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;
  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:	859
Committed:	Mon Nov 10 21:50:36 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	13601 byte(s)
Log Message:	reordered the rcut/ecr/boxSize initialization removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
#	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	618	ecr = 0.0;
41	mmeineke	619	est = 0.0;
42	mmeineke	377
43	mmeineke	859	haveRcut = 0;
44			haveEcr = 0;
45	mmeineke	626	boxIsInit = 0;
46
47	tim	781	resetTime = 1e99;
48	mmeineke	626
49	mmeineke	855	orthoTolerance = 1E-6;
50			useInitXSstate = true;
51
52	mmeineke	377	usePBC = 0;
53			useLJ = 0;
54			useSticky = 0;
55			useDipole = 0;
56			useReactionField = 0;
57			useGB = 0;
58			useEAM = 0;
59
60	mmeineke	670	myConfiguration = new SimState();
61
62	gezelter	457	wrapMeSimInfo( this );
63			}
64	mmeineke	377
65	mmeineke	670
66	tim	660	SimInfo::~SimInfo(){
67
68	mmeineke	670	delete myConfiguration;
69
70	tim	660	map<string, GenericData*>::iterator i;
71
72			for(i = properties.begin(); i != properties.end(); i++)
73			delete (*i).second;
74	mmeineke	670
75	tim	660	}
76
77	gezelter	457	void SimInfo::setBox(double newBox[3]) {
78	mmeineke	586
79	gezelter	588	int i, j;
80			double tempMat[3][3];
81	gezelter	463
82	gezelter	588	for(i=0; i<3; i++)
83			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
84	gezelter	463
85	gezelter	588	tempMat[0][0] = newBox[0];
86			tempMat[1][1] = newBox[1];
87			tempMat[2][2] = newBox[2];
88	gezelter	463
89	mmeineke	586	setBoxM( tempMat );
90	mmeineke	568
91	gezelter	457	}
92	mmeineke	377
93	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
94	mmeineke	568
95	mmeineke	787	int i, j;
96	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
97			// ordering in the array is as follows:
98			// [ 0 3 6 ]
99			// [ 1 4 7 ]
100			// [ 2 5 8 ]
101			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102	mmeineke	568
103	mmeineke	626	if( !boxIsInit ) boxIsInit = 1;
104	mmeineke	586
105	gezelter	588	for(i=0; i < 3; i++)
106			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107
108	mmeineke	568	calcBoxL();
109	gezelter	588	calcHmatInv();
110	mmeineke	568
111	gezelter	588	for(i=0; i < 3; i++) {
112			for (j=0; j < 3; j++) {
113			FortranHmat[3*j + i] = Hmat[i][j];
114			FortranHmatInv[3*j + i] = HmatInv[i][j];
115			}
116			}
117	mmeineke	586
118	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119	mmeineke	568
120	mmeineke	377	}
121	gezelter	458
122	mmeineke	568
123	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
124	mmeineke	568
125	gezelter	588	int i, j;
126			for(i=0; i<3; i++)
127			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128	mmeineke	568	}
129
130	gezelter	574
131			void SimInfo::scaleBox(double scale) {
132	gezelter	588	double theBox[3][3];
133			int i, j;
134	gezelter	574
135	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
136	mmeineke	586
137	gezelter	588	for(i=0; i<3; i++)
138			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139	gezelter	574
140			setBoxM(theBox);
141
142			}
143
144	gezelter	588	void SimInfo::calcHmatInv( void ) {
145	mmeineke	590
146	mmeineke	853	int oldOrtho;
147	mmeineke	590	int i,j;
148	mmeineke	569	double smallDiag;
149			double tol;
150			double sanity[3][3];
151	mmeineke	568
152	gezelter	588	invertMat3( Hmat, HmatInv );
153	mmeineke	568
154	gezelter	588	// check to see if Hmat is orthorhombic
155	mmeineke	568
156	mmeineke	853	oldOrtho = orthoRhombic;
157
158			smallDiag = fabs(Hmat[0][0]);
159			if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
160			if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
161	mmeineke	855	tol = smallDiag * orthoTolerance;
162	mmeineke	568
163	gezelter	588	orthoRhombic = 1;
164	mmeineke	568
165	gezelter	588	for (i = 0; i < 3; i++ ) {
166			for (j = 0 ; j < 3; j++) {
167			if (i != j) {
168			if (orthoRhombic) {
169	mmeineke	853	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
170	gezelter	588	}
171			}
172	mmeineke	568	}
173			}
174	mmeineke	853
175			if( oldOrtho != orthoRhombic ){
176
177			if( orthoRhombic ){
178			sprintf( painCave.errMsg,
179			"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
180	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
181			orthoTolerance);
182	mmeineke	853	simError();
183			}
184			else {
185			sprintf( painCave.errMsg,
186			"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
187	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
188			orthoTolerance);
189	mmeineke	853	simError();
190			}
191			}
192	gezelter	588	}
193	mmeineke	569
194	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
195			int i, j, k;
196			double determinant;
197	mmeineke	569
198	gezelter	588	determinant = 0.0;
199
200			for(i = 0; i < 3; i++) {
201			j = (i+1)%3;
202			k = (i+2)%3;
203
204			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
205	mmeineke	569	}
206
207	gezelter	588	return determinant;
208			}
209	mmeineke	569
210	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
211	mmeineke	569
212	gezelter	588	int i, j, k, l, m, n;
213			double determinant;
214	mmeineke	569
215	gezelter	588	determinant = matDet3( a );
216
217			if (determinant == 0.0) {
218			sprintf( painCave.errMsg,
219			"Can't invert a matrix with a zero determinant!\n");
220			painCave.isFatal = 1;
221			simError();
222			}
223
224			for (i=0; i < 3; i++) {
225			j = (i+1)%3;
226			k = (i+2)%3;
227			for(l = 0; l < 3; l++) {
228			m = (l+1)%3;
229			n = (l+2)%3;
230
231			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
232	mmeineke	569	}
233			}
234	mmeineke	568	}
235
236	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
237			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
238
239			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
240			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
241			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
242
243			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
244			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
245			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
246
247			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
248			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
249			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
250
251			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
252			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
253			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
254			}
255
256			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
257			double a0, a1, a2;
258
259			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
260
261			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
262			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
263			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
264			}
265	mmeineke	597
266			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
267			double temp[3][3];
268			int i, j;
269
270			for (i = 0; i < 3; i++) {
271			for (j = 0; j < 3; j++) {
272			temp[j][i] = in[i][j];
273			}
274			}
275			for (i = 0; i < 3; i++) {
276			for (j = 0; j < 3; j++) {
277			out[i][j] = temp[i][j];
278			}
279			}
280			}
281	gezelter	588
282	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
283
284			std::cerr
285			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
286			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
287			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
288			}
289
290			void SimInfo::printMat9(double A[9] ){
291
292			std::cerr
293			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
294			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
295			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
296			}
297
298	tim	781
299			void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
300
301			out[0] = a[1] * b[2] - a[2] * b[1];
302			out[1] = a[2] * b[0] - a[0] * b[2] ;
303			out[2] = a[0] * b[1] - a[1] * b[0];
304
305			}
306
307			double SimInfo::dotProduct3(double a[3], double b[3]){
308			return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
309			}
310
311			double SimInfo::length3(double a[3]){
312			return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
313			}
314
315	mmeineke	568	void SimInfo::calcBoxL( void ){
316
317			double dx, dy, dz, dsq;
318
319	gezelter	588	// boxVol = Determinant of Hmat
320	mmeineke	568
321	gezelter	588	boxVol = matDet3( Hmat );
322	mmeineke	568
323			// boxLx
324
325	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
326	mmeineke	568	dsq = dxdx + dydy + dz*dz;
327	gezelter	621	boxL[0] = sqrt( dsq );
328	tim	781	//maxCutoff = 0.5 * boxL[0];
329	mmeineke	568
330			// boxLy
331
332	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
333	mmeineke	568	dsq = dxdx + dydy + dz*dz;
334	gezelter	621	boxL[1] = sqrt( dsq );
335	tim	781	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
336	mmeineke	568
337	tim	781
338	mmeineke	568	// boxLz
339
340	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
341	mmeineke	568	dsq = dxdx + dydy + dz*dz;
342	gezelter	621	boxL[2] = sqrt( dsq );
343	tim	781	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
344
345			//calculate the max cutoff
346			maxCutoff = calcMaxCutOff();
347	chuckv	669
348			checkCutOffs();
349	mmeineke	626
350	mmeineke	568	}
351
352
353	tim	781	double SimInfo::calcMaxCutOff(){
354
355			double ri[3], rj[3], rk[3];
356			double rij[3], rjk[3], rki[3];
357			double minDist;
358
359			ri[0] = Hmat[0][0];
360			ri[1] = Hmat[1][0];
361			ri[2] = Hmat[2][0];
362
363			rj[0] = Hmat[0][1];
364			rj[1] = Hmat[1][1];
365			rj[2] = Hmat[2][1];
366
367			rk[0] = Hmat[0][2];
368			rk[1] = Hmat[1][2];
369			rk[2] = Hmat[2][2];
370
371			crossProduct3(ri,rj, rij);
372			distXY = dotProduct3(rk,rij) / length3(rij);
373
374			crossProduct3(rj,rk, rjk);
375			distYZ = dotProduct3(ri,rjk) / length3(rjk);
376
377			crossProduct3(rk,ri, rki);
378			distZX = dotProduct3(rj,rki) / length3(rki);
379
380			minDist = min(min(distXY, distYZ), distZX);
381			return minDist/2;
382
383			}
384
385	mmeineke	568	void SimInfo::wrapVector( double thePos[3] ){
386
387	mmeineke	787	int i;
388	mmeineke	568	double scaled[3];
389
390	mmeineke	569	if( !orthoRhombic ){
391			// calc the scaled coordinates.
392	gezelter	588
393
394			matVecMul3(HmatInv, thePos, scaled);
395	mmeineke	569
396			for(i=0; i<3; i++)
397	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
398	mmeineke	569
399			// calc the wrapped real coordinates from the wrapped scaled coordinates
400
401	gezelter	588	matVecMul3(Hmat, scaled, thePos);
402
403	mmeineke	569	}
404			else{
405			// calc the scaled coordinates.
406
407			for(i=0; i<3; i++)
408	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
409	mmeineke	569
410			// wrap the scaled coordinates
411
412			for(i=0; i<3; i++)
413	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
414	mmeineke	569
415			// calc the wrapped real coordinates from the wrapped scaled coordinates
416
417			for(i=0; i<3; i++)
418	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
419	mmeineke	569	}
420
421	mmeineke	568	}
422
423
424	gezelter	458	int SimInfo::getNDF(){
425	mmeineke	790	int ndf_local;
426	gezelter	457
427	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
428
429			#ifdef IS_MPI
430			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
431			#else
432			ndf = ndf_local;
433			#endif
434
435	mmeineke	674	ndf = ndf - 3 - nZconstraints;
436	gezelter	458
437			return ndf;
438			}
439
440			int SimInfo::getNDFraw() {
441	mmeineke	790	int ndfRaw_local;
442	gezelter	458
443			// Raw degrees of freedom that we have to set
444			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
445
446			#ifdef IS_MPI
447			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
448			#else
449			ndfRaw = ndfRaw_local;
450			#endif
451
452			return ndfRaw;
453			}
454	tim	767
455			int SimInfo::getNDFtranslational() {
456	mmeineke	790	int ndfTrans_local;
457	tim	767
458			ndfTrans_local = 3 * n_atoms - n_constraints;
459
460			#ifdef IS_MPI
461			MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
462			#else
463			ndfTrans = ndfTrans_local;
464			#endif
465
466			ndfTrans = ndfTrans - 3 - nZconstraints;
467
468			return ndfTrans;
469			}
470
471	mmeineke	377	void SimInfo::refreshSim(){
472
473			simtype fInfo;
474			int isError;
475	gezelter	490	int n_global;
476	mmeineke	424	int* excl;
477	mmeineke	626
478	mmeineke	469	fInfo.dielect = 0.0;
479	mmeineke	377
480	mmeineke	469	if( useDipole ){
481			if( useReactionField )fInfo.dielect = dielectric;
482			}
483
484	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
485	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
486	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
487	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
488			//fInfo.SIM_uses_sticky = 0;
489	chuckv	482	fInfo.SIM_uses_dipoles = useDipole;
490			//fInfo.SIM_uses_dipoles = 0;
491	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
492			fInfo.SIM_uses_RF = 0;
493	mmeineke	377	fInfo.SIM_uses_GB = useGB;
494			fInfo.SIM_uses_EAM = useEAM;
495
496	mmeineke	424	excl = Exclude::getArray();
497	mmeineke	377
498	gezelter	490	#ifdef IS_MPI
499			n_global = mpiSim->getTotAtoms();
500			#else
501			n_global = n_atoms;
502			#endif
503
504	mmeineke	377	isError = 0;
505
506	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
507	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
508			&isError );
509	mmeineke	377
510			if( isError ){
511
512			sprintf( painCave.errMsg,
513			"There was an error setting the simulation information in fortran.\n" );
514			painCave.isFatal = 1;
515			simError();
516			}
517
518			#ifdef IS_MPI
519			sprintf( checkPointMsg,
520			"succesfully sent the simulation information to fortran.\n");
521			MPIcheckPoint();
522			#endif // is_mpi
523	gezelter	458
524	gezelter	474	this->ndf = this->getNDF();
525			this->ndfRaw = this->getNDFraw();
526	tim	767	this->ndfTrans = this->getNDFtranslational();
527	mmeineke	377	}
528
529	mmeineke	841	void SimInfo::setDefaultRcut( double theRcut ){
530
531	mmeineke	859	haveRcut = 1;
532	mmeineke	841	rCut = theRcut;
533	mmeineke	843
534	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535
536	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537	mmeineke	841	}
538
539			void SimInfo::setDefaultEcr( double theEcr ){
540
541	mmeineke	859	haveEcr = 1;
542	mmeineke	841
543	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544
545	mmeineke	841	ecr = theEcr;
546	gezelter	845
547	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548	mmeineke	841	}
549
550			void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551	mmeineke	626
552	mmeineke	841	est = theEst;
553			setDefaultEcr( theEcr );
554			}
555
556
557	mmeineke	626	void SimInfo::checkCutOffs( void ){
558	gezelter	770
559	mmeineke	626	if( boxIsInit ){
560
561			//we need to check cutOffs against the box
562	mmeineke	859
563			if( rCut > maxCutoff ){
564	mmeineke	626	sprintf( painCave.errMsg,
565	mmeineke	859	"Box size is too small for the long range cutoff radius, "
566			"%lf, at time %lf\n",
567			rCut, currentTime );
568			painCave.isFatal = 1;
569	mmeineke	626	simError();
570			}
571	mmeineke	859
572			if( haveEcr ){
573			if( ecr > maxCutoff ){
574			sprintf( painCave.errMsg,
575			"Box size is too small for the electrostatic cutoff radius, "
576			"%lf, at time %lf\n",
577			ecr, currentTime );
578			painCave.isFatal = 1;
579			simError();
580	tim	781	}
581			}
582	tim	767	} else {
583			// initialize this stuff before using it, OK?
584	gezelter	770	sprintf( painCave.errMsg,
585			"Trying to check cutoffs without a box. Be smarter.\n" );
586			painCave.isFatal = 1;
587			simError();
588	mmeineke	626	}
589	gezelter	770
590	mmeineke	626	}
591	tim	658
592			void SimInfo::addProperty(GenericData* prop){
593
594			map<string, GenericData*>::iterator result;
595			result = properties.find(prop->getID());
596
597			//we can't simply use properties[prop->getID()] = prop,
598			//it will cause memory leak if we already contain a propery which has the same name of prop
599
600			if(result != properties.end()){
601
602			delete (*result).second;
603			(*result).second = prop;
604
605			}
606			else{
607
608			properties[prop->getID()] = prop;
609
610			}
611
612			}
613
614			GenericData* SimInfo::getProperty(const string& propName){
615
616			map<string, GenericData*>::iterator result;
617
618			//string lowerCaseName = ();
619
620			result = properties.find(propName);
621
622			if(result != properties.end())
623			return (*result).second;
624			else
625			return NULL;
626			}
627
628			vector<GenericData*> SimInfo::getProperties(){
629
630			vector<GenericData*> result;
631			map<string, GenericData*>::iterator i;
632
633			for(i = properties.begin(); i != properties.end(); i++)
634			result.push_back((*i).second);
635
636			return result;
637			}
638
639	tim	763	double SimInfo::matTrace3(double m[3][3]){
640			double trace;
641			trace = m[0][0] + m[1][1] + m[2][2];
642	tim	658
643	tim	763	return trace;
644			}