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;
  nZconstraints = 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;

  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::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];
  
  checkCutOffs();

}


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;
}
 
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 )&&(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\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)&&(usePBC)) {
      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:	674
Committed:	Mon Aug 11 18:29:46 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	12127 byte(s)
Log Message:	changed the number of degrees of freedom to account for zConstreints
#	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	674	nZconstraints = 0;
34	mmeineke	377	the_integrator = NULL;
35			setTemp = 0;
36			thermalTime = 0.0;
37	mmeineke	642	currentTime = 0.0;
38	mmeineke	420	rCut = 0.0;
39	mmeineke	618	ecr = 0.0;
40	mmeineke	619	est = 0.0;
41	mmeineke	626	oldEcr = 0.0;
42			oldRcut = 0.0;
43	mmeineke	377
44	mmeineke	626	haveOrigRcut = 0;
45			haveOrigEcr = 0;
46			boxIsInit = 0;
47
48
49
50	mmeineke	377	usePBC = 0;
51			useLJ = 0;
52			useSticky = 0;
53			useDipole = 0;
54			useReactionField = 0;
55			useGB = 0;
56			useEAM = 0;
57
58	mmeineke	670	myConfiguration = new SimState();
59
60	gezelter	457	wrapMeSimInfo( this );
61			}
62	mmeineke	377
63	mmeineke	670
64	tim	660	SimInfo::~SimInfo(){
65
66	mmeineke	670	delete myConfiguration;
67
68	tim	660	map<string, GenericData*>::iterator i;
69
70			for(i = properties.begin(); i != properties.end(); i++)
71			delete (*i).second;
72	mmeineke	670
73	tim	660	}
74
75	gezelter	457	void SimInfo::setBox(double newBox[3]) {
76	mmeineke	586
77	gezelter	588	int i, j;
78			double tempMat[3][3];
79	gezelter	463
80	gezelter	588	for(i=0; i<3; i++)
81			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
82	gezelter	463
83	gezelter	588	tempMat[0][0] = newBox[0];
84			tempMat[1][1] = newBox[1];
85			tempMat[2][2] = newBox[2];
86	gezelter	463
87	mmeineke	586	setBoxM( tempMat );
88	mmeineke	568
89	gezelter	457	}
90	mmeineke	377
91	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
92	mmeineke	568
93	gezelter	588	int i, j, status;
94	mmeineke	568	double smallestBoxL, maxCutoff;
95	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
96			// ordering in the array is as follows:
97			// [ 0 3 6 ]
98			// [ 1 4 7 ]
99			// [ 2 5 8 ]
100			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101	mmeineke	568
102	mmeineke	626
103			if( !boxIsInit ) boxIsInit = 1;
104	mmeineke	586
105	gezelter	588	for(i=0; i < 3; i++)
106			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107
108	mmeineke	568	calcBoxL();
109	gezelter	588	calcHmatInv();
110	mmeineke	568
111	gezelter	588	for(i=0; i < 3; i++) {
112			for (j=0; j < 3; j++) {
113			FortranHmat[3*j + i] = Hmat[i][j];
114			FortranHmatInv[3*j + i] = HmatInv[i][j];
115			}
116			}
117	mmeineke	586
118	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119	mmeineke	568
120	mmeineke	377	}
121	gezelter	458
122	mmeineke	568
123	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
124	mmeineke	568
125	gezelter	588	int i, j;
126			for(i=0; i<3; i++)
127			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128	mmeineke	568	}
129
130	gezelter	574
131			void SimInfo::scaleBox(double scale) {
132	gezelter	588	double theBox[3][3];
133			int i, j;
134	gezelter	574
135	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
136	mmeineke	586
137	gezelter	588	for(i=0; i<3; i++)
138			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139	gezelter	574
140			setBoxM(theBox);
141
142			}
143
144	gezelter	588	void SimInfo::calcHmatInv( void ) {
145	mmeineke	590
146			int i,j;
147	mmeineke	569	double smallDiag;
148			double tol;
149			double sanity[3][3];
150	mmeineke	568
151	gezelter	588	invertMat3( Hmat, HmatInv );
152	mmeineke	568
153	gezelter	588	// Check the inverse to make sure it is sane:
154	mmeineke	568
155	gezelter	588	matMul3( Hmat, HmatInv, sanity );
156
157			// check to see if Hmat is orthorhombic
158	mmeineke	568
159	gezelter	588	smallDiag = Hmat[0][0];
160			if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
161			if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
162			tol = smallDiag * 1E-6;
163	mmeineke	568
164	gezelter	588	orthoRhombic = 1;
165	mmeineke	568
166	gezelter	588	for (i = 0; i < 3; i++ ) {
167			for (j = 0 ; j < 3; j++) {
168			if (i != j) {
169			if (orthoRhombic) {
170			if (Hmat[i][j] >= tol) orthoRhombic = 0;
171			}
172			}
173	mmeineke	568	}
174			}
175	gezelter	588	}
176	mmeineke	569
177	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
178			int i, j, k;
179			double determinant;
180	mmeineke	569
181	gezelter	588	determinant = 0.0;
182
183			for(i = 0; i < 3; i++) {
184			j = (i+1)%3;
185			k = (i+2)%3;
186
187			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
188	mmeineke	569	}
189
190	gezelter	588	return determinant;
191			}
192	mmeineke	569
193	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
194	mmeineke	569
195	gezelter	588	int i, j, k, l, m, n;
196			double determinant;
197	mmeineke	569
198	gezelter	588	determinant = matDet3( a );
199
200			if (determinant == 0.0) {
201			sprintf( painCave.errMsg,
202			"Can't invert a matrix with a zero determinant!\n");
203			painCave.isFatal = 1;
204			simError();
205			}
206
207			for (i=0; i < 3; i++) {
208			j = (i+1)%3;
209			k = (i+2)%3;
210			for(l = 0; l < 3; l++) {
211			m = (l+1)%3;
212			n = (l+2)%3;
213
214			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
215	mmeineke	569	}
216			}
217	mmeineke	568	}
218
219	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
220			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
221
222			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
223			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
224			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
225
226			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
227			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
228			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
229
230			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
231			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
232			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
233
234			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
235			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
236			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
237			}
238
239			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
240			double a0, a1, a2;
241
242			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
243
244			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
245			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
246			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
247			}
248	mmeineke	597
249			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
250			double temp[3][3];
251			int i, j;
252
253			for (i = 0; i < 3; i++) {
254			for (j = 0; j < 3; j++) {
255			temp[j][i] = in[i][j];
256			}
257			}
258			for (i = 0; i < 3; i++) {
259			for (j = 0; j < 3; j++) {
260			out[i][j] = temp[i][j];
261			}
262			}
263			}
264	gezelter	588
265	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
266
267			std::cerr
268			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
269			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
270			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
271			}
272
273			void SimInfo::printMat9(double A[9] ){
274
275			std::cerr
276			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
277			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
278			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
279			}
280
281	mmeineke	568	void SimInfo::calcBoxL( void ){
282
283			double dx, dy, dz, dsq;
284			int i;
285
286	gezelter	588	// boxVol = Determinant of Hmat
287	mmeineke	568
288	gezelter	588	boxVol = matDet3( Hmat );
289	mmeineke	568
290			// boxLx
291
292	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
293	mmeineke	568	dsq = dxdx + dydy + dz*dz;
294	gezelter	621	boxL[0] = sqrt( dsq );
295	mmeineke	626	maxCutoff = 0.5 * boxL[0];
296	mmeineke	568
297			// boxLy
298
299	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
300	mmeineke	568	dsq = dxdx + dydy + dz*dz;
301	gezelter	621	boxL[1] = sqrt( dsq );
302	mmeineke	626	if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
303	mmeineke	568
304			// boxLz
305
306	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
307	mmeineke	568	dsq = dxdx + dydy + dz*dz;
308	gezelter	621	boxL[2] = sqrt( dsq );
309	mmeineke	626	if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
310	chuckv	669
311			checkCutOffs();
312	mmeineke	626
313	mmeineke	568	}
314
315
316			void SimInfo::wrapVector( double thePos[3] ){
317
318			int i, j, k;
319			double scaled[3];
320
321	mmeineke	569	if( !orthoRhombic ){
322			// calc the scaled coordinates.
323	gezelter	588
324
325			matVecMul3(HmatInv, thePos, scaled);
326	mmeineke	569
327			for(i=0; i<3; i++)
328	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
329	mmeineke	569
330			// calc the wrapped real coordinates from the wrapped scaled coordinates
331
332	gezelter	588	matVecMul3(Hmat, scaled, thePos);
333
334	mmeineke	569	}
335			else{
336			// calc the scaled coordinates.
337
338			for(i=0; i<3; i++)
339	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
340	mmeineke	569
341			// wrap the scaled coordinates
342
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			for(i=0; i<3; i++)
349	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
350	mmeineke	569	}
351
352	mmeineke	568	}
353
354
355	gezelter	458	int SimInfo::getNDF(){
356			int ndf_local, ndf;
357	gezelter	457
358	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
359
360			#ifdef IS_MPI
361			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
362			#else
363			ndf = ndf_local;
364			#endif
365
366	mmeineke	674	ndf = ndf - 3 - nZconstraints;
367	gezelter	458
368			return ndf;
369			}
370
371			int SimInfo::getNDFraw() {
372			int ndfRaw_local, ndfRaw;
373
374			// Raw degrees of freedom that we have to set
375			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
376
377			#ifdef IS_MPI
378			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
379			#else
380			ndfRaw = ndfRaw_local;
381			#endif
382
383			return ndfRaw;
384			}
385
386	mmeineke	377	void SimInfo::refreshSim(){
387
388			simtype fInfo;
389			int isError;
390	gezelter	490	int n_global;
391	mmeineke	424	int* excl;
392	mmeineke	626
393	mmeineke	469	fInfo.dielect = 0.0;
394	mmeineke	377
395	mmeineke	469	if( useDipole ){
396			if( useReactionField )fInfo.dielect = dielectric;
397			}
398
399	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
400	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
401	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
402	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
403			//fInfo.SIM_uses_sticky = 0;
404	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
405			//fInfo.SIM_uses_dipoles = 0;
406	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
407			fInfo.SIM_uses_RF = 0;
408	mmeineke	377	fInfo.SIM_uses_GB = useGB;
409			fInfo.SIM_uses_EAM = useEAM;
410
411	mmeineke	424	excl = Exclude::getArray();
412	mmeineke	377
413	gezelter	490	#ifdef IS_MPI
414			n_global = mpiSim->getTotAtoms();
415			#else
416			n_global = n_atoms;
417			#endif
418
419	mmeineke	377	isError = 0;
420
421	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
422	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
423			&isError );
424	mmeineke	377
425			if( isError ){
426
427			sprintf( painCave.errMsg,
428			"There was an error setting the simulation information in fortran.\n" );
429			painCave.isFatal = 1;
430			simError();
431			}
432
433			#ifdef IS_MPI
434			sprintf( checkPointMsg,
435			"succesfully sent the simulation information to fortran.\n");
436			MPIcheckPoint();
437			#endif // is_mpi
438	gezelter	458
439	gezelter	474	this->ndf = this->getNDF();
440			this->ndfRaw = this->getNDFraw();
441	gezelter	458
442	mmeineke	377	}
443
444	mmeineke	626
445			void SimInfo::setRcut( double theRcut ){
446
447			if( !haveOrigRcut ){
448			haveOrigRcut = 1;
449			origRcut = theRcut;
450			}
451
452			rCut = theRcut;
453			checkCutOffs();
454			}
455
456			void SimInfo::setEcr( double theEcr ){
457
458			if( !haveOrigEcr ){
459			haveOrigEcr = 1;
460			origEcr = theEcr;
461			}
462
463			ecr = theEcr;
464			checkCutOffs();
465			}
466
467			void SimInfo::setEcr( double theEcr, double theEst ){
468
469			est = theEst;
470			setEcr( theEcr );
471			}
472
473
474			void SimInfo::checkCutOffs( void ){
475
476			int cutChanged = 0;
477
478	chuckv	669
479
480	mmeineke	626	if( boxIsInit ){
481
482			//we need to check cutOffs against the box
483	chuckv	669
484			if(( maxCutoff > rCut )&&(usePBC)){
485	mmeineke	626	if( rCut < origRcut ){
486			rCut = origRcut;
487			if (rCut > maxCutoff) rCut = maxCutoff;
488
489			sprintf( painCave.errMsg,
490			"New Box size is setting the long range cutoff radius "
491			"to %lf\n",
492			rCut );
493			painCave.isFatal = 0;
494			simError();
495			}
496			}
497
498			if( maxCutoff > ecr ){
499			if( ecr < origEcr ){
500			rCut = origEcr;
501			if (ecr > maxCutoff) ecr = maxCutoff;
502
503			sprintf( painCave.errMsg,
504			"New Box size is setting the electrostaticCutoffRadius "
505			"to %lf\n",
506			ecr );
507			painCave.isFatal = 0;
508			simError();
509			}
510			}
511
512
513	chuckv	669	if ((rCut > maxCutoff)&&(usePBC)) {
514	mmeineke	626	sprintf( painCave.errMsg,
515			"New Box size is setting the long range cutoff radius "
516			"to %lf\n",
517			maxCutoff );
518			painCave.isFatal = 0;
519			simError();
520			rCut = maxCutoff;
521			}
522
523			if( ecr > maxCutoff){
524			sprintf( painCave.errMsg,
525			"New Box size is setting the electrostaticCutoffRadius "
526			"to %lf\n",
527			maxCutoff );
528			painCave.isFatal = 0;
529			simError();
530			ecr = maxCutoff;
531			}
532
533
534			}
535
536
537			if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
538
539			// rlist is the 1.0 plus max( rcut, ecr )
540
541			( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542
543			if( cutChanged ){
544
545			notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546			}
547
548			oldEcr = ecr;
549			oldRcut = rCut;
550			}
551	tim	658
552			void SimInfo::addProperty(GenericData* prop){
553
554			map<string, GenericData*>::iterator result;
555			result = properties.find(prop->getID());
556
557			//we can't simply use properties[prop->getID()] = prop,
558			//it will cause memory leak if we already contain a propery which has the same name of prop
559
560			if(result != properties.end()){
561
562			delete (*result).second;
563			(*result).second = prop;
564
565			}
566			else{
567
568			properties[prop->getID()] = prop;
569
570			}
571
572			}
573
574			GenericData* SimInfo::getProperty(const string& propName){
575
576			map<string, GenericData*>::iterator result;
577
578			//string lowerCaseName = ();
579
580			result = properties.find(propName);
581
582			if(result != properties.end())
583			return (*result).second;
584			else
585			return NULL;
586			}
587
588			vector<GenericData*> SimInfo::getProperties(){
589
590			vector<GenericData*> result;
591			map<string, GenericData*>::iterator i;
592
593			for(i = properties.begin(); i != properties.end(); i++)
594			result.push_back((*i).second);
595
596			return result;
597			}
598
599