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[Jmol-commits] SF.net SVN: jmol:[14862] trunk/Jmol/src/org/jmol/adapter/readers/xtal/ GulpReader.java
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From: <ha...@us...> - 2010-12-22 13:30:31
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Revision: 14862
http://jmol.svn.sourceforge.net/jmol/?rev=14862&view=rev
Author: hansonr
Date: 2010-12-22 13:30:24 +0000 (Wed, 22 Dec 2010)
Log Message:
-----------
GULP reader fixes
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java 2010-12-22 00:03:32 UTC (rev 14861)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/GulpReader.java 2010-12-22 13:30:24 UTC (rev 14862)
@@ -1,6 +1,7 @@
package org.jmol.adapter.readers.xtal;
import org.jmol.adapter.smarter.Atom;
+import org.jmol.adapter.smarter.AtomSetCollection;
import org.jmol.adapter.smarter.AtomSetCollectionReader;
/**
@@ -29,93 +30,180 @@
private boolean isSlab;
private boolean isPolymer;
private boolean isMolecular;
- private boolean isCrystal;
+ private boolean isPrimitive;
+ private String sep = "-------";
@Override
protected void initializeReader() throws Exception {
- setFractionalCoordinates(readType());
+ setFractionalCoordinates(readDimensionality());
+ isPrimitive = !checkFilter("CONV");
}
+ private boolean bTest;
+
@Override
protected boolean checkLine() throws Exception {
+ System.out.println(line);
if (line.contains("Space group ")) {
readSpaceGroup();
- } else if (line.contains("Cartesian lattice vectors")
- || line.contains("Surface cell parameters")) {
+ return true;
+ }
+
+ if (isSlab ? line.contains("Surface cell parameters")
+ : isPrimitive ? line.contains("Cartesian lattice vectors")
+ : line.contains("Cell parameters (Angstroms/Degrees)")) {
readCellParameters();
- } else if (line.contains("Final cell parameters and derivatives")) {
- readFinalCell();
- } else if (line.contains("Fractional coordinates of asymmetric unit :")
- || line.contains("Final fractional coordinates of atoms :")
+ return true;
+ }
+
+ if (line.contains("Fractional coordinates of asymmetric unit :")
|| line.contains("Final asymmetric unit coordinates")
- || line.contains("Final fractional coordinates ")
+ || (bTest = line.contains("Final fractional coordinates "))
|| line
.contains(" Mixed fractional/Cartesian coordinates of surface :")
|| line.contains("Cartesian coordinates of cluster ")
|| line.contains(" Final cartesian coordinates of atoms :")
&& isMolecular) {
if (doGetModel(++modelNumber))
- readAtomicPos();
- } else if (line.contains("Monopole - monopole (total)")) {
+ readAtomicPos(!bTest);
+ return true;
+ }
+ // past this point, we must already have coordinates defined
+ if (!doProcessLines)
+ return true;
+ if (line.contains("Final cell parameters and derivatives")) {
+ // this line comes AFTER atom positions
+ readFinalCell();
+ return true;
+ }
+ if (line.contains("Monopole - monopole (total)")) {
readEnergy();
- //} else if (line.contains(" Phonon Calculation : ")) {
- // readFrequency();
+ return true;
}
+
+ //if (line.contains(" Phonon Calculation : ")) {
+ // readFrequency();
+
return true;
}
- private boolean readType() throws Exception {
+ private boolean readDimensionality() throws Exception {
discardLinesUntilContains("Dimensionality");
String[] tokens = getTokens();
switch (parseInt(tokens[2])) {
case 0:
isMolecular = true;
+ isPrimitive = false;
return false;
case 1:
isPolymer = true;
+ isPrimitive = false;
break;
case 2:
isSlab = true;
+ isPrimitive = false;
break;
- case 3:
- isCrystal = true;
- break;
}
return true;
}
+ private void readSpaceGroup() throws Exception {
+ spaceGroup = (isPrimitive ? "P1"
+ : line.substring(line.indexOf(":") + 1).trim());
+ }
+ private float a, b, c, alpha, beta, gamma;
+ private float[] primitiveData;
+ private static String[] tags = AtomSetCollection.notionalUnitcellTags;
- private void readSpaceGroup() throws Exception {
- spaceGroup = line.substring(line.indexOf(":") + 1).trim();
- //spaceGroup = "P1";
+ private static int parameterIndex(String key) {
+ for (int i = tags.length; --i >= 0;)
+ if (tags[i].equals(key))
+ return i;
+ return -1;
+ }
+
+ private void setParameter(String key, float value) {
+ switch (parameterIndex(key)) {
+ case 0:
+ a = value;
+ break;
+ case 1:
+ b = value;
+ break;
+ case 2:
+ c = value;
+ break;
+ case 3:
+ alpha = value;
+ break;
+ case 4:
+ beta = value;
+ break;
+ case 5:
+ gamma = value;
+ break;
+ }
+ }
+
+ private void newAtomSet(boolean doSetUnitCell) {
+ atomSetCollection.newAtomSet();
+ if (doSetUnitCell)
+ setUnitCell();
+ }
+
+ private void setUnitCell() {
setSpaceGroupName(spaceGroup);
+ if (a == 0 && primitiveData == null)
+ return;
+ if (a == 0) {
+ addPrimitiveLatticeVector(0, primitiveData, 0);
+ addPrimitiveLatticeVector(1, primitiveData, 3);
+ addPrimitiveLatticeVector(2, primitiveData, 6);
+ } else {
+ if (isSlab) {
+ c = -1;
+ if (beta == 0)
+ beta = gamma = 90;
+ } else if (isPolymer) {
+ b = c = -1;
+ alpha = beta = gamma = 90;
+ }
+ setUnitCell(a, b, c, alpha, beta, gamma);
+ }
}
+ /*
+
+ Cartesian lattice vectors (Angstroms) :
+
+ 10.944693 0.000000 0.000000
+ 3.123705 4.493221 0.000000
+ 3.123705 1.632784 4.186054
+
+ Cell parameters (Angstroms/Degrees):
+
+ a = 10.9447 alpha = 55.1928
+ b = 5.4723 beta = 55.1928
+ c = 5.4723 gamma = 55.1928
+
+ */
+
private void readCellParameters() throws Exception {
discardLines(1);
- if (isCrystal) {
- float[] data = new float[9];
- fillFloatArray(data, null, 0);
- addPrimitiveLatticeVector(0, data, 0);
- addPrimitiveLatticeVector(1, data, 3);
- addPrimitiveLatticeVector(2, data, 6);
- } else if (isSlab) {
- //See example 31 I cannot remember How we did for CRYSTAL?
- discardLines(1);
- String[] tokens = getTokens(line.substring(line.indexOf("=")));
- float a = parseFloat(tokens[0]);
- float alpha = parseFloat(tokens[3]);
- tokens = getTokens(readLine());
- float b = parseFloat(tokens[2]);
- setUnitCell(a, b, -1, alpha, 90, 90);
- } else if (isPolymer) {
- //See example 32 I cannot recall How we did for CRYSTAL?
- discardLines(1);
- String[] tokens = getTokens(line.substring(line.indexOf("=")));
- float a = parseFloat(tokens[0]);
- setUnitCell(a, -1, -1, 90, 90, 90);
+ if (isPrimitive) {
+ primitiveData = new float[9];
+ fillFloatArray(primitiveData, null, 0);
+ a = 0;
+ return;
}
+ while (readLine() != null && line.contains("=")) {
+ String[] tokens = getTokens();
+ if (tokens.length >1 && tokens[1].equals("="))
+ setParameter(tokens[0], parseFloat(tokens[2]));
+ if (tokens.length > 5 && tokens[4].equals("="))
+ setParameter(tokens[3], parseFloat(tokens[5]));
+ }
}
/*
@@ -134,25 +222,12 @@
*/
private void readFinalCell() throws Exception {
- float cellArray[] = new float[6];
- int counter = 0;
-
- discardLines(2);
- while (readLine() != null && line.indexOf("----------") < 0) {
- String[] tokens = getTokens();
- cellArray[counter] = parseFloat(tokens[1]);
- counter++;
- }
-
- if (isCrystal) {
- setUnitCell(cellArray[0], cellArray[1], cellArray[2], cellArray[3],
- cellArray[4], cellArray[5]);
- } else if (isSlab) {
- setUnitCell(cellArray[0], cellArray[1], -1, cellArray[2], 90, 90);
- } else if (isPolymer) {
- setUnitCell(cellArray[0], -1, -1, 90, 90, 90);
- }
-
+ discardLinesUntilContains(sep);
+ String tokens[];
+ while (readLine() != null && (tokens = getTokens()).length >= 2)
+ setParameter(tokens[0], parseFloat(tokens[1]));
+ setUnitCell();
+ applySymmetryAndSetTrajectory();
}
/* Fractional coordinates of asymmetric unit :
@@ -206,11 +281,11 @@
*/
- private void readAtomicPos() throws Exception {
- discardLines(5);
- //atomSetCollection.newAtomSet();
- while (readLine() != null && line.indexOf("----------") < 0) {
- //This if is when the line contains extra *
+ private void readAtomicPos(boolean finalizeSymmetry) throws Exception {
+ newAtomSet(finalizeSymmetry);
+ discardLinesUntilContains(sep);
+ discardLinesUntilContains(sep);
+ while (readLine() != null && line.indexOf(sep) < 0) {
line = line.replace('*', ' ');
String[] tokens = getTokens();
if (!tokens[2].equals("c"))
@@ -220,9 +295,8 @@
setAtomCoord(atom, parseFloat(tokens[3]), parseFloat(tokens[4]),
parseFloat(tokens[5]));
}
- atomSetCollection.newAtomSet(); ///Not too sure it has to be here
- applySymmetryAndSetTrajectory();
-
+ if (finalizeSymmetry)
+ applySymmetryAndSetTrajectory();
}
/*
@@ -243,25 +317,27 @@
*/
private Double totEnergy;
+ private String energyUnits;
private void readEnergy() throws Exception {
- discardLines(2);
- if (line.contains("-------") || line.contains(":"))
- discardLines(1);
- totEnergy = Double.valueOf(Double.parseDouble(line.substring(line
- .indexOf("=") + 1, line.indexOf("eV") - 2)));
+ // question: Why read monopole-monopole energy as "totEnergy"?
+ // note that in some cases this is in Kcal/mol
+ if (line.indexOf("=") < 0)
+ discardLinesUntilContains("=");
+ String[] tokens = getTokens(line.substring(line.indexOf("=")));
+ totEnergy = Double.valueOf(Double.parseDouble(tokens[1]));
+ energyUnits = tokens[2];
//this avoid the class to re-reading the Total lattice energy expressed in other units
//don't change it to larger or smaller value
- discardLines(14);
- setEnergy();
-
+ discardLinesUntilContains(sep);
+ setEnergy();
}
private void setEnergy() {
atomSetCollection.setAtomSetEnergy("" + totEnergy, totEnergy.floatValue());
atomSetCollection.setAtomSetAuxiliaryInfo("Energy", totEnergy);
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("Energy", totEnergy);
- atomSetCollection.setAtomSetName("E = " + totEnergy + " eV");
+ atomSetCollection.setAtomSetName("E = " + totEnergy + " " + energyUnits);
}
/*
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