Merge pull request #399 from ReactionMechanismGenerator/level

Organize the level of theory representation in ARC

ARC.py

@@ -19,6 +19,9 @@ def parse_command_line_arguments(command_line_args=None):
 
     Args:
         command_line_args: The command line arguments.
+
+    Returns:
+        The parsed command-line arguments by key words.
     """
 
     parser = argparse.ArgumentParser(description='Automatic Rate Calculator (ARC)')
@@ -47,18 +50,18 @@ def main():
     input_file = args.file
     project_directory = os.path.abspath(os.path.dirname(args.file))
     input_dict = read_yaml_file(path=input_file, project_directory=project_directory)
-    try:
-        input_dict['project']
-    except KeyError:
-        print('A project name must be provided!')
+    if 'project' not in list(input_dict.keys()):
+        raise ValueError('A project name must be provided!')
 
     verbose = logging.INFO
     if args.debug:
         verbose = logging.DEBUG
     elif args.quiet:
         verbose = logging.WARNING
     input_dict['verbose'] = input_dict['verbose'] if 'verbose' in input_dict else verbose
-    arc_object = ARC(input_dict=input_dict, project_directory=project_directory)
+    if 'project_directory' not in input_dict or not input_dict['project_directory']:
+        input_dict['project_directory'] = project_directory
+    arc_object = ARC(**input_dict)
     arc_object.execute()
 
 

arc/__init__.py

@@ -1,10 +1,8 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 import arc.exceptions
 import arc.main
 from arc.main import ARC
 import arc.common
+import arc.level
 import arc.parser
 import arc.plotter
 import arc.processor

arc/exceptions.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 """
 This module contains classes which extend Exception for usage in the RMG module.
 """

arc/job/__init__.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 import arc.job.inputs
 import arc.job.job
 import arc.job.local

arc/job/inputs.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 """
 parameters for input files:
 
@@ -47,7 +44,7 @@
 %mem={memory}mb
 %NProcShared={cpus}
 
-#P {job_type_1} {restricted}{method}{slash}{basis}{slash_2}{auxiliary_basis} {job_type_2} {fine} {trsh} iop(2/9=2000) {job_options_keywords} {shortcut_keywords} {dispersion}
+#P {job_type_1} {restricted}{method}{slash}{basis}{slash_2}{auxiliary_basis} {job_type_2} {fine} iop(2/9=2000) {job_options_keywords} {dispersion}
 
 name
 
@@ -59,7 +56,7 @@
 
 """,
 
-    'orca': """!{restricted}{method_class} {method} {basis} {auxiliary_basis} {job_options_keywords} {shortcut_keywords}
+    'orca': """!{restricted}{method_class} {method} {basis} {auxiliary_basis} {job_options_keywords}
 ! NRSCF # using Newton–Raphson SCF algorithm 
 !{job_type_1} 
 {job_type_2}
@@ -88,7 +85,7 @@
    JOBTYPE       {job_type_1}
    METHOD        {method}
    UNRESTRICTED  {restricted}
-   BASIS         {basis}{fine}{trsh}{constraint}
+   BASIS         {basis}{fine}{job_options_keywords}{constraint}
 $end
 {scan}
 
@@ -117,7 +114,7 @@
     'terachem': """chkfile teracheck.chk
 jobname output
 run {job_type_1}
-{trsh}
+{job_options_keywords}
 coordinates coord.xyz
 gpumem {memory}
 
@@ -175,7 +172,7 @@
 
 opticalIsomers = {optical}
 
-energy = {{'{sp_level}': Log('{sp_path}')}}
+energy = Log('{sp_path}')
 
 geometry = Log('{opt_path}')
 

arc/job/local.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 """
 A module for running jobs on the local machine.
 When transitioning to Python 3, use

arc/job/ssh.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 """
 A module for SSHing into servers.
 Used for giving commands, uploading, and downloading files.
@@ -94,7 +91,7 @@ def __exit__(self, exc_type, exc_value, exc_traceback) -> None:
     @check_connections
     def _send_command_to_server(self, 
                                 command: Union[str, list], 
-                                remote_path: Optional[str] = '',
+                                remote_path: str = '',
                                 ) -> Tuple[list, list]:
         """
         A wrapper for exec_command in paramiko.SSHClient. Send commands to the server. 
@@ -123,20 +120,20 @@ def _send_command_to_server(self,
         try:
             _, stdout, stderr = self._ssh.exec_command(command)
         except Exception as e:  # SSHException: Timeout opening channel.
-            logger.debug(f'ssh timed-out in the first trial. Got:{e}')
+            logger.debug(f'ssh timed-out in the first trial. Got: {e}')
             try:  # try again
                 _, stdout, stderr = self._ssh.exec_command(command)
             except Exception as e:
-                logger.debug(f'ssh timed-out after two trials. Got:{e}')
-                return ['',], ['ssh timed-out after two trials',]
+                logger.debug(f'ssh timed-out after two trials. Got: {e}')
+                return ['', ], ['ssh timed-out after two trials', ]
         stdout = stdout.readlines()
         stderr = stderr.readlines()
         return stdout, stderr
 
     def upload_file(self,
                     remote_file_path: str,
-                    local_file_path: Optional[str] = '',
-                    file_string: Optional[str] = '',
+                    local_file_path: str = '',
+                    file_string: str = '',
                     ) -> None:
         """
         Upload a local file or contents from a string to the remote server.
@@ -257,7 +254,7 @@ def delete_jobs(self,
         Delete all of the jobs on a specific server.
 
         Args:
-                jobs (Optional[List[str, int]]): Specific ARC job IDs to delete.
+                jobs (List[str, int], optional): Specific ARC job IDs to delete.
         """
         jobs_message = f'{len(jobs)}' if jobs is not None else 'all'
         print(f'\nDeleting {jobs_message} ARC jobs from {self.server}...')
@@ -444,18 +441,18 @@ def list_available_nodes(self) -> list:
     def change_mode(self,
                     mode: str,
                     path: str,
-                    recursive: Optional[bool] = False,
-                    remote_path: Optional[str] = '',
+                    recursive: bool = False,
+                    remote_path: str = '',
                     ) -> None:
         """
         Change the mode to a file or a directory.
 
         Args:
             mode (str): The mode change to be applied, can be either octal or symbolic.
             path (str): The path to the file or the directory to be changed.
-            recursive (Optional[bool]): Whether to recursively change the mode to all files
+            recursive (bool, optional): Whether to recursively change the mode to all files
                                         under a directory.``True`` for recursively change.
-            remote_path (Optional[str]): The directory path at which the command will be executed.
+            remote_path (str, optional): The directory path at which the command will be executed.
         """
         recursive = '-R' if recursive else ''
         command = f'chmod {recursive} {mode} {path}'
@@ -549,7 +546,9 @@ def check_job_status_in_stdout(job_id: int,
             raise ValueError(f'Unknown cluster software {servers[server]["cluster_soft"]}')
 
 
-def delete_all_arc_jobs(server_list: list, jobs: Optional[List[str]] = None) -> None:
+def delete_all_arc_jobs(server_list: list,
+                        jobs: Optional[List[str]] = None,
+                        ) -> None:
     """
     Delete all ARC-spawned jobs (with job name starting with `a` and a digit) from :list:servers
     (`servers` could also be a string of one server name)

arc/job/submit.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python3
-# encoding: utf-8
-
 """
 Submit scripts
 sorted in a dictionary with server names as keys