Difference between revisions of "DisconnectionDPS"

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'''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.
−
'''disconnectionDPS''' is a hacked version of '''disconnection.f90''' that can read in pathsample generated output
  
−
files ''min.data'', and ''ts.data''. It also has the ability of producing postscripts with color.
  
−
The disconnection programs are currently only compiled with the Portland Fortran compilers.
  
−
The input parameters are read from a file called ''dinfo''.
  
   
  +
There's another program called '''manipulate''' (compiled from manipulate.f90) which can reorganize the minima horizontally.
−
A Minimal example of dinfo
  
−
delta 15
  
−
first -490.0
  
−
levels 10
  
−
minima min.data
  
−
ts ts.data
  
   
  +
==Basic usage==
−
delta - energy difference between levels
 
  +
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:
−
first - qualifies 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)
  
  +
<pre>
  +
delta 15
  +
first -490.0
  +
levels 10
  +
minima min.data
  +
ts ts.data
  +
connectmin <integer>
  +
identify
  +
</pre>
  +
  +
* ''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 - specifies number energy levels
 
   
  +
* ''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.
 +
* ''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.
−
(Note that the format of the minima and ts data files is different from that expected by the original disconnection program...)
  
   
  +
* ''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. May be used in conjunction with
  
−
pathsamples EXTRACTMIN keyword.
  
   
  +
* ''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, output files, output appearance.
 +
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.
+
e.g. ''TSTHRESH'' and ''NCONNMIN'', which have the same meaning as in [[PATHSAMPLE]].
   
  +
==Colouring disconnectivity graphs==
−
All the keywords are documented at the top of the disconnectionDPS.f90 file itself.
  
  +
The minima can be coloured with the keyword ''TRMIN''.
   
  +
<pre>
  +
TRMIN <n> <max> <file> <file>
  +
</pre>
   
−
The minima can be reorganized with '''manipulate.f90'''. Nodes are only moved horizontally.
  
−  
−
The minima can be coloured with the keyword TRMIN.
  
−  
−
TRMIN <n> <max> <file> <file>
  
−  
−
From Vanessa, '
 
 
Label n different sections of the graph in colour as specified by the minima in each 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.
 
one file for each section. Each file is a list of numbers of minima, one per line as for PICK.
Line 47: Line 48:
 
specified but colours can be specified individually at both COLOURMARKER in this file.
  
specified but colours can be specified individually at both COLOURMARKER in this file.
   
  +
==Additional useful keywords==
−
From Livia:
  
  +
* ''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 <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>
−  
−
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
 +
* ''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'''
  +
<pre>
  +
-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
  +
</pre>
  +
  +
'''ts.data'''
  +
<pre>
  +
-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
  +
</pre>
  +
  +
'''dinfo'''
  +
<pre>
  +
delta 1.0
  +
first 5
  +
levels 25
  +
minima min.data
  +
ts ts.data
  +
</pre>
  +
  +
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''.
   
  +
[[Image:Disconn_example2.png]]
−
--[[User:mp466]] 15:15, 1 July 2008 (BST)
  

Latest revision as of 14:36, 27 November 2014

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.

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