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;
  currentTime = 0.0;
  rCut = 0.0;
  ecr = 0.0;
  est = 0.0;
  oldEcr = 0.0;
  oldRcut = 0.0;

  haveOrigRcut = 0;
  haveOrigEcr = 0;
  boxIsInit = 0;
  
  
  usePBC = 0;
  useLJ = 0; 
  useSticky = 0;
  useDipole = 0;
  useReactionField = 0;
  useGB = 0;
  useEAM = 0;

  wrapMeSimInfo( this );
}

SimInfo::~SimInfo(){

  map<string, GenericData*>::iterator i;
  
  for(i = properties.begin(); i != properties.end(); i++)
    delete (*i).second;

  
}

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);

  
  if( !boxIsInit ) boxIsInit = 1;

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

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;
  boxL[0] = sqrt( dsq );
  maxCutoff = 0.5 * boxL[0];

  // boxLy
  
  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
  dsq = dx*dx + dy*dy + dz*dz;
  boxL[1] = sqrt( dsq );
  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];

  // boxLz
  
  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
  dsq = dx*dx + dy*dy + dz*dz;
  boxL[2] = sqrt( dsq );
  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];

}


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.dielect = 0.0;

  if( useDipole ){
    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();

}


void SimInfo::setRcut( double theRcut ){

  if( !haveOrigRcut ){
    haveOrigRcut = 1;
    origRcut = theRcut;
  }

  rCut = theRcut;
  checkCutOffs();
}

void SimInfo::setEcr( double theEcr ){

  if( !haveOrigEcr ){
    haveOrigEcr = 1;
    origEcr = theEcr;
  }

  ecr = theEcr;
  checkCutOffs();
}

void SimInfo::setEcr( double theEcr, double theEst ){

  est = theEst;
  setEcr( theEcr );
}


void SimInfo::checkCutOffs( void ){

  int cutChanged = 0;

  if( boxIsInit ){
    
    //we need to check cutOffs against the box
    
    if( maxCutoff > rCut ){
      if( rCut < origRcut ){
        rCut = origRcut;
        if (rCut > maxCutoff) rCut = maxCutoff;
        
        sprintf( painCave.errMsg,
                 "New Box size is setting the long range cutoff radius "
                 "to %lf\n",
                 rCut );
        painCave.isFatal = 0;
        simError();
      }
    }

    if( maxCutoff > ecr ){
      if( ecr < origEcr ){
        rCut = origEcr;
        if (ecr > maxCutoff) ecr = maxCutoff;
        
        sprintf( painCave.errMsg,
                 "New Box size is setting the electrostaticCutoffRadius "
                 "to %lf\n",
                 ecr );
        painCave.isFatal = 0;
        simError();
      }
    }


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

    if( ecr > maxCutoff){
      sprintf( painCave.errMsg,
               "New Box size is setting the electrostaticCutoffRadius "
               "to %lf\n",
               maxCutoff  );
      painCave.isFatal = 0;
      simError();      
      ecr = maxCutoff;
    }

    
  }
   

  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;

  // rlist is the 1.0 plus max( rcut, ecr )
  
  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;

  if( cutChanged ){
    
    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
  }

  oldEcr = ecr;
  oldRcut = rCut;
}

void SimInfo::addProperty(GenericData* prop){

  map<string, GenericData*>::iterator result;
  result = properties.find(prop->getID());
  
  //we can't simply use  properties[prop->getID()] = prop,
  //it will cause memory leak if we already contain a propery which has the same name of prop
  
  if(result != properties.end()){
    
    delete (*result).second;
    (*result).second = prop;
      
  }
  else{

    properties[prop->getID()] = prop;

  }
    
}

GenericData* SimInfo::getProperty(const string& propName){
 
  map<string, GenericData*>::iterator result;
  
  //string lowerCaseName = ();
  
  result = properties.find(propName);
  
  if(result != properties.end()) 
    return (*result).second;  
  else   
    return NULL;  
}

vector<GenericData*> SimInfo::getProperties(){

  vector<GenericData*> result;
  map<string, GenericData*>::iterator i;
  
  for(i = properties.begin(); i != properties.end(); i++)
    result.push_back((*i).second);
    
  return result;
}


Revision:	660
Committed:	Thu Jul 31 19:59:34 2003 UTC (20 years, 11 months ago) by tim
File size:	11978 byte(s)
Log Message:	add index range checking into ZConstraint
#	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	642	currentTime = 0.0;
37	mmeineke	420	rCut = 0.0;
38	mmeineke	618	ecr = 0.0;
39	mmeineke	619	est = 0.0;
40	mmeineke	626	oldEcr = 0.0;
41			oldRcut = 0.0;
42	mmeineke	377
43	mmeineke	626	haveOrigRcut = 0;
44			haveOrigEcr = 0;
45			boxIsInit = 0;
46
47
48
49	mmeineke	377	usePBC = 0;
50			useLJ = 0;
51			useSticky = 0;
52			useDipole = 0;
53			useReactionField = 0;
54			useGB = 0;
55			useEAM = 0;
56
57	gezelter	457	wrapMeSimInfo( this );
58			}
59	mmeineke	377
60	tim	660	SimInfo::~SimInfo(){
61
62			map<string, GenericData*>::iterator i;
63
64			for(i = properties.begin(); i != properties.end(); i++)
65			delete (*i).second;
66
67
68			}
69
70	gezelter	457	void SimInfo::setBox(double newBox[3]) {
71	mmeineke	586
72	gezelter	588	int i, j;
73			double tempMat[3][3];
74	gezelter	463
75	gezelter	588	for(i=0; i<3; i++)
76			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
77	gezelter	463
78	gezelter	588	tempMat[0][0] = newBox[0];
79			tempMat[1][1] = newBox[1];
80			tempMat[2][2] = newBox[2];
81	gezelter	463
82	mmeineke	586	setBoxM( tempMat );
83	mmeineke	568
84	gezelter	457	}
85	mmeineke	377
86	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
87	mmeineke	568
88	gezelter	588	int i, j, status;
89	mmeineke	568	double smallestBoxL, maxCutoff;
90	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
91			// ordering in the array is as follows:
92			// [ 0 3 6 ]
93			// [ 1 4 7 ]
94			// [ 2 5 8 ]
95			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
96	mmeineke	568
97	mmeineke	626
98			if( !boxIsInit ) boxIsInit = 1;
99	mmeineke	586
100	gezelter	588	for(i=0; i < 3; i++)
101			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
102
103	mmeineke	568	calcBoxL();
104	gezelter	588	calcHmatInv();
105	mmeineke	568
106	gezelter	588	for(i=0; i < 3; i++) {
107			for (j=0; j < 3; j++) {
108			FortranHmat[3*j + i] = Hmat[i][j];
109			FortranHmatInv[3*j + i] = HmatInv[i][j];
110			}
111			}
112	mmeineke	586
113	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
114	mmeineke	568
115	mmeineke	377	}
116	gezelter	458
117	mmeineke	568
118	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
119	mmeineke	568
120	gezelter	588	int i, j;
121			for(i=0; i<3; i++)
122			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
123	mmeineke	568	}
124
125	gezelter	574
126			void SimInfo::scaleBox(double scale) {
127	gezelter	588	double theBox[3][3];
128			int i, j;
129	gezelter	574
130	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
131	mmeineke	586
132	gezelter	588	for(i=0; i<3; i++)
133			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
134	gezelter	574
135			setBoxM(theBox);
136
137			}
138
139	gezelter	588	void SimInfo::calcHmatInv( void ) {
140	mmeineke	590
141			int i,j;
142	mmeineke	569	double smallDiag;
143			double tol;
144			double sanity[3][3];
145	mmeineke	568
146	gezelter	588	invertMat3( Hmat, HmatInv );
147	mmeineke	568
148	gezelter	588	// Check the inverse to make sure it is sane:
149	mmeineke	568
150	gezelter	588	matMul3( Hmat, HmatInv, sanity );
151
152			// check to see if Hmat is orthorhombic
153	mmeineke	568
154	gezelter	588	smallDiag = Hmat[0][0];
155			if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
156			if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
157			tol = smallDiag * 1E-6;
158	mmeineke	568
159	gezelter	588	orthoRhombic = 1;
160	mmeineke	568
161	gezelter	588	for (i = 0; i < 3; i++ ) {
162			for (j = 0 ; j < 3; j++) {
163			if (i != j) {
164			if (orthoRhombic) {
165			if (Hmat[i][j] >= tol) orthoRhombic = 0;
166			}
167			}
168	mmeineke	568	}
169			}
170	gezelter	588	}
171	mmeineke	569
172	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
173			int i, j, k;
174			double determinant;
175	mmeineke	569
176	gezelter	588	determinant = 0.0;
177
178			for(i = 0; i < 3; i++) {
179			j = (i+1)%3;
180			k = (i+2)%3;
181
182			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
183	mmeineke	569	}
184
185	gezelter	588	return determinant;
186			}
187	mmeineke	569
188	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
189	mmeineke	569
190	gezelter	588	int i, j, k, l, m, n;
191			double determinant;
192	mmeineke	569
193	gezelter	588	determinant = matDet3( a );
194
195			if (determinant == 0.0) {
196			sprintf( painCave.errMsg,
197			"Can't invert a matrix with a zero determinant!\n");
198			painCave.isFatal = 1;
199			simError();
200			}
201
202			for (i=0; i < 3; i++) {
203			j = (i+1)%3;
204			k = (i+2)%3;
205			for(l = 0; l < 3; l++) {
206			m = (l+1)%3;
207			n = (l+2)%3;
208
209			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
210	mmeineke	569	}
211			}
212	mmeineke	568	}
213
214	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
215			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
216
217			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
218			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
219			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
220
221			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
222			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
223			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
224
225			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
226			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
227			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
228
229			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
230			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
231			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
232			}
233
234			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
235			double a0, a1, a2;
236
237			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
238
239			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
240			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
241			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
242			}
243	mmeineke	597
244			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
245			double temp[3][3];
246			int i, j;
247
248			for (i = 0; i < 3; i++) {
249			for (j = 0; j < 3; j++) {
250			temp[j][i] = in[i][j];
251			}
252			}
253			for (i = 0; i < 3; i++) {
254			for (j = 0; j < 3; j++) {
255			out[i][j] = temp[i][j];
256			}
257			}
258			}
259	gezelter	588
260	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
261
262			std::cerr
263			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
264			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
265			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
266			}
267
268			void SimInfo::printMat9(double A[9] ){
269
270			std::cerr
271			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
272			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
273			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
274			}
275
276	mmeineke	568	void SimInfo::calcBoxL( void ){
277
278			double dx, dy, dz, dsq;
279			int i;
280
281	gezelter	588	// boxVol = Determinant of Hmat
282	mmeineke	568
283	gezelter	588	boxVol = matDet3( Hmat );
284	mmeineke	568
285			// boxLx
286
287	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
288	mmeineke	568	dsq = dxdx + dydy + dz*dz;
289	gezelter	621	boxL[0] = sqrt( dsq );
290	mmeineke	626	maxCutoff = 0.5 * boxL[0];
291	mmeineke	568
292			// boxLy
293
294	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
295	mmeineke	568	dsq = dxdx + dydy + dz*dz;
296	gezelter	621	boxL[1] = sqrt( dsq );
297	mmeineke	626	if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
298	mmeineke	568
299			// boxLz
300
301	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
302	mmeineke	568	dsq = dxdx + dydy + dz*dz;
303	gezelter	621	boxL[2] = sqrt( dsq );
304	mmeineke	626	if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
305
306	mmeineke	568	}
307
308
309			void SimInfo::wrapVector( double thePos[3] ){
310
311			int i, j, k;
312			double scaled[3];
313
314	mmeineke	569	if( !orthoRhombic ){
315			// calc the scaled coordinates.
316	gezelter	588
317
318			matVecMul3(HmatInv, thePos, scaled);
319	mmeineke	569
320			for(i=0; i<3; i++)
321	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
322	mmeineke	569
323			// calc the wrapped real coordinates from the wrapped scaled coordinates
324
325	gezelter	588	matVecMul3(Hmat, scaled, thePos);
326
327	mmeineke	569	}
328			else{
329			// calc the scaled coordinates.
330
331			for(i=0; i<3; i++)
332	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
333	mmeineke	569
334			// wrap the scaled coordinates
335
336			for(i=0; i<3; i++)
337	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
338	mmeineke	569
339			// calc the wrapped real coordinates from the wrapped scaled coordinates
340
341			for(i=0; i<3; i++)
342	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
343	mmeineke	569	}
344
345	mmeineke	568	}
346
347
348	gezelter	458	int SimInfo::getNDF(){
349			int ndf_local, ndf;
350	gezelter	457
351	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
352
353			#ifdef IS_MPI
354			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355			#else
356			ndf = ndf_local;
357			#endif
358
359			ndf = ndf - 3;
360
361			return ndf;
362			}
363
364			int SimInfo::getNDFraw() {
365			int ndfRaw_local, ndfRaw;
366
367			// Raw degrees of freedom that we have to set
368			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
369
370			#ifdef IS_MPI
371			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
372			#else
373			ndfRaw = ndfRaw_local;
374			#endif
375
376			return ndfRaw;
377			}
378
379	mmeineke	377	void SimInfo::refreshSim(){
380
381			simtype fInfo;
382			int isError;
383	gezelter	490	int n_global;
384	mmeineke	424	int* excl;
385	mmeineke	626
386	mmeineke	469	fInfo.dielect = 0.0;
387	mmeineke	377
388	mmeineke	469	if( useDipole ){
389			if( useReactionField )fInfo.dielect = dielectric;
390			}
391
392	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
393	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
394	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
395	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
396			//fInfo.SIM_uses_sticky = 0;
397	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
398			//fInfo.SIM_uses_dipoles = 0;
399	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
400			fInfo.SIM_uses_RF = 0;
401	mmeineke	377	fInfo.SIM_uses_GB = useGB;
402			fInfo.SIM_uses_EAM = useEAM;
403
404	mmeineke	424	excl = Exclude::getArray();
405	mmeineke	377
406	gezelter	490	#ifdef IS_MPI
407			n_global = mpiSim->getTotAtoms();
408			#else
409			n_global = n_atoms;
410			#endif
411
412	mmeineke	377	isError = 0;
413
414	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
415	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
416			&isError );
417	mmeineke	377
418			if( isError ){
419
420			sprintf( painCave.errMsg,
421			"There was an error setting the simulation information in fortran.\n" );
422			painCave.isFatal = 1;
423			simError();
424			}
425
426			#ifdef IS_MPI
427			sprintf( checkPointMsg,
428			"succesfully sent the simulation information to fortran.\n");
429			MPIcheckPoint();
430			#endif // is_mpi
431	gezelter	458
432	gezelter	474	this->ndf = this->getNDF();
433			this->ndfRaw = this->getNDFraw();
434	gezelter	458
435	mmeineke	377	}
436
437	mmeineke	626
438			void SimInfo::setRcut( double theRcut ){
439
440			if( !haveOrigRcut ){
441			haveOrigRcut = 1;
442			origRcut = theRcut;
443			}
444
445			rCut = theRcut;
446			checkCutOffs();
447			}
448
449			void SimInfo::setEcr( double theEcr ){
450
451			if( !haveOrigEcr ){
452			haveOrigEcr = 1;
453			origEcr = theEcr;
454			}
455
456			ecr = theEcr;
457			checkCutOffs();
458			}
459
460			void SimInfo::setEcr( double theEcr, double theEst ){
461
462			est = theEst;
463			setEcr( theEcr );
464			}
465
466
467			void SimInfo::checkCutOffs( void ){
468
469			int cutChanged = 0;
470
471			if( boxIsInit ){
472
473			//we need to check cutOffs against the box
474
475			if( maxCutoff > rCut ){
476			if( rCut < origRcut ){
477			rCut = origRcut;
478			if (rCut > maxCutoff) rCut = maxCutoff;
479
480			sprintf( painCave.errMsg,
481			"New Box size is setting the long range cutoff radius "
482			"to %lf\n",
483			rCut );
484			painCave.isFatal = 0;
485			simError();
486			}
487			}
488
489			if( maxCutoff > ecr ){
490			if( ecr < origEcr ){
491			rCut = origEcr;
492			if (ecr > maxCutoff) ecr = maxCutoff;
493
494			sprintf( painCave.errMsg,
495			"New Box size is setting the electrostaticCutoffRadius "
496			"to %lf\n",
497			ecr );
498			painCave.isFatal = 0;
499			simError();
500			}
501			}
502
503
504			if (rCut > maxCutoff) {
505			sprintf( painCave.errMsg,
506			"New Box size is setting the long range cutoff radius "
507			"to %lf\n",
508			maxCutoff );
509			painCave.isFatal = 0;
510			simError();
511			rCut = maxCutoff;
512			}
513
514			if( ecr > maxCutoff){
515			sprintf( painCave.errMsg,
516			"New Box size is setting the electrostaticCutoffRadius "
517			"to %lf\n",
518			maxCutoff );
519			painCave.isFatal = 0;
520			simError();
521			ecr = maxCutoff;
522			}
523
524
525			}
526
527
528			if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
529
530			// rlist is the 1.0 plus max( rcut, ecr )
531
532			( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
533
534			if( cutChanged ){
535
536			notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537			}
538
539			oldEcr = ecr;
540			oldRcut = rCut;
541			}
542	tim	658
543			void SimInfo::addProperty(GenericData* prop){
544
545			map<string, GenericData*>::iterator result;
546			result = properties.find(prop->getID());
547
548			//we can't simply use properties[prop->getID()] = prop,
549			//it will cause memory leak if we already contain a propery which has the same name of prop
550
551			if(result != properties.end()){
552
553			delete (*result).second;
554			(*result).second = prop;
555
556			}
557			else{
558
559			properties[prop->getID()] = prop;
560
561			}
562
563			}
564
565			GenericData* SimInfo::getProperty(const string& propName){
566
567			map<string, GenericData*>::iterator result;
568
569			//string lowerCaseName = ();
570
571			result = properties.find(propName);
572
573			if(result != properties.end())
574			return (*result).second;
575			else
576			return NULL;
577			}
578
579			vector<GenericData*> SimInfo::getProperties(){
580
581			vector<GenericData*> result;
582			map<string, GenericData*>::iterator i;
583
584			for(i = properties.begin(); i != properties.end(); i++)
585			result.push_back((*i).second);
586
587			return result;
588			}
589
590