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mytrim_bobmsq.cc
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mytrim_bobmsq.cc
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/***************************************************************************
* Copyright (C) 2008 by Daniel Schwen *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <queue>
#include "simconf.h"
#include "element.h"
#include "material.h"
#include "sample_solid.h"
#include "ion.h"
#include "trim.h"
#include "invert.h"
#include "functions.h"
int main(int argc, char *argv[])
{
char fname[200];
if( argc != 3 )
{
fprintf( stderr, "syntax:\n%s element energy[keV]\n",argv[0] );
return 1;
}
// PKA energy
double E = atof(argv[2])*1000.0;
// seed randomnumber generator from system entropy pool
FILE *urand = fopen( "/dev/random", "r" );
int seed;
fread( &seed, sizeof(int), 1, urand );
fclose( urand );
r250_init( seed<0 ? -seed : seed ); // random generator goes haywire with neg. seed
// initialize global parameter structure and read data tables from file
simconf = new simconfType;
simconf->fullTraj = false;
simconf->tmin = 0.2;
//simconf->tmin = 0.2;
// initialize sample structure
sampleSolid *sample = new sampleSolid( 200.0, 200.0, 200.0 );
// initialize trim engine for the sample
trimBase *trim = new trimBase( sample );
//trimBase *trim = new trimPrimaries( sample );
//sample->bc[0] = sampleBase::CUT; // no PBC in x (just clusterless matrix)
// double atp = 0.1; // 10at% Mo 90at%Cu
double v_sam = sample->w[0] * sample->w[1] * sample->w[2];
double s_sam = sample->w[1] * sample->w[2];
materialBase *material;
elementBase *element;
const char *choice[4] = {"Fe", "Si", "Cu", "Au"};
int i;
for(i=0; i<4 && strcmp(choice[i],argv[1])!=0; ++i);
if(i==4) {
fprintf( stderr, "Element choice not supported: %s\n",argv[1] );
return 1;
}
double A,Z;
switch(i) {
case 0:
// Fe
material = new materialBase( 7.87 ); // rho
element = new elementBase;
Z = 26.0;
A = 56.0;
element->z = Z;
element->m = A;
element->t = 1.0;
element->Edisp = 25.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
break;
case 1:
// Si
material = new materialBase( 2.33 ); // rho
element = new elementBase;
Z = 14.0;
A = 28.0;
element->z = Z;
element->m = A;
element->t = 1.0;
element->Edisp = 25.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
break;
case 2:
// Cu
material = new materialBase( 8.89 ); // rho
element = new elementBase;
Z = 29.0;
A = 63.5;
element->z = Z;
element->m = A;
element->t = 1.0;
element->Edisp = 25.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
break;
case 3:
// Au
material = new materialBase( 19.32 ); // rho
element = new elementBase;
Z = 79.0;
A = 197.0;
element->z = Z;
element->m = A;
element->t = 1.0;
element->Edisp = 25.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
break;
}
const int nstep = 1000;
// create a FIFO for recoils
queue<ionBase*> recoils;
double norm;
massInverter *m = new massInverter;
energyInverter *e = new energyInverter;
double A1, A2, Etot, E1, E2;
int Z1, Z2;
double pos1[3], pos2[3];
ionBase *ff1, *pka;
int id = 1;
// squared displacement
double sqd = 0.0, sqd2 = 0.0;
// main loop
for( int n = 0; n < nstep; n++ )
{
if( n % 10 == 0 ) fprintf( stderr, "pka #%d\n", n+1 );
ff1 = new ionBase;
ff1->gen = 0; // generation (0 = PKA)
ff1->tag = -1;
ff1->id = simconf->id++;
ff1->z1 = Z;
ff1->m1 = A;
ff1->e = E;
ff1->dir[0] = 1;
ff1->dir[1] = 0;
ff1->dir[2] = 0;
ff1->pos[0] = 0;
ff1->pos[1] = sample->w[1] / 2.0;
ff1->pos[2] = sample->w[2] / 2.0;
ff1->set_ef();
recoils.push( ff1 );
while( !recoils.empty() )
{
pka = recoils.front();
recoils.pop();
sample->averages( pka );
// store position
if( pka->gen > 0 )
for( int i = 0; i < 3; i++ )
pos2[i] = pka->pos[i];
// follow this ion's trajectory and store recoils
trim->trim( pka, recoils );
// do ion analysis/processing AFTER the cascade here
if( pka->gen > 0 )
for( int i = 0; i < 3; i++ )
sqd += (pos2[i]-pka->pos[i])*(pos2[i]-pka->pos[i]);
else if( pka->gen > 1 )
for( int i = 0; i < 3; i++ )
sqd2 += (pos2[i]-pka->pos[i])*(pos2[i]-pka->pos[i]);
// done with this recoil
delete pka;
}
}
// output full damage data
printf( "total sum of square displacements: %g Ang^2\n", sqd );
printf( "%d vacancies per %d ions = %d vac/ion\n", simconf->vacancies_created, nstep, simconf->vacancies_created/nstep );
double surf = sample->w[1] * sample->w[2];
double natom = v_sam * sample->material[0]->arho;
printf( "volume = %f Ang^3, surface area = %f Ang^2, containing %f atoms => %f dpa/(ion/Ang^2)\n",
v_sam, s_sam, natom, simconf->vacancies_created / ( natom * nstep/s_sam ) );
printf( "sqd/dpa = %g\n sqd/vac = %g\n sqd2/vac = %g\nnvac = %d", sqd/(simconf->vacancies_created/natom), sqd/simconf->vacancies_created, sqd2/simconf->vacancies_created,simconf->vacancies_created );
/*
// calculate modified kinchin pease data http://www.iue.tuwien.ac.at/phd/hoessinger/node47.html
// just for the PKA
double Zatoms = 26.0, Matoms = 56.0;
double Epka = 5.0e6;
double ed = 0.0115 * pow( Zatoms, -7.0/3.0) * Epka;
double g = 3.4008 * pow( ed, 1.0/6.0 ) + 0.40244 * pow( ed, 3.0/4.0 ) + ed;
double kd = 0.1337 * pow( Zatoms, 2.0/3.0 ) / pow( Matoms, 0.5); //Z,M
double Ev = Epka / ( 1.0 + kd * g );
double Ed = 40.0;
printf( "%f modified PKA kinchin-pease vacancies per 100 ions = %f vac/ion\n",
100*0.8*Ev/(2.0*Ed), 0.8*Ev/(2.0*Ed) );
// do Kinchin-Pease for all primary recoils
printf( "%f modified 1REC kinchin-pease vacancies per 100 ions = %f vac/ion\n",
simconf->KP_vacancies, simconf->KP_vacancies / 100.0 );
*/
return EXIT_SUCCESS;
}