# $Id: import_xtl.tcl 533 2009-12-04 23:07:46Z toby $

#-------------------------------------------------
# define info used in addcmds.tcl
set description "MSI .xtl file"
set extensions .xtl
set procname ReadMSIxtlFile
#-------------------------------------------------

proc ReadMSIxtlFile {filename} {
    set fp [open $filename r]
    set spg {}
    set cell {}
    set atomlist {}
    set shift {}
    set sgnum {}
    set sglbl {}
    set sgqual {}
    set head {}
    while {[gets $fp line] >= 0} {
	if {$head == ""} {
	    set token [string toupper [lindex $line 0] ]
	} else {
	    set token ParseAtom
	}
	switch $token {
	    TITLE {continue}
	    DIMENSION {continue}
	    CELL {
		# cell parameters are usually on the next line (always?)
		if {[lrange $line 1 end] == ""} {
		    gets $fp cell
		} else {
		    set cell [lrange $line 1 end]
		}
	    }
	    SYMMETRY {
		# scan line for either the flag number or label
		set i 0
		while {[lindex $line [incr i]] != ""} {
		    if {[string toupper [lindex $line $i]] == "NUMBER"} {
			set sgnum [lindex $line [incr i]]
		    } elseif {[string toupper [lindex $line $i]] == "LABEL"} {
			set sglbl [lindex $line [incr i]]
		    } elseif {[string toupper [lindex $line $i]] == "QUALIFIER"} {
			set sgqual [lindex $line [incr i]]
		    }
		}   
	    }
	    ATOMS {
		gets $fp head
		set head [string toupper $head]
		# process the space group now, so that we can establish 
		# a shift for coordinates
		set fp1 {}
		if {$sgnum !=  ""} {
		    global expgui
		    set fp1 [open [file join \
			    $expgui(scriptdir) spacegrp.ref] r]
		    while {[gets $fp1 line] >= 0} {
			if {$sgnum == [lindex $line 1]} {
			    set spg [lindex $line 8]
			    break
			}
		    }
		} elseif {$sglbl !=  ""} {
		    global expgui
		    set sgtmp [string toupper $sglbl]
		    # remove spaces from space group
		    regsub -all " " $sgtmp "" sgtmp
		    # make a copy where we treat bar 3 as the same as 3 
		    regsub -- "-3" $sgtmp "3" sgtmp3
		    set fp1 [open [file join \
			    $expgui(scriptdir) spacegrp.ref] r]
		    while {[gets $fp1 line] >= 0} {
			set testsg [string toupper [lindex $line 8]]
			regsub -all " " $testsg "" testsg
			if {$testsg == $sgtmp} {
			    set spg [lindex $line 8]
			    set sgnum [lindex $line 1]
			    break
			} elseif {[lindex $line 1] >= 200} {
			    regsub -- "-3" $testsg "3" testsg3
			    if {$testsg3 == $sgtmp3} {
				set spg [lindex $line 8]
				set sgnum [lindex $line 1]
				break
			    }
			} elseif {[lindex $line 1] <= 18} {
			    # monoclinic: change operators of form "1 xxx 1" to "xxx"
			    regsub -- " 1 (.*) 1" [string toupper [lindex $line 8]] "\\1" testsg
			    # remove spaces from space group
			    regsub -all " " $testsg "" testsg
			    if {$testsg == $sgtmp} {
				set spg [lindex $line 8]
				set sgnum [lindex $line 1]
				break
			    }
			}
		    }
		}
		# is this an origin 1 setting where a choice exists?
		if {$spg != "" && [string tolower $sgqual] == "origin_1"} {
		    # advance to the 2nd part of the file
		    while {[lindex $line 1] != 230} {
			if {[gets $fp1 line] < 0} break
		    }
		    while {[gets $fp1 line] >= 0} {
			if {$sgnum == [lindex $line 1]} {
			    set spg [lindex $line 8]
			    set shift [lindex $line 9]
			    break
			}
		    }
		}
		if {$fp1 != ""} {close $fp1}
	    }
	    ParseAtom {
		# ignore blank lines

		if {[string trim $line] == ""} continue
		set label {}
		set type {}
		# get label & element type from name or better -- Scat field
		set n [lsearch $head NAME]
		if {$n != -1} {
		    set label [lindex $line $n]
		    regsub -all {[0-9 ]} $label "" type
		}
		set l2 $label
		set n [lsearch $head SCAT]
		if {$n != -1} {
		    if {[lindex $line $n] != ""} {
			set type [lindex $line $n]
			regsub -all {[0-9 +-]} $type "" type
		    }
		}
		foreach p {X Y Z} s $shift {
		    set n [lsearch $head $p]
		    if {$n == -1} {
			lappend l2 {}
		    } else {
			set v [lindex $line $n]
			if {$s != ""} {set v [expr $v + $s]}
			lappend l2 $v
		    }
		}
		lappend l2 $type
		set n [lsearch $head OCCUP]
		if {$n == -1} {
		    lappend l2 {}
		} else {
		    lappend l2 [lindex $line $n]
		}
		set uiso {}
		# get temperature factor, if present
		set n [lsearch $head TEMP]
		if {$n != -1} {
		    if {[catch {
			set uiso [expr [lindex $line $n] / 78.9567]
			set uiso [format %.5f $uiso]
		    }]} {set uiso ""}
		}
		set n [lsearch $head UISO]
		if {$n != -1} {
		    if {[catch {
			set uiso [expr [lindex $line $n]]
			set uiso [format %.5f $uiso]
		    }]} {set uiso ""}
		}
		if {$uiso != ""} {
		    lappend l2 $uiso
		}
		lappend atomlist $l2
	    }
	    default {}
	}
    }
    close $fp

    set msg {}
    # spacegroup was not found
    if {$spg == ""} {
	# did not find the spacegroup
	if {$sglbl != ""} {
	    MyMessageBox -parent . -type ok -icon warning \
		-message "Error: The space group ($sglbl) in file $filename could not be converted to match GSAS input; please edit it"
	    set spg $sglbl
	    set msg "Note: You must check the space group & edit to conform to GSAS input"
	} else {
	    MyMessageBox -parent . -type ok -icon warning \
		-message "Error: The space group number information in file $filename is missing or invalid!"
	    set msg "Note: You must set the space group"
	}
    } elseif {$shift != ""} {
	# don't have the correct setting
	MyMessageBox -parent . -type ok -icon warning \
		-message "Note: an origin shift ($shift) has been added to the coordinates to convert them to the Origin Choice 2 setting (-1 at 000)"
    }
    # adjust space group for rhombohedral settings
    if {$spg != "" && [string tolower $sgqual] == "rhombohedral"} {
	append spg " R"
    }
    return "[list $spg] [list $cell] [list $atomlist] [list $msg]"
}