Revision: 20817
http://sourceforge.net/p/jmol/code/20817
Author: hansonr
Date: 2015-10-11 15:41:18 +0000 (Sun, 11 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.10.11"
new feature: unitcell() function
-- returns unitcell as an array in the form [origin, va, vb, vc]
-- first parameter is optional unitcell itself; absence uses current model's
unit cell.
-- optional last parameter: scale
-- signatures:
unitcell() // uses current unit cell
unitcell(uc) // copies unit cell
unitcell(uc, "reciprocal") // reciprocal lattice for specied unit cell
unitcell("reciprocal") // reciprocal lattice for current model's unit cell
unitcell(ucconv, "primitive","BCC"|"FCC") // convert primitive to
conventional
unitcell("primitive","BCC"|"FCC")
unitcell(ucprim, "conventional","BCC"|"FCC") // convert primitive to
conventional
unitcell("conventional","BCC"|"FCC")
unitcell(origin, [va, vb, vc])
unitcell(origin, pta, ptb, ptc)
new feature: point(unitcell, {i, j, k})
-- unitcell is an array of the form [origin, va, vb, vc]
-- {i j k} is a point in the unitcell
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -38,7 +38,7 @@
public boolean createSpaceGroup(int desiredSpaceGroupIndex,
String name,
- Object object);
+ Object data);
public String fcoord(T3 p);
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -8626,7 +8626,8 @@
float angstroms = floatParameterRange(index, 0, 2);
return (Float.isNaN(angstroms) ? Integer.MAX_VALUE : (int)
Math.floor(angstroms * 1000 * 2));
}
- errorStr(ERROR_booleanOrWhateverExpected, "\"DOTTED\"");
+ if (!chk)
+ errorStr(ERROR_booleanOrWhateverExpected, "\"DOTTED\"");
return 0;
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -227,7 +227,7 @@
// unitcell(uc)
// unitcell(uc, "reciprocal")
// unitcell(ucconv, "primitive","BCC"|"FCC")
- // unitcell(ucprim, "conventional","BCC"|"FCC"|...?) //not yet implemented
+ // unitcell(ucprim, "conventional","BCC"|"FCC")
// unitcell(origin, [va, vb, vc])
// unitcell(origin, pta, ptb, ptc)
int lastParam = args.length - 1;
@@ -280,27 +280,13 @@
}
}
}
- String op = (ptParam <= lastParam ? args[ptParam++].asString() : null);
- if ("reciprocal".equalsIgnoreCase(op)) {
+ String op = (ptParam <= lastParam ? args[ptParam].asString() : null);
+ boolean isPrimitive = "primitive".equalsIgnoreCase(op);
+ if (isPrimitive || "conventional".equalsIgnoreCase(op)) {
+ if (!SimpleUnitCell.transformCubic(isPrimitive,
args[++ptParam].asString(), ucnew))
+ return false;
+ } else if ("reciprocal".equalsIgnoreCase(op)) {
ucnew = SimpleUnitCell.getReciprocal(ucnew);
- } else if ("primitive".equalsIgnoreCase(op)) {
- String type = args[ptParam].asString();
- float[] f = null;
- if (type.equalsIgnoreCase("BCC"))
- f = new float[] { .5f, .5f, -.5f, -.5f, .5f, .5f, .5f, -.5f, .5f };
- else if (type.equalsIgnoreCase("FCC"))
- f = new float[] { .5f, .5f, 0, 0, .5f, .5f, .5f, 0, .5f };
- if (f == null)
- return false;
- P3[] b = new P3[3];
- for (int i = 0, p = 0; i < 3; i++) {
- b[i] = new P3();
- for (int j = 1; j < 4; j++)
- b[i].scaleAdd2(f[p++], ucnew[j], b[i]);
- }
- for (int i = 0; i < 3; i++)
- ucnew[i + 1] = b[i];
-
}
if (scale != 1)
for (int i = 1; i < 4; i++)
@@ -2268,6 +2254,12 @@
}
private boolean evaluatePoint(ScriptMathProcessor mp, SV[] args) {
+ // point(1.3) // rounds toward 0
+ // point(pt, true) // to screen coord
+ // point(pt, false) // from screen coord
+ // point(x, y, z)
+ // point(x, y, z, w)
+
switch (args.length) {
default:
return false;
@@ -2281,15 +2273,33 @@
return (pt instanceof P3 ? mp.addXPt((P3) pt) : mp.addXStr("" + pt));
case 2:
// to/from screen coordinates
- P3 pt3 = SV.ptValue(args[0]);
- if (pt3 == null)
- return false;
- if (args[1].tok == T.off) {
+ P3 pt3;
+ switch (args[1].tok) {
+ case T.off:
+ if ((pt3 = SV.ptValue(args[0])) == null)
+ return false;
// these are screen coordinates
vwr.tm.unTransformPoint(pt3, pt3);
- } else {
+ break;
+ case T.on:
+ if ((pt3 = SV.ptValue(args[0])) == null)
+ return false;
// this is TO screen coordinates
vwr.tm.transformPt3f(pt3, pt3);
+ break;
+ case T.point3f:
+ // unitcell transform
+ Lst<SV> sv = args[0].getList();
+ if (sv == null || sv.size() != 4)
+ return false;
+ P3 pt1 = SV.ptValue(args[1]);
+ pt3 = P3.newP(SV.ptValue(sv.get(0)));
+ pt3.scaleAdd2(pt1.x, SV.ptValue(sv.get(1)), pt3);
+ pt3.scaleAdd2(pt1.y, SV.ptValue(sv.get(2)), pt3);
+ pt3.scaleAdd2(pt1.z, SV.ptValue(sv.get(3)), pt3);
+ break;
+ default:
+ return false;
}
return mp.addXPt(pt3);
case 3:
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -116,9 +116,13 @@
boolean isBilbao;
- static SpaceGroup getNull(boolean doInit) {
+ static SpaceGroup getNull(boolean doInit, boolean doNormalize, boolean
doFinalize) {
getSpaceGroups();
- return new SpaceGroup(null, doInit);
+ SpaceGroup sg = new SpaceGroup(null, doInit);
+ sg.doNormalize = doNormalize;
+ if (doFinalize)
+ sg.setFinalOperations(null, 0, 0, false);
+ return sg;
}
private SpaceGroup(String cifLine, boolean doInit) {
@@ -128,11 +132,6 @@
buildSpaceGroup(cifLine);
}
- SpaceGroup set(boolean doNormalize) {
- this.doNormalize = doNormalize;
- return this;
- }
-
private void init(boolean addXYZ) {
xyzList = new Hashtable<String, Integer>();
operationCount = 0;
@@ -159,6 +158,12 @@
return sg;
}
+ /**
+ *
+ * @param name
+ * @param data Lst<SymmetryOperation> or Lst<M4>
+ * @return a new SpaceGroup if successful or null
+ */
private static SpaceGroup createSGFromList(String name, Lst<?> data) {
// try unconventional Hall symbol
SpaceGroup sg = new SpaceGroup("0;--;--;--", true);
@@ -352,7 +357,7 @@
/**
*
- * @return valid space group or null
+ * @return a known space group or null
*/
SpaceGroup getDerivedSpaceGroup() {
if (index >= 0 && index < SG.length
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -130,7 +130,7 @@
@Override
public void setSpaceGroup(boolean doNormalize) {
if (spaceGroup == null)
- spaceGroup = (SpaceGroup.getNull(true)).set(doNormalize);
+ spaceGroup = SpaceGroup.getNull(true, doNormalize, false);
}
@Override
@@ -160,11 +160,18 @@
spaceGroup = (SpaceGroup) symmetry.getSpaceGroup();
}
+ /**
+ *
+ * @param desiredSpaceGroupIndex
+ * @param name
+ * @param data a Lst<SymmetryOperation> or Lst<M4>
+ * @return true if a known space group
+ */
@Override
public boolean createSpaceGroup(int desiredSpaceGroupIndex, String name,
- Object object) {
+ Object data) {
spaceGroup = SpaceGroup.createSpaceGroup(desiredSpaceGroupIndex, name,
- object);
+ data);
if (spaceGroup != null && Logger.debugging)
Logger.debug("using generated space group " + spaceGroup.dumpInfo(null));
return spaceGroup != null;
@@ -321,8 +328,11 @@
@Override
public M4[] getSymmetryOperations() {
- return symmetryInfo == null ? spaceGroup.finalOperations
- : symmetryInfo.symmetryOperations;
+ if (symmetryInfo != null)
+ return symmetryInfo.symmetryOperations;
+ if (spaceGroup == null)
+ spaceGroup = SpaceGroup.getNull(true, false, true);
+ return spaceGroup.finalOperations;
}
@Override
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -1007,7 +1007,7 @@
} else {
isStandard = !isBio;
if (isBio)
- sym.spaceGroup = (SpaceGroup.getNull(false)).set(false);
+ sym.spaceGroup = SpaceGroup.getNull(false, false, false);
else
sym.setSpaceGroup(false);
strOperations = "\n" + ops.length + " symmetry operations:";
Modified: trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -400,4 +400,31 @@
}
return rabc;
}
+
+ /**
+ *
+ * @param isPrimitive or assumed conventional
+ * @param type FCC or BCC
+ * @param uc either [origin, va, vb, vc] or just [va, vb, vc]
+ * @return true if successful
+ */
+ public static boolean transformCubic(boolean isPrimitive, String type,
+ T3[] uc) {
+ int offset = uc.length - 3;
+ float[] f = (type.equalsIgnoreCase("BCC") ? (isPrimitive ? new float[] {
.5f, .5f, -.5f, -.5f, .5f, .5f, .5f, -.5f, .5f }
+ : new float[] { 1, 0, 1, 1, 1, 0, 0, 1, 1 })
+ : type.equalsIgnoreCase("FCC") ? (isPrimitive ? new float[] { .5f, .5f, 0,
0, .5f, .5f, .5f, 0, .5f }
+ : new float[] { 1, -1, 1, 1, 1, -1, -1, 1, 1 }) : null);
+ if (f == null)
+ return false;
+ P3[] b = new P3[3];
+ for (int i = 0, p = 0; i < 3; i++) {
+ b[i] = new P3();
+ for (int j = offset; j < 3 + offset; j++)
+ b[i].scaleAdd2(f[p++], uc[j], b[i]);
+ }
+ for (int i = 0; i < 3; i++)
+ uc[i + offset] = b[i];
+ return true;
+ }
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-10 16:49:59 UTC
(rev 20816)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-11 15:41:18 UTC
(rev 20817)
@@ -63,17 +63,28 @@
-Jmol.___JmolVersion="14.3.16_2015.10.09"
+Jmol.___JmolVersion="14.3.16_2015.10.11"
new feature: unitcell() function
- // optional last parameter: scale
- // unitcell()
- // unitcell(uc)
- // unitcell(uc, "reciprocal")
- // unitcell(ucconv, "primitive","BCC"|"FCC")
- // unitcell(ucprim, "conventional","BCC"|"FCC"|...?) //not yet implemented
- // unitcell(origin, [va, vb, vc])
- // unitcell(origin, pta, ptb, ptc)
+ -- returns unitcell as an array in the form [origin, va, vb, vc]
+ -- first parameter is optional unitcell itself; absence uses current model's
unit cell.
+ -- optional last parameter: scale
+ -- signatures:
+ unitcell() // uses current unit cell
+ unitcell(uc) // copies unit cell
+ unitcell(uc, "reciprocal") // reciprocal lattice for specied unit cell
+ unitcell("reciprocal") // reciprocal lattice for current model's unit cell
+ unitcell(ucconv, "primitive","BCC"|"FCC") // convert primitive to
conventional
+ unitcell("primitive","BCC"|"FCC")
+ unitcell(ucprim, "conventional","BCC"|"FCC") // convert primitive to
conventional
+ unitcell("conventional","BCC"|"FCC")
+
+ unitcell(origin, [va, vb, vc])
+ unitcell(origin, pta, ptb, ptc)
+
+new feature: point(unitcell, {i, j, k})
+ -- unitcell is an array of the form [origin, va, vb, vc]
+ -- {i j k} is a point in the unitcell
JmolVersion="14.3.16_2015.10.09"
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