Xmd Test Job

From UGP-Wiki

XMD is a molecular dynamics program package. box9.xm and cu.txt are input files to test XMD serial jobs.

box9.xm looks like:

####################################
#  Finding the optimum time step   #
#                                  #
#                                  # 
####################################                 
# BOX MADE OF COPPER 
# 
#
# 
# 
* 
* 2 PS IN EACH TEMP FIRST A PERIOD OF ADIABATIC MD
* 500 ATOMS PERIODIC BOUNDARIES
# 
# 
# Set EAM potential
#
#
POTENTIAL SET EAM 1
#
#
# Read Copper potential
#
read cu.txt
TYPENAME 1 CU
#
#
# Macro for output files
#
MACRO fname optimum_
#
# Making repeating box
#
box 9 9 9
fill particle 4
1 1/4 1/4 1/4
1 1/4 3/4 3/4
1 3/4 1/4 3/4
1 3/4 3/4 1/4 
fill go
#
#
# Scale up to Cu unit cell length
#
SCALE 3.61
#
#
# Save energies from every dynamics step in file "timestep_e.txt"
#
esave 50 w_timestep_e.txt
#
#
# set masses (in atomic mass units)
#
#
SELECT ALL
# 
MASS 63.54
#
#
# Set adiabatic simulation (total energy conserved) at starting
# temperature of 200K
# 
clamp off
itemp 2000
#
#
# Set time step (Varying)
#
#
# Set initial timestep size variable
#
calc stepsize = 1.5e-15
#
# Do 6 separate runs of 20 steps each
#repeat 20
  # Set timestep size using dtime command
  dtime stepsize
  # 20 steps of dynamics (energies are written to tempstep_e.txt file
  select all
  write file n_of_particles.txt np
  write pdb $(fname)_prior.pdb
  cmd 200
  write pdb $(fname)_after200.pdb
  cmd 10000
  write pdb $(fname)_final.pdb
  # Double the time step size
  #calc  stepsize = stepsize + 2e-16
#end

*SELECT SET 4

cu.txt looks like:

#
#  Johnson's Cu potential
#
#
potential set eam 1
eunit ev

POTENTIAL PAIR 1 1 3000 1 5.0000
7.303228e+01 7.268832e+01 7.234597e+01
7.200523e+01 7.166610e+01 7.132857e+01
...(2500 data lines omitted)

1. Use the Data Manager to copy box9.xm and cu.txt to the cluster on which you will run XMD.
2. Select "Applications" under the "Job Services" tab.
3. Select XMD under the cluster name from the frame on the left side of the page.
4. Fill in the Applications form as follows:
   1. Enter box9.xm the text field labeled "Arguments:".
   2. If box9.xm is not in your home directory, enter in the text field labeled "Directory:" either the full pathname of the directory containing cpmd.in or a path relatative to your home directory.
   3. Select serial for the "JobType" field.
   4. Enter 1 for the "Number of processors:".
   5. Click the "Submit Job" button.

The results will be in the chosen directory.