Thm segregate

.circleci/config.yml

@@ -3,7 +3,7 @@ jobs:
   build:
     working_directory: /home/cbgeo/research/mpm
     docker:
-      - image: quay.io/cbgeo/mpm
+      - image: quay.io/cbgeo/thm
     steps:
       - checkout
       # GCC-8
@@ -17,7 +17,7 @@ jobs:
             export MODULEPATH=$MODULEPATH:/usr/share/modulefiles
             module load mpi/openmpi-x86_64
             export CXX_COMPILER=mpicxx
-            cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_EXPORT_COMPILE_COMMANDS=On ..
+            cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_EXPORT_COMPILE_COMMANDS=On -DDEAL_II_DIR=/home/cbgeo/research/dealii/ ..
             make -j2
             ctest -VV
       # Clang-6.0
@@ -27,7 +27,7 @@ jobs:
             mkdir -p build
             [ "$(ls -A build)" ] && rm -rf build/*
             cd build
-            scan-build cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_EXPORT_COMPILE_COMMANDS=On ..
+            scan-build cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_EXPORT_COMPILE_COMMANDS=On -DDEAL_II_DIR=/home/cbgeo/research/dealii/ ..
             scan-build make -j2 
             ctest -VV
       # cppcheck
@@ -40,17 +40,4 @@ jobs:
       - run:
           name: clang-format
           command: |
-            python3 ./clang-tools/run-clang-format.py -r include/* src/* tests/*
-      # codecoverage
-      - run:
-          name: codecov.io
-          command: |
-            mkdir -p build
-            [ "$(ls -A build)" ] && rm -rf build/*
-            cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ -DCMAKE_EXPORT_COMPILE_COMMANDS=On -DENABLE_COVERAGE=On ..
-            make mpmtest_coverage -j2
-            ./mpmtest_coverage
-            make gcov -j2  --ignore-errors
-            make lcov
-            bash <(curl -s https://codecov.io/bash) -X gcov
+            python3 ./clang-tools/run-clang-format.py -r include/* src/*

.clang-format

@@ -0,0 +1,47 @@
+---
+# BasedOnStyle:  CUED GeoMechanics
+AccessModifierOffset: -1
+ConstructorInitializerIndentWidth: 4
+AlignEscapedNewlinesLeft: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakTemplateDeclarations: true
+AlwaysBreakBeforeMultilineStrings: true
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BinPackParameters: true
+ColumnLimit:     80
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+DerivePointerBinding: false
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: true
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 60
+PenaltyBreakString: 1000
+PenaltyBreakFirstLessLess: 120
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerBindsToType: true
+SpacesBeforeTrailingComments: 2
+Cpp11BracedListStyle: true
+Standard:        Auto
+IndentWidth:     2
+TabWidth:        8
+UseTab:          Never
+BreakBeforeBraces: Attach
+IndentFunctionDeclarationAfterType: true
+SpacesInParentheses: false
+SpacesInAngles:  false
+SpaceInEmptyParentheses: false
+SpacesInCStyleCastParentheses: false
+SpaceAfterControlStatementKeyword: true
+SpaceBeforeAssignmentOperators: true
+ContinuationIndentWidth: 4
+...
+

.gitignore

@@ -59,3 +59,11 @@ configure.scan
 *missing
 *stamp-h1
 benchmarks/
+build/*
+*copy*
+*.geo*
+*.db*
+*.nas*
+*.vscode/*
+grid-1.eps
+outputfiles/*

CMakeLists.txt

@@ -1,4 +1,6 @@
-project(thm LANGUAGES CXX)
+#project(thm LANGUAGES CXX)
+# Set the name of the project and target:
+SET(TARGET "thm")
 
 # Require C++14-compliant compiler; only available for CMake v3.10 and up
 set(CMAKE_CXX_STANDARD 14)
@@ -33,25 +35,58 @@ endif()
 # so we provide an option similar to BUILD_TESTING, but just for THM.
 option(THM_BUILD_TESTING "enable testing for thm" ON)
 
+# Add -O0 to remove optimizations when using gcc
+# IF(CMAKE_COMPILER_IS_GNUCC)
+  SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
+  SET(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
+# ENDIF(CMAKE_COMPILER_IS_GNUCC)
+
 # CMake Modules
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
+# Dealii
+FIND_PACKAGE(deal.II 8.5.0 QUIET
+  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
+  )
+if(NOT ${deal.II_FOUND})
+  MESSAGE(FATAL_ERROR "\n"
+    "*** Could not locate a (sufficiently recent) version of deal.II. ***\n\n"
+    "You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake\n"
+    "or set an environment variable \"DEAL_II_DIR\" that contains this path."
+    )
+endif()
+
+if (${deal.II_FOUND})
+  include_directories(${DEAL_II_DIR}/include/)
+endif()
+
+#thm executable
+SET(thm_src
+  ./src/main.cc
+  ./src/get_parameter.cc
+  ./src/interpolation1d.cc
+  ./src/linspace.cc
+)
 
+# aux_source_directory(./src/ thm_src)
 
 # Include directories
-include_directories(BEFORE
-  ${thm_SOURCE_DIR}/include/
-  ${thm_SOURCE_DIR}/external/
+include_directories(
+  ./include/
+  ./external/
+
 )
 
-# thm executable
-#SET(thm_src
-#  ${thm_SOURCE_DIR}/src/thm.cc
-#)
+SET(TARGET_SRC ${thm_src})
+
+DEAL_II_INITIALIZE_CACHED_VARIABLES()
+PROJECT(${TARGET})
+DEAL_II_INVOKE_AUTOPILOT()
+
 
 #add_library(lthm SHARED ${thm_src})
 
-add_executable(thm ${thm_SOURCE_DIR}/src/main.cc)
+# add_executable(geothm ${thm_SOURCE_DIR}/src/main.cc)
 #target_link_libraries(thm lthm)
 
 # Unit test

clang-tools/format.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 find ../include/ -iname *.h -o -iname *.tcc | xargs clang-format -i
 find ../src/ -iname *.h -o -iname *.cc | xargs clang-format -i
-find ../tests/ -iname *.h -o -iname *.cc | xargs clang-format -i
+#find ../tests/ -iname *.h -o -iname *.cc | xargs clang-format -i