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ksteube |
1809 |
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2 |
jfenwick |
3981 |
############################################################################## |
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ksteube |
1312 |
# |
4 |
uqaeller |
6939 |
# Copyright (c) 2003-2020 by The University of Queensland |
5 |
jfenwick |
3981 |
# http://www.uq.edu.au |
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ksteube |
1312 |
# |
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ksteube |
1809 |
# Primary Business: Queensland, Australia |
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jfenwick |
6112 |
# Licensed under the Apache License, version 2.0 |
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# http://www.apache.org/licenses/LICENSE-2.0 |
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ksteube |
1312 |
# |
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jfenwick |
3981 |
# Development until 2012 by Earth Systems Science Computational Center (ESSCC) |
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jfenwick |
4657 |
# Development 2012-2013 by School of Earth Sciences |
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# Development from 2014 by Centre for Geoscience Computing (GeoComp) |
14 |
uqaeller |
6939 |
# Development from 2019 by School of Earth and Environmental Sciences |
15 |
jfenwick |
3981 |
# |
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############################################################################## |
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gross |
899 |
|
18 |
sshaw |
5706 |
from __future__ import print_function, division |
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sshaw |
5571 |
|
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uqaeller |
6939 |
__copyright__="""Copyright (c) 2003-2020 by The University of Queensland |
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jfenwick |
3981 |
http://www.uq.edu.au |
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ksteube |
1809 |
Primary Business: Queensland, Australia""" |
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jfenwick |
6112 |
__license__="""Licensed under the Apache License, version 2.0 |
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http://www.apache.org/licenses/LICENSE-2.0""" |
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jfenwick |
2344 |
__url__="https://launchpad.net/escript-finley" |
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ksteube |
1809 |
|
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gross |
899 |
""" |
28 |
caltinay |
2180 |
Template for the Design which defines regions and features |
29 |
gross |
932 |
for a mesh generator. |
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gross |
899 |
|
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jfenwick |
2625 |
:var __author__: name of author |
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:var __copyright__: copyrights |
33 |
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:var __license__: licence agreement |
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:var __url__: url entry point on documentation |
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:var __version__: version |
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:var __date__: date of the version |
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gross |
899 |
""" |
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__author__="Lutz Gross, l.gross@uq.edu.au" |
40 |
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|
41 |
jfenwick |
3774 |
from .primitives import Primitive, ReversePrimitive, PropertySet, Point, Manifold1D, Manifold2D, Manifold3D |
42 |
gross |
944 |
from xml.dom import minidom |
43 |
gross |
2720 |
import tempfile, os |
44 |
gross |
931 |
|
45 |
gross |
944 |
class TagMap(object): |
46 |
|
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""" |
47 |
caltinay |
2180 |
A class that allows to map tags to names. |
48 |
gross |
944 |
|
49 |
caltinay |
2180 |
Example:: |
50 |
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51 |
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tm=TagMap({5 : x }) |
52 |
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tm.setMap(a=1,x=4) |
53 |
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assert tm.getTags("a") == [ 1 ] |
54 |
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assert tm.getTags("x") == [ 5, 4 ] |
55 |
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assert tm.map(x=10., a=20.) == { 5 : 10, 4: 10, 1 : 20 } |
56 |
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|
57 |
gross |
944 |
""" |
58 |
gross |
1052 |
def __init__(self, mapping={}): |
59 |
gross |
944 |
""" |
60 |
jfenwick |
2625 |
Initializes the mapping. ``mapping`` defines an initial mapping from tag |
61 |
caltinay |
2180 |
to a name. |
62 |
gross |
944 |
""" |
63 |
gross |
1052 |
self.__mapping={} |
64 |
sshaw |
5641 |
for tag, name in sorted(mapping.items(), key=lambda x: x[1]): |
65 |
gross |
944 |
if not isinstance(tag, int): |
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caltinay |
2180 |
raise TypeError("tag needs to be an int") |
67 |
gross |
944 |
if not isinstance(name, str): |
68 |
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raise TypeError("name needs to be a str.") |
69 |
gross |
1052 |
self.__mapping[tag]=name |
70 |
caltinay |
2180 |
|
71 |
gross |
944 |
def setMap(self,**kwargs): |
72 |
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""" |
73 |
caltinay |
2180 |
Sets a new map where <name>=<tag> assigns the tag <tag> to name <name>. |
74 |
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<tag> has to be an integer. If <tag> has been assigned to a name before |
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the mapping will be overwritten. Otherwise a new mapping <tag> -> <name> |
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is set. Notice that a single name can be assigned to different tags. |
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gross |
944 |
""" |
78 |
sshaw |
5641 |
for name, tag in sorted(kwargs.items(), key=lambda x: x[0]): |
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gross |
944 |
if not isinstance(tag, int): |
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caltinay |
2180 |
raise TypeError("tag needs to be an int") |
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gross |
1052 |
self.__mapping[tag]=name |
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caltinay |
2180 |
|
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gross |
944 |
def getTags(self,name=None): |
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""" |
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jfenwick |
2625 |
Returns a list of the tags assigned to ``name``. If name is not present |
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caltinay |
2180 |
a list of all tags is returned. |
87 |
gross |
944 |
""" |
88 |
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if name == None: |
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sshaw |
5641 |
out=sorted(self.__mapping.keys()) |
90 |
gross |
944 |
else: |
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out=[] |
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sshaw |
5641 |
for tag, arg in sorted(self.__mapping.items(), key=lambda x: x[0]): |
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gross |
944 |
if arg == name: out.append(tag) |
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return out |
95 |
caltinay |
2180 |
|
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gross |
999 |
def getName(self,tag=None): |
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gross |
944 |
""" |
98 |
jfenwick |
2625 |
Returns the name of a tag. If ``tag`` is not present a list of all names |
99 |
caltinay |
2180 |
is returned. |
100 |
gross |
944 |
""" |
101 |
gross |
999 |
if tag == None: |
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sshaw |
5641 |
return sorted(list(set(self.__mapping.values()))) |
103 |
gross |
999 |
else: |
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gross |
1052 |
return self.__mapping[tag] |
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gross |
997 |
|
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gross |
944 |
def getMapping(self): |
107 |
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""" |
108 |
caltinay |
2180 |
Returns a dictionary where the tags define the keys and the values the |
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corresponding names. |
110 |
gross |
944 |
""" |
111 |
gross |
1052 |
return self.__mapping |
112 |
gross |
997 |
|
113 |
gross |
944 |
def map(self,default=0,**kwargs): |
114 |
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""" |
115 |
caltinay |
2180 |
Returns a dictionary where the tags define the keys and the values give |
116 |
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the values assigned to the tag via name and kwargs:: |
117 |
gross |
944 |
|
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caltinay |
2180 |
tm=TagMap(x=5) |
119 |
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tm.setMap(a=1,x=4) |
120 |
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print tm.map(x=10., a=20.) |
121 |
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{ 5 : 10, 4: 10, 1 : 20 } |
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The default is used for tags which map onto name with unspecified |
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values. |
125 |
gross |
944 |
""" |
126 |
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out={} |
127 |
gross |
1052 |
for tag in self.__mapping: |
128 |
jfenwick |
3774 |
if self.__mapping[tag] in kwargs: |
129 |
gross |
1052 |
out[tag]=kwargs[self.__mapping[tag]] |
130 |
gross |
944 |
else: |
131 |
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out[tag]=default |
132 |
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return out |
133 |
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def insert(self,data,default=0,**kwargs): |
135 |
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""" |
136 |
jfenwick |
2625 |
Inserts values into the `esys.escript.Data` object according to the |
137 |
caltinay |
2180 |
given values assigned to the keywords. The default is used for tags |
138 |
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which map onto name with unspecified values. |
139 |
gross |
944 |
""" |
140 |
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d=self.map(default=default,**kwargs) |
141 |
sshaw |
5641 |
for t,v in sorted(d.items(), key=lambda x: x[0]): |
142 |
gross |
944 |
data.setTaggedValue(t,v) |
143 |
caltinay |
2180 |
|
144 |
gross |
1044 |
def passToDomain(self,domain): |
145 |
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""" |
146 |
jfenwick |
2625 |
Passes the tag map to the `esys.escript.Domain` ``domain``. |
147 |
gross |
1044 |
""" |
148 |
sshaw |
5641 |
for tag, name in sorted(self.__mapping.items(), key=lambda x: x[1]): |
149 |
jfenwick |
3774 |
print("Tag",name, "is mapped to id ", tag) |
150 |
gross |
1044 |
domain.setTagMap(name,tag) |
151 |
caltinay |
2180 |
|
152 |
gross |
944 |
def toDOM(self,dom): |
153 |
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""" |
154 |
jfenwick |
2625 |
Adds object to ``dom``. |
155 |
gross |
944 |
""" |
156 |
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tm=dom.createElement("TagMap") |
157 |
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dom.appendChild(tm) |
158 |
sshaw |
5641 |
for tag,name in sorted(self.getMapping().items(), key=lambda x: x[1]): |
159 |
gross |
944 |
item_dom=dom.createElement("map") |
160 |
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tag_dom=dom.createElement("tag") |
161 |
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name_dom=dom.createElement("name") |
162 |
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tag_dom.appendChild(dom.createTextNode(str(tag))) |
163 |
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name_dom.appendChild(dom.createTextNode(str(name))) |
164 |
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item_dom.appendChild(tag_dom) |
165 |
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item_dom.appendChild(name_dom) |
166 |
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tm.appendChild(item_dom) |
167 |
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return tm |
168 |
caltinay |
2180 |
|
169 |
gross |
944 |
def fromDom(self,node): |
170 |
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""" |
171 |
jfenwick |
2625 |
Fills names and tags from dom ``node``. |
172 |
gross |
944 |
""" |
173 |
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for node in node.childNodes: |
174 |
|
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if isinstance(node, minidom.Element): |
175 |
|
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if node.tagName == 'map': |
176 |
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tag=int(node.getElementsByTagName("tag")[0].firstChild.nodeValue.strip()) |
177 |
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name=str(node.getElementsByTagName("name")[0].firstChild.nodeValue.strip()) |
178 |
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self.setMap(**{ name : tag }) |
179 |
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return |
180 |
|
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|
181 |
gross |
999 |
def fillFromXML(self,iostream): |
182 |
gross |
944 |
""" |
183 |
caltinay |
2180 |
Uses the XML file or string to set the mapping. |
184 |
gross |
944 |
""" |
185 |
gross |
999 |
if isinstance(iostream,str): |
186 |
|
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dom=minidom.parseString(iostream) |
187 |
gross |
944 |
else: |
188 |
gross |
999 |
dom=minidom.parse(iostream) |
189 |
gross |
944 |
root=dom.getElementsByTagName('ESys')[0] |
190 |
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for node in root.childNodes: |
191 |
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if isinstance(node, minidom.Element): |
192 |
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if node.tagName == 'TagMap': |
193 |
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self.fromDom(node) |
194 |
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return |
195 |
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|
196 |
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def writeXML(self,iostream=None): |
197 |
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""" |
198 |
jfenwick |
2625 |
Serializes self as XML into ``iostream`` or if not present returns the |
199 |
caltinay |
2180 |
XML as string. |
200 |
gross |
944 |
""" |
201 |
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dom=minidom.Document() |
202 |
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esys=dom.createElement('ESys') |
203 |
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esys.appendChild(self.toDOM(dom)) |
204 |
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dom.appendChild(esys) |
205 |
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if iostream == None: |
206 |
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return dom.toprettyxml() |
207 |
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else: |
208 |
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iostream.write(dom.toprettyxml()) |
209 |
caltinay |
2180 |
|
210 |
sshaw |
4559 |
class AbstractDesign(object): |
211 |
gross |
899 |
""" |
212 |
caltinay |
2180 |
Template for a design which defines the input for a mesh generator. |
213 |
gross |
2717 |
|
214 |
jfenwick |
6647 |
:note: class variable GMSH - `gmsh <http://www.geuz.org/gmsh/>`_ file format |
215 |
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:note: class variable IDEAS - `I_DEAS <http://www.plm.automation.siemens.com/en_us/products/nx/>`_ universal file format |
216 |
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:note: class variable VRML - `VRML <http://www.w3.org/MarkUp/VRML/>`_ file format |
217 |
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:note: class variable STL - `STL <http://en.wikipedia.org/wiki/STL_(file_format)>`_ file format |
218 |
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:note: class variable NASTRAN - `Nastran <http://simcompanion.mscsoftware.com/infocenter/index?page=content&channel=DOCUMENTATION>`_ bulk data format |
219 |
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:note: class variable MEDIT - `Medit <http://www-rocq.inria.fr/OpenFEM/Doc/>`_ file format |
220 |
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:note: class variable CGNS - `CGNS <http://cgns.sourceforge.net/>`_ file format |
221 |
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:note: class variable PLOT3D - `Plot3D <http://www.plot3d.net/>`_ file format |
222 |
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:note: class variable DIFFPACK- `Diffpack <http://www.diffpack.com/>`_ file format |
223 |
gross |
899 |
""" |
224 |
gross |
2717 |
GMSH="msh" |
225 |
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IDEAS="unv" |
226 |
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VRML="vrml" |
227 |
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STL="stl" |
228 |
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NASTRAN="bdf" |
229 |
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MEDIT="mesh" |
230 |
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CGNS="cgns" |
231 |
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PLOT3D="p3d" |
232 |
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DIFFPACK="diff" |
233 |
gross |
932 |
def __init__(self,dim=3,element_size=1.,order=1,keep_files=False): |
234 |
gross |
899 |
""" |
235 |
caltinay |
2180 |
Initializes a design. |
236 |
gross |
932 |
|
237 |
jfenwick |
2625 |
:param dim: spatial dimension |
238 |
|
|
:param element_size: global element size |
239 |
|
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:param order: element order |
240 |
|
|
:param keep_files: flag to keep work files |
241 |
caltinay |
2180 |
""" |
242 |
gross |
932 |
self.clearItems() |
243 |
|
|
self.setElementSize(element_size) |
244 |
gross |
899 |
self.setDim(dim) |
245 |
gross |
932 |
self.setElementOrder(order) |
246 |
gross |
2717 |
self.setFileFormat() |
247 |
gross |
932 |
if keep_files: |
248 |
|
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self.setKeepFilesOn() |
249 |
|
|
else: |
250 |
|
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self.setKeepFilesOff() |
251 |
caltinay |
3734 |
self.__mshname="" |
252 |
|
|
self.setMeshFileName() |
253 |
caltinay |
2180 |
|
254 |
gross |
899 |
def setDim(self,dim=3): |
255 |
gross |
932 |
""" |
256 |
caltinay |
2180 |
Sets the spatial dimension. |
257 |
gross |
932 |
""" |
258 |
caltinay |
2180 |
if not dim in [1,2,3]: |
259 |
gross |
932 |
raise ValueError("only dimension 1, 2, 3 are supported.") |
260 |
gross |
899 |
self.__dim=dim |
261 |
caltinay |
2180 |
|
262 |
gross |
899 |
def getDim(self,dim=3): |
263 |
gross |
932 |
""" |
264 |
caltinay |
2180 |
Returns the spatial dimension. |
265 |
gross |
932 |
""" |
266 |
gross |
899 |
return self.__dim |
267 |
caltinay |
2180 |
|
268 |
gross |
899 |
def setElementOrder(self,order=1): |
269 |
gross |
932 |
""" |
270 |
caltinay |
2180 |
Sets the element order. |
271 |
gross |
932 |
""" |
272 |
|
|
if not order in [1,2]: |
273 |
caltinay |
2180 |
raise ValueError("only element order 1 or 2 is supported.") |
274 |
gross |
899 |
self.__order=order |
275 |
caltinay |
2180 |
|
276 |
gross |
999 |
def getElementOrder(self): |
277 |
gross |
932 |
""" |
278 |
caltinay |
2180 |
Returns the element order. |
279 |
gross |
932 |
""" |
280 |
gross |
899 |
return self.__order |
281 |
caltinay |
2180 |
|
282 |
gross |
999 |
def setElementSize(self,element_size=1.): |
283 |
gross |
932 |
""" |
284 |
caltinay |
2180 |
Sets the global element size. |
285 |
gross |
932 |
""" |
286 |
|
|
if element_size<=0.: |
287 |
gross |
999 |
raise ValueError("element size needs to be positive.") |
288 |
gross |
932 |
self.__element_size=element_size |
289 |
caltinay |
2180 |
|
290 |
gross |
999 |
def getElementSize(self): |
291 |
gross |
932 |
""" |
292 |
caltinay |
2180 |
Returns the global element size. |
293 |
gross |
932 |
""" |
294 |
|
|
return self.__element_size |
295 |
caltinay |
2180 |
|
296 |
gross |
932 |
def setKeepFilesOn(self): |
297 |
|
|
""" |
298 |
caltinay |
2180 |
Work files are kept at the end of the generation. |
299 |
gross |
932 |
""" |
300 |
|
|
self.__keep_files=True |
301 |
caltinay |
2180 |
|
302 |
gross |
932 |
def setKeepFilesOff(self): |
303 |
|
|
""" |
304 |
caltinay |
2180 |
Work files are deleted at the end of the generation |
305 |
gross |
932 |
""" |
306 |
|
|
self.__keep_files=False |
307 |
caltinay |
2180 |
|
308 |
gross |
932 |
def keepFiles(self): |
309 |
|
|
""" |
310 |
caltinay |
2180 |
Returns True if work files are kept, False otherwise. |
311 |
gross |
932 |
""" |
312 |
|
|
return self.__keep_files |
313 |
caltinay |
2180 |
|
314 |
gross |
932 |
def addItems(self,*items): |
315 |
|
|
""" |
316 |
caltinay |
2180 |
Adds items to the design. |
317 |
gross |
932 |
""" |
318 |
gross |
2683 |
new_items=[] |
319 |
gross |
932 |
for i in range(len(items)): |
320 |
|
|
if not isinstance(items[i],(Primitive, ReversePrimitive)): |
321 |
|
|
raise TypeError("%s-th argument is not a Primitive object"%i) |
322 |
gross |
2560 |
if isinstance(items[i],PropertySet): |
323 |
gross |
2683 |
q=items[i] |
324 |
|
|
else: |
325 |
|
|
q=PropertySet("__%s__"%(items[i].getID()), items[i]) |
326 |
|
|
for p in self.getAllPrimitives(): |
327 |
|
|
if isinstance(p, PropertySet): |
328 |
|
|
if q.getName() == p.getName(): |
329 |
|
|
raise ValueError("Property set name %s is allready in use."%q.getName()) |
330 |
|
|
new_items.append(q) |
331 |
|
|
for q in new_items: self.__items.append(q) |
332 |
caltinay |
2180 |
|
333 |
gross |
932 |
def getItems(self): |
334 |
|
|
""" |
335 |
caltinay |
2180 |
Returns a list of the items used in the design. |
336 |
gross |
932 |
""" |
337 |
gross |
899 |
return self.__items |
338 |
caltinay |
2180 |
|
339 |
gross |
932 |
def clearItems(self): |
340 |
|
|
""" |
341 |
caltinay |
2180 |
Removes all items from the design. |
342 |
gross |
932 |
""" |
343 |
|
|
self.__items=[] |
344 |
caltinay |
2180 |
|
345 |
gross |
932 |
def getAllPrimitives(self): |
346 |
|
|
""" |
347 |
caltinay |
2180 |
Returns a list of all primitives used to create the design. |
348 |
|
|
Each primitive appears once. The primitives are ordered by their |
349 |
|
|
order of generation. |
350 |
gross |
932 |
""" |
351 |
gross |
1021 |
prims=[] |
352 |
caltinay |
2180 |
for i in self.getItems(): |
353 |
gross |
1021 |
for p in i.getPrimitives(): |
354 |
|
|
if not p in prims: prims.append(p) |
355 |
gross |
932 |
prims.sort() |
356 |
|
|
return prims |
357 |
gross |
901 |
|
358 |
gross |
932 |
def setOptions(self,**kwargs): |
359 |
|
|
""" |
360 |
caltinay |
2180 |
Sets options of the mesh generator. |
361 |
gross |
932 |
|
362 |
jfenwick |
2625 |
:note: this method is typically overwritten by a particular design |
363 |
caltinay |
2180 |
implementation. |
364 |
gross |
932 |
""" |
365 |
|
|
pass |
366 |
gross |
2717 |
def generate(self): |
367 |
|
|
""" |
368 |
|
|
generate output file |
369 |
|
|
|
370 |
|
|
:note: this method may be overwritten by a particular design |
371 |
|
|
implementation. |
372 |
|
|
""" |
373 |
|
|
self.getMeshHandler() |
374 |
caltinay |
2180 |
|
375 |
gross |
932 |
def getMeshHandler(self): |
376 |
|
|
""" |
377 |
caltinay |
2180 |
Returns a handle to a mesh meshing the design. |
378 |
gross |
932 |
|
379 |
jfenwick |
2625 |
:note: this method has to be overwritten by a particular design |
380 |
caltinay |
2180 |
implementation. |
381 |
gross |
932 |
""" |
382 |
|
|
raise NotImplementedError() |
383 |
|
|
|
384 |
gross |
997 |
def getTagMap(self): |
385 |
gross |
944 |
""" |
386 |
jfenwick |
2625 |
Returns a `TagMap` to map the names of `PropertySet` s to tags. |
387 |
gross |
944 |
""" |
388 |
|
|
m={} |
389 |
|
|
for p in self.getAllPrimitives(): |
390 |
gross |
997 |
if isinstance(p, PropertySet): m[ p.getTag() ] = p.getName() |
391 |
gross |
944 |
return TagMap(m) |
392 |
caltinay |
2180 |
|
393 |
gross |
2717 |
def setFileFormat(self,format='msh'): |
394 |
|
|
""" |
395 |
|
|
Sets the file format to be used. |
396 |
|
|
|
397 |
|
|
:param format: format to be used. needs to be one of |
398 |
|
|
|
399 |
|
|
""" |
400 |
|
|
if not format in [ self.GMSH, self.IDEAS, self.VRML, self.STL, self.NASTRAN, self.MEDIT, self.CGNS, self.PLOT3D, self.DIFFPACK] : |
401 |
jfenwick |
3774 |
raise ValueError("unknown file format %s."%format) |
402 |
gross |
2717 |
self.__fileformat=format |
403 |
|
|
|
404 |
|
|
def getFileFormat(self): |
405 |
|
|
""" |
406 |
|
|
Returns the file format |
407 |
|
|
""" |
408 |
|
|
return self.__fileformat |
409 |
|
|
|
410 |
|
|
def setMeshFileName(self, name=None): |
411 |
|
|
""" |
412 |
|
|
Sets the name for the mesh file. If no name is given a name is generated. |
413 |
|
|
""" |
414 |
caltinay |
3734 |
if self.__mshname: |
415 |
|
|
os.unlink(self.__mshname) |
416 |
gross |
2717 |
if name == None: |
417 |
caltinay |
3782 |
self.__mshname_set=False |
418 |
gross |
2717 |
tmp_f_id=tempfile.mkstemp(suffix="."+self.getFileFormat()) |
419 |
|
|
self.__mshname=tmp_f_id[1] |
420 |
|
|
os.close(tmp_f_id[0]) |
421 |
|
|
else: |
422 |
|
|
self.__mshname=name |
423 |
caltinay |
3782 |
self.__mshname_set=True |
424 |
gross |
2717 |
|
425 |
|
|
def getMeshFileName(self): |
426 |
|
|
""" |
427 |
|
|
Returns the name of the mesh file. |
428 |
|
|
""" |
429 |
|
|
return self.__mshname |
430 |
|
|
|
431 |
|
|
|
432 |
|
|
|