breaking: add "force" to default cli Gaussian keywords; update cli do…

…cs (#141)
tongzhugroup · Jun 20, 2022 · b111176 · b111176
1 parent c222992
commit b111176
Showing 1 changed file with 12 additions and 12 deletions.
diff --git a/mddatasetbuilder/datasetbuilder.py b/mddatasetbuilder/datasetbuilder.py
@@ -539,41 +539,41 @@ def erroriter(self):
 
 
 def _commandline():
-    parser = argparse.ArgumentParser(description='MDDatasetBuilder')
+    parser = argparse.ArgumentParser(description='MDDatasetBuilder', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument('-d', '--dumpfile', nargs='*',
                         help='Input dump file, e.g. dump.reaxc', required=True)
     parser.add_argument(
-        '-b', '--bondfile', nargs='*', help='Input bond file, e.g. bonds.reaxc')
+        '-b', '--bondfile', nargs='*', help='Input bond file, e.g. bonds.reaxc. If not given, Open Babel will be used to determine bond connectivity.')
     parser.add_argument('-a', '--atomname',
                         help='Atomic names in the trajectory, e.g. C H O',
                         nargs='*', required=True)
     parser.add_argument(
-        '-np', '--nproc', help='Number of processes', type=int)
+        '-np', '--nproc', help='Number of processes used by MDDatasetBuilder', type=int)
     parser.add_argument(
-        '-c', '--cutoff', help='Cutoff radius (default is 5.0)', type=float,
+        '-c', '--cutoff', help='Cutoff radius to take clusters from the trajectory. Note that only a complete molecule or free radical will be taken.', type=float,
         default=5.)
     parser.add_argument(
-        '-i', '--interval', help='Step interval (default is 1)', type=int,
+        '-i', '--interval', help='Step interval to collect from the trajectory. 1 means collect from every step in the trajectory.', type=int,
         default=1)
     parser.add_argument(
-        '-s', '--size', help='Dataset size (default is 10,000)', type=int,
+        '-s', '--size', help='Collected dataset size for each bond type.', type=int,
         default=10000)
     parser.add_argument(
         '-k', '--qmkeywords',
-        help='QM keywords (default is mn15/6-31g**)',
-        default="mn15/6-31g**")
+        help='Gaussian QM keywords. Note that it shloud include "force" keyword to compute forces.',
+        default="force mn15/6-31g**")
     parser.add_argument(
         '--nprocjob',
-        help='CPU number that each job uses.',
+        help='CPU number that each Gaussian job uses.',
         default=4,
         type=int
     )
     parser.add_argument(
-        '-n', '--name', help='Dataset name (default is md)', default="md")
+        '-n', '--name', help='Dataset name', default="md")
     parser.add_argument(
-        '--errorfile', help='Error file generated by modified DeePMD', nargs='*')
+        '--errorfile', help='Model deviation file generated by DeePMD-kit plugin for LAMMPS. atomic should be enabled.', nargs='*')
     parser.add_argument(
-        '-e', '--errorlimit', help='Error Limit', type=float, default=0.)
+        '-e', '--errorlimit', help='Model deviation lower threshold. Atoms whose model deviation is less than the threshold will not be collected.', type=float, default=0.)
     args = parser.parse_args()
     DatasetBuilder(
         atomname=args.atomname, bondfilename=args.bondfile,