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Messages - Jin-Kyu Choi

Pages: [1] 2
1
Installation and License Questions / What version of ATK is this commercial license for ?
« on: August 18, 2014, 14:07 »
I'm a commercial user of ATK program.
In recent, I have purchased a upgraded license, 2 masters & 6 slaves (from 1 master & 6 slaves). (please find the attached license file)

But, I have faced a serious problem in the use of ATK package; "License Error: (Internal: 719 Feature: ATKPython (Err: 9) Feature not found"
I suspect that this license error may occur due to version mismatch between the license and ATK package, because I had been using ATK 12.2.2, the old version of ATK.

So, I would like to ask some questions:

1. What is the version of this license? (What version of ATK is suitable to be used using this commercial license?)
In the file, the version is appeared to be 14.2 but the latest official version of ATK is 13.8.1 as I know, so what is the meaning of version 14.2 of this license?

2. Can this license (please find the attached license file) run the latest official version of ATK 13.8.1?
In other word, can I use the latest official version of ATK 13.8.1 with this commercial license?

Please give some kind answers. Thank you very much.
Sincerely,

2
General Questions and Answers / Geometry optimization in Z-direction for two probe system
« on: June 17, 2014, 06:48 »
Dear all,
I would like to ask a question about geometry optimization for a two probe system.

Recently, I have been trying to obtain an optimized geometry of a molecular junction (two probe system), dimethylenebenzene sandwiched in two Au electrodes.

I have completed geometry optimization calculation as seen in the attached image file.
But, the distance between two Au electrodes is not changed (optimized); it is 10.43A before and after optimization while the geometry of the molecule is optimized.
Because the dimethylenebenzene is not a planar molecule, defining geometry including distance between electrode and molecule is very important to get right transmission information.

Therefore, I would like to ask a question that:
In ATK, is there no way to find optimum distance between two electrodes? and between molecule and electrode?
I mean how to optimize the geometry also in Z-direction?

I hope some advice.
Thank you very much.

I'm attaching the input of the optimization calculation, so please refer to it.
# -------------------------------------------------------------
# TwoProbe configuration
# -------------------------------------------------------------

# -------------------------------------------------------------
# Left electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
left_electrode_coordinates = [[ 0.75183977,  1.24918839,  1.17728937],
                              [ 3.635598  ,  1.24918839,  1.17728937],
                              [ 6.51935623,  1.24918839,  1.17728937],
                              [-0.69003934,  3.74659628,  1.17728937],
                              [ 2.19371889,  3.74659628,  1.17728937],
                              [ 5.07747712,  3.74659628,  1.17728937],
                              [-2.13191846,  6.24400417,  1.17728937],
                              [ 0.75183977,  6.24400417,  1.17728937],
                              [ 3.635598  ,  6.24400417,  1.17728937],
                              [-0.69003934,  2.08165769,  3.5318681 ],
                              [ 2.19371889,  2.08165769,  3.5318681 ],
                              [ 5.07747712,  2.08165769,  3.5318681 ],
                              [-2.13191846,  4.57906558,  3.5318681 ],
                              [ 0.75183977,  4.57906558,  3.5318681 ],
                              [ 3.635598  ,  4.57906558,  3.5318681 ],
                              [-3.57379757,  7.07647346,  3.5318681 ],
                              [-0.69003934,  7.07647346,  3.5318681 ],
                              [ 2.19371889,  7.07647346,  3.5318681 ],
                              [ 2.19371889,  0.4167191 ,  5.88644684],
                              [ 5.07747712,  0.4167191 ,  5.88644684],
                              [ 7.96123535,  0.4167191 ,  5.88644684],
                              [ 0.75183977,  2.91412699,  5.88644684],
                              [ 3.635598  ,  2.91412699,  5.88644684],
                              [ 6.51935623,  2.91412699,  5.88644684],
                              [-0.69003934,  5.41153487,  5.88644684],
                              [ 2.19371889,  5.41153487,  5.88644684],
                              [ 5.07747712,  5.41153487,  5.88644684]]*Angstrom

# Set up configuration
left_electrode = BulkConfiguration(
    bravais_lattice=left_electrode_lattice,
    elements=left_electrode_elements,
    cartesian_coordinates=left_electrode_coordinates
    )

# -------------------------------------------------------------
# Right electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                            Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                            Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
right_electrode_coordinates = [[-0.75184086,  2.08018876,  1.17728937],
                               [ 2.13191737,  2.08018876,  1.17728937],
                               [ 5.0156756 ,  2.08018876,  1.17728937],
                               [-2.19371998,  4.57759665,  1.17728937],
                               [ 0.69003825,  4.57759665,  1.17728937],
                               [ 3.57379648,  4.57759665,  1.17728937],
                               [-3.63559909,  7.07500453,  1.17728937],
                               [-0.75184086,  7.07500453,  1.17728937],
                               [ 2.13191737,  7.07500453,  1.17728937],
                               [ 2.13191737,  0.41525017,  3.5318681 ],
                               [ 5.0156756 ,  0.41525017,  3.5318681 ],
                               [ 7.89943383,  0.41525017,  3.5318681 ],
                               [ 0.69003825,  2.91265806,  3.5318681 ],
                               [ 3.57379648,  2.91265806,  3.5318681 ],
                               [ 6.45755472,  2.91265806,  3.5318681 ],
                               [-0.75184086,  5.41006594,  3.5318681 ],
                               [ 2.13191737,  5.41006594,  3.5318681 ],
                               [ 5.0156756 ,  5.41006594,  3.5318681 ],
                               [ 0.69003825,  1.24771946,  5.88644684],
                               [ 3.57379648,  1.24771946,  5.88644684],
                               [ 6.45755472,  1.24771946,  5.88644684],
                               [-0.75184086,  3.74512735,  5.88644684],
                               [ 2.13191737,  3.74512735,  5.88644684],
                               [ 5.0156756 ,  3.74512735,  5.88644684],
                               [-2.19371998,  6.24253524,  5.88644684],
                               [ 0.69003825,  6.24253524,  5.88644684],
                               [ 3.57379648,  6.24253524,  5.88644684]]*Angstrom

# Set up configuration
right_electrode = BulkConfiguration(
    bravais_lattice=right_electrode_lattice,
    elements=right_electrode_elements,
    cartesian_coordinates=right_electrode_coordinates
    )

# -------------------------------------------------------------
# Central region
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 21.6389764739]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Hydrogen, Hydrogen,
                           Carbon, Carbon, Hydrogen, Hydrogen, Carbon, Carbon, Carbon,
                           Carbon, Hydrogen, Hydrogen, Carbon, Carbon, Hydrogen, Hydrogen,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
central_region_coordinates = [[  0.75183977,   1.24918839,   1.17728937],
                              [  3.635598  ,   1.24918839,   1.17728937],
                              [  6.51935623,   1.24918839,   1.17728937],
                              [ -0.69003934,   3.74659628,   1.17728937],
                              [  2.19371889,   3.74659628,   1.17728937],
                              [  5.07747712,   3.74659628,   1.17728937],
                              [ -2.13191846,   6.24400417,   1.17728937],
                              [  0.75183977,   6.24400417,   1.17728937],
                              [  3.635598  ,   6.24400417,   1.17728937],
                              [ -0.69003934,   2.08165769,   3.5318681 ],
                              [  2.19371889,   2.08165769,   3.5318681 ],
                              [  5.07747712,   2.08165769,   3.5318681 ],
                              [ -2.13191846,   4.57906558,   3.5318681 ],
                              [  0.75183977,   4.57906558,   3.5318681 ],
                              [  3.635598  ,   4.57906558,   3.5318681 ],
                              [ -3.57379757,   7.07647346,   3.5318681 ],
                              [ -0.69003934,   7.07647346,   3.5318681 ],
                              [  2.19371889,   7.07647346,   3.5318681 ],
                              [  2.19371889,   0.4167191 ,   5.88644684],
                              [  5.07747712,   0.4167191 ,   5.88644684],
                              [  7.96123535,   0.4167191 ,   5.88644684],
                              [  0.75183977,   2.91412699,   5.88644684],
                              [  3.635598  ,   2.91412699,   5.88644684],
                              [  6.51935623,   2.91412699,   5.88644684],
                              [ -0.69003934,   5.41153487,   5.88644684],
                              [  2.19371889,   5.41153487,   5.88644684],
                              [  5.07747712,   5.41153487,   5.88644684],
                              [  2.68803462,   4.63813503,   7.48490567],
                              [  1.17074902,   3.73512826,   7.48579329],
                              [  2.19371889,   3.74659628,   7.88644684],
                              [  2.19371889,   3.74659628,   9.39796011],
                              [  2.19216958,   1.60034561,   9.58728037],
                              [  2.19102095,   5.89254533,   9.58831624],
                              [  2.17967176,   2.54790079,  10.12212133],
                              [  2.17903092,   4.94460065,  10.12265559],
                              [  2.14660645,   2.54752301,  11.516221  ],
                              [  2.14596317,   4.94422281,  11.51695525],
                              [  2.1346164 ,   1.59967832,  12.05056037],
                              [  2.13346654,   5.89187802,  12.05169624],
                              [  2.13191718,   3.74582735,  12.24101655],
                              [  2.13191737,   3.74512735,  13.75252964],
                              [  3.15489378,   3.73219537,  14.15317673],
                              [  1.61690008,   2.86518312,  14.15382052],
                              [ -0.75184086,   2.08018876,  15.75252964],
                              [  2.13191737,   2.08018876,  15.75252964],
                              [  5.0156756 ,   2.08018876,  15.75252964],
                              [ -2.19371998,   4.57759665,  15.75252964],
                              [  0.69003825,   4.57759665,  15.75252964],
                              [  3.57379648,   4.57759665,  15.75252964],
                              [ -3.63559909,   7.07500453,  15.75252964],
                              [ -0.75184086,   7.07500453,  15.75252964],
                              [  2.13191737,   7.07500453,  15.75252964],
                              [  2.13191737,   0.41525017,  18.10710837],
                              [  5.0156756 ,   0.41525017,  18.10710837],
                              [  7.89943383,   0.41525017,  18.10710837],
                              [  0.69003825,   2.91265806,  18.10710837],
                              [  3.57379648,   2.91265806,  18.10710837],
                              [  6.45755472,   2.91265806,  18.10710837],
                              [ -0.75184086,   5.41006594,  18.10710837],
                              [  2.13191737,   5.41006594,  18.10710837],
                              [  5.0156756 ,   5.41006594,  18.10710837],
                              [  0.69003825,   1.24771946,  20.46168711],
                              [  3.57379648,   1.24771946,  20.46168711],
                              [  6.45755472,   1.24771946,  20.46168711],
                              [ -0.75184086,   3.74512735,  20.46168711],
                              [  2.13191737,   3.74512735,  20.46168711],
                              [  5.0156756 ,   3.74512735,  20.46168711],
                              [ -2.19371998,   6.24253524,  20.46168711],
                              [  0.69003825,   6.24253524,  20.46168711],
                              [  3.57379648,   6.24253524,  20.46168711]]*Angstrom

# Set up configuration
central_region = BulkConfiguration(
    bravais_lattice=central_region_lattice,
    elements=central_region_elements,
    cartesian_coordinates=central_region_coordinates
    )

device_configuration = DeviceConfiguration(
    central_region,
    [left_electrode, right_electrode]
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
    GGABasis.Hydrogen_DoubleZetaPolarized,
    GGABasis.Carbon_DoubleZetaPolarized,
    GGABasis.Gold_SingleZetaPolarized,
    ]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE

#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=100.0*Rydberg,
    k_point_sampling=(3, 3, 100),
    )

right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=100.0*Rydberg,
    k_point_sampling=(3, 3, 100),
    )

device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=100.0*Rydberg,
    k_point_sampling=(3, 3, 100),
    )

#----------------------------------------
# Poisson Solver Settings
#----------------------------------------
left_electrode_poisson_solver = FastFourier2DSolver(
    boundary_conditions=[[PeriodicBoundaryCondition,PeriodicBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition]]
    )

right_electrode_poisson_solver = FastFourier2DSolver(
    boundary_conditions=[[PeriodicBoundaryCondition,PeriodicBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition]]
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    poisson_solver=left_electrode_poisson_solver,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    poisson_solver=right_electrode_poisson_solver,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('/pwork01/p037cjk/ATK_sinbaram/DMB-Au_GOA/DMB-Au_GOA.nc', device_configuration)

device_configuration = OptimizeGeometry(
        device_configuration,
        max_forces=0.04*eV/Ang,
        max_steps=200,
        max_step_length=0.4*Ang,
        trajectory_filename=None,
        disable_stress=True,
        optimizer_method=QuasiNewton(),
        )
nlsave('/pwork01/p037cjk/ATK_sinbaram/DMB-Au_GOA/DMB-Au_GOA.nc', device_configuration)
nlprint(device_configuration)

3
Installation and License Questions / Can this trial license be activated by floating server way?
« on: June 9, 2014, 07:05 »
Dear,

Currently, we have been using a trial license as attached.
Could you check whether this license is possible to be activated by floating server way or not?

Thank you very much.

Moderator edit: Private attachment removed

4
General Questions and Answers / Transmission calculation at different bias voltages
« on: June 6, 2014, 08:02 »
Dear all,
I would like ask a simple advice.

I'm interested in transport properties of molecular junctions (two probe systems).
To investigate them, I have divided the procedures into two steps: (1) geometry optimization (2) transmission calculations at a bias voltages.

So, first I have finished the optimization calculation of a two probe system.
Then, transmission spectrum calculation was applied with a given bias voltage.
To get I-V curve characteristic, I'm repeating the transmission calculation with different bias voltages.

Here, I have a question.
Because each calculation requires quite long time (transmission at a bias voltage), I'm trying to find a way to save time.
Is it necessary to run a calculation for a system at a given bias voltage?
I mean, "New Calculation" in VNL-Scriptor is required for the each bias condition?

Thank you for your reading.

5
Installation and License Questions / License Error: (Internal: 719 Feature: ATKPython)
« on: June 2, 2014, 05:09 »
Dear all,

I would like ask a question about licensing error.
First, for the full understanding, I would like to explain our calculation system briefly.

We belong to Department of Chemistry and are oriented to experimental research.
Therefore, We have very few knowledge on "computing".

We're using ATK program loaded on a supercomputing system operated by an institute in KOREA (ROK), Korea Institute of Science and Technology Information (KISTI).
And we are under guide of the KISTI for the usage of the supercomputing.

The name of the system is SINBARAM and its specifications are as follow:
- processor: Intel Xeon 2.5GHz
- node: 18
- OS: CentOS
- CPU(all): 512
- CPU(/node): 16
- Mem: 64GB

To run ATK calculations, we use job script specifying computing conditions, as below:
#!/bin/bash
#@ job_type = serial
#@ wall_clock_limit = 34:00:00
#@ step_name = ATK
#@ notification = complete
#@ class = normal
#@ error = $(step_name).$(jobid).$(stepid).err
#@ output = $(step_name).$(jobid).$(stepid).out
#@ resources = ConsumableCpus(4) ConsumableMemory(2000)
#@ queue

. /etc/profile

module load mpi/gcc/openmpi-1.6

# Load ATK
export ATK_ROOT=/home/applic/Applications/QuantumWise/atk-12.2.2/atkpython
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/applic/Applications/QuantumWise/atk-12.2.2/atkpython/lib
export PATH=$PATH:/home/applic/Applications/QuantumWise/atk-12.2.2/atkpython/bin

## QuantumWise Atk 12.2.2 ##
export QUANTUM_LICENSE_PATH="6201@134.75.117.31"
export QUANTUM_AUTOMATIC_SERVER_DISCOVERY="1"
export MKL_DYNAMIC="FALSE"

## CPU Setting same with ConsumableCpus ##
export OMP_NUM_THREADS=4

## ATK Run ##
$ATK_ROOT/bin/atkpython /pwork01/p037cjk/ATK_sinbaram/DTB-Au_GO_CPU4/DTB-Au_GO_CPU4.py

Here is the problem.
When we run a calculation, sometimes we have faced an error as below and sometimes not.
License Error: (Internal: 719 Feature: ATKPython)
(Err: 9) Feature not found
For assistance on resolving this matter, there are several options:
Consult the FAQ : http://www.quantumwise.com/support/faq
Find help on the forum : http://forum.quantumwise.com
The installation guide : http://www.quantumwise.com/support/manuals
Email support : support@quantumwise.com

And this is the license log:
...
[2014-06-02 10:15:15] SERVER DISCOVERY by p037cjk@sinbaram22.plsi.or.kr [134.75.117.184]
[2014-06-02 10:15:19] SERVER DISCOVERY by p037cjk@sinbaram22.plsi.or.kr [134.75.117.184]
[2014-06-02 10:15:20] SERVER DISCOVERY by p037cjk@sinbaram22.plsi.or.kr [134.75.117.184]
[2014-06-02 10:15:52] SERVER DISCOVERY by p037cjk@sinbaram24.plsi.or.kr [134.75.117.186]
[2014-06-02 10:15:57] SERVER DISCOVERY by p037cjk@sinbaram24.plsi.or.kr [134.75.117.186]

I have already discussed it with the manager at KISTI who guides us use of supercomputing,
and he suggested to ask to software expert (ATK, Quantumwise).

So, I would like to ask that
(1) Why does this error come? (I guess this occurs because the license is not called)
(2) Why sometimes does this error come? and sometimes does not?

I hope you give us detailed instruction.
Thank you very much.

6
General Questions and Answers / Re: After calculation of geometry optimization, no changes in geometry ??
« on: May 23, 2014, 08:42 »
Dear Umberto Martinez,

Thank you very much for your kind instruction.
I will discuss with the manager in the institute. I hope I could solve this issue.

Thank you again.

7
General Questions and Answers / Re: After calculation of geometry optimization, no changes in geometry ??
« on: May 23, 2014, 08:09 »
Dear Umberto Martinez,

I perform calculations using parallel-computing.
But, since I'm very poor at computing, I run the calculations under guide from a institute in Korea.

As you pointed, I may have run the same calculation jobs.
I have linked the log file. Please refer to it if it is necessary.
(http://bigmail.mail.daum.net/Mail-bin/bigfile_down?uid=4zBHnQlYkFZ2qzDJGrQPDxKdPKqR2K7X)

So... the calculation was run??
And the output was not save??

8
General Questions and Answers / After calculation of geometry optimization, no changes in geometry ??
« on: May 22, 2014, 14:05 »
Dear all,

I have run a calculation of geometry optimization for a molecular junction of two probe system, in which a phenylene molecule is sandwiched between two gold electrodes.
(please find the input file attached, input.py)

The calculation has been performed for around 40 hours then I have obtained a result file (nc file).
When I clicked the nc result file in VNL window, I could have seen 16 geometries: gID000 -> gID015
(please see the image named "Result_list.gif")

But I found the geometry after optimization is the same with that before optimization.
(please see the image named "geometry.gif")

Here, I would like to ask two questions;
1. Why are there 16 geometries in the nc file from gID000 to gID015? and What are they?
2. Why are the geometries before and after optimizaton calculation the same? and Can I believe that the initial geometry before optimization was optimum?

I hope your help.
Thank you very much.
Sincerely,

9
General Questions and Answers / Re: How to run a calculation to get conductance from transmission result?
« on: May 14, 2014, 03:17 »
I would like to thank you for your reply.

As you pointed, I droped the NC file containing the transmission spectrum on the dropzone of the "Conductance Plot" in the "Custom Analyzer", then I could have seen the conductance value. (problem solved  :o)

Previously, to see the conductance value, I droped the NC file of transmission spectrum to the "I-V Curve" in the "Custom Analyzer", then it showed the error message as mentioned in the first post.

Actually, I could have seen the current and conductance values simultaneously by dropping the NC file which was obtained using the keywords: [Device-New calculator-TransmissionSpectrum-ElectrostaticDifferencePotential] in "Script Generator", to the "I-V curve" in the "Custom Analyzer", of which process is introduced in the tutorial in Quantumwise.

Because I do not well understand the nanolanguage or coding in the ATK program, particularly VNL, I do not know the relation between input-keywords and output-results. Anyway now I can see the conductance.

Thank you very much.

10
General Questions and Answers / How to run a calculation to get conductance from transmission result?
« on: May 12, 2014, 13:39 »
Dear all,
I would like to ask a simple question on how to obtain conductance value from a result file including transmission.

First, I had obtained transmission spectrum using the keywords: [Device-New calculator-TransmissionSpectrum] as in the picture (1_transmission.png).
Then, I tried to obtain further information on the conductance value by running a calculation from the result file of transmission spectrum
I used keywords as [Device-Analysis from File-ElectrostaticDifferencePotential] as in the picture (2_conductance.png).

But, I faced a trouble when I tried to open the result file of the conductance calculation using the window of “Analyzer-IV curve”.
The error message is that:
Traceback (most recent call last):
File ".\zipdir\NL\GUI\Core\Runner.py", line 230, in run
File ".\zipdir\NL\GUI\Tools\CustomAnalyzer\Analyzers\IVCurve.py", line 27, in analyzer
File ".\zipdir\NL\IO\NLSaveUtilities.py", line 243, in nlread
NL.ComputerScienceUtilities.Exceptions.NLValueError: The filename must be given as a string - e.g. "my_file.nc".

Here I have two questions,
(1) is it not possible to calculate conductance value by running a calculation from transmission result?
(2) After just calculating the transmission spectrum [Device-New calculator-TransmissionSpectrum], I can see the current value by drag and drop the result file onto the I-V analyzer. Is this current value is right?

*I know the tutorial on how to calculate I-V (http://www.quantumwise.com/documents/tutorials/latest/ATKTutorialDevice/index.html/chap.iv.html)
I want to know how to run additional calculation to get conductance value from the transmission result.

Thank you very much.
Sincerely,

11
General Questions and Answers / Relation between MPSH and PDOS on molecule?
« on: September 7, 2013, 15:08 »
Dear all,

I would like to ask about how to understand the relation between MPSH and PDOS (projected density of states) on molecule of two probe system (electrode-molecule-electrode).

I have performed the calculation on dithiolbenzene molecule in gold electrode junction.

I compared the MPSH and PDOS on the molecule. Please refer to the Figure.

The thing that I have difficulty to understand is that the difference between them.
Especially, in the range of energy from 0 eV to 2 eV, there is no MPSH but DOS is.
How can this be understood?
No orbital state but DOS...?

Is it OK to think that existence of PDOS on molecule in 0~2 eV is from broadening of state related to the self-energy?

I would like to ask to give me some comment to understand it physically and theoretically.

Thank you very much.

12
General Questions and Answers / Electrons of different wavevectors from electrode to molecule can be counted?
« on: September 2, 2013, 15:30 »
Dear all,

Nowdays, I'm studying electron transport in a molecular junction (two probe system) with semiconducting silicon electrode.
As well-known, the bulk silicon is indirect band gap material (Eg=~1.1eV, direct band gap at Gamma=~3.4eV).

Especially, I'm considering the injection and ejection of electron from Si electrode (left) to molecule (central) and to Si electrode (right).
I'm wondering about how to understand the electron injection and ejection with the concept of band structure for the Si electrode.
With those concerns, I would like to ask few questions and comments:

1. Is it right to think that electron injects from valence band of the Si electrode to the molecule, at which the wavevector of the electron is kept?
   And the electron ejects from the molecule to the conduction band of the Si electrode. In this case, the electron ejects to the conduction band at Gamma point of the Si electrode?

2. As I know, ATK computes only for coherent transport and if it is right the electron transport occurs with the same wavevector?

I probably have some misunderstanding, please give me some correction.

Thank you very much.

13
General Questions and Answers / Re: How to calculate band gap energy of semiconductor electrodes in two probe system
« on: August 31, 2013, 08:49 »
So... there is no changes in the band structure of the electrode due to interaction with the centered molecule?
The interaction between the electrode and the molecule (self-energy) is just affecting on the molecule? not electrode?

And, there is no way to directly extract the information about electronic structure of the electrode in the molecular junction?
(I have already performed the calculations on the transmission spectrum and current-voltage)

14
General Questions and Answers / How to calculate band gap energy of semiconductor electrodes in two probe system
« on: August 30, 2013, 15:17 »
Dear all,

I'm studying charge transport properties of a single molecule in a junction with various kinds of electrodes (not only metallic).

I want to draw the schematic energy diagram for a molecular junction with semiconducting electrodes, for example, as shown in the Figure.

By the MPSH calculation in the ATK package, I can determine the molecular orbital energies but, I can not draw the simple band diagram for the semiconducting electrode (band gap).

In ATK package, is it possible to calculate band gap (conduction band minimum - valence band maximum) of the electrode in the molecular junction?? Not bulk case. For a simple bulk case, I can find the tutorial in the QW website.

Please give me any comments.

Thank you very much.

15
General Questions and Answers / How to calculate the total energy of only electrodes in a two probe system
« on: August 30, 2013, 15:02 »
Dear all,

Recently I have posted to ask about calculation of total energy, but no one answered...

There is no way to calculate the total energy for only electrodes in a molecular junction (two probe system)??

The following is my previous question please refer to it.

Thank you very much.

------------------------------------------------------------------------------------------------------------------------
How can I calculate total energy?
« on: August 26, 2013, 17:11 »
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Dear all,

I would like to ask how to calculate total energy, in not simple case.

For example, I have a general molecular junction (two-probe system): electrode-molecule-electrode.
In order to get "binding energy" between the electrode and molecule, I want compare the total energy of "electrode-molecule-electrode", "only molecule", and "only electrode".

Could you give me some advise for how to calculate the total energy especially for "only molecule" and "only electrode"?
Please help me.

Thank you very much.

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