Atomistic Simulations LAMMPS & VMD

Dr. Kasra Momeniwww.KNanoSys.com

PI: K. Momeni

Outline• HandsonExperiment

• LAMMPS• VMD• Binning

• DiffusionCoefficientfromMD

AdHiMad Lab 2

PI: K. Momeni

Hands on – LAMMPS

• Createthesimulationboxwithatoms

#---------- InitializeSimulation--------clearunitsljdimension2boundarysspatom_style atomic

#---------- CreateAtoms--------------latticesq21.0regionboxblock010101unitslatticecreate_box 1boxcreate_atoms 1box

mass*1write_dump allatomini.atomquit

AdHiMad Lab 3

PI: K. Momeni

Visualization – VMD

AdHiMadLab 4

(1) New Molecule

(c) Browse

(d) Load

(b) Molecule file browser

PI: K. Momeni

VMD – Rendering

AdHiMad Lab 5

(3) Draw style

(1) Current graphicalrepresentation

(4) Coloring

(5) Drawing method

(2) Selected Atoms

(6) Settings associated to particular drawing method

PI: K. Momeni

VMD – Practice

• VMD• Makeanimage

• File>Render...• Atomspositions• Bondlength

AdHiMad Lab 6

PI: K. Momeni

VMD – Command Line• Extensions >Tk Console• SomeCommands

• rotate• rock• scale• stage• translate• []• atomselect

• top• all

• measure• minmax

measureminmax [atomselect topall]

AdHiMad Lab 7

http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node105.html

PI: K. Momeni

Hands on LAMMPS – Dynamic Run • Createthesimulationboxwithatoms#---------- InitializeSimulation--------clearunitsljdimension2boundarysspatom_style atomic#---------- CreateAtoms--------------latticesq21.0regionboxblock010101unitslatticecreate_box 1boxcreate_atoms 1box

mass*1write_dump allatomini.atom

#---------- DefineInteratomicPotential-------pair_style lj/cut2.5pair_coeff **11

#---------- RunMinimization---------------------fix2allnverun_style verlet

#---------- DefineSettings---------------------thermo 1thermo_style customsteptempetotal

run100quit

AdHiMad Lab 8

PI: K. Momeni

Lammps.log FileLAMMPS(30Jul 2016)...

WARNING:...

…

Neighborlistinfo...1neighborlistrequests

updateevery1steps,delay10steps,checkyes

maxneighbors/atom:2000,pagesize:100000

masterlistdistancecutoff=2.8ghostatomcutoff=2.8

binsize =1.4->bins=222

Memoryusageperprocessor=2.33558Mbytes

StepTempTotEng0 0 -0.37460938

10.0057828055 -0.3746222

…

Looptimeof0.000486986on1procsfor100stepswith5atoms

Performance:88708918.567tau/day,205344.719timesteps/s

77.2%CPUusewith1MPItasksxnoOpenMP threads

MPItasktimingbreakdown:

Section| mintime | avg time | maxtime |%varavg|%total

---------------------------------------------------------------

Pair |3.8565e-05|3.8565e-05|3.8565e-05| 0.0| 7.92Neigh |1.657e-06 |1.657e-06 |1.657e-06 | 0.0| 0.34

Comm |1.1892e-05|1.1892e-05|1.1892e-05| 0.0| 2.44

Output |0.00035416|0.00035416|0.00035416| 0.0|72.72

Modify |1.9303e-05|1.9303e-05|1.9303e-05| 0.0| 3.96Other | |6.141e-05 | | |12.61

AdHiMad Lab 9

PI: K. Momeni

Hands on – LAMMPS #---------- DefineSettings---------------------thermo 1thermo_style customsteptempetotal

#---------- Definecalculatedvariables ---------------------computeperatom allpe/atomcomputepe allreducesumc_peratomcomputeperatomke allke/atomcomputeke allreducesumc_peratomke

variabletoteng equalpe+kevariablestepequalstep

#---------- RunMinimization---------------------fix2allnverun_style verlet

dump1allatom1my.atomdumpstr allcustom1my.dat idxyzc_peratomc_kefix3allprint1"${step}${toteng}"filetoteng.txt

run100

AdHiMad Lab 10

PI: K. Momeni

Homework 1 – Solution • CalculatethenumberofsurfaceatomsinaFCCcrystalwith10unitcellsineachdirection

• Hint1:Thereare4atomsinaFCCunitcell• Hint2:#surfaceatoms=#Total- #interioratoms

Total#atoms:4*10^3=4000Interior#atoms:4*(10-0.5-0.5)^3=2914%internalatoms=2914/4000*100=72.85%%atomsonthesurface=100-72.85=27.15%

AdHiMad Lab 11

n=10

n=10

PI: K. Momeni

Midterm Survey • Pleasetakethetimefillingoutthesurveyonmoodle

AdHiMad Lab 12

PI: K. Momeni AdHiMad Lab 13

Questions