Update dev/gp3_ipea (#146)

marcelmbn · jonathan-schoeps · web-flow · commit dfa2ea20f591 · 2026-01-22T15:43:01.000+01:00
* Remove need for constraints and specific compositions (#143) * initial implementation of constraint input Signed-off-by: Marcel Mueller <marcel.mueller@thch.uni-bonn.de> * improve code Signed-off-by: Marcel Mueller <marcel.mueller@thch.uni-bonn.de> * added CHANGELOG and formatted it Signed-off-by: Marcel Mueller <marcel.mueller@thch.uni-bonn.de> * remove need for fixed composition and exact number of atoms Signed-off-by: Marcel Mueller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Marcel Mueller <marcel.mueller@thch.uni-bonn.de> * If constrains are set in the refinement step now the same constrains are set in the postprocess via the usage of xtb with orca as a driver. (#145) * If constrains are set during refinement the postprocess step now uses xtb with orca as a driver to set the same constrains during postprocess. Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Implemented tests for the orca as a driver run when distance constrains are enabled Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Fix for the windows python crash in testsuit Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Try to fix for the windows python crash in testsuit Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Removal of copied code Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Implementation of comments from the Pull request, less complicated optimize in orca.py Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Implemented requested changes and updated tests Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * changed the test_orca.py testsuite to match the test_xtb.py tests Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> --------- Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> --------- Signed-off-by: Marcel Mueller <marcel.mueller@thch.uni-bonn.de> Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> Co-authored-by: Jonathan Schöps <106986430+jonathan-schoeps@users.noreply.github.com>
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Distance constraints for xTB (normalized parsing, config validation, runtime enforcement, and optional integration test).
+- Distance constrains for ORCA (uses xTB as as driver to set the same distance constrains for the postprocess).
 
 ## [0.6.0] - 2025-04-01
 
diff --git a/mindlessgen.toml b/mindlessgen.toml
@@ -106,6 +106,8 @@ basis = "def2-SVP"
 gridsize = 1
 # > Maximum number of SCF cycles: Options: <int>
 scf_cycles = 100
+# > Use xTB as an external ORCA driver to keep distance constraints during postprocessing. Options: <bool>
+use_xtb_driver = false
 
 [turbomole]
 # > Path to the ridft executable. The name `ridft` is automatically searched for. Options: <str | Path>
diff --git a/src/mindlessgen/generator/main.py b/src/mindlessgen/generator/main.py
@@ -508,7 +508,7 @@ def setup_engines(
                 raise ImportError("orca not found.")
         except ImportError as e:
             raise ImportError("orca not found.") from e
-        return ORCA(path, cfg.orca)
+        return ORCA(path, cfg.orca, cfg.xtb)
     elif engine_type == "turbomole":
         try:
             jobex_path = jobex_path_func(cfg.turbomole.jobex_path)
diff --git a/src/mindlessgen/prog/config.py b/src/mindlessgen/prog/config.py
@@ -1179,6 +1179,7 @@ def __init__(self: ORCAConfig) -> None:
         self._basis: str = "def2-SVP"
         self._gridsize: int = 1
         self._scf_cycles: int = 100
+        self._use_xtb_driver: bool = False
 
     def get_identifier(self) -> str:
         return "orca"
@@ -1269,6 +1270,22 @@ def scf_cycles(self, max_scf_cycles: int):
             raise ValueError("Max SCF cycles should be greater than 0.")
         self._scf_cycles = max_scf_cycles
 
+    @property
+    def use_xtb_driver(self) -> bool:
+        """
+        Determine whether the xTB external driver can be used during post-processing.
+        """
+        return self._use_xtb_driver
+
+    @use_xtb_driver.setter
+    def use_xtb_driver(self, enabled: bool):
+        """
+        Enable or disable the usage of the xTB external driver during post-processing.
+        """
+        if not isinstance(enabled, bool):
+            raise TypeError("use_xtb_driver should be a boolean.")
+        self._use_xtb_driver = enabled
+
 
 class TURBOMOLEConfig(BaseConfig):
     """
diff --git a/src/mindlessgen/qm/orca.py b/src/mindlessgen/qm/orca.py
@@ -8,16 +8,19 @@
 from tempfile import TemporaryDirectory
 
 from ..molecules import Molecule
-from ..prog import ORCAConfig
+from ..prog import ORCAConfig, XTBConfig
 from .base import QMMethod
+from .xtb import XTB, get_xtb_path
 
 
 class ORCA(QMMethod):
     """
     This class handles all interaction with the ORCA external dependency.
     """
 
-    def __init__(self, path: str | Path, orcacfg: ORCAConfig) -> None:
+    def __init__(
+        self, path: str | Path, orcacfg: ORCAConfig, xtb_config: XTBConfig | None = None
+    ) -> None:
         """
         Initialize the ORCA class.
         """
@@ -28,6 +31,7 @@ def __init__(self, path: str | Path, orcacfg: ORCAConfig) -> None:
         else:
             raise TypeError("orca_path should be a string or a Path object.")
         self.cfg = orcacfg
+        self.xtb_cfg = xtb_config
         # must be explicitly initialized in current parallelization implementation
         # as accessing parent class variables might not be possible
         self.tmp_dir = self.__class__.get_temporary_directory()
@@ -51,24 +55,38 @@ def optimize(
             # NOTE: "prefix" and "dir" are valid keyword arguments for TemporaryDirectory
             temp_path = Path(temp_dir).resolve()
             # write the molecule to a temporary file
-            molecule.write_xyz_to_file(temp_path / "molecule.xyz")
+            xyz_filename = "molecule.xyz"
+            molecule.write_xyz_to_file(temp_path / xyz_filename)
 
+            if self.cfg.use_xtb_driver:
+                optimized_molecule = self.optimize_xtb_driver(
+                    temp_path=temp_path,
+                    molecule=molecule,
+                    xyz_filename=xyz_filename,
+                    ncores=ncores,
+                    max_cycles=max_cycles,
+                    verbosity=verbosity,
+                )
+                return optimized_molecule
             inputname = "orca_opt.inp"
             orca_input = self._gen_input(
-                molecule, "molecule.xyz", ncores, True, max_cycles
+                molecule,
+                xyz_filename,
+                temp_path,
+                ncores,
+                True,
+                max_cycles,
             )
             if verbosity > 1:
                 print("ORCA input file:\n##################")
                 print(orca_input)
                 print("##################")
             with open(temp_path / inputname, "w", encoding="utf8") as f:
                 f.write(orca_input)
-
             # run orca
             arguments = [
                 inputname,
             ]
-
             orca_log_out, orca_log_err, return_code = self._run(
                 temp_path=temp_path, arguments=arguments
             )
@@ -78,7 +96,6 @@ def optimize(
                 raise RuntimeError(
                     f"ORCA failed with return code {return_code}:\n{orca_log_err}"
                 )
-
             # read the optimized molecule from the output file
             xyzfile = Path(temp_path / inputname).resolve().with_suffix(".xyz")
             optimized_molecule = molecule.copy()
@@ -103,10 +120,10 @@ def singlepoint(self, molecule: Molecule, ncores: int, verbosity: int = 1) -> st
 
             # write the input file
             inputname = "orca.inp"
-            orca_input = self._gen_input(molecule, molfile, ncores)
+            orca_input = self._gen_input(molecule, molfile, temp_path, ncores)
             if verbosity > 1:
                 print("ORCA input file:\n##################")
-                print(self._gen_input(molecule, molfile, ncores))
+                print(self._gen_input(molecule, molfile, temp_path, ncores))
                 print("##################")
             with open(temp_path / inputname, "w", encoding="utf8") as f:
                 f.write(orca_input)
@@ -174,6 +191,7 @@ def _gen_input(
         self,
         molecule: Molecule,
         xyzfile: str,
+        _temp_path: Path,
         ncores: int,
         optimization: bool = False,
         opt_cycles: int | None = None,
@@ -200,6 +218,145 @@ def _gen_input(
         orca_input += f"* xyzfile {molecule.charge} {molecule.uhf + 1} {xyzfile}\n"
         return orca_input
 
+    def optimize_xtb_driver(
+        self,
+        temp_path: Path,
+        molecule: Molecule,
+        xyz_filename: str,
+        ncores: int,
+        max_cycles: int | None = None,
+        verbosity: int = 1,
+    ) -> Molecule:
+        """
+        Optimize a molecule using ORCA through the xTB external driver.
+        """
+
+        xtb_input = temp_path / "xtb.inp"
+        inputname = "orca_opt.inp"
+        self._write_xtb_input(molecule, xtb_input, inputname)
+        orca_input = self._gen_input_xtb_driver(
+            molecule,
+            xyz_filename,
+            temp_path,
+            ncores,
+            True,
+            max_cycles,
+        )
+        if verbosity > 1:
+            print("ORCA input file:\n##################")
+            print(orca_input)
+            print("##################")
+            print("XTB input file:\n##################")
+            print(xtb_input)
+            print("##################")
+        with open(temp_path / inputname, "w", encoding="utf8") as f:
+            f.write(orca_input)
+        # run orca with xTB as a driver
+        orca_log_out, orca_log_err, return_code = self._run_xtb_driver(
+            temp_path=temp_path,
+            geometry_filename=xyz_filename,
+            xcontrol_name=xtb_input.name,
+            ncores=ncores,
+        )
+        if verbosity > 2:
+            print(orca_log_out)
+        if return_code != 0:
+            raise RuntimeError(
+                f"ORCA failed with return code {return_code}:\n{orca_log_err}"
+            )
+
+        # read the optimized molecule from the output file
+        xyzfile = temp_path / "xtbopt.xyz"
+        if not xyzfile.exists():
+            raise RuntimeError(
+                "xTB-driven ORCA optimization did not produce 'xtbopt.xyz'."
+            )
+        optimized_molecule = molecule.copy()
+        optimized_molecule.read_xyz_from_file(xyzfile)
+        return optimized_molecule
+
+    def _run_xtb_driver(
+        self,
+        temp_path: Path,
+        geometry_filename: str,
+        xcontrol_name: str,
+        ncores: int,
+    ) -> tuple[str, str, int]:
+        """
+        Run the optimization through the xTB external driver when constraints are requested.
+        """
+        xtb_executable = get_xtb_path()
+        if self.xtb_cfg is None:
+            raise RuntimeError(
+                "xTB driver requested but no xTB configuration provided."
+            )
+        xtb_runner = XTB(path=xtb_executable, xtb_config=self.xtb_cfg)
+        arguments = [
+            geometry_filename,
+            "--opt",
+        ]
+        opt_level = getattr(self.cfg, "optlevel", None)
+        if opt_level not in (None, ""):
+            arguments.append(str(opt_level))
+        arguments.extend(["--orca", "-I", xcontrol_name])
+        xtb_log_out, xtb_log_err, returncode = xtb_runner._run(
+            temp_path=temp_path, arguments=arguments
+        )
+        return xtb_log_out, xtb_log_err, returncode
+
+    def _write_xtb_input(
+        self, molecule: Molecule, xtb_input: Path, input_file: str
+    ) -> None:
+        """
+        Write the xcontrol file containing constraints and ORCA driver info.
+        """
+        if not self.xtb_cfg:
+            raise RuntimeError(
+                "xTB configuration missing but constraints were requested."
+            )
+        xtb_path = get_xtb_path()
+        xtb_writer = XTB(xtb_path, self.xtb_cfg)
+        generated = xtb_writer._prepare_distance_constraint_file(
+            molecule, xtb_input.parent
+        )
+        if not generated:
+            raise RuntimeError(
+                "xTB driver requested but no distance constraints were generated."
+            )
+        with xtb_input.open("a", encoding="utf8") as handle:
+            handle.write("$external\n")
+            handle.write(f"  orca input file= {input_file}\n")
+            handle.write(f"  orca bin= {self.path}\n")
+            handle.write("$end\n")
+
+    def _gen_input_xtb_driver(
+        self,
+        molecule: Molecule,
+        xyzfile: str,
+        temp_path: Path,
+        ncores: int,
+        optimization: bool = False,
+        opt_cycles: int | None = None,
+    ) -> str:
+        """
+        Generate a default input file for ORCA.
+        """
+        orca_input = f"! {self.cfg.functional} {self.cfg.basis}\n"
+        orca_input += f"! DEFGRID{self.cfg.gridsize}\n"
+        orca_input += "! MiniPrint\n"
+        orca_input += "! NoTRAH\n"
+        orca_input += "! Engrad\n"
+        # "! AutoAux" keyword for super-heavy elements as def2/J ends at Rn
+        if any(atom >= 86 for atom in molecule.ati):
+            orca_input += "! AutoAux\n"
+        orca_input += f"%scf\n\tMaxIter {self.cfg.scf_cycles}\n"
+        if not optimization:
+            orca_input += "\tConvergence Medium\n"
+        orca_input += "end\n"
+        orca_input += f"%pal nprocs {ncores} end\n\n"
+        orca_input += f"* xyzfile {molecule.charge} {molecule.uhf + 1} {xyzfile}\n"
+        return orca_input
+
 
 # TODO: 1. Convert this to a @staticmethod of Class ORCA
 #       2. Rename to `get_method` or similar to enable an abstract interface
diff --git a/test/test_qm/test_orca.py b/test/test_qm/test_orca.py
