Error when running crest for pyrene dimer molecules

[haobamkisan]

Dear All, I ran pyrene dimer molecules by implementing the spherical log fermi constraining potential and the command line I used is "crest struc.xyz -nocross -cinp constrain.inp". However, I have encountered the following error, and also I have attached the details of struc.xyz and constrain.inp file

Command line input:

crest struc.xyz -nocross -cinp constrain.inp

-nocross : skipping GC part. -cinp : constrain.inp

file present. content of the constraining file (sorted): > $wall > potential=logfermi > sphere: 17, all ------------------------- xTB Geometry Optimization ------------------------- Initial geometry optimization failed! Please check your input. ########### constrain.inp $wall potential=logfermi sphere: 17, all $end ######### struc.xyz 58 C 3.5632730000 -0.8309560000 -1.6793250000 C 4.3718880000 -0.6616260000 -0.5647920000 C 3.8358940000 -0.7478500000 0.7117640000 C 2.4768240000 -0.9998000000 0.8954720000 C 1.6469550000 -1.1644390000 -0.2365180000 C 2.1997740000 -1.0832760000 -1.5346510000 C 0.2503610000 -1.4054910000 -0.0689760000 C -0.3047270000 -1.4777410000 1.2284590000 C 0.5665920000 -1.3122950000 2.3640070000 C 1.8852820000 -1.0882170000 2.2069730000 C -0.5803540000 -1.5691600000 -1.2003630000 C -1.9430890000 -1.7964870000 -1.0158670000 C -2.4839740000 -1.8626370000 0.2587840000 C -1.6727530000 -1.7031490000 1.3715120000 C 0.0121000000 -1.4871940000 -2.5113250000 C 1.3293430000 -1.2559780000 -2.6705780000 H 3.9876670000 -0.7657730000 -2.6764310000 H 5.4310930000 -0.4644310000 -0.6922620000 H 4.4736420000 -0.6176270000 1.5805600000 H 0.1303840000 -1.3682990000 3.3561430000 H 2.5310180000 -0.9651370000 3.0709680000 H -2.5833820000 -1.9109450000 -1.8846490000 H -3.5485800000 -2.0228200000 0.3850640000 H -2.1008790000 -1.7429550000 2.3680010000 H -0.6347460000 -1.6102360000 -3.3740430000 H 1.7622460000 -1.1904830000 -3.6641020000 H -6.5295752900 4.4949024900 2.3962382100 C -6.1051712900 4.5600534900 1.3991352100 C -6.9137382900 4.3906104900 0.2845842100 C -6.3777062900 4.4767584900 -0.9919597900 H -7.0154532900 4.3465674900 -1.8607627900 C -5.0186702900 4.7289284900 -1.1756667900 C -4.4271422900 4.8174094900 -2.4871657900 H -5.0728482900 4.6941324900 -3.3511547900 C -3.1084592900 5.0415234900 -2.6441877900 H -2.6721572900 5.0974884900 -3.6362837900 C -2.2371372900 5.2068044900 -1.5086117900 C -0.8691392900 5.4323824900 -1.6516667900 H -0.4409992900 5.4721704900 -2.6481507900 C -0.0579402900 5.5919484900 -0.5389367900 H 1.0066827100 5.7520294900 -0.6651997900 C -0.5988182900 5.5257134900 0.7357122100 C -1.9615352900 5.2982894900 0.9202092100 C -2.5540012900 5.2162604900 2.2311632100 C -3.8712592900 4.9851324900 2.3904022100 H -4.3041502900 4.9195464900 3.3839252100 H -1.9071512900 5.3392434900 3.0938862100 H 0.0415237100 5.6398264900 1.6045032100 C -2.7922222900 5.1345074900 -0.2111767900 C -4.1888372900 4.8935744900 -0.0436577900 H -7.9729692900 4.1935354900 0.4120182100 C -4.7416752900 4.8124034900 1.2544662100 C 0.8098070000 -1.2328790000 0.3217870000 C 0.8098070000 -1.2328790000 0.3217870000 C 0.8098070000 -1.2328790000 0.3217870000 C 0.8098070000 -1.2328790000 0.3217870000 C 0.8098070000 -1.2328790000 0.3217870000 C 0.8098070000 -1.2328790000 0.3217870000 Thanks Kisan

[pprcht]

Hi, since the calculation fails in the initial xtb optimization there should be a file xtb.out that might give you some indication on what went wrong. Have a look in there and maybe try testing with xtb first before attempting to run the calculation with CREST.

A thing that occasionally happens with the wall potentials is that the sphere is too small, that could be a cause here. In the continuous release there is also a command line argument --wall/--wallxl/-wallxxl that automatically creates such a potential, maybe that's of interest for you.

[haobamkisan]

In the xtb.out the following lines are written

       -------------------------------------------------
      |                Calculation Setup                |
       -------------------------------------------------

      program call               : xtb tmpcoord --gfn2 --opt
      coordinate file            : tmpcoord
      omp threads                :                     1

ID Z sym. atoms 1 6 c 1-16, 28-30, 32, 33, 35, 37, 38, 40, 42-45, 49, 50, 52-58 2 1 h 17-27, 31, 34, 36, 39, 41, 46-48, 51 spherical wallpotenial with radius 8.9960134 Å

molecular fragmentation (1/2 indicates fragments): 1111111111111111111111111122222222222222222222222222111111

atoms in fragment 1/2: 32 26

fragment masses (1/2) : 274.32 202.25 CMA distance (Bohr) : 14.479 constraining FC (au) : 0.0500 ######################################################################## [ERROR] Program stopped due to fatal error -17- Some atoms in the start geometry are very close -16- XTB REFUSES TO CONTINUE WITH THIS CALCULATION! -15- Found very short distance of 0.000E+00 for c57-c58 -14- Found very short distance of 0.000E+00 for c56-c58 -13- Found very short distance of 0.000E+00 for c55-c58 -12- Found very short distance of 0.000E+00 for c54-c58 -11- Found very short distance of 0.000E+00 for c53-c58 -10- Found very short distance of 0.000E+00 for c56-c57 -9- Found very short distance of 0.000E+00 for c55-c57 -8- Found very short distance of 0.000E+00 for c54-c57 -7- Found very short distance of 0.000E+00 for c53-c57 -6- Found very short distance of 0.000E+00 for c55-c56 -5- Found very short distance of 0.000E+00 for c54-c56 -4- Found very short distance of 0.000E+00 for c53-c56 -3- Found very short distance of 0.000E+00 for c54-c55 -2- Found very short distance of 0.000E+00 for c53-c55 -1- Found very short distance of 0.000E+00 for c53-c54 ######################################################################## "xtb.out" 119L, 5657C

[pprcht]

Well, your input geometry is broken. You have specified the same Cartesian position for multiple atoms (the last six in your input file, it seems). No calculation will work with this, you need to repair it first.

[haobamkisan]

Thank You ! The error is there in the coordinates.

[haobamkisan]

Hi,

I used sphere logfermi potential with radius of 20 Bohr for dimer molecules, and the calculation is terminated normally and generates the conformers. How can I visualize the origin of the sphere potential and the molecule's center of mass coincide?

[pprcht]

Hi, Both the center of mass and the wall potential's center are automatically shifted to the origin on multiple occasions between calculations. You could (only for visualization!) add another atom (e.g. Xe) at the origin and then use your favorite molecule viewer.

[haobamkisan]

Thank You !

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