alert changes, updated notes

experiments/clas12/alert/He_bag/hebag__geometry_original.txt

@@ -1,5 +1,4 @@
-        mother_Hebag  |                root  |           ALERT He bag mother  |                              0*mm 0*mm 330.025*mm  |                                   0 0 0  | eeeegg   |                Tube  |                      0.0*mm 26.0*mm 150.03*mm 0*deg 360*deg  |               G4_He  |                  no  |     1   |     1   |     1   |   0   |   0   |                  no  |                  no  |                                      no 
-               Hebag  |        mother_Hebag  |              He bag for ALERT  |                                             0 0 0  |                                   0 0 0  | 00ff00   |                Tube  |                       25*mm 25.06*mm 150.0*mm 0*deg 360*deg  |               G4_Al  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 
-        Hebag_upst_w  |        mother_Hebag  |        He bag upstream window  |                             0*mm 0*mm -150.015*mm  |                                   0 0 0  | 00ff00   |                Tube  |                   3.1561*mm 25.06*mm 0.015*mm 0*deg 360*deg  |               G4_Al  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 
-        Hebag_dnst_w  |        mother_Hebag  |      He bag downstream window  |                              0*mm 0*mm 150.015*mm  |                                   0 0 0  | 00ff00   |                Tube  |                        0*mm 25.06*mm 0.015*mm 0*deg 360*deg  |               G4_Al  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 
-           Hebag_gas  |        mother_Hebag  |          He bag gas for ALERT  |                                             0 0 0  |                                   0 0 0  | ffff00   |                Tube  |                           0*mm 25*mm 150.0*mm 0*deg 360*deg  |               G4_He  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 
+        mother_Hebag  |                root  |           ALERT He bag mother  |                              0*mm 0*mm 641.635*mm  |                                   0 0 0  | eeeegg   |                Tube  |                     0.0*mm 20.0*mm 319.365*mm 0*deg 360*deg  |               HECO2  |                  no  |     1   |     1   |     1   |   0   |   0   |                  no  |                  no  |                                      no 
+               Hebag  |        mother_Hebag  |              He bag for ALERT  |                               0*mm 0*mm -0.015*mm  |                                   0 0 0  | 00ff00   |                Tube  |                       19*mm 19.1*mm 319.35*mm 0*deg 360*deg  |           G4_KAPTON  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 
+        Hebag_dnst_w  |        mother_Hebag  |      He bag downstream window  |                               0*mm 0*mm 319.35*mm  |                                   0 0 0  | 00ff00   |                Tube  |                         0*mm 19.1*mm 0.015*mm 0*deg 360*deg  |           G4_KAPTON  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 
+           Hebag_gas  |        mother_Hebag  |          He bag gas for ALERT  |                               0*mm 0*mm -0.015*mm  |                                   0 0 0  | ffff00   |                Tube  |                          0*mm 19*mm 319.35*mm 0*deg 360*deg  |               HECO2  |                  no  |     1   |     1   |     1   |   1   |   1   |                  no  |                  no  |                                      no 

experiments/clas12/alert/He_bag/hebag__materials_original.txt

@@ -1 +1,2 @@
             HeBagGas  |         Downstream He bag gas  |  0.000164  |         1  |                                           G4_He 1  | none  | none  | none  | none  | none  | none  | none  |   -1  |   -1  |   -1  |   -1  |   -1  | none  |   -1  | none  |   -1  |   -1  |   -1  
+               HECO2  |               Wires layer gas  |  0.000487  |         3  |                                      He 1 C 1 O 2  | none  | none  | none  | none  | none  | none  | none  |   -1  |   -1  |   -1  |   -1  |   -1  | none  |   -1  | none  |   -1  |   -1  |   -1  

experiments/clas12/alert/README.md

@@ -1,18 +1,17 @@
 # commands to generate text files for alert.gcard
 # copy and paste in your terminal all lines that do not start with:
-# this should be done from the directory where this file is located 
+# this should be done from the directory where this file is located
+
+```
 cd ../targets
 ./targets.pl config.dat
 cd ../alert/ahdc
-run-groovy factory.groovy --variation default --runnumber 11
-run-groovy factory.groovy --variation rga_fall2018 --runnumber 11
 ./ahdc.pl config.dat
 cd ../atof
-run-groovy factory.groovy --variation default --runnumber 11
-run-groovy factory.groovy --variation rga_fall2018 --runnumber 11
 ./atof.pl config.dat
 cd ../external_shell_nonActif
 ./alertshell.pl config.dat
 cd ../He_bag
 ./hebag.pl config.dat
 cd ../
+```