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