merge upstream from private

Author: sbryngelson

.gitignore

@@ -21,14 +21,26 @@ tests/*/silo*
 tests/*/restart*
 tests/*/*.out
 tests/*/binary
+<<<<<<< HEAD
+=======
+example_cases/*batch/*/
+>>>>>>> MFC_private/master
 example_cases/*/D/*
 example_cases/*/p*
 example_cases/*/D_*
 example_cases/*/*.inf
 example_cases/*/*.inp
 example_cases/*/*.dat
+<<<<<<< HEAD
+=======
+example_cases/*/*.o*
+>>>>>>> MFC_private/master
 example_cases/*/silo*
 example_cases/*/restart*
 example_cases/*/*.out
 example_cases/*/binary
 lib/fftw-3.3.8
+<<<<<<< HEAD
+=======
+lib/lapack-3.4.2
+>>>>>>> MFC_private/master

AUTHORS

@@ -1,6 +1,10 @@
 The MFC is distributed under the GNU GPLv3 license (or later).
 
+<<<<<<< HEAD
 Contributors: S. H. Bryngelson, K. Schmidmayer, V. Coralic, J. Meng, K. Maeda, T. Colonius
+=======
+Contributors: S. H. Bryngelson, K. Schmidmayer, V. Coralic, J. Meng, K. Maeda, T. Colonius, J.-S. Spratt, M. Rodriguez
+>>>>>>> MFC_private/master
 
 
 Spencer H. Bryngelson
@@ -10,6 +14,21 @@ California Institute of Technology
 Pasadena, California, USA 
 Email: [email protected]
 
+<<<<<<< HEAD
+=======
+Jean-Sebastien Spratt
+--------------------------------------------
+Graduate Researcher
+California Institute of Technology 
+Pasadena, California, USA 
+
+Mauro Rodriguez 
+--------------------------------------------
+Postdoctoral Scholar
+California Institute of Technology 
+Pasadena, California, USA 
+
+>>>>>>> MFC_private/master
 Kevin Schmidmayer
 --------------------------------------------
 Postdoctoral Scholar

CONFIGURE

@@ -21,11 +21,28 @@ If you already have FFTW compiled:
     include files in Makefile.user (fftw_lib_dir and
     fftw_include_dir)
 
+<<<<<<< HEAD
 If you do not have FFTW compiler, the library and 
+=======
+If you do not have FFTW compiled, the library and 
+>>>>>>> MFC_private/master
 installer are included in this package. Just:
     $$ cd installers
     $$ ./install_fftw.sh
 
+<<<<<<< HEAD
+=======
+## LAPACK ##
+If you already have LAPACK compiled:
+    - Specify the location of your LAPACK library and 
+    include files in Makefile.user (lapack_lib_dir) 
+
+If you do not have LAPACK compiled, the library and 
+installer are included in this package. Just:
+    $$ cd installers
+    $$ ./install_lapack.sh
+
+>>>>>>> MFC_private/master
 #> 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

Makefile.in

@@ -1,5 +1,17 @@
 include ../../Makefile.user
 
+<<<<<<< HEAD
+=======
+#######################  Lapack Flags ###########################
+
+# Linker flags 
+ifdef lapack_lib_dir
+ld_pre_flags = -L$(lapack_lib_dir) -llapack -lblas
+else
+ld_pre_flags =
+endif
+
+>>>>>>> MFC_private/master
 ########################## FFTW Flags ###########################
 # Linker flags 
 ifdef fftw_lib_dir
@@ -8,6 +20,13 @@ else
 ld_sim_flags = 
 endif
 
+<<<<<<< HEAD
+=======
+ifdef lapack_lib_dir
+ld_sim_flags += -L$(lapack_lib_dir) -llapack -lblas
+endif
+
+>>>>>>> MFC_private/master
 # Header flags
 ifdef fftw_include_dir
 hd_flags = -I$(fftw_include_dir)

Makefile.user

@@ -4,6 +4,7 @@ MFC_DIR:=$(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
 
 ### Compiler command ###
 FC = mpif90
+<<<<<<< HEAD
 
 ### Compiler flags [set according to your compiler] ### 
 ## Note: Requires -cpp (Intel/GCC/etc) or -eZ (Cray) to 
@@ -21,6 +22,28 @@ fftw_lib_dir     = $(MFC_DIR)/lib/fftw-3.3.8/lib
 fftw_include_dir = $(MFC_DIR)/lib/fftw-3.3.8/include
 
 ## Some other example locations
+=======
+#FC = mpiifort
+   
+### Compiler flags [set according to your compiler] ### 
+#Note: Requires -cpp to enable preprocessor 
+
+FFLAGS = -cpp -c -w -freal-4-real-8 -O3
+# FFLAGS = -cpp -c -w -fimplicit-none  -Wall  -Wline-truncation  -Wcharacter-truncation  -Wsurprising  -Waliasing  -Wimplicit-interface  -Wunused-parameter  -fwhole-file  -fcheck=all  -std=f2008  -pedantic  -fbacktrace
+#NOTE: Cray compilers require: -eZ
+
+######### LAPACK library location #########
+lapack_lib_dir = $(MFC_DIR)/lib/lapack-3.4.2/
+
+######### 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]
+>>>>>>> MFC_private/master
 #fftw_lib_dir = /usr/local/lib
 #fftw_include_dir = /usr/include
 #fftw_include_dir = /usr/local/include
@@ -32,6 +55,11 @@ fftw_include_dir = $(MFC_DIR)/lib/fftw-3.3.8/include
 silo_lib_dir = /usr/local/lib
 silo_include_dir = /usr/local/include
 
+<<<<<<< HEAD
 ## Some other example locations
 #silo_lib_dir = <SILO_DIR>/lib
 #silo_include_dir = <SILO_DIR>/include
+=======
+#silo_lib_dir = /home/spencer/packages/silo-4.10.2/lib
+#silo_include_dir = /home/spencer/packages/silo-4.10.2/include
+>>>>>>> MFC_private/master

README.md

@@ -5,10 +5,15 @@ for multi-component, multi-phase, and bubbly flows.
 
 # Authors
 
+<<<<<<< HEAD
   MFC was developed at Caltech by a group
   of post-doctoral scientists and graduate research students
   under the supervision of Professor Tim Colonius. These contributors 
   include:
+=======
+  MFC was developed at Caltech by a group of post-doctoral scientists and graduate research students under the supervision of Professor Tim Colonius.
+  These contributors include:
+>>>>>>> MFC_private/master
 * Dr. Spencer Bryngelson
 * Dr. Kevin Schmidmayer
 * Dr. Vedran Coralic
@@ -33,6 +38,7 @@ for multi-component, multi-phase, and bubbly flows.
 ## MFC paper
 
   The paper that describes the MFC's capabilities:
+<<<<<<< HEAD
 * <a href="http://dx.doi.org/https://doi.org/10.1016/j.cpc.2020.107396">
         S. H. Bryngelson, K. Schmidmayer, V. Coralic, K. Maeda, J. Meng, T. Colonius (2020) Computer Physics Communications 4655, 107396
         </a>
@@ -52,6 +58,12 @@ for multi-component, multi-phase, and bubbly flows.
 }
 ```
 
+=======
+* <a href="https://doi.org/10.1016/j.cpc.2020.107396">
+        S. H. Bryngelson, K. Schmidmayer, V. Coralic, K. Maeda, J. Meng, T. Colonius (2020) Computer Physics Communications 4655, 107396
+        </a>
+  
+>>>>>>> MFC_private/master
 ## Related publications
 
   Several publications have used the MFC in various stages of its 
@@ -113,14 +125,22 @@ Ph.D. Disserations:
 
 ### Main dependencies: MPI and Python 
   If you do not have Python, it can be installed via
+<<<<<<< HEAD
   <a href="https://brew.sh/">Homebrew on MacOS</a> as:  
+=======
+  <a href="https://brew.sh/">Homebrew on OSX</a> as:  
+>>>>>>> MFC_private/master
 `brew install python`
 
   or compiled via your favorite package manager on Unix systems.
 
   An MPI fortran compiler is required for all systems.
   If you do not have one, Homebrew can take care of this
+<<<<<<< HEAD
   on MacOS:  
+=======
+  on OSX:  
+>>>>>>> MFC_private/master
 `brew install open-mpi`  
 
   or compiled via another package manager on Unix systems.
@@ -144,7 +164,11 @@ If you do not have FFTW compiler, the library and
   but can indeed be handled with the MFC. For this, HDF5
   and Silo must be installed
 
+<<<<<<< HEAD
   On MacOS, a custom Homebrew tap for Silo is included in the installers
+=======
+  On OSX, a custom Homebrew tap for Silo is included in the installers
+>>>>>>> MFC_private/master
   directory. You can use it via  
 `cd installers`  
 `brew install silo.rb`  
@@ -203,16 +227,28 @@ Their contents, and a guide to filling them out, are documented
 in the user manual. A commented, tutorial script
 can also be found in `example_cases/3d_sphbubcollapse`.
 MFC can be executed as  
+<<<<<<< HEAD
 `python input.py pre_process`
 
 which will generate the restart and grid files that will be read 
 by the simulation code. Then  
 `python input.py simulation`
+=======
+`python pre_process`
+
+which will generate the restart and grid files that will be read 
+by the simulation code. Then  
+`python simulation`
+>>>>>>> MFC_private/master
 
 will execute the flow solver. The last (optional) step
 is to post treat the data files and output HDF5 databases
 for the flow variables via  
+<<<<<<< HEAD
 `python input.py post_process`
+=======
+`python post_process`
+>>>>>>> MFC_private/master
 
 Note that the post-processing step 
 requires installation of Silo and HDF5.

doc/basics_of_qbmm.md

@@ -0,0 +1,15 @@
+'qbmm'               : 'T',
+    * Turns on QBMM. It uses CHyQMOM.
+'nnode'              : 4,
+    * Number of quadrature points. 
+    * Currently 4 is the only option.
+'dist_type'          : 2,
+    * 1 = Binormal distribution
+    * 2 = Lognormal in R, Normal in V (Rdot)
+    * Both of these use mean in R = 1, mean in V = 0
+'sigR'               : 0.1,
+    * Standard deviation of distribution in R
+'sigV'               : 0.1,
+    * Standard deviation of distribution in V (Rdot)
+'rhoRV'              : 0.0,
+    * Initial covariance between R and V directions (usually 0)

doc/how_to_add_variable.md

@@ -0,0 +1,20 @@
+# How to add variable to MFC
+
+* Add variable to input.py
+* Add variable to src/master_scripts/m_python_proxy.py dictionary as appropriate (pre_process, simulation, and/or post_process)
+    * This will then write this variable to the \*.in input file that gets created by input.py
+* Go into the code that you added the variable for (pre_process / simulation / post_process)
+    * m_startup.f90
+      * Add variable to NAMELIST user_inputs in subroutine s_read_input_file
+      * Add appropriate checks to s_check_input_file 
+    * m_global_parameters.f90
+      * Make your new variable/parameter global so that the whole code can see it
+      * Add it to the header of this module (document as appropriate)
+      * In s_assign_default_values_to_user_inputs set the default value for this variable
+    * m_mpi_proxy.f90
+      * s_mpi_bcast_user_inputs
+      * This is where the variable is broadcasted to all processors 
+      * Add to list of broadcasted variables 
+      * e.g. CALL MPI_BCAST(weno_nn, 1, MPI_LOGICAL, 0, MPI_COMM_WORLD, ierr  )
+* You can now use your variable (e.g. weno_nn) in the code. At least anywhere that m_global_parameters is used (see header of module)
+

doc/richardson_MFC.md

@@ -0,0 +1,89 @@
+# How to get MFC up and running on Richardson
+
+* Log in
+    * $ ssh [email protected]
+    * Make this an alias! e.g. $ richardson
+        * Append 
+        alias richardson='ssh -Y <your_userid>@richardson.caltech.edu'
+        RICHARDSON="<user name>@richardson.caltech.edu"
+        to your ~/.bash_profile  
+        on your local computer
+    * Add your private key to your Richardson keychain
+        * $ cat ~/.ssh/id_rsa.pub | ssh <your_userid>@richardson.caltech.edu 'cat >> ~/.ssh/authorized_keys'
+
+=======
+        * [Generate](https://docs.joyent.com/public-cloud/getting-started/ssh-keys/generating-an-ssh-key-manually/manually-generating-your-ssh-key-in-mac-os-x) your private key if you don't have one 
+        * $ cat ~/.ssh/id_rsa.pub | ssh <your_userid>@richardson.caltech.edu 'cat >> ~/.ssh/authorized_keys'
+
+* Silo/HDF5, Visit, Paraview on Richardson
+    * Follow the `visit_paraview_richardson.pdf` document  
+    * Step 15. under 'visit on richardson' should use the following URL:  http://visit.ilight.com/svn/visit/branches/2.9RC/src/svn_bin/bv_support/
+
+>>>>>>> qbmm
+* Clone MFC, e.g.
+    * $ git clone https://github.com/ComputationalFlowPhysics/MFC_private.git 
+    * $ git status
+        * shows what branch you are on
+    * $ git checkout <branch>
+        * switch to branch <branch> 
+
+* Compile MFC
+    * Get open-mpi
+        * Show currently loaded modules
+            * $ module list  
+        * Show possible module files
+            * $ module avail
+        * Load open-mpi
+            * For example: $ module load openmpi-1.8/gcc 
+        * Add this to your .bashrc so it happens at login time
+            * Append 
+            module load openmpi-1.8/gcc
+            to your ~/.bashrc
+            on Richardson
+    * Install FFTW
+        * $ cd installers
+        * $ ./install_fftw.sh
+    * Install LAPACK [if QBMM]
+        * $ cd installers
+        * $ ./install_lapack.sh
+    * Make MFC
+        * $ cd ../    [or to MFC directory]
+        * make
+        * make test
+
+* Moving files from local computer to Richardson [While on local computer. Can't do other way around]
+    * $ rsync -rvz <local files> <user name>@richardson.caltech.edu:<richardson location>
+    * or $ rsync -rvz <local files> $RICHARDSON:<richardson location>
+    * Or from Richardson to local computer
+        * $ rsync -rvz <user name>@richardson.caltech.edu:<richardson location> <local files>
+        * or $ rsync -rvz $RICHARDSON:<richardson location> <local files>
+    * Can also use GUI-based tools like FileZilla 
+
+* How to visualize using gnuplot on Richardson
+    * You need XQuartz on your MacOS [or X11 on Linux]
+        * Install at https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.8.dmg
+        * Make sure you logged into Richardson using ssh -Y [or ssh -X] 
+        * Check if your X server is working by logging into Richardson and issuing
+            $ xclock
+            * I am aware this version is deprecated, but it appears that 2.7.11 does not work in some cases
+        * Make sure you logged into Richardson using ssh -Y [or ssh -X] 
+        * Check if your X server is working by logging into Richardson and issuing
+            $ xclock
+        * IF YOU USE MacOS CATALINA!
+            * Permissions can be an issue
+            * Go to System preferences -> Security and Privacy -> Privacy -> Full Disk Access 
+            * Add your terminal (e.g. Terminal, iTerm2, etc.) via the + button
+            * Add XQuartz (launchd_startx) and the app (XQuartz)
+
+    * Copy contents of https://raw.githubusercontent.com/sbryngelson/dotfiles/master/.gnuplotrc_x11
+    into your ~/.bashrc
+        * now you can use 
+        $ myplot cons.1.0000000
+        for, e.g., conservative and primitive serial data files cons.* prim.*
+        $ myplots X probe1.dat
+        for probe data [variable numeber X]
+        $ animate1d X cons.1.*
+        to animate cons.1.* X times
+
+
+