Materials Studio

Materials Studio is available on the following servers.

Parallel Computing and Informatics Server

Please contact us if you want to use it on your PC.
The following modules are available.

Module	Licenses	Functions
Visualizer	8	Construct structural models, creating and showing of input files for a simulation, calculation results, graphs, tables, etc.
CASTEP_Interface	2	Create input files for CASTEP execution, and analyze the result.
CASTEP	16	Simulate the wide range physical properties in ceramics, a semiconductor, the solid in the substance domain of science containing metal, an interface, and the surface.
DMol3_Interface	2	Create input files for DMol3 execution, and analyze the result.
DMol3-Solid_State	16	Predict physical properties in high reliability and at high speed by the ability of high precision computation based on quantum mechanics.
Forcite Plus	3	Predict a structure and molecule relations, an understanding of an intermolecular interaction, and the character of a solid, a liquid, and gas.
DFTB+	1	An improved implementation of the Density Functional based Tight Binding(DFTB) quantum simulation method for the study of electronic properties of materials and offers unique capabilities to study and understand systems containing hundreds of atoms.
Sorption	1	Predict fundamental properties, such as sorption isotherms(or loading curves) and Henry's constants needed for investigating separations phenomena.
FlexTS	1	Search for the position of a stationary point on the potential energy surface.

How to set License server

Select [BIOVIA]-[Licensing]-[License Administrator] from the start menu.
Select [License Server]-[Connections] and push [Set] or [Edit].

Set [Host name] to “10.1.0.2” and [Port] to “1715”, push [OK].

[Server Status] will be displayed as “Connected”.

How to set Gateway

Select [BIOVIA]-[Server Console] from the start menu.
Right click [Server Gateways] and create [Server Gateway].
Set [URL] to “10.1.4.3”, and [Port Number] to as bellow.

Version	Port Number
2022HF1	18893
2023	18894
2024	18895

It will added to [Server Gateway].

How to execute

Select [BIOVIA]-Materials Studio from the start menu.
The followings are examples of CASTEP, DMol3, DFTB+ and FlexTS.

How to execute CASTEP

This is an example of Si.
① Construction of a Model

② Setting Parameters
Select [Modules]-[CASTEP]-[Calculation] from the menu bar, and set parameters.

③ Submit Job 【In the case of submitting job from Materials Studio】
Select a machine you use on [Job Control] tab.

Gateway location	Machine
10.1.4.3_18893	Parallel Computing & Informatics Server(Materials Studio 2022HF1)
10.1.4.3_18894	Parallel Computing & Informatics Server(Materials Studio 2023)
10.1.4.3_18895	Parallel Computing & Informatics Server(Materials Studio 2024)

【In the case of submitting job from command line】
Select [Files]-[Save Files] in the [CASTEP Calculation] dialog to create input files. Since a job is submitted in the /work area, transfer them to the working directory in the supercomputing system.

*.params
*.cell

*The *.cell is a hidden file.
Use text transfer mode to transfer these files, and don't include space and parentheses as a part of the filenames.

Copy a script file to the current directory.
・Materials Studio 2022HF1

$ cp /work/app/MaterialsStudio2022HF1/MaterialsStudio22.1/etc/CASTEP/bin/RunCASTEP.sh ./

・Materials Studio 2023

$ cp /work/app/MaterialsStudio2023/MaterialsStudio23.1/etc/CASTEP/bin/RunCASTEP.sh ./

・Materials Studio 2024

$ cp /work/app/MaterialsStudio2024/MaterialsStudio24.1/etc/CASTEP/bin/RunCASTEP.sh ./

Please submit job from the front end node of Accelerator Server(gpu.sc.imr.tohoku.ac.jp).
Make a script file

#!/bin/sh
#PBS -l select=1
#PBS -l castep= round up (MPI tasks / 18)
#PBS -q C_002
#PBS -N castep

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunCASTEP.sh -np MPI tasks Si

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) parallel computing and informatics server
When you run Materials Studio 2023 or 2024, you must unload the intel module.

#!/bin/sh
#PBS -l select=1
#PBS -l castep=2     ※ 34/18 =1.888･･･ → 2
#PBS -q C_002
#PBS -N castep

# when you run version 2023 or 2024, uncomment the following line
# module unload intel

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunCASTEP.sh -np 34 Si

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Option -l castep is mandatory.
The argument after MPI tasks is an input file name without extension.
(example) Si.param / Si.cell → Si

④ Confirming Result
Copy output files to your PC.
Use text transfer mode if its format is text. Use binary transfer mode if not.
Select [Modules]-[CASTEP]-[Analysis] from the menu bar.

Density of States

How to execute DMol3

This is the example of benzene.
① Construction of a Model

② Setting Parameters
Select [Modules]-[DMol3]-[Calculation] from the menu bar, and set parameters.

③ Submit Job
【The case of submitting job from Materials Studio】
Select a machine you use on [Job Control] tab.

Gateway location	Machine
10.1.4.3_18893	Parallel Computing & Informatics Server(Materials Studio 2022HF1)
10.1.4.3_18894	Parallel Computing & Informatics Server(Materials Studio 2023)
10.1.4.3_18895	Parallel Computing & Informatics Server(Materials Studio 2024)

【The case of submitting job from command line】
Select [Files]-[Save Files] in the [DMol3 Calculation] dialog to create input files. Since a job is submitted in the /work area, transfer them to the working directory in the supercomputing system.

*.input
*.car

The *.car is a hidden file.
Use text transfer mode to transfer these files, and don't include space and parentheses as a part of the filenames. Copy a script file to the current directory.
・Materials Studio 2022HF1

$ cp /work/app/MaterialsStudio2022HF1/MaterialsStudio22.1/etc/DMol3/bin/RunDMol3.sh ./

・Materials Studio 2023

$ cp /work/app/MaterialsStudio2023/MaterialsStudio23.1/etc/DMol3/bin/RunDMol3.sh ./

・Materials Studio 2024

$ cp /work/app/MaterialsStudio2024/MaterialsStudio24.1/etc/DMol3/bin/RunDMol3.sh ./

Make a script file

#!/bin/sh
#PBS -l select=1
#PBS -l dmol3= round up (MPI tasks / 18)
#PBS -q C_002
#PBS -N dmol3

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunDMol3.sh -np MPI tasks benzene

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) parallel computing and informatics server
When you run Materials Studio 2023 or 2024, you must unload the intel module.

#!/bin/sh
#PBS -l select=1
#PBS -l dmol3=2     ※ 32/18 =1.777･･･ →2
#PBS -q C_002
#PBS -N dmol3

# when you run version 2023 or 2024, uncomment the following line
# module unload intel

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunDMol3.sh -np 32 benzene

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Option -l dmol3 is mandatory.

The argument after MPI tasks is an input file name without extension.
(example) benzene.input/benzene.car → benzene

④ Confirming Result
Copy output files to your PC.
Use text transfer mode if its format is text. Use binary transfer mode if not.
Select [Modules]-[DMol3]-[Analysis] from the menu bar.

Orbitals (HOMO:Right、LUMO:Left)

How to execute DFTB+

This is an example of SWNT.
① Construction of a Model

② Setting Parameters
Select [Modules]-[DFTB+]-[Calculation] from the menu bar, and set parameters.

③ Create a Perl script file
Right-click on the directory of input file in the project window, and select [New]-[Perl Script Document]. The following perl script will be generated.

#perl!
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);

Add the following line to the last line.

my $doc = $Documents{“input file”};

Click [Copy Script] next to [Run] button in the DFTB+ Calculation window and add it to the last line of the perl script.
The following is a final perl script.

#perl!
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);
my $doc = $Documents{“SWNT.xsd”};
my $results = Modules->DFTB->GeometryOptimization->Run($doc, Settings(
OptimizeCell => ‘Yes’,
SKFLibrary => ‘CHNO’,
CalculatiBandStructure => ‘DispersionAndDos’));

④Submit Job
You have to submit job from command line. Please note that you cannot submit job through Materials Studio. Since a job is submitted in the /work area, transfer them to the working directory in the supercomputing system.

*.pl
*.xsd

Use text transfer mode to transfer these files, and don’t include space and parentheses as a part of the filenames. Copy a script file to the current directory.
・Materials Studio 2022HF1

$ cp /work/app/MaterialsStudio2022HF1/MaterialsStudio22.1/etc/Scripting/bin/RunMatScript.sh ./

・Materials Studio 2023

$ cp /work/app/MaterialsStudio2023/MaterialsStudio23.1/etc/Scripting/bin/RunMatScript.sh ./

・Materials Studio 2024

$ cp /work/app/MaterialsStudio2024/MaterialsStudio24.1/etc/Scripting/bin/RunMatScript.sh ./

Make a script file.

#!/bin/sh
#PBS -l select=1
#PBS -l dftb=1
#PBS -q C_002
#PBS -N dftb
DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME
./RunMatScript.sh -np MPI tasks SWNT
cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) parallel computing and informatics server
When you run Materials Studio 2023 or 2024, you must unload the intel module.

#!/bin/sh
#PBS -l select=1
#PBS -l dftb=1
#PBS -q C_002
#PBS -N dftb

# when you run version 2023 or 2024, uncomment the following line
# module unload intel

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunMatScript.sh -np 36 SWNT

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Option -l dftb is mandatory.

The argument after MPI tasks is an input file name without extension.
.ex) SWNT.xsd/SWNT.pl → SWNT

⑤ Confirming Result
Copy output files to your PC. Use text transfer mode if its format is text. Use binary transfer mode if not.
Select [Modules]-[DFTB+]-[Analysis] from the menu bar.

Band Structure

How to execute FlexTS

This is an example of naphthalocyanine.
① Construction of a Model

② Create a Perl script file
Right-click on the directory of input file in the project window, and select [New]-[Perl Script Document]. The following perl script will be generated.

#perl!
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);

Add the following line to the last line.

my $doc = $Documents{“input file”};

The following is a perl script.

#perl!
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);
my $doc = $Documents{“input file”};

③Setting Parameters
FlexTS is available with [Minimum Energy Path] task with DFTB+ and DMol3 module.

・Using DMol3 module
Select [Modules]-[DMol3]-[Calculation] from the menu bar, and select [Minimum Energy Path] task.
Set the parameters.

・Using DFTB+ module
Select [Modules]-[DFTB+]-[Calculation] from the menu bar, and select [Minimum Energy Path] task.
Set the parameters.

④Create a Perl script file
Click [Copy Script] next to [Run] button in the Calculation window and add it to the last line of the perl script.
The following is a final perl script.
・Example) DMol3

#perl!
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);
my $doc = $Documents{“reactor-product.xsd”};
my $results = Modules->DMol3->MinimumEnergyPath->Run($doc, Settings(
Quality => ‘Medium’));

・Example) DFTB+

#perl!
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);
my $doc = $Documents{“reactor-product.xtd”};
my $results = Modules->DFTB+->MinimumEnergyPath->Run($doc, Settings(
Quality => ‘Fine’,
MEPRunMode => ‘TS Path’,
MEPCompareEnergiesOnly => ‘Yes’,
Charge => ‘2’,
UseDC => ‘Yes’,
SpinUnrestricted => ‘Yes’,
UseSmearing => ‘No’));

⑤Submit Job
You have to submit job from command line. Please note that you cannot submit job through Materials Studio. Since a job is submitted in the /work area, transfer them to the working directory in the supercomputing system.

*.pl
*.xsd / *.xtd
*.arc (Using DFTB+)

The *.arc file is a hidden file.
Use text transfer mode to transfer these files, and don’t include space and parentheses as a part of the filenames. Copy a script file to the current directory.
・Materials Studio 2022HF1

$ cp /work/app/MaterialsStudio2022HF1/MaterialsStudio22.1/etc/Scripting/bin/RunMatScript.sh ./

・Materials Studio 2023

$ cp /work/app/MaterialsStudio2023/MaterialsStudio23.1/etc/Scripting/bin/RunMatScript.sh ./

・Materials Studio 2024

$ cp /work/app/MaterialsStudio2024/MaterialsStudio24.1/etc/Scripting/bin/RunMatScript.sh ./

Make a script file.
・Example) DMol3

#PBS -l select=1
#PBS -l dmol3= round up MPI tasks / 18
#PBS -l flexts=1
#PBS -q C_002

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunMatScript.sh -np MPI tasks reactor-product

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) parallel computing and informatics server
When you run Materials Studio 2023 or 2024, you must unload the intel module.

#!/bin/sh
#PBS -l select=1
#PBS -l dmol3=2
#PBS -l flexts=1
#PBS -q C_002

# when you run version 2023 or 2024, uncomment the following line
# module unload intel

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunMatScript.sh -np 36 reactor-product

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Option -l dmol3 and -l flexts are mandatory.

The argument after MPI tasks is an input file name without extension.
.ex) reactor-product.xsd/ reactor-product.pl → reactor-product

・Example) DFTB+

#PBS -l select=1
#PBS -l dftb=1
#PBS -l flexts=1
#PBS -q C_002

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunMatScript.sh -np MPI tasks reactor-product

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) parallel computing and informatics server
When you run Materials Studio 2023 or 2024, you must unload the intel module.

#!/bin/sh
#PBS -l select=1
#PBS -l dftb=1
#PBS -l flexts=1
#PBS -q C_002

# when you run version 2023 or 2024, uncomment the following line
# module unload intel

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

./RunMatScript.sh -np 36 reactor-product

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Option -l dftb and -l flexts are mandatory.

The argument after MPI tasks is an input file name without extension.
.ex) reactor-product.xtd/ reactor-product.pl → reactor-product

⑥ Confirming Result
Copy output files to your PC. Use text transfer mode if its format is text. Use binary transfer mode if not.

Connected Path

Confirming Job Status

【The case of submitting job from Materials Studio】
See [Jobs] pane at the lower right of the screen on Materials Studio.

Canceling Job

【The case of submitting job from Materials Studio】
Right-click [Jobs] pane on Materials Studio, and select [Actions]-[Stop] from the pull-down menu.

[JobStatus] changes to “terminated” after a while, and your job stops with the following pop-up.

Materials Studio

Parallel Computing and Informatics Server

How to set License server

How to set Gateway

How to execute

How to execute CASTEP

How to execute DMol3

How to execute DFTB+

How to execute FlexTS

Confirming Job Status

Canceling Job