matvirdkit stands for Material virtual design kit. This toolkit has been developed for 3 purpose.
-
Describing the data schema
-
Parsing data from DFT calculation raw data
-
Supplying API request information.
matvirdkit
├── api
├── builder
├── creator
└── model
api api interface
builder basic parser for data generating
creator used for writing data into database
model define the model of material, task and properties
basic rules:
- properties definition:
if you want to add a set of properties named Abc into the model. You may add a new class for the new set Abc and corresponding document AbcDoc, e.g.
from typing import ClassVar, Dict
from pydantic import BaseModel, Field
from matvirdkit.model.provenance import LocalProvenance
from matvirdkit.model.common import MatvirdBase
class Abc(MatvirdBase):
provenance: Dict[str,LocalProvenance] = Field({}, description="Property provenance, make sure keep this!")
sub_property_1: float = Field(...)
sub_property_2: int = Field(...)
class AbcDoc(BaseModel):
"""
ABC property block
"""
property_name: ClassVar[str] = "Abc"
abc: Dict[str,Abc] = Field({}, description='abc information')
or, you may just add the sub_prop to the existed property class. For example, we can add new property update_time to the set Abc above.
from typing import ClassVar, Dict
from pydantic import BaseModel, Field
from matvirdkit.model.provenance import LocalProvenance
from matvirdkit.model.common import MatvirdBase
class Abc(MatvirdBase):
provenance: Dict[str,LocalProvenance] = Field({}, description="Property provenance, make sure keep this!")
sub_property_1: float = Field(...)
sub_property_2: int = Field(...)
update_time: str = Field(...)
class AbcDoc(BaseModel):
"""
ABC property block
"""
property_name: ClassVar[str] = "Abc"
abc: Dict[str,Abc] = Field({}, description='abc information')
To set up a instance of AbcDoc, we can use the following code:
doc=AbcDoc(
abc={'label': Abc(sub_property_1=0.2, sub_property_2=0.3, update_time= str(datetime.now()) ,description='This is a test')},
provenance={'label':{}}
)
print(doc.dict())
Generally speaking, the key of Dict for property AbcDoc.abc can be functional of calculation or calcuation method, such as "GGA-PBE", "GW", "PBE+U".
-
tasks definition:
Currently, we only support the VASP task.
The command line operation for preparing datasets and database operating are supported.
usage: mvdkit [-h] [-v] {build,create} ...
Desctiption:
------------
mvdkit is collection of toolkits for preparing and quering the data of matvird database.
To see the options for the sub-commands, type "mvdkit sub-command -h".
positional arguments:
{build,create}
build Generating data set for matvird.
create Write the data into database
optional arguments:
-h, --help show this help message and exit
-v, --version Display version
To prepare the dataset for specific database, you have to write your own info.json firstly, and
then run the cmd mvdkit build -c info.json
Generally, the repository location can be ~/.repository, which can be setted in then ~/.env.
The directory tree of repository:
.
├── datasets
│ └── mech2d
│ └── m2d-2
│ ├── 1794cb78e03147af65fb3a4f2110b8f92b915f12-mp-755811-dos.json
│ ├── c271afe290f282540eccf92dbd03530df9070de9-mp-755811-dos.png
│ ├── m2d-2.json
│ └── mechanics
│ ├── elc_energy
│ │ ├── Def_1
│ │ │ ├── Def_1_Energy.dat
│ │ │ └── Def_1_Energy_Strain.png
│ │ ├── Def_2
│ │ │ ├── Def_2_Energy.dat
│ │ │ └── Def_2_Energy_Strain.png
│ │ ├── Def_3
│ │ │ ├── Def_3_Energy.dat
│ │ │ └── Def_3_Energy_Strain.png
│ │ ├── Def_4
│ │ │ ├── Def_4_Energy.dat
│ │ │ └── Def_4_Energy_Strain.png
│ │ ├── energy-EV.png
│ │ ├── EV_theta.dat
│ │ ├── Mech2D.json
│ │ └── Result.json
│ ├── elc_stress
│ │ ├── Def_1
│ │ │ ├── Def_1_Lagrangian_Stress.dat
│ │ │ ├── Def_1_Lagrangian_Stress.png
│ │ │ └── Def_1_Physical_Stress.dat
│ │ ├── Def_2
│ │ │ ├── Def_2_Lagrangian_Stress.dat
│ │ │ ├── Def_2_Lagrangian_Stress.png
│ │ │ └── Def_2_Physical_Stress.dat
│ │ ├── EV_theta.dat
│ │ ├── Mech2D.json
│ │ ├── Result.json
│ │ └── stress-EV.png
│ └── ssc_stress
│ ├── Def_bi
│ │ ├── Def_bi_Lagrangian_Stress.dat
│ │ ├── Def_bi_Lagrangian_Stress.png
│ │ └── Def_bi_Physical_Stress.dat
│ ├── Def_xx
│ │ ├── Def_xx_Lagrangian_Stress.dat
│ │ ├── Def_xx_Lagrangian_Stress.png
│ │ └── Def_xx_Physical_Stress.dat
│ ├── Def_xy
│ │ ├── Def_xy_Lagrangian_Stress.dat
│ │ ├── Def_xy_Lagrangian_Stress.png
│ │ └── Def_xy_Physical_Stress.dat
│ ├── Def_yy
│ │ ├── Def_yy_Lagrangian_Stress.dat
│ │ ├── Def_yy_Lagrangian_Stress.png
│ │ └── Def_yy_Physical_Stress.dat
│ └── Mech2D.json
├── meta
└── tasks
├── qe
│ └── 3d3616d4-49f8-4c97-9084-5846e8dbc903
└── vasp
├── 007d2c20b64b678e0d0fa1ff3f6950c0ceef8d5b
│ ├── 1477eeae6f878e441588f86c42857c2b34580624-CONTCAR.gz
│ ├── 3fcf67030e2044f6a74da9611778c0d9e7281642-CONTCAR.json
│ ├── 81c8a4ade5c45aef52bb2eea3cdbf118d20c38bc-vasprun.xml.gz
│ ├── 832f638ae8029d0ca099be0aa08b8519e0e98548-vasprun.xml.json
│ └── task.json
├── 0446e56c-8f9c-49b9-9d09-a1bcfb24e585
├── 06a7163b7b14404c93f985bdf0079ff20edbefb7
│ ├── 771be761164e4c5841e0eca173bddb4a01b410a1-CONTCAR.json
│ ├── a6349f104781f34f1459d1ba6124cbebe291ef7d-vasprun.xml.json
│ ├── d67ee17be51577b948a74dfd7769562cb3733970-vasprun.xml.gz
│ ├── f6e1b58a62479f6db561a63af912ff8cb904af1d-CONTCAR.gz
│ └── task.json
├── 071a0189883132bd8541b9430d073ffca5111860
│ ├── 283126d3546db1a51aea3e9a2467ba893c0630d5-vasprun.xml.json
│ ├── 4d8ff43e2ebabefa45eb204c308ded6eedb93ef9-CONTCAR.json
│ ├── b3f32ff8e4d1a9fd9d3c489102e557f7fe9de57f-vasprun.xml.gz
│ ├── cabd3d9c80a6ca864fc37dc7ab2932528c64b880-CONTCAR.gz
│ └── task.json
├── 074cb012-764b-489f-bd0a-7dda570b907e