diff --git a/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree b/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree index 54d49255..060da115 100644 Binary files a/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree and b/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree differ diff --git a/docs/_build/doctrees/api/tcutility.data.doctree b/docs/_build/doctrees/api/tcutility.data.doctree index 906b5848..5e3bb8b3 100644 Binary files a/docs/_build/doctrees/api/tcutility.data.doctree and b/docs/_build/doctrees/api/tcutility.data.doctree differ diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 5ee82e8c..2a6ac28f 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/data/atom.html b/docs/_build/html/_modules/tcutility/data/atom.html index 8f3d9857..06d2b355 100644 --- a/docs/_build/html/_modules/tcutility/data/atom.html +++ b/docs/_build/html/_modules/tcutility/data/atom.html @@ -259,7 +259,7 @@

Source code for tcutility.data.atom

 
 
 # read data
-data_dir = pl.Path(__file__).parents[0] / "atom_data_info"
+data_dir = pl.Path(__file__).parents[0] / "_atom_data_info"
 
 with open(data_dir / "name.txt") as data:
     lines = data.readlines()
diff --git a/docs/_build/html/_sources/api/tcutility.data.rst.txt b/docs/_build/html/_sources/api/tcutility.data.rst.txt
index 44b0121c..3fb5b4e8 100644
--- a/docs/_build/html/_sources/api/tcutility.data.rst.txt
+++ b/docs/_build/html/_sources/api/tcutility.data.rst.txt
@@ -1,14 +1,6 @@
 tcutility.data package
 ======================
 
-Subpackages
------------
-
-.. toctree::
-   :maxdepth: 4
-
-   tcutility.data.atom_data_info
-
 Submodules
 ----------
 
diff --git a/docs/_build/html/api/modules.html b/docs/_build/html/api/modules.html
index 33727b6c..5abcebaf 100644
--- a/docs/_build/html/api/modules.html
+++ b/docs/_build/html/api/modules.html
@@ -216,11 +216,8 @@
 
  • tcutility.analysis.vibration package
    • 
 
 
-
  • tcutility.data package
-
    • 
-
  • tcutility.job package
      
+
    • tcutility.data package
      • 
+
    • tcutility.job package
 
      • 
@@ -294,7 +291,6 @@ 
      tcutilitytcutility.data package
 
-
    • tcutility.data package
-
      • 
-
    • tcutility.job package
 
      • 
-
    • tcutility.data package
-
      • 
-
    • tcutility.job package
 
      • 
-
    • tcutility.data package
-
      • 
-
    • tcutility.job package
 
      • 
-
    • tcutility.data package
-
      • 
-
    • tcutility.job package
        
+
      • tcutility.data package
        • 
+
      • tcutility.job package
 
        • 
@@ -290,17 +287,6 @@
                   
   
        
 
        tcutility.data package#
        
-
        
-
        Subpackages#
        
-
        
-
-
        
-
        
 
        
 
        Submodules#
        
 
        
@@ -470,11 +456,11 @@ 
        Submodules
       
        
         
        next
        
-        
        tcutility.data.atom_data_info package
        
+        
        tcutility.job package
        
       
        
       
             
@@ -496,7 +482,6 @@ 
        Submodules
     
          
-
        • Subpackages
          • 
 
        • Submodules
          • 
 
        • tcutility.data.atom module
            
 
          • parse_element()
            • 
diff --git a/docs/_build/html/api/tcutility.html b/docs/_build/html/api/tcutility.html
index 2c12952d..40669bce 100644
--- a/docs/_build/html/api/tcutility.html
+++ b/docs/_build/html/api/tcutility.html
@@ -217,11 +217,8 @@
 
          • tcutility.analysis.vibration package
            • 
 
          
 
          • 
-
        • tcutility.data package
-
          • 
-
        • tcutility.job package
            
+
          • tcutility.data package
            • 
+
          • tcutility.job package
 
            • 
@@ -313,13 +310,6 @@ 
            Subpackagestcutility.data package
              
-
            • Subpackages
-
              • 
 
            • Submodules
              • 
 
            • tcutility.data.atom module
                
 
              • parse_element()
                • 
diff --git a/docs/_build/html/api/tcutility.job.html b/docs/_build/html/api/tcutility.job.html
index d0fd76fa..2524e698 100644
--- a/docs/_build/html/api/tcutility.job.html
+++ b/docs/_build/html/api/tcutility.job.html
@@ -48,7 +48,7 @@
     
     
     
-    
+    
   
   
   
@@ -216,11 +216,8 @@
 
              • tcutility.analysis.vibration package
                • 
 
              
 
              • 
-
            • tcutility.data package
-
              • 
-
            • tcutility.job package
 
              • 
-
            • tcutility.data package
-
              • 
-
            • tcutility.job package
 
              • 
-
            • tcutility.data package
-
              • 
-
            • tcutility.job package
 
              • 
-
            • tcutility.data package
-
              • 
-
            • tcutility.job package
                
+
              • tcutility.data package
                • 
+
              • tcutility.job package
 
                • 
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
index 719ef83e..10e1ecc8 100644
--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -649,8 +649,6 @@ 
                M
                
         
              • tcutility.data
 
                • 
         
              • tcutility.data.atom
-
                • 
-        
              • tcutility.data.atom_data_info
 
                • 
         
              • tcutility.data.basis_sets
 
                • 
@@ -994,13 +992,6 @@ 
                T
                
 
       
-      
              • 
-    tcutility.data.atom_data_info
-
-      
                • 
       
              • 
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
index 2a323d52..b3c0072e 100644
Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ
diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html
index 8a44dafc..df03f7c4 100644
--- a/docs/_build/html/py-modindex.html
+++ b/docs/_build/html/py-modindex.html
@@ -287,11 +287,6 @@ 
                Python Module Index
                
           
        tcutility.data.atom
        
-     
-       
-          
-       tcutility.data.atom_data_info
-       
      
        
           
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 5dde47ad..427ff282 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
-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 v0.9.0 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], "exampl": [0, 1, 4, 9, 11, 13], "usag": [0, 4, 13, 18, 19], "below": [0, 4, 13, 18, 19], "i": [0, 1, 2, 4, 6, 7, 9, 11, 13, 16, 18, 19], "list": [0, 2, 4, 6, 7, 11, 13], "avail": [0, 4, 6, 9, 11, 18], "transit": [0, 7, 11, 16], "state": [0, 7, 11, 16], "vdd": [0, 1, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "charg": [0, 1, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "requir": 0, "api": [0, 18], "tcutil": [0, 1, 2, 19], "result": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19], "read": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18], "manag": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "vddchargemanag": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "vddcharg": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "change_unit": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "v0": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19], "7": 2, "2": [2, 4, 11, 13, 18], "text": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "cm": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "1": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "kcal": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "mol": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "km": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19], "code": [1, 4, 13, 16, 18], "document": [1, 4, 11, 18], "still": [1, 4, 11], "under": [1, 16], "construct": [1, 11], "when": [2, 4, 9, 11, 13, 18], "calcul": [2, 4, 7, 11, 13, 16, 18], "perform": [2, 13], "ha": [2, 4, 7, 11, 13], "succesfulli": [2, 11], "finish": [2, 3, 4, 11, 13, 18], "can": [2, 4, 6, 9, 11, 13, 18, 19], "us": [2, 4, 6, 7, 9, 11, 13, 16, 17, 18, 19], "extract": 2, "voronoi": [2, 13], "deform": [2, 13], "densiti": [2, 11, 18], "The": [2, 4, 6, 9, 11, 13, 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"tcutility.atom_data_info package": [[8, "tcutility-atom-data-info-package"]], "tcutility.data package": [[9, "tcutility-data-package"]], "tcutility.data.atom module": [[9, "module-tcutility.data.atom"]], "tcutility.data.basis_sets module": [[9, "module-tcutility.data.basis_sets"]], "tcutility.data.cosmo module": [[9, "module-tcutility.data.cosmo"]], "tcutility.data.functionals module": [[9, "module-tcutility.data.functionals"]], "tcutility.data.molecules module": [[9, "module-tcutility.data.molecules"]], "tcutility.data.atom_data_info package": [[10, "tcutility-data-atom-data-info-package"]], "tcutility.job package": [[11, "tcutility-job-package"], [15, "tcutility-job-package"]], "tcutility.job.adf module": [[11, "module-tcutility.job.adf"]], "tcutility.job.ams module": [[11, "module-tcutility.job.ams"]], "tcutility.job.crest module": [[11, "module-tcutility.job.crest"]], "tcutility.job.dftb module": [[11, "module-tcutility.job.dftb"]], "tcutility.job.generic module": [[11, "module-tcutility.job.generic"]], "tcutility.job.nmr module": [[11, "module-tcutility.job.nmr"]], "tcutility.job.orca module": [[11, "module-tcutility.job.orca"]], "tcutility.job.postscripts package": [[12, "tcutility-job-postscripts-package"]], "tcutility.job.postscripts.clean_workdir module": [[12, "module-tcutility.job.postscripts.clean_workdir"]], "tcutility.job.postscripts.split_crest_xyz module": [[12, "module-tcutility.job.postscripts.split_crest_xyz"]], "tcutility.job.postscripts.write_converged_geoms module": [[12, "module-tcutility.job.postscripts.write_converged_geoms"]], "tcutility.results package": [[13, "tcutility-results-package"], [15, "tcutility-results-package"]], "tcutility.results.adf module": [[13, "module-tcutility.results.adf"]], "tcutility.results.ams module": [[13, "module-tcutility.results.ams"]], "tcutility.results.cache module": [[13, "module-tcutility.results.cache"]], "tcutility.results.dftb module": [[13, "module-tcutility.results.dftb"]], 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(class in tcutility.log)": [[4, "tcutility.log.Emojis"]], "kabschtransform (class in tcutility.geometry)": [[4, "tcutility.geometry.KabschTransform"]], "noprint (class in tcutility.log)": [[4, "tcutility.log.NoPrint"]], "rmsd() (in module tcutility.geometry)": [[4, "tcutility.geometry.RMSD"]], "si (class in tcutility.report)": [[4, "tcutility.report.SI"]], "transform (class in tcutility.geometry)": [[4, "tcutility.geometry.Transform"]], "add_heading() (si method)": [[4, "tcutility.report.SI.add_heading"]], "add_xyz() (si method)": [[4, "tcutility.report.SI.add_xyz"]], "angstrom (emojis attribute)": [[4, "tcutility.log.Emojis.angstrom"]], "apply() (transform method)": [[4, "tcutility.geometry.Transform.apply"]], "apply_rotmat() (in module tcutility.geometry)": [[4, "tcutility.geometry.apply_rotmat"]], "boxed() (in module tcutility.log)": [[4, "tcutility.log.boxed"]], "cache() (in module tcutility.cache)": [[4, "tcutility.cache.cache"]], "caller_name() (in module tcutility.log)": [[4, "tcutility.log.caller_name"]], "cancel (emojis attribute)": [[4, "tcutility.log.Emojis.cancel"]], "check() (in module tcutility.spell_check)": [[4, "tcutility.spell_check.check"]], "combine_transforms() (transform method)": [[4, "tcutility.geometry.Transform.combine_transforms"]], "critical() (in module tcutility.log)": [[4, "tcutility.log.critical"]], "debug() (in module tcutility.log)": [[4, "tcutility.log.debug"]], "empty (emojis attribute)": [[4, "tcutility.log.Emojis.empty"]], "ensure_2d() (in module tcutility)": [[4, "tcutility.ensure_2d"]], "ensure_list() (in module tcutility)": [[4, "tcutility.ensure_list"]], "error() (in module tcutility.log)": [[4, "tcutility.log.error"]], "fail (emojis attribute)": [[4, "tcutility.log.Emojis.fail"]], "finish (emojis attribute)": [[4, "tcutility.log.Emojis.finish"]], "flow() (in module tcutility.log)": [[4, "tcutility.log.flow"]], "get_closest() (in module tcutility.spell_check)": [[4, "tcutility.spell_check.get_closest"]], "get_rotmat() (in 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"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"]], "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.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"]], "tcutility.data.atom_data_info": [[10, "module-tcutility.data.atom_data_info"]], "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_convergence() (adfjob method)": [[11, 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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 v0.9.0 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.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_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"]], "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"]], "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/docs/api/tcutility.data.rst b/docs/api/tcutility.data.rst
index 44b0121c..3fb5b4e8 100644
--- a/docs/api/tcutility.data.rst
+++ b/docs/api/tcutility.data.rst
@@ -1,14 +1,6 @@
 tcutility.data package
 ======================
 
-Subpackages
------------
-
-.. toctree::
-   :maxdepth: 4
-
-   tcutility.data.atom_data_info
-
 Submodules
 ----------