Messages

46

General Questions and Answers / Vacuum potential??

« on: July 27, 2012, 11:34 »

Hi,
   Can anyone let me know about the steps involved in calculating vacuum potential using ATK.

47

Scripts, Tutorials and Applications / Running from middle:

« on: July 17, 2012, 15:10 »

hi,
    I have attached two files here:
  1.Checkpoint.py (in this i can successfully save temporary .nc file in specified folder and at a given time)
  Problem with this script:
  a)as i have defined checkpoint file (ben.nc)for electrode calculation and (ben2.nc) for device calculation,however, the file is getting saved as ben2.nc only i.e for both electrode and device. Also,
ben2.nc is getting deleted after electrode calculation is finished and with the start of device calculation it is again saving temporary files as (ben2.nc). I want electrode calculated nc file and device calculated nc files separately. So that I can restart simulation from middle.

2.benzene_I_V2_resart.py( I want to restart it, using ben2.nc file, however, getting error as shown in third attachment.)
Problem:
 a)Can I restart from any point.

3. Screenshot.png(error file)
 
Plz correct the coding if possible.

48

Scripts, Tutorials and Applications / Re: Reusing same electrodes:

« on: July 17, 2012, 14:12 »

Thank you very much for the reply

49

Scripts, Tutorials and Applications / Re: Reusing same electrodes:

« on: July 17, 2012, 11:56 »

Sorry, I forgot to attach scripts.
I have tried [1] in first two lines instead

• , however got the error attached.

Now, I have attached
1.  (electrode_left_right.py)
2.(Au_Benzene_AU_IV.py)the full calculation as we normally do with some representative central region. I have used this one to create my (device.py) and (electrode_left_right.py)
3.Error.png, when tried [1] instead

• .

50

Scripts, Tutorials and Applications / Re: Reusing same electrodes:

« on: July 17, 2012, 06:46 »

Thanks for reply.I am attaching two file , Plz comment on them
1.  (electrode_left_right.py)
2.(Au_Benzene_AU_IV.py)the full calculation as we normally do with some representative central region. I have used this one to create my (device.py) and (electrode_left_right.py)

51

Scripts, Tutorials and Applications / Reusing same electrodes:

« on: July 16, 2012, 14:02 »

Hi,
    I am doing the tutorial " Reuse the same electrode for many different calculations " (http://www.quantumwise.com/publications/tutorials/mini-tutorials) I have created succesully the (left_electrode.nc) and (right_electrode.nc), however when I am using (device.py) for simulation , it is not bypassing the electrode calculation. I am attaching the script , if anyone can correct the code.

52

General Questions and Answers / Simulation Problem on cluster

« on: July 13, 2012, 07:09 »

We are running simulation on cluster machine,the cluster and License server are on the same LAN, however, recently we faced the problem as described in attached file. Can anyone help us to know that.

53

General Questions and Answers / Checkpoint handler...

« on: July 12, 2012, 13:51 »

I am running simulation on cluster machine having 20 nodes, each node is quadcore with 4 GB Ram, I am using swap of 100 GB in each..
while running log file is showing that .nc file is getting saved in /tmp, however there it is not saving actually. I have studied the manual how to change the checkpoint time and folder in which .nc files which are creating in between the simulation..bt unable to make it correctly.
Can anyone help..coz m new to quantumwise.I am getting problem with cluster as time to time m getting communication error with license server.
1. Can we restart simulation from any point or it can be restarted after certain point.

54

General Questions and Answers / Re: Script changed while running simulation

« on: July 9, 2012, 07:28 »

thanx Nordland.....

55

General Questions and Answers / can we start simulation from middle??

« on: July 9, 2012, 07:26 »

Is there any way to restart a simulation from middle, i mean if anyhow our simulation gets stop due to any reason, hence, to save time can we restart the simulation from the point where it was stopped.

56

General Questions and Answers / Script changed while running simulation

« on: July 7, 2012, 08:11 »

I am running simulation for IV characteristic , and in between running it i have realised that I have not saved .nc(i.e o/p file)correctly then i have opened the script and given the correct the path. Simulation is currently doing bulk caculation, Now I doubt whether  it will save the .nc file to new path or will have some problem.
Can anyone help.

57

Installation and License Questions / Re: License is lost due to heartbeat failure

« on: July 6, 2012, 09:35 »

Thanx, But I was running simulation on license server itself.

58

Installation and License Questions / License is lost due to heartbeat failure

« on: July 5, 2012, 09:25 »

I was running simulation on the license node itself, however during simulation its log file suddenly shows following error:

Connection to server [ License_Server_IP : 6200 ] lost - trying to reconnect.
Connection to server [ License_Server_IP: 6200 ] lost - trying to reconnect.
Server could not re-checkout feature because:
License is lost due to heartbeat failure

Can anyone plz help me get out of this problem,although i have restarted simulation,& it is working well.. i want to know the reason behind the above.

59

General Questions and Answers / Re: Communication error with rank 12???

« on: June 15, 2012, 10:02 »

Thanx Anders... , I utilize this knowledge for running my scripts.

60

General Questions and Answers / Communication error with rank 12???

« on: June 14, 2012, 12:50 »

1.I have installed MPICH2 1.3 in two nodes each node is having 12 cores, therefore running my script in 16 cores parallely, however after some time simulation is getting stopped and giving the following error.
2. When iam running my script parallely in the same node using CUI it is taking more time compare to if I am running it in GUI.what is the problem.Simulation time for that scipt is 0nly 4 minutes in GUI ,whereas in Parallely running it is taking double time 8 min.
Can anyone Plz suggest smthng, Iam new user in ATK.