+
fix_modify AtC output boundary_integral
-syntax
+fix_modify AtC output boundary_integral
+syntax
fix_modify AtC output boundary_integral [field] faceset [name]
- field (string) : name of hardy field
- name (string) : name of faceset
-examples
++examples
fix_modify AtC output boundary_integral stress faceset loop1
-description
++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
++restrictions
Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html index 16abc2593f..a74acda5e9 100644 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ b/doc/src/USER/atc/man_consistent_fe_initialization.html @@ -7,29 +7,43 @@ + +
+
fix_modify AtC consistent_fe_initialization
-syntax
+fix_modify AtC consistent_fe_initialization
+syntax
fix_modify AtC consistent_fe_initialization <on | off>
- <on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field
-examples
++examples
fix_modify atc consistent_fe_initialization on
-description
++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
++restrictions
Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes.
--related
--default
++related
++default
Default is off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html index da43a1d863..304b4bec66 100644 --- a/doc/src/USER/atc/man_contour_integral.html +++ b/doc/src/USER/atc/man_contour_integral.html @@ -7,32 +7,46 @@ + +
+
fix_modify AtC output contour_integral
-syntax
+fix_modify AtC output contour_integral
+syntax
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
++examples
fix_modify AtC output contour_integral stress faceset loop1
-description
++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
++restrictions
Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html index b63c07b327..2c42fa2d6a 100644 --- a/doc/src/USER/atc/man_control.html +++ b/doc/src/USER/atc/man_control.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC control
-syntax
+fix_modify AtC control
+syntax
fix_modify AtC control <physics_type> <solution_parameter>
-examples
++examples
fix_modify AtC control thermal max_iterations 10
fix_modify AtC control momentum tolerance 1.e-5
-description
++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
++restrictions
only for be used with specific controllers : thermal, momentum
They are ignored if a lumped solution is requested
-related
--default
++related
++default
max_iterations is the number of rows in the matrix
tolerance is 1.e-10
+
fix_modify AtC control momentum
-syntax
+fix_modify AtC control momentum
+syntax
fix_modify AtC control momentum none
fix_modify AtC control momentum rescale <frequency>
@@ -32,21 +46,21 @@ syntax
-examples
++examples
fix_modify AtC control momentum glc_velocity
fix_modify AtC control momentum flux faceset bndy_faces
-description
--restrictions
++description
++restrictions
only to be used with specific transfers : elastic
rescale not valid with time filtering activated
-related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html index 0f70c595cc..b6af089baf 100644 --- a/doc/src/USER/atc/man_control_thermal.html +++ b/doc/src/USER/atc/man_control_thermal.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC control thermal
-syntax
+fix_modify AtC control thermal
+syntax
fix_modify AtC control thermal <control_type> <optional_args>
- control_type (string) = none | rescale | hoover | flux
@@ -34,25 +48,25 @@ syntax - face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate
-examples
++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
++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
++restrictions
only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux)
rescale not valid with time filtering activated
-related
--default
++related
++default
none
rescale frequency is 1
flux boundary_integration_type is interpolate
+
fix_modify AtC control thermal correction_max_iterations
-syntax
+fix_modify AtC control thermal correction_max_iterations
+syntax
fix_modify AtC control thermal correction_max_iterations <max_iterations>
- max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers
-examples
++examples
fix_modify AtC control thermal correction_max_iterations 10
-description
++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
++restrictions
only for use with thermal physics using the fractional step method.
--related
--default
++related
++default
correction_max_iterations is 20
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html index b57a276e31..fd8986b19d 100644 --- a/doc/src/USER/atc/man_decomposition.html +++ b/doc/src/USER/atc/man_decomposition.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC decomposition
-syntax
+fix_modify AtC decomposition
+syntax
fix_modify AtC decomposition <type>
- <type> =
@@ -20,20 +34,20 @@ syntax distributed_memory: only owned nodal information on processor
-examples
++examples
fix_modify atc decomposition distributed_memory
-description
++description
Command for assigning the distribution of work and memory for parallel runs.
--restrictions
++restrictions
replicated_memory is appropriate for simulations were the number of nodes << number of atoms
--related
--default
++related
++default
replicated_memory
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html index bb9a4f72bd..ab00b5d45f 100644 --- a/doc/src/USER/atc/man_electron_integration.html +++ b/doc/src/USER/atc/man_electron_integration.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC extrinsic electron_integration
-syntax
+fix_modify AtC extrinsic electron_integration
+syntax
fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)>
-
@@ -20,20 +34,20 @@ syntax
- num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration
-examples
++examples
fix_modify AtC extrinsic electron_integration implicit
fix_modify AtC extrinsic electron_integration explicit 100
-description
++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
++restrictions
For use only with two_temperature type of AtC fix ( see fix atc command )
-default
++default
implicit
subcycle_steps = 1
+
fix_modify AtC equilibrium_start
-syntax
+fix_modify AtC equilibrium_start
+syntax
fix_modify AtC equilibrium_start <on|off>
--examples
++examples
fix_modify atc equilibrium_start on
-description
++description
Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.
--restrictions
++restrictions
only needed before filtering is begun
--related
++related
--default
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html index dca429e3b8..5b3b4315e1 100644 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ b/doc/src/USER/atc/man_extrinsic_exchange.html @@ -7,28 +7,42 @@ + +
+
fix_modify AtC extrinsic exchange
-syntax
+fix_modify AtC extrinsic exchange
+syntax
fix_modify AtC extrinsic exchange <on|off>
--examples
++examples
fix_modify AtC extrinsic exchange on
-description
++description
Switches energy exchange between the MD system and electron system on and off
--restrictions
++restrictions
Only valid for use with two_temperature type of AtC fix.
--related
++related
see fix atc command
--default
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html index d83821b867..aa1b6f6bb3 100644 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ b/doc/src/USER/atc/man_fe_md_boundary.html @@ -7,28 +7,42 @@ + +
+
fix_modify AtC fe_md_boundary
-syntax
+fix_modify AtC fe_md_boundary
+syntax
fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args]
--examples
++examples
fix_modify atc fe_md_boundary interpolate
-description
++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
++restrictions
If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.
--related
++related
see for how to specify the faceset name.
--default
++default
Interpolate.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html index 2abd84d6ce..3b6f0ddc34 100644 --- a/doc/src/USER/atc/man_fem_mesh.html +++ b/doc/src/USER/atc/man_fem_mesh.html @@ -3,21 +3,34 @@
fix_modify AtC fem create mesh
-syntax
+ ++ +
fix_modify AtC fem create mesh
+syntax
fix_modify AtC fem create mesh <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 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
++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
noneGenerated on Mon Aug 17 09:35:16 2009 for ATC by
1.3.9.1
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index bca799804f..68eb5ef370 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -7,33 +7,47 @@
+
++
fix_modify AtC filter scale
-syntax
+fix_modify AtC filter scale
+syntax
fix_modify AtC filter scale <scale>
- scale (real) = characteristic time scale of the filter
-examples
++examples
fix_modify AtC filter scale 10.0
-description
++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
++restrictions
only for be used with specific transfers: thermal, two_temperature
--related
++related
fix_modify AtC filter fix_modify AtC filter type
--default
++default
0.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html index 8b7d7ad58e..919dff505f 100644 --- a/doc/src/USER/atc/man_filter_type.html +++ b/doc/src/USER/atc/man_filter_type.html @@ -7,29 +7,43 @@ + +
+
fix_modify AtC filter type
-syntax
+fix_modify AtC filter type
+syntax
fix_modify AtC filter type <exponential | step | no_filter>
-examples
++examples
fix_modify AtC filter type exponential
-description
++description
Specifies the type of time filter used.
--restrictions
++restrictions
only for be used with specific transfers: thermal, two_temperature
--related
++related
fix_modify AtC filter fix_modify AtC filter scale
--default
++default
No default.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html index 0e14498ffe..9e82ded3de 100644 --- a/doc/src/USER/atc/man_fix_atc.html +++ b/doc/src/USER/atc/man_fix_atc.html @@ -7,12 +7,26 @@ + +
+
fix atc command
-syntax
+fix atc command
+syntax
fix <fixID> <group> atc <type> <parameter_file>
- fixID = name of fix @@ -26,15 +40,15 @@ syntax
- parameter_file = name of the file with material parameters.
note: Neither hardy nor field requires a parameter file
-examples
++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
++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:
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
++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
++related
fix_modify commands for setup:
-
@@ -231,8 +245,8 @@ related
- fix_modify AtC remove_molecule
Note: a set of example input files with the attendant material files are included with this package
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html index 46400e9103..a5b98d8c64 100644 --- a/doc/src/USER/atc/man_fix_flux.html +++ b/doc/src/USER/atc/man_fix_flux.html @@ -7,32 +7,46 @@ + +
+
fix_modify AtC fix_flux
-syntax
+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
++examples
fix_modify atc fix_flux temperature faceSet 10.0
-description
++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
++restrictions
Only normal fluxes (Neumann data) can be prescribed.
--related
++related
--default
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html index 4745e241c6..b8d20002b5 100644 --- a/doc/src/USER/atc/man_fix_nodes.html +++ b/doc/src/USER/atc/man_fix_nodes.html @@ -7,34 +7,48 @@ + +
+
fix_modify AtC fix
-syntax
+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
++examples
fix_modify AtC fix temperature groupNAME 10.
fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0
-description
++description
Creates a constraint on the values of the specified field at specified nodes.
--restrictions
++restrictions
keyword 'all' reserved in nodeset name
--related
++related
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html index e6fb1430a6..9c4ea9340d 100644 --- a/doc/src/USER/atc/man_hardy_computes.html +++ b/doc/src/USER/atc/man_hardy_computes.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC computes
-syntax
+fix_modify AtC computes
+syntax
fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number>
-
@@ -23,8 +37,8 @@ syntax
- volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions
-examples
++examples
compute virial all stress/atom
fix_modify AtC computes add virial volume
fix_modify AtC computes delete virial
@@ -32,20 +46,20 @@ examples
compute centrosymmetry all centro/atom
fix_modify AtC computes add centrosymmetry number
-description
++description
Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS
-restrictions
++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
++related
See manual page for compute
--default
++default
No defaults exist for this command
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html index c393bcba2a..79cbbb5d56 100644 --- a/doc/src/USER/atc/man_hardy_fields.html +++ b/doc/src/USER/atc/man_hardy_fields.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC fields
-syntax
+fix_modify AtC fields
+syntax
fix_modify AtC fields <all | none>
fix_modify AtC fields <add | delete> <list_of_fields>
-
-examples
++examples
fix_modify AtC fields add velocity temperature
-description
++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
++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
++related
See fix_modify AtC gradients , fix_modify AtC rates and fix_modify AtC computes
--default
++default
By default, no fields are output
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 12a80c2166..30016b591a 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC gradients
-syntax
+fix_modify AtC gradients
+syntax
fix_modify AtC gradients <add | delete> <list_of_fields>
-
@@ -21,21 +35,21 @@ syntax
- fields (keyword) =
gradients can be calculated for all fields listed in fix_modify AtC fields
-examples
++examples
fix_modify AtC gradients add temperature velocity stress
fix_modify AtC gradients delete velocity
-description
++description
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
++restrictions
Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++related
++default
No gradients are calculated by default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html index 6c8ddd9923..a37fdd22d9 100644 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ b/doc/src/USER/atc/man_hardy_kernel.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC kernel
-syntax
+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
@@ -28,22 +42,22 @@ syntax quartic_sphere = radius (double)
-examples
++examples
fix_modify AtC kernel cell 1.0 1.0 1.0
fix_modify AtC kernel quartic_sphere 10.0
-description
--restrictions
++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
++related
++default
No default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html index bc2d71a17b..043926d555 100644 --- a/doc/src/USER/atc/man_hardy_on_the_fly.html +++ b/doc/src/USER/atc/man_hardy_on_the_fly.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC on_the_fly
-syntax
+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
-examples
++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
++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
++restrictions
Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++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.
+
fix_modify AtC rates
-syntax
+fix_modify AtC rates
+syntax
fix_modify AtC rates <add | delete> <list_of_fields>
-
@@ -21,22 +35,22 @@ syntax
- fields (keyword) =
rates can be calculated for all fields listed in fix_modify AtC fields
-examples
++examples
fix_modify AtC rates add temperature velocity stress
fix_modify AtC rates delete stress
-description
++description
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
++restrictions
Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++related
++default
No rates are calculated by default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html index 539d8afd59..429bd25af6 100644 --- a/doc/src/USER/atc/man_initial.html +++ b/doc/src/USER/atc/man_initial.html @@ -7,29 +7,43 @@ + +
+
fix_modify AtC initial
-syntax
+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
++examples
fix_modify atc initial temperature groupNAME 10.
-description
++description
Sets the initial values for the specified field at the specified nodes.
--restrictions
++restrictions
keyword 'all' reserved in nodeset name
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html index 5a8704c46f..2f2987ec68 100644 --- a/doc/src/USER/atc/man_internal_atom_integrate.html +++ b/doc/src/USER/atc/man_internal_atom_integrate.html @@ -7,18 +7,32 @@ + +
+
fix_modify AtC internal_atom_integrate
-syntax
+fix_modify AtC internal_atom_integrate
+syntax
fix_modify AtC internal_atom_integrate <on | off> fix_modify AtC internal_atom_integrate on
-description
++description
Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms.
--default
++default
on for coupling methods, off for post-processors off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html index bf1cb007f6..dbd1d1e026 100644 --- a/doc/src/USER/atc/man_internal_element_set.html +++ b/doc/src/USER/atc/man_internal_element_set.html @@ -7,30 +7,44 @@ + +
+
fix_modify AtC internal_element_set
-syntax
+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
++examples
fix_modify AtC internal_element_set myElementSet fix_modify AtC internal_element_set off
-description
++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
++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
++related
see atom_element_map_type and boundary
--default
++default
off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html index 8ad3399e86..1a36ab4606 100644 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ b/doc/src/USER/atc/man_internal_quadrature.html @@ -7,28 +7,42 @@ + +
+
fix_modify AtC internal_quadrature
-syntax
+fix_modify AtC internal_quadrature
+syntax
fix_modify atc internal_quadrature <on | off> [region]
--examples
++examples
fix_modify atc internal_quadrature off
-description
++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
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
++restrictions
++related
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html index e2702cd9fc..f87735b38b 100644 --- a/doc/src/USER/atc/man_kernel_function.html +++ b/doc/src/USER/atc/man_kernel_function.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC kernel
-syntax
+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
@@ -28,21 +42,21 @@ syntax quartic_sphere = radius (double)
-examples
++examples
fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0
--description
--restrictions
++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
++related
++default
No default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html index e435504233..8b729f567b 100644 --- a/doc/src/USER/atc/man_localized_lambda.html +++ b/doc/src/USER/atc/man_localized_lambda.html @@ -7,26 +7,40 @@ + +
+
fix_modify AtC control localized_lambda
-syntax
+fix_modify AtC control localized_lambda
+syntax
fix_modify AtC control localized_lambda <on|off>
--examples
++examples
fix_modify atc control localized_lambda on
-description
++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
++restrictions
++related
++default
Default is off.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_lumped_lambda_solve.html b/doc/src/USER/atc/man_lumped_lambda_solve.html index 43eee362e2..a38edfff09 100644 --- a/doc/src/USER/atc/man_lumped_lambda_solve.html +++ b/doc/src/USER/atc/man_lumped_lambda_solve.html @@ -7,26 +7,40 @@ + +
+
fix_modify AtC control lumped_lambda_solve
-syntax
+fix_modify AtC control lumped_lambda_solve
+syntax
fix_modify AtC control lumped_lambda_solve <on|off>
--examples
++examples
fix_modify atc control lumped_lambda_solve on
-description
++description
Command to use or not use lumped matrix for lambda solve
--restrictions
--related
--default
++restrictions
++related
++default
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+
fix_modify AtC control mask_direction
-syntax
+fix_modify AtC control mask_direction
+syntax
fix_modify AtC control mask_direction <direction> <on|off>
--examples
++examples
fix_modify atc control mask_direction 0 on
-description
++description
Command to mask out certain dimensions from the atomic regulator
--restrictions
--related
--default
++restrictions
++related
++default
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+
fix_modify AtC mass_matrix
-syntax
+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
++examples
fix_modify atc mass_matrix fe
-description
++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
++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
++related
++default
Default is off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html index 8460b04a82..956642bd9d 100644 --- a/doc/src/USER/atc/man_material.html +++ b/doc/src/USER/atc/man_material.html @@ -7,27 +7,41 @@ + +
+
fix_modify AtC material
-syntax
+fix_modify AtC material
+syntax
fix_modify AtC material [elementset_name] [material_id]
-examples
++examples
fix_modify AtC material gap_region 2
-description
++description
Sets the material model in elementset_name to be of type material_id.
--restrictions
++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
++related
++default
All elements default to the first material in the material file.
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+
fix_modify AtC mesh add_to_nodeset
-syntax
+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
++examples
fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12
-description
++description
Command to add nodes to an already existing FE nodeset.
--restrictions
--related
--default
++restrictions
++related
++default
Coordinates are assumed to be in lattice units.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html index c128d03916..d4ea2be031 100644 --- a/doc/src/USER/atc/man_mesh_create.html +++ b/doc/src/USER/atc/man_mesh_create.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC mesh create
-syntax
+fix_modify AtC mesh create
+syntax
fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
-
@@ -20,21 +34,21 @@ syntax
- region-id = id of region that is to be meshed
- f p p = periodicity flags for x, y, z
-examples
++examples
fix_modify AtC mesh create 10 1 1 feRegion p p p
-description
++description
Creates a uniform mesh in a rectangular region
--restrictions
++restrictions
Creates only uniform rectangular grids in a rectangular region
--related
++related
fix_modify AtC mesh quadrature
--default
++default
When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style.
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+
fix_modify AtC mesh create_elementset
-syntax
+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
++examples
fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100
-description
++description
Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations.
--restrictions
++restrictions
Only viable for rectangular grids.
--related
--default
++related
++default
Coordinates are assumed to be in lattice units.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_create_faceset_box.html b/doc/src/USER/atc/man_mesh_create_faceset_box.html index ddbeb7eccf..a406cace8b 100644 --- a/doc/src/USER/atc/man_mesh_create_faceset_box.html +++ b/doc/src/USER/atc/man_mesh_create_faceset_box.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC mesh create_faceset box
-syntax
+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 @@ -20,19 +34,19 @@ syntax
- <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
++examples
fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out
-description
++description
Command to assign an id to a set of FE faces.
--restrictions
++restrictions
Only viable for rectangular grids.
--related
--default
++related
++default
The default options are units = lattice and the use of outer faces
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+
fix_modify AtC mesh create_faceset plane
-syntax
+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 @@ -20,19 +34,19 @@ syntax
- <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
++examples
fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0
-description
++description
Command to assign an id to a set of FE faces.
--restrictions
++restrictions
Only viable for rectangular grids.
--related
--default
++related
++default
The default option is units = lattice.
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+
fix_modify AtC mesh create_nodeset
-syntax
+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
++examples
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
-description
++description
Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions.
--restrictions
--related
--default
++restrictions
++related
++default
Coordinates are assumed to be in lattice units.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html index d43fe91565..071b67c1e1 100644 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ b/doc/src/USER/atc/man_mesh_delete_elements.html @@ -7,28 +7,42 @@ + +
+
fix_modify AtC mesh delete_elements
-syntax
+fix_modify AtC mesh delete_elements
+syntax
fix_modify AtC mesh delete_elements <element_set>
- <element_set> = name of an element set
-examples
++examples
fix_modify AtC delete_elements gap
-description
++description
Deletes a group of elements from the mesh.
--restrictions
--related
--default
++restrictions
++related
++default
none
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+
fix_modify AtC mesh nodeset_to_elementset
-syntax
+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
++examples
fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min
-description
++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
++restrictions
None.
--related
--default
++related
++default
Unless specified, the maximal element set is created
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+
fix_modify AtC mesh output
-syntax
+fix_modify AtC mesh output
+syntax
fix_modify AtC mesh output <file_prefix>
--examples
++examples
fix_modify AtC mesh output meshData
-description
++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
++restrictions
none
--related
--default
++related
++default
none
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+
fix_modify AtC mesh quadrature
-syntax
+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
++examples
fix_modify AtC mesh quadrature face
-description
++description
(Re-)assigns the quadrature style for the existing mesh.
--restrictions
--related
++restrictions
++related
--default
++default
none
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+
fix_modify AtC mesh read
-syntax
+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
++examples
fix_modify AtC mesh read myComponent.mesh p p p
fix_modify AtC mesh read myOtherComponent.exo
-description
++description
Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed.
--restrictions
--related
--default
++restrictions
++related
++default
periodicity flags are false by default
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+
fix_modify AtC mesh write
-syntax
+fix_modify AtC mesh write
+syntax
fix_modify AtC mesh write <filename>
- filename = name of file to write mesh
-examples
++examples
fix_modify AtC mesh write myMesh.mesh
-description
++description
Writes a mesh to a text file.
--restrictions
--related
--default
++restrictions
++related
++default
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+
fix_modify AtC time_integration (momentum)
-syntax
+fix_modify AtC time_integration (momentum)
+syntax
fix_modify AtC time_integration <descriptor>
-
@@ -21,24 +35,24 @@ syntax
various time integration methods for the finite elements
-description
++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
++examples
fix_modify atc time_integration verlet
fix_modify atc time_integration fractional_step
-description
--related
++description
++related
see fix atc command
--default
++default
none
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+
fix_modify AtC output
-syntax
+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 @@ -25,23 +39,23 @@ syntax tensor_components = outputs tensor as scalar components (use this for Paraview)
-examples
++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
++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
++restrictions
++related
see fix atc command
--default
++default
no default format output indexed by time
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+
fix_modify AtC output elementset
-syntax
+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
++examples
fix_modify AtC output eset1 mass_density
-description
++description
Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file.
--restrictions
--related
++restrictions
++related
see fix atc command
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html index 3005057d0d..90536b4cb9 100644 --- a/doc/src/USER/atc/man_output_nodeset.html +++ b/doc/src/USER/atc/man_output_nodeset.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC output nodeset
-syntax
+fix_modify AtC output nodeset
+syntax
fix_modify AtC output nodeset <nodeset_name> <operation>
- nodeset_name (string) = name of nodeset to be operated on @@ -20,20 +34,20 @@ syntax sum = creates nodal sum over nodes in specified nodeset
-examples
++examples
fix_modify AtC output nodeset nset1 sum
-description
++description
Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file.
--restrictions
--related
++restrictions
++related
see fix atc command
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html index 0393b29d56..3c6d65432c 100644 --- a/doc/src/USER/atc/man_pair_interactions.html +++ b/doc/src/USER/atc/man_pair_interactions.html @@ -7,28 +7,42 @@ + +
+
fix_modify AtC pair_interactions/bond_interactions
-syntax
+fix_modify AtC pair_interactions/bond_interactions
+syntax
fix_modify AtC pair_interactions <on|off>
fix_modify AtC bond_interactions <on|off>
-examples
++examples
fix_modify AtC bond_interactions on
-description
++description
include bonds and/or pairs in the stress and heat flux computations
--restrictions
--related
--default
++restrictions
++related
++default
pair interactions: on, bond interactions: off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html index 52022222f1..2aa4be52a5 100644 --- a/doc/src/USER/atc/man_poisson_solver.html +++ b/doc/src/USER/atc/man_poisson_solver.html @@ -7,31 +7,45 @@ + +
+
fix_modify AtC poisson_solver
-syntax
+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
++examples
fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p
-description
++description
Creates a uniform mesh in a rectangular region
--restrictions
++restrictions
creates only uniform rectangular grids in a rectangular region
--related
--default
++related
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html index b6da026bc8..1e7c0be0e8 100644 --- a/doc/src/USER/atc/man_read_restart.html +++ b/doc/src/USER/atc/man_read_restart.html @@ -7,29 +7,43 @@ + +
+
fix_modify AtC read_restart
-syntax
+fix_modify AtC read_restart
+syntax
fix_modify AtC read_restart [file_name]
-examples
++examples
fix_modify AtC read_restart ATC_state
-description
++description
Reads the current state of the fields from a named text-based restart file.
--restrictions
++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
++related
see write_restart fix_modify AtC write_restart
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html index 0e288c9bee..0a850dcac3 100644 --- a/doc/src/USER/atc/man_remove_molecule.html +++ b/doc/src/USER/atc/man_remove_molecule.html @@ -7,32 +7,46 @@ + +
+
fix_modify AtC remove_molecule
-syntax
+fix_modify AtC remove_molecule
+syntax
fix_modify_AtC remove_molecule <TAG>
- <TAG> = tag for tracking a molecule type
-examples
++examples
fix_modify AtC remove_molecule water
-description
++description
Removes tag designated for tracking a specified set of molecules.
-restrictions
--related
--default
++restrictions
++related
++default
No defaults for this command.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html index 837a2a94e4..f550e2d024 100644 --- a/doc/src/USER/atc/man_remove_source.html +++ b/doc/src/USER/atc/man_remove_source.html @@ -7,31 +7,45 @@ + +
+
fix_modify AtC remove_source
-syntax
+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
++examples
fix_modify atc remove_source temperature groupNAME
-description
++description
Remove a domain source.
--restrictions
++restrictions
keyword 'all' reserved in element_set name
--related
++related
--default
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html index 0fc06d1cf9..ad563fcd79 100644 --- a/doc/src/USER/atc/man_remove_species.html +++ b/doc/src/USER/atc/man_remove_species.html @@ -7,32 +7,46 @@ + +
+
fix_modify AtC remove_species
-syntax
+fix_modify AtC remove_species
+syntax
fix_modify_AtC delete_species <TAG>
- <TAG> = tag for tracking a species
-examples
++examples
fix_modify AtC remove_species gold
-description
++description
Removes tag designated for tracking a specified species.
-restrictions
--related
--default
++restrictions
++related
++default
No defaults for this command.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html index bc9ca16806..4262ce7b4a 100644 --- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html +++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html @@ -7,27 +7,41 @@ + +
+
fix_modify AtC reset_atomic_reference_positions
-syntax
+fix_modify AtC reset_atomic_reference_positions
+syntax
fix_modify AtC reset_atomic_reference_positions
--examples
++examples
fix_modify atc reset_atomic_reference_positions
-description
++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
++restrictions
-related
++related
-default
++default
Default is off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html index a20cf9d0bf..28a9559900 100644 --- a/doc/src/USER/atc/man_reset_time.html +++ b/doc/src/USER/atc/man_reset_time.html @@ -7,43 +7,57 @@ + +
+
fix_modify AtC reset_time
-syntax
+fix_modify AtC reset_time
+syntax
fix_modify AtC reset_time
--examples
++examples
fix_modify atc reset_time 0.0
-description
++description
Resets the simulation time counter.
--restrictions
--related
--default
--syntax
++restrictions
++related
++default
++syntax
fix_modify AtC kernel_bandwidth
--examples
++examples
fix_modify atc reset_time 8
-description
++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
++restrictions
Only is used if kernel functions are being used.
--related
--default
++related
++default
Number of sample locations.
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html index ba2544edc4..988a2cac50 100644 --- a/doc/src/USER/atc/man_sample_frequency.html +++ b/doc/src/USER/atc/man_sample_frequency.html @@ -7,30 +7,44 @@ + +
+
fix_modify AtC sample_frequency
-syntax
+fix_modify AtC sample_frequency
+syntax
fix_modify AtC sample_frequency [freq]
- freq (int) : frequency to sample field in number of steps
-examples
++examples
fix_modify AtC sample_frequency 10
-description
++description
Specifies a frequency at which fields are computed for the case where time filters are being applied.
-restrictions
++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
++related
-default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html index 993d9948d8..6543a6458a 100644 --- a/doc/src/USER/atc/man_set.html +++ b/doc/src/USER/atc/man_set.html @@ -7,34 +7,48 @@ + +
+
fix_modify AtC set
-syntax
+fix_modify AtC set
+syntax
fix_modify AtC set reference_potential_energy <value_or_filename(optional)>
- value (double) : optional user specified zero point for PE in native LAMMPS energy units
- filename (string) : optional user specified string for file of nodal PE values to be read-in
-examples
++examples
fix_modify AtC set reference_potential_energy
fix_modify AtC set reference_potential_energy -0.05
fix_modify AtC set reference_potential_energy myPEvalues
-description
++description
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.
--restrictions
++restrictions
Must be used with the hardy/field type of AtC fix ( see fix atc command )
--related
--default
++related
++default
Defaults to lammps zero point i.e. isolated atoms
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html index 81cb7cee4a..5b8f47f483 100644 --- a/doc/src/USER/atc/man_source.html +++ b/doc/src/USER/atc/man_source.html @@ -7,31 +7,45 @@ + +
+
fix_modify AtC source
-syntax
+fix_modify AtC source
+syntax
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
++examples
fix_modify atc source temperature middle temporal_ramp 10. 0.
-description
++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.
--restrictions
++restrictions
keyword 'all' reserved in element_set name
--related
++related
see fix_modify AtC remove_source
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html index 80b66edb80..3ce3342458 100644 --- a/doc/src/USER/atc/man_source_integration.html +++ b/doc/src/USER/atc/man_source_integration.html @@ -7,24 +7,38 @@ + +
+
fix_modify AtC source_integration
-syntax
+fix_modify AtC source_integration
+syntax
fix_modify AtC source_integration < fe | atom>
--examples
++examples
fix_modify atc source_integration atom
-description
--restrictions
--related
--default
++description
++restrictions
++related
++default
Default is fe
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html index 18f89798cc..f7d212cad2 100644 --- a/doc/src/USER/atc/man_temperature_definition.html +++ b/doc/src/USER/atc/man_temperature_definition.html @@ -7,25 +7,39 @@ + +
+
fix_modify AtC temperature_definition
-syntax
+fix_modify AtC temperature_definition
+syntax
fix_modify AtC temperature_definition <kinetic|total>
--examples
++examples
fix_modify atc temperature_definition kinetic
-description
++description
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.
--restrictions
++restrictions
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.
--default
++default
kinetic
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html index 8cceba845d..c9205550e9 100644 --- a/doc/src/USER/atc/man_thermal_time_integration.html +++ b/doc/src/USER/atc/man_thermal_time_integration.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC time_integration (thermal)
-syntax
+fix_modify AtC time_integration (thermal)
+syntax
fix_modify AtC time_integration <descriptor>
-
@@ -21,23 +35,23 @@ syntax
various time integration methods for the finite elements
-description
++description
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
-examples
++examples
fix_modify atc time_integration gear
fix_modify atc time_integration fractional_step
-description
--related
++description
++related
see fix atc command
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html index d75dc0703f..02b8bcabaa 100644 --- a/doc/src/USER/atc/man_time_filter.html +++ b/doc/src/USER/atc/man_time_filter.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC filter
-syntax
+fix_modify AtC filter
+syntax
fix_modify AtC filter <on | off | equilibrate>
-
@@ -20,22 +34,22 @@ syntax
- equilibrate = runs dynamics without filtering but initializes filtered quantities
-examples
++examples
fix_modify atc transfer filter on
-description
++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
++restrictions
only for be used with specific transfers: thermal, two_temperature
--related
++related
fix_modify AtC filter scale
fix_modify AtC equilibrium_start
-default
++default
off
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html index c9b13d4094..d77cf879c4 100644 --- a/doc/src/USER/atc/man_track_displacement.html +++ b/doc/src/USER/atc/man_track_displacement.html @@ -7,26 +7,40 @@ + +
+
fix_modify AtC track_displacement
-syntax
+fix_modify AtC track_displacement
+syntax
fix_modify AtC track_displacement <on/off>
-examples
++examples
fix_modify atc track_displacement on
-description
++description
Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.
--restrictions
++restrictions
Some constitutive models require the displacement field
--default
++default
on
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html index 786a3f243a..76d24653f1 100644 --- a/doc/src/USER/atc/man_unfix_flux.html +++ b/doc/src/USER/atc/man_unfix_flux.html @@ -7,31 +7,45 @@ + +
+
fix_modify AtC unfix_flux
-syntax
+fix_modify AtC unfix_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
++examples
fix_modify atc unfix_flux temperature faceSet
-description
++description
Command for removing prescribed normal fluxes e.g. heat_flux, stress.
--restrictions
--related
++restrictions
++related
--default
++default
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html index 08266b4012..4ef1460138 100644 --- a/doc/src/USER/atc/man_unfix_nodes.html +++ b/doc/src/USER/atc/man_unfix_nodes.html @@ -7,31 +7,45 @@ + +
+
fix_modify AtC unfix
-syntax
+fix_modify AtC unfix
+syntax
fix_modify AtC unfix <field> <nodeset>
- <field> = field name valid for type of physics
- <nodeset> = name of set of nodes
-examples
++examples
fix_modify AtC unfix temperature groupNAME
-description
++description
Removes constraint on field values for specified nodes.
--restrictions
++restrictions
keyword 'all' reserved in nodeset name
--related
++related
--default
++default
none
Generated on 21 Aug 2013 for ATC by diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html index c91a51487c..864b9e43f9 100644 --- a/doc/src/USER/atc/man_write_atom_weights.html +++ b/doc/src/USER/atc/man_write_atom_weights.html @@ -7,12 +7,26 @@ + +
+
fix_modify AtC write_atom_weights
-syntax
+fix_modify AtC write_atom_weights
+syntax
fix_modify AtC write_atom_weights <filename> <frequency>
- <filename> = name of file that atomic weights are written to
@@ -20,19 +34,19 @@ syntax - <frequency> = how often writes will occur
-examples
++examples
fix_modify atc write_atom_weights atm_wt_file.txt 10
-description
++description
Command for writing the values of atomic weights to a specified file.
--restrictions
--related
--default
++restrictions
++related
++default
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+
fix_modify AtC write_restart
-syntax
+fix_modify AtC write_restart
+syntax
fix_modify AtC write_restart [file_name]
-examples
++examples
fix_modify AtC write_restart restart.mydata
-description
++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.
--restrictions
++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
++related
see read_restart fix_modify AtC read_restart
--default
++default
none
Generated on 21 Aug 2013 for ATC by