velocity.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:  Setting linear and angular velocities with               #
#            the VELOCITY command                                     #
#                                                                     #
#######################################################################
#                                                                     #
#    The VELOCITY command sets the linear or angular velocity         #
#  of the center of mass of a group of selected particles.            #
#                                                                     #
#    In this example, we create two Ni FCC cubes, each 3.5x3.5x3.5    #
#  cell lengths and separated by 2 unit cell lengths.  Each           #
#  cube is given a velocity toward the other, and each is rotated in  #
#  opposite directions about an axis that runs through their center   #
#  of masses and points in the Z direction.                           #
#                                                                     #
#######################################################################
#     The format of the VELOCITY command is                           #
#                                                                     #
#          VELOCITY LINEAR  dx dy dz magnitude                        #
#     or                                                              #
#          VELOCITY ANGULAR dx dy dz magnitude                        #
#                                                                     #
#  where   dx dy dz    are the components of the axis direction       #
#                      (only the direction of the vector d is used)   #
#          magnitude   is either the linear velocity in (cm/sec)      #
#                      or the angular velocity (in radians/sec)       #
#                                                                     #
#######################################################################
#
#  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 13 13 13
#
#  Create a 3.5x3.5x3.5 FCC cube with one corner at the origin
#
particle 4
dup 3  1 0 0 
dup 3  0 1 0 
dup 3  0 0 1 
#
#  Trim off extra 0.5 unit 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 84
remove
***   NUMBER REMAINING 172
#
#  Store first cube in set 1
#
select all
***  NUMBER SELECTED 172
set add 1
#
#  Move cube toward center of box
#
select all
***  NUMBER SELECTED 172
move 2 4.75 4.75
#
#  Make second cube displaced 5.5 unit cells
#  Now the midpoint of the two cubes is centered in the box.
#
dup 1  5.5 0.0 0.0
#
#  Store second cube as set 2
#
select not set 1
***  NUMBER SELECTED 172
set add 2
#
#  Scale up to Ni unit cell length
#
scale 3.52
#
#  Set masses
#
select all
***  NUMBER SELECTED 344
#  MASS1 is set in nial.txt file
mass MASS1
#
#  Set linear velocities for first and second cube separately
#
select set 1
***  NUMBER SELECTED 172
velocity linear  1 0 0  2e4  
select set 2
***  NUMBER SELECTED 172
velocity linear  1 0 0  -2e4
#
#  Set angular velocities for first and second cube separately
#
select set 1
***  NUMBER SELECTED 172
velocity angular 0 0 1   2e11
select set 2
***  NUMBER SELECTED 172
velocity angular 0 0 1  -2e11
#
#  Set adiabatic simulation (total energy conserved) 
#
clamp -1
#
#  Save energy every 10 time steps (to insure conservation of energy)
#
esave 10 velocity.e
#
#  Write initial coordinates (for making movie after)
#
write cor velocity.cor
#
#   Perform 1000 simulations steps (50*20)
#   Save coordinates after every 20 steps
#
repeat 50
   cmd 20
   write cor +velocity.cor
end
***   Current step is 20
***   Current step is 40
***   Current step is 60
***   Current step is 80
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***   Current step is 740
***   Current step is 760
***   Current step is 780
***   Current step is 800
***   Current step is 820
***   Current step is 840
***   Current step is 860
***   Current step is 880
***   Current step is 900
***   Current step is 920
***   Current step is 940
***   Current step is 960
***   Current step is 980
***   Current step is 1000

TIME INFORMATION
   Ending   Time: 03/19/2001   13:41:28
   Elapsed  Time: 0 min 15 sec

DYNAMICS STATISTICS
   Number of MD Steps:                1000
   Number of Neighbor Searchs:          93
   Time spent on MD steps:              15 (secs)
   Time spent on Neighbor Search:        0 (secs)

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