fix spring doc page update
This commit is contained in:
Steve Plimpton
@ -1,163 +1,163 @@
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############################################################################
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# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
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# Christopher Barrett, March 2013
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# This script requires a Mg pair potential file to be in the same directory.
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# fname is the file name. It is necessary for loops to work correctly. (See jump command)
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variable fname index in.basal
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######################################
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# POTENTIAL VARIABLES
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# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
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variable lx equal 3.181269601
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variable b equal sqrt(3)
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variable c equal sqrt(8/3)
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variable ly equal ${b}*${lx}
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variable lz equal ${c}*${lx}
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variable pairlocation index almg.liu
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variable pairstyle index eam/alloy/opt
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######################################
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# EQUILIBRATION/DEFORMATION VARIABLES
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# eqpress = 10 bar = 1 MPa
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# tstep (the timestep) is set to a default value of 0.001 (1 fs)
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# seed randomizes the velocity
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# srate is the rate of strain in 1/s
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# Ndump is the number of timesteps in between each dump of the atom coordinates
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variable tstep equal 0.001
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variable seed equal 95812384
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variable srate equal 1e9
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######################################
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# INITIALIZATION
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units metal
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dimension 3
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boundary s s s
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atom_style atomic
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######################################
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# ATOM BUILD
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atom_modify map array
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# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
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lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
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variable multiple equal 20
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variable mx equal "v_lx*v_multiple"
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variable my equal "v_ly*v_multiple"
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variable mz equal "v_lz*v_multiple"
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# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
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region whole block 0 ${mz} 0 ${mx} 0 ${my} units box
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create_box 2 whole
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create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1
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region fixed1 block INF INF INF INF INF 10 units box
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region fixed2 block INF INF INF INF 100 INF units box
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group lower region fixed1
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group upper region fixed2
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group boundary union upper lower
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group mobile subtract all boundary
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variable natoms equal "count(all)"
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print "# of atoms are: ${natoms}"
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######################################
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# INTERATOMIC POTENTIAL
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pair_style ${pairstyle}
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pair_coeff * * ${pairlocation} Mg Mg
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######################################
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# COMPUTES REQUIRED
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compute csym all centro/atom 12
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compute eng all pe/atom
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compute eatoms all reduce sum c_eng
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compute basal all basal/atom
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######################################
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# MINIMIZATION
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# Primarily adjusts the c/a ratio to value predicted by EAM potential
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reset_timestep 0
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thermo 1
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thermo_style custom step pe c_eatoms
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min_style cg
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minimize 1e-15 1e-15 1000 2000
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variable eminimum equal "c_eatoms / count(all)"
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print "%%e(it,1)=${eminimum}"
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######################################
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# EQUILIBRATION
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reset_timestep 0
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timestep ${tstep}
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# atoms are given a random velocity based on a temperature of 100K.
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velocity all create 100 ${seed} mom yes rot no
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# temperature and pressure are set to 100 and 0
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fix 1 all nve
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# Set thermo output
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thermo 100
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thermo_style custom step lx ly lz press pxx pyy pzz pe temp
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# Run for at least 2 picosecond (assuming 1 fs timestep)
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run 2000
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# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
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label loopeq
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variable eq loop 100
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run 250
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variable converge equal press
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if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press"
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if "${converge} <= 50" then "jump ${fname} breakeq"
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next eq
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jump ${fname} loopeq
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label breakeq
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# Store length for strain rate calculations
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variable tmp equal "lx"
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variable L0 equal ${tmp}
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print "Initial Length, L0: ${L0}"
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unfix 1
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######################################
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# DEFORMATION
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reset_timestep 0
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timestep ${tstep}
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# Impose constant strain rate
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variable srate1 equal "v_srate / 1.0e10"
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velocity upper set 0.0 NULL 0.0 units box
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velocity lower set 0.0 NULL 0.0 units box
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fix 2 upper setforce 0.0 NULL 0.0
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fix 3 lower setforce 0.0 NULL 0.0
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fix 1 all nve
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# Output strain and stress info to file
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# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
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# p2 is in GPa
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variable strain equal "(lx - v_L0)/v_L0"
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variable p1 equal "v_strain"
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variable p2 equal "-pxz/10000"
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variable p3 equal "lx"
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variable p4 equal "temp"
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variable p5 equal "pe"
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variable p6 equal "ke"
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fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
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# Dump coordinates to file (for void size calculations)
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dump 1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
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# Display thermo
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thermo_style custom step v_strain pxz lx temp pe ke
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restart 50000 output.restart
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# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
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variable runtime equal 0
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label loop
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displace_atoms all ramp x 0.0 ${srate1} z 10 100 units box
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run 100
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variable runtime equal ${runtime}+100
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if "${runtime} < 100000" then "jump ${fname} loop"
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######################################
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# SIMULATION DONE
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print "All done"
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############################################################################
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# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
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# Christopher Barrett, March 2013
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# This script requires a Mg pair potential file to be in the same directory.
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# fname is the file name. It is necessary for loops to work correctly. (See jump command)
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variable fname index in.basal
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######################################
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# POTENTIAL VARIABLES
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# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
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variable lx equal 3.181269601
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variable b equal sqrt(3)
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variable c equal sqrt(8/3)
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variable ly equal ${b}*${lx}
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variable lz equal ${c}*${lx}
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variable pairlocation index almg.liu
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variable pairstyle index eam/alloy/opt
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######################################
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# EQUILIBRATION/DEFORMATION VARIABLES
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# eqpress = 10 bar = 1 MPa
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# tstep (the timestep) is set to a default value of 0.001 (1 fs)
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# seed randomizes the velocity
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# srate is the rate of strain in 1/s
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# Ndump is the number of timesteps in between each dump of the atom coordinates
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variable tstep equal 0.001
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variable seed equal 95812384
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variable srate equal 1e9
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######################################
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# INITIALIZATION
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units metal
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dimension 3
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boundary s s s
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atom_style atomic
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######################################
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# ATOM BUILD
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atom_modify map array
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# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
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lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
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variable multiple equal 20
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variable mx equal "v_lx*v_multiple"
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variable my equal "v_ly*v_multiple"
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variable mz equal "v_lz*v_multiple"
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# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
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region whole block 0 ${mz} 0 ${mx} 0 ${my} units box
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create_box 2 whole
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create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1
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region fixed1 block INF INF INF INF INF 10 units box
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region fixed2 block INF INF INF INF 100 INF units box
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group lower region fixed1
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group upper region fixed2
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group boundary union upper lower
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group mobile subtract all boundary
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variable natoms equal "count(all)"
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print "# of atoms are: ${natoms}"
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######################################
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# INTERATOMIC POTENTIAL
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pair_style ${pairstyle}
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pair_coeff * * ${pairlocation} Mg Mg
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######################################
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# COMPUTES REQUIRED
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compute csym all centro/atom 12
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compute eng all pe/atom
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compute eatoms all reduce sum c_eng
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compute basal all basal/atom
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######################################
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# MINIMIZATION
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# Primarily adjusts the c/a ratio to value predicted by EAM potential
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reset_timestep 0
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thermo 1
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thermo_style custom step pe c_eatoms
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min_style cg
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minimize 1e-15 1e-15 1000 2000
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variable eminimum equal "c_eatoms / count(all)"
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print "%%e(it,1)=${eminimum}"
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######################################
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# EQUILIBRATION
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reset_timestep 0
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timestep ${tstep}
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# atoms are given a random velocity based on a temperature of 100K.
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velocity all create 100 ${seed} mom yes rot no
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# temperature and pressure are set to 100 and 0
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fix 1 all nve
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# Set thermo output
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thermo 100
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thermo_style custom step lx ly lz press pxx pyy pzz pe temp
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# Run for at least 2 picosecond (assuming 1 fs timestep)
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run 2000
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# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
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label loopeq
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variable eq loop 100
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run 250
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variable converge equal press
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if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press"
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if "${converge} <= 50" then "jump ${fname} breakeq"
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next eq
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jump ${fname} loopeq
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label breakeq
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# Store length for strain rate calculations
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variable tmp equal "lx"
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variable L0 equal ${tmp}
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print "Initial Length, L0: ${L0}"
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unfix 1
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######################################
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# DEFORMATION
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reset_timestep 0
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timestep ${tstep}
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# Impose constant strain rate
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variable srate1 equal "v_srate / 1.0e10"
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velocity upper set 0.0 NULL 0.0 units box
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velocity lower set 0.0 NULL 0.0 units box
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fix 2 upper setforce 0.0 NULL 0.0
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fix 3 lower setforce 0.0 NULL 0.0
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fix 1 all nve
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# Output strain and stress info to file
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# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
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# p2 is in GPa
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variable strain equal "(lx - v_L0)/v_L0"
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variable p1 equal "v_strain"
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variable p2 equal "-pxz/10000"
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variable p3 equal "lx"
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variable p4 equal "temp"
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variable p5 equal "pe"
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variable p6 equal "ke"
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fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
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# Dump coordinates to file (for void size calculations)
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dump 1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
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# Display thermo
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thermo_style custom step v_strain pxz lx temp pe ke
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restart 50000 output.restart
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# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
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variable runtime equal 0
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label loop
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displace_atoms all ramp x 0.0 ${srate1} z 10 100 units box
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run 100
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variable runtime equal ${runtime}+100
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if "${runtime} < 100000" then "jump ${fname} loop"
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######################################
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# SIMULATION DONE
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print "All done"
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