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The
Modify functions (setenviron()
and edit*())
can be called only after the
setup()
function. Modify functions can be mixed with calls
to the Run functions.
The
first Modify function is slightly different from
the others. Unlike other Modify functions,
specifying some setenviron()
arguments go beyond storing keyword values. For
example, specifying the
set_velocities
keyword causes the velocities to be adjusted to the
value of start_temperature.
(Whether new velocities are generated or the
existing velocities are scaled depend on the value
assigned to set_velocities.)
Also, some keyword values are modified by other
functions. For example, the value of
start_temperature
is modified by calls to
montecarlo()
and dynamics().
The name of this function starts with
set
and the other function names start with
edit
to draw attention to these differences.
|
Function
|
Summary
|
Return
Values
|
|
setenviron()
|
Modify
the simulation (molecular)
environment
|
#0
|
|
Keyword
|
Argument
|
Type
or Values
|
Interpretation
|
Initial
Value
|
|
archive_type
|
#2
|
"both",
"coordinates",
"velocities"
|
what
to archive
|
"coordinates"
|
|
seed
|
#2
|
Unsigned
|
seed
value for the random number
generator
|
1
|
|
start_time
|
#2
|
Float
|
start
time [ps]
|
0
or (from archive file)
|
|
set_velocities
|
#2
|
"new",
"scale"
|
generate
new velocities or scale to starting
temperature
|
"new"
|
|
temperature
|
#2
|
Float,
>0
|
starting
and final temperatures
[K]
|
300
|
|
start_temperature
|
#2
|
Float,
>0
|
starting
temperature [K]
|
300
|
|
final_temperature
|
#2
|
Float,
>0
|
final
temperature [K]
|
300
|
|
lockset
|
#2
|
Unsigned
|
which
lock set to use, 0 = none
|
0
|
Notes:
#0 : none or no value
#1 : this argument must always be specified
#2 : this argument is optional
|