Add sp_composite focal-point/CBS single-point protocols

arc/checks/nmd.py

@@ -2,6 +2,7 @@
 A module for checking the normal mode displacement of a TS.
 """
 
+
 import numpy as np
 from collections import Counter
 from itertools import product

arc/checks/ts.py

@@ -2,6 +2,7 @@
 A module for checking the quality of TS-related calculations, contains helper functions for Scheduler.
 """
 
+
 from itertools import product
 import os
 

arc/family/family.py

@@ -2,6 +2,7 @@
 A module for working with RMG reaction families.
 """
 
+
 from typing import TYPE_CHECKING
 import ast
 import os

arc/job/adapters/cfour.py

@@ -7,6 +7,7 @@
 http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.ListOfKeywordsInAlphabeticalOrder
 """
 
+
 import datetime
 import math
 import os

arc/job/adapters/common.py

@@ -3,13 +3,13 @@
 As such, it should not import any other ARC modules to avoid circular imports.
 """
 
+
 import datetime
 import os
 import shutil
 import sys
 import re
 
-from pprint import pformat
 from typing import TYPE_CHECKING
 
 from arc.common import get_logger
@@ -470,21 +470,26 @@ def set_job_args(args: dict | None,
     """
     Set the job args considering args from ``level`` and from ``trsh``.
 
+    The caller (e.g. :meth:`arc.scheduler.Scheduler.run_job`) is expected to
+    have already merged any ``level.args`` content into ``args`` before calling
+    this function — ``run_job`` does so via ``args.update(level.args)``. When
+    the caller passes empty ``args`` and the level supplies ``args``, we fall
+    back to ``level.args`` for convenience.
+
     Args:
-        args (dict): The job specific arguments.
+        args (dict): The job-specific arguments.
         level (Level): The level of theory.
         job_name (str): The job name.
 
     Returns:
-        dict: The initialized job specific arguments.
+        dict: The initialized job-specific arguments, guaranteed to carry the
+        ``'keyword'``, ``'block'``, and ``'trsh'`` buckets (each a dict).
     """
-    # Ignore user-specified additional job arguments when troubleshooting.
-    if args is not None and args and any(val for val in args.values()) \
-            and level is not None and level.args and any(val for val in level.args.values()):
-        logger.warning(f'When troubleshooting {job_name}, ARC ignores the following user-specified options:\n'
-                       f'{pformat(level.args)}')
-    elif not args and level is not None:
+    # Convenience fallback: empty (or None) caller-args inherits level.args.
+    if not args and level is not None and level.args is not None:
         args = level.args
+    if args is None:
+        args = dict()
     for key in ['keyword', 'block', 'trsh']:
         if key not in args.keys():
             args[key] = dict()

arc/job/adapters/common_test.py

@@ -5,6 +5,7 @@
 This module contains unit tests of the arc.job.adapters.common module
 """
 
+import logging
 import os
 import shutil
 import unittest
@@ -166,6 +167,29 @@ def test_set_job_args(self):
         args = common.set_job_args(args={'keyword': 'k1'}, level=Level(repr='CBS-QB3'), job_name='j1')
         self.assertEqual(args, {'keyword':'k1', 'block': dict(), 'trsh': dict()})
 
+    def test_set_job_args_no_spurious_warning_when_level_has_args(self):
+        """Regression: the previous "ARC ignores user-specified options" warning
+        fired on every first-run job whose level carried args, because
+        ``run_job`` had already merged ``level.args`` into ``args`` before
+        calling — nothing was actually being ignored. The warning should now
+        be silent on a normal first-run path."""
+        merged_args = {'keyword': {'core': 'core,0,0,0,0,0,0,0,0;'}, 'block': {}}
+        level_with_args = Level(method='ccsd(t)', basis='cc-pCVTZ',
+                                args=merged_args)
+        with self.assertNoLogs(logger='arc', level=logging.WARNING):
+            result = common.set_job_args(args=merged_args,
+                                         level=level_with_args, job_name='j_first_run')
+        # Args content is preserved (not dropped).
+        self.assertEqual(result['keyword'], {'core': 'core,0,0,0,0,0,0,0,0;'})
+        self.assertEqual(result['trsh'], {})  # bucket added by guarantee
+
+    def test_set_job_args_args_none_preserves_level_args(self):
+        """When the caller passes None, fall back to level.args (legacy convenience)."""
+        level = Level(method='ccsd(t)', basis='cc-pVTZ',
+                      args={'keyword': {'general': 'foo'}, 'block': {}})
+        result = common.set_job_args(args=None, level=level, job_name='j1')
+        self.assertEqual(result['keyword'], {'general': 'foo'})
+
     def test_which(self):
         """Test the which() function"""
         ans = common.which(command='python', return_bool=True, raise_error=False)

arc/job/adapters/gaussian.py

@@ -4,6 +4,7 @@
 https://gaussian.com/
 """
 
+
 import datetime
 import math
 import os

arc/job/adapters/mockter.py

@@ -2,6 +2,7 @@
 An adapter for dummy jobs, meant for testing and debugging only.
 """
 
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/molpro.py

@@ -4,6 +4,7 @@
 https://www.molpro.net/
 """
 
+
 import datetime
 import math
 import os
@@ -35,6 +36,20 @@
     settings['default_job_settings'], settings['global_ess_settings'], settings['input_filenames'], \
     settings['output_filenames'], settings['servers'], settings['submit_filenames']
 
+# Methods that native Molpro does not support but its MRCC plugin does.
+# When the level's method matches one of these (case-insensitive), the adapter
+# emits a ``{mrcc,method=...}`` plugin call instead of a bare directive that
+# Molpro's input parser would reject with "Unknown command or directive".
+# Compared against the lowercased ``Level.method``.
+MRCC_ROUTED_METHODS = frozenset({
+    'ccsdt',
+    'ccsdt(q)',
+    'ccsdtq',
+    'ccsdtq(p)',
+    'ccsdtqp',
+})
+
+
 input_template = """***,${label}
 memory,Total=${memory},m;
 
@@ -47,7 +62,7 @@
 ${cabs}
 int;
 
-{hf;${shift}
+{${hf_method};${shift}
  maxit,999;
  wf,spin=${spin},charge=${charge};
 }
@@ -229,10 +244,37 @@ def write_input_file(self) -> None:
         input_dict['spin'] = self.multiplicity - 1
         input_dict['xyz'] = xyz_to_str(self.xyz)
         input_dict['orbitals'] = '\ngprint,orbitals;\n'
+        input_dict['hf_method'] = 'hf'  # default; overridden below for open-shell MRCC
 
         if not is_restricted(self):
             input_dict['restricted'] = 'u'
 
+        if self.level.method in MRCC_ROUTED_METHODS:
+            # Restriction is implicit from the preceding {hf;...} block; the
+            # MRCC plugin call does not accept a 'u'/'r' prefix.
+            input_dict['method'] = '{mrcc,method=' + self.level.method.upper() + '}'
+            input_dict['restricted'] = ''
+            if not is_restricted(self):
+                # Open-shell wavefunction + MRCC's approximate-CC family
+                # (CCSDT(Q), CCSDTQ(P), and the perturbative-(T) variants)
+                # refuses standard ROHF orbitals:
+                #   "Approximate CC methods are not implemented for standard
+                #    ROHF orbitals! Use semicanonical orbitals!"
+                # Solution: use UHF instead of (RO)HF as the SCF reference.
+                # UHF orbitals are semicanonical by construction (alpha and
+                # beta Fock matrices are separately diagonal) and live at the
+                # default record 2100.2, which MRCC reads. MRCC then reports
+                # ``Type=UHF/CANONICAL`` and accepts.
+                #
+                # An earlier attempt at this fix prepended ``{uccsd}`` to the
+                # MRCC call. {uccsd} does run UCCSD on top of ROHF, but the
+                # post-UCCSD canonical orbitals go to a separate record while
+                # the default 2100.2 still holds the original ROHF orbitals —
+                # MRCC reads 2100.2 by default and complained. Switching the
+                # SCF reference to UHF avoids this orbital-record bookkeeping
+                # entirely.
+                input_dict['hf_method'] = 'uhf'
+
         # Job type specific options
         if self.job_type in ['opt', 'optfreq', 'conf_opt']:
             keywords = ['optg', 'root=2', 'method=qsd', 'readhess', "savexyz='geometry.xyz'"] if self.is_ts \

arc/job/adapters/molpro_test.py

@@ -97,6 +97,24 @@ def setUpClass(cls):
                                                               'closed': [1, 0, 0, 0, 0, 0, 0, 0]})],
                                   testing=True,
                                   )
+        cls.job_mrcc_ccsdt = MolproAdapter(execution_type='queue',
+                                           job_type='sp',
+                                           level=Level(method='CCSDT', basis='cc-pVDZ'),
+                                           project='test',
+                                           project_directory=os.path.join(ARC_TESTING_PATH,
+                                                                          'test_MolproAdapter_mrcc_ccsdt'),
+                                           species=[ARCSpecies(label='spc1', xyz=['O 0 0 1'], multiplicity=3)],
+                                           testing=True,
+                                           )
+        cls.job_mrcc_ccsdtq = MolproAdapter(execution_type='queue',
+                                            job_type='sp',
+                                            level=Level(method='CCSDT(Q)', basis='cc-pVDZ'),
+                                            project='test',
+                                            project_directory=os.path.join(ARC_TESTING_PATH,
+                                                                           'test_MolproAdapter_mrcc_ccsdtq'),
+                                            species=[ARCSpecies(label='spc1', xyz=['O 0 0 1'], multiplicity=1)],
+                                            testing=True,
+                                            )
 
     def test_set_cpu_and_mem(self):
         """Test assigning number of cpu's and memory"""
@@ -441,6 +459,107 @@ def test_write_mrci_input_file(self):
 """
         self.assertEqual(content_7, job_7_expected_input_file)
 
+    def test_write_input_file_mrcc_routing(self):
+        """Methods unsupported by native Molpro but supported by MRCC are routed through the MRCC plugin.
+
+        For an open-shell wavefunction, the SCF reference is switched from
+        ``{hf;...}`` (which gives Molpro's ROHF for open-shell) to
+        ``{uhf;...}``. MRCC's approximate-CC family (``CCSDT(Q)``,
+        ``CCSDTQ(P)``, and the perturbative-``(T)`` variants) refuses
+        standard ROHF orbitals with the error::
+
+            Approximate CC methods are not implemented for standard ROHF orbitals!
+            Use semicanonical orbitals!
+
+        UHF orbitals are semicanonical by construction (alpha and beta Fock
+        matrices are separately diagonal), saved to the default record 2100.2
+        which MRCC reads — MRCC then reports ``Type=UHF/CANONICAL`` and runs
+        the requested approximate-CC method.
+        """
+        self.job_mrcc_ccsdt.cpu_cores = 48
+        self.job_mrcc_ccsdt.set_input_file_memory()
+        self.job_mrcc_ccsdt.write_input_file()
+        with open(os.path.join(self.job_mrcc_ccsdt.local_path,
+                               input_filenames[self.job_mrcc_ccsdt.job_adapter]), 'r') as f:
+            content_ccsdt = f.read()
+        # spc1 has multiplicity=3 (open-shell triplet) — UHF reference expected.
+        expected_ccsdt = """***,spc1
+memory,Total=438,m;
+
+geometry={angstrom;
+O       0.00000000    0.00000000    1.00000000}
+
+gprint,orbitals;
+
+basis=cc-pvdz
+
+
+
+int;
+
+{uhf;
+ maxit,999;
+ wf,spin=2,charge=0;
+}
+
+{mrcc,method=CCSDT}
+
+
+
+---;
+
+"""
+        self.assertEqual(content_ccsdt, expected_ccsdt)
+        # Sanity: the bare directive Molpro rejects must NOT appear on its own line.
+        self.assertNotIn('\nccsdt;\n', content_ccsdt)
+        self.assertNotIn('\nuccsdt;\n', content_ccsdt)
+        # An earlier (insufficient) fix used `{uccsd}` between HF and MRCC —
+        # this contract has been replaced with UHF, so {uccsd} must NOT appear.
+        self.assertNotIn('{uccsd}', content_ccsdt)
+        # UHF must replace HF as the only SCF reference (no {hf;...} block).
+        self.assertNotIn('{hf;', content_ccsdt)
+        self.assertIn('{uhf;', content_ccsdt)
+
+        self.job_mrcc_ccsdtq.cpu_cores = 48
+        self.job_mrcc_ccsdtq.set_input_file_memory()
+        self.job_mrcc_ccsdtq.write_input_file()
+        with open(os.path.join(self.job_mrcc_ccsdtq.local_path,
+                               input_filenames[self.job_mrcc_ccsdtq.job_adapter]), 'r') as f:
+            content_ccsdtq = f.read()
+        expected_ccsdtq = """***,spc1
+memory,Total=438,m;
+
+geometry={angstrom;
+O       0.00000000    0.00000000    1.00000000}
+
+gprint,orbitals;
+
+basis=cc-pvdz
+
+
+
+int;
+
+{hf;
+ maxit,999;
+ wf,spin=0,charge=0;
+}
+
+{mrcc,method=CCSDT(Q)}
+
+
+
+---;
+
+"""
+        self.assertEqual(content_ccsdtq, expected_ccsdtq)
+        self.assertNotIn('\nccsdt(q);\n', content_ccsdtq)
+        # spc1 here has multiplicity=1 (closed-shell) — RHF gives canonical
+        # orbitals MRCC accepts directly. No UHF/UCCSD pre-step needed.
+        self.assertNotIn('{uccsd}', content_ccsdtq)
+        self.assertNotIn('{uhf;', content_ccsdtq)
+        self.assertIn('{hf;', content_ccsdtq)
+
     def test_set_files(self):
         """Test setting files"""
         job_1_files_to_upload = [{'file_name': 'submit.sub',

arc/job/adapters/obabel.py

@@ -3,6 +3,7 @@
 http://openbabel.org/docs/current/
 """
 
+
 import datetime
 import os
 import subprocess

arc/job/adapters/orca.py

@@ -4,6 +4,7 @@
 https://orcaforum.kofo.mpg.de/app.php/portal
 """
 
+
 import datetime
 import math
 import os

arc/job/adapters/psi_4.py

@@ -4,6 +4,7 @@
 https://www.psicode.org/
 """
 
+
 import datetime
 import math
 import os

arc/job/adapters/qchem.py

@@ -4,6 +4,7 @@
 https://www.q-chem.com/
 """
 
+
 import datetime
 import os
 from typing import TYPE_CHECKING

arc/job/adapters/terachem.py

@@ -4,6 +4,7 @@
 http://www.petachem.com/products.html
 """
 
+
 import datetime
 import math
 import os

arc/job/adapters/torch_ani.py

@@ -6,6 +6,7 @@
 ASE: https://wiki.fysik.dtu.dk/ase/index.html, https://core.ac.uk/download/84004505.pdf
 """
 
+
 import datetime
 import os
 from typing import TYPE_CHECKING