Revision: 18620
http://sourceforge.net/p/jmol/code/18620
Author: hansonr
Date: 2013-08-22 15:12:02 +0000 (Thu, 22 Aug 2013)
Log Message:
-----------
incommensurate work
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-22
05:44:50 UTC (rev 18619)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-22
15:12:02 UTC (rev 18620)
@@ -47,6 +47,7 @@
import org.jmol.util.P3;
import org.jmol.util.SimpleUnitCell;
import org.jmol.util.TextFormat;
+import org.jmol.util.V3;
/**
@@ -818,6 +819,7 @@
final private static byte DISORDER_ASSEMBLY = 58;
final private static byte ASYM_ID = 59;
final private static byte SUBSYS_ID = 60;
+ final private static byte SITE_MULT = 61;
final private static String[] atomFields = {
@@ -881,7 +883,8 @@
"_chem_comp_atom_pdbx_model_cartn_z_ideal",
"_atom_site_disorder_assembly",
"_atom_site_label_asym_id",
- "_atom_site_subsystem_code"
+ "_atom_site_subsystem_code",
+ "_atom_site_symmetry_multiplicity"
};
/* to: hans...@stolaf.edu
@@ -933,6 +936,7 @@
int iAtom = -1;
int modelField = -1;
String subid = null;
+ int siteMult = 0;
while (tokenizer.getData()) {
Atom atom = new Atom();
assemblyId = '\0';
@@ -1141,6 +1145,9 @@
case SUBSYS_ID:
subid = field;
break;
+ case SITE_MULT:
+ if (incommensurate)
+ siteMult = parseIntStr(field);
}
}
if (isAnisoData)
@@ -1175,9 +1182,10 @@
htHetero);
htHetero = null;
}
- if (subid != null) {
+ if (subid != null)
addSubsystem(subid, null, atom.atomName);
- }
+ if (siteMult != 0)
+ atom.vib = V3.new3(siteMult, 0, Float.NaN);
}
if (isPDB)
@@ -2321,6 +2329,9 @@
private final static int FP_DISP_ID = 43;
private final static int FP_OCC_ID = 44;
private final static int FP_U_ID = 45;
+
+ private final static int JANA_OCC_ABS_LABEL = 46;
+ private final static int JANA_OCC_ABS_O_0 = 47;
final private static String[] modulationFields = {
"_cell_wave_vector_seq_id",
@@ -2372,6 +2383,9 @@
"_atom_site_displace_fourier_param_id",
"_atom_site_occ_fourier_param_id",
"_atom_site_u_fourier_param_id",
+
+ "_jana_atom_site_occ_fourier_absolute_site_label",
+ "_jana_atom_site_occ_fourier_absolute"
};
/**
@@ -2440,7 +2454,12 @@
}
id += field;
break;
+ case JANA_OCC_ABS_LABEL:
+ id = "J_O";
+ pt.x = pt.z = 1;
+ //$FALL-THROUGH$
case DISP_SPEC_LABEL:
+ if (id == null)
id = "D_S";
//$FALL-THROUGH$
case OCC_SPECIAL_LABEL:
@@ -2503,6 +2522,7 @@
case FWV_U_PHASE:
case OCC_CRENEL_W:
case DISP_SAW_AY:
+ case JANA_OCC_ABS_O_0:
pt.y = parseFloatStr(field);
break;
case WV_Z:
@@ -2529,6 +2549,7 @@
case 'D':
case 'O':
case 'U':
+ case 'J':
if (atomLabel == null || axis == null)
continue;
if (id.equals("D_S")) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-22 05:44:50 UTC (rev 18619)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-22 15:12:02 UTC (rev 18620)
@@ -320,6 +320,7 @@
private int iopLast = -1;
private Matrix3f gammaE;
private Matrix4f gammaIS;
+ private int nOps;
/**
* The displacement will be set as the atom vibration vector; the string
@@ -353,6 +354,7 @@
gammaE = new Matrix3f();
symmetry.getSpaceGroupOperation(iop).getRotationScale(gammaE);
gammaIS = symmetry.getOperationGammaIS(iop);
+ nOps = symmetry.getSpaceGroupOperationCount();
}
if (Logger.debugging) {
Logger.debug("setModulation iop = " + iop + " "
@@ -361,11 +363,32 @@
Matrix4f q123w = Matrix4f.newMV(q123, new V3());
setSubsystemMatrix(a.atomName, q123w);
ModulationSet ms = new ModulationSet(a.index + " " + a.atomName,
- P3.newP(a), a.foccupancy, modDim, list, gammaE, gammaIS, q123w, qlen);
- a.vib = ms;
+ P3.newP(a), modDim, list, gammaE, gammaIS, q123w, qlen);
ms.calculate();
if (!Float.isNaN(ms.vOcc)) {
- a.foccupancy = Math.min(1, Math.max(0, ms.vOcc0 + ms.vOcc));
+ P3 pt = getMod("J_O#0;" + a.atomName);
+ float occ0 = ms.vOcc0;
+ float occ;
+ if (Float.isNaN(occ0)) {
+ // Crenel
+ occ = ms.vOcc;
+ } else if (pt == null) {
+ // cif Fourier
+ // _atom_site_occupancy + SUM
+ occ = a.foccupancy + ms.vOcc;
+ } else if (a.vib != null) {
+ // cif with m40 Fourier
+ // occ_site * (occ_0 + SUM)
+ float site_mult = a.vib.x;
+ float o_site = a.foccupancy * site_mult / nOps / pt.y;
+ occ = o_site * (pt.y + ms.vOcc);
+ } else {
+ // m40 Fourier
+ // occ_site * (occ_0 + SUM)
+ occ = pt.x * (pt.y + ms.vOcc);
+ }
+ a.foccupancy = Math.min(1, Math.max(0, occ));
+ a.vib = ms;
// if (!modVib) {
// if (occ < 0.5f) {
// a.foccupancy = 0;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-22 05:44:50 UTC (rev 18619)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-22 15:12:02 UTC (rev 18620)
@@ -221,7 +221,9 @@
// 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 000000
// 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 000000
//
- // x y z CS? O D U
+ // SPECIAL COUNTS
+ // --- -------
+ // x y z ODU O D U
// Zn 5 1 0.500000 0.250000 0.406400 0.244000 000 0 2 0
//
// 0 1 2 3 4 5 6 7
@@ -231,7 +233,25 @@
// 0.015300 0.000000 0.000000-0.010100 0.000000 0.000000 000000
// 0.000000 0.000200-0.000100 0.000000 0.000500-0.000400 000000
// 0.000000 0
+ // ...
+ // [occ_site]
+ // Na1 1 2 0.500000 0.500000 0.000000 0.000000 000 1 1 1
+ // 0.034155-0.007468 0.002638 0.000000-0.005723 0.000000 0000111010
+ // [occ_0 for Fourier or width for crenel]
+ // 0.848047 1
+ // [center for Crenel; ]
+ // 0.000000 0.312670 01
+ // 0.029441 0.000000 0.003581 0.000000 0.000000 0.000000 101000
+ // 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 000000
+ // -0.051170 0.000624-0.008585 0.000000 0.014781 0.000000 111010
+ // 0.000000
+ //
+ /**
+ * read the M40 file
+ *
+ * @throws Exception
+ */
private void readM40Data() throws Exception {
String name = filePath;
int ipt = name.lastIndexOf(".");
@@ -266,7 +286,7 @@
iSub++;
addSubsystem("" + iSub, null, atom.atomName);
}
- atom.foccupancy = floats[2];
+ float o_site = atom.foccupancy = floats[2];
setAtomCoordXYZ(atom, floats[3], floats[4], floats[5]);
atomSetCollection.addAtom(atom);
if (!incommensurate)
@@ -296,20 +316,30 @@
// read occupancy parameters
P3 pt;
- if (nOcc > 0 && !haveSpecialOcc)
- r.readLine(); //"1.00000"
+ float o_0 = (nOcc > 0 && !haveSpecialOcc ? parseFloatStr(r.readLine()) :
1);
+ // we add a pt that save the original (unadjusted) o_0 and o_site
+ // will implement
+ //
+ // O = o_site (o_0 + SUM)
+ //
+ // However, first we need to adjust o_0 because the value given in m40
is
+ // divided by the number of operators giving this site.
+ if (o_0 != 1) {
+ addModulation(null, "J_O#0;" + atom.atomName, P3.new3(o_site, o_0, 0),
-1);
+ }
+ atom.foccupancy = o_0 * o_site;
int wv = 0;
float a1, a2;
for (int j = 0; j < nOcc; j++) {
if (haveSpecialOcc) {
float[][] data = readM40FloatLines(2, 1, r);
- a1 = data[1][0];
- a2 = data[0][0];
+ a2 = data[0][0]; // width (first line)
+ a1 = data[1][0]; // center (second line)
} else {
wv = j + 1;
readM40Floats(r);
- a1 = floats[1];
- a2 = floats[0];
+ a2 = floats[0]; // sin (first line)
+ a1 = floats[1]; // cos (second line)
}
id = "O_" + wv + "#0" + label;
pt = P3.new3(a1, a2, 0);
@@ -445,7 +475,9 @@
}
/**
- * M40 occupancies are divided by the site multiplicity
+ * M40 occupancies are divided by the site multiplicity;
+ * here we factor that back in.
+ *
*/
private void adjustM40Occupancies() {
Map<String, Integer> htSiteMult = new Hashtable<String, Integer>();
@@ -454,9 +486,8 @@
Atom a = atoms[i];
Integer ii = htSiteMult.get(a.atomName);
if (ii == null) {
- System.out.println(a.atomName);
htSiteMult.put(a.atomName, ii =
Integer.valueOf(atomSetCollection.getSymmetry().getSiteMultiplicity(a)));
- System.out.println(a.atomName + " " + ii + " " + a.bsSymmetry + " " +
a.foccupancy);
+ //System.out.println(a.atomName + " " + ii + " " + a.bsSymmetry + " "
+ a.foccupancy);
}
a.foccupancy *= ii.intValue();
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-08-22 05:44:50 UTC
(rev 18619)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-08-22 15:12:02 UTC
(rev 18620)
@@ -41,7 +41,7 @@
public String atomName;
public int formalCharge = Integer.MIN_VALUE;
public float partialCharge = Float.NaN;
- public V3 vib;
+ public V3 vib; // .x and .y can be used for in-reader purposes as long as
vib.z is left Float.NaN
public float bfactor = Float.NaN;
public float foccupancy = 1;
public float radius = Float.NaN;
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-22 05:44:50 UTC
(rev 18619)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-22 15:12:02 UTC
(rev 18620)
@@ -154,7 +154,7 @@
x -= Math.floor(x);
ms.vOcc = (range(x) ? 1 : 0);
- ms.vOcc0 = 0; // absolute
+ ms.vOcc0 = Float.NaN; // absolute
//System.out.println("MOD " + ms.r + " " + ms.delta + " " + ms.epsilon
+ " " + ms.id + " " + ms.v + " l=" + left + " x=" + x4 + " r=" + right);
return;
case TYPE_DISP_SAWTOOTH:
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-22 05:44:50 UTC
(rev 18619)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-22 15:12:02 UTC
(rev 18620)
@@ -45,11 +45,10 @@
*
*/
- public ModulationSet(String id, P3 r, float vocc0, int modDim,
+ public ModulationSet(String id, P3 r, int modDim,
JmolList<Modulation> mods, Matrix3f gammaE,
Matrix4f gammaIS, Matrix4f q123w, double[] qlen) {
this.id = id;
- this.vOcc0 = vocc0;
this.modDim = modDim;
this.mods = mods;
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