void
HeatConductionApp::associateSyntax(Syntax & syntax, ActionFactory & action_factory)
{
#undef registerAction
#define registerAction(tplt, action) action_factory.reg<tplt>(stringifyName(tplt), action)
// This registers an action to add the "slave_flux" vector to the system at the right time
registerTask("add_slave_flux_vector", false);
addTaskDependency("add_slave_flux_vector", "ready_to_init");
addTaskDependency("init_problem", "add_slave_flux_vector");
registerAction(AddSlaveFluxVectorAction, "add_slave_flux_vector");
syntax.registerActionSyntax("AddSlaveFluxVectorAction", "ThermalContact/*");
syntax.registerActionSyntax("ThermalContactAuxBCsAction", "ThermalContact/*", "add_aux_kernel");
syntax.registerActionSyntax("ThermalContactAuxVarsAction", "ThermalContact/*", "add_aux_variable");
syntax.registerActionSyntax("ThermalContactBCsAction", "ThermalContact/*", "add_bc");
syntax.registerActionSyntax("ThermalContactDiracKernelsAction", "ThermalContact/*", "add_dirac_kernel");
syntax.registerActionSyntax("ThermalContactMaterialsAction", "ThermalContact/*", "add_material");
registerAction(ThermalContactAuxBCsAction, "add_aux_kernel");
registerAction(ThermalContactAuxVarsAction, "add_aux_variable");
registerAction(ThermalContactBCsAction, "add_bc");
registerAction(ThermalContactDiracKernelsAction, "add_dirac_kernel");
registerAction(ThermalContactMaterialsAction, "add_material");
#undef registerAction
#define registerAction(tplt, action) action_factory.regLegacy<tplt>(stringifyName(tplt), action)
}
void initComUart(){
uartMessage.source = com_uart_user;
UCA0CTL1 = UCSWRST; //RESET
UCA0CTL1 |= UCSSEL_2; // SMCLK
UCA0CTL0 = 0x00;
UCA0BR0 = 104; // 1MHz 9600
UCA0BR1 = 0; // 1MHz 9600
UCA0MCTL = UCBRS0; // Modulation UCBRSx = 1
P1SEL |= (UART_TXD + UART_RXD); // Timer function for TXD/RXD pins
P1SEL2 |= (UART_TXD + UART_RXD); // Timer function for TXD/RXD pins
P1DIR |= UART_TXD;
P1DIR &= ~UART_RXD;
UCA0CTL1 &= ~UCSWRST; // **Initialize USCI state machine**
IE2 |= UCA0RXIE; // Enable USCI_A0 RX interrupt
//UCA0TXBUF = 0x35;
comUartTask.user = com_uart_user;
comUartTask.handler = &comUartHandler;
comUartTask.cmdName = comUartCmd;
registerTask( &comUartTask );
}
void
ContactApp::associateSyntax(Syntax & syntax, ActionFactory & action_factory)
{
syntax.registerActionSyntax("ContactAction", "Contact/*");
syntax.registerActionSyntax("ContactPenetrationAuxAction", "Contact/*");
syntax.registerActionSyntax("ContactPenetrationVarAction", "Contact/*");
syntax.registerActionSyntax("ContactPressureAuxAction", "Contact/*");
syntax.registerActionSyntax("ContactPressureVarAction", "Contact/*");
syntax.registerActionSyntax("NodalAreaAction", "Contact/*");
syntax.registerActionSyntax("NodalAreaVarAction", "Contact/*");
registerAction(ContactAction, "add_aux_kernel");
registerAction(ContactAction, "add_aux_variable");
registerAction(ContactAction, "add_dirac_kernel");
registerTask("output_penetration_info_vars", false);
registerAction(ContactAction, "output_penetration_info_vars");
syntax.addDependency("output_penetration_info_vars", "add_output");
registerAction(ContactPenetrationAuxAction, "add_aux_kernel");
registerAction(ContactPenetrationVarAction, "add_aux_variable");
registerAction(ContactPressureAuxAction, "add_aux_kernel");
registerAction(ContactPressureVarAction, "add_aux_variable");
registerAction(NodalAreaAction, "add_user_object");
registerAction(NodalAreaVarAction, "add_aux_variable");
}
void LOS_init(void)
{
if (media_init() == 0)
{
mSD_status = SD_ERR_INIT;
printf("ERROR: Media init failed\n");
return;
}
// Attach media access functions to library
if (fl_attach_media(media_read, media_write) != FAT_INIT_OK)
{
mSD_status = SD_ERR_ATTACH;
printf("ERROR: Media attach failed\n");
return;
}
#ifndef __LOCAL_STORE_ACCEL_MODE__
BQ_init(&LOS_queue, LOS_write_buffer, sizeof(LOS_write_buffer));
#endif
LOS_tid = registerTask(LOS_proc, 0, 0, 0xFF);
#ifdef FRAM_ENABLED
FRAM_WR_init();
#endif
// Delete File
int i = 0;
while ((i = fl_remove("/file.txt")) == -1);
if (!i)
{
//printf("ERROR: Delete file failed\n");
}
}
void
registerActions(Syntax & syntax,
ActionFactory & action_factory,
const std::set<std::string> & obj_labels)
{
Registry::registerActionsTo(action_factory, obj_labels);
// TODO: Why is this here?
registerTask("finish_input_file_output", false);
}
void initButton(){
buttonTask.user = button_user;
buttonTask.handler = &buttonHandler;
buttonTask.cmdName = buttonCmd;
registerTask( &buttonTask );
P1DIR &= ~BUTTON; //Button input
P1IE |= BUTTON; //interrupt for button enabled
P1IFG &= ~BUTTON; //Interrupt flag enabled
P1IES |= BUTTON; //Hi/lo edge
}
int main( void ){
disableWDT();// Stop watchdog timer
initQueue();
initScheduler();
initButton();
initLed();
initComUart();
initInfo();
mainTask.cmdName = cmdNameMain;
mainTask.user = main_user;
mainTask.handler = &mainHandler;
registerTask( &mainTask );
setDCOCLK( DCO_1M );
setSMCLK( SMCLK_DCO, CLK_DIV_1 );
if( getFreeMessage( &mainMessage ) == queue_ok ){
mainMessage->source = main_user;
mainMessage->destination = led_user;
mainMessage->id = MSG_ID_LED_GREEN;
mainMessage->priority = normal_priority;
mainMessage->event = undef_event;
putMessage( mainMessage );
}
if( getFreeMessage( &mainMessage ) == queue_ok){
mainMessage->destination = com_uart_user;
mainMessage->source = main_user;
mainMessage->id = MSG_ID_UART_WELCOME;
putMessage( mainMessage );
}
initCli();
enableTimerA0CCInterrupt();
setTimerA0Mode( TAMODE_CONT );
setTimerA0ClockSource( TA_SMCLK );
setTimerA0Divider( TA_DIV_1 );
__enable_interrupt();
__bis_SR_register( 0x18 );
//__bis_SR_register( 0x18 ); // LPM0 with interrupts enabled
while( 1 ){};
return 0;
}
void
XFEMApp::associateSyntax(Syntax & syntax, ActionFactory & action_factory)
{
registerTask("setup_xfem", false);
registerAction(XFEMAction, "setup_xfem");
syntax.addDependency("setup_xfem","setup_adaptivity");
registerAction(XFEMAction, "add_aux_variable");
registerAction(XFEMAction, "add_aux_kernel");
syntax.registerActionSyntax("XFEMAction", "XFEM");
syntax.registerActionSyntax("AddUserObjectAction", "XFEM/*");
}
void
NavierStokesApp::associateSyntax(Syntax & syntax, ActionFactory & action_factory)
{
#undef registerAction
#define registerAction(type, action) \
action_factory.reg<type>(stringifyName(type), action, __FILE__, __LINE__)
// Create the syntax
registerSyntax("AddNavierStokesVariablesAction", "Modules/NavierStokes/Variables");
registerSyntax("AddNavierStokesICsAction", "Modules/NavierStokes/ICs");
registerSyntax("AddNavierStokesKernelsAction", "Modules/NavierStokes/Kernels");
registerSyntax("AddNavierStokesBCsAction", "Modules/NavierStokes/BCs/*");
// add variables action
registerTask("add_navier_stokes_variables", /*is_required=*/false);
addTaskDependency("add_navier_stokes_variables", "add_variable");
registerAction(AddNavierStokesVariablesAction, "add_navier_stokes_variables");
// add ICs action
registerTask("add_navier_stokes_ics", /*is_required=*/false);
addTaskDependency("add_navier_stokes_ics", "add_ic");
registerAction(AddNavierStokesICsAction, "add_navier_stokes_ics");
// add Kernels action
registerTask("add_navier_stokes_kernels", /*is_required=*/false);
addTaskDependency("add_navier_stokes_kernels", "add_kernel");
registerAction(AddNavierStokesKernelsAction, "add_navier_stokes_kernels");
// add BCs actions
registerMooseObjectTask("add_navier_stokes_bcs", NSWeakStagnationInletBC, /*is_required=*/false);
appendMooseObjectTask("add_navier_stokes_bcs", NSNoPenetrationBC);
appendMooseObjectTask("add_navier_stokes_bcs", NSStaticPressureOutletBC);
addTaskDependency("add_navier_stokes_bcs", "add_bc");
registerAction(AddNavierStokesBCsAction, "add_navier_stokes_bcs");
#undef registerAction
#define registerAction(type, action) action_factory.regLegacy<type>(stringifyName(type), action)
}
void initAccelHandler(void) {
//unsigned short temp = 0;
// Initialize the platform
QfPlat_Init();
// Init QF4A512 and SPI hardware to which the QF4A512 is attached.
qf4a512_Init();
// Load the table of settings and FIR coefficients from the Quickfilter Pro PC
// software. (see header above for instructions on how to generate the table)
//num = QF_IMAGE_REGISTER_TABLE_DIMENSION;
qf4a512_LoadImageRegisterTable();
//QfPowerDown();
//QFPlat_PowerDownBase();
//for endless sampling
accelSampleHandle = registerTask(&sample, 0, (unsigned short) 0, -1);
//sleepHandle = registerTask(&sleep_WB, 0, (unsigned short) 100, -1);
//pauseTask(sleepHandle);
//temp = adis16209_get_status();
//temp = 0;
//temp = adis16209_get_sample_rate();
//temp = 0;
//temp = adis16209_get_status();
//temp = 0;
//temp = adis16209_get_sample_rate();
//temp = 0;
//canRegisterWhenWakeUp_WB(&AccelWakeUpByCAN);
//can peripheral off
//canSleep();
//can transceiver off
//QfPlat_ToggleActivityLED();
//put cpu asleep
//Sleep();
//QFPlat_Sleep();
}
/**
* Multiple Action class can be associated with a single input file section, in which case all associated Actions
* will be created and "acted" on when the associated input file section is seen.b *
* Example:
* "setup_mesh" <-----------> SetupMeshAction <---------
* \
* [Mesh]
* /
* "setup_mesh_complete" <---> SetupMeshCompleteAction <-
*
*
* Action classes can also be registered to act on more than one input file section for a different task
* if similar logic can work in multiple cases
*
* Example:
* "add_variable" <----- -> [Variables/ *]
* \ /
* CopyNodalVarsAction
* / \
* "add_aux_variable" <- -> [AuxVariables/ *]
*
*
* Note: Placeholder "no_action" actions must be put in places where it is possible to match an object
* with a star or a more specific parent later on. (i.e. where one needs to negate the '*' matching
* prematurely)
*/
void
registerActions(Syntax & syntax, ActionFactory & action_factory)
{
#undef registerAction
#define registerAction(tplt, action) action_factory.reg<tplt>(stringifyName(tplt), action)
registerAction(SetupPostprocessorDataAction, "setup_postprocessor_data");
registerAction(SetupMeshAction, "setup_mesh");
registerAction(SetupMeshCompleteAction, "prepare_mesh");
registerAction(AddMeshModifierAction, "add_mesh_modifier");
registerAction(AddMortarInterfaceAction, "add_mortar_interface");
registerAction(SetupMeshCompleteAction, "execute_mesh_modifiers");
registerAction(SetupMeshCompleteAction, "uniform_refine_mesh");
registerAction(SetupMeshCompleteAction, "setup_mesh_complete");
registerAction(AddFunctionAction, "add_function");
registerAction(CreateExecutionerAction, "setup_executioner");
registerAction(SetupTimeStepperAction, "setup_time_stepper");
registerAction(SetupTimeIntegratorAction, "setup_time_integrator");
registerAction(SetupTimePeriodsAction, "setup_time_periods");
registerAction(CreateDisplacedProblemAction, "init_displaced_problem");
registerAction(DetermineSystemType, "determine_system_type");
registerAction(CreateProblemAction, "create_problem");
registerAction(DynamicObjectRegistrationAction, "dynamic_object_registration");
registerAction(AddOutputAction, "add_output");
registerAction(CommonOutputAction, "common_output");
registerAction(SetupRecoverFileBaseAction, "setup_recover_file_base");
registerAction(GlobalParamsAction, "set_global_params");
registerAction(SetupPredictorAction, "setup_predictor");
registerAction(MaterialOutputAction, "setup_material_output");
registerAction(CheckOutputAction, "check_output");
/// Variable/AuxVariable Actions
registerAction(AddVariableAction, "add_variable");
registerAction(AddAuxVariableAction, "add_aux_variable");
registerAction(CopyNodalVarsAction, "check_copy_nodal_vars");
registerAction(CopyNodalVarsAction, "copy_nodal_vars");
registerAction(CopyNodalVarsAction, "copy_nodal_aux_vars");
// Initial Condition Actions
registerAction(AddICAction, "add_ic");
registerAction(AddInitialConditionAction, "add_ic");
registerAction(AddKernelAction, "add_kernel");
registerAction(AddKernelAction, "add_aux_kernel");
registerAction(AddScalarKernelAction, "add_scalar_kernel");
registerAction(AddScalarKernelAction, "add_aux_scalar_kernel");
registerAction(AddDGKernelAction, "add_dg_kernel");
registerAction(AddBCAction, "add_bc");
registerAction(EmptyAction, "no_action"); // placeholder
registerAction(AddPeriodicBCAction, "add_periodic_bc");
registerAction(AddMaterialAction, "add_material");
registerAction(AddPostprocessorAction, "add_postprocessor");
registerAction(AddVectorPostprocessorAction, "add_vector_postprocessor");
registerAction(AddDamperAction, "add_damper");
registerAction(AddSplitAction, "add_split");
registerAction(SetupPreconditionerAction, "add_preconditioning");
registerAction(SetupQuadratureAction, "setup_quadrature");
registerAction(DeprecatedBlockAction, "deprecated_block");
registerAction(AddConstraintAction, "add_constraint");
registerAction(AddUserObjectAction, "add_user_object");
registerAction(AddControlAction, "add_control");
registerAction(AddElementalFieldAction, "add_elemental_field_variable");
registerAction(AddIndicatorAction, "add_indicator");
registerAction(AddMarkerAction, "add_marker");
registerAction(SetAdaptivityOptionsAction, "set_adaptivity_options");
registerAction(AddNodalNormalsAction, "add_aux_variable");
registerAction(AddNodalNormalsAction, "add_postprocessor");
registerAction(AddNodalNormalsAction, "add_user_object");
#ifdef LIBMESH_ENABLE_AMR
registerAction(AdaptivityAction, "setup_adaptivity");
#endif
registerAction(AddDiracKernelAction, "add_dirac_kernel");
registerAction(SetupDebugAction, "setup_debug");
registerAction(SetupResidualDebugAction, "setup_residual_debug");
registerAction(AddBoundsVectorsAction, "add_bounds_vectors");
// NonParsedActions
registerAction(SetupDampersAction, "setup_dampers");
registerAction(EmptyAction, "ready_to_init");
registerAction(InitProblemAction, "init_problem");
registerAction(CheckIntegrityAction, "check_integrity");
registerAction(AddMultiAppAction, "add_multi_app");
registerAction(AddTransferAction, "add_transfer");
// TODO: Why is this here?
registerTask("finish_input_file_output", false);
registerAction(EmptyAction, "finish_input_file_output");
#undef registerAction
#define registerAction(tplt, action) action_factory.regLegacy<tplt>(stringifyName(tplt), action)
}
void
addActionTypes(Syntax & syntax)
{
/**
* The second param here indicates whether the task must be satisfied or not for a successful run.
* If set to true, then the ActionWarehouse will attempt to create "Action"s automatically if they have
* not been explicitly created by the parser or some other mechanism.
*
* Note: Many of the actions in the "Minimal Problem" section are marked as false. However, we can generally
* force creation of these "Action"s as needed by registering them to syntax that we expect to see even
* if those "Action"s don't normally pick up parameters from the input file.
*/
/**************************/
/**** Register Actions ****/
/**************************/
registerMooseObjectTask("create_problem", Problem, true);
registerMooseObjectTask("setup_executioner", Executioner, true);
// This task does not construct an object, but it needs all of the parameters that
// would normally be used to construct an object.
registerMooseObjectTask("determine_system_type", Executioner, true);
registerMooseObjectTask("setup_mesh", MooseMesh, false);
registerMooseObjectTask("add_mesh_modifier", MeshModifier, false);
registerMooseObjectTask("add_kernel", Kernel, false);
appendMooseObjectTask ("add_kernel", EigenKernel);
registerMooseObjectTask("add_material", Material, false);
registerMooseObjectTask("add_bc", BoundaryCondition, false);
registerMooseObjectTask("add_function", Function, false);
registerMooseObjectTask("add_aux_kernel", AuxKernel, false);
registerMooseObjectTask("add_elemental_field_variable", AuxKernel, false);
registerMooseObjectTask("add_scalar_kernel", ScalarKernel, false);
registerMooseObjectTask("add_aux_scalar_kernel", AuxScalarKernel, false);
registerMooseObjectTask("add_dirac_kernel", DiracKernel, false);
registerMooseObjectTask("add_dg_kernel", DGKernel, false);
registerMooseObjectTask("add_constraint", Constraint, false);
registerMooseObjectTask("add_ic", InitialCondition, false);
appendMooseObjectTask ("add_ic", ScalarInitialCondition);
registerMooseObjectTask("add_damper", Damper, false);
registerMooseObjectTask("setup_predictor", Predictor, false);
registerMooseObjectTask("setup_time_stepper", TimeStepper, false);
registerMooseObjectTask("setup_time_integrator", TimeIntegrator, false);
registerMooseObjectTask("add_preconditioning", MoosePreconditioner, false);
registerMooseObjectTask("add_split", Split, false);
registerMooseObjectTask("add_user_object", UserObject, false);
appendMooseObjectTask ("add_user_object", Postprocessor);
registerMooseObjectTask("add_postprocessor", Postprocessor, false);
registerMooseObjectTask("add_vector_postprocessor", VectorPostprocessor, false);
registerMooseObjectTask("add_indicator", Indicator, false);
registerMooseObjectTask("add_marker", Marker, false);
registerMooseObjectTask("add_multi_app", MultiApp, false);
registerMooseObjectTask("add_transfer", Transfer, false);
registerMooseObjectTask("add_output", Output, false);
registerMooseObjectTask("add_control", Control, false);
registerTask("dynamic_object_registration", false);
registerTask("common_output", true);
registerTask("setup_recover_file_base", true);
registerTask("add_bounds_vectors", false);
registerTask("add_periodic_bc", false);
registerTask("add_aux_variable", false);
registerTask("add_variable", false);
registerTask("execute_mesh_modifiers", false);
registerTask("uniform_refine_mesh", false);
registerTask("prepare_mesh", false);
registerTask("setup_mesh_complete", false); // calls prepare
registerTask("init_displaced_problem", false);
registerTask("init_problem", true);
registerTask("check_copy_nodal_vars", true);
registerTask("copy_nodal_vars", true);
registerTask("copy_nodal_aux_vars", true);
registerTask("setup_postprocessor_data", false);
registerTask("setup_dampers", true);
registerTask("check_integrity", true);
registerTask("setup_quadrature", true);
/// Additional Actions
registerTask("no_action", false); // Used for Empty Action placeholders
registerTask("set_global_params", false);
registerTask("setup_time_periods", true);
registerTask("setup_adaptivity", false);
registerTask("meta_action", false);
registerTask("setup_debug", false);
registerTask("setup_residual_debug", false);
registerTask("setup_oversampling", false);
registerTask("deprecated_block", false);
registerTask("set_adaptivity_options", false);
registerTask("add_mortar_interface", false);
// Dummy Actions (useful for sync points in the dependencies)
registerTask("setup_function_complete", false);
registerTask("setup_variable_complete", false);
registerTask("ready_to_init", true);
// Output related actions
registerTask("setup_material_output", true);
registerTask("check_output", true);
/**************************/
/****** Dependencies ******/
/**************************/
/**
* The following is the default set of action dependencies for a basic MOOSE problem. The formatting
* of this string is important. Each line represents a set of dependencies that depend on the previous
* line. Items on the same line have equal weight and can be executed in any order.
*
* Additional dependencies can be inserted later inside of user applications with calls to
* ActionWarehouse::addDependency("task", "pre_req")
*/
syntax.addDependencySets(
"(meta_action)"
"(dynamic_object_registration)"
"(common_output)"
"(set_global_params)"
"(setup_recover_file_base)"
"(check_copy_nodal_vars)"
"(setup_mesh)"
"(prepare_mesh)"
"(add_mesh_modifier)"
"(add_mortar_interface)"
"(execute_mesh_modifiers)"
"(uniform_refine_mesh)"
"(setup_mesh_complete)"
"(determine_system_type)"
"(create_problem)"
"(setup_time_integrator)"
"(setup_executioner)"
"(setup_time_stepper)"
"(setup_predictor)"
"(setup_postprocessor_data)"
"(setup_time_periods)"
"(init_displaced_problem)"
"(add_aux_variable, add_variable, add_elemental_field_variable)"
"(setup_variable_complete)"
"(setup_quadrature)"
"(add_function)"
"(add_periodic_bc)"
"(add_user_object)"
"(setup_function_complete)"
"(setup_adaptivity)"
"(set_adaptivity_options)"
"(add_ic)"
"(add_preconditioning, add_constraint, add_split)"
"(ready_to_init)"
"(setup_dampers)"
"(setup_residual_debug)"
"(add_bounds_vectors)"
"(add_multi_app)"
"(add_transfer)"
"(copy_nodal_vars, copy_nodal_aux_vars)"
"(add_material)"
"(setup_material_output)"
"(init_problem)"
"(setup_debug)"
"(add_output)"
"(add_postprocessor)"
"(add_vector_postprocessor)"
"(add_aux_kernel, add_bc, add_damper, add_dirac_kernel, add_kernel, add_dg_kernel, add_scalar_kernel, add_aux_scalar_kernel, add_indicator, add_marker)"
"(add_control)"
"(check_output)"
"(check_integrity)"
);
}
void QfSpi_Init(void) {
/*
// Sanity check SPI0 state.
Assert( Spi0State == Uninitialized );
SetBit( UCTL0, SWRST ); // Hold the USART in Reset while configuring
ClearBit( IE1, URXIE0 ); // Disable SPI0 Receive Interrupts
U0ME |= UTXE0 + URXE0; // Enable USART0 transmit and receive modules
P3SEL |= 0x0E; // Select the SPI option for USART0 pins (P3.1-3)
UCTL0 |= CHAR + // Character length is 8 bits
SYNC + // Synchronous Mode (as opposed to UART)
MM; // 8-bit SPI Master **SWRST**
UTCTL0 |= CKPH + // UCLK delayed by 1/2 cycle
SSEL1 + SSEL0 + // Clock source is SMCLK (implies Master mode)
// 00 UCLKI 10 SMCLK
// 01 ACLK (fastest) 11 SMCLK
STC; // 3-pin SPI mode (STE disabled)
URCTL0 = 0; // Receive control register
UMCTL0 = SPI0_MODULATION_CONTROL; // No modulation
UBR10 = GetHiByte( SPI0_BAUD_DIVISOR ); // Set baud rate
UBR00 = GetLoByte( SPI0_BAUD_DIVISOR );
URCTL0 = 0; // Init receiver contol register
ME1 |= UTXE0 + URXE0; // Enable USART0 SPI transmit and receive. (note that
// URXE0 and USPIE0 are one in the same on the '449)
ClearBit( UCTL0, SWRST ); // Release USART state machine (begin operation).
// Doesn't do anything in SPI mode until a write
// to TXBUF0 occurs.
*/
PIE1bits.SSPIE = 0;
IPR1bits.SSPIP = 0; //spi interrupt low priority
set_LIV_function(&Spi0ReadIsr);
TRISCbits.TRISC3 = 0; //sck output
TRISCbits.TRISC5 = 0; //sdo output
//TRISAbits.TRISA5 = 1; //ss input
QfPlat_DeactivateQF4A512ChipSelect();
OpenSPI(SPI_FOSC_16, MODE_00, SMPEND);
Spi0State = Idle;
//YEB
#ifndef __YEB_INTERRUPT__
#ifndef __YEB_IMMEDIATE__
rememberHandle = registerTask(&rememberCallback, 0, (unsigned short) 0, -1);
pauseTask(rememberHandle);
#endif
#endif
}
/**
* Multiple Action class can be associated with a single input file section, in which case all associated Actions
* will be created and "acted" on when the associated input file section is seen.b *
* Example:
* "setup_mesh" <-----------> SetupMeshAction <---------
* \
* [Mesh]
* /
* "setup_mesh_complete" <---> SetupMeshCompleteAction <-
*
*
* Action classes can also be registered to act on more than one input file section for a different task
* if similar logic can work in multiple cases
*
* Example:
* "add_variable" <----- -> [Variables/ *]
* \ /
* CopyNodalVarsAction
* / \
* "add_aux_variable" <- -> [AuxVariables/ *]
*
*
* Note: Placeholder "no_action" actions must be put in places where it is possible to match an object
* with a star or a more specific parent later on. (i.e. where one needs to negate the '*' matching
* prematurely)
*/
void
registerActions(Syntax & syntax, ActionFactory & action_factory)
{
registerAction(SetupPostprocessorDataAction, "setup_postprocessor_data");
registerAction(RecoverBaseAction, "recover_base");
registerAction(SetupMeshAction, "setup_mesh");
registerAction(SetupMeshCompleteAction, "prepare_mesh");
registerAction(AddMeshModifierAction, "add_mesh_modifier");
registerAction(AddMortarInterfaceAction, "add_mortar_interface");
registerAction(SetupMeshCompleteAction, "setup_mesh_complete");
registerAction(AddFunctionAction, "add_function");
registerAction(CreateExecutionerAction, "setup_executioner");
registerAction(SetupTimeStepperAction, "setup_time_stepper");
registerAction(SetupTimePeriodsAction, "setup_time_periods");
registerAction(InitDisplacedProblemAction, "init_displaced_problem");
registerAction(CreateProblemAction, "create_problem");
registerAction(SetupOutputAction, "setup_output"); /// \todo{remove w/ update system upgraded}
registerAction(SetupOutputNameAction, "setup_output_name"); /// \todo{remove w/ update system upgraded}
registerAction(AddOutputAction, "add_output");
registerAction(CommonOutputAction, "meta_action");
registerAction(GlobalParamsAction, "set_global_params");
registerAction(SetupPredictorAction, "setup_predictor");
/* The display of performance long is controlled by the Console outputter, if there is not one present
logging must be disable externally from the object, this action does this */
registerAction(PerfLogOutputAction, "perf_log_output");
/// Variable/AuxVariable Actions
registerAction(AddVariableAction, "add_variable");
registerAction(AddVariableAction, "add_ic"); // initial condition shortcut syntax
registerAction(AddAuxVariableAction, "add_aux_variable");
registerAction(AddAuxVariableAction, "add_ic"); // initial condition shortcut syntax
registerAction(CopyNodalVarsAction, "check_copy_nodal_vars");
registerAction(CopyNodalVarsAction, "copy_nodal_vars");
registerAction(CopyNodalVarsAction, "copy_nodal_aux_vars");
// Initial Condition Actions
registerAction(AddICAction, "add_ic");
registerAction(AddInitialConditionAction, "add_ic");
registerAction(AddKernelAction, "add_kernel");
registerAction(AddKernelAction, "add_aux_kernel");
registerAction(AddScalarKernelAction, "add_scalar_kernel");
registerAction(AddScalarKernelAction, "add_aux_scalar_kernel");
registerAction(AddDGKernelAction, "add_dg_kernel");
registerAction(AddBCAction, "add_bc");
registerAction(EmptyAction, "no_action"); // placeholder
registerAction(AddPeriodicBCAction, "add_periodic_bc");
registerAction(AddBCAction, "add_aux_bc");
registerAction(AddMaterialAction, "add_material");
registerAction(AddPostprocessorAction, "add_postprocessor");
registerAction(AddDamperAction, "add_damper");
registerAction(AddSplitAction, "add_split");
registerAction(SetupPreconditionerAction, "add_preconditioning");
registerAction(SetupQuadratureAction, "setup_quadrature");
registerAction(SetupOverSamplingAction, "setup_oversampling");
registerAction(DeprecatedBlockAction, "deprecated_block");
registerAction(AddConstraintAction, "add_constraint");
registerAction(AddUserObjectAction, "add_user_object");
registerAction(AddElementalFieldAction, "add_elemental_field_variable");
registerAction(AddIndicatorAction, "add_indicator");
registerAction(AddMarkerAction, "add_marker");
registerAction(SetAdaptivityOptionsAction, "set_adaptivity_options");
registerAction(AddNodalNormalsAction, "add_aux_variable");
registerAction(AddNodalNormalsAction, "add_postprocessor");
registerAction(AddNodalNormalsAction, "add_user_object");
#ifdef LIBMESH_ENABLE_AMR
registerAction(AdaptivityAction, "setup_adaptivity");
#endif
registerAction(AddDiracKernelAction, "add_dirac_kernel");
registerAction(SetupDebugAction, "setup_debug");
registerAction(SetupResidualDebugAction, "setup_residual_debug");
registerAction(AddBoundsVectorsAction, "add_bounds_vectors");
// NonParsedActions
registerAction(SetupDampersAction, "setup_dampers");
registerAction(EmptyAction, "ready_to_init");
registerAction(InitProblemAction, "init_problem");
registerAction(CheckIntegrityAction, "check_integrity");
// coupling
registerAction(AddFEProblemAction, "add_feproblem");
registerAction(AddCoupledVariableAction, "add_coupled_variable");
registerAction(AddMultiAppAction, "add_multi_app");
registerAction(AddTransferAction, "add_transfer");
// TODO: Why is this here?
registerTask("finish_input_file_output", false);
registerAction(EmptyAction, "finish_input_file_output");
}
void PhylipPlugin::processCmdlineOptions() {
CMDLineRegistry *cmdLineRegistry = AppContext::getCMDLineRegistry();
CHECK(cmdLineRegistry->hasParameter(PhylipCmdlineTask::PHYLIP_CMDLINE), );
CHECK(cmdLineRegistry->hasParameter(CmdlineInOutTaskRunner::OUT_DB_ARG), );
CHECK(cmdLineRegistry->hasParameter(CmdlineInOutTaskRunner::IN_DB_ARG), );
CHECK(cmdLineRegistry->hasParameter(CmdlineInOutTaskRunner::IN_ID_ARG), );
CreatePhyTreeSettings settings = fetchSettings();
QString outDbString = cmdLineRegistry->getParameterValue(CmdlineInOutTaskRunner::OUT_DB_ARG);
QString inDbString = cmdLineRegistry->getParameterValue(CmdlineInOutTaskRunner::IN_DB_ARG);
QString idString = cmdLineRegistry->getParameterValue(CmdlineInOutTaskRunner::IN_ID_ARG);
U2OpStatus2Log os;
U2DbiRef outDbiRef = CmdlineInOutTaskRunner::parseDbiRef(outDbString, os);
CHECK_OP(os, );
U2DbiRef inDbiRef = CmdlineInOutTaskRunner::parseDbiRef(inDbString, os);
CHECK_OP(os, );
U2DataId dataId = CmdlineInOutTaskRunner::parseDataId(idString, inDbiRef, os);
CHECK_OP(os, );
Task *t = new PhylipTask(U2EntityRef(inDbiRef, dataId), outDbiRef, settings);
connect(AppContext::getPluginSupport(), SIGNAL(si_allStartUpPluginsLoaded()), new TaskStarter(t), SLOT(registerTask()));
}
void
addActionTypes(Syntax & syntax)
{
/**
* The (optional) last param here indicates whether the task should trigger an Action auto-build.
* If a task is marked as "true". Then MOOSE will attempt to build the associated Action if one is
* not supplied by some other means (usually through the input file or custom Action). Only
* Actions that do not have required parameters and have defaults for all optional parameters can
* be built automatically (See ActionWarehouse.C).
*
* Note: Many of the actions in the "Minimal Problem" section are marked as false. However, we
* can generally force creation of these "Action"s as needed by registering them to syntax that we
* expect to see even if those "Action"s don't normally pick up parameters from the input file.
*/
// clang-format off
/**************************/
/**** Register Actions ****/
/**************************/
registerMooseObjectTask("create_problem", Problem, false);
registerMooseObjectTask("setup_executioner", Executioner, false);
// This task does not construct an object, but it needs all of the parameters that
// would normally be used to construct an object.
registerMooseObjectTask("determine_system_type", Executioner, true);
registerMooseObjectTask("setup_mesh", MooseMesh, false);
registerMooseObjectTask("init_mesh", MooseMesh, false);
registerMooseObjectTask("add_mesh_modifier", MeshModifier, false);
registerMooseObjectTask("add_kernel", Kernel, false);
appendMooseObjectTask ("add_kernel", EigenKernel);
appendMooseObjectTask ("add_kernel", VectorKernel);
registerMooseObjectTask("add_nodal_kernel", NodalKernel, false);
registerMooseObjectTask("add_material", Material, false);
registerMooseObjectTask("add_bc", BoundaryCondition, false);
registerMooseObjectTask("add_function", Function, false);
registerMooseObjectTask("add_distribution", Distribution, false);
registerMooseObjectTask("add_sampler", Sampler, false);
registerMooseObjectTask("add_aux_kernel", AuxKernel, false);
registerMooseObjectTask("add_elemental_field_variable", AuxKernel, false);
registerMooseObjectTask("add_scalar_kernel", ScalarKernel, false);
registerMooseObjectTask("add_aux_scalar_kernel", AuxScalarKernel, false);
registerMooseObjectTask("add_dirac_kernel", DiracKernel, false);
registerMooseObjectTask("add_dg_kernel", DGKernel, false);
registerMooseObjectTask("add_interface_kernel", InterfaceKernel, false);
registerMooseObjectTask("add_constraint", Constraint, false);
registerMooseObjectTask("add_ic", InitialCondition, false);
appendMooseObjectTask ("add_ic", ScalarInitialCondition);
registerMooseObjectTask("add_damper", Damper, false);
registerMooseObjectTask("setup_predictor", Predictor, false);
registerMooseObjectTask("setup_time_stepper", TimeStepper, false);
registerMooseObjectTask("setup_time_integrator", TimeIntegrator, false);
registerMooseObjectTask("add_preconditioning", MoosePreconditioner, false);
registerMooseObjectTask("add_field_split", Split, false);
registerMooseObjectTask("add_user_object", UserObject, false);
appendMooseObjectTask ("add_user_object", Postprocessor);
registerMooseObjectTask("add_postprocessor", Postprocessor, false);
registerMooseObjectTask("add_vector_postprocessor", VectorPostprocessor, false);
registerMooseObjectTask("add_indicator", Indicator, false);
registerMooseObjectTask("add_marker", Marker, false);
registerMooseObjectTask("add_multi_app", MultiApp, false);
registerMooseObjectTask("add_transfer", Transfer, false);
registerMooseObjectTask("add_output", Output, false);
registerMooseObjectTask("add_control", Control, false);
registerMooseObjectTask("add_partitioner", MoosePartitioner, false);
// clang-format on
registerTask("dynamic_object_registration", false);
registerTask("common_output", true);
registerTask("setup_recover_file_base", true);
registerTask("add_bounds_vectors", false);
registerTask("add_periodic_bc", false);
registerTask("add_aux_variable", false);
registerTask("add_external_aux_variables", true);
registerTask("add_variable", false);
registerTask("execute_mesh_modifiers", false);
registerTask("uniform_refine_mesh", false);
registerTask("prepare_mesh", false);
registerTask("add_geometric_rm", true);
registerTask("setup_mesh_complete", false); // calls prepare
registerTask("init_displaced_problem", false);
registerTask("add_algebraic_rm", true);
registerTask("init_problem", true);
registerTask("check_copy_nodal_vars", true);
registerTask("copy_nodal_vars", true);
registerTask("copy_nodal_aux_vars", true);
registerTask("setup_postprocessor_data", false);
registerTask("setup_dampers", true);
registerTask("check_integrity", true);
registerTask("check_integrity_early", true);
registerTask("setup_quadrature", true);
/// Additional Actions
registerTask("no_action", false); // Used for Empty Action placeholders
registerTask("set_global_params", false);
registerTask("setup_adaptivity", false);
registerTask("meta_action", false);
registerTask("setup_debug", false);
registerTask("setup_residual_debug", false);
registerTask("setup_oversampling", false);
registerTask("deprecated_block", false);
registerTask("set_adaptivity_options", false);
registerTask("add_mortar_interface", false);
// Dummy Actions (useful for sync points in the dependencies)
registerTask("setup_function_complete", false);
registerTask("setup_variable_complete", false);
registerTask("ready_to_init", true);
// Output related actions
registerTask("setup_material_output", true);
registerTask("check_output", true);
/**************************/
/****** Dependencies ******/
/**************************/
/**
* The following is the default set of action dependencies for a basic MOOSE problem. The
* formatting of this string is important. Each line represents a set of dependencies that depend
* on the previous line. Items on the same line have equal weight and can be executed in any
* order.
*
* Additional dependencies can be inserted later inside of user applications with calls to
* ActionWarehouse::addDependency("task", "pre_req")
*/
syntax.addDependencySets("(meta_action)"
"(dynamic_object_registration)"
"(common_output)"
"(set_global_params)"
"(setup_recover_file_base)"
"(check_copy_nodal_vars)"
"(setup_mesh)"
"(add_partitioner)"
"(add_geometric_rm)"
"(init_mesh)"
"(prepare_mesh)"
"(add_mesh_modifier)"
"(execute_mesh_modifiers)"
"(add_mortar_interface)"
"(uniform_refine_mesh)"
"(setup_mesh_complete)"
"(determine_system_type)"
"(create_problem)"
"(setup_postprocessor_data)"
"(setup_time_integrator)"
"(setup_executioner)"
"(check_integrity_early)"
"(setup_predictor)"
"(init_displaced_problem)"
"(add_aux_variable, add_variable, add_elemental_field_variable,"
" add_external_aux_variables)"
"(setup_variable_complete)"
"(setup_quadrature)"
"(add_function)"
"(add_distribution)"
"(add_sampler)"
"(add_periodic_bc)"
"(add_user_object)"
"(setup_function_complete)"
"(setup_adaptivity)"
"(set_adaptivity_options)"
"(add_ic)"
"(add_constraint, add_field_split)"
"(add_preconditioning)"
"(setup_time_stepper)"
"(ready_to_init)"
"(setup_dampers)"
"(setup_residual_debug)"
"(add_bounds_vectors)"
"(add_multi_app)"
"(add_transfer)"
"(copy_nodal_vars, copy_nodal_aux_vars)"
"(add_material)"
"(setup_material_output)"
"(add_algebraic_rm)"
"(init_problem)"
"(setup_debug)"
"(add_output)"
"(add_postprocessor)"
"(add_vector_postprocessor)" // MaterialVectorPostprocessor requires this
// to be after material objects are created.
"(add_aux_kernel, add_bc, add_damper, add_dirac_kernel, add_kernel,"
" add_nodal_kernel, add_dg_kernel, add_interface_kernel,"
" add_scalar_kernel, add_aux_scalar_kernel, add_indicator, add_marker)"
"(add_control)"
"(check_output)"
"(check_integrity)");
}
