Merge branch 'master' into poisson_disk

README.md

@@ -28,8 +28,6 @@ $ cd LaGriT/
 ### Building LaGriT ###
 ---
 
-#### Building LaGriT - long version 
-
 [Building LaGriT with cmake and exodus](cmake/README.md)
 
 

cmake/README.md

@@ -1,31 +1,65 @@
-# CMake Build System
+# LaGriT and ExodusII with cmake
 
-The CMake build system is a way of enabling LaGriT to
-be cross-platform, cross-architecture, and cross-compiler.
+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
+For additional help on ExodusII, see instructions at https://github.com/sandialabs/seacas
+**Note for Exodus with LaGriT, FORTRAN must be set to YES**
 
-See Build and Install Instructions: https://github.com/lanl/LaGriT#readme
 
 There's a really good tutorial-overview on CMake here, it covers how to handle multiple build configurations: https://cliutils.gitlab.io/modern-cmake/
 
 
-## Code Development
+## Download LaGriT
 
-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. One way to handle building both Debug and release is to make two build directories. Here's a short guide: https://riptutorial.com/cmake/example/7357/switching-between-build-types--e-g--debug-and-release
+Download the repo as shown under the Code button on git.
+For developers, be sure to use SSH version to clone. 
 
-You can set cmake and make to show verbose screen reporting. These are run from your buld directory with the following options:
 ```
-cmake -D CMAKE_FIND_DEBUG_MODE=ON ..
-make VERBOSE=1
+$ git clone [email protected]: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).
 ```
 
-For LANL developers, you may need to generate a token to use as password. See instructions at https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token
+## Build ExodusII (optional)
 
+See instructions in install-exodus.sh
+
+LaGriT will use libs and files located in TPLs/seacas
+
+Expected libs and include files:
+
+```
+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
+include/exodus_config.h  include/exodusII.h     include/exodusII.inc  include/exodusII_par.h
+include/netcdf.h         include/hdf5.h
+```
+
+Once the ExodusII is successful, build LaGriT as usual but with the EXODUS flag:
+
+```
+mkdir build/ && cd build/
+cmake .. -DCMAKE_BUILD_TYPE=Debug -DLAGRIT_BUILD_EXODUS=ON
+make
+```
 
 ## Create your build directory:
 
+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'
@@ -36,8 +70,14 @@ 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
+## 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.
@@ -55,7 +95,7 @@ make
 
 
       
-### Example Directory structure for development:
+### Example Directory structure for developers:
       
 ```
 LaGriT/
@@ -132,8 +172,11 @@ make[2]: Leaving directory '/project/eesdev/tam/LaGriT/build'
 [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
+### Header File configuration
 
 CMake automatically configures two header files:
 
@@ -164,3 +207,32 @@ configure_file(
 
 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)
+```
+
+
+
+

docs/index.md

@@ -16,9 +16,19 @@ title: LaGriT - Home
                 
     <div class="button" id="button-4">
     <div id="underline"></div>
-    <a href="https://lanl.github.io/LaGriT/pages/tutorial/index.html">Take the Tutorial</a>
+    <a href="https://lanl.github.io/LaGriT/pages/manual.html">LaGriT Manual</a>
     </div>
-            
+
+    <div class="button" id="button-4">
+    <div id="underline"></div>
+    <a href="https://lanl.github.io/LaGriT/pages/tutorial/index.html">LaGriT Tutorial</a>
+    </div>
+
+    <div class="button" id="button-4">
+    <div id="underline"></div>
+    <a href="https://lanl.github.io/LaGriT/pylagrit/original/index.html">PyLaGriT Manual</a>
+    </div>
+
   </div>
 </div>
 
@@ -69,12 +79,6 @@ incorporating uncertainty in system geometry and automatic mesh
 generation. 
 
 
-## Documentation
-
-
-- [LaGriT Manual](pages/manual.md)
-- [PyLaGriT Manual](/pylagrit/original/index.html)
-
 
 ## About LaGriT
 

docs/pages/development.md

@@ -1,21 +1,23 @@
 LaGriT Code Development Team
 ----------------------------
 
-[Carl W. Gable](http://www.lanl.gov/expertise/profiles/view/carl-gable), Geological Applications
+[Carl W. Gable](http://www.lanl.gov/search-capabilities/profiles/carl-gable.shtml) Author (Retired from LANL)
+
+[Terry Miller](http://www.lanl.gov/search-capabilities/profiles/terry-miller.shtml) Support
+
+[Jeffrey De'Haven Hyman](http://www.lanl.gov/search-capabilities/profiles/jeffrey-hyman.shtml) Applications
 
 [Tinka Gammel](http://public.lanl.gov/jtg/)
 
 Denise George (Retired)
 
 [Andrew Kuprat](http://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7019)
 
-[Terry Miller](http://www.lanl.gov/expertise/profiles/view/terry-miller)
-
 Frank A. Ortega 
 
-[Harold Trease](http://www.sysbio.org/resources/staff/trease.stm)
+[Harold Trease](http://www.sysbio.org/resources/staff/trease.stm) Retired from LANL
 
-[Lynn Trease](http://www.sysbio.org/resources/staff/l-trease.stm)
+[Lynn Trease](http://www.sysbio.org/resources/staff/l-trease.stm) Retired from LANL
 
 Robert B. Walker
 

docs/pages/docs/build.md

@@ -11,20 +11,22 @@ Tags: Manual Building an executable and running LaGriT
 The executable is built by linking a driver routine with the code and
 utility libraries. The driver routine must contain a call to initLaGriT
 and a call to control_command_lg and must contain a subroutine called
-user_sub.  The input arguments to initLaGriT are:
+user_sub.  
+
+The input arguments to initLaGriT are:
 
 **mode** - set to 'noisy' for output to be echoed to the screen - set to
 'silent' for no echo
 
 **log_file** - name of log file (if ' ' or '-def-' use default name which
-is logx3dgen)  This file will contain a list of commands.
+is lagrit.log)  This file will contain a list of commands.
 
 **batch_file** - name of batch file (if ' ' or '-def-' use default name
-which is outx3dgen). This file will contain a list of commands and the
+which is lagrit.out). This file will contain a list of commands and the
 error, warning and informational messages generated by the command.
 User_sub is used to implement user commands, see [User Commands](writing.md).
 
-A sample driver routine is listed below:
+A sample Fortran driver routine is listed below (C++ examples are in examples/liblagrit/):
 
 <pre>
 program adrivgen
@@ -82,11 +84,31 @@ C    For example
 
 ### Sample build scripts
 
-LaGriT can be compiled on most modern machines including Linux, Mac, and WINDOWS.
+LaGriT can be compiled on most modern machines including Linux, and Mac. WINDOWS is still under development, but pre-cmake versions were successful under Cygwin. LaGriT now uses cmake to build with or without external libraries such as Seacas Exodus. 
+
+The most recent instructions can be found on the github pages.
+
+
+Simple install, build, and test: [LaGriT Github README](https://github.com/lanl/LaGriT/blob/master/README.md)  
+
+Build options and instructions for developers: [LaGriT Github cmake README](https://github.com/lanl/LaGriT/blob/master/cmake/README.md)
+
+
+
+### Running LaGriT
 
-*Note examples may be out of date, see [LaGriT Github](https://github.com/lanl/LaGriT)*
+To execute, use standard unix file redirection for standard input and
+output. LaGriT will produce two additional files, lagrit.out and
+lagrit.log. The user can change the names of these files by supplying new
+names as arguments in the call to initLaGriT before compiling.  These files contain
+detailed output information and the list of commands respectively.
+LaGriT may also be run interactively in which case the user will be
+prompted to enter commands at the machine prompt.
 
+    lagrit < lagrit_command_file
+
 
+### The following are examples to build old releases (pre V3.2) but may be helpful on older machines.
 
 **Sun OS and Sun Solaris forte version 7 compiler:**
 
@@ -185,10 +207,4 @@ where fdate.f is
 
 
 
-To execute, use standard unix file redirection for standard input and
-output. LaGriT will produce two additional files, outx3dgen and
-logx3dgen. The names of these files can be changed by supplying the
-names as arguments in the call to initLaGriT.  These files contain
-detailed output information and the list of commands respectively.
-LaGriT may also be run interactively in which case the user will be
-prompted to enter commands from the workstation.
+

docs/pages/docs/commands/cmo/cmo_addatt.md

@@ -194,10 +194,10 @@ See also the command [**`QUALITY`**](../QUALITY.md) for adding attributes such a
 **ang_mind_solid** / `att_name` <br> create a scalar element attribute and fill it with the minimum solid angle (degrees) of the element
 
 <a name="ang_mind_solid"></a>
-**ang_maxd_solid** / `att_name` <br> create a scalar element attribute and fill it with the minimum solid angle (radian) of the element
+**ang_minr_solid** / `att_name` <br> create a scalar element attribute and fill it with the minimum solid angle (radian) of the element
 
 <a name="ang_mind_solid"></a>
-**ang_minr_solid** / `att_name` <br> create a scalar element attribute and fill it with the maximum solid angle (degrees) of the element
+**ang_maxd_solid** / `att_name` <br> create a scalar element attribute and fill it with the maximum solid angle (degrees) of the element
 
 <a name="ang_mind_solid"></a>
 **ang_maxr_solid** / `att_name` <br> create a scalar element attribute and fill it with the maximum solid angle (radian) of the element

docs/pages/docs/commands/createpts.md

@@ -16,6 +16,9 @@ This command adds points to a mesh object. For some special cases, it will also
 
 **[createpts/interp](createpts/createpts_interp.md)** Creates points by linear interpolation between two point sets.
 
+
+**[createpts/poisson_disk](createpts/createpts_poisson.md)** Use Poisson Disk sampling to create uniform or variable spaced points inside a polygon.
+
 **[createpts/sphere](createpts/cresphere.md)** Create points for a sphere.
 
 **[createpts/random](createpts/CRTPTRZRAN.md)** Add random points within region.