Revision: 18596
http://sourceforge.net/p/jmol/code/18596
Author: hansonr
Date: 2013-08-19 21:13:46 +0000 (Mon, 19 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.19"
code: Incommensurate modulated structure CIF and M50/40 file loading validation
-- includes d=1 and d=2
-- Fourier, sawtooth, crenel
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/modelset/LabelToken.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/thread/MoveToThread.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-19
04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-19
21:13:46 UTC (rev 18596)
@@ -2356,12 +2356,12 @@
/**
* creates entries in htModulation with a key of the form:
*
- * type_id_axis;atomLabel
+ * type_id_axis;atomLabel
*
- * where type = W|F|D|O (wave vector, Fourier index,
- * displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0),
- * sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant --
occupancy);
- * and ;atomLabel is only for D and O.
+ * where type = W|F|D|O (wave vector, Fourier index, displacement,
occupancy);
+ * id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) =
+ * 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for
D
+ * and O.
*
* @throws Exception
*/
@@ -2384,7 +2384,8 @@
case FA_ID:
case FO_ID:
case FU_ID:
- fid = "#=P" +
Character.toUpperCase(modulationFields[tok].charAt(11)) + "_" + field;
+ fid = "#=P" + Character.toUpperCase(modulationFields[tok].charAt(11))
+ + "_" + field;
pt.x = pt.y = pt.z = 0;
break;
case WV_ID:
@@ -2407,28 +2408,27 @@
case FWV_DISP_ID:
case FWV_OCC_ID:
case FWV_U_ID:
- id = "" + Character.toUpperCase(modulationFields[tok].charAt(11))
+ "_";
+ id = "" + Character.toUpperCase(modulationFields[tok].charAt(11))
+ + "_";
break;
case FP_DISP_ID:
case FP_OCC_ID:
case FP_U_ID:
- id = "P" + Character.toUpperCase(modulationFields[tok].charAt(11))
+ "_";
+ id = "P" + Character.toUpperCase(modulationFields[tok].charAt(11))
+ + "_";
}
id += field;
break;
case DISP_SPEC_LABEL:
id = "D_S";
- atomLabel = field;
- axis = "0";
- break;
+ //$FALL-THROUGH$
case OCC_SPECIAL_LABEL:
- id = "O_0";
+ if (id == null)
+ id = "O_0";
axis = "0";
//$FALL-THROUGH$
case FWV_DISP_LABEL:
case FWV_OCC_LABEL:
- atomLabel = field;
- break;
case FWV_U_LABEL:
atomLabel = field;
break;
@@ -2497,7 +2497,9 @@
w = parseFloatStr(field);
break;
}
- if (ignore || Float.isNaN(pt.x + pt.y + pt.z) || pt.x == 0 && pt.y ==
0 && pt.z == 0 || id == null)
+ if (ignore || Float.isNaN(pt.x + pt.y + pt.z) || pt.x == 0 && pt.y == 0
+ && pt.z == 0 || id == null || atomLabel != null
+ && rejectAtomName(atomLabel))
continue;
switch (id.charAt(0)) {
case 'W':
@@ -2527,8 +2529,7 @@
}
}
}
-
-
+
private void addMod(String id, String fid, P3 params) {
if (fid != null)
id += fid;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-19 04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-19 21:13:46 UTC (rev 18596)
@@ -41,7 +41,6 @@
import org.jmol.util.P3;
import org.jmol.util.SB;
import org.jmol.util.Tensor;
-import org.jmol.util.TextFormat;
import org.jmol.util.V3;
@@ -82,7 +81,6 @@
private V3 q1Norm;
private Map<String, P3> htModulation;
private Map<String, JmolList<Modulation>> htAtomMods;
- private int modT;
protected Map<String, Object> htSubsystems;
@@ -110,7 +108,7 @@
modDim = 0;
modAverage = true;
} else {
- appendLoadNote("Modulation dimension = " + modDim + (modDim > 1 ? " NOT
IMPLEMENTED YET " : ""));
+ appendLoadNote("Modulation dimension = " + modDim);
htModulation = new Hashtable<String, P3>();
}
incommensurate = (modDim > 0);
@@ -143,6 +141,8 @@
pt.x = pt.y = 0;
break;
}
+ if (pt.x == 0 && pt.y == 0 && pt.z == 0)
+ return;
if (map == null)
map = htModulation;
id += "@"
@@ -179,7 +179,7 @@
if (htModulation.containsKey("X_" + suffix))
return;
htModulation.put("X_" +suffix, new P3());
- q123 = new P3[modDim];
+ q123 = new P3[3];
qlen = new double[modDim];
for (int i = 0; i < modDim; i++) {
q123[i] = getMod("W_" + (i + 1));
@@ -189,8 +189,11 @@
}
qlen[i] = q123[i].length();
}
+ for (int i = modDim; i < 3; i++)
+ q123[i] = new P3();
q1 = q123[0];
q1Norm = V3.new3(q1.x == 0 ? 0 : 1, q1.y == 0 ? 0 : 1, q1.z == 0 ? 0 : 1);
+ P3 qlist100 = P3.new3(1, 0, 0);
P3 pt;
int n = atomSetCollection.getAtomCount();
Map<String, P3> map = new Hashtable<String, P3>();
@@ -225,23 +228,13 @@
// convert JAVA Fourier descriptions to standard descriptions
if (key.indexOf("_q_") >= 0) {
// d > 1 -- already set
- appendLoadNote("Wave vector " + key + "(n=" + (modDim == 1 ?
Integer.valueOf((int)pt.x) : pt)+")");
- P3 pf = new P3();
- if (pt.x != 0)
- pf.scaleAdd2(pt.x, getMod("W_1"), pf);
- if (pt.y != 0)
- pf.scaleAdd2(pt.y, getMod("W_2"), pf);
- if (pt.z != 0)
- pf.scaleAdd2(pt.z, getMod("W_3"), pf);
- key = TextFormat.simpleReplace(key, "_q_", "");
- addModulation(map, key, pf, iModel);
- appendLoadNote("Wave vector " + key + "(n=" + (modDim == 1 ?
Integer.valueOf((int)pt.x) : pt)+") = " + pf);
+ appendLoadNote("Wave vector " + key + "=" + pt);
} else {
int fn = (int) (pt.dot(q1) / q1.dot(q1) * 1.01f);
String k2 = key + "_q_";
if (!htModulation.containsKey(k2 + suffix)) {
addModulation(map, k2, P3.new3(fn, 0, 0), iModel);
- appendLoadNote("Wave vector " + key + " = " + pt + " n = " + fn);
+ //appendLoadNote("Wave vector " + key + " = " + pt + " n = " + fn);
}
}
break;
@@ -282,10 +275,13 @@
htAtomMods = new Hashtable<String, JmolList<Modulation>>();
int fn = (id == 'S' ? 0 : parseIntStr(key.substring(2)));
if (fn == 0) {
- addAtomModulation(atomName, axis, type, 1, params, utens, new int[]
{1});
+ addAtomModulation(atomName, axis, type, params, utens, qlist100);
} else {
- P3 qlist = getMod("F_" + fn + "_q_");
- addAtomModulation(atomName, axis, type, 1, params, utens, new int[]
{ (int) qlist.x, (int) qlist.y, (int) qlist.z } );
+ P3 qlist = getMod("F_" + fn + "_q_");
+ if (qlist == null) {
+ Logger.error("Missing qlist for F_" + fn);
+ }
+ addAtomModulation(atomName, axis, type, params, utens, qlist);
}
haveAtomMods = true;
break;
@@ -296,7 +292,6 @@
atoms = atomSetCollection.getAtoms();
symmetry = atomSetCollection.getSymmetry();
iopLast = -1;
- f4 = new float[4];
SB sb = new SB();
for (int i = atomSetCollection.getLastAtomSetAtomIndex(); i < n; i++)
modulateAtom(atoms[i], sb);
@@ -305,11 +300,11 @@
}
private void addAtomModulation(String atomName, char axis, int type,
- int fn, P3 params, String utens, int[]
qcoefs) {
+ P3 params, String utens, P3 qcoefs) {
JmolList<Modulation> list = htAtomMods.get(atomName);
if (list == null)
htAtomMods.put(atomName, list = new JmolList<Modulation>());
- list.addLast(new Modulation(axis, type, fn, params, utens, qcoefs));
+ list.addLast(new Modulation(axis, type, params, utens, qcoefs));
}
private String checkKey(String key) {
@@ -318,10 +313,8 @@
}
private int iopLast = -1;
- private Matrix3f rot;
- private float[] f4;
- float[] epsilon = new float[3];
- float[] delta = new float[3];
+ private Matrix3f gammaE;
+ private Matrix4f gammaIS;
/**
* The displacement will be set as the atom vibration vector; the string
@@ -352,37 +345,23 @@
if (iop != iopLast) {
//System.out.println("mdim=" + mdim + " op=" + (iop + 1) + " " +
symmetry.getSpaceGroupOperation(iop) + " " + symmetry.getSpaceGroupXyz(iop,
false));
iopLast = iop;
- rot = new Matrix3f();
- for (int i = 0; i < modDim; i++) {
- symmetry.getMod456Row(iop, i, f4);
- epsilon[i] = 0;
- if (modSelected > 0) {
- if (i == modSelected - 1)
- epsilon[i] = f4[i] * modSelected;
- continue;
- }
- for (int j = 0; j < modDim; j++)
- epsilon[i] += f4[j] * (j + 1);
- delta[i] = f4[3] - modT;
- }
+ gammaE = new Matrix3f();
+ symmetry.getSpaceGroupOperation(iop).getRotationScale(gammaE);
+ gammaIS = symmetry.getOperationGammaIS(iop);
}
- symmetry.getSpaceGroupOperation(iop).getRotationScale(rot);
if (Logger.debugging) {
Logger.debug("setModulation iop = " + iop + " "
+ symmetry.getSpaceGroupXyz(iop, false) + " " + a.bsSymmetry);
}
- ModulationSet ms = new ModulationSet(a.index + " " + a.atomName, list,
- modDim, q123, qlen);
+
+ float vocc0 = a.occupancy / 100f;
+ ModulationSet ms = new ModulationSet(a.index + " " + a.atomName,
+ P3.newP(a), vocc0, modDim, list, gammaE, gammaIS, q123, qlen);
a.vib = ms;
- ms.epsilon = epsilon;
- ms.delta = delta;
- ms.r = P3.newP(a);
- ms.vocc0 = a.occupancy / 100f;
- ms.rot = rot;
ms.calculate();
if (!Float.isNaN(ms.vocc)) {
- if (modVib && !Float.isNaN(ms.vocc0)) {
- a.occupancy = (int) ((ms.vocc0 + ms.vocc) * 100);
+ if (modVib && !Float.isNaN(vocc0)) {
+ a.occupancy = (int) ((vocc0 + ms.vocc) * 100);
} else if (ms.vocc < 0.5f) {
a.occupancy = 0;
if (bsAtoms != null)
@@ -391,7 +370,7 @@
a.occupancy = 100;
}
}
- if (ms.htValues != null) {
+ if (ms.htUij != null) {
// Uiso or Uij. We add the displacements, create the tensor, then rotate
it,
// replacing the tensor already present for that atom.
if (Logger.debuggingHigh) {
@@ -399,7 +378,7 @@
Logger.debug("setModulation tensor="
+ Escape.e(a.tensors.get(0).getInfo("all")));
}
- for (Entry<String, Float> e : ms.htValues.entrySet())
+ for (Entry<String, Float> e : ms.htUij.entrySet())
addUStr(a, e.getKey(), e.getValue().floatValue());
if (a.tensors != null)
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2013-08-19
04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2013-08-19
21:13:46 UTC (rev 18596)
@@ -201,7 +201,7 @@
atomTypePt0 = Integer.parseInt(tokens[0]) - 1;
int pt = tokens[1].indexOf("=");
if (pt >= 0) {
- filterAtomTypeStr = tokens[1].substring(pt + 1).toUpperCase();
+ setFilterAtomTypeStr(tokens[1].substring(pt + 1).toUpperCase());
} else {
pt = tokens[1].length();
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-19 04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-19 21:13:46 UTC (rev 18596)
@@ -139,9 +139,20 @@
private void qi() {
P3 pt = P3.new3(parseFloat(), parseFloat(), parseFloat());
- if (qicount == 0)
- addModulation(null, "W_1", pt, -1);
- addModulation(null, "F_" + (++qicount), pt, -1);
+ addModulation(null, "W_" + (++qicount), pt, -1);
+ pt = new P3();
+ switch (qicount) {
+ case 1:
+ pt.x = 1;
+ break;
+ case 2:
+ pt.y = 1;
+ break;
+ case 3:
+ pt.z = 1;
+ break;
+ }
+ addModulation(null, "F_" + qicount + "_q_", pt, -1);
}
private void lattvec(String data) throws Exception {
float[] a;
@@ -211,18 +222,21 @@
ipt = id.lastIndexOf("/");
id = id.substring(ipt + 1);
BufferedReader r = JmolBinary.getBufferedReaderForString((String)
viewer.getLigandModel(id, name, "_file", "----"));
- if (readM40Floats(r).startsWith("command")) {
- discardLinesUntilContains("end");
- readM40Floats(r);
- }
+ if (readM40Floats(r).startsWith("command"))
+ readM40WaveVectors(r);
int nAtoms = (int) floats[0];
for (int i = 0; i < nAtoms; i++) {
while (readM40Floats(r).length() == 0 || line.charAt(0) == ' '
|| line.charAt(0) == '-') {
}
- Atom atom = atomSetCollection.addNewAtom();
+
+
+ Atom atom = new Atom();
atom.atomName = line.substring(0, 9).trim();
+ if (!filterAtom(atom, 0))
+ continue;
setAtomCoordXYZ(atom, floats[3], floats[4], floats[5]);
+ atomSetCollection.addAtom(atom);
if (!incommensurate)
continue;
String label = ";" + atom.atomName;
@@ -305,6 +319,26 @@
r.close();
}
+ private void readM40WaveVectors(BufferedReader r) throws Exception {
+ while (!readM40Floats(r).contains("end"))
+ if (line.startsWith("wave")) {
+ String[] tokens = getTokens();
+ P3 pt = new P3();
+ switch (modDim) {
+ case 3:
+ pt.z = parseFloatStr(tokens[4]);
+ //$FALL-THROUGH$
+ case 2:
+ pt.y = parseFloatStr(tokens[3]);
+ //$FALL-THROUGH$
+ case 1:
+ pt.x = parseFloatStr(tokens[2]);
+ }
+ addModulation(null, "F_" + parseIntStr(tokens[1]) + "_q_", pt, -1);
+ }
+ readM40Floats(r);
+ }
+
private void addSinCos(int j, String key, String label, BufferedReader r)
throws Exception {
checkFourier(j);
readM40Floats(r);
@@ -323,10 +357,11 @@
}
private void checkFourier(int j) {
- if (j > 0 && getModulationVector("F_" + (j + 1)) == null) {
- P3 pt = P3.newP(getModulationVector("F_1"));
+ P3 pt;
+ if (j > 0 && getModulationVector("F_" + (j + 1) + "_q_") == null && (pt =
getModulationVector("F_1_q_")) != null) {
+ pt = P3.newP(pt);
pt.scale(j + 1);
- addModulation(null, "F_" + (j + 1), pt, -1);
+ addModulation(null, "F_" + (j + 1) + "_q_", pt, -1);
}
}
@@ -339,7 +374,8 @@
private String readM40Floats(BufferedReader r) throws Exception {
line = r.readLine();
- System.out.println(line);
+ if (Logger.debugging)
+ Logger.debug(line);
int ptLast = line.length() - 10;
for (int i = 0, pt = 0; i < 6 && pt <= ptLast; i++, pt += 9)
floats[i] = parseFloatStr(line.substring(pt, pt + 9));
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-08-19 04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-08-19 21:13:46 UTC (rev 18596)
@@ -790,7 +790,8 @@
private boolean filterChain;
private boolean filterAtomName;
private boolean filterAtomType;
- protected String filterAtomTypeStr;
+ private String filterAtomTypeStr;
+ private String filterAtomNameTerminator = ";";
private boolean filterElement;
protected boolean filterHetero;
private boolean filterEveryNth;
@@ -823,6 +824,12 @@
// Spartan: "INPUT", "ESPCHARGES"
//
+ protected void setFilterAtomTypeStr(String s) {
+ // PDB reader TYPE=...
+ filterAtomTypeStr = s;
+ filterAtomNameTerminator = "\0";
+ }
+
protected void setFilter(String filter0) {
if (filter0 == null) {
filter0 = (String) htParams.get("filter");
@@ -922,8 +929,7 @@
private boolean checkFilter(Atom atom, String f) {
return (!filterGroup3 || atom.group3 == null || !filterReject(f, "[",
atom.group3.toUpperCase() + "]"))
- && (!filterAtomName || atom.atomName == null || !filterReject(f, ".",
- atom.atomName.toUpperCase() + (filterAtomTypeStr == null ? ";" :
"\0")))
+ && (!filterAtomName || allowAtomName(atom.atomName, f))
&& (filterAtomTypeStr == null || atom.atomName == null
|| atom.atomName.toUpperCase().indexOf("\0" + filterAtomTypeStr)
>= 0)
&& (!filterElement || atom.elementSymbol == null || !filterReject(f,
"_",
@@ -936,6 +942,15 @@
atom.isHetero ? "HETATM" : "ATOM"));
}
+ protected boolean rejectAtomName(String name) {
+ return filterAtomName && !allowAtomName(name, filter);
+ }
+
+ private boolean allowAtomName(String atomName, String f) {
+ return (atomName == null || !filterReject(f, ".",
+ atomName.toUpperCase() + filterAtomNameTerminator));
+ }
+
protected boolean filterReject(String f, String code, String atomCode) {
return (f.indexOf(code) >= 0 && (f.indexOf("!" + code) >= 0 ? f
.indexOf(code + atomCode) >= 0 : f.indexOf(code + atomCode) < 0));
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -66,8 +66,6 @@
public Matrix4f getSpaceGroupOperation(int i);
- public void getMod456Row(int iop, int irow, float[] f4);
-
public String getSpaceGroupXyz(int i, boolean doNormalize);
public void newSpaceGroupPoint(int i, P3 atom1, P3 atom2,
@@ -178,5 +176,7 @@
public void addLatticeVectors(JmolList<float[]> lattvecs);
public boolean hasLatticeCentering();
+
+ public Matrix4f getOperationGammaIS(int iop);
}
Modified: trunk/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -342,6 +342,8 @@
private static int setToken(Viewer viewer, String strFormat, LabelToken lt,
int cch, int chAtom, Map<String, Object>
htValues) {
int ich = lt.pt + 1;
+ if (ich >= cch)
+ return ich;
char ch;
if (strFormat.charAt(ich) == '-') {
lt.alignLeft = true;
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -180,13 +180,6 @@
}
- public void getMod456Row(int iop, int rowPt, float[] f4) {
- spaceGroup.finalOperations[iop].getMod456Row(rowPt, f4);
- }
-
-
-
-
public String getSpaceGroupXyz(int i, boolean doNormalize) {
return spaceGroup.finalOperations[i].getXyz(doNormalize);
}
@@ -656,4 +649,11 @@
return spaceGroup.hasLatticeCentering;
}
+ public Matrix4f getOperationGammaIS(int iop) {
+ return spaceGroup.finalOperations[iop].gammaIS;
+ }
+
+
+
+
}
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-08-19
04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-08-19
21:13:46 UTC (rev 18596)
@@ -73,7 +73,7 @@
private String[] myLabels;
int modDim;
float[] rotTransMatrix;
- public Matrix4f mod456;
+ Matrix4f gammaIS;
/**
@@ -113,7 +113,7 @@
}
private void setMod456() {
- (mod456 = new Matrix4f()).setA(rotTransMatrix, 16);
+ (gammaIS = new Matrix4f()).setA(rotTransMatrix, 16);
}
void doFinalize() {
@@ -121,9 +121,9 @@
m13 /= 12;
m23 /= 12;
if (modDim > 0) {
- mod456.m03 /= 12;
- mod456.m13 /= 12;
- mod456.m23 /= 12;
+ gammaIS.m03 /= 12;
+ gammaIS.m13 /= 12;
+ gammaIS.m23 /= 12;
}
isFinalized = true;
}
@@ -266,7 +266,7 @@
setA(rotTransMatrix, 0);
if (rotTransMatrix.length == 32) {
rotTransMatrix[31] = 1;
- (mod456 = new Matrix4f()).setA(rotTransMatrix, 16);
+ (gammaIS = new Matrix4f()).setA(rotTransMatrix, 16);
}
isFinalized = true;
if (isReverse)
@@ -1315,8 +1315,4 @@
operation.m23 = ((int)operation.m23 + 12) % 12;
}
- public void getMod456Row(int rowPt, float[] f4) {
- mod456.getRow(rowPt, f4);
- }
-
}
Modified: trunk/Jmol/src/org/jmol/thread/MoveToThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/MoveToThread.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/thread/MoveToThread.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -233,7 +233,7 @@
}
private float getVal(Slider s) {
- return (s == null ? Float.MAX_VALUE : s.getVal(fStep));
+ return (s == null ? Float.NaN : s.getVal(fStep));
}
@Override
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -13,14 +13,13 @@
private static final double TWOPI = 2 * Math.PI;
- private int[] qCoefs;
+ private P3 qCoefs;
private double a1;
private double a2;
private double center;
private double left, right;
- private int fn; // power
private char axis;
private final int type;
@@ -40,17 +39,15 @@
*
* @param axis
* @param type
- * @param fn
* @param params
* @param utens TODO
* @param qCoefs
*/
- public Modulation(char axis, int type, int fn, P3 params, String utens,
int[] qCoefs) {
+ public Modulation(char axis, int type, P3 params, String utens, P3 qCoefs) {
if (Logger.debuggingHigh)
- Logger.debug("MOD create " + Escape.eAI(qCoefs) + " axis=" + axis + "
type=" + type + " fn=" + fn + " params=" + params + " utens=" + utens);
+ Logger.debug("MOD create " + Escape.eP(qCoefs) + " axis=" + axis + "
type=" + type + " params=" + params + " utens=" + utens);
this.axis = axis;
this.type = type;
- this.fn = fn;
this.utens = utens;
this.qCoefs = qCoefs;
switch (type) {
@@ -75,7 +72,7 @@
right -= 1;
if (left >= right && left - right < 0.01f)
left = right + 0.01f;
- a1 = 2 * params.z / width;
+ a1 = 2 * params.z / params.y;
break;
}
}
@@ -88,28 +85,64 @@
*
* where axis is x, y, or z, and theta = 2n pi x
*
- * @param i
+ * More generally, we have for a given rotation that is characterized by
+ *
+ * X {x4 x5 x6 ...}
+ *
+ * Gamma_E (R3 rotation)
+ *
+ * Gamma_I (X rotation)
+ *
+ * S_I (X translation)
+ *
+ * We allow here only up to x6, simply because we are using standard R3
+ * rotation objects Matrix3f, P3, V3.
+ *
+ * We desire:
+ *
+ * u'(X') = Gamma_E u(X)
+ *
+ * which is defined as [private communication, Vaclav Petricek]:
+ *
+ * u'(X') = Gamma_E sum[ U_c cos(2 pi (n m).Gamma_I^-1{X - S_I}) + U_s sin(2
+ * pi (n m).Gamma_I^-1{X - S_I}) ]
+ *
+ * where
+ *
+ * U_c and U_s are coefficients for cos and sin, respectively (will be a1 and
+ * a2 here)
+ *
+ * (n m) is an array of Fourier number coefficients, such as (1 0), (1 -1),
or
+ * (0 2)
+ *
+ * Offset here is only for d=1 case.
+ *
+ *
+ *
* @param ms
- * @param x4
+ * @param offset
*
+ *
*/
- void apply(int i, ModulationSet ms, double x4) {
+ void apply(ModulationSet ms, double offset) {
+ double x = qCoefs.dot(ms.x456) + qCoefs.x * offset;
double v = 0;
//if (type == TYPE_OCC_CRENEL)
//delta = 0;
-
+
switch (type) {
case TYPE_DISP_FOURIER:
case TYPE_OCC_FOURIER:
case TYPE_U_FOURIER:
- double theta = TWOPI * fn * x4;
+ double theta = TWOPI * x;
if (a1 != 0)
v += a1 * Math.cos(theta);
if (a2 != 0)
v += a2 * Math.sin(theta);
if (Logger.debuggingHigh)
- Logger.debug("MOD " + i + ":" + ms.id + " fn=" + fn + " " + " axis="
+ axis + " v=" + v + " ccos,csin=" + a1 + "," + a2 + " / theta=" + theta);
+ Logger.debug("MOD " + ms.id + " " + Escape.eP(qCoefs) + " axis=" + axis
+ + " v=" + v + " ccos,csin=" + a1 + "," + a2 + " / theta=" + theta);
break;
case TYPE_OCC_CRENEL:
@@ -119,8 +152,8 @@
// p(x4)=1 if x4 belongs to the interval [c-w/2,c+w/2]
// p(x4)=0 if x4 is outside the interval [c-w/2,c+w/2],
- x4 -= Math.floor(x4);
- ms.vocc = (range(x4) ? 1 : 0);
+ x -= Math.floor(x);
+ ms.vocc = (range(x) ? 1 : 0);
ms.vocc0 = Float.NaN; // don't add this in
//System.out.println("MOD " + ms.r + " " + ms.delta + " " + ms.epsilon
+ " " + ms.id + " " + ms.v + " l=" + left + " x=" + x4 + " r=" + right);
return;
@@ -140,8 +173,8 @@
// here we have set a1 = 2a_xyz/w
- x4 -= Math.floor(x4);
- if (!range(x4))
+ x -= Math.floor(x);
+ if (!range(x))
return;
// x < L < c
@@ -193,12 +226,12 @@
// |/
if (left > right) {
- if (x4 < left && left < center)
- x4 += 1;
- else if (x4 > right && right > center)
- x4 -= 1;
+ if (x < left && left < center)
+ x += 1;
+ else if (x > right && right > center)
+ x -= 1;
}
- v = a1 * (x4 - center);
+ v = a1 * (x - center);
break;
}
@@ -213,7 +246,7 @@
ms.z += v;
break;
case 'U':
- ms.addUTens(utens, (float) v, fn);
+ ms.addUTens(utens, (float) v);
break;
default:
if (Float.isNaN(ms.vocc))
@@ -234,25 +267,4 @@
|| x4 <= right);
}
- /** just guessing here....
- *
- * @param aq
- * @param q
- * @return pointer to last-used index
- */
- int getQ(P3[] aq, P3 q) {
- q.set(0, 0, 0);
- int eq = 0;
- fn = 0;
- for (int i = 0; i < aq.length; i++) {
- q.scaleAdd2(qCoefs[i], aq[i], q);
- if (qCoefs[i] != 0) {
- eq = i;
- fn+= Math.abs(qCoefs[i]);
- }
- }
- q.scale(1f/fn);
- return eq;
- }
-
}
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -13,149 +13,92 @@
public class ModulationSet extends Vibration {
- public JmolList<Modulation> mods;
- public float[] epsilon;
- public float[] delta;
- public int[] t = new int[3];
-
- public P3[] q123;
- public double[] qlen;
- private int modDim;
- public P3 r;
- public Matrix3f rot;
- public float vdisp = Float.NaN;
public float vocc = Float.NaN;
- public float vocc0 = Float.NaN;
- public Map<String, Float> htValues;
+ public Map<String, Float> htUij;
public boolean enabled = false;
public String id;
-
public V3 prevSetting;
- public ModulationSet(String id, JmolList<Modulation> list, int modDim, P3[]
q123, double[] qlen) {
- this.id = id;
- mods = list;
- this.modDim = modDim;
- this.q123 = q123;
- this.qlen = qlen;
- }
+ float vocc0 = Float.NaN;
+ private JmolList<Modulation> mods;
+ private Matrix3f gammaE;
+ private int t = Integer.MAX_VALUE;
+ private double[] qlen;
+
+ int modDim;
+ V3 x456;
+
/**
- * Determine the overall modulation.
+ * A collection of modulations for a specific atom.
*
- * 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):
+ * @param id
+ * @param r
+ * @param vocc0
+ * @param modDim
+ * @param mods
+ * @param gammaE
+ * @param gammaIS
+ * @param q123
+ * @param qlen
*
- * 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 = (x4' - delta) / epsilon = epsilon (x4' - delta)
- *
- * More generally, we might have something like:
- *
- * x4' = x5 + 1/2; x5' = x4 - 1/2
- *
- * so in those cases, we have to use the proper q.
- *
- *
*/
- public void calculate() {
- // Q: What about x4,x5 exchange?
- set(0, 0, 0);
- htValues = null;
- vdisp = vocc = Float.NaN;
- P3[] aq = new P3[modDim];
+
+ public ModulationSet(String id, P3 r, float vocc0, int modDim,
+ JmolList<Modulation> mods, Matrix3f gammaE, Matrix4f
gammaIS, P3[] q123, double[] qlen) {
+ this.id = id;
+ this.vocc0 = vocc0;
+ this.modDim = modDim;
+ this.mods = mods;
- for (int iq = 0; iq < modDim; iq++) {
- int eps = (int) epsilon[iq];
- if (eps == 0)
- continue;
- int qpt = (Math.abs(eps) - 1);
- aq[iq] = q123[qpt];
- }
- P3 q = new P3();
- int jmax = 1;
- for (int j = 0;j < modDim; j++) {
- // testing hypothesis that either one should work...
- // checks out for (0,1) (1,0), but not (1,1)
- if (j == jmax)continue;
-
- for (int i = mods.size(); --i >= 0;) {
+ // set up x456
+
+ this.gammaE = gammaE;
+ Matrix3f gammaIinv = new Matrix3f();
+ gammaIS.getRotationScale(gammaIinv);
+ V3 sI = new V3();
+
+ gammaIS.get(sI);
+ gammaIinv.invert();
+ x456 = V3.new3(q123[0].dot(r), q123[1].dot(r), q123[2].dot(r));
+ x456.sub(sI);
+ gammaIinv.transform(x456);
+ if (Logger.debuggingHigh)
+ Logger.debug("MODSET create r=" + Escape.eP(r) + " q0=" +
Escape.eP(q123[0])
+ + " si=" + Escape.eP(sI) + " ginv=" +
gammaIinv.toString().replace('\n',' ') + " x4=" + x456.x);
- int iq = mods.get(i).getQ(aq, q);
- int eps = (int) epsilon[iq];
- eps = (eps > 0 ? 1 : -1);
- //int qpt = (Math.abs(eps) - 1);
+ // temporary only - only for d=1:
+ this.qlen = qlen;
+
+ }
-
- double x4 = eps * (q.dot(r) - delta[iq] + qlen[iq] * t[iq]);
- System.out.println("MODSET q=" + q + " r=" + r
- + " epsilon=" + eps + " delta=" + delta[iq] + " t=" + t[iq]
- + " x4=" + x4);
-
- // here we are using the original specification for the function.
- // F2 = "(0)q1 + (1)q2"
- // even though we have switched q1 and q2
- mods.get(i).apply(i, this, x4);
- }
- }
- rot.transform(this);
+ public void calculate() {
+ x = y = z = 0;
+ htUij = null;
+ vocc = Float.NaN;
+ double offset = (t == Integer.MAX_VALUE ? 0 : qlen[0] * t);
+ for (int i = mods.size(); --i >= 0;)
+ mods.get(i).apply(this, offset);
+ gammaE.transform(this);
}
-//
http://nanocrystallography.research.pdx.edu/static/mcodcif/4/33/14/4331458.cif
-
-// _space_group_ssg_name_WJJ P-42_1m(a,a,0)00s(-a,a,0)000
-// loop_
-// _space_group_symop_ssg_id
-// _space_group_symop_ssg_operation_algebraic
-// 1 x1,x2,x3,x4,x5
-// 2 -x1,-x2,x3,-x4,-x5
-// 3 x2,-x1,-x3,x5,-x4
-// 4 -x2,x1,-x3,-x5,x4
-// 5 -x1+1/2,x2+1/2,-x3,x5+1/2,x4+1/2
-// 6 x1+1/2,-x2+1/2,-x3,-x5+1/2,-x4+1/2
-// 7 -x2+1/2,-x1+1/2,x3,-x4+1/2,x5+1/2
-// 8 x2+1/2,x1+1/2,x3,x4+1/2,-x5+1/2
-
-// _cell_wave_vector_seq_id
-// _cell_wave_vector_x
-// _cell_wave_vector_y
-// _cell_wave_vector_z
-// 1 0.216050 0.216050 0.000000
-// 2 -0.216050 0.216050 0.000000
-
-// loop_
-// _atom_site_Fourier_wave_vector_seq_id
-// _jana_atom_site_fourier_wave_vector_q1_coeff
-// _jana_atom_site_fourier_wave_vector_q2_coeff
-// 1 1 0
-// 2 0 1
-// 3 1 1
-// 4 -1 1
-// 5 2 0
-// 6 0 2
-
- public void addUTens(String utens, float v, int n) {
- if (htValues == null)
- htValues = new Hashtable<String, Float>();
- Float f = htValues.get(utens);
+ public void addUTens(String utens, float v) {
+ if (htUij == null)
+ htUij = new Hashtable<String, Float>();
+ Float f = htUij.get(utens);
if (Logger.debuggingHigh)
- Logger.debug("MODSET " + id + " n=" + n + " utens=" + utens + " f=" + f
+ " v="+ v);
+ Logger.debug("MODSET " + id + " utens=" + utens + " f=" + f + " v="+ v);
if(f != null)
v += f.floatValue();
- htValues.put(utens, Float.valueOf(v));
+ htUij.put(utens, Float.valueOf(v));
}
/**
- * Set modulation "t" value, which sets which unit cell in sequence we are
looking at.
+ * Set modulation "t" value, which sets which unit cell
+ * in sequence we are looking at; d=1 only.
*
* @param isOn
* @param t
@@ -170,15 +113,19 @@
scale(-1);
return (enabled ? 2 : 1);
}
- if (t == this.t[0])
+ if (modDim > 1 || t == this.t)
return 4;
if (prevSetting == null)
prevSetting = new V3();
prevSetting.setT(this);
- this.t[0] = t;
+ this.t = t;
calculate();
enabled = false;
return 3;
}
+ public String getState() {
+ return "modulation " + (!enabled ? "OFF" : t == Integer.MAX_VALUE ? "ON" :
"" + t);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -11,8 +11,12 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.18"
+___JmolVersion="13.3.4_dev_2013.08.19"
+code: Incommensurate modulated structure CIF and M50/40 file loading validation
+ -- includes d=1 and d=2
+ -- Fourier, sawtooth, crenel
+
bug fix: translation not read from state
new feature: set platformSpeed [0 to 10]
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-19 04:39:18 UTC
(rev 18595)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-19 21:13:46 UTC
(rev 18596)
@@ -365,8 +365,9 @@
if ((ivib = viewer.modelGetLastVibrationIndex(i, T.modulation)) >=
0)
for (int j = models[i].firstAtomIndex; j <= ivib; j++) {
ModulationSet mset = (ModulationSet) viewer.getVibration(j);
- if (mset != null && mset.enabled)
- BSUtil.setMapBitSet(temp, j, j, "modulation " + mset.t[0]);
+ if (mset != null && mset.enabled) {
+ BSUtil.setMapBitSet(temp, j, j, mset.getState());
+ }
}
}
String s = getCommands(temp, null, "select");
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-08-19
04:39:18 UTC (rev 18595)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-08-19
21:13:46 UTC (rev 18596)
@@ -1708,15 +1708,15 @@
matrixEnd.setAA(aaMoveTo);
}
}
- if (Float.isNaN(cameraX) || cameraX == cameraSetting.x)
- cameraX = Float.MAX_VALUE;
- if (Float.isNaN(cameraY) || cameraY == cameraSetting.y)
- cameraY = Float.MAX_VALUE;
+ if (cameraX == cameraSetting.x)
+ cameraX = Float.NaN;
+ if (cameraY == cameraSetting.y)
+ cameraY = Float.NaN;
if (cameraDepth == this.cameraDepth)
- cameraDepth = Float.MAX_VALUE;
- if (cameraX != Float.MAX_VALUE)
+ cameraDepth = Float.NaN;
+ if (!Float.isNaN(cameraX))
xTrans = cameraX * 50 / newRotationRadius / width * screenPixelCount;
- if (cameraY != Float.MAX_VALUE)
+ if (!Float.isNaN(cameraY))
yTrans = cameraY * 50 / newRotationRadius / height * screenPixelCount;
float pixelScale = (center == null ? scaleDefaultPixelsPerAngstrom
: defaultScaleToScreen(newRotationRadius));
@@ -2760,21 +2760,23 @@
moveRotationCenter(center, !windowCentered);
if (navCenter != null && mode == MODE_NAVIGATION)
navigationCenter.setT(navCenter);
- if (cameraDepth != Float.MAX_VALUE)
+ if (!Float.isNaN(cameraDepth))
setCameraDepthPercent(cameraDepth, false);
- if (cameraX != Float.MAX_VALUE && cameraY != Float.MAX_VALUE)
+ if (!Float.isNaN(cameraX) && !Float.isNaN(cameraY))
setCamera(cameraX, cameraY);
- if (zoom != Float.MAX_VALUE)
+ if (!Float.isNaN(zoom))
zoomToPercent(zoom);
- modelRadius = rotationRadius;
- scaleDefaultPixelsPerAngstrom = pixelScale;
- if (xTrans != Float.MAX_VALUE && yTrans != Float.MAX_VALUE) {
+ if (!Float.isNaN(rotationRadius))
+ modelRadius = rotationRadius;
+ if (!Float.isNaN(pixelScale))
+ scaleDefaultPixelsPerAngstrom = pixelScale;
+ if (!Float.isNaN(xTrans) && !Float.isNaN(yTrans)) {
translateToPercent('x', xTrans);
translateToPercent('y', yTrans);
}
- if (xNav != Float.MAX_VALUE && yNav != Float.MAX_VALUE)
+ if (!Float.isNaN(xNav) && !Float.isNaN(yNav))
navTranslatePercentOrTo(0, xNav, yNav);
- if (navDepth != Float.MAX_VALUE)
+ if (!Float.isNaN(navDepth))
setNavigationDepthPercent(navDepth);
}
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