common.h File Reference

#include <unistd.h>
#include <stdio.h>
#include <limits.h>
#include "converse.h"

Go to the source code of this file.

Macros
#define	NAMD_FILENAME_BUFFER_SIZE   4096
#define	COULOMB   332.0636
#define	BOLTZMANN   0.001987191
#define	TIMEFACTOR   48.88821
#define	PRESSUREFACTOR   6.95E4
#define	PDBVELFACTOR   20.45482706
#define	PDBVELINVFACTOR   (1.0/PDBVELFACTOR)
#define	PNPERKCALMOL   69.479
#define	namdnearbyint(x)   floor((x)+0.5)
#define	PI   3.141592653589793
#define	TWOPI   2.0 * PI
#define	ONE   1.000000000000000
#define	ZERO   0.000000000000000
#define	SMALLRAD   0.0005
#define	SMALLRAD2   SMALLRAD*SMALLRAD
#define	FALSE   0
#define	TRUE   1
#define	NO   0
#define	YES   1
#define	STRINGNULL   '\0'
#define	MAX_NEIGHBORS   27
#define	SIMPARAMSTAG   100
#define	STATICPARAMSTAG   101
#define	MOLECULETAG   102
#define	FULLTAG   104
#define	FULLFORCETAG   105
#define	DPMTATAG   106
#define	GRIDFORCEGRIDTAG   107
#define	COMPUTEMAPTAG   108
#define	CYCLE_BARRIER   0
#define	PME_BARRIER   0
#define	STEP_BARRIER   0
#define	USE_BARRIER   (CYCLE_BARRIER || PME_BARRIER || STEP_BARRIER)
#define	NAMD_SeparateWaters   0
#define	NAMD_ComputeNonbonded_SortAtoms   1
#define	NAMD_ComputeNonbonded_SortAtoms_LessBranches   1
#define	WAT_TIP3   0
#define	WAT_TIP4   1
#define	WAT_SWM4   2 /* Drude model (5 charge sites) */

Typedefs
typedef long long	int64
typedef float	Real
typedef double	BigReal
typedef int	Bool

Functions
void	NAMD_quit (const char *)
void	NAMD_die (const char *)
void	NAMD_err (const char *)
void	NAMD_bug (const char *)
int	NAMD_file_exists (const char *filename)
void	NAMD_backup_file (const char *filename, const char *extension=0)
int	NAMD_open_text (const char *fname, int append=0)
void	NAMD_write (int fd, const char *buf, size_t count, const char *fname="in NAMD_write()")
void	NAMD_close (int fd, const char *fname)
char *	NAMD_stringdup (const char *)
FILE *	Fopen (const char *filename, const char *mode)
int	Fclose (FILE *fout)

Macro Definition Documentation

#define BOLTZMANN   0.001987191

Definition at line 47 of file common.h.

Referenced by Controller::adaptTempUpdate(), Controller::Controller(), HomePatch::hardWallDrude(), Controller::langevinPiston1(), Controller::langevinPiston2(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), Controller::multigatorCalcEnthalpy(), Controller::multigratorPressure(), Controller::multigratorTemperature(), Controller::outputFepEnergy(), Sequencer::reassignVelocities(), Controller::receivePressure(), Sequencer::reinitVelocities(), Controller::stochRescaleCoefficient(), and Controller::writeFepEnergyData().

#define COMPUTEMAPTAG   108

Definition at line 159 of file common.h.

Referenced by WorkDistrib::recvComputeMapChanges(), and WorkDistrib::sendComputeMap().

#define COULOMB   332.0636

Definition at line 46 of file common.h.

Referenced by ComputeNonbondedUtil::calcGBIS(), ExclElem::computeForce(), ComputeMsm::ComputeMsm(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), HomePatch::gbisComputeAfterP2(), HomePatch::positionsReady(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), and ComputeQMMgr::recvPntChrg().

#define CYCLE_BARRIER   0

Definition at line 161 of file common.h.

#define DPMTATAG   106

Definition at line 157 of file common.h.

#define FALSE   0

Definition at line 118 of file common.h.

Referenced by Molecule::atoms_1to4(), ParseOptions::check_consistency(), GridforceFullMainGrid::compute_b(), ComputeCylindricalBC::ComputeCylindricalBC(), ComputeSphericalBC::ComputeSphericalBC(), ConfigList::ConfigList(), WorkDistrib::createAtomLists(), ParseOptions::DataElement::DataElement(), ParseOptions::defined(), Parameters::done_reading_files(), PDBData::field(), ParseOptions::get(), Parameters::get_table_pair_params(), Parameters::get_vdw_pair_params(), Molecule::go_restricted(), GridforceFullBaseGrid::GridforceFullBaseGrid(), GridforceFullMainGrid::initialize(), GridforceFullSubGrid::initialize(), Molecule::is_atom_constorqued(), Molecule::is_atom_constrained(), Molecule::is_atom_gridforced(), Molecule::is_atom_movdragged(), Molecule::is_atom_rotdragged(), Molecule::is_atom_stirred(), MGridforceParams::MGridforceParams(), Parameters::Parameters(), Molecule::read_go_file(), Vector::set(), ParseOptions::set(), and ParseOptions::units().

#define FULLFORCETAG   105

Definition at line 156 of file common.h.

Referenced by ComputeFullDirect::doWork().

#define FULLTAG   104

Definition at line 155 of file common.h.

Referenced by ComputeFullDirect::doWork().

#define GRIDFORCEGRIDTAG   107

Definition at line 158 of file common.h.

Referenced by Node::reloadGridforceGrid().

#define MAX_NEIGHBORS   27

Definition at line 131 of file common.h.

#define MOLECULETAG   102

Definition at line 154 of file common.h.

Referenced by Node::resendMolecule().

#define NAMD_ComputeNonbonded_SortAtoms   1

Definition at line 186 of file common.h.

#define NAMD_ComputeNonbonded_SortAtoms_LessBranches   1

Definition at line 187 of file common.h.

#define NAMD_FILENAME_BUFFER_SIZE   4096

Definition at line 38 of file common.h.

Referenced by Molecule::build_go_arrays(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), and Molecule::build_gridforce_params().

#define NAMD_SeparateWaters   0

Definition at line 173 of file common.h.

#define namdnearbyint

(

x

)

floor((x)+0.5)

Definition at line 76 of file common.h.

Referenced by Lattice::delta(), Lattice::nearest(), Parameters::read_ener_table(), Parameters::read_energy_type(), Parameters::read_energy_type_bothcubspline(), Parameters::read_energy_type_cubspline(), Lattice::wrap_delta(), and Lattice::wrap_nearest_delta().

#define NO   0

Definition at line 123 of file common.h.

#define ONE   1.000000000000000

Definition at line 91 of file common.h.

#define PDBVELFACTOR   20.45482706

Definition at line 50 of file common.h.

Referenced by ParallelIOMgr::bcastMolInfo(), and Sequencer::maximumMove().

#define PDBVELINVFACTOR   (1.0/PDBVELFACTOR)

Definition at line 51 of file common.h.

#define PI   3.141592653589793

Definition at line 83 of file common.h.

Referenced by calcOverlap(), ImproperElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), crossterm_setup(), ComputeEField::doForce(), ComputeLCPO::doForce(), GromacsTopFile::GromacsTopFile(), proc_getangle(), proc_getdihedral(), and vec_rotation_matrix().

#define PME_BARRIER   0

Definition at line 162 of file common.h.

#define PNPERKCALMOL   69.479

Definition at line 52 of file common.h.

#define PRESSUREFACTOR   6.95E4

Definition at line 49 of file common.h.

Referenced by PressureProfileReduction::getData(), Controller::printEnergies(), Controller::receivePressure(), Controller::rescaleaccelMD(), and SimParameters::scriptSet().

#define SIMPARAMSTAG   100

Definition at line 152 of file common.h.

#define SMALLRAD   0.0005

Definition at line 99 of file common.h.

#define SMALLRAD2   SMALLRAD*SMALLRAD

Definition at line 103 of file common.h.

#define STATICPARAMSTAG   101

Definition at line 153 of file common.h.

Referenced by Node::resendMolecule().

#define STEP_BARRIER   0

Definition at line 163 of file common.h.

#define STRINGNULL   '\0'

Definition at line 128 of file common.h.

Referenced by ParseOptions::get(), NAMD_find_first_word(), NAMD_pad(), NAMD_read_int(), NAMD_read_line(), NAMD_remove_comment(), and NAMD_truncate().

#define TIMEFACTOR   48.88821

Definition at line 48 of file common.h.

Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), Sequencer::addVelocityToPosition(), Sequencer::correctMomentum(), HomePatch::hardWallDrude(), Sequencer::maximumMove(), Sequencer::minimize(), HomePatch::minimize_rattle2(), Sequencer::newMinimizeDirection(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), ComputeQMMgr::recvPartQM(), and Sequencer::submitMinimizeReductions().

#define TRUE   1

Definition at line 119 of file common.h.

Referenced by Molecule::atoms_1to4(), ParseOptions::check_consistency(), GridforceFullMainGrid::compute_b(), ComputeCylindricalBC::ComputeCylindricalBC(), ComputeSphericalBC::ComputeSphericalBC(), ConfigList::ConfigList(), WorkDistrib::createAtomLists(), ParseOptions::defined(), Parameters::done_reading_files(), PDBData::field(), ParseOptions::get(), Parameters::get_table_pair_params(), Parameters::get_vdw_pair_params(), Molecule::go_restricted(), GridforceFullMainGrid::initialize(), GridforceFullSubGrid::initialize(), MGridforceParams::MGridforceParams(), ParseOptions::ParseOptions(), Parameters::read_charmm_parameter_file(), Molecule::read_go_file(), Parameters::read_parameter_file(), Parameters::receive_Parameters(), Vector::set(), ParseOptions::set(), and ParseOptions::units().

#define TWOPI   2.0 * PI

Definition at line 87 of file common.h.

Referenced by DihedralElem::computeForce(), ImproperElem::computeForce(), and ComputeEField::doForce().

#define USE_BARRIER   (CYCLE_BARRIER || PME_BARRIER || STEP_BARRIER)

Definition at line 165 of file common.h.

#define WAT_SWM4   2 /* Drude model (5 charge sites) */

Definition at line 192 of file common.h.

Referenced by HomePatch::buildRattleList(), HomePatch::minimize_rattle2(), HomePatch::rattle1old(), and HomePatch::rattle2().

#define WAT_TIP3   0

Definition at line 190 of file common.h.

Referenced by HomePatch::rattle1().

#define WAT_TIP4   1

Definition at line 191 of file common.h.

Referenced by HomePatch::buildRattleList(), HomePatch::minimize_rattle2(), Molecule::num_deg_freedom(), HomePatch::rattle1old(), and HomePatch::rattle2().

#define YES   1

Definition at line 124 of file common.h.

#define ZERO   0.000000000000000

Definition at line 95 of file common.h.

Referenced by ComputeNonbondedUtil::calcGBIS().

Typedef Documentation

typedef double BigReal

Definition at line 114 of file common.h.

typedef int Bool

Definition at line 133 of file common.h.

typedef long long int64

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

Definition at line 34 of file common.h.

typedef float Real

Definition at line 109 of file common.h.

Function Documentation

int Fclose

(

FILE *

fout

)

Definition at line 367 of file common.C.

Referenced by ConfigList::ConfigList(), parm::genclose(), PDB::PDB(), read_binary_file(), and Parameters::read_parameter_file().

{
  int rc = -1;
#if !defined(NOCOMPRESSED)
  rc = pclose(fout);
#endif
  if (rc == -1) // stream not associated with a popen()
    {
    rc = fclose(fout);
    }
  return rc;
} /* Fclose() */

FILE* Fopen	(	const char *	filename,
		const char *	mode
	)

Definition at line 273 of file common.C.

References endi(), and iout.

Referenced by ConfigList::ConfigList(), parm::genopen(), GridforceFullMainGrid::initialize(), PDB::PDB(), read_binary_file(), and Parameters::read_parameter_file().

{
  struct stat buf;
  // check if basic filename exists (and not a directory)

#if defined(NOCOMPRESSED)
  if (!stat(filename,&buf))
    {
      FILE *rval;
      while ( ! (rval = fopen(filename,mode)) ) {
        if ( errno != EINTR ) break;
      }
      return(rval);
    }
#else
  if (!stat(filename,&buf))
    {
      if (!S_ISDIR(buf.st_mode)) {
        FILE *rval;
        while ( ! (rval = fopen(filename,mode)) ) {
          if ( errno != EINTR ) break;
        }
        return(rval);
      }
    }
  // check for a compressed file
  char *realfilename;
  char *command;
  FILE *fout;
  command = (char *)malloc(strlen(filename)+25);
  // check for .Z (unix compress)
  sprintf(command,"zcat %s.Z",filename);
  realfilename = command+5;
  iout << "Command = " << command << "\n" << endi;
  iout << "Filename.Z = " << realfilename << "\n" << endi;
  if (!stat(realfilename,&buf))
        {
        if (!S_ISDIR(buf.st_mode))
                {
                fout = popen(command,mode);
                // on HP-UX, the first character(s) out of pipe may be
                // garbage!  (Argh!)
                int C;
                do
                  {
                  C = fgetc(fout);
                  // iout << "C is " << C << "\n" << endi;
                  if (isalnum(C) || isspace(C))
                        {
                        ungetc(C,fout);
                        C = -1; // outta loop
                        }
                  } while(C != -1);
                free(command);
                return(fout);
                }
        }
  // check for .gz (gzip)
  sprintf(command,"gzip -d -c %s.gz",filename);
  realfilename = command+11;
  iout << "Command = " << command << "\n" << endi;
  iout << "Filename.gz = " << realfilename << "\n" << endi;
  if (!stat(realfilename,&buf))
        {
        if (!S_ISDIR(buf.st_mode))
                {
                fout = popen(command,mode);
                // on HP-UX, the first character(s) out of pipe may be
                // garbage!  (Argh!)
                int C;
                do
                  {
                  C = fgetc(fout);
                  // iout << "C is " << C << "\n" << endi;
                  if (isalnum(C) || isspace(C))
                        {
                        ungetc(C,fout);
                        C = -1; // outta loop
                        }
                  } while(C != -1);
                free(command);
                return(fout);
                }
        }
  free(command);
#endif /* !defined(NOCOMPRESSED) */

  return(NULL);
} /* Fopen() */

void NAMD_backup_file	(	const char *	filename,
		const char *	extension = 0
	)

Definition at line 167 of file common.C.

References endi(), iERROR(), iout, and NAMD_file_exists().

Referenced by Controller::adaptTempInit(), colvarproxy_namd::backup_file(), ofstream_namd::open(), open_dcd_write(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), CollectionMaster::receiveDataStream(), and Controller::write_accelMDG_rest_file().

{
  if (NAMD_file_exists(filename)) {
    if ( ! extension ) extension = ".BAK";
    char *backup = new char[strlen(filename)+strlen(extension)+1];
    strcpy(backup, filename);
    strcat(backup, extension);
#if defined(WIN32) && !defined(__CYGWIN__)
    if ( remove(backup) ) if ( errno != ENOENT ) {
      char *sys_err_msg = strerror(errno);
      if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
      iout << iERROR << "Error on removing file "
        << backup << ": " << sys_err_msg << "\n" << endi;
      fflush(stdout);
    }
#endif
    while ( rename(filename,backup) )
    {
      if ( errno == EINTR ) continue;
      const char *sys_err_msg = strerror(errno);
      if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
      iout << iERROR << "Error on renaming file " << filename
        << " to " << backup << ": " << sys_err_msg << "\n" << endi;
      fflush(stdout);
      if ( errno == EXDEV ) continue;
      break;
      // char errmsg[256];
      // sprintf(errmsg, "Error on renaming file %s to %s",filename,backup);
      // NAMD_err(errmsg);
    }
    delete [] backup;
  }
}

void NAMD_bug

(

const char *

)

Definition at line 129 of file common.C.

Referenced by Sequencer::algorithm(), Controller::algorithm(), CollectProxyVectorInstance::append(), CudaComputeNonbonded::assignPatches(), CudaComputeNonbonded::assignPatchesOnPe(), PmePencilXYZ::backwardDone(), LdbCoordinator::barrier(), ComputeNonbondedCUDA::build_exclusions(), ComputeNonbondedCUDA::build_lj_table(), HomePatch::buildSpanningTree(), ReductionMgr::buildSpanTree(), ComputeNonbondedUtil::calc_error(), Controller::calcPressure(), ComputePmeMgr::chargeGridReady(), checkSum(), ofstream_namd::close(), Box< Patch, CompAtom >::close(), Controller::compareChecksums(), ComputeCUDAMgr::ComputeCUDAMgr(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputePmeCUDAMgr::ComputePmeCUDAMgr(), ComputeTclBC::ComputeTclBC(), CudaPmeTranspose::copyDataDeviceToDevice(), CudaPmeTranspose::copyDataDeviceToHost(), CudaPmeTranspose::copyDataHostToDevice(), WorkDistrib::createAtomLists(), ComputeCUDAMgr::createCudaComputeNonbonded(), ComputePmeCUDAMgr::createDevicesAndAtomFiler(), CsmAckHandler(), CsmHandler(), cuda_check_local_progress(), cuda_check_remote_progress(), cudaNAMD_bug(), CudaPmeRealSpaceCompute::CudaPmeRealSpaceCompute(), MigrateAtomsCombinedMsg::distribute(), ComputeGridForce::doForce(), HomePatch::doGroupSizeCheck(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), CudaComputeNonbonded::doWork(), WorkDistrib::enqueueAngles(), WorkDistrib::enqueueAniso(), WorkDistrib::enqueueBonds(), WorkDistrib::enqueueCrossterms(), WorkDistrib::enqueueDihedrals(), WorkDistrib::enqueueExcls(), WorkDistrib::enqueueGromacsPair(), WorkDistrib::enqueueImpropers(), WorkDistrib::enqueueLCPO(), WorkDistrib::enqueuePme(), WorkDistrib::enqueueSelfA1(), WorkDistrib::enqueueSelfA2(), WorkDistrib::enqueueSelfA3(), WorkDistrib::enqueueSelfB1(), WorkDistrib::enqueueSelfB2(), WorkDistrib::enqueueSelfB3(), WorkDistrib::enqueueThole(), WorkDistrib::enqueueWork(), WorkDistrib::enqueueWorkA1(), WorkDistrib::enqueueWorkA2(), WorkDistrib::enqueueWorkA3(), WorkDistrib::enqueueWorkB1(), WorkDistrib::enqueueWorkB2(), WorkDistrib::enqueueWorkB3(), WorkDistrib::enqueueWorkC(), ScriptTcl::eval(), ComputeMap::extendPtrs(), findRecipEvirPe(), CudaComputeNonbonded::finishReductions(), ofstream_namd::flush(), PmeAtomStorage::getAtomIndex(), getBlockDim(), CudaPmeTranspose::getBuffer(), ComputeCUDAMgr::getComputeCUDAMgr(), ComputeCUDAMgr::getCudaComputeNonbonded(), ComputePmeCUDAMgr::getDevice(), ComputePmeCUDAMgr::getDevicePencilY(), ComputePmeCUDAMgr::getDevicePencilZ(), ParseOptions::getfromptr(), ComputePmeCUDAMgr::getHomePencil(), Communicate::getMessage(), ComputePmeCUDAMgr::getNode(), getPencilDim(), GridforceFullBaseGrid::grid_index(), FFTCompute::init(), ComputePmeCUDA::initialize(), ComputePatch::initialize(), ComputeHomePatch::initialize(), ComputePme::initialize(), LdbCoordinator::initialize(), ParallelIOMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeMgr::initialize_computes(), IRSet::insert(), ParseOptions::issetfromptr(), ParseOptions::istruefromptr(), CudaComputeNonbonded::launchWork(), LdbCoordinator::LdbCoordinator(), ScriptTcl::load(), NamdState::loadStructure(), PatchMap::makePatches(), WorkDistrib::messageEnqueueWork(), CudaComputeNonbonded::messageEnqueueWork(), WorkDistrib::messageFinishCUDA(), WorkDistrib::messageFinishMIC(), HomePatch::minimize_rattle2(), Sequencer::multigratorPressure(), NAMD_write(), Node::Node(), PmeZPencil::node_process_untrans(), PmeYPencil::node_process_untrans(), ofstream_namd::open(), Box< Patch, CompAtom >::open(), CudaComputeNonbonded::openBoxesOnPe(), PatchMap::pack(), PatchMgr::PatchMgr(), CudaComputeNonbonded::patchReady(), PmePencilX::PmePencilX(), PmePencilXY::PmePencilXY(), PmePencilXYZ::PmePencilXYZ(), PmePencilY::PmePencilY(), PmePencilZ::PmePencilZ(), PmeTranspose::PmeTranspose(), ComputePmeMgr::pollChargeGridReady(), ComputePmeMgr::pollForcesReady(), PmePencilXYZMap::populateInitial(), PmePencilXMap::populateInitial(), PmePencilXYMap::populateInitial(), PmePencilMap::populateInitial(), Controller::printEnergies(), Rebalancer::printLoads(), PmePencilXMap::procNum(), PmePencilXYMap::procNum(), ProxyMgr::ProxyMgr(), HomePatch::rattle2(), Sequencer::reassignVelocities(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), ParallelIOMgr::receiveForces(), ParallelIOMgr::receivePositions(), ParallelIOMgr::receiveVelocities(), recursive_bisect_with_curve(), recvAck(), ComputePmeMgr::recvAck(), ComputePmeCUDADevice::recvAtoms(), ComputePmeCUDADevice::recvAtomsFromNeighbor(), recvBcast(), BroadcastMgr::recvBroadcast(), PatchMgr::recvCheckpointAck(), HomePatch::recvCheckpointLoad(), PatchMgr::recvCheckpointReq(), WorkDistrib::recvComputeMapChanges(), GlobalMasterServer::recvData(), recvData(), ComputePmeCUDAMgr::recvDevices(), recvEvalCommand(), recvEvalResult(), PatchMgr::recvExchangeReq(), ComputePmeCUDADevice::recvForcesFromNeighbor(), ComputePmeMgr::recvGrid(), ComputeQMMgr::recvPartQM(), ComputePmeMgr::recvRecipEvir(), Output::recvReplicaDcdData(), ComputeGlobal::recvResults(), ProxyMgr::recvResults(), ComputePmeMgr::recvUngrid(), NodePmeMgr::recvUngrid(), ReductionSet::ReductionSet(), register_cuda_compute_pair(), register_cuda_compute_self(), AtomMapper::registerIDsCompAtomExt(), AtomMapper::registerIDsFullAtom(), registerUserEventsForAllComputeObjs(), Node::reloadGridforceGrid(), ReductionMgr::remoteSubmit(), IRSet::remove(), replica_bcast(), replica_min_double(), CollectProxyVectorInstance::reset(), CollectionMgr::CollectVectorInstance::reset(), CollectionMaster::CollectVectorInstance::reset(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), ComputeNonbondedUtil::select(), PmeZPencil::send_ungrid(), PatchMgr::sendAtoms(), NodePmeMgr::sendDataHelper(), ComputePmeMgr::sendDataPart(), Communicate::sendMessage(), PatchMgr::sendMovePatches(), PatchMgr::sendOneHomePatch(), NodePmeMgr::sendPencilsHelper(), ComputePmeMgr::sendPencilsPart(), CudaPmeTranspose::setDataPtrsYZX(), CudaPmeTranspose::setDataPtrsZXY(), ComputePmeCUDADevice::setPencilProxy(), ComputePmeCUDAMgr::setupPencils(), SimpleBroadcastObject< Tensor >::SimpleBroadcastObject(), Box< Patch, CompAtom >::skip(), CudaComputeNonbonded::skipPatchesOnPe(), CudaPmeKSpaceCompute::solve(), Node::startup(), ComputeMap::storeCompute(), ComputePmeCUDA::storePmeForceMsg(), PmePencilXYZ::submitReductions(), PmePencilZ::submitReductions(), ComputePmeMgr::submitReductions(), Sync::Sync(), TopoManagerWrapper::TopoManagerWrapper(), CudaPmeTranspose::transposeXYZtoYZX(), CudaPmeTranspose::transposeXYZtoZXY(), IRSet::unchecked_insert(), ComputePme::ungridForces(), ComputeMap::unpack(), GridforceGrid::unpack_grid(), unregister_cuda_compute(), CudaComputeNonbonded::unregisterBoxesOnPe(), AtomMapper::unregisterIDsCompAtomExt(), AtomMapper::unregisterIDsFullAtom(), ComputeCUDAMgr::update(), ComputeMgr::updateComputes(), Node::updateGridScale(), WorkDistrib::WorkDistrib(), AtomMapper::~AtomMapper(), and Rebalancer::~Rebalancer().

{
  if ( ! err_msg ) err_msg = "(unknown error)";
  const char *bug_msg = 
    "FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html";
  CkPrintf("FATAL ERROR: %s\n%s\n",err_msg, bug_msg);
  fflush(stdout);
  char repstr[24] = "";
  if (CmiNumPartitions() > 1) {
    sprintf(repstr,"REPLICA %d ", CmiMyPartition());
    // CkAbort ensures that all replicas die
    CkAbort("%sFATAL ERROR: %s\n%s\n", repstr, err_msg, bug_msg);
  }
  CkError("%sFATAL ERROR: %s\n%s\n", repstr, err_msg, bug_msg);
#if CHARM_VERSION < 61000
  CkExit();
#else
  CkExit(2);
#endif
}

void NAMD_close	(	int	fd,
		const char *	fname
	)

Definition at line 247 of file common.C.

References NAMD_err().

                                           {
#ifdef WIN32
  while ( _close(fd) ) {
#else
  while ( close(fd) ) {
#endif
    if ( errno != EINTR ) {
      char errmsg[1024];
      sprintf(errmsg, "Error on closing file %s", fname);
      NAMD_err(errmsg);
    }
  }
}

void NAMD_die

(

const char *

)

Definition at line 85 of file common.C.

{
  if ( ! err_msg ) err_msg = "(unknown error)";
  CkPrintf("FATAL ERROR: %s\n", err_msg);
  fflush(stdout);
  char repstr[24] = "";
  if (CmiNumPartitions() > 1) {
    sprintf(repstr,"REPLICA %d ", CmiMyPartition());
    // CkAbort ensures that all replicas die
    CkAbort("%sFATAL ERROR: %s\n", repstr, err_msg);
  }
  CkError("%sFATAL ERROR: %s\n", repstr, err_msg);
#if CHARM_VERSION < 61000
  CkExit();
#else
  CkExit(1);
#endif
}

void NAMD_err

(

const char *

)

Definition at line 106 of file common.C.

Referenced by after_backend_init(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), close_dcd_write(), colvarproxy_namd::error(), NAMD_close(), NAMD_open(), NAMD_open_text(), NAMD_seek(), NAMD_write(), Controller::outputExtendedSystem(), PDB::PDB(), ComputeQMMgr::recvPartQM(), Output::recvReplicaDcdData(), and PDB::write().

{
  if ( ! err_msg ) err_msg = "(unknown error)";
  const char *sys_err_msg = strerror(errno);
  if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
  CkPrintf("FATAL ERROR: %s: %s\n", err_msg, sys_err_msg);
  fflush(stdout);
  char repstr[24] = "";
  if (CmiNumPartitions() > 1) {
    sprintf(repstr,"REPLICA %d ", CmiMyPartition());
    // CkAbort ensures that all replicas die
    CkAbort("%sFATAL ERROR: %s: %s\n", repstr, err_msg, sys_err_msg);
  }
  CkError("%sFATAL ERROR: %s: %s\n", repstr, err_msg, sys_err_msg);
#if CHARM_VERSION < 61000
  CkExit();
#else
  CkExit(1);
#endif
}

int NAMD_file_exists

(

const char *

filename

)

Definition at line 151 of file common.C.

References endi(), iERROR(), and iout.

Referenced by NAMD_backup_file().

                                           {
  int rval;
  do {
    rval = access(filename, F_OK);
  } while ( rval != 0 && errno == EINTR );
  if ( rval != 0 && errno != ENOENT ) {
    const char *sys_err_msg = strerror(errno);
    if ( ! sys_err_msg ) sys_err_msg = "(unknown error)";
    iout << iERROR << "Error on checking file "
      << filename << ": " << sys_err_msg << "\n" << endi;
    fflush(stdout);
  }
  return ! rval;
}

int NAMD_open_text	(	const char *	fname,
		int	append = 0
	)

Definition at line 202 of file common.C.

References NAMD_err().

Referenced by ofstream_namd::open().

                                                  {
  int fd;

  //  open the file and die if the open fails
#ifdef WIN32
  while ( (fd = _open(fname, O_WRONLY|(append?O_APPEND:O_EXCL)|O_CREAT|O_TEXT,_S_IREAD|_S_IWRITE)) < 0) {
#else
#ifdef NAMD_NO_O_EXCL
  while ( (fd = open(fname, O_WRONLY|(append?O_APPEND:O_TRUNC)|O_CREAT,
#else
  while ( (fd = open(fname, O_WRONLY|(append?O_APPEND:O_EXCL)|O_CREAT,
#endif
                           S_IRUSR|S_IWUSR|S_IRGRP|S_IROTH)) < 0) {
#endif
    if ( errno != EINTR ) {
      char errmsg[1024];
      sprintf(errmsg, "Unable to open text file %s", fname);
      NAMD_err(errmsg);
    }
  }

  return fd;
}

void NAMD_quit

(

const char *

)

Definition at line 64 of file common.C.

Referenced by GlobalMasterIMD::get_vmd_forces().

{
  if ( ! err_msg ) err_msg = "(unknown error)";
  CkPrintf("EXITING: %s\n", err_msg);
  fflush(stdout);
  char repstr[24] = "";
  if (CmiNumPartitions() > 1) {
    sprintf(repstr,"REPLICA %d ", CmiMyPartition());
    // CkAbort ensures that all replicas die
    CkAbort("%sEXITING: %s\n", repstr, err_msg);
  }
  CkError("%sEXITING: %s\n", repstr, err_msg);
#if CHARM_VERSION < 61000
  CkExit();
#else
  CkExit(0);
#endif
}

char* NAMD_stringdup

(

const char *

s

)

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

Definition at line 50 of file common.C.

                                    {
  char *rs;

  if(!s)
    return NULL;

  rs = new char[strlen(s) + 1];
  strcpy(rs,s);

  return rs;
}

void NAMD_write	(	int	fd,
		const char *	buf,
		size_t	count,
		const char *	fname = "in NAMD_write()"
	)

Definition at line 227 of file common.C.

References endi(), iout, iWARN(), NAMD_bug(), and NAMD_err().

                                                                          {
  while ( count ) {
#if defined(WIN32) && !defined(__CYGWIN__)
    long retval = _write(fd,buf,count);
#else
    ssize_t retval = write(fd,buf,count);
#endif
    if ( retval < 0 && errno == EINTR ) retval = 0;
    if ( retval < 0 ) {
      char errmsg[1024];
      sprintf(errmsg, "Error on writing to file %s", fname);
      NAMD_err(errmsg);
    }
    if ( retval > count ) NAMD_bug("extra bytes written in NAMD_write()");
    buf += retval;
    count -= retval;
  }
}