UcellTest Class Reference

Inheritance diagram for UcellTest:

Collaboration diagram for UcellTest:

Protected Member Functions
void	SetUp ()
void	TearDown ()
void	SetUp ()
void	TearDown ()
void	SetUp ()

Protected Attributes
std::unique_ptr< UnitCell >	ucell {new UnitCell}
std::string	output
UcellTestPrepare	utp = UcellTestLib["C1H2-Read"]
std::ofstream	ofs
std::string	pp_dir

Detailed Description

• Tested Functions:
  • Constructor:
    • UnitCell() and ~UnitCell()
  • Setup:
    • setup(): to set latname, ntype, lmaxmax, init_vel, and lc
    • if_cell_can_change(): judge if any lattice vector can change
  • SetupWarningQuit1:
    • setup(): deliver warning: "there are bugs in the old implementation; set relax_new to be 1 for fixed_volume relaxation"
  • SetupWarningQuit2:
    • setup(): deliver warning: "set relax_new to be 1 for fixed_shape relaxation"
  • RemakeCell
    • remake_cell(): rebuild cell according to its latName
  • RemakeCellWarnings
    • remake_cell(): deliver warnings when find wrong latname or cos12
  • JudgeParallel
    • judge_parallel: judge if two vectors a[3] and Vector3<double> b are parallel
  • Index
    • set_iat2iait(): set index relations in two arrays of Unitcell: iat2it[nat], iat2ia[nat]
    • iat2iait(): depends on the above function, but can find both ia & it from iat
    • ijat2iaitjajt(): find ia, it, ja, jt from ijat (ijat_max = nat*nat) which collapses it, ia, jt, ja loop into a single loop
    • step_ia(): periodically set ia to 0 when ia reaches atom[it].na - 1
    • step_it(): periodically set it to 0 when it reaches ntype -1
    • step_iait(): return true only the above two conditions are true
    • step_jajtiait(): return ture only two of the above function (for i and j) are true
  • GetAtomCounts
    • get_atomCounts(): get atomCounts, which is a map from atom type to atom number
  • GetOrbitalCounts
    • get_orbitalCounts(): get orbitalCounts, which is a map from atom type to orbital number
  • CheckDTau
    • check_dtau(): move all atomic coordinates into the first unitcell, i.e. in between [0,1)
  • CheckTau
    • check_tau(): check if any "two atoms are too close"
  • SelectiveDynamics
    • if_atoms_can_move():it is true if any coordinates of any atom can move, i.e. mbl = 1
  • PeriodicBoundaryAdjustment
    • periodic_boundary_adjustment(): move atoms inside the unitcell after relaxation
  • PrintCell
    • print_cell(ofs): print basic cell info into ofs
  • PrintSTRU
    • print_stru_file(): print STRU file of ABACUS
  • PrintTauDirect
  • PrintTauCartesian
    • print_tau(): print atomic coordinates, magmom and initial velocities
  • PrintUnitcellPseudo
    • Actually an integrated function to call UnitCell::print_cell and Atom::print_Atom
  • UpdateVel
    • update_vel(const ModuleBase::Vector3<double>* vel_in)
  • CalUx
    • cal_ux(UnitCell& ucell): calculate magnetic moments of cell
  • ReadOrbFile
    • read_orb_file(): read header part of orbital file
  • ReadOrbFileWarning
    • read_orb_file(): ABACUS Cannot find the ORBITAL file
  • ReadAtomSpecies
    • read_atom_species(): a successful case
  • ReadAtomSpeciesWarning1
    • read_atom_species(): unrecognized pseudopotential type.
  • ReadAtomSpeciesWarning2
    • read_atom_species(): lat0<=0.0
  • ReadAtomSpeciesWarning3
    • read_atom_species(): do not use LATTICE_PARAMETERS without explicit specification of lattice type
  • ReadAtomSpeciesWarning4
    • read_atom_species():do not use LATTICE_VECTORS along with explicit specification of lattice type
  • ReadAtomSpeciesWarning5
    • read_atom_species():latname not supported
  • ReadAtomSpeciesLatName
    • read_atom_species(): various latname
  • ReadAtomPositionsS1
    • read_atom_positions(): spin 1 case
  • ReadAtomPositionsS2
    • read_atom_positions(): spin 2 case
  • ReadAtomPositionsS4Noncolin
    • read_atom_positions(): spin 4 noncolinear case
  • ReadAtomPositionsS4Colin
    • read_atom_positions(): spin 4 colinear case
  • ReadAtomPositionsC
    • read_atom_positions(): Cartesian coordinates
  • ReadAtomPositionsCA
    • read_atom_positions(): Cartesian_angstrom coordinates
  • ReadAtomPositionsCACXY
    • read_atom_positions(): Cartesian_angstrom_center_xy coordinates
  • ReadAtomPositionsCACXZ
    • read_atom_positions(): Cartesian_angstrom_center_xz coordinates
  • ReadAtomPositionsCACXYZ
    • read_atom_positions(): Cartesian_angstrom_center_xyz coordinates
  • ReadAtomPositionsCAU
    • read_atom_positions(): Cartesian_au coordinates
  • ReadAtomPositionsWarning1
    • read_atom_positions(): unknown type of coordinates
  • ReadAtomPositionsWarning2
    • read_atom_positions(): atomic label inconsistency between ATOM_POSITIONS and ATOM_SPECIES
  • ReadAtomPositionsWarning3
    • read_atom_positions(): warning : atom number < 0
  • ReadAtomPositionsWarning4
    • read_atom_positions(): mismatch in atom number for atom type
  • ReadAtomPositionsWarning5
    • read_atom_positions(): no atoms can move in MD simulations!
• Tested Functions:
  • UpdatePosTaud
    • update_pos_tau(double* pos)
    • update_pos_taud(const double* pos)
    • bcast_atoms_tau() is also called in the above function, which calls Atom::bcast_atom with many atomic info in addition to tau
  • BcastUnitcell
    • bcast basic info of unitcell and basic info of atoms
  • BcastUnitcell2
    • calls bcast_atoms2() to bcast atomic pseudo info
  • ReadPseudo
    • read_pseudo()
• Tested Functions:
  • ReadCellPPWarning1
    • read_cell_pseudopots(): error when average the pseudopotential: error_ap
  • ReadCellPPWarning2
    • read_cell_pseudopots(): Couldn't find pseudopotential file:: error == 1
  • ReadCellPPWarning3
    • read_cell_pseudopots(): Pseudopotential data do not match: error ==2
    • error==3 is currently difficult to reach in read_pseudo_vwr
  • ReadCellPPWarning4
    • read_cell_pseudopots(): dft_functional from INPUT does not match that in pseudopot file
  • ReadCellPPWarning5
    • read_cell_pseudopots(): Unknown pseudopotential type
  • ReadCellPP
    • read_cell_pseudopots(): read pp files with flag_empty_element set
  • CalMeshx
    • cal_meshx(): calculate max mesh info from atomic pseudo potential file
  • CalNatomwfc1
    • cal_natomwfc(): calculate total number of atomic orbitals in pseudo potential file
    • NSPIN != 4
    • this corresponds to number_of_wfc, PP_CHI in pp file, and atoms[it].ncpp.lchi[ncpp.nchi]
    • setup the total number of PAOs: pseudopotential atomic orbitals
  • CalNatomwfc2
    • cal_natomwfc(): calculate total number of atomic orbitals in pseudo potential file
    • NSPIN ==4, has_so = false
  • CalNatomwfc3
    • cal_natomwfc(): calculate total number of atomic orbitals in pseudo potential file
    • NSPIN ==4, has_so = true
  • CalNwfc1
    • cal_nwfc(): calcuate the total number of local basis: NSPIN != 4
    • this corresponds to number_of_proj, PP_BETA in pp file, and atoms[it].l_nchi[nw], nw from orb file
    • setup PARAM.sys.nlocal
    • interfaces initialed in this function:
      • itia2iat
      • iat2iwt
      • itiaiw2iwt
      • iwt2iat
      • iwt2iw
  • CalNwfc2
    • cal_nwfc(): calcuate the total number of local basis: NSPIN == 4
  • CheckStructure
    • check_atomic_stru(): check if too atoms are two close
  • ReadPseudoWarning1
    • read_pseudo(): All DFT functional must consistent.
  • ReadPseudoWarning2
    • read_pseudo(): number valence electrons > corresponding minimum possible of an element
  • CalNelec: UnitCell::cal_nelec
    • calculate the total number of valence electrons from psp files
  • CalNbands: elecstate::cal_nbands()
    • calculate the number of bands
• Tested Functions:
  • ReadAtomSpecies
    • read_atom_species(): read header part of orbital file
  • ReadAtomPositions
    • read_atom_positions(): read atomic coordinates, velocities, magmoms
  • SetupCell
    • setup_cell(): the pw version

Member Function Documentation

SetUp() [1/3]

void UcellTest::SetUp ( )

inlineprotected

Here is the call graph for this function:

SetUp() [2/3]

void UcellTest::SetUp ( )

inlineprotected

Here is the call graph for this function:

SetUp() [3/3]

void UcellTest::SetUp ( )

inlineprotected

TearDown() [1/2]

void UcellTest::TearDown ( )

inlineprotected

TearDown() [2/2]

void UcellTest::TearDown ( )

inlineprotected

Member Data Documentation

ofs

std::ofstream UcellTest::ofs

protected

output

std::string UcellTest::output

protected

pp_dir

std::string UcellTest::pp_dir

protected

ucell

std::unique_ptr< UnitCell > UcellTest::ucell {new UnitCell}

protected

utp

UcellTestPrepare UcellTest::utp = UcellTestLib["C1H2-Read"]

protected

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

• /home/runner/work/abacus-develop/abacus-develop/source/source_cell/test/unitcell_test.cpp
• /home/runner/work/abacus-develop/abacus-develop/source/source_cell/test/unitcell_test_para.cpp
• /home/runner/work/abacus-develop/abacus-develop/source/source_cell/test/unitcell_test_readpp.cpp
• /home/runner/work/abacus-develop/abacus-develop/source/source_cell/test_pw/unitcell_test_pw.cpp