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Topics - kaypu

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1
Questions and Answers / DFT+MD with electric field
« on: May 15, 2019, 11:34 »
Dear QuantumWise staffs:
Using a 'post-step-hook' hook function,  as shown in https://forum.quantumatk.com/index.php?topic=4696.msg20375#msg20375,  the corresponding script as follows:
*********************************************************************
charges = PartialCharges(bulk_configuration).evaluate()
field = [0.01, 0.0, 0.0]*Volt/Ang
class ElectricFieldHook(object):
   def __init__(self, charges, electric_field):
      # Store the charges and the electric field.
      charges = charges.reshape(-1, 1)
      field = electric_field.reshape(1, 3)
      self.efield_forces = (charges*field).convertTo(eV/Ang)

   def __call__(self, step, time, configuration, forces, stress):
        # Add the electric field forces to the forces vector.
      forces += self.efield_forces

electric_field_hook = ElectricFieldHook(
    charges=partial_charges,
    electric_field=field
)

# -------------------------------------------------------------
# Molecular Dynamics
# -------------------------------------------------------------

initial_velocity = None

method = NVTBerendsen(
    time_step=1*femtoSecond,
    reservoir_temperature=300*Kelvin,
    thermostat_timescale=100*femtoSecond,
    initial_velocity=initial_velocity,
    heating_rate=0*Kelvin/picoSecond,
)

rigid_indices_0 = [203, 204, 205, 206, 207, 208, 209, 210, 211, 212,
                   213, 214, 215, 216, 217, 218, 219, 220, 221, 222,
                   223, 224, 225, 226, 227, 228, 229, 230, 231, 232,
                   233, 234, 235, 236, 237, 238, 239, 240, 241, 242]
rigid_indices_1 = [ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12,
                   13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
                   26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
                   39]

constraints = [RigidBody(rigid_indices_0),
               RigidBody(rigid_indices_1)]

md_trajectory = MolecularDynamics(
    bulk_configuration,
    constraints=constraints,
    trajectory_filename='trajectory.nc',
    steps=200,
    log_interval=1,
    post_step_hook=electric_field_hook,
    method=method
)

bulk_configuration = md_trajectory.lastImage()
nlsave('Device-AGNR-Tran1-MDopt.nc', md_trajectory)
*****************************************************************************
it doesn't work,  the error message is "NL.ComputerScienceUtilities.Exceptions.NLTypeError: The LCAOCalculator does not
support calculation of PartialCharges."
how to deal with it? Thanks

2
Questions and Answers / Question on Transmission Paths
« on: October 9, 2018, 04:34 »
Dear QuantumWise staff:
I have read the paper exploring local currents in molecular juctions. http://www.nature.com/nchem/journal/v2/n3/pdf/nchem.546.pdf

As the author said, the local currents could divide into sigma and pi systems, how could i do the same thing in ATK?

Thanks

3
Questions and Answers / VibrationalMode of molecule
« on: March 8, 2017, 14:23 »
Dear QuantumWise staff:

     The ATK can do VibrationalMode and PhononDensityofState of an isolate molecule,  whether the energy in phonon density of state corresponds to the vibration frequencies of the molecule (plus hbar)? Or, the vibrationalMode is the vibration frequencies of molecule?

4
Dear QuantumWise staff:
      In the process of gas adsorption, A stands for pristine adsorbate (such as graphene), B is gas molecule (for example CO), and C is the adsorbate with an absorbed gas molecule (graphene+CO). the adsorption process can be represent as A+B=C, the adsorption energy is defined as: Eads=EC-EA-EB. We can calculate the Total energy of A, B, and C respectively by ATK, and get adsorption energy. how to calculate enthalpy in the adsorption process by ATK?

5
Dear QuantumWise staff:

    How to set spin multiplicity in ATK? For example, the spin state of O2 molecule is triplet, using Dmol3 or Gaussian, we can use spin unrestricted and the mulitiplicity is chosen Triplet. Now, for ATK, how to set?

6
Dear Quantumwise staff:

according to the page from http://quantumwise.com/forum/index.php?topic=2203.msg10537#msg10537
i try to do it using atk 14.3, but something wrong with it. the script as follows:
**********************************************
from NanoLanguage import *
import NLEngine

def makeGridValues(datagrid, cell, origin, unit):

    n0, n1, n2 = datagrid.shape
    gA, gB, gC = cell
    u0 = NLEngine.Cartesian3D(gA[0],gA[1],gA[2])
    u1 = NLEngine.Cartesian3D(gB[0],gB[1],gB[2])
    u2 = NLEngine.Cartesian3D(gC[0],gC[1],gC[2])
    cell_origin = NLEngine.Cartesian3D(origin[0],origin[1],origin[2])

    grid_descriptor = NLEngine.GridDescriptor(n0,n1,n2,
                                              NLEngine.UnitCell(u0,u1,u2,cell_origin))
    grid3d = NLEngine.RealGrid3D(grid_descriptor,
                                 NLEngine.doubleSequenceToRealVector(datagrid.flatten()),True)

    return GridValues(grid3d,unit)

bulk_configuration = nlread("C:\Users\kaypu\Desktop/zigzag12-band.nc", BulkConfiguration)[0]
conf = nlread("C:\Users\kaypu\Desktop/zigzag12-band.nc", BulkConfiguration, read_state=False)[0]

dm = bulk_configuration.calculator()._densityMatrixCalculator()
number_of_electrons = int(dm.fermiDistribution().numberOfElectrons())

LUMO = number_of_electrons/2
LLUMO = LUMO+1

# Which state to compute?
spin = Spin.Up
state = LUMO
filename = "bloch_z12_LUMO_up.nc"

# Number of points to sample from G to Z
Nk = 100

density = None
for kz in numpy.linspace(0.2,0.5,Nk):
    b = BlochState(bulk_configuration, quantum_number=state, k_point=[0,0,kz], spin=spin)
    psi = b.toArray()
    if density == None:
        density = (psi*psi.conj()).real
    else:
        density += (psi*psi.conj()).real

cell = conf.bravaisLattice().primitiveVectors().inUnitsOf(Bohr)
origin = conf.bravaisLattice().origin().inUnitsOf(Bohr)
grid = makeGridValues(density,cell,origin,unit = eV/eV)

nlsave(filename, grid)
nlsave(filename, conf)
******************************************************
the wrong message shows as follows:

Traceback (most recent call last):
  File "c:\users\kaypu\appdata\local\temp\1676064135181985.py", line 52, in <module>
    grid = makeGridValues(density,cell,origin,unit = eV/eV)
  File "c:\users\kaypu\appdata\local\temp\1676064135181985.py", line 12, in makeGridValues
    u0 = NLEngine.Cartesian3D(gA[0],gA[1],gA[2])
AttributeError: 'module' object has no attribute 'Cartesian3D'

what's wrong with it, i use 2014.3

7
Dear QuantumWise staff

Following your advice(http://quantumwise.com/forum/index.php?topic=3385.0), I increase the scattering region and recalculate the s-PDOS. The negative s-PDOS is gone. thank you

in the attachment, there is a dip in the Fermi energy, is that QI or numerical artifact?
near -1.8eV, is there Fano resonance? how to explain it?

thank you

8
Questions and Answers / Question on negative s-PDOS
« on: May 4, 2015, 08:57 »
Dear QuantumWise staff:

In the attachment, the device is composed of carbon nanotube(m=n=4) and anthracene (certral molecule). all the device has been optmized using LBFGS(z vetor is not fixed).The corresponding script is also in the attachment. The self-energy is chosen recursionself energy to avoid negative transmission appearing. Integral lower bound is set to 4.0 hartree to  eliminate charge missing problem.

but there are still some problem...

in the s-PDOS.jpg, near -1 eV, the PDOS of s state is negative, is that right? could  you help me to figure out this problem?

                                             Thanks

9
Questions and Answers / Question on PDOS
« on: April 29, 2015, 08:52 »
Dear QuantumWise staff
Whether it is possible for ATK(2014.2) to calculate PDOS and project the density to s, px, py, pz of certain atom? if it is, how to compile  the script,
 thank you

10
Dear QuantumWise staff:
    How the left/right electrodes are modeled? it is done through a self-energy(Recursion self-energy)? And i want to know which model is used for it (wide band approximation, absorbing potential, etc.) in ATK

Thanks

11
Questions and Answers / Questions on Energy dependent LDOS
« on: November 9, 2014, 14:16 »
hi:
 i use this py(in the attachment) to plot the Energy dependent LDOS at bias of 0.4V. the LDOS in the different energy(-1eV~1eV) are saved to LDOS1-LDOS4. but it doesn't work.
*******************
File "LDOS-plot.py", line 25, in <module>
    X, Y = numpy.meshgrid(z, energies)
  File "./build/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3379, in meshgrid
  File "./zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 456, in __mul__
  File "./zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 249, in unit
AttributeError: 'PhysicalQuantity' object has no attribute '_PhysicalQuantity__unit'
*******************
atk version 2014.1

what's wrong? need to modify the py?

thanks

12
Dear QuantumWise staff
             
      What does the Electrostatic Potential consist of when the bias is applied? Does it equal to the Hartree energy?  or equal to the sum of Hartree energy and the electro-static external potential (bias potential)?

13
Questions and Answers / Question about zero charge at 0 bias
« on: December 16, 2013, 07:35 »
Dear QuantumWise staff:

    i want to test the polarization transport of the two-probe system of Ni-benzene-Ni.  but all the charges in the center scattering area are zero, as shown in the following:

+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0  Ni   [   0.623 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   1  Ni   [   3.115 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   2  Ni   [   5.608 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   3  Ni   [   0.623 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   4  Ni   [   3.115 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   5  Ni   [   5.608 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   6  Ni   [   0.623 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   7  Ni   [   3.115 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   8  Ni   [   5.608 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   9  Ni   [   1.869 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  10  Ni   [   4.361 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  11  Ni   [   6.854 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  12  Ni   [   1.869 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  13  Ni   [   4.361 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  14  Ni   [   6.854 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  15  Ni   [   1.869 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  16  Ni   [   4.361 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  17  Ni   [   6.854 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  18  Ni   [   0.623 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  19  Ni   [   3.115 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  20  Ni   [   5.608 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  21  Ni   [   0.623 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  22  Ni   [   3.115 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  23  Ni   [   5.608 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  24  Ni   [   0.623 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  25  Ni   [   3.115 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  26  Ni   [   5.608 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  27  Ni   [   1.869 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  28  Ni   [   4.361 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  29  Ni   [   6.854 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  30  Ni   [   1.869 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  31  Ni   [   4.361 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  32  Ni   [   6.854 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  33  Ni   [   1.869 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  34  Ni   [   4.361 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  35  Ni   [   6.854 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  36  Ni   [   0.623 ,   0.622 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  37  Ni   [   3.125 ,   0.623 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  38  Ni   [   5.598 ,   0.623 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  39  Ni   [   0.623 ,   3.123 ,   7.971 ]   -0.00000  -0.00000 -10.00000     |
|  40  Ni   [   3.084 ,   3.081 ,   8.044 ]   -0.00000  -0.00000 -10.00000     |
|  41  Ni   [   5.640 ,   3.081 ,   8.044 ]   -0.00000  -0.00000 -10.00000     |
|  42  Ni   [   0.623 ,   5.599 ,   7.971 ]   -0.00000  -0.00000 -10.00000     |
|  43  Ni   [   3.083 ,   5.642 ,   8.043 ]   -0.00000  -0.00000 -10.00000     |
|  44  Ni   [   5.641 ,   5.643 ,   8.043 ]   -0.00000  -0.00000 -10.00000     |
|  45   S   [   4.364 ,   4.366 ,   9.313 ]   -0.00000  -0.00000  -6.00000     |
|  46   C   [   4.364 ,   4.368 ,  11.106 ]   -0.00000  -0.00000  -4.00000     |
|  47   H   [   4.367 ,   6.532 ,  11.228 ]   -0.00000  -0.00000  -1.00000     |
|  48   H   [   4.367 ,   2.204 ,  11.228 ]   -0.00000  -0.00000  -1.00000     |
|  49   C   [   4.367 ,   3.145 ,  11.808 ]   -0.00000  -0.00000  -4.00000     |
|  50   C   [   4.366 ,   5.592 ,  11.807 ]   -0.00000  -0.00000  -4.00000     |
|  51   C   [   4.369 ,   5.591 ,  13.208 ]   -0.00000  -0.00000  -4.00000     |
|  52   C   [   4.369 ,   3.145 ,  13.208 ]   -0.00000  -0.00000  -4.00000     |
|  53   H   [   4.374 ,   2.203 ,  13.783 ]   -0.00000  -0.00000  -1.00000     |
|  54   H   [   4.374 ,   6.534 ,  13.783 ]   -0.00000  -0.00000  -1.00000     |
|  55   C   [   4.369 ,   4.368 ,  13.913 ]   -0.00000  -0.00000  -4.00000     |
|  56   S   [   4.368 ,   4.368 ,  15.711 ]   -0.00000  -0.00000  -6.00000     |
|  57  Ni   [   0.624 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  58  Ni   [   3.116 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  59  Ni   [   5.609 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  60  Ni   [   0.624 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  61  Ni   [   3.116 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  62  Ni   [   5.609 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  63  Ni   [   0.624 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  64  Ni   [   3.116 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  65  Ni   [   5.609 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  66  Ni   [   1.870 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  67  Ni   [   4.362 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  68  Ni   [   6.855 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  69  Ni   [   1.870 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  70  Ni   [   4.362 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  71  Ni   [   6.855 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  72  Ni   [   1.870 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  73  Ni   [   4.362 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  74  Ni   [   6.855 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  75  Ni   [   0.624 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  76  Ni   [   3.116 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  77  Ni   [   5.609 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  78  Ni   [   0.624 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  79  Ni   [   3.116 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  80  Ni   [   5.609 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  81  Ni   [   0.624 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  82  Ni   [   3.116 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  83  Ni   [   5.609 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  84  Ni   [   1.870 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  85  Ni   [   4.362 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  86  Ni   [   6.855 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  87  Ni   [   1.870 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  88  Ni   [   4.362 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  89  Ni   [   6.855 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  90  Ni   [   1.870 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  91  Ni   [   4.362 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  92  Ni   [   6.855 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
+------------------------------------------------------------------------------+
|  15 E =  0.000508546 dE =  7.311566e-08 dH =  7.445477e-05  

          
The script is in the attachment

whar's wrong with it? should i increase the integral lower bound?

14
Questions and Answers / Question about stacking
« on: December 9, 2013, 08:50 »
Dear QuantumWise staff

i made a two-probe system as shown in the attachment, it is stacking fault(i mean in the Z-direction the periodicity is broken)

left electrode: ABAB...
right electrode: BABA...

is it right to use this type of two-probe system? or can it lead to wrong electronic transport properties
?

15
Dear QuantumWise staff:
    Does the phase of electron change in the coherence transport ? 

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