common.h File Reference

#include <unistd.h>
#include <stdio.h>
#include <climits>
#include <vector>
#include <cstdint>

Go to the source code of this file.

Classes
struct	dcd_params
struct	per_atom_flags

Macros
#define	SEQUENCER_SOA
#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	RECIP_TIMEFACTOR   (1.0 / TIMEFACTOR)
#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
	DMK - Atom Separation (water vs. non-water) More...
#define	NAMD_ComputeNonbonded_SortAtoms   1
#define	NAMD_ComputeNonbonded_SortAtoms_LessBranches   1
#define	NAMD_HOST_DEVICE   inline
#define	NAMD_UNIFIED_REDUCTION
#define	CUDAGM_VERSION   2
#define	CUDAGM_PASTER(x, y)   x ## y
#define	CUDAGM_EVALUATOR(x, y)   CUDAGM_PASTER(x,y)
#define	CUDAGM_NS   CUDAGM_EVALUATOR(v, CUDAGM_VERSION)

Typedefs
typedef int8_t	int8
typedef int16_t	int16
typedef int32_t	int32
typedef int64_t	int64
typedef uint8_t	uint8
typedef uint16_t	uint16
typedef uint32_t	uint32
typedef uint64_t	uint64
typedef float	Real
typedef double	BigReal
typedef int	Bool
typedef struct dcd_params	DCDParams
typedef struct per_atom_flags	PerAtomFlags

Enumerations
enum	NAMD_ReleaseType { NAMD_UNKNOWN_RELEASE = 0, NAMD_ALPHA_RELEASE = 1, NAMD_BETA_RELEASE = 2, NAMD_FINAL_RELEASE = 3 }
enum	WaterModel { WaterModel::TIP3, WaterModel::TIP4, WaterModel::SWM4 }
enum	OUTPUTFILETYPE {   dcdType, forcedcdType, veldcdType, coorType,   forceType, velType }
enum	IMDversion_t { IMDv2 =2, IMDv3 =3 }

Functions
void	NAMD_version (int *major, int *minor, int *patchLevel, int *releaseType)
const char *	NAMD_version_string (void)
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)
int	NAMD_gcd (int a, int b)
constexpr int	getWaterModelGroupSize (const WaterModel &watmodel)

Macro Definition Documentation

BOLTZMANN

#define BOLTZMANN   0.001987191

Definition at line 54 of file common.h.

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

COMPUTEMAPTAG

#define COMPUTEMAPTAG   108

Definition at line 184 of file common.h.

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

COULOMB

#define COULOMB   332.0636

Definition at line 53 of file common.h.

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

CUDAGM_EVALUATOR

#define CUDAGM_EVALUATOR	(		x,
			y
	)		CUDAGM_PASTER(x,y)

Definition at line 279 of file common.h.

CUDAGM_NS

#define CUDAGM_NS   CUDAGM_EVALUATOR(v, CUDAGM_VERSION)

Definition at line 280 of file common.h.

CUDAGM_PASTER

#define CUDAGM_PASTER	(		x,
			y
	)		x ## y

Definition at line 278 of file common.h.

CUDAGM_VERSION

#define CUDAGM_VERSION   2

Definition at line 277 of file common.h.

CYCLE_BARRIER

#define CYCLE_BARRIER   0

Definition at line 186 of file common.h.

DPMTATAG

#define DPMTATAG   106

Definition at line 182 of file common.h.

FALSE

#define FALSE   0

Definition at line 127 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_dcd_selection(), Molecule::is_atom_gridforced(), Molecule::is_atom_movdragged(), Molecule::is_atom_rotdragged(), Molecule::is_atom_stirred(), MGridforceParams::MGridforceParams(), Parameters::Parameters(), Molecule::read_go_file(), ParseOptions::set(), Vector::set(), and ParseOptions::units().

FULLFORCETAG

#define FULLFORCETAG   105

Definition at line 181 of file common.h.

Referenced by ComputeFullDirect::doWork().

FULLTAG

#define FULLTAG   104

Definition at line 180 of file common.h.

Referenced by ComputeFullDirect::doWork().

GRIDFORCEGRIDTAG

#define GRIDFORCEGRIDTAG   107

Definition at line 183 of file common.h.

Referenced by Node::reloadGridforceGrid().

MAX_NEIGHBORS

#define MAX_NEIGHBORS   27

Definition at line 140 of file common.h.

MOLECULETAG

#define MOLECULETAG   102

Definition at line 179 of file common.h.

Referenced by Node::resendMolecule().

NAMD_ComputeNonbonded_SortAtoms

#define NAMD_ComputeNonbonded_SortAtoms   1

Definition at line 217 of file common.h.

NAMD_ComputeNonbonded_SortAtoms_LessBranches

#define NAMD_ComputeNonbonded_SortAtoms_LessBranches   1

Definition at line 218 of file common.h.

NAMD_FILENAME_BUFFER_SIZE

#define NAMD_FILENAME_BUFFER_SIZE   4096

Definition at line 45 of file common.h.

Referenced by Molecule::build_go_arrays(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), Molecule::build_gridforce_params(), Controller::outputExtendedSystem(), and ParallelIOMgr::recvDcdParams().

NAMD_HOST_DEVICE

#define NAMD_HOST_DEVICE   inline

Definition at line 237 of file common.h.

NAMD_SeparateWaters

#define NAMD_SeparateWaters   0

DMK - Atom Separation (water vs. non-water)

Setting this define to a non-zero value will cause the HomePatches to separate the hydrogen groups in their HomePatch::atom lists (all water molecules first, in arbitrary order, followed by all non-waters, in arbitrary order).

Note from DH: This macro appears to be broken. After fixing basic compilation issues (undefined reference to simParams), enabling it causes an infinite loop when trying to run STMV.

Definition at line 204 of file common.h.

NAMD_UNIFIED_REDUCTION

#define NAMD_UNIFIED_REDUCTION

Definition at line 273 of file common.h.

namdnearbyint

#define namdnearbyint

(

x

)

floor((x)+0.5)

Definition at line 85 of file common.h.

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

NO

#define NO   0

Definition at line 132 of file common.h.

ONE

#define ONE   1.000000000000000

Definition at line 100 of file common.h.

PDBVELFACTOR

#define PDBVELFACTOR   20.45482706

Definition at line 57 of file common.h.

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

PDBVELINVFACTOR

#define PDBVELINVFACTOR   (1.0/PDBVELFACTOR)

Definition at line 58 of file common.h.

PI

#define PI   3.141592653589793

Definition at line 92 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().

PME_BARRIER

#define PME_BARRIER   0

Definition at line 187 of file common.h.

PNPERKCALMOL

#define PNPERKCALMOL   69.479

Definition at line 59 of file common.h.

PRESSUREFACTOR

#define PRESSUREFACTOR   6.95E4

Definition at line 56 of file common.h.

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

RECIP_TIMEFACTOR

#define RECIP_TIMEFACTOR   (1.0 / TIMEFACTOR)

Definition at line 61 of file common.h.

Referenced by Sequencer::integrate_SOA().

SEQUENCER_SOA

#define SEQUENCER_SOA

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

Definition at line 15 of file common.h.

SIMPARAMSTAG

#define SIMPARAMSTAG   100

Definition at line 177 of file common.h.

SMALLRAD

#define SMALLRAD   0.0005

Definition at line 108 of file common.h.

SMALLRAD2

#define SMALLRAD2   SMALLRAD*SMALLRAD

Definition at line 112 of file common.h.

STATICPARAMSTAG

#define STATICPARAMSTAG   101

Definition at line 178 of file common.h.

Referenced by Node::resendMolecule().

STEP_BARRIER

#define STEP_BARRIER   0

Definition at line 188 of file common.h.

STRINGNULL

#define STRINGNULL   '\0'

Definition at line 137 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().

TIMEFACTOR

#define TIMEFACTOR   48.88821

Definition at line 55 of file common.h.

Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), Sequencer::addVelocityToPosition(), Sequencer::correctMomentum(), HomePatch::hardWallDrude(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), Sequencer::maximumMove(), Sequencer::minimize(), HomePatch::minimize_rattle2(), Sequencer::newMinimizeDirection(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), ComputeQMMgr::recvPartQM(), and Sequencer::submitMinimizeReductions().

TRUE

#define TRUE   1

Definition at line 128 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(), ParseOptions::set(), Vector::set(), and ParseOptions::units().

TWOPI

#define TWOPI   2.0 * PI

Definition at line 96 of file common.h.

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

USE_BARRIER

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

Definition at line 190 of file common.h.

YES

#define YES   1

Definition at line 133 of file common.h.

ZERO

#define ZERO   0.000000000000000

Definition at line 104 of file common.h.

Referenced by ComputeNonbondedUtil::calcGBIS().

Typedef Documentation

BigReal

typedef double BigReal

Definition at line 123 of file common.h.

Bool

typedef int Bool

Definition at line 142 of file common.h.

DCDParams

typedef struct dcd_params DCDParams

int16

typedef int16_t int16

Definition at line 37 of file common.h.

int32

typedef int32_t int32

Definition at line 38 of file common.h.

int64

typedef int64_t int64

Definition at line 39 of file common.h.

int8

typedef int8_t int8

Definition at line 36 of file common.h.

PerAtomFlags

typedef struct per_atom_flags PerAtomFlags

Real

typedef float Real

Definition at line 118 of file common.h.

uint16

typedef uint16_t uint16

Definition at line 41 of file common.h.

uint32

typedef uint32_t uint32

Definition at line 42 of file common.h.

uint64

typedef uint64_t uint64

Definition at line 43 of file common.h.

uint8

typedef uint8_t uint8

Definition at line 40 of file common.h.

Enumeration Type Documentation

IMDversion_t

enum IMDversion_t

Enumerator
IMDv2
IMDv3

Definition at line 275 of file common.h.

{IMDv2=2, IMDv3=3};

NAMD_ReleaseType

enum NAMD_ReleaseType

Enumerator
NAMD_UNKNOWN_RELEASE
NAMD_ALPHA_RELEASE
NAMD_BETA_RELEASE
NAMD_FINAL_RELEASE

Definition at line 147 of file common.h.

                      {
  NAMD_UNKNOWN_RELEASE = 0,
  NAMD_ALPHA_RELEASE   = 1,
  NAMD_BETA_RELEASE    = 2,
  NAMD_FINAL_RELEASE   = 3
};

OUTPUTFILETYPE

enum OUTPUTFILETYPE

Enumerator
dcdType
forcedcdType
veldcdType
coorType
forceType
velType

Definition at line 240 of file common.h.

                    {
        dcdType,
        forcedcdType,
        veldcdType,
        coorType,
        forceType,
        velType
};

WaterModel

enum WaterModel

strong

Enumerator
TIP3
TIP4
SWM4

Definition at line 221 of file common.h.

                      {
  TIP3,
  TIP4,
  SWM4, /* Drude model (5 charge sites) */
};

Function Documentation

Fclose()

int Fclose

(

FILE *

fout

)

Definition at line 436 of file common.C.

Referenced by ConfigList::ConfigList(), Ambertoppar::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() */

Fopen()

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

Definition at line 342 of file common.C.

References endi(), and iout.

Referenced by ConfigList::ConfigList(), Ambertoppar::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() */

getWaterModelGroupSize()

constexpr int getWaterModelGroupSize ( const WaterModel &  watmodel )

inline

Definition at line 228 of file common.h.

References SWM4, TIP3, and TIP4.

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

                                                                        {
  return (watmodel == WaterModel::TIP3) ? 3:
         (watmodel == WaterModel::TIP4) ? 4:
         (watmodel == WaterModel::SWM4) ? 5: -1;
}

NAMD_backup_file()

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

Definition at line 236 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;
  }
}

NAMD_bug()

void NAMD_bug

(

const char *

)

Definition at line 196 of file common.C.

References Node::Object().

Referenced by Sequencer::algorithm(), Controller::algorithm(), SynchronousCollectives::allGather(), SynchronousCollectives::allReduce(), SynchronousCollectives::alltoallv(), CollectProxyVectorInstance::append(), CudaComputeNonbonded::assignPatches(), CudaComputeNonbonded::assignPatchesOnPe(), PmePencilXYZ::backwardDone(), LdbCoordinator::barrier(), SynchronousCollectives::barrier(), SynchronousCollectives::broadcast(), HomePatch::buildRattleList_SOA(), HomePatch::buildSpanningTree(), ReductionMgr::buildSpanTree(), ComputeNonbondedUtil::calc_error(), Controller::calcPressure(), ComputePmeMgr::chargeGridReady(), checkSum(), ofstream_namd::close(), Box< Patch, CompAtom >::close(), Controller::compareChecksums(), ComputeCUDAMgr::ComputeCUDAMgr(), ComputePmeCUDAMgr::ComputePmeCUDAMgr(), ComputeTclBC::ComputeTclBC(), CudaPmeTranspose::copyDataDeviceToDevice(), CudaPmeTranspose::copyDataDeviceToHost(), CudaPmeTranspose::copyDataHostToDevice(), WorkDistrib::createAtomLists(), ComputeCUDAMgr::createCudaComputeNonbonded(), ComputePmeCUDAMgr::createDevicesAndAtomFiler(), CsmAckHandler(), CsmHandler(), cudaNAMD_bug(), CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeRealSpaceCompute::CudaPmeRealSpaceCompute(), MigrateAtomsCombinedMsg::distribute(), ComputeGridForce::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doGroupSizeCheck_SOA(), ComputePme::doWork(), CudaComputeNonbonded::doWork(), WorkDistrib::enqueueAngles(), WorkDistrib::enqueueAniso(), WorkDistrib::enqueueBonds(), WorkDistrib::enqueueCrossterms(), WorkDistrib::enqueueDihedrals(), WorkDistrib::enqueueExcls(), WorkDistrib::enqueueGromacsPair(), WorkDistrib::enqueueImpropers(), WorkDistrib::enqueueLCPO(), WorkDistrib::enqueueOneFourNbThole(), 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(), SimpleBroadcastObject< Tensor >::get(), PmeAtomStorage::getAtomIndex(), getBlockDim(), CudaPmeTranspose::getBuffer(), ComputeCUDAMgr::getComputeCUDAMgr(), ComputeCUDAMgr::getCudaComputeNonbonded(), ComputePmeCUDAMgr::getDevice(), ComputePmeCUDAMgr::getDevicePencilY(), ComputePmeCUDAMgr::getDevicePencilZ(), ParseOptions::getfromptr(), ComputePmeCUDAMgr::getHomePencil(), ComputeLjPmeSerialMgr::getLJparameters(), Communicate::getMessage(), ComputePmeCUDAMgr::getNode(), getPencilDim(), Controller::getTotalPotentialEnergy(), globalAtomIDToSOAID(), GlobalGPUMgr::GlobalGPUMgr(), 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_version(), 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(), ComputeMgr::recvCudaGlobalMasterUpdateResultMsg(), 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(), AtomMapper::registerIDsCompAtomExt(), AtomMapper::registerIDsFullAtom(), registerUserEventsForAllComputeObjs(), Node::reloadGridforceGrid(), ReductionMgr::remoteSubmit(), IRSet::remove(), replica_bcast(), replica_min_double(), RequireReductionShared::RequireReductionShared(), 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(), SubmitReductionShared::SubmitReductionShared(), Sync::Sync(), SynchronousCollectives::SynchronousCollectives(), TopoManagerWrapper::TopoManagerWrapper(), CudaPmeTranspose::transposeXYZtoYZX(), CudaPmeTranspose::transposeXYZtoZXY(), IRSet::unchecked_insert(), ComputePme::ungridForces(), ComputeMap::unpack(), GridforceGrid::unpack_grid(), 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 ||
      (Node::Object()->simParameters != 0 &&
       Node::Object()->simParameters->CUDASOAintegrateMode)) {
    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
}

NAMD_close()

void NAMD_close	(	int	fd,
		const char *	fname
	)

Definition at line 316 of file common.C.

References NAMD_err().

                                           {
#if defined(WIN32) && !defined(__CYGWIN__)
  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);
    }
  }
}

NAMD_die()

void NAMD_die

(

const char *

)

Definition at line 148 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 || 
      (Node::Object()->simParameters != 0 &&
       Node::Object()->simParameters->CUDASOAintegrateMode)) {
    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
}

NAMD_err()

void NAMD_err

(

const char *

)

Definition at line 171 of file common.C.

References Node::Object().

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(), AmberParm7Reader::read_amber_parm_stage1(), 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 ||
      (Node::Object()->simParameters != 0 &&
       Node::Object()->simParameters->CUDASOAintegrateMode)) {
    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
}

NAMD_file_exists()

int NAMD_file_exists

(

const char *

filename

)

Definition at line 220 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;
}

NAMD_gcd()

int NAMD_gcd	(	int	a,
		int	b
	)

Definition at line 103 of file common.C.

References NAMD_gcd().

Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), and NAMD_gcd().

{
   if(a == 0 || b == 0) return 0;
   else if(a == b) return a;
   else if(a > b) return NAMD_gcd(a-b,b);
   return NAMD_gcd(a, b-a);
}

NAMD_open_text()

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

Definition at line 271 of file common.C.

References NAMD_err().

Referenced by ofstream_namd::open().

                                                  {
  int fd;

  //  open the file and die if the open fails
#if defined(WIN32) && !defined(__CYGWIN__)
  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;
}

NAMD_quit()

void NAMD_quit

(

const char *

)

Definition at line 126 of file common.C.

References Node::Object().

Referenced by GlobalMasterIMD::get_vmd_forces(), and Controller::printTiming().

{
  if ( ! err_msg ) err_msg = "(unknown error)";
  CkPrintf("EXITING: %s\n", err_msg);
  fflush(stdout);
  char repstr[24] = "";
  if (CmiNumPartitions() > 1
      || Node::Object()->simParameters->CUDASOAintegrateMode) {
    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
}

NAMD_stringdup()

char* NAMD_stringdup

(

const char *

)

Definition at line 112 of file common.C.

                                    {
  char *rs;

  if(!s)
    return NULL;

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

  return rs;
}

NAMD_version()

void NAMD_version	(	int *	major,
		int *	minor,
		int *	patchLevel,
		int *	releaseType
	)

Definition at line 57 of file common.C.

References NAMD_ALPHA_RELEASE, NAMD_BETA_RELEASE, NAMD_bug(), NAMD_FINAL_RELEASE, NAMD_UNKNOWN_RELEASE, and NAMD_version_string().

{
  int NAMD_major = 0;
  int NAMD_minor = 0;
  int NAMD_patchLevel = 0;
  int NAMD_releaseType = NAMD_UNKNOWN_RELEASE;

  // have to parse the version string to determine numbers
  const char *vstr = NAMD_version_string();
  char dot[4] = "";  // expect to read "."
  char release[8] = "";  // expect to read "" or "."
                         // or "alpha" or "beta" or "final" or "release"
  char extra[4] = "";  // bad version string if we read an extra character
  int n = sscanf(vstr, "%d%3[^0-9]%d%7[^0-9]%d%c",
      &NAMD_major, dot, &NAMD_minor, release, &NAMD_patchLevel, extra);
  if (n < 3 || n > 5) {
    NAMD_bug("Unable to parse NAMD_VERSION from Makefile");
  }
  if (n >= 4) {
    if (strcmp(release, "a") == 0 || strcmp(release, "alpha") == 0) {
      NAMD_releaseType = NAMD_ALPHA_RELEASE;
    }
    else if (strcmp(release, "b") == 0 || strcmp(release, "beta") == 0) {
      NAMD_releaseType = NAMD_BETA_RELEASE;
    }
    else if (strcmp(release, ".") == 0 ||
             strcmp(release, "final") == 0 ||
             strcmp(release, "release") == 0 ||
             strcmp(release, "patch") == 0) {
      NAMD_releaseType = NAMD_FINAL_RELEASE;
    }
    else {
      NAMD_bug("Unable to parse NAMD_VERSION from Makefile");
    }
  }
  else {
    NAMD_releaseType = NAMD_FINAL_RELEASE;
  }
  // now return values to caller
  if (major != NULL) *major = NAMD_major;
  if (minor != NULL) *minor = NAMD_minor;
  if (patchLevel != NULL) *patchLevel = NAMD_patchLevel;
  if (releaseType != NULL) *releaseType = NAMD_releaseType;
}

NAMD_version_string()

const char* NAMD_version_string

(

void

)

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

Definition at line 52 of file common.C.

Referenced by NAMD_version().

                                  {
  return NAMD_VERSION;  // macro defined in toplevel Makefile
}

NAMD_write()

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

Definition at line 296 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;
  }
}