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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 "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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|
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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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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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NPTf::NPTf (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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|
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for(i = 0; i < 3; i++){ |
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for (j = 0; j < 3; j++){ |
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|
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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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|
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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->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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} |
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|
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NPTf::~NPTf() { |
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|
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// empty for now |
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} |
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|
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void NPTf::evolveEtaA() { |
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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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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) += 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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} |
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|
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} |
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|
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void NPTf::evolveEtaB() { |
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|
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int i; |
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int 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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} |
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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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} |
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|
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void NPTf::calcVelScale(){ |
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|
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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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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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void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel);{ |
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sc = vScale * vel; |
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} |
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|
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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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|
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void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, |
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int index, Vector3d& sc) { |
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|
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/**@todo */ |
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Vector3d rj = (oldPos[index] + pos[j])/2.0 -COM; |
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sc = eta * rj; |
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} |
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|
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void NPTf::scaleSimBox(){ |
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|
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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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Mat3x3d hm; |
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Mat3x3d hmnew; |
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|
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|
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|
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// Scale the box after all the positions have been moved: |
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|
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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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|
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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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|
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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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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 > 1.01) || (smallScale < 0.99)) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting a Box scaling of more than 1 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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" 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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painCave.isFatal = 1; |
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simError(); |
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} else if (offDiagMax > 0.01) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting an off-diagonal Box scaling of more than 1 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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" 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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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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} |
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|
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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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} |
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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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} |
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|
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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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|
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totalEnergy = tStats->getTotalE(); |
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|
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thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * eConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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|
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trEta = (eta.transpose() * eta).trace(); |
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|
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barostat_kinetic = NkBT * tb2 * trEta /(2.0 * eConvert); |
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|
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barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /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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return conservedQuantity; |
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|
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} |
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|
