Re: Formating of logfile

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Fri Nov 13 2009 - 02:55:02 CST

On Thursday 12 November 2009 21:07:56 you wrote:
> On Wed, Nov 11, 2009 at 8:07 AM, Bjoern Olausson
<namdlist_at_googlemail.com>wrote:
> > Ha namd users,
> >
> > can anybody tell me the formating of the output file, especially the
> > formatting of the following lines:
> >
> > PRESSURE:
> > GPRESSURE:
> > PRESSAVG:
> > GPRESSAVG:
> > ENERGY:
> >
> > Are the values in fixed columns or white space separated? Or is there any
> > criteria which can separate these values for 100%
> >
> > I used the following python synthax to extract the values, but today it
> > failed
> > for th first time because the formatting did no longer match:
> >
> > def Energy(line) :
> > TS.append(int(line[7:16].strip()))
> > BOND.append(float(line[16:31].strip()))
> > ANGLE.append(float(line[31:46].strip()))
> > DIHED.append(float(line[46:61].strip()))
> > IMPRP.append(float(line[61:76].strip()))
> > ELECT.append(float(line[76:96].strip()))
> > VDW.append(float(line[96:112].strip()))
> > BOUNDARY.append(float(line[112:126].strip()))
> > MISC.append(float(line[126:141].strip()))
> > KINETIC.append(float(line[141:156].strip()))
> > TOTAL.append(float(line[156:176].strip()))
> > TEMP.append(float(line[176:191].strip()))
> > TOTAL2.append(float(line[191:206].strip()))
> > TOTAL3.append(float(line[206:221].strip()))
> > TEMPAVG.append(float(line[221:236].strip()))
> > # If "minimization on" was used these values are not populated
> > if not MINo :
> > PRESSURE.append(float(line[236:256].strip()))
> > GPRESSURE.append(float(line[256:271].strip()))
> > VOLUME.append(float(line[271:286].strip()))
> > PRESSAVG.append(float(line[286:301].strip()))
> > GPRESSAVG.append(float(line[301:316].strip()))
> >
> > kind regards
> > Bjoern
> >
> awk '/^ENERGY/ {print $2 " " $12}' ./output > ./newfile
>
> to separate timestep and pot en. It is all one line per timestep or title.
> Hope this helps.
>
> Christi Young
>

Your answer implies that the lines are "white space" separated.
Are you sure about it? Would make life easier if you are right. *G*

Ah, whatever, I'll go for "white spaced" and use it until it fails some day,
then I know for sure :-)

Cheers
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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