Optional Keywords

• AUTORANGE : Choose FIRST and MAXTSENERGY to include all the connected minima with one level above and below the range. We try to arrange for zero to be an energy value on the vertical axis. The number of levels is chosen with the -1 option.

• BASINT energy: If this keyword is present, the outcome of a basin analysis at the specified energy is written to a file `basins'.

• CENTREGMIN: If this keyword is present, then when a node splits into its daughter nodes, the one containing the global minimum is always placed centrally (even if other nodes carry more minima). This does not guarantee that the global minimum is central in the overall diagram because other nodes may push the one containing the global minimum over to one side.

• CHOOSECOLOURS: Use in combination with TRMIN to have specific colours for groups of minima, rather than a rainbow spectrum.

• COLOURONLYMIN: only colour branches that correspond to single minima for TRVAL. The default behaviour is to use the darkest colour for branches between nodes that correspond to multiple minima. This keyword show also work with NEWTRVAL.

• COLOURFRONT: put the coloured branches in the front of default black branches.

• COLOURPRINT: For use with TRMIN, if present colour analysis written to `node_sections'. Not actually required for colour analysis.

• CONNECTMIN min: If present then the analysis for a connected database is based upon minimum number min. If absent then the global minimum is used to define the connected component to be plotted on the graph.

• DEFAULTCOLOUR r g b: sets the default line colour with
  r g b setrgbcolor
  The default is black, but coloured graphs may look better with default gray lines using 0.5 for each rgb entry.

• DUMPNUMBERS: If present, a file called `node_numbers' is written, listing the minima associated with each node in each level. Nodes are listed from left to right within each level.

• DUMPSIZES: If present, a file called `node_sizes' is written, listing how many minima are represented by each node in each level. Nodes are listed from left to right in each level.

• EXCLUDEALL: Removes all minima from the list of minima to be plotted. This is to be used in conjunction with the PICK command which can be used to specify exclusively which minima are to be included.

• IDENTIFY: If present, the branch ends are labelled with the lowest-energy minimum they represent.

• IDENTIFY_NODE max_min: If present, the nodes are labelled with the format N1_N2, where N1 is the number of level, N2 is the number of the node at that level. The label is only printed if the number of minima below that node is smaller than max_min. With this info you can pick the number of minima corresponding to that node from the `node_numbers' file, produced by using the keyword DUMPNUMBERS (and then print any branch of the graph separately).

• IDENTIFY_NODE_SIZE max_min2: If present, the nodes are labelled with number of minima corresponding to that node. The label is only printed if the number of minima below that node is smaller than max_min2.

• IDMIN min: Label the minimum min on the graph. Repeat to label more than one minimum.

• IDMINFILE file: Label the minima specified in file in the same way as IDMIN. Can use the same file as for PICK to label selected minima, e.g. using `min.include' and PERSIST keyword in PATHSAMPLE

• LABELFORMAT fmt: Specifies the Fortran format string for the energy level labels. The default is F6.1.

• LABELSIZE n: Set the size of the fonts in case of the labels (for IDENTIFY, IDENTIFY_NODE etc.). Default is 14 pt.

• LETTER: If present, the graph is formatted for American letter paper rather than ISO 216 A4.

• LOWEST n: If present, only the branches leading to the lowest n minima are drawn. The pruning occurs after the basin analysis, so the ``discarded'' minima can still influence the connectivities.

• MAXTSBARRIER threshold: Ignore transition states with both barriers above threshold.

• MAXTSENERGY threshold: Ignore transition states above threshold.

• MINBARRIER threshold: ignore transition states with either barrier below this threshold. Default is -1.0D100.

• MONOTONIC: If present, all minima not lying at the bottom of a monotonic sequences are not drawn. This tends to reduce the number of branches drastically. If the keyword LOWEST is also used, the MONOTONIC sequence analysis is applied after the high energy minima have been discarded.

• MONOEDIFF ediff: If present, all minima not lying at the bottom of a monotonic sequences are not drawn, as for MONOTONIC, but energy differences in defining basin bottoms must be greater than the ediff condition. This allows all degenerate minima corresponding to monotonic basin bottoms to be included.

• NCONNMIN n: Minima with n connections or fewer are discarded. Default is zero.

• NOBARRIERS: If present, all transition state energies are reset to the energy of the higher of the two minima they connect. This transforms the energy landscape to the type explored by GMIN.

• NOSPLIT: By default, every minimum is indicated by its own branch, which splits off from the parent basin even if the minimum and its lowest transition state do not straddle an energy level in the basin analysis. This is to avoid it being dependent on precisely where the levels are placed (bulk shifting of the levels would cause some branch ends to appear or disappear rather than change node if this were not the case). The NOSPLIT option turns this feature off, so that if two minima are separated by a barrier lower than the level above their own energy, they are grouped together. This option should probably never be used.

• ORDER_BY_ENERGY: If this keyword is present, then when a node splits into its daughter nodes, the lower energy nodes are closer to the centre.

• ORDER_BY_SIZE: If this keyword is present, then when a node splits into its daughter nodes, the nodes that represent larger basins are closer to the centre. This keyword is compatible with keyword CENTREGMIN

• PAIRS n max file file ...: Show the paths between pairs of minima in different colours and assign colours according to the connectivity of the graph. This is useful if you want to show how transitions of a particular type such as cagebreaks span the landscape. For simple colouring use TRMIN or TRVAL. This keyword works in two different ways dependent on the input. (a) Pairs of minima in the different files (number of files specified by n) are coloured, with a different colour for each file. (b) Pairs of minima in one file are all coloured differently. A value of zero for n requests this colour scheme. Each file should be a list of numbers of minima, two per line showing a pair. max is the number of lines in the longest file, currently used for array allocation. For both (a) and (b), these are the starting colours, and if pairs of minima are found to be connected together, colours are reassigned so that they have the same colour. Colours are chosen automatically to be as spread out as possible. Colours can be specified individually with CHOOSECOLOURS. This cannot be used at the same time as TRMIN/TRVAL.

• PAIRSONLY: Used with pairs, this keyword means that any min/nodes that are uncoloured will not be drawn. The tree is constructed as before with spaces left for the missing structure

• PICK file: Specifies the name of a list of numbers of minima, one per line. Minima on this list are included on the graph. Minima preceded with a minus sign are removed from the graph. This process is executed after the commands MONOTONIC, LOWEST and EXCLUDEALL have been executed, thereby making it possible to override them for particular minima. Examples: 1. To remove certain minima from a full plot, just specify PICK and a list of negative minima numbers. 2. To include only specific minima, use EXCLUDEALL and PICK plus a list of positive minima numbers. All basin analysis includes the full sample and is performed before minima are removed or added back in.

• PRINTCONNECTED: Writes file `connected' which lists all of the minima included in the subdatabase when a disconnectivity graph is produced (i.e. it lists all of the minima plotted on the tree itself).

• PS_PAGE_X n: Set the width of the output Postscript file.

• PS_PAGE_Y n: Set the height of the output Postscript file.

• SCALEBAR ndelta: specifies a scale bar instead of a vertical axis with height ndelta times dE.

• SCALEPOS x y: specifies bottom position of scale bar: x and y are integers. Use gv to determine a good placement. The default scale bar position is at the bottom left of the graph.

• SPREADTERMINI : Spread terminating minima out within the horizontal range for daughter node range. The default is to scale the horizontal position according to the energy by the fraction of the vertical range. May work best with ORDER_BY_ENERGY.

• SQUEEZELEVEL lev fac : squeezes nodes for level lev and lower by factor fac. This option helps to keep sets of nodes apart, especially if there are single minima branching from adjacent parents that come very close in the level below. May work best for lev set to the level where mode nodes branch off, with fac around 0.9 To see where the nodes branch look in the standard output for diconnectionDPS.

• TRMIN n max file file ...: Label n different sections of the graph in colour as specified by the minima in each file, one file for each section. Each file is a list of numbers of minima, one per line as for PICK. max is the total number of minima, not the number in the colour files, currently used for array allocation. In other words, max is the total number of minima in the entire database corresponding to the MINIMA keyword file. Colours are chosen automatically to spread over a rainbow spectrum (from red to purple) in the order the files are specified, unless CHOOSECOLOURS is also set, in which case colours are specified individually. Branches are coloured if all the minima below lie in the same set.

• NEWTRMIN n file file ...: same as TRMIN above, but does not require the number of minima. The MINIMA keyword must precede NEWTRVAL so that the number of minima can be determined from the specified file. Branches are coloured if all the minima below lie in the same set.

• TRVAL max filename cscale weightlower cshift: Colour the graph according to an order parameter value for each minimum. The order parameters are read in from the named file, which should contain one line per minimum. The expected range of the order parameters is [0,1] inclusive. max is the total number of minima in the entire database corresponding to the MINIMA keyword file. Colours are chosen automatically to be evenly distributed with order parameter value along the edges of the RBG colour cube: red -> yellow -> green -> cyan -> blue. The optional arguments cscale and cshift scale and shift order parameters that do not already lie in the range [0,1]. cscale=1/(max-min) multiplies the order parameters to give values between min and min+1 and if min is not zero, it should be combined with cshift=-min. The optional argument weightlower is true or false, and when true, shifts the colouring emphasis of the main branch to colours corresponding to lower values (i.e. towards red), rather than the default emphasising higher values (i.e. towards blue).

• NEWTRVAL filename cscale weightlower cshift: same as TRVAL above but does not require the number of minima. The MINIMA keyword must precede NEWTRVAL for allocation purposes. If the number of entries in file filename is less than the number of minima the program will stop with an error message. For TRVAL inconsistencies between the number of entries will lead to random colouring with no warnings. See NEWTRVALLIST for a way to colour only subsets of minima.

• NEWTRVALLIST filename cscale weightlower cshift: same as NEWTRVAL but only colours the minima listed in the file filename where each line must contain the position of the minimum in the min.data file followed by the value of the order parameter. The MINIMA keyword must precede NEWTRVALLIST for allocation purposes. See TRVALSCALE to scale order parameters to a given range.

• TRVALRANGE trmin trmax: Specify maximum and minimum values for order parameters that are not scaled to the range [0,1].

• TRVALSCALE x y: Currently only for use with TRVAL. Creates a colour scalebar displaying the order parameter values for each colour. x and y (in postscript units) are optional and overide the default values.

• TSTHRESH threshold: Ignore transition states above threshold.

• WEIGHTS file: If present, use weights in file to scale the horizontal width. The expected format of file is bin number Vmin Vmax ln weight

• WIDELINECOL x: For use with TRMIN. To highlight the coloured branches of the disconnectivity graph their width is set to x times 1.5 pt. The default value for x is three.

• ZEROGM: Shift all energies so that the global minimum (or the lowest-energy minimum in the connected component to be plotted) is at 0.