Periodic electrostatic embedded cluster setup question

[tsanan]

I'm attempting to set up a calculation using the periodic electrostatic embedded cluster method in Turbomole. Unfortunately, I'm not finding the manual to be particularly helpful describing the process by which one would properly do so. Here are the steps as described in the Turbomole 5.10 manual:

1. Dimensionality of the system is specified by the keyword periodic in the  $embed section: periodic 3 means a bulk three-dimensional system, periodic 2  denotes a two-dimensional surface with an aperiodic z direction.
2. Definition of the unit cell of periodic point charges field is specified in the  subsections cell and content of the $embed section.
3. Definition of the part of point charges field that will be replaced by the QM cluster together with the isolating shell (ECPs, explicit point charges) is specified in the subsection cluster of the $embed section.
4. Definition of the quantum mechanical cluster as well as the surrounding ECPs and anionic point charges is included in the usual $coord section.

I've been attempting to replicate the Al8O12 cluster described in the manual, and I'm not having success. Here are some uncertainties/questions I have:

The $embed keyword is obviously necessary, but where it should be specified is unclear. When I copy the $embed section from the manual into control, it never appears to be read in. Attempting to read it in using the 'cem' option in the basis submenu of define results in the script crashing. What, exactly, is the proper protocol for reading in this information? Am I expected to run define with the 'QM' described cluster, and then add the embed information to control manually? If so, is there any way (aside from just running single point calculations) to determine if the embed information has been properly inputed? A test optimization did not use the cluster information, so there's obviously something incorrect in the way I have been doing things. If someone could provide a more explicit and well documented protocol for setting up both the QM and embedded regions that would be greatly appreciated. Thank you,

Toby Sanan
Hadad Research Group
Ohio State University

[christof.haettig]

The $embed data group should be put into the control file anywhere before the data group $end.
An example input can be found in TURBOTEST/rdgrad/long/Al2O3.PC.DFT.E1.
The best check whether the input is meaningful is indeed to run a single point calculation with ridft.

Christof

[tsanan]

I am still having problems with the PEECM. Here is the control file I am trying to use to simulate a 2D zirconia (ZrO2) surface:

$title
Zirconia
$operating system unix
$symmetry ci
$redundant    file=coord
$coord    file=coord
$user-defined bonds    file=coord
$atoms
zr 1,3,7,9,13,15,19,21                                                       \
   basis =zr def-TZVP                                                          \
   ecp   =zr def-ecp                                                            \
   jbas  =zr def-TZVP
o  2,4-6,8,10-12,14,16-18,20,22-24                                     \
   basis =o def-SV(P)                                                          \
   jbas  =o def-SV(P)
$embed
periodic 2
wsicl 2.0
lmaxmom 25
cell angs
14.098 14.098 14.988 90.000 90.000 90.000
cluster ang
Zr                 4.39000000    6.14600000    6.23500000
O                  4.39000000    4.39000000    5.26234000
Zr                 6.14600000    4.39000000    8.72900000
O                  4.39000000    4.39000000    7.75634000
O                  6.14600000    6.14600000    9.70166000
O                  6.14600000    6.14600000    7.20766000
Zr                 7.90200000    6.14600000    6.23500000
O                  7.90200000    4.39000000    5.26234000
Zr                 9.65800000    4.39000000    8.72900000
O                  7.90200000    4.39000000    7.75634000
O                  9.65800000    6.14600000    9.70166000
O                  9.65800000    6.14600000    7.20766000
Zr                 4.39000000    9.65800000    6.23500000
O                  4.39000000    7.90200000    5.26234000
Zr                 6.14600000    7.90200000    8.72900000
O                  4.39000000    7.90200000    7.75634000
O                  6.14600000    9.65800000    9.70166000
O                  6.14600000    9.65800000    7.20766000
Zr                 7.90200000    9.65800000    6.23500000
O                  7.90200000    7.90200000    5.26234000
Zr                 9.65800000    7.90200000    8.72900000
O                  7.90200000    7.90200000    7.75634000
O                  9.65800000    9.65800000    9.70166000
O                  9.65800000    9.65800000    7.20766000
end
content ang
Zr                 0.87800000    2.63400000    6.23500000
O                  0.87800000    0.87800000    5.26234000
Zr                 2.63400000    0.87800000    8.72900000
O                  0.87800000    0.87800000    7.75634000
O                  2.63400000    2.63400000    9.70166000
O                  2.63400000    2.63400000    7.20766000
Zr                 4.39000000    2.63400000    6.23500000
O                  4.39000000    0.87800000    5.26234000
Zr                 6.14600000    0.87800000    8.72900000
O                  4.39000000    0.87800000    7.75634000
O                  6.14600000    2.63400000    9.70166000
O                  6.14600000    2.63400000    7.20766000
Zr                 7.90200000    2.63400000    6.23500000
O                  7.90200000    0.87800000    5.26234000
Zr                 9.65800000    0.87800000    8.72900000
O                  7.90200000    0.87800000    7.75634000
O                  9.65800000    2.63400000    9.70166000
O                  9.65800000    2.63400000    7.20766000
Zr                11.41400000    2.63400000    6.23500000
O                 11.41400000    0.87800000    5.26234000
Zr                13.17000000    0.87800000    8.72900000
O                 11.41400000    0.87800000    7.75634000
O                 13.17000000    2.63400000    9.70166000
O                 13.17000000    2.63400000    7.20766000
Zr                 0.87800000    6.14600000    6.23500000
O                  0.87800000    4.39000000    5.26234000
Zr                 2.63400000    4.39000000    8.72900000
O                  0.87800000    4.39000000    7.75634000
O                  2.63400000    6.14600000    9.70166000
O                  2.63400000    6.14600000    7.20766000
Zr                11.41400000    6.14600000    6.23500000
O                 11.41400000    4.39000000    5.26234000
Zr                13.17000000    4.39000000    8.72900000
O                 11.41400000    4.39000000    7.75634000
O                 13.17000000    6.14600000    9.70166000
O                 13.17000000    6.14600000    7.20766000
Zr                 0.87800000    9.65800000    6.23500000
O                  0.87800000    7.90200000    5.26234000
Zr                 2.63400000    7.90200000    8.72900000
O                  0.87800000    7.90200000    7.75634000
O                  2.63400000    9.65800000    9.70166000
O                  2.63400000    9.65800000    7.20766000
Zr                11.41400000    9.65800000    6.23500000
O                 11.41400000    7.90200000    5.26234000
Zr                13.17000000    7.90200000    8.72900000
O                 11.41400000    7.90200000    7.75634000
O                 13.17000000    9.65800000    9.70166000
O                 13.17000000    9.65800000    7.20766000
Zr                 0.87800000   13.17000000    6.23500000
O                  0.87800000   11.41400000    5.26234000
Zr                 2.63400000   11.41400000    8.72900000
O                  0.87800000   11.41400000    7.75634000
O                  2.63400000   13.17000000    9.70166000
O                  2.63400000   13.17000000    7.20766000
Zr                 4.39000000   13.17000000    6.23500000
O                  4.39000000   11.41400000    5.26234000
Zr                 6.14600000   11.41400000    8.72900000
O                  4.39000000   11.41400000    7.75634000
O                  6.14600000   13.17000000    9.70166000
O                  6.14600000   13.17000000    7.20766000
Zr                 7.90200000   13.17000000    6.23500000
O                  7.90200000   11.41400000    5.26234000
Zr                 9.65800000   11.41400000    8.72900000
O                  7.90200000   11.41400000    7.75634000
O                  9.65800000   13.17000000    9.70166000
O                  9.65800000   13.17000000    7.20766000
Zr                11.41400000   13.17000000    6.23500000
O                 11.41400000   11.41400000    5.26234000
Zr                13.17000000   11.41400000    8.72900000
O                 11.41400000   11.41400000    7.75634000
O                 13.17000000   13.17000000    9.70166000
O                 13.17000000   13.17000000    7.20766000
end
charges
Zr 4.0
O  -2.0
end
$basis    file=basis
$ecp    file=basis
$rundimensions
   dim(fock,dens)=124024
   natoms=24
   nshell=184
   nbf(CAO)=496
   nbf(AO)=456
   dim(trafo[SAO<-->AO/CAO])=1152
   rhfshells=1
$scfmo   file=mos
$closed shells
ag      1-56                                   ( 2 )
au      1-56                                   ( 2 )
$scfiterlimit       30
$thize     0.10000000E-04
$thime        5
$scfdump
$scfintunit
unit=30       size=0        file=twoint
$scfdiis
$scforbitalshift  automatic=.1
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$optimize
   internal   on
   redundant  on
   cartesian  off
   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
   functional b-p
   gridsize   m3
$scfconv   6
$scfdamp   start=0.700  step=0.050  min=0.050
$ricore      200
$rij
$jbas    file=auxbasis
$last step     define
$end

Can anyone point out any obvious (or not so obvious) problems with the control file?

The file coord contains only the QM region (Zr8O16). The basis, auxbasis, and mos files were generated using define in the usual way.

Here is the error message from job.last:

Extensions and centers of shell-pairs:
  number of shells with a single center:         6510
  number of shells with double centers:           339

Size of the simulation box:     28.32322 a.u.
Radius of 1st FMM zone:         84.96965 a.u.
Radius of QM cluster:           50.36950 a.u.
Radius of PC cluster:            8.20590 a.u.
Final radius of 1st FMM zone:   84.96965 a.u.

# of cells of 1st FMM zone:         37
# of PCs in 1st FMM zone:          810

MODTRACE: no modules on stack



Cell mismatch in nfpcstf
ridft ended abnormally
ridft step ended abnormally
next step = ridft

Another piece of information is the geometry for the QM region+PCs was generated using Gaussview, building up from the Zr2O4 crystal structure. I used Gaussview to build a 14.048x14.048x4.498A cluster, then added 10A to the z-axis and the crystal lattice is centered in the z-axis extra space. I do this because the manual says "the third dimension of the unit cell must be large enough to enclose the entire surface in this direction." I interpreted this as the z dimension should be the largest dimension, but I am not sure that is correct. Do you suggest any other methods for building the cluster and content regions?

Thanks,
Toby

[christof.haettig]

I don't see any obvious error. Maybe, you should send a bug report to the turbomole help desk.
Christof