Name change: AlignmentGroup -> BodyShiftGroup. (#175)

README.md

@@ -49,7 +49,7 @@ An individual element looks like:
 Ele: "qf" (b1>>2)   Quadrupole
   branch             Branch 1: "b1" 
   ix_ele             2 
-  AlignmentGroup:
+  BodyShiftGroup:
     offset               [0.0, 0.0, 0.0] m            offset_tot           [0.0, 0.0, 0.0] m
     x_rot                0 rad                        x_rot_tot            0 rad
     y_rot                0 rad                        y_rot_tot            0 rad

manual/construction.tex

@@ -21,4 +21,6 @@ \chapter{Constructing Lattices}
 
 * Show how to construct a Bmad replacement line using a function.
 
-* Show how to get the effect of a Bmad List by replacing elements after expansion.
+* Show how to get the effect of a Bmad List by replacing elements after expansion.
+
+* Default name for end element is \vn{"endN"} where N is the index of the branch.

manual/ele-anatomy.tex

@@ -69,7 +69,7 @@ \section{Element Parameter Groups}
 \begin{example}
   julia> subtypes(EleParameterGroup)
   28-element Vector{Any}:
-   AlignmentGroup
+   BodyShiftGroup
    ApertureGroup
    BMultipoleGroup
    ...
@@ -83,7 +83,7 @@ \section{Element Parameter Groups}
 
     Associated parameter groups
     ===========================
-      •  AlignmentGroup -> Element position/orientation shift.
+      •  BodyShiftGroup -> Element position/orientation shift.
       •  ApertureGroup -> Vacuum chamber aperture.
       •  BMultipoleGroup -> Magnetic multipoles.
       •  EMultipoleGroup -> Electric multipoles.

manual/ele-param-groups.tex

@@ -13,7 +13,7 @@ \chapter{Element Parameter Groups}
  {\it Group}          & {\it Section}             & {\it Group}          & {\it Section}            \\ 
  \midrule
  ACKickerGroup        & \sref{s:ackicker.g}       & LengthGroup          & \sref{s:length.g}        \\    
- AlignmentGroup       & \sref{s:alignment.g}      & LordSlaveStatusGroup & \sref{s:lord.slave.g}    \\
+ BodyShiftGroup       & \sref{s:alignment.g}      & LordSlaveStatusGroup & \sref{s:lord.slave.g}    \\
  ApertureGroup        & \sref{s:aperture.g}       & MasterGroup          & \sref{s:master.g}        \\
  BMultipoleGroup      & \sref{s:bmultipole.g}     & OrientationGroup     & \sref{s:orientation.g}   \\ 
  BeamBeamGroup        & \sref{s:beam.beam.g}      & OriginEleGroup       & \sref{s:origin.ele.g}    \\
@@ -44,7 +44,7 @@ \chapter{Element Parameter Groups}
 To see which element types contain a given group, use the \vn{info(::EleParameterGroup)}
 method. Example:
 \begin{example}
-  julia> info(AlignmentGroup)
+  julia> info(BodyShiftGroup)
   ApertureGroup: Vacuum chamber aperture.
   ...
   Found in:
@@ -104,13 +104,13 @@ \section{ACKickerGroup}
 \newpage
 
 %---------------------------------------------------------------------------------------------------
-\section{AlignmentGroup}
+\section{BodyShiftGroup}
 \label{s:alignment.g}
 
 \begin{figure}[bt]
 \centering \includegraphics{alignment-ref.pdf} 
 \caption[Element alignment.]  
-{AlignmentGroup parameters The reference point is the origin
+{BodyShiftGroup parameters The reference point is the origin
 about which the element alignment is calculated. 
 A) For straight elements, the reference point is in the center of the element. 
 For \vn{Bend} elements, the reference point is at the midpoint of the chord connecting
@@ -127,7 +127,7 @@ \section{AlignmentGroup}
 }  \label{f:alignment}
 \end{figure}
 
-The \vn{AlignmentGroup} gives the alignment (position and angular orientation) of the physical element 
+The \vn{BodyShiftGroup} gives the alignment (position and angular orientation) of the physical element 
 relative to the nominal position defined by the branch coordinates (\sref{s:orient}).
 Alignment is specified with respect to the ``alignment reference point'' of an element as shown
 in Fig~\ref{s:alignment}. The \vn{Bend} reference point is chosen to be the center of the chord
@@ -136,7 +136,7 @@ \section{AlignmentGroup}
 common simulation problem is to simulate a bend with a \vn{z_rot} keeping the entrance and exit
 endpoints fixed.
 
-The parameters of the \vn{AlignmentGroup} are:
+The parameters of the \vn{BodyShiftGroup} are:
 \begin{example}
   offset::Vector - $[x, y, z]$ offset.
   x_rot::Number  - Rotation around the x-axis.
@@ -148,12 +148,12 @@ \section{AlignmentGroup}
 parameters are with respect to the branch reference coordinates. There are output alignment
 parameters:
 \begin{example}
-  q_align::Quaternion     - Quaternion representation of x_rot, y_rot, z_rot.
+  q_shift::Quaternion     - Quaternion representation of x_rot, y_rot, z_rot.
   offset_tot::Vector      - $[x, y, z]$ offset.
   x_rot_tot::Number       - Rotation around the x-axis.
   y_rot_tot::Number       - Rotation around the z-axis.
   z_rot_tot::Number       - Rotation around the z-axis. 
-  q_align_tot::Quaternion - Quaternion  representation of tot rotations.
+  q_shift_tot::Quaternion - Quaternion  representation of tot rotations.
 \end{example}
 The ``total alignment'' parameters which have a \vn{_tot} suffix are always the alignment 
 of the element with with respect to the branch coordinates.
@@ -165,8 +165,8 @@ \section{AlignmentGroup}
 of any \vn{Girder}. \vn{Girder} elements themselves also have both relative and total
 alignments since Girders can support other Girders.
 
-The \vn{q_align} output parameter gives the quaternion representation of 
-\vn{x_rot}, \vn{y_rot} and \vn{z_rot}. Similarly, the\vn{q_align_tot} output parameter gives the
+The \vn{q_shift} output parameter gives the quaternion representation of 
+\vn{x_rot}, \vn{y_rot} and \vn{z_rot}. Similarly, the\vn{q_shift_tot} output parameter gives the
 quaternion representation of \vn{x_rot_tot}, \vn{y_rot_tot} and \vn{z_rot_tot}.
 
 %---------------------------------------------------------------------------------------------------
@@ -191,7 +191,7 @@ \section{ApertureGroup}
   aperture_at::BodyLoc.T        - Aperture location. Default: BodyLoc.ENTRANCE_END
   wall::Wall2D                  - Aperture defined by vertex array.
   custom_aperture::Dict         - Custom aperture information.
-  aperture_shifts_with_alignment::Bool 
+  aperture_shifts_with_body::Bool 
                                 - Alignment affects aperture? Default: false.
 \end{example}
 
@@ -895,7 +895,7 @@ \section{OriginEleGroup}
 
 The \vn{OriginEleGroup} is used with \vn{Fiducial}, \vn{FloorShift}, and \vn{Girder} elements.
 The \vn{OriginEleGroup} is used to set the coordinate reference frame from which 
-the orientation set by the \vn{AlignmentGroup} is measured. To specify that the floor coordinates are
+the orientation set by the \vn{BodyShiftGroup} is measured. To specify that the floor coordinates are
 to be used, set the \vn{origin_ele} to \vn{NULL_ELE}. Typically this is the same as using the
 beginning element of the first branch of a lattice as long as the first element does not have
 any orientation shifts.

manual/ele-types.tex

@@ -49,7 +49,7 @@ \section{ACKicker}
 Element parameter groups associated with this element type are:
 \TOPrule 
 \begin{example}
-  AlignmentGroup     -> Element position/orientation shift. \sref{s:align.g} 
+  BodyShiftGroup     -> Element position/orientation shift. \sref{s:align.g} 
   ApertureGroup      -> Vacuum chamber aperture. \sref{s:aperture.g} 
   BMultipoleGroup    -> Magnetic multipoles. \sref{s:bmultipole.g} 
   OrientationGroup -> Floor floor position and orientation. \sref{s:orientation.g} 
@@ -143,7 +143,7 @@ \section{Bend}
 Element parameter groups associated with this element type are:
 \TOPrule
 \begin{example}
-  AlignmentGroup     -> Element position/orientation shift. \sref{s:align.g} 
+  BodyShiftGroup     -> Element position/orientation shift. \sref{s:align.g} 
   ApertureGroup      -> Vacuum chamber aperture. \sref{s:aperture.g} 
   BMultipoleGroup    -> Magnetic multipoles. \sref{s:bmultipole.g} 
   BendGroup          -> Bend element parameters. \sref{s:bend.g} 
@@ -562,7 +562,7 @@ \section{Girder}
   OrientationGroup -> Floor floor position and orientation. \sref{s:orientation.g} 
   LengthGroup        -> Length and s-position parameters. \sref{s:length.g} 
   DescriptionGroup   -> Element descriptive strings. \sref{s:descrip.g} 
-  AlignmentGroup     -> Alignment with respect to the reference. \sref{s:alignment.g}
+  BodyShiftGroup     -> Alignment with respect to the reference. \sref{s:alignment.g}
 \end{example}
 \BOTTOMrule
 
@@ -601,7 +601,7 @@ \section{Girder}
 
 The reference frame from which a \vn{Girder}'s orientation is measured is set by the
 \vn{origin_ele} and \vn{origin_ele_ref_point} parameters (\sref{s:origin.ele.g}).
-Orientation shifts are controlled by the \vn{AlignmentGroup} (\sref{s:align.g}).
+Orientation shifts are controlled by the \vn{BodyShiftGroup} (\sref{s:align.g}).
 
 When a girder is shifted in space, the elements
 it supports are also shifted.  In this case, the orientation

src/AcceleratorLattice.jl

@@ -57,7 +57,6 @@ include("lat_construction.jl")
 include("output_lat.jl")
 include("query.jl")
 include("find.jl")
-include("external_ele.jl")
 
 # Note! Element types, enums, and Holy traits are exported automatically when constructed.
 
@@ -70,7 +69,7 @@ export split!, construct_ele_type, ele_at_s, toggle_integrated!
 export eles_search, eles_substitute_lords!, eles_sort!
 export next_ele, ele_at_offset, ele_param_value_str, strip_AL, ele_param_group_symbols
 export branch, matches_branch, create_ele_vars, eval_str, Vertex1, LatticeGlobal
-export EleParameterGroup, AlignmentGroup, OrientationGroup, BMultipole, BMultipoleGroup, BeamBeamGroup
+export EleParameterGroup, BodyShiftGroup, OrientationGroup, BMultipole, BMultipoleGroup, BeamBeamGroup
 export EMultipole, EMultipoleGroup, BendGroup, ApertureGroup, DescriptionGroup, RFGroup, SolenoidGroup
 export TrackingGroup, LengthGroup, ReferenceGroup, DownstreamReferenceGroup, ForkGroup
 export MasterGroup, LordSlaveStatusGroup, ACKickerGroup
@@ -83,7 +82,7 @@ export machine_location, body_location, EleRegion, holy_traits, output_parameter
 export BranchType, LordBranch, TrackingBranch, MultipassBranch, SuperBranch, transform
 export str_split, str_match, str_unquote, str_quote, str_to_int, associated_names
 export ELE_PARAM_GROUP_INFO, ELE_TYPE_INFO, PARAM_GROUPS_LIST, OPEN, CLOSED
-export rotX, rotY, rotZ, rot, rot!
+export rotX, rotY, rotZ, rot, rot!, bend_quaternion, lat_ele_dict
 
 # From LinearAlgebra
 export norm

src/accessor.jl

@@ -207,10 +207,11 @@ end
 """
   Base.getindex(lat::Lattice, name::AbstractString)
   Base.getindex(lat::Lattice, ix_branch::Int)
+  Base.getindex(lat::Lattice, typ::Type{T} where T <: BranchType)
 
 If `lat[name]` matches a branch name, return the branch. No wild cards permitted here.
 If `lat[name]` does not match a branch name, return list of matching lattice elements.
-In this case the returned vector is equivalent to `eles_search(lat, name)`.
+In this case, the returned vector is equivalent to `eles_search(lat, name)`.
 
 For `lat[ix_branch]`, return `lat.branch[ix_branch]`.
 """ Base.getindex(lat::Lattice, name::AbstractString)
@@ -223,26 +224,44 @@ function Base.getindex(lat::Lattice, name::AbstractString)
   return eles_search(lat, name)
 end
 
+#------------
+
 function Base.getindex(lat::Lattice, ix_branch::Int)
   if ix_branch > length(lat.branch); error("Index above length of lat.branch[] array."); end
   return lat.branch[ix_branch]
 end
 
+#------------
+
+Base.getindex(lat::Lattice, typ::Type{T} where T <: BranchType) = lat.branch[typ]
+
 #---------------------------------------------------------------------------------------------------
 # Base.getindex(branch::Vector{Branch}, name::AbstractString)
 
 """
   Base.getindex(branch::Vector{Branch}, name::AbstractString)
+  Base.getindex(branch::Vector{Branch}, typ::Type{T} where T <: BranchType)
 
-Match `branch[name]` to branch in `branch[]` array using the names of the branches.
-""" Base.getindex(branch::Vector{Branch}, name::AbstractString)
+Match `branch[name]` or `branch[type]` to branch in `branch[]` array using the names or types
+of the branches. If there are multiple matches the match with the smallest index is returned.
+""" Base.getindex(branch::Vector{Branch})
 
 function Base.getindex(branch::Vector{Branch}, name::AbstractString)
   for br in branch
     if br.name == name; return br; end
   end
 
-  error(f"No branch with name: {name}")
+  error("Cannot find branch with name: $name")
+end
+
+#-----------
+
+function Base.getindex(branch::Vector{Branch}, typ::Type{T} where T <: BranchType)
+  for br in branch
+    if br.type == typ; return br; end
+  end
+
+  error("Cannot find branch of type: $typ")
 end
 
 #---------------------------------------------------------------------------------------------------
@@ -459,49 +478,49 @@ function output_parameter(sym::Symbol, ele::Ele, output_group::Type{T}) where T
     if :DownstreamReferenceGroup ∉ keys(ele.pdict); return NaN; end
     return ele.E_tot_ref_downstream / massof(ele.species_ref_downstream)
 
-  elseif sym == :q_align
-    if :AlignmentGroup ∉ keys(ele.pdict); return NaN; end
-    ag = ele.pdict[:AlignmentGroup]
+  elseif sym == :q_shift
+    if :BodyShiftGroup ∉ keys(ele.pdict); return NaN; end
+    ag = ele.pdict[:BodyShiftGroup]
     return Quaternion(ag.x_rot, ag.y_rot, ag.z_rot)
 
   elseif sym == :offset_tot
-    if :AlignmentGroup ∉ keys(ele.pdict); return NaN; end
+    if :BodyShiftGroup ∉ keys(ele.pdict); return NaN; end
     if isnothing(girder(ele)); return ele.offset; end
-    ag = ele.pdict[:AlignmentGroup]
-    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_align_tot)
-    orient_ele = OrientationGroup(ele.offset, ele.q_align)
+    ag = ele.pdict[:BodyShiftGroup]
+    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_shift_tot)
+    orient_ele = OrientationGroup(ele.offset, ele.q_shift)
     return coord_transform(orient_ele, orient_girder).r
 
   elseif sym == :x_rot_tot
-    if :AlignmentGroup ∉ keys(ele.pdict); return NaN; end
+    if :BodyShiftGroup ∉ keys(ele.pdict); return NaN; end
     if isnothing(girder(ele)); return ele.x_rot; end
-    ag = ele.pdict[:AlignmentGroup]
-    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_align_tot)
-    orient_ele = OrientationGroup(ele.offset, ele.q_align)
+    ag = ele.pdict[:BodyShiftGroup]
+    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_shift_tot)
+    orient_ele = OrientationGroup(ele.offset, ele.q_shift)
     return rot_angles(coord_transform(orient_ele, orient_girder).q)[1]
 
   elseif sym == :y_rot_tot
-    if :AlignmentGroup ∉ keys(ele.pdict); return NaN; end
+    if :BodyShiftGroup ∉ keys(ele.pdict); return NaN; end
     if isnothing(girder(ele)); return ele.y_rot; end
-    ag = ele.pdict[:AlignmentGroup]
-    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_align_tot)
-    orient_ele = OrientationGroup(ele.offset, ele.q_align)
+    ag = ele.pdict[:BodyShiftGroup]
+    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_shift_tot)
+    orient_ele = OrientationGroup(ele.offset, ele.q_shift)
     return rot_angles(coord_transform(orient_ele, orient_girder).q)[2]
 
   elseif sym == :z_rot_tot
-    if :AlignmentGroup ∉ keys(ele.pdict); return NaN; end
+    if :BodyShiftGroup ∉ keys(ele.pdict); return NaN; end
     if isnothing(girder(ele)); return ele.z_rot; end
-    ag = ele.pdict[:AlignmentGroup]
-    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_align_tot)
-    orient_ele = OrientationGroup(ele.offset, ele.q_align)
+    ag = ele.pdict[:BodyShiftGroup]
+    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_shift_tot)
+    orient_ele = OrientationGroup(ele.offset, ele.q_shift)
     return rot_angles(coord_transform(orient_ele, orient_girder).q)[3]
 
-  elseif sym == :q_align_tot
-    if :AlignmentGroup ∉ keys(ele.pdict); return NaN; end
-    if isnothing(girder(ele)); return ele.q_align; end
-    ag = ele.pdict[:AlignmentGroup]
-    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_align_tot)
-    orient_ele = OrientationGroup(ele.offset, ele.q_align)
+  elseif sym == :q_shift_tot
+    if :BodyShiftGroup ∉ keys(ele.pdict); return NaN; end
+    if isnothing(girder(ele)); return ele.q_shift; end
+    ag = ele.pdict[:BodyShiftGroup]
+    orient_girder = OrientationGroup(girder(ele).offset_tot, girder(ele).q_shift_tot)
+    orient_ele = OrientationGroup(ele.offset, ele.q_shift)
     return coord_transform(orient_ele, orient_girder).q
   end