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 );
}

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:	658
Committed:	Thu Jul 31 15:35:07 2003 UTC (22 years, 3 months ago) by tim
File size:	11823 byte(s)
Log Message:	Added Z constraint.
#	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	gezelter	457	void SimInfo::setBox(double newBox[3]) {
61	mmeineke	586
62	gezelter	588	int i, j;
63			double tempMat[3][3];
64	gezelter	463
65	gezelter	588	for(i=0; i<3; i++)
66			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
67	gezelter	463
68	gezelter	588	tempMat[0][0] = newBox[0];
69			tempMat[1][1] = newBox[1];
70			tempMat[2][2] = newBox[2];
71	gezelter	463
72	mmeineke	586	setBoxM( tempMat );
73	mmeineke	568
74	gezelter	457	}
75	mmeineke	377
76	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
77	mmeineke	568
78	gezelter	588	int i, j, status;
79	mmeineke	568	double smallestBoxL, maxCutoff;
80	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
81			// ordering in the array is as follows:
82			// [ 0 3 6 ]
83			// [ 1 4 7 ]
84			// [ 2 5 8 ]
85			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
86	mmeineke	568
87	mmeineke	626
88			if( !boxIsInit ) boxIsInit = 1;
89	mmeineke	586
90	gezelter	588	for(i=0; i < 3; i++)
91			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
92
93	mmeineke	568	calcBoxL();
94	gezelter	588	calcHmatInv();
95	mmeineke	568
96	gezelter	588	for(i=0; i < 3; i++) {
97			for (j=0; j < 3; j++) {
98			FortranHmat[3*j + i] = Hmat[i][j];
99			FortranHmatInv[3*j + i] = HmatInv[i][j];
100			}
101			}
102	mmeineke	586
103	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
104	mmeineke	568
105	mmeineke	377	}
106	gezelter	458
107	mmeineke	568
108	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
109	mmeineke	568
110	gezelter	588	int i, j;
111			for(i=0; i<3; i++)
112			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
113	mmeineke	568	}
114
115	gezelter	574
116			void SimInfo::scaleBox(double scale) {
117	gezelter	588	double theBox[3][3];
118			int i, j;
119	gezelter	574
120	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
121	mmeineke	586
122	gezelter	588	for(i=0; i<3; i++)
123			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
124	gezelter	574
125			setBoxM(theBox);
126
127			}
128
129	gezelter	588	void SimInfo::calcHmatInv( void ) {
130	mmeineke	590
131			int i,j;
132	mmeineke	569	double smallDiag;
133			double tol;
134			double sanity[3][3];
135	mmeineke	568
136	gezelter	588	invertMat3( Hmat, HmatInv );
137	mmeineke	568
138	gezelter	588	// Check the inverse to make sure it is sane:
139	mmeineke	568
140	gezelter	588	matMul3( Hmat, HmatInv, sanity );
141
142			// check to see if Hmat is orthorhombic
143	mmeineke	568
144	gezelter	588	smallDiag = Hmat[0][0];
145			if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
146			if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
147			tol = smallDiag * 1E-6;
148	mmeineke	568
149	gezelter	588	orthoRhombic = 1;
150	mmeineke	568
151	gezelter	588	for (i = 0; i < 3; i++ ) {
152			for (j = 0 ; j < 3; j++) {
153			if (i != j) {
154			if (orthoRhombic) {
155			if (Hmat[i][j] >= tol) orthoRhombic = 0;
156			}
157			}
158	mmeineke	568	}
159			}
160	gezelter	588	}
161	mmeineke	569
162	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
163			int i, j, k;
164			double determinant;
165	mmeineke	569
166	gezelter	588	determinant = 0.0;
167
168			for(i = 0; i < 3; i++) {
169			j = (i+1)%3;
170			k = (i+2)%3;
171
172			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
173	mmeineke	569	}
174
175	gezelter	588	return determinant;
176			}
177	mmeineke	569
178	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
179	mmeineke	569
180	gezelter	588	int i, j, k, l, m, n;
181			double determinant;
182	mmeineke	569
183	gezelter	588	determinant = matDet3( a );
184
185			if (determinant == 0.0) {
186			sprintf( painCave.errMsg,
187			"Can't invert a matrix with a zero determinant!\n");
188			painCave.isFatal = 1;
189			simError();
190			}
191
192			for (i=0; i < 3; i++) {
193			j = (i+1)%3;
194			k = (i+2)%3;
195			for(l = 0; l < 3; l++) {
196			m = (l+1)%3;
197			n = (l+2)%3;
198
199			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
200	mmeineke	569	}
201			}
202	mmeineke	568	}
203
204	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
205			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
206
207			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
208			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
209			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
210
211			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
212			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
213			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
214
215			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
216			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
217			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
218
219			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
220			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
221			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
222			}
223
224			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
225			double a0, a1, a2;
226
227			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
228
229			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
230			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
231			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
232			}
233	mmeineke	597
234			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
235			double temp[3][3];
236			int i, j;
237
238			for (i = 0; i < 3; i++) {
239			for (j = 0; j < 3; j++) {
240			temp[j][i] = in[i][j];
241			}
242			}
243			for (i = 0; i < 3; i++) {
244			for (j = 0; j < 3; j++) {
245			out[i][j] = temp[i][j];
246			}
247			}
248			}
249	gezelter	588
250	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
251
252			std::cerr
253			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
254			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
255			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
256			}
257
258			void SimInfo::printMat9(double A[9] ){
259
260			std::cerr
261			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
262			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
263			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
264			}
265
266	mmeineke	568	void SimInfo::calcBoxL( void ){
267
268			double dx, dy, dz, dsq;
269			int i;
270
271	gezelter	588	// boxVol = Determinant of Hmat
272	mmeineke	568
273	gezelter	588	boxVol = matDet3( Hmat );
274	mmeineke	568
275			// boxLx
276
277	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
278	mmeineke	568	dsq = dxdx + dydy + dz*dz;
279	gezelter	621	boxL[0] = sqrt( dsq );
280	mmeineke	626	maxCutoff = 0.5 * boxL[0];
281	mmeineke	568
282			// boxLy
283
284	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
285	mmeineke	568	dsq = dxdx + dydy + dz*dz;
286	gezelter	621	boxL[1] = sqrt( dsq );
287	mmeineke	626	if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
288	mmeineke	568
289			// boxLz
290
291	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
292	mmeineke	568	dsq = dxdx + dydy + dz*dz;
293	gezelter	621	boxL[2] = sqrt( dsq );
294	mmeineke	626	if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
295
296	mmeineke	568	}
297
298
299			void SimInfo::wrapVector( double thePos[3] ){
300
301			int i, j, k;
302			double scaled[3];
303
304	mmeineke	569	if( !orthoRhombic ){
305			// calc the scaled coordinates.
306	gezelter	588
307
308			matVecMul3(HmatInv, thePos, scaled);
309	mmeineke	569
310			for(i=0; i<3; i++)
311	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
312	mmeineke	569
313			// calc the wrapped real coordinates from the wrapped scaled coordinates
314
315	gezelter	588	matVecMul3(Hmat, scaled, thePos);
316
317	mmeineke	569	}
318			else{
319			// calc the scaled coordinates.
320
321			for(i=0; i<3; i++)
322	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
323	mmeineke	569
324			// wrap the scaled coordinates
325
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			for(i=0; i<3; i++)
332	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
333	mmeineke	569	}
334
335	mmeineke	568	}
336
337
338	gezelter	458	int SimInfo::getNDF(){
339			int ndf_local, ndf;
340	gezelter	457
341	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
342
343			#ifdef IS_MPI
344			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
345			#else
346			ndf = ndf_local;
347			#endif
348
349			ndf = ndf - 3;
350
351			return ndf;
352			}
353
354			int SimInfo::getNDFraw() {
355			int ndfRaw_local, ndfRaw;
356
357			// Raw degrees of freedom that we have to set
358			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
359
360			#ifdef IS_MPI
361			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
362			#else
363			ndfRaw = ndfRaw_local;
364			#endif
365
366			return ndfRaw;
367			}
368
369	mmeineke	377	void SimInfo::refreshSim(){
370
371			simtype fInfo;
372			int isError;
373	gezelter	490	int n_global;
374	mmeineke	424	int* excl;
375	mmeineke	626
376	mmeineke	469	fInfo.dielect = 0.0;
377	mmeineke	377
378	mmeineke	469	if( useDipole ){
379			if( useReactionField )fInfo.dielect = dielectric;
380			}
381
382	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
383	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
384	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
385	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
386			//fInfo.SIM_uses_sticky = 0;
387	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
388			//fInfo.SIM_uses_dipoles = 0;
389	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
390			fInfo.SIM_uses_RF = 0;
391	mmeineke	377	fInfo.SIM_uses_GB = useGB;
392			fInfo.SIM_uses_EAM = useEAM;
393
394	mmeineke	424	excl = Exclude::getArray();
395	mmeineke	377
396	gezelter	490	#ifdef IS_MPI
397			n_global = mpiSim->getTotAtoms();
398			#else
399			n_global = n_atoms;
400			#endif
401
402	mmeineke	377	isError = 0;
403
404	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
405	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
406			&isError );
407	mmeineke	377
408			if( isError ){
409
410			sprintf( painCave.errMsg,
411			"There was an error setting the simulation information in fortran.\n" );
412			painCave.isFatal = 1;
413			simError();
414			}
415
416			#ifdef IS_MPI
417			sprintf( checkPointMsg,
418			"succesfully sent the simulation information to fortran.\n");
419			MPIcheckPoint();
420			#endif // is_mpi
421	gezelter	458
422	gezelter	474	this->ndf = this->getNDF();
423			this->ndfRaw = this->getNDFraw();
424	gezelter	458
425	mmeineke	377	}
426
427	mmeineke	626
428			void SimInfo::setRcut( double theRcut ){
429
430			if( !haveOrigRcut ){
431			haveOrigRcut = 1;
432			origRcut = theRcut;
433			}
434
435			rCut = theRcut;
436			checkCutOffs();
437			}
438
439			void SimInfo::setEcr( double theEcr ){
440
441			if( !haveOrigEcr ){
442			haveOrigEcr = 1;
443			origEcr = theEcr;
444			}
445
446			ecr = theEcr;
447			checkCutOffs();
448			}
449
450			void SimInfo::setEcr( double theEcr, double theEst ){
451
452			est = theEst;
453			setEcr( theEcr );
454			}
455
456
457			void SimInfo::checkCutOffs( void ){
458
459			int cutChanged = 0;
460
461			if( boxIsInit ){
462
463			//we need to check cutOffs against the box
464
465			if( maxCutoff > rCut ){
466			if( rCut < origRcut ){
467			rCut = origRcut;
468			if (rCut > maxCutoff) rCut = maxCutoff;
469
470			sprintf( painCave.errMsg,
471			"New Box size is setting the long range cutoff radius "
472			"to %lf\n",
473			rCut );
474			painCave.isFatal = 0;
475			simError();
476			}
477			}
478
479			if( maxCutoff > ecr ){
480			if( ecr < origEcr ){
481			rCut = origEcr;
482			if (ecr > maxCutoff) ecr = maxCutoff;
483
484			sprintf( painCave.errMsg,
485			"New Box size is setting the electrostaticCutoffRadius "
486			"to %lf\n",
487			ecr );
488			painCave.isFatal = 0;
489			simError();
490			}
491			}
492
493
494			if (rCut > maxCutoff) {
495			sprintf( painCave.errMsg,
496			"New Box size is setting the long range cutoff radius "
497			"to %lf\n",
498			maxCutoff );
499			painCave.isFatal = 0;
500			simError();
501			rCut = maxCutoff;
502			}
503
504			if( ecr > maxCutoff){
505			sprintf( painCave.errMsg,
506			"New Box size is setting the electrostaticCutoffRadius "
507			"to %lf\n",
508			maxCutoff );
509			painCave.isFatal = 0;
510			simError();
511			ecr = maxCutoff;
512			}
513
514
515			}
516
517
518			if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
519
520			// rlist is the 1.0 plus max( rcut, ecr )
521
522			( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
523
524			if( cutChanged ){
525
526			notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
527			}
528
529			oldEcr = ecr;
530			oldRcut = rCut;
531			}
532	tim	658
533			void SimInfo::addProperty(GenericData* prop){
534
535			map<string, GenericData*>::iterator result;
536			result = properties.find(prop->getID());
537
538			//we can't simply use properties[prop->getID()] = prop,
539			//it will cause memory leak if we already contain a propery which has the same name of prop
540
541			if(result != properties.end()){
542
543			delete (*result).second;
544			(*result).second = prop;
545
546			}
547			else{
548
549			properties[prop->getID()] = prop;
550
551			}
552
553			}
554
555			GenericData* SimInfo::getProperty(const string& propName){
556
557			map<string, GenericData*>::iterator result;
558
559			//string lowerCaseName = ();
560
561			result = properties.find(propName);
562
563			if(result != properties.end())
564			return (*result).second;
565			else
566			return NULL;
567			}
568
569			vector<GenericData*> SimInfo::getProperties(){
570
571			vector<GenericData*> result;
572			map<string, GenericData*>::iterator i;
573
574			for(i = properties.begin(); i != properties.end(); i++)
575			result.push_back((*i).second);
576
577			return result;
578			}
579
580