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 );
}
          

SimInfo* currentInfo;

SimInfo::SimInfo(){
  excludes = NULL;
  n_constraints = 0;
  nZconstraints = 0;
  n_oriented = 0;
  n_dipoles = 0;
  ndf = 0;
  ndfRaw = 0;
  nZconstraints = 0;
  the_integrator = NULL;
  setTemp = 0;
  thermalTime = 0.0;
  currentTime = 0.0;
  rCut = 0.0;
  origRcut = -1.0;
  ecr = 0.0;
  origEcr = -1.0;
  est = 0.0;
  oldEcr = 0.0;
  oldRcut = 0.0;

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

  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::setRcut( double theRcut ){

  rCut = theRcut;
  checkCutOffs();
}

void SimInfo::setDefaultRcut( double theRcut ){

  haveOrigRcut = 1;
  origRcut = theRcut;
  rCut = theRcut;

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

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

void SimInfo::setEcr( double theEcr ){

  ecr = theEcr;
  checkCutOffs();
}

void SimInfo::setDefaultEcr( double theEcr ){

  haveOrigEcr = 1;
  origEcr = theEcr;
  
  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;

  ecr = theEcr;

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

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

  est = theEst;
  setEcr( theEcr );
}

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

  est = theEst;
  setDefaultEcr( theEcr );
}


void SimInfo::checkCutOffs( void ){

  int cutChanged = 0;
  
  if( boxIsInit ){
    
    //we need to check cutOffs against the box

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


    //detect the change of ecr
    if( maxCutoff > ecr ){
      if( ecr < origEcr ){
        ecr = origEcr;
        if (ecr > maxCutoff) ecr = maxCutoff;
  
          sprintf( painCave.errMsg,
                    "New Box size is setting the electrostaticCutoffRadius "
                    "to %lf at time %lf\n",
                    ecr, currentTime );
            painCave.isFatal = 0;
            simError();
      }
    }
    else if( ecr > maxCutoff){
      sprintf( painCave.errMsg,
               "New Box size is setting the electrostaticCutoffRadius "
               "to %lf at time %lf\n",
               maxCutoff, currentTime  );
      painCave.isFatal = 0;
      simError();      
      ecr = maxCutoff;
    }

    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
    
    // rlist is the 1.0 plus max( rcut, ecr )
    
    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
    
    if( cutChanged ){
      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
    }
    
    oldEcr = ecr;
    oldRcut = rCut;
    
  } else {
    // initialize this stuff before using it, OK?
    sprintf( painCave.errMsg,
             "Trying to check cutoffs without a box. Be smarter.\n" );
    painCave.isFatal = 1;
    simError();      
  }
  
}

void SimInfo::addProperty(GenericData* prop){

  map<string, GenericData*>::iterator result;
  result = properties.find(prop->getID());
  
  //we can't simply use  properties[prop->getID()] = prop,
  //it will cause memory leak if we already contain a propery which has the same name of prop
  
  if(result != properties.end()){
    
    delete (*result).second;
    (*result).second = prop;
      
  }
  else{

    properties[prop->getID()] = prop;

  }
    
}

GenericData* SimInfo::getProperty(const string& propName){
 
  map<string, GenericData*>::iterator result;
  
  //string lowerCaseName = ();
  
  result = properties.find(propName);
  
  if(result != properties.end()) 
    return (*result).second;  
  else   
    return NULL;  
}

vector<GenericData*> SimInfo::getProperties(){

  vector<GenericData*> result;
  map<string, GenericData*>::iterator i;
  
  for(i = properties.begin(); i != properties.end(); i++)
    result.push_back((*i).second);
    
  return result;
}

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

  return trace;
}
Revision:	855
Committed:	Thu Nov 6 22:01:37 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	15332 byte(s)
Log Message:	added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
#	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
24	mmeineke	377	SimInfo* currentInfo;
25
26			SimInfo::SimInfo(){
27			excludes = NULL;
28			n_constraints = 0;
29	tim	699	nZconstraints = 0;
30	mmeineke	377	n_oriented = 0;
31			n_dipoles = 0;
32	gezelter	458	ndf = 0;
33			ndfRaw = 0;
34	mmeineke	674	nZconstraints = 0;
35	mmeineke	377	the_integrator = NULL;
36			setTemp = 0;
37			thermalTime = 0.0;
38	mmeineke	642	currentTime = 0.0;
39	mmeineke	420	rCut = 0.0;
40	mmeineke	690	origRcut = -1.0;
41	mmeineke	618	ecr = 0.0;
42	mmeineke	690	origEcr = -1.0;
43	mmeineke	619	est = 0.0;
44	mmeineke	626	oldEcr = 0.0;
45			oldRcut = 0.0;
46	mmeineke	377
47	mmeineke	626	haveOrigRcut = 0;
48			haveOrigEcr = 0;
49			boxIsInit = 0;
50
51	tim	781	resetTime = 1e99;
52	mmeineke	626
53	mmeineke	855	orthoTolerance = 1E-6;
54			useInitXSstate = true;
55
56	mmeineke	377	usePBC = 0;
57			useLJ = 0;
58			useSticky = 0;
59			useDipole = 0;
60			useReactionField = 0;
61			useGB = 0;
62			useEAM = 0;
63
64	mmeineke	670	myConfiguration = new SimState();
65
66	gezelter	457	wrapMeSimInfo( this );
67			}
68	mmeineke	377
69	mmeineke	670
70	tim	660	SimInfo::~SimInfo(){
71
72	mmeineke	670	delete myConfiguration;
73
74	tim	660	map<string, GenericData*>::iterator i;
75
76			for(i = properties.begin(); i != properties.end(); i++)
77			delete (*i).second;
78	mmeineke	670
79	tim	660	}
80
81	gezelter	457	void SimInfo::setBox(double newBox[3]) {
82	mmeineke	586
83	gezelter	588	int i, j;
84			double tempMat[3][3];
85	gezelter	463
86	gezelter	588	for(i=0; i<3; i++)
87			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
88	gezelter	463
89	gezelter	588	tempMat[0][0] = newBox[0];
90			tempMat[1][1] = newBox[1];
91			tempMat[2][2] = newBox[2];
92	gezelter	463
93	mmeineke	586	setBoxM( tempMat );
94	mmeineke	568
95	gezelter	457	}
96	mmeineke	377
97	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
98	mmeineke	568
99	mmeineke	787	int i, j;
100	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
101			// ordering in the array is as follows:
102			// [ 0 3 6 ]
103			// [ 1 4 7 ]
104			// [ 2 5 8 ]
105			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106	mmeineke	568
107	mmeineke	626
108			if( !boxIsInit ) boxIsInit = 1;
109	mmeineke	586
110	gezelter	588	for(i=0; i < 3; i++)
111			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
112
113	mmeineke	568	calcBoxL();
114	gezelter	588	calcHmatInv();
115	mmeineke	568
116	gezelter	588	for(i=0; i < 3; i++) {
117			for (j=0; j < 3; j++) {
118			FortranHmat[3*j + i] = Hmat[i][j];
119			FortranHmatInv[3*j + i] = HmatInv[i][j];
120			}
121			}
122	mmeineke	586
123	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
124	mmeineke	568
125	mmeineke	377	}
126	gezelter	458
127	mmeineke	568
128	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
129	mmeineke	568
130	gezelter	588	int i, j;
131			for(i=0; i<3; i++)
132			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
133	mmeineke	568	}
134
135	gezelter	574
136			void SimInfo::scaleBox(double scale) {
137	gezelter	588	double theBox[3][3];
138			int i, j;
139	gezelter	574
140	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
141	mmeineke	586
142	gezelter	588	for(i=0; i<3; i++)
143			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
144	gezelter	574
145			setBoxM(theBox);
146
147			}
148
149	gezelter	588	void SimInfo::calcHmatInv( void ) {
150	mmeineke	590
151	mmeineke	853	int oldOrtho;
152	mmeineke	590	int i,j;
153	mmeineke	569	double smallDiag;
154			double tol;
155			double sanity[3][3];
156	mmeineke	568
157	gezelter	588	invertMat3( Hmat, HmatInv );
158	mmeineke	568
159	gezelter	588	// check to see if Hmat is orthorhombic
160	mmeineke	568
161	mmeineke	853	oldOrtho = orthoRhombic;
162
163			smallDiag = fabs(Hmat[0][0]);
164			if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165			if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166	mmeineke	855	tol = smallDiag * orthoTolerance;
167	mmeineke	568
168	gezelter	588	orthoRhombic = 1;
169	mmeineke	568
170	gezelter	588	for (i = 0; i < 3; i++ ) {
171			for (j = 0 ; j < 3; j++) {
172			if (i != j) {
173			if (orthoRhombic) {
174	mmeineke	853	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175	gezelter	588	}
176			}
177	mmeineke	568	}
178			}
179	mmeineke	853
180			if( oldOrtho != orthoRhombic ){
181
182			if( orthoRhombic ){
183			sprintf( painCave.errMsg,
184			"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
186			orthoTolerance);
187	mmeineke	853	simError();
188			}
189			else {
190			sprintf( painCave.errMsg,
191			"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
192	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
193			orthoTolerance);
194	mmeineke	853	simError();
195			}
196			}
197	gezelter	588	}
198	mmeineke	569
199	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
200			int i, j, k;
201			double determinant;
202	mmeineke	569
203	gezelter	588	determinant = 0.0;
204
205			for(i = 0; i < 3; i++) {
206			j = (i+1)%3;
207			k = (i+2)%3;
208
209			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
210	mmeineke	569	}
211
212	gezelter	588	return determinant;
213			}
214	mmeineke	569
215	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216	mmeineke	569
217	gezelter	588	int i, j, k, l, m, n;
218			double determinant;
219	mmeineke	569
220	gezelter	588	determinant = matDet3( a );
221
222			if (determinant == 0.0) {
223			sprintf( painCave.errMsg,
224			"Can't invert a matrix with a zero determinant!\n");
225			painCave.isFatal = 1;
226			simError();
227			}
228
229			for (i=0; i < 3; i++) {
230			j = (i+1)%3;
231			k = (i+2)%3;
232			for(l = 0; l < 3; l++) {
233			m = (l+1)%3;
234			n = (l+2)%3;
235
236			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
237	mmeineke	569	}
238			}
239	mmeineke	568	}
240
241	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
242			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
243
244			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
245			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
246			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
247
248			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
249			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
250			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
251
252			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
253			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
254			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
255
256			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
257			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
258			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
259			}
260
261			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
262			double a0, a1, a2;
263
264			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
265
266			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
267			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
268			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
269			}
270	mmeineke	597
271			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272			double temp[3][3];
273			int i, j;
274
275			for (i = 0; i < 3; i++) {
276			for (j = 0; j < 3; j++) {
277			temp[j][i] = in[i][j];
278			}
279			}
280			for (i = 0; i < 3; i++) {
281			for (j = 0; j < 3; j++) {
282			out[i][j] = temp[i][j];
283			}
284			}
285			}
286	gezelter	588
287	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
288
289			std::cerr
290			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293			}
294
295			void SimInfo::printMat9(double A[9] ){
296
297			std::cerr
298			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301			}
302
303	tim	781
304			void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
305
306			out[0] = a[1] * b[2] - a[2] * b[1];
307			out[1] = a[2] * b[0] - a[0] * b[2] ;
308			out[2] = a[0] * b[1] - a[1] * b[0];
309
310			}
311
312			double SimInfo::dotProduct3(double a[3], double b[3]){
313			return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
314			}
315
316			double SimInfo::length3(double a[3]){
317			return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
318			}
319
320	mmeineke	568	void SimInfo::calcBoxL( void ){
321
322			double dx, dy, dz, dsq;
323
324	gezelter	588	// boxVol = Determinant of Hmat
325	mmeineke	568
326	gezelter	588	boxVol = matDet3( Hmat );
327	mmeineke	568
328			// boxLx
329
330	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
331	mmeineke	568	dsq = dxdx + dydy + dz*dz;
332	gezelter	621	boxL[0] = sqrt( dsq );
333	tim	781	//maxCutoff = 0.5 * boxL[0];
334	mmeineke	568
335			// boxLy
336
337	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
338	mmeineke	568	dsq = dxdx + dydy + dz*dz;
339	gezelter	621	boxL[1] = sqrt( dsq );
340	tim	781	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341	mmeineke	568
342	tim	781
343	mmeineke	568	// boxLz
344
345	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
346	mmeineke	568	dsq = dxdx + dydy + dz*dz;
347	gezelter	621	boxL[2] = sqrt( dsq );
348	tim	781	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349
350			//calculate the max cutoff
351			maxCutoff = calcMaxCutOff();
352	chuckv	669
353			checkCutOffs();
354	mmeineke	626
355	mmeineke	568	}
356
357
358	tim	781	double SimInfo::calcMaxCutOff(){
359
360			double ri[3], rj[3], rk[3];
361			double rij[3], rjk[3], rki[3];
362			double minDist;
363
364			ri[0] = Hmat[0][0];
365			ri[1] = Hmat[1][0];
366			ri[2] = Hmat[2][0];
367
368			rj[0] = Hmat[0][1];
369			rj[1] = Hmat[1][1];
370			rj[2] = Hmat[2][1];
371
372			rk[0] = Hmat[0][2];
373			rk[1] = Hmat[1][2];
374			rk[2] = Hmat[2][2];
375
376			crossProduct3(ri,rj, rij);
377			distXY = dotProduct3(rk,rij) / length3(rij);
378
379			crossProduct3(rj,rk, rjk);
380			distYZ = dotProduct3(ri,rjk) / length3(rjk);
381
382			crossProduct3(rk,ri, rki);
383			distZX = dotProduct3(rj,rki) / length3(rki);
384
385			minDist = min(min(distXY, distYZ), distZX);
386			return minDist/2;
387
388			}
389
390	mmeineke	568	void SimInfo::wrapVector( double thePos[3] ){
391
392	mmeineke	787	int i;
393	mmeineke	568	double scaled[3];
394
395	mmeineke	569	if( !orthoRhombic ){
396			// calc the scaled coordinates.
397	gezelter	588
398
399			matVecMul3(HmatInv, thePos, scaled);
400	mmeineke	569
401			for(i=0; i<3; i++)
402	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
403	mmeineke	569
404			// calc the wrapped real coordinates from the wrapped scaled coordinates
405
406	gezelter	588	matVecMul3(Hmat, scaled, thePos);
407
408	mmeineke	569	}
409			else{
410			// calc the scaled coordinates.
411
412			for(i=0; i<3; i++)
413	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
414	mmeineke	569
415			// wrap the scaled coordinates
416
417			for(i=0; i<3; i++)
418	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
419	mmeineke	569
420			// calc the wrapped real coordinates from the wrapped scaled coordinates
421
422			for(i=0; i<3; i++)
423	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
424	mmeineke	569	}
425
426	mmeineke	568	}
427
428
429	gezelter	458	int SimInfo::getNDF(){
430	mmeineke	790	int ndf_local;
431	gezelter	457
432	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
433
434			#ifdef IS_MPI
435			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
436			#else
437			ndf = ndf_local;
438			#endif
439
440	mmeineke	674	ndf = ndf - 3 - nZconstraints;
441	gezelter	458
442			return ndf;
443			}
444
445			int SimInfo::getNDFraw() {
446	mmeineke	790	int ndfRaw_local;
447	gezelter	458
448			// Raw degrees of freedom that we have to set
449			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
450
451			#ifdef IS_MPI
452			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
453			#else
454			ndfRaw = ndfRaw_local;
455			#endif
456
457			return ndfRaw;
458			}
459	tim	767
460			int SimInfo::getNDFtranslational() {
461	mmeineke	790	int ndfTrans_local;
462	tim	767
463			ndfTrans_local = 3 * n_atoms - n_constraints;
464
465			#ifdef IS_MPI
466			MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
467			#else
468			ndfTrans = ndfTrans_local;
469			#endif
470
471			ndfTrans = ndfTrans - 3 - nZconstraints;
472
473			return ndfTrans;
474			}
475
476	mmeineke	377	void SimInfo::refreshSim(){
477
478			simtype fInfo;
479			int isError;
480	gezelter	490	int n_global;
481	mmeineke	424	int* excl;
482	mmeineke	626
483	mmeineke	469	fInfo.dielect = 0.0;
484	mmeineke	377
485	mmeineke	469	if( useDipole ){
486			if( useReactionField )fInfo.dielect = dielectric;
487			}
488
489	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
490	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
491	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
492	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
493			//fInfo.SIM_uses_sticky = 0;
494	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
495			//fInfo.SIM_uses_dipoles = 0;
496	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
497			fInfo.SIM_uses_RF = 0;
498	mmeineke	377	fInfo.SIM_uses_GB = useGB;
499			fInfo.SIM_uses_EAM = useEAM;
500
501	mmeineke	424	excl = Exclude::getArray();
502	mmeineke	377
503	gezelter	490	#ifdef IS_MPI
504			n_global = mpiSim->getTotAtoms();
505			#else
506			n_global = n_atoms;
507			#endif
508
509	mmeineke	377	isError = 0;
510
511	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
512	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
513			&isError );
514	mmeineke	377
515			if( isError ){
516
517			sprintf( painCave.errMsg,
518			"There was an error setting the simulation information in fortran.\n" );
519			painCave.isFatal = 1;
520			simError();
521			}
522
523			#ifdef IS_MPI
524			sprintf( checkPointMsg,
525			"succesfully sent the simulation information to fortran.\n");
526			MPIcheckPoint();
527			#endif // is_mpi
528	gezelter	458
529	gezelter	474	this->ndf = this->getNDF();
530			this->ndfRaw = this->getNDFraw();
531	tim	767	this->ndfTrans = this->getNDFtranslational();
532	mmeineke	377	}
533
534	mmeineke	626
535			void SimInfo::setRcut( double theRcut ){
536
537			rCut = theRcut;
538			checkCutOffs();
539			}
540
541	mmeineke	841	void SimInfo::setDefaultRcut( double theRcut ){
542
543			haveOrigRcut = 1;
544			origRcut = theRcut;
545			rCut = theRcut;
546	mmeineke	843
547	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548
549	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550	mmeineke	841	}
551
552	mmeineke	626	void SimInfo::setEcr( double theEcr ){
553
554			ecr = theEcr;
555			checkCutOffs();
556			}
557
558	mmeineke	841	void SimInfo::setDefaultEcr( double theEcr ){
559
560			haveOrigEcr = 1;
561			origEcr = theEcr;
562
563	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564
565	mmeineke	841	ecr = theEcr;
566	gezelter	845
567	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
568	mmeineke	841	}
569
570	mmeineke	626	void SimInfo::setEcr( double theEcr, double theEst ){
571
572			est = theEst;
573			setEcr( theEcr );
574			}
575
576	mmeineke	841	void SimInfo::setDefaultEcr( double theEcr, double theEst ){
577	mmeineke	626
578	mmeineke	841	est = theEst;
579			setDefaultEcr( theEcr );
580			}
581
582
583	mmeineke	626	void SimInfo::checkCutOffs( void ){
584
585			int cutChanged = 0;
586	gezelter	770
587	mmeineke	626	if( boxIsInit ){
588
589			//we need to check cutOffs against the box
590	tim	781
591			//detect the change of rCut
592	chuckv	669	if(( maxCutoff > rCut )&&(usePBC)){
593	mmeineke	626	if( rCut < origRcut ){
594	tim	781	rCut = origRcut;
595
596			if (rCut > maxCutoff)
597			rCut = maxCutoff;
598
599			sprintf( painCave.errMsg,
600			"New Box size is setting the long range cutoff radius "
601			"to %lf at time %lf\n",
602			rCut, currentTime );
603			painCave.isFatal = 0;
604			simError();
605	mmeineke	626	}
606			}
607	tim	781	else if ((rCut > maxCutoff)&&(usePBC)) {
608	mmeineke	626	sprintf( painCave.errMsg,
609			"New Box size is setting the long range cutoff radius "
610	tim	781	"to %lf at time %lf\n",
611	gezelter	770	maxCutoff, currentTime );
612	mmeineke	626	painCave.isFatal = 0;
613			simError();
614			rCut = maxCutoff;
615			}
616	tim	781
617
618			//detect the change of ecr
619			if( maxCutoff > ecr ){
620			if( ecr < origEcr ){
621			ecr = origEcr;
622			if (ecr > maxCutoff) ecr = maxCutoff;
623
624			sprintf( painCave.errMsg,
625			"New Box size is setting the electrostaticCutoffRadius "
626			"to %lf at time %lf\n",
627			ecr, currentTime );
628			painCave.isFatal = 0;
629			simError();
630			}
631			}
632			else if( ecr > maxCutoff){
633	mmeineke	626	sprintf( painCave.errMsg,
634			"New Box size is setting the electrostaticCutoffRadius "
635	gezelter	770	"to %lf at time %lf\n",
636			maxCutoff, currentTime );
637	mmeineke	626	painCave.isFatal = 0;
638			simError();
639			ecr = maxCutoff;
640			}
641
642	tim	767	if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
643	gezelter	770
644	tim	767	// rlist is the 1.0 plus max( rcut, ecr )
645	mmeineke	626
646	tim	767	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647
648			if( cutChanged ){
649			notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650			}
651
652			oldEcr = ecr;
653			oldRcut = rCut;
654	gezelter	770
655	tim	767	} else {
656			// initialize this stuff before using it, OK?
657	gezelter	770	sprintf( painCave.errMsg,
658			"Trying to check cutoffs without a box. Be smarter.\n" );
659			painCave.isFatal = 1;
660			simError();
661	mmeineke	626	}
662	gezelter	770
663	mmeineke	626	}
664	tim	658
665			void SimInfo::addProperty(GenericData* prop){
666
667			map<string, GenericData*>::iterator result;
668			result = properties.find(prop->getID());
669
670			//we can't simply use properties[prop->getID()] = prop,
671			//it will cause memory leak if we already contain a propery which has the same name of prop
672
673			if(result != properties.end()){
674
675			delete (*result).second;
676			(*result).second = prop;
677
678			}
679			else{
680
681			properties[prop->getID()] = prop;
682
683			}
684
685			}
686
687			GenericData* SimInfo::getProperty(const string& propName){
688
689			map<string, GenericData*>::iterator result;
690
691			//string lowerCaseName = ();
692
693			result = properties.find(propName);
694
695			if(result != properties.end())
696			return (*result).second;
697			else
698			return NULL;
699			}
700
701			vector<GenericData*> SimInfo::getProperties(){
702
703			vector<GenericData*> result;
704			map<string, GenericData*>::iterator i;
705
706			for(i = properties.begin(); i != properties.end(); i++)
707			result.push_back((*i).second);
708
709			return result;
710			}
711
712	tim	763	double SimInfo::matTrace3(double m[3][3]){
713			double trace;
714			trace = m[0][0] + m[1][1] + m[2][2];
715	tim	658
716	tim	763	return trace;
717			}