[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/SimInfo.cpp

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 441 by chuckv, Tue Apr 1 16:50:14 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 2004 UTC

-<
+#include <cstdlib>
-<
+#include <cstring>
->
+#include <stdlib.h>
->
+#include <string.h>
->
+#include <math.h>
-+
+#include <iostream>
-+
+using namespace std;
+#include "SimInfo.hpp"
+#define __C
+#include "fortranWrappers.hpp"
-+
+#include "MatVec3.h"
-+
-+
+#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;
-+
+  rSw = 0.0;
-+
+  haveRcut = 0;
-+
+  haveRsw = 0;
-+
+  boxIsInit = 0;
-+
-+
+  resetTime = 1e99;
-+
-+
+  orthoRhombic = 0;
-+
+  orthoTolerance = 1E-6;
-+
+  useInitXSstate = true;
-+
+  usePBC = 0;
+  useLJ = 0;
+  useSticky = 0;
-<
+  useDipole = 0;
->
+  useCharges = 0;
->
+  useDipoles = 0;
+  useReactionField = 0;
+  useGB = 0;
+  useEAM = 0;
-+
-+
+  haveCutoffGroups = false;
-+
+  excludes = Exclude::Instance();
-+
+  myConfiguration = new SimState();
-+
+  has_minimizer = false;
-+
+  the_minimizer =NULL;
-+
-+
+  ngroup = 0;
-+
+  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,
-+
+               "OOPSE is switching from the default Non-Orthorhombic\n"
-+
+               "\tto the faster Orthorhombic periodic boundary computations.\n"
-+
+               "\tThis is usually a good thing, but if you wan't the\n"
-+
+               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
-+
+               "\tvariable ( currently set to %G ) smaller.\n",
-+
+               orthoTolerance);
-+
+      simError();
-+
+    }
-+
+    else {
-+
+      sprintf( painCave.errMsg,
-+
+               "OOPSE is switching from the faster Orthorhombic to the more\n"
-+
+               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
-+
+               "\tThis is usually because the box has deformed under\n"
-+
+               "\tNPTf integration. If you wan't to live on the edge with\n"
-+
+               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
-+
+               "\tvariable ( currently set to %G ) larger.\n",
-+
+               orthoTolerance);
-+
+      simError();
-+
+    }
-+
+  }
-+
+}
-+
-+
+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) / norm3(rij);
-+
-+
+  crossProduct3(rj,rk, rjk);
-+
+  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
-+
-+
+  crossProduct3(rk,ri, rki);
-+
+  distZX = dotProduct3(rj,rki) / norm3(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 = 0;
-+
-+
+  for(int i = 0; i < integrableObjects.size(); i++){
-+
+    ndf_local += 3;
-+
+    if (integrableObjects[i]->isDirectional()) {
-+
+      if (integrableObjects[i]->isLinear())
-+
+        ndf_local += 2;
-+
+      else
-+
+        ndf_local += 3;
-+
+    }
-+
+  }
-+
-+
+  // n_constraints is local, so subtract them on each processor:
-+
-+
+  ndf_local -= n_constraints;
-+
-+
+#ifdef IS_MPI
-+
+  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
-+
+#else
-+
+  ndf = ndf_local;
-+
+#endif
-+
-+
+  // nZconstraints is global, as are the 3 COM translations for the
-+
+  // entire system:
-+
-+
+  ndf = ndf - 3 - nZconstraints;
-+
-+
+  return ndf;
-+
+}
-+
-+
+int SimInfo::getNDFraw() {
-+
+  int ndfRaw_local;
-+
-+
+  // Raw degrees of freedom that we have to set
-+
+  ndfRaw_local = 0;
-+
-+
+  for(int i = 0; i < integrableObjects.size(); i++){
-+
+    ndfRaw_local += 3;
-+
+    if (integrableObjects[i]->isDirectional()) {
-+
+       if (integrableObjects[i]->isLinear())
-+
+        ndfRaw_local += 2;
-+
+      else
-+
+        ndfRaw_local += 3;
-+
+    }
-+
+  }
-+
-+
+#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 * integrableObjects.size() - 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;
-+
+}
-+
-+
+int SimInfo::getTotIntegrableObjects() {
-+
+  int nObjs_local;
-+
+  int nObjs;
-+
-+
+  nObjs_local =  integrableObjects.size();
-+
-+
-+
+#ifdef IS_MPI
-+
+  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
-+
+#else
-+
+  nObjs = nObjs_local;
-+
+#endif
-+
-+
-+
+  return nObjs;
-+
+}
-+
+void SimInfo::refreshSim(){
+  simtype fInfo;
+  int isError;
-+
+  int n_global;
+  int* excl;
-<
+  fInfo.box[0] = box_x;
-<
+  fInfo.box[1] = box_y;
-<
+  fInfo.box[2] = box_z;
->
+  fInfo.dielect = 0.0;
-<
+  fInfo.rlist = rList;
-<
+  fInfo.rcut = rCut;
-<
+  fInfo.rrf = ecr;
-<
+  fInfo.rt = ecr - est;
-<
+  fInfo.dielect = dielectric;
->
+  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_dipoles = useDipole;
->
+  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();
-<
->
+  n_exclude = excludes->getSize();
->
+  excl = excludes->getFortranArray();
->
->
+#ifdef IS_MPI
->
+  n_global = mpiSim->getTotAtoms();
->
+#else
->
+  n_global = n_atoms;
->
+#endif
->
+  isError = 0;
-<
-<
+//   fInfo;
-<
+//   n_atoms;
-<
+//   identArray;
-<
+//   n_exclude;
-<
+//   excludes;
-<
+//   nGlobalExcludes;
-<
+//   globalExcludes;
-<
+//   isError;
-<
-<
+  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
-<
+                  &nGlobalExcludes, globalExcludes, &isError );
-<
->
->
+  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
->
+  //it may not be a good idea to pass the address of first element in vector
->
+  //since c++ standard does not require vector to be stored continously in meomory
->
+  //Most of the compilers will organize the memory of vector continously
->
+  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
->
+                  &nGlobalExcludes, globalExcludes, molMembershipArray,
->
+                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
->
+  if( isError ){
-<
->
+    sprintf( painCave.errMsg,
-<
+             "There was an error setting the simulation information in fortran.\n" );
->
+             "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;
-+
+  rList = rCut + 1.0;
-+
-+
+  notifyFortranCutOffs( &rCut, &rSw, &rList );
-+
+}
-+
-+
+void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
-+
-+
+  rSw = theRsw;
-+
+  setDefaultRcut( theRcut );
-+
+}
-+
-+
-+
+void SimInfo::checkCutOffs( void ){
-+
-+
+  if( boxIsInit ){
-+
-+
+    //we need to check cutOffs against the box
-+
-+
+    if( rCut > maxCutoff ){
-+
+      sprintf( painCave.errMsg,
-+
+               "cutoffRadius is too large for the current periodic box.\n"
-+
+               "\tCurrent Value of cutoffRadius = %G at time %G\n "
-+
+               "\tThis is larger than half of at least one of the\n"
-+
+               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
-+
+               "\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();
-+
+    }
-+
+  } 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;
-+
+}
-+
-+
-+
+void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
-+
+                          vector<int>& groupList, vector<int>& groupStart){
-+
+  Molecule* myMols;
-+
+  Atom** myAtoms;
-+
+  int numAtom;
-+
+  int curIndex;
-+
+  double mtot;
-+
+  int numMol;
-+
+  int numCutoffGroups;
-+
+  CutoffGroup* myCutoffGroup;
-+
+  vector<CutoffGroup*>::iterator iterCutoff;
-+
+  Atom* cutoffAtom;
-+
+  vector<Atom*>::iterator iterAtom;
-+
+  int atomIndex;
-+
+  double totalMass;
-+
-+
+  mfact.clear();
-+
+  groupList.clear();
-+
+  groupStart.clear();
-+
-+
+  //Be careful, fortran array begin at 1
-+
+  curIndex = 1;
-+
-+
+  myMols = info->molecules;
-+
+  numMol = info->n_mol;
-+
+  for(int i  = 0; i < numMol; i++){
-+
+    numAtom = myMols[i].getNAtoms();
-+
+    myAtoms = myMols[i].getMyAtoms();
-+
-+
-+
+    for(int j = 0; j < numAtom; j++){
-+
-+
-+
+#ifdef IS_MPI
-+
+      atomIndex = myAtoms[j]->getGlobalIndex();
-+
+#else
-+
+      atomIndex = myAtoms[j]->getIndex();
-+
+#endif
-+
-+
+      if(myMols[i].belongToCutoffGroup(atomIndex))
-+
+        continue;
-+
+      else{
-+
+        // this is a fraction of the cutoff group's mass, not the mass itself!
-+
+        mfact.push_back(1.0);
-+
+        groupList.push_back(myAtoms[j]->getIndex() + 1);
-+
+        groupStart.push_back(curIndex++);
-+
+      }
-+
+    }
-+
-+
+    numCutoffGroups = myMols[i].getNCutoffGroups();
-+
+    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
-+
+                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
-+
-+
+      totalMass = myCutoffGroup->getMass();
-+
-+
+      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
-+
+                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
-+
+        mfact.push_back(cutoffAtom->getMass()/totalMass);
-+
+        groupList.push_back(cutoffAtom->getIndex() + 1);
-+
+      }
-+
-+
+      groupStart.push_back(curIndex);
-+
+      curIndex += myCutoffGroup->getNumAtom();
-+
-+
+    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
-+
-+
+  }//end for(int i  = 0; i < numMol; i++)
-+
-+
+  ngroup = groupStart.size();
-+
+}

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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents): Revision 441 by chuckv, Tue Apr 1 16:50:14 2003 UTC vs. Revision 1163 by gezelter, Wed May 12 14:30:12 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 441 by chuckv, Tue Apr 1 16:50:14 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 2004 UTC