// Set flags for this material being rigid and for if it ignores cracks
// Not that ignoring cracks only works for multimaterial mode. Rigid contact
// materials default to ignoring cracks while non rigid default to see them
int MaterialBase::GetMVFFlags(int matfld)
{ // check number errors
if(matfld>=(int)fieldMatIDs.size()) return 0;
MaterialBase *matID = theMaterials[fieldMatIDs[matfld]];
int flags = matID->Rigid() ? RIGID_FIELD_BIT : 0 ;
return flags;
}
// Archive the results if it is time
void ArchiveData::ArchiveHistoryFile(double atime,vector< int > quantity)
{
char fname[300],fline[600],subline[100];
// get relative path name to the file
sprintf(fname,"%s%s_History_%d.txt",outputDir,archiveRoot,fmobj->mstep);
// open the file
ofstream afile;
afile.open(fname, ios::out);
if(!afile.is_open())
FileError("Cannot open a particle history archive file",fname,"ArchiveData::ArchiveHistoryFile");
// header line
afile << "Particle History Data File" << endl;
// title
sprintf(fline,"step:%d time:%15.7e ms",fmobj->mstep,1000.*atime);
afile << fline << endl;
strcpy(fline,"#\tx\ty");
if(threeD) strcat(fline,"\tz");
unsigned int q;
for(q=0;q<quantity.size();q++)
{ sprintf(subline,"\t%d",quantity[q]);
strcat(fline,subline);
}
afile << fline << endl;
// each particle
int p;
for(p=0;p<nmpms;p++)
{ // number and position
afile << p+1 << "\t" << mpm[p]->pos.x << "\t" << mpm[p]->pos.y ;
if(threeD) afile << "\t" << mpm[p]->pos.z ;
// history data
MaterialBase *matptr = theMaterials[mpm[p]->MatID()];
char *hptr = mpm[p]->GetHistoryPtr();
for(q=0;q<quantity.size();q++)
{ afile << "\t" << matptr->GetHistory(quantity[q],hptr);
}
afile << endl;
}
// close the file
afile.close();
if(afile.bad())
FileError("File error closing a particle history archive file",fname,"ArchiveData::ArchiveHistoryFile");
}
MaterialBase *
SampleDynamic::lookupMaterial(Point & pos)
{
// std::cout << "lookuplayer" << std::endl;
MaterialBase * m = material[lookupLayer(pos)];
// std::cout << m << ' ' << m->_arho << ' ' << m->am << ' ' << m->az << ' ' << m->mu << std::endl;
// on-demand update
if (m->_dirty)
{
// std::cout << "on demand aver" << std::endl;
m->average(pka);
// std::cout << m << ' ' << m->_arho << ' ' << m->am << ' ' << m->az << ' ' << m->mu <<
// std::endl;
}
return m;
}
// Adjust time step now
CustomTask *CarnotCycle::StepCalculation(void)
{
int p;
MaterialBase *matID;
double Vrel = 0.;
int numgas = 0;
double Tgas = 0.;
// loop over nonrigid material points
for(p=0;p<nmpmsNR;p++)
{ numgas++;
Vrel += mpm[p]->GetRelativeVolume();
Tgas += mpm[p]->pPreviousTemperature;
}
// get averages
Vrel /= (double)numgas;
Tgas /= (double)numgas;
switch(carnotStep)
{ case 0:
carnotStep = 1;
cout << "# Step 1: isothermal expansion" << endl;
ConductionTask::adiabatic = FALSE;
break;
case 1:
// stop when Vrel reaches V1rel
if(Vrel >= V1rel)
{ // switch to adibatic expanion
carnotStep = 2;
ConductionTask::adiabatic = TRUE;
cout << "# Step 2: adibatic expansion" << endl;
}
break;
case 2:
// stop when T cools to T2
if(Tgas<=T2)
{ // switch to pause
carnotStep = 3;
ConductionTask::adiabatic = FALSE;
V2rel = Vrel;
// find velocity
for(p=0;p<nmpms;p++)
{ // verify material is defined and sets if field number (in in multimaterial mode)
matID=theMaterials[mpm[p]->MatID()]; // material object for this particle
if(matID->Rigid())
mpm[p]->ReverseParticle(false,false);
else
mpm[p]->StopParticle();
}
// estimate next volume
if(V3rel<1.)
V3rel = V2rel/V1rel;
cout << "# Step 2: isothermal compression to " << V3rel << "*V0" << endl;
}
break;
case 3:
// stop when Vrel reaches V3rel
if(Vrel <= V3rel)
{ // switch to adibatic compression
carnotStep = 4;
ConductionTask::adiabatic = TRUE;
cout << "# Step 4: adibatic compression" << endl;
}
break;
case 4:
// done when T increases to thermal.reference, or when volume returns to 1
if(Tgas>=thermal.reference)
throw CommonException("Carnot cycle is complete","CarnotCycle::StepCalculation()");
//if(Vrel<=1.)
// throw CommonException("Carnot cycle is complete","CarnotCycle::StepCalculation()");
break;
default:
break;
}
return nextTask;
}
// when set, return total number of materials if this is a new one, or 1 if not in multimaterial mode
// not thread safe due to push_back()
int MaterialBase::SetField(int fieldNum,bool multiMaterials,int matid,int &activeNum)
{ if(!multiMaterials)
{ if(field<0)
{ field=0;
activeField=activeNum;
fieldNum=1;
activeNum++;
activeMatIDs.push_back(matid);
int altBuffer,matBuffer = SizeOfMechanicalProperties(altBuffer);
if(matBuffer > maxPropertyBufferSize) maxPropertyBufferSize = matBuffer;
if(altBuffer > maxAltBufferSize) maxAltBufferSize = altBuffer;
}
}
else
{ if(field<0)
{ // if sharing a field, look up shared material.
if(shareMatField>0)
{ if(shareMatField>nmat)
{ throw CommonException("Material class trying to share velocity field with an undefined material type",
"MaterialBase::SetField");
}
// must match for rigid feature
MaterialBase *matRef = theMaterials[shareMatField-1];
if(matRef->Rigid() != Rigid())
{ throw CommonException("Material class trying to share velocity field with an incompatible material type",
"MaterialBase::SetField");
}
// base material cannot share too
if(matRef->GetShareMatField()>=0)
{ throw CommonException("Material class trying to share velocity field with a material that share's its field",
"MaterialBase::SetField");
}
// set field to other material (and set other material if needed
field = matRef->GetField();
if(field<0)
{ fieldNum = matRef->SetField(fieldNum,multiMaterials,shareMatField-1,activeNum);
field = fieldNum-1;
}
}
else
{ field=fieldNum;
fieldNum++;
// fieldMatIDs[i] for i=0 to # materials is material index for that material velocity field
// when materials share fields, it points to the based shared material
fieldMatIDs.push_back(matid);
}
// for first particle using this material, add to active material IDs and check required
// material buffer sizes
if(activeNum>=0)
{ activeField=activeNum;
activeNum++;
activeMatIDs.push_back(matid);
int altBuffer,matBuffer = SizeOfMechanicalProperties(altBuffer);
if(matBuffer > maxPropertyBufferSize) maxPropertyBufferSize = matBuffer;
if(altBuffer > maxAltBufferSize) maxAltBufferSize = altBuffer;
}
}
}
return fieldNum;
}
// increment external load on a particle
// input is analysis time in seconds
// (only called when diffusion is active)
MatPtFluxBC *MatPtFluxBC::AddMPFlux(double bctime)
{
// condition value is g/(mm^2-sec), Divide by rho*csat to get potential flux in mm/sec
// find this flux and then add (times area) to get mm^3-potential/sec
MPMBase *mpmptr = mpm[ptNum-1];
MaterialBase *matptr = theMaterials[mpmptr->MatID()];
// Flux is a scalar and we need int_(face) F Ni(x) dA
// Since F is constant, only need integral which is done by CPDI methods
// which has be generalized to work for GIMP too
// We use X_DIRECTION for bcDIR for efficiency. For Silent BC, change to
// Normal direction to all caculation of n
Vector fluxMag;
ZeroVector(&fluxMag);
int bcDir=X_DIRECTION;
if(style==SILENT)
{ TransportProperties t;
matptr->GetTransportProps(mpmptr,fmobj->np,&t);
Tensor *D = &(t.diffusionTensor);
// D in mm^2/sec, Dc in 1/mm
if(fmobj->IsThreeD())
{ fluxMag.x = D->xx*mpmptr->pDiffusion[gGRADx] + D->xy*mpmptr->pDiffusion[gGRADy] + D->xz*mpmptr->pDiffusion[gGRADz];
fluxMag.y = D->xy*mpmptr->pDiffusion[gGRADx] + D->yy*mpmptr->pDiffusion[gGRADy] + D->yz*mpmptr->pDiffusion[gGRADz];
fluxMag.z = D->xz*mpmptr->pDiffusion[gGRADx] + D->yz*mpmptr->pDiffusion[gGRADy] + D->zz*mpmptr->pDiffusion[gGRADz];
}
else
{ fluxMag.x = D->xx*mpmptr->pDiffusion[gGRADx] + D->xy*mpmptr->pDiffusion[gGRADy];
fluxMag.y = D->xy*mpmptr->pDiffusion[gGRADx] + D->yy*mpmptr->pDiffusion[gGRADy];
}
bcDir = N_DIRECTION;
}
else if(direction==EXTERNAL_FLUX)
{ // csatrho = rho0 V0 csat/V (units g/mm^3)
double csatrho = mpmptr->GetRho()*mpmptr->GetConcSaturation()/mpmptr->GetRelativeVolume();
fluxMag.x = BCValue(bctime)/csatrho;
}
else
{ // coupled surface flux and ftime is bath concentration
// time variable (t) is replaced by c-cbath, where c is the particle potential and cbath is bath potential
varTime = mpmptr->pPreviousConcentration-GetBCFirstTime();
GetPosition(&varXValue,&varYValue,&varZValue,&varRotValue);
double currentValue = fabs(scale*function->Val());
if(varTime>0.) currentValue=-currentValue;
// csatrho = rho0 V0 csat/V (units g/mm^3)
double csatrho = mpmptr->GetRho()*mpmptr->GetConcSaturation()/mpmptr->GetRelativeVolume();
fluxMag.x = currentValue/csatrho;
}
// get corners and direction from material point
int cElem[4],numDnds;
Vector corners[4],tscaled;
double ratio = mpmptr->GetTractionInfo(face,bcDir,cElem,corners,&tscaled,&numDnds);
// compact CPDI nodes into list of nodes (nds) and final shape function term (fn)
// May need up to 8 (in 3D) for each of the numDnds (2 in 2D or 4 in 3D)
int nds[8*numDnds+1];
double fn[8*numDnds+1];
int numnds = CompactCornerNodes(numDnds,corners,cElem,ratio,nds,fn);
// add force to each node
int i;
for(i=1;i<=numnds;i++)
diffusion->AddFluxCondition(nd[nds[i]],DotVectors(&fluxMag,&tscaled)*fn[i],false);
return (MatPtFluxBC *)GetNextObject();
}
int
main(int argc, char * argv[])
{
if (argc != 3)
{
fprintf(stderr, "syntax:\n%s element energy[keV]\n", argv[0]);
return 1;
}
// PKA energy
Real E = atof(argv[2]) * 1000.0;
// seed random number generator from system entropy pool
FILE * urand = fopen("/dev/random", "r");
unsigned int seed;
if (fread(&seed, sizeof(unsigned int), 1, urand) != 1)
return 1;
fclose(urand);
// initialize global parameter structure and read data tables from file
SimconfType * simconf = new SimconfType(seed);
simconf->fullTraj = false;
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(simconf, sample);
// TrimBase *trim = new TrimPrimaries(sample);
// sample->bc[0] = SampleBase::CUT; // no PBC in x (just clusterless matrix)
// Real atp = 0.1; // 10at% Mo 90at%Cu
Real v_sam = sample->w[0] * sample->w[1] * sample->w[2];
Real s_sam = sample->w[1] * sample->w[2];
MaterialBase * material;
Element 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;
}
Real A, Z;
switch (i)
{
case 0:
// Fe
material = new MaterialBase(simconf, 7.87); // rho
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(simconf, 2.33); // rho
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(simconf, 8.89); // rho
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(simconf, 19.32); // rho
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;
default:
return 1;
}
const int nstep = 1000;
// create a FIFO for recoils
std::queue<IonBase *> recoils;
Point pos2;
IonBase *ff1, *pka;
// squared displacement
Real 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->_Z = Z;
ff1->_m = 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->setEf();
recoils.push(ff1);
while (!recoils.empty())
{
pka = recoils.front();
recoils.pop();
sample->averages(pka);
// store position
if (pka->_gen > 0)
pos2 = pka->_pos;
// follow this ion's trajectory and store recoils
trim->trim(pka, recoils);
// do ion analysis/processing AFTER the cascade here
if (pka->_gen > 0)
sqd += (pos2 - pka->_pos).norm_sq();
else if (pka->_gen > 1)
sqd2 += (pos2 - pka->_pos).norm_sq();
// 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);
Real 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
Real Zatoms = 26.0, Matoms = 56.0;
Real Epka = 5.0e6;
Real ed = 0.0115 * std::pow(Zatoms, -7.0/3.0) * Epka;
Real g = 3.4008 * std::pow(ed, 1.0/6.0) + 0.40244 * std::pow(ed, 3.0/4.0) + ed;
Real kd = 0.1337 * std::pow(Zatoms, 2.0/3.0) / std::pow(Matoms, 0.5); //Z, M
Real Ev = Epka / (1.0 + kd * g);
Real 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;
}
int
main(int argc, char * argv[])
{
char fname[200];
if (argc != 2)
{
fprintf(stderr, "syntax:\n%s basename\n", argv[0]);
return 1;
}
// seed random number generator from system entropy pool
FILE * urand = fopen("/dev/random", "r");
unsigned int seed;
if (fread(&seed, sizeof(unsigned int), 1, urand) != 1)
return 1;
fclose(urand);
// initialize global parameter structure and read data tables from file
SimconfType * simconf = new SimconfType(seed);
simconf->fullTraj = false;
simconf->tmin = 0.2;
// initialize sample structure
SampleSolid * sample = new SampleSolid(200.0, 200.0, 200.0);
// 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(simconf, sample);
sample->bc[0] = SampleBase::CUT; // no PBC in x (just clusterless matrix)
// Real atp = 0.1; // 10at% Mo 90at%Cu
Real v_sam = sample->w[0] * sample->w[1] * sample->w[2];
Real s_sam = sample->w[1] * sample->w[2];
MaterialBase * material;
Element element;
/*
// Fe
material = new MaterialBase(simconf, 7.87); // rho
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
// ZrO2
material = new MaterialBase(simconf, 5.68); // rho
element._Z = 40; // Zr
element._m = 91.0;
element._t = 1.0;
material->_element.push_back(element);
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
*/
// ZrO2 Xe 0.01
material = new MaterialBase(simconf, 5.68); // rho
element._Z = 40; // Zr
element._m = 90.0; // 91?
element._t = 1.0;
material->_element.push_back(element);
element._Z = 8; // O
element._m = 16.0;
element._t = 2.0;
material->_element.push_back(element);
/*element._Z = 54; // Xe
element._m = 132.0;
element._t = 0.01;
material->_element.push_back(element);*/
material->prepare(); // all materials added
sample->material.push_back(material); // add material to sample
/*
// TiO2 precipitate
material = new MaterialBase(simconf, 4.23); // rho
element._Z = 22; // Ti
element._m = 48.0;
element._t = 1.0;
material->_element.push_back(element);
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(simconf, 4.6); // rho between 4.23 and 5.01
element._Z = 39; // Y
element._m = 89.0;
element._t = 2.0;
element._Edisp = 57.0;
material->_element.push_back(element);
element._Z = 22; // Ti
element._m = 48.0;
element._t = 2.0;
element._Edisp = 57.0;
material->_element.push_back(element);
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(simconf, 3.5); // rho
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
*/
const int nstep = 10000;
// create a FIFO for recoils
std::queue<IonBase *> recoils;
Real dif2[3];
snprintf(fname, 199, "%s.Erec", argv[1]);
FILE * erec = fopen(fname, "wt");
snprintf(fname, 199, "%s.dist", argv[1]);
FILE * rdist = fopen(fname, "wt");
Real pos2[3];
IonBase *ff1, *pka;
// Real A = 84.0, E = 1.8e6; int Z = 36; // 1.8MeV Kr
Real A = 131.0, E = 2.0e4;
int Z = 54; // 20keV Xe
// Real A = 58.0, E = 5.0e6; int Z = 28; // 5MeV Ni
// Real A = 56.0, E = 5.0e6; int Z = 26; // 5MeV Fe
// 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->_Z = Z;
ff1->_m = 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->setEf();
recoils.push(ff1);
while (!recoils.empty())
{
pka = 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->_Z == 8 || pka->_Z == 22 || pka->_Z == 39)
// pka is Xe
Real oerec = pka->_E;
if (pka->_Z == 542)
{
if (pka->_gen > 0)
{
// output energy and recoil generation
// fprintf(erec, "%f\t%d\t%d\n", pka->_E, pka->_gen, pka->_md);
}
for (int i = 0; i < 3; ++i)
{
pos2[i] = pka->_pos(i);
}
}
// follow this ion's trajectory and store recoils
// printf("%f\t%d\n", pka->_E, pka->_Z);
// pka->_md = id++;
trim->trim(pka, recoils);
fprintf(rdist, "%f 1\n", pka->_pos(0));
// do ion analysis/processing AFTER the cascade here
// pka is O or Ti
// if (pka->_Z == 8 || pka->_Z == 22 || pka->_Z == 39)
// pka is Xe
if (pka->_Z == 542)
{
// 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)
for (int i = 0; i < 3; ++i)
{
dif2[i] = pos2[i] - pka->_pos(i); // total distance it moved
}
fprintf(rdist,
"%d %f %f %f %f %f\n",
pka->_Z,
pos2[0],
pos2[1],
pos2[2],
std::sqrt(v_dot(dif2, dif2)),
oerec);
}
// 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);
Real 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)",
v_sam,
s_sam,
natom,
simconf->vacancies_created / (natom * nstep / s_sam));
/*
// calculate modified kinchin pease data http://www.iue.tuwien.ac.at/phd/hoessinger/node47.html
// just for the PKA
Real Zatoms = 26.0, Matoms = 56.0;
Real Epka = 5.0e6;
Real ed = 0.0115 * std::pow(Zatoms, -7.0/3.0) * Epka;
Real g = 3.4008 * std::pow(ed, 1.0/6.0) + 0.40244 * std::pow(ed, 3.0/4.0) + ed;
Real kd = 0.1337 * std::pow(Zatoms, 2.0/3.0) / std::pow(Matoms, 0.5); //Z, M
Real Ev = Epka / (1.0 + kd * g);
Real 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;
}
int
main(int argc, char * argv[])
{
char fname[200];
if (argc != 4) // 2
{
fprintf(
stderr, "syntax:\n%s basename r Cbfactor\n\nCbfactor=1 => 7e-4 bubbles/nm^3\n", argv[0]);
return 1;
}
// seed random number generator from system entropy pool
FILE * urand = fopen("/dev/random", "r");
unsigned int seed;
if (fread(&seed, sizeof(unsigned int), 1, urand) != 1)
return 1;
fclose(urand);
// initialize global parameter structure and read data tables from file
SimconfType * simconf = new SimconfType(seed);
simconf->fullTraj = false;
simconf->tmin = 0.2;
// initialize sample structure
sampleClusters * sample = new sampleClusters(400.0, 400.0, 400.0);
// 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(simconf, sample);
// TrimBase *trim = new TrimPrimaries(sample);
// Real r = 10.0;
Real r = atof(argv[2]); // 10.0;
Real Cbf = atof(argv[3]);
// sample->bc[0] = CUT; // no pbc in x dir
sample->initSpatialhash(
int(sample->w[0] / r) - 1, int(sample->w[1] / r) - 1, int(sample->w[2] / r) - 1);
Real v_sam = sample->w[0] * sample->w[1] * sample->w[2];
int n_cl;
n_cl = v_sam * 7.0e-7 * Cbf; // Ola06 7e-4/nm^3
fprintf(stderr, "adding %d clusters...\n", n_cl);
// cluster surfaces must be at least 25.0 Ang apart
sample->addRandomClusters(n_cl, r, 15.0, simconf);
// 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");
MaterialBase * material;
Element element;
// UO2
material = new MaterialBase(simconf, 10.0); // rho
element._Z = 92; // U
element._m = 235.0;
element._t = 1.0;
material->_element.push_back(element);
element._Z = 16; // O
element._m = 32.0;
element._t = 2.0;
material->_element.push_back(element);
material->prepare(); // all materials added
sample->material.push_back(material); // add material to sample
// xe bubble
material = new MaterialBase(simconf, 3.5); // rho
element._Z = 54; // Xe
element._m = 132.0;
element._t = 1.0;
// element._t = 0.002;
material->_element.push_back(element);
material->prepare();
sample->material.push_back(material); // add material to sample
// sample->material.push_back(material); // add material to sample
// create a FIFO for recoils
std::queue<IonBase *> recoils;
Real norm;
Point dif, dif2;
MassInverter * m = new MassInverter;
EnergyInverter * e = new EnergyInverter;
Real 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");
Point pos1, pos2;
IonMDTag *ff1, *ff2, *pka;
// 1000 fission events
for (int n = 0; n < 1000; n++) // 2000 ff
{
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++;
// generate fission fragment data
A1 = m->x(simconf->drand());
// A1 = 131;
A2 = 235.0 - A1;
Etot = e->x(simconf->drand());
E1 = Etot * A2 / (A1 + A2);
// E1 = 100;
E2 = Etot - E1;
Z1 = round((A1 * 92.0) / 235.0);
// Z1 = 54;
Z2 = 92 - Z1;
ff1->_Z = Z1;
ff1->_m = A1;
ff1->_E = E1 * 1.0e6;
// ff1->_Z = 53;
// ff1->_m = 127;
// ff1->_E = 70.0 * 1.0e6;
do
{
for (int i = 0; i < 3; ++i)
ff1->_dir(i) = simconf->drand() - 0.5;
norm = ff1->_dir.norm_sq();
} while (norm <= 0.0001 || norm > 0.25);
/*
norm = 1.0;
ff1->_dir(0) = 1.0;
ff1->_dir(1) = 0.0;
ff1->_dir(2) = 0.0;
*/
ff1->_dir /= std::sqrt(norm);
// random origin (outside cluster!)
do
{
for (int i = 0; i < 3; ++i)
ff1->_pos(i) = simconf->drand() * sample->w[i];
} while (sample->lookupCluster(ff1->_pos) >= 0);
ff1->setEf();
recoils.push(ff1);
ff2 = new IonMDTag(*ff1); // copy constructor
// ff1->_id = simconf->_id++;
// reverse direction
ff2->_dir = -ff2->_dir;
ff2->_Z = Z2;
ff2->_m = A2;
ff2->_E = E2 * 1.0e6;
ff2->setEf();
recoils.push(ff2);
// fprintf(stderr, "A1=%f Z1=%d (%f MeV)\tA2=%f Z2=%d (%f MeV)\n", A1, Z1, E1, A2, Z2, E2);
while (!recoils.empty())
{
pka = dynamic_cast<IonMDTag *>(recoils.front());
recoils.pop();
sample->averages(pka);
// do ion analysis/processing BEFORE the cascade here
if (pka->_Z == 54)
{
// mark the first recoil that falls into the MD energy gap with 1 (child generations
// increase the number)
if (pka->_E > 200 && pka->_E < 12000 && pka->_md == 0)
pka->_md = 1;
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->_Z == 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->_Z);
// pka->_md = id++;
// printf("\nstart %f %f %f %d %d %d\n", pka->_pos(0), pka->_pos(1), pka->_pos(2), pka->_Z,
// pka->_md, pka->_id);
trim->trim(pka, recoils);
// fprintf(phon, "%f %f %f %f %d %d\n", pka->_E, pka->_pos(0), pka->_pos(1), pka->_pos(2),
// pka->_Z, pka->_id);
// do ion analysis/processing AFTER the cascade here
// pka is Xe
if (pka->_Z == 54)
{
// 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)
{
dif = pos1 - pka->_pos; // distance to cluster center
dif2 = pos2 - pka->_pos; // total distance it moved
fprintf(rdist,
"%f %d %f %f %f %f\n",
dif.norm(),
pka->_md,
pka->_pos(0),
pka->_pos(1),
pka->_pos(2),
dif2.norm());
}
// 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) = simconf->drand() - 0.5;
norm = v_dot(pka->_dir, pka->_dir);
}
while (norm <= 0.0001);
v_scale(pka->_dir, jmp / std::sqrt(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);
return EXIT_SUCCESS;
}
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;
if (fread(&seed, sizeof(int), 1, urand) != 1) return 1;
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
SimconfType * 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(simconf, sample);
//TrimBase *trim = new TrimPrimaries(sample);
//Real r = 10.0;
Real r = atof(argv[2]); //10.0;
Real 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);
// Real atp = 0.1; // 10at% Mo 90at%Cu
Real v_sam = sample->w[0] * sample->w[1] * sample->w[2];
//Real 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(simconf, 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(simconf, 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
std::queue<IonBase*> recoils;
Real dif[3], dif2[3];
snprintf(fname, 199, "%s.Erec", argv[1]);
FILE *erec = fopen(fname, "wt");
snprintf(fname, 199, "%s.dist", argv[1]);
FILE *rdist = fopen(fname, "wt");
Real pos1[3], pos2[3];
IonMDTag *ff1, *pka;
Real A = 84.0, E = 1.8e6; int Z = 36; // 1.8MeV Kr
//Real A = 58.0, E = 5.0e6; int Z = 28; // 5MeV Ni
//Real 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->_Z = Z;
ff1->_m = 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->setEf();
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->_Z == 8 || pka->_Z == 22 || pka->_Z == 39)
// pka is Xe
//if (pka->_Z == 54)
// pka is B or Ti
if (pka->_Z == 5 || pka->_Z == 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->_Z == 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->_Z);
//pka->_md = id++;
trim->trim(pka, recoils);
// do ion analysis/processing AFTER the cascade here
// pka is O or Ti
//if (pka->_Z == 8 || pka->_Z == 22 || pka->_Z == 39)
// pka is Xe
//if (pka->_Z == 54)
// pka is B or Ti
if (pka->_Z == 5 || pka->_Z == 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", std::sqrt(v_dot(dif, dif)), pka->_Z, pka->_pos(0), pka->_pos(1), pka->_pos(2), std::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 / std::sqrt(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
Real Zatoms = 26.0, Matoms = 56.0;
Real Epka = 5.0e6;
Real ed = 0.0115 * std::pow(Zatoms, -7.0/3.0) * Epka;
Real g = 3.4008 * std::pow(ed, 1.0/6.0) + 0.40244 * std::pow(ed, 3.0/4.0) + ed;
Real kd = 0.1337 * std::pow(Zatoms, 2.0/3.0) / std::pow(Matoms, 0.5); //Z, M
Real Ev = Epka / (1.0 + kd * g);
Real 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;
}
int main(int argc, char *argv[])
{
if (argc != 8)
{
std::cerr << "syntax: " << argv[0] << " basename angle[deg] diameter(nm) burried[0, 1] numbermultiplier xyzout[0, 1] lbinout[0, 1]" << std::endl;
return 1;
}
Real theta = atof(argv[2]) * M_PI/180.0; // 0 = parallel to wire
Real diameter = 10.0*atof(argv[3]);
Real length = 11000.0; // 1.1 mu
bool burried = (atoi(argv[4]) != 0);
Real mult = atof(argv[5]);
bool xyz_out = (atoi(argv[6]) != 0);
bool ldat_out = (atoi(argv[7]) != 0);
// ion series
const int nstep = 5;
Real ion_dose[nstep] = { 3.0e13, 2.2e13, 1.5e13, 1.2e13, 2.5e13 }; // in ions/cm^2
int ion_count[nstep];
IonBase* ion_prototype[nstep];
ion_prototype[0] = new IonBase( 5, 11.0 , 320.0e3); // Z, m, E
ion_prototype[1] = new IonBase( 5, 11.0 , 220.0e3); // Z, m, E
ion_prototype[2] = new IonBase( 5, 11.0 , 160.0e3); // Z, m, E
ion_prototype[3] = new IonBase( 5, 11.0 , 120.0e3); // Z, m, E
ion_prototype[4] = new IonBase(15, 31.0 , 250.0e3); // Z, m, E
// seed randomnumber generator from system entropy pool
FILE *urand = fopen("/dev/random", "r");
int seed;
if (fread(&seed, sizeof(int), 1, urand) != 1) return 1;
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
SimconfType * simconf = new SimconfType;
//simconf->fullTraj = true;
// initialize sample structure
SampleWire *sample;
if (burried)
sample = new SampleBurriedWire(diameter, diameter, length);
else
{
sample = new SampleWire(diameter, diameter, length);
sample->bc[2] = SampleWire::CUT;
}
// calculate actual ion numbers
for (int s = 0; s < nstep; ++s)
{
Real A; // irradiated area in Ang^2
if (burried)
A =(length + sample->w[0]) * (length + sample->w[1]);
else
A = cos(theta) * M_PI * 0.25 * sample->w[0] * sample->w[1] + // slanted top face
sin(theta) * length * sample->w[0]; // + projected side
// 1cm^2 = 1e16 Ang**2, 1Ang^2 = 1e-16cm^2
ion_count[s] = ion_dose[s] * A * 1.0e-16 * mult;
std::cerr << "Ion " << s << ' ' << ion_count[s] << std::endl;
}
// initialize trim engine for the sample
/* const int z1 = 31;
const int z2 = 33;
TrimVacMap *trim = new TrimVacMap(sample, z1, z2); // GaAs
*/
//TrimBase *trim = new TrimBase(sample);
TrimBase *trim = new TrimPrimaries(simconf, sample);
MaterialBase *material;
ElementBase *element;
// Si
material = new MaterialBase(simconf, 2.329); // rho
element = new ElementBase;
element->_Z = 14; // Si
element->_m = 28.0;
element->_t = 1.0;
material->_element.push_back(element);
material->prepare(); // all materials added
sample->material.push_back(material); // add material to sample
// SiO2 (material[1] for the cover layer in SampleBurriedWire)
material = new MaterialBase(simconf, 2.634); // rho
element = new ElementBase;
element->_Z = 14; // Si
element->_m = 28.0;
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
// create a FIFO for recoils
std::queue<IonBase*> recoils;
IonBase *pka;
// map concentration along length
int *lbins[2];
int lx = 100; // 100 bins
int dl = length/Real(lx);
lbins[1] = new int[lx]; // P z=15
for (int i = 0; i < 2; ++i)
{
lbins[i] = new int[lx]; // 0=B (z=5), 1=P (z=15)
for (int l = 0; l < lx; ++l)
lbins[i][l] = 0;
}
// xyz data
int xyz_lines = 0;
std::stringstream xyz_data;
for (int s = 0; s < nstep; ++s)
{
for (int n = 0; n < ion_count[s]; ++n)
{
if (n % 10000 == 0)
std::cerr << "pka #" << n+1 << std::endl;
// generate new PKA from prototype ion
pka = new IonBase(ion_prototype[s]);
pka->gen = 0; // generation (0 = PKA)
pka->tag = -1;
pka->_dir(0) = 0.0;
pka->_dir(1) = sin(theta);
pka->_dir(2) = cos(theta);
v_norm(pka->_dir);
if (burried)
{
// cannot anticipate the straggling in the burrial layer, thus have to shoot onto a big surface
// TODO: take theta into account!
pka->_pos(0) = (dr250() - 0.5) * (length + sample->w[0]);
pka->_pos(1) = (dr250() - 0.5) * (length + sample->w[1]);
pka->_pos(2) = -250.0; // overcoat thickness
}
else
{
if (theta == 0.0)
{
// 0 degrees => start on top of wire!
pka->_pos(2) = 0.0;
do
{
pka->_pos(0) = dr250() * sample->w[0];
pka->_pos(1) = dr250() * sample->w[1];
} while (sample->lookupMaterial(pka->_pos) == 0);
}
else
{
// start on side _or_ top!
Real vpos[3], t;
do
{
do
{
vpos[0] = dr250() * sample->w[0];
vpos[1] = 0.0;
vpos[2] = (dr250() * (length + diameter/tan(theta))) - diameter/tan(theta);
t = (1.0 - std::sqrt(1.0 - sqr(2*vpos[0]/diameter - 1.0))) * diameter/(2.0*pka->_dir(1));
// if we start beyond wire length (that would be inside the substrate) then retry
} while (t*pka->_dir(2) + vpos[2] >= length);
// if first intersection with cylinder is at z<0 then check if we hit the top face instead
if (t*pka->_dir(2) + vpos[2] < 0.0)
t = -vpos[2]/pka->_dir(2);
// start PKA at calculated intersection point
for (int i = 0; i < 3; ++i)
pka->_pos(i) = t*pka->_dir(i) + vpos[i];
} while (sample->lookupMaterial(pka->_pos) == 0);
}
}
//cout << "START " << pka->_pos(0) << ' ' << pka->_pos(1) << ' ' << pka->_pos(2) << ' ' << std::endl;
//continue;
pka->setEf();
recoils.push(pka);
while (!recoils.empty())
{
pka = recoils.front();
recoils.pop();
sample->averages(pka);
// do ion analysis/processing BEFORE the cascade here
if (pka->_Z == ion_prototype[s]->_Z )
{
//printf( "p1 %f\t%f\t%f\n", pka->_pos(0), pka->_pos(1), pka->_pos(2));
}
// follow this ion's trajectory and store recoils
trim->trim(pka, recoils);
// do ion analysis/processing AFTER the cascade here
// ion is in the wire
if ( sample->lookupMaterial(pka->_pos) == sample->material[0])
{
int l = pka->_pos(2) / dl;
if (l >=0 && l < lx)
{
if (xyz_out)
{
xyz_data << simconf->scoef[pka->_Z-1].sym << ' '
<< pka->_pos(0)/100.0 << ' ' << pka->_pos(1)/100.0 << ' ' << pka->_pos(2)/100.0 << std::endl;
xyz_lines++;
}
if (ldat_out)
lbins[ (pka->_Z == 5) ? 0 : 1 ][l]++;
}
}
// done with this recoil
delete pka;
}
}
}
// write xyz file
if (xyz_out)
{
std::stringstream xyz_name;
xyz_name << argv[1] << ".xyz";
std::ofstream xyz(xyz_name.str().c_str());
xyz << xyz_lines << std::endl << std::endl << xyz_data.str();
xyz.close();
}
// write lbins file (atoms per nm^3)
if (ldat_out)
{
std::stringstream ldat_name;
ldat_name << argv[1] << ".ldat";
std::ofstream ldat(ldat_name.str().c_str());
Real dv = 1e-3 * dl * M_PI * 0.25 *sample->w[0] * sample->w[1]; // volume per bin in nm^3
for (int l = 0; l < lx; ++l)
ldat << l*dl << ' ' << lbins[0][l]/(mult*dv) << ' ' << lbins[1][l]/(mult*dv) << std::endl;
ldat.close();
}
delete[] lbins[0];
delete[] lbins[1];
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
char fname[200];
if (argc != 8)
{
fprintf(stderr, "syntax:\n%s basename Eion[eV] angle[deg] numpka zpka mpka r[nm]\n", argv[0]);
return 1;
}
Real epka = atof(argv[2]);
Real theta = atof(argv[3]) * M_PI/180.0; // 0 = perpendicular to wire
int numpka = atoi(argv[4]);
int zpka = atoi(argv[5]);
Real mpka = atof(argv[6]);
Real dwire = atof(argv[7])*20.0;
// seed randomnumber generator from system entropy pool
FILE *urand = fopen("/dev/random", "r");
int seed;
if (fread(&seed, sizeof(int), 1, urand) != 1) return 1;
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
SimconfType * simconf = new SimconfType;
// initialize sample structure
SampleWire *sample = new SampleWire(dwire, dwire, 100.0);
// initialize trim engine for the sample
const int z1 = 29; //Cu
const int z2 = 22; //Ti
const int z3 = 47; //Ag
TrimVacMap *trim = new TrimVacMap(simconf, sample, z1, z2, z3); // GaCW
MaterialBase *material;
ElementBase *element;
material = new MaterialBase(simconf, (56.0*8.920 + 38.0*4.507 + 8.0*10.490)/(56.0+38.0+8.0)); // rho
element = new ElementBase;
element->_Z = z1; // Cu
element->_m = 63.546;
element->_t = 56.0;
material->_element.push_back(element);
element = new ElementBase;
element->_Z = z2; // Ti
element->_m = 47.867;
element->_t = 38.0;
material->_element.push_back(element);
element = new ElementBase;
element->_Z = z3; // Ag
element->_m = 107.87;
element->_t = 8.0;
material->_element.push_back(element);
material->prepare(); // all materials added
sample->material.push_back(material); // add material to sample
// create a FIFO for recoils
std::queue<IonBase*> recoils;
IonBase *pka;
const int mx = 20, my = 20;
int imap[mx][my][3];
for (int e = 0; e < 3; e++)
for (int x = 0; x < mx; x++)
for (int y = 0; y < my; y++)
imap[x][y][e] = 0;
// 10000 ions
for (int n = 0; n < numpka; n++)
{
if (n % 1000 == 0) fprintf(stderr, "pka #%d\n", n+1);
pka = new IonBase;
pka->gen = 0; // generation (0 = PKA)
pka->tag = -1;
pka->_Z = zpka; // S
pka->_m = mpka;
pka->_E = epka;
pka->_dir(0) = 0.0;
pka->_dir(1) = -cos(theta);
pka->_dir(2) = sin(theta);
v_norm(pka->_dir);
pka->_pos(0) = dr250() * sample->w[0];
pka->_pos(2) = dr250() * sample->w[2];
// wire surface
pka->_pos(1) = sample->w[1] / 2.0 * (1.0 + std::sqrt(1.0 - sqr((pka->_pos(0) / sample->w[0]) * 2.0 - 1.0))) - 0.5;
pka->setEf();
recoils.push(pka);
while (!recoils.empty())
{
pka = recoils.front();
recoils.pop();
sample->averages(pka);
// do ion analysis/processing BEFORE the cascade here
if (pka->_Z == zpka )
{
//printf( "p1 %f\t%f\t%f\n", pka->_pos(0), pka->_pos(1), pka->_pos(2));
}
// follow this ion's trajectory and store recoils
// printf("%f\t%d\n", pka->_E, pka->_Z);
trim->trim(pka, recoils);
// do ion analysis/processing AFTER the cascade here
// ion is still in sample
if ( sample->lookupMaterial(pka->_pos) != 0)
{
int x, y;
x = ((pka->_pos(0) * mx) / sample->w[0]);
y = ((pka->_pos(1) * my) / sample->w[1]);
x -= int(x/mx) * mx;
y -= int(y/my) * my;
// keep track of interstitials for the two constituents
if (pka->_Z == z1) imap[x][y][0]++;
else if (pka->_Z == z2) imap[x][y][1]++;
else if (pka->_Z == z3) imap[x][y][2]++;
}
// done with this recoil
delete pka;
}
}
const char *elnam[3] = { "Cu", "Ti", "Ag" };
FILE *intf, *vacf, *netf;
// e<numberofelementsinwire
for (int e = 0; e < 3; e++)
{
snprintf(fname, 199, "%s.%s.int", argv[1], elnam[e]);
intf = fopen(fname, "wt");
snprintf(fname, 199, "%s.%s.vac", argv[1], elnam[e]);
vacf = fopen(fname, "wt");
snprintf(fname, 199, "%s.%s.net", argv[1], elnam[e]);
netf = fopen(fname, "wt");
for (int y = 0; y <= my; y++)
{
for (int x = 0; x <= mx; x++)
{
Real x1 = Real(x)/Real(mx)*sample->w[0];
Real y1 = Real(y)/Real(my)*sample->w[1];
fprintf(intf, "%f %f %d\n", x1, y1, (x<mx && y<my) ? imap[x][y][e] : 0);
fprintf(vacf, "%f %f %d\n", x1, y1, (x<mx && y<my) ? trim->vmap[x][y][e] : 0);
fprintf(netf, "%f %f %d\n", x1, y1, (x<mx && y<my) ? (imap[x][y][e] - trim->vmap[x][y][e]) : 0);
}
fprintf(intf, "\n");
fprintf(vacf, "\n");
fprintf(netf, "\n");
}
fclose(intf);
fclose(vacf);
fclose(netf);
}
return EXIT_SUCCESS;
}