LoadDefaultsDecoder::LoadDefaultsDecoder(const std::string& filename)
{
std::fstream stream;
stream.open(filename.c_str(), std::ios::in);
if (!stream) {
throw DefaultLoadingException("Failed to open file " + filename);
}
//replace following code with:
//getCodecByName(const std::string& name, Stream& stream, Bridge* bridge)
//typedef list<Atlas::Factory<Atlas::Codec<std::iostream> >*> FactoryCodecs;
//FactoryCodecs *myCodecs = Factory<Codec<std::iostream> >::factories();
//FactoryCodecs::iterator i;
//Atlas::Codec<std::iostream> *codec = NULL;
//for (i = myCodecs->begin(); i != myCodecs->end(); ++i)
//if((*i)->getName() == "XML")
//codec = (*i)->New(Codec<std::iostream>::Parameters((iostream&)stream, this));
//end of replace
Atlas::Codec *codec = new Atlas::Codecs::XML(stream, *this);
while(stream) {
codec->poll();
}
delete codec;
MapType anonymous_obj;
m_objects["anonymous"] = anonymous_obj;
MapType generic_obj;
m_objects["generic"] = generic_obj;
fillDefaults();
}
const IR::Node* DoDefaultArguments::postorder(IR::Declaration_Instance* inst) {
auto ii = Instantiation::resolve(inst, refMap, typeMap);
auto args = fillDefaults(&ii->substitution);
if (args != nullptr)
inst->arguments = args;
return inst;
}
const IR::Node* DoDefaultArguments::postorder(IR::MethodCallExpression* mce) {
auto mi = MethodInstance::resolve(mce, refMap, typeMap);
auto args = fillDefaults(&mi->substitution);
if (args != nullptr)
mce->arguments = args;
return mce;
}
const IR::Node* DoDefaultArguments::postorder(IR::ConstructorCallExpression* cce) {
auto cc = ConstructorCall::resolve(cce, refMap, typeMap);
auto args = fillDefaults(&cc->substitution);
if (args != nullptr)
cce->arguments = args;
return cce;
}
void ConfigSetup::Init(const char *fileName)
{
std::vector<std::string> line;
//ADDED LINES TO GET PREFIX PATH AND
//CONVERT CHAR ARRY TO STRING TYPE TO GET PREFIX PATH
//string prefix;
std::string inputString(fileName);
size_t found = inputString.rfind('/');
if (found != std::string::npos)
prefix = inputString.substr(0, inputString.find_last_of('/')) + '/';
//END ADD LINE
reader.Open(fileName);
while(reader.readNextLine(line))
{
if(line[0] == "Restart") {
in.restart.enable = checkBool(line[1]);
} else if(line[0] == "FirstStep") {
in.restart.step = stringtoi(line[1]);
} else if(line[0] == "PRNG") {
in.prng.kind = line[1];
} else if(line[0] == "Random_Seed") {
in.prng.seed = stringtoi(line[1]);
} else if(line[0] == "ParaTypeCHARMM") {
if(checkBool(line[1]))
{
in.ffKind.numOfKinds++;
in.ffKind.isEXOTIC = false;
in.ffKind.isMARTINI = false;
in.ffKind.isCHARMM = true;
std::cout << "REMINDER: CHARMM force field has been selected!" << std::endl;
}
} else if(line[0] == "ParaTypeEXOTIC") {
if(checkBool(line[1]))
{
in.ffKind.numOfKinds++;
in.ffKind.isCHARMM = false;
in.ffKind.isMARTINI = false;
in.ffKind.isEXOTIC = true;
std::cout << "REMINDER: EXOTIC force field has been selected!" << std::endl;
}
} else if(line[0] == "ParaTypeMARTINI") {
if(checkBool(line[1]))
{
in.ffKind.numOfKinds ++;
in.ffKind.isEXOTIC = false;
in.ffKind.isMARTINI = true;
in.ffKind.isCHARMM = true;
std::cout << "REMINDER: MARTINI force field has been selected!" << std::endl;
}
} else if(line[0] == "Parameters") {
in.files.param.name = prefix + line[1]; //ADDED PREFIX
} else if(line[0] == "Coordinates") {
uint boxnum = stringtoi(line[1]);
if(boxnum >= BOX_TOTAL)
{
std::cout<< "Error: This simulation requires only " << BOX_TOTAL << " number of PDB file(s)!" << std::endl;
exit(0);
}
in.files.pdb.name[boxnum] = prefix + line[2]; //ADDED PREFIX
} else if(line[0] == "Structure") {
uint boxnum = stringtoi(line[1]);
if(boxnum >= BOX_TOTAL)
{
std::cout<< "Error: This simulation requires only " << BOX_TOTAL << " number of PSF file(s)!" << std::endl;
exit(0);
}
in.files.psf.name[boxnum] = prefix + line[2]; //ADDED PREFIX
}
#if ENSEMBLE == GEMC
else if(line[0] == "GEMC")
{
if(line[1] == "NVT")
{
sys.gemc.kind = mv::GEMC_NVT;
std::cout<< " NVT_GEMC simulation has been selected " << std::endl;
}
else if(line[1] == "NPT")
{
sys.gemc.kind = mv::GEMC_NPT;
std::cout<< " NPT_GEMC simulation has been selected " << std::endl;
}
}
else if(line[0] == "Pressure")
{
sys.gemc.pressure = stringtod(line[1]);
std::cout<< " Pressure of system has been set to " << sys.gemc.pressure << " bar " << std::endl;
sys.gemc.pressure *= unit::BAR_TO_K_MOLECULE_PER_A3;
}
#endif
else if(line[0] == "Temperature")
{
sys.T.inKelvin = stringtod(line[1]);
}
else if(line[0] == "Potential")
{
if(line[1] == "VDW")
sys.ff.VDW_KIND = sys.ff.VDW_STD_KIND;
else if(line[1] == "SHIFT")
sys.ff.VDW_KIND = sys.ff.VDW_SHIFT_KIND;
else if(line[1] == "SWITCH")
sys.ff.VDW_KIND = sys.ff.VDW_SWITCH_KIND;
}
else if(line[0] == "LRC")
{
sys.ff.doTailCorr = checkBool(line[1]);
}
else if(line[0] == "Rswitch")
{
sys.ff.rswitch = stringtod(line[1]);
}
else if(line[0] == "Rcut")
{
sys.ff.cutoff = stringtod(line[1]);
}
else if(line[0] == "Exclude")
{
if(line[1] == sys.exclude.EXC_ONETWO)
sys.exclude.EXCLUDE_KIND = sys.exclude.EXC_ONETWO_KIND;
else if(line[1] == sys.exclude.EXC_ONETHREE)
sys.exclude.EXCLUDE_KIND = sys.exclude.EXC_ONETHREE_KIND;
else if(line[1] == sys.exclude.EXC_ONEFOUR)
sys.exclude.EXCLUDE_KIND = sys.exclude.EXC_ONEFOUR_KIND;
}
else if(line[0] == "Ewald")
{
sys.elect.ewald = checkBool(line[1]);
sys.elect.readEwald = true;
}
else if(line[0] == "ElectroStatic")
{
sys.elect.enable = checkBool(line[1]);
sys.elect.readElect = true;
}
else if(line[0] == "Tolerance")
{
sys.elect.tolerance = stringtod(line[1]);
sys.elect.alpha = sqrt(-1 * log(sys.elect.tolerance))/
sys.ff.cutoff;
sys.elect.recip_rcut = 2 * (-log(sys.elect.tolerance))/
sys.ff.cutoff;
}
else if(line[0] == "1-4scaling")
{
sys.elect.oneFourScale = stringtod(line[1]);
}
else if(line[0] == "Dielectric")
{
sys.elect.dielectric = stringtod(line[1]);
}
else if(line[0] == "RunSteps")
{
sys.step.total = stringtoi(line[1]);
}
else if(line[0] == "EqSteps")
{
sys.step.equil = stringtoi(line[1]);
}
else if(line[0] == "AdjSteps")
{
sys.step.adjustment = stringtoi(line[1]);
}
else if(line[0] == "DisFreq")
{
sys.moves.displace = stringtod(line[1]);
}
else if(line[0] == "IntraSwapFreq")
{
sys.moves.intraSwap = stringtod(line[1]);
}
else if(line[0] == "RotFreq")
{
sys.moves.rotate = stringtod(line[1]);
}
#ifdef VARIABLE_VOLUME
else if(line[0] == "VolFreq")
{
sys.moves.volume = stringtod(line[1]);
}
#endif
#ifdef VARIABLE_PARTICLE_NUMBER
else if(line[0] == "SwapFreq")
{
#if ENSEMBLE == NVT
sys.moves.transfer = 0.000;
#else
sys.moves.transfer = stringtod(line[1]);
#endif
}
#endif
else if(line[0] == "BoxDim") {
uint box = stringtoi(line[1]);
if(box < BOX_TOTAL)
{
XYZ temp;
sys.volume.boxCoordRead++;
sys.volume.hasVolume = (sys.volume.boxCoordRead == BOX_TOTAL);
temp.x = stringtod(line[2]);
temp.y = stringtod(line[3]);
temp.z = stringtod(line[4]);
sys.volume.axis.Set(box, temp);
}
else
{
std::cout<< "Error: This simulation requires only " << BOX_TOTAL << " number of box dimension(s)!" << std::endl;
exit(0);
}
}
#ifdef VARIABLE_PARTICLE_NUMBER
else if(line[0] == "CBMC_First")
{
sys.cbmcTrials.nonbonded.first = stringtoi(line[1]);
}
else if(line[0] == "CBMC_Nth")
{
sys.cbmcTrials.nonbonded.nth = stringtoi(line[1]);
}
else if(line[0] == "CBMC_Ang")
{
sys.cbmcTrials.bonded.ang = stringtoi(line[1]);
}
else if(line[0] == "CBMC_Dih")
{
sys.cbmcTrials.bonded.dih = stringtoi(line[1]);
}
#endif
#if ENSEMBLE == GCMC
else if(line[0] == "ChemPot") {
if(line.size() != 3)
{
std::cout << "Error: Chemical potential parameters have not been specified!" << std::endl;
exit(0);
}
std::string resName = line[1];
double val = stringtod(line[2]);
sys.chemPot.cp[resName] = val;
}
#endif
else if(line[0] == "OutputName")
{
out.statistics.settings.uniqueStr.val = line[1];
}
else if(line[0] == "CoordinatesFreq")
{
out.state.settings.enable = checkBool(line[1]);
out.state.settings.frequency = stringtoi(line[2]);
}
else if(line[0] == "RestartFreq")
{
out.restart.settings.enable = checkBool(line[1]);
out.restart.settings.frequency = stringtoi(line[2]);
}
else if(line[0] == "ConsoleFreq")
{
out.console.enable = checkBool(line[1]);
out.console.frequency = stringtoi(line[2]);
}
else if(line[0] == "BlockAverageFreq")
{
out.statistics.settings.block.enable = checkBool(line[1]);
out.statistics.settings.block.frequency = stringtoi(line[2]);
}
else if(line[0] == "FluctuationFreq")
{
out.statistics.settings.fluct.enable = checkBool(line[1]);
out.statistics.settings.fluct.frequency = stringtoi(line[2]);
}
#if ENSEMBLE == GCMC
else if(line[0] == "HistogramFreq")
{
out.statistics.settings.hist.enable = checkBool(line[1]);
out.statistics.settings.hist.frequency = stringtoi(line[2]);
}
else if(line[0] == "DistName")
{
out.state.files.hist.histName = line[1];
}
else if(line[0] == "HistName")
{
out.state.files.hist.sampleName = line[1];
}
else if(line[0] == "RunNumber")
{
out.state.files.hist.number = line[1];
}
else if(line[0] == "RunLetter")
{
out.state.files.hist.letter = line[1];
}
else if(line[0] == "SampleFreq")
{
out.state.files.hist.stepsPerHistSample = stringtoi(line[1]);
}
#endif
else if(line[0] == "OutEnergy") {
out.statistics.vars.energy.block = checkBool(line[1]);
out.statistics.vars.energy.fluct = checkBool(line[2]);
out.statistics.vars.energy.hist = checkBool(line[3]);
} else if(line[0] == "OutPressure") {
out.statistics.vars.pressure.block = checkBool(line[1]);
out.statistics.vars.pressure.fluct = checkBool(line[2]);
out.statistics.vars.pressure.hist = checkBool(line[3]);
}
#ifdef VARIABLE_PARTICLE_NUMBER
else if(line[0] == "OutMolNum") {
out.statistics.vars.molNum.block = checkBool(line[1]);
out.statistics.vars.molNum.fluct = checkBool(line[2]);
out.statistics.vars.molNum.hist = checkBool(line[3]);
} else if(line[0] == "OutAcceptAngles") {
out.statistics.vars.acceptAngles.block = checkBool(line[1]);
out.statistics.vars.acceptAngles.fluct = checkBool(line[2]);
out.statistics.vars.acceptAngles.hist = checkBool(line[3]);
}
#endif
#ifdef VARIABLE_DENSITY
else if(line[0] == "OutDensity") {
out.statistics.vars.density.block = checkBool(line[1]);
out.statistics.vars.density.fluct = checkBool(line[2]);
out.statistics.vars.density.hist = checkBool(line[3]);
}
#endif
#ifdef VARIABLE_VOLUME
else if(line[0] == "OutVolume") {
out.statistics.vars.volume.block = checkBool(line[1]);
out.statistics.vars.volume.fluct = checkBool(line[2]);
out.statistics.vars.volume.hist = checkBool(line[3]);
}
#endif
else{
cout << "Warning: Unknown input " << line[0] << "!" << endl;
}
// Clear and get ready for the next line
line.clear();
}
//*********** Fill in the default values if not specified ***********//
fillDefaults();
//*********** Verify inputs ***********//
verifyInputs();
}
