Revision: 18646
http://sourceforge.net/p/jmol/code/18646
Author: hansonr
Date: 2013-09-06 17:26:07 +0000 (Fri, 06 Sep 2013)
Log Message:
-----------
___JmolVersion="13.2.5_dev_2013.09.06"
bug fix: CRYSTAL reader not allowing vibration for conventional cell
Modified Paths:
--------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
branches/v13_2/Jmol/src/org/jmol/adapter/smarter/Atom.java
branches/v13_2/Jmol/src/org/jmol/script/ScriptCompiler.java
branches/v13_2/Jmol/src/org/jmol/util/Escape.java
branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-09-06 17:25:32 UTC (rev 18645)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-09-06 17:26:07 UTC (rev 18646)
@@ -99,7 +99,7 @@
private boolean isSlab;
private boolean isMolecular;
private boolean haveCharges;
- private boolean isFreqCalc;
+ //private boolean isFreqCalc;
private boolean inputOnly;
private boolean isLongMode;
private boolean getLastConventional;
@@ -111,7 +111,7 @@
private int[] atomFrag;
private int[] primitiveToIndex;
private float[] nuclearCharges;
- private JmolList<String> vInputCoords;
+ private JmolList<String> vCoords;
private Double energy;
private P3 ptOriginShift = new P3();
@@ -124,72 +124,68 @@
doProcessLines = false;
inputOnly = checkFilterKey("INPUT");
isPrimitive = !inputOnly && !checkFilterKey("CONV");
- addVibrations &= !inputOnly && isPrimitive; //
+ addVibrations &= !inputOnly;
getLastConventional = (!isPrimitive && desiredModelNumber == 0);
setFractionalCoordinates(readHeader());
}
@Override
protected boolean checkLine() throws Exception {
-
if (line.startsWith(" LATTICE PARAMETER")) {
boolean isConvLattice = (line.indexOf("- CONVENTIONAL") >= 0);
if (isConvLattice) {
// skip if we want primitive and this is the conventional lattice
if (isPrimitive)
return true;
- readCellParams(true);
+ readLatticeParams(true);
} else if (!isPrimitive && !havePrimitiveMapping &&
!getLastConventional) {
- if (readPrimitiveMapping())
+ readLines(3);
+ readPrimitiveMapping();
+ if (setPrimitiveMapping())
return true; // just for properties
// no input coordinates -- continue;
}
- readCellParams(true);
+ readLatticeParams(true);
if (!isPrimitive) {
discardLinesUntilContains(" TRANSFORMATION");
readTransformationMatrix();
discardLinesUntilContains(" CRYSTALLOGRAPHIC");
- readCellParams(false);
+ readLatticeParams(false);
discardLinesUntilContains(" CRYSTALLOGRAPHIC");
- readCrystallographicCoords();
- if (modelNumber == 1) {
- // done here
- } else if (!isFreqCalc) {
- // conventional cell and now the lattice has changed.
- // ignore? Can we convert a new primitive cell to conventional cell?
- //continuing = false;
- //Logger.error("Ignoring structure " + modelNumber + " due to FILTER
\"conventional\"");
- //return true;
- }
+ readCoordLines();
+// if (modelNumber == 1) {
+// // done here
+// } else if (!isFreqCalc) {
+// // conventional cell and now the lattice has changed.
+// // ignore? Can we convert a new primitive cell to conventional
cell?
+// //continuing = false;
+// //Logger.error("Ignoring structure " + modelNumber + " due to
FILTER \"conventional\"");
+// //return true;
+// }
if (!getLastConventional) {
- if (!doGetModel(++modelNumber, null)) {
- vInputCoords = null;
+ if (doGetModel(++modelNumber, null)) {
+ createAtomsFromCoordLines();
+ } else {
+ vCoords = null;
checkLastModel();
}
- processInputCoords();
}
}
return true;
}
- if (isPrimitive) {
- if (line.indexOf("VOLUME=") >= 0 && line.indexOf("- DENSITY") >= 0)
- return readVolumePrimCell();
- //if (line.startsWith(" TRANSFORMATION MATRIX"))
- //return getOrientationMatrix();
- } else {
+ if (!isPrimitive) {
if (line.startsWith(" SHIFT OF THE ORIGIN"))
return readShift();
if (line.startsWith(" INPUT COORDINATES")) {
- readCrystallographicCoords(); // note, these will not be the full set
of atoms, so we IGNORE VIBRATIONS
+ readCoordLines(); // note, these will not be the full set of atoms, so
we IGNORE VIBRATIONS
if (inputOnly)
continuing = false;
return true;
}
}
- if (line
- .startsWith(" DIRECT LATTICE VECTOR"))
+ if (line.startsWith(" DIRECT LATTICE VECTOR"))
return setDirect();
if (line.indexOf("DIMENSIONALITY OF THE SYSTEM") >= 0) {
@@ -200,13 +196,13 @@
return true;
}
- if (line.indexOf("FRQFRQ") >= 0) {
- isFreqCalc = true;
- return true;
- }
+// if (line.indexOf("FRQFRQ") >= 0) {
+// isFreqCalc = true;
+// return true;
+// }
- if (line.startsWith(" FREQUENCIES COMPUTED ON A FRAGMENT"))
- return readFragments();
+ if (addVibrations && line.startsWith(" FREQUENCIES COMPUTED ON A
FRAGMENT"))
+ return readFreqFragments();
if (line.indexOf("CONSTRUCTION OF A NANOTUBE FROM A SLAB") >= 0) {
isPolymer = true;
@@ -221,12 +217,17 @@
return true;
}
- if ((isPrimitive && line.startsWith(" ATOMS IN THE ASYMMETRIC UNIT"))
+ if (((isPrimitive || isMolecular) && line.startsWith(" ATOMS IN THE
ASYMMETRIC UNIT"))
|| isProperties && line.startsWith(" ATOM N.AT.")) {
if (!doGetModel(++modelNumber, null))
return checkLastModel();
return readAtoms();
}
+
+ if (line.startsWith(" * SUPERCELL OPTION")) {
+ discardLinesUntilContains("GENERATED");
+ return true;
+ }
if (!doProcessLines)
return true;
@@ -256,8 +257,7 @@
&& line.contains(isVersion3 ? "EIGENVALUES (EV) OF THE MASS"
: "EIGENVALUES (EIGV) OF THE MASS")
|| line.indexOf("LONGITUDINAL OPTICAL (LO)") >= 0) {
- if (vInputCoords != null)
- processInputCoords();
+ createAtomsFromCoordLines();
isLongMode = (line.indexOf("LONGITUDINAL OPTICAL (LO)") >= 0);
return readFrequencies();
}
@@ -266,18 +266,23 @@
return readGradient();
if (line.startsWith(" ATOMIC SPINS SET"))
- return readSpins();
+ return readData("spin", 3);
if (line.startsWith(" TOTAL ATOMIC SPINS :"))
- return readMagneticMoments();
+ return readData("magneticMoment", 1);
+ if (line.startsWith(" BORN CHARGE TENSOR."))
+ return readBornChargeTensors();
+
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 getQuadrupoleTensors();
+
+
if (line.startsWith(" MULTIPOLE ANALYSIS BY ATOMS")) {
appendLoadNote("Multipole Analysis");
@@ -289,30 +294,25 @@
@Override
protected void finalizeReader() throws Exception {
- if (vInputCoords != null)
- processInputCoords();
+ createAtomsFromCoordLines();
if (energy != null)
setEnergy();
finalizeReaderASCR();
}
- /*
- DIRECT LATTICE VECTORS CARTESIAN COMPONENTS (ANGSTROM)
- X Y Z
- 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
+ // DIRECT LATTICE VECTORS CARTESIAN COMPONENTS (ANGSTROM)
+ // X Y Z
+ // 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 {
boolean isBohr = (line.indexOf("(BOHR") >= 0);
directLatticeVectors = read3Vectors(isBohr);
@@ -352,19 +352,26 @@
return !isProperties;
}
- /*
- *
- TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL
- 1.0000 0.0000 1.0000 -1.0000 1.0000 1.0000 0.0000 -1.0000 1.0000
-
+ // TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL
+ // 1.0000 0.0000 1.0000 -1.0000 1.0000 1.0000 0.0000 -1.0000 1.0000
+
+ /**
+ * Read transform matrix primitive to conventional.
+ * @throws Exception
+ *
*/
-
private void readTransformationMatrix() throws Exception {
primitiveToCryst = Matrix3f.newA(fillFloatArray(null, 0, new float[9]));
}
+ // SHIFT OF THE ORIGIN : 3/4 1/4 0
+
+ /**
+ * Read the origin shift
+ *
+ * @return true
+ */
private boolean readShift() {
- // SHIFT OF THE ORIGIN : 3/4 1/4 0
String[] tokens = getTokens();
int pt = tokens.length - 3;
ptOriginShift.set(fraction(tokens[pt++]), fraction(tokens[pt++]),
@@ -377,93 +384,38 @@
return (ab.length == 2 ? parseFloatStr(ab[0]) / parseFloatStr(ab[1]) : 0);
}
- private boolean readGradient() throws Exception {
- /*MAX GRADIENT 0.000967 THRESHOLD
- RMS GRADIENT 0.000967 THRESHOLD
- MAX DISPLAC. 0.005733 THRESHOLD
- RMS DISPLAC. 0.005733 THRESHOLD */
+ private float primitiveVolume;
+ private float primitiveDensity;
+
+ //0 1 2 3 4 5 6 7
+
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
+ // PRIMITIVE CELL - CENTRING CODE 5/0 VOLUME= 30.176529 - DENSITY11.444
g/cm^3
- String key = null;
- while (line != null) {
- String[] tokens = getTokens();
- if (line.indexOf("MAX GRAD") >= 0)
- key = "maxGradient";
- else if (line.indexOf("RMS GRAD") >= 0)
- key = "rmsGradient";
- else if (line.indexOf("MAX DISP") >= 0)
- key = "maxDisplacement";
- else if (line.indexOf("RMS DISP") >= 0)
- key = "rmsDisplacement";
- else
- break;
- if (atomSetCollection.getAtomCount() > 0)
- atomSetCollection.setAtomSetModelProperty(key, tokens[2]);
- readLine();
- }
- return true;
- }
-
- private boolean readVolumePrimCell() {
- // line looks like: PRIMITIVE CELL - CENTRING CODE 1/0 VOLUME=
113.054442 - DENSITY 2.642 g/cm^3
- String[] tokens = getTokensStr(line);
- String volumePrim = tokens[7];
- // this is to avoid misreading
- //PRIMITIVE CELL - CENTRING CODE 5/0 VOLUME= 30.176529 - DENSITY11.444
g/cm^3
- if (tokens[9].length() > 7) {
- line = TextFormat.simpleReplace(line, "DENSITY", "DENSITY ");
- }
- String densityPrim = tokens[10];
- atomSetCollection.setAtomSetModelProperty("volumePrimitive",
- TextFormat.formatDecimal(parseFloatStr(volumePrim), 3));
- atomSetCollection.setAtomSetModelProperty("densityPrimitive",
- TextFormat.formatDecimal(parseFloatStr(densityPrim), 3));
- return true;
- }
-
- /*
-
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
- ATOMIC SPINS SET TO (ATOM, AT. N., SPIN)
- 1 26-1 2 8 0 3 8 0 4 8 0 5 26 1 6 26 1 7 8 0 8
8 0
- 9 8 0 10 26-1 11 26-1 12 8 0 13 8 0 14 8 0 15 26 1 16
26 1
- 17 8 0 18 8 0 19 8 0 20 26-1 21 26-1 22 8 0 23 8 0 24
8 0
- 25 26 1 26 26 1 27 8 0 28 8 0 29 8 0 30 26-1
- ALPHA-BETA ELECTRONS LOCKED TO 0 FOR 50 SCF CYCLES
-
+ /**
+ * Read the primitive cell volume and density.
+ * Not sure why we are rounding here.
+ *
*/
- private boolean readSpins() throws Exception {
- String data = "";
- while (readLine() != null && line.indexOf("ALPHA") < 0)
- data += line;
- data = TextFormat.simpleReplace(data, "-", " -");
- setData("spin", data, 2, 3);
- return true;
+ private void setPrimitiveVolumeAndDensity() {
+ if (primitiveVolume != 0)
+ atomSetCollection.setAtomSetModelProperty("volumePrimitive", TextFormat
+ .formatDecimal(primitiveVolume, 3));
+ if (primitiveDensity != 0)
+ atomSetCollection.setAtomSetModelProperty("densityPrimitive", TextFormat
+ .formatDecimal(primitiveDensity, 3));
}
+
+ // EEEEEEEEEE STARTING DATE 19 03 2010 TIME 22:00:45.6
+ // (title)
+ //
+ // CRYSTAL CALCULATION
+ // (INPUT ACCORDING TO THE INTERNATIONAL TABLES FOR X-RAY CRYSTALLOGRAPHY)
+ // CRYSTAL FAMILY : CUBIC
+ // CRYSTAL CLASS (GROTH - 1921) : CUBIC HEXAKISOCTAHEDRAL
+ //
+ // SPACE GROUP (CENTROSYMMETRIC) : I A 3 D
- private boolean readMagneticMoments() throws Exception {
- String data = "";
- while (readLine() != null && line.indexOf("TTTTTT") < 0)
- data += line;
- setData("magneticMoment", data, 0, 1);
- return true;
- }
- private void setData(String name, String data, int pt, int dp)
- throws Exception {
- if (vInputCoords != null)
- processInputCoords();
- String[] s = new String[atomCount];
- for (int i = 0; i < atomCount; i++)
- s[i] = "0";
- String[] tokens = getTokensStr(data);
- for (int i = 0; i < atomCount; i++, pt += dp) {
- int iConv = getAtomIndexFromPrimitiveIndex(i);
- if (iConv >= 0)
- s[iConv] = tokens[pt];
- }
- data = TextFormat.join(s, '\n', 0);
- atomSetCollection.setAtomSetAtomProperty(name, data, -1);
- }
-
private boolean readHeader() throws Exception {
discardLinesUntilContains("* CRYSTAL");
@@ -477,16 +429,13 @@
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) {
+ // GEOMETRY INPUT FROM EXTERNAL FILE (FORTRAN UNIT 34)
type = readLine().trim();
isPolymer = (type.equals("1D - POLYMER"));
isSlab = (type.equals("2D - SLAB"));
@@ -514,7 +463,7 @@
}
spaceGroupName = "P1";
if (!isPrimitive) {
- readLines(5);
+ discardLinesUntilContains2("SPACE GROUP", "****");
pt = line.indexOf(":");
if (pt >= 0)
spaceGroupName = line.substring(pt + 1).trim();
@@ -523,14 +472,42 @@
return !isProperties;
}
- private void readCellParams(boolean isNewSet) throws Exception {
+ // LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
+ // A B C ALPHA BETA GAMMA
+ // 3.97500 3.97500 5.02300 90.00000 90.00000 90.00000
+ //
+ //or
+ //
+ // LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - PRIMITIVE CELL
+ // A B C ALPHA BETA GAMMA
VOLUME
+ // 3.97500 3.97500 5.02300 90.00000 90.00000 90.00000
79.366539
+ //
+ //or
+ //
+ // LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
+ // PRIMITIVE CELL - CENTRING CODE 1/0 VOLUME= 79.366539 - DENSITY 9.372
g/cm^3
+ // A B C ALPHA BETA
GAMMA
+ // 3.97500000 3.97500000 5.02300000 90.000000 90.000000
90.000000
+
+
+ /**
+ * Read the lattice parameters.
+ *
+ * @param isNewSet
+ * @throws Exception
+ */
+ private void readLatticeParams(boolean isNewSet) throws Exception {
float f = (line.indexOf("(BOHR") >= 0 ? ANGSTROMS_PER_BOHR : 1);
if (isNewSet)
newAtomSet();
if (isPolymer && !isPrimitive) {
setUnitCell(parseFloatStr(line.substring(line.indexOf("CELL") + 4)) * f,
-1, -1, 90, 90, 90);
} else {
- discardLinesUntilContains("GAMMA");
+ while (readLine().indexOf("GAMMA") < 0)
+ if (line.indexOf("VOLUME=") >= 0) {
+ primitiveVolume = parseFloatStr(line.substring(43));
+ primitiveDensity = parseFloatStr(line.substring(66));
+ }
String[] tokens = getTokensStr(readLine());
if (isSlab) {
if (isPrimitive)
@@ -551,68 +528,81 @@
}
}
+ // COORDINATES OF THE EQUIVALENT ATOMS (FRACTIONAL UNITS)
+ //
+ // N. ATOM EQUIV AT. N. X Y Z
+ //
+ // 1 1 1 25 MN 2.50000000000E-01 3.75000000000E-01
1.25000000000E-01
+ // 2 1 2 25 MN -2.50000000000E-01 1.25000000000E-01
3.75000000000E-01
+ // ...
+ //
+
+
+ private JmolList<String> vPrimitiveMapping;
+ private void readPrimitiveMapping() throws Exception {
+ if (havePrimitiveMapping)
+ return;
+ vPrimitiveMapping = new JmolList<String>();
+ while (readLine() != null && line.indexOf("NUMBER") < 0)
+ vPrimitiveMapping.addLast(line);
+ }
+
/**
- * create arrays that maps primitive atoms to conventional atoms in a 1:1
- * fashion. Creates:
+ * Create arrays that maps primitive atoms to conventional atoms in a 1:1
+ * fashion. Creates int[] primitiveToIndex -- points to model-based atomIndex
*
- * int[] primitiveToIndex -- points to model-based atomIndex
+ * @return TRUE if coordinates have been created
*
- * @return TRUE
- *
* @throws Exception
*/
- private boolean readPrimitiveMapping() throws Exception {
- if (vInputCoords == null)
+ private boolean setPrimitiveMapping() throws Exception {
+ if (vCoords == null || vPrimitiveMapping == null || havePrimitiveMapping)
return false;
havePrimitiveMapping = true;
BS bsInputAtomsIgnore = new BS();
- int n = vInputCoords.size();
+ int n = vCoords.size();
int[] indexToPrimitive = new int[n];
primitiveToIndex = new int[n];
for (int i = 0; i < n; i++)
indexToPrimitive[i] = -1;
-
- readLines(3);
- while (readLine() != null && line.indexOf(" NOT IRREDUCIBLE") >= 0) {
- // example HA_BULK_PBE_FREQ.OUT
- // we remove unnecessary atoms. This is important, because
- // these won't get properties, and we don't know exactly which
- // other atom to associate with them.
-
- bsInputAtomsIgnore.set(parseIntRange(line, 21, 25) - 1);
- readLine();
- }
-
- // COORDINATES OF THE EQUIVALENT ATOMS
- readLines(3);
- int iPrim = 0;
int nPrim = 0;
- while (readLine() != null && line.indexOf("NUMBER") < 0) {
- if (line.length() == 0)
+ for (int iLine = 0; iLine < vPrimitiveMapping.size(); iLine++) {
+ line = vPrimitiveMapping.get(iLine);
+ if (line.indexOf(" NOT IRREDUCIBLE") >= 0) {
+ // example HA_BULK_PBE_FREQ.OUT
+ // we remove unnecessary atoms. This is important, because
+ // these won't get properties, and we don't know exactly which
+ // other atom to associate with them.
+ bsInputAtomsIgnore.set(parseIntRange(line, 21, 25) - 1);
continue;
- nPrim++;
- int iAtom = parseIntRange(line, 4, 8) - 1;
- if (indexToPrimitive[iAtom] < 0) {
- // no other primitive atom is mapped to a given conventional atom.
- indexToPrimitive[iAtom] = iPrim++;
}
+
+ while (readLine() != null && line.indexOf("NUMBER") < 0) {
+ if (line.length() < 2 || line.indexOf("ATOM") >= 0)
+ continue;
+ int iAtom = parseIntRange(line, 4, 8) - 1;
+ if (indexToPrimitive[iAtom] < 0) {
+ // no other primitive atom is mapped to a given conventional atom.
+ indexToPrimitive[iAtom] = nPrim++;
+ }
+ }
}
-
if (bsInputAtomsIgnore.nextSetBit(0) >= 0)
for (int i = n; --i >= 0;)
if (bsInputAtomsIgnore.get(i))
- vInputCoords.remove(i);
- atomCount = vInputCoords.size();
+ vCoords.remove(i);
+ atomCount = vCoords.size();
Logger.info(nPrim + " primitive atoms and " + atomCount
+ " conventionalAtoms");
primitiveToIndex = new int[nPrim];
for (int i = 0; i < nPrim; i++)
primitiveToIndex[i] = -1;
for (int i = atomCount; --i >= 0;) {
- iPrim = indexToPrimitive[parseIntStr(vInputCoords.get(i).substring(0,
4)) - 1];
+ int iPrim = indexToPrimitive[parseIntStr(vCoords.get(i).substring(0, 4))
- 1];
if (iPrim >= 0)
primitiveToIndex[iPrim] = i;
}
+ vPrimitiveMapping = null;
return true;
}
@@ -642,6 +632,7 @@
private boolean readAtoms() throws Exception {
if (isMolecular)
newAtomSet();
+ vCoords = null;
while (readLine() != null && line.indexOf("*") < 0) {
if (line.indexOf("X(ANGSTROM") >= 0) {
// fullerene from slab has this.
@@ -663,7 +654,7 @@
String[] tokens = getTokens();
int pt = (isProperties ? 1 : 2);
atom.elementSymbol = getElementSymbol(getAtomicNumber(tokens[pt++]));
- atom.atomName = getAtomName(tokens[pt++]);
+ atom.atomName = fixAtomName(tokens[pt++]);
if (isProperties)
pt++; // skip SHELL
float x = parseFloatStr(tokens[pt++]);
@@ -687,50 +678,74 @@
return true;
}
- private String getAtomName(String s) {
- String atomName = s;
- if (atomName.length() > 1 && Character.isLetter(atomName.charAt(1)))
- atomName = atomName.substring(0, 1)
- + Character.toLowerCase(atomName.charAt(1)) + atomName.substring(2);
- return atomName;
+ /**
+ * MN33 becomes Mn33
+ *
+ * @param s
+ * @return fixed atom name
+ */
+ private static String fixAtomName(String s) {
+ return (s.length() > 1 && Character.isLetter(s.charAt(1)) ?
+ s.substring(0, 1) + Character.toLowerCase(s.charAt(1)) +
s.substring(2)
+ : s);
}
/*
* Crystal adds 100 to the atomic number when the same atom will be described
- * with different basis sets. It also adds 200 when ECP are used:
+ * with different basis sets. It also adds 200 when ECP are used.
*
- * 1 T 282 PB 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 2 T 16
- * S -5.000000000000E-01 -5.000000000000E-01 -5.000000000000E-01
*/
private int getAtomicNumber(String token) {
- int atomicNumber = parseIntStr(token);
- while (atomicNumber >= 100)
- atomicNumber -= 100;
- return atomicNumber;
+ // 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
+ return parseIntStr(token) % 100;
}
- /*
- * INPUT COORDINATES
+ // INPUT COORDINATES
+ //
+ // ATOM AT. N. COORDINATES
+ // 1 25 1.250000000000E-01 0.000000000000E+00 2.500000000000E-01
+ // 2 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ // 3 14 3.750000000000E-01 0.000000000000E+00 2.500000000000E-01
+ // 4 8 3.444236601187E-02 4.682106125226E-02 -3.476426505505E-01
+ //
+ // or
+ //
+ // COORDINATES IN THE CRYSTALLOGRAPHIC CELL
+ // ATOM X/A Y/B Z/C
+ //
*******************************************************************************
+ // 1 T 25 MN 1.250000000000E-01 0.000000000000E+00 2.500000000000E-01
+ // 2 F 25 MN 3.750000000000E-01 4.012073555523E-17 -2.500000000000E-01
+ // 3 F 25 MN 2.500000000000E-01 1.250000000000E-01 0.000000000000E+00
+
+ /**
+ * Read coordinates, either input or crystallographic,
+ * just saving their lines in a vector for now.
*
- * 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
+ * @throws Exception
*/
- private void readCrystallographicCoords() throws Exception {
- // we only store them, because we may want to delete some
+ private void readCoordLines() throws Exception {
readLine();
readLine();
- vInputCoords = new JmolList<String>();
+ vCoords = new JmolList<String>();
while (readLine() != null && line.length() > 0)
- vInputCoords.addLast(line);
+ vCoords.addLast(line);
}
- private void processInputCoords() throws Exception {
+ /**
+ * Now create atoms from the coordinate lines.
+ *
+ * @throws Exception
+ */
+ private void createAtomsFromCoordLines() throws Exception {
+ if (vCoords == null)
+ return;
// here we may have deleted unnecessary input coordinates
- atomCount = vInputCoords.size();
+ atomCount = vCoords.size();
for (int i = 0; i < atomCount; i++) {
Atom atom = atomSetCollection.addNewAtom();
- String[] tokens = getTokensStr(vInputCoords.get(i));
+ String[] tokens = getTokensStr(vCoords.get(i));
+ atom.atomSerial = parseIntStr(tokens[0]);
int atomicNumber, offset;
if (tokens.length == 7) {
atomicNumber = getAtomicNumber(tokens[2]);
@@ -753,16 +768,18 @@
setAtomCoordXYZ(atom, x, y, z);
atom.elementSymbol = getElementSymbol(atomicNumber);
}
- vInputCoords = null;
+ vCoords = null;
+ setPrimitiveVolumeAndDensity();
}
private void newAtomSet() throws Exception {
- if (atomSetCollection.getAtomCount() > 0) {
+ if (atomCount > 0 && atomSetCollection.getAtomCount() > 0) {
applySymmetryAndSetTrajectory();
atomSetCollection.newAtomSet();
}
if (spaceGroupName != null)
setSpaceGroupName(spaceGroupName);
+ atomCount = 0;
}
private void readEnergy() {
@@ -832,18 +849,27 @@
return (primitiveToIndex == null ? iPrim : primitiveToIndex[iPrim]);
}
- private boolean readFragments() throws Exception {
- /*
- * 2 ( 8 O ) 3 ( 8 O ) 4 ( 8 O ) 85 ( 8 O ) 86 (
8 O )
- * 87( 8 O ) 89( 6 C ) 90( 8 O ) 91( 8 O ) 92( 1 H
)
- * 93( 1 H ) 94( 6 C ) 95( 1 H ) 96( 8 O ) 97( 1 H
)
- * 98( 8 O ) 99( 6 C ) 100( 8 O ) 101( 8 O ) 102( 1 H
)
- * 103( 1 H ) 104( 6 C ) 105( 1 H ) 106( 8 O ) 107( 8 O
)
- * 108( 1 H ) 109( 6 C ) 110( 1 H ) 111( 8 O ) 112( 8 O
)
- * 113( 1 H ) 114( 6 C ) 115( 1 H ) 116( 8 O ) 117( 8 O
)
- * 118( 1 H )
- *
- */
+ //
+ // FREQUENCIES COMPUTED ON A FRAGMENT OF 36 ATOMS
+ // 2( 8 O ) 3( 8 O ) 4( 8 O ) 85( 8 O ) 86( 8 O )
+ // 87( 8 O ) 89( 6 C ) 90( 8 O ) 91( 8 O ) 92( 1 H )
+ // 93( 1 H ) 94( 6 C ) 95( 1 H ) 96( 8 O ) 97( 1 H )
+ // 98( 8 O ) 99( 6 C ) 100( 8 O ) 101( 8 O ) 102( 1 H )
+ // 103( 1 H ) 104( 6 C ) 105( 1 H ) 106( 8 O ) 107( 8 O )
+ // 108( 1 H ) 109( 6 C ) 110( 1 H ) 111( 8 O ) 112( 8 O )
+ // 113( 1 H ) 114( 6 C ) 115( 1 H ) 116( 8 O ) 117( 8 O )
+ // 118( 1 H )
+ //
+
+ /**
+ * Select only specific atoms for frequency generation.
+ * (See freq_6for_001.out)
+ *
+ * @return true
+ * @throws Exception
+ *
+ */
+ private boolean readFreqFragments() throws Exception {
int numAtomsFrag = parseIntRange(line, 39, 44);
if (numAtomsFrag < 0)
return true;
@@ -864,31 +890,31 @@
return true;
}
- /*
- * Transverse:
- *
- 0 1 2 3 4 5 6 7
-
01234567890123456789012345678901234567890123456789012345678901234567890123456789
- MODES EV FREQUENCIES IRREP IR INTENS RAMAN
- (AU) (CM**-1) (THZ) (KM/MOL)
- 1- 1 -0.00004031 -32.6352 -0.9784 (A2 ) I ( 0.00) A
- 2- 2 -0.00003920 -32.1842 -0.9649 (B2 ) A ( 6718.50) A
- 3- 3 -0.00000027 -2.6678 -0.0800 (A1 ) A ( 3.62) A
- *
- * Longitudinal:
- *
- *
- 0 1 2 3 4 5 6 7
-
01234567890123456789012345678901234567890123456789012345678901234567890123456789
- MODES EIGV FREQUENCIES IRREP IR INTENS SHIFTS
- (HARTREE**2) (CM**-1) (THZ) (KM/MOL) (CM**-1)
(THZ)
- 4- 6 0.2370E-06 106.8457 3.2032 (F1U) 40.2 7.382
0.2213
- 16- 18 0.4250E-06 143.0817 4.2895 (F1U) 181.4 14.234
0.4267
- 31- 33 0.5848E-06 167.8338 5.0315 (F1U) 24.5 1.250
0.0375
- 41- 43 0.9004E-06 208.2551 6.2433 (F1U) 244.7 10.821
0.3244
- */
+ // not all crystal calculations include intensities values
+ // this feature is activated when the keyword INTENS is on the input
+ //
+ // transverse:
+ //
+ // 0 1 2 3 4 5 6 7
+ //
01234567890123456789012345678901234567890123456789012345678901234567890123456789
+ // MODES EV FREQUENCIES IRREP IR INTENS
RAMAN
+ // (AU) (CM**-1) (THZ) (KM/MOL)
+ // 1- 1 -0.00004031 -32.6352 -0.9784 (A2 ) I ( 0.00) A
+ // 2- 2 -0.00003920 -32.1842 -0.9649 (B2 ) A ( 6718.50) A
+ // 3- 3 -0.00000027 -2.6678 -0.0800 (A1 ) A ( 3.62) A
+ //
+ // Longitudinal:
+ //
+ // 0 1 2 3 4 5 6 7
+ //
01234567890123456789012345678901234567890123456789012345678901234567890123456789
+ // MODES EIGV FREQUENCIES IRREP IR INTENS
SHIFTS
+ // (HARTREE**2) (CM**-1) (THZ) (KM/MOL) (CM**-1)
(THZ)
+ // 4- 6 0.2370E-06 106.8457 3.2032 (F1U) 40.2 7.382
0.2213
+ // 16- 18 0.4250E-06 143.0817 4.2895 (F1U) 181.4 14.234
0.4267
+ // 31- 33 0.5848E-06 167.8338 5.0315 (F1U) 24.5 1.250
0.0375
+ // 41- 43 0.9004E-06 208.2551 6.2433 (F1U) 244.7 10.821
0.3244
+
private boolean readFrequencies() throws Exception {
-
energy = null; // don't set energy for these models
discardLinesUntilContains("MODES");
// This line is always there
@@ -904,9 +930,6 @@
String intens = (!haveIntensities ? "not available" : (isLongMode ? line
.substring(53, 61) : line.substring(59, 69).replace(')', '
')).trim());
- // not all crystal calculations include intensities values
- // this feature is activated when the keyword INTENS is on the input
-
String irActivity = (isLongMode ? "A" : line.substring(55, 58).trim());
String ramanActivity = (isLongMode ? "I" : line.substring(71,
73).trim());
@@ -963,56 +986,103 @@
+ " km/Mole), " + activity);
}
- /*
- DEFINITION OF TRACELESS QUADRUPOLE TENSORS:
+ // MAX GRADIENT 0.000967 THRESHOLD
+ // RMS GRADIENT 0.000967 THRESHOLD
+ // MAX DISPLAC. 0.005733 THRESHOLD
+ // RMS DISPLAC. 0.005733 THRESHOLD
- (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
+ /**
+ * Read minimization measures
+ *
+ * @return true
+ * @throws Exception
+ */
+ private boolean readGradient() throws Exception {
+ String key = null;
+ while (line != null) {
+ String[] tokens = getTokens();
+ if (line.indexOf("MAX GRAD") >= 0)
+ key = "maxGradient";
+ else if (line.indexOf("RMS GRAD") >= 0)
+ key = "rmsGradient";
+ else if (line.indexOf("MAX DISP") >= 0)
+ key = "maxDisplacement";
+ else if (line.indexOf("RMS DISP") >= 0)
+ key = "rmsDisplacement";
+ else
+ break;
+ if (atomSetCollection.getAtomCount() > 0)
+ atomSetCollection.setAtomSetModelProperty(key, tokens[2]);
+ readLine();
+ }
+ return true;
+ }
- *** ATOM N. 1 (Z=282) PB
+ //
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
+ // ATOMIC SPINS SET TO (ATOM, AT. N., SPIN)
+ // 1 26-1 2 8 0 3 8 0 4 8 0 5 26 1 6 26 1 7 8 0 8
8 0
+ // 9 8 0 10 26-1 11 26-1 12 8 0 13 8 0 14 8 0 15 26 1 16
26 1
+ // 17 8 0 18 8 0 19 8 0 20 26-1 21 26-1 22 8 0 23 8 0 24
8 0
+ // 25 26 1 26 26 1 27 8 0 28 8 0 29 8 0 30 26-1
+ // ALPHA-BETA ELECTRONS LOCKED TO 0 FOR 50 SCF CYCLES
+ //
+ // or (for magnetic moments)
+ //
+ // TOTAL ATOMIC SPINS :
+ // 5.0000000 -5.0000000 -5.0000000 5.0000000 0.0000000 0.0000000
+ // 0.0000000 0.0000000 0.0000000 0.0000000
+ // TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 233.11 TCPU
154.98
+
+ /**
+ * For spin and magnetic moment data, read the data block
+ * and save it as property_spin or propert_magneticMoment.
+ *
+ * @param name
+ * @param nfields
+ * @return true
+ * @throws Exception
+ */
+ private boolean readData(String name, int nfields) throws Exception {
+ createAtomsFromCoordLines();
+ String[] s = new String[atomCount];
+ for (int i = 0; i < atomCount; i++)
+ s[i] = "0";
+ String data = "";
+ while (readLine() != null && (line.length() < 4 ||
Character.isDigit(line.charAt(3))))
+ data += line;
+ data = TextFormat.simpleReplace(data, "-", " -");
+ String[] tokens = getTokensStr(data);
+ for (int i = 0, pt = nfields - 1; i < atomCount; i++, pt += nfields) {
+ int iConv = getAtomIndexFromPrimitiveIndex(i);
+ if (iConv >= 0)
+ s[iConv] = tokens[pt];
+ }
+ data = TextFormat.join(s, '\n', 0);
+ atomSetCollection.setAtomSetAtomProperty(name, data, -1);
+ return true;
+ }
- TENSOR IN PRINCIPAL AXIS SYSTEM
- AA 6.265724E-01 BB -2.651563E-01 CC -3.614161E-01
+
+ // 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
+ //...
+ // TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT POLI TELAPSE 0.05 TCPU
0.04
- *** 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 {
+ private boolean getQuadrupoleTensors() throws Exception {
readLines(6);
Atom[] atoms = atomSetCollection.getAtoms();
while (readLine() != null && line.startsWith(" *** ATOM")) {
@@ -1022,11 +1092,41 @@
atoms[index].addTensor(Tensor.getTensorFromEigenVectors(directLatticeVectors,
new float[] {parseFloatStr(tokens[1]),
parseFloatStr(tokens[3]),
- parseFloatStr(tokens[5]) }, "unknown", atoms[index].atomName),
null);
+ parseFloatStr(tokens[5]) }, "quadrupole", atoms[index].atomName),
null);
readLine();
}
+ appendLoadNote("Ellipsoids set \"quadrupole\": Quadrupole tensors");
return true;
}
+ // BORN CHARGE TENSOR. (DINAMIC CHARGE = 1/3 * TRACE)
+ //
+ // ATOM 2 O DYNAMIC CHARGE -1.274519
+ //
+ // 1 2 3
+ // 1 -1.3467E+00 -1.6358E-02 -6.0557E-01
+ // 2 1.3223E-01 -1.3781E+00 -2.1223E-02
+ // 3 -1.5921E-01 -1.4427E-01 -1.0988E+00
+ // ...
+ private boolean readBornChargeTensors() throws Exception {
+ createAtomsFromCoordLines();
+ readLine();
+ Atom[] atoms = atomSetCollection.getAtoms();
+ while (readLine().startsWith(" ATOM")) {
+ int index = parseIntStr(line.substring(5)) - 1;
+ Atom atom = atoms[index];
+ readLines(2);
+ double[][] a = new double[3][3];
+ for (int i = 0; i < 3; i++) {
+ String[] tokens = getTokensStr(readLine());
+ for (int j = 0; j < 3; j++)
+ a[i][j] = parseFloatStr(tokens[j + 1]);
+ }
+ atom.addTensor(Tensor.getTensorFromAsymmetricTensor(a, "charge",
atom.elementSymbol + (index + 1)), null);
+ readLine();
+ }
+ appendLoadNote("Ellipsoids set \"charge\": Born charge tensors");
+ return false;
+ }
}
Modified: branches/v13_2/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-09-06
17:25:32 UTC (rev 18645)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-09-06
17:26:07 UTC (rev 18646)
@@ -24,13 +24,18 @@
package org.jmol.adapter.smarter;
+import org.jmol.util.ArrayUtil;
import org.jmol.util.BS;
import org.jmol.util.JmolList;
import org.jmol.util.P3;
import org.jmol.util.Tensor;
public class Atom extends P3 implements Cloneable {
- public int atomSetIndex;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ public int atomSetIndex;
public int index;
public BS bsSymmetry;
public int atomSite;
@@ -79,9 +84,15 @@
}
public Atom getClone() throws CloneNotSupportedException {
- // note that anisoBorU and ellipsoid are not copied
- // we consider them "final" in a sense
- return (Atom)clone();
+ Atom a = (Atom)clone();
+ if (anisoBorU != null)
+ a.anisoBorU = ArrayUtil.arrayCopyF(anisoBorU, -1);
+ if (tensors != null) {
+ a.tensors = new JmolList<Tensor>();
+ for (int i = tensors.size(); --i >= 0;)
+ a.tensors.addLast(Tensor.copyTensor(tensors.get(i)));
+ }
+ return a;
}
public String getElementSymbol() {
Modified: branches/v13_2/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-09-06
17:25:32 UTC (rev 18645)
+++ branches/v13_2/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-09-06
17:26:07 UTC (rev 18646)
@@ -1209,6 +1209,10 @@
&& flowContext.var != null && theTok != T.casecmd
&& theTok != T.defaultcmd && lastToken.tok != T.switchcmd)
return ERROR(ERROR_badContext, ident);
+ if (lastToken.tok == T.define && theTok != T.leftbrace && nTokens != 1) {
+ addTokenToPrefix(T.o(T.string, ident));
+ return CONTINUE;
+ }
switch (theTok) {
case T.identifier:
if (nTokens == 0 && !checkImpliedScriptCmd) {
@@ -2331,12 +2335,6 @@
}
break;
}
- if (Character.isWhitespace(ch)) {
- if (ptSpace < 0)
- ptSpace = ichT;
- } else {
- ptLastChar = ichT;
- }
++ichT;
}
// message/echo/label @x
Modified: branches/v13_2/Jmol/src/org/jmol/util/Escape.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/util/Escape.java 2013-09-06 17:25:32 UTC
(rev 18645)
+++ branches/v13_2/Jmol/src/org/jmol/util/Escape.java 2013-09-06 17:26:07 UTC
(rev 18646)
@@ -1038,7 +1038,7 @@
String s = Parser.getQuotedStringNext(data, next);
if (s == null)
return null;
- v.addLast(s);
+ v.addLast(TextFormat.simpleReplace(s, "\\\"", "\""));
while (next[0] < data.length() && data.charAt(next[0]) != '"')
next[0]++;
}
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-09-06
17:25:32 UTC (rev 18645)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-09-06
17:26:07 UTC (rev 18646)
@@ -9,9 +9,14 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
+___JmolVersion="13.2.5_dev_2013.09.06"
-___JmolVersion="13.2.4"
+bug fix: CRYSTAL reader not allowing vibration for conventional cell
+bug fix: JavaScript binary for Safari and Opera
+bug fix: ID @id vector fails
+JmolVersion="13.2.4"
+
bug fix: select 1-5 broken
JmolVersion="13.2.4_dev_2013.08.20"
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