Materials Studio 2018 is a complete modeling and simulation software package designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and behavior.

Licenses for the following modules are available at NUS IT. Please take note the terms and conditions in the academic license and service agreement which we have signed with Dassault Systems. Your downloading and using of the software imply your acceptance/compliance to the license agreement.

MS Academic Standard Base

• Visualizer and Collections

• Conformers

• Forcite Plus

• QSAR

• Reflex

• VAMP and VAMP Interface

MS Academic Standard Quantum

• CASTEP Parallel and CASTEP Interface

• NMR CASTEP Parallel

• DBTB+

• DMOL3 Interface

• DSOLID State parallel

• ONETEP and ONETEP Interface

• QMERA and QMERA Interface

• GULP Parallel

• CANTERA

MS Academic Standard Classical & Mesoscale

• Adsorption Locator

• Amorphous Cell

• Blends

• Compass Parallel

• Gulp Parallel and Gulp Interface

• Mesocite and Mesocite interface

• Mesodyn and Mesodyn Interface

• Sorption

• Synthia

If you had installed the previous versions of MaterialsStudio on your Windows PC, please remove or uninstall it by going through the normal procedure of removing programs on Windows system: Control Panel ->Programs and Features -> Biovia MaterialsStudio 2016 and click Uninstall.

After that, go to https://bobcat.nus.edu.sg/hpc/support/MS2018/ and download the “MaterialsStudio2018.exe” to your local hard disk, double click to unzip the file, go to the directory and click on “Autorun” to start the installation.

The follows 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 at the end of the installation, or you can choose to start it later as one of the Services in the Windows System Tools. Please refer to the Help menu regarding gateway security and enhancement settings.
• • Check the “Configure Materials Studio 2018 Licensing” when you are asked to, otherwise, click on Configure Materials Studio 2018 Licensing under All Program menu later on to configure your license.

Currently, gateway job submission on MS visualizer is not supported. 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 PBS PRO batch job submission commands. Take CASTEP jobs as examples, 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 or /hpctmp2. Submit jobs to the PBS Pro batch queues as shown in next section.

The default New Project folder and Workspace folder are defined in Tools -> Options -> Locations. Transfer the whole working folder under the New Project over instead of going to the folder and transferring 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 pseudopotential files in /app1/biovia/MaterialsStudio18.1/share/Resources/Quantum/Castep/Potentials, copy them over to your working directory. You can also copy from your own Windows installation, the Potential may be found here: C:\Program Files (x86)\BIOVIA\Materials Studio 18.1 x64 Server\share\Resources\Quantum\Castep\Potentials.

Most of the times, files transferred from Windows PC to the Linux system have “carriage return signs” at the end of each line. In case your jobs execution is affected by this, you can do a “dos2unix filenames” to convert the DOS format to Unix format.

After the files are transferred over, login to any of the login nodes and change directory to /hpctmp2 and your subdirectory, submit your jobs to the batch queue using the following batch job submission script:

#!/bin/bash
#PBS -P ms2018
#PBS -j oe
#PBS -N ms2018castep
#PBS -q parallel2
#PBS -l select=1:ncpus=12:mpiprocs=12:mem=40GB

cd $PBS_O_WORKDIR
np=$( cat  ${PBS_NODEFILE} |wc -l );  ### get number of CPUs, do not change
DSD_MachineList="$PBS_O_WORKDIR/machines.LINUX"
export DSD_MachineList
cat $PBS_NODEFILE  > machines.LINUX
DSD_NumProc=12
export DSD_NumProc

/app1/biovia/MaterialsStudio18.1/etc/CASTEP/bin/RunCASTEP.sh -np ${np} my_castep_job

You can choose to use either “-np 12” or “-np 24”, for jobs submitted to parallel12 or parallel24. Batch jobs can also be submitted to “short” queue, if the jobs can be finished with 24 hours.

Replace the last line in the above script for other kind of jobs (DMOL3, ONETEP, DFTB+, GULP and QMERA) with their specific command scripts:

/app1/biovia/MaterialsStudio18.1/etc/DMol3/bin/RunDMol3.sh -np 24 my_dmol3_job
/app1/biovia/MaterialsStudio18.1/etc/ONETEP/bin/RunONETEP.sh -np 24 my_Onetep_job
/app1/biovia/MaterialsStudio18.1/etc/DFTBpara/bin/RunDFTBpara.sh -np 24 my_DFTP_job
/app1/biovia/MaterialsStudio18.1/etc/GULP/bin/RunGULP.sh -np 24 my_gulp_job
/app1/biovia/MaterialsStudio18.1/etc/QMERA/bin/RunQMERA.sh -np 24 my_qmera_job

First, prepare the .xsd file that contains the structure of the system you want to simulate and .pl file that contains MaterialsScript to execute Forcite:

The .pl file can be created by the following way:

1. Choose Files -> New… from toolbar and “Perl Script” and click OK.
2. New script file will be created. Rename the file to such as “TestForcite.pl”
3. In testForcite.pl file, add the following three lines after the “use MaterialsScript qw(:all);”

my %Args;
GetOptions(\%Args, "Structure=s");
my $doc = $Documents{"your_file.xsd"};

(Here “your_file.xsd” must be changed to your xsd filename)

4. Open the xsd file.
5. Open Forcite calculation dialogue and setup configuration as you do usually.
6. Click on the small down-arrow part that is on the right next to the Run button, and click “Copy Script”.
7. Open the TestForcite.pl file and right-click on the last blank line and choose “Paste”.

You will have something like this:

#!perl
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);
my %Args;
GetOptions(\%Args, "Structure=s");
my $doc = $Documents{"your_file.xsd"}; 

my $results = Modules->Forcite->Dynamics->Run($doc, Settings(
        CurrentForcefield => "COMPASSII",
        ChargeAssignment => "Forcefield assigned",
        Ensemble3D => "NVT",
        NumberOfSteps => 50000,
        TrajectoryFrequency => 10000));
my $outTrajectory = $results->Trajectory;

This example reflects the Forcite configuration and setting, it may differ from your script.

Once xsd and perl script files are prepared, which should be in the folder of the “New Projects” you define in Tools -> Options -> Locations. Transfer them from this location to the HPC server using scp or FileZilla on your PC.

Next, run the following commands on any HPC login server:

> cd /hpctmp2/
> qsub perl_script

The MESOCITE use similar perl script as the above for batch job submission.

Configure your licensing if you have not done so when you do the software installation: right click and choose “Run as administrator” to start “License Administrator 2018”. In the pop up window, Biovia Licence Administrator, choose Connections, to Edit and add the IP addresses (only IP addresses) of the following three license servers 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.

172.18.165.24 lion11.nus.edu.sg
172.18.165.25 lion12.nus.edu.sg
172.18.165.26 lion13.nus.edu.sg

Materials Studio 2018 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 submit a request via nTouch (https://ntouch.nus.edu.sg/)