--- branches/development/src/rnemd/RNEMD.cpp 2012/08/08 16:03:02 1774 +++ branches/development/src/rnemd/RNEMD.cpp 2012/10/03 14:20:07 1803 @@ -69,6 +69,9 @@ namespace OpenMD { Globals * simParams = info->getSimParams(); RNEMDParameters* rnemdParams = simParams->getRNEMDParameters(); + doRNEMD_ = rnemdParams->getUseRNEMD(); + if (!doRNEMD_) return; + stringToMethod_["Swap"] = rnemdSwap; stringToMethod_["NIVS"] = rnemdNIVS; stringToMethod_["VSS"] = rnemdVSS; @@ -77,6 +80,7 @@ namespace OpenMD { stringToFluxType_["Px"] = rnemdPx; stringToFluxType_["Py"] = rnemdPy; stringToFluxType_["Pz"] = rnemdPz; + stringToFluxType_["Pvector"] = rnemdPvector; stringToFluxType_["KE+Px"] = rnemdKePx; stringToFluxType_["KE+Py"] = rnemdKePy; stringToFluxType_["KE+Pvector"] = rnemdKePvector; @@ -98,8 +102,8 @@ namespace OpenMD { sprintf(painCave.errMsg, "RNEMD: No fluxType was set in the md file. This parameter,\n" "\twhich must be one of the following values:\n" - "\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n" - "\tuse RNEMD\n"); + "\tKE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector\n" + "\tmust be set to use RNEMD\n"); painCave.isFatal = 1; painCave.severity = OPENMD_ERROR; simError(); @@ -197,6 +201,7 @@ namespace OpenMD { break; case rnemdPvector: hasCorrectFlux = hasMomentumFluxVector; + break; case rnemdKePx: case rnemdKePy: hasCorrectFlux = hasMomentumFlux && hasKineticFlux; @@ -224,8 +229,7 @@ namespace OpenMD { } if (!hasCorrectFlux) { sprintf(painCave.errMsg, - "RNEMD: The current method,\n" - "\t%s, and flux type %s\n" + "RNEMD: The current method, %s, and flux type, %s,\n" "\tdid not have the correct flux value specified. Options\n" "\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n", methStr.c_str(), fluxStr.c_str()); @@ -235,7 +239,10 @@ namespace OpenMD { } if (hasKineticFlux) { - kineticFlux_ = rnemdParams->getKineticFlux(); + // convert the kcal / mol / Angstroms^2 / fs values in the md file + // into amu / fs^3: + kineticFlux_ = rnemdParams->getKineticFlux() + * PhysicalConstants::energyConvert; } else { kineticFlux_ = 0.0; } @@ -270,6 +277,7 @@ namespace OpenMD { // do some sanity checking int selectionCount = seleMan_.getSelectionCount(); + int nIntegrable = info->getNGlobalIntegrableObjects(); if (selectionCount > nIntegrable) { @@ -314,7 +322,7 @@ namespace OpenMD { outputMap_["TEMPERATURE"] = TEMPERATURE; OutputData velocity; - velocity.units = "amu/fs"; + velocity.units = "angstroms/fs"; velocity.title = "Velocity"; velocity.dataType = "Vector3d"; velocity.accumulator.reserve(nBins_); @@ -410,7 +418,7 @@ namespace OpenMD { } RNEMD::~RNEMD() { - + if (!doRNEMD_) return; #ifdef IS_MPI if (worldRank == 0) { #endif @@ -432,7 +440,7 @@ namespace OpenMD { } void RNEMD::doSwap() { - + if (!doRNEMD_) return; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); @@ -491,9 +499,6 @@ namespace OpenMD { + angMom[2]*angMom[2]/I(2, 2); } } //angular momenta exchange enabled - //energyConvert temporarily disabled - //make kineticExchange_ comparable between swap & scale - //value = value * 0.5 / PhysicalConstants::energyConvert; value *= 0.5; break; case rnemdPx : @@ -731,7 +736,6 @@ namespace OpenMD { switch(rnemdFluxType_) { case rnemdKE: - cerr << "KE\n"; kineticExchange_ += max_val - min_val; break; case rnemdPx: @@ -744,7 +748,6 @@ namespace OpenMD { momentumExchange_.z() += max_val - min_val; break; default: - cerr << "default\n"; break; } } else { @@ -767,7 +770,7 @@ namespace OpenMD { } void RNEMD::doNIVS() { - + if (!doRNEMD_) return; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); @@ -911,8 +914,7 @@ namespace OpenMD { if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients c = sqrt(c); - //std::cerr << "cold slab scaling coefficient: " << c << endl; - //now convert to hotBin coefficient + RealType w = 0.0; if (rnemdFluxType_ == rnemdFullKE) { x = 1.0 + px * (1.0 - c); @@ -950,8 +952,6 @@ namespace OpenMD { } } w = sqrt(w); - // std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z - // << "\twh= " << w << endl; for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { if (rnemdFluxType_ == rnemdFullKE) { vel = (*sdi)->getVel(); @@ -1216,7 +1216,7 @@ namespace OpenMD { } void RNEMD::doVSS() { - + if (!doRNEMD_) return; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); RealType time = currentSnap_->getTime(); Mat3x3d hmat = currentSnap_->getHmat(); @@ -1260,9 +1260,7 @@ namespace OpenMD { if (inA) { hotBin.push_back(sd); - //std::cerr << "before, velocity = " << vel << endl; Ph += mass * vel; - //std::cerr << "after, velocity = " << vel << endl; Mh += mass; Kh += mass * vel.lengthSquare(); if (rnemdFluxType_ == rnemdFullKE) { @@ -1310,10 +1308,6 @@ namespace OpenMD { Kh *= 0.5; Kc *= 0.5; - - // std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc - // << "\tKc= " << Kc << endl; - // std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl; #ifdef IS_MPI MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM); @@ -1345,8 +1339,7 @@ namespace OpenMD { if (hDenominator > 0.0) { RealType h = sqrt(hNumerator / hDenominator); if ((h > 0.9) && (h < 1.1)) { - // std::cerr << "cold slab scaling coefficient: " << c << "\n"; - // std::cerr << "hot slab scaling coefficient: " << h << "\n"; + vector::iterator sdi; Vector3d vel; for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { @@ -1394,7 +1387,7 @@ namespace OpenMD { } void RNEMD::doRNEMD() { - + if (!doRNEMD_) return; trialCount_++; switch(rnemdMethod_) { case rnemdSwap: @@ -1413,7 +1406,7 @@ namespace OpenMD { } void RNEMD::collectData() { - + if (!doRNEMD_) return; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); @@ -1421,7 +1414,7 @@ namespace OpenMD { seleMan_.setSelectionSet(evaluator_.evaluate()); - int selei; + int selei(0); StuntDouble* sd; int idx; @@ -1447,9 +1440,10 @@ namespace OpenMD { sd != NULL; sd = mol->nextIntegrableObject(iiter)) */ + for (sd = seleMan_.beginSelected(selei); sd != NULL; sd = seleMan_.nextSelected(selei)) { - + idx = sd->getLocalIndex(); Vector3d pos = sd->getPos(); @@ -1466,7 +1460,7 @@ namespace OpenMD { // The modulo operator is used to wrap the case when we are // beyond the end of the bins back to the beginning. int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_; - + RealType mass = sd->getMass(); Vector3d vel = sd->getVel(); @@ -1497,7 +1491,6 @@ namespace OpenMD { } } - #ifdef IS_MPI MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0], nBins_, MPI::INT, MPI::SUM); @@ -1524,10 +1517,13 @@ namespace OpenMD { vel.x() = binPx[i] / binMass[i]; vel.y() = binPy[i] / binMass[i]; vel.z() = binPz[i] / binMass[i]; - den = binCount[i] * nBins_ / currentSnap_->getVolume(); + + den = binMass[i] * nBins_ * PhysicalConstants::densityConvert + / currentSnap_->getVolume() ; + temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb * PhysicalConstants::energyConvert); - + for (unsigned int j = 0; j < outputMask_.size(); ++j) { if(outputMask_[j]) { switch(j) { @@ -1550,11 +1546,13 @@ namespace OpenMD { } void RNEMD::getStarted() { + if (!doRNEMD_) return; collectData(); writeOutputFile(); } void RNEMD::parseOutputFileFormat(const std::string& format) { + if (!doRNEMD_) return; StringTokenizer tokenizer(format, " ,;|\t\n\r"); while(tokenizer.hasMoreTokens()) { @@ -1575,6 +1573,7 @@ namespace OpenMD { } void RNEMD::writeOutputFile() { + if (!doRNEMD_) return; #ifdef IS_MPI // If we're the root node, should we print out the results @@ -1596,7 +1595,8 @@ namespace OpenMD { RealType time = currentSnap_->getTime(); RealType avgArea; areaAccumulator_->getAverage(avgArea); - RealType Jz = kineticExchange_ / (2.0 * time * avgArea); + RealType Jz = kineticExchange_ / (2.0 * time * avgArea) + / PhysicalConstants::energyConvert; Vector3d JzP = momentumExchange_ / (2.0 * time * avgArea); rnemdFile_ << "#######################################################\n"; @@ -1613,7 +1613,7 @@ namespace OpenMD { rnemdFile_ << "# fluxType = \"" << (*fi).first << "\";\n"; } - rnemdFile_ << "# exchangeTime = " << exchangeTime_ << "; fs\n"; + rnemdFile_ << "# exchangeTime = " << exchangeTime_ << ";\n"; rnemdFile_ << "# objectSelection = \"" << rnemdObjectSelection_ << "\";\n"; @@ -1625,17 +1625,28 @@ namespace OpenMD { rnemdFile_ << "# RNEMD report:\n"; rnemdFile_ << "# running time = " << time << " fs\n"; rnemdFile_ << "# target flux:\n"; - rnemdFile_ << "# kinetic = " << kineticFlux_ << "\n"; - rnemdFile_ << "# momentum = " << momentumFluxVector_ << "\n"; + rnemdFile_ << "# kinetic = " + << kineticFlux_ / PhysicalConstants::energyConvert + << " (kcal/mol/A^2/fs)\n"; + rnemdFile_ << "# momentum = " << momentumFluxVector_ + << " (amu/A/fs^2)\n"; rnemdFile_ << "# target one-time exchanges:\n"; - rnemdFile_ << "# kinetic = " << kineticTarget_ << "\n"; - rnemdFile_ << "# momentum = " << momentumTarget_ << "\n"; + rnemdFile_ << "# kinetic = " + << kineticTarget_ / PhysicalConstants::energyConvert + << " (kcal/mol)\n"; + rnemdFile_ << "# momentum = " << momentumTarget_ + << " (amu*A/fs)\n"; rnemdFile_ << "# actual exchange totals:\n"; - rnemdFile_ << "# kinetic = " << kineticExchange_ << "\n"; - rnemdFile_ << "# momentum = " << momentumExchange_ << "\n"; + rnemdFile_ << "# kinetic = " + << kineticExchange_ / PhysicalConstants::energyConvert + << " (kcal/mol)\n"; + rnemdFile_ << "# momentum = " << momentumExchange_ + << " (amu*A/fs)\n"; rnemdFile_ << "# actual flux:\n"; - rnemdFile_ << "# kinetic = " << Jz << "\n"; - rnemdFile_ << "# momentum = " << JzP << "\n"; + rnemdFile_ << "# kinetic = " << Jz + << " (kcal/mol/A^2/fs)\n"; + rnemdFile_ << "# momentum = " << JzP + << " (amu/A/fs^2)\n"; rnemdFile_ << "# exchange statistics:\n"; rnemdFile_ << "# attempted = " << trialCount_ << "\n"; rnemdFile_ << "# failed = " << failTrialCount_ << "\n"; @@ -1653,6 +1664,8 @@ namespace OpenMD { if (outputMask_[i]) { rnemdFile_ << "\t" << data_[i].title << "(" << data_[i].units << ")"; + // add some extra tabs for column alignment + if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t"; } } rnemdFile_ << std::endl; @@ -1716,6 +1729,7 @@ namespace OpenMD { } void RNEMD::writeReal(int index, unsigned int bin) { + if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); assert(bin < nBins_); RealType s; @@ -1734,6 +1748,7 @@ namespace OpenMD { } void RNEMD::writeVector(int index, unsigned int bin) { + if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); assert(bin < nBins_); Vector3d s; @@ -1752,6 +1767,7 @@ namespace OpenMD { } void RNEMD::writeRealStdDev(int index, unsigned int bin) { + if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); assert(bin < nBins_); RealType s; @@ -1770,6 +1786,7 @@ namespace OpenMD { } void RNEMD::writeVectorStdDev(int index, unsigned int bin) { + if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); assert(bin < nBins_); Vector3d s;