From: Joshua D. Moore (joshuadmoore_at_gmail.com)
Date: Tue Feb 08 2011 - 17:01:32 CST
Hey sorry Andrew. I didn't read your full message. You have clear variable
names there for everything.
Josh
On Tue, Feb 8, 2011 at 9:00 AM, Andrew Emerson <a.emerson_at_cineca.it> wrote:
> Dear Bjoern
>
> I dont know python but comparing your script with the fortran program I
> wrote some time ago,
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8441.html
>
> it looks as if you are lacking the box dimension information (an array of
> 6 doubles).
> As for the timestep DELTA I guess this depends on what units it has been
> stored in - I suspect it is a reduced time step and has been divided by some
> other quantity such as the system mass.
>
> regards
> Andy
>
>
>
> On 2/8/2011 12:24 PM, Bjoern Olausson wrote:
>
>> On Monday 07 February 2011 19:53:56 Joshua D. Moore wrote:
>>
>>> catdcd can tell you the number of frames in the trajectory
>>>
>>> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>>>
>>> The other information is written in the header of the dcd file. You can
>>> print that out if you wanted to using a simple C or fortran code.
>>>
>>> The format is here with one correct in that the the PBCs are written in
>>> double precision while the coordinates are in single precision (not
>>> double
>>> as is written on the page).
>>>
>>> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
>>>
>>> The format can also be ascertained fairly easily from the plugin in the
>>> VMD
>>> source code.
>>>
>>> Josh
>>>
>>> Interesting, thanks!
>>
>> So when I understand the header correctly I can get NSET (Number of
>> overall
>> frames?), integration time (DELTA), write out frequency (NSAVC) and the
>> first
>> timestep (not sure about the meaning of ISTRT - step 1).
>>
>> With these information every thing else I want is at ones hand :-)
>>
>> Since I am a noob regarding C or Fortran I'll played around with python
>> and
>> came up with the appended script. But after the "NSAVC" header, something
>> pops
>> up which is not documented on the above website. Does anyone know what it
>> exactly refers to?
>> Furthermore the "DELTA" looks messed up. It should be 2.0 fs.
>>
>> Any clue what went wrong?
>>
>> http://paste.pocoo.org/show/FeirO5JuypU7XzrUmQtK/
>> ----------------------------------------------------
>> #!/bin/env python
>> # -*- coding: utf-8 -*-
>> #
>> #
>>
>> import sys, struct
>>
>> #HDR NSET ISTRT NSAVC 5-ZEROS
>> NATOM-NFREAT
>> DELTA 9-ZEROS
>> #`CORD' #files step 1 step interv. zeroes
>> (zero)
>> timestep (zeroes)
>> #C*4 INT INT INT
>> 5INT INT
>> DOUBLE 9INT
>>
>> #==========================================================================
>> #NTITLE TITLE
>> #INT (=2) C*MAXTITL (=32)
>>
>> #==========================================================================
>> #NATOM
>> ##atoms
>> #INT
>>
>> #==========================================================================
>> #X(I), I=1,NATOM (SINGLE)
>> #Y(I), I=1,NATOM
>> #Z(I), I=1,NATOM
>>
>> #==========================================================================
>>
>>
>> f = open(sys.argv[1], 'rb')
>> HDR = struct.unpack('i4c',f.read(struct.calcsize('i4c')))
>> NSET = struct.unpack('i', f.read(struct.calcsize('i')))[0]
>> ISTART = struct.unpack('i', f.read(struct.calcsize('i')))[0]
>> NSAVC = struct.unpack('i', f.read(struct.calcsize('i')))[0]
>> ##NOTE: The following seems not to be documented on
>> ##NOTE:
>> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
>> UNDOC = struct.unpack('i', f.read(struct.calcsize('i')))[0]
>> ZEROS5 = struct.unpack('4i', f.read(struct.calcsize('4i')))
>> NFREAT = struct.unpack('i', f.read(struct.calcsize('i')))
>> DELTA = struct.unpack('d',f.read(struct.calcsize('d')))
>> ZEROS9 = struct.unpack('8i', f.read(struct.calcsize('8i')))
>>
>> ISTOP = ISTART + (NSET * NSAVC)
>> NSTP = ISTOP - ISTART
>>
>> print "%(ID)-13s %(DATA)s" %{"ID": "HDR:", "DATA": HDR}
>> print "%(ID)-13s %(DATA)i" %{"ID": "Coor Sets:", "DATA": NSET}
>> print "%(ID)-13s %(DATA)i" %{"ID": "First Step:", "DATA": ISTART}
>> print "%(ID)-13s %(DATA)i" %{"ID": "Save Int.:", "DATA": NSAVC}
>> print "%(ID)-13s %(DATA)i" %{"ID": "UNDOC:", "DATA": UNDOC}
>> print "%(ID)-13s %(DATA)s" %{"ID": "5-ZEROS:", "DATA": ZEROS5}
>> print "%(ID)-13s %(DATA)s" %{"ID": "NATOM-NFREAT:", "DATA": NFREAT}
>> print "%(ID)-13s %(DATA)s" %{"ID": "Int. Time:", "DATA": DELTA}
>> print "%(ID)-13s %(DATA)s" %{"ID": "9-ZEROS:", "DATA": ZEROS9}
>> print "\n%(ID)-13s %(DATA)i" %{"ID": "Last Step:", "DATA": ISTOP}
>> print "%(ID)-13s %(DATA)i" %{"ID": "Num Steps:", "DATA": NSTP}
>>
>> ----------------------------------------------------
>>
>> Cheers and kind regards,
>> Bjoern
>>
>>
> --
> Dr Andrew Emerson
> CINECA (High Performance Systems)
> via Magnanelli, 6/3
> 40033 Casalecchio di Reno (BO)-ITALY
> tel: +39-051-6171653, fax: +39-051-6137273
> e-mail: a.emerson_at_cineca.it
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:47 CST