diff --git a/doc/USER/atc/man_atom_element_map.html b/doc/USER/atc/man_atom_element_map.html index 33bd8e692a..3073c0f920 100644 --- a/doc/USER/atc/man_atom_element_map.html +++ b/doc/USER/atc/man_atom_element_map.html @@ -1,26 +1,52 @@ - - -ATC: fix_modify AtC transfer atom_element_map - - - -

fix_modify AtC transfer atom_element_map

+ + + + +ATC: fix_modify AtC atom_element_map + + + + + + +
+ + +

fix_modify AtC atom_element_map

syntax

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

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

-

+
  • frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian
    • + +

    examples

    - fix_modify atc transfer atom_element_map eulerian 100

    +

    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.

    +

    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.

    +

    Cannot change map type after initialization.

    +

    related

    -

    +

    default

    -lagrangian
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    lagrangian

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_boundary_integral.html b/doc/USER/atc/man_boundary_integral.html index 7f8379d9b0..3e78f12963 100644 --- a/doc/USER/atc/man_boundary_integral.html +++ b/doc/USER/atc/man_boundary_integral.html @@ -1,26 +1,53 @@ - - -ATC: fix_modify AtC boundary_integral - - - -

    fix_modify AtC boundary_integral

    + + + + +ATC: fix_modify AtC output boundary_integral + + + + + + +
    + + +

    fix_modify AtC output boundary_integral

    syntax

    -fix_modify AtC transfer boundary_integral [field] faceset [name] -

    +

    fix_modify AtC output boundary_integral [field] faceset [name]

    +
      +
    • field (string) : name of hardy field
      • +
    • name (string) : name of faceset
      • +
    +

    examples

    - fix_modify AtC transfer boundary_integral stress faceset loop1
    -

    +

    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

    +

    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 AtC transfer ( see fix atc command )

    +

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

    +

    related

    -

    +

    default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    none

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_contour_integral.html b/doc/USER/atc/man_contour_integral.html index b87b2567bf..c321605e88 100644 --- a/doc/USER/atc/man_contour_integral.html +++ b/doc/USER/atc/man_contour_integral.html @@ -1,26 +1,54 @@ - - -ATC: fix_modify AtC contour_integral - - - -

    fix_modify AtC contour_integral

    + + + + +ATC: fix_modify AtC output contour_integral + + + + + + +
    + + +

    fix_modify AtC output contour_integral

    syntax

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

    +

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

    +
      +
    • field (string) : name of hardy field
      • +
    • name (string) : name of faceset
      • +
    • axis (string) : x or y or z
      • +
    +

    examples

    - fix_modify AtC transfer contour_integral stress faceset loop1
    -

    +

    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

    +

    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 AtC transfer ( see fix atc command )

    +

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

    +

    related

    -

    +

    default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    none

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_electron_integration.html b/doc/USER/atc/man_electron_integration.html index dbde3d777a..b14c14d86d 100644 --- a/doc/USER/atc/man_electron_integration.html +++ b/doc/USER/atc/man_electron_integration.html @@ -1,30 +1,56 @@ - - + + + + ATC: fix_modify AtC extrinsic electron_integration - - - -

    fix_modify AtC extrinsic electron_integration

    + + + + + + +
    + + +

    fix_modify AtC extrinsic electron_integration

    syntax

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

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

    -

    -num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration

    +
  • integration_type (string) = explicit | implicit | steady
    +
    • +
  • num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration
    • + +

    examples

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

    +

    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.

    +

    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 )
    -

    +

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

    +

    default

    -implicit
    - subcycle_steps = 1
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    implicit
    + subcycle_steps = 1

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_equilibrium_start.html b/doc/USER/atc/man_equilibrium_start.html index 5aa645df6e..3723cf98bf 100644 --- a/doc/USER/atc/man_equilibrium_start.html +++ b/doc/USER/atc/man_equilibrium_start.html @@ -1,24 +1,50 @@ - - -ATC: fix_modify AtC transfer equilibrium_start - - - -

    fix_modify AtC transfer equilibrium_start

    + + + + +ATC: fix_modify AtC equilibrium_start + + + + + + +
    + + +

    fix_modify AtC equilibrium_start

    syntax

    -fix_modify AtC transfer equilibrium_start <on|off>

    +

    fix_modify AtC equilibrium_start <on|off>

    +

    examples

    - fix_modify atc transfer equilibrium_start on
    -

    +

    fix_modify atc equilibrium_start on
    +

    +

    description

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

    +

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

    +

    restrictions

    -only needed before filtering is begun

    +

    only needed before filtering is begun

    +

    related

    -see fix_modify AtC transfer filter

    +

    see fix_modify AtC filter

    +

    default

    -on
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    on

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_extrinsic_exchange.html b/doc/USER/atc/man_extrinsic_exchange.html index f8337a7cc9..8f6533ad64 100644 --- a/doc/USER/atc/man_extrinsic_exchange.html +++ b/doc/USER/atc/man_extrinsic_exchange.html @@ -1,24 +1,50 @@ - - + + + + ATC: fix_modify AtC extrinsic exchange - - - -

    fix_modify AtC extrinsic exchange

    + + + + + + +
    + + +

    fix_modify AtC extrinsic exchange

    syntax

    -fix_modify AtC extrinsic exchange <on|off>

    +

    fix_modify AtC extrinsic exchange <on|off>

    +

    examples

    - fix_modify AtC extrinsic exchange on
    -

    +

    fix_modify AtC extrinsic exchange on
    +

    +

    description

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

    +

    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.

    +

    Only valid for use with two_temperature type of AtC fix.

    +

    related

    -see fix atc command

    +

    see fix atc command

    +

    default

    -on
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    on

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_filter_scale.html b/doc/USER/atc/man_filter_scale.html index 606c41f17a..975f87e949 100644 --- a/doc/USER/atc/man_filter_scale.html +++ b/doc/USER/atc/man_filter_scale.html @@ -1,28 +1,55 @@ - - -ATC: fix_modify AtC transfer filter scale - - - -

    fix_modify AtC transfer filter scale

    + + + + +ATC: fix_modify AtC filter scale + + + + + + +
    + + +

    fix_modify AtC filter scale

    syntax

    -fix_modify AtC transfer filter scale <scale>
    +

    fix_modify AtC filter scale <scale>
    +

    -

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

    examples

    - fix_modify AtC transfer filter scale 10.0
    -

    +

    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

    +

    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

    +

    only for be used with specific transfers: thermal, two_temperature

    +

    related

    -fix_modify AtC transfer filter

    +

    fix_modify AtC filter fix_modify AtC filter type

    +

    default

    -0.
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    0.

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_fix_atc.html b/doc/USER/atc/man_fix_atc.html index f30b50349c..d6076a091a 100644 --- a/doc/USER/atc/man_fix_atc.html +++ b/doc/USER/atc/man_fix_atc.html @@ -1,119 +1,255 @@ - - + + + + ATC: fix atc command - - - -

    fix atc command

    + + + + + + +
    + + +

    fix atc command

    syntax

    -fix AtC transfer <type> <parameter_file> -

    +

    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_modify AtC transfer thermal Ar_thermal.dat
    - fix_modify AtC transfer hardy

    +

    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 Hardy/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 fem create mesh 12 2 2 mdRegion f p p
    -
    - # specify the control method for the type of coupling
    - # physics control_type
    - fix_modify AtC transfer thermal control flux
    -
    - # specify the initial values for the empirical field "temperature"
    - # field node_group value
    - fix_modify AtC transfer initial temperature all 30.
    -
    - # create an output stream for nodal fields
    - # filename output_frequency
    - fix_modify AtC transfer 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
    -
    - # create a uniform 1 x 1 x 1 mesh that covers region contain the group
    - # with periodicity this effectively creats a system average
    - fix_modify AtC fem create mesh 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
    - fix_modify AtC transfer fields none
    -
    - # add mass density, potential energy density, stress and temperature
    - fix_modify AtC transfer fields add density energy stress temperature
    -
    - # create an output stream for nodal fields
    - # filename output_frequency
    - fix_modify AtC transfer output nvtFE 100 text
    -

    - run 1000
    -

    -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:
    +

    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 creats 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
    -

    -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.

    +
  • 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.
    -

    +

    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 setup:
    +

    -

    -fix_modify commands for boundary and initial conditions:
    +

  • fix_modify AtC mesh create
    • +
  • fix_modify AtC mesh quadrature
    • +
  • fix_modify AtC mesh read
    • +
  • fix_modify AtC mesh write
    • +
  • fix_modify AtC mesh create_nodeset
    • +
  • fix_modify AtC mesh add_to_nodeset
    • +
  • fix_modify AtC mesh create_faceset box
    • +
  • fix_modify AtC mesh create_faceset plane
    • +
  • fix_modify AtC mesh create_elementset
    • +
  • fix_modify AtC mesh delete_elements
    • +
  • fix_modify AtC mesh nodeset_to_elementset
    • +
  • fix_modify AtC boundary
    • +
  • fix_modify AtC internal_quadrature
    • +
  • fix_modify AtC time_integration (thermal)
    • +
  • fix_modify AtC time_integration (momentum)
    • +
  • fix_modify AtC extrinsic electron_integration
    • +
  • fix_modify AtC internal_element_set
    • +
  • fix_modify AtC decomposition
    • + +

    fix_modify commands for boundary and initial conditions:
    +

    -

    -fix_modify commands for control and filtering:
    +

  • fix_modify AtC initial
    • +
  • fix_modify AtC fix
    • +
  • fix_modify AtC unfix
    • +
  • fix_modify AtC fix_flux
    • +
  • fix_modify AtC unfix_flux
    • +
  • fix_modify AtC source
    • +
  • fix_modify AtC remove_source
    • + +

    fix_modify commands for control and filtering:
    +

    -

    -fix_modify commands for output:
    +

  • fix_modify AtC control
    • +
  • fix_modify AtC control thermal
    • +
  • fix_modify AtC control thermal correction_max_iterations
    • +
  • fix_modify AtC control momentum
    • +
  • fix_modify AtC control localized_lambda
    • +
  • fix_modify AtC control lumped_lambda_solve
    • +
  • fix_modify AtC control mask_direction
    • +
  • fix_modify AtC filter
    • +
  • fix_modify AtC filter scale
    • +
  • fix_modify AtC filter type
    • +
  • fix_modify AtC equilibrium_start
    • +
  • fix_modify AtC extrinsic exchange
    • +
  • man_charge_control
    • +
  • fix_modify AtC poisson_solver
    • + +

    fix_modify commands for output:
    +

    -

    -fix_modify commands for post-processing:
    +

  • fix_modify AtC output
    • +
  • fix_modify AtC output nodeset
    • +
  • fix_modify AtC output elementset
    • +
  • fix_modify AtC output boundary_integral
    • +
  • fix_modify AtC output contour_integral
    • +
  • fix_modify AtC mesh output
    • +
  • fix_modify AtC write_restart
    • +
  • fix_modify AtC read_restart
    • + +

    fix_modify commands for post-processing:
    +

    -

    -miscellaneous fix_modify commands:
    +

  • fix_modify AtC kernel
    • +
  • fix_modify AtC fields
    • +
  • fix_modify AtC gradients
    • +
  • fix_modify AtC rates
    • +
  • fix_modify AtC computes
    • +
  • fix_modify AtC on_the_fly
    • +
  • fix_modify AtC pair_interactions/bond_interactions
    • +
  • fix_modify AtC sample_frequency
    • +
  • fix_modify AtC set
    • + +

    miscellaneous fix_modify commands:
    +

    -

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

    +
  • fix_modify AtC atom_element_map
    • +
  • fix_modify AtC atom_weight
    • +
  • fix_modify AtC write_atom_weights
    • +
  • fix_modify AtC reset_time
    • +
  • fix_modify AtC reset_atomic_reference_positions
    • +
  • fix_modify AtC fe_md_boundary
    • +
  • fix_modify AtC boundary_faceset
    • +
  • fix_modify AtC consistent_fe_initialization
    • +
  • fix_modify AtC mass_matrix
    • +
  • fix_modify AtC material
    • +
  • fix_modify AtC atomic_charge
    • +
  • fix_modify AtC source_integration
    • +
  • fix_modify AtC temperature_definition
    • +
  • fix_modify AtC track_displacement
    • +
  • fix_modify AtC boundary_dynamics
    • +
  • fix_modify AtC add_species
    • +
  • fix_modify AtC add_molecule
    • +
  • fix_modify AtC remove_species
    • +
  • fix_modify AtC remove_molecule
    • + +

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

    +

    default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_fix_flux.html b/doc/USER/atc/man_fix_flux.html index 44fdd73483..d8369a8785 100644 --- a/doc/USER/atc/man_fix_flux.html +++ b/doc/USER/atc/man_fix_flux.html @@ -1,26 +1,53 @@ - - -ATC: fix_modify AtC transfer fix_flux - - - -

    fix_modify AtC transfer fix_flux

    + + + + +ATC: fix_modify AtC fix_flux + + + + + + +
    + + +

    fix_modify AtC fix_flux

    syntax

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

    +

    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 transfer fix_flux temperature faceSet 10.0
    -

    +

    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.

    +

    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.

    +

    Only normal fluxes (Neumann data) can be prescribed.

    +

    related

    -see fix_modify AtC transfer unfix_flux

    +

    see fix_modify AtC unfix_flux

    +

    default

    -
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_fix_nodes.html b/doc/USER/atc/man_fix_nodes.html index 788e40d758..cf5c93590a 100644 --- a/doc/USER/atc/man_fix_nodes.html +++ b/doc/USER/atc/man_fix_nodes.html @@ -1,27 +1,56 @@ - - -ATC: fix_modify AtC transfer fix - - - -

    fix_modify AtC transfer fix

    + + + + +ATC: fix_modify AtC fix + + + + + + +
    + + +

    fix_modify AtC fix

    syntax

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

    +

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

    +

    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.

    +

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

    +

    restrictions

    -keyword 'all' reserved in nodeset name

    +

    keyword 'all' reserved in nodeset name

    +

    related

    -see fix_modify AtC transfer unfix

    +

    see fix_modify AtC unfix

    +

    default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_hardy_computes.html b/doc/USER/atc/man_hardy_computes.html index 5eba042b99..c16550742b 100644 --- a/doc/USER/atc/man_hardy_computes.html +++ b/doc/USER/atc/man_hardy_computes.html @@ -1,38 +1,67 @@ - - -ATC: fix_modify AtC transfer computes - - - -

    fix_modify AtC transfer computes

    + + + + +ATC: fix_modify AtC computes + + + + + + +
    + + +

    fix_modify AtC computes

    syntax

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

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

    +

    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
    -

    +

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

    +

    restrictions

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

    +

    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

    +

    See manual page for compute

    +

    default

    -No defaults exist for this command
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    No defaults exist for this command

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_hardy_fields.html b/doc/USER/atc/man_hardy_fields.html index fd23662f85..1f55fd5e37 100644 --- a/doc/USER/atc/man_hardy_fields.html +++ b/doc/USER/atc/man_hardy_fields.html @@ -1,46 +1,83 @@ - - -ATC: fix_modify AtC transfer fields - - - -

    fix_modify AtC transfer fields

    + + + + +ATC: fix_modify AtC fields + + + + + + +
    + + +

    fix_modify AtC fields

    syntax

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

    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 transfer fields add velocity temperature

    +

    fix_modify AtC fields add velocity temperature

    +

    description

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

    +

    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 AtC transfer, 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.

    +

    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 transfer gradients , fix_modify AtC transfer rates and fix_modify AtC transfer computes

    +

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

    +

    default

    -All fields are output by default
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    By default, no fields are output

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_hardy_gradients.html b/doc/USER/atc/man_hardy_gradients.html index caeb8b1749..708fecbca1 100644 --- a/doc/USER/atc/man_hardy_gradients.html +++ b/doc/USER/atc/man_hardy_gradients.html @@ -1,30 +1,57 @@ - - -ATC: fix_modify AtC transfer gradients - - - -

    fix_modify AtC transfer gradients

    + + + + +ATC: fix_modify AtC gradients + + + + + + +
    + + +

    fix_modify AtC gradients

    syntax

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

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

    +

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

    +

    description

    -Requests calculation and ouput of gradients of the fields from the Hardy 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 transfer atom_element_map )

    +

    Requests calculation and ouput 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 AtC transfer ( see fix atc command )

    +

    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 Mon Aug 17 09:35:16 2009 for ATC by  +

    No gradients are calculated by default

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_hardy_kernel.html b/doc/USER/atc/man_hardy_kernel.html index 20c9410e5c..3d81b367dd 100644 --- a/doc/USER/atc/man_hardy_kernel.html +++ b/doc/USER/atc/man_hardy_kernel.html @@ -1,36 +1,65 @@ - - + + + + ATC: fix_modify AtC kernel - - - -

    fix_modify AtC kernel

    + + + + + + +
    + + +

    fix_modify AtC kernel

    syntax

    -fix_modify AtC transfer kernel <type> <parameters> -

    +

    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 transfer kernel cell 1.0 1.0 1.0

    +

    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 transfer
    - For cylinder kernel types, cylindrical axis is assumed to be in z-direction
    - ( see fix atc command )

    +

    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

    -Default to the mesh based kernel
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    No default

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_hardy_on_the_fly.html b/doc/USER/atc/man_hardy_on_the_fly.html index 4d9645f1af..d140cf6840 100644 --- a/doc/USER/atc/man_hardy_on_the_fly.html +++ b/doc/USER/atc/man_hardy_on_the_fly.html @@ -1,34 +1,60 @@ - - -ATC: fix_modify AtC transfer on_the_fly - - - -

    fix_modify AtC transfer on_the_fly

    + + + + +ATC: fix_modify AtC on_the_fly + + + + + + +
    + + +

    fix_modify AtC on_the_fly

    syntax

    -fix_modify AtC transfer on_the_fly <bond | kernel> <optional on | off>
    +

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

    +

    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 and kernel atom-to-node matrices. If activated, will calculate elements of these 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 specified matrix. Can be deactivated using off flag.
    -

    +

    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 AtC transfer ( see fix atc command )

    +

    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 elements. If this allocation fails, on-the-fly is activated.
    -
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    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 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_hardy_rates.html b/doc/USER/atc/man_hardy_rates.html index f8d002d32f..ab0315cb65 100644 --- a/doc/USER/atc/man_hardy_rates.html +++ b/doc/USER/atc/man_hardy_rates.html @@ -1,31 +1,58 @@ - - -ATC: fix_modify AtC transfer rates - - - -

    fix_modify AtC transfer rates

    + + + + +ATC: fix_modify AtC rates + + + + + + +
    + + +

    fix_modify AtC rates

    syntax

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

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

    +

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

    +

    description

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

    +

    Requests calculation and ouput 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 AtC transfer ( see fix atc command )

    +

    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 Mon Aug 17 09:35:16 2009 for ATC by  +

    No rates are calculated by default

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_initial.html b/doc/USER/atc/man_initial.html index 73438c9252..c0a0be3852 100644 --- a/doc/USER/atc/man_initial.html +++ b/doc/USER/atc/man_initial.html @@ -1,25 +1,51 @@ - - -ATC: fix_modify AtC transfer initial - - - -

    fix_modify AtC transfer initial

    + + + + +ATC: fix_modify AtC initial + + + + + + +
    + + +

    fix_modify AtC initial

    syntax

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

    +

    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 transfer initial temperature groupNAME 10.

    +

    fix_modify atc initial temperature groupNAME 10.

    +

    description

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

    +

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

    +

    restrictions

    -keyword 'all' reserved in nodeset name

    -related

    -see fix_modify AtC transfer internal

    +

    keyword 'all' reserved in nodeset name

    +

    default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    none

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_internal_quadrature.html b/doc/USER/atc/man_internal_quadrature.html index beff89bddb..172187c298 100644 --- a/doc/USER/atc/man_internal_quadrature.html +++ b/doc/USER/atc/man_internal_quadrature.html @@ -1,23 +1,50 @@ - - -ATC: fix_modify AtC transfer internal_quadrature - - - -

    fix_modify AtC transfer internal_quadrature

    + + + + +ATC: fix_modify AtC internal_quadrature + + + + + + +
    + + +

    fix_modify AtC internal_quadrature

    syntax

    -fix_modify atc transfer internal_quadrature < on | off >

    +

    fix_modify atc internal_quadrature <on | off> [region]

    +

    examples

    - fix_modify atc transfer internal_quadrature off

    +

    fix_modify atc internal_quadrature off

    +

    description

    -Command 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.

    +

    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 Mon Aug 17 09:35:16 2009 for ATC by  +

    on

    +

    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_mesh_delete_elements.html b/doc/USER/atc/man_mesh_delete_elements.html index a4f025eedc..cc269c8e65 100644 --- a/doc/USER/atc/man_mesh_delete_elements.html +++ b/doc/USER/atc/man_mesh_delete_elements.html @@ -1,25 +1,50 @@ - - + + + + ATC: fix_modify AtC mesh delete_elements - - - -

    fix_modify AtC mesh delete_elements

    + + + + + + +
    + + +

    fix_modify AtC mesh delete_elements

    syntax

    -fix_modify AtC mesh delete_elements <element_set> -

    +

    fix_modify AtC mesh delete_elements <element_set>

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

    examples

    - fix_modify AtC delete_elements gap

    +

    fix_modify AtC delete_elements gap

    +

    description

    -Deletes a group of elements from the mesh.

    +

    Deletes a group of elements from the mesh.

    +

    restrictions

    -

    +

    related

    -

    +

    default

    -none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

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    +

    +
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    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_mesh_output.html b/doc/USER/atc/man_mesh_output.html index 5e336fb5ae..be1b4c194f 100644 --- a/doc/USER/atc/man_mesh_output.html +++ b/doc/USER/atc/man_mesh_output.html @@ -1,24 +1,49 @@ - - + + + + ATC: fix_modify AtC mesh output - - - -

    fix_modify AtC mesh output

    + + + + + + +
    + + +

    fix_modify AtC mesh output

    syntax

    -fix_modify AtC mesh output <file_prefix>

    +

    fix_modify AtC mesh output <file_prefix>

    +

    examples

    - fix_modify AtC mesh output meshData
    -

    +

    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.

    +

    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

    +

    none

    +

    related

    -

    +

    default

    -none
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    +

    +
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    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_read_restart.html b/doc/USER/atc/man_read_restart.html index c7c9a35f4f..96168fccc7 100644 --- a/doc/USER/atc/man_read_restart.html +++ b/doc/USER/atc/man_read_restart.html @@ -1,25 +1,51 @@ - - -ATC: fix_modify AtC transfer read_restart - - - -

    fix_modify AtC transfer read_restart

    + + + + +ATC: fix_modify AtC read_restart + + + + + + +
    + + +

    fix_modify AtC read_restart

    syntax

    -fix_modify AtC transfer read_restart [file_name]
    -

    +

    fix_modify AtC read_restart [file_name]
    +

    +

    examples

    - fix_modify AtC transfer read_restart ATC_state
    -

    +

    fix_modify AtC read_restart ATC_state
    +

    +

    description

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

    +

    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.

    +

    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 transfer write_restart

    +

    see write_restart fix_modify AtC write_restart

    +

    default

    -none
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    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_remove_source.html b/doc/USER/atc/man_remove_source.html index 7678d4ccef..d1d249eb76 100644 --- a/doc/USER/atc/man_remove_source.html +++ b/doc/USER/atc/man_remove_source.html @@ -1,25 +1,52 @@ - - -ATC: fix_modify AtC transfer remove_source - - - -

    fix_modify AtC transfer remove_source

    + + + + +ATC: fix_modify AtC remove_source + + + + + + +
    + + +

    fix_modify AtC remove_source

    syntax

    -fix_modify AtC transfer remove_source <field> <element_set> -

    +

    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 transfer remove_source temperature groupNAME

    +

    fix_modify atc remove_source temperature groupNAME

    +

    description

    -Remove a domain source.

    +

    Remove a domain source.

    +

    restrictions

    -keyword 'all' reserved in element_set name

    +

    keyword 'all' reserved in element_set name

    +

    related

    -see fix_modify AtC transfer source

    +

    see fix_modify AtC source

    +

    default

    -
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    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_source.html b/doc/USER/atc/man_source.html index d8070635c6..833b2a866f 100644 --- a/doc/USER/atc/man_source.html +++ b/doc/USER/atc/man_source.html @@ -1,25 +1,53 @@ - - -ATC: fix_modify AtC transfer source - - - -

    fix_modify AtC transfer source

    + + + + +ATC: fix_modify AtC source + + + + + + +
    + + +

    fix_modify AtC source

    syntax

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

    +

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

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

    examples

    - fix_modify atc transfer source temperature middle temporal_ramp 10. 0.

    +

    fix_modify atc source temperature middle temporal_ramp 10. 0.

    +

    description

    -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.

    +

    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.

    +

    restrictions

    -keyword 'all' reserved in element_set name

    +

    keyword 'all' reserved in element_set name

    +

    related

    -see fix_modify AtC transfer remove_source

    +

    see fix_modify AtC remove_source

    +

    default

    -none
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    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_time_filter.html b/doc/USER/atc/man_time_filter.html index 1d77773242..ec70fed871 100644 --- a/doc/USER/atc/man_time_filter.html +++ b/doc/USER/atc/man_time_filter.html @@ -1,29 +1,57 @@ - - -ATC: fix_modify AtC transfer filter - - - -

    fix_modify AtC transfer filter

    + + + + +ATC: fix_modify AtC filter + + + + + + +
    + + +

    fix_modify AtC filter

    syntax

    -fix_modify AtC transfer filter <on | off | equilibrate>
    +

    fix_modify AtC filter <on | off | equilibrate>
    +

    -

    +
  • on | off (keyword) = turns filter on or off
    +
    • +
  • equilibrate = runs dynamics without filtering but initializes filtered quantities
    • + +

    examples

    - fix_modify atc transfer filter on
    -

    +

    fix_modify atc transfer filter on
    +

    +

    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

    +

    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

    +

    only for be used with specific transfers: thermal, two_temperature

    +

    related

    -fix_modify AtC transfer filter scale
    - fix_modify AtC transfer equilibrium_start

    +

    fix_modify AtC filter scale
    + fix_modify AtC equilibrium_start

    +

    default

    -off
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  +

    off

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_unfix_flux.html b/doc/USER/atc/man_unfix_flux.html index cdea61b8fe..b2a19a7fd0 100644 --- a/doc/USER/atc/man_unfix_flux.html +++ b/doc/USER/atc/man_unfix_flux.html @@ -1,26 +1,52 @@ - - -ATC: fix_modify AtC transfer unfix_flux - - - -

    fix_modify AtC transfer unfix_flux

    + + + + +ATC: fix_modify AtC unfix_flux + + + + + + +
    + + +

    fix_modify AtC unfix_flux

    syntax

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

    +

    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 transfer unfix_flux temperature faceSet
    -

    +

    fix_modify atc unfix_flux temperature faceSet
    +

    +

    description

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

    +

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

    +

    restrictions

    -

    +

    related

    -see fix_modify AtC transfer unfix_flux

    +

    see fix_modify AtC unfix_flux

    +

    default

    -
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    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_unfix_nodes.html b/doc/USER/atc/man_unfix_nodes.html index 7a7d77c236..498d549f9e 100644 --- a/doc/USER/atc/man_unfix_nodes.html +++ b/doc/USER/atc/man_unfix_nodes.html @@ -1,25 +1,53 @@ - - -ATC: fix_modify AtC transfer unfix - - - -

    fix_modify AtC transfer unfix

    + + + + +ATC: fix_modify AtC unfix + + + + + + +
    + + +

    fix_modify AtC unfix

    syntax

    -fix_modify AtC transfer unfix <field> <nodeset> -

    +

    fix_modify AtC unfix <field> <nodeset>

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

    examples

    - fix_modify AtC transfer unfix temperature groupNAME

    +

    fix_modify AtC unfix temperature groupNAME

    +

    description

    -Removes constraint on field values for specified nodes.

    +

    Removes constraint on field values for specified nodes.

    +

    restrictions

    -keyword 'all' reserved in nodeset name

    +

    keyword 'all' reserved in nodeset name

    +

    related

    -see fix_modify AtC transfer fix

    +

    see fix_modify AtC fix

    +

    default

    -none
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    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  -doxygen 1.3.9.1
    +doxygen 1.6.1     diff --git a/doc/USER/atc/man_write_restart.html b/doc/USER/atc/man_write_restart.html index bd92e3e906..6ea350d5e8 100644 --- a/doc/USER/atc/man_write_restart.html +++ b/doc/USER/atc/man_write_restart.html @@ -1,25 +1,51 @@ - - -ATC: fix_modify AtC transfer write_restart - - - -

    fix_modify AtC transfer write_restart

    + + + + +ATC: fix_modify AtC write_restart + + + + + + +
    + + +

    fix_modify AtC write_restart

    syntax

    -fix_modify AtC transfer write_restart [file_name]
    -

    +

    fix_modify AtC write_restart [file_name]
    +

    +

    examples

    - fix_modify AtC transfer write_restart restart.mydata
    -

    +

    fix_modify AtC write_restart restart.mydata
    +

    +

    description

    -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.

    +

    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.

    +

    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.

    +

    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 read_restart fix_modify AtC transfer read_restart

    +

    see read_restart fix_modify AtC read_restart

    +

    default

    -none
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    +
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    +doxygen 1.6.1