OOPSE/libmdtools/SimInfo.cpp

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

#include <iostream>
using namespace std;

#include "SimInfo.hpp"
#define __C
#include "fSimulation.h"
#include "simError.h"

#include "fortranWrappers.hpp"

#ifdef IS_MPI
#include "mpiSimulation.hpp"
#endif

inline double roundMe( double x ){
  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
}
          
inline double min( double a, double b ){
  return (a < b ) ? a : b;
}

SimInfo* currentInfo;

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

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

  orthoTolerance = 1E-6;
  useInitXSstate = true;

  usePBC = 0;
  useLJ = 0; 
  useSticky = 0;
  useCharges = 0;
  useDipoles = 0;
  useReactionField = 0;
  useGB = 0;
  useEAM = 0;

  myConfiguration = new SimState();

  has_minimizer = false;
  the_minimizer =NULL;

  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 Box.\n"
               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
               "\tvariable ( currently set to %G ).\n",
               orthoTolerance);
      simError();
    }
    else {
      sprintf( painCave.errMsg,
               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
               "\tvariable ( currently set to %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( useDipoles ){
    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_charges = useCharges;
  fInfo.SIM_uses_dipoles = useDipoles;
  //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;
  ecr = theEcr;
  
  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;

  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, "
               "%G, at time %G\n"
               "\t[ %G %G %G ]\n"
               "\t[ %G %G %G ]\n"
               "\t[ %G %G %G ]\n",
               rCut, currentTime,
               Hmat[0][0], Hmat[0][1], Hmat[0][2],
               Hmat[1][0], Hmat[1][1], Hmat[1][2],
               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
      painCave.isFatal = 1;
      simError();
    }
    
    if( haveEcr ){
      if( ecr > maxCutoff ){
        sprintf( painCave.errMsg,
                 "Box size is too small for the electrostatic cutoff radius, "
                 "%G, at time %G\n"
                 "\t[ %G %G %G ]\n"
                 "\t[ %G %G %G ]\n"
                 "\t[ %G %G %G ]\n",
                 ecr, currentTime,
                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
        painCave.isFatal = 1;
        simError();
      }
    }
  } else {
    // initialize this stuff before using it, OK?
    sprintf( painCave.errMsg,
             "Trying to check cutoffs without a box.\n"
             "\tOOPSE should have better programmers than that.\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:	1031
Committed:	Fri Feb 6 18:58:06 2004 UTC (20 years, 5 months ago) by tim
File size:	14300 byte(s)
Log Message:	Add some lines into global.cpp to make it work with energy minimization
#	User	Rev	Content
1	gezelter	829	#include <stdlib.h>
2			#include <string.h>
3			#include <math.h>
4	mmeineke	377
5	mmeineke	572	#include <iostream>
6			using namespace std;
7	mmeineke	377
8			#include "SimInfo.hpp"
9			#define __C
10			#include "fSimulation.h"
11			#include "simError.h"
12
13			#include "fortranWrappers.hpp"
14
15	gezelter	490	#ifdef IS_MPI
16			#include "mpiSimulation.hpp"
17			#endif
18
19	mmeineke	572	inline double roundMe( double x ){
20			return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21			}
22
23	mmeineke	860	inline double min( double a, double b ){
24			return (a < b ) ? a : b;
25			}
26	mmeineke	572
27	mmeineke	377	SimInfo* currentInfo;
28
29			SimInfo::SimInfo(){
30			excludes = NULL;
31			n_constraints = 0;
32	tim	699	nZconstraints = 0;
33	mmeineke	377	n_oriented = 0;
34			n_dipoles = 0;
35	gezelter	458	ndf = 0;
36			ndfRaw = 0;
37	mmeineke	674	nZconstraints = 0;
38	mmeineke	377	the_integrator = NULL;
39			setTemp = 0;
40			thermalTime = 0.0;
41	mmeineke	642	currentTime = 0.0;
42	mmeineke	420	rCut = 0.0;
43	mmeineke	618	ecr = 0.0;
44	mmeineke	619	est = 0.0;
45	mmeineke	377
46	mmeineke	859	haveRcut = 0;
47			haveEcr = 0;
48	mmeineke	626	boxIsInit = 0;
49
50	tim	781	resetTime = 1e99;
51	mmeineke	626
52	mmeineke	855	orthoTolerance = 1E-6;
53			useInitXSstate = true;
54
55	mmeineke	377	usePBC = 0;
56			useLJ = 0;
57			useSticky = 0;
58	gezelter	941	useCharges = 0;
59			useDipoles = 0;
60	mmeineke	377	useReactionField = 0;
61			useGB = 0;
62			useEAM = 0;
63
64	mmeineke	670	myConfiguration = new SimState();
65
66	tim	1031	has_minimizer = false;
67			the_minimizer =NULL;
68
69	gezelter	457	wrapMeSimInfo( this );
70			}
71	mmeineke	377
72	mmeineke	670
73	tim	660	SimInfo::~SimInfo(){
74
75	mmeineke	670	delete myConfiguration;
76
77	tim	660	map<string, GenericData*>::iterator i;
78
79			for(i = properties.begin(); i != properties.end(); i++)
80			delete (*i).second;
81	mmeineke	670
82	tim	660	}
83
84	gezelter	457	void SimInfo::setBox(double newBox[3]) {
85	mmeineke	586
86	gezelter	588	int i, j;
87			double tempMat[3][3];
88	gezelter	463
89	gezelter	588	for(i=0; i<3; i++)
90			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
91	gezelter	463
92	gezelter	588	tempMat[0][0] = newBox[0];
93			tempMat[1][1] = newBox[1];
94			tempMat[2][2] = newBox[2];
95	gezelter	463
96	mmeineke	586	setBoxM( tempMat );
97	mmeineke	568
98	gezelter	457	}
99	mmeineke	377
100	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
101	mmeineke	568
102	mmeineke	787	int i, j;
103	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
104			// ordering in the array is as follows:
105			// [ 0 3 6 ]
106			// [ 1 4 7 ]
107			// [ 2 5 8 ]
108			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
109	mmeineke	568
110	mmeineke	626	if( !boxIsInit ) boxIsInit = 1;
111	mmeineke	586
112	gezelter	588	for(i=0; i < 3; i++)
113			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
114
115	mmeineke	568	calcBoxL();
116	gezelter	588	calcHmatInv();
117	mmeineke	568
118	gezelter	588	for(i=0; i < 3; i++) {
119			for (j=0; j < 3; j++) {
120			FortranHmat[3*j + i] = Hmat[i][j];
121			FortranHmatInv[3*j + i] = HmatInv[i][j];
122			}
123			}
124	mmeineke	586
125	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
126	mmeineke	568
127	mmeineke	377	}
128	gezelter	458
129	mmeineke	568
130	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
131	mmeineke	568
132	gezelter	588	int i, j;
133			for(i=0; i<3; i++)
134			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
135	mmeineke	568	}
136
137	gezelter	574
138			void SimInfo::scaleBox(double scale) {
139	gezelter	588	double theBox[3][3];
140			int i, j;
141	gezelter	574
142	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
143	mmeineke	586
144	gezelter	588	for(i=0; i<3; i++)
145			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
146	gezelter	574
147			setBoxM(theBox);
148
149			}
150
151	gezelter	588	void SimInfo::calcHmatInv( void ) {
152	mmeineke	590
153	mmeineke	853	int oldOrtho;
154	mmeineke	590	int i,j;
155	mmeineke	569	double smallDiag;
156			double tol;
157			double sanity[3][3];
158	mmeineke	568
159	gezelter	588	invertMat3( Hmat, HmatInv );
160	mmeineke	568
161	gezelter	588	// check to see if Hmat is orthorhombic
162	mmeineke	568
163	mmeineke	853	oldOrtho = orthoRhombic;
164
165			smallDiag = fabs(Hmat[0][0]);
166			if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
167			if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
168	mmeineke	855	tol = smallDiag * orthoTolerance;
169	mmeineke	568
170	gezelter	588	orthoRhombic = 1;
171	mmeineke	568
172	gezelter	588	for (i = 0; i < 3; i++ ) {
173			for (j = 0 ; j < 3; j++) {
174			if (i != j) {
175			if (orthoRhombic) {
176	mmeineke	853	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
177	gezelter	588	}
178			}
179	mmeineke	568	}
180			}
181	mmeineke	853
182			if( oldOrtho != orthoRhombic ){
183
184			if( orthoRhombic ){
185			sprintf( painCave.errMsg,
186	gezelter	965	"Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
187			"\tIf this is a bad thing, change the orthoBoxTolerance\n"
188			"\tvariable ( currently set to %G ).\n",
189	mmeineke	855	orthoTolerance);
190	mmeineke	853	simError();
191			}
192			else {
193			sprintf( painCave.errMsg,
194	gezelter	965	"Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
195			"\tIf this is a bad thing, change the orthoBoxTolerance\n"
196			"\tvariable ( currently set to %G ).\n",
197	mmeineke	855	orthoTolerance);
198	mmeineke	853	simError();
199			}
200			}
201	gezelter	588	}
202	mmeineke	569
203	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
204			int i, j, k;
205			double determinant;
206	mmeineke	569
207	gezelter	588	determinant = 0.0;
208
209			for(i = 0; i < 3; i++) {
210			j = (i+1)%3;
211			k = (i+2)%3;
212
213			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
214	mmeineke	569	}
215
216	gezelter	588	return determinant;
217			}
218	mmeineke	569
219	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
220	mmeineke	569
221	gezelter	588	int i, j, k, l, m, n;
222			double determinant;
223	mmeineke	569
224	gezelter	588	determinant = matDet3( a );
225
226			if (determinant == 0.0) {
227			sprintf( painCave.errMsg,
228			"Can't invert a matrix with a zero determinant!\n");
229			painCave.isFatal = 1;
230			simError();
231			}
232
233			for (i=0; i < 3; i++) {
234			j = (i+1)%3;
235			k = (i+2)%3;
236			for(l = 0; l < 3; l++) {
237			m = (l+1)%3;
238			n = (l+2)%3;
239
240			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
241	mmeineke	569	}
242			}
243	mmeineke	568	}
244
245	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
246			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
247
248			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
249			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
250			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
251
252			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
253			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
254			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
255
256			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
257			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
258			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
259
260			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
261			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
262			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
263			}
264
265			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
266			double a0, a1, a2;
267
268			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
269
270			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
271			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
272			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
273			}
274	mmeineke	597
275			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
276			double temp[3][3];
277			int i, j;
278
279			for (i = 0; i < 3; i++) {
280			for (j = 0; j < 3; j++) {
281			temp[j][i] = in[i][j];
282			}
283			}
284			for (i = 0; i < 3; i++) {
285			for (j = 0; j < 3; j++) {
286			out[i][j] = temp[i][j];
287			}
288			}
289			}
290	gezelter	588
291	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
292
293			std::cerr
294			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
295			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
296			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
297			}
298
299			void SimInfo::printMat9(double A[9] ){
300
301			std::cerr
302			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
303			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
304			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
305			}
306
307	tim	781
308			void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
309
310			out[0] = a[1] * b[2] - a[2] * b[1];
311			out[1] = a[2] * b[0] - a[0] * b[2] ;
312			out[2] = a[0] * b[1] - a[1] * b[0];
313
314			}
315
316			double SimInfo::dotProduct3(double a[3], double b[3]){
317			return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
318			}
319
320			double SimInfo::length3(double a[3]){
321			return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
322			}
323
324	mmeineke	568	void SimInfo::calcBoxL( void ){
325
326			double dx, dy, dz, dsq;
327
328	gezelter	588	// boxVol = Determinant of Hmat
329	mmeineke	568
330	gezelter	588	boxVol = matDet3( Hmat );
331	mmeineke	568
332			// boxLx
333
334	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
335	mmeineke	568	dsq = dxdx + dydy + dz*dz;
336	gezelter	621	boxL[0] = sqrt( dsq );
337	tim	781	//maxCutoff = 0.5 * boxL[0];
338	mmeineke	568
339			// boxLy
340
341	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
342	mmeineke	568	dsq = dxdx + dydy + dz*dz;
343	gezelter	621	boxL[1] = sqrt( dsq );
344	tim	781	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
345	mmeineke	568
346	tim	781
347	mmeineke	568	// boxLz
348
349	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
350	mmeineke	568	dsq = dxdx + dydy + dz*dz;
351	gezelter	621	boxL[2] = sqrt( dsq );
352	tim	781	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
353
354			//calculate the max cutoff
355			maxCutoff = calcMaxCutOff();
356	chuckv	669
357			checkCutOffs();
358	mmeineke	626
359	mmeineke	568	}
360
361
362	tim	781	double SimInfo::calcMaxCutOff(){
363
364			double ri[3], rj[3], rk[3];
365			double rij[3], rjk[3], rki[3];
366			double minDist;
367
368			ri[0] = Hmat[0][0];
369			ri[1] = Hmat[1][0];
370			ri[2] = Hmat[2][0];
371
372			rj[0] = Hmat[0][1];
373			rj[1] = Hmat[1][1];
374			rj[2] = Hmat[2][1];
375
376			rk[0] = Hmat[0][2];
377			rk[1] = Hmat[1][2];
378			rk[2] = Hmat[2][2];
379
380			crossProduct3(ri,rj, rij);
381			distXY = dotProduct3(rk,rij) / length3(rij);
382
383			crossProduct3(rj,rk, rjk);
384			distYZ = dotProduct3(ri,rjk) / length3(rjk);
385
386			crossProduct3(rk,ri, rki);
387			distZX = dotProduct3(rj,rki) / length3(rki);
388
389			minDist = min(min(distXY, distYZ), distZX);
390			return minDist/2;
391
392			}
393
394	mmeineke	568	void SimInfo::wrapVector( double thePos[3] ){
395
396	mmeineke	787	int i;
397	mmeineke	568	double scaled[3];
398
399	mmeineke	569	if( !orthoRhombic ){
400			// calc the scaled coordinates.
401	gezelter	588
402
403			matVecMul3(HmatInv, thePos, scaled);
404	mmeineke	569
405			for(i=0; i<3; i++)
406	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
407	mmeineke	569
408			// calc the wrapped real coordinates from the wrapped scaled coordinates
409
410	gezelter	588	matVecMul3(Hmat, scaled, thePos);
411
412	mmeineke	569	}
413			else{
414			// calc the scaled coordinates.
415
416			for(i=0; i<3; i++)
417	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
418	mmeineke	569
419			// wrap the scaled coordinates
420
421			for(i=0; i<3; i++)
422	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
423	mmeineke	569
424			// calc the wrapped real coordinates from the wrapped scaled coordinates
425
426			for(i=0; i<3; i++)
427	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
428	mmeineke	569	}
429
430	mmeineke	568	}
431
432
433	gezelter	458	int SimInfo::getNDF(){
434	mmeineke	790	int ndf_local;
435	gezelter	457
436	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
437
438			#ifdef IS_MPI
439			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
440			#else
441			ndf = ndf_local;
442			#endif
443
444	mmeineke	674	ndf = ndf - 3 - nZconstraints;
445	gezelter	458
446			return ndf;
447			}
448
449			int SimInfo::getNDFraw() {
450	mmeineke	790	int ndfRaw_local;
451	gezelter	458
452			// Raw degrees of freedom that we have to set
453			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
454
455			#ifdef IS_MPI
456			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
457			#else
458			ndfRaw = ndfRaw_local;
459			#endif
460
461			return ndfRaw;
462			}
463	tim	767
464			int SimInfo::getNDFtranslational() {
465	mmeineke	790	int ndfTrans_local;
466	tim	767
467			ndfTrans_local = 3 * n_atoms - n_constraints;
468
469			#ifdef IS_MPI
470			MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
471			#else
472			ndfTrans = ndfTrans_local;
473			#endif
474
475			ndfTrans = ndfTrans - 3 - nZconstraints;
476
477			return ndfTrans;
478			}
479
480	mmeineke	377	void SimInfo::refreshSim(){
481
482			simtype fInfo;
483			int isError;
484	gezelter	490	int n_global;
485	mmeineke	424	int* excl;
486	mmeineke	626
487	mmeineke	469	fInfo.dielect = 0.0;
488	mmeineke	377
489	gezelter	941	if( useDipoles ){
490	mmeineke	469	if( useReactionField )fInfo.dielect = dielectric;
491			}
492
493	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
494	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
495	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
496	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
497			//fInfo.SIM_uses_sticky = 0;
498	gezelter	941	fInfo.SIM_uses_charges = useCharges;
499			fInfo.SIM_uses_dipoles = useDipoles;
500	chuckv	482	//fInfo.SIM_uses_dipoles = 0;
501	chrisfen	999	fInfo.SIM_uses_RF = useReactionField;
502			//fInfo.SIM_uses_RF = 0;
503	mmeineke	377	fInfo.SIM_uses_GB = useGB;
504			fInfo.SIM_uses_EAM = useEAM;
505
506	mmeineke	424	excl = Exclude::getArray();
507	mmeineke	377
508	gezelter	490	#ifdef IS_MPI
509			n_global = mpiSim->getTotAtoms();
510			#else
511			n_global = n_atoms;
512			#endif
513
514	mmeineke	377	isError = 0;
515
516	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
517	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
518			&isError );
519	mmeineke	377
520			if( isError ){
521
522			sprintf( painCave.errMsg,
523			"There was an error setting the simulation information in fortran.\n" );
524			painCave.isFatal = 1;
525			simError();
526			}
527
528			#ifdef IS_MPI
529			sprintf( checkPointMsg,
530			"succesfully sent the simulation information to fortran.\n");
531			MPIcheckPoint();
532			#endif // is_mpi
533	gezelter	458
534	gezelter	474	this->ndf = this->getNDF();
535			this->ndfRaw = this->getNDFraw();
536	tim	767	this->ndfTrans = this->getNDFtranslational();
537	mmeineke	377	}
538
539	mmeineke	841	void SimInfo::setDefaultRcut( double theRcut ){
540
541	mmeineke	859	haveRcut = 1;
542	mmeineke	841	rCut = theRcut;
543	mmeineke	843
544	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545
546	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
547	mmeineke	841	}
548
549			void SimInfo::setDefaultEcr( double theEcr ){
550
551	mmeineke	859	haveEcr = 1;
552	chrisfen	872	ecr = theEcr;
553	mmeineke	841
554	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555
556	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
557	mmeineke	841	}
558
559			void SimInfo::setDefaultEcr( double theEcr, double theEst ){
560	mmeineke	626
561	mmeineke	841	est = theEst;
562			setDefaultEcr( theEcr );
563			}
564
565
566	mmeineke	626	void SimInfo::checkCutOffs( void ){
567	gezelter	770
568	mmeineke	626	if( boxIsInit ){
569
570			//we need to check cutOffs against the box
571	mmeineke	859
572			if( rCut > maxCutoff ){
573	mmeineke	626	sprintf( painCave.errMsg,
574	mmeineke	859	"Box size is too small for the long range cutoff radius, "
575	mmeineke	874	"%G, at time %G\n"
576	gezelter	965	"\t[ %G %G %G ]\n"
577			"\t[ %G %G %G ]\n"
578			"\t[ %G %G %G ]\n",
579	mmeineke	874	rCut, currentTime,
580			Hmat[0][0], Hmat[0][1], Hmat[0][2],
581			Hmat[1][0], Hmat[1][1], Hmat[1][2],
582			Hmat[2][0], Hmat[2][1], Hmat[2][2]);
583	mmeineke	859	painCave.isFatal = 1;
584	mmeineke	626	simError();
585			}
586	mmeineke	859
587			if( haveEcr ){
588			if( ecr > maxCutoff ){
589			sprintf( painCave.errMsg,
590			"Box size is too small for the electrostatic cutoff radius, "
591	mmeineke	874	"%G, at time %G\n"
592	gezelter	965	"\t[ %G %G %G ]\n"
593			"\t[ %G %G %G ]\n"
594			"\t[ %G %G %G ]\n",
595	mmeineke	874	ecr, currentTime,
596			Hmat[0][0], Hmat[0][1], Hmat[0][2],
597			Hmat[1][0], Hmat[1][1], Hmat[1][2],
598			Hmat[2][0], Hmat[2][1], Hmat[2][2]);
599	mmeineke	859	painCave.isFatal = 1;
600			simError();
601	tim	781	}
602			}
603	tim	767	} else {
604			// initialize this stuff before using it, OK?
605	gezelter	770	sprintf( painCave.errMsg,
606	gezelter	965	"Trying to check cutoffs without a box.\n"
607			"\tOOPSE should have better programmers than that.\n" );
608	gezelter	770	painCave.isFatal = 1;
609			simError();
610	mmeineke	626	}
611	gezelter	770
612	mmeineke	626	}
613	tim	658
614			void SimInfo::addProperty(GenericData* prop){
615
616			map<string, GenericData*>::iterator result;
617			result = properties.find(prop->getID());
618
619			//we can't simply use properties[prop->getID()] = prop,
620			//it will cause memory leak if we already contain a propery which has the same name of prop
621
622			if(result != properties.end()){
623
624			delete (*result).second;
625			(*result).second = prop;
626
627			}
628			else{
629
630			properties[prop->getID()] = prop;
631
632			}
633
634			}
635
636			GenericData* SimInfo::getProperty(const string& propName){
637
638			map<string, GenericData*>::iterator result;
639
640			//string lowerCaseName = ();
641
642			result = properties.find(propName);
643
644			if(result != properties.end())
645			return (*result).second;
646			else
647			return NULL;
648			}
649
650			vector<GenericData*> SimInfo::getProperties(){
651
652			vector<GenericData*> result;
653			map<string, GenericData*>::iterator i;
654
655			for(i = properties.begin(); i != properties.end(); i++)
656			result.push_back((*i).second);
657
658			return result;
659			}
660
661	tim	763	double SimInfo::matTrace3(double m[3][3]){
662			double trace;
663			trace = m[0][0] + m[1][1] + m[2][2];
664	tim	658
665	tim	763	return trace;
666			}