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[Jmol-commits] SF.net SVN: jmol:[12411] trunk/Jmol/src/org/jmol/adapter/readers/xtal/ CrystalReader.java
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From: <ha...@us...> - 2010-02-19 14:33:31
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Revision: 12411
http://jmol.svn.sourceforge.net/jmol/?rev=12411&view=rev
Author: hansonr
Date: 2010-02-19 14:33:22 +0000 (Fri, 19 Feb 2010)
Log Message:
-----------
preliminary CRYSTAL reader -- requires CRYSTAL:: prefix in LOAD command. -- still needs testing
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java 2010-02-19 05:35:31 UTC (rev 12410)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java 2010-02-19 14:33:22 UTC (rev 12411)
@@ -31,62 +31,53 @@
import java.io.BufferedReader;
/**
- *
+ *
* http://www.crystal.unito.it/
- *
- * @author Pieremanuele Canepa, Room 104, FM Group
- * School of Physical Sciences, Ingram Building,
- * University of Kent, Canterbury, Kent,
- * CT2 7NH
- * United Kingdom
- *
+ *
+ * @author Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences,
+ * Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United
+ * Kingdom
+ *
* @version 1.0
- *
- * This version works and has been well tested on several structures!
*
- * TODO: Needs adaptation to be more modular and flexible
- *
+ * This version works and has been well tested on several structures!
+ *
+ * TODO: Needs adaptation to be more modular and flexible
+ *
*/
public class CrystalReader extends AtomSetCollectionReader {
- private String calculationType;
- public void readAtomSetCollection(BufferedReader reader) {
+ private boolean isPrimitive = true;
+ private boolean isPolymer = false;
+ private boolean isSlab = false;
- boolean isPeriodic = true;
- boolean isFractional = true;
+ public void readAtomSetCollection(BufferedReader reader) {
+ this.reader = reader;
+ atomSetCollection = new AtomSetCollection("Crystal", this);
- atomSetCollection = new AtomSetCollection("Crystal", this);
+ isPrimitive = (filter == null || filter.indexOf("conv") >= 0);
+ atomSetCollection.setAtomSetAuxiliaryInfo("unitCellType", (isPrimitive ? "primitive" : "conventional"));
try {
- this.reader = reader;
- discardLinesUntilContains("* CRYSTAL");
- discardLinesUntilContains("EEEEEEEEEE");
- atomSetCollection.setCollectionName(readLine().trim());
- readLine();
- calculationType = readLine().trim();
- atomSetCollection.setAtomSetAuxiliaryInfo("calculationType", calculationType);
- if (calculationType.indexOf("MOLECULAR") >= 0) {
- isFractional = false;
- isPeriodic = false;
- }
+ setFractionalCoordinates(readHeader());
while (readLine() != null) {
- if (line.startsWith(" SPACE GROUP ") || line.startsWith(" CORRESPONDING SPACE GROUP")) {
- readSpaceGroup();
+ if (line.startsWith(" LATTICE PARAMETER") &&
+ (isPrimitive && line.contains("- PRIMITIVE") || !isPrimitive && line.contains("- CONVENTIONAL"))) {
+ readCellParams();
continue;
}
- if (line.startsWith(" LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL")) {
- isFractional = true;
- readCellParams();
- continue;
+ if (isPrimitive) {
+ if (line
+ .startsWith(" COORDINATES OF THE EQUIVALENT ATOMS")) {
+ readFractionalCoords();
+ continue;
+ }
+ } else {
+ if (line.startsWith(" INPUT COORDINATES")) {
+ readInputCoords();
+ continue;
+ }
}
- if (line.startsWith(" LATTICE PARAMETER (ANGSTROMS) - CONVENTIONAL CELL")) {
- isFractional = true;
- readPolymerCell();
- }
- if (line.startsWith(" INPUT COORDINATES")) {
- readAtomCoords(isFractional, isPeriodic);
- continue;
- }
}
applySymmetryAndSetTrajectory();
@@ -95,6 +86,26 @@
}
}
+ private boolean readHeader() throws Exception {
+ discardLinesUntilContains("* CRYSTAL");
+ discardLinesUntilContains("EEEEEEEEEE");
+ atomSetCollection.setCollectionName(readLine().trim());
+ readLine();
+ calculationType = readLine().trim();
+ isPolymer = (calculationType.equals("POLYMER CALCULATION"));
+ isSlab = (calculationType.equals("SLAB CALCULATION"));
+ atomSetCollection.setAtomSetAuxiliaryInfo("calculationType",
+ calculationType);
+ if (calculationType.indexOf("MOLECULAR") >= 0)
+ return false;
+ if (!isPrimitive) {
+ readLine();
+ readLine();
+ readSpaceGroup();
+ }
+ return true;
+ }
+
private void readSpaceGroup() {
// SPACE GROUP (CENTROSYMMETRIC) : F M 3 M
String name = line.substring(line.indexOf(":") + 1).trim();
@@ -102,35 +113,61 @@
}
private void readCellParams() throws Exception {
+ if (isPolymer) {
+ float a = parseFloat(line.substring(line.indexOf("CELL") + 4));
+ setUnitCell(a, 1, 1, 90, 90, 90);
+ return;
+ }
readLine();
String[] tokens = getTokens(readLine());
- if (calculationType.equals("SLAB CALCULATION")) {
- setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), 1, 90, 90,
- parseFloat(tokens[2]));
+ if (isSlab) {
+ setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), 1,
+ parseFloat(tokens[3]), parseFloat(tokens[4]), parseFloat(tokens[5]));
} else {
- setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]),
- parseFloat(tokens[2]), parseFloat(tokens[3]), parseFloat(tokens[4]),
- parseFloat(tokens[5]));
+ setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), parseFloat(tokens[2]),
+ parseFloat(tokens[3]), parseFloat(tokens[4]), parseFloat(tokens[5]));
}
}
- private void readPolymerCell() {
- float a = parseFloat(line.substring(line.indexOf("CELL") + 4));
- setUnitCell(a, 1, 1, 90, 90, 90);
-
- }
+ /*
+ COORDINATES OF THE EQUIVALENT ATOMS
+ (X AND Y IN FRACTIONARY UNITS, Z IN ANGSTROMS)
+ N. ATOM EQUIV AT. N. X Y Z
- /*
- INPUT COORDINATES
+ 1 1 1 26 FE 3.33130643604E-01 1.66339516481E-01 6.03501134235E+00
+ */
+ private void readFractionalCoords() throws Exception {
+ discardLinesUntilContains("ATOM EQUIV");
+ while (readLine() != null && line.indexOf("NUMBER OF SYMM") < 0) {
+ if (line.length() == 0)
+ continue;
+ Atom atom = atomSetCollection.addNewAtom();
+ String[] tokens = getTokens();
+ int atomicNumber = parseInt(tokens[3]);
+ float x = parseFloat(tokens[5]);
+ float y = parseFloat(tokens[6]);
+ float z = parseFloat(tokens[7]);
+ if (isPolymer || isSlab) {
+ if (x < 0)
+ x += 1;
+ if (y < 0)
+ y += 1;
+ }
+ setAtomCoord(atom, x, y, z);
+ atom.elementSymbol = getElementSymbol(atomicNumber);
+ }
+ }
- ATOM AT. N. COORDINATES
- 1 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
- 2 8 5.000000000000E-01 5.000000000000E-01 5.000000000000E-01
- */
- private void readAtomCoords(boolean isFractional, boolean isthisPeriodic)
+ /*
+ * INPUT COORDINATES
+ *
+ * ATOM AT. N. COORDINATES
+ * 1 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ * 2 8 5.000000000000E-01 5.000000000000E-01 5.000000000000E-01
+ */
+ private void readInputCoords()
throws Exception {
- setFractionalCoordinates(isFractional);
readLine();
readLine();
while (readLine() != null && line.length() > 0) {
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