Add new capabilities

- Overhaul source code.
- Overhaul configuration file.
- Overhaul output, now .sim format (compatible with Neper).
- Added parallelized multi-point constraints and periodic boundary conditions.
- Added 2-parameter anisotropic hardening (diagonal + off-diagonal values).
- Generalize code to take arbitrary domain shapes and boundary conditions.
- Added ability for 112-type slip in BCC crystals, added ability to specify
  anisotropic initial slip strengths, improved precipitate strengthening model
  (Orowan looping).
- Made various other changes and improvements.

Author: rquey

.gitignore

@@ -4,7 +4,6 @@
 *.x
 *~
 *.x.dSYM
-*.cp*
 *.fn*
 *.ky*
 *.pg*
@@ -14,17 +13,22 @@
 *.dvi
 *.info
 *.swp
+fort.75
 
 # Ignore FEPX build files
 /lib/libf95/modules
 /lib/libparallel/modules_serial
 /lib/libparallel/modules_parallel
 /src/build/
+/src/build.sim
 /build/
 /doc/build/
 
 # Ignore FEPX post files
+/tests/*/simulation.sim
 post.*
+rst*.*
+FAILED
 
 # Ignore AppleDouble files and Mac .DS_Store files
 ._*
@@ -69,3 +73,6 @@ docs
 
 # Sphinx files
 __pycache__
+
+doxygen
+

CMakeLists.txt

@@ -0,0 +1,218 @@
+# This file is part of the FEPX software package.
+# Copyright (C) 1996-2023, DPLab, ACME Lab.
+# See the COPYING file in the top-level directory.
+
+# Top-level CMakeLists.txt for building FEPX
+cmake_minimum_required(VERSION 3.0)
+project(fepx Fortran)
+set(FEPX_VERSION \"1.3.1-1553-devel\")
+
+# Prepare CMake for Fortran and locate MPI package
+enable_language(Fortran)
+find_package(MPI REQUIRED)
+
+# Set the build type for appropriate compile flags
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build: Debug Release" FORCE)
+endif()
+
+set(BUILD_TESTING_MODE "Normal" CACHE STRING "Choose the testing mode: Normal Minimal Writing")
+set(BUILD_TESTING_DIFF "Exact" CACHE STRING "Choose the testing method: Exact Neper")
+
+# Option for verbose build
+option(VERBOSE "Build verbose Makefiles" OFF)
+if(VERBOSE)
+    set(CMAKE_VERBOSE_MAKEFILE ON)
+else(VERBOSE)
+    set(CMAKE_VERBOSE_MAKEFILE OFF)
+endif(VERBOSE)
+
+# Option to suppress IEEE warnings on program exit
+option(IEEE_SUPPRESS "Suppress IEEE signals on program exit" ON)
+if(IEEE_SUPPRESS)
+    set(CMAKE_Fortran_FLAGS "-ffpe-summary='none'")
+else(IEEE_SUPPRESS)
+    set(CMAKE_Fortran_FLAGS "")
+endif(IEEE_SUPPRESS)
+
+# Code to silence warnings from RANLIB on OSX
+# From https://stackoverflow.com/questions/4929255/building-static-libraries-on-mac-using-cmake-and-gcc
+if (APPLE)
+  SET(CMAKE_Fortran_ARCHIVE_CREATE   "<CMAKE_AR> Scr <TARGET> <LINK_FLAGS> <OBJECTS>")
+  SET(CMAKE_Fortran_ARCHIVE_FINISH   "<CMAKE_RANLIB> -no_warning_for_no_symbols -c <TARGET>")
+endif ()
+
+# Check that this machine supports F90 compilation
+if(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+    message(FATAL_ERROR "Fortran compiler does not support F90")
+endif(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+
+if((${CMAKE_Fortran_COMPILER_ID} MATCHES Intel) OR (${CMAKE_Fortran_COMPILER_ID} MATCHES GNU))
+    message(STATUS "Fortran compiler: ${CMAKE_Fortran_COMPILER}, ${CMAKE_Fortran_COMPILER_ID}")
+else()
+    message(FATAL_ERROR "Unsupported Fortran compiler (use Intel or GNU).")
+endif()
+
+# Set compiler flag options depending on the compiler located
+if(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+    set(CMAKE_Fortran_MODDIR_FLAG   "-J")
+#    set(CMAKE_Fortran_FLAGS         "")
+    set(CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g -fcheck=all -fbacktrace -fbounds-check -Wall")
+    set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ftree-vectorize -funroll-loops")
+# IFORT is currently not supported, but will be in the future
+#ELSEIF(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+#   set(CMAKE_Fortran_MODDIR_FLAG   "")
+#   set(CMAKE_Fortran_FLAGS         "")
+#   set(CMAKE_Fortran_FLAGS_DEBUG   "")
+#   set(CMAKE_Fortran_FLAGS_RELEASE "")
+endif()
+
+# Set directories for CMake to access files
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/mod)
+
+# Preamble info
+STRING(TIMESTAMP CONFIG_DATE "%Y-%m-%d")
+message(STATUS "Configuring Makefiles for the FEPX software package...")
+message(STATUS "Built date: (${CONFIG_DATE})")
+message(STATUS "OS: ${CMAKE_SYSTEM_NAME} ${CMAKE_SYSTEM_VERSION}")
+message(STATUS "Build Type: ${CMAKE_BUILD_TYPE}") # Need to grab input cache here?
+message(STATUS "Version: ${VERSION}")
+
+# configure a header file to pass some of the CMake settings to the
+# source code
+configure_file(
+  "${PROJECT_SOURCE_DIR}/fepx_config.f90.in"
+  "${PROJECT_BINARY_DIR}/fepx_config.f90"
+)
+
+# Add in the subdirectories and includes
+
+file(GLOB fepx
+    ${PROJECT_BINARY_DIR}/fepx_config.f90
+    fepx.f90
+    fepx2.f90
+    read_input/read_input.f90
+    read_input/read_input_cfg.f90
+    read_input/read_input_msh.f90
+    read_input/read_input_msh2.f90
+    read_input/boundary_conditions_mod1.f90
+    read_input/boundary_conditions_mod2.f90
+    read_input/boundary_conditions_mod3.f90
+    read_input/boundary_conditions_mod2_legacy.f90
+    read_input/read_input_mpcs/multi_point_constraints_mod1.f90
+    read_input/read_input_mpcs/multi_point_constraints_mod2.f90
+    general/crys_type_mod.f90
+    general/crys_type_mod2.f90
+    general/crys_type_mod3.f90
+    general/general_mod.f90
+    general/types_mod.f90
+    general/printing_type_mod.f90
+    general/exec_type_mod.f90
+    general/loading_type_mod1.f90
+    general/loading_type_mod2.f90
+    general/loading_options_type_mod.f90
+    general/mesh_type_mod.f90
+    general/utils.f90
+    general/orientation_conversion_mod.f90
+    parallel/gather_scatter_mod.f90
+    parallel/parallel_mod.f90
+    res_init/res_init_mod1.f90
+    res_init/res_init_mod2.f90
+
+    triaxial/driver_triaxclr_mod.f90
+    triaxial/driver_triaxcsr_mod.f90
+    triaxial/driver_triax_utilities_mod.f90
+
+    libfepx/driver_uniaxial_control_mod1.f90
+    libfepx/driver_uniaxial_control_mod2.f90
+
+    libfepx/solveit_isovp/solveit_isovp_mod1.f90
+    libfepx/solveit_isovp/solveit_isovp_mod2.f90
+    libfepx/solveit_isovp/solveit_isovp_mod3.f90
+    libfepx/solveit_isovp/solveit_isovp_mod4.f90
+
+    libfepx/solveit_evp/solveit_evp_mod1.f90
+    libfepx/solveit_evp/solveit_evp_mod2.f90
+    libfepx/solveit_evp/solveit_evp_mod3.f90
+    libfepx/solveit_evp/solveit_evp_mod4.f90
+
+    libfepx/solveit_evp/solve_evp/solve_evp_mod1.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_mod2.f90
+
+    libfepx/solveit_evp/solve_evp/solve_evp_vpstress/solve_evp_vpstress_mod1.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_vpstress/solve_evp_vpstress_mod2.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_vpstress/solve_evp_vpstress_mod3.f90
+
+    libfepx/solveit_evp/solve_evp/solve_evp_stress/solve_evp_stress_mod1.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_stress/solve_evp_stress_mod2.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_stress/solve_evp_stress_mod3.f90
+
+    libfepx/solveit_evp/solve_evp/solve_evp_rstar/solve_evp_rstar_mod1.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_rstar/solve_evp_rstar_mod2.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_rstar/update_hardening/hardening_mod1.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_rstar/update_hardening/hardening_mod2.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_rstar/update_hardening/hardening_mod3.f90
+    libfepx/solveit_evp/solve_evp/solve_evp_rstar/update_hardening/hardening_mod4.f90
+
+    libfepx/solveit_evp/finalize_res/finalize_res_mod1.f90
+
+    libfepx/restart/restart.f90
+
+    libfepx/aniso_vp_lag.f90
+    libfepx/conjugate_gradient_mod.f90
+    libfepx/kinematics_mod.f90
+    libfepx/kinematics_mod_bis.f90
+
+    general/matrix_operations_mod.f90
+    general/shape_2d_mod.f90
+    general/shape_3d_mod.f90
+    general/quadrature_mod.f90
+    general/units_mod.f90
+
+    libfepx/stiffness_mod.f90
+    libfepx/surf_mod.f90
+    libfepx/write_res/write_res_mod1.f90
+    libfepx/write_res/write_res_mod2.f90
+)
+
+include_directories(${CMAKE_Fortran_MODULE_DIRECTORY} ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
+
+# Prepare MPI Fortan compiler for compilation of executable
+set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER})
+message(STATUS "Switching to MPI Fortran compiler: ${CMAKE_Fortran_COMPILER}, ${CMAKE_Fortran_COMPILER_ID}")
+
+message(STATUS "Preparing executable: fepx")
+add_executable(fepx ${fepx})
+
+
+# Install FEPX into bin on the local machine
+install(TARGETS fepx DESTINATION bin
+  PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ
+    GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+
+# Notify the user how to continue after `cmake ..`
+message(STATUS "FEPX is set to be installed in: ${CMAKE_INSTALL_PREFIX}/bin")
+
+# Testing ######################################################################
+
+include(CTest)
+
+file(GLOB_RECURSE tests ../tests/*/*.cmake)
+
+if(BUILD_TESTING)
+  foreach(test ${tests})
+    get_filename_component(test_name ${test} NAME)
+    string(REPLACE ".cmake" "" test_name ${test_name})
+    get_filename_component(test_dir ${test} DIRECTORY)
+    get_filename_component(test_path ${test} PATH)
+    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/../tests/" "" test_label ${test_dir})
+    add_test(NAME ${test_label}
+             COMMAND ${CMAKE_COMMAND}
+             -Dtest_prog=$<TARGET_FILE:fepx>
+             -Dtest_mode=${BUILD_TESTING_MODE}
+             -Dtest_diff=${BUILD_TESTING_DIFF}
+             -P ${test}
+             WORKING_DIRECTORY ${test_dir})
+  endforeach()
+endif()