initial upload

2025-12-17 11:00:57 +08:00
parent 2bc7b24a71
commit a09a73537f
4614 changed files with 3478433 additions and 2 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -32,3 +32,4 @@
 *.out
 *.app

+.DS_Store
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -0,0 +1,333 @@
+# Default build with Exodus OFF
+# for testing cmake options:
+# -DCMAKE_BUILD_TYPE=Debug
+# -DLAGRIT_BUILD_EXODUS=ON (detect Exodus?, default OFF)
+#
+# Some common cmake variables:
+# https://cmake.org/cmake/help/latest/manual/cmake-variables.7.html
+# -D CMAKE_FIND_DEBUG_MODE=ON
+#
+# Not supported yet but available:
+# -D CMAKE_INSTALL_PREFIX (default /usr/local if make install)
+# -D LaGriT_BUILD_STATIC=ON (default .a, use OFF for .so etc)
+#
+# Long version with explicit paths to build lagrit with Exodus 
+# This file is useful for debugging cmake with Exodus
+# Note Windows is not working and is commented out
+# Sep 28 2022 tamiller@lanl.gov lagrit.lanl.gov
+# SEACAS Exodus Gregory Sjaardema gsjaardema@gmail.com
+##############################################################################
+
+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
+
+# set cmake variables for version numbers and compilers
+project(LaGriT VERSION 3.3.4
+               DESCRIPTION "LaGriT Meshing Utilities"
+               LANGUAGES Fortran CXX C)
+
+option(LAGRIT_BUILD_STATIC "Compile as a static (fat) executable." ON)
+option(LAGRIT_BUILD_EXODUS "Build with Exodus." OFF)
+
+# Set Directories for lagrit compile and build 
+set(INSTALL_DIR "${CMAKE_SOURCE_DIR}/install")
+set(SRC_UTIL "${CMAKE_SOURCE_DIR}/lg_util/src")
+set(SRC_CORE "${CMAKE_SOURCE_DIR}/src")
+
+set(TPL_LIBRARIES "")
+set(TPL_INCLUDE_DIRS "")
+
+message(STATUS "==========================================")
+message(STATUS "============Configuring LaGriT============")
+message(STATUS "===================v${PROJECT_VERSION}=================")
+
+message(STATUS "Compile LaGriT as a static binary = ${LAGRIT_BUILD_STATIC}")
+message(STATUS "Compile LaGriT with ExodusII = ${LAGRIT_BUILD_EXODUS}")
+
+# Add Third Party Libraries here and add all to TPL_LIBRARIES
+# These include Exodus and PETSc (planned for Voronoi codes)
+
+if (LAGRIT_BUILD_EXODUS) 
+
+message(STATUS "-----Configuring Exodus-----")
+
+# this is the long version to build LAGRIT with Exodus
+# it is useful if Exodus cmake files or libs are not found
+# new versions of exodus should set definitions with find_package()
+# Look for SEACAS/ExodusII libraries
+# then set the "TPL_LIBRARIES" variable to full paths of found libs
+# NAMES exodus libexodus exoIIv2for netcdf hdf5_hl hdf5 libz
+
+set(EXODUS_ROOT "${CMAKE_SOURCE_DIR}/TPLs/seacas")
+set(Exodus_INCLUDE_DIR "${EXODUS_ROOT}/include")
+set(Exodus_LIBRARIES "${EXODUS_ROOT}/lib")
+
+if(EXISTS "${Exodus_INCLUDE_DIR}")
+  message(STATUS "  Found exodus include dir: ${Exodus_INCLUDE_DIR}")
+else()
+  message("FATAL_ERROR: exodus include dir not found in ${EXODUS_ROOT}")
+endif()
+
+if(EXISTS "${Exodus_INCLUDE_DIR}/exodusII.inc")
+  set(EXO_INC "${Exodus_INCLUDE_DIR}/exodusII.inc")
+  message(STATUS "  Found exodusII.inc : ${EXO_INC}")
+else()
+  message("FATAL_ERROR: exodusII.inc not found in ${EXO_INC}")
+endif()
+
+# set libraries with individual calls to each lib name
+if(EXISTS "${Exodus_LIBRARIES}")
+find_library(EXO_FOUND libexodus.a 
+    PATHS ${EXODUS_ROOT} ${Exodus_LIBRARIES} NO_DEFAULT_PATH)
+find_library(EXO_FORT_FOUND libexodus_for.a 
+    PATHS ${EXODUS_ROOT} ${Exodus_LIBRARIES} NO_DEFAULT_PATH)
+find_library(EXO_FORT32_FOUND libexoIIv2for32.a 
+    PATHS ${EXODUS_ROOT} ${Exodus_LIBRARIES} NO_DEFAULT_PATH)
+find_library(HDF5_FOUND libhdf5.a 
+    PATHS ${EXODUS_ROOT} ${Exodus_LIBRARIES} NO_DEFAULT_PATH)
+find_library(NETCDF_FOUND libnetcdf.a 
+    PATHS ${EXODUS_ROOT} ${Exodus_LIBRARIES} NO_DEFAULT_PATH)
+find_library(ZLIB_FOUND libz.a 
+    PATHS ${EXODUS_ROOT} ${Exodus_LIBRARIES} NO_DEFAULT_PATH)
+  message(STATUS "  Found Exodus      lib: ${EXO_FOUND}")
+  message(STATUS "  Found Exodus_fort lib: ${EXO_FORT_FOUND}")
+  message(STATUS "  Found HDF5        lib: ${HDF5_FOUND}")
+  message(STATUS "  Found NetCDF      lib: ${NETCDF_FOUND}")
+  message(STATUS "  Found ZLIB        lib: ${ZLIB_FOUND}")
+else()
+  message("FATAL_ERROR: Exodus libs not found in ${Exodus_LIBRARIES}")
+endif()
+
+# IF NOT FOUND hard-wire root and paths here
+# set(EXODUS_ROOT "/project/eesdev/tam/LaGriT-build/TPLs/seacas")
+# set(Exodus_LIBRARIES "${EXODUS_ROOT}/lib")
+# set(Exodus_INCLUDE_DIR "${EXODUS_ROOT}/include")
+# message(STATUS "Set Explicit Exodus ROOT: ${SEACASExodus_ROOT}")
+
+# trick cmake to add exodus libs correctly for linking
+# nc-config --static should pick up all link FLAGS from netcdf 
+# -lcurl needed for linking netcdf libs on linux 
+set(TPL_LINK_LIBS "-L${EXODUS_ROOT}/lib -lexodus_for -lexodus -lnetcdf -lhdf5_hl -lcurl -lhdf5 -lz -ldl -static-libgfortran -static-libgcc")
+
+message(STATUS "-----Done Exodus-----")
+
+# SET TPLS with exodus and petsc includes and libs
+if (Exodus_INCLUDE_DIR AND Exodus_LIBRARIES) # AND NetCDF_FOUND AND HDF5_FOUND AND ZLIB_FOUND
+  set(TPL_INCLUDE_DIRS "${Exodus_INCLUDE_DIR}")
+#  set(TPL_LIBRARIES ${HDF5_FOUND} ${NETCDF_FOUND} ${ZLIB_FOUND} ${EXO_FOUND} ${EXO_FORT32_FOUND} ${EXO_FORT_FOUND} )
+  set(TPL_LIBRARIES "${Exodus_LIBRARIES}" )
+
+else()
+  message("ERROR: ExodusII and/or other dependencies could not be found.")
+  message( FATAL_ERROR "Build ExodusII or use -DLaGriT_BUILD_EXODUS=OFF" )
+endif()
+
+endif()
+# END TPLs
+
+if (LAGRIT_BUILD_EXODUS)
+  add_definitions(-DLAGRIT_INCLUDE_EXODUSII)
+  message(STATUS "ExodusII support enabled: ${LAGRIT_BUILD_EXODUS}")
+  message(STATUS "ExodusII libraries      : ${Exodus_LIBRARIES}")
+  message(STATUS "ExodusII include        : ${Exodus_INCLUDE_DIR}")
+else()
+  message("LaGriT Compiling without ExodusII support.")
+  message("To include Exodus, use -DLAGRIT_BUILD_EXODUS=ON")
+endif()
+
+# message( FATAL_ERROR "Debug exit at STOP." )
+
+# ===== Detect local platform, bit-size, and compilers ==================== #
+message(STATUS "Detecting LaGriT build using local cmake files:")
+include("${CMAKE_SOURCE_DIR}/cmake/PlatformSettings.cmake")
+include("${CMAKE_SOURCE_DIR}/cmake/DetectBitSize.cmake")
+include("${CMAKE_SOURCE_DIR}/cmake/CompilerFlags-Fortran.cmake")
+include("${CMAKE_SOURCE_DIR}/cmake/CompilerFlags-C.cmake")
+
+if (LAGRIT_BUILD_STATIC)
+  set(LIBLAGRIT_BUILD_TYPE "STATIC")
+else()
+  set(LIBLAGRIT_BUILD_TYPE "SHARED")
+  set(BUILD_SHARED_LIBS TRUE)
+endif()
+
+# cmake variable to set DEBUG or RELEASE on command line 
+if (CMAKE_BUILD_TYPE)
+  message("LaGriT compile type set to: ${CMAKE_BUILD_TYPE}")
+endif()
+
+# ////////// BEGIN COMPILER SETTINGS //////////
+
+if (TPL_LIBRARIES)
+message(STATUS "Using Third Party Libraries.")
+message(STATUS "TPL libs: ${TPL_LIBRARIES}")
+message(STATUS "TPL include: ${TPL_INCLUDE_DIRS}")
+include_directories(${TPL_INCLUDE_DIRS})
+endif()
+
+## ////////// BEGIN LINKER CONFIGURATION //////////
+## Windows Extra linker and compile options
+#if(MSVC)
+#    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} /Dwin64")
+#    set(CMAKE_EXE_LINKER_FLAGS "/NODEFAULTLIB:msvcrtd.lib")
+#    set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+#    add_compile_options(
+#        $<$<CONFIG:>:/MT>
+#        $<$<CONFIG:Debug>:/MTd>
+#        $<$<CONFIG:Release>:/MT>
+#    )
+#endif()
+
+# create lagrit.h using PROJECT_VERSION_* in template lagrit.h.in
+string(TIMESTAMP CMAKE_DATE_COMPILE "%Y/%m/%d")
+configure_file(
+    ${SRC_CORE}/lagrit.h.in
+    ${SRC_CORE}/lagrit.h
+    @ONLY
+)
+
+# Validate compiler & symbol interop
+include(FortranCInterface)
+FortranCInterface_VERIFY()
+
+# Create fc_mangle.h for c-fortran routines to handle symbol mangling
+# Names here should also be declared in src/lg_f_interface.h
+# More information: https://www.netlib.org/lapack/lawnspdf/lawn270.pdf
+FortranCInterface_HEADER(
+    ${SRC_CORE}/fc_mangle.h
+    SYMBOLS
+        INITLAGRIT # syntax: <subroutine>
+        DOTASK
+        CMO_GET_NAME
+        CMO_GET_INFO
+        CMO_GET_INTINFO
+        FC_CMO_GET_INT
+        FC_CMO_GET_VINT
+        FC_CMO_GET_DOUBLE
+        FC_CMO_GET_VDOUBLE
+        FPASS_TYPES
+        INSIDE_TET
+        LINESEG_TRI)
+
+# ////////// BEGIN TARGET CONFIGURATION //////////
+# Grab `lg_util/` source files
+file(
+    GLOB_RECURSE
+    SRC_UTIL_FILES
+    "${SRC_UTIL}/*.c"
+    "${SRC_UTIL}/*.cpp"
+    "${SRC_UTIL}/*.f"
+    "${SRC_UTIL}/*.F"
+    "${SRC_UTIL}/*.f90"
+)
+
+# Grab `src/` source files
+file(
+    GLOB_RECURSE
+    SRC_CORE_FILES
+    "${SRC_CORE}/*.c"
+    "${SRC_CORE}/*.cpp"
+    "${SRC_CORE}/*.f"
+    "${SRC_CORE}/*.F"
+    "${SRC_CORE}/*.f90"
+)
+
+# Files we don't want compiled
+list(FILTER SRC_UTIL_FILES EXCLUDE REGEX ".*mm2000_header.F$")
+list(FILTER SRC_CORE_FILES EXCLUDE REGEX ".*lagrit_main.f$")
+
+message(STATUS "Using Compiler Settings:")
+message(STATUS "  FORTRAN [compiler = \"${CMAKE_Fortran_COMPILER}\"; flags = \"${CMAKE_Fortran_FLAGS}\"]")
+message(STATUS "  C [compiler = \"${CMAKE_C_COMPILER}\"; flags = \"${CMAKE_C_FLAGS}\"]")
+message(STATUS "  C++ [compiler = \"${CMAKE_CXX_COMPILER}\"; flags = \"${CMAKE_CXX_FLAGS}\"]")
+
+# This file has the `#ifdef EXODUS` preprocessor directive
+# The -cpp flag ensures the compiler can process those directives
+set_source_files_properties(
+    "${SRC_CORE}/dumpexodusII.f"
+    PROPERTIES COMPILE_OPTIONS "-cpp"
+)
+
+# Compile LaGriT routines as a library
+add_library(
+    liblagrit
+    ${LIBLAGRIT_BUILD_TYPE} # STATIC or SHARED
+    ${SRC_UTIL_FILES}
+    ${SRC_CORE_FILES}
+)
+
+# Set the shared library version
+set_target_properties(
+  liblagrit
+  PROPERTIES
+  OUTPUT_NAME "lagrit"
+  VERSION "${PROJECT_VERSION}"
+  SOVERSION "${PROJECT_VERSION_MAJOR}"
+)
+
+# Compile the main LaGriT binary
+add_executable(
+  lagrit
+  ${SRC_CORE}/lagrit_main.f
+)
+
+set_target_properties(
+  lagrit
+  PROPERTIES
+  OUTPUT_NAME "lagrit"
+  LINKER_LANGUAGE Fortran
+  Fortran_MODULE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/modules/"
+)
+
+# Change from 'lagrit' (OUTPUT_NAME) to 'lagrit.exe' on Windows
+if (WIN32)
+  set_target_properties(lagrit PROPERTIES SUFFIX ".exe")
+endif()
+
+if (LAGRIT_BUILD_STATIC)
+  set_target_properties(lagrit PROPERTIES LINK_SEARCH_START_STATIC 1)
+  set_target_properties(lagrit PROPERTIES LINK_SEARCH_END_STATIC 1)
+
+  if(WIN32)
+    set(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+  else()
+    set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+    set(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+  endif()
+
+endif()
+# end static build options
+
+target_include_directories(
+  lagrit
+  PUBLIC ${TPL_INCLUDE_DIRS} # includes 'exodusII.h' 'exodusII.inc'
+)
+
+target_link_libraries(lagrit
+   PRIVATE liblagrit           # liblagrit.[dylib|so|a|dll]
+   PUBLIC ${TPL_LINK_LIBS}     # Exodus / NetCDF / HDF5 / ZLIB
+)
+
+# this produces errors 
+#make[2]: *** No rule to make target '../TPLs/seacas/lib/libexoIIv2for.a', needed by 'lagrit'.  Stop.
+# target_link_libraries(lagrit
+#     PRIVATE
+#         liblagrit
+#         "${Exodus_LIBRARIES}/libexodus.a"
+#         "${Exodus_LIBRARIES}/libexoIIv2for.a"
+#         "${Exodus_LIBRARIES}/libnetcdf.a"
+#         "${Exodus_LIBRARIES}/libhdf5.a"
+#         "${Exodus_LIBRARIES}/libhdf5_hl.a"
+# )
+
+# Install lagrit to ${CMAKE_INSTALL_PATH}/bin/
+install(
+    TARGETS lagrit
+    DESTINATION "bin"
+)
+
+# Install liblagrit to ${CMAKE_INSTALL_PATH}/lib/
+install(
+    TARGETS liblagrit
+    DESTINATION "lib"
+)
+
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -0,0 +1,200 @@
+# Contributing to LaGriT
+
+Contributor: A contributor is someone from the outside not on the core development team of the project that wants to contribute some changes to a project. Before a pull request can be accepted, a external contributor must submit a Contributor License Agreement (CLA) as described below. 
+
+Collaborator: A collaborator is part of the LANL core development team and has commit access to the main repository.
+
+
+# External Contributions to LaGriT
+
+Before submitting a pull request, please make sure you have done the following:
+
+1. Fork the repository and fork your working branch from master
+2. Describe your test plan in your Pull Request
+3. Ensure all test suites pass (`test/suite.py`)
+4. Make sure you have completed the CLA
+
+## Copyright Notice for Files
+
+Copy and paste this to the top of any created source code (replacing `!` with any language-specific comment char):
+
+```
+!
+! Copyright (c) 2017 Los Alamos National Laboratory, LLC
+! All rights reserved.
+!
+! This source code is licensed under the BSD-style license found in the
+! LICENSE.md file in the root directory of this source tree.
+!
+```
+
+## Contributor License Agreement (CLA)
+
+In order to accept your pull request, we need you to submit a CLA. If you are submitting a pull request for the first time, just let us know after you have completed the CLA so that we can cross-check signers with your GitHub username. This license is for your protection as a Contributor as well as the protection of LANL and the LaGriT users; it does not change your rights to use your own Contributions for any other purpose.
+
+Sign the CLA here: https://www.clahub.com/agreements/lanl/LaGriT
+
+# Instructions for Contributors and Collaborators
+
+- anything in the master branch is always deployable
+- identify any issues including bugs and feature requests, use appropriate title and reproducable description
+- update your local repo, branch, or fork often to stay current with the master branch
+- use fork for off-site contributors and large number of repo changes
+- use branch for approved collaborators for specific code development to be saved and perhaps merged
+- use local clone for admin level collaborators updating the master branch
+- all code committed to LaGriT code must use or be compatible with our BSD-3 license 
+- all code must be tested before it can be merged into the mainstream
+
+
+## Large Files
+
+Git is designed for source code, scripts, and smaller datasets and is repositories are not more than a few gigabytes.
+Larger data files may occasionally need to accompany a repository, and if this is the case, consider these options:
+- a shared project data directory on an HPC resource or local disk space
+- include an empty directory that has a .gitignore file to ignore all of its contents and then share file transfer services
+- if repo absolutely must contain larger data files for unit testing needs, use the Git Large File Storage (LFS) extension so large files are not versioned (only the latest version is kept). 
+
+# Notes on Branches, Forks, and Clones
+
+## Create a Branch
+For collaborators such as students and visitors working on a specific feature or idea. This is good for code development that may or may not be merged with master, but allows you to keep the work with the repo.
+
+```
+LaGriT is my working directory from master branch
+clone is current repo (for synching my work)
+
+-------------------
+Create a branch in my own space
+
+  % git checkout -b tamiller_dev
+
+Switched to a new branch 'tamiller_dev'
+
+-------------------
+Show what branches local git can see
+  % git branch
+
+  master
+* tamiller_dev
+
+-------------------
+Make branch live on github repo (only local until this is done).
+  git push --set-upstream origin tamiller_dev
+
+-------------------
+Switch to master and update from git repo
+  % git checkout master
+
+Switched to branch 'master'
+Your branch is up-to-date with 'origin/master'.
+
+-------------------
+  % git pull
+
+remote: Enumerating objects: 6, done.
+remote: Counting objects: 100% (6/6), done.
+remote: Total 6 (delta 5), reused 6 (delta 5), pack-reused 0
+Unpacking objects: 100% (6/6), done.
+From https://github.com/lanl/LaGriT
+   c2477a8..42507ad  master     -> origin/master
+Updating c2477a8..42507ad
+Fast-forward
+ test/level01/single_triangle/reference/logx3dgen | 0
+ test/level01/single_triangle/reference/outx3dgen | 0
+ 2 files changed, 0 insertions(+), 0 deletions(-)
+ create mode 100644 test/level01/single_triangle/reference/logx3dgen
+ create mode 100644 test/level01/single_triangle/reference/outx3dgen
+
+-------------------
+Switch to branch and check status
+  % git checkout tamiller_dev
+  % git status
+
+On branch tamiller_dev
+Your branch is up-to-date with 'origin/tamiller_dev'.
+nothing to commit, working directory clean
+
+
+-------------------
+Get difference between master and branch
+  % git diff master..tamiller_dev
+
+diff --git a/test/level01/single_triangle/reference/logx3dgen b/test/level01/single_triangle/reference/logx3dgen
+deleted file mode 100644
+index e69de29..0000000
+diff --git a/test/level01/single_triangle/reference/outx3dgen b/test/level01/single_triangle/reference/outx3dgen
+deleted file mode 100644
+index e69de29..0000000
+es04:LaGriT:bsh% git diff master..
+diff --git a/test/level01/single_triangle/reference/logx3dgen b/test/level01/single_triangle/reference/logx3dgen
+deleted file mode 100644
+index e69de29..0000000
+diff --git a/test/level01/single_triangle/reference/outx3dgen b/test/level01/single_triangle/reference/outx3dgen
+deleted file mode 100644
+index e69de29..0000000
+```
+
+If there commits but you want to see them, status does not show.
+push so origin (github repo) is curent with your work directory.
+Once push is complete the commits will show under your  branch.
+You can now create a pull request (compare tamiller_dev to master)
+```
+illposed:src:bsh% git status
+On branch tamiller_dev
+Your branch is ahead of 'origin/tamiller_dev' by 5 commits.
+  (use "git push" to publish your local commits)
+nothing to commit, working directory clean
+
+illposed:src:bsh% git push
+To https://github.com/lanl/LaGriT.git
+   d7fcef5..149f303  tamiller_dev -> tamiller_dev
+```
+
+
+## Fork a project
+For off-site collaborators and changes involving many repo files.  This is very useful for editing a large number of files, such as git pages. This will keep all the notifications from emails and allow you to pull and merge into a single commit.
+
+The following are instructions for updating your fork from the master repo.
+```
+Fork millerta/LaGriT-1
+
+Use brower to Synch my fork with orginal so fork is current.
+
+Open your fork of the repository.
+
+Click the compare button under Clone button.
+
+This will open a page titled Comparing Changes NOTE you have jumped to the upstream original version of the repository.
+If you were to do a regular pull request then you would be bringing your changes into the original version.
+But in this case we want to flip the direction and pull changes from the original version to our fork.
+
+Change the base fork to your repository
+
+You're now back to your fork but showing branches not forks.
+Click on compare across forks to get back your base fork option.
+
+Change the head fork to the upstream (original) repository
+
+You'll see one of two options:
+
+1. "There isn't anything to compare" so you don't have to do anything.
+
+2. A list of commits.  Create a pull request
+Note that this pull request is to you!
+So you can confirm that it's ok and merge as necessary.
+If there are any merge conflicts then it's up to you to figure out what's gone wrong and sort them out.
+
+And now you're ready to continue working on your fork
+```
+
+## Working from a clone
+Pull requests are approved only by the development team. 
+
+This is a typical workflow for pushing code to be pulled to master branch.
+```
+git pull
+git add -A
+git commit -a
+git push
+```
+
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -0,0 +1,24 @@
+# License (BSD)
+
+LANL Software: LA-CC-15-069 Copyright No. C15097
+
+This software is open source available under the BSD-3 license.
+
+Copyright (c) 2016. Triad National Security, LLC. All rights reserved. 
+This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), 
+which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security 
+Administration.  All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of
+Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf 
+a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute
+copies to the public, perform publicly and display publicly, and to permit others to do so. If software is modified to
+produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version 
+available from LANL.
+ 
+Additionally, redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+* 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+* 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+* 3. Neither the name of Triad National Security, LLC, Los Alamos National Laboratory, LANL, the U.S. Government, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY TRIAD NATIONAL SECURITY, LLC AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL TRIAD NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
--- a/MAC_EnvironmentalVar.sh
+++ b/MAC_EnvironmentalVar.sh
@@ -0,0 +1,22 @@
+#
+#	Set Up Mac Specific Environmental Variables
+#
+#=====================================================
+
+fortran_var=$(find /opt/local/bin/gfortran-mp-*)
+cc_var=$(find /opt/local/bin/gcc-mp-*)
+cpp_var=$(find /opt/local/bin/g++-mp-*)
+
+echo "Environmental Variables set"
+
+FC="$fortran_var"
+find ${FC}
+export FC="$fortran_var"
+
+CC="$cc_var"
+find ${CC}
+export CC="$cc_var"
+
+CXX="$cpp_var"
+find ${CXX}
+export CXX="$cpp_var"
--- a/MAC_install-exodus.sh
+++ b/MAC_install-exodus.sh
@@ -0,0 +1,103 @@
+# script to install seacas-exodus for build with LaGriT
+# See detailed instructions at https://github.com/sandialabs/seacas
+# Seacas Contact Gregory Sjaardema gsjaardema@gmail.com
+#
+# LaGriT does not need full seacas but does require
+# exodus and associated libs with FORTRAN=YES
+# libexodus.a      libexoIIv2for32.a  libhdf5_hl.a     libnetcdf.a
+# libexodus_for.a  libhdf5.a          libhdf5_tools.a  libz.a
+# Preferable to use versions newer than July 2022
+set -e
+set -x
+
+# ==== USER SETTINGS ==============================
+# Suggest Installing seacas in LaGriT/TPLs
+SEACAS_INSTALL_DIR=${SEACAS_INSTALL_DIR:-"$(pwd)/TPLs/"}
+# EXO_COMMIT_HASH=${EXO_COMMIT_HASH:-v2021-10-11}
+# =================================================
+
+# ==== MAC SPECIFIC COMPILER EXPORTS ===============
+
+# ==== MAC SPECIFIC COMPILER EXPORTS ===============
+if [[ $(command -v brew) != "" ]]; then
+	echo "Homebrew found"
+	export PATH="/usr/bin/:/opt/homebrew/lib/:/opt/homebrew/bin:/opt/homebrew/sbin:$PATH"
+	export PATH="/opt/homebrew/opt/make/libexec/gnubin:$PATH"
+	export COMPILER=HomeBrew
+	fortran_var=/opt/homebrew/bin/gfortran
+	cc_var=/usr/bin/gcc
+	cpp_var=/usr/bin/g++
+
+elif [[ $(command -v port) != "" ]]; then
+	echo "MacPorts found"
+	export PATH="/opt/local/libexec/gnubin:/opt/local/bin:/opt/local/sbin:$PATH"
+	export COMPILER=MacPorts
+	fortran_var=$(find /opt/local/bin/gfortran-mp-*)
+	cc_var=$(find /opt/local/bin/gcc-mp-*)
+	cpp_var=$(find /opt/local/bin/g++-mp-*)
+
+else
+    echo "Please install compiler using Homebrew or MacPorts. Exiting."
+    exit 1
+fi
+
+echo "Fortran Compiler: $fortran_var"
+echo "C Compiler: $cc_var"
+echo "C++ Compiler: $cpp_var"
+
+FC="$fortran_var"
+export FC="$fortran_var"
+
+CC="$cc_var"
+export CC="$cc_var"
+
+CXX="$cpp_var"
+export CXX="$cpp_var"
+
+# ==== GET SOURCE  ================================
+mkdir -p ${SEACAS_INSTALL_DIR}
+cd ${SEACAS_INSTALL_DIR}
+
+git clone https://github.com/sandialabs/seacas.git
+cd seacas && export ACCESS=`pwd`
+
+# ==== INSTALL REQUIRED LIBRARIES  ==================
+# Use seacas/install-tpl.sh
+# These flags are recommended for LaGriT
+CGNS=NO MATIO=NO GNU_PARALLEL=NO FMT=NO SHARED=NO NEEDS_ZLIB=YES ./install-tpl.sh 
+
+# Result: lib/libhdf5.a lib/libhdf5_hl.a lib/libhdf5_tools.a lib/libnetcdf.a
+#
+# ==== RUN CMAKE  ====================================
+
+cd $ACCESS
+mkdir build && cd build
+FORTRAN=YES SHARED=NO ../cmake-exodus
+
+# result:
+# -- Build files have been written to: TPLs/seacas/build
+#    HAVE_NETCDF: YES
+
+# ==== BUILD and INSTALL EXODUS  =====================
+# In directory seacas/build
+make && make install
+
+# ==== SCRIPT DONE  ==================================
+# CHECK: libs and files used by lagrit located in TPLs/seacas
+# 
+# bsh% ls lib/*a
+# lib/libexodus.a      lib/libexoIIv2for32.a  lib/libhdf5_hl.a     lib/libnetcdf.a
+# lib/libexodus_for.a  lib/libhdf5.a        lib/libhdf5_tools.a  lib/libz.a
+# 
+# bsh% ls include/exo*
+# include/exodus_config.h  include/exodusII.h  include/exodusII.inc  include/exodusII_par.h
+# include/netcdf.h include/hdf5.h
+# 
+# Once Exodus is installed, use the following commands to build lagrit executable:
+# 
+# mkdir build/ && cd build/
+# cmake .. -DLAGRIT_BUILD_EXODUS=ON
+# make
+# or
+# make VERBOSE=1
+
--- a/241
+++ b/241
@@ -0,0 +1,241 @@
+#================================================================#
+#  LaGriT Makefile
+# -------------------------------------------------------------- #
+#  
+#  Targets:
+#    - release : build a LaGriT binary with shared libs
+#    - static : build a LaGriT binary with static libs
+#    - exodus : build the Exodus library
+#    - test : run the LaGriT test suite
+#    - help : show a help screen
+#    - header : build src/lagrit.h header file
+#    - clean : remove all object and mod files
+#    - clobber : remove all object and mod files *and* library
+#
+#  Variables:
+#    CC (default: gcc) : C source compiler
+#    FC (default: gfortran) : Fortran source compiler
+#    FC90 (default: gfortran) : Fortran90 source compiler
+#    WITH_EXODUS (default: 1) : Build with or without Exodus
+#    DEBUG (default: 0) : Built in debug (1) or optimized (0) mode
+#    EXO_LIB_DIR (default: LAGRIT_ROOT_DIR/seacas/lib) : ExodusII library location
+#    EXE_NAME (default: src/lagrit) : binary filename for LaGriT
+#    EXO_CMAKE_FLAGS (default: none) : Add custom CMake flags to pass to cmake-exodus
+#================================================================#
+#  TODO:
+#    - Add support for 32 bit machines
+
+CC := gcc
+CXX := g++
+FC := gfortran
+FC90 := $(FC)
+OBJDIR := objects/
+WITH_EXODUS := 1
+
+# Detect 64 or 32 bit arch; detect OS name
+BIT_SIZE := $(shell getconf LONG_BIT)
+OPSYS := $(shell uname -s)
+
+MAJOR_VERSION := 3
+MINOR_VERSION := 320
+BUILD_DATE := $(shell date +%Y/%m/%d)
+BUILD_TYPE := Release
+EXE_NAME := src/lagrit
+EXO_BUILD_DIR := $(shell pwd)
+EXO_LIB_DIR := $(shell pwd)/seacas/lib
+EXO_CMAKE_FLAGS := 
+
+LG_UTIL_LIB := lg_util_lib.a
+SRC_LIB := lagrit_lib.a
+
+define LAGRIT_H_TEXT
+c
+c----------------------------------------------------------------
+c Auto-generated LaGriT program banner
+c
+c Substitute the TAG strings with Date and Linux, Darwin, WIN, etc.
+c Compile library with updated lagrit.h used in writinit()
+c This template is preserved in lagrit.template.h
+c----------------------------------------------------------------
+c
+      integer        v_major, v_minor
+      parameter      (v_major=$(MAJOR_VERSION))
+      parameter      (v_minor=$(MINOR_VERSION))
+c
+      character*22   date_compile
+      character*8    os_name
+      character*16   my_name
+c
+      data my_name      /'lagrit'/
+c     os_name is used to find and write OS related files
+c     make sure it is a version recognized in Makefile
+c     and writinit.f for forming header info
+      data os_name      /'$(OPSYS)'/
+c
+      data date_compile /'$(BUILD_DATE) $(BUILD_TYPE) '/
+c
+      integer         NCall
+      save            NCall
+      character*8     Version
+      save            Version
+c
+c----------------------------------------------------------------
+c
+endef
+export LAGRIT_H_TEXT
+
+define LAGRIT_HELP
+----------------------- LAGRIT MAKEFILE -----------------------
+
+This is an automatic build tool for the Los Alamos Grid Toolbox.
+
+USAGE:
+
+  make [options] [target]
+
+TARGETS:
+
+- make release
+    Optimized build (with shared libraries)
+
+- make static
+    Optimized build (with static libraries)
+
+- make DEBUG=1 release
+    Debug build (with shared libraries)
+
+- make DEBUG=1 static
+    Debug build (with static libraries)
+
+- make exodus
+    Download and build the SANDIA ExodusII Fortran library.
+    By default, it will download to the current working directory.
+    This can be changed by running
+
+       make EXO_BUILD_DIR=/exodus/path/out/ exodus
+
+- make test
+    Run the LaGriT test suite on the created binary.
+    If you have changed or moved LaGriT from src/lagrit, use
+    the option EXE_NAME=/path/to/lagrit
+
+OPTIONS:
+
+    CC (default: gcc) : C source compiler
+    FC (default: gfortran) : Fortran source compiler
+    FC90 (default: gfortran) : Fortran90 source compiler
+    WITH_EXODUS (default: 1) : Build with or without Exodus
+    DEBUG (default: 0) : Built in debug (1) or optimized (0) mode
+    EXO_LIB_DIR (default: LAGRIT_ROOT_DIR/seacas/lib) : ExodusII library location
+    EXE_NAME (default: src/lagrit) : binary filename for LaGriT
+    EXO_CMAKE_FLAGS (default: none) : Add custom CMake flags to pass to cmake-exodus
+
+endef
+export LAGRIT_HELP
+
+# release, no exo, shared
+BUILDLIBS := src/lagrit_main.o src/lagrit_fdate.o src/$(SRC_LIB) lg_util/src/$(LG_UTIL_LIB)
+
+LINKERFLAGS := -fcray-pointer -fdefault-integer-8 -m64
+BUILDFLAGS  := -fcray-pointer -fdefault-integer-8 -m64 -fno-sign-zero -lm -lstdc++
+OSX_STATIC_LIBS := 
+SYS_LNK_FLAGS :=
+
+ifeq ($(OPSYS),Darwin)
+	LINKERFLAGS += -Dmacx64
+	BUILDFLAGS  += -Dmacx64
+	OSX_STATIC_LIBS := 
+else ifeq ($(OPSYS),Linux)
+	LINKERFLAGS += -Dlinx64
+	BUILDFLAGS  += -Dlinx64
+	SYS_LNK_FLAGS += -no-pie
+else ifeq ($(findstring CYGWIN_NT,$(OPSYS)),CYGWIN_NT)
+	LINKERFLAGS += -Dwin64
+	BUILDFLAGS  += -Dwin64
+endif
+
+ifeq ($(DEBUG),1)
+	LINKERFLAGS += -g -fbacktrace -ffpe-trap=invalid,zero,overflow,underflow,denormal
+	BUILDFLAGS +=  -g -fbacktrace -ffpe-trap=invalid,zero,overflow,underflow,denormal
+else
+	LINKERFLAGS += -O
+	BUILDFLAGS += -O
+endif
+
+ifeq ($(wildcard $(EXO_LIB_DIR)),)
+        EXO_LIB_DIR := /usr/lib
+endif
+
+ifeq ($(WITH_EXODUS),1)
+	BUILDFLAGS += -L$(EXO_LIB_DIR) -lexodus_for -lexodus -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl
+	FAIL_THRESH := 2
+else
+	FAIL_THRESH := 3
+endif
+
+.PHONY: release static header before clean clobber test exodus
+release: BUILD_TYPE = Release
+release: build
+
+build : header before
+	$(FC) -o $(EXE_NAME) $(SYS_LNK_FLAGS) $(BUILDLIBS) $(BUILDFLAGS)
+
+header :
+	@echo "$$LAGRIT_H_TEXT" > src/lagrit.h
+
+before : src/lagrit_main.o src/lagrit_fdate.o
+	make -C lg_util/src/ LIB=$(LG_UTIL_LIB) CC=$(CC) FC=$(FC) DEBUG=$(DEBUG)
+	make -C src/ LIB=$(SRC_LIB) WITHEXODUS=$(WITH_EXODUS) CC=$(CC) FC=$(FC) EXO_INCLUDE_DIR=$(EXO_LIB_DIR)/../include DEBUG=$(DEBUG)
+
+clean :
+	make -C lg_util/src/ clean
+	make -C src/ clean
+
+clobber : 
+	make -C lg_util/src/ clobber
+	make -C src/ clobber
+	rm src/*.o ; rm $(EXE_NAME)
+
+test :
+	@export LG_CWD=$(shell pwd); \
+	 cd test/; \
+	 python3 suite.py -f -l 1 -exe=$$LG_CWD/$(EXE_NAME) -hf=$(FAIL_THRESH);
+
+help : 
+	@echo "$$LAGRIT_HELP"
+
+exodus :
+	set -e; \
+	export CGNS=OFF; \
+	export MATIO=OFF; \
+	export SHARED=NO; \
+	export LG_DIR=`pwd`; \
+	export NEEDS_ZLIB=YES; \
+	export GNU_PARALLEL=OFF; \
+	export BUILD=YES; \
+	export CC=$(CC); export CXX=$(CXX); export FC=$(FC); export FC90=$(FC90); \
+	git clone https://github.com/gsjaardema/seacas.git $(EXO_BUILD_DIR)/seacas || true; \
+	cd $(EXO_BUILD_DIR)/seacas; \
+	git checkout ba60a4d19516c433967581fbb8525c56f03b7c3e; \
+	export ACCESS=`pwd`; \
+	if [[ `uname -s` == *"CYGWIN"* ]]; then \
+		BUILD=NO ./install-tpl.sh; \
+		sed -i 's/defined(_WIN32) || defined(__CYGWIN__)/defined(_WIN32)/g' `ls -t -d TPL/zlib-* | head -1`/gzguts.h; \
+		export DOWNLOAD=NO; \
+	fi; \
+	./install-tpl.sh; \
+	cd TPL; \
+	../cmake-exodus $(EXO_CMAKE_FLAGS) -DFORTRAN=YES; \
+	make && make install; \
+	cd $(LG_DIR); \
+	echo "Build directory:"; \
+	echo "   $(EXO_BUILD_DIR)/seacas/lib"; \
+	echo ""
+
+static: BUILD_TYPE = Static
+static: LINKERFLAGS += -static
+static: BUILDFLAGS += -static-libgfortran -static-libgcc
+static: build
+
+%.o : %.f
+	$(FC) $(LINKERFLAGS) -c -o $@ $<
--- a/PyLaGriT/README
+++ b/PyLaGriT/README
@@ -0,0 +1,14 @@
+PyLaGriT Class
+##############
+
+- The PyLaGriT class provides a python interface to the Los Alamos Grid Toolbox. 
+- The PyLaGrit class is derived class of the perplex packages spawn class, and its objects contains all of spawn's functionality. 
+- Commands can be sent using LaGriT syntax as string arguments to the sendline method. 
+- Direct access to the LaGriT shell is provided by the interact method. 
+- Subclasses of the PyLaGrit class include mesh object (MO), surface, and region and can be created using various methods to PyLaGriT objects. 
+- The mesh object subclass contains subclasses pset and eltset. 
+- Subclasses are contained in dictionaries in the parent class. 
+- The mesh object class contains gmv and paraview methods that dump the appropriate files and open them in viewer. 
+- PyLaGriT can be accessed in Julia using the Julia PyCall package (refer to PyLaGriT/examples/julia folder in the source code)
+
+See Documentation at https://lanl.github.io/LaGriT/pylagrit/original/index.html
--- a/PyLaGriT/documentation/Makefile
+++ b/PyLaGriT/documentation/Makefile
@@ -0,0 +1,233 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  epub3      to make an epub3"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  dummy      to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	rm -rf $(BUILDDIR)/html
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	find $(BUILDDIR)/html -name "*.html" | xargs sed -i'.original' -e 's/_static/static/g'
+	find $(BUILDDIR)/html -name "*.html" | xargs sed -i'.original' -e 's/_image/image/g'
+	find $(BUILDDIR)/html -name "*.html" | xargs sed -i'.original' -e 's/_sources/sources/g'
+	mv $(BUILDDIR)/html/_static $(BUILDDIR)/html/static
+	mv $(BUILDDIR)/html/_images $(BUILDDIR)/html/images
+	mv $(BUILDDIR)/html/_sources $(BUILDDIR)/html/sources
+	rm -f $(BUILDDIR)/html/*.original
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PyLaGriT.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyLaGriT.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PyLaGriT"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyLaGriT"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."
--- a/PyLaGriT/documentation/source/autodoc.rst
+++ b/PyLaGriT/documentation/source/autodoc.rst
@@ -0,0 +1,21 @@
+.. _class_docs:
+
+Class Documentation
+-------------------
+
+.. toctree::
+
+    PyLaGriT Class <autodoc_pylagrit.rst>
+
+    Mesh Class <autodoc_mo.rst>
+
+    Point Set Class <autodoc_pset.rst>
+
+    Element Set Class <autodoc_eltset.rst>
+
+    Face Set Class <autodoc_faceset.rst>
+
+    Region Class <autodoc_region.rst>
+
+    
+
--- a/PyLaGriT/documentation/source/autodoc_eltset.rst
+++ b/PyLaGriT/documentation/source/autodoc_eltset.rst
@@ -0,0 +1,8 @@
+Element Set Object
+------------------
+.. automodule:: pylagrit
+
+.. autoclass:: EltSet
+   :members:
+   :undoc-members:
+
--- a/PyLaGriT/documentation/source/autodoc_faceset.rst
+++ b/PyLaGriT/documentation/source/autodoc_faceset.rst
@@ -0,0 +1,8 @@
+Face Set Object
+---------------
+.. automodule:: pylagrit
+
+.. autoclass:: FaceSet
+   :members:
+   :undoc-members:
+
--- a/PyLaGriT/documentation/source/autodoc_mo.rst
+++ b/PyLaGriT/documentation/source/autodoc_mo.rst
@@ -0,0 +1,8 @@
+Mesh Object
+-----------
+.. automodule:: pylagrit
+
+.. autoclass:: MO
+   :members:
+   :undoc-members:
+
--- a/PyLaGriT/documentation/source/autodoc_pset.rst
+++ b/PyLaGriT/documentation/source/autodoc_pset.rst
@@ -0,0 +1,8 @@
+Point Set Object
+----------------
+.. automodule:: pylagrit
+
+.. autoclass:: PSet
+   :members:
+   :undoc-members:
+
--- a/PyLaGriT/documentation/source/autodoc_pylagrit.rst
+++ b/PyLaGriT/documentation/source/autodoc_pylagrit.rst
@@ -0,0 +1,8 @@
+PyLaGriT
+--------
+.. automodule:: pylagrit
+
+.. autoclass:: PyLaGriT
+   :members:
+   :undoc-members:
+
--- a/PyLaGriT/documentation/source/autodoc_region.rst
+++ b/PyLaGriT/documentation/source/autodoc_region.rst
@@ -0,0 +1,8 @@
+Region Object
+-------------
+.. automodule:: pylagrit
+
+.. autoclass:: Region
+   :members:
+   :undoc-members:
+
--- a/PyLaGriT/documentation/source/conf.py
+++ b/PyLaGriT/documentation/source/conf.py
@@ -0,0 +1,343 @@
+# -*- coding: utf-8 -*-
+#
+# PyLaGriT documentation build configuration file, created by
+# sphinx-quickstart on Tue Oct  4 10:10:46 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.mathjax',
+    #'sphinx.ext.githubpages',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'PyLaGriT'
+copyright = u'2016, Dylan R. Harp'
+author = u'Dylan R. Harp'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'0'
+# The full version, including alpha/beta/rc tags.
+release = u'0.0.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = u'PyLaGriT v0.0.0'
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+# html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = True
+
+# If false, no index is generated.
+#
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PyLaGriTdoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+     # The paper size ('letterpaper' or 'a4paper').
+     #
+     # 'papersize': 'letterpaper',
+
+     # The font size ('10pt', '11pt' or '12pt').
+     #
+     # 'pointsize': '10pt',
+
+     # Additional stuff for the LaTeX preamble.
+     #
+     # 'preamble': '',
+
+     # Latex figure (float) alignment
+     #
+     # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'PyLaGriT.tex', u'PyLaGriT Documentation',
+     u'Dylan R. Harp', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# It false, will not define \strong, \code, 	itleref, \crossref ... but only
+# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
+# packages.
+#
+# latex_keep_old_macro_names = True
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'pylagrit', u'PyLaGriT Documentation',
+     [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'PyLaGriT', u'PyLaGriT Documentation',
+     author, 'PyLaGriT', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False
--- a/PyLaGriT/documentation/source/cube.png
+++ b/PyLaGriT/documentation/source/cube.png
--- a/PyLaGriT/documentation/source/gettingstarted.rst
+++ b/PyLaGriT/documentation/source/gettingstarted.rst
@@ -0,0 +1,73 @@
+Getting Started
+===============
+
+Installation
+------------
+
+The Python module PyLaGriT allows LaGriT to be accessed interactively and in batch mode from Python. 
+To install PyLaGriT on your system, change to the PyLaGriT directory and run ``python setup.py install``. 
+Alternatively, the PyLaGriT folder can be added to your **PYTHONPATH** environment variable. 
+Due to the use of the pexpect Python module, PyLaGriT does not work on Windows. 
+It has been tested on Mac and Linux operating systems. 
+
+Since PyLaGriT is simply a frontend for LaGriT, you will need a lagrit executable to use PyLaGriT.
+To use the paraview and gmv methods, you will need ParaView (http://www.paraview.org) and GMV (http://www.generalmeshviewer.com) installed, respectively.
+
+To avoid specifying the LaGriT, ParaView, and GMV executable locations, copy the **pylagritrc_example** file:
+
+.. literalinclude:: ../../pylagritrc_example
+
+in the PyLaGriT folder to your home directory or working directory changing its name to either **pylagritrc** or **.pylagritrc** and uncomment and change the path locations.
+
+Simple example
+--------------
+
+The following is a PyLaGriT script for creating a simple cube shaped mesh using the :func:`gridder <pylagrit.PyLaGriT.gridder>` and `connect <pylagrit.PyLaGriT.connect>` methods:
+
+.. code-block:: python
+
+    # Import PyLaGriT class from pylagrit module
+    from pylagrit import PyLaGriT
+    
+    # Create PyLaGriT object
+    # This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified
+    l = PyLaGriT()
+
+    # Create x,y,z arrays for location of points
+    x = range(1,5)
+    y = range(1,5)
+    z = range(1,5)
+
+    # Create mesh object using x,y,z arrays
+    m = l.gridder(x,y,z)
+
+    # Connect points
+    m.connect()
+
+    # Visualize connected mesh using ParaView
+    # This assumes that pylagritrc is being used so that exe option does not need to be specified
+    m.paraview()
+
+The script can be pasted line by line into a Python or IPython terminal, or saved in a file (e.g., ``script.py``) and run on the command line as ``python script.py``.
+
+This will open up ParaView with the mesh loaded:
+
+.. image:: cube.png
+
+Next steps
+----------
+
+Additional example PyLaGriT scripts are provided in the PyLaGriT/examples folder and in the :ref:`class_docs`. 
+
+Combining LaGriT and Python functionality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+An example of using PyLaGriT to facilitate looping over LaGriT functionality is described in the :func:`merge method <pylagrit.PyLaGriT.merge>` documentation, where a mesh is successively copied, translated and merged into a larger mesh.
+Other examples of usage are provided for other methods and more will be added in the future.
+
+User defined error checking
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Since PyLaGriT stores the LaGriT terminal output from each command in the PyLaGriT object attribute ``before``, user-defined error checking can be easily implemented.
+The example provided with the :func:`refine method <pylagrit.EltSet.refine>` demonstrates this by checking for the string `The mesh is complete but could not include all points.` in the LaGriT output using ``lg.before``. 
+In this example, an error message is printed to the screen and the script is aborted.
--- a/PyLaGriT/documentation/source/index.rst
+++ b/PyLaGriT/documentation/source/index.rst
@@ -0,0 +1,42 @@
+.. PyLaGriT documentation master file, created by
+   sphinx-quickstart on Tue Oct  4 10:10:46 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PyLaGriT, Python interface for LaGriT
+=====================================
+
+.. include:: ../../README
+
+.. toctree::
+   :maxdepth: 2
+
+   Getting Started <gettingstarted.rst>    
+
+   Stratigraphic Hex Mesh Tutorial <stratigraphic.rst>
+
+   Class Documentation <autodoc.rst>
+
+PyLaGriT source code is packaged with LaGriT source code `here <https://github.com/lanl/LaGriT>`_.
+
+Example scripts can be found `here <https://github.com/lanl/LaGriT/tree/master/PyLaGriT/examples>`_.
+
+Development team
+################
+* Dylan Harp <dharp@lanl.gov>
+
+* Daniel Livingston <livingston@lanl.gov>
+
+* James (Joe) Beisman <jjbeisman@gmail.com>
+
+* Terry Miller <tamiller@lanl.gov>
+
+* Carl Gable <gable@lanl.gov>
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
--- a/PyLaGriT/documentation/source/stratigraphic.rst
+++ b/PyLaGriT/documentation/source/stratigraphic.rst
@@ -0,0 +1,11 @@
+Stratigraphic Hex Mesh Tutorial
+===============================
+Written by Guoyan Jiang (gyjiang@whu.edu.cn) with technical support from Dylan Harp (dharp@lanl.gov) and Terry Miller (tamiller@lanl.gov). 
+The associated LaGriT tutorial is `here <https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html>`_.
+This example script can be downloaded `here <https://github.com/lanl/LaGriT/blob/master/PyLaGriT/examples/stratigraphic_hex_mesh_tutorial.py>`_.
+
+.. literalinclude:: ../../examples/stratigraphic_hex_mesh_tutorial.py
+
+The final result:
+
+.. image:: stratigraphy.png
--- a/PyLaGriT/documentation/source/stratigraphy.png
+++ b/PyLaGriT/documentation/source/stratigraphy.png
--- a/PyLaGriT/examples/arctic_2D/bottom_peat2.avs
+++ b/PyLaGriT/examples/arctic_2D/bottom_peat2.avs
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--- a/PyLaGriT/examples/arctic_2D/mesh_pylagrit.py
+++ b/PyLaGriT/examples/arctic_2D/mesh_pylagrit.py
@@ -0,0 +1,109 @@
+from pylagrit import PyLaGriT
+import numpy
+
+# Variables
+nx = 50 # Number of points in x direction
+dy = 0.25 # width of cells in y direction
+distance = 12.34364319 # distance in x direction
+
+l = PyLaGriT()
+
+# Create base layer
+layer = l.create_qua()
+layer.createpts_xyz((nx,2,1),[0.,0.,0.],[distance,dy,0.],rz_switch=[1,1,1],connect=True)
+layer.setatt('itetclr',1)
+layer.minmax_xyz()
+
+# Create top of mesh
+# Collapse y values
+layer.addatt('y_save',vtype='vdouble',rank='scalar')
+layer.copyatt('yic','y_save')
+layer.setatt('yic',0.)
+
+# Read in lidar top elevations
+peat_surf_pts = l.read('surface_coords2.avs')
+peat_surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+peat_surf_pts.copyatt('zic','z_save')
+peat_surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to layer mo
+layer.addatt('z_val',vtype='vdouble',rank='scalar')
+layer.interpolate_voronoi('z_val',peat_surf_pts,'z_save')
+layer.copyatt('y_save','yic')
+layer.copyatt('z_val','zic')
+
+# Save peat top
+layer.setatt('imt',1)
+layer.setatt('itetclr',1)
+layer.dump('tmp_lay_peat_top.inp')
+peat_surf_pts.delete()
+
+# Read in peat bottom elevations
+peat_bot_pts = l.read('bottom_peat2.avs')
+peat_bot_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+peat_bot_pts.copyatt('zic','z_save')
+peat_bot_pts.setatt('zic',0.)
+
+# Interpolate peat bottom elevations to layer mo
+layer.setatt('yic',0.)
+layer.addatt('z_val',vtype='vdouble',rank='scalar')
+layer.interpolate_voronoi('z_val',peat_bot_pts,'z_save')
+layer.copyatt('y_save','yic')
+layer.delatt('y_save')
+layer.copyatt('z_val','zic')
+layer.delatt('z_val')
+
+# Save peat bot
+layer.dump('tmp_lay_peat_bot.inp')
+
+# Copy layer to peat_bot for use in generating additional layers
+peat_bot = layer.copy()
+
+stack_files = ['tmp_lay_peat_top.inp 1,5']
+stack_files.append('tmp_lay_peat_bot.inp 1,33')
+
+# Layer depths?
+#           1   2   3    4    5    6    7   8    9   10
+layers = [ 1.0, 0.16, 0.32, 0.64, 1.28, 3.2, 6.4, 8.0]
+addnum = [   3,    3,    3,    3,    4,   4,   3,   5]
+matnum = [2]*len(layers) 
+
+layer_interfaces = numpy.cumsum(layers)
+i = 1
+for li,m,a in zip(layer_interfaces,matnum,addnum):
+    layer.math('sub','zic',li,cmosrc=peat_bot)
+    stack_files.append('tmp_lay'+str(i)+'.inp '+str(int(m))+', '+str(a))
+    layer.dump('tmp_lay'+str(i)+'.inp')
+    i += 1
+
+layer.setatt('zic',-45.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+stack_files.reverse()
+
+# Create stacked layer mesh and fill
+stack = l.create()
+stack.stack_layers(stack_files,file_type='avs',flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('arctic_siteb_2d.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain peat',
+            20000:'computational domain upper mineral'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('arctic_siteb_2d_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('arctic_siteb_2d_par4_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.par',matnames=matnames,facenames=facenames)
--- a/PyLaGriT/examples/arctic_2D/surface_coords2.avs
+++ b/PyLaGriT/examples/arctic_2D/surface_coords2.avs
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--- a/PyLaGriT/examples/arctic_2D_new/Topo_Profile_NS_ERT.csv
+++ b/PyLaGriT/examples/arctic_2D_new/Topo_Profile_NS_ERT.csv
@@ -0,0 +1,142 @@
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--- a/PyLaGriT/examples/arctic_2D_new/transect.py
+++ b/PyLaGriT/examples/arctic_2D_new/transect.py
@@ -0,0 +1,118 @@
+from pylagrit import PyLaGriT
+import numpy as np
+
+lg = PyLaGriT()
+
+# Create base layer from x=10 to x=21 to match bert02 mesh
+x = np.linspace(10.,21,(21.-10.)/0.25+1)
+y = [0.,0.25]
+top = lg.gridder(x,y,elem_type='quad',connect=True)
+
+# Create top of mesh
+# Collapse y values
+top.addatt('y_save',vtype='vdouble',rank='scalar')
+top.copyatt('yic','y_save')
+top.setatt('yic',0.)
+
+# Read in top elevations
+d = np.genfromtxt("./Topo_Profile_NS_ERT.csv", delimiter=",", names=True)
+surf_pts = lg.points(x=d['Distance_m'],z=d['Z'],elem_type='quad')
+surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+surf_pts.copyatt('zic','z_save')
+surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to top
+top.addatt('z_val',vtype='vdouble',rank='scalar')
+top.interpolate_voronoi('z_val',surf_pts,'z_save')
+top.copyatt('y_save','yic')
+top.copyatt('z_val','zic')
+
+# Save top
+top.setatt('imt',1)
+top.setatt('itetclr',1)
+top.dump('tmp_lay_peat_top.inp')
+surf_pts.delete()
+
+# Copy top to create intermediate layers
+layer = top.copy()
+
+# Begin to construct stacked layer arrays
+# Names of layer files
+stack_files = ['tmp_lay_peat_top.inp']
+# Material id, should be same length as length of stack_files
+matids = [1]
+
+# Add (15) 2 cm thick layers
+layer.math('sub',0.02*15,'zic')
+layer.dump('tmp_lay1.inp')
+stack_files.append('tmp_lay1.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers = [14]
+matids.append(1)
+
+# Add (15) 5 cm thick layers
+layer.math('sub',0.05*15,'zic')
+layer.dump('tmp_lay2.inp')
+stack_files.append('tmp_lay2.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers.append(14)
+matids.append(2)
+
+# Add (15) 10 cm thick layers
+layer.math('sub',0.1*15,'zic')
+layer.dump('tmp_lay3.inp')
+stack_files.append('tmp_lay3.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers.append(14)
+matids.append(2)
+
+# Add (15) 1 c thick layers
+layer.math('sub',1*15,'zic')
+layer.dump('tmp_lay3.inp')
+stack_files.append('tmp_lay3.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers.append(14)
+matids.append(2)
+
+layer.math('sub',2.*15.,'zic')
+layer.dump('tmp_lay4.inp')
+stack_files.append('tmp_lay4.inp')
+nlayers.append(14)
+matids.append(2)
+ 
+layer.setatt('zic',-45.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+nlayers.append(1)
+matids.append(2)
+
+# Create stacked layer mesh and fill
+# Reverse arrays so that order is from bottom to top!!!
+stack_files.reverse()
+nlayers.reverse()
+matids.reverse()
+stack = lg.create()
+stack.stack_layers(stack_files,nlayers=nlayers,matids=matids,flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('arctic_siteb_2d.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain peat',
+            20000:'computational domain upper mineral'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('arctic_siteb_2d_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('arctic_siteb_2d_par4_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.par',matnames=matnames,facenames=facenames)
--- a/PyLaGriT/examples/arctic_w_ice_wedges/meshdoc_cabolt_v1.pdf
+++ b/PyLaGriT/examples/arctic_w_ice_wedges/meshdoc_cabolt_v1.pdf
--- a/PyLaGriT/examples/arctic_w_ice_wedges/transectNWSE.PY
+++ b/PyLaGriT/examples/arctic_w_ice_wedges/transectNWSE.PY
@@ -0,0 +1,160 @@
+from pylagrit import PyLaGriT
+import numpy as np
+
+lg = PyLaGriT()
+
+# Create base layer, with x matching s from the csv file 
+x = np.linspace(0.,29.75,(29.75-0.)/0.25+1)
+y = [0.,0.25]
+top = lg.gridder(x,y,elem_type='quad',connect=True)
+
+# Create top of mesh
+# Collapse y values
+top.addatt('y_save',vtype='vdouble',rank='scalar')
+top.copyatt('yic','y_save')
+top.setatt('yic',0.)
+
+# Read in top elevations
+d = np.genfromtxt("transectNWSE.csv", delimiter=",", names=True)
+coords = np.column_stack([d['s'],np.zeros_like(d['s']),d['z']])
+surf_pts = lg.points(coords,elem_type='quad')
+surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+surf_pts.copyatt('zic','z_save')
+surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to top
+top.addatt('z_val',vtype='vdouble',rank='scalar')
+top.interpolate_voronoi('z_val',surf_pts,'z_save')
+top.copyatt('y_save','yic')
+top.copyatt('z_val','zic')
+
+# Save top
+top.setatt('imt',1)
+top.setatt('itetclr',1)
+top.dump('tmp_lay_peat_top.inp')
+surf_pts.delete()
+
+# Copy top to create intermediate layers
+layer = top.copy()
+
+# Begin to construct stacked layer arrays
+# Names of layer files
+stack_files = ['tmp_lay_peat_top.inp']
+# Material id, should be same length as length of stack_files
+matids = [1]
+
+# Add (2) 1 cm thick layers
+layer.math('sub',0.01*2,'zic')
+layer.dump('tmp_lay1.inp')
+stack_files.append('tmp_lay1.inp')
+nlayers = [1]
+matids.append(1)
+
+# Add (6) 2 cm thick layers
+layer.math('sub',0.02*6,'zic')
+layer.dump('tmp_lay2.inp')
+stack_files.append('tmp_lay2.inp')
+nlayers.append(5)
+matids.append(2)
+
+# Add (8) 2 cm thick layers
+layer.math('sub',0.02*8,'zic')
+layer.dump('tmp_lay3.inp')
+stack_files.append('tmp_lay3.inp')
+nlayers.append(7)
+matids.append(3)
+
+# Add (15) 5 cm thick layers
+layer.math('sub',0.05*15,'zic')
+layer.dump('tmp_lay4.inp')
+stack_files.append('tmp_lay4.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add (15) 10 cm thick layers
+layer.math('sub',0.1*15,'zic')
+layer.dump('tmp_lay5.inp')
+stack_files.append('tmp_lay5.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add (15) 1 m thick layers
+layer.math('sub',1*15,'zic')
+layer.dump('tmp_lay6.inp')
+stack_files.append('tmp_lay6.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add (15) 2 m thick layers
+layer.math('sub',2.*15.,'zic')
+layer.dump('tmp_lay7.inp')
+stack_files.append('tmp_lay7.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add the bottom layer, and make the bottom boundary flat 
+layer.setatt('zic',29.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp')
+nlayers.append(0)
+matids.append(3)
+
+# Create stacked layer mesh and fill
+# Reverse arrays so that order is from bottom to top!!!
+stack_files.reverse()
+nlayers.reverse()
+matids.reverse()
+stack = lg.create()
+stack.stack_layers(stack_files,nlayers=nlayers,matids=matids,flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Define ice wedges
+def iceWedgePoints( vtxL, vtxB, vtxR, dx, dz ):
+    xnodes = np.arange( vtxL[0], vtxR[0], dx )
+    znodes = np.arange( vtxB[1], vtxR[1], dz )
+    xg, zg = np.meshgrid(xnodes, znodes)
+    xg = xg.flatten(); zg = zg.flatten()
+    m1 = (vtxB[1] - vtxL[1])/(vtxB[0] - vtxL[0])
+    b1 = vtxL[1] - m1*vtxL[0]
+    m2 = (vtxR[1] - vtxB[1])/(vtxR[0] - vtxB[0])
+    b2 = vtxR[1] - m2*vtxR[0]
+    idx = [ (zg[i] > m1*xg[i]+b1) & (zg[i] > m2*xg[i]+b2)  for i in range(len(zg)) ]
+    iwx = xg[np.array(idx)]; iwz = zg[np.array(idx)]
+    iwy = np.concatenate( (np.ones(iwx.size)*0.05, np.ones(iwx.size)*0.2) )    
+    iwx = np.tile(iwx, 2); iwz = np.tile(iwz, 2)
+   
+    return iwx, iwy, iwz
+
+iw1x, iw1y, iw1z = iceWedgePoints( [3.25, 78.3], [3.875, 75.0], [4.5, 78.3], 0.125, 0.01 )
+iw1pts = lg.points(np.column_stack([iw1x, iw1y, iw1z]), connect=True)
+iw1 = stack_hex.eltset_object(iw1pts)
+iw1.setatt('itetclr', 4)
+
+iw2x, iw2y, iw2z = iceWedgePoints( [18.5, 78.4], [19.125, 75.1], [19.75,78.4], 0.125, 0.01 )
+iw2pts = lg.points(np.column_stack([iw2x, iw2y, iw2z]), connect=True)
+iw2 = stack_hex.eltset_object(iw2pts)
+iw2.setatt('itetclr', 4)
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('transectNWSE.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain moss',
+            20000:'computational domain peat',
+            30000:'computational domain mineral',
+            40000:'computational domain ice wedge'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('transectNWSE_mesh.xml','../../mesh/transectNWSE.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('transectNWSE_parmesh.xml','../../mesh/4/transectNWSE.par',matnames=matnames,facenames=facenames)
--- a/PyLaGriT/examples/arctic_w_ice_wedges/transectNWSE.csv
+++ b/PyLaGriT/examples/arctic_w_ice_wedges/transectNWSE.csv
@@ -0,0 +1,121 @@
+s,x,y,z
+0,431503.263849712,7748935.90919019,79.01
+0.25,431503.436233142,7748935.72812679,79.01
+0.5,431503.608616571,7748935.5470634,79.01
+0.75,431503.781,7748935.366,79.01
+1,431503.953383429,7748935.1849366,79.01
+1.25,431504.125766858,7748935.00387321,79.03
+1.5,431504.298150288,7748934.82280981,79.0733333333333
+1.75,431504.470533717,7748934.64174642,79.1166666666667
+2,431504.642917146,7748934.46068302,79.16
+2.25,431504.815300575,7748934.27961962,79.165
+2.5,431504.987684004,7748934.09855623,79.17
+2.75,431505.160067433,7748933.91749283,79.17
+3,431505.332450863,7748933.73642944,79.13
+3.25,431505.504834292,7748933.55536604,79.09
+3.5,431505.677217721,7748933.37430265,79.035
+3.75,431505.84960115,7748933.19323925,78.98
+4,431506.021984579,7748933.01217585,78.97
+4.25,431506.194368009,7748932.83111246,79.03
+4.5,431506.366751438,7748932.65004906,79.09
+4.75,431506.539134867,7748932.46898567,79.12
+5,431506.711518296,7748932.28792227,79.118
+5.25,431506.883901725,7748932.10685887,79.116
+5.5,431507.056285155,7748931.92579548,79.114
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--- a/PyLaGriT/examples/basin_bnd_ply_rescale.inp
+++ b/PyLaGriT/examples/basin_bnd_ply_rescale.inp
@@ -0,0 +1,315 @@
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--- a/PyLaGriT/examples/create_exo.py
+++ b/PyLaGriT/examples/create_exo.py
@@ -0,0 +1,8 @@
+from pylagrit import PyLaGriT
+l = PyLaGriT()
+m = l.create()
+m.createpts_xyz((3,3,3),(0.,0.,0.),(1.,1.,1.),rz_switch=[1,1,1],connect=True)
+m.status ()
+m.status (brief=True)
+fs = m.create_boundary_facesets(base_name='faceset_bounds')
+m.dump_exo('cube.exo',facesets=fs.values())
--- a/PyLaGriT/examples/createpts_dxyz.py
+++ b/PyLaGriT/examples/createpts_dxyz.py
@@ -0,0 +1,28 @@
+from pylagrit import PyLaGriT
+l = PyLaGriT()
+
+# Create 2x2x2 cell mesh
+m = l.create()
+m.createpts_dxyz((0.5,0.5,0.5),(0.,0.,0.),(1.,1.,1.),rz_switch=[1,1,1],connect=True)
+m.paraview()
+#m.gmv()
+
+# Create 2x2x2 mesh where maxs will be truncated to nearest value under given maxs
+m_under = l.create()
+m_under.createpts_dxyz((0.4,0.4,0.4),(0.,0.,0.),(1.,1.,1.),rz_switch=[1,1,1],connect=True)
+m_under.paraview()
+#m_under.gmv()
+
+# Create 3x3x3 mesh where maxs will be truncated to nearest value over given maxs
+m_over = l.create()
+m_over.createpts_dxyz((0.4,0.4,0.4),(0.,0.,0.),(1.,1.,1.),clip='over',rz_switch=[1,1,1],connect=True)
+m_over.paraview()
+#m_over.gmv()
+
+# Create 3x3x3 mesh where x and y maxs will be truncated to nearest value over given maxs
+# and z min will be truncated  to nearest value 
+m_mixed = l.create()
+m_mixed.createpts_dxyz((0.4,0.4,0.4),(0.,0.,-1.),(1.,1.,0.),hard_bound=('min','min','max'),clip=('under','under','over'),rz_switch=[1,1,1],connect=True)
+m_mixed.paraview()
+#m_over.gmv()
+
--- a/PyLaGriT/examples/ex_convert_files.py
+++ b/PyLaGriT/examples/ex_convert_files.py
@@ -0,0 +1,17 @@
+#To use pylagrit, import the module.
+import pylagrit
+
+#Create your pylagrit session.
+lg = pylagrit.PyLaGriT()
+
+#Create a mesh object and dump it to a gmv file 'test.gmv'.
+mo = lg.create(name='test')
+mo.createpts_brick_xyz((5,5,5), (0,0,0), (5,5,5,))
+mo.dump('gmv', 'test.gmv')
+
+#Convert test.gmv to exoduce and contour files.
+lg.convert('test.gmv', 'exo')
+lg.convert('test.gmv', 'avs')
+
+
+
--- a/PyLaGriT/examples/ex_gridder.py
+++ b/PyLaGriT/examples/ex_gridder.py
@@ -0,0 +1,13 @@
+from pylagrit import PyLaGriT
+import numpy
+
+lg = PyLaGriT()
+
+x0 = -numpy.logspace(1,2,15,endpoint=True)
+x1 = numpy.arange(-10,10,1)
+x2 = -x0
+x = numpy.concatenate([x0,x1,x2])
+y = x
+mqua = lg.gridder(x,y,elem_type='quad',connect=True)
+
+mqua.paraview()
--- a/PyLaGriT/examples/ex_merge_mesh_objects.py
+++ b/PyLaGriT/examples/ex_merge_mesh_objects.py
@@ -0,0 +1,30 @@
+################################################################################
+# This example shows how to merge multiple mesh objects together.              #
+################################################################################
+
+#To use pylagrit, import the module.
+import pylagrit
+import numpy
+
+#Instantiate the lagrit object.
+lg = pylagrit.PyLaGriT()
+
+# Create list with mesh object as first element
+dxyz = numpy.array([0.25]*3)
+mins = numpy.array([0.]*3)
+maxs = numpy.array([1.]*3)
+ms = [lg.createpts_dxyz(dxyz,mins,maxs,'tet',connect=True)]
+
+# Create three new mesh objects, each one directly above the other
+for i in range(3):
+    ms.append(ms[-1].copy())
+    ms[-1].trans(ms[-1].mins,ms[-1].mins+numpy.array([0.,0.,1.]))
+
+# Merge list of mesh objects and clean up
+mo_merge = lg.merge(ms)
+for mo in ms: mo.delete()
+mo_merge.rmpoint_compress(filter_bool=True,resetpts_itp=True)
+
+mo_merge.paraview(filename='mo_merge.inp')
+
+
--- a/PyLaGriT/examples/ex_read_lagrit_binary_mos.py
+++ b/PyLaGriT/examples/ex_read_lagrit_binary_mos.py
@@ -0,0 +1,28 @@
+#To use pylagrit, import the module.
+import pylagrit
+import numpy
+
+#Instantiate the lagrit object.
+lg = pylagrit.PyLaGriT()
+
+# Create list with mesh object as first element
+dxyz = numpy.array([0.25]*3)
+mins = numpy.array([0.]*3)
+maxs = numpy.array([1.]*3)
+ms = [lg.createpts_dxyz(dxyz,mins,maxs,'tet',connect=True,name='testmo')]
+
+# Create three new mesh objects, each one directly above the other
+for i in range(3):
+    ms.append(ms[-1].copy())
+    ms[-1].trans(ms[-1].mins,ms[-1].mins+numpy.array([0.,0.,1.]))
+
+lg.dump('lagrit_binary.lg')
+lg.close()
+
+lg = pylagrit.PyLaGriT()
+ms_read = lg.read('lagrit_binary.lg')
+
+print('Name of mesh object read in should be testmo, is: ', ms_read.name)
+
+
+
--- a/PyLaGriT/examples/ex_read_mesh.py
+++ b/PyLaGriT/examples/ex_read_mesh.py
@@ -0,0 +1,18 @@
+#To use pylagrit, import the module.
+import pylagrit
+
+#Create your pylagrit session.
+lg = pylagrit.PyLaGriT()
+
+#Create a mesh object and dump it to a gmv file 'test.gmv'.
+mo = lg.create(name='test')
+mo.createpts_brick_xyz((5,5,5), (0,0,0), (5,5,5,))
+mo.dump('test.gmv')
+mo.dump('test.avs')
+mo.dump('test.lg')
+
+mo1 = lg.read('test.gmv')
+mo2 = lg.read('test.avs')
+mo3 = lg.read('test.lg',name='test')
+
+
--- a/PyLaGriT/examples/ex_refine_edge.py
+++ b/PyLaGriT/examples/ex_refine_edge.py
@@ -0,0 +1,42 @@
+from pylagrit import PyLaGriT
+import numpy
+import sys
+
+df = 0.0005 # Fault half aperture
+lr = 7 # Levels of refinement
+nx = 4 # Number of base mesh blocks in x direction
+nz = 20 # Number of base mesh blocks in z direction
+d_base = df*2**(lr+1) # Calculated dimension of base block
+w = d_base*nx # Calculated width of model
+d = d_base*nz # Calculated depth of model
+
+lg = PyLaGriT()
+
+# Create discrete fracture mesh
+dxyz = numpy.array([d_base,d_base,0.])
+mins = numpy.array([0.,-d,0.])
+maxs = numpy.array([w,0,0])
+mqua = lg.createpts_dxyz(dxyz,mins,maxs,'quad',hard_bound=('min','max','min'),connect=True)
+
+for i in range(lr):
+    prefine = mqua.pset_geom_xyz(mins-0.1,(0.0001,0.1,0))
+    erefine = prefine.eltset()
+    erefine.refine()
+    prefine.delete()
+    erefine.delete()
+
+mtri = mqua.copypts('triplane')
+mtri.connect()
+# Make sure that not nodes are lost during connect
+if 'The mesh is complete but could not include all points.' in str(lg.before):
+    print("Error: Lost some points during connect, not completing mesh and exiting workflow!\n")
+    sys.exit()
+mtri.tri_mesh_output_prep()
+mtri.reorder_nodes(cycle='xic yic zic')
+pfault = mtri.pset_geom_xyz(mins-0.1,(0.0001,0.1,0))
+psource = mtri.pset_geom_xyz(mins-0.1,mins+0.0001)
+mtri.setatt('imt',1)
+pfault.setatt('imt',10)
+psource.setatt('imt',20)
+
+mtri.paraview(filename='discrete_fracture.inp')
--- a/PyLaGriT/examples/ex_rotate.py
+++ b/PyLaGriT/examples/ex_rotate.py
@@ -0,0 +1,16 @@
+from pylagrit import PyLaGriT
+import numpy
+
+x = numpy.arange(0,10.1,1)
+y = x
+z = [0,1]
+
+lg = PyLaGriT()
+mqua = lg.gridder(x,y,z,elem_type='hex',connect=True)
+
+mqua.rotateln([mqua.xmin-0.1,0,0],[mqua.xmax+0.1,0,0],25)
+
+mqua.dump_exo('rotated.exo')
+mqua.dump_ats_xml('rotated.xml','rotated.exo')
+
+mqua.paraview()
--- a/PyLaGriT/examples/ex_rotate_stack.py
+++ b/PyLaGriT/examples/ex_rotate_stack.py
@@ -0,0 +1,47 @@
+from pylagrit import PyLaGriT
+import numpy
+
+x = numpy.arange(0,10.1,1)
+y = [0,1]
+#z = [0,1]
+
+lg = PyLaGriT()
+layer = lg.gridder(x=x,y=y,elem_type='quad',connect=True)
+layer.rotateln([0,layer.ymin-0.10,0],[0,layer.ymax+0.1,0],25)
+layer.dump('tmp_lay_top.inp')
+
+# Layer depths?
+#           1   2   3    4    5    6    7   8    9   10
+layers = [ .1, 1.]
+addnum = [  4, 2]
+#matnum = [2]*len(layers)
+matnum = [2, 1]
+layer_interfaces = numpy.cumsum(layers)
+
+mtop = layer.copy()
+stack_files = ['tmp_lay_top.inp 1,9']
+#stack_files.append('tmp_lay_peat_bot.inp 1,33')
+
+i = 1
+for li,m,a in zip(layer_interfaces,matnum,addnum):
+    layer.math('sub','zic',value=li,cmosrc=mtop)
+    stack_files.append('tmp_lay'+str(i)+'.inp '+str(int(m))+', '+str(a))
+    layer.dump('tmp_lay'+str(i)+'.inp')
+    i += 1
+
+layer.math('sub','zic',2,cmosrc=mtop)
+#layer.setatt('zic',-2.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+stack_files.reverse()
+
+# Create stacked layer mesh and fill
+stack = lg.create()
+stack.stack_layers(stack_files,file_type='avs',flip_opt=True)
+stack_hex = stack.stack_fill()
+
+
+stack_hex.dump_exo('rotated.exo')
+stack_hex.dump_ats_xml('rotated.xml','rotated.exo')
+
+stack_hex.paraview()
--- a/PyLaGriT/examples/ex_select_subset.py
+++ b/PyLaGriT/examples/ex_select_subset.py
@@ -0,0 +1,15 @@
+#To use pylagrit, import the module.
+import pylagrit
+
+#Start the lagrit session.
+lg = pylagrit.PyLaGriT()
+
+#Create a mesh object.
+mo = lg.create()
+mo.createpts_brick_xyz((5,5,5), (0,0,0), (5,5,5))
+
+#Take the subset from (3,3,3)
+mo.subset((3,3,3),(5,5,5))
+
+
+
--- a/PyLaGriT/examples/ex_triangulate.py
+++ b/PyLaGriT/examples/ex_triangulate.py
@@ -0,0 +1,41 @@
+from pylagrit import PyLaGriT
+
+# Create pylagrit object
+lg = PyLaGriT()
+
+# Define polygon points in clockwise direction
+# and create tri mesh object
+coords = [[0.0, 0.0, 0.0], 
+          [0.0, 1000.0, 0.0], 
+          [2200.0, 200.0, 0.0], 
+          [2200.0, 0.0, 0.0]]
+motri = lg.tri_mo_from_polyline(coords)
+
+# Triangulate polygon
+motri.triangulate()
+motri.setatt('imt',1)
+motri.setatt('itetclr',1)
+
+# refine mesh with successively smaller edge length constraints
+edge_length = [1000,500,250,125,75,40,20,15]
+for i,l in enumerate(edge_length):
+    motri.resetpts_itp()
+    motri.refine(refine_option='rivara',refine_type='edge',values=[l],inclusive_flag='inclusive')
+    motri.smooth()
+    motri.recon(0)
+
+# provide additional smoothing after the last refine
+for i in range(5):
+    motri.smooth()
+    motri.recon(0)
+
+# create delaunay mesh and clean up
+motri.tri_mesh_output_prep()
+
+# dump fehm files
+motri.dump_fehm('nk_mesh00')
+
+# view results
+motri.paraview()
+
+
--- a/PyLaGriT/examples/ideas_mesh/dem0.5m.dat
+++ b/PyLaGriT/examples/ideas_mesh/dem0.5m.dat
@@ -0,0 +1,38 @@
+ ncols         160
+ nrows          32
+ xllcorner 0.0
+ yllcorner 0.0
+ cellsize 0.5
+ NODATA_value -9999
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+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.55573988       4.46583986       4.38897991       4.31172991       4.22817993       4.15384007       4.12025023       4.07011986       4.01909018       3.96926999       3.91944003       3.88232994       3.84305000       3.80281997       3.76258993       3.73002005       3.69626999       3.66469002       3.65206003       3.64124990       3.63132000       3.64013004       3.64875007       3.65774012       3.67949009       3.68523002       3.69086003       3.69074011       3.69091010       3.69107008       3.69583011       3.70115995       3.70648003       3.71778989       3.72344995       3.72909999       3.73305988       3.73685002       3.74063993       3.74378991       3.74619007       3.74858999       3.75500989       3.75461006       3.75421000       3.75612998       3.75830007       3.76045990       3.76610994       3.77403998       3.78197002       3.79888010       3.81327009       3.82765007       3.85355997       3.87308002       3.89260006       3.91772008       3.93684006       3.95596004       3.96785998       3.97803998       3.98820996       3.99762988       4.00082016       4.00401020       4.00610018       4.00740004       4.00869989       4.00592995       4.00184011       3.99775004       3.99611998       3.99374008       3.99136996       3.98576999       3.97705007       3.96832991       3.95656991       3.94228005       3.92799997       3.92249990       3.91728997       3.91209006       3.90859008       3.90462995       3.90066004       3.89023995       3.87863994       3.86690998       3.84959006       3.83152008       3.81332994       3.78800011       3.75896001       3.73007011       3.70500994       3.68022990       3.65699005       3.65357995       3.65202999       3.65259004       3.66489005       3.67986989       3.68420005       3.68056989       3.67923999       3.66851997       3.65532994       3.64233994       3.61121988       3.58025002       3.54926991       3.51323009       3.46823001       3.42322993       3.39383006       3.36268997       3.33148003       3.30258989       3.27870011       3.25901008       3.24396992       3.22650003       3.20532990       3.17890000       3.14651990       3.10921001       3.07927990       3.05504990       3.03754997       3.02096009      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
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+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.64178991       4.59597015       4.55013990       4.49826002       4.44572020       4.38675022       4.30862999       4.23880005       4.20069981       4.16695023       4.13784981       4.12072992       4.11025000       4.09138012       4.07167006       4.06062984       4.05372000       4.04960012       4.04851007       4.05473995       4.06504011       4.07738018       4.09111023       4.09019995       4.08203983       4.06607008       4.05054998       4.04838991       4.05846024       4.07349014       4.08758020       4.09551001       4.09555006       4.08900976       4.08033991       4.07426023       4.07009983       4.07126999       4.07263994       4.07595015       4.07827997       4.08038998       4.08677006       4.09217978       4.08864021       4.07785988       4.06629992       4.07379007       4.08456993       4.09405994       4.10431004       4.11808014       4.11703014       4.11475992       4.11655998       4.11665010       4.11175013       4.10714006       4.10253000       4.10757017       4.11627007       4.12888002       4.13692999       4.13093996       4.10960007       4.08827019       4.07352018       4.06573009       4.05929995       4.05411005       4.04859018       4.03232002       4.01335001       3.99213004       3.97332001       3.96074009       3.95889997       3.95705009       3.95675993       3.95449996       3.95157003       3.94887996       3.94160008       3.90840006       3.86736012       3.82295990       3.78417993       3.75428009       3.73095012       3.70761991       3.68709993       3.68324995       3.68233991       3.68322992       3.69042993       3.71111989       3.73880005       3.76731992       3.78471994       3.78882003       3.78590012       3.78297997       3.77551007       3.75131011       3.72726989       3.70325994       3.67300010       3.64611006       3.63032007       3.62185001       3.61336994       3.60489988       3.59645009       3.60377002       3.61120009       3.60505009       3.56705999      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.63767004       4.55955982       4.48145008       4.40333986       4.32523012       4.29421997       4.26513004       4.23603010       4.20696020       4.18704987       4.16715002       4.14724016       4.12802982       4.12390995       4.11978006       4.11566019       4.11306000       4.12680006       4.14053011       4.15427017       4.16422987       4.14826012       4.13229990       4.11633015       4.10558987       4.12061977       4.13565016       4.15067005       4.16071987       4.15205002       4.14337015       4.13468981       4.12848997       4.12966013       4.13082981       4.13199997       4.13345003       4.13556004       4.13767004       4.13978004       4.13732004       4.12576008       4.11420012       4.10263014       4.09898996       4.10848999       4.11798000       4.12748003       4.13206005       4.12978983       4.12751007       4.12523985       4.12190008       4.11729002       4.11267996       4.10806990       4.11207008       4.12468004       4.13729000       4.14989996       4.14412022       4.12278986       4.10145998       4.08013010       4.06821012       4.06302023       4.05781984       4.05262995       4.03741980       4.01620007       3.99497008       3.97375011       3.96543002       3.96358991       3.96174002       3.95989990       3.95745993       3.95477009       3.95209002       3.94940996       3.91546988       3.87106991       3.82666993       3.78226995      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
--- a/PyLaGriT/examples/ideas_mesh/dem1m.dat
+++ b/PyLaGriT/examples/ideas_mesh/dem1m.dat
@@ -0,0 +1,22 @@
+ ncols          80
+ nrows          16
+ xllcorner 0.0
+ yllcorner 0.0
+ cellsize 1.0
+ NODATA_value -9999
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.67219996       3.68359995       3.69619012       3.71521997       3.72508001       3.72726989       3.71860003       3.70366001       3.69660997       3.69231009       3.69566989       3.70247006       3.70868993       3.73199010       3.73533010       3.72710991       3.71343994       3.69245005       3.67408991       3.66343999       3.66878009       3.67532992      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.75395012       3.75072002       3.77381992       3.80789995       3.83649993       3.83517003       3.80082989       3.76087999       3.72447991       3.71415997       3.73225999       3.73175001       3.73741007       3.73725009       3.73420000       3.72895002       3.72724009       3.71581006       3.70748997       3.70763993       3.71369004       3.71959996       3.72178006       3.71810007       3.71340990       3.72086000       3.70785999       3.69271994       3.68577003       3.69053006       3.71712995       3.73258996       3.73983002       3.75313997       3.72856998       3.71529007       3.69196010       3.68709993       3.68752003       3.71386003       3.74335003      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.84218001       3.85291004       3.85646009       3.84837008       3.81525993       3.78619003       3.77371001       3.78171992       3.78228998       3.80602002       3.82614994       3.81270003       3.78468990       3.75465989       3.72204995       3.70226002       3.71567988       3.71896005       3.70863008       3.68091989       3.66621995       3.66920996       3.69081998       3.66926003       3.65340996       3.64381003       3.64496994       3.65351009       3.63864994       3.62265992       3.62915993       3.64632010       3.64388990       3.63277006       3.61752009       3.63211012       3.69529009       3.71615005       3.71783996       3.72343993       3.73534012       3.74135995       3.71669006       3.71463990       3.72206998       3.73904991       3.77004004       3.81308007       3.82997990       3.79167008       3.74681997       3.68841004      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.89721990       3.89446998       3.88790989       3.88687992       3.87184000       3.87367010       3.86740994       3.85953999       3.83484006       3.80479002       3.77077007       3.74273992       3.75369000       3.75407004       3.74163008       3.73374009       3.72142005       3.70238996       3.66389990       3.62322998       3.58352995       3.61139011       3.61373997       3.59570003       3.54733992       3.50950003       3.49995995       3.51776004       3.51693010       3.49341989       3.46985006       3.47119999       3.47304010       3.45194006       3.44093990       3.43341994       3.44907999       3.46670008       3.46933007       3.44515991       3.49103999       3.54961991       3.60261011       3.60168004       3.63162994       3.67248011       3.69498992       3.69745994       3.67420006       3.68841004       3.72452998       3.75991011       3.76771998       3.78307009       3.76691008       3.74364996       3.69601989       3.65737009       3.62821007       3.62685990       3.64345002      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.97463989       3.96666002       3.94780993       3.94218993       3.91915011       3.91198993       3.89215994       3.87345004       3.85437989       3.83789992       3.80751991       3.77642989       3.73608994       3.69320011       3.66227007       3.66677999       3.65785003       3.62424994       3.58114004       3.54922009       3.52816010       3.49469995       3.42711997       3.39080000       3.37755990       3.37296009       3.36444998       3.31990004       3.25889993       3.24163008       3.26091003       3.27699995       3.26254010       3.23248005       3.22522998       3.22555995       3.22105002       3.21431994       3.18898010       3.19310999       3.22851992       3.24569988       3.25251007       3.25864005       3.30609012       3.36669993       3.40301991       3.44205999       3.51185012       3.56785989       3.57076001       3.55559993       3.58434010       3.63444996       3.67550993       3.68491006       3.69812012       3.71179008       3.70617008       3.68607998       3.66150999       3.64916992       3.66020989       3.67941999       3.70173001       3.72968006       3.72755003       3.70164990      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.02367020       4.01190996       4.02333021       4.00113010       3.97018003       3.93827009       3.90633988       3.86961007       3.84359002       3.81522989       3.77417994       3.73583007       3.69358993       3.66131997       3.60915995       3.54360008       3.49505997       3.47079992       3.45974994       3.40716004       3.35136008       3.30119991       3.28457999       3.26395988       3.23436999       3.18297005       3.15848994       3.15164995       3.13547993       3.10908008       3.07193995       3.04245996       3.05696988       3.06269002       3.06114006       3.05426002       3.03233004       3.03197002       3.03110003       3.03109002       3.02905989       3.02705002       3.04509997       3.07450008       3.08585000       3.09185004       3.10967994       3.16898990       3.20758009       3.22706008       3.24148989       3.28264999       3.35360003       3.37469006       3.42071009       3.46594000       3.52659988       3.55022001       3.57961988       3.60310006       3.63214993       3.63052011       3.62648010       3.64428997       3.67242002       3.70278001       3.71656990       3.73416996       3.74310994       3.71284008       3.69461989       3.66292000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000       4.08056021       4.03021002       3.97554994       3.96744990       3.96454000       3.96043992       3.93502998       3.88625002       3.80773997       3.75567007       3.71145010       3.68425012       3.62757993       3.54643989       3.47901011       3.43943000       3.39190006       3.33290005       3.27805996       3.24868989       3.23566008       3.20618010       3.16253996       3.11444998       3.09419990       3.07409000       3.05212998       3.02804995       3.00203991       2.98604012       2.98108006       2.98636007       2.98809004       2.98990989       2.99160004       2.99549007       3.01216006       3.01435995       3.00728011       3.00518990       3.00177002       3.01401997       3.01781988       3.00535011       3.00322008       3.00254011       3.00037003       2.99166989       2.98130989       3.01029992       3.06195998       3.07175994       3.07405996       3.11138010       3.16626000       3.20573997       3.21698999       3.24619007       3.31199002       3.36210990       3.40650010       3.44888997       3.49475002       3.52310991       3.56508994       3.60157990       3.64304996       3.68530989       3.70687008       3.72404003       3.72502995       3.72311997       3.70644999       3.69006991       3.67417002       3.66610003      -9999.00000      -9999.00000    
+  -9999.00000       4.17643976       4.10390997       3.97607994       3.89861989       3.85435009       3.81108999       3.78051996       3.75936007       3.75047994       3.64608002       3.54189992       3.46359992       3.44306993       3.39913011       3.31353998       3.23955011       3.20812011       3.18319011       3.14372993       3.09769011       3.05991006       3.03835011       3.00462008       2.98114991       2.98615003       2.98948002       2.99089003       2.99953008       3.00716996       3.01724005       3.00921011       3.01032996       3.02570009       3.03816009       3.03851008       3.04104996       3.06101990       3.08590007       3.09742999       3.09222007       3.07147002       3.08153009       3.10124993       3.10500002       3.08592010       3.07090998       3.07936001       3.09131002       3.07593989       3.04626989       3.03160000       3.01507998       3.00090003       2.98080993       3.00290990       3.03574991       3.06944990       3.08284998       3.10534000       3.15187001       3.20514011       3.24820995       3.29709005       3.35172009       3.40943003       3.45816994       3.50570989       3.56209993       3.59572005       3.62329006       3.67304993       3.69532990       3.69238997       3.70085001       3.70246005       3.69505000       3.68829012      -9999.00000      -9999.00000    
+  -9999.00000       4.24236012       4.09855986       3.91252995       3.76834989       3.70830011       3.59031010       3.51260996       3.49142003       3.51143003       3.42268991       3.23323011       3.17428994       3.17407990       3.12173009       3.05750990       3.01828003       2.99637008       2.98281002       2.99205995       2.99881005       2.99673009       3.00162005       3.01030993       3.02418995       3.03158998       3.03176999       3.03296995       3.04728007       3.06346011       3.07817006       3.07838011       3.09077001       3.12357998       3.15052009       3.16090012       3.16596007       3.18351007       3.21501994       3.23701000       3.24569988       3.22339010       3.23500991       3.25476003       3.25937009       3.23691010       3.20707989       3.21790004       3.21984005       3.20320010       3.16915011       3.13944006       3.12245989       3.09775996       3.06613994       3.03109002       3.01264000       2.99286008       2.98671007       3.01121998       3.04731989       3.09072995       3.11647010       3.16470003       3.22282004       3.28312993       3.32658005       3.36889005       3.41938996       3.45702004       3.49959993       3.55202007       3.60661006       3.63202000       3.66960001       3.69051003      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000       4.29971981       4.10629988       3.83737993       3.59399009       3.47365999       3.30367994       3.20103002       3.15771008       3.10987997       3.06352997       2.99652004       2.98945999       3.00626993       3.03315997       3.03697991       3.02785993       3.02589989       3.03076005       3.03990006       3.04690003       3.04946995       3.05135989       3.05876994       3.07023001       3.08350992       3.09370995       3.10203004       3.13198996       3.15823007       3.18322992       3.19155002       3.21530008       3.29510999       3.33300996       3.35775995       3.40023994       3.40590000       3.41758990       3.44348001       3.45841002       3.46871996       3.45460010       3.45779991       3.45900989       3.45091009       3.43195009       3.42033005       3.38880992       3.36106992       3.32400990       3.28205991       3.25758004       3.22212005       3.18089008       3.13333011       3.10859990       3.08309007       3.04491997       3.01049995       2.99011993       2.99732995       3.02582002       3.05786991       3.11262012       3.15846992       3.18129992       3.22334003       3.26321006       3.30721998       3.35206008       3.40335989       3.46203995       3.54347992       3.58182001      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000       4.43861008       4.17054987       3.86994004       3.53736997       3.25597000       3.20038009       3.08452010       3.03712010       3.10261011       3.12493992       3.10684991       3.07525992       3.07524991       3.09787011       3.10535002       3.11404991       3.11512995       3.10285997       3.12579989       3.15029001       3.16046000       3.16025996       3.17108989       3.19092989       3.20595002       3.21574998       3.22956991       3.27025008       3.31076002       3.37841010       3.39192009       3.45056009       3.51063991       3.55185008       3.59440994       3.64246011       3.64417005       3.62995005       3.64646006       3.66740990       3.68558002       3.66199994       3.64866996       3.63913012       3.64798999       3.64030004       3.60897994       3.56533003       3.52887988       3.48669004       3.44168997       3.40675998       3.36542010       3.33564997       3.28865004       3.25092006       3.21391010       3.15182996       3.08898997       3.06352997       3.03574991       2.99936008       2.98095012       3.01904011       3.05187011       3.07034993       3.08738995       3.12649989       3.16768003       3.20777988       3.26090002       3.31991005      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000       4.57731009       4.33658981       4.07664013       3.77132010       3.55111003       3.41736007       3.32752991       3.26822996       3.28042006       3.27336001       3.25344992       3.22819996       3.21158004       3.23557997       3.26879001       3.29426003       3.29137993       3.29047990       3.31513000       3.34335995       3.35736990       3.35695004       3.36314011       3.38662004       3.40035009       3.40897012       3.42754006       3.45870996       3.50495005       3.57962990       3.63894010       3.69623995       3.73137999       3.76063991       3.79294991       3.83254004       3.82194996       3.80666995       3.81192994       3.82526994       3.83078003       3.80167007       3.78429008       3.77467990       3.78880000       3.77147007       3.74549007       3.70541000       3.66699004       3.62378001       3.57565999       3.52970004       3.50422001       3.49130988       3.46569991       3.43094993       3.38494992       3.30970001       3.23032999       3.17314005       3.13644004       3.09240007       3.06037998       3.04159999       3.00019002       2.99084997       3.00775003       3.02535009       3.05351996       3.10082006      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000       4.57560015       4.37607002       4.20177984       4.01429987       3.87034988       3.77456999       3.71565008       3.64509010       3.57018995       3.50861001       3.47612000       3.46308994       3.48081994       3.51987004       3.54540992       3.54459000       3.55202007       3.56594992       3.58985996       3.59822989       3.60551000       3.61189008       3.62537003       3.63271999       3.63729000       3.64698005       3.66808009       3.71257997       3.76557994       3.81666994       3.87055993       3.89491010       3.91667008       3.93983006       3.94470000       3.94535995       3.93807006       3.93723011       3.93302011       3.92212009       3.90139008       3.88089991       3.87199998       3.86624002       3.85402012       3.83102989       3.79874992       3.75980997       3.71024990       3.65822005       3.62374997       3.61437988       3.62491989       3.62020993       3.60022998       3.56051993       3.48305011       3.40926003       3.33383012       3.27803993       3.21555996       3.16777992       3.14651990       3.11034989       3.05351996       3.00648999       2.98060989       3.00207996      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.51867008       4.35922003       4.26718998       4.18594980       4.07220984       3.97362995       3.88965988       3.82112002       3.77624011       3.75555992       3.77010012       3.78081989       3.79038000       3.79234004       3.79977012       3.80716991       3.81455994       3.82194996       3.83102989       3.83831000       3.83976007       3.83709002       3.83874011       3.85103011       3.86532998       3.89446998       3.92010999       3.95538998       3.99272990       4.02166986       4.03460979       4.04231977       4.04194021       4.04672003       4.03694010       4.03138018       4.01698017       4.00165987       3.97779989       3.95024991       3.93858004       3.92491007       3.91535997       3.89463997       3.86547995       3.81423998       3.75416994       3.70116997       3.67047000       3.66912007       3.69726992       3.71468997       3.71936989       3.69407010       3.65030003       3.58697009       3.49704003       3.43596005       3.38104010       3.33449006       3.29909992       3.24625993       3.17236996       3.10206008      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.58134985       4.48944998       4.39742994       4.28569984       4.18388987       4.09923983       4.03039980       4.00988007       3.99761009       3.97807002       3.98390007       3.99950004       4.01413012       3.99914002       3.99207997       3.99616003       4.02147007       4.02345991       4.02088022       4.01127005       4.01202011       4.01789999       4.04221010       4.03633022       4.03916979       4.06193018       4.08783007       4.10255003       4.11400986       4.10411978       4.10311985       4.11502981       4.11170006       4.08641005       4.06730986       4.05387020       4.03119993       3.99847007       3.96706009       3.95353007       3.95288992       3.94675994       3.90494990       3.83586001       3.76796007       3.71741009       3.68933010       3.68394995       3.71424007       3.75681996       3.78045988       3.77634001       3.74535990       3.69663000       3.62673998       3.58439994       3.55714011       3.53695989       3.51200008       3.42859006      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.55066013       4.39344978       4.29017019       4.23160982       4.18378019       4.14372015       4.12312984       4.11482000       4.12974977       4.15740013       4.14442015       4.11228991       4.12460995       4.15486002       4.14951992       4.13205004       4.13003016       4.13239002       4.13628006       4.14053011       4.12151003       4.09823990       4.11220980       4.13132000       4.12883997       4.12425995       4.11524010       4.10596991       4.13058996       4.15518999       4.11225986       4.07076979       4.06031990       4.04735994       4.00464010       3.96624994       3.96253991       3.95858002       3.95318007       3.93288994       3.84352994      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
--- a/PyLaGriT/examples/ideas_mesh/ideas_mesh.py
+++ b/PyLaGriT/examples/ideas_mesh/ideas_mesh.py
@@ -0,0 +1,194 @@
+import optparse
+import shutil, distutils.dir_util, os, sys, glob
+
+import numpy
+import math
+import matplotlib.pyplot as plt
+from pylagrit import PyLaGriT
+
+#
+#  Create parser and options
+#
+p = optparse.OptionParser()
+p.add_option('--dem-file', help='DEM data file name including path', type='string', dest='dem_filename' )
+p.add_option('--exo-file', help='Exodus II mesh output including path', type='string', dest='exo_filename')
+p.add_option('--dry-run', help='Show commands and diagnostics but no execution', default=False, dest='dry_run', action='store_true')
+p.add_option('--plot', help='Show commands and diagnostics but no execution', default=False, dest='plot', action='store_true')
+#
+(opts,args) = p.parse_args()
+
+print(opts.dem_filename)
+print(opts.dry_run)
+
+# Input: DEM data
+dem_file_fullname=opts.dem_filename
+dem_file_noext, dem_file_ext=os.path.splitext(opts.dem_filename)
+dem_file_base=os.path.basename(opts.dem_filename).rstrip(dem_file_ext)
+dem_file_path=os.path.dirname(opts.dem_filename)
+
+# Output: Exodus II mesh
+exo_file_fullname=opts.exo_filename
+exo_file_noext, exo_file_ext=os.path.splitext(opts.exo_filename)
+exo_file_base=os.path.basename(opts.exo_filename).rstrip(exo_file_ext)
+exo_file_path=os.path.dirname(opts.exo_filename)
+
+# Output: XML region specifications for the new mesh
+xml_file_fullname=exo_file_path+exo_file_base+'.xml'
+
+# DEM parsing
+# 
+with open(dem_file_fullname) as dem_header:
+    for line in dem_header:
+        if ("ncols" in line):
+            nx=int(line.split()[1])
+        elif ("nrows" in line):
+            ny=int(line.split()[1])
+        elif ("xllcorner" in line):
+            xll_corner=float(line.split()[1])
+        elif ("yllcorner" in line):
+            yll_corner=float(line.split()[1])
+        elif ("cellsize" in line):
+            dx=float(line.split()[1])
+            dy=dx
+        elif ("NODATA_value" in line):
+            no_data_value=int(line.split()[1])
+            break
+
+print(nx, ny, xll_corner, yll_corner, dx, dy, no_data_value)
+dem_header.close()
+
+d = numpy.flipud(numpy.genfromtxt(dem_file_fullname,skip_header=6))
+#plt.matshow(d)
+
+# Create mesh based on ncols and nrows in file, could automatically read
+x = numpy.linspace(xll_corner,dx*(nx-1),nx)
+y = numpy.linspace(yll_corner,dy*(ny-1),ny)
+
+x=numpy.arange(xll_corner,dx*nx,dx)
+y=numpy.arange(yll_corner,dy*ny,dy)
+
+xx, yy = numpy.meshgrid(x,y)
+
+# Write avs file
+fh = open(dem_file_base+'.avs','w')
+# Find number of data values and write avs header
+N = numpy.where(numpy.isnan(d)==False)[0].shape[0]
+fh.write(str(N)+' 0 0 0 0\n')
+# Collect data into avs format
+# JDM:  Not sure if this should be nx*ny? 
+davs = numpy.zeros([nx*ny,4])
+ind = 0
+for i,row in enumerate(d):
+    for j,v in enumerate(row):
+        davs[ind,:] = [ind + 1, xx[i,j], yy[i,j], v]
+        ind += 1
+# Write data to avs file 
+numpy.savetxt(fh,davs,fmt=['%4d','%.1lf','%.1lf','%.8lf'])   
+fh.close()
+
+# Crank up pylagrit
+lg = PyLaGriT()
+# Read in elevations in avs fromat
+m = lg.read(dem_file_base+'.avs')
+# Take a look, change paraview exe
+# Will need to use glyph filter to view points
+#m.paraview(exe='paraview')
+
+# Copy z values over to attribute
+m.addatt('z_save',vtype='vdouble',rank='scalar')
+m.copyatt('zic','z_save')
+# Not sure why this has to be done, but not data elements don't get removed otherwise
+m.setatt('zic',0.)
+
+# Create connected quad mesh surface
+m2 = lg.create()
+#m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1],connect=True)
+m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1])
+# Create temporary z value attribute
+m2.addatt('z_save',vtype='vdouble',rank='scalar')
+# Interpolate elevations to z_save
+m2.interpolate_voronoi('z_save',m,'z_save')
+# Find nodes associated with nodata
+pdel = m2.pset_attribute('z_save',-9999)
+# Create element set from these nodes and remove elements
+edel = pdel.eltset()
+m2.rmpoint_eltset(edel)
+# Copy temp z values over to actual a values
+#m2.copyatt('z_save','zic')
+# Take a look to make sure everything is ok
+#m2.paraview(exe='paraview')
+
+
+
+m3 = m2.copypts(elem_type='triplane')
+m3.connect()
+# To lazy to add to pylagrit now, and don't know how to make it intuitive
+# Creates edge_max element attribute containing max edge length
+m3.sendline('quality/edge_max/y')
+# Query created attribute
+#m3.printatt('edgemax')
+m3.minmax('edgemax')
+# Figure out max desired edge length
+max_edge = numpy.sqrt(dx**2+dy**2)
+# Identify elements with longer edges
+edel = m3.eltset_attribute('edgemax',max_edge*2.05,'gt')
+m3.rmpoint_eltset(edel)
+
+#m3 = m2.grid2grid_quadtotri2()
+#m3=m2
+# Create temporary z value attribute
+m3.addatt('z_save',vtype='vdouble',rank='scalar')
+# Interpolate elevations to z_save
+m3.interpolate_voronoi('z_save',m,'z_save')
+
+# Find nodes associated with nodata
+pdel = m3.pset_attribute('z_save',-9999)
+# Create element set from these nodes and remove elements
+edel = pdel.eltset()
+m3.rmpoint_eltset(edel)
+# Copy temp z values over to actual a values
+m3.copyatt('z_save','zic')
+# Take a look to make sure everything is ok
+#m2.paraview(exe='paraview')
+
+# Create top surface avs
+m3.dump('top.inp')
+## Subtract 1 from z values of top and dump into bottom surface avs
+m3.math('sub',1,'zic',cmosrc=m3)
+m3.dump('mid.inp')
+m3.setatt('zic',0.0)
+m3.dump('bot.inp')
+
+# Stack the layers in a new mesh object
+stack = lg.create()
+stack.stack_layers('avs',['bot.inp 1','mid.inp 1,3','top.inp 1,0'],flip_opt=True)
+stack_hex = stack.stack_fill()
+# Automatically create face sets based on normal vectors and layer id
+#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True)
+#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=False)
+# Diagnostic
+#stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+#stack_hex.dump_exo(exo_file_fullname,facesets=fs.values())
+stack_hex.dump_exo(exo_file_fullname)
+
+# Write region and faceset identifier file for ats_xml
+matnames = {10000:'computational domain peat'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+# Dump ats style xml for mesh, can provide options for other schemas easily also
+#stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
+
+# Take a look
+if opts.plot: 
+    stack_hex.paraview(exe='/Applications/paraview.app/Contents/MacOS/paraview')
+
+
+
--- a/PyLaGriT/examples/julia/calc_volume/calc_volume.jl
+++ b/PyLaGriT/examples/julia/calc_volume/calc_volume.jl
@@ -0,0 +1,47 @@
+using PyCall
+@pyimport pylagrit
+
+l = pylagrit.PyLaGriT(lagrit_exe="lagrit")
+
+# Create mesh object 'm'
+m = l[:create](elem_type="triplane")
+m[:read]("data.inp")
+
+# Set imt to 1 for all points
+m[:setatt]("imt",1)
+m[:minmax_xyz]()
+
+# Connect mesh
+m[:connect]()
+
+# Lift the triangulation by assigning the Z coordinate to the data value (value)
+m[:copyatt]("value","zic")
+m[:minmax_xyz]()
+
+# Dump surface to vis file
+m[:dump]("tmp_tri_surf.inp")
+
+# Extrude mesh to 0
+mprism = m[:extrude](0.1,offset_type="min",return_type="volume", direction=[0.,0.,-1.])
+
+# Diagnostic
+l[:sendline]("quality / volume")
+
+# Add e_volume attribute of type "volume"
+mprism[:addatt]("e_volume", keyword="volume")
+
+# Calculate volume
+mprism[:math]("sum","volume_sum",attsrc="e_volume")
+
+# Dump surface to vis file
+mprism[:dump]("tmp_prism.inp")
+
+# Just to check the math do this again and assign all the 'values' to 1.0 and see if we get the expected result.
+mprism[:delete]()
+m[:setatt]("value", 1.0)
+m[:copyatt]("value","zic")
+mprism = m[:extrude](0.1,offset_type="min",return_type="volume", direction=[0.,0.,-1.])
+l[:sendline]("quality / volume")
+mprism[:addatt]("e_volume", keyword="volume")
+mprism[:math]("sum","volume_sum",attsrc="e_volume")
+
--- a/PyLaGriT/examples/julia/calc_volume/data.inp
+++ b/PyLaGriT/examples/julia/calc_volume/data.inp
@@ -0,0 +1,13 @@
+5 0 1 0 0
+1 0. 0. 0.
+2 1. 0. 0.
+3 1. 1. 0.
+4 0. 1. 0.
+5 .3 .7 0.
+1 1
+value, real
+1 0.1
+2 0.2
+3 0.4
+4 0.4
+5 0.5
--- a/PyLaGriT/examples/julia/polygon_map/2d_mesh.avs
+++ b/PyLaGriT/examples/julia/polygon_map/2d_mesh.avs
@@ -0,0 +1,112 @@
+        36         34          4          0          0
+001   6.013520000000E+01  7.815840000000E+01  0.000000000000E+00
+002   6.225470000000E+01  7.304140000000E+01  0.000000000000E+00
+003   6.636100000000E+01  7.733150000000E+01  0.000000000000E+00
+004   6.743270000000E+01  7.545220000000E+01  0.000000000000E+00
+005   6.859450000000E+01  7.817220000000E+01  0.000000000000E+00
+006   6.951440000000E+01  7.399160000000E+01  0.000000000000E+00
+007   7.084420000000E+01  7.675250000000E+01  0.000000000000E+00
+008   7.160620000000E+01  7.163580000000E+01  0.000000000000E+00
+009   7.446970000000E+01  7.667770000000E+01  0.000000000000E+00
+010   7.634490000000E+01  6.771360000000E+01  0.000000000000E+00
+011   7.675880000000E+01  6.338200000000E+01  0.000000000000E+00
+012   7.897770000000E+01  6.857050000000E+01  0.000000000000E+00
+013   7.901310000000E+01  6.423670000000E+01  0.000000000000E+00
+014   8.278350000000E+01  6.370140000000E+01  0.000000000000E+00
+015   8.581780000000E+01  6.354890000000E+01  0.000000000000E+00
+016   8.837110000000E+01  6.236630000000E+01  0.000000000000E+00
+017   9.139940000000E+01  5.620000000000E+01  0.000000000000E+00
+018   9.220260000000E+01  5.174260000000E+01  0.000000000000E+00
+019   9.029090000000E+01  5.127020000000E+01  0.000000000000E+00
+020   8.814240000000E+01  4.745050000000E+01  0.000000000000E+00
+021   8.651860000000E+01  4.605400000000E+01  0.000000000000E+00
+022   8.447390000000E+01  4.624540000000E+01  0.000000000000E+00
+023   8.032490000000E+01  4.764650000000E+01  0.000000000000E+00
+024   7.972940000000E+01  5.571550000000E+01  0.000000000000E+00
+025   7.884580000000E+01  5.498510000000E+01  0.000000000000E+00
+026   7.671340000000E+01  5.763060000000E+01  0.000000000000E+00
+027   7.543020000000E+01  5.673740000000E+01  0.000000000000E+00
+028   7.536320000000E+01  5.840850000000E+01  0.000000000000E+00
+029   7.325510000000E+01  6.345750000000E+01  0.000000000000E+00
+030   7.111320000000E+01  6.315590000000E+01  0.000000000000E+00
+031   7.113480000000E+01  6.613580000000E+01  0.000000000000E+00
+032   7.012260000000E+01  6.643770000000E+01  0.000000000000E+00
+033   6.865560000000E+01  6.764970000000E+01  0.000000000000E+00
+034   6.784250000000E+01  6.752880000000E+01  0.000000000000E+00
+035   6.589600000000E+01  6.792520000000E+01  0.000000000000E+00
+036   6.262800000000E+01  6.655140000000E+01  0.000000000000E+00
+001        0   tri  1  2  3
+002        0   tri  3  4  5
+003        0   tri  5  6  7
+004        0   tri  9 10 11
+005        0   tri 13 14 15
+006        0   tri 15 16 17
+007        0   tri 17 18 19
+008        0   tri 19 20 21
+009        0   tri 21 22 23
+010        0   tri 23 24 25
+011        0   tri 25 26 27
+012        0   tri 28 29 30
+013        0   tri 34 35 36
+014        0   tri  1  3  5
+015        0   tri  5  7  8
+016        0   tri  8  9 11
+017        0   tri 13 15 17
+018        0   tri 17 19 21
+019        0   tri 21 23 25
+020        0   tri 25 27 28
+021        0   tri 28 30 31
+022        0   tri  1  5  8
+023        0   tri  8 11 12
+024        0   tri 13 17 21
+025        0   tri 21 25 28
+026        0   tri 28 31 32
+027        0   tri  1  8 12
+028        0   tri 12 13 21
+029        0   tri 21 28 32
+030        0   tri 12 21 32
+031        0   tri 12 32 33
+032        0   tri  1 12 33
+033        0   tri  1 33 34
+034        0   tri  1 34 36
+00004  1  1  1  1
+imt1, integer 
+itp1, integer 
+icr1, integer 
+isn1, integer 
+0000000001  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000002  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000003  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000004  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000005  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000006  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000007  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000008  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000009  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000010  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000011  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000012  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000013  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000014  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000015  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000016  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000017  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000018  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000019  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000020  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000021  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000022  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000023  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000024  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000025  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000026  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000027  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000028  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000029  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000030  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000031  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000032  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000033  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000034  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000035  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000036  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
--- a/PyLaGriT/examples/julia/polygon_map/README
+++ b/PyLaGriT/examples/julia/polygon_map/README
@@ -0,0 +1 @@
+This example demonstrates how PyLaGriT can be used within a Julia script. The julia script "polygon_map.jl" and the python script "polygon_map.py" perform the same LaGriT operations. The two scripts can be compared to see how the syntax is modified for the Julia languange.
--- a/PyLaGriT/examples/julia/polygon_map/polygon_map.jl
+++ b/PyLaGriT/examples/julia/polygon_map/polygon_map.jl
@@ -0,0 +1,43 @@
+using PyCall
+@pyimport pylagrit 
+@pyimport numpy as np
+
+# User parameters #######################
+# Discretization
+nx = 61; ny = 61
+# Polygon delineation filename
+polygon_file = "2d_mesh.avs"
+# User parameters #######################
+
+l = pylagrit.PyLaGriT()
+
+# Read in polygon delineation mesh
+mopoly = l[:read](polygon_file)
+
+# Create quad using polygon min and max coordinates
+xs = linspace(mopoly[:xmin],mopoly[:xmax],nx)
+ys = linspace(mopoly[:ymin],mopoly[:ymax],ny)
+#xs = np.linspace(mopoly.xmin,mopoly.xmax,nx)
+#ys = np.linspace(mopoly.ymin,mopoly.ymax,ny)
+moquad = l[:gridder](xs,ys,elem_type="quad",connect=true)
+mopoly[:setatt]("itetclr",1)
+
+# Create extruded quad to tet and center at z=0
+moprism = mopoly[:extrude](1.0)
+moprism[:trans]((0.,0.,0.),(0.,0.,0.5))
+motet = moprism[:grid2grid_prismtotet3]()
+
+# Clean up a little
+mopoly[:delete]()
+moprism[:delete]()
+
+# Add attribute to moquad to store if in polygon or not
+moquad[:addatt]("if_in_poly",vtype="vint")
+moquad[:setatt]("if_in_poly", 0) # Make sure attr starts as zero
+
+# Interpolate motet's itetclr into moquad's if_in_poly
+moquad[:interpolate_map]("if_in_poly",motet,"itetclr")
+moquad[:intersect_elements](motet,attr_name="if_inter")
+
+# Write out file, mapping is stored as cell attribute in if_inter
+moquad[:dump]("polygon_map_julia.inp")
--- a/PyLaGriT/examples/julia/polygon_map/polygon_map.py
+++ b/PyLaGriT/examples/julia/polygon_map/polygon_map.py
@@ -0,0 +1,40 @@
+from pylagrit import PyLaGriT
+import numpy as np
+
+# User parameters #######################
+# Discretization
+nx = 61; ny = 61
+# Polygon delineation filename
+polygon_file = '2d_mesh.avs'
+# User parameters #######################
+
+l = PyLaGriT()
+
+# Read in polygon delineation mesh
+mopoly = l.read(polygon_file)
+
+# Create quad using polygon min and max coordinates
+xs = np.linspace(mopoly.xmin,mopoly.xmax,nx)
+ys = np.linspace(mopoly.ymin,mopoly.ymax,ny)
+moquad = l.gridder(xs,ys,elem_type='quad',connect=True)
+mopoly.setatt('itetclr',1)
+
+# Create extruded quad to tet and center at z=0
+mopoly.extrude(1.0)
+moprism = mopoly.extrude(1.0)
+moprism.trans((0.,0.,0.),(0.,0.,0.5))
+motet = moprism.grid2grid_prismtotet3()
+
+# Clean up a little
+mopoly.delete()
+moprism.delete()
+
+# Add attribute to moquad to store if in polygon or not
+moquad.addatt('if_in_poly',vtype='vint')
+moquad.setatt('if_in_poly', 0) # Make sure attr starts as zero
+
+# Interpolate motet's itetclr into moquad's if_in_poly
+moquad.interpolate_map('if_in_poly',motet,'itetclr')
+moquad.intersect_elements(motet,attr_name='if_inter')
+
+moquad.dump('polygon_map_python.inp')
--- a/PyLaGriT/examples/read_fehm_mesh/fehm.grid
+++ b/PyLaGriT/examples/read_fehm_mesh/fehm.grid
--- a/PyLaGriT/examples/read_fehm_mesh/read_fehm_mesh.py
+++ b/PyLaGriT/examples/read_fehm_mesh/read_fehm_mesh.py
@@ -0,0 +1,11 @@
+from pylagrit import PyLaGriT
+l = PyLaGriT()
+mhex = l.read_fehm('fehm.grid')
+#mhex.paraview()
+
+mtet = l.create(elem_type='tet')
+mtet = mhex.copypts()
+mtet.connect()
+mtet.paraview()
+
+
--- a/PyLaGriT/examples/refine_to_object.py
+++ b/PyLaGriT/examples/refine_to_object.py
@@ -0,0 +1,96 @@
+# Set up a five spot co2 injection and brine production problem
+import os,sys
+#from fdata import*
+#from fpost import*
+import zipfile
+import time
+from glob import glob
+import pylagrit
+import numpy as np
+
+batch = False
+dip = 90. # Degrees, dip of fault, angle is measured from horizontal
+pars = {'k_cap':-18,
+    'k_res':-12.,
+    'k_aq':-14,
+    'k_leak':-12,
+    'zcap1':100.,
+    'zcap2':100.,       
+    'fx':3000.,
+    'fw':380,
+    'fl':1.e3,
+    'injection_rate':10.,
+    'specific_storage':1.e-4,
+    'failure_pressure':3.,
+    }
+
+# dimensions
+xmin, xmax = -2000., 6000.
+zmin, zmax = -1000.,0.
+print('zmin = '+str(zmin)+' zmax '+str(zmax))
+zmid = -1.e3        # 1 km depth
+
+fx = pars['fx']         # distance between fault and injector
+fw = pars['fw']
+fl = pars['fl']
+
+############################################## generate grid
+
+# ndivisions
+nxbase = 11
+nzbase = int((zmax-zmin)/25.)
+
+xmm = np.linspace(xmin,xmax,nxbase)
+ymm = [0.,25.]
+zmm = np.linspace(zmin,zmax,nzbase+1)
+
+#N = len(xmm)*len(ymm)*len(zmm)
+#print('Grid will contain '+str(N) +' nodes')
+#print(str(len(zmm))+' in the z direction')
+#
+## assemble parameters and root names
+#dat = fdata()
+#dat.work_dir='.'
+#
+#dat.grid.make(dat.work_dir+os.sep+'GRID.inp',x=xmm,y=ymm,z=zmm)
+#dat.grid.write('AVS.inp', format='avs')
+l = pylagrit.PyLaGriT(batch=batch)
+mtemp = l.gridder(xmm,ymm,zmm,connect=True)
+mtemp.dump("AVS.inp")
+m = l.read('AVS.inp')
+#z_inj = dat.grid.node_nearest_point((0,0,zmid)).position[2]
+#m_l = l.create_line(2, (0.1,0.1,zmin), (0.1,0.1,zmax))
+#m_l.connect_delaunay()
+#m.refine_to_object(m_l,level=3)
+#m_l.delete()
+
+#for i in range(4):
+#    prefine = m.pset_geom( (-.1,-.1,zmin), (.1,.1,zmax))
+#    prefine.refine('constant','element',inclusive_flag='inclusive',prd_choice=12)
+#    prefine.delete()
+
+m_l = l.create_line(2, [fx+fw/2.,-fl/2.,zmax+.1], [fx+fw/2.,fl/2.,zmax+.1])
+m_h = m_l.extrude(fw, direction=[1,0,0])
+m_l.delete()
+m_c = m_h.extrude((zmax-zmin)*2, direction=[np.tan(np.radians(90.-dip)),0.,-1])
+m_h.delete()
+m_c.connect_delaunay()
+for i in range(4): m.refine_to_object(m_c,prd_choice=1)
+
+m2 = m.grid2grid_tree_to_fe()
+#m2.gmv()
+m2.connect_delaunay()
+
+# Set imt at injector
+#p_inj = m.pset_geom( (-.1,-.1,z_inj-0.1), (.1,.1,z_inj+0.1))
+#p_inj.setatt('imt',10)
+ 
+# set imt of fault
+attr_name = m2.intersect_elements(m_c)
+e_fault = m2.eltset_attribute(attr_name,0,boolstr='gt')
+p_fault = e_fault.pset()
+p_fault.setatt('imt',20)
+
+if batch: l.run_batch()
+else: m2.paraview()
+
--- a/PyLaGriT/examples/region_example.py
+++ b/PyLaGriT/examples/region_example.py
@@ -0,0 +1,21 @@
+from pylagrit import PyLaGriT
+lg = PyLaGriT()
+mesh = lg.create()
+mins = (0,0,0)
+maxs = (5,5,5)
+eighth = mesh.surface_box(mins,maxs)
+boolstr1 = 'le '+eighth.name
+boolstr2 = 'gt '+eighth.name
+reg1 = mesh.region(boolstr1)
+reg2 = mesh.region(boolstr2)
+mreg1 = mesh.mregion(boolstr1)
+mreg2 = mesh.mregion(boolstr2)
+mesh.createpts_brick_xyz((10,10,10), (0,0,0), (10,10,10))
+mesh.rmregion(reg1)
+mesh.dump('reg_test.gmv')
+
+
+
+
+
+
--- a/PyLaGriT/examples/stratigraphic_hex_mesh_tutorial.py
+++ b/PyLaGriT/examples/stratigraphic_hex_mesh_tutorial.py
@@ -0,0 +1,479 @@
+# -*- coding: utf-8
+# This script is the PyLaGriT version of LaGriT tutorial example at
+# https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html.
+# Written by Guoyan Jiang (gyjiang@whu.edu.cn) with technical support
+# from Dylan Harp (dharp@lanl.gov) and Terry Miller (tamiller@lanl.gov). 
+
+# Import PyLaGriT class from pylagrit module
+from pylagrit import PyLaGriT
+import numpy
+
+# Variables
+maxX  = 4000              # Max value in x direction
+maxY  = 4000              # Max value in y direction
+maxZ  = 3000              # Max value in z direction
+numX = 51                 # Number of points in x direction
+numY = 51                 # Number of points in y direction
+numZ = 26                 # Number of points in z direction
+
+# Create PyLaGriT object
+# This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified
+lg = PyLaGriT()
+
+#********************************************
+# 01 Built HEX Mesh
+#********************************************
+# Create mesh object 
+mo = lg.create_hex()
+mo.createpts_brick_xyz((numX, numY, numZ), (0,0,0), (maxX, maxY, maxZ))
+
+# Save the mesh object
+mo.dump('tmp_hex_01.inp')
+
+# Set vertices (imt) and cells (itetlcr) to 1
+mo.setatt('imt', 1)
+mo.setatt('itetclr', 1)
+
+# Set node type from connectivity of mesh
+mo.resetpts_itp()
+
+#********************************************
+# 02 Use pset’s to identify (for setting boundary conditions, 
+# initial conditions, etc.) a set of vertices on the top 
+# surface of the mesh
+#********************************************
+# Create a pset named p_top, which contains all nodes (stride = 1 0 0) 
+# where the node’s Z value (zic) is greater than or equal to (ge) the top of the mesh (maxZ) 
+pset0 = mo.pset_attribute('zic', maxZ, 'ge', (1,0,0), 'p_top')
+
+# Define three cylindrical objects
+pset1 = mo.pset_geom((0,0,-1), (1100,360,10000), (1500,1500,0), 'rtz', (1,0,0), 'p_circle1')
+pset2 = mo.pset_geom((0,0,-1), (1100,360,10000), (2500,2500,0), 'rtz', (1,0,0), 'p_circle2')
+pset3 = mo.pset_geom((0,0,-1), (1100,360,10000), (2500,1500,0), 'rtz', (1,0,0), 'p_circle3')
+
+# Intersect four psets, points belonging to the union of all given sets are preserved into the pset p_region
+pset4 = mo.pset_inter([pset0, pset1, pset2, pset3], 'p_region')
+
+# Map psets to an attribute
+mo.addatt('id_top_region', vtype='vint', rank='scalar')     # Creat a node-based attribute id_top_region within the mesh object
+mo.setatt('id_top_region', 1)              #Fill the entire attribute with 1
+pset1.setatt('id_top_region', 2)           #Color all nodes in the pset p_circle1 with the value 2
+pset2.setatt('id_top_region', 3)
+pset3.setatt('id_top_region', 4)
+pset4.setatt('id_top_region', 5)
+
+# Release the psets from memory
+pset0.delete()
+pset1.delete()
+pset2.delete()
+pset3.delete()
+pset4.delete()
+
+#********************************************
+# 03 Build some surfaces to define stratigraphy.
+# In a real model, the surfaces would come from some geologic framework model
+# and would define geologic or hydro-geologic horizons and topography.
+#********************************************
+mosurf1 = lg.create_qua()       # Create the top surface
+p1 = (-20, -20, 1000)
+p2 = (4020, -20, 1500)
+p3 = (4020, 4020, 2500)
+p4 = (-20, 4020, 500)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf1.quadxy(nnodes, pts)
+#mosurf1.paraview()
+mosurf1.minmax_xyz()
+mosurf1.dump('tmp_surf1_quad.inp')
+
+mosurf2 = lg.create_qua()       # Create the bottom surface
+p1 = (-20, -20, 1800)
+p2 = (4020, -20, 2100)
+p3 = (4020, 4020, 2800)
+p4 = (-20, 4020, 800)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf2.quadxy(nnodes, pts)
+#mosurf2.paraview()
+mosurf2.minmax_xyz()
+mosurf2.dump('tmp_surf2_quad.inp')
+
+#********************************************
+# 04 Use the surfaces to define regions and set
+# vertex and cell ids
+#********************************************
+# Define Regions
+sf1 = mosurf1.surface('sf1')
+sf2 = mosurf2.surface('sf2')
+
+r1 = mo.region('le ' + str(sf1))
+r2 = mo.region('gt ' + str(sf1) + ' and ' + 'le ' + str(sf2))
+r3 = mo.region('gt ' + str(sf2))
+
+mosurf1.delete()
+mosurf2.delete()
+
+# Create Eltsets and PSets from Regions
+pset1 = mo.pset_region(r1)
+pset2 = mo.pset_region(r2)
+pset3 = mo.pset_region(r3)
+
+eltset1 = mo.eltset_region(r1)
+eltset2 = mo.eltset_region(r2)
+eltset3 = mo.eltset_region(r3)
+
+#Set Attributes from Eltsets and PSets
+pset1.setatt('imt', 1)
+pset2.setatt('imt', 2)
+pset3.setatt('imt', 3)
+
+eltset1.setatt('itetclr', 1)
+eltset2.setatt('itetclr', 2)
+eltset3.setatt('itetclr', 3)
+
+#********************************************
+# 05 Build a fault surface and define stratigraphy 
+# on each side of the fault
+#********************************************
+# Create fault surface and surfaces to either side of fault
+mosurf1_fminus = lg.create_qua()       
+p1 = (-20, -20, 1000)
+p2 = (4020, -20, 1500)
+p3 = (4020, 4020, 2500)
+p4 = (-20, 4020, 500)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf1_fminus .quadxy(nnodes, pts)
+#mosurf1_fminus .paraview()
+mosurf1_fminus .minmax_xyz()
+mosurf1_fminus .dump('tmp_s1_fm.inp')
+
+mosurf2_fminus = lg.create_qua()      
+p1 = (-20, -20, 1800)
+p2 = (4020, -20, 2100)
+p3 = (4020, 4020, 2800)
+p4 = (-20, 4020, 800)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf2_fminus.quadxy(nnodes, pts)
+#mosurf2_fminus.paraview()
+mosurf2_fminus.minmax_xyz()
+mosurf2_fminus.dump('tmp_s2_fm.inp')
+
+mosurf1_fplus = lg.create_qua()      
+p1 = (-20, -20, 1400)
+p2 = (4020, -20, 1900)
+p3 = (4020, 4020, 2900)
+p4 = (-20, 4020, 900)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf1_fplus.quadxy(nnodes, pts)
+#mosurf1_fplus.paraview()
+mosurf1_fplus.minmax_xyz()
+mosurf1_fplus.dump('mosurf1_fplus.inp')
+
+mosurf2_fplus = lg.create_qua()      
+p1 = (-20, -20, 2200)
+p2 = (4020, -20, 2500)
+p3 = (4020, 4020, 3200)
+p4 = (-20, 4020, 1200)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf2_fplus.quadxy(nnodes, pts)
+#mosurf2_fplus.paraview()
+mosurf2_fplus.minmax_xyz()
+mosurf2_fplus.dump('mosurf2_fplus.inp')
+
+mosurf_fault = lg.create_qua()      
+p1 = (-20, -20, -1.e4)
+p2 = (4020, -20, -1.e4)
+p3 = (4020, 4020, 1.e4)
+p4 = (-20, 4020, 1.e4)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf_fault.quadxy(nnodes, pts)
+#mosurf_fault.paraview()
+mosurf_fault.minmax_xyz()
+mosurf_fault.dump('mosurf_fault.inp')
+
+# Define geometry of hydrostratigraphic model
+sf1_fm = mosurf1_fminus.surface('sf1_fm')
+sf2_fm = mosurf2_fminus.surface('sf2_fm')
+sf1_fp = mosurf1_fplus.surface('sf1_fp')
+sf2_fp = mosurf2_fplus.surface('sf2_fp')
+sf_f = mosurf_fault.surface('sf_f')
+
+r1_fm = mo.region('le ' + str(sf1_fm) + ' and ' + 'le ' + str(sf_f))
+r2_fm = mo.region('gt ' + str(sf1_fm) + ' and ' + 'le ' + str(sf2_fm) + ' and ' + 'le ' + str(sf_f))
+r3_fm = mo.region('gt ' + str(sf2_fm) + ' and ' + 'le ' + str(sf_f))
+r1_fp = mo.region('le ' + str(sf1_fp) + ' and ' + 'gt ' + str(sf_f))
+r2_fp = mo.region('gt ' + str(sf1_fp) + ' and ' + 'le ' + str(sf2_fp) + ' and ' + 'gt ' + str(sf_f))
+r3_fp = mo.region('gt ' + str(sf2_fp) + ' and ' + 'gt ' + str(sf_f))
+
+mosurf1_fminus.delete()
+mosurf2_fminus.delete()
+mosurf1_fplus.delete()
+mosurf2_fplus.delete()
+mosurf_fault.delete()
+
+# Set fault node and element materials
+pset1_fm = mo.pset_region(r1_fm)
+pset2_fm = mo.pset_region(r2_fm)
+pset3_fm = mo.pset_region(r3_fm)
+pset1_fp = mo.pset_region(r1_fp)
+pset2_fp = mo.pset_region(r2_fp)
+pset3_fp = mo.pset_region(r3_fp)
+
+eltset1_fm = mo.eltset_region(r1_fm)
+eltset2_fm = mo.eltset_region(r2_fm)
+eltset3_fm = mo.eltset_region(r3_fm)
+eltset1_fp = mo.eltset_region(r1_fp)
+eltset2_fp = mo.eltset_region(r2_fp)
+eltset3_fp = mo.eltset_region(r3_fp)
+
+#Set Attributes from Eltsets and PSets
+mo.setatt('imt', 7)
+mo.setatt('itetclr', 7)
+
+pset1_fm.setatt('imt', 1)
+pset2_fm.setatt('imt', 2)
+pset3_fm.setatt('imt', 3)
+pset1_fp.setatt('imt', 4)
+pset2_fp.setatt('imt', 5)
+pset3_fp.setatt('imt', 6)
+
+eltset1_fm.setatt('itetclr', 1)
+eltset2_fm.setatt('itetclr', 2)
+eltset3_fm.setatt('itetclr', 3)
+eltset1_fp.setatt('itetclr', 4)
+eltset2_fp.setatt('itetclr', 5)
+eltset3_fp.setatt('itetclr', 6)
+
+#********************************************
+# 06 Define a polyline and truncate the exterior boundary of the mesh with the polyline
+#********************************************
+# Read boundary polygon file
+mobndry = lg.read('basin_bnd_ply_rescale.inp')
+
+# Extrude the polyline into a vertical surface
+mofence = mobndry.extrude(3200, 'const', 'volume', [0, 0, -1])
+
+mobndry.minmax_xyz()
+mofence.minmax_xyz()
+
+# Translate the extrusion to make it cover the vertical extent of the hex mesh
+mofence.trans((0, 0, -3100), (0, 0 ,0))
+
+mofence.minmax_xyz()
+#mofence.paraview()
+#mofence.dump('3D_vertical_surface.inp')
+#mo.dump('cube.inp')
+
+# Truncate mesh
+sf_bndry = mofence.surface('sf_bndry')
+r_bndry = mo.region('ge ' + str(sf_bndry))
+pset_bndry = mo.pset_region(r_bndry)
+
+mobndry.delete()
+mofence.delete()
+
+# Method 1: Only remove a cell if ALL vertices are outside
+e_delete1 = pset_bndry.eltset('exclusive')
+
+# Method 2: Remove a cell if the centroid (average of all vertices) is outside
+e_delete2 = mo.eltset_region(r_bndry)
+
+# Method 3: Remove a cell if one or more vertices are outside
+e_delete3 = pset_bndry.eltset('inclusive')
+
+#mo.addatt('id_in_out_bndry', vtype='vint', rank='scalar', length='nelements')
+mo.add_element_attribute('id_in_out_bndry', vtype='vint')
+mo.setatt('id_in_out_bndry', 4)              #Fill the entire attribute with 4
+e_delete3.setatt('id_in_out_bndry', 3)          
+e_delete2.setatt('id_in_out_bndry', 2)
+e_delete1.setatt('id_in_out_bndry', 1)
+
+eltset4 = mo.eltset_attribute('id_in_out_bndry', 4, 'eq')
+eltset3 = mo.eltset_attribute('id_in_out_bndry', 3, 'eq')
+#eltset2 = mo.eltset_attribute('id_in_out_bndry', 2, 'eq')
+#eltset1 = mo.eltset_attribute('id_in_out_bndry', 1, 'eq')
+
+mo.rmpoint_eltset(eltset4, False, False)
+mo.rmpoint_eltset(eltset3, True, True)
+
+#********************************************
+# 07 Refine the mesh around the fault
+#********************************************
+f_zone = mo.intersect_elements(sf_f, 'f_zone')
+fz_i = mo.eltset_attribute('f_zone', 0, 'gt')     #Non-zero indicates intersection
+fz_i.refine()
+
+mo.delatt('f_zone')
+
+mo.status (brief=True)
+
+#sf_f.delete()
+#sf1_fm.delete()
+#sf2_fm.delete()
+#sf1_fp.delete()
+#sf1_fp.delete()
+#sf_bndry.delete()
+
+#********************************************
+# 08 Insert a couple of 'wells' by refining the mesh and identifying a line of nodes
+# that will be the well source/sink for boundary conditions.
+#********************************************
+Well1X = 1234.56
+Well1Y = 1987.65
+Well2X = 2243.21
+Well2Y = 1212.34
+Radius = 25
+NRadius = 2
+
+#Well 1
+mowell1 = lg.create_tet()
+mowell1.createpts_rtz((NRadius, 9, numZ), (0, 0, 3100), (Radius, 360, 1500))   #Create a cylindrical point cloud 
+
+mowell1.filter()              # Filter (delete) points that are too close ( default distance <=1.e-16) or duplicate points
+mowell1.rmpoint_compress()    # Remove all marked nodes and correct the itet array
+mowell1.setatt('imt', 1)
+
+mowell1.connect()             # Connect the point cloud
+mowell1.resetpts_itp()
+mowell1.minmax_xyz()
+
+mowell1.trans((0, 0, 0), (Well1X, Well1Y, 0))
+mowell1.minmax_xyz()
+#mowell1.paraview()
+mowell1.dump('tmp_well1.inp')
+
+#Well 2
+mowell2 = lg.create_tet()
+mowell2.createpts_rtz((NRadius, 9, numZ), (0, 0, 3100), (Radius, 360, 2200))   
+
+mowell2.filter()              
+mowell2.rmpoint_compress()    
+mowell2.setatt('imt', 1)
+
+mowell2.connect()             
+mowell2.resetpts_itp()
+mowell2.minmax_xyz()
+
+mowell2.trans((0, 0, 0), (Well2X, Well2Y, 0))
+mowell2.minmax_xyz()
+#mowell2.paraview()
+mowell2.dump('tmp_well2.inp')
+
+# Join the two distinct wells into a single mesh object 
+mowells = lg.merge([mowell1, mowell2])
+mowells.dump('tmp_wells.inp') 
+#mowells.paraview()
+
+# Refine the mo around the wells
+# First pass refinement
+w_zone = mo.intersect_elements(mowells, 'w_zone')
+wz_i = mo.eltset_attribute('w_zone', 0, 'gt')     #Non-zero indicates intersection
+wz_i.refine()
+mo.setatt('w_zone', 0)
+#wz_i.delete()
+
+# Second pass refinement
+w_zone = mo.intersect_elements(mowells, 'w_zone')
+wz_i = mo.eltset_attribute('w_zone', 0, 'gt')     #Non-zero indicates intersection
+wz_i.refine()
+mo.setatt('w_zone', 0)
+#wz_i.delete()
+
+mohex = mo.grid2grid_tree_to_fe()                         #Quadtree or octree grid to grid
+
+#mo.status (brief=True)
+
+# Identify the column of vertices closest to the well center.
+#Well1
+mo_pts1 = lg.create()
+mo_pts1.createpts_rtz((2, 2, 1000), (0, 0, 3100), (Radius, 360, 2200))   
+mo_pts1.trans((0, 0, 0), (Well1X, Well1Y, 0))
+
+#Well2
+mo_pts2 = lg.create()
+mo_pts2.createpts_rtz((2, 2, 1000), (0, 0, 3100), (Radius, 360, 2200))   
+mo_pts2.trans((0, 0, 0), (Well2X, Well2Y, 0))
+
+mo_pts = lg.merge([mo_pts1, mo_pts2])
+mo_pts.filter()              
+mo_pts.rmpoint_compress()   
+
+# Compute a distance field attribute
+mo.compute_distance(mo_pts, option='distance_field', attname='dfield_well')
+
+mo_pts1.delete()
+mo_pts2.delete()
+mo_pts.delete()
+mowell1.delete()
+mowell2.delete()
+mowells.delete()
+
+# Describe all nodes within 32, 16, 8, 4, 2 and 1 meters of the wells.
+pwell = mo.pset_attribute('dfield_well', 1.0, 'le', (1,0,0), 'pwell1')
+pwell.dump('zone_radius_01.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 2.0, 'le', (1,0,0), 'pwell2')
+pwell.dump('zone_radius_02.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 4.0, 'le', (1,0,0), 'pwell4')
+pwell.dump('zone_radius_04.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 8.0, 'le', (1,0,0), 'pwell8')
+pwell.dump('zone_radius_08.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 16.0, 'le', (1,0,0), 'pwell16')
+pwell.dump('zone_radius_16.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 32.0, 'le', (1,0,0), 'pwell32')
+pwell.dump('zone_radius_32.0.zone')
+
+mo.dump('Hex_mesh.inp') 
+
+#********************************************
+# 09 Convert hex mesh to tet mesh
+#********************************************
+motet = mohex.copypts()
+motet.setatt('imt', 1)
+motet.setatt('itp', 0)
+motet.connect(option1='check_interface')
+motet.resetpts_itp()
+
+motet.interpolate_voronoi('imt', mohex, 'imt')
+motet.interpolate_map('itetclr', mohex, 'itetclr')
+
+#Remove all nodes and elements with imt and itetclr values of 7
+motet.rmmat(7)
+#pset7 = motet.pset_attribute('imt', 7, 'eq', (1,0,0), 'pset7')
+#motet.rmpoint_pset(pset7)
+#eltset7 = motet.eltset_attribute('itetclr', 7, 'eq')
+#motet.rmpoint_eltset(eltset7, True, True)
+
+motet.rmpoint_compress() 
+motet.resetpts_itp()
+
+# Visualize connected mesh using ParaView
+# This assumes that pylagritrc is being used so that exe option does not need to be specified
+#motet.paraview()
+
+motet.dump('Tet_mesh.inp')
+
+#********************************************
+# 10 Write tet mesh files for FEHM
+# FEHM uses node based materials and properties
+#********************************************
+#motet.resetpts_parent()
+motet.filter() 
+motet.rmpoint_compress() 
+motet.resetpts_itp()
+motet.minmax('imt')
+motet.setatt('itetclr', 1)
+#motet. tri_mesh_output_prep()
+motet.dump_fehm('Example3')
+
+
+
--- a/PyLaGriT/pylagrit/init.py
+++ b/PyLaGriT/pylagrit/init.py
@@ -0,0 +1,3 @@
+from pylagrit.pylagrit import *
+
+__xall__ = ["PyLaGriT"]
--- a/PyLaGriT/pylagrit/pylagrit.py
+++ b/PyLaGriT/pylagrit/pylagrit.py
--- a/PyLaGriT/pylagrit/utilities.py
+++ b/PyLaGriT/pylagrit/utilities.py
@@ -0,0 +1,231 @@
+import os
+import numpy as np
+from datetime import datetime
+
+
+def zone_to_zonn(zonefile):
+    zonnfile = os.path.splitext(zonefile)[0] + ".zonn"
+    with open(zonefile, "r") as fh:
+        fh.readline()
+        lns = fh.readlines()
+    with open(zonnfile, "w") as fout:
+        fout.write("zonn\n")
+        for l in lns:
+            fout.write(l)
+
+
+def spherical_writeFEHM(node_locations, filename_base, title="default"):
+    """
+    Create FEHM .stor and .fehmn input files for 1d spherical simulations.
+    Assumes logical 1D structure.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array(float)
+    :arg filename_base: base name for the .stor and .fehmn files
+    :type filename_base: str
+    :arg title: optional title for simulation
+    :type title: str
+
+    Example:
+    from pylagrit import utilities as util
+    import numpy as np
+    nodes = np.linspace(0.0,200.0)
+    filename_base = "test"
+    title = "test sim"
+    # write .stor and .fehmn files
+    util.spherical_writeFEHM(nodes,filename_base,title)
+    """
+    # stor file header
+    now = datetime.now()
+    print_datetime = now.strftime("%m/%d/%Y  %H:%M:%S")
+    header = (
+        "FEHM .stor file generated by PyLaGriT  "
+        + print_datetime
+        + "\n"
+        + "title:  "
+        + title
+        + "\n"
+    )
+
+    # calculate dx, face locations, face areas, volumes, and geometric coefficients
+    dx = spherical_dx(node_locations)
+    faces = spherical_faces(node_locations)
+    area = spherical_areas(faces)
+    volumes = spherical_volumes(node_locations)
+    coeffs = area / dx
+
+    # matrix metadata header info
+    neq = np.size(node_locations)
+    num_coeffs = neq - 1
+    FEHM_mem = (neq - 2) * 3 + 4 + neq + 1
+    num_area_coeff = 1
+    max_connect = 3
+    matrix_params = (num_coeffs, neq, FEHM_mem, num_area_coeff, max_connect)
+    params_header = "        " + "        ".join(str(s) for s in matrix_params) + "\n"
+
+    # row count
+    row_count = np.empty([neq + 1])
+    start = neq + 1
+    row_count[0] = start
+    row_count[1] = row_count[0] + 2
+    for i in range(2, neq):
+        row_count[i] = row_count[i - 1] + 3
+    row_count[neq] = row_count[neq - 1] + 2
+
+    # row entries
+    row_entries = []
+    row_entries.append(1)
+    row_entries.append(2)
+    for i in range(1, neq - 1):
+        row_entries.append(i)
+        row_entries.append(i + 1)
+        row_entries.append(i + 2)
+    row_entries.append(neq - 1)
+    row_entries.append(neq)
+
+    # index into geometric coefficient matrix
+    coeff_indices = []
+    coeff_indices.append(0)
+    coeff_indices.append(1)
+    for i in range(1, neq - 1):
+        coeff_indices.append(i)
+        coeff_indices.append(0)
+        coeff_indices.append(i + 1)
+    coeff_indices.append(neq - 1)
+    coeff_indices.append(0)
+    # neq + 1 extra 0s for padding
+    for i in range(0, neq + 1):
+        coeff_indices.append(0)
+
+    # index of diagonal entries
+    diagonal_indices = np.empty([neq])
+    diagonal_indices[0] = neq + 2
+    for i in range(1, neq):
+        diagonal_indices[i] = diagonal_indices[i - 1] + 3
+
+    # open stor file, write header and matrix parameters
+    storfile = filename_base + ".stor"
+    sfile = open(storfile, "w")
+    _ = sfile.write(header)
+    _ = sfile.write(params_header)
+
+    # write Voronoi volumes
+    count = 1
+    for vol in volumes:
+        print("  %1.12e" % vol, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write row counts
+    count = 1
+    for row in row_count:
+        print(" %9d" % row, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write row entries
+    count = 1
+    for row in row_entries:
+        print(" %9d" % row, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write geometric coefficient indices
+    count = 1
+    for idx in coeff_indices:
+        print(" %9d" % idx, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write diagonal indices
+    count = 1
+    for idx in diagonal_indices:
+        print(" %9d" % idx, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write geometric coefficients
+    count = 1
+    for coef in coeffs:
+        print("  %1.12e" % coef, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+
+    # close stor file
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+    _ = sfile.close()
+
+    # open fehmn file
+    fehmnfile = filename_base + ".fehmn"
+    ifile = open(fehmnfile, "w")
+    # write header and neq
+    _ = ifile.write("coor\n%d\n" % neq)
+    # write node number and radial location
+    for i in range(1, neq + 1):
+        print(
+            "        %3d        %12f        0        0" % (i, node_locations[i - 1]),
+            file=ifile,
+        )
+    # write connectivity
+    _ = ifile.write("\nelem\n")
+    _ = ifile.write("%d %d\n" % (2, neq - 1))
+    for i in range(1, neq):
+        print("%3d   %3d   %3d" % (i, i, i + 1), file=ifile)
+    # close fehmn file
+    _ = ifile.write("\nstop\n")
+    _ = ifile.close()
+
+
+def spherical_faces(node_locations):
+    """
+    Calculate radial interface locations given radial node locations.
+    Assumes 1st and last nodes lie on domain boundary.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array_like(float)
+    Returns: array of radial interface locations of size node_locations - 1
+    """
+    interface_locations = node_locations[:-1] + np.diff(node_locations) / 2.0
+    return interface_locations
+
+
+def spherical_areas(interface_locations):
+    """
+    Calculate spherical area of each interface given radial interface locations.
+    :arg interface_locations: radial location of interfaces
+    :type interface_locations: array_like(float)
+    Returns: array of spherical interface areas of size interface_locations
+    """
+    areas = 4.0 * np.pi * interface_locations ** 2
+    return areas
+
+
+def spherical_dx(node_locations):
+    """
+    Calculate Delaunay edge lengths given radial node locations.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array_like(float)
+    Returns: array of Delaunay edge lengths of size node_locations - 1
+    """
+    delaunay = np.diff(node_locations)
+    return delaunay
+
+
+def spherical_volumes(node_locations):
+    """
+    Calculate Voronoi volume associated with each node given radial node locations.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array_like(float)
+    Returns: array of Voronoi volumes of size node_locations
+    """
+    coeff = np.pi * 4.0 / 3.0
+    edges = spherical_faces(node_locations)
+    edges = np.insert(edges, 0, node_locations[0])
+    edges = np.append(edges, node_locations[np.size(node_locations) - 1])
+    spheres = coeff * edges ** 3
+    volumes = np.diff(spheres)
+    assert np.all(volumes > 0), "ERROR: Negative volumes are not good."
+    return volumes
--- a/PyLaGriT/pylagritrc_example
+++ b/PyLaGriT/pylagritrc_example
@@ -0,0 +1,7 @@
+# This is an example pylagritrc file. 
+# To use, change its name to pylagritrc or .pylagritrc, uncomment and modify attributes and move to your working directory or your home directory. 
+# The rc file in the working directory will take precedence over the one in your home directory. 
+
+#lagrit_exe : '/lagrit/executable/location/lagrit' 
+#gmv_exe : '/gmv/executable/location/gmv' 
+#paraview_exe : '/paraview/executable/location/paraview' 
--- a/PyLaGriT/setup.py
+++ b/PyLaGriT/setup.py
@@ -0,0 +1,27 @@
+"""
+Build script for PyLaGriT
+"""
+
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+import os
+
+setup(
+    name="pylagrit",
+    version="1.0.1",
+    description="Python interface for LaGriT",
+    author="Dylan R. Harp",
+    author_email="dharp@lanl.gov",
+    url="lagrit.lanl.gov",
+    license="LGPL",
+    install_requires=[
+        "pexpect>=4.6.0",
+        "numpy",
+    ],
+    packages=[
+        "pylagrit",
+    ],
+)
--- a/PyLaGriT/tests/.directory
+++ b/PyLaGriT/tests/.directory
@@ -0,0 +1,3 @@
+[Dolphin]
+Timestamp=2014,7,24,15,5,28
+ViewMode=1
--- a/PyLaGriT/tests/contour_file.avs
+++ b/PyLaGriT/tests/contour_file.avs
--- a/PyLaGriT/tests/old_formatF
+++ b/PyLaGriT/tests/old_formatF
--- a/PyLaGriT/tests/test_convert/test.avs
+++ b/PyLaGriT/tests/test_convert/test.avs
--- a/PyLaGriT/tests/test_convert/test.exo
+++ b/PyLaGriT/tests/test_convert/test.exo
--- a/PyLaGriT/tests/test_convert/test.gmv
+++ b/PyLaGriT/tests/test_convert/test.gmv
--- a/PyLaGriT/tests/test_merge/test.avs
+++ b/PyLaGriT/tests/test_merge/test.avs
--- a/PyLaGriT/tests/test_pylagrit.py
+++ b/PyLaGriT/tests/test_pylagrit.py
@@ -0,0 +1,204 @@
+import unittest
+import pylagrit
+import glob
+import sys
+import os
+from contextlib import contextmanager
+import itertools
+
+class TestPyLaGriT(unittest.TestCase):
+    '''
+    A PyLagriT Test
+    
+    Represents a test of PyLaGriT functionality.
+    '''
+
+    def setUp(self):
+        #Sets upt a lagrit object to be used during tests.
+        with suppress_stdout():
+            self.lg = pylagrit.PyLaGriT('../../build/lagrit')
+
+    def test_read_script(self):
+        '''
+        Test the Read Script Function
+        
+        Tests that pylagrit can read a lagrit script. 
+        '''
+        
+        lg = self.lg
+        for f in glob.glob('/test_scripts/*.lg'):
+            with suppress_stdout():
+                lg.read_script(f)
+                
+    def test_convert(self):
+        '''
+        Test the Conversion Function
+        
+        Tests that pylagrit can convert files from one format to a new one.
+        '''
+        
+        lg = self.lg      
+        
+        old_formats = ['avs', 'gmv']
+        new_formats = ['avs', 'gmv', 'exo']
+        
+        for old_ft, new_ft in itertools.product(old_formats, new_formats):
+            #Convert all avs files to gmv with pylagrit
+            with suppress_stdout():
+                lg.convert('test_convert/*.%s'%old_ft, new_ft)
+            
+            #If the file did not get generated, assume fail.
+            if not os.path.isfile('test.%s'%new_ft): 
+                raise OSError('Failed Conversion.')         
+            os.remove('test.%s'%new_ft)
+            
+    def test_merge(self):
+        '''
+        Tests the Merge Function
+        
+        Tests that pylagrit can merge 3 mesh objects and return a single mesh
+        object.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo1 = lg.read('avs', 'contour_file.avs')
+            mo2 = lg.read('avs', 'contour_file.avs')
+            mo3 = lg.read('avs', 'contour_file.avs')
+            new_mo = lg.merge([mo1, mo2, mo3]) 
+        #Test that the merge created a new mesh object.
+        if type(new_mo) is type(None):
+            raise ValueError('An expected mesh object was not created.')
+                    
+    def test_create(self):
+        '''
+        Tests the Create Function
+        
+        Tests that the create function returns a mesh object.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo1 = lg.create() 
+            mo2 = lg.create_hex() 
+            mo3 = lg.create(elem_type='pri') 
+        if any([type(x) is type(None) for x in [mo1, mo2, mo3]]):
+            raise ValueError('An expected mesh object was not created.')
+            
+    def test_createpts_brick(self):
+        '''
+        Test the Create Points Function
+        
+        Tests that a mesh object can run the createpts method with fail.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo = lg.create()
+            npts = (4, 4, 4)
+            mins = (0, 0, 0)
+            maxs = (4, 4, 4)
+            mo.createpts_brick('xyz', npts, mins, maxs)    
+            
+    def test_pset_geom(self):
+        '''
+        Test the MO Geometry Function
+        
+        Tests that each geom method returns a PSet.
+        '''
+        
+        lg = self.lg
+        mins = (1, 1, 1)
+        maxs = (2, 2, 2)
+        with suppress_stdout():
+            mo = lg.create()
+            ps = []
+            ps.append(mo.pset_geom(mins, maxs))
+            ps.append(mo.pset_geom_xyz(mins, maxs))
+            ps.append(mo.pset_geom_rtz(mins, maxs))
+            ps.append(mo.pset_geom_rtp(mins, maxs))
+             
+        if any([not isinstance(x, pylagrit.PSet) for x in ps]):
+            raise ValueError('PSet not returned.')
+            
+    def test_copy(self):
+        '''
+        Test the Copy Function
+        
+        Tests that the copy function returns a mesh object.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo = lg.create()
+            mo_clone = lg.copy(mo)
+        if not isinstance(mo_clone, pylagrit.MO):
+            raise ValueError('MO not returned.')
+            
+    def test_pset_not(self):
+        '''
+        Test the Mesh Object Not Function
+        
+        Tests that a mesh object can return a PSet using the pset_not function.
+        '''
+        
+        lg = self.lg
+        mins = (1, 1, 1)
+        maxs = (2, 2, 2)
+        with suppress_stdout():
+            mo = lg.create()
+            ps1 = mo.pset_geom(mins, maxs)
+            ps2 = mo.pset_not(ps1)
+        if not isinstance(ps2, pylagrit.PSet):
+            raise ValueError('PSet not returned.')
+            
+    def test_subset(self):
+        '''
+        Test the MO Subset Function
+        
+        Tests that a mesh object can return another mesh object with the subset
+        methods.
+        '''
+        
+        lg = self.lg
+        mins = (1,1,1)
+        maxs = (2,2,2)
+        with suppress_stdout():
+            mo = lg.create()
+            mo_subs = []
+            mo_subs = mo_subs + [mo.subset(mins, maxs)]
+            mo_subs = mo_subs + [mo.subset(mins, maxs, geom='rtz')]
+            mo_subs = mo_subs + [mo.subset(mins, maxs, geom='rtp')]
+            mo_subs = mo_subs + [mo.subset_rtp(mins, maxs)]
+            mo_subs = mo_subs + [mo.subset_rtz(mins, maxs)]
+            
+        if any([not isinstance(x, pylagrit.MO) for x in mo_subs]):
+            raise ValueError('MO not returned.')
+                     
+@contextmanager
+def suppress_stdout():
+    #Utility to supress standard output.
+    with open(os.devnull, 'w') as devnull:
+        old_stdout = sys.stdout
+        sys.stdout = devnull
+        try:
+            yield
+        finally:
+            sys.stdout = old_stdout
+                               
+if __name__ == '__main__':    
+    runner = unittest.TextTestRunner(verbosity=2)    
+    suite = unittest.TestSuite()
+    suite.addTest(TestPyLaGriT('test_read_script'))
+    suite.addTest(TestPyLaGriT('test_convert'))
+    suite.addTest(TestPyLaGriT('test_merge'))
+    suite.addTest(TestPyLaGriT('test_create'))
+    suite.addTest(TestPyLaGriT('test_createpts_brick'))
+    suite.addTest(TestPyLaGriT('test_pset_geom'))
+    suite.addTest(TestPyLaGriT('test_copy'))
+    suite.addTest(TestPyLaGriT('test_pset_not'))
+    suite.addTest(TestPyLaGriT('test_subset'))
+    runner.run(suite)
+    
+    
+    
--- a/PyLaGriT/tests/test_scripts/test_script1.lg
+++ b/PyLaGriT/tests/test_scripts/test_script1.lg
@@ -0,0 +1 @@
+cmo / create / cmotri / / / tri
--- a/PyLaGriT/tests/test_scripts/test_script2.lg
+++ b/PyLaGriT/tests/test_scripts/test_script2.lg
@@ -0,0 +1,6 @@
+*Example Comment
+cmo / create / cmotri / / / tri
+read / avs / input.inp / cmotri
+*
+
+finish
--- a/PyLaGriT/tests/test_scripts/test_script3.lg
+++ b/PyLaGriT/tests/test_scripts/test_script3.lg
@@ -0,0 +1,8 @@
+* Example of Some Comments
+* More Comments
+* 
+define/nx/20
+define/ny/20
+define/nz/20
+   
+finish
--- a/README.md
+++ b/README.md
@@ -1,3 +1,192 @@
-# LaGriT
+## LaGriT: Los Alamos Grid Toolbox ##

-A personal copy of the original LaGriT
+**LANL Software: LA-CC-15-069  No. C15097**
+
+[![Latest Version](https://img.shields.io/github/release/lanl/lagrit.svg?style=flat-square)](https://github.com/lanl/lagrit/releases) [![PyPI](https://img.shields.io/pypi/l/Django.svg)](https://lanl.github.io/LaGriT/pages/licensing.html)
+
+[![dockerhub](https://img.shields.io/static/v1?label=Docker&message=Download%20V3.3.3&color=blue&style=for-the-badge&logo=docker)](https://hub.docker.com/r/ees16/lagrit) <br/>
+[![readthedocs](https://img.shields.io/static/v1?label=Documentation&message=Read%20online&color=blue&style=for-the-badge&logo=read-the-docs)](https://lanl.github.io/LaGriT/) <br/>
+[![readthedocs](https://img.shields.io/static/v1?label=LaGriT%20Home&message=Read%20online&color=blue&style=for-the-badge&logo=read-the-docs)](https://lagrit.lanl.gov/) <br/>
+[![readthedocs](https://img.shields.io/static/v1?label=Meshing%20Portfolio&message=Read%20online&color=blue&style=for-the-badge&logo=read-the-docs)](https://meshing.lanl.gov/) <br/>
+
+
+> [!NOTE]
+> We are currently working on developing Poisson-disk for 3D.
+
+
+Los Alamos Grid Toolbox (**LaGriT**) is a library of user callable tools that provide mesh generation, mesh optimization and dynamic mesh maintenance in two and three dimensions. LaGriT is used for a variety of geology and geophysics modeling applications including porous flow and transport model construction, finite element modeling of stress/strain in crustal fault systems, seismology, discrete fracture networks, asteroids and hydrothermal systems.
+
+The general capabilities of LaGriT can also be used outside of earth science applications and applied to nearly any system that requires a grid/mesh and initial and boundary conditions, setting of material properties and other model setup functions. It can also be use as a tool to pre- and post-process and analyze vertex and mesh based data.
+
+**PyLaGriT** is a Python interface for LaGriT that allows LaGriT functionality to be accessed interactively and in batch mode from Python.
+This allows the meshing capabilities of LaGriT to be combined with the numeric and scientific functionality of Python.
+PyLaGriT allows interactive and automated querying of mesh properties, enhanced looping functionality, and user defined error checking based on LaGriT output.
+
+---
+
+### Quick Start
+
+#### Docker Container
+
+The easiest way to get started with LaGriT is through [Docker](https://hub.docker.com/r/ees16/lagrit):
+
+    $ docker pull ees16/lagrit:latest
+    $ docker run -it -v $(pwd):/docker_user/work ees16/lagrit:latest
+
+After the container launches, navigate to:
+
+    $ cd bin
+    $ ./lagrit
+
+
+*Docker is no longer available from LANL EES servers as of Sep 1 2025.*
+
+---
+
+### Building LaGriT
+
+#### Dependencies ####
+
+- CMake is used to generate the build system.
+- C, C++, and compatible Fortran compilers. MacOS may need command line tools updated.
+- OPTIONAL Exodus libraries installed in TPLs, requires bash and wget.
+
+**Note:** There is an issue with Poisson Disk Commands using any Brew installed compilers and Gnu 10-12. Works on Clang 14-15 and Gnu 9.4.
+
+#### Download LaGriT ####
+
+Download the Https repo by running:
+
+```bash
+git clone https://github.com/lanl/LaGriT.git
+cd LaGriT/
+```
+
+Note for developers, you will need the SSH version to enable Git version control to this repository.
+
+[Detailed Instructions for Building LaGriT with cmake and exodus](cmake/README.md)
+
+
+The simplest way to build LaGriT uses cmake with auto dectection and no options.
+Type the following (you can name the build directory anything you want).
+
+```bash
+mkdir build/ && cd build/
+cmake .. && make
+```
+
+The cmake command creates the configuration and build files for lagrit and will look similar to this:
+```
+-- ==========================================
+-- ============Configuring LaGriT============
+-- ===================v3.3.3=================
+-- Compile LaGriT as a static binary = ON
+-- Compile LaGriT with ExodusII = OFF
+LaGriT Compiling without ExodusII support.
+
+-- Configuring done
+-- Generating done
+```
+
+The make command will compile the libraries and build lagrit. Use `make VERBOSE=1` to view compile progress.
+The `lagrit` executable is installed in the `build/` directory.
+
+
+- Type `./lagrit` to make sure the executable is working.
+- On the LaGriT command line type `test` which will execute a set of LaGriT commands.
+- Type `finish` to exit.
+
+The result will look like:
+```
+nnodes:              27                                                         
+nelements:            8                                                         
+xic(1:3):  1.00 1.25 1.50                                                       
+imt(1:3):     1    1    1                                                       
+epsilonl:   1.9229627E-13                                                       
+     Released Mesh Object: test_hex                                             
+lagrit test done.                                                               
+ 
+ Enter a command
+finish                                                                          
+LaGriT successfully completed             
+```
+
+### Testing LaGriT
+
+To test LaGriT, start from top and simply run:
+
+```bash
+$ python test/runtests.py
+```
+
+Test output can be found in the `test/lagrit-tests.log` file.
+
+Additional options are available by running:
+
+```bash
+$ python test/runtests.py --help
+```
+
+
+### (Optional) Build LaGriT with ExodusII ###
+
+
+The only LaGriT command used with ExodusII libs is `dump/exodus` and associated face set and node set commands.
+To include these commands you will need to install Seacas-Exodus.
+
+Use the install-exodus.sh or MAC_install-exodus.sh to Install Exodus and associated libraries. You can run the file or use the file as a guide to copy and paste commands for installation. The script provides the flags needed by LaGriT and will install seacas in the directory TPLs.
+
+For full and current Exodus Installation instructions, go to:
+[Seacas ExodusII](https://github.com/sandialabs/seacas)
+
+Install, configure, and build ExodusII with script (use MAC_install-exodus.sh for mac machines):
+
+```bash
+$ ./install-exodus.sh
+```
+
+Configure and build LaGriT using ExodusII libs:
+
+```bash
+mkdir build/ && cd build/
+cmake .. -DLAGRIT_BUILD_EXODUS=ON
+make
+```
+
+[Detailed Instructions for Building LaGriT with cmake and exodus](cmake/README.md)
+
+
+### CMake Build Options
+
+You can make changes in the CMakeLists.txt file, but your build directory must be empty for globals to take effect. These options are available on the command line and will update cmake global variables.
+
+To use cmake options, use -D as shown in this example:
+
+```bash
+mkdir dir_name/ && cd dir_name/
+cmake .. -DCMAKE_BUILD_TYPE=Debug -DLAGRIT_BUILD_EXODUS=ON
+make
+```
+
+- `-D CMAKE_BUILD_TYPE`
+  - Sets the build type. Choose between `Debug` and `Release`.
+- `-D LAGRIT_BUILD_EXODUS=ON`
+  - Builds LaGriT with ExodusII if installed.
+- `-D CMAKE_INSTALL_PREFIX`
+  - Sets where to install LaGriT when running `make install`. Defaults to `/usr/local/`.
+- `-D LaGriT_BUILD_STATIC`
+  - Builds LaGriT as a static binary (default; `ON`) or as a shared library (`.so`, `.dylib`, `.dll`)
+
+### Supporting Documentation ###
+---
+* [LaGriT Documentation](https://lanl.github.io/LaGriT/)
+* [PyLaGriT documentation](https://lanl.github.io/LaGriT/pylagrit/original/index.html)
+* [lagrit.lanl.gov: Web Page](http://lagrit.lanl.gov)
+* [Contribution Agreement for External Collaborators](CONTRIBUTING.md)
+* [Copyright License](LICENSE.md)
+* [Code Development with cmake](cmake/README.md)
+* [Installation for old LaGriT V2](documentation/INSTALL.md)
+
+![Refine Samples](screenshots/refine_samples_TN1000.png)
+
+##### LaGriT Mesh Images at https://meshing.lanl.gov/proj/screenshots/GRID_GALLERY.html
--- a/cmake/CompilerFlags-C.cmake
+++ b/cmake/CompilerFlags-C.cmake
@@ -0,0 +1,58 @@
+# removing legacy flags like -m64
+# flag -m64 may be needed for C code lg_util/opsys.h
+ 
+# ======= C flags =========================================
+if("${CMAKE_C_COMPILER_ID}" MATCHES "Clang")
+  MESSAGE(STATUS "  C compiler: Clang")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w -m64")
+
+  execute_process(COMMAND clang --version OUTPUT_VARIABLE clang_version_output)
+  string(REGEX MATCH "[0-9]+" clang_version "${clang_version_output}")
+
+  if (clang_version AND clang_version GREATER_EQUAL 15)
+      set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-error=implicit-int")
+  endif()
+
+elseif ("${CMAKE_C_COMPILER_ID}" STREQUAL "GNU")
+  MESSAGE(STATUS "  C compiler: GNU GCC")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w -m64")
+
+elseif ("${CMAKE_C_COMPILER_ID}" STREQUAL "Intel")
+  MESSAGE(STATUS "  C compiler: Intel C")
+
+elseif ("${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC")
+  MESSAGE(STATUS "  C compiler: Microsoft Visual C")
+
+else()
+  message(STATUS "  C compiler not recognized: ${CMAKE_C_COMPILER_ID}")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w -m64")
+
+endif()
+
+# ======= C++ flags =======================================
+if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+  message(STATUS "  C++ compiler: Clang")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w -stdlib=libc++ -std=c++0x")
+
+  execute_process(COMMAND clang --version OUTPUT_VARIABLE clang_version_output)
+  string(REGEX MATCH "[0-9]+" clang_version "${clang_version_output}")
+  
+  if (clang_version AND clang_version GREATER_EQUAL 15)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-error=implicit-int")
+  endif()
+
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+  message(STATUS "  C++ compiler: GNU G++")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w")
+
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  message(STATUS "  C++ compiler: Intel C++")
+
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
+  message(STATUS "  C++ compiler: Microsoft Visual C++")
+
+else()
+  message(STATUS "  C++ compiler not recognized: ${CMAKE_CXX_COMPILER_ID}")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w")
+
+endif()
--- a/cmake/CompilerFlags-Fortran.cmake
+++ b/cmake/CompilerFlags-Fortran.cmake
@@ -0,0 +1,28 @@
+# if not found, try -DCMAKE_fortran_PATH="path/gfortran"
+# remove unused option -m64
+
+include(CheckFortranCompilerFlag)
+
+# set known compiler flags
+if ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
+  message(STATUS "  Fortran compiler: GNU GFORTRAN")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer -fdefault-integer-8 -std=legacy -fno-sign-zero -fno-range-check")
+
+elseif ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Intel")
+  message(STATUS "  Fortran compiler: Intel Fortran")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -O -Qsafe-cray-ptr -integer-size=64 -assume:nominus0 -QRimplicit-import-")
+
+
+# try using flags for unknown compiler
+else()
+
+message(STATUS "  Fortran compiler: ${CMAKE_Fortran_COMPILER_ID}")
+check_fortran_compiler_flag("${CMAKE_Fortran_FLAGS}" _my_flags)
+if(_my_flags)
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer -fdefault-integer-8 -std=legacy -fno-sign-zero -fno-range-check")
+else()
+  message(STATUS "  cmake/CompilerFlags-Fortran.cmake: FLAGS NOT SET")
+endif()
+
+endif()
+
--- a/cmake/DetectBitSize.cmake
+++ b/cmake/DetectBitSize.cmake
@@ -0,0 +1,24 @@
+# === DETECT BIT SIZE ======================== #
+if(CMAKE_SIZEOF_VOID_P EQUAL 8)
+  message(STATUS "  Architecture: 64-bit")
+  set(LAGRIT_RMAX_ALLOCATE 18446744073709551615.00)
+  set(LAGRIT_BYTES_PER_INT 8)
+  set(LAGRIT_BYTES_PER_REAL 8)
+  set(LAGRIT_BYTES_PER_CHAR 32)
+  set(LAGRIT_BYTES_PER_PTR 8)
+  set(LAGRIT_AD_SIZE 6)
+elseif(CMAKE_SIZEOF_VOID_P EQUAL 4)
+  message(STATUS "  Architecture: 32-bit")
+  set(LAGRIT_RMAX_ALLOCATE 4294967295.00)
+  set(LAGRIT_BYTES_PER_INT 4)
+  set(LAGRIT_BYTES_PER_REAL 8)
+  set(LAGRIT_BYTES_PER_CHAR 32)
+  set(LAGRIT_BYTES_PER_PTR 4)
+  set(LAGRIT_AD_SIZE 6)
+endif()
+
+configure_file(
+    "${SRC_UTIL}/mm2000.h.in"
+    "${SRC_UTIL}/mm2000.h"
+    @ONLY
+)
--- a/cmake/Linux.md
+++ b/cmake/Linux.md
@@ -0,0 +1,35 @@
+# Linux Helps and Hints
+
+Versions of LaGriT have been developed and tested on our local Linux Ubuntu servers using GNU compilers for many years. 
+This platform is very stable and should not require any special changes to cmake or associated files.
+
+### LaGriT build without Exodus
+
+No known issues.
+
+### LaGriT V3.3.3 build with Exodus
+
+**install-exodus.sh**
+
+Modifications for Exodus install, cmake, build were suggested by Greg at Seacas.
+
+```
+# FIX TPL/netcdf/runcmake.sh and cmake-exodus as described above
+sed -i '69i \         -DENABLE_PLUGINS:BOOL=OFF \\\n         -DENABLE_MULTIFILTERS:BOOL=NO \\\n         -DENABLE_NCZARR_FILTERS:BOOL=OFF \\\n         -DENABLE_TESTS:BOOL=OFF \\' TPL/netcdf/runcmake.sh
+sed -ie 's/DSeacas_EXTRA_LINK_FLAGS=z;dl/DSeacas_EXTRA_LINK_FLAGS=curl;z;dl/g' cmake-exodus
+```
+
+**CMakeLists.txt**
+
+Exodus for LaGriT requires Exodus Fortran libraries, not always installed on systems.
+For this reason we recommend installing Exodus in the local directory "TPLs".
+CMakeLists.txt will look for needed libraries locally rather than system versions that may not work.
+
+```
+set(EXODUS_ROOT "${CMAKE_SOURCE_DIR}/TPLs/seacas")
+set(Exodus_INCLUDE_DIR "${EXODUS_ROOT}/include")
+set(Exodus_LIBRARIES "${EXODUS_ROOT}/lib")
+```
+
+See detailed instructions at https://github.com/sandialabs/seacas
+Seacas Contact Gregory Sjaardema gsjaardema@gmail.com
--- a/cmake/PlatformSettings.cmake
+++ b/cmake/PlatformSettings.cmake
@@ -0,0 +1,27 @@
+# https://gitlab.kitware.com/cmake/community/-/wikis/doc/tutorials/How-To-Write-Platform-Checks#platform-variables
+
+if(UNIX)
+    if(APPLE)
+        message(STATUS "  Operating System: macOS")
+        add_definitions(-Dmacx64)
+    elseif(CYGWIN)
+        message(STATUS "  Operating System: Windows (Cygwin)")
+        add_definitions(-Dwin64)
+    else()
+        message(STATUS "  Operating System: Linux")
+        add_definitions(-Dlinx64)
+    endif()
+
+    set(LaGriT_STATIC_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+
+elseif(WIN32)
+    message(STATUS "  Operating System: Windows")
+    add_definitions(-Dwin64)
+
+elseif(MINGW)
+    message(STATUS "  Operating System: Windows (MinGW)")
+    add_definitions(-Dwin64)
+
+else()
+    message("cmake/PlatformSettings.cmake OPERATING SYSTEM UNDEFINED")
+endif()
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -0,0 +1,312 @@
+# LaGriT and ExodusII with cmake
+
+The CMake build system is a way of enabling LaGriT to be cross-platform, cross-architecture, and cross-compiler. This page is a verbose description of building LaGriT and includes instructions for building the optional library for ExodusII.
+
+The CMake build is controlled by CMakeLists.txt and files in directory /cmake
+
+The ExodusII libraries can be built using install-exodus.sh or MAC_install-exodus.sh
+For additional help on ExodusII, see instructions at https://github.com/sandialabs/seacas
+**Note for Exodus with LaGriT, FORTRAN must be set to YES**
+
+
+There's a really good tutorial-overview on CMake here, it covers how to handle multiple build configurations: https://cliutils.gitlab.io/modern-cmake/
+
+
+## Download LaGriT
+
+Download the repo as shown under the Code button on git.
+For developers, be sure to use SSH version to clone. 
+
+```
+$ git clone git@github.com:lanl/LaGriT.git 
+$ cd LaGriT/
+```
+
+If SSH Key needed, generate a key for your machine.
+[See GitHub Docs for SSH Key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
+```
+Generate a SSH key (NOT RSA) in your .ssh directory.
+ssh-keygen -t ed25519 -C "email.lanl.gov"
+Copy contents of id_ed25519.pub into your SSH Keys on github (under settings).
+```
+
+## Build With ExodusII (optional)
+
+ 
+From the top directory run: ```./install-exodus.sh``` or for a mac use: ```./MAC_install-exodus.sh```
+The script will take some time to clone, configure, and build the necessary lib and include files.
+Read comments in the script for hints if things go wrong.
+For additional help on ExodusII, see instructions at https://github.com/sandialabs/seacas
+
+LaGriT requires the following:
+```
+/seacas/lib/ libexodus.a  libexodus_for.a  libexoIIv2for32.a
+/seacas/include/ exodus_config.h  exodusII.h  exodusII.inc  exodusII_int.h  exodusII_par.h
+```
+
+Once the ExodusII is successful, build LaGriT as usual using the EXODUS flag:
+
+```
+mkdir build/ && cd build/
+cmake .. -DLAGRIT_BUILD_EXODUS=ON
+make
+```
+
+## Build Without ExodusII
+
+If you do not need to write an Exodus formatted file, you can build LaGriT without the ExodusII libraries.
+Create a directory for your lagrit executable, then use cmake to create the configuration files and directories.
+
+From the top directory in LaGriT:
+```
+mkdir build
+cd build
+cmake ..
+```
+
+Cmake will use settings defined in LaGriT/CMakeLists.txt and should look something like this:
+
+```
+-- ==========================================
+-- ============Configuring LaGriT============
+-- ===================v3.3.3=================
+-- Compile LaGriT as a static binary = ON
+-- Compile LaGriT with ExodusII = OFF
+LaGriT Compiling without ExodusII support.
+To include Exodus, use -DLAGRIT_BUILD_EXODUS=ON
+-- Detecting LaGriT build using local cmake files:
+--   Operating System: Linux
+--   Architecture: 64-bit
+--   Fortran compiler: GNU GFORTRAN
+--   C compiler: GNU GCC
+--   C++ compiler: GNU G++
+-- Configuring done
+-- Generating done
+-- Build files have been written to: /project/eesdev/tam/clone/LaGriT/build
+```
+
+Once cmake has configured the directory files, type *make* to compile the lagrit executable:
+
+```
+make
+```
+
+This directory will create the **lagrit** executable using the files created by cmake.
+
+```
+Scanning dependencies of target liblagrit
+[  0%] Building Fortran object CMakeFiles/liblagrit.dir/src/ColoredGraphModule.f90.o
+...
+[100%] Built target liblagrit
+Scanning dependencies of target lagrit
+[100%] Building Fortran object CMakeFiles/lagrit.dir/src/lagrit_main.f.o
+[100%] Linking Fortran executable lagrit
+[100%] Built target lagrit
+```
+
+
+## Run LaGriT Test Suite
+
+Go to LaGriT/test and run the test script. See the README file for further instructions.
+
+```
+$ cd test
+$ python runtests.py
+```
+
+
+## Create your build directory:
+
+By default, most the scripts will expect the lagrit executable to be in the "build" directory. But you build in directories with other names.
+You can build as Debug (-g) or as Release with the CMake flag "-D CMAKE_BUILD_TYPE=[Debug|Release]".
+There's two stages in CMake; the 'configure' stage (where you run 'cmake ..') and the build stage (where you run 'make' using the Makefile created by cmake)
+
+The build type can only be set in the configure stage (with cmake) and will apply to all files in your build directory. If you make a change to cmake, you will need to run in a new directory, or remove all the files and directories created with your previous cmake configuration.
+
+Setup a work directory for dev and debug work (example using name "debug").
+Use cmake to create Makefiles and build files. You will do this only once.
+Compile the lagrit executable using 'make' or 'make VERBOSE=1'
+```
+mkdir debug && cd debug
+cmake .. -D CMAKE_BUILD_TYPE=Debug
+make
+```
+
+Run ./lagrit and type command **test** which creates hex mesh and reports expected values.
+
+For debugging the build process, set cmake and make to show verbose screen reporting. These are run from your build directory with the following options:
+```
+cmake -D CMAKE_FIND_DEBUG_MODE=ON ..
+make VERBOSE=1
+```
+      
+## Modify code and update **lagrit** executable
+
+Modify code by working with lagrit source files in LaGriT/src
+Do not add any non-code develpment files in the /src directory, they may be detected and attempted to use during compile time.
+
+When you want to compile, do not run cmake again, it already created your makefiles, .o, and other dependencies.
+
+Go to LaGriT/*your_build_name* directory and type
+```
+make
+```
+
+**lagrit** will be built in LaGriT/*your_build_name* directory.
+
+*If you add new files to /src you will need to run cmake again. This will detect all files in src/ and create a new set of Makefiles.*
+
+
+      
+### Example Directory structure for developers:
+      
+```
+LaGriT/
+|
+└── build/
+    └── lagrit executable, Makefiles built by cmake, cmake files    
+└── src/
+    └── file.cpp, file.f, file.c, lagrit.h, etc
+|
+├── CMakeLists.txt
+└── cmake/
+    └── CompilerFlags-C.cmake, CompilerFlags-Fortran.cmake, DetectBitSize.cmake, PlatformSettings.cmake
+```
+
+### Example Screen Output for cmake .. -DLAGRIT_BUILD_EXODUS=ON
+
+```
+-- The Fortran compiler identification is GNU 7.5.0
+-- The CXX compiler identification is GNU 7.5.0
+-- The C compiler identification is GNU 7.5.0
+-- ==========================================
+-- ============Configuring LaGriT============
+-- ===================v3.3.3=================
+-- Compile LaGriT as a static binary = ON
+-- Compile LaGriT with ExodusII = ON
+-- ExodusII libraries      : /project/eesdev/tam/LaGriT/TPLs/seacas/lib
+-- ExodusII include        : /project/eesdev/tam/LaGriT/TPLs/seacas/include
+-- Detected System:
+--   Operating System: Linux
+--   Architecture: 64-bit
+--   Fortran compiler: GNU GFORTRAN
+--   C compiler: GNU GCC
+--   C++ compiler: GNU G++
+-- Using Third Party Libraries.
+-- TPL libs: /project/eesdev/tam/LaGriT/TPLs/seacas/lib
+-- TPL include: /project/eesdev/tam/LaGriT/TPLs/seacas/include
+-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
+-- Verifying Fortran/C Compiler Compatibility - Success
+-- Compilers:
+--   FORTRAN [compiler = "/usr/bin/f95"; flags = " -m64 -fcray-pointer -fdefault-integer-8 -std=legacy -fno-sign-zero -fno-range-check"]
+--   C [compiler = "/usr/bin/cc"; flags = " -w -m64"]
+--   C++ [compiler = "/usr/bin/c++"; flags = " -w -m64"]
+-- Configuring done
+-- Generating done
+-- Build files have been written to: /project/eesdev/tam/LaGriT/build
+```
+
+### Example Screen Output for make VERBOSE=1
+
+```
+[  2%] Building C object CMakeFiles/liblagrit.dir/lg_util/src/gmvwrite.c.o
+/usr/bin/cc -DLAGRIT_INCLUDE_EXODUSII -Dlinx64 -I/project/eesdev/tam/LaGriT/TPLs/seacas/include -w -m64 -MD -MT CMakeFiles/liblagrit.dir/lg_util/src/gmvwrite.c.o -MF CMakeFiles/liblagrit.dir/lg_util/src/gmvwrite.c.o.d -o CMakeFiles/liblagrit.dir/lg_util/src/gmvwrite.c.o -c /project/eesdev/tam/LaGriT/lg_util/src/gmvwrite.c
+
+[ 36%] Building Fortran object CMakeFiles/liblagrit.dir/src/dumpexodusII.f.o
+/usr/bin/f95 -DLAGRIT_INCLUDE_EXODUSII -Dlinx64 -I/project/eesdev/tam/LaGriT/TPLs/seacas/include -m64 -fcray-pointer -fdefault-integer-8 -std=legacy -fno-sign-zero -fno-range-check -cpp -c /project/eesdev/tam/LaGriT/src/dumpexodusII.f -o CMakeFiles/liblagrit.dir/src/dumpexodusII.f.o
+
+[ 70%] Building CXX object CMakeFiles/liblagrit.dir/src/poi_helperFunctions.cpp.o
+/usr/bin/c++ -DLAGRIT_INCLUDE_EXODUSII -Dlinx64 -I/project/eesdev/tam/LaGriT/TPLs/seacas/include -w -m64 -MD -MT CMakeFiles/liblagrit.dir/src/poi_helperFunctions.cpp.o -MF CMakeFiles/liblagrit.dir/src/poi_helperFunctions.cpp.o.d -o CMakeFiles/liblagrit.dir/src/poi_helperFunctions.cpp.o -c /project/eesdev/tam/LaGriT/src/poi_helperFunctions.cpp
+
+[100%] Linking CXX static library liblagrit.a
+/n/swdev/packages/Ubuntu-18.04-x86_64/cmake/cmake-3.22.1/bin/cmake -P CMakeFiles/liblagrit.dir/cmake_clean_target.cmake
+
+/n/swdev/packages/Ubuntu-18.04-x86_64/cmake/cmake-3.22.1/bin/cmake -E cmake_link_script CMakeFiles/liblagrit.dir/link.txt
+
+/usr/bin/ranlib liblagrit.a
+make[2]: Leaving directory '/project/eesdev/tam/LaGriT/build'
+[100%] Built target liblagrit
+
+[100%] Linking Fortran executable lagrit
+/n/swdev/packages/Ubuntu-18.04-x86_64/cmake/cmake-3.22.1/bin/cmake -E cmake_link_script CMakeFiles/lagrit.exe.dir/link.txt
+
+/usr/bin/f95 -static-libgcc -static-libstdc++  -m64 -fcray-pointer -fdefault-integer-8 -std=legacy -fno-sign-zero -fno-range-check CMakeFiles/lagrit.exe.dir/src/lagrit_main.f.o -o lagrit  liblagrit.a -L/project/eesdev/tam/LaGriT/TPLs/seacas/lib -lexodus_for -lexodus -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl -static-libgfortran -static-libgcc -lstdc++ 
+
+[100%] Built target lagrit
+```
+
+## Automatic Configurations
+
+This is work performed by cmake and is usually not modified. Cmake is used to do some automatic file edits that depend on the machine or platform you are using. 
+
+### Header File configuration
+
+CMake automatically configures two header files:
+
+- `lg_util/src/mm2000.h`
+- `src/lagrit.h`
+
+The original files have the same name, but ending with `.in`.
+
+CMake configures the files as following. Consider a line from `lagrit.h.in`:
+
+```fortran
+      parameter      (v_major=@PROJECT_VERSION_MAJOR@)
+```
+
+Here, `@PROJECT_VERSION_MAJOR@` is a CMake variable which will be replaced by CMake.
+
+Here is how CMake configures the file:
+
+```cmake
+configure_file(
+    ${SRC_CORE}/lagrit.h.in
+    ${SRC_CORE}/lagrit.h
+    @ONLY
+)
+```
+
+`${SRC_CORE}/lagrit.h.in` is the 'template' file, and `${SRC_CORE}/lagrit.h` is the output file. The `@ONLY` line means to **only** replace variables between the `@` symbol.
+
+The variable above - `@PROJECT_VERSION_MAJOR@` is an instrinsic CMake variable. You can define your own. For example, CMake code within `SetBitSize.cmake` configures the `lg_util/src/mm2000.h.in` file.
+
+### C-Fortran Compatibility
+
+LaGriT codes include both Fortran and C/C++ code files. The driver routines are Fortran, the C/C++ files use wrapper functions and definitions set by cmake before code is compiled. These are set during the configuration and should not need to be modified unless new routines are added.
+
+cmake writes fc_mangle.h for c-fortran routines. This file handles the symbol mangling for routines declared in src/lg_f_interface.h include file. For more information on this method visit https://www.netlib.org/lapack/lawnspdf/lawn270.pdf
+
+The C++ wrapper routines need to be listed in CMakeLists.txt:
+
+```
+FortranCInterface_HEADER(
+    ${SRC_CORE}/fc_mangle.h
+    SYMBOLS
+        INITLAGRIT # syntax: <subroutine>
+        DOTASK
+        CMO_GET_NAME
+        CMO_GET_INFO
+        CMO_GET_INTINFO
+        FC_CMO_GET_INT
+        FC_CMO_GET_VINT
+        FC_CMO_GET_DOUBLE
+        FC_CMO_GET_VDOUBLE
+        FPASS_TYPES
+        INSIDE_TET
+        LINESEG_TRI)
+```
+
+### LaGriT command TEST
+
+The following commands have been added as tests during execution. These are especially useful in testing and to debug the c-fortran codes on various machines.
+
+```
+test (no second word) - easy test using createpts to check executable
+test list - list available options
+cpp -  call dotask and c-fortran wrappers using get_info calls to get pointers from fortran
+fortran - call dotask and get_info pointers used by cpp
+dotask - call dotask_test which avoids global commands and just tests dotask parameters
+```
+
+
+
--- a/cmake/Windows.md
+++ b/cmake/Windows.md
@@ -0,0 +1,36 @@
+# Windows Helps and Hints
+
+LaGriT V3.3.3 was not tested on Windows. 
+Earlier versions of LaGriT worked on Windows using CYGWIN.
+
+## LaGrit V3.3.3 Windows 10 with gcc/gfortran
+From User cean wang ceanwang@gmail.com Dec 11 2023
+
+Cean compiled LaGriT under WIndows 10 with gcc/gfortran.
+
+Cean followed instructions at https://lanl.github.io/LaGriT/pages/docs/build.html
+and copied the example driver function into adrivgen.f and had a successful compile.
+
+Cean noticed an error message suggesting to add a '' at the end of a function name, that is: initlagrit to initlagrit. This is normal for C & Fortran mixed programing.
+
+
+## LaGriT V3.2 with C++ main on Windows with Microsoft Visual Studio
+
+GOLDER Project has a forked version of LaGriT V3.2 that builds on Windows and includes instructions for their work: See repo at https://github.com/daniellivingston/LaGriT-Windows
+
+Daniel Livingston developed a branch working on windows that is an update to the Golder project. See https://github.com/lanl/LaGriT/tree/windows
+
+The code on the windows branch uses C++ as main calling LaGriT fortran and c codes. The branch has not been merged with master because of compile failures on Linux and Mac systems.
+
+## ERROR: Undefined references to srand48() and drand48()
+
+Complaint using WIndows 10 with gcc/gfortran edit src/metis_lg.c
+Functions srand48() and drand48() are Linux or some flavor of Windows with MinGW as compiler system.
+Solution at https://stackoverflow.com/questions/74274179/i-cant-use-drand48-and-srand48-in-c
+
+Note metis codes are no longer used and will be updated or removed.
+
+
+
+
+*Check LaGriT Github Issues for help and hints for  Windows systems.*
--- a/cmake/macOS.md
+++ b/cmake/macOS.md
@@ -0,0 +1,246 @@
+# MacOS Helps and Hints
+
+LaGriT has been developed and used on MacOS machines for many years, using both Clang and GNU compilers.
+For MacOS compilers and systems newer than those used in 2019, there may be issues finding the correct compilers.
+See below for known issues.
+
+LaGriT V3.3.3 builds with and without Exodus on MacOS Intel and M1 machines on Monterey, Ventura, and Sonoma.
+
+LaGriT builds without Exodus are usually successful and recommended before building a version with Exodus.
+
+See **LaGriT/MAC-install-exodus.sh** which works for brew as well as macports. This script finds and sets compiler paths due to location and naming changes between homebrew and macports.
+
+See also **LaGriT/MAC_EnvironmentalVar.sh** for setting your compilers.
+
+
+### Compiler Errors
+
+LaGriT uses C, C++, and Fortran compilers. You may have to set the correct compilers for your build environment. The build may fail for newer models due to differences in naming conventions for both file structure and compilers. 
+
+Find or install your preferred compilers and set your environment, for example:
+
+```
+export CC=/opt/local/bin/gcc-mp-12
+export CXX=/opt/local/bin/g++-mp-12
+export FC=/opt/local/bin/gfortran-mp-12
+```
+
+On newer machines, the problem is that mac / osx has stolen the name gcc and g++ for the Apple clang compiler.   And they don't provide fortran.
+There are quite a few ways to work around this issue, but in any given case you have to be careful to make sure things are self-consistent.
+
+Below are instructions for installing a set of compilers using MacPorts (Homebrew also works). 
+
+
+
+## Fortran Compiler Not Found or Incompatible with C compilers (macports example)
+
+For LaGriT V3.3.3 on MacOS the Builds for LaGriT and Exodus were successful on Ventura and Sonoma using MacPorts and Homebrew. This example uses macports.
+
+To use Macports you will need to install XCode command line tools.
+Go to:https://developer.apple.com/download/all/ and select Sonoma Xcode 15.1, Ventura Xcode 14.3, or Early macOS 13.2.
+
+Download and install macports:https://www.macports.org/install.php
+
+Once Downloaded, Check to see if port command is found:
+```
+% port version
+Version: 2.8.1
+``` 
+
+If port not found, set path. This should be in your appropriate login file such as .bash_profile.
+
+```
+export PATH="/opt/local/bin:/opt/local/sbin:$PATH"
+```
+
+selfupdate with verbose will take some time:
+```sudo -E port -v selfupdate```
+
+Use macports, Install CMake, GNU make, GNU compilers, (and wget for Exodus). Use the -E option to preserve environment varables such as your Proxies.
+
+```
+sudo -E port install cmake
+sudo -E port install gmake
+sudo -E port install gcc12
+sudo -E port install wget
+```
+
+When done should have:
+
+```
+cmake version 3.24.4
+gmake version 4.4.1
+gcc version Apple Clang version 14.0.3
+g++ version Apple Clang version 14.0.3
+gfortran version 12.2.0
+wget version 1.21.4
+```
+
+Make sure Cmake configurations for LaGriT and Exodus are using these tools and compilers.
+
+
+ 
+## Exodus Build Fails with CommandLineTools Error (macports example)
+
+Usually these strange permission errors are related to XCode resource management and parallel builds.   In the older XCode (14.x) these were all resolved with the gnu tools (particularly gmake) coming from macports. 
+
+```
+[ 93%] Built target h5dump
+[ 93%] Built target h5watch
+[ 93%] Built target h5perf_serial
+make[1]: /Library/Developer/CommandLineTools/usr/bin/make: Permission denied
+```
+
+
+Switch MacPort installed gmake to 4.4 release.
+See also: https://trac.macports.org/wiki/howto/InstallingOlderPort
+
+```
+git clone --single-branch https://github.com/macports/macports-ports.git
+cd macports-ports
+find . -name gmake
+```
+
+Now either in a web browser or from the command line identify the hash of the version you want.
+Then checkout that commit, the commands below will checkout version 4.4
+
+```
+git checkout 4423959
+cd devel/gmake
+sudo -E port install
+```
+
+The tail end of the output shows that the newer version is deactivated and replaced with the older version:
+```
+--->  Building gmake
+--->  Staging gmake into destroot
+--->  Installing gmake @4.4_0
+--->  Deactivating gmake @4.4.1_0
+--->  Cleaning gmake
+--->  Activating gmake @4.4_0
+--->  Cleaning gmake
+--->  Scanning binaries for linking errors
+--->  No broken files found.
+--->  No broken ports found.
+```
+
+
+If you experience a weird permission error, and you have admin permissions set. You still might not have access to the files you just installed. 
+
+```
+Error: Unable to execute port: Could not open file: /Users/l113691/macports/macports-ports/devel/gmake/Portfile
+```
+
+Suggested fix, move the directory away from root and inherited permissions:
+See suggestion at: https://superuser.com/questions/598824/previous-version-of-cgal-with-macports-error-unable-to-execute-port-could-no
+
+```
+cd macports-ports/devel
+sudo mv gmake /private/tmp
+cd /private/tmp
+sudo -E port install
+```
+
+```
+gmake --version
+GNU Make 4.4
+```
+
+This solution worked on MacOS Intel and M1, Ventura and Sonoma for building LaGriT and Exodus.
+
+## Exodus Build Fails with a make error that mentions an "sdk"
+
+The error looks like this using macports:
+```
+/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/_wchar.h:90,
+             	from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/wchar.h:67,
+             	from /opt/local/include/gcc14/c++/cwchar:44,
+             	from /opt/local/include/gcc14/c++/bits/postypes.h:40,
+             	from /opt/local/include/gcc14/c++/bits/char_traits.h:42,
+             	from /opt/local/include/gcc14/c++/string:42,
+             	from /Users/elm/packages/amanzi/repos/amanzi-1.5.1/src/error_handling/exceptions.hh:13,
+             	from /Users/elm/packages/amanzi/repos/amanzi-1.5.1/src/error_handling/dbc.hh:13,
+             	from /Users/elm/packages/amanzi/repos/amanzi-1.5.1/src/error_handling/dbc.cc:10:
+/opt/local/lib/gcc14/gcc/aarch64-apple-darwin23/14.2.0/include-fixed/stdio.h:83:8: error: 'FILE' does not name a type
+   83 | extern FILE *__stdinp;
+  	|    	^~~~
+```
+
+or this using brew:
+```
+Building CXX object CMakeFiles/cmTC_c85e6.dir/testCXXCompiler.cxx.o
+    /Library/Developer/CommandLineTools/usr/bin/g++   “-I/opt/homebrew/opt/llvm/include”  -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk -mmacosx-version-min=14.7 -MD -MT CMakeFiles/cmTC_c85e6.dir/testCXXCompiler.cxx.o -MF CMakeFiles/cmTC_c85e6.dir/testCXXCompiler.cxx.o.d -o CMakeFiles/cmTC_c85e6.dir/testCXXCompiler.cxx.o -c /Users/jhyman/src/LaGriT/TPLs/seacas/TPL/netcdf/netcdf-c/build/CMakeFiles/CMakeScratch/TryCompile-sEGBRU/testCXXCompiler.cxx
+    clang++: error: no such file or directory: '“-I/opt/homebrew/opt/llvm/include”'
+    gmake[1]: *** [CMakeFiles/cmTC_c85e6.dir/build.make:79: CMakeFiles/cmTC_c85e6.dir/testCXXCompiler.cxx.o] Error 1
+    gmake[1]: Leaving directory '/Users/jhyman/src/LaGriT/TPLs/seacas/TPL/netcdf/netcdf-c/build/CMakeFiles/CMakeScratch/TryCompile-sEGBRU'
+    gmake: *** [Makefile:127: cmTC_c85e6/fast] Error 2
+```
+
+**This error happens because newer Mac's require a newer version of x-code Command Line Tools to be installed. These tools don't work nicely with gcc-14. The sdk's for the newer tools are incompatible.** 
+
+To fix the error:
+
+1. Verify that you have an older MacOSX14.sdk installation
+   ```
+   ls /Library/Developer/CommandLineTools/SDKs
+   ```
+2. export older sds:
+   ```
+   export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/
+   ```
+ 
+## New Compilers show precision error for very small numbers
+
+The XCode 15.0 compilers are showing a precision error for very small numbers.
+This does not alter the meshing results but can show differences in how diagonals are crossed and reporting statistics.
+
+This issue was observed using the following:
+```
+Cmake 3.24.4
+Gmake 3.81
+gcc 15.0.0
+gcc-mp-13
+g++-mp-13
+gfortran-mp-13
+```
+
+The MacPorts compilers shown above do not have this precision issue.
+
+
+## Compilers using Homebrew
+
+Prior to installing compilers, you must have a working git, https://github.com/git-guides/install-git, and homebrew, https://github.com/homebrew, install.
+
+```
+brew install cmake
+brew install make
+brew install gcc
+brew install wget
+```
+It may be necessary to export your compiler path as MACs like to use Clang whenever possible
+
+```
+export PATH=/usr/local/bin:$PATH
+```
+
+It some cases, creating an alias also helps:
+```
+alias gcc="gcc-13"
+alias g++="g++-13"
+alias cc="cc-13"
+alias c++="c++-13"
+```
+
+When you run 
+```
+gcc –version
+```
+it should now list homebrew rather than clang.
+
+## Clang and Implicit-int error
+
+Newer versions of Clang have moved away from implicit-int and have begun reporting it as an error rather then a warning. It may be necessary to use the flag
+
+```
+-Wno-error=implicit-int
+```
--- a/cmake/modules/FindExodus.cmake
+++ b/cmake/modules/FindExodus.cmake
@@ -0,0 +1,27 @@
+#
+# Find the Exodus finite element data model library from Sandia
+#
+#  EXODUS_FOUND - System has Exodus
+#  EXODUS_INCLUDE_DIR - The LibXml2 include directory
+#  EXODUS_LIBRARIES - The libraries needed to use LibXml2
+#
+# Original author: https://gitlab.kitware.com/xdmf/xdmf/blob/master/CMake/FindExodus.cmake
+
+#FIND_PACKAGE(NetCDF REQUIRED)
+# Original lagrit build line: -L$(EXO_LIB_DIR) -lexodus_for -lexodus -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl
+
+FIND_PATH(Exodus_INCLUDE_DIR NAMES exodusII.h)
+
+#FIND_LIBRARY(EXODUS_LIBRARIES NAMES exodusii exodusIIv2c exodus_for exodus)
+FIND_LIBRARY(Exodus_LIBRARIES
+    NAMES exodus_for exodus
+)
+
+INCLUDE(FindPackageHandleStandardArgs)
+
+# handle the QUIETLY and REQUIRED arguments and set EXODUS_FOUND to TRUE if
+# all listed variables are TRUE
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Exodus DEFAULT_MSG Exodus_LIBRARIES Exodus_INCLUDE_DIR)
+
+MARK_AS_ADVANCED(Exodus_INCLUDE_DIR Exodus_LIBRARIES)
+
--- a/cmake/modules/FindNetCDF.cmake
+++ b/cmake/modules/FindNetCDF.cmake
@@ -0,0 +1,30 @@
+#
+# Find NetCDF include directories and libraries
+#
+# NetCDF_FOUND - System has NetCDF
+# NetCDF_INCLUDE_DIR - The NetCDF include directory
+# NetCDF_LIBRARIES - The libraries needed to use NetCDF
+
+FIND_PATH(NetCDF_INCLUDE_DIR netcdf.h)
+
+FIND_LIBRARY(NetCDF_LIBRARIES
+  NAMES netcdf
+  ${NetCDF_PREFIX}
+  ${NetCDF_PREFIX}/lib64
+  ${NetCDF_PREFIX}/lib
+  /usr/local/lib64
+  /usr/lib64
+  /usr/lib64/netcdf-3
+  /usr/local/lib
+  /usr/lib
+  /usr/lib/netcdf-3
+)
+
+INCLUDE(FindPackageHandleStandardArgs)
+
+# handle the QUIETLY and REQUIRED arguments and set EXODUS_FOUND to TRUE if 
+# all listed variables are TRUE
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NetCDF_INCLUDE_DIR NetCDF_LIBRARIES)
+
+MARK_AS_ADVANCED(NetCDF_INCLUDE_DIR NetCDF_LIBRARIES)
+
--- a/docs/.README.swp
+++ b/docs/.README.swp
--- a/docs/Gemfile
+++ b/docs/Gemfile
@@ -0,0 +1,37 @@
+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "minima", "~> 2.5"
+
+gem "github-pages", "~> 232", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "html-proofer"
+  gem "jekyll-sitemap"
+  gem "rubocop-github"
+  gem "jekyll-seo-tag"
+  gem "w3c_validators"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", "~> 1.2"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+gem "webrick", "~> 1.7"
+gem "liquid", "~> 4.0.4"
+
+# kramdown v2 ships without the gfm parser by default. If you're using
+# kramdown v1, comment out this line.
+gem "kramdown-parser-gfm"
--- a/docs/Gemfile.lock
+++ b/docs/Gemfile.lock
@@ -0,0 +1,395 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    Ascii85 (2.0.1)
+    activesupport (8.0.1)
+      base64
+      benchmark (>= 0.3)
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.3.1)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      logger (>= 1.4.2)
+      minitest (>= 5.1)
+      securerandom (>= 0.3)
+      tzinfo (~> 2.0, >= 2.0.5)
+      uri (>= 0.13.1)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    afm (0.2.2)
+    ast (2.4.2)
+    async (2.21.1)
+      console (~> 1.29)
+      fiber-annotation
+      io-event (~> 1.6, >= 1.6.5)
+    base64 (0.2.0)
+    benchmark (0.4.0)
+    bigdecimal (3.1.9)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
+    colorator (1.1.0)
+    commonmarker (0.23.11)
+    concurrent-ruby (1.3.4)
+    connection_pool (2.5.0)
+    console (1.29.2)
+      fiber-annotation
+      fiber-local (~> 1.1)
+      json
+    csv (3.3.2)
+    dnsruby (1.72.3)
+      base64 (~> 0.2.0)
+      simpleidn (~> 0.2.1)
+    drb (2.2.1)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
+    eventmachine (1.2.7)
+    execjs (2.10.0)
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
+    ffi (1.17.1-aarch64-linux-gnu)
+    ffi (1.17.1-aarch64-linux-musl)
+    ffi (1.17.1-arm-linux-gnu)
+    ffi (1.17.1-arm-linux-musl)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-darwin)
+    ffi (1.17.1-x86_64-linux-gnu)
+    ffi (1.17.1-x86_64-linux-musl)
+    fiber-annotation (0.2.0)
+    fiber-local (1.1.0)
+      fiber-storage
+    fiber-storage (1.0.0)
+    forwardable-extended (2.6.0)
+    gemoji (4.1.0)
+    github-pages (232)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.10.0)
+      jekyll-avatar (= 0.8.0)
+      jekyll-coffeescript (= 1.2.2)
+      jekyll-commonmark-ghpages (= 0.5.1)
+      jekyll-default-layout (= 0.1.5)
+      jekyll-feed (= 0.17.0)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.16.1)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
+      jemoji (= 0.13.0)
+      kramdown (= 2.4.0)
+      kramdown-parser-gfm (= 1.1.0)
+      liquid (= 4.0.4)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.16.2, < 2.0)
+      rouge (= 3.30.0)
+      terminal-table (~> 1.4)
+      webrick (~> 1.8)
+    github-pages-health-check (1.18.2)
+      addressable (~> 2.3)
+      dnsruby (~> 1.60)
+      octokit (>= 4, < 8)
+      public_suffix (>= 3.0, < 6.0)
+      typhoeus (~> 1.3)
+    hashery (2.1.2)
+    html-pipeline (2.14.3)
+      activesupport (>= 2)
+      nokogiri (>= 1.4)
+    html-proofer (5.0.9)
+      addressable (~> 2.3)
+      async (~> 2.1)
+      nokogiri (~> 1.13)
+      pdf-reader (~> 2.11)
+      rainbow (~> 3.0)
+      typhoeus (~> 1.3)
+      yell (~> 2.0)
+      zeitwerk (~> 2.5)
+    http_parser.rb (0.8.0)
+    i18n (1.14.6)
+      concurrent-ruby (~> 1.0)
+    io-event (1.7.5)
+    jekyll (3.10.0)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      csv (~> 3.0)
+      em-websocket (~> 0.5)
+      i18n (>= 0.7, < 2)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 2.0)
+      kramdown (>= 1.17, < 3)
+      liquid (~> 4.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (>= 1.7, < 4)
+      safe_yaml (~> 1.0)
+      webrick (>= 1.0)
+    jekyll-avatar (0.8.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-coffeescript (1.2.2)
+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.12)
+    jekyll-commonmark (1.4.0)
+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.5.1)
+      commonmarker (>= 0.23.7, < 1.1.0)
+      jekyll (>= 3.9, < 4.0)
+      jekyll-commonmark (~> 1.4.0)
+      rouge (>= 2.0, < 5.0)
+    jekyll-default-layout (0.1.5)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-feed (0.17.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-gist (1.5.0)
+      octokit (~> 4.2)
+    jekyll-github-metadata (2.16.1)
+      jekyll (>= 3.4, < 5.0)
+      octokit (>= 4, < 7, != 4.4.0)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-mentions (1.6.0)
+      html-pipeline (~> 2.3)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-optional-front-matter (0.3.2)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-paginate (1.1.0)
+    jekyll-readme-index (0.3.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-remote-theme (0.4.3)
+      addressable (~> 2.0)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+      rubyzip (>= 1.3.0, < 3.0)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-swiss (1.0.0)
+    jekyll-theme-architect (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-cayman (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-dinky (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-hacker (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-leap-day (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-merlot (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-midnight (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-minimal (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-modernist (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-primer (0.6.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-github-metadata (~> 2.9)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-slate (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-tactile (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-time-machine (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-titles-from-headings (0.5.3)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    jemoji (0.13.0)
+      gemoji (>= 3, < 5)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0, < 5.0)
+    json (2.9.1)
+    kramdown (2.4.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    language_server-protocol (3.17.0.3)
+    liquid (4.0.4)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.4)
+    mercenary (0.3.6)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    minitest (5.25.4)
+    net-http (0.6.0)
+      uri
+    nokogiri (1.18.1-aarch64-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-aarch64-linux-musl)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm-linux-musl)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.18.1-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.18.1-x86_64-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-x86_64-linux-musl)
+      racc (~> 1.4)
+    octokit (4.25.1)
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
+    parallel (1.26.3)
+    parser (3.3.6.0)
+      ast (~> 2.4.1)
+      racc
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    pdf-reader (2.13.0)
+      Ascii85 (>= 1.0, < 3.0, != 2.0.0)
+      afm (~> 0.2.1)
+      hashery (~> 2.0)
+      ruby-rc4
+      ttfunk
+    public_suffix (5.1.1)
+    racc (1.8.1)
+    rack (3.1.8)
+    rainbow (3.1.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    regexp_parser (2.10.0)
+    rexml (3.4.0)
+    rouge (3.30.0)
+    rubocop (1.69.2)
+      json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
+      parallel (~> 1.10)
+      parser (>= 3.3.0.2)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.37.0)
+      parser (>= 3.3.1.0)
+    rubocop-github (0.20.0)
+      rubocop (>= 1.37)
+      rubocop-performance (>= 1.15)
+      rubocop-rails (>= 2.17)
+    rubocop-performance (1.23.1)
+      rubocop (>= 1.48.1, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
+    rubocop-rails (2.28.0)
+      activesupport (>= 4.2.0)
+      rack (>= 1.1)
+      rubocop (>= 1.52.0, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
+    ruby-progressbar (1.13.0)
+    ruby-rc4 (0.1.5)
+    rubyzip (2.4.1)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sawyer (0.9.2)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    securerandom (0.4.1)
+    simpleidn (0.2.3)
+    terminal-table (1.6.0)
+    ttfunk (1.8.0)
+      bigdecimal (~> 3.1)
+    typhoeus (1.4.1)
+      ethon (>= 0.9.0)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (3.1.3)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
+    uri (1.0.2)
+    w3c_validators (1.3.7)
+      json (>= 1.8)
+      nokogiri (~> 1.6)
+      rexml (~> 3.2)
+    webrick (1.9.1)
+    yell (2.2.2)
+    zeitwerk (2.7.1)
+
+PLATFORMS
+  aarch64-linux-gnu
+  aarch64-linux-musl
+  arm-linux-gnu
+  arm-linux-musl
+  arm64-darwin
+  x86_64-darwin
+  x86_64-linux-gnu
+  x86_64-linux-musl
+
+DEPENDENCIES
+  github-pages (~> 232)
+  html-proofer
+  jekyll-seo-tag
+  jekyll-sitemap
+  kramdown-parser-gfm
+  liquid (~> 4.0.4)
+  minima (~> 2.5)
+  rubocop-github
+  tzinfo (~> 1.2)
+  tzinfo-data
+  w3c_validators
+  wdm (~> 0.1.1)
+  webrick (~> 1.7)
+
+BUNDLED WITH
+   2.6.2
--- a/docs/README.md
+++ b/docs/README.md
@@ -0,0 +1,36 @@
+## Jekyll
+
+The LaGriT site uses Jekyll which is a simple, blog-aware, static site generator perfect for personal, project, or organization sites. Think of it like a file-based CMS, without all the complexity. Jekyll takes your content, renders Markdown and Liquid templates, and spits out a complete, static website ready to be served. Jekyll is the engine behind GitHub Pages, which you can use to host sites from your GitHub repositories.
+
+### Installation
+
+One of the benifits to Jekyll is that you can view your site edits locally prior to commiting them and making them live. You can find detailed information for installation at [https://jekyllrb.com/docs/installation/](https://jekyllrb.com/docs/installation/).
+
+### Development
+
+This folder contains a _config.yml file which contains settings that control your site. It is not usually updated unless there is a major theme update. Any changes to this file will require you to restart the server process (see below).
+
+This folder also contains a Gemfile. This is where you manage which Jekyll version is used to run. When you want to use a different version, change it in your Gemfile, save the file and run `bundle install`. Then restart the server. This will help ensure the proper Jekyll version is running.
+
+There is a Gemfile.lock. This file should not be modified unless you really know what you are doing. It contains all of the versions for the necessary dependencies.
+
+#### Starting the Jekyll server
+
+To start your server you should ensure that you are in the /docs folder and then run
+
+```
+bundle exec jekyll serve
+```
+
+This will start the server and make it viewable on your localhost. The address will be given on the terminal. For example:
+
+```
+Server address: http://127.0.0.1:4000
+Server running... press ctrl-c to stop.
+```
+
+Prior to pushing updates to Github, you should preform a build.
+
+```
+bundle exec jekyll build
+```
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -0,0 +1,26 @@
+exclude: [".rvmrc", ".rbenv-version", "ReadMe.md", "Rakefile", "changelog.md", "License.md"]
+highlighter: rouge
+
+title : LaGriT
+description: LaGriT is a library providing mesh generation and optimization for a variety of polyhedra and dimensions.
+
+author :
+  name : Terry Miller, Carl Gable, Nathaniel Knapp, Daniel Livingston, Erica Hinrichs
+  email : tamiller@lanl.gov
+  github : lanl
+
+theme: jekyll-theme-slate
+
+production_url : https://lanl.github.io/LaGriT
+base_url : https://lanl.github.io/LaGriT
+
+kramdown:
+   input: GFM
+   hard_wrap: false
+
+plugins:
+  - jekyll-sitemap
+
+tipue_search:
+      include:
+              pages: true
--- a/docs/_layouts/default.html
+++ b/docs/_layouts/default.html
@@ -0,0 +1,164 @@
+<html lang="en-gb" dir="ltr">
+
+<head>
+    <title>{{ page.title | default: site.title }}</title>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <meta name="description" content="{{ site.title | default: site.github.repository_name }} : {{ site.description | default: site.github.project_tagline }}">
+    <link href="https://fonts.googleapis.com/css?family=Do+Hyeon|Fira+Sans" rel="stylesheet">
+    <link rel="preload" href="https://getuikit.com/fonts/ProximaNova-Reg-webfont.woff2" as="font" type="font/woff2" crossorigin="">
+    <link rel="preload" href="https://getuikit.com/fonts/ProximaNova-Light-webfont.woff2" as="font" type="font/woff2" crossorigin="">
+    <link rel="stylesheet" href="{{ "/assets/css/uikit_theme.css" | relative_url }}">
+    <link rel="icon" type="image/x-icon" href="https://www.lanl.gov/favicon.ico">
+    <link rel="stylesheet" type="text/css" href="{{ "/assets/css/footer.css" | relative_url }}">
+
+    <!-- load stylesheets -->
+    <script type="text/javascript" async="" src="https://www.google-analytics.com/analytics.js"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" defer=""></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/he/1.2.0/he.min.js" defer=""></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/marked/0.6.2/marked.min.js" defer=""></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/vue/2.6.10/vue.min.js" defer=""></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/vue-router/3.0.2/vue-router.min.js" defer=""></script>
+    <script src="https://getuikit.com/assets/uikit/dist/js/uikit.min.js?1180" defer=""></script>
+    <script src="https://getuikit.com/assets/uikit/dist/js/uikit-icons.min.js?1180" defer=""></script>
+    <script src="https://getuikit.com/assets/highlightjs/highlight.min.js" defer=""></script>
+    <script src="https://getuikit.com/app/main.min.js?1180" defer=""></script>
+    <script src="https://www.googletagmanager.com/gtag/js?id=UA-42150424-1" async=""></script>
+
+    <!-- tipuesearch files -->
+    <link rel="stylesheet" href="{{ "/assets/tipuesearch/css/normalize.css" | relative_url }}">
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
+    <script src="{{ "/assets/tipuesearch/tipuesearch_content.js" | relative_url }}"></script>
+    <link rel="stylesheet" href="{{ "/assets/tipuesearch/css/tipuesearch.css" | relative_url }}">
+    <script src="{{ "/assets/tipuesearch/tipuesearch_set.js" | relative_url }}"></script>
+    <script src="{{ "/assets/tipuesearch/tipuesearch.min.js" | relative_url }}"></script>
+
+    <!-- Finally, load global style to overwrite template, tipuesearch, etc. -->
+    <!--<link rel="stylesheet" href="{{ "/assets/globalstyle.css" | relative_url }}">-->
+</head>
+
+<body>
+    <div>
+        <!-- Header -->
+        <div uk-sticky="media: 960" class="uk-navbar-container tm-navbar-container uk-sticky uk-sticky-fixed" style="position: fixed; top: 0px; width: 100%; color: #212328;">
+            <div class="uk-container uk-container-expand">
+                <nav class="uk-navbar">
+                    <div class="uk-navbar-left">
+                        <a href="{{ "/" | relative_url }}" class="uk-navbar-item uk-logo" style="font-family: 'Do Hyeon', sans-serif; color: white;">
+                            <img uk-img src="{{ "/assets/img/logo.png" | relative_url }}" width="50" class="uk-margin-small-right" alt="LANL logo">
+                            LaGriT
+                        </a>
+                    </div>
+                    <div class="uk-navbar-right">
+                        <ul class="uk-navbar-nav uk-visible@m">
+                            <li><a href="{{ "/pages/commands" | relative_url }}">Commands</a></li>
+                            <li><a href="{{ "/pages/tutorial/index" | relative_url }}">Tutorials</a></li>
+                            <li><a href="{{ "/pages/release" | relative_url }}">Release Notes</a></li>
+                            <li><a href="{{ "/pages/publications" | relative_url }}">Publications</a></li>
+                            <li><a href="http://github.com/lanl/LaGriT"><span uk-icon="github"></span></a></li>
+
+                            <!-- Begin search bar -->
+                            <div class="nav-overlay uk-navbar-right">
+                                <a class="uk-navbar-toggle" uk-search-icon uk-toggle="target: .nav-overlay; animation: uk-animation-fade" href="#"></a>
+                            </div>
+
+                            <div class="nav-overlay uk-navbar-left uk-flex-1" hidden>
+                                <div class="uk-navbar-item uk-width-expand">
+                                    <form class="uk-search uk-search-navbar uk-width-1-1" action="https://lanl.github.io/LaGriT/search/">
+                                        <input class="uk-search-input" name="q" type="search" id="tipue_search_input" placeholder="Search..." autofocus>
+                                    </form>
+                                </div>
+                                <a class="uk-navbar-toggle" uk-close uk-toggle="target: .nav-overlay; animation: uk-animation-fade" href="#"></a>
+                            </div>
+
+                            <script>
+                                $(document).ready(function() {
+                                  $('#tipue_search_input').tipuesearch({
+                                        'show': 10,
+                                        'newWindow'  : true,
+                                        'showURL' : true,
+                                        'showTitleCount' : true,
+                                        'descriptiveWords' : 20,
+                                        'highlightTerms' : true,
+                                        'mode': 'static',
+                                  });
+                                });
+                            </script>
+                            <!-- End search bar -->
+
+                        </ul>
+                        
+                        <a uk-navbar-toggle-icon="" href="#offcanvas" uk-toggle="" class="uk-navbar-toggle uk-hidden@m uk-icon uk-navbar-toggle-icon">
+                            <svg width="20" height="20" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg" data-svg="navbar-toggle-icon">
+                                <rect y="9" width="20" height="2"></rect>
+                                <rect y="3" width="20" height="2"></rect>
+                                <rect y="15" width="20" height="2"></rect>
+                            </svg>
+                        </a>
+                    </div>
+                </nav>
+            </div>
+        </div>
+        <div class="uk-sticky-placeholder" style="height: 80px; margin: 0px;"></div>
+        <!-- End Header -->
+
+        <!-- Main Body text -->
+        <div class="tm-main uk-section uk-section-default">
+            <div class="uk-container uk-container-small uk-position-relative">
+
+                {{ content }}
+
+            </div>
+        </div>
+
+        <!-- Begin footer -->
+        <footer class="footer-distributed">
+            <div class="footer-right">
+              <div><img src="{{ "/assets/img/lanl_logo_white.png" | relative_url }}" height="80"></div>
+            </div>
+
+            <div class="footer-left lg-background-color">
+                <p class="footer-links" style="font-family: 'Fira Sans', sans-serif; color: white;">
+                    <a href="{{ "/" | relative_url }}">Home</a>
+                    ·
+                    <a href="{{ "/pylagrit/original/index.html" | relative_url }}">PyLaGriT</a>
+                    ·
+                    <a href="https://int.lanl.gov/org/ddste/aldcels/ees/index.shtml">EES-16</a>
+                    ·
+                    <a href="{{ "/pages/licensing.html" | relative_url }}">License</a>
+                    ·
+                    <a href="https://lagrit.lanl.gov/">Contact</a>
+                </p>
+
+                <p>&copy; 2019 Los Alamos National Laboratory</p>
+                <p>EES-16 | Computational Earth Science</p>
+                <p>LA-CC-15-069</p>
+            </div>
+        </footer>
+
+        <!-- Begin Navigation Bar -->
+        <div id="offcanvas" uk-offcanvas="mode: push; overlay: true" class="uk-offcanvas">
+            <div class="uk-offcanvas-bar">
+                <div class="uk-panel">
+                    <ul class="uk-nav uk-nav-default tm-nav">
+                        <form class="uk-search uk-search-default" action="https://lanl.github.io/LaGriT/search/">
+                            <a href="" uk-search-icon></a>
+                            <input class="uk-search-input" type="search" placeholder="" name="q" id="tipue_search_input_mobile">
+                        </form>
+                        <li class="uk-nav-header">General</li>
+                        <li><a href="{{ "/" | relative_url }}">Home</a></li>
+                        <li><a href="{{ "/pages/commands" | relative_url }}">Commands</a></li>
+                        <li><a href="{{ "/pages/release" | relative_url }}">Release Notes</a></li>
+                        <li><a href="{{ "/pages/publications" | relative_url }}">Publications</a></li>
+                        <li><a href="http://github.com/lanl/LaGriT">GitHub</a></li>
+                    </ul>
+                </div>
+            </div>
+        </div>
+        <!-- End Navigation Bar -->
+
+    </div>
+
+</body>
+
+</html>
--- a/docs/_site/Gemfile
+++ b/docs/_site/Gemfile
@@ -0,0 +1,37 @@
+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "minima", "~> 2.5"
+
+gem "github-pages", "~> 232", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "html-proofer"
+  gem "jekyll-sitemap"
+  gem "rubocop-github"
+  gem "jekyll-seo-tag"
+  gem "w3c_validators"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", "~> 1.2"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+gem "webrick", "~> 1.7"
+gem "liquid", "~> 4.0.4"
+
+# kramdown v2 ships without the gfm parser by default. If you're using
+# kramdown v1, comment out this line.
+gem "kramdown-parser-gfm"
--- a/docs/_site/Gemfile.lock
+++ b/docs/_site/Gemfile.lock
@@ -0,0 +1,395 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    Ascii85 (2.0.1)
+    activesupport (8.0.1)
+      base64
+      benchmark (>= 0.3)
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.3.1)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      logger (>= 1.4.2)
+      minitest (>= 5.1)
+      securerandom (>= 0.3)
+      tzinfo (~> 2.0, >= 2.0.5)
+      uri (>= 0.13.1)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    afm (0.2.2)
+    ast (2.4.2)
+    async (2.21.1)
+      console (~> 1.29)
+      fiber-annotation
+      io-event (~> 1.6, >= 1.6.5)
+    base64 (0.2.0)
+    benchmark (0.4.0)
+    bigdecimal (3.1.9)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
+    colorator (1.1.0)
+    commonmarker (0.23.11)
+    concurrent-ruby (1.3.4)
+    connection_pool (2.5.0)
+    console (1.29.2)
+      fiber-annotation
+      fiber-local (~> 1.1)
+      json
+    csv (3.3.2)
+    dnsruby (1.72.3)
+      base64 (~> 0.2.0)
+      simpleidn (~> 0.2.1)
+    drb (2.2.1)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
+    eventmachine (1.2.7)
+    execjs (2.10.0)
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
+    ffi (1.17.1-aarch64-linux-gnu)
+    ffi (1.17.1-aarch64-linux-musl)
+    ffi (1.17.1-arm-linux-gnu)
+    ffi (1.17.1-arm-linux-musl)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-darwin)
+    ffi (1.17.1-x86_64-linux-gnu)
+    ffi (1.17.1-x86_64-linux-musl)
+    fiber-annotation (0.2.0)
+    fiber-local (1.1.0)
+      fiber-storage
+    fiber-storage (1.0.0)
+    forwardable-extended (2.6.0)
+    gemoji (4.1.0)
+    github-pages (232)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.10.0)
+      jekyll-avatar (= 0.8.0)
+      jekyll-coffeescript (= 1.2.2)
+      jekyll-commonmark-ghpages (= 0.5.1)
+      jekyll-default-layout (= 0.1.5)
+      jekyll-feed (= 0.17.0)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.16.1)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
+      jemoji (= 0.13.0)
+      kramdown (= 2.4.0)
+      kramdown-parser-gfm (= 1.1.0)
+      liquid (= 4.0.4)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.16.2, < 2.0)
+      rouge (= 3.30.0)
+      terminal-table (~> 1.4)
+      webrick (~> 1.8)
+    github-pages-health-check (1.18.2)
+      addressable (~> 2.3)
+      dnsruby (~> 1.60)
+      octokit (>= 4, < 8)
+      public_suffix (>= 3.0, < 6.0)
+      typhoeus (~> 1.3)
+    hashery (2.1.2)
+    html-pipeline (2.14.3)
+      activesupport (>= 2)
+      nokogiri (>= 1.4)
+    html-proofer (5.0.9)
+      addressable (~> 2.3)
+      async (~> 2.1)
+      nokogiri (~> 1.13)
+      pdf-reader (~> 2.11)
+      rainbow (~> 3.0)
+      typhoeus (~> 1.3)
+      yell (~> 2.0)
+      zeitwerk (~> 2.5)
+    http_parser.rb (0.8.0)
+    i18n (1.14.6)
+      concurrent-ruby (~> 1.0)
+    io-event (1.7.5)
+    jekyll (3.10.0)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      csv (~> 3.0)
+      em-websocket (~> 0.5)
+      i18n (>= 0.7, < 2)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 2.0)
+      kramdown (>= 1.17, < 3)
+      liquid (~> 4.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (>= 1.7, < 4)
+      safe_yaml (~> 1.0)
+      webrick (>= 1.0)
+    jekyll-avatar (0.8.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-coffeescript (1.2.2)
+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.12)
+    jekyll-commonmark (1.4.0)
+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.5.1)
+      commonmarker (>= 0.23.7, < 1.1.0)
+      jekyll (>= 3.9, < 4.0)
+      jekyll-commonmark (~> 1.4.0)
+      rouge (>= 2.0, < 5.0)
+    jekyll-default-layout (0.1.5)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-feed (0.17.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-gist (1.5.0)
+      octokit (~> 4.2)
+    jekyll-github-metadata (2.16.1)
+      jekyll (>= 3.4, < 5.0)
+      octokit (>= 4, < 7, != 4.4.0)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-mentions (1.6.0)
+      html-pipeline (~> 2.3)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-optional-front-matter (0.3.2)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-paginate (1.1.0)
+    jekyll-readme-index (0.3.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-remote-theme (0.4.3)
+      addressable (~> 2.0)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+      rubyzip (>= 1.3.0, < 3.0)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-swiss (1.0.0)
+    jekyll-theme-architect (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-cayman (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-dinky (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-hacker (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-leap-day (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-merlot (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-midnight (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-minimal (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-modernist (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-primer (0.6.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-github-metadata (~> 2.9)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-slate (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-tactile (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-time-machine (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-titles-from-headings (0.5.3)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    jemoji (0.13.0)
+      gemoji (>= 3, < 5)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0, < 5.0)
+    json (2.9.1)
+    kramdown (2.4.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    language_server-protocol (3.17.0.3)
+    liquid (4.0.4)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.4)
+    mercenary (0.3.6)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    minitest (5.25.4)
+    net-http (0.6.0)
+      uri
+    nokogiri (1.18.1-aarch64-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-aarch64-linux-musl)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm-linux-musl)
+      racc (~> 1.4)
+    nokogiri (1.18.1-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.18.1-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.18.1-x86_64-linux-gnu)
+      racc (~> 1.4)
+    nokogiri (1.18.1-x86_64-linux-musl)
+      racc (~> 1.4)
+    octokit (4.25.1)
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
+    parallel (1.26.3)
+    parser (3.3.6.0)
+      ast (~> 2.4.1)
+      racc
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    pdf-reader (2.13.0)
+      Ascii85 (>= 1.0, < 3.0, != 2.0.0)
+      afm (~> 0.2.1)
+      hashery (~> 2.0)
+      ruby-rc4
+      ttfunk
+    public_suffix (5.1.1)
+    racc (1.8.1)
+    rack (3.1.8)
+    rainbow (3.1.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    regexp_parser (2.10.0)
+    rexml (3.4.0)
+    rouge (3.30.0)
+    rubocop (1.69.2)
+      json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
+      parallel (~> 1.10)
+      parser (>= 3.3.0.2)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.37.0)
+      parser (>= 3.3.1.0)
+    rubocop-github (0.20.0)
+      rubocop (>= 1.37)
+      rubocop-performance (>= 1.15)
+      rubocop-rails (>= 2.17)
+    rubocop-performance (1.23.1)
+      rubocop (>= 1.48.1, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
+    rubocop-rails (2.28.0)
+      activesupport (>= 4.2.0)
+      rack (>= 1.1)
+      rubocop (>= 1.52.0, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
+    ruby-progressbar (1.13.0)
+    ruby-rc4 (0.1.5)
+    rubyzip (2.4.1)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sawyer (0.9.2)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    securerandom (0.4.1)
+    simpleidn (0.2.3)
+    terminal-table (1.6.0)
+    ttfunk (1.8.0)
+      bigdecimal (~> 3.1)
+    typhoeus (1.4.1)
+      ethon (>= 0.9.0)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (3.1.3)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
+    uri (1.0.2)
+    w3c_validators (1.3.7)
+      json (>= 1.8)
+      nokogiri (~> 1.6)
+      rexml (~> 3.2)
+    webrick (1.9.1)
+    yell (2.2.2)
+    zeitwerk (2.7.1)
+
+PLATFORMS
+  aarch64-linux-gnu
+  aarch64-linux-musl
+  arm-linux-gnu
+  arm-linux-musl
+  arm64-darwin
+  x86_64-darwin
+  x86_64-linux-gnu
+  x86_64-linux-musl
+
+DEPENDENCIES
+  github-pages (~> 232)
+  html-proofer
+  jekyll-seo-tag
+  jekyll-sitemap
+  kramdown-parser-gfm
+  liquid (~> 4.0.4)
+  minima (~> 2.5)
+  rubocop-github
+  tzinfo (~> 1.2)
+  tzinfo-data
+  w3c_validators
+  wdm (~> 0.1.1)
+  webrick (~> 1.7)
+
+BUNDLED WITH
+   2.6.2
--- a/docs/_site/README.md
+++ b/docs/_site/README.md
@@ -0,0 +1,36 @@
+## Jekyll
+
+The LaGriT site uses Jekyll which is a simple, blog-aware, static site generator perfect for personal, project, or organization sites. Think of it like a file-based CMS, without all the complexity. Jekyll takes your content, renders Markdown and Liquid templates, and spits out a complete, static website ready to be served. Jekyll is the engine behind GitHub Pages, which you can use to host sites from your GitHub repositories.
+
+### Installation
+
+One of the benifits to Jekyll is that you can view your site edits locally prior to commiting them and making them live. You can find detailed information for installation at [https://jekyllrb.com/docs/installation/](https://jekyllrb.com/docs/installation/).
+
+### Development
+
+This folder contains a _config.yml file which contains settings that control your site. It is not usually updated unless there is a major theme update. Any changes to this file will require you to restart the server process (see below).
+
+This folder also contains a Gemfile. This is where you manage which Jekyll version is used to run. When you want to use a different version, change it in your Gemfile, save the file and run `bundle install`. Then restart the server. This will help ensure the proper Jekyll version is running.
+
+There is a Gemfile.lock. This file should not be modified unless you really know what you are doing. It contains all of the versions for the necessary dependencies.
+
+#### Starting the Jekyll server
+
+To start your server you should ensure that you are in the /docs folder and then run
+
+```
+bundle exec jekyll serve
+```
+
+This will start the server and make it viewable on your localhost. The address will be given on the terminal. For example:
+
+```
+Server address: http://127.0.0.1:4000
+Server running... press ctrl-c to stop.
+```
+
+Prior to pushing updates to Github, you should preform a build.
+
+```
+bundle exec jekyll build
+```
--- a/docs/_site/assets/css/bootstrap.min.css
+++ b/docs/_site/assets/css/bootstrap.min.css
--- a/docs/_site/assets/css/datepicker.css
+++ b/docs/_site/assets/css/datepicker.css
@@ -0,0 +1,207 @@
+.qs-datepicker {
+  color: black;
+  position: absolute;
+  width: 250px;
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-direction: column;
+      flex-direction: column;
+  font-family: sans-serif;
+  font-size: 14px;
+  z-index: 9001;
+  -webkit-user-select: none;
+     -moz-user-select: none;
+      -ms-user-select: none;
+          user-select: none;
+  border: 1px solid gray;
+  border-radius: 4.22275px;
+  overflow: hidden;
+  background: white;
+  box-shadow: 0 20px 20px -15px rgba(0, 0, 0, 0.3);
+}
+.qs-datepicker * {
+  box-sizing: border-box;
+}
+.qs-datepicker.qs-hidden {
+  display: none;
+}
+.qs-datepicker .qs-overlay {
+  position: absolute;
+  top: 0;
+  left: 0;
+  background: rgba(0, 0, 0, 0.75);
+  color: white;
+  width: 100%;
+  height: 100%;
+  padding: .5em;
+  z-index: 1;
+  opacity: 1;
+  transition: opacity 0.3s;
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-direction: column;
+      flex-direction: column;
+  -ms-flex-align: center;
+      align-items: center;
+}
+.qs-datepicker .qs-overlay.qs-hidden {
+  opacity: 0;
+  z-index: -1;
+}
+.qs-datepicker .qs-overlay .qs-close {
+  -ms-flex-item-align: end;
+      align-self: flex-end;
+  display: inline-table;
+  padding: .5em;
+  line-height: .77;
+  cursor: pointer;
+  position: absolute;
+}
+.qs-datepicker .qs-overlay .qs-overlay-year {
+  display: block;
+  border: none;
+  background: transparent;
+  border-bottom: 1px solid white;
+  border-radius: 0;
+  color: white;
+  font-size: 14px;
+  padding: .25em 0;
+  margin: auto 0 .5em;
+  width: calc(100% - 1em);
+}
+.qs-datepicker .qs-overlay .qs-overlay-year::-webkit-inner-spin-button {
+  -webkit-appearance: none;
+}
+.qs-datepicker .qs-overlay .qs-submit {
+  border: 1px solid white;
+  border-radius: 4.22275px;
+  padding: .5em;
+  margin: 0 auto auto;
+  cursor: pointer;
+  background: rgba(128, 128, 128, 0.4);
+}
+.qs-datepicker .qs-overlay .qs-submit.qs-disabled {
+  color: gray;
+  border-color: gray;
+  cursor: not-allowed;
+}
+.qs-datepicker .qs-controls {
+  width: 100%;
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-pack: justify;
+      justify-content: space-between;
+  -ms-flex-align: center;
+      align-items: center;
+  -ms-flex-positive: 1;
+      flex-grow: 1;
+  -ms-flex-negative: 0;
+      flex-shrink: 0;
+  background: lightgray;
+  filter: blur(0px);
+  transition: filter 0.3s;
+}
+.qs-datepicker .qs-controls.qs-blur {
+  filter: blur(5px);
+}
+.qs-datepicker .qs-arrow {
+  height: 25px;
+  width: 25px;
+  position: relative;
+  cursor: pointer;
+  border-radius: 5px;
+  transition: background .15s;
+}
+.qs-datepicker .qs-arrow:hover {
+  background: rgba(0, 0, 0, 0.1);
+}
+.qs-datepicker .qs-arrow:hover.qs-left:after {
+  border-right-color: black;
+}
+.qs-datepicker .qs-arrow:hover.qs-right:after {
+  border-left-color: black;
+}
+.qs-datepicker .qs-arrow:after {
+  content: '';
+  border: 6.25px solid transparent;
+  position: absolute;
+  top: 50%;
+  transition: border .2s;
+}
+.qs-datepicker .qs-arrow.qs-left:after {
+  border-right-color: gray;
+  right: 50%;
+  transform: translate(25%, -50%);
+}
+.qs-datepicker .qs-arrow.qs-right:after {
+  border-left-color: gray;
+  left: 50%;
+  transform: translate(-25%, -50%);
+}
+.qs-datepicker .qs-month-year {
+  font-weight: bold;
+  transition: border .2s;
+  border-bottom: 1px solid transparent;
+  cursor: pointer;
+}
+.qs-datepicker .qs-month-year:hover {
+  border-bottom: 1px solid gray;
+}
+.qs-datepicker .qs-month-year:focus,
+.qs-datepicker .qs-month-year:active:focus {
+  outline: none;
+}
+.qs-datepicker .qs-month {
+  padding-right: .5ex;
+}
+.qs-datepicker .qs-year {
+  padding-left: .5ex;
+}
+.qs-datepicker .qs-squares {
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-wrap: wrap;
+      flex-wrap: wrap;
+  padding: 5px;
+  filter: blur(0px);
+  transition: filter 0.3s;
+}
+.qs-datepicker .qs-squares.qs-blur {
+  filter: blur(5px);
+}
+.qs-datepicker .qs-square {
+  width: 14.28571429%;
+  height: 25px;
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-align: center;
+      align-items: center;
+  -ms-flex-pack: center;
+      justify-content: center;
+  cursor: pointer;
+  transition: background .1s;
+  border-radius: 4.22275px;
+}
+.qs-datepicker .qs-square.qs-current {
+  font-weight: bold;
+}
+.qs-datepicker .qs-square.qs-active {
+  background: lightblue;
+}
+.qs-datepicker .qs-square.qs-disabled span {
+  opacity: .2;
+}
+.qs-datepicker .qs-square.qs-empty {
+  cursor: default;
+}
+.qs-datepicker .qs-square.qs-disabled {
+  cursor: not-allowed;
+}
+.qs-datepicker .qs-square.qs-day {
+  cursor: default;
+  font-weight: bold;
+  color: gray;
+}
+.qs-datepicker .qs-square:not(.qs-empty):not(.qs-disabled):not(.qs-day):hover {
+  background: orange;
+}
--- a/docs/_site/assets/css/footer.css
+++ b/docs/_site/assets/css/footer.css
@@ -0,0 +1,88 @@
+/*
+
+Begin footer CSS
+
+*/
+
+li {
+  margin-bottom: 5px;
+}
+
+.lg-output {
+  font-size: 0.9em;
+  background-color: rgb(40,40,40);
+  color: rgba(255,255,255);
+}
+
+.footer-distributed{
+  background-color: #1F252A;
+  box-shadow: 0 1px 1px 0 rgba(0, 0, 0, 0.12);
+  box-sizing: border-box;
+  width: 100%;
+  text-align: left;
+  font: normal 16px sans-serif;
+
+  padding: 45px 50px;
+  margin-top: 80px;
+}
+
+.footer-distributed .footer-left p{
+  color:  #8f9296;
+  font-size: 12px;
+  margin: 3px;
+}
+
+/* Footer links */
+
+.footer-distributed p.footer-links{
+  font-size:14px;
+  font-weight: bold;
+  color:  #ffffff;
+  margin: 0 0 10px;
+  padding: 0;
+}
+
+.footer-distributed p.footer-links a{
+  display:inline-block;
+  line-height: 1.8;
+  text-decoration: none;
+  color:  inherit;
+}
+
+.footer-distributed .footer-right{
+  float: right;
+  margin-top: 6px;
+  max-width: 180px;
+}
+
+.footer-distributed .footer-right a{
+  display: inline-block;
+  width: 35px;
+  height: 35px;
+  background-color:  #33383b;
+  border-radius: 2px;
+
+  font-size: 20px;
+  color: #ffffff;
+  text-align: center;
+  line-height: 35px;
+
+  margin-left: 3px;
+}
+
+@media (max-width: 600px) {
+
+  .footer-distributed .footer-left,
+  .footer-distributed .footer-right{
+    text-align: center;
+  }
+
+  .footer-distributed .footer-right{
+    float: none;
+    margin: 0 auto 20px;
+  }
+
+  .footer-distributed .footer-left p.footer-links{
+    line-height: 1.8;
+  }
+}
--- a/docs/_site/assets/css/index_page_style.css
+++ b/docs/_site/assets/css/index_page_style.css
@@ -0,0 +1,152 @@
+.extended-content-container {
+    width: 100vw;
+    position: relative;
+    left: 50%;
+    right: 50%;
+    top: -70px;
+    margin-left: -50vw;
+    margin-right: -50vw;
+    background-color:#68A5F3;
+    padding-bottom: 15px;
+    padding-top: 15px;
+}
+
+@media only screen and (max-width: 960px) {
+  .extended-content-container {
+    top: -70px;
+  }
+}
+    
+.extended-content {
+    width: 100%;
+    background-color:#68A5F3;
+    text-align:center;
+    color: white;
+    font-size: 25pt;
+}
+
+/*
+    Button Styles
+    Inspired by 'CSS Button Animations' by Alex Loomer
+    
+    https://codepen.io/atloomer/pen/JEaRWX
+*/
+
+.button {
+    display: inline-flex;
+    height: 40px;
+    width: 165px;
+    /*border: 2px solid #BFC0C0;*/
+    margin: 20px 20px 20px 20px;
+    color: #BFC0C0;
+    text-transform: uppercase;
+    text-decoration: none;
+    font-size: 10pt;
+    letter-spacing: 1.5px;
+    align-items: center;
+    justify-content: center;
+    overflow: hidden;
+}
+    
+/* Third Button */
+
+#button-3 {
+    position: relative;
+    overflow: hidden;
+    cursor: pointer;
+    border: 2px solid white;
+    background: #3570B3;
+}
+
+#button-3 a {
+  position: relative;
+  transition: all .45s ease-Out;
+  color: white;
+  text-decoration: none;
+}
+
+#circle {
+    width: 0%;
+    height: 0%;
+    opacity: 0;
+    line-height: 40px;
+    border-radius: 50%;
+    background: #F0D451;
+    position: absolute;
+    transition: all .5s ease-Out;
+    top: 20px;
+    left: 70px;
+}
+
+#button-3:hover #circle {
+    width: 200%;
+    height: 500%;
+    opacity: 1;
+    top: -70px;
+    left: -70px;
+}
+
+#button-3:hover a {
+    color: #2D3142;
+    text-decoration: none;
+}
+
+/* Fourth Button */
+
+#button-4 {
+    position: relative;
+    overflow: hidden;
+    cursor: pointer;
+}
+
+#button-4 a {
+    position: relative;
+    transition: all .45s ease-Out;
+    color: white;
+}
+
+#underline {
+    width: 100%;
+    height: 2.5px;
+    margin-top: 15px;
+    align-self: flex-end;
+    left: -200px;
+    background: #F0D451;
+    position: absolute;
+    transition: all .3s ease-Out;
+    bottom: 0;
+}
+
+#button-4:hover #underline {
+    left: 0;
+}
+
+#button-4:hover a {
+    text-decoration: none;
+}
+
+.accordion-item input {
+  display: none;
+}
+
+.accordion-header {
+  display: block;
+  cursor: pointer;
+  padding: 10px;
+  #background-color: #f1f1f1;
+  border: 1px solid #ddd;
+  font-weight: bold;
+}
+
+.accordion-content {
+  max-height: 0;
+  overflow: hidden;
+  transition: max-height 0.3s ease;
+  padding: 0 10px;
+  background-color: #fff;
+  border-top: 1px solid #ddd;
+}
+
+.accordion-item input:checked ~ .accordion-content {
+  max-height: 800px; /* Set a reasonable max-height */
+}
--- a/docs/_site/assets/css/style.css
+++ b/docs/_site/assets/css/style.css
@@ -0,0 +1,2 @@
+/*@import "jekyll-theme-slate";*/
+pre, code { display: inline-block; width: 100%; font: 14px 'Source Code Pro', monospace; color: #111; border: 0; background-color: #f9f9f9; resize: none; outline: 0; }
--- a/docs/_site/assets/css/templatemo-style.css
+++ b/docs/_site/assets/css/templatemo-style.css
@@ -0,0 +1,652 @@
+/* 
+
+Journey Template 
+http://www.templatemo.com/tm-511-journey
+
+Primary color (light blue)  : #69c6ba
+Highlight color (pink)		: #c66995
+--------------------------------------
+
+*/
+
+.tm-page-wrap { 
+    max-width: 1400px;
+    box-shadow: 0 0 3px rgba(0, 0, 0, 0.15);
+    background: white;
+}
+
+.tm-container-outer {
+    max-width: 1400px;
+    margin: 0 auto;    
+}
+
+.tm-content-box { box-shadow: 0 0 3px rgba(0, 0, 0, 0.15); }
+.tm-text-gray { color: #787676; }
+
+.tm-text-highlight {
+    color: #c66995;
+    font-weight: 600;
+}
+
+.tm-bg-primary { background: #69c6ba; }
+.tm-bg-highlight { background: #c66995; }
+
+.btn-primary {
+    background: #69c6ba;
+    border: none;
+    border-radius: 0;
+    outline: none;
+}
+
+.btn-primary:hover { background: #c66995; }
+.tm-top-bar .navbar-expand-lg .navbar-nav .nav-link { padding: 50px 35px; }
+
+.tm-top-bar {
+    position: fixed;
+    top: 0;
+    left: 0;
+    width: 100%;
+    padding: 0;
+    z-index: 10000;
+    transition: all 0.2s ease-in-out;
+    height: 119px;
+
+    /* Navigation bar BG color */
+    background: #212329;
+}
+
+.tm-top-bar.active {
+    height: 60px;
+    box-shadow: 0 1px 5px rgba(0, 0, 0, 0.25);
+}
+
+.tm-top-bar.active .navbar-expand-lg .navbar-nav .nav-link { padding: 20px 35px; }
+.tm-top-bar.active .navbar-brand { font-size: 1.4rem; }
+
+.tm-top-bar .navbar-brand img {
+    width: 60px;
+    height: auto;
+}
+
+.tm-top-bar.active .navbar-brand img { width: 40px; }
+.tm-top-bar-bg { height: 119px; }
+.tm-top-bar a { color: rgb(255,255,255); }
+
+.navbar-brand {
+	font-size: 2.2rem;    
+    /*text-transform: uppercase;    */
+}
+
+.navbar {
+    font-weight: 700;
+    width: 100%;
+    padding-top: 0;
+    padding-bottom: 0;
+}
+ 
+/* TODO : change color here! */
+.nav-link.active, .nav-link:hover {	color: rgb(102,219,249);	}
+
+.navbar-toggler-icon {
+    background-image: url("data:image/svg+xml;charset=utf8,%3Csvg viewBox='0 0 32 32' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath stroke='rgb(255, 255, 255)' stroke-width='2' stroke-linecap='round' stroke-miterlimit='10' d='M4 8h24M4 16h24M4 24h24'/%3E%3C/svg%3E");
+}
+
+.navbar-toggler { 
+    border-color: rgb(255,255,255);/*rgb(104, 199, 187);*/
+    border-radius: 0;
+    cursor: pointer;
+}
+
+.tm-banner-title {
+    font-size: 2rem;
+    margin-bottom: 10px;
+}
+.tm-banner-subtitle {
+    font-size: 1.5rem;
+    margin-top: 10px;
+    letter-spacing: 1px;
+}
+
+.tm-banner-header { color: white; }
+.tm-banner-overlay {
+    z-index: 1;
+    height: 100%;
+    width: 100%;
+    position: absolute;
+    overflow: auto;
+    top: 0px;
+    left: 0px;
+    background: rgba(0, 0, 0, 0.7);
+}
+.tm-banner-bg {
+    background: url(../img/banner.jpg) center top no-repeat;    
+    min-height: 720px;
+    position: relative;
+}
+.tm-banner-row { 
+    position: relative;
+    z-index: 100;
+    justify-content: center;
+    padding-top: 100px;
+}
+.tm-banner-row-header { text-align: center; }
+.tm-down-arrow-link { 
+    color: white;
+    background-color: #69c6ba;
+    border-radius: 50%;
+    padding: 10px 15px;
+    margin-top: 0px;
+    display: inline-block;
+}
+
+.tm-down-arrow-link:hover,
+.tm-down-arrow-link:focus {
+    color: white;
+    background-color: #c66995;
+}
+
+/* Search form */
+select.tm-select.form-control:not([size]):not([multiple]) { height: 45px; }
+.form-control {
+    font-size: 0.8rem;
+    padding: .75rem;
+}
+label { font-weight: 700; }
+.tm-search-form {
+    background-color: #f5f6f6;
+    padding: 25px 25px 15px;
+    width: 100%;
+    max-width: 830px;
+    margin-left: 15px;
+    margin-right: 15px;
+}
+
+.tm-form-group { float: left; }
+.tm-form-group-pad { padding: 0 8px; }
+.tm-form-group-1 { width: 50%; }
+.tm-form-group-2 { width: 50%; }
+.tm-form-group-3 { width: 25%; }
+.form-control { border-radius: 0; }
+
+.tm-btn {
+    cursor: pointer;
+    display: inline-block;
+    font-size: 0.85rem;
+    font-weight: 400;  
+    padding: 12px 20px;
+}
+
+.tm-btn-white { background: white; }
+.tm-btn-white-primary { color: #69c6ba; }
+.tm-btn-white-highlight { color: #c66995; }
+
+.tm-btn-white-primary:hover,
+.tm-btn-white-primary:focus,
+.tm-btn-white-primary:active {
+    background: #c66995;
+    color: white;
+}
+
+.tm-btn-white-highlight:hover,
+.tm-btn-white-highlight:focus,
+.tm-btn-white-highlight:active {
+    background: #69c6ba;
+    color: white;
+}
+
+.tm-btn-search { width: 100%; }
+
+.tm-btn-search:hover,
+.tm-btn-search:active,
+.tm-btn-search:focus {
+    background: #c66995;
+}
+
+.tm-bg-gray { background-color: #efefef; }
+.tm-about-text-wrap { max-width: 830px; }
+
+.tm-right {
+    display: inline-block;
+    float: right;
+}
+
+.tm-slideshow-section {
+    display: -webkit-box;
+    display: -webkit-flex;
+    display: -ms-flexbox;
+    display: flex;
+    -webkit-box-align: center;
+    -webkit-align-items: center;
+    -ms-flex-align: center;
+    align-items: center;
+}
+
+.tm-slideshow-section-reverse {
+    -webkit-box-orient: horizontal;
+    -webkit-box-direction: reverse;
+    -webkit-flex-direction: row-reverse;
+    -ms-flex-direction: row-reverse;
+    flex-direction: row-reverse;
+}
+
+.tm-slideshow { width: 50%; }
+
+.tm-slideshow-description {
+    padding: 50px;
+    color: white;
+    width: 48%;
+    z-index: 100;
+    margin-left: -42px;
+}
+
+.tm-slideshow-description-left {
+    margin-left: auto;
+    margin-right: -42px;    
+}
+
+.tm-position-relative { position: relative; }
+
+.slick-prev, .slick-next {
+    width: 50px;
+    height: 50px;
+}
+
+.slick-prev, .slick-next,
+.slick-prev:focus,
+.slick-prev:active,
+.slick-next:focus,
+.slick-next:active {
+    background: rgba(0,0,0,0.5);    
+}
+
+.slick-prev:before, .slick-next:before { font-size: 22px; }
+
+.slick-prev:hover,
+.slick-next:hover {
+    background: #69c6ba;
+}
+
+.tm-slideshow-highlight .slick-prev:hover, 
+.tm-slideshow-highlight .slick-next:hover {
+    background: #c66995;
+}
+
+.slick-prev {
+    left: auto;
+    right: 95px;
+    z-index: 1000;
+}
+
+.tm-right .slick-prev {
+    left: 42px;
+    right: auto;
+}
+
+.slick-next { right: 42px; }
+
+.tm-right .slick-next {
+    right: auto;
+    left: 94px;
+}
+
+/* Tabs */
+.tm-tabs-links {
+    display: -webkit-box;
+    display: -webkit-flex;
+    display: -ms-flexbox;
+    display: flex;
+    -webkit-box-align: stretch;
+    -webkit-align-items: stretch;
+    -ms-flex-align: stretch;
+    align-items: stretch;
+    -webkit-box-pack: space-evenly;
+    -webkit-justify-content: space-evenly;
+    -ms-flex-pack: space-evenly;
+    justify-content: space-evenly;
+    background: #69c6ba;
+}
+
+.tm-tab-link {
+    padding: 30px 25px;
+    text-align: center;
+    display: -webkit-box;
+    display: -webkit-flex;
+    display: -ms-flexbox;
+    display: flex;
+    -webkit-box-orient: vertical;
+    -webkit-box-direction: normal;
+    -webkit-flex-direction: column;
+    -ms-flex-direction: column;
+    flex-direction: column;
+    -webkit-box-align: center;
+    -webkit-align-items: center;
+    -ms-flex-align: center;
+    align-items: center;
+    -webkit-box-pack: center;
+    -webkit-justify-content: center;
+    -ms-flex-pack: center;
+    justify-content: center;
+    text-transform: uppercase;
+    color: white;
+    font-weight: 400;
+    font-size: 0.9rem;
+    height: 100%;
+}
+
+.tm-tab-link:hover { color: white; }
+
+.tm-tab-link-li {
+    background: transparent;
+    -webkit-box-flex: 1;
+    -webkit-flex: 1 1 auto;
+    -ms-flex: 1 1 auto;
+    flex: 1 1 auto;
+    transition: all 0.3s ease;    
+}
+
+.tm-tab-link:hover,
+.tm-tab-link.active {
+    background: #c66995;
+}
+
+.tab-pane {
+    max-width: 970px;
+    margin: 60px auto;
+}
+
+.tm-recommended-place {
+    box-shadow: 0 0 3px rgba(0, 0, 0, 0.15);
+    display: -webkit-box;
+    display: -webkit-flex;
+    display: -ms-flexbox;
+    display: flex;
+    align-items: stretch;
+    justify-content: space-around;
+    margin-bottom: 25px;
+}
+
+.tm-recommended-title {
+    font-size: 1.2rem;
+    font-weight: 600;
+    text-transform: uppercase;    
+}
+
+.tm-recommended-img { width: 270px; }
+
+.tm-recommended-description-box {
+    padding: 30px;
+    width: 500px;
+}
+
+.tm-recommended-price-box {    
+    background-color: #69c6ba;
+    background-image: url(../img/button-curve.png);
+    background-repeat: no-repeat;
+    background-size: auto 100%;
+    font-weight: 400;
+    display: -webkit-box;
+    display: -webkit-flex;
+    display: -ms-flexbox;
+    display: flex;
+    -webkit-box-orient: vertical;
+    -webkit-box-direction: normal;
+    -webkit-flex-direction: column;
+    -ms-flex-direction: column;
+    flex-direction: column;
+    -webkit-box-align: center;
+    -webkit-align-items: center;
+    -ms-flex-align: center;
+    align-items: center;
+    -webkit-box-pack: center;
+    -webkit-justify-content: center;
+    -ms-flex-pack: center;
+    justify-content: center;
+    padding-left: 20px;
+    width: 200px;
+    transition: all 0.3s ease;
+}
+
+.tm-recommended-price-box:hover { background-color: #c66995; }
+
+.tm-recommended-price {
+    color: white;
+    font-size: 1.6rem;
+    font-weight: 600;
+}
+
+.tm-recommended-price-link {
+    color: white;
+    font-size: 0.8rem;
+    font-weight: 600;
+    text-transform: uppercase;
+}
+
+.tm-d-table { display: table; }
+
+footer {
+    background: #69c6ba;
+    padding-top: 40px;
+    padding-bottom: 40px;
+    text-align: center;    
+    font-size: 0.8rem;
+}
+
+footer a { color: #fff; }
+
+footer a:hover { color: #900; }
+
+footer p { color: white; }
+
+.tm-footer-text-highlight {
+    color: white;
+    font-weight: 600;
+}
+
+.tm-footer-text-highlight:hover { color: #c66995; }
+
+.tm-contact-form {
+    background: white;
+    width: 470px;
+    position: absolute;
+    top: 100px;
+    right: 100px;
+    padding: 20px;
+    z-index: 1000;
+}
+
+.form-control {
+    background-color: #f5f5f5;
+    border: none;
+}
+
+.form-control:focus {
+    border-color: #69c6ba;
+    box-shadow: 0 0 0 0.1rem #69c6babf;
+}
+
+.tm-name-container,
+.tm-email-container {
+    width: 210px;
+    float: left;    
+}
+
+.tm-email-container { margin-left: 10px; }
+
+.tm-btn-send {
+    width: 100%;
+    padding-top: 10px;
+    padding-bottom: 10px;
+    cursor: pointer;
+    font-size: 0.8rem;
+    font-weight: 600;
+}
+
+#google-map { height: 600px; }
+
+@media screen and (max-width: 1080px) {
+    .tm-tab-link-li { width: 25%; }
+}
+
+@media screen and (max-width: 1033px) {
+    .tm-slideshow-description { width: 55%; }
+}
+
+/* TODO */
+@media screen and (max-width: 991px) {
+    .tm-top-bar .navbar-expand-lg .navbar-nav .nav-link {
+        padding: 15px 20px;
+        background: rgb(33,36,41);
+    }
+
+    .tm-top-bar, .tm-top-bar-bg { height: auto; }
+
+    #mainNav {
+        width: 250px;
+        position: absolute;
+        top: 53px;
+        right: 15px;
+    }
+
+    .tm-top-bar {
+        height: 60px;
+        box-shadow: 0 1px 5px rgba(0, 0, 0, 0.25);
+        display: flex;
+        align-items: center;
+    }
+
+    .tm-top-bar.active .navbar-expand-lg .navbar-nav .nav-link,
+    .tm-top-bar .navbar-expand-lg .navbar-nav .nav-link { padding: 15px; }
+
+    .tm-top-bar .navbar-brand { font-size: 1.4rem; }
+
+    .tm-top-bar .navbar-brand img {
+        width: 60px;
+        height: auto;
+    }
+
+    .tm-top-bar .navbar-brand img { width: 40px; }
+
+    .tab-pane {
+        margin-left: 20px;
+        margin-right: 20px;
+    }
+
+    .tm-recommended-description-box { width: 450px; }
+}
+
+@media screen and (max-width: 986px) {
+    .tm-slideshow-section { flex-direction: column; }
+    
+    .tm-slideshow,
+    .tm-slideshow-description {
+        width: 100%;
+        max-width: 700px;
+    }
+
+    .tm-slideshow-description {        
+        margin-right: auto;
+        margin-left: auto;
+    }
+
+    .slick-prev, .slick-next {
+        bottom: 0;
+        top: auto;
+    }
+
+    .tm-contact-form {
+        position: static;
+        width: 100%;
+    }
+
+    .tm-name-container,
+    .tm-email-container {
+        width: 49%;
+    }
+
+    .tm-email-container {
+        margin-left: 0;
+        float: right;
+    }
+
+}
+
+@media screen and (max-width: 860px) {
+    .tm-recommended-description-box { width: 350px; }
+}
+
+@media screen and (max-width: 826px) {
+
+    .body {
+        padding-top: 300px;
+        content: "test\nsdfg\nsdfg\nsdfg\nsfg\n";
+    }
+
+    .tm-banner-row-header { padding-top: 120px; }
+
+    .tm-recommended-place-wrap {
+        display: flex;
+        flex-wrap: wrap;
+        max-width: 600px;
+        margin: 0 auto 15px;
+    }
+
+    .tm-recommended-place {
+        display: block;
+        margin-left: auto;
+        margin-right: auto;
+        width: 270px;
+    }
+
+    .tm-recommended-price,
+    .tm-recommended-price-link {
+        position: relative;
+        z-index: 1000;
+    }
+
+    .tm-recommended-price { padding-top: 50px; }
+
+    .tm-recommended-price-box {
+        width: 270px;
+        height: 180px;        
+        position: relative;
+        overflow: hidden;
+        padding-left: 0;
+        background-image: none;
+    }
+
+    .tm-recommended-price-box:after {
+        content: "";
+        position: absolute;
+        width: 180px;
+        height: 270px;
+        top: -45px;
+        left: 45px;
+        z-index: 27;
+        background: url(../img/button-curve.png) 0 0 no-repeat;
+        -webkit-transform: rotate(90deg);
+        transform: rotate(90deg);
+        background-size: auto 100%;      
+    }
+
+    .tm-recommended-price-box,
+    .tm-recommended-price-box:hover {
+        background-size: cover;
+    }
+
+    .tm-recommended-description-box { width: 270px; }
+}
+
+@media screen and (max-width: 767px) {
+    .tm-banner-row {
+        padding-top: 80px;
+        padding-bottom: 50px;
+    }
+
+    .tm-banner-header { margin-top: 100px; }
+
+    .tm-form-group-1,
+    .tm-form-group-2,
+    .tm-form-group-3 {
+        width: 100%;
+    }    
+}
--- a/docs/_site/assets/css/uikit_theme.css
+++ b/docs/_site/assets/css/uikit_theme.css
--- a/Show More
+++ b/Show More
				`@@ -0,0 +1 @@`
				`This example demonstrates how PyLaGriT can be used within a Julia script. The julia script "polygon_map.jl" and the python script "polygon_map.py" perform the same LaGriT operations. The two scripts can be compared to see how the syntax is modified for the Julia languange.`