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Topics - fanjiaping

Pages: [1] 2
1
General Questions and Answers / the question about quantum number
« on: August 23, 2011, 14:32 »
    I have obtained the molecularEnergySpectrum.  A part of content as below:
           # Line 31 in data set 0
  2.000000e-01  -1.013910e+00
  8.000000e-01  -1.013910e+00

# Line 32 in data set 0
  2.000000e-01  -2.222022e-01
  8.000000e-01  -2.222022e-01

# Line 33 in data set 0
  2.000000e-01   2.435497e+00
  8.000000e-01   2.435497e+00

# Line 34 in data set 0
  2.000000e-01   3.346397e+00
  8.000000e-01   3.346397e+00

# Line 35 in data set 0
  2.000000e-01   3.420903e+00
  8.000000e-01   3.420903e+00

# Line 36 in data set 0
  2.000000e-01   3.620254e+00
  8.000000e-01   3.620254e+00
Does it mean the quantum number of LUMO and HOMO are 33 and 32,respectively?

2
General Questions and Answers / is this possible?
« on: May 28, 2011, 10:34 »
Dears:     
 I get the I-V curve which contained a strange phenomenon. I doublt that this case can't be occurred. So I want to get authority reply from you. the picture was in additional information. thank you!

3
General Questions and Answers / the periodic boundry of system
« on: April 15, 2011, 12:45 »
Dir sir:
      As we know, the electrode is periodic at x,y directions. And we should make the size of electrode larger than the molecule at X,Y directions to avoid the interation between the molecule and its mirror. But in some paper , the figure shows that the molecule size is larger than electrode. So I am confused by this case. Could you show me more tips on this?
      the additional figure is the case which I mentioned!

4
General Questions and Answers / error from the cluster of computer
« on: April 7, 2011, 08:22 »
Dear sir:
        we have installed the lastest version of atk 11.2.1. A error appeared as below:
       terminate called after throwing an instance of 'MathException'
       terminate called after throwing an instance of 'MathException'
       terminate called after throwing an instance of 'MathException'
       terminate called after throwing an instance of 'MathException'
I have search the same error from the internet.　　　　　　　　　　　　　　　　　　　　　http://quantumwise.com/forum/index.php?topic=975.msg4885#msg4885
(the error nearly same as mine).　
But it didn't give us a hint. So I need your help.
thanks!

5
General Questions and Answers / confused on the spin value(relative)
« on: April 3, 2011, 14:18 »
Dear sir :     
      in the initial module of the scripter panel, We can set the spin value(relative) of each atom. the value range from -1 to 1. But my confusion is what is the value stand for? My understanding on the meaning of value which set to 1 or -1 is all the unpaired electrons directed to one direction.And the value equal to 0.5 means half of the unpaired electrons directed to one direction. If my understanding is right, my problem is when someone set the value to 0.77, how does  the software work?
        thanks for any advices!

6
General Questions and Answers / inquiring on the memory settings and multi-task running on a single cluster
« on: March 23, 2011, 04:38 »
Dear sir:
  We are runing the ATK package on a cluster with 22 nodes. However, we find that we are allowed to run only one task each time. And if we submit another new task, the currrent job will be killed automatically. Furthermore, based on our calculation, each task is usually  time consuming and expensive, that is, for runing an individual ATK task, it cost a  great amount of memory. Can you kindly make some modification of the default envionment settings for us, then we can use the soruces properly. Or is there some options we can apply to monitor the working processing?

    Any kind of suggestiong would be greatly appreciated.
 Thanks in advance.

7
General Questions and Answers / how build the model which contains proton transfer?
« on: January 4, 2011, 16:14 »
      I read a paper calculating the transmission of the compound which contains the proton transfer? So I want to know how to build the model in this case? the addtional information includes the molecule which existed in center region excluded the electrode atoms.
      Thank you !

8
General Questions and Answers / net error
« on: December 25, 2010, 16:19 »
     Recently, the problem about net error always appeared. The information was attached below.

Connection to server [ localhost : 6200 ] lost - trying to reconnect.
Server could not re-checkout feature because:
Unexpected network-related error occurred
rank 0 in job 20  master_52926   caused collective abort of all ranks
  exit status of rank 0: return code 1

could you kindly tell me what is the reason of the question? how to fix it ?
Thank you!

the second question:

+------------------------------------------------------------------------------+
|  12 E = -252.188 dE =  9.504735e-06 dH =  7.931225e-08                       |
+------------------------------------------------------------------------------+
| Calculation Converged in 12 steps                                            |
|                                                                              |
| Fermi Level  = -0.065674 Ha                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Right Electrode Calculation  [Finished Fri Dec 24 22:35:05 2010]             |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Device Density Matrix Calculation   [Started Fri Dec 24 22:35:05 2010]       |
|                                                                              |
+------------------------------------------------------------------------------+
| Left electrode chemical potential  = -0.065674 Ha                            |
| Right electrode chemical potential = -0.065674 Ha                            |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Equivalent Bulk  [Started Fri Dec 24 22:35:36 2010]                          |
|                                                                              |
+------------------------------------------------------------------------------+
rank 0 in job 1  compute-0-6_35793   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9

does it mean there is no enough memory of computer?

9
General Questions and Answers / some bugs in my script
« on: November 21, 2010, 05:46 »
Dear: 
   I want to adjust the distance between the electrode and molecule. Here ,A central region, contained Lithium and Hydrogen, was adopted as my example. The file "li_h2_prototype.py" is the script got from the VNL without any change !
the second script "test.py" is the script which I want to test my code.
I split the central region into three parts,first part contained the left five Lithium atoms, second part contained two hydrogen atoms, third part contained right five lithium.
first:
     I adjust the distance between the first part and second part by moving the coordinates of second part and third part.(if coordinate[2]>=12.1*Ang:
                                     coordinate[2]+=add*Ang)
second:
      I adjust the distance between the second part and third part by moving the coordinates of  third part. ( if coordinate[2]>(12.8+add)*Ang:
            coordinate[2]+=add*Ang)
third :
     we get the new coordinates to define the new central_region_coordinates, then get the central_region.
    But maybe here exist some errors. So, could you give me some guidance?

Thank you!

10
General Questions and Answers / the problem about index out of bound
« on: November 19, 2010, 07:01 »
Dear professor
       My calculation appeared a problem. I don't know what happened ! So I copy the message to here.

+------------------------------------------------------------------------------+
|  12 E = -189.203 dE =  2.329186e-05 dH =  3.725734e-07                       |
+------------------------------------------------------------------------------+
| Calculation Converged in 12 steps                                            |
|                                                                              |
| Fermi Level  = -0.068148 Ha                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Right Electrode Calculation  [Finished Thu Nov 18 10:06:56 2010]             |
|                                                                              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Device Density Matrix Calculation   [Started Thu Nov 18 10:06:56 2010]       |
|                                                                              |
+------------------------------------------------------------------------------+
| Left electrode chemical potential  = -0.068148 Ha                            |
| Right electrode chemical potential = -0.068148 Ha                            |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Equivalent Bulk  [Started Thu Nov 18 10:07:39 2010]                          |
|                                                                              |
+------------------------------------------------------------------------------+
0 : ML_CommInfoOP_GenUsingGIDExternals warning : index out of bound              = 827(1) 324395 268450802(0)
rank 11 in job 1  master_36287   caused collective abort of all ranks
  exit status of rank 11: killed by signal 9



Above all is the imformation the output file given. Could you kindly tell me how to solve the problem?

my second question:
 The ATK software installed in my computer unnormally run. If I clicked the modules of  builder or custom, the main window will close! I uninstall the software and then install again,but the problem still exist! the bug appeared like:
  /opt/QuantumWise/atk-10.8.2/vnl/bin/vnl: line 3: 13080 Segmentation fault      VNL_PATH=$EXEC_DIR/../.. PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../../atkpython/share/pseudopotentials PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/vnl_exec $*



Thank you for you help!

11
General Questions and Answers / how to get the PPT of the hefei meeting
« on: November 14, 2010, 12:55 »
        This week I attended the ATK meeting in hefei in china. But I forgot to get the PPT written by professor kurt about "Nano-device simulations with the new ATK: From field effect to Single Electron Organic Transistors."
Could you kindly tell me how can I get it or send a copy to me ? my email address is  359220837@qq.com
  Thanks a lot!
 

12
General Questions and Answers / the question about "the quick tutorial of ATK"
« on: November 6, 2010, 16:41 »
         in the tutorial of the quick tutorial of ATK",
(http://www.quantumwise.com/documents/tutorials/ATKTutorialDevice/ATKTutorialDevice.pdf)
I am confused on the part of how to calculate the device of density states. The tutorial tell us that "The Device Density of States also contains information on the Partial Density of States (PDOS)
which can be displayed by pushing PDOS Show from the lower right panel of the VNL main
window." But I can't find the PDOS from the lower right panel of the VNL main window. Also we can see from the upper left panel if is the word "vnl",not the "options" which appears in the tutorial. Maybe there are some mistakes I made. could you kindly tell me how to solve the problem?

13
General Questions and Answers / Is there a convenient way to constraint atoms?
« on: October 28, 2010, 16:51 »
   dear
     when I want to optimize the bulk of my own, it is so trivial to constraint the atoms of electrode which have so many atoms. Is there any convenient way to select the atoms which we want to constraint instead of clicking the atoms one by one using the mouse!!!!! ???

14
General Questions and Answers / the question about script in VNL tutorial
« on: October 22, 2010, 15:42 »
   In the part of Custom builder for the Li-H2-Li device system, there are some codes list as "builder.double('distance_h_h'  , 0.804, 'H/H  distance (Ang)' , min=0.01, max=1000)"
the queation I want to ask is why we set the min equal to 0.01? can we change it to others value,such as 0.02?

15
General Questions and Answers / confused by how to set the distance between molecule and electrode again :'(
« on: October 21, 2010, 13:44 »
   Dear
   I have learned the method about how to obtain the distance by calculating the total energy of the bulk (or we can call it as molecule-extend). That is to say, the distance could be obtained when the lowest total energy is reached. Unfortunately, the calculated energy can’t reach the lowest one point, and instead of that several points on a line are obtained. Therefore, I cannot get the exact distance between the certain molecule and the gold electrode. I am confused by the phenomenon and wonder how I can get the right distance. Could you give me some advices? Additionally, the script and the table of the total energy versus distance are in the attachment.
Thank you!

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