linux杀dmol3进程,求助DMol3在Linux下提交任务 - 【Materials Studio】 - 分子模拟论坛 Molecular Simulation Forums - Power...

请看Help文件，如下所示

Transfer the input files to the server

If you generated the input files manually using a text editor on the server machine, then no file transfer is required. However, if you generated the files on your PC using Materials Studio, you must transfer them to the server before you can start the calculation. If you can access the hard drive of the server machine directly from the client PC, you can use the Map Network Drive... option on the Windows Explorer Tools menu to help you transfer the files. This allows you to copy and paste files from one location to another. Alternatively, you can use the hard drive on the server as a location for Materials Studio projects.

If you are unable to access the hard drive on the server, you should use the File Transfer tool to transfer files from the client to the server.

To transfer input files to the server using the File Transfer tool

Select the folder containing the input files you wish to transfer using the Project Explorer.

Select Tools | File Transfer from the menu bar. The File Transfer dialog is displayed.

If necessary, supply or update the values for User name, Password, Remote host, Remote folder, and Arguments.

Choose Upload files to server.

Optionally, check the Edit script before executing checkbox. When Edit script before executing is enabled, the script generated when you press Run is opened in a text window immediately after it is created, allowing you to inspect and edit it before it is passed to the FTP client.

Optionally, use the AdditionalFiles option to specify extra files not present in the selected project folder for upload.

Press the Run button. This generates a script that lists all of the files present in the selected project folder and any additional files specified. The FTP client on the local computer is then launched using the command specified in the FTP command text box and the script is executed.

If you checked the Edit script before executing checkbox, a text window containing the script is opened after the script is generated. Make any desired changes, e.g., remove the names of any files you do not wish to transfer to the remote server, and ensure that you save the updated script. As soon as the text window is closed, the FTP client is launched and the script is executed.

Execute the job

To assist you in running DMol3 in standalone mode, a batch/shell file called RunDMol3 is supplied. It can be found in the directory in which the DMol3 executables are located, usually DMol3/bin in the main Materials Studio directory. RunDMol3 scripts are used to start DMol3 jobs in standalone serial or parallel mode. RunDMol3.sh is provided for UNIX and Linux servers, while RunDMol3.bat is provided for Windows servers.

Usage:

RunDMol3.sh [-h] [-nodelete] [-np parallel processes] seedname (UNIX)

or

RunDMol3.bat [-h] [-nodelete] [-np parallel processes] seedname (Windows)

ArgumentDescription

-hDisplays the help text.

-nodeleteSpecifies whether job and scratch files created during DMol3 execution are deleted. When this option is used, all temporary and scratch files are retained on the server. If the option is not used, the script deletes these files upon the termination of the job.

-npSpecifies whether to use a parallel (MPI-based) version of DMol3. When this option is not used, a serial version is of DMol3 is started. When this option is used, an MPI version of DMol3 is invoked, even if only one process is requested.

parallel processesNumber of parallel execution threads to be used.

seednameThe seed used to identify the set of DMol3 input and output files. The input files should be present in the directory in which the DMol3 script is started.

If you wish to calculate properties, you should execute the script for the main run first:

RunDMol3.sh -nodelete seedname

When that run is complete, you should make copies of the .car, .tpvec, .tpdensk and .tpotl files that will be used in all subsequent properties runs:

cp seedname.car seedname_BandStr.car

cp seedname.car seedname_DOS.car

cp seedname.tpvec seedname_BandStr.tpvec

cp seedname.tpvec seedname_DOS.tpvec

etc

Specifically, one needs the following files for a DOS calculation:

seedname_DOS.tpvec

seedname_DOS.tpotl

seedname_DOS.car

seedname_DOS.kpoints (for periodic structures only)

seedname_DOS.tpdensk (for periodic structures only)

and the following files for a Band structure calculation:

seedname_BandStr.tpvec

seedname_BandStr.tpotl

seedname_BandStr.car

seedname_BandStr.kpoints (for periodic structures only)

seedname_BandStr.tpdensk (for periodic structures only)

When the appropriate copies have been made, execute RunDMol3 for each properties run:

RunDMol3.sh -nodelete seedname_DOS

RunDMol3.sh -nodelete seedname_BandStr

These jobs can be run independently because they do not share input or output files.