# | Line 20 | Line 20 | inline double roundMe( double x ){ | |
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20 | return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); | |
21 | } | |
22 | ||
23 | + | inline double min( double a, double b ){ |
24 | + | return (a < b ) ? a : b; |
25 | + | } |
26 | ||
27 | SimInfo* currentInfo; | |
28 | ||
# | Line 37 | Line 40 | SimInfo::SimInfo(){ | |
40 | thermalTime = 0.0; | |
41 | currentTime = 0.0; | |
42 | rCut = 0.0; | |
40 | – | origRcut = -1.0; |
43 | ecr = 0.0; | |
42 | – | origEcr = -1.0; |
44 | est = 0.0; | |
44 | – | oldEcr = 0.0; |
45 | – | oldRcut = 0.0; |
45 | ||
46 | < | haveOrigRcut = 0; |
47 | < | haveOrigEcr = 0; |
46 | > | haveRcut = 0; |
47 | > | haveEcr = 0; |
48 | boxIsInit = 0; | |
49 | ||
50 | resetTime = 1e99; | |
52 | – | |
51 | ||
52 | + | orthoTolerance = 1E-6; |
53 | + | useInitXSstate = true; |
54 | + | |
55 | usePBC = 0; | |
56 | useLJ = 0; | |
57 | useSticky = 0; | |
58 | < | useDipole = 0; |
58 | > | useCharges = 0; |
59 | > | useDipoles = 0; |
60 | useReactionField = 0; | |
61 | useGB = 0; | |
62 | useEAM = 0; | |
# | Line 102 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){ | |
104 | // [ 2 5 8 ] | |
105 | double FortranHmatInv[9]; // the inverted Hmat (for Fortran); | |
106 | ||
105 | – | |
107 | if( !boxIsInit ) boxIsInit = 1; | |
108 | ||
109 | for(i=0; i < 3; i++) | |
# | Line 146 | Line 147 | void SimInfo::calcHmatInv( void ) { | |
147 | ||
148 | void SimInfo::calcHmatInv( void ) { | |
149 | ||
150 | + | int oldOrtho; |
151 | int i,j; | |
152 | double smallDiag; | |
153 | double tol; | |
# | Line 153 | Line 155 | void SimInfo::calcHmatInv( void ) { | |
155 | ||
156 | invertMat3( Hmat, HmatInv ); | |
157 | ||
156 | – | // Check the inverse to make sure it is sane: |
157 | – | |
158 | – | matMul3( Hmat, HmatInv, sanity ); |
159 | – | |
158 | // check to see if Hmat is orthorhombic | |
159 | ||
160 | < | smallDiag = Hmat[0][0]; |
163 | < | if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
164 | < | if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
165 | < | tol = smallDiag * 1E-6; |
160 | > | oldOrtho = orthoRhombic; |
161 | ||
162 | + | smallDiag = fabs(Hmat[0][0]); |
163 | + | if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
164 | + | if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
165 | + | tol = smallDiag * orthoTolerance; |
166 | + | |
167 | orthoRhombic = 1; | |
168 | ||
169 | for (i = 0; i < 3; i++ ) { | |
170 | for (j = 0 ; j < 3; j++) { | |
171 | if (i != j) { | |
172 | if (orthoRhombic) { | |
173 | < | if (Hmat[i][j] >= tol) orthoRhombic = 0; |
173 | > | if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
174 | } | |
175 | } | |
176 | + | } |
177 | + | } |
178 | + | |
179 | + | if( oldOrtho != orthoRhombic ){ |
180 | + | |
181 | + | if( orthoRhombic ){ |
182 | + | sprintf( painCave.errMsg, |
183 | + | "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n" |
184 | + | "\tIf this is a bad thing, change the orthoBoxTolerance\n" |
185 | + | "\tvariable ( currently set to %G ).\n", |
186 | + | orthoTolerance); |
187 | + | simError(); |
188 | + | } |
189 | + | else { |
190 | + | sprintf( painCave.errMsg, |
191 | + | "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n" |
192 | + | "\tIf this is a bad thing, change the orthoBoxTolerance\n" |
193 | + | "\tvariable ( currently set to %G ).\n", |
194 | + | orthoTolerance); |
195 | + | simError(); |
196 | } | |
197 | } | |
198 | } | |
# | Line 463 | Line 483 | void SimInfo::refreshSim(){ | |
483 | ||
484 | fInfo.dielect = 0.0; | |
485 | ||
486 | < | if( useDipole ){ |
486 | > | if( useDipoles ){ |
487 | if( useReactionField )fInfo.dielect = dielectric; | |
488 | } | |
489 | ||
# | Line 472 | Line 492 | void SimInfo::refreshSim(){ | |
492 | fInfo.SIM_uses_LJ = useLJ; | |
493 | fInfo.SIM_uses_sticky = useSticky; | |
494 | //fInfo.SIM_uses_sticky = 0; | |
495 | < | fInfo.SIM_uses_dipoles = useDipole; |
495 | > | fInfo.SIM_uses_charges = useCharges; |
496 | > | fInfo.SIM_uses_dipoles = useDipoles; |
497 | //fInfo.SIM_uses_dipoles = 0; | |
498 | //fInfo.SIM_uses_RF = useReactionField; | |
499 | fInfo.SIM_uses_RF = 0; | |
# | Line 510 | Line 531 | void SimInfo::refreshSim(){ | |
531 | this->ndf = this->getNDF(); | |
532 | this->ndfRaw = this->getNDFraw(); | |
533 | this->ndfTrans = this->getNDFtranslational(); | |
513 | – | } |
514 | – | |
515 | – | |
516 | – | void SimInfo::setRcut( double theRcut ){ |
517 | – | |
518 | – | rCut = theRcut; |
519 | – | checkCutOffs(); |
534 | } | |
535 | ||
536 | void SimInfo::setDefaultRcut( double theRcut ){ | |
537 | ||
538 | < | haveOrigRcut = 1; |
525 | < | origRcut = theRcut; |
538 | > | haveRcut = 1; |
539 | rCut = theRcut; | |
527 | – | } |
540 | ||
541 | < | void SimInfo::setEcr( double theEcr ){ |
541 | > | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
542 | ||
543 | < | ecr = theEcr; |
532 | < | checkCutOffs(); |
543 | > | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
544 | } | |
545 | ||
546 | void SimInfo::setDefaultEcr( double theEcr ){ | |
547 | ||
548 | < | haveOrigEcr = 1; |
538 | < | origEcr = theEcr; |
539 | < | |
548 | > | haveEcr = 1; |
549 | ecr = theEcr; | |
550 | < | } |
550 | > | |
551 | > | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
552 | ||
553 | < | void SimInfo::setEcr( double theEcr, double theEst ){ |
544 | < | |
545 | < | est = theEst; |
546 | < | setEcr( theEcr ); |
553 | > | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
554 | } | |
555 | ||
556 | void SimInfo::setDefaultEcr( double theEcr, double theEst ){ | |
# | Line 554 | Line 561 | void SimInfo::checkCutOffs( void ){ | |
561 | ||
562 | ||
563 | void SimInfo::checkCutOffs( void ){ | |
557 | – | |
558 | – | int cutChanged = 0; |
564 | ||
565 | if( boxIsInit ){ | |
566 | ||
567 | //we need to check cutOffs against the box | |
568 | < | |
569 | < | //detect the change of rCut |
565 | < | if(( maxCutoff > rCut )&&(usePBC)){ |
566 | < | if( rCut < origRcut ){ |
567 | < | rCut = origRcut; |
568 | < | |
569 | < | if (rCut > maxCutoff) |
570 | < | rCut = maxCutoff; |
571 | < | |
572 | < | sprintf( painCave.errMsg, |
573 | < | "New Box size is setting the long range cutoff radius " |
574 | < | "to %lf at time %lf\n", |
575 | < | rCut, currentTime ); |
576 | < | painCave.isFatal = 0; |
577 | < | simError(); |
578 | < | } |
579 | < | } |
580 | < | else if ((rCut > maxCutoff)&&(usePBC)) { |
568 | > | |
569 | > | if( rCut > maxCutoff ){ |
570 | sprintf( painCave.errMsg, | |
571 | < | "New Box size is setting the long range cutoff radius " |
572 | < | "to %lf at time %lf\n", |
573 | < | maxCutoff, currentTime ); |
574 | < | painCave.isFatal = 0; |
571 | > | "Box size is too small for the long range cutoff radius, " |
572 | > | "%G, at time %G\n" |
573 | > | "\t[ %G %G %G ]\n" |
574 | > | "\t[ %G %G %G ]\n" |
575 | > | "\t[ %G %G %G ]\n", |
576 | > | rCut, currentTime, |
577 | > | Hmat[0][0], Hmat[0][1], Hmat[0][2], |
578 | > | Hmat[1][0], Hmat[1][1], Hmat[1][2], |
579 | > | Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
580 | > | painCave.isFatal = 1; |
581 | simError(); | |
587 | – | rCut = maxCutoff; |
582 | } | |
583 | < | |
584 | < | |
585 | < | //detect the change of ecr |
586 | < | if( maxCutoff > ecr ){ |
587 | < | if( ecr < origEcr ){ |
588 | < | ecr = origEcr; |
589 | < | if (ecr > maxCutoff) ecr = maxCutoff; |
590 | < | |
591 | < | sprintf( painCave.errMsg, |
592 | < | "New Box size is setting the electrostaticCutoffRadius " |
593 | < | "to %lf at time %lf\n", |
594 | < | ecr, currentTime ); |
595 | < | painCave.isFatal = 0; |
596 | < | simError(); |
583 | > | |
584 | > | if( haveEcr ){ |
585 | > | if( ecr > maxCutoff ){ |
586 | > | sprintf( painCave.errMsg, |
587 | > | "Box size is too small for the electrostatic cutoff radius, " |
588 | > | "%G, at time %G\n" |
589 | > | "\t[ %G %G %G ]\n" |
590 | > | "\t[ %G %G %G ]\n" |
591 | > | "\t[ %G %G %G ]\n", |
592 | > | ecr, currentTime, |
593 | > | Hmat[0][0], Hmat[0][1], Hmat[0][2], |
594 | > | Hmat[1][0], Hmat[1][1], Hmat[1][2], |
595 | > | Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
596 | > | painCave.isFatal = 1; |
597 | > | simError(); |
598 | } | |
599 | } | |
605 | – | else if( ecr > maxCutoff){ |
606 | – | sprintf( painCave.errMsg, |
607 | – | "New Box size is setting the electrostaticCutoffRadius " |
608 | – | "to %lf at time %lf\n", |
609 | – | maxCutoff, currentTime ); |
610 | – | painCave.isFatal = 0; |
611 | – | simError(); |
612 | – | ecr = maxCutoff; |
613 | – | } |
614 | – | |
615 | – | if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
616 | – | |
617 | – | // rlist is the 1.0 plus max( rcut, ecr ) |
618 | – | |
619 | – | ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
620 | – | |
621 | – | if( cutChanged ){ |
622 | – | |
623 | – | notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
624 | – | } |
625 | – | |
626 | – | oldEcr = ecr; |
627 | – | oldRcut = rCut; |
628 | – | |
600 | } else { | |
601 | // initialize this stuff before using it, OK? | |
602 | sprintf( painCave.errMsg, | |
603 | < | "Trying to check cutoffs without a box. Be smarter.\n" ); |
603 | > | "Trying to check cutoffs without a box.\n" |
604 | > | "\tOOPSE should have better programmers than that.\n" ); |
605 | painCave.isFatal = 1; | |
606 | simError(); | |
607 | } |
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