Init

.gitignore

@@ -0,0 +1,34 @@
+doc/Doxygen/*/html
+doc/Doxygen/*logo*
+doc/Doxygen/*icon*
+src/*/*.mod
+src/*/*.o
+src/pre_process_code/pre_process
+src/simulation_code/simulation
+src/post_process_code/post_process
+src/master_scripts/*.pyc
+src/master_scripts/__*
+make_doc.sh
+cases/
+.DS_Store
+tests/*/D/*
+tests/*/p*
+tests/*/D_*
+tests/*/*.inf
+tests/*/*.inp
+tests/*/*.dat
+tests/*/silo*
+tests/*/restart*
+tests/*/*.out
+tests/*/binary
+example_cases/*/D/*
+example_cases/*/p*
+example_cases/*/D_*
+example_cases/*/*.inf
+example_cases/*/*.inp
+example_cases/*/*.dat
+example_cases/*/silo*
+example_cases/*/restart*
+example_cases/*/*.out
+example_cases/*/binary
+lib/fftw-3.3.8

AUTHORS

@@ -0,0 +1,46 @@
+The MFC is distributed under the GNU GPLv3 license (or later).
+
+Contributors: S. H. Bryngelson, K. Schmidmayer, V. Coralic, J. Meng, K. Maeda, T. Colonius
+
+
+Spencer H. Bryngelson
+--------------------------------------------
+Senior Postdoctoral Scholar 
+California Institute of Technology 
+Pasadena, California, USA 
+Email: spencer@caltech.edu
+
+Kevin Schmidmayer
+--------------------------------------------
+Postdoctoral Scholar
+California Institute of Technology 
+Pasadena, California, USA
+Email: kevin.schmidmayer@gmail.com
+
+Vedran Coralic
+--------------------------------------------
+Senior Research Scientist
+Prime Air, Amazon Inc.
+Seattle, Washington, USA
+Email: vcoralic@amazon.com
+
+Jomela Meng
+--------------------------------------------
+Research Engineer
+Bosch Research and Technology Center
+Sunnyvale, California, USA
+Email: jomela.meng@gmail.com
+
+Kazuki Maeda
+--------------------------------------------
+Acting Assistant Professor
+University of Washington
+Seattle, Washington, USA
+Email: kazuki.e.maeda@gmail.com
+
+Tim Colonius
+--------------------------------------------
+Frank and Ora Lee Marble Professor of Mechanical Engineering 
+California Institute of Technology
+Pasadena, California, USA
+Email: colonius@caltech.edu

CONFIGURE

@@ -0,0 +1,62 @@
+#> Simulations using MFC depend upon Python, MPI,
+#> and FFTW.
+
+## Python ##
+If you do not have Python, it can be installed via 
+Homebrew on OSX (https://www.brew.sh) as:
+    $$ brew install python
+or compiled via your favorite package manager on Unix 
+systems.
+
+## MPI ##
+An MPI fortran compiler is required for all systems.
+If you do not have one, Homebrew can take care of this
+on OSX:
+    $$ brew install open-mpi
+or compiled via another package manager on Unix systems.
+
+## FFTW ##
+If you already have FFTW compiled:
+    - Specify the location of your FFTW library and 
+    include files in Makefile.user (fftw_lib_dir and
+    fftw_include_dir)
+
+If you do not have FFTW compiler, the library and 
+installer are included in this package. Just:
+    $$ cd installers
+    $$ ./install_fftw.sh
+
+#> Post-processing of parallel data files is not required,
+#> but can indeed be handled with the MFC. For this, HDF5
+#> and Silo must be installed
+
+On OSX, a custom tap for Silo is included in the installers
+directory. You can use it via
+    $$ cd lib
+    $$ brew install silo.rb
+This will install silo and its dependences (including HDF5)
+in their usual locations (/usr/local/lib and 
+/usr/local/include) 
+
+On Unix systems, you can install via a package manager or
+from source. On CentOS (also Windows 7), HDF5
+binaries can be found at 
+    https://support.hdfgroup.org/ftp/HDF5/current18/bin/
+Untar this archive in your intended location via 
+    $$ tar -zxf [your HDF5 archive]
+
+Silo should be downloaded at
+    https://wci.llnl.gov/simulation/computer-codes/silo/downloads
+then 
+    $$ tar -zxf [your Silo archive]
+    $$ cd [your Silo archive]
+    $$ ./configure --prefix=[target installation directory] --enable-pythonmodule --enable-optimization --disable-hzip --disable-fpzip --enableportable-binary FC=mpif90 F77=mpif77 -with-hdf5=[your hdf5 directory]/include,/[your hdf5 directory]/lib --disable-silex
+    $$ make
+    $$ make install
+then add this line to your ~/.bash_profile
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/[your silo directory]/lib:/[your hdf5 directory]/lib
+and
+    $$ source ~/.bash_profile
+
+You will then need to modify silo_lib_dir and silo_include_dir in 
+Makefile.user to point to your silo directory

COPYRIGHT

@@ -0,0 +1,3 @@
+MFC
+
+Copyright © 2019    Spencer Bryngelson, Kevin Schmidmayer, Vedran Coralic, Jomela Meng, Kazuki Maeda, Timothy Colonius

INSTALL

@@ -0,0 +1,18 @@
+
+READ "CONFIGURE" BEFORE PROCEEDING WITH INSTALL
+
+Once all dependencies have been installed, the MFC can be built via
+
+    $$ make
+
+from the MFC directory. This will build all MFC components. Individual
+components can be built via
+
+    $$ make [component]
+
+where [component] is one of "pre_process,simulation,post_process". 
+
+Once this is completed, you can ensure that the software is working 
+as intended by running
+
+    $$ make test

Makefile

@@ -0,0 +1,43 @@
+include Makefile.user 
+
+default: all
+
+include installers/Makefile.messages
+
+all: pre_process simulation post_process
+
+pre_process:
+	@$(MAKE) -C src/pre_process_code -f makefile
+
+simulation:
+
+ifneq ("$(wildcard $(fftw_include_dir)/fftw3.*)","")
+ifneq ("$(wildcard $(fftw_lib_dir)/libfftw*.la)","")
+	@$(MAKE) -C src/simulation_code -f makefile
+else
+	@echo "$$FFTW_LIB_ERR"
+endif
+else
+	@echo "$$FFTW_INC_ERR"
+endif
+
+post_process:
+
+ifneq ("$(wildcard $(silo_include_dir)/silo_*.inc)","")
+ifneq ("$(wildcard $(silo_lib_dir)/libsilo*.*a)","")
+	@$(MAKE) -C src/post_process_code -f makefile
+else
+	@echo "$$SILO_LIB_ERR"
+endif
+else
+	@echo "$$SILO_INC_ERR"
+endif
+
+test:
+	./tests/checks.sh
+
+.PHONY: clean
+clean:
+	@$(MAKE) -C src/pre_process_code -f makefile clean
+	@$(MAKE) -C src/simulation_code -f makefile clean
+	@$(MAKE) -C src/post_process_code -f makefile clean

Makefile.in

@@ -0,0 +1,38 @@
+include ../../Makefile.user
+
+########################## FFTW Flags ###########################
+# Linker flags 
+ifdef fftw_lib_dir
+ld_sim_flags = -L$(fftw_lib_dir) -lfftw3 -lm
+else
+ld_sim_flags = 
+endif
+
+# Header flags
+ifdef fftw_include_dir
+hd_flags = -I$(fftw_include_dir)
+else
+hd_flags = 
+endif
+
+# Compiler flags
+f90_flags = $(FFLAGS) $(hd_flags)
+
+#################### Post-process Silo Flags #####################
+# Linker flags
+ifdef silo_lib_dir
+silo_flags = -L$(silo_lib_dir) -lsiloh5 -lm
+else
+silo_flags =
+endif
+ld_post_flags = $(ld_sim_flags) $(silo_flags)
+
+# Header flags
+ifdef silo_include_dir
+hd_post_flags = -I$(silo_include_dir)
+else
+hd_post_flags =
+endif
+
+# Compiler flags
+f90_post_flags = $(f90_flags) $(hd_post_flags)

Makefile.user

@@ -0,0 +1,35 @@
+################ Compiler options ####################
+# Gets the MFC directory [do not modify]
+MFC_DIR:=$(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+
+### Compiler command ###
+FC = mpif90
+#FC = mpiifort
+
+### Compiler flags [set according to your compiler] ### 
+#Note: Requires -cpp to enable preprocessor 
+
+FFLAGS = -cpp -c -w 
+#NOTE: Cray compilers require: -eZ
+
+######### FFTW library and include locations #########
+######### Set these to the location of FFTW  #########
+
+## For the FFTW included in the MFC package
+fftw_lib_dir     = $(MFC_DIR)/lib/fftw-3.3.8/lib
+fftw_include_dir = $(MFC_DIR)/lib/fftw-3.3.8/include
+
+## Other possible locatins [only use absolute paths]
+#fftw_lib_dir = /usr/local/lib
+#fftw_include_dir = /usr/include
+#fftw_include_dir = /usr/local/include
+
+######### Silo library and include locations #########
+######### Set these to the location of Silo  #########
+#########   [  only use absolute paths   ]   #########
+
+silo_lib_dir = /usr/local/lib
+silo_include_dir = /usr/local/include
+
+#silo_lib_dir = /home/spencer/packages/silo-4.10.2/lib
+#silo_include_dir = /home/spencer/packages/silo-4.10.2/include