From e818ba5bcc461af545665c78157be4e52252aa1c Mon Sep 17 00:00:00 2001
From: Miha <miha.fosnaric@fe.uni-lj.si>
Date: Mon, 11 Jul 2016 11:52:30 +0000
Subject: [PATCH] Merge branch 'master' of https://bitbucket.org/samop/trisurf-ng
---
python/trisurf/Remote.py | 73 +++++
src/main.c | 6
python/tape | 12
python/trisurf/trisurf.py | 8
src/io.c | 72 ----
src/tape | 18
python/pythonvtk.py | 42 +++
python/trisurf/__init__.py | 0
python/trisurf/WebTrisurf.py | 59 ++++
python/networkedExample.py | 27 +
src/timestep.c | 5
python/trisurf/tsmgr.py | 316 +++++++++++++++++----
python/trisurf/VTKRendering.py | 155 +++++++++++
13 files changed, 638 insertions(+), 155 deletions(-)
diff --git a/python/networkedExample.py b/python/networkedExample.py
new file mode 100755
index 0000000..74c0a04
--- /dev/null
+++ b/python/networkedExample.py
@@ -0,0 +1,27 @@
+from trisurf import trisurf
+from trisurf import tsmgr
+
+
+
+
+#Ok... Configure your keys:
+#ssh-keygen
+#and copy them to all the remote hosts
+#ssh-copy-id -i ./ssh/id_rsa.pub username@remotehost
+
+run2=trisurf.Runner(tape='tape')
+run2.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
+run2.setSubdir("run1")
+
+run3=trisurf.Runner(tape='tape')
+run3.setMaindir(("N","k","V","Np","Nm"),("nshell","xk0","constvolswitch","npoly","nmono"))
+run3.setSubdir("run2")
+
+
+
+Runs=[run2, run3]
+
+hosts=({'name':'natalie','address':'kabinet.penic.eu', 'runs':Runs, 'username':'samo'},
+ {'name':'Hestia','address':'127.0.0.1', 'runs':Runs, 'username':'samo'})
+
+tsmgr.start(hosts)
diff --git a/python/pythonvtk.py b/python/pythonvtk.py
new file mode 100644
index 0000000..b50ff7c
--- /dev/null
+++ b/python/pythonvtk.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# by Panos Mavrogiorgos, email: pmav99 <> gmail
+
+from vtk import *
+
+# The source file
+#file_name = "uGridEx.vtk"
+file_name="timestep.vtu"
+# Read the source file.
+#reader = vtkUnstructuredGridReader()
+reader=vtkXMLUnstructuredGridReader()
+reader.SetFileName(file_name)
+reader.Update() # Needed because of GetScalarRange
+output = reader.GetOutput()
+scalar_range = output.GetScalarRange()
+
+# Create the mapper that corresponds the objects of the vtk file
+# into graphics elements
+mapper = vtkDataSetMapper()
+mapper.SetInput(output)
+mapper.SetScalarRange(scalar_range)
+
+# Create the Actor
+actor = vtkActor()
+actor.SetMapper(mapper)
+
+# Create the Renderer
+renderer = vtkRenderer()
+renderer.AddActor(actor)
+renderer.SetBackground(0, 0, 0) # Set background to white
+
+# Create the RendererWindow
+renderer_window = vtkRenderWindow()
+renderer_window.AddRenderer(renderer)
+
+# Create the RendererWindowInteractor and display the vtk_file
+interactor = vtkRenderWindowInteractor()
+interactor.SetRenderWindow(renderer_window)
+interactor.Initialize()
+interactor.Start()
diff --git a/python/tape b/python/tape
index f207db2..35b52e6 100644
--- a/python/tape
+++ b/python/tape
@@ -1,6 +1,6 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
-nshell=5
+nshell=10
# dmax is the max. bond length (in units l_min)
dmax=1.7
# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
@@ -17,15 +17,15 @@
pressure=0.0
#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol)
-constvolswitch=2
+constvolswitch=0
constvolprecision=1e-14
#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
-constareaswitch=2
+constareaswitch=0
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=2
+npoly=60
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
@@ -55,7 +55,7 @@
mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
-inititer=0
+inititer=10
#how many records do you want on the disk iteration are there in a run?
#10000
iterations=100
@@ -63,7 +63,7 @@
###### Spherical harmonics ###########
# If 0 then spherical harmonics are not calculated at all.
-spherical_harmonics_coefficients=21
+spherical_harmonics_coefficients=0
#shut up if we are using cluster!!!
quiet=false
diff --git a/python/trisurf/Remote.py b/python/trisurf/Remote.py
new file mode 100644
index 0000000..8da08be
--- /dev/null
+++ b/python/trisurf/Remote.py
@@ -0,0 +1,73 @@
+import paramiko
+
+
+
+class Connection:
+ def __init__(self, hostname, port=22, username=None, password=None):
+ self.hostname=hostname
+ self.port=port
+ if(username!=None):
+ self.username=username
+ else:
+ self.username=''
+ if(password!=None):
+ self.password=password
+ else:
+ self.password=''
+ self.ssh=paramiko.SSHClient()
+ self.ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+ self.connected=False
+ return
+
+ def connect(self, Timeout=5):
+ if(not self.connected):
+ try:
+ print("Trying to connect to: "+self.username+"@"+self.hostname+":"+str(self.port)+".")
+ self.ssh.connect(self.hostname, username=self.username, password=self.password, port=self.port, timeout=Timeout)
+ self.connected=True
+ except:
+ print("Error establishing connection with "+self.username+"@"+self.hostname+":"+str(self.port)+".")
+ exit(1)
+ else:
+ print("Already connected!")
+ return
+
+ def disconnect(self):
+ if(self.connected):
+ try:
+ self.ssh.close()
+ except:
+ print("Cannot disconect. Unknown error.")
+ else:
+ print("Cannot disconect. Already disconnected.")
+ self.connected=False
+
+ def execute(self,command):
+ if(self.connected):
+ try:
+ stdin,stdout,stderr=self.ssh.exec_command(command)
+ output=stdout.readlines()
+ errors=stderr.readlines()
+ # print(errors)
+ return(output)
+ except:
+ print("Cannot execute remote commands")
+ else:
+ print("Cannot execute remote commands. Connect first.")
+
+ def send_file(self, local, remote):
+ sftp=self.ssh.open_sftp()
+ sftp.put(local,remote)
+ sftp.close()
+
+ def receive_file(self,remote,local):
+ sftp=self.ssh.open_sftp()
+ sftp.get(remote,local)
+ sftp.close()
+
+ def mkdir_remote(self,directory):
+ sftp=self.ssh.open_sftp()
+ sftp.mkdir(directory)
+ sftp.close()
+
+
diff --git a/python/trisurf/VTKRendering.py b/python/trisurf/VTKRendering.py
new file mode 100644
index 0000000..5e72b98
--- /dev/null
+++ b/python/trisurf/VTKRendering.py
@@ -0,0 +1,155 @@
+import os,sys
+from . import trisurf
+if sys.version_info<(3,0):
+ from vtk import *
+
+
+
+class MultiRender:
+ def __init__(self,args,host):
+ target_runs=getRargetRunIdxList(args)
+ if target_runs==None:
+ target_runs=list(range(1,len(host['runs'])+1))
+ nruns=len(target_runs)
+ #prepare rendering window
+ self.renderer_window = vtkRenderWindow()
+ self.renderer_window.AddRenderer(self.renderer)
+ self.renderer_window.SetSize(1200,600)
+ interactor = vtkRenderWindowInteractor()
+ interactor.SetRenderWindow(self.renderer_window)
+ interactor.Initialize()
+ interactor.AddObserver("TimerEvent", self.RenderUpdate)
+ timerIDR = interactor.CreateRepeatingTimer(1000)
+ self.filename=[]
+ self.renderer=[]
+ i=0
+ for run in target_runs:
+ #for each target run calculate renderer location
+ r.vtkRenderer()
+ r.SetBackground(0,0,0)
+ p=1.0/float(nruns)
+ x1=i*p
+ x2=(i+1)*p
+ r.SetViewport(x1,0.0,x2,1.0)
+ self.renderer.Append(r)
+ self.renderer_window.AddRenderer(r)
+ i=i+1
+ #call Renderer object with Run, renderer
+ #start endless loop of interactor
+ interactor.Start()
+
+ def lastVTU(self,run):
+ Dir=trisurf.Directory(maindir=run.maindir,simdir=run.subdir)
+ filename=os.path.join("./",Dir.fullpath(),run.getLastVTU())
+ return filename
+
+ def lastActorForRun(self,run):
+ filename=self.lastVTU(run)
+ reader=vtkXMLUnstructuredGridReader()
+ reader.SetFileName(self.filename)
+ reader.Update() # Needed because of GetScalarRange
+ output = reader.GetOutput()
+ scalar_range = output.GetScalarRange()
+ mapper = vtkDataSetMapper()
+ mapper.SetInput(output)
+ mapper.SetScalarRange(scalar_range)
+
+ # Create the Actor
+ actor = vtkActor()
+ actor.SetMapper(mapper)
+ return actor
+
+
+
+ def RenderUpdate(self, obj, event):
+ i=0
+ for run in runs:
+ if(self.lastVTU(run)!=self.filename[i]):
+ #print("updejt")
+ self.renderer.RemoveActor(self.actor)
+ self.renderer.RemoveActor(self.textactor)
+ self.actor=self.lastActor()
+ self.textactor=self.textActor()
+ self.renderer.AddActor(self.actor)
+ self.renderer.AddActor(self.textactor)
+ self.renderer_window.Render()
+ #self.render.RemoveActor(self.actor)
+ i=i+1
+ return
+
+
+class Renderer:
+ def __init__(self,args,host):
+ self.host=host
+ self.args=args
+ self.renderer = vtkRenderer()
+ self.actor=self.lastActor()
+ self.textactor=self.textActor()
+ self.renderer.AddActor(self.actor)
+ self.renderer.AddActor(self.textactor)
+ self.renderer.SetBackground(0, 0, 0) # Set background to white
+ # Create the RendererWindow
+ self.renderer_window = vtkRenderWindow()
+ self.renderer_window.AddRenderer(self.renderer)
+ self.renderer_window.SetSize(1200,600)
+
+ self.renderer.SetViewport(0.0,0.0,0.5,1.0)
+ rend=vtk.vtkRenderer()
+ rend.AddActor(self.actor)
+ rend.SetViewport(0.5,0.0,1.0,1.0)
+ self.renderer_window.AddRenderer(rend)
+# Set up a check for aborting rendering.
+ # Create the RendererWindowInteractor and display the vtk_file
+ interactor = vtkRenderWindowInteractor()
+ interactor.SetRenderWindow(self.renderer_window)
+ interactor.Initialize()
+ interactor.AddObserver("TimerEvent", self.RenderUpdate)
+ timerIDR = interactor.CreateRepeatingTimer(1000)
+ interactor.Start()
+
+ return
+
+ def lastVTU(self):
+ Dir=trisurf.Directory(maindir=self.host['runs'][0].maindir,simdir=self.host['runs'][0].subdir)
+ filename=os.path.join("./",Dir.fullpath(),self.host['runs'][0].getLastVTU())
+ return filename
+
+ def textActor(self):
+ textactor=vtkTextActor()
+ textactor.SetInput(self.filename)
+ tp=textactor.GetTextProperty()
+ tp.SetColor(1,1,1)
+ tp.SetFontSize(11)
+ textactor.SetDisplayPosition(20,30)
+ return textactor
+
+ def lastActor(self):
+ self.filename=self.lastVTU()
+ reader=vtkXMLUnstructuredGridReader()
+ reader.SetFileName(self.filename)
+ reader.Update() # Needed because of GetScalarRange
+ output = reader.GetOutput()
+ scalar_range = output.GetScalarRange()
+ mapper = vtkDataSetMapper()
+ mapper.SetInput(output)
+ mapper.SetScalarRange(scalar_range)
+
+ # Create the Actor
+ actor = vtkActor()
+ actor.SetMapper(mapper)
+ return actor
+
+
+ def RenderUpdate(self, obj, event):
+ if(self.lastVTU()!=self.filename):
+ #print("updejt")
+ self.renderer.RemoveActor(self.actor)
+ self.renderer.RemoveActor(self.textactor)
+ self.actor=self.lastActor()
+ self.textactor=self.textActor()
+ self.renderer.AddActor(self.actor)
+ self.renderer.AddActor(self.textactor)
+ self.renderer_window.Render()
+ #self.render.RemoveActor(self.actor)
+
+ return
diff --git a/python/trisurf/WebTrisurf.py b/python/trisurf/WebTrisurf.py
new file mode 100644
index 0000000..4b36ec9
--- /dev/null
+++ b/python/trisurf/WebTrisurf.py
@@ -0,0 +1,59 @@
+import subprocess
+import sys, os
+if sys.version_info>=(3,0):
+ from urllib.parse import urlparse
+else:
+ from urlparse import urlparse
+import http.server
+import socketserver
+
+#Web server
+class TsWEB(http.server.BaseHTTPRequestHandler):
+ def do_GET(self):
+ parsed_path=urlparse(self.path)
+ """ message_parts = [
+ 'CLIENT VALUES:',
+ 'client_address=%s (%s)' % (self.client_address, self.address_string()),
+ 'command=%s' % self.command,
+ 'path=%s' % self.path,
+ 'real path=%s' % parsed_path.path,
+ 'query=%s' % parsed_path.query,
+ 'request_version=%s' % self.request_version,
+ '',
+ 'SERVER VALUES:',
+ 'server_version=%s' % self.server_version,
+ 'sys_version=%s' % self.sys_version,
+ 'protocol_version=%s' % self.protocol_version,
+ '',
+ 'HEADERS RECEIVED:',
+ ]
+ for name, value in sorted(self.headers.items()):
+ message_parts.append('%s=%s' % (name, value.rstrip()))
+ message_parts.append('')
+ message = '<br>'.join(message_parts) """
+ self.send_response(200)
+ self.end_headers()
+ self.wfile.write(b"<h1>Trisurf-ng manager web interface</h1><hr>")
+ oldstdout=sys.stdout
+ process=subprocess.Popen (['/usr/bin/python3', sys.argv[0], '-s', '--html'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr= process.communicate()
+ output=stdout.decode('ascii')
+ output=output.replace('\n','<BR>')
+ output=bytearray(output,'ascii')
+ self.wfile.write(output)
+
+
+
+
+class WebServer():
+ def __init__(self, port=8000):
+ http_server = socketserver.TCPServer(('', port), TsWEB)
+ try:
+ http_server.serve_forever()
+ except KeyboardInterrupt:
+ print('^C received, shutting down the web server')
+ http_server.socket.close()
+
+
+
+
diff --git a/python/trisurf/__init__.py b/python/trisurf/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/python/trisurf/__init__.py
diff --git a/python/trisurf/trisurf.py b/python/trisurf/trisurf.py
index ddcb7f9..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
@@ -350,7 +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
@@ -443,6 +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
@@ -493,7 +495,7 @@
def getLastVTU(self):
- vtuidx=self.getLastIteration()
+ vtuidx=self.getLastIteration() -int(self.tape.getValue("inititer"))
if vtuidx<0:
return None
else:
diff --git a/python/trisurf/tsmgr.py b/python/trisurf/tsmgr.py
index fa7d20f..d973360 100644
--- a/python/trisurf/tsmgr.py
+++ b/python/trisurf/tsmgr.py
@@ -1,21 +1,61 @@
-import sys, getopt
+import argparse
+import paramiko
+from . import Remote
+from . import trisurf
+import socket
+import os,sys
import tabulate
import subprocess,re
import psutil
-
-def printHelp():
- print('Python module tsmgr accept following switches:\n')
- print('tsmgr [-n process number] [-R] [-h] [-r] [-s] [-c comment text] [-a comment text]\n')
- print('[-n process number]: number of process for which -s -r -c or -a switch apply. Should be placed before any other switch');
- print('[-R] : raw output for -s switch');
- print('[-r] : run process');
- print('[-s] : process status');
- print('[-k] : kill process');
- print('[-c comment text] : write new comment for process');
- print('[-a comment text] : append additional comment for process');
- print('[-h] : print help');
+#import http.server
+#import socketserver
+if sys.version_info>=(3,0):
+ from urllib.parse import urlparse
+ from . import WebTrisurf
+else:
+ from urlparse import urlparse
+ from vtk import *
+ from . import VTKRendering
+#import io
+
+#Color definitions for terminal
+class bcolors:
+ HEADER = '\033[95m'
+ OKBLUE = '\033[94m'
+ OKGREEN = '\033[92m'
+ WARNING = '\033[93m'
+ FAIL = '\033[91m'
+ ENDC = '\033[0m'
+ BOLD = '\033[1m'
+ UNDERLINE = '\033[4m'
+
+#parses Command Line Arguments and returns the list of parsed values
+def ParseCLIArguments(arguments):
+ parser = argparse.ArgumentParser(description='Manages (start, stop, status) multiple simulation processes of trisurf according to the configuration file.')
+ parser.add_argument('proc_no', metavar='PROC_NO', nargs='*',
+ help='process number at host. If hostname is not specified, localhost is assumed. If no processes are specified all processes on all hosts are assumed.')
+ action_group=parser.add_mutually_exclusive_group(required=True)
+ action_group.add_argument('-c','--comment',nargs=1, help='append comment to current comment')
+ action_group.add_argument('--delete-comment', help='delete comment',action='store_true')
+ action_group.add_argument('-k','--kill','--stop','--suspend', help='stop/kill the process', action='store_true')
+ action_group.add_argument('-r','--run','--start','--continue', help='start/continue process', action='store_true')
+ action_group.add_argument('-s','--status',help='print status of the processes',action='store_true')
+ action_group.add_argument('-v','--version', help='print version information and exit', action='store_true')
+ action_group.add_argument('--web-server', type=int,metavar="PORT", nargs=1, help='EXPERIMENTAL: starts web server and never exist.')
+ action_group.add_argument('-p','--preview',help='preview last VTU shape',action='store_true')
+ parser.add_argument('--force', help='if dangerous operation (killing all the processes) is requested, this flag is required to execute the operation. Otherwise, the request will be ignored.', action="store_true")
+ parser.add_argument('-H', '--host', nargs=1, help='specifies which host is itended for the operation. Defauts to localhost for all operations except --status and --version, where all configured hosts are assumed.')
+ parser.add_argument('--html', help='Generate HTML output', action="store_true")
+ parser.add_argument('-n', nargs='+', metavar='PROC_NO', type=int, help='OBSOLETE. Specifies process numbers.')
+ parser.add_argument('-R','--raw',help='print status and the rest of the information in raw format', action="store_true")
+ parser.add_argument('-x','--local-only',help='do not attempt to contact remote hosts. Run all operations only on local machine',action='store_true')
+ args = parser.parse_args(arguments)
+ return args
+
+
+#gets version of trisurf currently running
def getTrisurfVersion():
p = subprocess.Popen('trisurf --version', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
lines=p.stdout.readlines()
@@ -26,67 +66,205 @@
else:
return "unknown version"
-def start(Runs):
- argv=sys.argv[1:]
- processno=0
- raw=False
- try:
- opts, args = getopt.getopt(argv,"Ra:n:hrskc:")
- except getopt.GetoptError:
- printHelp()
- sys.exit(2)
- for opt, arg in opts:
- if opt == '-R':
- raw=True
- elif opt == '-h':
- printHelp()
- sys.exit()
- elif opt == '-r':
- if processno:
- localRuns=[Runs[processno-1]]
- else:
- localRuns=Runs
- for run in localRuns:
- run.start()
- elif opt == '-s':
- report=[]
- i=1
- if processno:
- localRuns=[Runs[processno-1]]
- else:
- localRuns=Runs
- for run in localRuns:
- line=run.getStatistics()
- line.insert(0,i)
- report.append(line)
- i=i+1
- if(raw):
- print(report)
- else:
- print ("\n\nTrisurf running processes report\n")
- print (tabulate.tabulate(report,headers=["Run no.", "Run start time", "ETA", "Status", "PID", "Path", "Comment"], tablefmt='fancy_grid'))
- elif opt == '-n':
- processno=int(arg)
- if processno<1 or processno>len(Runs) :
- processno=0
- elif opt == '-c':
- comment = arg
- if processno:
- Runs[processno-1].writeComment(arg)
- elif opt == '-a':
- comment = arg
- if processno:
- Runs[processno-1].writeComment("\n"+arg, 'a')
- elif opt == '-k':
- if processno:
- Runs[processno-1].stop()
+
+def copyConfigAndConnect(hosts):
+ print("Connecting to remote hosts and copying config files, tapes and snapshots")
+ for host in hosts:
+ if(host['name'] !=socket.gethostname()): #if I am not the computer named in host name
+ try:
+ username=host['username']
+ except:
+ username=os.getusername() #default username is current user user's name
+ try:
+ port=host['port']
+ except:
+ port=22 #default ssh port
+ rm=Remote.Connection(hostname=host['address'],username=username, port=port)
+ rm.connect()
+ rm.send_file(__file__,'remote_control.py')
+ for run in host['runs']:
+ try:
+ rm.send_file(run.tapeFile,run.tapeFile)
+ except:
+ pass
+ try:
+ rm.send_file(run.snapshotFile,run.snapshotFile)
+ except:
+ pass
+ host['_conn']= rm
+ # we are connected to all hosts...
+ return hosts
+
+
+
+def getTargetRunIdxList(args):
+ target_runs=list(map(int,args['proc_no']))
+ if len(target_runs)==0:
+ #check if obsolete -n flags have numbers
+ target_runs=args['n']
+ if target_runs==None:
+ return None
+ target_runs=list(set(target_runs))
+ return target_runs
+
+
+
+def status_processes(args,host):
+ target_runs=getTargetRunIdxList(args)
+ if target_runs==None:
+ target_runs=list(range(1,len(host['runs'])+1))
+ report=[]
+ for i in target_runs:
+ line=host['runs'][i-1].getStatistics()
+ line.insert(0,i)
+ report.append(line)
+ if(args['raw']):
+ print(report)
+ else:
+ if(args['html']):
+ tablefmt='html'
else:
- printHelp()
- sys.exit(2)
+ tablefmt='fancy_grid'
+ print(tabulate.tabulate(report,headers=["Run no.", "Run start time", "ETA", "Status", "PID", "Path", "Comment"], tablefmt=tablefmt))
+ return
+
+def run_processes(args,host):
+ target_runs=getTargetRunIdxList(args)
+ if target_runs==None:
+ target_runs=list(range(1,len(host['runs'])+1))
+ for i in target_runs:
+ host['runs'][i-1].start()
+ return
+
+def kill_processes(args,host):
+ target_runs=getTargetRunIdxList(args)
+ if target_runs==None:
+ if args['force']==True:
+ target_runs=list(range(1,len(host['runs'])+1))
+ else:
+ print("Not stopping all processes on the host. Run with --force flag if you are really sure to stop all simulations")
+ return
+ for i in target_runs:
+ host['runs'][i-1].stop()
+ return
+
+def comment_processes(args,host):
+ target_runs=getTargetRunIdxList(args)
+ if target_runs==None:
+ target_runs=list(range(1,len(host['runs'])+1))
+ for i in target_runs:
+ host['runs'][i-1].writeComment(args['comment'][0],'a')
+ print("Comment added")
+ return
+
+def delete_comments(args,host):
+ target_runs=getTargetRunIdxList(args)
+ if target_runs==None:
+ if args['force']==True:
+ target_runs=list(range(1,len(host['runs'])+1))
+ else:
+ print("Not deleting comments on all posts on the host. Run with --force flag if you are really sure to delete all comments")
+ return
+ for i in target_runs:
+ host['runs'][i-1].writeComment("")
+ print("Comment deleted")
+ return
+
+
+def start_web_server(args,host):
+ print('Server listening on port {}'.format(args['web_server'][0]))
+ if sys.version_info>=(3,0):
+ WebTrisurf.WebServer(port=args['web_server'][0])
+ else:
+ print("Cannot start WebServer in python 2.7")
+ exit(0)
+
+def perform_action(args,host):
+ #find which flags have been used and act upon them. -r -s -k -v -c --delete-comment are mutually exclusive, so only one of them is active
+ if args['run']:
+ run_processes(args,host)
+ elif args['kill']:
+ kill_processes(args,host)
+ elif args['status']:
+ status_processes(args,host)
+ elif args['comment']!= None:
+ comment_processes(args,host)
+ elif args['delete_comment']:
+ delete_comments(args,host)
+ elif args['web_server']!=None:
+ start_web_server(args,host)
+ elif args['preview']:
+ preview_vtu(args,host)
+ else: #version requested
+ print(getTrisurfVersion())
+ return
+def preview_vtu(args,host):
+ #only for localhost at the moment
+ if sys.version_info>=(3,0):
+ print("Preview works only with python 2.7")
+ exit(1)
+ if host['name'] == socket.gethostname():
+ VTKRendering.Renderer(args,host)
+
+def getListOfHostConfigurationByHostname(hosts,host):
+ rhost=[]
+ for chost in hosts:
+ if chost['name'] in host:
+ rhost.append(chost)
+ return rhost
+
+
+
+def start(hosts,argv=sys.argv[1:]):
+ args=vars(ParseCLIArguments(argv))
+ #print(vars(args))
+
+ #Backward compatibility... If running just on localmode, the host specification is unnecessary. Check if only Runs are specified
+ try:
+ test_host=hosts[0]['name']
+ except:
+ print("Network mode disabled. Old syntax detected.")
+ host={'name':socket.gethostname(),'address':'127.0.0.1', 'runs':hosts}
+ perform_action(args,host)
+ exit(0)
+
+
+ #find the host at which the action is attended
+ if args['host']==None:
+ if(args['status']==False and args['version']==False):
+ hosts=getListOfHostConfigurationByHostname(hosts,socket.gethostname())
+ else:
+ hosts=getListOfHostConfigurationByHostname(hosts,args['host'])
+ if len(hosts)==0:
+ print ('Hostname "{}" does not exist in configuration file. Please check the spelling'.format(args['host'][0]))
+ exit(1)
+
+ if not args['local_only']:
+ hosts=copyConfigAndConnect(hosts)
+
+ #do local stuff:
+ for host in hosts:
+ if host['name'] == socket.gethostname():
+ if(args['html']):
+ print("Host <font color='orange'>"+host['name']+"</font> reports the following:")
+ else:
+ print("Host "+bcolors.WARNING+host['name']+bcolors.ENDC+" reports the following:")
+ perform_action(args,host)
+ elif not args['local_only']:
+ output=host['_conn'].execute('python3 ./remote_control.py -x '+" ".join(argv))
+ for line in output:
+ print(line.replace('\n',''))
+
+
+ if not args['local_only']:
+ print("Closing connections to remote hosts")
+ for host in hosts:
+ if(host['name'] !=socket.gethostname()):
+ host['_conn'].disconnect()
diff --git a/src/io.c b/src/io.c
index f0207ac..6d6cbbb 100644
--- a/src/io.c
+++ b/src/io.c
@@ -861,8 +861,8 @@
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
xml_trisurf_data(fh,vesicle);
fprintf(fh, " <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
- fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
+ fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
@@ -887,61 +887,6 @@
}
fprintf(fh,"</DataArray>\n");
-
- //here comes additional data as needed. Currently only spontaneous curvature
- fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
- for(i=0;i<vlist->n;i++){
- fprintf(fh,"%.17e ",vtx[i]->c);
- }
- //polymeres
- if(poly){
- poly_idx=vlist->n;
- for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
- fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
- }
- }
- }
- //filaments
- if(fil){
- poly_idx=vlist->n+monono*polyno;
- for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
- // fprintf(stderr,"was here\n");
- fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
- }
- }
- }
- fprintf(fh,"</DataArray>\n");
-
- //here comes additional data. Energy!
- fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
- for(i=0;i<vlist->n;i++){
- fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
- }
- //polymeres
- if(poly){
- poly_idx=vlist->n;
- for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
- fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
- }
- }
- }
- //filaments
- if(fil){
- poly_idx=vlist->n+monono*polyno;
- for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
- // fprintf(stderr,"was here\n");
- fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
- }
- }
- }
- fprintf(fh,"</DataArray>\n");
-
-
-
fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
@@ -994,17 +939,24 @@
}
}
-
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
+ }
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
+ for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
+ fprintf(fh,"%u ", j);
+ }
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
+ for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++){
fprintf(fh,"3 ");
}
-
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"5 ");
+ }
fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
fclose(fh);
return TS_SUCCESS;
diff --git a/src/main.c b/src/main.c
index 7c1ff29..c2e51af 100644
--- a/src/main.c
+++ b/src/main.c
@@ -54,13 +54,13 @@
if(fd!=NULL){
arguments_no=fscanf(fd,"%u", &start_iteration);
if(arguments_no==0){
- ts_fprintf(stdout,"No information of start iteration in .status file");
+ ts_fprintf(stdout,"No information of start iteration in .status file\n");
}
fclose(fd);
- start_iteration++;
+ start_iteration++;
}
else
- ts_fprintf(stdout,"No .status file. The iteration count will start from 0");
+ ts_fprintf(stdout,"No .status file. The iteration count will start from 0\n");
/* Here you should read new tape file, reassign some values in vertex from the tape and assign read tape to vesicle->tape */
// tape=parsetape(command_line_args.tape_fullfilename);
// vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape);
diff --git a/src/tape b/src/tape
index 0784fac..2e8b8c7 100644
--- a/src/tape
+++ b/src/tape
@@ -1,6 +1,6 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
-nshell=17
+nshell=5
# dmax is the max. bond length (in units l_min)
dmax=1.7
# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
@@ -25,26 +25,26 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=3
+npoly=0
# nmono is a number of monomers in each polymer
-nmono=10
+nmono=2
# Spring constant between monomers of the polymer
k_spring=800
####### Filament (inside the vesicle) definitions ###########
# nfil is a number of filaments inside the vesicle
-nfil=2
+nfil=0
# nfono is a number of monomers in each filament
-nfono=300
+nfono=3
# Persistence lenght of the filaments (in units l_min)
xi=100
####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
R_nucleus=0
-R_nucleusX=6.0
-R_nucleusY=12.0
-R_nucleusZ=6.0
+R_nucleusX=0
+R_nucleusY=0
+R_nucleusZ=0
####### Cell definitions ############
nxmax=60
nymax=60
@@ -57,7 +57,7 @@
mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
-inititer=0
+inititer=10
#how many records do you want on the disk iteration are there in a run?
#10000
iterations=100
diff --git a/src/timestep.c b/src/timestep.c
index 6328b0f..be14619 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -60,11 +60,6 @@
/* RANDOM SEED SET BY CURRENT TIME */
epochtime=get_epoch();
srand48(epochtime);
-/*Nir Gov: randomly add spontaneous curvature for some vertices */
- for(i=0;i<20;i++){
- int b=rand() % vesicle->vlist->n;
- vesicle->vlist->vtx[b]->c=-0.5;
- }
centermass(vesicle);
cell_occupation(vesicle);
vesicle_volume(vesicle); //needed for constant volume at this moment
--
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