Changes between Version 2 and Version 3 of ManyBodyBondOrder

Timestamp:

Aug 18, 2008, 11:45:22 AM (16 years ago)

Author:

FrederikHeber

Comment:

changed to current BOSSANOVA scheme

ManyBodyBondOrder

@@ -5 +5 @@
 ./molecuilder <PathToConfig>/acetanilide.conf
 }}}
- 1. Create the connection matrix by entering: '''o 1.55'''
- 1. Create the Atomic and Bond Fragments by entering: '''f 1 b'''. This will use the ''!BottomUp''-approach to 1st order.
+ 1. Create the Bond Fragments by entering: '''f 1.55 1'''. This will look for bonds between atoms at most 1.55 units apart and fragment to first order.
  1. Quit ''MoleCuilder''.
  1. The config files of the fragments reside in the directory given as the defaultpath in the father config file (must exist).
  1. Go to this directory and create all the necessary subdirs with:
 {{{
-i=0
-while [ -e AtomicFragment${i}.conf ]; do 
-  mkdir AtomicFragment${i}
-  let i=$i+1
-done
 i=0
 while [ -e BondFragment${i}.conf ]; do
@@ -23 +17 @@
 }}}
  1. Start the simulations ...
- 1. Add the resulting total energy of each fragment according to the created file ''TE-Factors.dat.conf''.
+ 1. Use '''joiner''' to evaluate total energy and forces in the files ''pcp.energy.all'' and ''pcp.forces.all'':
+{{{
+joiner <PathToConfig>/ pcp
+}}}