Revision: 18424
http://sourceforge.net/p/jmol/code/18424
Author: hansonr
Date: 2013-07-04 20:52:57 +0000 (Thu, 04 Jul 2013)
Log Message:
-----------
temp name only
Added Paths:
-----------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagRessReader.java
Copied: trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagRessReader.java (from
rev 18423, trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java)
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagRessReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagRessReader.java
2013-07-04 20:52:57 UTC (rev 18424)
@@ -0,0 +1,316 @@
+package org.jmol.adapter.readers.xtal;
+
+/**
+ * MagRes reader for magnetic resonance files produced by CASTEP
+ *
+ * @author Bob Hanson hans...@stolaf.edu, Simone Sturniolo 6/27/2013
+ *
+ */
+
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.util.Escape;
+import org.jmol.util.JmolList;
+import org.jmol.util.Logger;
+import org.jmol.util.SB;
+import org.jmol.util.Tensor;
+import org.jmol.util.TextFormat;
+
+import org.jmol.adapter.smarter.AtomSetCollectionReader;
+import org.jmol.adapter.smarter.Atom;
+
+public class MagRessReader extends AtomSetCollectionReader {
+
+ private final static int BLOCK_NEW = -2;
+ private final static int BLOCK_NONE = -1;
+ private final static int BLOCK_CALC = 0;
+ private final static int BLOCK_ATOMS = 1;
+ private final static int BLOCK_MAGRES = 2;
+
+ private int currentBlock = BLOCK_NONE;
+
+ private float[] cellParams;
+ //private static float maxIso = 10000; // the old code was checking for this.
+
+ private Map<String, String> magresUnits = new Hashtable<String, String>();
+ private JmolList<Tensor> interactionTensors = new JmolList<Tensor>();
+ private SB header = new SB();
+
+ /**
+ * not sure how to work with symmetry here...
+ *
+ */
+ @Override
+ protected void initializeReader() {
+ setFractionalCoordinates(false);
+ //doApplySymmetry = false;
+ ignoreFileSpaceGroupName = true;
+ }
+
+ /**
+ * Set final auxiliary info and symmetry, including
+ * "fileHeader", "magresUnits", and "interactionTensors";
+ * note that print getProperty("auxiliaryInfo.models[1].magresUnits")
+ * should return a catalog of tensor types.
+ *
+ */
+ @Override
+ protected void finalizeReader() throws Exception {
+ //doApplySymmetry = true;
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("fileHeader",
+ header.toString());
+ finalizeReaderASCR();
+ if (interactionTensors.size() > 0)
+ atomSetCollection.setAtomSetAuxiliaryInfo("interactionTensors",
interactionTensors);
+ }
+
+ /**
+ * Valid blocks include [calculation] [atoms] [magres];
+ * all magres entries must be prefaced with a corresponding unit;
+ * Use of < > instead of [ ] is allowed.
+ *
+ * @return true to read another line (some readers return false because they
have over-read a line)
+ */
+ @Override
+ protected boolean checkLine() throws Exception {
+ if (!trimLine())
+ return true;
+ switch (checkBlock()) {
+ case BLOCK_CALC:
+ header.append(line).append("\n");
+ appendLoadNote(line);
+ break;
+ case BLOCK_ATOMS:
+ if (cellParams == null && line.startsWith("lattice"))
+ return readCellParams();
+ if (line.startsWith("symmetry"))
+ return readSymmetry();
+ if (line.startsWith("units"))
+ return setUnits(false);
+ if (line.startsWith("atom"))
+ return readAtom();
+ break;
+ case BLOCK_MAGRES:
+ if (line.startsWith("units"))
+ return setUnits(true);
+ return readTensor();
+ }
+ return true;
+ }
+
+ /**
+ * All characters after hash ignored; lines are trimmed.
+ *
+ * @return true if line has content
+ *
+ */
+ private boolean trimLine() {
+ int pt = line.indexOf("#");
+ if (pt >= 0)
+ line = line.substring(0, pt);
+ line = line.trim();
+ return (line.length() > 0);
+ }
+
+ /**
+ * looking for tags here.
+ *
+ * @return currentBlock if not a tag or BLOCK_NEW otherwise
+ */
+ private int checkBlock() {
+ // please don't use RegEx here, because of issues with JavaScript version
+ if (!(line.startsWith("<") && line.endsWith(">"))
+ && !(line.startsWith("[") && line.endsWith("]")))
+ return currentBlock;
+ line = TextFormat.simpleReplace(line, "<", "[");
+ line = TextFormat.simpleReplace(line, ">", "]");
+ switch (("..............." +
+ "[calculation].." +
+ "[/calculation]." +
+ "[atoms]........" +
+ "[/atoms]......." +
+ "[magres]......." +
+ "[/magres]......").indexOf(line + ".") / 15) {
+ case 0:
+ Logger.info("block indicator ignored: " + line);
+ break;
+ case 1:
+ if (currentBlock == BLOCK_NONE)
+ currentBlock = BLOCK_CALC;
+ break;
+ case 2:
+ if (currentBlock == BLOCK_CALC)
+ currentBlock = BLOCK_NONE;
+ break;
+ case 3:
+ if (currentBlock == BLOCK_NONE) {
+ currentBlock = BLOCK_ATOMS;
+ atomSetCollection.newAtomSet();
+ magresUnits = new Hashtable<String, String>();
+ }
+ break;
+ case 4:
+ if (currentBlock == BLOCK_ATOMS)
+ currentBlock = BLOCK_NONE;
+ break;
+ case 5:
+ if (currentBlock == BLOCK_NONE) {
+ currentBlock = BLOCK_MAGRES;
+ magresUnits = new Hashtable<String, String>();
+ atomSetCollection.setAtomSetAuxiliaryInfo("magresUnits",
+ magresUnits);
+ }
+ break;
+ case 6:
+ if (currentBlock == BLOCK_MAGRES)
+ currentBlock = BLOCK_NONE;
+ break;
+ }
+ return BLOCK_NEW;
+ }
+
+ /**
+ * catalog units
+ *
+ * @param isMagresBlock
+ *
+ * @return true
+ */
+ private boolean setUnits(boolean isMagresBlock) {
+ String[] tokens = getTokens();
+ String id = tokens[1];
+ if (isMagresBlock)
+ appendLoadNote("Ellipsoid set " + Escape.eS(id) + ": "
+ + (id.startsWith("ms") ? "Magnetic Shielding"
+ : id.startsWith("efg") ? "Electric Field Gradient" : id
+ .startsWith("isc") ? "J-Coupling" : "?"));
+ magresUnits.put(id, tokens[2]);
+ return true;
+ }
+
+ // 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
+
+ /**
+ * not doing anything with this -- P1 assumed
+ * @return true
+ */
+ private boolean readSymmetry() {
+ // not used
+ setSymmetryOperator(getTokens()[1]);
+ return true;
+ }
+
+ // lattice 6.0000000000000009E+00 0.0000000000000000E+00
0.0000000000000000E+00 0.0000000000000000E+00 6.0000000000000009E+00
0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00
6.0000000000000009E+00
+
+ /**
+ *
+ * @return true;
+ * @throws Exception
+ */
+ private boolean readCellParams() throws Exception {
+ String[] tokens = getTokens();
+ cellParams = new float[9];
+ for (int i = 0; i < 9; i++)
+ cellParams[i] = parseFloatStr(tokens[i + 1]);
+ addPrimitiveLatticeVector(0, cellParams, 0);
+ addPrimitiveLatticeVector(1, cellParams, 3);
+ addPrimitiveLatticeVector(2, cellParams, 6);
+ setSpaceGroupName("P1");
+ return true;
+ }
+
+ /*
+ C 1 Coordinates 2.054 0.000 0.000 A
+ */
+
+ /**
+ *
+ * Allowing for BOHR units here; probably unnecessary.
+ *
+ * @return true
+ */
+ private boolean readAtom() {
+ String units = magresUnits.get("atom");
+ if (units == null)
+ return true;
+ float f = (units.startsWith("A") ? 1 : ANGSTROMS_PER_BOHR);
+ String[] tokens = getTokens();
+ Atom atom = new Atom();
+ int pt = 1;
+ atom.elementSymbol = tokens[pt++];
+ atom.atomName = getAtomName(tokens[pt++], tokens[pt++]);
+ atomSetCollection.addAtomWithMappedName(atom);
+ 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);
+ return true;
+ }
+
+ /**
+ * combine name and index
+ * @param name
+ * @param index
+ * @return name_index
+ */
+ private static String getAtomName(String name, String index) {
+ return name + "_" + index;
+ }
+
+ // 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
+ // 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
+ // isc_fc C 2 H 3
-1.0414024145274923E+00 5.9457737246691622E-02
1.3323917584132525E-01 5.9457737246692129E-02
-8.0480723469752380E-01 5.4194562595693906E-02
1.3323917584132525E-01 5.4194562595693989E-02
-8.1674287041188620E-01
+
+ /**
+ * Read a tensor line. Note that a corresponding unit line must have
appeared first.
+ * @return true;
+ * @throws Exception
+ */
+ private boolean readTensor() throws Exception {
+ String[] tokens = getTokens();
+ String id = tokens[0];
+ String units = magresUnits.get(id);
+ if (units == null) {
+ Logger.warn(id + " ignored; no units defined; line: " + line);
+ return true;
+ }
+ boolean isIsc = id.startsWith("isc");
+ if (tokens.length == 10) {
+ // raw vector - you get ONE
+ magresUnits.remove(id);
+ float[] data = new float[9];
+ for (int i = 0; i < 9;)
+ data[i] = parseFloatStr(tokens[++i]);
+ Logger.info("Magres reader creating magres_" + id + ": " +
Escape.eAF(data));
+ atomSetCollection.setAtomSetAuxiliaryInfo("magres_" + id, data);
+ }
+ String atomName1 = getAtomName(tokens[1], tokens[2]);
+ int pt = 3;
+ String atomName2 = (isIsc ? getAtomName(tokens[pt++], tokens[pt++]) :
null);
+ if (atomName1.equals(atomName2)) {
+ Logger.warn(id + " ignored; atom1 == atom2 for " + atomName1 + " line: "
+ line);
+ return true;
+ }
+ double[][] a = new double[3][3];
+ for (int i = 0; i < 3; i++)
+ for (int j = 0; j < 3; j++)
+ a[i][j] = Double.valueOf(tokens[pt++]).doubleValue();
+ int index1 = atomSetCollection.getAtomIndexFromName(atomName1);
+ int index2;
+ Tensor t = Tensor.getTensorFromAsymmetricTensor(a, id);
+ if (atomName2 == null) {
+ index2 = -1;
+ atomSetCollection.getAtoms()[index1].addTensor(t, null);
+ } else {
+ index2 = atomSetCollection.getAtomIndexFromName(atomName2);
+ interactionTensors.addLast(t);
+ }
+ t.setAtomIndexes(index1, index2);
+ return true;
+ }
+}
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