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In response to referee's comment:
"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in
rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked
automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."
I made the following changes:
- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in
rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked
automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."
I made the following changes:
- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
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<!--
$Rev$: Revision of last commit
$Author$: Author of last commit
$Source$: Source file
$Date$: Date of last commit
This file is part of the Virtual Leaf.
The Virtual Leaf is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
The Virtual Leaf is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with the Virtual Leaf. If not, see <http://www.gnu.org/licenses/>.
Copyright 2010 Michael Guravage.
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="vl" targetNamespace="vl"
elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:annotation>
<xs:documentation> Virtual Leaf </xs:documentation>
</xs:annotation>
<!-- A precooked comment element -->
<xs:element name="comment" type="xs:string"/>
<!-- An element with a integer value named 'v.' -->
<xs:complexType name="iValueType">
<xs:attribute name="v" type="xs:integer"/>
</xs:complexType>
<!-- An element with a real value named 'v.' -->
<xs:complexType name="rValueType">
<xs:attribute name="v" type="xs:float"/>
</xs:complexType>
<!-- Leaf is the root element -->
<xs:element name="leaf">
<xs:complexType>
<xs:sequence>
<xs:element name="comment" minOccurs="0"/>
<xs:element name="parameter" type="ParameterType" minOccurs="0"/>
<xs:element name="code" type="CodeType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="nodes" type="NodesType" minOccurs="0"/>
<xs:element name="cells" type="CellsType" minOccurs="0"/>
<xs:element name="walls" type="WallsType" minOccurs="0"/>
<xs:element name="nodesets" type="NodesetsType" minOccurs="0"/>
<xs:element name="settings" type="SettingsType" minOccurs="0"/>
</xs:sequence>
<xs:attributeGroup ref="leafAttrubutes"/>
</xs:complexType>
</xs:element>
<!-- List of leaf attributes -->
<xs:attributeGroup name="leafAttrubutes">
<xs:attribute name="uri" type="xs:anyURI"/>
<xs:attribute name="date" type="xs:dateTime"/>
<xs:attribute name="simtime" type="xs:integer"/>
</xs:attributeGroup>
<!-- Parameters -->
<xs:complexType name="ParameterType">
<xs:sequence>
<xs:element name="comment" minOccurs="0"/>
<xs:element name="par" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="valarray" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="val" type="rValueType" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="val" type="xs:string"/>
<xs:anyAttribute processContents="skip"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
<!-- Code -->
<xs:complexType name="CodeType">
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="name" type="xs:string" use="required"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<!-- Nodes -->
<xs:complexType name="NodesType">
<xs:sequence>
<xs:element name="comment" minOccurs="0"/>
<xs:element name="node" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attributeGroup ref="nodeAttributes"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attributeGroup ref="nodesAttributes"/>
</xs:complexType>
<!-- A list of node attributes -->
<xs:attributeGroup name="nodeAttributes">
<xs:attribute name="x" type="xs:float" use="required"/>
<xs:attribute name="y" type="xs:float" use="required"/>
<xs:attribute name="fixed" type="xs:boolean"/>
<xs:attribute name="boundary" type="xs:boolean"/>
<xs:attribute name="sam" type="xs:boolean"/>
</xs:attributeGroup>
<!-- A list of nodes attributes -->
<xs:attributeGroup name="nodesAttributes">
<xs:attribute name="n" type="xs:integer" use="required"/>
<xs:attribute name="target_length" type="xs:float" use="required"/>
</xs:attributeGroup>
<!-- Cells -->
<xs:complexType name="CellsType">
<xs:sequence>
<xs:element name="comment" minOccurs="0"/>
<xs:element name="cell" type="CellType" maxOccurs="unbounded"/>
<xs:element name="boundary_polygon" type="CellType"/>
</xs:sequence>
<xs:attributeGroup ref="cellsAttributes"/>
</xs:complexType>
<!-- A list of cells attributes and their types -->
<xs:attributeGroup name="cellsAttributes">
<xs:attribute name="n" type="xs:integer" use="required"/>
<xs:attribute name="offsetx" type="xs:float"/>
<xs:attribute name="offsety" type="xs:float"/>
<xs:attribute name="magnification" type="xs:float"/>
<xs:attribute name="base_area" type="xs:float" use="required"/>
<xs:attribute name="nchem" type="xs:integer" use="required"/>
</xs:attributeGroup>
<!-- Cell -->
<xs:complexType name="CellType">
<xs:sequence>
<xs:element name="node" type="CellNodeType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="wall" type="CellWallType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="chem" type="CellChemType" minOccurs="0"/>
</xs:sequence>
<xs:attributeGroup ref="cellAttributes"/>
</xs:complexType>
<!-- A list of cell attributes and their types. -->
<xs:attributeGroup name="cellAttributes">
<xs:attribute name="index" type="xs:integer" use="required"/>
<xs:attribute name="area" type="xs:float"/>
<xs:attribute name="target_area" type="xs:float" use="required"/>
<xs:attribute name="target_length" type="xs:float"/>
<xs:attribute name="lambda_celllength" type="xs:float"/>
<xs:attribute name="stiffness" type="xs:float"/>
<xs:attribute name="fixed" type="xs:boolean"/>
<xs:attribute name="pin_fixed" type="xs:boolean"/>
<xs:attribute name="at_boundary" type="xs:boolean"/>
<xs:attribute name="dead" type="xs:boolean"/>
<xs:attribute name="source" type="xs:boolean"/>
<xs:attribute name="boundary" type="xs:boolean"/>
<xs:attribute name="div_counter" type="xs:integer"/>
<xs:attribute name="cell_type" type="xs:integer"/>
</xs:attributeGroup>
<!-- Cell Node -->
<xs:complexType name="CellNodeType">
<xs:attribute name="n" type="xs:integer" use="required"/>
</xs:complexType>
<!-- Cell Wall -->
<xs:complexType name="CellWallType">
<xs:attribute name="w" type="xs:integer" use="required"/>
</xs:complexType>
<!-- Cell Chemical -->
<xs:complexType name="CellChemType">
<xs:sequence>
<xs:element name="val" type="rValueType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="n" type="xs:integer" use="required"/>
</xs:complexType>
<!-- Walls -->
<xs:complexType name="WallsType">
<xs:sequence>
<xs:element name="comment" minOccurs="0"/>
<xs:element name="wall" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="transporter1" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="val" type="rValueType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="transporter2" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="val" type="rValueType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="apoplast" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="val" type="rValueType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="index" type="xs:integer" use="required"/>
<xs:attribute name="c1" type="xs:integer" use="required"/>
<xs:attribute name="c2" type="xs:integer" use="required"/>
<xs:attribute name="n1" type="xs:integer" use="required"/>
<xs:attribute name="n2" type="xs:integer" use="required"/>
<xs:attribute name="length" type="xs:float"/>
<xs:attribute name="viz_flux" type="xs:integer"/>
<xs:attribute name="wall_type">
<xs:simpleType>
<xs:restriction base="xs:normalizedString">
<xs:enumeration value="normal"/>
<xs:enumeration value="aux_source"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="n" type="xs:integer" use="required"/>
</xs:complexType>
<!-- Nodesets -->
<xs:complexType name="NodesetsType">
<xs:attribute name="n" type="xs:integer" use="required"/>
</xs:complexType>
<!-- Settings -->
<xs:complexType name="SettingsType">
<xs:sequence>
<xs:element name="comment" minOccurs="0"/>
<xs:element name="setting" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="val" type="xs:boolean" use="required"/>
<xs:anyAttribute processContents="skip"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:schema>
|