MaterialsStudio

2017.05

version 1.8

Materials Studio 1

1. 1

1.1 1

1.2 1

1.3 2

2. TSUBAME 2

2.1 Materials Studio 2

2.2 2

2.3 Visualizer 3

3. 3

3.1 3

3.2 8

4. 12

4.1 12

4.2 15

5. PBS 27

5.1 27

5.2 PBS 29

31

Materials Studio

1. Materials Studio TSUBAME TSUBAME TSUBAME

Materials StudioWeb

http://accelrys.co.jp/

1.1 TSUBAME

Materials Studio 5.0.1, 5.5.3, 6.0 SP1, 7.0 SP1, 8.0 SP1, 2017 R2

1.2 Materials Studio Materials VisualizerMaterials Visualizer Materials Studio (GUI)

Materials Studio

Forcite ( Discover )MMMD

Compass

CASTEP(Density Functional Theory, DFT) //

DMol3(Density Functional Theory, DFT) /

Amorphous Cell

Reflex PlusReflexPowder Solve ReflexPowder indexing

Materials Studio

1

http://accelrys.co.jp/

X-CellIndexing Indexing Indexing IndexingIndexing

1.3 Windows Materials Studio

Materials Studio Help

2. TSUBAME

2.1 Materials Studio Materials Studio AccelrysMaterials Studio () Materials Studio

Welcome to Materials StudioCreate a new project Open an existing project Create a new project Open an existing project

[File]-[Exit]

2.2 TSUBAME token (Materials Studio, Discovery Studio 40token12280token) TSUBAME

$ lmutil lmstat -S msi -c 27060@t2zlic01

1.3

2

20 token

CASTEP 4 token []

Biovia(Materials Studio/Discovery Studio) - http://tsubame.gsic.titech.ac.jp/node/1493

BIOVIA(Materials Studio/Discovery Studio)() - http://tsubame.gsic.titech.ac.jp/node/1510

2.3 Visualizer Accelrys Status Cannot connect

Materials Studio Visualizer

Cannot connect Visualizer

3. .

3.1 . Materials StudioWelcome to Materials Studio Create a new project.

2.3 Visualizer

3

http://tsubame.gsic.titech.ac.jp/node/1493http://tsubame.gsic.titech.ac.jp/node/1493http://tsubame.gsic.titech.ac.jp/node/1510http://tsubame.gsic.titech.ac.jp/node/1510

New Project. ()OK. .

FileNew.

New Document. 3D Atomistic.

..

2.3 Visualizer

4

. Sketch Atom. (). .

(3D Atomistic ).. . . . Esc..

2.3 Visualizer

5

. ViewDisplay Style.

Display StyleBall and stick.

.

. Sketch Atom Oxygen.

2.3 Visualizer

6

. Esc.

. Adjust Hydrogen.

.

Clean.

2.3 Visualizer

7

.

3.2 .

3.1 . .Sketch Ring. 6 Member.

3.2

8

(3D Atomistic ). 6.

. ViewDisplay Style.

Display StyleBall and stick.

.

3.2

9

6.

3D Viewer Selection Mode .

Modify Bond TypePartial Double Bond 6.

3.2

10

. Adjust Hydrogen.

.

Clean.

..

3.2

11

.

4.

4.1 3.

4.

12

Discover

Discovery ModulesDiscoverSetup

Discover Setup

compass Discover SetupEnergyForcefieldcompass

Discover SetupJob Control

4.

13

1CPU

ModulesDiscoverMinimizer

Discover Minimization Minimize

Job Completed OK

4.

14

4.2 (AlAs)

AlAs

AlAsF-43m216

2AlAsfractional(0,0,0)(0.25,0.25,0.25)

5.6622

Materials Studio

FileNew3D Atomistic Document

Project Explorer3D Atomistic Document Rename AlAs

4.2

15

BuildCrystalsBuild Crystal

Build Crystal

Enter group216f-43mTAB TAB

4.2

16

Lattice ParametersA10.005.662

Build 3D3D

4.2

17

BuildAdd Atoms Add Atoms

OptionCoordinate SystemFractional

AtomsElement textAl Add

4.2

18

Al

Element textAsa,b,c0.25 Add

4.2

19

BuildCrystalsRebuild Crystal Rebuild CrystalRebuild

Ball and StickViewDisplay Style Ball and stick

4.2

20

BuildSymmetryPrimitive Cell

CASTEP

4.2

21

CASTEP ModulesCASTEPCalculation CASTEP Calculation

TaskGeometry OptimizationQualityFine

TaskMore CASTEP Geometry Optimization Optimization cell

CASTEP CalculationProperties

Properties Band structureDensity of states

4.2

22

CASTEP CalculationJob Control

Run in parallel 4

2016104 CASTEP 4 token CASTEP 1 processor TSUBAME

[]

BIOVIA(Materials Studio/Discovery Studio)() - http://tsubame.gsic.titech.ac.jp/node/1510

Run

Job Completed OK

4.2

23

http://tsubame.gsic.titech.ac.jp/node/1510http://tsubame.gsic.titech.ac.jp/node/1510

Analysis(DOS)()

(AlAs.xsd)() ModuleCASTEPAnalysis

CASTEP Analysis Band structureView

4.2

24

AlAs

(AlAs.xsd)() ModuleCASTEPAnalysis

CASTEP Analysis Density of statesMore

4.2

25

Integration methodInterpolation Accuracy levelFineOK

CASTEP AnalysisView

4.2

26

5. PBSPBS 4

Amorphous CellCASTEPDMol3Discover ( 7.0SP1 )

5.1 Discover DiscoverDynamics

Discover Molecular Dynamics File

5. PBS

27

Dynamics Job Files Save Files

5. PBS

28

.inp.car.mdf 3

1. Materials StudioHelpTutorials

2. Remote jobsRunning in standalone mode

5.2 PBS(1)

5.1TSUBAME

(2)

CRLF

5.2 PBS

29

$ file benzene.inp benzene.car benzene.mdfbenzene.inp: ASCII text, with CRLF line terminatorsbenzene.car: ASCII text, with CRLF line terminatorsbenzene.mdf: ASCII text, with CRLF line terminators

CRLFLF dos2unix

$ dos2unix benzene.inp benzene.car benzene.mdfdos2unix: converting file benzene.inp to UNIX format ...dos2unix: converting file benzene.car to UNIX format ...dos2unix: converting file benzene.mdf to UNIX format ...

$ file benzene.inp benzene.car benzene.mdfbenzene.inp: ASCII textbenzene.car: ASCII textbenzene.mdf: ASCII text

(3)PBS

(a). Discover

cp /usr/apps/isv/MaterialsStudio/5.0.1/etc/Discover/bin/RunDiscover.sh .

5.0.1 Discover .

2017 R2Amorphous Cell /usr/apps.sp3/isv/MaterialsStudio/2017R2/MaterialsStudio17.2/etc/AmorphousCell/bin/RunAmorphousCell.shCASTEP /usr/apps.sp3/isv/MaterialsStudio/2017R2/MaterialsStudio17.2/etc/CASTEP/bin/RunCASTEP.shDMol3 /usr/apps.sp3/isv/MaterialsStudio/2017R2/MaterialsStudio17.2/etc/DMol3/bin/RunDMol3.sh

8.0 SP1Amorphous Cell /usr/apps.sp3/isv/MaterialsStudio/8.0.SP1/MaterialsStudio8.0/etc/AmorphousCell/bin/RunAmorphousCell.shCASTEP /usr/apps.sp3/isv/MaterialsStudio/8.0.SP1/MaterialsStudio8.0/etc/CASTEP/bin/RunCASTEP.shDMol3 /usr/apps.sp3/isv/MaterialsStudio/8.0.SP1/MaterialsStudio8.0/etc/DMol3/bin/RunDMol3.sh

7.0SP1Amorphous Cell /usr/apps.sp3/isv/MaterialsStudio/7.0.SP1/MaterialsStudio7.0/etc/AmorphousCell/bin/RunAmorphousCell.shCASTEP /usr/apps.sp3/isv/MaterialsStudio/7.0.SP1/MaterialsStudio7.0/etc/CASTEP/bin/RunCASTEP.shDMol3 /usr/apps.sp3/isv/MaterialsStudio/7.0.SP1/MaterialsStudio7.0/etc/DMol3/bin/RunDMol3.shDiscover /usr/apps.sp3/isv/MaterialsStudio/7.0.SP1/MaterialsStudio7.0/etc/Discover/bin/RunDiscover.sh

6.0 SP1Amorphous Cell /usr/apps/isv/MaterialsStudio/6.0.SP1/MaterialsStudio6.0/etc/AmorphousCell/bin/RunAmorphousCell.shCASTEP /usr/apps/isv/MaterialsStudio/6.0.SP1/MaterialsStudio6.0/etc/CASTEP/bin/RunCASTEP.shDMol3 /usr/apps/isv/MaterialsStudio/6.0.SP1/MaterialsStudio6.0/etc/DMol3/bin/RunDMol3.shDiscover /usr/apps/isv/MaterialsStudio/6.0.SP1/MaterialsStudio6.0/etc/Discover/bin/RunDiscover.sh

5.5.3Amorphous Cell /usr/apps/isv/MaterialsStudio/5.5.3/etc/AmorphousCell/bin/RunAmorphousCell.shCASTEP /usr/apps/isv/MaterialsStudio/5.5.3/etc/CASTEP/bin/RunCASTEP.shDMol3 /usr/apps/isv/MaterialsStudio/5.5.3/etc/DMol3/bin/RunDMol3.shDiscover /usr/apps/isv/MaterialsStudio/5.5.3/etc/Discover/bin/RunDiscover.sh

5.0.1Amorphous Cell /usr/apps/isv/MaterialsStudio/5.0.1/etc/AmorphousCell/bin/RunAmorphousCell.shCASTEP /usr/apps/isv/MaterialsStudio/5.0.1/etc/CASTEP/bin/RunCASTEP.shDMol3 /usr/apps/isv/MaterialsStudio/5.0.1/etc/DMol3/bin/RunDMol3.shDiscover /usr/apps/isv/MaterialsStudio/5.0.1/etc/Discover/bin/RunDiscover.sh

(b). test_rundiscover.sh

5.2 PBS

30

#!/bin/bashcd ${PBS_O_WORKDIR}

./RunDiscover.sh

12 CPU CPU 13 12 CPU AmorphousCell 1 CPU

#!/bin/bashcd ${PBS_O_WORKDIR}

./RunDiscover.sh -np

benzene.inp benzene

(c).

chmod +x test_rundiscover.sh

(d).

$ t2sub test_rundiscover.sh

$ t2sub -l select=1:ncpus=:mpiprocs= test_rundiscover.sh

version 1.0 2010 11 1 --

version 1.1 2011 9 1 2.2, 5 : 5.5.3

version 1.2 2012 9 10 2.2, 5 : 6.0 SP1

version 1.3 2013 1 24 5 : CPU4CPU12CPU

version 1.4 2013 4 3 2 : 2012

version 1.4 2013 6 6 2.3 :

version 1.5 2014 5 13 2.2, 5 : 7.0 SP1

version 1.5 2014 5 13 4 : 4

version 1.6 2015 7 16 5 : 8.0 SP1

version 1.7 2017 2 28 2.2, 4.2 :

31

version 1.8 2017 5 11 5 : 2017 R2

32

Materials Studio 1. 1.1 1.2 1.3

2. TSUBAME 2.1 Materials Studio 2.2 2.3 Visualizer

3. 3.1 3.2

4. 4.1 4.2

5. PBS5.1 5.2 PBS