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ISU / Dec 10 th. Joaquin Peralta, Rupa Dumpala , and Scott Broderick. First simulations / QE. Quantum espresso Convergence parameters Technical Issues Undefined ‘ input_file ’ to add initial velocities. Defining by modifying source code. Alternatives VASP/QE Coding. Initial Simulations.

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isu dec 10 th

ISU / Dec 10th

Joaquin Peralta, RupaDumpala, and Scott Broderick

first simulations qe
First simulations / QE
  • Quantum espresso
    • Convergence parameters
  • Technical Issues
    • Undefined ‘input_file’ to add initial velocities.
    • Defining by modifying source code.
    • Alternatives VASP/QE Coding

Initial

Simulations

using vasp
Using VASP
  • Available VASP versions : 5.3.2 and 4.X
  • Pseudo potentials
    • PAW – PBE/LDA
    • Alternative of request all-electron (very small number of atoms)
  • Convergence settings
    • Molecules with considerable vacuum space
    • Plane Waves must be around 50% more than the used in classical crystalline structures (RAM memory)
    • Partial occupancies (smearing). In particular for the case of molecules and DM, Fermi-smearing or Gaussian-smearing will be used.
  • Compilation Issues
    • Performance
    • Gamma Point
si9 cluster
Si9 Cluster
  • Original Adri’s group Si cluster of 9 atoms.
  • Reducing vacuum space size to improve convergence and plane waves.
  • A cubic cell of 30A it was the first option.
  • Silicon first because :
    • Performance Input : ISPIN / ENCUT / NGX
    • Performance Compiling : Gamma Point / Settings
    • Vacuum Space, Plane waves and Memory requirements
si9 cluster1
Si9 / Cluster
  • Trying to fit best parameters for simulation time
  • Technical issues with
    • Cluster platform fails with NPAR major than eight
    • Compiled version don’t run with a wrong number of NGX, NGY, and NGZ
    • Not considerable performance improvement with more aggressive compilation
  • 1 Ionic step/minute  1fs each step  5ps = 83 hours
  • 1 Ionic step/minute  0.25fs  5ps = 13 days!

* Vasp 5.2.11** The simulation didn’t finish.

si9 o
Si9 - O
  • Incorporation of Oxygen in the system
  • Using ISMEAR Associated to the temperature of the input file from Adri’s group. T = 338 K
  • Oxygen ENCUT increased the time of the RUN.
  • Technical initial problems / Times
    • Using 64 CPU / NPAR 4  Work ~1 step/min.
    • Using 64 CPU / NPAR 8  Faster, but suddenly simulation stop.
    • Using 128 and 256 CPU
      • NPAR > 8  Simulation faster ~ 1.5 to 2.0 step/min
      • Principal problem, after a couple of hours the simulation stop for different problems
        • Zombie process (Cluster environment problem)
        • Setup ENCUT / NGX / etc.
si9 o3
Si9-O
  • Temperature response
slide10
Si-9
  • Energy
next steps
Next steps
  • Reduce vacuum space to improve simulation times.
  • Reduce compiling optimization and disk I/O
    • Cluster problem(s)
    • FFT size grid  Better accuracy, slower simulation time.
  • Based on old NPAR and CPU studies to compare.
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