Devel

.gitignore

@@ -0,0 +1,62 @@
+# Compiled object files
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Static libraries
+*.lib
+*.a
+
+# Compiled Dynamic libraries
+*.dll
+*.so
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Fortran module files
+*.mod
+*.smod
+
+# Debug files
+*.dSYM/
+*.stackdump
+
+# Build directories
+/build/
+/bin/
+/lib/
+/CMakeFiles/
+/cmake-build-*/
+
+/EXAMPLES/*/OUTPUT_FILES/
+
+# CMake generated files
+CMakeCache.txt
+CMakeFiles/
+Makefile
+cmake_install.cmake
+CTestTestfile.cmake
+install_manifest.txt
+
+# IDE files
+*.swp
+*.swo
+*.user
+*.workspace
+*.project
+*.idea/
+.vscode/
+
+# Logs
+*.log
+
+# OS generated files
+.DS_Store
+Thumbs.db

.vscode/c_cpp_properties.json

@@ -1,13 +1,13 @@
 {
     "configurations": [
         {
-            "name": "LINUX",
+            "name": "macOS",
             "includePath": [
                 "${workspaceFolder}/**",
                 "~/software/eigen-3.4.0",
-                "/opt/homebrew/Cellar/open-mpi/5.0.7/include",
-                "/Users/nqdu/software/miniconda3/include/python3.11",
-                "/Users/nqdu/software/miniconda3/lib/python3.11/site-packages/pybind11/include"
+                "/opt/homebrew/Cellar/open-mpi/5.0.8/include",
+                "/Users/nqdu/software/miniconda3/include/python3.12",
+                "/Users/nqdu/software/miniconda3/lib/python3.12/site-packages/pybind11/include"
             ],
             "compilerPath": "/usr/bin/g++",
             "cStandard": "gnu17",

.vscode/launch.json

@@ -1,17 +1,20 @@
 {
     "version": "0.2.0",
     "configurations": [
-      {
-        "name": "Python + LLDB",
-        "type":"debugpy",
-        "request": "launch",
-        "program": "${workspaceFolder}/example/love1/step0_database.py",
-        "args": ["model.txt", 
-                "1", "1", "1", "0"],
+        {
+            "name": "(lldb) Launch",
+            "type": "cppdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/bin/surfani",
+            "args": ["model.txt","0.01","0.5","100","0"],
+            "cwd": "${workspaceFolder}/example/orthorhombic",
+            "stopAtEntry": false,
+            // "program": "${workspaceFolder}/a.out",
+            // "cwd": "${workspaceFolder}",
+            "environment": [],
+            "externalConsole": false,
+            "MIMode": "lldb"
+        }
 
-        "cwd": "${workspaceFolder}/example/love1",
-        "stopOnEntry": false
-      }
     ]
-  }
-
+}

CMakeLists.txt

@@ -35,7 +35,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/build/obj)
 
 ################# cmake setup #################
-set(CMAKE_CXX_FLAGS  "-g -Wall")
+set(CMAKE_CXX_FLAGS  "-g -Wall -DEIGEN_DONT_PARALLELIZE")
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/bin)
 if (CMAKE_CXX_COMPILER_ID MATCHES "GNU") 
   set(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -march=native")
@@ -53,9 +53,6 @@ endif()
 set(CMAKE_VERBOSE_MAKEFILE on)
 
 ################# find packages #################
-# path of *.cmake files
-#set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/include/cmake)
-
 # eigen
 include_directories(${EIGEN_INC})
 
@@ -65,6 +62,13 @@ find_package(LAPACK REQUIRED)
 find_package(LAPACKE REQUIRED)
 set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -DEIGEN_USE_LAPACKE")
 
+#find_package(OpenMP REQUIRED)
+if (OPENMP_FOUND)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+    include_directories(${OpenMP_CXX_INCLUDE_DIRS})
+endif()
+
 ################# include paths #################
 include_directories(${PROJECT_SOURCE_DIR}/src)
 #include_directories(${PROJECT_SOURCE_DIR}/include)
@@ -73,7 +77,7 @@ include_directories(${PROJECT_SOURCE_DIR}/src)
 add_subdirectory(${PROJECT_SOURCE_DIR}/src/shared)
 add_subdirectory(${PROJECT_SOURCE_DIR}/src/mesh)
 add_subdirectory(${PROJECT_SOURCE_DIR}/src/vti)
-# add_subdirectory(${PROJECT_SOURCE_DIR}/src/tti)
+add_subdirectory(${PROJECT_SOURCE_DIR}/src/aniso)
 # add_subdirectory(${PROJECT_SOURCE_DIR}/src/multiphysics)
 
 # check build libraries

README.md

@@ -1,8 +1,9 @@
 # SpecSWD
-**SpecSWD**  is a software to compute surface wave dispersions and do sensitivity analysis for 1-D fully anisotropic, wealy anelastic media. It utilizes spectral element method and quadratic eigenvalue solver to handle multiphysics (elastic-acoustic coupling), strong anisotropy and discontinuities inside the study region.  
 
-**SpecSWD** also provides high-level sensitivity analysis framework (adjoint methods) for any user-defined quantities.
+**SpecSWD** is a software designed to compute surface wave dispersions and perform sensitivity analysis for 1-D fully anisotropic, weakly anelastic media. It utilizes the spectral element method and a quadratic eigenvalue solver to effectively handle multiphysics (elastic-acoustic coupling), strong anisotropy, and discontinuities within the study region.
 
-For installation, user manual, please refer to [docs](https://nqdu.github.io/SpecSWD/).
+SpecSWD also offers a high-level sensitivity analysis framework (using adjoint methods) for any user-defined quantities.
+
+For installation instructions and the user manual, please refer to the [documentation](https://nqdu.github.io/SpecSWD/).
 
 For theoretical background and implementation details, please refer to this [EarthArXiv link](https://doi.org/10.31223/X57J37).

code_gen/aniso_code_gen.ipynb

@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -130,7 +130,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -142,7 +142,7 @@
        "-2*U*c11*k*cos(phi)**2*conjugate(U) - 2*U*c12*k*sin(phi)*cos(phi)*conjugate(W) + I*U*c13*cos(phi)*conjugate(Vdot) - 2*U*c14*k*sin(phi)*cos(phi)*conjugate(V) + I*U*c14*cos(phi)*conjugate(Wdot) - 2*U*c15*k*cos(phi)**2*conjugate(V) + I*U*c15*cos(phi)*conjugate(Udot) - 4*U*c16*k*sin(phi)*cos(phi)*conjugate(U) - 2*U*c16*k*cos(phi)**2*conjugate(W) - 2*U*c26*k*sin(phi)**2*conjugate(W) + I*U*c36*sin(phi)*conjugate(Vdot) - 2*U*c46*k*sin(phi)**2*conjugate(V) + I*U*c46*sin(phi)*conjugate(Wdot) - 2*U*c56*k*sin(phi)*cos(phi)*conjugate(V) + I*U*c56*sin(phi)*conjugate(Udot) - 2*U*c66*k*sin(phi)**2*conjugate(U) - 2*U*c66*k*sin(phi)*cos(phi)*conjugate(W) - I*Udot*c15*cos(phi)*conjugate(U) - I*Udot*c25*sin(phi)*conjugate(W) - I*Udot*c45*sin(phi)*conjugate(V) - I*Udot*c55*cos(phi)*conjugate(V) - I*Udot*c56*sin(phi)*conjugate(U) - I*Udot*c56*cos(phi)*conjugate(W) - 2*V*c14*k*sin(phi)*cos(phi)*conjugate(U) - 2*V*c15*k*cos(phi)**2*conjugate(U) - 2*V*c24*k*sin(phi)**2*conjugate(W) - 2*V*c25*k*sin(phi)*cos(phi)*conjugate(W) + I*V*c34*sin(phi)*conjugate(Vdot) + I*V*c35*cos(phi)*conjugate(Vdot) - 2*V*c44*k*sin(phi)**2*conjugate(V) + I*V*c44*sin(phi)*conjugate(Wdot) - 4*V*c45*k*sin(phi)*cos(phi)*conjugate(V) + I*V*c45*sin(phi)*conjugate(Udot) + I*V*c45*cos(phi)*conjugate(Wdot) - 2*V*c46*k*sin(phi)**2*conjugate(U) - 2*V*c46*k*sin(phi)*cos(phi)*conjugate(W) - 2*V*c55*k*cos(phi)**2*conjugate(V) + I*V*c55*cos(phi)*conjugate(Udot) - 2*V*c56*k*sin(phi)*cos(phi)*conjugate(U) - 2*V*c56*k*cos(phi)**2*conjugate(W) - I*Vdot*c13*cos(phi)*conjugate(U) - I*Vdot*c23*sin(phi)*conjugate(W) - I*Vdot*c34*sin(phi)*conjugate(V) - I*Vdot*c35*cos(phi)*conjugate(V) - I*Vdot*c36*sin(phi)*conjugate(U) - I*Vdot*c36*cos(phi)*conjugate(W) - 2*W*c12*k*sin(phi)*cos(phi)*conjugate(U) - 2*W*c16*k*cos(phi)**2*conjugate(U) - 2*W*c22*k*sin(phi)**2*conjugate(W) + I*W*c23*sin(phi)*conjugate(Vdot) - 2*W*c24*k*sin(phi)**2*conjugate(V) + I*W*c24*sin(phi)*conjugate(Wdot) - 2*W*c25*k*sin(phi)*cos(phi)*conjugate(V) + I*W*c25*sin(phi)*conjugate(Udot) - 2*W*c26*k*sin(phi)**2*conjugate(U) - 4*W*c26*k*sin(phi)*cos(phi)*conjugate(W) + I*W*c36*cos(phi)*conjugate(Vdot) - 2*W*c46*k*sin(phi)*cos(phi)*conjugate(V) + I*W*c46*cos(phi)*conjugate(Wdot) - 2*W*c56*k*cos(phi)**2*conjugate(V) + I*W*c56*cos(phi)*conjugate(Udot) - 2*W*c66*k*sin(phi)*cos(phi)*conjugate(U) - 2*W*c66*k*cos(phi)**2*conjugate(W) - I*Wdot*c14*cos(phi)*conjugate(U) - I*Wdot*c24*sin(phi)*conjugate(W) - I*Wdot*c44*sin(phi)*conjugate(V) - I*Wdot*c45*cos(phi)*conjugate(V) - I*Wdot*c46*sin(phi)*conjugate(U) - I*Wdot*c46*cos(phi)*conjugate(W)"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -153,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -230,7 +230,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -443,6 +443,13 @@
     "fileid.close()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -453,7 +460,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },
@@ -467,7 +474,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.2"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,