cavity.xmo

一个很好的分子动力学程序

XMD (Version 2.5.29 Nov 27 2000)

Not using pthread library.
Not using asm("finit"); patch in thread routines.
#######################################################################
#                                                           17 Jul 96 #
#                                                                     #
#  Example:  Constraining particle with the CONSTRAIN CAVITY command  #
#                                                                     #
#######################################################################
#                                                                     #
#    The CONSTRAIN CAVITY command creates a cavity constraint which   #
#  imposes a spring-like force on atoms that try to exit through the  #
#  wall.                                                              #
#                                                                     #
#    In this example, we create a single Ni FCC 3.5x3.5x3.5 cube.     #
#  This cube is started with its atoms at 16000K and its is placed    #
#  in an ellipsoidal cavity.  Molecular dynamics is performed for     #
#  2000 steps, during which time atoms 'boil' off the cube into       #
#  space and are reflected back by the ellipsoid walls.               #
#                                                                     #
#    A COR file cavity.cor is written so that a movie can be made.    #
#  Also an ESAVE file cavity.e is written to every 10 steps to check  #
#  that energy is conserved.                                          #
#                                                                     #
#######################################################################
#     The format of the CONSTRAIN CAVITY command is                   #
#                                                                     #
#         CONSTRAIN ELLIPSOID  spring  xc yc zc  xa ya za             #
#     or                                                              #
#         CONSTRAIN SPHERE     spring  xc yc zc  radius               #
#                                                                     #
#  where   spring      is the spring constant (dynes/cm)              #
#          xc yc zc    is the center of the cavity (angstroms)        #
#          xa ya za    are the ellipsoidal half-axises (angstroms)    #
#                      (analogous to spherical radii)                 #
#          radius      is the sphere radius (angstroms)               #
#                                                                     #
#######################################################################
#
#  Allocate space for particles
#
allocate 10000 100000
WARNING:  Allocate command is now obsolete.
#
#  Read Nickel-Aluminum potential
#
read ../nial.txt
#
#  Set large box (most of box will be empty)
#
box 12 12 12
#
#  Create a 3.5x3.5x3.5 FCC cube with one corner at the origin
#
particle 4
dup 4  1 0 0 
dup 4  0 1 0 
dup 4  0 0 1 
#
#  Trim off remaining 0.5 cells
#
#     NOTE:  This leaves 'extra' layer on trailing surfaces,
#     so that every surface atom is one of the fcc unit cell
#     'corners'.  The result is the cube looks more symetrical.
#
select not box  0 0 0 3.5 3.5 3.5
***  NUMBER SELECTED 328
remove
***   NUMBER REMAINING 172
#
#  Move cube toward center of box
#
select all
***  NUMBER SELECTED 172
move 4.25 4.25 4.25
#
#  Add ellipsoid cavity
#
constrain cavity sphere  1e5  6.0 6.0 6.0   4.0 2.0 2.0
#
#  Scale up to Ni unit cell length
#
scale 3.52
#
#  Set masses
#
select all
***  NUMBER SELECTED 172
#  MASS1 is set in nialh.txt file
mass MASS1
#
#  Set adiabatic simulation (total energy conserved) 
#
clamp -1
#
#  Initialize high temperature
#
itemp 16000
#
#  Save energy every 10 time steps (to check conservation of energy)
#
esave 10 cavity.e
#
#  Write initial coordinates (for make movie after)
#
write cor cavity.cor
#
#   Perform 2000 simulations steps 
#   Save coordinates after every 20 steps
#
repeat 100
   cmd 20
   write cor +cavity.cor
end
***   Current step is 20
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***   Current step is 2000

TIME INFORMATION
   Ending   Time: 03/19/2001   13:37:07
   Elapsed  Time: 0 min 11 sec

DYNAMICS STATISTICS
   Number of MD Steps:                2000
   Number of Neighbor Searchs:         873
   Time spent on MD steps:              10 (secs)
   Time spent on Neighbor Search:        2 (secs)

ERROR STATISTICS
   Number of Fatal Errors:               0
   Number of Unknown Command Errors:     0
   Number of Misc. Warnings:             1   <=======  !!!