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;

  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;

  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:	670
Committed:	Thu Aug 7 21:47:18 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	12090 byte(s)
Log Message:	switched SimInfo to use a system configuration from SimState rather than arrays from Atom
#	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	mmeineke	670	myConfiguration = new SimState();
58
59	gezelter	457	wrapMeSimInfo( this );
60			}
61	mmeineke	377
62	mmeineke	670
63	tim	660	SimInfo::~SimInfo(){
64
65	mmeineke	670	delete myConfiguration;
66
67	tim	660	map<string, GenericData*>::iterator i;
68
69			for(i = properties.begin(); i != properties.end(); i++)
70			delete (*i).second;
71	mmeineke	670
72	tim	660	}
73
74	gezelter	457	void SimInfo::setBox(double newBox[3]) {
75	mmeineke	586
76	gezelter	588	int i, j;
77			double tempMat[3][3];
78	gezelter	463
79	gezelter	588	for(i=0; i<3; i++)
80			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
81	gezelter	463
82	gezelter	588	tempMat[0][0] = newBox[0];
83			tempMat[1][1] = newBox[1];
84			tempMat[2][2] = newBox[2];
85	gezelter	463
86	mmeineke	586	setBoxM( tempMat );
87	mmeineke	568
88	gezelter	457	}
89	mmeineke	377
90	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
91	mmeineke	568
92	gezelter	588	int i, j, status;
93	mmeineke	568	double smallestBoxL, maxCutoff;
94	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
95			// ordering in the array is as follows:
96			// [ 0 3 6 ]
97			// [ 1 4 7 ]
98			// [ 2 5 8 ]
99			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
100	mmeineke	568
101	mmeineke	626
102			if( !boxIsInit ) boxIsInit = 1;
103	mmeineke	586
104	gezelter	588	for(i=0; i < 3; i++)
105			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
106
107	mmeineke	568	calcBoxL();
108	gezelter	588	calcHmatInv();
109	mmeineke	568
110	gezelter	588	for(i=0; i < 3; i++) {
111			for (j=0; j < 3; j++) {
112			FortranHmat[3*j + i] = Hmat[i][j];
113			FortranHmatInv[3*j + i] = HmatInv[i][j];
114			}
115			}
116	mmeineke	586
117	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
118	mmeineke	568
119	mmeineke	377	}
120	gezelter	458
121	mmeineke	568
122	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
123	mmeineke	568
124	gezelter	588	int i, j;
125			for(i=0; i<3; i++)
126			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
127	mmeineke	568	}
128
129	gezelter	574
130			void SimInfo::scaleBox(double scale) {
131	gezelter	588	double theBox[3][3];
132			int i, j;
133	gezelter	574
134	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
135	mmeineke	586
136	gezelter	588	for(i=0; i<3; i++)
137			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
138	gezelter	574
139			setBoxM(theBox);
140
141			}
142
143	gezelter	588	void SimInfo::calcHmatInv( void ) {
144	mmeineke	590
145			int i,j;
146	mmeineke	569	double smallDiag;
147			double tol;
148			double sanity[3][3];
149	mmeineke	568
150	gezelter	588	invertMat3( Hmat, HmatInv );
151	mmeineke	568
152	gezelter	588	// Check the inverse to make sure it is sane:
153	mmeineke	568
154	gezelter	588	matMul3( Hmat, HmatInv, sanity );
155
156			// check to see if Hmat is orthorhombic
157	mmeineke	568
158	gezelter	588	smallDiag = Hmat[0][0];
159			if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
160			if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
161			tol = smallDiag * 1E-6;
162	mmeineke	568
163	gezelter	588	orthoRhombic = 1;
164	mmeineke	568
165	gezelter	588	for (i = 0; i < 3; i++ ) {
166			for (j = 0 ; j < 3; j++) {
167			if (i != j) {
168			if (orthoRhombic) {
169			if (Hmat[i][j] >= tol) orthoRhombic = 0;
170			}
171			}
172	mmeineke	568	}
173			}
174	gezelter	588	}
175	mmeineke	569
176	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
177			int i, j, k;
178			double determinant;
179	mmeineke	569
180	gezelter	588	determinant = 0.0;
181
182			for(i = 0; i < 3; i++) {
183			j = (i+1)%3;
184			k = (i+2)%3;
185
186			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
187	mmeineke	569	}
188
189	gezelter	588	return determinant;
190			}
191	mmeineke	569
192	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
193	mmeineke	569
194	gezelter	588	int i, j, k, l, m, n;
195			double determinant;
196	mmeineke	569
197	gezelter	588	determinant = matDet3( a );
198
199			if (determinant == 0.0) {
200			sprintf( painCave.errMsg,
201			"Can't invert a matrix with a zero determinant!\n");
202			painCave.isFatal = 1;
203			simError();
204			}
205
206			for (i=0; i < 3; i++) {
207			j = (i+1)%3;
208			k = (i+2)%3;
209			for(l = 0; l < 3; l++) {
210			m = (l+1)%3;
211			n = (l+2)%3;
212
213			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
214	mmeineke	569	}
215			}
216	mmeineke	568	}
217
218	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
219			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
220
221			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
222			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
223			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
224
225			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
226			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
227			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
228
229			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
230			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
231			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
232
233			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
234			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
235			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
236			}
237
238			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
239			double a0, a1, a2;
240
241			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
242
243			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
244			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
245			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
246			}
247	mmeineke	597
248			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
249			double temp[3][3];
250			int i, j;
251
252			for (i = 0; i < 3; i++) {
253			for (j = 0; j < 3; j++) {
254			temp[j][i] = in[i][j];
255			}
256			}
257			for (i = 0; i < 3; i++) {
258			for (j = 0; j < 3; j++) {
259			out[i][j] = temp[i][j];
260			}
261			}
262			}
263	gezelter	588
264	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
265
266			std::cerr
267			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
268			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
269			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
270			}
271
272			void SimInfo::printMat9(double A[9] ){
273
274			std::cerr
275			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
276			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
277			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
278			}
279
280	mmeineke	568	void SimInfo::calcBoxL( void ){
281
282			double dx, dy, dz, dsq;
283			int i;
284
285	gezelter	588	// boxVol = Determinant of Hmat
286	mmeineke	568
287	gezelter	588	boxVol = matDet3( Hmat );
288	mmeineke	568
289			// boxLx
290
291	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
292	mmeineke	568	dsq = dxdx + dydy + dz*dz;
293	gezelter	621	boxL[0] = sqrt( dsq );
294	mmeineke	626	maxCutoff = 0.5 * boxL[0];
295	mmeineke	568
296			// boxLy
297
298	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
299	mmeineke	568	dsq = dxdx + dydy + dz*dz;
300	gezelter	621	boxL[1] = sqrt( dsq );
301	mmeineke	626	if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
302	mmeineke	568
303			// boxLz
304
305	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
306	mmeineke	568	dsq = dxdx + dydy + dz*dz;
307	gezelter	621	boxL[2] = sqrt( dsq );
308	mmeineke	626	if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
309	chuckv	669
310			checkCutOffs();
311	mmeineke	626
312	mmeineke	568	}
313
314
315			void SimInfo::wrapVector( double thePos[3] ){
316
317			int i, j, k;
318			double scaled[3];
319
320	mmeineke	569	if( !orthoRhombic ){
321			// calc the scaled coordinates.
322	gezelter	588
323
324			matVecMul3(HmatInv, thePos, scaled);
325	mmeineke	569
326			for(i=0; i<3; i++)
327	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
328	mmeineke	569
329			// calc the wrapped real coordinates from the wrapped scaled coordinates
330
331	gezelter	588	matVecMul3(Hmat, scaled, thePos);
332
333	mmeineke	569	}
334			else{
335			// calc the scaled coordinates.
336
337			for(i=0; i<3; i++)
338	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
339	mmeineke	569
340			// wrap the scaled coordinates
341
342			for(i=0; i<3; i++)
343	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
344	mmeineke	569
345			// calc the wrapped real coordinates from the wrapped scaled coordinates
346
347			for(i=0; i<3; i++)
348	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
349	mmeineke	569	}
350
351	mmeineke	568	}
352
353
354	gezelter	458	int SimInfo::getNDF(){
355			int ndf_local, ndf;
356	gezelter	457
357	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
358
359			#ifdef IS_MPI
360			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
361			#else
362			ndf = ndf_local;
363			#endif
364
365			ndf = ndf - 3;
366
367			return ndf;
368			}
369
370			int SimInfo::getNDFraw() {
371			int ndfRaw_local, ndfRaw;
372
373			// Raw degrees of freedom that we have to set
374			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
375
376			#ifdef IS_MPI
377			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378			#else
379			ndfRaw = ndfRaw_local;
380			#endif
381
382			return ndfRaw;
383			}
384
385	mmeineke	377	void SimInfo::refreshSim(){
386
387			simtype fInfo;
388			int isError;
389	gezelter	490	int n_global;
390	mmeineke	424	int* excl;
391	mmeineke	626
392	mmeineke	469	fInfo.dielect = 0.0;
393	mmeineke	377
394	mmeineke	469	if( useDipole ){
395			if( useReactionField )fInfo.dielect = dielectric;
396			}
397
398	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
399	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
400	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
401	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
402			//fInfo.SIM_uses_sticky = 0;
403	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
404			//fInfo.SIM_uses_dipoles = 0;
405	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
406			fInfo.SIM_uses_RF = 0;
407	mmeineke	377	fInfo.SIM_uses_GB = useGB;
408			fInfo.SIM_uses_EAM = useEAM;
409
410	mmeineke	424	excl = Exclude::getArray();
411	mmeineke	377
412	gezelter	490	#ifdef IS_MPI
413			n_global = mpiSim->getTotAtoms();
414			#else
415			n_global = n_atoms;
416			#endif
417
418	mmeineke	377	isError = 0;
419
420	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
421	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
422			&isError );
423	mmeineke	377
424			if( isError ){
425
426			sprintf( painCave.errMsg,
427			"There was an error setting the simulation information in fortran.\n" );
428			painCave.isFatal = 1;
429			simError();
430			}
431
432			#ifdef IS_MPI
433			sprintf( checkPointMsg,
434			"succesfully sent the simulation information to fortran.\n");
435			MPIcheckPoint();
436			#endif // is_mpi
437	gezelter	458
438	gezelter	474	this->ndf = this->getNDF();
439			this->ndfRaw = this->getNDFraw();
440	gezelter	458
441	mmeineke	377	}
442
443	mmeineke	626
444			void SimInfo::setRcut( double theRcut ){
445
446			if( !haveOrigRcut ){
447			haveOrigRcut = 1;
448			origRcut = theRcut;
449			}
450
451			rCut = theRcut;
452			checkCutOffs();
453			}
454
455			void SimInfo::setEcr( double theEcr ){
456
457			if( !haveOrigEcr ){
458			haveOrigEcr = 1;
459			origEcr = theEcr;
460			}
461
462			ecr = theEcr;
463			checkCutOffs();
464			}
465
466			void SimInfo::setEcr( double theEcr, double theEst ){
467
468			est = theEst;
469			setEcr( theEcr );
470			}
471
472
473			void SimInfo::checkCutOffs( void ){
474
475			int cutChanged = 0;
476
477	chuckv	669
478
479	mmeineke	626	if( boxIsInit ){
480
481			//we need to check cutOffs against the box
482	chuckv	669
483			if(( maxCutoff > rCut )&&(usePBC)){
484	mmeineke	626	if( rCut < origRcut ){
485			rCut = origRcut;
486			if (rCut > maxCutoff) rCut = maxCutoff;
487
488			sprintf( painCave.errMsg,
489			"New Box size is setting the long range cutoff radius "
490			"to %lf\n",
491			rCut );
492			painCave.isFatal = 0;
493			simError();
494			}
495			}
496
497			if( maxCutoff > ecr ){
498			if( ecr < origEcr ){
499			rCut = origEcr;
500			if (ecr > maxCutoff) ecr = maxCutoff;
501
502			sprintf( painCave.errMsg,
503			"New Box size is setting the electrostaticCutoffRadius "
504			"to %lf\n",
505			ecr );
506			painCave.isFatal = 0;
507			simError();
508			}
509			}
510
511
512	chuckv	669	if ((rCut > maxCutoff)&&(usePBC)) {
513	mmeineke	626	sprintf( painCave.errMsg,
514			"New Box size is setting the long range cutoff radius "
515			"to %lf\n",
516			maxCutoff );
517			painCave.isFatal = 0;
518			simError();
519			rCut = maxCutoff;
520			}
521
522			if( ecr > maxCutoff){
523			sprintf( painCave.errMsg,
524			"New Box size is setting the electrostaticCutoffRadius "
525			"to %lf\n",
526			maxCutoff );
527			painCave.isFatal = 0;
528			simError();
529			ecr = maxCutoff;
530			}
531
532
533			}
534
535
536			if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
537
538			// rlist is the 1.0 plus max( rcut, ecr )
539
540			( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
541
542			if( cutChanged ){
543
544			notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
545			}
546
547			oldEcr = ecr;
548			oldRcut = rCut;
549			}
550	tim	658
551			void SimInfo::addProperty(GenericData* prop){
552
553			map<string, GenericData*>::iterator result;
554			result = properties.find(prop->getID());
555
556			//we can't simply use properties[prop->getID()] = prop,
557			//it will cause memory leak if we already contain a propery which has the same name of prop
558
559			if(result != properties.end()){
560
561			delete (*result).second;
562			(*result).second = prop;
563
564			}
565			else{
566
567			properties[prop->getID()] = prop;
568
569			}
570
571			}
572
573			GenericData* SimInfo::getProperty(const string& propName){
574
575			map<string, GenericData*>::iterator result;
576
577			//string lowerCaseName = ();
578
579			result = properties.find(propName);
580
581			if(result != properties.end())
582			return (*result).second;
583			else
584			return NULL;
585			}
586
587			vector<GenericData*> SimInfo::getProperties(){
588
589			vector<GenericData*> result;
590			map<string, GenericData*>::iterator i;
591
592			for(i = properties.begin(); i != properties.end(); i++)
593			result.push_back((*i).second);
594
595			return result;
596			}
597
598