Revision: 20816
http://sourceforge.net/p/jmol/code/20816
Author: hansonr
Date: 2015-10-10 16:49:59 +0000 (Sat, 10 Oct 2015)
Log Message:
-----------
new feature: unitcell() function
// optional last parameter: scale
// unitcell()
// unitcell(uc)
// unitcell(uc, "reciprocal")
// unitcell(ucconv, "primitive","BCC"|"FCC")
// unitcell(ucprim, "conventional","BCC"|"FCC"|...?) //not yet implemented
// unitcell(origin, [va, vb, vc])
// unitcell(origin, pta, ptb, ptc)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/Subsystem.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/Subsystem.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/Subsystem.java 2015-10-09
23:01:06 UTC (rev 20815)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/Subsystem.java 2015-10-10
16:49:59 UTC (rev 20816)
@@ -5,11 +5,13 @@
import javajs.util.Lst;
import javajs.util.M4;
import javajs.util.Matrix;
+import javajs.util.T3;
import javajs.util.V3;
import org.jmol.api.SymmetryInterface;
import org.jmol.symmetry.Symmetry;
import org.jmol.util.Logger;
+import org.jmol.util.SimpleUnitCell;
class Subsystem {
@@ -72,8 +74,8 @@
// Part 2: Get the new unit cell and symmetry operators
SymmetryInterface s0 = msRdr.cr.asc.getSymmetry();
- V3[] vu43 = s0.getUnitCellVectors();
- V3[] vr43 = reciprocalsOf(vu43);
+ T3[] vu43 = s0.getUnitCellVectors();
+ T3[] vr43 = SimpleUnitCell.getReciprocal(vu43);
// using full matrix math here:
//
@@ -96,11 +98,11 @@
// back to vector notation and direct lattice
- V3[] uc_nu = new V3[4];
+ T3[] uc_nu = new T3[4];
uc_nu[0] = vu43[0]; // origin
for (int i = 0; i < 3; i++)
uc_nu[i + 1] = V3.new3((float) a[i][0], (float) a[i][1], (float)
a[i][2]);
- uc_nu = reciprocalsOf(uc_nu);
+ uc_nu = SimpleUnitCell.getReciprocal(uc_nu);
symmetry = ((Symmetry)
msRdr.cr.getInterface("org.jmol.symmetry.Symmetry")).getUnitCell(uc_nu, false,
null);
modMatrices = new Matrix[] { sigma_nu, tFactor };
if (!setOperators)
@@ -160,17 +162,6 @@
return false;
}
- private V3[] reciprocalsOf(V3[] abc) {
- V3[] rabc = new V3[4];
- rabc[0] = abc[0]; // origin
- for (int i = 0; i < 3; i++) {
- rabc[i + 1] = new V3();
- rabc[i + 1].cross(abc[((i + 1) % 3) + 1], abc[((i + 2) % 3) + 1]);
- rabc[i + 1].scale(1/abc[i + 1].dot(rabc[i + 1]));
- }
- return rabc;
- }
-
@Override
public String toString() {
return "Subsystem " + code + "\n" + w;
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-10-09 23:01:06 UTC
(rev 20815)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-10-10 16:49:59 UTC
(rev 20816)
@@ -112,7 +112,7 @@
public String getUnitCellState();
- public V3[] getUnitCellVectors();
+ public P3[] getUnitCellVectors();
public P3[] getUnitCellVerticesNoOffset();
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-10-09 23:01:06 UTC (rev
20815)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-10-10 16:49:59 UTC (rev
20816)
@@ -271,13 +271,13 @@
public final static int throwcmd = 6 | mathExpressionCommand;
//public final static int prompt see mathfunc
- public final static int echo = 1 /* must be odd */ | implicitStringCommand
| shapeCommand | setparam;
+ public final static int echo = 1 /* must be odd */ |
implicitStringCommand | shapeCommand | setparam;
public final static int help = 2 /* must be even */ |
implicitStringCommand;
- public final static int hover = 3 /* must be odd */ | implicitStringCommand
| defaultON;
+ public final static int hover = 3 /* must be odd */ |
implicitStringCommand | defaultON;
//public final static int javascript see mathfunc
//public final static int label see mathfunc
public final static int message = 5 /* must be odd */ |
implicitStringCommand;
- public final static int pause = 7 /* must be odd */ | implicitStringCommand;
+ public final static int pause = 7 /* must be odd */ |
implicitStringCommand;
//these commands control flow
//sorry about GOTO!
@@ -389,10 +389,10 @@
public final static int nbo = shapeCommand | 19 | misc;
public final static int pmesh = shapeCommand | 20;
public final static int plot3d = shapeCommand | 22;
-// public final static int polyhedra = shapeCommand | 24 | predefinedset;
- //public final static int spacefill see floatproperty
+ // public final static int polyhedra see mathfunc
+ // public final static int spacefill see floatproperty
public final static int struts = shapeCommand | 26 | defaultON;
- public final static int unitcell = shapeCommand | 28 | deprecatedparam |
predefinedset | defaultON;
+ // public final static int unitcell see mathfunc
public final static int vector = shapeCommand | 30;
public final static int wireframe = shapeCommand | 32 | defaultON;
@@ -657,7 +657,8 @@
//
// maximum number of parameters is set by the << 9 shift
// the min/max mask requires that the first number here must not exceed 63
- // the only other requirement is that these numbers be unique
+ // the only other requirement is that these numbers be unique, so the
initial
+ // number can be duplicated if necessary, as long as other flags are
different
static int getMaxMathParams(int tokCommand) {
@@ -669,41 +670,40 @@
// xxx(a,b,c,d,e,...)
- public final static int in = 1 | 0 << 9 | mathfunc |
mathproperty;
public final static int angle = 1 | 0 << 9 | mathfunc;
public final static int array = 2 | 0 << 9 | mathfunc |
mathproperty;
public final static int axisangle = 3 | 0 << 9 | mathfunc;
- public final static int bin = 3 | 0 << 9 | mathfunc |
mathproperty;
- public final static int color = 4 | 0 << 9 | mathfunc |
intproperty | scriptCommand | deprecatedparam | settable;
- public final static int compare = 5 | 0 << 9 | mathfunc |
scriptCommand;
- public final static int connected = 6 | 0 << 9 | mathfunc;
- public final static int polyhedra = 7 | 0 << 9 | mathfunc |
mathproperty | shapeCommand;
+ public final static int bin = 4 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int cache = 5 | 0 << 9 | mathfunc |
scriptCommand; // new in Jmol 13.1.2
+ public final static int color = 6 | 0 << 9 | mathfunc |
intproperty | scriptCommand | deprecatedparam | settable;
+ public final static int compare = 7 | 0 << 9 | mathfunc |
scriptCommand;
+ public final static int connected = 8 | 0 << 9 | mathfunc;
+ public final static int count = 9 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int data = 10 | 0 << 9 | mathfunc |
scriptCommand;
+ public final static int find = 11 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int format = 12 | 0 << 9 | mathfunc |
mathproperty | strproperty | settable;
+ public final static int function = 13 | 0 << 9 | mathfunc |
flowCommand;
+ public final static int getproperty = 14 | 0 << 9 | mathfunc |
mathproperty | scriptCommand;
+ public final static int helix = 15 | 0 << 9 | mathfunc |
predefinedset;
+ public final static int in = 16 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int label = 18 /* must NOT be odd */| 0 << 9
| mathfunc | mathproperty | strproperty | settable | implicitStringCommand |
shapeCommand | defaultON | deprecatedparam;
+ public final static int measure = 19 | 0 << 9| mathfunc |
shapeCommand | deprecatedparam | defaultON;
+ public final static int modulation = 20 | 0 << 9 | mathfunc |
mathproperty | scriptCommand;
+ public final static int now = 21 | 0 << 9 | mathfunc;
+ public final static int plane = 22 | 0 << 9 | mathfunc;
+ public final static int point = 23 | 0 << 9 | mathfunc;
+ public final static int polyhedra = 24 | 0 << 9 | mathfunc |
mathproperty | shapeCommand;
+ public final static int pop = 25 | 0 << 9 | mathfunc |
mathproperty | scriptCommand | noArgs; //internal only;
+ public final static int quaternion = 26 | 0 << 9 | mathfunc |
scriptCommand;
+ public final static int replace = 27 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int sort = 28 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int tensor = 29 | 0 << 9 | mathfunc |
mathproperty;
+ public final static int unitcell = 30 | 0 << 9 | mathfunc |
shapeCommand | deprecatedparam | predefinedset | defaultON;
+ public final static int within = 31 | 0 << 9 | mathfunc;
+ public final static int write = 32 | 0 << 9 | mathfunc |
scriptCommand;
+ public final static int _ = 33 | 0 << 9 | mathfunc |
mathproperty; // same as getProperty
- public final static int data = 8 | 0 << 9 | mathfunc |
scriptCommand;
- public final static int format = 7 | 0 << 9 | mathfunc |
mathproperty | strproperty | settable;
- public final static int function = 9 | 0 << 9 | mathfunc |
flowCommand;
- public final static int getproperty = 10 | 0 << 9 | mathfunc |
mathproperty | scriptCommand;
- public final static int helix = 11 | 0 << 9 | mathfunc |
predefinedset;
- public final static int label = 12 /* must NOT be odd */| 0 << 9
| mathfunc | mathproperty | strproperty | settable | implicitStringCommand |
shapeCommand | defaultON | deprecatedparam;
- public final static int measure = 13 | 0 << 9| mathfunc |
shapeCommand | deprecatedparam | defaultON;
- public final static int now = 14 | 0 << 9 | mathfunc;
- public final static int plane = 15 | 0 << 9 | mathfunc;
- public final static int point = 16 | 0 << 9 | mathfunc;
- public final static int pop = 17 | 0 << 9 | mathfunc |
mathproperty | scriptCommand | noArgs; //internal only;
- public final static int quaternion = 18 | 0 << 9 | mathfunc |
scriptCommand;
- public final static int sort = 19 | 0 << 9 | mathfunc |
mathproperty;
- public final static int count = 20 | 0 << 9 | mathfunc |
mathproperty;
- public final static int within = 21 | 0 << 9 | mathfunc;
- public final static int write = 22 | 0 << 9 | mathfunc |
scriptCommand;
- public final static int cache = 23 | 0 << 9 | mathfunc |
scriptCommand; // new in Jmol 13.1.2
- public final static int tensor = 24 | 0 << 9 | mathfunc |
mathproperty;
- public final static int modulation = 25 | 0 << 9 | mathfunc |
mathproperty | scriptCommand;
- public final static int _ = 26 | 0 << 9 | mathfunc |
mathproperty; // same as getProperty
- public final static int find = 27 | 0 << 9 | mathfunc | mathproperty;
- public final static int replace = 28 | 0 << 9 | mathfunc | mathproperty;
-
-
// xxx(a)
public final static int acos = 2 | 1 << 9 | mathfunc;
@@ -725,22 +725,22 @@
// two parameters and it CAN be a dot-function (but not both together)
public final static int div = 0 | 1 << 9 | mathfunc | mathproperty;
- public final static int mul = 3 | 1 << 9 | mathfunc | mathproperty;
- public final static int mul3 = 4 | 1 << 9 | mathfunc | mathproperty;
- public final static int sub = 7 | 1 << 9 | mathfunc | mathproperty;
- public final static int trim = 8 | 1 << 9 | mathfunc | mathproperty;
- public final static int volume = 9 | 1 << 9 | mathfunc | mathproperty
| floatproperty;
- public final static int col = 10 | 1 << 9 | mathfunc | mathproperty;
- public final static int row = 11 | 1 << 9 | mathfunc | mathproperty;
+ public final static int mul = 1 | 1 << 9 | mathfunc | mathproperty;
+ public final static int mul3 = 2 | 1 << 9 | mathfunc | mathproperty;
+ public final static int sub = 3 | 1 << 9 | mathfunc | mathproperty;
+ public final static int trim = 4 | 1 << 9 | mathfunc | mathproperty;
+ public final static int volume = 5 | 1 << 9 | mathfunc | mathproperty
| floatproperty;
+ public final static int col = 6 | 1 << 9 | mathfunc | mathproperty;
+ public final static int row = 7 | 1 << 9 | mathfunc | mathproperty;
// xxx(a,b)
- public final static int load = 3 | 2 << 9 | mathfunc | scriptCommand;
- public final static int script = 5 | 2 << 9 | mathfunc | scriptCommand;
- public final static int substructure = 6 | 2 << 9 | mathfunc | intproperty |
strproperty;
- public final static int search = 7 | 2 << 9 | mathfunc;
- public final static int smiles = 8 | 2 << 9 | mathfunc;
- public final static int contact = 9 | 2 << 9 | mathfunc | shapeCommand;
+ public final static int load = 1 | 2 << 9 | mathfunc | scriptCommand;
+ public final static int script = 2 | 2 << 9 | mathfunc | scriptCommand;
+ public final static int substructure = 3 | 2 << 9 | mathfunc | intproperty |
strproperty;
+ public final static int search = 4 | 2 << 9 | mathfunc;
+ public final static int smiles = 5 | 2 << 9 | mathfunc;
+ public final static int contact = 6 | 2 << 9 | mathfunc | shapeCommand;
// ___.xxx(a,b)
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-09 23:01:06 UTC
(rev 20815)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-10-10 16:49:59 UTC
(rev 20816)
@@ -35,6 +35,7 @@
import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolNMRInterface;
import org.jmol.api.JmolPatternMatcher;
+import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
import org.jmol.bspt.Bspt;
@@ -58,6 +59,7 @@
import org.jmol.util.Edge;
import org.jmol.util.Parser;
import org.jmol.util.Point3fi;
+import org.jmol.util.SimpleUnitCell;
import javajs.util.AU;
import javajs.util.Lst;
@@ -140,6 +142,8 @@
case T.connected:
case T.polyhedra:
return evaluateConnected(mp, args, tok);
+ case T.unitcell:
+ return evaluateUnitCell(mp, args);
case T.contact:
return evaluateContact(mp, args);
case T.data:
@@ -217,6 +221,93 @@
return false;
}
+ private boolean evaluateUnitCell(ScriptMathProcessor mp, SV[] args) {
+ // optional last parameter: scale
+ // unitcell()
+ // unitcell(uc)
+ // unitcell(uc, "reciprocal")
+ // unitcell(ucconv, "primitive","BCC"|"FCC")
+ // unitcell(ucprim, "conventional","BCC"|"FCC"|...?) //not yet implemented
+ // unitcell(origin, [va, vb, vc])
+ // unitcell(origin, pta, ptb, ptc)
+ int lastParam = args.length - 1;
+ float scale = 1;
+ switch (lastParam < 0 ? T.nada : args[lastParam].tok) {
+ case T.integer:
+ case T.decimal:
+ scale = args[lastParam].asFloat();
+ lastParam--;
+ break;
+ }
+ int tok0 = (lastParam < 0 ? T.nada : args[0].tok);
+ Lst<SV> uc = (tok0 == T.varray ? args[0].getList() : null);
+ SymmetryInterface u = null;
+ boolean haveUC = (uc != null);
+ if (haveUC && uc.size() < 4)
+ return false;
+ int ptParam = (haveUC ? 1 : 0);
+ T3[] ucnew = null;
+ if (!haveUC && tok0 != T.point3f) {
+ u = vwr.getCurrentUnitCell();
+ ucnew = (u == null ? new P3[] { P3.new3(0, 0, 0), P3.new3(1, 0, 0),
+ P3.new3(0, 1, 0), P3.new3(0, 0, 1) } : u.getUnitCellVectors());
+ }
+ if (ucnew == null) {
+ ucnew = new P3[4];
+ if (haveUC) {
+ ucnew[0] = P3.newP(SV.ptValue(uc.get(0)));
+ for (int i = 1; i < 4; i++)
+ ucnew[i] = P3.newP(SV.ptValue(uc.get(i)));
+ } else {
+ ucnew[0] = SV.ptValue(args[0]);
+ switch (lastParam) {
+ case 3:
+ // unitcell(origin, pa, pb, pc)
+ for (int i = 1; i < 4; i++)
+ (ucnew[i] = P3.newP(SV.ptValue(args[i]))).sub(ucnew[0]);
+ break;
+ case 1:
+ // unitcell(origin, [va, vb, vc])
+ Lst<SV> l = args[1].getList();
+ if (l != null && l.size() == 3) {
+ for (int i = 0; i < 3; i++)
+ ucnew[i + 1] = SV.ptValue(l.get(i));
+ break;
+ }
+ //$FALL-THROUGH$
+ default:
+ return false;
+ }
+ }
+ }
+ String op = (ptParam <= lastParam ? args[ptParam++].asString() : null);
+ if ("reciprocal".equalsIgnoreCase(op)) {
+ ucnew = SimpleUnitCell.getReciprocal(ucnew);
+ } else if ("primitive".equalsIgnoreCase(op)) {
+ String type = args[ptParam].asString();
+ float[] f = null;
+ if (type.equalsIgnoreCase("BCC"))
+ f = new float[] { .5f, .5f, -.5f, -.5f, .5f, .5f, .5f, -.5f, .5f };
+ else if (type.equalsIgnoreCase("FCC"))
+ f = new float[] { .5f, .5f, 0, 0, .5f, .5f, .5f, 0, .5f };
+ if (f == null)
+ return false;
+ P3[] b = new P3[3];
+ for (int i = 0, p = 0; i < 3; i++) {
+ b[i] = new P3();
+ for (int j = 1; j < 4; j++)
+ b[i].scaleAdd2(f[p++], ucnew[j], b[i]);
+ }
+ for (int i = 0; i < 3; i++)
+ ucnew[i + 1] = b[i];
+
+ }
+ if (scale != 1)
+ for (int i = 1; i < 4; i++)
+ ucnew[i].scale(scale);
+ return mp.addXObj(ucnew);
+ }
+
@SuppressWarnings("unchecked")
private boolean evaluateArray(ScriptMathProcessor mp, SV[] args, boolean
isSelector) throws ScriptException {
if (isSelector) {
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-09 23:01:06 UTC
(rev 20815)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-10-10 16:49:59 UTC
(rev 20816)
@@ -521,7 +521,7 @@
}
@Override
- public V3[] getUnitCellVectors() {
+ public P3[] getUnitCellVectors() {
return unitCell.getUnitCellVectors();
}
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2015-10-09 23:01:06 UTC
(rev 20815)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2015-10-10 16:49:59 UTC
(rev 20816)
@@ -478,13 +478,13 @@
return unitCellMultiplier;
}
- public V3[] getUnitCellVectors() {
+ public P3[] getUnitCellVectors() {
M4 m = matrixFractionalToCartesian;
- return new V3[] {
- V3.newV(cartesianOffset),
- V3.new3(fix(m.m00), fix(m.m10), fix(m.m20)),
- V3.new3(fix(m.m01), fix(m.m11), fix(m.m21)),
- V3.new3(fix(m.m02), fix(m.m12), fix(m.m22)) };
+ return new P3[] {
+ P3.newP(cartesianOffset),
+ P3.new3(fix(m.m00), fix(m.m10), fix(m.m20)),
+ P3.new3(fix(m.m01), fix(m.m11), fix(m.m21)),
+ P3.new3(fix(m.m02), fix(m.m12), fix(m.m22)) };
}
private float fix(float x) {
Modified: trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-10-09 23:01:06 UTC
(rev 20815)
+++ trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2015-10-10 16:49:59 UTC
(rev 20816)
@@ -388,4 +388,16 @@
f /= 2;
return f;
}
+
+ public static P3[] getReciprocal(T3[] abc) {
+ P3[] rabc = new P3[4];
+ int off = (abc.length == 4 ? 1 : 0);
+ rabc[0] = (off == 1 ? P3.newP(abc[0]) : new P3()); // origin
+ for (int i = 0; i < 3; i++) {
+ rabc[i + 1] = new P3();
+ rabc[i + 1].cross(abc[((i + off) % 3) + off], abc[((i + off + 1) % 3) +
off]);
+ rabc[i + 1].scale(1/abc[i + off].dot(rabc[i + 1]));
+ }
+ return rabc;
+ }
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-09 23:01:06 UTC
(rev 20815)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-10 16:49:59 UTC
(rev 20816)
@@ -62,8 +62,21 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
+
Jmol.___JmolVersion="14.3.16_2015.10.09"
+new feature: unitcell() function
+ // optional last parameter: scale
+ // unitcell()
+ // unitcell(uc)
+ // unitcell(uc, "reciprocal")
+ // unitcell(ucconv, "primitive","BCC"|"FCC")
+ // unitcell(ucprim, "conventional","BCC"|"FCC"|...?) //not yet implemented
+ // unitcell(origin, [va, vb, vc])
+ // unitcell(origin, pta, ptb, ptc)
+
+JmolVersion="14.3.16_2015.10.09"
+
bug fix: print 'CCC'.find("SMILES") should throw a ScriptException, not a
Java exception
new feature: Gaussian log file reader reads spin density scalars as
property_spin
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