Messages

1

General Questions and Answers / Calculation time in several methods.

« on: July 17, 2012, 11:40 »

Would you please to explane how does the calculation time depends on number of atoms (basis functions) in ATK in
1) DFT/PAO/LDA-PZ
2) DFTB
3) DFTB-nonit
4) EHT
  methods.
And one more question. How does the memory size influence the maximum number of atoms which is possiple to calculate by these methods?
Thank you in advance.

2

General Questions and Answers / Parallel calculation

« on: July 13, 2012, 11:07 »

We calculate graphene molecule with 92 atoms by DFT on cluster. There are 3 node with 4 12-core processes on each in the cluster. What type of parallelize should we use for best acceleration? Our input file is here (atoms xyz is cut out):

Code

molecule_configuration = MoleculeConfiguration(xyz_format=
"""60
geometry
C         -4.27910    -2.53300     0.00000
…
H          8.21480     2.31410     0.00000
H          4.49440     4.49970    -0.00000
H          6.97860     4.47250    -0.00000""")

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
calculator = LCAOCalculator()

molecule_configuration.setCalculator(calculator)
nlprint(molecule_configuration)
molecule_configuration.update()
nlsave('nh3.nc', molecule_configuration)

# -------------------------------------------------------------
# Molecular energy spectrum
# -------------------------------------------------------------
molecular_energy_spectrum = MolecularEnergySpectrum(
    configuration=molecule_configuration,
    energy_zero_parameter=FermiLevel,
    projection_list=ProjectionList(All)
    )
nlsave('c42h18.nc', molecular_energy_spectrum)
nlprint(molecular_energy_spectrum)

We tried to run it in two threades by MVAPICH (

Code

mpiexec –n 4 atkpython graphen.py > out.out

) on one node and have had deceleration from 32 to 34 min. Could you please to advise us something.

3

General Questions and Answers / Re: Maximum number of atoms

« on: July 13, 2012, 10:29 »

I see. Thank you.

4

General Questions and Answers / Re: Writing to scratch directory, not to tmp.

« on: July 12, 2012, 13:43 »

Thank you very much.

5

General Questions and Answers / Maximum number of atoms

« on: July 12, 2012, 13:41 »

What is the maximum number of atoms in molecule wich it is possible to calculate by DFT/LDA/PW?

6

General Questions and Answers / Writing to scratch directory, not to tmp.

« on: July 9, 2012, 15:44 »

I work on cluster. How to make ATK write to scratch direcrory, that I create. Now ATK try to write in ./tmp