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------------------------------------------------------------
revno: 2045
committer: Anton Gladky <gladky.anton@xxxxxxxxx>
branch nick: trunk
timestamp: Sun 2010-02-21 01:04:22 +0100
message:
  1. spheresToFile() has been fixed and moved to export file. Do we need "consider=lambda id: True" there?
  2. ymport.ascii() was renamed to spheresFromFile; wenjieFormat was deleted there. The function is rewritten, comments are available now.
  3. Added export.spheresToFile() and ymport.ascii() examples to regular-sphere-pack.py.
  4. In timing.py InteractionDispatcher->InteractionDispatchers
  5. Some default values in scons were changed to make YADE compilable with "standard" Ubuntu machine with 4GB RAM: chunkSize=7, jobs=2
added:
  scripts/test/regular-sphere-pack-FromFile
modified:
  SConstruct
  py/SConscript
  py/export.py
  py/timing.py
  py/utils.py
  py/ymport.py
  scripts/test/regular-sphere-pack.py


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=== modified file 'SConstruct'
--- SConstruct	2010-02-18 07:59:29 +0000
+++ SConstruct	2010-02-21 00:04:22 +0000
@@ -140,11 +140,11 @@
 	ListVariable('exclude','Yade components that will not be built','none',names=['gui','extra','common','dem','lattice','snow']),
 	EnumVariable('PGO','Whether to "gen"erate or "use" Profile-Guided Optimization','',['','gen','use'],{'no':'','0':'','false':''},1),
 	ListVariable('features','Optional features that are turned on','log4cxx,opengl,gts,openmp,vtk',names=['opengl','log4cxx','cgal','openmp','gts','vtk','python','eigen','nowm3','never_use_this_one']),
-	('jobs','Number of jobs to run at the same time (same as -j, but saved)',4,None,int),
+	('jobs','Number of jobs to run at the same time (same as -j, but saved)',2,None,int),
 	#('extraModules', 'Extra directories with their own SConscript files (must be in-tree) (whitespace separated)',None,None,Split),
 	('buildPrefix','Where to create build-[version][variant] directory for intermediary files','..'),
 	EnumVariable('linkStrategy','How to link plugins together',defOptions['linkStrategy'],['per-class','per-pkg[broken]','monolithic','static[broken]']),
-	('chunkSize','Maximum files to compile in one translation unit when building plugins.',20,None,int),
+	('chunkSize','Maximum files to compile in one translation unit when building plugins.',7,None,int),
 	('version','Yade version (if not specified, guess will be attempted)',None),
 	('CPPPATH', 'Additional paths for the C preprocessor (colon-separated)','/usr/include/vtk-5.2:/usr/include/vtk-5.4:/usr/include/eigen2'),
 	('LIBPATH','Additional paths for the linker (colon-separated)',None),

=== modified file 'py/SConscript'
--- py/SConscript	2010-02-15 19:35:41 +0000
+++ py/SConscript	2010-02-21 00:04:22 +0000
@@ -24,6 +24,7 @@
 	env.AlwaysBuild(env.ScanReplace('config.py.in')),
 	env.File('utils.py'),
 	env.File('ymport.py'),
+	env.File('export.py'),
 	env.File('eudoxos.py'),
 	env.File('plot.py'),
 	env.File('linterpolation.py'),

=== modified file 'py/export.py'
--- py/export.py	2009-12-13 20:30:13 +0000
+++ py/export.py	2010-02-21 00:04:22 +0000
@@ -1,3 +1,6 @@
+"""
+Export geometry to various formats.
+"""
 # encoding: utf-8
 from yade.wrapper import *
 
@@ -117,3 +120,26 @@
 		outFile.close()
 		self.snapCount+=1
 
+def spheresToFile(filename, consider=lambda id: True):
+	"""Save sphere coordinates into a text file; the format of the line is: x y z r.
+	Non-spherical bodies are silently skipped.
+	Returns number of spheres which were written.
+	Example added to scripts/test/regular-sphere-pack.py
+	"""
+	O=Omega()
+	
+	try:
+		out=open(filename,'w')
+	except:
+		raise RuntimeError("Problem to write into the file")
+	
+	count=0
+	for b in O.bodies:
+		try:
+			if ((b.shape.name=="Sphere") and consider(b.id)):
+				out.write('%g\t%g\t%g\t%g\n'%(b.state.pos[0],b.state.pos[1],b.state.pos[2],b.shape['radius']))
+				count+=1
+		except AttributeError:
+			pass
+	out.close()
+	return count

=== modified file 'py/timing.py'
--- py/timing.py	2010-01-24 16:27:40 +0000
+++ py/timing.py	2010-02-21 00:04:22 +0000
@@ -57,7 +57,7 @@
 			else: execTime=e.execTime
 			lines+=_delta_stats(e.timingDeltas,execTime,level+1)
 		if isinstance(e,Dispatcher): lines+=_engines_stats(e.functors,e.execTime,level+1)
-		if isinstance(e,InteractionDispatcher):
+		if isinstance(e,InteractionDispatchers):
 			lines+=_engines_stats(e.geomDispatcher.functors,e.execTime,level+1)
 			lines+=_engines_stats(e.physDispatcher.functors,e.execTime,level+1)
 			lines+=_engines_stats(e.lawDispatcher.functors,e.execTime,level+1)

=== modified file 'py/utils.py'
--- py/utils.py	2010-02-14 19:36:17 +0000
+++ py/utils.py	2010-02-21 00:04:22 +0000
@@ -399,23 +399,6 @@
 		color=(random.random(),random.random(),random.random())
 		if b.dynamic or not onlyDynamic: b.shape.diffuseColor=color
 
-
-
-def spheresToFile(filename,consider=lambda id: True):
-	"""Save sphere coordinates into ASCII file; the format of the line is: x y z r.
-	Non-spherical bodies are silently skipped.
-	
-	Returns number of spheres that were written."""
-	o=Omega()
-	out=open(filename,'w')
-	count=0
-	for b in o.bodies:
-		if not b.shape or not b.shape.name=='Sphere' or not consider(b.id): continue
-		out.write('%g\t%g\t%g\t%g\n'%(b.phys.pos[0],b.phys.pos[1],b.phys.pos[2],b.shape.radius))
-		count+=1
-	out.close()
-	return count
-
 def avgNumInteractions(cutoff=0.):
 	nums,counts=bodyNumInteractionsHistogram(aabbExtrema(cutoff))
 	return sum([nums[i]*counts[i] for i in range(len(nums))])/(1.*sum(counts))
@@ -577,7 +560,7 @@
 def spheresFromFile(*args,**kw):
 	_deprecatedUtilsFunction('spheresFromFile','yade.import.text')
 	import yade.ymport
-	return yade.ymport.text(*args,**kw)
+	return yade.ymport.spheresFromFile(*args,**kw)
 def import_stl_geometry(*args,**kw):
 	_deprecatedUtilsFunction('import_stl_geometry','yade.import.stl')
 	import yade.ymport

=== modified file 'py/ymport.py'
--- py/ymport.py	2010-01-24 16:27:40 +0000
+++ py/ymport.py	2010-02-21 00:04:22 +0000
@@ -7,23 +7,20 @@
 from yade import utils
 
 
-def ascii(filename,scale=1.,wenjieFormat=False,**kw):
+def spheresFromFile(fileName,shift=[0.0,0.0,0.0],scale=1.0,**kw):
 	"""Load sphere coordinates from file, create spheres, insert them to the simulation.
-
-	filename is the file holding ASCII numbers (at least 4 colums that hold x_center, y_center, z_center, radius).
-	All remaining arguments are passed the the yade.utils.sphere function that creates the bodies.
-
-	wenjieFormat will skip all lines that have exactly 5 numbers and where the 4th one is exactly 1.0 -
-	this was used by a fellow developer called Wenjie to mark box elements.
-	
-	Returns list of body ids that were inserted into simulation."""
-	from yade.utils import sphere
-	o=Omega()
+	filename is the file which has 4 colums [x, y, z, radius].
+	All remaining arguments are passed the the yade.utils.sphere function which creates bodies.
+	Comments, started from # are supported
+	"""
+	infile = open(fileName,"r")
+	lines = infile.readlines()
+	infile.close()
 	ret=[]
-	for l in open(filename):
-		ss=[float(i) for i in l.split()]
-		if wenjieFormat and len(ss)==5 and ss[4]==1.0: continue
-		ret.append(sphere([scale*ss[0],scale*ss[1],scale*ss[2]],scale*ss[3],**kw))
+	for line in lines:
+		data = line.split()
+		if (data[0][0] != "#"):
+			ret.append(utils.sphere([shift[0]+scale*float(data[0]),shift[1]+scale*float(data[1]),shift[2]+scale*float(data[2])],scale*float(data[3]),**kw))
 	return ret
 
 def stl(file, dynamic=False,wire=True,color=None,highlight=False,noBound=False,material=0):

=== added file 'scripts/test/regular-sphere-pack-FromFile'
--- scripts/test/regular-sphere-pack-FromFile	1970-01-01 00:00:00 +0000
+++ scripts/test/regular-sphere-pack-FromFile	2010-02-21 00:04:22 +0000
@@ -0,0 +1,4 @@
+#This is the file with the geometry, which can be imported into the simulation script
+-1.69	-0.880052	3.53564	1.15
+-1.69	-3.880052	4.0899	0.55
+-1.69	-5.741487	3.25851	0.95

=== modified file 'scripts/test/regular-sphere-pack.py'
--- scripts/test/regular-sphere-pack.py	2010-01-26 15:45:20 +0000
+++ scripts/test/regular-sphere-pack.py	2010-02-21 00:04:22 +0000
@@ -1,4 +1,4 @@
-from yade import pack,ymport
+from yade import pack,ymport,export
 
 """ This script demonstrates how to use 2 components of creating packings:
 
@@ -66,6 +66,11 @@
 """Import regular-sphere-pack-LSMGenGeo.geo into the YADE simulation"""
 O.bodies.append(ymport.gengeoFile('regular-sphere-pack-LSMGenGeo.geo',shift=[-7.0,-7.0,-5.9],scale=1.0,color=(1,0,1),**kw))
 
+"""spheresToFile saves coordinates and radiuses of all spheres of the simulation into the text file"""
+print "Saved into the OutFile " + str (export.spheresToFile("OutFile")) + " spheres";
+
+"""spheresFromFile function imports coordinates and radiuses of all spheres of the simulation into the text file"""
+O.bodies.append(ymport.spheresFromFile('regular-sphere-pack-FromFile',shift=[6.0,6.0,-2.9],scale=0.7,color=(1,1,1),**kw))
 
 try:
 	from yade import qt