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

NAMD_HOST_DEVICE Vector (void)
 
NAMD_HOST_DEVICE Vector (BigReal newx, BigReal newy, BigReal newz)
 
NAMD_HOST_DEVICE Vector (BigReal newv)
 
NAMD_HOST_DEVICE Vector (const FloatVector &v)
 
NAMD_HOST_DEVICE Vector (double3 vec)
 
NAMD_HOST_DEVICE operator double3 () const
 
NAMD_HOST_DEVICE BigRealoperator[] (int i)
 
NAMD_HOST_DEVICE Vectoroperator= (const BigReal &v2)
 
NAMD_HOST_DEVICE void operator+= (const Vector &v2)
 
NAMD_HOST_DEVICE void operator-= (const Vector &v2)
 
NAMD_HOST_DEVICE void operator*= (const BigReal &v2)
 
NAMD_HOST_DEVICE void operator/= (const BigReal &v2)
 
NAMD_HOST_DEVICE BigReal length (void) const
 
NAMD_HOST_DEVICE BigReal length2 (void) const
 
NAMD_HOST_DEVICE BigReal rlength (void) const
 
NAMD_HOST_DEVICE Vector unit (void) const
 
NAMD_HOST_DEVICE void cross (const Vector &v2)
 
NAMD_HOST_DEVICE BigReal dot (const Vector &v2) const
 
Bool set (const char *s)
 

Public Attributes

BigReal x
 
BigReal y
 
BigReal z
 

Friends

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

Detailed Description

Definition at line 72 of file Vector.h.

Constructor & Destructor Documentation

◆ Vector() [1/5]

NAMD_HOST_DEVICE Vector::Vector ( void  )
inline

Definition at line 77 of file Vector.h.

Referenced by unit().

77 : x(-99999), y(-99999), z(-99999) { ; }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ Vector() [2/5]

NAMD_HOST_DEVICE Vector::Vector ( BigReal  newx,
BigReal  newy,
BigReal  newz 
)
inline

Definition at line 82 of file Vector.h.

83  : x(newx), y(newy), z(newz) { ; }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ Vector() [3/5]

NAMD_HOST_DEVICE Vector::Vector ( BigReal  newv)
inline

Definition at line 85 of file Vector.h.

86  : x(newv), y(newv), z(newv) { ; }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ Vector() [4/5]

NAMD_HOST_DEVICE Vector::Vector ( const FloatVector v)
inline

Definition at line 88 of file Vector.h.

88 : x(v.x), y(v.y), z(v.z) { ; }
BigReal z
Definition: Vector.h:74
float y
Definition: Vector.h:26
float x
Definition: Vector.h:26
float z
Definition: Vector.h:26
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ Vector() [5/5]

NAMD_HOST_DEVICE Vector::Vector ( double3  vec)
inline

Definition at line 93 of file Vector.h.

94  : x(vec.x), y(vec.y), z(vec.z) { ; }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

Member Function Documentation

◆ cross()

NAMD_HOST_DEVICE void Vector::cross ( const Vector v2)
inline

Definition at line 245 of file Vector.h.

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

245  {
246  BigReal xx = y*v2.z-v2.y*z;
247  // BigReal yy = -x*v2.z+v2.x*z;
248  BigReal yy = v2.x*z-x*v2.z;
249  z = x*v2.y-v2.x*y;
250  y=yy;
251  x=xx;
252  }
BigReal z
Definition: Vector.h:74
virial xx
BigReal x
Definition: Vector.h:74
virial yy
BigReal y
Definition: Vector.h:74
double BigReal
Definition: common.h:123

◆ dot()

NAMD_HOST_DEVICE BigReal Vector::dot ( const Vector v2) const
inline

Definition at line 255 of file Vector.h.

References x, y, and z.

Referenced by ComputeStir::doForce().

255  {
256  return x*v2.x + y*v2.y + z*v2.z;
257  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ length()

NAMD_HOST_DEVICE BigReal Vector::length ( void  ) const
inline

◆ length2()

NAMD_HOST_DEVICE BigReal Vector::length2 ( void  ) const
inline

◆ operator double3()

NAMD_HOST_DEVICE Vector::operator double3 ( ) const
inline

Definition at line 97 of file Vector.h.

References x, y, and z.

97  {
98  double3 res;
99  res.x = x;
100  res.y = y;
101  res.z = z;
102  return res;
103  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator*=()

NAMD_HOST_DEVICE void Vector::operator*= ( const BigReal v2)
inline

Definition at line 146 of file Vector.h.

References x, y, and z.

146  {
147  x *= v2;
148  y *= v2;
149  z *= v2;
150  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator+=()

NAMD_HOST_DEVICE void Vector::operator+= ( const Vector v2)
inline

Definition at line 132 of file Vector.h.

References x, y, and z.

132  {
133  x += v2.x;
134  y += v2.y;
135  z += v2.z;
136  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator-=()

NAMD_HOST_DEVICE void Vector::operator-= ( const Vector v2)
inline

Definition at line 139 of file Vector.h.

References x, y, and z.

139  {
140  x -= v2.x;
141  y -= v2.y;
142  z -= v2.z;
143  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator/=()

NAMD_HOST_DEVICE void Vector::operator/= ( const BigReal v2)
inline

Definition at line 153 of file Vector.h.

References namd_reciprocal, x, y, and z.

153  {
154  BigReal v2_recip = namd_reciprocal(v2);
155  x *= v2_recip;
156  y *= v2_recip;
157  z *= v2_recip;
158  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74
#define namd_reciprocal(x)
Definition: Vector.h:69
double BigReal
Definition: common.h:123

◆ operator=()

NAMD_HOST_DEVICE Vector& Vector::operator= ( const BigReal v2)
inline

Definition at line 124 of file Vector.h.

References x, y, and z.

124  {
125  x = v2;
126  y = v2;
127  z = v2;
128  return *this;
129  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator[]()

NAMD_HOST_DEVICE BigReal& Vector::operator[] ( int  i)
inline

Definition at line 107 of file Vector.h.

References x, y, and z.

107  {
108  return i==0 ? x
109  :i==1 ? y
110  :i==2 ? z : x
111  ;
112  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ rlength()

NAMD_HOST_DEVICE BigReal Vector::rlength ( void  ) const
inline

Definition at line 210 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().

210  {
211  return namd_rsqrt (x*x + y*y + z*z);
212  }
BigReal z
Definition: Vector.h:74
#define namd_rsqrt(x)
Definition: Vector.h:68
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ set()

Bool Vector::set ( const char *  s)
inline

Definition at line 261 of file Vector.h.

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

Referenced by colvarproxy_namd::calculate(), ParseOptions::get(), GroupRestraintParam::SetGroup1RefPosition(), and GroupRestraintParam::SetResCenter().

261  {
262  double a[3]; // read into doubles, since I don't know what
263  char tmp[100]; // a "BigReal" is in real life
264  // cheap way to get commas, etc. a poor regex
265  int i=sscanf(s, "%lf%99[ \t,]%lf%99[ \t,]%lf%99s",
266  a, tmp, a+1, tmp, a+2, tmp);
267  if (i != 5) return FALSE;
268  const char *t = s; // now count commas (for "1,,,,2, , 3")
269  int flg = 0; // and check for "1 2,,3"
270  i = 0;
271  for (;*t;t++) {
272  if (*t == ',') {
273  if (flg == 0) { // expecting non-whitespace
274  return FALSE; // so error
275  }
276  flg = 0; // now expect non-whitespace
277  i++; // and increment comma counter
278  }
279  else if (*t != ' ' && *t != '\t') { // got non-whitespace
280  flg = 1; // so the next can be whitespace or commas
281  }
282  }
283  if (i == 0 || i == 2) { // allow "1 2 3" or "1, 2,3" forms
284  x = a[0]; y = a[1]; z = a[2];
285  return TRUE;
286  }
287  return FALSE;
288  }
BigReal z
Definition: Vector.h:74
#define FALSE
Definition: common.h:127
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74
#define TRUE
Definition: common.h:128

◆ unit()

NAMD_HOST_DEVICE Vector Vector::unit ( void  ) const
inline

Friends And Related Function Documentation

◆ cross [1/3]

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

Definition at line 221 of file Vector.h.

221  {
222  return Vector( v1.y*v2.z-v2.y*v1.z,
223  // -v1.x*v2.z+v2.x*v1.z,
224  v2.x*v1.z-v1.x*v2.z,
225  v1.x*v2.y-v2.x*v1.y );
226  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ cross [2/3]

NAMD_HOST_DEVICE friend Vector cross ( const Real k,
const Vector v1,
const Vector v2 
)
friend

Definition at line 230 of file Vector.h.

230  {
231  return Vector( k*(v1.y*v2.z-v2.y*v1.z),
232  // k*(-v1.x*v2.z+v2.x*v1.z),
233  k*(v2.x*v1.z-v1.x*v2.z),
234  k*(v1.x*v2.y-v2.x*v1.y) );
235  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ cross [3/3]

NAMD_HOST_DEVICE friend Vector cross ( const BigReal k,
const Vector v1,
const Vector v2 
)
friend

Definition at line 237 of file Vector.h.

237  {
238  return Vector( k*(v1.y*v2.z-v2.y*v1.z),
239  // k*(-v1.x*v2.z+v2.x*v1.z),
240  k*(v2.x*v1.z-v1.x*v2.z),
241  k*(v1.x*v2.y-v2.x*v1.y) );
242  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator!=

NAMD_HOST_DEVICE friend int operator!= ( const Vector v1,
const Vector v2 
)
friend

Definition at line 163 of file Vector.h.

163  {
164  // return !(v1.x == v2.x && v1.y == v2.y && v1.z == v2.z);
165  return v1.x != v2.x || v1.y != v2.y || v1.z != v2.z;
166  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator* [1/3]

NAMD_HOST_DEVICE friend BigReal operator* ( const Vector v1,
const Vector v2 
)
friend

Definition at line 183 of file Vector.h.

183  {
184  return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z;
185  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

◆ operator* [2/3]

NAMD_HOST_DEVICE friend Vector operator* ( const BigReal f,
const Vector v1 
)
friend

Definition at line 187 of file Vector.h.

187  {
188  return Vector(f*v1.x, f*v1.y, f*v1.z);
189  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator* [3/3]

NAMD_HOST_DEVICE friend Vector operator* ( const Vector v1,
const BigReal f 
)
friend

Definition at line 191 of file Vector.h.

191  {
192  return Vector(f*v1.x, f*v1.y, f*v1.z);
193  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator+

NAMD_HOST_DEVICE friend Vector operator+ ( const Vector v1,
const Vector v2 
)
friend

Definition at line 169 of file Vector.h.

169  {
170  return Vector( v1.x+v2.x, v1.y+v2.y, v1.z+v2.z);
171  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator- [1/2]

NAMD_HOST_DEVICE friend Vector operator- ( const Vector v1)
friend

Definition at line 174 of file Vector.h.

174  {
175  return Vector( -v1.x, -v1.y, -v1.z);
176  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator- [2/2]

NAMD_HOST_DEVICE friend Vector operator- ( const Vector v1,
const Vector v2 
)
friend

Definition at line 179 of file Vector.h.

179  {
180  return Vector( v1.x-v2.x, v1.y-v2.y, v1.z-v2.z);
181  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator/

NAMD_HOST_DEVICE friend Vector operator/ ( const Vector v1,
const BigReal f 
)
friend

Definition at line 195 of file Vector.h.

195  {
196 // if (!f)
197 // NAMD_die("Division by 0 on a vector operation.");
198  return Vector(v1.x/f, v1.y/f, v1.z/f);
199  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
NAMD_HOST_DEVICE Vector(void)
Definition: Vector.h:77
BigReal y
Definition: Vector.h:74

◆ operator==

NAMD_HOST_DEVICE friend int operator== ( const Vector v1,
const Vector v2 
)
friend

Definition at line 160 of file Vector.h.

160  {
161  return v1.x == v2.x && v1.y == v2.y && v1.z == v2.z;
162  }
BigReal z
Definition: Vector.h:74
BigReal x
Definition: Vector.h:74
BigReal y
Definition: Vector.h:74

Member Data Documentation

◆ x

BigReal Vector::x

Definition at line 74 of file Vector.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), Sequencer::berendsenPressure_SOA(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), CudaPmeOneDevice::compute(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Controller::correctMomentum(), cross(), Lattice::delta_from_diff(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeSphericalBC::doForce(), ComputeGridForce::doForce(), ComputeCylindricalBC::doForce(), ComputeRestraints::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), 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(), colvarproxy_namd::GridForceGridLoop(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap_by_name(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), Sequencer::integrate_SOA(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Lattice::nearest(), obj_3D_vector(), operator double3(), sortop_x::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlistFromAll(), partition(), partition_SOA(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), PRINT_VECTOR(), Controller::printEnergies(), GroupRestraintParam::PrintSummary(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGlobal::recvResults(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeMsmSerial::saveResults(), ComputeLjPmeSerial::saveResults(), ComputeFmmSerial::saveResults(), ComputeGlobal::saveTotalForces(), scale_coordinates(), Lattice::scale_force(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), GroupRestraintParam::SetResDirection(), LjPmeMgr::setScaledCoordinates(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), Lattice::wrap_delta_scaled(), and Controller::writeExtendedSystemData().

◆ y

BigReal Vector::y

Definition at line 74 of file Vector.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), Sequencer::berendsenPressure_SOA(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::compute(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Controller::correctMomentum(), cross(), Lattice::delta_from_diff(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeSphericalBC::doForce(), ComputeGridForce::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), 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(), colvarproxy_namd::GridForceGridLoop(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap_by_name(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), Sequencer::integrate_SOA(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Lattice::nearest(), obj_3D_vector(), operator double3(), sortop_y::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlistFromAll(), partition(), partition_SOA(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), PRINT_VECTOR(), print_vel_AOS(), Controller::printEnergies(), GroupRestraintParam::PrintSummary(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGlobal::recvResults(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeFmmSerial::saveResults(), ComputeMsmSerial::saveResults(), ComputeLjPmeSerial::saveResults(), ComputeGlobal::saveTotalForces(), scale_coordinates(), Lattice::scale_force(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), GroupRestraintParam::SetResDirection(), LjPmeMgr::setScaledCoordinates(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), Lattice::wrap_delta_scaled(), and Controller::writeExtendedSystemData().

◆ z

BigReal Vector::z

Definition at line 74 of file Vector.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), Sequencer::berendsenPressure_SOA(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::compute(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Controller::correctMomentum(), cross(), Lattice::delta_from_diff(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeSphericalBC::doForce(), ComputeNonbondedSelf::doForce(), ComputeGridForce::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), 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(), colvarproxy_namd::GridForceGridLoop(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap_by_name(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), Sequencer::integrate_SOA(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Lattice::nearest(), obj_3D_vector(), operator double3(), sortop_z::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlistFromAll(), partition(), partition_SOA(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), PRINT_VECTOR(), print_vel_AOS(), Controller::printEnergies(), GroupRestraintParam::PrintSummary(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGlobal::recvResults(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeMsmSerial::saveResults(), ComputeLjPmeSerial::saveResults(), ComputeFmmSerial::saveResults(), ComputeGlobal::saveTotalForces(), scale_coordinates(), Lattice::scale_force(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), GroupRestraintParam::SetResDirection(), LjPmeMgr::setScaledCoordinates(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), Lattice::wrap_delta_scaled(), and Controller::writeExtendedSystemData().


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