QMD analysis code

Just Got Here

4:08:17 PM PDT - Mon, Jul 9th 2018

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

4:46:08 AM PDT - Tue, Jul 10th 2018
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

5:02:15 AM PDT - Tue, Aug 14th 2018
Please take a look at the response to this post, http://nwchemgit.github.io/Special_AWCforum/st/id2750/Errors_in_using_qmd_analysis... I believe it will fix your problem

Just Got Here

9:17:26 AM PST - Fri, Nov 9th 2018
Thank you very much!

Just Got Here

12:08:34 AM PDT - Sat, Oct 12th 2019
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

10:41:25 AM PDT - Thu, Oct 24th 2019
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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