Revision: 18536
http://sourceforge.net/p/jmol/code/18536
Author: hansonr
Date: 2013-08-11 01:01:29 +0000 (Sun, 11 Aug 2013)
Log Message:
-----------
* abstract modulation class for CIF and Jana
*
* Current status:
*
* -- d=1 only
* -- includes Fourier, Crenel, Sawtooth; displacement, occupancy, and Uiso
* -- reading composite subsystem files such as ms-fit-1.cif
*
* TODO: Uij, d > 1
* TODO: handle subsystems properly
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-11 00:05:54 UTC (rev 18535)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-11 01:01:29 UTC (rev 18536)
@@ -49,7 +49,13 @@
* Current status:
*
* -- d=1 only
- * -- only simple atom displacement, no occupation crenel, no sawtooth
+ * -- includes Fourier, Crenel, Sawtooth; displacement, occupancy, and Uiso
+ * -- reading composite subsystem files such as ms-fit-1.cif
+ *
+ * TODO: Uij, d > 1
+ * TODO: handle subsystems properly
+ *
+ * No plan to implement rigid-body rotation
*
* @author Bob Hanson hans...@stolaf.edu 8/7/13
*
@@ -238,6 +244,7 @@
return;
atoms = atomSetCollection.getAtoms();
symmetry = atomSetCollection.getSymmetry();
+ iopLast = -1;
SB sb = new SB();
for (int i = atomSetCollection.getLastAtomSetAtomIndex(); i < n; i++)
modulateAtom(atoms[i], sb);
@@ -250,6 +257,9 @@
return (pt_ < 0 ? null : key.substring(0, pt_));
}
+ private int iopLast = -1;
+ private Matrix3f rot;
+
/**
* The displacement will be set as the atom vibration vector; the string
* buffer will be appended with the t value for a given unit cell.
@@ -271,7 +281,10 @@
float epsilon = symmetry.getModParam(iop, 0);
float delta = symmetry.getModParam(iop, 1);
delta -= modT;
- Matrix3f rot = new Matrix3f();
+ if (iop != iopLast) {
+ iopLast = iop;
+ rot = new Matrix3f();
+ }
symmetry.getSpaceGroupOperation(iop).getRotationScale(rot);
System.out.println("=========MR i=" + a.index + " " + a.atomName + " " + a
+ " " + a.occupancy);
System.out.println("op=" + (iop + 1) + " " +
symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de=" + delta);
@@ -294,7 +307,7 @@
if (key.equalsIgnoreCase("Uiso")) {
setU(a, 7, v);
} else {
-
+ //TODO
}
}
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