4. Basic Operation Flow¶
Here, we introduce the basic operation flow of quantum chemical calculation, molecular dynamics calculation, or first principles calculation using Winmostar.
- Create initial structureFollow the procedure described at Structure Building to create the system you want to calculate.
- Configure simulation conditions
Select the solver you want to use at Sovlver pull-down menu , and click Configure button .
For some solvers, if you put a pointer over the keyword column, the meaning of that keyword will appear.
- Run simulation
To execute calculations on Windows PC with Winmostar installed ( **Local job** )
- With the configure window open, press the Run button.
- Press the OK button to close the configure window. So if you want to modify the keywords directly, enter at Keyword Editor or edit the input file from the Open in Text Editor using any text editor. Then click the Run button on the tool bar .
After clicking Run, if the input file is not saved, entering the name of the input file will be saved, then the job will be registered in Winmostar Job Manager.
Winmostar Job Manager will process the registered jobs in order.
When running on a Linux machine connected to the network on Winmostar installed PC (Remote job)
Press the OK button to close the configure window.
Next, click the Submit Remote Job button on the tool bar to set up connection to the server. After that, press the Send & Submit button on the Submit Remoet Job window to save and transfer (send) the input file and register the job at the remote server (submit) at once.
Registered jobs are executed in order on the remote server.
When the job ends on the remote server Press the Get All Files button to transfer the file output from the calculation to the Windows PC where Winmostar is installed.
For details, see Submitting remote job.
- Confirm log
Press the Open Log File button on the toolbar.
You are asked which file to open. If the input file of the calculation you want to check log is displayed in the main window, open the file selected by default.
The log file is displayed with a text editor, then check whether the job has ended normally or abnormally.
- Display and analyze physical quantities
If the job has ended normally, press the Analysis button on the toolbar and select the menu of physical quantities you want to display.
You will be asked which file to open, so choose as appropriate. As with log checking, the one associated with the file displayed in the main window is selected by default.
When you specify a file, a window for the result display is displayed.
- To visualize the structure optimization process or trajectory, press the Animation button on the tool bar .
- To plot changes of energies and temperature during SCF or MD calculation, press the Energy Plot button on the tool bar.
- For analysis of molecular shape, use functions below Tool menu.
- Extend job
If it is necessary to extend or continue the job, open the configure window again and start the job.
- For MD, check Extending Simulation in the configure window.
- For Quantum ESPRESSO, set Continue to Output Direcotory in the configure window.
- If you want to run simulation after the structure optimization for semi-empirical QM or QM solvers, press the Animation button on the toolbar, display the final structure on the main window and configure for the next job.