Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Messages - luke419

Pages: [1]
1
General Questions and Answers / handling of symmetry during the calculation
« on: October 15, 2012, 05:43 »
I think that symmetry should be kept during running the work.
If so, how can I run the work without imposing the symmetry?

Otherwise, will it be running without symmetry by default?
In this case, how can I impose the symmtery in running the work?

Thanks for your help in advance.

Best

  Young


2
Installation and License Questions / Re: lincense error for running the program using demo license
« on: September 26, 2012, 14:17 »
I've used the license tool to install the trial license file. However, it showed the same error message.
How can I remove the ATK installation completely so that I can install in naive system condition?
I've used uninstall program but it seems that I should some other things to remove it completely.

Best

  Young
 

3
Installation and License Questions / Re: lincense error for running the program using demo license
« on: September 25, 2012, 12:15 »
I've got the trial license and test it well using it but it showed error message suddenly today. It does not expired due date. Is there any other thing to be checked?

Best

  Young

4
Installation and License Questions / lincense error for running the program using demo license
« on: September 25, 2012, 09:55 »
I'd like to run windows ATK using demo license file offered by qunatumwise.
I've installed demo license file using license installation tools but it showed the following error.

License Error: (Internal: 693 Feature: VNL)

(Err: 19) Feature not allowed to run on terminal server clients

For assistance on resolving this matter, there are several options:
  Consult the FAQ        : http://www.quantumwise.com/support/faq
  Find help on the forum : http://forum.quantumwise.com
  The installation guide : http://www.quantumwise.com/support/manuals
  Email support          : support@quantumwise.com

I've removed all and reboot and install it again but it showed the error message still.
Incidentally, I cound not remove the quantumwise/vnl/lib/site/pyc of the pevious installed program.

What's the problem with it and what should I do for it?

Best

  Young

5
General Questions and Answers / Re: the setting for the parallel computing of ATK
« on: September 14, 2012, 18:58 »
First many thanks for all your previous help, Anderson Blom.
The hostname test was done again and it runs well in the comupter system.
It seems that mpich2 is the best for ATK but I'd like to use "mpich intel" if possible since there is some probelm in mpich2 of our system.
It is written that mpich intel will be all right for running ATK.
However, if I run it, only one process (one core) is running in the submitted node and it is not distributed to other cores nor the other machcines.
If you know about this issue, would you let me know of it?
Incidentally, mpich intel in our system works well for many other programs.

Best

  Young


6
General Questions and Answers / Re: the setting for the parallel computing of ATK
« on: August 27, 2012, 13:38 »
1. I've tested the script with and without includinig machinefile list and the output is the same as follows.

master -p4pg /home/yijhon/ATK/test/PI9492 -p4wd /home/yijhon/ATK/test

PI9492 was changed to PIxxxx, it is just numbering of the job.

2. Please, let me know of your email address by sending the information to luke419@google.com so that the system adiministrator contact to you, if possible.

Best regards,

  Young

7
General Questions and Answers / Re: the setting for the parallel computing of ATK
« on: August 27, 2012, 05:20 »
1. The output is as follows.
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 12.2.2 [Build 144eba5]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Master node master

In the a pevious test, it was node45 instead of master but it didn't show Slave node, either.

2. The email address is "hidden" in your profile of the forum.
I'd like to ask you send the information on your email address to luke419@google.com, please.

3. What was the version of MPICH2 which was used to compile ATK 12.2.2?


Best regards,

  Young


8
General Questions and Answers / Re: the setting for the parallel computing of ATK
« on: August 24, 2012, 08:02 »
Thanks for your answers, Anders Blom.
I've asked about MPI system to the system administrator and he said MPICH2 was installed. Mpirun works well generally in this system (e.g., VASP etc.) and I think it needs some modification for ATK but I don't know what it is.
I am not an expert on the system details and I will ask the administrator to upload his question using my ID and talk with you on this point.

If possible, you may let me know of your email address (informing your email adress by sending it to my email) for the direct discussion with him.
By the way, in case that it is hard to solve, may I ask you connect to our computer system and check the detail?

Many thanks for all your helps again.

Best regards,

  Young

 

9
General Questions and Answers / continued to the previous post, the setting for parallel computing
« on: August 23, 2012, 05:35 »
I didn't compile it and I've used a binary file provided by quantumwise for the execution.
The commands for the execution was as follows.

mpirun -np 16 -machinefile nodefile /opt/QuantumWise/atk-12.2.2/atkpython/bin/atkpython test.py > test.log &

nodefile contains three nodes.

I've got the following result using the test script.

+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 12.2.2 [Build 144eba5]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Master node node45

Slave node and its specific host name was not shown and it seems that something is wrong.

What should I do for it?
Can I compile the source files of ATK in my system?

Best regards,

  Young


10
General Questions and Answers / Re: the setting for the parallel computing of ATK
« on: August 23, 2012, 03:40 »
I didn't compile it and I've used a binary file provided by quantumwise for the execution.
The commands for the execution was as follows.

mpirun -np 16 -machinefile nodefile /opt/QuantumWise/atk-12.2.2/atkpython/bin/atkpython test.py > out &

nodefile contains three nodes.

I've got the following result using the test script.

+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 12.2.2 [Build 144eba5]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Master node node45

Slave node and its specific host name was not shown and it seems that something is wrong.

What should I do for it?
Can I compile the source files of ATK in my system?

Best regards,

  Young


11
General Questions and Answers / the setting for the parallel computing of ATK
« on: August 22, 2012, 06:24 »
Hello,

I'd like to perform ATK in parallel based on MPI using 4 node systems in which each has 8 cores (total 32 cores).
I've make input file (python) for ATK and performed it using queue system in  as way that VASP was performed.

My questions are as follows.

1. Despite parallel computing, the speed is not good.
The queue state showed that it assigned to 4 nodes, however, if I connected the corresponding nodes, running program for ATK is not shown by "top" or "ps" command.
Only one node showed one running job of "atkexec".
What's the problem with it and what should I do for it?

Should I add the commands for the node number or core number in input python file for correct running?
Otherwise, is it working correctly though they are not shown?
I ask your answers as in detail as possible, please.

2. Incidentally, the job stopped during the process without the completion after 4 days.
Can restart it? If so, what should I do for it?


Best reagrds,

  Young


12
General Questions and Answers / question on GPAW installation
« on: August 19, 2012, 16:16 »
Hello,

I've installed GPAW to atk 11.8.2 following the instruction of the website.
But in vnl, I can' see "GPAW" item  in the menu of calculators in new calculator block while the tutorial indicates that it is available.
Isn't VNL modified by GPAW installation script file?
Should I add GPAW calculation code to the script file of ATK manually?

2. While intall-GPAW scipt file exists in binary directory of ATK 11.8.2, it doesn't in the directory of ATK 12.2.2.
For what does such a difference exist and if possible, what should I do to install GPAW to ATK 12.2.2?

Thanks for your answer in advance.

  Young


13
General Questions and Answers / the question on the error message
« on: August 17, 2012, 19:14 »
Helllo,

I've got the error message after the running as follows.

Traceback (most recent call last):
  File "FLG_MD_1L.py", line 19, in <module>
    bulk_configuration.setCalculator(calculator)
NameError: name 'bulk_configuration' is not defined

My script is given below.


# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = GGABasis.DoubleZetaPolarized

#----------------------------------------
# Exchange-Correlation   
#----------------------------------------
exchange_correlation = GGA.PBE
                         
calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    )                   
                         
bulk_configuration.setCalculator(calculator) 
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('analysis.nc', bulk_configuration)
                         
# -------------------------------------------------------------
# Bulk configuration     
# -------------------------------------------------------------
                         
# Set up lattice         
lattice = Triclinic(12.741*Angstrom, 12.26*Angstrom, 20.0*Angstrom, 90.0*Degrees, 90.0*Degrees, 90.0*Degrees)
                         
# Define elements       
elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon]   
                         
# Define coordinates     
cartesian_coordinates = [[  3.53919498e+00,   1.22587740e+00,   1.00000000e+01],
                         [  1.41590733e+00,   6.12323400e-16,   1.00000000e+01],
                         [  2.12366988e+00,   1.22612260e+00,   1.00000000e+01],
                         [  6.12323400e-16,   6.12323400e-16,   1.00000000e+01],
                         [  7.78627992e+00,   1.22587740e+00,   1.00000000e+01],
 [  5.66286486e+00,   6.12323400e-16,   1.00000000e+01],
                         [  6.37062741e+00,   1.22612260e+00,   1.00000000e+01],
                         [  4.24695753e+00,   6.12323400e-16,   1.00000000e+01],
                         [  1.20332374e+01,   1.22587740e+00,   1.00000000e+01],
                         [  9.90994980e+00,   6.12323400e-16,   1.00000000e+01],
                         [  1.06177123e+01,   1.22612260e+00,   1.00000000e+01],
                         [  8.49404247e+00,   6.12323400e-16,   1.00000000e+01],
                         [  3.53919498e+00,   3.67787740e+00,   1.00000000e+01],
                         [  1.41590733e+00,   2.45200000e+00,   1.00000000e+01],
                         [  2.12366988e+00,   3.67812260e+00,   1.00000000e+01],
                         [  7.62465097e-16,   2.45200000e+00,   1.00000000e+01],
                         [  7.78627992e+00,   3.67787740e+00,   1.00000000e+01],
                         [  5.66286486e+00,   2.45200000e+00,   1.00000000e+01],
                         [  6.37062741e+00,   3.67812260e+00,   1.00000000e+01],
                         [  4.24695753e+00,   2.45200000e+00,   1.00000000e+01],
                         [  1.20332374e+01,   3.67787740e+00,   1.00000000e+01],
                         [  9.90994980e+00,   2.45200000e+00,   1.00000000e+01],
                         [  1.06177123e+01,   3.67812260e+00,   1.00000000e+01],
                         [  8.49404247e+00,   2.45200000e+00,   1.00000000e+01],
                         [  3.53919498e+00,   6.12987740e+00,   1.00000000e+01],
                         [  1.41590733e+00,   4.90400000e+00,   1.00000000e+01],
                         [  2.12366988e+00,   6.13012260e+00,   1.00000000e+01],
                         [  9.12606795e-16,   4.90400000e+00,   1.00000000e+01],
                         [  7.78627992e+00,   6.12987740e+00,   1.00000000e+01],
                         [  5.66286486e+00,   4.90400000e+00,   1.00000000e+01],
                         [  6.37062741e+00,   6.13012260e+00,   1.00000000e+01],
                         [  4.24695753e+00,   4.90400000e+00,   1.00000000e+01],
                         [  1.20332374e+01,   6.12987740e+00,   1.00000000e+01],
                         [  9.90994980e+00,   4.90400000e+00,   1.00000000e+01],
                         [  1.06177123e+01,   6.13012260e+00,   1.00000000e+01],
                         [  8.49404247e+00,   4.90400000e+00,   1.00000000e+01],
                         [  3.53919498e+00,   8.58187740e+00,   1.00000000e+01],
                         [  1.41590733e+00,   7.35600000e+00,   1.00000000e+01],
                         [  2.12366988e+00,   8.58212260e+00,   1.00000000e+01],
                         [  1.06274849e-15,   7.35600000e+00,   1.00000000e+01],
                         [  7.78627992e+00,   8.58187740e+00,   1.00000000e+01],
                         [  5.66286486e+00,   7.35600000e+00,   1.00000000e+01],
                         [  6.37062741e+00,   8.58212260e+00,   1.00000000e+01],
                         [  4.24695753e+00,   7.35600000e+00,   1.00000000e+01],
                         [  1.20332374e+01,   8.58187740e+00,   1.00000000e+01],
                         [  9.90994980e+00,   7.35600000e+00,   1.00000000e+01],                     
                         [  1.06177123e+01,   6.13012260e+00,   1.00000000e+01],
                         [  8.49404247e+00,   4.90400000e+00,   1.00000000e+01],
                         [  3.53919498e+00,   8.58187740e+00,   1.00000000e+01],
                         [  1.41590733e+00,   7.35600000e+00,   1.00000000e+01],
                         [  2.12366988e+00,   8.58212260e+00,   1.00000000e+01],
                         [  1.06274849e-15,   7.35600000e+00,   1.00000000e+01],
                         [  7.78627992e+00,   8.58187740e+00,   1.00000000e+01],
                         [  5.66286486e+00,   7.35600000e+00,   1.00000000e+01],
                         [  6.37062741e+00,   8.58212260e+00,   1.00000000e+01],
                         [  4.24695753e+00,   7.35600000e+00,   1.00000000e+01],
                         [  1.20332374e+01,   8.58187740e+00,   1.00000000e+01],
                         [  9.90994980e+00,   7.35600000e+00,   1.00000000e+01],
                         [  1.06177123e+01,   8.58212260e+00,   1.00000000e+01],
                         [  8.49404247e+00,   7.35600000e+00,   1.00000000e+01],
                         [  3.53919498e+00,   1.10338774e+01,   1.00000000e+01],
                         [  1.41590733e+00,   9.80800000e+00,   1.00000000e+01],
                         [  2.12366988e+00,   1.10341226e+01,   1.00000000e+01],
                         [  1.21289019e-15,   9.80800000e+00,   1.00000000e+01],
                         [  7.78627992e+00,   1.10338774e+01,   1.00000000e+01],
                         [  5.66286486e+00,   9.80800000e+00,   1.00000000e+01],
                         [  6.37062741e+00,   1.10341226e+01,   1.00000000e+01],
                         [  4.24695753e+00,   9.80800000e+00,   1.00000000e+01],
                         [  1.20332374e+01,   1.10338774e+01,   1.00000000e+01],
                         [  9.90994980e+00,   9.80800000e+00,   1.00000000e+01],
                         [  1.06177123e+01,   1.10341226e+01,   1.00000000e+01],
                         [  8.49404247e+00,   9.80800000e+00,   1.00000000e+01]]*Angstrom

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    cartesian_coordinates=cartesian_coordinates
    )



initial_velocity = MaxwellBoltzmannDistribution(
        temperature=300.0*Kelvin
    )
method = VelocityVerlet(
        time_step=1.0*femtoSecond,
        initial_velocity=initial_velocity
    )
molecular_dynamics = MolecularDynamics(
        bulk_configuration,
        constraints=[],                                                                                         
        log_filename='trajectory.nc',
        steps=100,
        log_interval=10,
        method=method
    )
nlsave('analysis.nc', molecular_dynamics)
nlprint(molecular_dynamics)

# -------------------------------------------------------------
# Stress
# -------------------------------------------------------------
stress = Stress(bulk_configuration)
nlsave('analysis.nc', stress)
nlprint(stress)

# -------------------------------------------------------------
# Total energy
# -------------------------------------------------------------
total_energy = TotalEnergy(bulk_configuration)
nlsave('/home/yijhon/ATK/FLG_MD/1L/1L_FLG_MD.nc', total_energy)
nlprint(total_energy)




The block named Bulk existed originally in script section when I moved to building step to script generator step.
What's wrong and what should I do for it?


Best regards,

  Young


                                             




















The block named Bulk was present originally in script section when I move to script generator step from buiding step.
What's wrong and what should I do for it?










The block named Bulk was present originally in script section when I move to script generator step from buiding step.
What's wrong and what should I do for it?


14
General Questions and Answers / questions on the setting in VNL
« on: August 17, 2012, 15:38 »
First many thanks for the answer to my previous post, Dr. Anders Blom.
I have several questions on the use of VNL as follows.

1. We can add the blocks we want to script section.
However, it seems that we cannot remove the added blocks from the script section. Is it right?

When I add the same blocks to the script windows, I'd like to remove one of them.
Will the double writing due to the double blocks not influence the runing generally, though we can remove the doubled contents in the script file manually?

2. ATK calculation can be peformed either of at command line or using VNL.
In the first case, I can assign the core number and node list as I want.
However, it seems that there are not the options for them in job manager of VNL.
How can we assign the core number and the queue system (e.g., among queue_system1 of nodelist 1 and queue2_system2 of node list2 etc.) for the running in VNL?

3. I'd like to know atomic stress tensor in addition to total stress tensor of the system.
If it is possible, will it be provided basically in the output file by adding the stress analaysis block?

Otherwise, should we add additionional command manually in the script file?
If so, would you let me know what I should do for it?

4. It is written that DFT-D2 is available in the recent version of ATK.
For this, what I should do?

5. It seems that it ATK does not supprot temerature control yet. Is it right?
If it is availablee, where should I assign the value for the damping parameter?


Thanks a lot for your help in advance.

Best regards,

  Young


15
General Questions and Answers / the questions on NVT MD
« on: August 17, 2012, 06:05 »
I'd like to perform molecular dynamics simulation of graphene at 298 K and I have some questions it as follows.

1. Is it available to perform NVT simulation in ATK in addition to NVE?
   If so, can we perform in it in VNL as one of the basic tasks?

   It is written that assignment of temperature is not described in the manual in the previous post of the forum.
   What does it mean in detail? Should we assign the temperature using the script file only or does it mean NVT is not provided yet?

2. Is it possible to perform MD using DFTB in DFT-ATK (not semiempirical-ATK)?


Thanks for your answer in advance.

Young

Pages: [1]