| 1 |
#include <cstdlib> |
| 2 |
#include <cstring> |
| 3 |
#include <cmath> |
| 4 |
|
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#include <iostream> |
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using namespace std; |
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|
| 8 |
#include "SimInfo.hpp" |
| 9 |
#define __C |
| 10 |
#include "fSimulation.h" |
| 11 |
#include "simError.h" |
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|
| 13 |
#include "fortranWrappers.hpp" |
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|
| 15 |
#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
| 17 |
#endif |
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|
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inline double roundMe( double x ){ |
| 20 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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|
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|
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SimInfo* currentInfo; |
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|
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SimInfo::SimInfo(){ |
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excludes = NULL; |
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n_constraints = 0; |
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n_oriented = 0; |
| 30 |
n_dipoles = 0; |
| 31 |
ndf = 0; |
| 32 |
ndfRaw = 0; |
| 33 |
the_integrator = NULL; |
| 34 |
setTemp = 0; |
| 35 |
thermalTime = 0.0; |
| 36 |
rCut = 0.0; |
| 37 |
|
| 38 |
usePBC = 0; |
| 39 |
useLJ = 0; |
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useSticky = 0; |
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useDipole = 0; |
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useReactionField = 0; |
| 43 |
useGB = 0; |
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useEAM = 0; |
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|
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wrapMeSimInfo( this ); |
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} |
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|
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void SimInfo::setBox(double newBox[3]) { |
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|
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double smallestBoxL, maxCutoff; |
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int status; |
| 53 |
int i; |
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|
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for(i=0; i<9; i++) Hmat[i] = 0.0;; |
| 56 |
|
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Hmat[0] = newBox[0]; |
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Hmat[4] = newBox[1]; |
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Hmat[8] = newBox[2]; |
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|
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calcHmatI(); |
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calcBoxL(); |
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|
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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|
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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|
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maxCutoff = smallestBoxL / 2.0; |
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|
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if (rList > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing neighborlist radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
| 77 |
simError(); |
| 78 |
|
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rList = maxCutoff; |
| 80 |
|
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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rCut = rList - 1.0; |
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|
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// list radius changed so we have to refresh the simulation structure. |
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refreshSim(); |
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} |
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|
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if (rCut > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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status = 0; |
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LJ_new_rcut(&rCut, &status); |
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if (status != 0) { |
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sprintf( painCave.errMsg, |
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"Error in recomputing LJ shifts based on new rcut\n"); |
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painCave.isFatal = 1; |
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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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void SimInfo::setBoxM( double theBox[9] ){ |
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|
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int i, status; |
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double smallestBoxL, maxCutoff; |
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|
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for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
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calcHmatI(); |
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calcBoxL(); |
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|
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
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|
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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|
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maxCutoff = smallestBoxL / 2.0; |
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|
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if (rList > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing neighborlist radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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rList = maxCutoff; |
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|
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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rCut = rList - 1.0; |
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|
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// list radius changed so we have to refresh the simulation structure. |
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refreshSim(); |
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} |
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|
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if (rCut > maxCutoff) { |
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sprintf( painCave.errMsg, |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
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simError(); |
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|
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status = 0; |
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LJ_new_rcut(&rCut, &status); |
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if (status != 0) { |
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sprintf( painCave.errMsg, |
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"Error in recomputing LJ shifts based on new rcut\n"); |
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painCave.isFatal = 1; |
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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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|
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void SimInfo::getBoxM (double theBox[9]) { |
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|
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int i; |
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for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
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} |
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|
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|
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void SimInfo::scaleBox(double scale) { |
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double theBox[9]; |
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int i; |
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|
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for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale; |
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|
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setBoxM(theBox); |
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|
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} |
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|
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void SimInfo::calcHmatI( void ) { |
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|
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double C[3][3]; |
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double detHmat; |
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int i, j, k; |
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double smallDiag; |
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double tol; |
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double sanity[3][3]; |
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|
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// calculate the adjunct of Hmat; |
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|
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C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
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C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
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C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
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|
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C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
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C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
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C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
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|
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C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
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C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
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C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
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|
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// calcutlate the determinant of Hmat |
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|
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detHmat = 0.0; |
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for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
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|
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|
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// H^-1 = C^T / det(H) |
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|
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i=0; |
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for(j=0; j<3; j++){ |
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for(k=0; k<3; k++){ |
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|
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HmatI[i] = C[j][k] / detHmat; |
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i++; |
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} |
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} |
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|
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// sanity check |
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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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sanity[i][j] = 0.0; |
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for(k=0; k<3; k++){ |
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sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
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} |
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} |
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} |
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|
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cerr << "sanity => \n" |
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<< sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
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<< sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
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<< sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
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<< "\n"; |
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|
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|
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// check to see if Hmat is orthorhombic |
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|
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smallDiag = Hmat[0]; |
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if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
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if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
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tol = smallDiag * 1E-6; |
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|
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orthoRhombic = 1; |
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for(i=0; (i<9) && orthoRhombic; i++){ |
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|
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if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
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orthoRhombic = (Hmat[i] <= tol); |
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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 SimInfo::calcBoxL( void ){ |
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|
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double dx, dy, dz, dsq; |
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int i; |
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|
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// boxVol = h1 (dot) h2 (cross) h3 |
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|
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boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
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+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
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+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
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|
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|
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// boxLx |
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|
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dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxLx = sqrt( dsq ); |
| 278 |
|
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// boxLy |
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|
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dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
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dsq = dx*dx + dy*dy + dz*dz; |
| 283 |
boxLy = sqrt( dsq ); |
| 284 |
|
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// boxLz |
| 286 |
|
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dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
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dsq = dx*dx + dy*dy + dz*dz; |
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boxLz = sqrt( dsq ); |
| 290 |
|
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} |
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|
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|
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void SimInfo::wrapVector( double thePos[3] ){ |
| 295 |
|
| 296 |
int i, j, k; |
| 297 |
double scaled[3]; |
| 298 |
|
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if( !orthoRhombic ){ |
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// calc the scaled coordinates. |
| 301 |
|
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for(i=0; i<3; i++) |
| 303 |
scaled[i] = |
| 304 |
thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
| 305 |
|
| 306 |
// wrap the scaled coordinates |
| 307 |
|
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for(i=0; i<3; i++) |
| 309 |
scaled[i] -= roundMe(scaled[i]); |
| 310 |
|
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 312 |
|
| 313 |
for(i=0; i<3; i++) |
| 314 |
thePos[i] = |
| 315 |
scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
| 316 |
} |
| 317 |
else{ |
| 318 |
// calc the scaled coordinates. |
| 319 |
|
| 320 |
for(i=0; i<3; i++) |
| 321 |
scaled[i] = thePos[i]*HmatI[i*4]; |
| 322 |
|
| 323 |
// wrap the scaled coordinates |
| 324 |
|
| 325 |
for(i=0; i<3; i++) |
| 326 |
scaled[i] -= roundMe(scaled[i]); |
| 327 |
|
| 328 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 329 |
|
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for(i=0; i<3; i++) |
| 331 |
thePos[i] = scaled[i]*Hmat[i*4]; |
| 332 |
} |
| 333 |
|
| 334 |
|
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} |
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|
| 337 |
|
| 338 |
int SimInfo::getNDF(){ |
| 339 |
int ndf_local, ndf; |
| 340 |
|
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ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
| 342 |
|
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#ifdef IS_MPI |
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MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 345 |
#else |
| 346 |
ndf = ndf_local; |
| 347 |
#endif |
| 348 |
|
| 349 |
ndf = ndf - 3; |
| 350 |
|
| 351 |
return ndf; |
| 352 |
} |
| 353 |
|
| 354 |
int SimInfo::getNDFraw() { |
| 355 |
int ndfRaw_local, ndfRaw; |
| 356 |
|
| 357 |
// Raw degrees of freedom that we have to set |
| 358 |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
| 359 |
|
| 360 |
#ifdef IS_MPI |
| 361 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 362 |
#else |
| 363 |
ndfRaw = ndfRaw_local; |
| 364 |
#endif |
| 365 |
|
| 366 |
return ndfRaw; |
| 367 |
} |
| 368 |
|
| 369 |
void SimInfo::refreshSim(){ |
| 370 |
|
| 371 |
simtype fInfo; |
| 372 |
int isError; |
| 373 |
int n_global; |
| 374 |
int* excl; |
| 375 |
|
| 376 |
fInfo.rrf = 0.0; |
| 377 |
fInfo.rt = 0.0; |
| 378 |
fInfo.dielect = 0.0; |
| 379 |
|
| 380 |
fInfo.rlist = rList; |
| 381 |
fInfo.rcut = rCut; |
| 382 |
|
| 383 |
if( useDipole ){ |
| 384 |
fInfo.rrf = ecr; |
| 385 |
fInfo.rt = ecr - est; |
| 386 |
if( useReactionField )fInfo.dielect = dielectric; |
| 387 |
} |
| 388 |
|
| 389 |
fInfo.SIM_uses_PBC = usePBC; |
| 390 |
//fInfo.SIM_uses_LJ = 0; |
| 391 |
fInfo.SIM_uses_LJ = useLJ; |
| 392 |
fInfo.SIM_uses_sticky = useSticky; |
| 393 |
//fInfo.SIM_uses_sticky = 0; |
| 394 |
fInfo.SIM_uses_dipoles = useDipole; |
| 395 |
//fInfo.SIM_uses_dipoles = 0; |
| 396 |
//fInfo.SIM_uses_RF = useReactionField; |
| 397 |
fInfo.SIM_uses_RF = 0; |
| 398 |
fInfo.SIM_uses_GB = useGB; |
| 399 |
fInfo.SIM_uses_EAM = useEAM; |
| 400 |
|
| 401 |
excl = Exclude::getArray(); |
| 402 |
|
| 403 |
#ifdef IS_MPI |
| 404 |
n_global = mpiSim->getTotAtoms(); |
| 405 |
#else |
| 406 |
n_global = n_atoms; |
| 407 |
#endif |
| 408 |
|
| 409 |
isError = 0; |
| 410 |
|
| 411 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 412 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 413 |
&isError ); |
| 414 |
|
| 415 |
if( isError ){ |
| 416 |
|
| 417 |
sprintf( painCave.errMsg, |
| 418 |
"There was an error setting the simulation information in fortran.\n" ); |
| 419 |
painCave.isFatal = 1; |
| 420 |
simError(); |
| 421 |
} |
| 422 |
|
| 423 |
#ifdef IS_MPI |
| 424 |
sprintf( checkPointMsg, |
| 425 |
"succesfully sent the simulation information to fortran.\n"); |
| 426 |
MPIcheckPoint(); |
| 427 |
#endif // is_mpi |
| 428 |
|
| 429 |
this->ndf = this->getNDF(); |
| 430 |
this->ndfRaw = this->getNDFraw(); |
| 431 |
|
| 432 |
} |
| 433 |
|
