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Messages - esp

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286
General Questions and Answers / Re: saving calcs with device?
« on: January 24, 2012, 23:57 »
Ok I see what I was doing, I wanted to save the calc seperately inside the nc file then reopen that .. that must be where i got the error . here is that error ...

There is no support for writing this object <class 'NL.Calculators.LCAOCalculator.DeviceLCAOCalculator.DeviceLCAOCalculator'> to a NetCDF file

i think what you are saying though is that the code i posted previously is correct and should work, to save the calc within the device object .. i will check again .. thank you. 

287
General Questions and Answers / Re: saving calcs with device?
« on: January 24, 2012, 23:02 »
oh ok .. actually i got an error saying that saving of LCAO calcs is not supported .. ?  i changed my script but if i see it again i will post it. 

ed

288
General Questions and Answers / saving calcs with device?
« on: January 24, 2012, 22:23 »
It seems that when you set the device calculator object, then save the object, it does not save the calculator .. is this correct? 

example: 

Code
	device_configuration = nlread(outFileName,DeviceConfiguration)[0]
	device_configuration.setCalculator(calculator)
	device_configuration.update()
	nlsave(outFileName, device_configuration, object_id="cfg")

when i open the "cfg" object later and try to run a calc it says i did not set a calculator ... why?


289
General Questions and Answers / Re: Error message - mem error running in parallel
« on: January 24, 2012, 19:32 »
thank you that is very helpful

290
General Questions and Answers / running in parallel question
« on: January 24, 2012, 03:41 »
Maybe this is a dumb question, but what I am doing now is running a script such as :

1) make cfg
2) setup calcs
3) run calcs
4) make plots

If I run in parallel, do I need to seperate these?  for example, I noticed that a print message i put in the routine to make the cfg was printed 8 times, meaning it was run by each of the parallel threads ... is that bad?  do i need to only run calculations in parallel?  How do i know what to seperate exactly? i was assumming the program knew how to do that, but since my make config script seems to have run 8 times, that seems sort of strange ... it should not have to make the sonfiguration objects more than once ... please advice


291
General Questions and Answers / Re: MKL ?
« on: January 23, 2012, 21:54 »
Thank you. 

292
General Questions and Answers / MKL ?
« on: January 23, 2012, 20:42 »
on this page: http://quantumwise.com/documents/tutorials/latest/ParallelGuide/index.html/chap.quick.html

it talks about parallel implementation, then at the bottom it mentions:

"MKL will detect the presence of a multi-core processor and enable OpenMP automatically. It is recommended to let the software figure out itself how many threads to use optimally."

So I have a machine which has an equivalent of 24 cores ... so then should I run my jobs with the mpiexec -n parameter or not? should I .. "let the software figure out itself" ?

 ???

293
General Questions and Answers / Re: GNR topology
« on: January 22, 2012, 21:23 »
the tutorial mentioned above just disappeared:

"We're sorry…
The page you requested cannot be displayed. Possible reasons are: ... "

294
General Questions and Answers / Re: Error message - mem error running in parallel
« on: January 20, 2012, 22:36 »
Good tips .. I will check on that and try again.  Thank you. 

295
General Questions and Answers / Error message - mem error running in parallel
« on: January 20, 2012, 21:05 »
I am running atk in parallel on a machine with an equivalent of 24 cores ...

i got the following after an hour:


  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 287, in _update
  File "./zipdir/NL/Calculators/DeviceCalculatorInterface.py", line 287, in _update
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1632, in scfLoopDevice
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 588, in scfLoopDeviceHamiltonian
  File "./zipdir/NL/Calculators/CommonBuilder/DeviceBuilder.py", line 461, in createElectrostaticCalculator
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1632, in scfLoopDevice
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 588, in scfLoopDeviceHamiltonian
  File "./zipdir/NL/Calculators/CommonBuilder/DeviceBuilder.py", line 461, in createElectrostaticCalculator
  File "./zipdir/NL/CommonConcepts/PoissonSolvers/MultigridSolver.py", line 55, in calculateFunctionOnGrid
MemoryError
  File "./zipdir/NL/CommonConcepts/PoissonSolvers/MultigridSolver.py", line 55, in calculateFunctionOnGrid
MemoryError



Now there are still many processes running, so ... i am not sure, will the results be valid, or if i got this i should kill the processes and start over?


296
General Questions and Answers / Re: imports
« on: January 20, 2012, 05:53 »
ok got it .. you need this:

Code
from NanoLanguage import *
import numpy
import pylab
import ase

then you can put your parms in another file

297
General Questions and Answers / imports
« on: January 20, 2012, 05:43 »
I wanted to organize my code where i put parameters into a parms.py file, then use the following in the main program file:

Code
from parms import *

but i am having a problem where some of my parms use NanoLanguage units, etc .. and they are not available there ... i tried importing numpy and NanoLanguage but it is not working ... how can I accomplish this?

298
General Questions and Answers / Re: GNR topology
« on: January 19, 2012, 01:00 »
great, i look forward to it

299
General Questions and Answers / Re: GNR topology
« on: January 19, 2012, 00:46 »
regarding doping being done in the builder .. i am not sure i can agree to that being easier .. it seems that you have to select each atom, one by one, then go to the list of atoms, double click and select the new atom type, then go back and repeat ... to do this on say 20 atoms takes a considerable amount of time ... doing it programatically takes no time, except that since the order of each atom in the lists is not clear, the program can be somewhat complex to get a good distribution of new atoms .. is there an easier way to do this in builder or is it as much of a manual process as it seems to be?

300
General Questions and Answers / Re: Warning Message
« on: January 18, 2012, 21:36 »
what if it is not that small?

The computed multigrid residual is greater than the required accuracy
# Computed residual :   5.79742e-09                                            #
# Required accuracy :   1.00000e-12 

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