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;
  

  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 * 1E-6;

  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 ortho tolerance in SimInfo.\n" );
      simError();
    }
    else {
      sprintf( painCave.errMsg,
               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
      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:	853
Committed:	Thu Nov 6 19:11:38 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	15212 byte(s)
Log Message:	did a merge by hand from the new-templateless branch to the main trunk. bug Fixes include: * fixed the switching function from ortho to non-ortho box. !!!!! THis was responsible for all of the sudden deaths we saw. * some formating in the string when we write out the extended system state. * added NPT.cpp to the makefile.in
#	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
54	mmeineke	377	usePBC = 0;
55			useLJ = 0;
56			useSticky = 0;
57			useDipole = 0;
58			useReactionField = 0;
59			useGB = 0;
60			useEAM = 0;
61
62	mmeineke	670	myConfiguration = new SimState();
63
64	gezelter	457	wrapMeSimInfo( this );
65			}
66	mmeineke	377
67	mmeineke	670
68	tim	660	SimInfo::~SimInfo(){
69
70	mmeineke	670	delete myConfiguration;
71
72	tim	660	map<string, GenericData*>::iterator i;
73
74			for(i = properties.begin(); i != properties.end(); i++)
75			delete (*i).second;
76	mmeineke	670
77	tim	660	}
78
79	gezelter	457	void SimInfo::setBox(double newBox[3]) {
80	mmeineke	586
81	gezelter	588	int i, j;
82			double tempMat[3][3];
83	gezelter	463
84	gezelter	588	for(i=0; i<3; i++)
85			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
86	gezelter	463
87	gezelter	588	tempMat[0][0] = newBox[0];
88			tempMat[1][1] = newBox[1];
89			tempMat[2][2] = newBox[2];
90	gezelter	463
91	mmeineke	586	setBoxM( tempMat );
92	mmeineke	568
93	gezelter	457	}
94	mmeineke	377
95	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
96	mmeineke	568
97	mmeineke	787	int i, j;
98	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
99			// ordering in the array is as follows:
100			// [ 0 3 6 ]
101			// [ 1 4 7 ]
102			// [ 2 5 8 ]
103			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
104	mmeineke	568
105	mmeineke	626
106			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	gezelter	588	tol = smallDiag * 1E-6;
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			" If this is a bad thing change the ortho tolerance in SimInfo.\n" );
184			simError();
185			}
186			else {
187			sprintf( painCave.errMsg,
188			"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
189			" If this is a bad thing change the ortho tolerance in SimInfo.\n" );
190			simError();
191			}
192			}
193	gezelter	588	}
194	mmeineke	569
195	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
196			int i, j, k;
197			double determinant;
198	mmeineke	569
199	gezelter	588	determinant = 0.0;
200
201			for(i = 0; i < 3; i++) {
202			j = (i+1)%3;
203			k = (i+2)%3;
204
205			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
206	mmeineke	569	}
207
208	gezelter	588	return determinant;
209			}
210	mmeineke	569
211	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212	mmeineke	569
213	gezelter	588	int i, j, k, l, m, n;
214			double determinant;
215	mmeineke	569
216	gezelter	588	determinant = matDet3( a );
217
218			if (determinant == 0.0) {
219			sprintf( painCave.errMsg,
220			"Can't invert a matrix with a zero determinant!\n");
221			painCave.isFatal = 1;
222			simError();
223			}
224
225			for (i=0; i < 3; i++) {
226			j = (i+1)%3;
227			k = (i+2)%3;
228			for(l = 0; l < 3; l++) {
229			m = (l+1)%3;
230			n = (l+2)%3;
231
232			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
233	mmeineke	569	}
234			}
235	mmeineke	568	}
236
237	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239
240			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
241			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
242			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
243
244			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
245			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
246			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
247
248			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
249			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
250			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
251
252			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255			}
256
257			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258			double a0, a1, a2;
259
260			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
261
262			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
263			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
264			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
265			}
266	mmeineke	597
267			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268			double temp[3][3];
269			int i, j;
270
271			for (i = 0; i < 3; i++) {
272			for (j = 0; j < 3; j++) {
273			temp[j][i] = in[i][j];
274			}
275			}
276			for (i = 0; i < 3; i++) {
277			for (j = 0; j < 3; j++) {
278			out[i][j] = temp[i][j];
279			}
280			}
281			}
282	gezelter	588
283	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
284
285			std::cerr
286			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289			}
290
291			void SimInfo::printMat9(double A[9] ){
292
293			std::cerr
294			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297			}
298
299	tim	781
300			void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301
302			out[0] = a[1] * b[2] - a[2] * b[1];
303			out[1] = a[2] * b[0] - a[0] * b[2] ;
304			out[2] = a[0] * b[1] - a[1] * b[0];
305
306			}
307
308			double SimInfo::dotProduct3(double a[3], double b[3]){
309			return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
310			}
311
312			double SimInfo::length3(double a[3]){
313			return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
314			}
315
316	mmeineke	568	void SimInfo::calcBoxL( void ){
317
318			double dx, dy, dz, dsq;
319
320	gezelter	588	// boxVol = Determinant of Hmat
321	mmeineke	568
322	gezelter	588	boxVol = matDet3( Hmat );
323	mmeineke	568
324			// boxLx
325
326	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
327	mmeineke	568	dsq = dxdx + dydy + dz*dz;
328	gezelter	621	boxL[0] = sqrt( dsq );
329	tim	781	//maxCutoff = 0.5 * boxL[0];
330	mmeineke	568
331			// boxLy
332
333	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
334	mmeineke	568	dsq = dxdx + dydy + dz*dz;
335	gezelter	621	boxL[1] = sqrt( dsq );
336	tim	781	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
337	mmeineke	568
338	tim	781
339	mmeineke	568	// boxLz
340
341	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
342	mmeineke	568	dsq = dxdx + dydy + dz*dz;
343	gezelter	621	boxL[2] = sqrt( dsq );
344	tim	781	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
345
346			//calculate the max cutoff
347			maxCutoff = calcMaxCutOff();
348	chuckv	669
349			checkCutOffs();
350	mmeineke	626
351	mmeineke	568	}
352
353
354	tim	781	double SimInfo::calcMaxCutOff(){
355
356			double ri[3], rj[3], rk[3];
357			double rij[3], rjk[3], rki[3];
358			double minDist;
359
360			ri[0] = Hmat[0][0];
361			ri[1] = Hmat[1][0];
362			ri[2] = Hmat[2][0];
363
364			rj[0] = Hmat[0][1];
365			rj[1] = Hmat[1][1];
366			rj[2] = Hmat[2][1];
367
368			rk[0] = Hmat[0][2];
369			rk[1] = Hmat[1][2];
370			rk[2] = Hmat[2][2];
371
372			crossProduct3(ri,rj, rij);
373			distXY = dotProduct3(rk,rij) / length3(rij);
374
375			crossProduct3(rj,rk, rjk);
376			distYZ = dotProduct3(ri,rjk) / length3(rjk);
377
378			crossProduct3(rk,ri, rki);
379			distZX = dotProduct3(rj,rki) / length3(rki);
380
381			minDist = min(min(distXY, distYZ), distZX);
382			return minDist/2;
383
384			}
385
386	mmeineke	568	void SimInfo::wrapVector( double thePos[3] ){
387
388	mmeineke	787	int i;
389	mmeineke	568	double scaled[3];
390
391	mmeineke	569	if( !orthoRhombic ){
392			// calc the scaled coordinates.
393	gezelter	588
394
395			matVecMul3(HmatInv, thePos, scaled);
396	mmeineke	569
397			for(i=0; i<3; i++)
398	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
399	mmeineke	569
400			// calc the wrapped real coordinates from the wrapped scaled coordinates
401
402	gezelter	588	matVecMul3(Hmat, scaled, thePos);
403
404	mmeineke	569	}
405			else{
406			// calc the scaled coordinates.
407
408			for(i=0; i<3; i++)
409	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
410	mmeineke	569
411			// wrap the scaled coordinates
412
413			for(i=0; i<3; i++)
414	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
415	mmeineke	569
416			// calc the wrapped real coordinates from the wrapped scaled coordinates
417
418			for(i=0; i<3; i++)
419	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
420	mmeineke	569	}
421
422	mmeineke	568	}
423
424
425	gezelter	458	int SimInfo::getNDF(){
426	mmeineke	790	int ndf_local;
427	gezelter	457
428	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429
430			#ifdef IS_MPI
431			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
432			#else
433			ndf = ndf_local;
434			#endif
435
436	mmeineke	674	ndf = ndf - 3 - nZconstraints;
437	gezelter	458
438			return ndf;
439			}
440
441			int SimInfo::getNDFraw() {
442	mmeineke	790	int ndfRaw_local;
443	gezelter	458
444			// Raw degrees of freedom that we have to set
445			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
446
447			#ifdef IS_MPI
448			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
449			#else
450			ndfRaw = ndfRaw_local;
451			#endif
452
453			return ndfRaw;
454			}
455	tim	767
456			int SimInfo::getNDFtranslational() {
457	mmeineke	790	int ndfTrans_local;
458	tim	767
459			ndfTrans_local = 3 * n_atoms - n_constraints;
460
461			#ifdef IS_MPI
462			MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
463			#else
464			ndfTrans = ndfTrans_local;
465			#endif
466
467			ndfTrans = ndfTrans - 3 - nZconstraints;
468
469			return ndfTrans;
470			}
471
472	mmeineke	377	void SimInfo::refreshSim(){
473
474			simtype fInfo;
475			int isError;
476	gezelter	490	int n_global;
477	mmeineke	424	int* excl;
478	mmeineke	626
479	mmeineke	469	fInfo.dielect = 0.0;
480	mmeineke	377
481	mmeineke	469	if( useDipole ){
482			if( useReactionField )fInfo.dielect = dielectric;
483			}
484
485	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
486	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
487	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
488	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
489			//fInfo.SIM_uses_sticky = 0;
490	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
491			//fInfo.SIM_uses_dipoles = 0;
492	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
493			fInfo.SIM_uses_RF = 0;
494	mmeineke	377	fInfo.SIM_uses_GB = useGB;
495			fInfo.SIM_uses_EAM = useEAM;
496
497	mmeineke	424	excl = Exclude::getArray();
498	mmeineke	377
499	gezelter	490	#ifdef IS_MPI
500			n_global = mpiSim->getTotAtoms();
501			#else
502			n_global = n_atoms;
503			#endif
504
505	mmeineke	377	isError = 0;
506
507	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
508	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
509			&isError );
510	mmeineke	377
511			if( isError ){
512
513			sprintf( painCave.errMsg,
514			"There was an error setting the simulation information in fortran.\n" );
515			painCave.isFatal = 1;
516			simError();
517			}
518
519			#ifdef IS_MPI
520			sprintf( checkPointMsg,
521			"succesfully sent the simulation information to fortran.\n");
522			MPIcheckPoint();
523			#endif // is_mpi
524	gezelter	458
525	gezelter	474	this->ndf = this->getNDF();
526			this->ndfRaw = this->getNDFraw();
527	tim	767	this->ndfTrans = this->getNDFtranslational();
528	mmeineke	377	}
529
530	mmeineke	626
531			void SimInfo::setRcut( double theRcut ){
532
533			rCut = theRcut;
534			checkCutOffs();
535			}
536
537	mmeineke	841	void SimInfo::setDefaultRcut( double theRcut ){
538
539			haveOrigRcut = 1;
540			origRcut = theRcut;
541			rCut = theRcut;
542	mmeineke	843
543	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544
545	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546	mmeineke	841	}
547
548	mmeineke	626	void SimInfo::setEcr( double theEcr ){
549
550			ecr = theEcr;
551			checkCutOffs();
552			}
553
554	mmeineke	841	void SimInfo::setDefaultEcr( double theEcr ){
555
556			haveOrigEcr = 1;
557			origEcr = theEcr;
558
559	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560
561	mmeineke	841	ecr = theEcr;
562	gezelter	845
563	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
564	mmeineke	841	}
565
566	mmeineke	626	void SimInfo::setEcr( double theEcr, double theEst ){
567
568			est = theEst;
569			setEcr( theEcr );
570			}
571
572	mmeineke	841	void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573	mmeineke	626
574	mmeineke	841	est = theEst;
575			setDefaultEcr( theEcr );
576			}
577
578
579	mmeineke	626	void SimInfo::checkCutOffs( void ){
580
581			int cutChanged = 0;
582	gezelter	770
583	mmeineke	626	if( boxIsInit ){
584
585			//we need to check cutOffs against the box
586	tim	781
587			//detect the change of rCut
588	chuckv	669	if(( maxCutoff > rCut )&&(usePBC)){
589	mmeineke	626	if( rCut < origRcut ){
590	tim	781	rCut = origRcut;
591
592			if (rCut > maxCutoff)
593			rCut = maxCutoff;
594
595			sprintf( painCave.errMsg,
596			"New Box size is setting the long range cutoff radius "
597			"to %lf at time %lf\n",
598			rCut, currentTime );
599			painCave.isFatal = 0;
600			simError();
601	mmeineke	626	}
602			}
603	tim	781	else if ((rCut > maxCutoff)&&(usePBC)) {
604	mmeineke	626	sprintf( painCave.errMsg,
605			"New Box size is setting the long range cutoff radius "
606	tim	781	"to %lf at time %lf\n",
607	gezelter	770	maxCutoff, currentTime );
608	mmeineke	626	painCave.isFatal = 0;
609			simError();
610			rCut = maxCutoff;
611			}
612	tim	781
613
614			//detect the change of ecr
615			if( maxCutoff > ecr ){
616			if( ecr < origEcr ){
617			ecr = origEcr;
618			if (ecr > maxCutoff) ecr = maxCutoff;
619
620			sprintf( painCave.errMsg,
621			"New Box size is setting the electrostaticCutoffRadius "
622			"to %lf at time %lf\n",
623			ecr, currentTime );
624			painCave.isFatal = 0;
625			simError();
626			}
627			}
628			else if( ecr > maxCutoff){
629	mmeineke	626	sprintf( painCave.errMsg,
630			"New Box size is setting the electrostaticCutoffRadius "
631	gezelter	770	"to %lf at time %lf\n",
632			maxCutoff, currentTime );
633	mmeineke	626	painCave.isFatal = 0;
634			simError();
635			ecr = maxCutoff;
636			}
637
638	tim	767	if( (oldEcr != ecr) \|\| ( oldRcut != rCut ) ) cutChanged = 1;
639	gezelter	770
640	tim	767	// rlist is the 1.0 plus max( rcut, ecr )
641	mmeineke	626
642	tim	767	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643
644			if( cutChanged ){
645			notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646			}
647
648			oldEcr = ecr;
649			oldRcut = rCut;
650	gezelter	770
651	tim	767	} else {
652			// initialize this stuff before using it, OK?
653	gezelter	770	sprintf( painCave.errMsg,
654			"Trying to check cutoffs without a box. Be smarter.\n" );
655			painCave.isFatal = 1;
656			simError();
657	mmeineke	626	}
658	gezelter	770
659	mmeineke	626	}
660	tim	658
661			void SimInfo::addProperty(GenericData* prop){
662
663			map<string, GenericData*>::iterator result;
664			result = properties.find(prop->getID());
665
666			//we can't simply use properties[prop->getID()] = prop,
667			//it will cause memory leak if we already contain a propery which has the same name of prop
668
669			if(result != properties.end()){
670
671			delete (*result).second;
672			(*result).second = prop;
673
674			}
675			else{
676
677			properties[prop->getID()] = prop;
678
679			}
680
681			}
682
683			GenericData* SimInfo::getProperty(const string& propName){
684
685			map<string, GenericData*>::iterator result;
686
687			//string lowerCaseName = ();
688
689			result = properties.find(propName);
690
691			if(result != properties.end())
692			return (*result).second;
693			else
694			return NULL;
695			}
696
697			vector<GenericData*> SimInfo::getProperties(){
698
699			vector<GenericData*> result;
700			map<string, GenericData*>::iterator i;
701
702			for(i = properties.begin(); i != properties.end(); i++)
703			result.push_back((*i).second);
704
705			return result;
706			}
707
708	tim	763	double SimInfo::matTrace3(double m[3][3]){
709			double trace;
710			trace = m[0][0] + m[1][1] + m[2][2];
711	tim	658
712	tim	763	return trace;
713			}