Index

_

__init__() (chemsh.base.restraint.Angle method) (chemsh.base.restraint.Bond method) (chemsh.base.restraint.BondDifference2 method) (chemsh.base.restraint.BondDifference3 method) (chemsh.base.restraint.BondDifference4 method) (chemsh.base.restraint.Torsion method) (chemsh.Psi4 method)

A

a accumulate() (chemsh.base.restraint.Angle method) (chemsh.base.restraint.Bond method) (chemsh.base.restraint.BondDifference2 method) (chemsh.base.restraint.BondDifference3 method) (chemsh.base.restraint.BondDifference4 method) (chemsh.base.restraint.Restraint method) (chemsh.base.restraint.Torsion method) accuracy active active_radius

addCharges() (Fragment method) addShells() (Fragment method) adjust_charge, [1] adsorbate algorithm alpha angle Angle (class in chemsh.base.restraint) angle() (Fragment method) atom_display auxbasis

B

b basis, [1], [2], [3] (chemsh.Psi4 attribute) basis_de_dloge basis_file basis_precision berendsen binary bond Bond (class in chemsh.base.restraint)

BondDifference2 (class in chemsh.base.restraint) BondDifference3 (class in chemsh.base.restraint) BondDifference4 (class in chemsh.base.restraint) boundary, [1] bq_density, [1] bq_margin, [1] bq_symbol, [1] bqs built-in function construct_cluster() partition()

C

CASTEP (built-in class) cdft cell centroid() (Fragment method) charge (chemsh.Psi4 attribute) ChargeFitting (built-in class) charges, [1] (Fragment.bqs attribute) (Fragment.shells attribute) check check_qm_region chk conjugate connect() (Fragment method) connect_mode connect_scale connect_toler connIJ() (Fragment method) conserve constant_area constrain constraints, [1]

constraints_ref construct_cluster() built-in function consts (Fragment.cell attribute) convdyn convergence, [1], [2] (chemsh.Psi4 attribute) conversion coor coordinates coords (Fragment.bqs attribute) (Fragment.shells attribute) coreatoms (Fragment.shells attribute) counterions coupling CP2K (built-in class) crystal_type cut_off_energy cutoff cutoff_boundary, [1] cutoff_coulomb cutoff_vdw

D

d3 damping dcd delete() (Fragment method) delr delta densvar DFTBplus (built-in class) diag_method dihedral() (Fragment method) diis dimer dipole_adjust

direct directory dispersion dispersion_param displace (Fragment.shells attribute) distance DL_FIELD (built-in class) dl_field_charges dl_field_types dl_poly 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 eps_diff

eps_inorg eps_org equilibration eroots estate ewald excited exclude, [1] extra_info

F

fcidump (chemsh.Psi4 attribute) ff, [1] ff_dir FHIaims (built-in class) field_by_chemsh filename finalgridsize finite_basis_corr finite_basis_npoints finite_basis_spacing fix fix_occupancy fixed_atoms fixed_atoms_forces flexible_cell

fractional (Fragment.cell attribute) frag (chemsh.Psi4 attribute) frag2 Fragment (built-in class) fragmovecs freeze freq_chk freq_dcd freq_full_elect freq_nonbonded freq_out_energy freq_out_pressure freq_xst frozen, [1] functional, [1], [2] (chemsh.Psi4 attribute)

G

GAMESS_UK (built-in class) 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

hl_tol hubbard_derivs hydrogen_correction hydrogen_damping

I

indices (chemsh.base.restraint.Angle property) (chemsh.base.restraint.Bond property) (chemsh.base.restraint.BondDifference2 property) (chemsh.base.restraint.BondDifference3 property) (chemsh.base.restraint.BondDifference4 property) (chemsh.base.restraint.Torsion property) initial

initial_hessian inner_atoms input, [1], [2], [3], [4] input_file_name (chemsh.Psi4 attribute) input_qm insert() (Fragment method) interface_exclude, [1] interface_rigid

J

jobname

K

k (chemsh.base.restraint.Angle attribute) (chemsh.base.restraint.Bond attribute) (chemsh.base.restraint.BondDifference2 attribute) (chemsh.base.restraint.BondDifference3 attribute) (chemsh.base.restraint.BondDifference4 attribute) (chemsh.base.restraint.Torsion attribute)

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) lshift

M

margin masses max_angular_momentum maxcycle maxene maxinners maxiter, [1], [2], [3] (chemsh.Psi4 attribute) maxiter_outer maxmicrocycle maxstep MD (built-in class) mem_global mem_heap mem_stack memory merge() (Fragment method) merge_cross metals_method method, [1], [2] (chemsh.Psi4 attribute)

micro_esp_fit microiterative min_distance minimisation_npt minimisation_nvt minimise mixing_alpha mixing_gmix_p mixing_method mixing_scheme mm mm_energy MNDO (built-in class) module tools moinp molecule Molpro (built-in class) mult (chemsh.Psi4 attribute)

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

nfock ngrids nimages nlayers NLayerSubtractive (built-in class) nmos_added npoints nprocs, [1] (chemsh.Psi4 attribute) nshells nsnapshots nsteps nsteps_per_cycle num_dump_cycles NWChem (built-in class)

O

Opt (built-in class) opt_strategy optimise optstr ORCA (built-in class) origin, [1] origin_bulk

origin_qm original_tip3p outer_scf output, [1], [2], [3] output_file_name (chemsh.Psi4 attribute) output_prefix override_builtin

P

padding pairlist_dist par partition() built-in function partition_mode patch_target path, [1] pbc pbc_wrap pdb pdb2pqr periodic phi0 (chemsh.base.restraint.Torsion property) pme pme_grid_sizes

poisson_solver pot (Field attribute) potential potential_file precision_all precision_gvg precision_rho prefix prefix_restart print print_warnings pseudopotential, [1] psf psfgen() (NAMD method) psfgen_options Psi4 (class in chemsh) PySCF (built-in class)

Q

qm qm_region

qmatoms QMMM (built-in class) qmmm_interface, [1]

R

r0 (chemsh.base.restraint.Bond attribute) (chemsh.base.restraint.BondDifference2 attribute) (chemsh.base.restraint.BondDifference3 attribute) (chemsh.base.restraint.BondDifference4 attribute) radius radius() (Fragment method) radius_active, [1] radius_cluster, [1] rand_seed rcut recentre relax_residues_npt relax_residues_nvt remove_unused_definitions

residues restart, [1] restart_from_md Restraint (class in chemsh.base.restraint) restraints, [1] rigid rigid_body rpad run() (ChargeFitting method) (MD method) (Opt method) (SP method) run_only_once rvdw

S

save() (Fragment method) save_path scalapack scale scale_coul scale_vdw scaling14 scc 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) selectByNeighbours() (Fragment method) selectByRadius() (Fragment method) selectByRegions() (Fragment method) selectByShell() (Fragment method) separate_ecps set_options (chemsh.Psi4 attribute) settings shape shell_charge shell_species shells shl_maxcycles shl_tolerance

sig_diff sig_inorg sig_org, [1] skf_path skzcam_anion_tol skzcam_cation skzcam_shells smear, [1] smear_method, [1] smear_mp_order smear_temperature, [1] smear_window smearing_width solute solution solution_cutoff solution_den solution_unit solvent, [1] solvents SP (built-in class) spheric_exponent spheric_k spheric_r0 stack stats steps surface switch_dist switching symmetry syscmd (chemsh.Psi4 attribute)

T

takeSnapshots() (in module tools) tda temperature, [1] tether theory theta0 (chemsh.base.restraint.Angle property) third_order threshold, [1] timestep, [1] tol tol_density tol_energy tol_gradient

tol_inner tolerance tolerance_e tools module Torsion (class in chemsh.base.restraint) torsion_angle() (chemsh.base.restraint.Torsion static method) torsion_angle_and_derivative() (chemsh.base.restraint.Torsion static method) totalcharge trust_radius tsrelative TURBOMOLE (built-in class) type

U

udff unit, [1] update_method

use_finalgrid use_ri, [1] (chemsh.Psi4 attribute) user_control

V

valence_matrix vdw_format vdw_incr vdw_scale

vectors (Fragment.cell attribute) vel velocity verbosity version

W

wavefunction waveplot wrap_all

wrap_water write_checkpoint write_formatted_density

X

xc_derivative xc_finer_grid

xc_smooth_rho xsc xst

Z

znums

zora zora_cutoff