Topics

1

General Questions and Answers / why the equivalent bulk density matrix are still used for neutralAtom method

« on: April 10, 2017, 14:04 »

Dear Quantumwisestaffs:
           Recently i decided to calculate heterojunctions, i learned from post http://quantumwise.com/forum/index.php?topic=4038.msg18443#msg18443that the NeutralAtoms option should be used for the heterogeneous system, but what confused me most is that the phrase in the Atomistix ToolKit Reference Manual"Length over which the atoms in the electrode copy within the central region will be initialized with a linear combination of the converged density matrix of the electrodes and the equivalent bulk density matrix. The weight of the electrode density matrix is 1 at the boundary and 0 at the distance electrode_constraint length from the boundary"from http://www.quantumwise.com/documents/manuals/ATK-2015/ReferenceManual/index.html/ref.neutralatom.html.
            The question is that since the  equivalent bulk is replaced by NeutralAtoms for heterojunctions, why the equivalent bulk calculation  is still involved to get the  equivalent bulk density matrix before the first device electronic convergence. On the other hand, how should we pick appropriate electrode_constraint _length for NeutralAtoms option, or how the magnitude of electrode_constraint_length influence the speed for the subsequent device eletronic convergence. for example, convergence speed will be accelerated if we use the electrode length in the Z direction or just set zero value for electrode_constraint_length?

2

General Questions and Answers / Problems of the Normalization of the frontier wave functions of MPSH analysis

« on: June 29, 2016, 11:35 »

           Recently i  did  the MPSH and calculated the correspponding FMO of the eigenstate.Then i exported  the cube of the FMO.In my opinion ,if  i  want to compare the expansibility of two FMO ,we should square the absolute cube and normalize the squared  cube .So i pick the fourth option，but i can not figure out  if it is normalied? Here is export picture of the FMO.

3

General Questions and Answers / problems about the calculation max steps in the restarting calculation

« on: April 4, 2016, 08:47 »

Dear quantumwise staff:
          Recently i confronted a convergence problems in MoS2 ,so i referred to the forum  and increase the max steps ,the problem is as follows:
if i don't restart from the convergened state ,that is i calculate it from zero bias ,here is my max steps setting.

Code

#----------------------------------------
# Iteration Control Settings
#----------------------------------------
left_electrode_iteration_control_parameters = IterationControlParameters(
    max_steps=500,
    )

right_electrode_iteration_control_parameters = IterationControlParameters(
    max_steps=500,
    )

device_iteration_control_parameters = IterationControlParameters(
    damping_factor=0.31,
    max_steps=2000,
    number_of_history_steps=10,
    )

#----------------------------------------
# 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]]
    )

#----------------------------------------
# Contour Integral Settings
#----------------------------------------
contour_parameters = DoubleContourIntegralParameters(
    real_axis_infinitesimal=1e-06*Rydberg,
    real_axis_point_density=0.02*eV,
    integral_lower_bound=50.0*eV,
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    iteration_control_parameters=left_electrode_iteration_control_parameters,
    poisson_solver=left_electrode_poisson_solver,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    iteration_control_parameters=right_electrode_iteration_control_parameters,
    poisson_solver=right_electrode_poisson_solver,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    iteration_control_parameters=device_iteration_control_parameters,
    contour_parameters=contour_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    )

device_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
initial_spin = InitialSpin(scaled_spins=[0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, -1.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, -1.0, 0.0, -1.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0])
device_configuration.setCalculator(
    calculator,
    initial_spin=initial_spin,
)
device_configuration.update()
nlsave('CONFIG.nc', device_configuration)
nlprint(device_configuration)

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations_bias_%g.nc" % bias.inUnitsOf(Volt), device_configuration)

My calculation is slowly converged in the step =635 ,

Code

350627:| 615 E = -447.349 dE =  4.819839e-04 dH =  2.388363e-04
350846:| 616 E =  -447.35 dE =  9.950206e-04 dH =  8.781832e-04
351065:| 617 E =  -447.35 dE =  1.495225e-04 dH =  1.050059e-03
351284:| 618 E = -447.349 dE =  7.514605e-04 dH =  2.417407e-04
351503:| 619 E = -447.349 dE =  8.285889e-05 dH =  1.792596e-04
351722:| 620 E = -447.348 dE =  6.273245e-04 dH =  1.333994e-04
351941:| 621 E = -447.348 dE =  4.864245e-04 dH =  3.458751e-04
352160:| 622 E = -447.348 dE =  1.074768e-04 dH =  2.376046e-04
352379:| 623 E = -447.349 dE =  6.705824e-04 dH =  3.217824e-04
352598:| 624 E = -447.348 dE =  6.934614e-04 dH =  3.254210e-04
352817:| 625 E = -447.348 dE =  3.242197e-04 dH =  2.692547e-04
353036:| 626 E = -447.348 dE =  1.095985e-04 dH =  1.103893e-04
353255:| 627 E = -447.349 dE =  7.666417e-04 dH =  1.624413e-04
353474:| 628 E = -447.349 dE =  1.769304e-05 dH =  4.870540e-04
353693:| 629 E = -447.348 dE =  8.042218e-04 dH =  1.483390e-04
353912:| 630 E = -447.348 dE =  1.963235e-06 dH =  2.435271e-04
354131:| 631 E = -447.349 dE =  6.199732e-04 dH =  5.196899e-04
354350:| 632 E = -447.348 dE =  5.375404e-04 dH =  1.000946e-04
354569:| 633 E = -447.348 dE =  1.350441e-05 dH =  1.004250e-04
354788:| 634 E = -447.348 dE =  1.106934e-04 dH =  1.264113e-04
355007:| 635 E = -447.348 dE =  3.390452e-05 dH =  9.519258e-05
355462:|   0 E = -428.204 dE =  1.917845e+01 dH =  1.470380e-01
355681:|   1 E = -439.981 dE =  1.177661e+01 dH =  3.916571e+00
355900:|   2 E = -445.977 dE =  5.996319e+00 dH =  7.775032e-01
356119:|   3 E = -446.527 dE =  5.499668e-01 dH =  2.842024e-01
356338:|   4 E = -446.857 dE =  3.301646e-01 dH =  8.742580e-02
356557:|   5 E = -446.732 dE =  1.250417e-01 dH =  1.973932e-01
356776:|   6 E = -446.928 dE =  1.960541e-01 dH =  8.639483e-02
356995:|   7 E = -446.951 dE =  2.286883e-02 dH =  8.455163e-02
357214:|   8 E = -447.205 dE =  2.537133e-01 dH =  9.177060e-02
357433:|   9 E = -447.073 dE =  1.319129e-01 dH =  7.540765e-02
357652:|  10 E = -447.258 dE =  1.854489e-01 dH =  5.404163e-02
357871:|  11 E = -447.261 dE =  3.214866e-03 dH =  8.341868e-02
358090:|  12 E = -447.239 dE =  2.249815e-02 dH =  6.084702e-02
358309:|  13 E = -447.096 dE =  1.428855e-01 dH =  5.987770e-02
358528:|  14 E = -447.068 dE =  2.819535e-02 dH =  4.608637e-02
358747:|  15 E = -447.118 dE =  5.013750e-02 dH =  8.704623e-02
358966:|  16 E = -447.188 dE =  6.975315e-02 dH =  6.939250e-02
359185:|  17 E = -447.285 dE =  9.755813e-02 dH =  1.863129e-01

but when i  set  same max step in another restarting py ,

Code

#----------------------------------------
# Iteration Control Settings
#----------------------------------------
left_electrode_iteration_control_parameters = IterationControlParameters(
    max_steps=1000,
    )

right_electrode_iteration_control_parameters = IterationControlParameters(
    max_steps=1000,
    )

device_iteration_control_parameters = IterationControlParameters(
    damping_factor=0.36,
    max_steps=2000,
    number_of_history_steps=8,
    )

#----------------------------------------
# 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]]
    )

#----------------------------------------
# Contour Integral Settings
#----------------------------------------
contour_parameters = DoubleContourIntegralParameters(
    real_axis_infinitesimal=1e-06*Rydberg,
    real_axis_point_density=0.02*eV,
    integral_lower_bound=50.0*eV,
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    iteration_control_parameters=left_electrode_iteration_control_parameters,
    poisson_solver=left_electrode_poisson_solver,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    iteration_control_parameters=right_electrode_iteration_control_parameters,
    poisson_solver=right_electrode_poisson_solver,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    iteration_control_parameters=device_iteration_control_parameters,
    contour_parameters=contour_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    )

device_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
initial_spin = InitialSpin(scaled_spins=[0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0])
device_configuration.setCalculator(
    calculator,
    initial_spin=initial_spin,
)
device_configuration = nlread("ivcurve_selfconsistent_configurations_bias_-0.1.nc")[0]
device_configuration.update(force_restart=True)
nlsave('CONFIG.nc', device_configuration)
nlprint(device_configuration)

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [-0.200000, -0.300000, -0.400000, -0.500000,
          -0.600000, -0.700000, -0.800000, -0.900000, -1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations_bias_%g.nc" % bias.inUnitsOf(Volt), device_configuration)

it stopped in the step=499 （i should mentioned that in the previous V= -0.1,i used max steps as 500) ,so i wonder if it is because the restarting for -0.1 make the new max step =2000 invalid ,can anyone explain about it ?

4

General Questions and Answers / Restarting a device configuration

« on: March 22, 2016, 06:28 »

hello,quantumwise staff :
1.i also met the restarting problems ,here is my confusion:
   there are so many verisions of restart a bias dependent calculation ,but i can't get the uniform answer about it ,there is basically two answers  in the forum :
   first solution ,

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()
device_configuration = nlread("ivcurve_selfconsistent_configurations_bias_0.nc",)[0]

     second solution,

Code

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration = nlread("ivcurve_selfconsistent_configurations_bias_0.nc")[0]
device_configuration.update(force_restart=True)
nlsave('CONFIG.nc', device_configuration)

     
      I don't know  the accuracy and differences between these two solutions  and in the

Code

 nlread("ivcurve_selfconsistent_configurations_bias_0.nc")[0]

,what is the exact meaning of

• and [-1],or when should i use
• and [-1],what is the exact meaning of 
  Code

  force_restart=True

  .
  2.i am also very confused about the restarting procedure ,can you explain about it ?In another posthttp://quantumwise.com/forum/index.php?topic=1374.msg6752#msg6752 ,it tells me that the restarting procedure includes these steps :
  1.) read Electrode
  2.) read checkpoint-file  (== equiv. bulk)
  3.) create Device from equiv. Bulk and electrodes
  4.) attach a new device calculator
  5.) update
   Hope you can give us a detailed description of the equiv bulk and the  restarting procedure .

5

General Questions and Answers / How to get the electrode band structure under a certain bias ?

« on: March 11, 2016, 05:06 »

Hello ,every one .For a  spin dependent two-probe  deviceI, i am running  the I-V calculation and  confused about how  to calculate the bandstructure under a certain bias for the electrode after the I-V calculation  .This is my thought: i need to analyse the iv-scf converged device configuration ,but how should i apply it to my left/right electrode ,in another words, how should i write in my code to read the bias left/right electrode configuration and its spin state for my iv-scf converged device configuration  . I can't find any information in the forum and toturial about the detailed items.

Code

# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [37.2364702358, 0.0, 0.0]*Angstrom
vector_b = [0.0, 23.17211, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.43074]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum, Molybdenum,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum,
            Molybdenum, Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum, Molybdenum, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum,
            Molybdenum, Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Molybdenum, Molybdenum, Molybdenum, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Molybdenum,
            Molybdenum, Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur]

# Define coordinates
fractional_coordinates = [[ 0.292994142293,  0.43155327676 ,  0.083333333329],
                          [ 0.439217461613,  0.43155327676 ,  0.083333333329],
                          [ 0.585440780933,  0.43155327676 ,  0.083333333329],
                          [ 0.731664100254,  0.43155327676 ,  0.083333333329],
                          [ 0.34199604229 ,  0.499999999998,  0.083333333329],
                          [ 0.48821936161 ,  0.499999999998,  0.083333333329],
                          [ 0.634442680931,  0.499999999998,  0.083333333329],
                          [ 0.292994142293,  0.568446723236,  0.083333333329],
                          [ 0.439217461613,  0.568446723236,  0.083333333329],
                          [ 0.585440780933,  0.568446723236,  0.083333333329],
                          [ 0.731664100254,  0.568446723236,  0.083333333329],
                          [ 0.366105801953,  0.43155327676 ,  0.249999999997],
                          [ 0.512329121273,  0.43155327676 ,  0.249999999997],
                          [ 0.658552440594,  0.43155327676 ,  0.249999999997],
                          [ 0.26888438263 ,  0.499999999998,  0.249999999997],
                          [ 0.41510770195 ,  0.499999999998,  0.249999999997],
                          [ 0.561331021271,  0.499999999998,  0.249999999997],
                          [ 0.707554340591,  0.499999999998,  0.249999999997],
                          [ 0.366105801953,  0.568446723236,  0.249999999997],
                          [ 0.512329121273,  0.568446723236,  0.249999999997],
                          [ 0.658552440594,  0.568446723236,  0.249999999997],
                          [ 0.292994142293,  0.43155327676 ,  0.416666666664],
                          [ 0.439217461613,  0.43155327676 ,  0.416666666664],
                          [ 0.585440780933,  0.43155327676 ,  0.416666666664],
                          [ 0.731664100254,  0.43155327676 ,  0.416666666664],
                          [ 0.34199604229 ,  0.499999999998,  0.416666666664],
                          [ 0.48821936161 ,  0.499999999998,  0.416666666664],
                          [ 0.634442680931,  0.499999999998,  0.416666666664],
                          [ 0.292994142293,  0.568446723236,  0.416666666664],
                          [ 0.439217461613,  0.568446723236,  0.416666666664],
                          [ 0.585440780933,  0.568446723236,  0.416666666664],
                          [ 0.731664100254,  0.568446723236,  0.416666666664],
                          [ 0.366105801953,  0.43155327676 ,  0.583333333331],
                          [ 0.512329121273,  0.43155327676 ,  0.583333333331],
                          [ 0.658552440594,  0.43155327676 ,  0.583333333331],
                          [ 0.26888438263 ,  0.499999999998,  0.583333333331],
                          [ 0.41510770195 ,  0.499999999998,  0.583333333331],
                          [ 0.561331021271,  0.499999999998,  0.583333333331],
                          [ 0.707554340591,  0.499999999998,  0.583333333331],
                          [ 0.366105801953,  0.568446723236,  0.583333333331],
                          [ 0.512329121273,  0.568446723236,  0.583333333331],
                          [ 0.658552440594,  0.568446723236,  0.583333333331],
                          [ 0.292994142293,  0.43155327676 ,  0.74999999999 ],
                          [ 0.439217461613,  0.43155327676 ,  0.74999999999 ],
                          [ 0.585440780933,  0.43155327676 ,  0.74999999999 ],
                          [ 0.731664100254,  0.43155327676 ,  0.74999999999 ],
                          [ 0.34199604229 ,  0.499999999998,  0.74999999999 ],
                          [ 0.48821936161 ,  0.499999999998,  0.74999999999 ],
                          [ 0.634442680931,  0.499999999998,  0.74999999999 ],
                          [ 0.292994142293,  0.568446723236,  0.74999999999 ],
                          [ 0.439217461613,  0.568446723236,  0.74999999999 ],
                          [ 0.585440780933,  0.568446723236,  0.74999999999 ],
                          [ 0.731664100254,  0.568446723236,  0.74999999999 ],
                          [ 0.366105801953,  0.43155327676 ,  0.916666666657],
                          [ 0.512329121273,  0.43155327676 ,  0.916666666657],
                          [ 0.658552440594,  0.43155327676 ,  0.916666666657],
                          [ 0.26888438263 ,  0.499999999998,  0.916666666657],
                          [ 0.41510770195 ,  0.499999999998,  0.916666666657],
                          [ 0.561331021271,  0.499999999998,  0.916666666657],
                          [ 0.707554340591,  0.499999999998,  0.916666666657],
                          [ 0.366105801953,  0.568446723236,  0.916666666657],
                          [ 0.512329121273,  0.568446723236,  0.916666666657],
                          [ 0.658552440594,  0.568446723236,  0.916666666657]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# Add tags
bulk_configuration.addTags('Left')

# -------------------------------------------------------------
# Analysis from File
# -------------------------------------------------------------
bulk_configuration = nlread('ivcurve_selfconsistent_configurations_bias_0.4.nc', object_id='gID000')[0]

# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=bulk_configuration,
    route=['G', 'Z'],
    points_per_segment=20,
    bands_above_fermi_level=All
    )
nlsave('Device Device-1-7 (1) (left electrode).nc', bandstructure)

.
This is my code  and i am not sure if it is right or wrong .

6

General Questions and Answers / problems abou the spin density visualization

« on: March 7, 2016, 09:42 »

Hello,i recently learned the spin density from the http://www.quantumwise.com/documents/tutorials/latest/GrapheneBloch/index.html/electrondensity.spin.html,The block state and the band structure is normal ,but when i calculated the spin density difference and visualize it in the view  subframe,it turned out that the color and the pattern is not consistent with the the Mulliken populations that the numbers 0 and 1) have a surplus population of 0.25 of either spin-up or spin-down.I read some literatures that the spin density is usually red and blue ,i change the color map ,it still exhibited wrong  color.can anyone help me fix it ?

7

General Questions and Answers / problem about optimizing lattice constant in the new ATK2015

« on: February 24, 2016, 14:49 »

Hello, i tried to optimize the lattice constant of the MoS2 recently ,i read the tutorial http://quantumwise.com/forum/index.php?topic=29.0.I used the easy  GaN.py example  and modified it as

Code

from stress_optimizers import *
import ATK; ATK.setVerbosityLevel(1)
from ATK.KohnSham import *
# Select Bravais lattice and define lattice constants
bravais_lattice = Hexagonal(
    a=3.160400 * Angstrom,
    c=12.29500 * Angstrom
    )

# Define bulk elements and unit cell coordinates
elements = [Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur]
coordinates = [[ 1.5802      ,  0.9123289,  3.073750   ],
               [ 1.5802      , -0.9123289,  9.221250   ],
               [ 1.5802      ,  0.9123289,  7.635195   ],
               [ 1.5802      , -0.9123289,  1.487695   ],
               [ 1.5802      ,  0.9123289,  10.80730   ], 
               [ 1.5802      , -0.9123289,  4.659805   ]]*Angstrom  
# Set up bulk configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice,
    elements,
    cartesian_coordinates=coordinates
    )

method = KohnShamMethod(brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((5,5,5)),
                        basis_set_parameters = basisSetParameters())
opt_conf = calculateOptimizedBulkConfiguration(bulk_configuration, method, runtimeParameters(1))

.
 runed it on my cluster  and the version is ATK2015.It quickly returned the error message:

Code

Traceback (most recent call last):
  File "MoS2.py", line 1, in <module>
Traceback (most recent call last):
  File "MoS2.py", line 1, in <module>
Traceback (most recent call last):
  File "MoS2.py", line 1, in <module>
Traceback (most recent call last):
  File "MoS2.py", line 1, in <module>
    from stress_optimizers import *
    from stress_optimizers import *
    from stress_optimizers import *
ImportError: No module named stress_optimizersImportError: No module named stress_optimizers
ImportError: No module named stress_optimizers

.
I am not aware about the program codes in ATK and can't fix this problem.

Thanks.

8

General Questions and Answers / Server could not re-checkout feature because:Software expired

« on: January 22, 2016, 04:39 »

Recently i ran two  device with wo - dimensional materials ,it has  340 atoms .They both return the error message.

Code

Server could not re-checkout feature because:
Software expired

.Some detailed maeesage are :

Code

|  332   S   [  13.649 ,  13.172 ,  50.033 ]    3.09984   3.07110   0.17094    |
|  333   S   [  19.123 ,  13.172 ,  50.033 ]    3.08572   3.08115   0.16687    |
|  334   S   [  24.597 ,  13.172 ,  50.033 ]    3.11573   3.03993   0.15566    |
|  335   S   [  30.071 ,  13.172 ,  50.033 ]    3.45875   2.63973   0.09848    |
+------------------------------------------------------------------------------+
|  99 E = -711.003 dE =  1.849073e-04 dH =  2.930977e-04                       |
+------------------------------------------------------------------------------+
|                                                                              |
| Fermi Level  = -4.229089 eV                                                  |
+------------------------------------------------------------------------------+
################################################################################
#                                                                              #
# Warning: The calculation did not converge to the requested tolerance!        #
#                                                                              #
################################################################################
+------------------------------------------------------------------------------+
|                                                                              |
| DFT Calculation  [Finished Thu Jan 21 23:48:51 2016]                         |
|                                                                              |
+------------------------------------------------------------------------------+

Code

+------------------------------------------------------------------------------+
|   1 E = -710.931 dE =  1.668908e-01 dH =  8.603409e-02                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Eigenvalues    : Connection to server [ localhost : 6200 ] lost - trying to reconnect.
Server could not re-checkout feature because:
Software expired

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

.
I have another problems that i set

Code

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
indices_0 = [192, 193, 194, 195, 196, 197, 198, 199, 200, 201,
             202, 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, 243, 244, 245, 246, 247, 248, 249, 250, 251,
             252, 253, 254, 255, 256, 257, 258, 259, 260, 261,
             262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
             272, 273, 274, 275, 276, 277, 278, 279, 280, 281,
             282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
             292, 293, 294, 295, 296, 297, 298, 299, 300, 301,
             302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
             312, 313, 314, 315, 316, 317, 318, 319, 320, 321,
             322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
             332, 333, 334, 335]
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,
              40,  41,  42,  43,  44,  45,  46,  47,  48,  49,
              50,  51,  52,  53,  54,  55,  56,  57,  58,  59,
              60,  61,  62,  63,  64,  65,  66,  67,  68,  69,
              70,  71,  72,  73,  74,  75,  76,  77,  78,  79,
              80,  81,  82,  83,  84,  85,  86,  87,  88,  89,
              90,  91,  92,  93,  94,  95,  96,  97,  98,  99,
             100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
             110, 111, 112, 113, 114, 115, 116, 117, 118, 119,
             120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
             130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
             140, 141, 142, 143]
constraints = [RigidBody(indices_0), RigidBody(indices_1)]

bulk_configuration = OptimizeGeometry(
        bulk_configuration,
        max_forces=0.05*eV/Ang,
        max_steps=500,
        max_step_length=0.2*Ang,
        constraints=constraints,
        trajectory_filename='trajectory.nc',
        disable_stress=True,
        optimizer_method=LBFGS(),
        )
nlsave('Device-heterojunctions2.nc', bulk_configuration)
nlprint(bulk_configuration)

my max_steps=500,why it stops when the step=99 and

Code

 the dE =  1.849073e-04 dH =  2.930977e-04    

.

9

General Questions and Answers / where is the unit cell in the view interface?

« on: January 18, 2016, 11:09 »

Recently itested the tutorial http://www.quantumwise.com/documents/tutorials/latest/GrapheneBloch/index.html/chap.spin.html.When i analyse the nc in the viewer to visualize the Spin up (right) and down (left) states at the Z point  in Fig6. I couldn't find theUnit cell ,i.e, I couldn't find the cell tick.All the subsequent analyse such as Electron density ,i couldn.t see the unit cell in the viewer .Hope anyone could help me!
attachments are the analyse nc file.

10

General Questions and Answers / How to save selfconsistent_configurations for every voltage

« on: January 10, 2016, 11:21 »

Dear sir:
       Recently i tested to  restart I-V calculations from a checkpoint . i learned from http://quantumwise.com/forum/index.php?topic=3306.msg15142#msg15142 andhttp://quantumwise.com/forum/index.php?topic=1358.msg9062#msg9062 about how to restart a suspended job.i modify the code as

Code

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
calculator=device_configuration.calculator()

biases = [0.000000, 0.100000, 0.200000, 0.300000, 0.400000, 0.500000,
          0.600000, 0.700000, 0.800000, 0.900000, 1.000000]*Volt
for bias in biases:
    calculator=calculator(
            electrode_voltages=(bias/2, -bias/2))

    device_configuration.setCalculator(
          calculator(),
          initial_state=device_configuration)
    device_configuration.update()
    nlsave("ivcurve_selfconsistent_configurations.nc", device_configuration)
    
#----------------------------------------
# Transmission spectrum
#----------------------------------------
configurations = nlread('ivcurve_selfconsistent_configurations.nc', DeviceConfiguration)
     for device_configuration in configurations:
         transmission_spectrum = TransmissionSpectrum(
             configuration=device_configuration,
             energies=numpy.linspace(-2,2,201)*eV,
             kpoints=MonkhorstPackGrid(4, 4),
             energy_zero_parameter=AverageFermiLevel,
             infinitesimal=1e-06*eV,
             self_energy_calculator=RecursionSelfEnergy(),
             )
         nlsave("TS_analysis.nc", transmission_spectrum)
         nlprint(transmission_spectrum)

.

So here is my idea:
For the initial calculation script(not restaring script) i want to use "nlsave" statement to make a new file for each converged bias and calculate the transmission spectrum for each bias using each converged bias(i want to exactly know output bias file and restart from it ),
my problem is :
How to modify the above code in the I-V and transmission module  to realise the these two underlined functions.

11

General Questions and Answers / problem about restarting from a check point

« on: January 9, 2016, 06:48 »

Hello,recently i run a test script[Device.py] to set the

Code

DeviceLCAOCalculator( checkpoint_handler= CheckpointHandler('checkpoint-2.nc', 1*Minute),

and kille the job for restarting the jobs.i also get the [checkpoint-2.nc],but when i run the new py script[Device-restart.py], i get the  error message instantly

Code

Traceback (most recent call last):
  File "Device.py", line 495, in <module>
    device_configuration.setCalculator(DeviceLCAOCalculator(), initial_state= device_configuration)
  File "./zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1222, in setCalculator
  File "./zipdir/NL/CommonConcepts/Calculator.py", line 58, in _supportConfiguration
  File "./zipdir/NL/CommonConcepts/Calculator.py", line 48, in _supportConfigurationType
  File "./zipdir/NL/Analysis/AnalysisUtilities.py", line 78, in checkConfiguration
NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter, configuration, must be an instance of one of the following SurfaceConfiguration, DeviceConfiguration, NudgedElasticBand.

I have already read the Restarting stopped calculations toturial ,forum ,and the manual and i can't fix the problem in my code. Hope anyone could help! me!

12

General Questions and Answers / how to print out the default parameter in the .out file

« on: December 18, 2015, 04:57 »

Hello,i am eager to know the default Double Contour Integral Parameters ,ie .fermi_ function_poles 、circle_points， and fermi_line_points.but i am not farmiliar with the python language.Can anyone tell me what code should i use in .py to print out it.

13

General Questions and Answers / transmission-spectrum output differences running on cluster using VNL-ATK2015

« on: December 15, 2015, 06:00 »

Hello,i tested the example on the quantumwise website-Transmission spectrum of a graphene nanoribbon with a distortion  on our cluster by parallel computing(i watched the viedo and follow the steps and set the same parameter as it sets).I found the apparent differences of  transmission-spectrum output  .Hope anyone can explain it , thanks a lot .

14

General Questions and Answers / How to get the transmission spectrum data by K-point average

« on: December 10, 2015, 14:29 »

I used VNL-ATK 2015 to calculate the transmission spectrum ,but i don't understand the export  data of the  transmisison spectrum .What  does the data in  Line2D(_line0,1,2,3,4,5,6) mean?It is extraordinary  to see that data corresponding to  line6 only has two lines(see the attachment [transmission in ATK]).In addition ,what code should i write in the input  py  script to  get the transmision data averaged by K-point (see the attachments [input.py,transmission in siesta]).

15

General Questions and Answers / Question about difference between ATK and Siesta transmission spectrum data

« on: December 9, 2015, 15:25 »

Dear QuantumWise Staff :
              I used  ATK  and Siesta to  run transmission spectrum of the same gold-dtb-gold device under zero bias voltage .When i compare the two  transmisison coefficient data and graph ,i am confused with several differences between  the two graphs and datas:
             1. T(e,v) <1  in SIESTA .T(e,v) can be 2 or more in ATK. I learned the transmission spectrum in ATK is the sum of probabilities for all the states that exist at the given energy, but i don't know what the T(e,v) means in SIESTA exactly and
             2. the two graph has two instinct  differences under E<-1.5 and E=1.8
             3  i don't understand the ATK output  transmission spectrum data .In detail ,why it has line 0 -6  ,ie,seven group data ,and how should i pick the correct line to analyse my system. In addition , i used the Line2D(_line0) data in the graph plotted above .
              4.how do i use the transmission spectrum to analyse my system.

              Hope for your answers sincerely! Thank you very much !