[Pw_forum] gipaw.x

Manuel Otero oteromn at gmail.com
Thu May 12 21:14:49 CEST 2016


Hello
I'm trying to obtain the NMR spectrum of ethanol using the gipaw.x program.
I managed to install gipaw.x in the espresso-5.4.0 version. I think it is
working fine. But I can not find any tutorial that explains how to extract
the spectrum from the output file.

My input is:
------------------------------------------------------------------------------------
&inputgipaw
        job = 'nmr'
        tmp_dir = './'
        q_gipaw = 0.01
        spline_ps = .true.
        use_nmr_macroscopic_shape = .true.
/
-------------------------------------------------------------------------------------

And the output:
-------------------------------------------------------------------------------------

     Program QE v.5.4.0 starts on 12May2016 at  8:28:47

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details
at
     http://www.quantum-espresso.org/quote

     Parallel version (MPI), running on     1 processors

     ***** This is GIPAW svn revision unknown      *****

     Parallelizing q-star over 1 images

     Reading data from directory:
     ./pwscf.save

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1, nr2, nr3 values from input

     IMPORTANT: XC functional enforced from input :
     Exchange-correlation      =  SLA  PW   PBX  PBC ( 1  4  3  4 0 0)
     Any further DFT definition will be discarded
     Please, verify this is what you really want


     G-vector sticks info
     --------------------
     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
     Sum         641     641    193                12053    12053    2103


     Subspace diagonalization in iterative solution of the eigenvalue
problem:
     a serial algorithm will be used

     GIPAW projectors -----------------------------------------------
     atom=  H    l=0  rc=    1.2000  rs=    0.8000
     atom=  H    l=0  rc=    1.2000  rs=    0.8000
     projs nearly linearly dependent: l=0  n1,n2= 1, 2  s= -0.99707079

     atom=  C    l=0  rc=    1.7500  rs=    1.1667
     atom=  C    l=0  rc=    1.7500  rs=    1.1667
     atom=  C    l=1  rc=    1.7500  rs=    1.1667
     atom=  C    l=1  rc=    1.7500  rs=    1.1667
     projs nearly linearly dependent: l=1  n1,n2= 1, 2  s= -0.99430547

     atom=  O    l=0  rc=    1.4500  rs=    0.9667
     atom=  O    l=0  rc=    1.4500  rs=    0.9667
     atom=  O    l=1  rc=    1.4500  rs=    0.9667
     atom=  O    l=1  rc=    1.4500  rs=    0.9667
     projs nearly linearly dependent: l=1  n1,n2= 1, 2  s= -0.99382826
     -----------------------------------------------------------------


     smearing ngauss=   0  degauss=  0.0050 Ry
     alpha_pv=     27.9815 eV

     GIPAW job:
nmr

     NMR macroscopic correction: yes
             0.6667          0.0000          0.0000
             0.0000          0.6667          0.0000
             0.0000          0.0000          0.6667


     Largest allocated arrays     est. size (Mb)     dimensions
        KS wavefunctions at k           0.31 Mb     (    1472,   14)
        KS wavefunctions at k+q         0.31 Mb     (    1472,   14)
        First-order wavefunctions       3.14 Mb     (    1472,   14, 10)
        Charge/spin density             0.21 Mb     (   27000,    1)
        Induced current                 1.85 Mb     (   27000,    3,3,1)
        Induced magnetic field          1.85 Mb     (   27000,    3,3,1)
        NL pseudopotentials             0.07 Mb     (    1472,    3)
        GIPAW NL terms                  0.81 Mb     (    1472,   36)

     Computing the magnetic susceptibility     isolve=0    ethr=  0.1000E-13
     k-point #    1 of     1      pool #  1    cpu time:       3.1
     End of magnetic susceptibility calculation

     f-sum rule (1st term):
           -20.1385          0.0343          0.0018
             0.0396        -20.7667         -0.0482
            -0.0279         -0.0556        -19.5381

     f-sum rule (2nd term):
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     f-sum rule (should be   -20.0000):
           -20.1385          0.0343          0.0018
             0.0396        -20.7667         -0.0482
            -0.0279         -0.0556        -19.5381

     chi_bare pGv (HH) in paratec units:
        -8.111321     -0.089278     -0.162804
         0.084689     -4.403855     -1.881381
        -0.019083     -1.907482     -5.571525

        -8.111321     -0.089278     -0.162804
         0.084689     -4.403855     -1.881381
        -0.019083     -1.907482     -5.571525

     chi_bare vGv (VV) in paratec units:
        -8.396255      0.008744     -0.247577
         0.033452     -5.035034     -1.627866
        -0.213776     -1.644906     -6.067375

        -8.396255      0.008744     -0.247577
         0.033452     -5.035034     -1.627866
        -0.213776     -1.644906     -6.067375

     chi_bare pGv (HH) in 10^{-6} cm^3/mol:
           -38.5458         -0.4243         -0.7737
             0.4025        -20.9275         -8.9405
            -0.0907         -9.0645        -26.4764

     chi_bare vGv (VV) in 10^{-6} cm^3/mol:
           -39.8998          0.0416         -1.1765
             0.1590        -23.9270         -7.7358
            -1.0159         -7.8167        -28.8327

     Contributions to the NMR chemical shifts:
-------------------------------

     Macroscopic shape contribution in ppm:                    2.69
             3.6186          0.0000          0.0000
            -0.0000          1.9646          0.0000
             0.0000          0.0000          2.4856


     Core contribution in ppm:

     Atom  1  H   pos: (  0.752224  0.789592  0.622680)  core
sigma:           0.00
     Atom  2  H   pos: (  0.951174  0.648257  0.851276)  core
sigma:           0.00
     Atom  3  H   pos: (  1.080748  0.860252  0.626511)  core
sigma:           0.00
     Atom  4  H   pos: (  0.703023  1.007130  1.041222)  core
sigma:           0.00
     Atom  5  H   pos: (  0.833779  1.215769  0.815795)  core
sigma:           0.00
     Atom  6  H   pos: (  1.117133  0.950964  1.179605)  core
sigma:           0.00
     Atom  7  C   pos: (  0.915939  0.822150  0.744767)  core
sigma:         200.33
     Atom  8  C   pos: (  0.869846  1.042890  0.922665)  core
sigma:         200.33
     Atom  9  O   pos: (  1.085885  1.098442  1.074706)  core
sigma:         270.67

     Bare contribution in ppm:

     Atom  1  H   pos: (  0.752224  0.789592  0.622680)  bare
sigma:          25.09
            26.0625          1.8273          4.4375
             1.7774         23.1239          1.9122
             2.5439          2.5552         26.0825

     Atom  2  H   pos: (  0.951174  0.648257  0.851276)  bare
sigma:          25.76
            22.9144         -1.9826          0.3695
            -0.9485         30.2608         -2.4861
            -0.2162         -1.1068         24.1123

     Atom  3  H   pos: (  1.080748  0.860252  0.626511)  bare
sigma:          24.69
            25.4475          1.3890         -3.8302
            -1.4758         21.3844         -0.2736
            -4.5261         -0.9285         27.2391

     Atom  4  H   pos: (  0.703023  1.007130  1.041222)  bare
sigma:          22.75
            26.3109          0.0354         -1.9862
             1.5735         19.1495          1.7562
            -0.4490          1.5663         22.7875

     Atom  5  H   pos: (  0.833779  1.215769  0.815795)  bare
sigma:          23.69
            22.4615         -2.8223          2.1746
            -1.2684         24.6928          0.0325
             3.0915         -1.9351         23.9174

     Atom  6  H   pos: (  1.117133  0.950964  1.179605)  bare
sigma:          26.96
            24.0411         -2.9849          5.2775
            -2.2403         26.3910         -4.4965
             5.3174         -4.2014         30.4409

     Atom  7  C   pos: (  0.915939  0.822150  0.744767)  bare
sigma:          18.21
            28.7528        -24.7475         -5.8478
            -6.3080         15.1127         21.5440
            -4.1815         17.5814         10.7596

     Atom  8  C   pos: (  0.869846  1.042890  0.922665)  bare
sigma:         -20.95
           -18.7502          9.8457         21.7863
            16.4429        -35.2450          8.1922
            21.4969          7.9533         -8.8401

     Atom  9  O   pos: (  1.085885  1.098442  1.074706)  bare
sigma:          59.24
            75.0512          6.2968         37.5933
           -19.4634         58.3954        -19.4878
            16.3500          5.1516         44.2657

     Diamagnetic contribution in ppm:

     Atom  1  H   pos: (  0.752224  0.789592  0.622680)  dia
sigma:           0.30
             0.3018          0.0000          0.0000
             0.0000          0.3018         -0.0000
             0.0000         -0.0000          0.3018

     Atom  2  H   pos: (  0.951174  0.648257  0.851276)  dia
sigma:           0.31
             0.3081          0.0000          0.0000
             0.0000          0.3081         -0.0000
             0.0000         -0.0000          0.3081

     Atom  3  H   pos: (  1.080748  0.860252  0.626511)  dia
sigma:           0.30
             0.3040          0.0000          0.0000
             0.0000          0.3040         -0.0000
             0.0000         -0.0000          0.3040

     Atom  4  H   pos: (  0.703023  1.007130  1.041222)  dia
sigma:           0.31
             0.3147          0.0000          0.0000
             0.0000          0.3147         -0.0000
             0.0000         -0.0000          0.3147

     Atom  5  H   pos: (  0.833779  1.215769  0.815795)  dia
sigma:           0.31
             0.3139          0.0000          0.0000
             0.0000          0.3139         -0.0000
             0.0000         -0.0000          0.3139

     Atom  6  H   pos: (  1.117133  0.950964  1.179605)  dia
sigma:           0.27
             0.2700          0.0000          0.0000
             0.0000          0.2700         -0.0000
             0.0000         -0.0000          0.2700

     Atom  7  C   pos: (  0.915939  0.822150  0.744767)  dia
sigma:           3.13
             3.1353          0.0020          0.0014
             0.0020          3.1158         -0.0088
             0.0014         -0.0088          3.1262

     Atom  8  C   pos: (  0.869846  1.042890  0.922665)  dia
sigma:           3.13
             3.1388          0.0028          0.0057
             0.0028          3.1229         -0.0069
             0.0057         -0.0069          3.1372

     Atom  9  O   pos: (  1.085885  1.098442  1.074706)  dia
sigma:           2.72
             2.7126         -0.0097         -0.0161
            -0.0097          2.7328         -0.0080
            -0.0161         -0.0080          2.7259

     Paramagnetic contribution in ppm:

     Atom  1  H   pos: (  0.752224  0.789592  0.622680)  para
sigma:           0.00
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     Atom  2  H   pos: (  0.951174  0.648257  0.851276)  para
sigma:           0.00
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     Atom  3  H   pos: (  1.080748  0.860252  0.626511)  para
sigma:           0.00
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     Atom  4  H   pos: (  0.703023  1.007130  1.041222)  para
sigma:           0.00
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     Atom  5  H   pos: (  0.833779  1.215769  0.815795)  para
sigma:           0.00
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     Atom  6  H   pos: (  1.117133  0.950964  1.179605)  para
sigma:           0.00
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000
             0.0000          0.0000          0.0000

     Atom  7  C   pos: (  0.915939  0.822150  0.744767)  para
sigma:         -24.59
           -18.3800        -12.6293         -2.7974
            -2.2746        -25.5132         10.7372
            -0.7003          7.6236        -29.8855

     Atom  8  C   pos: (  0.869846  1.042890  0.922665)  para
sigma:         -43.39
           -43.5635          4.4329          7.3253
             8.0071        -48.3291          2.5162
             8.2612          2.6681        -38.2718

     Atom  9  O   pos: (  1.085885  1.098442  1.074706)  para
sigma:         -10.83
            -4.5779          1.6409         14.5155
           -10.5485         -9.9291        -10.1861
             3.8350          2.1952        -17.9841


     Total NMR chemical shifts in ppm:
---------------------------------------
     (adopting the Simpson convention for anisotropy and
asymmetry)-----------

     Atom  1  H   pos: (  0.752224  0.789592  0.622680)  Total
sigma:          28.08
            29.9829          1.8273          4.4375
             1.7774         25.3903          1.9122
             2.5439          2.5552         28.8698

     H    1    anisotropy:      8.73    eta:   -0.3008
     H    1    sigma_11=   26.0467    axis=( -0.705509  0.279308  0.651341)
     H    1    sigma_22=   24.2962    axis=( -0.029258  0.906800 -0.420545)
     H    1    sigma_33=   33.9002    axis=(  0.708097  0.315755  0.631583)

     Atom  2  H   pos: (  0.951174  0.648257  0.851276)  Total
sigma:          28.76
            26.8411         -1.9826          0.3695
            -0.9485         32.5335         -2.4861
            -0.2162         -1.1068         26.9059

     H    2    anisotropy:      6.92    eta:   -0.1464
     H    2    sigma_11=   26.7922    axis=( -0.761295  0.008534  0.648350)
     H    2    sigma_22=   26.1171    axis=( -0.612014 -0.339731 -0.714158)
     H    2    sigma_33=   33.3712    axis=(  0.214170 -0.940484  0.263858)

     Atom  3  H   pos: (  1.080748  0.860252  0.626511)  Total
sigma:          27.68
            29.3701          1.3890         -3.8302
            -1.4758         23.6530         -0.2736
            -4.5261         -0.9285         30.0286

     H    3    anisotropy:      9.33    eta:   -0.3323
     H    3    sigma_11=   25.6063    axis=(  0.724076 -0.217504  0.654527)
     H    3    sigma_22=   23.5384    axis=( -0.133577 -0.975230 -0.176306)
     H    3    sigma_33=   33.9071    axis=( -0.676662 -0.040230  0.735194)

     Atom  4  H   pos: (  0.703023  1.007130  1.041222)  Total
sigma:          25.75
            30.2442          0.0354         -1.9862
             1.5735         21.4289          1.7562
            -0.4490          1.5663         25.5878

     H    4    anisotropy:     -7.58    eta:   -0.9036
     H    4    sigma_11=   25.9970    axis=(  0.191997  0.365094  0.910958)
     H    4    sigma_22=   30.5608    axis=(  0.973701  0.045146 -0.223314)
     H    4    sigma_33=   20.7031    axis=(  0.122657 -0.929875  0.346824)

     Atom  5  H   pos: (  0.833779  1.215769  0.815795)  Total
sigma:          26.69
            26.3940         -2.8223          2.1746
            -1.2684         26.9714          0.0325
             3.0915         -1.9351         26.7169

     H    5    anisotropy:      5.68    eta:   -0.6120
     H    5    sigma_11=   25.9592    axis=(  0.114791  0.793597  0.597517)
     H    5    sigma_22=   23.6409    axis=(  0.767373  0.311133 -0.560656)
     H    5    sigma_33=   30.4821    axis=(  0.630842 -0.522877  0.573270)

     Atom  6  H   pos: (  1.117133  0.950964  1.179605)  Total
sigma:          29.92
            27.9296         -2.9849          5.2775
            -2.2403         28.6256         -4.4965
             5.3174         -4.2014         33.1964

     H    6    anisotropy:     13.58    eta:   -0.1652
     H    6    sigma_11=   26.1398    axis=( -0.267495 -0.896968 -0.351988)
     H    6    sigma_22=   24.6444    axis=(  0.840565 -0.038638 -0.540331)
     H    6    sigma_33=   38.9673    axis=(  0.471059 -0.440405  0.764295)

     Atom  7  C   pos: (  0.915939  0.822150  0.744767)  Total
sigma:         199.76
           217.4594        -37.3747         -8.6438
            -8.5806        195.0127         32.2724
            -4.8805         25.1962        186.8186

     C    7    anisotropy:     62.04    eta:   -0.9279
     C    7    sigma_11=  198.2724    axis=(  0.692401  0.401818  0.599268)
     C    7    sigma_22=  159.8972    axis=( -0.195965 -0.694619  0.692172)
     C    7    sigma_33=  241.1212    axis=( -0.694391  0.596696  0.402213)

     Atom  8  C   pos: (  0.869846  1.042890  0.922665)  Total
sigma:         141.82
           144.7764         14.2814         29.1172
            24.4528        121.8462         10.7015
            29.7639         10.6145        158.8435

     C    8    anisotropy:     69.89    eta:   -0.3743
     C    8    sigma_11=  127.2460    axis=(  0.516158  0.541519 -0.663579)
     C    8    sigma_22=  109.8058    axis=(  0.589762 -0.786541 -0.183123)
     C    8    sigma_33=  188.4143    axis=(  0.621097  0.296833  0.725347)

     Atom  9  O   pos: (  1.085885  1.098442  1.074706)  Total
sigma:         324.49
           347.4733          7.9280         52.0927
           -30.0215        323.8325        -29.6819
            20.1690          7.3387        302.1619

     O    9    anisotropy:     71.54    eta:   -0.7953
     O    9    sigma_11=  319.6078    axis=( -0.315490 -0.947791 -0.046461)
     O    9    sigma_22=  281.6751    axis=( -0.463904  0.111337  0.878861)
     O    9    sigma_33=  372.1849    axis=(  0.827804 -0.298825  0.474810)

     *** ATTENTION: system is metallic, Knight shift not included ***
     Initialization:
     gipaw_setup  :      0.50s CPU      0.73s WALL (       1 calls)

     Linear response
     greenf       :     11.23s CPU     12.90s WALL (      21 calls)
     cgsolve      :     11.15s CPU     12.82s WALL (      21 calls)
     ch_psi       :     10.89s CPU     12.52s WALL (     588 calls)
     h_psiq       :     10.04s CPU     11.44s WALL (     588 calls)

     Apply operators
     h_psi        :     12.95s CPU     14.71s WALL (     897 calls)
     apply_vel    :      0.09s CPU      0.11s WALL (      21 calls)

     Induced current
     j_para       :      1.26s CPU      1.49s WALL (      12 calls)
     biot_savart  :      0.03s CPU      0.03s WALL (       1 calls)

     Other routines

     General routines
     calbec       :      0.37s CPU      0.38s WALL (    2170 calls)
     fft          :      0.04s CPU      0.18s WALL (      29 calls)
     fftw         :     12.62s CPU     14.41s WALL (   16772 calls)
     davcio       :      0.00s CPU      0.00s WALL (      15 calls)

     Parallel routines
     fft_scatter  :      0.65s CPU      1.01s WALL (   16801 calls)

     Plugins

     GIPAW        :     18.54s CPU     23.44s WALL (       1 calls)
-------------------------------------------------------------------------------------------------------

I found some helpful slides, but none of them explains how to plot the
spectrum peaks positions, width and intensity.

-
http://media.quantum-espresso.org/santa_barbara_2009_07/slides-exercices/Seitsonen-nmr_lecture.pdf
-
https://github.com/NNemec/quantum-espresso/tree/master/examples/GIPAW_example

Can someone help me with this last step?

Thanks you very much
Manuel Otero
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