diff --git a/_sources/advanced.rst.txt b/_sources/advanced.rst.txt index 86953f9b98..91bbe5f2aa 100644 --- a/_sources/advanced.rst.txt +++ b/_sources/advanced.rst.txt @@ -18,7 +18,7 @@ __ xyz_format_ Specify a specific job type to execute ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ To run ARC with a particular job type **only**, set ``specific_job_type`` to the job type you want. -Currently, ARC supports the following job types: ``conformers``, ``opt``, ``fine``, ``freq``, +Currently, ARC supports the following job types: ``conf_opt``, ``conf_sp``, ``opt``, ``fine``, ``freq``, ``sp``, ``rotors``, ``onedmin``, ``orbitals``, ``bde``, ``irc``. Note: ``specific_job_type`` takes higher precedence than ``job_types``. If you specify both attributes, ARC will @@ -53,7 +53,8 @@ a level of theory. ARC allows users to specify a level of theory per job type, w as described below. Job types for which levels of theory may be specified (otherwise ARC will assume defaults values) are: - - ``conformer_level`` + - ``conformer_opt_level`` + - ``conformer_sp_level`` - ``ts_guess_level`` - ``opt_level`` - ``freq_level`` @@ -72,9 +73,9 @@ arguments to be defined: ``method``, ``basis``, ``auxiliary_basis``, ``dispersio For example:: - conformer_level: {'method': 'b3lyp', - 'basis': '6-31g(d,p)', - 'dispersion': 'empiricaldispersion=gd3bj', + conformer_opt_level: {'method': 'b3lyp', + 'basis': '6-31g(d,p)', + 'dispersion': 'empiricaldispersion=gd3bj', } specifies ``b3lyp/6-31g(d,p)`` model chemistry along with the @@ -101,8 +102,8 @@ THe following are examples for **equivalent** definitions:: opt_level = 'apfd/def2tzvp' opt_level = {'method': 'apfd', 'basis': 'def2tzvp'} - conformer_level = 'PM6' - conformer_level = {'method': 'PM6'} + conformer_opt_level = 'PM6' + conformer_opt_level = {'method': 'PM6'} Note that the ``cabs`` and ``solvation_scheme_level`` arguments currently have no effect @@ -499,7 +500,7 @@ but just be an arbitrary conformer with the required chiralities to be preserved Don't generate conformers for specific species ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The ``conformers`` entry in the ``job_types`` dictionary is a global flag, +The ``conf_opt`` entry in the ``job_types`` dictionary is a global flag, affecting conformer generation of all species in the project. If you'd like to avoid generating conformers just for selected species, @@ -616,7 +617,7 @@ The above code generated the following input file:: job_types: rotors: true - conformers: true + conf_opt: true fine: true freq: true lennard_jones: false @@ -715,7 +716,7 @@ Below is an example requesting all hydrogen BDEs in ethanol including the ``C--O job_types: rotors: true - conformers: true + conf_opt: true fine: true freq: true opt: true diff --git a/_sources/examples.rst.txt b/_sources/examples.rst.txt index 86899a99cb..7c9b245cf4 100644 --- a/_sources/examples.rst.txt +++ b/_sources/examples.rst.txt @@ -28,7 +28,7 @@ Multiple species are defined using SMILES / an XYZ list / InChI:: job_types: rotors: true - conformers: true + conf_opt: true fine: true freq: true opt: true @@ -130,7 +130,7 @@ The same example as above ran via the API (e.g., in `Jupyter notebooks`__) would max_job_time=24, level_of_theory='CCSD(T)-F12/cc-pVTZ-F12//wb97xd/def2tzvp', scan_level='wb97xd/def2tzvp', - conformer_level='b3lyp/6-311+g(d,p)', + conformer_opt_level='b3lyp/6-311+g(d,p)', species=[spc1, spc2, spc3], ) diff --git a/advanced.html b/advanced.html index 93b93984a5..211f3dc1d8 100644 --- a/advanced.html +++ b/advanced.html @@ -204,7 +204,7 @@

Specify a specific job type to execute

To run ARC with a particular job type only, set specific_job_type to the job type you want. -Currently, ARC supports the following job types: conformers, opt, fine, freq, +Currently, ARC supports the following job types: conf_opt, conf_sp, opt, fine, freq, sp, rotors, onedmin, orbitals, bde, irc.

Note: specific_job_type takes higher precedence than job_types. If you specify both attributes, ARC will dismiss the given job_types and will only populate the job_types dictionary using the given @@ -234,7 +234,8 @@

Specify a specific job type to execute -

  • conformer_level

    • +

  • conformer_opt_level

    • +

  • conformer_sp_level

  • ts_guess_level

  • opt_level

  • freq_level

    • @@ -252,9 +253,9 @@

    Specify a specific job type to executecabs (complementary auxiliary basis set for F12 calculations), software, software_version (not used), solvation_method, solvent, solvation_scheme_level, args.

    For example:

    -
    conformer_level: {'method': 'b3lyp',
-                  'basis': '6-31g(d,p)',
-                  'dispersion': 'empiricaldispersion=gd3bj',
+
    conformer_opt_level: {'method': 'b3lyp',
+                      'basis': '6-31g(d,p)',
+                      'dispersion': 'empiricaldispersion=gd3bj',
                   }
 
    
 
    
@@ -278,8 +279,8 @@ 
    Specify a specific job type to execute
    opt_level = 'apfd/def2tzvp'
 opt_level = {'method': 'apfd', 'basis': 'def2tzvp'}
 
-conformer_level = 'PM6'
-conformer_level = {'method': 'PM6'}
+conformer_opt_level = 'PM6'
+conformer_opt_level = {'method': 'PM6'}

    Note that the cabs and solvation_scheme_level arguments currently have no effect @@ -639,7 +640,7 @@

    Consider a specific diastereomer

    Don’t generate conformers for specific species

    -

    The conformers entry in the job_types dictionary is a global flag, +

    The conf_opt entry in the job_types dictionary is a global flag, affecting conformer generation of all species in the project.

    If you’d like to avoid generating conformers just for selected species, pass their labels to ARC in the dont_gen_confs list, e.g.:

    @@ -751,7 +752,7 @@

    Writing an ARC input file using the APIjob_types: rotors: true - conformers: true + conf_opt: true fine: true freq: true lennard_jones: false @@ -850,7 +851,7 @@

    Calculating BDEs (bond dissociation energies)job_types: rotors: true - conformers: true + conf_opt: true fine: true freq: true opt: true diff --git a/examples.html b/examples.html index c01f705b1f..82459b5c37 100644 --- a/examples.html +++ b/examples.html @@ -191,7 +191,7 @@

    Calculating thermodynamic propertiesjob_types: rotors: true - conformers: true + conf_opt: true fine: true freq: true opt: true @@ -290,7 +290,7 @@

    Calculating thermodynamic propertiesmax_job_time=24, level_of_theory='CCSD(T)-F12/cc-pVTZ-F12//wb97xd/def2tzvp', scan_level='wb97xd/def2tzvp', - conformer_level='b3lyp/6-311+g(d,p)', + conformer_opt_level='b3lyp/6-311+g(d,p)', species=[spc1, spc2, spc3], ) diff --git a/searchindex.js b/searchindex.js index fcdb1bbf30..8d0586a8e8 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["advanced", "api/common", "api/conformers", "api/converter", "api/index", "api/job", "api/level", "api/local", "api/main", "api/parser", "api/plotter", "api/processor", "api/reaction", "api/rmgdb", "api/scale", "api/scheduler", "api/species", "api/ssh", "api/trsh", "api/vectors", "api/zmat", "cite", "contribute", "credits", "examples", "index", "installation", "licence", "media", "output", "release", "running", "tools"], "filenames": ["advanced.rst", "api/common.rst", "api/conformers.rst", "api/converter.rst", "api/index.rst", "api/job.rst", "api/level.rst", 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