From 80f2a33e4b55c7259bdb4bff66a0ce12b96edd80 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 11 Jul 2016 19:29:28 +0000
Subject: [PATCH] Merge branch 'master' of bitbucket.org:samop/trisurf-ng
---
python/trisurf/trisurf.py | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++++++----
1 files changed, 54 insertions(+), 4 deletions(-)
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index 8b36d27..3fe4adb 100644
--- a/python/trisurf/trisurf.py
+++ b/python/trisurf/trisurf.py
@@ -2,7 +2,7 @@
import xml.etree.ElementTree as ET
import base64
import zlib
-import io
+import sys,io
import os
from itertools import islice
import mmap
@@ -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.
'''
@@ -318,7 +350,7 @@
return int(status)
def isCompleted(self):
- if (int(self.tape.getValue("iterations"))==self.getLastIteration()+1):
+ if int(self.tape.getValue("iterations"))+int(self.tape.getValue("inititer"))==self.getLastIteration()+1:
return True
else:
return False
@@ -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):
@@ -403,6 +443,8 @@
for p,v in zip(prefix,variables):
if(v=="xk0"):
tv=str(round(float(self.tape.config[v])))
+ if sys.version_info<(3,0):
+ tv=str(int(float(self.tape.config[v])))
else:
tv=self.tape.config[v]
maindir=maindir+p+tv
@@ -451,6 +493,14 @@
self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
self.Comment.writefile(data,mode=mode)
+
+ def getLastVTU(self):
+ vtuidx=self.getLastIteration() -int(self.tape.getValue("inititer"))
+ 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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