Trouble with negative frequencies

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Just Got Here
Threads 1
Posts 3
9:55:31 AM PST - Tue, Jan 16th 2018
Dear developers and users of nwchem,
We are investigating small cluster systems via global optimisation on the DFT level (TPSS, PBE0, B3LYP, B3P86 with basis set def2-TZVPP or ccPVTZ-pp) of theorie with the goal to find the Global Minimum. After analysing the system, we often find that our predicted GM show negative frequencies. Even for a system with only three atoms the problems occur. Higher level QC calculations like CCSD(T) show the structure to be real minima with properties matching the experimental data. We have tried different methods to get rid of the negative frequencies like:

-elongation along the negative frequency modes
-elongation along positive real frequency modes
-random displacements and distortions
-with different driver trust settings, different grids and convergence criteria.
Unfortunately nothing of this helps.

By coincidence we found the other day, that it is also possible to calculate the frequencies numerically instead of analytically using the statement “task dft frequencies numerical”. With this numerical statement all frequencies are positive for a lot of found GM’s.
Sometimes other Isomers, for which we performed geometry optimisation, show purely negative frequencies with the analytical method, which should not be the case after geometry optimisation. We suspect that NWChem has issues with the derivatives needed for the analytic frequency analysis.
Is the analytic frequency analysis known to cause these kind of problems? Is the numerical calculations of the frequencies of equal quality to the analytical?

Thank you in advance!

Forum Vet
Threads 9
Posts 1459
11:00:02 AM PST - Tue, Jan 16th 2018
Could you share one the input files?

Just Got Here
Threads 1
Posts 3
4:03:16 AM PST - Wed, Jan 17th 2018
Yes, gladly. This is one of the submitted NWChem input files:
Example 1


echo
start Iso1_Cd1Se2
memory total 8000 mb
charge 1
#Iso1_Cd1Se2_2_B3LYP_cc-pVTZ-PP
geometry units angstrom noautoz noautosym
Cd    0.082077410000      1.420620500000     -1.402792040000
Se    0.413989940000     -0.953124550000     -0.044427640000
Se   -0.531980300000     -0.924193230000      1.918203620000
end
#  cc-pVTZ-PP  EMSL  Basis Set Exchange Library  12/31/17 9:22 AM
# Elements                             References
# --------                             ----------
# Ga-As,In-Sb, Tl-Bi   : K.A. Peterson, J. Chem. Phys. 119, 11099 (2003).
# Se-Kr, Te-Xe, Po-Rn  : K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and
# M. Dolg, J. Chem. Phys. 119, 11113 (2003).
# Cu, Zn, Pd, Ag, Au, Hg: K.A. Peterson and C. Puzzarini, Theor. Chem. Acc., 114, 283 (2005)
# Y Zr Nb Mo Tc Ru Rh Pd     : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I    : K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
BASIS "ao basis" PRINT
#BASIS SET: (10s,11p,9d,1f) -> [5s,4p,3d,1f]
Se    S
   8991.8000000              0.0004210             -0.0001650        
   1355.2000000              0.0029330             -0.0011040        
    303.4980000              0.0098700             -0.0040150        
     44.3870000              0.0808600             -0.0276280        
     17.1581000             -0.3914900              0.1415820        
      3.5026200              0.6863270             -0.3316090        
      1.6158300              0.4855820             -0.3848760        
Se    S
      0.5046210              1.0000000        
Se    S
      0.2407280              1.0000000        
Se    S
      0.1025980              1.0000000        
Se    P
    491.8970000              0.0003680             -0.0001150        
     89.2328000              0.0048720             -0.0011020        
     25.5069000             -0.0885470              0.0230250        
      6.6999200              0.3466370             -0.1044220        
      3.1877200              0.5068780             -0.1640980        
      1.4838500              0.2515060             -0.0724090        
      0.5621350              0.0219950              0.3278190        
      0.2210550             -0.0012350              0.5611980        
      0.0822520              0.0006100              0.2784910        
Se    P
      0.6364000              1.0000000        
Se    P
      0.0978000              1.0000000        
Se    D
    301.8680000              0.0016370        
     92.1254000              0.0169670        
     37.9081000              0.0741760        
     16.4171000              0.1894830        
      7.4149600              0.3234940        
      3.3373800              0.3715420        
      1.4643800              0.2597780        
Se    D
      0.5825160              1.0000000        
Se    D
      0.2162000              1.0000000        
Se    F
      0.4696000              1.0000000        
#BASIS SET: (10s,9p,8d,2f,1g) -> [5s,5p,4d,2f,1g]
Cd    S
    257.4970000              0.0007680             -0.0002310              0.0004270              0.0014390        
     21.3546000             -0.0781940              0.0222790             -0.0241760             -0.1719290        
     13.4806000              0.4609280             -0.1382050              0.2190290              0.9499110        
      8.4865100             -0.5362100              0.1777840             -0.1984150             -1.5172470        
      5.3255100             -0.4008230              0.1056950             -0.5647670              0.1055120        
      1.6268600              0.8553620             -0.3259540              1.8215160              3.3939830        
      0.7404690              0.4898680             -0.2993250             -0.8098690             -4.0474090        
      0.1809330              0.0220290              0.2821000             -1.9098510              2.4869710        
      0.0850960             -0.0083600              0.6020440              1.4360880             -0.5824690        
Cd    S
      0.0363840              1.0000000        
Cd    P
    243.1650000              0.0001130             -0.0000370             -0.0000610             -0.0000860        
     13.9588000              0.0696720             -0.0165070             -0.0330520             -0.0719040        
      8.3100100             -0.2536750              0.0636620              0.1255300              0.2712270        
      2.2020000              0.4824920             -0.1465210             -0.3052730             -0.9039590        
      1.1007200              0.4845500             -0.1561870             -0.3223690             -0.2760210        
      0.5359750              0.1796400             -0.0273550              0.1819080              1.4946140        
      0.2136540              0.0152290              0.3226010              0.6863790             -0.2070140        
      0.0854690             -0.0001880              0.5566980              0.3216860             -0.7304040        
Cd    P
      0.0338230              1.0000000        
Cd    D
     86.0666000              0.0004430              0.0006330             -0.0003260        
     22.6386000              0.0050060              0.0073050             -0.0146770        
     12.1384000             -0.0160770             -0.0238720              0.0459900        
      3.4408100              0.1771520              0.3340440             -0.6525580        
      1.7176100              0.3666560              0.5448850             -0.2130730        
      0.8148490              0.3772260             -0.1745820              1.1468110        
      0.3660070              0.2339200             -0.6047310             -0.2158710        
Cd    D
      0.1502820              1.0000000        
Cd    F
      2.9086000              1.0000000        
Cd    F
      0.8508000              1.0000000        
Cd    G
      1.8019000              1.0000000        
END
# ELEMENTS                      REFERENCES
# ---------                       ----------
# O: B. Metz and H. Stoll, private communication (KAP)
# Tl: B. Metz, M. Schweizer, H. Stoll, M. Dolg, W. Liu, Theor. Chem. Acc. 104, 22 (2000).
# Ga-As, In-Sb, Pb-Bi: B. Metz, H. Stoll, M. Dolg, J. Chem. Phys. 113, 2563 (2000).
# Se-Kr, Te-Xe, Po-Rn: K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and M. Dolg, J. Chem. Phys., in press (2003).
# Cu, Zn, Ag, Cd, Au, Hg: D. Figgen, G. Rauhut, M. Dolg, and H. Stoll, Chem. Phys. 311, 227 (2005).
# Y Zr Nb Mo Tc Ru Rh Pd : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I: K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
ECP
Se nelec 10
Se ul
2      1.0000000              0.0000000        
Se S
2     30.0469900            370.1228880        
2      6.9186880             10.4561680        
Se P
2     45.7730140             99.1350590        
2     45.2946420            198.2924830        
2     20.7396480             28.3387470        
2     20.0286010             56.7497470        
Se D
2     50.9417680            -18.5265560        
2     49.5947400            -28.3349210        
2     16.3235220             -0.6960890        
2     14.4651960             -1.1678910        
2      3.7753300              0.0414430        
2      3.5019530              0.2355830        
Se F
2     11.9508670             -0.7662620        
2     17.8107800             -2.1027420        
Cd nelec 28
Cd ul
2      1.0000000              0.0000000        
Cd S
2     13.3551760            270.0394480        
2      7.3083780             38.8777660        
Cd P
2     12.6597280             64.6074700        
2     12.2896390            129.2194450        
2      6.7861760             10.6225580        
2      6.4007430             21.2650460        
Cd D
2     11.1617220             31.6639650        
2     11.2196150             47.4892160        
2      4.5377330              5.1862000        
2      4.3357270              7.5660630        
Cd F
2     11.4789860            -12.6327850        
2     11.4870270            -16.7601710        
END
#B3LYP
dft
 xc b3lyp
 direct
 grid xfine
 mult 2
 convergence ncydp 0 dampon 1d99 dampoff 1d-7 damp 70
 iterations 3000
 noio
end
driver
 xyz Iso1_Cd1Se2
 trust 0.3
 tight
 maxiter 200
end
set lindep:tol 1.0d-7
set int:txs:limxmem  28307786
set dft:diisreset 25              
task dft optimize
task dft frequencies


The resulting frequencies are:

----------------------------------------------------------------------------

Normal Eigenvalue ||           Projected Infra Red Intensities

 Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]

------ ---------- || -------------- ----------------- ---------- -----------

   1     -272.983 ||    0.000572           0.013         0.557       2.255

   2     -136.209 ||    0.002082           0.048         2.030       8.214

   3       -0.000 ||    0.000871           0.020         0.849       3.434

   4       -0.000 ||    0.001649           0.038         1.608       6.505

   5       -0.000 ||    0.003059           0.071         2.982      12.067

   6        0.000 ||    0.001711           0.039         1.668       6.751

   7        0.000 ||    0.003323           0.077         3.239      13.107

   8        0.000 ||    0.001331           0.031         1.297       5.249

   9      161.271 ||    0.008218           0.190         8.011      32.417

----------------------------------------------------------------------------

If I only switch the task dft frequencies to task dft frequencies numerical than all frequencies are positve:

----------------------------------------------------------------------------
 
Normal Eigenvalue ||           Projected Infra Red Intensities

 Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]

------ ---------- || -------------- ----------------- ---------- -----------

   1       -0.000 ||    0.000617           0.014         0.602       2.471

   2        0.000 ||    0.004188           0.097         4.083      16.771

   3        0.000 ||    0.002311           0.053         2.253       9.255

   4        0.000 ||    0.002829           0.065         2.758      11.329

   5        0.000 ||    0.000959           0.022         0.935       3.839

   6        0.000 ||    0.002369           0.055         2.310       9.488

   7       69.530 ||    0.000462           0.011         0.451       1.851

   8      134.561 ||    0.001121           0.026         1.093       4.488

   9      368.364 ||    0.007618           0.176         7.426      30.507

----------------------------------------------------------------------------




Example 2:

The following input file produces an even more strange result, because after geometry optimisation one obtains only negative frequencies:

echo
start Iso1_Se4
memory total 8000 mb
charge 1
#Iso1_Se4_2_PBE0_cc-pVTZ-PP
geometry units angstrom noautoz noautosym
Se   -0.473825546110      1.717840275589      1.028941993772
Se    0.000485660781     -0.845265976921     -1.029893516657
Se    1.180466149055     -1.332002348834      1.032100843165
Se   -0.707214508724      0.459516226371     -1.031237602320
end
#  cc-pVTZ-PP  EMSL  Basis Set Exchange Library  12/31/17 9:21 AM
# Elements                             References
# --------                             ----------
# Ga-As,In-Sb, Tl-Bi   : K.A. Peterson, J. Chem. Phys. 119, 11099 (2003).
# Se-Kr, Te-Xe, Po-Rn  : K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and
# M. Dolg, J. Chem. Phys. 119, 11113 (2003).
# Cu, Zn, Pd, Ag, Au, Hg: K.A. Peterson and C. Puzzarini, Theor. Chem. Acc., 114, 283 (2005)
# Y Zr Nb Mo Tc Ru Rh Pd     : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I    : K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
BASIS "ao basis" PRINT
#BASIS SET: (10s,11p,9d,1f) -> [5s,4p,3d,1f]
Se    S
   8991.8000000              0.0004210             -0.0001650        
   1355.2000000              0.0029330             -0.0011040        
    303.4980000              0.0098700             -0.0040150        
     44.3870000              0.0808600             -0.0276280        
     17.1581000             -0.3914900              0.1415820        
      3.5026200              0.6863270             -0.3316090        
      1.6158300              0.4855820             -0.3848760        
Se    S
      0.5046210              1.0000000        
Se    S
      0.2407280              1.0000000        
Se    S
      0.1025980              1.0000000        
Se    P
    491.8970000              0.0003680             -0.0001150        
     89.2328000              0.0048720             -0.0011020        
     25.5069000             -0.0885470              0.0230250        
      6.6999200              0.3466370             -0.1044220        
      3.1877200              0.5068780             -0.1640980        
      1.4838500              0.2515060             -0.0724090        
      0.5621350              0.0219950              0.3278190        
      0.2210550             -0.0012350              0.5611980        
      0.0822520              0.0006100              0.2784910        
Se    P
      0.6364000              1.0000000        
Se    P
      0.0978000              1.0000000        
Se    D
    301.8680000              0.0016370        
     92.1254000              0.0169670        
     37.9081000              0.0741760        
     16.4171000              0.1894830        
      7.4149600              0.3234940        
      3.3373800              0.3715420        
      1.4643800              0.2597780        
Se    D
      0.5825160              1.0000000        
Se    D
      0.2162000              1.0000000        
Se    F
      0.4696000              1.0000000        
END
# ELEMENTS                      REFERENCES
# ---------                       ----------
# O: B. Metz and H. Stoll, private communication (KAP)
# Tl: B. Metz, M. Schweizer, H. Stoll, M. Dolg, W. Liu, Theor. Chem. Acc. 104, 22 (2000).
# Ga-As, In-Sb, Pb-Bi: B. Metz, H. Stoll, M. Dolg, J. Chem. Phys. 113, 2563 (2000).
# Se-Kr, Te-Xe, Po-Rn: K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and M. Dolg, J. Chem. Phys., in press (2003).
# Cu, Zn, Ag, Cd, Au, Hg: D. Figgen, G. Rauhut, M. Dolg, and H. Stoll, Chem. Phys. 311, 227 (2005).
# Y Zr Nb Mo Tc Ru Rh Pd : K.A. Peterson, D. Figgen, M. Dolg, H. Stoll, Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd, Journal of Chemical Physics 126, 124101 (2007).
# I: K. A. Peterson, B. C. Shepler, D. Figgen, H. Stoll, On the spectroscopic and thermochemical properties of ClO, BrO, IO, and their anions, Journal of Physical Chemistry A 110, 13877 (2006).
# Hf Ta W Re Os Ir Pt: D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf-Pt, Journal of Chemical Physics 130, 164108 (2009).
#
ECP
Se nelec 10
Se ul
2      1.0000000              0.0000000        
Se S
2     30.0469900            370.1228880        
2      6.9186880             10.4561680        
Se P
2     45.7730140             99.1350590        
2     45.2946420            198.2924830        
2     20.7396480             28.3387470        
2     20.0286010             56.7497470        
Se D
2     50.9417680            -18.5265560        
2     49.5947400            -28.3349210        
2     16.3235220             -0.6960890        
2     14.4651960             -1.1678910        
2      3.7753300              0.0414430        
2      3.5019530              0.2355830        
Se F
2     11.9508670             -0.7662620        
2     17.8107800             -2.1027420        
END
#PBE0
dft
 xc pbe0
 direct
 grid xfine
 mult 2
 convergence ncydp 0 dampon 1d99 dampoff 1d-7 damp 70
 iterations 3000
 noio
end
driver
 xyz Iso1_Se4
 trust 0.3
 tight
 maxiter 300
end
set lindep:tol 1.0d-7
set int:txs:limxmem  28307786
set dft:diisreset 25              
task dft optimize
task dft frequencies



The output frequencies are:

----------------------------------------------------------------------------
 
Normal Eigenvalue ||           Projected Infra Red Intensities

 Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]

------ ---------- || -------------- ----------------- ---------- -----------

   1     -472.151 ||    0.006800           0.157         6.629      37.931

   2     -460.248 ||    0.000000           0.000         0.000       0.000

   3     -448.696 ||    0.000000           0.000         0.000       0.000

   4     -401.204 ||    0.000000           0.000         0.000       0.000

   5     -343.142 ||    0.005197           0.120         5.066      28.986

   6     -289.069 ||    0.000000           0.000         0.000       0.000

   7       -0.000 ||    0.002430           0.056         2.369      13.557

   8       -0.000 ||    0.000273           0.006         0.266       1.520

   9       -0.000 ||    0.002348           0.054         2.289      13.099

  10       -0.000 ||    0.000810           0.019         0.789       4.516

  11       -0.000 ||    0.001915           0.044         1.867      10.681

  12        0.000 ||    0.001741           0.040         1.697       9.710

----------------------------------------------------------------------------

Again by performing a numerical frequency analysis, all frequencies are positive, which I would expect after a geometry optimisation.

Thank you in advance

Forum Vet
Threads 9
Posts 1459
7:51:51 PM PST - Fri, Jan 19th 2018
Please try the following input changes (I am only showing the bottom part of the input file). Adoption of this huge radial grids has made all the negative frequencies disappear in my runs. Please let me know if you see the same
Example 1
set lindep:tol 1.0d-7
set int:txs:limxmem  28307786
set dft:diisreset 25
task dft optimize
dft
grid lebedev se 750 16 cd 250 16 
end
task dft frequencies


Example 2
set lindep:tol 1.0d-7
set int:txs:limxmem  28307786
set dft:diisreset 25
dft
grid lebedev se 750 16
end
task dft optimize
task dft frequencies

Just Got Here
Threads 1
Posts 3
5:13:15 AM PST - Tue, Jan 23rd 2018
Many thanks,
this is working fine and all frequencies are now positive.

I have just a few questions concerning this adaption. How did you hit on that ? Are there some lines in the outputfile, which show excplicitly that one must adjust the grid ? If yes how do these output lines look like ?

What does the numerical frequency analysis of NWChem do different from the analytical? Was this a hint for this being a grid issue?

How did you specify the values for the elements that is: se 750 and cd 250 ?

How can I specify appropriate lebedev grid values fo other elements for example for Sn ?


And just for my common understanding: With your adaption we have changed the angular grid haven't we? Is it now bigger or smaller than before?
Does the grid for the radial integration remain unchanged ?

I am very grateful for your reply. Thank you in advance.
Edited On 7:47:09 AM PST - Wed, Jan 24th 2018 by ChemHunter

Forum Vet
Threads 9
Posts 1459
4:23:38 PM PST - Tue, Jan 30th 2018
Chemhunter

The modification to the input file I suggested you increase greatly the radial size of the grid.
https://github.com/nwchemgit/nwchem/wiki/Density-Functional-Theory-for-Molecules#grid----n...
The number of radial grid point I have chosen are around three times larger than the xfine grid available in NWChem 6.8 (and earlier version). I did not suggest any change to the angular grid.

I reached the conclusion that the cause for negative frequencies ad to be traced back to the inadequacy of the radial grid after exploring a series of computational parameters that are involved in the evaluation of the DFT hessian. I had observed similar results with negative frequencies with some of my own calculations, but your test case were smaller and, therefore, better for debugging. The negative frequency issue seems more likely to appear the basis set has a combination of diffuse functions and high angular momentum functions (Therefore, once can get cleaner frequency by adopting a more modest basis set).

I have introduced a new grid (labeled as "huge") in the master branch. I am testing this new feature and it might be released as part of the 6.8.1 maintenance release.

PS Please do NOT try to use the input line "grid huge" in 6.8 or earlier release since a bug in the input code might make NWChem accept the input line without really adopting the huge grid itself.
Edited On 4:25:19 PM PST - Tue, Jan 30th 2018 by Edoapra

Clicked A Few Times
Threads 4
Posts 12
9:29:34 AM PST - Thu, Feb 1st 2018
Hello,
I am having a similar problem with tin copper molecules. The structure is the result of a global optimization and should thus be the global minimum. However the analytic frequency calculation yield negative values, while the numeric calculation results in positive values. I further tried to adopt your values for Sn and Cu, however even with this grid the structure displays negative frequency values.

Should I use an even bigger grid?
Is the result of the numerical frequency calculation "trusthworthy"?
What does the numerical frequency calculation do different than the analytical one?
Does the numerical calculation use a different grid?

best wishes

Forum Vet
Threads 9
Posts 1459
10:44:19 AM PST - Thu, Feb 1st 2018
Sparks
Could you share your input file?
Thanks

Clicked A Few Times
Threads 4
Posts 12
8:17:11 AM PST - Fri, Feb 2nd 2018
Yes, gladly.

The input file for the numerical frequency analysis results in positive frequencies, while the analytical calculation results in negative frequencies.

Quote:

start Sn11Cu_1Frequencies

memory total 32000 mb

charge 0

geometry units angstrom noautoz noautosym
Sn                    0.74774404    -0.36320969     3.24551488

Sn                   -1.86493613     0.41518897     1.98309726

Sn                   -0.86440318    -2.48096166     1.30970699

Sn                    1.23978879     1.74470426     1.28844186

Sn                    2.10057095    -1.56558239     0.84780881

Cu                   -0.05124385    -0.07174558    -0.05357672

Sn                    1.03144315     2.86595826    -1.39746308

Sn                   -1.71605355     2.10670460    -0.44952184

Sn                   -2.52030147    -0.91688207    -0.79233695

Sn                    0.23660325    -2.29391942    -1.58159748

Sn                    2.24883501     0.12627981    -1.58462070

Sn                   -0.61074657     0.40716217    -2.84330112
end

basis
Cu S
  1946.3500000              0.0001730             -0.0000430             -0.0000850             -0.0003310        

   277.9450000              0.0009580             -0.0001730             -0.0004180              0.0007840        

    60.0108000             -0.0139320              0.0021820              0.0051250             -0.0199370        

    37.5138000              0.0666720             -0.0132150             -0.0280790             -0.0064730        

    10.9688000             -0.4144860              0.0954600              0.2066260              0.4304630        

     2.3353600              0.7319850             -0.2048920             -0.6763950             -2.3103570        

     0.9775800              0.4735590             -0.2429550              0.0068900              2.2981990        

     0.1858870              0.0288600              0.2128160              1.6771590              0.3918090        

     0.0948510             -0.0143780              0.5320730             -0.4592680             -2.2238270
Cu S
     0.0403630              1.0000000
Cu P
   395.0250000              0.0002060             -0.0000510             -0.0001220             -0.0003940        

    64.7808000              0.0038720             -0.0007000             -0.0012420             -0.0013450        

    17.8335000             -0.0831640              0.0170850              0.0352160              0.0791750        

     4.3595800              0.3467890             -0.0814680             -0.1894850             -0.5949390        

     2.0181600              0.4867620             -0.1198010             -0.2432280             -0.4104190        

     0.9023120              0.2722850             -0.0599620              0.0252340              1.0418980        

     0.3122900              0.0339860              0.2354600              0.5801290              0.3430100        

     0.1156800             -0.0036900              0.5603760              0.4825400             -0.8397400
Cu P
     0.0417450              1.0000000
Cu D
   134.0680000              0.0029660             -0.0036790              0.0045260        

    42.2407000              0.0273300             -0.0338610              0.0423250        

    16.5467000              0.1001680             -0.1283960              0.1662100        

     7.0122700              0.2319250             -0.3011240              0.4031220        

     3.0244600              0.3392610             -0.3197480              0.0713050        

     1.2646100              0.3452250              0.0845510             -0.7108880        

     0.4962380              0.2466370              0.5018780             -0.1463320
Cu D
     0.1731340              1.0000000
Cu F
     5.1411000              1.0000000
Cu F
     1.2848000              1.0000000
Cu G
     3.4525000              1.0000000
  1. BASIS SET: (12s,11p,9d,1f) -> [5s,4p,3d,1f]
Sn S
  3672.4000000              0.0001170              0.0000430        

   558.1430000              0.0006870              0.0003070        

   114.0890000              0.0021300              0.0004960        

    31.4006000             -0.0376690             -0.0091050        

    19.6318000              0.1591490              0.0498980        

     6.7720500             -0.6517540             -0.2498540        

     1.8335100              0.8376920              0.4440970        

     0.8777150              0.4884260              0.3520250        

     0.0517570              0.0018720             -0.1655790
Sn S
     0.2373960              1.0000000
Sn S
     0.1120680              1.0000000
Sn S
     0.0638000              1.0000000
Sn P
   216.9700000              0.0002260             -0.0000810        

    20.9102000              0.0229170             -0.0054570        

     8.7961100             -0.1971460              0.0530050        

     2.5673700              0.4679170             -0.1546650        

     1.3145100              0.4960430             -0.1589400        

     0.6535910              0.1766100             -0.0497030        

     0.2721500              0.0128500              0.3271270        

     0.1107360              0.0001190              0.5670890        

     0.0440340              0.0001730              0.2642970
Sn P
     0.3451000              1.0000000
Sn P
     0.0568000              1.0000000
Sn D
   130.2430000              0.0003190        

    36.7762000              0.0026780        

    14.6321000             -0.0101090        

     4.6969500              0.1197680        

     2.5307800              0.3226000        

     1.3017400              0.3842380        

     0.6465750              0.2653580
Sn D
     0.3023160              1.0000000
Sn D
     0.1160000              1.0000000
Sn F
     0.2822000              1.0000000
end

ecp
Cu nelec 10
Cu ul
2 1.0000000 0.0000000
Cu S
2 30.1105430 355.7505120
2 13.0763100 70.9309060
Cu P
2 32.6926140 77.9699310
2 32.7703390 155.9274480
2 13.7510670 18.0211320
2 13.3221660 36.0943720
Cu D
2 38.9965110 -12.3434100
2 39.5397880 -18.2733620
2 12.2875110 -0.9847050
2 11.4593000 -1.3187470
Cu F
2 6.1901020 -0.2272640
2 8.1187800 -0.4687730
Sn nelec 28
Sn ul
2 1.0000000 0.0000000
Sn S
2 17.4204140 279.9886820
2 7.6311550 62.3778100
Sn P
2 16.1310240 66.1625230
2 15.6280770 132.1743960
2 7.3256080 16.3394170
2 6.9425190 32.4889590
Sn D
2 15.5149760 36.3874410
2 15.1881600 54.5078410
2 5.4560240 8.6968230
2 5.3631050 12.8402080
Sn F
2 12.2823480 -12.5763330
2 12.2721500 -16.5959440
end

dft
xc pbe0

direct grid xfine

mult 2

convergence ncydp 0 dampon 1d99 dampoff 1d-7 damp 70

iterations 750
  1. print "final evals" "final vectors"
noio
  1. smear 0.001
end

set int:txs:limxmem 30379684
task dft frequencies numerical


The same input file without keyword numerical and the grid
Quote:
grid lebedev sn 250 16 cu 750 16

results also in negative frequencies.

I further noticed, that the frequency calculation with PBE0 is very memory demanding as soon as copper or gold are involved. Is this a bug or a feature?

best wishes
Edited On 8:19:07 AM PST - Fri, Feb 2nd 2018 by Sparks

Forum Vet
Threads 9
Posts 1459
8:49:45 PM PST - Fri, Feb 2nd 2018
Sparks
Please try the following input
memory stack 1750 mb heap 100 mb global 425 mb noverify
geometry 
  Sn                    2.83057294     0.00000000     1.79084262
  Sn                    1.48326322    -2.28741950     0.38664881
  Sn                    2.53215310     0.00000000    -1.48542974
  Sn                    0.00000000     0.00000000     2.49952371
  Sn                    1.48326322     2.28741950     0.38664881
  Cu                    0.00000000     0.00000000    -0.10161326
  Sn                   -2.83057294     0.00000000     1.79084262
  Sn                   -1.48326322    -2.28741950     0.38664881
  Sn                    0.00000000    -1.59009764    -2.29900451
  Sn                    0.00000000     1.59009764    -2.29900451
  Sn                   -1.48326322     2.28741950     0.38664881
  Sn                   -2.53215310     0.00000000    -1.48542974
 zcoord ; cvr_scaling 0.85d0 ;end
end
basis spherical
* library cc-pvtz-pp
end
ecp
* library cc-pvtz-pp
end
set tolguess 1d-3
dft
 mult 2
 xc pbe0
 convergence energy 5d-9 damp 45 ncydp 0 dampon 1d99 dampoff 1d-4
 smear
 grid fine
 maxiter 999
end
driver
 clear
 tight
end
task dft optimize
set int:txs:limxmem               29379684
dft
grid Sn 750 18 Cu 400 18
end
task dft freq

Clicked A Few Times
Threads 4
Posts 12
3:14:55 AM PST - Wed, Feb 14th 2018
Hello,

the calculation took a while to converge, that is why I am only answering now.
The calculation results now in positive frequencies :

Quote:


Normal Eigenvalue ||           Projected Infra Red Intensities

 Mode   [cm**-1]  || [atomic units] [(debye/angs)**2] [(KM/mol)] [arbitrary]

------ ---------- || -------------- ----------------- ---------- -----------

   1        0.000 ||    0.000000           0.000         0.000       0.002

   2        0.000 ||    0.000003           0.000         0.003       0.062

   3        0.000 ||    0.000004           0.000         0.004       0.078

   4        0.000 ||    0.000001           0.000         0.001       0.022

   5        0.000 ||    0.000001           0.000         0.001       0.018

   6        0.000 ||    0.000003           0.000         0.003       0.051

   7       36.978 ||    0.000707           0.016         0.689      13.364

   8       41.025 ||    0.000018           0.000         0.018       0.340

   9       44.622 ||    0.000000           0.000         0.000       0.000

  10       48.339 ||    0.000090           0.002         0.087       1.693

  11       62.376 ||    0.000032           0.001         0.031       0.596

  12       66.355 ||    0.000217           0.005         0.212       4.108

  13       73.788 ||    0.000000           0.000         0.000       0.000

  14       78.852 ||    0.000064           0.001         0.062       1.211

  15       85.201 ||    0.000102           0.002         0.099       1.921

  16       92.155 ||    0.000014           0.000         0.014       0.263

  17       92.340 ||    0.000000           0.000         0.000       0.000

  18       94.873 ||    0.000034           0.001         0.033       0.645

  19       96.902 ||    0.000115           0.003         0.112       2.171

  20       99.945 ||    0.000013           0.000         0.013       0.248

  21      100.391 ||    0.000066           0.002         0.064       1.246

  22      109.354 ||    0.000004           0.000         0.004       0.071

  23      115.161 ||    0.000000           0.000         0.000       0.000

  24      120.202 ||    0.000820           0.019         0.799      15.496

  25      120.615 ||    0.000522           0.012         0.509       9.866

  26      121.296 ||    0.000000           0.000         0.000       0.005

  27      123.603 ||    0.000023           0.001         0.022       0.430

  28      125.202 ||    0.000038           0.001         0.037       0.712

  29      130.179 ||    0.001205           0.028         1.175      22.785

  30      134.724 ||    0.000006           0.000         0.006       0.113

  31      144.670 ||    0.000067           0.002         0.065       1.268

  32      151.020 ||    0.000126           0.003         0.123       2.382

  33      163.944 ||    0.000144           0.003         0.141       2.725

  34      171.920 ||    0.005047           0.116         4.920      95.409

  35      207.843 ||    0.005772           0.133         5.627     109.104

  36      216.643 ||    0.003788           0.087         3.692      71.596

----------------------------------------------------------------------------

Which of your changes made my negative frequencies disappear?
Thank you in advance!

Forum Vet
Threads 9
Posts 1459
11:37:44 AM PST - Wed, Feb 14th 2018
Thank you very much for the feedback.
The major reason for the positive frequencies is the use of the huge grid.
The other input changes I suggested you helped in getting a more stable optimized geometry and its corresponding density/orbitals
Edited On 11:40:26 AM PST - Wed, Feb 14th 2018 by Edoapra

Clicked A Few Times
Threads 4
Posts 12
6:16:47 AM PDT - Mon, Mar 12th 2018
Hello again,
we noticed additional problems regarding this issue. It seems the I/O output of the calculations is enormous. One of the jobs even created 160 GB of data in one day. The jobs were waiting around 80% of the time for IO.

We tried to reduce this strain by inserting the "no disk" option behind both grid parameters, but it does not seem to have any effect. Is there away to reduce this problem?

best wishes,
Sparks

Forum Vet
Threads 9
Posts 1459
10:01:23 AM PDT - Mon, Mar 12th 2018
Direct
Please add the direct keyword in the dft field
dft
 direct
end


https://github.com/nwchemgit/nwchem/wiki/Density-Functional-Theory-for-Molecules#direct-se...
Edited On 10:04:30 AM PDT - Mon, Mar 12th 2018 by Edoapra

Clicked A Few Times
Threads 4
Posts 12
3:01:59 AM PDT - Wed, Mar 14th 2018
Hello,

thank you for your help. Adding that keyword as well as "noio" did solve the problem.

best wishes,
Sparks


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