Formating of logfile

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Nov 11 2009 - 06:58:44 CST

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

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

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