[ase-users] ase-users Digest, Vol 125, Issue 26
Alexander Sougaard Tygesen
alexty at dtu.dk
Fri Nov 23 10:43:25 CET 2018
Hi,
The VTST tools just use a set folder structure, and some POSCAR's in that folder structure, so you could use ASE to generate the pathway like we normally would, and then save each image in the corresponding folder, i.e. if you have 5 images in total, you would have a folder structure of
01/ 02/ 03/ 04/ 05/
you then set up your structures with ASE, and save each image into each folder, like 01/POSCAR, 02/POSCAR, etc.
Once you have done that setup, you just start the VTST VASP like normal, with images=5 from the outer-folder. All that the "nebmake.pl" script does, it exactly that: Set up the POSCAR's in the corresponding folder _before_ we start doing any VASP execution.
Best,
Alexander
________________________________
From: ase-users-bounces at listserv.fysik.dtu.dk <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Abid Channa via ase-users <ase-users at listserv.fysik.dtu.dk>
Sent: Tuesday, November 20, 2018 11:03 AM
To: ase-users at listserv.fysik.dtu.dk
Subject: Re: [ase-users] ase-users Digest, Vol 125, Issue 26
Hi Dear All,
Thanks for your suggestions on Willem's query about ABINIT calculator and parallel run. My query was on IDPP interpolation which is only incorporated in ASE not VTSTTools. I'm dealing with crystals and surfaces using VASP so I have two options
1- By using VASP with interfaces ASE because IDPP in only part of ASE (For this, I'm looking for template script)
2- By using VASP in VTSTTools where I will get only linear interpolation by using command "nebmake.pl" not IDPP , Is there any way we convert linear interpolation (getting from VTSTTools) to IDPP using ASE.
Thanks again for your suggestions and response.
Best,
_________________________________
ABID ALI
PhD (Marie Curie-ITN) Fellow
Theoretical Chemistry
Dunhagi 3, VR-II1,
Science Institute, 107 Reykjavik
University of Iceland.
Mobile : +3547835935
On Monday, November 19, 2018, 7:10:49 PM GMT, ase-users-request at listserv.fysik.dtu.dk <ase-users-request at listserv.fysik.dtu.dk> wrote:
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Today's Topics:
1. Re: NEB parallel with Abinit parallel (Ask Hjorth Larsen)
2. Re: NEB parallel with Abinit parallel (Ask Hjorth Larsen)
3. Re: ASE error in VASP calculations (Offermans Willem)
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Nov 2018 16:39:13 +0100
From: Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>>
To: "Kondov, Ivan (SCC)" <ivan.kondov at kit.edu<mailto:ivan.kondov at kit.edu>>
Cc: ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Subject: Re: [ase-users] NEB parallel with Abinit parallel
Message-ID:
<CACu53wkvPaFxpg7+rc74VmmeML+cxJma-=YqAvBca29d6Aq1HQ at mail.gmail.com<mailto:YqAvBca29d6Aq1HQ at mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"
Hi,
Am Mo., 19. Nov. 2018 um 14:51 Uhr schrieb Kondov, Ivan (SCC) via
ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>:
>
> Dear all,
>
>
>
> I think that the ASE/NEB and the Calculator can run both in parallel only if the Calculator is GPAW. This is because the NEB and the process spawned by the Calculator have to share an MPI communicator (I am not sure about any existing tricks with application/machinefiles and mpirun options). Thus parallel NEB will work with VASP or Abinit in serial mode only. Also serial NEB will work with the parallel versions of VASP, Abinit etc.
>
>
>
> In order to run a parallel NEB with parallel VASP, the NEB implementation in the VTST package can be used (http://theory.cm.utexas.edu/vasp/) and VASP has to be patched. For Abinit I do not know such a solution.
>
>
>
> A generic solution with ASE could be to split the calculations of the images in each BFGS iteration into several jobs and distribute them on the cluster. After all jobs are ready then their outputs are collected and passed to BFGS and the next image geometries are computed, distributed and so on until BFGS converges. Unfortunately I do not have an implementation yet but I would prefer (and recommend) to use a workflow system such as FireWorks for this.
We can perhaps modify the new SocketIOCalculator to accept and control
multiple connections. That would make it possible to launch a server
(on any computer) and then a job with, say, 10 nodes, and each node
connects to the server in order to receive positions and then
calculate forces. I can help if any of you are willing to take the
initiative.
Best regards
Ask
>
>
>
> Best regards,
>
> Ivan
>
>
>
------------------------------
Message: 2
Date: Mon, 19 Nov 2018 18:19:59 +0100
From: Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>>
To: Offermans Willem <willem.offermans at vito.be<mailto:willem.offermans at vito.be>>
Cc: ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Subject: Re: [ase-users] NEB parallel with Abinit parallel
Message-ID:
<CACu53wkKqMkBoFVkdXpOc4kaYseYH849mBwBhRoDKGnFJqqsgw at mail.gmail.com<mailto:CACu53wkKqMkBoFVkdXpOc4kaYseYH849mBwBhRoDKGnFJqqsgw at mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"
Dear both,
Am Mo., 19. Nov. 2018 um 17:39 Uhr schrieb Offermans Willem
<willem.offermans at vito.be<mailto:willem.offermans at vito.be>>:
>
> Dear Ask, Ivan, and ASE-users,
>
> I?m not sure that I understand the response of Ask.
>
> I like to run both NEB and ABINIT in parallel. So, for example, I would reserve 85 nodes and run 5 images on 13 nodes (= number of k-points) separately. ASE coordinates the NEB and optimisation of the NEB, ABINIT is the calculator and runs for several images. Each ABINIT calculation runs in parallel and is distributed over nodes by individual k-point. That is the basic idea.
>
> If I understood correctly, this is not yet supported by ASE. However, Ask is willing to support us (me), if I take the initiative to develop this.
>
> What do I need to do? And how can Ask support me?
The ase.calculators.socketio.SocketIOCalculator is a calculator which
wraps a server. This server currently supports a single connection.
The connection represents a remote calculator. If/when we need it, we
can expand it so it runs with multiple connections and hence can
control multiple remote calculators. That would be useful for a NEB
run.
Now if a client process runs an ase.calculators.socketio.SocketClient
on an Atoms object with Abinit(command='mpirun ....') attached as
calculator, then the client's subprocess will run its calculations in
parallel, and yet communicate with the server as a single entity.
If you try it out on something simple like a relaxation, it should be
more clear. It will work locally on a desktop computer.
https://wiki.fysik.dtu.dk/ase/ase/calculators/socketio/socketio.html
So the goal would be to set up a NEB run where each atoms object
contains a SocketIOCalculator (which preferably would run a single
server rather than a server for each image; this is where something
needs to be modified), and then different processes can connect to it
and run independently. Right now the processes may end up waiting for
each other inefficiently or something like that, but one would need to
see those problems first in order to fix them :)
Best regards
Ask
>
>
>
> Met vriendelijke groeten,
> Mit freundlichen Gr??en,
>
>
> Willem Offermans
> Researcher Electrocatalysis SCT
> VITO NV | Boeretang 200 | 2400 Mol
> Phone:+32(0)14335263 Mobile:+32(0)492182073
>
> Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>
>
>
> On 19 Nov 2018, at 16:39, Ask Hjorth Larsen via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:
>
> Hi,
>
> Am Mo., 19. Nov. 2018 um 14:51 Uhr schrieb Kondov, Ivan (SCC) via
> ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>:
>
>
> Dear all,
>
>
>
> I think that the ASE/NEB and the Calculator can run both in parallel only if the Calculator is GPAW. This is because the NEB and the process spawned by the Calculator have to share an MPI communicator (I am not sure about any existing tricks with application/machinefiles and mpirun options). Thus parallel NEB will work with VASP or Abinit in serial mode only. Also serial NEB will work with the parallel versions of VASP, Abinit etc.
>
>
>
> In order to run a parallel NEB with parallel VASP, the NEB implementation in the VTST package can be used (http://theory.cm.utexas.edu/vasp/) and VASP has to be patched. For Abinit I do not know such a solution.
>
>
>
> A generic solution with ASE could be to split the calculations of the images in each BFGS iteration into several jobs and distribute them on the cluster. After all jobs are ready then their outputs are collected and passed to BFGS and the next image geometries are computed, distributed and so on until BFGS converges. Unfortunately I do not have an implementation yet but I would prefer (and recommend) to use a workflow system such as FireWorks for this.
>
>
> We can perhaps modify the new SocketIOCalculator to accept and control
> multiple connections. That would make it possible to launch a server
> (on any computer) and then a job with, say, 10 nodes, and each node
> connects to the server in order to receive positions and then
> calculate forces. I can help if any of you are willing to take the
> initiative.
>
> Best regards
> Ask
>
>
>
>
> Best regards,
>
> Ivan
>
>
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
> Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, niet vanuit richting Mol, zie vito.be/route.
> If you plan to visit VITO at Mol, then please note that the main entrance can only be reached coming from Dessel-Retie and no longer coming from Mol, see vito.be/en/contact/locations.
> VITO Disclaimer: http://www.vito.be/e-maildisclaimer
------------------------------
Message: 3
Date: Mon, 19 Nov 2018 15:52:22 +0000
From: Offermans Willem <willem.offermans at vito.be<mailto:willem.offermans at vito.be>>
To: Veenu Mehta <veenumehta634 at gmail.com<mailto:veenumehta634 at gmail.com>>
Cc: Abid Channa via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>
Subject: Re: [ase-users] ASE error in VASP calculations
Message-ID: <87A8D2C2-186C-424D-A225-82E6F98C6B87 at Vito.be<mailto:87A8D2C2-186C-424D-A225-82E6F98C6B87 at Vito.be>>
Content-Type: text/plain; charset="utf-8"
Dear Veenu Mehta,
Try to keep the conversion through the mailing list.
Others will certainly benefit from your questions and possible solutions.
If you want to learn about python scripting (programming), www.python.org<http://www.python.org> might be a good starting point.
Follow the link to the documentation on the python site and you can start learning how to code.
Met vriendelijke groeten,
Mit freundlichen Gr??en,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be><mailto:Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>>
[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local<mailto:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local>]
On 19 Nov 2018, at 12:40, Veenu Mehta <veenumehta634 at gmail.com<mailto:veenumehta634 at gmail.com><mailto:veenumehta634 at gmail.com<mailto:veenumehta634 at gmail.com>>> wrote:
Sir:
I am getting error again. I am new to python and want to learn python-ase. from where can I learn about python and these python scripts so that I can run them easily without any error. whenever I run the calculations of siesta and vasp with the python scripts, always an error come. Kindly give me the python tutorials notes.
thank you
On Sat, Nov 17, 2018 at 4:44 PM Offermans Willem <willem.offermans at vito.be<mailto:willem.offermans at vito.be><mailto:willem.offermans at vito.be<mailto:willem.offermans at vito.be>>> wrote:
Dear Veenu Mehta,
Did you notice that the error messages, you provided, are different?
One is complaining about missing POTCAR file (RuntimeError: No pseudopotential for Al!), the other has some problems with finding VASP (sh: 1: vasp: not found).
Try to build up the complexity of your python script: Test the concept of the script with easy settings. This sounds easier than it is; take some seconds to consider this. Try to specify the whole path to the vasp executable and include this. So for example:
<snip>
?.
calc = VASP(command='/data/users/Public/USERNAME/VASP/bin/vasp > vasp.log?,
?
</snip>
Instead of:
<snip>
?.
calc = VASP(command='vasp > vasp.log?,
?
</snip>
Try to copy the POTCAR into the WORKING_DIRECTORY.
And keep an eye on the error messages and how they change with every change of the python script and/or presence of POTCAR file.
Try to change one thing after each other and look to the error or log messages.
Met vriendelijke groeten,
Mit freundlichen Gr??en,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be><mailto:Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>>
[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local<mailto:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local>]
On 17 Nov 2018, at 11:57, Veenu Mehta <veenumehta634 at gmail.com<mailto:veenumehta634 at gmail.com><mailto:veenumehta634 at gmail.com<mailto:veenumehta634 at gmail.com>>> wrote:
sir,
actually I have given the POTCAR file. I have put the folders potpwa_LDA and potpaw_PBE in /hoem/mehta/VASP firectory...but it always show this type of error. (whether I have to put the POTCAR file in the folder where I am running this example?) and also with another example file I obtain the error:
python vasp_co.py
sh: 1: vasp: not found
Traceback (most recent call last):
File "vasp_co.py", line 37, in <module>
en = co.get_potential_energy()
File "/home/mehta/.local/lib/python2.7/site-packages/ase/atoms.py", line 685, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/home/mehta/.local/lib/python2.7/site-packages/ase/calculators/vasp/vasp.py", line 231, in get_potential_energy
self.update(atoms)
File "/home/mehta/.local/lib/python2.7/site-packages/ase/calculators/vasp/vasp.py", line 83, in update
self.calculate(atoms)
File "/home/mehta/.local/lib/python2.7/site-packages/ase/calculators/vasp/vasp.py", line 106, in calculate
self.run()
File "/home/mehta/.local/lib/python2.7/site-packages/ase/calculators/vasp/vasp.py", line 177, in run
raise RuntimeError('Vasp exited with exit code: %d. ' % exitcode)
RuntimeError: Vasp exited with exit code: 32512.
On Sat, Nov 17, 2018 at 4:22 PM Offermans Willem <willem.offermans at vito.be<mailto:willem.offermans at vito.be><mailto:willem.offermans at vito.be<mailto:willem.offermans at vito.be>>> wrote:
Dear Veenu Mehta,
What is not clear about the error message?
You need to provide a pseudo potential file, i.e. POTCAR file.
Met vriendelijke groeten,
Mit freundlichen Gr??en,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be><mailto:Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>>
[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local<mailto:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local>]
On 17 Nov 2018, at 08:56, Veenu Mehta via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk><mailto:ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>> wrote:
Respected Sir/Mam:
I have successfully installed ASE-python-2.7 in my system. but whenever I run the vasp calculations for example files then I always obtain the error as:
ython vasp_Al_volrelax.py
Looking for potpaw/Al/POTCAR
The pseudopotentials are expected to be in:
LDA: /home/mehta/VASP/potpaw/
PBE: /home/mehta/VASP/potpaw_PBE/
PW91: /home/mehta/VASP/potpaw_GGA/
Traceback (most recent call last):
File "vasp_Al_volrelax.py", line 66, in <module>
Al_vasp = vasp_vol_relax()
File "vasp_Al_volrelax.py", line 25, in vasp_vol_relax
calc.calculate(Al)
File "/home/mehta/.local/lib/python2.7/site-packages/ase/calculators/vasp/vasp.py", line 100, in calculate
self.initialize(atoms)
File "/home/mehta/.local/lib/python2.7/site-packages/ase/calculators/vasp/create_input.py", line 1107, in initialize
raise RuntimeError('No pseudopotential for %s!' % symbol)
RuntimeError: No pseudopotential for Al!
Kinldy resolve the issue.
Thank you
--
With Regards,
Veenu Mehta
Assistant Professor
Dept. of Physics,
Govt. College, Hisar
Research Scholar
Department of Physics
GJUS&T, Hisar
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Indien u VITO Mol bezoekt, hou aub er dan rekening mee dat de hoofdingang voortaan enkel bereikbaar is vanuit de richting Dessel-Retie, niet vanuit richting Mol, zie vito.be/route.<http://www.vito.be/route>
If you plan to visit VITO at Mol, then please note that the main entrance can only be reached coming from Dessel-Retie and no longer coming from Mol, see vito.be/en/contact/locations.<http://www.vito.be/en/contact/locations>
VITO Disclaimer: http://www.vito.be/e-maildisclaimer
--
With Regards,
Veenu Mehta
Assistant Professor
Dept. of Physics,
Govt. College, Hisar
Research Scholar
Department of Physics
GJUS&T, Hisar
<vito.jpg><vito.jpg>
--
With Regards,
Veenu Mehta
Assistant Professor
Dept. of Physics,
Govt. College, Hisar
Research Scholar
Department of Physics
GJUS&T, Hisar
<vito.jpg>
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