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 in project mode or 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
A description of the files that make up the project can be found in New Project.
Create initial structure
Click New Project and follow the Structure Building procedure to create the system you want to calculate.
Click New project with current structure to switch from file mode to project mode, for example, with an existing structure file open.
If you want to run calculations on an existing structure file, you can click New Project and then use Import File to load the structure.
Configure simulation conditions
Select the solver you want to use at Sovlver pull-down menu
, and click Workflow Setup button
.
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.
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. Enter the number of processes or threads to use in parallel number. (For parameter and structure scan functions, enter the number of parallels for each calculation.) 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.
To stop a job, right-click on the job you want to stop in the working folder in the project view area and click Stop.
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 in file mode 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.
Enter the number of processes or threads to use in parallel number. (For parameter and structure scan functions, enter the number of parallels for each calculation.)
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.
To stop a job, right-click on the job you want to stop in the working folder in the project view area and click Stop.
If you want to check the end of the log or retrieve and visualize some files while the job is running, right-click the target job in the working folder of the project view area and click Control Remote Job/Server ` in the :guilabel:`Project View Area. See Each function of the Submit Remote Job window for instructions on how to operate the Control Remote Job/Server window that opens.
If you do not want to run the calculation directly from Winmostar and only want to save the file
Configure Job window, set up as you would for a local or remote job, then check Do not run own part after saving file and click Save at the bottom right. Then click to see the set of saved input files, batch files, and shell scripts.
Display and analyze physical quantities
Extend job
Create initial structure
Click New File and follow the Structure Building procedure to create the system you want to calculate.
Configure simulation conditions
Select the solver you want to use at Sovlver pull-down menu
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 you want to abort a job, close the appropriate console window or perform Ctrl-C while the appropriate console window is active.
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. See Remote Job Setup Procedures in file mode for how to set it up. After that, press the Send & Submit button on the Submit Remote 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 Remote Job Operation Procedures in File Mode for other detailed operations.
If you want to abort a job, remember the job ID that appears immediately after you run Send & Submit, and in the Submit Remote Job window, click and enter the job ID.
If you do not want to run the calculation directly from Winmostar and only want to save the file
For LAMMPS, Gromacs, and Quantum ESPRESSO:
Go to the Options tab in the keyword configuration window, press the Dump all files for remote button, enter a file name and save it.
For other solvers:
Close the Keyword Setup window by clicking the OK button. Then click to save the file. If you want to save not only the input file but also accompanying files such as shell scripts, use the project mode.
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 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