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();

  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( 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"
               "  [ %G %G %G ]\n"
               "  [ %G %G %G ]\n"
               "  [ %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"
                 "  [ %G %G %G ]\n"
                 "  [ %G %G %G ]\n"
                 "  [ %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. 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:	941
Committed:	Tue Jan 13 23:01:43 2004 UTC (20 years, 5 months ago) by gezelter
File size:	14120 byte(s)
Log Message:	Changes for adding direct charge-charge interactions (with switching function)
#	User	Rev	Content
1	gezelter	829	#include <stdlib.h>
2			#include <string.h>
3			#include <math.h>
4	mmeineke	377
5	mmeineke	572	#include <iostream>
6			using namespace std;
7	mmeineke	377
8			#include "SimInfo.hpp"
9			#define __C
10			#include "fSimulation.h"
11			#include "simError.h"
12
13			#include "fortranWrappers.hpp"
14
15	gezelter	490	#ifdef IS_MPI
16			#include "mpiSimulation.hpp"
17			#endif
18
19	mmeineke	572	inline double roundMe( double x ){
20			return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21			}
22
23	mmeineke	860	inline double min( double a, double b ){
24			return (a < b ) ? a : b;
25			}
26	mmeineke	572
27	mmeineke	377	SimInfo* currentInfo;
28
29			SimInfo::SimInfo(){
30			excludes = NULL;
31			n_constraints = 0;
32	tim	699	nZconstraints = 0;
33	mmeineke	377	n_oriented = 0;
34			n_dipoles = 0;
35	gezelter	458	ndf = 0;
36			ndfRaw = 0;
37	mmeineke	674	nZconstraints = 0;
38	mmeineke	377	the_integrator = NULL;
39			setTemp = 0;
40			thermalTime = 0.0;
41	mmeineke	642	currentTime = 0.0;
42	mmeineke	420	rCut = 0.0;
43	mmeineke	618	ecr = 0.0;
44	mmeineke	619	est = 0.0;
45	mmeineke	377
46	mmeineke	859	haveRcut = 0;
47			haveEcr = 0;
48	mmeineke	626	boxIsInit = 0;
49
50	tim	781	resetTime = 1e99;
51	mmeineke	626
52	mmeineke	855	orthoTolerance = 1E-6;
53			useInitXSstate = true;
54
55	mmeineke	377	usePBC = 0;
56			useLJ = 0;
57			useSticky = 0;
58	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	gezelter	457	wrapMeSimInfo( this );
67			}
68	mmeineke	377
69	mmeineke	670
70	tim	660	SimInfo::~SimInfo(){
71
72	mmeineke	670	delete myConfiguration;
73
74	tim	660	map<string, GenericData*>::iterator i;
75
76			for(i = properties.begin(); i != properties.end(); i++)
77			delete (*i).second;
78	mmeineke	670
79	tim	660	}
80
81	gezelter	457	void SimInfo::setBox(double newBox[3]) {
82	mmeineke	586
83	gezelter	588	int i, j;
84			double tempMat[3][3];
85	gezelter	463
86	gezelter	588	for(i=0; i<3; i++)
87			for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
88	gezelter	463
89	gezelter	588	tempMat[0][0] = newBox[0];
90			tempMat[1][1] = newBox[1];
91			tempMat[2][2] = newBox[2];
92	gezelter	463
93	mmeineke	586	setBoxM( tempMat );
94	mmeineke	568
95	gezelter	457	}
96	mmeineke	377
97	gezelter	588	void SimInfo::setBoxM( double theBox[3][3] ){
98	mmeineke	568
99	mmeineke	787	int i, j;
100	gezelter	588	double FortranHmat[9]; // to preserve compatibility with Fortran the
101			// ordering in the array is as follows:
102			// [ 0 3 6 ]
103			// [ 1 4 7 ]
104			// [ 2 5 8 ]
105			double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106	mmeineke	568
107	mmeineke	626	if( !boxIsInit ) boxIsInit = 1;
108	mmeineke	586
109	gezelter	588	for(i=0; i < 3; i++)
110			for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
111
112	mmeineke	568	calcBoxL();
113	gezelter	588	calcHmatInv();
114	mmeineke	568
115	gezelter	588	for(i=0; i < 3; i++) {
116			for (j=0; j < 3; j++) {
117			FortranHmat[3*j + i] = Hmat[i][j];
118			FortranHmatInv[3*j + i] = HmatInv[i][j];
119			}
120			}
121	mmeineke	586
122	mmeineke	590	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123	mmeineke	568
124	mmeineke	377	}
125	gezelter	458
126	mmeineke	568
127	gezelter	588	void SimInfo::getBoxM (double theBox[3][3]) {
128	mmeineke	568
129	gezelter	588	int i, j;
130			for(i=0; i<3; i++)
131			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
132	mmeineke	568	}
133
134	gezelter	574
135			void SimInfo::scaleBox(double scale) {
136	gezelter	588	double theBox[3][3];
137			int i, j;
138	gezelter	574
139	gezelter	617	// cerr << "Scaling box by " << scale << "\n";
140	mmeineke	586
141	gezelter	588	for(i=0; i<3; i++)
142			for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
143	gezelter	574
144			setBoxM(theBox);
145
146			}
147
148	gezelter	588	void SimInfo::calcHmatInv( void ) {
149	mmeineke	590
150	mmeineke	853	int oldOrtho;
151	mmeineke	590	int i,j;
152	mmeineke	569	double smallDiag;
153			double tol;
154			double sanity[3][3];
155	mmeineke	568
156	gezelter	588	invertMat3( Hmat, HmatInv );
157	mmeineke	568
158	gezelter	588	// check to see if Hmat is orthorhombic
159	mmeineke	568
160	mmeineke	853	oldOrtho = orthoRhombic;
161
162			smallDiag = fabs(Hmat[0][0]);
163			if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
164			if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
165	mmeineke	855	tol = smallDiag * orthoTolerance;
166	mmeineke	568
167	gezelter	588	orthoRhombic = 1;
168	mmeineke	568
169	gezelter	588	for (i = 0; i < 3; i++ ) {
170			for (j = 0 ; j < 3; j++) {
171			if (i != j) {
172			if (orthoRhombic) {
173	mmeineke	853	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
174	gezelter	588	}
175			}
176	mmeineke	568	}
177			}
178	mmeineke	853
179			if( oldOrtho != orthoRhombic ){
180
181			if( orthoRhombic ){
182			sprintf( painCave.errMsg,
183			"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
184	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
185			orthoTolerance);
186	mmeineke	853	simError();
187			}
188			else {
189			sprintf( painCave.errMsg,
190			"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191	mmeineke	855	" If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
192			orthoTolerance);
193	mmeineke	853	simError();
194			}
195			}
196	gezelter	588	}
197	mmeineke	569
198	gezelter	588	double SimInfo::matDet3(double a[3][3]) {
199			int i, j, k;
200			double determinant;
201	mmeineke	569
202	gezelter	588	determinant = 0.0;
203
204			for(i = 0; i < 3; i++) {
205			j = (i+1)%3;
206			k = (i+2)%3;
207
208			determinant += a[0][i] * (a[1][j]a[2][k] - a[1][k]a[2][j]);
209	mmeineke	569	}
210
211	gezelter	588	return determinant;
212			}
213	mmeineke	569
214	gezelter	588	void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215	mmeineke	569
216	gezelter	588	int i, j, k, l, m, n;
217			double determinant;
218	mmeineke	569
219	gezelter	588	determinant = matDet3( a );
220
221			if (determinant == 0.0) {
222			sprintf( painCave.errMsg,
223			"Can't invert a matrix with a zero determinant!\n");
224			painCave.isFatal = 1;
225			simError();
226			}
227
228			for (i=0; i < 3; i++) {
229			j = (i+1)%3;
230			k = (i+2)%3;
231			for(l = 0; l < 3; l++) {
232			m = (l+1)%3;
233			n = (l+2)%3;
234
235			b[l][i] = (a[j][m]a[k][n] - a[j][n]a[k][m]) / determinant;
236	mmeineke	569	}
237			}
238	mmeineke	568	}
239
240	gezelter	588	void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241			double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242
243			r00 = a[0][0]b[0][0] + a[0][1]b[1][0] + a[0][2]*b[2][0];
244			r01 = a[0][0]b[0][1] + a[0][1]b[1][1] + a[0][2]*b[2][1];
245			r02 = a[0][0]b[0][2] + a[0][1]b[1][2] + a[0][2]*b[2][2];
246
247			r10 = a[1][0]b[0][0] + a[1][1]b[1][0] + a[1][2]*b[2][0];
248			r11 = a[1][0]b[0][1] + a[1][1]b[1][1] + a[1][2]*b[2][1];
249			r12 = a[1][0]b[0][2] + a[1][1]b[1][2] + a[1][2]*b[2][2];
250
251			r20 = a[2][0]b[0][0] + a[2][1]b[1][0] + a[2][2]*b[2][0];
252			r21 = a[2][0]b[0][1] + a[2][1]b[1][1] + a[2][2]*b[2][1];
253			r22 = a[2][0]b[0][2] + a[2][1]b[1][2] + a[2][2]*b[2][2];
254
255			c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256			c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
257			c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
258			}
259
260			void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261			double a0, a1, a2;
262
263			a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2];
264
265			outVec[0] = m[0][0]a0 + m[0][1]a1 + m[0][2]*a2;
266			outVec[1] = m[1][0]a0 + m[1][1]a1 + m[1][2]*a2;
267			outVec[2] = m[2][0]a0 + m[2][1]a1 + m[2][2]*a2;
268			}
269	mmeineke	597
270			void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271			double temp[3][3];
272			int i, j;
273
274			for (i = 0; i < 3; i++) {
275			for (j = 0; j < 3; j++) {
276			temp[j][i] = in[i][j];
277			}
278			}
279			for (i = 0; i < 3; i++) {
280			for (j = 0; j < 3; j++) {
281			out[i][j] = temp[i][j];
282			}
283			}
284			}
285	gezelter	588
286	mmeineke	597	void SimInfo::printMat3(double A[3][3] ){
287
288			std::cerr
289			<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290			<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291			<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292			}
293
294			void SimInfo::printMat9(double A[9] ){
295
296			std::cerr
297			<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298			<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299			<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300			}
301
302	tim	781
303			void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
304
305			out[0] = a[1] * b[2] - a[2] * b[1];
306			out[1] = a[2] * b[0] - a[0] * b[2] ;
307			out[2] = a[0] * b[1] - a[1] * b[0];
308
309			}
310
311			double SimInfo::dotProduct3(double a[3], double b[3]){
312			return a[0]b[0] + a[1]b[1]+ a[2]*b[2];
313			}
314
315			double SimInfo::length3(double a[3]){
316			return sqrt(a[0]a[0] + a[1]a[1] + a[2]*a[2]);
317			}
318
319	mmeineke	568	void SimInfo::calcBoxL( void ){
320
321			double dx, dy, dz, dsq;
322
323	gezelter	588	// boxVol = Determinant of Hmat
324	mmeineke	568
325	gezelter	588	boxVol = matDet3( Hmat );
326	mmeineke	568
327			// boxLx
328
329	gezelter	588	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
330	mmeineke	568	dsq = dxdx + dydy + dz*dz;
331	gezelter	621	boxL[0] = sqrt( dsq );
332	tim	781	//maxCutoff = 0.5 * boxL[0];
333	mmeineke	568
334			// boxLy
335
336	gezelter	588	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
337	mmeineke	568	dsq = dxdx + dydy + dz*dz;
338	gezelter	621	boxL[1] = sqrt( dsq );
339	tim	781	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
340	mmeineke	568
341	tim	781
342	mmeineke	568	// boxLz
343
344	gezelter	588	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
345	mmeineke	568	dsq = dxdx + dydy + dz*dz;
346	gezelter	621	boxL[2] = sqrt( dsq );
347	tim	781	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
348
349			//calculate the max cutoff
350			maxCutoff = calcMaxCutOff();
351	chuckv	669
352			checkCutOffs();
353	mmeineke	626
354	mmeineke	568	}
355
356
357	tim	781	double SimInfo::calcMaxCutOff(){
358
359			double ri[3], rj[3], rk[3];
360			double rij[3], rjk[3], rki[3];
361			double minDist;
362
363			ri[0] = Hmat[0][0];
364			ri[1] = Hmat[1][0];
365			ri[2] = Hmat[2][0];
366
367			rj[0] = Hmat[0][1];
368			rj[1] = Hmat[1][1];
369			rj[2] = Hmat[2][1];
370
371			rk[0] = Hmat[0][2];
372			rk[1] = Hmat[1][2];
373			rk[2] = Hmat[2][2];
374
375			crossProduct3(ri,rj, rij);
376			distXY = dotProduct3(rk,rij) / length3(rij);
377
378			crossProduct3(rj,rk, rjk);
379			distYZ = dotProduct3(ri,rjk) / length3(rjk);
380
381			crossProduct3(rk,ri, rki);
382			distZX = dotProduct3(rj,rki) / length3(rki);
383
384			minDist = min(min(distXY, distYZ), distZX);
385			return minDist/2;
386
387			}
388
389	mmeineke	568	void SimInfo::wrapVector( double thePos[3] ){
390
391	mmeineke	787	int i;
392	mmeineke	568	double scaled[3];
393
394	mmeineke	569	if( !orthoRhombic ){
395			// calc the scaled coordinates.
396	gezelter	588
397
398			matVecMul3(HmatInv, thePos, scaled);
399	mmeineke	569
400			for(i=0; i<3; i++)
401	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
402	mmeineke	569
403			// calc the wrapped real coordinates from the wrapped scaled coordinates
404
405	gezelter	588	matVecMul3(Hmat, scaled, thePos);
406
407	mmeineke	569	}
408			else{
409			// calc the scaled coordinates.
410
411			for(i=0; i<3; i++)
412	gezelter	588	scaled[i] = thePos[i]*HmatInv[i][i];
413	mmeineke	569
414			// wrap the scaled coordinates
415
416			for(i=0; i<3; i++)
417	mmeineke	572	scaled[i] -= roundMe(scaled[i]);
418	mmeineke	569
419			// calc the wrapped real coordinates from the wrapped scaled coordinates
420
421			for(i=0; i<3; i++)
422	gezelter	588	thePos[i] = scaled[i]*Hmat[i][i];
423	mmeineke	569	}
424
425	mmeineke	568	}
426
427
428	gezelter	458	int SimInfo::getNDF(){
429	mmeineke	790	int ndf_local;
430	gezelter	457
431	gezelter	458	ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
432
433			#ifdef IS_MPI
434			MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
435			#else
436			ndf = ndf_local;
437			#endif
438
439	mmeineke	674	ndf = ndf - 3 - nZconstraints;
440	gezelter	458
441			return ndf;
442			}
443
444			int SimInfo::getNDFraw() {
445	mmeineke	790	int ndfRaw_local;
446	gezelter	458
447			// Raw degrees of freedom that we have to set
448			ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
449
450			#ifdef IS_MPI
451			MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
452			#else
453			ndfRaw = ndfRaw_local;
454			#endif
455
456			return ndfRaw;
457			}
458	tim	767
459			int SimInfo::getNDFtranslational() {
460	mmeineke	790	int ndfTrans_local;
461	tim	767
462			ndfTrans_local = 3 * n_atoms - n_constraints;
463
464			#ifdef IS_MPI
465			MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
466			#else
467			ndfTrans = ndfTrans_local;
468			#endif
469
470			ndfTrans = ndfTrans - 3 - nZconstraints;
471
472			return ndfTrans;
473			}
474
475	mmeineke	377	void SimInfo::refreshSim(){
476
477			simtype fInfo;
478			int isError;
479	gezelter	490	int n_global;
480	mmeineke	424	int* excl;
481	mmeineke	626
482	mmeineke	469	fInfo.dielect = 0.0;
483	mmeineke	377
484	gezelter	941	if( useDipoles ){
485	mmeineke	469	if( useReactionField )fInfo.dielect = dielectric;
486			}
487
488	mmeineke	377	fInfo.SIM_uses_PBC = usePBC;
489	mmeineke	443	//fInfo.SIM_uses_LJ = 0;
490	chuckv	439	fInfo.SIM_uses_LJ = useLJ;
491	mmeineke	443	fInfo.SIM_uses_sticky = useSticky;
492			//fInfo.SIM_uses_sticky = 0;
493	gezelter	941	fInfo.SIM_uses_charges = useCharges;
494			fInfo.SIM_uses_dipoles = useDipoles;
495	chuckv	482	//fInfo.SIM_uses_dipoles = 0;
496	mmeineke	443	//fInfo.SIM_uses_RF = useReactionField;
497			fInfo.SIM_uses_RF = 0;
498	mmeineke	377	fInfo.SIM_uses_GB = useGB;
499			fInfo.SIM_uses_EAM = useEAM;
500
501	mmeineke	424	excl = Exclude::getArray();
502	mmeineke	377
503	gezelter	490	#ifdef IS_MPI
504			n_global = mpiSim->getTotAtoms();
505			#else
506			n_global = n_atoms;
507			#endif
508
509	mmeineke	377	isError = 0;
510
511	gezelter	490	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
512	gezelter	483	&nGlobalExcludes, globalExcludes, molMembershipArray,
513			&isError );
514	mmeineke	377
515			if( isError ){
516
517			sprintf( painCave.errMsg,
518			"There was an error setting the simulation information in fortran.\n" );
519			painCave.isFatal = 1;
520			simError();
521			}
522
523			#ifdef IS_MPI
524			sprintf( checkPointMsg,
525			"succesfully sent the simulation information to fortran.\n");
526			MPIcheckPoint();
527			#endif // is_mpi
528	gezelter	458
529	gezelter	474	this->ndf = this->getNDF();
530			this->ndfRaw = this->getNDFraw();
531	tim	767	this->ndfTrans = this->getNDFtranslational();
532	mmeineke	377	}
533
534	mmeineke	841	void SimInfo::setDefaultRcut( double theRcut ){
535
536	mmeineke	859	haveRcut = 1;
537	mmeineke	841	rCut = theRcut;
538	mmeineke	843
539	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
540
541	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
542	mmeineke	841	}
543
544			void SimInfo::setDefaultEcr( double theEcr ){
545
546	mmeineke	859	haveEcr = 1;
547	chrisfen	872	ecr = theEcr;
548	mmeineke	841
549	gezelter	845	( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
550
551	mmeineke	843	notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
552	mmeineke	841	}
553
554			void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555	mmeineke	626
556	mmeineke	841	est = theEst;
557			setDefaultEcr( theEcr );
558			}
559
560
561	mmeineke	626	void SimInfo::checkCutOffs( void ){
562	gezelter	770
563	mmeineke	626	if( boxIsInit ){
564
565			//we need to check cutOffs against the box
566	mmeineke	859
567			if( rCut > maxCutoff ){
568	mmeineke	626	sprintf( painCave.errMsg,
569	mmeineke	859	"Box size is too small for the long range cutoff radius, "
570	mmeineke	874	"%G, at time %G\n"
571			" [ %G %G %G ]\n"
572			" [ %G %G %G ]\n"
573			" [ %G %G %G ]\n",
574			rCut, currentTime,
575			Hmat[0][0], Hmat[0][1], Hmat[0][2],
576			Hmat[1][0], Hmat[1][1], Hmat[1][2],
577			Hmat[2][0], Hmat[2][1], Hmat[2][2]);
578	mmeineke	859	painCave.isFatal = 1;
579	mmeineke	626	simError();
580			}
581	mmeineke	859
582			if( haveEcr ){
583			if( ecr > maxCutoff ){
584			sprintf( painCave.errMsg,
585			"Box size is too small for the electrostatic cutoff radius, "
586	mmeineke	874	"%G, at time %G\n"
587			" [ %G %G %G ]\n"
588			" [ %G %G %G ]\n"
589			" [ %G %G %G ]\n",
590			ecr, currentTime,
591			Hmat[0][0], Hmat[0][1], Hmat[0][2],
592			Hmat[1][0], Hmat[1][1], Hmat[1][2],
593			Hmat[2][0], Hmat[2][1], Hmat[2][2]);
594	mmeineke	859	painCave.isFatal = 1;
595			simError();
596	tim	781	}
597			}
598	tim	767	} else {
599			// initialize this stuff before using it, OK?
600	gezelter	770	sprintf( painCave.errMsg,
601			"Trying to check cutoffs without a box. Be smarter.\n" );
602			painCave.isFatal = 1;
603			simError();
604	mmeineke	626	}
605	gezelter	770
606	mmeineke	626	}
607	tim	658
608			void SimInfo::addProperty(GenericData* prop){
609
610			map<string, GenericData*>::iterator result;
611			result = properties.find(prop->getID());
612
613			//we can't simply use properties[prop->getID()] = prop,
614			//it will cause memory leak if we already contain a propery which has the same name of prop
615
616			if(result != properties.end()){
617
618			delete (*result).second;
619			(*result).second = prop;
620
621			}
622			else{
623
624			properties[prop->getID()] = prop;
625
626			}
627
628			}
629
630			GenericData* SimInfo::getProperty(const string& propName){
631
632			map<string, GenericData*>::iterator result;
633
634			//string lowerCaseName = ();
635
636			result = properties.find(propName);
637
638			if(result != properties.end())
639			return (*result).second;
640			else
641			return NULL;
642			}
643
644			vector<GenericData*> SimInfo::getProperties(){
645
646			vector<GenericData*> result;
647			map<string, GenericData*>::iterator i;
648
649			for(i = properties.begin(); i != properties.end(); i++)
650			result.push_back((*i).second);
651
652			return result;
653			}
654
655	tim	763	double SimInfo::matTrace3(double m[3][3]){
656			double trace;
657			trace = m[0][0] + m[1][1] + m[2][2];
658	tim	658
659	tim	763	return trace;
660			}