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#include <cstdlib> |
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#include <cstring> |
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#include <cmath> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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#include <iostream> |
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using namespace std; |
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haveOrigEcr = 0; |
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boxIsInit = 0; |
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resetTime = 1e99; |
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usePBC = 0; |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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int i, j, status; |
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double smallestBoxL, maxCutoff; |
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int i, j; |
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double FortranHmat[9]; // to preserve compatibility with Fortran the |
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// ordering in the array is as follows: |
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// [ 0 3 6 ] |
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<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
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<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
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<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
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} |
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void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
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out[0] = a[1] * b[2] - a[2] * b[1]; |
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out[1] = a[2] * b[0] - a[0] * b[2] ; |
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out[2] = a[0] * b[1] - a[1] * b[0]; |
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} |
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double SimInfo::dotProduct3(double a[3], double b[3]){ |
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return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
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} |
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|
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double SimInfo::length3(double a[3]){ |
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return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
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} |
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void SimInfo::calcBoxL( void ){ |
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double dx, dy, dz, dsq; |
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int i; |
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// boxVol = Determinant of Hmat |
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dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[0] = sqrt( dsq ); |
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maxCutoff = 0.5 * boxL[0]; |
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//maxCutoff = 0.5 * boxL[0]; |
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// boxLy |
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dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[1] = sqrt( dsq ); |
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if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
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//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
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// boxLz |
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dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxL[2] = sqrt( dsq ); |
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if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
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//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
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|
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//calculate the max cutoff |
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maxCutoff = calcMaxCutOff(); |
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checkCutOffs(); |
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} |
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double SimInfo::calcMaxCutOff(){ |
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double ri[3], rj[3], rk[3]; |
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double rij[3], rjk[3], rki[3]; |
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double minDist; |
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|
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ri[0] = Hmat[0][0]; |
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ri[1] = Hmat[1][0]; |
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ri[2] = Hmat[2][0]; |
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|
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rj[0] = Hmat[0][1]; |
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rj[1] = Hmat[1][1]; |
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rj[2] = Hmat[2][1]; |
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rk[0] = Hmat[0][2]; |
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rk[1] = Hmat[1][2]; |
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rk[2] = Hmat[2][2]; |
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crossProduct3(ri,rj, rij); |
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distXY = dotProduct3(rk,rij) / length3(rij); |
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crossProduct3(rj,rk, rjk); |
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distYZ = dotProduct3(ri,rjk) / length3(rjk); |
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crossProduct3(rk,ri, rki); |
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distZX = dotProduct3(rj,rki) / length3(rki); |
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minDist = min(min(distXY, distYZ), distZX); |
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return minDist/2; |
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} |
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void SimInfo::wrapVector( double thePos[3] ){ |
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int i, j, k; |
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int i; |
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double scaled[3]; |
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if( !orthoRhombic ){ |
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int SimInfo::getNDF(){ |
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int ndf_local, ndf; |
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int ndf_local; |
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ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
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} |
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int SimInfo::getNDFraw() { |
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int ndfRaw_local, ndfRaw; |
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int ndfRaw_local; |
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// Raw degrees of freedom that we have to set |
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ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
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return ndfRaw; |
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} |
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int SimInfo::getNDFtranslational() { |
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int ndfTrans_local; |
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ndfTrans_local = 3 * n_atoms - n_constraints; |
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#ifdef IS_MPI |
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MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndfTrans = ndfTrans_local; |
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#endif |
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ndfTrans = ndfTrans - 3 - nZconstraints; |
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return ndfTrans; |
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} |
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void SimInfo::refreshSim(){ |
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simtype fInfo; |
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this->ndf = this->getNDF(); |
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this->ndfRaw = this->getNDFraw(); |
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this->ndfTrans = this->getNDFtranslational(); |
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} |
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void SimInfo::setRcut( double theRcut ){ |
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if( !haveOrigRcut ){ |
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haveOrigRcut = 1; |
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origRcut = theRcut; |
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} |
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rCut = theRcut; |
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checkCutOffs(); |
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} |
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void SimInfo::setEcr( double theEcr ){ |
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void SimInfo::setDefaultRcut( double theRcut ){ |
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if( !haveOrigEcr ){ |
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haveOrigEcr = 1; |
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origEcr = theEcr; |
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} |
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haveOrigRcut = 1; |
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origRcut = theRcut; |
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rCut = theRcut; |
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
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} |
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void SimInfo::setEcr( double theEcr ){ |
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ecr = theEcr; |
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checkCutOffs(); |
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} |
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void SimInfo::setDefaultEcr( double theEcr ){ |
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|
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haveOrigEcr = 1; |
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origEcr = theEcr; |
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|
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ecr = theEcr; |
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
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} |
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void SimInfo::setEcr( double theEcr, double theEst ){ |
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est = theEst; |
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setEcr( theEcr ); |
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} |
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void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
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void SimInfo::checkCutOffs( void ){ |
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est = theEst; |
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setDefaultEcr( theEcr ); |
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} |
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int cutChanged = 0; |
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void SimInfo::checkCutOffs( void ){ |
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int cutChanged = 0; |
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|
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if( boxIsInit ){ |
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//we need to check cutOffs against the box |
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|
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//detect the change of rCut |
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if(( maxCutoff > rCut )&&(usePBC)){ |
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if( rCut < origRcut ){ |
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rCut = origRcut; |
571 |
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if (rCut > maxCutoff) rCut = maxCutoff; |
572 |
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|
573 |
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sprintf( painCave.errMsg, |
574 |
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"New Box size is setting the long range cutoff radius " |
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"to %lf\n", |
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rCut ); |
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painCave.isFatal = 0; |
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simError(); |
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rCut = origRcut; |
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|
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if (rCut > maxCutoff) |
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rCut = maxCutoff; |
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|
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sprintf( painCave.errMsg, |
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"New Box size is setting the long range cutoff radius " |
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"to %lf at time %lf\n", |
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rCut, currentTime ); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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|
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if( maxCutoff > ecr ){ |
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if( ecr < origEcr ){ |
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rCut = origEcr; |
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if (ecr > maxCutoff) ecr = maxCutoff; |
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|
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sprintf( painCave.errMsg, |
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"New Box size is setting the electrostaticCutoffRadius " |
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"to %lf\n", |
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ecr ); |
510 |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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|
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|
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if ((rCut > maxCutoff)&&(usePBC)) { |
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else if ((rCut > maxCutoff)&&(usePBC)) { |
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sprintf( painCave.errMsg, |
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"New Box size is setting the long range cutoff radius " |
586 |
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"to %lf\n", |
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maxCutoff ); |
586 |
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"to %lf at time %lf\n", |
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maxCutoff, currentTime ); |
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painCave.isFatal = 0; |
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simError(); |
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rCut = maxCutoff; |
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} |
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|
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if( ecr > maxCutoff){ |
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|
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//detect the change of ecr |
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if( maxCutoff > ecr ){ |
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if( ecr < origEcr ){ |
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ecr = origEcr; |
598 |
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if (ecr > maxCutoff) ecr = maxCutoff; |
599 |
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|
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sprintf( painCave.errMsg, |
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"New Box size is setting the electrostaticCutoffRadius " |
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"to %lf at time %lf\n", |
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ecr, currentTime ); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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else if( ecr > maxCutoff){ |
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sprintf( painCave.errMsg, |
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"New Box size is setting the electrostaticCutoffRadius " |
611 |
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"to %lf\n", |
612 |
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maxCutoff ); |
611 |
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"to %lf at time %lf\n", |
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maxCutoff, currentTime ); |
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painCave.isFatal = 0; |
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simError(); |
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ecr = maxCutoff; |
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} |
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if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
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} |
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539 |
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|
540 |
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if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
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|
542 |
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// rlist is the 1.0 plus max( rcut, ecr ) |
543 |
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|
544 |
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
545 |
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|
546 |
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if( cutChanged ){ |
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// rlist is the 1.0 plus max( rcut, ecr ) |
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
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|
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if( cutChanged ){ |
625 |
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|
626 |
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
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} |
628 |
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|
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oldEcr = ecr; |
630 |
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oldRcut = rCut; |
631 |
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|
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} else { |
633 |
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// initialize this stuff before using it, OK? |
634 |
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sprintf( painCave.errMsg, |
635 |
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"Trying to check cutoffs without a box. Be smarter.\n" ); |
636 |
> |
painCave.isFatal = 1; |
637 |
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simError(); |
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} |
639 |
< |
|
551 |
< |
oldEcr = ecr; |
552 |
< |
oldRcut = rCut; |
639 |
> |
|
640 |
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} |
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|
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void SimInfo::addProperty(GenericData* prop){ |