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--- scripts:modxyz [2009/11/27 12:43]
prokop
+++ scripts:modxyz [2011/02/18 13:13]
@@ Line 1: / Line 1: @@
-==== usage ====
-  * Copy wf2state to bin directory
-  * copy particular cel.lvs into same directory as your *.xyz file
-  * run with *.xyz file name as 1st parameter and shift by lattice vectors da, db, dc, example:
-    <code> wf2state scan.xyz 0.5 0.5 0.0 </code>
-  * script generate ''scan.xyz.s.xyz'' file
-=== how it works ===
-  * compute inverse matrix of lattice
-  * transform geometry by the inverse lattice (make it rectangular)
-  * shift by da,db,dz in this rectangularized space
-  * modulo by cel size a,b,c
-  * transform back by forward lattice matrix
-==== wf2state: ====
-<code>
-#! /bin/bash
-#input="scan-.xyz"
-input=$1
-output=$input.s.xyz"
-da=$2
-db=$3
-dc=$4
-p=`cat $input | head -1`
-let p=$p+2
-awk -v p=$p -v da=$da -v db=$db -v dc=$dc '
-function deter(a){
-det= a[1,1]*(a[3,3]*a[2,2]-a[3,2]*a[2,3])-a[2,1]*(a[3,3]*a[1,2]-a[3,2]*a[1,3])+a[3,1]*(a[2,3]*a[1,2]-a[2,2]*a[1,3])
-return det
-}
-function invert(a,b){
-det = deter(a)
-b[1,1] =  (a[3,3]*a[2,2]-a[3,2]*a[2,3]) / det
-b[1,2] = -(a[3,3]*a[1,2]-a[3,2]*a[1,3]) /det
-b[1,3] =  (a[2,3]*a[1,2]-a[2,2]*a[1,3]) /det
-b[2,1] = -(a[3,3]*a[2,1]-a[3,1]*a[2,3]) /det
-b[2,2] =  (a[3,3]*a[1,1]-a[3,1]*a[1,3]) /det
-b[2,3] = -(a[2,3]*a[1,1]-a[2,1]*a[1,3]) /det
-b[3,1] =  (a[3,2]*a[2,1]-a[3,1]*a[2,2]) /det
-b[3,2] = -(a[3,2]*a[1,1]-a[3,1]*a[1,2]) /det
-b[3,3] =  (a[2,2]*a[1,1]-a[2,1]*a[1,2]) /det
-}
-function Mvec(M,v,out){
-out[1]=v[1]*M[1,1]+v[2]*M[1,2]+v[3]*M[1,3]
-out[2]=v[1]*M[2,1]+v[2]*M[2,2]+v[3]*M[2,3]
-out[3]=v[1]*M[3,1]+v[2]*M[3,2]+v[3]*M[3,3]
-}
-function Mvec2(M,v,out){
-out[1]=v[1]*M[1,1]+v[2]*M[2,1]+v[3]*M[3,1]
-out[2]=v[1]*M[1,2]+v[2]*M[2,2]+v[3]*M[3,2]
-out[3]=v[1]*M[1,3]+v[2]*M[2,3]+v[3]*M[3,3]
-}
-BEGIN{
-getline < "cel.lvs"
-A[1,1]=$1;A[1,2]=$2;A[1,3]=$3
-getline < "cel.lvs"
-A[2,1]=$1;A[2,2]=$2;A[2,3]=$3
-getline < "cel.lvs"
-A[3,1]=$1;A[3,2]=$2;A[3,3]=$3
-invert(A,B)
-}
-#(NR==1){print $0}
-#(NR==2){print $0}
-(NR>0){ if ($4!=""){
-v[1]=$2;v[2]=$3;v[3]=$4;
-Mvec2(B,v,v_)
-v_[1]=(v_[1]+da)%1.0
-v_[2]=(v_[2]+db)%1.0
-v_[3]=(v_[3]+dc)%1.0
-#print $1,"   ",v_[1],"    ",v_[2],"   ",v_[3]
-Mvec2(A,v_,v__)
-print $1,"   ",v__[1],"    ",v__[2],"   ",v__[3]
-}else{print $0}
-}
-END{
-}
-' $input > $output
-</code>

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