resolved material model merge

.github/workflows/ubuntu-build.yaml

@@ -0,0 +1,49 @@
+name: Ubuntu Build
+
+on: workflow_dispatch
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: update the package list
+      run:
+        sudo apt-get update
+      shell: bash
+    - name: Install build tools
+      run:
+        sudo apt-get install build-essential
+      shell: bash
+    - name: Install LaPack
+      run:
+        sudo apt-get install libblas-dev liblapack-dev
+      shell: bash
+    - name: Install MPI
+      run: |
+        sudo apt-get install libopenmpi-dev openmpi-bin
+        echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
+    - name: Install cmake
+      run:
+        sudo apt-get -y install cmake
+      shell: bash
+    - name: Install python
+      run:
+        sudo apt-get install python3.6
+      shell: bash
+    - name: Run build script
+      run: |
+         chmod +x ./scripts/build-fierro.sh
+         ./scripts/build-fierro.sh --build_action=full-app --solver=all --kokkos_build_type=openmp --build_cores=2
+      shell: bash
+
+    - name: Run tests
+      run: |
+         python3 test_fierro.py
+      working-directory: ./integrated-tests/Test-scripts
+      shell: bash

.gitmodules

@@ -2,3 +2,6 @@
 	path = lib/Elements
 	url = https://github.com/lanl/ELEMENTS.git
     branch = master
+[submodule "dev-utils/uncrustify"]
+	path = dev-utils/uncrustify
+	url = https://github.com/uncrustify/uncrustify.git

docs/formatting/ClassDefinitionComment.txt

@@ -0,0 +1,11 @@
+/////////////////////////////////////////////////////////////////////////////
+///
+/// \class $(class)
+///
+/// \brief <insert brief description>
+/// 
+/// < Insert longer more detailed 
+/// description which can span 
+/// multiple lines if needed >
+///
+/////////////////////////////////////////////////////////////////////////////

docs/formatting/FunctionDefinitionComment.txt

@@ -0,0 +1,16 @@
+/////////////////////////////////////////////////////////////////////////////
+///
+/// \fn $(function)
+///
+/// \brief <insert brief description>
+/// 
+/// <Insert longer more detailed description which
+/// can span multiple lines if needed>
+/// 
+/// \param <function parameter description>
+/// \param <function parameter description>
+/// \param <function parameter description>
+/// 
+/// \return <return type and definition description if not void>
+/// 
+/////////////////////////////////////////////////////////////////////////////

docs/formatting/HeaderForSources.txt

@@ -0,0 +1,34 @@
+ /**********************************************************************************************
+ © 2020. 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.
+ This program is open source under the BSD-3 License.
+ 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 the copyright holder 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 THE COPYRIGHT HOLDERS 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 THE COPYRIGHT HOLDER 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.
+ **********************************************************************************************/
+

docs/formatting/uncrustify.cfg

@@ -26,6 +26,12 @@ indent_func_call_param          = true     # false/true
 # Same as indent_func_call_param, but for function defs
 indent_func_def_param           = false    # false/true
 
+# for function definitions, only if indent_func_def_param is false
+# Allows to align params when appropriate and indent them when not
+# behave as if it was true if paren position is more than this value
+# if paren position is more than the option value
+indent_func_def_param_paren_pos_threshold = 6        # unsigned number
+
 # Same as indent_func_call_param, but for function protos
 indent_func_proto_param         = false    # false/true
 
@@ -94,13 +100,13 @@ nl_struct_brace                 = force      # ignore/add/remove/force
 nl_union_brace                  = force      # ignore/add/remove/force
 
 # Add or remove newline between 'if' and '{'
-nl_if_brace                     = force      # ignore/add/remove/force
+nl_if_brace                     = remove     # ignore/add/remove/force
 
 # Add or remove newline between '}' and 'else'
 nl_brace_else                   = force      # ignore/add/remove/force
 
 # Add or remove newline between 'else' and '{'
-nl_else_brace                   = force      # ignore/add/remove/force
+nl_else_brace                   = remove     # ignore/add/remove/force
 
 # Add or remove newline between 'else' and 'if'
 nl_else_if                      = remove   # ignore/add/remove/force
@@ -115,7 +121,7 @@ nl_finally_brace                = force      # ignore/add/remove/force
 nl_try_brace                    = force      # ignore/add/remove/force
 
 # Add or remove newline between 'for' and '{'
-nl_for_brace                    = force      # ignore/add/remove/force
+nl_for_brace                    = remove      # ignore/add/remove/force
 
 # Add or remove newline between 'catch' and '{'
 nl_catch_brace                  = force      # ignore/add/remove/force
@@ -130,7 +136,7 @@ nl_do_brace                     = force      # ignore/add/remove/force
 nl_brace_while                  = force      # ignore/add/remove/force
 
 # Add or remove newline between 'switch' and '{'
-nl_switch_brace                 = force      # ignore/add/remove/force
+nl_switch_brace                 = remove      # ignore/add/remove/force
 
 # Add or remove newline between function signature and '{'
 nl_fdef_brace                   = force      # ignore/add/remove/force
@@ -369,18 +375,36 @@ align_var_class_span            = 1        # number
 align_var_class_thresh          = 6        # number
 
 # Whether to align variable definitions in prototypes and functions.
-align_func_params               = true    # true/false
+align_func_params               = false   # true/false
+
+# The span for aligning parameter definitions in function on parameter name.
+#
+# 0: Don't align (default).
+align_func_params_span          = 1        # unsigned number
+
+
+# The threshold for aligning function parameter definitions.
+# Use a negative number for absolute thresholds.
+#
+# 0: No limit (default).
+align_func_params_thresh        = -5        # number
 
 # The span for aligning on '=' in assignments.
 #
 # 0 = Don't align (default).
 align_assign_span               = 1        # unsigned number
 
+# The span for aligning function prototypes (0=don't align)
+align_func_proto_span           = 0        # number
+
 # The threshold for aligning on '=' in assignments.
 # Use a negative number for absolute thresholds.
 #
 # 0 = No limit (default).
-align_assign_thresh             = 6        # number
+align_assign_thresh             = 4        # number
+
+# The threshold for aligning variable definitions (0=no limit)
+align_var_def_thresh            = 4        # number
 
 # Whether to align lines that start with '<<' with previous '<<'.
 #
@@ -440,7 +464,20 @@ cmt_indent_multi                = false    # false/true
 
 # The filename that contains text to insert at the head of a file if the file doesn't start with a C/C++ comment.
 # Will substitute $(filename) with the current file's name.
-# cmt_insert_file_header          = "../HeaderForSources.txt"
+cmt_insert_file_header          = "HeaderForSources.txt"
+
+# Path to a file that contains text to insert before a function definition if
+# the function isn't preceded by a C/C++ comment. If the inserted text
+# contains '$(function)', '$(javaparam)' or '$(fclass)', these will be
+# replaced with, respectively, the name of the function, the javadoc '@param'
+# and '@return' stuff, or the name of the class to which the member function
+# belongs.
+cmt_insert_func_header          = "FunctionDefinitionComment.txt"         # string
+
+# Path to a file that contains text to insert before a class if the class
+# isn't preceded by a C/C++ comment. If the inserted text contains '$(class)',
+# that will be replaced with the class name.
+cmt_insert_class_header         = ""         # string
 
 # If a namespace body exceeds the specified number of newlines and doesn't have a comment after
 # the close brace, a comment will be added.

integrated-tests/Test-scripts/Solver-Inputs/SGH_Noh_simple.yaml

@@ -0,0 +1,70 @@
+num_dims: 3
+dynamic_options:
+  time_final: 0.6
+  dt_min: 1.e-8
+  dt_max: 1.e-2
+  dt_start: 1.e-5
+  cycle_stop: 2000000
+
+mesh_generation_options:
+  type: Box
+  origin: [0, 0, 0]
+  length: [1.0, 1.0, 1.0]
+  num_elems: [10, 10, 10]
+
+output_options:
+  timer_output_level: thorough
+  output_file_format: vtk
+  graphics_step: 0.6
+  write_initial: false
+  write_final: true
+
+
+fea_module_parameters:
+  - type: SGH
+    material_id: 0
+    boundary_conditions:
+      # Tag X plane
+      - surface: 
+          type: x_plane
+          plane_position: 0.0
+        type: reflected
+
+        # Tag Y plane
+      - surface: 
+          type: y_plane
+          plane_position: 0.0
+        type: reflected
+
+        # Tag Z plane
+      - surface: 
+          type: z_plane
+          plane_position: 0.0
+        type: reflected
+
+
+materials:
+  - id: 0
+    eos_model: ideal_gas
+    strength_model: none
+    elastic_modulus: 10
+    poisson_ratio: 0.3
+    q1: 0.06
+    q2: 1.2
+    q1ex: 0.06
+    q2ex: 1.2
+    eos_global_vars:
+      - 1.666666666666667
+      - 1.0E-14
+      - 1.0
+
+regions:
+  - volume: 
+      type: global
+    material_id: 0
+    den: 1.0
+    sie: 1.e-10
+
+    velocity: spherical
+    speed: -1.0
+

integrated-tests/Test-scripts/Solver-Inputs/SGH_Sedov_simple.yaml

@@ -0,0 +1,82 @@
+num_dims: 3
+dynamic_options:
+  time_final: 1.0
+  dt_min: 1.e-8
+  dt_max: 1.e-2
+  dt_start: 1.e-5
+  cycle_stop: 2000000
+
+mesh_generation_options:
+  type: Box
+  origin: [0, 0, 0]
+  length: [1.2, 1.2, 1.2]
+  num_elems: [12, 12, 12]
+
+output_options:
+  timer_output_level: thorough
+  output_file_format: vtk
+  graphics_step: 1.0
+  write_initial: false
+  write_final: true
+
+fea_module_parameters:
+  - type: SGH
+    material_id: 0
+    boundary_conditions:
+      # Tag X plane
+      - surface: 
+          type: x_plane
+          plane_position: 0.0
+        type: reflected
+
+        # Tag Y plane
+      - surface: 
+          type: y_plane
+          plane_position: 0.0
+        type: reflected
+
+        # Tag Z plane
+      - surface: 
+          type: z_plane
+          plane_position: 0.0
+        type: reflected
+
+
+materials:
+  - id: 0
+    eos_model: ideal_gas
+    strength_model: none
+    elastic_modulus: 10
+    poisson_ratio: 0.3
+    q1: 0.06
+    q2: 1.0
+    q1ex: 0.06
+    q2ex: 1.0
+    eos_global_vars:
+      - 1.666666666666667
+      - 1.0E-14
+      - 1.0
+
+regions:
+  - volume: 
+      type: global
+    material_id: 0
+    den: 1.0
+    sie: 1.e-10
+
+    velocity: cartesian
+    u: 0.0
+    v: 0.0
+    w: 0.0
+    # energy source initial conditions
+  - volume: 
+      type: sphere
+      radius1: 0.0
+      radius2: 0.1
+    material_id: 0
+    den: 1.0
+    ie:  0.25833839995946534
+    velocity: cartesian
+    u: 0.0
+    v: 0.0
+    w: 0.0