Changeset 1829 for branches/blt4

Timestamp:

Jul 16, 2010 3:47:24 PM (14 years ago)

Author:

gah

Message:

 

Location:

branches/blt4

Files:

• gui/scripts/analyzer.tcl (modified) (5 diffs)
• gui/scripts/molvisviewer.tcl (modified) (3 diffs)
• packages/vizservers/nanovis/FlowCmd.cpp (modified) (1 diff)
• packages/vizservers/nanovis/Makefile.in (modified) (1 diff)

branches/blt4/gui/scripts/analyzer.tcl

@@ -508 +508 @@
 
     foreach item [$xmlobj children -type run output.include] {
-        set id [$xmlobj element -as id output.include.$item]
-        set inclfile [$xmlobj get output.include.$item]
-        set inclobj [Rappture::library $inclfile]
-        foreach c [$inclobj children output] {
-            switch -glob -- $c {
-                # we don't want to include these tags
-                include* - time* - status* - user* {
-                    continue
-                }
-                default {
-                    set oldid [$inclobj element -as id output.$c]
-                    set oldtype [$inclobj element -as type output.$c]
-                    set newcomp "$oldtype\($id-$oldid\)"
-                    $xmlobj copy output.$newcomp from $inclobj output.$c
-                }
-            }
-        }
+        set id [$xmlobj element -as id output.include.$item]
+        set inclfile [$xmlobj get output.include.$item]
+        set inclobj [Rappture::library $inclfile]
+        foreach c [$inclobj children output] {
+            switch -glob -- $c {
+                # We don't want to include these tags.
+                include* - time* - status* - user* {
+                    continue
+                }
+                default {
+                    set oldid [$inclobj element -as id output.$c]
+                    set oldtype [$inclobj element -as type output.$c]
+                    set newcomp "$oldtype\($id-$oldid\)"
+                    $xmlobj copy output.$newcomp from $inclobj output.$c
+                }
+            }
+        }
     }
 
     lappend _runs $xmlobj
 
-    # detect molecule elements that contain trajectory data and convert
+    # Detect molecule elements that contain trajectory data and convert
     # to sequences.
     _trajToSequence $xmlobj output
 
-    # go through the analysis and find all result sets
+    # Go through the analysis and find all result sets.
     set haveresults 0
     foreach item [_reorder [$xmlobj children output]] {
@@ -1256 +1256 @@
 }
 
+# ----------------------------------------------------------------------
+# USAGE: _lammpsToSequence <xmlobj> ?<path>?
+#
+# If the molecule element is a trajectory, delete the original
+# and create a sequence of individual molecules.
+# Used internally to detect any molecule output elements that contain
+# trajectory data.  Trajectories will be converted into sequences of
+# individual molecules.  All other elements will be unaffected. Scans
+# the entire xml tree if a starting path is not specified.
+# ----------------------------------------------------------------------
 itcl::body Rappture::Analyzer::_lammpsToSequence {xmlobj path id child data} {
 
@@ -1308 +1318 @@
 
 # ----------------------------------------------------------------------
-# USAGE: _trajtosequence <xmlobj> ?<path>?
+# USAGE: _trajToSequence <xmlobj> ?<path>?
 #
 #       Check for PDB and LAMMPS trajectories in molecule data and rewrite 
@@ -1328 +1338 @@
         set current ${path}.${child}
         if { [string match "structure*" $child] } {
+            set isTraj [$xmlobj get ${current}.components.molecule.trajectory]
+            if { !$isTraj } {
+                continue;               # Not a trajectory.
+            }
             # Look for trajectory if molecule element found.  Check both pdb
             # data and lammps data.
@@ -1347 +1361 @@
             continue
         }
+        if 0 {
         # Recurse over all child nodes.
-        #_trajToSequence $xmlobj $current
+        _trajToSequence $xmlobj $current
+        }
     }
 }

branches/blt4/gui/scripts/molvisviewer.tcl

@@ -778 +778 @@
                 # We know we're buffered here, so append the "loadpdb" command
                 # with the data payload immediately afterwards.
-                append _outbuf "loadpdb -defer $nBytes $model $state\n"
+                append _outbuf "loadpdb -defer NA $state $nBytes\n"
                 append _outbuf $data1
                 set _dataobjs($model-$state)  1
@@ -791 +791 @@
                 # We know we're buffered here, so append the "loadpdb" command
                 # with the data payload immediately afterwards.
-                append _outbuf "loadpdb -defer $nBytes $model $state\n"
+                append _outbuf "loadpdb -defer NA $state $nBytes\n"
                 append _outbuf $data2
                 set _dataobjs($model-$state)  1
@@ -841 +841 @@
                     # We know we're buffered here, so append the "loadpdb" 
                     # command with the data payload immediately afterwards.
-                    append _outbuf "loadpdb -defer $nBytes $model $state\n"
+                    append _outbuf "loadpdb -defer NA $model $state $nBytes\n"
                     append _outbuf $data3
                 }

branches/blt4/packages/vizservers/nanovis/FlowCmd.cpp

@@ -4 +4 @@
 #include <stddef.h>
 #include <limits.h>
+#include <stdint.h>
 #include <poll.h>
 #include <tcl.h>

branches/blt4/packages/vizservers/nanovis/Makefile.in

@@ -107 +107 @@
 CFLAGS          = @CFLAGS@
 EXTRA_CFLAGS    = -Wall
-DEFINES         = @DEFINES@
-CC_SWITCHES     = $(CFLAGS) $(EXTRA_CFLAGS) $(INCLUDES)
+DEFINES         = -D__STDC_CONSTANT_MACROS=1
+CC_SWITCHES     = $(CFLAGS) $(EXTRA_CFLAGS) $(DEFINES) $(INCLUDES)
 
 OBJS            = \