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exp/Adsorption_Graphene/Graphene.POSCAR

@@ -0,0 +1,40 @@
+ Position data Generated by SPaMD
+1.0
+ 9.872700 0.000000 0.000000
+ -4.936348 8.550008 0.000000
+ 0.000000 0.000000 4.000000
+ C 
+ 32 
+Cartesian
+ 1.234087 0.712501 2.000000
+ 0.000000 0.000000 2.000000
+ 0.000000 2.850003 2.000000
+ -1.234087 2.137502 2.000000
+ -1.234087 4.987505 2.000000
+ -2.468174 4.275004 2.000000
+ -2.468174 7.125007 2.000000
+ -3.702261 6.412506 2.000000
+ 3.702262 0.712501 2.000000
+ 2.468175 0.000000 2.000000
+ 2.468175 2.850003 2.000000
+ 1.234088 2.137502 2.000000
+ 1.234088 4.987505 2.000000
+ 0.000001 4.275004 2.000000
+ 0.000001 7.125007 2.000000
+ -1.234086 6.412506 2.000000
+ 6.170437 0.712501 2.000000
+ 4.936350 0.000000 2.000000
+ 4.936350 2.850003 2.000000
+ 3.702263 2.137502 2.000000
+ 3.702263 4.987505 2.000000
+ 2.468176 4.275004 2.000000
+ 2.468176 7.125007 2.000000
+ 1.234089 6.412506 2.000000
+ 8.638612 0.712501 2.000000
+ 7.404525 0.000000 2.000000
+ 7.404525 2.850003 2.000000
+ 6.170438 2.137502 2.000000
+ 6.170438 4.987505 2.000000
+ 4.936351 4.275004 2.000000
+ 4.936351 7.125007 2.000000
+ 3.702264 6.412506 2.000000

exp/Adsorption_Graphene/H20.poscar

@@ -0,0 +1,15 @@
+ Position data Generated by SPaMD
+1.0
+ 8.000000 0.000000 0.000000
+ 0.000000 8.000000 0.000000
+ 0.000000 0.000000 8.000000
+ O H 
+ 1 2 
+Selective dynamics
+C
+ 4.000000 4.000000 4.000000 
+ 4.000000 4.000000 3.0473 
+ 3.077729064 4.000000 4.250717936
+
+
+

exp/Adsorption_Graphene/run.sh

@@ -0,0 +1,4 @@
+#step 1 get site list from surface slab
+./../../bin/Surfkit --site2D Graphene.POSCAR 2D.POSCAR 1 3
+#step 2 adsorb H2O to surface slab
+./../../bin/Surfkit --adsorb -file Graphene.POSCAR 2D.POSCAR Slab.POSCAR 1 5 H20.poscar H 1 1 0 0 0 1 0 0 0 1

exp/Adsorption_Pt/Pt211.POSCAR

@@ -0,0 +1,44 @@
+ Position data Generated by SPaMD
+1.0
+ 10.224509 0.000000 0.000000
+ -5.112255 6.261208 0.000000
+ 0.000000 0.000000 15.903123
+ E0 
+ 36 
+Cartesian
+ 10.224509 0.000000 5.000000
+ 1.278064 0.000000 7.213671
+ 8.946446 0.000000 7.213671
+ 0.000000 2.087069 6.475781
+ 7.668382 2.087069 6.475781
+ -1.278064 2.087069 8.689452
+ 6.390318 2.087069 8.689452
+ -2.556127 4.174139 7.951562
+ 5.112255 4.174139 7.951562
+ 6.390318 4.174139 10.165233
+ 3.834191 4.174139 10.165233
+ 0.000000 0.000000 9.427342
+ 7.668382 0.000000 9.427342
+ 7.668382 2.087069 10.903123
+ 5.112255 2.087069 10.903123
+ 2.556127 2.087069 6.475781
+ 3.834191 2.087069 8.689452
+ 1.278064 2.087069 8.689452
+ 2.556127 4.174139 7.951562
+ 0.000000 4.174139 7.951562
+ 1.278064 4.174139 10.165233
+ -1.278064 4.174139 10.165233
+ 5.112255 0.000000 9.427342
+ 2.556127 0.000000 9.427342
+ 2.556127 2.087069 10.903123
+ 0.000000 2.087069 10.903123
+ -1.278064 4.174139 5.737890
+ 6.390318 4.174139 5.737890
+ 2.556127 0.000000 5.000000
+ 5.112255 2.087069 6.475781
+ 3.834191 0.000000 7.213671
+ 6.390318 0.000000 7.213671
+ 5.112255 0.000000 5.000000
+ 7.668382 0.000000 5.000000
+ 1.278064 4.174139 5.737890
+ 3.834191 4.174139 5.737890

exp/Adsorption_Pt/run.sh

@@ -0,0 +1,4 @@
+#step 1 get site list from surface slab
+./../../bin/Surfkit --site3D Pt211.POSCAR 3D.POSCAR 1 9
+#step 2 adsorb H atom to surface slab
+./../../bin/Surfkit --adsorb -ele Pt211.POSCAR 3D.POSCAR Slab.POSCAR 3 1 H 

exp/Al2O3/Al2O3.POSCAR

@@ -0,0 +1,38 @@
+ Position data Generated by SPaMD
+1.0
+ 4.808483 0.000000 0.000000
+ -2.404241 4.164268 0.000000
+ 0.000000 0.000000 13.122423
+ Al O 
+ 12 18 
+Cartesian
+ -0.000002 2.776180 5.127238
+ 2.404244 1.388088 3.433973
+ -0.000002 2.776180 1.246912
+ 0.000000 0.000000 2.940163
+ 0.000000 0.000000 9.501375
+ -0.000002 2.776180 7.808123
+ 0.000000 0.000000 5.621048
+ 2.404244 1.388088 7.314300
+ 2.404244 1.388088 0.753088
+ 0.000000 0.000000 12.182260
+ 2.404244 1.388088 9.995185
+ -0.000002 2.776180 11.688450
+ 3.876472 1.388088 2.093531
+ 1.668130 0.113102 2.093531
+ 1.668130 2.663074 2.093531
+ 3.336255 0.000000 4.280606
+ 0.736114 1.274986 4.280606
+ -1.668127 2.889282 4.280606
+ 1.472226 2.776180 6.467681
+ -0.736116 1.501194 6.467681
+ -0.736116 4.051166 6.467681
+ 0.932016 1.388088 8.654742
+ 3.140358 2.663074 8.654742
+ 3.140358 0.113102 8.654742
+ 1.472228 0.000000 10.841817
+ 1.668128 2.889282 10.841817
+ -0.736114 1.274986 10.841817
+ -1.472230 2.776180 13.028892
+ 0.736112 4.051166 13.028892
+ 0.736112 1.501194 13.028892

exp/Al2O3/run.sh

@@ -0,0 +1,16 @@
+#step 1 align Al2O3.POSCAR to desired condition
+./../../bin/Surfkit --align Al2O3.POSCAR step1.POSCAR a x b y
+#step 2 align Al2O3.POSCAR to desired condition
+./../../bin/Surfkit --prim2D step1.POSCAR step2.POSCAR
+#step 3 scan Al2O3.POSCAR for atomic layer
+./../../bin/Surfkit --scan step2.POSCAR -7 7 
+#step 4 we found a non-polar center at 1 so we shift model by -1
+./../../bin/Surfkit --shift step2.POSCAR step3.POSCAR -1
+#step 5 scan modified Al2O3.POSCAR for atomic layer
+./../../bin/Surfkit --scan step3.POSCAR -3 3 
+#step 6 cleave model to Al2O3 slab
+./../../bin/Surfkit --cleav step3.POSCAR step4.POSCAR -2 2
+#step 7 adding vacuum layer for Al2O3 
+./../../bin/Surfkit --vacuum step4.POSCAR step5.POSCAR 5
+
+

exp/BN/BN.POSCAR

@@ -0,0 +1,12 @@
+ Position data Generated by SPaMD
+1.0
+ 2.489016 0.000000 0.000000
+ 0.000000 2.489016 0.000000
+ 0.000000 0.000000 3.520000
+ B N 
+ 2 2 
+Cartesian
+ 0.000000 1.244508 0.880000
+ 1.244508 0.000000 2.640000
+ 1.244508 1.244508 1.760000
+ 0.000000 0.000000 0.000000

exp/BN/Layer_Scan.csv

@@ -0,0 +1,11 @@
+Layer_Type,Height,Contains,Integration
+Atomic_Layer,4.064546,N4,B20N20
+Atomic_Layer,3.556478,B4,B20N16
+Atomic_Layer,2.032273,N4,B16N16
+Atomic_Layer,1.524205,B4,B16N12
+Atomic_Layer,0.000000,N4,B12N12
+Atomic_Layer,-0.508068,B4,B12N8
+Atomic_Layer,-2.032273,N4,B8N8
+Atomic_Layer,-2.540341,B4,B8N4
+Atomic_Layer,-4.064546,N4,B4N4
+Atomic_Layer,-4.572614,B4,B4

exp/BN/run.sh

@@ -0,0 +1,12 @@
+#step 1 convert BN.POSCAR to conventioal cell
+./../../bin/Surfkit --conv BN.POSCAR BN_conv.POSCAR 
+#step 1.5 convert BN.POSCAR to 2D primitive cell
+./../../bin/Surfkit --prim2D BN.POSCAR BN_prim2D.POSCAR 
+#step 2 convert conventioal cell to supercell
+./../../bin/Surfkit --proj -mat BN_conv.POSCAR BN_slab0.POSCAR 1 -1 0 1 0 -1 1 1 1 
+#step 3 scan atomic layer of BN_slab0.POSCAR
+./../../bin/Surfkit --scan BN_slab0.POSCAR -5 5
+#step 4 redefine slab thickness
+./../../bin/Surfkit --cleav BN_slab0.POSCAR BN_slab1.POSCAR -2 3
+#step 5 redefine Vacuum thickness
+./../../bin/Surfkit --vacuum BN_slab1.POSCAR BN_slab2.POSCAR 10

exp/FeS2/FeS2.POSCAR

@@ -0,0 +1,20 @@
+ Position data Generated by SPaMD
+1.0
+ 5.417900 0.0 0.0
+ 0.0 5.417900 0.0
+ 0.0 0.0 5.417900
+ E0 E1 
+ 4 8 
+Cartesian
+ 0.000000 0.000000 0.000000
+ 2.708950 0.000000 2.708950
+ 0.000000 2.708950 2.708950
+ 2.708950 2.708950 0.000000
+ 2.080474 2.080474 2.080474
+ 3.337426 3.337426 3.337426
+ 0.628476 3.337426 4.789424
+ 4.789424 2.080474 0.628476
+ 3.337426 4.789424 0.628476
+ 2.080474 0.628476 4.789424
+ 4.789424 0.628476 3.337426
+ 0.628476 4.789424 2.080474

exp/FeS2/run.sh

@@ -0,0 +1,8 @@
+#add adsorbtion on FeS2
+./../../bin/Surfkit --proj -mat FeS2.POSCAR step1.POSCAR 1 0 0 0 1 0 0 0 1
+./../../bin/Surfkit --align step1.POSCAR step1.POSCAR a x b y 
+./../../bin/Surfkit --cleav step1.POSCAR step2.POSCAR 0 15
+./../../bin/Surfkit --vacuum step2.POSCAR step3.POSCAR 15
+./../../bin/Surfkit --site3D step3.POSCAR 3D.POSCAR 3 9
+./../../bin/Surfkit --adsorb -ele step3.POSCAR 3D.POSCAR Slab.POSCAR 1 1 H 
+rm step*.POSCAR

exp/Graphene-MoS2/GRAPHENE.POSCAR

@@ -0,0 +1,10 @@
+ Position data Generated by SPaMD
+1.0
+ 2.468175 0.000000 0.000000
+ -1.234087 2.137502 0.000000
+ 0.000000 0.000000 2.000000
+ C 
+ 2 
+Cartesian
+ 1.234087 0.712501 1.000000
+ 0.000000 0.000000 1.000000

exp/Graphene-MoS2/Layer_Scan.csv

@@ -0,0 +1,4 @@
+Layer_Type,Height,Contains,Integration
+Atomic_Layer,4.577506,S19,C74S19
+Atomic_Layer,1.000000,C74,C74
+Nonpolar_Center,1.000000

exp/Graphene-MoS2/MoS2.POSCAR

@@ -0,0 +1,11 @@
+ Position data Generated by SPaMD
+1.0
+ 3.402500 0.000000 0.000000
+ -1.701250 2.946651 0.000000
+ 0.000000 0.000000 8.284989
+ Mo S 
+ 1 2 
+Cartesian
+ 0.000000 1.964434 4.142494
+ 1.701250 0.982217 5.707483
+ 1.701250 0.982217 2.577506