From 8c91d2bcad7df7c647f1379483673183329ddfe8 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 05 Jul 2016 10:53:31 +0000
Subject: [PATCH] Fixed some bugs in cluster.c, added a line in cluster.h
---
python/trisurf/trisurf.py | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++--
1 files changed, 50 insertions(+), 2 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 8b36d27..ddcb7f9 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -212,8 +212,40 @@
lines=0
f.close()
return lines
-
+
+ def tail(self,filename,n=2):
+ with open(filename,'r') as myfile:
+ lines=myfile.readlines()
+ return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')]
+
def read(self):
+ try:
+ lines=self.tail(self.fullname)
+ except:
+ return(False)
+ if len(lines)<2:
+ return(False)
+ #print (line)
+ fields=shlex.split(lines[0])
+ epoch1=fields[0]
+ n1=fields[1]
+
+ fields=shlex.split(lines[1])
+ epoch2=fields[0]
+ n2=fields[1]
+ try:
+ self.dT=int(epoch2)-int(epoch1)
+ self.last=n2
+ #print(epoch1)
+ #print(epoch2)
+ #print(self.dT)
+ #print(self.last)
+ self.startDate=os.path.getmtime(os.path.join(self.path,'.lock'))
+ except:
+ return(False)
+ return(True)
+
+ def read_old(self):
'''
Method read() reads the statistics if it exists. It sets local variable dT storing the time differential between two intervals of simulation (outer loops). It also stores last simulation loop and the start of the run.
'''
@@ -382,10 +414,18 @@
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):
@@ -451,6 +491,14 @@
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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