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;
  nZconstraints = 0;
  n_oriented = 0;
  n_dipoles = 0;
  ndf = 0;
  ndfRaw = 0;
  nZconstraints = 0;
  the_integrator = NULL;
  setTemp = 0;
  thermalTime = 0.0;
  currentTime = 0.0;
  rCut = 0.0;
  origRcut = -1.0;
  ecr = 0.0;
  origEcr = -1.0;
  est = 0.0;
  oldEcr = 0.0;
  oldRcut = 0.0;

  haveOrigRcut = 0;
  haveOrigEcr = 0;
  boxIsInit = 0;
  
  resetTime = 1e99;
  

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

  myConfiguration = new SimState();

  wrapMeSimInfo( this );
}


SimInfo::~SimInfo(){

  delete myConfiguration;

  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::crossProduct3(double a[3],double b[3], double out[3]){

      out[0] = a[1] * b[2] - a[2] * b[1];
      out[1] = a[2] * b[0] - a[0] * b[2] ;
      out[2] = a[0] * b[1] - a[1] * b[0];
      
}

double SimInfo::dotProduct3(double a[3], double b[3]){
  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
}

double SimInfo::length3(double a[3]){
  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
}

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];

  //calculate the max cutoff
  maxCutoff =  calcMaxCutOff(); 
  
  checkCutOffs();

}


double SimInfo::calcMaxCutOff(){

  double ri[3], rj[3], rk[3];
  double rij[3], rjk[3], rki[3];
  double minDist;

  ri[0] = Hmat[0][0];
  ri[1] = Hmat[1][0];
  ri[2] = Hmat[2][0];

  rj[0] = Hmat[0][1];
  rj[1] = Hmat[1][1];
  rj[2] = Hmat[2][1];

  rk[0] = Hmat[0][2];
  rk[1] = Hmat[1][2];
  rk[2] = Hmat[2][2];
  
  crossProduct3(ri,rj, rij);
  distXY = dotProduct3(rk,rij) / length3(rij);

  crossProduct3(rj,rk, rjk);
  distYZ = dotProduct3(ri,rjk) / length3(rjk);

  crossProduct3(rk,ri, rki);
  distZX = dotProduct3(rj,rki) / length3(rki);

  minDist = min(min(distXY, distYZ), distZX);
  return minDist/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 - nZconstraints;

  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;
}

int SimInfo::getNDFtranslational() {
  int ndfTrans_local, ndfTrans;

  ndfTrans_local = 3 * n_atoms - n_constraints;

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

  ndfTrans = ndfTrans - 3 - nZconstraints;

  return ndfTrans;
}

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();
  this->ndfTrans = this->getNDFtranslational();
}


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

    //detect the change of rCut
    if(( maxCutoff > rCut )&&(usePBC)){
      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 at time %lf\n",
                    rCut, currentTime );
          painCave.isFatal = 0;
          simError();
      }
    }
    else if ((rCut > maxCutoff)&&(usePBC)) {
      sprintf( painCave.errMsg,
               "New Box size is setting the long range cutoff radius "
               "to %lf at time %lf\n",
               maxCutoff, currentTime );
      painCave.isFatal = 0;
      simError();
      rCut = maxCutoff;
    }


    //detect the change of ecr
    if( maxCutoff > ecr ){
      if( ecr < origEcr ){
        ecr = origEcr;
        if (ecr > maxCutoff) ecr = maxCutoff;
  
          sprintf( painCave.errMsg,
                    "New Box size is setting the electrostaticCutoffRadius "
                    "to %lf at time %lf\n",
                    ecr, currentTime );
            painCave.isFatal = 0;
            simError();
      }
    }
    else if( ecr > maxCutoff){
      sprintf( painCave.errMsg,
               "New Box size is setting the electrostaticCutoffRadius "
               "to %lf at time %lf\n",
               maxCutoff, currentTime  );
      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;
    
  } else {
    // initialize this stuff before using it, OK?
    sprintf( painCave.errMsg,
             "Trying to check cutoffs without a box. Be smarter.\n" );
    painCave.isFatal = 1;
    simError();      
  }
  
}

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;
}

double SimInfo::matTrace3(double m[3][3]){
  double trace;
  trace = m[0][0] + m[1][1] + m[2][2];

  return trace;
}
Revision:	781
Committed:	Mon Sep 22 23:07:57 2003 UTC (20 years, 9 months ago) by tim
File size:	14402 byte(s)
Log Message:	fix bug in calculating maxCutoff
#	Content
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;
28	n_constraints = 0;
29	nZconstraints = 0;
30	n_oriented = 0;
31	n_dipoles = 0;
32	ndf = 0;
33	ndfRaw = 0;
34	nZconstraints = 0;
35	the_integrator = NULL;
36	setTemp = 0;
37	thermalTime = 0.0;
38	currentTime = 0.0;
39	rCut = 0.0;
40	origRcut = -1.0;
41	ecr = 0.0;
42	origEcr = -1.0;
43	est = 0.0;
44	oldEcr = 0.0;
45	oldRcut = 0.0;
46
47	haveOrigRcut = 0;
48	haveOrigEcr = 0;
49	boxIsInit = 0;
50
51	resetTime = 1e99;
52
53
54	usePBC = 0;
55	useLJ = 0;
56	useSticky = 0;
57	useDipole = 0;
58	useReactionField = 0;
59	useGB = 0;
60	useEAM = 0;
61
62	myConfiguration = new SimState();
63
64	wrapMeSimInfo( this );
65	}
66
67
68	SimInfo::~SimInfo(){
69
70	delete myConfiguration;
71
72	map<string, GenericData*>::iterator i;
73
74	for(i = properties.begin(); i != properties.end(); i++)
75	delete (*i).second;
76
77	}
78
79	void SimInfo::setBox(double newBox[3]) {
80
81	int i, j;
82	double tempMat[3][3];
83
84	for(i=0; i<3; i++)
85	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
86
87	tempMat[0][0] = newBox[0];
88	tempMat[1][1] = newBox[1];
89	tempMat[2][2] = newBox[2];
90
91	setBoxM( tempMat );
92
93	}
94
95	void SimInfo::setBoxM( double theBox[3][3] ){
96
97	int i, j, status;
98	double smallestBoxL, maxCutoff;
99	double FortranHmat[9]; // to preserve compatibility with Fortran the
100	// ordering in the array is as follows:
101	// [ 0 3 6 ]
102	// [ 1 4 7 ]
103	// [ 2 5 8 ]
104	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
105
106
107	if( !boxIsInit ) boxIsInit = 1;
108
109	for(i=0; i < 3; i++)
110	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
111
112	calcBoxL();
113	calcHmatInv();
114
115	for(i=0; i < 3; i++) {
116	for (j=0; j < 3; j++) {
117	FortranHmat[3*j + i] = Hmat[i][j];
118	FortranHmatInv[3*j + i] = HmatInv[i][j];
119	}
120	}
121
122	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123
124	}
125
126
127	void SimInfo::getBoxM (double theBox[3][3]) {
128
129	int i, j;
130	for(i=0; i<3; i++)
131	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
132	}
133
134
135	void SimInfo::scaleBox(double scale) {
136	double theBox[3][3];
137	int i, j;
138
139	// cerr << "Scaling box by " << scale << "\n";
140
141	for(i=0; i<3; i++)
142	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
143
144	setBoxM(theBox);
145
146	}
147
148	void SimInfo::calcHmatInv( void ) {
149
150	int i,j;
151	double smallDiag;
152	double tol;
153	double sanity[3][3];
154
155	invertMat3( Hmat, HmatInv );
156
157	// Check the inverse to make sure it is sane:
158
159	matMul3( Hmat, HmatInv, sanity );
160
161	// check to see if Hmat is orthorhombic
162
163	smallDiag = Hmat[0][0];
164	if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
165	if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
166	tol = smallDiag * 1E-6;
167
168	orthoRhombic = 1;
169
170	for (i = 0; i < 3; i++ ) {
171	for (j = 0 ; j < 3; j++) {
172	if (i != j) {
173	if (orthoRhombic) {
174	if (Hmat[i][j] >= tol) orthoRhombic = 0;
175	}
176	}
177	}
178	}
179	}
180
181	double SimInfo::matDet3(double a[3][3]) {
182	int i, j, k;
183	double determinant;
184
185	determinant = 0.0;
186
187	for(i = 0; i < 3; i++) {
188	j = (i+1)%3;
189	k = (i+2)%3;
190
191	determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
192	}
193
194	return determinant;
195	}
196
197	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
198
199	int i, j, k, l, m, n;
200	double determinant;
201
202	determinant = matDet3( a );
203
204	if (determinant == 0.0) {
205	sprintf( painCave.errMsg,
206	"Can't invert a matrix with a zero determinant!\n");
207	painCave.isFatal = 1;
208	simError();
209	}
210
211	for (i=0; i < 3; i++) {
212	j = (i+1)%3;
213	k = (i+2)%3;
214	for(l = 0; l < 3; l++) {
215	m = (l+1)%3;
216	n = (l+2)%3;
217
218	b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
219	}
220	}
221	}
222
223	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
224	double r00, r01, r02, r10, r11, r12, r20, r21, r22;
225
226	r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
227	r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
228	r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
229
230	r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
231	r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
232	r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
233
234	r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
235	r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
236	r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
237
238	c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
239	c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
240	c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
241	}
242
243	void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
244	double a0, a1, a2;
245
246	a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
247
248	outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
249	outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
250	outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
251	}
252
253	void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
254	double temp[3][3];
255	int i, j;
256
257	for (i = 0; i < 3; i++) {
258	for (j = 0; j < 3; j++) {
259	temp[j][i] = in[i][j];
260	}
261	}
262	for (i = 0; i < 3; i++) {
263	for (j = 0; j < 3; j++) {
264	out[i][j] = temp[i][j];
265	}
266	}
267	}
268
269	void SimInfo::printMat3(double A[3][3] ){
270
271	std::cerr
272	<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
273	<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
274	<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
275	}
276
277	void SimInfo::printMat9(double A[9] ){
278
279	std::cerr
280	<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
281	<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
282	<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
283	}
284
285
286	void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
287
288	out[0] = a[1] * b[2] - a[2] * b[1];
289	out[1] = a[2] * b[0] - a[0] * b[2] ;
290	out[2] = a[0] * b[1] - a[1] * b[0];
291
292	}
293
294	double SimInfo::dotProduct3(double a[3], double b[3]){
295	return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
296	}
297
298	double SimInfo::length3(double a[3]){
299	return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
300	}
301
302	void SimInfo::calcBoxL( void ){
303
304	double dx, dy, dz, dsq;
305	int i;
306
307	// boxVol = Determinant of Hmat
308
309	boxVol = matDet3( Hmat );
310
311	// boxLx
312
313	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314	dsq = dxdx + dydy + dz*dz;
315	boxL[0] = sqrt( dsq );
316	//maxCutoff = 0.5 * boxL[0];
317
318	// boxLy
319
320	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321	dsq = dxdx + dydy + dz*dz;
322	boxL[1] = sqrt( dsq );
323	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
324
325
326	// boxLz
327
328	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
329	dsq = dxdx + dydy + dz*dz;
330	boxL[2] = sqrt( dsq );
331	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
332
333	//calculate the max cutoff
334	maxCutoff = calcMaxCutOff();
335
336	checkCutOffs();
337
338	}
339
340
341	double SimInfo::calcMaxCutOff(){
342
343	double ri[3], rj[3], rk[3];
344	double rij[3], rjk[3], rki[3];
345	double minDist;
346
347	ri[0] = Hmat[0][0];
348	ri[1] = Hmat[1][0];
349	ri[2] = Hmat[2][0];
350
351	rj[0] = Hmat[0][1];
352	rj[1] = Hmat[1][1];
353	rj[2] = Hmat[2][1];
354
355	rk[0] = Hmat[0][2];
356	rk[1] = Hmat[1][2];
357	rk[2] = Hmat[2][2];
358
359	crossProduct3(ri,rj, rij);
360	distXY = dotProduct3(rk,rij) / length3(rij);
361
362	crossProduct3(rj,rk, rjk);
363	distYZ = dotProduct3(ri,rjk) / length3(rjk);
364
365	crossProduct3(rk,ri, rki);
366	distZX = dotProduct3(rj,rki) / length3(rki);
367
368	minDist = min(min(distXY, distYZ), distZX);
369	return minDist/2;
370
371	}
372
373	void SimInfo::wrapVector( double thePos[3] ){
374
375	int i, j, k;
376	double scaled[3];
377
378	if( !orthoRhombic ){
379	// calc the scaled coordinates.
380
381
382	matVecMul3(HmatInv, thePos, scaled);
383
384	for(i=0; i<3; i++)
385	scaled[i] -= roundMe(scaled[i]);
386
387	// calc the wrapped real coordinates from the wrapped scaled coordinates
388
389	matVecMul3(Hmat, scaled, thePos);
390
391	}
392	else{
393	// calc the scaled coordinates.
394
395	for(i=0; i<3; i++)
396	scaled[i] = thePos[i]*HmatInv[i][i];
397
398	// wrap the scaled coordinates
399
400	for(i=0; i<3; i++)
401	scaled[i] -= roundMe(scaled[i]);
402
403	// calc the wrapped real coordinates from the wrapped scaled coordinates
404
405	for(i=0; i<3; i++)
406	thePos[i] = scaled[i]*Hmat[i][i];
407	}
408
409	}
410
411
412	int SimInfo::getNDF(){
413	int ndf_local, ndf;
414
415	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
416
417	#ifdef IS_MPI
418	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
419	#else
420	ndf = ndf_local;
421	#endif
422
423	ndf = ndf - 3 - nZconstraints;
424
425	return ndf;
426	}
427
428	int SimInfo::getNDFraw() {
429	int ndfRaw_local, ndfRaw;
430
431	// Raw degrees of freedom that we have to set
432	ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
433
434	#ifdef IS_MPI
435	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
436	#else
437	ndfRaw = ndfRaw_local;
438	#endif
439
440	return ndfRaw;
441	}
442
443	int SimInfo::getNDFtranslational() {
444	int ndfTrans_local, ndfTrans;
445
446	ndfTrans_local = 3 * n_atoms - n_constraints;
447
448	#ifdef IS_MPI
449	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
450	#else
451	ndfTrans = ndfTrans_local;
452	#endif
453
454	ndfTrans = ndfTrans - 3 - nZconstraints;
455
456	return ndfTrans;
457	}
458
459	void SimInfo::refreshSim(){
460
461	simtype fInfo;
462	int isError;
463	int n_global;
464	int* excl;
465
466	fInfo.dielect = 0.0;
467
468	if( useDipole ){
469	if( useReactionField )fInfo.dielect = dielectric;
470	}
471
472	fInfo.SIM_uses_PBC = usePBC;
473	//fInfo.SIM_uses_LJ = 0;
474	fInfo.SIM_uses_LJ = useLJ;
475	fInfo.SIM_uses_sticky = useSticky;
476	//fInfo.SIM_uses_sticky = 0;
477	fInfo.SIM_uses_dipoles = useDipole;
478	//fInfo.SIM_uses_dipoles = 0;
479	//fInfo.SIM_uses_RF = useReactionField;
480	fInfo.SIM_uses_RF = 0;
481	fInfo.SIM_uses_GB = useGB;
482	fInfo.SIM_uses_EAM = useEAM;
483
484	excl = Exclude::getArray();
485
486	#ifdef IS_MPI
487	n_global = mpiSim->getTotAtoms();
488	#else
489	n_global = n_atoms;
490	#endif
491
492	isError = 0;
493
494	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
495	&nGlobalExcludes, globalExcludes, molMembershipArray,
496	&isError );
497
498	if( isError ){
499
500	sprintf( painCave.errMsg,
501	"There was an error setting the simulation information in fortran.\n" );
502	painCave.isFatal = 1;
503	simError();
504	}
505
506	#ifdef IS_MPI
507	sprintf( checkPointMsg,
508	"succesfully sent the simulation information to fortran.\n");
509	MPIcheckPoint();
510	#endif // is_mpi
511
512	this->ndf = this->getNDF();
513	this->ndfRaw = this->getNDFraw();
514	this->ndfTrans = this->getNDFtranslational();
515	}
516
517
518	void SimInfo::setRcut( double theRcut ){
519
520	if( !haveOrigRcut ){
521	haveOrigRcut = 1;
522	origRcut = theRcut;
523	}
524
525	rCut = theRcut;
526	checkCutOffs();
527	}
528
529	void SimInfo::setEcr( double theEcr ){
530
531	if( !haveOrigEcr ){
532	haveOrigEcr = 1;
533	origEcr = theEcr;
534	}
535
536	ecr = theEcr;
537	checkCutOffs();
538	}
539
540	void SimInfo::setEcr( double theEcr, double theEst ){
541
542	est = theEst;
543	setEcr( theEcr );
544	}
545
546
547	void SimInfo::checkCutOffs( void ){
548
549	int cutChanged = 0;
550
551	if( boxIsInit ){
552
553	//we need to check cutOffs against the box
554
555	//detect the change of rCut
556	if(( maxCutoff > rCut )&&(usePBC)){
557	if( rCut < origRcut ){
558	rCut = origRcut;
559
560	if (rCut > maxCutoff)
561	rCut = maxCutoff;
562
563	sprintf( painCave.errMsg,
564	"New Box size is setting the long range cutoff radius "
565	"to %lf at time %lf\n",
566	rCut, currentTime );
567	painCave.isFatal = 0;
568	simError();
569	}
570	}
571	else if ((rCut > maxCutoff)&&(usePBC)) {
572	sprintf( painCave.errMsg,
573	"New Box size is setting the long range cutoff radius "
574	"to %lf at time %lf\n",
575	maxCutoff, currentTime );
576	painCave.isFatal = 0;
577	simError();
578	rCut = maxCutoff;
579	}
580
581
582	//detect the change of ecr
583	if( maxCutoff > ecr ){
584	if( ecr < origEcr ){
585	ecr = origEcr;
586	if (ecr > maxCutoff) ecr = maxCutoff;
587
588	sprintf( painCave.errMsg,
589	"New Box size is setting the electrostaticCutoffRadius "
590	"to %lf at time %lf\n",
591	ecr, currentTime );
592	painCave.isFatal = 0;
593	simError();
594	}
595	}
596	else if( ecr > maxCutoff){
597	sprintf( painCave.errMsg,
598	"New Box size is setting the electrostaticCutoffRadius "
599	"to %lf at time %lf\n",
600	maxCutoff, currentTime );
601	painCave.isFatal = 0;
602	simError();
603	ecr = maxCutoff;
604	}
605
606	if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
607
608	// rlist is the 1.0 plus max( rcut, ecr )
609
610	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
611
612	if( cutChanged ){
613
614	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
615	}
616
617	oldEcr = ecr;
618	oldRcut = rCut;
619
620	} else {
621	// initialize this stuff before using it, OK?
622	sprintf( painCave.errMsg,
623	"Trying to check cutoffs without a box. Be smarter.\n" );
624	painCave.isFatal = 1;
625	simError();
626	}
627
628	}
629
630	void SimInfo::addProperty(GenericData* prop){
631
632	map<string, GenericData*>::iterator result;
633	result = properties.find(prop->getID());
634
635	//we can't simply use properties[prop->getID()] = prop,
636	//it will cause memory leak if we already contain a propery which has the same name of prop
637
638	if(result != properties.end()){
639
640	delete (*result).second;
641	(*result).second = prop;
642
643	}
644	else{
645
646	properties[prop->getID()] = prop;
647
648	}
649
650	}
651
652	GenericData* SimInfo::getProperty(const string& propName){
653
654	map<string, GenericData*>::iterator result;
655
656	//string lowerCaseName = ();
657
658	result = properties.find(propName);
659
660	if(result != properties.end())
661	return (*result).second;
662	else
663	return NULL;
664	}
665
666	vector<GenericData*> SimInfo::getProperties(){
667
668	vector<GenericData*> result;
669	map<string, GenericData*>::iterator i;
670
671	for(i = properties.begin(); i != properties.end(); i++)
672	result.push_back((*i).second);
673
674	return result;
675	}
676
677	double SimInfo::matTrace3(double m[3][3]){
678	double trace;
679	trace = m[0][0] + m[1][1] + m[2][2];
680
681	return trace;
682	}