The ABINIT Users Mailing List ( CLOSED )

["Josef W. Zwanziger" <jzwanzig@dal.ca>]

Dear Colleagues,

I have written a Perl script called "abchk" (attached) to aid in 
checking abinit input files. Several times I have had trouble with 
abinit calculations, only to find that I had mistyped the name of a 
variable in the input file; it would appear that abinit more or less 
ignores such input, at least for some variables ("rfstrs" for example), 
and the program runs with the offending variable set to its default 
value. I would prefer that, if the program encountered a variable it 
didn't recogize, it just stopped and gave an exit warning. I couldn't 
figure out how to code this simply into abinit, so instead I wrote the 
attached perl script. This code steps through the input file, compares 
the variable names (after suitably ignoring initial "#" characters and 
trailing numbers) to a glossary of abinit variables. If it fails to find 
a match, it prints the name of variable it couldn't match; the return 
status is the number of unmatched variables. That way you can also run 
it from a shell script (as I always  have to do on our Linux cluster 
with Sun Grid Engine queuing) and basically abort if the program returns 
with any unknown variables in the input file.

Doubtless the program can be improved, but I hope some of you find it 
helpful.

Joe

--
Josef W. Zwanziger
Prof. of Chemistry and Canada Research Chair in NMR Studies of Materials
Director, Atlantic Region Magnetic Resonance Centre
Dalhousie University
Halifax, NS B3H 4J3
Canada

tel: 902.494.1960     net: jzwanzig@dal.ca
fax: 902.494.1867     web: http://jwz.chem.dal.ca
#!/usr/bin/perl

# this program reads through an abinit input file, and checks to see
# whether each variable encountered can be matched to a variable in the
# abinit input list. The purpose is to avoid input errors of the type
# "rfstr" instead of the correct "rfstrs"; since abinit has defaults for
# many variables, if it reads an unknown name it seems to just ignore the
# input and continue on with the default.

# usage: abchk <input file name>
# output: variables in the input file that didn't match the glossary
# program returns the number of unmatched variables, which makes it
# also useful in shell scripts

# By: Josef Zwanziger, Dept. of Chemistry and Institute for Research
# in Materials, Dalhousie University, Halifax, NS B3H 4J3
# jzwanzig@dal.ca

# have fun!!


# here are many of the abinit variables. You can add more.
@abinit_variables = ("acell","angdeg","amu","algalch",
                     "brvltt","bdberry","berryopt","boxcenter","boxcutmin",
                     "cmlfile","chkexit","chkrprim","cpus","cpum","cpuh",
                     "delayperm","dilatmx","dtion","dsikpt","diecut",
                     "diegap","dielam","dielng","diemac","diemix","dosdeltae",
                     "ecut","ecutsm","efield","enunit",
                     "friction","fband","fixmom",
                     "getddk","getden","getkss","getocc","getscr",
                     "getwfk","getwfq","get1den","get1wf","get1wfden",
                     "genafm","getcell","getxcart","getxred",
                     "iscf","ixc","iatcon","iatfix","iatfixx","iatfixy",
                     "iatfixz","ionmov","irdddk","irdkss","irdscr","irdwfk",
                     "irdwfq","ird1wf","iatsph","iprcel",
                     "jdtset",
                     "kpt","kptnrm","kptopt","kssform","kberry","kptbounds",
                     "kptrlatt","kptrlen",
                     "localrdwf",
                     "mdftemp","mditemp","mdwall","mffmem","mkmem",
                     "mkqmem","mk1mem","mixalch",
                     "natfix","natfixx","natfixy","natfixz","natcon",
                     "nconeq","ntime",
                     "natom","nband","ndtset","ngkpt","nkpt","nshiftk",
                     "natsph","nberry","nbdbuf","ndivk","ngfft","nline",
                     "npsp","nqpt","nspinor","ntypalch",
                     "nspol","nstep","nsym","ntypat","natrd","nobj",
                     "occopt","objatt","objbat","objaax","objbax","objan",
                     "objbn","objarf","objbrf","objaro","objbro","obfatr",
                     "objbtr","optcell","occ","optdriver",
                     "prtcml","prtden","prtdos","prteig","prtfsurf","prtgeo",
                     "prtkpt","prtpot","prtstm","prtvha","prtvhxc",
                     "prtvol","prtvxc","prtwf","prt1dm","prepanl","prtbbb",
                     "pspso",
                     "qpt","qptnrm",
                     "rprim","restartxf","rfasr","rfatpol","rfdir","rfelfd",
                     "rfphon","rfstrs","rfthrd","rfuser","rf1atpol",
                     "rf1dir","rf1elfd","rf1phon","rf2atpol","rf2dir",
                     "rf2elfd","rf2phon","rf3atpol","rf3dir","rf3elfd",
                     "rf3phon","ratsph",
                     "shiftk","symrel","spgaxor","spgorig","spgroup",
                     "spgroupma","signperm","strfact","strprecon",
                     "strtarget","sciss","so_typat","spinat","stmbias",
                     "symafm",
                     "tnons","toldfe","toldff","tolvrs","tolwfr","typat",
                     "tolmxf","td_maxene","td_mexcit","timopt",
                     "tphysel","tsmear",
                     "udtset",
                     "vel","vis","vacuum","vacwidth",
                     "wtk","wtatcon",
                     "xangst","xcart","xred",
                     "znucl");

#now set number of unknown variables to 0.
$unknown_variables = 0;
while (<>) { # loop over lines in the input file...
      @fields = split; # split each line on white space...
      if ( @fields[0] =~ /^[a-z]/ ) { # check for a match on lowercase 
characters. These are variables
         while( @fields[0] =~ /[0-9]\b/ ) { chop(@fields[0]); } # if the 
trailing character is a number, 
                                                                # strip it 
off. These are the variables in multiple data sets
         $known = 0;
         foreach $abinit_variable (@abinit_variables) { # if the variable 
matches a glossary entry EXACTLY, it's known.
                 if (@fields[0] =~ /\b$abinit_variable\b/) { $known = 1; }
        }
        if(!$known) { #if the variable is not known, tell us about it. 
                    print "do not know variable @fields[0]\n";
                    ++$unknown_variables;
                    };
        }
}
exit($unknown_variables); # finally, tell us the total number of unknown 
variables