Revision: 18528
http://sourceforge.net/p/jmol/code/18528
Author: hansonr
Date: 2013-08-08 14:09:49 +0000 (Thu, 08 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.08"
code: incommensurate crystal work
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/util/Measure.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/Tuple3f.java
trunk/Jmol/src/org/jmol/util/V3.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-08 11:06:19 UTC (rev 18527)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-08 14:09:49 UTC (rev 18528)
@@ -32,7 +32,6 @@
import org.jmol.util.Logger;
import org.jmol.util.Matrix3f;
-import org.jmol.util.Matrix4f;
import org.jmol.util.Modulation;
import org.jmol.util.P3;
import org.jmol.util.SB;
@@ -42,6 +41,11 @@
/**
* abstract modulation class for CIF and Jana
+ *
+ * Current status:
+ *
+ * -- d=1 only
+ * -- only simple atom displacement, no occupation crenel, no sawtooth
*
* @author Bob Hanson hans...@stolaf.edu 8/7/13
*
@@ -54,12 +58,15 @@
protected boolean modAverage;
protected boolean checkSpecial = true;
protected int modDim;
- //protected boolean modCentered;
- //protected boolean modOffset;
protected boolean incommensurate;
- private Map<String, P3> htModulation;
protected Atom[] atoms;
+ private JmolList<float[]> lattvecs;
+ private V3 modT;
+ private Matrix3f rot;
+ private Map<String, P3> htModulation;
+ private Map<String, JmolList<Modulation>> htAtomMods;
+
protected void initializeMod() throws Exception {
modAxes = getFilter("MODAXES=");
modVib = checkFilterKey("MODVIB");
@@ -67,16 +74,8 @@
checkSpecial = !checkFilterKey("NOSPECIAL");
atomSetCollection.setCheckSpecial(checkSpecial);
allowRotations = !checkFilterKey("NOSYM");
- //modOffset = !checkFilterKey("NOMODOFFSET");
- //modCentered = !checkFilterKey("NOMODCENT");
- //if (!modCentered) {
- // if (doCentralize && filter.indexOf("CENTER") ==
filter.lastIndexOf("CENTER"))
- // doCentralize = false;
- // appendLoadNote("CIF reader not using delta to recenter modulation.");
- // }
}
- private JmolList<float[]> lattvecs;
protected void addLatticeVector(String data) {
if (lattvecs == null)
@@ -124,8 +123,13 @@
map = htModulation;
map.put(id, pt);
Logger.info("Adding " + id + " " + pt);
- if (id.charAt(0) == 'W' || id.charAt(0) == 'F')
- appendLoadNote("Wave vector " + id +" = " + pt);
+ if (id.charAt(0) == 'W' || id.charAt(0) == 'F') {
+ appendLoadNote("Wave vector " + id +" = " + pt);
+ if (id.equals("W_1")) {
+ modT = V3.newV(pt);
+ modT.normalize();
+ }
+ }
}
/**
@@ -185,12 +189,19 @@
if (key.charAt(2) == 'S') {
// TODO -- sawtooth, so now what?
} else {
+ if (htAtomMods == null)
+ htAtomMods = new Hashtable<String, JmolList<Modulation>>();
P3 coefs = e.getValue();
String label = key.substring(key.indexOf(";") + 1);
int n = key.charAt(2) - '0';
key = "F_" + n;
- P3 q = htModulation.get(key);
- addAtomModulation(label, q, axis, coefs, n);
+ //TODO -- THIS IS WRONG. n is just a label. It will break in 2D
+ // but I don't know to determine "n" any other way in a CIF
file.
+ P3 nq = htModulation.get(key);
+ JmolList<Modulation> list = htAtomMods.get(label);
+ if (list == null)
+ htAtomMods.put(label, list = new JmolList<Modulation>());
+ list.addLast(new Modulation(nq, n, axis, coefs));
haveAtomMods = true;
}
break;
@@ -200,94 +211,53 @@
return;
atoms = atomSetCollection.getAtoms();
symmetry = atomSetCollection.getSymmetry();
- mtemp3 = new Matrix3f();
- //mtemp3i = new Matrix3f();
- ptemp = new P3();
- offset = new V3();
- //opTrans = new V3();
- // step one: All base atoms.
- int n = atomSetCollection.baseSymmetryAtomCount;
- P3[] pts = new P3[n];
+ rot = new Matrix3f();
SB sb = new SB();
- for (int i = 0; i < n; i++) {
- pts[i] = P3.newP(atoms[i]);
- modulateAtom(i, modVib, null, sb);
- }
- // step two: All other atoms.
- int n1 = atomSetCollection.getAtomCount();
- for (int i = n1; --i >= n;)
- modulateAtom(i, modVib, pts[atoms[i].atomSite], sb);
+ int n = atomSetCollection.getAtomCount();
+ for (int i = 0; i < n; i++)
+ modulateAtom(atoms[i], sb);
atomSetCollection.setAtomSetAtomProperty("modt", sb.toString(), -1);
}
- private Matrix3f mtemp3;
- private P3 ptemp;
- private V3 offset;
- private Map<String, JmolList<Modulation>> htAtomMods;
-
- public void addAtomModulation(String label, P3 q, char axis, P3 coefs, int
n) {
- if (htAtomMods == null)
- htAtomMods = new Hashtable<String, JmolList<Modulation>>();
- JmolList<Modulation> list = htAtomMods.get(label);
- if (list == null)
- htAtomMods.put(label, list = new JmolList<Modulation>());
- list.addLast(new Modulation(q, n, axis, coefs));
- }
-
- private V3 qNorm;
-
/**
- * Modulation generally involves u(x4) = u(q.r + t). Here we arbitrarily set
t
- * = 0, making this u(x4) = u(q.r). For symmetry- related atoms, including
- * lattice shifts, we need to apply this as:
- *
- * u'(x4') = R'u(q.r + q.s')
- *
- * where s' is the sum of all shifts, and R' is the product of all rotations.
- * We already track symmetry, so we should be able to figure this out.
- *
- * @param i
- * @param modvib
- * @param pt0
+ * Modulation generally involves x4 = q.r + t. Here we arbitrarily set t =
0,
+ * but t could be a FILTER option MODT=n. There would need to be one t per
dimension.
+ * The displacement will be set as the atom vibration vector.
+ *
+ * @param a
* @param sb
*/
- public void modulateAtom(int i, boolean modvib, P3 pt0, SB sb) {
- Atom a = atoms[i];
- a.vib = new V3();
+ public void modulateAtom(Atom a, SB sb) {
JmolList<Modulation> list = htAtomMods.get(a.atomName);
- if (list == null || symmetry == null)
+ if (list == null || symmetry == null || a.bsSymmetry == null)
return;
- // if (pt0 != null) {
int iop = a.bsSymmetry.nextSetBit(0);
if (iop < 0)
iop = 0;
- Matrix4f m = symmetry.getSpaceGroupOperation(iop);
- m.getRotationScale(mtemp3);
- //mtemp3i.invertM(mtemp3);
- //opTrans = symmetry.getOriginalTranslation(iop);
- //m.get(opTrans);
float epsilon = symmetry.getModParam(iop, 0);
float delta = symmetry.getModParam(iop, 1);
- ptemp.setT(a);
- symmetry.unitize(ptemp);
- offset.sub2(a, ptemp);
- //System.out.println("=========CIF i=" + i + " " + a.atomName + " " + a);
- //System.out.println("op=" + (iop + 1) + " "
- // + symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de="
- //+ delta + " a=" + a);
- qNorm = V3.newV(list.get(0).getWaveVector());
- qNorm.normalize();
- Modulation.modulateAtom(ptemp, offset, list, epsilon, delta, a.vib);
- System.out.println("a.vib(abc)=" + a.vib);
- mtemp3.transform(a.vib);
- sb.append((int) (qNorm.dot(offset) * 1.01f) + "\n");
- if (!modvib) {
+ symmetry.getSpaceGroupOperation(iop).getRotationScale(rot);
+ a.vib = new V3();
+ Modulation.modulateAtom(list, a, epsilon, delta, rot, a.vib);
+ //System.out.println("=========MR i=" + i + " " + a.atomName + " " + a);
+ //System.out.println("op=" + (iop + 1) + " " +
symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de=" + delta);
+ //System.out.println("a.vib(abc)=" + a.vib);
+
+ // set property_modT to be Math.floor (q.r/|q|) -- really only for d=1
+
+ float t = modT.dot(a);
+ if (Math.abs(t - (int) t) > 0.001f)
+ t = (int) Math.floor(t);
+ sb.append(((int) t) + "\n");
+
+ // displace the atom if not filter "MODVIB"
+ if (!modVib) {
a.add(a.vib);
a.vib.scale(-1);
}
symmetry.toCartesian(a.vib, true);
//System.out.println("a.vib(xyz)=" + a.vib);
- //if (i == 98 || i == 99)
- //System.out.println("CIFTEST");
+
}
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-08 11:06:19 UTC (rev 18527)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-08 14:09:49 UTC (rev 18528)
@@ -197,8 +197,10 @@
private int qicount;
private void qi() {
- addModulation(null, "F_" + (++qicount), P3.new3(parseFloat(),
- parseFloat(), parseFloat()));
+ P3 pt = P3.new3(parseFloat(), parseFloat(), parseFloat());
+ if (qicount == 0)
+ addModulation(null, "W_1", pt);
+ addModulation(null, "F_" + (++qicount), pt);
}
private void ndim() {
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-08 11:06:19 UTC (rev 18527)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-08 14:09:49 UTC (rev 18528)
@@ -473,7 +473,6 @@
atomSetNumbers = new int[16];
atomSymbolicMap = new Hashtable<Object, Integer>();
bonds = null;
- cartesians = null;
connectLast = null;
currentAtomSetIndex = -1;
latticeCells = null;
@@ -1139,7 +1138,7 @@
: symmetryRange < 0 ? 1 // checking against symop=1555 set; just a box
: 1 // not checking
);
- cartesians = new P3[cartesianCount];
+ P3[] cartesians = new P3[cartesianCount];
for (int i = 0; i < noSymmetryCount; i++)
atoms[i + iAtomFirst].bsSymmetry = BSUtil.newBitSet(operationCount
* (nCells + 1));
@@ -1197,7 +1196,7 @@
rmaxz += absRange;
}
cell555Count = pt = symmetryAddAtoms(iAtomFirst, noSymmetryCount, 0,
- 0, 0, 0, pt, iCell * operationCount);
+ 0, 0, 0, pt, iCell * operationCount, cartesians);
}
if (checkRange111) {
rminx -= absRange;
@@ -1217,7 +1216,7 @@
iCell++;
if (tx != 0 || ty != 0 || tz != 0)
pt = symmetryAddAtoms(iAtomFirst, noSymmetryCount, tx, ty, tz,
- cell555Count, pt, iCell * operationCount);
+ cell555Count, pt, iCell * operationCount, cartesians);
}
if (iCell * noSymmetryCount == atomCount - iAtomFirst)
appendAtomProperties(iCell);
@@ -1256,7 +1255,6 @@
setAtomSetAuxiliaryInfo("symmetryCount", Integer.valueOf(operationCount));
}
- private P3[] cartesians;
private int bondCount0;
private int bondIndex0;
private boolean applySymmetryToBonds = false;
@@ -1272,7 +1270,7 @@
private int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX,
int transY, int transZ, int baseCount, int pt,
- int iCellOpPt) throws Exception {
+ int iCellOpPt, P3[] cartesians) throws
Exception {
boolean isBaseCell = (baseCount == 0);
boolean addBonds = (bondCount0 > bondIndex0 && applySymmetryToBonds);
int[] atomMap = (addBonds ? new int[noSymmetryCount] : null);
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-08 11:06:19 UTC
(rev 18527)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-08 14:09:49 UTC
(rev 18528)
@@ -11,7 +11,6 @@
import org.jmol.util.Matrix4f;
import org.jmol.util.P3;
import org.jmol.util.P3i;
-import org.jmol.util.P4;
import org.jmol.util.Tensor;
import org.jmol.util.Tuple3f;
import org.jmol.util.V3;
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-08-08 11:06:19 UTC (rev
18527)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-08-08 14:09:49 UTC (rev
18528)
@@ -199,7 +199,7 @@
}
public static void getPlaneThroughPoint(P3 pt, V3 normal, P4 plane) {
- plane.set(normal.x, normal.y, normal.z, -normal.dot(V3.newV(pt)));
+ plane.set(normal.x, normal.y, normal.z, -normal.dot(pt));
}
public static float distanceToPlane(P4 plane, P3 pt) {
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-08 11:06:19 UTC
(rev 18527)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-08 14:09:49 UTC
(rev 18528)
@@ -14,25 +14,28 @@
private double ccos;
private double csin;
- private V3 q; // wave vector
+ private V3 nq; // wave vector
private int n; // power
+ private char axis;
+
public V3 getWaveVector() {
- return q;
+ return nq;
}
- private char axis;
-
+
/**
- * Each atomic modulation involves a fractional coordinate wave vector q,
- * a modulation axis (x, y, or, z), and specified coefficients for cos and
sin.
+ * Each atomic modulation involves a fractional coordinate wave vector q, a
+ * Fourier power n, a modulation axis (x, y, or, z), and specified
+ * coefficients for cos and sin.
*
- * @param q
+ *
+ * @param nq
* @param n
* @param axis
* @param coefs
*/
- public Modulation(P3 q, int n, char axis, P3 coefs) {
- this.q = V3.newV(q);
+ public Modulation(P3 nq, int n, char axis, P3 coefs) {
+ this.nq = V3.newV(nq);
//this.q.scale(1f/n); leave this nq.
this.n = n;
this.axis = axis;
@@ -41,34 +44,62 @@
}
/**
- * Starting with fractional coordinates, determine the overall modulation
vector.
+ * Starting with fractional coordinates, determine the overall modulation
displacement.
*
- * @param pt fractional xyz
- * @param offset
- * @param mods a given atom's modulations
- * @param epsilon TODO
- * @param delta TODO
- * @param vecMod will be filled;
+ * @param mods a given atom's modulations
+ * @param r fractional xyz
+ * @param epsilon as in x4´ = epsilon x4 + delta
+ * @param delta as in x4´ = epsilon x4 + delta
+ * @param rot symmetry rotation to be applied
+ * @param d displacement return
*/
- public static void modulateAtom(P3 pt, V3 offset, JmolList<Modulation> mods,
float epsilon, float delta, V3 vecMod) {
- V3 r = V3.newV(pt);
- if (offset != null && offset.length() > 0.0001f)
- r.add(offset);
- vecMod.set(0, 0, 0);
+ public static void modulateAtom(JmolList<Modulation> mods, Tuple3f r, float
epsilon, float delta, Matrix3f rot, V3 d) {
+ d.set(0, 0, 0);
for (int i = mods.size(); --i >= 0;)
- mods.get(i).addTo(r, epsilon, delta, vecMod);
+ mods.get(i).apply(r, epsilon, delta, d);
+ rot.transform(d);
}
/**
+ *
+ * In general, we have:
+ *
+ * u_axis(x) = sum[A1 cos(theta) + B1 sin(theta)]
+ *
+ * where axis is x, y, or z, and theta = 2n pi x
+ *
+ * However, for symmetry-related atoms, we need to do a 4D transformation,
+ * not just a 3D one. We need to operate on x first BEFORE applying u(x):
+ *
+ * u(x4') = Ru(x4)
+ *
+ * where we need to express x4 in terms of a "transformed" x4', because
+ * x4' is for our rotated point.
+ *
+ * x4' = epsilon x4 + delta
+ *
+ * where epsilon = +/-1, so
+ *
+ * x4 = epsilon (x4' - delta)
+ *
+ * More generally, we might have something like:
+ *
+ * x4' = x5 + 1/2; x5' = x4 - 1/2
+ *
+ * Will have to work on that later!
+ *
+ *
* @param r
* @param epsilon
* @param delta
* @param vecMod
*
*/
- private void addTo(V3 r, float epsilon, float delta, V3 vecMod) {
- // pt[axis]' = pt[axis] + A1 cos(2pi * q.r) + B1 sin(2pi * q.r)
- double theta = TWOPI * (epsilon * q.dot(r) + n * delta);
+ private void apply(Tuple3f r, float epsilon, float delta, V3 vecMod) {
+
+ // TODO: must be adapted for d > 1 modulation
+
+ double theta = TWOPI * (epsilon * (nq.dot(r) + n * delta));
double v = 0;
if (ccos != 0)
v += ccos * Math.cos(theta);
@@ -85,6 +116,7 @@
vecMod.z += v;
break;
}
- System.out.println("MOD q=" + q + " r=" + r + " axis=" + axis + " theta="
+ theta + " ccos=" + ccos + " csin=" + csin + " delta=" + delta + " v=" + v);
+ //System.out.println("MOD q=" + nq + " r=" + r + " axis=" + axis + "
theta=" + theta + " ccos=" + ccos + " csin=" + csin + " delta=" + delta + " v="
+ v);
}
+
}
Modified: trunk/Jmol/src/org/jmol/util/Tuple3f.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tuple3f.java 2013-08-08 11:06:19 UTC (rev
18527)
+++ trunk/Jmol/src/org/jmol/util/Tuple3f.java 2013-08-08 14:09:49 UTC (rev
18528)
@@ -188,6 +188,17 @@
y = s * y + t1.y;
z = s * z + t1.z;
}
+
+ /**
+ * Was in Vector3f; more useful here, though.
+ *
+ * @param v
+ * the other vector
+ * @return this.dot.v
+ */
+ public final float dot(Tuple3f v) {
+ return x * v.x + y * v.y + z * v.z;
+ }
/**
* Returns a hash number based on the data values in this object. Two
Modified: trunk/Jmol/src/org/jmol/util/V3.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/V3.java 2013-08-08 11:06:19 UTC (rev
18527)
+++ trunk/Jmol/src/org/jmol/util/V3.java 2013-08-08 14:09:49 UTC (rev
18528)
@@ -80,17 +80,6 @@
}
/**
- * Computes the dot product of the this vector and vector v.
- *
- * @param v
- * the other vector
- * @return this.dot.v
- */
- public final float dot(V3 v) {
- return x * v.x + y * v.y + z * v.z;
- }
-
- /**
* Normalizes this vector in place.
*/
public final void normalize() {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-08 11:06:19 UTC
(rev 18527)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-08 14:09:49 UTC
(rev 18528)
@@ -11,8 +11,10 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.07"
+___JmolVersion="13.3.4_dev_2013.08.08"
+code: incommensurate crystal work
+
bug fix: shapeInfo not reporting visibility of isosurface
code: pdb, cif readers separated into separate packages; p2n, pqr readers with
pdb now
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