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Subsections


Subsetting

This is the basis of divide and conquer methodology[,,]. Subsetting can be performed by hand through the SUB parameters, or automatically through the keywords listed below. Subsystems consists of a core surrounded by an inner and outer buffer.


CLUSTER

Execute cluster based subsetting. Specification of the cluster based subsetting is through the cluster parameter block:

CLUSTER

  NCORE=3 DBUFF1=4.0 DBUFF2=2.0

END_CLUSTER
This means that the cores will be build from 3 residues, the first buffer region extends 4.0 Å from the core, the second buffer region 2.0 Å from the first buffer region. Multiple cores (i.e. multiple cluster groups) can be defined by:

CLUSTER

  NCORE=2 (1-6 7 8 12-14)

  NCORE=3 (9 10 15-25 )

  NCORE=1 (26 27)

  DBUFF1=4.3 DBUFF2=2.0

END_CLUSTER
Cores will be build from 2 residues for residues 1-6, 7, 8, 12-14, from 3 residues for residues 9, 10, 15-25 and from 1 core for residue 26 and 27. The first buffer region is 4.3 Å, the second 2.0 Å. Note that all residues should be used (and only once) in this syntax.

CLUSTER

  NCORE=1 (1-20) [-1]

  NCORE=1 (21-100) [0]

END_CLUSTER
Cores will be built from 1 residue for residues 1-20 and from 1 residue for residues 21-100. Moreover, the charge of the subsystems build from residues 1-20 will be constrained to -1 electron and the charge of the subsystems build from residues 21-100 to 0 electrons. Only effective when the NO-OVERLAP keyword is used. Charges are constrained by use of multiple Fermi energies[].

The NEIGHBORS parameter block can only be used in conjunction with the CLUSTER subsetting (only used with the multiple core and Fermi feature) and NO-OVERLAP keyword.

NEIGHBORS

  NEIGHBORS=2 1

  NEIGHBORS=1 3

END_NEIGHBORS
Specifies the overlap of residues in the first and third cluster groups. Residues in the first cluster group only overlap with residues of the first cluster group if they are within 2 residues away from each other. Residues in the third cluster group only overlap with residues of the third cluster group if they are within 1 residue away from each other. For example:

CLUSTER

  NCORE=1 (1-10) [0]

  NCORE=1 (11-20) [0]

  NCORE=1 (21-30) [0]

  DBUFF1=4.0 DBUFF2=2.0

END_CLUSTER

NEIGHBORS

  NEIGHBORS=2 1

  NEIGHBORS=1 3

END_NEIGHBORS
Here atoms of residue 1 (which is in the first cluster group) will only overlap with atoms of residue 1, 2 and 3 (that is, if they are within the buffer region). Atoms of residue 5 will only overlap with atoms of residue 3, 4, 5, 6 and 7 and atoms of residue 30 only with atoms of residues 29 and 30.


NO-OVERLAP

Can only be used in combination with the CLUSTER keyword.

CLUSTER

  NCORE=1 (1-10)

  NCORE=1 (11-20)

END_CLUSTER
When the NO-OVERLAP keyword is used, subsystems made from residues 1-10 only overlap with subsystems made from residues 1-10 and subsystems made from residues 11-20 only overlap with subsystems made from residues 11-20. In other words, density matrix elements between subsystems 1-10 and 11-20 are zero.


ATGRID

Execute a grid-based, atom-wise subsetting (core and buffers will be build from atoms).


RESGRID

Execute grid-based, residue-wise subsetting (core and buffers will be build from residues).


MIXGRID

Do grid based, residue-wise subsetting for cores, grid based, atom-wise subsetting for buffers.

NOTE: Specify Grid parameters when a grid based subsetting is selected. The syntax for these parameters is:

GRID

  XCORE=4.0 YCORE=4.0 ZCORE=4.0 OVERLAP=0.5

  DBUFF1=2.5 DBUFF2=1.0

END_GRID
Meaning that the total system will be divided into rectangular boxes of 4.0 \ensuremath{×}4.0 \ensuremath{×}4.0 Å that overlap 0.5 Å in each dimension. The first buffer region is 2.5 Å wide, the second 1.0 Å.


COMBSUB

Execute a combination subsetting; certain residues will be subsetted grid based, others cluster based. Use the combsub parameters to specify this subsetting:

COMBSUB

  CLUSTER

    1-10 13

  RESGRID

    11-12 14-20

END_COMBSUB
Here, cluster based subsetting will be done for residues 1-10 and 13, grid-based residue-wise subsetting will be done for residues 11-12 and 14-20. The cores of the subsystems will be selected from the specified residues, buffers from all residues / atoms of the system. COMBSUB can only be defined as a combination of CLUSTER with one of RESGRID, ATGRID of MIXGRID. Note that you have to specify the CLUSTER and GRID parameters when you use COMBSUB. Note that all residues should be used (and only once) in COMBSUB.


PBC

Periodic boundary conditions in effect. This only works when a box is specified through the BOX parameters:

BOX

  XBOX=20.0 YBOX=20.0 ZBOX=20.0

END_BOX
This means that the box dimensions are 20 \ensuremath{×}20 \ensuremath{×}20 Å.

Note that for a single point calculation / geometry optimization where RESGRID was not specified all atoms should be contained within the box, for all other cases all center of masses of the residues should be within the box.


STANDARD (-standard)

Standard closed-shell calculation (no divide and conquer). All subsetting parameters are ignored, only one subsystem containing all atoms will be generated.

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