int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
char *FileIn = NULL;
if (argc != 2) {
cerr << " Usage: " << program_name << " <input file>\n";
exit(-1);
}
else {
FileIn = argv[1];
}
// Find Input filetype
OBConversion conv(&cin, &cout);
OBFormat *inFormat = conv.FormatFromExt(FileIn);
if (!inFormat || !conv.SetInFormat(inFormat)) {
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
// If we can't also use this for an output format, use XYZ
if (!conv.SetOutFormat(inFormat))
conv.SetOutFormat(conv.FindFormat("xyz"));
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBPointGroup pg;
for (c = 1;; ++c)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
// not needed by OBPointGroup, but useful for external programs
pg.Setup(&mol);
cerr << "Point Group: " << pg.IdentifyPointGroup() << endl;
pg.Symmetrize(&mol);
conv.Write(&mol, &cout);
} // end for loop
return(1);
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
char *FileIn = NULL;
if (argc != 2) {
cerr << " Usage: " << program_name << " <input file>\n";
exit(-1);
}
else {
FileIn = argv[1];
}
// Find Input filetype
OBConversion conv;
OBFormat *inFormat = conv.FormatFromExt(FileIn);
if (!inFormat || !conv.SetInFormat(inFormat)) {
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBPointGroup pg;
for (c = 1;; ++c)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
// not needed by OBPointGroup, but useful for external programs
mol.Center();
mol.ToInertialFrame();
pg.Setup(&mol);
cout << "Point Group: " << pg.IdentifyPointGroup() << endl;
} // end for loop
return(1);
}
int main(int argc,char **argv)
{
char *program_name = argv[0];
int Nsymm = 0, Nrot = 0;
bool bKJ = false;
double dBdT = 0;
string filename, option;
OBConversion conv;
double unit_factor = 1;
string e_unit("kcal/mol");
string s_unit("cal/mol K");
if (argc < 2) {
cout << "Usage: obthermo [options] <filename>" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " --symm N override symmetry number used in input file" << endl;
cout << endl;
cout << " --nrot N number of rotatable bonds for conformational entropy" << endl;
cout << endl;
cout << " --dbdt x temperature derivative of second virial coefficient for cp calculation" << endl;
cout << endl;
cout << " --kj output kJ/mol related units (default kcal/mol)" << endl;
cout << endl;
exit(-1);
} else {
int i;
for (i = 1; i < argc; ) {
option = argv[i];
if ((option == "--symm") && (argc > (i+1))) {
Nsymm = atoi(argv[i+1]);
if (Nsymm < 1) {
cerr << program_name << ": the symmetry number should be >= 1!" << endl;
exit(-1);
}
i += 2;
}
else if ((option == "--nrot") && (argc > (i+1))) {
Nrot = atoi(argv[i+1]);
if (Nrot < 0) {
cerr << program_name << ": the number of rotatable bonds should be >= 0!" << endl;
exit(-1);
}
i += 2;
}
else if ((option == "--dbdt") && (argc > (i+1))) {
dBdT = atof(argv[i+1]);
if (dBdT < 0) {
cerr << program_name << ": the derivative of the second virial coefficient with respect to temperature should be >= 0!" << endl;
exit(-1);
}
i += 2;
}
else if (option == "--kj") {
bKJ = true;
unit_factor = 4.184;
e_unit.assign("kJ/mol");
s_unit.assign("J/mol K");
i += 1;
}
else {
filename.assign(argv[i]);
i += 1;
}
}
}
if (filename.size() == 0) {
cerr << program_name << ": no filename specified" << endl;
exit (-1);
}
// Find Input filetype
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !conv.SetInFormat(format_in)) {
cerr << program_name << ": cannot read input format in file \"" << filename << "\"" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
if ((conv.Read(&mol, &ifs)) && ! mol.Empty())
{
OBPointGroup obPG;
double temperature, DeltaHf0, DeltaHfT, DeltaGfT, DeltaSfT, S0T, CVT, CPT, ZPVE;
std::vector<double> Scomponents;
obPG.Setup(&mol);
printf("obthermo - extract thermochemistry data from quantum chemistry logfiles\n");
printf("Number of rotatable bonds: %d\n", Nrot);
if (dBdT == 0)
{
printf("Please supply --dbdt option to get reliable heat capacity at constant pressure.\n");
}
printf("Point group according to OpenBabel: %s\n",
obPG.IdentifyPointGroup());
bool bVerbose = true;
if (extract_thermochemistry(mol,
bVerbose,
&Nsymm,
Nrot,
dBdT,
&temperature,
&DeltaHf0,
&DeltaHfT,
&DeltaGfT,
&DeltaSfT,
&S0T,
&CVT,
&CPT,
Scomponents,
&ZPVE))
{
double Rgas = 1.9872041; // cal/mol K
printf("DeltaHform(0K) %10g %s\n", DeltaHf0*unit_factor, e_unit.c_str());
printf("Temperature %10g K\n", temperature);
printf("DeltaHform(T) %10g %s\n", DeltaHfT*unit_factor, e_unit.c_str());
printf("DeltaGform(T) %10g %s\n", DeltaGfT*unit_factor, e_unit.c_str());
printf("DeltaSform(T) %10g %s\n", DeltaSfT*unit_factor, s_unit.c_str());
printf("cv(T) %10g %s\n", CVT*unit_factor, s_unit.c_str());
printf("cp(T) %10g %s\n", CPT*unit_factor, s_unit.c_str());
printf("Strans(T) %10g %s\n", Scomponents[0]*unit_factor, s_unit.c_str());
printf("Srot(T) %10g %s\n", Scomponents[1]*unit_factor, s_unit.c_str());
printf("Svib(T) %10g %s\n", Scomponents[2]*unit_factor, s_unit.c_str());
if (Scomponents[3] != 0)
{
printf("Ssymm %10g %s\n", Scomponents[3]*unit_factor, s_unit.c_str());
}
if (Scomponents[4] != 0)
{
printf("Sconf %10g %s\n", Scomponents[4]*unit_factor, s_unit.c_str());
}
printf("S0(T) %10g %s\n", S0T*unit_factor, s_unit.c_str());
}
else
{
printf("Could not find all necessary information to determine thermochemistry values.\n");
}
}
ifs.close();
return 0;
}
static int extract_thermo(OpenBabel::OBMol *mol,string method,double temperature,
double ezpe,double Hcorr,double Gcorr,double E0,double CV,
int RotSymNum,std::vector<double> Scomponents)
{
// Initiate correction database
OpenBabel::OBAtomicHeatOfFormationTable *ahof = new OpenBabel::OBAtomicHeatOfFormationTable();
OpenBabel::OBAtomIterator OBai;
OpenBabel::OBAtom *OBa;
OpenBabel::OBElementTable *OBet;
char valbuf[128];
int ii,atomid,atomicnumber,found,foundall;
double dhofM0, dhofMT, S0MT, DeltaSMT;
double eFactor = HARTEE_TO_KCALPERMOL;
OBet = new OpenBabel::OBElementTable();
// Now loop over atoms in order to correct the Delta H formation
OBai = mol->BeginAtoms();
atomid = 0;
foundall = 0;
dhofM0 = E0*eFactor;
dhofMT = dhofM0+(Hcorr-ezpe)*eFactor;
S0MT = 0;
if (temperature > 0)
{
// Multiply by 1000 to make the unit cal/mol K
S0MT += 1000*eFactor*(Hcorr-Gcorr)/temperature;
}
// Check for symmetry
OBPointGroup obPG;
obPG.Setup(mol);
const char *pg = obPG.IdentifyPointGroup();
double Rgas = 1.9872041; // cal/mol K http://en.wikipedia.org/wiki/Gas_constant
double Srot = -Rgas * log(RotSymNum);
//printf("DHf(M,0) = %g, DHf(M,T) = %g, S0(M,T) = %g\nPoint group = %s RotSymNum = %d Srot = %g\n",
// dhofM0, dhofMT, S0MT, pg, RotSymNum, Srot);
if (RotSymNum > 1)
{
// We assume Gaussian has done this correctly!
Srot = 0;
}
S0MT += Srot;
DeltaSMT = S0MT;
for (OBa = mol->BeginAtom(OBai); (NULL != OBa); OBa = mol->NextAtom(OBai))
{
double dhfx0, dhfxT, S0xT;
atomicnumber = OBa->GetAtomicNum();
found = ahof->GetHeatOfFormation(OBet->GetSymbol(atomicnumber),
0,
method,
temperature,
&dhfx0, &dhfxT, &S0xT);
if (1 == found)
{
dhofM0 += dhfx0;
dhofMT += dhfxT;
DeltaSMT += S0xT;
foundall ++;
}
atomid++;
}
if (foundall == atomid)
{
std::string attr[5];
double result[5];
char buf[32];
attr[0].assign("DeltaHform(0K)");
result[0] = dhofM0;
snprintf(buf, sizeof(buf), "DeltaHform(%gK)", temperature);
attr[1].assign(buf);
result[1] = dhofMT;
snprintf(buf, sizeof(buf), "DeltaSform(%gK)", temperature);
attr[2].assign(buf);
result[2] = DeltaSMT;
snprintf(buf, sizeof(buf), "DeltaGform(%gK)", temperature);
attr[3].assign(buf);
result[3] = dhofMT - temperature*result[2]/1000;
snprintf(buf, sizeof(buf), "S0(%gK)", temperature);
attr[4].assign(buf);
result[4] = S0MT;
add_unique_pairdata_to_mol(mol, "method", method, 0);
for(ii=0; (ii<5); ii++)
{
// Add to molecule properties
sprintf(valbuf,"%f", result[ii]);
add_unique_pairdata_to_mol(mol, attr[ii], valbuf, 0);
}
sprintf(valbuf, "%f", CV);
add_unique_pairdata_to_mol(mol, "cv", valbuf, 0);
sprintf(valbuf, "%f", CV+Rgas);
add_unique_pairdata_to_mol(mol, "cp", valbuf, 0);
// Entropy components
if (Scomponents.size() == 3)
{
const char *comps[3] = { "Strans", "Srot", "Svib" };
for(int i=0; (i<3); i++)
{
sprintf(valbuf, "%f", Scomponents[i]);
add_unique_pairdata_to_mol(mol, comps[i], valbuf, 0);
}
}
// Finally store the energy in internal data structures as well.
mol->SetEnergy(dhofMT);
}
else
{
// Debug message?
}
// Clean up
delete OBet;
delete ahof;
if (foundall == atomid)
return 1;
else
return 0;
}
