4. Basic Operation Flow

Here, we introduce the basic operation flow of quantum chemical calculation, molecular dynamics calculation, or first principles calculation using Winmostar.

Start Winmostar and click on file ‣ new project in project mode or file ‣ new file in file mode.

Project Mode

You can manage jobs without being aware of individual files. We recommend using this mode for non-free users.

File Mode

Explicitly operates on individual files, with procedures compatible with V10 and earlier. Use this mode when using the free version or a solver/job scheduler that does not support project mode, or when running calculations using input files for each solver created outside of Winmostar.

4.1. For project mode

  1. Create initial structure

Follow the procedure described at Structure Building to create the system you want to calculate.

  1. Configure simulation conditions

Select the solver you want to use at Sovlver pull-down menu solver , and click Workflow Setup button toolbar_configure.

The # of Jobs specifies the number of jobs to be executed this time. If # of Jobs is 2 or more, jobs are executed sequentially, with the final structure of each job being used as the initial structure of the next job.

In the central part of the workflow settings window, you specify the calculation conditions for each job.

Finally, click OK.

  1. Run simulation

  • To execute calculations on Windows PC with Winmostar installed ( **Local job** )

    Job setup window, check Run job on this machine and click Run. The Winmostar Job Manager will process the registered jobs in order.

    After executing, check the status of each working folder in the project display area. If the computation proceeded normally, the state will change from NEW to PEND to RUN to END. If there is an anomaly, the state will be ABORT.

    Project Display Area, hovering the cursor over a working folder will display an error message. Click on the working folder and in the Actions click on Log to see the log of the calculation.

  • When running on a Linux machine connected to the network on Winmostar installed PC (Remote job)

    You can also check the instructions at Remote Job Tutorial (Japanese only).

    In the Job Settings window, check the Run job on remote machine checkbox. In the Profile select the server settings you want to use.

    If there is no appropriate profile, click Config and enter the server information. See Remote Job Setup Procedures for more information.

    If you need to specify a separate environment variable to use the solver on a remote server, click New in the Template Script, edit the shell script to use when submitting jobs, and select it in Template Script.

    options are arguments for commands (such as qsub) to submit jobs on remote servers. Typically, options are entered that depend on the type of queue you want to use and your machine configuration. You can use Alias string available for remote job function in this field to abstractly specify the number of parallels, etc.

    Profile and Options can be tested with Test Connection. You can also use Control to check for free queues, etc.

    Finally, click Run. The registered jobs will be executed in order on the remote server.

    After executing, check the status of each working folder in the project display area. If the computation proceeded normally, the state will change from NEW to SEND to PEND to RUN to END(Rem)→RECV to END(-). If there is an anomaly, the state will be ABORT.

    Error message appears when hovering the cursor over the working folder in the project display area. Right-click on the working folder and click Open Remote stdout or Open Remote stderr to see the standard output and standard error when executed remotely. You can see the log of the calculation by clicking on the working folder and clicking Log in Actions.

    If the status is END(-) and you have finished successfully on the remote server, click on the working folder and under Actions click Receive All Remote Output Files and all output files will be saved to the local Transfer to machine.

  1. Display and analyze physical quantities

  1. Extend job

  1. Create initial structure

Follow the procedure described at Structure Building to create the system you want to calculate.

  1. Configure simulation conditions

Select the solver you want to use at Sovlver pull-down menu solver , and click Keyword Setup button toolbar_configure.

For some solvers, if you put a pointer over the keyword column, the meaning of that keyword will appear.

  1. 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 toolbar_run.

    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 toolbar_submit on the tool bar to set up connection to the server. See Remote Job Setup Procedures for how to set it up. 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.

    See Advanced Operation of Remote Jobs for other detailed operations.

  1. Confirm log

Press the Open Log File button toolbar_openlog 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.

  1. Display and analyze physical quantities

If the job has ended normally, press the Analysis button toolbar_analysis 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 toolbar_animation.

  • To plot changes of energies and temperature during SCF or MD calculation, press the Energy Plot button toolbar_energyplot on the tool bar.

  • For analysis of molecular shape, use functions below Tool menu.

  1. Extend job

If it is necessary to extend or continue the job, open the configure window again and start the job.

  • For MD, check Continue 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 toolbar_animation on the toolbar, display the final structure on the main window and configure for the next job.