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[Jmol-commits] SF.net SVN: jmol:[16027] trunk/Jmol/src/org/jmol/adapter/readers/xtal/ CrystalReader.java
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From: <ha...@us...> - 2011-09-03 10:40:15
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Revision: 16027
http://jmol.svn.sourceforge.net/jmol/?rev=16027&view=rev
Author: hansonr
Date: 2011-09-03 10:40:08 +0000 (Sat, 03 Sep 2011)
Log Message:
-----------
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 2011-09-03 10:36:13 UTC (rev 16026)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java 2011-09-03 10:40:08 UTC (rev 16027)
@@ -111,6 +111,7 @@
private Point3f ptOriginShift = new Point3f();
private Matrix3f primitiveToCryst;
private Vector3f[] directLatticeVectors;
+ private String spaceGroupName;
@Override
protected void initializeReader() throws Exception {
@@ -119,17 +120,12 @@
addVibrations &= !inputOnly;
isPrimitive = !inputOnly && !checkFilter("CONV");
getLastConventional = (!isPrimitive && desiredModelNumber == 0);
- setFractionalCoordinates(!isProperties ? readHeader() : false);
+ setFractionalCoordinates(readHeader());
}
@Override
protected boolean checkLine() throws Exception {
- if (line.startsWith(" CRYSTAL - PROPERTIES - TYPE OF CALCULATION")) {
- isProperties = true;
- return true;
- }
-
if (line.startsWith(" LATTICE PARAMETER")) {
boolean isConvLattice = (line.indexOf("- CONVENTIONAL") >= 0);
if (isConvLattice) {
@@ -189,7 +185,7 @@
}
if (line
- .startsWith(" DIRECT LATTICE VECTORS CARTESIAN COMPONENTS (ANGSTROM)"))
+ .startsWith(" DIRECT LATTICE VECTOR"))
return setDirect();
if (line.indexOf("DIMENSIONALITY OF THE SYSTEM") >= 0) {
@@ -225,7 +221,7 @@
|| isProperties && line.startsWith(" ATOM N.AT.")) {
if (!doGetModel(++modelNumber))
return checkLastModel();
- return readFractionalCoords();
+ return readAtoms();
}
if (!doProcessLines)
@@ -271,8 +267,14 @@
if (line.startsWith(" TOTAL ATOMIC SPINS :"))
return readMagneticMoments();
+ if (!isProperties)
+ return true;
+
/// From here on we are considering only keywords of properties output files
+ if (line.startsWith(" DEFINITION OF TRACELESS")) {
+ return getPropertyTensors();
+ }
return true;
}
@@ -291,14 +293,27 @@
0.290663292155E+01 0.000000000000E+00 0.460469095849E+01
-0.145331646077E+01 0.251721794953E+01 0.460469095849E+01
-0.145331646077E+01 -0.251721794953E+01 0.460469095849E+01
+
+ or
+
+ DIRECT LATTICE VECTOR COMPONENTS (BOHR)
+ 11.12550 0.00000 0.00000
+ 0.00000 10.45091 0.00000
+ 0.00000 0.00000 8.90375
+
+
*/
private boolean setDirect() throws Exception {
- readLine();
+ boolean isBohr = (line.indexOf("(BOHR") >= 0);
+ if (!isBohr)
+ readLine();
directLatticeVectors = new Vector3f[3];
- directLatticeVectors[0] = getPoint3f(null, 0);
- directLatticeVectors[1] = getPoint3f(null, 0);
- directLatticeVectors[2] = getPoint3f(null, 0);
+ for (int i = 0; i < 3; i++) {
+ directLatticeVectors[i] = getPoint3f(null, 0);
+ if (isBohr)
+ directLatticeVectors[i].scale(ANGSTROMS_PER_BOHR);
+ }
if (Logger.debugging) {
addJmolScript("draw va vector {0 0 0} "
@@ -333,7 +348,7 @@
.getMatrix();
Logger.info("oriented unit cell is in model "
+ atomSetCollection.getAtomSetCount());
- return true;
+ return !isProperties;
}
private Vector3f getPoint3f(float[] f, int pt) throws Exception {
@@ -459,16 +474,26 @@
private boolean readHeader() throws Exception {
discardLinesUntilContains("* CRYSTAL");
+
isVersion3 = (line.indexOf("CRYSTAL03") >= 0);
discardLinesUntilContains("EEEEEEEEEE");
- atomSetCollection.setCollectionName(readLine().trim()
- + (desiredModelNumber == 0 ? " (optimized)" : ""));
- readLine();
+ String name;
+ if (readLine().length() == 0) {
+ name = readLines(2).trim();
+ } else {
+ name = line.trim();
+ readLine();
+ }
String type = readLine().trim();
/*
* This is when the initial geometry is read from an external file GEOMETRY
* INPUT FROM EXTERNAL FILE (FORTRAN UNIT 34)
*/
+ int pt = type.indexOf("- PROPERTIES");
+ if (pt >= 0) {
+ isProperties = true;
+ type = type.substring(0, pt).trim();
+ }
if (type.indexOf("EXTERNAL FILE") >= 0) {
type = readLine().trim();
isPolymer = (type.equals("1D - POLYMER"));
@@ -477,6 +502,8 @@
isPolymer = (type.equals("POLYMER CALCULATION"));
isSlab = (type.equals("SLAB CALCULATION"));
}
+ atomSetCollection.setCollectionName(name
+ + (!isProperties && desiredModelNumber == 0 ? " (optimized)" : ""));
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("symmetryType", type);
if ((isPolymer || isSlab) && !isPrimitive) {
Logger.error("Cannot use FILTER \"conventional\" with POLYMER or SLAB");
@@ -493,54 +520,45 @@
line.substring(line.indexOf(" OR ") + 4).trim());
return false;
}
+ spaceGroupName = "P1";
if (!isPrimitive) {
- discardLines(5);
- setSpaceGroupName(line.indexOf(":") >= 0 ? line.substring(
- line.indexOf(":") + 1).trim() : "P1");
+ readLines(5);
+ pt = line.indexOf(":");
+ if (pt >= 0)
+ spaceGroupName = line.substring(pt + 1).trim();
}
-
- return true;
+ doApplySymmetry = isProperties;
+ return !isProperties;
}
private void readCellParams(boolean isNewSet) throws Exception {
- directLatticeVectors = null;
+ float f = (line.indexOf("(BOHR") >= 0 ? ANGSTROMS_PER_BOHR : 1);
if (isNewSet)
newAtomSet();
if (isPolymer && !isPrimitive) {
- float a = parseFloat(line.substring(line.indexOf("CELL") + 4));
- setUnitCell(a, -1, -1, 90, 90, 90);
+ setUnitCell(parseFloat(line.substring(line.indexOf("CELL") + 4)) * f, -1, -1, 90, 90, 90);
} else {
discardLinesUntilContains("GAMMA");
String[] tokens = getTokens(readLine());
if (isSlab) {
if (isPrimitive)
- setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), -1,
+ setUnitCell(parseFloat(tokens[0]) * f, parseFloat(tokens[1]) * f, -1,
parseFloat(tokens[3]), parseFloat(tokens[4]),
parseFloat(tokens[5]));
else
- setUnitCell(parseFloat(tokens[0]), parseFloat(tokens[1]), -1, 90, 90,
+ setUnitCell(parseFloat(tokens[0]) * f, parseFloat(tokens[1]) * f, -1, 90, 90,
parseFloat(tokens[2]));
} else if (isPolymer) {
- setUnitCell(parseFloat(tokens[0]), -1, -1, parseFloat(tokens[3]),
+ setUnitCell(parseFloat(tokens[0]) * f, -1, -1, parseFloat(tokens[3]),
parseFloat(tokens[4]), parseFloat(tokens[5]));
} else {
- setUnitCell(convertCellParam(tokens[0]), convertCellParam(tokens[1]),
- convertCellParam(tokens[2]), parseFloat(tokens[3]),
+ setUnitCell(parseFloat(tokens[0]) * f, parseFloat(tokens[1]) * f,
+ parseFloat(tokens[2]) * f, parseFloat(tokens[3]),
parseFloat(tokens[4]), parseFloat(tokens[5]));
}
}
}
- private float convertCellParam(String tokens) {
- float cellParam;
- if (isProperties) {
- cellParam = parseFloat(tokens) * ANGSTROMS_PER_BOHR;
- } else {
- cellParam = parseFloat(tokens);
- }
- return cellParam;
- }
-
/**
* create arrays that maps primitive atoms to conventional atoms in a 1:1
* fashion. Creates:
@@ -562,7 +580,7 @@
for (int i = 0; i < n; i++)
indexToPrimitive[i] = -1;
- discardLines(3);
+ readLines(3);
while (readLine() != null && line.indexOf(" NOT IRREDUCIBLE") >= 0) {
// example HA_BULK_PBE_FREQ.OUT
// we remove unnecessary atoms. This is important, because
@@ -574,7 +592,7 @@
}
// COORDINATES OF THE EQUIVALENT ATOMS
- discardLines(3);
+ readLines(3);
int iPrim = 0;
int nPrim = 0;
while (readLine() != null && line.indexOf("NUMBER") < 0) {
@@ -607,49 +625,67 @@
}
/*
- * ATOMS IN THE ASYMMETRIC UNIT 30 - ATOMS IN THE UNIT CELL: 30 ATOM X/A Y/B
- * Z(ANGSTROM)
- * ***************************************************************** 1 T 26 FE
- * 3.332220233571E-01 1.664350001467E-01 5.975038441891E+00 2 T 8 O
- * -3.289334452690E-01 1.544678332212E-01 5.601153565811E+00
+ ATOMS IN THE ASYMMETRIC UNIT 2 - ATOMS IN THE UNIT CELL: 4
+ ATOM X/A Y/B Z/C
+ *******************************************************************************
+ 1 T 282 PB 0.000000000000E+00 5.000000000000E-01 2.385000000000E-01
+ 2 F 282 PB 5.000000000000E-01 0.000000000000E+00 -2.385000000000E-01
+ 3 T 8 O 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ 4 F 8 O 5.000000000000E-01 5.000000000000E-01 0.000000000000E+00
+
+ or
+
+ ATOM N.AT. SHELL X(A) Y(A) Z(A) EXAD N.ELECT.
+ *******************************************************************************
+ 1 282 PB 4 1.331 -0.077 1.178 1.934E-01 2.891
+ 2 282 PB 4 -1.331 0.077 -1.178 1.934E-01 2.891
+ 3 282 PB 4 1.331 -2.688 -1.178 1.934E-01 2.891
+ 4 282 PB 4 -1.331 2.688 1.178 1.934E-01 2.891
+ 5 8 O 5 -0.786 0.522 1.178 6.500E-01 9.109
+ 6 8 O 5 0.786 -0.522 -1.178 6.500E-01 9.109
+ 7 8 O 5 -0.786 2.243 -1.178 6.500E-01 9.109
+ 8 8 O 5 0.786 -2.243 1.178 6.500E-01 9.109
+
*/
- private boolean readFractionalCoords() throws Exception {
+ private boolean readAtoms() throws Exception {
if (isMolecular)
newAtomSet();
- readLine();
- readLine();
+ discardLinesUntilContains("*");
int i = atomIndexLast;
- boolean doNormalizePrimitive = isPrimitive && !isMolecular && !isPolymer
- && !isSlab && (!doApplySymmetry || latticeCells[2] != 0);
+ // I turned off normalization -- proper way to do this is to
+ // add the "packed" keyword. As it was, it was impossible to
+ // load the file with its original coordinates
+
+ boolean doNormalizePrimitive =
+ false && isPrimitive && !isMolecular && !isPolymer
+ && !isSlab && (!doApplySymmetry || latticeCells[2] != 0);
atomIndexLast = atomSetCollection.getAtomCount();
- while (readLine() != null && !isProperties ? line.length() > 0
- : getTokens().length > 1) { ///&& !isPrimitive ? line.indexOf("=") < 0 : line.indexOf("*") < 0 )
+ while (readLine() != null && line.length() > 0 && line.indexOf(isPrimitive ? "*" : "=") < 0) {
Atom atom = atomSetCollection.addNewAtom();
String[] tokens = getTokens();
- int atomicNumber = !isProperties ? getAtomicNumber(tokens[2])
- : getAtomicNumber(tokens[1]);
- atom.atomName = !isProperties ? getAtomName(tokens[3])
- : getAtomName(tokens[2]);
-
- float x = parseFloat(tokens[4]);
- float y = parseFloat(tokens[5]);
- float z = parseFloat(tokens[6]);
+ int pt = (isProperties ? 1 : 2);
+ atom.elementSymbol = getElementSymbol(getAtomicNumber(tokens[pt++]));
+ atom.atomName = getAtomName(tokens[pt++]);
+ if (isProperties)
+ pt++; // skip SHELL
+ float x = parseFloat(tokens[pt++]);
+ float y = parseFloat(tokens[pt++]);
+ float z = parseFloat(tokens[pt]);
if (haveCharges)
atom.partialCharge = atomSetCollection.getAtom(i++).partialCharge;
- // note: this normalization is unique to this reader -- all other
- // readers operate through symmetry application
- if (x < 0 && (isPolymer || isSlab || doNormalizePrimitive))
- x += 1;
- if (y < 0 && (isSlab || doNormalizePrimitive))
- y += 1;
- if (z < 0 && doNormalizePrimitive)
- z += 1;
+ if (!isProperties) {
+ // note: this normalization is unique to this reader -- all other
+ // readers operate through symmetry application
+ if (x < 0 && (isPolymer || isSlab || doNormalizePrimitive))
+ x += 1;
+ if (y < 0 && (isSlab || doNormalizePrimitive))
+ y += 1;
+ if (z < 0 && doNormalizePrimitive)
+ z += 1;
+ }
setAtomCoord(atom, x, y, z);
- atom.elementSymbol = getElementSymbol(atomicNumber);
}
- if (isProperties)
- applySymmetryAndSetTrajectory();
atomCount = atomSetCollection.getAtomCount() - atomIndexLast;
return true;
}
@@ -724,15 +760,12 @@
}
private void newAtomSet() throws Exception {
- if (atomSetCollection.getAtomCount() == 0)
- return;
- if (isProperties) {
- setFractionalCoordinates(false);
- setSpaceGroupName("P1");
- } else {
+ if (atomSetCollection.getAtomCount() > 0) {
applySymmetryAndSetTrajectory();
+ atomSetCollection.newAtomSet();
}
- atomSetCollection.newAtomSet();
+ if (spaceGroupName != null)
+ setSpaceGroupName(spaceGroupName);
}
private void readEnergy() {
@@ -760,7 +793,7 @@
if (haveCharges || atomSetCollection.getAtomCount() == 0)
return true;
haveCharges = true;
- discardLines(3);
+ readLines(3);
Atom[] atoms = atomSetCollection.getAtoms();
int i0 = atomSetCollection.getLastAtomSetAtomIndex();
int iPrim = 0;
@@ -932,4 +965,71 @@
+ " km/Mole), " + activity);
}
+ /*
+ DEFINITION OF TRACELESS QUADRUPOLE TENSORS:
+
+ (3XX-RR)/2=(2,2)/4-(2,0)/2
+ (3YY-RR)/2=-(2,2)/4-(2,0)/2
+ (3ZZ-RR)/2=(2,0)
+ 3XY/2=(2,-2)/4 3XZ/2=(2,1)/2 3YZ/2=(2,-1)/2
+
+ *** ATOM N. 1 (Z=282) PB
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 6.265724E-01 BB -2.651563E-01 CC -3.614161E-01
+
+ *** ATOM N. 2 (Z=282) PB
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 6.265724E-01 BB -2.651563E-01 CC -3.614161E-01
+
+ *** ATOM N. 3 (Z=282) PB
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 6.265724E-01 BB -2.651563E-01 CC -3.614161E-01
+
+ *** ATOM N. 4 (Z=282) PB
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 6.265724E-01 BB -2.651563E-01 CC -3.614161E-01
+
+ *** ATOM N. 5 (Z= 8) O
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 3.258167E-01 BB -1.529525E-01 CC -1.728642E-01
+
+ *** ATOM N. 6 (Z= 8) O
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 3.258167E-01 BB -1.529525E-01 CC -1.728642E-01
+
+ *** ATOM N. 7 (Z= 8) O
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 3.258167E-01 BB -1.529525E-01 CC -1.728642E-01
+
+ *** ATOM N. 8 (Z= 8) O
+
+ TENSOR IN PRINCIPAL AXIS SYSTEM
+ AA 3.258167E-01 BB -1.529525E-01 CC -1.728642E-01
+ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT POLI TELAPSE 0.05 TCPU 0.04
+ */
+ private boolean getPropertyTensors() throws Exception {
+ readLines(6);
+ Atom[] atoms = atomSetCollection.getAtoms();
+ while (readLine() != null && line.startsWith(" *** ATOM")) {
+ String[] tokens = getTokens();
+ int index = parseInt(tokens[3]) - 1;
+ Atom atom = atoms[index];
+ tokens = getTokens(readLines(3));
+ atom.ellipsoid = symmetry.getEllipsoid(directLatticeVectors,
+ parseFloat(tokens[1]),
+ parseFloat(tokens[3]),
+ parseFloat(tokens[5]));
+ readLine();
+ }
+ return true;
+ }
+
+
}
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