wiki - User contributions [en]

Online Calculation

2020-07-10T07:39:43Z

Moq:

<div style="margin-left:30px;margin-right:30px">

For online calculation, Matgen combines with two computing software: VASP and Gaussian. For VASP, users can choose [https://matgen.nscc-gz.cn/3DStructGen_help.html#section-19 VASP Online Calculation] and [[Workflow Online Calculation]]For Gaussian, users can choose [https://matgen.nscc-gz.cn/3DStructGen_help.html#section-20 Gaussian Calculation] 
</div>

Online Calculation

2020-07-10T07:39:05Z

Moq:

Online Calculation

2020-07-10T07:38:25Z

Moq:

<div style="margin-left:30px;margin-right:30px">

For online calculation, Matgen combines with two computing software: VASP and Gaussian. For VASP, users can choose [https://matgen.nscc-gz.cn/3DStructGen_help.html#section-19] and [[Workflow Online Calculation]]For Gaussian, users can choose [[Gaussian Calculation]] 
</div>

Talk:Main Page

2020-07-09T06:57:11Z

Moq:

= Question1: can't submit online calculation =
Answer:
* You have starlight account and have logged in. Manual [[:login]]
* Your account have been associated with system account. Manual [[:associate with system account]]
* You have bought computing resource on Tianhe-2c Work cluster
* Clear cache may help you

Talk:Main Page

2020-07-09T06:25:23Z

Moq: Created page with "= Question1: can't submit online calculation = Answer: * You have starlight account and have logged in. Manual :login * Your account have been associated with system acco..."

Workflow Online Calculation

2020-07-09T01:08:40Z

Moq:

<div style="margin-left:30px;margin-right:30px">

Matgen also provides module to run and analyze Density Functional Theory (DFT) calculations. It relies on Tianhe-2 computing cluster to run simulation jobs, so users need to [[:login]] with their starlight account, [[:associate system account]] and make sure they have bought computing resources on Tianhe-2c WORK cluster before running DFT calculations through Matgen. Currently, Matgen only support DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have valid VASP license.
This module mainly supports workflow design, workflow submission and workflow status monitoring, analyzed data visualization and workflow cancellation.
<div>__TOC__</div>

= Choose System for DFT calculation =
To run DFT simulation for a particular system, users can enter this module through “Inorganic Crystal Materials” module in the main page, and then users can search and choose the material for DFT calculation.
[[Image:1.png|500px|frameless|center]]
Pic 1 Enter “Inorganic Crystal Materials” module
[[Image:2.png|500px|frameless|center]]
Pic 2 Search the target material and enter material detail page
[[Image:3.png|500px|frameless|center]]
Pic 3 Enter DFT calculation page: click “RERUN

= Workflow Design =
Matgen provides a whole workflow which includes Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. Users can choose any calculation to run and modify Input Files for each calculation.
== Calculation Process Design ==
Though Matgen provide five calculations in the workflow, it is not necessary to run all in reality and users may choose part of properties for simulation. In this case, users can click the calculation name and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
VASP has four input files, INCAR, KPOINTS, POSCAR and POTCAR. For INCAR, KPOINTS, and POSCAR, Matgen provides a default content so that the VASP calculation result can be more physically meaningful. Users can adjust file content directly through choosing calculation, click the file name users want to edit and modifying content in the right side. For POTCAR, as POTCAR file can be generated by combining POTCAR files of each element in the system together, users choose pseudo potential of each element instead of editing the whole POTCAR file.
[[Image:5.png|500px|frameless|center]]
Pic 5 Edit “Geometry Optimization” input files: click “Geometry Optimization”; click “Settings”; click the file to modify; modify directly

== Calculation Configuration Setting ==
For high-throughput jobs, users need to set calculation configurations to better run VASP. The main configuration is node number. In Matgen, users can choose node number less than 4 for each calculation except Band Structure Calculation.
[[Image:6.png|500px|frameless|center]]
Pic 6 Set node number for each calculation: click “submit” button after editing input files; click “submit”; choose node number for each calculation; click submit to submit workflow

= Workflow Status Monitoring =
After workflow submission, users will enter job list page, and can check workflow status and status of each step in workflow.
[[Image:7.png|500px|frameless|center]]
Pic 7 Get status of each calculation in a workflow: click “refresh” button; click “W” button; click “check” button
[[Image:8.png|500px|frameless|center]]
Pic 8 Status of each calculation in a workflow

= Data Visualization =
Once each calculation in a workflow is finished and there is no error in calculation, users can see results which have been processed after calculation.
[[Image:9.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

= Workflow Cancellation =
To cancel a running workflow, users can select this workflow from job list, and then cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Workflow Online Calculation

2020-07-09T00:58:44Z

Moq:

<div style="margin-left:30px;margin-right:30px">

Matgen also provides module to run and analyze Density Functional Theory (DFT) calculations. It relies on Tianhe-2 computing cluster to run simulation jobs, so users need to [[:login]] with their starlight account, [[:associate system account]] and make sure they have bought computing resources on Tianhe-2c WORK cluster before running DFT calculations through Matgen. Currently, Matgen only support DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have valid VASP license.
This module mainly supports workflow design, workflow submission and workflow status monitoring, analyzed data visualization and workflow cancellation.

== 1.0 Choose System for DFT calculation ==
To run DFT simulation for a particular system, users can enter this module through “Inorganic Crystal Materials” module in the main page, and then users can search and choose the material for DFT calculation.
[[Image:1.png|500px|frameless|center]]
Pic 1 Enter “Inorganic Crystal Materials” module
[[Image:2.png|500px|frameless|center]]
Pic 2 Search the target material and enter material detail page
[[Image:3.png|500px|frameless|center]]
Pic 3 Enter DFT calculation page: click “RERUN

1.1 Workflow Design
Matgen provides a whole workflow which includes Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. Users can choose any calculation to run and modify Input Files for each calculation.
1.1.1 Calculation Process Design
Though Matgen provide five calculations in the workflow, it is not necessary to run all in reality and users may choose part of properties for simulation. In this case, users can click the calculation name and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

1.1.2 Input Parameter Setting
VASP has four input files, INCAR, KPOINTS, POSCAR and POTCAR. For INCAR, KPOINTS, and POSCAR, Matgen provides a default content so that the VASP calculation result can be more physically meaningful. Users can adjust file content directly through choosing calculation, click the file name users want to edit and modifying content in the right side. For POTCAR, as POTCAR file can be generated by combining POTCAR files of each element in the system together, users choose pseudo potential of each element instead of editing the whole POTCAR file.
[[Image:5.png|500px|frameless|center]]
Pic 5 Edit “Geometry Optimization” input files: click “Geometry Optimization”; click “Settings”; click the file to modify; modify directly

1.1.3 Calculation Configuration Setting
For high-throughput jobs, users need to set calculation configurations to better run VASP. The main configuration is node number. In Matgen, users can choose node number smaller than 4 for each calculation except Band Structure Calculation.
[[Image:6.png|500px|frameless|center]]
Pic 6 Set node number for each calculation: click “submit” button after editing input files; click “submit”; choose node number for each calculation; click submit to submit workflow

1.2 Workflow Status Monitoring
After workflow submission, users will enter job list page, and can check workflow status and status of each calculation.
[[Image:7.png|500px|frameless|center]]
Pic 7 Get status of each calculation in a workflow: click “refresh” button; click “W” button; click “check” button
[[Image:8.png|500px|frameless|center]]
Pic 8 Status of each calculation in a workflow

1.3 Data Visualization
Once each calculation in a workflow is finished and there is no error in calculation, users can see results which have been processed after calculation.
[[Image:9.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

1.4 Workflow Cancellation
To cancel a running workflow, users can select this workflow from job list, and then cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Workflow Online Calculation

2020-07-08T09:58:34Z

Moq:

<div style="margin-left:30px;margin-right:30px">

Matgen also provides module to run and analyze Density Functional Theory (DFT) calculations. It relies on Tianhe-2 computing cluster to run simulation jobs, so users need to [[:login]] with their starlight account, [[:associate system account]] and make sure they have bought computing resources on Tianhe-2c WORK cluster before running DFT calculations through Matgen. Currently, Matgen only support DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have valid VASP license.
This module mainly supports workflow design, workflow submission and workflow status monitoring, analyzed data visualization and workflow cancellation.

1.0 Choose System for DFT calculation
To run DFT simulation for a particular system, users can enter this module through “Inorganic Crystal Materials” module in the main page, and then users can search and choose the material for DFT calculation.
[[Image:1.png|500px|frameless|center]]
Pic 1 Enter “Inorganic Crystal Materials” module
[[Image:2.png|500px|frameless|center]]
Pic 2 Search the target material and enter material detail page
[[Image:3.png|500px|frameless|center]]
Pic 3 Enter DFT calculation page: click “RERUN

1.1 Workflow Design
Matgen provides a whole workflow which includes Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. Users can choose any calculation to run and modify Input Files for each calculation.
1.1.1 Calculation Process Design
Though Matgen provide five calculations in the workflow, it is not necessary to run all in reality and users may choose part of properties for simulation. In this case, users can click the calculation name and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

1.1.2 Input Parameter Setting
VASP has four input files, INCAR, KPOINTS, POSCAR and POTCAR. For INCAR, KPOINTS, and POSCAR, Matgen provides a default content so that the VASP calculation result can be more physically meaningful. Users can adjust file content directly through choosing calculation, click the file name users want to edit and modifying content in the right side. For POTCAR, as POTCAR file can be generated by combining POTCAR files of each element in the system together, users choose pseudo potential of each element instead of editing the whole POTCAR file.
[[Image:5.png|500px|frameless|center]]
Pic 5 Edit “Geometry Optimization” input files: click “Geometry Optimization”; click “Settings”; click the file to modify; modify directly

1.1.3 Calculation Configuration Setting
For high-throughput jobs, users need to set calculation configurations to better run VASP. The main configuration is node number. In Matgen, users can choose node number smaller than 4 for each calculation except Band Structure Calculation.
[[Image:6.png|500px|frameless|center]]
Pic 6 Set node number for each calculation: click “submit” button after editing input files; click “submit”; choose node number for each calculation; click submit to submit workflow

1.2 Workflow Status Monitoring
After workflow submission, users will enter job list page, and can check workflow status and status of each calculation.
[[Image:7.png|500px|frameless|center]]
Pic 7 Get status of each calculation in a workflow: click “refresh” button; click “W” button; click “check” button
[[Image:8.png|500px|frameless|center]]
Pic 8 Status of each calculation in a workflow

1.3 Data Visualization
Once each calculation in a workflow is finished and there is no error in calculation, users can see results which have been processed after calculation.
[[Image:9.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

1.4 Workflow Cancellation
To cancel a running workflow, users can select this workflow from job list, and then cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Main Page

2020-07-08T09:58:14Z

Moq:

Welcome to the Matgen wiki.

The content here is still under construction...

== UCSD Database ==
* [[Database information]]

== Tools ==
* [[3DStructGen]]
* [[Matgen toolkit]]

== Applications ==
* [[Inorganic Crystal Material]] - Search for DFT calculated data on inorganic crystal materials.
* [[Molten Salt Material]] - Search for calculated data based on molecular dynamics method on molten salt materials.
* [[Porous Material]] - Search for calculated data based on Monte Carlo method on Metal-Organic Frameworks (MOFs) materials.

== Manual ==
* [[Online Calculation]]

Main Page

2020-07-08T09:49:38Z

Moq: /* Tools */

Welcome to the Matgen wiki.

The content here is still under construction...

== UCSD Database ==
* [[Database information]]

== Tools ==
* [[3DStructGen]]
* [[Matgen toolkit]]
* [[Online Calculation]]

== Applications ==
* [[Inorganic Crystal Material]] - Search for DFT calculated data on inorganic crystal materials.
* [[Molten Salt Material]] - Search for calculated data based on molecular dynamics method on molten salt materials.
* [[Porous Material]] - Search for calculated data based on Monte Carlo method on Metal-Organic Frameworks (MOFs) materials.

Online Calculation

2020-07-08T09:49:23Z

Moq: Created page with "<div style="margin-left:30px;margin-right:30px"> For online calculation, Matgen combines with two computing software: VASP and Gaussian..."

<div style="margin-left:30px;margin-right:30px">

For online calculation, Matgen combines with two computing software: VASP and Gaussian. For VASP, users can choose [[VASP Calculation]] and [[Workflow Online Calculation]]For Gaussian, users can choose [[Gaussian Calculation]] 
</div>

Main Page

2020-07-08T09:45:31Z

Moq: /* Tools */

Welcome to the Matgen wiki.

The content here is still under construction...

== UCSD Database ==
* [[Database information]]

== Tools ==
* [[3DStructGen]]
* [[Matgen toolkit]]
* [[Online Calculation]]
* [[Workflow Online Calculation]]

== Applications ==
* [[Inorganic Crystal Material]] - Search for DFT calculated data on inorganic crystal materials.
* [[Molten Salt Material]] - Search for calculated data based on molecular dynamics method on molten salt materials.
* [[Porous Material]] - Search for calculated data based on Monte Carlo method on Metal-Organic Frameworks (MOFs) materials.

Main Page

2020-07-08T09:45:19Z

Moq: /* Tools */

Welcome to the Matgen wiki.

The content here is still under construction...

== UCSD Database ==
* [[Database information]]

== Tools ==
* [[3DStructGen]]
* [[Matgen toolkit]]
* [[Onlise Calculation]]
* [[Workflow Online Calculation]]

== Applications ==
* [[Inorganic Crystal Material]] - Search for DFT calculated data on inorganic crystal materials.
* [[Molten Salt Material]] - Search for calculated data based on molecular dynamics method on molten salt materials.
* [[Porous Material]] - Search for calculated data based on Monte Carlo method on Metal-Organic Frameworks (MOFs) materials.

Main Page

2020-07-08T09:44:46Z

Moq: /* Tools */

Welcome to the Matgen wiki.

The content here is still under construction...

== UCSD Database ==
* [[Database information]]

== Tools ==
* [[3DStructGen]]
* [[Matgen toolkit]]
* [[Workflow Online Calculation]]

== Applications ==
* [[Inorganic Crystal Material]] - Search for DFT calculated data on inorganic crystal materials.
* [[Molten Salt Material]] - Search for calculated data based on molecular dynamics method on molten salt materials.
* [[Porous Material]] - Search for calculated data based on Monte Carlo method on Metal-Organic Frameworks (MOFs) materials.

Workflow Online Calculation

2020-07-08T09:43:21Z

Moq: Moq moved page Matgen Online Calculation to Workflow Online Calculation

<div style="margin-left:30px;margin-right:30px">

Matgen also provide module to run and analyze Density Functional Theory (DFT) calculations. It relies on Tianhe-2 computing cluster to run simulation jobs, so users need to [[:login]] with their starlight account, [[:associate system account]] and make sure they have bought computing resources on Tianhe-2c WORK cluster before running DFT calculations through Matgen. Currently, Matgen only support DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have valid VASP license.
This module mainly supports workflow design, workflow submission and workflow status monitoring, analyzed data visualization and workflow cancellation.

1.0 Choose System for DFT calculation
To run DFT simulation for a particular system, users can enter this module through “Inorganic Crystal Materials” module in the main page, and then users can search and choose the material for DFT calculation.
[[Image:1.png|500px|frameless|center]]
Pic 1 Enter “Inorganic Crystal Materials” module
[[Image:2.png|500px|frameless|center]]
Pic 2 Search the target material and enter material detail page
[[Image:3.png|500px|frameless|center]]
Pic 3 Enter DFT calculation page: click “RERUN

1.1 Workflow Design
Matgen provides a whole workflow which includes Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. Users can choose any calculation to run and modify Input Files for each calculation.
1.1.1 Calculation Process Design
Though Matgen provide five calculations in the workflow, it is not necessary to run all in reality and users may choose part of properties for simulation. In this case, users can click the calculation name and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

1.1.2 Input Parameter Setting
VASP has four input files, INCAR, KPOINTS, POSCAR and POTCAR. For INCAR, KPOINTS, and POSCAR, Matgen provides a default content so that the VASP calculation result can be more physically meaningful. Users can adjust file content directly through choosing calculation, click the file name users want to edit and modifying content in the right side. For POTCAR, as POTCAR file can be generated by combining POTCAR files of each element in the system together, users choose pseudo potential of each element instead of editing the whole POTCAR file.
[[Image:5.png|500px|frameless|center]]
Pic 5 Edit “Geometry Optimization” input files: click “Geometry Optimization”; click “Settings”; click the file to modify; modify directly

1.1.3 Calculation Configuration Setting
For high-throughput jobs, users need to set calculation configurations to better run VASP. The main configuration is node number. In Matgen, users can choose node number smaller than 4 for each calculation except Band Structure Calculation.
[[Image:6.png|500px|frameless|center]]
Pic 6 Set node number for each calculation: click “submit” button after editing input files; click “submit”; choose node number for each calculation; click submit to submit workflow

1.2 Workflow Status Monitoring
After workflow submission, users will enter job list page, and can check workflow status and status of each calculation.
[[Image:7.png|500px|frameless|center]]
Pic 7 Get status of each calculation in a workflow: click “refresh” button; click “W” button; click “check” button
[[Image:8.png|500px|frameless|center]]
Pic 8 Status of each calculation in a workflow

1.3 Data Visualization
Once each calculation in a workflow is finished and there is no error in calculation, users can see results which have been processed after calculation.
[[Image:9.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

1.4 Workflow Cancellation
To cancel a running workflow, users can select this workflow from job list, and then cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Matgen Online Calculation

2020-07-08T09:43:21Z

Moq: Moq moved page Matgen Online Calculation to Workflow Online Calculation

#REDIRECT [[Workflow Online Calculation]]

Workflow Online Calculation

2020-07-08T09:41:19Z

Moq:

File:10.png

2020-07-08T09:39:13Z

Moq:

File:9.png

2020-07-08T09:38:58Z

Moq:

File:8.png

2020-07-08T09:38:43Z

Moq:

File:7.png

2020-07-08T09:38:23Z

Moq:

File:6.png

2020-07-08T09:38:03Z

Moq:

File:5.png

2020-07-08T09:37:44Z

Moq:

File:4.png

2020-07-08T09:37:21Z

Moq:

File:3.png

2020-07-08T09:37:02Z

Moq:

Workflow Online Calculation

2020-07-08T09:36:30Z

Moq:

<div style="margin-left:30px;margin-right:30px">

Matgen also provide module to run and analyze Density Functional Theory (DFT) calculations. It relies on Tianhe-2 computing cluster to run simulation jobs, so users need to [[:login]] with their starlight account, [[:associate system account]] and make sure they have bought computing resources on Tianhe-2c WORK cluster before running DFT calculations through Matgen. Currently, Matgen only support DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have valid VASP license.
This module mainly supports workflow design, workflow submission and workflow status monitoring, analyzed data visualization and workflow cancellation.
 

1.0 Choose System for DFT calculation
To run DFT simulation for a particular system, users can enter this module through “Inorganic Crystal Materials” module in the main page, and then users can search and choose the material for DFT calculation.
[[Image:1.png|500px|frameless|center]]
Pic 1 Enter “Inorganic Crystal Materials” module
[[Image:1.png|500px|frameless|center]]
Pic 2 Search the target material and enter material detail page
[[Image:1.png|500px|frameless|center]]
Pic 3 Enter DFT calculation page: click “RERUN
 

1.1 Workflow Design
Matgen provides a whole workflow which includes Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. Users can choose any calculation to run and modify Input Files for each calculation.
1.1.1 Calculation Process Design
Though Matgen provide five calculations in the workflow, it is not necessary to run all in reality and users may choose part of properties for simulation. In this case, users can click the calculation name and delete it.
[[Image:1.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

1.1.2 Input Parameter Setting
VASP has four input files, INCAR, KPOINTS, POSCAR and POTCAR. For INCAR, KPOINTS, and POSCAR, Matgen provides a default content so that the VASP calculation result can be more physically meaningful. Users can adjust file content directly through choosing calculation, click the file name users want to edit and modifying content in the right side. For POTCAR, as POTCAR file can be generated by combining POTCAR files of each element in the system together, users choose pseudo potential of each element instead of editing the whole POTCAR file.
[[Image:1.png|500px|frameless|center]]
Pic 5 Edit “Geometry Optimization” input files: click “Geometry Optimization”; click “Settings”; click the file to modify; modify directly

1.1.3 Calculation Configuration Setting
For high-throughput jobs, users need to set calculation configurations to better run VASP. The main configuration is node number. In Matgen, users can choose node number smaller than 4 for each calculation except Band Structure Calculation.
[[Image:1.png|500px|frameless|center]]
Pic 6 Set node number for each calculation: click “submit” button after editing input files; click “submit”; choose node number for each calculation; click submit to submit workflow

1.2 Workflow Status Monitoring
After workflow submission, users will enter job list page, and can check workflow status and status of each calculation.
[[Image:1.png|500px|frameless|center]]
Pic 7 Get status of each calculation in a workflow: click “refresh” button; click “W” button; click “check” button
[[Image:1.png|500px|frameless|center]]
Pic 8 Status of each calculation in a workflow

1.3 Data Visualization
Once each calculation in a workflow is finished and there is no error in calculation, users can see results which have been processed after calculation.
[[Image:1.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

1.4 Workflow Cancellation
To cancel a running workflow, users can select this workflow from job list, and then cancel it.
[[Image:1.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Workflow Online Calculation

2020-07-08T08:28:46Z

Moq:

[[Image:1.png|500px|frameless|center]]
test2test3