6.46.3.2 Output filesIn addition to the standard output file SlapAf will use the following output files.
SlapAf will as standard
provided with an energy and a corresponding gradient
update the geometry (optimize).
Possible update methods include different quasiNewton methods.
The program will also provide for updates of the Hessian.
The program has a number of different variable metric methods available for
the Hessian update.
This section describes the input to the SlapAf program.

Keyword  Meaning 
ITERations  Maximum number of iterations which will be allowed in the relaxation procedure. Default is 500 iterations, however, if environment variable MAXITER has been exported by the user this is the assumed default value. 
THRShld  Enter two real numbers which specifies the convergence criterion with respect to the energy change and the norm of the gradient. The defaults are 1.0D6 and 3.0D4. 
BAKEr  Activate convergence criterions according to Baker [145]. Default is to use the convergence criterions as in the Gaussian program [146]. 
MAXStep  This keyword is followed by the value which defines the seed of largest change of the internal coordinates which will be accepted. A change which is larger is reduced to the max value. The value is dynamically modified each iterations. The default value is 0.3 au or rad. 
CNWEight  Sets the maximum weight assigned to the fulfillment of the constraints, relative to the step taken in the complementary space for energy minimization. The step in the constraint space is truncated to be at most as large as the step in the minimization space, or half the maximum total step, whichever is larger, multiplied by this value. Default is 1.0. 
Optional coordinate selection keywords
Optional Hessian update keywords
Keyword  Meaning 
NOUPdate  No update is applied to the Hessian matrix. Default is that the BroydenFletcherGoldfarbShanno update is applied. 
BFGS  Activate update according to BroydenFletcherGoldfarbShanno. This is the default. 
MSPupdate  Activate the MurtaghSargentPowell update according to Bofill [147]. This update is preferred for the location of transition states. 
EUUpdate  Activate the EU update according to Bofill [148]. This update can be used for the location of transition states. 
TSBFGS  Activate the TSBFGS update according to Bofill [148]. This update can be used for the location of minima transition states. 
UORDer  Order the gradients and displacements vectors according to Schlegel prior to the update of the Hessian. Default is no reorder. 
WINDow  Maximum number of previous iterations to include in the Hessian update. Default is 5. 
Optional optimization procedure keywords
Keyword  Meaning 
NOLIne  Disable line search. Default is to use line search for minima. 
RATIonal  Activate geometry optimization using the restricted step Rational Functional optimization [149,150], this is the default. 
C1Diis  Activate geometry optimization using the C1GDIIS method [151,152,153]. The default is to use the Rational Functional approach. 
C2Diis  Activate geometry optimization using the C2GDIIS method [154]. The default is to use the Rational Functional approach. 
DXDX  This option is associated to the use of the C1 and C2GDIIS procedures. This option will activate the computation of the socalled error matrix elements as , where is the displacement vector. 
DXG  This option is associated to the use of the C1 and C2GDIIS procedures. This option will activate the computation of the socalled error matrix elements as , where is the displacement vector and g is the gradient vector. 
GDX  See above. 
GG  This option is associated to the use of the C1 and C2GDIIS procedures. This option will activate the computation of the socalled error matrix elements as , where g is the gradient vector. This is the default. 
NEWTon  Activate geometry optimization using the standard quasiNewton approach. The default is to use the Rational Functional approach. 
RSPrfo  Activate RSPRFO [150] as default for TSsearch. Default is RSIRFO. 
TS  Keyword for optimization of transition states. This flag will activate the use of the mode following rational functional approach [155]. The mode to follow can either be the one with the lowest eigenvalue (if positive it will be changed to a negative value) or by the eigenvector which index is specified by the MODE keyword (see below). The keyword will also activate the MurtaghSargentPowell update of the Hessian and inactivate line search. This keyword will also enforce that the Hessian has the right index (i.e. one negative eigenvalue). 
MODE  Specification of the Hessian eigenvector index, this mode will be followed by the mode following RF method for optimization of transition states. The keyword card is followed by a single card specifying the eigenvector index. 
FINDTS  Enable a constrained optimization to release the constraints and locate a transition state if negative curvature is encountered and the gradient norm is below a specific threshold (see the GNRM option). Note that with the FINDTS keyword at least one of the constraints should be ``soft''. 
GNRM  Modify the gradient norm threshold associated with the FINDTS option. The actual threshold is specified on the subsequent line. The default value is 0.2. 
MEPsearch  Enable a minimum energy path (MEP) search. MEP is a valid synonym. 
NMEP  Maximum number of points to find in a minimum energy path search or intrinsic reaction coordinate analysis. Synonym of NIRC. 
MEPStep  The keyword is used to specify the step length done in the MEP search or IRC analysis. The step length can be followed with the unit BOHR or ANGSTROM. The default is 0.1 a.u. (in normalized massweighted coordinates). Synonym of IRCStep. 
MEPType  Specifies what kind of constraint will be used for optimizing the points during the MEP search or IRC analysis. The possibilities are SPHERE, the default, which uses the Sphere constraint (each structure is at a given distance in coordinate space from the reference), or PLANE which uses the Transverse constraint (each structure is at a given distance from the hyperplane defined by the reference and the path direction). The reference structure changes at each step, according to the MEPAlgorithm keyword. Synonym of IRCType. 
MEPAlgorithm  Selects the algorithm for a MEP search or IRC analysis. The possibilities are GS for the GonzálezSchlegel algorithm, the default, or MB for the MüllerBrown algorithm. Synonym of IRCAlgorithm. 
REFErence  The keyword is followed by a list of the symmetry unique coordinates (in au) of the origin of the hyper sphere. The default origin is the structure of the first iteration. 
GRADient of reference  The keyword is followed by a list of the gradient vector components. This keyword is compulsory when using the Transverse kind of constraint. The optimization is performed in a space orthogonal to the given vector. 
CIOPtimization  The keyword is used to perform a conical intersection search. It has to be followed by a line containing the two roots of a previous RASSCF or MSCASPT2 run, which are used to look for the intersection. Optionally, on the same entry the keyword NUMERICAL can be specified to request a numerical procedure, default in case of MSCASPT2. It will call the module CIISCMNG, which will produce the required gradients before returning to SLAPAF. See section for help on how to write the input. 
ISCOptimization  The keyword is used to perform an intersystem crossing search. It has to be followed by an entry containing the two roots of two previous RASSCF or CASPT2 runs, which are used to look for the crossing. Optionally, on the same entry the keyword NUMERICAL can be specified to request a numerical procedure, default in case of CASPT2. It will call the module CIISCMNG, which will produce the required gradients before returning to SLAPAF. See section for help on how to write the input. 
IRC  The keyword is used to perform an intrinsic reaction coordinate (IRC) analysis of a transition state structure. The analysis will follow the reaction path forward and backward until the energy increases. The keyword requires that the starting structure be that of a transition state and that the reaction vector be specified explicitly (check the keyword REACtion vector) or implicitly if it can be found on RUNOLD. Note that the user should not specify any explicit constraints! 
NIRC  Maximum number of points to find in an intrinsic reaction coordinate analysis or minimum energy path search. Synonym of NMEP. 
IRCStep  The keyword is used to specify the step length done in the IRC analysis or MEP search. The step length can be followed with the unit BOHR or ANGSTROM. The default is 0.1 a.u. (in normalized massweighted coordinates). Synonym of MEPStep. 
IRCType  Specifies what kind of constraint will be used for optimizing the points during the IRC analysis or MEP search. The possibilities are SPHERE, the default, which uses the Sphere constraint (each structure is at a given distance in coordinate space from the reference), or PLANE which uses the Transverse constraint (each structure is at a given distance from the hyperplane defined by the reference and the path direction). The reference structure changes at each step, according to the IRCAlgorithm keyword. Synonym of MEPType 
IRCAlgorithm  Selects the algorithm for a MEP search or IRC analysis. The possibilities are GS for the GonzálezSchlegel algorithm, the default, or MB for the MüllerBrown algorithm. Synonym of MEPAlgorithm. 
REACtion vector  The keyword is followed by the reaction vector specified as the Cartesian vector components on each of the symmetry unique atoms. 
Optional force constant keywords
Keyword  Meaning 
OLDForce  The Hessian matrix is read from the file RUNOLD. This Hessian is either an analytic or approximative Hessian updated by Slapaf. Note that for this option to work properly the type of internal coordinates must be the same! 
FCONstant  Input of Hessian in internal coordinates.
There are two different syntaxes.

XFCOnstant  Input of an external Hessian matrix in cartesian coordinates. The syntax is the same as for the FCONSTANT keyword. 
NUMErical  This invokes as calculation of the force constant matrix by a twopoint finite difference formula. The resulting force constant matrix is used for an analysis of the harmonic frequencies. Observe that in case of the use of internal coordinates defined as Cartesian coordinates that these has to be linear combinations which are free from translational and rotational components for the harmonic frequency analysis to be valid. Alternative: see keyword RowH in the section about Internal coordinates. 
CUBIc  This invokes a calculation of the 2nd and the 3rd order force constant matrix by finite difference formula. 
DELTa  This keyword is followed by a real number which defines the step length used in the finite differentiation. Default: 1.0D2. 
PRFC  The eigenvalues and eigenvectors of the Hessian matrix are printed. The internal coordinates definitions are also printed. 
RHIDden  Define the hidden atoms selection radius in order to improve a QM/MM Hessian. It can be followed by Angstrom. 
Optional miscellaneous keywords
Keyword  Meaning 
CTOF  Coordinates TO Follow defines an internal coordinate whose values will be printed in the output during the optimization. Both the original and the new values will be printed. The keyword must be followed by the definition on the primitive coordinate. 
RTRN  Maximum number of atoms for which bond lengths, angles and dihedral angles are listed, and the radius defining the maximum length of a bond follows. The latter is used as a threshold when printing out angles and dihedral angles. The length can be followed by Bohr or Angstrom which indicates the unit in which the length was specified, the default is Bohr. The default values are 15 and 3.0 au. 
THERmochemistry  Request frequencies to be computed followed by an user specified thermochemical analysis. The keyword must be followed by different entries containing the Rotational Symmetry Number, the Pressure (in atm), and one entry per Temperature (in K) for which the thermochemistry will be calculated. The section is ended by the keyword End of PT. 
LASTenergy  Specifies the quantum chemical method requested for the Last_Energy module (e.g., SCF, CASSCF, CASPT2, etc.) The keyword must be followed by the name of the module. Moreover, the EMIL command COPY needs to be used in the global input to provide a file named LASTEN, containing the input for the specified module. 
Example: A complete set of input decks for a CASSCF geometry
optimization. These are the input decks for the optimization
of the enediyne molecule.
&GATEWAY
Title= Enediyne
Coord= $MOLCAS/Coord/enediyne.xyz
Basis= ANOLVQZP
Group= x z
> DoWhile
&SEWARD
&SCF
ITERATIONS= 30; Occupied= 9 8 2 1; Thresholds= 1.0d8 1.0d3 1.5d3 0.2d3; IVO
&RASSCF
Symmetry= 1; Spin= 1
NactEl= 12 0 0; Inactive= 7 7 0 0; Ras2= 3 3 3 3
Iterations= 50 50; CiRoot= 1 1; 1; Thrs= 1.0e08 1.0e05 1.0e05
Lumorb
&SLAPAF; Iterations= 20
> EndDo
Example: Thermochemistry for an asymmetric top (Rotational Symmetry Number
= 1), at 1.0 atm and 273.15, 298.15, 398.15 and 498.15 K.
&SLAPAF; THERmochemistry= 1; 1.0; 273.15; 298.15; 398.15; 498.15; End of PT
End of input
The input section defining the internal coordinates always start with the keyword Internal coordinates and the definition of the constraints starts with the keyword Constraints. Note that the latter is an input section for the GATEWAY module.
The input is always sectioned into two parts where the first section defines a set of primitive internal coordinates and the second part defines the actual internal coordinates as any arbitrary linear combination of the primitive internal coordinates that was defined in the first section. In case of constraints the second part does also assign values to the constraints.
In the first section we will refer to the atoms by their atom label (SEWARD will make sure that there is no redundancy). In case of symmetry one will have to augment the atom label with a symmetry operation in parenthesis in order to specify a symmetry related center. Note that the user only have to specify distinct internal coordinates (ALASKA will make the symmetry adaptation).
In the specification below rLabel is a user defined label with no more than 8 (eight) characters. The specifications atom1, atom2, atom3, and atom4 are the unique atom labels as specified in the input to SEWARD.
The primitive internal coordinates are defined as
The second section starts with the label Vary or in the case of constraints with the label Values.
In case of a definition of internal coordinates in this section the user specifies all symmetric internal coordinates excluding translation and rotation using a list of expressions like
label = f1 rLabel1 + f2 rLabel2 + ....
which defines an internal coordinate label as the linear combination of the primitive internal coordinates rLabel1, rLabel2, ... with the coefficients f1, f2, ..., respectively. If the internal coordinate just corresponds to the primitive internal coordinate, the same label can be used
label
If some internal coordinates are chosen to be fixed they should be defined after
the label Fix. The fixed internal coordinate are defined with
expressions as in the section Vary. Observe: using expression can
introduce linear dependence and/or undefined nuclear coordinates, so use with care.
For the internal coordinates defined after Vary (and Fix, if present)
a numerical estimation of rows and columns of the hessian matrix can be performed. The
label of internal coordinates (max 10) must be specified after keyword RowH.
Keywords NUMErical and RowH are mutually exclusive.
In case of a definition of constraints the sections contains either a direct reference to a rLabel as in
rLabel = rValue [Angstrom,Degrees] [Soft,Hard]
or one can also use expressions like
f1 rLabel1 + f2 rLabel2 + .... = Value [Angstrom,Degrees] [Soft,Hard]
where rValue is the desired value of the constraint in au or rad, or in angstrom or degrees if the corresponding keyword is added. The ``Hard'' and ``Soft'' keywords are only meaningful for numerical differentiation: the coordinates corresponding to soft constraints are differentiated, those of hard constraints are not. By default almost all constraints are hard, only constraints of the type ``Sphere``, ``Transverse`` and ``Ediff`` default to soft. The ``Hard'' and ``Soft'' keywords override the default. When using constraints in combination with the FINDTS keyword, one should use soft constraints, at least for the constraint most similar to the expected reaction vector.
Alternatively, if the current value of an internal coordinate is to be used, i.e. no change is to be allowed (frozen), this is expressed as
rLabel = FIX
Example: A definition of user specified internal coordinates of benzene. The molecule is
in D_{6h} and since MOLCAS only uses up to D_{2h} the
Fix option is used to
constrain the relaxation to the higher point group. Observe that this will
only restrict the nuclear coordinates to D_{6h}. The electronic wavefunction,
however, can have lower symmetry.
Internal coordinates
r1 = Bond C1 C2
r2 = Bond C1 H1
r3 = Bond C2 H2
r4 = Bond C2 C2(x)
f1 = Angle H1 C1 C2
f2 = Angle H2 C2 C1
Vary
a = 1.0 r1 + 1.0 r4
b = 1.0 r2 + 1.0 r3
c = 1.0 f1 + 1.0 f2
Fix
a = 1.0 r1 + 1.0 r4
b = 1.0 r2 + 1.0 r3
c = 1.0 f1 + 1.0 f2
End of Internal
Example: A input for the optimization of water constraining the structure to be linear
at convergence.
&GATEWAY
Title= H2O geom optim, using the ANOS basis set.
Coord=$MOLCAS/Coord/Water.xyz
Basis=ANOSVDZ
Group= c1
Constraints
a1 = langle(1) H2 O1 H3
Values
a1 = 179.99 degrees
End of Constraints
>>> DO WHILE <<<
&SEWARD; &SCF
&SLAPAF
>>> END DO <<<
Example: A complete set of input decks for a UHF transition
structure geometry optimization of an identity hydrogen
transfer reaction (HO + H_{2}O > H_{2}O + OH).
&GATEWAY
ZMAT
O.STO3G....
H.STO3G....
H1
Z2 1 1.0
O3 1 1.15 2 92.
O4 1 1.15 2 92. 3 180.
H5 3 0.98 4 105.4 2 120.
H6 4 0.98 3 105.4 2 120.
>>> DO WHILE <<<
&SEWARD;
&SCF; UHF
&SLAPAF; TS; PRFC
Internal
bOO4 = Bond O3 O4
bOH5 = Bond H5 O3
bOH6 = Bond H6 O4
bOH1 = Bond O3 H1
aOOH5 = Angle O4 O3 H5
aOOH6 = Angle O3 O4 H6
aHOH1 = Angle H5 O3 H1
dH6 = Dihedral H6 O4 O3 H5
dH1 = Dihedral O4 H5 O3 H1
Vary; bOO4; bOH5; bOH6; bOH1; aOOH5; aOOH6; aHOH1; dH6; dH1
RowH; bOH1
End of Internal
>>> ENDDO <<<
vibrot.tex
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