Added the option to change the name of the auxiliary file for NEB cal…

…culations

ccinput/calculation.py

@@ -9,7 +9,9 @@ class Calculation:
     """
         Holds all the data required to generate an input file. Its fields are the parameters likely to change (charge, multiplicity, xyz, calculation type...). The other parameters are contained in the Parameters class (accessed through self.parameters).
     """
-    def __init__(self, xyz, parameters, type, constraints="", nproc=0, mem=0, charge=0, multiplicity=1, name="calc", header="File created by ccinput", software=""):
+    def __init__(self, xyz, parameters, type, constraints="", nproc=0, mem=0,
+            charge=0, multiplicity=1, aux_name="calc2", name="calc",
+            header="File created by ccinput", software=""):
         self.xyz = xyz
         self.parameters = parameters
         self.type = type
@@ -58,6 +60,7 @@ def __init__(self, xyz, parameters, type, constraints="", nproc=0, mem=0, charge
         self.constraints = constraints
 
         self.name = name
+        self.aux_name = aux_name
         self.header = header
 
     def verify_charge_mult(self):
@@ -81,7 +84,9 @@ class Parameters:
         Holds all the parameters about the computational method. These parameters do not depend on the particular system (e.g. regarding the charge and multiplicity) and can be reused.
     """
 
-    def __init__(self, software, solvent="", solvation_model="", solvation_radii="", basis_set="", method="", specifications="", density_fitting="", custom_basis_sets="", **kwargs):
+    def __init__(self, software, solvent="", solvation_model="",
+            solvation_radii="", basis_set="", method="", specifications="",
+            density_fitting="", custom_basis_sets="", **kwargs):
 
         if solvent.strip() != "":
             self.solvent = get_abs_solvent(solvent)

ccinput/packages/orca.py

@@ -202,14 +202,14 @@ def handle_command(self):
         elif self.calc.type == CalcType.MEP:#### Second structure to handle
             self.command_line = "NEB "
             neb_block = """%neb
-                        product "struct2.xyz"
+                        product "{}.xyz"
                         nimages {}
                         end"""
             if 'nimages' in self.specifications:
                 nimages = self.specifications['nimages']
             else:
                 nimages = 8
-            self.blocks.append(neb_block.format(nimages))
+            self.blocks.append(neb_block.format(self.calc.aux_name, nimages))
 
         method = get_method(self.calc.parameters.method, "orca")
         if self.calc.parameters.theory_level not in ['xtb', 'semi-empirical', 'special']:

ccinput/tests/test_orca.py

@@ -1184,7 +1184,7 @@ def test_NEB(self):
         H         -1.82448        0.94856        3.28105
         *
         %neb
-        product "struct2.xyz"
+        product "calc2.xyz"
         nimages 8
         end
         %pal
@@ -1222,7 +1222,46 @@ def test_NEB2(self):
         H         -1.82448        0.94856        3.28105
         *
         %neb
-        product "struct2.xyz"
+        product "calc2.xyz"
+        nimages 12
+        end
+        %pal
+        nprocs 8
+        end
+
+        """
+        self.assertTrue(self.is_equivalent(REF, inp.input_file))
+
+    def test_NEB_aux_name(self):
+        params = {
+                'nproc': 8,
+                'type': 'Minimum Energy Path',
+                'in_file': 'elimination_substrate.xyz',
+                'auxiliary_file': 'elimination_product.xyz',
+                'software': 'ORCA',
+                'specifications': '--nimages 12',
+                'charge': -1,
+                'method': 'gfn2-xtb',
+                'aux_name': 'product',
+                }
+
+        inp = self.generate_calculation(**params)
+
+        REF = """!NEB xtb2
+        *xyz -1 1
+        C         -0.74277        0.14309        0.12635
+        C          0.71308       -0.12855       -0.16358
+        Cl         0.90703       -0.47793       -1.61303
+        H         -0.84928        0.38704        1.20767
+        H         -1.36298       -0.72675       -0.06978
+        H         -1.11617        0.99405       -0.43583
+        H          1.06397       -0.95639        0.44985
+        H          1.30839        0.75217        0.07028
+        O         -0.91651        0.74066        3.00993
+        H         -1.82448        0.94856        3.28105
+        *
+        %neb
+        product "product.xyz"
         nimages 12
         end
         %pal

ccinput/wrapper.py

@@ -20,8 +20,8 @@ def process_calculation(calc):
 def generate_calculation(software=None, type=None, method="", basis_set="", \
             solvent="", solvation_model="", solvation_radii="",  specifications="", \
             density_fitting="", custom_basis_sets="", xyz="", in_file="", \
-            constraints="", nproc=0, mem="", charge=0, multiplicity=1, name="calc", \
-            header="File created by ccinput", **kwargs):
+            constraints="", nproc=0, mem="", charge=0, multiplicity=1, aux_name="calc2", \
+            name="calc", header="File created by ccinput", **kwargs):
 
     if software is None:
         raise InvalidParameter("Specify a software package to use (software=...)")
@@ -46,7 +46,7 @@ def generate_calculation(software=None, type=None, method="", basis_set="", \
 
     calc = Calculation(xyz_structure, params, calc_type, constraints=constraints, \
             nproc=nproc, mem=mem, charge=charge, multiplicity=multiplicity, \
-            name=name, header=header, software=abs_software)
+            aux_name=aux_name, name=name, header=header, software=abs_software)
 
     return process_calculation(calc)
 
@@ -112,6 +112,9 @@ def get_parser():
     parser.add_argument('--name', default="calc", type=str,
             help='Name of the produced file (unused by some packages)')
 
+    parser.add_argument('--aux_name', default="calc2", type=str,
+            help='Name of the auxiliary file (some calculation types only)')
+
     parser.add_argument('--header', default="File created by ccinput", type=str,
             help='Header in produced file (unused by some packages)')
 
@@ -128,7 +131,7 @@ def cmd():
                 solvation_radii=args.solvation_radii,  specifications=args.specifications, density_fitting=args.density_fitting, \
                 custom_basis_sets=args.custom_basis_sets, xyz=args.xyz, in_file=args.file, constraints=args.constraints, \
                 nproc=args.nproc, mem=args.mem, charge=args.charge, multiplicity=args.mult, \
-                name=args.name, header=args.header)
+                aux_name=args.aux_name, name=args.name, header=args.header)
     except CCInputException as e:
         print("*** {} ***".format(str(e)))
         return