import java.io.*; import java.lang.Math; public class alphaQuartz2jmol { public static void main( String[] args ) { int i,j,k, icoord, iatom; int nXcell = 2, nYcell = 2, nZcell = 2; double aa = 4.9134, cc = 5.4052; double x,y,z, x_cart, y_cart, z_cart; double [][] base, silicon, oxygene, Si_cart, Ox_cart; double [] vector, tempo; FileOutputStream out; // declare a file output object FileOutputStream parsec_out; // declare a file output object PrintStream p; // declare a print stream object System.out.println("This program generates the structure of alpha-Quartz"); System.out.println("Taking the parameters from the Navy"); System.out.println("Written by carrier@cs.umn.edu"); System.out.println("Group #154; P6(_3)/mmc"); int num_atoms_Si = 3; int num_atoms_Ox = 6; silicon = new double [num_atoms_Si][3]; oxygene = new double [num_atoms_Ox][3]; Si_cart = new double [num_atoms_Si][3]; Ox_cart = new double [num_atoms_Ox][3]; base = new double [3][3]; vector = new double [3]; tempo = new double [3]; // The basis base[0][0] = 0.5; base[0][1] = -Math.sqrt(3.0)/2.0; base[0][2] = 0.000; base[1][0] = 0.5; base[1][1] = Math.sqrt(3.0)/2.0; base[1][2] = 0.000; base[2][0] = 0.0; base[2][1] = 0.0; base[2][2] = cc/aa; // print the basis System.out.println("The lattice basis"); System.out.printf( "%2.12f %2.12f %2.12f\n",base[0][0], base[0][1], base[0][2] ); System.out.printf( "%2.12f %2.12f %2.12f\n",base[1][0], base[1][1], base[1][2] ); System.out.printf( "%2.12f %2.12f %2.12f\n",base[2][0], base[2][1], base[2][2] ); // prints to file out try { // Create a new file output stream out = new FileOutputStream("alphaQuartz.xyz"); // Connect print stream to the output stream p = new PrintStream( out ); p.println (num_atoms_Si + num_atoms_Ox); p.println(); System.out.println( "6c ; O" ); // Data from the Amer. Mineralogy society: Type in mineral "quartz" at http://rruff.geo.arizona.edu/AMS/amcsd.php // x = 0.4135; // y = 0.2669; // z = 0.1191; // That one makes no sense as it is. According to the Navy, it is 0.7854 which is + 2/3 // the value given by Levien-Prewitt // Data from the Navy http://cst-www.nrl.navy.mil/lattice/struk/sio2a.html x = 0.4141; y = 0.2681; z = 0.1187 + 0.6666; // Int. Tables for Cryst. #154, 6c oxygene[ 0][0] = ( x ); oxygene[ 0][1] = ( y ); oxygene[ 0][2] = ( z ); oxygene[ 1][0] = ( -y ); oxygene[ 1][1] = ( x-y ); oxygene[ 1][2] = ( z+2./3. ); oxygene[ 2][0] = ( -x+y ); oxygene[ 2][1] = ( -x ); oxygene[ 2][2] = ( z+1./3. ); oxygene[ 3][0] = ( y ); oxygene[ 3][1] = ( x ); oxygene[ 3][2] = ( -z ); oxygene[ 4][0] = ( -x ); oxygene[ 4][1] = ( -x+y ); oxygene[ 4][2] = ( -z+2./3. ); oxygene[ 5][0] = ( x-y ); oxygene[ 5][1] = ( -y ); oxygene[ 5][2] = ( -z+1./3. ); // Check for the elements outside the unit cell for( i = 0; i < num_atoms_Ox; i++ ) { for( icoord=0; icoord <=2; icoord++) { if (oxygene[i][icoord] >= 1.0) oxygene[i][icoord] -= 1.0; if (oxygene[i][icoord] <= -1.0) oxygene[i][icoord] += 1.0; } } // Transform in cartesian coordinates for( i = 0; i < num_atoms_Ox; i++ ) { Ox_cart[i][0] = aa*(oxygene[i][0]*base[0][0] + oxygene[i][1]*base[1][0] + oxygene[i][2]*base[2][0]); Ox_cart[i][1] = aa*(oxygene[i][0]*base[0][1] + oxygene[i][1]*base[1][1] + oxygene[i][2]*base[2][1]); Ox_cart[i][2] = aa*(oxygene[i][0]*base[0][2] + oxygene[i][1]*base[1][2] + oxygene[i][2]*base[2][2]); } for( i = 0; i < num_atoms_Ox; i++ ) { p.printf ("O %2.8f %2.8f %2.8f %2.8f %2.8f %2.8f\n", oxygene[i][0], oxygene[i][1], oxygene[i][2], Ox_cart[i][0], Ox_cart[i][1], Ox_cart[i][2]); } System.out.println( "3 a ; Si" ); x = 0.4699 ; // Int. Tables for Cryst. #154, 3a: silicon[0][0] = ( x ); silicon[0][1] = ( 0 ); silicon[0][2] = ( 2./3. ); silicon[1][0] = ( 0 ); silicon[1][1] = ( x ); silicon[1][2] = ( 1./3. ); silicon[2][0] = ( -x ); silicon[2][1] = ( -x ); silicon[2][2] = ( 0. ); // Check for the elements outside the unit cell for( i = 0; i < num_atoms_Si; i++ ) { for( icoord=0; icoord <=2; icoord++) { if (silicon[i][icoord] >= 1.0) silicon[i][icoord] -= 1.0; if (silicon[i][icoord] <= -1.0) silicon[i][icoord] += 1.0; } } // Transform in cartesian coordinates for( i = 0; i < num_atoms_Si; i++ ) { Si_cart[i][0] = aa*(silicon[i][0]*base[0][0] + silicon[i][1]*base[1][0] + silicon[i][2]*base[2][0]); Si_cart[i][1] = aa*(silicon[i][0]*base[0][1] + silicon[i][1]*base[1][1] + silicon[i][2]*base[2][1]); Si_cart[i][2] = aa*(silicon[i][0]*base[0][2] + silicon[i][1]*base[1][2] + silicon[i][2]*base[2][2]); } for( i = 0; i< num_atoms_Si; i++ ) { p.printf ("Si %2.8f %2.8f %2.8f %2.8f %2.8f %2.8f\n", silicon[i][0], silicon[i][1], silicon[i][2], Si_cart[i][0], Si_cart[i][1], Si_cart[i][2]); } p.close(); } catch (Exception e) { System.err.println ("Error writing to file alphaQuartz.xyz"); } // supercell generation next try { // Create a new file output stream out = new FileOutputStream("supercell.xyz"); // Connect print stream to the output stream p = new PrintStream( out ); p.println ( (num_atoms_Si + num_atoms_Ox)*(nXcell+1)*(nYcell+1)*(nZcell+1) ); p.println(); // oxygen for(iatom=0 ; iatom < num_atoms_Ox; iatom++ ) { for( i=0 ; i<=nXcell; i++ ) { for( j=0 ; j<=nYcell; j++ ) { for( k=0 ; k<=nZcell; k++ ) { // Transform in cartesian coordinates for( icoord=0; icoord <=2; icoord++) { tempo[icoord] = (oxygene[iatom][0] + i)*base[0][icoord] + (oxygene[iatom][1] + j)*base[1][icoord] + (oxygene[iatom][2] + k)*base[2][icoord]; } p.printf ("O %2.8f %2.8f %2.8f\n",tempo[0]*aa, tempo[1]*aa, tempo[2]*aa); } } } } // silicon for(iatom=0 ; iatom < num_atoms_Si; iatom++ ) { for( i=0 ; i<=nXcell; i++ ) { for( j=0 ; j<=nYcell; j++ ) { for( k=0 ; k<=nZcell; k++ ) { // Transform in cartesian coordinates for( icoord=0; icoord <=2; icoord++) { tempo[icoord] = (silicon[iatom][0] + i)*base[0][icoord] + (silicon[iatom][1] + j)*base[1][icoord] + (silicon[iatom][2] + k)*base[2][icoord]; } p.printf ("Si %2.8f %2.8f %2.8f\n",tempo[0]*aa, tempo[1]*aa, tempo[2]*aa); } } } } p.close(); } catch (Exception e) { System.err.println ("Error writing to file"); } } }