special group upgrade - final update prior to 16.3.0

src/org/jmol/modelkit/ModelKit.java

@@ -4227,40 +4227,49 @@ private String getDrawAxes(String id, String swidth) {
         "originPoint", 0);
     P3d[] axisPoints = (P3d[]) vwr.shm.getShapePropertyIndex(JC.SHAPE_AXES,
         "axisPoints", 0);
+
     String s = "";
     String[] colors = new String[] { "red", "green", "blue" };
     int nDim = sym.getDimensionality();
-    int per = sym.getPeriodicity();
-    boolean shiftA = (per == 0x4 && nDim == 3); // rod group
-    boolean shiftB = (shiftA || per == 0x1 && nDim == 2); // rod or frieze
-    boolean shiftC = (per == 0x1 && nDim == 2 || per == 0x3 && nDim == 3); // frieze or layer
+    int periodicity = sym.getPeriodicity();
+    boolean shiftA = ((periodicity & 0x1) == 0); // rod (ab)c, rod b(ca)
+    boolean shiftB = ((periodicity & 0x2) == 0); // frieze a(b), rod (ab)c, rod a(bc)
+    boolean shiftC = ((periodicity & 0x4) == 0); // plane ab, layer ab(c), frieze a(b), rod a(bc), rod b(ca)
     P3d[] pts = axisPoints;
     P3d[] opts = null;
     if (shiftA || shiftB || shiftC) {
       pts = new P3d[] { new P3d(), new P3d(), new P3d() };
       opts = new P3d[] { new P3d(), new P3d(), new P3d() };
+
       if (shiftA) {
         opts[0].sub2(origin, axisPoints[0]);
         opts[0].scale(0.5d);
         pts[0].sub2(origin, opts[0]);
+      } else if (nDim == 3) {
+        pts[0] = axisPoints[0];
       }
       if (shiftB) {
         opts[1].sub2(origin, axisPoints[1]);
         opts[1].scale(0.5d);
         pts[1].sub2(origin, opts[1]);
+      } else if (nDim == 3) {
+        pts[1] = axisPoints[1];
       }
       if (shiftC) {
         opts[2].sub2(origin, axisPoints[2]);
         opts[2].scale(0.5d);
         pts[2].sub2(origin, opts[2]);
+      } else if (nDim == 3) {
+        pts[2] = axisPoints[2];
       }
     }
     for (int i = 0, a = JC.AXIS_A; i < 3; i++, a++) {
       s += "\ndraw ID " + PT.esc(id + "_axis_" + JC.axisLabels[a]) + " "
           + swidth + " line "
           + (opts == null 
           || i == 0 && !shiftA
-          || i == 1 && !shiftB ? origin : opts[i])
+          || i == 1 && !shiftB 
+          || i == 2 && !shiftC ? origin : opts[i])
           + " " + pts[i] + " color " + colors[i];
     }
     return s;

src/org/jmol/render/CageRenderer.java

@@ -51,7 +51,7 @@ abstract class CageRenderer extends FontLineShapeRenderer {
   protected BS bsPeriod; 
   protected P3d pt = new P3d();
 
-  protected P3d[] vvert, vvertA;
+  protected P3d[] vvert;
 
   /**
    * Uccage only
@@ -165,9 +165,9 @@ protected void setBSPeriod() {}
   protected boolean shiftA, shiftB, shiftC, shifting;
 
   protected void setShifts() {
-    shiftA = (nDims == 3 && periodicity == 0x4); // rod
-    shiftB = shiftA || (nDims == 2 && periodicity == 0x1); // rod or frieze
-    shiftC = (nDims == 3 && periodicity == 0x3); // layer
+    shiftA = ((periodicity & 0x1) == 0); // rod (ab)c, rod (a)b(c)
+    shiftB = ((periodicity & 0x2) == 0); // frieze a(b), rod (ab)c, rod a(bc)
+    shiftC = ((periodicity & 0x4) == 0); // plane ab, layer ab(c), frieze a(b), rod (a)b(c)
     shifting = (shiftA || shiftB || shiftC);
   }
 }

src/org/jmol/render/UccageRenderer.java

@@ -47,6 +47,8 @@ public class UccageRenderer extends CageRenderer {
 
   private final P3d[] verticesT = new P3d[8];
 
+  private P3d[] vvertA;
+
   @Override
   protected void initRenderer() {
     for (int i = 8; --i >= 0; ) 
@@ -58,6 +60,7 @@ protected void initRenderer() {
   @Override
   protected void setPeriodicity(P3d[] vertices, double scale) {
     setShifts();
+    P3d p0;
     if (shifting) {
       // layer group shifts axes and unit cell down 50%
       if (vvert == null) { //v[1] is c, v[2,3] is b, v[4,5] is a 
@@ -66,9 +69,25 @@ protected void setPeriodicity(P3d[] vertices, double scale) {
           vvert[i] = new P3d();
         }
       }
-      P3d p0;
-      P3d p1;
-      if (shiftA) {
+
+      if (shiftC && periodicity == 0x1) {
+        if (vvertA == null) { //v[1] is c, v[2,3] is b, v[4,5] is a 
+          vvertA = new P3d[8];
+          for (int i = 8; --i >= 0;) {
+            vvertA[i] = new P3d();
+          }
+        }
+        p0 = P3d.newP(vertices[1]);
+        p0.sub(vertices[0]);
+        p0.scale(0.5);
+        for (int i = 8; --i >= 0;) {
+          pt.setT(vertices[i]);
+          pt.sub(vertices[0]);
+          pt.scaleAdd2(scale, pt, vertices[0]);
+          pt.sub(p0);
+          tm.transformPtNoClip(pt, vvertA[i]);
+        }
+      } else if (shiftA) {
         if (vvertA == null) { //v[1] is c, v[2,3] is b, v[4,5] is a 
           vvertA = new P3d[8];
           for (int i = 8; --i >= 0;) {
@@ -156,6 +175,7 @@ private void render1(int mad10) {
     Axes axes = (Axes) vwr.shm.getShape(JC.SHAPE_AXES);
     if (axes != null && vwr.areAxesTainted())
       axes.reinitShape();
+
     P3d[] axisPoints = (axes == null
         || vwr.getObjectMad10(StateManager.OBJ_AXIS1) == 0 
         || axes.axisXY.z != 0 && (axes.axes2 == null || axes.axes2.length() == 3)
@@ -213,12 +233,14 @@ private void render1(int mad10) {
     renderInfo();
   }
 
+
   @Override
   protected void renderCageLine(int i, int edge0, int edge1, int d, boolean drawTicks) {
     P3d p1;
     P3d p2;
     if (bsVerticals != null && bsVerticals.get(i)) {
-      if (vvertA != null && (i == 4 || i == 8)) {
+      if (vvertA != null && (i == 4 || i == 8 || i == 12 || i == 16 
+          || i == 0 && periodicity != 0x2)) {
         p1 = vvertA[edge0];
         p2 = vvertA[edge1];
       } else {
@@ -246,9 +268,10 @@ protected void setBSPeriod() {
     case 0x7:
       return;
     case 0x3:
+      // plane, layer ab(c)
       bs = (bsPeriod == null ? (bsPeriod = new BS()) : bsPeriod);
       if (nDims == 3) {
-        // verticals
+        // verticals for four layer c-posts, all set the same direction
        bs.set(0);
        bs.set(10);
        bs.set(16);
@@ -267,9 +290,9 @@ protected void setBSPeriod() {
     case 0x4:
       // rod
       bs = (bsPeriod == null ? (bsPeriod = new BS()) : bsPeriod);
-      bs.set(2);
-      bs.set(4);
+      bs.set(2); // these offset in b
       bs.set(6);
+      bs.set(4); // these two offset in a
       bs.set(8);
       if (bsVerticals == null) {
         bsVerticals = new BS();
@@ -279,17 +302,34 @@ protected void setBSPeriod() {
       bs.set(0);
       break;
     case 0x1:
+      // rod-a, frieze
       bs = (bsPeriod == null ? (bsPeriod = new BS()) : bsPeriod);
-      if (nDims == 2) {
-        // frieze
-        bs.set(2);
-        bs.set(18);
-        if (bsVerticals == null) {
-          bsVerticals = new BS();
-        }
-        BSUtil.copy2(bs, bsVerticals);
-        bs.set(4);
+      bs.set(2);
+      bs.set(18);
+      if (nDims == 3) {
+        //rod-a
+        bs.set(0);
+        bs.set(16);
+      }
+      if (bsVerticals == null) {
+        bsVerticals = new BS();
       }
+      BSUtil.copy2(bs, bsVerticals);
+      bs.set(4);
+      break;
+    case 0x2:
+      // rod-b
+      bs = (bsPeriod == null ? (bsPeriod = new BS()) : bsPeriod);
+      bs.set(0); 
+      bs.set(4);
+      bs.set(12); //"A" shift 
+      bs.set(10);
+      //bs.set(16);
+      if (bsVerticals == null) {
+        bsVerticals = new BS();
+      }
+      BSUtil.copy2(bs, bsVerticals);
+      bs.set(2);      
       break;
     }
   }

src/org/jmol/scriptext/IsoExt.java

@@ -467,10 +467,13 @@ private void draw() throws ScriptException {
             int[][] faces;
             switch (uc.getPeriodicity()) {
             case 0x1:
-              faces = Triangulator.friezeEdge;
+              faces = Triangulator.edgeA;
+              break;
+            case 0x2: 
+              faces = Triangulator.edgeB;
               break;
             case 0x4:
-              faces = Triangulator.rodEdge;
+              faces = Triangulator.edgeC;
               break;
             case 0x3:
               faces = Triangulator.abFace;

src/org/jmol/shape/Axes.java

@@ -183,8 +183,10 @@ public P3d getAxisPoint(int i, boolean actual, P3d ptTemp) {
   public Object getProperty(String property, int index) {
     if (property == "originPoint")
       return originPoint;
-    if (property == "axisPoints")
+    if (property == "axisPoints") {
+      setPoints(vwr.g.axesMode);
       return axisPoints;
+    }
     if (property == "axesTypeXY")
       return (axisXY.z == 0 ? Boolean.FALSE : Boolean.TRUE);
     if (property == "origin")

src/org/jmol/symmetry/CLEG.java

@@ -46,7 +46,7 @@
  * org.jmol.modelkit.Modelkit to process CLEG strings.
  * 
  * This code access multiple methods in Jmol, so it is not independently
- * implemented outside that context. But it encapsulates the essentals of 
+ * implemented outside that context. But it enca  psulates the essentals of 
  * 
  */
 final public class CLEG {
@@ -259,11 +259,6 @@ public ClegNode(ClegData data, int index, String name) {
         if (name == null)
           return;
         this.index = index;
-        int pt = isProbableClegSetting(name);
-        if (pt > 0) {
-          myIta = name.substring(0, pt);
-          myTrm = name.substring(pt + 1);
-        }
         // sets this.name
         init(data, name);
       }
@@ -304,7 +299,11 @@ private String checkSpecial(String name) {
     }
 
     private void init(ClegData data, String name) {
-      int pt;
+      int pt = isProbableClegSetting(name);
+      if (pt > 0) {
+        myIta = name.substring(0, pt);
+        myTrm = name.substring(pt + 1);
+      }
       if (name.equals(TYPE_REFERENCE)) {
         isThisModelCalc = true;
       }
@@ -374,7 +373,7 @@ private void init(ClegData data, String name) {
           myIta = (String) data.sym.getSpaceGroupInfoObj("itaNumber", specialPrefix + name,
               false, false);
         if (myTrm == null)
-          myTrm = (String) data.sym.getSpaceGroupInfoObj("itaTransform", name,
+          myTrm = (String) data.sym.getSpaceGroupInfoObj("itaTransform", specialPrefix + name,
               false, false);
 
         if (hallSymbol != null && hallTrm != null) {
@@ -1292,7 +1291,7 @@ && isTransformOnly(tokens[index + 1])
     }
     // ready to roll....
     boolean isP1 = (token.equalsIgnoreCase("P1") || token.equals("ITA/1.1"));
-
+    // TODO: P1 is only for space groups need isP1(token) or node.isP1
     try {
       BS bsAtoms;
       boolean noAtoms;