forked from lijiext/lammps
fix spring doc page update
This commit is contained in:
Steve Plimpton
parent
c31f1e9f22
commit
5cd856c97f
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@ -89,11 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
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group can straddle a periodic boundary. See the "dump"_dump.html doc
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page for a discussion of unwrapped coordinates. It also means that a
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spring connecting two groups or a group and the tether point can cross
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a periodic boundary and its length be calculated correctly. One
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exception is for rigid bodies, which should not be used with the fix
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spring command, if the rigid body will cross a periodic boundary.
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This is because image flags for rigid bodies are used in a different
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way, as explained on the "fix rigid"_fix_rigid.html doc page.
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a periodic boundary and its length be calculated correctly.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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@ -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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@ -51,7 +51,7 @@ void AtomVecAtomic::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -118,7 +118,7 @@ void AtomVecBody::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -53,7 +53,7 @@ void AtomVecCharge::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -72,7 +72,7 @@ void AtomVecEllipsoid::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -144,7 +144,7 @@ void AtomVecHybrid::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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// sub-styles perform all reallocation
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@ -83,7 +83,7 @@ void AtomVecLine::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -84,7 +84,7 @@ void AtomVecSphere::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -88,7 +88,7 @@ void AtomVecTri::grow(int n)
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0)
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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@ -51,10 +51,14 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
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/* ---------------------------------------------------------------------- */
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CommBrick::CommBrick(LAMMPS *lmp) : Comm(lmp),
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sendnum(NULL), recvnum(NULL), sendproc(NULL), recvproc(NULL), size_forward_recv(NULL),
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size_reverse_send(NULL), size_reverse_recv(NULL), slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
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cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL), sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
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CommBrick::CommBrick(LAMMPS *lmp) :
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Comm(lmp),
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sendnum(NULL), recvnum(NULL), sendproc(NULL), recvproc(NULL),
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size_forward_recv(NULL),
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size_reverse_send(NULL), size_reverse_recv(NULL),
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slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
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cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL),
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sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
|
||||
{
|
||||
style = 0;
|
||||
layout = LAYOUT_UNIFORM;
|
||||
|
|
|
|||
|
|
@ -1102,6 +1102,40 @@ int Domain::closest_image(int i, int j)
|
|||
return closest;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return local index of atom J or any of its images that is closest to pos
|
||||
if J is not a valid index like -1, just return it
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Domain::closest_image(double *pos, int j)
|
||||
{
|
||||
if (j < 0) return j;
|
||||
|
||||
int *sametag = atom->sametag;
|
||||
double **x = atom->x;
|
||||
|
||||
int closest = j;
|
||||
double delx = pos[0] - x[j][0];
|
||||
double dely = pos[1] - x[j][1];
|
||||
double delz = pos[2] - x[j][2];
|
||||
double rsqmin = delx*delx + dely*dely + delz*delz;
|
||||
double rsq;
|
||||
|
||||
while (sametag[j] >= 0) {
|
||||
j = sametag[j];
|
||||
delx = pos[0] - x[j][0];
|
||||
dely = pos[1] - x[j][1];
|
||||
delz = pos[2] - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
if (rsq < rsqmin) {
|
||||
rsqmin = rsq;
|
||||
closest = j;
|
||||
}
|
||||
}
|
||||
|
||||
return closest;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
find and return Xj image = periodic image of Xj that is closest to Xi
|
||||
for triclinic, add/subtract tilt factors in other dims as needed
|
||||
|
|
|
|||
|
|
@ -113,6 +113,7 @@ class Domain : protected Pointers {
|
|||
void minimum_image(double &, double &, double &);
|
||||
void minimum_image(double *);
|
||||
int closest_image(int, int);
|
||||
int closest_image(double *, int);
|
||||
void closest_image(const double * const, const double * const,
|
||||
double * const);
|
||||
void remap(double *, imageint &);
|
||||
|
|
|
|||
|
|
@ -40,6 +40,7 @@ namespace MathExtra {
|
|||
inline void sub3(const double *v1, const double *v2, double *ans);
|
||||
inline double len3(const double *v);
|
||||
inline double lensq3(const double *v);
|
||||
inline double distsq3(const double *v1, const double *v2);
|
||||
inline double dot3(const double *v1, const double *v2);
|
||||
inline void cross3(const double *v1, const double *v2, double *ans);
|
||||
|
||||
|
|
@ -265,6 +266,18 @@ inline double MathExtra::lensq3(const double *v)
|
|||
return v[0]*v[0] + v[1]*v[1] + v[2]*v[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
ans = distance squared between pts v1 and v2
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
inline double MathExtra::distsq3(const double *v1, const double *v2)
|
||||
{
|
||||
double dx = v1[0] - v2[0];
|
||||
double dy = v1[1] - v2[1];
|
||||
double dz = v1[2] - v2[2];
|
||||
return dx*dx + dy*dy + dz*dz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
dot product of 2 vectors
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
|
|||
|
|
@ -149,7 +149,7 @@ void NPair::build_setup()
|
|||
------------------------------------------------------------------------- */
|
||||
|
||||
int NPair::exclusion(int i, int j, int itype, int jtype,
|
||||
int *mask, tagint *molecule) const {
|
||||
int *mask, tagint *molecule) const {
|
||||
int m;
|
||||
|
||||
if (nex_type && ex_type[itype][jtype]) return 1;
|
||||
|
|
|
|||
|
|
@ -28,8 +28,10 @@ using namespace LAMMPS_NS;
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Region::Region(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp),
|
||||
id(NULL), style(NULL), contact(NULL), list(NULL), xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
|
||||
Region::Region(LAMMPS *lmp, int narg, char **arg) :
|
||||
Pointers(lmp),
|
||||
id(NULL), style(NULL), contact(NULL), list(NULL),
|
||||
xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
|
||||
{
|
||||
int n = strlen(arg[0]) + 1;
|
||||
id = new char[n];
|
||||
|
|
|
|||
Loading…
Reference in New Issue