[ase-users] ase-db output limit and sorting
Peter Bjerre Jensen
pbjen at dtu.dk
Fri Oct 24 13:22:35 CEST 2014
Thank you for fixing :-)
I will let you know if I encounter further problems.. (please see the
previous email regarding doubling the output when specifying the columns
to show..)
/Peter
Den 24-10-2014 kl. 13:20 skrev Tristan Maxson:
> I have just committed a fix for this. Revision 3882 properly sort
> even when encountering None.
>
> Thank you for reporting this,
> Tristan Maxson
>
> On Fri, Oct 24, 2014 at 7:05 AM, Peter Bjerre Jensen <pbjen at dtu.dk
> <mailto:pbjen at dtu.dk>> wrote:
>
> Hi Tristan
>
> I have pasted the full output of "ase-db fcc_alloys.db
> -c+hof,raw_score -s raw_score --limit 0" below.
>
> As you can see the first 180 structures do not have a defined
> raw_score, and are therefore shown first (I am not sure whether
> this is the preferred result - when sorting you are normally only
> interested in the entries with a value for the parameter you sort
> after?)
>
> So the sorting seems be correct (except the issue regarding not
> defined parameters).
>
> But normally one would be interested in the structures with the
> highest value of a sorted parameter, and therefore I think this
> should be shown as standard.
>
> I hope this made it more clear?
>
> Best regards
> Peter
>
> The full output is this:
>
> id|age|user |formula |pbc|volume| mass| hof|raw_score
> 1|15m|pbjen| |---| 1.000| 0.000| |
> 2|15m|pbjen|AgAl2Pt |---| 1.000|356.911| |
> 3|15m|pbjen|Ag3Cu |---| 1.000|387.150| |
> 4|15m|pbjen|AgAlAuCu|---| 1.000|395.362| |
> 5|15m|pbjen|AgAlAuPd|---| 1.000|438.236| |
> 6|15m|pbjen|Ag2AuPt |---| 1.000|607.783| |
> 7|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 8|15m|pbjen|AgNiPdPt|---| 1.000|468.061| |
> 9|15m|pbjen|NiPt3 |---| 1.000|643.933| |
> 10|15m|pbjen|AuCuPd2 |---| 1.000|473.353| |
> 11|15m|pbjen|AgNiPt2 |---| 1.000|556.721| |
> 22|15m|pbjen|AgAuNiPt|---| 1.000|558.608| |
> 24|15m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 26|15m|pbjen|CuPt3 |---| 1.000|648.786| |
> 28|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 30|15m|pbjen|AgCuNiPt|---| 1.000|425.187| |
> 32|15m|pbjen|Al2Pt2 |---| 1.000|444.123| |
> 34|15m|pbjen|Au2Pd2 |---| 1.000|606.773| |
> 36|15m|pbjen|AgPt3 |---| 1.000|693.108| |
> 38|15m|pbjen|AlPt3 |---| 1.000|612.222| |
> 40|15m|pbjen|AlAuCuPd|---| 1.000|393.914| |
> 42|15m|pbjen|Ag2AlAu |---| 1.000|439.684| |
> 44|15m|pbjen|AgCuNi2 |---| 1.000|288.801| |
> 46|15m|pbjen|NiPt3 |---| 1.000|643.933| |
> 48|15m|pbjen|Cu2Pd2 |---| 1.000|339.932| |
> 50|15m|pbjen|CuNiPdPt|---| 1.000|423.739| |
> 52|15m|pbjen|AgAuCuPd|---| 1.000|474.800| |
> 54|15m|pbjen|AuNiPd2 |---| 1.000|468.500| |
> 56|15m|pbjen|NiPt3 |---| 1.000|643.933| |
> 58|15m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 60|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 62|15m|pbjen|Pt4 |---| 1.000|780.320| |
> 64|15m|pbjen|CuPt3 |---| 1.000|648.786| |
> 66|15m|pbjen|AlCuNiPt|---| 1.000|344.301| |
> 68|15m|pbjen|AgAlPdPt|---| 1.000|436.350| |
> 70|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 72|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 74|15m|pbjen|Cu2Pt2 |---| 1.000|517.252| |
> 76|15m|pbjen|CuNiPdPt|---| 1.000|423.739| |
> 78|15m|pbjen|CuPt3 |---| 1.000|648.786| |
> 80|15m|pbjen|AgAlAu2 |---| 1.000|528.783| |
> 82|15m|pbjen|CuPdPt2 |---| 1.000|560.126| |
> 84|15m|pbjen|CuNiPdPt|---| 1.000|423.739| |
> 86|15m|pbjen|AlCuPt2 |---| 1.000|480.688| |
> 88|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 90|15m|pbjen|Ni2Pt2 |---| 1.000|507.547| |
> 92|15m|pbjen|AuNi2Pt |---| 1.000|509.433| |
> 94|15m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 96|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 98|15m|pbjen|CuPt3 |---| 1.000|648.786| |
> 100|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 102|15m|pbjen|AuCuNiPt|---| 1.000|514.286| |
> 104|15m|pbjen|AuCu2Pt |---| 1.000|519.139| |
> 106|15m|pbjen|AgNiPt2 |---| 1.000|556.721| |
> 108|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 110|15m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 112|15m|pbjen|AgCuNi2 |---| 1.000|288.801| |
> 114|15m|pbjen|AgNi2Pt |---| 1.000|420.335| |
> 116|15m|pbjen|AlCuNiPt|---| 1.000|344.301| |
> 118|14m|pbjen|Cu2PdPt |---| 1.000|428.592| |
> 120|14m|pbjen|AuNiPt2 |---| 1.000|645.820| |
> 122|14m|pbjen|Ni2PdPt |---| 1.000|418.887| |
> 124|14m|pbjen|AuCuPt2 |---| 1.000|650.673| |
> 126|14m|pbjen|Cu2Pt2 |---| 1.000|517.252| |
> 128|14m|pbjen|AlCuNiPt|---| 1.000|344.301| |
> 130|14m|pbjen|AgCuPt2 |---| 1.000|561.574| |
> 132|14m|pbjen|AlCu2Pt |---| 1.000|349.154| |
> 134|14m|pbjen|Cu2NiPt |---| 1.000|380.865| |
> 136|14m|pbjen|AuCu2Pt |---| 1.000|519.139| |
> 138|14m|pbjen|Ni3Pt |---| 1.000|371.160| |
> 140|14m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 142|14m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 144|14m|pbjen|AuCuNiPt|---| 1.000|514.286| |
> 146|14m|pbjen|CuPdPt2 |---| 1.000|560.126| |
> 148|14m|pbjen|AgCuNiPt|---| 1.000|425.187| |
> 150|14m|pbjen|Cu2NiPt |---| 1.000|380.865| |
> 152|14m|pbjen|Ni2Pt2 |---| 1.000|507.547| |
> 154|14m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 156|14m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 158|14m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 160|14m|pbjen|AuNi2Pt |---| 1.000|509.433| |
> 162|14m|pbjen|Cu2NiPt |---| 1.000|380.865| |
> 164|14m|pbjen|Cu3Ni |---| 1.000|249.331| |
> 166|14m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 168|14m|pbjen|AgNi2Pt |---| 1.000|420.335| |
> 170|14m|pbjen|CuNiPt2 |---| 1.000|512.399| |
> 172|14m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 174|14m|pbjen|CuNi2Pt |---| 1.000|376.013| |
> 176|14m|pbjen|AlNi2Pt |---| 1.000|339.448| |
> 178|14m|pbjen|Pt4 |---| 1.000|780.320| |
> 180|14m|pbjen|Cu2Pt2 |---| 1.000|517.252| |
> 177|14m|pbjen|AlNi2Pt |---| 1.000|339.448| 0.136| -0.136
> 45|15m|pbjen|AgCuNi2 |---| 1.000|288.801| 0.105| -0.105
> 113|15m|pbjen|AgCuNi2 |---| 1.000|288.801| 0.105| -0.105
> 129|14m|pbjen|AlCuNiPt|---| 1.000|344.301| 0.098| -0.098
> 67|15m|pbjen|AlCuNiPt|---| 1.000|344.301| 0.098| -0.098
> 117|14m|pbjen|AlCuNiPt|---| 1.000|344.301| 0.098| -0.098
> 23|15m|pbjen|AgAuNiPt|---| 1.000|558.608| 0.064| -0.064
> 18|15m|pbjen|AgNiPdPt|---| 1.000|468.061| 0.055| -0.055
> 115|15m|pbjen|AgNi2Pt |---| 1.000|420.335| 0.054| -0.054
> 169|14m|pbjen|AgNi2Pt |---| 1.000|420.335| 0.054| -0.054
> 133|14m|pbjen|AlCu2Pt |---| 1.000|349.154| 0.052| -0.052
> 55|15m|pbjen|AuNiPd2 |---| 1.000|468.500| 0.047| -0.047
> 39|15m|pbjen|AlPt3 |---| 1.000|612.222| 0.043| -0.043
> 41|15m|pbjen|AlAuCuPd|---| 1.000|393.914| 0.042| -0.042
> 37|15m|pbjen|AgPt3 |---| 1.000|693.108| 0.040| -0.040
> 33|15m|pbjen|Al2Pt2 |---| 1.000|444.123| 0.040| -0.040
> 69|15m|pbjen|AgAlPdPt|---| 1.000|436.350| 0.035| -0.035
> 21|15m|pbjen|AgNiPt2 |---| 1.000|556.721| 0.035| -0.035
> 107|15m|pbjen|AgNiPt2 |---| 1.000|556.721| 0.035| -0.035
> 87|15m|pbjen|AlCuPt2 |---| 1.000|480.688| 0.032| -0.032
> 13|15m|pbjen|Ag3Cu |---| 1.000|387.150| 0.026| -0.026
> 16|15m|pbjen|Ag2AuPt |---| 1.000|607.783| 0.024| -0.024
> 14|15m|pbjen|AgAlAuCu|---| 1.000|395.362| 0.024| -0.024
> 149|14m|pbjen|AgCuNiPt|---| 1.000|425.187| 0.023| -0.023
> 31|15m|pbjen|AgCuNiPt|---| 1.000|425.187| 0.023| -0.023
> 121|14m|pbjen|AuNiPt2 |---| 1.000|645.820| 0.019| -0.019
> 165|14m|pbjen|Cu3Ni |---| 1.000|249.331| 0.019| -0.019
> 93|15m|pbjen|AuNi2Pt |---| 1.000|509.433| 0.017| -0.017
> 161|14m|pbjen|AuNi2Pt |---| 1.000|509.433| 0.017| -0.017
> 35|15m|pbjen|Au2Pd2 |---| 1.000|606.773| 0.009| -0.009
> 53|15m|pbjen|AgAuCuPd|---| 1.000|474.800| 0.009| -0.009
> 12|15m|pbjen|AgAl2Pt |---| 1.000|356.911| 0.008| -0.008
> 15|15m|pbjen|AgAlAuPd|---| 1.000|438.236| 0.001| -0.001
> 63|15m|pbjen|Pt4 |---| 1.000|780.320|-0.000| 0.000
> 179|14m|pbjen|Pt4 |---| 1.000|780.320|-0.000| 0.000
> 103|15m|pbjen|AuCuNiPt|---| 1.000|514.286|-0.003| 0.003
> 145|14m|pbjen|AuCuNiPt|---| 1.000|514.286|-0.003| 0.003
> 20|15m|pbjen|AuCuPd2 |---| 1.000|473.353|-0.005| 0.005
> 131|14m|pbjen|AgCuPt2 |---| 1.000|561.574|-0.007| 0.007
> 125|14m|pbjen|AuCuPt2 |---| 1.000|650.673|-0.017| 0.017
> 81|15m|pbjen|AgAlAu2 |---| 1.000|528.783|-0.025| 0.025
> 43|15m|pbjen|Ag2AlAu |---| 1.000|439.684|-0.030| 0.030
> 49|15m|pbjen|Cu2Pd2 |---| 1.000|339.932|-0.032| 0.032
> 137|14m|pbjen|AuCu2Pt |---| 1.000|519.139|-0.034| 0.034
> 105|15m|pbjen|AuCu2Pt |---| 1.000|519.139|-0.034| 0.034
> 123|14m|pbjen|Ni2PdPt |---| 1.000|418.887|-0.042| 0.042
> 77|15m|pbjen|CuNiPdPt|---| 1.000|423.739|-0.051| 0.051
> 85|15m|pbjen|CuNiPdPt|---| 1.000|423.739|-0.051| 0.051
> 51|15m|pbjen|CuNiPdPt|---| 1.000|423.739|-0.051| 0.051
> 19|15m|pbjen|NiPt3 |---| 1.000|643.933|-0.056| 0.056
> 47|15m|pbjen|NiPt3 |---| 1.000|643.933|-0.056| 0.056
> 57|15m|pbjen|NiPt3 |---| 1.000|643.933|-0.056| 0.056
> 83|15m|pbjen|CuPdPt2 |---| 1.000|560.126|-0.059| 0.059
> 147|14m|pbjen|CuPdPt2 |---| 1.000|560.126|-0.059| 0.059
> 119|14m|pbjen|Cu2PdPt |---| 1.000|428.592|-0.072| 0.072
> 27|15m|pbjen|CuPt3 |---| 1.000|648.786|-0.073| 0.073
> 65|15m|pbjen|CuPt3 |---| 1.000|648.786|-0.073| 0.073
> 79|15m|pbjen|CuPt3 |---| 1.000|648.786|-0.073| 0.073
> 99|15m|pbjen|CuPt3 |---| 1.000|648.786|-0.073| 0.073
> 135|14m|pbjen|Cu2NiPt |---| 1.000|380.865|-0.088| 0.088
> 163|14m|pbjen|Cu2NiPt |---| 1.000|380.865|-0.088| 0.088
> 151|14m|pbjen|Cu2NiPt |---| 1.000|380.865|-0.088| 0.088
> 143|14m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 155|14m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 173|14m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 175|14m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 25|15m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 59|15m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 95|15m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 157|14m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 167|14m|pbjen|CuNi2Pt |---| 1.000|376.013|-0.096| 0.096
> 29|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 61|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 73|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 89|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 97|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 159|14m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 171|14m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 17|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 71|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 101|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 109|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 141|14m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 111|15m|pbjen|CuNiPt2 |---| 1.000|512.399|-0.101| 0.101
> 91|15m|pbjen|Ni2Pt2 |---| 1.000|507.547|-0.107| 0.107
> 153|14m|pbjen|Ni2Pt2 |---| 1.000|507.547|-0.107| 0.107
> 127|14m|pbjen|Cu2Pt2 |---| 1.000|517.252|-0.110| 0.110
> 75|15m|pbjen|Cu2Pt2 |---| 1.000|517.252|-0.110| 0.110
> 181|14m|pbjen|Cu2Pt2 |---| 1.000|517.252|-0.110| 0.110
> 139|14m|pbjen|Ni3Pt |---| 1.000|371.160|-0.118| 0.118
>
> Den 24-10-2014 kl. 12:56 skrev Tristan Maxson:
>> To be clear, you are saying that ase-db discards extra results
>> (past the limit) BEFORE sorting rather than after?...This seems
>> like a bug if so. I will look into it and see if its easily
>> fixable if this is the case.
>>
>> Thank you,
>> Tristan Maxson
>>
>> On Fri, Oct 24, 2014 at 6:52 AM, Peter Bjerre Jensen
>> <pbjen at dtu.dk <mailto:pbjen at dtu.dk>> wrote:
>>
>> Hi
>>
>> According to the help of ase-db (ase-db --help) one can
>> specify the number of entries to show with the keyword limit;
>> however I do not think it works very well in combination with
>> the sort function.
>>
>> For example I have created a database following the ase-ga
>> toturial
>> (https://wiki.fysik.dtu.dk/ase/tutorials/ga/ga_fcc_alloys.html )
>> and generated a database where the 5 best structures
>> according to raw_score are these:
>>
>> id|age|user |formula |pbc|volume| mass| hof|raw_score
>> 153|22s|pbjen|Ni2Pt2 |---| 1.000|507.547|-0.107| 0.107
>> 127|34s|pbjen|Cu2Pt2 |---| 1.000|517.252|-0.110| 0.110
>> 75|54s|pbjen|Cu2Pt2 |---| 1.000|517.252|-0.110| 0.110
>> 181| 9s|pbjen|Cu2Pt2 |---| 1.000|517.252|-0.110| 0.110
>> 139|29s|pbjen|Ni3Pt |---| 1.000|371.160|-0.118| 0.118
>>
>> This was obtained by using "ase-db fcc_alloys.db --limit 0
>> -c+hof,raw_score -s raw_score" to show all entries and sort
>> by raw_score(=-hof); which should be as high as possible for
>> the best candidates.
>>
>> However, if I now do "ase-db fcc_alloys.db --limit 5
>> -c+hof,raw_score -s raw_score" I obtain the top of the list
>> (which are the unrelaxed structures from the tutorial with no
>> defined raw_score):
>>
>> id| age|user |formula |pbc|volume| mass|hof|raw_score
>> 1|248s|pbjen| |---| 1.000| 0.000| |
>> 2|248s|pbjen|AgAl2Pt |---| 1.000|356.911| |
>> 3|248s|pbjen|Ag3Cu |---| 1.000|387.150| |
>> 4|247s|pbjen|AgAlAuCu|---| 1.000|395.362| |
>> 5|247s|pbjen|AgAlAuPd|---| 1.000|438.236| |
>>
>> I think this is very unpractical, and I think it would make
>> most sense to show the last entries if one specifies a limit.
>>
>> I think a simple solution could be to add an extra keyword
>> specifying the sorting to be reverse?
>>
>> Best regards
>> Peter
>>
>> Peter Bjerre Jensen
>> PhD Student
>> DTU Energy Conversion
>>
>> Technical University of Denmark
>>
>>
>> Department of Energy Conversion and Storage
>> Fysikvej, Building 307
>> 2800 Kgs. Lyngby
>> Direct +45 45253204 <tel:%2B45%2045253204>
>> pbjen at dtu.dk <mailto:pbjen at dtu.dk>
>> www.ecs.dtu.dk <http://www.ecs.dtu.dk>
>>
>>
>> --
>> Peter Bjerre Jensen
>> Gyngemose Parkvej 6C ST TH
>> 2860 Søborg
>> Tlf. 21 26 13 90
>>
>>
>> _______________________________________________
>> 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
>>
>>
>
>
>
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