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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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sjplimp
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f81f0da734
commit
ce3676677e
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# Rodrigo Freitas - rodrigohb@gmail.com
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#-------------------------- Initial Setup -------------------------------------#
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units metal
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atom_modify map array
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#------------------------------------------------------------------------------#
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#-------------------------- Atomic Setup --------------------------------------#
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lattice sc 10.0
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region my_region block 0 8 0 8 0 8
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create_box 1 my_region
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create_atoms 1 box
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mass * 50.0
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atom_modify sort 0 0
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#------------------------------------------------------------------------------#
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#---------------------- Thermostat & Barostat ---------------------------------#
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fix f1 all nve
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fix f2 all spring/self 10.0
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fix f3 all ti/rs 1.0 0.5 2000 1000 function 2
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fix f4 all langevin 100.0 100.0 0.5 1230917 zero yes
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#------------------------------------------------------------------------------#
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#------------------ Computes, variables & modifications -----------------------#
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compute Tcm all temp/com
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fix_modify f4 temp Tcm
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variable step equal step
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variable U equal f_f2/atoms
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variable lambda equal f_f3[1]
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variable dlambda equal f_f3[2]
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#------------------------------------------------------------------------------#
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#------------------------- Thermo stuff ---------------------------------------#
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thermo 0
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timestep 0.001
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#------------------------------------------------------------------------------#
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#------------------------- Running the Simulation -----------------------------#
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velocity all create 200.0 8128481 mom yes rot yes dist gaussian
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# Forward.
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run 999
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fix f5 all print 1 "${step} ${U} ${lambda} ${dlambda}" &
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screen no file forward_rs.dat &
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title '# step U lambda dlambda'
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run 2001
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unfix f5
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# Backward.
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run 999
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fix f5 all print 1 "${step} ${U} ${lambda} ${dlambda}" &
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screen no file backward_rs.dat &
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title '# step U lambda dlmabda'
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run 2001
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unfix f5
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#------------------------------------------------------------------------------#
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@ -1,64 +1,59 @@
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# Rodrigo Freitas - rodrigohb@gmail.com
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# Rodrigo Freitas - rodrigof@berkeley.edu
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#
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# Description: nonequilibrium thermodynamic integration. Further details in:
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# R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016)
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# http://dx.doi.org/10.1016/j.commatsci.2015.10.050
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#-------------------------- Initial Setup -------------------------------------#
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#--------------------------- System setup -------------------------------------#
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units metal
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atom_modify map array
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#------------------------------------------------------------------------------#
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#-------------------------- Atomic Setup --------------------------------------#
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lattice sc 10.0
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region my_region block 0 8 0 8 0 8
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create_box 1 my_region
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lattice fcc 3.621
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region sim_box block 0 4 0 4 0 4
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create_box 1 sim_box
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create_atoms 1 box
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mass * 50.0
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atom_modify sort 0 0
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pair_style eam/alloy
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pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu
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#------------------------------------------------------------------------------#
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#---------------------- Thermostat & Barostat ---------------------------------#
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#---------------------- Simulation setup --------------------------------------#
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# The order of the fix commands is important: thermostat AFTER thermodynamic integration force interpolation.
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fix f1 all nve
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fix f2 all spring/self 10.0
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fix f3 all ti/spring 50.0 2000 1000 function 2
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fix f4 all langevin 100.0 100.0 0.5 1230917 zero yes
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#------------------------------------------------------------------------------#
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fix f2 all ti/spring 3.728 2000 1000 function 2
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fix f3 all langevin 100.0 100.0 0.1 666 zero yes
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# Compute temperature using center-of-mass coordinates.
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compute c1 all temp/com
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fix_modify f3 temp c1
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#------------------ Computes, variables & modifications -----------------------#
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compute Tcm all temp/com
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fix_modify f4 temp Tcm
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# Output variables.
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variable step equal step
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variable dU equal (f_f2-f_f3)/atoms
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variable lambda equal f_f3[1]
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variable dlambda equal f_f3[2]
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variable dU equal pe-f_f2 # Used on the integration.
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variable lambda equal f_f2[1] # For reference or integration.
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variable dlambda equal f_f2[2] # For reference or integration.
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# Thermo output.
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thermo_style custom step pe
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thermo 100
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#------------------------------------------------------------------------------#
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#------------------------- Thermo stuff ---------------------------------------#
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thermo 0
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timestep 0.001
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#------------------------------------------------------------------------------#
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#------------------------- Running the Simulation -----------------------------#
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velocity all create 200.0 8128481 mom yes rot yes dist gaussian
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# Forward.
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run 999
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fix f5 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
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screen no file forward_fl.dat &
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title '# step dU lambda dlambda'
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run 2001
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unfix f5
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# Backward.
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run 999
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fix f5 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
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screen no file backward_fl.dat &
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title '# step dU lambda dlambda'
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run 2001
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unfix f5
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#------------------------- Running the simulation -----------------------------#
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# Setup initial velocities to accelerate equilibration.
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velocity all create 200.0 9999 mom yes rot yes dist gaussian
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# Forward nonequilibrium thermodynamic integration.
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run 1000 # Equilibrate system at lambda = 0.
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fix f4 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
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screen no file forward.dat title '# step dU lambda dlambda'
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run 2000 # Lambda switching: 0 -> 1.
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unfix f4
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# Backward nonequilibrium thermodynamic integration.
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run 1000 # Equilibrate system at lambda = 1.
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fix f4 all print 1 "${step} ${dU} ${lambda} ${dlambda}" &
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screen no file backward.dat title '# step dU lambda dlambda'
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run 2000 # Lambda switching: 1 -> 0.
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unfix f4
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#------------------------------------------------------------------------------#
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