Merge branch 'main' into pdep_spin_conservation

Author: donerancl

arkane/ess/adapter.py

@@ -45,10 +45,11 @@ class ESSAdapter(ABC):
     An abstract ESS Adapter class
     """
 
-    def __init__(self, path, check_for_errors=True):
+    def __init__(self, path, check_for_errors=True, scratch_directory=None):
         self.path = path
         if check_for_errors:
             self.check_for_errors()
+        self.scratch_directory = scratch_directory if scratch_directory is not None else os.path.join(os.path.abspath('.'), str('scratch'))
 
     @abstractmethod
     def check_for_errors(self):
@@ -174,7 +175,7 @@ def get_symmetry_properties(self):
         coordinates, atom_numbers, _ = self.load_geometry()
         unique_id = '0'  # Just some name that the SYMMETRY code gives to one of its jobs
         # Scratch directory that the SYMMETRY code writes its files in:
-        scr_dir = os.path.join(os.path.abspath('.'), str('scratch'))
+        scr_dir = self.scratch_directory
         if not os.path.exists(scr_dir):
             os.makedirs(scr_dir)
         try:

arkane/ess/factory.py

@@ -61,6 +61,7 @@ def register_ess_adapter(ess: str,
 
 def ess_factory(fullpath: str,
                 check_for_errors: bool = True,
+                scratch_directory: str = None,
                 ) -> Type[ESSAdapter]:
     """
     A factory generating the ESS adapter corresponding to ``ess_adapter``.
@@ -106,4 +107,4 @@ def ess_factory(fullpath: str,
         raise InputError(f'The file at {fullpath} could not be identified as a '
                          f'Gaussian, Molpro, Orca, Psi4, QChem, or TeraChem log file.')
 
-    return _registered_ess_adapters[ess_name](path=fullpath, check_for_errors=check_for_errors)
+    return _registered_ess_adapters[ess_name](path=fullpath, check_for_errors=check_for_errors, scratch_directory=scratch_directory)

environment.yml

@@ -16,7 +16,7 @@
 #   made dependency list more explicit (@JacksonBurns).
 # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
 #   moved diffeqpy to pip and (temporarily) removed chemprop
-#
+# - August 4, 2024 Restricted pyrms to <2
 name: rmg_env
 channels:
   - defaults
@@ -88,7 +88,7 @@ dependencies:
 # packages we maintain
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
-  - rmg::pyrms
+  - rmg::pyrms <2
   - rmg::symmetry
 
 # packages we would like to stop maintaining (and why)

rmgpy/molecule/draw.py

@@ -1644,6 +1644,7 @@ def __init__(self, options=None):
         self.options = MoleculeDrawer().options.copy()
         self.options.update({
             'arrowLength': 36,
+            'drawReversibleArrow': True
         })
         if options:
             self.options.update(options)
@@ -1744,11 +1745,30 @@ def draw(self, reaction, file_format, path=None):
         rxn_cr.save()
         rxn_cr.set_source_rgba(0.0, 0.0, 0.0, 1.0)
         rxn_cr.set_line_width(1.0)
-        rxn_cr.move_to(rxn_x + 8, rxn_top + 0.5 * rxn_height)
-        rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height)
-        rxn_cr.move_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height - 3.0)
-        rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height)
-        rxn_cr.line_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height + 3.0)
+        if self.options['drawReversibleArrow'] and reaction.reversible:  # draw double harpoons
+            TOP_HARPOON_Y = rxn_top + (0.5 * rxn_height - 1.75)
+            BOTTOM_HARPOON_Y = rxn_top + (0.5 * rxn_height + 1.75)
+
+            # Draw top harpoon
+            rxn_cr.move_to(rxn_x + 8, TOP_HARPOON_Y)
+            rxn_cr.line_to(rxn_x + arrow_width - 8, TOP_HARPOON_Y)
+            rxn_cr.move_to(rxn_x + arrow_width - 14, TOP_HARPOON_Y - 3.0)
+            rxn_cr.line_to(rxn_x + arrow_width - 8, TOP_HARPOON_Y)
+
+            # Draw bottom harpoon
+            rxn_cr.move_to(rxn_x + arrow_width - 8, BOTTOM_HARPOON_Y)
+            rxn_cr.line_to(rxn_x + 8, BOTTOM_HARPOON_Y)
+            rxn_cr.move_to(rxn_x + 14, BOTTOM_HARPOON_Y + 3.0)
+            rxn_cr.line_to(rxn_x + 8, BOTTOM_HARPOON_Y)
+
+            
+        else:  # draw forward arrow
+            rxn_cr.move_to(rxn_x + 8, rxn_top + 0.5 * rxn_height)
+            rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height)
+            rxn_cr.move_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height - 3.0)
+            rxn_cr.line_to(rxn_x + arrow_width - 8, rxn_top + 0.5 * rxn_height)
+            rxn_cr.line_to(rxn_x + arrow_width - 14, rxn_top + 0.5 * rxn_height + 3.0)
+
         rxn_cr.stroke()
         rxn_cr.restore()
         rxn_x += arrow_width