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#include <cmath> |
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#include "Atom.hpp" |
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#include "Molecule.hpp" |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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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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// The NPTfm variant scales the molecular center-of-mass coordinates |
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// instead of the atomic coordinates |
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NPTfm::NPTfm ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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template<typename T> NPTfm<T>::NPTfm ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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int i, j; |
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chi = 0.0; |
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integralOfChidt = 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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eta[i][j] = 0.0; |
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have_target_pressure = 0; |
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} |
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void NPTfm::moveA() { |
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template<typename T> void NPTfm<T>::moveA() { |
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int i, j, k; |
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DirectionalAtom* dAtom; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double sc[3]; |
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double eta2ij; |
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double eta2ij, smallScale, bigScale, offDiagMax; |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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int nInMol; |
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for (k = 0; k < 3; k++ ) |
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pos[k] += dt * (vel[k] + sc[k]); |
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myAtoms[j]->setPos( pos ); |
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if( myAtoms[j]->isDirectional() ){ |
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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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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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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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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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info->getBoxM(hm); |
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info->matMul3(hm, scaleMat, hmnew); |
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info->setBoxM(hmnew); |
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTf 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 if (offDiagMax > 0.1) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting an off-diagonal 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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info->matMul3(hm, scaleMat, hmnew); |
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info->setBoxM(hmnew); |
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} |
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} |
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void NPTfm::moveB( void ){ |
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template<typename T> void NPTfm<T>::moveB( void ){ |
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int i, j; |
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DirectionalAtom* dAtom; |
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} |
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} |
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int NPTfm::readyCheck() { |
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template<typename T> void NPTfm<T>::resetIntegrator() { |
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int i,j; |
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chi = 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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eta[i][j] = 0.0; |
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} |
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template<typename T> int NPTfm<T>::readyCheck() { |
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//check parent's readyCheck() first |
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if (T::readyCheck() == -1) |
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return -1; |
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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return 1; |
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} |
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template<typename T> double NPTfm<T>::getConservedQuantity(void){ |
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double conservedQuantity; |
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double tb2; |
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double trEta; |
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//HNVE |
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conservedQuantity = tStats->getTotalE(); |
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//HNVT |
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conservedQuantity += (info->getNDF() * kB * targetTemp * |
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(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0)) / eConvert ; |
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//HNPT |
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tb2 = tauBarostat *tauBarostat; |
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trEta = info->matTrace3(eta); |
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conservedQuantity += (targetPressure * tStats->getVolume() / p_convert + |
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3*NkBT/2 * tb2 * trEta * trEta) / eConvert; |
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return conservedQuantity; |
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} |
