solid-bathymetry/Snakefile

@@ -0,0 +1,134 @@
+SPECFEM_BIN = "specfem2d"
+MESHFEM_BIN = "xmeshfem2D"
+
+
+rule all:
+    input:
+        plot="OUTPUT_FILES/results/plot.png",
+    localrule: True
+
+rule generate_mesh:
+    input:
+        "Par_File",
+    output:
+        database="OUTPUT_FILES/database.bin",
+        stations="OUTPUT_FILES/STATIONS",
+    localrule: True
+    shell:
+        """
+            mkdir -p OUTPUT_FILES
+            {MESHFEM_BIN} -p {input}
+        """
+
+rule generate_line_sources:
+    input:
+        jinja_file = "line_sources.yaml.j2",
+        jinja_variables = "jinja_variables.yaml",
+    output:
+        source_file = "line_sources.yaml",
+    localrule: True
+    run:
+        import jinja2
+        import yaml
+
+        def generate_sources():
+            # read jinja2 variables yaml file
+            with open(input.jinja_variables, 'r') as f:
+                jinja_vars = yaml.safe_load(f)
+
+            with open(input.jinja_file, 'r') as f:
+                template = jinja2.Template(f.read())
+
+            variables = jinja_vars['variables']
+            with open(output.source_file, 'w') as f:
+                f.write(template.render(variables))
+
+        generate_sources()
+
+rule run_simulation:
+    input:
+        database="OUTPUT_FILES/database.bin",
+        stations="OUTPUT_FILES/STATIONS",
+        line_sources="line_sources.yaml",
+        specfem_config="specfem_config.yaml",
+    output:
+        pressure_siesmograms=expand(
+            "OUTPUT_FILES/results/{station_name}{network_name}{component}.semp",
+            station_name=[
+                "S0001",
+                "S0002",
+            ],
+            network_name=["AA"],
+            component=["PRE"],
+        ),
+    resources:
+        nodes=1,
+        tasks=1,
+        cpus_per_task=1,
+        runtime=40,
+    shell:
+        """
+            module purge
+            module load boost/1.73.0
+            mkdir -p OUTPUT_FILES/results
+            mkdir -p OUTPUT_FILES/display
+            echo "Hostname: $(hostname)" > output.log
+            {SPECFEM_BIN} -p {input.specfem_config} >> output.log
+        """
+
+rule plot_seismogram:
+    input:
+        pressure_siesmograms=expand(
+            "OUTPUT_FILES/results/{station_name}{network_name}{component}.semp",
+            station_name=[
+                "S0001",
+                "S0002",
+            ],
+            network_name=["AA"],
+            component=["PRE"],
+        ),
+    output:
+        traces="OUTPUT_FILES/results/plot.png",
+    localrule: True
+    run:
+        import glob
+        import os
+        import numpy as np
+        import obspy
+
+        # Set matplotlib gui off
+        import matplotlib
+        matplotlib.use("Agg")
+
+        def get_traces(directory):
+            traces = []
+            files = glob.glob(directory + "/*.sem*")
+            ## iterate over all seismograms
+            for filename in files:
+                station_name = os.path.splitext(filename)[0]
+                station_name = station_name.split("/")[-1]
+                trace = np.loadtxt(filename, delimiter=" ")
+                starttime = trace[0, 0]
+                dt = trace[1, 0] - trace[0, 0]
+                traces.append(
+                    obspy.Trace(
+                        trace[:, 1],
+                        {"network": station_name, "starttime": starttime, "delta": dt},
+                    )
+                )
+
+            stream = obspy.Stream(traces)
+
+            return stream
+
+
+        stream = get_traces("OUTPUT_FILES/results")
+        stream.plot(size=(800, 1000)).savefig(output.traces)
+
+rule clean:
+    localrule: True
+    shell:
+        """
+            rm -rf OUTPUT_FILES
+            rm -f line_sources.yaml
+        """

examples/fluid-solid-bathymetry/jinja_variables.yaml

@@ -0,0 +1,4 @@
+
+variables:
+  number_of_sources_x: 197
+  number_of_sources_z: 37