{+ file: merge.inp +} {+ directory: xtal_util +} {+ description: Dataset merging, renaming, data set expansion and reduction +} {+ authors: Axel T. Brunger +} {+ copyright: Yale University +} {- Guidelines for using this file: - all strings must be quoted by double-quotes - logical variables (true/false) are not quoted - do not remove any evaluate statements from the file -} {- begin block parameter definition -} define( {====================== crystallographic data ========================} {* space group *} {* use International Table conventions with subscripts substituted by parenthesis *} {===>} sg="P2(1)"; {* unit cell parameters in Angstroms and degrees *} {+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +} {===>} a=45.2896; {===>} b=100.0178; {===>} c=71.9303; {===>} alpha=90; {===>} beta=104.4158; {===>} gamma=90; {* reflection input files followed by the names of reciprocal-space objects as they appear in the file, and, optionally, new names and data types as they will appear in the merged file. Only specified objects will be written to the merged file *} {* leave the "new_name_xxx" and/or "new_type_xxx" entries blank if the name and/or type is to be inherited from the original data file *} {* possible data types are: complex, real or integer *} {* important: specify non-anomalous files (if any) first *} {======================== reflection file 1 ==========================} {* reflection file *} {===>} reflection_infile_1="iso_mpr1_p21_13.hkl"; {* arrays *} {+ table: rows=20 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_1="Ffoo"; new_name_1_1="F_nat"; new_type_1_1="real"; {===>} old_name_2_1="SIGfoo"; new_name_2_1="S_nat"; new_type_2_1=""; {===>} old_name_3_1=""; new_name_3_1=""; new_type_3_1=""; {===>} old_name_4_1=""; new_name_4_1=""; new_type_4_1=""; {===>} old_name_5_1=""; new_name_5_1=""; new_type_5_1=""; {===>} old_name_6_1=""; new_name_6_1=""; new_type_6_1=""; {===>} old_name_7_1=""; new_name_7_1=""; new_type_7_1=""; {===>} old_name_8_1=""; new_name_8_1=""; new_type_8_1=""; {===>} old_name_9_1=""; new_name_9_1=""; new_type_9_1=""; {===>} old_name_10_1=""; new_name_10_1=""; new_type_10_1=""; {===>} old_name_11_1=""; new_name_11_1=""; new_type_11_1=""; {===>} old_name_12_1=""; new_name_12_1=""; new_type_12_1=""; {===>} old_name_13_1=""; new_name_13_1=""; new_type_13_1=""; {===>} old_name_14_1=""; new_name_14_1=""; new_type_14_1=""; {===>} old_name_15_1=""; new_name_15_1=""; new_type_15_1=""; {===>} old_name_16_1=""; new_name_16_1=""; new_type_16_1=""; {===>} old_name_17_1=""; new_name_17_1=""; new_type_17_1=""; {===>} old_name_18_1=""; new_name_18_1=""; new_type_18_1=""; {===>} old_name_19_1=""; new_name_19_1=""; new_type_19_1=""; {===>} old_name_20_1=""; new_name_20_1=""; new_type_20_1=""; {======================== reflection file 2 ==========================} {* reflection file *} {===>} reflection_infile_2="iso_mpr78_p21_11.hkl"; {* arrays *} {+ table: rows=20 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_2="Ffoo"; new_name_1_2="F_mal"; new_type_1_2="real"; {===>} old_name_2_2="SIGfoo"; new_name_2_2="S_mal"; new_type_2_2=""; {===>} old_name_3_2=""; new_name_3_2=""; new_type_3_2=""; {===>} old_name_4_2=""; new_name_4_2=""; new_type_4_2=""; {===>} old_name_5_2=""; new_name_5_2=""; new_type_5_2=""; {===>} old_name_6_2=""; new_name_6_2=""; new_type_6_2=""; {===>} old_name_7_2=""; new_name_7_2=""; new_type_7_2=""; {===>} old_name_8_2=""; new_name_8_2=""; new_type_8_2=""; {===>} old_name_9_2=""; new_name_9_2=""; new_type_9_2=""; {===>} old_name_10_2=""; new_name_10_2=""; new_type_10_2=""; {===>} old_name_11_2=""; new_name_11_2=""; new_type_11_2=""; {===>} old_name_12_2=""; new_name_12_2=""; new_type_12_2=""; {===>} old_name_13_2=""; new_name_13_2=""; new_type_13_2=""; {===>} old_name_14_2=""; new_name_14_2=""; new_type_14_2=""; {===>} old_name_15_2=""; new_name_15_2=""; new_type_15_2=""; {===>} old_name_16_2=""; new_name_16_2=""; new_type_16_2=""; {===>} old_name_17_2=""; new_name_17_2=""; new_type_17_2=""; {===>} old_name_18_2=""; new_name_18_2=""; new_type_18_2=""; {===>} old_name_19_2=""; new_name_19_2=""; new_type_19_2=""; {===>} old_name_20_2=""; new_name_20_2=""; new_type_20_2=""; {======================== reflection file 3 ==========================} {* reflection file *} {===>} reflection_infile_3=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_3=""; new_name_1_3=""; new_type_1_3="real"; {===>} old_name_2_3=""; new_name_2_3=""; new_type_2_3=""; {===>} old_name_3_3=""; new_name_3_3=""; new_type_3_3=""; {===>} old_name_4_3=""; new_name_4_3=""; new_type_4_3=""; {===>} old_name_5_3=""; new_name_5_3=""; new_type_5_3=""; {===>} old_name_6_3=""; new_name_6_3=""; new_type_6_3=""; {===>} old_name_7_3=""; new_name_7_3=""; new_type_7_3=""; {===>} old_name_8_3=""; new_name_8_3=""; new_type_8_3=""; {======================== reflection file 4 ==========================} {* reflection file *} {===>} reflection_infile_4=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_4=""; new_name_1_4=""; new_type_1_4="real"; {===>} old_name_2_4=""; new_name_2_4=""; new_type_2_4=""; {===>} old_name_3_4=""; new_name_3_4=""; new_type_3_4=""; {===>} old_name_4_4=""; new_name_4_4=""; new_type_4_4=""; {===>} old_name_5_4=""; new_name_5_4=""; new_type_5_4=""; {===>} old_name_6_4=""; new_name_6_4=""; new_type_6_4=""; {===>} old_name_7_4=""; new_name_7_4=""; new_type_7_4=""; {===>} old_name_8_4=""; new_name_8_4=""; new_type_8_4=""; {======================== reflection file 5 ==========================} {* reflection file *} {===>} reflection_infile_5=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_5="FAu"; new_name_1_5="F_Au"; new_type_1_5="real"; {===>} old_name_2_5="SIGAu"; new_name_2_5="S_Au"; new_type_2_5=""; {===>} old_name_3_5=""; new_name_3_5=""; new_type_3_5=""; {===>} old_name_4_5=""; new_name_4_5=""; new_type_4_5=""; {===>} old_name_5_5=""; new_name_5_5=""; new_type_5_5=""; {===>} old_name_6_5=""; new_name_6_5=""; new_type_6_5=""; {===>} old_name_7_5=""; new_name_7_5=""; new_type_7_5=""; {===>} old_name_8_5=""; new_name_8_5=""; new_type_8_5=""; {======================== reflection file 6 ==========================} {* reflection file *} {===>} reflection_infile_6=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_6="FPb"; new_name_1_6="F_Pb"; new_type_1_6="real"; {===>} old_name_2_6="SIGPb"; new_name_2_6="S_Pb"; new_type_2_6=""; {===>} old_name_3_6=""; new_name_3_6=""; new_type_3_6=""; {===>} old_name_4_6=""; new_name_4_6=""; new_type_4_6=""; {===>} old_name_5_6=""; new_name_5_6=""; new_type_5_6=""; {===>} old_name_6_6=""; new_name_6_6=""; new_type_6_6=""; {===>} old_name_7_6=""; new_name_7_6=""; new_type_7_6=""; {===>} old_name_8_6=""; new_name_8_6=""; new_type_8_6=""; {======================== reflection file 7 ==========================} {* reflection file *} {===>} reflection_infile_7=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_7="FcisPt2"; new_name_1_7="F_cisPt2"; new_type_1_7="real"; {===>} old_name_2_7="SIGcisPt2"; new_name_2_7="S_cisPt2"; new_type_2_7=""; {===>} old_name_3_7=""; new_name_3_7=""; new_type_3_7=""; {===>} old_name_4_7=""; new_name_4_7=""; new_type_4_7=""; {===>} old_name_5_7=""; new_name_5_7=""; new_type_5_7=""; {===>} old_name_6_7=""; new_name_6_7=""; new_type_6_7=""; {===>} old_name_7_7=""; new_name_7_7=""; new_type_7_7=""; {===>} old_name_8_7=""; new_name_8_7=""; new_type_8_7=""; {======================== reflection file 8 ==========================} {* reflection file *} {===>} reflection_infile_8=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_8="FSm"; new_name_1_8="F_Sm"; new_type_1_8="real"; {===>} old_name_2_8="SIGSm"; new_name_2_8="S_Sm"; new_type_2_8=""; {===>} old_name_3_8=""; new_name_3_8=""; new_type_3_8=""; {===>} old_name_4_8=""; new_name_4_8=""; new_type_4_8=""; {===>} old_name_5_8=""; new_name_5_8=""; new_type_5_8=""; {===>} old_name_6_8=""; new_name_6_8=""; new_type_6_8=""; {===>} old_name_7_8=""; new_name_7_8=""; new_type_7_8=""; {===>} old_name_8_8=""; new_name_8_8=""; new_type_8_8=""; {======================== reflection file 9 ==========================} {* reflection file *} {===>} reflection_infile_9=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_9="FHg"; new_name_1_9="F_Hg"; new_type_1_9="real"; {===>} old_name_2_9="SIGHg"; new_name_2_9="S_Hg"; new_type_2_9=""; {===>} old_name_3_9=""; new_name_3_9=""; new_type_3_9=""; {===>} old_name_4_9=""; new_name_4_9=""; new_type_4_9=""; {===>} old_name_5_9=""; new_name_5_9=""; new_type_5_9=""; {===>} old_name_6_9=""; new_name_6_9=""; new_type_6_9=""; {===>} old_name_7_9=""; new_name_7_9=""; new_type_7_9=""; {===>} old_name_8_9=""; new_name_8_9=""; new_type_8_9=""; {======================== reflection file 10 ==========================} {* reflection file *} {===>} reflection_infile_10=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_10="FcisPt3"; new_name_1_10="F_cisPt3"; new_type_1_10="real"; {===>} old_name_2_10="SIGcisPt3"; new_name_2_10="S_cisPt3"; new_type_2_10=""; {===>} old_name_3_10=""; new_name_3_10=""; new_type_3_10=""; {===>} old_name_4_10=""; new_name_4_10=""; new_type_4_10=""; {===>} old_name_5_10=""; new_name_5_10=""; new_type_5_10=""; {===>} old_name_6_10=""; new_name_6_10=""; new_type_6_10=""; {===>} old_name_7_10=""; new_name_7_10=""; new_type_7_10=""; {===>} old_name_8_10=""; new_name_8_10=""; new_type_8_10=""; {======================== reflection file 11 ==========================} {* reflection file *} {===>} reflection_infile_11=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_11="FAu2"; new_name_1_11="F_Au2"; new_type_1_11="real"; {===>} old_name_2_11="SIGAu2"; new_name_2_11="S_Au2"; new_type_2_11=""; {===>} old_name_3_11=""; new_name_3_11=""; new_type_3_11=""; {===>} old_name_4_11=""; new_name_4_11=""; new_type_4_11=""; {===>} old_name_5_11=""; new_name_5_11=""; new_type_5_11=""; {===>} old_name_6_11=""; new_name_6_11=""; new_type_6_11=""; {===>} old_name_7_11=""; new_name_7_11=""; new_type_7_11=""; {===>} old_name_8_11=""; new_name_8_11=""; new_type_8_11=""; {======================== reflection file 12 ==========================} {* reflection file *} {===>} reflection_infile_12=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_12="FCo2"; new_name_1_12="F_Co2"; new_type_1_12="real"; {===>} old_name_2_12="SIGCo2"; new_name_2_12="S_Co2"; new_type_2_12=""; {===>} old_name_3_12=""; new_name_3_12=""; new_type_3_12=""; {===>} old_name_4_12=""; new_name_4_12=""; new_type_4_12=""; {===>} old_name_5_12=""; new_name_5_12=""; new_type_5_12=""; {===>} old_name_6_12=""; new_name_6_12=""; new_type_6_12=""; {===>} old_name_7_12=""; new_name_7_12=""; new_type_7_12=""; {===>} old_name_8_12=""; new_name_8_12=""; new_type_8_12=""; {======================== reflection file 13 ==========================} {* reflection file *} {===>} reflection_infile_13=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_13=""; new_name_1_13=""; new_type_1_13=""; {===>} old_name_2_13=""; new_name_2_13=""; new_type_2_13=""; {===>} old_name_3_13=""; new_name_3_13=""; new_type_3_13=""; {===>} old_name_4_13=""; new_name_4_13=""; new_type_4_13=""; {===>} old_name_5_13=""; new_name_5_13=""; new_type_5_13=""; {===>} old_name_6_13=""; new_name_6_13=""; new_type_6_13=""; {===>} old_name_7_13=""; new_name_7_13=""; new_type_7_13=""; {===>} old_name_8_13=""; new_name_8_13=""; new_type_8_13=""; {======================== reflection file 14 ==========================} {* reflection file *} {===>} reflection_infile_14=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_14=""; new_name_1_14=""; new_type_1_14=""; {===>} old_name_2_14=""; new_name_2_14=""; new_type_2_14=""; {===>} old_name_3_14=""; new_name_3_14=""; new_type_3_14=""; {===>} old_name_4_14=""; new_name_4_14=""; new_type_4_14=""; {===>} old_name_5_14=""; new_name_5_14=""; new_type_5_14=""; {===>} old_name_6_14=""; new_name_6_14=""; new_type_6_14=""; {===>} old_name_7_14=""; new_name_7_14=""; new_type_7_14=""; {===>} old_name_8_14=""; new_name_8_14=""; new_type_8_14=""; {======================== reflection file 15 ==========================} {* reflection file *} {===>} reflection_infile_15=""; {* arrays *} {+ table: rows=8 cols=3 "old name" "new name" "new type" +} {===>} old_name_1_15=""; new_name_1_15=""; new_type_1_15=""; {===>} old_name_2_15=""; new_name_2_15=""; new_type_2_15=""; {===>} old_name_3_15=""; new_name_3_15=""; new_type_3_15=""; {===>} old_name_4_15=""; new_name_4_15=""; new_type_4_15=""; {===>} old_name_5_15=""; new_name_5_15=""; new_type_5_15=""; {===>} old_name_6_15=""; new_name_6_15=""; new_type_6_15=""; {===>} old_name_7_15=""; new_name_7_15=""; new_type_7_15=""; {===>} old_name_8_15=""; new_name_8_15=""; new_type_8_15=""; {========================expansion/reduction==========================} {* average Friedel mates and write a non-anomalous diffraction file *} {* operates on real, integer, complex and HL reciprocal space objects *} {+ choice: true false +} {===>} make_non_anomalous=false; {* create Friedel mates starting from non-anomalous data *} {+ choice: true false +} {===>} make_anomalous=false; {* expand data set to P1 *} {+ choice: true false +} {===>} expand=false; {========================== output options ===========================} {* resolution range of reflections that will be written *} {+ table: rows=1 "resolution" cols=2 "lowest" "highest" +} {===>} low_res=500; {===>} high_res=2.8; {* merged/renamed/expanded/reduced data output file *} {===>} reflection_outfile="merge.hkl"; {===========================================================================} { things below this line do not normally need to be changed } {===========================================================================} ) {- end block parameter definition -} checkversion 1.1 evaluate ($log_level=quiet) xray @CNS_XTALLIB:spacegroup.lib (sg=&sg;) a=&a b=&b c=&c alpha=&alpha beta=&beta gamma=&gamma {- first step: read all data and copy into temporary arrays -} if ( $log_level = verbose ) then set message=normal echo=on end else set message=off echo=off end end if evaluate ($ii=1) while (&exist%reflection_infile_$ii=true) loop firs if ( &BLANK%reflection_infile_$ii = false ) then reflection @@&reflection_infile_$ii end evaluate ($jj=1) while (&exist%old_name_$jj_$ii=true) loop cpp if ( &BLANK%old_name_$jj_$ii = false ) then query name=&strip%old_name_$jj_$ii domain=reciprocal end if ( $object_exist = false ) then display Error: specified reciprocal space array &old_name_$jj_$ii is missing abort end if evaluate ($temp_name_$jj_$ii="tmpx_"+encode($jj)+"_"+encode($ii)) if ( &BLANK%new_type_$jj_$ii = true ) then {- no new type specified: just rename into temporary name -} rename old=&strip%old_name_$jj_$ii new=$strip%temp_name_$jj_$ii domain=reciprocal end elseif ($object_type = &strip%new_type_$jj_$ii) then {- new type specified but same type as old type: just rename -} rename old=&strip%old_name_$jj_$ii new=$strip%temp_name_$jj_$ii domain=reciprocal end elseif (&new_type_$jj_$ii="real") then {- new type specified: copy and delete old object -} declare name=$strip%temp_name_$jj_$ii domain=reciprocal type=real end do ($strip%temp_name_$jj_$ii=amplitude(&strip%old_name_$jj_$ii)) ( all ) undeclare name=&strip%old_name_$jj_$ii domain=reciprocal end elseif (&new_type_$jj_$ii="complex") then {- new type specified: copy and delete old object -} declare name=$strip%temp_name_$jj_$ii domain=reciprocal type=complex end do ($strip%temp_name_$jj_$ii=&strip%old_name_$jj_$ii) ( all ) undeclare name=&strip%old_name_$jj_$ii domain=reciprocal end elseif (&new_type_$jj_$ii="integer") then {- new type specified: copy and delete old object -} declare name=$strip%temp_name_$jj_$ii domain=reciprocal type=integer end do ($strip%temp_name_$jj_$ii=int(amplitude(&strip%old_name_$jj_$ii))) ( all ) undeclare name=&strip%old_name_$jj_$ii domain=reciprocal end else {- unknown type - abort -} display Error: unrecognized data type &new_type_$jj_$ii for &strip%old_name_$jj_$ii abort end if end if evaluate ($jj=$jj+1) end loop cpp {- undeclare all unspecified objects -} undeclare name # tmpx* domain=reciprocal end end if evaluate ($ii=$ii+1) end loop firs {- second step: rename arrays into target destinations -} evaluate ($ii=1) while (&exist%reflection_infile_$ii=true) loop seco if ( &BLANK%reflection_infile_$ii = false ) then evaluate ($jj=1) while (&exist%old_name_$jj_$ii=true) loop cpp2 if ( &BLANK%old_name_$jj_$ii = false ) then if ( &BLANK%new_name_$jj_$ii = false ) then rename old=$strip%temp_name_$jj_$ii new=&strip%new_name_$jj_$ii domain=reciprocal end else rename old=$strip%temp_name_$jj_$ii new=&strip%old_name_$jj_$ii domain=reciprocal end end if end if evaluate ($jj=$jj+1) end loop cpp2 end if evaluate ($ii=$ii+1) end loop seco set message=on echo=on end anomalous ? evaluate ($current_ano=$result) if (&make_non_anomalous=true) then if ($current_ano=true) then anomalous=false end if end if if (&make_anomalous=true) then if ($current_ano=false) then anomalous=true end if end if if (&expand=true) then expand end if write reflection output=&reflection_outfile selection=( &low_res > d > &high_res ) end end stop