diff --git a/docs/_build/doctrees/api/tcutility.job.doctree b/docs/_build/doctrees/api/tcutility.job.doctree index 70aa03ad..050bc905 100644 Binary files a/docs/_build/doctrees/api/tcutility.job.doctree and b/docs/_build/doctrees/api/tcutility.job.doctree differ diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index b0bdce16..8d7cf867 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/html/_modules/tcutility/job/ams.html b/docs/_build/html/_modules/tcutility/job/ams.html index 54d45a65..00e3edfd 100644 --- a/docs/_build/html/_modules/tcutility/job/ams.html +++ b/docs/_build/html/_modules/tcutility/job/ams.html @@ -275,7 +275,7 @@

Source code for tcutility.job.ams

     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.single_point()
-        self.geometry_convergence('Good')
+        self.geometry_convergence()
 
     def __str__(self):
         return f'{self._task}({self._functional}/{self._basis_set}), running in {os.path.join(os.path.abspath(self.rundir), self.name)}'
@@ -380,28 +380,20 @@ 
Source code for tcutility.job.ams
 
 

 [docs]
-    def geometry_convergence(self, quality: str = None, gradients: float = 1e-5, energy: float = 1e-5, step: float = 1e-2):
+    def geometry_convergence(self, gradients: float = 1e-5, energy: float = 1e-5, step: float = 1e-2, stress: float = 5e-4):
         '''
         Set the convergence criteria for the geometry optimization.
 
         Args:
-            quality: convergence criteria preset. Must be one of [``VeryBasic``, ``Basic``, ``Normal``, ``Good``, ``VeryGood``]. 
-                Default ``None`` will not use a threshold. If it is given, it will overwrite the other arguments. 
-            gradients: the convergence criteria for the gradients during geometry optimizations. Defaults to 1e-5.
-            energy: the convergence criteria for the energy during geometry optimizations. Defaults to 1e-5.
-            step: the convergence criteria for the step-size during geometry optimizations. Defaults to 1e-2.
+            gradients: the convergence criteria for the gradients during geometry optimizations. Defaults to ``1e-5``.
+            energy: the convergence criteria for the energy during geometry optimizations. Defaults to ``1e-5``.
+            step: the convergence criteria for the step-size during geometry optimizations. Defaults to ``1e-2``.
+            stress: the convergence criteria for the stress-energy per atom during geometry optimizations. Defaults to ``5e-4``
         '''
-        if quality:
-            allowed_qualities = ['verybasic', 'basic', 'normal', 'good', 'verygood']
-            if quality.lower() not in [q.lower() for q in allowed_qualities]:
-                log.error(f'Argument "quality" must be one of {allowed_qualities}, not {quality}')
-                raise
-            self.settings.input.ams.GeometryOptimization.Convergence.Quality = quality
-        else:
-            self.settings.input.ams.GeometryOptimization.Convergence.Quality = 'Custom'
-            self.settings.input.ams.GeometryOptimization.Convergence.Gradients = gradients
-            self.settings.input.ams.GeometryOptimization.Convergence.Energy = energy
-            self.settings.input.ams.GeometryOptimization.Convergence.Step = step

+        self.settings.input.ams.GeometryOptimization.Convergence.Gradients = gradients
+        self.settings.input.ams.GeometryOptimization.Convergence.Energy = energy
+        self.settings.input.ams.GeometryOptimization.Convergence.Step = step
+        self.settings.input.ams.GeometryOptimization.Convergence.StressEnergyPerAtom = stress

 
 
 

diff --git a/docs/_build/html/api/tcutility.job.html b/docs/_build/html/api/tcutility.job.html
index b7ff7077..6a320329 100644
--- a/docs/_build/html/api/tcutility.job.html
+++ b/docs/_build/html/api/tcutility.job.html
@@ -605,16 +605,15 @@ 
Submodules
 

-geometry_convergence(quality: str = None, gradients: float = 1e-05, energy: float = 1e-05, step: float = 0.01)[source]#

+geometry_convergence(gradients: float = 1e-05, energy: float = 1e-05, step: float = 0.01, stress: float = 0.0005)[source]#
 
Set the convergence criteria for the geometry optimization.

 

 
Parameters:

 
    
-
  • quality – convergence criteria preset. Must be one of [VeryBasic, Basic, Normal, Good, VeryGood].
-Default None will not use a threshold. If it is given, it will overwrite the other arguments.
    • 
-
  • gradients – the convergence criteria for the gradients during geometry optimizations. Defaults to 1e-5.
    • 
-
  • energy – the convergence criteria for the energy during geometry optimizations. Defaults to 1e-5.
    • 
-
  • step – the convergence criteria for the step-size during geometry optimizations. Defaults to 1e-2.
    • 
+
  • gradients – the convergence criteria for the gradients during geometry optimizations. Defaults to 1e-5.
    • 
+
  • energy – the convergence criteria for the energy during geometry optimizations. Defaults to 1e-5.
    • 
+
  • step – the convergence criteria for the step-size during geometry optimizations. Defaults to 1e-2.
    • 
+
  • stress – the convergence criteria for the stress-energy per atom during geometry optimizations. Defaults to 5e-4
    • 
 

 

 

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 68772a7e..5f42cb6a 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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[[4, "tcutility.formula.molecule"]], "naive_recursive() (in module tcutility.spell_check)": [[4, "tcutility.spell_check.naive_recursive"]], "parse_molecule() (in module tcutility.formula)": [[4, "tcutility.formula.parse_molecule"]], "parse_str() (in module tcutility.molecule)": [[4, "tcutility.molecule.parse_str"]], "question (emojis attribute)": [[4, "tcutility.log.Emojis.question"]], "random_points_in_anular_sphere() (in module tcutility.geometry)": [[4, "tcutility.geometry.random_points_in_anular_sphere"]], "random_points_on_sphere() (in module tcutility.geometry)": [[4, "tcutility.geometry.random_points_on_sphere"]], "rarrow (emojis attribute)": [[4, "tcutility.log.Emojis.rarrow"]], "receive (emojis attribute)": [[4, "tcutility.log.Emojis.receive"]], "rlarrow (emojis attribute)": [[4, "tcutility.log.Emojis.rlarrow"]], "rotate() (transform method)": [[4, "tcutility.geometry.Transform.rotate"]], "rotate() (in module tcutility.geometry)": [[4, "tcutility.geometry.rotate"]], "save() (in module tcutility.molecule)": [[4, "tcutility.molecule.save"]], "sbatch() (in module tcutility.slurm)": [[4, "tcutility.slurm.sbatch"]], "scale() (transform method)": [[4, "tcutility.geometry.Transform.scale"]], "send (emojis attribute)": [[4, "tcutility.log.Emojis.send"]], "sleep (emojis attribute)": [[4, "tcutility.log.Emojis.sleep"]], "split_all() (in module tcutility.pathfunc)": [[4, "tcutility.pathfunc.split_all"]], "squeeze_list() (in module tcutility)": [[4, "tcutility.squeeze_list"]], "squeue() (in module tcutility.slurm)": [[4, "tcutility.slurm.squeue"]], "table() (in module tcutility.log)": [[4, "tcutility.log.table"]], "tcutility": [[4, "module-tcutility"]], "tcutility.cache": [[4, "module-tcutility.cache"]], "tcutility.constants": [[4, "module-tcutility.constants"]], "tcutility.formula": [[4, "module-tcutility.formula"]], "tcutility.geometry": [[4, "module-tcutility.geometry"]], "tcutility.log": [[4, "module-tcutility.log"]], "tcutility.molecule": [[4, "module-tcutility.molecule"]], "tcutility.pathfunc": [[4, "module-tcutility.pathfunc"]], "tcutility.report": [[4, "module-tcutility.report"]], "tcutility.slurm": [[4, "module-tcutility.slurm"]], "tcutility.spell_check": [[4, "module-tcutility.spell_check"]], "time_stamp() (in module tcutility.log)": [[4, "tcutility.log.time_stamp"]], "timed_cache() (in module tcutility.cache)": [[4, "tcutility.cache.timed_cache"]], "translate() (transform method)": [[4, "tcutility.geometry.Transform.translate"]], "vector_align_rotmat() (in module tcutility.geometry)": [[4, "tcutility.geometry.vector_align_rotmat"]], "wagner_fischer() (in module tcutility.spell_check)": [[4, "tcutility.spell_check.wagner_fischer"]], "wait (emojis attribute)": [[4, "tcutility.log.Emojis.wait"]], "wait_for_job() (in module tcutility.slurm)": [[4, "tcutility.slurm.wait_for_job"]], "warn() (in module tcutility.log)": [[4, "tcutility.log.warn"]], "warning (emojis attribute)": [[4, "tcutility.log.Emojis.warning"]], "workdir_info() (in module tcutility.slurm)": [[4, "tcutility.slurm.workdir_info"]], "tcutility.analysis": [[5, "module-tcutility.analysis"]], "vddcharge (class in tcutility.analysis.vdd.charge)": [[6, "tcutility.analysis.vdd.charge.VDDCharge"]], "vddchargemanager (class in tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager"]], "atom_index (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.atom_index"]], "atom_symbol (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.atom_symbol"]], "calc_dir (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.calc_dir"]], "change_unit() (vddcharge method)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.change_unit"]], "change_unit() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.change_unit"]], "change_unit_decorator() (in module tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.change_unit_decorator"]], "charge (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.charge"]], "charge_is_conserved() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.charge_is_conserved"]], "create_vdd_charge_manager() (in module tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.create_vdd_charge_manager"]], "frag_index (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.frag_index"]], "get_summed_vdd_charges() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges"]], "get_summed_vdd_charges_dataframe() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges_dataframe"]], "get_summed_vdd_charges_table() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges_table"]], "get_vdd_charges() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges"]], "get_vdd_charges_dataframe() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges_dataframe"]], "get_vdd_charges_table() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges_table"]], "irreps (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.irreps"]], "is_fragment_calculation (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.is_fragment_calculation"]], "mol_charge (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.mol_charge"]], "name (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.name"]], "plot_vdd_charges_per_atom() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.plot_vdd_charges_per_atom"]], "tcutility.analysis.vdd": [[6, "module-tcutility.analysis.vdd"]], "tcutility.analysis.vdd.charge": [[6, "module-tcutility.analysis.vdd.charge"]], "tcutility.analysis.vdd.manager": [[6, "module-tcutility.analysis.vdd.manager"]], "unit (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.unit"]], "vdd_charges (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.vdd_charges"]], "write_to_excel() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.write_to_excel"]], "write_to_txt() (vddchargemanager static method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.write_to_txt"]], "avg_relative_bond_length_delta() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.avg_relative_bond_length_delta"]], "determine_ts_reactioncoordinate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.determine_ts_reactioncoordinate"]], "tcutility.analysis.vibration": [[7, "module-tcutility.analysis.vibration"]], "tcutility.analysis.vibration.ts_vibration": [[7, "module-tcutility.analysis.vibration.ts_vibration"]], "validate_transitionstate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.validate_transitionstate"]], "color() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.color"]], "functional_name_from_path_safe_name() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.functional_name_from_path_safe_name"]], "get() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.get"]], "get() (in module tcutility.data.molecules)": [[9, "tcutility.data.molecules.get"]], "get_available_functionals() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.get_available_functionals"]], "get_molecules() (in module tcutility.data.molecules)": [[9, "tcutility.data.molecules.get_molecules"]], "parse_element() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.parse_element"]], "radius() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.radius"]], "tcutility.data": [[9, "module-tcutility.data"]], "tcutility.data.atom": [[9, "module-tcutility.data.atom"]], "tcutility.data.basis_sets": [[9, "module-tcutility.data.basis_sets"]], "tcutility.data.cosmo": [[9, "module-tcutility.data.cosmo"]], "tcutility.data.functionals": [[9, "module-tcutility.data.functionals"]], "tcutility.data.molecules": [[9, "module-tcutility.data.molecules"]], "adffragmentjob (class in tcutility.job.adf)": [[11, "tcutility.job.adf.ADFFragmentJob"]], "adfjob (class in tcutility.job.adf)": [[11, "tcutility.job.adf.ADFJob"]], "amsjob (class in tcutility.job.ams)": [[11, "tcutility.job.ams.AMSJob"]], "crestjob (class in tcutility.job.crest)": [[11, "tcutility.job.crest.CRESTJob"]], "dftbjob (class in tcutility.job.dftb)": [[11, "tcutility.job.dftb.DFTBJob"]], "irc() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.IRC"]], "job (class in tcutility.job.generic)": [[11, "tcutility.job.generic.Job"]], "nmrjob (class in tcutility.job.nmr)": [[11, "tcutility.job.nmr.NMRJob"]], "orcajob (class in tcutility.job.orca)": [[11, "tcutility.job.orca.ORCAJob"]], "qcgjob (class in tcutility.job.crest)": [[11, "tcutility.job.crest.QCGJob"]], "scf() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.SCF"]], "scf_convergence() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.SCF_convergence"]], "add_fragment() (adffragmentjob method)": [[11, "tcutility.job.adf.ADFFragmentJob.add_fragment"]], "add_nics_point() (nmrjob method)": [[11, "tcutility.job.nmr.NMRJob.add_nics_point"]], "add_postamble() (job method)": [[11, "tcutility.job.generic.Job.add_postamble"]], "add_postscript() (job method)": [[11, "tcutility.job.generic.Job.add_postscript"]], "add_preamble() (job method)": [[11, "tcutility.job.generic.Job.add_preamble"]], "alpb() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.alpb"]], "basis_set() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.basis_set"]], "best_conformer_path (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.best_conformer_path"]], "best_ensemble_path (qcgjob property)": [[11, "tcutility.job.crest.QCGJob.best_ensemble_path"]], "can_skip() (job method)": [[11, "tcutility.job.generic.Job.can_skip"]], "charge() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.charge"]], "charge() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.charge"]], "charge() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.charge"]], "conformer_directory (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.conformer_directory"]], "dependency() (job method)": [[11, "tcutility.job.generic.Job.dependency"]], "ensemble_directory (qcgjob property)": [[11, "tcutility.job.crest.QCGJob.ensemble_directory"]], "ensemble_mode() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.ensemble_mode"]], "functional() (adfjob 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\ No newline at end of file
+Search.setIndex({"docnames": ["analysis/analysis", "analysis/transition_state_analysis", "analysis/vdd_charge_analysis", "api/modules", "api/tcutility", "api/tcutility.analysis", "api/tcutility.analysis.vdd", "api/tcutility.analysis.vibration", "api/tcutility.atom_data_info", "api/tcutility.data", "api/tcutility.data.atom_data_info", "api/tcutility.job", "api/tcutility.job.postscripts", "api/tcutility.results", "api/tcutility.typing", "examples", "index", "tcutility.constants", "tcutility.job", "tcutility.results"], "filenames": ["analysis/analysis.rst", "analysis/transition_state_analysis.rst", "analysis/vdd_charge_analysis.rst", "api/modules.rst", "api/tcutility.rst", "api/tcutility.analysis.rst", "api/tcutility.analysis.vdd.rst", "api/tcutility.analysis.vibration.rst", "api/tcutility.atom_data_info.rst", "api/tcutility.data.rst", "api/tcutility.data.atom_data_info.rst", "api/tcutility.job.rst", "api/tcutility.job.postscripts.rst", "api/tcutility.results.rst", "api/tcutility.typing.rst", "examples.rst", "index.rst", "tcutility.constants.rst", "tcutility.job.rst", "tcutility.results.rst"], "titles": ["Overview of the analysis module", "Transition State Analysis module", "VDD Charge Analysis module", "tcutility", "tcutility package", "tcutility.analysis package", "tcutility.analysis.vdd package", "tcutility.analysis.vibration package", "tcutility.atom_data_info package", "tcutility.data package", "tcutility.data.atom_data_info package", "tcutility.job package", "tcutility.job.postscripts package", "tcutility.results package", "tcutility.typing package", "Examples", "TCutility v0.10.2 documentation", "tcutility.constants package", "Setup workflows with tcutility.job", "Reading a calculation"], "terms": {"thi": [0, 1, 2, 4, 7, 9, 11, 13, 16, 18, 19], "chapter": 0, "contain": [0, 1, 2, 4, 7, 9, 11, 13, 16, 17], "descript": [0, 4], "all": [0, 4, 7, 9, 11, 18], "function": [0, 2, 3, 4, 7, 11, 13, 16, 18, 19], "includ": [0, 2, 4, 9, 13, 18, 19], 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"tcutility.analysis.vibration": [[7, "module-tcutility.analysis.vibration"]], "tcutility.analysis.vibration.ts_vibration": [[7, "module-tcutility.analysis.vibration.ts_vibration"]], "validate_transitionstate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.validate_transitionstate"]], "color() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.color"]], "functional_name_from_path_safe_name() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.functional_name_from_path_safe_name"]], "get() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.get"]], "get() (in module tcutility.data.molecules)": [[9, "tcutility.data.molecules.get"]], "get_available_functionals() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.get_available_functionals"]], "get_molecules() (in module tcutility.data.molecules)": [[9, "tcutility.data.molecules.get_molecules"]], "parse_element() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.parse_element"]], "radius() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.radius"]], "tcutility.data": [[9, "module-tcutility.data"]], "tcutility.data.atom": [[9, "module-tcutility.data.atom"]], "tcutility.data.basis_sets": [[9, "module-tcutility.data.basis_sets"]], "tcutility.data.cosmo": [[9, "module-tcutility.data.cosmo"]], "tcutility.data.functionals": [[9, "module-tcutility.data.functionals"]], "tcutility.data.molecules": [[9, "module-tcutility.data.molecules"]], "adffragmentjob (class in tcutility.job.adf)": [[11, "tcutility.job.adf.ADFFragmentJob"]], "adfjob (class in tcutility.job.adf)": [[11, "tcutility.job.adf.ADFJob"]], "amsjob (class in tcutility.job.ams)": [[11, "tcutility.job.ams.AMSJob"]], "crestjob (class in tcutility.job.crest)": [[11, "tcutility.job.crest.CRESTJob"]], "dftbjob (class in tcutility.job.dftb)": [[11, "tcutility.job.dftb.DFTBJob"]], "irc() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.IRC"]], "job (class in tcutility.job.generic)": [[11, "tcutility.job.generic.Job"]], "nmrjob (class in tcutility.job.nmr)": [[11, "tcutility.job.nmr.NMRJob"]], "orcajob (class in tcutility.job.orca)": [[11, "tcutility.job.orca.ORCAJob"]], "qcgjob (class in tcutility.job.crest)": [[11, "tcutility.job.crest.QCGJob"]], "scf() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.SCF"]], "scf_convergence() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.SCF_convergence"]], "add_fragment() (adffragmentjob method)": [[11, "tcutility.job.adf.ADFFragmentJob.add_fragment"]], "add_nics_point() (nmrjob method)": [[11, "tcutility.job.nmr.NMRJob.add_nics_point"]], "add_postamble() (job method)": [[11, "tcutility.job.generic.Job.add_postamble"]], "add_postscript() (job method)": [[11, "tcutility.job.generic.Job.add_postscript"]], "add_preamble() (job method)": [[11, "tcutility.job.generic.Job.add_preamble"]], "alpb() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.alpb"]], "basis_set() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.basis_set"]], "best_conformer_path (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.best_conformer_path"]], "best_ensemble_path (qcgjob property)": [[11, "tcutility.job.crest.QCGJob.best_ensemble_path"]], "can_skip() (job method)": [[11, "tcutility.job.generic.Job.can_skip"]], "charge() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.charge"]], "charge() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.charge"]], "charge() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.charge"]], "conformer_directory (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.conformer_directory"]], "dependency() (job method)": [[11, "tcutility.job.generic.Job.dependency"]], "ensemble_directory (qcgjob property)": [[11, "tcutility.job.crest.QCGJob.ensemble_directory"]], "ensemble_mode() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.ensemble_mode"]], "functional() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.functional"]], "geometry_convergence() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.geometry_convergence"]], "get_conformer_xyz() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.get_conformer_xyz"]], "get_ensemble_xyz() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.get_ensemble_xyz"]], "get_input() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.get_input"]], "get_memory_usage() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.get_memory_usage"]], "get_rotamer_xyz() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.get_rotamer_xyz"]], "guess_fragments() (adffragmentjob method)": [[11, "tcutility.job.adf.ADFFragmentJob.guess_fragments"]], "inputfile_path (job property)": [[11, "tcutility.job.generic.Job.inputfile_path"]], "kspace() (dftbjob method)": [[11, "tcutility.job.dftb.DFTBJob.kspace"]], "md_length() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.md_length"]], "md_temperature() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.md_temperature"]], "model() (dftbjob method)": [[11, "tcutility.job.dftb.DFTBJob.model"]], "molecule() (job method)": [[11, "tcutility.job.generic.Job.molecule"]], "multiplicity() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.multiplicity"]], "multiplicity() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.multiplicity"]], "multiplicity() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.multiplicity"]], "nofix() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.nofix"]], "nsolv() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.nsolv"]], "optimization() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.optimization"]], "optimization() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.optimization"]], "output_mol_path (amsjob property)": [[11, "tcutility.job.ams.AMSJob.output_mol_path"]], "output_mol_path (job property)": [[11, "tcutility.job.generic.Job.output_mol_path"]], "quality() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.quality"]], "relativity() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.relativity"]], "rotamer_directory (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.rotamer_directory"]], "run() (adffragmentjob method)": [[11, "tcutility.job.adf.ADFFragmentJob.run"]], "run() (job method)": [[11, "tcutility.job.generic.Job.run"]], "runfile_path (job property)": [[11, "tcutility.job.generic.Job.runfile_path"]], "sbatch() (job method)": [[11, "tcutility.job.generic.Job.sbatch"]], "single_point() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.single_point"]], "single_point() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.single_point"]], "solvent() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.solvent"]], "solvent() (dftbjob method)": [[11, "tcutility.job.dftb.DFTBJob.solvent"]], "solvent() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.solvent"]], "spin_polarization() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.spin_polarization"]], "spin_polarization() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.spin_polarization"]], "spin_polarization() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.spin_polarization"]], "symmetry() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.symmetry"]], "tcutility.job": [[11, "module-tcutility.job"]], "tcutility.job.adf": [[11, "module-tcutility.job.adf"]], "tcutility.job.ams": [[11, "module-tcutility.job.ams"]], "tcutility.job.crest": [[11, "module-tcutility.job.crest"]], "tcutility.job.dftb": [[11, "module-tcutility.job.dftb"]], "tcutility.job.generic": [[11, "module-tcutility.job.generic"]], "tcutility.job.nmr": [[11, "module-tcutility.job.nmr"]], "tcutility.job.orca": [[11, "module-tcutility.job.orca"]], "transition_state() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.transition_state"]], "transition_state() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.transition_state"]], "unrestricted() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.unrestricted"]], "vibrations() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.vibrations"]], "vibrations() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.vibrations"]], "workdir (job property)": [[11, "tcutility.job.generic.Job.workdir"]], "tcutility.job.postscripts": [[12, "module-tcutility.job.postscripts"]], "tcutility.job.postscripts.clean_workdir": [[12, "module-tcutility.job.postscripts.clean_workdir"]], "tcutility.job.postscripts.split_crest_xyz": [[12, "module-tcutility.job.postscripts.split_crest_xyz"]], "tcutility.job.postscripts.write_converged_geoms": [[12, "module-tcutility.job.postscripts.write_converged_geoms"]], "result (class in tcutility.results.result)": [[13, "tcutility.results.result.Result"]], "trackkfreader (class in tcutility.results.cache)": [[13, "tcutility.results.cache.TrackKFReader"]], "as_plams_settings() (result method)": [[13, "tcutility.results.result.Result.as_plams_settings"]], "get() (in module tcutility.results.cache)": [[13, "tcutility.results.cache.get"]], "get_ams_info() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_ams_info"]], "get_ams_input() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_ams_input"]], "get_ams_version() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_ams_version"]], "get_calc_files() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_calc_files"]], "get_calc_files() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_calc_files"]], "get_calc_settings() (in module tcutility.results.adf)": [[13, "tcutility.results.adf.get_calc_settings"]], "get_calc_settings() (in module tcutility.results.dftb)": [[13, "tcutility.results.dftb.get_calc_settings"]], "get_calc_settings() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_calc_settings"]], "get_calculation_status() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_calculation_status"]], "get_calculation_status() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_calculation_status"]], "get_history() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_history"]], "get_info() (in module tcutility.results)": [[13, "tcutility.results.get_info"]], "get_info() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_info"]], "get_input() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_input"]], "get_input_blocks() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_input_blocks"]], "get_level_of_theory() (in module tcutility.results.adf)": [[13, "tcutility.results.adf.get_level_of_theory"]], "get_level_of_theory() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_level_of_theory"]], "get_molecules() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_molecules"]], "get_molecules() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_molecules"]], "get_multi_key() (result method)": [[13, "tcutility.results.result.Result.get_multi_key"]], "get_parent_tree() (result method)": [[13, "tcutility.results.result.Result.get_parent_tree"]], "get_properties() (in module tcutility.results.adf)": [[13, "tcutility.results.adf.get_properties"]], "get_properties() (in module tcutility.results.dftb)": [[13, "tcutility.results.dftb.get_properties"]], "get_properties() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_properties"]], "get_timing() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_timing"]], "get_version() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_version"]], "get_vibrations() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_vibrations"]], "items() (result method)": [[13, "tcutility.results.result.Result.items"]], "keys() (result method)": [[13, "tcutility.results.result.Result.keys"]], "prune() (result method)": [[13, "tcutility.results.result.Result.prune"]], "read() (trackkfreader method)": [[13, "tcutility.results.cache.TrackKFReader.read"]], "read() (in module tcutility.results)": [[13, "tcutility.results.read"]], "store() (in module tcutility.results.cache)": [[13, "tcutility.results.cache.store"]], "tcutility.results": [[13, "module-tcutility.results"]], "tcutility.results.adf": [[13, "module-tcutility.results.adf"]], "tcutility.results.ams": [[13, "module-tcutility.results.ams"]], "tcutility.results.cache": [[13, "module-tcutility.results.cache"]], "tcutility.results.dftb": [[13, "module-tcutility.results.dftb"]], "tcutility.results.orca": [[13, "module-tcutility.results.orca"]], "tcutility.results.result": [[13, "module-tcutility.results.result"]], "unload() (in module tcutility.results.cache)": [[13, "tcutility.results.cache.unload"]], "tcutility.typing": [[14, "module-tcutility.typing"]], "tcutility.typing.arrays": [[14, "module-tcutility.typing.arrays"]]}})
\ No newline at end of file
diff --git a/src/tcutility/job/ams.py b/src/tcutility/job/ams.py
index 3b4ec248..d8172dc7 100644
--- a/src/tcutility/job/ams.py
+++ b/src/tcutility/job/ams.py
@@ -16,7 +16,7 @@ class AMSJob(Job):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.single_point()
-        self.geometry_convergence('Good')
+        self.geometry_convergence()
 
     def __str__(self):
         return f'{self._task}({self._functional}/{self._basis_set}), running in {os.path.join(os.path.abspath(self.rundir), self.name)}'
@@ -135,28 +135,20 @@ def vibrations(self, enable: bool = True, NegativeFrequenciesTolerance: float =
         self.settings.input.ams.PESPointCharacter.NegativeFrequenciesTolerance = NegativeFrequenciesTolerance
         self.settings.input.ams.NormalModes.ReScanFreqRange = '-10000000.0 10.0'
 
-    def geometry_convergence(self, quality: str = None, gradients: float = 1e-5, energy: float = 1e-5, step: float = 1e-2):
+    def geometry_convergence(self, gradients: float = 1e-5, energy: float = 1e-5, step: float = 1e-2, stress: float = 5e-4):
         '''
         Set the convergence criteria for the geometry optimization.
 
         Args:
-            quality: convergence criteria preset. Must be one of [``VeryBasic``, ``Basic``, ``Normal``, ``Good``, ``VeryGood``]. 
-                Default ``None`` will not use a threshold. If it is given, it will overwrite the other arguments. 
-            gradients: the convergence criteria for the gradients during geometry optimizations. Defaults to 1e-5.
-            energy: the convergence criteria for the energy during geometry optimizations. Defaults to 1e-5.
-            step: the convergence criteria for the step-size during geometry optimizations. Defaults to 1e-2.
-        '''
-        if quality:
-            allowed_qualities = ['verybasic', 'basic', 'normal', 'good', 'verygood']
-            if quality.lower() not in [q.lower() for q in allowed_qualities]:
-                log.error(f'Argument "quality" must be one of {allowed_qualities}, not {quality}')
-                raise
-            self.settings.input.ams.GeometryOptimization.Convergence.Quality = quality
-        else:
-            self.settings.input.ams.GeometryOptimization.Convergence.Quality = 'Custom'
-            self.settings.input.ams.GeometryOptimization.Convergence.Gradients = gradients
-            self.settings.input.ams.GeometryOptimization.Convergence.Energy = energy
-            self.settings.input.ams.GeometryOptimization.Convergence.Step = step
+            gradients: the convergence criteria for the gradients during geometry optimizations. Defaults to ``1e-5``.
+            energy: the convergence criteria for the energy during geometry optimizations. Defaults to ``1e-5``.
+            step: the convergence criteria for the step-size during geometry optimizations. Defaults to ``1e-2``.
+            stress: the convergence criteria for the stress-energy per atom during geometry optimizations. Defaults to ``5e-4``
+        '''
+        self.settings.input.ams.GeometryOptimization.Convergence.Gradients = gradients
+        self.settings.input.ams.GeometryOptimization.Convergence.Energy = energy
+        self.settings.input.ams.GeometryOptimization.Convergence.Step = step
+        self.settings.input.ams.GeometryOptimization.Convergence.StressEnergyPerAtom = stress
 
     def charge(self, val: int):
         '''
diff --git a/src/tcutility/results/ams.py b/src/tcutility/results/ams.py
index 846b8935..5d61c033 100644
--- a/src/tcutility/results/ams.py
+++ b/src/tcutility/results/ams.py
@@ -229,6 +229,7 @@ def get_calculation_status(calc_dir: str) -> Result:
         return ret
 
     if termination_status == "IN PROGRESS":
+        ret.fatal = False
         ret.reasons.append("Calculation in progress")
         ret.name = "RUNNING"
         ret.code = "R"