Makerestart - Revision history

import>Csw34 at 15:14, 14 May 2008

2008-05-14T15:14:45Z

← Older revision		Revision as of 15:14, 14 May 2008
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	That should do it!		That should do it!

	'''NOTE''': I had to put a lot of hashes in as for some reason the wiki was splitting the code into blocks when I had blank lines there :( Anyone know how to fix that?
	<pre>		<pre>
	#!/bin/bash		#!/bin/bash

import>Csw34 at 15:14, 14 May 2008

2008-05-14T15:14:31Z

Show changes

import>Csw34 at 12:16, 9 May 2008

2008-05-09T12:16:53Z

← Older revision		Revision as of 12:16, 9 May 2008
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	GMIN creates a file, ''GMIN.dump'' ~~after each~~ 1000 steps which allows you to restart the run if, for example, your job crashed of if you simply want to run more quenches to see if you find a lower minimum. This script can be run in a directory containing the output from a CGMIN run to automatically setup a restart. The directory you run it in must include the following files:		GMIN creates a file, ''GMIN.dump'' every 1000 steps which allows you to restart the run if, for example, your job crashed of if you simply want to run more quenches to see if you find a lower minimum. This script can be run in a directory containing the output from a CGMIN run to automatically setup a restart. The directory you run it in must include the following files:

	* ''input.crd''		* ''input.crd''

import>Csw34 at 12:16, 9 May 2008

2008-05-09T12:16:34Z

← Older revision		Revision as of 12:16, 9 May 2008
Line 1:		Line 1:
	GMIN ~~is set tp create~~ a file, ''GMIN.dump'' after each 1000 steps which allows you to restart the run if, for example, your job crashed of if you simply want to run more quenches to see if you find a lower minimum. This script can be run in a directory containing the output from a CGMIN run to automatically setup a restart. The directory you run it in must include the following files:		GMIN creates a file, ''GMIN.dump'' after each 1000 steps which allows you to restart the run if, for example, your job crashed of if you simply want to run more quenches to see if you find a lower minimum. This script can be run in a directory containing the output from a CGMIN run to automatically setup a restart. The directory you run it in must include the following files:

	* ''input.crd''		* ''input.crd''

import>Csw34 at 12:16, 9 May 2008

2008-05-09T12:16:01Z

← Older revision		Revision as of 12:16, 9 May 2008
Line 1:		Line 1:
	This script can be run in a directory containing the output from a CGMIN run to automatically setup a restart. The directory you run it in must include the following files:		GMIN is set tp create a file, ''GMIN.dump'' after each 1000 steps which allows you to restart the run if, for example, your job crashed of if you simply want to run more quenches to see if you find a lower minimum. This script can be run in a directory containing the output from a CGMIN run to automatically setup a restart. The directory you run it in must include the following files:

	* ''input.crd''		* ''input.crd''
Line 5:		Line 5:
	* ''GMIN.dump'' - if your run crashed and you only have ''GMIN.dump.save'', copy it to GMIN.dump and then run the script		* ''GMIN.dump'' - if your run crashed and you only have ''GMIN.dump.save'', copy it to GMIN.dump and then run the script

	This script works for [[CHARMM]] with [[GMIN]] only but it is very simple to modify it for use with [[AMBER]]! All you need to change is the files that are copied across in the file handling section!		This script works for [[CHARMM]] with [[GMIN]] only but it is very simple to modify it for use with [[AMBER]]! All you need to change is the files that are copied across in the file handling section! The usage is extremely simple, copy the below text into your favourite editor and save it as ''makerestart''. You then need to make it executable and I recommend moving it into your ''bin'' directory i.e.

			chmod a+x makerestart
			mv makerestart ~/bin

			Now change to the directory containing your [[GMIN]] output and type:
⚫	NOTE: I had to put a lot of hashes in as for some reason the wiki was splitting the code into blocks when I had blank lines there :( Anyone know how to fix that?

			makerestart <number of steps in restart run>

			That should do it!

		⚫	'''NOTE''': I had to put a lot of hashes in as for some reason the wiki was splitting the code into blocks when I had blank lines there :( Anyone know how to fix that?

	#!/bin/bash		#!/bin/bash
Line 52:		Line 61:
	sed -n '2,$p' data.top > restart/data		sed -n '2,$p' data.top > restart/data
	rm data.top		rm data.top

			You should now have a subdirectory called ''restart'' where you ran the script. Running [[GMIN]] here will begin the restart run. Also, the script is designed so that you can of course run it in the directory of a previous restart run!

import>Csw34 at 12:06, 9 May 2008

2008-05-09T12:06:13Z

← Older revision		Revision as of 12:06, 9 May 2008
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	# NOTE that the last sed command ensures that if the data file has been used in a restart run before,		# NOTE that the last sed command ensures that if the data file has been used in a restart run before,
	# the 'RESTORE' line is removed to ensure it only appears once in the new file!		# the 'RESTORE' line is removed to ensure it only appears once in the new file!
			#
	# Prints the top of the data file up to (but not including) the line containing 'STEPS' to a new file, 'data.top'		# Prints the top of the data file up to (but not including) the line containing 'STEPS' to a new file, 'data.top'
	awk 'NR==1,/STEPS/{print x};{x=$0}' data \| sed -n '/RESTORE/!p' > data.top		awk 'NR==1,/STEPS/{print x};{x=$0}' data \| sed -n '/RESTORE/!p' > data.top

import>Csw34 at 12:04, 9 May 2008

2008-05-09T12:04:37Z

← Older revision		Revision as of 12:04, 9 May 2008
Line 7:		Line 7:
	This script works for [[CHARMM]] with [[GMIN]] only but it is very simple to modify it for use with [[AMBER]]! All you need to change is the files that are copied across in the file handling section!		This script works for [[CHARMM]] with [[GMIN]] only but it is very simple to modify it for use with [[AMBER]]! All you need to change is the files that are copied across in the file handling section!

			NOTE: I had to put a lot of hashes in as for some reason the wiki was splitting the code into blocks when I had blank lines there :( Anyone know how to fix that?
⚫	#!/bin/bash

		⚫	#!/bin/bash
			#
	###########################################################################		###########################################################################
	# Created by Chris Whittleston (csw34@cam.ac.uk) on 9th May 2008 ##		# Created by Chris Whittleston (csw34@cam.ac.uk) on 9th May 2008 ##

import>Csw34 at 12:03, 9 May 2008

2008-05-09T12:03:43Z

← Older revision		Revision as of 12:03, 9 May 2008
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	# e.g. if you want to do another 1000 steps then use './makerestart 1000'##		# e.g. if you want to do another 1000 steps then use './makerestart 1000'##
	###########################################################################		###########################################################################
			#

	# VARIABLE ASSIGNMENT		# VARIABLE ASSIGNMENT
			#

	## Prints the line in the data file containing 'STEPS' and assigns $oldsteps to the second column		# Prints the line in the data file containing 'STEPS' and assigns $oldsteps to the second column
	oldsteps=$(sed -n '/STEPS/p' data \| awk '{print $2'})		oldsteps=$(sed -n '/STEPS/p' data \| awk '{print $2'})
	steps=$oldsteps		steps=$oldsteps
	# This increments the $steps variable by the number used in the first arguement		# This increments the $steps variable by the number used in the first arguement
	let "steps += $1"		let "steps += $1"
			#

	# SOME PRINTING		# SOME PRINTING
			#

	echo 'Setting up restart run in the current directory'		echo 'Setting up restart run in the current directory'
	echo 'Number of steps completed='$oldsteps		echo 'Number of steps completed='$oldsteps
	echo 'Number of additional steps requested='$1		echo 'Number of additional steps requested='$1
	echo 'Total number of steps after restart='$steps		echo 'Total number of steps after restart='$steps
			#

	# CREATING THE NEW DATA FILE		# CREATING THE NEW DATA FILE
			#

	# NOTE that the last sed command ensures that if the data file has been used in a restart run before,		# NOTE that the last sed command ensures that if the data file has been used in a restart run before,
	# the 'RESTORE' line is removed to ensure it only appears once in the new file!		# the 'RESTORE' line is removed to ensure it only appears once in the new file!
Line 42:		Line 42:
	# Adds the bottom bit of the data file back on (NOT including the 'STEPS' line from the old one)		# Adds the bottom bit of the data file back on (NOT including the 'STEPS' line from the old one)
	awk '/STEPS/,0' data \| sed -n '2,$p' \| sed -n '/RESTORE/!p' >> data.top		awk '/STEPS/,0' data \| sed -n '2,$p' \| sed -n '/RESTORE/!p' >> data.top
			#

	# FILE HANDLING		# FILE HANDLING
			#

	mkdir restart		mkdir restart
	cp GMIN.dump input.crd restart/		cp GMIN.dump input.crd restart/

import>Csw34 at 12:02, 9 May 2008

2008-05-09T12:02:51Z

← Older revision		Revision as of 12:02, 9 May 2008
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	###########################################################################		###########################################################################

			# VARIABLE ASSIGNMENT
	# Variable assignment

	## Prints the line in the data file containing 'STEPS' and assigns $oldsteps to the second column		## Prints the line in the data file containing 'STEPS' and assigns $oldsteps to the second column

import>Csw34 at 12:02, 9 May 2008

2008-05-09T12:02:35Z

← Older revision		Revision as of 12:02, 9 May 2008
Line 16:		Line 16:
	###########################################################################		###########################################################################

			# Variable assignment
	## VARIABLE ASSIGNMENT

	## Prints the line in the data file containing 'STEPS' and assigns $oldsteps to the second column		## Prints the line in the data file containing 'STEPS' and assigns $oldsteps to the second column
	oldsteps=$(sed -n '/STEPS/p' data \| awk '{print $2'})		oldsteps=$(sed -n '/STEPS/p' data \| awk '{print $2'})
	steps=$oldsteps		steps=$oldsteps
	## This increments the $steps variable by the number used in the first arguement		# This increments the $steps variable by the number used in the first arguement
	let "steps += $1"		let "steps += $1"

	## SOME PRINTING		# SOME PRINTING

	echo 'Setting up restart run in the current directory'		echo 'Setting up restart run in the current directory'
Line 31:		Line 31:
	echo 'Total number of steps after restart='$steps		echo 'Total number of steps after restart='$steps

	## CREATING THE NEW DATA FILE		# CREATING THE NEW DATA FILE

	## NOTE that the last sed command ensures that if the data file has been used in a restart run before,		# NOTE that the last sed command ensures that if the data file has been used in a restart run before,
	## the 'RESTORE' line is removed to ensure it only appears once in the new file!		# the 'RESTORE' line is removed to ensure it only appears once in the new file!
	## Prints the top of the data file up to (but not including) the line containing 'STEPS' to a new file, 'data.top'		# Prints the top of the data file up to (but not including) the line containing 'STEPS' to a new file, 'data.top'
	awk 'NR==1,/STEPS/{print x};{x=$0}' data \| sed -n '/RESTORE/!p' > data.top		awk 'NR==1,/STEPS/{print x};{x=$0}' data \| sed -n '/RESTORE/!p' > data.top
	## Adds back in the 'STEPS' keyword and also the 'RESTORE' command to specify a restart		# Adds back in the 'STEPS' keyword and also the 'RESTORE' command to specify a restart
	echo 'STEPS '$steps' 1.0' >> data.top		echo 'STEPS '$steps' 1.0' >> data.top
	echo 'RESTORE GMIN.dump' >> data.top		echo 'RESTORE GMIN.dump' >> data.top
	## Adds the bottom bit of the data file back on (NOT including the 'STEPS' line from the old one)		# Adds the bottom bit of the data file back on (NOT including the 'STEPS' line from the old one)
	awk '/STEPS/,0' data \| sed -n '2,$p' \| sed -n '/RESTORE/!p' >> data.top		awk '/STEPS/,0' data \| sed -n '2,$p' \| sed -n '/RESTORE/!p' >> data.top

	## FILE HANDLING		# FILE HANDLING

	mkdir restart		mkdir restart