National University of Singapore

1. Introduction

Materials Studio 6.1 from Accelrys Inc is Materials Studio's modeling and simulation product suite, and is designed for structural and computational researchers in chemicals and materials R&D who need to perform expert-level modeling and simulations tasks in an easy to learn yet powerful environment. It provides flexible and validated tools for the study of materials at various length and time scales.

2. License

License for the following modules are available at Computer Centre. Please take note the terms and conditions in the academic license and service agreement we have signed with Accelrys. Your download and usage of the software implies your acceptance/compliance.

Materials Visualizer - the core MS Modeling product, provides all of the tools that are required to construct graphical models of molecules, crystalline materials, and polymers. Additionally, the Visualizer lets you view and analyze these models and provides the software infrastructure and analysis tools to support the full range of Materials Studio products (10 licenses)

CASTEP - a premier density functional theory quantum mechanical code to simulate the properties of solids, interfaces, and surfaces. (8 licenses available for CASTEP)

Discover - molecular mechanics and dynamics methods for structure and property prediction (3 licenses are available for Discover).

DMol3 - a unique density functional theory quantum mechanical code for gas phase, solvent, and solid state simulations (8 licenses available for DMol3).

Forcite - a molecular mechanics product for energy calculation and geometry optimization of molecules and periodic systems (Forcite shares the same license as Discover).

 

3. Install MS Visualizer on your PC

If you had installed the previous versions of Materials Studio on your PC, please remove or uninstall it by going through the normal procedures of removing programs on Windows systems: Control Panel  ->Programs and Features ->Accelrys MS Modeling 5.5 and click Uninstall.

After that, go to http://bobcat.nus.edu.sg/mswin and download  the “MaterialsStudio61.zip” to your local hard disk, unzip the file,  go to the directory and click on “Autorun” to start the installation.

The following are some scenarios you need to take note:

• Choose Complete installation to install all modules, this will ensure you view the help and tutorial for all modules, also allow you run simple jobs on your local PC.
• Check the "Start Gateway" box will start Gateway service on your local PC, or you can choose to start later as one of the Services in the System Tools. Please refer to the on line help manual regarding gateway security and enhancement settings.
• Check the "Configure Materials Studio 6.1 Licensing" when you are asked to, otherwise, click on Licensing under Accelrys from  the All Program menu  later on to configure your license.
  
  

4. Create Job files and Submit Jobs at the HPC Systems

Currently, we don’t support job submission through MS visualizer. You need to build your models using the Materials Studio Visualizer, save and transfer all files to HPC servers, and submit your jobs to the batch queues using LSF commands. Take CASTEP jobs as example, once you build your model, go to Modules, CASTEP and Calculation. Set up your CASTEP calculation, choose Files in the CASTEP Calculation panel, click Files..., the CASTEP Job Files window will pop up, click Save File to save the jobs files to your default New Project Folder. Login to any of the login nodes and transfer your files to the common working directory: /hpctmp. Submit jobs to the LSF queues as shown in next section.

The default New Project folder and workspace folder are defined in Tools -> Options -> Locations. You can edit those folders by click on the Edit button. Transfer the whole folder over instead of going to the folder and transfer individual files. Please refer to the new users guide for instructions on how to transfer files to HPC systems.

The Materials Studio project folder does not contain the pseudopotential files required to run a CASTEP job. Therefore, you must determine which pseudopotential files are required by examining the .cell file. Find the files in /app1/Accelrys/MaterialsStudio6.1/Potentials, copy them over to your working directory.

Most of the times, files transferred from Windows PC to the Linux system have "carriage return signs" at the end of each line. You can do a "dos2unix filename" to convert the DOS format to Unix format. Otherwise, your jobs could be terminated.

5. Submit Jobs Through LSF

Login to any of the login nodes and change directory to /hpctmp and your subdirectory, then submit your jobs to the LSF batch system:

• bsub -q linux64 -m atlas5cluster -o my_job.eo "/app1/Accelrys/MaterialsStudio6.1/etc/Discover/bin/RunDiscover.sh -np 4 my_job"   
• bsub -q linux64 -m atlas5cluster -o my_job.eo "/app1/Accelrys/MaterialsStudio6.1/etc/DMol3/bin/RunDMol3.sh -np 4 my_job"   
• bsub -q linux64 -m atlas5cluster -o my_job.eo "/app1/Accelrys/MaterialsStudio6.1/etc/DMol3/bin/RunDMol3.sh -np 4 my_job"   
  
  

Large memory jobs can be submitted to atlas5_large or atlas6_large queues. In this case, you don’t need to specify the hosts using “-m atlas5cluster”. Jobs submitted to atlas5 queues can choose to use either “-np 4” or “-np 8”, and jobs submitted to atlas6 queues can choose to use either “-np 6” or “-np 12”, which will draw 1 or 2 software licenses per job.

6. Extra Notes on Calculating Material Properties Using CASTEP

When the first CASTEP job run is complete, make copies of the *.check file that will be used in all subsequent properties runs:

• cp my_job.check  my_job_BandStr.check
• cp my_job.check  my_job_DOS.check
• cp my_job.check  my_job_Optics.check
  
  

When the appropriate copies have been made, execute RunCASTEP for each property run:

• bsub -q linux64 -m atlas5cluster -o my_job.eo "/app1/Accelrys/MaterialsStudio6.1/etc/CASTEP/bin/RunCASTEP.sh my_job_DOS"
• bsub -q linux64 -m atlas5cluster -o my_job.eo "/app1/Accelrys/MaterialsStudio6.1/etc/CASTEP/bin/RunCASTEP.sh my_job_BandStr"

• bsub -q linux64 -m atlas5cluster -o my_job.eo "/app1/Accelrys/MaterialsStudio6.1/etc/CASTEP/bin/RunCASTEP.sh my_job_Optics"
  

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

7. Getting License from the License Server "lion4" “lion2” and “lion3”

Configure your licensing if you have not done so when you do the software installation.  Click All Programms -> Accelrys -> Configure Materials Studio 6.1 Licensing. In the pop up window, Accelrys Licensing, choose Connect to a Remote Server, add "lion4" "lion2" and "lion3" as the hostnames (click and check the "Redundant Servers" box) and keep the default 1715 as the port number and click OK to exit. You'll see a "started" as the status of the license server connection.

For Windows Vista and Windows 7 users, you when you start the License Administrator 7.6.8, you need to right click on the License Administrator 7.6.8 button and choose "Run as administrator" if you want to modify the license hosts.

Before this, you need to modify your "hosts" file on your PC to add this line under the line "172.0.0.1 localhost":

172.18.173.56  lion4.nus.edu.sg  lion4
172.18.165.5  lion2.nus.edu.sg  lion2
172.18.165.160  lion3.nus.edu.sg  lion3

The "hosts" file can be found at C:\WINDOWS\system32\drivers\etc. For Window 7 users, you need to open the text editor, i.g., Wordpad by “Run as Administrator” to read and modify the file. .

8. Help

Materials Studio 6.1 on-line help and tutorials are available by clicking on the Help button on the Materials Studio Visualizer Interface. If you have any problems or queries, please send emails to