#!/bin/bash # (c) S. Parkin 15/02/19 -- 15/04/24: SADABS-AUTO - a SADABS automator. # # A 'bash' script that automates George Sheldrick's SADABS absorption correction # program. SADABS-AUTO sets a few parameters and then calls a separate 'expect' # script, SADABS-AUTO-RUN, which in turn spawns a SADABS job. SADABS-AUTO-RUN is # used to bypass the usual interactive SADABS session. SADABS-AUTO launches via # a command-line call like this: # # sadabs-auto filename even odd muR Laue weights # # Where 'filename' is the filename used for the dataset (without the extension), # 'even' is an even integer (2,4,6,8), 'odd' is an odd integer (1,3,5,7) and muR # is a real (non-negative) value for equivalent muR. 'Laue' sets the Laue group # number for SADABS using one of Sheldrick's 14 categories. The 'Laue' entry is # optional on the command line but if you use it you should try to get it right. # Automated SADABS will fail if you use too high a Laue class. If no 'Laue' type # is given then SADABS-AUTO will try to figure it out using information given in # a CIF (if a CIF is available). Failing that it will ask for manual input. The # 'weights' input allows you to alter the SADABS weighting scheme, but will only # accept choices (0-6) because (7-11) require manual input and thus are not good # for automation. # # The script will also attempt to figure out a reasonable number for muR if none # is specified on the command line. The error trapping seems to work quite well, # but it is probably better to enter it on the command line. # # NOTE: There are lots of different versions of SADABS around. This version of # SADABS-AUTO is specific to SADABS version 14.4. Other SADABS versions require # changes to the companion 'expect' script, SADABS-AUTO-RUN. # Add a header for SADABS-AUTO to the usual SADABS header. # echo " " echo " ==========================================================================" echo " SADABS-AUTO: SADABS automation by bash/expect scripts: S.Parkin 2015/02/19" echo " --------------------------------------------------------------------------" # The first task is to pull some information from the command line that was used # to start SADABS-AUTO. Currently this is the filename, the even & odd spherical # harmonic order, an average muR value, the Laue group number, and the weighting # scheme type (if suitable values were supplied). If no number for muR is given, # SADABS-AUTO tries to calculate a sensible value so long as a suitable CIF file # is present. If no weighting scheme entry is given, or if the supplied value is # nonsense, then the default [5] is used. See the section starting below at line # 215 or so. # filename=$1 highest_even_order=$2 highest_odd_order=$3 muR_equivalent=$4 sadabs_laue_group_number=$5 weighting_scheme=$6 refinement_cycles=$7 if [ ! $filename ]; then echo echo " No filename was given. SADABS-AUTO is launched like this: " echo echo " sadabs-auto filename even odd muR Laue weight" echo echo " 'filename' is the filename used for the dataset (no extension) " echo " 'even' is an even integer [2,4,6,8] " echo " 'odd' is an odd integer [1,3,5,7] " echo " 'muR' is a reasonable value for the equivalent muR " echo " 'Laue' sets the Laue group number for SADABS [1 - 14] " echo " 'weight' sets the type of weighting scheme [1 - 6] " echo echo " For the Laue group, use one of the following numbers: " echo echo " [1] -1 [8] -3m (rhombohedral axes) " echo " [2] 2/m (Y unique) [9] -31m (Z unique) " echo " [3] mmm [10] -3m1 (Z unique) " echo " [4] 4/m (Z unique) [11] 6/m (Z unique) " echo " [5] 4/mmm (Z unique) [12] 6/mmm (Z unique) " echo " [6] -3 (rhombohedral axes) [13] m3 " echo " [7] -3 (Z unique) [14] m3m " echo echo " You need to at least specify a filename. SADABS-AUTO will now quit. " echo " ==========================================================================" echo exit fi # The stem of the filename is used to set the filename for the CIF [used to find # some information about the structure (see below)]. It is also used to set the # name of the file that contains all the integrated data. For kappaCCD data this # is a file with a '.sad' suffix (created by Sheldrick's x2sad program), whereas # for Bruker machines it is a file with '_0m.raw' appended to the filename stem. # The machine_flag is set to the first letter of the filename (either 'k' or 'x' # for the UK X-Ray Laboratory) so that the right file (either *.sad or *_0m.raw) # is used for the SADABS job. Datafiles from a synchrotron (e.g. the ALS) should # start with the letter 's', and the assumption is that the data files come from # a Bruker instrument. # cif_file=$filename".cif" machine_flag=${filename:0:1} if [ $machine_flag == "k" ]; then raw_file=$filename".sad" #elif [ $machine_flag == "x" ]; then # raw_file=$filename"_0m.raw" #elif [ $machine_flag == "s" ]; then # raw_file=$filename"_0m.raw" else raw_file=$filename"_0m.raw" fi # Check that the Laue group number from the command line is an integer between 1 # and 14. Write a warning about setting too high a value. If no value was found, # then write a different message. # if [[ $5 =~ ^[0-9]+$ ]] && [ "$5" -ge 1 -a "$5" -le 14 ]; then echo echo " If the Laue group number supplied on the command line is too high then the " echo " automated SADABS process will fail! A Laue group number of "$sadabs_laue_group_number" was supplied. " else echo echo " Either no Laue group number was supplied, or the value was outside of the " echo " acceptable range. SADABS-AUTO will either figure it out or it will ask. " # For fully automated use, SADABS-AUTO will either get the Laue group number off # the command line or it must figure it out from a SHELXL-written CIF. If there # is no suitable CIF available, SADABS-AUTO asks the user to enter it. # if [ ! -f "$cif_file" ]; then echo echo " For fully automated use SADABS-AUTO requires that the 'Laue group number'" echo " is either given on the command line or that a suitable SHELXL-written CIF" echo " is available in the current directory. No suitable CIF was found, so you" echo " need to enter the Laue group number now. Please enter a number [1-14], as" echo " per the following SADABS classifications: " echo " " echo " [1] -1 [8] -3m (rhombohedral axes) " echo " [2] 2/m (Y unique) [9] -31m (Z unique) " echo " [3] mmm [10] -3m1 (Z unique) " echo " [4] 4/m (Z unique) [11] 6/m (Z unique) " echo " [5] 4/mmm (Z unique) [12] 6/mmm (Z unique) " echo " [6] -3 (rhombohedral axes) [13] m3 " echo " [7] -3 (Z unique) [14] m3m " echo echo -n " Enter Laue group number: " read sadabs_laue_group_number while [[ "1 2 3 4 5 6 7 8 9 10 11 12 13 14" != *"$sadabs_laue_group_number"* ]] || [[ $sadabs_laue_group_number == 0 ]]; do echo -n " An integer between 1 and 14 (inclusive) is required: " read sadabs_laue_group_number done else # Assign a few variables. Not all of these will be needed for the final version. # NOTE: Those that are not used will be removed once everything works properly. # In the meantime, any unused variables do no harm and so can be ignored. # lambda=`echo $(grep "_diffrn_radiation_wavelength" $cif_file) | cut -d' ' -f 2` a=`echo $(grep "_cell_length_a" $cif_file) | awk '{print $2}' | sed 's/(.*//'` b=`echo $(grep "_cell_length_b" $cif_file) | awk '{print $2}' | sed 's/(.*//'` c=`echo $(grep "_cell_length_c" $cif_file) | awk '{print $2}' | sed 's/(.*//'` alpha=`echo $(grep "_cell_angle_alpha" $cif_file) | awk '{print $2}' | sed 's/(.*//'` beta=`echo $(grep "_cell_angle_beta" $cif_file) | awk '{print $2}' | sed 's/(.*//'` gamma=`echo $(grep "_cell_angle_gamma" $cif_file) | awk '{print $2}' | sed 's/(.*//'` mu=`echo $(grep "_exptl_absorpt_coefficient_mu" $cif_file) | awk '{print $2}'` max_size=`echo $(grep "_exptl_crystal_size_max" $cif_file) | awk '{print $2}'` mid_size=`echo $(grep "_exptl_crystal_size_mid" $cif_file) | awk '{print $2}'` min_size=`echo $(grep "_exptl_crystal_size_min" $cif_file) | awk '{print $2}'` crystal_system=`echo $(grep "_space_group_crystal_system" $cif_file) | awk '{print $2}'` space_group_number=`echo $(grep "_space_group_IT_number" $cif_file) | awk '{print $2}'` three_bar_one_m="149 151 153 157 159 162 164" three_bar_m_one="150 152 154 156 158 163 165" # If it was not entered on the command line, or was not entered manually, then a # value for the Laue group number will be obtained from information taken from a # CIF. The series of if...fi conditional tests below seem to work well but they # need to be tested with higher symmetry, especially for trigonal space groups. # if [ $crystal_system == "triclinic" ]; then sadabs_laue_group_number=1 elif [ $crystal_system == "monoclinic" ]; then sadabs_laue_group_number=2 elif [ $crystal_system == "orthorhombic" ]; then sadabs_laue_group_number=3 elif [ $crystal_system == "tetragonal" ]; then if [ $space_group_number -le 88 ]; then sadabs_laue_group_number=4 elif [ $space_group_number -ge 89 ]; then sadabs_laue_group_number=5 fi elif [ $crystal_system == "trigonal" ]; then if [[ $alpha == $gamma ]] && [[ $space_group_number -le 148 ]]; then sadabs_laue_group_number=6 elif [[ $gamma == "120" ]] && [[ $space_group_number -le 147 ]]; then sadabs_laue_group_number=7 elif [[ $alpha == $gamma ]] && [[ $space_group_number -ge 155 ]]; then sadabs_laue_group_number=8 elif [[ $gamma == "120" ]] && [[ $three_bar_one_m == *"$space_group_number"* ]]; then sadabs_laue_group_number=9 elif [[ $gamma == "120" ]] && [[ $three_bar_m_one == *"$space_group_number"* ]]; then sadabs_laue_group_number=10 fi elif [ $crystal_system == "hexagonal" ]; then if [ $space_group_number -le 176 ]; then sadabs_laue_group_number=11 elif [ $space_group_number -ge 177 ]; then sadabs_laue_group_number=12 fi elif [ $crystal_system == "cubic" ]; then if [ $space_group_number -le 206 ]; then sadabs_laue_group_number=13 elif [ $space_group_number -ge 207 ]; then sadabs_laue_group_number=14 fi fi fi fi # The muR equivalent is best set from the command line. However, it is possible # to calculate a good starting point for muR using something like the following: # # muR_equivalent=`echo "scale=3; (($max_size + $mid_size + $min_size) / 6) * $mu" | bc` # muR_equivalent=`echo "scale=3; (($max_size + $mid_size + ($min_size * 5.5)) / 15) * $mu" | bc` # # NOTE: Sheldrick recommends a value for R that is biased closer to half the min # dimension. The example in the SADABS paper [J. Appl. Cryst. (2015), 48, 3-10] # suggests that for a 0.1 mm x 0.2 mm x 0.3 mm crystal, a value for R of 0.07 mm # is appropriate. In that example, the smallest dimension is up-weighted by 5.5 # times. This is an approximation of course, but if we take this recommendation # at face value, the second assignment above would be preferred (see below). # if ! echo "$muR_equivalent" | grep -qE ^\-?[0-9]?\.?[0-9]+$; then echo echo " muR was either not given or it was invalid. Either the default will be used " echo " or if a suitable CIF file is present an attempt will be made to calculate a " echo " suitable value. " echo muR_equivalent=`echo "scale=3; (($max_size + $mid_size + ($min_size * 5.5)) / 15) * $mu" | bc` fi # Include an option to change the type of weighting scheme used by SADABS. There # are 11 choices, which are explained in the usual SADABS interactive blurbs but # weighting schemes 7--11 require manual input, and so they are not suitable for # automation. If no entry is made on the command line, if 7--11 is specified, or # if the entry is garbage then SADABS-AUTO will default to weighting scheme (5). # In my tests, which are fairly extensive, the default (5) is the most general. # if ! ( [[ $6 =~ ^[0-9]+$ ]] && [[ $6 -ge 0 ]] && [[ $6 -le 6 ]] ); then echo " Weighting scheme either not given or invalid. Will use default value of 5. " weighting_scheme="" fi # Run SADABS using SADABS-AUTO-RUN (i.e. the companion 'expect' script) with the # Laue group number, the even/odd spherical harmonic orders and the mean muR all # specified on the command line. # NOTE: For kappaCCD data, $raw_file is a *.sad file. # NOTE: For X8 Proteum data, $raw_file is a *_0m.raw file. # sadabs-auto-run $raw_file $sadabs_laue_group_number $highest_even_order $highest_odd_order $muR_equivalent $weighting_scheme $refinement_cycles #sadabs-auto-run-2012 $raw_file $sadabs_laue_group_number $highest_even_order $highest_odd_order $muR_equivalent #sadabs-auto-run-2014 $raw_file $sadabs_laue_group_number $highest_even_order $highest_odd_order $muR_equivalent # Clean up the filenames: # if [ -f "sadabs-auto-temp" ]; then if [ $machine_flag == "k" ]; then mv $filename".sad.abs" $filename.abs mv $filename".sad.hkl" $filename.hkl elif [ $machine_flag == "x" ]; then mv $filename"_0m.raw.abs" $filename.abs mv $filename"_0m.raw.hkl" $filename.hkl fi echo fi echo " SADABS-AUTO-RUN, and hence SADABS, was fed the following parameters: " echo echo " Highest even spherical harmonic " $highest_even_order echo " Highest odd spherical harmonic " $highest_odd_order echo " Mean equivalent-sphere muR value " $muR_equivalent echo " SADABS-specific Laue group number " $sadabs_laue_group_number if [ $weighting_scheme ]; then echo " SADABS weighting scheme used type " $weighting_scheme else echo " SADABS weighting scheme used type 5 (default) " fi if [ -f "sadabs-auto-temp" ]; then echo echo " SADABS-AUTO has renamed the output files to" $filename.hkl "and" $filename.abs rm sadabs-auto-temp else echo echo " SADABS-AUTO failed because too high of a Laue group number was specified. " rm $raw_file.abs fi if [ -f "$cif_file" ]; then # Grep the Tmin and Tmax values from the appropriate *.abs file. The values are # the 6th and 7th fields, and truncate them to three decimal places. # tminmax=`grep "Estimated minimum and maximum transmission:" $filename.abs` tmin=`echo $tminmax | awk '{printf($6)}'` tmax=`echo $tminmax | awk '{printf($7)}'` mu=`echo $(grep "_exptl_absorpt_coefficient_mu" $cif_file) | awk '{print $2}'` longest=`echo "scale=3; l($tmin)/-$mu" | bc -l` shortest=`echo "scale=3; l($tmax)/-$mu" | bc -l` echo echo " Based on the max. transmission coefficient, the shortest crystal dimension " echo " is predicted to be about "$shortest" mm. If this isn't close then something isn't " echo " right, so you should try a different muR value. If the estimate is too big" echo " then use a smaller muR. Spherical harmonic orders could also be tweaked." fi # Add a SADABS/SADABS-AUTO footer to the SADABS screen output. # echo echo " --------------------------------------------------------------------------" echo " SADABS-2014/4 - Bruker AXS area detector scaling and absorption correction" echo " SADABS-AUTO: SADABS automation by bash/expect scripts: S.Parkin 2015/02/19" echo " ==========================================================================" echo exit