From 4a06ce08d7dbe999c1deac0a6778bd4789536adf Mon Sep 17 00:00:00 2001
From: Blake Walters <blakerwalters@gmail.com>
Date: Mon, 9 Aug 2021 11:49:48 -0700
Subject: [PATCH 01/14] Fix many small transport bugs in synchdmlc

---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 203 +++++---
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      | 476 ++++++++++++++----
 .../omega/progs/gui/beamnrc/synchdmlc.tcl     |  20 +-
 3 files changed, 516 insertions(+), 183 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 1565b296e..0b33392d6 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -1144,16 +1144,12 @@ $REAL INDEXTMP; "T>temporary input variable for field indices in dynamic and
                 "  step-and-shoot simulations
 $LOGICAL check_full_qtr;
 
-"a flag indicating whether a sector of a given leaf cross-section has"
-"an alternative definition to that specified in the BEAMnrc Manual"
-"indexing: LEAFTYPE, 1 (Y bound) or 2 (Z bound), boundary no.
-$INTEGER I_LEAF_ALT_DEF(5,2,10);
 $REAL YTMP;
 
 DO I=1,5[
   DO J=1,2[
    DO K=1,10[
-     I_LEAF_ALT_DEF(I,J,K)=0;
+     I_LEAF_ALT_DEF_$SYNCHDMLC(I,J,K)=0;
    ]
   ]
 ]
@@ -1609,7 +1605,7 @@ IF(NUM_HLF>0) [
       ' WRAILBOT_$SYNCHDMLC(2) > WGROOVE_$SYNCHDMLC(2)+WTIP_$SYNCHDMLC(2).'/
       ' Leaf cross-section differs from that specified in the BEAMnrc'/
       ' Manual.'//);
-   I_LEAF_ALT_DEF(2,1,4) = 1;
+   I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,4) = 1;
  ]
  IF(WRAILTOP_$SYNCHDMLC(2)>WRAILBOT_$SYNCHDMLC(2))[
    OUTPUT ICM_$SYNCHDMLC;
@@ -1617,7 +1613,7 @@ IF(NUM_HLF>0) [
       ' WRAILTOP_$SYNCHDMLC(2) > WRAILBOT_$SYNCHDMLC(2).'/
       ' This differs from the cross-section specified in the BEAMnrc'/
       ' Manual.'//);
-   I_LEAF_ALT_DEF(2,1,6) = 1;
+   I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,6) = 1;
  ]
  IF(WRAILTOP_$SYNCHDMLC(2)<WRAILBOT_$SYNCHDMLC(2)-WGROOVE_$SYNCHDMLC(2))[
    OUTPUT ICM_$SYNCHDMLC;
@@ -1714,7 +1710,7 @@ IF(NUM_HLF>0) [
    (//' ***WARNING IN CM ',I3,' ($SYNCHDMLC) in HALF ISO leaf definition:'/
 ' WRAILBOT_$SYNCHDMLC(3) > WRAILTOP_$SYNCHDMLC(3).'/
 ' This differs from the cross-section specified in the BEAMnrc Manual.'//);
-         I_LEAF_ALT_DEF(3,1,1) = 1;
+         I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1) = 1;
  ]
  IF(WRAILBOT_$SYNCHDMLC(3)<WRAILTOP_$SYNCHDMLC(3)-WTONGUE_$SYNCHDMLC(3))[
    OUTPUT ICM_$SYNCHDMLC;
@@ -1832,22 +1828,22 @@ IF(NUM_QTR>0) [
       ' WRAILBOT_$SYNCHDMLC(4) > WGROOVE_$SYNCHDMLC(4)+WTIP_$SYNCHDMLC(4).'/
       ' This differs from the cross-section specified in the BEAMnrc'/
       ' Manual.'//);
-        I_LEAF_ALT_DEF(4,1,4) = 1;
+        I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,4) = 1;
  ]
  IF(WRAILTOP_$SYNCHDMLC(4)>WRAILBOT_$SYNCHDMLC(4))[
    OUTPUT ICM_$SYNCHDMLC;
    (//' ***WARNING IN CM ',I3,' ($SYNCHDMLC) in QTR TARGET leaf definition:'/
    ' WRAILTOP_$SYNCHDMLC(4) > WRAILBOT_$SYNCHDMLC(4).'/
    ' This differs from the cross-section specified in the BEAMnrc Manual.'//);
-       I_LEAF_ALT_DEF(4,1,6) = 1;
+       I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,6) = 1;
  ]
  IF(WRAILTOP_$SYNCHDMLC(4)<WRAILBOT_$SYNCHDMLC(4)-WGROOVE_$SYNCHDMLC(4))[
    OUTPUT ICM_$SYNCHDMLC;
    (//' ***WARNING IN CM ',I3,' ($SYNCHDMLC) in QTR TARGET leaf definition:'/
    ' WRAILTOP_$SYNCHDMLC(4) < WRAILBOT_$SYNCHDMLC(4)-WGROOVE_$SYNCHDMLC(4).'/
    ' This differs from the cross-section defined in the BEAMnrc Manual.'//);
-       I_LEAF_ALT_DEF(4,1,5) = 1;
-   IF(I_LEAF_ALT_DEF(4,1,4) = 1 & WRAILTOP_$SYNCHDMLC(4) <
+       I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,5) = 1;
+   IF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,4) = 1 & WRAILTOP_$SYNCHDMLC(4) <
        WRAILBOT_$SYNCHDMLC(4) - WGROOVE_$SYNCHDMLC(4) - WTIP_$SYNCHDMLC(4))[
        OUTPUT ICM_$SYNCHDMLC;
        (//' ***ERROR IN CM ',I3,' ($SYNCHDMLC) in QTR TARGET leaf definition:'/
@@ -1949,7 +1945,7 @@ IF(NUM_QTR>0) [
    (//' ***WARNING IN CM ',I5,' ($SYNCHDMLC) in QTR ISO leaf definition:'/
    ' WRAILBOT_$SYNCHDMLC(5) < WRAILTOP_$SYNCHDMLC(5)-WTONGUE_$SYNCHDMLC(5).'/
    ' Cross-section definition differs from BEAMnrc Manual.'//);
-         I_LEAF_ALT_DEF(5,1,2) = 1;
+         I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2) = 1;
    IF(WRAILBOT_$SYNCHDMLC(5)<WRAILTOP_$SYNCHDMLC(5)-WTONGUE_$SYNCHDMLC(5)-
       WTIP_$SYNCHDMLC(5))[
       OUTPUT ICM_$SYNCHDMLC;
@@ -1981,7 +1977,7 @@ IF(NUM_QTR>0) [
    (//' ***WARNING IN CM ',I5,' ($SYNCHDMLC) in QTR ISO leaf definition:'/
    ' ZGROOVE_$SYNCHDMLC(5) > ZTONGUE_$SYNCHDMLC(5).'/
    ' This differs from the cross-section specified in the BEAMnrc Manual.'//);
-         I_LEAF_ALT_DEF(5,2,4) = 1;
+         I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4) = 1;
  ]
  IF(ZHOLETOP_$SYNCHDMLC(5)<ZGROOVE_$SYNCHDMLC(5))[
    OUTPUT ICM_$SYNCHDMLC;
@@ -2402,7 +2398,7 @@ DO J=1,NGROUP_$SYNCHDMLC[
     ELSE ["qtr isocenter"
       ZREG_$SYNCHDMLC(I,2)=ZTIP_$SYNCHDMLC(5);
       ZREG_$SYNCHDMLC(I,3)=ZLEAF_$SYNCHDMLC(5);
-      IF(I_LEAF_ALT_DEF(5,2,4)=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
          ZREG_$SYNCHDMLC(I,5)=ZGROOVE_$SYNCHDMLC(5);
          ZREG_$SYNCHDMLC(I,4)=ZTONGUE_$SYNCHDMLC(5);
       ]
@@ -2471,13 +2467,13 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
        YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(2);
        YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-
                             ABS(WRAILBOT_$SYNCHDMLC(2)-WRAILTOP_$SYNCHDMLC(2));
-       IF(I_LEAF_ALT_DEF(2,1,6)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,6)=1)[
           YTMP = YREG_$SYNCHDMLC(I,6);
        ]
        ELSE[
           YTMP = YREG_$SYNCHDMLC(I,7);
        ]
-       IF(I_LEAF_ALT_DEF(2,1,4)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,4)=1)[
           YREG_$SYNCHDMLC(I,4)=YTMP-WGROOVE_$SYNCHDMLC(2)-WTIP_$SYNCHDMLC(2);
           YREG_$SYNCHDMLC(I,3)=YTMP-WRAILBOT_$SYNCHDMLC(2);
        ]
@@ -2492,7 +2488,7 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
                           WRAILBOT_$SYNCHDMLC(3));
        YREG_$SYNCHDMLC(I,3)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(3);
        YREG_$SYNCHDMLC(I,4)=YREG_$SYNCHDMLC(I,3)+WTIP_$SYNCHDMLC(3);
-       IF(I_LEAF_ALT_DEF(3,1,1)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
           YREG_$SYNCHDMLC(I,5)=YREG_$SYNCHDMLC(I,1)+WRAILBOT_$SYNCHDMLC(3);
        ]
        ELSE[
@@ -2505,20 +2501,20 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=4)["qtr target leaf"
        YREG_$SYNCHDMLC(I,2)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(4);
        YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(4);
-       IF(I_LEAF_ALT_DEF(4,1,5)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,5)=1)[
           YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-WGROOVE_$SYNCHDMLC(4);
        ]
        ELSE[
           YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-
                             ABS(WRAILBOT_$SYNCHDMLC(4)-WRAILTOP_$SYNCHDMLC(4));
        ]
-       IF(I_LEAF_ALT_DEF(4,1,6)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,6)=1)[
           YTMP = YREG_$SYNCHDMLC(I,6);
        ]
        ELSE[
           YTMP = YREG_$SYNCHDMLC(I,7);
        ]
-       IF(I_LEAF_ALT_DEF(4,1,4)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,4)=1)[
           YREG_$SYNCHDMLC(I,4)=YTMP-WGROOVE_$SYNCHDMLC(4)-WTIP_$SYNCHDMLC(4);
           YREG_$SYNCHDMLC(I,3)=YTMP-WRAILBOT_$SYNCHDMLC(4);
        ]
@@ -2526,7 +2522,7 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
           YREG_$SYNCHDMLC(I,3)=YTMP-WGROOVE_$SYNCHDMLC(4)-WTIP_$SYNCHDMLC(4);
           YREG_$SYNCHDMLC(I,4)=YTMP-WRAILBOT_$SYNCHDMLC(4);
        ]
-       IF(I_LEAF_ALT_DEF(4,1,5)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,5)=1)[
           YREG_$SYNCHDMLC(I,5)=YTMP-WRAILBOT_$SYNCHDMLC(4)+
                                WRAILTOP_$SYNCHDMLC(4);
        ]
@@ -2535,7 +2531,7 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
        ]
      ]
      ELSE ["qtr isocenter leaf"
-       IF(I_LEAF_ALT_DEF(5,1,2)=1)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[
           YREG_$SYNCHDMLC(I,3)=YREG_$SYNCHDMLC(I,1)+WRAILTOP_$SYNCHDMLC(5)-
                           WRAILBOT_$SYNCHDMLC(5);
           YREG_$SYNCHDMLC(I,2)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(5);
@@ -2556,8 +2552,8 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
 
      DO J = 1, 7 [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
-     "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
-     " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
+     OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
+      OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
  ]; "End of L loop"
@@ -2896,14 +2892,14 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
       SUBINDEX_$SYNCHDMLC(L,I,2,6)=2;
       SUBINDEX_$SYNCHDMLC(L,I,2,7)=2;
       SUBINDEX_$SYNCHDMLC(L,I,3,1)=2;
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),1,4)~=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,4)~=1)[
          SUBINDEX_$SYNCHDMLC(L,I,3,2)=2;
       ]
       SUBINDEX_$SYNCHDMLC(L,I,3,3)=2;
       SUBINDEX_$SYNCHDMLC(L,I,3,5)=2;
       SUBINDEX_$SYNCHDMLC(L,I,3,6)=2;
       SUBINDEX_$SYNCHDMLC(L,I,3,7)=2;
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),1,4)~=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,4)~=1)[
          SUBINDEX_$SYNCHDMLC(L,I,3,8)=2;
       ]
       SUBINDEX_$SYNCHDMLC(L,I,4,1)=2;
@@ -2912,13 +2908,13 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
       SUBINDEX_$SYNCHDMLC(L,I,4,6)=2;
       SUBINDEX_$SYNCHDMLC(L,I,4,7)=2;
       SUBINDEX_$SYNCHDMLC(L,I,4,8)=2;
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),1,5)~=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,5)~=1)[
          SUBINDEX_$SYNCHDMLC(L,I,5,1)=2;
       ]
       SUBINDEX_$SYNCHDMLC(L,I,5,3)=2;
       SUBINDEX_$SYNCHDMLC(L,I,5,5)=2;
       SUBINDEX_$SYNCHDMLC(L,I,5,6)=2;
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),1,6)=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,6)=1)[
          SUBINDEX_$SYNCHDMLC(L,I,6,1)=2;
       ]
       ELSE[
@@ -2963,12 +2959,12 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
     ] ELSE [
       "This is an Half or Quarter Isocenter Leaf"
       "Common to both Half and Quarter"
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),1,1)=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,1)=1)[
         SUBINDEX_$SYNCHDMLC(L,I,1,9)=2;
       ]
       ELSE[
         IF (LEAFTYPE_$SYNCHDMLC(L)=3 |
-            I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),2,4)=1) [
+            I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),2,4)=1) [
           "either 1) half isocentre or 2) quarter isocentre with zg>zt"
           SUBINDEX_$SYNCHDMLC(L,I,1,4)=2;
         ]
@@ -2976,13 +2972,13 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
         SUBINDEX_$SYNCHDMLC(L,I,1,7)=2;
       ]
       IF(LEAFTYPE_$SYNCHDMLC(L)=3 |
-          I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),2,4)=1)[
+          I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),2,4)=1)[
          "either 1) half isocentre or 2) quarter isocentre with zg>zt"
          SUBINDEX_$SYNCHDMLC(L,I,2,4)=2;
       ]
       SUBINDEX_$SYNCHDMLC(L,I,2,5)=2;
       SUBINDEX_$SYNCHDMLC(L,I,2,7)=2;
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),1,2)~=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,2)~=1)[
          SUBINDEX_$SYNCHDMLC(L,I,2,9)=2;
       ]
       SUBINDEX_$SYNCHDMLC(L,I,3,2)=2;
@@ -3007,7 +3003,7 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
       SUBINDEX_$SYNCHDMLC(L,I,6,8)=2;
       SUBINDEX_$SYNCHDMLC(L,I,6,9)=2;
 
-      IF(I_LEAF_ALT_DEF(LEAFTYPE_$SYNCHDMLC(L),2,4)~=1) [
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),2,4)~=1) [
         "Quarter Isocenter with zg<zt"
         SUBINDEX_$SYNCHDMLC(L,I,6,4)=2;
       ];
@@ -3721,22 +3717,64 @@ IF(LEAFIS~=0) [
    "Set minimum and maximum Z boundaries"
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
       "Quarter or Half Target leaf"
-
-      IF((NY=1|NY=2) & NZ<=3) [I1=1; I2=4;]
-      ELSEIF(NY=1 & NZ=5) [I1=5; I2=6;]
-      ELSEIF(NY=1 & NZ>=6) [I1=6; I2=10;]
-      ELSEIF(NZ=4) [I1=4; I2=5;]
-      ELSEIF((NY=2|NY=3) & NZ>=8) [I1=8; I2=10;]
-      ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [I1=1; I2=2;]
-      ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [I1=2; I2=3;]
-      ELSEIF(NY>=3 & NZ=3) [I1=3; I2=4;]
-      ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [I1=5; I2=8;]
-      ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [I1=5; I2=9;]
-      ELSEIF(NY=4 & NZ=9) [I1=9; I2=10;]
-      ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [I1=5; I2=7;]
-      ELSEIF((NY=5|NY=6) & NZ>=7) [I1=7; I2=10;]
-      ELSEIF(NY=6 & NZ<=2) [I1=1; I2=3;]
-
+      "Deal with each NY case"
+      IF(NY=1) [
+        IF(NZ<=3) [I1=1; I2=4;]
+        ELSEIF(NZ=4) [I1=4; I2=5;]
+        ELSEIF(NZ=5) [I1=5; I2=6;]
+        ELSE [I1=6; I2=10;]
+      ]
+      ELSEIF(NY=2) [
+        IF(NZ<=3) [I1=1; I2=4;]
+        ELSEIF(NZ=4) [I1=4; I2=5;]
+        ELSEIF(NZ<=7) [I1=5; I2=8;]
+        ELSE [I1=8; I2=10;]
+      ]
+      ELSEIF(NY=3) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
+           IF(NZ=1) [I1=1; I2=2;]
+           ELSEIF(NZ=2) [I1=2; I2=3;]
+           ELSEIF(NZ=3) [I1=3; I2=4;]
+           ELSEIF(NZ=4) [I1=4; I2=5;]
+           ELSEIF(NZ<=7) [I1=5; I2=8;]
+           ELSE [I1=8; I2=10;]
+        ]
+        ELSE [
+           IF(NZ<=3) [I1=1; I2=4;]
+           ELSEIF(NZ=4) [I1=4; I2=5;]
+           ELSEIF(NZ<=8) [I1=5; I2=9;]
+           ELSE [I1=9; I2=10;]
+        ]
+      ]
+      ELSEIF(NY=4) [
+        IF(NZ=1) [I1=1; I2=2;]
+        ELSEIF(NZ=2) [I1=2; I2=3;]
+        ELSEIF(NZ=3) [I1=3; I2=4;]
+        ELSEIF(NZ=4) [I1=4; I2=5;]
+        ELSEIF(NZ<=7) [I1=5; I2=8;]
+        ELSE [I1=8; I2=10;]
+      ]
+      ELSEIF(NY=5) [
+        IF(NZ=1) [I1=2; I2=3;]
+        ELSEIF(NZ=2) [I1=2; I2=3;]
+        ELSEIF(NZ=3) [I1=3; I2=4;]
+        ELSEIF(NZ=4) [I1=4; I2=5;]
+        ELSEIF(NZ<=6) [I1=5; I2=7;]
+        ELSE [I1=7; I2=10;]
+      ]
+      ELSEIF(NY=6) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          IF(NZ=1) [I1=1; I2=1;]
+          ELSE[ I1=2; I2=10;]
+        ]
+        ELSE [
+          IF(NZ<=2) [I1=1; I2=3;]
+          ELSEIF(NZ=3) [I1=3; I2=4;]
+          ELSEIF(NZ=4) [I1=4; I2=5;]
+          ELSEIF(NZ<=6) [I1=5; I2=7;]
+          ELSE [ I1=7; I2=10;]
+        ]
+      ]
     ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) [
       "Full leaf"
 
@@ -3758,22 +3796,55 @@ IF(LEAFIS~=0) [
 
     ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
       "Half Isocenter leaf"
-
-      IF((NY=1|NY=2) & NZ<=3) [I1=1; I2=4;]
-      ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [I1=4; I2=6;]
-      ELSEIF(NZ=6) [I1=6; I2=7;]
-      ELSEIF(NY<=4 & NZ=7) [I1=7; I2=8;]
-      ELSEIF(NY=1 & NZ>=8) [I1=8; I2=10;]
-      ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [I1=8; I2=9;]
-      ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [I1=9; I2=10;]
-      ELSEIF(NY=3 & NZ=1) [I1=1; I2=2;]
-      ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [I1=2; I2=6;]
-      ELSEIF((NY=4|NY=5) & NZ<=2) [I1=1; I2=3;]
-      ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [I1=3; I2=6;]
-      ELSEIF((NY=5|NY=6) & NZ>=7) [I1=7; I2=10;]
-      ELSEIF(NY=6 & NZ<=4) [I1=1; I2=5;]
-      ELSEIF(NY=6 & NZ=5) [I1=5; I2=6;]
-
+      IF(NY=1) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+          IF(NZ<=8) [I1=1; I2=9;]
+          ELSE [I1=9; I2=10;]
+        ]
+        ELSE [
+          IF(NZ<=3) [I1=1; I2=4;]
+          ELSEIF(NZ<=5) [I1=4; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSE [I1=8; I2=10;]
+        ]
+      ]
+      ELSEIF(NY=2) [
+        IF(NZ<=3) [I1=1; I2=4;]
+        ELSEIF(NZ<=5) [I1=4; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSEIF(NZ=8) [I1=8; I2=9;]
+        ELSE [I1=9; I2=10;]
+      ]
+      ELSEIF(NY=3) [
+        IF(NZ=1) [I1=1; I2=2;]
+        ELSEIF(NZ<=5) [I1=2; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSEIF(NZ=8) [I1=8; I2=9;]
+        ELSE [I1=9; I2=10;]
+      ]
+      ELSEIF(NY=4) [
+        IF(NZ<=2) [I1=1; I2=3;]
+        ELSEIF(NZ<=5) [I1=3; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSEIF(NZ=8) [I1=8; I2=9;]
+        ELSE [I1=9; I2=10;]
+      ]
+      ELSEIF(NY=5) [
+        IF(NZ<=2) [I1=1; I2=3;]
+        ELSEIF(NZ<=5) [I1=3; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSE [I1=7; I2=10;]
+      ]
+      ELSEIF(NY=6) [
+        IF(NZ<=4) [I1=1; I2=5;]
+        ELSEIF(NZ=5) [I1=5; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSE [I1=7; I2=10;]
+      ]
     ] ELSE [
       "Quarter Isocenter leaf"
 
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index fadb53e88..2a865de4f 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -182,6 +182,11 @@ REPLACE {$MAXFIELDLEAF} WITH {{COMPUTE $MAXLEAF*$MAXFIELD_$SYNCHDMLC}}
 "I>                    when doing range rejection
 "V>                    for particles in the leaves and beyond the most open
 "V>                    leaf.  0 (default) otherwise.
+"V>I_LEAF_ALT_DEF_$SYNCHDMLC An array of flags indicating whether a sector
+"V>                    of a given leaf cross-section has an alternative
+"V>                    definition to that specified in the BEAMnrc Manual"
+"V>                    indexing: LEAFTYPE, 1 (Y bound) or 2 (Z bound),
+"V>                    boundary no.
 ;
 REPLACE{;COMIN/CM_$SYNCHDMLC/;} WITH {
 ;COMMON/CM_$SYNCHDMLC/
@@ -206,6 +211,7 @@ REPLACE{;COMIN/CM_$SYNCHDMLC/;} WITH {
       IR_$SYNCHDMLC,NUM_LEAF_$SYNCHDMLC, ORIENT_$SYNCHDMLC,
       SUBINDEX_$SYNCHDMLC,NGROUP_$SYNCHDMLC,
       LEAFTYPE_$SYNCHDMLC,
+      I_LEAF_ALT_DEF_$SYNCHDMLC,
       TITLE_$SYNCHDMLC;
    DOUBLE PRECISION
       ZMAX_$SYNCHDMLC,
@@ -230,7 +236,8 @@ REPLACE{;COMIN/CM_$SYNCHDMLC/;} WITH {
       N_GAP_$SYNCHDMLC,IR_$SYNCHDMLC,NUM_LEAF_$SYNCHDMLC($MAXLEAF),
       ORIENT_$SYNCHDMLC,SUBINDEX_$SYNCHDMLC($MAXLEAF,5,6,9),
       NGROUP_$SYNCHDMLC,
-      LEAFTYPE_$SYNCHDMLC($MAXLEAF);
+      LEAFTYPE_$SYNCHDMLC($MAXLEAF),
+      I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,10);
   CHARACTER*1 TITLE_$SYNCHDMLC(60);
 
 }
@@ -685,20 +692,63 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
 				   "Target leaf"
 
-    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
-    ELSEIF(NY=1 & NZ=5) [ZLHS=5; ZRHS=6;]
-    ELSEIF(NY=1 & NZ>=6) [ZLHS=6; ZRHS=10;]
-    ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-    ELSEIF((NY=2|NY=3) & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [ZLHS=2; ZRHS=3;]
-    ELSEIF(NY>=3 & NZ=3) [ZLHS=3; ZRHS=4;]
-    ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [ZLHS=5; ZRHS=8;]
-    ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [ZLHS=5; ZRHS=9;]
-    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [ZLHS=5; ZRHS=7;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=2) [ZLHS=1; ZRHS=3;]
+    IF(NY=1) [
+        IF(NZ<=3) [ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+        ELSEIF(NZ=5) [ZLHS=5; ZRHS=6;]
+        ELSE [ZLHS=6; ZRHS=10;]
+    ]
+    ELSEIF(NY=2) [
+        IF(NZ<=3) [ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+        ELSEIF(NZ<=7) [ZLHS=5; ZRHS=8;]
+        ELSE [ZLHS=8; ZRHS=10;]
+    ]
+    ELSEIF(NY=3) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
+           IF(NZ=1) [ZLHS=1; ZRHS=2;]
+           ELSEIF(NZ=2) [ZLHS=2; ZRHS=3;]
+           ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
+           ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+           ELSEIF(NZ<=7) [ZLHS=5; ZRHS=8;]
+           ELSE [ZLHS=8; ZRHS=10;]
+        ]
+        ELSE [
+           IF(NZ<=3) [ZLHS=1; ZRHS=4;]
+           ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+           ELSEIF(NZ<=8) [ZLHS=5; ZRHS=9;]
+           ELSE [ZLHS=9; ZRHS=10;]
+        ]
+    ]
+    ELSEIF(NY=4) [
+        IF(NZ=1) [ZLHS=1; ZRHS=2;]
+        ELSEIF(NZ=2) [ZLHS=2; ZRHS=3;]
+        ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
+        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+        ELSEIF(NZ<=7) [ZLHS=5; ZRHS=8;]
+        ELSE [ZLHS=8; ZRHS=10;]
+    ]
+    ELSEIF(NY=5) [
+        IF(NZ=1) [ZLHS=2; ZRHS=3;]
+        ELSEIF(NZ=2) [ZLHS=2; ZRHS=3;]
+        ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
+        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+        ELSEIF(NZ<=6) [ZLHS=5; ZRHS=7;]
+        ELSE [ZLHS=7; ZRHS=10;]
+    ]
+    ELSEIF(NY=6) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          IF(NZ=1) [ZLHS=1; ZRHS=1;]
+          ELSE[ ZLHS=2; ZRHS=10;]
+        ]
+        ELSE [
+          IF(NZ<=2) [ZLHS=1; ZRHS=3;]
+          ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
+          ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+          ELSEIF(NZ<=6) [ZLHS=5; ZRHS=7;]
+          ELSE [ ZLHS=7; ZRHS=10;]
+        ]
+    ]
 
   ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["Full leaf"
 
@@ -720,21 +770,55 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
 
   ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
     "Half Isocenter leaf"
-
-    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
-    ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
-    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
-    ELSEIF(NY=1 & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
-    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
-    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
-    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
+    IF(NY=1) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+          IF(NZ<=8) [ZLHS=1; ZRHS=9;]
+          ELSE [ZLHS=9; ZRHS=10;]
+        ]
+        ELSE [
+          IF(NZ<=3) [ZLHS=1; ZRHS=4;]
+          ELSEIF(NZ<=5) [ZLHS=4; ZRHS=6;]
+          ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+          ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
+          ELSE [ZLHS=8; ZRHS=10;]
+        ]
+    ]
+    ELSEIF(NY=2) [
+        IF(NZ<=3) [ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ<=5) [ZLHS=4; ZRHS=6;]
+        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
+        ELSEIF(NZ=8) [ZLHS=8; ZRHS=9;]
+        ELSE [ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=3) [
+        IF(NZ=1) [ZLHS=1; ZRHS=2;]
+        ELSEIF(NZ<=5) [ZLHS=2; ZRHS=6;]
+        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
+        ELSEIF(NZ=8) [ZLHS=8; ZRHS=9;]
+        ELSE [ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=4) [
+        IF(NZ<=2) [ZLHS=1; ZRHS=3;]
+        ELSEIF(NZ<=5) [ZLHS=3; ZRHS=6;]
+        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
+        ELSEIF(NZ=8) [ZLHS=8; ZRHS=9;]
+        ELSE [ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=5) [
+        IF(NZ<=2) [ZLHS=1; ZRHS=3;]
+        ELSEIF(NZ<=5) [ZLHS=3; ZRHS=6;]
+        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+        ELSE [ZLHS=7; ZRHS=10;]
+    ]
+    ELSEIF(NY=6) [
+        IF(NZ<=4) [ZLHS=1; ZRHS=5;]
+        ELSEIF(NZ=5) [ZLHS=5; ZRHS=6;]
+        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+        ELSE [ZLHS=7; ZRHS=10;]
+    ]
 
   ] ELSE [
     "Quarter Isocenter leaf"
@@ -768,51 +852,127 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
   ELSE [ ZDIST = 1.0E20; ];
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
      "Target leaf"
-     IF(NZ=1 & NY<=5) [
+     IF(NZ=1) [
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          LHS=1; J=LEAFIS;
+          RHS=7; I=LEAFIS;
+       ]
+       ELSE [
+          IF(NY<=5) [
+            LHS=1; J=LEAFIS;
+            RHS=6; I=LEAFIS;
+          ]
+          ELSE [
+            LHS=6; J=LEAFIS;
+            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+            ELSE [RHS=3; I=LEAFIS+1;]
+          ]
+       ]
+     ]
+     ELSEIF(NZ=2) [
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
+          IF(NY<=2) [
+            LHS=1; J=LEAFIS;
+            RHS=3; I=LEAFIS;
+          ]
+          ELSE[
+            LHS=3; J=LEAFIS;
+            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+            ELSE [RHS=3; I=LEAFIS+1;]
+          ]
+       ]
+       ELSE[
+          IF(NY<=3) [
+            LHS=1; J=LEAFIS;
+            RHS=4; I=LEAFIS;
+          ]
+          ELSE[
+            LHS=4; J=LEAFIS;
+            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+            ELSE [RHS=3; I=LEAFIS+1;]
+          ]
+       ]
+    ]
+    ELSEIF(NZ=3)[
        LHS=1; J=LEAFIS;
-       RHS=6; I=LEAFIS;
-     ] ELSEIF(NZ=1 & NY=6) [
-        LHS=6; J=LEAFIS;
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-        ELSE [RHS=3; I=LEAFIS+1;]
-     ] ELSEIF(NZ=2 & NY<=2) [
-        LHS=1; J=LEAFIS;
-        RHS=3; I=LEAFIS;
-     ] ELSEIF(NZ=2 & NY>=3) [
-        LHS=3; J=LEAFIS;
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-        ELSE [RHS=3; I=LEAFIS+1;]
-     ] ELSEIF(NZ=3|NZ=4|NZ=5) [
-        LHS=1; J=LEAFIS;
-        RHS=7; I=LEAFIS;
-     ] ELSEIF(NY=1 & (NZ=6|NZ=7)) [
-        IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-        ELSE [LHS=7; J=LEAFIS-1;]
-        RHS=2; I=LEAFIS;
-     ] ELSEIF(NY>=2 & NZ=6) [
-       LHS=2; J=LEAFIS;
        RHS=7; I=LEAFIS;
-     ] ELSEIF(NZ=7 & (NY=2|NY=3|NY=4)) [
-       LHS=2; J=LEAFIS;
-       RHS=5; I=LEAFIS;
-     ] ELSEIF((NZ=7|NZ=8) & NY>=5) [
-       LHS=5; J=LEAFIS;
-       IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-       ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF(NZ=8 & NY<=3) [
-       IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-       ELSE [LHS=7; J=LEAFIS-1;]
-       RHS=4; I=LEAFIS;
-     ] ELSEIF(NZ=8 & NY=4) [
-       LHS=4; J=LEAFIS;
-       RHS=5; I=LEAFIS;
-     ] ELSEIF(NZ=9) [
+    ]
+    ELSEIF(NZ=4)[
+       LHS=1; J=LEAFIS;
+       RHS=7; I=LEAFIS;
+    ]
+    ELSEIF(NZ=5)[
+       LHS=1; J=LEAFIS;
+       RHS=7; I=LEAFIS;
+    ]
+    ELSEIF(NZ=6)[
+       IF(NY=1)[
+         IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+         ELSE [LHS=7; J=LEAFIS-1;]
+         RHS=2; I=LEAFIS;
+       ]
+       ELSE[
+         LHS=2; J=LEAFIS;
+         RHS=7; I=LEAFIS;
+       ]
+    ]
+    ELSEIF(NZ=7)[
+       IF(NY=1)[
+         IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+         ELSE [LHS=7; J=LEAFIS-1;]
+         RHS=2; I=LEAFIS;
+       ]
+       ELSEIF(NY<=4)[
+         LHS=2; J=LEAFIS;
+         RHS=5; I=LEAFIS;
+       ]
+       ELSE[
+         LHS=5; J=LEAFIS;
+         IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+         ELSE [RHS=1; I=LEAFIS+1;]
+       ]
+    ]
+    ELSEIF(NZ=8)[
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
+         IF(NY<=3)[
+          IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+          ELSE [LHS=7; J=LEAFIS-1;]
+          RHS=4; I=LEAFIS;
+         ]
+         ELSEIF(NY=4)[
+          LHS=4; J=LEAFIS;
+          RHS=5; I=LEAFIS;
+         ]
+         ELSE[
+          LHS=5; J=LEAFIS;
+          IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+          ELSE [RHS=1; I=LEAFIS+1;]
+         ]
+       ]
+       ELSE[
+         IF(NY<=2)[
+          IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+          ELSE [LHS=7; J=LEAFIS-1;]
+          RHS=4; I=LEAFIS;
+         ]
+         ELSEIF(NY<=4)[
+          LHS=4; J=LEAFIS;
+          RHS=5; I=LEAFIS;
+         ]
+         ELSE[
+          LHS=5; J=LEAFIS;
+          IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+          ELSE [RHS=1; I=LEAFIS+1;]
+         ]
+       ]
+    ]
+    ELSEIF(NZ=9)[
        IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
        ELSE [LHS=7; J=LEAFIS-1;]
        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
        ELSE [RHS=1; I=LEAFIS+1;]
-     ]
-   ]
+    ]
+  ]
   ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["full leaf"
      IF(NZ=1) [IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
         ELSE [LHS=6; J=LEAFIS-1;]
@@ -866,44 +1026,146 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
         ELSE [LHS=7; J=LEAFIS-1;]
         IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
         ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF((NZ=2|NZ=3) & (NY=1|NY=2)) [
-        IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-        ELSE [LHS=7; J=LEAFIS-1;]
-        RHS=3; I=LEAFIS;
-     ] ELSEIF(NZ=2 & NY=3) [
-        LHS=3; J=LEAFIS;
-        RHS=4; I=LEAFIS;
-     ] ELSEIF(NZ=2 & NY>=4) [
-        LHS=4; J=LEAFIS;
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-        ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF(NZ=3 & (NY=3|NY=4|NY=5)) [
-        LHS=3; J=LEAFIS;
-        RHS=6; I=LEAFIS;
-     ] ELSEIF((NZ=3|NZ=4) & NY=6) [
-        LHS=6; J=LEAFIS;
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-        ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF(NZ=4 & NY<=5) [
-        LHS=1; J=LEAFIS;
-        RHS=6; I=LEAFIS;
-     ] ELSEIF(NZ=5|NZ=6|NZ=7) [
-        LHS=1; J=LEAFIS;
-        RHS=7; I=LEAFIS;
-     ] ELSEIF(NZ=8 & NY<=4) [
-        IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-        ELSE [LHS=5; J=LEAFIS-1;]
-        RHS=5; I=LEAFIS;
-     ] ELSEIF(NZ=8 & NY>=5) [
-        LHS=5; J=LEAFIS;
-        RHS=7; I=LEAFIS;
-     ] ELSEIF(NZ=9 & NY=1) [
-       IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-       ELSE [LHS=5; J=LEAFIS-1;]
-       RHS=2; I=LEAFIS;
-     ] ELSEIF(NZ=9 & NY>=2) [
-       LHS=2; J=LEAFIS;
-       RHS=7; I=LEAFIS;
+     ]
+     ELSEIF(NZ=2)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+           ELSE [LHS=7; J=LEAFIS-1;]
+           RHS=3; I=LEAFIS;
+        ]
+        IF(NY=3)[
+           LHS=3; J=LEAFIS;
+           RHS=4; I=LEAFIS;
+        ]
+        ELSE[
+           LHS=4; J=LEAFIS;
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+           ELSE [RHS=1; I=LEAFIS+1;]
+        ]
+     ]
+     ELSEIF(NZ=3)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+           ELSE [LHS=7; J=LEAFIS-1;]
+           RHS=3; I=LEAFIS;
+        ]
+        IF(NY<=5)[
+           LHS=3; J=LEAFIS;
+           RHS=6; I=LEAFIS;
+        ]
+        ELSE[
+           LHS=6; J=LEAFIS;
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+           ELSE [RHS=1; I=LEAFIS+1;]
+        ]
+     ]
+     ELSEIF(NZ=4)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+             ELSE [LHS=7; J=LEAFIS-1;]
+             RHS=2; I=LEAFIS;
+           ]
+           ELSEIF(NY<=5)[
+             LHS=2; J=LEAFIS;
+             RHS=6; I=LEAFIS;
+           ]
+           ELSE[
+             LHS=6; J=LEAFIS;
+             IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+             ELSE [RHS=1; I=LEAFIS+1;]
+           ]
+        ]
+        ELSE[
+           IF(NY<=5)[
+              LHS=1; J=LEAFIS;
+              RHS=6; I=LEAFIS;
+           ]
+           ELSE[
+              LHS=6; J=LEAFIS;
+              IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+              ELSE [RHS=1; I=LEAFIS+1;]
+           ]
+        ]
+     ]
+     ELSEIF(NZ=5)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+             ELSE [LHS=7; J=LEAFIS-1;]
+             RHS=2; I=LEAFIS;
+           ]
+           ELSE[
+             LHS=2; J=LEAFIS;
+             RHS=7; I=LEAFIS;
+           ]
+        ]
+        ELSE[
+           LHS=2; J=LEAFIS;
+           RHS=7; I=LEAFIS;
+        ]
+     ]
+     ELSEIF(NZ=6)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+             ELSE [LHS=7; J=LEAFIS-1;]
+             RHS=2; I=LEAFIS;
+           ]
+           ELSE[
+             LHS=2; J=LEAFIS;
+             RHS=7; I=LEAFIS;
+           ]
+        ]
+        ELSE[
+           LHS=2; J=LEAFIS;
+           RHS=7; I=LEAFIS;
+        ]
+     ]
+     ELSEIF(NZ=7)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+             ELSE [LHS=7; J=LEAFIS-1;]
+             RHS=2; I=LEAFIS;
+           ]
+           ELSE[
+             LHS=2; J=LEAFIS;
+             RHS=7; I=LEAFIS;
+           ]
+        ]
+        ELSE[
+           LHS=2; J=LEAFIS;
+           RHS=7; I=LEAFIS;
+        ]
+     ]
+     ELSEIF(NZ=8)[
+        IF(NY<=4)[
+           IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+           ELSE [LHS=5; J=LEAFIS-1;]
+           RHS=5; I=LEAFIS;
+        ]
+        ELSE[
+           LHS=5; J=LEAFIS;
+           RHS=7; I=LEAFIS;
+        ]
+     ]
+     ELSEIF(NZ=9)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           LHS=1; J=LEAFIS;
+           RHS=7; I=LEAFIS;
+        ]
+        ELSE[
+           IF(NY=1)[
+             IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+             ELSE [LHS=5; J=LEAFIS-1;]
+             RHS=2; I=LEAFIS;
+           ]
+           ELSE[
+             LHS=2; J=LEAFIS;
+             RHS=7; I=LEAFIS;
+           ]
+        ]
      ]
    ] ELSE [
      "Isocenter Quarter"
diff --git a/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl b/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
index 69ea67cae..fd9b88ab2 100644
--- a/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
+++ b/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
@@ -296,9 +296,9 @@ proc edit_SYNCHDMLC { id zmax } {
     set top .synchdmlc$id.top
 
 
-    label $top.mainlabel -text "Multi-leaf collimator $cm_ident($id)" \
-	    -font $helvfont
-    pack $top.mainlabel -side top -padx 10
+    #label $top.mainlabel -text "Multi-leaf collimator $cm_ident($id)" \
+#	    -font $helvfont
+   # pack $top.mainlabel -side top -padx 10
 
     # SYNCHDMLC_macros.mortran:REPLACE {$MAXLEAF} WITH {64}
     # read the macro file for CM SYNCHDMLC to get defaults and put a label on the
@@ -330,9 +330,9 @@ proc edit_SYNCHDMLC { id zmax } {
 	tk_dialog .nope "Too bad" "Couldn't get the defaults" info 0 OK
     }
 
-    label $top.default1 -text "The default maximum number\
-	    of leaves is $default1." -font $helvfont
-    pack $top.default1 -side top
+   # label $top.default1 -text "The default maximum number\
+#	    of leaves is $default1." -font $helvfont
+ #   pack $top.default1 -side top
 
     label $top.zmax -text $zmax -font $helvfont
     pack $top.zmax -pady 5
@@ -481,11 +481,11 @@ proc edit_SYNCHDMLC { id zmax } {
     pack $top.openings.label $top.openings.inps -side top
     pack $top.openings -side top -fill x
 
-    pack $top -side top -pady 5
+    pack $top -side top -pady 0
 
 #now get ecut,pcut,materials,etc
 
-    frame .synchdmlc$id.bottom -bd 4
+    frame .synchdmlc$id.bottom -bd 0
 
     frame .synchdmlc$id.bottom.ecut
     button .synchdmlc$id.bottom.ecut.b -text "?" -command \
@@ -597,7 +597,7 @@ proc edit_SYNCHDMLC { id zmax } {
 
     pack .synchdmlc$id.bottom -side top -pady 5
 
-    frame .synchdmlc$id.buts -bd 4
+    frame .synchdmlc$id.buts -bd 1
     button .synchdmlc$id.buts.okb -text "OK" -command "destroy .synchdmlc$id"\
 	    -relief groove -bd 8
     button .synchdmlc$id.buts.helpb -text "Help" -command\
@@ -2315,7 +2315,7 @@ proc draw_SYNCHDMLC { id } {
 
     # put the canvas up
     set ncan 3
-    set width 200.0
+    set width 150.0
     set canwidth [expr $width+150.0]
     set scrlheight [expr 2*$canwidth]
     set scrlwidth [expr 2*$canwidth]

From 32710544574e9a53f7373b560fd4adb1fc7f8824 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakerwalters@gmail.com>
Date: Mon, 13 Sep 2021 10:12:22 -0700
Subject: [PATCH 02/14] Address input override bugs for M120 Millenium MLC

---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    |  39 ++-
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      | 233 +++++++++---------
 2 files changed, 145 insertions(+), 127 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 0b33392d6..ae59bacfe 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -712,7 +712,7 @@ REPLACE {$GEO_SHIFT_1_(#)} WITH {
 }
 
 ;IMPLICIT NONE;
-;COMIN/CMs,CM_$SYNCHDMLC,EPCONT,STACK,USER,EGS-IO/;
+;COMIN/MISC,SCORE,CMs,CM_$SYNCHDMLC,EPCONT,STACK,USER,EGS-IO/;
 "T>
 "T>**********************************
 "T>TYPE DECLARATIONS FOR HOWFAR_$SYNCHDMLC
@@ -764,6 +764,13 @@ IF(ORIENT_$SYNCHDMLC=1) [
 ELSE[ XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);]
 ;
 
+"IF(Z(NP)>47.62001 & Z(NP)<54.37999)["
+        "IF(med(irl) = 0)["
+         " write(*,*)' iq,x,y,z ',iq(np),x(np),y(np),z(np);"
+         " write(*,*)' ir,med ',ir(np),med(irl);"
+         " write(*,*)'  ihstry ',ihstry;"
+       " ]"
+  " ]"
 STEP_UNIT=0.0;
 COUNT = 0;
 OUTOFCMFLAG=0;
@@ -968,6 +975,10 @@ ELSEIF( (STEP_UNIT>DIST1) & (DIST1>=0)) [
           ]
 
           IRNEW = NEWREGION_$SYNCHDMLC;
+          "Holy assumption: If there is no airgap between leaves, we could"
+          "have the situation where we do not transport as far as the new"
+          "region but the region no. is changed anyway"
+          "Consider using the _FIND macro to get the reg. no. anyway"
           RETURN;
        ] ELSE [
          $SYNCHDMLC_MINDISTANCE(DIST2);
@@ -2439,8 +2450,16 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
                           WTONGUE_$SYNCHDMLC(2);
      ]
      ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=3)["half isocenter leaf"
-         YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
+              "here we are saying that leaf gap is defined wrt tongue/groove"
+              YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+                          WTONGUE_$SYNCHDMLC(3)-
+                          ABS(WRAILBOT_$SYNCHDMLC(3)-WRAILTOP_$SYNCHDMLC(3));
+         ]
+         ELSE[
+              YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(3);
+         ]
      ]
      ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=4)["qtr target leaf"
          YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
@@ -2486,7 +2505,12 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=3)["half isocenter leaf"
        YREG_$SYNCHDMLC(I,2)=YREG_$SYNCHDMLC(I,1)+ABS(WRAILTOP_$SYNCHDMLC(3)-
                           WRAILBOT_$SYNCHDMLC(3));
-       YREG_$SYNCHDMLC(I,3)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(3);
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
+          YREG_$SYNCHDMLC(I,3)=YREG_$SYNCHDMLC(I,2)+WTONGUE_$SYNCHDMLC(3);
+       ]
+       ELSE[
+          YREG_$SYNCHDMLC(I,3)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(3);
+       ]
        YREG_$SYNCHDMLC(I,4)=YREG_$SYNCHDMLC(I,3)+WTIP_$SYNCHDMLC(3);
        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
           YREG_$SYNCHDMLC(I,5)=YREG_$SYNCHDMLC(I,1)+WRAILBOT_$SYNCHDMLC(3);
@@ -2552,8 +2576,8 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
 
      DO J = 1, 7 [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
-     OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
-      OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
+     "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
+     " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
  ]; "End of L loop"
@@ -3717,7 +3741,7 @@ IF(LEAFIS~=0) [
    "Set minimum and maximum Z boundaries"
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
       "Quarter or Half Target leaf"
-      "Deal with each NY case"
+
       IF(NY=1) [
         IF(NZ<=3) [I1=1; I2=4;]
         ELSEIF(NZ=4) [I1=4; I2=5;]
@@ -3764,7 +3788,7 @@ IF(LEAFIS~=0) [
       ]
       ELSEIF(NY=6) [
         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
-          IF(NZ=1) [I1=1; I2=1;]
+          IF(NZ=1) [I1=1; I2=2;]
           ELSE[ I1=2; I2=10;]
         ]
         ELSE [
@@ -3775,6 +3799,7 @@ IF(LEAFIS~=0) [
           ELSE [ I1=7; I2=10;]
         ]
       ]
+
     ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) [
       "Full leaf"
 
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index 2a865de4f..b4a6b67df 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -521,7 +521,9 @@ ELSE ["inside leaf bank"
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
        "Originally on Target (Quarter or Half) Leaf"
 
-       IF((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9) & (LEAFIS~=TOT_LEAF_$SYNCHDMLC)) [
+       IF(LEAFIS~=TOT_LEAF_$SYNCHDMLC & (((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9)) |
+           (I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1 &
+            NY=6 & NZ>1))) [
 
          "In groove check if on next leaf"
          IF(XYFL(1)>SURPARA1_$SYNCHDMLC(LEAFIS+1,1)*
@@ -628,7 +630,32 @@ ELSE ["inside leaf bank"
            ];
          ]
        ];
-     ];
+     ]
+     ELSEIF(LEAFIS ~=1 &
+           I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,1)=1 &
+           NY=1 & NZ<9)[
+       "check if particle is in region of previous leaf"
+       IF(XYFL(1)<SURPARA1_$SYNCHDMLC(LEAFIS-1,7)*
+             (ZFL-ZFOCUS_$SYNCHDMLC(1))) [
+
+         LEAFIS=LEAFIS-1;
+         NY=6;
+         IF(XYFL(1)<SURPARA1_$SYNCHDMLC(LEAFIS,6)*
+             (ZFL-ZFOCUS_$SYNCHDMLC(1))) [
+              NY=5;
+         ]
+         IF(ZFL<ZREG_$SYNCHDMLC(LEAFIS,1))[
+              NZ=1;
+         ] ELSEIF(ZFL>ZREG_$SYNCHDMLC(LEAFIS,10))[
+              NZ=9;
+         ] ELSE[
+             DO I=1,9 ["recheck Z region"
+              IF((ZFL>=ZREG_$SYNCHDMLC(LEAFIS,I)) &
+                (ZREG_$SYNCHDMLC(LEAFIS,I+1)>=ZFL)) [NZ=I; EXIT];
+              ];
+         ]
+       ]
+     ]
     ];
 "Now determine X region index"
   IF(ENDTYPE_$SYNCHDMLC=1)[
@@ -689,65 +716,32 @@ ELSE ["inside leaf bank"
 "{P1}: The change value for ir region #"
 
 REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
+  "Note: some of these will underestimate dZ when input dimension"
+  "restrictions are overridden--this should not result in transport"
+  "errors, but will potentially slow transport"
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
-				   "Target leaf"
+                                   "Target leaf"
 
-    IF(NY=1) [
-        IF(NZ<=3) [ZLHS=1; ZRHS=4;]
-        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-        ELSEIF(NZ=5) [ZLHS=5; ZRHS=6;]
-        ELSE [ZLHS=6; ZRHS=10;]
-    ]
-    ELSEIF(NY=2) [
-        IF(NZ<=3) [ZLHS=1; ZRHS=4;]
-        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-        ELSEIF(NZ<=7) [ZLHS=5; ZRHS=8;]
-        ELSE [ZLHS=8; ZRHS=10;]
-    ]
-    ELSEIF(NY=3) [
-        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
-           IF(NZ=1) [ZLHS=1; ZRHS=2;]
-           ELSEIF(NZ=2) [ZLHS=2; ZRHS=3;]
-           ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
-           ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-           ELSEIF(NZ<=7) [ZLHS=5; ZRHS=8;]
-           ELSE [ZLHS=8; ZRHS=10;]
-        ]
-        ELSE [
-           IF(NZ<=3) [ZLHS=1; ZRHS=4;]
-           ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-           ELSEIF(NZ<=8) [ZLHS=5; ZRHS=9;]
-           ELSE [ZLHS=9; ZRHS=10;]
-        ]
-    ]
-    ELSEIF(NY=4) [
-        IF(NZ=1) [ZLHS=1; ZRHS=2;]
-        ELSEIF(NZ=2) [ZLHS=2; ZRHS=3;]
-        ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
-        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-        ELSEIF(NZ<=7) [ZLHS=5; ZRHS=8;]
-        ELSE [ZLHS=8; ZRHS=10;]
-    ]
-    ELSEIF(NY=5) [
-        IF(NZ=1) [ZLHS=2; ZRHS=3;]
-        ELSEIF(NZ=2) [ZLHS=2; ZRHS=3;]
-        ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
-        ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-        ELSEIF(NZ<=6) [ZLHS=5; ZRHS=7;]
-        ELSE [ZLHS=7; ZRHS=10;]
-    ]
-    ELSEIF(NY=6) [
-        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
-          IF(NZ=1) [ZLHS=1; ZRHS=1;]
-          ELSE[ ZLHS=2; ZRHS=10;]
-        ]
-        ELSE [
-          IF(NZ<=2) [ZLHS=1; ZRHS=3;]
-          ELSEIF(NZ=3) [ZLHS=3; ZRHS=4;]
-          ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-          ELSEIF(NZ<=6) [ZLHS=5; ZRHS=7;]
-          ELSE [ ZLHS=7; ZRHS=10;]
-        ]
+    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
+    ELSEIF(NY=1 & NZ=5) [ZLHS=5; ZRHS=6;]
+    ELSEIF(NY=1 & NZ>=6) [ZLHS=6; ZRHS=10;]
+    ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+    ELSEIF((NY=2|NY=3) & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [ZLHS=2; ZRHS=3;]
+    ELSEIF(NY>=3 & NZ=3) [ZLHS=3; ZRHS=4;]
+    ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [ZLHS=5; ZRHS=8;]
+    ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [ZLHS=5; ZRHS=9;]
+    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [ZLHS=5; ZRHS=7;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=2) [
+      "dZ potentially overestimated--deal with it!"
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1)[
+         IF(NZ=1)[ZLHS=1; ZRHS=2;]
+         ELSE[ZLHS=2; ZRHS=10;]
+      ]
+      ELSE[ZLHS=1; ZRHS=3;]
     ]
 
   ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["Full leaf"
@@ -770,55 +764,28 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
 
   ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
     "Half Isocenter leaf"
-    IF(NY=1) [
-        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
-          IF(NZ<=8) [ZLHS=1; ZRHS=9;]
-          ELSE [ZLHS=9; ZRHS=10;]
-        ]
-        ELSE [
-          IF(NZ<=3) [ZLHS=1; ZRHS=4;]
-          ELSEIF(NZ<=5) [ZLHS=4; ZRHS=6;]
-          ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-          ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
-          ELSE [ZLHS=8; ZRHS=10;]
-        ]
-    ]
-    ELSEIF(NY=2) [
-        IF(NZ<=3) [ZLHS=1; ZRHS=4;]
-        ELSEIF(NZ<=5) [ZLHS=4; ZRHS=6;]
-        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
-        ELSEIF(NZ=8) [ZLHS=8; ZRHS=9;]
-        ELSE [ZLHS=9; ZRHS=10;]
-    ]
-    ELSEIF(NY=3) [
-        IF(NZ=1) [ZLHS=1; ZRHS=2;]
-        ELSEIF(NZ<=5) [ZLHS=2; ZRHS=6;]
-        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
-        ELSEIF(NZ=8) [ZLHS=8; ZRHS=9;]
-        ELSE [ZLHS=9; ZRHS=10;]
-    ]
-    ELSEIF(NY=4) [
-        IF(NZ<=2) [ZLHS=1; ZRHS=3;]
-        ELSEIF(NZ<=5) [ZLHS=3; ZRHS=6;]
-        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7) [ZLHS=7; ZRHS=8;]
-        ELSEIF(NZ=8) [ZLHS=8; ZRHS=9;]
-        ELSE [ZLHS=9; ZRHS=10;]
-    ]
-    ELSEIF(NY=5) [
-        IF(NZ<=2) [ZLHS=1; ZRHS=3;]
-        ELSEIF(NZ<=5) [ZLHS=3; ZRHS=6;]
-        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-        ELSE [ZLHS=7; ZRHS=10;]
-    ]
-    ELSEIF(NY=6) [
-        IF(NZ<=4) [ZLHS=1; ZRHS=5;]
-        ELSEIF(NZ=5) [ZLHS=5; ZRHS=6;]
-        ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-        ELSE [ZLHS=7; ZRHS=10;]
+
+    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
+    ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
+    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
+    "potential overestimate of dZ below--correct it"
+    ELSEIF(NY=1 & NZ>=8) [
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
+        IF(NZ=9)[ZLHS=9; ZRHS=10;]
+        ELSE[ZLHS=1; ZRHS=9;]
+      ]
+      ELSE[ZLHS=8; ZRHS=10;]
     ]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
+    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
+    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
+    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
 
   ] ELSE [
     "Quarter Isocenter leaf"
@@ -842,7 +809,6 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
     "!= from Half Isocenter"
     ELSEIF(NY=6 & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
   ]
-
   IF(W(NP)~=0) [
      ZP = (ZREG_$SYNCHDMLC(LEAFIS,ZRHS)-ZFL)/W(NP);
      ZN = (ZREG_$SYNCHDMLC(LEAFIS,ZLHS)-ZFL)/W(NP);
@@ -953,10 +919,10 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
          IF(NY<=2)[
           IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
           ELSE [LHS=7; J=LEAFIS-1;]
-          RHS=4; I=LEAFIS;
+          RHS=3; I=LEAFIS;
          ]
          ELSEIF(NY<=4)[
-          LHS=4; J=LEAFIS;
+          LHS=3; J=LEAFIS;
           RHS=5; I=LEAFIS;
          ]
          ELSE[
@@ -1024,6 +990,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
      IF(NZ=1) [
         IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
         ELSE [LHS=7; J=LEAFIS-1;]
+        "possibly use LHS=6?"
         IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
         ELSE [RHS=1; I=LEAFIS+1;]
      ]
@@ -1046,7 +1013,15 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
      ELSEIF(NZ=3)[
         IF(NY<=2)[
            IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
-           ELSE [LHS=7; J=LEAFIS-1;]
+           ELSE [
+              J=LEAFIS-1;
+              IF(ZFL>ZREG_$SYNCHDMLC(J,7))[
+                LHS = 5;
+              ]
+              ELSE[
+                LHS = 7;
+              ]
+           ]
            RHS=3; I=LEAFIS;
         ]
         IF(NY<=5)[
@@ -1056,14 +1031,22 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
         ELSE[
            LHS=6; J=LEAFIS;
            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-           ELSE [RHS=1; I=LEAFIS+1;]
+           ELSE [
+             I=LEAFIS+1;
+             IF(ZFL<ZREG_$SYNCHDMLC(I,6))[
+                RHS=1;
+             ]
+             ELSE[
+                RHS=2;
+             ]
+           ]
         ]
      ]
      ELSEIF(NZ=4)[
         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
            IF(NY=1)[
              IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
-             ELSE [LHS=7; J=LEAFIS-1;]
+             ELSE [LHS=5; J=LEAFIS-1;]
              RHS=2; I=LEAFIS;
            ]
            ELSEIF(NY<=5)[
@@ -1073,7 +1056,15 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
            ELSE[
              LHS=6; J=LEAFIS;
              IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-             ELSE [RHS=1; I=LEAFIS+1;]
+             ELSE [
+               I=LEAFIS+1;
+               IF(ZFL<ZREG_$SYNCHDMLC(I,6))[
+                  RHS=1;
+               ]
+               ELSE[
+                  RHS=2;
+               ]
+             ]
            ]
         ]
         ELSE[
@@ -1092,7 +1083,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
            IF(NY=1)[
              IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
-             ELSE [LHS=7; J=LEAFIS-1;]
+             ELSE [LHS=5; J=LEAFIS-1;]
              RHS=2; I=LEAFIS;
            ]
            ELSE[
@@ -1101,7 +1092,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
            ]
         ]
         ELSE[
-           LHS=2; J=LEAFIS;
+           LHS=1; J=LEAFIS;
            RHS=7; I=LEAFIS;
         ]
      ]
@@ -1109,7 +1100,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
            IF(NY=1)[
              IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
-             ELSE [LHS=7; J=LEAFIS-1;]
+             ELSE [LHS=5; J=LEAFIS-1;]
              RHS=2; I=LEAFIS;
            ]
            ELSE[
@@ -1118,7 +1109,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
            ]
         ]
         ELSE[
-           LHS=2; J=LEAFIS;
+           LHS=1; J=LEAFIS;
            RHS=7; I=LEAFIS;
         ]
      ]
@@ -1126,7 +1117,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
            IF(NY=1)[
              IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
-             ELSE [LHS=7; J=LEAFIS-1;]
+             ELSE [LHS=5; J=LEAFIS-1;]
              RHS=2; I=LEAFIS;
            ]
            ELSE[
@@ -1135,7 +1126,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
            ]
         ]
         ELSE[
-           LHS=2; J=LEAFIS;
+           LHS=1; J=LEAFIS;
            RHS=7; I=LEAFIS;
         ]
      ]
@@ -1159,6 +1150,8 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
            IF(NY=1)[
              IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
              ELSE [LHS=5; J=LEAFIS-1;]
+             "here we are ignoring the possibility that Z could be"
+             ">Ztip(LEAFIS-1) but should be okay"
              RHS=2; I=LEAFIS;
            ]
            ELSE[

From 7e5d0f7597516e75ddcd8585389a56cd3bfa1685 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakerwalters@gmail.com>
Date: Fri, 15 Oct 2021 08:15:29 -0700
Subject: [PATCH 03/14] Fix y boundary for synchdmlc target overrides

Restore some code from DYNVMLC that seemed necessary to avoid changing
regions when the particle had not actually traveled as far as the region
boundary.
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 60 ++++++++++---------
 1 file changed, 33 insertions(+), 27 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index ae59bacfe..6e882dce3 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -764,13 +764,6 @@ IF(ORIENT_$SYNCHDMLC=1) [
 ELSE[ XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);]
 ;
 
-"IF(Z(NP)>47.62001 & Z(NP)<54.37999)["
-        "IF(med(irl) = 0)["
-         " write(*,*)' iq,x,y,z ',iq(np),x(np),y(np),z(np);"
-         " write(*,*)' ir,med ',ir(np),med(irl);"
-         " write(*,*)'  ihstry ',ihstry;"
-       " ]"
-  " ]"
 STEP_UNIT=0.0;
 COUNT = 0;
 OUTOFCMFLAG=0;
@@ -943,7 +936,7 @@ ELSEIF( (STEP_UNIT>DIST1) & (DIST1>=0)) [
       DIST1=DIST1+1.0E-5; "we have to shift it regardless to avoid "
                           "infinite loops"
     "OUTPUT REGION_$SYNCHDMLC;(I3);-prints 67 to 69"
-    "  IF(DIST1>=STEP_UNIT)[EXIT;]"
+      IF(DIST1>=STEP_UNIT)[EXIT;]
     "  ELSE["
         $SYNCHDMLC_FIND(NEWREGION_$SYNCHDMLC,DIST1);
 
@@ -1155,7 +1148,7 @@ $REAL INDEXTMP; "T>temporary input variable for field indices in dynamic and
                 "  step-and-shoot simulations
 $LOGICAL check_full_qtr;
 
-$REAL YTMP;
+$REAL YTMP,YLEAFEND;
 
 DO I=1,5[
   DO J=1,2[
@@ -2436,38 +2429,44 @@ I=0;
 IF(TOT_LEAF_$SYNCHDMLC>0) [
   DO L = 1,NGROUP_$SYNCHDMLC[
    DO K = 1,NUM_LEAF_$SYNCHDMLC(L) [
-
      I=I+1;
      IF(I=1)[
        YREG_$SYNCHDMLC(I,1)=START_$SYNCHDMLC;
      ]
-     ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=1)[
-       YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+     ELSE[
+       YLEAFEND=YREG_$SYNCHDMLC(I-1,7);
+       "possible exceptions"
+       IF(LEAFTYPE_$SYNCHDMLC(I-1)=2 & I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,6)=1)[
+          YLEAFEND=YREG_$SYNCHDMLC(I-1,6);
+       ]
+       IF(LEAFTYPE_$SYNCHDMLC(I)=1)[
+          YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(1);
-     ]
-     ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=2)["half target leaf"
-         YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+       ]
+       ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=2)["half target leaf"
+          YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(2);
-     ]
-     ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=3)["half isocenter leaf"
+       ]
+       ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=3)["half isocenter leaf"
          IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
               "here we are saying that leaf gap is defined wrt tongue/groove"
-              YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+              YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(3)-
                           ABS(WRAILBOT_$SYNCHDMLC(3)-WRAILTOP_$SYNCHDMLC(3));
          ]
          ELSE[
-              YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+              YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(3);
          ]
-     ]
-     ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=4)["qtr target leaf"
-         YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+       ]
+       ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=4)["qtr target leaf"
+         YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(4);
-     ]
-     ELSE ["qtr iso leaf"
-         YREG_$SYNCHDMLC(I,1)=YREG_$SYNCHDMLC(I-1,7)+LEAFGAP_$SYNCHDMLC-
+       ]
+       ELSE ["qtr iso leaf"
+         YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(5);
+       ]
      ]
      "we have now defined YREG_$SYNCHDMLC(I,1)"
 
@@ -2483,9 +2482,16 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      ]
      ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=2)["half target leaf"
        YREG_$SYNCHDMLC(I,2)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(2);
-       YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(2);
-       YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,6)=1)[
+          YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(2);
+          YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,6)+
                             ABS(WRAILBOT_$SYNCHDMLC(2)-WRAILTOP_$SYNCHDMLC(2));
+       ]
+       ELSE[
+          YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(2);
+          YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-
+                            ABS(WRAILBOT_$SYNCHDMLC(2)-WRAILTOP_$SYNCHDMLC(2));
+       ]
        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,6)=1)[
           YTMP = YREG_$SYNCHDMLC(I,6);
        ]

From 88828acc02ba74cbb37b827889ba3da74967f239 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakerwalters@gmail.com>
Date: Fri, 29 Oct 2021 14:39:29 -0700
Subject: [PATCH 04/14] Fix target leaf in synchdmlc

Note that commented out debug write statements are still present in the
source code.
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 393 +++++++++++++++---
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      |  46 +-
 2 files changed, 382 insertions(+), 57 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 6e882dce3..35ec1d5fa 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -764,6 +764,15 @@ IF(ORIENT_$SYNCHDMLC=1) [
 ELSE[ XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);]
 ;
 
+"write(*,*)' in howfar ';
+
+"IF(Z(NP)>47.62001 & Z(NP)<54.37999)["
+        "IF(med(irl) = 0)["
+         " write(*,*)' iq,x,y,z ',iq(np),x(np),y(np),z(np);"
+         " write(*,*)' ir,med ',ir(np),med(irl);"
+         " write(*,*)'  ihstry ',ihstry;"
+       " ]"
+  " ]"
 STEP_UNIT=0.0;
 COUNT = 0;
 OUTOFCMFLAG=0;
@@ -823,6 +832,7 @@ ELSEIF(IR_$SYNCHDMLC=1 | IR_$SYNCHDMLC=2 | IR_$SYNCHDMLC=3) [
    ELSEIF(W(NP) < 0.0) [
      "particle going backward"
       DIST = (ZMIN_$SYNCHDMLC - Z(NP))/W(NP); "distance to back of CM "
+      "write(*,*)' dist, ustep ',dist,ustep;
       IF(DIST>USTEP) [ STEP_UNIT=USTEP;  ]
       ELSE [ STEP_UNIT=DIST; ]
       IF(DIST <= 0.0) [
@@ -840,6 +850,8 @@ ELSEIF(IR_$SYNCHDMLC=1 | IR_$SYNCHDMLC=2 | IR_$SYNCHDMLC=3) [
 
 $SYNCHDMLC_FIND(REGION_$SYNCHDMLC,0.0);
 
+"write(*,*)' leafis, region ',leafis,REGION_$SYNCHDMLC;
+
 IF(REGION_$SYNCHDMLC=4) [ "Particle is in the air gap "
   REGION_$SYNCHDMLC=IRSTART_$SYNCHDMLC-1+REGION_$SYNCHDMLC;
    IF(W(NP) > 0.0)[
@@ -911,6 +923,10 @@ IF(OUTOFMLCFLAG=1) [
 
 $SYNCHDMLC_MINDISTANCE(DIST1);
 
+"write(*,*)' x,y,z ',x(np),y(np),z(np);
+"write(*,*)' leafis,nx,ny,nz ',leafis,nx,ny,nz;
+"write(*,*)' dist1,step_unit ',DIST1,STEP_UNIT;
+
 "OUTPUT REGION_$SYNCHDMLC;(I3);"
 
 IF((DIST1>=STEP_UNIT) | (DIST1<0)) [
@@ -943,6 +959,9 @@ ELSEIF( (STEP_UNIT>DIST1) & (DIST1>=0)) [
         NEWREGION_$SYNCHDMLC=NEWREGION_$SYNCHDMLC+IRSTART_$SYNCHDMLC-1;
        " OUTPUT REGION_$SYNCHDMLC;(I3);"
 
+       "write(*,*)' region, newregion, dist1 ',REGION_$SYNCHDMLC,
+       "     NEWREGION_$SYNCHDMLC,DIST1;
+
         IF( OUTOFCMFLAG=1 ) [
           EXIT;
         ] ELSEIF( (NEWREGION_$SYNCHDMLC~=REGION_$SYNCHDMLC)
@@ -975,6 +994,7 @@ ELSEIF( (STEP_UNIT>DIST1) & (DIST1>=0)) [
           RETURN;
        ] ELSE [
          $SYNCHDMLC_MINDISTANCE(DIST2);
+         "write(*,*)' dist1, dist2 ',dist1,dist2;
          DIST1=DIST1+DIST2;
        ];
 
@@ -2583,6 +2603,8 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      DO J = 1, 7 [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
      "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
+     write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,
+            YREG_$SYNCHDMLC(I,J);
      " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
@@ -3613,7 +3635,9 @@ IF(LEAFIS~=0) [
   "Check if we are in groove on leaf and move to adjacent leaf"
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
 				   "target leaf"
-    IF((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9) & LEAFIS~=TOT_LEAF_$SYNCHDMLC) [
+    IF(LEAFIS~=TOT_LEAF_$SYNCHDMLC & (((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9)) |
+        (I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1 &
+          NY=6 & NZ>1))) [
        IF(XYL1>SURPARA1_$SYNCHDMLC(LEAFIS+1,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1)))[
           LEAFIS=LEAFIS+1;
           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1));
@@ -3703,7 +3727,32 @@ IF(LEAFIS~=0) [
                  ];
                 ]
            ];
-         ];
+         ]
+         ELSEIF(LEAFIS ~=1 &
+           I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,1)=1 &
+           NY=1 & NZ<9)[
+           "check if particle is in region of previous leaf"
+           IF(XYL1<SURPARA1_$SYNCHDMLC(LEAFIS-1,7)*
+             (Z(NP)-ZFOCUS_$SYNCHDMLC(1))) [
+
+              LEAFIS=LEAFIS-1;
+              NY=6;
+              IF(XYL1<SURPARA1_$SYNCHDMLC(LEAFIS,6)*
+                 (Z(NP)-ZFOCUS_$SYNCHDMLC(1))) [
+                 NY=5;
+              ]
+              IF(Z(NP)<ZREG_$SYNCHDMLC(LEAFIS,1))[
+                 NZ=1;
+              ] ELSEIF(Z(NP)>ZREG_$SYNCHDMLC(LEAFIS,10))[
+                 NZ=9;
+              ] ELSE[
+                 DO I=1,9 ["recheck Z region"
+                    IF((Z(NP)>=ZREG_$SYNCHDMLC(LEAFIS,I)) &
+                   (ZREG_$SYNCHDMLC(LEAFIS,I+1)>=Z(NP))) [NZ=I; EXIT];
+                 ];
+              ]
+           ]
+         ]
       ];
 
   "Determine which X region we are in"
@@ -3747,6 +3796,8 @@ IF(LEAFIS~=0) [
    "Set minimum and maximum Z boundaries"
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
       "Quarter or Half Target leaf"
+      "take care of distance to corners possibly being min. distance"
+      "here."
 
       IF(NY=1) [
         IF(NZ<=3) [I1=1; I2=4;]
@@ -3755,8 +3806,11 @@ IF(LEAFIS~=0) [
         ELSE [I1=6; I2=10;]
       ]
       ELSEIF(NY=2) [
-        IF(NZ<=3) [I1=1; I2=4;]
+        IF(NZ=1) [I1=1; I2=2;]
+        ELSEIF(NZ=2) [I1=1; I2=4;]
+        ELSEIF(NZ=3) [I1=3; I2=4;]
         ELSEIF(NZ=4) [I1=4; I2=5;]
+        ELSEIF(NZ=5) [I1=5; I2=6;]
         ELSEIF(NZ<=7) [I1=5; I2=8;]
         ELSE [I1=8; I2=10;]
       ]
@@ -3766,13 +3820,19 @@ IF(LEAFIS~=0) [
            ELSEIF(NZ=2) [I1=2; I2=3;]
            ELSEIF(NZ=3) [I1=3; I2=4;]
            ELSEIF(NZ=4) [I1=4; I2=5;]
-           ELSEIF(NZ<=7) [I1=5; I2=8;]
+           ELSEIF(NZ<=6) [I1=5; I2=7;]
+           ELSEIF(NZ=7) [I1=5; I2=8;]
            ELSE [I1=8; I2=10;]
         ]
         ELSE [
-           IF(NZ<=3) [I1=1; I2=4;]
+           IF(NZ=1) [I1=1; I2=2;]
+           ELSEIF(NZ=2) [I1=1; I2=4;]
+           ELSEIF(NZ=3) [I1=3; I2=4;]
            ELSEIF(NZ=4) [I1=4; I2=5;]
-           ELSEIF(NZ<=8) [I1=5; I2=9;]
+           ELSEIF(NZ=5) [I1=5; I2=6;]
+           ELSEIF(NZ=6) [I1=5; I2=7;]
+           ELSEIF(NZ=7) [I1=5; I2=8;]
+           ELSEIF(NZ=8) [I1=5; I2=9;]
            ELSE [I1=9; I2=10;]
         ]
       ]
@@ -3781,8 +3841,10 @@ IF(LEAFIS~=0) [
         ELSEIF(NZ=2) [I1=2; I2=3;]
         ELSEIF(NZ=3) [I1=3; I2=4;]
         ELSEIF(NZ=4) [I1=4; I2=5;]
-        ELSEIF(NZ<=7) [I1=5; I2=8;]
-        ELSE [I1=8; I2=10;]
+        ELSEIF(NZ<=6) [I1=5; I2=7;]
+        ELSEIF(NZ=7) [I1=5; I2=8;]
+        ELSEIF(NZ=8) [I1=5; I2=9;]
+        ELSE [I1=9; I2=10;]
       ]
       ELSEIF(NY=5) [
         IF(NZ=1) [I1=2; I2=3;]
@@ -3902,6 +3964,9 @@ IF(LEAFIS~=0) [
 
     DIST=MIN(ABS(ZREG_$SYNCHDMLC(LEAFIS,I1)-Z(NP)),
              ABS(ZREG_$SYNCHDMLC(LEAFIS,I2)-Z(NP)));
+    "write(*,*)' x,y,z ',x(np),y(np),z(np);
+    "write(*,*)' nx,ny,nz ',nx,ny,nz;
+    "write(*,*)' leafis,i1,i2,zdist ',leafis,i1,i2,dist;
 
     "Calculates distance to closest boundary in z direction"
     "--> 3) 7 Jul 2009"
@@ -3909,36 +3974,62 @@ IF(LEAFIS~=0) [
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
       "Target leaf"
 
-       IF(NZ=1 & NY<=5) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
-
-      ] ELSEIF(NZ=1 & NY=6) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+       IF(NZ=1)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
-        ] ELSE [
-          TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,3);
         ]
+        ELSE[
+          IF(NY<=5) [
 
-      ] ELSEIF(NZ=2 & NY<=2) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+            TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
 
-      ] ELSEIF(NZ=2 & NY>=3) [
+          ] ELSEIF(NY=6) [
 
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
-          TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
-        ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,3);]
+            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+              TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+            ] ELSE [
+              TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,3);
+            ]
+         ]
+       ]
+      ] ELSEIF(NZ=2) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
+           IF(NY<=2) [
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+             IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+                TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+             ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,3);]
+           ]
+        ]
+        ELSE[
+           IF(NY<=3)[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+             IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+                TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+             ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,3);]
+           ]
+        ]
 
       ] ELSEIF(NZ=3|NZ=4|NZ=5) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+          TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+        ]
+        ELSE[
+          TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+          TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
 
       ] ELSEIF(NY=1 & (NZ=6|NZ=7)) [
 
@@ -3947,33 +4038,62 @@ IF(LEAFIS~=0) [
         TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
 
       ] ELSEIF(NY>=2 & NZ=6) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
-
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
       ] ELSEIF(NZ=7 & (NY=2|NY=3|NY=4)) [
 
         TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
         TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
 
-      ] ELSEIF((NZ=7|NZ=8) & NY>=5) [
+      ] ELSEIF(NZ=7 & NY>=5) [
 
         TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,5);
         IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
         ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
 
-      ] ELSEIF(NZ=8 & NY<=3) [IF(LEAFIS=1) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
-        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,4);
-
-      ]
-     ELSEIF(NZ=8 & NY=4) [
-       TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,4);
-       TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
-      ]
+      ] ELSEIF(NZ=8)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,4)=1) [
+          IF(NY<=3)[
+            IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1); ]
+            ELSE[ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
+            TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+          ]
+          ELSEIF(NY=4)[
+            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+            TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+          ]
+          ELSE[
+            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+               TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+            ELSE[TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+          ]
+        ]
+        ELSE[
+          IF(NY<=2)[
+            IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1); ]
+            ELSE[ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
+            TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+          ]
+          ELSEIF(NY<=4)[
+            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+            TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+          ]
+          ELSE[
+            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+               TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+            ELSE[TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+          ]
+        ]
+     ]
      ELSEIF(NZ=9) [IF(LEAFIS=1) [
        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
@@ -4038,10 +4158,184 @@ IF(LEAFIS~=0) [
         TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
        ]
      ]
-    ELSE ["Isocenter leaf"
+    ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
+      "half isocenter leaf
+      IF(NZ=1) [
+        IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
+        "possibly use LHS=6?"
+        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+        ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+     ]
+     ELSEIF(NZ=2)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+        ]
+        IF(NY=3)[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+           ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+        ]
+     ]
+     ELSEIF(NZ=3)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [
+              IF(Z(NP)>ZREG_$SYNCHDMLC(J,7))[
+                TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);
+              ]
+              ELSE[
+                TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);
+              ]
+           ]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+        ]
+        IF(NY<=5)[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+           ELSE [
+             IF(Z(NP)<ZREG_$SYNCHDMLC(I,6))[
+                TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);
+             ]
+             ELSE[
+                TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,2);
+             ]
+           ]
+        ]
+     ]
+     ELSEIF(NZ=4)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           ]
+           ELSEIF(NY<=5)[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+             IF(LEAFIS=TOT_LEAF_$SYNCHDMLC)[
+                   TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+             ELSE [
+               IF(Z(NP)<ZREG_$SYNCHDMLC(I,6))[
+                  TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);
+               ]
+               ELSE[
+                  TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,2);
+               ]
+             ]
+           ]
+        ]
+        ELSE[
+           IF(NY<=5)[
+              TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+              TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+           ]
+           ELSE[
+              TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+              IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+                     TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+              ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+           ]
+        ]
+     ]
+     ELSEIF(NZ=5)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+           ]
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
+     ]
+     ELSEIF(NZ=6)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+           ]
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
+     ]
+     ELSEIF(NZ=7)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           IF(NY=1)[
+             IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+           ]
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
+     ]
+     ELSEIF(NZ=8)[
+        IF(NY<=4)[
+           IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
+     ]
+     ELSEIF(NZ=9)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1) [
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
+        ELSE[
+           IF(NY=1)[
+             IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             "here we are ignoring the possibility that Z could be"
+             ">Ztip(LEAFIS-1) but should be okay"
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+           ]
+        ]
+     ]
+    ]
+    ELSE ["Quarter Isocenter leaf"
       "EH - because the quarter and half leaves are slightly different"
       "     you will need a modification for NZ=4 and NY=6"
-
       IF(NZ=1) [
         IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
         ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);];
@@ -4121,6 +4415,7 @@ IF(LEAFIS~=0) [
           SQRT(1+TEMP2**2));
 
     DIST = MIN(DIST,TEMP1,TEMP2);
+    "write(*,*)' ydist ',dist;
  "NOW CHECK DISTANCE IN X DIRECTION"
     IF(ENDTYPE_$SYNCHDMLC=1) [ "focused leaf end"
       TEMP1=SURPARA2_B_$SYNCHDMLC(LEAFIS);
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index b4a6b67df..dd752ff1b 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -518,6 +518,8 @@ ELSE ["inside leaf bank"
       NY=NY+1;
     ];
 
+    "write(*,*)' leafis, xyfl1, ny ',leafis,xyfl(1),ny;"
+
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
        "Originally on Target (Quarter or Half) Leaf"
 
@@ -814,6 +816,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
      ZN = (ZREG_$SYNCHDMLC(LEAFIS,ZLHS)-ZFL)/W(NP);
      IF( (ZP>=0.0) & (ZN>=0.0) ) [ ZDIST =MIN(ZP, ZN); ]
      ELSE [ ZDIST = MAX(ZP, ZN); ]
+     "write(*,*)' zdist,leafis ',zdist,leafis;"
    ]
   ELSE [ ZDIST = 1.0E20; ];
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
@@ -860,16 +863,34 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
        ]
     ]
     ELSEIF(NZ=3)[
-       LHS=1; J=LEAFIS;
-       RHS=7; I=LEAFIS;
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          LHS=1; J=LEAFIS;
+          RHS=6; I=LEAFIS;
+       ]
+       ELSE[
+          LHS=1; J=LEAFIS;
+          RHS=7; I=LEAFIS;
+       ]
     ]
     ELSEIF(NZ=4)[
-       LHS=1; J=LEAFIS;
-       RHS=7; I=LEAFIS;
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          LHS=1; J=LEAFIS;
+          RHS=6; I=LEAFIS;
+       ]
+       ELSE[
+          LHS=1; J=LEAFIS;
+          RHS=7; I=LEAFIS;
+       ]
     ]
     ELSEIF(NZ=5)[
-       LHS=1; J=LEAFIS;
-       RHS=7; I=LEAFIS;
+       IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+          LHS=1; J=LEAFIS;
+          RHS=6; I=LEAFIS;
+       ]
+       ELSE[
+          LHS=1; J=LEAFIS;
+          RHS=7; I=LEAFIS;
+       ]
     ]
     ELSEIF(NZ=6)[
        IF(NY=1)[
@@ -878,8 +899,14 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
          RHS=2; I=LEAFIS;
        ]
        ELSE[
-         LHS=2; J=LEAFIS;
-         RHS=7; I=LEAFIS;
+         IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
+            LHS=2; J=LEAFIS;
+            RHS=6; I=LEAFIS;
+         ]
+         ELSE[
+            LHS=2; J=LEAFIS;
+            RHS=7; I=LEAFIS;
+         ]
        ]
     ]
     ELSEIF(NZ=7)[
@@ -1222,6 +1249,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
   ELSE [ YN = 1.0E20; ];
   IF((YP>=0.0) & (YN>=0.0) ) [ YDIST =MIN(YP, YN); ]
   ELSE [ YDIST = MAX(YP,YN);];
+  "write(*,*)' ydist ',ydist;"
  IF(ENDTYPE_$SYNCHDMLC = 1) ["focused leaf end"
       HOLE=HOLEPOS_$SYNCHDMLC(LEAFIS);
       TEMP3=LEAFB_$SYNCHDMLC(LEAFIS)-HOLE;
@@ -1276,6 +1304,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
     TEMP3 = UVL(2)*(XYFL(2)-XoP)+W(NP)*(ZFL-Zo); "B in eqn"
     TEMP4 = (XYFL(2)-XoN)**2 + (ZFL-Zo)**2; "part of C"
     TEMP5 = (XYFL(2)-XoP)**2 + (ZFL-Zo)**2; "part of C"
+    "write(*,*)' nx ',nx;"
     IF((XYFL(2)>=XoN) & (SQRT((XYFL(2)-XoN)**2+(ZFL-Zo)**2)-
       LEAFRADIUS_$SYNCHDMLC=0.0) & (UVL(2)*(XYFL(2)-XoN)+W(NP)*(ZFL-Zo)=0.0)) [
          XN=0.0;  XP=1.0E20; "on edge of negative leaf"
@@ -1391,6 +1420,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
  ];
 IF( (XP>=0.0) & (XN>=0.0) ) [ XDIST =MIN(XP, XN); ]
 ELSE [ XDIST = MAX(XP,XN); ];
+"write(*,*)' xdist ',xdist;"
 IF( ZDIST>=0.0) [TEMP=ZDIST;
     IF( YDIST>=0.0 ) [TEMP=MIN(TEMP,YDIST);];
     IF( XDIST>=0.0 ) [TEMP=MIN(TEMP,XDIST);];

From bd607021f113fe1d4611abf784ef40978ebb8ccc Mon Sep 17 00:00:00 2001
From: Blake Walters <blakerwalters@gmail.com>
Date: Sat, 30 Oct 2021 11:21:31 -0700
Subject: [PATCH 05/14] Fix HOWNEAR for half isocenter leaves

Note that commented out debug write statements are still present in the
source code.
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 26 +++++++++++++------
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      |  2 ++
 2 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 35ec1d5fa..460b2c722 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -2603,8 +2603,8 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      DO J = 1, 7 [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
      "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
-     write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,
-            YREG_$SYNCHDMLC(I,J);
+     "write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,
+         "   YREG_$SYNCHDMLC(I,J);
      " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
@@ -3055,7 +3055,8 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
       SUBINDEX_$SYNCHDMLC(L,I,6,8)=2;
       SUBINDEX_$SYNCHDMLC(L,I,6,9)=2;
 
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),2,4)~=1) [
+      IF(LEAFTYPE_$SYNCHDMLC(L)=5 &
+          I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)~=1) [
         "Quarter Isocenter with zg<zt"
         SUBINDEX_$SYNCHDMLC(L,I,6,4)=2;
       ];
@@ -3912,7 +3913,9 @@ IF(LEAFIS~=0) [
       ]
       ELSEIF(NY=3) [
         IF(NZ=1) [I1=1; I2=2;]
-        ELSEIF(NZ<=5) [I1=2; I2=6;]
+        ELSEIF(NZ=2)[I1=2; I2=6;]
+        ELSEIF(NZ=3) [I1=3; I2=6;]
+        ELSEIF(NZ<=5) [I1=4; I2=6;]
         ELSEIF(NZ=6) [I1=6; I2=7;]
         ELSEIF(NZ=7) [I1=7; I2=8;]
         ELSEIF(NZ=8) [I1=8; I2=9;]
@@ -3920,7 +3923,9 @@ IF(LEAFIS~=0) [
       ]
       ELSEIF(NY=4) [
         IF(NZ<=2) [I1=1; I2=3;]
-        ELSEIF(NZ<=5) [I1=3; I2=6;]
+        ELSEIF(NZ=3) [I1=3; I2=6;]
+        ELSEIF(NZ=4) [I1=4; I2=6;]
+        ELSEIF(NZ=5) [I1=5; I2=6;]
         ELSEIF(NZ=6) [I1=6; I2=7;]
         ELSEIF(NZ=7) [I1=7; I2=8;]
         ELSEIF(NZ=8) [I1=8; I2=9;]
@@ -3928,15 +3933,20 @@ IF(LEAFIS~=0) [
       ]
       ELSEIF(NY=5) [
         IF(NZ<=2) [I1=1; I2=3;]
-        ELSEIF(NZ<=5) [I1=3; I2=6;]
+        ELSEIF(NZ<=4) [I1=3; I2=6;]
+        ELSEIF(NZ=5) [I1=5; I2=6;]
         ELSEIF(NZ=6) [I1=6; I2=7;]
-        ELSE [I1=7; I2=10;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSEIF(NZ=8) [I1=7; I2=10;]
+        ELSE [I1=9; I2=10;]
       ]
       ELSEIF(NY=6) [
         IF(NZ<=4) [I1=1; I2=5;]
         ELSEIF(NZ=5) [I1=5; I2=6;]
         ELSEIF(NZ=6) [I1=6; I2=7;]
-        ELSE [I1=7; I2=10;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSEIF(NZ=8) [I1=7; I2=10;]
+        ELSE [I1=9; I2=10;]
       ]
     ] ELSE [
       "Quarter Isocenter leaf"
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index dd752ff1b..6f24721b2 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -698,6 +698,8 @@ ELSE ["inside leaf bank"
     ELSEIF((XYFL(2)>TEMP4) | (XYFL(2)=TEMP4 & UVL(2)>=0)) [
          NX=5;]
  ];
+ "write(*,*)' leafis, x, y, z ',leafis,xyfl(2),xyfl(1),zfl;"
+ "write(*,*)' nx, ny, nz ',nx,ny,nz;"
  {P1}=SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);
 
  "OUTPUT LEAFIS,XYFL(2),XYFL(1),ZFL,{P1};"

From 1df517fecd50762897b50dd0f4cb8d205158d610 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakerwalters@gmail.com>
Date: Thu, 11 Nov 2021 22:07:04 -0800
Subject: [PATCH 06/14] Add debugging information output for synchdmlc

---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    |   4 +-
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      |   3 +-
 HEN_HOUSE/src/egsnrc.mortran                  | 212 ++++++++++++++++++
 3 files changed, 216 insertions(+), 3 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 460b2c722..8698e0cca 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -2603,8 +2603,8 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      DO J = 1, 7 [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
      "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
-     "write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,
-         "   YREG_$SYNCHDMLC(I,J);
+     write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,
+            YREG_$SYNCHDMLC(I,J);
      " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index 6f24721b2..cb282f234 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -699,7 +699,8 @@ ELSE ["inside leaf bank"
          NX=5;]
  ];
  "write(*,*)' leafis, x, y, z ',leafis,xyfl(2),xyfl(1),zfl;"
- "write(*,*)' nx, ny, nz ',nx,ny,nz;"
+ "write(*,*)' nx, ny, nz, subindex ',nx,ny,nz,"
+ "            SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);"
  {P1}=SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);
 
  "OUTPUT LEAFIS,XYFL(2),XYFL(1),ZFL,{P1};"
diff --git a/HEN_HOUSE/src/egsnrc.mortran b/HEN_HOUSE/src/egsnrc.mortran
index ed3bc507a..039d83e63 100644
--- a/HEN_HOUSE/src/egsnrc.mortran
+++ b/HEN_HOUSE/src/egsnrc.mortran
@@ -1041,6 +1041,111 @@ $start_new_particle;
 
 :NEWELECTRON:LOOP
 [
+"IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
+"    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' test 1';
+"  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
+"    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' test 2';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
+"   MED(IR(NP))=2)[
+"  write(*,*)' test 3';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
+"  MED(IR(NP))=2)[
+"  write(*,*)' test 4';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 5';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 6';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 7';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 8';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 9';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+IF(Y(NP) > -0.72751 & Y(NP) <-0.728 & Z(NP) <54.284 & Z(NP)>47.621 &
+  MED(IR(NP))=2)[
+  write(*,*)' test 10';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.72751 & Y(NP) <-0.690 & Z(NP) <51.103 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 11';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 12';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.493 & Y(NP) <-0.4566 & Z(NP) <51.204 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 13';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7276 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 14';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7276 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 15';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7265 & Y(NP) <-0.4566 & Z(NP) <54.019 & Z(NP)>51.206 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 16';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 17';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <51.206 & Z(NP)>51.105 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 18';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 19';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6105 & Y(NP) <-0.4566 & Z(NP) <54.284 & Z(NP)>54.021 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 20';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7275 & Y(NP) <-0.4566 & Z(NP) <54.379 & Z(NP)>54.286 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 21';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
     "Go once through this loop for each 'new' electron whose charge and
     "energy has not been checked
 
@@ -1182,6 +1287,7 @@ $start_new_particle;
                 $SET-TUSTEP-EM-FIELD; "optional tustep restriction in EM field
 
                 $CALL-HOWNEAR(tperp);
+                "write(*,*)'ustep, tperp ',ustep,tperp;
                 dnear(np) = tperp;
                 $RANGE-DISCARD;       "optional regional range rejection for"
                                       "particles below e_max_rr if i_do_rr set"
@@ -6480,6 +6586,112 @@ $EVALUATE GMFPR0 USING GMFP(GLE);]
 
 :PTRANS:
 LOOP["PHOTON TRANSPORT LOOP"
+"IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
+"    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' test 1';
+"  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
+"    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' test 2';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
+"  MED(IR(NP))=2)[
+"  write(*,*)' test 3';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
+"  MED(IR(NP))=2)[
+"  write(*,*)' test 4';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 5';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 6';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 7';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 8';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
+"  MED(IR(NP))=1)[
+"  write(*,*)' test 9';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+IF(Y(NP) > -0.72751 & Y(NP) <-0.728 & Z(NP) <54.284 & Z(NP)>47.621 &
+  MED(IR(NP))=2)[
+  write(*,*)' test 10';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.72751 & Y(NP) <-0.690 & Z(NP) <51.103 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 11';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 12';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.493 & Y(NP) <-0.4566 & Z(NP) <51.204 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 13';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7276 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 14';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7276 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' test 15';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7265 & Y(NP) <-0.4566 & Z(NP) <54.019 & Z(NP)>51.206 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 16';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 17';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <51.206 & Z(NP)>51.105 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 18';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 19';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.6105 & Y(NP) <-0.4566 & Z(NP) <54.284 & Z(NP)>54.021 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 20';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.7275 & Y(NP) <-0.4566 & Z(NP) <54.379 & Z(NP)>54.286 &
+  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' test 21';
+  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+
 IF (MEDIUM.EQ.0)[TSTEP=VACDST;]
 ELSE [$SET-RHOF;    "DENSITY RATIO SCALING TEMPLATE"
 GMFP=GMFPR0/RHOF;

From 25d24eb66536be0e245c0f1a56dfedf7b8a3f5e7 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakewalters@Blakes-MacBook-Air.local>
Date: Fri, 10 Dec 2021 15:03:15 -0800
Subject: [PATCH 07/14] Debug half target and half iso cross sections

Also comment out debug write statements.
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    |  48 ++-
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      |   2 +-
 HEN_HOUSE/src/egsnrc.mortran                  | 342 +++++++++---------
 3 files changed, 213 insertions(+), 179 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 8698e0cca..9272365c0 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -701,11 +701,14 @@
 "V>$GEO_SHIFT_1_(#)
 "V>=============
 "V>{p1} the value to compare with ustep
-"V> if {p1}+1.0e-5 < ustep shift it, otherwise no shift
+"V> if {p1}+1.0e-5 < ustep shift it, otherwise set it to ustep
+"V> Note: if above condition failed, this used to leave {p1}
+"V> unshifted, which led to transport errors 
 ;
 REPLACE {$GEO_SHIFT_1_(#)} WITH {
   ;IF({P1}~=0.00 ) [
     IF({P1}+1.0E-5< USTEP) [{P1}={P1}+1.0E-5;]
+    ELSE [{P1}=USTEP;]
    ]
    ELSE [{P1}={P1}+1.0E-5;];
 
@@ -764,7 +767,7 @@ IF(ORIENT_$SYNCHDMLC=1) [
 ELSE[ XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);]
 ;
 
-"write(*,*)' in howfar ';
+"write(*,*)' in howfar, ir, med ',IR_$SYNCHDMLC,med(IRL);
 
 "IF(Z(NP)>47.62001 & Z(NP)<54.37999)["
         "IF(med(irl) = 0)["
@@ -801,6 +804,7 @@ OUTOFMLCFLAG=0;
 IF(N_GAP_$SYNCHDMLC=1 & IR_$SYNCHDMLC=4 ) ["Check the air gap first"
    IF(W(NP)>0.0) ["Particle going forward"
       DIST = (ZMIN_$SYNCHDMLC - Z(NP))/W(NP); "distance to front of CM"
+      "write(*,*)' dist ',dist;
       IF(DIST <= 0.0) [
           USTEP=0.0;
           $SYNCHDMLC_FIND(IR_$SYNCHDMLC, 0.0);
@@ -850,15 +854,18 @@ ELSEIF(IR_$SYNCHDMLC=1 | IR_$SYNCHDMLC=2 | IR_$SYNCHDMLC=3) [
 
 $SYNCHDMLC_FIND(REGION_$SYNCHDMLC,0.0);
 
-"write(*,*)' leafis, region ',leafis,REGION_$SYNCHDMLC;
+"write(*,*)' leafis, region, dist ',leafis,REGION_$SYNCHDMLC,DIST;
 
 IF(REGION_$SYNCHDMLC=4) [ "Particle is in the air gap "
   REGION_$SYNCHDMLC=IRSTART_$SYNCHDMLC-1+REGION_$SYNCHDMLC;
    IF(W(NP) > 0.0)[
     IF(DIST <= USTEP ) ["particle to be moved to region boundary"
+      "write(*,*)' ustep, dist here ',ustep,dist;
       $GEO_SHIFT_1_(DIST);
+      "write(*,*)' and ustep, dist here ',ustep,dist;
       USTEP = DIST;
       $SYNCHDMLC_FIND(NEWREGION_$SYNCHDMLC,USTEP);
+      "write(*,*)' ustep, newregion ',ustep,NEWREGION_$SYNCHDMLC;
       IF( NEWREGION_$SYNCHDMLC=1) [IRNEW =IRSTART_$SYNCHDMLC; RETURN;]
       ELSE[IRNEW =IRSTART_$SYNCHDMLC+1; RETURN;]
     ]
@@ -923,6 +930,7 @@ IF(OUTOFMLCFLAG=1) [
 
 $SYNCHDMLC_MINDISTANCE(DIST1);
 
+"write(*,*)' dist1 ',dist1;
 "write(*,*)' x,y,z ',x(np),y(np),z(np);
 "write(*,*)' leafis,nx,ny,nz ',leafis,nx,ny,nz;
 "write(*,*)' dist1,step_unit ',DIST1,STEP_UNIT;
@@ -3077,6 +3085,18 @@ DO L=1,TOT_LEAF_$SYNCHDMLC[
      ]
    ];
 
+   "reset some driving screw regions to air for some
+   "input dimension overrides
+   IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,1)=1)[
+     "an isocenter leaf override"
+     SUBINDEX_$SYNCHDMLC(L,2,1,6)=1;
+     SUBINDEX_$SYNCHDMLC(L,5,1,6)=1;
+   ]
+   ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(L),1,6)=1)[
+     SUBINDEX_$SYNCHDMLC(L,2,6,4)=1;
+     SUBINDEX_$SYNCHDMLC(L,5,6,4)=1;
+   ]
+
    IF(LEAFTYPE_$SYNCHDMLC(L)=1) [
      "Full Leaf"
      SUBINDEX_$SYNCHDMLC(L,2,1,6)=1;
@@ -3545,7 +3565,6 @@ $INTEGER I,J, "T> looping index"
          LEAFIS, "T> leaf no. where particle is located"
          I1,I2; "T> used to mark min. max. Z boundaries for calculating dist"
 
-
 IR_$SYNCHDMLC=IR(NP)-IRSTART_$SYNCHDMLC +1;
 "IR_$SYNCHDMLC=IR(NP)-IRSTART_$SYNCHDMLC; CB"
 IF(IR_$SYNCHDMLC=4) [ "in the air gap at the top"
@@ -3634,12 +3653,15 @@ IF(LEAFIS~=0) [
   ]
 
   "Check if we are in groove on leaf and move to adjacent leaf"
+"write(*,*)' before check leafis, leaftype ',leafis,LEAFTYPE_$SYNCHDMLC(LEAFIS);
+"write(*,*)' nx, ny, nz ',nx,ny,nz; 
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
 				   "target leaf"
-    IF(LEAFIS~=TOT_LEAF_$SYNCHDMLC & (((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9)) |
-        (I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1 &
-          NY=6 & NZ>1))) [
-       IF(XYL1>SURPARA1_$SYNCHDMLC(LEAFIS+1,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1)))[
+    IF(LEAFIS~=TOT_LEAF_$SYNCHDMLC & ((((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9)) &
+       XYL1>SURPARA1_$SYNCHDMLC(LEAFIS+1,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1))) |
+      (I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1 & 
+       NY=6 & NZ>1 & 
+       XYL1>SURPARA1_$SYNCHDMLC(LEAFIS+1,3)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1))))) [
           LEAFIS=LEAFIS+1;
           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1));
           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1));
@@ -3669,7 +3691,6 @@ IF(LEAFIS~=0) [
             ];
           ]
          ];
-       ];
       ]
     ELSE [ "we are on a full leaf or isocenter leaf"
        IF((NY=6 & NZ<=4 & LEAFIS~=TOT_LEAF_$SYNCHDMLC &
@@ -3729,9 +3750,10 @@ IF(LEAFIS~=0) [
                 ]
            ];
          ]
-         ELSEIF(LEAFIS ~=1 &
-           I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,1)=1 &
-           NY=1 & NZ<9)[
+         ELSEIF(LEAFIS ~=1 & NY<=2 & 
+           ((LEAFTYPE_$SYNCHDMLC(LEAFIS) = 3 & NZ<=3) |
+            (LEAFTYPE_$SYNCHDMLC(LEAFIS) = 5 & NZ<=4)))[ 
+           "here we are in an isocenter leaf
            "check if particle is in region of previous leaf"
            IF(XYL1<SURPARA1_$SYNCHDMLC(LEAFIS-1,7)*
              (Z(NP)-ZFOCUS_$SYNCHDMLC(1))) [
@@ -3848,7 +3870,7 @@ IF(LEAFIS~=0) [
         ELSE [I1=9; I2=10;]
       ]
       ELSEIF(NY=5) [
-        IF(NZ=1) [I1=2; I2=3;]
+        IF(NZ=1) [I1=1; I2=2;]
         ELSEIF(NZ=2) [I1=2; I2=3;]
         ELSEIF(NZ=3) [I1=3; I2=4;]
         ELSEIF(NZ=4) [I1=4; I2=5;]
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index cb282f234..932ce8a27 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -698,7 +698,7 @@ ELSE ["inside leaf bank"
     ELSEIF((XYFL(2)>TEMP4) | (XYFL(2)=TEMP4 & UVL(2)>=0)) [
          NX=5;]
  ];
- "write(*,*)' leafis, x, y, z ',leafis,xyfl(2),xyfl(1),zfl;"
+ "write(*,*)' find: leafis, x, y, z ',leafis,xyfl(2),xyfl(1),zfl;"
  "write(*,*)' nx, ny, nz, subindex ',nx,ny,nz,"
  "            SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);"
  {P1}=SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);
diff --git a/HEN_HOUSE/src/egsnrc.mortran b/HEN_HOUSE/src/egsnrc.mortran
index 039d83e63..1ca92ccf5 100644
--- a/HEN_HOUSE/src/egsnrc.mortran
+++ b/HEN_HOUSE/src/egsnrc.mortran
@@ -1041,111 +1041,117 @@ $start_new_particle;
 
 :NEWELECTRON:LOOP
 [
-"IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
-"    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' test 1';
-"  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
-"    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' test 2';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
-"   MED(IR(NP))=2)[
-"  write(*,*)' test 3';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
-"  MED(IR(NP))=2)[
-"  write(*,*)' test 4';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 5';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 6';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 7';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 8';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 9';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-IF(Y(NP) > -0.72751 & Y(NP) <-0.728 & Z(NP) <54.284 & Z(NP)>47.621 &
-  MED(IR(NP))=2)[
-  write(*,*)' test 10';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.72751 & Y(NP) <-0.690 & Z(NP) <51.103 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 11';
+IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
+    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' half air test 1';
+  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
+    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' half air test 2';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 12';
+IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
+   MED(IR(NP))=2)[
+  write(*,*)' half air test 3';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.493 & Y(NP) <-0.4566 & Z(NP) <51.204 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 13';
+IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
+  MED(IR(NP))=2)[
+  write(*,*)' half air test 4';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7276 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 14';
+IF(Y(NP) > -0.9632 & Y(NP) < -0.689 & Z(NP) >54.1161 & ABS(X(NP))<10.0 &
+  MED(IR(NP))=2)[
+  write(*,*)' half air test 5';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7276 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 15';
+IF(Y(NP) > -0.9632 & Y(NP) < -0.926 & Z(NP) >50.996 & ABS(X(NP))<10.0 &
+  MED(IR(NP))=2)[
+  write(*,*)' half air test 6';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7265 & Y(NP) <-0.4566 & Z(NP) <54.019 & Z(NP)>51.206 &
+IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 16';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+  write(*,*)' half med test 7';
+ write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
+IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 17';
+  write(*,*)' half med test 8';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <51.206 & Z(NP)>51.105 &
+IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 18';
+  write(*,*)' half med test 9';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
+IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 19';
+  write(*,*)' half med test 10';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6105 & Y(NP) <-0.4566 & Z(NP) <54.284 & Z(NP)>54.021 &
+IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 20';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.7275 & Y(NP) <-0.4566 & Z(NP) <54.379 & Z(NP)>54.286 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 21';
+  write(*,*)' half med test 11';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
+"   ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 1';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.7266 & Z(NP) <54.284 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 2';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"  stop;
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.6893 & Z(NP) <51.103 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 3';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 4';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 5';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.4936 & Y(NP) <-0.4566 & Z(NP) <51.2 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 6';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>54.286 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 7';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6104 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>51.206 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 8';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <54.02 & Z(NP)>51.105 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 9';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 10';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 11';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
     "Go once through this loop for each 'new' electron whose charge and
     "energy has not been checked
 
@@ -6586,111 +6592,117 @@ $EVALUATE GMFPR0 USING GMFP(GLE);]
 
 :PTRANS:
 LOOP["PHOTON TRANSPORT LOOP"
-"IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
-"    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' test 1';
-"  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
-"    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' test 2';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
-"  MED(IR(NP))=2)[
-"  write(*,*)' test 3';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
-"  MED(IR(NP))=2)[
-"  write(*,*)' test 4';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 5';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 6';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 7';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 8';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
-"  MED(IR(NP))=1)[
-"  write(*,*)' test 9';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-IF(Y(NP) > -0.72751 & Y(NP) <-0.728 & Z(NP) <54.284 & Z(NP)>47.621 &
-  MED(IR(NP))=2)[
-  write(*,*)' test 10';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.72751 & Y(NP) <-0.690 & Z(NP) <51.103 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 11';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 12';
+IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
+    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' half air test 1';
+  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+]
+IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
+    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+  write(*,*)' half air test 2';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.493 & Y(NP) <-0.4566 & Z(NP) <51.204 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 13';
+IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
+   MED(IR(NP))=2)[
+  write(*,*)' half air test 3';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7276 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 14';
+IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
+  MED(IR(NP))=2)[
+  write(*,*)' half air test 4';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7276 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' test 15';
+IF(Y(NP) > -0.9632 & Y(NP) < -0.689 & Z(NP) >54.1161 & ABS(X(NP))<10.0 &
+  MED(IR(NP))=2)[
+  write(*,*)' half air test 5';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7265 & Y(NP) <-0.4566 & Z(NP) <54.019 & Z(NP)>51.206 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 16';
+IF(Y(NP) > -0.9632 & Y(NP) < -0.926 & Z(NP) >50.996 & ABS(X(NP))<10.0 &
+  MED(IR(NP))=2)[
+  write(*,*)' half air test 6';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 17';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
+ ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' half med test 7';
+ write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <51.206 & Z(NP)>51.105 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 18';
+IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
+ ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' half med test 8';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 19';
+IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
+ ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+  write(*,*)' half med test 9';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.6105 & Y(NP) <-0.4566 & Z(NP) <54.284 & Z(NP)>54.021 &
+IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 20';
+  write(*,*)' half med test 10';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
-IF(Y(NP) > -0.7275 & Y(NP) <-0.4566 & Z(NP) <54.379 & Z(NP)>54.286 &
+IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
   ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' test 21';
+  write(*,*)' half med test 11';
   write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
 ]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
+"   ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 1';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.7266 & Z(NP) <54.284 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 2';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.6893 & Z(NP) <51.103 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 3';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"  stop;
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 4';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 5';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.4936 & Y(NP) <-0.4566 & Z(NP) <51.2 & Z(NP)>47.621 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
+"  write(*,*)' iso air test 6';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>54.286 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 7';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6104 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>51.206 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 8';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <54.02 & Z(NP)>51.105 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 9';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 10';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
+"IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
+"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
+"  write(*,*)' iso med test 11';
+"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
+"]
 
 IF (MEDIUM.EQ.0)[TSTEP=VACDST;]
 ELSE [$SET-RHOF;    "DENSITY RATIO SCALING TEMPLATE"

From 39d85c951ce69e2d50a1e37fae8b3176aeed6edb Mon Sep 17 00:00:00 2001
From: Blake Walters <blakewalters@Blakes-MacBook-Air.local>
Date: Fri, 4 Mar 2022 16:39:29 -0800
Subject: [PATCH 08/14] Add new leaf orientation option for synchdmlc

Add $SYNCHDMLC_ORIENT options to flip leaf numbering and cross-sections
with respect to the axis perpendicular to the opening axis, so that the
MLC coordinate system matches that in the manufacturer (Varian) specs
for 120MLC and HD120.

This reflection reverses the order of leaf numbering, hence leaf opening
sequences are automatically "flipped" so that the opening coordinate
applied to leaf i is instead applied to leaf N-i+1, where N is the total
number of leaves. See the updated BEAMnrc manual for more details.

Also, add new ORIENT=2,3 options to SYNCHDMLC gui
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 103 ++++++++----
 .../omega/progs/gui/beamnrc/synchdmlc.tcl     | 154 +++++++++++++++---
 2 files changed, 200 insertions(+), 57 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 9272365c0..417ecbed7 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -238,6 +238,13 @@
 "I>
 "I>            ORIENT_$SYNCHDMLC = 0 for leaves parallel to Y direction
 "I>                            = 1 for leaves parallel to X direction
+"I>                            = 2 same as 0 but with leaf numbering and cross-
+"I>                              sections reversed--Note: This makes the
+"I>                              +ve leaves equivalent to leaf bank A
+"I>                              -ve leaves equivalent to bank B in TrueBeam
+"I>                              specs
+"I>                            = 3 same as 1 but with leaf numbering and cross-
+"I>                              sections reversed similar to option 2
 "I>            NGROUP_$SYNCHDMLC = number of groups of adjacent leaves where
 "I>                              all leaves in a group are:
 "I>                              1. FULL leaves
@@ -488,19 +495,18 @@
 "I>
 "I>   Repeat 14 until coordinates of all leaves are defined once.  Leaves
 "I>   are numbered 1,2,...TOT_LEAF_$SYNCHDMLC, where numbering goes from leaf
-"I>   1 to leaf TOT_LEAF_$SYNCHDMLC. Convention is lower to upper or
-"I>   left to right depending on ORIENT_$SYNCHDMLC i.e from negative to
-"I>   positive.
+"I>   1 to leaf TOT_LEAF_$SYNCHDMLC. Convention is -ve to +ve 
+"I>   (ORIENT_$SYNCHDMLC=0,2) or +ve to -ve (ORIENT_$SYNCHDMLC=1,3) 
 "I>
 "I>  14a  NEG_$SYNCHDMLC, POS_$SYNCHDMLC, NUM_$SYNCHDMLC (2F15.5,I5)
 "I>
-"I>    NEG_$SYNCHDMLC:   Min. Y (ORIENT_$SYNCHDMLC=0) or X (ORIENT_$SYNCHDMLC=1)
-"I>                   of front opening in leaf I (ie the opening at
-"I>                   ZMIN_$SYNCHDMLC) if ENDTYPE=1, or of rounded end
-"I>                   of leaf I if ENDTYPE=0.
-"I>    POS_$SYNCHDMLC:   Max. Y (ORIENT_$SYNCHDMLC=0) or X (ORIENT_$SYNCHDMLC=1)
-"I>                   of front opening in leaf I if ENDTYPE=1, or of
+"I>    NEG_$SYNCHDMLC:   Min. Y (ORIENT_$SYNCHDMLC=0,2) or X 
+"I>                   (ORIENT_$SYNCHDMLC=1,3) of front opening in leaf I (ie 
+"I>                   the opening at ZMIN_$SYNCHDMLC) if ENDTYPE=1, or of 
 "I>                   rounded end of leaf I if ENDTYPE=0.
+"I>    POS_$SYNCHDMLC:   Max. Y (ORIENT_$SYNCHDMLC=0,2) or X 
+"I>                   (ORIENT_$SYNCHDMLC=1,3) of front opening in leaf I if 
+"I>                   ENDTYPE=1, or of rounded end of leaf I if ENDTYPE=0.
 "I>    NUM_$SYNCHDMLC:   Apply NEG_$SYNCHDMLC and POS_$SYNCHDMLC to leaves
 "I>                   I,...,I+NUM_$SYNCHDMLC-1.  Defaults to 1 if set <=0.
 "I>                   Defaults to TOT_LEAF_$SYNCHDMLC-I+1 if set >
@@ -535,13 +541,13 @@
 "I>                         number is compared to a random number on (0,1) at
 "I>                         the start of each history; if the random number is
 "I>                         <= INDEX_$SYNCHDMLC(I), then field I is used.
-"I>          NEG_$SYNCHDMLC:  Min. Y (ORIENT_$SYNCHDMLC=0) or
-"I>			      X (ORIENT_$SYNCHDMLC=1)
+"I>          NEG_$SYNCHDMLC:  Min. Y (ORIENT_$SYNCHDMLC=0,2) or
+"I>			      X (ORIENT_$SYNCHDMLC=1,3)
 "I>                         of front opening in leaf (ie the opening at
 "I>                         ZMIN_$SYNCHDMLC) if ENDTYPE=1, or of rounded end
 "I>                         of leaf if ENDTYPE=0 for leaf J in field I.
-"I>          POS_$SYNCHDMLC:  Max. Y (ORIENT_$SYNCHDMLC=0) or
-"I> 			      X (ORIENT_$SYNCHDMLC=1)
+"I>          POS_$SYNCHDMLC:  Max. Y (ORIENT_$SYNCHDMLC=0,2) or
+"I> 			      X (ORIENT_$SYNCHDMLC=1,3)
 "I>                         of front opening in leaf if ENDTYPE=1, or of
 "I>                         rounded end of leaf if ENDTYPE=0 for leaf J in
 "I>                         field I.
@@ -575,10 +581,10 @@
 "I>                      rejection in leaf material when the particle X position
 "I>                      is < min X of all leaf openings (not including leaf
 "I>                      ends) or > max X of leaf openings (not including ends)
-"I>                      (ORIENT_$SYNCHDMLC=1) or if the particle Y position
+"I>                      (ORIENT_$SYNCHDMLC=1,3) or if the particle Y position
 "I>                      is < min Y of all leaf openings (not including leaf
 "I>                      ends) or > max Y of leaf openings (not including ends)
-"I>                      (ORIENT_$SYNCHDMLC=0). This approximation is designed
+"I>                      (ORIENT_$SYNCHDMLC=0,2). This approximation is designed
 "I>                      to make range rejection more efficient deep in the
 "I>                      leaves, while still preserving accurate transport
 "I>                      in the leaf ends.  Note that if you have significant
@@ -762,9 +768,19 @@ parameter (one = 1);
 IRL = IR(NP); "local region number (absolute)"
 IR_$SYNCHDMLC = IRL - IRSTART_$SYNCHDMLC + 1; "rel. local region number"
 "IR_$SYNCHDMLC = IRL - IRSTART_$SYNCHDMLC; rel. local region number"
-IF(ORIENT_$SYNCHDMLC=1) [
-    XYL(1)=Y(NP); XYL(2)=X(NP);UVL(1)=V(NP);UVL(2)=U(NP);]
-ELSE[ XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);]
+
+IF(ORIENT_$SYNCHDMLC=0)[
+    XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);
+]
+ELSEIF(ORIENT_$SYNCHDMLC=1)[
+    XYL(1)=Y(NP); XYL(2)=X(NP);UVL(1)=V(NP);UVL(2)=U(NP);
+]
+ELSEIF(ORIENT_$SYNCHDMLC=2)[
+    XYL(1)=-X(NP); XYL(2)=Y(NP);UVL(1)=-U(NP);UVL(2)=V(NP);
+]
+ELSEIF(ORIENT_$SYNCHDMLC=3)[
+    XYL(1)=-Y(NP); XYL(2)=X(NP);UVL(1)=-V(NP);UVL(2)=U(NP);
+]
 ;
 
 "write(*,*)' in howfar, ir, med ',IR_$SYNCHDMLC,med(IRL);
@@ -1090,9 +1106,18 @@ INTEGER NX,NY,NZ,   "T>Indices of subregions
 DOUBLE PRECISION   XYL(2), XYFL(2), ZFL, UVL(2), XoN, XoP, Zo, TEMP1, TEMP2,
                    TEMP3, TEMP4, HOLE;
 
-IF(ORIENT_$SYNCHDMLC=1)
-    [ XYL(1)=Y(NP); XYL(2)=X(NP);UVL(1)=V(NP);UVL(2)=U(NP);]
-ELSE[ XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);];
+IF(ORIENT_$SYNCHDMLC=0)[
+    XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);
+]
+ELSEIF(ORIENT_$SYNCHDMLC=1)[ 
+    XYL(1)=Y(NP); XYL(2)=X(NP);UVL(1)=V(NP);UVL(2)=U(NP);
+]
+ELSEIF(ORIENT_$SYNCHDMLC=2)[
+    XYL(1)=-X(NP); XYL(2)=Y(NP);UVL(1)=-U(NP);UVL(2)=V(NP);
+]
+ELSEIF(ORIENT_$SYNCHDMLC=3)[ 
+    XYL(1)=-Y(NP); XYL(2)=X(NP);UVL(1)=-V(NP);UVL(2)=U(NP);
+]
 IF (IDIR=1) [
  "particle entering this CM through front face (upstream)"
    IF(N_GAP_$SYNCHDMLC = 0) [ "no air gap this CM"
@@ -1208,12 +1233,12 @@ OUTPUT TITLE_$SYNCHDMLC;(' ',60A1);
 "II. CHOOSE THE SYNCHDMLC ORIENTATION "
 "============================== "
 
-OUTPUT; (' Input leaf orientation (0=parallel to y, 1=parallel to x) and '/
+OUTPUT; (' Input leaf orientation (0,2=parallel to y, 1,3=parallel to x) and '/
          ' no. of groups of leaves with equal width on one line'/' :',$);
 MINPUT ($SYNCHDMLC) ORIENT_$SYNCHDMLC, NGROUP_$SYNCHDMLC,
        MODE_$SYNCHDMLC; (3I5);
 OUTPUT ORIENT_$SYNCHDMLC,NGROUP_$SYNCHDMLC,MODE_$SYNCHDMLC; (3I5/);
-IF(ORIENT_$SYNCHDMLC~=1) [
+IF(ORIENT_$SYNCHDMLC<0 | ORIENT_$SYNCHDMLC>3) [
       ORIENT_$SYNCHDMLC=0;
       OUTPUT;(/' Orientation defaults to 0.'/);
  ];
@@ -2119,8 +2144,8 @@ IF(check_full_qtr) [ "Ya never know"
 " III. START POSITION OF LEAVES"
 " ============================="
 ;
-OUTPUT ZMIN_$SYNCHDMLC; (/' Input the starting X (ORIENT_$SYNCHDMLC=0) or '/
-         ' Y (ORIENT_$SYNCHDMLC=1) position at z = ',F12.5, ' cm : ', $);
+OUTPUT ZMIN_$SYNCHDMLC; (/' Input the starting X (ORIENT_$SYNCHDMLC=0,2) or '/
+         ' Y (ORIENT_$SYNCHDMLC=1,3) position at z = ',F12.5, ' cm : ', $);
 MINPUT ($SYNCHDMLC) START_$SYNCHDMLC; (F15.0);
 OUTPUT START_$SYNCHDMLC; (F12.5);
 
@@ -2611,8 +2636,8 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      DO J = 1, 7 [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
      "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
-     write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,
-            YREG_$SYNCHDMLC(I,J);
+     "write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,"
+            "YREG_$SYNCHDMLC(I,J);"
      " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
@@ -2688,7 +2713,7 @@ IF(MODE_$SYNCHDMLC=1|MODE_$SYNCHDMLC=2)["dynamic or step-and-shoot leaf inputs"
 ]
 ELSE[
 OUTPUT; (' Input for MLC A and B leaf tips '/);
-IF(ORIENT_$SYNCHDMLC=1)[
+IF(ORIENT_$SYNCHDMLC=1 | ORIENT_$SYNCHDMLC=3)[
     IF(ENDTYPE_$SYNCHDMLC=1)[
       OUTPUT;(' Input min. X, max. X of top of opening in leaves,');
     ]
@@ -2809,7 +2834,7 @@ DO IR_$SYNCHDMLC = 1,N_$SYNCHDMLC ["loop through regions to get information"
 ;
 
 IF(IGNOREGAPS_$SYNCHDMLC=1 & IREJCT_GLOBAL>0)[
-   IF(ORIENT_$SYNCHDMLC=1)["leaves parallel to X"
+   IF(ORIENT_$SYNCHDMLC=1 | ORIENT_$SYNCHDMLC=3)["leaves parallel to X"
        OUTPUT;(/' *******Range rejection in $SYNCHDMLC will ignore all'/
                ' air gaps if the particle is in the leaves and has'/
                ' X < min. X of leaf openings (not including leaf ends)'/
@@ -3345,7 +3370,7 @@ IF(N_GAP_$SYNCHDMLC~=0) [
                        ZMIN_$SYNCHDMLC-Z_min_CM(ICM_$SYNCHDMLC);
   ];
 WRITE(IOUTLIST,122) ZTHICK_$SYNCHDMLC;
-IF(ORIENT_$SYNCHDMLC~=0) [
+IF(ORIENT_$SYNCHDMLC~=0 & ORIENT_$SYNCHDMLC~=2) [
    WRITE(IOUTLIST,123) 'X';
 ]
 ELSE[
@@ -3376,7 +3401,7 @@ WRITE(IOUTLIST,128) (LEAFWIDTH_$SYNCHDMLC(I),I=1,3),
                      HOLEPOS_ISO_$SYNCHDMLC,
                     (ZRAILTOP_$SYNCHDMLC(I),I=1,3),
                     (ZRAILBOT_$SYNCHDMLC(I),I=1,3);
-IF(ORIENT_$SYNCHDMLC~=0) [
+IF(ORIENT_$SYNCHDMLC~=0 & ORIENT_$SYNCHDMLC~=2) [
       WRITE(IOUTLIST,129)'Y','X';
  ]
 ELSE [
@@ -3451,7 +3476,7 @@ IF(N_GAP_$SYNCHDMLC~=0) [
  ];
 
 IF(IGNOREGAPS_$SYNCHDMLC=1 & IREJCT_GLOBAL>0)[
-  IF(ORIENT_$SYNCHDMLC=1)["leaves parallel to X"
+  IF(ORIENT_$SYNCHDMLC=1 | ORIENT_$SYNCHDMLC=3)["leaves parallel to X"
    WRITE(IOUTLIST,'(/'' *******Range rejection in $SYNCHDMLC will ignore all''/
                    '' air gaps if the particle is in the leaves and has''/
                    '' X < min. X of leaf openings (not including leaf ends)''/
@@ -3572,8 +3597,18 @@ IF(IR_$SYNCHDMLC=4) [ "in the air gap at the top"
   ]
 
 ELSE [
-  IF(ORIENT_$SYNCHDMLC=1) [ XYL1=Y(NP);XYL2=X(NP);UVL1=V(NP);UVL2=U(NP); ]
-  ELSE [ XYL1=X(NP);XYL2=Y(NP);UVL1=U(NP);UVL2=V(NP);];
+  IF(ORIENT_$SYNCHDMLC=0) [
+     XYL1=X(NP);XYL2=Y(NP);UVL1=U(NP);UVL2=V(NP);
+  ]
+  ELSEIF(ORIENT_$SYNCHDMLC=1) [
+     XYL1=Y(NP);XYL2=X(NP);UVL1=V(NP);UVL2=U(NP);
+  ]
+  ELSEIF(ORIENT_$SYNCHDMLC=2) [
+     XYL1=-X(NP);XYL2=Y(NP);UVL1=-U(NP);UVL2=V(NP);
+  ]
+  ELSEIF(ORIENT_$SYNCHDMLC=3) [
+     XYL1=-Y(NP);XYL2=X(NP);UVL1=-V(NP);UVL2=U(NP);
+  ]
 
   IF(IGNOREGAPS_$SYNCHDMLC=1 & XYL2 < MIN_PLANE_$SYNCHDMLC &
   XYL1 > SURPARA1_$SYNCHDMLC(1,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1)) &
diff --git a/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl b/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
index fd9b88ab2..9f2dede13 100644
--- a/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
+++ b/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
@@ -345,14 +345,30 @@ proc edit_SYNCHDMLC { id zmax } {
     # for range rejection in leaves
     frame $top.inp2 -bd 2
     frame $top.inp2.left
-    radiobutton $top.inp2.left.r1 -text "Leaves parallel to y"\
+    frame $top.inp2.left.ll
+    checkbutton $top.inp2.left.ll.help -bitmap @$GUI_DIR/help_icon.xbm \
+          -command "help_leaf_mfg_specs_synchdmlc [winfo parent $top.inp2.left]"
+    pack $top.inp2.left.ll.help -padx 5
+    frame $top.inp2.left.l
+    label $top.inp2.left.l.l1 -text {Leaves || to Y}
+    label $top.inp2.left.l.l2 -text {Leaves || to X}
+    pack $top.inp2.left.l.l1 $top.inp2.left.l.l2 -side top
+    frame $top.inp2.left.m
+    radiobutton $top.inp2.left.m.r1 -text "default orient."\
             -variable cmval($id,2,0) -value 0
-    radiobutton $top.inp2.left.r2 -text "Leaves parallel to x"\
+    radiobutton $top.inp2.left.m.r2 -text "default orient."\
             -variable cmval($id,2,0) -value 1
-    pack $top.inp2.left.r1 $top.inp2.left.r2 -side top
+    pack $top.inp2.left.m.r1 $top.inp2.left.m.r2 -side top
+    frame $top.inp2.left.r
+    radiobutton $top.inp2.left.r.r1 -text "mfg orient."\
+            -variable cmval($id,2,0) -value 2
+    radiobutton $top.inp2.left.r.r2 -text "mfg orient."\
+            -variable cmval($id,2,0) -value 3
+    pack $top.inp2.left.r.r1 $top.inp2.left.r.r2 -side top
+    pack $top.inp2.left.ll $top.inp2.left.l $top.inp2.left.m $top.inp2.left.r -side left
+
     frame $top.inp2.right
-    checkbutton $top.inp2.right.c1 -text "Ignore air gaps for range \
-                   rejection in leaves" -variable cmval($id,17,4)
+    checkbutton $top.inp2.right.c1 -text "Ignore air gaps for range rejection" -variable cmval($id,17,4)
     button $top.inp2.right.help -bitmap @$GUI_DIR/help_icon.xbm \
             -command "help_ignoregaps_synchdmlc [winfo parent $top.inp2.right]"
     pack $top.inp2.right.help $top.inp2.right.c1 -side right
@@ -735,7 +751,7 @@ proc define_synchdmlc_leaves { id } {
     frame $top.f -bd 10
     set w $top.f
 
-    if $cmval($id,2,0)==1 {
+    if {$cmval($id,2,0)==1 || $cmval($id,2,0)==3} {
         set porient X
         set xorient Y
     } else {
@@ -1938,7 +1954,7 @@ proc define_synchdmlc_openings { id } {
     frame $top.f -bd 10
     set w $top.f
 
-    if $cmval($id,2,0)==1 {
+    if {$cmval($id,2,0)==1 || $cmval($id,2,0)==3} {
 	set orientation X
     } else {
 	set orientation Y
@@ -2315,7 +2331,7 @@ proc draw_SYNCHDMLC { id } {
 
     # put the canvas up
     set ncan 3
-    set width 150.0
+    set width 180.0
     set canwidth [expr $width+150.0]
     set scrlheight [expr 2*$canwidth]
     set scrlwidth [expr 2*$canwidth]
@@ -2341,7 +2357,7 @@ proc draw_SYNCHDMLC { id } {
 
     # Put some text in the upper left corner, just to fill the gap.
     if {$cmval($id,2,2)==1 | $cmval($id,2,2)==2} {
-      .synchdmlc$id.show.frm.can create text 225 225 -text "xz\
+      .synchdmlc$id.show.frm.can create text 160 160 -text "xz\
             cross-section shows only those leaves that\
             are intersected by y=0, and yz cross-section shows only those\
             leaves intersected by x=0.  In the case where only a portion\
@@ -2353,9 +2369,9 @@ proc draw_SYNCHDMLC { id } {
 NOTE: This is a dynamic or step-and-shoot delivery, with leaf opening\
       coordinates defined in a file.  Leaf opening coordinates are shown for the\
       first field defined in this file."\
-            -font $helvfont -width 300
+            -font $helvfont -width 300 
     } else {
-    .synchdmlc$id.show.frm.can create text 225 225 -text "xz\
+    .synchdmlc$id.show.frm.can create text 160 160 -text "xz\
             cross-section shows only those leaves that\
 	    are intersected by y=0, and yz cross-section shows only those\
             leaves intersected by x=0.  In the case where only a portion\
@@ -2363,7 +2379,7 @@ NOTE: This is a dynamic or step-and-shoot delivery, with leaf opening\
             is shown.  The xy view is at a plane at Z=ZMIN\
             (straight leaf ends) or Z=ZMIN+ZTHICK/2 (cylindrical\
             leaf ends)."\
-	    -font $helvfont -width 300
+	    -font $helvfont -width 300 
     }
 
     set xscale [expr $width/double(abs($xrange(1)-$xrange(0)))]
@@ -2416,7 +2432,7 @@ NOTE: This is a dynamic or step-and-shoot delivery, with leaf opening\
     add_air $id .synchdmlc$id.show.frm.can.two $xrange(0) $zrange(0)\
 	    $xscale $zscale $l $m
 
-    if $cmval($id,2,0)==0 {
+    if {$cmval($id,2,0)==0 || $cmval($id,2,0)==2} {
 	add_SYNCHDMLC_sides $id $xscale $zscale $xrange(0) $zrange(0) $zrange(1)\
 		$l $m .synchdmlc$id.show.frm.can.two
     } else {
@@ -2458,7 +2474,7 @@ NOTE: This is a dynamic or step-and-shoot delivery, with leaf opening\
     add_air $id .synchdmlc$id.show.frm.can.three $yrange(0) $zrange(0)\
 	    $yscale $zscale $l $m
 
-    if $cmval($id,2,0)==0 {
+    if {$cmval($id,2,0)==0 || $cmval($id,2,0)==2} {
 	add_SYNCHDMLC_ends $id $yscale $zscale $yrange(0) $zrange(0) $zrange(1)\
 		$l $m .synchdmlc$id.show.frm.can.three
     } else {
@@ -2577,6 +2593,17 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
 	}
 	incr i
     }
+    #now flip leaf opening sequence if ORIENT=2 or 3
+    if {$cmval($id,2,0) == 2 || $cmval($id,2,0) == 3} {
+        for {set i 1} {$i <= $nleaf($id)/2} {incr i} {
+          set tmp_coord $neg($i)
+          set neg($i) $neg([expr $nleaf($id)-$i+1])
+          set neg([expr $nleaf($id)-$i+1]) $tmp_coord
+          set tmp_coord $pos($i)
+          set pos($i) $pos([expr $nleaf($id)-$i+1])
+          set pos([expr $nleaf($id)-$i+1]) $tmp_coord
+        }
+    }
 
     set color [lindex $colorlist $med(leaves)]
 
@@ -2635,7 +2662,7 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
     set wg(5) $cmval($id,31,2)
     set wtot(5) [expr $cmval($id,31,0)+$cmval($id,31,1)]
   }
-    if {$cmval($id,2,0)==1} {
+    if {$cmval($id,2,0)==1 || $cmval($id,2,0)==3} {
 	# leaves parallel to x
 	set lstart $cmval($id,9)
 	set rmin [expr (-$cmval($id,0)-$xmin)*$xscale+$l]
@@ -2645,9 +2672,17 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
             set color [lindex $colorlist $med(leaves)]
 
             set a [expr ($neg($i)-$xmin)*$xscale+$l]
-            set b [expr ($lstart-$ymin)*$yscale+$m]
+            if {$cmval($id,2,0)==3} {
+               set b [expr (-$lstart-$ymin)*$yscale+$m] 
+            } else {
+               set b [expr ($lstart-$ymin)*$yscale+$m]
+            }
             set c [expr ($pos($i)-$xmin)*$xscale+$l]
-            set d [expr ($lstart+$wtot($type($i))-$ymin)*$yscale+$m]
+            if {$cmval($id,2,0)==3} {
+               set d [expr (-($lstart+$wtot($type($i)))-$ymin)*$yscale+$m]
+            } else {
+               set d [expr ($lstart+$wtot($type($i))-$ymin)*$yscale+$m]
+            }
             $parent_w create rectangle $rmin $b $a $d -fill $color -outline black
             $parent_w create rectangle $rmax $b $c $d -fill $color -outline black
 
@@ -2657,10 +2692,19 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
                   #draw the air space
                   set color [lindex $colorlist $med(in)]
                   set a [expr ($neg($i)-$xmin)*$xscale+$l]
-                  set b [expr ($lstart+$wtot($type($i))-$ymin)*$yscale+$m]
+                  if {$cmval($id,2,0)==3} {
+                     set b [expr (-($lstart+$wtot($type($i)))-$ymin)*$yscale+$m]
+                  } else {
+                     set b [expr ($lstart+$wtot($type($i))-$ymin)*$yscale+$m]
+                  }
                   set c [expr ($pos($i)-$xmin)*$xscale+$l]
-                  set d [expr ($lstart+$wtot($type($i))+$cmval($id,10) \
+                  if {$cmval($id,2,0)==3} {
+                     set d [expr (-($lstart+$wtot($type($i))+$cmval($id,10) \
+                               -$wt($type([expr $i+1])))-$ymin)*$yscale+$m]
+                  } else {
+                     set d [expr ($lstart+$wtot($type($i))+$cmval($id,10) \
                                -$wt($type([expr $i+1]))-$ymin)*$yscale+$m]
+                  }
                   $parent_w create rectangle $rmin $b $a $d -fill $color -outline {}
                   $parent_w create rectangle $rmax $b $c $d -fill $color -outline {}
               }
@@ -2678,9 +2722,17 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
             # now make rectangles for the top view of the leaf
 
             set a [expr ($neg($i)-$ymin)*$yscale+$m]
-            set b [expr ($lstart-$xmin)*$xscale+$l]
+            if {$cmval($id,2,0)==2} {
+               set b [expr (-$lstart-$xmin)*$xscale+$l]
+            } else {
+               set b [expr ($lstart-$xmin)*$xscale+$l]
+            }
             set c [expr ($pos($i)-$ymin)*$yscale+$m]
-            set d [expr ($lstart+$wtot($type($i))-$xmin)*$xscale+$l]
+            if {$cmval($id,2,0)==2} {
+               set d [expr (-($lstart+$wtot($type($i)))-$xmin)*$xscale+$l]
+            } else {
+               set d [expr ($lstart+$wtot($type($i))-$xmin)*$xscale+$l]
+            }
             $parent_w create rectangle $b $rmax $d $c -fill $color -outline black
             $parent_w create rectangle $b $a $d $rmin -fill $color -outline black
             if {$i<$nleaf($id)} {
@@ -2689,10 +2741,19 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
                   #draw the air space
                   set color [lindex $colorlist $med(in)]
                   set a [expr ($neg($i)-$ymin)*$yscale+$m]
-                  set b [expr ($lstart-$xmin)*$xscale+$l]
+                  if {$cmval($id,2,0)==2} {
+                     set b [expr (-$lstart-$xmin)*$xscale+$l]
+                  } else {
+                     set b [expr ($lstart-$xmin)*$xscale+$l]
+                  }
                   set c [expr ($pos($i)-$ymin)*$yscale+$m]
-                  set d [expr ($lstart+$wtot($type($i))+$cmval($id,10) \
+                  if {$cmval($id,2,0)==2} {
+                     set d [expr (-($lstart+$wtot($type($i))+$cmval($id,10) \
+                               -$wt($type([expr $i+1])))-$xmin)*$xscale+$l]
+                  } else {
+                     set d [expr ($lstart+$wtot($type($i))+$cmval($id,10) \
                                -$wt($type([expr $i+1]))-$xmin)*$xscale+$l]
+                  }
                   $parent_w create rectangle $b $rmax $d $c -fill $color -outline {}
                   $parent_w create rectangle $b $a $d $rmin -fill $color -outline {}
               }
@@ -2792,6 +2853,17 @@ proc add_SYNCHDMLC_ends {id xscale zscale xmin zmin zmax l m parent_w} {
              }
              incr i
     }
+    #now flip leaf opening sequence if ORIENT=2 or 3
+    if {$cmval($id,2,0) == 2 || $cmval($id,2,0) == 3} {
+        for {set i 1} {$i <= $nleaf($id)/2} {incr i} {
+          set tmp_coord $neg($i)
+          set neg($i) $neg([expr $nleaf($id)-$i+1])
+          set neg([expr $nleaf($id)-$i+1]) $tmp_coord
+          set tmp_coord $pos($i)
+          set pos($i) $pos([expr $nleaf($id)-$i+1])
+          set pos([expr $nleaf($id)-$i+1]) $tmp_coord
+        }
+    }
 
     #set up an array of widths and Z positions for the leaf types
     #FULL leaf
@@ -3170,6 +3242,17 @@ proc add_SYNCHDMLC_sides {id yscale zscale ymin zmin zmax l m parent_w} {
         }
         incr i
     }
+    #now flip leaf opening sequence if ORIENT=2 or 3
+    if {$cmval($id,2,0) == 2 || $cmval($id,2,0) == 3} {
+        for {set i 1} {$i <= $nleaf($id)/2} {incr i} {
+          set tmp_coord $neg($i)
+          set neg($i) $neg([expr $nleaf($id)-$i+1])
+          set neg([expr $nleaf($id)-$i+1]) $tmp_coord 
+          set tmp_coord $pos($i)     
+          set pos($i) $pos([expr $nleaf($id)-$i+1])
+          set pos([expr $nleaf($id)-$i+1]) $tmp_coord
+        }
+    }
 
     # set up an array of leaf types
         set k 0; #leaf k
@@ -3542,6 +3625,11 @@ proc add_SYNCHDMLC_sides {id yscale zscale ymin zmin zmax l m parent_w} {
             set y($j) [max_nrc $rmin $y($j)]
             set y($j) [min_nrc $rmax $y($j)]
 
+            #flip cross-sections around Z if ORIENT = 2 or 3 (hope this works!)
+            if {$cmval($id,2,0)==2 || $cmval($id,2,0)==3} {
+                set y($j) [expr -1*$y($j)]
+            }
+            
             # set y and z scale and relative position
             set y($j) [expr ($y($j)-$ymin)*$yscale+$l]
             set z($j) [expr ($z($j)-$zmin)*$zscale+$m]
@@ -3563,6 +3651,9 @@ proc add_SYNCHDMLC_sides {id yscale zscale ymin zmin zmax l m parent_w} {
             set y($j) [expr ($ls+$hy($type($i),$j))*($z($j)-$zf)/($ztop-$zf)]
             set y($j) [max_nrc $rmin $y($j)]
             set y($j) [min_nrc $rmax $y($j)]
+            if {$cmval($id,2,0)==2 || $cmval($id,2,0)==3} {
+                set y($j) [expr -1*$y($j)]
+            }
 
             # set y and z scale and relative position
             set y($j) [expr ($y($j)-$ymin)*$yscale+$l]
@@ -3638,6 +3729,23 @@ to have exact transport throughout the entire multi-leaf collimator.}
     help_dialog $w.help "Help" $text info 0 OK
 }
 
+proc help_leaf_mfg_specs_synchdmlc { w } {
+
+    set text {
+Choose "default orientation" for leaf cross-sections and numbering as shown in\
+the BEAMnrc manual for leaves parallel to Y (ORIENT=0) or X (ORIENT=1).  Choose\
+"mfg orientation" to reflect leaves parallel to Y about the X-axis (ORIENT=2)\
+or to reflect leaves parallel to X about the Y-axis (ORIENT=3).  The\
+"mfg orientation" option effectively reflects leaf banks so that the MLC\
+coordinate system accords with that used in the manufacturer (Varian)\
+specifications for the 120MLC and HD120 multileaf collimators.\
+Note that because the leaf banks have been reflected, leaf opening sequences\
+are automaticaly "flipped," so that opening coordinates for leaf i are instead\
+applied to leaf N-i+1, where N is the total no. of leaves.  See the BEAMnrc\
+Manual for more details.}
+    help_dialog $w.help "Help" $text info 0 OK
+} 
+
 proc help_screwdist { w } {
 
 # help procedure put here because it is only for SYNCHDMLC

From 7c0e351918ea6adec97a867c66eea44cb0f56c6c Mon Sep 17 00:00:00 2001
From: Blake Walters <blakewalters@Blakes-MacBook-Air.local>
Date: Fri, 11 Mar 2022 13:44:01 -0800
Subject: [PATCH 09/14] Reverse definition of leaf opening sequence

Reverse leaf opening sequence definition for option
ORIENT_$SYNCHDMLC=2,3
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 32 ++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 417ecbed7..fff689d5c 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -1180,7 +1180,9 @@ EGS-IO/;
 DOUBLE PRECISION  NEG_$SYNCHDMLC,     "T>Leaf B tip
                   POS_$SYNCHDMLC,     "T>Leaf A Tip
                   TEMP1,
-                  TEMP2;
+                  TEMP2,
+                  tmp_coord;          "a variable to hold values while"
+                                      "reversing leaf opening definitions"
 
 INTEGER I,J,K,L,        "T>DO loop indices
         IRA,            "T>Absolute region number
@@ -2700,6 +2702,23 @@ IF(MODE_$SYNCHDMLC=1|MODE_$SYNCHDMLC=2)["dynamic or step-and-shoot leaf inputs"
        ]
        J=K;
      ]WHILE(J<=TOT_LEAF_$SYNCHDMLC);
+     IF(ORIENT_$SYNCHDMLC>=2)[
+       "reverse order of leaf opening coordinates"
+       DO K=1,TOT_LEAF_$SYNCHDMLC/2[
+         tmp_coord = LEAFNEG_$SYNCHDMLC(K+(I-1)*TOT_LEAF_$SYNCHDMLC);
+         LEAFNEG_$SYNCHDMLC(K+(I-1)*TOT_LEAF_$SYNCHDMLC) =
+             LEAFNEG_$SYNCHDMLC((TOT_LEAF_$SYNCHDMLC-K+1)+
+                      (I-1)*TOT_LEAF_$SYNCHDMLC);
+         LEAFNEG_$SYNCHDMLC((TOT_LEAF_$SYNCHDMLC-K+1)+
+                      (I-1)*TOT_LEAF_$SYNCHDMLC) = tmp_coord;
+         tmp_coord = LEAFPOS_$SYNCHDMLC(K+(I-1)*TOT_LEAF_$SYNCHDMLC);
+         LEAFPOS_$SYNCHDMLC(K+(I-1)*TOT_LEAF_$SYNCHDMLC) =
+             LEAFPOS_$SYNCHDMLC((TOT_LEAF_$SYNCHDMLC-K+1)+
+                      (I-1)*TOT_LEAF_$SYNCHDMLC);
+         LEAFPOS_$SYNCHDMLC((TOT_LEAF_$SYNCHDMLC-K+1)+
+                      (I-1)*TOT_LEAF_$SYNCHDMLC) = tmp_coord;
+       ]
+     ]   
   ]
   CLOSE(UNIT=mlc_unit);
 
@@ -2761,6 +2780,17 @@ LOOP[
   ]
   I=J;
 ]WHILE(I<=TOT_LEAF_$SYNCHDMLC);"End of Coordinate inputs for || direction "
+IF(ORIENT_$SYNCHDMLC>=2)[
+  "reverse leaf opening definitions"
+  DO I=1,TOT_LEAF_$SYNCHDMLC/2 [
+    tmp_coord = LEAFB_$SYNCHDMLC(I);
+    LEAFB_$SYNCHDMLC(I) = LEAFB_$SYNCHDMLC(TOT_LEAF_$SYNCHDMLC-I+1);
+    LEAFB_$SYNCHDMLC(TOT_LEAF_$SYNCHDMLC-I+1) = tmp_coord;
+    tmp_coord = LEAFA_$SYNCHDMLC(I);
+    LEAFA_$SYNCHDMLC(I) = LEAFA_$SYNCHDMLC(TOT_LEAF_$SYNCHDMLC-I+1);
+    LEAFA_$SYNCHDMLC(TOT_LEAF_$SYNCHDMLC-I+1) = tmp_coord;
+  ]
+] 
 
 IF(ENDTYPE_$SYNCHDMLC=1)[
 DO I=1, TOT_LEAF_$SYNCHDMLC [

From 5230f76ad13fb6a9a7c0553fe65df4bcffba14d7 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakewalters@Blakes-MacBook-Air.local>
Date: Fri, 18 Mar 2022 09:47:35 -0700
Subject: [PATCH 10/14] Fix synchdmlc QUARTER leaf restriction relaxation

Reorder cross section y boundaries when input restrictions are relaxed.
---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 332 +++++++++----
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      | 445 ++++++++++++------
 2 files changed, 531 insertions(+), 246 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index fff689d5c..1ff09fbf8 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -2489,11 +2489,16 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
        YREG_$SYNCHDMLC(I,1)=START_$SYNCHDMLC;
      ]
      ELSE[
+
        YLEAFEND=YREG_$SYNCHDMLC(I-1,7);
        "possible exceptions"
        IF(LEAFTYPE_$SYNCHDMLC(I-1)=2 & I_LEAF_ALT_DEF_$SYNCHDMLC(2,1,6)=1)[
           YLEAFEND=YREG_$SYNCHDMLC(I-1,6);
        ]
+       ELSEIF(LEAFTYPE_$SYNCHDMLC(I-1)=4 & I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,6)=1)[
+          YLEAFEND=YREG_$SYNCHDMLC(I-1,6);
+       ]
+
        IF(LEAFTYPE_$SYNCHDMLC(I)=1)[
           YREG_$SYNCHDMLC(I,1)=YLEAFEND+LEAFGAP_$SYNCHDMLC-
                           WTONGUE_$SYNCHDMLC(1);
@@ -2585,11 +2590,18 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
      ]
      ELSEIF(LEAFTYPE_$SYNCHDMLC(I)=4)["qtr target leaf"
        YREG_$SYNCHDMLC(I,2)=YREG_$SYNCHDMLC(I,1)+WTONGUE_$SYNCHDMLC(4);
-       YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(4);
        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,5)=1)[
+          YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(4);
           YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-WGROOVE_$SYNCHDMLC(4);
        ]
+       ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(4,1,6)=1)[
+          "this exception and the above are mutually exclusive"
+          YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(2);
+          YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,6)+
+                            ABS(WRAILBOT_$SYNCHDMLC(4)-WRAILTOP_$SYNCHDMLC(4));
+       ]
        ELSE[
+          YREG_$SYNCHDMLC(I,7)=YREG_$SYNCHDMLC(I,2)+LEAFWIDTH_$SYNCHDMLC(4);
           YREG_$SYNCHDMLC(I,6)=YREG_$SYNCHDMLC(I,7)-
                             ABS(WRAILBOT_$SYNCHDMLC(4)-WRAILTOP_$SYNCHDMLC(4));
        ]
@@ -2639,7 +2651,7 @@ IF(TOT_LEAF_$SYNCHDMLC>0) [
        SURPARA1_$SYNCHDMLC(I,J)=YREG_$SYNCHDMLC(I,J)/TEMP1;
      "OUTPUT I, J, YREG_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      "write(*,*)' i, leafis, j, yreg ',i,LEAFTYPE_$SYNCHDMLC(I),j,"
-            "YREG_$SYNCHDMLC(I,J);"
+     "       YREG_$SYNCHDMLC(I,J);"
      " OUTPUT I, J, SURPARA1_$SYNCHDMLC(I,J); (I5, I5, F12.6, ' ', $/);"
      ];"End of J Loop"
   ]; "End of K Loop"
@@ -4037,26 +4049,98 @@ IF(LEAFIS~=0) [
       ]
     ] ELSE [
       "Quarter Isocenter leaf"
-
-      "!= from Half Isocenter"
-      IF((NY=1|NY=2) & NZ<=4) [I1=1; I2=5;]
-      "!= from Half Isocenter"
-      ELSEIF((NY=1|NY=2) & (NZ=5)) [I1=5; I2=6;]
-      ELSEIF(NZ=6) [I1=6; I2=7;]
-      ELSEIF(NY<=4 & NZ=7) [I1=7; I2=8;]
-      ELSEIF(NY=1 & NZ>=8) [I1=8; I2=10;]
-      ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [I1=8; I2=9;]
-      ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [I1=9; I2=10;]
-      ELSEIF(NY=3 & NZ=1) [I1=1; I2=2;]
-      ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [I1=2; I2=6;]
-      ELSEIF((NY=4|NY=5) & NZ<=2) [I1=1; I2=3;]
-      ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [I1=3; I2=6;]
-      ELSEIF((NY=5|NY=6) & NZ>=7) [I1=7; I2=10;]
-      "!= from Half Isocenter"
-      ELSEIF(NY=6 & NZ<=3) [I1=1; I2=4;]
-      "!= from Half Isocenter"
-      ELSEIF(NY=6 & (NZ=4|NZ=5)) [I1=4; I2=6;]
-
+      IF(NY=1) [
+        IF(NZ<=3) [I1=1; I2=4;]
+        ELSEIF(NZ<=5) [I1=4; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSE [I1=8; I2=10;]
+      ]
+      ELSEIF(NY=2) [
+        IF(NZ<=3) [I1=1; I2=4;]
+        ELSEIF(NZ<=5) [I1=4; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSE[
+          IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[
+            I1=8; I2=10;
+          ]
+          ELSE[
+            IF(NZ=8) [I1=8; I2=9;]
+            ELSE [I1=9; I2=10;]
+          ]
+        ]
+      ]
+      ELSEIF(NY=3) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+          IF(NZ=1) [I1=1; I2=2;]
+          ELSEIF(NZ=2)[I1=2; I2=6;]
+          ELSEIF(NZ=3) [I1=3; I2=6;]
+          ELSEIF(NZ<=5) [I1=4; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSEIF(NZ=8) [I1=8; I2=9;]
+          ELSE [I1=9; I2=10;]
+        ]
+        ELSE[ "Zg > Zt"
+          IF(NZ=1) [I1=1; I2=2;]
+          ELSEIF(NZ=2)[I1=2; I2=6;]
+          ELSEIF(NZ<=4) [I1=3; I2=6;]
+          ELSEIF(NZ=5) [I1=5; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSEIF(NZ=8) [I1=8; I2=9;]
+          ELSE [I1=9; I2=10;]
+        ]
+      ]
+      ELSEIF(NY=4) [
+        IF(NZ<=2) [I1=1; I2=3;]
+        ELSEIF(NZ=3) [I1=3; I2=6;]
+        ELSEIF(NZ=4) [I1=4; I2=6;]
+        ELSEIF(NZ=5) [I1=5; I2=6;]
+        ELSEIF(NZ=6) [I1=6; I2=7;]
+        ELSEIF(NZ=7) [I1=7; I2=8;]
+        ELSEIF(NZ=8) [I1=8; I2=9;]
+        ELSE [I1=9; I2=10;]
+      ]
+      ELSEIF(NY=5) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+          IF(NZ<=2) [I1=1; I2=3;]
+          ELSEIF(NZ<=4) [I1=3; I2=6;]
+          ELSEIF(NZ=5) [I1=5; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSEIF(NZ=8) [I1=7; I2=10;]
+          ELSE [I1=9; I2=10;]
+        ]
+        ELSE[
+          IF(NZ<=2) [I1=1; I2=3;]
+          ELSEIF(NZ=3) [I1=3; I2=6;]
+          ELSEIF(NZ<=5) [I1=4; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSEIF(NZ=8) [I1=7; I2=10;]
+          ELSE [I1=9; I2=10;]
+        ]
+      ]
+      ELSEIF(NY=6) [
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+          IF(NZ<=4) [I1=1; I2=5;]
+          ELSEIF(NZ=5) [I1=5; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSEIF(NZ=8) [I1=7; I2=10;]
+          ELSE [I1=9; I2=10;]
+        ]
+        ELSE[
+          IF(NZ<=3) [I1=1; I2=4;]
+          ELSEIF(NZ<=5) [I1=4; I2=6;]
+          ELSEIF(NZ=6) [I1=6; I2=7;]
+          ELSEIF(NZ=7) [I1=7; I2=8;]
+          ELSEIF(NZ=8) [I1=7; I2=10;]
+          ELSE [I1=9; I2=10;]
+        ]
+      ]
     ];
 
     DIST=MIN(ABS(ZREG_$SYNCHDMLC(LEAFIS,I1)-Z(NP)),
@@ -4284,7 +4368,7 @@ IF(LEAFIS~=0) [
         IF(NY<=2)[
            IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
            ELSE [
-              IF(Z(NP)>ZREG_$SYNCHDMLC(J,7))[
+              IF(Z(NP)>ZREG_$SYNCHDMLC(LEAFIS-1,7))[
                 TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);
               ]
               ELSE[
@@ -4300,8 +4384,8 @@ IF(LEAFIS~=0) [
         ELSE[
            TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
            IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
-           ELSE [
-             IF(Z(NP)<ZREG_$SYNCHDMLC(I,6))[
+           ELSE [ "ignores that LEAFIS+1 might be FULL"
+             IF(Z(NP)<ZREG_$SYNCHDMLC(LEAFIS+1,6))[
                 TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);
              ]
              ELSE[
@@ -4431,81 +4515,141 @@ IF(LEAFIS~=0) [
      ]
     ]
     ELSE ["Quarter Isocenter leaf"
-      "EH - because the quarter and half leaves are slightly different"
-      "     you will need a modification for NZ=4 and NY=6"
       IF(NZ=1) [
-        IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
-        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);];
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
-        ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);];
-       ]
-      ELSEIF(((NZ=2|NZ=3) & (NY=1|NY=2)) |
-          ((NY<3) & (NZ=4) & LEAFTYPE_$SYNCHDMLC(LEAFIS)=5)) [
-        IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
-        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);];
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
-       ]
-      ELSEIF(NZ=2 & NY=3) [
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,4);
-       ]
-      ELSEIF(NZ=2 & NY>=4) [
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,4);
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
-        ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);];
-       ]
-      ELSEIF(NZ=3 & (NY=3|NY=4|NY=5)) [
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
-       ]
-      ELSEIF((NZ=3 & NY=6)
-              | (NZ=4 & NY=6 & (LEAFTYPE_$SYNCHDMLC(LEAFIS)=3))) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+        IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
+        "possibly use LHS=6?"
         IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
-        ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);];
-       ]
-      ELSEIF (NZ=4 & NY>=3
-              & (LEAFTYPE_$SYNCHDMLC(LEAFIS)=5)) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
-       ]
-     " ELSEIF (NZ=4 & NY<3"
-      "        & (LEAFTYPE_$SYNCHDMLC(LEAFIS)=5)) ["
-
-      "  IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]"
-      "  ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);];"
-      "  TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);"
-     " ]"
-      ELSEIF(NZ=4 & NY<=5 & (LEAFTYPE_$SYNCHDMLC(LEAFIS)=3)) [
-
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
-       ]
-      ELSEIF(NZ=5|NZ=6|NZ=7) [
+        ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+     ]
+     ELSEIF(NZ=2)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [ TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+        ]
+        IF(NY=3)[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,4);
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+           ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+        ]
+     ]
+     ELSEIF(NZ=3)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [
+              IF(Z(NP)>ZREG_$SYNCHDMLC(LEAFIS-1,7))[
+                TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);
+              ]
+              ELSE[
+                TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);
+              ]
+           ]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+        ]
+        IF(NY<=5)[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+           ELSE [ "ignores that LEAFIS+1 might be FULL"
+             IF(Z(NP)<ZREG_$SYNCHDMLC(LEAFIS+1,6))[
+                TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);
+             ]
+             ELSE[
+                TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,2);
+             ]
+           ]
+        ]
+     ]
+     ELSEIF(NZ=4)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+           IF(NY<=5)[
+              TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
+              TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+           ]
+           ELSE[
+              TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,6);
+              IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [
+                     TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);]
+              ELSE [TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS+1,1);]
+           ]
+        ]
+        ELSE[ "Zt > Zg"
+         IF(NY<=2)[
+           IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [
+              IF(Z(NP)>ZREG_$SYNCHDMLC(LEAFIS-1,7))[
+                TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);
+              ]
+              ELSE[
+                TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,7);
+              ]
+           ]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+         ]
+         ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+         ]
+        ]
+     ]
+     ELSEIF(NZ=5)[
         TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
         TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
-       ]
-      ELSEIF(NZ=8 & NY<=4) [
-        IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
-        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);];
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
-       ]
-      ELSEIF(NZ=8 & NY>=5) [
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+     ]
+     ELSEIF(NZ=6)[
+        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
         TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
-       ]
-      ELSEIF(NZ=9 & NY=1) [
-        IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
-        ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
-        TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
-       ]
-      ELSEIF(NZ=9 & NY>=2) [
-        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+     ]
+     ELSEIF(NZ=7)[
+        TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);
         TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
-       ]
-     ];
+     ]
+     ELSEIF(NZ=8)[
+        IF(NY<=4)[
+           IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+           ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+        ]
+        ELSE[
+           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,5);
+           TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+        ]
+     ]
+     ELSEIF(NZ=9)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1) [
+           IF(NY<=2)[
+             IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             "here we are ignoring the possibility that Z could be"
+             ">Ztip(LEAFIS-1) but should be okay"
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,3);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+           ]
+        ]
+        ELSE[
+           IF(NY=1)[
+             IF(LEAFIS=1) [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1);]
+             ELSE [TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS-1,5);]
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+           ]
+           ELSE[
+             TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,2);
+             TEMP2=SURPARA1_$SYNCHDMLC(LEAFIS,7);
+           ]
+        ]
+     ]
+    ];
     TEMP1=ABS((TEMP1*(Z(NP)-ZFOCUS_$SYNCHDMLC(1))-XYL1)/
           SQRT(1+TEMP1**2));
     TEMP2=ABS((TEMP2*(Z(NP)-ZFOCUS_$SYNCHDMLC(1))-XYL1)/
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index 932ce8a27..67e67aac9 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -713,116 +713,10 @@ ELSE ["inside leaf bank"
 ;}
 ;
 
-" $SYNCHDMLC_MINDISTANCE;            "
-"===============================   "
-" The following macro will give the nearest distance the particle"
-" can travel along its given direction before it strikes the boundary"
-" in the x, y or z direction."
-"{P1}: The change value for ir region #"
-
-REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
-  "Note: some of these will underestimate dZ when input dimension"
-  "restrictions are overridden--this should not result in transport"
-  "errors, but will potentially slow transport"
-  IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
-                                   "Target leaf"
-
-    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
-    ELSEIF(NY=1 & NZ=5) [ZLHS=5; ZRHS=6;]
-    ELSEIF(NY=1 & NZ>=6) [ZLHS=6; ZRHS=10;]
-    ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-    ELSEIF((NY=2|NY=3) & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [ZLHS=2; ZRHS=3;]
-    ELSEIF(NY>=3 & NZ=3) [ZLHS=3; ZRHS=4;]
-    ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [ZLHS=5; ZRHS=8;]
-    ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [ZLHS=5; ZRHS=9;]
-    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [ZLHS=5; ZRHS=7;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=2) [
-      "dZ potentially overestimated--deal with it!"
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1)[
-         IF(NZ=1)[ZLHS=1; ZRHS=2;]
-         ELSE[ZLHS=2; ZRHS=10;]
-      ]
-      ELSE[ZLHS=1; ZRHS=3;]
-    ]
-
-  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["Full leaf"
-
-    IF((NY=1|NY=2) & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF(NY=1 & (NZ=2|NZ=3)) [ZLHS=2; ZRHS=4;]
-    ELSEIF(NY=1 & NZ>=4) [ZLHS=4; ZRHS=10;]
-    ELSEIF(NY=2 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
-    ELSEIF(NY>=2 & NZ=6) [ZLHS=6; ZRHS=7;]
-    ELSEIF(NY=2 & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=3|NY=4|NY=5) & (NZ=1|NZ=2)) [ZLHS=1; ZRHS=3;]
-    ELSEIF((NY=3|NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
-    ELSEIF(NY=3 & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=7) [ZLHS=7; ZRHS=8;]
-    ELSEIF(NY=4 & NZ=8) [ZLHS=8; ZRHS=9;]
-    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
-    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
-
-  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
-    "Half Isocenter leaf"
-
-    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
-    ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
-    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
-    "potential overestimate of dZ below--correct it"
-    ELSEIF(NY=1 & NZ>=8) [
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
-        IF(NZ=9)[ZLHS=9; ZRHS=10;]
-        ELSE[ZLHS=1; ZRHS=9;]
-      ]
-      ELSE[ZLHS=8; ZRHS=10;]
-    ]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
-    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
-    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
-    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
-
-  ] ELSE [
-    "Quarter Isocenter leaf"
-
-    "!= from Half Isocenter"
-    IF((NY=1|NY=2) & NZ<=4) [ZLHS=1; ZRHS=5;]
-    "!= from Half Isocenter"
-    ELSEIF((NY=1|NY=2) & (NZ=5)) [ZLHS=5; ZRHS=6;]
-    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
-    ELSEIF(NY=1 & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
-    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
-    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    "!= from Half Isocenter"
-    ELSEIF(NY=6 & NZ<=3) [ZLHS=1; ZRHS=4;]
-    "!= from Half Isocenter"
-    ELSEIF(NY=6 & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
-  ]
-  IF(W(NP)~=0) [
-     ZP = (ZREG_$SYNCHDMLC(LEAFIS,ZRHS)-ZFL)/W(NP);
-     ZN = (ZREG_$SYNCHDMLC(LEAFIS,ZLHS)-ZFL)/W(NP);
-     IF( (ZP>=0.0) & (ZN>=0.0) ) [ ZDIST =MIN(ZP, ZN); ]
-     ELSE [ ZDIST = MAX(ZP, ZN); ]
-     "write(*,*)' zdist,leafis ',zdist,leafis;"
-   ]
-  ELSE [ ZDIST = 1.0E20; ];
-  IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
+"Macro to find I, LHS, J, RHS, indices of boundaries in Y-direction"
+"Put in a separate macro to prevent the parent macro from getting too long"
+REPLACE {$SYNCHDMLC_FIND_Y_BOUNDS;} WITH{;
+IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
      "Target leaf"
      IF(NZ=1) [
        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1) [
@@ -1190,56 +1084,303 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
            ]
         ]
      ]
-   ] ELSE [
+   ] 
+   ELSE[
      "Isocenter Quarter"
      IF(NZ=1) [
         IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
         ELSE [LHS=7; J=LEAFIS-1;]
+        "possibly use LHS=6?"
         IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
         ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF((NZ=2|NZ=3|NZ=4) & (NY=1|NY=2)) [
-        "!= from Half Isocenter - Block 2"
-        IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-        ELSE [LHS=7; J=LEAFIS-1;]
-        RHS=3; I=LEAFIS;
-     ] ELSEIF(NZ=2 & NY=3) [
-        LHS=3; J=LEAFIS;
-        RHS=4; I=LEAFIS;
-     ] ELSEIF(NZ=2 & NY>=4) [
-        LHS=4; J=LEAFIS;
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-        ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF(NZ=3 & (NY=3|NY=4|NY=5)) [
-        LHS=3; J=LEAFIS;
-        RHS=6; I=LEAFIS;
-     ] ELSEIF(NZ=3 & NY=6) [
-        "!= from Half Isocenter - Block 5"
-        LHS=6; J=LEAFIS;
-        IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
-        ELSE [RHS=1; I=LEAFIS+1;]
-     ] ELSEIF(NZ=4 & (NY>=3)) [
-        "!= from Half Isocenter - Block 7"
-        LHS=3; J=LEAFIS;
-        RHS=7; I=LEAFIS;
-     ] ELSEIF(NZ=5|NZ=6|NZ=7) [
+     ]
+     ELSEIF(NZ=2)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+           ELSE [LHS=7; J=LEAFIS-1;]
+           RHS=3; I=LEAFIS;
+        ]
+        IF(NY=3)[
+           LHS=3; J=LEAFIS;
+           RHS=4; I=LEAFIS;
+        ]
+        ELSE[
+           LHS=4; J=LEAFIS;
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+           ELSE [RHS=1; I=LEAFIS+1;]
+        ]
+     ]
+     ELSEIF(NZ=3)[
+        IF(NY<=2)[
+           IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+           ELSE [
+              J=LEAFIS-1;
+              IF(ZFL>ZREG_$SYNCHDMLC(J,7))[
+                LHS = 5;
+              ]
+              ELSE[
+                LHS = 7;
+              ]
+           ]
+           RHS=3; I=LEAFIS;
+        ]
+        IF(NY<=5)[
+           LHS=3; J=LEAFIS;
+           RHS=6; I=LEAFIS;
+        ]
+        ELSE[
+           LHS=6; J=LEAFIS;
+           IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+           ELSE [
+             I=LEAFIS+1;
+             IF(ZFL<ZREG_$SYNCHDMLC(I,6))[
+                RHS=1;
+             ]
+             ELSE[
+                RHS=2;
+             ]
+           ]
+        ]
+     ]
+     ELSEIF(NZ=4)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[ 
+           IF(NY<=5)[
+              LHS=1; J=LEAFIS;
+              RHS=6; I=LEAFIS;
+           ]
+           ELSE[
+              LHS=6; J=LEAFIS;
+              IF(LEAFIS=TOT_LEAF_$SYNCHDMLC) [RHS=7; I=LEAFIS;]
+              ELSE [RHS=1; I=LEAFIS+1;]
+           ]
+        ]
+        ELSE[
+           IF(NY<=2)[
+              IF(LEAFIS=1) [ LHS=1; J=LEAFIS;]
+              ELSE [
+                 J=LEAFIS-1;
+                 IF(ZFL>ZREG_$SYNCHDMLC(J,7))[
+                   LHS = 5;
+                 ]
+                 ELSE[ 
+                   LHS = 7;
+                 ]
+              ]
+              RHS=3; I=LEAFIS;
+           ]
+           ELSE[
+              LHS=3; J=LEAFIS;
+              RHS=7; I=LEAFIS;
+           ]
+        ] 
+     ]
+     ELSEIF(NZ<=7)[
         LHS=1; J=LEAFIS;
         RHS=7; I=LEAFIS;
-     ] ELSEIF(NZ=8 & NY<=4) [
-        IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-        ELSE [LHS=5; J=LEAFIS-1;]
-        RHS=5; I=LEAFIS;
-     ] ELSEIF(NZ=8 & NY>=5) [
-        LHS=5; J=LEAFIS;
-        RHS=7; I=LEAFIS;
-     ] ELSEIF(NZ=9 & NY=1) [
-       IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
-       ELSE [LHS=5; J=LEAFIS-1;]
-       RHS=2; I=LEAFIS;
-     ] ELSEIF(NZ=9 & NY>=2) [
-       LHS=2; J=LEAFIS;
-       RHS=7; I=LEAFIS;
      ]
-   ];
+     ELSEIF(NZ=8)[
+        IF(NY<=4)[
+           IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+           ELSE [LHS=5; J=LEAFIS-1;]
+           RHS=5; I=LEAFIS;
+        ]
+        ELSE[
+           LHS=5; J=LEAFIS;
+           RHS=7; I=LEAFIS;
+        ]
+     ]
+     ELSEIF(NZ=9)[
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1) [
+           IF(NY<=2)[
+              IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+              ELSE [LHS=5; J=LEAFIS-1;]
+              RHS=3; I=LEAFIS;
+           ]
+           ELSE[
+              LHS=3; J=LEAFIS;
+              RHS=7; I=LEAFIS;
+           ]    
+        ]
+        ELSE[
+           IF(NY=1)[
+              IF(LEAFIS=1) [LHS=1; J=LEAFIS;]
+              ELSE [LHS=5; J=LEAFIS-1;]
+              RHS=2; I=LEAFIS;
+           ]
+           ELSE[
+              LHS=2; J=LEAFIS;
+              RHS=7; I=LEAFIS;
+           ]
+        ]
+     ]
+];
+};
+
+" $SYNCHDMLC_MINDISTANCE;            "
+"===============================   "
+" The following macro will give the nearest distance the particle"
+" can travel along its given direction before it strikes the boundary"
+" in the x, y or z direction."
+"{P1}: The change value for ir region #"
+
+REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
+  "Note: some of these will underestimate dZ when input dimension"
+  "restrictions are overridden--this should not result in transport"
+  "errors, but will potentially slow transport"
+  IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
+                                   "Target leaf"
+
+    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
+    ELSEIF(NY=1 & NZ=5) [ZLHS=5; ZRHS=6;]
+    ELSEIF(NY=1 & NZ>=6) [ZLHS=6; ZRHS=10;]
+    ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+    ELSEIF((NY=2|NY=3) & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [ZLHS=2; ZRHS=3;]
+    ELSEIF(NY>=3 & NZ=3) [ZLHS=3; ZRHS=4;]
+    ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [ZLHS=5; ZRHS=8;]
+    ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [ZLHS=5; ZRHS=9;]
+    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [ZLHS=5; ZRHS=7;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=2) [
+      "dZ potentially overestimated--deal with it!"
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1)[
+         IF(NZ=1)[ZLHS=1; ZRHS=2;]
+         ELSE[ZLHS=2; ZRHS=10;]
+      ]
+      ELSE[ZLHS=1; ZRHS=3;]
+    ]
+
+  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["Full leaf"
+
+    IF((NY=1|NY=2) & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF(NY=1 & (NZ=2|NZ=3)) [ZLHS=2; ZRHS=4;]
+    ELSEIF(NY=1 & NZ>=4) [ZLHS=4; ZRHS=10;]
+    ELSEIF(NY=2 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
+    ELSEIF(NY>=2 & NZ=6) [ZLHS=6; ZRHS=7;]
+    ELSEIF(NY=2 & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=3|NY=4|NY=5) & (NZ=1|NZ=2)) [ZLHS=1; ZRHS=3;]
+    ELSEIF((NY=3|NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
+    ELSEIF(NY=3 & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=7) [ZLHS=7; ZRHS=8;]
+    ELSEIF(NY=4 & NZ=8) [ZLHS=8; ZRHS=9;]
+    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
+    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
+
+  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
+    "Half Isocenter leaf"
+
+    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
+    ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
+    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
+    "potential overestimate of dZ below--correct it"
+    ELSEIF(NY=1 & NZ>=8) [
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
+        IF(NZ=9)[ZLHS=9; ZRHS=10;]
+        ELSE[ZLHS=1; ZRHS=9;]
+      ]
+      ELSE[ZLHS=8; ZRHS=10;]
+    ]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
+    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
+    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
+    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
+
+  ] ELSE [
+    "Quarter Isocenter leaf"
+    IF(NY=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+        IF(NZ<=3)[ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSE[ZLHS=8; ZRHS=10;]
+      ]
+      ELSE[
+        IF(NZ<=4)[ZLHS=1; ZRHS=5;]
+        ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSE[ZLHS=8; ZRHS=10;]
+      ]
+    ]
+    ELSEIF(NY=2)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+        IF(NZ<=3)[ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[ZLHS=8; ZRHS=10;]
+        ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+        ELSE[ZLHS=9; ZRHS=10;]
+      ]
+      ELSE[
+        IF(NZ<=4)[ZLHS=1; ZRHS=5;]
+        ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[ZLHS=8; ZRHS=10;]
+        ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+        ELSE[ZLHS=9; ZRHS=10;]
+      ]
+    ]
+    ELSEIF(NY=3)[
+      IF(NZ=1)[ZLHS=1; ZRHS=2;]
+      ELSEIF(NZ<=5)[ZLHS=2; ZRHS=6;]
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]  
+      ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+      ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+      ELSE[ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=4)[
+      IF(NZ<=2)[ZLHS=1; ZRHS=3;]
+      ELSEIF(NZ<=5)[ZLHS=3; ZRHS=6;]
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+      ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+      ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+      ELSE[ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=5)[
+      IF(NZ<=2)[ZLHS=1; ZRHS=3;]
+      ELSEIF(NZ<=5)[ZLHS=3; ZRHS=6;]
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+      ELSE[ZLHS=7; ZRHS=10;]
+    ]
+    ELSEIF(NY=6)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+         IF(NZ<=4)[ZLHS=1; ZRHS=5;]
+         ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
+         ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+         ELSE[ZLHS=7; ZRHS=10;]
+      ]
+      ELSE[
+         IF(NZ<=3)[ZLHS=1; ZRHS=4;]
+         ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
+         ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+         ELSE[ZLHS=7; ZRHS=10;]
+      ]
+    ] 
+  ]
+  IF(W(NP)~=0) [
+     ZP = (ZREG_$SYNCHDMLC(LEAFIS,ZRHS)-ZFL)/W(NP);
+     ZN = (ZREG_$SYNCHDMLC(LEAFIS,ZLHS)-ZFL)/W(NP);
+     IF( (ZP>=0.0) & (ZN>=0.0) ) [ ZDIST =MIN(ZP, ZN); ]
+     ELSE [ ZDIST = MAX(ZP, ZN); ]
+     "write(*,*)' zdist,leafis ',zdist,leafis;"
+   ]
+  ELSE [ ZDIST = 1.0E20; ];
+
+  $SYNCHDMLC_FIND_Y_BOUNDS;
+
   IF((UVL(1)-SURPARA1_$SYNCHDMLC(I,RHS)*W(NP))~ = 0 ) [
      YP = (SURPARA1_$SYNCHDMLC(I,RHS)*(ZFL-ZFOCUS_$SYNCHDMLC(1))-XYFL(1));
      YP = YP/(UVL(1) - SURPARA1_$SYNCHDMLC(I,RHS)*W(NP));
@@ -1252,7 +1393,7 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
   ELSE [ YN = 1.0E20; ];
   IF((YP>=0.0) & (YN>=0.0) ) [ YDIST =MIN(YP, YN); ]
   ELSE [ YDIST = MAX(YP,YN);];
-  "write(*,*)' ydist ',ydist;"
+  "write(*,*)' i,j, rhs, lhs, ydist ',i,j,rhs,lhs,ydist;"
  IF(ENDTYPE_$SYNCHDMLC = 1) ["focused leaf end"
       HOLE=HOLEPOS_$SYNCHDMLC(LEAFIS);
       TEMP3=LEAFB_$SYNCHDMLC(LEAFIS)-HOLE;

From b64d4f2f053220371ec8fe1f84c324ddede55792 Mon Sep 17 00:00:00 2001
From: Frederic Tessier <ftessier@gmail.com>
Date: Thu, 30 Jun 2022 17:25:52 -0400
Subject: [PATCH 11/14] Add new FIND_Z_BOUNDS macro in synchdmlc

---
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      | 300 +++++++++---------
 1 file changed, 154 insertions(+), 146 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index 67e67aac9..fd4ad6c09 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -713,6 +713,158 @@ ELSE ["inside leaf bank"
 ;}
 ;
 
+"Macro to find ZLHS and ZRHS, upper and lower indices of boundaries in"
+"Z-direction"
+"Put in a separate macro to prevent the parent macro from getting too long"
+REPLACE {$SYNCHDMLC_FIND_Z_BOUNDS;} WITH{;
+"Note: some of these will underestimate dZ when input dimension"
+"restrictions are overridden--this should not result in transport"
+"errors, but will potentially slow transport"
+IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
+                                   "Target leaf"
+
+    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
+    ELSEIF(NY=1 & NZ=5) [ZLHS=5; ZRHS=6;]
+    ELSEIF(NY=1 & NZ>=6) [ZLHS=6; ZRHS=10;]
+    ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
+    ELSEIF((NY=2|NY=3) & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [ZLHS=2; ZRHS=3;]
+    ELSEIF(NY>=3 & NZ=3) [ZLHS=3; ZRHS=4;]
+    ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [ZLHS=5; ZRHS=8;]
+    ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [ZLHS=5; ZRHS=9;]
+    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [ZLHS=5; ZRHS=7;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=2) [
+      "dZ potentially overestimated--deal with it!"
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1)[
+         IF(NZ=1)[ZLHS=1; ZRHS=2;]
+         ELSE[ZLHS=2; ZRHS=10;]
+      ]
+      ELSE[ZLHS=1; ZRHS=3;]
+    ]
+
+  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["Full leaf"
+
+    IF((NY=1|NY=2) & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF(NY=1 & (NZ=2|NZ=3)) [ZLHS=2; ZRHS=4;]
+    ELSEIF(NY=1 & NZ>=4) [ZLHS=4; ZRHS=10;]
+    ELSEIF(NY=2 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
+    ELSEIF(NY>=2 & NZ=6) [ZLHS=6; ZRHS=7;]
+    ELSEIF(NY=2 & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=3|NY=4|NY=5) & (NZ=1|NZ=2)) [ZLHS=1; ZRHS=3;]
+    ELSEIF((NY=3|NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
+    ELSEIF(NY=3 & NZ>=8) [ZLHS=8; ZRHS=10;]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=7) [ZLHS=7; ZRHS=8;]
+    ELSEIF(NY=4 & NZ=8) [ZLHS=8; ZRHS=9;]
+    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
+    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
+
+  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
+    "Half Isocenter leaf"
+
+    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
+    ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
+    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
+    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
+    "potential overestimate of dZ below--correct it"
+    ELSEIF(NY=1 & NZ>=8) [
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
+        IF(NZ=9)[ZLHS=9; ZRHS=10;]
+        ELSE[ZLHS=1; ZRHS=9;]
+      ]
+      ELSE[ZLHS=8; ZRHS=10;]
+    ]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
+    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
+    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
+    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
+    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
+    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
+    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
+    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
+    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
+
+  ] ELSE [
+    "Quarter Isocenter leaf"
+    IF(NY=1)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+        IF(NZ<=3)[ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSE[ZLHS=8; ZRHS=10;]
+      ]
+      ELSE[
+        IF(NZ<=4)[ZLHS=1; ZRHS=5;]
+        ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSE[ZLHS=8; ZRHS=10;]
+      ]
+    ]
+    ELSEIF(NY=2)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+        IF(NZ<=3)[ZLHS=1; ZRHS=4;]
+        ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[ZLHS=8; ZRHS=10;]
+        ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+        ELSE[ZLHS=9; ZRHS=10;]
+      ]
+      ELSE[
+        IF(NZ<=4)[ZLHS=1; ZRHS=5;]
+        ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
+        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+        ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[ZLHS=8; ZRHS=10;]
+        ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+        ELSE[ZLHS=9; ZRHS=10;]
+      ]
+    ]
+    ELSEIF(NY=3)[
+      IF(NZ=1)[ZLHS=1; ZRHS=2;]
+      ELSEIF(NZ<=5)[ZLHS=2; ZRHS=6;]
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]  
+      ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+      ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+      ELSE[ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=4)[
+      IF(NZ<=2)[ZLHS=1; ZRHS=3;]
+      ELSEIF(NZ<=5)[ZLHS=3; ZRHS=6;]
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+      ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
+      ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
+      ELSE[ZLHS=9; ZRHS=10;]
+    ]
+    ELSEIF(NY=5)[
+      IF(NZ<=2)[ZLHS=1; ZRHS=3;]
+      ELSEIF(NZ<=5)[ZLHS=3; ZRHS=6;]
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+      ELSE[ZLHS=7; ZRHS=10;]
+    ]
+    ELSEIF(NY=6)[
+      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
+         IF(NZ<=4)[ZLHS=1; ZRHS=5;]
+         ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
+         ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+         ELSE[ZLHS=7; ZRHS=10;]
+      ]
+      ELSE[
+         IF(NZ<=3)[ZLHS=1; ZRHS=4;]
+         ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
+         ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
+         ELSE[ZLHS=7; ZRHS=10;]
+      ]
+    ] 
+]
+};
+
 "Macro to find I, LHS, J, RHS, indices of boundaries in Y-direction"
 "Put in a separate macro to prevent the parent macro from getting too long"
 REPLACE {$SYNCHDMLC_FIND_Y_BOUNDS;} WITH{;
@@ -1223,159 +1375,15 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
 " in the x, y or z direction."
 "{P1}: The change value for ir region #"
 
-REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {; "boundaries in Z direction"
-  "Note: some of these will underestimate dZ when input dimension"
-  "restrictions are overridden--this should not result in transport"
-  "errors, but will potentially slow transport"
-  IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
-                                   "Target leaf"
-
-    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
-    ELSEIF(NY=1 & NZ=5) [ZLHS=5; ZRHS=6;]
-    ELSEIF(NY=1 & NZ>=6) [ZLHS=6; ZRHS=10;]
-    ELSEIF(NZ=4) [ZLHS=4; ZRHS=5;]
-    ELSEIF((NY=2|NY=3) & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=3|NY=4|NY=5) & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF((NY=3|NY=4|NY=5) & NZ=2) [ZLHS=2; ZRHS=3;]
-    ELSEIF(NY>=3 & NZ=3) [ZLHS=3; ZRHS=4;]
-    ELSEIF((NY=2|NY=3) & (NZ=5|NZ=6|NZ=7)) [ZLHS=5; ZRHS=8;]
-    ELSEIF(NY=4 & (NZ=5|NZ=6|NZ=7|NZ=8)) [ZLHS=5; ZRHS=9;]
-    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF((NY=5|NY=6) & (NZ=5|NZ=6)) [ZLHS=5; ZRHS=7;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=2) [
-      "dZ potentially overestimated--deal with it!"
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1)[
-         IF(NZ=1)[ZLHS=1; ZRHS=2;]
-         ELSE[ZLHS=2; ZRHS=10;]
-      ]
-      ELSE[ZLHS=1; ZRHS=3;]
-    ]
-
-  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=1) ["Full leaf"
-
-    IF((NY=1|NY=2) & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF(NY=1 & (NZ=2|NZ=3)) [ZLHS=2; ZRHS=4;]
-    ELSEIF(NY=1 & NZ>=4) [ZLHS=4; ZRHS=10;]
-    ELSEIF(NY=2 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
-    ELSEIF(NY>=2 & NZ=6) [ZLHS=6; ZRHS=7;]
-    ELSEIF(NY=2 & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=3|NY=4|NY=5) & (NZ=1|NZ=2)) [ZLHS=1; ZRHS=3;]
-    ELSEIF((NY=3|NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
-    ELSEIF(NY=3 & NZ>=8) [ZLHS=8; ZRHS=10;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=7) [ZLHS=7; ZRHS=8;]
-    ELSEIF(NY=4 & NZ=8) [ZLHS=8; ZRHS=9;]
-    ELSEIF(NY=4 & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
-    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
-
-  ] ELSEIF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=3) [
-    "Half Isocenter leaf"
+REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {;
 
-    IF((NY=1|NY=2) & NZ<=3) [ZLHS=1; ZRHS=4;]
-    ELSEIF((NY=1|NY=2) & (NZ=4|NZ=5)) [ZLHS=4; ZRHS=6;]
-    ELSEIF(NZ=6) [ZLHS=6; ZRHS=7;]
-    ELSEIF(NY<=4 & NZ=7) [ZLHS=7; ZRHS=8;]
-    "potential overestimate of dZ below--correct it"
-    ELSEIF(NY=1 & NZ>=8) [
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(3,1,1)=1)[
-        IF(NZ=9)[ZLHS=9; ZRHS=10;]
-        ELSE[ZLHS=1; ZRHS=9;]
-      ]
-      ELSE[ZLHS=8; ZRHS=10;]
-    ]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=8) [ZLHS=8; ZRHS=9;]
-    ELSEIF((NY=2|NY=3|NY=4) & NZ=9) [ZLHS=9; ZRHS=10;]
-    ELSEIF(NY=3 & NZ=1) [ZLHS=1; ZRHS=2;]
-    ELSEIF(NY=3 & (NZ=2|NZ=3|NZ=4|NZ=5)) [ZLHS=2; ZRHS=6;]
-    ELSEIF((NY=4|NY=5) & NZ<=2) [ZLHS=1; ZRHS=3;]
-    ELSEIF((NY=4|NY=5) & (NZ=3|NZ=4|NZ=5)) [ZLHS=3; ZRHS=6;]
-    ELSEIF((NY=5|NY=6) & NZ>=7) [ZLHS=7; ZRHS=10;]
-    ELSEIF(NY=6 & NZ<=4) [ZLHS=1; ZRHS=5;]
-    ELSEIF(NY=6 & NZ=5) [ZLHS=5; ZRHS=6;]
+  $SYNCHDMLC_FIND_Z_BOUNDS;
 
-  ] ELSE [
-    "Quarter Isocenter leaf"
-    IF(NY=1)[
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
-        IF(NZ<=3)[ZLHS=1; ZRHS=4;]
-        ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
-        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
-        ELSE[ZLHS=8; ZRHS=10;]
-      ]
-      ELSE[
-        IF(NZ<=4)[ZLHS=1; ZRHS=5;]
-        ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
-        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
-        ELSE[ZLHS=8; ZRHS=10;]
-      ]
-    ]
-    ELSEIF(NY=2)[
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
-        IF(NZ<=3)[ZLHS=1; ZRHS=4;]
-        ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
-        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
-        ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[ZLHS=8; ZRHS=10;]
-        ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
-        ELSE[ZLHS=9; ZRHS=10;]
-      ]
-      ELSE[
-        IF(NZ<=4)[ZLHS=1; ZRHS=5;]
-        ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
-        ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-        ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
-        ELSEIF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,1,2)=1)[ZLHS=8; ZRHS=10;]
-        ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
-        ELSE[ZLHS=9; ZRHS=10;]
-      ]
-    ]
-    ELSEIF(NY=3)[
-      IF(NZ=1)[ZLHS=1; ZRHS=2;]
-      ELSEIF(NZ<=5)[ZLHS=2; ZRHS=6;]
-      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]  
-      ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
-      ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
-      ELSE[ZLHS=9; ZRHS=10;]
-    ]
-    ELSEIF(NY=4)[
-      IF(NZ<=2)[ZLHS=1; ZRHS=3;]
-      ELSEIF(NZ<=5)[ZLHS=3; ZRHS=6;]
-      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-      ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
-      ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
-      ELSE[ZLHS=9; ZRHS=10;]
-    ]
-    ELSEIF(NY=5)[
-      IF(NZ<=2)[ZLHS=1; ZRHS=3;]
-      ELSEIF(NZ<=5)[ZLHS=3; ZRHS=6;]
-      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-      ELSE[ZLHS=7; ZRHS=10;]
-    ]
-    ELSEIF(NY=6)[
-      IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
-         IF(NZ<=4)[ZLHS=1; ZRHS=5;]
-         ELSEIF(NZ=5)[ZLHS=5; ZRHS=6;]
-         ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-         ELSE[ZLHS=7; ZRHS=10;]
-      ]
-      ELSE[
-         IF(NZ<=3)[ZLHS=1; ZRHS=4;]
-         ELSEIF(NZ<=5)[ZLHS=4; ZRHS=6;]
-         ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
-         ELSE[ZLHS=7; ZRHS=10;]
-      ]
-    ] 
-  ]
   IF(W(NP)~=0) [
      ZP = (ZREG_$SYNCHDMLC(LEAFIS,ZRHS)-ZFL)/W(NP);
      ZN = (ZREG_$SYNCHDMLC(LEAFIS,ZLHS)-ZFL)/W(NP);
      IF( (ZP>=0.0) & (ZN>=0.0) ) [ ZDIST =MIN(ZP, ZN); ]
      ELSE [ ZDIST = MAX(ZP, ZN); ]
-     "write(*,*)' zdist,leafis ',zdist,leafis;"
    ]
   ELSE [ ZDIST = 1.0E20; ];
 

From 5f5143b067440cfbba886b05e4db7f5165caf23e Mon Sep 17 00:00:00 2001
From: Frederic Tessier <ftessier@gmail.com>
Date: Thu, 30 Jun 2022 17:26:41 -0400
Subject: [PATCH 12/14] Remove debug output inserted to fix synchdmlc

---
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    |  31 ---
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      |   8 -
 HEN_HOUSE/src/egsnrc.mortran                  | 224 ------------------
 3 files changed, 263 deletions(-)

diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 1ff09fbf8..4418208af 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -783,15 +783,6 @@ ELSEIF(ORIENT_$SYNCHDMLC=3)[
 ]
 ;
 
-"write(*,*)' in howfar, ir, med ',IR_$SYNCHDMLC,med(IRL);
-
-"IF(Z(NP)>47.62001 & Z(NP)<54.37999)["
-        "IF(med(irl) = 0)["
-         " write(*,*)' iq,x,y,z ',iq(np),x(np),y(np),z(np);"
-         " write(*,*)' ir,med ',ir(np),med(irl);"
-         " write(*,*)'  ihstry ',ihstry;"
-       " ]"
-  " ]"
 STEP_UNIT=0.0;
 COUNT = 0;
 OUTOFCMFLAG=0;
@@ -820,7 +811,6 @@ OUTOFMLCFLAG=0;
 IF(N_GAP_$SYNCHDMLC=1 & IR_$SYNCHDMLC=4 ) ["Check the air gap first"
    IF(W(NP)>0.0) ["Particle going forward"
       DIST = (ZMIN_$SYNCHDMLC - Z(NP))/W(NP); "distance to front of CM"
-      "write(*,*)' dist ',dist;
       IF(DIST <= 0.0) [
           USTEP=0.0;
           $SYNCHDMLC_FIND(IR_$SYNCHDMLC, 0.0);
@@ -852,7 +842,6 @@ ELSEIF(IR_$SYNCHDMLC=1 | IR_$SYNCHDMLC=2 | IR_$SYNCHDMLC=3) [
    ELSEIF(W(NP) < 0.0) [
      "particle going backward"
       DIST = (ZMIN_$SYNCHDMLC - Z(NP))/W(NP); "distance to back of CM "
-      "write(*,*)' dist, ustep ',dist,ustep;
       IF(DIST>USTEP) [ STEP_UNIT=USTEP;  ]
       ELSE [ STEP_UNIT=DIST; ]
       IF(DIST <= 0.0) [
@@ -870,18 +859,13 @@ ELSEIF(IR_$SYNCHDMLC=1 | IR_$SYNCHDMLC=2 | IR_$SYNCHDMLC=3) [
 
 $SYNCHDMLC_FIND(REGION_$SYNCHDMLC,0.0);
 
-"write(*,*)' leafis, region, dist ',leafis,REGION_$SYNCHDMLC,DIST;
-
 IF(REGION_$SYNCHDMLC=4) [ "Particle is in the air gap "
   REGION_$SYNCHDMLC=IRSTART_$SYNCHDMLC-1+REGION_$SYNCHDMLC;
    IF(W(NP) > 0.0)[
     IF(DIST <= USTEP ) ["particle to be moved to region boundary"
-      "write(*,*)' ustep, dist here ',ustep,dist;
       $GEO_SHIFT_1_(DIST);
-      "write(*,*)' and ustep, dist here ',ustep,dist;
       USTEP = DIST;
       $SYNCHDMLC_FIND(NEWREGION_$SYNCHDMLC,USTEP);
-      "write(*,*)' ustep, newregion ',ustep,NEWREGION_$SYNCHDMLC;
       IF( NEWREGION_$SYNCHDMLC=1) [IRNEW =IRSTART_$SYNCHDMLC; RETURN;]
       ELSE[IRNEW =IRSTART_$SYNCHDMLC+1; RETURN;]
     ]
@@ -946,11 +930,6 @@ IF(OUTOFMLCFLAG=1) [
 
 $SYNCHDMLC_MINDISTANCE(DIST1);
 
-"write(*,*)' dist1 ',dist1;
-"write(*,*)' x,y,z ',x(np),y(np),z(np);
-"write(*,*)' leafis,nx,ny,nz ',leafis,nx,ny,nz;
-"write(*,*)' dist1,step_unit ',DIST1,STEP_UNIT;
-
 "OUTPUT REGION_$SYNCHDMLC;(I3);"
 
 IF((DIST1>=STEP_UNIT) | (DIST1<0)) [
@@ -983,9 +962,6 @@ ELSEIF( (STEP_UNIT>DIST1) & (DIST1>=0)) [
         NEWREGION_$SYNCHDMLC=NEWREGION_$SYNCHDMLC+IRSTART_$SYNCHDMLC-1;
        " OUTPUT REGION_$SYNCHDMLC;(I3);"
 
-       "write(*,*)' region, newregion, dist1 ',REGION_$SYNCHDMLC,
-       "     NEWREGION_$SYNCHDMLC,DIST1;
-
         IF( OUTOFCMFLAG=1 ) [
           EXIT;
         ] ELSEIF( (NEWREGION_$SYNCHDMLC~=REGION_$SYNCHDMLC)
@@ -1018,7 +994,6 @@ ELSEIF( (STEP_UNIT>DIST1) & (DIST1>=0)) [
           RETURN;
        ] ELSE [
          $SYNCHDMLC_MINDISTANCE(DIST2);
-         "write(*,*)' dist1, dist2 ',dist1,dist2;
          DIST1=DIST1+DIST2;
        ];
 
@@ -3730,8 +3705,6 @@ IF(LEAFIS~=0) [
   ]
 
   "Check if we are in groove on leaf and move to adjacent leaf"
-"write(*,*)' before check leafis, leaftype ',leafis,LEAFTYPE_$SYNCHDMLC(LEAFIS);
-"write(*,*)' nx, ny, nz ',nx,ny,nz; 
   IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
 				   "target leaf"
     IF(LEAFIS~=TOT_LEAF_$SYNCHDMLC & ((((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9)) &
@@ -4145,9 +4118,6 @@ IF(LEAFIS~=0) [
 
     DIST=MIN(ABS(ZREG_$SYNCHDMLC(LEAFIS,I1)-Z(NP)),
              ABS(ZREG_$SYNCHDMLC(LEAFIS,I2)-Z(NP)));
-    "write(*,*)' x,y,z ',x(np),y(np),z(np);
-    "write(*,*)' nx,ny,nz ',nx,ny,nz;
-    "write(*,*)' leafis,i1,i2,zdist ',leafis,i1,i2,dist;
 
     "Calculates distance to closest boundary in z direction"
     "--> 3) 7 Jul 2009"
@@ -4656,7 +4626,6 @@ IF(LEAFIS~=0) [
           SQRT(1+TEMP2**2));
 
     DIST = MIN(DIST,TEMP1,TEMP2);
-    "write(*,*)' ydist ',dist;
  "NOW CHECK DISTANCE IN X DIRECTION"
     IF(ENDTYPE_$SYNCHDMLC=1) [ "focused leaf end"
       TEMP1=SURPARA2_B_$SYNCHDMLC(LEAFIS);
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index fd4ad6c09..a3345da38 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -518,8 +518,6 @@ ELSE ["inside leaf bank"
       NY=NY+1;
     ];
 
-    "write(*,*)' leafis, xyfl1, ny ',leafis,xyfl(1),ny;"
-
     IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
        "Originally on Target (Quarter or Half) Leaf"
 
@@ -698,9 +696,6 @@ ELSE ["inside leaf bank"
     ELSEIF((XYFL(2)>TEMP4) | (XYFL(2)=TEMP4 & UVL(2)>=0)) [
          NX=5;]
  ];
- "write(*,*)' find: leafis, x, y, z ',leafis,xyfl(2),xyfl(1),zfl;"
- "write(*,*)' nx, ny, nz, subindex ',nx,ny,nz,"
- "            SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);"
  {P1}=SUBINDEX_$SYNCHDMLC(LEAFIS,NX,NY,NZ);
 
  "OUTPUT LEAFIS,XYFL(2),XYFL(1),ZFL,{P1};"
@@ -1401,7 +1396,6 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {;
   ELSE [ YN = 1.0E20; ];
   IF((YP>=0.0) & (YN>=0.0) ) [ YDIST =MIN(YP, YN); ]
   ELSE [ YDIST = MAX(YP,YN);];
-  "write(*,*)' i,j, rhs, lhs, ydist ',i,j,rhs,lhs,ydist;"
  IF(ENDTYPE_$SYNCHDMLC = 1) ["focused leaf end"
       HOLE=HOLEPOS_$SYNCHDMLC(LEAFIS);
       TEMP3=LEAFB_$SYNCHDMLC(LEAFIS)-HOLE;
@@ -1456,7 +1450,6 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {;
     TEMP3 = UVL(2)*(XYFL(2)-XoP)+W(NP)*(ZFL-Zo); "B in eqn"
     TEMP4 = (XYFL(2)-XoN)**2 + (ZFL-Zo)**2; "part of C"
     TEMP5 = (XYFL(2)-XoP)**2 + (ZFL-Zo)**2; "part of C"
-    "write(*,*)' nx ',nx;"
     IF((XYFL(2)>=XoN) & (SQRT((XYFL(2)-XoN)**2+(ZFL-Zo)**2)-
       LEAFRADIUS_$SYNCHDMLC=0.0) & (UVL(2)*(XYFL(2)-XoN)+W(NP)*(ZFL-Zo)=0.0)) [
          XN=0.0;  XP=1.0E20; "on edge of negative leaf"
@@ -1572,7 +1565,6 @@ REPLACE {$SYNCHDMLC_MINDISTANCE(#);} WITH {;
  ];
 IF( (XP>=0.0) & (XN>=0.0) ) [ XDIST =MIN(XP, XN); ]
 ELSE [ XDIST = MAX(XP,XN); ];
-"write(*,*)' xdist ',xdist;"
 IF( ZDIST>=0.0) [TEMP=ZDIST;
     IF( YDIST>=0.0 ) [TEMP=MIN(TEMP,YDIST);];
     IF( XDIST>=0.0 ) [TEMP=MIN(TEMP,XDIST);];
diff --git a/HEN_HOUSE/src/egsnrc.mortran b/HEN_HOUSE/src/egsnrc.mortran
index 1ca92ccf5..ed3bc507a 100644
--- a/HEN_HOUSE/src/egsnrc.mortran
+++ b/HEN_HOUSE/src/egsnrc.mortran
@@ -1041,117 +1041,6 @@ $start_new_particle;
 
 :NEWELECTRON:LOOP
 [
-IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
-    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' half air test 1';
-  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
-    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' half air test 2';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
-   MED(IR(NP))=2)[
-  write(*,*)' half air test 3';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
-  MED(IR(NP))=2)[
-  write(*,*)' half air test 4';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) < -0.689 & Z(NP) >54.1161 & ABS(X(NP))<10.0 &
-  MED(IR(NP))=2)[
-  write(*,*)' half air test 5';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) < -0.926 & Z(NP) >50.996 & ABS(X(NP))<10.0 &
-  MED(IR(NP))=2)[
-  write(*,*)' half air test 6';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 7';
- write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 8';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 9';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 10';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 11';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
-"   ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 1';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.7266 & Z(NP) <54.284 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 2';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"  stop;
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.6893 & Z(NP) <51.103 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 3';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 4';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 5';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.4936 & Y(NP) <-0.4566 & Z(NP) <51.2 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 6';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>54.286 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 7';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6104 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>51.206 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 8';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <54.02 & Z(NP)>51.105 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 9';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 10';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 11';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
     "Go once through this loop for each 'new' electron whose charge and
     "energy has not been checked
 
@@ -1293,7 +1182,6 @@ IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
                 $SET-TUSTEP-EM-FIELD; "optional tustep restriction in EM field
 
                 $CALL-HOWNEAR(tperp);
-                "write(*,*)'ustep, tperp ',ustep,tperp;
                 dnear(np) = tperp;
                 $RANGE-DISCARD;       "optional regional range rejection for"
                                       "particles below e_max_rr if i_do_rr set"
@@ -6592,118 +6480,6 @@ $EVALUATE GMFPR0 USING GMFP(GLE);]
 
 :PTRANS:
 LOOP["PHOTON TRANSPORT LOOP"
-IF(Y(NP) > -0.73059 & Y(NP) < -0.689 &
-    Z(NP) > 50.998 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' half air test 1';
-  write(*,*)' e,x,y,z,ir ',E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.8258 & Y(NP) < -0.689 &
-    Z(NP) > 47.716 & Z(NP) < 47.979 & ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-  write(*,*)' half air test 2';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.693 & Y(NP) < -0.689 & ABS(X(NP))<10.0 & Z(NP) > 47.716 &
-   MED(IR(NP))=2)[
-  write(*,*)' half air test 3';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9259 & Y(NP) <-0.8234 & Z(NP) >53.998 & ABS(X(NP))<10.0 &
-  MED(IR(NP))=2)[
-  write(*,*)' half air test 4';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) < -0.689 & Z(NP) >54.1161 & ABS(X(NP))<10.0 &
-  MED(IR(NP))=2)[
-  write(*,*)' half air test 5';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) < -0.926 & Z(NP) >50.996 & ABS(X(NP))<10.0 &
-  MED(IR(NP))=2)[
-  write(*,*)' half air test 6';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9259 & Y(NP) <-0.7306 & Z(NP) <53.996 & Z(NP)>47.981 &
- ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 7';
- write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9259 & Y(NP) <-0.6933 & Z(NP) <50.996 & Z(NP)>47.981 &
- ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 8';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) <-0.689 & Z(NP) <47.714 & Z(NP)>47.6201 &
- ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 9';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.9632 & Y(NP) <-0.826 & Z(NP) <50.994 & Z(NP)>47.6201 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 10';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-IF(Y(NP) > -0.823 & Y(NP) <-0.7306 & Z(NP) <54.116 & Z(NP)>53.998 &
-  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-  write(*,*)' half med test 11';
-  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <47.884 & Z(NP)>47.621 &
-"   ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 1';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.7266 & Z(NP) <54.284 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 2';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.6893 & Z(NP) <51.103 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 3';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"  stop;
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.6106 & Z(NP) <54.284 & Z(NP)>54.021 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 4';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6142 & Y(NP) <-0.4566 & Z(NP) <48.00 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 5';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.4936 & Y(NP) <-0.4566 & Z(NP) <51.2 & Z(NP)>47.621 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=2)[
-"  write(*,*)' iso air test 6';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7274 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>54.286 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 7';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6104 & Y(NP) <-0.4566 & Z(NP) <54.375 & Z(NP)>51.206 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 8';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.7265 & Y(NP) <-0.4938 & Z(NP) <54.02 & Z(NP)>51.105 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 9';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6892 & Y(NP) <-0.4938 & Z(NP) <51.103 & Z(NP)>48.005 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 10';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-"IF(Y(NP) > -0.6892 & Y(NP) <-0.6143 & Z(NP) <48.003 & Z(NP)>47.886 &
-"  ABS(X(NP))<10.0 & MED(IR(NP))=1)[
-"  write(*,*)' iso med test 11';
-"  write(*,*)' iq,e,x,y,z,ir ',IQ(NP),E(NP),X(NP),Y(NP),Z(NP),IR(NP);
-"]
-
 IF (MEDIUM.EQ.0)[TSTEP=VACDST;]
 ELSE [$SET-RHOF;    "DENSITY RATIO SCALING TEMPLATE"
 GMFP=GMFPR0/RHOF;

From 11cf3b82d7d538bc33d2eec90262fb59cef7bc02 Mon Sep 17 00:00:00 2001
From: Blake Walters <blakewalters@Blakes-MacBook-Air.local>
Date: Fri, 20 May 2022 11:40:21 -0700
Subject: [PATCH 13/14] Update documentation to reflect synchdmlc changes

---
 .../pirs509a-beamnrc/figures/synchdmlcd.fig   | 364 +++++++++---------
 .../pirs509a-beamnrc/figures/synchdmlcd.pdf   | Bin 26102 -> 25511 bytes
 .../src/pirs509a-beamnrc/pirs509a-beamnrc.tex | 139 ++++---
 3 files changed, 258 insertions(+), 245 deletions(-)

diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/synchdmlcd.fig b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/synchdmlcd.fig
index 090e190a1..6c11a4e30 100644
--- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/synchdmlcd.fig
+++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/synchdmlcd.fig
@@ -1,4 +1,4 @@
-#FIG 3.2  Produced by xfig version 3.2.5b
+#FIG 3.2  Produced by xfig version 3.2.8b
 Portrait
 Center
 Inches
@@ -178,22 +178,10 @@ Single
 	1 1 1.00 60.00 90.00
 	1 1 1.00 60.00 90.00
 	 6815 14424 7527 14424
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 1014 499 1014 5747
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 1289 499 1289 5778
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 1777 5290 -419 5290
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 1838 2666 -359 2666
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 1868 835 -327 835
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 1534 499 1534 5778
-2 1 1 1 0 6 50 0 20 4.000 0 0 -1 0 0 2
-	 1831 2929 -366 2929
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 1892 3904 -457 3904
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 1800 3649 -395 3649
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
@@ -215,10 +203,6 @@ Single
 	1 1 1.00 94.50 94.50
 	1 1 1.00 94.50 94.50
 	 -181 967 557 967
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 1838 1140 -359 1140
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 -64 1036 520 1036 520 1237 -64 1237 -64 1036
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 66.00 36.00
 	1 1 1.00 66.00 36.00
@@ -242,26 +226,12 @@ Single
 	1 1 1.00 66.00 36.00
 	1 1 1.00 66.00 36.00
 	 818 5228 1012 5228
-2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 96.00 96.00
-	1 1 1.00 96.00 96.00
-	 21 4066 1513 4066
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 673 4966 1138 4966 1138 5176 673 5176 673 4966
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
 	1 1 1.00 96.00 96.00
 	 1662 4253 1664 4676
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
 	1 1 1.00 96.00 96.00
 	 1735 4922 1742 5299
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 283 4411 748 4411 748 4621 283 4621 283 4411
-2 2 0 0 -1 7 0 0 20 0.000 0 0 -1 0 0 5
-	 171 2002 921 2002 921 2266 171 2266 171 2002
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 801 499 801 5747
-2 1 1 1 0 7 51 0 -1 4.000 0 0 -1 0 0 2
-	 588 499 588 5747
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 13577 5526 11774 5526
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
@@ -274,14 +244,6 @@ Single
 	 13652 827 11851 827
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 13603 4765 11799 4765
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 13636 591 11836 591
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 12776 491 12776 5740
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 13177 491 13177 5771
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 12125 491 12125 5740
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 94.50 94.50
 	1 1 1.00 94.50 94.50
@@ -308,8 +270,6 @@ Single
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
 	1 1 1.00 96.00 96.00
 	 12921 561 12924 1120
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 13627 2901 11825 2901
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 66.00 36.00
 	1 1 1.00 66.00 36.00
@@ -319,14 +279,6 @@ Single
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
 	1 1 1.00 96.00 96.00
 	 13305 2168 13298 2527
-2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 96.00 96.00
-	1 1 1.00 96.00 96.00
-	 12338 1794 13355 1794
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 12653 1686 12930 1686 12930 1903 12653 1903 12653 1686
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
-	 11881 4196 13333 4196
 2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
 	 11922 3862 13374 3862
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
@@ -352,18 +304,10 @@ Single
 	 14717 600 14725 5505
 2 2 0 0 0 7 50 -1 20 0.000 0 0 -1 0 0 5
 	 14273 2737 15443 2737 15443 3067 14273 3067 14273 2737
-2 1 1 1 0 6 50 0 20 4.000 0 0 -1 0 0 2
-	 7 499 7 5747
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 1777 4680 -419 4680
-2 3 0 2 0 6 51 0 20 0.000 0 0 -1 0 0 17
-	 -205 865 -205 2666 7 2666 7 4680 1014 4680 1014 5290
-	 801 5290 801 5533 1534 5533 1534 2910 1289 2910 1289 1140
-	 588 1140 588 835 -205 835 -205 897 -205 865
 2 1 1 1 0 7 52 0 -1 4.000 0 0 -1 0 0 2
 	 -208 484 -208 5732
-2 2 0 2 0 14 51 0 20 0.000 0 0 -1 0 0 5
-	 -4 3642 1511 3642 1511 3904 -4 3904 -4 3642
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 0 0 2
 	 -566 4694 244 3734
 2 3 0 2 0 6 51 0 20 0.000 0 0 -1 0 0 17
@@ -392,22 +336,14 @@ Single
 	 4477 8983 4443 9087 4789 9087 4809 8977 4477 8983
 2 3 0 2 0 13 50 0 20 0.000 0 0 -1 0 0 5
 	 4754 9625 4737 9724 5064 9719 5064 9624 4754 9625
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
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 2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
 	 2755 1655 4523 1655
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 4795 1655 2605 1655
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 4523 436 4523 5707
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 4795 1929 2605 1929
-2 1 1 1 0 7 52 0 -1 4.000 0 0 -1 0 0 2
-	 2753 405 2753 5645
 2 2 0 2 0 14 51 0 20 0.000 0 0 -1 0 0 5
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 3003 407 3003 5647
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
 	1 1 1.00 96.00 96.00
 	 4583 314 4586 873
@@ -446,8 +382,6 @@ Single
 	 4208 2536 4507 2536
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 0 0 2
 	 4355 2569 4659 2936
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 4757 5077 2567 5077
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 4779 2296 2522 2304
 2 3 0 2 0 6 51 0 20 0.000 0 0 -1 0 0 15
@@ -562,14 +496,10 @@ Single
 	 10918 8760 11283 8760 11283 12020 10918 12020 10918 8760
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 10706 5267 8928 5267
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
-	 9100 1934 10534 1934
 2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
 	 9075 1661 10510 1661
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 10731 1661 8953 1661
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 10731 1934 8953 1934
 2 2 0 2 0 14 51 0 20 0.000 0 0 -1 0 0 5
 	 9069 1661 10510 1661 10510 1920 9069 1920 9069 1661
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
@@ -601,10 +531,6 @@ Single
 	1 1 1.00 66.00 36.00
 	1 1 1.00 66.00 36.00
 	 10255 2561 10505 2561
-2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 96.00 96.00
-	1 1 1.00 96.00 96.00
-	 9285 3770 10505 3773
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 0 2
 	1 1 1.00 96.00 96.00
 	 10355 4499 10355 5054
@@ -633,10 +559,6 @@ Single
 	 5097 6830 5097 10745
 2 4 2 1 -1 7 0 0 -1 3.000 0 0 7 0 0 5
 	 1151 8456 9332 8456 9332 10196 1151 10196 1151 8456
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 6865 481 6865 5760
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 7355 481 7355 5791
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 7845 5545 5640 5545
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
@@ -649,18 +571,6 @@ Single
 	 7906 1126 5702 1126
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 7937 819 5734 819
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
-	 5825 3886 7600 3886
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 2
-	 5825 4197 7600 4197
-2 3 0 2 0 6 51 0 20 0.000 0 0 -1 0 0 15
-	 6314 819 6314 2662 5942 2661 5942 4776 6865 4779 6865 5299
-	 6069 5299 6069 5545 7600 5545 7600 2905 7355 2905 7355 1126
-	 6652 1126 6652 819 6314 819
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 7814 3886 5717 3883
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 7937 4197 5680 4198
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 7877 4779 5672 4779
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
@@ -705,8 +615,6 @@ Single
 	1 1 1.00 66.00 36.00
 	1 1 1.00 66.00 36.00
 	 7367 2986 7566 2986
-2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 0 0 2
-	 8067 2306 7465 2966
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 94.50 94.50
 	1 1 1.00 94.50 94.50
@@ -715,46 +623,16 @@ Single
 	1 1 1.00 94.50 94.50
 	1 1 1.00 94.50 94.50
 	 5965 4686 6848 4686
-2 2 0 0 -1 7 0 0 20 0.000 0 0 -1 0 0 5
-	 6408 3903 7158 3903 7158 4167 6408 4167 6408 3903
-2 1 1 1 0 7 52 0 -1 4.000 0 0 -1 0 0 2
-	 5942 466 5942 5745
-2 2 0 2 0 14 51 0 20 0.000 0 0 -1 0 0 5
-	 5935 3883 7593 3883 7593 4201 5935 4201 5935 3883
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 6314 481 6314 5760
-2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 96.00 96.00
-	1 1 1.00 96.00 96.00
-	 6310 1809 7606 1809
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 6652 481 6652 5760
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 6069 481 6069 5760
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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 2 2 0 0 0 7 50 -1 20 0.000 0 0 -1 0 0 5
 	 5628 1478 6213 1478 6213 1703 5628 1703 5628 1478
 2 2 0 0 0 7 50 -1 20 0.000 0 0 -1 0 0 5
 	 11643 1455 12250 1455 12250 1747 11643 1747 11643 1455
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 12325 491 12325 5740
-2 3 0 2 0 6 51 0 20 0.000 0 0 -1 0 0 15
-	 12325 827 12325 2660 12020 2659 12020 4762 12776 4765 12776 5282
-	 12125 5282 12125 5526 13378 5526 13388 2542 13178 2542 13177 1132
-	 12601 1132 12601 827 12325 827
 2 2 0 0 0 7 50 -1 20 0.000 0 0 -1 0 0 5
 	 12003 1837 12258 1837 12258 2070 12003 2070 12003 1837
 2 2 0 0 0 7 50 -1 20 0.000 0 0 -1 0 0 5
 	 10250 4257 10505 4257 10505 4490 10250 4490 10250 4257
-2 1 1 1 0 7 52 0 -1 4.000 0 0 -1 0 0 2
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 13651 4190 11806 4191
-2 2 0 2 0 14 51 0 20 0.000 0 0 -1 0 0 5
-	 12015 3875 13369 3875 13369 4182 12015 4182 12015 3875
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 94.50 94.50
 	1 1 1.00 94.50 94.50
@@ -771,14 +649,12 @@ Single
 	 9945 1305 10486 1305
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 4818 1237 2626 1237
-2 3 0 2 0 6 52 0 20 0.000 0 0 -1 0 0 15
+2 3 0 2 0 6 57 0 20 0.000 0 0 -1 0 0 15
 	 4187 5281 4186 2459 4531 2461 4523 1228 3825 1230 3828 894
 	 4400 893 4400 589 2755 589 2739 2304 2996 2309 2994 5069
 	 3705 5070 3705 5280 4187 5281
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 4400 436 4400 5707
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 4766 893 2574 893
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 94.50 94.50
 	1 1 1.00 94.50 94.50
@@ -787,27 +663,19 @@ Single
 	1 1 1.00 66.00 66.00
 	1 1 1.00 66.00 66.00
 	 3714 5352 4164 5352
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 12601 491 12601 5740
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
+2 2 0 0 0 7 47 0 20 0.000 0 0 -1 0 0 5
 	 12214 4410 12594 4410 12594 4619 12214 4619 12214 4410
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 12282 4926 12634 4926 12634 5130 12282 5130 12282 4926
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
+2 2 0 0 0 7 47 0 20 0.000 0 0 -1 0 0 5
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 13400 493 13400 5773
 2 2 0 0 0 7 50 -1 20 0.000 0 0 -1 0 0 5
 	 13260 1873 13590 1873 13590 2120 13260 2120 13260 1873
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 7600 481 7600 5791
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 4187 436 4187 5676
 2 1 1 1 0 7 55 0 -1 4.000 0 0 -1 0 0 2
 	 14814 591 -245 581
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
+2 2 0 0 0 7 47 0 20 0.000 0 0 -1 0 0 5
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-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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 	 3975 1380 4440 1380 4440 1590 3975 1590 3975 1380
 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
 	 3697 400 3697 5640
@@ -817,46 +685,178 @@ Single
 	1 1 1.00 96.00 96.00
 	1 1 1.00 96.00 96.00
 	 3021 3748 4521 3766
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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 2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
+2 1 1 1 0 7 49 0 -1 4.000 0 0 -1 0 0 2
 	 10706 904 8928 904
 2 1 1 1 0 7 55 0 -1 4.000 0 0 -1 0 0 2
 	 10706 601 8928 601
-2 3 0 2 0 6 52 0 20 0.000 0 0 -1 0 0 15
+2 3 0 2 0 6 57 0 20 0.000 0 0 -1 0 0 15
 	 10236 5267 10235 2460 10516 2462 10510 1237 9930 1236 9930 906
 	 10409 904 10409 601 9075 601 9061 2307 9269 2312 9268 5056
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 10236 449 10236 5660
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 10409 449 10409 5691
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 9960 1380 10478 1380 10478 1609 9960 1609 9960 1380
-2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
-	 9773 435 9773 5646
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 9631 3637 9973 3637 9973 3870 9631 3870 9631 3637
 2 1 0 2 0 7 50 0 -1 0.000 0 0 -1 1 1 2
 	1 1 1.00 66.00 66.00
 	1 1 1.00 66.00 66.00
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-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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 2 2 0 0 -1 7 6 0 20 0.000 0 0 -1 0 0 5
 	 -384 4769 366 4769 366 5033 -384 5033 -384 4769
-2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
-	 495 3937 833 3937 833 4155 495 4155 495 3937
 2 2 0 0 0 7 50 0 20 0.000 0 0 -1 0 0 5
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+2 1 1 1 0 6 50 0 20 4.000 0 0 -1 0 0 2
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+	1 1 1.00 96.00 96.00
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+2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
+	 645 507 645 5755
+2 2 0 0 0 7 48 0 20 0.000 0 0 -1 0 0 5
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+2 3 0 2 0 6 57 0 20 0.000 0 0 -1 0 0 15
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+2 1 1 1 0 7 50 0 -1 4.000 0 0 -1 0 0 2
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diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/synchdmlcd.pdf b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/synchdmlcd.pdf
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DU8UE*

diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex b/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex
index 49d0629ff..dbc365e78 100644
--- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex
+++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex
@@ -64,6 +64,8 @@
 \usepackage{moreverb}   %this is used for the boxedverbatim environment
                         %used to box the listing files for tutor programs
 
+\renewcommand{\labelenumi}{\theenumi}
+
 \renewcommand{\footrulewidth}{0.4pt}
 \renewcommand{\headrulewidth}{0.4pt}
 \lhead[{\sffamily \thepage}]{{\sffamily BEAMnrc Users Manual}}
@@ -8491,6 +8493,12 @@ \subsubsection{SYNCHDMLC}
 similar to the TARGET/ISOCENTER leaves in DYNVMLC, with HALF TARGET/HALF ISOCENTER leaves being
 wider than the QUARTER TARGET/QUARTER ISOCENTER leaves.
 
+In addition to the option to specify leaves opening in either the Y- ({\tt ORIENT}=0) or X-direction ({\tt ORIENT}=1)
+shared with other dynamic MLCs, SYNCHDMLC provides two additional possible settings of {\tt ORIENT} which
+will automatically transform the SYNCHDMLC coordinate system to match that given in the manufacturers specifications
+for the 120MLC and HD120 MLCs for leaves opening in the Y- ({\tt ORIENT}=2) or X-direction ({\tt ORIENT}=3).  More
+details on {\tt ORIENT}=2,3 are given below.
+
 \begin{figure}[htpb]
 \begin{center}
 \vspace*{-0.7cm}
@@ -8525,57 +8533,15 @@ \subsubsection{SYNCHDMLC}
 have the same meanings as those used for DYNVMLC (See Section~\ref{dynvmlcsect} and
 Table~\ref{dynvmlc_tab}).  In general, QUARTER leaves
 are used closer to middle of the mlc, and, while their Z-dimensions are similar to those for their HALF counterparts, they
-are significantly thinner in the X- ({\tt ORIENT}=0) or Y- ({\tt ORIENT}=1)
+are significantly thinner in the X- ({\tt ORIENT}=0,2) or Y- ({\tt ORIENT}=1,3)
 dimension.
 
-\index{SYNCHDMLC!Relaxation of leaf cross-section input restrictions}
-In general, SYNCHDMLC is similar to DYNVMLC and SYNCVMLC in that leaf cross-section dimensions must be defined so that
-the grid lines shown in Figure~\ref{synchdmlc_fig}, defining the cross-section regions, remain in the same order
-shown in the figure.  This should allow modeling of the HD120 based on manufacturer specifications assuming either
-non-divergent leaves ({\em i.e.,} leaves in which the vertical cross-section boundaries are parallel as opposed
-to intersecting at some value of Z$<${\tt ZMIN}), as shown in
-Figure~\ref{synchdmlc_fig}, or else minimal divergence.  Leaves may diverge to a significant extent, however,
-and it has
-come to our attention that, in an effort to more accurately model this, users may project manufacturer-specified
-cross-section widths ({\em e.g.,} {\tt wtip}, {\tt wts}, {\tt wbs}, etc) from the Z values at which they are defined
-back to {\tt ZMIN}.  This results in a change in order in some of the vertical cross-section boundaries.  In an effort
-to accommodate this in SYNCHDMLC, we have recently introduced the following relaxations of prior input restrictions:
-\begin{enumerate}
-\item {\bf For HALF TARGET and QUARTER TARGET leaves}: The bottom of the support rail can extend to the left of the
-leaf tip ({\tt wbs} $>$ {\tt wg} + {\tt wtip}), changing the
-order of the 3rd and 4th (counting from the right) vertical cross-section boundaries shown in Figure~\ref{synchdmlc_fig}.
-\item {\bf For HALF TARGET and QUARTER TARGET leaves}: The top of the support rail can extend past the right edge
-of the leaf ({\tt wts} $>$ {\tt wbs}), changing the order of the
-6th and 7th vertical cross-section boundaries.
-\item {\bf For QUARTER TARGET leaves}: The top of the support rail need not extend past the beginning (left edge)
-of the groove ({\tt wts} $<$ {\tt wbs} - {\tt wg}),
-effectively changing the order of vertical boundries 5 and
-6, provided that, if relaxation 1 above is in effect, it does extend past the left edge of the leaf tip.
-\item {\bf For HALF ISOCENTER leaves}: The bottom of the support rail can extend past the left edge of the leaf
-({\tt wbs} $>$ {\tt wts}), changing the order of the 1st and 2nd vertical cross-section boundaries.
-\item {\bf For QUARTER ISOCENTER leaves}: The bottom of the support rail need not extend (to the right) as far as
-the right edge of the tongue ({\tt wbs} $<$ {\tt wts} - {\tt wt}), changing
-the order of the 2nd and 3rd vertical cross-section boundaries, provided that it still extends past the
-right edge of the leaf tip.
-\item {\bf For QUARTER ISOCENTER leaves}: The Z-position of the groove, {\tt zg}, can be greater than that of the tongue,
-{\tt zt}, allowing for duelling interpretations of manufacturer specifications for this leaf type in which the
-relative Z-positions of these structures are not entirely clear.
-\end{enumerate}
-If user input dimensions require any of the above relaxations, a warning message will be output stating which restriction
-is being relaxed and indicating that the input cross-section differs from that shown in this manual.
-It is important to note that, while these relaxations in boundary ordering may allow the user to input
-accurate dimensions consistent with divergent MLC leaves, leaves are still modeled as if they are non-divergent,
-with all side surfaces focused at {\tt ZFOCUS(1)}, and, thus, the geometry remains an approximation.
-Many thanks to Dr. Jarkko Ojala at Tampere University
-Hospital, Finland, who, through detailed examination of manufacturer specifications and measurement of MLC leaves,
-determined which restrictions needed to be relaxed and who helped test the modified code.
-
 \index{SYNCHDMLC!restrictions on leaf dimensions}
-Similar to DYNVMLC, leaf cross-section dimensions must be defined so that the Z and X ({\tt ORIENT}=0) or Y ({\tt ORIENT}=1) grid lines
+Leaf cross-section dimensions must be defined so that the Z and X ({\tt ORIENT}=0,2) or Y ({\tt ORIENT}=1,3) grid lines
 shown on the cross-sections at the top of Figure~\ref{synchdmlc_fig} do not change order.
 The Z-positions of tongues and grooves must allow leaves to fit
 together in the following
-combinations: \\
+combinations:\\~~\\
 FULL/FULL ({\tt zt}$_{FULL}$ $\leq$ {\tt zg}$_{FULL}$)\\
 FULL/HALF TARGET ({\tt zg}$_{FULL}$ $\geq$ {\tt zt}$_{HALF~TARGET}$)\\
 HALF TARGET/HALF ISOCENTER ({\tt zg}$_{HALF~TARGET}$ $\leq$ {\tt zt}$_{HALF~ISOCENTER}$)\\
@@ -8586,22 +8552,11 @@ \subsubsection{SYNCHDMLC}
 QUARTER ISOCENTER/HALF TARGET ({\tt zg}$_{QUARTER~ISOCENTER}$ $\geq$ {\tt zt}$_{HALF~TARGET}$)\\
 and HALF ISOCENTER/FULL (ie {\tt zg}$_{HALF~ISOCENTER}$ $\geq$ {\tt zt}$_{FULL}$).
 
-
-
-As in DYNVMLC and SYNCVMLC, rather than specifying the type of each leaf in the MLC, the user is able to specify groups
-of adjacent leaves of the same type.  Since TARGET leaves always alternate with ISOCENTER leaves within a group,
-for the purpose of defining a leaf group, HALF or QUARTER TARGET/ISOCENTER leaves are considered one type.
-Unlike DYNVMLC and SYNCVMLC, however, the number of TARGET/ISOCENTER leaves in a group does not have to be even.  Thus,
-the final TARGET or ISOCENTER leaf in a group need not be matched by its ISOCENTER or TARGET (respectively)
-counterpart.  If a group of TARGET/ISOCENTER is defined adjacent to another group of TARGET/ISOCENTER leaves, the
-first leaf in the group will automatically be chosen to match the last leaf of the previous group.  Thus, if
-the last leaf of the previous group was a QUARTER or HALF TARGET leaf, then the first leaf of the current
-group will be a QUARTER or HALF ISOCENTER leaf, and vice versa.  In terms of leaf groups, the only restriction
-is that the numbers and types of leaves cannot be specified so that a QUARTER or HALF TARGET leaf ends up
-immediately adjacent to a FULL leaf on the -X (ORIENT=0) or -Y (ORIENT=1) side.
-Finally, note that the user need not use all leaf types in a simulated MLC.  Thus, there may be no FULL leaves, HALF TARGET/ISOCENTER
-leaves, or QUARTER TARGET/ISOCENTER leaves in the simulation.  In this case, inputs for the
-cross-section parameters of the unused leaves can be left as blanks or zeros.
+The default cross-sections for each leaf type are shown in Figure~\ref{synchdmlc_fig}.  The width of
+each vertical region is specified as back projected to {\tt ZMIN}.  Thus, for any width, $w_i$,
+the user inputs the value, $w_i\times\left(\frac{{\tt ZMIN}}{Z_i}\right)$, where $Z_i$ is the value of Z
+where $w_i$ is defined.  For example, for any leaf type, to define the groove width, $wg$, 
+the user would input $wg\times\left(\frac{{\tt ZMIN}}{zg}\right)$.
 
 Similar to DYNVMLC and SYNCVMLC, leaf ends can be straight, focused ({\tt ENDTYPE}=1) or cylindrical
 ({\tt ENDTYPE}=0).  For straight, focused ends, the user must specify the Z-position of the
@@ -8636,9 +8591,67 @@ \subsubsection{SYNCHDMLC}
 leaves when determining the perpendicular
 distance to the nearest region boundary for
 charged particle range rejection.  For this option to be in effect, charged particles must be in the leaf medium and have:\\
-particle Y ({\tt ORIENT}=0) or X ({\tt ORIENT}=1) $<$ minimum Y ({\tt ORIENT}=0) or X ({\tt ORIENT}=1) of all leaf openings
+particle Y ({\tt ORIENT}=0,2) or X ({\tt ORIENT}=1,3) $<$ minimum Y ({\tt ORIENT}=0,2) or X ({\tt ORIENT}=1,3) of all leaf openings
 (excluding rounded or focused leaf end) or\\
-particle Y ({\tt ORIENT}=0) or X ({\tt ORIENT}=1) $>$ maximum Y ({\tt ORIENT}=0) or X ({\tt ORIENT}=1) of all leaf openings (excluding leaf end)\\
+particle Y ({\tt ORIENT}=0,2) or X ({\tt ORIENT}=1,3) $>$ maximum Y ({\tt ORIENT}=0,2) or X ({\tt ORIENT}=1,3) of all leaf openings (excluding leaf end)\\
+
+\subsubsubsection{More accurate modeling of manufacturer specifications for 120MLC and HD120 collimators}
+\index{SYNCHDMLC!And manufacturer MLC specifications}
+
+\index{SYNCHDMLC!Relaxation of leaf cross-section input restrictions}
+The default cross-sections were originally implemented assuming that leaf divergence ({\em i.e.}, due
+to all leaf sides being focused at a single Z-value, {\tt ZFOCUS(1)}) is sufficiently small that
+the order of vertical boundaries does not change when widths are back projected to {\tt ZMIN}, and
+restrictions have been placed on cross-section inputs based on this assumption.  However, recent work
+by Dr. Jarkko Ojala (2018, Tampere University Hospital, Finland) involving detailed measurements
+of leaf cross-sections and reference to the manufacturer's (Varian) specifications has shown
+that this assumption does not hold for a number of vertical regions.  To facilitate more accurate modelling
+of leaf cross-sections, then, we have implemented the following exceptions to the original cross-section
+input restrictions:
+
+For accurate modelling of HALF TARGET and HALF ISOCENTER leaves (Varian MLC120 and HDMLC):
+\renewcommand{\theenumi}{\roman{enumi}}%
+\begin{enumerate}
+\item In HALF TARGET leaves, the bottom of the support rail is allowed to extend to the left of the
+leaf tip ({\tt wbs} $>$ {\tt wg} + {\tt wtip}), changing the
+order of the 3rd and 4th (counting from the right) vertical cross-section boundaries shown in Figure~\ref{synchdmlc_fig}.
+\item In HALF TARGET leaves, the top of the support rail can extend past the right edge
+of the leaf ({\tt wts} $>$ {\tt wbs}), changing the order of the
+6th and 7th vertical cross-section boundaries.
+\item In HALF ISOCENTER leaves, the bottom of the support rail can extend past the left edge of the leaf
+({\tt wbs} $>$ {\tt wts}), changing the order of the 1st and 2nd vertical cross-section boundaries.
+\end{enumerate}
+
+For accurate modeling of QUARTER TARGET and QUARTER ISOCENTER leaves (Varian HDMLC only):
+\begin{enumerate}
+\item In QUARTER TARGET leaves, the bottom of the support rail is allowed to extend to the left of the
+leaf tip ({\tt wbs} $>$ {\tt wg} + {\tt wtip}).  This is similar to the exception for HALF TARGET leaves (see above).
+\item In QUARTER TARGET leaves, the top of the support rail can extend past the right edge
+of the leaf ({\tt wts} $>$ {\tt wbs}).  This is also similar to the exception for HALF TARGET leaves (see above).
+\end{enumerate}
+
+In addition, in the past there has been some doubt interpreting the manufacturer's specifications for the relative Z-positions
+of the tongue ({\tt zt}) and groove ({\tt zg}) of QUARTER ISOCENTER leaves, with one interpretation consistent with the
+cross-section shown in Figure~\ref{synchdmlc_fig} ({\tt i.e.}, {\tt zg} $<$ {\tt zt}) and another indicating
+that {\tt zg} $>$ {\tt zt}.  Ojala's work has shown that the latter interpretation is correct, and so we have implemented
+an input exception for QUARTER ISOCENTER leaves allowing {\tt zg} $>$ {\tt zt}.
+
+Each of the exceptions above will generate a warning message on input making clear that the leaf cross-section now differs
+from that shown in this manual.
+
+\index{SYNCHDMLC!{\tt ORIENT}=2 and 3}
+More recent comparisons between simulated and measured dose results using the Varian
+MLC120 and HDMLC collimators (Ojala, 2022) have revealed a mismatch between the BEAMnrc coordinate system and
+that used in the manufacturer specifications for these MLCs.  While the BEAMnrc coordinate system is right-handed, that used by in the manufacturer specifications is left-handed.  As a result, for the definitions of positive
+and negative leaf banks in BEAMnrc-space to
+be consistent with specifications, leaf cross-sections must be flipped about the Z-axis and leaf ordering
+must be reversed.  This is best pictured by considering the X cross-section view shown in Figure~\ref{synchdmlc_fig}
+with the X-axis replaced by the -X-axis.  In order to preserve leaf opening sequences, however,
+we must then ``flip'' the
+leaf opening coordinates so that the opening coordinates formerly applied to leaf i are now applied to leaf
+{\tt TOT\_LEAF} - i + 1, where {\tt TOT\_LEAF} is the total number of leaves in the bank.
+These transformations are done automatically if
+the user sets {\tt ORIENT=2} (for leaves opening in X-direction) or {\tt ORIENT=3} (for leaves opening in Y-direction).
 
 An example of a file specifying dynamic leaf settings for SYNCHDMLC
 is included with the distribution.  This file is {\tt \$OMEGA\_HOME/beamnrc/CMs/sample\_synchdmlc.sequence}.

From 5e0b12234d93029d715a8c977a35888dac6a9fd7 Mon Sep 17 00:00:00 2001
From: Frederic Tessier <ftessier@gmail.com>
Date: Thu, 30 Jun 2022 18:12:36 -0400
Subject: [PATCH 14/14] Remove EOL whitespace in updated synchdmlc files

---
 .../src/pirs509a-beamnrc/pirs509a-beamnrc.tex |  2 +-
 .../omega/beamnrc/CMs/SYNCHDMLC_cm.mortran    | 32 +++++++++----------
 .../beamnrc/CMs/SYNCHDMLC_macros.mortran      | 14 ++++----
 .../omega/progs/gui/beamnrc/synchdmlc.tcl     | 14 ++++----
 4 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex b/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex
index dbc365e78..ea3afe440 100644
--- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex
+++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex
@@ -8555,7 +8555,7 @@ \subsubsection{SYNCHDMLC}
 The default cross-sections for each leaf type are shown in Figure~\ref{synchdmlc_fig}.  The width of
 each vertical region is specified as back projected to {\tt ZMIN}.  Thus, for any width, $w_i$,
 the user inputs the value, $w_i\times\left(\frac{{\tt ZMIN}}{Z_i}\right)$, where $Z_i$ is the value of Z
-where $w_i$ is defined.  For example, for any leaf type, to define the groove width, $wg$, 
+where $w_i$ is defined.  For example, for any leaf type, to define the groove width, $wg$,
 the user would input $wg\times\left(\frac{{\tt ZMIN}}{zg}\right)$.
 
 Similar to DYNVMLC and SYNCVMLC, leaf ends can be straight, focused ({\tt ENDTYPE}=1) or cylindrical
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
index 4418208af..28d4a1c9a 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_cm.mortran
@@ -495,17 +495,17 @@
 "I>
 "I>   Repeat 14 until coordinates of all leaves are defined once.  Leaves
 "I>   are numbered 1,2,...TOT_LEAF_$SYNCHDMLC, where numbering goes from leaf
-"I>   1 to leaf TOT_LEAF_$SYNCHDMLC. Convention is -ve to +ve 
-"I>   (ORIENT_$SYNCHDMLC=0,2) or +ve to -ve (ORIENT_$SYNCHDMLC=1,3) 
+"I>   1 to leaf TOT_LEAF_$SYNCHDMLC. Convention is -ve to +ve
+"I>   (ORIENT_$SYNCHDMLC=0,2) or +ve to -ve (ORIENT_$SYNCHDMLC=1,3)
 "I>
 "I>  14a  NEG_$SYNCHDMLC, POS_$SYNCHDMLC, NUM_$SYNCHDMLC (2F15.5,I5)
 "I>
-"I>    NEG_$SYNCHDMLC:   Min. Y (ORIENT_$SYNCHDMLC=0,2) or X 
-"I>                   (ORIENT_$SYNCHDMLC=1,3) of front opening in leaf I (ie 
-"I>                   the opening at ZMIN_$SYNCHDMLC) if ENDTYPE=1, or of 
+"I>    NEG_$SYNCHDMLC:   Min. Y (ORIENT_$SYNCHDMLC=0,2) or X
+"I>                   (ORIENT_$SYNCHDMLC=1,3) of front opening in leaf I (ie
+"I>                   the opening at ZMIN_$SYNCHDMLC) if ENDTYPE=1, or of
 "I>                   rounded end of leaf I if ENDTYPE=0.
-"I>    POS_$SYNCHDMLC:   Max. Y (ORIENT_$SYNCHDMLC=0,2) or X 
-"I>                   (ORIENT_$SYNCHDMLC=1,3) of front opening in leaf I if 
+"I>    POS_$SYNCHDMLC:   Max. Y (ORIENT_$SYNCHDMLC=0,2) or X
+"I>                   (ORIENT_$SYNCHDMLC=1,3) of front opening in leaf I if
 "I>                   ENDTYPE=1, or of rounded end of leaf I if ENDTYPE=0.
 "I>    NUM_$SYNCHDMLC:   Apply NEG_$SYNCHDMLC and POS_$SYNCHDMLC to leaves
 "I>                   I,...,I+NUM_$SYNCHDMLC-1.  Defaults to 1 if set <=0.
@@ -709,7 +709,7 @@
 "V>{p1} the value to compare with ustep
 "V> if {p1}+1.0e-5 < ustep shift it, otherwise set it to ustep
 "V> Note: if above condition failed, this used to leave {p1}
-"V> unshifted, which led to transport errors 
+"V> unshifted, which led to transport errors
 ;
 REPLACE {$GEO_SHIFT_1_(#)} WITH {
   ;IF({P1}~=0.00 ) [
@@ -1084,13 +1084,13 @@ DOUBLE PRECISION   XYL(2), XYFL(2), ZFL, UVL(2), XoN, XoP, Zo, TEMP1, TEMP2,
 IF(ORIENT_$SYNCHDMLC=0)[
     XYL(1)=X(NP); XYL(2)=Y(NP);UVL(1)=U(NP);UVL(2)=V(NP);
 ]
-ELSEIF(ORIENT_$SYNCHDMLC=1)[ 
+ELSEIF(ORIENT_$SYNCHDMLC=1)[
     XYL(1)=Y(NP); XYL(2)=X(NP);UVL(1)=V(NP);UVL(2)=U(NP);
 ]
 ELSEIF(ORIENT_$SYNCHDMLC=2)[
     XYL(1)=-X(NP); XYL(2)=Y(NP);UVL(1)=-U(NP);UVL(2)=V(NP);
 ]
-ELSEIF(ORIENT_$SYNCHDMLC=3)[ 
+ELSEIF(ORIENT_$SYNCHDMLC=3)[
     XYL(1)=-Y(NP); XYL(2)=X(NP);UVL(1)=-V(NP);UVL(2)=U(NP);
 ]
 IF (IDIR=1) [
@@ -2705,7 +2705,7 @@ IF(MODE_$SYNCHDMLC=1|MODE_$SYNCHDMLC=2)["dynamic or step-and-shoot leaf inputs"
          LEAFPOS_$SYNCHDMLC((TOT_LEAF_$SYNCHDMLC-K+1)+
                       (I-1)*TOT_LEAF_$SYNCHDMLC) = tmp_coord;
        ]
-     ]   
+     ]
   ]
   CLOSE(UNIT=mlc_unit);
 
@@ -2777,7 +2777,7 @@ IF(ORIENT_$SYNCHDMLC>=2)[
     LEAFA_$SYNCHDMLC(I) = LEAFA_$SYNCHDMLC(TOT_LEAF_$SYNCHDMLC-I+1);
     LEAFA_$SYNCHDMLC(TOT_LEAF_$SYNCHDMLC-I+1) = tmp_coord;
   ]
-] 
+]
 
 IF(ENDTYPE_$SYNCHDMLC=1)[
 DO I=1, TOT_LEAF_$SYNCHDMLC [
@@ -3709,8 +3709,8 @@ IF(LEAFIS~=0) [
 				   "target leaf"
     IF(LEAFIS~=TOT_LEAF_$SYNCHDMLC & ((((NY=5|NY=6) & (NZ=7|NZ=8|NZ=9)) &
        XYL1>SURPARA1_$SYNCHDMLC(LEAFIS+1,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1))) |
-      (I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1 & 
-       NY=6 & NZ>1 & 
+      (I_LEAF_ALT_DEF_$SYNCHDMLC(LEAFTYPE_$SYNCHDMLC(LEAFIS),1,6)=1 &
+       NY=6 & NZ>1 &
        XYL1>SURPARA1_$SYNCHDMLC(LEAFIS+1,3)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1))))) [
           LEAFIS=LEAFIS+1;
           TEMP1=SURPARA1_$SYNCHDMLC(LEAFIS,1)*(Z(NP)-ZFOCUS_$SYNCHDMLC(1));
@@ -3800,9 +3800,9 @@ IF(LEAFIS~=0) [
                 ]
            ];
          ]
-         ELSEIF(LEAFIS ~=1 & NY<=2 & 
+         ELSEIF(LEAFIS ~=1 & NY<=2 &
            ((LEAFTYPE_$SYNCHDMLC(LEAFIS) = 3 & NZ<=3) |
-            (LEAFTYPE_$SYNCHDMLC(LEAFIS) = 5 & NZ<=4)))[ 
+            (LEAFTYPE_$SYNCHDMLC(LEAFIS) = 5 & NZ<=4)))[
            "here we are in an isocenter leaf
            "check if particle is in region of previous leaf"
            IF(XYL1<SURPARA1_$SYNCHDMLC(LEAFIS-1,7)*
diff --git a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
index a3345da38..c9452d9b8 100644
--- a/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
+++ b/HEN_HOUSE/omega/beamnrc/CMs/SYNCHDMLC_macros.mortran
@@ -824,7 +824,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
     ELSEIF(NY=3)[
       IF(NZ=1)[ZLHS=1; ZRHS=2;]
       ELSEIF(NZ<=5)[ZLHS=2; ZRHS=6;]
-      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]  
+      ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
       ELSEIF(NZ=7)[ZLHS=7; ZRHS=8;]
       ELSEIF(NZ=8)[ZLHS=8; ZRHS=9;]
       ELSE[ZLHS=9; ZRHS=10;]
@@ -856,7 +856,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
          ELSEIF(NZ=6)[ZLHS=6; ZRHS=7;]
          ELSE[ZLHS=7; ZRHS=10;]
       ]
-    ] 
+    ]
 ]
 };
 
@@ -1231,7 +1231,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
            ]
         ]
      ]
-   ] 
+   ]
    ELSE[
      "Isocenter Quarter"
      IF(NZ=1) [
@@ -1290,7 +1290,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
         ]
      ]
      ELSEIF(NZ=4)[
-        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[ 
+        IF(I_LEAF_ALT_DEF_$SYNCHDMLC(5,2,4)=1)[
            IF(NY<=5)[
               LHS=1; J=LEAFIS;
               RHS=6; I=LEAFIS;
@@ -1309,7 +1309,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
                  IF(ZFL>ZREG_$SYNCHDMLC(J,7))[
                    LHS = 5;
                  ]
-                 ELSE[ 
+                 ELSE[
                    LHS = 7;
                  ]
               ]
@@ -1319,7 +1319,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
               LHS=3; J=LEAFIS;
               RHS=7; I=LEAFIS;
            ]
-        ] 
+        ]
      ]
      ELSEIF(NZ<=7)[
         LHS=1; J=LEAFIS;
@@ -1346,7 +1346,7 @@ IF(LEAFTYPE_$SYNCHDMLC(LEAFIS)=2 | LEAFTYPE_$SYNCHDMLC(LEAFIS)=4) [
            ELSE[
               LHS=3; J=LEAFIS;
               RHS=7; I=LEAFIS;
-           ]    
+           ]
         ]
         ELSE[
            IF(NY=1)[
diff --git a/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl b/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
index 9f2dede13..d0e19c92e 100644
--- a/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
+++ b/HEN_HOUSE/omega/progs/gui/beamnrc/synchdmlc.tcl
@@ -2369,7 +2369,7 @@ proc draw_SYNCHDMLC { id } {
 NOTE: This is a dynamic or step-and-shoot delivery, with leaf opening\
       coordinates defined in a file.  Leaf opening coordinates are shown for the\
       first field defined in this file."\
-            -font $helvfont -width 300 
+            -font $helvfont -width 300
     } else {
     .synchdmlc$id.show.frm.can create text 160 160 -text "xz\
             cross-section shows only those leaves that\
@@ -2379,7 +2379,7 @@ NOTE: This is a dynamic or step-and-shoot delivery, with leaf opening\
             is shown.  The xy view is at a plane at Z=ZMIN\
             (straight leaf ends) or Z=ZMIN+ZTHICK/2 (cylindrical\
             leaf ends)."\
-	    -font $helvfont -width 300 
+	    -font $helvfont -width 300
     }
 
     set xscale [expr $width/double(abs($xrange(1)-$xrange(0)))]
@@ -2673,7 +2673,7 @@ proc add_SYNCHDMLC_xy {id xscale yscale xmin ymin l m parent_w} {
 
             set a [expr ($neg($i)-$xmin)*$xscale+$l]
             if {$cmval($id,2,0)==3} {
-               set b [expr (-$lstart-$ymin)*$yscale+$m] 
+               set b [expr (-$lstart-$ymin)*$yscale+$m]
             } else {
                set b [expr ($lstart-$ymin)*$yscale+$m]
             }
@@ -3247,8 +3247,8 @@ proc add_SYNCHDMLC_sides {id yscale zscale ymin zmin zmax l m parent_w} {
         for {set i 1} {$i <= $nleaf($id)/2} {incr i} {
           set tmp_coord $neg($i)
           set neg($i) $neg([expr $nleaf($id)-$i+1])
-          set neg([expr $nleaf($id)-$i+1]) $tmp_coord 
-          set tmp_coord $pos($i)     
+          set neg([expr $nleaf($id)-$i+1]) $tmp_coord
+          set tmp_coord $pos($i)
           set pos($i) $pos([expr $nleaf($id)-$i+1])
           set pos([expr $nleaf($id)-$i+1]) $tmp_coord
         }
@@ -3629,7 +3629,7 @@ proc add_SYNCHDMLC_sides {id yscale zscale ymin zmin zmax l m parent_w} {
             if {$cmval($id,2,0)==2 || $cmval($id,2,0)==3} {
                 set y($j) [expr -1*$y($j)]
             }
-            
+
             # set y and z scale and relative position
             set y($j) [expr ($y($j)-$ymin)*$yscale+$l]
             set z($j) [expr ($z($j)-$zmin)*$zscale+$m]
@@ -3744,7 +3744,7 @@ are automaticaly "flipped," so that opening coordinates for leaf i are instead\
 applied to leaf N-i+1, where N is the total no. of leaves.  See the BEAMnrc\
 Manual for more details.}
     help_dialog $w.help "Help" $text info 0 OK
-} 
+}
 
 proc help_screwdist { w } {