Wrong symmetry with desy (and energies)

[asaf]

Hi,
1) I am using desy in order to define the symmetry of a one squared surface slab composed of two types of atoms in the xy plan, and another atom above the slab in the z  direction, between the x and y axes on the diagonal of the surface.
The symmetry of the configuration is c1v in which the plan crosses (parallel) to  c1 between the x and y axes.
desy gives cs with an xy plan wich is definitely wrong (there is no yielding of new atoms) - what is the problem?
The energies with this symmetry and without any use of symmetry are slightly different which is wrong:
-6973.526711143 and -6973.525884277
What is the problem?
Thanks.

[asaf]

Sorry,
I was wrong,
Desy manipulate the geometry and the new cs with xy plan is good.
However,
The differences in energy with using this symmetry and without using any symmetry are still a problem.
Thanks.

[uwe]

Hi,

can you post the structure, i.e. the coord file here?

Regards,

Uwe

[asaf]

$coord
  -17.20736325947312     17.20736325947312      0.00000000000000      li
  -17.67727440792691     13.94098772913550      0.00000000000000      f
  -17.57299777885308     10.46995876956571      0.00000000000000      li
  -17.84927600603095      7.01677752244211      0.00000000000000      f
  -17.69001324433830      3.50782155976300      0.00000000000000      li
  -17.90748960281839      0.00000000000000      0.00000000000000      f
  -17.69001324433830     -3.50782155976300      0.00000000000000      li
  -17.84927600603095     -7.01677752244211      0.00000000000000      f
  -17.57299777885308    -10.46995876956571      0.00000000000000      li
  -17.67727440792691    -13.94098772913550      0.00000000000000      f
  -17.20736325947312    -17.20736325947312      0.00000000000000      li
  -13.94098772913550     17.67727440792691      0.00000000000000      f
  -14.00644521514217     14.00644521514217      0.00000000000000      li
  -14.08132090986711     10.51386203324838      0.00000000000000      f
  -14.19533983578200      7.00254561299388      0.00000000000000      li
  -14.19931298609203      3.50631129021353      0.00000000000000      f
  -14.26051688635180      0.00000000000000      0.00000000000000      li
  -14.19931298609203     -3.50631129021353      0.00000000000000      f
  -14.19533983578200     -7.00254561299388      0.00000000000000      li
  -14.08132090986711    -10.51386203324838      0.00000000000000      f
  -14.00644521514217    -14.00644521514217      0.00000000000000      li
  -13.94098772913550    -17.67727440792691      0.00000000000000      f
  -10.46995876956571     17.57299777885308      0.00000000000000      li
  -10.51386203324838     14.08132090986711      0.00000000000000      f
  -10.52769974571460     10.52769974571460      0.00000000000000      li
  -10.59856071614291      7.01831802761820      0.00000000000000      f
  -10.61768588381363      3.50546374780494      0.00000000000000      li
  -10.64844213012559      0.00000000000000      0.00000000000000      f
  -10.61768588381363     -3.50546374780494      0.00000000000000      li
  -10.59856071614291     -7.01831802761820      0.00000000000000      f
  -10.52769974571460    -10.52769974571460      0.00000000000000      li
  -10.51386203324838    -14.08132090986711      0.00000000000000      f
  -10.46995876956571    -17.57299777885308      0.00000000000000      li
   -7.01677752244211     17.84927600603095      0.00000000000000      f
   -7.00254561299388     14.19533983578200      0.00000000000000      li
   -7.01831802761820     10.59856071614291      0.00000000000000      f
   -7.04493256000175      7.04493256000175      0.00000000000000      li
   -7.06721394914587      3.51836528968206      0.00000000000000      f
   -7.07720134353519      0.00000000000000      0.00000000000000      li
   -7.06721394914587     -3.51836528968206      0.00000000000000      f
   -7.04493256000175     -7.04493256000175      0.00000000000000      li
   -7.01831802761820    -10.59856071614291      0.00000000000000      f
   -7.00254561299388    -14.19533983578200      0.00000000000000      li
   -7.01677752244211    -17.84927600603095      0.00000000000000      f
   -3.50782155976300     17.69001324433830      0.00000000000000      li
   -3.50631129021353     14.19931298609203      0.00000000000000      f
   -3.50546374780494     10.61768588381363      0.00000000000000      li
   -3.51836528968206      7.06721394914587      0.00000000000000      f
   -3.52720788765862      3.52720788765862      0.00000000000000      li
   -3.53309967745012      0.00000000000000      0.00000000000000      f
   -3.52720788765862     -3.52720788765862      0.00000000000000      li
 -3.51836528968206     -7.06721394914587      0.00000000000000      f
   -3.50546374780494    -10.61768588381363      0.00000000000000      li
   -3.50631129021353    -14.19931298609203      0.00000000000000      f
   -3.50782155976300    -17.69001324433830      0.00000000000000      li
    0.00000000000000     17.90748960281839      0.00000000000000      f
    0.00000000000000     14.26051688635180      0.00000000000000      li
    0.00000000000000     10.64844213012559      0.00000000000000      f
    0.00000000000000      7.07720134353519      0.00000000000000      li
    0.00000000000000      3.53309967745012      0.00000000000000      f
    0.00000000000000      0.00000000000000      0.00000000000000      li
    0.00000000000000     -3.53309967745012      0.00000000000000      f
    0.00000000000000     -7.07720134353519      0.00000000000000      li
    0.00000000000000    -10.64844213012559      0.00000000000000      f
    0.00000000000000    -14.26051688635180      0.00000000000000      li
    0.00000000000000    -17.90748960281839      0.00000000000000      f
    3.50782155976300     17.69001324433830      0.00000000000000      li
    3.50631129021353     14.19931298609203      0.00000000000000      f
    3.50546374780494     10.61768588381363      0.00000000000000      li
    3.51836528968206      7.06721394914587      0.00000000000000      f
    3.52720788765862      3.52720788765862      0.00000000000000      li
    3.53309967745012      0.00000000000000      0.00000000000000      f
    3.52720788765862     -3.52720788765862      0.00000000000000      li
    3.51836528968206     -7.06721394914587      0.00000000000000      f
    3.50546374780494    -10.61768588381363      0.00000000000000      li
    3.50631129021353    -14.19931298609203      0.00000000000000      f
    3.50782155976300    -17.69001324433830      0.00000000000000      li
    7.01677752244211     17.84927600603095      0.00000000000000      f
    7.00254561299388     14.19533983578200      0.00000000000000      li
    7.01831802761820     10.59856071614291      0.00000000000000      f
    7.04493256000175      7.04493256000175      0.00000000000000      li
    7.06721394914587      3.51836528968206      0.00000000000000      f
    7.07720134353519      0.00000000000000      0.00000000000000      li
    7.06721394914587     -3.51836528968206      0.00000000000000      f
    7.04493256000175     -7.04493256000175      0.00000000000000      li
    7.01831802761820    -10.59856071614291      0.00000000000000      f
    7.00254561299388    -14.19533983578200      0.00000000000000      li
    7.01677752244211    -17.84927600603095      0.00000000000000      f
   10.46995876956571     17.57299777885308      0.00000000000000      li
   10.51386203324838     14.08132090986711      0.00000000000000      f
   10.52769974571460     10.52769974571460      0.00000000000000      li
   10.59856071614291      7.01831802761820      0.00000000000000      f
   10.61768588381363      3.50546374780494      0.00000000000000      li
   10.64844213012559      0.00000000000000      0.00000000000000      f
   10.61768588381363     -3.50546374780494      0.00000000000000      li
   10.59856071614291     -7.01831802761820      0.00000000000000      f
   10.52769974571460    -10.52769974571460      0.00000000000000      li
   10.51386203324838    -14.08132090986711      0.00000000000000      f
   10.46995876956571    -17.57299777885308      0.00000000000000      li
   13.94098772913550     17.67727440792691      0.00000000000000      f
   14.00644521514217     14.00644521514217      0.00000000000000      li
   14.08132090986711     10.51386203324838      0.00000000000000      f
   14.19533983578200      7.00254561299388      0.00000000000000      li
   14.19931298609203      3.50631129021353      0.00000000000000      f
   14.26051688635180      0.00000000000000      0.00000000000000      li
   14.19931298609203     -3.50631129021353      0.00000000000000      f
   14.19533983578200     -7.00254561299388      0.00000000000000      li
   14.08132090986711    -10.51386203324838      0.00000000000000      f
   14.00644521514217    -14.00644521514217      0.00000000000000      li
   13.94098772913550    -17.67727440792691      0.00000000000000      f
   17.20736325947312     17.20736325947312      0.00000000000000      li
   17.67727440792691     13.94098772913550      0.00000000000000      f
   17.57299777885308     10.46995876956571      0.00000000000000      li
   17.84927600603095      7.01677752244211      0.00000000000000      f
   17.69001324433830      3.50782155976300      0.00000000000000      li
   17.90748960281839      0.00000000000000      0.00000000000000      f
   17.69001324433830     -3.50782155976300      0.00000000000000      li
   17.84927600603095     -7.01677752244211      0.00000000000000      f
   17.57299777885308    -10.46995876956571      0.00000000000000      li
   17.67727440792691    -13.94098772913550      0.00000000000000      f
   17.20736325947312    -17.20736325947312      0.00000000000000      li
    3.53553390593274      3.53553390593274      5.00000000000000      ar
$user-defined bonds
$end

[asaf]

The calculation was done at dft level (pbe functional) grid m4 ,ri + marij(maxlmom=18) and $disp in control file,scfconv=9
Thanks.

[uwe]

Hi,

the structure is not the one of the C4v symmetric case, since the Ar is not positioned in the middle of the Li-F plane. So this has Cs (or C1v) only.

If I move the argon to the middle position, I get C4v. With this structure, the energies are:

C4v	-6973.0631895
Cs	-6973.0631895
C1v	-6973.0631895
C1	-6973.0631895

But for the structure in Cs you have posted:

Cs	-6973.06432419522

Obviously we have used a different basis set, and I have chosen a total charge of +1 to make it a closed shell case. However, the difference you see is quite similar to what I see when I put the argon on two different positions.

Could it be that your argon is placed differently in the C1v case?

Regards,

Uwe

[asaf]

Hi,
The Ar is not placed differently:
I have calculated two different configurations:
1)When the Ar placed on the middle of the surface (c4v symmetry)
2)When the Ar is along the diagonal of the surface (cs symmetry)
In case 1, c4v, c2v and c1 give the same results, but slightly different from c1v.
In case 2, cs and c1 give slightly different results.
Regards,
Asaf

[asaf]

Clarifying:
In case 1, following your instructions from the previous topic gives the same results for c1v as c4v, c2v and c1 (when i have used susy). without using susy I get what I have wrote above.
In case 2, cs and c1 gives slightly different results. (In this case I am using desy to determine cs. probably if I could used susy for this case too, the problem would not be seen as in case 1).
Thanks.

[asaf]

It will be interesting what you will get if you will calculate for the structure which I have posted here, the energy with c1.
In my calculation it is different from the result with using cs.

[uwe]

Hi,

which basis set did you use?

Uwe

[asaf]

Hi,
The basis set which was used is the default of TM: def-SV(P)

[uwe]

Hi,

I do not get your energy. I guess before I start to try which occupation/charge you have, it would be much easier if you could also post the control file.

Regards,

Uwe

[asaf]

Hi
1)The following is for c1 (after calculation):



$title
$operating system unix
$symmetry c1
$coord    file=coord
$user-defined bonds    file=coord
$atoms
li 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53 \
   55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,   \
   103,105,107,109,111,113,115,117,119,121                                     \
   basis =li def-SV(P)                                                         \
   jbas  =li def-SV(P)
f  2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,  \
   54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,   \
   102,104,106,108,110,112,114,116,118,120                                     \
   basis =f def-SV(P)                                                          \
   jbas  =f def-SV(P)
ar 122                                                                         \
   basis =ar def-SV(P)                                                         \
   jbas  =ar def-SV(P)
$basis    file=basis
$rundimensions
   dim(fock,dens)=827722
   natoms=122
   nshell=612
   nbf(CAO)=1285
   nbf(AO)=1224
   dim(trafo[SAO<-->AO/CAO])=1407
   rhfshells=2
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$alpha shells
 a       1-371                                  ( 1 )
$beta shells
 a       1-370                                  ( 1 )
$scfiterlimit      300
$thize     0.10000000E-04
$thime        5
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$optimize
   internal   off
   cartesian  on
   global     off
   basis      off   logarithm
$coordinateupdate
   dqmax=0.3
   interpolate  on
   statistics    5
$forceupdate
   ahlrichs numgeo=0  mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
   threig=0.005  reseig=0.005  thrbig=3.0  scale=1.00  damping=0.0
$forceinit on
   diag=default
$energy    file=energy
$grad    file=gradient
$forceapprox    file=forceapprox
$lock off
$dft
   weight derivatives
   functional pbe
   gridsize   m4
$disp
$scfconv        9
$scfdamp   start=0.700  step=0.050  min=0.050
$scforbitalshift  closedshell=.05
$ricore     1500
$rij
$jbas    file=auxbasis
$marij
  lmaxmom            18
$last step     rdgrad
$orbital_max_rnorm 0.19784832412769E-06
$last SCF energy change = -6973.5259
$dipole from ridft
  x     0.00688705924863    y     0.00688705073305    z     0.16207396037241    a.u.
   | dipole | =    0.4126972166  debye
$end





2)The following is for cs (after calculation):



$title
$operating system unix
$symmetry cs
$coord    file=coord
$user-defined bonds    file=coord
$atoms
li 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53 \
   55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,   \
   103,105,107,109,111,113,115,117,119,121                                     \
   basis =li def-SV(P)                                                         \
   jbas  =li def-SV(P)
f  2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,  \
   54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,   \
   102,104,106,108,110,112,114,116,118,120                                     \
   basis =f def-SV(P)                                                          \
   jbas  =f def-SV(P)
ar 122                                                                         \
   basis =ar def-SV(P)                                                         \
   jbas  =ar def-SV(P)
$basis    file=basis
$rundimensions
   dim(fock,dens)=827722
   natoms=122
   nshell=612
   nbf(CAO)=1285
   nbf(AO)=1224
   dim(trafo[SAO<-->AO/CAO])=2727
   rhfshells=2
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$alpha shells
 a'      1-194                                  ( 1 )
 a"      1-177                                  ( 1 )
$beta shells
 a'      1-193                                  ( 1 )
 a"      1-177                                  ( 1 )
$scfiterlimit      300
$thize     0.10000000E-04
$thime        5
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$optimize
   internal   off
   cartesian  on
   global     off
   basis      off   logarithm
$coordinateupdate
   dqmax=0.3
   interpolate  on
   statistics    5
$forceupdate
   ahlrichs numgeo=0  mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
   threig=0.005  reseig=0.005  thrbig=3.0  scale=1.00  damping=0.0
$forceinit on
   diag=default
$energy    file=energy
$grad    file=gradient
$forceapprox    file=forceapprox
$lock off
$dft
   weight derivatives
   functional pbe
   gridsize   m4
$disp
$scfconv        9
$scfdamp   start=0.700  step=0.050  min=0.050
$scforbitalshift  closedshell=.05
$ricore     1500
$rij
$jbas    file=auxbasis
$marij
  lmaxmom            18
$last step     rdgrad
$orbital_max_rnorm 0.19671757652964E-06
$last SCF energy change = -6973.5267
$dipole from ridft
  x     0.00975456986373    y     0.16242638323577    z    -0.00000000001391    a.u.
   | dipole | =    0.4135936372  debye
$end



Regards.

[uwe]

Hi,

took a while but now I understand what happened.

The problem is that your C1 and C1v or Cs structure is slightly different. The coordinates you have posted are not exactly symmetric. So if you first run a job in C1 symmetry, you get the energy for exactly those coordinates.

If you afterwards run define and call desy - and desy is described in the menu of define as:

desy <eps>       : DETERMINE MOLECULAR SYMMETRY AND ADJUST
                     COORDINATES (default for eps=1d-6)

it does ADJUST the coordinates to Cs or C1v symmetry. define MOVES your coordinates into the given symmetry. So calling desy results in Cs, but if you look at the screen you will see:

symmetry group of the molecule :   cs

 the group has the following generators :
   c1(z)
   mirror plane sigma(xy)

    2 symmetry operations found

 THE MOLECULAR GEOMETRY WILL BE SYMMETRIZED !

This also explains why we both get the exactly same energy when going down from C4v to a smaller point group: The coordinates are already in C2, Cs, C1v, ... and do not have to be moved there.

The same happens when you call sy instead of desy. sy either adds atoms such that the symmetry is being enforced, or it moves the atoms. The decision whether to add or move can be controlled by the threshold <eps>:

sy <group> <eps> : DEFINE MOLECULAR SYMMETRY (default for eps=3d-1)

Regards,

Uwe

[asaf]

Thanks a lot,
Asaf