Add support for directory for Q-Chem (#318)

* Add support for `directory` for Q-Chem

* fix

* pre-commit auto-fixes

* Update handlers.py

* fix

* fix

* fix

* fix

* fix

* fix

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

custodian/qchem/handlers.py

@@ -1,4 +1,4 @@
-"""This module implements new error handlers for QChem runs."""
+"""This module implements error handlers for QChem runs."""
 
 import os
 
@@ -55,9 +55,10 @@ def __init__(
         self.errors = []
         self.opt_error_history = []
 
-    def check(self):
+    def check(self, directory="./"):
         """Checks output file for errors."""
-        self.outdata = QCOutput(self.output_file).data
+        self._output_path = os.path.join(directory, self.output_file)
+        self.outdata = QCOutput(self._output_path).data
         self.errors = self.outdata.get("errors")
         self.warnings = self.outdata.get("warnings")
         # If we aren't out of optimization cycles, but we were in the past, reset the history
@@ -68,11 +69,13 @@ def check(self):
             return False
         return len(self.errors) > 0
 
-    def correct(self):
+    def correct(self, directory="./"):
         """Perform corrections."""
-        backup({self.input_file, self.output_file})
+        self._input_path = os.path.join(directory, self.input_file)
+        self._output_path = os.path.join(directory, self.output_file)
+        backup({self._input_path, self._output_path})
         actions = []
-        self.qcinp = QCInput.from_file(self.input_file)
+        self.qcinp = QCInput.from_file(self._input_path)
 
         if "SCF_failed_to_converge" in self.errors:
             # Given defaults, the first handlers will typically be skipped.
@@ -380,6 +383,7 @@ def correct(self):
         ) and str(self.qcinp.geom_opt["initial_hessian"]).lower() == "read":
             del self.qcinp.geom_opt["initial_hessian"]
             actions.append({"initial_hessian": "deleted"})
-        os.replace(self.input_file, f"{self.input_file}.last")
-        self.qcinp.write_file(self.input_file)
+
+        os.replace(self._input_path, os.path.join(directory, self.input_file + ".last"))
+        self.qcinp.write_file(self._input_path)
         return {"errors": self.errors, "warnings": self.warnings, "actions": actions}

custodian/qchem/jobs.py

@@ -5,6 +5,7 @@
 import shutil
 import subprocess
 import warnings
+from pathlib import Path
 
 import numpy as np
 from pymatgen.core import Molecule
@@ -99,26 +100,29 @@ def __init__(
             print("SLURM_CPUS_ON_NODE not in environment")
 
     @property
-    def current_command(self):
+    def current_command(self, directory="./"):
         """The command to run QChem."""
+        self._input_path = os.path.join(directory, self.input_file)
+        self._output_path = os.path.join(directory, self.output_file)
         multi = {"openmp": "-nt", "mpi": "-np"}
         if self.multimode not in multi:
             raise RuntimeError("ERROR: Multimode should only be set to openmp or mpi")
-        command = [multi[self.multimode], str(self.max_cores), self.input_file, self.output_file, "scratch"]
+        command = [multi[self.multimode], str(self.max_cores), self._input_path, self._output_path, "scratch"]
         command = self.qchem_command + command
         return " ".join(command)
 
-    def setup(self):
+    def setup(self, directory="./"):
         """Sets up environment variables necessary to efficiently run QChem."""
+        self._input_path = os.path.join(directory, self.input_file)
         if self.backup:
-            shutil.copy(self.input_file, f"{self.input_file}.orig")
+            shutil.copy(self._input_path, os.path.join(directory, f"{self.input_file}.orig"))
         if self.multimode == "openmp":
             os.environ["QCTHREADS"] = str(self.max_cores)
             os.environ["OMP_NUM_THREADS"] = str(self.max_cores)
-        os.environ["QCSCRATCH"] = os.getcwd()
+        os.environ["QCSCRATCH"] = str(Path(directory).resolve())
         if self.calc_loc is not None:
             os.environ["QCLOCALSCR"] = self.calc_loc
-        qcinp = QCInput.from_file(self.input_file)
+        qcinp = QCInput.from_file(self._input_path)
         if (
             qcinp.rem.get("run_nbo6", "none").lower() == "true"
             or qcinp.rem.get("nbo_external", "none").lower() == "true"
@@ -128,17 +132,20 @@ def setup(self):
                 raise RuntimeError("Trying to run NBO7 without providing NBOEXE in fworker! Exiting...")
             os.environ["NBOEXE"] = self.nboexe
 
-    def postprocess(self):
+    def postprocess(self, directory="./"):
         """Renames and removes scratch files after running QChem."""
+        self._input_path = os.path.join(directory, self.input_file)
+        self._output_path = os.path.join(directory, self.output_file)
+        self._qclog_path = os.path.join(directory, self.qclog_file)
         scratch_dir = os.path.join(os.environ["QCSCRATCH"], "scratch")
         for file in ["HESS", "GRAD", "plots/dens.0.cube", "131.0", "53.0", "132.0"]:
             file_path = os.path.join(scratch_dir, file)
             if os.path.isfile(file_path):
-                shutil.copy(file_path, os.getcwd())
+                shutil.copy(file_path, directory)
         if self.suffix != "":
-            shutil.move(self.input_file, self.input_file + self.suffix)
-            shutil.move(self.output_file, self.output_file + self.suffix)
-            shutil.move(self.qclog_file, self.qclog_file + self.suffix)
+            shutil.move(self._input_path, os.path.join(directory, self.input_file + self.suffix))
+            shutil.move(self._output_path, os.path.join(directory, self.output_file + self.suffix))
+            shutil.move(self._qclog_path, os.path.join(directory, self.qclog_file + self.suffix))
             for file in ["HESS", "GRAD", "dens.0.cube"]:
                 if os.path.isfile(file):
                     shutil.move(file, file + self.suffix)

tests/qchem/test_jobs.py

@@ -44,10 +44,10 @@ def tearDown(self):
     def test_defaults(self):
         with patch("custodian.qchem.jobs.shutil.copy") as copy_patch:
             job = QCJob(qchem_command="qchem", max_cores=32)
-            assert job.current_command == "qchem -nt 32 mol.qin mol.qout scratch"
+            assert job.current_command == "qchem -nt 32 ./mol.qin ./mol.qout scratch"
             job.setup()
-            assert copy_patch.call_args_list[0][0][0] == "mol.qin"
-            assert copy_patch.call_args_list[0][0][1] == "mol.qin.orig"
+            assert copy_patch.call_args_list[0][0][0] == "./mol.qin"
+            assert copy_patch.call_args_list[0][0][1] == "./mol.qin.orig"
             assert os.environ["QCSCRATCH"] == os.getcwd()
             assert os.environ["QCTHREADS"] == "32"
             assert os.environ["OMP_NUM_THREADS"] == "32"
@@ -63,7 +63,7 @@ def test_not_defaults(self):
             nboexe="/path/to/nbo7.i4.exe",
             backup=False,
         )
-        assert job.current_command == "qchem -slurm -np 12 different.qin not_default.qout scratch"
+        assert job.current_command == "qchem -slurm -np 12 ./different.qin ./not_default.qout scratch"
         job.setup()
         assert os.environ["QCSCRATCH"] == os.getcwd()
         assert os.environ["QCLOCALSCR"] == "/not/default/"
@@ -78,10 +78,10 @@ def test_save_scratch(self):
                 calc_loc="/tmp/scratch",
                 save_scratch=True,
             )
-            assert job.current_command == "qchem -slurm -nt 32 mol.qin mol.qout scratch"
+            assert job.current_command == "qchem -slurm -nt 32 ./mol.qin ./mol.qout scratch"
             job.setup()
-            assert copy_patch.call_args_list[0][0][0] == "mol.qin"
-            assert copy_patch.call_args_list[0][0][1] == "mol.qin.orig"
+            assert copy_patch.call_args_list[0][0][0] == "./mol.qin"
+            assert copy_patch.call_args_list[0][0][1] == "./mol.qin.orig"
             assert os.environ["QCSCRATCH"] == os.getcwd()
             assert os.environ["QCTHREADS"] == "32"
             assert os.environ["OMP_NUM_THREADS"] == "32"