[1166] | 1 | #============================================================================ |
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| 2 | # Rigid body utility routines |
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| 3 | #============================================================================ |
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| 4 | # RigidBodyGetVarNums: Returns a list of the variable numbers in use |
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| 5 | # for rigid body variable parameters. |
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| 6 | # RigidBodyAtomNums: returns a list of atom numbers that are mapped to |
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| 7 | # rigid bodies in a selected phase |
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| 8 | # RigidStartAtoms: returns a list of atoms that are allowed for creation of RB |
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| 9 | # ExtractRigidBody: Use the GSAS geometry program to cartesian coordinates & |
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| 10 | # setting info for a RB from fractional coordinates for atoms in a phase |
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| 11 | # RunRecalcRBCoords: updates the coordinates in all phases after changes have |
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| 12 | # been made to rigid parameters. |
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| 13 | # CalcBody: Convert ortho to fractional coordinates using RB parameters |
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| 14 | # FitBody: Optimize the origin and Euler angles to match a rigid body to a |
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| 15 | # set of fractional coordinates |
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| 16 | # zmat2coord: convert a z-matrix to a set of cartesian coordinates |
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| 17 | # RB2cart: convert the representation used for rigid bodies into |
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| 18 | # cartesian coordinates |
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| 19 | # PlotRBtype: plot a rigid body with DRAWxtl |
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| 20 | # PlotRBcoords: plot orthogonal coordinates with DRAWxtl |
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| 21 | # DRAWxtlPlotRBFit: plot a set of fraction coordinates superimposed |
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| 22 | # on a structure read from a phase with DRAWxtl |
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| 23 | #============================================================================ |
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| 24 | #============================================================================ |
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| 25 | # RigidBodyGetVarNums: Returns a list of the variable numbers used already |
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| 26 | # for rigid body variable parameters |
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| 27 | proc RigidBodyGetVarNums {} { |
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| 28 | set varlist {} |
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| 29 | foreach type [RigidBodyList] { |
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| 30 | set typelist [lindex [ReadRigidBody $type] 1] |
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| 31 | foreach item $typelist { |
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| 32 | lappend varlist [lindex $item 2] |
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| 33 | } |
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| 34 | foreach phase $::expmap(phaselist) { |
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| 35 | foreach i [RigidBodyMappingList $phase $type] { |
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| 36 | set items [ReadRigidBodyMapping $phase $type $i] |
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| 37 | set varlist [concat $varlist [lindex $items 3]] |
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| 38 | if {[llength [lindex $items 6]] > 0} { |
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| 39 | set varlist [concat $varlist [lindex $items 6]] |
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| 40 | } |
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| 41 | } |
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| 42 | } |
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| 43 | } |
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| 44 | return [lsort -integer -unique $varlist] |
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| 45 | } |
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| 46 | |
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| 47 | # RigidBodyAtomNums: Returns a list of the atoms mapped to rigid bodies in |
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| 48 | # phase $phase |
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| 49 | proc RigidBodyAtomNums {phase} { |
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| 50 | if {[lsearch $::expmap(phaselist) $phase] == -1} {return ""} |
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| 51 | set allatoms $::expmap(atomlist_$phase) |
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| 52 | # get matching atoms coordinate range |
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| 53 | set mappedlist {} |
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| 54 | foreach type [RigidBodyList] { |
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| 55 | foreach i [RigidBodyMappingList $phase $type] { |
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| 56 | # get the number of atoms in this type of body |
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| 57 | set natoms [llength [lindex [lindex [lindex [ReadRigidBody $type] 1] 0] 3]] |
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| 58 | set natom1 [expr {$natoms - 1}] |
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| 59 | set items [ReadRigidBodyMapping $phase $type $i] |
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| 60 | set firstatom [lindex $items 0] |
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| 61 | set firstind [lsearch $allatoms $firstatom] |
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| 62 | set mappedlist [concat $mappedlist \ |
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| 63 | [lrange \ |
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| 64 | [lrange $allatoms $firstind end] \ |
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| 65 | 0 $natom1] \ |
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| 66 | ] |
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| 67 | } |
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| 68 | } |
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| 69 | return [lsort -integer $mappedlist] |
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| 70 | } |
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| 71 | |
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| 72 | # RigidStartAtoms: Find allowed starting atoms for a rigid body in a phase |
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| 73 | # Input: |
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| 74 | # phase is the phase number |
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| 75 | # natoms is the number of atoms in the RB to be mapped |
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| 76 | # Returns a list of valid "start" atoms. |
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| 77 | # Example: if the atom numbers in the phase are {2 4 5 6 7 8} and no rigid bodies |
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| 78 | # are mapped, then a 4-atom body can be mapped starting with atom 2, 4 or 5 only, |
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| 79 | # so {2 4 5} is returned |
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| 80 | # If atoms 2-6 were already mapped, then this routine would return an empty |
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| 81 | # list, as it is not possible to map the body. |
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| 82 | proc RigidStartAtoms {phase natoms} { |
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| 83 | if {[lsearch $::expmap(phaselist) $phase] == -1} {return ""} |
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| 84 | set allatoms $::expmap(atomlist_$phase) |
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| 85 | set usedatoms [RigidBodyAtomNums $phase] |
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| 86 | set startatomlist {} |
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| 87 | for {set i 0} {$i < [llength $allatoms]} {incr i} { |
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| 88 | set al [lrange $allatoms $i [expr {$i+$natoms-1}]] |
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| 89 | if {[llength $al] < $natoms} break |
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| 90 | set ok 1 |
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| 91 | foreach atom $al { |
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| 92 | if {[lsearch $usedatoms $atom] != -1} { |
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| 93 | set ok 0 |
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| 94 | break |
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| 95 | } |
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| 96 | } |
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| 97 | if $ok {lappend startatomlist [lindex $al 0]} |
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| 98 | } |
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| 99 | return $startatomlist |
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| 100 | } |
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| 101 | |
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| 102 | # ExtractRigidBody: Use the GSAS geometry program to compute a set of cartesian coordinates for a |
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| 103 | # set of atoms in a .EXP file and provide the origin shift and Euler angles needed to |
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| 104 | # place the cartesian system into the crystal coordinates. Used for setting up a rigid body. |
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| 105 | # Returns a nested list of lists: |
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| 106 | # element 0: a list of the origin location {x y z} in fraction coordinates |
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| 107 | # element 1: a list of three rotation angles in form {a1 a2 a3} |
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| 108 | # where a1, a2 and a3 are rotations around the cartesian x, y and z axes |
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| 109 | # element 2: a list of $natom cartesian coordinate triples {{x1 y1 z1} {x2 y2 z2}...} |
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| 110 | # arguments: |
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| 111 | # phase: phase # |
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| 112 | # natom: number of atoms in group |
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| 113 | # firstatom: sequence # in phase (may be > than number of the atom) |
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| 114 | # originlist: atoms to define origin (where 1 is first atom in group; <= natom) |
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| 115 | # vector1: list of 3 values with X, Y or Z, atom #a and #b (number as in origin) (for example {X 1 3}) |
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| 116 | # vector2: list of 3 values with X, Y or Z, atom #a and #b (number as in origin) |
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| 117 | # note that vector2 must define a different axis than vector1 |
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| 118 | # also and vector1 and vector2 cannot use the same atom pair |
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| 119 | proc ExtractRigidBody {phase natom firstatom originlist vector1 vector2} { |
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| 120 | global expgui |
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| 121 | set fp [open "geom.inp" "w"] |
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| 122 | puts $fp "N" |
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| 123 | if {[llength ::expmap(phaselist)] > 1} { |
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| 124 | # select phase |
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| 125 | puts $fp "N" |
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| 126 | puts $fp $phase |
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| 127 | puts $fp "N" |
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| 128 | } |
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| 129 | puts $fp "R" |
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| 130 | puts $fp "$natom" |
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| 131 | puts $fp "$firstatom" |
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| 132 | puts $fp [llength $originlist] |
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| 133 | foreach i $originlist { |
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| 134 | puts $fp $i |
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| 135 | } |
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| 136 | foreach i [concat $vector1 $vector2] { |
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| 137 | puts $fp $i |
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| 138 | } |
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| 139 | puts $fp "0" |
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| 140 | puts $fp "X" |
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| 141 | close $fp |
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| 142 | #puts "[file join $expgui(gsasexe) geometry] $expgui(expfile) < geom.inp > geom.out" |
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[1175] | 143 | # Save any change sin the current exp file |
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| 144 | savearchiveexp |
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[1166] | 145 | catch { |
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| 146 | exec [file join $expgui(gsasexe) geometry] $expgui(expfile) < geom.inp > geom.out |
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| 147 | } err |
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| 148 | #puts $err |
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| 149 | file delete geom.inp |
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| 150 | set fp [open geom.out r] |
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| 151 | set origin {} |
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| 152 | set Euler {} |
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| 153 | set coordlist {} |
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| 154 | while {[gets $fp line] >= 0} { |
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| 155 | if {[string first "Cell coordinates of origin" $line] != -1} { |
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| 156 | set origin [lrange [string range $line [string first "are" $line] end] 1 3] |
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| 157 | #puts "origin in rb = $origin" |
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| 158 | } |
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| 159 | if {[string first "Rotation angles" $line] != -1} { |
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| 160 | set Euler {} |
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| 161 | foreach i [lrange [split $line "="] 1 3] { |
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| 162 | lappend Euler [lindex $i 0] |
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| 163 | } |
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| 164 | #puts $line |
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| 165 | #puts $Euler |
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| 166 | } |
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| 167 | if {[string first "Atom Orthon" $line] != -1} { |
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| 168 | set coordlist {} |
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| 169 | for {set i 1} {$i <= $natom} {incr i} { |
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| 170 | gets $fp line |
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| 171 | set coord {} |
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| 172 | lappend coord [string trim [string range $line 9 15]] |
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| 173 | lappend coord [string trim [string range $line 16 22]] |
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| 174 | lappend coord [string trim [string range $line 23 29]] |
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| 175 | lappend coord [string trim [string range $line 0 8]] |
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| 176 | #puts $line |
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| 177 | #puts $coord |
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| 178 | lappend coordlist $coord |
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| 179 | } |
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| 180 | #puts $coordlist |
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| 181 | } |
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| 182 | } |
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| 183 | #file delete geom.out |
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| 184 | if {[llength $origin] == 0 || [llength $Euler] == 0 || [llength $coordlist] == 0} { |
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| 185 | puts "Error: run of GEOMETRY failed" |
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[1175] | 186 | error "Run of Program GEOMETRY failed, cannot continue" |
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[1166] | 187 | } |
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| 188 | return [list $origin $Euler $coordlist] |
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| 189 | } |
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| 190 | |
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| 191 | # RunRecalcRBCoords: updates the coordinates in a .EXP file after a rigid |
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| 192 | # body has been changed, mapped or the setting info is changed |
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| 193 | proc RunRecalcRBCoords { } { |
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| 194 | global expgui tcl_platform |
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| 195 | set input [open resetmult.inp w] |
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| 196 | puts $input "Y" |
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| 197 | puts $input "l b" |
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| 198 | puts $input "n" |
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| 199 | puts $input "x x x" |
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| 200 | puts $input "x" |
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| 201 | close $input |
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| 202 | # Save the current exp file |
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| 203 | savearchiveexp |
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| 204 | # disable the file changed monitor |
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| 205 | set expgui(expModifiedLast) 0 |
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| 206 | set expnam [file root [file tail $expgui(expfile)]] |
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| 207 | set err [catch { |
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| 208 | if {$tcl_platform(platform) == "windows"} { |
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| 209 | exec [file join $expgui(gsasexe) expedt.exe] $expnam < resetmult.inp >& resetmult.out |
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| 210 | } else { |
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| 211 | exec [file join $expgui(gsasexe) expedt] $expnam < resetmult.inp >& resetmult.out |
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| 212 | } |
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| 213 | } errmsg] |
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| 214 | loadexp $expgui(expfile) |
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| 215 | set fp [open resetmult.out r] |
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| 216 | set out [read $fp] |
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| 217 | close $fp |
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| 218 | set expgui(exptoolout) $out |
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| 219 | catch {file delete resetmult.inp resetmult.out} |
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| 220 | if {$err} { |
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| 221 | return $errmsg |
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| 222 | } else { |
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| 223 | return "" |
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| 224 | } |
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| 225 | } |
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| 226 | |
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| 227 | |
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| 228 | # compute a rotation matrix for orthogonal coordinates (based on MAKMATD in GSAS) |
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| 229 | # rotate angle degrees around axis (1, 2 or 3) for (x, y, or z) |
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| 230 | # returns a list that can be used as a matrix in the La package |
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| 231 | proc RotMatrix {axis angle} { |
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| 232 | set ang [expr {$angle * acos(0) / 90.}] |
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| 233 | set mat "1 0 0 0 1 0 0 0 1" |
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| 234 | if {$axis == 1} { |
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| 235 | set i1 1 |
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| 236 | set i2 2 |
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| 237 | } elseif {$axis == 2} { |
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| 238 | set i1 2 |
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| 239 | set i2 0 |
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| 240 | } else { |
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| 241 | set i1 0 |
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| 242 | set i2 1 |
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| 243 | } |
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| 244 | proc imat {i1 i2} {return [expr {(3*$i2) + $i1}]} |
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| 245 | foreach item { |
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| 246 | {$i1 $i1 [expr {cos($ang)}]} |
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| 247 | {$i2 $i2 [expr {cos($ang)}]} |
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| 248 | {$i1 $i2 [expr {-sin($ang)}]} |
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| 249 | {$i2 $i1 [expr {sin($ang)}]} |
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| 250 | } { |
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| 251 | foreach {c r val} [subst $item] {} |
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| 252 | set mat [lreplace $mat [imat $c $r] [imat $c $r] $val] |
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| 253 | } |
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| 254 | return "2 3 3 $mat" |
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| 255 | } |
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| 256 | |
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| 257 | # compute the derivative of the rotation matrix with respect to the angle, see RotMatrix |
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| 258 | # (based on MAKMATD in GSAS) |
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| 259 | # returns a list that can be used as a matrix in the La package |
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| 260 | proc DerivRotMatrix {axis angle} { |
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| 261 | set ang [expr {$angle * acos(0) / 90.}] |
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| 262 | set mat "0 0 0 0 0 0 0 0 0" |
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| 263 | if {$axis == 1} { |
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| 264 | set i1 1 |
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| 265 | set i2 2 |
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| 266 | } elseif {$axis == 2} { |
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| 267 | set i1 2 |
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| 268 | set i2 0 |
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| 269 | } else { |
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| 270 | set i1 0 |
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| 271 | set i2 1 |
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| 272 | } |
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| 273 | proc imat {i1 i2} {return [expr {(3*$i2) + $i1}]} |
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| 274 | foreach item { |
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| 275 | {$i1 $i1 [expr {-sin($ang) * acos(0) / 90.}]} |
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| 276 | {$i2 $i2 [expr {-sin($ang) * acos(0) / 90.}]} |
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| 277 | {$i1 $i2 [expr {-cos($ang) * acos(0) / 90.}]} |
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| 278 | {$i2 $i1 [expr {cos($ang) * acos(0) / 90.}]} |
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| 279 | } { |
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| 280 | foreach {c r val} [subst $item] {} |
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| 281 | set mat [lreplace $mat [imat $c $r] [imat $c $r] $val] |
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| 282 | } |
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| 283 | return "2 3 3 $mat" |
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| 284 | } |
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| 285 | |
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| 286 | # compute an orthogonalization matrix from cell parameters (based on AMATRX in GSAS) |
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| 287 | # returns a list that can be used as a matrix in the La package |
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| 288 | proc OrthoMatrix {a b c alpha beta gamma} { |
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| 289 | set CA [expr {cos($alpha * acos(0) / 90.)}] |
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| 290 | set CB [expr {cos($beta * acos(0) / 90.)}] |
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| 291 | set CG [expr {cos($gamma * acos(0) / 90.)}] |
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| 292 | set SA [expr {sin($alpha * acos(0) / 90.)}] |
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| 293 | set SB [expr {sin($beta * acos(0) / 90.)}] |
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| 294 | set SC [expr {sin($gamma * acos(0) / 90.)}] |
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| 295 | set CASTAR [expr { ($CB*$CG-$CA)/($SB*$SC) }] ;#! cos(Alpha*) |
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| 296 | set CBSTAR [expr { ($CA*$CG-$CB)/($SA*$SC) }] ;#! cos(Beta*) |
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| 297 | set CCSTAR [expr { ($CA*$CB-$CG)/($SA*$SB) }] ;#! cos(Gamma*) |
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| 298 | set SASTAR [expr { sqrt(1.0-($CASTAR*$CASTAR*2)) }] ;#! sin(Alpha*) |
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| 299 | set SBSTAR [expr { sqrt(1.0-($CBSTAR*$CBSTAR*2)) }] ;#! sin(Beta*) |
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| 300 | set SCSTAR [expr { sqrt(1.0-($CCSTAR*$CCSTAR*2)) }] ;#! sin(Gamma*) |
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| 301 | |
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| 302 | set A "2 3 3 $a 0 0 0 $b 0 0 0 $c" |
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| 303 | set A1 "2 3 3 1.0 0 0 $CG [expr {$SASTAR*$SC}] [expr {-$CASTAR*$SC}] $CB 0.0 $SB" |
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| 304 | #!This matrix is |
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| 305 | #! (1.0 0.0 0.0 ) |
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| 306 | #! (cos(G) sin(A*)*sin(G) -cos(A*)*sin(G) ) |
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| 307 | #! (cos(B) 0.0 sin(B) ) |
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| 308 | return [La::transpose [La::mmult $A $A1]] |
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| 309 | } |
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| 310 | |
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| 311 | # compute the transformation matrix that converts a rigid body coordinates into fractional |
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| 312 | # coordinates |
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| 313 | # arguments: |
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| 314 | # rotations: a list of axes and angles to rotate: { {axis1 angle1} {axis2 angle2} ...} |
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| 315 | # where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes |
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| 316 | # cellprms: a list with "a b c alpha beta gamma" in Angstroms and degrees |
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| 317 | # returns a list that can be used as a matrix in the La package |
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| 318 | proc CalcXformMatrix {rotations cellprms} { |
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| 319 | set prod {} |
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| 320 | foreach item $rotations { |
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| 321 | #puts $item |
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| 322 | set mat [eval RotMatrix $item] |
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| 323 | if {$prod == ""} { |
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| 324 | set prod $mat |
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| 325 | } else { |
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| 326 | set prod [La::mmult $prod $mat] |
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| 327 | } |
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| 328 | } |
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| 329 | #puts "--- rotation product ---" |
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| 330 | #puts [La::show $prod] |
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| 331 | |
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| 332 | set ortho [eval OrthoMatrix $cellprms] |
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| 333 | #puts "--- ortho ---" |
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| 334 | #puts [La::show $ortho] |
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| 335 | set deortho [La::msolve $ortho [La::mident 3] ] |
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| 336 | #puts "--- deortho ---" |
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| 337 | #puts [La::show $deortho] |
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| 338 | #puts "--- xform ---" |
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| 339 | set xform [La::mmult $deortho $prod] |
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| 340 | return $xform |
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| 341 | } |
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| 342 | |
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| 343 | # transforms a triplet of orthogonal coordinates into fractional ones using |
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| 344 | # arguments: |
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| 345 | # xform: a transformation matrix from CalcXformMatrix |
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| 346 | # origin: a list of fraction coordinates {x y z} describing the location of the |
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| 347 | # origin of the orthogonal coordinates in the crystal system |
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| 348 | # ortho: a triplet of othogonal coordinates |
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| 349 | # returns a triplet of fractional coordinates |
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| 350 | proc Ortho2Xtal {xform origin ortho} { |
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| 351 | set ocv "2 3 0 $ortho" |
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| 352 | set frac [La::mmult $xform $ocv] |
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| 353 | #puts [La::show [La::transpose $frac]] |
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| 354 | #puts $frac |
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| 355 | set frac [La::madd $frac "[lrange $frac 0 2] $origin"] |
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| 356 | #puts [La::show [La::transpose $frac]] |
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| 357 | return $frac |
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| 358 | } |
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| 359 | |
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| 360 | # compute the derivative of the transformation matrix (see CalcXformMatrix) |
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| 361 | # with respect to every rotation in the $rotations list |
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| 362 | # arguments: |
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| 363 | # rotations: a list of axes and angles to rotate: { {axis1 angle1} {axis2 angle2} ...} |
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| 364 | # where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes |
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| 365 | # cellprms: a list with "a b c alpha beta gamma" in Angstroms and degrees |
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| 366 | # returns a list of matrices where each matrix is a list that can be used as a |
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| 367 | # matrix in the La package |
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| 368 | proc CalcDerivMatrix {rotations cellprms} { |
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| 369 | set ortho [eval OrthoMatrix $cellprms] |
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| 370 | set deortho [La::msolve $ortho [La::mident 3] ] |
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| 371 | set derivlist {} |
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| 372 | |
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| 373 | foreach item $rotations { |
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| 374 | #puts $item |
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| 375 | set mat [eval DerivRotMatrix $item] |
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| 376 | #puts $item |
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| 377 | #puts [La::show $mat] |
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| 378 | set xform [La::mmult $deortho $mat] |
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| 379 | lappend derivlist $xform |
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| 380 | } |
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| 381 | return $derivlist |
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| 382 | } |
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| 383 | |
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| 384 | # CalcBody: Calculate fractional coordinates using rigid body setting parameters |
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| 385 | # arguments: |
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| 386 | # Euler: a list of axes and angles to rotate: { {axis1 angle1} {axis2 angle2} ...} |
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| 387 | # where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes |
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| 388 | # cell: a list with "a b c alpha beta gamma" in Angstroms and degrees |
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| 389 | # ortholist: list containing triplets with orthogonal coordinates |
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| 390 | # origin: a list of fraction coordinates {x y z} describing the location of the |
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| 391 | # origin of the orthogonal coordinates in the crystal system |
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| 392 | # note that the length of ortholist, useflag and fraclist should be the same |
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| 393 | # Returns a list with the computed fractional coordinates for all atoms |
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| 394 | proc CalcBody {Euler cell ortholist origin} { |
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| 395 | set xform [CalcXformMatrix $Euler $cell] |
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| 396 | set i 0 |
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| 397 | set sumdvs 0 |
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| 398 | set fracout {} |
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| 399 | set rmsout {} |
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| 400 | foreach oc $ortholist { |
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| 401 | set frac [lrange [Ortho2Xtal $xform $origin $oc] 3 end] |
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| 402 | lappend fracout $frac |
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| 403 | } |
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| 404 | return $fracout |
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| 405 | } |
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| 406 | |
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| 407 | |
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| 408 | # fit a rigid body's origin |
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| 409 | # arguments: |
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| 410 | # Euler: a list of axes and angles to rotate: { {axis1 angle1} {axis2 angle2} ...} |
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| 411 | # where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes |
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| 412 | # cell: a list with "a b c alpha beta gamma" in Angstroms and degrees |
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| 413 | # ortholist: list containing triplets with orthogonal coordinates |
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| 414 | # useflag: list of flags to indicate if an atom should be used (1) or ignored (0) |
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| 415 | # fraclist: list containing triplets with fractional coordinates |
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| 416 | # origin: a list of fraction coordinates {x y z} describing the location of the |
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| 417 | # origin of the orthogonal coordinates in the crystal system |
---|
| 418 | # note that the length of ortholist, useflag and fraclist should be the same |
---|
| 419 | # Returns a list with the following elements |
---|
| 420 | # 0: a list with three new origin values |
---|
| 421 | # 1: the root-mean square difference between the fraclist coordinates and those computed |
---|
| 422 | # using the input values for those atoms where $use is one (in Angstroms) |
---|
| 423 | # 2: the computed fractional coordinates for all atoms |
---|
| 424 | # 3: individual rms values for all atoms (in Angstroms) |
---|
| 425 | # note that items 1-3 are computed with the imput origin, not the revised one |
---|
| 426 | proc FitBodyOrigin {Euler cell ortholist useflag fraclist origin} { |
---|
| 427 | puts $fraclist |
---|
| 428 | set xform [CalcXformMatrix $Euler $cell] |
---|
| 429 | #puts "entering FitBodyOrigin" |
---|
| 430 | foreach var {x y z} {set sum($var) 0.0} |
---|
| 431 | set i 0 |
---|
| 432 | set sumdvs 0 |
---|
| 433 | set fracout {} |
---|
| 434 | set rmsout {} |
---|
| 435 | foreach oc $ortholist use $useflag coord $fraclist { |
---|
| 436 | #puts "ortho: $oc" |
---|
| 437 | set frac [lrange [Ortho2Xtal $xform $origin $oc] 3 end] |
---|
| 438 | lappend fracout $frac |
---|
| 439 | if {$use} {incr i} |
---|
| 440 | set dvs 0 |
---|
| 441 | foreach var {x y z} v1 $frac v2 $coord abc [lrange $cell 0 2] { |
---|
| 442 | #puts "v2 = $v2" |
---|
| 443 | #puts "v1 = $v1" |
---|
| 444 | #puts "abc = $abc" |
---|
| 445 | set dv [expr {($v2 - $v1)*$abc}] |
---|
| 446 | set dvs [expr {$dvs + $dv*$dv}] |
---|
| 447 | set sumdvs [expr {$sumdvs + $dv*$dv}] |
---|
| 448 | if {$use} {set sum($var) [expr {$sum($var) + $dv/$abc}]} |
---|
| 449 | #puts "round and round" |
---|
| 450 | } |
---|
| 451 | lappend rmsout [expr {sqrt($dvs)}] |
---|
| 452 | } |
---|
| 453 | set rms 0 |
---|
| 454 | if {$i > 1} {set rms [expr {sqrt($sumdvs)/$i}]} |
---|
| 455 | set neworig {} |
---|
| 456 | foreach var {x y z} o $origin { |
---|
| 457 | lappend neworig [expr {$o + ($sum($var)/$i)}] |
---|
| 458 | } |
---|
| 459 | return [list $neworig $rms $fracout $rmsout] |
---|
| 460 | } |
---|
| 461 | |
---|
| 462 | # fit a rigid body's Euler angles using least-squares |
---|
| 463 | # arguments: |
---|
| 464 | # Euler: a list of axes and angles to rotate: { {axis1 angle1} {axis2 angle2} ...} |
---|
| 465 | # where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes |
---|
| 466 | # cell: a list with "a b c alpha beta gamma" in Angstroms and degrees |
---|
| 467 | # ortholist: list containing triplets with orthogonal coordinates |
---|
| 468 | # useflag: list of flags to indicate if an atom should be used (1) or ignored (0) |
---|
| 469 | # fraclist: list containing triplets with fractional coordinates |
---|
| 470 | # origin: a list of fraction coordinates {x y z} describing the location of the |
---|
| 471 | # origin of the orthogonal coordinates in the crystal system |
---|
| 472 | # note that the length of ortholist, useflag and fraclist should be the same |
---|
| 473 | # Returns a list of new Euler angles |
---|
| 474 | proc FitBodyRot {Euler cell ortholist useflag fraclist origin} { |
---|
| 475 | set xform [CalcXformMatrix $Euler $cell] |
---|
| 476 | set derivlist [CalcDerivMatrix $Euler $cell] |
---|
| 477 | set A "2 [expr 3*[llength $ortholist]] 3" |
---|
| 478 | foreach oc $ortholist use $useflag coord $fraclist { |
---|
| 479 | if {! $use} continue |
---|
| 480 | foreach deriv $derivlist { |
---|
| 481 | foreach xyz [lrange [Ortho2Xtal $deriv "0 0 0" $oc] 3 end] { |
---|
| 482 | lappend A $xyz |
---|
| 483 | } |
---|
| 484 | } |
---|
| 485 | } |
---|
| 486 | #puts "A: [La::show $A]" |
---|
| 487 | set y "2 [expr 3*[llength $ortholist]] 1" |
---|
| 488 | foreach oc $ortholist use $useflag coord $fraclist { |
---|
| 489 | if {! $use} continue |
---|
| 490 | set frac [lrange [Ortho2Xtal $xform $origin $oc] 3 end] |
---|
| 491 | foreach xyz $coord XYZ $frac { |
---|
| 492 | lappend y [expr {$XYZ - $xyz}] |
---|
| 493 | } |
---|
| 494 | } |
---|
| 495 | |
---|
| 496 | set AtA [La::mmult [La::transpose $A] $A] |
---|
| 497 | set Aty [La::mmult [La::transpose $A] $y] |
---|
| 498 | |
---|
| 499 | set l {} |
---|
| 500 | #set shifts {} |
---|
| 501 | foreach delta [lrange [La::msolve $AtA $Aty] 3 end] item $Euler { |
---|
| 502 | #lappend shifts $delta |
---|
| 503 | lappend l "[lindex $item 0] [expr {$delta + [lindex $item 1]}]" |
---|
| 504 | } |
---|
| 505 | #puts "shifts = $shifts" |
---|
| 506 | return $l |
---|
| 507 | } |
---|
| 508 | |
---|
| 509 | # FitBody: fit a rigid body's Origin and Euler angles |
---|
| 510 | # arguments: |
---|
| 511 | # Euler: a list of axes and angles to rotate: { {axis1 angle1} {axis2 angle2} ...} |
---|
| 512 | # where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes |
---|
| 513 | # cell: a list with "a b c alpha beta gamma" in Angstroms and degrees |
---|
| 514 | # ortholist: list containing triplets with orthogonal coordinates |
---|
| 515 | # useflag: list of flags to indicate if an atom should be used (1) or ignored (0) |
---|
| 516 | # fraclist: list containing triplets with fractional coordinates |
---|
| 517 | # origin: a list of fraction coordinates {x y z} describing the location of the |
---|
| 518 | # origin of the orthogonal coordinates in the crystal system |
---|
| 519 | # note that the length of ortholist, useflag and fraclist should be the same |
---|
| 520 | # Returns a list containing |
---|
| 521 | # new origin |
---|
| 522 | # new Euler angles |
---|
| 523 | # total rms |
---|
| 524 | # fractional coordinates |
---|
| 525 | # rms deviation in fractional coordinates of new Euler angles |
---|
| 526 | proc FitBody {Euler cell ortholist useflag fraclist origin "ncycle 5"} { |
---|
| 527 | #puts "start origin = $origin" |
---|
| 528 | foreach { |
---|
| 529 | origin |
---|
| 530 | startrms |
---|
| 531 | fracout |
---|
| 532 | rmsout } [FitBodyOrigin $Euler $cell $ortholist $useflag $fraclist $origin] {} |
---|
| 533 | #puts "start rms = $startrms" |
---|
| 534 | set rmsprev $startrms |
---|
| 535 | #puts "new origin = $origin" |
---|
| 536 | for {set i 0} {$i < $ncycle} {incr i} { |
---|
| 537 | set Eulerprev $Euler |
---|
| 538 | set Euler [FitBodyRot $Euler $cell $ortholist $useflag $fraclist $origin] |
---|
| 539 | #puts "New Euler $Euler" |
---|
| 540 | #puts "after fit" |
---|
| 541 | foreach { |
---|
| 542 | origin |
---|
| 543 | rms |
---|
| 544 | fracout |
---|
| 545 | rmsout } [FitBodyOrigin $Euler $cell $ortholist $useflag $fraclist $origin] {} |
---|
| 546 | if {$rms > (1.1 * $rmsprev) + 0.01} { |
---|
| 547 | #puts "rms = $rms, new origin = $origin" |
---|
| 548 | set rmsprev $rms |
---|
| 549 | } |
---|
| 550 | } |
---|
| 551 | #proc FitBodyOrigin {Euler cell ortholist useflag fraclist origin} |
---|
| 552 | #return "$neworig $rms $fracout $rmsout" |
---|
| 553 | set fmt {"%8.5f %8.5f %8.5f %8.5f %8.5f %8.5f %6.3f"} |
---|
| 554 | #foreach fracin $fraclist fraccalc $fracout rmsi $rmsout { |
---|
| 555 | #puts "[eval format $fmt $fracin $fraccalc $rmsi]" |
---|
| 556 | #} |
---|
| 557 | return [list $origin $Euler $rms $fracout $rmsout] |
---|
| 558 | } |
---|
| 559 | |
---|
| 560 | # zmat2coord: convert a z-matrix to a set of cartesian coordinates |
---|
| 561 | # a z-matrix is also known as "internal coordinates" or "torsion space" |
---|
| 562 | # (see Journal of Computational Chemistry, Vol 26, #10, p. 1063â1068, 2005 or |
---|
| 563 | # http://www.cmbi.ru.nl/molden/zmat/zmat.html) |
---|
| 564 | # INPUT: |
---|
| 565 | # atmlist is a list of ascii lines where each line contains |
---|
| 566 | # lbl c1 distance c2 angle c3 torsion |
---|
| 567 | # where each atom is computed from the previous where the new atom is: |
---|
| 568 | # distance $distance from atom $c1 (angstrom) |
---|
| 569 | # angle $angle from $c1--$c2 (degrees) |
---|
| 570 | # torsion $torsion from $c1--$c2--$c3 (degrees) |
---|
| 571 | # OUTPUT: |
---|
| 572 | # zmat2coord returns a list of atom labels and cartesian coordinates, |
---|
| 573 | # with 4 items in each element (label, x, y, z) |
---|
| 574 | # this routine was tested against results from Babel via the web interface at |
---|
| 575 | # http://www.shodor.org/chemviz/zmatrices/babel.html and sample input at |
---|
| 576 | # http://iopenshell.usc.edu/howto/zmatrix/ |
---|
| 577 | proc zmat2coord {atmlist} { |
---|
| 578 | set torad [expr {acos(0)/90.}] |
---|
| 579 | set i 0 |
---|
| 580 | foreach line $atmlist { |
---|
| 581 | incr i |
---|
| 582 | foreach {lbl c1 dist c2 angle c3 torsion} $line {} |
---|
| 583 | if {$i == 1} { |
---|
| 584 | set atm(1) [list $lbl 0 0 0] ; # 1st atom is at origin |
---|
| 585 | } elseif {$i == 2} { |
---|
| 586 | set dist1 $dist |
---|
| 587 | set atm(2) [list $lbl $dist1 0 0] ; # 2nd atom is along x-axis |
---|
| 588 | } elseif {$i == 3} { |
---|
| 589 | # 3rd atom can be bonded to the 1st or 2nd |
---|
| 590 | if {$c1 == 1} { |
---|
| 591 | set atm(3) [list $lbl \ |
---|
| 592 | [expr {$dist * cos($torad * $angle)}] \ |
---|
| 593 | [expr {$dist * sin($torad * $angle)}] \ |
---|
| 594 | 0] |
---|
| 595 | } else { |
---|
| 596 | set atm(3) [list $lbl \ |
---|
| 597 | [expr {$dist1 - $dist * cos($torad * $angle)}] \ |
---|
| 598 | [expr {$dist * sin($torad * $angle)}] \ |
---|
| 599 | 0] |
---|
| 600 | } |
---|
| 601 | } else { |
---|
| 602 | set atm($i) [concat $lbl \ |
---|
| 603 | [ahcat "atm" $c1 $dist $c2 $angle $c3 $torsion]] |
---|
| 604 | } |
---|
| 605 | } |
---|
| 606 | set coordlist {} |
---|
| 607 | foreach key [lsort -integer [array names atm]] { |
---|
| 608 | lappend coordlist $atm($key) |
---|
| 609 | } |
---|
| 610 | return $coordlist |
---|
| 611 | } |
---|
| 612 | # Compute the length of a vector |
---|
| 613 | proc vlen {a} { |
---|
| 614 | set sum 0.0 |
---|
| 615 | foreach ai $a { |
---|
| 616 | set sum [expr {$sum + $ai*$ai}] |
---|
| 617 | } |
---|
| 618 | return [expr sqrt($sum)] |
---|
| 619 | } |
---|
| 620 | # compute vector (a + z * b) and optionally normalize to length d |
---|
| 621 | proc vadd {a b d z} { |
---|
| 622 | set c {} |
---|
| 623 | foreach ai $a bi $b { |
---|
| 624 | lappend c [expr {$bi + $z * $ai}] |
---|
| 625 | } |
---|
| 626 | set v [vlen $c] |
---|
| 627 | if {$d != 0} { |
---|
| 628 | set r {} |
---|
| 629 | foreach ci $c { |
---|
| 630 | lappend r [expr {$d * $ci / $v}] |
---|
| 631 | } |
---|
| 632 | return [list $v $r] |
---|
| 633 | } |
---|
| 634 | return [list $v $c] |
---|
| 635 | } |
---|
| 636 | # normalize a vector |
---|
| 637 | proc vnrm {x} { |
---|
| 638 | set v [vlen $x] |
---|
| 639 | if {abs($v) < 1e-8} {return [list 0 0 0]} |
---|
| 640 | set y {} |
---|
| 641 | foreach xi $x { |
---|
| 642 | lappend y [expr {$xi / $v}] |
---|
| 643 | } |
---|
| 644 | return $y |
---|
| 645 | } |
---|
| 646 | # compute the coordinates for an atom that is bonded: |
---|
| 647 | # distance $dist from atom $nc |
---|
| 648 | # angle $bondang from $nc--$nb |
---|
| 649 | # torsion $torsang from $nc--$nb--$na |
---|
| 650 | # coordinates are found in array $atmarr in the calling routine |
---|
| 651 | # based on a Fortran routine provided by Peter Zavalij (Thanks Peter!) |
---|
| 652 | proc ahcat {atmarr nc dist nb bondang na torsang} { |
---|
| 653 | upvar 1 $atmarr atm |
---|
| 654 | set xa [lrange $atm($na) 1 3] |
---|
| 655 | set xb [lrange $atm($nb) 1 3] |
---|
| 656 | set xc [lrange $atm($nc) 1 3] |
---|
| 657 | set torad [expr {acos(0)/90.}] |
---|
| 658 | # x = unit Vector A-B |
---|
| 659 | foreach {x1 x2 x3} [lindex [vadd $xb $xa 1. -1.] 1] {} |
---|
| 660 | # y = unit Vector C-B |
---|
| 661 | set y [lindex [vadd $xb $xc 1. -1.] 1] |
---|
| 662 | foreach {y1 y2 y3} $y {} |
---|
| 663 | set z1 [expr {$x2*$y3 - $x3*$y2}] |
---|
| 664 | set z2 [expr {$x3*$y1 - $x1*$y3}] |
---|
| 665 | set z3 [expr {$x1*$y2 - $x2*$y1}] |
---|
| 666 | set z [vnrm [list $z1 $z2 $z3]] |
---|
| 667 | set q1 [expr {$y2*$z3 - $y3*$z2}] |
---|
| 668 | set q2 [expr {$y3*$z1 - $y1*$z3}] |
---|
| 669 | set q3 [expr {$y1*$z2 - $y2*$z1}] |
---|
| 670 | set q [vnrm [list $q1 $q2 $q3]] |
---|
| 671 | set th [expr {$bondang * $torad}] |
---|
| 672 | set ph [expr {-1. * $torsang * $torad}] |
---|
| 673 | set cth [expr {cos($th)}] |
---|
| 674 | set sth [expr {sin($th)}] |
---|
| 675 | set cph [expr {cos($ph)}] |
---|
| 676 | set sph [expr {sin($ph)}] |
---|
| 677 | set xh {} |
---|
| 678 | foreach xci $xc xi $q zi $z yi $y { |
---|
| 679 | lappend xh [expr { |
---|
| 680 | $xci + |
---|
| 681 | $dist*($sth*($cph*$xi + $sph*$zi)-$cth*$yi) |
---|
| 682 | }] |
---|
| 683 | } |
---|
| 684 | return $xh |
---|
| 685 | } |
---|
| 686 | |
---|
| 687 | # RB2cart: convert the rigid body representation reported as the 2nd element |
---|
| 688 | # in ReadRigidBody into cartesian coordinates |
---|
| 689 | # rblist: a list containing an element for each scaling factor |
---|
| 690 | # in each element there are four items: |
---|
| 691 | # a multiplier value for the rigid body coordinates |
---|
| 692 | # a damping value (0-9) for the refinement of the multiplier (not used) |
---|
| 693 | # a variable number if the multiplier will be refined (not used) |
---|
| 694 | # a list of cartesian coordinates coordinates |
---|
| 695 | # each cartesian coordinate contains 4 items: x,y,z and a label |
---|
| 696 | # returns a list of coordinate triplets |
---|
| 697 | proc RB2cart {rblist} { |
---|
| 698 | foreach item $rblist { |
---|
| 699 | foreach {mult damp ref coords} $item {} |
---|
| 700 | set i 0 |
---|
| 701 | foreach xyz $coords { |
---|
| 702 | foreach {x y z} [lrange $xyz 0 2] {} |
---|
| 703 | foreach val [lrange $xyz 0 2] var {X Y Z} { |
---|
| 704 | if {[array names $var $i] == ""} { |
---|
| 705 | set ${var}($i) [expr {$mult * $val}] |
---|
| 706 | } else { |
---|
| 707 | set ${var}($i) [expr {[set ${var}($i)] + $mult * $val}] |
---|
| 708 | } |
---|
| 709 | } |
---|
| 710 | incr i |
---|
| 711 | } |
---|
| 712 | } |
---|
| 713 | set out "" |
---|
| 714 | foreach i [lsort -integer [array names X]] { |
---|
| 715 | lappend out [list $X($i) $Y($i) $Z($i)] |
---|
| 716 | } |
---|
| 717 | return $out |
---|
| 718 | } |
---|
| 719 | |
---|
| 720 | # get the name of the DRAWxtl application, if installed |
---|
| 721 | proc GetDRAWxtlApp {} { |
---|
| 722 | # is DRAWxtl installed? |
---|
| 723 | set app {} |
---|
| 724 | if {![catch {set fp [open [file join $::env(HOME) .drawxtlrc] r]}]} { |
---|
| 725 | # line 12 is name of executable |
---|
| 726 | set i 0 |
---|
| 727 | while {$i < 12} { |
---|
| 728 | incr i |
---|
| 729 | gets $fp appname |
---|
| 730 | } |
---|
| 731 | close $fp |
---|
| 732 | set app [auto_execok $appname] |
---|
| 733 | } |
---|
| 734 | if {$app != ""} { |
---|
| 735 | return $appname |
---|
| 736 | } |
---|
| 737 | return "" |
---|
| 738 | } |
---|
| 739 | |
---|
| 740 | # DRAWxtlPlotOrtho: plot orthogonal coordinates in DRAWxtl |
---|
| 741 | # input: |
---|
| 742 | # filename: file name for the .str file to create |
---|
| 743 | # title: string for title in .str file |
---|
| 744 | # coords: cartesian coordinates |
---|
| 745 | # bondlist: list of bonds to draw as min, max length (A) and |
---|
| 746 | # an optional color; for example: {{1.4 1.6} {1.2 1.3 Red}} |
---|
| 747 | proc DRAWxtlPlotOrtho {filename title coords bondlist} { |
---|
| 748 | foreach {xmin ymin zmin} {"" "" ""} {} |
---|
| 749 | foreach {xmax ymax zmax} {"" "" ""} {} |
---|
| 750 | foreach xyz $coords { |
---|
| 751 | foreach {x y z} $xyz {} |
---|
| 752 | foreach s {x y z} { |
---|
| 753 | foreach t {min max} { |
---|
| 754 | if {[set ${s}${t}] == ""} {set ${s}${t} [set $s]} |
---|
| 755 | } |
---|
| 756 | if {[set ${s}min] > [set $s]} {set ${s}min [set $s]} |
---|
| 757 | if {[set ${s}max] < [set $s]} {set ${s}max [set $s]} |
---|
| 758 | } |
---|
| 759 | } |
---|
| 760 | #puts "$xmin $xmax $ymin $ymax $zmin $zmax" |
---|
| 761 | set max $xmin |
---|
| 762 | foreach val "$xmin $xmax $ymin $ymax $zmin $zmax" { |
---|
| 763 | if {$max < abs($val)} {set max $val} |
---|
| 764 | } |
---|
| 765 | set scale [expr {4.*$max}] |
---|
| 766 | set a 10. |
---|
| 767 | lappend range [expr -0.01+($xmin/$scale)] [expr 0.01+($xmax/$scale)] \ |
---|
| 768 | [expr -0.01+($ymin/$scale)] [expr 0.01+($ymax/$scale)] \ |
---|
| 769 | [expr -0.01+($zmin/$scale)] [expr 0.01+($zmax/$scale)] |
---|
| 770 | set fp [open $filename w] |
---|
| 771 | puts $fp "title $title" |
---|
| 772 | puts $fp "box 0.000 Black" |
---|
| 773 | puts $fp "background White" |
---|
| 774 | #puts $fp "nolabels" |
---|
| 775 | puts $fp "cell $a $a $a 90 90 90" |
---|
| 776 | puts $fp "spgr P 1" |
---|
| 777 | puts $fp "pack $range" |
---|
| 778 | set i 0 |
---|
| 779 | foreach xyz $coords { |
---|
| 780 | foreach {x y z} $xyz {} |
---|
| 781 | incr i |
---|
| 782 | puts $fp "atom c $i [expr {$x/$scale}] [expr {$y/$scale}] [expr {$z/$scale}]" |
---|
| 783 | puts $fp "labeltext [expr {0.02 + $x/$scale}] [expr {0.01 + $y/$scale}] [expr {0.01 + $z/$scale}] $i" |
---|
| 784 | } |
---|
| 785 | puts $fp "sphere c [expr 0.100*($a/$scale)] Red" |
---|
| 786 | puts $fp "finish 0.70 0.30 0.08 0.01" |
---|
| 787 | foreach bondpair $bondlist { |
---|
| 788 | foreach {b1 b2 color} $bondpair {} |
---|
| 789 | if {$color == ""} {set color Red} |
---|
| 790 | puts $fp "bond c c [expr {0.01*$a/$scale}] [expr {$b1*$a/$scale}] [expr {$b2*$a/$scale}] $color" |
---|
| 791 | } |
---|
| 792 | puts $fp "frame" |
---|
| 793 | set range {} |
---|
| 794 | lappend range -0.01 [expr 0.01+(0.1*$a/$scale)] \ |
---|
| 795 | -0.01 [expr 0.01+(0.1*$a/$scale)] \ |
---|
| 796 | -0.01 [expr 0.01+(0.1*$a/$scale)] |
---|
| 797 | puts $fp "cell $a $a $a 90 90 90" |
---|
| 798 | puts $fp "spgr P 1" |
---|
| 799 | puts $fp "pack $range" |
---|
| 800 | puts $fp "atom o 1 0 0 0" |
---|
| 801 | puts $fp "atom o 2 [expr {0.1*$a/$scale}] 0 0" |
---|
| 802 | puts $fp "atom o 3 0 [expr {0.1*$a/$scale}] 0" |
---|
| 803 | puts $fp "atom o 4 0 0 [expr {0.1*$a/$scale}]" |
---|
| 804 | puts $fp "bond o o [expr {0.01*$a/$scale}] [expr {-0.1 + $a/$scale}] [expr {0.1 + $a/$scale}] Black" |
---|
| 805 | puts $fp "labelscale 0.5" |
---|
| 806 | puts $fp "labeltext [expr {0.11*$a/$scale}] 0 0 x" |
---|
| 807 | puts $fp "labeltext 0 [expr {0.11*$a/$scale}] 0 y" |
---|
| 808 | puts $fp "labeltext 0 0 [expr {0.11*$a/$scale}] z" |
---|
| 809 | puts $fp "sphere o [expr {0.02*$a/$scale}] Blue" |
---|
| 810 | puts $fp "origin .0 .0 .0" |
---|
| 811 | puts $fp "end" |
---|
| 812 | close $fp |
---|
| 813 | } |
---|
| 814 | |
---|
| 815 | # PlotRBtype: plot a rigid body in DRAWxtl |
---|
| 816 | # input: |
---|
| 817 | # rbtype: # of rigid body |
---|
| 818 | # bondlist: list of bonds to draw as min, max length (A) and |
---|
| 819 | # an optional color; for example: {{1.4 1.6} {1.2 1.3 Red}} |
---|
| 820 | # file: file name for the .str file to create |
---|
| 821 | proc PlotRBtype {rbtype "bondlist {}" "file {}"} { |
---|
| 822 | set app [GetDRAWxtlApp] |
---|
| 823 | if {$app == ""} { |
---|
| 824 | MyMessageBox -parent . -title "No DRAWxtl" \ |
---|
| 825 | -message "Sorry, DRAWxtl is not installed" \ |
---|
| 826 | -icon warning |
---|
| 827 | return |
---|
| 828 | } |
---|
| 829 | if {$::tcl_platform(platform) == "windows" && $file == ""} { |
---|
| 830 | set file [file join [pwd] rbplot.str] |
---|
| 831 | } else { |
---|
| 832 | set file "/tmp/rbplot.str" |
---|
| 833 | } |
---|
| 834 | set coords [RB2cart [lindex [ReadRigidBody $rbtype] 1]] |
---|
| 835 | DRAWxtlPlotOrtho $file "" $coords $bondlist |
---|
| 836 | if {$app != ""} {exec $app $file &} |
---|
| 837 | } |
---|
| 838 | |
---|
| 839 | # PlotRBcoords: plot orthogonal coordinates in DRAWxtl |
---|
| 840 | # input: |
---|
| 841 | # coords: cartesian coordinates |
---|
| 842 | # bondlist: list of bonds to draw as min, max length (A) and |
---|
| 843 | # an optional color; for example: {{1.4 1.6} {1.2 1.3 Red}} |
---|
| 844 | # file: file name for the .str file to create |
---|
| 845 | proc PlotRBcoords {coords "bondlist {}" "file {}"} { |
---|
| 846 | set app [GetDRAWxtlApp] |
---|
| 847 | if {$app == ""} { |
---|
| 848 | MyMessageBox -parent . -title "No DRAWxtl" \ |
---|
| 849 | -message "Sorry, DRAWxtl is not installed" \ |
---|
| 850 | -icon warning |
---|
| 851 | return |
---|
| 852 | } |
---|
| 853 | if {$::tcl_platform(platform) == "windows" && $file == ""} { |
---|
| 854 | set file [file join [pwd] rbplot.str] |
---|
| 855 | } else { |
---|
| 856 | set file "/tmp/rbplot.str" |
---|
| 857 | } |
---|
| 858 | DRAWxtlPlotOrtho $file "" $coords $bondlist |
---|
| 859 | if {$app != ""} {exec $app $file &} |
---|
| 860 | } |
---|
| 861 | |
---|
| 862 | # DRAWxtlPlotRBFit: plot a set of fraction coordinates superimposed |
---|
| 863 | # on a structure read from a phase |
---|
| 864 | # input: |
---|
| 865 | # RBcoords: fractional coordinates for rigid body |
---|
| 866 | # phase:# of phase to plot |
---|
| 867 | # firstatom: seq # of 1st atom in structure to be mapped to rigid body |
---|
| 868 | # allatoms: 0 to plot only atoms in phase that are in the rigid body, |
---|
| 869 | # otherwise plot all atoms |
---|
| 870 | # bondlist: list of bonds to draw for the phase as min, max length (A) and |
---|
| 871 | # an optional color; for example: {{1.4 1.6} {1.2 1.3 Red}} |
---|
| 872 | # rbbondlist: list of bonds to draw for the phase as min, max length (A) and |
---|
| 873 | # an optional color; for example: {{1.4 1.6} {1.2 1.3 Red}} |
---|
| 874 | # file: optional file name for the .str file to create |
---|
| 875 | proc DRAWxtlPlotRBFit {RBcoords phase firstatom "allatoms 0" \ |
---|
| 876 | "bondlist {}" "rbbondlist {}" "file {}"} { |
---|
| 877 | set natom [llength $RBcoords] |
---|
| 878 | set app [GetDRAWxtlApp] |
---|
| 879 | if {$app == ""} { |
---|
| 880 | MyMessageBox -parent . -title "No DRAWxtl" \ |
---|
| 881 | -message "Sorry, DRAWxtl is not installed" \ |
---|
| 882 | -icon warning |
---|
| 883 | return |
---|
| 884 | } |
---|
| 885 | if {$::tcl_platform(platform) == "windows" && $file == ""} { |
---|
| 886 | set file [file join [pwd] rbplot.str] |
---|
| 887 | } else { |
---|
| 888 | set file "/tmp/rbfit.str" |
---|
| 889 | } |
---|
| 890 | |
---|
| 891 | # get rigid body coordinate range |
---|
| 892 | foreach {xmin ymin zmin} {"" "" ""} {} |
---|
| 893 | foreach {xmax ymax zmax} {"" "" ""} {} |
---|
| 894 | foreach xyz $RBcoords { |
---|
| 895 | foreach {x y z} $xyz {} |
---|
| 896 | foreach s {x y z} { |
---|
| 897 | foreach t {min max} { |
---|
| 898 | if {[set ${s}${t}] == ""} {set ${s}${t} [set $s]} |
---|
| 899 | } |
---|
| 900 | if {[set ${s}min] > [set $s]} {set ${s}min [set $s]} |
---|
| 901 | if {[set ${s}max] < [set $s]} {set ${s}max [set $s]} |
---|
| 902 | } |
---|
| 903 | } |
---|
| 904 | set rbrange {} |
---|
| 905 | foreach val [list [expr -0.01+$xmin] [expr 0.01+$xmax] \ |
---|
| 906 | [expr -0.01+$ymin] [expr 0.01+$ymax] \ |
---|
| 907 | [expr -0.01+$zmin] [expr 0.01+$zmax] ] { |
---|
| 908 | append rbrange [format " %8.4f" $val] |
---|
| 909 | } |
---|
| 910 | set rbcenter [list [expr {($xmin+$xmax)/2}] \ |
---|
| 911 | [expr {($ymin+$ymax)/2}] \ |
---|
| 912 | [expr {($zmin+$zmax)/2}] ] |
---|
| 913 | # get matching atoms coordinate range |
---|
| 914 | set firstind [lsearch $::expmap(atomlist_$phase) $firstatom] |
---|
| 915 | set matchedatomlist [lrange \ |
---|
| 916 | [lrange $::expmap(atomlist_$phase) $firstind end] \ |
---|
| 917 | 0 [expr {$natom-1}]] |
---|
| 918 | foreach atom $matchedatomlist { |
---|
| 919 | foreach s {x y z} { |
---|
| 920 | set $s [atominfo $phase $atom $s] |
---|
| 921 | foreach t {min max} { |
---|
| 922 | if {[set ${s}${t}] == ""} {set ${s}${t} [set $s]} |
---|
| 923 | } |
---|
| 924 | if {[set ${s}min] > [set $s]} {set ${s}min [set $s]} |
---|
| 925 | if {[set ${s}max] < [set $s]} {set ${s}max [set $s]} |
---|
| 926 | } |
---|
| 927 | } |
---|
| 928 | # expand to cover at least one unit cell |
---|
| 929 | foreach var {xmin ymin zmin} { |
---|
| 930 | if {[set $var] > 0.0} {set $var 0.0} |
---|
| 931 | } |
---|
| 932 | foreach var {xmax ymax zmax} { |
---|
| 933 | if {[set $var] < 1.} {set $var 1.} |
---|
| 934 | } |
---|
| 935 | set range {} |
---|
| 936 | foreach val [list [expr -0.01+$xmin] [expr 0.01+$xmax] \ |
---|
| 937 | [expr -0.01+$ymin] [expr 0.01+$ymax] \ |
---|
| 938 | [expr -0.01+$zmin] [expr 0.01+$zmax]] { |
---|
| 939 | append range [format " %8.4f" $val] |
---|
| 940 | } |
---|
| 941 | |
---|
| 942 | set fp [open $file w] |
---|
| 943 | puts $fp "title structure/rigid-body fit plot" |
---|
| 944 | # plot the structure |
---|
| 945 | puts -nonewline $fp "cell" |
---|
| 946 | foreach p {a b c alpha beta gamma} { |
---|
| 947 | puts -nonewline $fp " [phaseinfo $phase $p]" |
---|
| 948 | } |
---|
| 949 | puts $fp "" |
---|
| 950 | puts $fp "spgp [phaseinfo $phase spacegroup]" |
---|
| 951 | puts $fp "pack $range" |
---|
| 952 | if {$allatoms != 0} { |
---|
| 953 | set atoms $::expmap(atomlist_$phase) |
---|
| 954 | } else { |
---|
| 955 | set firstind [lsearch $::expmap(atomlist_$phase) $firstatom] |
---|
| 956 | set atoms [lrange \ |
---|
| 957 | [lrange $::expmap(atomlist_$phase) $firstind end] \ |
---|
| 958 | 0 [expr {$natom-1}]] |
---|
| 959 | } |
---|
| 960 | |
---|
| 961 | # set origin at center of rigid body |
---|
| 962 | puts $fp "origin $rbcenter" |
---|
| 963 | # now loop over atoms |
---|
| 964 | foreach atom $atoms { |
---|
| 965 | set type [atominfo $phase $atom type] |
---|
| 966 | set typelist($type) 1 |
---|
| 967 | set xyz "" |
---|
| 968 | foreach v {x y z} { |
---|
| 969 | append xyz "[atominfo $phase $atom $v] " |
---|
| 970 | } |
---|
| 971 | puts $fp "atom $type $atom $xyz" |
---|
| 972 | if {[lsearch $matchedatomlist $atom] != -1} { |
---|
| 973 | puts $fp "labeltext $xyz $atom" |
---|
| 974 | } |
---|
| 975 | |
---|
| 976 | set uiso [atominfo $phase $atom Uiso] |
---|
| 977 | # are there anisotropic atoms? If so convert them to Uequiv |
---|
| 978 | if {[atominfo $phase $atom temptype] == "A"} { |
---|
| 979 | puts -nonewline $fp "Uij [atominfo $phase $atom type] $atom " |
---|
| 980 | foreach v {U11 U22 U33 U12 U13 U23} { |
---|
| 981 | puts -nonewline $fp "[atominfo $phase $atom $v] " |
---|
| 982 | } |
---|
| 983 | puts $fp "" |
---|
| 984 | } |
---|
| 985 | } |
---|
| 986 | |
---|
| 987 | foreach type [array names typelist] color {Green Blue Magenta Cyan} { |
---|
| 988 | if {$type == ""} break |
---|
| 989 | puts $fp "sphere $type 0.1 $color" |
---|
| 990 | } |
---|
| 991 | foreach type [array names typelist] color1 {Green Blue Magenta Cyan} { |
---|
| 992 | foreach bondpair $bondlist { |
---|
| 993 | foreach {b1 b2 color} $bondpair {} |
---|
| 994 | if {$color == ""} {set color $color1} |
---|
| 995 | puts $fp "bond $type $type 0.02 $b1 $b2 $color" |
---|
| 996 | } |
---|
| 997 | foreach type1 [array names typelist] { |
---|
| 998 | if {$type1 == $type} break |
---|
| 999 | foreach bondpair $bondlist { |
---|
| 1000 | foreach {b1 b2 color} $bondpair {} |
---|
| 1001 | if {$color == ""} {set color $color1} |
---|
| 1002 | puts $fp "bond $type $type1 0.02 $b1 $b2 $color" |
---|
| 1003 | } |
---|
| 1004 | } |
---|
| 1005 | } |
---|
| 1006 | # plot the rigid body |
---|
| 1007 | puts $fp "frame" |
---|
| 1008 | puts -nonewline $fp "cell" |
---|
| 1009 | foreach p {a b c alpha beta gamma} { |
---|
| 1010 | puts -nonewline $fp " [phaseinfo $phase $p]" |
---|
| 1011 | } |
---|
| 1012 | puts $fp "" |
---|
| 1013 | puts $fp "background White" |
---|
| 1014 | #puts $fp "nolabels" |
---|
| 1015 | puts $fp "labelscale 0.5" |
---|
| 1016 | puts $fp "spgr P 1" |
---|
| 1017 | puts $fp "pack $rbrange" |
---|
| 1018 | set i 0 |
---|
| 1019 | foreach xyz $RBcoords { |
---|
| 1020 | foreach {x y z} $xyz {} |
---|
| 1021 | incr i |
---|
| 1022 | puts $fp "atom c $i $x $y $z" |
---|
| 1023 | puts $fp "labeltext $x $y $z r$i" |
---|
| 1024 | } |
---|
| 1025 | foreach bondpair $rbbondlist { |
---|
| 1026 | foreach {b1 b2 color} $bondpair {} |
---|
| 1027 | if {$color == ""} {set color Red} |
---|
| 1028 | puts $fp "bond c c 0.02 $b1 $b2 $color" |
---|
| 1029 | } |
---|
| 1030 | |
---|
| 1031 | puts $fp "sphere c 0.05 Red" |
---|
| 1032 | puts $fp "finish 0.70 0.30 0.08 0.01" |
---|
| 1033 | puts $fp "end" |
---|
| 1034 | |
---|
| 1035 | #puts $fp "bond o o [expr {0.01*$a/$scale}] [expr {-0.1 + $a/$scale}] [expr {0.1 + $a/$scale}] Black" |
---|
| 1036 | close $fp |
---|
| 1037 | MyMessageBox -parent . -title "Info" \ |
---|
| 1038 | -message "Note that the phase is drawn in green, blue, cyan & magenta and the rigid body in red." |
---|
| 1039 | if {$app != ""} {exec $app $file &} |
---|
| 1040 | } |
---|
| 1041 | |
---|
| 1042 | |
---|
| 1043 | #AddRigidBody {1} { {{0 0 0 xe} {1 1 1 o} {2 2 2 si+4}} } |
---|
| 1044 | #puts [GetRB 1 6 8 "1 2" "X 1 2" "Y 1 3"] |
---|
| 1045 | #puts [GetRB 1 4 8 "1" "X 1 2" "Z 3 4"] |
---|
| 1046 | #MapRigidBody 1 1 7 ".11 .22 .33" "11 12 13" |
---|
| 1047 | |
---|
| 1048 | |
---|
| 1049 | #AddRigidBody {1} { { |
---|
| 1050 | # {1 1 1 o} {-1 1 1 o} {1 -1 1 o} {-1 -1 1 o} |
---|
| 1051 | # {1 1 -1 o} {-1 1 -1 o} {1 -1 -1 o} {-1 -1 -1 o} |
---|
| 1052 | #} } |
---|
| 1053 | #set n [MapRigidBody 1 1 1 ".2 .3 .4" "13 17 19"] |
---|
| 1054 | #puts "body $n created" |
---|
| 1055 | #incr expgui(changed) |
---|
| 1056 | #RunRecalcRBCoords |
---|
| 1057 | #puts "press Enter to continue" |
---|
| 1058 | #gets stdin line |
---|
| 1059 | #MapRigidBody 1 1 $n ".5 .5 .5" "0 0 0" |
---|
| 1060 | #incr expgui(changed) |
---|
| 1061 | #RunRecalcRBCoords |
---|
| 1062 | |
---|
| 1063 | #puts "Test FitBody" |
---|
| 1064 | set fraclist { |
---|
| 1065 | { 0.5483305238484277 0.4887545024531055 0.6167996784631056 } |
---|
| 1066 | { 0.1036801409356145 0.5954016321779562 0.5129448102437683 } |
---|
| 1067 | { 0.26404665760133855 0.09455414439078394 0.612655365147539 } |
---|
| 1068 | { -0.18060372531147473 0.20120127411563465 0.5088004969282018 } |
---|
| 1069 | { 0.5806037253114747 0.3987987258843653 0.2911995030717982 } |
---|
| 1070 | { 0.13595334239866147 0.5054458556092161 0.18734463485246095 } |
---|
| 1071 | { 0.2963198590643855 0.004598367822043814 0.2870551897562318 } |
---|
| 1072 | { -0.1483305238484277 0.1112454975468945 0.1832003215368945 } |
---|
| 1073 | } |
---|
| 1074 | set ortholist { |
---|
| 1075 | {1 1 1} |
---|
| 1076 | {-1 1 1} |
---|
| 1077 | { 1.000000 -1.000000 1.000000} |
---|
| 1078 | { -1.000000 -1.000000 1.000000} |
---|
| 1079 | { 1.000000 1.000000 -1.000000} |
---|
| 1080 | { -1.000000 1.000000 -1.000000} |
---|
| 1081 | { 1.000000 -1.000000 -1.000000} |
---|
| 1082 | { -1.000000 -1.000000 -1.000000} |
---|
| 1083 | } |
---|
| 1084 | # test code, generates DRAWxtl imput file from orthogonal coordinate list |
---|
| 1085 | # with bonds of ~2, 2.8 and 3.4 A |
---|
| 1086 | #DRAWxtlPlotOrtho test4.str "test file" $ortholist {{1.9 2.1} {3.4 3.5 Blue} {2.8 2.83 Green} } |
---|
| 1087 | |
---|
| 1088 | # test code, plots rigid body type #2 with bonds drawn at ~1.3 & 2 A |
---|
| 1089 | #PlotRBtype 2 {{1.9 2.1} {1.28 1.32}} |
---|
| 1090 | |
---|
| 1091 | # test code, plots rigid body coords in ortholist with bonds @ ~2, 2.8 and 3.4 A |
---|
| 1092 | #PlotRBcoords $ortholist {{1.9 2.1} {3.4 3.5 Blue} {2.8 2.83 Green} } |
---|
| 1093 | |
---|
| 1094 | |
---|
| 1095 | set useflag {1 1 1 1 1 1 1 1} |
---|
| 1096 | set cell {4. 5. 6. 95. 100. 105.} |
---|
| 1097 | #set origin ".20 .30 .40" |
---|
| 1098 | set origin ".0 .0 .0" |
---|
| 1099 | #set Euler {{1 13} {2 17} {3 19}} |
---|
| 1100 | #set Euler {{1 0} {2 180} {3 0}} |
---|
| 1101 | set Euler {{1 0} {2 0} {3 0}} |
---|
| 1102 | |
---|
| 1103 | #puts [La::show $xform] |
---|
| 1104 | #puts "out: [FitBody $Euler $cell $ortholist $useflag $fraclist $origin 30]" |
---|
| 1105 | |
---|
| 1106 | |
---|
| 1107 | # test zmat2coord |
---|
| 1108 | set atmlist { |
---|
| 1109 | {C1 0 0.0 0 0.0 0 0.0} |
---|
| 1110 | {O2 1 1.20 0 0.0 0 0.0} |
---|
| 1111 | {H3 1 1.10 2 120.0 0 0.0} |
---|
| 1112 | {C4 1 1.50 2 120.0 3 180.0} |
---|
| 1113 | {H5 4 1.10 1 110.0 2 0.00} |
---|
| 1114 | {H6 4 1.10 1 110.0 2 120.0} |
---|
| 1115 | {H7 4 1.10 1 110.0 2 -120.0} |
---|
| 1116 | } |
---|
| 1117 | # C 0.00000 0.00000 0.00000 |
---|
| 1118 | # O 1.20000 0.00000 0.00000 |
---|
| 1119 | # H -0.55000 0.95263 0.00000 |
---|
| 1120 | # C -0.75000 -1.29904 -0.00000 |
---|
| 1121 | # H -0.04293 -2.14169 -0.00000 |
---|
| 1122 | # H -1.38570 -1.36644 0.89518 |
---|
| 1123 | # H -1.38570 -1.36644 -0.89518 |
---|
| 1124 | # set coordlist [zmat2coord $atmlist] |
---|
| 1125 | set i 0 |
---|
| 1126 | # puts "\nZmatrix in" |
---|
| 1127 | # foreach line $atmlist { |
---|
| 1128 | # incr i |
---|
| 1129 | # puts "$i) $line" |
---|
| 1130 | # } |
---|
| 1131 | # puts "Cartesian out" |
---|
| 1132 | # foreach line $coordlist { |
---|
| 1133 | # puts [eval format "%-4s%10.5f%10.5f%10.5f" $line] |
---|
| 1134 | # } |
---|
| 1135 | |
---|
| 1136 | # AddRigidBody {1 0.75} { |
---|
| 1137 | # { |
---|
| 1138 | # {1 1 1 c} |
---|
| 1139 | # {-1 1 1 c} |
---|
| 1140 | # { 1.000000 -1.000000 1.000000 c} |
---|
| 1141 | # { -1.000000 -1.000000 1.000000 c} |
---|
| 1142 | # { 1.000000 1.000000 -1.000000 c} |
---|
| 1143 | # { -1.000000 1.000000 -1.000000 c} |
---|
| 1144 | # { 1.000000 -1.000000 -1.000000 c} |
---|
| 1145 | # { -1.000000 -1.000000 -1.000000 c} |
---|
| 1146 | # {1 1 1 h} |
---|
| 1147 | # {1 -1 -1 h} |
---|
| 1148 | # {-1 1 -1 h} |
---|
| 1149 | # {-1 -1 1 h} |
---|
| 1150 | # } { |
---|
| 1151 | # {0 0 0 c } |
---|
| 1152 | # {0 0 0 c} |
---|
| 1153 | # {0 0 0 c} |
---|
| 1154 | # {0 0 0 c} |
---|
| 1155 | # {0 0 0 c} |
---|
| 1156 | # {0 0 0 c} |
---|
| 1157 | # {0 0 0 c} |
---|
| 1158 | # {0 0 0 c} |
---|
| 1159 | # {1 1 1 h} |
---|
| 1160 | # {1 -1 -1 h} |
---|
| 1161 | # {-1 1 -1 h} |
---|
| 1162 | # {-1 -1 1 h} |
---|
| 1163 | # } |
---|
| 1164 | # } |
---|
| 1165 | # MapRigidBody 2 2 1 {0 0 0} {10 15 20} |
---|