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            "18": {
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                "title": "Scripting",
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                        "*": "\n\n* Prev: [[Warming up with Unix commands]]\n* Next: [[LabQSM#Link to Selected Laboratories]]\n\n\n[[File:Bash.png|left| 180px]]\n\nCommands (to be interpreted and executed) can be placed in a text file, called script, to be executed by means of an interpreter\n\nThe interpreter is specified in the first line of the script, e.g. by:\n  #! /bin/sh\n  #! /bin/bash\n  #! /bin/tcsh\n  #! /usr/bin/awk -f\n  #! /usr/bin/env python\n  ...\n(Note that while # is in all the above languages a comment, #! is actually used to identify the interpreter).\n\n== Bash scripting ==\n\nAmong the many, '''bash scripting''' is particularly relevant to us (bash is also the interpreter of the command-line shell\nwe have been using so far).\n\nUnix commands (enriched by bash built-in functions & structures) can be used in bash scripts:\n\n $> vi ./get_users.sh\n \n #! /bin/bash  -x\n filein=/etc/passwd\n #\n # extract user names\n cat $filein | awk -v FS=\":\" '{print $1}'\n\nNote that in order to execute <code>get_users.sh</code>, we need to change its permissions,\n  $> chmod a+x ./get_users.sh\nWhen executing, the output fo the script can also be redirected to a file, \n  $> ./get_users.sh > users.dat\n\nWithin the script, $0 corresponds to the invocation name (./get_users.sh, in the example above), $1, $2, .. $n\nto the n-th arguments if present. $# is the number of command line arguments passed to the script.\n\n $> cat ./get_users2.sh\n \n #! /bin/bash\n if [ $# == 0 ] ; then echo \"Usage:  ./get_users2.sh  <filename>\" ; exit 1 ; fi\n filein=$1\n # \n # extract user names\n cat $filein | awk -v FS=\":\" '{print $1}'\n\nNow, this second version of the script needs to be run as:\n $> ./get_users2.sh /etc/passwd\n\n== Sed & Awk ==\n\nThese two commands, available almost everywhere, are extremely used in bash scripting.\n\n=== sed ===  \nsubstitutes regular expressions in files or strings. Examples follow:\n\n $> echo \u201cCiao Ciao\u201d | sed \u2018s/C/M/\u2019\n      ->  \u201cMiao Ciao\u201d\n $> echo \u201cCiao Ciao\u201d | sed \u2018s/C/M/g\u2019\n      ->  \u201cMiao Miao\u201d                  # g stands for \u201cglobal substitution\u201d\n\nRegular expressions can also be used in the search. \n\n* \".\"  in the regular expr means all characters (wild card) and needs to be protected as \\. to be treated as a regular character\n* \\n   means newline\n* \\t   tab\n\n\n=== awk ===\nline by line operations (number & strings, syntax similar to c)\n $> echo 10 4.0 | awk '{print $1 * sqrt($2)}'\n $> echo \u201cLabQSM 2020\u201d | awk '{print $1; print \"Year\", $2}'\n\nAwk has its own scripting, useful eg for parsing or data post-processing (the same operation/search is done line by line)\n\nActions are automatically performed line by line.\n* NR      current line number\n* NF      current number of fields, separated by FS \n* FS      field separator, space by default, can be changed e.g. to , or :, or tab\n* $1, $2, ... $NF   refer to different fields in the parsed line\n* Arithmetic, string (and many more) operations.\n* next    skips to the next line\n\nTake eg the file <code>apt.txt</code> with the list of tennis players that we have used in previous examples:\n  9850, Nadal,  Rafael \n  6630, Federer,  Roger\n  3075, Berrettini,  Matteo \n 12030, Djokovic,  Novak\n\nThe problem can be solved by awk as follows:\n\n #! /usr/bin/awk -f\n BEGIN{ i=ind; nlines=0; FS=\",\" }\n {\n   if (NF != 3) next\n   nlines++\n   if (nlines == i) {printf \"%s, %s\\n\", $3,$2}\n }\n END{\n # place here any operation to be done at the end\n }\n\nRun as:\n $> ./solution.awk -v ind=2  apt.txt\n\nNote that comma-separated columns are no longer needed, and one can avoid using commas by simply dropping the redefinition of the field-separator FS=\",\".\n\n== Bash control statements ==\n\n'''Conditionals'''\n\n if [ \"$var1\" = \"$var2\" ] ; then\n    <some-statements>\n else\n    <some-statements>\n fi\n \n if [ -n \"$var\" ] ; then echo \"var is non-empty\" ; fi \n if [ -z \"$var\" ] ; then echo \"var is empty\" ; fi\n if [ -e \"$file\" ] ; then echo \"File exists\" ; fi\n if [ ! -e \"$file\" ] ; then echo \"File does not exist\" ; fi\n if [ -d \"$dir\" ] ;  then echo \"Dir exists\" ; fi\n if [ -x \"$file\" ] ; then echo \"File exists and is exec\" ; fi\n\n'''Loops'''\n list=\"item1 item2 item3\"\n for item in $list\n do\n    echo $item\n done\n\n'''Input from command line'''\n\n #! /bin/bash\n echo \"number of arguments : $#\"\n echo \"        \tcommand : $0\"\n echo \"        \t1st arg : $1\"\n echo \"        \t2nd arg : $2\"\n echo \"            \t... \"\n echo \"       \tall args : $*\"\n\n Execute as:\n $> ./example.sh  p1 p2 p3\n\n'''Dealing with extended text'''\n(Useful eg to write input files)\n\nThis can be used for a few lines\n echo line1 >  file.txt \n echo line2 >> file.txt\n echo line3 >> file.txt\n\nInstead, when text becomes extended\n cat >file.txt << EOF\n    line1\n    line2\n    line3\n EOF\n\n== Exercises ==\n\n=== Exercise 1 ===\nJob Script: Write a script (run.sh) to run <code>pw.x</code> once an input file is provided\n\n[[Solution_1_1 | Solution 1]]\n\n[[Solution_1_2 | Solution 2]]\n\n\n=== Exercise 2 ===\n\n* Modify the ruh.sh script of Problem 1 to loop over different lattice parameters.\n* Consider the grid:  -3%, -2%, -1%, 0, +1%, +2%, + 3%\n* Keep trace of the parameters used in the file names\n\n* '''Hint1''': create a template input file, where the <code>celldm1</code> field is assigned <code>@alat@</code>, which you will substitute in the script\n* '''Hint2''': save both input and output files;    \n* '''Hint3''':   <code>$ basename <name>.dat  .dat   ->  <name></code>\n\n'''Solution''': have a look at   \n* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/run_lattice.sh LAB_1/test_diamond/run_lattice.sh]    and\n* [https://github.com/max-centre/LabQSM/blob/main/LAB_1/test_diamond/scf.tmpl LAB_1/test_diamond/scf.tmpl]\n\n\n\n=== Exercise 3 ===\n\nLattice parameter revised\n* Same at Exercise 2\n* Include the input file in the script, meaning that the substitution of parameters in the template input file can be done via shell variables and loops\n\n'''Solution''': have a look at \n* [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]"
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                "pageid": 22,
                "ns": 0,
                "title": "Solution 0 1 1",
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                        "*": "* Back to the previous page: [[Scripting#Exercises|Exercises]]\n\n #! /bin/bash -x\n filein=scf.diamond.in\n bindir=/usr/local/bin\n #\n # fileout=scf.diamond.out\n fileout=`echo $filein | sed 's/\\.in/\\.out/' `\n #\n $bindir/pw.x < $filein > $fileout\n exit 0"
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