the error of the .vnl result document

[Roc]

Dear everyone,
    I have optimized the structure of two molecules(foe examples M1, M2) with the same method. however, I can only open the optimized .vnl document of M1, which is about 78MB. when I open the .vnl of M2, which is about 109MB, the error occures like picture1. The scripts .py and out document .txt have been uploaded as attachment M1.py and M2.py, whether is the method I choose reasonable, how to deal with the error. The ATK and VNL version is 2008.10.

thanks! （sorry,the M1opt.txt is too bigger than 256KB, just the M2opt.txt is uploaded）

[Anders Blom]

This might be a reflection of a memory problem. It is known that loading large files into VNL can causes memory issues. To avoid this, one can attempt to putt the eigenstates (the 3D grids) into separate files, or to restart VNL between loading different large files. This is obviously not an ideal solution, but it's a work-around for now, that hopefully can solve the problem. To recalculate the eigenstates should be very fast, and can easily be done from the checkpoint file, for example using something like

Code

from ATK.KohnSham import *
from ATK.MPI import processIsMaster

# Opening vnlfile
if processIsMaster(): file = VNLFile('TET_1.vnl')

scf = restoreSelfConsistentCalculation ('tet.nc')

eigenstates = calculateEigenstates(
    self_consistent_calculation = scf,
    quantum_numbers = (33)
)
for state_index,state in enumerate(eigenstates):
    label='Eigenstate'+' '+str(state_index)
    if processIsMaster(): file.addToSample(state, 'New Molecule', label)

[Roc]

thank you Anders Blom  for your advice.  I have tried to open the M2.vnl using my PC owning 4G physical memory, also the virtual memory is set to 4G, however, the error still occurs. how much memory is enough?
your advice would be my helpless choice. thank you again.
another, have you run the script M2.py, does the error occur in your powerful super computer.
 

[Anders Blom]

We have to admit that VNL doesn't manage memory properly in this case. I know, it's weird that a 100 Mb cannot be opened with 4 Gb of RAM, but that seems to be the case (for some types of grids). Later versions will of course resolve the problem.

[Roc]

thank you very much! I expect this problem could be resovled as soon as possible! best wishes!