wiki - User contributions [en]

Workflow Online Calculation

2021-06-21T05:50:29Z

Chengxili:

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

The Matgen platform also provides a module to run and analyze Density Functional Theory (DFT) calculations. Because the Matgen platform relies on the Tianhe-2 computing cluster to run simulation jobs, users need to log in with their Starlight account, associate their private account with a system account, and make sure they have bought computing resources on the Tianhe-2c WORK cluster before running DFT calculations. Currently, the Matgen platform only supports DFT calculations running with the Vienna Ab initio Simulation Package (VASP), and users also need to have a valid VASP license. Please click [[:here|log in] to log in. Please click [[:here]] to associate your account with the system account.
This module mainly supports workflow design, workflow submission, workflow status monitoring, analyzed data visualization, and workflow cancellation.
<div>__TOC__</div>

= Choose System for DFT calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 =
The Matgen platform provides a whole workflow, including Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. You can choose the calculations above to run and modify your Input Files for each calculation.
== Calculation Process Design ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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, you need to set calculation configurations manually to run the VASP better. The main configuration is the node number. In the Matgen platform, you can choose node numbers 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, you will enter the job list page, and you can check the workflow status and the status of each step.
[[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 =
If one of the calculations in a workflow is finished without error, you can see processed results in the job lists by clicking the "view" button.
[[Image:9.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

= Workflow Cancellation =
If you want to cancel a running workflow, you can select the specific workflow from the job list and cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Workflow Online Calculation

2021-06-21T05:27:55Z

Chengxili: /* Workflow Cancellation */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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, you need to set calculation configurations manually to run the VASP better. The main configuration is the node number. In the Matgen platform, you can choose node numbers 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, you will enter the job list page, and you can check the workflow status and the status of each step.
[[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 =
If one of the calculations in a workflow is finished without error, you can see processed results in the job lists by clicking the "view" button.
[[Image:9.png|500px|frameless|center]]
Pic 9 Get data after workflow calculation: click “view” button in job lists

= Workflow Cancellation =
If you want to cancel a running workflow, you can select the specific workflow from the job list and cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Workflow Online Calculation

2021-06-21T05:27:16Z

Chengxili: /* Data Visualization */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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, you need to set calculation configurations manually to run the VASP better. The main configuration is the node number. In the Matgen platform, you can choose node numbers 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, you will enter the job list page, and you can check the workflow status and the status of each step.
[[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 =
If one of the calculations in a workflow is finished without error, you can see processed results in the job lists by clicking the "view" button.
[[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 the 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

2021-06-21T05:26:52Z

Chengxili: /* Data Visualization */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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, you need to set calculation configurations manually to run the VASP better. The main configuration is the node number. In the Matgen platform, you can choose node numbers 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, you will enter the job list page, and you can check the workflow status and the status of each step.
[[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 =
If one of the calculations in a workflow is finished without error, you can see processed results in the job lists by clicking the <button>view</button> button.
[[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 the 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

2021-06-21T05:26:14Z

Chengxili: /* Workflow Status Monitoring */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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, you need to set calculation configurations manually to run the VASP better. The main configuration is the node number. In the Matgen platform, you can choose node numbers 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, you will enter the job list page, and you can check the workflow status and the status of each step.
[[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 that 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 the 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

2021-06-21T05:25:56Z

Chengxili: /* Calculation Configuration Setting */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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, you need to set calculation configurations manually to run the VASP better. The main configuration is the node number. In the Matgen platform, you can choose node numbers 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 the job list page, and can check workflow status and status of each step in the 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 that 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 the 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

2021-06-21T05:25:32Z

Chengxili: /* Input Parameter Setting */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need and delete it.
[[Image:4.png|500px|frameless|center]]
Pic 4 Delete “Magnetic Testing”: click “Magnetic Testing”; click “delete”

== Input Parameter Setting ==
The VASP has four kinds of input files, INCAR, KPOINTS, POSCAR, and POTCAR. For INCAR, KPOINTS, and POSCAR, the Matgen platform provides default content so that the VASP calculation result can be more physically meaningful. You can adjust file content directly by choosing calculation, clicking the file name you want to edit, and modifying content on the right side. For POTCAR, because the POTCAR file can generate by combining each element of other POTCAR files in the system, you can modify the pseudopotential 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 numbers 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 the job list page, and can check workflow status and status of each step in the 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 that 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 the 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

2021-06-21T05:24:57Z

Chengxili: /* Calculation Process Design */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
If you don't need to run all of the calculations, you can choose parts of properties for simulation by clicking the name of calculations you don’t need 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 on the right side. For POTCAR, as the POTCAR file can be generated by combining the POTCAR files of each element in the system together, users choose pseudopotential 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 numbers 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 the job list page, and can check workflow status and status of each step in the 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 that 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 the 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

2021-06-21T05:24:30Z

Chengxili: /* Calculation Process Design */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 ==
The Matgen platform provides a whole workflow, including Magnetic Testing, Geometry Optimization, Static Calculation, Band Structure Calculation, Density of States Calculation, and Magnetic Calculation. You can choose the calculations above to run and modify your Input Files for each calculation..
[[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 on the right side. For POTCAR, as the POTCAR file can be generated by combining the POTCAR files of each element in the system together, users choose pseudopotential 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 numbers 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 the job list page, and can check workflow status and status of each step in the 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 that 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 the 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

2021-06-21T05:23:17Z

Chengxili: /* Choose System for DFT calculation */

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

Matgen also provides a 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|log in]] 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 supports DFT calculations which run with Vienna Ab initio Simulation Package (VASP), so to use this module, users must have a 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 calculations =
To run a DFT simulation for a particular system, you can enter this module through the “Inorganic Crystal Materials” module on the main page, then search and choose the material for your DFT calculations.
[[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 provides five calculations in the workflow, it is not necessary to run all in reality and users can choose parts 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 on the right side. For POTCAR, as the POTCAR file can be generated by combining the POTCAR files of each element in the system together, users choose pseudopotential 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 numbers 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 the job list page, and can check workflow status and status of each step in the 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 that 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 the job list, and then cancel it.
[[Image:10.png|500px|frameless|center]]
Pic 10 Cancel workflow: select from job list; click “X” button

</div>

Molten Salt Material

2021-06-17T15:26:07Z

Chengxili: Undo revision 197 by Chengxili (talk)

=== Background ===
Molten salts are promising thermal energy storage materials. The structures and thermophysical properties of pure molten halide salts are essential for complementing the basic thermodynamic data and developing new types of high-performance multi-component halide molten salts. Although the thermophysical properties of multi-components molten halide salts can be roughly estimated by additive principle and other empirical methods without any experiments, the corresponding properties of individual components are momentous in exploiting new compounds. Furthermore, microstructures of molten halide salts need to be simulated and measured to elucidate the evolution law of thermophysical properties under different temperatures. Unfortunately, people could not measure all the thermophysical properties by experiment so far. As an alternative, molecular simulations are proposed and used to predict thermophysical properties over the entire operating temperature range.

=== Results ===
In this work, we use high-throughput molecular dynamics (HT-MD) to compute thermophysical properties and glean microstructural information about thirty MXn systems of pure molten halide salts exhaustively. These systems include most cations from groups I, II, as well as parts of transition metal elements in lanthanides, and anions from group Ⅶ in the periodic table. Thermophysical properties of these systems, including constant pressure specific heat capacity, density, thermal expansion coefficient, self-diffusion coefficient, viscosity, and microstructure information, which comprises partial radial distribution function and coordination curve under an atmospheric pressure condition, are obtained under a range of temperatures by simulation. These calculations are automated by our own codes called Molten Salt Simulation Toolkit (MSST), developed in the National Supercomputer Center, Guangzhou. Building upon Tianhe-2 high-performance computing (HPC) clusters, MSST can automatically handle input/output processing of CP2K molecular dynamics and manage job submission to cluster queues. Fig. 2 shows the workflow used to implement the HT-MD. (https://raw.githubusercontent.com/pangchq/Molten-Salt-Simulation-Toolkit/master/Fig.2.jpg)

=== Conclusions ===
The simulated constant pressure specific heat capacity, density, viscosity, thermal expansion coefficient, self-diffusion coefficient, and microstructures are in good agreement with experimental values.

=== Usage notes ===
We recommend usage of the fitting formula of thermophysical properties in the database as some viscosities of simulations near the melting point are not very accurate due to the reason mentioned above. Researchers who concern the precision and would like to obtain more accurate results can rerun the code (https://github.com/pangchq/Molten-Salt-Simulation-Toolkit/) and increase the simulation time.

Molten Salt Material

2021-06-17T15:25:25Z

Chengxili: Undo revision 196 by Chengxili (talk)

=== Background ===
Molten salts are promising thermal energy storage materials. The structures and thermophysical properties of pure molten halide salts are essential for complementing the basic thermodynamic data and developing new types of high-performance multi-component halide molten salts. Although the thermophysical properties of multi-components molten halide salts can be roughly estimated by additive principle and other empirical methods without any experiments, the corresponding properties of individual components are momentous in exploiting new compounds. Furthermore, microstructures of molten halide salts need to be simulated and measured to elucidate the evolution law of thermophysical properties under different temperatures. Unfortunately, people could not measure all the thermophysical properties by experiment so far. As an alternative, molecular simulations are proposed and used to predict thermophysical properties over the entire operating temperature range.

=== Results ===
In this work, we use high-throughput molecular dynamics (HT-MD) to compute thermophysical properties and microstructure information of molten halide salts in an exhaustive manner. Thirty MXn systems are simulated in total. Of which cations cover majority of group I and II and minority of transition metal elements, lanthanides and actinicles while anions cover majority of halogen (see Fig. 1 (https://github.com/pangchq/Molten-Salt-Simulation-Toolkit/raw/master/Fig.1.jpg)
). Thermophysical properties (~2,500) including constant pressure specific heat capacity, density, thermal expansion coefficient, self-diffusion coefficient, and viscosity as well as microstructure information including partial radial distribution function and coordination curve under atmospheric pressure condition are obtained with respect to different temperature. These calculations are automated using our own code, Molten Salt Simulation Toolkit (MSST), developed at the National Supercomputer Center in Guangzhou. MSST is built upon Tianhe-2 high-performance computing (HPC) clusters and can automatically handle input/output processing of CP2K molecular dynamics and manage job submission to cluster queues. Fig. 2 shows the workflow used to implement the HT-MD. (https://raw.githubusercontent.com/pangchq/Molten-Salt-Simulation-Toolkit/master/Fig.2.jpg)

=== Conclusions ===
The simulated constant pressure specific heat capacity, density, viscosity, thermal expansion coefficient, self-diffusion coefficient, and microstructures are in good agreement with experimental values.

=== Usage notes ===
We recommend usage of the fitting formula of thermophysical properties in the database as some viscosities of simulations near the melting point are not very accurate due to the reason mentioned above. Researchers who concern the precision and would like to obtain more accurate results can rerun the code (https://github.com/pangchq/Molten-Salt-Simulation-Toolkit/) and increase the simulation time.

Molten Salt Material

2021-06-17T15:24:31Z

Chengxili: /* Results */

=== Background ===
Molten salts are promising thermal energy storage materials. The structures and thermophysical properties of pure molten halide salts are essential for complementing the basic thermodynamic data and developing new types of high-performance multi-component halide molten salts. Although the thermophysical properties of multi-components molten halide salts can be roughly estimated by additive principle and other empirical methods without any experiments, the corresponding properties of individual components are momentous in exploiting new compounds. Furthermore, microstructures of molten halide salts need to be simulated and measured to elucidate the evolution law of thermophysical properties under different temperatures. Unfortunately, people could not measure all the thermophysical properties by experiment so far. As an alternative, molecular simulations are proposed and used to predict thermophysical properties over the entire operating temperature range.

=== Results ===
In this work, we use high-throughput molecular dynamics (HT-MD) to compute thermophysical properties and glean microstructural information about thirty MXn systems of pure molten halide salts exhaustively. These systems include most cations from groups I, II, as well as parts of transition metal elements in lanthanides, and anions from group Ⅶ in the periodic table. Thermophysical properties of these systems, including constant pressure specific heat capacity, density, thermal expansion coefficient, self-diffusion coefficient, viscosity, and microstructure information, which comprises partial radial distribution function and coordination curve under an atmospheric pressure condition, are obtained under a range of temperatures by simulation. These calculations are automated by our own codes called Molten Salt Simulation Toolkit (MSST), developed in the National Supercomputer Center, Guangzhou. Building upon Tianhe-2 high-performance computing (HPC) clusters, MSST can automatically handle input/output processing of CP2K molecular dynamics and manage job submission to cluster queues. Fig. 2 shows the workflow used to implement the HT-MD.(https://raw.githubusercontent.com/pangchq/Molten-Salt-Simulation-Toolkit/master/Fig.2.jpg)

=== Conclusions ===
The simulated constant pressure specific heat capacity, density, viscosity, thermal expansion coefficient, self-diffusion coefficient, and microstructures are in good agreement with experimental values.

=== Usage notes ===
We recommend usage of the fitting formula of thermophysical properties in the database as some viscosities of simulations near the melting point are not very accurate due to the reason mentioned above. Researchers who concern the precision and would like to obtain more accurate results can rerun the code (https://github.com/pangchq/Molten-Salt-Simulation-Toolkit/) and increase the simulation time.

Molten Salt Material

2021-06-17T15:24:08Z

Chengxili: /* Background */

=== Background ===
Molten salts are promising thermal energy storage materials. The structures and thermophysical properties of pure molten halide salts are essential for complementing the basic thermodynamic data and developing new types of high-performance multi-component halide molten salts. Although the thermophysical properties of multi-components molten halide salts can be roughly estimated by additive principle and other empirical methods without any experiments, the corresponding properties of individual components are momentous in exploiting new compounds. Furthermore, microstructures of molten halide salts need to be simulated and measured to elucidate the evolution law of thermophysical properties under different temperatures. Unfortunately, people could not measure all the thermophysical properties by experiment so far. As an alternative, molecular simulations are proposed and used to predict thermophysical properties over the entire operating temperature range.

=== Results ===
In this work, we use high-throughput molecular dynamics (HT-MD) to compute thermophysical properties and microstructure information of molten halide salts in an exhaustive manner. Thirty MXn systems are simulated in total. Of which cations cover majority of group I and II and minority of transition metal elements, lanthanides and actinicles while anions cover majority of halogen (see Fig. 1 (https://github.com/pangchq/Molten-Salt-Simulation-Toolkit/raw/master/Fig.1.jpg)
). Thermophysical properties (~2,500) including constant pressure specific heat capacity, density, thermal expansion coefficient, self-diffusion coefficient, and viscosity as well as microstructure information including partial radial distribution function and coordination curve under atmospheric pressure condition are obtained with respect to different temperature. These calculations are automated using our own code, Molten Salt Simulation Toolkit (MSST), developed at the National Supercomputer Center in Guangzhou. MSST is built upon Tianhe-2 high-performance computing (HPC) clusters and can automatically handle input/output processing of CP2K molecular dynamics and manage job submission to cluster queues. Fig. 2 shows the workflow used to implement the HT-MD. (https://raw.githubusercontent.com/pangchq/Molten-Salt-Simulation-Toolkit/master/Fig.2.jpg)

=== Conclusions ===
The simulated constant pressure specific heat capacity, density, viscosity, thermal expansion coefficient, self-diffusion coefficient, and microstructures are in good agreement with experimental values.

=== Usage notes ===
We recommend usage of the fitting formula of thermophysical properties in the database as some viscosities of simulations near the melting point are not very accurate due to the reason mentioned above. Researchers who concern the precision and would like to obtain more accurate results can rerun the code (https://github.com/pangchq/Molten-Salt-Simulation-Toolkit/) and increase the simulation time.

3DStructGen

2021-06-17T15:22:24Z

Chengxili: /* Conclusions */

== 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal ==
=== Backgroud ===
Nowadays, increasingly more organic as well as inorganic structures not only promote the development of “Big Data” in chemistry and material science, but also raise the demand for cross-platform and web-based tools to search, view, and edit these structures online. Many available web-based tools, which can show three-dimensional (3D) structures of specific materials, have been put forward for displaying existing models, building new models, and preparing initial input files for external calculations, but few of these tools can deal with crystal structures.

=== Results ===
Based on standard web techniques, such as HyperText Markup Language 5 (HTML 5), Cascade Style Sheet (CSS), and JavaScript, we have developed a versatile and user-friendly program called 3DStructGen. In this program, the structure of the non-periodic organic molecules and long-range order crystal materials can both be visualized, built, and edited interactively. Users can view and modify the atoms, bonds, angles, and dihedrals in any molecule or material by some simple mouse operations. Especially, equipped with cheminformatics algorithms for crystal structures, including cleaving surfaces, establishing vacuum layers, and building supercells, four displayed styles, “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell in this program. Moreover, the initial input files of Vienna Ab-initio Simulation Package (VASP) and Gaussian can also be obtained through interacting with dialog boxes in 3DStructGen.

=== Conclusions ===
Other than local desktop software, this program does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

== References ==
1.Chen, P., Wang, Y., Yan, H. et al. 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. J Cheminform 12, 7 (2020). https://doi.org/10.1186/s13321-020-0411-2

3DStructGen

2021-06-17T15:20:50Z

Chengxili: /* Results */

== 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal ==
=== Backgroud ===
Nowadays, increasingly more organic as well as inorganic structures not only promote the development of “Big Data” in chemistry and material science, but also raise the demand for cross-platform and web-based tools to search, view, and edit these structures online. Many available web-based tools, which can show three-dimensional (3D) structures of specific materials, have been put forward for displaying existing models, building new models, and preparing initial input files for external calculations, but few of these tools can deal with crystal structures.

=== Results ===
Based on standard web techniques, such as HyperText Markup Language 5 (HTML 5), Cascade Style Sheet (CSS), and JavaScript, we have developed a versatile and user-friendly program called 3DStructGen. In this program, the structure of the non-periodic organic molecules and long-range order crystal materials can both be visualized, built, and edited interactively. Users can view and modify the atoms, bonds, angles, and dihedrals in any molecule or material by some simple mouse operations. Especially, equipped with cheminformatics algorithms for crystal structures, including cleaving surfaces, establishing vacuum layers, and building supercells, four displayed styles, “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell in this program. Moreover, the initial input files of Vienna Ab-initio Simulation Package (VASP) and Gaussian can also be obtained through interacting with dialog boxes in 3DStructGen.

=== Conclusions ===
3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

== References ==
1.Chen, P., Wang, Y., Yan, H. et al. 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. J Cheminform 12, 7 (2020). https://doi.org/10.1186/s13321-020-0411-2

3DStructGen

2021-06-17T15:20:17Z

Chengxili: /* Backgroud */

== 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal ==
=== Backgroud ===
Nowadays, increasingly more organic as well as inorganic structures not only promote the development of “Big Data” in chemistry and material science, but also raise the demand for cross-platform and web-based tools to search, view, and edit these structures online. Many available web-based tools, which can show three-dimensional (3D) structures of specific materials, have been put forward for displaying existing models, building new models, and preparing initial input files for external calculations, but few of these tools can deal with crystal structures.

=== Results ===
We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen.
=== Conclusions ===
3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

== References ==
1.Chen, P., Wang, Y., Yan, H. et al. 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. J Cheminform 12, 7 (2020). https://doi.org/10.1186/s13321-020-0411-2

3DStructGen

2021-06-17T15:20:07Z

Chengxili: /* Backgroud */

== 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal ==
=== Backgroud ===
Nowadays, increasingly more organic as well as inorganic structures not only promote the development of “Big Data” in chemistry and material science, but also raise the demand for cross-platform and web-based tools to search, view, and edit these structures online. Many available web-based tools, which can show three-dimensional (3D) structures of specific materials, have been put forward for displaying existing models, building new models, and preparing initial input files for external calculations, but few of these tools can deal with crystal structures.

=== Results ===
We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen.
=== Conclusions ===
3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

== References ==
1.Chen, P., Wang, Y., Yan, H. et al. 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. J Cheminform 12, 7 (2020). https://doi.org/10.1186/s13321-020-0411-2

3DStructGen

2021-06-17T15:19:54Z

Chengxili: /* Backgroud */

== 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal ==
=== Backgroud ===
Nowadays, increasingly more organic as well as inorganic structures not only promote the development of “Big Data” in chemistry and material science, but also raise the demand for cross-platform and web-based tools to search, view, and edit these structures online. Many available web-based tools, which can show three-dimensional (3D) structures of specific materials, have been put forward for displaying existing models, building new models, and preparing initial input files for external calculations, but few of these tools can deal with crystal structures.

=== Results ===
We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen.
=== Conclusions ===
3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

== References ==
1.Chen, P., Wang, Y., Yan, H. et al. 3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. J Cheminform 12, 7 (2020). https://doi.org/10.1186/s13321-020-0411-2

Talk:Main Page

2021-06-17T15:19:07Z

Chengxili: /* Question1: Why can’t I submit online calculations? */

= Question1: Why can’t I submit online calculations? =
Answers:
* This website only provides services for users who have bought computing resources on the Tianhe-2c Work cluster, please click [[:here]] to check your certification.
* Users need to have their own Starlight accounts, please click [[:here]] to log in.
* Users need to associate their personal accounts with the system account, please click [[:here]] to associate your account with the system account manually.
* If you meet all the conditions above, please try to clear the cache.

Talk:Main Page

2021-06-17T15:18:39Z

Chengxili: /* Question1: Why can’t I submit online calculations? */

= Question1: Why can’t I submit online calculations? =
Answers:
* This website only provides services for users who have bought computing resources on the Tianhe-2c Work cluster, please click [[:here]] to check your certification.
* Users need to have their own Starlight accounts, please click [[:here]] to log in.
* Users need to associate their personal accounts with the system account, please click [[:here] to associate your account with the system account manually.
* If you meet all the conditions above, please try to clear the cache.

Talk:Main Page

2021-06-17T15:17:00Z

Chengxili: /* Question1: Why can’t I submit online calculations? */

= Question1: Why can’t I submit online calculations? =
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