test the jigsaw workflow

examples/susquehanna/run_simulation_mpas.py

@@ -3,7 +3,7 @@
 
 
 from pyflowline.configuration.read_configuration_file import pyflowline_read_configuration_file
-from pyflowline.configuration.change_json_key_value import pyflowline_change_json_key_value
+from pyflowline.configuration.change_json_key_value import change_json_key_value
 from pyflowline.configuration import path_manager as pyflowline_path_manager
 
 

pyflowline/classes/_hpc.py

@@ -1,20 +1,25 @@
 import os
 import stat
 from pathlib import Path
-
-
+from pyearth.system.python.retrieve_python_environment import retrieve_python_environment
 def _pyflowline_create_hpc_job(self, sSlurm_in=None):
     """create a HPC job for this simulation
     """
     os.chdir(self.sWorkspace_output)
-
+    sConda_env_path , sConda_env_name = retrieve_python_environment()
     # part 1 python script
 
     sFilename_pyflowline = os.path.join(
         str(Path(self.sWorkspace_output)), "run_pyflowline.py")
     ofs_pyflowline = open(sFilename_pyflowline, 'w')
 
-    sLine = '#!/qfs/people/liao313/.conda/envs/pyflowline/bin/' + 'python3' + '\n'
+    sLine = '#!/qfs/people/liao313/.conda/envs/' +  sConda_env_name + '/bin/' + 'python3' + '\n'
+    ofs_pyflowline.write(sLine)
+    sLine = 'import os' + '\n'
+    ofs_pyflowline.write(sLine)
+    sLine = "os.environ['PROJ_LIB']=" + '"'+ sConda_env_path  + '/share/proj' +'"'+ '\n'
+    ofs_pyflowline.write(sLine)
+    sLine = "os.environ['LD_LIBRARY_PATH']=" + '"' + sConda_env_path + '/lib:${LD_LIBRARY_PATH}"' + '\n'
     ofs_pyflowline.write(sLine)
     sLine = 'from pyflowline.configuration.read_configuration_file import pyflowline_read_configuration_file' + '\n'
     ofs_pyflowline.write(sLine)
@@ -64,7 +69,7 @@ def _pyflowline_create_hpc_job(self, sSlurm_in=None):
     ofs.write(sLine)
     sLine = '#SBATCH --job-name=' + self.sCase + '\n'
     ofs.write(sLine)
-    sLine = '#SBATCH -t 1:00:00' + '\n'
+    sLine = '#SBATCH -t 4:00:00' + '\n'
     ofs.write(sLine)
     sLine = '#SBATCH --nodes=1' + '\n'
     ofs.write(sLine)
@@ -93,7 +98,7 @@ def _pyflowline_create_hpc_job(self, sSlurm_in=None):
     ofs.write(sLine)
     sLine = 'source /share/apps/python/miniconda4.12.0/etc/profile.d/conda.sh' + '\n'
     ofs.write(sLine)
-    sLine = 'conda activate hexwatershed' + '\n'
+    sLine = 'conda activate '+ sConda_env_name + '\n'
     ofs.write(sLine)
     sLine = 'cd $SLURM_SUBMIT_DIR\n'
     ofs.write(sLine)

pyflowline/classes/pycase.py

@@ -1,4 +1,5 @@
 import os
+import shutil
 import stat
 from pathlib import Path
 import json
@@ -559,6 +560,11 @@ def pyflowline_setup(self):
                 sWorkspace_output = self.sWorkspace_output + slash + '..'+ slash + 'jigsaw'
                 sWorkspace_output = os.path.abspath(sWorkspace_output)
 
+            #check if the folder exists
+            if os.path.exists(sWorkspace_output):
+                #delete the folder
+                shutil.rmtree(sWorkspace_output)
+
             Path(sWorkspace_output).mkdir(parents=True, exist_ok=True)
             self.sWorkspace_jigsaw = sWorkspace_output
             #then copy the binary file to the folder
@@ -567,6 +573,10 @@ def pyflowline_setup(self):
                 sFilename_new = sWorkspace_output + slash + 'jigsaw'
                 copy2(self.sFilename_dggrid, sFilename_new)
                 os.chmod(sFilename_new, stat.S_IREAD | stat.S_IWRITE | stat.S_IXUSR)
+                #make this binary as the default one and overwrite other binaries
+                # Add the destination directory ahead of the system PATH
+                os.environ["PATH"] = sWorkspace_output + os.pathsep + os.environ["PATH"]
+                # Verify that the binary is in the PATH and is the default
                 pass
             else:
                 if system == 'Windows':
@@ -600,6 +610,10 @@ def pyflowline_setup(self):
                 sWorkspace_output = self.sWorkspace_output + slash + '..'+ slash + 'dggrid'
                 sWorkspace_output = os.path.abspath(sWorkspace_output)
 
+            if os.path.exists(sWorkspace_output):
+                #delete the folder
+                shutil.rmtree(sWorkspace_output)
+
             Path(sWorkspace_output).mkdir(parents=True, exist_ok=True)
             self.sWorkspace_dggrid = sWorkspace_output
             #then copy the binary file to the folder
@@ -996,22 +1010,23 @@ def pyflowline_mesh_generation(self, iFlag_antarctic_in=None, iFlag_arctic_in=No
 
                             if self.iFlag_run_jigsaw == 1: #run the jigsaw mesh generation workflow, the user also need to provide a json configuration file for jisgaw
 
-                                sFilename_jigsaw_geometry_in = os.path.join(self.sWorkspace_jigsaw, 'jigsaw.msh')
+                                sWorkspace_jigsaw = self.sWorkspace_jigsaw
                                 aFilename_river = list()
                                 aFilename_watershed_boundary = list()
                                 aFilenamae_lake_boundary = list()
                                 aFilename_coastline = list()
 
-                                run_jigsaw_mpas_workflow(sFilename_jigsaw_geometry_in,
-                                                         aConfig_jigsaw_in = self.aConfig_jissaw,
+                                sFilename_mesh_netcdf = run_jigsaw_mpas_workflow(sWorkspace_jigsaw,
+                                                         aConfig_in = self.aConfig_jissaw,
                                     aFilename_river_in=aFilename_river,
                                     aFilename_watershed_boundary_in= aFilename_watershed_boundary,
                                     aFilenamae_lake_boundary_in = aFilenamae_lake_boundary,
                                     aFilename_coastline_in = aFilename_coastline)
 
-                                pass
+                                print('The generated MPAS mesh is: ',sFilename_mesh_netcdf)
+
                             iFlag_use_mesh_dem = self.iFlag_use_mesh_dem
-                            sFilename_mesh_netcdf = self.sFilename_mesh_netcdf
+                            self.sFilename_mesh_netcdf = sFilename_mesh_netcdf
                             dLatitude_top    = self.dLatitude_top
                             dLatitude_bot    = self.dLatitude_bot
                             dLongitude_left  = self.dLongitude_left
@@ -1028,7 +1043,7 @@ def pyflowline_mesh_generation(self, iFlag_antarctic_in=None, iFlag_arctic_in=No
                                     #create a polygon based on
                                     #read boundary
                                     pBoundary_wkt, aExtent = gdal_read_geojson_boundary(self.sFilename_mesh_boundary_geojson)
-
+                                    print(sFilename_mesh_netcdf)
                                     aMpas = create_mpas_mesh(iFlag_global, iFlag_use_mesh_dem, iFlag_save_mesh,
                                                              sFilename_mesh_netcdf,  sFilename_mesh,
                                                              iFlag_antarctic_in=iFlag_antarctic_in,

pyflowline/classes/vertex.py

@@ -75,6 +75,10 @@ def __init__(self, aParameter):
         except:
             print('Initialization of vertex failed!')
 
+        #calcualte x y z based on dLongitude and dLatitude and earth radius
+        self.dX_meter, self.dY_meter, self.dZ_meter = self.calculate_xyz()
+
+
         return
 
     def toNvector(self):
@@ -179,6 +183,22 @@ def calculate_distance(self, other):
         dDistance = calculate_distance_based_on_longitude_latitude(lon1, lat1, lon2, lat2)
         return dDistance
 
+    def calculate_xyz(self):
+        """
+        Calculate the x, y, z based on dLongitude and dLatitude
+
+        Returns:
+            tuple: The x, y, z
+        """
+        dX_meter = 0.0
+        dY_meter = 0.0
+        dZ_meter = 0.0
+        dRadius = 6371000.0 #earth radius in meter
+        dX_meter = dRadius * np.cos(self.dLatitude_radian) * np.cos(self.dLongitude_radian)
+        dY_meter = dRadius * np.cos(self.dLatitude_radian) * np.sin(self.dLongitude_radian)
+        dZ_meter = dRadius * np.sin(self.dLatitude_radian)
+        return dX_meter, dY_meter, dZ_meter
+
     def tojson(self):
         """
         Convert a vecter object to a json string