readpar()
{
init_read_par() ;
readparam( TWMC ) ;
readparam( USER ) ;
process_readpar() ;
}
readParFile()
{
init_read_par() ;
readparam( PART ) ;
readparam( USER ) ;
process_readpar() ;
}
/* This function returns 1 on success, and 0 on failure
*/
int readParams(char *datFileName) {
int printFlag = 1;
char title[128], parStr[128], *str;
int gCount,i,Nkind;
char unitCellFile[64];
atom *tempCell;
if (!parOpen(datFileName)) {
printf("Could not open data input file %s\n",datFileName);
return 0;
}
resetParamFile();
while(readparam("crystal:",parStr,0)) nGrains++;
resetParamFile();
while(readparam("amorph:",parStr,0)) nGrains++;
resetParamFile();
while(readparam("special:",parStr,0)) nGrains++;
printf("Found data for %d grain(s) (crystalline frame work and amorphous)\n",nGrains);
if (nGrains == 0) return 0;
grains = (grainBox *)malloc(nGrains*sizeof(grainBox));
/* Now we will loop through all the grains and lok for the necessary
* data for each grain
*/
if (readparam("box:",parStr,1)) {
sscanf(parStr,"%lf %lf %lf",&(superCell.ax),&(superCell.by),&(superCell.cz));
}
else {
printf("Size of super cell box not defined - exit!\n");
exit(0);
}
/* reset the input file and advance to the next crystal row */
resetParamFile();
/*
readparam("crystal:",parStr,0);
grains[0].name = (char *)malloc(NAME_BUF_LEN);
strcpy(grains[0].name,parStr);
grains[0].nplanes = 0;
grains[0].planes = NULL;
*/
gCount = -1;
/* We will look for the following tokens:
* tilt: tiltx,tilty,tiltz;
* translation: shiftx shifty shiftz
* plane: vectX vectY vectZ pointX pointY pointZ
*/
while (readNextParam(title,parStr)) {
// printf("%s\n",parStr);
/* if we found a new crystal ... */
if (strncmp(title,"crystal:",8) == 0) {
gCount++;
grains[gCount].name = (char *)malloc(NAME_BUF_LEN);
grains[gCount].amorphFlag = 0;
grains[gCount].density = 0;
grains[gCount].rmin = 0;
grains[gCount].rFactor = 1.0;
grains[gCount].sphereRadius = 0;
/* first we want to extract crystal name and file name for
* unit cell data file from this one line
*/
strcpy(grains[gCount].name,parStr);
str = strnext(parStr," \t");
if (str != NULL) {
grains[gCount].name[str-parStr-1]='\0';
// printf("%s, name: %s\n",parStr,grains[gCount].name);
//str = strnext(str," \t");
//if (str != NULL) {
strcpy(unitCellFile,str);
if ((str = strchr(unitCellFile,' ')) != NULL)
*str = '\0';
if ((str = strchr(unitCellFile,'\t')) != NULL)
*str = '\0';
}
else {
printf("Error: no unit cell data file specified for crystal %s\n",
grains[gCount].name);
return 0;
}
// sscanf(parStr,"%s %s",grains[gCount].name,unitCellFile);
grains[gCount].nplanes = 0;
grains[gCount].planes = NULL;
muls->nCellX = 1;
muls->nCellY = 1;
muls->nCellZ = 1;
muls->ctiltx = 0;
muls->ctilty = 0;
muls->ctiltz = 0;
muls->tds = 0;
tempCell = readUnitCell(&(grains[gCount].natoms), unitCellFile, muls, 0);
if (tempCell == NULL) {
printf("Error reading unit cell data - exit!\n");
exit(0);
}
/*****************************************************
* Test code
*
printf("ax: %g, by: %g, cz: %g\n",muls->ax,muls->by,muls->c);
for (i=0;i<grains[gCount].natoms;i++) {
printf("%d: %d (%g,%g,%g)\n",i,tempCell[i].Znum,tempCell[i].x,tempCell[i].y,tempCell[i].z);
}
*
*****************************************************/
grains[gCount].unitCell = (atom *)malloc(grains[gCount].natoms*sizeof(atom));
memcpy(grains[gCount].unitCell,tempCell,grains[gCount].natoms*sizeof(atom));
grains[gCount].alpha = muls->cAlpha;
grains[gCount].beta = muls->cBeta;
grains[gCount].gamma = muls->cGamma;
grains[gCount].ax = muls->ax;
grains[gCount].by = muls->by;
grains[gCount].cz = muls->c;
}
/***************************************************
* amorphous stuff
*/
else if (strncmp(title,"amorph:",7) == 0) {
gCount++;
grains[gCount].name = (char *)malloc(NAME_BUF_LEN);
grains[gCount].amorphFlag = AMORPHOUS;
grains[gCount].density = 0;
grains[gCount].rmin = 1000;
grains[gCount].rFactor = 1.2;
grains[gCount].sphereRadius = 0;
/* first we want to extract crystal name and file name for
* unit cell data file from this one line
*/
strcpy(grains[gCount].name,parStr);
str = strnext(parStr," \t");
if (str != NULL) {
grains[gCount].name[str-parStr-1]='\0';
// printf("%s, name: %s\n",parStr,grains[gCount].name);
//str = strnext(str," \t");
//if (str != NULL) {
strcpy(unitCellFile,str);
if ((str = strchr(unitCellFile,' ')) != NULL)
*str = '\0';
if ((str = strchr(unitCellFile,'\t')) != NULL)
*str = '\0';
}
else {
printf("Error: no unit cell data file specified for crystal %s\n",
grains[gCount].name);
return 0;
}
// sscanf(parStr,"%s %s",grains[gCount].name,unitCellFile);
grains[gCount].nplanes = 0;
grains[gCount].planes = NULL;
muls->nCellX = 1;
muls->nCellY = 1;
muls->nCellZ = 1;
muls->ctiltx = 0;
muls->ctilty = 0;
tempCell = readUnitCell(&(grains[gCount].natoms), unitCellFile, muls, 0);
grains[gCount].unitCell = (atom *)malloc(grains[gCount].natoms * sizeof(atom));
memcpy(grains[gCount].unitCell, tempCell, grains[gCount].natoms * sizeof(atom));
grains[gCount].alpha = 0;
grains[gCount].beta = 0;
grains[gCount].gamma = 0;
grains[gCount].ax = 0;
grains[gCount].by = 0;
grains[gCount].cz = 0;
}
/***************************************************
* code for specially distributed amorphous stuff
*/
else if (strncmp(title,"special:",8) == 0) {
gCount++;
grains[gCount].name = (char *)malloc(NAME_BUF_LEN);
grains[gCount].amorphFlag = SPECIAL_GRAIN;
grains[gCount].density = 0;
grains[gCount].rmin = 1000;
grains[gCount].rFactor = 1.2;
grains[gCount].sphereRadius = 0;
/* first we want to extract crystal name and file name for
* unit cell data file from this one line
*/
strcpy(grains[gCount].name,parStr); // name of this grain
// don't need cfg input file
grains[gCount].natoms = 0;
grains[gCount].unitCell = NULL;
// sscanf(parStr,"%s %s",grains[gCount].name,unitCellFile);
grains[gCount].nplanes = 0;
grains[gCount].planes = NULL;
grains[gCount].alpha = 0;
grains[gCount].beta = 0;
grains[gCount].gamma = 0;
grains[gCount].ax = 0;
grains[gCount].by = 0;
grains[gCount].cz = 0;
} // end of "special"
/* if we found tilt data */
else if (gCount >= 0) {
if (strncmp(title,"tilt:",5) == 0) {
sscanf(parStr,"%lf %lf %lf",&(grains[gCount].tiltx),
&(grains[gCount].tilty),&(grains[gCount].tiltz));
if (strstr(parStr,"degree") != NULL) {
grains[gCount].tiltx *= PI180;
grains[gCount].tilty *= PI180;
grains[gCount].tiltz *= PI180;
}
}
/* assign density */
else if (strncmp(title,"density:",8) == 0) {
sscanf(parStr,"%lf",&(grains[gCount].density));
grains[gCount].rmin = pow(sqrt(15.0/144.0)/grains[gCount].density,1.0/3.0);
}
/* assign density factor */
else if (strncmp(title,"rmin:",5) == 0) {
sscanf(parStr,"%lf",&(grains[gCount].rmin));
grains[gCount].density = sqrt(15.0/144)*pow(grains[gCount].rmin,3);
}
else if (strncmp(title,"r-factor:",9) == 0) {
sscanf(parStr,"%lf",&(grains[gCount].rFactor));
}
/* if we found shift data */
else if (strncmp(title,"translation:",12) == 0) {
sscanf(parStr,"%lf %lf %lf",&(grains[gCount].shiftx),
&(grains[gCount].shifty),&(grains[gCount].shiftz));
}
else if (strncmp(title,"sphere:",7) == 0) {
sscanf(parStr,"%lf %lf %lf %lf",&(grains[gCount].sphereRadius),
&(grains[gCount].sphereX),&(grains[gCount].sphereY),&(grains[gCount].sphereZ));
}
/* if we found a new plane for this crystal */
else if (strncmp(title,"plane:",6) == 0) {
grains[gCount].nplanes++;
grains[gCount].planes = (plane *) realloc(grains[gCount].planes,
grains[gCount].nplanes*sizeof(plane));
if (grains[gCount].planes == NULL) {
printf("Sorry, could not allocate memory for new plane\n");
return 0;
}
sscanf(parStr,"%lf %lf %lf %lf %lf %lf %lf %lf %lf",
&(grains[gCount].planes[grains[gCount].nplanes-1].pointX),
&(grains[gCount].planes[grains[gCount].nplanes-1].pointY),
&(grains[gCount].planes[grains[gCount].nplanes-1].pointZ),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect1X),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect1Y),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect1Z),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect2X),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect2Y),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect2Z));
crossProduct(&(grains[gCount].planes[grains[gCount].nplanes-1].vect1X),
&(grains[gCount].planes[grains[gCount].nplanes-1].vect2X),
&(grains[gCount].planes[grains[gCount].nplanes-1].normX));
} /* end of if plane ... */
else if (strncmp(title,"atom:",5) == 0) {
grains[gCount].natoms++;
grains[gCount].unitCell = (atom *)realloc(grains[gCount].unitCell,
grains[gCount].natoms*sizeof(atom));
// Now read Znum, r (->z), and count (->y)
sscanf(parStr,"%d %f %d %f",&(grains[gCount].unitCell[grains[gCount].natoms-1].Znum),
&(grains[gCount].unitCell[grains[gCount].natoms-1].z),&Nkind,
&(grains[gCount].unitCell[grains[gCount].natoms-1].y));
// assign number of atoms directly, if specified in input file
if (Nkind > 0) grains[gCount].unitCell[grains[gCount].natoms-1].y = (float)Nkind;
for (i=0;i<muls->atomKinds;i++)
if (muls->Znums[i] == grains[gCount].unitCell[grains[gCount].natoms-1].Znum) break;
if (i == muls->atomKinds) {
muls->atomKinds++;
muls->Znums = (int *) realloc(muls->Znums,muls->atomKinds*sizeof(int));
muls->Znums[i] = grains[gCount].unitCell[grains[gCount].natoms-1].Znum;
}
} /* end of if "atom:" */
} /* end of if gCount >=0 */
}
parClose();
if (printFlag) showData();
return 1;
}