NamdState.C

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/*
***  Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by
***  The Board of Trustees of the University of Illinois.
***  All rights reserved.
**/

/*
   Holds pointers to large molecule data structure, simulation parameters...
*/

#include "InfoStream.h"
#include "common.h"
#include "Molecule.h"
#include "Parameters.h"
#include "SimParameters.h"
#include "ConfigList.h"
#include "PDB.h"
#include "NamdState.h"
#include "Controller.h"
#include "ScriptTcl.h"
#ifndef WIN32
#include <unistd.h>
#endif
#include <sys/stat.h>
#include "parm.h"

//#define DEBUGM
#include "Debug.h"

#include "CompressPsf.h"
#include "PluginIOMgr.h"

NamdState::NamdState()
{
    configList = NULL;
    simParameters = NULL;
    parameters = NULL;
    molecule = NULL;
    pdb = NULL;
}

int
NamdState::status()
{
    int ret=0;
    if (configList != NULL) {
      DebugM(1, "Config List exists\n");
    } else ret++;

    if (simParameters != NULL) {
      DebugM(1, "SimParameters exists\n");
    }
    else ret++;

    if (parameters != NULL) {
      DebugM(1,"Parameters exists\n");
    }
    else ret++;

    if (molecule != NULL) {
      DebugM(1, "Molecule exists\n");
    }
    else ret++;

    if (pdb != NULL) {
      DebugM(1,"PDB exists \n");
    }
    else ret++;
    
    return(ret);
}

void NamdState:: useController(Controller *controllerPtr)
{
  controller=controllerPtr;
}

void NamdState:: runController(void)
{
  controller->run();
}

extern void read_binary_coors(char *fname, PDB *pdbobj);

#ifdef MEM_OPT_VERSION
 //Check features that are not supported in the memory optimized 
 //version.  --Chao Mei
void NamdState::checkMemOptCompatibility(){
    if(simParameters->genCompressedPsf) {
        iout << "In the memory optimized version, the compression of molecule information is not supported! "
                << "Please use the non-memory optimized version.\n" <<endi;
        NAMD_die("MEMOPT: unsupported usage");
    }

    if(simParameters->langevinOn && simParameters->langevinDamping == 0.0) {
        iout << iWARN << "langevinDamping MUST NOT BE 0.0 IF LANGEVIN IS"
            <<" TURNED ON IN MEMORY OPTIMIZED VERSION\n" <<endi;
        NAMD_die("MEMOPT: unsupported feature");
    }
    if(simParameters->tCoupleOn)
        NAMD_die("MEMOPT: tCouple is not supported in memory optimized version");
    if(simParameters->pairInteractionOn)
        NAMD_die("MEMOPT: pairInteractionOn could not be enabled in memory optimized version");
    if(simParameters->alchFepOn || simParameters->alchOn){
        iout << iWARN << "ALCH: AUTOMATIC DELETION OF BONDED INTERACTIONS "
        << "BETWEEN INITIAL AND FINAL GROUPS IS NOT SUPPORTED IN MEMORY "
        << "OPTIMISED VERSION - MANUAL PROCESSING IS NECESSARY\n" << endi;
        NAMD_die("MEMOPT: unsupported feature");
    }
    if(simParameters->alchThermIntOn)
        NAMD_die("MEMOPT: alchThermIntOn could not be enabled in memory optimized version");
    if(simParameters->lesOn)
        NAMD_die("MEMOPT: lesOn could not be enabled in memory optimized version");
    if(simParameters->lonepairs) {
        NAMD_die("MEMOPT: lonepairs could not be enabled in memory optimized version");
    }
}
#endif

int NamdState::configListInit(ConfigList *cfgList) {
  configList = cfgList;
  if (!configList->okay()) {
    NAMD_die("Simulation config file is incomplete or contains errors.");
  }
  DebugM(1,"NamdState::configFileInit configList okay\n");

  char *currentdir = 0;
  simParameters =  new SimParameters(configList,currentdir);
  fflush(stdout);
  lattice = simParameters->lattice;

 //Check features that are not supported in the memory optimized 
 //version.  --Chao Mei
#ifdef MEM_OPT_VERSION
  checkMemOptCompatibility();
#endif

  //Check rigidBonds type when generating the compressed psf files.
  if(simParameters->genCompressedPsf) {
      if(simParameters->rigidBonds == RIGID_NONE){
          //default to RIGID_ALL
          simParameters->rigidBonds = RIGID_ALL;
      }
  }

  StringList *molInfoFilename;
  // If it's AMBER force field, read the AMBER style files;
  // if it's GROMACS, read the GROMACS files;
  // Otherwise read the CHARMM style files

  if (simParameters->amberOn)
  { StringList *parmFilename = configList->find("parmfile");
    molInfoFilename = parmFilename;
    StringList *coorFilename = configList->find("ambercoor");
    // "amber" is a temporary data structure, which records all
    // the data from the parm file. After copying them into
    // molecule, parameter and pdb structures, it will be deleted.
    Ambertoppar *amber;
    amber = new Ambertoppar;
    if (amber->readparm(parmFilename->data))
    { parameters = new Parameters(amber, simParameters->vdwscale14);
      molecule = new Molecule(simParameters, parameters, amber);
      if (coorFilename != NULL)
        pdb = new PDB(coorFilename->data,amber);
      delete amber;
    }
    else
      NAMD_die("Failed to read AMBER parm file!");
    parameters->print_param_summary();
  }
  else if (simParameters->gromacsOn) {
    StringList *topFilename = configList->find("grotopfile");
    molInfoFilename = topFilename;
    StringList *coorFilename = configList->find("grocoorfile");
    // "gromacsFile" is a temporary data structure, which records all
    // the data from the topology file. After copying it into the
    // molecule and parameter and pdb, it will be deleted.
    GromacsTopFile *gromacsFile;
    gromacsFile = new GromacsTopFile(topFilename->data);
    parameters = new Parameters(gromacsFile,simParameters->minimizeCGOn);
    if (coorFilename != NULL)
      pdb = new PDB(coorFilename->data,gromacsFile);

    molecule = new Molecule(simParameters, parameters, gromacsFile);
    // XXX does Molecule(needAll,these,arguments)?

    delete gromacsFile; // XXX unimplemented

    // XXX add error handling when the file doesn't exist
    // XXX make sure the right things happen when the parameters are
    // not even specified.
    // NAMD_die("Failed to read AMBER parm file!");
    parameters->print_param_summary();
  }
  else if (simParameters->usePluginIO){
#ifdef MEM_OPT_VERSION          
        NAMD_die("Using plugin IO is not supported in memory optimized version!");
#else    
    PluginIOMgr *pIOMgr = new PluginIOMgr();
    
    iout << iWARN << "Plugin-based I/O is still in development and may still have bugs\n" << endi;

    molfile_plugin_t *pIOHandle = pIOMgr->getPlugin();
    if (pIOHandle == NULL) {
        NAMD_die("ERROR: Failed to match requested plugin type");
    }
    if ( pIOHandle->open_file_read == NULL )
       NAMD_die("ERROR: Selected plugin type cannot open files"); 
    if ( pIOHandle->read_structure == NULL )
       NAMD_die("ERROR: Selected plugin type cannot read structures"); 
    if ( pIOHandle->read_next_timestep == NULL )
       NAMD_die("ERROR: Selected plugin type cannot read coordinates"); 

    StringList *moleculeFilename = configList->find("structure");
    molInfoFilename = moleculeFilename;
    StringList *parameterFilename = configList->find("parameters");
    //****** BEGIN CHARMM/XPLOR type changes
    // For AMBER use different constructor based on parm_struct!!!  -JCP
    parameters = new Parameters(simParameters, parameterFilename);
    parameters->print_param_summary();

    int numAtoms = 0;
    //TODO: not sure about the name field in the handler
    void *plgFile = pIOHandle->open_file_read(moleculeFilename->data, 
                                              pIOHandle->name, &numAtoms);
    if(plgFile ==  NULL) {
        NAMD_die("ERROR: Opening structure file failed!");
    }

    double fileReadTime = CmiWallTimer();
    molecule = new Molecule(simParameters, parameters, pIOHandle, plgFile, numAtoms);
    iout << iINFO << "TIME FOR LOAD MOLECULE STRUCTURE INFORMATION: " << CmiWallTimer() - fileReadTime << "\n" << endi;

    /* If we are only generating compressed molecule information, the PDB object is not needed */
    if(!simParameters->genCompressedPsf) {        
        fileReadTime = CmiWallTimer();
        //get the occupancy data from the Molecule object and then free it
        //as it is stored in the Molecule object.
        pdb = new PDB(pIOHandle, plgFile, molecule->numAtoms, molecule->getOccupancyData(), molecule->getBFactorData());
        molecule->freeOccupancyData();
        molecule->freeBFactorData();
        iout << iINFO << "TIME FOR LOADING ATOMS' COORDINATES INFORMATION: " << CmiWallTimer() - fileReadTime << "\n" << endi;
    }

    pIOHandle->close_file_read(plgFile);
    delete pIOMgr;
#endif    
  }
  else
  { 
    StringList *moleculeFilename = configList->find("structure");
    molInfoFilename = moleculeFilename; 
    StringList *parameterFilename = configList->find("parameters");
    //****** BEGIN CHARMM/XPLOR type changes
    // For AMBER use different constructor based on parm_struct!!!  -JCP
    parameters = new Parameters(simParameters, parameterFilename);
    //****** END CHARMM/XPLOR type changes    

    parameters->print_param_summary();

    double fileReadTime = CmiWallTimer();
    molecule = new Molecule(simParameters, parameters, moleculeFilename->data, configList);
    iout << iINFO << "TIME FOR READING PSF FILE: " << CmiWallTimer() - fileReadTime << "\n" << endi;
}

  fflush(stdout);

#ifdef MEM_OPT_VERSION
  //upon knowing the number of atoms, it's good time to estimate the number of
  //input/output processors if their value is not set
  if(simParameters->numinputprocs==0){
    int numatoms = molecule->numAtoms;
    long estval = (sizeof(InputAtom)+2*sizeof(int)+1)*((long)(numatoms));
    int numprocs = estval>>26; //considering every input proc consumes about 64M.
    if(numprocs==0){
        numprocs=1;
    }else if(numprocs>CkNumPes()){
        numprocs=CkNumPes();
    }
    simParameters->numinputprocs=numprocs;
  }
  if(simParameters->numoutputprocs==0){
    int numatoms = molecule->numAtoms;
    long estval = (sizeof(Vector)*2)*((long)(numatoms));
    int numprocs = estval>>26; //considering every input proc consumes about 64M.
    if(numprocs==0){
      numprocs=1;
    }else if(numprocs>CkNumPes()){
      numprocs=CkNumPes();
    }
    simParameters->numoutputprocs=numprocs;    
  }
  //check the number of output procs that simultaneously write to a file
  if(simParameters->numoutputwrts > simParameters->numoutputprocs) {
      simParameters->numoutputwrts = simParameters->numoutputprocs;
  }

  if (simParameters->fixedAtomsOn){
      double fileReadTime = CmiWallTimer();
      molecule->load_fixed_atoms(configList->find("fixedAtomListFile"));
      iout << iINFO << "TIME FOR READING FIXED ATOMS FILE: " << CmiWallTimer() - fileReadTime << "\n" << endi;
  }
#else
  if (simParameters->extraBondsOn) {        
    //The extra bonds building will be executed in read_compressed_psf in
    //the memory optimized version, so avoid calling this function in the 
    //memory optimized run.
    if(!simParameters->useCompressedPsf)
      molecule->build_extra_bonds(parameters, configList->find("extraBondsFile"));         
  }
  if(simParameters->genCompressedPsf) {
      double fileReadTime = CmiWallTimer();
      compress_molecule_info(molecule, molInfoFilename->data, parameters, simParameters, configList);
      iout << "Finished compressing molecule information, which takes " << CmiWallTimer()-fileReadTime <<"(s)\n"<<endi;
      CkExit();
  }

  //If using plugin-based IO, the PDB object is already created!
  StringList *coordinateFilename = NULL;
  if(!simParameters->usePluginIO) {
      //In the memory opt version, the coordinates of atoms
      //are read during startup in parallel with a bincoordinates input
      //-Chao Mei
      coordinateFilename = configList->find("coordinates");    
      double fileReadTime = CmiWallTimer();
      if (coordinateFilename != NULL)
        pdb = new PDB(coordinateFilename->data);
      if (pdb->num_atoms() != molecule->numAtoms) {
        NAMD_die("Number of pdb and psf atoms are not the same!");
      }
      iout << iINFO << "TIME FOR READING PDB FILE: " << CmiWallTimer() - fileReadTime << "\n" << endi;
      iout << iINFO << "\n" << endi;
  }

        //  If constraints are active, build the parameters necessary
        if (simParameters->constraintsOn)
        {
           StringList *consRefFile = configList->find("consref");
           StringList *consKFile = configList->find("conskfile");

          if (coordinateFilename != NULL) {
           if(strcasecmp(coordinateFilename->data, consRefFile->data)==0)
                consRefFile = NULL;
           if(strcasecmp(coordinateFilename->data, consKFile->data)==0)
                consKFile = NULL;
          }

           molecule->build_constraint_params(consRefFile, consKFile,
                                             configList->find("conskcol"),
                                             pdb,
                                             NULL);
        }
        //CkPrintf ("DEBUG--check if StirOn to build stir params..\n");

        if (simParameters->stirOn)
        {       
        //CkPrintf ("DEBUG--now to build stir params..\n");
          
           molecule->build_stirred_atoms(configList->find("stirFilename"),
                                       configList->find("stirredAtomsCol"),
                                       pdb,
                                       NULL);
        }


        if (simParameters->fixedAtomsOn)
        {
           molecule->build_fixed_atoms(configList->find("fixedatomsfile"),
                                        configList->find("fixedatomscol"),
                                        pdb,
                                        NULL);
        }
        
        /* BEGIN gf */
        if (simParameters->mgridforceOn)
        {
            molecule->build_gridforce_params(configList->find("gridforcefile"),
                                             configList->find("gridforcecol"),
                                             configList->find("gridforcechargecol"),
                                             configList->find("gridforcepotfile"),
                                             pdb,
                                             NULL);
        }
        /* END gf */

        // If constant forces are active, read the forces necessary
        if (simParameters->consForceOn) {
    char *filename = NULL;
    if (configList->find("consforcefile"))
      filename = configList->find("consforcefile")->data;
    molecule->build_constant_forces(filename);
  }

        if (simParameters->excludeFromPressure) {
           molecule->build_exPressure_atoms(
             configList->find("excludeFromPressureFile"),
             configList->find("excludeFromPressureCol"),
             pdb, NULL);
        }

        // If moving drag is active, build the parameters necessary
        if (simParameters->movDragOn) {
          molecule->build_movdrag_params(configList->find("movDragFile"),
                                         configList->find("movDragCol"),
                                         configList->find("movDragVelFile"),
                                         pdb,
                                         NULL);
        }

        // If rotating drag is active, build the parameters necessary
        if (simParameters->rotDragOn) {
          molecule->build_rotdrag_params(configList->find("rotDragFile"),
                                         configList->find("rotDragCol"),
                                         configList->find("rotDragAxisFile"),
                                         configList->find("rotDragPivotFile"),
                                         configList->find("rotDragVelFile"),
                                         configList->find("rotDragVelCol"),
                                         pdb,
                                         NULL);
        }

        // If "constant" torque is active, build the parameters necessary
        if (simParameters->consTorqueOn) {
          molecule->build_constorque_params(configList->find("consTorqueFile"),
                                       configList->find("consTorqueCol"),
                                       configList->find("consTorqueAxisFile"),
                                       configList->find("consTorquePivotFile"),
                                       configList->find("consTorqueValFile"),
                                       configList->find("consTorqueValCol"),
                                       pdb,
                                       NULL);
        }

        //  If langevin dynamics or temperature coupling are active, build 
        //  the parameters necessary
        if (simParameters->langevinOn)
        {
          if (simParameters->langevinDamping == 0.0) {
            molecule->build_langevin_params(configList->find("langevinfile"),
                                            configList->find("langevincol"),
                                            pdb,
                                            NULL);
          } else {
            molecule->build_langevin_params(simParameters->langevinDamping,
                                            simParameters->drudeDamping,
                                            simParameters->langevinHydrogen);
          }
        }
        else if (simParameters->tCoupleOn)
        {
           //  Temperature coupling uses the same parameters, but with different
           //  names . . .
           molecule->build_langevin_params(configList->find("tcouplefile"),
                                            configList->find("tcouplecol"),
                                            pdb,
                                            NULL);
        }

//Modifications for alchemical fep
     //identify the mutant atoms for fep simulation
        if (simParameters->alchOn) {
           molecule->build_fep_flags(configList->find("alchfile"),
                configList->find("alchcol"), pdb, NULL, "alch" );
           molecule->delete_alch_bonded();
        }
//fepe
        if (simParameters->lesOn) {
           if (simParameters->alchFepOn || simParameters->alchThermIntOn) NAMD_bug("FEP/TI and LES are incompatible!");
           molecule->build_fep_flags(configList->find("lesfile"),
                configList->find("lescol"), pdb, NULL, "les");
        }
        if (simParameters->pairInteractionOn) {
           molecule->build_fep_flags(configList->find("pairInteractionFile"),
                configList->find("pairInteractionCol"), pdb, NULL, "pairInteraction");
        }      
        if (simParameters->pressureProfileAtomTypes > 1) {
          molecule->build_fep_flags(configList->find("pressureProfileAtomTypesFile"),
                configList->find("pressureProfileAtomTypesCol"), pdb, NULL, "pressureProfileAtomTypes");
        }
       
        #ifdef OPENATOM_VERSION
        if (simParameters->openatomOn) {
          molecules->build_qmmm_flags(configList->find("openatomPdbFile",
                configList->find("openatomPdbCol"), pdb, NULL, "openatomPdb")
        }
        #endif // OPENATOM_VERSION

        // JLai checks to see if Go Forces are turned on
        if (simParameters->goForcesOn) {
#ifdef MEM_OPT_VERSION
          NAMD_die("Go forces are not supported in memory-optimized builds.");
#else
          StringList *moleculeFilename = configList->find("structure");
          StringList *parameterFilename = configList->find("parameters");
          StringList *goFilename = configList->find("goParameters");
          StringList *goStructureFilename = configList->find("goCoordinates");
          
          // Added by JLai -- 1.10.12 -- Code to build the Go parameters (from within the Go molecule instead of the parameters object)
          molecule->build_go_params(goFilename);
          // Added by JLai -- 6.3.11 -- flag to switch between the different goMethodologies
          int goMethod = simParameters->goMethod;
          if (goMethod == 1) { // should probably replace with switch statement
            iout << iINFO << "Using Go method matrix\n" << endi;
            molecule->build_go_sigmas(goStructureFilename, NULL);
          } else if (goMethod == 2) {
            iout << iINFO << "Using Go method sparse matrix\n" << endi;
            NAMD_die("Go method sparse not yet implemented.  Crashing");
            // Insert code to build sparse matrix
          } else if (goMethod == 3) {
            iout << iINFO << "Using Go method lowmem\n" << endi;
            molecule->build_go_arrays(goStructureFilename, NULL);
          } else {
            NAMD_die("Failed to read goMethod variable in NamdState.C");
          }
#endif
        }
        // End of Go code -- JLai

        iout << iINFO << "****************************\n";
        iout << iINFO << "STRUCTURE SUMMARY:\n";
        iout << iINFO << molecule->numAtoms << " ATOMS\n";
        iout << iINFO << molecule->numBonds << " BONDS\n";
        iout << iINFO << molecule->numAngles << " ANGLES\n";
        iout << iINFO << molecule->numDihedrals << " DIHEDRALS\n";
        iout << iINFO << molecule->numImpropers << " IMPROPERS\n";
        iout << iINFO << molecule->numCrossterms << " CROSSTERMS\n";
        iout << iINFO << molecule->numExclusions << " EXCLUSIONS\n";

        //****** BEGIN CHARMM/XPLOR type changes
        if ((molecule->numMultipleDihedrals) && (simParameters->paraTypeXplorOn))
        {
                iout << iINFO << molecule->numMultipleDihedrals 
             << " DIHEDRALS WITH MULTIPLE PERIODICITY (BASED ON PSF FILE)\n";
        }
        if ((molecule->numMultipleDihedrals) && (simParameters->paraTypeCharmmOn))
        {
                iout << iINFO << molecule->numMultipleDihedrals 
         << " DIHEDRALS WITH MULTIPLE PERIODICITY IGNORED (BASED ON PSF FILE) \n";
                iout << iINFO  
         << " CHARMM MULTIPLICITIES BASED ON PARAMETER FILE INFO! \n";
        }
        //****** END CHARMM/XPLOR type changes

        if (molecule->numMultipleImpropers)
        {
                iout << iINFO << molecule->numMultipleImpropers 
                         << " IMPROPERS WITH MULTIPLE PERIODICITY\n";
        }
        
        if (simParameters->constraintsOn)
        {
           iout << iINFO << molecule->numConstraints << " CONSTRAINTS\n";
        }

        if (simParameters->consForceOn)
          iout << iINFO << molecule->numConsForce << " CONSTANT FORCES\n";

        if (simParameters->stirOn)
          iout << iINFO << molecule->numStirredAtoms << " STIRRED ATOMS\n";

        if (simParameters->fixedAtomsOn)
        {
           iout << iINFO << molecule->numFixedAtoms << " FIXED ATOMS\n";
        }

        if (simParameters->rigidBonds)
        {
           iout << iINFO << molecule->numRigidBonds << " RIGID BONDS\n";
        }

        if (simParameters->fixedAtomsOn && simParameters->rigidBonds)
        {
           iout << iINFO << molecule->numFixedRigidBonds <<
                        " RIGID BONDS BETWEEN FIXED ATOMS\n";
        }
        
        /* BEGIN gf */
        if (simParameters->mgridforceOn)
        {
            int i;
            iout << iINFO << molecule->numGridforceGrids 
                 << " GRIDS ACTIVE\n";
        }
        /* END gf */

//Modifications for alchemical fep
        if (simParameters->alchFepOn || simParameters->alchThermIntOn) {
          iout << iINFO << "ALCH: " 
               << molecule->numFepInitial <<
               " ATOMS TO DISAPPEAR IN FINAL STATE\n";
           iout << iINFO << "ALCH: " 
               <<  molecule->numFepFinal <<
               " ATOMS TO APPEAR IN FINAL STATE\n";
           if (molecule->suspiciousAlchBonds) {
             iout << iWARN << "ALCH: SUSPICIOUS BONDS BETWEEN INITIAL AND " <<
             "FINAL GROUPS WERE FOUND" << "\n" << endi;
           }
           if (molecule->alchDroppedAngles) {
             iout << iINFO << "ALCH: " 
                 << molecule->alchDroppedAngles <<
                 " ANGLES LINKING INITIAL AND FINAL ATOMS DELETED\n";
           }
           if (molecule->alchDroppedDihedrals) {
             iout << iINFO << "ALCH: "
                 << molecule->alchDroppedDihedrals <<
                 " DIHEDRALS LINKING INITIAL AND FINAL ATOMS DELETED\n";
           }
           if (molecule->alchDroppedImpropers) {
             iout << iINFO << "ALCH: "
                 << molecule->alchDroppedImpropers <<
                 " IMPROPERS LINKING INITIAL AND FINAL ATOMS DELETED\n";
           }
        }
//fepe

        if (simParameters->lesOn) {
           iout << iINFO << molecule->numFepInitial <<
               " LOCALLY ENHANCED ATOMS ENABLED\n";
        }
       
        if (simParameters->pairInteractionOn) {
           iout << iINFO << "PAIR INTERACTION GROUP 1 CONTAINS "
                <<  molecule->numFepInitial << " ATOMS\n";
           if (!simParameters->pairInteractionSelf) {
             iout << iINFO << "PAIR INTERACTION GROUP 2 CONTAINS "
                  <<  molecule->numFepFinal << " ATOMS\n";
           }
        }
           
#if 1
        if (molecule->numLonepairs != 0) {
          iout << iINFO << molecule->numLonepairs << " LONE PAIRS\n";
        }
        if (molecule->numDrudeAtoms != 0) {
          iout << iINFO << molecule->numDrudeAtoms << " DRUDE ATOMS\n";
        }
        iout << iINFO << molecule->num_deg_freedom(1)
             << " DEGREES OF FREEDOM\n";
        if (simParameters->drudeOn) {
          int g_bond = 3 * molecule->numDrudeAtoms;
          int g_com = molecule->num_deg_freedom(1) - g_bond;
          iout << iINFO << g_com << " DRUDE COM DEGREES OF FREEDOM\n";
          iout << iINFO << g_bond << " DRUDE BOND DEGREES OF FREEDOM\n";
        }
#endif
#if 0
        {
          // Copied from Controller::printEnergies()
          int numAtoms = molecule->numAtoms;
          int numDegFreedom = 3 * numAtoms;
    int numLonepairs = molecule->numLonepairs;
          int numFixedAtoms = molecule->numFixedAtoms;
          if ( numFixedAtoms ) numDegFreedom -= 3 * numFixedAtoms;
          if ( ! ( numFixedAtoms || molecule->numConstraints
                || simParameters->comMove || simParameters->langevinOn ) ) {
            numDegFreedom -= 3;
          }
    if (numLonepairs) numDegFreedom -= 3 * numLonepairs;
          int numRigidBonds = molecule->numRigidBonds;
          int numFixedRigidBonds = molecule->numFixedRigidBonds;
    // numLonepairs is subtracted here because all lonepairs have a rigid bond
    // to oxygen, but all of the LP degrees of freedom are dealt with above
    numDegFreedom -= ( numRigidBonds - numFixedRigidBonds - numLonepairs);
          iout << iINFO << numDegFreedom << " DEGREES OF FREEDOM\n";
        }
#endif

        iout << iINFO << molecule->numHydrogenGroups << " HYDROGEN GROUPS\n";
        iout << iINFO << molecule->maxHydrogenGroupSize
                << " ATOMS IN LARGEST HYDROGEN GROUP\n";
        iout << iINFO << molecule->numMigrationGroups << " MIGRATION GROUPS\n";
        iout << iINFO << molecule->maxMigrationGroupSize
                << " ATOMS IN LARGEST MIGRATION GROUP\n";
        if (simParameters->fixedAtomsOn)
        {
           iout << iINFO << molecule->numFixedGroups <<
                        " HYDROGEN GROUPS WITH ALL ATOMS FIXED\n";
        }

        {
          BigReal totalMass = 0;
          BigReal totalCharge = 0;
          int i;
          for ( i = 0; i < molecule->numAtoms; ++i ) {
            totalMass += molecule->atommass(i);
            totalCharge += molecule->atomcharge(i);
          }
          iout << iINFO << "TOTAL MASS = " << totalMass << " amu\n"; 
          iout << iINFO << "TOTAL CHARGE = " << totalCharge << " e\n"; 

          BigReal volume = lattice.volume();
          if ( volume ) {
            iout << iINFO << "MASS DENSITY = "
              << ((totalMass/volume) / 0.6022) << " g/cm^3\n";
            iout << iINFO << "ATOM DENSITY = "
              << (molecule->numAtoms/volume) << " atoms/A^3\n";
          }
        }

        iout << iINFO << "*****************************\n";
        iout << endi;
        fflush(stdout);

  StringList *binCoordinateFilename = configList->find("bincoordinates");
  if ( binCoordinateFilename ) {
    read_binary_coors(binCoordinateFilename->data, pdb);
  }

  DebugM(4, "::configFileInit() - printing Molecule Information\n");

  molecule->print_atoms(parameters);
  molecule->print_bonds(parameters);
  molecule->print_exclusions();
  fflush(stdout);
#endif

  DebugM(4, "::configFileInit() - done printing Molecule Information\n");
  DebugM(1, "::configFileInit() - done\n");

  return(0);
}

---