Merge pull request #44 from GES-lbabetto/main

code now takes nproc from OMP_NUM_THREADS if available

compechem/algorithms/oneeloxidation.py

@@ -48,6 +48,9 @@ def calculate_deprotomers(
         List containing all the deprotomers with pKa < 20 for the given molecule
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     mol_list = []
 
     if conformer_search:
@@ -144,6 +147,9 @@ def generate_species(
         Species object with the singlets and radicals for the given input molecule
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     species = Species()
 
     molname = base_mol.name
@@ -250,6 +256,9 @@ def one_electron_oxidation_potentials(
     pH_step: float = 1.0,
 ):
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     os.makedirs("pickle_files", exist_ok=True)
 
     species = generate_species(

compechem/calculators/crest.py

@@ -32,6 +32,9 @@ def tautomer_search(
         list containing the found tautomers, in order of ascending energy
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     parent_dir = os.getcwd()
     logger.info(f"{mol.name}, charge {mol.charge} spin {mol.spin} - CREST tautomer search")
 
@@ -102,6 +105,9 @@ def conformer_search(
         list containing the found conformers, in order of ascending energy
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     parent_dir = os.getcwd()
     logger.info(f"{mol.name}, charge {mol.charge} spin {mol.spin} - CREST conformer search")
 
@@ -170,6 +176,9 @@ def deprotonate(
         list containing the found deprotomers, in order of ascending energy
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     parent_dir = os.getcwd()
     logger.info(f"{mol.name}, charge {mol.charge} spin {mol.spin} - CREST deprotonation")
 
@@ -247,6 +256,9 @@ def protonate(
         list containing the found protomers, in order of ascending energy
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     parent_dir = os.getcwd()
     logger.info(f"{mol.name}, charge {mol.charge} spin {mol.spin} - CREST protonation")
 
@@ -341,6 +353,9 @@ def qcg_grow(
         Molecule object containing the explicitly solvated input molecule
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     if charge is None:
         charge = solute.charge
     if spin is None:
@@ -434,6 +449,9 @@ def qcg_ensemble(
         is taken as the weighted average of all generated ensembles.
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     if charge is None:
         charge = solute.charge
     if spin is None:

compechem/calculators/orca.py

@@ -43,6 +43,9 @@ def __init__(
             optional keywords, by default ""
         """
 
+        if os.environ["OMP_NUM_THREADS"]:
+            nproc = int(os.environ["OMP_NUM_THREADS"])
+
         self.method = method
         self.basis_set = basis_set
         self.aux_basis = aux_basis

compechem/calculators/xtb.py

@@ -34,6 +34,9 @@ def __init__(
             optional keywords/flags, by default ""
         """
 
+        if os.environ["OMP_NUM_THREADS"]:
+            nproc = int(os.environ["OMP_NUM_THREADS"])
+
         self.method = method
 
         self.nproc = nproc

compechem/tools.py

@@ -295,7 +295,7 @@ def split_multixyz(mol: Molecule, file: str, suffix: str, charge: int = None, sp
 
 def reorder_energies(
     molecule_list: list,
-    nproc: int = 1,
+    nproc: int = len(os.sched_getaffinity(0)),
     maxcore: int = 350,
     method_opt: str = None,
     method_el: str = None,
@@ -325,6 +325,9 @@ def reorder_energies(
         molecule list, reordered at the new level of theory.
     """
 
+    if os.environ["OMP_NUM_THREADS"]:
+        nproc = int(os.environ["OMP_NUM_THREADS"])
+
     if method_opt is None:
         method_opt = XtbInput(nproc=nproc)
     if method_el is None:

meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "GES-comp-echem" %}
-{% set version = "0.1.29a" %}
+{% set version = "0.1.30a" %}
 
 
 

setup.py

@@ -3,7 +3,7 @@
 
 setuptools.setup(
     name="GES-comp-echem",
-    version="0.1.29a",
+    version="0.1.30a",
     description="",
     long_description="",
     packages=["compechem"],