Index

A

a accuracy addCharges() (Fragment method) addShells() (Fragment method) adjust_charge

adsorbate algorithm alpha angle() (Fragment method) auxbasis

B

b basis, [1], [2], [3] basis_de_dloge basis_file basis_precision berendsen binary

boundary, [1] bq_density bq_margin bq_symbol, [1] bqs built-in function construct_cluster() partition()

C

CASTEP (built-in class) cell centroid() (Fragment method) charge ChargeFitting (built-in class) charges (Fragment.bqs attribute) (Fragment.shells attribute) check chk conjugate connect() (Fragment method) connect_mode connect_scale connect_toler connIJ() (Fragment method) conserve constant_area

constraints, [1] constraints_ref construct_cluster() built-in function consts (Fragment.cell attribute) convdyn convergence, [1], [2] coor coordinates coords (Fragment.bqs attribute) (Fragment.shells attribute) coreatoms (Fragment.shells attribute) coupling CP2K (built-in class) crystal_type cut_off_energy cutoff cutoff_boundary

D

d3 damping dcd delete() (Fragment method), [1] delr delta densvar DFTBplus (built-in class) diag_method dihedral() (Fragment method) diis

dimer dipole_adjust direct dispersion dispersion_param displace (Fragment.shells attribute) dl_field_charges dl_field_types DL_POLY (built-in class) driver, [1] dryrun

E

ecp efield (Field attribute) elec_convergence_win elec_energy_tol electronic_minimizer embedding, [1] energy (Result attribute)

ensemble equilibration eroots estate ewald excited exclude

F

fcidump ff ff_dir FHIaims (built-in class) finalgridsize finite_basis_corr finite_basis_npoints finite_basis_spacing fix fix_occupancy fixed_atoms fixed_atoms_forces

flexible_cell fractional (Fragment.cell attribute) frag2 Fragment (built-in class) freq_chk freq_dcd freq_full_elect freq_nonbonded freq_out_energy freq_out_pressure freq_xst frozen functional, [1]

G

Gaussian (built-in class) gradients (Result attribute) grid (Field attribute) grid_cutoff

grid_real_cutoff grid_scale gridsize, [1] group_pressure guess GULP (built-in class)

H

harmonic hascharges() (Fragment method) hessian

hubbard_derivs hydrogen_correction hydrogen_damping

I

initial input, [1], [2]

interface_exclude interface_rigid

J

jobname

K

kpoints_method

L

label_active label_bq label_inactive label_interface label_qm langevin langevin_damping langevin_H langevin_piston langevin_piston_decay langevin_piston_period

langevin_piston_target langevin_piston_temp langevin_temperature lattice_scale Layer (built-in class) layers length_npt length_nvt length_production list_option LSDalton (built-in class)

M

margin masses max_angular_momentum maxcycle maxene maxinners maxiter, [1], [2], [3] maxiter_outer maxstep MD (built-in class) mem_global mem_heap mem_stack memory merge() (Fragment method) merge_cross

metals_method method, [1], [2] minimisation_npt minimisation_nvt minimise mixing_alpha mixing_gmix_p mixing_method mixing_scheme mm MNDO (built-in class) module tools moinp molecule Molpro (built-in class) mult

N

NAMD (built-in class) names (Fragment.bqs attribute) (Fragment.shells attribute) natoms nbands nbqs ndimensions (Fragment attribute) neb nebk neutralise neutralise_anion neutralise_cation

newscf ngrids nimages nlayers NLayerSubtractive (built-in class) nmos_added npoints nprocs, [1] nshells nsnapshots nsteps nsteps_per_cycle num_dump_cycles NWChem (built-in class)

O

Opt (built-in class) opt_strategy optstr ORCA (built-in class)

origin origin_atom origin_point outer_scf output, [1], [2]

P

padding pairlist_dist par partition() built-in function path, [1] pbc_wrap pdb pdb2pqr periodic pme pme_grid_sizes poisson_solver

pot (Field attribute) potential potential_file precision_all precision_gvg precision_rho prefix prefix_restart print pseudopotential, [1] psf psfgen() (NAMD method) psfgen_options PySCF (built-in class)

Q

qm qm_region

QMMM (built-in class) qmmm_interface

R

radius() (Fragment method) radius_active, [1] radius_cluster rand_seed rcut relax_residues_npt relax_residues_nvt residues

restart, [1] restart_from_md rigid rpad run() (ChargeFitting method) (MD method) (Opt method) (SP method) rvdw

S

save() (Fragment method) scalapack scale scaling14 scc scf scf_threshold, [1] scftype, [1] scheme seed, [1] select() (Fragment method) selectByAtoms() (Fragment method) selectByBackbone() (Fragment method) selectByCommonNames() (Fragment method) selectByIndices() (Fragment method) selectByIons() (Fragment method) selectByRadius() (Fragment method) selectByRegions() (Fragment method) selectByShell() (Fragment method) separate_ecps settings shape

shells shl_maxcycles shl_tolerance skf_path smear, [1] smear_method, [1] smear_mp_order smear_temperature, [1] smear_window smearing_width solute solvent SP (built-in class) spheric_exponent spheric_k spheric_r0 stack stats steps surface switch_dist switching symmetry

T

takeSnapshots() (in module tools) tda temperature theory third_order threshold timestep, [1] tol_density tol_energy tol_gradient

tol_inner tolerance tolerance_e tools module totalcharge trust_radius tsrelative TURBOMOLE (built-in class) type

U

unit use_finalgrid

use_ri, [1] user_control

V

valence_matrix vdw_incr vdw_scale

vectors (Fragment.cell attribute) vel version

W

wavefunction wrap_all

wrap_water write_checkpoint write_formatted_density

X

xc_derivative xc_finer_grid

xc_smooth_rho xsc xst

Z

znums