Input files

This page describes the allowed input parameters, and a description of what they do. Please note the following:

• Note that input-file keywords are case-sensitive - everything should be lower-case!
• In the input file, lines beginning with '#' are comments.
• Blank lines are ignored.
• Keywords can appear in any order.

General input parameters

These parameters are used to control input, number of images, and other general aspects of the calculation.

Keyword	Type	Required	Description
calctype	string	Yes	Calculation type: • optpath - Minimum energy path optimization. • pathfind - Double-ended reaction-path finding.
startfile	string	Yes	Start-point / reactant xyz coordinate file used to initialize reaction-paths and pathfinding.
endfile	string	Yes	End-point xyz coordinate file.
pathfile	string	No	Initial path file in xyz format - used when startfrompath = .TRUE.
ranseed	integer	Yes	Random number seed (positive integer).
startfrompath	logical	Yes	Indicates whether to start from end-point files only (.FALSE.) or from a full path (.TRUE.).

Path optimization control

The following parameters are used to control the calculation when performing a path-optimization simulation (calctype optpath), for example using climbing-image nudged elastic band.

Keyword	Type	Required	Description
pathinit	string	No	If startfrompath = .FALSE., specifies the initial interpolation method: - linear is linear Cartesian interpolation. - idpp is image-dependent pair potential.
nimage	integer	No	Number of nudged elastic band images.
pathoptmethod	string	No	Path-optimization method - currently cineb only.
nebmethod	string	Yes	(CI)NEB optimization method. Options are: - fire for FIRE algorithm. - quickmin for QuickMin algorithm, - steepest for steepest-descent method (generally slow).
nebiter	integer	No	Number of (CI)NEB optimization iterations.
cithresh	float	No	RMS force threshold (in atomic units) at which climbing-image is activated.
nebspring	float	No	(CI)NEB spring constant in atomic units (Eh/bohr²).
nebstep	float	No	Step size for steepest descent or QuickMin (in atomic units).
neboutfreq	integer	No	Output frequency during (CI)NEB optimization.
optendsbefore	logical	No	Flag indicating whether to optimize reaction end-points before NEB refinement.
optendsduring	logical	No	Flag indicating whether to optimize end points simultaneously with path optimization.
nebrestrend	logical	No	Flag indicating whether to apply the graph-restraining potential during NEB optimization (also used in GDS).
vsthresh	logical	No	RMS force threshold (atomic units) at which variable spring strength is switched on.
reconnect	logical	No	For images 2 through N−1, linearly interpolates the coordinates of beads 1 and N after minimization (if optendsbefore is .TRUE.).
idppguess	logical	No	Performs NEB starting from an Image-Dependent Pair Potential (IDPP) guess (generally better idea).
projforcetype	integer	No	Selects the type of NEB projected force: - 1 is original formulation, - 2 is from Henkelman et al. (2000), - 3 is Kolsbjerg et al. (2016).
stripinactive	logical	No	Controls whether "inactive" molecules are removed from the initial NEB path before refinement.
nebconv	float	No	NEB RMF force convergence threshold (in atomic units).
nebmaxconv	float	No	Maximum-force convergence threshold (in atomic units) for NEB optimization.

Constraint controls

These inputs controls the constrained atoms and degrees-of-freedom in GDS calculations and geometry-optimization calculations.

Tip

None of the following are required input parameters.

• dofconstraints

The dofconstraints input comprises two lines, as in the following example:

 dofconstraints 6
 1 2 3 5 6 9

This input gives the number of fixed DoFs (in this case, 6), with the second line in the input file listing the integer-values of the fixed DoFS. Here, counting starts at 1 for the x-coordinate of atom 1. The z-coordinate of atom 2 has the integer value of 6, and so on.

Warning

Once defined, the constrained DoFs will remain fixed throughout any NEB calculation; these DoFs are simply not optimized.

• atomconstraints

The atomconstraints input has the same format as dofconstraints, but the integers now refer to the number of fixed atoms, and the indices of the fixed atoms. In the following, 1 atom is fixed - atom number 13:

 atomconstraints 1
 13

• alignedatoms (experimental)

The alignedatoms input allows one to define three atoms which will be used to position and orient any input molecular structure in space. This can be very useful when performing NEB calculations as it helps remove overall translations and orientations of the molecules in the optimized string. Note that the NEB routines will automatically select 3 atoms to position and orient if you don't input anything as alignedatoms. In the following example, atoms 1, 2 and 3 are chosen to define the relative position and orientation.

 alignedatoms
 1 2 3

Warning

The alignedatoms are not fixed during optimization; they are just used during initial path approximation.

PES controls

These input parameters control potential energy evaluations during GDS and NEB calculations.

Keyword	Type	Required	Description
pesfull	logical	Yes	If .TRUE., we perform PES evaluations and geometry optimizations for the full system (that is, all atoms) each time. If .FALSE., we separately calculate the energy for each independent molecule in the structure.
pestype	string	Yes	Defines single-point PES evaluation code to use. options are: - orca for the ORCA code, - dftb for DFTB, - lammps for LAMMPS, - null for no PES evaluation (GRP optimization only).
pesfile	string	No	Defines the filename containing the header information to be used for PES single-point calculation.
pesopttype	string	No	Defines the geometry optimization PES code to be used. Options are: - orca for ORCA, - dftb for DFT, - uff for universal force-field implemented in OpenBabel, - null for no optimization.
pesoptfile	string	No	Defines the filename containing the header for geometry-optimization calculation.
pesexecutable	string	No	Defines the executable to use to for single-point PES evaluation (full path or alias).
pesoptexecutable	string	No	Defines the executable to use to for geometry optimization (full path or alias).

Warning

For NEB calculations, pesfull must be set to .TRUE. because uniquely identifying independent molecules along a reaction path becomes tricky.

Graph-driven sampling controls

The following control the varisou (single-ended and double-ended) GDS calculations.

Keyword	Type	Required	Description
movefile	string	No	Identifies the filename of the move-file used to define allowed graph moves.
gdsspring	float	No	Inter-bead spring constant for GRP (defaul: 0.025 Eh/Bohr**2).
gdsrestspring	float	No	Spring constant for harmonic graph enforcement terms (default: 0.1 Eh/Bohr**2).
nbstrength	float	No	Repulsion strength for non-bonded atoms, where: \(V = nbstrength * exp(-r_{ij}^2 / (2 * nbrange^2))\).
nbrange	float	No	Range parameter for non-bonded atoms (default: 2.0 Bohr).
kradius	float	No	Spring constant for non-interacting molecules in GDS simulations (defaul: 0.1 Eh/Bohr**2).
ngdsrelax	integer	No	Number of steepest-descent optimization steps to minimize graph restraint potential (default: 2000).
gdsdtrelax	float	No	Step-size for GDS relaxation (default: 0.05 Bohr).
gdsoutfreq	integer	No	Information output frequency during GDS simulation.
nebrestrend	logical	No	Flag indicating weather to apply to it duing the optimization of molecules during GDS, if optaftermove is .TRUE. (also used in CINEB).
optaftermove	logical	No	Optimizes every molecule involved in the path formation - if the resulting optimised molecule does not conform to the graph, the proposed path is rejected. If nebrestrend .TRUE., the graph constraining potential are also included during the optimization, and then switched off during a second, in the hope to find a minima in agreement with the graphs (would recommend to set nebrestrend .TRUE. for this).

In addition to the keywords above, GDS calculations can also be controlled by the following complex optional inputs:

• valencerange

This input defines the allowed valence ranges of each element, as in the following example:

valencerange{
C 1 4
O 1 2
H 0 1
Pt 0 3 fz
}

Here, carbon atoms can only be bonded to between 1 and 4 other atoms, oxygen can be bonded to 1-to-2 other atoms, and so on. These constraints are applied when generating new reaction species in GDS simulations.

The fz keyword applies only to frozen atoms, either by being defined in the fixedbonds{} input (see below), or by the atomcontraints keyword. In the example given above, only Pt-X bonds (X = any atom) which can be formed or broken during the GDS calculation are counted into the 'valence'. If a cluster of Pt atoms are not moving during a GDS calculation, and they are bonded to each other (to varying degrees), the above keyword will allow for up to 3 more bonds, not counting the Pt-Pt bonds, to be formed on the Pt atoms.

• reactiveatomtypes

This keyword defines which elements are allowed to react during GDS runs, as follows:

reactiveatomtypes{
C
O
H
}

Warning

If no reactive atoms are defined explicitly, cde assumes that nothing can react!

• reactiveatoms

This keyword defines which atom numbers (indices) are allowed to react. These can be given as an inclusive range (range XX YY), or by individual atom-index number (id XX), as in the following example:

reactiveatoms{
range 1 4
id 7
}

Warning

Atom indices start at 1!

• reactivevalence

This keyword defines the valence range that one element can have while bonded to another element, as follows:

reactivevalence{
Fe Fe 6 8
    H C 0 1
    H O 0 1
}

In the above, Fe must be bonded between 6 to 8 other Fe atoms to be an acceptable molecule. Similarly, the second line indicates that hydrogen can only be bonded up to 1 carbon atom.

• fixedbonds

This keyword defines fixed bonds, which are not allowed to change during a chemical reaction (although they can vibrate, translate, etc.):

fixedbonds{
C O
3 4
}

In the above example, all C-O bond orders are fixed at whatever they are in the starting structure. So, if a C-O bond is present in the starting structure, it cannot change during the GDS simulation. Similarly, the bond between atoms 3 and 4 is also fixed at the starting structure value.

• essentialmoveatoms

Defines a list of atoms of which AT LEAST ONE OF THEM MUST be included in any possible graph moves. The formatting options are the same as the reactiveatoms block described above, for example:

essentialmoveatoms{
range 1 2
}

In the above example, the atoms in the range 1-2 must be included amogst the moves chosen.

• essentialatoms

Defines atoms of which AT LEAST ONE OF THEM MUST be included in molecules that are involved in the reactions. The formatting options are the same as the reactiveatoms block described above, for example:

essentialatoms{
id 5
id 7
}

In the above example, the atoms 5 and 7 must be in any of the molecules that are involved in the reaction (from chemical species image 1 changing to nimage)

Warning

In the latest version of CDE, the implementation of essentialatoms and essentialmoveatoms needs debugging....

• allowedbonds

Allows definition of bond-number constraints in the structures generated by graph moves. The format is as given in the following example:

allowedbonds{
O O 1
}

Here, the constraint indicates that an oxygen atom cannot be bonded to more than 1 other oxygen atom.

• forbidgraphs

This is a logical flag which indicates whether or not to use the forbidden graph pattern file. If .TRUE., then a GDS simulation will not allow any graph-patterns to form which are input into the forbidfile defined below. By adding entries to the forbidfile, users can force GDS to stop generating user-defined bonding patterns.

• forbidfile forbid.in

Identifies the file (here, forbid.in) which contains the library of forbidden bonding patterns which are used if forbidgraphs = .TRUE..

Path-finding controls

The following parameters control the double-ended reaction-path finding algorithm.

Keyword	Type	Required	Description
nrxn	integer	No	Total number of elementary steps allowed in mechanism.
nmcrxn	integer	No	Maximum number of Monte Carlo moves to attempt during simulated annealing optimization.
nmechmove	integer	No	Maximum number of mechanism updates in each MC step.
mcrxntemp	integer	No	Initial temperature (in K) for simulated annealing optimization (decreases linearly during run).
graphfunctype	integer	No	Determines the optimization function used for the path-finding calculation. This should be an integer, as follows: (1) Standard element-wise comparison, (2) Eigenvalue comparison, (3) Histogram comparison, (4) Eigenvalue comparison for single molecule. You should preferably use either (2) or (4)!

Warning

In addition to the keywords above, the following keywords cna be defined to influence charge constraints. Note that these options have not yet been thoroughly tested.

Keyword	Type	Required	Description
minmolcharge	integer	No	Minimum allowed molecular charge (if electron transfer moves are allowed in the movefile).
maxmolcharge	integer	No	As above, but maximum value.
nchargemol	integer	No	Maximum number of molecules which can be charged.
maxstepcharge	integer	No	Maximum number of reation steps which can involve charge changes.
maxtotalcharge	integer	No	Maximum total charge in a given reaction step.