Minor improvements for generation of dataset of reaction profiles. (#359

)

* tight criteria

* csv output

* single point refinement bool

* bug #358

* Revert "csv output"

This reverts commit 1f4c6e0.

* Revert "tight criteria"

This reverts commit 675b82e.

* template

* update changelog and readme

* parentheses

* provisional patch

---------

Co-authored-by: t-young31 <[email protected]>

README.md

@@ -97,3 +97,4 @@ If **autodE** is used in a publication please consider citing the [paper](https:
 - Daniel Hollas ([@danielhollas](https://github.com/danielhollas))
 - Nils Heunemann ([@nilsheunemann](https://github.com/NilsHeunemann))
 - Sijie Fu ([@sijiefu](https://github.com/SijieFu))
+- Javier Alfonso ([@javialra97](https://github.com/javialra97))

autode/reactions/reaction.py

@@ -119,6 +119,7 @@ def __str__(self):
     def calculate_reaction_profile(
         self,
         units: Union["Unit", str] = "kcal mol-1",
+        single_point_refinement: bool = True,
         with_complexes: bool = False,
         free_energy: bool = False,
         enthalpy: bool = False,
@@ -132,6 +133,9 @@ def calculate_reaction_profile(
         Keyword Arguments:
             units (autode.units.Unit | str):
 
+            single_point_refinement (bool): Calculate single point at a
+                                            higher level of theory
+
             with_complexes (bool): Calculate the lowest energy conformers
                                    of the reactant and product complexes
 
@@ -161,7 +165,8 @@ def calculate(reaction):
                 reaction.calculate_complexes()
             if free_energy or enthalpy:
                 reaction.calculate_thermochemical_cont()
-            reaction.calculate_single_points()
+            if single_point_refinement:
+                reaction.calculate_single_points()
             reaction.print_output()
             return None
 

autode/wrappers/G09.py

@@ -546,7 +546,9 @@ def coordinates_from(self, calc: "CalculationExecutor") -> Coordinates:
         coords: List[List[float]] = []
 
         for i, line in enumerate(calc.output.file_lines):
-            if "Input orientation" in line:
+            if "Input orientation" in line or (
+                "Standard orientation" in line and len(coords) == 0
+            ):
                 coords.clear()
                 xyz_lines = calc.output.file_lines[
                     i + 5 : i + 5 + calc.molecule.n_atoms

doc/changelog.rst

@@ -7,11 +7,11 @@ Changelog
 
 Functionality improvements
 **************************
-- ...
+- Adds a boolean option for calculating single points refinements
 
 Bug Fixes
 *********
-- ...
+- Fixes coordinate extraction in some G16 output files
 
 
 1.4.4