Merge pull request #61 from GES-lbabetto/main

minor bugfixes and improvements

Author: lbabetto

compechem/algorithms/__init__.py

@@ -1 +1,2 @@
-from compechem.algorithms.oneeloxidation import one_electron_oxidation_potentials
+from compechem.algorithms.oneeloxidation import one_electron_oxidation_potential
+from compechem.algorithms.oneeloxidation import generate_potential_data

compechem/algorithms/oneeloxidation.py

@@ -1,5 +1,7 @@
 import os, pickle
+from unicodedata import name
 import numpy as np
+from collections import namedtuple
 
 from compechem.config import get_ncores
 from compechem.systems import System
@@ -17,6 +19,7 @@
 
 xtb = XtbInput()
 
+Point = namedtuple("Point", "pH V")
 
 class Species:
     """Class containing the singlets and radicals lists"""
@@ -408,10 +411,10 @@ def generate_potential_data(
 
         last_potential = potential
 
-        yield current_pH, potential
+        yield Point(current_pH, potential)
 
 
-def one_electron_oxidation_potentials(
+def one_electron_oxidation_potential(
     system: System,
     method,
     ncores: int = None,

compechem/tools/externalutilities.py

@@ -84,7 +84,7 @@ def compress_dftb_trajectory(filename, md_out="md.out", geo_xyz="geo_end.xyz"):
                 if linenum % (atomcount + 2) == 0:
                     out.write(f"{line.split()[0]}\n")
                 if linenum % (atomcount + 2) == 1:
-                    out.write(f"Step: {line.split()[0]} Energy: {energies.pop(0)} Eh\n")
+                    out.write(f"Step: {line.split()[2]} Energy: {energies.pop(0)} Eh\n")
                 if linenum % (atomcount + 2) > 1:
                     out.write(
                         f"{line.split()[0]} {round(float(line.split()[1]),3)} {round(float(line.split()[2]),3)} {round(float(line.split()[3]),3)}\n"

compechem/wrappers/crest.py

@@ -65,7 +65,7 @@ def tautomer_search(
                 tautomer.write_xyz(f"{tautomer.name}.xyz")
                 if cyclization_check("geom.xyz", f"{tautomer.name}.xyz") is True:
                     logger.warning(
-                        f"Cyclization change spotted for {tautomer.name}. Removing from list."
+                        f"Cyclization change spotted for {tautomer.name}, charge {mol.charge} spin {mol.spin}. Removing from list."
                     )
                     add_flag(
                         mol,
@@ -81,7 +81,7 @@ def tautomer_search(
 
         else:
             logger.warning(
-                f"No tautomers possible for {mol.name}. Ignoring tautomer search."
+                f"No tautomers possible for {mol.name}, charge {mol.charge} spin {mol.spin}. Ignoring tautomer search."
             )
             add_flag(mol, "No possible tautomers. Tautomer search was ignored.")
             process_output(mol, "CREST", "tautomers", mol.charge, mol.spin)
@@ -146,7 +146,7 @@ def conformer_search(
                 conformer.write_xyz(f"{conformer.name}.xyz")
                 if cyclization_check("geom.xyz", f"{conformer.name}.xyz") is True:
                     logger.warning(
-                        f"Cyclization change spotted for {conformer.name}. Removing from list."
+                        f"Cyclization change spotted for {conformer.name}, charge {mol.charge} spin {mol.spin}. Removing from list."
                     )
                     add_flag(
                         mol,
@@ -162,7 +162,7 @@ def conformer_search(
 
         else:
             logger.error(
-                f"{mol.name}, conformer search failed. Reverting to original molecule."
+                f"{mol.name}, charge {mol.charge} spin {mol.spin}, conformer search failed. Reverting to original molecule."
             )
             add_flag(mol, "Conformer search failed.")
             return [mol]
@@ -223,7 +223,7 @@ def deprotonate(
                 deprotomer.write_xyz(f"{deprotomer.name}.xyz")
                 if cyclization_check("geom.xyz", f"{deprotomer.name}.xyz") is True:
                     logger.warning(
-                        f"Cyclization change spotted for {deprotomer.name}. Removing from list."
+                        f"Cyclization change spotted for {deprotomer.name}, charge {mol.charge} spin {mol.spin}. Removing from list."
                     )
                     add_flag(
                         mol,
@@ -239,12 +239,16 @@ def deprotonate(
             if deprotomers:
                 return deprotomers
             else:
-                logger.error(f"{mol.name}, no suitable deprotomers found.")
+                logger.error(
+                    f"{mol.name}, charge {mol.charge} spin {mol.spin}, no suitable deprotomers found."
+                )
                 add_flag(mol, "No suitable deprotomers.")
                 return None
 
         else:
-            logger.error(f"{mol.name}, deprotomer search failed.")
+            logger.error(
+                f"{mol.name}, charge {mol.charge} spin {mol.spin}, deprotomer search failed."
+            )
             add_flag(mol, "Deprotomer search failed.")
             return None
 
@@ -305,7 +309,7 @@ def protonate(
                 protomer.write_xyz(f"{protomer.name}.xyz")
                 if cyclization_check("geom.xyz", f"{protomer.name}.xyz") is True:
                     logger.warning(
-                        f"Cyclization change spotted for {protomer.name}. Removing from list."
+                        f"Cyclization change spotted for {protomer.name}, charge {mol.charge} spin {mol.spin}. Removing from list."
                     )
                     add_flag(
                         mol,
@@ -321,11 +325,15 @@ def protonate(
             if protomers:
                 return protomers
             else:
-                logger.error(f"{mol.name}, no suitable protomers found.")
+                logger.error(
+                    f"{mol.name}, charge {mol.charge} spin {mol.spin}, no suitable protomers found."
+                )
                 add_flag(mol, "No suitable protomers.")
                 return None
         else:
-            logger.error(f"{mol.name}, protomer search failed.")
+            logger.error(
+                f"{mol.name}, charge {mol.charge} spin {mol.spin}, protomer search failed."
+            )
             add_flag(mol, "Protomer search failed.")
             return None
 
@@ -406,7 +414,9 @@ def qcg_grow(
         try:
             cluster.update_geometry("grow/cluster.xyz")
         except:
-            logger.error(f"{solute.name}, cluster growth failed.")
+            logger.error(
+                f"{solute.name}, charge {solute.charge} spin {solute.spin}, cluster growth failed."
+            )
             add_flag(solute, "Cluster growth failed.")
             return None
 
@@ -507,7 +517,9 @@ def qcg_ensemble(
             )
 
         except:
-            logger.error(f"{solute.name}, cluster growth failed.")
+            logger.error(
+                f"{solute.name}, charge {solute.charge} spin {solute.spin}, cluster growth failed."
+            )
             add_flag(solute, "Cluster growth failed.")
             return None
 

docs/intro.md

@@ -1,6 +1,6 @@
 # GES-comp-echem User Guide
 
-Version 0.2.0
+Version 0.2.1
 
 This is the user guide for the `GES-comp-echem` Python module. The philosophy of this software package is to provide: i) a simple interface for carrying out calculations with a number of computational chemistry programs, and ii) a selection of higher level algorithms for calculating experimental observables.
 

meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "GES-comp-echem" %}
-{% set version = "0.2.0a" %}
+{% set version = "0.2.1" %}
 
 
 
@@ -45,4 +45,4 @@ about:
 
 extra:
   recipe-maintainers:
-    - GES-compchem
+    - GES-compchem

setup.py

@@ -3,7 +3,7 @@
 
 setuptools.setup(
     name="GES-comp-echem",
-    version="0.2.0",
+    version="0.2.1",
     description="",
     long_description="",
     packages=["compechem"],