cmiss_cellml.f90 File Reference

This module is a OpenCMISS(cm) buffer module to OpenCMISS(cellml). More...

Go to the source code of this file.

Data Types
interface	cmiss_cellml::map_cellml_variable_type_to_field_type
	Map a CellML variable type from OpenCMISS(cellml) to a CellML field type. More...
interface	cmiss_cellml::map_cellml_field_type_to_variable_type
	Map a CellML field type to a CellML variable type from OpenCMISS(cellml). More...
interface	cmiss_cellml::cellml_model_import
interface	cmiss_cellml::cellml_variable_set_as_known
interface	cmiss_cellml::cellml_variable_set_as_wanted
interface	cmiss_cellml::cellml_create_cellml_to_field_map
interface	cmiss_cellml::cellml_create_field_to_cellml_map
interface	cmiss_cellml::cellml_field_component_get

Modules
module	cmiss_cellml
	This module is a OpenCMISS(cm) buffer module to OpenCMISS(cellml).

Functions/Subroutines
subroutine, public	cmiss_cellml::cellml_cellml_to_field_update (CELLML, ERR, ERROR,)
	Updates any mapped fields from the cellml fields. More...
subroutine, public	cmiss_cellml::cellml_create_start (CELLML_USER_NUMBER, REGION, CELLML, ERR, ERROR,)
	Set up the CellML environment in the given region. For a given region, create a CellML environment that will be used to define CellML models in openCMISS. This will simply create and initialise an empty CellML environment object in the specified region with the specified unique identifier number. Also set some flag to indicate the CellML environment object is in the process of being created and should not yet be used. More...
subroutine, public	cmiss_cellml::cellml_create_finish (CELLML, ERR, ERROR,)
	Finish creating the CellML environment. At this point we know all the variables that are known and wanted so can generate the final code. Check the provided CellML environment object and if it all looks good clear the "in progress" flag to indicate the object is now ready for use. More...
subroutine, public	cmiss_cellml::cellml_destroy (CELLML, ERR, ERROR,)
	Destroys the given CellML environment. More...
subroutine, public	cmiss_cellml::cellml_field_to_cellml_update (CELLML, ERR, ERROR,)
	Updates any cellml fields from the mapped fields. More...
subroutine	cmiss_cellml::cellml_finalise (CELLML, ERR, ERROR,)
	Finalise a CellML environment and deallocate all memory. More...
subroutine	cmiss_cellml::cellml_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment and deallocate all memory. More...
subroutine, public	cmiss_cellml::cellml_field_maps_create_finish (CELLML, ERR, ERROR,)
	Finish creating the field maps for a CellML environment. More...
subroutine, public	cmiss_cellml::cellml_field_maps_create_start (CELLML, ERR, ERROR,)
	Start the creation of field maps for a CellML environment. More...
subroutine	cmiss_cellml::cellml_field_maps_finalise (CELLML_FIELD_MAPS, ERR, ERROR,)
	Finalise a CellML maps and deallocate all memory. More...
subroutine	cmiss_cellml::cellml_field_maps_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML field mpas. More...
subroutine	cmiss_cellml::cellml_model_finalise (CELLML_MODEL, ERR, ERROR,)
	Finalise a CellML model and deallocate all memory. More...
subroutine	cmiss_cellml::cellml_model_initialise (CELLML_MODEL, ERR, ERROR,)
	Initialise a CellML model. More...
subroutine	cmiss_cellml::cellml_model_map_finalise (CELLML_MODEL_MAP, ERR, ERROR,)
	Finalise a CellML model map and deallocate all memory. More...
subroutine	cmiss_cellml::cellml_model_map_initialise (CELLML_MODEL_MAP, ERR, ERROR,)
	Initialise a CellML model map. More...
subroutine	cmiss_cellml::cellml_model_maps_finalise (CELLML_MODEL_MAPS, ERR, ERROR,)
	Finalise a CellML model maps and deallocate all memory. More...
subroutine	cmiss_cellml::cellml_model_maps_initialise (CELLML_MODEL_MAPS, ERR, ERROR,)
	Initialise a CellML model maps. More...
subroutine	cmiss_cellml::cellml_model_import_c (CELLML, URI, MODEL_INDEX, ERR, ERROR,)
	Import the specified CellML model into the given CellML environment object. More...
subroutine	cmiss_cellml::cellml_model_import_vs (CELLML, URI, MODEL_INDEX, ERR, ERROR,)
	Import the specified CellML model into the given CellML environment object. More...
subroutine	cmiss_cellml::cellml_variable_set_as_known_c (CELLML, MODEL_INDEX, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be known - i.e., the variable's value will be set by an OpenCMISS field. More...
subroutine	cmiss_cellml::cellml_variable_set_as_known_vs (CELLML, MODEL_USER_NUMBER, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be known - i.e., the variable's value will be set by an OpenCMISS field. More...
subroutine	cmiss_cellml::cellml_variable_set_as_wanted_c (CELLML, MODEL_INDEX, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be wanted - i.e., the variable's value will used by an OpenCMISS field. More...
subroutine	cmiss_cellml::cellml_variable_set_as_wanted_vs (CELLML, MODEL_USER_NUMBER, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be wanted - i.e., the variable's value will be used by an OpenCMISS field. More...
subroutine	cmiss_cellml::cellml_create_cellml_to_field_map_c (CELLML, MODEL_INDEX, VARIABLE_ID, CELLML_PARAMETER_SET, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, ERR, ERROR,)
	Create a CellML model variable to field variable component map. More...
subroutine	cmiss_cellml::cellml_create_cellml_to_field_map_vs (CELLML, MODEL_USER_NUMBER, VARIABLE_ID, CELLML_PARAMETER_SET, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, ERR, ERROR,)
	Create a CellML model variable to field variable component map. More...
subroutine	cmiss_cellml::cellml_create_field_to_cellml_map_c (CELLML, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, MODEL_INDEX, VARIABLE_ID, CELLML_PARAMETER_SET, ERR, ERROR,)
	Create a field variable component to CellML model variable map. More...
subroutine	cmiss_cellml::cellml_create_field_to_cellml_map_vs (CELLML, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, MODEL_USER_NUMBER, VARIABLE_ID, CELLML_PARAMETER_SET, ERR, ERROR,)
	Create a field variable component to CellML model variable map. More...
subroutine, public	cmiss_cellml::cellml_fieldmodeldofset (modelVariable, modelDofIdx, field, variableType, parameterSetIdx, componentIdx, value, err, error,)
	Set the dof in a field specified by a model DOF and component to a value. More...
subroutine	cmiss_cellml::cellml_models_field_check (MODELS_FIELD, ERR, ERROR,)
	Checks a CellML environment models field for correctness. More...
subroutine, public	cmiss_cellml::cellml_models_field_create_start (MODEL_FIELD_USER_NUMBER, CELLML, MODELS_FIELD, ERR, ERROR,)
	Start the creation of the models field for the given CellML environment. More...
subroutine, public	cmiss_cellml::cellml_models_field_create_finish (CELLML, ERR, ERROR,)
	Finish the creation of the models field for the given CellML environment. More...
subroutine	cmiss_cellml::cellml_models_field_finalise (MODELS_FIELD, ERR, ERROR,)
	Finalise a CellML environment models field and deallocate all memory. More...
subroutine, public	cmiss_cellml::cellml_models_field_get (CELLML, MODELS_FIELD, ERR, ERROR,)
	Returns the models field for the given CellML environment. More...
subroutine	cmiss_cellml::cellml_models_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment models field. More...
subroutine, public	cmiss_cellml::cellml_state_field_create_start (STATE_FIELD_USER_NUMBER, CELLML, STATE_FIELD, ERR, ERROR,)
	Start the creation of the state field for the given CellML environment. More...
subroutine, public	cmiss_cellml::cellml_state_field_create_finish (CELLML, ERR, ERROR,)
	Finialse the creation of the state field for the given CellML environment. Finish creating the state variable field for the provided CellML environment. More...
subroutine	cmiss_cellml::cellml_state_field_finalise (STATE_FIELD, ERR, ERROR,)
	Finalise a CellML environment state field and deallocate all memory. More...
subroutine, public	cmiss_cellml::cellml_state_field_get (CELLML, STATE_FIELD, ERR, ERROR,)
	Returns the state field for the given CellML environment. More...
subroutine	cmiss_cellml::cellml_state_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment models field. More...
subroutine	cmiss_cellml::cellml_field_component_get_c (CELLML, MODEL_INDEX, CELLML_FIELD_TYPE, VARIABLE_ID, COMPONENT_USER_NUMBER, ERR, ERROR,)
	Find the component ID in the given field for the variable defined by the given variable ID in the provided CellML environment. This generic routine will be used to map variable ID's in CellML models to components in the various fields defined in the CellML models defined for the provided CellML environment. More...
subroutine	cmiss_cellml::cellml_field_component_get_vs (CELLML, MODEL_INDEX, CELLML_FIELD_TYPE, VARIABLE_ID, COMPONENT_USER_NUMBER, ERR, ERROR,)
	Find the component ID in the given field for the variable defined by the given variable ID in the provided CellML environment. This generic routine will be used to map variable ID's in CellML models to components in the various fields defined in the CellML models defined for the provided CellML environment. More...
subroutine, public	cmiss_cellml::cellml_intermediate_field_create_start (INTERMEDIATE_FIELD_USER_NUMBER, CELLML, INTERMEDIATE_FIELD, ERR, ERROR,)
	Create a field used to store intermediate variables of interest. More...
subroutine, public	cmiss_cellml::cellml_intermediate_field_create_finish (CELLML, ERR, ERROR,)
	Finialse the creation of the intermediate field for the given CellML environment. Finish creating the intermediate variable field for the provided CellML environment. More...
subroutine	cmiss_cellml::cellml_intermediate_field_finalise (INTERMEDIATE_FIELD, ERR, ERROR,)
	Finalise a CellML environment models field and deallocate all memory. More...
subroutine, public	cmiss_cellml::cellml_intermediate_field_get (CELLML, INTERMEDIATE_FIELD, ERR, ERROR,)
	Returns the intermediate field for the given CellML environment. More...
subroutine	cmiss_cellml::cellml_intermediate_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment intermediate field. More...
subroutine, public	cmiss_cellml::cellml_parameters_field_create_start (PARAMETERS_FIELD_USER_NUMBER, CELLML, PARAMETERS_FIELD, ERR, ERROR,)
	Start the creation of the parameters field for the given CellML environment. More...
subroutine, public	cmiss_cellml::cellml_parameters_field_create_finish (CELLML, ERR, ERROR,)
	Finish the creation of the parameters field for the given CellML environment. More...
subroutine	cmiss_cellml::cellml_parameters_field_finalise (PARAMETERS_FIELD, ERR, ERROR,)
	Finalise a CellML environment parameters field and deallocate all memory. More...
subroutine, public	cmiss_cellml::cellml_parameters_field_get (CELLML, PARAMETERS_FIELD, ERR, ERROR,)
	Returns the parameters field for the given CellML environment. More...
subroutine	cmiss_cellml::cellml_parameters_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment parameters field. More...
subroutine, public	cmiss_cellml::cellml_generate (CELLML, ERR, ERROR,)
	Validate and instantiate the specified CellML environment. Users should call this routine once they have set up the CellML environment to allow the CellML environment to be validated and instantiated into computable code. More...
subroutine, public	cmiss_cellml::cellml_user_number_find (USER_NUMBER, REGION, CELLML, ERR, ERROR,)
	Finds and returns in CELLML a pointer to the CellML environment identified by USER_NUMBER on a region. If no CellML environment with that USER_NUMBER exists CELLML is left nullified. More...
subroutine, public	cmiss_cellml::cellml_environments_finalise (CELLML_ENVIRONMENTS, ERR, ERROR,)
	Finalises the CellML environments and deallocates all memory. More...
subroutine, public	cmiss_cellml::cellml_environments_initialise (REGION, ERR, ERROR,)
	Initialises the CellML environments. More...
integer(intg) function	cmiss_cellml::map_cellml_variable_type_to_field_type_intg (CELLML_VARIABLE_TYPE, ERR, ERROR)
	Maps a CellML variable type to a CellML field type (. More...
integer(intg) function	cmiss_cellml::map_cellml_field_type_to_variable_type_intg (CELLML_FIELD_TYPE, ERR, ERROR)
	Maps a CellML field type to a CellML variable type (. More...

Variables
integer(intg), parameter, public	cmiss_cellml::cellml_models_field = 1
	CellML models field. More...
integer(intg), parameter, public	cmiss_cellml::cellml_state_field = 2
	CellML state field. More...
integer(intg), parameter, public	cmiss_cellml::cellml_intermediate_field = 3
	CellML intermediate field. More...
integer(intg), parameter, public	cmiss_cellml::cellml_parameters_field = 4
	CellML parameters field. More...
integer(intg), parameter	cmiss_cellml::cellml_map_to_field_type = 1
	A CellML to field mapping type. More...
integer(intg), parameter	cmiss_cellml::cellml_map_from_field_type = 2
	A field to CellML mapping type. More...
integer(intg), parameter	cmiss_cellml::cellml_models_field_not_checked = -2
	The CellML environment models field has not been checked. More...
integer(intg), parameter, public	cmiss_cellml::cellml_models_field_not_constant =-1
	The CellML environement models field is not constant. More...

Detailed Description

This module is a OpenCMISS(cm) buffer module to OpenCMISS(cellml).

Author

David Nickerson nicke.nosp@m.rso@.nosp@m.users.nosp@m..sou.nosp@m.rcefo.nosp@m.rge..nosp@m.net

LICENSE

Version: MPL 1.1/GPL 2.0/LGPL 2.1

The contents of this file are subject to the Mozilla Public License Version 1.1 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.mozilla.org/MPL/

Software distributed under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License.

The Original Code is OpenCMISS

The Initial Developer of the Original Code is University of Auckland, Auckland, New Zealand, the University of Oxford, Oxford, United Kingdom and King's College, London, United Kingdom. Portions created by the University of Auckland, the University of Oxford and King's College, London are Copyright (C) 2007-2010 by the University of Auckland, the University of Oxford and King's College, London. All Rights Reserved.

Contributor(s): Chris Bradley

Alternatively, the contents of this file may be used under the terms of either the GNU General Public License Version 2 or later (the "GPL"), or the GNU Lesser General Public License Version 2.1 or later (the "LGPL"), in which case the provisions of the GPL or the LGPL are applicable instead of those above. If you wish to allow use of your version of this file only under the terms of either the GPL or the LGPL, and not to allow others to use your version of this file under the terms of the MPL, indicate your decision by deleting the provisions above and replace them with the notice and other provisions required by the GPL or the LGPL. If you do not delete the provisions above, a recipient may use your version of this file under the terms of any one of the MPL, the GPL or the LGPL.

Definition in file cmiss_cellml.f90.