Changes between Version 13 and Version 14 of StartersTutorial

Timestamp:

Aug 13, 2010, 4:23:37 PM (15 years ago)

Author:

FrederikHeber

Comment:

subgraph lacked -v 3 switch and notice that storing is molecule-wise

StartersTutorial

@@ -109 +109 @@
 If we then parse in the config files again, we will not have two separate molecules, addressable by indices 0 and 1, but a single one. This is bad. Let's do a graph analysis of the system
 {{{
-./src/molecuilder -i test.conf -I
+./src/molecuilder -i test.conf -v 3 -I
 }}}
 
 Note that we have specified here a verbosity level (''-v'') of 3 such that one sees a bit of what's going on.
-Somewhere along the output, you will notice ''Disconnected subgraph ranges from ...'' appears twice. These are two water molecules that have been recognized as separated.
+Somewhere along the output, you will notice ''Disconnected subgraph ranges from ...'' appears twice. These are two water molecules that have been recognized as separated: '''I scanned 2 molecules.'''
+
+Also, the sequence of the atoms has changed again. Their affiliation with a molecule supercedes the order--by-element of the ''pcp'' type, i.e. first all atoms of molecule 1, then of molecule 2.
 
 == Tesselate the second molecule ==