Messages

1

General Questions and Answers / Wrong GGA-NCPP of Ga

« on: September 7, 2010, 16:42 »

I find the NCPP in file GA.GGAPBE.ZIP is LDA-type, not GGA-type.

2

General Questions and Answers / How to Do A Parallel Calculation?(v 2010.8)

« on: July 22, 2010, 11:41 »

Feel so puzzled!!!!!

Read the the manuals "Parallel calculations using ATK" for 2008.10. Error got from test_mpi.py

Code

from ATK.MPI import *
 
if processIsMaster():
    print '# Master node'
else:
    print '# Slave node'

like

Code

+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 10.8.0                                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "test.py", line 1, in <module>
    from ATK.MPI import *
ImportError: No module named ATK.MPI
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 10.8.0                                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "test.py", line 1, in <module>
    from ATK.MPI import *
ImportError: No module named ATK.MPI

And 2010.8 version released "Fully parallel for DFT and SE, on two levels: MPI parallelization over clusters, and OpenMP threading for multi-core machines".

So I want to know the differences between the two version(2008.10,2010.8 ).I install the ATK 2010.8 on multi-cpus single node,  which mode do I chose? which parallel code i must use? Openmpi,mpich2? And which paralled version?

Code

[root@node1 ~]# mpiexec -n 2 atkpython test_mpi.py

or

Code

[root@node1 ~]# MKL_NUM_THREADS=2 MKL_DYNAMIC=FALSE atkpython test_mpi.py

3

General Questions and Answers / Re: Can ATK simulate the Surface system？

« on: July 16, 2010, 04:27 »

Thank you, zh. I want to simulate electrical transport properties of surface system,Could you tell me about the element "Poisson solver". For the surface system, How to set the Solver and Boundary condition?

Another question about the electrostatic potential, it there a element to calculate it?  'ElectrostaticDifferencePotential' can calculate the difference of two systems?

4

General Questions and Answers / Can ATK simulate the Surface system？

« on: July 15, 2010, 15:55 »

If can, How to?

5

Installation and License Questions / Re: error when running ATKSE to examine the molecular energy spectrum of water

« on: November 14, 2009, 07:40 »

It’s OK in ATK200911, ubunut-64bit-9.10 . However, another error when running input file from the Quick Tour "Properties of a Nano-ribbon Transistor" 

windysoul@ubuntu:~$ nlpython nanowire_device.py
Traceback (most recent call last):
  File "nanowire_device.py", line 245, in <module>
    difference_density = ElectronDifferenceDensity(device_configuration)
  File "./zipdir/NL/Analysis/ElectronDifferenceDensity.py", line 34, in __init__
  File "./zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 182, in update
  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 118, in _update
  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 107, in _upgrade
  File "./zipdir/NL/Calculators/HuckelCalculator/DeviceHuckelCalculator.py", line 223, in _customUpgrade
TypeError: isinstance() arg 2 must be a class, type, or tuple of classes and types

how to solve it?

6

Installation and License Questions / error when running ATKSE to examine the molecular energy spectrum of water

« on: November 4, 2009, 12:31 »

In .log file

Traceback (most recent call last):
  File "/tmp/2123880816936393.py", line 43, in <module>
    nlsave('analysis.nc', molecular_energy_spectrum)
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 7270, in nlsave
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 8050, in nlsaveMolecularEnergySpectrum
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 8460, in write1DArray
IndexError: list index out of range

how to solve it? Thanks!