bool ConfigScanner::readInConfig(string configpath) {
isSafeToContinue = true;
enviro = Environment();
numOfSteps = 0;
configPath = configpath;
if (configPath.empty()) {
std::cerr << "Configuration File path is empty" << std::endl;
return false;
}
ifstream configscanner(configPath.c_str());
if (!configscanner.is_open()) {
std::cerr << "Unable to open configuration file (" << configPath << ")"
<< std::endl;
return false;
} else {
string line;
int currentLine = 1;
while (configscanner.good()) {
getline(configscanner,line);
trim(line);
//assigns attributes based on line number
switch(currentLine) {
case 2: // read in x size of environment
if (line.length() > 0) {
enviro.x = atof(line.c_str());
} else {
throwScanError("Error: Config File: Missing environment X value.");
return false;
}
break;
case 3: // read in y size of environment
if (line.length() > 0) {
enviro.y = atof(line.c_str());
} else {
throwScanError("Error: Config File: Missing environment Y value.");
return false;
}
break;
case 4: // read in z size of environment
if (line.length() > 0) {
enviro.z = atof(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment z value.");
return false;
}
break;
case 6: // read in the temperature of the environment
if (line.length() > 0) {
enviro.temp = atof(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment temperature value.");
return false;
}
break;
case 8: // read in the maximum translation an atom can have.
if (line.length() > 0) {
enviro.maxTranslation = atof(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment max translation value.");
return false;
}
break;
case 10: // read in the number of steps to perform.
if (line.length() > 0) {
numOfSteps = atoi(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing number of steps value.");
return false;
}
break;
case 12: // read in the number of molecules.
if (line.length() > 0) {
enviro.numOfMolecules = atoi(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing number of molecules value.");
return false;
}
break;
case 14: // read in the oplsua.par path.
if (line.length() > 0) {
oplsuaparPath = line;
} else {
throwScanError("Configuration file not well formed. Missing oplsuapar path value.");
return false;
}
break;
case 16: // read in the z matrix path.
if (line.length() > 0) {
zmatrixPath = line;
useZMatrixSetup = true;
useStatefileSetup = true;
} else {
throwScanError("INFO: Configuration file not well formed. Missing z-matrix path value. Attempting to rely on prior state information...");
isSafeToContinue = false; //now that it is false, check if there is a state file
useZMatrixSetup = false;
useStatefileSetup = true;
}
break;
case 18: // read in the state file path.
if (line.length() > 0) {
statePath = line;
useZMatrixSetup = false; //we will go ahead and use the statefile, since the path was provided
useStatefileSetup = true;
} else if (isSafeToContinue == false) { // If no z matrix was provided, and no state file, there is a problem.
throwScanError("Configuration file not well formed. Missing value pointing to prior state file path. Cannot safely continue with program execution.");
useStatefileSetup = false; //we can't even hope to find the state file, so don't use it
useZMatrixSetup = false;
return false; //preferable to simply exiting, as we want to give the program a chance to do...whatever?
} else { // If we don't have a state file, but do have a z-matrix, use the z-matrix.
throwScanError("INFO: Value pointing to prior state file path not found in main config file. Environment setup defaulting to clean simulation.");
useZMatrixSetup = true; //revert to using the Zmatrix file for all setup
useStatefileSetup = false;
isSafeToContinue = true;
}
break;
case 20: // read in the path to output state files to.
if (line.length() > 0) {
stateOutputPath = line;
} else {
throwScanError("Configuration file not well formed. Missing state file output path value.");
return false;
}
break;
case 22: // read in the path to output pdb files to.
if (line.length() > 0) {
pdbOutputPath = line;
} else {
throwScanError("Configuration file not well formed. Missing PDB output path value.");
return false;
}
break;
case 24: // read in the energy calculation cutoff value.
if (line.length() > 0) {
enviro.cutoff = atof(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment cutoff value.");
return false;
}
break;
case 26: // read in the max rotation value.
if (line.length() > 0) {
enviro.maxRotation = atof(line.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment max rotation value.");
return false;
}
break;
case 28: // read in the random seed.
if (line.length() > 0) {
enviro.randomseed=atoi(line.c_str());
} else {
enviro.randomseed = (unsigned int) time(NULL);
//throwScanError("Configuration file not well formed. Missing random seed value.");
//return false;
}
break;
case 30: // Get the primary atom index definitions.
if (line.length() > 0) {
// Convert to a zero-based index
parsePrimaryIndexDefinitions(line);
} else {
throwScanError("Configuration file not well formed. Missing environment primary atom index value.");
return false;
}
break;
}
currentLine++;
}
}
configscanner.close();
return true;
}
bool ConfigScanner::readInConfig(string configpath) {
isSafeToContinue = true;
enviro = Environment();
numOfSteps = 0;
configPath = configpath;
if (configPath.empty()) {
std::cerr << "Configuration File path is empty" << std::endl;
return false;
}
ifstream configscanner(configPath.c_str());
if (!configscanner.is_open()) {
std::cerr << "Unable to open configuration file (" << configPath << ")"
<< std::endl;
return false;
}
string line;
while (configscanner.good()) {
getline(configscanner, line);
trim(line);
// Ignore blank lines and comments
if (line.empty() || line[0] == '#' || line[0] == ';') {
continue;
}
// Sections are supported, but don't have any additional functionality
if (line[0] == '[' && line.find(']') == line.length()) {
continue;
}
int splitPos = line.find('=');
if (splitPos == -1) {
throwScanError("Error: Configuration File not well formed.\n"
"Offending line: \"" + line + "\"");
return false;
}
string key = line.substr(0, splitPos);
string value = line.substr(splitPos+1, line.length());
// Assign attributes based on key
if (key == "x") {
if (value.length() > 0) {
enviro.x = atof(value.c_str());
} else {
throwScanError("Error: Config File: Missing environment X value.");
return false;
}
} else if (key == "y") {
if (value.length() > 0) {
enviro.y = atof(value.c_str());
} else {
throwScanError("Error: Config File: Missing environment Y value.");
return false;
}
} else if (key == "z") {
if (value.length() > 0) {
enviro.z = atof(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment z value.");
return false;
}
} else if (key == "temp") {
if (value.length() > 0) {
enviro.temp = atof(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment temperature value.");
return false;
}
} else if (key == "max-translation") {
if (value.length() > 0) {
enviro.maxTranslation = atof(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment max translation value.");
return false;
}
} else if (key == "steps") {
if (value.length() > 0) {
numOfSteps = atoi(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing number of steps value.");
return false;
}
} else if (key == "molecules") {
if (value.length() > 0) {
enviro.numOfMolecules = atoi(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing number of molecules value.");
return false;
}
} else if (key == "opla.par") {
if (value.length() > 0) {
oplsuaparPath = value;
} else {
throwScanError("Configuration file not well formed. Missing oplsuapar path value.");
return false;
}
} else if (key == "z-matrix") {
if (value.length() > 0) {
zmatrixPath = value;
useZMatrixSetup = true;
useStatefileSetup = true;
} else {
throwScanError("INFO: Configuration file not well formed. Missing z-matrix path value. Attempting to rely on prior state information...");
isSafeToContinue = false; //now that it is false, check if there is a state file
useZMatrixSetup = false;
useStatefileSetup = true;
}
} else if (key == "state-input") {
if (value.length() > 0) {
statePath = value;
useZMatrixSetup = false; //we will go ahead and use the statefile, since the path was provided
useStatefileSetup = true;
} else if (isSafeToContinue == false) { // If no z matrix was provided, and no state file, there is a problem.
throwScanError("Configuration file not well formed. Missing value pointing to prior state file path. Cannot safely continue with program execution.");
useStatefileSetup = false; //we can't even hope to find the state file, so don't use it
useZMatrixSetup = false;
return false; //preferable to simply exiting, as we want to give the program a chance to do...whatever?
} else { // If we don't have a state file, but do have a z-matrix, use the z-matrix.
throwScanError("INFO: Value pointing to prior state file path not found in main config file. Environment setup defaulting to clean simulation.");
useZMatrixSetup = true; //revert to using the Zmatrix file for all setup
useStatefileSetup = false;
isSafeToContinue = true;
}
} else if (key == "state-output") {
if (value.length() > 0) {
stateOutputPath = value;
} else {
throwScanError("Configuration file not well formed. Missing state file output path value.");
return false;
}
} else if (key == "pdb-output") {
if (value.length() > 0) {
pdbOutputPath = value;
} else {
throwScanError("Configuration file not well formed. Missing PDB output path value.");
return false;
}
} else if (key == "cutoff") {
if (value.length() > 0) {
enviro.cutoff = atof(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment cutoff value.");
return false;
}
} else if (key == "max-rotation") {
if (value.length() > 0) {
enviro.maxRotation = atof(value.c_str());
} else {
throwScanError("Configuration file not well formed. Missing environment max rotation value.");
return false;
}
} else if (key == "random-seed") {
if (value.length() > 0) {
enviro.randomseed=atoi(value.c_str());
} else {
enviro.randomseed = (unsigned int) time(NULL);
}
} else if (key == "primary-atom") {
if (value.length() > 0) {
// Convert to a zero-based index
parsePrimaryIndexDefinitions(value);
} else {
throwScanError("Configuration file not well formed. Missing "
"environment primary atom index value.");
return false;
}
} else if (key == "sim-name") {
if (value.length() > 0) {
simName = value;
}
} else if (key == "strategy") {
if (value.length() > 0) {
strategy = value;
}
} else if (key == "max-bond-delta") {
enviro.maxBondDelta = atof(value.c_str());
} else if (key == "max-angle-delta") {
enviro.maxAngleDelta = atof(value.c_str());
} else {
throwScanError("Unexpected key encountered: " + key);
return false;
}
}
configscanner.close();
return true;
}
