OOPSE/libmdtools/SimInfo.cpp

#include <stdlib.h>
#include <string.h>
#include <math.h>

#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 );
}
          
inline double min( double a, double b ){
  return (a < b ) ? a : b;
}

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;
  ecr = 0.0;
  est = 0.0;

  haveRcut = 0;
  haveEcr = 0;
  boxIsInit = 0;
  
  resetTime = 1e99;

  orthoTolerance = 1E-6;
  useInitXSstate = true;

  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;
  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 oldOrtho;
  int i,j;
  double smallDiag;
  double tol;
  double sanity[3][3];

  invertMat3( Hmat, HmatInv );

  // check to see if Hmat is orthorhombic
  
  oldOrtho = orthoRhombic;

  smallDiag = fabs(Hmat[0][0]);
  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
  tol = smallDiag * orthoTolerance;

  orthoRhombic = 1;
  
  for (i = 0; i < 3; i++ ) {
    for (j = 0 ; j < 3; j++) {
      if (i != j) {
        if (orthoRhombic) {
          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
        }        
      }
    }
  }

  if( oldOrtho != orthoRhombic ){
    
    if( orthoRhombic ){
      sprintf( painCave.errMsg,
               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
               orthoTolerance);
      simError();
    }
    else {
      sprintf( painCave.errMsg,
               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
               orthoTolerance);
      simError();
    }
  }
}

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;

  // 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;
  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_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;

  // 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_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::setDefaultRcut( double theRcut ){

  haveRcut = 1;
  rCut = theRcut;

  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;

  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
}

void SimInfo::setDefaultEcr( double theEcr ){

  haveEcr = 1;
  
  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;

  ecr = theEcr;

  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
}

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

  est = theEst;
  setDefaultEcr( theEcr );
}


void SimInfo::checkCutOffs( void ){
  
  if( boxIsInit ){
    
    //we need to check cutOffs against the box
    
    if( rCut > maxCutoff ){
      sprintf( painCave.errMsg,
               "Box size is too small for the long range cutoff radius, "
               "%lf, at time %lf\n",
               rCut, currentTime );
      painCave.isFatal = 1;
      simError();
    }
    
    if( haveEcr ){
      if( ecr > maxCutoff ){
        sprintf( painCave.errMsg,
                 "Box size is too small for the electrostatic cutoff radius, "
                 "%lf, at time %lf\n",
                 ecr, currentTime );
        painCave.isFatal = 1;
        simError();
      }
    }
  } 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:	860
Committed:	Tue Nov 11 17:20:12 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	13671 byte(s)
Log Message:	added a routine to SimInfo.cpp to inline a min function.
#	User	Rev	Content
1	gezelter	829	#include <stdlib.h>
2			#include <string.h>
3			#include <math.h>
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	mmeineke	860	inline double min( double a, double b ){
24			return (a < b ) ? a : b;
25			}
26	mmeineke	572
27	mmeineke	377	SimInfo* currentInfo;
28
29			SimInfo::SimInfo(){
30			excludes = NULL;
31			n_constraints = 0;
32	tim	699	nZconstraints = 0;
33	mmeineke	377	n_oriented = 0;
34			n_dipoles = 0;
35	gezelter	458	ndf = 0;
36			ndfRaw = 0;
37	mmeineke	674	nZconstraints = 0;
38	mmeineke	377	the_integrator = NULL;
39			setTemp = 0;
40			thermalTime = 0.0;
41	mmeineke	642	currentTime = 0.0;
42	mmeineke	420	rCut = 0.0;
43	mmeineke	618	ecr = 0.0;
44	mmeineke	619	est = 0.0;
45	mmeineke	377
46	mmeineke	859	haveRcut = 0;
47			haveEcr = 0;
48	mmeineke	626	boxIsInit = 0;
49
50	tim	781	resetTime = 1e99;
51	mmeineke	626
52	mmeineke	855	orthoTolerance = 1E-6;
53			useInitXSstate = true;
54
55	mmeineke	377	usePBC = 0;
56			useLJ = 0;
57			useSticky = 0;
58			useDipole = 0;
59			useReactionField = 0;
60			useGB = 0;
61			useEAM = 0;
62
63	mmeineke	670	myConfiguration = new SimState();
64
65	gezelter	457	wrapMeSimInfo( this );
66			}
67	mmeineke	377
68	mmeineke	670
69	tim	660	SimInfo::~SimInfo(){
70
71	mmeineke	670	delete myConfiguration;
72
73	tim	660	map<string, GenericData*>::iterator i;
74
75			for(i = properties.begin(); i != properties.end(); i++)
76			delete (*i).second;
77	mmeineke	670
78	tim	660	}
79
80	gezelter	457	void SimInfo::setBox(double newBox[3]) {
81	mmeineke	586
82	gezelter	588	int i, j;
83			double tempMat[3][3];
84	gezelter	463
85	gezelter	588	for(i=0; i<3; i++)
86			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
87	gezelter	463
88	gezelter	588	tempMat[0][0] = newBox[0];
89			tempMat[1][1] = newBox[1];
90			tempMat[2][2] = newBox[2];
91	gezelter	463
92	mmeineke	586	setBoxM( tempMat );
93	mmeineke	568
94	gezelter	457	}
95	mmeineke	377
96	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
97	mmeineke	568
98	mmeineke	787	int i, j;
99	gezelter	588	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	mmeineke	568
106	mmeineke	626	if( !boxIsInit ) boxIsInit = 1;
107	mmeineke	586
108	gezelter	588	for(i=0; i < 3; i++)
109			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
110
111	mmeineke	568	calcBoxL();
112	gezelter	588	calcHmatInv();
113	mmeineke	568
114	gezelter	588	for(i=0; i < 3; i++) {
115			for (j=0; j < 3; j++) {
116			FortranHmat[3*j + i] = Hmat[i][j];
117			FortranHmatInv[3*j + i] = HmatInv[i][j];
118			}
119			}
120	mmeineke	586
121	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122	mmeineke	568
123	mmeineke	377	}
124	gezelter	458
125	mmeineke	568
126	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
127	mmeineke	568
128	gezelter	588	int i, j;
129			for(i=0; i<3; i++)
130			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
131	mmeineke	568	}
132
133	gezelter	574
134			void SimInfo::scaleBox(double scale) {
135	gezelter	588	double theBox[3][3];
136			int i, j;
137	gezelter	574
138	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
139	mmeineke	586
140	gezelter	588	for(i=0; i<3; i++)
141			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
142	gezelter	574
143			setBoxM(theBox);
144
145			}
146
147	gezelter	588	void SimInfo::calcHmatInv( void ) {
148	mmeineke	590
149	mmeineke	853	int oldOrtho;
150	mmeineke	590	int i,j;
151	mmeineke	569	double smallDiag;
152			double tol;
153			double sanity[3][3];
154	mmeineke	568
155	gezelter	588	invertMat3( Hmat, HmatInv );
156	mmeineke	568
157	gezelter	588	// check to see if Hmat is orthorhombic
158	mmeineke	568
159	mmeineke	853	oldOrtho = orthoRhombic;
160
161			smallDiag = fabs(Hmat[0][0]);
162			if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
163			if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
164	mmeineke	855	tol = smallDiag * orthoTolerance;
165	mmeineke	568
166	gezelter	588	orthoRhombic = 1;
167	mmeineke	568
168	gezelter	588	for (i = 0; i < 3; i++ ) {
169			for (j = 0 ; j < 3; j++) {
170			if (i != j) {
171			if (orthoRhombic) {
172	mmeineke	853	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
173	gezelter	588	}
174			}
175	mmeineke	568	}
176			}
177	mmeineke	853
178			if( oldOrtho != orthoRhombic ){
179
180			if( orthoRhombic ){
181			sprintf( painCave.errMsg,
182			"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
184			orthoTolerance);
185	mmeineke	853	simError();
186			}
187			else {
188			sprintf( painCave.errMsg,
189			"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
190	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
191			orthoTolerance);
192	mmeineke	853	simError();
193			}
194			}
195	gezelter	588	}
196	mmeineke	569
197	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
198			int i, j, k;
199			double determinant;
200	mmeineke	569
201	gezelter	588	determinant = 0.0;
202
203			for(i = 0; i < 3; i++) {
204			j = (i+1)%3;
205			k = (i+2)%3;
206
207			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
208	mmeineke	569	}
209
210	gezelter	588	return determinant;
211			}
212	mmeineke	569
213	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
214	mmeineke	569
215	gezelter	588	int i, j, k, l, m, n;
216			double determinant;
217	mmeineke	569
218	gezelter	588	determinant = matDet3( a );
219
220			if (determinant == 0.0) {
221			sprintf( painCave.errMsg,
222			"Can't invert a matrix with a zero determinant!\n");
223			painCave.isFatal = 1;
224			simError();
225			}
226
227			for (i=0; i < 3; i++) {
228			j = (i+1)%3;
229			k = (i+2)%3;
230			for(l = 0; l < 3; l++) {
231			m = (l+1)%3;
232			n = (l+2)%3;
233
234			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
235	mmeineke	569	}
236			}
237	mmeineke	568	}
238
239	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
240			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
241
242			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
243			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
244			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
245
246			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
247			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
248			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
249
250			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
251			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
252			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
253
254			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
255			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
256			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
257			}
258
259			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
260			double a0, a1, a2;
261
262			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
263
264			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
265			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
266			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
267			}
268	mmeineke	597
269			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
270			double temp[3][3];
271			int i, j;
272
273			for (i = 0; i < 3; i++) {
274			for (j = 0; j < 3; j++) {
275			temp[j][i] = in[i][j];
276			}
277			}
278			for (i = 0; i < 3; i++) {
279			for (j = 0; j < 3; j++) {
280			out[i][j] = temp[i][j];
281			}
282			}
283			}
284	gezelter	588
285	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
286
287			std::cerr
288			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
289			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
290			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
291			}
292
293			void SimInfo::printMat9(double A[9] ){
294
295			std::cerr
296			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
297			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
298			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
299			}
300
301	tim	781
302			void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
303
304			out[0] = a[1] * b[2] - a[2] * b[1];
305			out[1] = a[2] * b[0] - a[0] * b[2] ;
306			out[2] = a[0] * b[1] - a[1] * b[0];
307
308			}
309
310			double SimInfo::dotProduct3(double a[3], double b[3]){
311			return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
312			}
313
314			double SimInfo::length3(double a[3]){
315			return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
316			}
317
318	mmeineke	568	void SimInfo::calcBoxL( void ){
319
320			double dx, dy, dz, dsq;
321
322	gezelter	588	// boxVol = Determinant of Hmat
323	mmeineke	568
324	gezelter	588	boxVol = matDet3( Hmat );
325	mmeineke	568
326			// boxLx
327
328	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
329	mmeineke	568	dsq = dxdx + dydy + dz*dz;
330	gezelter	621	boxL[0] = sqrt( dsq );
331	tim	781	//maxCutoff = 0.5 * boxL[0];
332	mmeineke	568
333			// boxLy
334
335	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
336	mmeineke	568	dsq = dxdx + dydy + dz*dz;
337	gezelter	621	boxL[1] = sqrt( dsq );
338	tim	781	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
339	mmeineke	568
340	tim	781
341	mmeineke	568	// boxLz
342
343	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
344	mmeineke	568	dsq = dxdx + dydy + dz*dz;
345	gezelter	621	boxL[2] = sqrt( dsq );
346	tim	781	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
347
348			//calculate the max cutoff
349			maxCutoff = calcMaxCutOff();
350	chuckv	669
351			checkCutOffs();
352	mmeineke	626
353	mmeineke	568	}
354
355
356	tim	781	double SimInfo::calcMaxCutOff(){
357
358			double ri[3], rj[3], rk[3];
359			double rij[3], rjk[3], rki[3];
360			double minDist;
361
362			ri[0] = Hmat[0][0];
363			ri[1] = Hmat[1][0];
364			ri[2] = Hmat[2][0];
365
366			rj[0] = Hmat[0][1];
367			rj[1] = Hmat[1][1];
368			rj[2] = Hmat[2][1];
369
370			rk[0] = Hmat[0][2];
371			rk[1] = Hmat[1][2];
372			rk[2] = Hmat[2][2];
373
374			crossProduct3(ri,rj, rij);
375			distXY = dotProduct3(rk,rij) / length3(rij);
376
377			crossProduct3(rj,rk, rjk);
378			distYZ = dotProduct3(ri,rjk) / length3(rjk);
379
380			crossProduct3(rk,ri, rki);
381			distZX = dotProduct3(rj,rki) / length3(rki);
382
383			minDist = min(min(distXY, distYZ), distZX);
384			return minDist/2;
385
386			}
387
388	mmeineke	568	void SimInfo::wrapVector( double thePos[3] ){
389
390	mmeineke	787	int i;
391	mmeineke	568	double scaled[3];
392
393	mmeineke	569	if( !orthoRhombic ){
394			// calc the scaled coordinates.
395	gezelter	588
396
397			matVecMul3(HmatInv, thePos, scaled);
398	mmeineke	569
399			for(i=0; i<3; i++)
400	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
401	mmeineke	569
402			// calc the wrapped real coordinates from the wrapped scaled coordinates
403
404	gezelter	588	matVecMul3(Hmat, scaled, thePos);
405
406	mmeineke	569	}
407			else{
408			// calc the scaled coordinates.
409
410			for(i=0; i<3; i++)
411	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
412	mmeineke	569
413			// wrap the scaled coordinates
414
415			for(i=0; i<3; i++)
416	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
417	mmeineke	569
418			// calc the wrapped real coordinates from the wrapped scaled coordinates
419
420			for(i=0; i<3; i++)
421	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
422	mmeineke	569	}
423
424	mmeineke	568	}
425
426
427	gezelter	458	int SimInfo::getNDF(){
428	mmeineke	790	int ndf_local;
429	gezelter	457
430	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
431
432			#ifdef IS_MPI
433			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
434			#else
435			ndf = ndf_local;
436			#endif
437
438	mmeineke	674	ndf = ndf - 3 - nZconstraints;
439	gezelter	458
440			return ndf;
441			}
442
443			int SimInfo::getNDFraw() {
444	mmeineke	790	int ndfRaw_local;
445	gezelter	458
446			// Raw degrees of freedom that we have to set
447			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
448
449			#ifdef IS_MPI
450			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
451			#else
452			ndfRaw = ndfRaw_local;
453			#endif
454
455			return ndfRaw;
456			}
457	tim	767
458			int SimInfo::getNDFtranslational() {
459	mmeineke	790	int ndfTrans_local;
460	tim	767
461			ndfTrans_local = 3 * n_atoms - n_constraints;
462
463			#ifdef IS_MPI
464			MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
465			#else
466			ndfTrans = ndfTrans_local;
467			#endif
468
469			ndfTrans = ndfTrans - 3 - nZconstraints;
470
471			return ndfTrans;
472			}
473
474	mmeineke	377	void SimInfo::refreshSim(){
475
476			simtype fInfo;
477			int isError;
478	gezelter	490	int n_global;
479	mmeineke	424	int* excl;
480	mmeineke	626
481	mmeineke	469	fInfo.dielect = 0.0;
482	mmeineke	377
483	mmeineke	469	if( useDipole ){
484			if( useReactionField )fInfo.dielect = dielectric;
485			}
486
487	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
488	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
489	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
490	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
491			//fInfo.SIM_uses_sticky = 0;
492	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
493			//fInfo.SIM_uses_dipoles = 0;
494	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
495			fInfo.SIM_uses_RF = 0;
496	mmeineke	377	fInfo.SIM_uses_GB = useGB;
497			fInfo.SIM_uses_EAM = useEAM;
498
499	mmeineke	424	excl = Exclude::getArray();
500	mmeineke	377
501	gezelter	490	#ifdef IS_MPI
502			n_global = mpiSim->getTotAtoms();
503			#else
504			n_global = n_atoms;
505			#endif
506
507	mmeineke	377	isError = 0;
508
509	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
510	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
511			&isError );
512	mmeineke	377
513			if( isError ){
514
515			sprintf( painCave.errMsg,
516			"There was an error setting the simulation information in fortran.\n" );
517			painCave.isFatal = 1;
518			simError();
519			}
520
521			#ifdef IS_MPI
522			sprintf( checkPointMsg,
523			"succesfully sent the simulation information to fortran.\n");
524			MPIcheckPoint();
525			#endif // is_mpi
526	gezelter	458
527	gezelter	474	this->ndf = this->getNDF();
528			this->ndfRaw = this->getNDFraw();
529	tim	767	this->ndfTrans = this->getNDFtranslational();
530	mmeineke	377	}
531
532	mmeineke	841	void SimInfo::setDefaultRcut( double theRcut ){
533
534	mmeineke	859	haveRcut = 1;
535	mmeineke	841	rCut = theRcut;
536	mmeineke	843
537	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
538
539	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
540	mmeineke	841	}
541
542			void SimInfo::setDefaultEcr( double theEcr ){
543
544	mmeineke	859	haveEcr = 1;
545	mmeineke	841
546	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
547
548	mmeineke	841	ecr = theEcr;
549	gezelter	845
550	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
551	mmeineke	841	}
552
553			void SimInfo::setDefaultEcr( double theEcr, double theEst ){
554	mmeineke	626
555	mmeineke	841	est = theEst;
556			setDefaultEcr( theEcr );
557			}
558
559
560	mmeineke	626	void SimInfo::checkCutOffs( void ){
561	gezelter	770
562	mmeineke	626	if( boxIsInit ){
563
564			//we need to check cutOffs against the box
565	mmeineke	859
566			if( rCut > maxCutoff ){
567	mmeineke	626	sprintf( painCave.errMsg,
568	mmeineke	859	"Box size is too small for the long range cutoff radius, "
569			"%lf, at time %lf\n",
570			rCut, currentTime );
571			painCave.isFatal = 1;
572	mmeineke	626	simError();
573			}
574	mmeineke	859
575			if( haveEcr ){
576			if( ecr > maxCutoff ){
577			sprintf( painCave.errMsg,
578			"Box size is too small for the electrostatic cutoff radius, "
579			"%lf, at time %lf\n",
580			ecr, currentTime );
581			painCave.isFatal = 1;
582			simError();
583	tim	781	}
584			}
585	tim	767	} else {
586			// initialize this stuff before using it, OK?
587	gezelter	770	sprintf( painCave.errMsg,
588			"Trying to check cutoffs without a box. Be smarter.\n" );
589			painCave.isFatal = 1;
590			simError();
591	mmeineke	626	}
592	gezelter	770
593	mmeineke	626	}
594	tim	658
595			void SimInfo::addProperty(GenericData* prop){
596
597			map<string, GenericData*>::iterator result;
598			result = properties.find(prop->getID());
599
600			//we can't simply use properties[prop->getID()] = prop,
601			//it will cause memory leak if we already contain a propery which has the same name of prop
602
603			if(result != properties.end()){
604
605			delete (*result).second;
606			(*result).second = prop;
607
608			}
609			else{
610
611			properties[prop->getID()] = prop;
612
613			}
614
615			}
616
617			GenericData* SimInfo::getProperty(const string& propName){
618
619			map<string, GenericData*>::iterator result;
620
621			//string lowerCaseName = ();
622
623			result = properties.find(propName);
624
625			if(result != properties.end())
626			return (*result).second;
627			else
628			return NULL;
629			}
630
631			vector<GenericData*> SimInfo::getProperties(){
632
633			vector<GenericData*> result;
634			map<string, GenericData*>::iterator i;
635
636			for(i = properties.begin(); i != properties.end(); i++)
637			result.push_back((*i).second);
638
639			return result;
640			}
641
642	tim	763	double SimInfo::matTrace3(double m[3][3]){
643			double trace;
644			trace = m[0][0] + m[1][1] + m[2][2];
645	tim	658
646	tim	763	return trace;
647			}