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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 "utils/simError.h" |
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#include "integrators/NPTxyz.hpp" |
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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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namespace oopse { |
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/* |
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NPTxyz::NPTxyz (SimInfo* info): NPT(info) { |
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GenericData* data; |
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DoubleVectorGenericData * etaValue; |
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int 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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eta[i][j] = 0.0; |
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oldEta[i][j] = 0.0; |
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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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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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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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template<typename T> NPTxyz<T>::~NPTxyz() { |
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// empty for now |
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} |
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template<typename T> void NPTxyz<T>::resetIntegrator() { |
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void NPTxyz::evolveEtaA() { |
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int 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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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 NPTxyz<T>::evolveEtaA() { |
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int 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] += 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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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/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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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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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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template<typename T> void NPTxyz<T>::evolveEtaB() { |
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void NPTxyz::evolveEtaB() { |
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int 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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prevEta[i][j] = eta[i][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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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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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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void NPTxyz::calcVelScale(void) { |
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int 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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vScale[i][j] = eta[i][j]; |
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vScale(i, j) = eta(i, j); |
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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 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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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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matVecMul3( vScale, myVel, sc ); |
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void NPTxyz::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 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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matVecMul3( eta, rj, sc ); |
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void NPTxyz::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 NPTxyz<T>::scaleSimBox( void ){ |
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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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|
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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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|
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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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} |
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} |
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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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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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// for(i=0; i<3; i++){ |
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// for(j=0; j<3; j++){ |
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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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// 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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// 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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// 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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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; |
| 232 |
< |
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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void NPTxyz::getPosScale(const Vector3d& pos, const Vector3d& COM, |
| 117 |
> |
int index, Vector3d& sc) { |
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> |
|
| 119 |
> |
Vector3d rj = (oldPos[index] + pos[j])/2.0 -COM; |
| 120 |
> |
sc = eta * rj; |
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} |
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|
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< |
template<typename T> bool NPTxyz<T>::etaConverged() { |
| 123 |
> |
bool NPTxyz::etaConverged() { |
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int i; |
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double diffEta, sumEta; |
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|
| 127 |
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sumEta = 0; |
| 128 |
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for(i = 0; i < 3; i++) |
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< |
sumEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 129 |
> |
sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
| 130 |
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|
| 131 |
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diffEta = sqrt( sumEta / 3.0 ); |
| 132 |
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| 133 |
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return ( diffEta <= etaTolerance ); |
| 134 |
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} |
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template<typename T> double NPTxyz<T>::getConservedQuantity(void){ |
| 136 |
> |
*/ |
| 137 |
> |
|
| 138 |
> |
double NPTxyz::calcConservedQuantity(){ |
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|
| 140 |
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double conservedQuantity; |
| 141 |
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double totalEnergy; |
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double barostat_kinetic; |
| 145 |
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double barostat_potential; |
| 146 |
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double trEta; |
| 147 |
< |
double a[3][3], b[3][3]; |
| 147 |
> |
Mat3x3d a; |
| 148 |
> |
Mat3x3d b; |
| 149 |
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|
| 150 |
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totalEnergy = tStats->getTotalE(); |
| 151 |
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| 167 |
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conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
| 168 |
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barostat_kinetic + barostat_potential; |
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|
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// cout.width(8); |
| 285 |
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// cout.precision(8); |
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| 287 |
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// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 288 |
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// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 289 |
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// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 290 |
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|
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return conservedQuantity; |
| 172 |
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| 173 |
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} |
| 174 |
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| 175 |
< |
template<typename T> string NPTxyz<T>::getAdditionalParameters(void){ |
| 176 |
< |
string parameters; |
| 297 |
< |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 298 |
< |
char buffer[BUFFERSIZE]; |
| 175 |
> |
|
| 176 |
> |
void NPTxyz::scaleSimBox(){ |
| 177 |
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|
| 178 |
< |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
| 179 |
< |
parameters += buffer; |
| 178 |
> |
int i,j,k; |
| 179 |
> |
Mat3x3d scaleMat; |
| 180 |
> |
double eta2ij, scaleFactor; |
| 181 |
> |
double bigScale, smallScale, offDiagMax; |
| 182 |
> |
Mat3x3d hm; |
| 183 |
> |
Mat3x3d hmnew; |
| 184 |
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|
| 185 |
< |
for(int i = 0; i < 3; i++){ |
| 186 |
< |
sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]); |
| 187 |
< |
parameters += buffer; |
| 185 |
> |
|
| 186 |
> |
|
| 187 |
> |
// Scale the box after all the positions have been moved: |
| 188 |
> |
|
| 189 |
> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 190 |
> |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 191 |
> |
|
| 192 |
> |
bigScale = 1.0; |
| 193 |
> |
smallScale = 1.0; |
| 194 |
> |
offDiagMax = 0.0; |
| 195 |
> |
|
| 196 |
> |
for(i=0; i<3; i++){ |
| 197 |
> |
for(j=0; j<3; j++){ |
| 198 |
> |
scaleMat(i, j) = 0.0; |
| 199 |
> |
if(i==j) scaleMat(i, j) = 1.0; |
| 200 |
> |
} |
| 201 |
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} |
| 202 |
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|
| 203 |
< |
return parameters; |
| 203 |
> |
for(i=0;i<3;i++){ |
| 204 |
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|
| 205 |
+ |
// calculate the scaleFactors |
| 206 |
+ |
|
| 207 |
+ |
scaleFactor = exp(dt*eta(i, i)); |
| 208 |
+ |
|
| 209 |
+ |
scaleMat(i, i) = scaleFactor; |
| 210 |
+ |
|
| 211 |
+ |
if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i); |
| 212 |
+ |
if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i); |
| 213 |
+ |
} |
| 214 |
+ |
|
| 215 |
+ |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 216 |
+ |
sprintf( painCave.errMsg, |
| 217 |
+ |
"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n" |
| 218 |
+ |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 219 |
+ |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 220 |
+ |
" [%lf\t%lf\t%lf]\n" |
| 221 |
+ |
" [%lf\t%lf\t%lf]\n", |
| 222 |
+ |
scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2), |
| 223 |
+ |
scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2), |
| 224 |
+ |
scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2)); |
| 225 |
+ |
painCave.isFatal = 1; |
| 226 |
+ |
simError(); |
| 227 |
+ |
} else { |
| 228 |
+ |
info->getBoxM(hm); |
| 229 |
+ |
matMul3(hm, scaleMat, hmnew); |
| 230 |
+ |
info->setBoxM(hmnew); |
| 231 |
+ |
} |
| 232 |
|
} |
| 233 |
+ |
|
| 234 |
+ |
} |
