Scripting - Revision history

Andrea Ferretti: /* Bash control statements */

2021-11-23T14:22:58Z

Bash control statements

← Older revision		Revision as of 14:22, 23 November 2021
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	fi		fi

			if [ -n "$var" ] ; then echo "var is non-empty" ; fi
			if [ -z "$var" ] ; then echo "var is empty" ; fi
	if [ -e "$file" ] ; then echo "File exists" ; fi		if [ -e "$file" ] ; then echo "File exists" ; fi
	if [ ! -e "$file" ] ; then echo "File does not exist" ; fi		if [ ! -e "$file" ] ; then echo "File does not exist" ; fi

2020-12-04T08:10:52Z

Exercises

← Older revision		Revision as of 08:10, 4 December 2020
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	[[Solution_1_2 \| Solution 2]]		[[Solution_1_2 \| Solution 2]]


	=== Exercise 2 ===		=== Exercise 2 ===
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	* Keep trace of the parameters used in the file names		* Keep trace of the parameters used in the file names

	* Hint1: create a template input file, where the celldm1 field is assigned @alat@, which you will substitute in the script		* '''Hint1''': create a template input file, where the <code>celldm1</code> field is assigned <code>@alat@</code>, which you will substitute in the script
	* Hint2: save both input and output files;		* '''Hint2''': save both input and output files;
	* Hint3: <code>$ basename <name>.dat .dat -> <name></code>		* '''Hint3''': <code>$ basename <name>.dat .dat -> <name></code>

	'''Solution''': have a look at		'''Solution''': have a look at
	* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice.sh LAB_1/test_diamond/run_lattice.sh] and		* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice.sh LAB_1/test_diamond/run_lattice.sh] and
	* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/scf.tmpl LAB_1/test_diamond/scf.tmpl]		* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/scf.tmpl LAB_1/test_diamond/scf.tmpl]



	=== Exercise 3 ===		=== Exercise 3 ===

2020-12-02T13:35:19Z

Bash scripting

← Older revision		Revision as of 13:35, 2 December 2020
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	Unix commands (enriched by bash built-in functions & structures) can be used in bash scripts:		Unix commands (enriched by bash built-in functions & structures) can be used in bash scripts:

	$> ~~cat~~ ./get_users.sh		$> vi ./get_users.sh

	#! /bin/bash -x		#! /bin/bash -x
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	Now, this second version of the script needs to be run as:		Now, this second version of the script needs to be run as:
	$> ./get_users2.sh /etc/passwd		$> ./get_users2.sh /etc/passwd


	== Sed & Awk ==		== Sed & Awk ==

2020-12-02T12:55:13Z

Exercise 4

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	'''Solution''': have a look at		'''Solution''': have a look at
	* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice_with_input.sh LAB_1/test_diamond/run_lattice_with_input.sh]		* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice_with_input.sh LAB_1/test_diamond/run_lattice_with_input.sh]

	~~=== Exercise 4 ===~~
	~~Parsing pw output files~~

	* Write a script to extract the total energy and the lattice parameter from a pw output file
	* Print them on the same output line
	* Solve the problem using a bash script (e.g. called <code>extract.sh</code>)
	* Try to do the same also using a awk script (<code>extract.awk</code>)
	* If you are a python expert you can give it a try (<code>extract.py</code>)

	~~Note that .sh and .py scripts can be made easily working on multiple files~~

	* Hint1: the total energy is marked by "!", while the lattice parameter can be taken from celldm1 (marked by "lattice parameter")
	* Hint2: look at an example and build the scripts checking step by step, use e.g. scf.diamond.out

	~~[[Solution_4_1 \| Solution]]~~

2020-12-02T11:02:19Z

Exercise 3

← Older revision		Revision as of 11:02, 2 December 2020
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	'''Solution''': have a look at		'''Solution''': have a look at
	* LAB_1/test_diamond/run_lattice_with_input.sh		* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice_with_input.sh LAB_1/test_diamond/run_lattice_with_input.sh]



	=== Exercise 4 ===		=== Exercise 4 ===

2020-12-02T11:01:03Z

Exercise 2

← Older revision		Revision as of 11:01, 2 December 2020
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	'''Solution''': have a look at		'''Solution''': have a look at
	* LAB_1/test_diamond/run_lattice.sh and		* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice.sh LAB_1/test_diamond/run_lattice.sh] and
	* LAB_1/test_diamond/scf.tmpl		* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/scf.tmpl LAB_1/test_diamond/scf.tmpl]


	=== Exercise 3 ===		=== Exercise 3 ===

2020-12-01T10:00:19Z

Exercise 1

2020-12-01T09:59:11Z

Exercise 1

← Older revision		Revision as of 09:59, 1 December 2020
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	Job Script: Write a script (run.sh) to run <code>pw.x</code> once an input file is provided		Job Script: Write a script (run.sh) to run <code>pw.x</code> once an input file is provided

	[[~~Solution 1~~ \| Solution 1]]		[[Solution_1_1 \| Solution 1]]

	[[Solution 2 \| Solution 2]]		[[Solution 2 \| Solution 2]]

2020-12-01T09:51:14Z

Exercise 4

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	* Hint2: look at an example and build the scripts checking step by step, use e.g. scf.diamond.out		* Hint2: look at an example and build the scripts checking step by step, use e.g. scf.diamond.out

	~~'''~~Solution~~'''~~		[[Solution_4_1 \| Solution]]
	~~Using bash scripting~~

	~~#!/bin/bash~~
	#
	~~filein=$1~~
	#
	~~ene=`grep ! $filein \| awk '{print $(NF-1)}'`~~
	~~alat=`grep "lattice parameter" $filein \| awk '{print $(NF-1)}'`~~
	#
	~~echo $alat $ene~~

	~~Probably more elegant and general using awk or (as today's standard) python.~~

2020-12-01T09:49:45Z

Exercise 1

← Older revision		Revision as of 09:49, 1 December 2020
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	Job Script: Write a script (run.sh) to run <code>pw.x</code> once an input file is provided		Job Script: Write a script (run.sh) to run <code>pw.x</code> once an input file is provided

	[[~~Solution1~~ \| Solution 1]]		[[Solution 1 \| Solution 1]]

	[[~~Solution2~~ \| Solution 2]]		[[Solution 2 \| Solution 2]]

	=== Exercise 2 ===		=== Exercise 2 ===