Revision: 18360
http://sourceforge.net/p/jmol/code/18360
Author: hansonr
Date: 2013-06-26 09:06:29 +0000 (Wed, 26 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.25"
code: MagRes/CASTEP reader upgrades
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/util/Eigen.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-06-25 01:43:16 UTC (rev 18359)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-06-26 09:06:29 UTC (rev 18360)
@@ -88,7 +88,6 @@
private boolean isPhonon;
private boolean isOutput;
private boolean isCell;
- private boolean isDispersion;
private float a, b, c, alpha, beta, gamma;
private V3[] abc = new V3[3];
@@ -241,9 +240,7 @@
protected boolean checkLine() throws Exception {
// only for .phonon, castep output, or other BEGIN HEADER type files
if (isOutput) {
- if (line.contains("DFT+D: Semi-empirical")){
- isDispersion = true;
- } else if (line.contains("Real Lattice(A)")) {
+ if (line.contains("Real Lattice(A)")) {
readOutputUnitCell();
} else if (line.contains("Fractional coordinates of atoms")) {
if (doGetModel(++modelNumber, null)) {
@@ -255,8 +252,12 @@
readOutputCharges();
} else if (doProcessLines && line.contains("Born Effective Charges")) {
readOutputBornChargeTensors();
- } else if (line.contains("Final energy")) {
- readEnergy();
+ } else if (line.contains("Final energy ")) { // not "Final energy, E"
+ readEnergy(3);
+ } else if (line.contains("Dispersion corrected final energy*")) {
+ readEnergy(5);
+ } else if (line.contains("Total energy corrected")) {
+ readEnergy(8);
}
return true;
}
@@ -290,7 +291,6 @@
private void readOutputUnitCell() throws Exception {
applySymmetryAndSetTrajectory();
- //atomSetCollection.newAtomSet();
setFractionalCoordinates(true);
abc = read3Vectors(false);
setLatticeVectors();
@@ -318,21 +318,16 @@
}
- private void readEnergy() throws Exception {
+ private void readEnergy(int pt) throws Exception {
tokens = getTokens();
- Double energy;
-
- if (!isDispersion) {
- energy = Double.valueOf(Double.parseDouble(tokens[3]));
- } else {
- discardLinesUntilContains("Dispersion corrected final energy*");
- tokens = getTokens();
- energy = Double.valueOf(Double.parseDouble(tokens[5]));
+ try {
+ Double energy = Double.valueOf(Double.parseDouble(tokens[pt]));
+ atomSetCollection.setAtomSetName("Energy = " + energy + " eV");
+ atomSetCollection.setAtomSetEnergy("" + energy, energy.floatValue());
+ atomSetCollection.setAtomSetAuxiliaryInfo("Energy", energy);
+ } catch (Exception e) {
+ appendLoadNote("CASTEP Energy could not be read: " + line);
}
-
- atomSetCollection.setAtomSetName("Energy = " + energy + " eV");
- atomSetCollection.setAtomSetEnergy("" + energy, energy.floatValue());
- atomSetCollection.setAtomSetAuxiliaryInfo("Energy", energy);
/*
is better to do this also here
in case the output is only a
@@ -340,7 +335,7 @@
both volume and geometry
*/
applySymmetryAndSetTrajectory();
- atomSetCollection.newAtomSet();
+ atomSetCollection.newAtomSetClear(false);
setLatticeVectors();
}
@@ -348,7 +343,7 @@
isTrajectory = (desiredVibrationNumber <= 0);
doApplySymmetry = true;
while (line != null && line.contains("<-- E")) {
- atomSetCollection.newAtomSet();
+ atomSetCollection.newAtomSetClear(false);
discardLinesUntilContains("<-- h");
setSpaceGroupName("P1");
abc = read3Vectors(true);
@@ -547,6 +542,7 @@
if (readLine().indexOf("--------") < 0)
return;
Atom[] atoms = atomSetCollection.getAtoms();
+ appendLoadNote("Ellipsoids: Born Charge Tensors");
while (readLine().indexOf('=') < 0)
getOutputEllipsoid(atoms[readOutputAtomIndex()], line.substring(12));
}
@@ -554,7 +550,8 @@
private int readOutputAtomIndex() {
tokens = getTokensStr(line);
- return atomSetCollection.getAtomIndexFromName(tokens[0] + tokens[1]);
+ String name = tokens[0] + tokens[1];
+ return atomSetCollection.getAtomIndexFromName(name);
}
private void getOutputEllipsoid(Atom atom, String line0) throws Exception {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
2013-06-25 01:43:16 UTC (rev 18359)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
2013-06-26 09:06:29 UTC (rev 18360)
@@ -12,6 +12,10 @@
* @version 1.0
*/
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.util.Quadric;
import org.jmol.util.TextFormat;
import org.jmol.adapter.smarter.AtomSetCollectionReader;
@@ -22,6 +26,9 @@
private float[] cellParams;
private float maxIso = 10000;
+ private String tensorTypes = "";
+ private boolean isNew;
+ private Map<String, String> mapUnits = new Hashtable<String, String>();
@Override
protected void initializeReader() {
@@ -31,21 +38,95 @@
}
@Override
+ protected void finalizeReader() throws Exception {
+ doApplySymmetry = true;
+ finalizeReaderASCR();
+ }
+
+ @Override
protected boolean checkLine() throws Exception {
- if (line.startsWith("lattice")) {
+ if (!isNew && line.indexOf("<calculation>") >= 0) {
+ isNew = true;
+ ignoreFileSpaceGroupName = true;
+ //setSpaceGroupName("P1");
+ }
+ if (cellParams == null && line.startsWith("lattice")) {
readCellParams();
- } else if (line.contains("Coordinates")) {
- readAtom();
- } else if (line.contains("J-coupling Total") || line.contains("TOTAL
tensor")) {
- readTensor();
+ return true;
}
+ if (isNew) {
+ if (line.startsWith("units")) {
+ setUnitsNew();
+ } else if (line.startsWith("atom")) {
+ readAtom(true);
+ atom.ellipsoid = new Quadric[2];
+ } else if (line.startsWith("symmetry")) {
+ readSymmetryNew();
+ } else if (line.startsWith("ms")) {
+ readTensorNew(0);
+ } else if (line.startsWith("efg")) {
+ readTensorNew(1);
+ } else if (line.startsWith("<magres_old>")) {
+ continuing = false;
+ }
+ return true;
+ }
+ if (line.contains("Coordinates")) {
+ readAtom(false);
+ } else if (line.contains("J-coupling Total")
+ || line.contains("TOTAL tensor")) {
+ readTensorOld();
+ }
return true;
}
+ // 0 ms H 1 1.9115355485265077E+01
-6.8441521786256319E+00 1.9869475943756368E-01
-7.4231606832789883E+00 3.5078237789073569E+01
1.6453141184608533E+00 -8.4492087560280138E-01
1.4000600350356041E+00 1.7999188282948701E+01
+ // 1 efg H 1 -9.7305664267778647E-02
-1.3880930041098827E-01 8.3161631703720738E-03
-1.3880930041098827E-01 2.5187188360357782E-01
-4.4856574290225361E-02 8.3161631703720738E-03
-4.4856574290225361E-02 -1.5456621933580317E-01
+ private void readTensorNew(int iType) throws Exception {
+ float[] data = new float[9];
+ String[] tokens = getTokens();
+ String atomName = (tokens[1] + tokens[2]);
+ fillFloatArray(line.substring(30), 0, data);
+ float f = (iType == 0 ? 0.04f : 1f);
+ // if (isJ) {
+ // discardLinesUntilContains("Isotropic");
+ // float iso = parseFloatStr(getTokens()[3]);
+ // if (Math.abs(iso) > maxIso)
+ // return;
+ // f = 0.04f;
+ // }
+ double[][] a = new double[3][3];
+ for (int i = 0, pt = 0; i < 3; i++)
+ for (int j = 0; j < 3; j++)
+ a[i][j] = data[pt++];
+ atom =
atomSetCollection.getAtoms()[atomSetCollection.getAtomIndexFromName(atomName)];
+ atom.ellipsoid[iType] = Eigen.getEllipsoidDD(a);
+ atom.ellipsoid[iType].scale(f);
+ if (tensorTypes.indexOf("" + iType) < 0) {
+ tensorTypes += "" + iType;
+ appendLoadNote("Ellipsoids set " + (iType + 1) + ": "
+ + (iType == 0 ? "Magnetic Shielding" : "Electric Field Gradient"));
+ }
+ }
+
+ // symmetry x,y,z
+ // symmetry x+1/2,-y+1/2,-z
+ // symmetry -x,y+1/2,-z+1/2
+ // symmetry -x+1/2,-y,z+1/2
+
+ private void readSymmetryNew() {
+ setSymmetryOperator(getTokens()[1]);
+ }
+
+ private void setUnitsNew() {
+ String[] tokens = getTokens();
+ mapUnits.put(tokens[1], tokens[2]);
+ }
+
private void readCellParams() throws Exception {
String[] tokens = getTokens();
- cellParams = new float[9];
+ cellParams = new float[9];
for (int i = 0; i < 9; i++)
cellParams[i] = parseFloatStr(tokens[i + 1]) * ANGSTROMS_PER_BOHR;
addPrimitiveLatticeVector(0, cellParams, 0);
@@ -59,15 +140,21 @@
*/
private Atom atom;
- private void readAtom() throws Exception {
- float f = line.trim().endsWith("A") ? 1 : ANGSTROMS_PER_BOHR;
+
+ private void readAtom(boolean isNew) {
+ float f = ((isNew ? mapUnits.get("atom").startsWith("A") : line.trim()
+ .endsWith("A")) ? 1 : ANGSTROMS_PER_BOHR);
+ int pt = (isNew ? 2 : 0);
String[] tokens = getTokens();
- atom = atomSetCollection.addNewAtom();
- atom.elementSymbol = tokens[0];
- atom.atomName = tokens[0] + tokens[1];
- float x = parseFloatStr(tokens[3]) * f;
- float y = parseFloatStr(tokens[4]) * f;
- float z = parseFloatStr(tokens[5]) * f;
+ atom = new Atom();
+ atom.elementSymbol = tokens[pt];
+ atom.atomName = tokens[pt++] + tokens[pt++];
+ atomSetCollection.addAtomWithMappedName(atom);
+ if (!isNew)
+ pt++;
+ float x = parseFloatStr(tokens[pt++]) * f;
+ float y = parseFloatStr(tokens[pt++]) * f;
+ float z = parseFloatStr(tokens[pt++]) * f;
atom.set(x, y, z);
setAtomCoord(atom);
}
@@ -82,19 +169,25 @@
W 1 Eigenvalue sigma_zz -432981.4974
W 1 Eigenvector sigma_zz 0.0000 0.0000 1.0000
-TOTAL tensor
+ TOTAL tensor
-0.0216 -0.1561 -0.0137
-0.1561 -0.1236 -0.0359
-0.0137 -0.0359 0.1452
*/
- private void readTensor() throws Exception {
+ private void readTensorOld() throws Exception {
+ line = line.trim();
+ if (tensorTypes.indexOf(line) < 0) {
+ tensorTypes += line;
+ appendLoadNote("Ellipsoids: " + line);
+ }
+ atomSetCollection.setAtomSetName(line);
boolean isJ = (line.indexOf("J-") >= 0);
- atomSetCollection.setAtomSetName(line.trim());
float[] data = new float[9];
readLine();
- String s = TextFormat.simpleReplace(readLine() + readLine() + readLine(),
"-", " -");
+ String s = TextFormat.simpleReplace(readLine() + readLine() + readLine(),
+ "-", " -");
fillFloatArray(s, 0, data);
float f = 3;
if (isJ) {
@@ -107,7 +200,7 @@
double[][] a = new double[3][3];
for (int i = 0, pt = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
- a[i][j] = data[pt++];
+ a[i][j] = data[pt++];
atom.setEllipsoid(Eigen.getEllipsoidDD(a));
atom.ellipsoid[0].scale(f);
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-06-25 01:43:16 UTC
(rev 18359)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-06-26 09:06:29 UTC
(rev 18360)
@@ -56,8 +56,6 @@
public void setEllipsoid(Quadric e) {
if (e == null)
return;
- //if (atomIndex < 5)
- //System.out.println("Atom: ellipsoid " + e);
if (ellipsoid != null && ellipsoid.length == 3)
ellipsoid[0] = e;
else
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-25 01:43:16 UTC (rev 18359)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-26 09:06:29 UTC (rev 18360)
@@ -1469,14 +1469,16 @@
//TODO: need to clone bonds
}
- Map<Object, Integer> atomSymbolicMap = new Hashtable<Object, Integer>();
+ private Map<Object, Integer> atomSymbolicMap = new Hashtable<Object,
Integer>();
private void mapMostRecentAtomName() {
if (atomCount > 0) {
int index = atomCount - 1;
String atomName = atoms[index].atomName;
- if (atomName != null)
+ if (atomName != null) {
atomSymbolicMap.put(atomName, Integer.valueOf(index));
+ System.out.println(this + " " + atomName);
+ }
}
}
@@ -1509,27 +1511,19 @@
haveMappedSerials = true;
}
- void mapAtomName(String atomName, int atomIndex) {
- atomSymbolicMap.put(atomName, Integer.valueOf(atomIndex));
- }
-
public int getAtomIndexFromName(String atomName) {
- //for new Bond -- inconsistent with mmCIF altLoc
- int index = -1;
- Object value = atomSymbolicMap.get(atomName);
- if (value != null)
- index = ((Integer)value).intValue();
- return index;
+ return getMapIndex(atomName);
}
public int getAtomIndexFromSerial(int serialNumber) {
- int index = -1;
- Object value = atomSymbolicMap.get(Integer.valueOf(serialNumber));
- if (value != null)
- index = ((Integer)value).intValue();
- return index;
+ return getMapIndex(Integer.valueOf(serialNumber));
}
+ private int getMapIndex(Object nameOrNum) {
+ Integer value = atomSymbolicMap.get(nameOrNum);
+ return (value == null ? -1 : value.intValue());
+ }
+
public void setAtomSetCollectionAuxiliaryInfo(String key, Object value) {
if (value == null)
atomSetCollectionAuxiliaryInfo.remove(key);
@@ -1647,6 +1641,11 @@
}
public void newAtomSet() {
+ newAtomSetClear(true);
+ }
+
+ public void newAtomSetClear(boolean doClearMap) {
+
if (!allowMultiple && currentAtomSetIndex >= 0)
discardPreviousAtoms();
bondIndex0 = bondCount;
@@ -1669,7 +1668,8 @@
} else {
atomSetNumbers[currentAtomSetIndex] = atomSetCount;
}
- atomSymbolicMap.clear();
+ if (doClearMap)
+ atomSymbolicMap.clear();
setAtomSetAuxiliaryInfo("title", collectionName);
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-06-25
01:43:16 UTC (rev 18359)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-06-26
09:06:29 UTC (rev 18360)
@@ -723,7 +723,7 @@
{"ZMatrix", "#ZMATRIX"};
private final static String[] magResFileStartRecords =
- {"MagRes", "# magres"};
+ {"MagRes", "# magres", "#$magres"};
private final static String[] pymolStartRecords =
{"PyMOL", "}q" };
Modified: trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-06-25 01:43:16 UTC (rev 18359)
+++ trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-06-26 09:06:29 UTC (rev 18360)
@@ -331,7 +331,7 @@
private void fillConeScreen(P3i p1, P3i p2, boolean isPositive) {
if (diameter == 0)
return;
- float diam = (diameter == 0 ? 1 : diameter) * 4;
+ float diam = (diameter == 0 ? 1 : diameter) * 8;
v1.set(p2.x - p1.x, p2.y - p1.y, p2.z - p1.z);
v1.normalize();
v1.scale(diam);
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-06-25 01:43:16 UTC (rev
18359)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-06-26 09:06:29 UTC (rev
18360)
@@ -2382,6 +2382,7 @@
"justifyMeasurements", T.t(justifymeasurements),
"languageTranslation", T.t(languagetranslation),
"legacyAutoBonding", T.t(legacyautobonding),
+ "legacyHAddtion", T.t(legacyhaddition),
"logCommands", T.t(logcommands),
"logGestures", T.t(loggestures),
"measureAllModels", T.t(measureallmodels),
Modified: trunk/Jmol/src/org/jmol/util/Eigen.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Eigen.java 2013-06-25 01:43:16 UTC (rev
18359)
+++ trunk/Jmol/src/org/jmol/util/Eigen.java 2013-06-26 09:06:29 UTC (rev
18360)
@@ -1073,15 +1073,15 @@
n.setT(evec[i]);
m.transform(n);
cross.cross(n, evec[i]);
- Logger.info("v[i], n, n x v[i]"+ evec[i] + " " + n + " " + cross);
+ //Logger.info("v[i], n, n x v[i]"+ evec[i] + " " + n + " " + cross);
n.setT(evec[i]);
n.normalize();
cross.cross(evec[i], evec[(i + 1)%3]);
- Logger.info("draw id eigv" + i + " " + Escape.eP(evec[i]) + " color " +
(i == 0 ? "red": i == 1 ? "green" : "blue") + " # " + n + " " + cross);
+ //Logger.info("draw id eigv" + i + " " + Escape.eP(evec[i]) + " color "
+ (i == 0 ? "red": i == 1 ? "green" : "blue") + " # " + n + " " + cross);
}
- Logger.info("eigVl (" + eigen.d[0] + " + " + eigen.e[0]
- + "I) (" + eigen.d[1] + " + " + eigen.e[1]
- + "I) (" + eigen.d[2] + " + " + eigen.e[2] + "I)");
+ Logger.info("eigVal+vec (" + eigen.d[0] + " + " + eigen.e[0]
+ + ")\n (" + eigen.d[1] + " + " + eigen.e[1]
+ + ")\n (" + eigen.d[2] + " + " + eigen.e[2] + ")");
V3[] unitVectors = new V3[3];
float[] lengths = new float[3];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-25 01:43:16 UTC
(rev 18359)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-26 09:06:29 UTC
(rev 18360)
@@ -11,6 +11,7 @@
___JmolVersion="13.1.17_dev_2013.06.25"
+code: MagRes/CASTEP reader upgrades
bug fix: PyMOL movie start frame
bug fix: PyMOL putty broken
bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-25 01:43:16 UTC
(rev 18359)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-26 09:06:29 UTC
(rev 18360)
@@ -853,7 +853,7 @@
//setParameterValue("edsUrlOptions", edsUrlOptions);
setS("edsUrlCutoff", edsUrlCutoff);
setB("ellipsoidArcs", ellipsoidArcs);
- setB("ellipsoidArrrow", ellipsoidArrows);
+ setB("ellipsoidArrows", ellipsoidArrows);
setB("ellipsoidAxes", ellipsoidAxes);
setF("ellipsoidAxisDiameter", ellipsoidAxisDiameter);
setB("ellipsoidBall", ellipsoidBall);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-25 01:43:16 UTC (rev
18359)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-26 09:06:29 UTC (rev
18360)
@@ -6490,6 +6490,11 @@
private void setBooleanPropertyTok(String key, int tok, boolean value) {
boolean doRepaint = true;
switch (tok) {
+ case T.ellipsoidarrows:
+ // 13.1.17 TRUE for little points on ellipsoids showing sign of
+ // eigenvalues (in --> negative; out --> positive)
+ global.ellipsoidArrows = value;
+ break;
case T.translucent:
// 13.1.17 false -> translucent objects are opaque among themselves
(Pymol transparency_mode 2)
global.translucent = value;
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