From 8cfc3df7d817194f7f667ec2b64cb9642e504802 Mon Sep 17 00:00:00 2001 From: Mark Payne Date: Mon, 24 Jun 2019 11:26:05 -0400 Subject: [PATCH] Automatically generate a restart from seed file --- rmgpy/rmg/main.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py index a469926261d..38c1ce9910a 100644 --- a/rmgpy/rmg/main.py +++ b/rmgpy/rmg/main.py @@ -1251,7 +1251,7 @@ def makeSeedMech(self,firstTime=False): q += 1 self.name = name + str(q) - seedDir = os.path.join(self.outputDirectory,'seed') + seedDir = os.path.join(self.outputDirectory, 'seed') filter_dir = os.path.join(seedDir, 'Filters') temp_seed_dir = os.path.join(self.outputDirectory, 'seed_tmp') @@ -1360,6 +1360,15 @@ def makeSeedMech(self,firstTime=False): with open(os.path.join(filter_dir, 'family_map.yml'), 'w') as f: yaml.dump(data=family_map, stream=f) + # Generate a file for restarting from a seed mechanism if this is not a restart job + if firstTime and (not self.restart_seed_path): + with open(self.inputFile, 'r') as f: + input_text = f.readlines() + + with open(os.path.join(self.outputDirectory, 'restart_from_seed.py'), 'w') as f: + f.write('restartFromSeed(\n path=\'seed\'\n)\n\n') + f.write(''.join(input_text)) + # Finally, delete the seed mechanism from the previous iteration (if it exists) if os.path.exists(temp_seed_dir): shutil.rmtree(temp_seed_dir)