QMD analysis code

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Just Got Here
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Hi,

I am trying to use the QMD analysis code on NWChem 6.8 with the command:

./qmd_analysis -xyz dih15.xyz -steps 1000 -skip 0 -ts 10

However I am getting this error message:

Input file:                    dih15.xyz
Ouput files: dih15_VDOS.dat
dih15_IR.dat
Number of steps to analyze: 100
Number of steps to be skipped: 0
Temperature: 298.15 K
Time step of simulation: 10.00 a.u.
FWHM of resulting spectrum: 10.00 cm^{-1}
Found 1 unique elements in trajectory file
READ ERROR



First two steps of the dih15.xyz file:

  19
0 -28649.8153065200 2.594822E-02 -6.693869E-02 3.272520E-02
Ni 0.60759863 2.77272964 -0.24368466 0.00063862 0.00181864 -0.00041117
Ni 0.32875775 -0.68502774 -1.90343107 0.00119789 -0.00118340 -0.00076219
Ni -1.59429017 -1.15210969 -0.52806100 -0.00014335 0.00219514 0.00072139
Ni -2.69694697 0.93277344 -0.12194816 -0.00029078 -0.00173376 0.00066038
Ni 0.49990340 -0.87149495 0.39741214 -0.00019444 0.00160586 0.00234631
Ni 0.18229075 -2.75693056 -0.69760032 -0.00112161 0.00288267 0.00172067
Ni 0.32776657 1.68071647 -2.28980379 -0.00170683 -0.00282290 -0.00241871
Ni 1.79467925 0.72989453 -0.65262333 0.00307254 0.00053927 -0.00173366
Ni 2.22416672 -1.62007140 -0.77657590 -0.00282916 -0.00135158 0.00047512
Ni -1.26420447 2.31438708 1.09015881 -0.00021066 -0.00104561 0.00172778
Ni 2.50055562 -0.52527326 1.26725616 0.00174180 0.00005289 0.00443869
Ni 1.54125971 -2.68714234 1.22905757 0.00206648 -0.00207317 -0.00087110
Ni 0.63238510 -0.98668293 2.60351243 0.00068088 -0.00108798 -0.00201098
Ni -0.49826617 0.86974232 -0.40209993 0.00131352 0.00430850 -0.00312590
Ni -1.30618902 -0.02664815 1.57940596 0.00033680 -0.00148346 0.00095855
Ni -1.53863247 2.68994845 -1.22834823 -0.00223494 0.00001772 0.00030751
Ni 0.78057179 1.13480944 1.50232344 -0.00325188 -0.00042652 -0.00083667
Ni -1.71448846 0.54776216 -2.21111898 0.00146415 0.00173117 -0.00112310
Ni -0.80691756 -2.36138251 1.38616887 -0.00052903 -0.00194348 -0.00006293
19
10 -28649.8147287343 8.588848E-02 4.446748E-02 -7.249883E-02
Ni 0.62435892 2.91368401 -0.36413013 -0.00325890 -0.00368344 -0.00212649
Ni 0.29204621 -0.63857995 -1.90974590 -0.00138708 0.00255839 0.00386435
Ni -1.58423180 -1.11994882 -0.55646551 0.00330548 0.00102099 0.00064075
Ni -2.76635948 0.94121749 -0.09925614 0.00343457 0.00126318 -0.00099430
Ni 0.57455886 -0.87297392 0.43881976 -0.00347227 0.00134337 -0.00035827
Ni 0.08136302 -2.85028338 -0.63287225 0.00134151 0.00050331 0.00091911
Ni 0.38366914 1.74220229 -2.49902716 -0.00150305 0.00100496 0.00502704
Ni 1.82291997 0.77576835 -0.63726426 -0.00544310 -0.00035823 0.00244357
Ni 2.33006413 -1.69625893 -0.71746529 0.00058805 0.00058254 0.00135510
Ni -1.35766935 2.33215717 1.10621332 0.00103855 -0.00156185 -0.00373246
Ni 2.52546782 -0.56306762 1.36005150 -0.00294691 -0.00074552 -0.00237749
Ni 1.60688001 -2.77308926 1.23588679 -0.00224602 0.00159966 0.00009519
Ni 0.65841477 -1.18468958 2.70097589 -0.00085618 -0.00121457 -0.00192265
Ni -0.47920355 1.00523541 -0.49435223 0.00116497 -0.00352939 0.00108723
Ni -1.30670225 -0.10471161 1.60270581 0.00458388 0.00053092 -0.00420350
Ni -1.65842846 2.75335407 -1.21028847 0.00164495 -0.00127569 0.00004014
Ni 0.86185434 1.23052727 1.56048242 0.00034881 -0.00231648 -0.00318326
Ni -1.80231528 0.56855890 -2.30755835 0.00121209 0.00096153 0.00416877
Ni -0.80668704 -2.45910190 1.42329021 0.00245066 0.00331634 -0.00074283



Thanks!

Forum Regular
Threads 1
Posts 185
I was a little lazy when writing that code as far as providing information if something goes wrong. Getting that message indicates that there was some problem while looping through the file, in particular when reading the first two lines of a frame (i.e. the number of atoms line and the line containing the time, energy, and dipole moment). If you make two small modifications to the source and remake it, it should help with your debugging. Find the two lines that output the error statement you are seeing

write(*,*) 'READ ERROR'

change the first one to

write(*,*) 'READ ERROR 1', is+1, ioerror

and the second one to

write(*,*) 'READ ERROR 2', is+1, ioerror

If you make these changes, rebuild the analysis code, and run it again, the error message will now tell you which frame in your trajectory is causing problems and will give you the IOSTAT value. Hopefully this is enough for you to figure out what is going wrong.

Forum Regular
Threads 1
Posts 185
Please take a look at the response to this post,
http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id2750/Errors_in_using_qmd_analysis...
I believe it will fix your problem

Just Got Here
Threads 1
Posts 2
Thank you very much!

Just Got Here
Threads 0
Posts 1
Prnt_xyz command does not provide an output
I am new to Nwchem, I was trying to run the sample input given for ground state MD in the documentation, this input lines have print_xyz 5, which I expect would output an xyz file with all the trajectory details.I could not obtain this file even after successful completion of MD run.Do we have to specify something else in the script?

Forum Regular
Threads 1
Posts 185
The code will always produce an xyz trajectory file with the exception being if

print_xyz n
nsteps_nucl m
where n>m

e.g. you tell the code to run 100 steps but also tell it to only print the trajectory file every 200 steps. By default the print_xyz keyword is set to 1, so the code will output the coordinates, etc to the xyz file every step by default.

If you are running one of the examples from the documentation, are you getting any of the output files back (*.db, *.movecs, etc)? Are you receiving any error messages either in the NWChem output or from your system that indicates that files could not be created/modified/copied?


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