CamCASP/Notes/4 - Revision history

import>Am592: /* Converting units */

2009-04-08T16:33:48Z

Converting units

@@ Line 12: / Line 12: @@
 Energy
   Read energy_file.dat
   Write energy_file_kJ.dat
 End

import>Am592: /* VIM tricks */

2009-03-30T13:39:06Z

VIM tricks

← Older revision		Revision as of 13:39, 30 March 2009
Line 39:		Line 39:
	:map t ^vllly$a Type ^[p^[		:map t ^vllly$a Type ^[p^[
	</pre>		</pre>
			The first '^' is the usual '^' character, but the '^[' at the end are obtained using <CRTL>-v-<ESC>. So cut-and-paste will not work. You've got to type in this sequence.

	Then search for ''Rank'' and type ''t''.		Then search for ''Rank'' and type ''t''.

import>Am592: /* Creating an energy file */

2008-12-02T16:35:46Z

Creating an energy file

← Older revision		Revision as of 16:35, 2 December 2008
Line 78:		Line 78:
	The file ''energy_saptdft.dat'' should look something like:		The file ''energy_saptdft.dat'' should look something like:
	<pre>		<pre>
			TITLE
	Energies in kJ/mol
			MOL-A
			MOL-B
			POINTS 500
			ENERGY-UNITS KJ/MOL
			LENGTH-UNITS
			ANGLE-UNITS

	LABELS INDEX Rx Ry Rz alpha Nx Ny Nz		LABELS INDEX Rx Ry Rz alpha Nx Ny Nz
Line 88:		Line 94:
	...		...
	</pre>		</pre>
	So it is in almost the correct format. You need to ~~add~~ the preamble:		So it is in almost the correct format. You need to fill up the preamble. For example, the complete pre-amble might look like:
	<pre>		<pre>
	TITLE Energy scan of MOL-A by MOL-B		TITLE Energy scan of MOL-A by MOL-B
Line 101:		Line 107:
	ANGLE-UNITS DEGREE		ANGLE-UNITS DEGREE
	</pre>		</pre>
	Or ~~whatever~~ is ~~appropriate~~ in ~~your~~ ~~case~~. ~~These~~ ~~fields~~ ~~are~~ used by CamCASP, so make sure they are correct.		Yes, you can have multiple ''TITLE'' fields. The first few will be used by CamCASP, the rest will be ignored. The other fields are more important, so make sure they are correct. In particular, get your units correct!

	And you will also need to add the last two lines:
	<pre>
	END
	END-FILE
	</pre>
	That is all you need do, unless you want to fill up the ''Elst-Asymp'', ''Ind2-Asymp'', ''Disp-Asymp'' and		That is all you need do, unless you want to fill up the ''Elst-Asymp'', ''Ind2-Asymp'', ''Disp-Asymp'' and
	''Delta'' fields. For the first three you will need to use '''ORIENT''' and the '''batch_ORIENT.pl''' script. The last one, ''Delta'', is any energy correction you would like to include. See [[ CamCASP/Notes/6 \| Overlap Models ]] for more details.		''Delta'' fields. For the first three you will need to use '''ORIENT''' and the '''batch_ORIENT.pl''' script. The last one, ''Delta'', is any energy correction you would like to include. See [[ CamCASP/Notes/6 \| Overlap Models ]] for more details.

import>Am592: /* Converting units */

2008-12-02T16:13:36Z

Converting units

← Older revision		Revision as of 16:13, 2 December 2008
Line 19:		Line 19:
	NOTES:		NOTES:
	# The advantage of this over any script is first of all speed --- the code's already written for you so why bother writing your own.		# The advantage of this over any script is first of all speed --- the code's already written for you so why bother writing your own.
			# '''PROCESS''' can read in multiple files --- say, from multiple energy-scan runs --- each with its own set of units (encoded in the files), and it (should) all work correctly. '''PROCESS''' will write out ''one'' energy file containing all the data.
	# ~~Second~~, '''PROCESS''' will convert from ''any'' of the recognised energy units to kJ/mol and it knows what units the energies are in as this information is in the energy file. Here's an example of the header of an energy file:		# Third, '''PROCESS''' will convert from ''any'' of the recognised energy units to kJ/mol and it knows what units the energies are in as this information is in the energy file. Here's an example of the header of an energy file:
	<pre>		<pre>
	TITLE Energy scan of MOL-A by MOL-B		TITLE Energy scan of MOL-A by MOL-B
Line 32:		Line 33:
	ANGLE-UNITS DEGREE		ANGLE-UNITS DEGREE
	</pre>		</pre>
	# And you could have read in multiple files, each with its own set of units and it (should) all work correctly.

	==VIM tricks==		==VIM tricks==

import>Am592: /* VIM tricks */

2008-12-02T16:07:49Z

VIM tricks

← Older revision		Revision as of 16:07, 2 December 2008
Line 40:		Line 40:
	</pre>		</pre>
	Then search for ''Rank'' and type ''t''.		Then search for ''Rank'' and type ''t''.

			==Creating an energy file==
			You will need an energy file (and overlap file) when creating an overlap model. The energy file should be in a the format (for example):
			<pre>
			TITLE Energy scan of MOL-A by MOL-B
			TITLE pyridine1 and pyridine2
			TITLE Basis sadlej and type MC
			TITLE Midbonds NONE and type weighted
			MOL-A pyridine1
			MOL-B pyridine2
			POINTS 500
			ENERGY-UNITS KJ/MOL
			LENGTH-UNITS BOHR
			ANGLE-UNITS DEGREE
			LABELS INDEX Rx Ry Rz alphaNx Ny Nz
			E(1)elst E(2)ind E(2)disp E(1)exch E(2)exind E(2)exdisp
			TotOverlap Elst-Asymp Ind2-Asymp Disp-Asymp Delta
			1 -5.870040E-01 3.957260E+00 9.016280E+00 1.227930E+02 -9.097780E-01 -1.008600E-01 4.026560E-01
			1.087500E-01 -2.364920E+00 -9.875980E+00 4.871440E+00 0.0E+00 0.0E+00 0.0E+00
			0.0E+00 0.0E+00 0.0E+00 0.0E+00
			...
			...
			END
			END-FILE
			</pre>
			If you have performed the energy scan using the '''ENERGY-SCAN''' module in CamCASP, then this file will be in such a format. But if you have performed a number of single-point (dimer geometry) calculations at specific dimer geometries using the ''batch_SAPT.pl'' script, you will not have such a file.

			So, how do you construct it?

			Use the ''batch_search.pl'' script as follows.
			# Create a file called ''keys'' containing just ''saptdft-camcasp''. This keyword will tell the ''search.pl'' script to search for SAPT(DFT) energies in the format used by CamCASP.
			# Run the ''batch_search.pl'' script using a command like:
			<pre>
			batch_search.pl pyridine2 -geom random-scan2.dat -d 6 -camcasp > energy_saptdft.dat
			</pre>

			The file ''energy_saptdft.dat'' should look something like:
			<pre>
			Energies in kJ/mol

			LABELS INDEX Rx Ry Rz alpha Nx Ny Nz
			E(1)elst E(2)ind E(2)disp E(1)exch E(2)exind E(2)exdisp TotOverlap
			Elst-Asymp Ind2-Asymp Disp-Asymp Delta
			1 -5.870040E-01 3.957260E+00 9.016280E+00 1.227930E+02 -9.097780E-01 -1.008600E-01 4.026560E-01
			1.087500E-01 -2.364920E+00 -9.875980E+00 4.871440E+00 0.0E+00 0.0E+00 0.0E+00
			0.0E+00 0.0E+00 0.0E+00 0.0E+00
			...
			</pre>
			So it is in almost the correct format. You need to add the preamble:
			<pre>
			TITLE Energy scan of MOL-A by MOL-B
			TITLE pyridine1 and pyridine2
			TITLE Basis sadlej and type MC
			TITLE Midbonds NONE and type weighted
			MOL-A pyridine1
			MOL-B pyridine2
			POINTS 500
			ENERGY-UNITS KJ/MOL
			LENGTH-UNITS BOHR
			ANGLE-UNITS DEGREE
			</pre>
			Or whatever is appropriate in your case. These fields are used by CamCASP, so make sure they are correct.
			And you will also need to add the last two lines:
			<pre>
			END
			END-FILE
			</pre>
			That is all you need do, unless you want to fill up the ''Elst-Asymp'', ''Ind2-Asymp'', ''Disp-Asymp'' and
			''Delta'' fields. For the first three you will need to use '''ORIENT''' and the '''batch_ORIENT.pl''' script. The last one, ''Delta'', is any energy correction you would like to include. See [[ CamCASP/Notes/6 \| Overlap Models ]] for more details.

import>Am592: /* Converting units */

2008-11-28T14:28:17Z

Converting units

← Older revision		Revision as of 14:28, 28 November 2008
Line 33:		Line 33:
	</pre>		</pre>
	# And you could have read in multiple files, each with its own set of units and it (should) all work correctly.		# And you could have read in multiple files, each with its own set of units and it (should) all work correctly.

			==VIM tricks==
			* Inserting the ''Type'' field in the *.mom files
			<pre>
			:map t ^vllly$a Type ^[p^[
			</pre>
			Then search for ''Rank'' and type ''t''.

import>Am592: /* Converting units */

2008-11-25T10:57:12Z

Converting units

← Older revision		Revision as of 10:57, 25 November 2008
Line 17:		Line 17:
	Finish		Finish
	</pre>		</pre>
			NOTES:
	The advantage of this over any script is first of all speed, it's already done for you so why bother, second, '''PROCESS''' will convert from ''any'' of the recognised energy units to kJ/mol. And you could have read in multiple files, each with its own set of units and it (should) all work correctly.
			# The advantage of this over any script is first of all speed --- the code's already written for you so why bother writing your own.
			# Second, '''PROCESS''' will convert from ''any'' of the recognised energy units to kJ/mol and it knows what units the energies are in as this information is in the energy file. Here's an example of the header of an energy file:
			<pre>
			TITLE Energy scan of MOL-A by MOL-B
			TITLE pyridine1 and pyridine2
			TITLE Basis sadlej and type MC
			TITLE Midbonds NONE and type weighted
			MOL-A pyridine1
			MOL-B pyridine2
			POINTS 500
			ENERGY-UNITS KJ/MOL
			LENGTH-UNITS BOHR
			ANGLE-UNITS DEGREE
			</pre>
			# And you could have read in multiple files, each with its own set of units and it (should) all work correctly.

import>Am592 at 14:52, 24 November 2008

2008-11-24T14:52:42Z

New page

[[ CamCASP ]] => [[ CamCASP/Notes | Notes ]] => Odds and Ends
== Converting units ==
The energy file produced by the '''ENERGY-SCAN''' module will probably use the units: Bohr, Degree, cm-1. These may not be appropriate and may need changing. It is easy enough to do this using a script, but there is a more convenient and probably more reliable way of converting the units in this file. That is to use the '''PROCESS''' program.

Here's the '''PROCESS''' command file to convert the energies in file ''energy_file.dat'' to kJ/mol.
<pre>
Global
Units kJ/mol
CamCASP /home/am592/CamCASP/current
End

Energy
Read energy_file.dat
Write energy_file_kJ.dat
End

Finish
</pre>
The advantage of this over any script is first of all speed, it's already done for you so why bother, second, '''PROCESS''' will convert from ''any'' of the recognised energy units to kJ/mol. And you could have read in multiple files, each with its own set of units and it (should) all work correctly.