Merge pull request #140 from ReactionMechanismGenerator/gen_input

Added a function to save an input file (and not run ARC on spot)

arc/common.py

@@ -252,3 +252,29 @@ def log_footer(execution_time, level=logging.INFO):
     logger.log(level, '')
     logger.log(level, 'Total execution time: {0}'.format(execution_time))
     logger.log(level, 'ARC execution terminated on {0}'.format(time.asctime()))
+
+
+def save_dict_file(path, restart_dict):
+    """
+    Save an input / restart YAML file
+    """
+    yaml.add_representer(str, string_representer)
+    yaml.add_representer(unicode, unicode_representer)
+    logger.debug('Creating a restart file...')
+    content = yaml.dump(data=restart_dict, encoding='utf-8', allow_unicode=True)
+    with open(path, 'w') as f:
+        f.write(content)
+
+
+def string_representer(dumper, data):
+    """Add a custom string representer to use block literals for multiline strings"""
+    if len(data.splitlines()) > 1:
+        return dumper.represent_scalar(tag='tag:yaml.org,2002:str', value=data, style='|')
+    return dumper.represent_scalar(tag='tag:yaml.org,2002:str', value=data)
+
+
+def unicode_representer(dumper, data):
+    """Add a custom unicode representer to use block literals for multiline strings"""
+    if len(data.splitlines()) > 1:
+        return yaml.ScalarNode(tag='tag:yaml.org,2002:str', value=data, style='|')
+    return yaml.ScalarNode(tag='tag:yaml.org,2002:str', value=data)

arc/main.py

@@ -21,7 +21,8 @@
 import arc.rmgdb as rmgdb
 from arc.settings import arc_path, default_levels_of_theory, servers, valid_chars, default_job_types
 from arc.scheduler import Scheduler
-from arc.common import VERSION, read_file, time_lapse, check_ess_settings, initialize_log, log_footer, get_logger
+from arc.common import VERSION, read_file, time_lapse, check_ess_settings, initialize_log, log_footer, get_logger,\
+    save_dict_file
 from arc.arc_exceptions import InputError, SettingsError, SpeciesError
 from arc.species.species import ARCSpecies
 from arc.reaction import ARCReaction
@@ -601,6 +602,21 @@ def from_dict(self, input_dict, project=None, project_directory=None):
         else:
             self.arc_rxn_list = list()
 
+    def write_input_file(self, path=None):
+        """
+        Save the current attributes as an ARC input file.
+
+        Args:
+             path (str, unicode, optional): The full path for the generated input file.
+        """
+        if path is None:
+            path = os.path.join(self.project_directory, 'input.yml')
+        base_path = os.path.dirname(path)
+        if not os.path.isdir(base_path):
+            os.makedirs(base_path)
+        logger.info('\n\nWriting input file to {0}'.format(path))
+        save_dict_file(path=path, restart_dict=self.restart_dict)
+
     def execute(self):
         """Execute ARC"""
         logger.info('\n')

arc/scheduler.py

@@ -13,7 +13,6 @@
 import numpy as np
 import math
 import shutil
-import yaml
 import logging
 from IPython.display import display
 
@@ -23,7 +22,7 @@
 from rmgpy.reaction import Reaction
 from rmgpy.exceptions import InputError as RMGInputError
 
-from arc.common import get_logger
+from arc.common import get_logger, save_dict_file
 import arc.rmgdb as rmgdb
 from arc import plotter
 from arc import parser
@@ -1857,8 +1856,6 @@ def save_restart_dict(self):
         Update the restart_dict and save the restart.yml file
         """
         if self.save_restart and self.restart_dict is not None:
-            yaml.add_representer(str, string_representer)
-            yaml.add_representer(unicode, unicode_representer)
             logger.debug('Creating a restart file...')
             self.restart_dict['output'] = self.output
             self.restart_dict['species'] = [spc.as_dict() for spc in self.species_dict.values()]
@@ -1870,10 +1867,8 @@ def save_restart_dict(self):
                          for job_name in self.running_jobs[spc.label] if 'conformer' not in job_name]\
                         + [self.job_dict[spc.label]['conformers'][int(job_name.split('mer')[1])].as_dict()
                            for job_name in self.running_jobs[spc.label] if 'conformer' in job_name]
-            content = yaml.dump(data=self.restart_dict, encoding='utf-8', allow_unicode=True)
-            with open(self.restart_path, 'w') as f:
-                f.write(content)
             logger.debug('Dumping restart dictionary:\n{0}'.format(self.restart_dict))
+            save_dict_file(path=self.restart_path, restart_dict=self.restart_dict)
 
     def make_reaction_labels_info_file(self):
         """A helper function for creating the `reactions labels.info` file"""
@@ -1964,20 +1959,6 @@ def min_list(lst):
     return min([entry for entry in lst if entry is not None])
 
 
-def string_representer(dumper, data):
-    """Add a custom string representer to use block literals for multiline strings"""
-    if len(data.splitlines()) > 1:
-        return dumper.represent_scalar(tag='tag:yaml.org,2002:str', value=data, style='|')
-    return dumper.represent_scalar(tag='tag:yaml.org,2002:str', value=data)
-
-
-def unicode_representer(dumper, data):
-    """Add a custom unicode representer to use block literals for multiline strings"""
-    if len(data.splitlines()) > 1:
-        return yaml.ScalarNode(tag='tag:yaml.org,2002:str', value=data, style='|')
-    return yaml.ScalarNode(tag='tag:yaml.org,2002:str', value=data)
-
-
 def sum_time_delta(timedelta_list):
     """A helper function for summing datetime.timedelta objects"""
     result = datetime.timedelta(0)