//BASIS file creation functions
void LICHEM2BASIS(int& argc,char**& argv)
{
//Writes a BASIS file based on a LICHEM regions file
fstream regfile,ofile; //File streams
string dummy; //Generic string
regfilename = "NOFILE"; //Global regions filename
//Read arguments
Nqm = 0; //For safety
Npseudo = 0; //For safety
bool DoQuit = 0; //Exit with an error
cout << "Reading LICHEM input: ";
for (int i=0;i<argc;i++)
{
dummy = string(argv[i]);
//Check regions file
if (dummy == "-b")
{
stringstream file;
file << argv[i+1];
if (!CheckFile(file.str()))
{
cout << "Error: Could not open regions file!!!";
cout << '\n';
DoQuit = 1;
}
regfilename = file.str();
regfile.open(argv[i+1],ios_base::in);
cout << argv[i+1];
}
}
cout << '\n' << '\n'; //Terminate output
//Error check
if (!CheckFile(regfilename))
{
cout << "Error: Missing region file!!!";
cout << '\n' << '\n';
DoQuit = 1;
}
//Parse input
if (!DoQuit)
{
//Parse region file
bool FoundWrapper = 0;
bool FoundBasis = 0;
bool FoundQM = 0;
bool FoundPB = 0;
vector<int> QMatoms;
vector<int> PBatoms;
string BasisSetName = "???";
string WrapperName = "N/A";
ofile.open("BASIS",ios_base::out);
if (regfile.good())
{
//Loop over the lines
while (!regfile.eof())
{
//Look for key words
stringstream line; //Generic stream
getline(regfile,dummy); //Read the line
line << dummy; //Copy to a better container
line >> dummy; //Read first item in the string
LICHEMLowerText(dummy);
if (dummy == "qm_type:")
{
//Read basis set information
line >> WrapperName;
LICHEMLowerText(WrapperName);
FoundWrapper = 1;
}
if (dummy == "qm_basis:")
{
//Read basis set information
line >> BasisSetName;
FoundBasis = 1;
}
if (dummy == "qm_atoms:")
{
//Read the list QM atoms
line >> Nqm;
for (int i=0;i<Nqm;i++)
{
//Save ID to the array
int AtNum = 0;
regfile >> AtNum;
QMatoms.push_back(AtNum);
}
FoundQM = 1;
}
//Parsers
void TINK2LICHEM(int& argc, char**& argv)
{
//Local variables
fstream TINKxyz,TINKkey,paramfile; //Input
fstream posfile,confile,regfile; //Output
stringstream line;
string dummy; //Generic string
int Ninact = 0;
bool SomeFroz = 0;
bool SomeAct = 0;
int ct; //Generic counter
//Open files
posfile.open("xyzfile.xyz",ios_base::out);
confile.open("connect.inp",ios_base::out);
regfile.open("regions.inp",ios_base::out);
//Read arguments
PBCon = 0;
cout << '\n';
cout << "Reading files: ";
for (int i=0;i<argc;i++)
{
dummy = string(argv[i]);
if (dummy == "-t")
{
//TINKER XYZ file
TINKxyz.open(argv[i+1],ios_base::in);
cout << argv[i+1];
cout << " ";
}
if (dummy == "-k")
{
//TINKER key file
TINKkey.open(argv[i+1],ios_base::in);
cout << argv[i+1];
cout << " ";
}
if (dummy == "-p")
{
//Flag for PBC
dummy = string(argv[i+1]);
LICHEMLowerText(dummy);
if ((dummy == "yes") or (dummy == "true"))
{
PBCon = 1;
}
}
}
//Start writing the files
if (PBCon)
{
//Remind forgetful users that they said the system was periodic
cout << '\n';
cout << " with PBC";
}
cout << "...";
cout << '\n';
getline(TINKxyz,dummy);
line.str(dummy);
line >> Natoms;
line >> Nqm;
if (!line.eof())
{
//Read QMMM information
//NB: This only works if the atoms are in the correct order:
// QM->PB->BA->MM
line >> Npseudo;
line >> Nbound;
}
