Adjust graphene island position on Cu surface
==============

::

	import numpy as np
	import os
	center=np.array([23.1136519648,19.7414802492])   #rotation center

	a1=np.array([2.5523713014,0.00])       #surface lattice constant
	a2=np.array([1.2708864505,2.2132145881])       #surface lattice constant

	data_pos=np.loadtxt("pos")    #graphene island coordinates
	ii=0
	for i in np.arange(0,1,0.1):
		for j in np.arange(0,1,0.1):
			tx,ty=i*a1+j*a2
			for theta in np.arange(0,np.pi/3,np.pi/60):
			#for theta in [np.pi]:
				ii+=1
				rot=np.eye(3)
				rot[0,0]=np.cos(theta)
				rot[0,1]=-np.sin(theta)
				rot[1,0]=np.sin(theta)
				rot[1,1]=np.cos(theta)
				
				data=data_pos.copy()
				for data_i in data:
					trans=np.eye(3)
					trans[:2,2]=center
					inv_trans=np.eye(3)
					inv_trans[:2,2]=-center
					data_temp=np.insert(data_i[:2],2,values=1).reshape(-1,1)
					data_temp=np.matmul(inv_trans,data_temp)
					data_temp=np.matmul(rot,data_temp)
					data_temp=np.matmul(trans,data_temp)
					data_temp=data_temp.T[0]
					#data_temp=data_temp.reshape(1,-1)
					data_i[:2]=data_temp[:2]
					data_i[0]+=tx
					data_i[1]+=ty

				np.savetxt("pos_temp",data)
				os.system("cat pos_head pos_temp > POSCAR_"+str(ii)+".vasp")

	os.system("mkdir POS;mv POSCAR* POS")