Messages

1

General Questions and Answers / Re: Why the number of electrons is so large

« on: October 19, 2011, 13:50 »

But, why can the ATK 11.x convergence well? I want to know, for two very different leads, how the code deals with. For my systems, the left/right leads can not coincide with the simple translation. So it does not convergence.  What do you think?

2

General Questions and Answers / Re: Why the number of electrons is so large

« on: October 13, 2011, 02:11 »

We test the initial_density_type paremeter and find that the EquivalentBulk and the NeutralAtom give nearly the same results. They all don't convergen. In principle, the more regular the system is, the faster the convergence runs. However, nowdays, more and more studies began to care about the complex system. Do you have some techniques which make the self-consistent convergence easier?

3

General Questions and Answers / Re: Why the number of electrons is so large

« on: October 11, 2011, 13:58 »

I have read a lot of notices in the forum, there are many questions about the missing electrodes. But this is the first time the electrons are increased. Is this relative to the self-consistent process? The basis sets we used are DZP, and I find that for Carbon elements, the 3d orbitals are also occupied. I send the structure file to you by email. Thanks for your suggestions.

4

General Questions and Answers / Re: Why the number of electrons is so large

« on: October 11, 2011, 13:18 »

We use the ATK 2008.10. How to decide the length of the electrode?  And in the code, how to match the Fermi level of the scattering region?

5

General Questions and Answers / Re: Why the number of electrons is so large

« on: October 11, 2011, 12:58 »

central_edp=electronDensityParameters(mesh_cutoff        = 200*Rydberg,
                                      initial_scaled_spin= [0.0]*10+[1.0]+[0.0]*10+[1.0]+[0.0]*10+[1.0]+[0.0]*10+[1.0]+[0.0]*60+[1.0]+[0.0]*10+[1.0]+[0.0]*10+[1.0]+[0.0]*10+[1.0]+[0.0]*10+[1.0])
central_tcip=twoCenterIntegralParameters(cutoff= 2500.0*Rydberg,
                                         points= 1024)
central_imp=iterationMixingParameters(algorithm                = IterationMixing.Pulay,
                                      diagonal_mixing_parameter= 0.001,
                                      quantity                 = IterationMixing.Hamiltonian,
                                      history_steps            = 12)
#Tolerance for convergence
central_icp=iterationControlParameters(tolerance= 1.0e-4,
                                       criterion= IterationControl.DensityMatrix,
                                       max_steps= 500)
central_ecip=energyContourIntegralParameters(circle_points          = 100,
                                             integral_lower_bound   = 15*Rydberg,
                                             fermi_line_points      = 10,
                                             fermi_function_poles   = 10,
                                             real_axis_infinitesimal= 0.01*eV,
                                             real_axis_point_density= 0.02*eV)
# Define methods for constrained algorithm
central_ap=twoProbeAlgorithmParameters(electrode_constraint = ElectrodeConstraints.Off,
                                       initial_density_type = InitialDensityType.NeutralAtom)
#Collect parameters into a two-probe calculation method
constrained_method=TwoProbeMethod((lelectrode_parameters,relectrode_parameters),
                                   basis_set_parameters              = [bsp_c,bsp_h,bsp_fe],
                                   exchange_correlation_type         = LDA.PZ,
                                   electron_density_parameters       = central_edp,
                                   two_center_integral_parameters    = central_tcip,
                                   iteration_mixing_parameters       = central_imp,
                                   iteration_control_parameters      = central_icp,
                                   energy_contour_integral_parameters= central_ecip,
                                   electrode_voltages                = (0.0,0.0)*Volt,
                                   algorithm_parameters              = central_ap)

All the basis sets are DZP.

6

General Questions and Answers / Why the number of electrons is so large

« on: October 11, 2011, 12:18 »

This is the self-consistent output file.

# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  512.00000 e
# sc  1 : q = 3131.32021 e  Ebs =        nan Ry  dRho =  5.3144E+02
# sc  2 : q = 3013.32101 e  Ebs =        nan Ry  dRho =  1.4456E+02
The total number of electrons of the two-probe system is 512. But why it changes to 3131.32021, when it runs the second self-consistent loops.
How to solve this problem?

7

General Questions and Answers / It's memory's question

« on: January 7, 2010, 03:26 »

  Our new cluster has 8 cpu/node, the total memory of each node is 24 Gb. How many atoms we calculate per node are? Because recently the calculation always leads to the cumputer dead.

8

General Questions and Answers / Re: ATKError: inverse(DZMatrix const &) : Could not LU factorize!

« on: December 24, 2009, 01:37 »

The structure is not right. Two atoms may be at the same position.

9

General Questions and Answers / Re: It's memory's question

« on: December 24, 2009, 01:34 »

But my senior fellow apprentice run well and I run only one work in the cluster well, too. When I put the second or the third in the computer ,the question is ocurring .
    Thanks a lot.

10

General Questions and Answers / Re: It's memory's question

« on: December 23, 2009, 01:35 »

rank 0 in job 1  cu107-ib_48955   caused collective abort of all ranks
  exit status of rank 0: return code 137


We use Intel mpi in our cluster. Doesn't this cause the problem?

11

General Questions and Answers / It's memory's question

« on: December 22, 2009, 01:22 »

     rank 15 in job 1  cu108-ib_38172   caused collective abort of all ranks
     Is this question cased by the litter memory? In every cpu, the memory is about 3Gb.

12

General Questions and Answers / Re: the converge problem when using gatedtwoprobemethod

« on: September 2, 2009, 09:35 »

   You don't understand my question.
   I understand that the surface layers act as the screening effect to avoid the interaction between electrodes and molecule, so the surface layers must be as long as the electrode supercell. In that case,  "ElectrodeConstraint.RealSpaceDensity" and "ElectrodeConstraint.Off" are the same.
   Thanks.

13

General Questions and Answers / Re: the converge problem when using gatedtwoprobemethod

« on: August 31, 2009, 11:00 »

I think if we want to use the option "ElectrodeConstraint.RealSpaceDensity", then I think the scattering region should have such a structure:

"one left electrode cell + left surface layers + molecule + right surface layers + one right electrode cell"

so that we can replace the charge density in the "one left electrode cell" and "one right electrode cell" in the scattering region by that of the bulk lead. Here if the left and right surface layers are thick enough,  then "ElectrodeConstraint.RealSpaceDensity" and ""ElectrodeConstraint.Off" will give the same results, if not, then maybe big difference exists.

Is my understanding right?  If my understanding is right and if the surface layers(here I mean, the total lenghth of "one left electrode cell + left surface layers" in the scattering region)  are not as thick as one electrode cell, then I think we can not use the option "ElectrodeConstraint.RealSpaceDensity" at all.  In this case, I think only "ElectrodeConstraint.Off" can be used.  Am I right?

14

General Questions and Answers / Re: the converge problem when using gatedtwoprobemethod

« on: August 31, 2009, 05:20 »

    In the parameters of twoProbeAlgorithmParameters, the parameters of electrode_constraint may be set up ElectrodeConstraints.Off or ElectrodeConstraint.RealSpaceDensity. The difference between the two setting? In the procedure, how to make up the two different parameters? In my opinion, the electrode density is calculated to be identical to the bulk calculations.
     Thanks!

15

General Questions and Answers / the converge problem when using gatedtwoprobemethod

« on: August 25, 2009, 03:39 »

    when I apply 1 voltage gated bias to the central region, the scf calculation is not coverged. Why it happens?  The possible reason.