[ase-users] ase-db output limit and sorting
Peter Bjerre Jensen
pbjen at dtu.dk
Fri Oct 24 13:05:07 CEST 2014
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
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