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update IO classes to latest upstream pymatgen #141

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Jun 8, 2022
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update IO classes to latest upstream pymatgen #141

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e8f0d3f
update IO classes to latest upstream pymatgen
rkingsbury Jun 6, 2022
83d0939
inherit InputSet and InputGenerator from pymatgen
rkingsbury Jun 7, 2022
e95c50d
linting
rkingsbury Jun 7, 2022
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10 changes: 5 additions & 5 deletions docs/user/codes/vasp.md
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Expand Up @@ -229,7 +229,7 @@ Modifying input sets
--------------------

The inputs for a calculation can be modified in several ways. Every VASP job
takes a {obj}`.VaspInputSetGenerator` as an argument (`input_set_generator`). One
takes a {obj}`.VaspInputGenerator` as an argument (`input_set_generator`). One
option is to specify an alternative input set generator:

```python
Expand Down Expand Up @@ -295,13 +295,13 @@ Powerups return a copy of the original flow or Maker and do not modify it in pla
```

In addition to the ability to change INCAR parameters on-the-fly, the
{obj}`.VaspInputSetGenerator`, `Maker` object, and "powerups" allow for the manual
{obj}`.VaspInputGenerator`, `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
arguments (`config_dict`) that can be provided to the {obj}`.VaspInputGenerator`.
By default, the {obj}`.VaspInputGenerator` uses a base set of VASP input parameters
from {obj}`.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.
An example of how this can be done is shown below for a representative static
Expand All @@ -310,7 +310,7 @@ calculation.
```
from atomate2.vasp.sets.core import StaticSetGenerator
from atomate2.vasp.jobs.core import StaticMaker
from atomate2.vasp.jobs.base import VaspInputSetGenerator
from atomate2.vasp.jobs.base import VaspInputGenerator
from monty.serialization import loadfn

# read in a custom config file
Expand Down
77 changes: 0 additions & 77 deletions src/atomate2/common/sets.py
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6 changes: 3 additions & 3 deletions src/atomate2/vasp/files.py
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Expand Up @@ -13,7 +13,7 @@
from atomate2.common.files import copy_files, get_zfile, gunzip_files, rename_files
from atomate2.utils.file_client import FileClient, auto_fileclient
from atomate2.utils.path import strip_hostname
from atomate2.vasp.sets.base import VaspInputSetGenerator
from atomate2.vasp.sets.base import VaspInputGenerator

__all__ = ["copy_vasp_outputs", "get_largest_relax_extension"]

Expand Down Expand Up @@ -143,7 +143,7 @@ def get_largest_relax_extension(

def write_vasp_input_set(
structure: Structure,
input_set_generator: VaspInputSetGenerator,
input_set_generator: VaspInputGenerator,
directory: Union[str, Path] = ".",
from_prev: bool = False,
apply_incar_updates: bool = True,
Expand All @@ -158,7 +158,7 @@ def write_vasp_input_set(
----------
structure : .Structure
A structure.
input_set_generator : .VaspInputSetGenerator
input_set_generator : .VaspInputGenerator
A VASP input set generator.
directory : str or Path
The directory to write the input files to.
Expand Down
18 changes: 9 additions & 9 deletions src/atomate2/vasp/jobs/amset.py
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Expand Up @@ -21,7 +21,7 @@
from atomate2.utils.path import strip_hostname
from atomate2.vasp.jobs.base import BaseVaspMaker
from atomate2.vasp.jobs.core import HSEBSMaker, NonSCFMaker
from atomate2.vasp.sets.base import VaspInputSetGenerator
from atomate2.vasp.sets.base import VaspInputGenerator
from atomate2.vasp.sets.core import (
HSEBSSetGenerator,
HSEStaticSetGenerator,
Expand Down Expand Up @@ -50,7 +50,7 @@ class DenseUniformMaker(NonSCFMaker):
----------
name : str
The job name.
input_set_generator : .VaspInputSetGenerator
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
Expand All @@ -71,7 +71,7 @@ class DenseUniformMaker(NonSCFMaker):
"""

name: str = "dense uniform"
input_set_generator: VaspInputSetGenerator = field(
input_set_generator: VaspInputGenerator = field(
default_factory=lambda: NonSCFSetGenerator(
mode="uniform", reciprocal_density=1000, user_incar_settings={"LWAVE": True}
)
Expand All @@ -91,7 +91,7 @@ class StaticDeformationMaker(BaseVaspMaker):
----------
name : str
The job name.
input_set_generator : .VaspInputSetGenerator
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
Expand All @@ -112,7 +112,7 @@ class StaticDeformationMaker(BaseVaspMaker):
"""

name: str = "static deformation"
input_set_generator: VaspInputSetGenerator = field(
input_set_generator: VaspInputGenerator = field(
default_factory=lambda: StaticSetGenerator(
user_kpoints_settings={"reciprocal_density": 100},
user_incar_settings={"KSPACING": None},
Expand All @@ -133,7 +133,7 @@ class HSEStaticDeformationMaker(BaseVaspMaker):
----------
name : str
The job name.
input_set_generator : .VaspInputSetGenerator
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
Expand All @@ -154,7 +154,7 @@ class HSEStaticDeformationMaker(BaseVaspMaker):
"""

name: str = "static deformation"
input_set_generator: VaspInputSetGenerator = field(
input_set_generator: VaspInputGenerator = field(
default_factory=lambda: HSEStaticSetGenerator(
user_kpoints_settings={"reciprocal_density": 100},
user_incar_settings={"KSPACING": None},
Expand All @@ -171,7 +171,7 @@ class HSEDenseUniformMaker(HSEBSMaker):
----------
name : str
The job name.
input_set_generator : .VaspInputSetGenerator
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
Expand All @@ -192,7 +192,7 @@ class HSEDenseUniformMaker(HSEBSMaker):
"""

name: str = "dense uniform"
input_set_generator: VaspInputSetGenerator = field(
input_set_generator: VaspInputGenerator = field(
default_factory=lambda: HSEBSSetGenerator(
mode="uniform_dense",
zero_weighted_reciprocal_density=1000,
Expand Down
8 changes: 3 additions & 5 deletions src/atomate2/vasp/jobs/base.py
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Expand Up @@ -20,7 +20,7 @@
from atomate2.vasp.files import copy_vasp_outputs, write_vasp_input_set
from atomate2.vasp.run import run_vasp, should_stop_children
from atomate2.vasp.schemas.task import TaskDocument
from atomate2.vasp.sets.base import VaspInputSetGenerator
from atomate2.vasp.sets.base import VaspInputGenerator

__all__ = ["BaseVaspMaker", "vasp_job"]

Expand Down Expand Up @@ -83,7 +83,7 @@ class BaseVaspMaker(Maker):
----------
name : str
The job name.
input_set_generator : .VaspInputSetGenerator
input_set_generator : .VaspInputGenerator
A generator used to make the input set.
write_input_set_kwargs : dict
Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
Expand All @@ -104,9 +104,7 @@ class BaseVaspMaker(Maker):
"""

name: str = "base vasp job"
input_set_generator: VaspInputSetGenerator = field(
default_factory=VaspInputSetGenerator
)
input_set_generator: VaspInputGenerator = field(default_factory=VaspInputGenerator)
write_input_set_kwargs: dict = field(default_factory=dict)
copy_vasp_kwargs: dict = field(default_factory=dict)
run_vasp_kwargs: dict = field(default_factory=dict)
Expand Down
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