Azure server

.gitignore

@@ -149,3 +149,4 @@ htmlcov/*
 #VSCode files
 .vscode/*
 .vscode/launch.json
+.code-workspace

.vscode/launch.json

@@ -1,17 +1,58 @@
-{
+{    
     // Use IntelliSense to learn about possible attributes.
     // Hover to view descriptions of existing attributes.
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
         {
-            "name": "Python: Current File",
+            "name": "Python: RMG_Env",
             "type": "python",
             "request": "launch",
-            "program": "${file}",
-            "env": {"PYDEVD_WARN_EVALUATION_TIMEOUT": "500"},
+            "program": "~/Code/RMG-Py/rmg.py",
             "console": "integratedTerminal",
-            "justMyCode": true
+            "justMyCode": false,
+            "args": ["${input:pickDir}/input.py"]
+        },
+        {
+            "name": "Python: ARC_Env",
+            "type": "python",
+            "request": "launch",
+            "program": "~/Code/ARC/ARC.py",
+            "console": "integratedTerminal",
+            "justMyCode": false,
+            "args": ["${input:pickDir}/input.yml"]
+        },
+        {
+            "name": "Python: Restart_ARC_Env",
+            "type": "python",
+            "request": "launch",
+            "program": "~/Code/ARC/ARC.py",
+            "console": "integratedTerminal",
+            "justMyCode": false,
+            "args": ["${input:pickDir}/restart.yml"]
+        },
+        {
+            "name": "Python: T3_Env",
+            "type": "python",
+            "request": "launch",
+            "program": "~/Code/T3/T3.py",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "args": ["${input:pickDir}/input.yml"]
+        }
+    ],
+    "inputs": [
+        {
+            "id": "pickDir",
+            "type": "command",
+            "command": "extension.commandvariable.file.pickFile",
+            "args":{
+                "include":"**/*",
+                "display": "fileName",
+                "description": "Subdirectory to process",
+                "showDirs": true,
+                "fromFolder":{"fixed":"/home/calvin/Code/Runs/"}
+            }
         }
     ]
-}
+}

T3.code-workspace

@@ -1,13 +1,10 @@
 {
 	"folders": [
 		{
-			"path": "."
-		},
-		{
-			"path": "../ARC"
+			"path": "../../../../.t3"
 		},
 		{
-			"path": "../RMG-Py"
+			"path": "."
 		}
 	],
 	"settings": {}

t3/main.py

@@ -52,6 +52,7 @@
 from t3.common import PROJECTS_BASE_PATH, VALID_CHARS, delete_root_rmg_log, get_species_by_label, time_lapse
 from t3.logger import Logger
 from t3.runners.rmg_runner import rmg_runner
+from t3.runners.rmg_adapter import RMGAdapter
 from t3.schema import InputBase
 from t3.simulate.factory import simulate_factory
 from t3.utils.writer import write_pdep_network_file, write_rmg_input_file
@@ -618,29 +619,29 @@ def run_rmg(self, restart_rmg: bool = False):
                 and not os.path.isdir(self.paths['RMG T3 kinetics lib']):
             self.rmg['database']['kinetics_libraries'].pop(self.rmg['database']['kinetics_libraries'].index(t3_kinetics_lib))
 
-        write_rmg_input_file(
-            rmg=self.rmg,
-            t3=self.t3,
-            iteration=self.iteration,
-            path=self.paths['RMG input'],
-            walltime=self.t3['options']['max_RMG_walltime'],
-        )
+
+    # Creating the RMG Adapter class - allow for SSH
+        # We will need self.rmg
+        rmg_adapter = RMGAdapter(
+                                rmg=self.rmg,
+                                t3=self.t3,
+                                iteration=self.iteration,
+                                paths=self.paths,
+                                logger=self.logger,
+                                walltime=self.t3['options']['max_RMG_walltime'],
+                                max_iterations=self.t3['options']['max_rmg_iterations'],
+                                verbose=self.verbose,
+                                t3_project_name=self.project,
+                                restart_rmg=restart_rmg,
+                                )
+        rmg_adapter.run_rmg()
         if not os.path.isfile(self.paths['RMG input']):
             raise ValueError(f"The RMG input file {self.paths['RMG input']} could not be written.")
         tic = datetime.datetime.now()
-
+        
         max_rmg_exceptions_allowed = self.t3['options']['max_RMG_exceptions_allowed']
-        rmg_exception_encountered = rmg_runner(rmg_input_file_path=self.paths['RMG input'],
-                                               job_log_path=self.paths['RMG job log'],
-                                               logger=self.logger,
-                                               memory=self.rmg['memory'] * 1000 if self.rmg['memory'] is not None else None,
-                                               max_iterations=self.t3['options']['max_rmg_iterations'],
-                                               verbose=self.verbose,
-                                               t3_project_name=self.project,
-                                               rmg_execution_type=self.rmg['rmg_execution_type'],
-                                               restart_rmg=restart_rmg,
-                                               )
-        if rmg_exception_encountered:
+
+        if rmg_adapter.rmg_exception_encountered:
             self.rmg_exceptions_counter += 1
             if self.rmg_exceptions_counter > max_rmg_exceptions_allowed:
                 self.logger.error(f'This is the {get_number_with_ordinal_indicator(self.rmg_exceptions_counter)} '
@@ -652,10 +653,14 @@ def run_rmg(self, restart_rmg: bool = False):
                                     f'This is the {get_number_with_ordinal_indicator(self.rmg_exceptions_counter)} '
                                     f'exception raised by RMG.\n'
                                     f'The maximum number of exceptions allowed is {max_rmg_exceptions_allowed}.')
-
         elapsed_time = time_lapse(tic)
         self.logger.info(f'RMG terminated, execution time: {elapsed_time}')
 
+
+
+
+
+    #
     def determine_species_and_reactions_to_calculate(self) -> bool:
         """
         Determine which species and reactions in the executed RMG job should be calculated.