Modeling Controls¶

POSCAR Controls¶

Read files in POSCAR、cif、xsf and xyz formats.

Input	Output
None	Structure: pymatgen class

Parameter Configuration：mainly used to load and display atomic structure information, double-click the icon to open the parameter configuration.

Open                                   Open and load the file

Reload                                 Reload file

Info                                   Show atomic structure information

Apply automatically                    If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Apply for transmission, which is checked by default.

Builder Controls¶

Complex models such as grain boundary, doping and vacancy can be constructed.Various methods such as finding grain boundaries, constructing grain boundaries, Interstitial doping, vacancy doping, substitution atom doping and arbitrary location doping are supported.

Input	Output
Structure	Structure	Build Structures

Note

The following parameters configuration, with * is required, and with no * is optional.

4.1.2.1 Find Grain Boundary：find grain boundary¶

Rotation axis*                         Specify the axis of rotation between two grains, such as 0 0 1

Maximum Σ*                             Maximum fitting degrees of freedom

find                                   Click to find the specified boundary conditions

Information                            Show grain boundary structure information

Build Grain Boundary：build grain boundary¶

Choose File*                           Choose the initial structure

Rotation axis*                         The common rotation axis of two grains, such as 0 0 1

Σ*                                     Fit the degree of freedom, such as 5

GB plane*                              Grain boundary orientation, such as 1 2 0

Grain A size(u. c.)                    The size of grain A

Grain B size(u. c.)                    The size of grain B

Delete layer                           Delete the surface layer on either side of each grain. 8 characters must be input. The first four characters are for grain A and the last four characters are for grain B. ‘b’ for the bottom and ‘t’ for the top. The integer represents the number of layers to remove. The default is：0b0t0b0t，which means there are no layers to remove.

Vacuum size(Å)                         Set the thickness of the vacuum layer at the grain boundary (for grain boundaries with plate models)

Extra IF distance(Å)                   Add an extra distance between the interfaces of the two grains

Tolerance factor(Å)                    A tolerance factor that determines whether two atoms are in the same plane

primitive GB                           Whether to get the primitive structure of grain boundary

Output format                          Choose output format

Build                                  Build grain boundary

Information                            Show the constructed grain boundary structure information

Build vacancy：build vacancy¶

Choose File*                           Choose the initial structure

Scaling matrix*                        Scaling matrix used to build supercells. The options include: one integer, representing expand multiple; three vectors，representing three directions at the same time to enlarge the corresponding multiples; nine matrices，representing to enlarge corresponding multiple in matrix.

Summary                                Offer all the information necessary to build a vacancy

Output format                          Choose output format

Build                                  Build vacancy

Information                            Show vacancy structure information

Build Substitution：build substitution atom¶

Element*                               Choose the element to substitute

Choose File*                           Choose the initial structure

Scaling matrix*                        Scaling matrix used to build supercells. The options include: one integer, representing expand multiple; three vectors，representing three directions at the same time to enlarge the corresponding multiples; nine matrices，representing to enlarge corresponding multiple in matrix.

Summary                                Offer all the information necessary to build substitution structure

Output format                          Choose output format

Build                                  Build substitution

Information                            Show information about the substitution structure

Build Interstitution：build interstitial atom¶

Element*                               Choose the element to insert interstice

Choose File*                           Choose the initial structure

Scaling matrix*                        Scaling matrix used to build supercells. The options include: one integer, representing expand multiple; three vectors，representing three directions at the same time to enlarge the corresponding multiples; nine matrices，representing to enlarge corresponding multiple in matrix.

Summary                                Offer all the information necessary to build interstitution structure

Output format                          Choose output format

Build                                  Build interstitial atom

Information                            Show information about structure of the interstitial atoms

Build Doping：build doping¶

Element*                               Choose the element to be doped

Choose File*                           Choose the initial structure

Add*                                   Choose the coordinates of the doped atom. Default is fractional coordinates.

cartesian coordinate                   Checking indicates that Cartesian coordinates are selected.

validate proximity                     Checking indicates whether the doping atom position overlaps with the existing atom.

Output format                          Choose output format

Build                                  Build doping

Information                            Show information about the structure of doped atoms

Send data：pass the constructed structure information to the next control¶

Multi POSCAR Controls¶

Read multiple files in POSCAR、cif、xsf and xyz formats.

Input	Output
None	Structure: pymatgen class	Many Structures

Parameter Configuration：mainly used to load and display atomic structure information, double-click the icon to open the parameter configuration.

Open                                   Open and load multiple files.Drop-down box to select the specified POSCAR file to view.

Reload                                 Reload files

Info                                   Show atomic structure information

Apply automatically                    If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Apply for transmission, which is checked by default.

Finder Controls¶

Find all possible structures for the specified element in database and generate the corresponding structure file.

Input	Output
None	Data

Sever info（Server information）:

Sever                                  The server address to connect

Port                                   Server port number

Database                               Database

collection                             Collection of MongoDB

Username                               The user name

Password                               Password

Refresh DB                             Refresh database

Structures path                        The path to local structure files

Send data                              Send the above data

Search（Find the structure needed）:

    Click elements in periodic table to find the structure that contains or does not contain the corresponding element, controlled by Setup.

Setup                                  Contains four options, And，And Not，Or，Or Not

Query Method                           Query methods, including chemical symbols, chemical formulas, regular expressions

Query Input                            Show the query criteria input

Clear                                  Clear all query conditions

Search                                 Find structures that satisfy the condition

Results                                Show information of all structures that meet the criteria. Double-click the results you want to view, and can be viewed in visualization software such as Vesta

Finder（send data）:

Auto-run                               If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Get finder for transmission, which is checked by default.

HT Preprocessor Controls¶

High-throughput pretreatment control that is similar to a structural container. All generated structures must be transferred to this control before the next calculation take place.

Input			Output
Structure	Many Structures	Table	Data

Parameter Configuration:

Show the basic information of input structure file

Auto-Run                               If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Send data for transmission, which is checked by default.

Data Table Controls¶

Display data sets in the form of tables(similar to Excel)

Input	Output
Data	Data	Selected Data

Parameter Configuration:

Info                                                 Show information about input data

Variables --> Show variable labels（if present）     If checked, variable labels will be showed if present
Variables --> Visualize numeric values               Check for visualize numeric values
Variables --> Color by instance classes              If checked, the color will be showed by instance classes

Selection --> Select full rows                       If checked, a whole line will be choosed at a time

Restore Original Order                               Restore original order

Send Automatically                                   If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Send Automatically for transmission, which is checked by default.

File Controls¶

Read data from input file or network and output a data table.

Input	Output
None	Data

Parameter Configuration:

File                                   Open and load file

Reload                                 Reload file

URL                                    Input the URL of the network file

Info                                   Show information about the file

Columns（Double click to edit）        Columns display data information, double-click to edit

Browse documentation datasets          Browse documentation datasets

Data Info Controls¶

Show the basic information of the dataset, such as the number and type of variables in each column, how many rows there are, and so on.

Input	Output
Data	None

Parameter Configuration:

Data Set Name                          Dataset name

Data Set Size                          Dataset size

Features                               Dataset features

Targets

Meta Attributes                        Meta attributes

Location                               Dataset storage location

Data Attributes                        Data attributes

LDA-1/2 Controls¶

Generate special LDA-1/2 potential function

Input	Output
file path	file path

The following three calculation methods can be choosed for LDA-1/2 calculation:

LDA-1/2

shLDA-1/2r_in

shLDA-1/2r_out

Parameter Configuration:

Element                                Choose element

Strip                                  Set self-energy potential modification value

Power Index                            Set power index

Fix outer cutoff radius                Fix outer cutoff radius

Scan inner cutoff radius               Scan inner cutoff radius

XC                                     Choosed hybrid functional

Open File                              Choose to upload the POTCAR file

Calculate                              Calculate the uploaded POTCAR

Information                            Related introduction of LDA-1/2 calculation method

Reference                              Reference for calculation methods

Send data                              Click Send data to send data when all settings are completed

POTCAR Controls¶

Choose the desired POTCAR file

Input	Output
file path	file path

Parameter Configuration:

Open                                   Open and load the file

Reload                                 Reload file

Info                                   Show POTCAR file information

Apply automatically                    If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Apply for transmission, which is checked by default.

1 to 4 Controls¶

Input binary material AB file in cif format, and output AA,AB,BA,BB,4 POSCAR files.

Input	Output
file path	list:many structures

Parameter Configuration:

Open                                   Open and load the file

Reload                                 Reload file

Info                                   Show information of 4 generated POSCAR files

Apply automatically                    If checked, the output of the control can be automatically passed to the next control. If unchecked, you can manually click Apply for transmission, which is checked by default.