Merge pull request #102 from PrincetonUniversity/devel

Added comments to parameter files

.jenkins/regression_tests.gvy

@@ -36,7 +36,8 @@ pipeline {
                                     steps {
                                         echo " Building SPECFEM "
                                         sh """
-                                            cmake -S . -B build_cpu -DCMAKE_BUILD_TYPE=Release
+                                            module load boost/1.73.0
+                                            cmake -S . -B build_cpu -DCMAKE_BUILD_TYPE=Release -D BUILD_TESTS=ON
                                             cmake3 --build build_cpu
                                         """
                                     }
@@ -48,7 +49,7 @@ pipeline {
                                         sh """
                                             module load cudatoolkit/11.7
                                             module load boost/1.73.0
-                                            cmake -S . -B build_gpu -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_CUDA=ON -DKokkos_ARCH_AMPERE80=ON -DKokkos_ENABLE_OPENMP=ON
+                                            cmake -S . -B build_gpu -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_CUDA=ON -DKokkos_ARCH_AMPERE80=ON -DKokkos_ENABLE_OPENMP=ON -D BUILD_TESTS=ON
                                             cmake3 --build build_gpu
                                         """
                                     }
@@ -146,7 +147,7 @@ pipeline {
                 stage (' Checkout main branch '){
                     steps {
                         checkout([$class: 'GitSCM',
-                                branches: [[name: 'code-along']],
+                                branches: [[name: 'main']],
                                 extensions: [lfs()],
                                 userRemoteConfigs: [[url: 'https://github.com/PrincetonUniversity/specfempp']]])
                     }
@@ -168,7 +169,8 @@ pipeline {
                                     steps {
                                         echo " Building SPECFEM "
                                         sh """
-                                            cmake -S . -B build_cpu -DCMAKE_BUILD_TYPE=Release
+                                            module load boost/1.73.0
+                                            cmake -S . -B build_cpu -DCMAKE_BUILD_TYPE=Release -D BUILD_TESTS=ON
                                             cmake3 --build build_cpu
                                         """
                                     }
@@ -180,7 +182,7 @@ pipeline {
                                         sh """
                                             module load cudatoolkit/11.7
                                             module load boost/1.73.0
-                                            cmake -S . -B build_gpu -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_CUDA=ON -DKokkos_ARCH_AMPERE80=ON -DKokkos_ENABLE_OPENMP=ON
+                                            cmake -S . -B build_gpu -DCMAKE_BUILD_TYPE=Release -DKokkos_ENABLE_CUDA=ON -DKokkos_ARCH_AMPERE80=ON -DKokkos_ENABLE_OPENMP=ON -D BUILD_TESTS=ON
                                             cmake3 --build build_gpu
                                         """
                                     }

examples/fluid-solid-interface/sources.yaml

@@ -1,13 +1,13 @@
 number-of-sources: 1
 sources:
   - force:
-      x : 1575.0
-      z : 2900.0
-      source_surf: false
-      angle : 0.0
-      vx : 0.0
-      vz : 0.0
+      x : 1575.0 # (meters)
+      z : 2900.0 # (meters)
+      source_surf: false # Place the source at the surface (true)
+      angle : 0.0 # (degrees)
+      vx : 0.0 # (m/s)
+      vz : 0.0 # (m/s)
       Ricker:
         factor: 1e9
-        tshift: 0.0
-        f0: 10.0
+        tshift: 0.0 # (seconds)
+        f0: 10.0 # (Hz)

examples/fluid-solid-interface/specfem_config.yaml.in

@@ -13,38 +13,40 @@ parameters:
   simulation-setup:
     ## quadrature setup
     quadrature:
-      alpha: 0.0
-      beta: 0.0
-      ngllx: 5
-      ngllz: 5
+      quadrature-type: GLL4 # fourth order Gauss-Lobatto-Legendre quadrature (5 GLL points)
 
     ## Solver setup
     solver:
       time-marching:
-        type-of-simulation: forward
+        type-of-simulation: forward # forward simulation (adjoint simulation is not supported yet)
         time-scheme:
-          type: Newmark
-          dt: 0.85e-3
-          nstep: 800
+          type: Newmark # Newmark time integration scheme
+          dt: 0.85e-3 # (seconds)
+          nstep: 800 # number of time steps
 
   receivers:
     stations-file: "@CMAKE_SOURCE_DIR@/examples/fluid_solid_interface/OUTPUT_FILES/STATIONS"
-    angle: 0.0
+    angle: 0.0 # angle of the receiver line (degrees)
     seismogram-type:
       - displacement
       - velocity
-    nstep_between_samples: 1
+    nstep_between_samples: 1 # number of time steps between seismogram samples (sampling rate = dt * nstep_between_samples)
+                             # seismograms are only written to disk at the end of the simulation
 
   ## Runtime setup
   run-setup:
-    number-of-processors: 1
-    number-of-runs: 1
+    # only single MPI processor is supported at the moment
+    number-of-processors: 1 # number of MPI processors
+    number-of-runs: 1 # number of concurrent runs (only single run is supported at the moment)
 
   ## databases
   databases:
+    # Database files are generated by the meshing tool (xmeshfem2D)
     mesh-database: "@CMAKE_SOURCE_DIR@/examples/fluid-solid-interface/OUTPUT_FILES/database.bin"
+    # YAML file describing the sources See examples/fluid-solid-interface/sources.yaml for details
     source-file: "@CMAKE_SOURCE_DIR@/examples/fluid-solid-interface/sources.yaml"
 
   seismogram:
-    seismogram-format: ascii
-    output-folder: "."
+    # seismogram output format
+    seismogram-format: ascii # ascii (text) - Only ascii format is supported at the moment
+    output-folder: "." # output folder for seismograms