atomate.common.powerups.add_metadata(wf, meta_dict, fw_name_constraint=None)¶Add a metadata dictionary to a Workflow and all its Fireworks. The dictionary +is merged into the “metadata” key of the Workflow and into the “_spec” key of +each Firework in the workflow.
+Can be used in combination with add_additional_fields_to_taskdocs to add the +same set of key-value pairs to Workflows, Fireworks and Tasks collections.
+wf (Workflow) +meta_dict: dictionary of custom metadata
+Workflow
+atomate.common.powerups.add_namefile(original_wf, use_slug=True)¶__init__(materials_write)¶Starting with an existing materials collection, adds some averages and +
Starting with an existing materials collection, adds some averages and eigenvalues for dielectric constants rather than just the tensor
materials_write: mongodb collection for materials (write access needed)
@@ -194,7 +194,7 @@from_file(db_file, m='materials', **kwargs)¶Get a MaterialsEhullBuilder using only a db file.
+Get a DielectricBuilder using only a db file.
db_file: (str) path to db file m: (str) name of “materials” collection @@ -504,8 +504,8 @@
atomate.vasp.builders.tasks_materials.module_dir = '/Users/ajain/Documents/code_lbl/atomate/atomate/vasp/builders'¶This class collects all “tasks” (individual calculations) on a single compound and produces a -summary report in a new collection (“materials”). The tasks are matched based on having the same +
This class collects all “tasks” (individual calculations) on a single compound and produces a +summary report in a new collection (“materials”). The tasks are matched based on having the same crystal structure, with some options for overriding this.
There is lots of config for this builder in the accompanying “tasks_materials_settings.yaml” file.
atomate.vasp.firetasks.neb_tasks.RunNEBVaspFake(*args, **kwargs)¶Bases: fireworks.core.firework.FiretaskBase
Vasp Emulator for NEB, which has a different file arrangement. Similar to RunVaspFake class.
-‘inputs’ and output files in the folder named ‘outputs’.
-params_to_check (list): optional list of incar parameters to check.
-optional_params = ['params_to_check']¶required_params = ['ref_dir']¶run_task(fw_spec)¶This method gets called when the Firetask is run. It can take in a -Firework spec, perform some task using that data, and then return an -output in the form of a FWAction.
-In addition, this spec contains a special “_fw_env” key that -contains the env settings of the FWorker calling this method. -This provides for abstracting out certain commands or -settings. For example, “foo” may be named “foo1” in resource -1 and “foo2” in resource 2. The FWorker env can specify { -“foo”: “foo1”}, which maps an abstract variable “foo” to the -relevant “foo1” or “foo2”. You can then write a task that -uses fw_spec[“_fw_env”][“foo”] that will work across all -these multiple resources.
-(FWAction)
-atomate.vasp.firetasks.neb_tasks.TransferNEBTask(*args, **kwargs)¶Bases: fireworks.core.firework.FiretaskBase
This class transfers NEB outputs from current directory to destination directory. “label” is -used to determine the step of calculation and hence the final path. The corresponding structure -will be updated in fw_spec before files transferring.
-“ep1”, “neb1”, “neb2” and etc..
-if “IMAGES” not provided in user_incar_settings, in Angstrom.
-optional_params = ['d_img']¶required_params = ['label']¶run_task(fw_spec)¶This method gets called when the Firetask is run. It can take in a -Firework spec, perform some task using that data, and then return an -output in the form of a FWAction.
-In addition, this spec contains a special “_fw_env” key that -contains the env settings of the FWorker calling this method. -This provides for abstracting out certain commands or -settings. For example, “foo” may be named “foo1” in resource -1 and “foo2” in resource 2. The FWorker env can specify { -“foo”: “foo1”}, which maps an abstract variable “foo” to the -relevant “foo1” or “foo2”. You can then write a task that -uses fw_spec[“_fw_env”][“foo”] that will work across all -these multiple resources.
-(FWAction)
-atomate.vasp.firetasks.neb_tasks.WriteNEBFromEndpoints(*args, **kwargs)¶Bases: fireworks.core.firework.FiretaskBase
Generate NEB input sets using endpoint structures, default writes CI-NEB input. -MVLCINEBSet is the only vasp_input_set supported now.
-search in “user_incar_settings”;
otherwise, calculated using “d_img”.
user_incar_settings (dict): additional INCAR settings.
-user_kpoints_settings (dict): additional KPOINTS settings. -sort_tol (float): Distance tolerance (in Angstrom) used to match the atomic indices between
---start and end structures. If it is set 0, then no sorting will be performed.
-
Angstrom.
-Choose from [“IDPP”, “linear”], default “IDPP”
-optional_params = ['user_kpoints_settings', 'sort_tol', 'd_img', 'interpolation_type']¶required_params = ['user_incar_settings']¶run_task(fw_spec)¶This method gets called when the Firetask is run. It can take in a -Firework spec, perform some task using that data, and then return an -output in the form of a FWAction.
-In addition, this spec contains a special “_fw_env” key that -contains the env settings of the FWorker calling this method. -This provides for abstracting out certain commands or -settings. For example, “foo” may be named “foo1” in resource -1 and “foo2” in resource 2. The FWorker env can specify { -“foo”: “foo1”}, which maps an abstract variable “foo” to the -relevant “foo1” or “foo2”. You can then write a task that -uses fw_spec[“_fw_env”][“foo”] that will work across all -these multiple resources.
-(FWAction)
-atomate.vasp.firetasks.neb_tasks.WriteNEBFromImages(*args, **kwargs)¶Bases: fireworks.core.firework.FiretaskBase
Generate CI-NEB input sets using given images and endpoints structures. The structures -correspond to structures nested in subfolders (“00”, “01”, “02”, etc.)
-neb_label (str): “1”, “2”, etc., labels the running sequence of NEB
-user_incar_settings (dict): Additional INCAR settings. -user_kpoints_settings (dict): Additional KPOINTS settings.
-optional_params = ['user_incar_settings', 'user_kpoints_settings']¶required_params = ['neb_label']¶run_task(fw_spec)¶This method gets called when the Firetask is run. It can take in a -Firework spec, perform some task using that data, and then return an -output in the form of a FWAction.
-In addition, this spec contains a special “_fw_env” key that -contains the env settings of the FWorker calling this method. -This provides for abstracting out certain commands or -settings. For example, “foo” may be named “foo1” in resource -1 and “foo2” in resource 2. The FWorker env can specify { -“foo”: “foo1”}, which maps an abstract variable “foo” to the -relevant “foo1” or “foo2”. You can then write a task that -uses fw_spec[“_fw_env”][“foo”] that will work across all -these multiple resources.
-(FWAction)
-atomate.vasp.drones.VaspDrone(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False, parse_potcar_file=True, store_volumetric_data=(), store_additional_json=False)¶atomate.vasp.drones.VaspDrone(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=False, parse_chgcar=False, parse_aeccar=False, parse_potcar_file=True, store_volumetric_data=(), store_additional_json=False)¶
Bases: pymatgen.apps.borg.hive.AbstractDrone
pymatgen-db VaspToDbTaskDrone with updated schema and documents processing methods. Please refer to matgendb.creator.VaspToDbTaskDrone documentation.
__init__(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=None, parse_chgcar=False, parse_aeccar=False, parse_potcar_file=True, store_volumetric_data=(), store_additional_json=False)¶__init__(runs=None, parse_dos='auto', bandstructure_mode='auto', parse_locpot=True, additional_fields=None, use_full_uri=True, parse_bader=False, parse_chgcar=False, parse_aeccar=False, parse_potcar_file=True, store_volumetric_data=(), store_additional_json=False)¶
Initialize a Vasp drone to parse vasp outputs Args:
@@ -448,8 +454,8 @@atomate.vasp.powerups module
atomate.vasp.vasp_config module¶
--@@ -187,7 +187,7 @@atomate.vasp.vasp_powerups module¶
++atomate.vasp.vasp_powerups module¶
diff --git a/docs/atomate.vasp.tests.html b/docs/atomate.vasp.tests.html index 5d08b8677..4fea6f40d 100644 --- a/docs/atomate.vasp.tests.html +++ b/docs/atomate.vasp.tests.html @@ -5,7 +5,7 @@ -Module contents¶
@@ -474,7 +480,7 @@Table of Contents
- atomate.vasp.powerups module
- atomate.vasp.submission_filter module
- atomate.vasp.vasp_config module
-- atomate.vasp.vasp_powerups module
+- atomate.vasp.vasp_powerups module
- Module contents
@@ -510,7 +516,7 @@Navigation
- modules |
- +atomate.vasp.tests package — atomate 1.0.0 documentation +atomate.vasp.tests package — atomate 1.0.1 documentation @@ -28,7 +28,7 @@Navigation
- modules |
- +Navigation
- modules |
- +
atomate.vasp.firetasks.glue_tasksatomate.vasp.firetasks.neb_tasksatomate.vasp.vasp_configatomate.vasp.vasp_powerups