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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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thermalTime = 0.0; |
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currentTime = 0.0; |
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rCut = 0.0; |
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origRcut = -1.0; |
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ecr = 0.0; |
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origEcr = -1.0; |
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est = 0.0; |
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oldEcr = 0.0; |
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oldRcut = 0.0; |
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haveOrigRcut = 0; |
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haveOrigEcr = 0; |
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haveRcut = 0; |
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haveEcr = 0; |
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boxIsInit = 0; |
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resetTime = 1e99; |
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orthoTolerance = 1E-6; |
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useInitXSstate = true; |
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usePBC = 0; |
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useLJ = 0; |
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useSticky = 0; |
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// [ 2 5 8 ] |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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if( !boxIsInit ) boxIsInit = 1; |
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for(i=0; i < 3; i++) |
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void SimInfo::calcHmatInv( void ) { |
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int oldOrtho; |
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int i,j; |
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double smallDiag; |
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double tol; |
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invertMat3( Hmat, HmatInv ); |
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// Check the inverse to make sure it is sane: |
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matMul3( Hmat, HmatInv, sanity ); |
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// check to see if Hmat is orthorhombic |
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smallDiag = Hmat[0][0]; |
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if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
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if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
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tol = smallDiag * 1E-6; |
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oldOrtho = orthoRhombic; |
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smallDiag = fabs(Hmat[0][0]); |
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if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
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if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
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tol = smallDiag * orthoTolerance; |
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orthoRhombic = 1; |
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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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if (orthoRhombic) { |
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if (Hmat[i][j] >= tol) orthoRhombic = 0; |
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if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
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} |
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} |
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} |
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} |
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if( oldOrtho != orthoRhombic ){ |
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if( orthoRhombic ){ |
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sprintf( painCave.errMsg, |
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"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
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" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
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orthoTolerance); |
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simError(); |
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} |
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else { |
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sprintf( painCave.errMsg, |
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"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
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" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n", |
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orthoTolerance); |
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simError(); |
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} |
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} |
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} |
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double SimInfo::matDet3(double a[3][3]) { |
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this->ndfTrans = this->getNDFtranslational(); |
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} |
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void SimInfo::setDefaultRcut( double theRcut ){ |
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void SimInfo::setRcut( double theRcut ){ |
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haveRcut = 1; |
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rCut = 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 > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
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rCut = theRcut; |
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checkCutOffs(); |
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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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void SimInfo::setDefaultEcr( double theEcr ){ |
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haveEcr = 1; |
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
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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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ecr = theEcr; |
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checkCutOffs(); |
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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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void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
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est = theEst; |
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setEcr( theEcr ); |
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setDefaultEcr( theEcr ); |
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} |
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void SimInfo::checkCutOffs( void ){ |
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int cutChanged = 0; |
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if( boxIsInit ){ |
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//we need to check cutOffs against the box |
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| 563 |
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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; |
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|
| 558 |
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if (rCut > maxCutoff) |
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rCut = maxCutoff; |
| 560 |
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|
| 561 |
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sprintf( painCave.errMsg, |
| 562 |
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"New Box size is setting the long range cutoff radius " |
| 563 |
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"to %lf at time %lf\n", |
| 564 |
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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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else if ((rCut > maxCutoff)&&(usePBC)) { |
| 562 |
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|
| 563 |
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if( rCut > maxCutoff ){ |
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sprintf( painCave.errMsg, |
| 565 |
< |
"New Box size is setting the long range cutoff radius " |
| 566 |
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"to %lf at time %lf\n", |
| 567 |
< |
maxCutoff, currentTime ); |
| 568 |
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painCave.isFatal = 0; |
| 565 |
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"Box size is too small for the long range cutoff radius, " |
| 566 |
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"%lf, at time %lf\n", |
| 567 |
> |
rCut, currentTime ); |
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painCave.isFatal = 1; |
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simError(); |
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rCut = maxCutoff; |
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} |
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| 572 |
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| 573 |
< |
//detect the change of ecr |
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< |
if( maxCutoff > ecr ){ |
| 575 |
< |
if( ecr < origEcr ){ |
| 576 |
< |
ecr = origEcr; |
| 577 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
| 578 |
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| 579 |
< |
sprintf( painCave.errMsg, |
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< |
"New Box size is setting the electrostaticCutoffRadius " |
| 588 |
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"to %lf at time %lf\n", |
| 589 |
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ecr, currentTime ); |
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painCave.isFatal = 0; |
| 591 |
< |
simError(); |
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> |
|
| 572 |
> |
if( haveEcr ){ |
| 573 |
> |
if( ecr > maxCutoff ){ |
| 574 |
> |
sprintf( painCave.errMsg, |
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> |
"Box size is too small for the electrostatic cutoff radius, " |
| 576 |
> |
"%lf, at time %lf\n", |
| 577 |
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ecr, currentTime ); |
| 578 |
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painCave.isFatal = 1; |
| 579 |
> |
simError(); |
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} |
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} |
| 594 |
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else if( ecr > maxCutoff){ |
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sprintf( painCave.errMsg, |
| 596 |
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"New Box size is setting the electrostaticCutoffRadius " |
| 597 |
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"to %lf at time %lf\n", |
| 598 |
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maxCutoff, currentTime ); |
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painCave.isFatal = 0; |
| 600 |
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simError(); |
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ecr = maxCutoff; |
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} |
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| 604 |
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if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
| 605 |
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| 606 |
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// rlist is the 1.0 plus max( rcut, ecr ) |
| 607 |
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| 608 |
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( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 609 |
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| 610 |
– |
if( cutChanged ){ |
| 611 |
– |
|
| 612 |
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notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 613 |
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} |
| 614 |
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|
| 615 |
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oldEcr = ecr; |
| 616 |
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oldRcut = rCut; |
| 617 |
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|
| 582 |
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} else { |
| 583 |
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// initialize this stuff before using it, OK? |
| 584 |
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sprintf( painCave.errMsg, |
