add ability to pass more flags to crest

cctk/molecule.py

@@ -1664,7 +1664,7 @@ def compute_energy(self, nprocs=1):
         energy = opt.get_energy(self, nprocs=nprocs)
         return energy
 
-    def csearch(self, nprocs=1, constraints=[], logfile=None, noncovalent=False, use_tempdir=True, gfn=2):
+    def csearch(self, nprocs=1, constraints=[], logfile=None, noncovalent=False, use_tempdir=True, gfn=2, additional_flags=None):
         """
         Optimize molecule at the GFN2-xtb level of theory.
 
@@ -1674,14 +1674,15 @@ def csearch(self, nprocs=1, constraints=[], logfile=None, noncovalent=False, use
             noncovalent (bool): whether or not to use non-covalent settings
             logfile (str): file to write ongoing ``crest`` output to
             use_tempdir (bool): write intermediate files to hidden directory (as opposed to current directory)
-            gfn (int or ``ff``): level of theory, either 1, 2, or ``ff``:w
+            gfn (int or ``ff``): level of theory, either 1, 2, or ``ff``
+            additional_flags (str): additional flags for command line
 
         Returns
             ConformationalEnsemble
         """
         import cctk.optimize as opt
         assert isinstance(nprocs, int), "nprocs must be int!"
-        return opt.csearch(molecule=self, nprocs=nprocs, constraints=constraints, noncovalent=noncovalent, logfile=logfile, use_tempdir=use_tempdir, gfn=gfn)
+        return opt.csearch(molecule=self, nprocs=nprocs, constraints=constraints, noncovalent=noncovalent, logfile=logfile, use_tempdir=use_tempdir, gfn=gfn, additional_flags=additional_flags)
 
     def num_neighbors_by_atom(self):
         """

cctk/optimize.py

@@ -121,6 +121,7 @@ def csearch(use_tempdir=True, **kwargs):
         nprocs (int): number of processors to use
         noncovalent (Bool): whether or not to use non-covalent settings
         logfile (str): file to write ongoing ``crest`` output to
+        additional_flags (str): flags to pass to command line
 
     Returns:
         cctk.ConformationalEnsemble
@@ -139,7 +140,7 @@ def csearch(use_tempdir=True, **kwargs):
 
     return ensemble
 
-def _do_csearch(molecule, directory, gfn=2, nprocs=1, logfile=None, noncovalent=False, constraints=None):
+def _do_csearch(molecule, directory, gfn=2, nprocs=1, logfile=None, noncovalent=False, constraints=None, additional_flags=None):
     assert isinstance(molecule, cctk.Molecule), "need a valid molecule!"
     assert isinstance(nprocs, int)
     assert isinstance(logfile, str)
@@ -163,6 +164,9 @@ def _do_csearch(molecule, directory, gfn=2, nprocs=1, logfile=None, noncovalent=
     else:
         command = f"crest xtb-in.xyz --gfn{gfn} --chrg {molecule.charge} --uhf {molecule.multiplicity - 1} -T {nprocs} {nci}"
 
+    if additional_flags is not None:
+        command = command + " " + additional_flags
+
     if logfile:
         with open(logfile, "w") as f:
             result = sp.run(command, stdout=f, stderr=f, cwd=directory, shell=True)