Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Anton Gladky
 +
 +       Example invocation:
 +                O.engines[5].porosity
 +               0.3901808
 +                utils.voxelPorosityTriaxial(O.engines[5],200,0)
 +               0.3908145
 +                utils.voxelPorosityTriaxial(O.engines[5],800,0)
 +               0.3902078
 +                utils.voxelPorosityTriaxial(O.engines[5],200,avg_radius)
 +               0.3604238
 +                utils.voxelPorosityTriaxial(O.engines[5],800,avg_radius)
 +               0.3604175
 +


Janek, your commit broke --test check. See buildbot logs.
https://yade-dem.org/buildbot/builders/yade-full/builds/433/steps/test/logs/stdio
Please, fix it.

Anton.

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Re: [Yade-dev] farewell

2011-03-17 Thread Sergei D.

Vaclav, you did a great job! I wish you good luck!
But do not say goodbye! Maybe you change your mind and come back!



I will be working now on a new project (unnamed so far), forked from 
current Yade code, which will be less DEM-centric (and more coupling 
with FEM, fluids, meshfree, ... -- big plans as usual, small fraction 
eventually realized) 


Sorry, but seems, you are going to make Yade as it was far in the past. No?
Is not the most promising pairing of different packages as, for example, 
LIGGGHTS-OpenFOAM, EDEM-FLUENT and so on?



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Re: [Yade-dev] farewell

2011-03-17 Thread Anton Gladky
Vaclav, I would like you to thank for all your job, what you have done
for this project and wish you everything the best with new targets!

I hope, yade will survive without your contribution.

But it would be good if you will be able to give your
comments/suggestions on resolving of some critical bugs, as you are
one of the most experienced programmers of this project. But, anyway,
it is up to you...

Also it would be interesting to know about your new project.

All the best!

Anton




On Thu, Mar 17, 2011 at 8:40 AM, Sergei D. sj2...@yandex.ru wrote:
 Vaclav, you did a great job! I wish you good luck!
 But do not say goodbye! Maybe you change your mind and come back!


 I will be working now on a new project (unnamed so far), forked from
 current Yade code, which will be less DEM-centric (and more coupling with
 FEM, fluids, meshfree, ... -- big plans as usual, small fraction eventually
 realized)

 Sorry, but seems, you are going to make Yade as it was far in the past. No?
 Is not the most promising pairing of different packages as, for example,
 LIGGGHTS-OpenFOAM, EDEM-FLUENT and so on?


 --
 Best regards,
 Sergei D.


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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Janek Kozicki
Anton Gladky said: (by the date of Thu, 17 Mar 2011 08:18:41 +0100)

 Janek, your commit broke --test check. See buildbot logs.
 https://yade-dem.org/buildbot/builders/yade-full/builds/433/steps/test/logs/stdio
 Please, fix it.

I did a test build of sphinx doc locally, and it was working. So
certainly I didn't expect this error. I'll try to fix, but can you
help me to reproduce this error on my machine?

How this doctest is invoked?

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Janek Kozicki
Janek Kozicki said: (by the date of Thu, 17 Mar 2011 09:53:24 +0100)

 Anton Gladky said: (by the date of Thu, 17 Mar 2011 08:18:41 +0100)
 
  Janek, your commit broke --test check. See buildbot logs.
  https://yade-dem.org/buildbot/builders/yade-full/builds/433/steps/test/logs/stdio
  Please, fix it.
 
 I did a test build of sphinx doc locally, and it was working. So
 certainly I didn't expect this error. I'll try to fix, but can you
 help me to reproduce this error on my machine?
 
 How this doctest is invoked?

oh, that's `yade --test`  :-)

Every time when I discover something about new incarnation of
yade, I am pleasantly surprised.

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Janek Kozicki
I committed a standalone example. It works if I copy-paste each line
into freshly launched yade, but still doesn't work in `yade --test`.

Maybe you have some idea about that.

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Anton Gladky
I think you should delete those results, because it is impossible to
obtain the same values on different machines.

Your script is better suitable for --checks section (see
test/scripts/checks/README), because it has no any analytical
solution.

Anton




On Thu, Mar 17, 2011 at 10:42 AM, Janek Kozicki janek_li...@wp.pl wrote:
 I committed a standalone example. It works if I copy-paste each line
 into freshly launched yade, but still doesn't work in `yade --test`.

 Maybe you have some idea about that.

 --
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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2787: 1. Small changes in installation section.

2011-03-17 Thread noreply

revno: 2787
committer: Anton Gladky gladky.an...@gmail.com
branch nick: yade
timestamp: Thu 2011-03-17 13:56:51 +0100
message:
  1. Small changes in installation section. 
  2. voxelPorosityTriaxial doctests are transformed to a simple source code 
demonstration due to results instability (candidate to --checks section 
http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg06635.html )
  3. Added initial sqlite database of performances on different machines.
added:
  scripts/test/performance/performance.db
modified:
  doc/sphinx/installation.rst
  py/utils.py


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=== modified file 'doc/sphinx/installation.rst'
--- doc/sphinx/installation.rst	2011-03-15 08:17:29 +
+++ doc/sphinx/installation.rst	2011-03-17 12:56:51 +
@@ -124,7 +124,9 @@
 			mkdir /etc/portage -p;\
 			echo media-libs/gd fontconfig jpeg png truetype /etc/portage/package.use
 			
+		* Some additional commands, which can be usefull::
 			
+			ln -s /usr/lib/python2.6/site-packages/numpy/core/include/numpy/ /usr/include/
 
 Compilation
 ^^^

=== modified file 'py/utils.py'
--- py/utils.py	2011-03-17 09:40:47 +
+++ py/utils.py	2011-03-17 12:56:51 +
@@ -512,18 +512,18 @@
 	:param offset: offset distance
 	:return: the porosity of the sample inside given volume
 
-	Example invocation:
-		 from yade import utils
-		 O.reset()
-		 rAvg=0.03
-		 TriaxialTest(numberOfGrains=200,radiusMean=rAvg).load()
-		 O.dt=-1
-		 O.run(1000)
-		 O.engines[4].porosity
+	Example invocation::
+	
+		from yade import utils
+		rAvg=0.03
+		TriaxialTest(numberOfGrains=200,radiusMean=rAvg).load()
+		O.dt=-1
+		O.run(1000)
+		O.engines[4].porosity
 		0.44007807740143889
-		 utils.voxelPorosityTriaxial(O.engines[4],200,0)
+		utils.voxelPorosityTriaxial(O.engines[4],200,0)
 		0.4405541250002
-		 utils.voxelPorosityTriaxial(O.engines[4],200,rAvg)
+		utils.voxelPorosityTriaxial(O.engines[4],200,rAvg)
 		0.367981998
 	
 	p_bottom	= O.bodies[triax.wall_bottom_id].state.se3[0]

=== added file 'scripts/test/performance/performance.db'
Binary files scripts/test/performance/performance.db	1970-01-01 00:00:00 + and scripts/test/performance/performance.db	2011-03-17 12:56:51 + differ
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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Janek Kozicki
Anton Gladky said: (by the date of Thu, 17 Mar 2011 11:03:18 +0100)

 test/scripts/checks/README

how do I mark the example provided in the documentation to be executed
as --check, not as --test ?

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Anton Gladky
There is no way to execute doc-script in --check section.
It should be separated script which provides a more-less stable
results and placed in test/scripts/checks/ folder.

I tried your script and gives different results on my computer. That
is why --test are failed.

Anton




On Thu, Mar 17, 2011 at 2:27 PM, Janek Kozicki janek_li...@wp.pl wrote:
 Anton Gladky said:     (by the date of Thu, 17 Mar 2011 11:03:18 +0100)

 test/scripts/checks/README

 how do I mark the example provided in the documentation to be executed
 as --check, not as --test ?

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[Yade-dev] [Bug 724396] Re: crash after add particles in parallel mode

2011-03-17 Thread Launchpad Bug Tracker
** Branch linked: lp:yade

-- 
You received this bug notification because you are a member of Yade
developers, which is the registrant for Yade.
https://bugs.launchpad.net/bugs/724396

Title:
  crash after add particles in parallel mode

Status in Yet Another Dynamic Engine:
  Fix Released

Bug description:
  Yade crash in parallel mode if to add particles after run of simulation.
  Attached script runs without errors in serial mode (-j 1 option),
  but in parallel mode (-j 2 or more) it crash at second O.run.

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[Yade-dev] [Bug 724396] Re: crash after add particles in parallel mode

2011-03-17 Thread Anton Gladky
Fixed in r2788.

Thanks all!

** Changed in: yade
   Status: Confirmed = Fix Released

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https://bugs.launchpad.net/bugs/724396

Title:
  crash after add particles in parallel mode

Status in Yet Another Dynamic Engine:
  Fix Released

Bug description:
  Yade crash in parallel mode if to add particles after run of simulation.
  Attached script runs without errors in serial mode (-j 1 option),
  but in parallel mode (-j 2 or more) it crash at second O.run.

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Re: [Yade-dev] farewell

2011-03-17 Thread Luc SIBILLE
Hi Vaclav,

Thank you for your important contribution in Yade. The python layer, among
other nice improvements, is very appreciable. Good luck for your new
project!

Best regards,
Luc

 Dear colleagues,

 most open-source projects are either abandoned, or developed forever,
 without ever getting to the done state. Yade is widely used now and,
 in my eyes, fully functional and completed. I am happy about that. I
 decided to retire from the development, not wanting to stay in some
 undefined suspended state as I've been for a few months now. Big thanks
 for cooperation and contributions.

 I will be working now on a new project (unnamed so far), forked from
 current Yade code, which will be less DEM-centric (and more coupling
 with FEM, fluids, meshfree, ... -- big plans as usual, small fraction
 eventually realized) and only developed in a small group; the extent of
 necessary changes is such that keeping continuity with Yade would not be
 possible, or uneconomically painful. You will be notified if it ever
 becomes released, but it is also possible that it will die underways or
 simply never happen at all, time will tell.

 Have a nice time with Yade. Adieu.

 Vaclav

 http://www.youtube.com/watch?v=zorktkN4DC0t=4m33s


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Université de Nantes - Laboratoire GeM

Adresse/address:
IUT de Saint Nazaire - Département de Génie-Civil
58, rue Michel-Ange - BP 420
44606 Saint-Nazaire Cedex   France

Tel: +33 2 40 17 81 78


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[Yade-dev] [Bug 721107] Re: InsertionSortCollider memory leaks

2011-03-17 Thread Anton Gladky
** Also affects: yade/0.60
   Importance: Undecided
   Status: New

** Also affects: yade/trunk
   Importance: High
   Status: Fix Committed

** Changed in: yade/0.60
   Status: New = Fix Released

** Changed in: yade/trunk
   Status: Fix Committed = Fix Released

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https://bugs.launchpad.net/bugs/721107

Title:
  InsertionSortCollider memory leaks

Status in Yet Another Dynamic Engine:
  Fix Released
Status in Yade 0.60 series:
  Fix Released
Status in Yade trunk series:
  Fix Released

Bug description:
  If  add a particles after start a simulation, InsertionSortCollider's memory 
leak occurs.
  If set verletDist=0 in ISC, no memory leak.

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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2789: 1.Add utils.trackPerfomance; 2.Small fix

2011-03-17 Thread noreply

revno: 2789
committer: Sergei D. sega@think
branch nick: yade
timestamp: Thu 2011-03-17 18:50:01 +0300
message:
  1.Add utils.trackPerfomance; 2.Small fix
modified:
  py/pack/pack.py
  py/utils.py


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=== modified file 'py/pack/pack.py'
--- py/pack/pack.py	2011-02-23 10:28:42 +
+++ py/pack/pack.py	2011-03-17 15:50:01 +
@@ -176,7 +176,7 @@
 def gtsSurface2Facets(surf,**kw):
 	Construct facets from given GTS surface. **kw is passed to utils.facet.
 	import gts
-	return [utils.facet([v.coords() for v in face.vertices()],**kw) for face in surf]
+	return [utils.facet([v.coords() for v in face.vertices()],**kw) for face in surf.faces()]
 
 def sweptPolylines2gtsSurface(pts,threshold=0,capStart=False,capEnd=False):
 	Create swept suface (as GTS triangulation) given same-length sequences of points (as 3-tuples).

=== modified file 'py/utils.py'
--- py/utils.py	2011-03-17 12:56:51 +
+++ py/utils.py	2011-03-17 15:50:01 +
@@ -544,6 +544,38 @@
 	return voxelPorosity(resolution,a,b)
 
 
+def trackPerfomance(updateTime=5):
+	
+	Track perfomance of a simulation. (Experimental)
+	Will create new thread to produce some plots.
+	Useful for track perfomance of long run simulations (in bath mode for example).
+	
+
+	def __track_perfomance(updateTime):
+		pid=os.getpid()
+		threadsCpu={}
+		lastTime,lastIter=-1,-1
+		while 1:
+			time.sleep(updateTime)
+			if not O.running: 
+lastTime,lastIter=-1,-1
+continue
+			if lastTime==-1: 
+lastTime=time.time();lastIter=O.iter
+plot.plots.update({'Iteration':('Perfomance',None,'Bodies','Interactions')})
+continue
+			curTime=time.time();curIter=O.iter
+			perf=(curIter-lastIter)/(curTime-lastTime)
+			out=subprocess.Popen(['top','-bH','-n1', ''.join(['-p',str(pid)])],stdout=subprocess.PIPE).communicate()[0].splitlines()
+			for s in out[7:-1]:
+w=s.split()
+threadsCpu[w[0]]=float(w[8])
+			plot.addData(Iteration=curIter,Iter=curIter,Perfomance=perf,Bodies=len(O.bodies),Interactions=len(O.interactions),**threadsCpu)
+			plot.plots.update({'Iter':threadsCpu.keys()})
+			lastTime=time.time();lastIter=O.iter
+
+	thread.start_new_thread(__track_perfomance,(updateTime))
+
 
 def NormalRestitution2DampingRate(en):
 	rCompute the normal damping rate as a function of the normal coefficient of restitution $e_n$. For $e_n\in\langle0,1\rangle$ damping rate equals

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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2790: 1. Make trunk compilable with Eigen3 (coming soon). No performance test results yet.

2011-03-17 Thread noreply

revno: 2790
committer: Anton Gladky gladky.an...@gmail.com
branch nick: yade
timestamp: Thu 2011-03-17 16:57:57 +0100
message:
  1. Make trunk compilable with Eigen3 (coming soon). No performance test 
results yet.
modified:
  core/Cell.hpp


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=== modified file 'core/Cell.hpp'
--- core/Cell.hpp	2011-02-02 08:13:42 +
+++ core/Cell.hpp	2011-03-17 15:57:57 +
@@ -105,7 +105,8 @@
 	// temporary, will be removed in favor of more descriptive setBox(...)
 	void setRefSize(const Vector3r s){
 		// if refSize is set to the current size and the cell is a box (used in older scripts), say it is not necessary
-		if(s==_size  hSize==hSize.diagonal().asDiagonal()){ LOG_WARN(Setting O.cell.refSize=O.cell.size is useless, O.trsf=Matrix3.Identity is enough now.); }
+		Matrix3r hSizeEigen3=hSize.diagonal().asDiagonal();		//Eigen3 support
+		if(s==_size  hSize==hSizeEigen3){ LOG_WARN(Setting O.cell.refSize=O.cell.size is useless, O.trsf=Matrix3.Identity is enough now.); }
 		else {LOG_WARN(Setting Cell.refSize is deprecated, use Cell.setBox(...) instead.);}
 		setBox(s); postLoad(*this);
 	} 

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2784: Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosi...

2011-03-17 Thread Bruno Chareyre

 There is no way to execute doc-script in --check section.
 It should be separated script which provides a more-less stable
 results and placed in test/scripts/checks/ folder.
I have the impression that this script is not even candidate for check
tests since it is highly random by nature.
Disabling the doc-test is ok.
Janek, you can use an existing position file from checkTest dir if you
want to check this sort of things.

Bruno



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[Yade-dev] buildbot failure in Yade on yade-full

2011-03-17 Thread buildbot
The Buildbot has detected a failed build of yade-full on Yade.
Full details are available at:
 http://yade-dem.org/buildbot/builders/yade-full/builds/434

Buildbot URL: http://yade-dem.org/buildbot/

Buildslave for this Build: r0calcul5

Build Reason: 
Build Source Stamp: 2785
Blamelist: Anton Gladky gladky.an...@gmail.com,Janek Kozicki 
cosu...@berlios.de

BUILD FAILED: failed test

sincerely,
 -The Buildbot


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Re: [Yade-dev] farewell

2011-03-17 Thread Bruno Chareyre
Dear Vaclav,

You are right, Yade is functional and will most probably be used more
and more. Many do/will benefit from what you've done. Thank you very much.
It's been a very instructing experience to see the evolution of Yade in
the last years, thank you very much for that too.
I'm sure it will be very usefull if you can advise or explain some
technical aspects from time to time. I know it can be a time-consuming
activity, however.
I wish you good luck for the next project.

I have the impression that, you being retired + the current state of
functionality, most developments will focus on physics more than core
development.
Some of your last developments are still largely unknown to me (namely
the L3Geom series), how far are they validated and functional?

Ciao.

Bruno


On 16/03/11 23:45, Václav Šmilauer wrote:
 Dear colleagues,

 most open-source projects are either abandoned, or developed forever,
 without ever getting to the done state. Yade is widely used now and,
 in my eyes, fully functional and completed. I am happy about that. I
 decided to retire from the development, not wanting to stay in some
 undefined suspended state as I've been for a few months now. Big
 thanks for cooperation and contributions.

 I will be working now on a new project (unnamed so far), forked from
 current Yade code, which will be less DEM-centric (and more coupling
 with FEM, fluids, meshfree, ... -- big plans as usual, small fraction
 eventually realized) and only developed in a small group; the extent
 of necessary changes is such that keeping continuity with Yade would
 not be possible, or uneconomically painful. You will be notified if it
 ever becomes released, but it is also possible that it will die
 underways or simply never happen at all, time will tell.

 Have a nice time with Yade. Adieu.

 Vaclav

 http://www.youtube.com/watch?v=zorktkN4DC0t=4m33s


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Re: [Yade-dev] Web site buildbot disruption

2011-03-17 Thread Rémi Cailletaud
Hi,

Le 16/03/2011 22:27, Anton Gladky a écrit :
 buildbot does not build automatically every revision. r2781 was the
 last built revision.

Fixed.

++
rémi


 
 Anton
 
 
 
 
 On Wed, Mar 16, 2011 at 2:57 PM, Sergei D. sj2...@yandex.ru wrote:
 Hi,

 I can't login to wiki. I forgot the password, so I request email new passw
 but don't receive it.

 --
 Best regards,
 Sergei D.


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Re: [Yade-dev] farewell

2011-03-17 Thread Václav Šmilauer


Sorry, but seems, you are going to make Yade as it was far in the 
past. No?

Come on... I am not reverting all my commits.
Is not the most promising pairing of different packages as, for 
example, LIGGGHTS-OpenFOAM, EDEM-FLUENT and so on?
I am sure other people on the list know better -- and can comment -- 
about what is promising. I would tend to think that combination (of some 
kind) of the classical DEM with some mathematically better established 
theories can be a step forward, but that's a rookie's opinion. It does 
not seem to me, however, that Yade lends itself in that direction very 
well, but I did not make any serious efforts in that direction.


v

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Re: [Yade-dev] farewell

2011-03-17 Thread Václav Šmilauer



Some of your last developments are still largely unknown to me (namely
the L3Geom series), how far are they validated and functional?
They were mostly sketches. I will certainly build on them myself in the 
fork, because I consider tham as a step forward, but cannot recommend 
them for wide use. OTOH everybody is free to read/use/modify that code, 
I don't need to say that.


v

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Re: [Yade-dev] farewell

2011-03-17 Thread Václav Šmilauer

I hope, yade will survive without your contribution.

http://www.youtube.com/watch?v=XM1fDkC4c0Q

Are we having mailing-list funeral?! Cheer up, it is just a piece of code!

Also it would be interesting to know about your new project.
I will let you know on the list, but (if ever) it will not be before 
many months will have passed. There is no sense announcing project 
which is not even clearly defined; you can search freshmeat / 
sourceforge, plenty open-source projects have just written their title 
and description, never commited any code, only to have their homepage 
become their epitaph of sorts, after a few years.


v

PS. http://www.youtube.com/watch?v=__OSyznVDOY


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Re: [Yade-dev] farewell

2011-03-17 Thread Klaus Thoeni
Hi Vaclav!

I am sure we will miss you! Anyway, good luck with your new plans.

Regarding your new plans, please keep us updated since coupling is a very 
interesting topic. I am already looking forward to see some nice animations 
from your new developments on youtube ;-)

Cheers

Klaus

On Fri, 18 Mar 2011 08:09:40 am Václav Šmilauer wrote:
  I hope, yade will survive without your contribution.
 
 http://www.youtube.com/watch?v=XM1fDkC4c0Q
 
 Are we having mailing-list funeral?! Cheer up, it is just a piece of
 code!
 
  Also it would be interesting to know about your new project.
 
 I will let you know on the list, but (if ever) it will not be before
 many months will have passed. There is no sense announcing project
 which is not even clearly defined; you can search freshmeat /
 sourceforge, plenty open-source projects have just written their title
 and description, never commited any code, only to have their homepage
 become their epitaph of sorts, after a few years.
 
 v
 
 PS. http://www.youtube.com/watch?v=__OSyznVDOY
 
 
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