OOPSE/libmdtools/SimInfo.cpp

#include <cstdlib>
#include <cstring>
#include <cmath>

#include <iostream>
using namespace std;

#include "SimInfo.hpp"
#define __C
#include "fSimulation.h"
#include "simError.h"

#include "fortranWrappers.hpp"

#ifdef IS_MPI
#include "mpiSimulation.hpp"
#endif

inline double roundMe( double x ){
  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
}
          

SimInfo* currentInfo;

SimInfo::SimInfo(){
  excludes = NULL;
  n_constraints = 0;
  n_oriented = 0;
  n_dipoles = 0;
  ndf = 0;
  ndfRaw = 0;
  the_integrator = NULL;
  setTemp = 0;
  thermalTime = 0.0;
  rCut = 0.0;

  usePBC = 0;
  useLJ = 0; 
  useSticky = 0;
  useDipole = 0;
  useReactionField = 0;
  useGB = 0;
  useEAM = 0;

  wrapMeSimInfo( this );
}

void SimInfo::setBox(double newBox[3]) {
  
  int i, j;
  double tempMat[3][3];

  for(i=0; i<3; i++) 
    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;

  tempMat[0][0] = newBox[0];
  tempMat[1][1] = newBox[1];
  tempMat[2][2] = newBox[2];

  setBoxM( tempMat );

}

void SimInfo::setBoxM( double theBox[3][3] ){
  
  int i, j, status;
  double smallestBoxL, maxCutoff;
  double FortranHmat[9]; // to preserve compatibility with Fortran the
                         // ordering in the array is as follows:
                         // [ 0 3 6 ]
                         // [ 1 4 7 ]
                         // [ 2 5 8 ]
  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);


  for(i=0; i < 3; i++) 
    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
  
  cerr 
    << "setting Hmat ->\n"
    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";

  calcBoxL();
  calcHmatInv();

  for(i=0; i < 3; i++) {
    for (j=0; j < 3; j++) {
      FortranHmat[3*j + i] = Hmat[i][j];
      FortranHmatInv[3*j + i] = HmatInv[i][j];
    }
  }

  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
 
  smallestBoxL = boxLx;
  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
  if (boxLz < smallestBoxL) smallestBoxL = boxLz;

  maxCutoff = smallestBoxL / 2.0;

  if (rList > maxCutoff) {
    sprintf( painCave.errMsg,
             "New Box size is forcing neighborlist radius down to %lf\n",
             maxCutoff );
    painCave.isFatal = 0;
    simError();

    rList = maxCutoff;

    sprintf( painCave.errMsg,
             "New Box size is forcing cutoff radius down to %lf\n",
             maxCutoff - 1.0 );
    painCave.isFatal = 0;
    simError();

    rCut = rList - 1.0;

    // list radius changed so we have to refresh the simulation structure.
    refreshSim();
  }

  if (rCut > maxCutoff) {
    sprintf( painCave.errMsg,
             "New Box size is forcing cutoff radius down to %lf\n",
             maxCutoff );
    painCave.isFatal = 0;
    simError();

    status = 0;
    LJ_new_rcut(&rCut, &status);
    if (status != 0) {
      sprintf( painCave.errMsg,
               "Error in recomputing LJ shifts based on new rcut\n");
      painCave.isFatal = 1;
      simError();
    }
  }
}
 

void SimInfo::getBoxM (double theBox[3][3]) {

  int i, j;
  for(i=0; i<3; i++) 
    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
}


void SimInfo::scaleBox(double scale) {
  double theBox[3][3];
  int i, j;

  cerr << "Scaling box by " << scale << "\n";

  for(i=0; i<3; i++) 
    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;

  setBoxM(theBox);

}

void SimInfo::calcHmatInv( void ) {
  
  int i,j;
  double smallDiag;
  double tol;
  double sanity[3][3];

  invertMat3( Hmat, HmatInv );

  // Check the inverse to make sure it is sane:

  matMul3( Hmat, HmatInv, sanity );
    
  // check to see if Hmat is orthorhombic
  
  smallDiag = Hmat[0][0];
  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
  tol = smallDiag * 1E-6;

  orthoRhombic = 1;
  
  for (i = 0; i < 3; i++ ) {
    for (j = 0 ; j < 3; j++) {
      if (i != j) {
        if (orthoRhombic) {
          if (Hmat[i][j] >= tol) orthoRhombic = 0;
        }        
      }
    }
  }
}

double SimInfo::matDet3(double a[3][3]) {
  int i, j, k;
  double determinant;

  determinant = 0.0;

  for(i = 0; i < 3; i++) {
    j = (i+1)%3;
    k = (i+2)%3;

    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
  }

  return determinant;
}

void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
  
  int  i, j, k, l, m, n;
  double determinant;

  determinant = matDet3( a );

  if (determinant == 0.0) {
    sprintf( painCave.errMsg,
             "Can't invert a matrix with a zero determinant!\n");
    painCave.isFatal = 1;
    simError();
  }

  for (i=0; i < 3; i++) {
    j = (i+1)%3;
    k = (i+2)%3;
    for(l = 0; l < 3; l++) {
      m = (l+1)%3;
      n = (l+2)%3;
      
      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
    }
  }
}

void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
  double r00, r01, r02, r10, r11, r12, r20, r21, r22;

  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
  
  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
  
  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
  
  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
}

void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
  double a0, a1, a2;

  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];

  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
}

void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
  double temp[3][3];
  int i, j;

  for (i = 0; i < 3; i++) {
    for (j = 0; j < 3; j++) {
      temp[j][i] = in[i][j];
    }
  }
  for (i = 0; i < 3; i++) {
    for (j = 0; j < 3; j++) {
      out[i][j] = temp[i][j];
    }
  }
}
  
void SimInfo::printMat3(double A[3][3] ){

  std::cerr 
            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
}

void SimInfo::printMat9(double A[9] ){

  std::cerr 
            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
}

void SimInfo::calcBoxL( void ){

  double dx, dy, dz, dsq;
  int i;

  // boxVol = Determinant of Hmat

  boxVol = matDet3( Hmat );

  // boxLx
  
  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
  dsq = dx*dx + dy*dy + dz*dz;
  boxLx = sqrt( dsq );

  // boxLy
  
  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
  dsq = dx*dx + dy*dy + dz*dz;
  boxLy = sqrt( dsq );

  // boxLz
  
  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
  dsq = dx*dx + dy*dy + dz*dz;
  boxLz = sqrt( dsq );
  
}


void SimInfo::wrapVector( double thePos[3] ){

  int i, j, k;
  double scaled[3];

  if( !orthoRhombic ){
    // calc the scaled coordinates.
  

    matVecMul3(HmatInv, thePos, scaled);
    
    for(i=0; i<3; i++)
      scaled[i] -= roundMe(scaled[i]);
    
    // calc the wrapped real coordinates from the wrapped scaled coordinates
    
    matVecMul3(Hmat, scaled, thePos);

  }
  else{
    // calc the scaled coordinates.
    
    for(i=0; i<3; i++)
      scaled[i] = thePos[i]*HmatInv[i][i];
    
    // wrap the scaled coordinates
    
    for(i=0; i<3; i++)
      scaled[i] -= roundMe(scaled[i]);
    
    // calc the wrapped real coordinates from the wrapped scaled coordinates
    
    for(i=0; i<3; i++)
      thePos[i] = scaled[i]*Hmat[i][i];
  }
    
}


int SimInfo::getNDF(){
  int ndf_local, ndf;
  
  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;

#ifdef IS_MPI
  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
  ndf = ndf_local;
#endif

  ndf = ndf - 3;

  return ndf;
}

int SimInfo::getNDFraw() {
  int ndfRaw_local, ndfRaw;

  // Raw degrees of freedom that we have to set
  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
  
#ifdef IS_MPI
  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
  ndfRaw = ndfRaw_local;
#endif

  return ndfRaw;
}
 
void SimInfo::refreshSim(){

  simtype fInfo;
  int isError;
  int n_global;
  int* excl;
  
  fInfo.rrf = 0.0;
  fInfo.rt = 0.0;
  fInfo.dielect = 0.0;

  fInfo.rlist = rList;
  fInfo.rcut = rCut;

  if( useDipole ){
    fInfo.rrf = ecr;
    fInfo.rt = ecr - est;
    if( useReactionField )fInfo.dielect = dielectric;
  }

  fInfo.SIM_uses_PBC = usePBC;
  //fInfo.SIM_uses_LJ = 0;
  fInfo.SIM_uses_LJ = useLJ;
  fInfo.SIM_uses_sticky = useSticky;
  //fInfo.SIM_uses_sticky = 0;
  fInfo.SIM_uses_dipoles = useDipole;
  //fInfo.SIM_uses_dipoles = 0;
  //fInfo.SIM_uses_RF = useReactionField;
  fInfo.SIM_uses_RF = 0;
  fInfo.SIM_uses_GB = useGB;
  fInfo.SIM_uses_EAM = useEAM;

  excl = Exclude::getArray();

#ifdef IS_MPI
  n_global = mpiSim->getTotAtoms();
#else
  n_global = n_atoms;
#endif

  isError = 0;

  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
                  &nGlobalExcludes, globalExcludes, molMembershipArray, 
                  &isError );

  if( isError ){

    sprintf( painCave.errMsg,
             "There was an error setting the simulation information in fortran.\n" );
    painCave.isFatal = 1;
    simError();
  }

#ifdef IS_MPI
  sprintf( checkPointMsg,
           "succesfully sent the simulation information to fortran.\n");
  MPIcheckPoint();
#endif // is_mpi

  this->ndf = this->getNDF();
  this->ndfRaw = this->getNDFraw();

}

Revision:	597
Committed:	Mon Jul 14 21:28:54 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	10085 byte(s)
Log Message:	found a bug. Unit vectors were not being updated
#	User	Rev	Content
1	mmeineke	377	#include <cstdlib>
2			#include <cstring>
3	mmeineke	568	#include <cmath>
4	mmeineke	377
5	mmeineke	572	#include <iostream>
6			using namespace std;
7	mmeineke	377
8			#include "SimInfo.hpp"
9			#define __C
10			#include "fSimulation.h"
11			#include "simError.h"
12
13			#include "fortranWrappers.hpp"
14
15	gezelter	490	#ifdef IS_MPI
16			#include "mpiSimulation.hpp"
17			#endif
18
19	mmeineke	572	inline double roundMe( double x ){
20			return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21			}
22
23
24	mmeineke	377	SimInfo* currentInfo;
25
26			SimInfo::SimInfo(){
27			excludes = NULL;
28			n_constraints = 0;
29			n_oriented = 0;
30			n_dipoles = 0;
31	gezelter	458	ndf = 0;
32			ndfRaw = 0;
33	mmeineke	377	the_integrator = NULL;
34			setTemp = 0;
35			thermalTime = 0.0;
36	mmeineke	420	rCut = 0.0;
37	mmeineke	377
38			usePBC = 0;
39			useLJ = 0;
40			useSticky = 0;
41			useDipole = 0;
42			useReactionField = 0;
43			useGB = 0;
44			useEAM = 0;
45
46	gezelter	457	wrapMeSimInfo( this );
47			}
48	mmeineke	377
49	gezelter	457	void SimInfo::setBox(double newBox[3]) {
50	mmeineke	586
51	gezelter	588	int i, j;
52			double tempMat[3][3];
53	gezelter	463
54	gezelter	588	for(i=0; i<3; i++)
55			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56	gezelter	463
57	gezelter	588	tempMat[0][0] = newBox[0];
58			tempMat[1][1] = newBox[1];
59			tempMat[2][2] = newBox[2];
60	gezelter	463
61	mmeineke	586	setBoxM( tempMat );
62	mmeineke	568
63	gezelter	457	}
64	mmeineke	377
65	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
66	mmeineke	568
67	gezelter	588	int i, j, status;
68	mmeineke	568	double smallestBoxL, maxCutoff;
69	gezelter	588	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 ]
74			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
75	mmeineke	568
76	mmeineke	586
77	gezelter	588	for(i=0; i < 3; i++)
78			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
79
80	mmeineke	586	cerr
81			<< "setting Hmat ->\n"
82	gezelter	588	<< "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83			<< "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84			<< "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85	mmeineke	586
86	mmeineke	568	calcBoxL();
87	gezelter	588	calcHmatInv();
88	mmeineke	568
89	gezelter	588	for(i=0; i < 3; i++) {
90			for (j=0; j < 3; j++) {
91			FortranHmat[3*j + i] = Hmat[i][j];
92			FortranHmatInv[3*j + i] = HmatInv[i][j];
93			}
94			}
95	mmeineke	586
96	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
97	mmeineke	568
98			smallestBoxL = boxLx;
99			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",
107			maxCutoff );
108			painCave.isFatal = 0;
109			simError();
110
111			rList = maxCutoff;
112
113			sprintf( painCave.errMsg,
114			"New Box size is forcing cutoff radius down to %lf\n",
115			maxCutoff - 1.0 );
116			painCave.isFatal = 0;
117			simError();
118
119			rCut = rList - 1.0;
120
121			// list radius changed so we have to refresh the simulation structure.
122			refreshSim();
123			}
124
125			if (rCut > maxCutoff) {
126			sprintf( painCave.errMsg,
127			"New Box size is forcing cutoff radius down to %lf\n",
128			maxCutoff );
129			painCave.isFatal = 0;
130			simError();
131
132			status = 0;
133			LJ_new_rcut(&rCut, &status);
134			if (status != 0) {
135			sprintf( painCave.errMsg,
136			"Error in recomputing LJ shifts based on new rcut\n");
137			painCave.isFatal = 1;
138			simError();
139			}
140			}
141	mmeineke	377	}
142	gezelter	458
143	mmeineke	568
144	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
145	mmeineke	568
146	gezelter	588	int i, j;
147			for(i=0; i<3; i++)
148			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
149	mmeineke	568	}
150
151	gezelter	574
152			void SimInfo::scaleBox(double scale) {
153	gezelter	588	double theBox[3][3];
154			int i, j;
155	gezelter	574
156	mmeineke	586	cerr << "Scaling box by " << scale << "\n";
157
158	gezelter	588	for(i=0; i<3; i++)
159			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
160	gezelter	574
161			setBoxM(theBox);
162
163			}
164
165	gezelter	588	void SimInfo::calcHmatInv( void ) {
166	mmeineke	590
167			int i,j;
168	mmeineke	569	double smallDiag;
169			double tol;
170			double sanity[3][3];
171	mmeineke	568
172	gezelter	588	invertMat3( Hmat, HmatInv );
173	mmeineke	568
174	gezelter	588	// Check the inverse to make sure it is sane:
175	mmeineke	568
176	gezelter	588	matMul3( Hmat, HmatInv, sanity );
177
178			// check to see if Hmat is orthorhombic
179	mmeineke	568
180	gezelter	588	smallDiag = Hmat[0][0];
181			if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
182			if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
183			tol = smallDiag * 1E-6;
184	mmeineke	568
185	gezelter	588	orthoRhombic = 1;
186	mmeineke	568
187	gezelter	588	for (i = 0; i < 3; i++ ) {
188			for (j = 0 ; j < 3; j++) {
189			if (i != j) {
190			if (orthoRhombic) {
191			if (Hmat[i][j] >= tol) orthoRhombic = 0;
192			}
193			}
194	mmeineke	568	}
195			}
196	gezelter	588	}
197	mmeineke	569
198	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
199			int i, j, k;
200			double determinant;
201	mmeineke	569
202	gezelter	588	determinant = 0.0;
203
204			for(i = 0; i < 3; i++) {
205			j = (i+1)%3;
206			k = (i+2)%3;
207
208			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
209	mmeineke	569	}
210
211	gezelter	588	return determinant;
212			}
213	mmeineke	569
214	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215	mmeineke	569
216	gezelter	588	int i, j, k, l, m, n;
217			double determinant;
218	mmeineke	569
219	gezelter	588	determinant = matDet3( a );
220
221			if (determinant == 0.0) {
222			sprintf( painCave.errMsg,
223			"Can't invert a matrix with a zero determinant!\n");
224			painCave.isFatal = 1;
225			simError();
226			}
227
228			for (i=0; i < 3; i++) {
229			j = (i+1)%3;
230			k = (i+2)%3;
231			for(l = 0; l < 3; l++) {
232			m = (l+1)%3;
233			n = (l+2)%3;
234
235			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
236	mmeineke	569	}
237			}
238	mmeineke	568	}
239
240	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242
243			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
244			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
245			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
246
247			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
248			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
249			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
250
251			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
252			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
253			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
254
255			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256			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;
258			}
259
260			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261			double a0, a1, a2;
262
263			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
264
265			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;
267			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
268			}
269	mmeineke	597
270			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271			double temp[3][3];
272			int i, j;
273
274			for (i = 0; i < 3; i++) {
275			for (j = 0; j < 3; j++) {
276			temp[j][i] = in[i][j];
277			}
278			}
279			for (i = 0; i < 3; i++) {
280			for (j = 0; j < 3; j++) {
281			out[i][j] = temp[i][j];
282			}
283			}
284			}
285	gezelter	588
286	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
287
288			std::cerr
289			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292			}
293
294			void SimInfo::printMat9(double A[9] ){
295
296			std::cerr
297			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300			}
301
302	mmeineke	568	void SimInfo::calcBoxL( void ){
303
304			double dx, dy, dz, dsq;
305			int i;
306
307	gezelter	588	// boxVol = Determinant of Hmat
308	mmeineke	568
309	gezelter	588	boxVol = matDet3( Hmat );
310	mmeineke	568
311			// boxLx
312
313	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314	mmeineke	568	dsq = dxdx + dydy + dz*dz;
315			boxLx = sqrt( dsq );
316
317			// boxLy
318
319	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
320	mmeineke	568	dsq = dxdx + dydy + dz*dz;
321			boxLy = sqrt( dsq );
322
323			// boxLz
324
325	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
326	mmeineke	568	dsq = dxdx + dydy + dz*dz;
327			boxLz = sqrt( dsq );
328
329			}
330
331
332			void SimInfo::wrapVector( double thePos[3] ){
333
334			int i, j, k;
335			double scaled[3];
336
337	mmeineke	569	if( !orthoRhombic ){
338			// calc the scaled coordinates.
339	gezelter	588
340
341			matVecMul3(HmatInv, thePos, scaled);
342	mmeineke	569
343			for(i=0; i<3; i++)
344	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
345	mmeineke	569
346			// calc the wrapped real coordinates from the wrapped scaled coordinates
347
348	gezelter	588	matVecMul3(Hmat, scaled, thePos);
349
350	mmeineke	569	}
351			else{
352			// calc the scaled coordinates.
353
354			for(i=0; i<3; i++)
355	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
356	mmeineke	569
357			// wrap the scaled coordinates
358
359			for(i=0; i<3; i++)
360	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
361	mmeineke	569
362			// calc the wrapped real coordinates from the wrapped scaled coordinates
363
364			for(i=0; i<3; i++)
365	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
366	mmeineke	569	}
367
368	mmeineke	568	}
369
370
371	gezelter	458	int SimInfo::getNDF(){
372			int ndf_local, ndf;
373	gezelter	457
374	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
375
376			#ifdef IS_MPI
377			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378			#else
379			ndf = ndf_local;
380			#endif
381
382			ndf = ndf - 3;
383
384			return ndf;
385			}
386
387			int SimInfo::getNDFraw() {
388			int ndfRaw_local, ndfRaw;
389
390			// Raw degrees of freedom that we have to set
391			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
392
393			#ifdef IS_MPI
394			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395			#else
396			ndfRaw = ndfRaw_local;
397			#endif
398
399			return ndfRaw;
400			}
401
402	mmeineke	377	void SimInfo::refreshSim(){
403
404			simtype fInfo;
405			int isError;
406	gezelter	490	int n_global;
407	mmeineke	424	int* excl;
408	mmeineke	469
409			fInfo.rrf = 0.0;
410			fInfo.rt = 0.0;
411			fInfo.dielect = 0.0;
412	mmeineke	377
413			fInfo.rlist = rList;
414			fInfo.rcut = rCut;
415
416	mmeineke	469	if( useDipole ){
417			fInfo.rrf = ecr;
418			fInfo.rt = ecr - est;
419			if( useReactionField )fInfo.dielect = dielectric;
420			}
421
422	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
423	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
424	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
425	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
426			//fInfo.SIM_uses_sticky = 0;
427	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
428			//fInfo.SIM_uses_dipoles = 0;
429	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
430			fInfo.SIM_uses_RF = 0;
431	mmeineke	377	fInfo.SIM_uses_GB = useGB;
432			fInfo.SIM_uses_EAM = useEAM;
433
434	mmeineke	424	excl = Exclude::getArray();
435	mmeineke	377
436	gezelter	490	#ifdef IS_MPI
437			n_global = mpiSim->getTotAtoms();
438			#else
439			n_global = n_atoms;
440			#endif
441
442	mmeineke	377	isError = 0;
443
444	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
445	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
446			&isError );
447	mmeineke	377
448			if( isError ){
449
450			sprintf( painCave.errMsg,
451			"There was an error setting the simulation information in fortran.\n" );
452			painCave.isFatal = 1;
453			simError();
454			}
455
456			#ifdef IS_MPI
457			sprintf( checkPointMsg,
458			"succesfully sent the simulation information to fortran.\n");
459			MPIcheckPoint();
460			#endif // is_mpi
461	gezelter	458
462	gezelter	474	this->ndf = this->getNDF();
463			this->ndfRaw = this->getNDFraw();
464	gezelter	458
465	mmeineke	377	}
466