$EFRAG group (optional)
The Effective Fragment Potential (EFP) is a potential
extracted from rigorous quantum mechanics, permitting the
treatment of solvent molecules (or other types of
subsystems) with a potential. There are two models, EFP1
and EFP2, with more accurate physics in the latter. For
more information, see chapter 4 of this manual.
EFP1 calculations are typically limited to a QM system
with water molecules, the latter modeled by RHF-based or
DFT-based potentials which are built into the program. The
following EFP1/QM calculations are possible:
QM/EFP1 method1 method2 SCF
RHF (and DFT) gradient x
UHF (and DFT) gradient x
ROHF(and DFT) gradient x
MP2(RHF/UHF/ROHF) gradient x x
CCSD energy x x
CCSD(T) energy x
CR-CCL energy x
EOM-CCSD energy x x
CR-EOML energy x
CITYP=CIS (only) gradient x x
TDDFT(RHF) gradient x x
GVB gradient x
MCSCF gradient x
Here, SCF means the QM calculation and the EFP particle's
polarizability terms are made fully self-consistent.
Otherwise, the QM density felt by the EFP particles is that
of the reference (ground) state, termed "method 1". A more
accurate and detailed energy calculation is possible when
the QM's density is available for a specific correlation
treatment and/or a specific excited state. Such "method 2"
calculations are available only for RUNTYP=QMEFPEA. The
"method 1" calculations can be used for any relevant run
type using the energy or analytic nuclear gradients, as
indicated. For example, after MP2 geometry optimization,
numerical differentiation can produce solvated MP2-level
frequencies.
EFP2 calculations should use COORD=FRAGONLY at the
present time, as the QM/EFP2 interaction terms are
currently under active development. The programming for
EFP2/EFP2 interactions is completed. See RUNTYP=MAKEFP to
create EFP2 potentials.
In most cases, the entire EFP1, QM/EFP1, or EFP2 system
can be embedded in a PCM continuum (see $PCM).
This group gives the name and position of one or more
effective fragment potentials. It consists of a series of
free format card images, which may not be combined onto a
single line! The position of a fragment is defined by
giving any three points within the fragment, relative to
the ab initio system defined in $DATA, since the effective
fragments have a frozen internal geometry. All other atoms
within the fragment are defined by information in the
$FRAGNAME input group.
----------------------------------------------------------
-1- a line containing one or more of these options:
If you choose more options than are able to be fit on a
single 80 character line, type an > character to continue
onto the next line.
If you do not choose any of these options, input a blank
line to accept defaults.
COORD =CART selects use of Cartesians coords
to define the fragment position at
line -3-. (default)
=INT selects use of Z-matrix internal
coordinates at line -3-.
POLMETHD=SCF indicates the induced dipole for
each fragment due to the ab initio
electric field and other fragment
fields is updated only once during
each SCF iteration.
=FRGSCF requests microiterations during
each SCF iteration to make induced
dipoles due to ab initio and other
fragment fields self consistent
among the fragments. (default)
Both methods converge to the same
dipolar interaction.
POSITION=OPTIMIZE Allows full optimization within the
ab initio part, and optimization of
the rotational and translational
motions of each fragment. (default)
=FIXED Allows full optimization of the
ab initio system, but freezes the
position of the fragments. This
makes sense only with two or more
fragments, as what is frozen is the
fragments' relative orientation.
FIXED may be used with RUNTYP being
OPTIMIZE, SADPOINT, HESSIAN and IRC.
=EFOPT the same as OPTIMIZE, but if the
fragment gradient is large, up to
5 geometry steps in which only the
fragments move may occur, before
the geometry of the ab initio piece
is relaxed. This may save time by
reusing the two electron integrals
for the ab initio system.
NBUFFMO = n First n orbitals in the MO matrix
are deemed to belong to the QM/MM
buffer and will be excluded from
the interaction with the EFP region.
This makes sense only if these first
MOs are frozen via the $MOFRZ.
The next few inputs apply periodic boundary conditions,
which is only possible if the system contains only EFP
particles, with no ab initio atoms. The default is to use
the minimum image convention, for all terms in the
potentials, but see also the $EWALD input group in order to
perform the long range electrostatic interactions in a more
accurate manner. You may choose no more than one of the
possible sets of cutoffs, with the switching function
SWR1/SWR2 being the most physically reasonable.
XBOX, YBOX, ZBOX = dimensions of the periodic box,
which must be given in Angstroms.
If these sizes are omitted, the
simulation is an isolated cluster.
SWR1, SWR2 = distance cutoffs for the switching
function that gradually drops the
interactions from full strength at
SWR1 to zero at SWR2. Choose
SWR2 <= min(XBOX/2,YBOX/2,ZBOX/2)
and SWR1 <= SWR2 (typically 80%),
to cut off interactions within a
single box. In Angstrom
RCUT a radial cutoff, implemented as a
step function, which should be
chosen like SWR2. In Angstrom
XCUT, YCUT, ZCUT = cutoffs (as step functions) beyond
which effective fragment potential
interactions are not computed,
XCUT <= XBOX/2, etc. Angstroms
For a simulation of 64 CCl4 molecules, PBC input might be
xbox=21.77 ybox=21.77 zbox=21.77 swr1=8.0 swr2=10.0
Box sizes are typically chosen to give a correct value for
the density of the system.
The following turn off selected terms in the potentials,
even if data for the term is found in the various $FRAGNAME
input groups. These keywords are standalone strings,
without a value assigned to them. They allow data from
potentials generated by MAKEFP runs to be kept in the
$FRAGNAME, for possible future use. The first two are of
interest in production runs, while the others are primarily
meant for debugging purposes, as the latter terms are
normally quite large.
NOCHTR = switch off charge transfer in EFP2
NODISP = switch off dispersion in EFP2
NOEXREP = switch off exchange repulsion (EFP1/EFP2)
NOPOL = switch off polarization (implies NOPSCR)
NOPSCR = switch off polarization screening, only
The following parameters are related to screening of some
terms in the potentials, when fragments are at close
distances. Note that they are relevant only to EFP2 runs.
Prior to May 2009, the defaults were
ISCRELEC=0 ISCRPOL=0 ISCRDISP=0
at which time the defaults were changed to
ISCRELEC=0 ISCRPOL=1 ISCRDISP=1
If you need to reproduce results or continue an ongoing set
of computations, simply input the old defaults.
ISCRELEC = fragment-fragment electrostatic screening,
a correction for "charge penetration":
E(elec) = E(multipoles) + E(chg.pen.)
= 0 damping by various formulae is controlled
by SCREEN1, SCREEN2, or SCREEN3 input
sections in the $FRAGNAME input(s). If
none are found, there will be no charge
penetration screening of electrostatics.
(default)
= 1 use an overlap based damping correction
E(chg.pen.)= -2(S**2/R)/sqrt(-2ln|S|)
to the classical multipole energy. Since
the overlap integrals used here, as well as
in ISCRDISP must be evaluated as part of
the exchange repulsion energy, there is
essentially no overhead for selecting this.
ISCRPOL = fragment-fragment polarization screening.
= 0 damping is controlled by POLSCR sections in
the $FRAGNAME inputs. If not found, there
will be no screening. If POLSCR is found,
you must also use ISCRELEC=0 and SCREEN3.
= 1 damping will use a Tang-Toennis style
Gaussian formula,
(1-exp(aR**2)(1+aR**2)
where the default value of a=0.6. In order
to change the 'a' parameter, give
POLAB
STOP
in the $FRAGNAME input. A smaller value
may be useful for ionic EFPs. (default)
ISCRDISP = fragment-fragment dispersion screening
= 0 Use Tang-Toennies damping, with a fixed
parameter a=1.5.
= 1 use an overlap based damping factor,
1-S**2(1-2ln|S|+2ln**2|S|)
instead. There is no parameterization, so
there's no other input. (default)
It is possible to choose ISCRELEC, ISCRPOL, and ISCRDISP
independently, as they apply to distinct parts of the
fragment-fragment effective potential, and apart from
POLSCR/SCREEN3, are independently implemented.
FRCPNT this keyword activates decomposing and
printing the forces at the desired points in
the EFP fragments, in additional to the
traditional summing of the forces at the
fragments' center-of-masses. This is useful
for coarse graining the EFP data. If this
option is selected, FORCE POINT section(s)
must be given in the $FRAGNAME input(s).
The following keywords are for use with the EFP2-AI (a.k.a.
EFP2-QM) dispersion calculation, that is, the calculation
of the dispersion energy in a mixed system containing one
or more EFP2 fragment(s) and a molecule modeled with a
fully ab initio method (e.g. Hartree-Fock).
QMDISP specify whether to perform the calculation
of EFP2-AI dispersion
= 0 do not calculate dispersion, even if both
an EFP2 fragment and an ab initio part are
present (default)
= 1 perform the EFP2-AI dispersion calculation
ISCRQMDS specify type of screening to use with
EFP2-AI damping
=-1 turn off damping (for debugging or benchmark
comparison purposes)
= 0 use Tang-Toennies damping, with a fixed
parameter a=1.5
= 1 use a parameter-free, overlap-based damping
factor, 1-S**2(1-2ln|S|+2ln**2|S|) (default)
NODSGRD skip calculation of the EFP2-AI dispersion
gradient, even if a gradient calculation is
specified with RUNTYP=GRADIENT
Note that localized orbitals are necessary for the
dispersion energy calculation. Boys localization will be
performed by default if QMDISP=1 is specified, with no
additional input keywords necessary. An alternate
localization method may be specified using the LOCAL
keyword in $CONTRL.
NIDISP7 skip computating the 7th power dispersion.
----------------------------------------------------------
-2- FRAGNAME=XXX
XXX is the name of the fragment whose coordinates are to be
given next, and whose potential may also be in the input
stream, as $XXX groups. XXX may not exceed 6 characters.
Below, the actual $XXX groups are referred to generically
as $FRAGNAME. Specific examples of $FRAGNAME are $C6H6,
$BENZEN, $DMSO, ...
All information defining the EFP2-type fragment potential
is given in its $FRAGNAME. A few standard EFP2 potentials
are provided: see ~/gamess/auxdata/EFP. These are used by
placing the desired file(s) into your input.
Two different EFP1-type water potentials are internally
stored. FRAGNAME=H2ORHF will select a water potential
developed at the RHF/DZP level, while FRAGNAME=H2ODFT will
select a potential corresponding to B3LYP/DZP (see $BASIS
for the precise meaning of DZP). If you choose either of
these internally stored potentials, you need not give any
further input to define them.
Since the EFP model consists of distributed multipoles and
distributed polarizabilities, it is trivial to map some of
the literature's simplified water potentials onto the EFP1
programming. For example, the octupole expansions used in
EFP can be truncated to point charges (monopole term). So,
FRAGNAME may also be any of the following water models:
SPC, SPCE, TIP5P, TIP5PE, or POL5P
Their EFP/EFP repulsion term is a typical 6-12 Lennard-
Jones form. Repulsion between the QM and EFP particles
follows the EFP1 style, if any QM atoms are input.
----------------------------------------------------------
-3- NAME, X, Y, Z (COORD=CART)
NAME, I, DISTANCE, J, BEND, K, TORSION (COORD=INT)
NAME = the name of a fragment point. The name used
here must match one of the points in $FRAGNAME.
For the internally stored H2ORHF and H2ODFT
potential, the atom names are O1, H2, and H3.
X, Y, Z = Cartesian coordinates defining the position of
this fragment point RELATIVE TO THE COORDINATE
ORIGIN used in $DATA. The choice of units is
controlled by UNITS in $CONTRL.
I, DISTANCE, J, BEND, K, TORSION = the usual Z-matrix
connectivity internal coordinate definition.
The atoms I, J, K must be atoms in the ab
initio system from in $DATA, or fragment points
already defined in the current fragment or
previously defined fragments.
If COORD=INT, line -3- must be given a total of three times
to define this fragment's position.
If COORD=CART, line -3- must be given three times, which is
sufficient to orient the rigid EFP particle. However, it
is good form to read in any remaining nuclei in the EFP,
for example all 12 atoms in a benzene EFP, although only
the first three lines determine the entire EFP's position,
whenever you have the data for the extra nuclei.
----------------------------------------------------------
Repeat lines -2- and -3- to enter as many fragments as you
desire, and then end the group with a $END line.
Note that it is quite typical to repeat the same fragment
name at line -2-, to use the same type of fragment system
at many different positions.
==========================================================
* * * * * * * * * * * * * * * * * * * * *
For tips on effective fragment potentials
see the 'further information' section
* * * * * * * * * * * * * * * * * * * * *
==========================================================
356 lines are written.
Edited by Shiro KOSEKI on Thu Mar 5 10:25:38 2020.