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#include <math.h> |
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|
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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/NPTf.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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|
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#ifdef IS_MPI |
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#include "brains/mpiSimulation.hpp" |
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#endif |
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namespace oopse { |
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static IntegratorBuilder<NPTf>* NPTfCreator = new IntegratorBuilder<NPTf>("NPTf"); |
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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> NPTf<T>::NPTf ( 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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void NPTf::evolveEtaA() { |
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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int i, j; |
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eta[i][j] = 0.0; |
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oldEta[i][j] = 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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if( i == j) { |
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eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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} |
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} |
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} |
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} |
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|
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if( theInfo->useInitXSstate ){ |
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// retrieve eta array from simInfo if it exists |
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data = info->getProperty(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleVectorGenericData*>(data); |
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if(etaValue){ |
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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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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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} |
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} |
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|
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} |
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template<typename T> NPTf<T>::~NPTf() { |
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void NPTf::evolveEtaB() { |
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// empty for now |
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} |
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int i; |
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int j; |
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template<typename T> void NPTf<T>::resetIntegrator() { |
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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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} |
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} |
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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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eta[i][j] = 0.0; |
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|
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T::resetIntegrator(); |
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} |
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|
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template<typename T> void NPTf<T>::evolveEtaA() { |
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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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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] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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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/OOPSEConstant::pressureConvert) / (NkBT*tb2); |
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} else { |
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eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2); |
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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 (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 NPTf<T>::evolveEtaB() { |
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void NPTf::calcVelScale(){ |
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int i,j; |
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for (int i = 0; i < 3; i++ ) { |
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for (int j = 0; j < 3; j++ ) { |
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vScale(i, j) = eta(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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prevEta[i][j] = eta[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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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] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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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 NPTf<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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vScale(i, j) += chi; |
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} |
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} |
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} |
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} |
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template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) { |
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matVecMul3( vScale, vel, sc ); |
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void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){ |
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sc = vScale * vel; |
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} |
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template<typename T> void NPTf<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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matVecMul3( vScale, myVel, sc ); |
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void NPTf::getVelScaleB(Vector3d& sc, int index ) { |
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sc = vScale * oldVel[index]; |
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} |
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template<typename T> void NPTf<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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void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) { |
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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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matVecMul3( eta, rj, sc ); |
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/**@todo */ |
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Vector3d rj = (oldPos[index] + pos)/2.0 -COM; |
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sc = eta * rj; |
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} |
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template<typename T> void NPTf<T>::scaleSimBox( void ){ |
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void NPTf::scaleSimBox(){ |
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int i,j,k; |
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double scaleMat[3][3]; |
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int i; |
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int j; |
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int k; |
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Mat3x3d scaleMat; |
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double eta2ij; |
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double bigScale, smallScale, offDiagMax; |
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double hm[3][3], hmnew[3][3]; |
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Mat3x3d hm; |
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Mat3x3d hmnew; |
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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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eta2ij += eta(i, k) * eta(k, j); |
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} |
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scaleMat[i][j] = 0.0; |
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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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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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scaleMat(i, j) += dt*eta(i, j) + 0.5*dt*dt*eta2ij; |
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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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if (fabs(scaleMat(i, j)) > offDiagMax) |
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offDiagMax = fabs(scaleMat(i, j)); |
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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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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 ((bigScale > 1.01) || (smallScale < 0.99)) { |
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" eta = [%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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eta[0][0],eta[0][1],eta[0][2], |
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eta[1][0],eta[1][1],eta[1][2], |
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eta[2][0],eta[2][1],eta[2][2]); |
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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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eta(0, 0),eta(0, 1),eta(0, 2), |
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eta(1, 0),eta(1, 1),eta(1, 2), |
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eta(2, 0),eta(2, 1),eta(2, 2)); |
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painCave.isFatal = 1; |
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simError(); |
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} else if (offDiagMax > 0.01) { |
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" eta = [%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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eta[0][0],eta[0][1],eta[0][2], |
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eta[1][0],eta[1][1],eta[1][2], |
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eta[2][0],eta[2][1],eta[2][2]); |
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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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eta(0, 0),eta(0, 1),eta(0, 2), |
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eta(1, 0),eta(1, 1),eta(1, 2), |
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eta(2, 0),eta(2, 1),eta(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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|
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template<typename T> bool NPTf<T>::etaConverged() { |
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int i; |
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double diffEta, sumEta; |
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> |
bool NPTf::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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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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|
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diffEta = sqrt( sumEta / 3.0 ); |
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diffEta = sqrt( sumEta / 3.0 ); |
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|
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return ( diffEta <= etaTolerance ); |
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return ( diffEta <= etaTolerance ); |
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} |
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|
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template<typename T> double NPTf<T>::getConservedQuantity(void){ |
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double NPTf::calcConservedQuantity(){ |
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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; |
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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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> |
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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totalEnergy = tStats->getTotalE(); |
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> |
totalEnergy = thermo.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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> |
thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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> |
thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert; |
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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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> |
SquareMatrix<double, 3> tmp = eta.transpose() * eta; |
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> |
trEta = tmp.trace(); |
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> |
|
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> |
barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert); |
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|
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< |
barostat_kinetic = NkBT * tb2 * trEta / |
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(2.0 * eConvert); |
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> |
barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert; |
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|
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< |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
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< |
eConvert; |
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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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< |
conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
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< |
barostat_kinetic + barostat_potential; |
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> |
return conservedQuantity; |
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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 NPTf<T>::getAdditionalParameters(void){ |
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< |
string parameters; |
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< |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 299 |
< |
char buffer[BUFFERSIZE]; |
| 236 |
> |
void NPTf::loadEta() { |
| 237 |
> |
eta= currentSnapshot_->getEta(); |
| 238 |
|
|
| 239 |
< |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 240 |
< |
parameters += buffer; |
| 239 |
> |
if (!eta.isDiagonal()) { |
| 240 |
> |
sprintf( painCave.errMsg, |
| 241 |
> |
"NPTi error: the diagonal elements of are eta matrix is not same or etaMat is not a diagonal matrix"); |
| 242 |
> |
painCave.isFatal = 1; |
| 243 |
> |
simError(); |
| 244 |
> |
} |
| 245 |
> |
} |
| 246 |
|
|
| 247 |
< |
for(int i = 0; i < 3; i++){ |
| 248 |
< |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 249 |
< |
parameters += buffer; |
| 307 |
< |
} |
| 247 |
> |
void NPTf::saveEta() { |
| 248 |
> |
currentSnapshot_->setEta(eta); |
| 249 |
> |
} |
| 250 |
|
|
| 309 |
– |
return parameters; |
| 310 |
– |
|
| 251 |
|
} |
