update to v0.9

.github/workflows/deploys.yml

@@ -0,0 +1,50 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    branches: [devel]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Install doc tools
+        run: |
+          sudo apt install -y doxygen
+          pip install sphinx myst-parser sphinx_rtd_theme 
+
+      - name: Build libaries
+        run: |
+          sudo apt install cmake build-essential gfortran liblapack-dev liblapacke-dev 
+          wget https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
+          tar -xvf eigen-3.4.0.tar.gz
+          pip install pybind11-global
+          mkdir -p build
+          cd build 
+          cmake .. -DCXX=g++ -DFC=gfortran -DEIGEN_INC=./eigen-3.4.0/  -DBUILD_LIBS=ON  -DPython3_EXECUTABLE=`which python`
+          make -j4 
+          make install
+          cd ..
+
+
+      - name: Build Doxygen C++ API Docs
+        run: doxygen misc/doxygen/doxygen.cfg 
+
+      - name: Build Python docs (Sphinx)
+        run: |
+          sphinx-apidoc -o misc/source/python ./specd
+
+      - name: Build master docs (Sphinx)
+        run: |
+          pip install numpy scipy
+           sphinx-build -b html misc/source docs
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs

.vscode/c_cpp_properties.json

@@ -1,16 +1,17 @@
 {
     "configurations": [
         {
-            "name": "MACOS",
+            "name": "LINUX",
             "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"
             ],
             "compilerPath": "/usr/bin/g++",
             "cStandard": "gnu17",
-            "cppStandard": "gnu++14",
+            "cppStandard": "gnu++17",
             "intelliSenseMode": "linux-gcc-x64"
         }
     ],

.vscode/launch.json

@@ -5,10 +5,12 @@
             "name": "(lldb) Launch",
             "type": "cppdbg",
             "request": "launch",
-            "program": "${workspaceFolder}/bin/surfvti_ac",
-            "args": ["model.txt","0.01","0.5","100"],
+            "program": "${workspaceFolder}/bin/surfrayl",
+            "args": ["model.txt","0.01","1","1"],
+            "cwd": "${workspaceFolder}/example/rayleigh",
             "stopAtEntry": false,
-            "cwd": "${workspaceFolder}/example/ac",
+            // "program": "${workspaceFolder}/a.out",
+            // "cwd": "${workspaceFolder}",
             "environment": [],
             "externalConsole": false,
             "MIMode": "lldb"

.vscode/settings.json

@@ -116,4 +116,5 @@
         "eigenvalues": "cpp"
     },
     //"C_Cpp.errorSquiggles": "disabled"
+    "fortran.linter.includePaths": ["/opt/homebrew/Cellar/open-mpi/5.0.7/include"]
 }

CMakeLists.txt

@@ -1,6 +1,6 @@
 #  CMakeLists.txt
 
-cmake_minimum_required(VERSION 3.13.0)
+cmake_minimum_required(VERSION 3.25.0)
 
 ################## compiler options ##################
 # compiler
@@ -13,8 +13,8 @@ set(CMAKE_CXX_FLAGS             ${CXXFLAGS})
 ################## dependencies ##################
 # preferred installation prefix of dependencies
 set(EIGEN_INC                 ${EIGEN_INC})
-set(USE_LAPACK             ${USE_LAPACK}) 
-set(BUILD_PYLIB             ${BUILD_PYLIB})
+
+option(BUILD_LIBS "BUILD_LIBS" OFF)
 
 
 # set default values
@@ -24,59 +24,61 @@ set(${var} ${val})
 endif()
 endmacro()
 setDefault(EIGEN_INC   "~/software/eigen-3.4.0")
-setDefault(USE_LAPACK FALSE)
-setDefault(BUILD_PYLIB FALSE)
 
 # project
 project(SWDTTI LANGUAGES CXX Fortran)
 
 # build type 
 set(CMAKE_BUILD_TYPE RELEASE)
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/build/obj)
 
 ################# cmake setup #################
-set(CMAKE_CXX_FLAGS  "-g")
+set(CMAKE_CXX_FLAGS  "-g -Wall")
 set(EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/bin)
-if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU") 
-  set(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -march=native -ffast-math")
+if (CMAKE_CXX_COMPILER_ID MATCHES "GNU") 
+  set(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -march=native")
   set(CMAKE_Fortran_FLAGS  "${CMAKE_Fortran_FLAGS} -march=native -ffixed-line-length-none")
-  set(CMAKE_CXX_FLAGS_RELEASE  "-O2")
-elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  #set(CMAKE_CXX_FLAGS_RELEASE  "-O0 -D_GLIBCXX_DEBUG")
+elseif (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
   set(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -xHost -DEIGEN_STRONG_INLINE=inline")
   set(CMAKE_Fortran_FLAGS  "${CMAKE_Fortran_FLAGS} -xHost -extend-source")
+else ()
+  set(CMAKE_Fortran_FLAGS  "${CMAKE_Fortran_FLAGS} -march=native -ffixed-line-length-none")
+  #set(CMAKE_CXX_FLAGS_RELEASE  "-O0 -D_GLIBCXX_DEBUG")
+  set(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -march=native")
 endif()
 
-set(CMAKE_VERBOSE_MAKEFILE off)
+set(CMAKE_VERBOSE_MAKEFILE on)
 
 ################# find packages #################
 # path of *.cmake files
-set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/include/cmake)
+#set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/include/cmake)
 
 # eigen
 include_directories(${EIGEN_INC})
 
 # lapack
-if(${USE_LAPACK})
-  find_package(LAPACK)
-  set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -DEIGEN_USE_LAPACKE")
-endif()
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+find_package(LAPACK REQUIRED)
+find_package(LAPACKE REQUIRED)
+set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -DEIGEN_USE_LAPACKE")
 
 ################# include paths #################
 include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/include)
+#include_directories(${PROJECT_SOURCE_DIR}/include)
 
 # subs
 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(${PROJECT_SOURCE_DIR}/src/multiphysics)
+# add_subdirectory(${PROJECT_SOURCE_DIR}/src/tti)
+# add_subdirectory(${PROJECT_SOURCE_DIR}/src/multiphysics)
 
-# check build pylib
-if(${BUILD_PYLIB}) 
-  #find_package(pybind11 REQUIRED)
-  find_package(Python COMPONENTS Interpreter Development)
+# check build libraries
+if(BUILD_LIBS) 
+  find_package(Python3 COMPONENTS Interpreter Development)
   find_package(pybind11 CONFIG)
   add_subdirectory(src/cps330)
   add_subdirectory(src/libswd)

README.md

@@ -1,39 +1,6 @@
-# SPECSWD
-**SpecSWD** utilizes spectral element method and quadratic eigenvalue solver to compute surface wave dispersion, eigen function and sensitivity kernels for **general layered models**.
+# 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.  
 
-It can handle dispersion values for several type of complex media, such as VTI, TTI(Tilted Transversely Isotropic), acoustic-VTI coupling, and at any frequency, and any mode. And it can support both 1-D layered
-model (1-D model with discontinuities) and gradient model (continous variation in both fluid and elastic domain).
-
-## Requirements and Installation
-1. **Compilers:** C++/Fortran compilers which support c++14 (tested on `GCC >=7.5`), `cmake >= 3.12`
-
-2. packages:
-* [Eigen](https://eigen.tuxfamily.org/index.php?title=Main_Page) >= 3.4.0
-* [MKL/LAPACK](https://www.netlib.org/lapack/lapacke.html), optional.
-* [doxygen](https://www.doxygen.nl/) for api document generation, optional.
-
-3. Install:
-```bash
-mkdir -p build; cd build;
-cmake .. -DCXX=g++ -DFC=gfortran  -DEIGEN_INC=/path/to/eigen/ -DUSE_LAPACK=FALSE
-make -j4; make install 
-```
-If you want to use `LAPACKE/MKL`, you can set `-DUSE_LAPACK=TRUE`. This program also provides python libraries (`.so`) and you can install them by adding ```-DBUILD_PYLIB=TRUE -DPYTHON_EXECUTABLE=`which python` ```
-
-4. install API docs
-```bash
-cd doxygen
-doxygen config.cfg
-```
-
-# Gallery
-### Benchmark: SWDTTI with CPS330
-![image](example//rayleigh/phase.jpg)
-### HTI model: Phase velocity vs. Azimuthal angle
-![image](example/tti/group-direc.jpg)
-
-### Fluid-Elastic Coupling phase and group velocity
-![image](example/ac/phase.jpg)
-![image](example/ac/group.jpg)
-### Acoustic 
+**SpecSWD** also provides high-level sensitivity analysis framework (adjoint methods) for any user-defined quantities.
 
+For installation, user manual, please refer to [docs](https://nqdu.github.io/SpecSWD/).

bak/src.bak/solver.bak/CMakeLists.txt

@@ -0,0 +1,8 @@
+file(GLOB SOURCE "*.cpp" )
+list(FILTER SOURCE EXCLUDE REGEX "main*.cpp")
+
+add_library(libsolver ${SOURCE})
+
+
+add_executable(surflove ${PROJECT_SOURCE_DIR}/src/solver/main_love.cpp)
+target_link_libraries(surflove libsolver shared ${LAPACK_LIBRARIES})