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APPENDIX A. Parameters

Table I lists the parameters and their currently used default values. The
entries are mostly self-explanatory. The code uses the convention that the
reaction core in a microiterative transition state search must be the first
fragment. Therefore, the connectivity of this fragment can be defined
separately by a special parameter (ctfirst). If there is only a single
fragment, this parameter can be used to select an optimisation in DLC (rather
than HDLC).

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TABLE I.
List of the parameters used by the HDLC optimiser. See the documentation on
how to access them from a particular implementation (currently available: MNDO
and ChemShell). The number of atoms excluding frozen atoms is N. The number of
constraints is N_c. Parameters without default values are mandatory input.
Defaults assume atomic units for lengths and energies.

Param	Type	Default	Scope	Purpose and special values
-----	----	-------	-----	--------------------------
nvar	int	0	all	number of degrees of freedom of reaction core
maxfun	int	1000000	all	maximum number of energy / gradient evaluations
reghdl	int	0	all	number of optimisation cycles until a restart
				0: never restart

mstart	int	0	all	startup procedure, value:
				0: start up from scratch, no checkpoint is used
				1: start up using coordinates from checkpoint
				2: as mstart=1, residues and parameters too
				3: as mstart=2, optimiser's memory image too
				4: as mstart=3, electronic state too

idump	int	0	all	dump the memory every idump cycles
				0: never
mdump	int	0	all	mode of dump (see mstart)
				0: optimiser only
				1: as mdump=0, electronic state too (if avail.)

printl	int	0	all	print level

precon	real(N)	(1.0)	all	preconditioning vector for the gradient

attypes	real(N)	none	HDLC	nuclear charge of the atoms

contyp	int	0	HDLC	connectivity type of primitive internals
				0: primitives
				1: total connection
ctfirst	int	0	HDLC	connectivity type of the first residue
				0: primitives
				1: total connection
				2: Cartesians
				3: DLC from primitives

nincon	int	0	HDLC	number of user connections
incon	int(2,)	()	HDLC	user connections connections

mconstr	int	0	HDLC	type of constraints
				0: initially satisfied
				1: initially unsatisfied, not yet implemented
nconstr	int	0	HDLC	number of constraints, N_c
iconstr	int(4,)			constraints (bonds, angles, torsions)
		()	HDLC
vconstr	real()	()	HDLC	target values of constraints (if mconstr>0)

cfact	real	0.0	HDLC	scale factor for Cartesians
				0: 1/M, (M=number of primitives in the residue)
				<0: -cfact/M
				>0: cfact

dmax	real	0.02	L-BFGS	initial step size
			P-RFO	initial step size
ddmax	real	1.0	L-BFGS	maximum step size
			P-RFO	maximum step size
toler	real	0.00045	L-BFGS	tolerance, see table II
			P-RFO	tolerance, see table II

memory	int	(*)	L-BFGS	number of remembered L-BFGS steps

rmin	real	0.0	P-RFO	min. ratio actual / predicted energy difference
rmax	real	10.0	P-RFO	max. ratio actual / predicted energy difference

osmin	real	0.0002	P-RFO	minimum step size
omin	real	0.6	P-RFO	minimum overlap criterion

mode	real	1	P-RFO	eigenmode to be followed
				0: minimise the core

recalc	real		P-RFO	recompute the Hessian every recalc P-RFO cycles
		-1 (nvar=0)	-1: never
		0 (nvar>0)	0: only at the initialisation

iupd	int		P-RFO	Hessian update scheme
		1 (mode=1)	1: Powell
		2 (mode=0)	2: BFGS

mhess	int	0	P-RFO	Calculation of the Hessian
				0: finite difference
				1: use analytical Hessian if available

prjhes	int		P-RFO	project out R/T modes if no internal coords
		0 (nvar<3N)	0: off
		1 (nvar=3N)	1: on

lock	int	0	P-RFO	Hessian mode locking switch
				0: mode switching allowed
				1: lock the mode followed regardless of overlap
(*): min(40,3N-N_c)
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The default convergence criteria are taken from Gaussian94 (for reference, see
article). For completeness, they are listed in table II. The values are given
in atomic units. Note that HDLC cannot be expressed in atomic units; their
values are usually somewhat larger, but in a similar range as those of the
Cartesians.

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Table II.
Convergence criteria applied by the HDLC optimiser. They are all based on the
parameter toler whose default is 0.000450.

Quantity			Part of the system	Value
--------			------------------	----- 
Maximum step component		total system or core	4*toler
RMS step			total system or core	(8/3)*toler
Maximum gradient component	total system or core	toler
RMS gradient			total system or core	(2/3)*toler

Maximum step component		environment		1.0
RMS step			environment		1.0
Maximum gradient component	environment		(1/3)*toler
RMS gradient			environment		(2/9)*toler
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