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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