speudos and phonon plotter #30

setten · 2015-08-21T12:23:12Z

No description provided.

onit message for your changes. Lines starting

gmatteo · 2015-08-21T18:13:54Z

pseudo_dojo/dojo/works.py

@@ -55,7 +55,7 @@ def write_dojo_report(self, report, overwrite_data=False):
        old_report[dojo_trial][dojo_ecut] = report
        try:
            self.pseudo.write_dojo_report(old_report)
-        except (OSError, IOError, TypeError):
+        except None: #(OSError, IOError, TypeError):


Please use

try:

except:

if you want to trap all the possible exceptions.
In python3, one cannot use arbitrary objects wit except, only subclasses of BaseException are allowed

you can revert it.

I only put the

except none

in when I'm debugging. I forgot to remove this one. It's the fastest way to
circumvent the except doning anything. Except None: literally does what it
says: it does not except anything and any raised exception causes the code
to stop.

Université catholique de Louvain
SST/IMCN - Institute of Condensed Matter and Nanosciences (IMCN)

Dr. Michiel J. van Setten

NAPS - Chemin des Étoiles 8 bte L7.03.01
1348 Louvain-la-Neuve (Belgium)
Email: michiel.vansetten@uclouvain.be mjvansetten@gmail.com

Telefon: +32 10 478681

2015-08-21 20:13 GMT+02:00 gmatteo notifications@github.com:

In pseudo_dojo/dojo/works.py
#30 (comment):

@@ -55,7 +55,7 @@ def write_dojo_report(self, report, overwrite_data=False):
old_report[dojo_trial][dojo_ecut] = report
try:
self.pseudo.write_dojo_report(old_report)

except (OSError, IOError, TypeError):

except None: #(OSError, IOError, TypeError):

Please use

try:

except:

if you want to trap all the possible exceptions.
In python3, one cannot use arbitrary objects wit except, only subclasses
of BaseException are allowed

—
Reply to this email directly or view it on GitHub
https://github.com/gmatteo/pseudo_dojo/pull/30/files#r37661866.

I still have a pull request open, there are some more commits added

Université catholique de Louvain
SST/IMCN - Institute of Condensed Matter and Nanosciences (IMCN)

Dr. Michiel J. van Setten

NAPS - Chemin des Étoiles 8 bte L7.03.01
1348 Louvain-la-Neuve (Belgium)
Email: michiel.vansetten@uclouvain.be mjvansetten@gmail.com

Telefon: +32 10 478681

2015-08-21 20:13 GMT+02:00 gmatteo notifications@github.com:

In pseudo_dojo/dojo/works.py
#30 (comment):

@@ -55,7 +55,7 @@ def write_dojo_report(self, report, overwrite_data=False):
old_report[dojo_trial][dojo_ecut] = report
try:
self.pseudo.write_dojo_report(old_report)

except (OSError, IOError, TypeError):

except None: #(OSError, IOError, TypeError):

Please use

try:

except:

if you want to trap all the possible exceptions.
In python3, one cannot use arbitrary objects wit except, only subclasses
of BaseException are allowed

—
Reply to this email directly or view it on GitHub
https://github.com/gmatteo/pseudo_dojo/pull/30/files#r37661866.

dojodata.py make_hints adds hints to the psp8 based on the df prime, refactoring, debugging cleaning of the old validate new validate under consruction... pt plot of the ecut hints ecut_hints added to the data frame. still some work to do there, now both ecuts and ecuthints exist

speudos and phonon plotter

setten · 2015-08-26T16:09:47Z

did you try the dojodata.py figures . ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 18:05, gmatteo wrote:

Merged #30.

—
Reply to this email directly or view it on GitHub.

gmatteo · 2015-08-26T19:00:53Z

→ ../scripts/dojodata.py figures ONCVPSP-PBE-MC2/
Traceback (most recent call last):
File "../scripts/dojodata.py", line 709, in
sys.exit(main())
File "../scripts/dojodata.py", line 692, in main
globals()"dojo_" + options.command
File "../scripts/dojodata.py", line 47, in dojo_figures
'low_ecut_hint', 'normal_ecut_hint', 'high_ecut_hint')}
File "../scripts/dojodata.py", line 44, in
l = {k: getattr(best, k) for k in ('name', 'Z', 'high_b0_GPa',
'high_b1', 'high_v0', 'high_dfact_meV',
File
"/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/pandas/core/generic.py",
line 2150, in getattr
(type(self).name, name))
AttributeError: 'Series' object has no attribute 'low_phonon'

On Wed, Aug 26, 2015 at 6:09 PM, Michiel van Setten <
notifications@github.com> wrote:

did you try the dojodata.py figures . ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 18:05, gmatteo wrote:

Merged #30.

—
Reply to this email directly or view it on GitHub.

—
Reply to this email directly or view it on GitHub
#30 (comment).

Nel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è riuscito
a sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,
serve 1GB di RAM... qualcosa deve essere andato storto

setten · 2015-08-26T21:07:46Z

did you also merge my pymatgen pull request ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 21:00, gmatteo wrote:

→ ../scripts/dojodata.py figures ONCVPSP-PBE-MC2/
Traceback (most recent call last):
File "../scripts/dojodata.py", line 709, in
sys.exit(main())
File "../scripts/dojodata.py", line 692, in main
globals()"dojo_" + options.command
File "../scripts/dojodata.py", line 47, in dojo_figures
'low_ecut_hint', 'normal_ecut_hint', 'high_ecut_hint')}
File "../scripts/dojodata.py", line 44, in
l = {k: getattr(best, k) for k in ('name', 'Z', 'high_b0_GPa',
'high_b1', 'high_v0', 'high_dfact_meV',
File
"/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/pandas/core/generic.py",
line 2150, in getattr
(type(self).name, name))
AttributeError: 'Series' object has no attribute 'low_phonon'

On Wed, Aug 26, 2015 at 6:09 PM, Michiel van Setten <
notifications@github.com> wrote:

did you try the dojodata.py figures . ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 18:05, gmatteo wrote:

Merged #30.

—
Reply to this email directly or view it on GitHub.

—
Reply to this email directly or view it on GitHub
#30 (comment).

Nel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è riuscito
a sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,
serve 1GB di RAM... qualcosa deve essere andato storto
—
Reply to this email directly or view it on GitHub.

gmatteo · 2015-08-26T22:08:43Z

It works if I do

cd pseudo_dojo/pseudos/ONCVPSP-PBE && dojodata.py figures .

whereas

cd seudo_dojo/pseudos/ && dojodata.py figures ONCVPSP-PBE

fails because of

outfile = name+'/'+out

that is relative and not absolute (btw: os.path.join instead of "/")

btw: the plots are nice and very useful

On Wed, Aug 26, 2015 at 11:07 PM, Michiel van Setten <
notifications@github.com> wrote:

did you also merge my pymatgen pull request ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 21:00, gmatteo wrote:

→ ../scripts/dojodata.py figures ONCVPSP-PBE-MC2/
Traceback (most recent call last):
File "../scripts/dojodata.py", line 709, in
sys.exit(main())
File "../scripts/dojodata.py", line 692, in main
globals()"dojo_" + options.command
File "../scripts/dojodata.py", line 47, in dojo_figures
'low_ecut_hint', 'normal_ecut_hint', 'high_ecut_hint')}
File "../scripts/dojodata.py", line 44, in
l = {k: getattr(best, k) for k in ('name', 'Z', 'high_b0_GPa',
'high_b1', 'high_v0', 'high_dfact_meV',
File

"/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/pandas/core/generic.py",
line 2150, in getattr
(type(self).name, name))
AttributeError: 'Series' object has no attribute 'low_phonon'

On Wed, Aug 26, 2015 at 6:09 PM, Michiel van Setten <
notifications@github.com> wrote:

did you try the dojodata.py figures . ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 18:05, gmatteo wrote:

Merged #30.

—
Reply to this email directly or view it on GitHub.

—
Reply to this email directly or view it on GitHub
<#30 (comment)
.

Nel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è
riuscito
a sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,
serve 1GB di RAM... qualcosa deve essere andato storto
—
Reply to this email directly or view it on GitHub.

—
Reply to this email directly or view it on GitHub
#30 (comment).

Nel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è riuscito
a sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,
serve 1GB di RAM... qualcosa deve essere andato storto

setten · 2015-08-27T07:11:26Z

I'll fix that

I'm now working on different sortings. now we take the pseudo per element that has the lowest df, I'm adding options for the selecting based on the amount of valence electrons.

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 27 Aug 2015, at 00:08, gmatteo wrote:

It works if I do

cd pseudo_dojo/pseudos/ONCVPSP-PBE && dojodata.py figures .

whereas

cd seudo_dojo/pseudos/ && dojodata.py figures ONCVPSP-PBE

fails because of

outfile = name+'/'+out

that is relative and not absolute (btw: os.path.join instead of "/")

btw: the plots are nice and very useful

On Wed, Aug 26, 2015 at 11:07 PM, Michiel van Setten <
notifications@github.com> wrote:

did you also merge my pymatgen pull request ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 21:00, gmatteo wrote:

→ ../scripts/dojodata.py figures ONCVPSP-PBE-MC2/
Traceback (most recent call last):
File "../scripts/dojodata.py", line 709, in
sys.exit(main())
File "../scripts/dojodata.py", line 692, in main
globals()"dojo_" + options.command
File "../scripts/dojodata.py", line 47, in dojo_figures
'low_ecut_hint', 'normal_ecut_hint', 'high_ecut_hint')}
File "../scripts/dojodata.py", line 44, in
l = {k: getattr(best, k) for k in ('name', 'Z', 'high_b0_GPa',
'high_b1', 'high_v0', 'high_dfact_meV',
File

"/Users/gmatteo/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/pandas/core/generic.py",
line 2150, in getattr
(type(self).name, name))
AttributeError: 'Series' object has no attribute 'low_phonon'

On Wed, Aug 26, 2015 at 6:09 PM, Michiel van Setten <
notifications@github.com> wrote:

did you try the dojodata.py figures . ?

Michiel van Setten
UCL, NAPS
mjvansetten@gmail.com
michiel.vansetten@uclouvain.be
010 478824

'"Although the way may not be obvious at first unless you're Dutch"
from The Zen of Python

On 26 Aug 2015, at 18:05, gmatteo wrote:

Merged #30.

—
Reply to this email directly or view it on GitHub.

—
Reply to this email directly or view it on GitHub
<#30 (comment)
.

Nel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è
riuscito
a sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,
serve 1GB di RAM... qualcosa deve essere andato storto
—
Reply to this email directly or view it on GitHub.

—
Reply to this email directly or view it on GitHub
#30 (comment).

Nel 1969, con la potenza di calcolo di due Commodore 64, l'uomo è riuscito
a sbarcare sulla luna. Oggi, per far girare decentemente Windows Vista,
serve 1GB di RAM... qualcosa deve essere andato storto
—
Reply to this email directly or view it on GitHub.

setten added 3 commits August 21, 2015 14:10

pseudos and dojodata stuff

36a73f3

Merge remote branch 'matteos-dojo/master'

24d7a89

correction

407c46f

onit message for your changes. Lines starting

gmatteo reviewed Aug 21, 2015
View reviewed changes

setten added 2 commits August 25, 2015 16:10

noble gas hints and minor corrections in plotting

6f9a5ef

gmatteo added a commit that referenced this pull request Aug 26, 2015

Merge pull request #30 from setten/master

1f23271

speudos and phonon plotter

gmatteo merged commit 1f23271 into abinit:master Aug 26, 2015

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

speudos and phonon plotter #30

speudos and phonon plotter #30

setten commented Aug 21, 2015

gmatteo Aug 21, 2015

setten Aug 21, 2015

setten Aug 26, 2015

setten commented Aug 26, 2015

gmatteo commented Aug 26, 2015

setten commented Aug 26, 2015

gmatteo commented Aug 26, 2015

setten commented Aug 27, 2015

speudos and phonon plotter #30

speudos and phonon plotter #30

Conversation

setten commented Aug 21, 2015

gmatteo Aug 21, 2015

Choose a reason for hiding this comment

setten Aug 21, 2015

Choose a reason for hiding this comment

Telefon: +32 10 478681

setten Aug 26, 2015

Choose a reason for hiding this comment

Telefon: +32 10 478681

setten commented Aug 26, 2015

gmatteo commented Aug 26, 2015

setten commented Aug 26, 2015

gmatteo commented Aug 26, 2015

setten commented Aug 27, 2015