NAMD
Public Member Functions | Public Attributes | Friends | List of all members
Vector Class Reference

#include <Vector.h>

Inheritance diagram for Vector:
AlignVector zVector

Public Member Functions

 Vector (void)
 
 Vector (BigReal newx, BigReal newy, BigReal newz)
 
 Vector (BigReal newv)
 
 Vector (const FloatVector &v)
 
BigRealoperator[] (int i)
 
Vectoroperator= (const BigReal &v2)
 
void operator+= (const Vector &v2)
 
void operator-= (const Vector &v2)
 
void operator*= (const BigReal &v2)
 
void operator/= (const BigReal &v2)
 
BigReal length (void) const
 
BigReal length2 (void) const
 
BigReal rlength (void)
 
Vector unit (void) const
 
void cross (const Vector &v2)
 
BigReal dot (const Vector &v2)
 
Bool set (const char *s)
 

Public Attributes

BigReal x
 
BigReal y
 
BigReal z
 

Friends

int operator== (const Vector &v1, const Vector &v2)
 
int operator!= (const Vector &v1, const Vector &v2)
 
Vector operator+ (const Vector &v1, const Vector &v2)
 
Vector operator- (const Vector &v1)
 
Vector operator- (const Vector &v1, const Vector &v2)
 
BigReal operator* (const Vector &v1, const Vector &v2)
 
Vector operator* (const BigReal &f, const Vector &v1)
 
Vector operator* (const Vector &v1, const BigReal &f)
 
Vector operator/ (const Vector &v1, const BigReal &f)
 
Vector cross (const Vector &v1, const Vector &v2)
 
Vector cross (const Real &k, const Vector &v1, const Vector &v2)
 
Vector cross (const BigReal &k, const Vector &v1, const Vector &v2)
 

Detailed Description

Definition at line 64 of file Vector.h.

Constructor & Destructor Documentation

Vector::Vector ( void  )
inline

Definition at line 69 of file Vector.h.

Referenced by unit().

69 : x(-99999), y(-99999), z(-99999) { ; }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
Vector::Vector ( BigReal  newx,
BigReal  newy,
BigReal  newz 
)
inline

Definition at line 74 of file Vector.h.

75  : x(newx), y(newy), z(newz) { ; }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
Vector::Vector ( BigReal  newv)
inline

Definition at line 77 of file Vector.h.

78  : x(newv), y(newv), z(newv) { ; }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
Vector::Vector ( const FloatVector v)
inline

Definition at line 80 of file Vector.h.

80 : x(v.x), y(v.y), z(v.z) { ; }
BigReal z
Definition: Vector.h:66
float y
Definition: Vector.h:18
float x
Definition: Vector.h:18
float z
Definition: Vector.h:18
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66

Member Function Documentation

void Vector::cross ( const Vector v2)
inline

Definition at line 212 of file Vector.h.

References x, xx, y, yy, and z.

212  {
213  BigReal xx = y*v2.z-v2.y*z;
214  // BigReal yy = -x*v2.z+v2.x*z;
215  BigReal yy = v2.x*z-x*v2.z;
216  z = x*v2.y-v2.x*y;
217  y=yy;
218  x=xx;
219  }
BigReal z
Definition: Vector.h:66
virial xx
BigReal x
Definition: Vector.h:66
virial yy
BigReal y
Definition: Vector.h:66
double BigReal
Definition: common.h:112
BigReal Vector::dot ( const Vector v2)
inline

Definition at line 222 of file Vector.h.

References x, y, and z.

Referenced by ComputeStir::doForce().

222  {
223  return x*v2.x + y*v2.y + z*v2.z;
224  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
BigReal Vector::length ( void  ) const
inline
BigReal Vector::length2 ( void  ) const
inline
void Vector::operator*= ( const BigReal v2)
inline

Definition at line 113 of file Vector.h.

References x, y, and z.

113  {
114  x *= v2;
115  y *= v2;
116  z *= v2;
117  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
void Vector::operator+= ( const Vector v2)
inline

Definition at line 99 of file Vector.h.

References x, y, and z.

99  {
100  x += v2.x;
101  y += v2.y;
102  z += v2.z;
103  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
void Vector::operator-= ( const Vector v2)
inline

Definition at line 106 of file Vector.h.

References x, y, and z.

106  {
107  x -= v2.x;
108  y -= v2.y;
109  z -= v2.z;
110  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
void Vector::operator/= ( const BigReal v2)
inline

Definition at line 120 of file Vector.h.

References namd_reciprocal, x, y, and z.

120  {
121  BigReal v2_recip = namd_reciprocal(v2);
122  x *= v2_recip;
123  y *= v2_recip;
124  z *= v2_recip;
125  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
#define namd_reciprocal(x)
Definition: Vector.h:61
double BigReal
Definition: common.h:112
Vector& Vector::operator= ( const BigReal v2)
inline

Definition at line 91 of file Vector.h.

References x, y, and z.

91  {
92  x = v2;
93  y = v2;
94  z = v2;
95  return *this;
96  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
BigReal& Vector::operator[] ( int  i)
inline

Definition at line 82 of file Vector.h.

References NAMD_die(), x, y, and z.

82  {
83  return i==0 ? x
84  :i==1 ? y
85  :i==2 ? z
86  :(NAMD_die("Vector reference out of bounds."), x);
87 
88  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
void NAMD_die(const char *err_msg)
Definition: common.C:83
BigReal y
Definition: Vector.h:66
BigReal Vector::rlength ( void  )
inline

Definition at line 177 of file Vector.h.

References namd_rsqrt, x, y, and z.

Referenced by AngleElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), and rescale_nonperiodic_cell().

177  {
178  return namd_rsqrt (x*x + y*y + z*z);
179  }
BigReal z
Definition: Vector.h:66
#define namd_rsqrt(x)
Definition: Vector.h:60
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
Bool Vector::set ( const char *  s)
inline

Definition at line 228 of file Vector.h.

References FALSE, TRUE, x, y, and z.

Referenced by colvarproxy_namd::calculate(), and ParseOptions::get().

228  {
229  double a[3]; // read into doubles, since I don't know what
230  char tmp[100]; // a "BigReal" is in real life
231  // cheap way to get commas, etc. a poor regex
232  int i=sscanf(s, "%lf%99[ \t,]%lf%99[ \t,]%lf%99s",
233  a, tmp, a+1, tmp, a+2, tmp);
234  if (i != 5) return FALSE;
235  const char *t = s; // now count commas (for "1,,,,2, , 3")
236  int flg = 0; // and check for "1 2,,3"
237  i = 0;
238  for (;*t;t++) {
239  if (*t == ',') {
240  if (flg == 0) { // expecting non-whitespace
241  return FALSE; // so error
242  }
243  flg = 0; // now expect non-whitespace
244  i++; // and increment comma counter
245  }
246  else if (*t != ' ' && *t != '\t') { // got non-whitespace
247  flg = 1; // so the next can be whitespace or commas
248  }
249  }
250  if (i == 0 || i == 2) { // allow "1 2 3" or "1, 2,3" forms
251  x = a[0]; y = a[1]; z = a[2];
252  return TRUE;
253  }
254  return FALSE;
255  }
BigReal z
Definition: Vector.h:66
#define FALSE
Definition: common.h:116
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
#define TRUE
Definition: common.h:117
Vector Vector::unit ( void  ) const
inline

Friends And Related Function Documentation

Vector cross ( const Vector v1,
const Vector v2 
)
friend

Definition at line 188 of file Vector.h.

188  {
189  return Vector( v1.y*v2.z-v2.y*v1.z,
190  // -v1.x*v2.z+v2.x*v1.z,
191  v2.x*v1.z-v1.x*v2.z,
192  v1.x*v2.y-v2.x*v1.y );
193  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector cross ( const Real k,
const Vector v1,
const Vector v2 
)
friend

Definition at line 197 of file Vector.h.

197  {
198  return Vector( k*(v1.y*v2.z-v2.y*v1.z),
199  // k*(-v1.x*v2.z+v2.x*v1.z),
200  k*(v2.x*v1.z-v1.x*v2.z),
201  k*(v1.x*v2.y-v2.x*v1.y) );
202  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector cross ( const BigReal k,
const Vector v1,
const Vector v2 
)
friend

Definition at line 204 of file Vector.h.

204  {
205  return Vector( k*(v1.y*v2.z-v2.y*v1.z),
206  // k*(-v1.x*v2.z+v2.x*v1.z),
207  k*(v2.x*v1.z-v1.x*v2.z),
208  k*(v1.x*v2.y-v2.x*v1.y) );
209  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
int operator!= ( const Vector v1,
const Vector v2 
)
friend

Definition at line 130 of file Vector.h.

130  {
131  // return !(v1.x == v2.x && v1.y == v2.y && v1.z == v2.z);
132  return v1.x != v2.x || v1.y != v2.y || v1.z != v2.z;
133  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
BigReal operator* ( const Vector v1,
const Vector v2 
)
friend

Definition at line 150 of file Vector.h.

150  {
151  return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z;
152  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66
Vector operator* ( const BigReal f,
const Vector v1 
)
friend

Definition at line 154 of file Vector.h.

154  {
155  return Vector(f*v1.x, f*v1.y, f*v1.z);
156  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector operator* ( const Vector v1,
const BigReal f 
)
friend

Definition at line 158 of file Vector.h.

158  {
159  return Vector(f*v1.x, f*v1.y, f*v1.z);
160  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector operator+ ( const Vector v1,
const Vector v2 
)
friend

Definition at line 136 of file Vector.h.

136  {
137  return Vector( v1.x+v2.x, v1.y+v2.y, v1.z+v2.z);
138  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector operator- ( const Vector v1)
friend

Definition at line 141 of file Vector.h.

141  {
142  return Vector( -v1.x, -v1.y, -v1.z);
143  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector operator- ( const Vector v1,
const Vector v2 
)
friend

Definition at line 146 of file Vector.h.

146  {
147  return Vector( v1.x-v2.x, v1.y-v2.y, v1.z-v2.z);
148  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
Vector operator/ ( const Vector v1,
const BigReal f 
)
friend

Definition at line 162 of file Vector.h.

162  {
163 // if (!f)
164 // NAMD_die("Division by 0 on a vector operation.");
165  return Vector(v1.x/f, v1.y/f, v1.z/f);
166  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
Vector(void)
Definition: Vector.h:69
BigReal y
Definition: Vector.h:66
int operator== ( const Vector v1,
const Vector v2 
)
friend

Definition at line 127 of file Vector.h.

127  {
128  return v1.x == v2.x && v1.y == v2.y && v1.z == v2.z;
129  }
BigReal z
Definition: Vector.h:66
BigReal x
Definition: Vector.h:66
BigReal y
Definition: Vector.h:66

Member Data Documentation

BigReal Vector::x

Definition at line 66 of file Vector.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), Controller::correctMomentum(), cross(), Lattice::delta(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), ComputeRestraints::doForce(), ComputeLCPO::doForce(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeNonbondedCUDA::finishWork(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), ComputeMsmMgr::gc_c1hermite_elem_accum(), get_3D_vector(), PDB::get_all_positions(), get_lattice_from_ts(), PDB::get_position_for_atom(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Lattice::nearest(), obj_3D_vector(), sortop_x::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlist_from_pairlist(), pairlistFromAll(), partition(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), PRINT_VECTOR(), Controller::printEnergies(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), register_cuda_compute_pair(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeMsmSerial::saveResults(), ComputeFmmSerial::saveResults(), scale_coordinates(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), and Controller::writeExtendedSystemData().

BigReal Vector::y

Definition at line 66 of file Vector.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), Controller::correctMomentum(), cross(), Lattice::delta(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeNonbondedCUDA::finishWork(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), ComputeMsmMgr::gc_c1hermite_elem_accum(), get_3D_vector(), PDB::get_all_positions(), get_lattice_from_ts(), PDB::get_position_for_atom(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Lattice::nearest(), obj_3D_vector(), sortop_y::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlist_from_pairlist(), pairlistFromAll(), partition(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), PRINT_VECTOR(), Controller::printEnergies(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), register_cuda_compute_pair(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeFmmSerial::saveResults(), ComputeMsmSerial::saveResults(), scale_coordinates(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), and Controller::writeExtendedSystemData().

BigReal Vector::z

Definition at line 66 of file Vector.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), Controller::correctMomentum(), cross(), Lattice::delta(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeNonbondedPair::doForce(), ComputeSphericalBC::doForce(), ComputeNonbondedSelf::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeNonbondedCUDA::finishWork(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), ComputeMsmMgr::gc_c1hermite_elem_accum(), get_3D_vector(), PDB::get_all_positions(), get_lattice_from_ts(), PDB::get_position_for_atom(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Lattice::nearest(), obj_3D_vector(), sortop_z::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlist_from_pairlist(), pairlistFromAll(), partition(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), PRINT_VECTOR(), Controller::printEnergies(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), register_cuda_compute_pair(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeFmmSerial::saveResults(), ComputeMsmSerial::saveResults(), scale_coordinates(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), and Controller::writeExtendedSystemData().


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