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Re: {Spam?} Re: [abinit-forum] negative Phonon frequency at gamma and wrongPHDOS

From: "Matteo Giantomassi" <Matteo.Giantomassi@uclouvain.be>
To: forum@abinit.org
Subject: Re: {Spam?} Re: [abinit-forum] negative Phonon frequency at gamma and wrongPHDOS
Date: Sun, 26 Jul 2009 21:19:32 +0200
Importance: Normal

> Dear Matteo,
> I simply plot the omega ,PHDOS ,PJDOS[1],PJDOS[2] columes and compare
> results with A.H.Romero et al.(PRB2008,78,224302). Their x axis is phonon
> frequency from 0 to 250cm-1, my x axis is omega. The overall agreement is
> bad.Should I convert omega to phonon frequency? I'm not sure about the
> formula. The output PHDOS file pls see the attached document.

Omega is the phonon frequency. By default it is given in Hartree.
The header of the PHDOS file indeed reports:

# Phonon density of states and projected DOS generated by anaddb
#
# energy in Ha , DOS in states/Ha
# Gaussian method with smearing = 2.27816763E-05Ha , nqibz = 256

If you want to compare with the results reported in the paper, you
have to convert from Hartree to cm-1 both the x- and the y-axis.

Ha_cmm1=219474.6313705 ! 1 Hartree, in cm^-1

I had a look at your file and the weird results you are getting are due
to a problem with the output format used to write the results,
in particular the first and the second column (omega and PHDOS,
respectively).
The two columns should be separated by a blank. In your case,
some values of PHDOS (2nd column) reach the maximum width specified in
the code (f11.5).
As a consequence the first and the second column are joined together and
the plotter
doesn't read correctly the values.

I'm attaching the modified PHDOS.txt in which the two columns have been
separated by hand using vi. The results now seem reasonable.

The output format (f11.5) is not safe and I've fixed it in 5.8.4
In the case you want to patch your version of m_phdos, this is the diff
file:

=== modified file 'src/77_ddb/m_phdos.F90'
--- src/77_ddb/m_phdos.F90 2009-05-04 20:03:40 +0000
+++ src/77_ddb/m_phdos.F90 2009-07-26 18:05:29 +0000
@@ -161,9 +161,9 @@
! call wrtout(unt,msg,'COLL')
write(msg,'(5a)')'# ',ch10,'# omega PHDOS IPHDOS PJDOS[1]
IPJDOS[1] ... ',ch10,'# '
call wrtout(unt,msg,'COLL')
- write(frmt,*)'(',phonon_dos%ntypat,'(2f11.5))'
+ write(frmt,*)'(',phonon_dos%ntypat,'(2es17.8))'
do io=1,phonon_dos%nomega
-
write(unt,'(3f11.5)',advance='NO')phonon_dos%omega(io)*cfact,phonon_dos%phdos(io)/cfact,phonon_dos%phdos_int(io)/cfact
+
write(unt,'(3es17.8)',advance='NO')phonon_dos%omega(io)*cfact,phonon_dos%phdos(io)/cfact,phonon_dos%phdos_int(io)/cfact
do itype=1,phonon_dos%ntypat

write(unt,frmt,advance='NO')phonon_dos%pjdos_typ(io,itype)/cfact,phonon_dos%pjdos_typ_int(io,itype)/cfact
end do

The non-zero contribution to the PHDOS at negative frequencies is not a
problem.
The values are small and due to the fact that you are using a Gaussian
to approximate the delta function.
You might try the tetrahedron method (prtdos 2) or a gaussian with a smaller
broadening (and a denser interpolating q-mesh) in order to have a nicer
PHDOS
curve with a smaller contribution for omega < 0.

Best Regards
Matteo Giantomassi

#
# Phonon density of states and projected DOS generated by anaddb
#
# energy in Ha , DOS in states/Ha
# Gaussian method with smearing = 2.27816763E-05Ha , nqibz = 256
#
# omega PHDOS IPHDOS PJDOS[1] IPJDOS[1] ...
#
-0.00001 10.30077 0.00002 6.55177 0.00001 3.74900 0.00001
-0.00001 13.61581 0.00009 8.72099 0.00006 4.89482 0.00003
-0.00000 18.12167 0.00017 11.69143 0.00011 6.43024 0.00006
0.00000 24.27741 0.00028 15.77536 0.00018 8.50205 0.00010
0.00001 32.64944 0.00043 21.36187 0.00028 11.28757 0.00015
0.00001 43.90887 0.00063 28.91958 0.00041 14.98929 0.00022
0.00002 58.83887 0.00090 39.00787 0.00059 19.83100 0.00031
0.00002 78.36880 0.00125 52.30769 0.00083 26.06111 0.00043
0.00003 103.65050 0.00173 69.68208 0.00114 33.96842 0.00058
0.00003 136.18373 0.00235 92.27039 0.00156 43.91334 0.00078
0.00003 177.98234 0.00316 121.60993 0.00212 56.37242 0.00104
0.00004 231.75458 0.00421 159.76626 0.00285 71.98832 0.00137
0.00004 301.05483 0.00559 209.44264 0.00380 91.61219 0.00179
0.00005 390.35827 0.00736 274.03493 0.00505 116.32334 0.00232
0.00005 505.01774 0.00966 357.60397 0.00668 147.41377 0.00299
0.00006 651.08546 0.01263 464.75307 0.00880 186.33238 0.00384
0.00006 835.01529 0.01644 600.42133 0.01153 234.59397 0.00490
0.00007 1063.29455 0.02128 769.62635 0.01504 293.66821 0.00624
0.00007 1342.07632 0.02740 977.20567 0.01949 364.87065 0.00791
0.00008 1676.88310 0.03504 1227.60589 0.02508 449.27721 0.00995
0.00008 2072.42683 0.04448 1524.75060 0.03203 547.67623 0.01245
0.00008 2532.54370 0.05602 1871.98548 0.04056 660.55823 0.01546
0.00009 3060.18920 0.06996 2272.06081 0.05091 788.12839 0.01905
0.00009 3657.39971 0.08663 2727.08440 0.06334 930.31532 0.02329
0.00010 4325.12092 0.10633 3238.37325 0.07809 1086.74767 0.02824
0.00010 5062.83894 0.12940 3806.15911 0.09544 1256.67983 0.03396
0.00011 5868.02270 0.15614 4429.15519 0.11562 1438.86750 0.04052
0.00011 6735.47058 0.18683 5104.05325 0.13887 1631.41733 0.04795
0.00012 7656.72068 0.22171 5825.06708 0.16541 1831.65361 0.05630
0.00012 8619.70049 0.26099 6583.64962 0.19541 2036.05087 0.06558
0.00013 9608.74846 0.30477 7368.47744 0.22898 2240.27102 0.07578
0.00013 10605.04816 0.35309 8165.72849 0.26619 2439.31967 0.08690
0.00013 11587.41224 0.40588 8959.60514 0.30701 2627.80710 0.09887
0.00014 12533.28089 0.46299 9733.00529 0.35136 2800.27560 0.11163
0.00014 13419.78917 0.5241310468.24378 0.39906 2951.54539 0.12508
0.00015 14224.81064 0.5889511147.77329 0.44985 3077.03735 0.13910
0.00015 14927.96987 0.6569611754.92163 0.50341 3173.04824 0.15356
0.00016 15511.68340 0.7276412274.71165 0.55934 3236.97175 0.16830
0.00016 15962.29181 0.8003712694.82358 0.61718 3267.46823 0.18319
0.00017 16271.27121 0.8745113006.68898 0.67644 3264.58223 0.19807
0.00017 16436.38733 0.9494013206.59235 0.73661 3229.79498 0.21278
0.00018 16462.53895 1.0244113296.55187 0.79720 3165.98709 0.22721
0.00018 16361.99281 1.0989613284.70714 0.85773 3077.28567 0.24123
0.00018 16153.77676 1.1725613184.99198 0.91780 2968.78478 0.25476
0.00019 15862.16162 1.2448313016.00657 0.97711 2846.15504 0.26772
0.00019 15514.37244 1.3155212799.18377 1.03543 2715.18867 0.28010
0.00020 15137.85464 1.3844912556.50752 1.09264 2581.34712 0.29186
0.00020 14757.51823 1.4517312308.13571 1.14872 2449.38252 0.30302
0.00021 14393.37263 1.5173212070.28378 1.20371 2323.08885 0.31360
0.00021 14058.86302 1.5813711853.65266 1.25772 2205.21036 0.32365
0.00022 13760.07560 1.6440711662.57340 1.31086 2097.50220 0.33321
0.00022 13495.84342 1.7055611494.93259 1.36324 2000.91083 0.34232
0.00023 13258.68931 1.7659711342.86334 1.41492 1915.82597 0.35105
0.00023 13036.48917 1.8253711194.13650 1.46592 1842.35267 0.35945
0.00024 12814.70584 1.8837611034.14579 1.51620 1780.56005 0.36756
0.00024 12579.00109 1.9410710848.32399 1.56563 1730.67710 0.37545
0.00024 12317.96283 1.9972010624.74150 1.61404 1693.22133 0.38316
0.00025 12025.59604 2.0519910356.53737 1.66122 1669.05867 0.39077
0.00025 11703.15514 2.1053110043.75445 1.70699 1659.40069 0.39833
0.00026 11359.89512 2.15707 9694.14663 1.75116 1665.74849 0.40592
0.00026 11012.43259 2.20725 9322.63895 1.79363 1689.79365 0.41361
0.00027 10682.64468 2.25592 8949.35649 1.83441 1733.28819 0.42151
0.00027 10394.35617 2.30328 8596.45616 1.87358 1797.90000 0.42970
0.00028 10169.38989 2.34962 8284.31236 1.91132 1885.07752 0.43829
0.00028 10023.78061 2.39529 8027.82497 1.94790 1995.95563 0.44739
0.00029 9964.99485 2.44069 7833.65497 1.98359 2131.33988 0.45710
0.00029 9990.82455 2.48621 7699.01974 2.01867 2291.80481 0.46754
0.00029 10090.26472 2.53219 7612.33337 2.05336 2477.93135 0.47883
0.00030 10246.23536 2.57887 7555.54877 2.08778 2690.68659 0.49109
0.00030 10439.58446 2.62644 7507.66682 2.12199 2931.91765 0.50445
0.00031 10653.52092 2.67498 7448.62986 2.15593 3204.89106 0.51905
0.00031 10877.53820 2.72454 7362.77229 2.18948 3514.76591 0.53507
0.00032 11110.00897 2.77516 7241.15893 2.22247 3868.85004 0.55269
0.00032 11358.91252 2.82692 7082.44328 2.25474 4276.46925 0.57218
0.00033 11640.52643 2.87996 6892.23084 2.28614 4748.29559 0.59381
0.00033 11976.29540 2.93453 6681.24401 2.31658 5295.05139 0.61794
0.00034 12388.42187 2.99097 6462.78611 2.34603 5925.63576 0.64494
0.00034 12894.96679 3.04972 6250.06804 2.37451 6644.89875 0.67522
0.00034 13505.37694 3.11126 6053.90359 2.40209 7451.47335 0.70917
0.00035 14217.34459 3.17604 5881.13740 2.42889 8336.20719 0.74715
0.00035 15015.73424 3.24446 5733.98807 2.45501 9281.74617 0.78944
0.00036 15873.97393 3.31678 5610.30607 2.4805810263.66786 0.83621
0.00036 16757.83412 3.39314 5504.58862 2.5056611253.24551 0.88748
0.00037 17630.98430 3.47347 5409.47813 2.5303112221.50616 0.94316
0.00037 18461.24627 3.55759 5317.40829 2.5545313143.83798 1.00305
0.00038 19226.18726 3.64519 5222.05970 2.5783314004.12755 1.06686
0.00038 19916.71528 3.73593 5119.34747 2.6016514797.36781 1.13428
0.00039 20537.68563 3.82951 5007.77555 2.6244715529.91009 1.20504
0.00039 21105.14354 3.92567 4888.13843 2.6467416217.00511 1.27893
0.00039 21640.58336 4.02427 4762.69642 2.6684416877.88694 1.35583
0.00040 22163.32905 4.12526 4634.06512 2.6895617529.26393 1.43570
0.00040 22682.66325 4.22861 4504.11499 2.7100818178.54826 1.51853
0.00041 23191.52490 4.33428 4373.16212 2.7300018818.36278 1.60427
0.00041 23663.38999 4.44209 4239.65028 2.7493219423.73970 1.69277
0.00042 24053.36123 4.55169 4100.39846 2.7680019952.96278 1.78368
0.00042 24303.61753 4.66242 3951.34768 2.7860120352.26986 1.87642
0.00043 24352.38993 4.77338 3788.61931 2.8032720563.77061 1.97011
0.00043 24144.76613 4.88339 3609.62352 2.8197220535.14261 2.06368
0.00044 23643.10941 4.99112 3413.94772 2.8352720229.16169 2.15585
0.00044 22834.87310 5.09516 3203.81230 2.8498719631.06079 2.24529
0.00044 21736.13259 5.19420 2983.98729 2.8634718752.14530 2.33073
0.00045 20390.11972 5.28710 2761.19130 2.8760517628.92842 2.41106
0.00045 18861.17322 5.37304 2543.10818 2.8876316318.06504 2.48541
0.00046 17225.50514 5.45153 2337.22966 2.8982814888.27548 2.55324
0.00046 15560.76594 5.52243 2149.75045 2.9080813411.01549 2.61435
0.00047 13936.44613 5.58593 1984.70811 2.9171211951.73802 2.66881
0.00047 12406.72474 5.64246 1843.49238 2.9255210563.23236 2.71694
0.00048 11006.64704 5.69261 1724.76954 2.93338 9281.87750 2.75923
0.00048 9751.72480 5.73704 1624.79801 2.94078 8126.92679 2.79626
0.00049 8640.40963 5.77641 1538.06125 2.94779 7102.34838 2.82862
0.00049 7658.50638 5.81130 1458.11404 2.95443 6200.39234 2.85687
0.00049 6784.47806 5.84221 1378.52238 2.96071 5405.95568 2.88150
0.00050 5994.68139 5.86953 1293.77015 2.96661 4700.91125 2.90292
0.00050 5267.77704 5.89353 1200.00763 2.97208 4067.76942 2.92145
0.00051 4587.81154 5.91443 1095.53248 2.97707 3492.27907 2.93736
0.00051 3945.73272 5.93241 980.92836 2.98154 2964.80436 2.95087
0.00052 3339.35995 5.94763 858.84163 2.98545 2480.51832 2.96217
0.00052 2772.06797 5.96026 733.44275 2.98879 2038.62522 2.97146
0.00053 2250.62864 5.97051 609.68121 2.99157 1640.94743 2.97894
0.00053 1782.75435 5.97863 492.48242 2.99382 1290.27193 2.98482
0.00054 1374.87199 5.98490 386.03847 2.99557 988.83353 2.98932
0.00054 1030.53260 5.98959 293.31248 2.99691 737.22013 2.99268
0.00054 749.66150 5.99301 215.81687 2.99789 533.84462 2.99512
0.00055 528.63623 5.99542 153.65951 2.99859 374.97672 2.99682
0.00055 361.00323 5.99706 105.79685 2.99908 255.20638 2.99799
0.00056 238.54774 5.99815 70.40282 2.99940 168.14492 2.99875
0.00056 152.42513 5.99884 45.25975 2.99960 107.16539 2.99924
0.00057 94.12604 5.99927 28.09756 2.99973 66.02849 2.99954
0.00057 56.14723 5.99953 16.83884 2.99981 39.30838 2.99972
0.00058 32.33972 5.99968 9.73902 2.99985 22.60071 2.99982
0.00058 17.97971 5.99976 5.43455 2.99988 12.54516 2.99988
0.00059 9.64575 5.99980 2.92521 2.99989 6.72054 2.99991
0.00059 4.99208 5.99983 1.51847 2.99990 3.47361 2.99993
0.00059 2.49182 5.99984 0.76002 2.99990 1.73180 2.99994
0.00060 1.19936 5.99984 0.36673 2.99990 0.83263 2.99994
0.00060 0.55654 5.99984 0.17056 2.99990 0.38598 2.99994
0.00061 0.24893 5.99985 0.07645 2.99990 0.17248 2.99994
0.00061 0.10731 5.99985 0.03302 2.99990 0.07429 2.99994
0.00062 0.04458 5.99985 0.01374 2.99990 0.03083 2.99994
0.00062 0.01784 5.99985 0.00551 2.99990 0.01233 2.99994
0.00063 0.00688 5.99985 0.00213 2.99990 0.00475 2.99994
0.00063 0.00255 5.99985 0.00079 2.99990 0.00176 2.99994

{Spam?} Re: [abinit-forum] negative Phonon frequency at gamma and wrongPHDOS, 徐, 07/25/2009
- Re: {Spam?} Re: [abinit-forum] negative Phonon frequency at gamma and wrongPHDOS, Matteo Giantomassi, 07/26/2009