13 June 2014

582. Briefly: freecall.com using linphone

I've covered how to set up linphone in the past: http://verahill.blogspot.com.au/2011/08/linphone-with-iinet-iitalk-voip-service.html

This is thus going to be a very brief post with just the settings for freecall.com, which offers a SIP service.

The specific settings that you need to make are (this is from my ~/.linphonerc
[auth_info_0] username=myUserId userid=myUserId passwd=PasswordInPlainText realm="sip.freecall.com" [proxy_0] reg_proxy=sip:sip.freecall.com reg_identity=sip:myUserID@sip.freecall.com reg_expires=3600 reg_sendregister=1 publish=0 dial_escape_plus=0

Yes, that's it. So, there you go - you now have a reasonably priced alternative to Skype for international calling.

I've charged my account with 10 Euro, and I've made a few test phone calls. So far so good.

See http://verahill.blogspot.com.au/2014/06/581-obi200-and-debian-and-iinet.html for how to use the obihai 200 ATA with freecall.

12 June 2014

581. Obihai Obi200 ATA and iinet Australia (and freecall)

I've had iitalk sip service as part of my naked DSL via iinet for years, but haven't really done much with it (apart from writing a post: http://verahill.blogspot.com.au/2011/08/linphone-with-iinet-iitalk-voip-service.html). I decided that it might be time to get something akin to a landline, and if it involves buying a new toy, so much better. The toy in question is an ATA device, which allows you to connect your regular old landline phone to your fancy internet router.

I ordered an Obihai OBI200 from Amazon US and had it delivered to Australia.

Getting started was pretty straightforward:
I unpacked the device, plugged in the power cable, and hooked it up to my router via an ethernet cable. I then gave it a static IP address, 192.168.2.131

Next I registered on the obitalk.com website, confirmed my email address, and logged in. You're then offered to set up your device. Note that you'll need to have a phone plugged into your obi device at this point. I bought a $32 Panasonic KX-TG1611 from JB HiFi.

Anyway, go to http://www.obitalk.com




go to dashboard

click on SP1

click on Next in the bottom right


select Generic Service Provider
The settings are as follows:
(state=vic, nsw etc. i.e. three-letter code)
Service Provider Proxy Server: sip.state.iinet.net.au
Service Provider Proxy Server port: 5060
Outbound Proxy Server: sip.state.iinet.net.au
Outbound Provider Proxy Server port: 5060
User Name: your phone number (e.g. 03 xxxx xxxx; look it up on your iinet toolbox)
Password: your VOIP password which you set up at some point
URI: yourphonenumber@sip.state.iinet.net.au

Hit submit

If all went well you'll show up as being registered.


freecall.com
I'm thinking about replacing skype with sip, and one provider is freecall.com. I originally signed up with them many years ago because I got a free number, but my account has expired, and they won't let me reactivate it. Either way,  you can still call pretty cheaply using their service.

The settings for the OBI200 and freecall are:
Service Provider Proxy Server: sip.freecall.com
Outbound Proxy Server: sip.freecall.com
User Name: your user name
Password: your password
URI: yourusername@freecall.com

I will work on setting it up for international calls at a later stage.

To select a specific service when making a call, type **1 for SP1, **2 for SP2 etc. See http://www.obihai.com/faq/About-the-OBi/How-do-I-make-calls-with-OBi

10 June 2014

580. Python script: Interpolate between structures in a multi-xyz file

I'm doing a lot of NEB (nudged elastic band) calculations using nwchem at the moment, and while getting 'neb convergence' is simple enough, I often get an error along the lines of
3965547 @neb NEB calculation converged
3965548 @neb However NEB Gmax not converged...Try increasing the number of beads.

While that sounds simple enough it's nicer if you don't have to go back to the beginning and e.g. run a more fine-grained PES job to generate a reasonable trajectory (straight linear interpolation often doesn't work), then keep on running neb iterations. One way to cut down on time (presumably) is to simply pad the neb path xyz with intermediate structures, and that is what this python (2.7) script does.

Oh, and I really wish blogspot would support code inclusion better...

How to use:
python nebinterpolate.py -i neb_A_F.neb_final.xyz  -o test.xyz

Example:
Say we have the structure of methanol, and methanol in which the oxygen-carbon distance is 3.0 Ångström:

Here's the corresponding xyz file, which we'll call first.xyz:
6 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 0.83960 0.81877 0.83960 H 1.38912 0.20156 1.38912 6 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.76087 1.75017 1.76087 H 2.31039 1.13296 2.31039

Run nebinterpolate -i first.xyz -o second.xyz and you'll get a new xyz file with three structures -- the first one plus an intermediate structure:

Here's the new file, second.xyz:
6 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 0.83960 0.81877 0.83960 H 1.38912 0.20156 1.38912 6 structure 2 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.30024 1.28447 1.30024 H 1.84976 0.66726 1.84976 6 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.76087 1.75017 1.76087 H 2.31039 1.13296 2.31039

 Run it again, nebinterpolate -i second.xyz -o third.xyz, and you'll get:

Here's the new file, third.xyz:
6 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 0.83960 0.81877 0.83960 H 1.38912 0.20156 1.38912 6 structure 2 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.06992 1.05162 1.06992 H 1.61944 0.43441 1.61944 6 structure 2 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.30024 1.28447 1.30024 H 1.84976 0.66726 1.84976 6 structure 4 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.53056 1.51732 1.53056 H 2.08007 0.90011 2.08007 6 C 0.03517 0.00549 0.03517 H -0.61778 -0.63407 0.66798 H 0.66798 -0.63407 -0.61778 H -0.60514 0.64647 -0.60514 O 1.76087 1.75017 1.76087 H 2.31039 1.13296 2.31039

Now, the real use for this is when you've been optimising a string of structures using NEB and want to increase the number of images because you're not getting gmax convergence, or if you want to do a quick and rough optimisation and then get a prettier looking set of coordinates.

You can load the multi-xyz file in nwchem by using

NEB
   ...
  XYZ_PATH path.xyz
END


nebinterpolate.py 

#!/usr/bin/python

import sys

def getvars(arguments):
 switches={}

 version='0.1'
 
 try:
  if "-i" in arguments:
   switches['in_one']=arguments[arguments.index('-i')+1]
   print 'Input: %s '% (switches['in_one'])
  else:
   arguments="--help";
 except:
  arguments="--help";
  
 try:
  if "-o" in arguments:
   switches['o']=arguments[arguments.index('-o')+1].lower()
   print 'Output: %s'% switches['o']
  else:
   arguments="--help";
 except:
  arguments="--help";

 try:
  if "-w" in arguments:
   switches['w']=float(arguments[arguments.index('-w')+1])
   print 'Weighting: %i'% switches['w']
  else:
   print 'Assuming no weighting'
   switches['w']=1.0;
 except:
  switches['w']=1.0;

 doexit=0
 try:
  if ("-h" in arguments) or ("--help" in arguments):
   print '\t\t bytes2words version %s' % version
   print 'Creates interpolated structures'
   print 'from an multixyz file'
   print '--input \t-i\t multi-xyz file to morph'
   print '--output\t-o\t output file'
   print '--weight\t-w\t weight first structure vs second one (1=average; 0=start; 2=end)'
   print 'Exiting'
   doexit=1
 except:
  a=0 # do nothing
 if doexit==1:
  sys.exit(0)

 return switches

def getcmpds(switches):
 
 cmpds={}
 
 g=open(switches['in_one'],'r') 
 n=0
 xyz=[]
 atoms=[]
 structure_id=1

 for line in g:

  try:
   if len(xyz)==cmpds['atoms_'+str(structure_id)]:
    cmpds['coords_'+str(structure_id)]=xyz
    cmpds['elements_'+str(structure_id)]=atoms   
    structure_id+=2
    n=0
    atoms=[]
    xyz=[]
  except:
   pass

  n+=1
  line=line.rstrip('\n')
   
  if n==1:
   cmpds['atoms_'+str(structure_id)]=int(line)
  elif n==2:
   cmpds['title_'+str(structure_id)]=line
  else:
   line=line.split(' ')
   line=filter(None,line)
   xyz+=[[float(line[1]),float(line[2]),float(line[3])]]
   atoms+=[line[0].capitalize()]
 g.close

 cmpds['coords_'+str(structure_id)]=xyz
 cmpds['elements_'+str(structure_id)]=atoms   
 cmpds['w']=switches['w']
 cmpds['structures']=(structure_id)
 
 return cmpds

def morph(cmpds,structure_id):
 coords_one=cmpds['coords_'+str(structure_id)]
 coords_two=cmpds['coords_'+str(structure_id+2)]
 
 coords_morph=[]
 coords_diff=[]
 for n in range(0,cmpds['atoms_'+str(structure_id)]):
  morph_x=coords_one[n][0]+cmpds['w']*(coords_two[n][0]-coords_one[n][0])/2.0
  morph_y=coords_one[n][1]+cmpds['w']*(coords_two[n][1]-coords_one[n][1])/2.0
  morph_z=coords_one[n][2]+cmpds['w']*(coords_two[n][2]-coords_one[n][2])/2.0
  diff_x=coords_two[n][0]-coords_one[n][0]
  diff_y=coords_two[n][1]-coords_one[n][1]
  diff_z=coords_two[n][2]-coords_one[n][2]
  coords_morph+=[[morph_x,morph_y,morph_z]]
  coords_diff+=[[diff_x,diff_y,diff_z]]

 cmpds['atoms_'+str(structure_id+1)]=cmpds['atoms_'+str(structure_id)]
 cmpds['elements_'+str(structure_id+1)]=cmpds['elements_'+str(structure_id)]
 cmpds['title_'+str(structure_id+1)]='structure '+str(structure_id+1)
 cmpds['coords_'+str(structure_id+1)]=coords_morph

 return cmpds

def genxyzstring(coords,element):
 x_str='%10.5f'% coords[0]
 y_str='%10.5f'% coords[1]
 z_str='%10.5f'% coords[2]
 
 xyz_string=element+(3-len(element))*' '+10*' '+\
 (8-len(x_str))*' '+x_str+10*' '+(8-len(y_str))*' '+y_str+10*' '+(8-len(z_str))*' '+z_str+'\n'
 
 return xyz_string

def writemorph(cmpds,outfile):
 g=open(outfile,'w') 

 for m in range(1,cmpds['structures']+1):
  g.write(str(cmpds['atoms_'+str(m)])+'\n')
  g.write(str(cmpds['title_'+str(m)])+'\n')
  for n in range(0,cmpds['atoms_'+str(m)]):
   coords=cmpds['coords_'+str(m)][n]
   g.write(genxyzstring(coords, cmpds['elements_'+str(m)][n]))
 g.close

 return 0

if __name__=="__main__":
 arguments=sys.argv[1:len(sys.argv)]
 switches=getvars(arguments)
 cmpds=getcmpds(switches)

#check that the structures are compatible
 for n in range(1,cmpds['structures'],2):

  if cmpds['atoms_'+str(n)]!=cmpds['atoms_'+str(n+2)]:
   print 'The number of atoms differ. Exiting'
   sys.exit(1)
  elif cmpds['elements_'+str(n)]!=cmpds['elements_'+str(n+2)]:
   print 'The types of atoms differ. Exiting'
   sys.exit(1)
  cmpds=morph(cmpds,n)
 success=writemorph(cmpds,switches['o'])
 if success==0:
  print 'Conversion seems successful'