PYGEOSX_ to PYGEOS_

Author: rrsettgast

examples/pygeosxExamples/hydraulicFractureWithMonitor/hydraulicFractureWithMonitor.py

@@ -1,18 +1,18 @@
 
-# PYGEOSX_SETUP
+# PYGEOS_SETUP
 from mpi4py import MPI
 import pygeosx
 from pygeosx_tools import wrapper
 from geosx_xml_tools.main import preprocess_parallel
 import matplotlib.pyplot as plt
-# PYGEOSX_SETUP_END
+# PYGEOS_SETUP_END
 
 
 def run_problem(plot_frequency=1):
     """
     Run the GEOSX problem
     """
-    # PYGEOSX_INITIALIZATION
+    # PYGEOS_INITIALIZATION
     # Get the MPI rank
     comm = MPI.COMM_WORLD
     rank = comm.Get_rank()
@@ -21,21 +21,21 @@ def run_problem(plot_frequency=1):
     args = preprocess_parallel()
     problem = pygeosx.initialize(rank, args)
     pygeosx.apply_initial_conditions()
-    # PYGEOSX_INITIALIZATION_END
+    # PYGEOS_INITIALIZATION_END
 
-    # PYGEOSX_KEY_SEARCH
+    # PYGEOS_KEY_SEARCH
     # Rather than specifying the wrapper paths explicitly,
     # search for them using a set of filters
     fracture_location_key = wrapper.get_matching_wrapper_path(problem, ['Fracture', 'elementCenter'])
     fracture_aperture_key = wrapper.get_matching_wrapper_path(problem, ['Fracture', 'effectiveAperture'])
-    # PYGEOSX_KEY_SEARCH_END
+    # PYGEOS_KEY_SEARCH_END
 
     # Note: we will be plotting our results.
     # This will modify the fonts so that they a bit easier to read
     plot_font = {'weight': 'normal', 'size': 8}
     plt.rc('font', **plot_font)
 
-    # PYGEOSX_QUERY_SETUP
+    # PYGEOS_QUERY_SETUP
     # Setup values to record
     records = {fracture_location_key: {'label': 'Fracture Extents (m)',
                                        'scale': 1.0,
@@ -48,17 +48,17 @@ def run_problem(plot_frequency=1):
                'time': {'label': 'Time (min)',
                         'scale': 1.0 / 60.0,
                         'history': []}}
-    # PYGEOSX_QUERY_SETUP_END
+    # PYGEOS_QUERY_SETUP_END
 
-    # PYGEOSX_MAIN_LOOP
+    # PYGEOS_MAIN_LOOP
     # Run the code
     query_count = 0
     while pygeosx.run() != pygeosx.COMPLETED:
         wrapper.run_queries(problem, records)
         query_count += 1
         if (query_count % plot_frequency == 0):
             wrapper.plot_history(records)
-    # PYGEOSX_MAIN_LOOP_END
+    # PYGEOS_MAIN_LOOP_END
 
 
 if __name__ == '__main__':

examples/pygeosxExamples/sedovWithStressFunction/run_sedov_problem.py

@@ -6,7 +6,7 @@
 from geosx_xml_tools.main import preprocess_parallel
 
 
-# PYGEOSX_STRESS_FN
+# PYGEOS_STRESS_FN
 def stress_fn(x):
     """
     Function to set stress values
@@ -19,14 +19,14 @@ def stress_fn(x):
     """
     R = x[:, 0]**2 + x[:, 1]**2 + x[:, 2]**2
     return np.sin(2.0 * np.pi * R / np.amax(R))
-# PYGEOSX_STRESS_FN_END
+# PYGEOS_STRESS_FN_END
 
 
 def run_problem():
     """
     Run the GEOSX problem
     """
-    # PYGEOSX_INITIALIZATION
+    # PYGEOS_INITIALIZATION
     # Get the MPI rank
     comm = MPI.COMM_WORLD
     rank = comm.Get_rank()
@@ -41,9 +41,9 @@ def run_problem():
     location_key = wrapper.get_matching_wrapper_path(problem, ['Region2', 'elementCenter'])
     stress_key = wrapper.get_matching_wrapper_path(problem, ['Region2', 'shale', 'stress'])
     ghost_key = wrapper.get_matching_wrapper_path(problem, ['Region2', 'cb1', 'ghostRank'])
-    # PYGEOSX_INITIALIZATION_END
+    # PYGEOS_INITIALIZATION_END
 
-    # PYGEOSX_STRESS_IC
+    # PYGEOS_STRESS_IC
     # Print initial stress
     wrapper.print_global_value_range(problem, stress_key, 'stress')
 
@@ -56,9 +56,9 @@ def run_problem():
     wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=1)
     wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=2)
     wrapper.print_global_value_range(problem, stress_key, 'stress')
-    # PYGEOSX_STRESS_IC_END
+    # PYGEOS_STRESS_IC_END
 
-    # PYGEOSX_MAIN_LOOP
+    # PYGEOS_MAIN_LOOP
     # Run the code
     while pygeosx.run() != pygeosx.COMPLETED:
         wrapper.print_global_value_range(problem, stress_key, 'stress')
@@ -72,7 +72,7 @@ def run_problem():
 
         tmp = wrapper.allgather_wrapper(problem, stress_key, ghost_key=ghost_key)
         print(wrapper.rank, 'allgather_ghost_filtered', np.shape(tmp), flush=True)
-    # PYGEOSX_MAIN_LOOP_END
+    # PYGEOS_MAIN_LOOP_END
 
 
 if __name__ == '__main__':

scripts/automatic_xml_preprocess.sh

@@ -9,7 +9,7 @@ COMPILED_XML_NAME_OVERRIDE=""
 PARAMETER_ARGS=""
 NEW_ARGS=""
 USE_PYGEOSX=1
-PYGEOSX_WARNINGS=0
+PYGEOS_WARNINGS=0
 SCRIPT_DIR=$(dirname "$0")
 PYGEOSX=$SCRIPT_DIR/../lib/PYGEOSX/bin/python
 
@@ -37,7 +37,7 @@ do
         shift
         ;;
         -w|--pygeosx-warnings)
-        PYGEOSX_WARNINGS=$2
+        PYGEOS_WARNINGS=$2
         shift
         ;;
         -h|--help)
@@ -75,12 +75,12 @@ if [ "$USE_PYGEOSX" -eq "1" ]
 then
    if [ -f $PYGEOSX ]
    then
-      if [ "$PYGEOSX_WARNINGS" -eq "1" ]
+      if [ "$PYGEOS_WARNINGS" -eq "1" ]
       then
          echo "Using pygeosx to preprocess the xml file"
       fi
    else
-      if [ "$PYGEOSX_WARNINGS" -eq "1" ]
+      if [ "$PYGEOS_WARNINGS" -eq "1" ]
       then
          echo "Pygeosx installation not found... reverting to non-pygeosx version"
       fi

scripts/pygeosx_preprocess.py

@@ -7,7 +7,7 @@ def run_problem():
     """
     Run the GEOSX problem
     """
-    # PYGEOSX_INITIALIZATION
+    # PYGEOS_INITIALIZATION
     # Get the MPI rank
     comm = MPI.COMM_WORLD
     rank = comm.Get_rank()

src/docs/sphinx/advancedExamples/pygeosxExamples/inSituDataMonitor/AdvancedExample.rst

@@ -63,8 +63,8 @@ The custom packages include pygeosx, which provides an interface to GEOS, and py
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/hydraulicFractureWithMonitor/hydraulicFractureWithMonitor.py
   :language: python
-  :start-after: # PYGEOSX_SETUP
-  :end-before: # PYGEOSX_SETUP_END
+  :start-after: # PYGEOS_SETUP
+  :end-before: # PYGEOS_SETUP_END
 
 In the next step, we apply the xml preprocessor to resolve the advanced xml features.
 Note that this step will modify the input arguments to reflect the location of the compiled xml file, which is processed directly by GEOS.
@@ -73,8 +73,8 @@ There is an opportunity to interact with the GEOS before the initial conditions
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/hydraulicFractureWithMonitor/hydraulicFractureWithMonitor.py
   :language: python
-  :start-after: # PYGEOSX_INITIALIZATION
-  :end-before: # PYGEOSX_INITIALIZATION_END
+  :start-after: # PYGEOS_INITIALIZATION
+  :end-before: # PYGEOS_INITIALIZATION_END
 
 To extract information from the problem, you need to know the full path (or 'key') to the target object.
 These keys can be quite long, and can change depending on the xml input.
@@ -84,8 +84,8 @@ Note that these functions will throw an error if they do not find a matching key
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/hydraulicFractureWithMonitor/hydraulicFractureWithMonitor.py
   :language: python
-  :start-after: # PYGEOSX_KEY_SEARCH
-  :end-before: # PYGEOSX_KEY_SEARCH_END
+  :start-after: # PYGEOS_KEY_SEARCH
+  :end-before: # PYGEOS_KEY_SEARCH_END
 
 Next, we setup a dictionary that will allow us to use pygeosx_tools to automatically query the problem.
 The root level of this dictionary contains the target keys (fracture location and aperture) and the required `time` key.
@@ -94,8 +94,8 @@ The target dictionaries also hold an entry `fhandle`, which contains a matplotli
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/hydraulicFractureWithMonitor/hydraulicFractureWithMonitor.py
   :language: python
-  :start-after: # PYGEOSX_QUERY_SETUP
-  :end-before: # PYGEOSX_QUERY_SETUP_END
+  :start-after: # PYGEOS_QUERY_SETUP
+  :end-before: # PYGEOS_QUERY_SETUP_END
 
 After setting up the problem, we enter the main problem loop.
 Upon calling `pygeosx.run()`, the code will execute until a Python event is triggered in the Event loop.
@@ -104,8 +104,8 @@ Here, we use pygeosx_tools to query the datastructure and occasionaly plot the r
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/hydraulicFractureWithMonitor/hydraulicFractureWithMonitor.py
   :language: python
-  :start-after: # PYGEOSX_QUERY_SETUP
-  :end-before: # PYGEOSX_QUERY_SETUP_END
+  :start-after: # PYGEOS_QUERY_SETUP
+  :end-before: # PYGEOS_QUERY_SETUP_END
 
 
 ---------------------------------

src/docs/sphinx/advancedExamples/pygeosxExamples/initialConditionModification/AdvancedExample.rst

@@ -59,32 +59,32 @@ Similar to the previous example, the python script begins by importing the requi
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/sedovWithStressFunction/run_sedov_problem.py
   :language: python
-  :start-after: # PYGEOSX_INITIALIZATION
-  :end-before: # PYGEOSX_INITIALIZATION_END
+  :start-after: # PYGEOS_INITIALIZATION
+  :end-before: # PYGEOS_INITIALIZATION_END
 
 The next steps rely on a python function that we use to set stress.
 The argument to this function, x, is assumed to be a numpy array of element centers:
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/sedovWithStressFunction/run_sedov_problem.py
   :language: python
-  :start-after: # PYGEOSX_STRESS_FN
-  :end-before: # PYGEOSX_STRESS_FN_END
+  :start-after: # PYGEOS_STRESS_FN
+  :end-before: # PYGEOS_STRESS_FN_END
 
 In the following section, we zero out the initial stress and then set it based on `stress_fn`.
 While doing this, we use `wrapper.print_global_value_range` to check on the process.
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/sedovWithStressFunction/run_sedov_problem.py
   :language: python
-  :start-after: # PYGEOSX_STRESS_IC
-  :end-before: # PYGEOSX_STRESS_IC_END
+  :start-after: # PYGEOS_STRESS_IC
+  :end-before: # PYGEOS_STRESS_IC_END
 
 Finally, we run the simulation.
 As an optional step, we extract numpy arrays from the datastructure using different parallel approaches:
 
 .. literalinclude:: ../../../../../../examples/pygeosxExamples/sedovWithStressFunction/run_sedov_problem.py
   :language: python
-  :start-after: # PYGEOSX_MAIN_LOOP
-  :end-before: # PYGEOSX_MAIN_LOOP_END
+  :start-after: # PYGEOS_MAIN_LOOP
+  :end-before: # PYGEOS_MAIN_LOOP_END
 
 
 ---------------------------------

src/pygeosx/pygeosx.hpp

@@ -13,8 +13,8 @@
  */
 
 // Source includes
-#ifndef GEOS_PYGEOSX_PYGEOSX_HPP_
-#define GEOS_PYGEOSX_PYGEOSX_HPP_
+#ifndef GEOS_PYGEOS_PYGEOS_HPP_
+#define GEOS_PYGEOS_PYGEOS_HPP_
 
 #include "LvArray/src/python/pythonForwardDeclarations.hpp"
 #include "mainInterface/GeosxState.hpp"