DisconnectionDPS
disconnectionDPS reads in PATHSAMPLE-generated output files min.data, and ts.data and produces disconnectivity graphs as postscripts with the lines coloured if required. The source code you need to compile to use it, disconnectionDPS.f90 can be found in svn/DISCONNECT/source and evolved out of disconnection.f90, by Dr Mark Miller, which read in database files in a pre-PATHSAMPLE format.
There's another program called manipulate (compiled from manipulate.f90) which can reorganize the minima horizontally.
Basic usage
The keyword-driven input parameters are read from a file called dinfo. All the keywords are well documented at the top of disconnectionDPS.f90 itself so please check there for more info.
A minimal example of dinfo:
delta 15 first -490.0 levels 10 minima min.data ts ts.data connectmin <integer> identify
- delta - energy difference between levels
- first - the highest energy state (the energy at the top of the graph, which should be chosen in combination with delta and levels so that you include everything you need to in the graph)
- levels - number of energy levels
- minima - file name of pathsample-style database file for minima. The first column must contain the energies; other columns are ignored.
- ts - file name of pathsample-style database file for transition states. 1st column: ts energy, 2nd and 3rd columns ignored, 4th and 5th must contain the indices of the connected minima. Other columns ignored.
- connectmin - in case there are disjoint sets of stationary points in the network (2 or more "islands" of stationary points connected only among themselves), we need to specify a minimum in the one set we are using to plot the tree (other islands will be ignored). It's usual to choose the index of one of the end point minima here.
- identify - branch endpoints are labeled with the index of the minima. Commonly used in conjunction with
PATHSAMPLE's EXTRACTMIN keyword.
There are many other flags for centering the trunk, specifying output appearance etc.
e.g. TSTHRESH and NCONNMIN, which have the same meaning as in PATHSAMPLE.
Colouring disconnectivity graphs
The minima can be coloured with the keyword TRMIN.
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, currently used for array allocation. Colours are chosen automatically to spread over a rainbow spectrum from red to purple) in the order the files are specified but colours can be specified individually at both COLOURMARKER in this file.
Additional useful keywords
- IDENTIFY_NODE <max_min> - If present, the nodes are labelled with the format N1_N2, where N1 is the number of the level, N2 is the number of the node at that level. The label is only printed if the number of minima corresponding to that node is smaller than <max_min>. With this information you can pick the numbers of minima correspondig to that node from the node_numbers file, if you also use the keyword DUMPNUMBERS (this allows you to print lonely any branch of the graph)
- IDENTIFY_NODE_SIZE <max_min2> - If present, the nodes are labelled with number of minima corresponding to them. The label is only printed if the number of minima below that node is smaller than <max_min2>
- LABELSIZE <n> - Set the size of the fonts in case of the labels (for IDENTIFY, IDENTIFY_NODE ...) Default is 10 pt
Example input and tree
The disconnectivity graph at the end of this page is generated using the following minimal data.
min.data
-15.7913383765
-15.3716324466
-15.2784553206
-14.8659752677
-14.6100290941
-14.8438888038
-14.6764387368
-13.0780207279
-13.4244465071
-13.9001397862
-14.5806991903
-13.6343028913
-13.5476311019
-13.5126028070
-13.0539318357
-13.0163471646
-12.7055024827
-12.6813905441
-13.4050227255
-12.1526874944
-9.7569601664
-9.7148834959
-8.7968335848
-2.0878308039
ts.data
-14.2438874029 5826.5019096289 1 1 2
-15.2517267073 5827.5883722365 1 3 2
-10.2756028420 5827.4074472537 1 2 4
-11.0550139083 5825.3479865211 1 5 5
-13.8074137761 5826.9428935509 1 5 5
-7.6472310832 5826.9433203303 1 1 6
-12.8852878968 5824.8742593541 1 7 8
-13.3238664334 5825.6041392600 1 9 1
-12.9444594557 5825.1824609061 1 9 8
-12.7805774208 5826.8177504070 1 4 5
-13.7400373656 5825.4148653061 1 10 11
-13.8959304882 5826.6450829981 1 10 1
-3.2396889015 5828.5328625030 1 12 3
-13.2619122721 5824.3361632898 1 13 13
48.4726283410 5818.2346547985 1 8 8
-12.8887781792 5827.1724658342 1 8 13
-13.0953446099 5826.7702086467 1 5 14
-13.0215442112 5826.6120915114 1 15 14
0.7698391921 5824.4745501501 1 1 16
-12.6932634722 5825.9036641463 1 12 17
-12.4325102543 5821.7090181589 1 10 18
-6.3998183560 5827.2535916747 1 6 19
-11.3289351693 5829.2973732454 1 20 19
-2.8817399907 5826.4760021864 1 14 21
-13.1335758793 5824.1488659044 1 9 9
-9.6073361906 5824.0565145759 1 13 22
43.8029317350 5823.6592937778 1 1 1
-13.6311667473 5823.3016775888 1 10 10
-8.7957862666 5824.6265631264 1 11 23
-15.5132994561 5828.0978042406 1 1 1
46.0819609649 5824.3818189221 1 6 6
-1.8455167037 5823.9083945062 1 2 24
-12.6466356094 5826.9370977040 1 6 17
dinfo
delta 1.0 first 5 levels 25 minima min.data ts ts.data
Other columns may be present in min.data and ts.data to the right of those given above; they will just be ignored by disconnectionDPS. There will be more columns in the files produced by PATHSAMPLE. The energy of the stationary point is the first column in both cases. The line number is the index within the database. In ts.data, column 2 is the log-product of positive Hessian eigenvalues (ignored here), column 3 is the order of the point group (also ignored) and columns 4 and 5 are the indices of the connected minima (referring to min.data).
Note that transition states that connect a minimum to itself (e.g. TS's 14, 15, etc) are ignored. Parameter first in dinfo is set to a value greater than the maximum TS energy. Parameters levels and delta are set such that delta x levels > max(TS) - gmin. In the above example:
max(TS) = 0.7698391921 < first
gmin = -15.7913383765
max(TS) - gmin = 16.56 < delta x levels.