[ase-users] Installation error using macOS Sierra 10.12.1

Thu Dec 1 19:49:10 CET 2016

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 fiWe should probably add a note to this effect in the documentation?All the best,Adam

Dr Adam J. Jackson
Post-doctoral research associate
Dept of Chemistry
University College London

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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 &lt;G.Donval at bath.ac.uk&gt; 
To: "ase-users at listserv.fysik.dtu.dk" 
    &lt;ase-users at listserv.fysik.dtu.dk&gt; 
Subject: Re: [ase-users] Installation error using macOS Sierra 10.12.1 
Message-ID: &lt;1480605727.1377.1.camel at bath.ac.uk&gt; 
Content-Type: text/plain; charset="utf-8" 

Hi, 

&gt; Based on the tutorial, I have create both a ~/.bashrc and ~/.cshrc 
&gt; files 
&gt; 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. 

&gt; The only error is "db.py" and it seems that it does not recognize the 
&gt; ase-gui and ase-build, thinking that its location is in bin/sh 
&gt; (underline). 

Anyway, that is not very important: as long as you can access these 
files from your terminal, it is fine. 

&gt; Copying these two files to the bin/sh would solve it but I do not 
&gt; think 
&gt; that this is the right way to go, e.g. I already modified the PATH 
&gt; variable. 

You are right. 

&gt; 
&gt; 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 &lt;esb at phys.au.dk&gt; 
To: "Iyemperumal, Satish Kumar" &lt;siyemperumal at wpi.edu&gt;, "Kondov, Ivan 
    (SCC)"    &lt;ivan.kondov at kit.edu&gt;, "ase-users at listserv.fysik.dtu.dk" 
    &lt;ase-users at listserv.fysik.dtu.dk&gt; 
Subject: Re: [ase-users] Clarifications on genetic algorithm 
Message-ID: &lt;CE85F5E6-8F46-41DB-AAE3-963FCEBFDEB0 at phys.au.dk&gt; 
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" &lt;siyemperumal at wpi.edu&gt; 
Dato: onsdag den 30. november 2016 kl. 16.50 
Til: Esben Leonhard Kolsbjerg &lt;esb at phys.au.dk&gt;, "Kondov, Ivan (SCC)" &lt;ivan.kondov at kit.edu&gt;, "ase-users at listserv.fysik.dtu.dk" &lt;ase-users at listserv.fysik.dtu.dk&gt; 
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 &lt;esb at phys.au.dk&gt; 
Sent: Wednesday, November 30, 2016 5:09:04 AM 
To: Iyemperumal, Satish Kumar; Kondov, Ivan (SCC); 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" &lt;siyemperumal at wpi.edu&gt; 
Dato: mandag den 28. november 2016 kl. 02.15 
Til: "Kondov, Ivan (SCC)" &lt;ivan.kondov at kit.edu&gt;, Esben Leonhard Kolsbjerg &lt;esb at phys.au.dk&gt;, "ase-users at listserv.fysik.dtu.dk" &lt;ase-users at listserv.fysik.dtu.dk&gt; 
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) &lt;ivan.kondov at kit.edu&gt; 
Sent: Tuesday, November 22, 2016 3:19:09 AM 
To: Iyemperumal, Satish Kumar; Esben Leonhard Kolsbjerg; ase-users at listserv.fysik.dtu.dk 
Subject: RE: Clarifications on genetic algorithm 

Dear all, 

&gt; 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 
&gt; 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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