fix: rewrite gaussian files

mddatasetbuilder/datasetbuilder.py

@@ -46,7 +46,7 @@ def __init__(
             clusteratom=None, bondfilename=None,
             dumpfilename="dump.reaxc", dataset_name="md", cutoff=5,
             stepinterval=1, n_clusters=10000,
-            qmkeywords="%nproc=4\n#mn15/6-31g(d,p)", nproc=None, pbc=True,
+            qmkeywords="%nproc=4\n#mn15/6-31g(d,p) force", nproc=None, pbc=True,
             fragment=True, errorfilename=None, errorlimit=0.):
         """Init the builder."""
         print(__doc__)
@@ -72,6 +72,8 @@ def __init__(
         self.writegjf = True
         self.gjfdir = f'{self.dataset_dir}_gjf'
         self.qmkeywords = qmkeywords
+        if type(self.qmkeywords) == str:
+            self.qmkeywords = [self.qmkeywords]
         self.fragment = fragment
         self._coulumbdiag = dict(map(lambda symbol: (
             symbol, atomic_numbers[symbol]**2.4/2), atomname))
@@ -292,31 +294,30 @@ def _convertgjf(self, gjffilename, takenatomidindex, atoms_whole):
         multiplicities = list(map(lambda atoms: (3 if atoms_whole[atoms].get_chemical_symbols() == [
                               "O", "O"] else(Counter(atoms_whole[atoms].get_chemical_symbols())['H'] % 2 + 1)), takenatomidindex))
         multiplicity_whole = sum(multiplicities)-len(takenatomidindex)+1
-        title = '\nGenerated by MDDatasetMaker\n'
+        multiplicity_whole_str = f'0 {multiplicity_whole}'
+        qmkeywords = self.qmkeywords
+        title = '\nGenerated by MDDatasetMaker (Author: Jinzhe Zeng)\n'
+        if len(qmkeywords) > 1:
+            connect = '\n--link1--\n'
+            chk = [f'%chk={os.path.splitext(os.path.basename(gjffilename))[0]}.chk']
+        else:
+            chk = []
         if len(takenatomidindex) == 1 or not self.fragment:
-            buff.extend((self.qmkeywords, title))
-            buff.append(f'0 {multiplicity_whole}')
+            buff.extend((*chk, qmkeywords[0], title, multiplicity_whole_str))
             buff.extend(map(lambda atom: "{} {:.5f} {:.5f} {:.5f}".format(
                 atom.symbol, *atom.position), atoms_whole))
-            buff.append('\n')
         else:
-            chk = f'%chk={os.path.splitext(os.path.basename(gjffilename))[0]}.chk'
-            connect = '\n--link1--\n'
-            kw1 = f'{self.qmkeywords} guess=fragment={len(takenatomidindex)}'
-            kw2 = f'{self.qmkeywords} force geom=chk guess=read'
-            multiplicities_str = ' '.join(
-                map(
-                    lambda
-                    multiplicity: f'0 {multiplicity}',
-                    itertools.chain(
-                        (multiplicity_whole,),
-                        multiplicities)))
-            buff.extend((chk, kw1, title, multiplicities_str))
+            qmkeywords[0] = f'{qmkeywords[0]} guess=fragment={len(takenatomidindex)}'
+            multiplicities_str = multiplicity_whole_str + ' '.join(
+                [f'0 {multiplicity}' for multiplicity in multiplicities])
+            buff.extend((*chk, qmkeywords[0], title, multiplicities_str))
             for index, atoms in enumerate(takenatomidindex, 1):
                 buff.extend(map(lambda atom: '{}(Fragment={}) {:.5f} {:.5f} {:.5f}'.format(
                     atom.symbol, index, *atom.position), atoms_whole[atoms]))
-            buff.extend((connect, chk, kw2,
-                         title, multiplicities_str, '\n'))
+        for kw in itertools.islice(qmkeywords, 1, None):
+            buff.extend((connect, *chk, kw,
+                         title, f'0 {multiplicity_whole}', '\n'))
+        buff.append('\n')
         with open(gjffilename, 'w') as f:
             f.write('\n'.join(buff))