Generate required files for examples/Tromp2005 from CMake

examples/Tromp_2005/.gitignore

@@ -3,9 +3,6 @@ OUTPUT_FILES/*
 *.semd
 *.adj
 Par_File
-Snakefile
 *.pyc
-forward_source.yaml
 forward_config.yaml
-adjoint_source.yaml
 adjoint_config.yaml

examples/Tromp_2005/templates/specfem_config.yaml → examples/Tromp_2005/CMakeFiles/adjoint_config.yaml.in

@@ -1,40 +1,52 @@
 parameters:
-
+  databases:
+    mesh-database: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/database.bin"
+    source-file: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/adjoint_source.yaml"
   header:
-    title: "Tromp-Tape-Liu (GJI 2005)"
-    description: |
-      Material systems : Elastic domain (1)
+    description: 'Material systems : Elastic domain (1)
+
       Interfaces : None
+
       Sources : Force source (1)
+
       Boundary conditions : Free surface (1)
+
       Mesh : 2D Cartesian grid (1)
+
       Receiver : Displacement seismogram (1)
+
       Output : Wavefield at the last time step (1)
+
       Output : Seismograms in ASCII format (1)
 
+      '
+    title: Tromp-Tape-Liu (GJI 2005)
+  receivers:
+    angle: 0.0
+    nstep_between_samples: 1
+    seismogram-type:
+    - displacement
+    stations-file: placeholder/for/path/to/STATIONS
+  run-setup:
+    number-of-processors: 1
+    number-of-runs: 1
   simulation-setup:
     quadrature:
       quadrature-type: GLL4
-
+    simulation-mode:
+      combined:
+        reader:
+          wavefield:
+            directory: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES"
+            format: HDF5
+        writer:
+          kernels:
+            directory: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES"
+            format: ASCII
     solver:
       time-marching:
         time-scheme:
-          type: Newmark
           dt: 0.02
           nstep: 2004
           t0: 8.0
-
-  receivers:
-    stations-file: placeholder/for/path/to/STATIONS
-    angle: 0.0
-    seismogram-type:
-      - displacement
-    nstep_between_samples: 1
-
-  run-setup:
-    number-of-processors: 1
-    number-of-runs: 1
-
-  databases:
-    mesh-database: placeholder/for/path/to/database.bin
-    source-file: placeholder/for/path/to/source.yaml
+          type: Newmark

examples/Tromp_2005/CMakeFiles/forward_config.yaml.in

@@ -0,0 +1,51 @@
+parameters:
+  databases:
+    mesh-database: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/database.bin"
+    source-file: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/forward_source.yaml"
+  header:
+    description: 'Material systems : Elastic domain (1)
+
+      Interfaces : None
+
+      Sources : Force source (1)
+
+      Boundary conditions : Free surface (1)
+
+      Mesh : 2D Cartesian grid (1)
+
+      Receiver : Displacement seismogram (1)
+
+      Output : Wavefield at the last time step (1)
+
+      Output : Seismograms in ASCII format (1)
+
+      '
+    title: Tromp-Tape-Liu (GJI 2005)
+  receivers:
+    angle: 0.0
+    nstep_between_samples: 1
+    seismogram-type:
+    - displacement
+    stations-file: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/STATIONS"
+  run-setup:
+    number-of-processors: 1
+    number-of-runs: 1
+  simulation-setup:
+    quadrature:
+      quadrature-type: GLL4
+    simulation-mode:
+      forward:
+        writer:
+          seismogram:
+            directory: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/results"
+            format: ASCII
+          wavefield:
+            directory: "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES"
+            format: HDF5
+    solver:
+      time-marching:
+        time-scheme:
+          dt: 0.02
+          nstep: 2004
+          t0: 8.0
+          type: Newmark

examples/Tromp_2005/CMakeLists.txt

@@ -2,4 +2,5 @@
 CMAKE_MINIMUM_REQUIRED(VERSION 3.17.5)
 
 configure_file(CMakeFiles/Par_File.in ${CMAKE_SOURCE_DIR}/examples/Tromp_2005/Par_File)
-configure_file(CMakeFiles/Snakefile.in ${CMAKE_SOURCE_DIR}/examples/Tromp_2005/Snakefile)
+configure_file(CMakeFiles/forward_config.yaml.in ${CMAKE_SOURCE_DIR}/examples/Tromp_2005/forward_config.yaml)
+configure_file(CMakeFiles/adjoint_config.yaml.in ${CMAKE_SOURCE_DIR}/examples/Tromp_2005/adjoint_config.yaml)

examples/Tromp_2005/Snakefile

@@ -0,0 +1,126 @@
+SPECFEM_BIN = "specfem2d"
+MESHFEM_BIN = "xmeshfem2D"
+ADJ_SEISMOGRAM_BIN = "xadj_seismogram"
+
+
+rule all:
+    input:
+        kernels="OUTPUT_FILES/Kernels.png",
+
+
+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 forward_simulation:
+    input:
+        database="OUTPUT_FILES/database.bin",
+        stations="OUTPUT_FILES/STATIONS",
+        source="forward_source.yaml",
+        config="forward_config.yaml",
+    output:
+        siesmograms=expand(
+            "OUTPUT_FILES/results/{station_name}{network_name}{component}.semd",
+            station_name=["S0001"],
+            network_name=["AA"],
+            component=["BXX", "BXZ"],
+        ),
+        forward_wavefield="OUTPUT_FILES/ForwardWavefield.h5",
+    resources:
+        nodes=1,
+        tasks=1,
+        cpus_per_task=1,
+        runtime=10,
+    shell:
+        """
+            # module purge
+            # module load boost/1.73.0
+            mkdir -p OUTPUT_FILES/results
+            echo "Hostname: $(hostname)" > output.log
+            {SPECFEM_BIN} -p {input.config} >> output.log
+        """
+
+
+rule compute_adjoint_sources:
+    input:
+        seismograms=expand(
+            "OUTPUT_FILES/results/{station_name}{network_name}{component}.semd",
+            station_name=["S0001"],
+            network_name=["AA"],
+            component=["BXX", "BXZ"],
+        ),
+    output:
+        adjoint_sources=expand(
+            "adjoint_sources/{station_name}{network_name}.{component}.adj",
+            station_name=["S0001"],
+            network_name=["AA"],
+            component=["BXX", "BXZ"],
+        ),
+    shell:
+        """
+            mkdir -p adjoint_sources
+            echo "Hostname: $(hostname)" > output.log
+            {ADJ_SEISMOGRAM_BIN} 27.0 32.0 S0001AA OUTPUT_FILES/results/ adjoint_sources/ 1
+        """
+
+
+rule adjoint_simulation:
+    input:
+        database="OUTPUT_FILES/database.bin",
+        stations="OUTPUT_FILES/STATIONS",
+        source="adjoint_source.yaml",
+        config="adjoint_config.yaml",
+        adjoint_sources=expand(
+            "adjoint_sources/{station_name}{network_name}.{component}.adj",
+            station_name=["S0001"],
+            network_name=["AA"],
+            component=["BXX", "BXZ"],
+        ),
+    output:
+        kernels=directory("OUTPUT_FILES/Kernels"),
+    resources:
+        nodes=1,
+        tasks=1,
+        cpus_per_task=1,
+        runtime=10,
+    shell:
+        """
+            # module purge
+            # module load boost/1.73.0
+            mkdir -p OUTPUT_FILES/results
+            echo "Hostname: $(hostname)" > output.log
+            {SPECFEM_BIN} -p {input.config} >> output.log
+        """
+
+
+rule plot_kernels:
+    input:
+        kernels="OUTPUT_FILES/Kernels",
+        plot_script="plot.py",
+    output:
+        plot="OUTPUT_FILES/Kernels.png",
+    run:
+        from plot import plot_kernels
+
+        # Set matplotlib gui off
+        import matplotlib
+        matplotlib.use("Agg")
+
+        plot_kernels(input.kernels, output.plot)
+
+
+rule clean:
+    shell:
+        """
+            rm -rf OUTPUT_FILES adjoint_sources
+        """

examples/Tromp_2005/adjoint_source.yaml

@@ -0,0 +1,27 @@
+number-of-sources: 2
+sources:
+- force:
+    Ricker:
+      f0: 0.42
+      factor: 7500000000.0
+      tshift: 0.0
+    angle: 270.0
+    source_surf: false
+    vx: 0.0
+    vz: 0.0
+    x: 50000
+    z: 40000
+- adjoint-source:
+    External:
+      format: ASCII
+      stf:
+        X-component: adjoint_sources/S0001AA.BXX.adj
+        Z-component: adjoint_sources/S0001AA.BXZ.adj
+    angle: 0.0
+    network_name: S0001
+    source-surf: false
+    station_name: AA
+    vx: 0.0
+    vz: 0.0
+    x: 150000.0
+    z: 40000.0

examples/Tromp_2005/CMakeFiles/Snakefile.in → examples/Tromp_2005/examples/Tromp_2005/Snakefile

@@ -40,11 +40,11 @@ rule forward_configuration:
                             "writer": {
                                 "wavefield": {
                                     "format": "HDF5",
-                                    "directory": "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES",
+                                    "directory": "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES",
                                 },
                                 "seismogram": {
                                     "format": "ASCII",
-                                    "directory": "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/results",
+                                    "directory": "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES/results",
                                 },
                             }
                         }
@@ -56,9 +56,9 @@ rule forward_configuration:
 
             ## Add forward node to the simulation setup
         config["parameters"]["simulation-setup"].update(forward)
-        config["parameters"]["databases"]["source-file"] = "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/forward_source.yaml"
-        config["parameters"]["receivers"]["stations-file"] = "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/STATIONS"
-        config["parameters"]["databases"]["mesh-database"] = "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/database.bin"
+        config["parameters"]["databases"]["source-file"] = "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/forward_source.yaml"
+        config["parameters"]["receivers"]["stations-file"] = "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES/STATIONS"
+        config["parameters"]["databases"]["mesh-database"] = "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES/database.bin"
 
         with open(output.config, "w") as f:
             yaml.safe_dump(config, f)
@@ -140,13 +140,13 @@ rule adjoint_configuration:
                             "writer": {
                                 "kernels": {
                                     "format": "ASCII",
-                                    "directory": "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES",
+                                    "directory": "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES",
                                 }
                             },
                             "reader": {
                                 "wavefield": {
                                     "format": "HDF5",
-                                    "directory": "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES",
+                                    "directory": "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES",
                                 }
                             },
                         }
@@ -158,8 +158,8 @@ rule adjoint_configuration:
 
             ## Add adjoint node to the simulation setup
         config["parameters"]["simulation-setup"].update(adjoint)
-        config["parameters"]["databases"]["source-file"] = "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/adjoint_source.yaml"
-        config["parameters"]["databases"]["mesh-database"] = "@CMAKE_SOURCE_DIR@/examples/Tromp_2005/OUTPUT_FILES/database.bin"
+        config["parameters"]["databases"]["source-file"] = "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/adjoint_source.yaml"
+        config["parameters"]["databases"]["mesh-database"] = "/Users/ccui/Documents/SPECFEMPP/examples/Tromp_2005/examples/Tromp_2005/OUTPUT_FILES/database.bin"
 
         with open(output.config, "w") as f:
             yaml.safe_dump(config, f)

examples/Tromp_2005/forward_source.yaml

@@ -0,0 +1,13 @@
+number-of-sources: 1
+sources:
+- force:
+    Ricker:
+      f0: 0.42
+      factor: 7500000000.0
+      tshift: 0.0
+    angle: 270.0
+    source_surf: false
+    vx: 0.0
+    vz: 0.0
+    x: 50000
+    z: 40000