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mytrim_ODS.cc
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mytrim_ODS.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 <stdlib.h>
#include <queue>
#include "simconf.h"
#include "element.h"
#include "material.h"
#include "sample_clusters.h"
#include "ion.h"
#include "trim.h"
#include "invert.h"
#include "functions.h"
int main(int argc, char *argv[])
{
char fname[200];
if( argc != 4 ) // 2
{
fprintf( stderr, "syntax:\nmytrim_ODS basename r Cbfactor\n\nCbfactor=1 => 1.5e-4 clusters/nm^3\n" );
return 1;
}
// 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 []
//sampleClusters *sample = new sampleClusters( 50000.0, 400.0, 400.0 );
sampleClusters *sample = new sampleClusters( 500.0, 1000.0, 1000.0 );
// initialize trim engine for the sample
snprintf( fname, 199, "%s.phon", argv[1] );
//FILE *phon = fopen( fname, "wt" );
//trimPhononOut *trim = new trimPhononOut( sample, phon );
trimBase *trim = new trimBase( sample );
//trimBase *trim = new trimPrimaries( sample );
//double r = 10.0;
double r = atof( argv[2] ); //10.0;
double Cbf = atof( argv[3] );
sample->bc[0] = sampleBase::INF; // no PBC in x (just clusterless matrix)
sample->initSpatialhash( int( sample->w[0] / r ) - 1,
int( sample->w[1] / r ) - 1,
int( sample->w[2] / r ) - 1 );
// double atp = 0.1; // 10at% Mo 90at%Cu
double v_sam = sample->w[0] * sample->w[1] * sample->w[2];
double v_cl = 4.0/3.0 * M_PI * cub(r);
int n_cl; // = atp * scoef[29-1].atrho * v_sam / ( v_cl * ( ( 1.0 - atp) * scoef[42-1].atrho + atp * scoef[29-1].atrho ) );
n_cl = v_sam * 1.5e-7 * Cbf ; // Allen08 1.5e-4/nm^3
//fprintf( stderr, "adding %d clusters to reach %fat%% Mo\n", n_cl, atp * 100.0 );
// cluster surfaces must be at least 25.0 Ang apart
fprintf( stderr, "adding %d clusters...\n", n_cl );
sample->addRandomClusters( n_cl, r, 15.0 );
// write cluster coords with tag numbers
snprintf( fname, 199, "%s.clcoor", argv[1] );
FILE *ccf = fopen( fname, "wt" );
for( int i = 0; i < sample->cn; i++)
fprintf( ccf, "%f %f %f %f %d\n", sample->c[0][i], sample->c[1][i], sample->c[2][i], sample->c[3][i], i );
fclose( ccf );
fprintf( stderr, "sample built.\n" );
//return 0;
materialBase *material;
elementBase *element;
/*
// Fe
material = new materialBase( 7.87 ); // rho
element = new elementBase;
element->z = 26; // Fe
element->m = 56.0;
element->t = 1.0;
element->Edisp = 40.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
*/
// Cu
material = new materialBase( 8.94 ); // rho
element = new elementBase;
element->z = 29; // Fe
element->m = 63.0;
element->t = 1.0;
element->Edisp = 40.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
/*
// ZrO2
material = new materialBase( 5.68 ); // rho
element = new elementBase;
element->z = 40; // Zr
element->m = 91.0;
element->t = 1.0;
material->element.push_back( element );
element = new elementBase;
element->z = 8; // O
element->m = 16.0;
element->t = 2.0;
material->element.push_back( element );
material->prepare(); // all materials added
sample->material.push_back( material ); // add material to sample
// TiO2 precipitate
material = new materialBase( 4.23 ); // rho
element = new elementBase;
element->z = 22; // Ti
element->m = 48.0;
element->t = 1.0;
material->element.push_back( element );
element = new elementBase;
element->z = 8; // O
element->m = 16.0;
element->t = 2.0;
material->element.push_back( element );
material->prepare();
sample->material.push_back( material ); // add material to sample
// Y2Ti2O7 precipitate
material = new materialBase( 4.6 ); // rho between 4.23 and 5.01
element = new elementBase;
element->z = 39; // Y
element->m = 89.0;
element->t = 2.0;
element->Edisp = 57.0;
material->element.push_back( element );
element = new elementBase;
element->z = 22; // Ti
element->m = 48.0;
element->t = 2.0;
element->Edisp = 57.0;
material->element.push_back( element );
element = new elementBase;
element->z = 8; // O
element->m = 16.0;
element->t = 7.0;
element->Edisp = 57.0;
material->element.push_back( element );
material->prepare();
sample->material.push_back( material ); // add material to sample
*/
/*
// xe bubble
material = new materialBase( 3.5 ); // rho
element = new elementBase;
element->z = 54; // Xe
element->m = 132.0;
element->t = 1.0;
material->element.push_back( element );
material->prepare();
sample->material.push_back( material ); // add material to sample
*/
// TiB2 precipitate
material = new materialBase( 4.52 ); // rho
element = new elementBase;
element->z = 22; // Ti
element->m = 48.0;
element->t = 1.0;
material->element.push_back( element );
element = new elementBase;
element->z = 5; // B
element->m = 11.0;
element->t = 2.0;
material->element.push_back( element );
material->prepare();
sample->material.push_back( material ); // add material to sample
const int nstep = 1000;
// create a FIFO for recoils
queue<ionBase*> recoils;
double norm;
double jmp = 2.7; // diffusion jump distance
int jumps;
double dif[3], dif2[3];
double A1, A2, Etot, E1, E2;
int Z1, Z2;
snprintf( fname, 199, "%s.Erec", argv[1] );
FILE *erec = fopen( fname, "wt" );
snprintf( fname, 199, "%s.dist", argv[1] );
FILE *rdist = fopen( fname, "wt" );
double pos1[3], pos2[3];
ionMDtag *ff1, *pka;
int id = 1;
double A = 84.0, E = 1.8e6; int Z = 36; // 1.8MeV Kr
//double A = 58.0, E = 5.0e6; int Z = 28; // 5MeV Ni
//double A = 56.0, E = 5.0e6; int Z = 26; // 5MeV Fe
// 1000 ions
for( int n = 0; n < nstep; n++ )
{
if( n % 10 == 0 ) fprintf( stderr, "pka #%d\n", n+1 );
ff1 = new ionMDtag;
ff1->gen = 0; // generation (0 = PKA)
ff1->tag = -1;
ff1->md = 0;
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 = dynamic_cast<ionMDtag*>(recoils.front());
recoils.pop();
sample->averages( pka );
// do ion analysis/processing BEFORE the cascade here
//fprintf( erec, "%f\t%d\t%d\n", pka->e, pka->gen, pka->md );
// pka is O or Ti
//if( pka->z1 == 8 || pka->z1 == 22 || pka->z1 == 39 )
// pka is Xe
//if( pka->z1 == 54 )
// pka is B or Ti
if( pka->z1 == 5 || pka->z1 == 22 )
{
if( pka->gen > 0 )
{
// output energy and recoil generation
fprintf( erec, "%f\t%d\t%d\n", pka->e, pka->gen, pka->md );
}
if( pka->tag >= 0 )
{
for( int i = 0; i < 3; i++ )
{
dif[i] = sample->c[i][pka->tag] - pka->pos[i];
pos2[i] = pka->pos[i];
if( sample->bc[i] == sampleBase::PBC ) dif[i] -= round( dif[i] / sample->w[i] ) * sample->w[i];
pos1[i] = pka->pos[i] + dif[i];
//printf( "%f\t%f\t%f\n", sample->c[i][pka->tag], pka->pos[i], pos1[i] );
}
//printf( "\n" );
//if(pka->z1 == 54 && pka->gen > 0 && pka->tag >= 0 ) printf( "clust %f %f %f %d", pos1[0], pos1[1], pos1[2], pka->id );
}
}
// follow this ion's trajectory and store recoils
// printf( "%f\t%d\n", pka->e, pka->z1 );
//pka->md = id++;
trim->trim( pka, recoils );
// do ion analysis/processing AFTER the cascade here
// pka is O or Ti
//if( pka->z1 == 8 || pka->z1 == 22 || pka->z1 == 39 )
// pka is Xe
//if( pka->z1 == 54 )
// pka is B or Ti
if( pka->z1 == 5 || pka->z1 == 22 )
{
// output
//printf( "%f %f %f %d\n", pka->pos[0], pka->pos[1], pka->pos[2], pka->tag );
// print out distance to cluster of origin center (and depth of recoil)
if( pka->tag >= 0 )
{
for( int i = 0; i < 3; i++ )
{
dif[i] = pos1[i] - pka->pos[i]; // distance to cluster center
dif2[i] = pos2[i] - pka->pos[i]; // total distance it moved
}
fprintf( rdist, "%f %d %f %f %f %f\n", sqrt( v_dot( dif, dif ) ), pka->z1, pka->pos[0], pka->pos[1], pka->pos[2], sqrt( v_dot( dif2, dif2 ) ) );
}
// do a random walk
/* jumps = 0;
do
{
material = sample->lookupLayer( pka->pos );
if( material->tag >= 0 ) break;
do
{
for( int i = 0; i < 3; i++ ) pka->dir[i] = dr250() - 0.5;
norm = v_dot( pka->dir, pka->dir );
}
while( norm <= 0.0001 );
v_scale( pka->dir, jmp / sqrtf( norm ) );
for( int i = 0; i < 3; i++ ) pka->pos[i] += pka->dir[i];
jumps++;
}
while ( pka->pos[0] > 0 && pka->pos[0] < sample->w[0] );
if( material->tag >= 0 && jumps > 0 )
fprintf( stderr, "walked to cluster %d (originated at %d, %d jumps)\n", material->tag, pka->tag, jumps ); */
}
// done with this recoil
delete pka;
// this should rather be done with spawnRecoil returning false
//if( simconf->primariesOnly ) while( !recoils.empty() ) { delete recoils.front(); recoils.pop(); };
}
}
fclose( rdist );
fclose( erec );
// output full damage data
printf( "%d vacancies per %d ions = %d vac/ion\n", simconf->vacancies_created, nstep, simconf->vacancies_created/nstep );
/*
// 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;
}