Implemented basic tinker parser

tinker @ ba8dd1a8

-Subproject commit eae5d87390863b72875087b1e69cfe15a516a5b9
+Subproject commit ba8dd1a8f5b4a976e84c31fd9a69bbcaf309d0f1

nomad/parsing/file_parser/basic_parser.py

@@ -62,6 +62,8 @@ class BasicParser(FairdiParser):
         self.mainfile_parser.logger = self.logger
 
         auxilliary_files = self.mainfile_parser.get('auxilliary_files', os.listdir(self.maindir))
+        # remove duplicates, maintain order
+        auxilliary_files = [f for n, f in enumerate(auxilliary_files) if f not in auxilliary_files[:n]]
         self.auxilliary_parsers = []
         for filename in auxilliary_files:
             filename = os.path.basename(filename)
@@ -133,11 +135,10 @@ class BasicParser(FairdiParser):
         for key, values in self.mainfile_parser.items():
             if values is None:
                 # get if from auxiliary files
+                values = []
                 for parser in self.auxilliary_parsers:
-                    values = parser.get(key)
-                    if values is not None:
-                        break
-            if values is None:
+                    values.extend(parser.get(key, []))
+            if values is None or len(values) == 0:
                 continue
             # set header quantities
             set_value(sec_run, key, values[0])

nomad/parsing/parsers.py

@@ -66,6 +66,7 @@ from mopacparser import MopacParser
 from namdparser import NAMDParser
 from onetepparser import OnetepParser
 from siestaparser import SiestaParser
+from tinkerparser import TinkerParser
 
 try:
     # these packages are not available without parsing extra, which is ok, if the
@@ -214,11 +215,7 @@ parsers = [
         parser_class_name='openkimparser.OpenKIMParser',
         mainfile_contents_re=r'OPENKIM'
     ),
-    LegacyParser(
-        name='parsers/tinker', code_name='TINKER', domain='dft',
-        parser_class_name='tinkerparser.TinkerParser',
-        mainfile_contents_re=r'TINKER  ---  Software Tools for Molecular Design'
-    ),
+    TinkerParser(),
     LammpsParser(),
     AmberParser(),
     GromacsParser(),