More ring design tutorial devel. (#1110)

* python -> python3

* More ring design tutorial devel.

bmad-doc/tao_examples/custom_tao_with_measured_data/README

@@ -1,6 +1,11 @@
 Example of How to Create a Customized Version of Tao 
 ---------------------------------------------------
 
+This example uses real data from the Fermilab Recycler NOvA Ring curtesy of Meiqin Xiao.
+Paper:
+	Linear Modelling and Lattice Correction from Betatron Phase Measurements at the Fermilab Recycler NOvA Ring
+	Meiqin Xiao(Fermilab), Kyle Hazelwood(Fermilab), Ming-Jen Yang(Fermilab), R. Ainsword(Fermilab)
+
 Directory:
 	tao/examples/custom_tao_with_measured_data
 

bmad-doc/tutorial_ring_design/doc/macros.tex

@@ -119,6 +119,7 @@
 \newcommand{\ltt}{{\sl Long Term Tracking}\xspace}
 \newcommand{\da}{{\sl Dynamic Aperture}\xspace}
 \newcommand{\sodom}{{\sl SODOM-2}\xspace}
+\newcommand{\spinstrob}{{\sl spin_stroboscope}\xspace}
 \newcommand{\bmad}{{\sl Bmad}\xspace}
 \newcommand{\mad}{{\sl MAD}\xspace}
 \newcommand{\quickplot}{{\sl Quick Plot}\xspace}

bmad-doc/tutorial_ring_design/doc/tutorial_ring_design.tex

@@ -1654,13 +1654,13 @@ \subsection{Example: tao.init for the Tune Cell}
 \begin{code}
 ! Require periodic betas in center FoDo cells of 2 o'clock tune cell
 datum(1) = 'expression: lat::beta.a[QFSS_2##4] - lat::beta.a[QFSS_2##5]' 
-                                                  '' '0' 'end' 'target' 0 10
+                                                  '' '' '' 'target' 0 10
 datum(2) = 'expression: lat::beta.b[QFSS_2##4] - lat::beta.b[QFSS_2##5]' 
-                                                  '' '0' 'end' 'target' 0 10
+                                                  '' '' '' 'target' 0 10
 datum(3) = 'expression: lat::alpha.a[QFSS_2##4] - lat::alpha.a[QFSS_2##5]' 
-                                                   '' '0' 'end' 'target' 0 10
+                                                   '' '' '' 'target' 0 10
 datum(4) = 'expression: lat::alpha.b[QFSS_2##4] - lat::alpha.b[QFSS_2##5]' 
-                                                   '' '0' 'end' 'target' 0 10
+                                                   '' '' '' 'target' 0 10
 \end{code}
 
 The syntax \vn{lat::beta.a[QFSS_2\#\#4]} evaluates to the value of the \vn{a}-mode beta function at the fourth lattice element named \vn{QFSS_2}.
@@ -1835,10 +1835,10 @@ \subsection{Example}
       Values at End of Element:
  Index  name      key           ...           orbit  ...          spin 
                                 ...               x  ...             x 
-     0  BEGINNING Beginning_Ele ...    0.000000E+00  ...  0.000000E+00 
-     1  B         Sbend         ...    5.027722E-03  ... -1.414516E-01 
-     2  Q         Quadrupole    ...   -1.599068E-02  ... -7.350543E-02 
-     3  END       Marker        ...   -1.599068E-02  ... -7.350543E-02 
+     0  BEGINNING Beginning_Ele ...    0.000000E+00  ...  1.000000E+00 
+     1  B         Sbend         ...    2.888946E-02  ...  9.886413E-01 
+     2  Q         Quadrupole    ...   -1.847740E-02  ...  9.768026E-01 
+     3  END       Marker        ...   -1.847740E-02  ...  9.768026E-01 
 \end{code}
 
 or the \vn{show element} command
@@ -1863,7 +1863,7 @@ \subsection{Exercises:}
 
 \begin{enumerate}[leftmargin=*]
 \item {\bf Phase Space:} Construct a lattice with a single drift of 2 meters length.
-Set the particle species to be protons with a reference energy of $10^12$~eV (so the approximation
+Set the particle species to be protons with a reference energy of $10^{12}$~eV (so the approximation
 that the particle velocity is speed of light can be made), and
 Set the initial particle position to have $p_x = 0.2$, $p_z = 1$ with all other coordinates
 zero. Calculate from first principles what the phase space coordinates will be at the end of the
@@ -1988,7 +1988,7 @@ \subsection{Adding RF Cavities}
 
 The example files for this section can be found at \vn{/lattices/9_RF/AddingRF/}
 
-In a real machine, electrons emit synchrotron radiation as they bend around the ring, so we need to replenish the energy with an RF system. Let’s put RF cavities in the 10 o’clock straight section of our ring. We will design a special FODO cellwith RF cavities \vn{FODORF} and replace 4 FODO cells in the 10 o’clock straight section. 
+In a real machine, electrons emit synchrotron radiation as they bend around the ring, so we need to replenish the energy with an RF system. Let’s put RF cavities in the 10 o’clock straight section of our ring. We will design a special FODO cell with RF cavities \vn{FODORF} and replace 4 FODO cells in the 10 o’clock straight section. 
 
 In the ESR, there are two RF cavities of length $4.017 \textrm{m}$ between each quadrupole with equal drift spaces between each element. We will follow these dimensions as shown in Fig.~\ref{f:fodorf}.
 
@@ -2015,7 +2015,7 @@ \subsection{Example: Consturcting the FODO cell with RF cavities}
 FODORF: line = (QFSS, DRF, RF0, DRF, RF0, DRF, QDSS, DRF, RF0, DRF, RF0, DRF)
     \end{code}
 
-    \item Replace 4 FODO cells in the 10 o'clock section with \vn{FODORF} by modifying \vn{SEXTANT9} and \vn{SEXTANT9}:
+    \item Replace 4 FODO cells in the 10 o'clock section with \vn{FODORF} by modifying \vn{SEXTANT9} and \vn{SEXTANT11}:
     \begin{code}
 SEXTANT9:  line = (4*FODOSSF, SS_TO_ARCF, 20*FODOAF, 
                               ARC_TO_SSF, 2*FODOSSF, 2*FODORF)
@@ -2036,7 +2036,7 @@ \subsection{Exercises}
 %
 \item 
 Modify the \vn{lcavity} in the \vn{cavity.bmad} to have a small length (so the transit time is
-small), and set the beginning momentum small enough so the relativistic beta is significantly than
+small), and set the beginning momentum small enough so the relativistic beta is significantly less than
 one. Starting the particle with a finite $z$, calculate the ending $z$ after the cavity and verity
 that the change in $z$ is consistent with what Bmad calculates.
 %
@@ -3214,32 +3214,12 @@ \subsection{Exercises}
 \begin{enumerate}[leftmargin=*]
 %
 \item {\bf Zero orbit at IP:}
-Use 4 horizontal/vertical kickers around the IP (CH/V_104 to CH/V_107, 8 total kickers) to make the orbit exactly 0 at the IP without affecting the rest of the ring.
+Use 4 horizontal/vertical kickers around the IP (CH/V\_104 to CH/V\_107, 8 total kickers) to make the orbit exactly 0 at the IP without affecting the rest of the ring.
 %
 \end{enumerate}
 
 \newpage
 
-%------------------------------------------------------------------------------
-%------------------------------------------------------------------------------
-%\section{Tracking with Ramping and Spin Tracking}
-
-%------------------------------------------------------------------------------
-%\subsection{Tracking with Ramping}
-%The ESR will not be used to accelerate, however to show what ramping in Bmad might look like we include this section.
-
-%------------------------------------------------------------------------------
-%\subsection{Adding Siberian Snakes}
-%Taylor element overview
-
-
-
-%------------------------------------------------------------------------------
-%\subsection{Invariant Spin Field Calculations}
-%\sodom $\rightarrow$ \ltt
-
-%\newpage
-
 %------------------------------------------------------------------------------
 %------------------------------------------------------------------------------
 \appendix

bmad-doc/tutorial_ring_design/lattices/8_PhaseSpace/orbit.bmad

@@ -2,7 +2,7 @@
 beginning[beta_a] = 10.   ! m  a-mode beta function
 beginning[beta_b] = 10.   ! m  b-mode beta function
 beginning[e_tot] = 10e6   ! eV
-parameter[geometry] = open  ! or closed
+parameter[geometry] = open  з! or closed
 bmad_com[spin_tracking_on] = T
 
 particle_start[y] = 0.01

bmad/calculations/exact_bend_multipole/convert.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Script for processing the Mathematica output for exact bend multipoles into Fortran form.
 # The output is a temporary that must be cut and pasted as appropriate.

bmad/doc/cover-page.tex

@@ -3,7 +3,7 @@
 
 \begin{flushright}
 \large
-  Revision: July 14, 2024 \\
+  Revision: July 30, 2024 \\
 \end{flushright}
 
 \pdfbookmark[0]{Preamble}{Preamble} 

bmad/doc/example-program.tex

@@ -24,7 +24,7 @@ \section{A First Program}
 Consider the example program shown in \fig{f:program}. The source code for this program is provided
 with \bmad in the directory:
 \begin{example}
-  \$ACC_ROOT_DIR/examples/simple_bmad_program
+  \$ACC_ROOT_DIR/code_examples/simple_bmad_program
 \end{example}
 [Note: \vn{\$ACC_ROOT_DIR} is the root directory of the \bmad \vn{Distribution} when you are running
 ``off-site'' and is root directory of the \vn{Release} when you are running ``on-site''.]

bmad/doc/list-element-attributes.tex

@@ -84,24 +84,25 @@ \chapter{List of Element Attributes}
  \label{s:list.beambeam}
 
  \begin{tabular}{llll} \toprule
-alias                            & crab_x3 [1/m$^2$]                & p0c [eV]                         & wrap_superimpose                 \\
-alpha_a_strong                   & crab_x4 [1/m$^3$]                & ptc_integration_type             & x1_limit [m]                     \\
-alpha_b_strong                   & crab_x5 [1/m$^4$]                & ref_origin                       & x2_limit [m]                     \\
-aperture [m]                     & create_jumbo_slave               & ref_time_start [sec]             & x_limit [m]                      \\
-aperture_at                      & delta_ref_time [sec]             & reference                        & x_offset [m]                     \\
-aperture_type                    & descrip                          & repetition_frequency [Hz]        & x_offset_tot [m]                 \\
-bbi_constant                     & e_tot [eV]                       & sig_x [m]                        & x_pitch [rad]                    \\
-beta_a_strong [m]                & e_tot_strong [eV]                & sig_y [m]                        & x_pitch_tot [rad]                \\
-beta_b_strong [m]                & ele_origin                       & sig_z [m]                        & y1_limit [m]                     \\
-bs_field [T]                     & field_calc                       & species_strong                   & y2_limit [m]                     \\
-charge                           & is_on                            & spin_tracking_method             & y_limit [m]                      \\
-cmat_11                          & ks [1/m]                         & superimpose                      & y_offset [m]                     \\
-cmat_12                          & l [m]                            & symplectify                      & y_offset_tot [m]                 \\
-cmat_21                          & mat6_calc_method                 & tilt [rad]                       & y_pitch [rad]                    \\
-cmat_22                          & n_particle                       & tilt_tot [rad]                   & y_pitch_tot [rad]                \\
-crab_tilt [rad]                  & n_slice                          & tracking_method                  & z_crossing [m]                   \\
-crab_x1                          & offset [m]                       & type                             & z_offset [m]                     \\
-crab_x2 [1/m]                    & offset_moves_aperture            & wall                             & z_offset_tot [m]                 \\
+alias                            & crab_x4 [1/m$^3$]                & ref_origin                       & x2_limit [m]                     \\
+alpha_a_strong                   & crab_x5 [1/m$^4$]                & ref_time_start [sec]             & x_limit [m]                      \\
+alpha_b_strong                   & create_jumbo_slave               & reference                        & x_offset [m]                     \\
+aperture [m]                     & delta_ref_time [sec]             & repetition_frequency [Hz]        & x_offset_tot [m]                 \\
+aperture_at                      & descrip                          & s_twiss_ref [m]                  & x_pitch [rad]                    \\
+aperture_type                    & e_tot [eV]                       & sig_x [m]                        & x_pitch_tot [rad]                \\
+bbi_constant                     & e_tot_strong [eV]                & sig_y [m]                        & y1_limit [m]                     \\
+beta_a_strong [m]                & ele_origin                       & sig_z [m]                        & y2_limit [m]                     \\
+beta_b_strong [m]                & field_calc                       & species_strong                   & y_limit [m]                      \\
+bs_field [T]                     & is_on                            & spin_tracking_method             & y_offset [m]                     \\
+charge                           & ks [1/m]                         & superimpose                      & y_offset_tot [m]                 \\
+cmat_11                          & l [m]                            & symplectify                      & y_pitch [rad]                    \\
+cmat_12                          & mat6_calc_method                 & tilt [rad]                       & y_pitch_tot [rad]                \\
+cmat_21                          & n_particle                       & tilt_tot [rad]                   & z_crossing [m]                   \\
+cmat_22                          & n_slice                          & tracking_method                  & z_offset [m]                     \\
+crab_tilt [rad]                  & offset [m]                       & type                             & z_offset_tot [m]                 \\
+crab_x1                          & offset_moves_aperture            & wall                             &                                  \\
+crab_x2 [1/m]                    & p0c [eV]                         & wrap_superimpose                 &                                  \\
+crab_x3 [1/m$^2$]                & ptc_integration_type             & x1_limit [m]                     &                                  \\
  \bottomrule
  \end{tabular}
  \vfill

bsim/bbu/collect_thresholds.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os, sys
 

bsim/bbu/test_run.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import os, sys, shutil, glob, tempfile, time
 from bbu import bbu_main, find_threshold, drscan, phase_scan  #imports bbu package in user python path
 

bsim/spin_stroboscope/plotting/invariant_spin.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import numpy as np

bsim/tune_scan/plotting/tune_scan_density_plot.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # To execute this file from within the Python interpreter:
 #   execfile('this_file_name')

cpp_bmad_interface/scripts/bmad_enums_to_c.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Note: 
 #   Run this script in the cpp_bmad_interface directory.

cpp_bmad_interface/scripts/create_interface.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Note: Run this script in the cpp_bmad_interface directory.
 

lux/doc/lux.tex

@@ -879,7 +879,7 @@ \section{Python Scripting}
 
 Example:
 \begin{listing}{1}
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import subprocess
 import glob

lux/scripts/combine_det_pix_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Script to combine det_pix output files from Lux into one det_pix file.
 # This is useful when a simulation has to be broken up into multiple runs.

lux/scripts/plot_det_pix.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # To execute this file from within the Python interpreter:
 #   execfile('this_file_name')

regression_tests/scripts/run_tests.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # Script to run regression tests for the Bmad libraries.

tao/doc/generate_tex_for_python_commands.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # coding: utf-8
 
 # # Generate documentation for Tao python commands.

tao/version/tao_version_mod.f90

@@ -6,5 +6,5 @@
 !-
 
 module tao_version_mod
-character(*), parameter :: tao_version_date = "2024/07/26 21:59:14"
+character(*), parameter :: tao_version_date = "2024/07/30 17:00:42"
 end module

util/create_searchf_namelist

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # Script to create the searchf.namelist files so that getf and listf can do faster searches.

util/getf

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # See searchf.py for all documentation

util/listf

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # See searchf.py for all documentation

util/raw_list

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # Script for finding and printing structure definitions.

util/searchf.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # searchf.py is the file that holds the code for the scripts:

util_programs/elegant_to_bmad/elegant_to_bmad.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # Script to convert from Elegant lattice format to Bmad lattice format.

util_programs/mad_to_bmad/mad8_to_bmad.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # Script to convert from MAD8 lattice format to Bmad lattice format.

util_programs/mad_to_bmad/madx_to_bmad.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #+
 # Script to convert from MADX lattice format to Bmad lattice format.

util_programs/slicktrack_to_bmad/slicktrack_to_bmad.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 from itertools import tee
 import sys