Revision: 18396
http://sourceforge.net/p/jmol/code/18396
Author: hansonr
Date: 2013-07-02 06:07:51 +0000 (Tue, 02 Jul 2013)
Log Message:
-----------
block reader for magres reader
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
2013-07-01 22:25:55 UTC (rev 18395)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
2013-07-02 06:07:51 UTC (rev 18396)
@@ -3,14 +3,17 @@
/**
* MagRes reader for magnetic resonance files produced by CASTEP
*
- * @author Bob Hanson hans...@stolaf.edu 6/27/2013
+ * @author Bob Hanson hans...@stolaf.edu, Simone Sturniolo 6/27/2013
*
*/
import java.util.Hashtable;
import java.util.Map;
+import jspecview.util.Logger;
+
import org.jmol.util.JmolList;
+import org.jmol.util.SB;
import org.jmol.util.Tensor;
import org.jmol.util.TextFormat;
@@ -19,118 +22,181 @@
public class MagResReader 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;
private String tensorTypes = "";
- private boolean isNew;
- private Map<String, String> mapUnits = new Hashtable<String, String>();
+ //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;
- atomSetCollection.newAtomSet();
- try {
- readLine();
- isNew = line.startsWith("#$magres");
- if (isNew) {
- ignoreFileSpaceGroupName = true;
- //setSpaceGroupName("P1");
- }
- } catch (Exception e) {
- }
+ ignoreFileSpaceGroupName = true;
}
+ /**
+ * Set final auxiliary info and symmetry, including "fileHeader",
"magresUnits", and "interactionTensors";
+ * note that getProperty("auxiliaryInfo","magresUnits") should then return
catalog of units
+ *
+ */
@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
+ *
+ * @return true to read another line (some readers return false because they
have over-read a line)
+ */
@Override
protected boolean checkLine() throws Exception {
- line = line.trim();
- if (cellParams == null && line.startsWith("lattice")) {
- readCellParams();
- return true;
+ trimLine();
+ if (currentBlock != BLOCK_NONE && line.startsWith("units"))
+ return setUnits();
+ switch (checkBlock()) {
+ case BLOCK_CALC:
+ header.append(line).append("\n");
+ appendLoadNote(line);
+ break;
+ case BLOCK_ATOMS:
+ if (cellParams == null && line.startsWith("lattice"))
+ return readCellParams();
+ else if (line.startsWith("atom"))
+ return readAtom();
+ else if (line.startsWith("symmetry"))
+ return readSymmetry();
+ break;
+ case BLOCK_MAGRES:
+ return readTensor();
}
- if (isNew) {
- if (line.startsWith("units")) {
- setUnitsNew();
- } else if (line.startsWith("atom")) {
- readAtom(true);
- } else if (line.startsWith("symmetry")) {
- readSymmetryNew();
- } else if (line.startsWith("ms") || line.startsWith("efg") ||
line.startsWith("isc")) {
- readTensorNew();
- } 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")|| line.contains("TOTAL Shielding
Tensor")) {
- readTensorOld();
- }
return true;
}
- // 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
+ /**
+ * All characters after hash ignored; lines are trimmed.
+ *
+ */
+ private void trimLine() {
+ int pt = line.indexOf("#");
+ if (pt >= 0)
+ line = line.substring(0, pt);
+ line = line.trim();
+ }
- private void readTensorNew() throws Exception {
- String[] tokens = getTokens();
- String id = tokens[0];
- String atomName1 = getAtomName(tokens[1], tokens[2]);
- int pt = 3;
- String atomName2 = (id.startsWith("isc") ? getAtomName(tokens[pt++],
tokens[pt++]) : null);
- // TODO: maxIso for isc?
- 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);
- interactionTensors.addLast(t);
- } else {
- index2 = atomSetCollection.getAtomIndexFromName(atomName2);
+ /**
+ * 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;
}
- t.setAtomIndexes(index1, index2);
- String key = ";" + id +";";
- if (tensorTypes.indexOf(key) < 0) {
- tensorTypes += key;
- appendLoadNote("Ellipsoids set \"" + id + "\": "
- + (id.startsWith("ms") ? "Magnetic Shielding" :
- id.startsWith("efg") ? "Electric Field Gradient" :
id.startsWith("isc") ? "J-Coupling" : "?"));
- }
+ return BLOCK_NEW;
}
+ /**
+ * catalog units
+ *
+ * @return true
+ */
+ private boolean setUnits() {
+ String[] tokens = getTokens();
+ magresUnits.put(tokens[1], 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
- private void readSymmetryNew() {
+ /**
+ * not doing anything with this -- P1 assumed
+ * @return true
+ */
+ private boolean readSymmetry() {
+ // not used
setSymmetryOperator(getTokens()[1]);
+ return true;
}
- private void setUnitsNew() {
- String[] tokens = getTokens();
- mapUnits.put(tokens[1], tokens[2]);
- }
+ // 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
- private void readCellParams() throws Exception {
- String[] tokens = getTokens();
-
+ /**
+ *
+ * @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]);
@@ -138,78 +204,89 @@
addPrimitiveLatticeVector(1, cellParams, 3);
addPrimitiveLatticeVector(2, cellParams, 6);
setSpaceGroupName("P1");
+ return true;
}
/*
C 1 Coordinates 2.054 0.000 0.000 A
*/
- private Atom atom;
-
- private void readAtom(boolean isNew) {
- float f = ((isNew ? mapUnits.get("atom").startsWith("A") : line.trim()
- .endsWith("A")) ? 1 : ANGSTROMS_PER_BOHR);
+ /**
+ *
+ * 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 = new Atom();
- int pt = (isNew ? 1 : 0);
- atom.elementSymbol = tokens[isNew ? pt++ : pt];
+ Atom atom = new Atom();
+ int pt = 1;
+ atom.elementSymbol = tokens[pt++];
atom.atomName = getAtomName(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);
+ return true;
}
- private String getAtomName(String name, String index) {
+ /**
+ * combine name and index
+ * @param name
+ * @param index
+ * @return name_index
+ */
+ private static String getAtomName(String name, String index) {
return name + "_" + index;
}
- /*
- J-coupling Total
+ // 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
- W 1 Eigenvalue sigma_xx -412163.5628
- W 1 Eigenvector sigma_xx 0.1467 -0.9892 0.0000
- W 1 Eigenvalue sigma_yy -412163.6752
- W 1 Eigenvector sigma_yy 0.9892 0.1467 0.0000
- W 1 Eigenvalue sigma_zz -432981.4974
- W 1 Eigenvector sigma_zz 0.0000 0.0000 1.0000
-
- TOTAL tensor
-
- -0.0216 -0.1561 -0.0137
- -0.1561 -0.1236 -0.0359
- -0.0137 -0.0359 0.1452
-
+ /**
+ * Read a tensor line. Note that a corresponding unit line must have
appeared first.
+ * @return true;
+ * @throws Exception
*/
- private void readTensorOld() throws Exception {
- line = line.trim();
- if (tensorTypes.indexOf(line) < 0) {
- tensorTypes += line;
- appendLoadNote("Ellipsoids: " + line);
+ private boolean readTensor() throws Exception {
+ String[] tokens = getTokens();
+ String id = tokens[0];
+ String units = magresUnits.get(id);
+ if (units == null)
+ return true;
+ String atomName1 = getAtomName(tokens[1], tokens[2]);
+ int pt = 3;
+ String atomName2 = (id.startsWith("isc") ? getAtomName(tokens[pt++],
tokens[pt++]) : null);
+ // TODO: maxIso for isc?
+ 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);
+ interactionTensors.addLast(t);
+ } else {
+ index2 = atomSetCollection.getAtomIndexFromName(atomName2);
}
- atomSetCollection.setAtomSetName(line);
- String type = (line.indexOf("J-") >= 0 ? "isc" : line.indexOf("Shielding")
>= 0 ? "ms" : "efg");
- float[] data = new float[9];
- readLine();
- String s = TextFormat.simpleReplace(readLine() + readLine() + readLine(),
- "-", " -");
- fillFloatArray(s, 0, data);
- //float f = 3;
- if (type.equals("isc")) {
- discardLinesUntilContains("Isotropic");
- float iso = parseFloatStr(getTokens()[3]);
- if (Math.abs(iso) > maxIso)
- return;
- //f = 0.04f;
+ t.setAtomIndexes(index1, index2);
+ String key = ";" + id +";";
+ if (tensorTypes.indexOf(key) < 0) {
+ tensorTypes += key;
+ appendLoadNote("Ellipsoids set \"" + id + "\": "
+ + (id.startsWith("ms") ? "Magnetic Shielding" :
+ id.startsWith("efg") ? "Electric Field Gradient" :
id.startsWith("isc") ? "J-Coupling" : "?"));
}
- 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.addTensor(Tensor.getTensorFromAsymmetricTensor(a, type), null);
+ return true;
}
}
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