NamdState Class Reference

#include <NamdState.h>

List of all members.

Public Member Functions
	NamdState (void)
	~NamdState ()
int	configFileInit (char *)
int	configListInit (ConfigList *)
int	status ()
void	useController (Controller *controllerPtr)
void	runController (void)
Friends
class	Namd
class	Node
class	Controller
class	ScriptTcl

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Constructor & Destructor Documentation

NamdState::NamdState (  void   )

Definition at line 33 of file NamdState.C. { configList = NULL; simParameters = NULL; parameters = NULL; molecule = NULL; pdb = NULL; }

NamdState::~NamdState (   )  [inline]

Definition at line 43 of file NamdState.h. {}

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Member Function Documentation

int NamdState::configFileInit (  char *   )

int NamdState::configListInit (  ConfigList *   )

Definition at line 120 of file NamdState.C. References Molecule::alchDroppedAngles, Molecule::alchDroppedDihedrals, Molecule::alchDroppedImpropers, SimParameters::alchFepOn, SimParameters::alchOn, SimParameters::alchThermIntOn, SimParameters::amberOn, Ambertoppar, Molecule::atomcharge(), Molecule::atommass(), BigReal, Molecule::build_constant_forces(), Molecule::build_constorque_params(), Molecule::build_constraint_params(), Molecule::build_exPressure_atoms(), Molecule::build_extra_bonds(), Molecule::build_fep_flags(), Molecule::build_fixed_atoms(), Molecule::build_go_arrays(), Molecule::build_go_params(), Molecule::build_go_sigmas(), Molecule::build_gridforce_params(), Molecule::build_langevin_params(), Molecule::build_movdrag_params(), Molecule::build_rotdrag_params(), Molecule::build_stirred_atoms(), SimParameters::comMove, compress_molecule_info(), SimParameters::consForceOn, SimParameters::consTorqueOn, SimParameters::constraintsOn, StringList::data, DebugM, Molecule::delete_alch_bonded(), SimParameters::drudeDamping, SimParameters::drudeOn, SimParameters::excludeFromPressure, SimParameters::extraBondsOn, ConfigList::find(), SimParameters::fixedAtomsOn, Molecule::freeBFactorData(), Molecule::freeOccupancyData(), SimParameters::genCompressedPsf, Molecule::getBFactorData(), Molecule::getOccupancyData(), PluginIOMgr::getPlugin(), SimParameters::goForcesOn, SimParameters::goMethod, SimParameters::gromacsOn, iINFO(), iout, iWARN(), SimParameters::langevinDamping, SimParameters::langevinHydrogen, SimParameters::langevinOn, SimParameters::lattice, SimParameters::lesOn, Molecule::maxHydrogenGroupSize, Molecule::maxMigrationGroupSize, SimParameters::mgridforceOn, SimParameters::minimizeCGOn, SimParameters::movDragOn, NAMD_bug(), NAMD_die(), PDB::num_atoms(), Molecule::num_deg_freedom(), Molecule::numAngles, Molecule::numAtoms, Molecule::numBonds, Molecule::numConsForce, Molecule::numConstraints, Molecule::numCrossterms, Molecule::numDihedrals, Molecule::numDrudeAtoms, Molecule::numExclusions, Molecule::numFepFinal, Molecule::numFepInitial, Molecule::numFixedAtoms, Molecule::numFixedGroups, Molecule::numFixedRigidBonds, Molecule::numGridforceGrids, Molecule::numHydrogenGroups, Molecule::numImpropers, SimParameters::numinputprocs, Molecule::numLonepairs, Molecule::numMigrationGroups, Molecule::numMultipleDihedrals, Molecule::numMultipleImpropers, SimParameters::numoutputprocs, SimParameters::numoutputwrts, Molecule::numRigidBonds, Molecule::numStirredAtoms, ConfigList::okay(), SimParameters::pairInteractionOn, SimParameters::pairInteractionSelf, SimParameters::paraTypeCharmmOn, SimParameters::paraTypeXplorOn, SimParameters::pressureProfileAtomTypes, Molecule::print_atoms(), Molecule::print_bonds(), Molecule::print_exclusions(), Parameters::print_param_summary(), read_binary_coors(), parm::readparm(), SimParameters::rigidBonds, SimParameters::rotDragOn, SimParameters::stirOn, Molecule::suspiciousAlchBonds, SimParameters::tCoupleOn, SimParameters::useCompressedPsf, SimParameters::usePluginIO, SimParameters::vdwscale14, and Lattice::volume(). { 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); }

void NamdState::runController (  void   )

Definition at line 78 of file NamdState.C. References Controller::run(). Referenced by Node::run(). { controller->run(); }

int NamdState::status (   )

Definition at line 43 of file NamdState.C. References DebugM. { 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  )

Definition at line 73 of file NamdState.C. { controller=controllerPtr; }

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Friends And Related Function Documentation

friend class Controller [friend]

Definition at line 25 of file NamdState.h.

friend class Namd [friend]

Definition at line 23 of file NamdState.h.

friend class Node [friend]

Definition at line 24 of file NamdState.h.

friend class ScriptTcl [friend]

Definition at line 45 of file NamdState.h.

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The documentation for this class was generated from the following files:

• NamdState.h
• NamdState.C

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