OOPSE/libmdtools/SimSetup.cpp

#include <algorithm>
#include <cstdlib>
#include <iostream>
#include <cmath>
#include <string>
#include <sprng.h> 

#include "SimSetup.hpp"
#include "ReadWrite.hpp"
#include "parse_me.h"
#include "Integrator.hpp"
#include "simError.h"

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

// some defines for ensemble and Forcefield  cases

#define NVE_ENS        0 
#define NVT_ENS        1
#define NPTi_ENS       2
#define NPTf_ENS       3
#define NPTxyz_ENS     4


#define FF_DUFF 0
#define FF_LJ   1
#define FF_EAM  2

using namespace std;

SimSetup::SimSetup(){
  isInfoArray = 0;
  nInfo = 1;

  stamps = new MakeStamps();
  globals = new Globals();


#ifdef IS_MPI
  strcpy(checkPointMsg, "SimSetup creation successful");
  MPIcheckPoint();
#endif // IS_MPI
}

SimSetup::~SimSetup(){
  delete stamps;
  delete globals;
}

void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
  info = the_info;
  nInfo = theNinfo;
  isInfoArray = 1;
}


void SimSetup::parseFile(char* fileName){
#ifdef IS_MPI
  if (worldRank == 0){
#endif // is_mpi

    inFileName = fileName;
    set_interface_stamps(stamps, globals);

#ifdef IS_MPI
    mpiEventInit();
#endif

    yacc_BASS(fileName);

#ifdef IS_MPI
    throwMPIEvent(NULL);
  }
  else{
    receiveParse();
  }
#endif

}

#ifdef IS_MPI
void SimSetup::receiveParse(void){
  set_interface_stamps(stamps, globals);
  mpiEventInit();
  MPIcheckPoint();
  mpiEventLoop();
}

#endif // is_mpi

void SimSetup::createSim(void){

  // gather all of the information from the Bass file

  gatherInfo();

  // creation of complex system objects

  sysObjectsCreation();

  // check on the post processing info

  finalInfoCheck();

  // initialize the system coordinates

  if (!isInfoArray){
    initSystemCoords();

    if( !(globals->getUseInitTime()) )
      info[0].currentTime = 0.0;
  }  

  // make the output filenames

  makeOutNames();

  // make the integrator

  makeIntegrator();

#ifdef IS_MPI
  mpiSim->mpiRefresh();
#endif

  // initialize the Fortran

  initFortran();
}


void SimSetup::makeMolecules(void){
  int k;
  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
  molInit molInfo;
  DirectionalAtom* dAtom;
  LinkedAssign* extras;
  LinkedAssign* current_extra;
  AtomStamp* currentAtom;
  BondStamp* currentBond;
  BendStamp* currentBend;
  TorsionStamp* currentTorsion;

  bond_pair* theBonds;
  bend_set* theBends;
  torsion_set* theTorsions;


  //init the forceField paramters

  the_ff->readParams();


  // init the atoms

  double ux, uy, uz, u, uSqr;

  for (k = 0; k < nInfo; k++){
    the_ff->setSimInfo(&(info[k]));

    atomOffset = 0;
    excludeOffset = 0;
    for (i = 0; i < info[k].n_mol; i++){
      stampID = info[k].molecules[i].getStampID();

      molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
      molInfo.nBonds = comp_stamps[stampID]->getNBonds();
      molInfo.nBends = comp_stamps[stampID]->getNBends();
      molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
      molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;

      molInfo.myAtoms = &(info[k].atoms[atomOffset]);
      molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
      molInfo.myBonds = new Bond * [molInfo.nBonds];
      molInfo.myBends = new Bend * [molInfo.nBends];
      molInfo.myTorsions = new Torsion * [molInfo.nTorsions];

      theBonds = new bond_pair[molInfo.nBonds];
      theBends = new bend_set[molInfo.nBends];
      theTorsions = new torsion_set[molInfo.nTorsions];

      // make the Atoms

      for (j = 0; j < molInfo.nAtoms; j++){
        currentAtom = comp_stamps[stampID]->getAtom(j);
        if (currentAtom->haveOrientation()){
          dAtom = new DirectionalAtom((j + atomOffset),
                                      info[k].getConfiguration());
          info[k].n_oriented++;
          molInfo.myAtoms[j] = dAtom;

          ux = currentAtom->getOrntX();
          uy = currentAtom->getOrntY();
          uz = currentAtom->getOrntZ();

          uSqr = (ux * ux) + (uy * uy) + (uz * uz);

          u = sqrt(uSqr);
          ux = ux / u;
          uy = uy / u;
          uz = uz / u;

          dAtom->setSUx(ux);
          dAtom->setSUy(uy);
          dAtom->setSUz(uz);
        }
        else{
          molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
                                               info[k].getConfiguration());
        }
        molInfo.myAtoms[j]->setType(currentAtom->getType());

#ifdef IS_MPI

        molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);

#endif // is_mpi
      } 

      // make the bonds
      for (j = 0; j < molInfo.nBonds; j++){
        currentBond = comp_stamps[stampID]->getBond(j);
        theBonds[j].a = currentBond->getA() + atomOffset;
        theBonds[j].b = currentBond->getB() + atomOffset;

        exI = theBonds[j].a;
        exJ = theBonds[j].b;

        // exclude_I must always be the smaller of the pair
        if (exI > exJ){
          tempEx = exI;
          exI = exJ;
          exJ = tempEx;
        }
#ifdef IS_MPI
        tempEx = exI;
        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
        tempEx = exJ;
        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;

        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
#else  // isn't MPI

        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
#endif  //is_mpi
      }
      excludeOffset += molInfo.nBonds;

      //make the bends
      for (j = 0; j < molInfo.nBends; j++){
        currentBend = comp_stamps[stampID]->getBend(j);
        theBends[j].a = currentBend->getA() + atomOffset;
        theBends[j].b = currentBend->getB() + atomOffset;
        theBends[j].c = currentBend->getC() + atomOffset;

        if (currentBend->haveExtras()){
          extras = currentBend->getExtras();
          current_extra = extras;

          while (current_extra != NULL){
            if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
              switch (current_extra->getType()){
                case 0:
                  theBends[j].ghost = current_extra->getInt() + atomOffset;
                  theBends[j].isGhost = 1;
                  break;

                case 1:
                  theBends[j].ghost = (int) current_extra->getDouble() +
                                      atomOffset;
                  theBends[j].isGhost = 1;
                  break;

                default:
                  sprintf(painCave.errMsg,
                          "SimSetup Error: ghostVectorSource was neither a "
                          "double nor an int.\n"
                          "-->Bend[%d] in %s\n",
                          j, comp_stamps[stampID]->getID());
                  painCave.isFatal = 1;
                  simError();
              }
            }
            else{
              sprintf(painCave.errMsg,
                      "SimSetup Error: unhandled bend assignment:\n"
                      "    -->%s in Bend[%d] in %s\n",
                      current_extra->getlhs(), j, comp_stamps[stampID]->getID());
              painCave.isFatal = 1;
              simError();
            }

            current_extra = current_extra->getNext();
          }
        }

        if (!theBends[j].isGhost){
          exI = theBends[j].a;
          exJ = theBends[j].c;
        }
        else{
          exI = theBends[j].a;
          exJ = theBends[j].b;
        }

        // exclude_I must always be the smaller of the pair
        if (exI > exJ){
          tempEx = exI;
          exI = exJ;
          exJ = tempEx;
        }
#ifdef IS_MPI
        tempEx = exI;
        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
        tempEx = exJ;
        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;

        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
#else  // isn't MPI
        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
#endif  //is_mpi
      }
      excludeOffset += molInfo.nBends;

      for (j = 0; j < molInfo.nTorsions; j++){
        currentTorsion = comp_stamps[stampID]->getTorsion(j);
        theTorsions[j].a = currentTorsion->getA() + atomOffset;
        theTorsions[j].b = currentTorsion->getB() + atomOffset;
        theTorsions[j].c = currentTorsion->getC() + atomOffset;
        theTorsions[j].d = currentTorsion->getD() + atomOffset;

        exI = theTorsions[j].a;
        exJ = theTorsions[j].d;

        // exclude_I must always be the smaller of the pair
        if (exI > exJ){
          tempEx = exI;
          exI = exJ;
          exJ = tempEx;
        }
#ifdef IS_MPI
        tempEx = exI;
        exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
        tempEx = exJ;
        exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;

        info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
#else  // isn't MPI
        info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
#endif  //is_mpi
      }
      excludeOffset += molInfo.nTorsions;


      // send the arrays off to the forceField for init.

      the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
      the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
      the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
      the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
                                 theTorsions);


      info[k].molecules[i].initialize(molInfo);


      atomOffset += molInfo.nAtoms;
      delete[] theBonds;
      delete[] theBends;
      delete[] theTorsions;
    }
  }

#ifdef IS_MPI
  sprintf(checkPointMsg, "all molecules initialized succesfully");
  MPIcheckPoint();
#endif // is_mpi

  // clean up the forcefield

  the_ff->calcRcut();
  the_ff->cleanMe();
}

void SimSetup::initFromBass(void){
  int i, j, k;
  int n_cells;
  double cellx, celly, cellz;
  double temp1, temp2, temp3;
  int n_per_extra;
  int n_extra;
  int have_extra, done;

  double vel[3];
  vel[0] = 0.0;
  vel[1] = 0.0;
  vel[2] = 0.0;

  temp1 = (double) tot_nmol / 4.0;
  temp2 = pow(temp1, (1.0 / 3.0));
  temp3 = ceil(temp2);

  have_extra = 0;
  if (temp2 < temp3){
    // we have a non-complete lattice
    have_extra = 1;

    n_cells = (int) temp3 - 1;
    cellx = info[0].boxL[0] / temp3;
    celly = info[0].boxL[1] / temp3;
    cellz = info[0].boxL[2] / temp3;
    n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
    temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
    n_per_extra = (int) ceil(temp1);

    if (n_per_extra > 4){
      sprintf(painCave.errMsg,
              "SimSetup error. There has been an error in constructing"
              " the non-complete lattice.\n");
      painCave.isFatal = 1;
      simError();
    }
  }
  else{
    n_cells = (int) temp3;
    cellx = info[0].boxL[0] / temp3;
    celly = info[0].boxL[1] / temp3;
    cellz = info[0].boxL[2] / temp3;
  }

  current_mol = 0;
  current_comp_mol = 0;
  current_comp = 0;
  current_atom_ndx = 0;

  for (i = 0; i < n_cells ; i++){
    for (j = 0; j < n_cells; j++){
      for (k = 0; k < n_cells; k++){
        makeElement(i * cellx, j * celly, k * cellz);

        makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);

        makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);

        makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
      }
    }
  }

  if (have_extra){
    done = 0;

    int start_ndx;
    for (i = 0; i < (n_cells + 1) && !done; i++){
      for (j = 0; j < (n_cells + 1) && !done; j++){
        if (i < n_cells){
          if (j < n_cells){
            start_ndx = n_cells;
          }
          else
            start_ndx = 0;
        }
        else
          start_ndx = 0;

        for (k = start_ndx; k < (n_cells + 1) && !done; k++){
          makeElement(i * cellx, j * celly, k * cellz);
          done = (current_mol >= tot_nmol);

          if (!done && n_per_extra > 1){
            makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
                        k * cellz);
            done = (current_mol >= tot_nmol);
          }

          if (!done && n_per_extra > 2){
            makeElement(i * cellx, j * celly + 0.5 * celly,
                        k * cellz + 0.5 * cellz);
            done = (current_mol >= tot_nmol);
          }

          if (!done && n_per_extra > 3){
            makeElement(i * cellx + 0.5 * cellx, j * celly,
                        k * cellz + 0.5 * cellz);
            done = (current_mol >= tot_nmol);
          }
        }
      }
    }
  }

  for (i = 0; i < info[0].n_atoms; i++){
    info[0].atoms[i]->setVel(vel);
  }
}

void SimSetup::makeElement(double x, double y, double z){
  int k;
  AtomStamp* current_atom;
  DirectionalAtom* dAtom;
  double rotMat[3][3];
  double pos[3];

  for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
    current_atom = comp_stamps[current_comp]->getAtom(k);
    if (!current_atom->havePosition()){
      sprintf(painCave.errMsg,
              "SimSetup:initFromBass error.\n"
              "\tComponent %s, atom %s does not have a position specified.\n"
              "\tThe initialization routine is unable to give a start"
              " position.\n",
              comp_stamps[current_comp]->getID(), current_atom->getType());
      painCave.isFatal = 1;
      simError();
    }

    pos[0] = x + current_atom->getPosX();
    pos[1] = y + current_atom->getPosY();
    pos[2] = z + current_atom->getPosZ();

    info[0].atoms[current_atom_ndx]->setPos(pos);

    if (info[0].atoms[current_atom_ndx]->isDirectional()){
      dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];

      rotMat[0][0] = 1.0;
      rotMat[0][1] = 0.0;
      rotMat[0][2] = 0.0;

      rotMat[1][0] = 0.0;
      rotMat[1][1] = 1.0;
      rotMat[1][2] = 0.0;

      rotMat[2][0] = 0.0;
      rotMat[2][1] = 0.0;
      rotMat[2][2] = 1.0;

      dAtom->setA(rotMat);
    }

    current_atom_ndx++;
  }

  current_mol++;
  current_comp_mol++;

  if (current_comp_mol >= components_nmol[current_comp]){
    current_comp_mol = 0;
    current_comp++;
  }
}


void SimSetup::gatherInfo(void){
  int i;

  ensembleCase = -1;
  ffCase = -1;

  // set the easy ones first

  for (i = 0; i < nInfo; i++){
    info[i].target_temp = globals->getTargetTemp();
    info[i].dt = globals->getDt();
    info[i].run_time = globals->getRunTime();
  }
  n_components = globals->getNComponents();


  // get the forceField

  strcpy(force_field, globals->getForceField());

  if (!strcasecmp(force_field, "DUFF")){
    ffCase = FF_DUFF;
  }
  else if (!strcasecmp(force_field, "LJ")){
    ffCase = FF_LJ;
  }
  else if (!strcasecmp(force_field, "EAM")){
    ffCase = FF_EAM;
  }
  else{
    sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
            force_field);
         painCave.isFatal = 1;
         simError();
  }

    // get the ensemble

  strcpy(ensemble, globals->getEnsemble());

  if (!strcasecmp(ensemble, "NVE")){
    ensembleCase = NVE_ENS;
  }
  else if (!strcasecmp(ensemble, "NVT")){
    ensembleCase = NVT_ENS;
  }
  else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
    ensembleCase = NPTi_ENS;
  }
  else if (!strcasecmp(ensemble, "NPTf")){
    ensembleCase = NPTf_ENS;
  }
  else if (!strcasecmp(ensemble, "NPTxyz")){
    ensembleCase = NPTxyz_ENS;
  }
  else{
    sprintf(painCave.errMsg,
            "SimSetup Warning. Unrecognized Ensemble -> %s, "
            "reverting to NVE for this simulation.\n",
            ensemble);
         painCave.isFatal = 0;
         simError();
         strcpy(ensemble, "NVE");
         ensembleCase = NVE_ENS;
  }  

  for (i = 0; i < nInfo; i++){
    strcpy(info[i].ensemble, ensemble);

    // get the mixing rule

    strcpy(info[i].mixingRule, globals->getMixingRule());
    info[i].usePBC = globals->getPBC();
  }

  // get the components and calculate the tot_nMol and indvidual n_mol

  the_components = globals->getComponents();
  components_nmol = new int[n_components];


  if (!globals->haveNMol()){
    // we don't have the total number of molecules, so we assume it is
    // given in each component

    tot_nmol = 0;
    for (i = 0; i < n_components; i++){
      if (!the_components[i]->haveNMol()){
        // we have a problem
        sprintf(painCave.errMsg,
                "SimSetup Error. No global NMol or component NMol"
                " given. Cannot calculate the number of atoms.\n");
        painCave.isFatal = 1;
        simError();
      }

      tot_nmol += the_components[i]->getNMol();
      components_nmol[i] = the_components[i]->getNMol();
    }
  }
  else{
    sprintf(painCave.errMsg,
            "SimSetup error.\n"
            "\tSorry, the ability to specify total"
            " nMols and then give molfractions in the components\n"
            "\tis not currently supported."
            " Please give nMol in the components.\n");
    painCave.isFatal = 1;
    simError();
  }

  // set the status, sample, and thermal kick times

  for (i = 0; i < nInfo; i++){
    if (globals->haveSampleTime()){
      info[i].sampleTime = globals->getSampleTime();
      info[i].statusTime = info[i].sampleTime;
      info[i].thermalTime = info[i].sampleTime;
    }
    else{
      info[i].sampleTime = globals->getRunTime();
      info[i].statusTime = info[i].sampleTime;
      info[i].thermalTime = info[i].sampleTime;
    }

    if (globals->haveStatusTime()){
      info[i].statusTime = globals->getStatusTime();
    }

    if (globals->haveThermalTime()){
      info[i].thermalTime = globals->getThermalTime();
    }

    info[i].resetIntegrator = 0;
    if( globals->haveResetTime() ){
      info[i].resetTime = globals->getResetTime();
      info[i].resetIntegrator = 1;
    }

    // check for the temperature set flag

    if (globals->haveTempSet())
      info[i].setTemp = globals->getTempSet();

    // get some of the tricky things that may still be in the globals

    double boxVector[3];
    if (globals->haveBox()){
      boxVector[0] = globals->getBox();
      boxVector[1] = globals->getBox();
      boxVector[2] = globals->getBox();

      info[i].setBox(boxVector);
    }
    else if (globals->haveDensity()){
      double vol;
      vol = (double) tot_nmol / globals->getDensity();
      boxVector[0] = pow(vol, (1.0 / 3.0));
      boxVector[1] = boxVector[0];
      boxVector[2] = boxVector[0];

      info[i].setBox(boxVector);
    }
    else{
      if (!globals->haveBoxX()){
        sprintf(painCave.errMsg,
                "SimSetup error, no periodic BoxX size given.\n");
        painCave.isFatal = 1;
        simError();
      }
      boxVector[0] = globals->getBoxX();

      if (!globals->haveBoxY()){
        sprintf(painCave.errMsg,
                "SimSetup error, no periodic BoxY size given.\n");
        painCave.isFatal = 1;
        simError();
      }
      boxVector[1] = globals->getBoxY();

      if (!globals->haveBoxZ()){
        sprintf(painCave.errMsg,
                "SimSetup error, no periodic BoxZ size given.\n");
        painCave.isFatal = 1;
        simError();
      }
      boxVector[2] = globals->getBoxZ();

      info[i].setBox(boxVector);
    }
  }

  //setup seed for random number generator
  int seedValue;

  if (globals->haveSeed()){
    seedValue = globals->getSeed();

    if(seedValue / 1E9 == 0){
      sprintf(painCave.errMsg,
              "Seed for sprng library should contain at least 9 digits\n"
              "OOPSE will generate a seed for user\n");
      painCave.isFatal = 0;
      simError();

      //using seed generated by system instead of invalid seed set by user 
#ifndef IS_MPI
      seedValue = make_sprng_seed();
#else 
      if (worldRank == 0){
        seedValue = make_sprng_seed();
      }
      MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);   
#endif      
    }
  }//end of if branch of globals->haveSeed()
  else{
    
#ifndef IS_MPI
    seedValue = make_sprng_seed();
#else 
    if (worldRank == 0){
      seedValue = make_sprng_seed();
    }
    MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);   
#endif
  }//end of globals->haveSeed()

  for (int i = 0; i < nInfo; i++){
    info[i].setSeed(seedValue);
  }

#ifdef IS_MPI
  strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
  MPIcheckPoint();
#endif // is_mpi
}


void SimSetup::finalInfoCheck(void){
  int index;
  int usesDipoles;
  int i;

  for (i = 0; i < nInfo; i++){
    // check electrostatic parameters

    index = 0;
    usesDipoles = 0;
    while ((index < info[i].n_atoms) && !usesDipoles){
      usesDipoles = (info[i].atoms[index])->hasDipole();
      index++;
    }

#ifdef IS_MPI
    int myUse = usesDipoles;
    MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
#endif //is_mpi

    double theEcr, theEst;

    if (globals->getUseRF()){
      info[i].useReactionField = 1;

      if (!globals->haveECR()){
        sprintf(painCave.errMsg,
                "SimSetup Warning: using default value of 1/2 the smallest "
                "box length for the electrostaticCutoffRadius.\n"
                "I hope you have a very fast processor!\n");
        painCave.isFatal = 0;
        simError();
        double smallest;
        smallest = info[i].boxL[0];
        if (info[i].boxL[1] <= smallest)
          smallest = info[i].boxL[1];
        if (info[i].boxL[2] <= smallest)
          smallest = info[i].boxL[2];
        theEcr = 0.5 * smallest;
      }
      else{
        theEcr = globals->getECR();
      }

      if (!globals->haveEST()){
        sprintf(painCave.errMsg,
                "SimSetup Warning: using default value of 0.05 * the "
                "electrostaticCutoffRadius for the electrostaticSkinThickness\n");
        painCave.isFatal = 0;
        simError();
        theEst = 0.05 * theEcr;
      }
      else{
        theEst = globals->getEST();
      }

      info[i].setEcr(theEcr, theEst);

      if (!globals->haveDielectric()){
        sprintf(painCave.errMsg,
                "SimSetup Error: You are trying to use Reaction Field without"
                "setting a dielectric constant!\n");
        painCave.isFatal = 1;
        simError();
      }
      info[i].dielectric = globals->getDielectric();
    }
    else{
      if (usesDipoles){
        if (!globals->haveECR()){
          sprintf(painCave.errMsg,
                  "SimSetup Warning: using default value of 1/2 the smallest "
                  "box length for the electrostaticCutoffRadius.\n"
                  "I hope you have a very fast processor!\n");
          painCave.isFatal = 0;
          simError();
          double smallest;
          smallest = info[i].boxL[0];
          if (info[i].boxL[1] <= smallest)
            smallest = info[i].boxL[1];
          if (info[i].boxL[2] <= smallest)
            smallest = info[i].boxL[2];
          theEcr = 0.5 * smallest;
        }
        else{
          theEcr = globals->getECR();
        }

        if (!globals->haveEST()){
          sprintf(painCave.errMsg,
                  "SimSetup Warning: using default value of 0.05 * the "
                  "electrostaticCutoffRadius for the "
                  "electrostaticSkinThickness\n");
          painCave.isFatal = 0;
          simError();
          theEst = 0.05 * theEcr;
        }
        else{
          theEst = globals->getEST();
        }

        info[i].setEcr(theEcr, theEst);
      }
    }
  }

#ifdef IS_MPI
  strcpy(checkPointMsg, "post processing checks out");
  MPIcheckPoint();
#endif // is_mpi
}

void SimSetup::initSystemCoords(void){
  int i;

  char* inName;

  (info[0].getConfiguration())->createArrays(info[0].n_atoms);

  for (i = 0; i < info[0].n_atoms; i++)
    info[0].atoms[i]->setCoords();

  if (globals->haveInitialConfig()){
    InitializeFromFile* fileInit;
#ifdef IS_MPI // is_mpi
    if (worldRank == 0){
#endif //is_mpi
      inName = globals->getInitialConfig();
      fileInit = new InitializeFromFile(inName);
#ifdef IS_MPI
    }
    else
      fileInit = new InitializeFromFile(NULL);
#endif
    fileInit->readInit(info); // default velocities on

    delete fileInit;
  }
  else{
#ifdef IS_MPI 

    // no init from bass

    sprintf(painCave.errMsg,
            "Cannot intialize a parallel simulation without an initial configuration file.\n");
    painCave.isFatal = 1;;
    simError();

#else

    initFromBass();


#endif
  }

#ifdef IS_MPI
  strcpy(checkPointMsg, "Successfully read in the initial configuration");
  MPIcheckPoint();
#endif // is_mpi
}


void SimSetup::makeOutNames(void){
  int k;


  for (k = 0; k < nInfo; k++){
#ifdef IS_MPI
    if (worldRank == 0){
#endif // is_mpi

      if (globals->haveFinalConfig()){
        strcpy(info[k].finalName, globals->getFinalConfig());
      }
      else{
        strcpy(info[k].finalName, inFileName);
        char* endTest;
        int nameLength = strlen(info[k].finalName);
        endTest = &(info[k].finalName[nameLength - 5]);
        if (!strcmp(endTest, ".bass")){
          strcpy(endTest, ".eor");
        }
        else if (!strcmp(endTest, ".BASS")){
          strcpy(endTest, ".eor");
        }
        else{
          endTest = &(info[k].finalName[nameLength - 4]);
          if (!strcmp(endTest, ".bss")){
            strcpy(endTest, ".eor");
          }
          else if (!strcmp(endTest, ".mdl")){
            strcpy(endTest, ".eor");
          }
          else{
            strcat(info[k].finalName, ".eor");
          }
        }
      }

      // make the sample and status out names

      strcpy(info[k].sampleName, inFileName);
      char* endTest;
      int nameLength = strlen(info[k].sampleName);
      endTest = &(info[k].sampleName[nameLength - 5]);
      if (!strcmp(endTest, ".bass")){
        strcpy(endTest, ".dump");
      }
      else if (!strcmp(endTest, ".BASS")){
        strcpy(endTest, ".dump");
      }
      else{
        endTest = &(info[k].sampleName[nameLength - 4]);
        if (!strcmp(endTest, ".bss")){
          strcpy(endTest, ".dump");
        }
        else if (!strcmp(endTest, ".mdl")){
          strcpy(endTest, ".dump");
        }
        else{
          strcat(info[k].sampleName, ".dump");
        }
      }

      strcpy(info[k].statusName, inFileName);
      nameLength = strlen(info[k].statusName);
      endTest = &(info[k].statusName[nameLength - 5]);
      if (!strcmp(endTest, ".bass")){
        strcpy(endTest, ".stat");
      }
      else if (!strcmp(endTest, ".BASS")){
        strcpy(endTest, ".stat");
      }
      else{
        endTest = &(info[k].statusName[nameLength - 4]);
        if (!strcmp(endTest, ".bss")){
          strcpy(endTest, ".stat");
        }
        else if (!strcmp(endTest, ".mdl")){
          strcpy(endTest, ".stat");
        }
        else{
          strcat(info[k].statusName, ".stat");
        }
      }

#ifdef IS_MPI

    }
#endif // is_mpi
  }
}


void SimSetup::sysObjectsCreation(void){
  int i, k;

  // create the forceField

  createFF();

  // extract componentList

  compList();

  // calc the number of atoms, bond, bends, and torsions

  calcSysValues();

#ifdef IS_MPI
  // divide the molecules among the processors

  mpiMolDivide();
#endif //is_mpi

  // create the atom and SRI arrays. Also initialize Molecule Stamp ID's

  makeSysArrays();

  // make and initialize the molecules (all but atomic coordinates)

  makeMolecules();

  for (k = 0; k < nInfo; k++){
    info[k].identArray = new int[info[k].n_atoms];
    for (i = 0; i < info[k].n_atoms; i++){
      info[k].identArray[i] = info[k].atoms[i]->getIdent();
    }
  }
}


void SimSetup::createFF(void){
  switch (ffCase){
    case FF_DUFF:
      the_ff = new DUFF();
      break;

    case FF_LJ:
      the_ff = new LJFF();
      break;

    case FF_EAM:
      the_ff = new EAM_FF();
      break;

    default:
      sprintf(painCave.errMsg,
              "SimSetup Error. Unrecognized force field in case statement.\n");
      painCave.isFatal = 1;
      simError();
  }

#ifdef IS_MPI
  strcpy(checkPointMsg, "ForceField creation successful");
  MPIcheckPoint();
#endif // is_mpi
}


void SimSetup::compList(void){
  int i;
  char* id;
  LinkedMolStamp* headStamp = new LinkedMolStamp();
  LinkedMolStamp* currentStamp = NULL;
  comp_stamps = new MoleculeStamp * [n_components];

  // make an array of molecule stamps that match the components used.
  // also extract the used stamps out into a separate linked list

  for (i = 0; i < nInfo; i++){
    info[i].nComponents = n_components;
    info[i].componentsNmol = components_nmol;
    info[i].compStamps = comp_stamps;
    info[i].headStamp = headStamp;
  }


  for (i = 0; i < n_components; i++){
    id = the_components[i]->getType();
    comp_stamps[i] = NULL;

    // check to make sure the component isn't already in the list

    comp_stamps[i] = headStamp->match(id);
    if (comp_stamps[i] == NULL){
      // extract the component from the list;

      currentStamp = stamps->extractMolStamp(id);
      if (currentStamp == NULL){
        sprintf(painCave.errMsg,
                "SimSetup error: Component \"%s\" was not found in the "
                "list of declared molecules\n",
                id);
        painCave.isFatal = 1;
        simError();
      }

      headStamp->add(currentStamp);
      comp_stamps[i] = headStamp->match(id);
    }
  }

#ifdef IS_MPI
  strcpy(checkPointMsg, "Component stamps successfully extracted\n");
  MPIcheckPoint();
#endif // is_mpi
}

void SimSetup::calcSysValues(void){
  int i;

  int* molMembershipArray;

  tot_atoms = 0;
  tot_bonds = 0;
  tot_bends = 0;
  tot_torsions = 0;
  for (i = 0; i < n_components; i++){
    tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
    tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
    tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
    tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
  }

  tot_SRI = tot_bonds + tot_bends + tot_torsions;
  molMembershipArray = new int[tot_atoms];

  for (i = 0; i < nInfo; i++){
    info[i].n_atoms = tot_atoms;
    info[i].n_bonds = tot_bonds;
    info[i].n_bends = tot_bends;
    info[i].n_torsions = tot_torsions;
    info[i].n_SRI = tot_SRI;
    info[i].n_mol = tot_nmol;

    info[i].molMembershipArray = molMembershipArray;
  }
}

#ifdef IS_MPI

void SimSetup::mpiMolDivide(void){
  int i, j, k;
  int localMol, allMol;
  int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;

  mpiSim = new mpiSimulation(info);

  globalIndex = mpiSim->divideLabor();

  // set up the local variables 

  mol2proc = mpiSim->getMolToProcMap();
  molCompType = mpiSim->getMolComponentType();

  allMol = 0;
  localMol = 0;
  local_atoms = 0;
  local_bonds = 0;
  local_bends = 0;
  local_torsions = 0;
  globalAtomIndex = 0;


  for (i = 0; i < n_components; i++){
    for (j = 0; j < components_nmol[i]; j++){
      if (mol2proc[allMol] == worldRank){
        local_atoms += comp_stamps[i]->getNAtoms();
        local_bonds += comp_stamps[i]->getNBonds();
        local_bends += comp_stamps[i]->getNBends();
        local_torsions += comp_stamps[i]->getNTorsions();
        localMol++;
      }      
      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
        info[0].molMembershipArray[globalAtomIndex] = allMol;
        globalAtomIndex++;
      }

      allMol++;
    }
  }
  local_SRI = local_bonds + local_bends + local_torsions;

  info[0].n_atoms = mpiSim->getMyNlocal();  

  if (local_atoms != info[0].n_atoms){
    sprintf(painCave.errMsg,
            "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
            " localAtom (%d) are not equal.\n",
            info[0].n_atoms, local_atoms);
    painCave.isFatal = 1;
    simError();
  }

  info[0].n_bonds = local_bonds;
  info[0].n_bends = local_bends;
  info[0].n_torsions = local_torsions;
  info[0].n_SRI = local_SRI;
  info[0].n_mol = localMol;

  strcpy(checkPointMsg, "Passed nlocal consistency check.");
  MPIcheckPoint();
}

#endif // is_mpi


void SimSetup::makeSysArrays(void){
 
#ifndef IS_MPI
  int k, j;
#endif // is_mpi
  int i, l;

  Atom** the_atoms;
  Molecule* the_molecules;
  Exclude** the_excludes;


  for (l = 0; l < nInfo; l++){
    // create the atom and short range interaction arrays

    the_atoms = new Atom * [info[l].n_atoms];
    the_molecules = new Molecule[info[l].n_mol];
    int molIndex;

    // initialize the molecule's stampID's

#ifdef IS_MPI


    molIndex = 0;
    for (i = 0; i < mpiSim->getTotNmol(); i++){
      if (mol2proc[i] == worldRank){
        the_molecules[molIndex].setStampID(molCompType[i]);
        the_molecules[molIndex].setMyIndex(molIndex);
        the_molecules[molIndex].setGlobalIndex(i);
        molIndex++;
      }
    }

#else // is_mpi

    molIndex = 0;
    globalAtomIndex = 0;
    for (i = 0; i < n_components; i++){
      for (j = 0; j < components_nmol[i]; j++){
        the_molecules[molIndex].setStampID(i);
        the_molecules[molIndex].setMyIndex(molIndex);
        the_molecules[molIndex].setGlobalIndex(molIndex);
        for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
          info[l].molMembershipArray[globalAtomIndex] = molIndex;
          globalAtomIndex++;
        }
        molIndex++;
      }
    }


#endif // is_mpi


    if (info[l].n_SRI){
      Exclude::createArray(info[l].n_SRI);
      the_excludes = new Exclude * [info[l].n_SRI];
      for (int ex = 0; ex < info[l].n_SRI; ex++){
        the_excludes[ex] = new Exclude(ex);
      }
      info[l].globalExcludes = new int;
      info[l].n_exclude = info[l].n_SRI;
    }
    else{
      Exclude::createArray(1);
      the_excludes = new Exclude * ;
      the_excludes[0] = new Exclude(0);
      the_excludes[0]->setPair(0, 0);
      info[l].globalExcludes = new int;
      info[l].globalExcludes[0] = 0;
      info[l].n_exclude = 0;
    }

    // set the arrays into the SimInfo object

    info[l].atoms = the_atoms;
    info[l].molecules = the_molecules;
    info[l].nGlobalExcludes = 0;
    info[l].excludes = the_excludes;

    the_ff->setSimInfo(info);
  }
}

void SimSetup::makeIntegrator(void){
  int k;

  NVE<RealIntegrator>* myNVE = NULL;
  NVT<RealIntegrator>* myNVT = NULL;
  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
  
  for (k = 0; k < nInfo; k++){
    switch (ensembleCase){
      case NVE_ENS:
        if (globals->haveZconstraints()){
          setupZConstraint(info[k]);
          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
        }
        else{
          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
        }
        
        info->the_integrator = myNVE;
        break;

      case NVT_ENS:
        if (globals->haveZconstraints()){
          setupZConstraint(info[k]);
          myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
        }
        else
          myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);

        myNVT->setTargetTemp(globals->getTargetTemp());

        if (globals->haveTauThermostat())
          myNVT->setTauThermostat(globals->getTauThermostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use the NVT\n"
                  "    ensemble, you must set tauThermostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        info->the_integrator = myNVT;
        break;

      case NPTi_ENS:
        if (globals->haveZconstraints()){
          setupZConstraint(info[k]);
          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
        }
        else
          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);

        myNPTi->setTargetTemp(globals->getTargetTemp());

        if (globals->haveTargetPressure())
          myNPTi->setTargetPressure(globals->getTargetPressure());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use a constant pressure\n"
                  "    ensemble, you must set targetPressure in the BASS file.\n");
          painCave.isFatal = 1;
          simError();
        }

        if (globals->haveTauThermostat())
          myNPTi->setTauThermostat(globals->getTauThermostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use an NPT\n"
                  "    ensemble, you must set tauThermostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        if (globals->haveTauBarostat())
          myNPTi->setTauBarostat(globals->getTauBarostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use an NPT\n"
                  "    ensemble, you must set tauBarostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        info->the_integrator = myNPTi;
        break;

      case NPTf_ENS:
        if (globals->haveZconstraints()){
          setupZConstraint(info[k]);
          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
        }
        else
          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);

        myNPTf->setTargetTemp(globals->getTargetTemp());

        if (globals->haveTargetPressure())
          myNPTf->setTargetPressure(globals->getTargetPressure());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use a constant pressure\n"
                  "    ensemble, you must set targetPressure in the BASS file.\n");
          painCave.isFatal = 1;
          simError();
        }    

        if (globals->haveTauThermostat())
          myNPTf->setTauThermostat(globals->getTauThermostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use an NPT\n"
                  "    ensemble, you must set tauThermostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        if (globals->haveTauBarostat())
          myNPTf->setTauBarostat(globals->getTauBarostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use an NPT\n"
                  "    ensemble, you must set tauBarostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        info->the_integrator = myNPTf;
        break;

      case NPTxyz_ENS:
        if (globals->haveZconstraints()){
          setupZConstraint(info[k]);
          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
        }
        else
          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);

        myNPTxyz->setTargetTemp(globals->getTargetTemp());

        if (globals->haveTargetPressure())
          myNPTxyz->setTargetPressure(globals->getTargetPressure());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use a constant pressure\n"
                  "    ensemble, you must set targetPressure in the BASS file.\n");
          painCave.isFatal = 1;
          simError();
        }    

        if (globals->haveTauThermostat())
          myNPTxyz->setTauThermostat(globals->getTauThermostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use an NPT\n"
                  "    ensemble, you must set tauThermostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        if (globals->haveTauBarostat())
          myNPTxyz->setTauBarostat(globals->getTauBarostat());
        else{
          sprintf(painCave.errMsg,
                  "SimSetup error: If you use an NPT\n"
                  "    ensemble, you must set tauBarostat.\n");
          painCave.isFatal = 1;
          simError();
        }

        info->the_integrator = myNPTxyz;
        break;

      default:
        sprintf(painCave.errMsg,
                "SimSetup Error. Unrecognized ensemble in case statement.\n");
        painCave.isFatal = 1;
        simError();
    }
  }
}

void SimSetup::initFortran(void){
  info[0].refreshSim();

  if (!strcmp(info[0].mixingRule, "standard")){
    the_ff->initForceField(LB_MIXING_RULE);
  }
  else if (!strcmp(info[0].mixingRule, "explicit")){
    the_ff->initForceField(EXPLICIT_MIXING_RULE);
  }
  else{
    sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
            info[0].mixingRule);
    painCave.isFatal = 1;
    simError();
  }


#ifdef IS_MPI
  strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
  MPIcheckPoint();
#endif // is_mpi
}

void SimSetup::setupZConstraint(SimInfo& theInfo){
  int nZConstraints;
  ZconStamp** zconStamp;

  if (globals->haveZconstraintTime()){
    //add sample time of z-constraint  into SimInfo's property list                    
    DoubleData* zconsTimeProp = new DoubleData();
    zconsTimeProp->setID(ZCONSTIME_ID);
    zconsTimeProp->setData(globals->getZconsTime());
    theInfo.addProperty(zconsTimeProp);
  }
  else{
    sprintf(painCave.errMsg,
            "ZConstraint error: If you use an ZConstraint\n"
            " , you must set sample time.\n");
    painCave.isFatal = 1;
    simError();
  }

  //push zconsTol into siminfo, if user does not specify
  //value for zconsTol, a default value will be used
  DoubleData* zconsTol = new DoubleData();
  zconsTol->setID(ZCONSTOL_ID);
  if (globals->haveZconsTol()){
    zconsTol->setData(globals->getZconsTol());
  }
  else{
    double defaultZConsTol = 0.01;
    sprintf(painCave.errMsg,
            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
            " , default value %f is used.\n",
            defaultZConsTol);
    painCave.isFatal = 0;
    simError();      

    zconsTol->setData(defaultZConsTol);
  }
  theInfo.addProperty(zconsTol);

  //set Force Subtraction Policy
  StringData* zconsForcePolicy = new StringData();
  zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);

  if (globals->haveZconsForcePolicy()){
    zconsForcePolicy->setData(globals->getZconsForcePolicy());
  }
  else{
    sprintf(painCave.errMsg,
            "ZConstraint Warning: User does not set force Subtraction policy, "
            "PolicyByMass is used\n");
    painCave.isFatal = 0;
    simError(); 
    zconsForcePolicy->setData("BYMASS");
  }

  theInfo.addProperty(zconsForcePolicy);

  //Determine the name of ouput file and add it into SimInfo's property list 
  //Be careful, do not use inFileName, since it is a pointer which
  //point to a string at master node, and slave nodes do not contain that string

  string zconsOutput(theInfo.finalName);

  zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";

  StringData* zconsFilename = new StringData();
  zconsFilename->setID(ZCONSFILENAME_ID);
  zconsFilename->setData(zconsOutput);

  theInfo.addProperty(zconsFilename);

  //setup index, pos and other parameters of z-constraint molecules
  nZConstraints = globals->getNzConstraints();
  theInfo.nZconstraints = nZConstraints;

  zconStamp = globals->getZconStamp();
  ZConsParaItem tempParaItem;

  ZConsParaData* zconsParaData = new ZConsParaData();
  zconsParaData->setID(ZCONSPARADATA_ID);

  for (int i = 0; i < nZConstraints; i++){
    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
    tempParaItem.zPos = zconStamp[i]->getZpos();
    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
    tempParaItem.kRatio = zconStamp[i]->getKratio();

    zconsParaData->addItem(tempParaItem);
  }

  //check the uniqueness of index  
  if(!zconsParaData->isIndexUnique()){
    sprintf(painCave.errMsg,
            "ZConstraint Error: molIndex is not unique\n");
    painCave.isFatal = 1;
    simError(); 
  }

  //sort the parameters by index of molecules
  zconsParaData->sortByIndex();
  
  //push data into siminfo, therefore, we can retrieve later
  theInfo.addProperty(zconsParaData);
}
Revision:	812
Committed:	Wed Oct 22 21:17:32 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	43816 byte(s)
Log Message:	added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.