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Offline ATK-user-zuox

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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 ?
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Offline Anders Blom

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Re: problems about the calculation max steps in the restarting calculation
« Reply #1 on: April 5, 2016, 15:01 »
Just declaring the max_steps has no effect. You also need to use the parameter class "device_iteration_control_parameters" in the calculator actually used. Keep in mind your script is code, just setting a=1 doesn't do anything if you don't use a for anything. When you restart at higher bias, depending on HOW you do it, it will use the calculator of the zero bias if you only change the electrode voltages.
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Offline ATK-user-zuox

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Re: problems about the calculation max steps in the restarting calculation
« Reply #2 on: April 7, 2016, 16:11 »
I used my original job and found that my change of
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,
    )
is effective in my calculation and  my calculation accelerates to convergence because of the large damping_factor ,but the  max_steps is not changed .so i am quite confused .As you said , if i  redefine the  Iteration Control Settings in the I-V block ,will it be effective on the max_steps?
Code
# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
#----------------------------------------
# Iteration Control Settings
#----------------------------------------
left_electrode_iteration_control_parameters = IterationControlParameters(
    max_steps=3000,
    )

right_electrode_iteration_control_parameters = IterationControlParameters(
    max_steps=3000,
    )

device_iteration_control_parameters = IterationControlParameters(
    damping_factor=0.25,
    max_steps=3000,
    number_of_history_steps=12,
    )

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)
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Re: problems about the calculation max steps in the restarting calculation
« Reply #3 on: April 7, 2016, 18:40 »
No, because your variable device_iteration_control_parameters is only defined, never used by the calculator.

You need create a new calculator by cloning the old one,

new_calculator = calculator(iteration_control_parameters=device_iteration_control_parameters)

and then use this in the bias loop.
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