void BasisSet::initCalculation()
{
if (m_init)
return;
// This currently just involves normalising all contraction coefficients
m_numAtoms = m_atomPos.size();
m_gtoCN.clear();
// Initialise the new data structures that are hopefully more efficient
unsigned int indexMO = 0;
m_moIndices.resize(m_symmetry.size());
// Add a final entry to the gtoIndices
m_gtoIndices.push_back(m_gtoA.size());
for(unsigned int i = 0; i < m_symmetry.size(); ++i) {
switch (m_symmetry[i]) {
case S:
m_moIndices[i] = indexMO++;
m_cIndices.push_back(m_gtoCN.size());
// Normalization of the S-type orbitals (normalization used in JMol)
// (8 * alpha^3 / pi^3)^0.25 * exp(-alpha * r^2)
for(unsigned j = m_gtoIndices[i]; j < m_gtoIndices[i+1]; ++j) {
m_gtoCN.push_back(m_gtoC[j] * pow(m_gtoA[j], 0.75) * 0.71270547);
}
break;
case P:
m_moIndices[i] = indexMO;
indexMO += 3;
m_cIndices.push_back(m_gtoCN.size());
// Normalization of the P-type orbitals (normalization used in JMol)
// (128 alpha^5 / pi^3)^0.25 * [x|y|z]exp(-alpha * r^2)
for(unsigned j = m_gtoIndices[i]; j < m_gtoIndices[i+1]; ++j) {
m_gtoCN.push_back(m_gtoC[j] * pow(m_gtoA[j], 1.25) * 1.425410941);
m_gtoCN.push_back(m_gtoCN.back());
m_gtoCN.push_back(m_gtoCN.back());
}
break;
case D:
// Cartesian - 6 d components
// Order in xx, yy, zz, xy, xz, yz
m_moIndices[i] = indexMO;
indexMO += 6;
m_cIndices.push_back(m_gtoCN.size());
// Normalization of the P-type orbitals (normalization used in JMol)
// xx|yy|zz: (2048 alpha^7/9pi^3)^0.25 [xx|yy|zz]exp(-alpha r^2)
// xy|xz|yz: (2048 alpha^7/pi^3)^0.25 [xy|xz|yz]exp(-alpha r^2)
for(unsigned j = m_gtoIndices[i]; j < m_gtoIndices[i+1]; ++j) {
m_gtoCN.push_back(m_gtoC[j] * pow(m_gtoA[j], 1.75) * 1.645922781);
m_gtoCN.push_back(m_gtoCN.back());
m_gtoCN.push_back(m_gtoCN.back());
m_gtoCN.push_back(m_gtoC[j] * pow(m_gtoA[j], 1.75) * 2.850821881);
m_gtoCN.push_back(m_gtoCN.back());
m_gtoCN.push_back(m_gtoCN.back());
}
break;
case D5:
// Spherical - 5 d components
// Order in d0, d+1, d-1, d+2, d-2
// Form d(z^2-r^2), dxz, dyz, d(x^2-y^2), dxy
m_moIndices[i] = indexMO;
indexMO += 5;
m_cIndices.push_back(m_gtoCN.size());
for(unsigned j = m_gtoIndices[i]; j < m_gtoIndices[i+1]; ++j) {
m_gtoCN.push_back(m_gtoC[j] * pow(2048.0 * pow(m_gtoA[j], 7.0)
/ (9.0 * M_PI*M_PI*M_PI), 0.25));
m_gtoCN.push_back(m_gtoC[j] * pow(2048.0 * pow(m_gtoA[j], 7.0)
/ (M_PI*M_PI*M_PI), 0.25));
m_gtoCN.push_back(m_gtoCN.back());
// I think this is correct but reaally need to check...
m_gtoCN.push_back(m_gtoC[j] * pow(128.0 * pow(m_gtoA[j], 7.0)
/ (M_PI*M_PI*M_PI), 0.25));
m_gtoCN.push_back(m_gtoC[j] * pow(2048.0 * pow(m_gtoA[j], 7.0)
/ (M_PI*M_PI*M_PI), 0.25));
}
break;
case F:
m_moIndices[i] = indexMO;
indexMO += 8;
m_cIndices.push_back(m_gtoCN.size());
qDebug() << "F Basis set not handled - results may be incorrect.";
break;
case F7:
m_moIndices[i] = indexMO;
indexMO += 7;
m_cIndices.push_back(m_gtoCN.size());
qDebug() << "F7 Basis set not handled - results may be incorrect.";
break;
default:
qDebug() << "Basis set not handled - results may be incorrect.";
}
}
m_init = true;
outputAll();
}
int main(int argc, char **argv)
{
char *outputFile = argv[1];
char *pathName = argv[2];
char ans[0];
char strp[999];
struct stat status;
struct dirent *pDirent;
//struct dirent *ini;
DIR* dir;
SortedListPtr list = SLCreate(compareStrings);
int st = 0;
if(argc != 3)
{
printf("Incorrect amount of arguments");
return 0;
}
FILE *ofp;
ofp = fopen(outputFile, "w");
if(!ofp)
{
perror("Cannot open output file");
exit(EXIT_FAILURE);
}
st = stat(pathName,&status);
if(st != 0)
{
printf("Error");
return 1;
}
if(S_ISREG(status.st_mode))
{
readprocess(pathName, list);
outputAll(list, ofp, pathName);
fclose(ofp);
return 1;
}
dir = opendir(pathName); //returns pointer to stream
if(dir == NULL)
printf("Could not open directory: %s\n", pathName);
else
printf("\nWe are inside: %s \n", pathName);
char *currentPath = malloc(strlen(pathName)+1);
currentPath = pathName;
pDirent = readdir(dir);
while(pDirent != NULL)
{
if(pDirent->d_type == DT_REG)
{
char thePath[9999];
strcpy(thePath, currentPath);
strcat(strcat(thePath,"/"),pDirent->d_name);
char *sv = thePath;
strcpy(charptr[i], sv);
readprocess(charptr[i], list);
i++;
}
if(pDirent->d_type == DT_DIR && strcmp(pDirent->d_name, ".") != 0 && strcmp(pDirent->d_name, "..") != 0 )
{
//printf("%s\n\n", pDirent->d_name);
subDirectory(pDirent->d_name, currentPath, list);
}
pDirent = readdir(dir);
}
//closes parent directory
closedir(dir);
//-=-=-=-=--=-==-=-=-==-THIS WILL OUTPUT TO FILE-=-=--=-==-=-=-==-==--=-=
//pass the list and print it
outputAll(list, ofp, pathName);
fclose(ofp);
printf("Goodbye\n");
//-=-=-=-=-=-=--=-==-=-=-=-=-=-=--=-==-=-=-==-==--=-=-===-==-=-=-=-==-=-=-
return 0;
}
