[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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