TURBOMOLE Users Forum
TURBOMOLE Modules => Ridft, Rdgrad, Dscf, Grad => Topic started by: asaf on October 21, 2010, 12:33:34 PM
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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.
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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.
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Hi,
can you post the structure, i.e. the coord file here?
Regards,
Uwe
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$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
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-14.26051688635180 0.00000000000000 0.00000000000000 li
-14.19931298609203 -3.50631129021353 0.00000000000000 f
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-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
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-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
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-7.01677752244211 -17.84927600603095 0.00000000000000 f
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-3.51836528968206 -7.06721394914587 0.00000000000000 f
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-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
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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
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10.64844213012559 0.00000000000000 0.00000000000000 f
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10.59856071614291 -7.01831802761820 0.00000000000000 f
10.52769974571460 -10.52769974571460 0.00000000000000 li
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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
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The calculation was done at dft level (pbe functional) grid m4 ,ri + marij(maxlmom=18) and $disp in control file,scfconv=9
Thanks.
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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:
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
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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
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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.
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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.
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Hi,
which basis set did you use?
Uwe
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Hi,
The basis set which was used is the default of TM: def-SV(P)
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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
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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.
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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
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Thanks a lot,
Asaf