Messages

1

General Questions and Answers / Re: Noncollinear transmission calculation

« on: December 4, 2013, 07:30 »

Thank you very much for the reply. The size of the .nc file is very large and thus I am herewith sending the snapshot of the screen and the corresponding exported data as an attachment.
In the right panel of the figure of the snapshot, clicking the right button of the mouse, gives an option to export data and I did that.

with best regards,
Mausumi

2

General Questions and Answers / Noncollinear transmission calculation

« on: December 3, 2013, 11:21 »

Hi all,
I have performed a noncollinear transmission calculation for a complex molecule and found a plot which describes the transmission coefficient along with KA and KB (in the right side of the vnl window). By saving the corresponding data I found three columns describing three parameters KA, KB and transmission coefficients, respectively. But in the saved data the value of transmission coefficients are different from the given plot. e.g. I found in the vnl_plot that a color bar shows the value of transmission coefficient in the order of 0.071 but in the saved data I found the value is only 7.1. I do not understand the problem. Please help me to resolve it.
Thanks in advance.

With best regards,
Mausumi Chattopadhyaya  

3

General Questions and Answers / visualization of local spin polarization vector is inactive

« on: November 23, 2013, 09:49 »

Hi,
Thank you for the reply. I tried the example file for noncollinear calculation (carbon chain). I got the Tr(rhoS) and Tr(K, epsilon). I have noticed while clicking on the Tr(K, epsilon) the transmission analyser is active but doing the same procedure on Tr(rhoS) I did not find the "spin polarization visualiser". Please help us sort  out the problem.
Thanks in advance.

4

General Questions and Answers / How to specify theta for specific atoms?

« on: November 22, 2013, 13:33 »

Hi,
I want to perform a noncollinear calculation by specifying theta only for two atoms. Because in my system the total spin polarization is confined only on the two atoms and rest of the atoms are not spin polarized at all (I have a molecule of 78 atoms). I found in the example of noncollinear calculation that the theta have been mentioned for all the atoms of the central region sequentially. Could you please tell me how can I define the theta for only for two particular atoms? whether it is feasible or not? If yes what will be the exact script file.
Waiting for your reply.
Thanks in advance.

5

General Questions and Answers / visualization of local spin polarization vector

« on: November 22, 2013, 10:00 »

Hi,
I have performed a non-collinear calculation in vnl 13.8 and I have the corresponding nc file. I want to visualize the local spin direction of that system. How can I do that? I have checked it from internet and they suggest to see it by polarization visualizer plug in. Unfortunately I could not find it out. I am recently using this 13.8 version and accustomed with the older version. So please help me to sort out this problem.
Thanks in advance.

6

General Questions and Answers / addition of more than one gate

« on: May 15, 2013, 13:28 »

Dear all,
Could please let me know whether we can add more than one gate at a time? if yes please let me know how.

7

General Questions and Answers / regarding mulliken populations and noncollinear spin

« on: April 4, 2013, 16:05 »

Hi,
We want to perform spin-polarized Mulliken population analysis for a certain Fe-complex by using ATK 12.8.2. After the calculation we have found in the output file that in the "Mulliken Population Report" section it printed only the total spin value instead of printing spin up and spin down values of electrons separately. I want to see the "Mulliken Population Report" for spin-up and spin-down electrons separately. A certain portion of the output file is given below:
                                     xy     zy  zz-rr     zx  xx-yy   
 27  Fe   7.578  1.103        0.162  0.248  0.195  0.222  0.275
                                     s
                      0.027        0.027
                                     xy     zy  zz-rr     zx  xx-yy
                      5.166        0.566  1.247  0.834  1.061  1.457
                                     s
                      0.569        0.569
                                     y      z      x         
                      0.713        0.237  0.248  0.228

Please tell me how can I get the Mulliken Population Report separately for up and down spin electrons and what I have to write exactly in the .py file?

My next query is about the noncollinear spin calculation on the same complex. We have performed the noncollinear spin calculation by using the block:

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = NCLDA.PZ

Apart from that we have specified the spin direction in physical spherical coordinates and orbital Mulliken population by using the blocks:
 
# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
bulk_configuration.setCalculator(
    calculator = LCAOCalculator( ),
    initial_spin = InitialSpin(scaled_spins=[(Carbon, 0.0, 0.0*numpy.pi*Radians, 0.0*numpy.pi*Radians), (Hydrogen, 0.0, 0.0*numpy.pi*Radians, 0.0*numpy.pi*Radians), (Nitrogen, 0.0, 0.0*numpy.pi*Radians, 0.0*numpy.pi*Radians), (Selenium, 0.0, 0.0*numpy.pi*Radians, 0.0*numpy.pi*Radians), (Iron, 1.0, 0.5*numpy.pi*Radians, 0.4*numpy.pi*Radians)])
)
bulk_configuration.update()
nlsave('C:\Documents and Settings\Administrator\Desktop\fefe-hs-0v-ncspin-lda-final.nc', bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Mulliken population
# -------------------------------------------------------------
mulliken_population = MullikenPopulation(bulk_configuration)
nlsave('C:\Documents and Settings\Administrator\Desktop\fefe-hs-0v-ncspin-lda-final.nc', mulliken_population)
nlprint(mulliken_population)

It is already mentioned in the ATK 12.8.2 manual that "The atom Mulliken Population can be diagonalized to give a local spin direction, and this direction is reported by the nlprint command for noncollinear systems. The nlprint report for noncollinear spin also shows the orbital mulliken populations in the local spin direction." But unfortunately we could not find any spin direction in the "Mulliken Population Report" section of the output file and it looks exactly similar as that obtained earlier for spin-polarized calculation (see the selected portion of the output file above). I want to know how can I see the local spin direction in the output file? What is the correct .py file from which one can visualize the spin direction?
Is it possible to get the spin-up and spin-down values separately for a noncollinear system instead of total spin value? If yes please tell me the proper keyword/block in the .py file.

Thanks in advance.

8

General Questions and Answers / extraction of potential drop between two metal centres calculated in a loop

« on: February 18, 2013, 08:54 »

I have calculated the potential difference between two atomic centres and transmission spectrum for different bias using the following script:

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
def transmission(configuration):
    # Calculate the transmission spectrum and save it in a file
    transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-3,3,200)*eV,
    kpoints=MonkhorstPackGrid(1,1),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=KrylovSelfEnergy(),
    )
    nlsave('/home/swapanchem/Desktop/Fe-Fe-complex/fefe-ls-dz/fefe-ls-loop-transmission-iv.nc', transmission_spectrum)

# Read in the converged zero-bias calculation
device_configuration = nlread('/home/swapanchem/Desktop/Fe-Fe-complex/fefe-ls-dz/fefe-ls-loop-iv.nc', DeviceConfiguration)[0]
calculator = device_configuration.calculator()
   
# Calculate and save the transmission spectrum for zero bias
transmission(device_configuration)

# Define the bias voltages for the I-V curve
voltage_list=[0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,-0.1,-0.15,-0.2,-0.25,-0.3,-0.35,-0.4,-0.45,-0.5,]*Volt

# Loop over the bias voltages
for voltage in voltage_list:
    # Set electrode voltages and use the self-consistent state
    # of the previous calculation as starting guess
    device_configuration.setCalculator(
          calculator(electrode_voltages=(voltage, 0.0*Volt)),
          initial_state=device_configuration)

    # Calculate and save the transmission spectrum for each bias
    transmission(device_configuration)

# -------------------------------------------------------------
# Effective potential
# -------------------------------------------------------------
def EfffectivePotential(configuration):
    # Calculate the transmission spectrum and save it in a file
    effective_potential = EffectivePotential(
    configuration=device_configuration,
    )
    nlsave('fefe-ls-loop-pd.nc', effective_potential)

# Read in the converged zero-bias calculation
device_configuration = nlread('fefe-ls-loop-iv.nc', DeviceConfiguration)[0]
calculator = device_configuration.calculator()
   
# Calculate and save the Electrostatic difference potential for zero bias
EfffectivePotential(device_configuration)

# Define the bias voltages for the I-V curve
voltage_list=[0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,-0.1,-0.15,-0.2,-0.25,-0.3,-0.35,-0.4,-0.45,-0.5,]*Volt

# Loop over the bias voltages
for voltage in voltage_list:
    # Set electrode voltages and use the self-consistent state
    # of the previous calculation as starting guess
    device_configuration.setCalculator(
          calculator(electrode_voltages=(voltage, 0.0*Volt)),
          initial_state=device_configuration)

    # Calculate and save the esdp for each bias
    EfffectivePotential(device_configuration)

Now I want to extract the value of potential drop between the two centres at different bias. I know how to calculate the said potential difference at a single bias. For this I uses the following script:

echo "pot = nlread('ti2c66-fm-epot1v-1v.nc', EffectivePotential)[0]
p1 = pot.evaluate(2.07218823*Ang,3.57884614*Ang,13.28806914*Ang)
p2 = pot.evaluate(2.38069829*Ang,3.55537652*Ang,22.30382852*Ang)
print p1
print p2
print (p2-p1)*27.2" > pot-ti2c66-fm-epot1v-1v.py

atkpython pot-ti2c66-fm-epot1v-1v.py > pot-ti2c66-fm-epot1v-1v.out

Now my question is how to extract the value of potential difference from a single netcdf file where it has been calculated for different biases in a loop.  kindly help me to sort out this problem.

9

General Questions and Answers / effective potential difference measurement from a loop run

« on: January 22, 2013, 13:54 »

Even after calculating effective potential in a loop over a range of bias I could not extract potential difference between any two points for a given bias. Kindly suggest me the correct script file so that I can estimate it at each voltage from the .nc file generated in the loop calculation.

10

General Questions and Answers / current for up and down spin channels at different bias from a single nc file

« on: December 21, 2012, 12:54 »

we have done  some current calculations where the bias was supplied in a loop and right now we are interested to extract the current contribution for the up and down spin channel separately at each bias. I know how to calculate this contribution from a single .nc file that contains the results for a particular bias. I would like to know how one could calculate the current contribution of the separate spin channels using a .nc file in a situation where the job has been submitted with a loop. Please note this .nc file contains all the relevant transmission spectra so in principle, one should able to make a script to evaluate  the spin polarized currents at the given range of bias from this single .nc file.