Merge pull request #13 from arosen93/rosen-docs

Add more information to docs about modifying input settings

docs/src/user/codes/vasp.rst

@@ -18,7 +18,8 @@ differences are:
 .. warning::
 
     The different input sets used in atomate2 mean total energies cannot be compared
-    against energies taken from the Materials Project.
+    against energies taken from the Materials Project unless the default settings are 
+    modified accordingly.
 
 Configuration
 -------------
@@ -220,7 +221,7 @@ written:
 
     static_job.maker.input_set_generator.user_incar_settings["LOPTICS"] = True
 
-Finally, sometimes you have workflow containing many VASP jobs. In this case it can be
+Finally, sometimes you have a workflow containing many VASP jobs. In this case it can be
 tedious to update the input sets for each job individually. Atomate2 provides helper
 functions called "powerups" that can apply settings updates to all VASP jobs in a flow.
 These powerups also contain filters for the name of the job and the maker used to
@@ -244,6 +245,43 @@ generate them.
     # only update VASP jobs which were generated by an ElasticRelaxMaker
     update_user_incar_settings(elastic_flow, {"ENCUT": 200}, class_filter=ElasticRelaxMaker)
 
+In addition to the ability to change INCAR parameters on-the-fly, the :obj:`.VaspInputSetGenerator`, 
+``Maker`` object, and "powerups" allow for the manual modification of several additional VASP 
+settings, such as the k-points (``user_kpoints_settings``) and choice of pseudopotentials 
+(``user_potcar_settings``). 
+
+If a greater degree of flexibility is needed, the user can define a default set of input
+arguments (``config_dict``) that can be provided to the :obj:`.VaspInputSetGenerator`. By default, 
+the :obj:`.VaspInputSetGenerator` uses a base set of VASP input parameters from [BaseVaspSet.yaml](/src/atomate2/vasp/sets/BaseVaspSet.yaml), 
+which each ``Maker`` is built upon. If desired, the user can define a custom ``.yaml`` file 
+that contains a different base set of VASP settings to use (e.g. ``MPRelaxSet``). An example of how 
+this can be done is shown below for a reprsentative static calculation.
+
+.. code-block:: python
+
+    from atomate2.vasp.sets.core import StaticSetGenerator
+    from atomate2.vasp.jobs.core import StaticMaker
+    from atomate2.vasp.jobs.base import VaspInputSetGenerator
+    from monty.serialization import loadfn
+
+    # read in a custom config dictionary
+    user_config_dict = loadfn("/path/to/my/CustomVaspSet.yaml")
+    
+    # create a custom input set generator with user-defined defaults
+    # also change the NELMIN parmaeter to 6 if it wasn't already
+    # this value in the config_dict (for demonstration purposes)
+    vis_generator = VaspInputSetGenerator(
+        user_incar_settings={"NELMIN": 6},
+        config_dict=user_config_dict,
+        )
+    my_custom_set = StaticSetGenerator(vis_generator)
+
+    # initialise the static maker to use the custom input set generator
+    static_maker = StaticMaker(input_set_generator=my_custom_set)
+
+    # create a job using the customised maker
+    static_job = static_maker.make(structure)
+
 .. _connecting_vasp_jobs:
 
 Chaining workflows

docs/src/user/fireworks.rst

@@ -33,7 +33,7 @@ submit an MgO band structure workflow using FireWorks:
     )
 
     # make a band structure flow to optimise the structure and obtain the band structure
-    bandstructure_flow = RelaxBandStructureMaker().make(si_structure)
+    bandstructure_flow = RelaxBandStructureMaker().make(mgo_structure)
 
     # convert the flow to a fireworks WorkFlow object
     wf = flow_to_workflow(bandstructure_flow)

src/atomate2/vasp/sets/base.py

@@ -203,7 +203,7 @@ class VaspInputSetGenerator(InputSetGenerator):
         when generating the input set from a previous VASP directory.
     constrain_total_magmom
         Whether to constrain the total magmom (NUPDOWN in INCAR) to be the sum of the
-        expected MAGMOM for all species.
+        initial MAGMOM guess for all species.
     validate_magmom
         Ensure that missing magmom values are filled in with the default value of 1.0.
     use_structure_charge