/* cgiInit()
*
* Read from io.input if no string is provided via CGI. Variables that
* doesn't have a value associated with it doesn't get stored.
*/
bool CGI::Init( )
{
//if ( res && !res->vars && !res->files)
if ( ! ReadVariables () )
{
return false;
}
return true;
}
Language* LanguageReader::Read( string p_definitionFilePath )
{
ifstream eye;
eye.open(p_definitionFilePath.c_str());
if(eye.is_open())
{
ReadVariables(eye);
ReadTokenTypes(eye);
ReadStates(eye);
ReadTags(eye);
eye.close();
return new Language(new DFA(m_startState, m_errorState, m_states), m_reservedWordsToTokenTypeIdMap);
}
return NULL;
}
bool GAMESSUKOutputFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) {
/*
Read in coordinates after any reorientation due to the symmetry code
- if there is a field called "input z-matrix" then we read the initial zmatrix in here
This geometry is not needed if we are optimising as we can use the optimised geometry
However, we need to keep this geometry as it's the only one we have if it's not an opt.
- if there is no zmat, we need to read the "molecular geometry" field. This geometry
only needs to be used if we are not in an optimisation.
Read the RUN TYPE field to work out whether we need to use the first geometry.
If it's a single point caculation, we can return the molecule at this point
If it's some form of structure search, we need to go and find the final structure
*/
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if (pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream& ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
// Get a default title as the filename
const char* title = pConv->GetTitle();
mol.BeginModify();
mol.SetTitle(title);
mol.EndModify();
vector<string> tokens, geomList; // list of lines and list of tokens on a line
string line; // For convenience so we can refer to lines from the iterator as 'line'
//ReadMode_t ReadMode=SKIP;
enum RunType_t { UNKNOWN, SINGLEPOINT, OPTXYZ, OPTZMAT, SADDLE };
RunType_t RunType=UNKNOWN;
bool ok;
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)) {
/* The zmatrix entered by the user
* REM: need to add stuff for "automatic z-matrix generation" as we currently
* ignore the zmatrix & just read the cartesian coordinates
*/
if (strstr(buffer," input z-matrix") != NULL){
// Set Runtype to SINGLEPOINT so we don't read in the cartesians
RunType=SINGLEPOINT;
geomList.clear();
// skip 2 lines
ifs.getline(buffer, BUFF_SIZE) && ifs.getline(buffer, BUFF_SIZE);
// Stick a header line first
geomList.push_back("zmatrix bohr");
// Read zmatrix into list until blank line
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE) && strlen(buffer) != 0){
line = buffer;
// transform(method.begin(), method.end(), method.begin(), ::tolower);
ToLower(line);
Trim(line);
geomList.push_back(line);
}
// Skip 3 lines
ifs.getline(buffer, BUFF_SIZE) &&
ifs.getline(buffer, BUFF_SIZE) &&
ifs.getline(buffer, BUFF_SIZE);
// Read in the variables till we hit blank line
if (! ReadVariables(ifs, BOHR_TO_ANGSTROM, "")) return false;
// Now go and process the geometry
ok = ReadGeometry(mol, geomList);
} // End Reading user z-matrix
// Read the cartesian coordinates if we've not read in the ZMATRIX
if (strstr(buffer,"* charge x y z shells") != NULL &&
RunType==UNKNOWN){
// Skip 3 lines
ifs.getline(buffer, BUFF_SIZE) &&
ifs.getline(buffer, BUFF_SIZE) &&
ifs.getline(buffer, BUFF_SIZE);
// Create regex for the coords
regex_t *myregex = new regex_t;
int iok;
iok = regcomp( myregex,
// ------label-------- -------charge-------- < seems enough for a match
" *\\* *[a-zA-Z]{1,2}[0-9]* *[0-9]{1,3}\\.[0-9]{1}",
REG_EXTENDED | REG_NOSUB);
if (iok !=0) cerr << "Error compiling regex in GUK OUTPUT!\n";
// Read in the coordinates - we process them directly rather
// then use ReadGeometry as we probably should do...
mol.BeginModify();
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)){
// End of geometry block
if (strstr(buffer,"*************************")!=NULL)break;
if (regexec( myregex, buffer, 0, 0, 0)==0) {
//cerr << "Got Coord line: " << buffer << endl;
OBAtom *atom = mol.NewAtom();
tokenize(tokens,buffer," ");
atom->SetAtomicNum(atoi(tokens[2].c_str()));
double x=atof(tokens[3].c_str())*BOHR_TO_ANGSTROM;
double y=atof(tokens[4].c_str())*BOHR_TO_ANGSTROM;
double z=atof(tokens[5].c_str())*BOHR_TO_ANGSTROM;
atom->SetVector(x, y, z);
}
}
mol.EndModify();
regfree(myregex);
} // End Read Cartesian Coords
// Determine the RunType - affects how we move on from here.
if (strstr(buffer," * RUN TYPE") != NULL){
tokenize(tokens,buffer," \t\n");
if(tokens[3].compare(0,6,"optxyz")==0){
//cerr << "runtype is optxyz\n";
RunType=OPTXYZ;
break;
} else if (tokens[3].compare(0,8,"optimize")==0){
//cerr << "runtype is optimise\n";
RunType=OPTZMAT;
break;
} else if (tokens[3].compare(0,6,"saddle")==0){
//cerr << "runtype is optimise\n";
RunType=SADDLE;
break;
} else {
RunType=SINGLEPOINT;
break;
}
}
} // End First Reading loop
if(RunType==SINGLEPOINT){
// We can return the molecule that we've read in
if (mol.NumAtoms() == 0) { // e.g., if we're at the end of a file PR#1737209
mol.EndModify();
return false;
} else {
return true;
}
}
// Clear the Molecule as we're going to start from scratch again.
mol.BeginModify();
mol.Clear();
mol.EndModify();
// Start trundling through the file again - just get the last geometry
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)) {
if (strstr(buffer,"optimization converged") != NULL)
{
if (RunType==OPTXYZ){
//cerr << "Got converged for OPTXYZ\n";
// FF to start of coordinate specification
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)) {
if (strstr(buffer,
"atom znuc x y z") != NULL) break;
}
// Skip 3 lines - should then be at the coordinates
ifs.getline(buffer, BUFF_SIZE) &&
ifs.getline(buffer, BUFF_SIZE) &&
ifs.getline(buffer, BUFF_SIZE);
// Read in the coordinates - we process them directly rather
// then use ReadGeometry as we probably should do...
mol.BeginModify();
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)){
// End of geometry block
if (strstr(buffer,"*************************")!=NULL)break;
//cerr << "Got Coord line: " << buffer << endl;
OBAtom *atom = mol.NewAtom();
tokenize(tokens,buffer," ");
atom->SetAtomicNum(atoi(tokens[2].c_str()));
double x=atof(tokens[3].c_str())*BOHR_TO_ANGSTROM;
double y=atof(tokens[4].c_str())*BOHR_TO_ANGSTROM;
double z=atof(tokens[5].c_str())*BOHR_TO_ANGSTROM;
atom->SetVector(x, y, z);
}
mol.EndModify();
return true;
} else if (RunType==OPTZMAT || RunType==SADDLE) {
// Original geometry specification should still be in geomList
// So just update the variables
//cerr << "Got converged for OPTZMAT\n";
// FF to variable specification
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)) {
if (strstr(buffer,
" variable value hessian") != NULL) break;
}
// Skip a line - should then be at variable specification
ifs.getline(buffer, BUFF_SIZE);
// Process them
if (! ReadVariables(ifs, BOHR_TO_ANGSTROM,
"===============================================")) return false;
// Now go and process with the geometry we read before
return ReadGeometry(mol, geomList);
}
}
} // End Second Reading loop
return true;
} // End GAMESSUKOutputFormat::ReadMolecule
bool GAMESSUKInputFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
/*
* Stuff to think about:
* - At outset check whether we are in zmatrix, cartesian or nw-chem format
* (we currently only suppot homogeneous formats - not mixed).
*
* For each line need to check:
* - Is this a comment (?,#)
* - Are the tokens separated by commas, if so use tokenize to split at commas
* - Is there an 'end' token on the line
*
* For each line we want to check that we haven't hit a change from c to zm or vv
*
*/
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if (pmol==NULL)
return false;
//Define some references so we can use the old parameter names
istream& ifs = *pConv->GetInStream();
OBMol &mol = *pmol;
// Get a default title as the filename
const char* title = pConv->GetTitle();
mol.BeginModify();
mol.SetTitle(title);
mol.EndModify();
vector<string> geomList, tokens; // list of lines and list of tokens on a line
string line; // For convenience so we can refer to lines from the iterator as 'line'
ReadMode_t ReadMode=SKIP;
double factor=BOHR_TO_ANGSTROM;
// Read File and copy geometry specification into geomList
while (ifs.good() && ifs.getline(buffer, BUFF_SIZE)) {
// Skip commnents
if (EQn(buffer, "#", 1) || EQn(buffer, "?", 1)) continue;
// Copy line to a C++ string and convert to lower case
// & remove leading and trailing spaces
line = buffer;
// transform(method.begin(), method.end(), method.begin(), ::tolower);
ToLower(line);
Trim(line);
// Start of coordinate specifiation
if (line.compare(0, 4, "zmat")==0) {
ReadMode=ZMATRIX;
geomList.push_back(line);
continue;
} else if (line.compare(0, 4, "geom")==0) {
ReadMode=CARTESIAN;
geomList.push_back(line);
continue;
}
// Reading the coordinate specification into the list
if (ReadMode==ZMATRIX || ReadMode==CARTESIAN) {
// Variables specification - process directly from filestream
// and then remove from the geometry specification
if (line.compare(0, 4, "vari")==0 || line.compare(0, 4, "const")==0) {
// Check for commas & split with that as the separator if necessary
if (line.find(',')!=string::npos) {
tokenize(tokens, line, ",");
} else {
tokenize(tokens, line, " \t\n");
}
// See if we need to rescale
if (IsUnits(tokens[1])) factor=Rescale(tokens[1]);
if (! ReadVariables(ifs, factor, "end")) return false;
ReadMode=SKIP;
geomList.push_back("end\n");
continue;
}
if (line.compare(0, 3, "end")==0) ReadMode=SKIP;
geomList.push_back(line);
}
}// End while reading loop
// Now go and process the coordinate specification if we got any
bool ok = ReadGeometry(mol, geomList);
if (mol.NumAtoms() == 0) { // e.g., if we're at the end of a file PR#1737209
mol.EndModify();
return false;
} else {
return ok;
}
} // End ReadMolecule
