Fix bug related to solvent in xtb_gaussian runs

.gitignore

@@ -2,3 +2,4 @@
 src/reaction_profile_generator/__pycache__/*
 .autode_calculations
 __pycache__/
+src/ts_tools/__pycache__/*.pyc

run_scripts/run_ts_searcher.py

@@ -118,7 +118,7 @@ def obtain_transition_states(target_dir, reaction_list, xtb_external_path, solve
     setup_dir(args.target_dir)
     reaction_list = get_reaction_list(args.input_file)
     start_time = time.time()
-    xtb_external_path = f'"{os.path.join(os.getcwd(), args.xtb_external_path)}"'
+    xtb_external_path = f'{os.path.join(os.getcwd(), args.xtb_external_path)}'
 
     # run all reactions in parallel
     successful_reactions = obtain_transition_states(args.target_dir, reaction_list, 

run_scripts/run_ts_searcher_dft.py

@@ -126,7 +126,7 @@ def obtain_transition_states(target_dir, reaction_list, xtb_external_path, solve
     setup_dir(args.target_dir)
     reaction_list = get_reaction_list(args.input_file)
     start_time = time.time()
-    xtb_external_path = f'"{os.path.join(os.getcwd(), args.xtb_external_path)}"'
+    xtb_external_path = f'{os.path.join(os.getcwd(), args.xtb_external_path)}'
 
     # run all reactions in parallel
     successful_reactions = obtain_transition_states(args.target_dir, reaction_list, 

src/ts_tools/irc_search.py

@@ -333,15 +333,13 @@ def generate_gaussian_irc_input(xyz_file, output_prefix='irc_calc', method='B3LY
                 f'\n\nIRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n' 
     else:
         if solvent is not None:
-            input_content_f = f'%Chk={xyz_file.split("/")[-1][:-4]}.chk\n#p IRC(calcfc, maxpoint=50, stepsize=15, Forward) {method} SCRF=(Solvent={solvent})\n\n' \
-                f'IRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n'
-            input_content_r = f'%Chk={xyz_file.split("/")[-1][:-4]}.chk\n#p IRC(calcfc, maxpoint=50, stepsize=15, Reverse) {method} SCRF=(Solvent={solvent})\n\n' \
-                f'IRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n' 
+            external_method = f'external="{method} alpb={solvent}"'
         else:
-            input_content_f = f'%Chk={xyz_file.split("/")[-1][:-4]}.chk\n#p IRC(calcfc, maxpoint=50, stepsize=15, Forward) {method}\n\n' \
-                f'IRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n'
-            input_content_r = f'%Chk={xyz_file.split("/")[-1][:-4]}.chk\n#p IRC(calcfc, maxpoint=50, stepsize=15, Reverse) {method}\n\n' \
-                f'IRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n' 
+            external_method = f'external="{method}"'
+        input_content_f = f'%Chk={xyz_file.split("/")[-1][:-4]}.chk\n#p IRC(calcfc, maxpoint=50, stepsize=15, Forward) {external_method}\n\n' \
+            f'IRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n'
+        input_content_r = f'%Chk={xyz_file.split("/")[-1][:-4]}.chk\n#p IRC(calcfc, maxpoint=50, stepsize=15, Reverse) {external_method}\n\n' \
+            f'IRC Calculation\n\n{charge} {multiplicity}\n{"".join(atom_coords)}\n\n' 
 
     # Write the input content to a Gaussian input file -- forward
     input_filename_f = os.path.join(os.path.dirname(xyz_file), f'{output_prefix}_forward.com')

src/ts_tools/ts_optimizer.py

@@ -75,10 +75,13 @@ def determine_ts(self, xtb=True, method='UB3LYP', basis_set='6-31G**'):
             return False
 
         if xtb:
-            method = f'external={self.xtb_external_path}'
+            if self.solvent is not None:
+                method = f'external="{self.xtb_external_path} alpb={self.solvent}"'
+            else:
+                method = f'external="{self.xtb_external_path}"'
             basis_set = ''
 
-        if self.solvent is not None:
+        if self.solvent is not None and not xtb:
             extra_commands = f'opt=(ts, calcall, noeigen, nomicro) SCRF=(Solvent={self.solvent})'
         else:
             extra_commands = f'opt=(ts, calcall, noeigen, nomicro)'
@@ -292,7 +295,7 @@ def confirm_opt_transition_state(self, log_file, xtb=True, method='UB3LYP', basi
                 irc_input_file_f, irc_input_file_r = generate_gaussian_irc_input(
                     f'{os.path.splitext(log_file)[0]}.xyz',
                     output_prefix=f'{os.path.splitext(log_file)[0]}_irc',
-                    method=f'external={self.xtb_external_path}',
+                    method=self.xtb_external_path,
                     mem=self.mem, proc=self.proc,
                     solvent=self.solvent, charge=self.charge, multiplicity=self.multiplicity
                 )
@@ -321,7 +324,6 @@ def confirm_opt_transition_state(self, log_file, xtb=True, method='UB3LYP', basi
             return reaction_correct
 
         except Exception as e:
-            #print(e)
             return False
 
     def reaction_is_intramolecular(self):