Topics

1

General Questions and Answers / what's wrong with the displaying of bond by using ATK 2015.0?

« on: December 16, 2016, 04:36 »

I get one strange picture  of  all  structures as the append file, the bond display abnormal by using ATK 2015.0, waht's wrong?
However,the bond of all structures display correct by using ATK 2013.8 in the same computer!
How can I solve the problem by using ATK 2015.0?

2

General Questions and Answers / Why I get error optmized structure when I use the ATK optmized method of LBFGS

« on: June 9, 2016, 10:53 »

I get error optmized structure  when I use the ATK optmized method of  LBFGS ,maybe also I get the error one when I use the ATK optmized method of  QuasiNewton, which are the hydrogens go away to the error position: or no band with the original of the bonding atoms. I  also have been  meet the phenomenon of atoms  running free，Why？
The structure of the initial and the  0ptimized structur are as the append file.
Thanks a lot.

3

General Questions and Answers / How can I get the beautiful bloch state figure?

« on: May 22, 2014, 21:24 »

Hi
  I have been repeat the tutorial----Graphene Bloch State Tutorial by ATK 13.8.1:
http://quantumwise.com/documents/tutorials/latest/GrapheneBloch/index.html/chap.blochstates.html#sect1.graphene_bloch.analysis

but I found that my color bar(Phase(radians)) in bloch state figure is from 0 to 2π as append files，how can I change my color bar(Phase(radians)) in bloch state figure as the tutorial  from 0 to 0.16?

4

General Questions and Answers / How can we improve the convergence of ATK 11.8?

« on: December 2, 2013, 12:00 »

I have been optmized the same geometry with the same parameters, and the ATK 13.8 convergence faster than ATK 11.8,
how can we improve the convergence of ATK 11.8?

5

General Questions and Answers / How can I get the same spin bandstructure use ATK 11.8?

« on: November 13, 2013, 03:11 »

I have been use ATK 11.8 compute the spin bandstructure of N doped  ZGNR, but I can't get the same results as the append spin bandstructure wiht same geometry.
How can I get the same spin bandstructure use ATK 11.8?

By the way,I have been use GGA method ,the gap become larger than LDA method, what can  I do?

6

General Questions and Answers / two questiones about the checkpoint file name in ATK 2008.10

« on: April 22, 2011, 05:44 »

  Hi,every one ,I have two questiones about the checkpoint file name in ATK 2008.10

Frist:
In the script:
import ATK
import numpy
for voltage in numpy.arange(0.0, 1.01, 0.1):
  # Store each calculation in a separate NetCDF file
 
  ATK.setCheckpointFilename('nonsy-tmr--anti-dn-%.2f.nc' % voltage)
  scf = restoreSelfConsistentCalculation(m)   .......
what is the correct string that can be substitute for  m ?  CheckpointFilename? checkpointFilename ?checkpoint_filename?seems are all incorrect?why?
Second:
  After the sentence"ATK.setCheckpointFilename('nonsy-tmr--anti-dn-%.2f.nc' % voltage)",why I can't use"print checkpointFilename()"  in which the error pointed out that he "checkpointFilename" was not defined?

Thanks a lot

7

General Questions and Answers / Could we change the atom's shape and color in vnl 2008.10?

« on: June 8, 2010, 04:12 »

 
  Hi,everyone . May be I want to change the atom's shape and color  in vnl 2008.10 to special foucs on our view , could someone tell me how can I do that?

8

General Questions and Answers / How can we achieved this in ATK?

« on: May 31, 2010, 14:29 »

Hi, everyone

The junction of connections through a charge neutral 5-member ring as below, our calculations yield local spin polarization connected to the nominally unpaired pz electron on the apex C atom. In one article they say that the local spin polarization can be compensated by doping the CNTs. Experimentally, doping could be achieved either chemically with alkali atoms or by applying a back-gate voltage.To simulate this, they dope the junction with two electrons which are then compensated by an equivalent background charge spread uniformly over the whole extended molecule. And they find that doping indeed leads to additional charge around the two apex C atoms which compensates the local spin.

And my question is  how can we achieved that dope the junction with two electrons in ATK?


And I also want to know the meaning and the using method of charge in Basis set parameters of ATK.
Thanks!

9

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 16, 2010, 15:40 »

I don't know why I can't reply that topic ?

By the way ,The upload folder of the forum is full ,please check it !

This time I make the sufficent screen layers ,but the same thing happen, waht's wrong?

I have been checked the http://quantumwise.com/forum/index.php?topic=21.0 carefully, and I also notice the setup of electrode_constraint = ElectrodeConstraints.RealSpaceDensity, but the same thing happen , what 's wrong ?

Could you check my scripts and run them to see what's happen?





from ATK.TwoProbe import *
from ATK.MPI import processIsMaster

# Generate time stamp
if processIsMaster():
    import platform, time
    print '#',time.ctime()
    print '#',platform.node(),platform.platform()+'\n'

# Opening vnlfile
if processIsMaster(): file = VNLFile('D:/voltage/new2/sufficent.vnl')

# Scattering elements and coordinates
scattering_elements = [Lithium,  Lithium,  Lithium,  Lithium, 
                       Lithium,  Lithium,  Lithium,  Lithium, 
                       Lithium,  Lithium,  Hydrogen, Hydrogen,
                       Lithium,  Lithium,  Lithium,  Lithium, 
                       Lithium,  Lithium,  Lithium,  Lithium, 
                       Lithium,  Lithium]
scattering_coordinates = [[  4.80000019,   4.80000019,   5.76000023],
                          [  4.80000019,   4.80000019,   8.64000034],
                          [  4.80000019,   4.80000019,  11.52000046],
                          [  4.80000019,   4.80000019,  14.40000057],
                          [  4.80000019,   4.80000019,  17.28000069],
                          [  4.80000019,   4.80000019,  20.15999985],
                          [  4.80000019,   4.80000019,  23.04000092],
                          [  4.80000019,   4.80000019,  25.92000008],
                          [  4.80000019,   4.80000019,  28.79999996],
                          [  4.80000019,   4.80000019,  31.68000008],
                          [  4.80000019,   4.80000019,  34.83999992],
                          [  4.80000019,   4.80000019,  33.85999943],
                          [  4.80000019,   4.80000019,  37.02000023],
                          [  4.80000019,   4.80000019,  39.90000034],
                          [  4.80000019,   4.80000019,  60.06000264],
                          [  4.80000019,   4.80000019,  62.94000299],
                          [  4.80000019,   4.80000019,  54.30000241],
                          [  4.80000019,   4.80000019,  57.18000252],
                          [  4.80000019,   4.80000019,  48.54000218],
                          [  4.80000019,   4.80000019,  51.42000325],
                          [  4.80000019,   4.80000019,  42.78000195],
                          [  4.80000019,   4.80000019,  45.66000302]]*Angstrom
       

electrode_elements = [Lithium, Lithium]
electrode_coordinates = [[ 4.80000019,  4.80000019,  0.        ],
                         [ 4.80000019,  4.80000019,  2.88000011]]*Angstrom

electrode_cell = [[ 9.6 ,  0.  ,  0.  ],
                  [ 0.  ,  9.6 ,  0.  ],
                  [ 0.  ,  0.  ,  5.76]]*Angstrom

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
    electrode_cell,
    electrode_elements,
    electrode_coordinates
    )

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
    (electrode_configuration,electrode_configuration),
    scattering_elements,
    scattering_coordinates,
    electrode_repetitions=[[1,1],[1,1]],
    equivalent_atoms=([0,0],[1,15])
    )
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'twoprobe_configuration')

######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = LDA.PZ

iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.1,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 150.0*Rydberg
)

basis_set_parameters = basisSetParameters(
    type = SingleZetaPolarized,
    radial_sampling_dr = 0.001*Bohr,
    energy_shift = 0.01*Rydberg,
    delta_rinn = 0.8,
    v0 = 40.0*Rydberg,
    charge = 0.0,
    split_norm = 0.15
)

iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 100
)

electrode_voltages = (1.0,0.0)*Volt

two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
    electrode_constraint = ElectrodeConstraints.RealSpaceDensity,
    initial_density_type = InitialDensityType.EquivalentBulk
)

energy_contour_integral_parameters = energyContourIntegralParameters(
    circle_points = 30,
    integral_lower_bound = 3*Rydberg,
    fermi_line_points = 10,
    fermi_function_poles = 4,
    real_axis_infinitesimal = 0.01*electronVolt,
    real_axis_point_density = 0.02*electronVolt
)

two_center_integral_parameters = twoCenterIntegralParameters(
    cutoff = 2500.0*Rydberg,
    points = 1024
)

######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 150.0*Rydberg
)

left_electrode_iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 100
)

left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
    monkhorst_pack_parameters = (1, 1, 200)
)

left_electrode_iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.1,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
    temperature = 300.0*Kelvin
)

######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
    brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
    electron_density_parameters = left_electrode_electron_density_parameters,
    eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
    iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
    iteration_control_parameters = left_electrode_iteration_control_parameters
)

######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 150.0*Rydberg
)

right_electrode_iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 100
)

right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
    monkhorst_pack_parameters = (1, 1, 200)
)

right_electrode_iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.1,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
    temperature = 300.0*Kelvin
)

######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
    brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
    electron_density_parameters = right_electrode_electron_density_parameters,
    eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
    iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
    iteration_control_parameters = right_electrode_iteration_control_parameters
)

######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
    electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
    exchange_correlation_type = exchange_correlation_type,
    iteration_mixing_parameters = iteration_mixing_parameters,
    electron_density_parameters = electron_density_parameters,
    basis_set_parameters = basis_set_parameters,
    iteration_control_parameters = iteration_control_parameters,
    energy_contour_integral_parameters = energy_contour_integral_parameters,
    two_center_integral_parameters = two_center_integral_parameters,
    electrode_voltages = electrode_voltages,
    algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)

# Restore self consistent calculation from check point file
scf = restoreSelfConsistentCalculation(
    filename = 'D:/voltage/new2/0.nc'
)

runtime_parameters = runtimeParameters(
    verbosity_level = 10,
    checkpoint_filename = 'D:/voltage/new2/1.nc'
)

# Using initial density from self consistent calculation
scf = executeSelfConsistentCalculation(
    twoprobe_configuration,
    two_probe_method,
    initial_calculation = scf,
    runtime_parameters = runtime_parameters
)

10

General Questions and Answers / what's happen when I compute the voltage drop?

« on: April 16, 2010, 05:34 »

 
Hi,everyone

I use the three scripts compute the voltage drop,but  why I get two strange images?What's happen?Could someone help me ?

The voltage drop script is append  here:
"""
Script for calculating the voltage drop given a zero bias twoprobe calculation
and a finite bias calculation for the same system.

The script will write to the voltage drop to the file specified by vnl_filename,
and it will write to screen the xy-average effective potential.

Specifiy the zero bias calculation by giving the name of the file as zero_bias_filename.
Specifiy the finite bias calculation by giving the name of the file as finiate_bias_filename.
Specify the destination output VNL file for storage of the 3D dataset.

Example of usage:
    atk voltagedrop.py > my_voltage_drop.dat
"""

zero_bias_filename = 'D:/voltage/0.nc'
finiate_bias_filename = 'D:/voltage/1.nc'
vnl_filename = 'D:/voltage/voltage_drop.vnl'


""" ------------ No need to modify anything below this point --------------------- """
# Implementation of the voltage drop.
from ATK.TwoProbe import *; import numpy

# Zero bias calculation.
zero_bias = restoreSelfConsistentCalculation(zero_bias_filename)
# Finite bias calculation.
finite_bias = restoreSelfConsistentCalculation(finiate_bias_filename)
# Calculate the voltage drop.
voltage_drop = calculateEffectivePotential(finite_bias) - calculateEffectivePotential(zero_bias)

# Store the results in a VNL file.
file = VNLFile(vnl_filename)
file.addToSample(voltage_drop,'Voltage Drop','Voltage Drop')

# Get the raw number of the potential, and print the average potential to the screen.
raw_data = voltage_drop.toArray()
z_axis_length = voltage_drop._cell().c().z()
print '### Voltage drop ###'
print '# z(bohr) V(Ry)'
# Loop over all the data and calculate the average in the xy-plane.
for i in range(raw_data.shape[2]):
    print i*z_axis_length/float(raw_data.shape[2]), numpy.average(raw_data[:,:,i])

11

General Questions and Answers / How can I bulid such two-probe system as the append files?

« on: April 9, 2010, 16:49 »

Hi,everyone:

    Could someone tell me how can I bulid such two-probe system as the append files?
I have been read an atricle(PRB 81, 045425(2010)), and I try many ways want to build（4,4）CNT/20-UZCNT/CNT MTJ
as in FIG. 1 of PRB 81, 045425(2010) , but I couldn't get it . Could you have some ideas to help me build a two-probe system
as 4,4）CNT/20-UZCNT/CNT MTJ?
I have been use the free CoNTub software to create a heterojunction of of cnt(4,4) and cnt(6,6).,but  I wonder what I can do next step?

ps :the append files is schematic structure of (4,4)CNT/20-UZCNT/CNT MTJ.

Many thanks!

12

General Questions and Answers / one question about the MOLECULAR BUILDER in ATK-SE 2009.12

« on: January 15, 2010, 10:30 »

 
Hi,

In ATK-SE 2009.12 I didn't find the MOLECULAR BUILDER ,and I am puzzled about how can we conveniently build the Molecule through the function of join 、fuse and others as the early version of ATK?

13

General Questions and Answers / one question about the CUSTOM BUILDER SCRIPT in ATK-SE 2009.12

« on: January 15, 2010, 07:42 »

  Hi,everyone:
   First, I congratulate the released of the  new version of ATK-SE 2009.12.The new version has so many powerful tools , and I think it will be more popular.
  When I use the CUSTOM BUILDER in Custom,I have encounter one problem:
  the append file is a script that CEO Kurt Stokbro wrote in HeFei of China, it  worked well of the time in HeFei, however, when I dragged it into the CUSTOM BUILDER in Custom of ATK-SE 2009.12,it does't work, and it give the follow error message:
Traceback (most recent call last):
  File ".\zipdir\NL\GUI\Core\Runner.py", line 232, in run
  File "<string>", line 20, in configuration
AttributeError: 'BulkConfiguration' object has no attribute 'get_bravais_lattice'

Info: Script generator function does not generate a valid configuration.

how can I solve it ?

By the way,maybe we want to write some other scripts like above which has the parameters that influence the lattice constants or the coordinates of the atoms, i.e. maybe the lattice constants or the coordinates of the atoms in our own scripts are dynamic ,how can I do so that we can conveniently control the parameters in our own scripts?

14

General Questions and Answers / How can we get the detailed MullikenPopulations after scf ?

« on: November 17, 2009, 15:23 »

Hi ,every one
 

I have finished the scf, and have the convergence .nc files,but I have not save the log files (I know we can get the detailed MullikenPopulations using verbosity level 10),so how can do to get  the detailed MullikenPopulations as (0 H q = 1.00000 [ s: 1.014, s: -0.014, y: 0.000, z: 0.000, x: 0.000 ),not the H 1.14273929774 by using calculateMullikenPopulation?

 May be we only need the scattering region elements's detailed MullikenPopulations ,so I  want to know why when I ues twoprobe_configuration.scattering_elements() is not right to print but the twoprobe_configuration.elements can implement to print, in this  I am confused  that twoprobe_configuration.elements represent the  scattering_elements or all the twoprobe configuration's elements?

By the way , I want to know how can we expertly use the RETURNED OBJECT METHODS in ATK ? Could someone show me the trick?

15

Future Releases / My suggestion to the next VNL version about optimization

« on: November 11, 2009, 16:11 »

 
Hi, everyone

I think may be you need strengthen the function of the optimization in the next VNl version:
1,we can conveniently optimize the lattice constants and the coordinates of atoms in the bulk system at one time , of course we also can optimize one of them at one time;
2,we can conveniently optimize the lattice constants and the coordinates of atoms in the bulk system with one direction(for example , the transport direction,i.e. Z direction) ,but the other directions of the lattice constants and the coordinates of atoms in the bulk system  we can impose the constraint.

Wish you best and succeed!