Descriptor File Format

lock: atom lock set definition

The lock record defines Nset sets of atoms that may be locked during a simulation. The lock record in the descriptor file has the form

lock
Nset

Nlock

atomi
atomj
...

...

The lock record starts with the keyword lock followed by the number of lock sets Nset. This is followed by Nset sub-records consisting first of the number of atoms in the lock set Nlock then the atoms in the set atomi, atomj, atomk and so on.

The lock sets are dormant until a set is selected during a simulation. When a lock set is selected before the application of certain simulation methods, the atoms in the set are locked into their current positions (whatever that may be). The lock-friendly methods are Monte Carlo and some energy minimization methods. If other simulation methods (molecular dynamics in particular and some energy minimization methods) are used the locked atoms will move along with every other atoms, i.e., the locks will have no effect. When a lock-friendly simulation method is applied later on, the atoms in the chosen lock set are locked at their new positions. Choosing lock set 0 removes all atom locking. Example


lock 3
3
     9   17   18
10
     3   6   7   8   9   11   16   17   18   19
7
     7   8   9   11   17   18   19

Three lock sets are defined with three, ten and seven candidate atoms respectively. In a simulation, one could for example, choose lock set 2, then 3, then 1 and finally 0 to refine a system with most of the atoms locked in the beginning and then to progressively relax the constraints until with the final choice of lock set 0, all atoms are released.


Details of Descriptor Records
intro
DES1
note
type
ivms
name
bond
mors
angl
angn
tors
itor
iton
nbn+
nbn-
ele+
ele-
vdw+
vdw-
abhb
noen
surf
stud
vlat
boun
lock

des format
arc format
yammp shell
exam commands
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arc
arcedit
arctransform
checkspider
des
elec2vlat

exam
mimesis
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mkchaindes
mkd3c
mkd3d
mkr2cc
mksnac
mksnad
xmd3
xmr2
ympf

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