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Commit ce367667 authored by sjplimp's avatar sjplimp
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15604 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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examples/USER/misc/ti/in.ti_rs deleted 100755 → 0
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# Rodrigo Freitas - rodrigohb@gmail.com
#-------------------------- Initial Setup -------------------------------------#
units metal
atom_modify map array
#------------------------------------------------------------------------------#
#-------------------------- Atomic Setup --------------------------------------#
lattice sc 10.0
region my_region block 0 8 0 8 0 8
create_box 1 my_region
create_atoms 1 box
mass * 50.0
atom_modify sort 0 0
#------------------------------------------------------------------------------#
#---------------------- Thermostat & Barostat ---------------------------------#
fix f1 all nve
fix f2 all spring/self 10.0
fix f3 all ti/rs 1.0 0.5 2000 1000 function 2
fix f4 all langevin 100.0 100.0 0.5 1230917 zero yes
#------------------------------------------------------------------------------#
#------------------ Computes, variables & modifications -----------------------#
compute Tcm all temp/com
fix_modify f4 temp Tcm
variable step equal step
variable U equal f_f2/atoms
variable lambda equal f_f3[1]
variable dlambda equal f_f3[2]
#------------------------------------------------------------------------------#
#------------------------- Thermo stuff ---------------------------------------#
thermo 0
timestep 0.001
#------------------------------------------------------------------------------#
#------------------------- Running the Simulation -----------------------------#
velocity all create 200.0 8128481 mom yes rot yes dist gaussian
# Forward.
run 999
fix f5 all print 1 "${step} ${U} ${lambda} ${dlambda}" &
screen no file forward_rs.dat &
title '# step U lambda dlambda'
run 2001
unfix f5
# Backward.
run 999
fix f5 all print 1 "${step} ${U} ${lambda} ${dlambda}" &
screen no file backward_rs.dat &
title '# step U lambda dlmabda'
run 2001
unfix f5
#------------------------------------------------------------------------------#
examples/USER/misc/ti/in.ti_spring
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View file @ ce367667
# Rodrigo Freitas - rodrigohb@gmail.com # Rodrigo Freitas - rodrigof@berkeley.edu
#
# Description: nonequilibrium thermodynamic integration. Further details in:
# R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016)
# http://dx.doi.org/10.1016/j.commatsci.2015.10.050
#-------------------------- Initial Setup -------------------------------------# #--------------------------- System setup -------------------------------------#
units metal units metal
atom_modify map array lattice fcc 3.621
#------------------------------------------------------------------------------# region sim_box block 0 4 0 4 0 4
create_box 1 sim_box
#-------------------------- Atomic Setup --------------------------------------#
lattice sc 10.0
region my_region block 0 8 0 8 0 8
create_box 1 my_region
create_atoms 1 box create_atoms 1 box
mass * 50.0 pair_style eam/alloy
atom_modify sort 0 0 pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
#---------------------- Thermostat & Barostat ---------------------------------# #---------------------- Simulation setup --------------------------------------#
# The order of the fix commands is important: thermostat AFTER thermodynamic integration force interpolation.
fix f1 all nve fix f1 all nve
fix f2 all spring/self 10.0 fix f2 all ti/spring 3.728 2000 1000 function 2
fix f3 all ti/spring 50.0 2000 1000 function 2 fix f3 all langevin 100.0 100.0 0.1 666 zero yes
fix f4 all langevin 100.0 100.0 0.5 1230917 zero yes
#------------------------------------------------------------------------------#
# Compute temperature using center-of-mass coordinates.
compute c1 all temp/com
fix_modify f3 temp c1
#------------------ Computes, variables & modifications -----------------------# # Output variables.
compute Tcm all temp/com
fix_modify f4 temp Tcm
variable step equal step variable step equal step
variable dU equal (f_f2-f_f3)/atoms variable dU equal pe-f_f2 # Used on the integration.
variable lambda equal f_f3[1] variable lambda equal f_f2[1] # For reference or integration.
variable dlambda equal f_f3[2] variable dlambda equal f_f2[2] # For reference or integration.
#------------------------------------------------------------------------------#
#------------------------- Thermo stuff ---------------------------------------# # Thermo output.
thermo 0 thermo_style custom step pe
timestep 0.001 thermo 100
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
#------------------------- Running the Simulation -----------------------------# #------------------------- Running the simulation -----------------------------#
velocity all create 200.0 8128481 mom yes rot yes dist gaussian # Setup initial velocities to accelerate equilibration.
velocity all create 200.0 9999 mom yes rot yes dist gaussian
# Forward. # Forward nonequilibrium thermodynamic integration.
run 999 run 1000 # Equilibrate system at lambda = 0.
fix f5 all print 1 "${step} ${dU} ${lambda} ${dlambda}" & fix f4 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
screen no file forward_fl.dat & screen no file forward.dat title '# step dU lambda dlambda'
title '# step dU lambda dlambda' run 2000 # Lambda switching: 0 -> 1.
run 2001 unfix f4
unfix f5
# Backward. # Backward nonequilibrium thermodynamic integration.
run 999 run 1000 # Equilibrate system at lambda = 1.
fix f5 all print 1 "${step} ${dU} ${lambda} ${dlambda}" & fix f4 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
screen no file backward_fl.dat & screen no file backward.dat title '# step dU lambda dlambda'
title '# step dU lambda dlambda' run 2000 # Lambda switching: 1 -> 0.
run 2001 unfix f4
unfix f5
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
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