some changes from a while ago...

kinbot/optimize.py

@@ -161,8 +161,8 @@ def do_optimization(self):
             if self.sconf == 1:  # conf search is finished
                 # if the conformers were already done in a previous run
                 # not clear what the purpose of these lines were
-                #if self.par['conformer_search'] == 1:
-                #    status, lowest_conf, geom, low_energy, conformers, energies = self.species.confs.check_conformers(wait=self.wait)
+                if self.par['conformer_search'] == 1:
+                    status, lowest_conf, geom, low_energy, conformers, energies = self.species.confs.check_conformers(wait=self.wait)
 
                 while self.restart <= self.max_restart:
                     # do the high level calculations

kinbot/parameters.py

@@ -144,7 +144,7 @@ def __init__(self, inpfile=None):
             # nwchem-specific parameter
             'methodclass': 'dft',  # or scf or mp2
             # Command for the quantum chemistry code
-            'qc_command': 'g09',
+            'qc_command': 'g16',
             # Quantum chemistry method to use as L1
             'method': 'b3lyp',
             # Basis set to use

kinbot/reaction_finder.py

@@ -500,6 +500,7 @@ def search_intra_OH_migration_Exocyclic_F(self, natom, atom, bond, rad):
         """ 
         This is the same as search_intra_OH_migration but for double bonds only
 
+          0 .....-2-1
         R=R~~~~~~~O-OH <==> R=R~~?? + ??~~=O
                               |
                               OH

reactions/reac_intra_OH_migration_Exocyclic_F.py

@@ -0,0 +1,58 @@
+from kinbot.reac_General import GeneralReac
+from kinbot.geometry import calc_dihedral
+
+
+class IntraOHMigrationExocyclicF(GeneralReac):
+    max_step = 14
+    scan = 0
+    skip = 1
+    dihstep = max_step - 2
+
+    def __init__(self, species, qc, par, instance, instance_name):  # special
+        GeneralReac.__init__(self, species, qc, par, instance, instance_name)
+        self.cistrans = self.instance[-1]  # (nominal) cis -1, trans -2
+        self.double = self.instance[0]  # the dangling atom with double bond
+        self.instance = self.instance[1:-1]  # cut off both
+        self.dih0, _ = calc_dihedral(self.species.geom[self.double],  # the original dihedral
+                                     self.species.geom[self.instance[0]], 
+                                     self.species.geom[self.instance[1]],
+                                     self.species.geom[self.instance[2]])
+
+    def get_constraints(self, step, geom):
+        fix = []
+        change = []
+        release = []
+        if step < self.max_step:
+            self.fix_bonds(fix)
+            #if self.cistrans == -1:
+            #    self.fix_dihedral_single(self.double, self.instance[0], self.instance[1], self.instance[2], fix)
+            #else:
+            if self.cistrans == -2:
+                val = self.dih0 + 180. / self.max_step * step
+                self.set_dihedral_single(self.double, self.instance[0], self.instance[1], self.instance[2], val, change)
+
+        if step < self.dihstep:
+            self.set_dihedrals(change, step)
+
+        elif step == self.dihstep:
+            self.fix_dihedrals(fix)
+            #self.set_dihedral_single(self.instance[0], self.instance[-1], self.instance[-2], self.instance[-3], 0., change)
+            self.set_angles(change) 
+
+        elif step == self.dihstep + 1:
+            self.release_angles(release)
+            self.release_dihedrals(release)
+
+            if self.species.atom[self.instance[0]] == 'C':
+                fval1 = 1.5
+                fval2 = 1.9
+            else:
+                fval1 = 1.7 
+                fval2 = 2.0
+
+            self.set_bond(0, -1, fval1, change)
+            self.set_bond(-2, -1, fval2, change)
+
+        self.clean_constraints(change, fix)
+
+        return step, fix, change, release