From: <ha...@us...> - 2010-08-18 07:25:41
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Revision: 14033 http://jmol.svn.sourceforge.net/jmol/?rev=14033&view=rev Author: hansonr Date: 2010-08-18 07:25:34 +0000 (Wed, 18 Aug 2010) Log Message: ----------- 12.1.5 VERSION # bug fix: CRYSTAL reader FREQUENCY needs fragment numbers sorted # bug fix: rotation QUATERNION broken by 11.9.36, Mar 25, 2009 - Does not rotation about {0 0 0} # bug fix: CURSOR_WAIT hourglass not turning off automatically after set picking JmolScript operation # bug fix: associative array function .keys should report sorted key list # bug fix: associative arrays as ScriptVariables must be checked for type # new feature: color() function: # color("") -- full details on current propertyColorScheme # color("$someID") -- full details on isosurface ID "someID" color scheme # color("xxx") -- full details for a named scheme where "xxx" is "rwb", for instance # color("myscale = [xFF0000] [ x00FF00] [x0000FF]") creation of a scheme and return of details # color("roygb", n) -- nth color of a standard color scheme # color("", x.y) -- color for a property value x.y # color("$someID", x.y) -- color for isosurface ID "someID" value x.y # color("roygb", min, max) -- color/value pairs (two arrays) # color("roygb", min, max, value) -- color for specific value # print color("myscale = [xFF0000] [x00FF00] [x0000FF]") # colors : # {255.0 0.0 0.0} # {0.0 255.0 0.0} # {0.0 0.0 255.0} # # max : 4.0 # min : 1.0 # name : myscale # reversed : false # values : # 1.0 # 2.0 # 3.0 # 4.0 # # print color("myscale = [xFF0000] [x00FF00] [x0000FF]", 0, 10, 0) # {255.0 0.0 0.0} # # The scheme is constructed, so it can be used later: # # print color("myscale", 0, 10, 5) # {0.0 255.0 0.0} # # bug fix: associative array key sorting, new line for arrayed values # new feature: getProperty shapeInfo reports colorKey for isosurfaces: # getproperty shapeInfo.isosurface[1].colorKey # # shapeinfo.isosurface[1].colorkey.colors *List[31] # shapeinfo.isosurface[1].colorkey.colors[1] {255.0 0.0 0.0} # shapeinfo.isosurface[1].colorkey.colors[2] {255.0 0.0 0.0} # ... # shapeinfo.isosurface[1].colorkey.colors[31] {16.0 16.0 255.0} # shapeinfo.isosurface[1].colorkey.color {255.0 165.0 0.0} # shapeinfo.isosurface[1].colorkey.values *float[32] [50.0,48.387096,46.774193,...,0.0] # shapeinfo.isosurface[1].colorkey.name "roygb" # shapeinfo.isosurface[1].colorkey.max 31 # shapeinfo.isosurface[1].colorkey.min 1 # # bug fix: isosurface color range should not carry over to general "color property" # bug fix: isosurface colorscheme TRANSLUCENT "xxx" fillTriangle error # bug fix: should not allow isosurface ... map colorscheme "xxx" TRANSLUCENT # bug fix: CRYSTAL reader FREQUENCY when input deck is missing VIBRATION record Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java 2010-08-18 07:21:53 UTC (rev 14032) +++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java 2010-08-18 07:25:34 UTC (rev 14033) @@ -34,6 +34,7 @@ import org.jmol.util.TextFormat; import java.util.ArrayList; +import java.util.Arrays; import java.util.BitSet; import java.util.List; @@ -778,6 +779,8 @@ String[] tokens = getTokens(Sfrag); for (int i = 0, pos = 0; i < numAtomsFrag; i++, pos += 5) atomFrag[i] = getAtomIndexFromPrimitiveIndex(parseInt(tokens[pos]) - 1); + + Arrays.sort(atomFrag); // the frequency module needs these sorted // note: atomFrag[i] will be -1 if this atom is being ignored due to FILTER "conventional" Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-08-18 07:21:53 UTC (rev 14032) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-08-18 07:25:34 UTC (rev 14033) @@ -1,8 +1,9 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.1.5_dev +version=12.1.5 +# bug fix: CRYSTAL reader FREQUENCY needs fragment numbers sorted # bug fix: rotation QUATERNION broken by 11.9.36, Mar 25, 2009 - Does not rotation about {0 0 0} # bug fix: CURSOR_WAIT hourglass not turning off automatically after set picking JmolScript operation # bug fix: associative array function .keys should report sorted key list @@ -11,7 +12,7 @@ # color("") -- full details on current propertyColorScheme # color("$someID") -- full details on isosurface ID "someID" color scheme # color("xxx") -- full details for a named scheme where "xxx" is "rwb", for instance -# color("myscale = [xFF0000] [x00FF00] [x0000FF]") creation of a scheme and return of details +# color("myscale = [xFF0000] [ x00FF00] [x0000FF]") creation of a scheme and return of details # color("roygb", n) -- nth color of a standard color scheme # color("", x.y) -- color for a property value x.y # color("$someID", x.y) -- color for isosurface ID "someID" value x.y This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |