| 1 |
#include <cstdlib> |
| 2 |
#include <cstring> |
| 3 |
#include <cmath> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "SimInfo.hpp" |
| 9 |
#define __C |
| 10 |
#include "fSimulation.h" |
| 11 |
#include "simError.h" |
| 12 |
|
| 13 |
#include "fortranWrappers.hpp" |
| 14 |
|
| 15 |
#ifdef IS_MPI |
| 16 |
#include "mpiSimulation.hpp" |
| 17 |
#endif |
| 18 |
|
| 19 |
inline double roundMe( double x ){ |
| 20 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 21 |
} |
| 22 |
|
| 23 |
|
| 24 |
SimInfo* currentInfo; |
| 25 |
|
| 26 |
SimInfo::SimInfo(){ |
| 27 |
excludes = NULL; |
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n_constraints = 0; |
| 29 |
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; |
| 40 |
useSticky = 0; |
| 41 |
useDipole = 0; |
| 42 |
useReactionField = 0; |
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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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int i, j; |
| 52 |
double tempMat[3][3]; |
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|
| 54 |
for(i=0; i<3; i++) |
| 55 |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
| 56 |
|
| 57 |
tempMat[0][0] = newBox[0]; |
| 58 |
tempMat[1][1] = newBox[1]; |
| 59 |
tempMat[2][2] = newBox[2]; |
| 60 |
|
| 61 |
setBoxM( tempMat ); |
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|
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} |
| 64 |
|
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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|
| 67 |
int i, j, status; |
| 68 |
double smallestBoxL, maxCutoff; |
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double FortranHmat[9]; // to preserve compatibility with Fortran the |
| 70 |
// ordering in the array is as follows: |
| 71 |
// [ 0 3 6 ] |
| 72 |
// [ 1 4 7 ] |
| 73 |
// [ 2 5 8 ] |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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|
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|
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for(i=0; i < 3; i++) |
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for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
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|
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cerr |
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<< "setting Hmat ->\n" |
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<< "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
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<< "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
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<< "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
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|
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calcBoxL(); |
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calcHmatInv(); |
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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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FortranHmat[3*j + i] = Hmat[i][j]; |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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} |
| 94 |
} |
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|
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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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|
| 98 |
smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
| 100 |
if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
| 101 |
|
| 102 |
maxCutoff = smallestBoxL / 2.0; |
| 103 |
|
| 104 |
if (rList > maxCutoff) { |
| 105 |
sprintf( painCave.errMsg, |
| 106 |
"New Box size is forcing neighborlist radius down to %lf\n", |
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maxCutoff ); |
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painCave.isFatal = 0; |
| 109 |
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[3][3]) { |
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|
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int i, j; |
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for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
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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[3][3]; |
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int i, j; |
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|
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cerr << "Scaling box by " << scale << "\n"; |
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|
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for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*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::calcHmatInv( void ) { |
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|
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int i,j; |
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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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invertMat3( Hmat, HmatInv ); |
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|
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// Check the inverse to make sure it is sane: |
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|
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matMul3( Hmat, HmatInv, sanity ); |
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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][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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|
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orthoRhombic = 1; |
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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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if (i != j) { |
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if (orthoRhombic) { |
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if (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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} |
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|
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double SimInfo::matDet3(double a[3][3]) { |
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int i, j, k; |
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double determinant; |
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|
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determinant = 0.0; |
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|
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for(i = 0; i < 3; i++) { |
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j = (i+1)%3; |
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k = (i+2)%3; |
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|
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determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
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} |
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|
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return determinant; |
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} |
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|
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void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
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|
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int i, j, k, l, m, n; |
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double determinant; |
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|
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determinant = matDet3( a ); |
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|
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if (determinant == 0.0) { |
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sprintf( painCave.errMsg, |
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"Can't invert a matrix with a zero determinant!\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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for (i=0; i < 3; i++) { |
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j = (i+1)%3; |
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k = (i+2)%3; |
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for(l = 0; l < 3; l++) { |
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m = (l+1)%3; |
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n = (l+2)%3; |
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|
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b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
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} |
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} |
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} |
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|
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void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
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double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
| 242 |
|
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r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
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r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
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r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
| 246 |
|
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r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
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r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
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r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
| 250 |
|
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r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
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r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
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r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
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|
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c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
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c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
| 257 |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
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} |
| 259 |
|
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void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
| 261 |
double a0, a1, a2; |
| 262 |
|
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a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
| 264 |
|
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outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
| 266 |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
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outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
| 268 |
} |
| 269 |
|
| 270 |
void SimInfo::calcBoxL( void ){ |
| 271 |
|
| 272 |
double dx, dy, dz, dsq; |
| 273 |
int i; |
| 274 |
|
| 275 |
// boxVol = Determinant of Hmat |
| 276 |
|
| 277 |
boxVol = matDet3( Hmat ); |
| 278 |
|
| 279 |
// boxLx |
| 280 |
|
| 281 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
| 282 |
dsq = dx*dx + dy*dy + dz*dz; |
| 283 |
boxLx = sqrt( dsq ); |
| 284 |
|
| 285 |
// boxLy |
| 286 |
|
| 287 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
| 288 |
dsq = dx*dx + dy*dy + dz*dz; |
| 289 |
boxLy = sqrt( dsq ); |
| 290 |
|
| 291 |
// boxLz |
| 292 |
|
| 293 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
| 294 |
dsq = dx*dx + dy*dy + dz*dz; |
| 295 |
boxLz = sqrt( dsq ); |
| 296 |
|
| 297 |
} |
| 298 |
|
| 299 |
|
| 300 |
void SimInfo::wrapVector( double thePos[3] ){ |
| 301 |
|
| 302 |
int i, j, k; |
| 303 |
double scaled[3]; |
| 304 |
|
| 305 |
if( !orthoRhombic ){ |
| 306 |
// calc the scaled coordinates. |
| 307 |
|
| 308 |
|
| 309 |
matVecMul3(HmatInv, thePos, scaled); |
| 310 |
|
| 311 |
for(i=0; i<3; i++) |
| 312 |
scaled[i] -= roundMe(scaled[i]); |
| 313 |
|
| 314 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 315 |
|
| 316 |
matVecMul3(Hmat, scaled, thePos); |
| 317 |
|
| 318 |
} |
| 319 |
else{ |
| 320 |
// calc the scaled coordinates. |
| 321 |
|
| 322 |
for(i=0; i<3; i++) |
| 323 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
| 324 |
|
| 325 |
// wrap the scaled coordinates |
| 326 |
|
| 327 |
for(i=0; i<3; i++) |
| 328 |
scaled[i] -= roundMe(scaled[i]); |
| 329 |
|
| 330 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 331 |
|
| 332 |
for(i=0; i<3; i++) |
| 333 |
thePos[i] = scaled[i]*Hmat[i][i]; |
| 334 |
} |
| 335 |
|
| 336 |
} |
| 337 |
|
| 338 |
|
| 339 |
int SimInfo::getNDF(){ |
| 340 |
int ndf_local, ndf; |
| 341 |
|
| 342 |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
| 343 |
|
| 344 |
#ifdef IS_MPI |
| 345 |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 346 |
#else |
| 347 |
ndf = ndf_local; |
| 348 |
#endif |
| 349 |
|
| 350 |
ndf = ndf - 3; |
| 351 |
|
| 352 |
return ndf; |
| 353 |
} |
| 354 |
|
| 355 |
int SimInfo::getNDFraw() { |
| 356 |
int ndfRaw_local, ndfRaw; |
| 357 |
|
| 358 |
// Raw degrees of freedom that we have to set |
| 359 |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
| 360 |
|
| 361 |
#ifdef IS_MPI |
| 362 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 363 |
#else |
| 364 |
ndfRaw = ndfRaw_local; |
| 365 |
#endif |
| 366 |
|
| 367 |
return ndfRaw; |
| 368 |
} |
| 369 |
|
| 370 |
void SimInfo::refreshSim(){ |
| 371 |
|
| 372 |
simtype fInfo; |
| 373 |
int isError; |
| 374 |
int n_global; |
| 375 |
int* excl; |
| 376 |
|
| 377 |
fInfo.rrf = 0.0; |
| 378 |
fInfo.rt = 0.0; |
| 379 |
fInfo.dielect = 0.0; |
| 380 |
|
| 381 |
fInfo.rlist = rList; |
| 382 |
fInfo.rcut = rCut; |
| 383 |
|
| 384 |
if( useDipole ){ |
| 385 |
fInfo.rrf = ecr; |
| 386 |
fInfo.rt = ecr - est; |
| 387 |
if( useReactionField )fInfo.dielect = dielectric; |
| 388 |
} |
| 389 |
|
| 390 |
fInfo.SIM_uses_PBC = usePBC; |
| 391 |
//fInfo.SIM_uses_LJ = 0; |
| 392 |
fInfo.SIM_uses_LJ = useLJ; |
| 393 |
fInfo.SIM_uses_sticky = useSticky; |
| 394 |
//fInfo.SIM_uses_sticky = 0; |
| 395 |
fInfo.SIM_uses_dipoles = useDipole; |
| 396 |
//fInfo.SIM_uses_dipoles = 0; |
| 397 |
//fInfo.SIM_uses_RF = useReactionField; |
| 398 |
fInfo.SIM_uses_RF = 0; |
| 399 |
fInfo.SIM_uses_GB = useGB; |
| 400 |
fInfo.SIM_uses_EAM = useEAM; |
| 401 |
|
| 402 |
excl = Exclude::getArray(); |
| 403 |
|
| 404 |
#ifdef IS_MPI |
| 405 |
n_global = mpiSim->getTotAtoms(); |
| 406 |
#else |
| 407 |
n_global = n_atoms; |
| 408 |
#endif |
| 409 |
|
| 410 |
isError = 0; |
| 411 |
|
| 412 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 413 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 414 |
&isError ); |
| 415 |
|
| 416 |
if( isError ){ |
| 417 |
|
| 418 |
sprintf( painCave.errMsg, |
| 419 |
"There was an error setting the simulation information in fortran.\n" ); |
| 420 |
painCave.isFatal = 1; |
| 421 |
simError(); |
| 422 |
} |
| 423 |
|
| 424 |
#ifdef IS_MPI |
| 425 |
sprintf( checkPointMsg, |
| 426 |
"succesfully sent the simulation information to fortran.\n"); |
| 427 |
MPIcheckPoint(); |
| 428 |
#endif // is_mpi |
| 429 |
|
| 430 |
this->ndf = this->getNDF(); |
| 431 |
this->ndfRaw = this->getNDFraw(); |
| 432 |
|
| 433 |
} |
| 434 |
|
