DisconnectionDPS - Revision history

import>Jmc49 at 13:36, 27 November 2014

2014-11-27T13:36:07Z

← Older revision		Revision as of 13:36, 27 November 2014
Line 29:		Line 29:
	* ''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.		* ''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		* ''identify'' - branch endpoints are labeled with the index of the minima. Commonly used in conjunction with [[PATHSAMPLE]]'s ''EXTRACTMIN'' keyword.
	[[PATHSAMPLE]]'s ''EXTRACTMIN'' keyword.

	There are many other flags for centering the trunk, specifying output appearance etc.		There are many other flags for centering the trunk, specifying output appearance etc.

import>Csw34 at 17:04, 26 November 2014

2014-11-26T17:04:26Z

Show changes

import>Jmc49 at 16:11, 26 November 2014

2014-11-26T16:11:59Z

← Older revision		Revision as of 16:11, 26 November 2014
Line 56:		Line 56:

	--[[User:mp466]]		--[[User:mp466]]

			'''Example'''

			Disconnectivity graph at the end of this page is generated using the following minimal data.

			<pre>
			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

			</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]]

import>Jmc49 at 11:33, 26 November 2014

2014-11-26T11:33:40Z

← Older revision		Revision as of 11:33, 26 November 2014
Line 53:		Line 53:
	N.B. disconnectionDPS.f90 evolved out of '''disconnection.f90''', by Dr Mark Miller, which read in database files in a pre-PATHSAMPLE format.		N.B. disconnectionDPS.f90 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''' (manipulate.f90) which can reorganize the minima horizontally.		There's another program called '''manipulate''' (compiled from manipulate.f90) which can reorganize the minima horizontally.

	--[[User:mp466]]		--[[User:mp466]]

import>Jmc49 at 15:50, 25 November 2014

2014-11-25T15:50:02Z

← Older revision		Revision as of 15:50, 25 November 2014
Line 53:		Line 53:
	N.B. disconnectionDPS.f90 evolved out of '''disconnection.f90''', by Dr Mark Miller, which read in database files in a pre-PATHSAMPLE format.		N.B. disconnectionDPS.f90 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''' (manipulate.f90) which can ~~reorganized~~ the minima horizontally.		There's another program called '''manipulate''' (manipulate.f90) which can reorganize the minima horizontally.

	--[[User:mp466]]		--[[User:mp466]]

import>Jmc49 at 15:46, 25 November 2014

2014-11-25T15:46:16Z

← Older revision		Revision as of 15:46, 25 November 2014
Line 1:		Line 1:
	'''disconnectionDPS''' ~~is a hacked version of '''disconnection.f90''' that can read~~ in ~~pathsample~~ generated output		'''disconnectionDPS''' reads in PATHSAMPLE-generated output
	files ''min.data'', and ''ts.data''. It also has the ability of producing postscripts with ~~color~~.		files ''min.data'', and ''ts.data''. It also has the ability of producing postscripts with the lines coloured.
	The disconnection programs are currently only compiled with the Portland Fortran compilers.
	The input parameters are read from a file called ''dinfo''.

		⚫	The keyword-driven input parameters are read from a file called ''dinfo''. All the keywords are documented at the top of disconnectionDPS.f90 itself.
⚫	A ~~Minimal~~ example of dinfo

		⚫	A minimal example of dinfo:
	delta 15		delta 15
	first -490.0		first -490.0
Line 15:		Line 15:
	delta - energy difference between levels		delta - energy difference between levels

	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)		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.		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.		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.		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		identify - branch endpoints are labeled with the index of the minima. Commonly used in conjunction with
	pathsample's EXTRACTMIN keyword.		pathsample's EXTRACTMIN keyword.

		⚫	There are many other flags for centering the trunk, specifying output appearance etc.

⚫	There are many other flags for centering the trunk, ~~output files,~~ output appearance.

	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.

⚫	All the keywords are documented at the top of ~~the~~ disconnectionDPS.f90 ~~file~~ itself.


	The minima can be reorganized with '''manipulate.f90'''. Nodes are only moved horizontally.

	The minima can be coloured with the keyword TRMIN.		The minima can be coloured with the keyword TRMIN.
Line 59:		Line 51:
	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

			N.B. disconnectionDPS.f90 evolved out of '''disconnection.f90''', by Dr Mark Miller, which read in database files in a pre-PATHSAMPLE format.
	--[[User:mp466]] 15:15, 1 July 2008 (BST)

			There's another program called '''manipulate''' (manipulate.f90) which can reorganized the minima horizontally.

			--[[User:mp466]]

import>Jmc49 at 10:18, 6 September 2011

2011-09-06T10:18:39Z

← Older revision		Revision as of 10:18, 6 September 2011
Line 29:		Line 29:
	identify - branch endpoints are labeled with the index of the minima. May be used in conjunction with		identify - branch endpoints are labeled with the index of the minima. May be used in conjunction with
	pathsample's EXTRACTMIN keyword.		pathsample's EXTRACTMIN keyword.

import>Jmc49 at 10:17, 6 September 2011

2011-09-06T10:17:18Z

← Older revision		Revision as of 10:17, 6 September 2011
Line 10:		Line 10:
	minima min.data		minima min.data
	ts ts.data		ts ts.data
			connectmin <integer>

			identify

	delta - energy difference between levels		delta - energy difference between levels

Line 22:		Line 24:

	(Note that the format of the minima and ts data files is different from that expected by the original disconnection program...)		(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		identify - branch endpoints are labeled with the index of the minima. May be used in conjunction with
	~~pathsamples~~ EXTRACTMIN keyword.		pathsample's EXTRACTMIN keyword.

import>Jmc49 at 11:56, 4 May 2011

2011-05-04T11:56:35Z

← Older revision		Revision as of 11:56, 4 May 2011
Line 1:		Line 1:
	'''~~disconnection_DPS~~''' is a hacked version of '''disconnection.f90''' that can read in pathsample generated output		'''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.		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 disconnection programs are currently only compiled with the Portland Fortran compilers.
Line 30:		Line 30:

	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.

			All the keywords are documented at the top of the disconnectionDPS.f90 file itself.


	The minima can be reorganized with '''manipulate.f90'''. Nodes are only moved horizontally.		The minima can be reorganized with '''manipulate.f90'''. Nodes are only moved horizontally.

import>Jmc49 at 11:51, 4 May 2011

2011-05-04T11:51:19Z

← Older revision		Revision as of 11:51, 4 May 2011
Line 13:		Line 13:
	delta - energy difference between levels		delta - energy difference between levels

	first - qualifies highest energy state		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)

	levels - specifies number energy levels		levels - specifies number energy levels