7.10. Input Output Region

This section is referenced in the following other sections

7.10.1. Input_Output Region

Scope

Fuego Procedure

Summary

Example:

BEGIN INPUT TRANSFER model_name
   USE FINITE ELEMENT MODEL fred
   START TIME       is 0
   OFFSET TIME      is 1
   PERIODICITY TIME is 10
END INPUT TRANSFER model_name

begin Input_Output Region Parameter_block_name

   Create Element Field Field_name Of Type {asym_tensor_03 | complex | full_tensor_22 | full_tensor_36 | integer | long_integer | matrix_22 | matrix_33 | real | sym_tensor_21 | sym_tensor_31 | sym_tensor_33 | unsigned_integer | unsigned_integer_64 | vector_2d | vector_3d} And Dimension Dimension [ Value {=} Number...  ]

   Create Nodal Field Field_name Of Type {asym_tensor_03 | complex | full_tensor_22 | full_tensor_36 | integer | long_integer | matrix_22 | matrix_33 | real | sym_tensor_21 | sym_tensor_31 | sym_tensor_33 | unsigned_integer | unsigned_integer_64 | vector_2d | vector_3d} And Dimension Dimension [ Value {=} Number...  ]

   Fixed Time [ {=} Fixed_time  ]

   Offset Time {=} Period_offset_time

   Periodicity Time {=} Periodicity_time

   Start Time {=} Start_time

   Time Interpolation Method {=} {closest | linear}

   Timestep Adjustment Interval {=} Nsteps

   Use Finite Element Model ModelName [ Model Coordinates Are Nodal_variable_name  ]

   begin Heartbeat Label
   end

   begin Heartbeat Output Label
   end

   begin History Output Label
   end

   begin Restart Data Label
   end

   begin Results Output Label
   end

end Input_Output Region Parameter_block_name

7.10.1.1. Line Commands

Create Element Field

Syntax: Create Element Field Field_name Of Type {asym_tensor_03 | complex | full_tensor_22 | full_tensor_36 | integer | long_integer | matrix_22 | matrix_33 | real | sym_tensor_21 | sym_tensor_31 | sym_tensor_33 | unsigned_integer | unsigned_integer_64 | vector_2d | vector_3d} And Dimension Dimension [ Value {=} Number… ]
Summary: Creates a Element Field name field_name on the region.

Parameter	Value	Default
Field_name	string	–
Option	{asym_tensor_03 \| complex \| full_tensor_22 \| full_tensor_36 \| integer \| long_integer \| matrix_22 \| matrix_33 \| real \| sym_tensor_21 \| sym_tensor_31 \| sym_tensor_33 \| unsigned_integer \| unsigned_integer_64 \| vector_2d \| vector_3d}	–
Dimension	integer	–

Create Nodal Field

Syntax: Create Nodal Field Field_name Of Type {asym_tensor_03 | complex | full_tensor_22 | full_tensor_36 | integer | long_integer | matrix_22 | matrix_33 | real | sym_tensor_21 | sym_tensor_31 | sym_tensor_33 | unsigned_integer | unsigned_integer_64 | vector_2d | vector_3d} And Dimension Dimension [ Value {=} Number… ]
Summary: Creates a Nodal Field name field_name on the region.

Parameter	Value	Default
Field_name	string	–
Option	{asym_tensor_03 \| complex \| full_tensor_22 \| full_tensor_36 \| integer \| long_integer \| matrix_22 \| matrix_33 \| real \| sym_tensor_21 \| sym_tensor_31 \| sym_tensor_33 \| unsigned_integer \| unsigned_integer_64 \| vector_2d \| vector_3d}	–
Dimension	integer	–

Fixed Time

Syntax

Fixed Time [ {=} Fixed_time ]

Summary

The line specifies that the database will be read for a single, fixed time. Specifying the actual time is optional. If the time is not specified, the final time plane in the database will be read.

NOTE:

This option takes precedence over the periodic specifications given by START TIME, PERIODICITY TIME, and OFFSET TIME.

if FIXED TIME is specified then
   if FIXED TIME value is given then (eg., FIXED TIME is 1.)
      DATABASE TIME = FIXED TIME
   else (eg., FIXED TIME)
      DATABASE TIME = last time in database
else
   if PERIODICITY TIME greater than 0 then
      if APPLICATION TIME less than or equal to START TIME then
         DATABASE TIME = APPLICATION TIME
      else
         DATABASE TIME = START TIME +
          (APPLICATION TIME - START TIME) modulo PERIODICITY TIME
   else
      DATABASE TIME = APPLICATION TIME
   now add OFFSET TIME to the computed DATABASE TIME

Offset Time

Syntax

Offset Time {=} Period_offset_time

Summary

This value is added to the application time to determine what database time slice to input. If OFFSET TIME were 15 than at application time 0 database time slice 15 would be read from the file and used for the initial values. At application time 1, database time slice 16 would be read.

NOTES:

The OFFSET TIME is added in after the START TIME and PERIODICITY TIME are used.
The FIXED TIME option takes precedence over this option.

if FIXED TIME is specified then
   if FIXED TIME value is given then (eg., FIXED TIME is 1.)
      DATABASE TIME = FIXED TIME
   else (eg., FIXED TIME)
      DATABASE TIME = last time in database
else
   if PERIODICITY TIME greater than 0 then
      if APPLICATION TIME less than or equal to START TIME then
         DATABASE TIME = APPLICATION TIME
      else
         DATABASE TIME = START TIME +
          (APPLICATION TIME - START TIME) modulo PERIODICITY TIME
   else
      DATABASE TIME = APPLICATION TIME
   now add OFFSET TIME to the computed DATABASE TIME

Parameter	Value	Default
{=}	{= \| are \| is}	–
Period_offset_time	real	–

Periodicity Time

Syntax

Periodicity Time {=} Periodicity_time

Summary

START TIME and PERIODICITY TIME taken together give the time frame from the input database to use to initialize the application values. If START TIME is 25 and PERIODICITY TIME is 10, then time slices from 25 to 35 will be used over and over again as the application time runs from 0 to whatever. In general

DATABASE TIME is (APPLICATION TIME - START TIME) modulo PERIODICITY TIME

after the application time reaches the START TIME.

NOTES:

The OFFSET TIME is added in after the START TIME and PERIODICITY TIME are used.
The FIXED TIME option takes precedence over this option.

if FIXED TIME is specified then
   if FIXED TIME value is given then (eg., FIXED TIME is 1.)
      DATABASE TIME = FIXED TIME
   else (eg., FIXED TIME)
      DATABASE TIME = last time in database
else
   if PERIODICITY TIME greater than 0 then
      if APPLICATION TIME less than or equal to START TIME then
         DATABASE TIME = APPLICATION TIME
      else
         DATABASE TIME = START TIME +
          (APPLICATION TIME - START TIME) modulo PERIODICITY TIME
   else
      DATABASE TIME = APPLICATION TIME
   now add OFFSET TIME to the computed DATABASE TIME

Parameter	Value	Default
{=}	{= \| are \| is}	–
Periodicity_time	real	–

Start Time

Syntax

Start Time {=} Start_time

Summary

The time in which to start applying PERIODICITY TIME. If PERIODICITY TIME is not specified then START TIME is ignored.

NOTES:

The OFFSET TIME is added in after the START TIME and PERIODICITY TIME are used.
The FIXED TIME option takes precedence over this option.

if FIXED TIME is specified then
   if FIXED TIME value is given then (eg., FIXED TIME is 1.)
      DATABASE TIME = FIXED TIME
   else (eg., FIXED TIME)
      DATABASE TIME = last time in database
else
   if PERIODICITY TIME greater than 0 then
      if APPLICATION TIME less than or equal to START TIME then
         DATABASE TIME = APPLICATION TIME
      else
         DATABASE TIME = START TIME +
          (APPLICATION TIME - START TIME) modulo PERIODICITY TIME
   else
      DATABASE TIME = APPLICATION TIME
   now add OFFSET TIME to the computed DATABASE TIME

Parameter	Value	Default
{=}	{= \| are \| is}	–
Start_time	real	–

Time Interpolation Method

Syntax: Time Interpolation Method {=} {closest | linear}
Summary: This line specifies how interpolation in time in the database will be handled. If linear (the default option) is specified, quantities at a given point are linearly interpolated from the bounding known time points. If the closest option is selected, then the closest known time point will be taken.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Method	{closest \| linear}	–

Timestep Adjustment Interval

Syntax: Timestep Adjustment Interval {=} Nsteps
Summary: Specify the number of steps to ‘look ahead’ and adjust the timestep to ensure that the specified output times or simulation end time will be hit ‘exactly’.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Nsteps	integer	–

Use Finite Element Model

Syntax: Use Finite Element Model ModelName [ Model Coordinates Are Nodal_variable_name ]
Summary: Associates a predefined finite element model with this region.

Parameter	Value	Default
ModelName	string	–

7.10.2. Results Output

Scope: Average Region, Fuego Region, Input_Output Region, Particle Region
Summary: Describes the location and type of the output stream used for outputting results for the enclosing region.

begin Results Output Label

   Additional Steps {=} List_of_steps...

   Additional Times {=} List_of_times...

   At Step n {increment | interval} {=} m

   At Time Dt1 {increment | interval} {=} Dt2

   Auto Output {all | element | global | nodal} User Defined Variables [ In UserOutputResultsList...  ]

   Auto Output {all | element | global | nodal} Variables

   Component Separator Character {=} Separator

   Database Name {=} StreamName

   Database Type {=} {catalyst | catalyst_exodus | cgns | dof | dof_exodus | exodus | exodusii | exonull | generated | genesis | null | parallel_exodus | textmesh}

   Edge VariableList...

   Element VariableList...

   Enable Large Ids

   Exclude {=} [ ElementBlockList...  ]

   Exists {=} {abort | add_suffix | append | overwrite}

   Face VariableList...

   Flush Interval {=} Option

   Global VariableList...

   Include {=} [ ElementBlockList...  ]

   Nodal VariableList...

   Node VariableList...

   Nodeset VariableList...

   Output Mesh {=} {exposed surface | refined | unrefined}

   Output On Signal {=} {sigabrt | sigalrm | sigfpe | sighup | sigill | sigint | sigkill | sigpipe | sigquit | sigsegv | sigterm | sigusr1 | sigusr2}

   Overwrite {=} {false | no | off | on | true | yes}

   Property PropertyName {=} PropertyValue

   Sideset VariableList...

   Start Time {=} Start_time

   Surface VariableList...

   Synchronize Output

   Termination Time {=} Final_time

   Timeseries Name {=} filename

   Timestep Adjustment Interval {=} Nsteps

   Title

   Use Dynamic Topology Io

   Use Output Scheduler Timer_name

   begin Catalyst Label
   end

end Results Output Label

7.10.2.1. Line Commands

Additional Steps

Syntax: Additional Steps {=} List_of_steps…
Summary: Additional simulation steps when output should occur.

Parameter	Value	Default
{=}	{= \| are \| is}	–
List_of_steps	integer…	–

Additional Times

Syntax: Additional Times {=} List_of_times…
Summary: Additional simulation times when output should occur.

Parameter	Value	Default
{=}	{= \| are \| is}	–
List_of_times	real…	–

At Step

Syntax: At Step n {increment | interval} {=} m
Summary: Specify an output interval in terms of the internal iteration step count. The first step specifies the step count at the beginning of this interval and the second step specifies the output frequency to be used within this interval.

Parameter	Value	Default
n	integer	–
Option	{increment \| interval}	–
{=}	{= \| are \| is}	–
m	integer	–

At Time

Syntax: At Time Dt1 {increment | interval} {=} Dt2
Summary: Specify an output interval in terms of the internal simulation time. The first time specifies the time at the beginning of this time interval and the second time specifies the output frequency to be used within this interval.

Parameter	Value	Default
Dt1	real	–
Option	{increment \| interval}	–
{=}	{= \| are \| is}	–
Dt2	real	–

Auto Output

Syntax: Auto Output {all | element | global | nodal} User Defined Variables [ In UserOutputResultsList… ]
Summary: Allows users to automatically output all user output defined variables for the type requested.

Parameter	Value	Default
auto_output_type_3	{all \| element \| global \| nodal}	–

Auto Output

Syntax: Auto Output {all | element | global | nodal} Variables
Summary: Allows users to automatically output all user output defined variables for the type requested.

Parameter	Value	Default
auto_output_type_3	{all \| element \| global \| nodal}	–

Component Separator Character

Syntax: Component Separator Character {=} Separator
Summary: The separator is the single character used to separate the output variable basename (e.g. “stress”) from the suffices (e.g. “xx”, “yy”) when displaying the names of the individual variable components. For example, the default separator is “_”, which results in names similar to “stress_xx”, “stress_yy”, … “stress_zx”. To eliminate the separator, specify an empty string (“”) or NONE.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Separator	string	–

Database Name

Syntax: Database Name {=} StreamName
Summary: The base name of the database containing the output results. If the filename begins with the ‘/’ character, it is an absolute path; otherwise, the path to the current directory will be prepended to the name. If this line is omitted, then a filename will be created from the basename of the input file with a “.e” suffix appended.

Parameter	Value	Default
{=}	{= \| are \| is}	–
StreamName	string	–

Database Type

Syntax: Database Type {=} {catalyst | catalyst_exodus | cgns | dof | dof_exodus | exodus | exodusii | exonull | generated | genesis | null | parallel_exodus | textmesh}
Summary: The database type/format to be used for the output results.

Parameter	Value	Default
{=}	{= \| are \| is}	–
DatabaseType	{catalyst \| catalyst_exodus \| cgns \| dof \| dof_exodus \| exodus \| exodusii \| exonull \| generated \| genesis \| null \| parallel_exodus \| textmesh}	–

Edge

Syntax: Edge VariableList…
Summary: Define the variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line. The entities that this variable are written to can also be limited or specified with “exclude list_of_entities” or “include list_of_entities”. Edge variables are not supported for all database types.

Parameter	Value	Default
VariableList	string…	–

Element

Syntax: Element VariableList…
Summary: Define the variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line. The entities that this variable are written to can also be limited or specified with “exclude list_of_entities” or “include list_of_entities”

Parameter	Value	Default
VariableList	string…	–

Enable Large Ids

Syntax: Enable Large Ids
Summary: Enable 64 bit entity IDs for output

Exclude

Syntax: Exclude {=} [ ElementBlockList… ]
Summary: Specify that the results file will only contain a subset of the element blocks in the analysis model. The element_block_list lists only the blocks which will not be output to the results database.

Parameter	Value	Default
{=}	{= \| are \| is}	–

Exists

Syntax: Exists {=} {abort | add_suffix | append | overwrite}
Summary: Specify the behavior when creating this database and there is an existing file with the same name. The default behavior is “OVERWRITE” which deletes the existing file and creates a new file of the same name. “APPEND” will (if possible) append the new data to the end of the existing file. “ABORT” will print an error message and end the analysis. “ADD_SUFFIX” will add a -s???? suffix where the ???? is replaced by a sequential number starting at 0002.

Parameter	Value	Default
{=}	{= \| is}	–
Option2	{abort \| add_suffix \| append \| overwrite}	–

Face

Syntax: Face VariableList…
Summary: Define the variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line. The entities that this variable are written to can also be limited or specified with “exclude list_of_entities” or “include list_of_entities”. Face variables are not supported for all database types.

Parameter	Value	Default
VariableList	string…	–

Flush Interval

Syntax: Flush Interval {=} Option
Summary: The minimum time interval (in seconds) at which output will be explicitly flushed to disk. The default is 10 seconds.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Option	integer	10

Global

Syntax: Global VariableList…
Summary: Define the global variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line.

Parameter	Value	Default
VariableList	string…	–

Include

Syntax: Include {=} [ ElementBlockList… ]
Summary: Specify that the results file will only contain a subset of the element blocks in the analysis model. The element_block_list lists only the blocks which will be output to the results database.

Parameter	Value	Default
{=}	{= \| are \| is}	–

Nodal

Syntax: Nodal VariableList…
Summary: Define the nodal variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line.

Parameter	Value	Default
VariableList	string…	–

Node

Syntax: Node VariableList…
Summary: Define the nodal variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line.

Parameter	Value	Default
VariableList	string…	–

Nodeset

Syntax: Nodeset VariableList…
Summary: Define the variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line. The entities that this variable are written to can also be limited or specified with “exclude list_of_entities” or “include list_of_entities”. Nodeset variables are not supported for all database types.

Parameter	Value	Default
VariableList	string…	–

Output Mesh

Syntax: Output Mesh {=} {exposed surface | refined | unrefined}
Summary: Use this command to turn on “unrefined” as the output mesh. The default behavior is “refined”, in which field variables are output on the current mesh, which may have been refined (either uniformly or adaptively) or had its topology altered in some way (e.g., dynamic load balancing) with respect to the original mesh read from the input file. By specifying “Output Mesh = unrefined”, all output variables are output only on the original mesh objects read from the input file.

Parameter	Value	Default
{=}	{= \| are \| is}	–
OutputMesh	{exposed surface \| refined \| unrefined}	–

Output On Signal

Syntax: Output On Signal {=} {sigabrt | sigalrm | sigfpe | sighup | sigill | sigint | sigkill | sigpipe | sigquit | sigsegv | sigterm | sigusr1 | sigusr2}
Summary: When the specified signal is raised, the output stream associated with this block will be output.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Signals	{sigabrt \| sigalrm \| sigfpe \| sighup \| sigill \| sigint \| sigkill \| sigpipe \| sigquit \| sigsegv \| sigterm \| sigusr1 \| sigusr2}	–

Overwrite

Syntax: Overwrite {=} {false | no | off | on | true | yes}
Summary: (DEPRECATED, Use EXISTS) Specify whether the database should be overwritten if it exists. The default behavior is to overwrite unless this command is specified in the output block and either off, false, or no is specified.

Parameter	Value	Default
{=}	{= \| is}	–
Option2	{false \| no \| off \| on \| true \| yes}	–

Property

Syntax

Property PropertyName {=} PropertyValue

Summary

Define a database property named “PropertyName” with the value “PropertyValue”. If PropertyValue consists of all digits, it will define an integer property. If PropertyValue is “true” or “yes” or “false” or “no”, it will define a logical property; otherwise it will define a string property. Supported properties are typically database dependent; Current properties are:

COMPRESSION_LEVEL = [0..9] (off)
COMPRESSION_SHUFFLE = true|false|on|off (off)
FILE_TYPE = netcdf4 (forces use of netcdf-4 hdf5-based file) (netcdf3)
INTEGER_SIZE_DB = 4|8 (4)
INTEGER_SIZE_API = 4|8 (4)
REAL_SIZE_DB = 4|8 (8 is default)
LOGGING = true|false|on|off (off)
MAX_NAME_LENGTH = value (32)

Parameter	Value	Default
PropertyName	string	–
{=}	{= \| are \| is}	–
PropertyValue	string	–

Sideset

Syntax: Sideset VariableList…
Summary: Define the variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line. The entities that this variable are written to can also be limited or specified with “exclude list_of_entities” or “include list_of_entities”. Face variables are not supported for all database types.

Parameter	Value	Default
VariableList	string…	–

Start Time

Syntax: Start Time {=} Start_time
Summary: Specify the time to start outputting results from this output request block. This time overrides all ‘at time’ and ‘at step’ specifications.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Start_time	real	–

Surface

Syntax: Surface VariableList…
Summary: Define the variables that should be written to the results database. If “variable” is entered, then its name will be used on the output database. If “variable as db_name” is entered, then “db_name” will be the name used on the database for the internal variable “variable”. Multiple “variable” or “variable as db_name” entries are allowed on the same line. The entities that this variable are written to can also be limited or specified with “exclude list_of_entities” or “include list_of_entities”. Face variables are not supported for all database types.

Parameter	Value	Default
VariableList	string…	–

Synchronize Output

Syntax

Synchronize Output

Summary

In an analysis with multiple regions, it is sometimes desirable to synchronize the output of results data between the regions. This can be done by adding the SYNCHRONIZE OUTPUT command line to the results output block. If a results block has this set, then it will write output whenever a previous region writes output. The ordering of regions is based on the order in the input file, algorithmic considerations, or by solution control specifications.

Although the USE OUTPUT SCHEDULER command line can also synchronize output between regions, the SYNCHRONIZE OUTPUT command line will synchronize the output with regions where the output frequency is not under the direct control of the Sierra IO system. Examples of this are typically coupled applications where one or more of the codes are not Sierra-based applications such as Alegra and CTH. A results block with SYNCHRONIZE OUTPUT specified will also synchronize its output with the output of the external code.

The SYNCHRONIZE OUTPUT command can be used with other output scheduling commands such as time-based or step-based output specifications.

Termination Time

Syntax: Termination Time {=} Final_time
Summary: Specify the time to stop outputting results from this output request block.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Final_time	real	–

Timeseries Name

Syntax: Timeseries Name {=} filename
Summary: Optionally specify a filename for a timeseries file that outputs the root database filename in the order that they are written. This is useful when running on large numbers of processors with many mesh-mods that cause simple disk operations to hang.

Parameter	Value	Default
{=}	{= \| are \| is}	–
filename	string	–

Timestep Adjustment Interval

Syntax: Timestep Adjustment Interval {=} Nsteps
Summary: Specify the number of steps to ‘look ahead’ and adjust the timestep to ensure that the specified output times or simulation end time will be hit ‘exactly’.

Parameter	Value	Default
{=}	{= \| are \| is}	–
Nsteps	integer	–

Title

Syntax: Title
Summary: Specify the title to be used for this specific output block.

Use Dynamic Topology Io

Syntax: Use Dynamic Topology Io
Summary: Specify that the app use IO for dynamic topology modifications where the output files are stored in a single database. Legacy file format for dynamically changing topology results in the creation of multiple files for each output on a mesh modification. This option leverages the ability of netCDF to create mesh groups within a single database and concatenate all mesh files into one. The names of each mesh group are of the form IOSS_MESH_GROUP-??? where ??? is the 1-based output index 1, 2, …, 10, …., 100, … Please note that netCDF has a current limit of 65,536 groups

Use Output Scheduler

Syntax: Use Output Scheduler Timer_name
Summary: Associates a predefined output scheduler with this output block (results, restart, heartbeat, or history).

Parameter	Value	Default
Timer_name	string	–