Author Topic: The problem about charge being zero in the central region has been solved.  (Read 13970 times)

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postnikov

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I have a test calculation using the atk code. I find the charge in the central region become zero even if the  paramter
    integral_lower_bound has been set as 100*Rydberg.

100 Ry should be enough for the central region, however, the charge has also been zero in the two-probe calculatio.
By the way, the circle_points has also increase (100).
« Last Edit: August 7, 2009, 05:22 by postnikov »

postnikov

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Re: charge becomes zero in the central region
« Reply #1 on: August 4, 2009, 04:32 »
I have a test calculation using the atk code. I find the charge in the central region become zero even if the  paramter
    integral_lower_bound has been set as 100*Rydberg.

100 Ry should be enough for the central region, however, the charge has also been zero in the two-probe calculatio.
By the way, the circle_points has also increase (100).


The structure has been checked carefully and it seems ok.

Offline zh

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Re: charge becomes zero in the central region
« Reply #2 on: August 4, 2009, 06:39 »
Did you try to increase the size of k-point grid and to use the DZP basis set?

Offline Anders Blom

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Re: charge becomes zero in the central region
« Reply #3 on: August 4, 2009, 09:19 »
Although it's not a really critical point, I would consider shifting the coordinates in the X direction. If you visualize the system in the Nanoscope in VNL, you will find that half of the atoms are outside the unit cell. ATK will shift them inside, but it can cause some problems, and at any rate it will be a bit tricky to visualize the results later on.

Otherwise the key to this system is most likely indeed the k-point sampling, as zh pointed out. In the X direction, that is. The system is periodic in this direction, and graphene typically requires a relatively large k-point sampling, if not for convergence then at any rate to obtain accurate results.

There is no need to increase the circle to 100 Ry, you will just lose accuracy, even with 100 points. If you fail to converge with a circle of, say, 10 Ry, then the problem lies elsewhere. Since there appears to be enough electrode layers in your setup, I think the k-point sampling will be very helpful. In addition, you can experiment with increasing the temperature.

Increasing the k-point sampling increases the computation time quite a bit if you run in serial. If you have possibility, consider running the calculation in parallel.

postnikov

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Re: charge becomes zero in the central region
« Reply #4 on: August 4, 2009, 09:32 »
zh and Blom, thanks!

I am performing the  KP 10x10X200  case calculations.

The obtained results are also very bad as follows:

#-------------------------------------------------------------------------------
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  576.00000 e
#-------------------------------------------------------------------------------
# Mulliken Population for sc 0
#-------------------------------------------------------------------------------
48  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
....
63  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
......
89  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
90  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
91  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
92  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
93  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
94  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
95  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
96  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
97  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
98  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
......
124  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
125  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
126  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
127  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
128  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
129  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
130  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
131  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
132  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
133  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
134  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
135  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
136  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
137  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
138  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
........
168  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
169  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
170  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
171  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
172  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
173  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
174  C     q =  4.00000 [ s:  2.000, py:  0.667, pz:  0.667, px:  0.667 ]
......
189  C     q =  7.98406 [ s:  1.994, py:  1.997, pz:  1.997, px:  1.995 ]
190  C     q =  7.67588 [ s:  1.920, py:  1.948, pz:  1.869, px:  1.939 ]
191  C     q =  7.98417 [ s:  1.994, py:  1.998, pz:  1.997, px:  1.995 ]
#-------------------------------------------------------------------------------
# Total Charge =  927.80288
#-------------------------------------------------------------------------------
# sc  2 : q =   -2.32246 e  dRho =  7.9168E+00
#-------------------------------------------------------------------------------
# Mulliken Population for sc 2
#-------------------------------------------------------------------------------
48  C     q = -0.00113 [ s: -0.000, py: -0.000, pz:  0.000, px: -0.001 ]
49  C     q = -0.20335 [ s: -0.056, py: -0.023, pz: -0.087, px: -0.037 ]
50  C     q = -0.00110 [ s: -0.001, py: -0.000, pz:  0.000, px: -0.001 ]
51  C     q = -0.20361 [ s: -0.057, py: -0.023, pz: -0.088, px: -0.037 ]
52  C     q = -0.00110 [ s: -0.001, py: -0.000, pz:  0.000, px: -0.001 ]
53  C     q = -0.20364 [ s: -0.057, py: -0.023, pz: -0.087, px: -0.037 ]
54  C     q = -0.00110 [ s: -0.001, py: -0.000, pz:  0.000, px: -0.001 ]
55  C     q = -0.20364 [ s: -0.057, py: -0.023, pz: -0.087, px: -0.037 ]
56  C     q = -0.00110 [ s: -0.001, py: -0.000, pz:  0.000, px: -0.001 ]
57  C     q = -0.20361 [ s: -0.057, py: -0.023, pz: -0.088, px: -0.037 ]
58  C     q = -0.00113 [ s: -0.000, py: -0.000, pz:  0.000, px: -0.001 ]
59  C     q = -0.20335 [ s: -0.056, py: -0.023, pz: -0.087, px: -0.037 ]
60  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
61  C     q = -0.00017 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
62  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
63  C     q = -0.00016 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
64  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
65  C     q = -0.00016 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
66  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
67  C     q = -0.00016 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
68  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
69  C     q = -0.00016 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
70  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
71  C     q = -0.00017 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
72  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
73  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
74  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
75  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
76  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
77  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
78  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
79  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
80  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
81  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
82  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
83  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
84  C     q =  0.00000 [ s:  0.000, py:  0.000, pz:  0.000, px:  0.000 ]
......
175  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
176  C     q = -0.00014 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
177  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
178  C     q = -0.00015 [ s: -0.000, py: -0.000, pz: -0.000, px: -0.000 ]
179  C     q = -0.00001 [ s: -0.000, py:  0.000, pz: -0.000, px: -0.000 ]
180  C     q = -0.18116 [ s: -0.044, py: -0.023, pz: -0.080, px: -0.034 ]
181  C     q = -0.00068 [ s: -0.000, py:  0.000, pz:  0.000, px: -0.001 ]
182  C     q = -0.18142 [ s: -0.044, py: -0.023, pz: -0.080, px: -0.034 ]
183  C     q = -0.00068 [ s: -0.000, py:  0.000, pz:  0.000, px: -0.001 ]
184  C     q = -0.18187 [ s: -0.044, py: -0.023, pz: -0.080, px: -0.034 ]
185  C     q = -0.00067 [ s: -0.000, py:  0.000, pz:  0.000, px: -0.001 ]
186  C     q = -0.18187 [ s: -0.044, py: -0.023, pz: -0.080, px: -0.034 ]
187  C     q = -0.00067 [ s: -0.000, py:  0.000, pz:  0.000, px: -0.001 ]
188  C     q = -0.18142 [ s: -0.044, py: -0.023, pz: -0.080, px: -0.034 ]
189  C     q = -0.00068 [ s: -0.000, py:  0.000, pz:  0.000, px: -0.001 ]
190  C     q = -0.18116 [ s: -0.044, py: -0.023, pz: -0.080, px: -0.034 ]
191  C     q = -0.00068 [ s: -0.000, py:  0.000, pz:  0.000, px: -0.001 ]
#-------------------------------------------------------------------------------
# Total Charge =   -2.32246
#-------------------------------------------------------------------------------
« Last Edit: August 4, 2009, 09:43 by postnikov »

Offline Anders Blom

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Re: charge becomes zero in the central region
« Reply #5 on: August 4, 2009, 09:39 »
There is no need to use more than 1 k-point in the Y direction, it just makes the calculation run slower, without changing or improving the results in any way!

So, try something like 10x1x200 instead.

postnikov

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Re: charge becomes zero in the central region
« Reply #6 on: August 4, 2009, 09:49 »
thanks again!

Now, I am trying the 16x1x200,
and the integral_lower_bound has been set as 10*Rydberg, circle_points = 100
« Last Edit: August 4, 2009, 10:07 by postnikov »

postnikov

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Re: charge becomes zero in the central region
« Reply #7 on: August 4, 2009, 12:22 »
thanks again!

Now, I am trying the 16x1x200,
and the integral_lower_bound has been set as 10*Rydberg, circle_points = 100

in  the case of 16x1x200, the charge variation in the calculation:

# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  576.00000
# Total Charge =  927.83657
# Total Charge =   -2.32268
# Total Charge =   38.14169
# Total Charge = 1150.31016
# Total Charge =  120.60376
# Total Charge =   97.44324
# Total Charge =   -5.98985
# Total Charge =   -5.60166
# Total Charge =   11.28651
# Total Charge =  739.07469
# Total Charge =  889.81866
# Total Charge =  765.27955
# Total Charge =  885.32093
# Total Charge =  215.58614
# Total Charge =  231.24017
# Total Charge =  375.51966
# Total Charge =  550.63754
# Total Charge =  481.29176
# Total Charge =  689.45979
# Total Charge =  195.55278
# Total Charge =  326.48935
# Total Charge =  589.78465
# Total Charge =  485.65247
# Total Charge =  428.85457
# Total Charge =  436.84078
# Total Charge =  377.56452


postnikov

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Re: charge becomes zero in the central region
« Reply #8 on: August 4, 2009, 12:24 »


in  the case of 10x1x200, the charge variation in the calculation:


# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  192.00000
# Total Charge =  576.00000
# Total Charge =  927.80347
# Total Charge =   -2.32289
# Total Charge =   38.15299
# Total Charge = 1150.30976
# Total Charge =  120.64785
# Total Charge =   97.38514
# Total Charge =   -5.95919
# Total Charge =   -5.59841
# Total Charge =   38.45065
# Total Charge =  768.23992
# Total Charge =  996.36881
# Total Charge =  913.11851
# Total Charge = 1108.56319
# Total Charge =  929.81157
# Total Charge =  345.36823
# Total Charge =  360.73868
# Total Charge =  141.53380
# Total Charge =  610.70247
# Total Charge =  565.37767
# Total Charge =  552.51291
# Total Charge =  581.16821
# Total Charge =  569.63964
# Total Charge =  538.48649
# Total Charge =  548.40624
# Total Charge =  571.78094
# Total Charge =  574.82316
# Total Charge =  577.37777
# Total Charge =  580.78817
# Total Charge =  580.76599
# Total Charge =  581.45682

Offline Anders Blom

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Re: charge becomes zero in the central region
« Reply #9 on: August 4, 2009, 12:53 »
Try increasing the temperature, and lowering the diagonal mixing to 0.05. Is this SingleZeta? I'd use SingleZetaPolarized.

Offline zh

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Re: charge becomes zero in the central region
« Reply #10 on: August 4, 2009, 13:33 »
How did you specify the "electrode_parameters" in the "TwoProbeMethod()"? Could you paste it here? If the left and right electrodes are identical to each other, one had better specify the same entity to the "electrode_parameters" in the "TwoProbeMethod()", as shown in follows:
electrode_params = ...
basis_set = ...
initial_density = ...
twoprobe_method = TwoProbeMethod(
    electrode_parameters=(electrode_parms, electrode_parms),
    basis_set_parameters=basis_set,
    electron_density_parameters=initial_density,
    ......
    )


Although the definitions of "left_electrode_params" and "right_electrode_params" in the followings example are identical to each other, it is not recommended to specify the "electrode_parameters" in the "TwoProbeMethod()" in the following way:
left_electrode_params = ...
right_electrode_params=
basis_set = ...
initial_density = ...
twoprobe_method = TwoProbeMethod(
    electrode_parameters=(left_electrode_parms, right_electrode_parms),
    basis_set_parameters=basis_set,
    electron_density_parameters=initial_density,
    ......
    )

.

Offline ipsecog

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Re: charge becomes zero in the central region
« Reply #11 on: August 4, 2009, 13:40 »
Well, the second way is how VNL produces the scripts, whether the setup is homogeneous or not...!

I doubt changing the setup this way will change the convergence, but if the system is homogeneous (left electrode == right electrode), then the calculation will run faster if you set it up using the same electrode parameters, since it uses FFT rather than the multigrid method for the electrostatics.

This should be the default for homogeneous systems, but it isn't. So, you have to edit the script by hand, after VNL has provided the "template".

postnikov

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Re: charge becomes zero in the central region
« Reply #12 on: August 4, 2009, 14:42 »
from ATK.TwoProbe import *
from ATK.MPI import processIsMaster

# Generate time stamp
if processIsMaster():
    import platform, time
    print '#',time.ctime()
    print '#',platform.node(),platform.platform()+'\n'

# Opening vnlfile
if processIsMaster(): file = VNLFile('sample_tp.vnl')

# Scattering elements and coordinates
scattering_elements = [Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
  .....
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon,
                       Carbon, Carbon, Carbon, Carbon]
scattering_coordinates = [[  7.755,   0.   ,  10.99 ],
                          [  8.46 ,   0.   ,   9.769],
                          [ 10.575,   0.   ,  10.99 ],
                          [  9.87 ,   0.   ,   9.769],
....
                          [ 14.805,   0.   ,  18.316],
                          [ 14.1  ,   0.   ,  17.095],
                          [ 16.215,   0.   ,  18.316],
                          [ 16.92 ,   0.   ,  17.095],
                          [ 19.035,   0.   ,  18.316],
                          [ 18.33 ,   0.   ,  17.095],
                          [  7.755,   0.   ,  20.759],
                          [  8.46 ,   0.   ,  19.538],
                          [ 10.575,   0.   ,  20.759],
                          [  9.87 ,   0.   ,  19.538],
                          [ 11.985,   0.   ,  20.759],
                          [ 12.69 ,   0.   ,  19.538],
                          [ 14.805,   0.   ,  20.759],
                          [ 14.1  ,   0.   ,  19.538],
                          [ 16.215,   0.   ,  20.759],
                          [ 16.92 ,   0.   ,  19.538],
                          [ 19.035,   0.   ,  20.759],
                          [ 18.33 ,   0.   ,  19.538],
                          [  7.755,   0.   ,  23.201],
                          [  8.46 ,   0.   ,  21.98 ],
                          [ 10.575,   0.   ,  23.201],
                          [  9.87 ,   0.   ,  21.98 ],
                          [ 11.985,   0.   ,  23.201],
                          [ 12.69 ,   0.   ,  21.98 ],
                          [ 14.805,   0.   ,  23.201],
                          [ 14.1  ,   0.   ,  21.98 ],
                          [ 16.215,   0.   ,  23.201],
                          [ 16.92 ,   0.   ,  21.98 ],
                          [ 19.035,   0.   ,  23.201],
 ...
                          [ 16.215,   0.   ,  28.085],
                          [ 16.92 ,   0.   ,  26.864],
                          [ 19.035,   0.   ,  28.085],
                          [ 18.33 ,   0.   ,  26.864],
                          [  7.755,   0.   ,  30.527],
                          [  8.46 ,   0.   ,  29.306],
                          [ 10.575,   0.   ,  30.527],
                          [  9.87 ,   0.   ,  29.306],
                          [ 11.985,   0.   ,  30.527],
                          [ 12.69 ,   0.   ,  29.306],
                          [ 14.805,   0.   ,  30.527],
                          [ 14.1  ,   0.   ,  29.306],
                          [ 16.215,   0.   ,  30.527],
                          [ 16.92 ,   0.   ,  29.306],
                          [ 19.035,   0.   ,  30.527],
                          [ 18.33 ,   0.   ,  29.306],
                          [  7.755,   0.   ,  32.97 ],
                          [  8.46 ,   0.   ,  31.748],
                          [ 10.575,   0.   ,  32.97 ],
                          [  9.87 ,   0.   ,  31.748],
                          [ 11.985,   0.   ,  32.97 ],
                          [ 12.69 ,   0.   ,  31.748],
                          [ 14.805,   0.   ,  32.97 ],
                          [ 14.1  ,   0.   ,  31.748],
                          [ 16.215,   0.   ,  32.97 ],
                          [ 16.92 ,   0.   ,  31.748],
                          [ 19.035,   0.   ,  32.97 ],
                          [ 18.33 ,   0.   ,  31.748],
                          [  7.755,   0.   ,  35.412],
                          [  8.46 ,   0.   ,  34.191],
                          [ 10.575,   0.   ,  35.412],
.....
                          [ 16.92 ,   0.   ,  36.633],
                          [ 19.035,   0.   ,  37.854],
                          [ 18.33 ,   0.   ,  36.633]]*Angstrom
        

electrode_elements = [Carbon, Carbon, Carbon, Carbon,
                      Carbon, Carbon, Carbon, Carbon,
...
                      Carbon, Carbon, Carbon, Carbon,
                      Carbon, Carbon, Carbon, Carbon,
                      Carbon, Carbon, Carbon, Carbon]
electrode_coordinates = [[  7.755,   0.   ,   1.221],
                         [  8.46 ,   0.   ,   0.   ],
                         [ 10.575,   0.   ,   1.221],
                         [  9.87 ,   0.   ,   0.   ],
                         [ 11.985,   0.   ,   1.221],
                         [ 12.69 ,   0.   ,   0.   ],
                         [ 14.805,   0.   ,   1.221],
 ....
                         [  7.755,   0.   ,   3.663],
                         [  8.46 ,   0.   ,   2.442],
                         [ 10.575,   0.   ,   3.663],
                         [  9.87 ,   0.   ,   2.442],
                         [ 11.985,   0.   ,   3.663],
                         [ 12.69 ,   0.   ,   2.442],
                         [ 14.805,   0.   ,   3.663],
                         [ 14.1  ,   0.   ,   2.442],
                         [ 16.215,   0.   ,   3.663],
                         [ 16.92 ,   0.   ,   2.442],
                         [ 19.035,   0.   ,   3.663],
                         [ 18.33 ,   0.   ,   2.442],
                         [  7.755,   0.   ,   6.105],
                         [  8.46 ,   0.   ,   4.884],
                         [ 10.575,   0.   ,   6.105],
                         [  9.87 ,   0.   ,   4.884],
                         [ 11.985,   0.   ,   6.105],
                         [ 12.69 ,   0.   ,   4.884],
                         [ 14.805,   0.   ,   6.105],
 ...
                         [  9.87 ,   0.   ,   7.327],
                         [ 11.985,   0.   ,   8.548],
                         [ 12.69 ,   0.   ,   7.327],
                         [ 14.805,   0.   ,   8.548],
                         [ 14.1  ,   0.   ,   7.327],
                         [ 16.215,   0.   ,   8.548],
                         [ 16.92 ,   0.   ,   7.327],
                         [ 19.035,   0.   ,   8.548],
                         [ 18.33 ,   0.   ,   7.327]]*Angstrom

electrode_cell = [[ 12.78774,   0.     ,   0.     ],
                  [  0.     ,  30.     ,   0.     ],
                  [  0.     ,   0.     ,   9.844  ]]*Angstrom

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
    electrode_cell,
    electrode_elements,
    electrode_coordinates
    )

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
    (electrode_configuration,electrode_configuration),
    scattering_elements,
    scattering_coordinates,
    electrode_repetitions=[[1,1],[1,1]],
    equivalent_atoms=([0,0],[47,143])
    )
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'sample_tp')

######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = LDA.PZ

iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.05,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 150.0*Rydberg
)

basis_set_parameters = basisSetParameters(
    type = SingleZetaPolarizedPolarized,
    radial_sampling_dr = 0.001*Bohr,
    energy_shift = 0.01*Rydberg,
    delta_rinn = 0.8,
    v0 = 40.0*Rydberg,
    charge = 0.0,
    split_norm = 0.15
)

iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 100
)

electrode_voltages = (0.0,0.0)*Volt

two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
    electrode_constraint = ElectrodeConstraints.Off,
    initial_density_type = InitialDensityType.NeutralAtom
)

energy_contour_integral_parameters = energyContourIntegralParameters(
    circle_points = 100,
    integral_lower_bound = 10*Rydberg,
    fermi_line_points = 10,
    fermi_function_poles = 4,
    real_axis_infinitesimal = 0.01*electronVolt,
    real_axis_point_density = 0.02*electronVolt
)

two_center_integral_parameters = twoCenterIntegralParameters(
    cutoff = 2500.0*Rydberg,
    points = 1024
)

######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 150.0*Rydberg
)

left_electrode_iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 100
)

left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
    monkhorst_pack_parameters = (16, 1, 200)
)

left_electrode_iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.05,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
    temperature = 300.0*Kelvin
)

######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
    brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
    electron_density_parameters = left_electrode_electron_density_parameters,
    eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
    iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
    iteration_control_parameters = left_electrode_iteration_control_parameters
)

######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 150.0*Rydberg
)

right_electrode_iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 100
)

right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
    monkhorst_pack_parameters = (16, 1, 200)
)

right_electrode_iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.05,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
    temperature = 300.0*Kelvin
)

######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
    brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
    electron_density_parameters = right_electrode_electron_density_parameters,
    eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
    iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
    iteration_control_parameters = right_electrode_iteration_control_parameters
)

######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
    electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
    exchange_correlation_type = exchange_correlation_type,
    iteration_mixing_parameters = iteration_mixing_parameters,
    electron_density_parameters = electron_density_parameters,
    basis_set_parameters = basis_set_parameters,
    iteration_control_parameters = iteration_control_parameters,
    energy_contour_integral_parameters = energy_contour_integral_parameters,
    two_center_integral_parameters = two_center_integral_parameters,
    electrode_voltages = electrode_voltages,
    algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)

runtime_parameters = runtimeParameters(
    verbosity_level = 10,
    checkpoint_filename = None
)

# Perform self-consistent field calculation
scf = executeSelfConsistentCalculation(
    twoprobe_configuration,
    two_probe_method,
    runtime_parameters = runtime_parameters
)






This is the used script file in my ongoing calculation, in which the diagonal mixing has been changed into 0.05 and the SingleZetaPolarized orbital has been adopted.

In the previous calculation, the diagonal mixing is 0.1 and the SingleZeta orbital is used.
« Last Edit: August 4, 2009, 15:09 by postnikov »

postnikov

  • Guest
Re: charge becomes zero in the central region
« Reply #13 on: August 4, 2009, 14:52 »
It is just a simple test calculation using ATK code.
However, I think it may be a good choice for atk users and developers to check electron loss problem.
I have found there are many posts about such a problem in this forum.

I have also test the case, in which electrode_constraint has been set as ElectrodeConstraints.RealSpaceDensity.
In such a case, everything is Ok.
« Last Edit: August 4, 2009, 14:57 by postnikov »

Offline Anders Blom

  • QuantumWise Staff
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    • QuantumWise
Re: charge becomes zero in the central region
« Reply #14 on: August 4, 2009, 15:26 »
You are right about the charge loss being a problem, but most of the time the solution is quite simple (increase the k-points sampling or the number of electrode layers).

Let us know when you get a parameter setting that works, it will, as you say, be very useful as an instructive system for other users. :)

I should also say, that when calculating a similar system, we found that you need a really high k-point sampling for the transmission spectrum to get accurate results. Therefore I'm not surprised if many k-points are also needed for the SCF loop.

In general, SingleZeta should be reserved for cases when the system uses so much memory that it's the only option, or if you have already tested a small system with this basis set and obtained accurate results. I wouldn't expect many systems to pass this test, however, the SingleZeta set is simply too limited for any serious work.