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User Guide
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System Settings
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AtomicSystem
AtomicSystem.box
AtomicSystem.volume
AtomicSystem.density
AtomicSystem.total_charge
AtomicSystem.total_mass
AtomicSystem.masses
AtomicSystem.charges
AtomicSystem.elements
AtomicSystem.ff_keys
AtomicSystem.ff_params
AtomicSystem.num_atoms
AtomicSystem.num_bonds
AtomicSystem.num_angles
AtomicSystem.num_dihedrals
AtomicSystem.num_impropers
AtomicSystem.num_atom_types
AtomicSystem.num_bond_types
AtomicSystem.num_angle_types
AtomicSystem.num_dihedral_types
AtomicSystem.num_improper_types
AtomicSystem.atom_types
AtomicSystem.bond_types
AtomicSystem.angle_types
AtomicSystem.dihedral_types
AtomicSystem.improper_types
AtomicSystem.summary
AtomicSystem.get_count
AtomicSystem.get_center_of_mass
AtomicSystem.copy
AtomicSystem.view
AtomicSystem.from_file
AtomicSystem.from_smiles
AtomicSystem.from_cod
AtomicSystem.from_pubchem
AtomicSystem.from_mda
AtomicSystem.from_pmg
AtomicSystem.to_mda
AtomicSystem.to_pmg
AtomicSystem.write
AtomicSystem.set_types
AtomicSystem.set_type2atoms
AtomicSystem.set_types_from_elements
AtomicSystem.set_topology
AtomicSystem.remove_all_connections
AtomicSystem.remove_connection_types
AtomicSystem.keep_connection_types
AtomicSystem.guess_connections
AtomicSystem.guess_angles
AtomicSystem.guess_dihedrals
AtomicSystem.guess_impropers
AtomicSystem.add_bond
AtomicSystem.add_angle
AtomicSystem.add_dihedral
AtomicSystem.add_improper
AtomicSystem.set_masses
AtomicSystem.set_charges
AtomicSystem.neutralize_charge
AtomicSystem.set_ff_from_database
AtomicSystem.explore_ff_database
AtomicSystem.set_pair_params
AtomicSystem.set_bond_params
AtomicSystem.set_angle_params
AtomicSystem.set_dihedral_params
AtomicSystem.set_improper_params
AtomicSystem.apply_pair_mixing_rules
AtomicSystem.set_ff_keys
AtomicSystem.set_atom_ff_keys
AtomicSystem.set_bond_ff_keys
AtomicSystem.set_angle_ff_keys
AtomicSystem.set_dihedral_ff_keys
AtomicSystem.set_improper_ff_keys
AtomicSystem.add_structure
AtomicSystem.add_liquid_layer
AtomicSystem.add_droplet
AtomicSystem.add_atom
AtomicSystem.add_atoms
AtomicSystem.protonate_atom
AtomicSystem.protonate_atoms
AtomicSystem.remove_atom
AtomicSystem.remove_atoms
AtomicSystem.set_atom_position
AtomicSystem.set_box
AtomicSystem.orthogonalize
AtomicSystem.unskew
AtomicSystem.replicate
AtomicSystem.wrap
AtomicSystem.center_on_com
Build Module
cemd.build.SolutionBuilder
SolutionBuilder.build
SolutionBuilder.build_hemisphere
SolutionBuilder.from_water
SolutionBuilder.get_solute_mass
SolutionBuilder.get_water_count
SolutionBuilder.to_counts
cemd.build.SurfaceBuilder
SurfaceBuilder.build
SurfaceBuilder.explore
cemd.build.Splitter
Splitter.add_solution
Splitter.best_coordinate
Splitter.build
Splitter.count_broken_bonds
Splitter.count_broken_ionic
Splitter.find_broken_bonds
Splitter.scan_broken_bonds
Splitter.side_mask
Splitter.split
Splitter.with_coordinate
cemd.build.GlassBuilder
GlassBuilder.build
GlassBuilder.from_elements
GlassBuilder.from_oxides
GlassBuilder.from_stoichiometry
GlassBuilder.get_actual_density
GlassBuilder.get_coefficient
GlassBuilder.get_components
GlassBuilder.get_elemental_composition
GlassBuilder.get_mass_per_formula_unit
GlassBuilder.get_num_formula_units
GlassBuilder.get_total_charge
GlassBuilder.is_pure
GlassBuilder.normalize
cemd.build.CSHBuilder
CSHBuilder.analyze
CSHBuilder.build
CSHBuilder.from_system
CSHBuilder.to_cash
cemd.build.AFBuilder
AFBuilder.build
AFBuilder.build_afm
AFBuilder.build_aft
Analysis Module
compute_rdf
analyze_silicates
msd
msd_profile
diffusion_coefficient
diffusion_coefficient_profile
plot_msd
plot_diffusion_profile
bondcorr
lifetime
density_profile
density_map
electrostatic_potential
find_interfaces_coordinates
shift_profile
API Reference
AtomicSystem
AtomicSystem.summary
AtomicSystem.summary
#
AtomicSystem.
summary
(
)
[source]
#
Print a complete summary of the AtomicSystem.
