NAMD
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#include "largefiles.h"
#include <string.h>
#include <stdlib.h>
#include "InfoStream.h"
#include "IMDOutput.h"
#include "Output.h"
#include "dcdlib.h"
#include "strlib.h"
#include "Molecule.h"
#include "Node.h"
#include "Parameters.h"
#include "PDB.h"
#include "SimParameters.h"
#include "Vector.h"
#include "structures.h"
#include "MStream.h"
#include "Communicate.h"
#include "PatchMap.h"
#include "PatchMap.inl"
#include "ScriptTcl.h"
#include "Lattice.h"
#include "DataExchanger.h"
#include <fcntl.h>
#include <sys/stat.h>
Go to the source code of this file.
Macros | |
#define | PATHSEPSTR "/" |
#define | MKDIR(X) mkdir(X,0777) |
#define | NAMD_open NAMD_open64 |
#define | NAMD_write NAMD_write64 |
#define | NAMD_close NAMD_close64 |
#define | O_LARGEFILE 0x0 |
#define | seek_dcdfile NAMD_seek |
#define | namdMyNode Node::Object() |
#define | simParams simParameters |
#define | pdbData pdb |
#define | RAD2DEG 180.0/3.14159265359 |
Functions | |
int | NAMD_open (const char *fname) |
void | NAMD_write (int fd, const char *buf, size_t count, const char *errmsg="NAMD_write64") |
void | NAMD_close (int fd, const char *fname) |
static void | lattice_to_unitcell (const Lattice *lattice, double *unitcell) |
template<class xVector , class xDone > | |
void | wrap_coor_int (xVector *coor, Lattice &lattice, xDone *done) |
void | wrap_coor (Vector *coor, Lattice &lattice, double *done) |
void | wrap_coor (FloatVector *coor, Lattice &lattice, float *done) |
#define NAMD_close NAMD_close64 |
Definition at line 52 of file Output.C.
Referenced by ofstream_namd::close().
#define namdMyNode Node::Object() |
#define O_LARGEFILE 0x0 |
Definition at line 55 of file Output.C.
Referenced by NAMD_open().
#define PATHSEPSTR "/" |
#define simParams simParameters |
Definition at line 127 of file Output.C.
Referenced by ComputeCylindricalBC::ComputeCylindricalBC(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), GromacsPairElem::computeForce(), ComputeFullDirect::ComputeFullDirect(), ComputeLCPO::ComputeLCPO(), ComputeRestraints::ComputeRestraints(), ComputeSphericalBC::ComputeSphericalBC(), ComputeStir::ComputeStir(), ComputeTclBC::ComputeTclBC(), Output::coordinate(), Output::coordinateNeeded(), LdbCoordinator::createLoadBalancer(), CudaComputeNonbonded::CudaComputeNonbonded(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeGridForce::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeRestraints::doForce(), ComputeTclBC::doWork(), ComputeNonbondedCUDA::doWork(), dumpbench(), ComputeNonbondedCUDA::finishReductions(), ComputeNonbondedCUDA::finishWork(), Output::force(), Output::forceNeeded(), Molecule::get_fep_bonded_type(), ComputePmeMgr::gridCalc2(), ComputePmeCUDA::initialize(), LdbCoordinator::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), isPmeProcessor(), NamdHybridLB::NamdHybridLB(), ComputeNonbondedCUDA::noWork(), Molecule::num_deg_freedom(), Molecule::num_fixed_atoms(), Molecule::num_group_deg_freedom(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), ComputeNonbondedCUDA::registerPatches(), ComputeNonbondedUtil::select(), ComputeNonbondedCUDA::skip(), NamdHybridLB::splitComputes(), NamdCentLB::Strategy(), ComputeMgr::updateLocalComputes4(), Output::velocity(), Output::velocityNeeded(), wrap_coor_int(), and Controller::write_accelMDG_rest_file().
Definition at line 131 of file Output.C.
References Lattice::a(), Lattice::a_p(), Lattice::b(), Lattice::b_p(), Lattice::c(), Lattice::c_p(), and Vector::length().
void NAMD_close | ( | int | fd, |
const char * | fname | ||
) |
int NAMD_open | ( | const char * | fname | ) |
Definition at line 59 of file Output.C.
References NAMD_err(), and O_LARGEFILE.
void NAMD_write | ( | int | fd, |
const char * | buf, | ||
size_t | count, | ||
const char * | errmsg = "NAMD_write64" |
||
) |
Definition at line 84 of file Output.C.
References endi(), iout, iWARN(), NAMD_bug(), and NAMD_err().
Definition at line 269 of file Output.C.
References wrap_coor_int().
Referenced by Output::coordinate().
void wrap_coor | ( | FloatVector * | coor, |
Lattice & | lattice, | ||
float * | done | ||
) |
Definition at line 273 of file Output.C.
References wrap_coor_int().
void wrap_coor_int | ( | xVector * | coor, |
Lattice & | lattice, | ||
xDone * | done | ||
) |
Definition at line 237 of file Output.C.
References Molecule::get_cluster(), Molecule::get_clusterSize(), Molecule::is_water(), Node::molecule, Molecule::numAtoms, Node::Object(), Node::simParameters, simParams, Lattice::wrap_delta(), Lattice::wrap_nearest_delta(), SimParameters::wrapAll, SimParameters::wrapNearest, and SimParameters::wrapWater.
Referenced by wrap_coor().