duu... at gmail.com
Tue Jan 26 22:45:13 CET 2010
Thanks alot, all is fine now!
On Jan 26, 2:39 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> thanks Lepka,
> Indeed there is a bug in fes.sop after a minor change to the METADYN
> code done last week.
> I have the fix but unfortunately BerliOS has the authenticated CVS
> server down :(.
> I will commit the fix as soon as the server will be up again.
> In the meanwhile, as a temporary work-around, please do execute this
> command on your shell:
> sed -e 's/SPAWNED_HILLS_SCALE/SPAWNED_HILLS_AMPL/g'
> YOUR_RESTART_FILE.restart > tmp
> mv tmp YOUR_RESTART_FILE.restart
> Use the processed restart file with your version of fes and it should work.
> Will send a further message once the patch to fes is in the CVS.
> yimanu wrote:
> > This is what I get from just running fes
> > USAGE:
> > graf
> > [-ngrid 50 .. ..] (Mesh dimension. Default :: 100)
> > [-dp 0.05 .. ..] (Alternative to -ngrid, allows the specification
> > of the mesh dx)
> > [-ndim 3 ] (Number of collective variables NCV)
> > [-ndw 1 3 .. ] (CVs for the free energy surface)
> > [-periodic 2 3 ..] (CVs with periodic boundary conditions (-
> > pi,pi] )
> > [-stride 10 ] (How often the FES is written)
> > [-fix 1.1 .. ..] (Define the region for the FES)
> > (If omitted this is automatically calculated)
> > [-cutoff 2. ] (The hills are cutoffed at 2)
> > [-file filename]
> > [-out filename]
> > [-orac] (If energies are written in orac intern units)
> > [-cp2k] (Specify if a CP2K restart file is provided)
> > [-cpmd] (Specify if CPMD colvar_mtd and parvar_mtd are
> > provided)
> > (With CPMD you do not need to specify -file,
> > parvar_mtd and
> > colvar_mtd are expected to be present in the
> > working directory)
> > [-mathlab] (File storing FES in Mathlab format. Default
> > format Gnuplot)
> > [-find-minima] (Tries to finds all minima in the computed FES)
> > [-find-path] (Finds MEP between all minima (found) in the
> > computed FES)
> > [-point-a] (Specifies point (a) when using -find-path
> > option)
> > [-point-b] (Specifies point (b) when using -find-path
> > option)
> > DEFAULT OUTPUT: fes.dat
> > STOP Please provide arguments to run FES!
> > I will attack the gzipped file on the main page
> > Thanks
> > Lekpa
> > On Jan 26, 2:17 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> >> could you please attach as well your restart file (please gzip first).
> >> Thanks
> >> Teo
> >> Lekpa Duukori wrote:
> >>> Hi all,
> >>> I am trying to use fes.sopt on a restart but I get the following error
> >>> fes.sopt -cp2k -ndim 3 -ndw 1 3 -file 2hno3_dftb_mtd_3cv-1.restart
> >>> **********************************************************************
> >>> FES| Parsing file: <2hno3_dftb_mtd_3cv-1.restart>
> >>> At line 374 of file
> >>> /opt/cp2k_gfortran/makefiles/../tools/metadyn/graph.F (unit = 10, file
> >>> = '2hno3_dftb_mtd_3cv-1.restart')
> >>> Fortran runtime error: End of file
> >>> fes.sopt was compiled using make fes.sopt ARCH=Linux-x86-64-gfortran
> >>> VERSION=sopt on a cp2k gfortran compilation from the CVS snapshot of
> >>> 2010-01-21
> >>> Using several other intermediate restart files does not help, so I am
> >>> guessing that somehow fes.sopt was not properly compiled or maybe my
> >>> cp2k compilation is not writing what fes.sopt expects.
> >>> Any thoughts is appreciated.
> >>> Thanks!
> >>> Lekpa
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