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Simulation.cpp
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Simulation.cpp
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/*
* Simulation.cpp
*
* Created on: May 4, 2012
* Author: dstuck
*/
#include "Simulation.h"
Simulation::Simulation(string inFileName, string logFileName, string prmFile) : autoCorr(1000) {
//*******************************************************
//* Default Parameters *
//*******************************************************
/*
stepNum = 0;
maxStep = 1000000;
sampleStart = 1000;
sampleFreq = 5;
convFreq = 10000;
storeFreq = 100000;
// beta = 21000; //21000 corresponds to 15 K
beta = 10500; //30 K
// beta = 5250; //60 K
*/
// DES Temp:
// tempNum = 0;
maxSim = 1;
epsInit = -1.0;
bool readOmega = false;
bool readGeom = false;
bool internalCoords = false;
bool scaleGeom = false;
int nPart = 0;
int pSlice = 0;
int nMode;
int coorDim;
bool deltaAI;
// I had been running this previously with the wrong intended mass (3500 instead of 35000)
// double m = 3500.0; // 35000 me corresponds to ~20 nuclei
// The line below is false, w = 0.00868 corresponds to 11976 wavenumber
// double w = 2.0*sqrt(2.0*0.033/3500.0); //.0026 corresponds to 3600 wavenumber
vector<double> kFreq;
vector<double> omega;
// for(int j=0; j<nPart; j++){
// omega.push_back(w);
// }
// int a = 1; // Atomic number
levyNum = 30;
levyModes = 0;
levyNumInit = -1;
levyModesInit = -1;
numTI = 0;
numGeomPrint = 0;
errorThresh = 0.05;
tau = -1.0;
storeNum = -1;
maxStep = -1;
sampleStart = -1;
initLen = -1;
autoCorrLen = 20000;
//autoCorrLen = -1;
sampleFreq = 1;
noEnergy = false;
vector<double> mass;
vector<string> atomType;
vector<int> paramType;
vector< vector<int> > connectivity;
vector< vector<double> > initPos;
vector< vector< vector<double> > > modes; //modes[i][j][k] will the the kth coordinate of the jth atom of the ith normal mode
PhysicsUtil * physicsParams = new PhysicsUtil();
//*******************************************************
//* Reading in input *
//*******************************************************
// Open the infile
ifstream input;
input.open(inFileName.c_str());
// DES Temp:
// string tempstr = "potential.txt";
// vFile.open(tempstr.c_str());
// Read in and parse the file
string lineRead;
while(std::getline(input, lineRead)) { // Reads next line until it reaches end of file
// Read molecule section from .pin file
if(lineRead.find("$molecule") != std::string::npos) { //If line contains $molecule
while(!(std::getline(input, lineRead).eof()) && (lineRead.find("$end") == std::string::npos)) { //Reads next line always, goes through parsing if line isn't $end
// cout << lineRead << endl;
vector<string> lineTokens;
Tokenize(lineRead, lineTokens);
int tokenShift = 0;
// Ignore first token if it is just an integer
if(atoi(lineTokens[0].c_str())) {
tokenShift++;
}
if(int(lineTokens.size()) < 4+tokenShift) {
cout << "Error in input file: $molecule" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
atomType.push_back(lineTokens[tokenShift]);
tokenShift++;
vector<double> p0;
for(int k=0; k< 3; k++) {
p0.push_back(atof(lineTokens[k+tokenShift].c_str()));
}
tokenShift += 3;
initPos.push_back(p0);
vector<int> con0;
for(int c=0; c<int(lineTokens.size()-tokenShift); c++) {
con0.push_back(atoi(lineTokens[c+tokenShift].c_str()));
}
connectivity.push_back(con0);
}
} // end of reading molecule section
// Read in parameters from .pin file
if(lineRead.find("$params") != std::string::npos) {
while(!(std::getline(input, lineRead).eof()) && (lineRead.find("$end") == std::string::npos)) {
// cout << lineRead << endl;
if(lineRead.find("!") != std::string::npos) {
}
else if(lineRead.find_first_not_of(" \t\r\n") == std::string::npos) {
}
else {
vector<string> lineTokens;
Tokenize(lineRead, lineTokens);
if(lineTokens.size() != 2) {
cout << "Error in input file: $params" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
if(lineTokens[0].find("maxSim") != std::string::npos) {
maxSim = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("maxStep") != std::string::npos) {
maxStep = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("initLen") != std::string::npos) {
initLen = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("autoCorrLen") != std::string::npos) {
autoCorrLen = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("sampleStart") != std::string::npos) {
sampleStart = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("sampleFreq") != std::string::npos) {
sampleFreq = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("convFreq") != std::string::npos) {
convFreq = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("storeFreq") != std::string::npos) {
storeFreq = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("storeNum") != std::string::npos) {
storeNum = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("errorThresh") != std::string::npos) {
errorThresh = atof(lineTokens[1].c_str())/100.0;
}
else if(lineTokens[0].find("beta") != std::string::npos) {
beta = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("temperature") != std::string::npos) {
// Atomic temperature units from http://en.wikipedia.org/wiki/Atomic_units 4/18/15
beta = 315774.65/atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("tempInit") != std::string::npos) {
epsInit = 315774.65/atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("initTemp") != std::string::npos) {
epsInit = 315774.65/atof(lineTokens[1].c_str());
}
// TODO: merge nPart read with $molecule section
else if(lineTokens[0].find("nPart") != std::string::npos) {
nPart = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("pSlice") != std::string::npos) {
pSlice = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("levyNum") != std::string::npos) {
if(lineTokens[0].find("levyNumInit") != std::string::npos) {
levyNumInit = atoi(lineTokens[1].c_str());
}
else {
levyNum = atoi(lineTokens[1].c_str());
}
}
else if(lineTokens[0].find("levyModes") != std::string::npos) {
if(lineTokens[0].find("levyModesInit") != std::string::npos) {
levyModesInit = atoi(lineTokens[1].c_str());
}
else {
levyModes = atoi(lineTokens[1].c_str());
}
}
else if(lineTokens[0].find("levyInit") != std::string::npos) {
physicsParams->numInit = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("internalCoords") != std::string::npos) {
if(atof(lineTokens[1].c_str())>0) {
internalCoords = true;
}
}
else if(lineTokens[0].find("rhoType") != std::string::npos) {
physicsParams->rhoType = lineTokens[1];
}
else if(lineTokens[0].find("vType") != std::string::npos) {
physicsParams->vType = lineTokens[1];
}
else if(lineTokens[0].find("morseDE") != std::string::npos) {
physicsParams->morseDE = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("morseAlpha") != std::string::npos) {
physicsParams->morseAlpha = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("morseMass") != std::string::npos) {
physicsParams->morseMass = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("freqCutoff") != std::string::npos) {
physicsParams->freqCutoff = atof(lineTokens[1].c_str())*0.00000455633;
}
else if(lineTokens[0].find("numFrozModes") != std::string::npos) {
physicsParams->lowFrozModes = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("lowFrozModes") != std::string::npos) {
physicsParams->lowFrozModes = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("highFrozModes") != std::string::npos) {
physicsParams->highFrozModes = atof(lineTokens[1].c_str());
}
else if(lineTokens[0].find("numTI") != std::string::npos) {
numTI=atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("numGeomPrint") != std::string::npos) {
numGeomPrint=atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("noEnergy") != std::string::npos) {
if(atof(lineTokens[1].c_str())>0) {
noEnergy = true;
}
}
else if(lineTokens[0].find("readGeom") != std::string::npos) {
if(atof(lineTokens[1].c_str())>0) {
readGeom = true;
}
}
else if(lineTokens[0].find("readOmega") != std::string::npos) {
if(atof(lineTokens[1].c_str())>0) {
readOmega = true;
}
}
else if(lineTokens[0].find("scaleGeom") != std::string::npos) {
if(atof(lineTokens[1].c_str())>0) {
scaleGeom = true;
}
}
else if(lineTokens[0].find("charge") != std::string::npos) {
physicsParams->charge = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("multiplicity") != std::string::npos || lineTokens[0].find("spin") != std::string::npos) {
physicsParams->multiplicity = atoi(lineTokens[1].c_str());
}
else if(lineTokens[0].find("deltaAI") != std::string::npos) {
if(atof(lineTokens[1].c_str())>0) {
physicsParams->deltaAbInit = true;
}
}
else {
cout << "Unrecognized input name " << lineTokens[0] << " skipped." << endl;
}
}
}
} // end of reading $params section
// Read in normal modes from .pin file
if(lineRead.find("$modes") != std::string::npos) {
while(!(std::getline(input, lineRead).eof()) && (lineRead.find("$end") == std::string::npos)) {
vector<string> lineTokens;
Tokenize(lineRead, lineTokens);
if(lineTokens.size() >= 1) {
// Ignore mode number
if(lineTokens[0].find("Mode:") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
// Set up frequencies
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("Frequency:") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
for(int w = 1; w < int(lineTokens.size()); w++) {
omega.push_back(atof(lineTokens[w].c_str())*0.00000455633); // 0.00000455633 is the conversion factor from cm^-1 to (atomic seconds)^-1
}
// Ignore force constants
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("Force") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
// Set up reduced masses of oscillators
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("Red.") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
for(int w = 2; w < int(lineTokens.size()); w++) {
mass.push_back(atof(lineTokens[w].c_str())*1822.8886); // 1822.8886 is the conversion factor from amu to atomic mass units (i.e. electron masses)
}
// Ignore IR Active
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("IR") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
// Ignore IR Intens
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("IR") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
// Ignore Raman Active
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("Raman") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
// Skip XYZ line
std::getline(input, lineRead);
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens[0].find("X") == std::string::npos) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
// Store harmonic modes
int columns = 0;
vector<double> tempModeInner;
vector< vector<double> > tempModeMid[3];
while(!(std::getline(input, lineRead).eof()) && (lineRead.find("TransDip") == std::string::npos)) { // Important: Keeps reading until TransDip line
lineTokens.clear();
Tokenize(lineRead, lineTokens);
if(lineTokens.size()%3 != 1) {
cout << "Error in input file: $modes" << endl;
cout << "Found line: " << lineRead << endl;
exit(-1);
}
columns = (lineTokens.size()-1)/3;
for(int j = 0; j < columns; j++) {
for(int i = 0; i < 3; i++) {
tempModeInner.push_back(atof(lineTokens[1+i+3*j].c_str()));
}
tempModeMid[j].push_back(tempModeInner);
tempModeInner.clear();
}
}
for(int j=0; j<columns; j++){
modes.push_back(tempModeMid[j]);
tempModeMid[j].clear();
}
} //end of not empty line check
}
} //end of reading $modes section
} // end of reading .pin file
//**********************
//* Variable Cleanup
//**********************
// Set up job length parameters(
if(autoCorrLen<=0 || maxSim > 1) {
cout << "Warning: Not using new standard of autoCorrLen > 0 and maxSim = 1. Continue at your own risk!" << endl;
}
if(initLen<0 && autoCorrLen > 0) {
initLen = autoCorrLen/4;
}
if(sampleStart>=0) {
if(initLen < 0) {
initLen = sampleStart;
}
else if((initLen+autoCorrLen) != sampleStart) {
cout << "Error: sampleStart != initLen+autoCorrLen" << endl;
exit(-1);
}
}
if(autoCorrLen > 0) {
sampleStart = initLen + autoCorrLen;
}
else {
sampleStart = initLen;
numSamples = maxStep - initLen;
}
// For autocorrelation based jobs, we don't know maxStep yet so set it after init
maxStep = max(maxStep,sampleStart+1);
// )
if(int(omega.size())!=int(mass.size())){
cout << "Error: Number of reduced masses not equal to number of frequencies" << endl;
cout << "omega dim = " << omega.size() << " but mass dim = " << mass.size() << endl;
exit (-1);
}
if(nPart == 0) {
nPart = connectivity.size();
}
else if(int(connectivity.size()) != nPart) {
cout << "Error: Number of atoms not equal to number of coordinates" << endl;
cout << "connectivity dim = " << connectivity.size() << " but nPart = " << nPart << endl;
exit (-1);
}
//DES Temp
// cout << "DES: connectivity" << endl;
// for(int i=0; i<connectivity.size(); i++) {
// for(int j=0; j< connectivity[i].size(); j++) {
// cout << connectivity[i][j] << "\t";
// }
// cout << endl;
// }
// exit(-1);
if(nPart==2) {
nMode = 1; //Linear case!
}
else {
// TODO: Doesn't work for linear molecules!
nMode = nPart*3-6;
}
if(levyModes==0) {
levyModes = nMode - (physicsParams->lowFrozModes+physicsParams->highFrozModes);
}
else if(levyModes>nMode - (physicsParams->lowFrozModes+physicsParams->highFrozModes)) {
cout << "Error: Total modes moved > number of modes!" << endl;
exit(-1);
}
if(levyModesInit==0) {
levyModesInit = nMode - (physicsParams->lowFrozModes+physicsParams->highFrozModes);
}
else if(levyModesInit>nMode - (physicsParams->lowFrozModes+physicsParams->highFrozModes)) {
cout << "Error: Total modes moved in initialization > number of modes!" << endl;
exit(-1);
}
if(physicsParams->lowFrozModes+physicsParams->highFrozModes > nMode) {
cout << "Error: Total frozen modes > number of modes!" << endl;
exit(-1);
}
coorDim = 1;
// nMode = nPart;
// coorDim = 3;
// mass.clear();
// for(int i=0; i<nPart; i++) {
// if(!atomType[i].compare("H")) {
// mass.push_back(1.0*1822.8886+1.0);
// }
// else if(!atomType[i].compare("O")) {
// mass.push_back(16.0*1822.8886+8.0);
// }
// else if(!atomType[i].compare("S")) {
// mass.push_back(32.0*1822.8886+16.0);
// }
// else {
// cout << "Unimplemented atom type. See Simulation.cpp" << endl;
// exit(-1);
// }
// }
if(physicsParams->numInit<0) {
physicsParams->numInit = pSlice-1;
}
if(physicsParams->isDeltaAI() && numTI<1) {
numTI=1;
cout << "DES: Setting numTI to 1 for deltaAI" << endl;
}
outName = logFileName.substr(0, logFileName.find_first_of("."));
epsilon = beta/((double)pSlice);
if(epsInit > 0) {
epsInit /= ((double)pSlice);
}
if(levyNumInit < 1) {
levyNumInit = levyNum;
}
if(levyModesInit < 1) {
levyModesInit = levyModes;
}
// double eZPE=0;
// double eFull=0;
// for(int i=0; i<nMode; i++){
// eZPE += omega[i]/2.0;
// eFull += omega[i]/2.0/tanh(beta*omega[i]/2.0);
// }
// cout << "Harmonic ZPE:\t" << eZPE << endl;
// cout << "Harmonic Energy:\t" << eFull << endl;
/*
for(int i = 0; i < nPart; i++) {
for (int k = 0; k < coorDim; k++) {
p0.push_back(0.0);
}
initPos.push_back(p0);
mass.push_back(m);
atomType.push_back(a);
}
*/
CoordUtil * coords = new CoordUtil(nMode, nPart, internalCoords, modes, omega, mass, initPos, atomType, paramType, connectivity, outName, prmFile, readGeom, readOmega);
coords->scaleGeom = scaleGeom;
sys = new TestSystem(pSlice, beta, coords, physicsParams);
simStats = new Stats();
simPotStats = new Stats();
// simComboStats = new Stats();
energyStats = new Stats();
potentialStats = new Stats();
// comboStats = new Stats();
convergenceStats = new Stats();
acceptanceStats = new Stats();
// xStats = new Stats();
// posFileName = "SHO.xyz";
// posFile.open(posFileName.c_str());
outFileName = logFileName;
logFile.open(outFileName.c_str(), ios::out | ios::app); //Append logFile
// Write Parameters to logFile
time_t t = time(0);
struct tm * current = localtime( & t );
// cout << outFileName << endl;
logFile << "-------------------------------------------------------------------------------" << endl;
logFile << (current->tm_mon+1) << "/" << (current->tm_mday) << "/" << (current->tm_year+1900) << " " << current->tm_hour << ":" << current->tm_min << ":" << current->tm_sec << endl;
logFile << inFileName << endl;
logFile << "Potential: " << sys->GetVType() << "\t Propagator: " << sys->GetRhoType() << endl;
//logFile << "P: "<< pSlice << ", N: "<< nPart << ", Beta: " << beta << ", levyModes: " << levyModes << ", levyNum: " << levyNum << "\n" << "maxSim: " << maxSim << ", maxStep: " << maxStep << ", sampleFreq: " << sampleFreq << ", convFreq: " << convFreq << ", storeFreq: " << storeFreq << endl;
logFile << "P: "<< pSlice << ", N: "<< nPart << ", Beta: " << beta << ", Internals: " << internalCoords << ", levyNum: " << levyNum << ", levyModes: " << levyModes << "\n" << "initLen: " << initLen << ", autoCorrLen: " << autoCorrLen << ", errorThresh: " << errorThresh << ", storeNum: " << storeNum;
if(autoCorrLen > 0) {
logFile << endl;
} else {
logFile << ", maxStep: " << maxStep << endl;
}
if(physicsParams->lowFrozModes+physicsParams->highFrozModes>0) {
logFile << "Frozen Modes:" << endl;
}
for(int i=0; i<physicsParams->lowFrozModes; i++) {
logFile << coords->omega[i]/0.00000455633 << "\t";
if((i)%10==9) {
logFile << "\n";
}
}
for(int i=(int)coords->omega.size()-physicsParams->highFrozModes; i<(int)coords->omega.size(); i++) {
logFile << coords->omega[i]/0.00000455633 << "\t";
if((i)%10==9) {
logFile << "\n";
}
}
if(physicsParams->lowFrozModes+physicsParams->highFrozModes>0) {
logFile << endl;
}
logFile << "Active Modes:" << endl;
for(int i=physicsParams->lowFrozModes; i<(int)coords->omega.size()-physicsParams->highFrozModes; i++) {
logFile << coords->omega[i]/0.00000455633 << "\t";
if((i-physicsParams->lowFrozModes)%10==9) {
logFile << "\n";
}
}
logFile << endl;
if(!coords->readGeom) {
logFile << "Coords after opt" << endl;
for(int j=0; j<coords->numPart; j++) {
for(int k=0; k<3; k++) {
logFile << coords->initCart[j][k] << "\t";
}
logFile << endl;
}
}
logFile << "Harmonic Energy is: " << sys->GetHarmonicE() << endl;
// srand(time(NULL));
idum = new int;
*idum = -time(0);
input.close();
// cout << "Initialization successful! Exiting for now" << endl;
// exit(0);
}
Simulation::~Simulation() {
// posFile.close();
logFile.close();
// DES Temp:
// vFile.close();
delete simStats;
delete simPotStats;
delete energyStats;
delete potentialStats;
delete convergenceStats;
delete acceptanceStats;
delete idum;
delete sys;
}
void Simulation::TakeStep(){
// rand();
vector<double> x;
// x.push_back(RandomNum::rangau(0,1,idum));
// for(int n = 0; n < 4; n++){
// for(int n = 0; n < 3+levyModes; n++){
if(epsInit>0 && stepNum < initLen) {
for(int n = 0; n < levyModesInit+1; n++){
x.push_back(RandomNum::rand3(idum));
}
sys->Move(x, epsInit, levyNumInit, levyModesInit);
}
else {
for(int n = 0; n < levyModes+1; n++){
x.push_back(RandomNum::rand3(idum));
}
sys->Move(x, epsilon, levyNum, levyModes);
}
}
bool Simulation::Check(double epsVal){
// double pTest = ((double)rand()/(double)RAND_MAX);
double pTest = (RandomNum::rand3(idum));
// cout<<"Weight: " << sys->GetWeight() << endl;
double checkVal = exp(-epsVal*(sys->GetWeight() - sys->GetOldWeight()));
// double checkVal = 1.0;
// cout << "V diff\t" << sys->GetWeight() - sys->GetOldWeight() << endl;
if (checkVal > pTest) {
acceptanceStats->AddVal(1.0);
// cout << "\tT" << endl;
return true;
} else {
acceptanceStats->AddVal(0.0);
// cout << "\tF" << endl;
// cout << "False: " << checkVal << endl;
return false;
}
}
void Simulation::Update() {
sys->Forget();
}
void Simulation::Revert() {
sys->Undo();
}
void Simulation::Sample() {
if(numTI==0) {
// If not TI use E
if(!noEnergy){
autoCorr.AddVal(sys->EstimatorE());
}
else{
autoCorr.AddVal(0.0);
}
}
else {
autoCorr.AddVal(sys->EstimatorAnharmonicV());
}
if(stepNum == initLen) {
autoCorr.Reset();
acceptanceStats->Reset();
if(autoCorrLen <= 0) {
if(storeNum>0) {
storeFreq = int((maxStep-initLen)/storeNum);
}
}
}
// Estimate remaining steps once autocorrelation estimated
if(stepNum == sampleStart && autoCorrLen>0) {
//sampleFreq = int(autoCorr.GetTau()*2+1);
tau = autoCorr.GetTau();
sampleFreq = 1;
//cout << "DES: Working out sampling" << endl;
//cout << "HarmoincE = " << sys->GetHarmonicE() << endl;
if(numTI < 1 ) {
numSamples = int(autoCorr.GetTotalVariance()/pow(((autoCorr.GetTotalMean()-sys->GetHarmonicE())*errorThresh),2)*(2*tau)*1.96*1.96);
}
else {
numSamples = int(autoCorr.GetTotalVariance()/pow((autoCorr.GetTotalMean()*errorThresh),2)*(2*tau)*1.96*1.96);
}
if(maxStep != sampleStart+1) {
numSamples = min(numSamples,maxStep);
if(numSamples == maxStep) {
cout << "Error: required number of steps > maxStep. Continuing for " << maxStep << " steps." << endl;
}
}
if(storeNum>0) {
storeFreq = int(numSamples/storeNum);
}
// if(maxStep == sampleStart) {
// maxStep = sampleStart + numSamples*sampleFreq;
// }
// else {
// maxStep = sampleStart + min(numSamples*sampleFreq,maxStep);
// }
if(maxStep == sampleStart+1) {
maxStep = initLen + numSamples;
}
else {
maxStep = sampleStart + min(numSamples-autoCorrLen,maxStep);
}
// Setting numSamples to the number of remaining samples here
numSamples = max(0,numSamples-autoCorrLen);
time_t t = time(0);
struct tm * current = localtime( & t );
logFile << "****Error Estimation****" << endl;
if(numTI < 1 ) {
logFile << "Tau: " << tau << ", Approx. Mean: " << autoCorr.GetTotalMean()-sys->GetHarmonicE() << ", Approx. St. Dev.: " << autoCorr.GetTotalStDev() << endl;
}
else {
logFile << "Tau: " << tau << ", Approx. Mean: " << autoCorr.GetTotalMean() << ", Approx. St. Dev.: " << autoCorr.GetTotalStDev() << endl;
}
logFile << "numSamples: " << numSamples+autoCorrLen << ", maxStep: " << maxStep << ", sampleFreq: " << sampleFreq << endl;
logFile << (current->tm_mon+1) << "/" << (current->tm_mday) << "/" << (current->tm_year+1900) << " " << current->tm_hour << ":" << current->tm_min << ":" << current->tm_sec << endl;
logFile << "************************" << endl;
}
// DES TODO: Don't estimate E if doing TI
if(autoCorrLen <=0) {
if((stepNum >= sampleStart)&&((stepNum-sampleStart)%sampleFreq==0)) {
//cout << "Sampling Step = " << (stepNum-sampleStart) << endl;
//energyStats->AddVal(sys->EstimatorE());
if(!noEnergy){
energyStats->AddVal(sys->EstimatorE());
}
else{
energyStats->AddVal(0.0);
}
if(!sys->GetPhysics()->isDeltaAI()) {
potentialStats->AddVal(sys->EstimatorAnharmonicV());
}
else {
double tempV = sys->EstimatorAnharmonicV();
potentialStats->AddVal(tempV);
// vFile << tempNum << "\t" << tempV << endl;
// tempNum++;
}
vector< vector<Particle> > part = sys->GetParticle();
/* xstats
double tempX = 0.0;
for(int i=0; i<(int)part.size(); i++) {
for(int j=0; j<(int)part[0].size(); j++) {
tempX += part[i][j].pos[0];
//xStats->AddVal(part[i][j].pos[0]-part[(i+1)%part.size()][j].pos[0]);
}
}
xStats->AddVal(tempX/part.size()/part[0].size());
*/
// To restore function uncomment posFile above
// if((stepNum-sampleStart)/(double)sampleFreq < 5000) {
// WritePathToFile(sys->GetParticle(),posFileName);
// }
}
if(numGeomPrint > 0) {
if(stepNum >= sampleStart && (stepNum-sampleStart+1)%((maxStep-sampleStart)/numGeomPrint)==0) {
//cout << "DES: sampling point = " << (maxStemp-sampleStart) << endl;
/*
vector< vector<Particle> > tempParts = sys->GetParticle();
vector<Particle> averagePart = tempParts[0];
for(int j=0; j<tempParts[0].size(); j++) {
for(int k=0; k<tempParts[0][0].pos.size(); k++) {
averagePart[j].pos[k] = 0.0;
for(int i=0; i<tempParts.size(); i++) {
averagePart[j].pos[k] += tempParts[i][j].pos[k];
}
averagePart[j].pos[k] /= tempParts.size();
}
}
*/
ostringstream convert;
convert << int((stepNum-sampleStart+1)/((maxStep-sampleStart)/numGeomPrint));
string geomNum = convert.str();
string partFileName = outName + "." + geomNum + ".xyz";
//WritePartToFile(averagePart,partFileName);
sys->WritePartToFile(partFileName);
}
}
}
// if(stepNum == initLen || stepNum == sampleStart) {
// autoCorr.Reset();
// }
}
void Simulation::WritePathToFile(vector< vector<Particle> > part, string pFileName) {
//vector< vector<Particle> > part = sys->GetParticle();
ofstream pFile;
pFile.open(pFileName.c_str());
if((int)part[0][0].pos.size()>3){
cout << "Warning! Turn off write to file if dim > 3!!!!" << endl;
}
else{
pFile << part.size()*part[0].size() << "\n" << endl;
for(int i=0; i<(int)part.size(); i++) {
for(int j=0; j<(int)part[0].size(); j++) {
// pFile << 1 << "\t";
pFile << part[i][j].atomType << "\t";
for(int k=0; k<(int)part[0][0].pos.size(); k++) {
pFile << part[i][j].pos[k] << "\t";
}
for(int k=0; k<(3-(int)part[0][0].pos.size()); k++) {
pFile << 0 << "\t";
}
pFile << endl;
}
}
}
pFile.close();
}
void Simulation::WritePartToFile(vector<Particle> part, string pFileName) {
ofstream pFile;
pFile.open(pFileName.c_str());
int dim = (int)part[0].pos.size();
if(dim>3){
cout << "Warning! Turn off write to file if dim > 3!!!!" << endl;
exit(-1);
}
else{
pFile << part.size() << "\n" << endl;
for(int i=0; i<(int)part.size(); i++) {
pFile << part[i].atomType << "\t";
for(int k=0; k<dim; k++) {
pFile << part[i].pos[k] << "\t";
}
// For printing carts if dim == 2
for(int k=0; k<(3-dim); k++) {
pFile << 0 << "\t";
}
pFile << endl;
}
}
pFile.close();
}
void Simulation::Log() {
time_t t = time(0);
struct tm * current = localtime( & t );
if(numTI <= 0) {
if(autoCorrLen > 0) {
logFile << "Mean Anharmonic Energy: " << autoCorr.GetTotalMean() - sys->GetHarmonicE() << endl;
logFile << "Energy St. Dev.: " << autoCorr.GetTotalStDev() << endl;
if(stepNum >= maxStep) {
logFile << "95% Confidence Bounds: " << autoCorr.GetTotalStDev()/sqrt(double(numSamples+autoCorrLen))*sqrt(tau*2)*1.96 << endl;
}
}
else {
logFile << "Mean Anharmonic Energy: " << energyStats->GetMean() - sys->GetHarmonicE() << endl;
logFile << "Energy St. Dev.: " << energyStats->GetStDev() << endl;
logFile << "Mean Potential: " << potentialStats->GetMean() << endl;
logFile << "Potential St. Dev.: " << potentialStats->GetStDev() << endl;
}
}
else {
if(autoCorrLen > 0) {
logFile << "Mean Anharmonic Free Energy: " << autoCorr.GetTotalMean() << endl;
logFile << "Free Energy St. Dev.: " << autoCorr.GetTotalStDev() << endl;
if(stepNum >= maxStep) {
logFile << "95% Confidence Bounds: " << autoCorr.GetTotalStDev()/sqrt(double(numSamples+autoCorrLen))*sqrt(tau*2)*1.96 << endl;
}
}
else {
logFile << "Mean Potential: " << potentialStats->GetMean() << endl;
logFile << "Potential St. Dev.: " << potentialStats->GetStDev() << endl;
}
}
// logFile << "Mean X Position: " << xStats->GetMean() << endl;
// logFile << "RMS X Position: " << xStats->GetRMS() << endl;
logFile << "Acceptance probability: " << acceptanceStats->GetMean() << endl;
logFile << (current->tm_mon+1) << "/" << (current->tm_mday) << "/" << (current->tm_year+1900) << " " << current->tm_hour << ":" << current->tm_min << ":" << current->tm_sec << endl;
}
void Simulation::FinalLog() {
time_t t = time(0);
struct tm * current = localtime( & t );
logFile << "****** " << maxSim << " Jobs Finished ******" << endl;
logFile << "Mean Energy: " << simStats->GetMean() << endl;
logFile << "Mean Potential: " << simPotStats->GetMean() << endl;
logFile << "Standard Deviation: " << simStats->GetStDev() << endl;
logFile << "Potential Standard Deviation: " << simPotStats->GetStDev() << endl;
logFile << (current->tm_mon+1) << "/" << (current->tm_mday) << "/" << (current->tm_year+1900) << " " << current->tm_hour << ":" << current->tm_min << ":" << current->tm_sec << endl;
}
void Simulation::TILog(double dG, double dGstdev, double taudGstdev) {
time_t t = time(0);
struct tm * current = localtime( & t );
logFile << "****** " << numTI << " TI Points Finished ******" << endl;
logFile << "Free Energy: " << dG << endl;
logFile << "Standard Deviation: " << dGstdev << endl;
if(maxSim == 1) {
logFile << "95% Confidence Bounds: " << taudGstdev/sqrt(double(numSamples+autoCorrLen))*sqrt(2.0)*1.96 << endl;
//logFile << "95% Confidence Bounds: " << dGstdev/sqrt(double(numSamples+autoCorrLen))*sqrt(tau*2)*1.96 << endl;
}
logFile << (current->tm_mon+1) << "/" << (current->tm_mday) << "/" << (current->tm_year+1900) << " " << current->tm_hour << ":" << current->tm_min << ":" << current->tm_sec << endl;
}
void Simulation::Store() {
if (storeFreq!=0 && (stepNum > sampleStart) && (stepNum-sampleStart+1)%storeFreq==0){
// time_t t = time(0);
// struct tm * current = localtime( & t );
// logFile << "Mean Energy: " << energyStats->GetMean() << endl;
// logFile << "Energy Convergence: " << convergenceStats->GetStDev() << endl;
// logFile << "Mean Potential: " << potentialStats->GetMean() << endl;
// logFile << "Acceptance probability: " << acceptanceStats->GetMean() << endl;
// logFile << (current->tm_mon+1) << "/" << (current->tm_mday) << "/" << (current->tm_year+1900) << " " << current->tm_hour << ":" << current->tm_min << ":" << current->tm_sec << endl;
Log();
}
}
void Simulation::Run() {
double savedMax = maxStep;
if(numTI==0) {
double runEps = epsilon;
for(int simNum = 0; simNum<maxSim; simNum++) {
if(epsInit>0) {
runEps = epsInit;
//cout << "DES Temp: epsInit = " << epsInit << "\t epsilon = " << epsilon << endl;
}
for(stepNum=0; stepNum<maxStep; stepNum++){
if(stepNum==initLen) {
runEps = epsilon;
}
TakeStep();
if (Check(runEps)) {
Update();
} else {
Revert();
}
Sample();
// if (storeFreq!=0 && (stepNum+1)%storeFreq==0 && (stepNum > (sampleStart))){
// Store(); //Write statistics to the log.txt file every storeFreq step
// }
Store();
}
logFile << "****Final Tau****" << endl;
tau = autoCorr.GetTau();
logFile << "Tau: " << tau << "\t numSamples: " << numSamples + autoCorrLen << endl;
if(maxSim==1) {
logFile << " ****Simulation Finished****" << endl;
}
else {
logFile << "****** Finished Simulation " << simNum << " ******" << endl;
}
Log();
simStats->AddVal(energyStats->GetMean());
simPotStats->AddVal(potentialStats->GetMean());
// simComboStats->AddVal(comboStats->GetMean());
if(maxSim>1) {
sys->Reset();
maxStep = savedMax;
}
energyStats->Reset();
potentialStats->Reset();
// comboStats->Reset();
}
if(maxSim>1) {
FinalLog();
}
}
// Running thermodynamic integration
else {
vector<double> gPoints;
vector<double> gWeights;
if(numTI==11) {
GetLinearQuad(numTI,gPoints,gWeights);
}
else {
GetGaussianQuad(numTI,gPoints,gWeights);
}
// double energyPoints = 0.0; //TODO: Remove this
// double energyStDevPoints = 0.0; //TODO: Remove this