From 223bfac229c142d15fa8c510d064dc244494e45f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 19 Mar 2020 15:44:53 -0400 Subject: [PATCH] remove ATC html files that are no longer needed --- doc/src/USER/atc/man_add_molecule.html | 57 ---- doc/src/USER/atc/man_add_species.html | 57 ---- doc/src/USER/atc/man_atom_element_map.html | 50 ---- doc/src/USER/atc/man_atom_weight.html | 59 ---- doc/src/USER/atc/man_atomic_charge.html | 49 ---- doc/src/USER/atc/man_boundary.html | 46 ---- doc/src/USER/atc/man_boundary_dynamics.html | 44 --- doc/src/USER/atc/man_boundary_faceset.html | 45 ---- doc/src/USER/atc/man_boundary_integral.html | 51 ---- .../atc/man_consistent_fe_initialization.html | 49 ---- doc/src/USER/atc/man_contour_integral.html | 52 ---- doc/src/USER/atc/man_control.html | 70 ----- doc/src/USER/atc/man_control_momentum.html | 66 ----- doc/src/USER/atc/man_control_thermal.html | 74 ----- ...rol_thermal_correction_max_iterations.html | 51 ---- doc/src/USER/atc/man_decomposition.html | 53 ---- .../USER/atc/man_electron_integration.html | 54 ---- doc/src/USER/atc/man_equilibrium_start.html | 48 ---- doc/src/USER/atc/man_extrinsic_exchange.html | 48 ---- doc/src/USER/atc/man_fe_md_boundary.html | 48 ---- doc/src/USER/atc/man_fem_mesh.html | 46 ---- doc/src/USER/atc/man_filter_scale.html | 53 ---- doc/src/USER/atc/man_filter_type.html | 49 ---- doc/src/USER/atc/man_fix_atc.html | 252 ------------------ doc/src/USER/atc/man_fix_flux.html | 51 ---- doc/src/USER/atc/man_fix_nodes.html | 54 ---- doc/src/USER/atc/man_hardy_computes.html | 65 ----- doc/src/USER/atc/man_hardy_fields.html | 81 ------ doc/src/USER/atc/man_hardy_gradients.html | 55 ---- doc/src/USER/atc/man_hardy_kernel.html | 63 ----- doc/src/USER/atc/man_hardy_on_the_fly.html | 58 ---- doc/src/USER/atc/man_hardy_rates.html | 56 ---- doc/src/USER/atc/man_initial.html | 49 ---- .../USER/atc/man_internal_atom_integrate.html | 38 --- .../USER/atc/man_internal_element_set.html | 50 ---- doc/src/USER/atc/man_internal_quadrature.html | 48 ---- doc/src/USER/atc/man_kernel_function.html | 62 ----- doc/src/USER/atc/man_localized_lambda.html | 46 ---- doc/src/USER/atc/man_lumped_lambda_solve.html | 45 ---- doc/src/USER/atc/man_mask_direction.html | 45 ---- doc/src/USER/atc/man_mass_matrix.html | 49 ---- doc/src/USER/atc/man_material.html | 47 ---- doc/src/USER/atc/man_mesh_add_to_nodeset.html | 49 ---- doc/src/USER/atc/man_mesh_create.html | 54 ---- .../USER/atc/man_mesh_create_elementset.html | 50 ---- .../USER/atc/man_mesh_create_faceset_box.html | 52 ---- .../atc/man_mesh_create_faceset_plane.html | 52 ---- doc/src/USER/atc/man_mesh_create_nodeset.html | 49 ---- .../USER/atc/man_mesh_delete_elements.html | 48 ---- .../atc/man_mesh_nodeset_to_elementset.html | 51 ---- doc/src/USER/atc/man_mesh_output.html | 47 ---- doc/src/USER/atc/man_mesh_quadrature.html | 49 ---- doc/src/USER/atc/man_mesh_read.html | 50 ---- doc/src/USER/atc/man_mesh_write.html | 48 ---- .../atc/man_momentum_time_integration.html | 58 ---- doc/src/USER/atc/man_output.html | 61 ----- doc/src/USER/atc/man_output_elementset.html | 52 ---- doc/src/USER/atc/man_output_nodeset.html | 53 ---- doc/src/USER/atc/man_pair_interactions.html | 48 ---- doc/src/USER/atc/man_poisson_solver.html | 51 ---- doc/src/USER/atc/man_read_restart.html | 49 ---- doc/src/USER/atc/man_remove_molecule.html | 52 ---- doc/src/USER/atc/man_remove_source.html | 50 ---- doc/src/USER/atc/man_remove_species.html | 52 ---- .../man_reset_atomic_reference_positions.html | 47 ---- doc/src/USER/atc/man_reset_time.html | 63 ----- doc/src/USER/atc/man_sample_frequency.html | 50 ---- doc/src/USER/atc/man_set.html | 54 ---- doc/src/USER/atc/man_source.html | 51 ---- doc/src/USER/atc/man_source_integration.html | 44 --- .../USER/atc/man_temperature_definition.html | 45 ---- .../atc/man_thermal_time_integration.html | 57 ---- doc/src/USER/atc/man_time_filter.html | 55 ---- doc/src/USER/atc/man_track_displacement.html | 46 ---- doc/src/USER/atc/man_unfix_flux.html | 50 ---- doc/src/USER/atc/man_unfix_nodes.html | 51 ---- doc/src/USER/atc/man_write_atom_weights.html | 51 ---- doc/src/USER/atc/man_write_restart.html | 49 ---- 78 files changed, 4271 deletions(-) delete mode 100644 doc/src/USER/atc/man_add_molecule.html delete mode 100644 doc/src/USER/atc/man_add_species.html delete mode 100644 doc/src/USER/atc/man_atom_element_map.html delete mode 100644 doc/src/USER/atc/man_atom_weight.html delete mode 100644 doc/src/USER/atc/man_atomic_charge.html delete mode 100644 doc/src/USER/atc/man_boundary.html delete mode 100644 doc/src/USER/atc/man_boundary_dynamics.html delete mode 100644 doc/src/USER/atc/man_boundary_faceset.html delete mode 100644 doc/src/USER/atc/man_boundary_integral.html delete mode 100644 doc/src/USER/atc/man_consistent_fe_initialization.html delete mode 100644 doc/src/USER/atc/man_contour_integral.html delete mode 100644 doc/src/USER/atc/man_control.html delete mode 100644 doc/src/USER/atc/man_control_momentum.html delete mode 100644 doc/src/USER/atc/man_control_thermal.html delete mode 100644 doc/src/USER/atc/man_control_thermal_correction_max_iterations.html delete mode 100644 doc/src/USER/atc/man_decomposition.html delete mode 100644 doc/src/USER/atc/man_electron_integration.html delete mode 100644 doc/src/USER/atc/man_equilibrium_start.html delete mode 100644 doc/src/USER/atc/man_extrinsic_exchange.html delete mode 100644 doc/src/USER/atc/man_fe_md_boundary.html delete mode 100644 doc/src/USER/atc/man_fem_mesh.html delete mode 100644 doc/src/USER/atc/man_filter_scale.html delete mode 100644 doc/src/USER/atc/man_filter_type.html delete mode 100644 doc/src/USER/atc/man_fix_atc.html delete mode 100644 doc/src/USER/atc/man_fix_flux.html delete mode 100644 doc/src/USER/atc/man_fix_nodes.html delete mode 100644 doc/src/USER/atc/man_hardy_computes.html delete mode 100644 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100644 doc/src/USER/atc/man_poisson_solver.html delete mode 100644 doc/src/USER/atc/man_read_restart.html delete mode 100644 doc/src/USER/atc/man_remove_molecule.html delete mode 100644 doc/src/USER/atc/man_remove_source.html delete mode 100644 doc/src/USER/atc/man_remove_species.html delete mode 100644 doc/src/USER/atc/man_reset_atomic_reference_positions.html delete mode 100644 doc/src/USER/atc/man_reset_time.html delete mode 100644 doc/src/USER/atc/man_sample_frequency.html delete mode 100644 doc/src/USER/atc/man_set.html delete mode 100644 doc/src/USER/atc/man_source.html delete mode 100644 doc/src/USER/atc/man_source_integration.html delete mode 100644 doc/src/USER/atc/man_temperature_definition.html delete mode 100644 doc/src/USER/atc/man_thermal_time_integration.html delete mode 100644 doc/src/USER/atc/man_time_filter.html delete mode 100644 doc/src/USER/atc/man_track_displacement.html delete mode 100644 doc/src/USER/atc/man_unfix_flux.html delete mode 100644 doc/src/USER/atc/man_unfix_nodes.html delete mode 100644 doc/src/USER/atc/man_write_atom_weights.html delete mode 100644 doc/src/USER/atc/man_write_restart.html diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html deleted file mode 100644 index 4e7810aa61..0000000000 --- a/doc/src/USER/atc/man_add_molecule.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC add_molecule - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC add_molecule

-syntax

-

fix_modify_AtC add_molecule <small|large> <TAG> <GROUP_NAME>
-

- -

-examples

-

group WATERGROUP type 1 2
- fix_modify AtC add_molecule small water WATERGROUP
-

-

-description

-

Associates a tag with all molecules corresponding to a specified group.
-

-

-restrictions

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html deleted file mode 100644 index a990ab626f..0000000000 --- a/doc/src/USER/atc/man_add_species.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC add_species - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC add_species

-syntax

-

fix_modify_AtC add_species <TAG> <group|type> <ID>
-

- -

-examples

-

fix_modify AtC add_species gold type 1
- group GOLDGROUP type 1
- fix_modify AtC add_species gold group GOLDGROUP

-

-description

-

Associates a tag with all atoms of a specified type or within a specified group.
-

-

-restrictions

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html deleted file mode 100644 index a5707d280e..0000000000 --- a/doc/src/USER/atc/man_atom_element_map.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC atom_element_map - - - - -
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- -
- - - -
- - -

fix_modify AtC atom_element_map

-syntax

-

fix_modify AtC atom_element_map <eulerian|lagrangian> <frequency>
-

- -

-examples

-

fix_modify atc atom_element_map eulerian 100

-

-description

-

Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated.

-

-restrictions

-

Cannot change map type after initialization.

-

-related

-

-default

-

lagrangian

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html deleted file mode 100644 index 350ab13b92..0000000000 --- a/doc/src/USER/atc/man_atom_weight.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - -ATC: fix_modify AtC atom_weight - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC atom_weight

-syntax

-

fix_modify AtC atom_weight <method> <arguments>

- -

-examples

-

fix_modify atc atom_weight constant myatoms 11.8
- fix_modify atc atom_weight lattice
- fix_modify atc atom_weight read-in atm_wt_file.txt
-

-

-description

-

Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations.

-

-restrictions

-

Use of lattice option requires a lattice type and parameter is already specified.

-

-related

-

-default

-

lattice

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html deleted file mode 100644 index 17e854a37f..0000000000 --- a/doc/src/USER/atc/man_atomic_charge.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC atomic_charge - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC atomic_charge

-syntax

-

fix_modify AtC <include | omit> atomic_charge

- -

-examples

-

fix_modify atc compute include atomic_charge

-

-description

-

Determines whether AtC tracks the total charge as a finite element field

-

-restrictions

-

Required for: electrostatics

-

-related

-

-default

-

if the atom charge is defined, default is on, otherwise default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html deleted file mode 100644 index c4448bc191..0000000000 --- a/doc/src/USER/atc/man_boundary.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC boundary - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC boundary

-syntax

-

fix_modify AtC boundary type <atom-type-id>

- -

-examples

-

fix_modify AtC boundary type ghost_atoms

-

-description

-

Command to define the atoms that represent the fictitious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined.

-

-restrictions

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html deleted file mode 100644 index 335ff2d209..0000000000 --- a/doc/src/USER/atc/man_boundary_dynamics.html +++ /dev/null @@ -1,44 +0,0 @@ - - - - -ATC: fix_modify AtC boundary_dynamics - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC boundary_dynamics

-syntax

-

fix_modify AtC boundary_dynamics < on | damped_harmonic | prescribed | coupled | none > [args]
-

-

-description

-

Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same.

-

-restrictions

-

Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two.

-

-related

-

-default

-

prescribed on

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html deleted file mode 100644 index 6c2fb84940..0000000000 --- a/doc/src/USER/atc/man_boundary_faceset.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC boundary_faceset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC boundary_faceset

-syntax

-

fix_modify AtC boundary_faceset <is | add> [args]

-

-examples

-

fix_modify AtC boundary_faceset is obndy

-

-description

-

This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist.

-

-restrictions

-

This is only valid when fe_md_boundary is set to faceset.

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html deleted file mode 100644 index c4b0d4865e..0000000000 --- a/doc/src/USER/atc/man_boundary_integral.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC output boundary_integral - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output boundary_integral

-syntax

-

fix_modify AtC output boundary_integral [field] faceset [name]

- -

-examples

-

fix_modify AtC output boundary_integral stress faceset loop1
-

-

-description

-

Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html deleted file mode 100644 index baa306a1c8..0000000000 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC consistent_fe_initialization - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC consistent_fe_initialization

-syntax

-

fix_modify AtC consistent_fe_initialization <on | off>

- -

-examples

-

fix_modify atc consistent_fe_initialization on

-

-description

-

Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations.

-

-restrictions

-

Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes.

-

-related

-

-default

-

Default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html deleted file mode 100644 index 16f6d9abad..0000000000 --- a/doc/src/USER/atc/man_contour_integral.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC output contour_integral - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output contour_integral

-syntax

-

fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]>

- -

-examples

-

fix_modify AtC output contour_integral stress faceset loop1
-

-

-description

-

Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html deleted file mode 100644 index e94a9a52ef..0000000000 --- a/doc/src/USER/atc/man_control.html +++ /dev/null @@ -1,70 +0,0 @@ - - - - -ATC: fix_modify AtC control - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control

-syntax

-

fix_modify AtC control <physics_type> <solution_parameter>

-


-

- -

fix_modify AtC transfer <physics_type> control max_iterations <max_iterations>
-

- -

fix_modify AtC transfer <physics_type> control tolerance <tolerance>
-

- -

-examples

-

fix_modify AtC control thermal max_iterations 10
- fix_modify AtC control momentum tolerance 1.e-5
-

-

-description

-

Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance.

-

-restrictions

-

only for be used with specific controllers : thermal, momentum
- They are ignored if a lumped solution is requested

-

-related

-

-default

-

max_iterations is the number of rows in the matrix
- tolerance is 1.e-10

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html deleted file mode 100644 index e3074eae8f..0000000000 --- a/doc/src/USER/atc/man_control_momentum.html +++ /dev/null @@ -1,66 +0,0 @@ - - - - -ATC: fix_modify AtC control momentum - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control momentum

-syntax

-

fix_modify AtC control momentum none
-

-

fix_modify AtC control momentum rescale <frequency>
-

- -

fix_modify AtC control momentum glc_displacement
-

-

fix_modify AtC control momentum glc_velocity
-

-

fix_modify AtC control momentum hoover
-

-

fix_modify AtC control momentum flux [faceset face_set_id, interpolate]

- -

-examples

-

fix_modify AtC control momentum glc_velocity
- fix_modify AtC control momentum flux faceset bndy_faces
-

-

-description

-

-restrictions

-

only to be used with specific transfers : elastic
- rescale not valid with time filtering activated

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html deleted file mode 100644 index 8d32f1c4f9..0000000000 --- a/doc/src/USER/atc/man_control_thermal.html +++ /dev/null @@ -1,74 +0,0 @@ - - - - -ATC: fix_modify AtC control thermal - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control thermal

-syntax

-

fix_modify AtC control thermal <control_type> <optional_args>

- -

fix_modify AtC control thermal rescale <frequency>
-

- -

fix_modify AtC control thermal hoover
-

-

fix_modify AtC control thermal flux <boundary_integration_type(optional)> <face_set_id(optional)>
-

- -

-examples

-

fix_modify AtC control thermal none
- fix_modify AtC control thermal rescale 10
- fix_modify AtC control thermal hoover
- fix_modify AtC control thermal flux
- fix_modify AtC control thermal flux faceset bndy_faces
-

-

-description

-

Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms.

-

-restrictions

-

only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux)
- rescale not valid with time filtering activated

-

-related

-

-default

-

none
- rescale frequency is 1
- flux boundary_integration_type is interpolate

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html deleted file mode 100644 index d28ec334f5..0000000000 --- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC control thermal correction_max_iterations - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control thermal correction_max_iterations

-syntax

-

fix_modify AtC control thermal correction_max_iterations <max_iterations>

- -

-examples

-

fix_modify AtC control thermal correction_max_iterations 10
-

-

-description

-

Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver.

-

-restrictions

-

only for use with thermal physics using the fractional step method.

-

-related

-

-default

-

correction_max_iterations is 20

-
-
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- - diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html deleted file mode 100644 index 98eedafa6c..0000000000 --- a/doc/src/USER/atc/man_decomposition.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC decomposition - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC decomposition

-syntax

-

fix_modify AtC decomposition <type>

- -

-examples

-

fix_modify atc decomposition distributed_memory
-

-

-description

-

Command for assigning the distribution of work and memory for parallel runs.

-

-restrictions

-

replicated_memory is appropriate for simulations were the number of nodes << number of atoms

-

-related

-

-default

-

replicated_memory

-
-
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- - diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html deleted file mode 100644 index 7cf40f6813..0000000000 --- a/doc/src/USER/atc/man_electron_integration.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC extrinsic electron_integration - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC extrinsic electron_integration

-syntax

-

fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)>
-

- -

-examples

-

fix_modify AtC extrinsic electron_integration implicit
- fix_modify AtC extrinsic electron_integration explicit 100
-

-

-description

-

Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.

-

-restrictions

-

For use only with two_temperature type of AtC fix ( see fix atc command )
-

-

-default

-

implicit
- subcycle_steps = 1

-
-
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- - diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html deleted file mode 100644 index 8c81ce5925..0000000000 --- a/doc/src/USER/atc/man_equilibrium_start.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC equilibrium_start - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC equilibrium_start

-syntax

-

fix_modify AtC equilibrium_start <on|off>

-

-examples

-

fix_modify atc equilibrium_start on
-

-

-description

-

Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.

-

-restrictions

-

only needed before filtering is begun

-

-related

-

see fix_modify AtC filter

-

-default

-

on

-
-
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- - diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html deleted file mode 100644 index f4d1b01e88..0000000000 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC extrinsic exchange - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC extrinsic exchange

-syntax

-

fix_modify AtC extrinsic exchange <on|off>

-

-examples

-

fix_modify AtC extrinsic exchange on
-

-

-description

-

Switches energy exchange between the MD system and electron system on and off

-

-restrictions

-

Only valid for use with two_temperature type of AtC fix.

-

-related

-

see fix atc command

-

-default

-

on

-
-
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- - diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html deleted file mode 100644 index e39ddd3cec..0000000000 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC fe_md_boundary - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fe_md_boundary

-syntax

-

fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args]

-

-examples

-

fix_modify atc fe_md_boundary interpolate
-

-

-description

-

Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed.

-

-restrictions

-

If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.

-

-related

-

see for how to specify the faceset name.

-

-default

-

Interpolate.

-
-
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- - diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html deleted file mode 100644 index 485b8c95a0..0000000000 --- a/doc/src/USER/atc/man_fem_mesh.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC fem create mesh - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- -

fix_modify AtC fem create mesh

-syntax

-fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p> -

-examples

-

fix_modify AtC fem create mesh 10 1 1 feRegion p p p
-

-

-description

-

Creates a uniform mesh in a rectangular region

-

-restrictions

-

creates only uniform rectangular grids in a rectangular region

-

-related

-

-default

-none -
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- - diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html deleted file mode 100644 index e2190dea21..0000000000 --- a/doc/src/USER/atc/man_filter_scale.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC filter scale - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC filter scale

-syntax

-

fix_modify AtC filter scale <scale>
-

-
    -
  • scale (real) = characteristic time scale of the filter
    -
    • -
-

-examples

-

fix_modify AtC filter scale 10.0
-

-

-description

-

Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics

-

-restrictions

-

only for be used with specific transfers: thermal, two_temperature

-

-related

-

fix_modify AtC filter fix_modify AtC filter type

-

-default

-

0.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html deleted file mode 100644 index 0928139d7d..0000000000 --- a/doc/src/USER/atc/man_filter_type.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC filter type - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC filter type

-syntax

-

fix_modify AtC filter type <exponential | step | no_filter>
-

-

-examples

-

fix_modify AtC filter type exponential
-

-

-description

-

Specifies the type of time filter used.

-

-restrictions

-

only for be used with specific transfers: thermal, two_temperature

-

-related

-

fix_modify AtC filter fix_modify AtC filter scale

-

-default

-

No default.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html deleted file mode 100644 index 7c5afd645a..0000000000 --- a/doc/src/USER/atc/man_fix_atc.html +++ /dev/null @@ -1,252 +0,0 @@ - - - - -ATC: fix atc command - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix atc command

-syntax

-

fix <fixID> <group> atc <type> <parameter_file>

-
    -
  • fixID = name of fix
    • -
  • group = name of group fix is to be applied
    • -
  • type
    - = thermal : thermal coupling with fields: temperature
    - = two_temperature : electron-phonon coupling with field: temperature and electron_temperature
    - = hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
    - = field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
    -
    • -
  • parameter_file = name of the file with material parameters.
    - note: Neither hardy nor field requires a parameter file
    • -
-

-examples

-

fix AtC internal atc thermal Ar_thermal.dat
- fix AtC internal atc two_temperature Ar_ttm.mat
- fix AtC internal atc hardy
- fix AtC internal atc field
-

-

-description

-

This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.

-

The following coupling example is typical, but non-exhaustive:
-

-

# ... commands to create and initialize the MD system
-

-

# initial fix to designate coupling type and group to apply it to
- # tag group physics material_file
- fix AtC internal atc thermal Ar_thermal.mat
-
- # create a uniform 12 x 2 x 2 mesh that covers region contain the group
- # nx ny nz region periodicity
- fix_modify AtC mesh create 12 2 2 mdRegion f p p
-
- # specify the control method for the type of coupling
- # physics control_type
- fix_modify AtC thermal control flux
-
- # specify the initial values for the empirical field "temperature"
- # field node_group value
- fix_modify AtC initial temperature all 30.
-
- # create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output atc_fe_output 100
-
-

-

run 1000
-

-

likewise for this post-processing example:
-

-

# ... commands to create and initialize the MD system
-

-

# initial fix to designate post-processing and the group to apply it to
- # no material file is allowed nor required
- fix AtC internal atc hardy
-
- # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
- fix AtC kernel quartic_sphere 10.0
-
- # create a uniform 1 x 1 x 1 mesh that covers region contain the group
- # with periodicity this effectively creates a system average
- fix_modify AtC mesh create 1 1 1 box p p p
-
- # change from default lagrangian map to eulerian
- # refreshed every 100 steps
- fix_modify AtC atom_element_map eulerian 100
-
- # start with no field defined
- # add mass density, potential energy density, stress and temperature
- fix_modify AtC fields add density energy stress temperature
-
- # create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output nvtFE 100 text
-

-

run 1000
-

-

the mesh's linear interpolation functions can be used as the localization function
- by using the field option:
-

-

fix AtC internal atc field
-
- fix_modify AtC mesh create 1 1 1 box p p p
-
- ...
-
-

-

Note coupling and post-processing can be combined in the same simulations using separate fixes.
- For detailed exposition of the theory and algorithms please see:
-

-
    -
  • Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, An atomistic-to-continuum coupling method for heat transfer in solids. Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
    -
    • -
  • Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, Calculation of stress in atomistic simulation. Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
    -
    • -
  • Zimmerman, JA; Jones, RE; Templeton, JA, A material frame approach for evaluating continuum variables in atomistic simulations. Journal of Computational Physics (2010), 229:2364.
    -
    • -
  • Templeton, JA; Jones, RE; Wagner, GJ, Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
    -
    • -
  • Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, Electron transport enhanced molecular dynamics for metals and semi-metals. International Journal for Numerical Methods in Engineering (2010), 83:940.
    -
    • -
  • Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. Journal of Chemical Theory and Computation (2011), 7:1736.
    -
    • -
  • Mandadapu, KK; Templeton, JA; Lee, JW, Polarization as a field variable from molecular dynamics simulations. Journal of Chemical Physics (2013), 139:054115.
    -
    • -
-

Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element method , Dover 2003, for the basics of FE simulation.

-

-restrictions

-

Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.

-

Currently,

-
    -
  • the coupling is restricted to thermal physics
    • -
  • the FE computations are done in serial on each processor.
    • -
-

-related

-

fix_modify commands for setup:
-

- -

fix_modify commands for boundary and initial conditions:
-

- -

fix_modify commands for control and filtering:
-

- -

fix_modify commands for output:
-

- -

fix_modify commands for post-processing:
-

- -

miscellaneous fix_modify commands:
-

- -

Note: a set of example input files with the attendant material files are included with this package

-

-default

-

none

-
-
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- - diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html deleted file mode 100644 index 31bd5619a3..0000000000 --- a/doc/src/USER/atc/man_fix_flux.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC fix_flux - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fix_flux

-syntax

-

fix_modify AtC fix_flux <field> <face_set> <value | function>

-
    -
  • <field> = field name valid for type of physics, temperature | electron_temperature
    • -
  • <face_set> = name of set of element faces
    • -
-

-examples

-

fix_modify atc fix_flux temperature faceSet 10.0
-

-

-description

-

Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales.

-

-restrictions

-

Only normal fluxes (Neumann data) can be prescribed.

-

-related

-

see fix_modify AtC unfix_flux

-

-default

-
-
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- - diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html deleted file mode 100644 index 2245e32607..0000000000 --- a/doc/src/USER/atc/man_fix_nodes.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC fix - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fix

-syntax

-

fix_modify AtC fix <field> <nodeset> <constant | function>

-
    -
  • <field> = field name valid for type of physics
    • -
  • <nodeset> = name of set of nodes to apply boundary condition
    • -
  • <constant | function> = value or name of function followed by its parameters
    • -
-

-examples

-

fix_modify AtC fix temperature groupNAME 10.
- fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0
-

-

-description

-

Creates a constraint on the values of the specified field at specified nodes.

-

-restrictions

-

keyword 'all' reserved in nodeset name

-

-related

-

see fix_modify AtC unfix

-

-default

-

none

-
-
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- - diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html deleted file mode 100644 index ec2dc3ccb9..0000000000 --- a/doc/src/USER/atc/man_hardy_computes.html +++ /dev/null @@ -1,65 +0,0 @@ - - - - -ATC: fix_modify AtC computes - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC computes

-syntax

-

fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number>
-

-
    -
  • add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity
    -
    • -
  • per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS
    -
    • -
  • volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions
    -
    • -
-

-examples

-

compute virial all stress/atom
- fix_modify AtC computes add virial volume
- fix_modify AtC computes delete virial
-
- compute centrosymmetry all centro/atom
- fix_modify AtC computes add centrosymmetry number
-

-

-description

-

Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS
-

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )
- Per-atom compute must be specified before corresponding continuum field can be requested
-

-

-related

-

See manual page for compute

-

-default

-

No defaults exist for this command

-
-
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- - diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html deleted file mode 100644 index 483e5be6bd..0000000000 --- a/doc/src/USER/atc/man_hardy_fields.html +++ /dev/null @@ -1,81 +0,0 @@ - - - - -ATC: fix_modify AtC fields - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fields

-syntax

-

fix_modify AtC fields <all | none>
- fix_modify AtC fields <add | delete> <list_of_fields>
-

-
    -
  • all | none (keyword) = output all or no fields
    -
    • -
  • add | delete (keyword) = add or delete the listed output fields
    -
    • -
  • fields (keyword) =
    - density : mass per unit volume
    - displacement : displacement vector
    - momentum : momentum per unit volume
    - velocity : defined by momentum divided by density
    - projected_velocity : simple kernel estimation of atomic velocities
    - temperature : temperature derived from the relative atomic kinetic energy (as done by )
    - kinetic_temperature : temperature derived from the full kinetic energy
    - number_density : simple kernel estimation of number of atoms per unit volume
    - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
    - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
    - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
    - potential_energy : potential energy per unit volume
    - kinetic_energy : kinetic energy per unit volume
    - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume
    - internal_energy : total internal energy (potential + thermal) per unit volume
    - energy : total energy (potential + kinetic) per unit volume
    - number_density : number of atoms per unit volume
    - eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
    - vacancy_concentration: volume fraction of vacancy content
    - type_concentration: volume fraction of a specific atom type
    -
    • -
-

-examples

-

fix_modify AtC fields add velocity temperature

-

-description

-

Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.
- fix_modify AtC fields none
- followed by
- fix_modify AtC fields add velocity temperature
- will only output the velocity and temperature fields.

-

-restrictions

-

Must be used with the hardy/field type of AtC fix, see fix atc command. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber.

-

-related

-

See fix_modify AtC gradients , fix_modify AtC rates and fix_modify AtC computes

-

-default

-

By default, no fields are output

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html deleted file mode 100644 index 1ecfade0ea..0000000000 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC gradients - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC gradients

-syntax

-

fix_modify AtC gradients <add | delete> <list_of_fields>
-

-
    -
  • add | delete (keyword) = add or delete the calculation of gradients for the listed output fields
    -
    • -
  • fields (keyword) =
    - gradients can be calculated for all fields listed in fix_modify AtC fields
    • -
-

-examples

-

fix_modify AtC gradients add temperature velocity stress
- fix_modify AtC gradients delete velocity
-

-

-description

-

Requests calculation and output of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see fix_modify AtC atom_element_map )

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

No gradients are calculated by default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html deleted file mode 100644 index 620b9b1d36..0000000000 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - -ATC: fix_modify AtC kernel - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC kernel

-syntax

-

fix_modify AtC kernel <type> <parameters>

-
    -
  • type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
    -
    • -
  • parameters :
    - step = radius (double)
    - cell = hx, hy, hz (double) or h (double)
    - cubic_bar = half-width (double)
    - cubic_cylinder = radius (double)
    - cubic_sphere = radius (double)
    - quartic_bar = half-width (double)
    - quartic_cylinder = radius (double)
    - quartic_sphere = radius (double)
    -
    • -
-

-examples

-

fix_modify AtC kernel cell 1.0 1.0 1.0
- fix_modify AtC kernel quartic_sphere 10.0

-

-description

-

-restrictions

-

Must be used with the hardy AtC fix
- For bar kernel types, half-width oriented along x-direction
- For cylinder kernel types, cylindrical axis is assumed to be in z-direction
- ( see fix atc command )

-

-related

-

-default

-

No default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html deleted file mode 100644 index 04d24ff029..0000000000 --- a/doc/src/USER/atc/man_hardy_on_the_fly.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - -ATC: fix_modify AtC on_the_fly - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC on_the_fly

-syntax

-

fix_modify AtC on_the_fly <bond | kernel> <optional on | off>
- - bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements
-

-
    -
  • on | off (keyword) = activate or discontinue on-the-fly mode
    -
    • -
-

-examples

-

fix_modify AtC on_the_fly bond on
- fix_modify AtC on_the_fly kernel
- fix_modify AtC on_the_fly kernel off
-

-

-description

-

Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use.
- on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag.
-

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated.
-

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html deleted file mode 100644 index 8066543485..0000000000 --- a/doc/src/USER/atc/man_hardy_rates.html +++ /dev/null @@ -1,56 +0,0 @@ - - - - -ATC: fix_modify AtC rates - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC rates

-syntax

-

fix_modify AtC rates <add | delete> <list_of_fields>
-

-
    -
  • add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields
    -
    • -
  • fields (keyword) =
    - rates can be calculated for all fields listed in fix_modify AtC fields
    • -
-

-examples

-

fix_modify AtC rates add temperature velocity stress
- fix_modify AtC rates delete stress
-

-

-description

-

Requests calculation and output of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.
-

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

No rates are calculated by default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html deleted file mode 100644 index c8348c45ed..0000000000 --- a/doc/src/USER/atc/man_initial.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC initial - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC initial

-syntax

-

fix_modify AtC initial <field> <nodeset> <constant | function>

-
    -
  • <field> = field name valid for type of physics, temperature | electron_temperature
    • -
  • <nodeset> = name of set of nodes to apply initial condition
    • -
  • <constant | function> = value or name of function followed by its parameters
    • -
-

-examples

-

fix_modify atc initial temperature groupNAME 10.

-

-description

-

Sets the initial values for the specified field at the specified nodes.

-

-restrictions

-

keyword 'all' reserved in nodeset name

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html deleted file mode 100644 index f76607cc91..0000000000 --- a/doc/src/USER/atc/man_internal_atom_integrate.html +++ /dev/null @@ -1,38 +0,0 @@ - - - - -ATC: fix_modify AtC internal_atom_integrate - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC internal_atom_integrate

-syntax

-

fix_modify AtC internal_atom_integrate <on | off> fix_modify AtC internal_atom_integrate on

-

-description

-

Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms.

-

-default

-

on for coupling methods, off for post-processors off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html deleted file mode 100644 index a5d893f2a3..0000000000 --- a/doc/src/USER/atc/man_internal_element_set.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC internal_element_set - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC internal_element_set

-syntax

-

fix_modify AtC internal_element_set <element-set-name>

-
    -
  • <element-set-name> = name of element set defining internal region, or off
    • -
-

-examples

-

fix_modify AtC internal_element_set myElementSet fix_modify AtC internal_element_set off

-

-description

-

Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise.

-

-restrictions

-

If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency

-

-related

-

see atom_element_map_type and boundary

-

-default

-

off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html deleted file mode 100644 index 6af543cbae..0000000000 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC internal_quadrature - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC internal_quadrature

-syntax

-

fix_modify atc internal_quadrature <on | off> [region]

-

-examples

-

fix_modify atc internal_quadrature off

-

-description

-

Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data.

-

-optional

-

Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off.

-

-restrictions

-

-related

-

-default

-

on

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html deleted file mode 100644 index cb02c05c23..0000000000 --- a/doc/src/USER/atc/man_kernel_function.html +++ /dev/null @@ -1,62 +0,0 @@ - - - - -ATC: fix_modify AtC kernel - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC kernel

-syntax

-

fix_modify AtC kernel <type> <parameters>

-
    -
  • type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
    -
    • -
  • parameters :
    - step = radius (double)
    - cell = hx, hy, hz (double) or h (double)
    - cubic_bar = half-width (double)
    - cubic_cylinder = radius (double)
    - cubic_sphere = radius (double)
    - quartic_bar = half-width (double)
    - quartic_cylinder = radius (double)
    - quartic_sphere = radius (double)
    -
    • -
-

-examples

-

fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0

-

-description

-

-restrictions

-

Must be used with the hardy AtC fix
- For bar kernel types, half-width oriented along x-direction
- For cylinder kernel types, cylindrical axis is assumed to be in z-direction
- ( see fix atc command )

-

-related

-

-default

-

No default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html deleted file mode 100644 index 88442d63a1..0000000000 --- a/doc/src/USER/atc/man_localized_lambda.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC control localized_lambda - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control localized_lambda

-syntax

-

fix_modify AtC control localized_lambda <on|off>

-

-examples

-

fix_modify atc control localized_lambda on
-

-

-description

-

Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation.

-

-restrictions

-

-related

-

-default

-

Default is off.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_lumped_lambda_solve.html b/doc/src/USER/atc/man_lumped_lambda_solve.html deleted file mode 100644 index 89aabebd3c..0000000000 --- a/doc/src/USER/atc/man_lumped_lambda_solve.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC control lumped_lambda_solve - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control lumped_lambda_solve

-syntax

-

fix_modify AtC control lumped_lambda_solve <on|off>

-

-examples

-

fix_modify atc control lumped_lambda_solve on
-

-

-description

-

Command to use or not use lumped matrix for lambda solve

-

-restrictions

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html deleted file mode 100644 index ea5a6e357b..0000000000 --- a/doc/src/USER/atc/man_mask_direction.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC control mask_direction - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control mask_direction

-syntax

-

fix_modify AtC control mask_direction <direction> <on|off>

-

-examples

-

fix_modify atc control mask_direction 0 on
-

-

-description

-

Command to mask out certain dimensions from the atomic regulator

-

-restrictions

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html deleted file mode 100644 index fd744e5bbf..0000000000 --- a/doc/src/USER/atc/man_mass_matrix.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mass_matrix - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mass_matrix

-syntax

-

fix_modify AtC mass_matrix <fe | md_fe>

-
    -
  • <fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region
    • -
-

-examples

-

fix_modify atc mass_matrix fe

-

-description

-

Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency.

-

-restrictions

-

Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate

-

-related

-

-default

-

Default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html deleted file mode 100644 index 1646abc671..0000000000 --- a/doc/src/USER/atc/man_material.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC material - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC material

-syntax

-

fix_modify AtC material [elementset_name] [material_id]
-

-

-examples

-

fix_modify AtC material gap_region 2

-

-description

-

Sets the material model in elementset_name to be of type material_id.

-

-restrictions

-

The element set must already be created and the material must be specified in the material file given the the atc fix on construction

-

-related

-

-default

-

All elements default to the first material in the material file.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_add_to_nodeset.html b/doc/src/USER/atc/man_mesh_add_to_nodeset.html deleted file mode 100644 index c4976f699d..0000000000 --- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh add_to_nodeset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh add_to_nodeset

-syntax

-

fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

-
    -
  • <id> = id of FE nodeset to be added to
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added
    • -
-

-examples

-

fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12

-

-description

-

Command to add nodes to an already existing FE nodeset.

-

-restrictions

-

-related

-

-default

-

Coordinates are assumed to be in lattice units.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html deleted file mode 100644 index 98989bd015..0000000000 --- a/doc/src/USER/atc/man_mesh_create.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create

-syntax

-

fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
-

-
    -
  • nx ny nz = number of elements in x, y, z
    • -
  • region-id = id of region that is to be meshed
    • -
  • f p p = periodicity flags for x, y, z
    • -
-

-examples

-

fix_modify AtC mesh create 10 1 1 feRegion p p p
-

-

-description

-

Creates a uniform mesh in a rectangular region

-

-restrictions

-

Creates only uniform rectangular grids in a rectangular region

-

-related

-

fix_modify AtC mesh quadrature

-

-default

-

When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html deleted file mode 100644 index 735d462b73..0000000000 --- a/doc/src/USER/atc/man_mesh_create_elementset.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_elementset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_elementset

-syntax

-

fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

-
    -
  • <id> = id to assign to the collection of FE element
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements
    • -
-

-examples

-

fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100

-

-description

-

Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations.

-

-restrictions

-

Only viable for rectangular grids.

-

-related

-

-default

-

Coordinates are assumed to be in lattice units.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_faceset_box.html b/doc/src/USER/atc/man_mesh_create_faceset_box.html deleted file mode 100644 index 0ae68435e5..0000000000 --- a/doc/src/USER/atc/man_mesh_create_faceset_box.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_faceset box - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_faceset box

-syntax

-

fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]

-
    -
  • <id> = id to assign to the collection of FE faces
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces
    • -
  • <in|out> = "in" gives inner faces to the box, "out" gives the outer faces to the box
    • -
  • units = option to specify real as opposed to lattice units
    • -
-

-examples

-

fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out

-

-description

-

Command to assign an id to a set of FE faces.

-

-restrictions

-

Only viable for rectangular grids.

-

-related

-

-default

-

The default options are units = lattice and the use of outer faces

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_faceset_plane.html b/doc/src/USER/atc/man_mesh_create_faceset_plane.html deleted file mode 100644 index cd78816bae..0000000000 --- a/doc/src/USER/atc/man_mesh_create_faceset_plane.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_faceset plane - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_faceset plane

-syntax

-

fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]

-
    -
  • <id> = id to assign to the collection of FE faces
    • -
  • <x|y|z> = coordinate directions that define plane on which faceset lies
    • -
  • <val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]
    • -
  • units = option to specify real as opposed to lattice units
    • -
-

-examples

-

fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0

-

-description

-

Command to assign an id to a set of FE faces.

-

-restrictions

-

Only viable for rectangular grids.

-

-related

-

-default

-

The default option is units = lattice.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html deleted file mode 100644 index 0e3624cf8a..0000000000 --- a/doc/src/USER/atc/man_mesh_create_nodeset.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_nodeset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_nodeset

-syntax

-

fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

-
    -
  • <id> = id to assign to the collection of FE nodes
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes
    • -
-

-examples

-

fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12

-

-description

-

Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions.

-

-restrictions

-

-related

-

-default

-

Coordinates are assumed to be in lattice units.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html deleted file mode 100644 index e39cc54d41..0000000000 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC mesh delete_elements - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh delete_elements

-syntax

-

fix_modify AtC mesh delete_elements <element_set>

-
    -
  • <element_set> = name of an element set
    • -
-

-examples

-

fix_modify AtC delete_elements gap

-

-description

-

Deletes a group of elements from the mesh.

-

-restrictions

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html deleted file mode 100644 index 66b55a48fb..0000000000 --- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC mesh nodeset_to_elementset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh nodeset_to_elementset

-syntax

-

fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>

-
    -
  • <nodeset_id> = id of desired nodeset from which to create elementset
    • -
  • <elementset_id> = id to assign to the collection of FE element
    • -
  • <max/min> = flag to choose either the maximal or minimal elementset
    • -
-

-examples

-

fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min

-

-description

-

Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created

-

-restrictions

-

None.

-

-related

-

-default

-

Unless specified, the maximal element set is created

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html deleted file mode 100644 index 1d2983afff..0000000000 --- a/doc/src/USER/atc/man_mesh_output.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC mesh output - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh output

-syntax

-

fix_modify AtC mesh output <file_prefix>

-

-examples

-

fix_modify AtC mesh output meshData
-

-

-description

-

Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data.

-

-restrictions

-

none

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_quadrature.html b/doc/src/USER/atc/man_mesh_quadrature.html deleted file mode 100644 index 821e50e4cf..0000000000 --- a/doc/src/USER/atc/man_mesh_quadrature.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh quadrature - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh quadrature

-syntax

-

fix_modify AtC mesh quadrature <quad>

-
    -
  • quad = one of <nodal|gauss1|gauss2|gauss3|face> --- when a mesh is created it defaults to gauss2, use this call to change it after the fact
    • -
-

-examples

-

fix_modify AtC mesh quadrature face

-

-description

-

(Re-)assigns the quadrature style for the existing mesh.

-

-restrictions

-

-related

-

fix_modify AtC mesh create

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html deleted file mode 100644 index 315180e1db..0000000000 --- a/doc/src/USER/atc/man_mesh_read.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC mesh read - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh read

-syntax

-

fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p>

-
    -
  • filename = name of file containing mesh to be read
    • -
  • f p p = periodicity flags for x, y, z
    • -
-

-examples

-

fix_modify AtC mesh read myComponent.mesh p p p
- fix_modify AtC mesh read myOtherComponent.exo

-

-description

-

Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed.

-

-restrictions

-

-related

-

-default

-

periodicity flags are false by default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html deleted file mode 100644 index f709c02a84..0000000000 --- a/doc/src/USER/atc/man_mesh_write.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC mesh write - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh write

-syntax

-

fix_modify AtC mesh write <filename>

-
    -
  • filename = name of file to write mesh
    • -
-

-examples

-

fix_modify AtC mesh write myMesh.mesh
-

-

-description

-

Writes a mesh to a text file.

-

-restrictions

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html deleted file mode 100644 index ee0505847c..0000000000 --- a/doc/src/USER/atc/man_momentum_time_integration.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - -ATC: fix_modify AtC time_integration (momentum) - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC time_integration (momentum)

-syntax

-

fix_modify AtC time_integration <descriptor>
-

-
    -
  • descriptor (string) = time integration type
    -
    • -
-

various time integration methods for the finite elements
-

-

-description

-

verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force
- fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes
- gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power
-

-

-examples

-

fix_modify atc time_integration verlet
- fix_modify atc time_integration fractional_step
-

-

-description

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html deleted file mode 100644 index d0a08fa0da..0000000000 --- a/doc/src/USER/atc/man_output.html +++ /dev/null @@ -1,61 +0,0 @@ - - - - -ATC: fix_modify AtC output - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output

-syntax

-

fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]

-
    -
  • filename_prefix (string) = prefix for data files
    • -
  • frequency (integer) = frequency of output in time-steps
    • -
  • options (keyword/s):
    - text = creates text output of index, step and nodal variable values for unique nodes
    - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes
    - binary = creates binary Ensight output
    - vector_components = outputs vectors as scalar components
    - tensor_components = outputs tensor as scalar components (use this for Paraview)
    -
    • -
-

-examples

-

fix_modify AtC output heatFE 100
- fix_modify AtC output hardyFE 1 text tensor_components
- fix_modify AtC output hardyFE 10 text binary tensor_components
- fix_modify AtC output index step
-

-

-description

-

Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible.

-

-restrictions

-

-related

-

see fix atc command

-

-default

-

no default format output indexed by time

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html deleted file mode 100644 index 18afe0aa97..0000000000 --- a/doc/src/USER/atc/man_output_elementset.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC output elementset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output elementset

-syntax

-

fix_modify AtC output volume_integral <eset_name> <field> {`

-
    -
  • set_name (string) = name of elementset to be integrated over
    • -
  • fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset
    -
    • -
-

-examples

-

fix_modify AtC output eset1 mass_density
-

-

-description

-

Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file.

-

-restrictions

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html deleted file mode 100644 index 7906c5fc52..0000000000 --- a/doc/src/USER/atc/man_output_nodeset.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC output nodeset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output nodeset

-syntax

-

fix_modify AtC output nodeset <nodeset_name> <operation>

-
    -
  • nodeset_name (string) = name of nodeset to be operated on
    • -
  • operation (keyword/s):
    - sum = creates nodal sum over nodes in specified nodeset
    -
    • -
-

-examples

-

fix_modify AtC output nodeset nset1 sum
-

-

-description

-

Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file.

-

-restrictions

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html deleted file mode 100644 index 3ec2eecc60..0000000000 --- a/doc/src/USER/atc/man_pair_interactions.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC pair_interactions/bond_interactions - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC pair_interactions/bond_interactions

-syntax

-

fix_modify AtC pair_interactions <on|off>
- fix_modify AtC bond_interactions <on|off>
-

-

-examples

-

fix_modify AtC bond_interactions on
-

-

-description

-

include bonds and/or pairs in the stress and heat flux computations

-

-restrictions

-

-related

-

-default

-

pair interactions: on, bond interactions: off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html deleted file mode 100644 index 3e22a51f3e..0000000000 --- a/doc/src/USER/atc/man_poisson_solver.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC poisson_solver - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC poisson_solver

-syntax

-

fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>

-
    -
  • nx ny nz = number of elements in x, y, z
    • -
  • region-id = id of region that is to be meshed
    • -
  • f p p = perioidicity flags for x, y, z
    • -
-

-examples

-

fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p

-

-description

-

Creates a uniform mesh in a rectangular region

-

-restrictions

-

creates only uniform rectangular grids in a rectangular region

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html deleted file mode 100644 index d13151a12e..0000000000 --- a/doc/src/USER/atc/man_read_restart.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC read_restart - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC read_restart

-syntax

-

fix_modify AtC read_restart [file_name]
-

-

-examples

-

fix_modify AtC read_restart ATC_state
-

-

-description

-

Reads the current state of the fields from a named text-based restart file.

-

-restrictions

-

The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.

-

-related

-

see write_restart fix_modify AtC write_restart

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html deleted file mode 100644 index 54e4e3419f..0000000000 --- a/doc/src/USER/atc/man_remove_molecule.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC remove_molecule - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC remove_molecule

-syntax

-

fix_modify_AtC remove_molecule <TAG>
-

-
    -
  • <TAG> = tag for tracking a molecule type
    -
    • -
-

-examples

-

fix_modify AtC remove_molecule water
-

-

-description

-

Removes tag designated for tracking a specified set of molecules.
-

-

-restrictions

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html deleted file mode 100644 index c15e0ca46d..0000000000 --- a/doc/src/USER/atc/man_remove_source.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC remove_source - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC remove_source

-syntax

-

fix_modify AtC remove_source <field> <element_set>

-
    -
  • <field> = field name valid for type of physics
    • -
  • <element_set> = name of set of elements
    • -
-

-examples

-

fix_modify atc remove_source temperature groupNAME

-

-description

-

Remove a domain source.

-

-restrictions

-

keyword 'all' reserved in element_set name

-

-related

-

see fix_modify AtC source

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html deleted file mode 100644 index ee063ce57f..0000000000 --- a/doc/src/USER/atc/man_remove_species.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC remove_species - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC remove_species

-syntax

-

fix_modify_AtC delete_species <TAG>
-

-
    -
  • <TAG> = tag for tracking a species
    -
    • -
-

-examples

-

fix_modify AtC remove_species gold
-

-

-description

-

Removes tag designated for tracking a specified species.
-

-

-restrictions

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html deleted file mode 100644 index 3c43861054..0000000000 --- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC reset_atomic_reference_positions - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC reset_atomic_reference_positions

-syntax

-

fix_modify AtC reset_atomic_reference_positions

-

-examples

-

fix_modify atc reset_atomic_reference_positions

-

-description

-

Resets the atomic positions ATC uses to perform point to field operations. In can be used to use perfect lattice sites in ATC but a thermalized or deformed lattice in LAMMPS.

-

-restrictions

-

-

-related

-

-

-default

-

Default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html deleted file mode 100644 index 9607848e1a..0000000000 --- a/doc/src/USER/atc/man_reset_time.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - -ATC: fix_modify AtC reset_time - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC reset_time

-syntax

-

fix_modify AtC reset_time

-

-examples

-

fix_modify atc reset_time 0.0
-

-

-description

-

Resets the simulation time counter.

-

-restrictions

-

-related

-

-default

-

-syntax

-

fix_modify AtC kernel_bandwidth

-

-examples

-

fix_modify atc reset_time 8
-

-

-description

-

Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations.

-

-restrictions

-

Only is used if kernel functions are being used.

-

-related

-

-default

-

Number of sample locations.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html deleted file mode 100644 index 9a9a8e3a02..0000000000 --- a/doc/src/USER/atc/man_sample_frequency.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC sample_frequency - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC sample_frequency

-syntax

-

fix_modify AtC sample_frequency [freq]

-
    -
  • freq (int) : frequency to sample field in number of steps
    • -
-

-examples

-

fix_modify AtC sample_frequency 10

-

-description

-

Specifies a frequency at which fields are computed for the case where time filters are being applied.

-

-restrictions

-

Must be used with the hardy/field AtC fix ( see fix atc command ) and is only relevant when time filters are being used.

-

-related

-

-

-default

-

none

-
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Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html deleted file mode 100644 index 55ad8d952b..0000000000 --- a/doc/src/USER/atc/man_set.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC set - - - - -
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fix_modify AtC set

-syntax

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fix_modify AtC set reference_potential_energy <value_or_filename(optional)>

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    -
  • value (double) : optional user specified zero point for PE in native LAMMPS energy units
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    • -
  • filename (string) : optional user specified string for file of nodal PE values to be read-in
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-examples

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fix_modify AtC set reference_potential_energy
- fix_modify AtC set reference_potential_energy -0.05
- fix_modify AtC set reference_potential_energy myPEvalues
-

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-description

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Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename.

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-restrictions

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Must be used with the hardy/field type of AtC fix ( see fix atc command )

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-related

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-default

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Defaults to lammps zero point i.e. isolated atoms

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- - diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html deleted file mode 100644 index 78fb1652eb..0000000000 --- a/doc/src/USER/atc/man_source.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC source - - - - -
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fix_modify AtC source

-syntax

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fix_modify AtC source <field> <element_set> <value | function>

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  • <field> = field name valid for type of physics
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  • <element_set> = name of set of elements
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-examples

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fix_modify atc source temperature middle temporal_ramp 10. 0.

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-description

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Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time.

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-restrictions

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keyword 'all' reserved in element_set name

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-related

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see fix_modify AtC remove_source

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-default

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none

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- - diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html deleted file mode 100644 index 3b261b7810..0000000000 --- a/doc/src/USER/atc/man_source_integration.html +++ /dev/null @@ -1,44 +0,0 @@ - - - - -ATC: fix_modify AtC source_integration - - - - -
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fix_modify AtC source_integration

-syntax

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fix_modify AtC source_integration < fe | atom>

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-examples

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fix_modify atc source_integration atom

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-description

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-restrictions

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-related

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-default

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Default is fe

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- - diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html deleted file mode 100644 index c317c06c00..0000000000 --- a/doc/src/USER/atc/man_temperature_definition.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC temperature_definition - - - - -
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fix_modify AtC temperature_definition

-syntax

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fix_modify AtC temperature_definition <kinetic|total>

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-examples

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fix_modify atc temperature_definition kinetic
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-description

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Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.

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-restrictions

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This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.

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-default

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kinetic

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- - diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html deleted file mode 100644 index 830591921e..0000000000 --- a/doc/src/USER/atc/man_thermal_time_integration.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC time_integration (thermal) - - - - -
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fix_modify AtC time_integration (thermal)

-syntax

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fix_modify AtC time_integration <descriptor>
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  • descriptor (string) = time integration type
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various time integration methods for the finite elements
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-description

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gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power
- fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes
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-examples

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fix_modify atc time_integration gear
- fix_modify atc time_integration fractional_step
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-description

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-related

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see fix atc command

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-default

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none

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- - diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html deleted file mode 100644 index 5000fb079d..0000000000 --- a/doc/src/USER/atc/man_time_filter.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC filter - - - - -
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fix_modify AtC filter

-syntax

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fix_modify AtC filter <on | off | equilibrate>
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  • on | off (keyword) = turns filter on or off
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  • equilibrate = runs dynamics without filtering but initializes filtered quantities
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-examples

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fix_modify atc transfer filter on
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-description

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Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics

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-restrictions

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only for be used with specific transfers: thermal, two_temperature

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-related

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fix_modify AtC filter scale
- fix_modify AtC equilibrium_start

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-default

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off

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- - diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html deleted file mode 100644 index 2c7cf26150..0000000000 --- a/doc/src/USER/atc/man_track_displacement.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC track_displacement - - - - -
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fix_modify AtC track_displacement

-syntax

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fix_modify AtC track_displacement <on/off>
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-examples

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fix_modify atc track_displacement on
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-description

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Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.

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-restrictions

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Some constitutive models require the displacement field

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-default

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on

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- - diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html deleted file mode 100644 index 551896431a..0000000000 --- a/doc/src/USER/atc/man_unfix_flux.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC unfix_flux - - - - -
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fix_modify AtC unfix_flux

-syntax

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fix_modify AtC fix_flux <field> <face_set> <value | function>

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  • <field> = field name valid for type of physics, temperature | electron_temperature
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  • <face_set> = name of set of element faces
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-examples

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fix_modify atc unfix_flux temperature faceSet
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-description

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Command for removing prescribed normal fluxes e.g. heat_flux, stress.

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-restrictions

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-related

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see fix_modify AtC unfix_flux

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-default

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- - diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html deleted file mode 100644 index 4dfd9b3cfc..0000000000 --- a/doc/src/USER/atc/man_unfix_nodes.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC unfix - - - - -
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fix_modify AtC unfix

-syntax

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fix_modify AtC unfix <field> <nodeset>

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  • <field> = field name valid for type of physics
    • -
  • <nodeset> = name of set of nodes
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-examples

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fix_modify AtC unfix temperature groupNAME

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-description

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Removes constraint on field values for specified nodes.

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-restrictions

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keyword 'all' reserved in nodeset name

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-related

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see fix_modify AtC fix

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-default

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none

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- - diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html deleted file mode 100644 index 1722d74f67..0000000000 --- a/doc/src/USER/atc/man_write_atom_weights.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC write_atom_weights - - - - -
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fix_modify AtC write_atom_weights

-syntax

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fix_modify AtC write_atom_weights <filename> <frequency>

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  • <filename> = name of file that atomic weights are written to
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  • <frequency> = how often writes will occur
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-examples

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fix_modify atc write_atom_weights atm_wt_file.txt 10
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-description

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Command for writing the values of atomic weights to a specified file.

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-restrictions

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-related

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-default

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- - diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html deleted file mode 100644 index 74c6e2d289..0000000000 --- a/doc/src/USER/atc/man_write_restart.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC write_restart - - - - -
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fix_modify AtC write_restart

-syntax

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fix_modify AtC write_restart [file_name]
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-examples

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fix_modify AtC write_restart restart.mydata
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-description

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Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command.

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-restrictions

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The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.

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-related

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see read_restart fix_modify AtC read_restart

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-default

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none

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