Revision: 20596
http://sourceforge.net/p/jmol/code/20596
Author: hansonr
Date: 2015-06-19 17:14:06 +0000 (Fri, 19 Jun 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.15_2015.06.19b"
new feature: MACRO command
-- runs predefined script, generally defining new functions of general use
-- contributions welcome!
-- will be expanded
$ macro aflow
running
http://aflowlib.mems.duke.edu/users/jmolers/jmol/spt/AFLOW.spt
aflowLoad(binaryAlloy) loaded
aflowBinaries loaded
aflowDualArray(binaryAlloy, a, b) loaded
aflowDualWrite loaded
aflowConvexHull(binaryAlloy) loaded
aflowCheckBinary(binaryAlloy) loaded
aflowGetPG(binaryAlloy, a, range1, range2,radius) loaded
$ aflowLoad("AgAu")
294 models
$ print aflowConvexHull
{
"Cb" : 0.0
"Hf_eV_VASP" : 0.0
"modelNumber" : 2
}
{
"Cb" : 0.25
"Hf_eV_VASP" : -0.0472733
"modelNumber" : 26
}
{
"Cb" : 0.5
"Hf_eV_VASP" : -0.085589
"modelNumber" : 180
}
{
"Cb" : 0.75
"Hf_eV_VASP" : -0.0463823
"modelNumber" : 25
}
{
"Cb" : 1.0
"Hf_eV_VASP" : 0.0
"modelNumber" : 260
}
bug fix: AFLOW binary file reader can fail with certain VASP formats containing
both in-line atom labels and atom elements prior to #elements line.
(AlPd#5, for example)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-06-19 15:45:34 UTC
(rev 20595)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-06-19 17:14:06 UTC
(rev 20596)
@@ -2520,6 +2520,7 @@
case T.hbond: // hbond connect
case T.image:
case T.stereo:
+ case T.macro:
case T.mapproperty:
case T.minimize:
case T.modulation:
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-06-19 15:45:34 UTC (rev
20595)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-06-19 17:14:06 UTC (rev
20596)
@@ -330,7 +330,8 @@
public final static int invertSelected = scriptCommand | 26;
//public final static int load see mathfunc
public final static int loop = scriptCommand | 27 | defaultON;
- public final static int mapproperty = scriptCommand | 28 | expression;
+ public final static int macro = scriptCommand | 28;
+ public final static int mapproperty = scriptCommand | 29 | expression;
public final static int minimize = scriptCommand | 30;
//public final static int model see mathfunc
//public final static int measure see mathfunc
@@ -2250,6 +2251,7 @@
"lonePair",
"lp",
"lumo",
+ "macro",
"manifest",
"mapProperty",
"map",
@@ -3280,6 +3282,7 @@
lonepair, // "lonePair"
lp, // "lp"
lumo, // "lumo"
+ macro, // "macro" // added in
Jmol 14.3.15
manifest, // "manifest"
mapproperty, // "mapProperty"
-1, // "map"
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-06-19 15:45:34 UTC
(rev 20595)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-06-19 17:14:06 UTC
(rev 20596)
@@ -142,6 +142,9 @@
case T.image:
image();
break;
+ case T.macro:
+ macro();
+ break;
case T.mapproperty:
mapProperty();
break;
@@ -190,6 +193,22 @@
}
+ private void macro() throws ScriptException {
+ String key = e.optParameterAsString(1);
+ if (key.length() == 0)
+ return;
+ if (chk)
+ return;
+ String macro = JC.getMacro(key);
+ if (macro == null) {
+ showString("macro " + key + " could not be found. Current macros
include:\n" + JC.getMacroList());
+ return;
+ }
+ showString("running " + macro);
+ macro = vwr.getFileAsString3(macro, false, null);
+ e.runScript(macro);
+ }
+
/**
* used for TRY command
*
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-06-19 15:45:34 UTC (rev
20595)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-06-19 17:14:06 UTC (rev
20596)
@@ -32,6 +32,7 @@
import javajs.J2SRequireImport;
import javajs.util.PT;
+import javajs.util.SB;
import javajs.util.V3;
import java.io.BufferedInputStream;
@@ -64,7 +65,25 @@
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";
};
+
+ public static String[] macros = {
+ "aflow", "http://aflowlib.mems.duke.edu/users/jmolers/jmol/spt/AFLOW.spt";
+ };
+ public static String getMacroList() {
+ SB s = new SB();
+ for (int i = 0; i < macros.length; i += 2)
+ s.append(macros[i]).append("\t").append(macros[i + 1]).append("\n");
+ return s.toString();
+ }
+
+
+ public static String getMacro(String key) {
+ for (int i = 0; i < macros.length; i += 2)
+ if (macros[i].equals(key))
+ return macros[i + 1];
+ return null;
+ }
public final static String copyright = "(C) 2015 Jmol Development";
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-19 15:45:34 UTC
(rev 20595)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-19 17:14:06 UTC
(rev 20596)
@@ -17,6 +17,50 @@
Jmol.___JmolVersion="14.3.15_2015.06.19b"
+new feature: MACRO command
+ -- runs predefined script, generally defining new functions of general use
+ -- contributions welcome!
+ -- will be expanded
+
+ $ macro aflow
+ running
http://aflowlib.mems.duke.edu/users/jmolers/jmol/spt/AFLOW.spt
+ aflowLoad(binaryAlloy) loaded
+ aflowBinaries loaded
+ aflowDualArray(binaryAlloy, a, b) loaded
+ aflowDualWrite loaded
+ aflowConvexHull(binaryAlloy) loaded
+ aflowCheckBinary(binaryAlloy) loaded
+ aflowGetPG(binaryAlloy, a, range1, range2,radius) loaded
+ $ aflowLoad("AgAu")
+ 294 models
+
+ $ print aflowConvexHull
+ {
+ "Cb" : 0.0
+ "Hf_eV_VASP" : 0.0
+ "modelNumber" : 2
+ }
+ {
+ "Cb" : 0.25
+ "Hf_eV_VASP" : -0.0472733
+ "modelNumber" : 26
+ }
+ {
+ "Cb" : 0.5
+ "Hf_eV_VASP" : -0.085589
+ "modelNumber" : 180
+ }
+ {
+ "Cb" : 0.75
+ "Hf_eV_VASP" : -0.0463823
+ "modelNumber" : 25
+ }
+ {
+ "Cb" : 1.0
+ "Hf_eV_VASP" : 0.0
+ "modelNumber" : 260
+ }
+
bug fix: AFLOW binary file reader can fail with certain VASP formats
containing
both in-line atom labels and atom elements prior to #elements line.
(AlPd#5, for example)
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