Folder structure (#1)

* Changed folder structure to resemble the one on the AFS SPS repository

* Changed references for folder structure and added a 'TODO' comment for referenced files not on the repository

matchtune.cmdx → cmd/matchtune.cmdx

@@ -12,7 +12,7 @@
 !        column=name,s,betx,alfx,x,dx,dpx,bety,alfy;
 
 !TWISS, DELTAP=0.0;
-!write, table=twiss, file=twiss_before.prt;
+!write, table=twiss, file="out/twiss_before.prt";
 
 
 
@@ -34,7 +34,7 @@ Endmatch;
 
 select, flag=twiss, clear;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy;
-twiss,  sequence=sps, file=twiss_ideal_se.tfs, save;
+twiss,  sequence=sps, file="out/twiss_ideal_se.tfs", save;
 
 value, KQD, KQF1, KQF2;
 

general_se.madx → madx/general_se.madx

@@ -67,7 +67,7 @@ call, file = '/afs/cern.ch/eng/sps/2014/beams/cngs_extraction.beamx';
 !--------------------------------------------------------------------------
 ! aperture of individual elements
 !--------------------------------------------------------------------------
- call, file = 'aperturedb_3.dbx';
+ call, file = 'aperture/aperturedb_3.dbx';
 
 
 !--------------------------------------------------------------------------
@@ -152,16 +152,16 @@ option, -echo;
 !--------------------------------------------------------------------------
 use, period=sps;
 
-call, file = 'matchtune.cmdx';
-call, file = 'matchchroma.cmdx';
+call, file = '../cmd/matchtune.cmdx';
+call, file = '../cmd/matchchroma.cmdx';
 
-!call, file = "lss1_q171819_displacement.madx";
+!call, file = "lss1_q171819_displacement.madx";  ! TODO file missing?
 option, -echo;
 
 select, flag=twiss, range=#E,column=name,s,betx,alfx,mux,x,px,dx,dpx,bety,alfy,muy,y,py,dy,dpy;
 TWISS, DELTAP=0.0;
 !savebeta,label=start, place=SPS$START;
-write, table=twiss, file=twiss_nominal_se.tfs;
+write, table=twiss, file="../out/twiss_nominal_se.tfs";
 
 
 !==========================================================
@@ -287,20 +287,20 @@ activate_bump(knob_value) : macro = {
     select, flag=twiss, clear;
     select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
     TWISS, DELTAP=0.0;
-    write, table=twiss, file=twiss_before_extr_knob_value.tfs;
+    write, table=twiss, file="../out/twiss_before_extr_knob_value.tfs";
 
 };
 !********/
 
 exec, activate_bump(1);
-call, file = 'matchchroma.cmdx';
-call, file = 'matchtune.cmdx';
+call, file = '../cmd/matchchroma.cmdx';
+call, file = '../cmd/matchtune.cmdx';
 
 select, flag=twiss, clear;
 savebeta, label = zs_start, place = ap.up.zs21633;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 TWISS, DELTAP=0.0;
-write, table=twiss, file=twiss_before_extr_normal.tfs;
+write, table=twiss, file="../out/twiss_before_extr_normal.tfs";
 
 
 dpp_extreme = -1.5e-3;
@@ -321,13 +321,13 @@ select, flag=twiss, clear;
 savebeta, label = zs_start, place = ap.up.zs21633;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 TWISS, DELTAP=0.0;
-write, table=twiss, file=twiss_test_twiss1.tfs;
+write, table=twiss, file="../out/twiss_test_twiss1.tfs";
 
 select, flag=twiss, clear;
 savebeta, label = zs_start, place = ap.up.zs21633;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 TWISS, DELTAP=dpp_extreme;
-write, table=twiss, file=twiss_test_twiss12.tfs;
+write, table=twiss, file="../out/twiss_test_twiss12.tfs";
 stop;
 
 
@@ -338,7 +338,7 @@ select, flag=twiss, clear;
 savebeta, label = zs_start2, place = ap.up.zs21633;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 TWISS, DELTAP=0.0;
-write, table=twiss, file=twiss_from_zs.tfs;
+write, table=twiss, file="../out/twiss_from_zs.tfs";
 
 /**********
 select, flag=twiss, clear;
@@ -349,7 +349,7 @@ select, flag=twiss, class = vmonitor, column=name,s,l,x,betx,dx,aper_1,y,bety,dy
 select, flag=twiss, class = instrument, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 
 TWISS, DELTAP=0.0, centre;
-write, table=twiss, file=twiss_centre_before_extr.tfs;
+write, table=twiss, file="../out/twiss_centre_before_extr.tfs";
 **************/
 
 create, table = spiral_step, column = knob_value, delta_x, delta_px, x_zs, px_zs,  final_x, final_px;
@@ -368,19 +368,19 @@ get_spiral_step(x0_bump, px0_bump) : macro = {
     savebeta, label=turn1, place=SPS2AP.UP.ZS21633_P_;
     select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
     TWISS, DELTAP=0.0, beta0=zs_start2;
-    write, table=twiss, file="twiss_bump_1_turn.tfs";
+    write, table=twiss, file="../out/twiss_bump_1_turn.tfs";
 
     select, flag=twiss, clear;
     savebeta, label=turn2, place=SPS2AP.UP.ZS21633_P_;
     select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
     TWISS, DELTAP=0.0, beta0=turn1;
-    write, table=twiss, file="twiss_bump_2_turn.tfs";
+    write, table=twiss, file="../out/twiss_bump_2_turn.tfs";
 
     select, flag=twiss, clear;
     savebeta, label=turn3, place=SPS2AP.UP.ZS21633_P_;
     select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
     TWISS, DELTAP=0.0, beta0=turn2;
-    write, table=twiss, file="twiss_bump_3_turn.tfs";
+    write, table=twiss, file="../out/twiss_bump_3_turn.tfs";
 
     delta_x = table(twiss, SPS2AP.UP.ZS21633_P_, x) - x_zs;
     delta_px = table(twiss, SPS2AP.UP.ZS21633_P_, px) - px_zs;
@@ -416,7 +416,7 @@ while(i <= 40){
 
 };
 
-write, table = spiral_step, file = "spiral_step.tfs";
+write, table = spiral_step, file = "../out/spiral_step.tfs";
 **********************/
 
 ! Extraction bump LSS2

makethin.madx → madx/makethin.madx

@@ -10,11 +10,11 @@ find_misa_macro(correct_x, correct_y, orbit_name): macro = {
     select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2,alfx,alfy,mux,muy,dpx,dpy;
     !select, flag=twiss, class=bpcn, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2,alfx,alfy,mux,muy,dpx,dpy;
     TWISS,  deltap=0.00;
-    write, table = twiss, file = "before_test.tfs";
+    write, table = twiss, file = "../out/before_test.tfs";
     twiss, table=my_model;                                                                                                
 
-    readmytable, file="yasp_orbit_name_h.tfs", table=x_target;                                                                 
-    readmytable, file="yasp_orbit_name_v.tfs", table=y_target;
+    readmytable, file="../in/yasp_orbit_name_h.tfs", table=x_target; ! TODO file missing
+    readmytable, file="../in/yasp_orbit_name_v.tfs", table=y_target; ! TODO file missing
 
 
     ! disable monitors and correctors                                                                                     
@@ -56,11 +56,11 @@ find_misa_macro(correct_x, correct_y, orbit_name): macro = {
     select, flag=twiss, class=bph, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2,alfx,alfy,mux,muy,dpx,dpy;
     select, flag=twiss, class=bpcn, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2,alfx,alfy,mux,muy,dpx,dpy;
     TWISS,  deltap=0.00;
-    write, table = twiss, file = "after_correction_orbit_name.tfs";
+    write, table = twiss, file = "../out/after_correction_orbit_name.tfs";
 
 };
 
-call, file = "virtual_cor.madx";
+call, file = "virtual_cor.madx"; ! TODO file missing
 use, sequence = sps;
 
 select, flag = makethin, clear;
@@ -78,12 +78,12 @@ select, flag=twiss, class = hmonitor, column=name,s,l,x,betx,dx,aper_1,y,bety,dy
 select, flag=twiss, class = vmonitor, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 select, flag=twiss, class = instrument, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 TWISS, DELTAP=0.0;
-write, table=twiss, file="twiss_before_rematch_thin.tfs";
+write, table=twiss, file="../out/twiss_before_rematch_thin.tfs";
 
 knob_ext_sext = 0;
 
-call, file = 'matchtune.cmdx';
-call, file = 'matchchroma.cmdx';
+call, file = '../cmd/matchtune.cmdx';
+call, file = '../cmd/matchchroma.cmdx';
 
 
 select, flag=twiss, clear;
@@ -92,7 +92,7 @@ select, flag=twiss, class = hmonitor, column=name,s,l,x,betx,dx,aper_1,y,bety,dy
 select, flag=twiss, class = vmonitor, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 select, flag=twiss, class = instrument, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy,k2l;
 TWISS, DELTAP=0.0;
-write, table=twiss, file="twiss_after_rematch_thin.tfs";
+write, table=twiss, file="../out/twiss_after_rematch_thin.tfs";
 
 !value, kqf1, kqd;
 !stop;
@@ -152,7 +152,7 @@ extr_bump_knob = extr_bump_knob / 4;
 
 !exec, find_misa_macro(1, 1, sftpro_ft);
 
-!call, file = "stren.out";
+!call, file = "../in/stren.out"; ! TODO file missing
 
 knob_ext_sext = sex_knob_value;
 
@@ -175,5 +175,5 @@ Endmatch;
 select, flag=twiss, clear;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy, dpx, dpy;
 TWISS, DELTAP=0.0;
-write, table=twiss, file="twiss_thin_nom.tfs";
+write, table=twiss, file="../out/twiss_thin_nom.tfs";
 

thin_tracking.madx → madx/thin_tracking.madx

@@ -2,10 +2,10 @@
 !Read input and create output tables
 !------------------------------------------------------------
 
-!readmytable,file=initial_distribution_fat_halo_60.txt, table=initial_distribution;
-readmytable,file=initial_distribution.txt, table=initial_distribution;
-readmytable,file=dpp_dist_after_gym.tsv, table=initial_dpp;
-!readmytable,file=initial_distribution_halo_chain10.txt, table=initial_distribution;
+!readmytable,file="../in/initial_distribution_fat_halo_60.txt", table=initial_distribution; ! TODO file missing
+readmytable,file="../in/initial_distribution.txt", table=initial_distribution; ! TODO file missing
+readmytable,file="../in/dpp_dist_after_gym.tsv", table=initial_dpp; ! TODO file missing
+!readmytable,file="../in/initial_distribution_halo_chain10.txt", table=initial_distribution; ! TODO file missing
 
 SELECT, FLAG= ERROR, PATTERN= "TIDH.11795";
 EALIGN, DX= -0.00425, DY= -0.00611;
@@ -129,7 +129,7 @@ kqd = kqd_start ;
 select, flag=twiss, clear;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy, dpx, dpy;
 TWISS, DELTAP=0.0;
-write, table=twiss, file="twiss_before_track_thin.tfs";
+write, table=twiss, file="../out/twiss_before_track_thin.tfs";
 
 
 !Nturns = 204565;
@@ -163,7 +163,7 @@ Nparticles = 1000 ;
 !Nturns = 1;
 
 TRACK, dump, onetable=true, onepass, aperture,  recloss, 
-update, file = "track_out_ship_newset_se_";
+update, file = "../out/track_out_ship_newset_se_";
 
     j = 1;
     while(j <= Nparticles)
@@ -183,6 +183,6 @@ update, file = "track_out_ship_newset_se_";
 
 ENDTRACK;
 
-write, table = trackloss, file = "losses_se_ship_newset_se.tfs";
+write, table = trackloss, file = "../out/losses_se_ship_newset_se.tfs";
 
-write, table = tune_var, file = "tune_flat_top_newset_se.tfs";
+write, table = tune_var, file = "../out/tune_flat_top_newset_se.tfs";

thin_tracking_phase_space_analysis.madx → madx/thin_tracking_phase_space_analysis.madx

@@ -2,7 +2,7 @@
 !Read input and create output tables
 !------------------------------------------------------------
 
-!readmytable,file=initial_distribution_fat_halo_60.txt, table=initial_distribution;
+!readmytable,file="../in/initial_distribution_fat_halo_60.txt", table=initial_distribution;
 
 !================================
 ! Misa in Sextant 2
@@ -68,14 +68,14 @@ kqd_end =     -0.01463733464 ;
 !kqd_start =     -0.01463244145 ;
 
 
-call, file = 'matchtune.cmdx';
+call, file = '../cmd/matchtune.cmdx';
 !kqf1 = kqf1_start ;
 !kqd  = kqd_start ;
 
 select, flag=twiss, clear;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy, dpx, dpy;
 TWISS, DELTAP=0.0;
-write, table=twiss, file="twiss_before_track_thin.tfs";
+write, table=twiss, file="../out/twiss_before_track_thin.tfs";
 
 m_f = (kqf1_start_nom - kqf1_end_nom) / (1 - 204565);
 m_d = (kqd_start_nom - kqd_end_nom) / (1 - 204565);
@@ -87,8 +87,8 @@ n_d = kqd_start - m_d;
 !kqd := m_d * tr$turni + n_d ;
 
 
-!readmytable,file=initial_distribution.txt, table=initial_distribution;
-!readmytable,file=initial_dis_1sigma_.txt, table=initial_distribution;
+!readmytable,file="../in/initial_distribution.txt", table=initial_distribution; ! TODO file missing
+!readmytable,file="../in/initial_dis_1sigma_.txt", table=initial_distribution; ! TODO file missing
 
 option,-info;   
                         ! otherwise you get warnings
@@ -150,7 +150,7 @@ Nparticles = 40 ;
 
 
 TRACK, onetable=true, onepass, recloss, aperture, 
-file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/track_out_action_angle_";      
+file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/track_out_action_angle_"; ! TODO access missing
 
     j = 1;
     while(j <= Nparticles)
@@ -173,6 +173,6 @@ file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/track_out_action_angle_"
 
 ENDTRACK;
 
-write, table = trackloss, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/losses_action_angle.tfs";
+write, table = trackloss, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/losses_action_angle.tfs"; ! TODO access missing
 
 stop;

thin_tracking_sample.madx → madx/thin_tracking_sample.madx

@@ -2,10 +2,10 @@
 !Read input and create output tables
 !------------------------------------------------------------
 
-!readmytable,file=initial_distribution_fat_halo_60.txt, table=initial_distribution;
-readmytable,file=initial_distribution_parab.txt, table=initial_distribution;
-!readmytable,file=dpp_dist_after_gym.tsv, table=initial_dpp;
-!readmytable,file=initial_distribution_halo_chain10.txt, table=initial_distribution;
+!readmytable,file="../in/initial_distribution_fat_halo_60.txt", table=initial_distribution; ! TODO file missing
+readmytable,file="../in/initial_distribution_parab.txt", table=initial_distribution; ! TODO file missing
+!readmytable,file="../in/dpp_dist_after_gym.tsv", table=initial_dpp; ! TODO file missing
+!readmytable,file="../in/initial_distribution_halo_chain10.txt", table=initial_distribution; ! TODO file missing
 
 SELECT, FLAG= ERROR, PATTERN= "TIDH.11795";
 EALIGN, DX= -0.00425, DY= -0.00611;
@@ -129,7 +129,7 @@ kqd = kqd_start ;
 select, flag=twiss, clear;
 select, flag=twiss, column=name,s,l,x,betx,dx,aper_1,y,bety,dy,aper_2, alfx, alfy, px, py, mux, muy, dpx, dpy;
 TWISS, DELTAP=0.0;
-write, table=twiss, file="twiss_before_track_thin.tfs";
+write, table=twiss, file="../out/twiss_before_track_thin.tfs";
 
 
 Nturns = 204565;
@@ -162,7 +162,7 @@ Nparticles = 100000 ;
 Nturns = 100;
 
 TRACK, dump, onetable=true, onepass, aperture,  recloss, 
-update, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/track_out_sample_se_";
+update, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/track_out_sample_se_"; ! TODO file access
 
     j = 1;
     while(j <= Nparticles)
@@ -183,7 +183,7 @@ update, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/track_out_sample
 
 ENDTRACK;
 
-write, table = trackloss, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/losses_sample_se.tfs";
+write, table = trackloss, file = "/home/fvelotti/Dropbox/Slow_extraction/tracking/losses_sample_se.tfs"; ! TODO file access
 
 
 value, Ex, (beam->exn);