int main(int argc, char *argv[]) {
char outFileName[64],datFileName[64],moldyName[128];
char *str;
// atom *atomPtr;
int g,nstart,j,ak,count;
FILE *fp;
double charge;
int moldyFlag = 0; // suppress creation of ..._moldy.in file
int distPlotFlag = 0; // suppress creation of disList.dat
/* Let's set the radii of certain elements by hand:
*/
// atRad = (double *)realloc(atRadf, 109*sizeof(double));
// covRad = (double *)realloc(covRadf,109*sizeof(double));
atRad = (double *)malloc(109*sizeof(double));
covRad = (double *)malloc(109*sizeof(double));
memcpy(atRad, atRadf,36*sizeof(double));
memcpy(covRad,covRadf,36*sizeof(double));
atRad[39-1]=2.27; covRad[39-1]=2.62; // Y
atRad[57-1]=2.74; covRad[57-1]=1.69; // La
atRad[71-1]=2.25; covRad[71-1]=1.56; // Lu
if (argc < 2)
sprintf(datFileName,"gb.gbm");
else
strcpy(datFileName,argv[1]);
// read a flag:
if (argc > 2) {
if (strncmp(argv[2],"-m",2) == 0) {
moldyFlag = 1; // also write a moldy file!
printf("Saving moldy input file!\n");
}
}
muls->nCellX = 1;
muls->nCellY = 1;
muls->nCellZ = 1;
muls->ctiltx = 0;
muls->ctilty = 0;
muls->ctiltz = 0;
superCell.atoms = NULL;
superCell.natoms = 0;
if (!readParams(datFileName))
exit(0);
if (nGrains > 0) {
// loop, until we find crystalline grains:
for (g=0; g<nGrains; g++) if (grains[g].amorphFlag == CRYSTALLINE) break;
/* make the crystalline part of the super cell */
if (g<nGrains) makeSuperCell();
/* if there is also an amorphous part, then add it now, and also write a
* MD input file, so that the amorphous phase atoms can be relaxed
*/
for (g=0; g<nGrains; g++) if (grains[g].amorphFlag != CRYSTALLINE) break;
if (g<nGrains) {
if (moldyFlag) {
sprintf(moldyName,"%s",datFileName);
moldyName[strlen(datFileName)-4] = '\0';
strcat(moldyName,"_moldy.in");
if ((fp=fopen(moldyName,"w")) == NULL) {
printf("Could not open moldy input file %s!\n",moldyName);
exit(0);
}
}
else {
fp = NULL;
}
if (nGrains > 1) {
writeFrameWork(fp,superCell);
computeCenterofMass();
nstart = superCell.natoms;
switch (grains[g].amorphFlag) {
case 1: makeAmorphous();
break;
case 2: makeSpecial(distPlotFlag);
break;
}
writeAmorphous(fp,superCell,nstart,superCell.natoms);
}
else {
switch (grains[g].amorphFlag) {
case 1: makeAmorphous();
break;
case 2: makeSpecial(distPlotFlag);
break;
}
writeAmorphous(fp,superCell,0,superCell.natoms);
}
if (moldyFlag) fclose(fp);
}
}
if (0) { // (moldyFlag) {
///////////////////////////////////////////////////////////////
// write Moldy input file, without presence of amorphous phase:
sprintf(moldyName,"%s",datFileName);
moldyName[strlen(datFileName)-4] = '\0';
strcat(moldyName,"_moldy.in");
if ((fp=fopen(moldyName,"w")) == NULL) {
printf("Could not open moldy input file %s!\n",moldyName);
exit(0);
}
// writeFrameWork(fp,superCell);
// computeCenterofMass();
// superCell2Moldy(fp,superCell);
fclose(fp);
} // end of: if moldyFlag ...
strcpy(outFileName,datFileName);
// atomPtr = readUnitCell(&natoms,fileName,&muls);
// writePDB(atomPtr,nat /* reset the input file and advance to the next crystal row */
str = strchr(outFileName,'.');
if (str == NULL) str=outFileName+strlen(outFileName);
sprintf(str,".cfg");
muls->ax = (float)superCell.ax;
muls->by = (float)superCell.by;
muls->c = (float)superCell.cz;
superCell.natoms = removeVacancies(superCell.atoms,superCell.natoms);
printf("will write cfg file to %s\n",outFileName);
writeCFG(superCell.atoms, superCell.natoms, outFileName, muls);
printf("wrote cfg file to %s\n",outFileName);
/**************************************************************
* find the charge for the Y-atoms, in order to remain neutral:
*/
charge = 0.0;
if (0) {
for (ak=0;ak<muls->atomKinds;ak++) {
count =0;
for (j=0;j<superCell.natoms;j++) {
if (muls->Znums[ak] == superCell.atoms[j].Znum) count++;
}
printf("Z=%3d: %d\n",muls->Znums[ak],count);
switch (muls->Znums[ak]) {
case 7: charge += count*(-3.0); break;
case 8: charge += count*(-2.0); break;
case 38: charge += count*(2.0); break;
case 22: charge += count*(4.0); break;
case 14: charge += count* 4.0; break;
}
}
}
else {
for (j=0;j<superCell.natoms;j++) {
charge += superCell.atoms[j].q*superCell.atoms[j].occ;
}
}
// printf("Total charge: %g, i.e. %g %s\n",charge,charge,(charge > 0) ? "holes" : "electrons");
printf("Total charge: %g",charge);
if (charge > 0) printf(", i.e. %g holes\n",charge);
if (charge < 0) printf(", i.e. %g electrons\n",-charge);
delete(muls);
return 0;
}
void
write_htmlFnctPages::writePage(void)
{
// most of the informations can be write only if the function has a body !
dataDrawerListIterator p; // browse the list
string fnctName; // name of the function
// Browse list one function for time
p = dataBL->begin();
while (p != dataBL->end()) {
dataB = *p;
p++;
fData = dataB->getFnctData();
cout << "Generating html page for function "
<< (fnctName = fData->getName()) << "...\n";
htmlpage.open((HTMLfilesRegister::htmlFile(*fData)).c_str());
// begin of the page
pageTitle = fnctName ;
writeHead();
writeIndex();
htmlpage << "<br><br>\n";
if (fnctName != "")
htmlpage << "This is the page of the function "
<< fnctName << ".<br><br>\n";
htmlpage << *fData
<< "<br><l><br>\n\n";
if (fData->hasBody()) {
writePageIndex();
// write body graph
if (!noBodyGraph) {
htmlpage << "<A name=\"bodyGraph\">\n";
writeSectionTitle("Graph of the body");
writeBodyGraph();
}
// write CFG
if (!noCFG) {
htmlpage << "<A name=\"CFG\">\n";
writeSectionTitle("Control flow graph");
writeCFG();
}
// write stmt stat
if (!noStmtStat) {
htmlpage << "<A name=\"stmtStatistics\">\n";
writeSectionTitle("Statements statistics");
htmlpage << *(dataB->getStmtNumData());
}
// write decl list
if ( (!noDeclsList) && (dataB->hasDeclsList()) ) {
htmlpage << "<A name=\"declsList\">\n";
writeSectionTitle("Declarations into the function");
htmlpage << *(dataB->getDeclsList());
}
// write var used
if ( (!noVarUsed) && (dataB->hasVarUsedList()) ) {
htmlpage << "<A name=\"varUsedList\">\n";
writeSectionTitle("Variables used by the function");
htmlpage << *(dataB->getVarUsedList());
}
// write exprs list
if ( (!noExprsList) && (dataB->hasExprsList()) ) {
htmlpage << "<A name=\"exprsList\">\n";
writeSectionTitle("List of the expressions");
htmlpage << *(dataB->getExprsList());
}
// write expr stat
if (!noExprStat) {
htmlpage << "<A name=\"exprStatistics\">\n";
writeSectionTitle("Expression statistics");
htmlpage << *(dataB->getExprNumData());
}
// write call graph
if (!noCallGraph) {
htmlpage << "<A name=\"callGraph\">\n";
writeSectionTitle("Call graph");
writeCallGraph();
}
}
// end of the page
writeIndex();
writeFoot();
htmlpage.close();
}
return;
}
