[ase-users] Installation error using macOS Sierra 10.12.1
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Fri Dec 2 10:22:20 CET 2016
On 12/01/2016 07:49 PM, Adam Jackson via ase-users wrote:
> Terminal sessions on Mac OSX don't load .bashrc automatically, they
> use .bash_profile.
> This commonly causes issues when following directions written for
> other Unix-like operating systems!
> I suggest adding a block to your .bash_profile which sources .bashrc,
> i.e.
>
> if [ -f ~/.bashrc ]; then source ~/.bashrc fi
> We should probably add a note to this effect in the documentation?
That's a good idea. Please do:
https://wiki.fysik.dtu.dk/ase/development/writing_documentation_ase.html
Jens Jørgen
> All the best,
> Adam
> Dr Adam J. Jackson
> Post-doctoral research associate
> Dept of Chemistry
> University College London
>
> ---- On Thu, 01 Dec 2016 16:29:03 +0000
> *<ase-users-request at listserv.fysik.dtu.dk>* wrote ----
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> Today's Topics:
>
> 1. Re: Installation error using macOS Sierra 10.12.1 (Ga?l Donval)
> 2. Re: Clarifications on genetic algorithm (Esben Leonhard Kolsbjerg)
>
>
> ----------------------------------------------------------------------
>
>
> Message: 1
> Date: Thu, 1 Dec 2016 15:22:07 +0000
> From: Ga?l Donval <G.Donval at bath.ac.uk <mailto:G.Donval at bath.ac.uk>>
> To: "ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>"
> <ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>>
> Subject: Re: [ase-users] Installation error using macOS Sierra
> 10.12.1
> Message-ID: <1480605727.1377.1.camel at bath.ac.uk
> <mailto:1480605727.1377.1.camel at bath.ac.uk>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> > Based on the tutorial, I have create both a ~/.bashrc and ~/.cshrc
> > files
> > that follows the command to include a new path.
>
> You only need one. Since you can `source` your file, I suppose
> that it
> is ~/.bashrc.
>
> As the doc said, just add:
>
> export
> PYTHONPATH=/Users/cennaradipa/Library/Python/2.7/python2.7/site-packages:$PYTHONPATH
>
> export PATH=/Users/cennaradipa/Library/Python/2.7/bin:$PATH
>
> to ~/.bashrc, then start a new terminal and check that everything is
> fine.
>
> > The only error is "db.py" and it seems that it does not
> recognize the
> > ase-gui and ase-build, thinking that its location is in bin/sh
> > (underline).
>
> Anyway, that is not very important: as long as you can access these
> files from your terminal, it is fine.
>
> > Copying these two files to the bin/sh would solve it but I do not
> > think
> > that this is the right way to go, e.g. I already modified the PATH
> > variable.
>
> You are right.
>
> >
> > Is there something missing here?
>
> Did you think of restarting the terminal once the changes are
> done? If
> not, this is certainly it: /bin/bash reads its configuration when it
> starts.
>
> There might be some problems with the way /bin/sh handle things or
> the
> way it is called within python on MacOS. But I don't have a Mac so I
> can't try that myself.
>
> Cheers,
> Ga?l
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 1 Dec 2016 16:28:52 +0000
> From: Esben Leonhard Kolsbjerg <esb at phys.au.dk
> <mailto:esb at phys.au.dk>>
> To: "Iyemperumal, Satish Kumar" <siyemperumal at wpi.edu
> <mailto:siyemperumal at wpi.edu>>, "Kondov, Ivan
> (SCC)" <ivan.kondov at kit.edu <mailto:ivan.kondov at kit.edu>>,
> "ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>"
> <ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>>
> Subject: Re: [ase-users] Clarifications on genetic algorithm
> Message-ID: <CE85F5E6-8F46-41DB-AAE3-963FCEBFDEB0 at phys.au.dk
> <mailto:E6-8F46-41DB-AAE3-963FCEBFDEB0 at phys.au.dk>>
> Content-Type: text/plain; charset="utf-8"
>
> You are, as you say, always optimizing the raw score and you have
> to manually set the raw_score. I have personally never optimized
> anything but the calculated energy but this should really not be
> an issue.
>
> When you call ?get_all_relaxed_candidates? it will return list of
> all the relaxed candidates sorted for the raw_score.
>
> What I don?t understand is why the raw score and the energy isn?t
> the same as you (I guess) just sat the energy manually in the
> calculator to the exact same value as the raw_score.
>
> To answer your question! No, I don?t think it is an issure!
>
> (Now I?m speculating!)
> If the wrong files are saved in the database I think the error
> must come from the fact that the atoms object normally called
> ?a?/?a3? are not updated in the script you are running. If the
> relaxation happens outside of the ga-script this could explain
> both why the wrong energy and structures are not displayed in the
> database. Could you maybe as an ugly hack (but maybe prettier than
> what you are doing now) try to load in the relaxed trajectory file
> after it is relaxed as ?a?/?a3? and the set the raw_score and then
> add it to the db?
> I don?t totally get your relaxation procedure but I don?t think it
> is a standard way and this might be why.
>
> Esben
>
>
>
> Fra: "Iyemperumal, Satish Kumar" <siyemperumal at wpi.edu
> <mailto:siyemperumal at wpi.edu>>
> Dato: onsdag den 30. november 2016 kl. 16.50
> Til: Esben Leonhard Kolsbjerg <esb at phys.au.dk
> <mailto:esb at phys.au.dk>>, "Kondov, Ivan (SCC)"
> <ivan.kondov at kit.edu <mailto:ivan.kondov at kit.edu>>,
> "ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>"
> <ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>>
> Emne: Re: Clarifications on genetic algorithm
>
>
> Thanks again for your input, Esben.
>
>
>
> The code does work. However, it leads to another question as you
> indicated. Does changing the (1) energy as
> a.calc.results['energy']=actual_energy*Hartree and (2) manually
> defining what raw_score is by setting
> a.info['key_value_pairs']['raw_score'] = -actual_energy * Hartree
> affect GA procedure.
>
>
>
> I do not think (1) will be affected since, as you also mentioned
> earlier that in GA, it is the raw score that is being maximized.
>
>
>
> In the case of (2), I am manually defining the correct raw scores
> within the GA script. This however, leads to all_candidates.traj
> file being generated that is not sorted from low to high energy
> structures (see attached for example traj file). Moreover, the
> geometries that are in all_candidates.traj file are not the final
> ground state geometries (not sure if they are the first ionic step
> geometries for each relaxed candidate). This makes me think that
> setting raw_scores perhaps affects the output files like
> all_candidates.traj generated by ASE. Anyways, due to this
> trouble, I manually save all the relaxed candidate structures from
> my NWChem run in separate directories. Finally, for getting the
> correct structure and energy, I just loop over these NWChem
> directories to read the correct results instead of postprocessing
> from ASE generated output files like all_candidates.traj and gadb.db.
>
>
>
> Do you think this approach is reliable? or do you think changing
> raw scores inherently messes something up within the GA procedure
> itself?
>
>
>
> Thank you for your time again!
>
> Best,
> Satish
> ________________________________
> From: Esben Leonhard Kolsbjerg <esb at phys.au.dk
> <mailto:esb at phys.au.dk>>
> Sent: Wednesday, November 30, 2016 5:09:04 AM
> To: Iyemperumal, Satish Kumar; Kondov, Ivan (SCC);
> ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>
> Subject: Re: Clarifications on genetic algorithm
>
> I?m not an expert in this database thing. But I took a look in the
> ase.db.core and as I see it you are not allowed through ase to
> update values like the energy in a database-file in a row already
> there.
>
> So
> con = connect('gadb.db')
> con.update(ids=53, **{'energy':100})
>
> will give you:
>
> ValueError: Bad key: energy
>
> What you might be able to do is directly set ?new? results in the
> calculator attached to the atoms object.
>
> It will then look something like this:
> ...
> with open('in.out') as f:
> for line in f:
> line = line.rstrip()
> if re.search('Total.DFT', line):
> actual_energy = float(line.strip().split()[-1])
> a.info['key_value_pairs']['raw_score'] = -actual_energy * Hartree
> a.calc.results['energy'] = -actual_energy * Hartree # setting the
> actual calculated property in the results dict of the calculator
> da.add_relaxed_step(a)
> ...
>
> Be aware that this hack might course you trouble elsewhere.
>
> I just ran a GA with the EMT potential where I think what you are
> looking for are working.
>
> Hope it helps?
>
> Esben
>
> Fra: "Iyemperumal, Satish Kumar" <siyemperumal at wpi.edu
> <mailto:siyemperumal at wpi.edu>>
> Dato: mandag den 28. november 2016 kl. 02.15
> Til: "Kondov, Ivan (SCC)" <ivan.kondov at kit.edu
> <mailto:ivan.kondov at kit.edu>>, Esben Leonhard Kolsbjerg
> <esb at phys.au.dk <mailto:esb at phys.au.dk>>,
> "ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>"
> <ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>>
> Emne: Re: Clarifications on genetic algorithm
>
>
> I was able to read in the right energies from the output file of
> nwchem calculations as the raw_scores in the genetic algorithm.
> But I also wanted to display the correct energy when I enter
> "ase-db gadb.db", which prints out id, age, user...magmom. To
> change raw_scores to read correct values, I did
>
>
>
> ...
>
> with open('in.out') as f:
>
> for line in f:
>
> line = line.rstrip()
>
> if re.search('Total.DFT', line):
>
> actual_energy = float(line.strip().split()[-1])
>
> a.info['key_value_pairs']['raw_score'] = -actual_energy * Hartree
>
> #a.info['energy'] = -actual_energy * Hartree
>
> da.add_relaxed_step(a)
>
> ...
>
>
> But, when I say a.info['energy'] = -actual_energy * Hartree, the
> energy is not updated by the actual_energy. I tried ase.db.connect
> but I could not find a way to modify the energy entry in gadb.db
> by the actual_energy values. How can I fix this?
>
>
>
> Thank you for your time on this. Complete updated script is attached.
>
>
>
> Best,
> Satish
> ________________________________
> From: Kondov, Ivan (SCC) <ivan.kondov at kit.edu
> <mailto:ivan.kondov at kit.edu>>
> Sent: Tuesday, November 22, 2016 3:19:09 AM
> To: Iyemperumal, Satish Kumar; Esben Leonhard Kolsbjerg;
> ase-users at listserv.fysik.dtu.dk
> <mailto:ase-users at listserv.fysik.dtu.dk>
> Subject: RE: Clarifications on genetic algorithm
>
> Dear all,
>
> > 2) I think I found the reason. get_potential_energy() gives the
> energy
> corresponding to task=energy. So even if I set task=optimize, the
> energy
> corresponds to the energy after first ionic step. I can read the
> correct
> energy corresponding to task=optimize
> > using some readlines() method, but I wanted to know if just
> updating
> raw_score of a row in the database file would be sufficient to
> make a GA run
> as follows.
>
> Apropos: task='optimize' with NWChem does not work properly. See
> my post
> from 17 October 2016 on this list:
>
> https://listserv.fysik.dtu.dk/pipermail/ase-users/2016-October/003187.html
>
>
> Meanwhile I have a local fix which I am testing in operation and
> will soon
> make a merge request to include it.
>
> Best regards,
> Ivan
>
>
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