Add beaker clusterX notebook and data

example-data/sige1/allcorr.out

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example-data/sige1/allenergy.out

+-0.00188363765642
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+-0.000629710976682
+-0.00254821906265
+-0.00166373171885
+-0.00239358781255
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+-0.00181605046885

example-data/sige1/atoms.xsf

+CRYSTAL
+PRIMVEC
+ 0.00000000000000 5.45937500000000 5.45937500000000
+ 5.45937500000000 0.00000000000000 5.45937500000000
+ 5.45937500000000 5.45937500000000 0.00000000000000
+PRIMCOORD
+ 16 1
+ 14     0.00000000000000     0.00000000000000     0.00000000000000
+ 14     0.00000000000000     2.72968750000000     2.72968750000000
+ 14     2.72968750000000     0.00000000000000     2.72968750000000
+ 14     2.72968750000000     2.72968750000000     0.00000000000000
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+ 14     4.09453125000000     1.36484375000000     4.09453125000000
+ 14     1.36484375000000     4.09453125000000     4.09453125000000
+ 14     6.82421875000000     4.09453125000000     4.09453125000000
+ 14     4.09453125000000     6.82421875000000     4.09453125000000
+ 14     4.09453125000000     4.09453125000000     6.82421875000000
+ 32     6.82421875000000     6.82421875000000     6.82421875000000
+ 14     5.45937500000000     2.72968750000000     2.72968750000000
+ 14     2.72968750000000     5.45937500000000     2.72968750000000
+ 14     2.72968750000000     2.72968750000000     5.45937500000000
+ 14     5.45937500000000     5.45937500000000     5.45937500000000

example-data/sige1/atomstolattice.log

+16
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+13 4 0.000000000000

example-data/sige1/clusters.out

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+

example-data/sige1/config.py

+# ab-initio
+CALCULATOR = "exciting"
+EXCITINGBIN = "/home/tutorials/exciting/bin"
+ENERGY_UNITS = "Ha"
+
+# crystal
+PAR_LAT_FILE = "lat.in"
+MET_LAT_FILE = "lat.in.met"
+VEGARDS_LAW = True
+
+CELL_PAR_0 = [[0.0000, 5.4310, 5.4310],
+              [5.4310, 0.0000, 5.4310],
+              [5.4310, 5.4310, 0.0000]]
+
+CELL_PAR_1 = [[0.0000, 5.6580, 5.6580],
+              [5.6580, 0.0000, 5.6580],
+              [5.6580, 5.6580, 0.0000]]
+
+
+# cluster expansion
+ENERGY_CE = "mixingPerSite"
+#ENERGY_CE = "total"
+MAX_RADIUS = 5.0
+MAX_POINTS = 4  
+
+E0 = -4623.87413289
+E1 = -33537.6274125
+
+
+# Ground-state search
+TEMP = 1000 # temperature [K] for the Metropolis sampling
+MAX_N_CONF = 300 # number of configuratons to sample after the last LND structure was found
+

example-data/sige1/config.py~

+# ab-initio
+CALCULATOR = "exciting"
+EXCITINGBIN = "/home/tutorials/exciting/bin"
+ENERGY_UNITS = "Ha"
+
+# crystal
+PAR_LAT_FILE = "lat.in"
+MET_LAT_FILE = "lat.in.met"
+VEGARDS_LAW = True
+
+CELL_PAR_0 = [[0.0000, 5.4310, 5.4310],
+              [5.4310, 0.0000, 5.4310],
+              [5.4310, 5.4310, 0.0000]]
+
+CELL_PAR_1 = [[0.0000, 5.6580, 5.6580],
+              [5.6580, 0.0000, 5.6580],
+              [5.6580, 5.6580, 0.0000]]
+
+
+# cluster expansion
+ENERGY_CE = "mixingPerSite"
+#ENERGY_CE = "total"
+MAX_RADIUS = 5.0
+MAX_POINTS = 4  
+
+# Ground-state search
+TEMP = 1000 # temperature [K] for the Metropolis sampling
+MAX_N_CONF = 300 # number of configuratons to sample after the last LND structure was found
+

example-data/sige1/corrdump.log

+strain=
+0.993121042322 0.000000000000 0.000000000000 
+0.000000000000 0.993121042322 0.000000000000 
+0.000000000000 0.000000000000 0.993121042322 
+
+Ge atom at 0.125000000000 0.125000000000 0.125000000000 mapped onto lattice site at 0.125000000000 0.125000000000 0.125000000000 distance= 0.000000000000
+Ge atom at 1.000000000000 1.000000000000 1.000000000000 mapped onto lattice site at 1.000000000000 1.000000000000 1.000000000000 distance= 0.000000000000
+Si atom at 0.500000000000 1.000000000000 1.000000000000 mapped onto lattice site at 0.500000000000 1.000000000000 1.000000000000 distance= 0.000000000000
+Si atom at 1.000000000000 0.500000000000 1.000000000000 mapped onto lattice site at 1.000000000000 0.500000000000 1.000000000000 distance= 0.000000000000
+Si atom at 1.000000000000 1.000000000000 0.500000000000 mapped onto lattice site at 1.000000000000 1.000000000000 0.500000000000 distance= 0.000000000000
+Si atom at 0.125000000000 0.625000000000 0.625000000000 mapped onto lattice site at 0.125000000000 0.625000000000 0.625000000000 distance= 0.000000000000
+Si atom at 0.625000000000 0.125000000000 0.625000000000 mapped onto lattice site at 0.625000000000 0.125000000000 0.625000000000 distance= 0.000000000000
+Si atom at 0.625000000000 0.625000000000 0.125000000000 mapped onto lattice site at 0.625000000000 0.625000000000 0.125000000000 distance= 0.000000000000
+Ge atom at 0.625000000000 0.625000000000 0.625000000000 mapped onto lattice site at 0.625000000000 0.625000000000 0.625000000000 distance= 0.000000000000
+Ge atom at 0.500000000000 0.500000000000 0.500000000000 mapped onto lattice site at 0.500000000000 0.500000000000 0.500000000000 distance= 0.000000000000
+Si atom at 0.125000000000 0.625000000000 0.125000000000 mapped onto lattice site at 0.125000000000 0.625000000000 0.125000000000 distance= 0.000000000000
+Si atom at 0.625000000000 0.125000000000 0.125000000000 mapped onto lattice site at 0.625000000000 0.125000000000 0.125000000000 distance= 0.000000000000
+Si atom at 0.125000000000 0.125000000000 0.625000000000 mapped onto lattice site at 0.125000000000 0.125000000000 0.625000000000 distance= 0.000000000000
+Si atom at 0.500000000000 0.500000000000 1.000000000000 mapped onto lattice site at 0.500000000000 0.500000000000 1.000000000000 distance= 0.000000000000
+Si atom at 1.000000000000 0.500000000000 0.500000000000 mapped onto lattice site at 1.000000000000 0.500000000000 0.500000000000 distance= 0.000000000000
+Si atom at 0.500000000000 1.000000000000 0.500000000000 mapped onto lattice site at 0.500000000000 1.000000000000 0.500000000000 distance= 0.000000000000

example-data/sige1/ece.dat

+0.75	-0.00186361
+0.0625	-0.000589423
+0.125	-0.00108791
+0.1875	-0.00142138
+0.3125	-0.00201775
+0.375	-0.0021786
+0.4375	-0.00246155
+0.5625	-0.00254402
+0.625	-0.00218765
+0.6875	-0.00198126
+0.8125	-0.00136058
+0.875	-0.000981573
+0.9375	-0.000504293
+0.5	-0.00255568
+0.25	-0.00158986
+0.5	-0.00237243
+0.75	-0.00180824
+0.25	-0.00185689

example-data/sige1/energy.eci

+-0.002166441514498
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+0.000023531336357
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+0.000000000000000
+0.000000000000000
+0.000000000000000
+0.000000000000000

example-data/sige1/energy.eci.out

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+2	-0.002126061863397	0.000030489728474	0.000312519119416	0.000068013935805	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000
+3	-0.002166441514498	0.000024322845195	0.000263280336765	0.000068662272477	0.000023531336357	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000
+4	-0.002126605172504	0.000044037544551	0.000308330159536	0.000070207474243	-0.000000181138273	-0.000007092111389	-0.000007092111389	0.000000000000000	0.000000000000000	0.000000000000000	0.000000000000000
+5	-0.002124323206848	0.000083780907737	0.000294553140343	0.000061701181839	0.000013690238068	-0.000014727804435	0.000000847968920	0.000000847968863	0.000007031969775	-0.000009182027403	-0.000018364054654

example-data/sige1/energy.eci.tmp

+3
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+0.000000000000000
+0.000000000000000
+0.000000000000000
+0.000000000000000

example-data/sige1/info_opt.out

+1	0.000326482344	0.000824339124	7.000000000000	0.000299216595	0.000293444287	0.000358762725	0.000249088287	2	2.359919225313	3
+2	0.000124046347	0.000288776031	7.000000000000	0.000130335713	0.000122347720	0.000122506124	0.000082625566	2	3.853731957467	4
+3	0.000093329104	0.000224048277	12.000000000000	0.000095893336	0.000105278356	0.000108406983	0.000056956874	2	4.518901276859	5
+4	0.000131713865	0.000274961105	7.000000000000	0.000121595653	0.000122328872	0.000156710543	0.000075580006	3	3.853731957467	7
+5	0.000099011391	0.000228221637	0.000000000000	0.000094955292	0.000101798507	0.000109090810	0.000035393105	3	4.518901276859	11

example-data/sige1/lat.in

+0.00 5.45 5.45
+5.45 0.00 5.45
+5.45 5.45 0.00
+0.5 0.0 0.0
+0.0 0.5 0.0
+0.0 0.0 0.5
+0.00000000 0.00000000 0.00000000 Si,Ge
+0.12500000 0.12500000 0.12500000 Si,Ge

example-data/sige1/lat.in.met

+0.00 5.45 5.45
+5.45 0.00 5.45
+5.45 5.45 0.00
+1.0 0.0 0.0
+0.0 1.0 0.0
+0.0 0.0 1.0
+0.00000000 0.00000000 0.00000000 Si,Ge
+0.50000000 0.00000000 0.00000000 Si,Ge
+0.00000000 0.50000000 0.00000000 Si,Ge
+0.00000000 0.00000000 0.50000000 Si,Ge
+0.12500000 0.12500000 0.12500000 Si,Ge
+0.12500000 0.12500000 0.62500000 Si,Ge
+0.12500000 0.62500000 0.12500000 Si,Ge
+0.62500000 0.12500000 0.12500000 Si,Ge
+0.12500000 0.62500000 0.62500000 Si,Ge
+0.62500000 0.12500000 0.62500000 Si,Ge
+0.62500000 0.62500000 0.12500000 Si,Ge
+0.62500000 0.62500000 0.62500000 Si,Ge
+0.00000000 0.50000000 0.50000000 Si,Ge
+0.50000000 0.00000000 0.50000000 Si,Ge
+0.50000000 0.50000000 0.00000000 Si,Ge
+0.50000000 0.50000000 0.50000000 Si,Ge

example-data/sige1/plot_gs_search.gp

+set terminal png
+set output "gs_search.png" 
+set format y "%2.1e"
+set ylabel "Energy [Ha]"
+set xlabel "Composition x"
+set label "Si" at graph -0.01,-0.12 
+set label "Ge" at graph 0.98,-0.12 
+set border linewidth 1.5
+set style line 1 linecolor rgb '#0060ad' linetype 1 linewidth 2
+set style line 2 linecolor rgb '#dd181f' linetype 1 linewidth 2
+set grid ytics lc rgb "#333333" lw 1 lt 0
+set grid xtics lc rgb "#333333" lw 1 lt 0
+plot "metropolis.log" w p pointtype 7 ps 0.7 lc rgb "red" title "GS search",\
+"abi.dat" w p pointtype 6 ps 2 lc rgb "blue" title "Ab-initio",\
+"ece.dat" u 1:2 w p pointtype 7 ps 1.4 lc rgb "blue" title "Predicted"
\ No newline at end of file

example-data/sige1/plot_optimize_clusters.gp

+set terminal png
+set output "optimize_clusters.png" 
+set format y "%2.1e"
+set ylabel "Energy [Ha]"
+set xlabel "Number of clusters"
+set border linewidth 1.5
+set style line 1 linecolor rgb '#0060ad' linetype 1 linewidth 2
+set style line 2 linecolor rgb '#dd181f' linetype 1 linewidth 2
+set grid ytics lc rgb "#333333" lw 1 lt 0
+set grid xtics lc rgb "#333333" lw 1 lt 0
+plot "info_opt.out" u 11:2 w lp pointtype 6 ps 2 lc rgb "red" title "CV score",\
+"info_opt.out" u 11:8 w lp pointtype 7 ps 1.4 lc rgb "blue" title "RMSE"
\ No newline at end of file