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#include <math.h> |
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#include "math/MatVec3.h" |
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#include "primitives/Atom.hpp" |
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#include "primitives/SRI.hpp" |
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#include "primitives/AbstractClasses.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "UseTheForce/ForceFields.hpp" |
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#include "brains/Thermo.hpp" |
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#include "io/ReadWrite.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "integrators/IntegratorCreator.hpp" |
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#include "integrators/NPTxyz.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/simError.h" |
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#ifdef IS_MPI |
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#include "brains/mpiSimulation.hpp" |
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#endif |
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|
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// Basic non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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template<typename T> NPTxyz<T>::NPTxyz ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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DoubleVectorGenericData * etaValue; |
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int i,j; |
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namespace oopse { |
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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static IntegratorBuilder<NPTxyz>* NPTxyzCreator = new IntegratorBuilder<NPTxyz>("NPTxyz"); |
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|
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double NPTxyz::calcConservedQuantity(){ |
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eta[i][j] = 0.0; |
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oldEta[i][j] = 0.0; |
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} |
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} |
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
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// than the barostat (when there are particles with orientational degrees |
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// of freedom). |
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fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp; |
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|
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if( theInfo->useInitXSstate ){ |
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double conservedQuantity; |
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double totalEnergy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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double barostat_kinetic; |
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double barostat_potential; |
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double trEta; |
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|
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// retrieve eta array from simInfo if it exists |
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data = info->getPropertyByName(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleVectorGenericData*>(data); |
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|
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if(etaValue){ |
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|
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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eta[i][j] = (*etaValue)[3*i+j]; |
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oldEta[i][j] = eta[i][j]; |
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} |
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} |
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} |
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} |
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} |
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} |
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totalEnergy = thermo.getTotalE(); |
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template<typename T> NPTxyz<T>::~NPTxyz() { |
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thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
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// empty for now |
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} |
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thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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template<typename T> void NPTxyz<T>::resetIntegrator() { |
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SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
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trEta = tmp.trace(); |
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int i, j; |
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barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
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T::resetIntegrator(); |
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} |
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conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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template<typename T> void NPTxyz<T>::evolveEtaA() { |
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int i, j; |
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return conservedQuantity; |
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) |
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eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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else |
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eta[i][j] = 0.0; |
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} |
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} |
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|
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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oldEta[i][j] = eta[i][j]; |
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} |
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template<typename T> void NPTxyz<T>::evolveEtaB() { |
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|
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void NPTxyz::scaleSimBox(){ |
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int i,j; |
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int i,j,k; |
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Mat3x3d scaleMat; |
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double eta2ij, scaleFactor; |
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double bigScale, smallScale, offDiagMax; |
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Mat3x3d hm; |
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Mat3x3d hmnew; |
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for(i = 0; i < 3; i++) |
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for (j = 0; j < 3; j++) |
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prevEta[i][j] = eta[i][j]; |
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for(i = 0; i < 3; i ++){ |
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for(j = 0; j < 3; j++){ |
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if( i == j) { |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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} else { |
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eta[i][j] = 0.0; |
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} |
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} |
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} |
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} |
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template<typename T> void NPTxyz<T>::calcVelScale(void) { |
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int i,j; |
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|
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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale[i][j] = eta[i][j]; |
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|
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if (i == j) { |
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vScale[i][j] += chi; |
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} |
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} |
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} |
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} |
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|
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template<typename T> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) { |
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matVecMul3( vScale, vel, sc ); |
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} |
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|
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template<typename T> void NPTxyz<T>::getVelScaleB(double sc[3], int index ){ |
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int j; |
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double myVel[3]; |
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|
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for (j = 0; j < 3; j++) |
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myVel[j] = oldVel[3*index + j]; |
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|
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matVecMul3( vScale, myVel, sc ); |
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} |
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|
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template<typename T> void NPTxyz<T>::getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]){ |
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int j; |
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double rj[3]; |
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|
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for(j=0; j<3; j++) |
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rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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|
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matVecMul3( eta, rj, sc ); |
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} |
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|
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template<typename T> void NPTxyz<T>::scaleSimBox( void ){ |
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|
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int i,j,k; |
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double scaleMat[3][3]; |
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double eta2ij, scaleFactor; |
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double bigScale, smallScale, offDiagMax; |
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double hm[3][3], hmnew[3][3]; |
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// Scale the box after all the positions have been moved: |
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// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
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// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
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bigScale = 1.0; |
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smallScale = 1.0; |
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offDiagMax = 0.0; |
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bigScale = 1.0; |
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smallScale = 1.0; |
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offDiagMax = 0.0; |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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scaleMat[i][j] = 0.0; |
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if(i==j) scaleMat[i][j] = 1.0; |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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scaleMat(i, j) = 0.0; |
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if(i==j) { |
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scaleMat(i, j) = 1.0; |
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} |
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} |
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} |
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} |
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for(i=0;i<3;i++){ |
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for(i=0;i<3;i++){ |
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// calculate the scaleFactors |
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scaleFactor = exp(dt*eta[i][i]); |
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scaleFactor = exp(dt*eta(i, i)); |
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scaleMat[i][i] = scaleFactor; |
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scaleMat(i, i) = scaleFactor; |
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if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
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if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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} |
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if (scaleMat(i, i) > bigScale) { |
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bigScale = scaleMat(i, i); |
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} |
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|
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if (scaleMat(i, i) < smallScale) { |
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smallScale = scaleMat(i, i); |
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} |
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} |
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// for(i=0; i<3; i++){ |
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// for(j=0; j<3; j++){ |
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
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scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
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scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2)); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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|
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// // Calculate the matrix Product of the eta array (we only need |
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// // the ij element right now): |
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|
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// eta2ij = 0.0; |
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// for(k=0; k<3; k++){ |
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// eta2ij += eta[i][k] * eta[k][j]; |
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// } |
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|
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// scaleMat[i][j] = 0.0; |
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// // identity matrix (see above): |
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// if (i == j) scaleMat[i][j] = 1.0; |
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// // Taylor expansion for the exponential truncated at second order: |
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// scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
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|
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// if (i != j) |
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// if (fabs(scaleMat[i][j]) > offDiagMax) |
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// offDiagMax = fabs(scaleMat[i][j]); |
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// } |
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|
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// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
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// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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// } |
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|
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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info->getBoxM(hm); |
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matMul3(hm, scaleMat, hmnew); |
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info->setBoxM(hmnew); |
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} |
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Mat3x3d hmat = currentSnapshot_->getHmat(); |
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hmat = hmat *scaleMat; |
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currentSnapshot_->setHmat(hmat); |
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} |
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} |
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|
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template<typename T> bool NPTxyz<T>::etaConverged() { |
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int i; |
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double diffEta, sumEta; |
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|
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sumEta = 0; |
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for(i = 0; i < 3; i++) |
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sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
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|
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diffEta = sqrt( sumEta / 3.0 ); |
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|
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return ( diffEta <= etaTolerance ); |
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> |
void NPTxyz::loadEta() { |
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eta= currentSnapshot_->getEta(); |
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} |
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|
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template<typename T> double NPTxyz<T>::getConservedQuantity(void){ |
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|
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double conservedQuantity; |
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double totalEnergy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
| 259 |
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double barostat_kinetic; |
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double barostat_potential; |
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double trEta; |
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double a[3][3], b[3][3]; |
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|
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totalEnergy = tStats->getTotalE(); |
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|
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thermostat_kinetic = fkBT * tt2 * chi * chi / |
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(2.0 * eConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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|
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transposeMat3(eta, a); |
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matMul3(a, eta, b); |
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trEta = matTrace3(b); |
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|
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barostat_kinetic = NkBT * tb2 * trEta / |
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(2.0 * eConvert); |
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|
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barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
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eConvert; |
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|
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conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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// cout.width(8); |
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// cout.precision(8); |
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|
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// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
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// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
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// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
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|
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return conservedQuantity; |
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|
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} |
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|
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template<typename T> string NPTxyz<T>::getAdditionalParameters(void){ |
| 296 |
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string parameters; |
| 297 |
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const int BUFFERSIZE = 2000; // size of the read buffer |
| 298 |
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char buffer[BUFFERSIZE]; |
| 299 |
– |
|
| 300 |
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sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
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parameters += buffer; |
| 302 |
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|
| 303 |
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for(int i = 0; i < 3; i++){ |
| 304 |
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sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
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parameters += buffer; |
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} |
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|
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return parameters; |
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|
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} |
