From 5c3143e7b7d0979d6eed07b6dfbe9f214159bdbb Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 31 May 2016 19:42:00 +0000
Subject: [PATCH] Use nucleus displaced centre in vertex move
---
python/trisurf/trisurf.py | 25 ++++++++++++++++++++++---
1 files changed, 22 insertions(+), 3 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index bed6f7d..46a3624 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -382,10 +382,18 @@
return
cwd=Directory(maindir=os.getcwd())
+ lastVTU=self.getLastVTU() #we get last VTU file in case we need to continue the simulation from last snapshot. Need to be done before the Dir.goto() call.
self.Dir.goto()
print("Starting trisurf-ng executable in "+self.Dir.fullpath())
if(self.fromSnapshot==True):
- params=["trisurf", "--restore-from-vtk","initial_snapshot.vtu"]+self.runArgs
+ #here we try to determine whether we should continue the simulation or start from last known VTU snapshot.
+ if(lastVTU==None):
+ initSnap="initial_snapshot.vtu"
+ else:
+ initSnap=lastVTU
+ print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle")
+ params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs
+ print("InitSnap is: "+initSnap)
else:
#veify if dump exists. If not it is a first run and shoud be run with --force-from-tape
if(os.path.isfile("dump.bin")==False):
@@ -397,8 +405,6 @@
print("Process in "+self.Dir.fullpath()+" already running. Not starting.")
return
- def stop(self):
- pass
def setMaindir(self,prefix,variables):
maindir=""
@@ -443,11 +449,24 @@
report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
return report
+
+ def stop(self):
+ p=psutil.Process(self.getPID())
+ p.kill()
+
def writeComment(self, data, mode='w'):
self.Dir=Directory(maindir=self.maindir,simdir=self.subdir)
self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
self.Comment.writefile(data,mode=mode)
+
+ def getLastVTU(self):
+ vtuidx=self.getLastIteration()
+ if vtuidx<0:
+ return None
+ else:
+ return 'timestep_{:06d}.vtu'.format(vtuidx)
+
def __str__(self):
if(self.getStatus()==0):
str=" not running."
--
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