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libAtoms

Subsections

Copyright
Introduction
- Purpose and Philosophy
- Requirements
- Example Program -- Classical Molecular Dynamics
- Controlling Output Verbosity
Program md
- Purpose
- Uses
Program xyz2pdb
- Purpose
- Uses
- Subroutine delete_metal_connects
- Subroutine print_usage
- Subroutine write_xsc_file
Module atoms_module
- Purpose
- Usage
- Uses
- Module variables
- Type Table_pointer
  - Elements
- Type Connection
  - Elements
- Type Atoms
  - Elements
- Interface initialise
- Interface finalise
- Interface wipe
- Interface zero
- Interface assignment(=)
- Interface set_atoms
- Interface set_cutoff_minimum
- Interface set_cutoff
- Interface set_cutoff_factor
- Interface add_atoms
- Interface remove_atoms
- Interface add_property
- Interface has_property
- Interface remove_property
- Interface assign_pointer
- Interface distance_min_image
- Interface diff_min_image
- Interface write_binary
- Interface read_binary
- Interface print
- Interface print_xyz
- Interface print_cfg
- Interface read_xyz
- Interface set_lattice
- Interface select
- Interface cell_volume
- Interface map_into_cell
- Subroutine atoms_copy_without_connect
- Subroutine calc_dists
- Subroutine connection_fill
- Subroutine test_form_bond
- Subroutine set_bonds
- Subroutine add_bond
- Subroutine remove_bond
- Subroutine calc_connect_hysteretic
- Subroutine connection_remove_atom
- Subroutine calc_connect
- Subroutine partition_atoms
- Subroutine divide_cell
- Subroutine fit_box_in_cell
- Subroutine get_lattice_params
- Subroutine directionality
- Subroutine parse_line_io_es
- Subroutine atoms_read_xyz
- Subroutine parse_atom_mask
- Subroutine property_to_list
- Subroutine list_to_property
- Subroutine complement
- Subroutine difference
- Subroutine coalesce_in_one_periodic_image
- Function atoms_cutoff
- Function atoms_cutoff_break
- Function atoms_n_neighbours
- Function atoms_neighbour
- Function diff
- Function realpos
- Function distance
- Function cosine
- Function cosine_neighbour
- Function direction_cosines
- Function direction_cosines_min_image
- Function is_in_subregion
- Function is_nearest_neighbour
- Function test_break_bond
- Function max_cutoff
- Function make_lattice
- Function centre_of_mass
- Function cosangle_to_line
- Function prop_names_string
- Function dict_prop_names_string
- Function read_line_io_es
- Function bond_length
- Function termination_bond_rescale
Module CInOutput_module
- Purpose
- Usage
- Uses
- Type CInOutput
  - Elements
- Interface
- Interface initialise
- Interface finalise
- Interface close
- Interface read
- Interface write
- Interface query
- Interface update
- Subroutine f_string_to_c_array
- Function c_array_to_f_string
- Function c_string_to_f_string
Module constraints_module
- Purpose
- Usage
- Uses
- Module variables
- Type Constraint
  - Elements
- Interface initialise
- Interface finalise
- Interface assignment(=)
- Interface print
- Interface write_binary
- Interface read_binary
- Subroutine constraint_amend
- Subroutine constraint_calculate_values
- Subroutine constraint_calculate_values_at
- Subroutine constraint_store_gradient
- Subroutine shake
- Subroutine rattle
- Subroutine BONDLENGTH
- Subroutine RELAX_BOND
- Subroutine CUBIC_BOND
- Subroutine PLANE
- Subroutine BONDLENGTH_DIFF
- Function register_constraint
Module dictionary_module
- Purpose
- Usage
- Uses
- Module variables
- Type DictData
  - Elements
- Type Dictionary
  - Elements
- Interface initialise
- Interface finalise
- Interface print
- Interface set_value
- Interface get_value
- Interface remove_value
- Interface write_binary
- Interface read_binary
- Interface write_string
- Interface read_string
- Interface subset
- Interface swap
- Interface assignment(=)
- Interface has_key
- Subroutine dictionary_get_type_and_size
- Function dictionary_parse_value
- Function lower_case
Module dynamicalsystem_module
- Purpose
- Usage
- Uses
- Module variables
- Type DynamicalSystem
  - Elements
- Interface assignment(=)
- Interface add_atoms
- Interface remove_atoms
- Interface write_binary
- Interface read_binary
- Interface print
- Interface initialise
- Interface finalise
- Interface kinetic_energy
- Interface angular_momentum
- Interface momentum
- Interface add_thermostat
- Subroutine ds_free_groups
- Subroutine ds_save_state
- Subroutine ds_restore_state
- Subroutine add_group_members
- Subroutine enable_damping
- Subroutine disable_damping
- Subroutine add_heat
- Subroutine rescale_velo
- Subroutine reinitialise_velo_normal
- Subroutine zero_momentum
- Subroutine zero_angular_momentum
- Subroutine advance_verlet1
- Subroutine advance_verlet2
- Subroutine advance_verlet
- Subroutine constrain_bond
- Subroutine constrain_bond_diff
- Subroutine ds_add_constraint
- Subroutine ds_amend_constraint
- Subroutine distance_relative_velocity
- Subroutine fix_atoms
- Function atom_type
- Function moment_of_inertia
- Function moment_of_inertia_tensor
- Function torque
- Function temperature
- Function gaussian_velocity_component
- Function gaussian_velocity
- Function centre_of_mass_velo
- Function centre_of_mass_acc
- Function degrees_of_freedom
Module extendable_str_module
- Purpose
- Usage
- Uses
- Type extendable_str
  - Elements
- Interface len
- Interface concat
- Interface string
- Interface read
- Interface initialise
- Interface zero
- Interface finalise
- Interface print
- Interface read_line
- Interface parse_line
- Interface index
- Subroutine extendable_str_bcast
- Function is_iostat_end
- Function is_iostat_eor
Module group_module
- Purpose
- Usage
- Uses
- Type Group
  - Elements
- Interface print
- Interface initialise
- Interface finalise
- Interface assignment(=)
- Interface write_binary
- Interface read_binary
- Interface set_type
- Subroutine merge_groups
- Subroutine group_delete_atom
- Subroutine group_delete_object
- Subroutine group_add_atom
- Subroutine group_add_object
- Subroutine groups_create_lookup
- Subroutine tidy_groups
- Function group_n_atoms
- Function group_nth_atom
- Function group_n_objects
- Function group_nth_object
- Function free_group
- Function num_free_groups
Module paramreader_module
- Purpose
- Usage
- Uses
- Module variables
- Interface param_register
- Interface assignment(=)
- Subroutine param_print
- Function param_read_line
- Function param_read_file
- Function param_read_args
- Function process_arguments
- Function param_write_string
- Function param_check
Module periodictable_module
- Purpose
- Usage
- Uses
- Module variables
- Interface atomic_number
- Function ElementFormat
Module quaternions_module
- Purpose
- Usage
- Uses
- Type Quaternion
  - Elements
- Interface norm
- Interface norm2
- Interface operator(+)
- Interface operator(-)
- Interface operator(*)
- Interface operator(/)
- Interface assignment(=)
- Interface operator(.conj.)
- Interface operator(.feq.)
- Interface operator(.fne.)
- Interface operator(.dot.)
- Interface rotate
- Interface print
- Subroutine rotation_parameters
- Function rotation
- Function orientation
- Function rotation_matrix
Module rigidbody_module
- Purpose
- Usage
- Uses
- Module variables
- Type RigidBodyModel
  - Elements
- Type RigidBody
  - Elements
- Interface initialise
- Interface finalise
- Interface assignment(=)
- Interface print
- Subroutine rigidbodymodel_initialise
- Subroutine rigidbodymodel_finalise
- Subroutine no_squish_free_rotor
- Function inertia_tensor
- Function P0
- Function P1
- Function P2
- Function P3
- Function no_squish_S
- Function no_squish_A_dot_transpose
Module sparse_module
- Purpose
- Usage
- Uses
- Module variables
- Type Sparse
  - Elements
- Interface assignment(=)
- Interface operator(.mult.)
- Interface print
- Interface print_full
- Subroutine sparse_init
- Subroutine sparse_finalise
- Subroutine sparse_zero
- Subroutine sparse_set_element
- Subroutine sparse_delete_element
- Subroutine sparse_check_bounds
- Subroutine sparse_check
- Subroutine sparse_test
- Function sparse_element
- Function sparse_stored_elements
- Function trace_sparse_mult_matrix
- Function sparse_cfct
Module spline_module
- Purpose
- Usage
- Uses
- Type Spline
  - Elements
- Interface initialise
- Interface finalise
- Interface print
- Subroutine spline_y2calc
- Subroutine spline_compute_matrices
- Function spline_value
- Function spline_deriv
- Function min_knot
- Function max_knot
Module structures_module
- Purpose
- Usage
- Uses
- Interface slab
- Subroutine fcc_11b2_edge_disloc
- Subroutine fcc_disloc_malc
- Subroutine disloc_noam
- Subroutine fcc_z111_ortho
- Subroutine fcc_z111
- Subroutine unit_slab
- Subroutine Graphene_Slab
- Subroutine Graphene_Sheet
- Subroutine supercell
- Subroutine diamond
- Subroutine fcc
- Subroutine bcc
- Subroutine a15
- Subroutine graphite
- Subroutine transform
- Subroutine find_motif
- Function Graphene_Cubic
- Function Tube_Radius
- Function gcd
- Function Graphene_Tube
- Function water
- Function make_structure
Module system_module
- Purpose
- Usage
- Uses
- Module variables
- Type Stack
  - Elements
- Type Inoutput
  - Elements
- Interface initialise
- Interface finalise
- Interface activate
- Interface deactivate
- Interface mpi_all_inoutput
- Interface print_mpi_id
- Interface print
- Interface write_binary
- Interface read_binary
- Interface read_line
- Interface parse_line
- Interface reallocate
- Interface operator(//)
- Interface system_command
- Interface
- Interface Initialise
- Interface Finalise
- Interface push
- Interface pop
- Interface value
- Interface Print
- Interface optional_default
- Subroutine inoutput_close
- Subroutine print_title
- Subroutine parse_string
- Subroutine parse_string_orig
- Subroutine rewind
- Subroutine backspace
- Subroutine system_initialise
- Subroutine get_cmd_arg
- Subroutine system_finalise
- Subroutine system_abort
- Subroutine print_warning
- Subroutine system_set_random_seeds
- Subroutine hello_world
- Subroutine system_resync_rng
- Subroutine system_reseed_rng
- Subroutine system_timer
- Subroutine verbosity_push
- Subroutine verbosity_pop
- Subroutine verbosity_push_increment
- Subroutine verbosity_push_decrement
- Subroutine verbosity_set_minimum
- Subroutine verbosity_unset_minimum
- Subroutine enable_timing
- Subroutine disable_timing
- Subroutine abort_on_mpi_error
- Subroutine parallel_print
- Subroutine ALLOC_TRACE
- Subroutine DEALLOC_TRACE
- Function isnan
- Function inoutput_do_output
- Recursive functionfind_closing_delimiter
- Function string_to_int
- Function string_to_logical
- Function string_to_real
- Function mpi_id
- Function mpi_n_procs
- Function round
- Function int_format_length
- Function real_sci_format_length
- Function real_format_length
- Function complex_format_length
- Function cmd_arg_count
- Function date_and_time_string
- Function th
- Function system_get_random_seed
- Function ran
- Function ran_uniform
- Function ran_normal
- Function ran_exp
- Function ran_string
- Function is_file_readable
- Function verbosity_to_str
- Function str_to_verbosity
- Function current_verbosity
- Function increase_stack
Module table_module
- Purpose
- Usage
- Uses
- Module variables
- Type Table
  - Elements
- Interface allocate
- Interface initialise
- Interface finalise
- Interface set_increment
- Interface append
- Interface append_column
- Interface remove_columns
- Interface insert
- Interface find
- Interface sort
- Interface search
- Interface print
- Interface int_part
- Interface real_part
- Interface str_part
- Interface logical_part
- Interface delete
- Interface delete_multiple
- Interface wipe
- Interface zero
- Interface write_binary
- Interface read_binary
- Interface rms_diff
- Interface select
- Subroutine reduce_allocation
- Subroutine table_append_row
- Subroutine table_append_arrays
- Subroutine table_extend_int_cols
- Subroutine table_extend_real_cols
- Subroutine table_extend_str_cols
- Subroutine table_extend_logical_cols
- Subroutine table_address
- Function subtable
- Function real_subtable
- Function int_subtable
Module thermostat_module
- Purpose
- Usage
- Uses
- Module variables
- Type thermostat
  - Elements
- Interface initialise
- Interface finalise
- Interface assignment(=)
- Interface print
- Interface add_thermostat
- Interface set_degrees_of_freedom
- Interface nose_hoover_mass
- Interface write_binary
- Interface read_binary
- Subroutine thermostat1
- Subroutine thermostat2
- Subroutine thermostat3
- Subroutine thermostat4
Module topology_module
- Purpose
- Usage
- Uses
- Module variables
- Subroutine create_CHARMM
- Subroutine next_motif
- Subroutine write_brookhaven_pdb_file
- Subroutine write_psf_file
- Subroutine write_psf_section
- Subroutine create_bond_list
- Subroutine create_angle_list
- Subroutine create_dihedral_list
- Subroutine create_improper_list
- Subroutine create_pos_dep_charges
- Subroutine calc_connect_danny
- Subroutine delete_bond
- Function get_property
- Function calc_fc
- Function danny_cutoff
Module units_module
- Purpose
- Usage
- Uses
- Module variables
Module clusters_module
- Purpose
- Usage
- Uses
- Module variables
- Interface create_hybrid_weights
- Interface bfs_grow
- Subroutine bfs_step
- Subroutine discard_non_min_images
- Subroutine make_convex
- Subroutine estimate_origin_extent
- Subroutine create_embed_and_fit_lists
- Subroutine select_hysteretic_quantum_region
- Subroutine construct_buffer
- Subroutine update_active
- Subroutine add_cut_hydrogens
- Subroutine constrained_to_quantum
- Subroutine thermalize_bond
- Subroutine quantum_to_constrained
- Subroutine thermalize_group
- Function multiple_images
- Function create_cluster_info
- Function carve_cluster
- Function create_cluster_info_from_hybrid_mark
- Function bond_energy
Module frametools_module
- Purpose
- Usage
- Uses
- Subroutine atoms_mark
- Subroutine ft_rotate
- Function is_in_cylinder
Module libAtoms_module
- Purpose
- Usage
- Uses
Module libatoms_misc_utils_module
- Purpose
- Usage
- Uses
- Function dipole_moment
Module linearalgebra_module
- Purpose
- Usage
- Uses
- Module variables
- Type LA_Matrix
  - Elements
- Interface Initialise
- Interface Finalise
- Interface Matrix_Solve
- Interface find
- Interface sign
- Interface diag
- Interface print
- Interface print_mathematica
- Interface operator(.mult.)
- Interface matrix_product
- Interface matrix_product_sub
- Interface operator(.multd.)
- Interface matrix_product_vect_asdiagonal_sub
- Interface matrix_product_vect_asdiagonal_RL_sub
- Interface matrix_mvmt
- Interface operator(.dot.)
- Interface operator(.feq.)
- Interface operator(.fne.)
- Interface diagonalise
- Interface inverse
- Interface operator(.outer.)
- Interface operator(.realouter.)
- Interface operator(.cross.)
- Interface is_symmetric
- Interface is_hermitian
- Interface is_square
- Interface symmetrise
- Interface trace
- Interface trace_mult
- Interface add_identity
- Interface add_xidentity
- Interface norm
- Interface norm2
- Interface randomise
- Interface find_in_array
- Interface rms_diff
- Interface histogram
- Interface sort_array
- Interface insertion_sort
- Interface check_size
- Interface update_exponential_average
- Subroutine matrix_nonsymmetric_diagonalise
- Subroutine test_eigensys
- Subroutine LA_Matrix_Factorise
- Subroutine LA_Matrix_Inverse
- Subroutine Matrix_CholFactorise
- Subroutine Matrix_BackSubstitute
- Subroutine Matrix_Solve_Upper_Triangular
- Subroutine Matrix_Factorised_Inverse
- Subroutine fit_cubic
- Subroutine logical_array_print
- Subroutine uniq
- Subroutine zero_sum
- Subroutine least_squares
- Subroutine update_running_average_and_variance
- Subroutine polar_decomposition
- Subroutine matrix3x3_inverse
- Function delta
- Function matrix_multT
- Function LA_Matrix_LogDet
- Function LA_Matrix_Det
- Function is_diagonal
- Function angle
- Function sqrt_cut
- Function ran_normal3
- Function array3_triple
- Function scalar_triple_product
- Function vector_triple_product
- Function unit_vector
- Function random_unit_vector
- Function linear_interpolate
- Function cubic_interpolate
- Function is_in_array
- Function binary_search
- Function average_array
- Function bin
- Function bin_centre
- Function int_array_ge
- Function int_array_gt
- Function int_array_lt
- Function sphere_intersection_vol
- Function permutation_symbol
- Function matrix3x3_det
Module minimization_module
- Purpose
- Usage
- Uses
- Module variables
- Interface minim
- Interface test_gradient
- Interface n_test_gradient
- Subroutine n_linmin
- Function linmin
- Function linmin_fast
- Function linmin_deriv
- Function linmin_deriv_iter
- Function linmin_deriv_iter_simple
- Function damped_md_minim
- Function fire_minim
- Function n_minim
Module mpi_module
- Purpose
- Usage
- Subroutine get_mpi_size_rank
- Function decode_mpi_error
Module nye_tensor_module
- Purpose
- Usage
- Uses
- Subroutine calc_nye_tensor
- Subroutine find_lattice_correspondence
- Subroutine get_nn_list
Module test_force_model_module
- Purpose
- Usage
- Uses
- Module variables
- Subroutine test_force_model
Miscellaneous Subroutines and Functions
- Subroutine matrix_general_diagonlise_lobpcg_sandia
- Subroutine rr_solve
- Subroutine orthogonalise_col_vectors

gabor 2009-06-30