Optimized Dynamical Matrix
This commit is contained in:
charlie sievers
48
examples/USER/phonon/dynamical_matrix_command/Manual.md
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48
examples/USER/phonon/dynamical_matrix_command/Manual.md
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# dynamical_matrix command
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## Syntax
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```
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dynamical_matrix group-ID style args keyword value ...
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```
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* group-ID = ID of group of atoms to displace
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* style = *regular* or *eskm*
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```
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*regular* args = gamma
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gamma = finite difference displacement length
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*eskm* args = gamma
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gamma = finite difference displacement length
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```
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* zero or more keyword/value pairs may be appended
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* keyword = *file* or *binary*
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```
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*file* value = output_file
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output_file = name of file to dump the dynamical matrix into
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*binary* values = *yes* or *no* or *gzip*
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```
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## Examples
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```
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dynamical_matrix 1 regular 0.000001
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dynamical_matrix 1 eskm 0.000001
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dynamical_matrix 3 regular 0.00004 file dynmat.dat
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dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes
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```
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## Description
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Calculate the dynamical matrix of the selected group.
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## Restrictions
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None
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## Related commands
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None
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## Default
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The option defaults are file = "dynmat.dyn", binary = no
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21
examples/USER/phonon/dynamical_matrix_command/README.md
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21
examples/USER/phonon/dynamical_matrix_command/README.md
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# LAMMPS LATTICE DYNAMICS COMMANDS
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## DYNAMICAL MATRIX CALCULATOR
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This directory contains the ingredients to calculate a dynamical matrix.
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Example:
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```
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NP=4 #number of processors
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mpirun -np $NP lmp_mpi < in.silicon > out.silicon
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```
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To test out a different silicon example:
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```
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LMP_FILE=amorphous_silicon.lmp
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cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
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NP=4 #number of processors
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mpirun -np $NP lmp_mpi < in.silicon > out.silicon
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```
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## Requires: MANYBODY and MOLECULE packages
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66
examples/USER/phonon/dynamical_matrix_command/Si.opt.tersoff
Executable file
66
examples/USER/phonon/dynamical_matrix_command/Si.opt.tersoff
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# Tersoff parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
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# other quantities are unitless
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# Aidan Thompson (athomps at sandia.gov) takes full blame for this
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# file. It specifies various potentials published by J. Tersoff for
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# silicon, carbon and germanium. Since Tersoff published several
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# different silicon potentials, I refer to them using atom types
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# Si(B), Si(C) and Si(D). The last two are almost almost identical but
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# refer to two different publications. These names should be used in
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# the LAMMPS command when the file is invoked. For example:
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# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials
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# can be used pure silicon, pure carbon, pure germanium, binary SiC,
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# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
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# generate an error if this file is used with any combination
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# involving C and Ge, since there are no entries for the GeC
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# interactions (Tersoff did not publish parameters for this
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# cross-interaction.)
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# format of a single entry (one or more lines):
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# element 1, element 2, element 3,
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# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
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# The original Tersoff potential for Silicon, Si(B)
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# J. Tersoff, PRB, 37, 6991 (1988)
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Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
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0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
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# The later Tersoff potential for Silicon, Si(C)
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# J. Tersoff, PRB, 38, 9902 (1988)
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Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
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1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
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# The later Tersoff potential for Carbon, Silicon, and Germanium
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# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
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# The Si and C parameters are very close to those in SiC.tersoff
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C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6
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Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
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Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0
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C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
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C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0
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C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
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Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
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Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
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Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
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Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
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Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
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Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
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Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
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Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0
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Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
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# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010)
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# element 1, element 2, element 3,
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# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
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C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6
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19
examples/USER/phonon/dynamical_matrix_command/ff-silicon.lmp
Executable file
19
examples/USER/phonon/dynamical_matrix_command/ff-silicon.lmp
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#############################
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#Atoms types - mass - charge#
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#############################
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#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
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variable Si equal 1
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#############
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#Atom Masses#
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#############
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mass ${Si} 28.08550
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###########################
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#Pair Potentials - Tersoff#
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###########################
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pair_style tersoff
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pair_coeff * * Si.opt.tersoff Si(D)
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89
examples/USER/phonon/dynamical_matrix_command/in.silicon
Executable file
89
examples/USER/phonon/dynamical_matrix_command/in.silicon
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###############################mm
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# Atom style - charge/vdw/bonded#
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#################################
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atom_style full
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##############################################
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#Units Metal : eV - ps - angstrom - bar#
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# Real : kcal/mol - fs - angstrom - atm#
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##############################################
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units metal
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############
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#Run number#
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############
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variable run_no equal 0 # is it a restart?
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variable res_no equal ${run_no}-1 # restart file number
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#######################################
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#Random Seeds and Domain Decomposition#
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#######################################
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variable iseed0 equal 2357
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variable iseed1 equal 26488
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variable iseed2 equal 10669
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processors * * *
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###########
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#Data File#
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###########
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variable inpfile string silicon_input_file.lmp
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variable resfile string final_restart.${res_no}
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variable ff_file string ff-silicon.lmp
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##########
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#Run Type#
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##########
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variable minimise equal 0 #Energy Minimization
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###############################
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#Molecular Dynamics Parameters#
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###############################
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neighbor 1 bin
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################################
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#Energy Minimization Parameters#
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################################
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variable mtraj equal 1 # trajectory output frequency - all system
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variable etol equal 1e-5 # % change in energy
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variable ftol equal 1e-5 # max force threshold (force units)
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variable maxiter equal 10000 # max # of iterations
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########################
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#3D Periodic Simulation#
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########################
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boundary p p p
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#############################
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#Reading the input structure#
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#############################
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if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
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#############
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#Force Field#
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#############
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include ${ff_file}
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######################
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#Thermodynamic Output#
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######################
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variable str_basic string 'step time pe temp press'
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#####################
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#Energy Minimization#
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#####################
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if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
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print "Doing CG minimisation"
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dump mdcd all dcd ${mtraj} min.dcd
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dump_modify mdcd unwrap yes
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min_style cg
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min_modify line quadratic
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minimize ${etol} ${ftol} ${maxiter} ${maxiter}
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reset_timestep 0
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undump mdcd
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label end_minimise
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##################
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#Dynamical Matrix#
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##################
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dynamical_matrix all eskm 0.000001 file dynmat.dat binary no
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534
examples/USER/phonon/dynamical_matrix_command/lmp_bank/amorphous_silicon.lmp
Executable file
534
examples/USER/phonon/dynamical_matrix_command/lmp_bank/amorphous_silicon.lmp
Executable file
@ -0,0 +1,534 @@
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LAMMPS description
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512 atoms
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0 bonds
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0 angles
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0 dihedrals
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0 impropers
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1 atom types
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0 bond types
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0 angle types
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0 dihedral types
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0 improper types
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0.0000000 21.848000 xlo xhi
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0.0000000 21.848000 ylo yhi
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0.0000000 21.848000 zlo zhi
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Atoms
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1 1 1 0.0000000 6.2030000 5.5980000 12.9980000
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2 2 1 0.0000000 21.3100000 5.6310000 21.1380000
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3 3 1 0.0000000 19.5320000 6.1170000 3.6940000
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4 4 1 0.0000000 4.3700000 14.0260000 0.0900000
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5 5 1 0.0000000 10.1930000 7.4590000 2.3530000
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|
6 6 1 0.0000000 17.5070000 14.1860000 3.6790000
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|
7 7 1 0.0000000 11.2050000 15.9160000 15.0480000
|
||||||
|
8 8 1 0.0000000 8.6050000 19.8970000 21.0040000
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||||||
|
9 9 1 0.0000000 15.0360000 17.5650000 1.3640000
|
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|
10 10 1 0.0000000 12.0450000 3.3600000 7.2720000
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||||||
|
11 11 1 0.0000000 7.1330000 17.4130000 18.0480000
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12 12 1 0.0000000 8.7340000 6.3830000 3.8480000
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13 13 1 0.0000000 13.0940000 3.2490000 3.5840000
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|
14 14 1 0.0000000 11.3200000 7.2770000 20.4120000
|
||||||
|
15 15 1 0.0000000 19.7770000 8.9110000 0.3000000
|
||||||
|
16 16 1 0.0000000 11.9710000 20.8500000 1.5140000
|
||||||
|
17 17 1 0.0000000 10.4480000 10.3650000 15.4040000
|
||||||
|
18 18 1 0.0000000 9.2060000 9.4670000 10.2240000
|
||||||
|
19 19 1 0.0000000 8.4360000 13.6240000 17.6570000
|
||||||
|
20 20 1 0.0000000 18.2020000 21.1230000 0.1380000
|
||||||
|
21 21 1 0.0000000 3.2970000 19.5740000 14.7410000
|
||||||
|
22 22 1 0.0000000 12.5330000 17.3580000 7.5960000
|
||||||
|
23 23 1 0.0000000 1.4040000 18.1060000 3.1510000
|
||||||
|
24 24 1 0.0000000 17.7440000 13.1530000 16.7940000
|
||||||
|
25 25 1 0.0000000 12.1070000 12.6630000 18.0340000
|
||||||
|
26 26 1 0.0000000 8.7270000 17.1140000 10.4200000
|
||||||
|
27 27 1 0.0000000 13.2330000 16.0380000 13.9210000
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||||||
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28 28 1 0.0000000 15.2360000 14.8650000 7.0150000
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||||||
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29 29 1 0.0000000 5.5190000 20.8660000 19.9260000
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||||||
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30 30 1 0.0000000 16.5810000 9.7460000 15.1710000
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||||||
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31 31 1 0.0000000 2.0500000 13.8550000 21.8010000
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||||||
|
32 32 1 0.0000000 21.2670000 20.8970000 13.6740000
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33 33 1 0.0000000 9.6900000 6.7650000 0.1950000
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34 34 1 0.0000000 11.2570000 13.2440000 2.8190000
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||||||
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35 35 1 0.0000000 10.7810000 12.7310000 12.1920000
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36 36 1 0.0000000 16.2630000 7.4100000 1.5360000
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37 37 1 0.0000000 19.6100000 18.1440000 19.6830000
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38 38 1 0.0000000 8.1790000 0.1200000 10.1620000
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39 39 1 0.0000000 17.0520000 20.4210000 15.0450000
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||||||
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40 40 1 0.0000000 12.3690000 12.6710000 4.8320000
|
||||||
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41 41 1 0.0000000 7.8300000 16.6790000 14.2470000
|
||||||
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42 42 1 0.0000000 1.6790000 9.9500000 1.2660000
|
||||||
|
43 43 1 0.0000000 16.6160000 14.6580000 13.2790000
|
||||||
|
44 44 1 0.0000000 13.7430000 11.9730000 21.5360000
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||||||
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45 45 1 0.0000000 5.2590000 15.1850000 9.5720000
|
||||||
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46 46 1 0.0000000 20.5980000 14.7930000 20.4140000
|
||||||
|
47 47 1 0.0000000 1.5640000 16.8080000 13.0450000
|
||||||
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48 48 1 0.0000000 21.3670000 11.4610000 20.6420000
|
||||||
|
49 49 1 0.0000000 14.5890000 5.9510000 7.1950000
|
||||||
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50 50 1 0.0000000 1.0870000 13.5410000 11.3300000
|
||||||
|
51 51 1 0.0000000 6.2040000 4.8970000 16.9420000
|
||||||
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52 52 1 0.0000000 0.4800000 4.1450000 0.8710000
|
||||||
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||||||
|
313 313 1 0.0000000 4.0640000 19.1000000 1.8260000
|
||||||
|
314 314 1 0.0000000 21.7520000 10.6160000 14.7710000
|
||||||
|
315 315 1 0.0000000 1.3090000 11.5200000 16.3780000
|
||||||
|
316 316 1 0.0000000 5.1840000 20.6560000 0.4260000
|
||||||
|
317 317 1 0.0000000 10.7630000 2.3920000 17.0100000
|
||||||
|
318 318 1 0.0000000 4.7970000 15.9920000 1.2450000
|
||||||
|
319 319 1 0.0000000 11.1370000 0.4590000 11.8330000
|
||||||
|
320 320 1 0.0000000 14.5870000 13.6170000 1.1610000
|
||||||
|
321 321 1 0.0000000 9.8660000 0.7940000 8.6450000
|
||||||
|
322 322 1 0.0000000 17.7650000 19.2430000 7.2990000
|
||||||
|
323 323 1 0.0000000 6.0610000 1.2430000 19.3000000
|
||||||
|
324 324 1 0.0000000 18.2200000 12.8760000 13.2170000
|
||||||
|
325 325 1 0.0000000 18.0460000 13.1700000 9.1450000
|
||||||
|
326 326 1 0.0000000 3.3530000 3.3130000 15.2040000
|
||||||
|
327 327 1 0.0000000 10.4090000 19.4890000 16.3660000
|
||||||
|
328 328 1 0.0000000 15.6710000 1.1260000 19.9260000
|
||||||
|
329 329 1 0.0000000 10.8900000 7.3650000 7.1060000
|
||||||
|
330 330 1 0.0000000 13.4480000 20.2870000 5.0130000
|
||||||
|
331 331 1 0.0000000 16.0530000 0.3050000 0.2340000
|
||||||
|
332 332 1 0.0000000 9.8430000 17.8410000 14.6670000
|
||||||
|
333 333 1 0.0000000 13.0150000 10.2370000 1.1400000
|
||||||
|
334 334 1 0.0000000 4.2090000 16.6330000 8.0040000
|
||||||
|
335 335 1 0.0000000 4.5530000 4.3630000 11.8090000
|
||||||
|
336 336 1 0.0000000 12.4370000 18.2310000 5.4180000
|
||||||
|
337 337 1 0.0000000 4.6660000 4.4220000 5.9770000
|
||||||
|
338 338 1 0.0000000 9.5670000 9.6790000 2.7600000
|
||||||
|
339 339 1 0.0000000 17.6640000 17.0250000 16.2770000
|
||||||
|
340 340 1 0.0000000 20.3640000 13.8280000 13.4210000
|
||||||
|
341 341 1 0.0000000 10.0140000 7.4130000 9.2700000
|
||||||
|
342 342 1 0.0000000 2.1350000 7.0370000 14.8450000
|
||||||
|
343 343 1 0.0000000 10.1280000 17.9060000 5.2690000
|
||||||
|
344 344 1 0.0000000 9.9640000 11.7180000 21.3790000
|
||||||
|
345 345 1 0.0000000 3.9300000 18.4910000 10.9740000
|
||||||
|
346 346 1 0.0000000 4.4370000 0.9780000 3.9700000
|
||||||
|
347 347 1 0.0000000 3.3540000 11.6180000 13.2880000
|
||||||
|
348 348 1 0.0000000 10.1490000 8.5100000 18.7440000
|
||||||
|
349 349 1 0.0000000 20.0030000 12.0850000 0.6000000
|
||||||
|
350 350 1 0.0000000 8.1370000 7.5880000 17.8300000
|
||||||
|
351 351 1 0.0000000 4.9940000 4.9580000 9.5900000
|
||||||
|
352 352 1 0.0000000 5.3170000 14.3610000 19.8350000
|
||||||
|
353 353 1 0.0000000 9.3030000 10.0320000 5.0540000
|
||||||
|
354 354 1 0.0000000 15.9060000 19.0210000 11.2850000
|
||||||
|
355 355 1 0.0000000 4.7750000 3.1100000 20.1740000
|
||||||
|
356 356 1 0.0000000 12.3120000 9.1080000 6.4970000
|
||||||
|
357 357 1 0.0000000 10.4810000 4.6620000 17.6350000
|
||||||
|
358 358 1 0.0000000 4.7080000 13.6970000 16.3300000
|
||||||
|
359 359 1 0.0000000 12.2970000 5.5490000 6.5760000
|
||||||
|
360 360 1 0.0000000 17.9900000 5.6590000 1.9370000
|
||||||
|
361 361 1 0.0000000 15.7760000 13.0220000 8.3090000
|
||||||
|
362 362 1 0.0000000 17.0960000 9.8020000 6.8980000
|
||||||
|
363 363 1 0.0000000 14.4040000 20.5780000 7.1330000
|
||||||
|
364 364 1 0.0000000 10.5700000 7.4740000 12.5610000
|
||||||
|
365 365 1 0.0000000 7.1880000 17.4800000 12.1560000
|
||||||
|
366 366 1 0.0000000 19.2640000 6.6050000 0.0900000
|
||||||
|
367 367 1 0.0000000 2.4860000 20.3860000 7.9620000
|
||||||
|
368 368 1 0.0000000 1.6540000 17.4650000 21.0330000
|
||||||
|
369 369 1 0.0000000 0.8570000 14.9180000 7.7750000
|
||||||
|
370 370 1 0.0000000 15.6360000 3.0200000 12.0780000
|
||||||
|
371 371 1 0.0000000 20.9520000 6.0750000 16.1620000
|
||||||
|
372 372 1 0.0000000 6.5150000 10.9720000 15.0530000
|
||||||
|
373 373 1 0.0000000 1.6150000 2.1220000 0.1040000
|
||||||
|
374 374 1 0.0000000 12.4880000 14.7040000 1.3780000
|
||||||
|
375 375 1 0.0000000 1.8720000 14.8200000 18.2130000
|
||||||
|
376 376 1 0.0000000 1.3840000 6.3060000 16.9560000
|
||||||
|
377 377 1 0.0000000 13.1420000 8.3550000 21.5020000
|
||||||
|
378 378 1 0.0000000 10.3950000 19.1540000 12.7720000
|
||||||
|
379 379 1 0.0000000 18.9350000 15.8660000 19.2180000
|
||||||
|
380 380 1 0.0000000 19.6110000 0.3890000 20.4600000
|
||||||
|
381 381 1 0.0000000 1.6460000 14.9430000 1.9780000
|
||||||
|
382 382 1 0.0000000 16.9420000 8.7780000 9.0500000
|
||||||
|
383 383 1 0.0000000 15.0770000 11.3050000 19.7190000
|
||||||
|
384 384 1 0.0000000 6.2370000 17.3890000 15.8170000
|
||||||
|
385 385 1 0.0000000 14.6890000 16.8390000 8.2540000
|
||||||
|
386 386 1 0.0000000 5.9660000 6.4540000 15.1720000
|
||||||
|
387 387 1 0.0000000 6.1100000 4.8320000 21.2820000
|
||||||
|
388 388 1 0.0000000 5.9710000 14.6570000 4.7110000
|
||||||
|
389 389 1 0.0000000 3.1780000 19.7080000 5.8410000
|
||||||
|
390 390 1 0.0000000 5.7600000 19.5340000 14.8080000
|
||||||
|
391 391 1 0.0000000 18.1190000 11.5110000 15.1550000
|
||||||
|
392 392 1 0.0000000 17.0450000 3.0230000 19.5700000
|
||||||
|
393 393 1 0.0000000 11.7520000 21.8180000 19.7610000
|
||||||
|
394 394 1 0.0000000 15.5870000 18.5610000 6.9700000
|
||||||
|
395 395 1 0.0000000 6.0680000 8.8370000 18.0920000
|
||||||
|
396 396 1 0.0000000 14.2730000 18.8060000 21.1250000
|
||||||
|
397 397 1 0.0000000 14.8640000 7.7480000 18.0510000
|
||||||
|
398 398 1 0.0000000 7.1970000 14.3360000 8.4160000
|
||||||
|
399 399 1 0.0000000 12.4080000 8.9750000 12.3640000
|
||||||
|
400 400 1 0.0000000 15.7690000 0.5910000 7.2330000
|
||||||
|
401 401 1 0.0000000 14.1880000 18.6730000 16.7170000
|
||||||
|
402 402 1 0.0000000 0.1070000 17.0650000 14.8780000
|
||||||
|
403 403 1 0.0000000 1.2690000 21.0730000 19.1580000
|
||||||
|
404 404 1 0.0000000 8.3320000 15.5390000 0.1550000
|
||||||
|
405 405 1 0.0000000 3.4890000 20.2250000 18.9410000
|
||||||
|
406 406 1 0.0000000 16.7760000 7.8120000 16.6050000
|
||||||
|
407 407 1 0.0000000 0.5070000 4.7570000 5.2510000
|
||||||
|
408 408 1 0.0000000 19.1810000 3.0200000 9.7780000
|
||||||
|
409 409 1 0.0000000 4.7160000 9.7900000 16.3110000
|
||||||
|
410 410 1 0.0000000 2.4040000 18.9600000 12.6390000
|
||||||
|
411 411 1 0.0000000 3.3380000 4.6500000 7.9680000
|
||||||
|
412 412 1 0.0000000 17.7990000 4.9620000 9.4940000
|
||||||
|
413 413 1 0.0000000 12.7390000 16.3390000 11.5840000
|
||||||
|
414 414 1 0.0000000 17.5550000 6.7730000 20.3200000
|
||||||
|
415 415 1 0.0000000 14.1770000 9.8840000 3.2060000
|
||||||
|
416 416 1 0.0000000 14.4790000 10.5810000 15.6890000
|
||||||
|
417 417 1 0.0000000 14.7570000 21.0200000 10.8010000
|
||||||
|
418 418 1 0.0000000 19.6820000 0.5930000 12.8140000
|
||||||
|
419 419 1 0.0000000 8.6600000 0.3420000 21.6710000
|
||||||
|
420 420 1 0.0000000 9.6300000 4.0130000 11.4620000
|
||||||
|
421 421 1 0.0000000 21.1990000 7.8220000 3.8780000
|
||||||
|
422 422 1 0.0000000 1.0220000 15.3220000 20.3160000
|
||||||
|
423 423 1 0.0000000 19.5230000 9.5210000 18.2400000
|
||||||
|
424 424 1 0.0000000 6.0420000 4.8470000 1.8140000
|
||||||
|
425 425 1 0.0000000 19.0970000 2.7310000 20.7130000
|
||||||
|
426 426 1 0.0000000 20.7220000 12.9310000 18.9570000
|
||||||
|
427 427 1 0.0000000 12.0420000 5.2830000 19.3670000
|
||||||
|
428 428 1 0.0000000 12.3510000 14.1340000 10.8070000
|
||||||
|
429 429 1 0.0000000 0.6760000 0.6980000 4.6080000
|
||||||
|
430 430 1 0.0000000 17.9010000 21.6070000 7.6530000
|
||||||
|
431 431 1 0.0000000 12.9910000 4.6940000 10.9090000
|
||||||
|
432 432 1 0.0000000 4.1650000 0.3790000 10.2450000
|
||||||
|
433 433 1 0.0000000 11.0350000 2.5880000 2.7230000
|
||||||
|
434 434 1 0.0000000 0.8260000 16.8030000 9.2410000
|
||||||
|
435 435 1 0.0000000 1.2930000 1.5320000 19.6910000
|
||||||
|
436 436 1 0.0000000 3.6360000 0.6300000 7.9720000
|
||||||
|
437 437 1 0.0000000 18.7690000 21.6650000 18.3160000
|
||||||
|
438 438 1 0.0000000 15.9900000 1.2130000 10.5660000
|
||||||
|
439 439 1 0.0000000 3.6880000 0.2170000 17.3680000
|
||||||
|
440 440 1 0.0000000 15.4550000 13.7970000 16.7760000
|
||||||
|
441 441 1 0.0000000 13.6260000 0.3920000 16.0690000
|
||||||
|
442 442 1 0.0000000 2.2090000 7.7760000 18.5900000
|
||||||
|
443 443 1 0.0000000 7.5390000 1.2670000 1.6990000
|
||||||
|
444 444 1 0.0000000 5.8870000 7.1350000 20.9610000
|
||||||
|
445 445 1 0.0000000 3.5460000 9.4970000 8.9750000
|
||||||
|
446 446 1 0.0000000 1.7030000 10.1450000 12.4300000
|
||||||
|
447 447 1 0.0000000 4.5220000 7.2320000 19.0140000
|
||||||
|
448 448 1 0.0000000 12.0790000 18.5320000 17.7390000
|
||||||
|
449 449 1 0.0000000 11.8150000 12.7440000 20.4040000
|
||||||
|
450 450 1 0.0000000 14.1450000 16.3300000 20.6400000
|
||||||
|
451 451 1 0.0000000 13.9790000 11.9100000 13.7820000
|
||||||
|
452 452 1 0.0000000 5.7860000 9.0870000 8.2180000
|
||||||
|
453 453 1 0.0000000 5.7610000 18.5920000 3.4730000
|
||||||
|
454 454 1 0.0000000 17.1860000 12.2100000 20.2580000
|
||||||
|
455 455 1 0.0000000 19.9590000 17.8190000 5.1360000
|
||||||
|
456 456 1 0.0000000 17.0590000 15.4900000 5.5810000
|
||||||
|
457 457 1 0.0000000 3.6710000 3.1920000 4.2290000
|
||||||
|
458 458 1 0.0000000 9.3110000 4.4320000 0.2320000
|
||||||
|
459 459 1 0.0000000 7.2900000 10.5480000 9.3640000
|
||||||
|
460 460 1 0.0000000 3.1990000 11.3340000 19.5640000
|
||||||
|
461 461 1 0.0000000 18.7960000 19.0310000 15.8960000
|
||||||
|
462 462 1 0.0000000 16.4530000 21.1730000 18.6370000
|
||||||
|
463 463 1 0.0000000 19.0360000 1.4790000 16.6070000
|
||||||
|
464 464 1 0.0000000 15.1190000 6.7220000 5.0610000
|
||||||
|
465 465 1 0.0000000 14.6980000 6.3460000 10.8900000
|
||||||
|
466 466 1 0.0000000 9.5270000 15.6660000 5.6890000
|
||||||
|
467 467 1 0.0000000 9.8670000 0.7250000 18.4290000
|
||||||
|
468 468 1 0.0000000 3.5070000 11.8220000 15.5670000
|
||||||
|
469 469 1 0.0000000 5.2170000 0.8530000 1.6550000
|
||||||
|
470 470 1 0.0000000 14.2830000 11.9310000 17.5860000
|
||||||
|
471 471 1 0.0000000 21.4650000 11.2840000 8.7140000
|
||||||
|
472 472 1 0.0000000 0.2700000 13.5140000 17.1240000
|
||||||
|
473 473 1 0.0000000 8.7330000 20.7300000 17.4130000
|
||||||
|
474 474 1 0.0000000 7.4140000 12.9760000 3.8660000
|
||||||
|
475 475 1 0.0000000 8.5520000 8.7210000 12.3480000
|
||||||
|
476 476 1 0.0000000 7.4770000 9.7280000 1.7090000
|
||||||
|
477 477 1 0.0000000 16.9200000 14.6800000 20.0740000
|
||||||
|
478 478 1 0.0000000 6.5920000 20.9910000 6.6400000
|
||||||
|
479 479 1 0.0000000 18.3870000 7.4290000 18.2380000
|
||||||
|
480 480 1 0.0000000 21.2320000 15.1360000 2.5810000
|
||||||
|
481 481 1 0.0000000 16.7390000 8.6780000 21.4380000
|
||||||
|
482 482 1 0.0000000 18.2260000 6.2380000 5.6140000
|
||||||
|
483 483 1 0.0000000 12.7550000 3.5820000 20.8720000
|
||||||
|
484 484 1 0.0000000 14.8870000 9.0010000 20.0300000
|
||||||
|
485 485 1 0.0000000 6.1970000 16.3000000 3.0880000
|
||||||
|
486 486 1 0.0000000 6.9450000 13.1810000 15.8140000
|
||||||
|
487 487 1 0.0000000 20.1770000 18.7700000 1.5020000
|
||||||
|
488 488 1 0.0000000 19.8750000 14.4220000 0.7710000
|
||||||
|
489 489 1 0.0000000 13.0770000 5.0280000 14.9330000
|
||||||
|
490 490 1 0.0000000 10.9540000 0.5380000 0.0170000
|
||||||
|
491 491 1 0.0000000 0.3310000 3.0520000 18.1720000
|
||||||
|
492 492 1 0.0000000 8.8200000 14.8310000 10.0110000
|
||||||
|
493 493 1 0.0000000 6.9570000 20.3870000 8.9230000
|
||||||
|
494 494 1 0.0000000 21.4900000 6.8560000 12.0490000
|
||||||
|
495 495 1 0.0000000 8.1550000 13.1990000 21.7210000
|
||||||
|
496 496 1 0.0000000 2.1970000 4.5290000 11.8290000
|
||||||
|
497 497 1 0.0000000 14.2880000 5.5560000 18.5960000
|
||||||
|
498 498 1 0.0000000 15.0910000 15.4110000 18.5470000
|
||||||
|
499 499 1 0.0000000 18.9760000 15.1930000 16.8970000
|
||||||
|
500 500 1 0.0000000 19.4100000 5.3490000 17.7540000
|
||||||
|
501 501 1 0.0000000 0.5430000 8.3990000 13.7700000
|
||||||
|
502 502 1 0.0000000 18.0770000 19.1690000 4.8770000
|
||||||
|
503 503 1 0.0000000 3.3760000 17.8650000 19.2940000
|
||||||
|
504 504 1 0.0000000 16.3760000 0.5870000 3.6340000
|
||||||
|
505 505 1 0.0000000 10.4990000 18.5190000 21.1770000
|
||||||
|
506 506 1 0.0000000 15.7320000 12.7570000 3.0200000
|
||||||
|
507 507 1 0.0000000 16.9190000 8.1780000 5.2430000
|
||||||
|
508 508 1 0.0000000 6.9450000 7.4210000 6.8040000
|
||||||
|
509 509 1 0.0000000 11.6120000 21.2610000 15.3620000
|
||||||
|
510 510 1 0.0000000 18.0500000 0.6840000 14.5470000
|
||||||
|
511 511 1 0.0000000 20.4340000 4.0240000 4.2040000
|
||||||
|
512 512 1 0.0000000 18.0190000 10.7210000 0.2160000
|
||||||
|
|
||||||
238
examples/USER/phonon/dynamical_matrix_command/lmp_bank/silicon_216.lmp
Executable file
238
examples/USER/phonon/dynamical_matrix_command/lmp_bank/silicon_216.lmp
Executable file
@ -0,0 +1,238 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
216 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 16.293000 xlo xhi
|
||||||
|
0.0000000 16.293000 ylo yhi
|
||||||
|
0.0000000 16.293000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 0.0000000 2.7160000 2.7160000
|
||||||
|
3 3 1 0.0000000 2.7160000 2.7160000 0.0000000
|
||||||
|
4 4 1 0.0000000 2.7160000 0.0000000 2.7160000
|
||||||
|
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
|
||||||
|
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
|
||||||
|
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
|
||||||
|
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
|
||||||
|
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
|
||||||
|
10 10 1 0.0000000 0.0000000 2.7160000 8.1460000
|
||||||
|
11 11 1 0.0000000 2.7160000 2.7160000 5.4310000
|
||||||
|
12 12 1 0.0000000 2.7160000 0.0000000 8.1460000
|
||||||
|
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
|
||||||
|
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
|
||||||
|
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
|
||||||
|
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
|
||||||
|
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
|
||||||
|
18 18 1 0.0000000 0.0000000 2.7160000 13.5780000
|
||||||
|
19 19 1 0.0000000 2.7160000 2.7160000 10.8620000
|
||||||
|
20 20 1 0.0000000 2.7160000 0.0000000 13.5780000
|
||||||
|
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
|
||||||
|
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
|
||||||
|
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
|
||||||
|
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
|
||||||
|
25 25 1 0.0000000 0.0000000 5.4310000 0.0000000
|
||||||
|
26 26 1 0.0000000 0.0000000 8.1460000 2.7160000
|
||||||
|
27 27 1 0.0000000 2.7160000 8.1460000 0.0000000
|
||||||
|
28 28 1 0.0000000 2.7160000 5.4310000 2.7160000
|
||||||
|
29 29 1 0.0000000 4.0730000 6.7890000 4.0730000
|
||||||
|
30 30 1 0.0000000 1.3580000 6.7890000 1.3580000
|
||||||
|
31 31 1 0.0000000 1.3580000 9.5040000 4.0730000
|
||||||
|
32 32 1 0.0000000 4.0730000 9.5040000 1.3580000
|
||||||
|
33 33 1 0.0000000 0.0000000 5.4310000 5.4310000
|
||||||
|
34 34 1 0.0000000 0.0000000 8.1460000 8.1460000
|
||||||
|
35 35 1 0.0000000 2.7160000 8.1460000 5.4310000
|
||||||
|
36 36 1 0.0000000 2.7160000 5.4310000 8.1460000
|
||||||
|
37 37 1 0.0000000 4.0730000 6.7890000 9.5040000
|
||||||
|
38 38 1 0.0000000 1.3580000 6.7890000 6.7890000
|
||||||
|
39 39 1 0.0000000 1.3580000 9.5040000 9.5040000
|
||||||
|
40 40 1 0.0000000 4.0730000 9.5040000 6.7890000
|
||||||
|
41 41 1 0.0000000 0.0000000 5.4310000 10.8620000
|
||||||
|
42 42 1 0.0000000 0.0000000 8.1460000 13.5780000
|
||||||
|
43 43 1 0.0000000 2.7160000 8.1460000 10.8620000
|
||||||
|
44 44 1 0.0000000 2.7160000 5.4310000 13.5780000
|
||||||
|
45 45 1 0.0000000 4.0730000 6.7890000 14.9350000
|
||||||
|
46 46 1 0.0000000 1.3580000 6.7890000 12.2200000
|
||||||
|
47 47 1 0.0000000 1.3580000 9.5040000 14.9350000
|
||||||
|
48 48 1 0.0000000 4.0730000 9.5040000 12.2200000
|
||||||
|
49 49 1 0.0000000 0.0000000 10.8620000 0.0000000
|
||||||
|
50 50 1 0.0000000 0.0000000 13.5780000 2.7160000
|
||||||
|
51 51 1 0.0000000 2.7160000 13.5780000 0.0000000
|
||||||
|
52 52 1 0.0000000 2.7160000 10.8620000 2.7160000
|
||||||
|
53 53 1 0.0000000 4.0730000 12.2200000 4.0730000
|
||||||
|
54 54 1 0.0000000 1.3580000 12.2200000 1.3580000
|
||||||
|
55 55 1 0.0000000 1.3580000 14.9350000 4.0730000
|
||||||
|
56 56 1 0.0000000 4.0730000 14.9350000 1.3580000
|
||||||
|
57 57 1 0.0000000 0.0000000 10.8620000 5.4310000
|
||||||
|
58 58 1 0.0000000 0.0000000 13.5780000 8.1460000
|
||||||
|
59 59 1 0.0000000 2.7160000 13.5780000 5.4310000
|
||||||
|
60 60 1 0.0000000 2.7160000 10.8620000 8.1460000
|
||||||
|
61 61 1 0.0000000 4.0730000 12.2200000 9.5040000
|
||||||
|
62 62 1 0.0000000 1.3580000 12.2200000 6.7890000
|
||||||
|
63 63 1 0.0000000 1.3580000 14.9350000 9.5040000
|
||||||
|
64 64 1 0.0000000 4.0730000 14.9350000 6.7890000
|
||||||
|
65 65 1 0.0000000 0.0000000 10.8620000 10.8620000
|
||||||
|
66 66 1 0.0000000 0.0000000 13.5780000 13.5780000
|
||||||
|
67 67 1 0.0000000 2.7160000 13.5780000 10.8620000
|
||||||
|
68 68 1 0.0000000 2.7160000 10.8620000 13.5780000
|
||||||
|
69 69 1 0.0000000 4.0730000 12.2200000 14.9350000
|
||||||
|
70 70 1 0.0000000 1.3580000 12.2200000 12.2200000
|
||||||
|
71 71 1 0.0000000 1.3580000 14.9350000 14.9350000
|
||||||
|
72 72 1 0.0000000 4.0730000 14.9350000 12.2200000
|
||||||
|
73 73 1 0.0000000 5.4310000 0.0000000 0.0000000
|
||||||
|
74 74 1 0.0000000 5.4310000 2.7160000 2.7160000
|
||||||
|
75 75 1 0.0000000 8.1460000 2.7160000 0.0000000
|
||||||
|
76 76 1 0.0000000 8.1460000 0.0000000 2.7160000
|
||||||
|
77 77 1 0.0000000 9.5040000 1.3580000 4.0730000
|
||||||
|
78 78 1 0.0000000 6.7890000 1.3580000 1.3580000
|
||||||
|
79 79 1 0.0000000 6.7890000 4.0730000 4.0730000
|
||||||
|
80 80 1 0.0000000 9.5040000 4.0730000 1.3580000
|
||||||
|
81 81 1 0.0000000 5.4310000 0.0000000 5.4310000
|
||||||
|
82 82 1 0.0000000 5.4310000 2.7160000 8.1460000
|
||||||
|
83 83 1 0.0000000 8.1460000 2.7160000 5.4310000
|
||||||
|
84 84 1 0.0000000 8.1460000 0.0000000 8.1460000
|
||||||
|
85 85 1 0.0000000 9.5040000 1.3580000 9.5040000
|
||||||
|
86 86 1 0.0000000 6.7890000 1.3580000 6.7890000
|
||||||
|
87 87 1 0.0000000 6.7890000 4.0730000 9.5040000
|
||||||
|
88 88 1 0.0000000 9.5040000 4.0730000 6.7890000
|
||||||
|
89 89 1 0.0000000 5.4310000 0.0000000 10.8620000
|
||||||
|
90 90 1 0.0000000 5.4310000 2.7160000 13.5780000
|
||||||
|
91 91 1 0.0000000 8.1460000 2.7160000 10.8620000
|
||||||
|
92 92 1 0.0000000 8.1460000 0.0000000 13.5780000
|
||||||
|
93 93 1 0.0000000 9.5040000 1.3580000 14.9350000
|
||||||
|
94 94 1 0.0000000 6.7890000 1.3580000 12.2200000
|
||||||
|
95 95 1 0.0000000 6.7890000 4.0730000 14.9350000
|
||||||
|
96 96 1 0.0000000 9.5040000 4.0730000 12.2200000
|
||||||
|
97 97 1 0.0000000 5.4310000 5.4310000 0.0000000
|
||||||
|
98 98 1 0.0000000 5.4310000 8.1460000 2.7160000
|
||||||
|
99 99 1 0.0000000 8.1460000 8.1460000 0.0000000
|
||||||
|
100 100 1 0.0000000 8.1460000 5.4310000 2.7160000
|
||||||
|
101 101 1 0.0000000 9.5040000 6.7890000 4.0730000
|
||||||
|
102 102 1 0.0000000 6.7890000 6.7890000 1.3580000
|
||||||
|
103 103 1 0.0000000 6.7890000 9.5040000 4.0730000
|
||||||
|
104 104 1 0.0000000 9.5040000 9.5040000 1.3580000
|
||||||
|
105 105 1 0.0000000 5.4310000 5.4310000 5.4310000
|
||||||
|
106 106 1 0.0000000 5.4310000 8.1460000 8.1460000
|
||||||
|
107 107 1 0.0000000 8.1460000 8.1460000 5.4310000
|
||||||
|
108 108 1 0.0000000 8.1460000 5.4310000 8.1460000
|
||||||
|
109 109 1 0.0000000 9.5040000 6.7890000 9.5040000
|
||||||
|
110 110 1 0.0000000 6.7890000 6.7890000 6.7890000
|
||||||
|
111 111 1 0.0000000 6.7890000 9.5040000 9.5040000
|
||||||
|
112 112 1 0.0000000 9.5040000 9.5040000 6.7890000
|
||||||
|
113 113 1 0.0000000 5.4310000 5.4310000 10.8620000
|
||||||
|
114 114 1 0.0000000 5.4310000 8.1460000 13.5780000
|
||||||
|
115 115 1 0.0000000 8.1460000 8.1460000 10.8620000
|
||||||
|
116 116 1 0.0000000 8.1460000 5.4310000 13.5780000
|
||||||
|
117 117 1 0.0000000 9.5040000 6.7890000 14.9350000
|
||||||
|
118 118 1 0.0000000 6.7890000 6.7890000 12.2200000
|
||||||
|
119 119 1 0.0000000 6.7890000 9.5040000 14.9350000
|
||||||
|
120 120 1 0.0000000 9.5040000 9.5040000 12.2200000
|
||||||
|
121 121 1 0.0000000 5.4310000 10.8620000 0.0000000
|
||||||
|
122 122 1 0.0000000 5.4310000 13.5780000 2.7160000
|
||||||
|
123 123 1 0.0000000 8.1460000 13.5780000 0.0000000
|
||||||
|
124 124 1 0.0000000 8.1460000 10.8620000 2.7160000
|
||||||
|
125 125 1 0.0000000 9.5040000 12.2200000 4.0730000
|
||||||
|
126 126 1 0.0000000 6.7890000 12.2200000 1.3580000
|
||||||
|
127 127 1 0.0000000 6.7890000 14.9350000 4.0730000
|
||||||
|
128 128 1 0.0000000 9.5040000 14.9350000 1.3580000
|
||||||
|
129 129 1 0.0000000 5.4310000 10.8620000 5.4310000
|
||||||
|
130 130 1 0.0000000 5.4310000 13.5780000 8.1460000
|
||||||
|
131 131 1 0.0000000 8.1460000 13.5780000 5.4310000
|
||||||
|
132 132 1 0.0000000 8.1460000 10.8620000 8.1460000
|
||||||
|
133 133 1 0.0000000 9.5040000 12.2200000 9.5040000
|
||||||
|
134 134 1 0.0000000 6.7890000 12.2200000 6.7890000
|
||||||
|
135 135 1 0.0000000 6.7890000 14.9350000 9.5040000
|
||||||
|
136 136 1 0.0000000 9.5040000 14.9350000 6.7890000
|
||||||
|
137 137 1 0.0000000 5.4310000 10.8620000 10.8620000
|
||||||
|
138 138 1 0.0000000 5.4310000 13.5780000 13.5780000
|
||||||
|
139 139 1 0.0000000 8.1460000 13.5780000 10.8620000
|
||||||
|
140 140 1 0.0000000 8.1460000 10.8620000 13.5780000
|
||||||
|
141 141 1 0.0000000 9.5040000 12.2200000 14.9350000
|
||||||
|
142 142 1 0.0000000 6.7890000 12.2200000 12.2200000
|
||||||
|
143 143 1 0.0000000 6.7890000 14.9350000 14.9350000
|
||||||
|
144 144 1 0.0000000 9.5040000 14.9350000 12.2200000
|
||||||
|
145 145 1 0.0000000 10.8620000 0.0000000 0.0000000
|
||||||
|
146 146 1 0.0000000 10.8620000 2.7160000 2.7160000
|
||||||
|
147 147 1 0.0000000 13.5780000 2.7160000 0.0000000
|
||||||
|
148 148 1 0.0000000 13.5780000 0.0000000 2.7160000
|
||||||
|
149 149 1 0.0000000 14.9350000 1.3580000 4.0730000
|
||||||
|
150 150 1 0.0000000 12.2200000 1.3580000 1.3580000
|
||||||
|
151 151 1 0.0000000 12.2200000 4.0730000 4.0730000
|
||||||
|
152 152 1 0.0000000 14.9350000 4.0730000 1.3580000
|
||||||
|
153 153 1 0.0000000 10.8620000 0.0000000 5.4310000
|
||||||
|
154 154 1 0.0000000 10.8620000 2.7160000 8.1460000
|
||||||
|
155 155 1 0.0000000 13.5780000 2.7160000 5.4310000
|
||||||
|
156 156 1 0.0000000 13.5780000 0.0000000 8.1460000
|
||||||
|
157 157 1 0.0000000 14.9350000 1.3580000 9.5040000
|
||||||
|
158 158 1 0.0000000 12.2200000 1.3580000 6.7890000
|
||||||
|
159 159 1 0.0000000 12.2200000 4.0730000 9.5040000
|
||||||
|
160 160 1 0.0000000 14.9350000 4.0730000 6.7890000
|
||||||
|
161 161 1 0.0000000 10.8620000 0.0000000 10.8620000
|
||||||
|
162 162 1 0.0000000 10.8620000 2.7160000 13.5780000
|
||||||
|
163 163 1 0.0000000 13.5780000 2.7160000 10.8620000
|
||||||
|
164 164 1 0.0000000 13.5780000 0.0000000 13.5780000
|
||||||
|
165 165 1 0.0000000 14.9350000 1.3580000 14.9350000
|
||||||
|
166 166 1 0.0000000 12.2200000 1.3580000 12.2200000
|
||||||
|
167 167 1 0.0000000 12.2200000 4.0730000 14.9350000
|
||||||
|
168 168 1 0.0000000 14.9350000 4.0730000 12.2200000
|
||||||
|
169 169 1 0.0000000 10.8620000 5.4310000 0.0000000
|
||||||
|
170 170 1 0.0000000 10.8620000 8.1460000 2.7160000
|
||||||
|
171 171 1 0.0000000 13.5780000 8.1460000 0.0000000
|
||||||
|
172 172 1 0.0000000 13.5780000 5.4310000 2.7160000
|
||||||
|
173 173 1 0.0000000 14.9350000 6.7890000 4.0730000
|
||||||
|
174 174 1 0.0000000 12.2200000 6.7890000 1.3580000
|
||||||
|
175 175 1 0.0000000 12.2200000 9.5040000 4.0730000
|
||||||
|
176 176 1 0.0000000 14.9350000 9.5040000 1.3580000
|
||||||
|
177 177 1 0.0000000 10.8620000 5.4310000 5.4310000
|
||||||
|
178 178 1 0.0000000 10.8620000 8.1460000 8.1460000
|
||||||
|
179 179 1 0.0000000 13.5780000 8.1460000 5.4310000
|
||||||
|
180 180 1 0.0000000 13.5780000 5.4310000 8.1460000
|
||||||
|
181 181 1 0.0000000 14.9350000 6.7890000 9.5040000
|
||||||
|
182 182 1 0.0000000 12.2200000 6.7890000 6.7890000
|
||||||
|
183 183 1 0.0000000 12.2200000 9.5040000 9.5040000
|
||||||
|
184 184 1 0.0000000 14.9350000 9.5040000 6.7890000
|
||||||
|
185 185 1 0.0000000 10.8620000 5.4310000 10.8620000
|
||||||
|
186 186 1 0.0000000 10.8620000 8.1460000 13.5780000
|
||||||
|
187 187 1 0.0000000 13.5780000 8.1460000 10.8620000
|
||||||
|
188 188 1 0.0000000 13.5780000 5.4310000 13.5780000
|
||||||
|
189 189 1 0.0000000 14.9350000 6.7890000 14.9350000
|
||||||
|
190 190 1 0.0000000 12.2200000 6.7890000 12.2200000
|
||||||
|
191 191 1 0.0000000 12.2200000 9.5040000 14.9350000
|
||||||
|
192 192 1 0.0000000 14.9350000 9.5040000 12.2200000
|
||||||
|
193 193 1 0.0000000 10.8620000 10.8620000 0.0000000
|
||||||
|
194 194 1 0.0000000 10.8620000 13.5780000 2.7160000
|
||||||
|
195 195 1 0.0000000 13.5780000 13.5780000 0.0000000
|
||||||
|
196 196 1 0.0000000 13.5780000 10.8620000 2.7160000
|
||||||
|
197 197 1 0.0000000 14.9350000 12.2200000 4.0730000
|
||||||
|
198 198 1 0.0000000 12.2200000 12.2200000 1.3580000
|
||||||
|
199 199 1 0.0000000 12.2200000 14.9350000 4.0730000
|
||||||
|
200 200 1 0.0000000 14.9350000 14.9350000 1.3580000
|
||||||
|
201 201 1 0.0000000 10.8620000 10.8620000 5.4310000
|
||||||
|
202 202 1 0.0000000 10.8620000 13.5780000 8.1460000
|
||||||
|
203 203 1 0.0000000 13.5780000 13.5780000 5.4310000
|
||||||
|
204 204 1 0.0000000 13.5780000 10.8620000 8.1460000
|
||||||
|
205 205 1 0.0000000 14.9350000 12.2200000 9.5040000
|
||||||
|
206 206 1 0.0000000 12.2200000 12.2200000 6.7890000
|
||||||
|
207 207 1 0.0000000 12.2200000 14.9350000 9.5040000
|
||||||
|
208 208 1 0.0000000 14.9350000 14.9350000 6.7890000
|
||||||
|
209 209 1 0.0000000 10.8620000 10.8620000 10.8620000
|
||||||
|
210 210 1 0.0000000 10.8620000 13.5780000 13.5780000
|
||||||
|
211 211 1 0.0000000 13.5780000 13.5780000 10.8620000
|
||||||
|
212 212 1 0.0000000 13.5780000 10.8620000 13.5780000
|
||||||
|
213 213 1 0.0000000 14.9350000 12.2200000 14.9350000
|
||||||
|
214 214 1 0.0000000 12.2200000 12.2200000 12.2200000
|
||||||
|
215 215 1 0.0000000 12.2200000 14.9350000 14.9350000
|
||||||
|
216 216 1 0.0000000 14.9350000 14.9350000 12.2200000
|
||||||
|
|
||||||
534
examples/USER/phonon/dynamical_matrix_command/lmp_bank/silicon_512.lmp
Executable file
534
examples/USER/phonon/dynamical_matrix_command/lmp_bank/silicon_512.lmp
Executable file
@ -0,0 +1,534 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
512 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 21.724000 xlo xhi
|
||||||
|
0.0000000 21.724000 ylo yhi
|
||||||
|
0.0000000 21.724000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 0.0000000 2.7150000 2.7150000
|
||||||
|
3 3 1 0.0000000 2.7150000 2.7150000 0.0000000
|
||||||
|
4 4 1 0.0000000 2.7150000 0.0000000 2.7150000
|
||||||
|
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
|
||||||
|
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
|
||||||
|
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
|
||||||
|
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
|
||||||
|
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
|
||||||
|
10 10 1 0.0000000 0.0000000 2.7150000 8.1460000
|
||||||
|
11 11 1 0.0000000 2.7150000 2.7150000 5.4310000
|
||||||
|
12 12 1 0.0000000 2.7150000 0.0000000 8.1460000
|
||||||
|
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
|
||||||
|
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
|
||||||
|
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
|
||||||
|
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
|
||||||
|
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
|
||||||
|
18 18 1 0.0000000 0.0000000 2.7150000 13.5770000
|
||||||
|
19 19 1 0.0000000 2.7150000 2.7150000 10.8620000
|
||||||
|
20 20 1 0.0000000 2.7150000 0.0000000 13.5770000
|
||||||
|
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
|
||||||
|
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
|
||||||
|
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
|
||||||
|
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
|
||||||
|
25 25 1 0.0000000 0.0000000 0.0000000 16.2930000
|
||||||
|
26 26 1 0.0000000 0.0000000 2.7150000 19.0080000
|
||||||
|
27 27 1 0.0000000 2.7150000 2.7150000 16.2930000
|
||||||
|
28 28 1 0.0000000 2.7150000 0.0000000 19.0080000
|
||||||
|
29 29 1 0.0000000 4.0730000 1.3580000 20.3660000
|
||||||
|
30 30 1 0.0000000 1.3580000 1.3580000 17.6510000
|
||||||
|
31 31 1 0.0000000 1.3580000 4.0730000 20.3660000
|
||||||
|
32 32 1 0.0000000 4.0730000 4.0730000 17.6510000
|
||||||
|
33 33 1 0.0000000 0.0000000 5.4310000 0.0000000
|
||||||
|
34 34 1 0.0000000 0.0000000 8.1460000 2.7150000
|
||||||
|
35 35 1 0.0000000 2.7150000 8.1460000 0.0000000
|
||||||
|
36 36 1 0.0000000 2.7150000 5.4310000 2.7150000
|
||||||
|
37 37 1 0.0000000 4.0730000 6.7890000 4.0730000
|
||||||
|
38 38 1 0.0000000 1.3580000 6.7890000 1.3580000
|
||||||
|
39 39 1 0.0000000 1.3580000 9.5040000 4.0730000
|
||||||
|
40 40 1 0.0000000 4.0730000 9.5040000 1.3580000
|
||||||
|
41 41 1 0.0000000 0.0000000 5.4310000 5.4310000
|
||||||
|
42 42 1 0.0000000 0.0000000 8.1460000 8.1460000
|
||||||
|
43 43 1 0.0000000 2.7150000 8.1460000 5.4310000
|
||||||
|
44 44 1 0.0000000 2.7150000 5.4310000 8.1460000
|
||||||
|
45 45 1 0.0000000 4.0730000 6.7890000 9.5040000
|
||||||
|
46 46 1 0.0000000 1.3580000 6.7890000 6.7890000
|
||||||
|
47 47 1 0.0000000 1.3580000 9.5040000 9.5040000
|
||||||
|
48 48 1 0.0000000 4.0730000 9.5040000 6.7890000
|
||||||
|
49 49 1 0.0000000 0.0000000 5.4310000 10.8620000
|
||||||
|
50 50 1 0.0000000 0.0000000 8.1460000 13.5770000
|
||||||
|
51 51 1 0.0000000 2.7150000 8.1460000 10.8620000
|
||||||
|
52 52 1 0.0000000 2.7150000 5.4310000 13.5770000
|
||||||
|
53 53 1 0.0000000 4.0730000 6.7890000 14.9350000
|
||||||
|
54 54 1 0.0000000 1.3580000 6.7890000 12.2200000
|
||||||
|
55 55 1 0.0000000 1.3580000 9.5040000 14.9350000
|
||||||
|
56 56 1 0.0000000 4.0730000 9.5040000 12.2200000
|
||||||
|
57 57 1 0.0000000 0.0000000 5.4310000 16.2930000
|
||||||
|
58 58 1 0.0000000 0.0000000 8.1460000 19.0080000
|
||||||
|
59 59 1 0.0000000 2.7150000 8.1460000 16.2930000
|
||||||
|
60 60 1 0.0000000 2.7150000 5.4310000 19.0080000
|
||||||
|
61 61 1 0.0000000 4.0730000 6.7890000 20.3660000
|
||||||
|
62 62 1 0.0000000 1.3580000 6.7890000 17.6510000
|
||||||
|
63 63 1 0.0000000 1.3580000 9.5040000 20.3660000
|
||||||
|
64 64 1 0.0000000 4.0730000 9.5040000 17.6510000
|
||||||
|
65 65 1 0.0000000 0.0000000 10.8620000 0.0000000
|
||||||
|
66 66 1 0.0000000 0.0000000 13.5770000 2.7150000
|
||||||
|
67 67 1 0.0000000 2.7150000 13.5770000 0.0000000
|
||||||
|
68 68 1 0.0000000 2.7150000 10.8620000 2.7150000
|
||||||
|
69 69 1 0.0000000 4.0730000 12.2200000 4.0730000
|
||||||
|
70 70 1 0.0000000 1.3580000 12.2200000 1.3580000
|
||||||
|
71 71 1 0.0000000 1.3580000 14.9350000 4.0730000
|
||||||
|
72 72 1 0.0000000 4.0730000 14.9350000 1.3580000
|
||||||
|
73 73 1 0.0000000 0.0000000 10.8620000 5.4310000
|
||||||
|
74 74 1 0.0000000 0.0000000 13.5770000 8.1460000
|
||||||
|
75 75 1 0.0000000 2.7150000 13.5770000 5.4310000
|
||||||
|
76 76 1 0.0000000 2.7150000 10.8620000 8.1460000
|
||||||
|
77 77 1 0.0000000 4.0730000 12.2200000 9.5040000
|
||||||
|
78 78 1 0.0000000 1.3580000 12.2200000 6.7890000
|
||||||
|
79 79 1 0.0000000 1.3580000 14.9350000 9.5040000
|
||||||
|
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||||||
|
341 341 1 0.0000000 14.9350000 12.2200000 14.9350000
|
||||||
|
342 342 1 0.0000000 12.2200000 12.2200000 12.2200000
|
||||||
|
343 343 1 0.0000000 12.2200000 14.9350000 14.9350000
|
||||||
|
344 344 1 0.0000000 14.9350000 14.9350000 12.2200000
|
||||||
|
345 345 1 0.0000000 10.8620000 10.8620000 16.2930000
|
||||||
|
346 346 1 0.0000000 10.8620000 13.5770000 19.0080000
|
||||||
|
347 347 1 0.0000000 13.5770000 13.5770000 16.2930000
|
||||||
|
348 348 1 0.0000000 13.5770000 10.8620000 19.0080000
|
||||||
|
349 349 1 0.0000000 14.9350000 12.2200000 20.3660000
|
||||||
|
350 350 1 0.0000000 12.2200000 12.2200000 17.6510000
|
||||||
|
351 351 1 0.0000000 12.2200000 14.9350000 20.3660000
|
||||||
|
352 352 1 0.0000000 14.9350000 14.9350000 17.6510000
|
||||||
|
353 353 1 0.0000000 10.8620000 16.2930000 0.0000000
|
||||||
|
354 354 1 0.0000000 10.8620000 19.0080000 2.7150000
|
||||||
|
355 355 1 0.0000000 13.5770000 19.0080000 0.0000000
|
||||||
|
356 356 1 0.0000000 13.5770000 16.2930000 2.7150000
|
||||||
|
357 357 1 0.0000000 14.9350000 17.6510000 4.0730000
|
||||||
|
358 358 1 0.0000000 12.2200000 17.6510000 1.3580000
|
||||||
|
359 359 1 0.0000000 12.2200000 20.3660000 4.0730000
|
||||||
|
360 360 1 0.0000000 14.9350000 20.3660000 1.3580000
|
||||||
|
361 361 1 0.0000000 10.8620000 16.2930000 5.4310000
|
||||||
|
362 362 1 0.0000000 10.8620000 19.0080000 8.1460000
|
||||||
|
363 363 1 0.0000000 13.5770000 19.0080000 5.4310000
|
||||||
|
364 364 1 0.0000000 13.5770000 16.2930000 8.1460000
|
||||||
|
365 365 1 0.0000000 14.9350000 17.6510000 9.5040000
|
||||||
|
366 366 1 0.0000000 12.2200000 17.6510000 6.7890000
|
||||||
|
367 367 1 0.0000000 12.2200000 20.3660000 9.5040000
|
||||||
|
368 368 1 0.0000000 14.9350000 20.3660000 6.7890000
|
||||||
|
369 369 1 0.0000000 10.8620000 16.2930000 10.8620000
|
||||||
|
370 370 1 0.0000000 10.8620000 19.0080000 13.5770000
|
||||||
|
371 371 1 0.0000000 13.5770000 19.0080000 10.8620000
|
||||||
|
372 372 1 0.0000000 13.5770000 16.2930000 13.5770000
|
||||||
|
373 373 1 0.0000000 14.9350000 17.6510000 14.9350000
|
||||||
|
374 374 1 0.0000000 12.2200000 17.6510000 12.2200000
|
||||||
|
375 375 1 0.0000000 12.2200000 20.3660000 14.9350000
|
||||||
|
376 376 1 0.0000000 14.9350000 20.3660000 12.2200000
|
||||||
|
377 377 1 0.0000000 10.8620000 16.2930000 16.2930000
|
||||||
|
378 378 1 0.0000000 10.8620000 19.0080000 19.0080000
|
||||||
|
379 379 1 0.0000000 13.5770000 19.0080000 16.2930000
|
||||||
|
380 380 1 0.0000000 13.5770000 16.2930000 19.0080000
|
||||||
|
381 381 1 0.0000000 14.9350000 17.6510000 20.3660000
|
||||||
|
382 382 1 0.0000000 12.2200000 17.6510000 17.6510000
|
||||||
|
383 383 1 0.0000000 12.2200000 20.3660000 20.3660000
|
||||||
|
384 384 1 0.0000000 14.9350000 20.3660000 17.6510000
|
||||||
|
385 385 1 0.0000000 16.2930000 0.0000000 0.0000000
|
||||||
|
386 386 1 0.0000000 16.2930000 2.7150000 2.7150000
|
||||||
|
387 387 1 0.0000000 19.0080000 2.7150000 0.0000000
|
||||||
|
388 388 1 0.0000000 19.0080000 0.0000000 2.7150000
|
||||||
|
389 389 1 0.0000000 20.3660000 1.3580000 4.0730000
|
||||||
|
390 390 1 0.0000000 17.6510000 1.3580000 1.3580000
|
||||||
|
391 391 1 0.0000000 17.6510000 4.0730000 4.0730000
|
||||||
|
392 392 1 0.0000000 20.3660000 4.0730000 1.3580000
|
||||||
|
393 393 1 0.0000000 16.2930000 0.0000000 5.4310000
|
||||||
|
394 394 1 0.0000000 16.2930000 2.7150000 8.1460000
|
||||||
|
395 395 1 0.0000000 19.0080000 2.7150000 5.4310000
|
||||||
|
396 396 1 0.0000000 19.0080000 0.0000000 8.1460000
|
||||||
|
397 397 1 0.0000000 20.3660000 1.3580000 9.5040000
|
||||||
|
398 398 1 0.0000000 17.6510000 1.3580000 6.7890000
|
||||||
|
399 399 1 0.0000000 17.6510000 4.0730000 9.5040000
|
||||||
|
400 400 1 0.0000000 20.3660000 4.0730000 6.7890000
|
||||||
|
401 401 1 0.0000000 16.2930000 0.0000000 10.8620000
|
||||||
|
402 402 1 0.0000000 16.2930000 2.7150000 13.5770000
|
||||||
|
403 403 1 0.0000000 19.0080000 2.7150000 10.8620000
|
||||||
|
404 404 1 0.0000000 19.0080000 0.0000000 13.5770000
|
||||||
|
405 405 1 0.0000000 20.3660000 1.3580000 14.9350000
|
||||||
|
406 406 1 0.0000000 17.6510000 1.3580000 12.2200000
|
||||||
|
407 407 1 0.0000000 17.6510000 4.0730000 14.9350000
|
||||||
|
408 408 1 0.0000000 20.3660000 4.0730000 12.2200000
|
||||||
|
409 409 1 0.0000000 16.2930000 0.0000000 16.2930000
|
||||||
|
410 410 1 0.0000000 16.2930000 2.7150000 19.0080000
|
||||||
|
411 411 1 0.0000000 19.0080000 2.7150000 16.2930000
|
||||||
|
412 412 1 0.0000000 19.0080000 0.0000000 19.0080000
|
||||||
|
413 413 1 0.0000000 20.3660000 1.3580000 20.3660000
|
||||||
|
414 414 1 0.0000000 17.6510000 1.3580000 17.6510000
|
||||||
|
415 415 1 0.0000000 17.6510000 4.0730000 20.3660000
|
||||||
|
416 416 1 0.0000000 20.3660000 4.0730000 17.6510000
|
||||||
|
417 417 1 0.0000000 16.2930000 5.4310000 0.0000000
|
||||||
|
418 418 1 0.0000000 16.2930000 8.1460000 2.7150000
|
||||||
|
419 419 1 0.0000000 19.0080000 8.1460000 0.0000000
|
||||||
|
420 420 1 0.0000000 19.0080000 5.4310000 2.7150000
|
||||||
|
421 421 1 0.0000000 20.3660000 6.7890000 4.0730000
|
||||||
|
422 422 1 0.0000000 17.6510000 6.7890000 1.3580000
|
||||||
|
423 423 1 0.0000000 17.6510000 9.5040000 4.0730000
|
||||||
|
424 424 1 0.0000000 20.3660000 9.5040000 1.3580000
|
||||||
|
425 425 1 0.0000000 16.2930000 5.4310000 5.4310000
|
||||||
|
426 426 1 0.0000000 16.2930000 8.1460000 8.1460000
|
||||||
|
427 427 1 0.0000000 19.0080000 8.1460000 5.4310000
|
||||||
|
428 428 1 0.0000000 19.0080000 5.4310000 8.1460000
|
||||||
|
429 429 1 0.0000000 20.3660000 6.7890000 9.5040000
|
||||||
|
430 430 1 0.0000000 17.6510000 6.7890000 6.7890000
|
||||||
|
431 431 1 0.0000000 17.6510000 9.5040000 9.5040000
|
||||||
|
432 432 1 0.0000000 20.3660000 9.5040000 6.7890000
|
||||||
|
433 433 1 0.0000000 16.2930000 5.4310000 10.8620000
|
||||||
|
434 434 1 0.0000000 16.2930000 8.1460000 13.5770000
|
||||||
|
435 435 1 0.0000000 19.0080000 8.1460000 10.8620000
|
||||||
|
436 436 1 0.0000000 19.0080000 5.4310000 13.5770000
|
||||||
|
437 437 1 0.0000000 20.3660000 6.7890000 14.9350000
|
||||||
|
438 438 1 0.0000000 17.6510000 6.7890000 12.2200000
|
||||||
|
439 439 1 0.0000000 17.6510000 9.5040000 14.9350000
|
||||||
|
440 440 1 0.0000000 20.3660000 9.5040000 12.2200000
|
||||||
|
441 441 1 0.0000000 16.2930000 5.4310000 16.2930000
|
||||||
|
442 442 1 0.0000000 16.2930000 8.1460000 19.0080000
|
||||||
|
443 443 1 0.0000000 19.0080000 8.1460000 16.2930000
|
||||||
|
444 444 1 0.0000000 19.0080000 5.4310000 19.0080000
|
||||||
|
445 445 1 0.0000000 20.3660000 6.7890000 20.3660000
|
||||||
|
446 446 1 0.0000000 17.6510000 6.7890000 17.6510000
|
||||||
|
447 447 1 0.0000000 17.6510000 9.5040000 20.3660000
|
||||||
|
448 448 1 0.0000000 20.3660000 9.5040000 17.6510000
|
||||||
|
449 449 1 0.0000000 16.2930000 10.8620000 0.0000000
|
||||||
|
450 450 1 0.0000000 16.2930000 13.5770000 2.7150000
|
||||||
|
451 451 1 0.0000000 19.0080000 13.5770000 0.0000000
|
||||||
|
452 452 1 0.0000000 19.0080000 10.8620000 2.7150000
|
||||||
|
453 453 1 0.0000000 20.3660000 12.2200000 4.0730000
|
||||||
|
454 454 1 0.0000000 17.6510000 12.2200000 1.3580000
|
||||||
|
455 455 1 0.0000000 17.6510000 14.9350000 4.0730000
|
||||||
|
456 456 1 0.0000000 20.3660000 14.9350000 1.3580000
|
||||||
|
457 457 1 0.0000000 16.2930000 10.8620000 5.4310000
|
||||||
|
458 458 1 0.0000000 16.2930000 13.5770000 8.1460000
|
||||||
|
459 459 1 0.0000000 19.0080000 13.5770000 5.4310000
|
||||||
|
460 460 1 0.0000000 19.0080000 10.8620000 8.1460000
|
||||||
|
461 461 1 0.0000000 20.3660000 12.2200000 9.5040000
|
||||||
|
462 462 1 0.0000000 17.6510000 12.2200000 6.7890000
|
||||||
|
463 463 1 0.0000000 17.6510000 14.9350000 9.5040000
|
||||||
|
464 464 1 0.0000000 20.3660000 14.9350000 6.7890000
|
||||||
|
465 465 1 0.0000000 16.2930000 10.8620000 10.8620000
|
||||||
|
466 466 1 0.0000000 16.2930000 13.5770000 13.5770000
|
||||||
|
467 467 1 0.0000000 19.0080000 13.5770000 10.8620000
|
||||||
|
468 468 1 0.0000000 19.0080000 10.8620000 13.5770000
|
||||||
|
469 469 1 0.0000000 20.3660000 12.2200000 14.9350000
|
||||||
|
470 470 1 0.0000000 17.6510000 12.2200000 12.2200000
|
||||||
|
471 471 1 0.0000000 17.6510000 14.9350000 14.9350000
|
||||||
|
472 472 1 0.0000000 20.3660000 14.9350000 12.2200000
|
||||||
|
473 473 1 0.0000000 16.2930000 10.8620000 16.2930000
|
||||||
|
474 474 1 0.0000000 16.2930000 13.5770000 19.0080000
|
||||||
|
475 475 1 0.0000000 19.0080000 13.5770000 16.2930000
|
||||||
|
476 476 1 0.0000000 19.0080000 10.8620000 19.0080000
|
||||||
|
477 477 1 0.0000000 20.3660000 12.2200000 20.3660000
|
||||||
|
478 478 1 0.0000000 17.6510000 12.2200000 17.6510000
|
||||||
|
479 479 1 0.0000000 17.6510000 14.9350000 20.3660000
|
||||||
|
480 480 1 0.0000000 20.3660000 14.9350000 17.6510000
|
||||||
|
481 481 1 0.0000000 16.2930000 16.2930000 0.0000000
|
||||||
|
482 482 1 0.0000000 16.2930000 19.0080000 2.7150000
|
||||||
|
483 483 1 0.0000000 19.0080000 19.0080000 0.0000000
|
||||||
|
484 484 1 0.0000000 19.0080000 16.2930000 2.7150000
|
||||||
|
485 485 1 0.0000000 20.3660000 17.6510000 4.0730000
|
||||||
|
486 486 1 0.0000000 17.6510000 17.6510000 1.3580000
|
||||||
|
487 487 1 0.0000000 17.6510000 20.3660000 4.0730000
|
||||||
|
488 488 1 0.0000000 20.3660000 20.3660000 1.3580000
|
||||||
|
489 489 1 0.0000000 16.2930000 16.2930000 5.4310000
|
||||||
|
490 490 1 0.0000000 16.2930000 19.0080000 8.1460000
|
||||||
|
491 491 1 0.0000000 19.0080000 19.0080000 5.4310000
|
||||||
|
492 492 1 0.0000000 19.0080000 16.2930000 8.1460000
|
||||||
|
493 493 1 0.0000000 20.3660000 17.6510000 9.5040000
|
||||||
|
494 494 1 0.0000000 17.6510000 17.6510000 6.7890000
|
||||||
|
495 495 1 0.0000000 17.6510000 20.3660000 9.5040000
|
||||||
|
496 496 1 0.0000000 20.3660000 20.3660000 6.7890000
|
||||||
|
497 497 1 0.0000000 16.2930000 16.2930000 10.8620000
|
||||||
|
498 498 1 0.0000000 16.2930000 19.0080000 13.5770000
|
||||||
|
499 499 1 0.0000000 19.0080000 19.0080000 10.8620000
|
||||||
|
500 500 1 0.0000000 19.0080000 16.2930000 13.5770000
|
||||||
|
501 501 1 0.0000000 20.3660000 17.6510000 14.9350000
|
||||||
|
502 502 1 0.0000000 17.6510000 17.6510000 12.2200000
|
||||||
|
503 503 1 0.0000000 17.6510000 20.3660000 14.9350000
|
||||||
|
504 504 1 0.0000000 20.3660000 20.3660000 12.2200000
|
||||||
|
505 505 1 0.0000000 16.2930000 16.2930000 16.2930000
|
||||||
|
506 506 1 0.0000000 16.2930000 19.0080000 19.0080000
|
||||||
|
507 507 1 0.0000000 19.0080000 19.0080000 16.2930000
|
||||||
|
508 508 1 0.0000000 19.0080000 16.2930000 19.0080000
|
||||||
|
509 509 1 0.0000000 20.3660000 17.6510000 20.3660000
|
||||||
|
510 510 1 0.0000000 17.6510000 17.6510000 17.6510000
|
||||||
|
511 511 1 0.0000000 17.6510000 20.3660000 20.3660000
|
||||||
|
512 512 1 0.0000000 20.3660000 20.3660000 17.6510000
|
||||||
|
|
||||||
29
examples/USER/phonon/dynamical_matrix_command/lmp_bank/silicon_8.lmp
Executable file
29
examples/USER/phonon/dynamical_matrix_command/lmp_bank/silicon_8.lmp
Executable file
@ -0,0 +1,29 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
8 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 5.4310000 xlo xhi
|
||||||
|
0.0000000 5.4310000 ylo yhi
|
||||||
|
0.0000000 5.4310000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
|
||||||
|
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
|
||||||
|
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
|
||||||
|
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
|
||||||
|
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
|
||||||
|
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
|
||||||
|
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500
|
||||||
192
examples/USER/phonon/dynamical_matrix_command/results/dynmat.dat
Executable file
192
examples/USER/phonon/dynamical_matrix_command/results/dynmat.dat
Executable file
@ -0,0 +1,192 @@
|
|||||||
|
5409.83472486 3.05075234 0.00000214
|
||||||
|
-1277.48270695 -863.24917964 -862.95613831
|
||||||
|
-193.14095266 0.11071645 0.00000015
|
||||||
|
-1277.48270619 -863.24917934 862.95613793
|
||||||
|
-193.17613831 0.34066975 -0.00000031
|
||||||
|
-1276.01088244 861.54715125 -861.62537402
|
||||||
|
83.46959051 -0.09801326 0.00000000
|
||||||
|
-1276.01088167 861.54715064 861.62537387
|
||||||
|
3.05073556 5409.83419867 0.00000137
|
||||||
|
-863.13224993 -1277.34160622 -862.92133430
|
||||||
|
0.12865796 -193.14095472 -0.00000023
|
||||||
|
-863.13224825 -1277.34160485 862.92133392
|
||||||
|
-0.23661028 83.46934214 -0.00000046
|
||||||
|
861.66402909 -1276.15172701 861.66024333
|
||||||
|
-0.00634065 -193.17585981 -0.00000015
|
||||||
|
861.66402909 -1276.15172686 -861.66024394
|
||||||
|
0.00000031 0.00000031 5410.11037330
|
||||||
|
-862.89766079 -862.97973912 -1277.71823542
|
||||||
|
0.00000000 -0.00000008 83.84059083
|
||||||
|
862.89766018 862.97973851 -1277.71823557
|
||||||
|
0.00000015 0.00000015 -193.17558390
|
||||||
|
-861.60900269 861.52691291 -1276.08157137
|
||||||
|
-0.00000015 -0.00000031 -193.17573821
|
||||||
|
861.60900330 -861.52691284 -1276.08157236
|
||||||
|
-1277.48271824 -863.13225435 -862.89768596
|
||||||
|
5409.83567916 3.04882502 2.82007861
|
||||||
|
-1277.34161080 -863.24919475 862.97975804
|
||||||
|
-193.14089260 0.11950100 0.11994134
|
||||||
|
-1277.52243157 863.24943259 -863.11331046
|
||||||
|
-193.17597070 0.16713301 -0.02106496
|
||||||
|
-1274.64156872 859.96385388 860.17328202
|
||||||
|
83.46945758 -0.16730525 -0.06100253
|
||||||
|
-863.24919444 -1277.34161103 -862.97975804
|
||||||
|
3.04882666 5409.83567944 -2.82007731
|
||||||
|
-863.13225496 -1277.48271916 862.89768688
|
||||||
|
0.11950094 -193.14089255 -0.11994043
|
||||||
|
863.24943320 -1277.52243118 863.11331076
|
||||||
|
-0.16730522 83.46945778 0.06100314
|
||||||
|
859.96385365 -1274.64156819 -860.17328225
|
||||||
|
0.16713979 -193.17596607 0.02106008
|
||||||
|
-862.95611199 -862.92132598 -1277.71824411
|
||||||
|
2.82004085 -2.82004013 5410.11000835
|
||||||
|
862.92132743 862.95611344 -1277.71824587
|
||||||
|
-0.11994722 0.11994786 83.84083834
|
||||||
|
-862.88110757 862.88110699 -1277.34764097
|
||||||
|
0.02099713 0.06108924 -193.17561785
|
||||||
|
860.25587487 -860.25587502 -1274.81548840
|
||||||
|
-0.06108897 -0.02099687 -193.17561808
|
||||||
|
-193.14095465 0.12865765 0.00000015
|
||||||
|
-1277.34160508 -863.13224794 862.92133361
|
||||||
|
5409.83419867 3.05073968 0.00000092
|
||||||
|
-1277.34160584 -863.13224924 -862.92133483
|
||||||
|
83.46934214 -0.23660998 -0.00000076
|
||||||
|
-1276.15172724 861.66402917 861.66024325
|
||||||
|
-193.17585988 -0.00634042 -0.00000031
|
||||||
|
-1276.15172694 861.66402940 -861.66024325
|
||||||
|
0.11071645 -193.14095243 0.00000046
|
||||||
|
-863.24917949 -1277.48270718 862.95613831
|
||||||
|
3.05075524 5409.83472478 -0.00000046
|
||||||
|
-863.24918117 -1277.48270825 -862.95613923
|
||||||
|
0.34066922 -193.17613823 0.00000046
|
||||||
|
861.54715094 -1276.01088228 -861.62537295
|
||||||
|
-0.09801303 83.46959035 0.00000015
|
||||||
|
861.54713538 -1276.01088145 861.62537387
|
||||||
|
-0.00000046 -0.00000023 83.84059068
|
||||||
|
862.97973867 862.89766010 -1277.71823633
|
||||||
|
-0.00000214 -0.00000053 5410.11037574
|
||||||
|
-862.97973943 -862.89766079 -1277.71823633
|
||||||
|
0.00000015 0.00000008 -193.17558374
|
||||||
|
861.52691291 -861.60900269 -1276.08157198
|
||||||
|
-0.00000015 -0.00000015 -193.17573814
|
||||||
|
-861.52691368 861.60900261 -1276.08157243
|
||||||
|
-1277.48271786 -863.13225450 862.89768520
|
||||||
|
-193.14089232 0.11950085 -0.11994115
|
||||||
|
-1277.34161255 -863.24919673 -862.97975957
|
||||||
|
5409.83568051 3.04882517 -2.82007644
|
||||||
|
-1277.52243110 863.24943259 863.11330990
|
||||||
|
83.46945732 -0.16730494 0.06100319
|
||||||
|
-1274.64156796 859.96385342 -860.17328103
|
||||||
|
-193.17597041 0.16713331 0.02106477
|
||||||
|
-863.24919482 -1277.34161057 862.97975774
|
||||||
|
0.11950077 -193.14089270 0.11994160
|
||||||
|
-863.13225473 -1277.48271839 -862.89768673
|
||||||
|
3.04882502 5409.83568081 2.82007903
|
||||||
|
863.24943084 -1277.52242966 -863.11330868
|
||||||
|
0.16713324 -193.17597064 -0.02106522
|
||||||
|
859.96385510 -1274.64156926 860.17328255
|
||||||
|
-0.16730411 83.46945641 -0.06100350
|
||||||
|
862.95611161 862.92132537 -1277.71824365
|
||||||
|
0.11994725 -0.11994740 83.84083859
|
||||||
|
-862.92132606 -862.95611207 -1277.71824548
|
||||||
|
-2.82003936 2.82004013 5410.11000806
|
||||||
|
862.88110509 -862.88110547 -1277.34764015
|
||||||
|
0.06108893 0.02099703 -193.17561792
|
||||||
|
-860.25587388 860.25587441 -1274.81548916
|
||||||
|
-0.02099726 -0.06108878 -193.17561777
|
||||||
|
-193.17613465 -0.23660693 0.00000015
|
||||||
|
-1277.52241409 863.24943328 -862.88111478
|
||||||
|
83.46934549 0.34066334 -0.00000015
|
||||||
|
-1277.52241425 863.24943335 862.88111508
|
||||||
|
5404.58897235 -9.71806749 0.00000015
|
||||||
|
-1273.31333522 -858.38273960 -858.96245956
|
||||||
|
-193.21062369 -0.11938368 0.00000000
|
||||||
|
-1273.31333598 -858.38273967 858.96245926
|
||||||
|
0.34066342 83.46934572 0.00000015
|
||||||
|
863.24943335 -1277.52241402 862.88111478
|
||||||
|
-0.23660723 -193.17613480 -0.00000046
|
||||||
|
863.24943320 -1277.52241425 -862.88111432
|
||||||
|
-9.71806582 5404.58897135 -0.00000183
|
||||||
|
-858.38273891 -1273.31333552 -858.96245926
|
||||||
|
-0.11938338 -193.21062369 0.00000000
|
||||||
|
-858.38273937 -1273.31333598 858.96245987
|
||||||
|
-0.00000031 -0.00000008 -193.17559595
|
||||||
|
-863.11328229 863.11328297 -1277.34763999
|
||||||
|
0.00000000 -0.00000015 -193.17559595
|
||||||
|
863.11328305 -863.11328282 -1277.34763984
|
||||||
|
0.00000122 -0.00000259 5404.30470550
|
||||||
|
-858.80486827 -858.80486866 -1273.17865241
|
||||||
|
-0.00000031 0.00000000 83.09905870
|
||||||
|
858.80486827 858.80486812 -1273.17865272
|
||||||
|
-1276.01089136 861.66402482 -861.60900483
|
||||||
|
-193.17596134 -0.16730494 0.02099535
|
||||||
|
-1276.15175745 861.54714988 861.52691337
|
||||||
|
83.46947097 0.16714109 0.06108436
|
||||||
|
-1273.31334651 -858.38273311 -858.80488185
|
||||||
|
5404.58493608 -3.04507687 -2.81778617
|
||||||
|
-1276.19187193 -861.66399965 861.74280750
|
||||||
|
-193.21058304 -0.11920641 -0.12012575
|
||||||
|
861.54714972 -1276.15175730 861.52691337
|
||||||
|
0.16714140 83.46947120 0.06108451
|
||||||
|
861.66402345 -1276.01089022 -861.60900330
|
||||||
|
-0.16730487 -193.17596164 0.02099489
|
||||||
|
-858.38273281 -1273.31334681 -858.80488063
|
||||||
|
-3.04507603 5404.58493554 -2.81778617
|
||||||
|
-861.66400079 -1276.19187270 861.74280887
|
||||||
|
-0.11920511 -193.21058281 -0.12012498
|
||||||
|
-861.62536929 861.66025668 -1276.08157121
|
||||||
|
-0.02106026 0.06099877 -193.17561197
|
||||||
|
861.66025752 -861.62537051 -1276.08157274
|
||||||
|
0.06099923 -0.02106049 -193.17561227
|
||||||
|
-858.96244980 -858.96244965 -1273.17866523
|
||||||
|
-2.81780608 -2.81780615 5404.30474272
|
||||||
|
861.58531232 861.58531248 -1275.71087663
|
||||||
|
0.12013467 0.12013460 83.09915619
|
||||||
|
83.46958166 -0.00634218 -0.00000023
|
||||||
|
-1274.64157002 859.96383191 860.25587098
|
||||||
|
-193.17585332 -0.09802844 0.00000023
|
||||||
|
-1274.64157155 859.96383290 -860.25587243
|
||||||
|
-193.21062064 -0.11939070 -0.00000008
|
||||||
|
-1276.19189573 -861.66398638 861.58531118
|
||||||
|
5404.58377546 3.62403097 0.00000015
|
||||||
|
-1276.19189558 -861.66398615 -861.58531103
|
||||||
|
-0.09802859 -193.17585355 -0.00000015
|
||||||
|
859.96383206 -1274.64156979 -860.25587113
|
||||||
|
-0.00634187 83.46958204 -0.00000008
|
||||||
|
859.96383282 -1274.64157132 860.25587212
|
||||||
|
-0.11939055 -193.21062041 0.00000000
|
||||||
|
-861.66398576 -1276.19189528 861.58531087
|
||||||
|
3.62402982 5404.58377698 -0.00000076
|
||||||
|
-861.66398927 -1276.19189772 -861.58531331
|
||||||
|
0.00000000 0.00000000 -193.17573654
|
||||||
|
860.17327676 -860.17327637 -1274.81551212
|
||||||
|
0.00000031 0.00000023 -193.17573676
|
||||||
|
-860.17327615 860.17327645 -1274.81551258
|
||||||
|
0.00000000 0.00000015 83.09907327
|
||||||
|
861.74281299 861.74281299 -1275.71086763
|
||||||
|
-0.00000046 -0.00000015 5404.30514861
|
||||||
|
-861.74281406 -861.74281421 -1275.71086938
|
||||||
|
-1276.01088968 861.66402284 861.60900330
|
||||||
|
83.46947136 0.16714109 -0.06108436
|
||||||
|
-1276.15175722 861.54714957 -861.52691391
|
||||||
|
-193.17596141 -0.16730510 -0.02099527
|
||||||
|
-1273.31334666 -858.38273281 858.80488124
|
||||||
|
-193.21058304 -0.11920641 0.12012636
|
||||||
|
-1276.19187285 -861.66400087 -861.74280773
|
||||||
|
5404.58493638 -3.04507565 2.81778602
|
||||||
|
861.54715133 -1276.15175913 -861.52691490
|
||||||
|
-0.16730502 -193.17596118 -0.02099497
|
||||||
|
861.66402314 -1276.01088976 861.60900383
|
||||||
|
0.16714125 83.46947151 -0.06108497
|
||||||
|
-858.38273296 -1273.31334681 858.80488139
|
||||||
|
-0.11920686 -193.21058311 0.12012605
|
||||||
|
-861.66400079 -1276.19187255 -861.74280811
|
||||||
|
-3.04506703 5404.58493432 2.81779319
|
||||||
|
861.62536952 -861.66025637 -1276.08157175
|
||||||
|
-0.06099938 0.02106080 -193.17561235
|
||||||
|
-861.66025645 861.62536929 -1276.08157213
|
||||||
|
0.02106049 -0.06099862 -193.17561189
|
||||||
|
858.96245049 858.96245041 -1273.17866553
|
||||||
|
-0.12013444 -0.12013475 83.09915550
|
||||||
|
-861.58531232 -861.58531217 -1275.71087655
|
||||||
|
2.81780737 2.81780753 5404.30474547
|
||||||
58
examples/USER/phonon/dynamical_matrix_command/results/out.silicon
Executable file
58
examples/USER/phonon/dynamical_matrix_command/results/out.silicon
Executable file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (16 Jul 2018)
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (5.431 5.431 5.431)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
8 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4
|
||||||
|
ghost atom cutoff = 4
|
||||||
|
binsize = 2, bins = 3 3 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Calculating Dynamical Matrix...
|
||||||
|
Dynamical Matrix calculation took 0.001183 seconds
|
||||||
|
Finished Calculating Dynamical Matrix
|
||||||
|
Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.00016781 | 0.00041345 | 0.00051464 | 0.0 | 0.00
|
||||||
|
Bond | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.00056143 | 0.00066602 | 0.00090865 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.224e+06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 3 max 1 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Nghost: 56 ave 57 max 55 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 32 ave 48 max 16 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 128
|
||||||
|
Ave neighs/atom = 16
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
29
examples/USER/phonon/dynamical_matrix_command/silicon_input_file.lmp
Executable file
29
examples/USER/phonon/dynamical_matrix_command/silicon_input_file.lmp
Executable file
@ -0,0 +1,29 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
8 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 5.4310000 xlo xhi
|
||||||
|
0.0000000 5.4310000 ylo yhi
|
||||||
|
0.0000000 5.4310000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
|
||||||
|
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
|
||||||
|
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
|
||||||
|
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
|
||||||
|
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
|
||||||
|
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
|
||||||
|
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500
|
||||||
48
examples/USER/phonon/third_order_command/Manual.md
Executable file
48
examples/USER/phonon/third_order_command/Manual.md
Executable file
@ -0,0 +1,48 @@
|
|||||||
|
# third_order command
|
||||||
|
|
||||||
|
## Syntax
|
||||||
|
|
||||||
|
```
|
||||||
|
third_order group-ID style args keyword value ...
|
||||||
|
```
|
||||||
|
|
||||||
|
* group-ID = ID of group of atoms to displace
|
||||||
|
* style = *regular* or *ballistico*
|
||||||
|
```
|
||||||
|
*regular* args = gamma
|
||||||
|
gamma = finite difference displacement length
|
||||||
|
*ballistico* args = gamma
|
||||||
|
gamma = finite difference displacement length
|
||||||
|
```
|
||||||
|
* zero or more keyword/value pairs may be appended
|
||||||
|
* keyword = *file* or *binary*
|
||||||
|
```
|
||||||
|
*file* value = output_file
|
||||||
|
output_file = name of file to dump the dynamical matrix into
|
||||||
|
*binary* values = *no* or *gzip*
|
||||||
|
```
|
||||||
|
|
||||||
|
## Examples
|
||||||
|
|
||||||
|
```
|
||||||
|
third_order 1 regular 0.000001
|
||||||
|
third_order 1 ballistico 0.000001
|
||||||
|
third_order 3 regular 0.00004 file third_order.dat
|
||||||
|
third_order 5 ballistico 0.00000001 file third_order.dat binary gzip
|
||||||
|
```
|
||||||
|
|
||||||
|
## Description
|
||||||
|
|
||||||
|
Calculate the finite difference third order tensor of the selected group.
|
||||||
|
|
||||||
|
## Restrictions
|
||||||
|
|
||||||
|
None
|
||||||
|
|
||||||
|
## Related commands
|
||||||
|
|
||||||
|
None
|
||||||
|
|
||||||
|
## Default
|
||||||
|
|
||||||
|
The option defaults are file = "third_order.dat", binary = no
|
||||||
25
examples/USER/phonon/third_order_command/README.md
Executable file
25
examples/USER/phonon/third_order_command/README.md
Executable file
@ -0,0 +1,25 @@
|
|||||||
|
# LAMMPS LATTICE DYNAMICS COMMANDS
|
||||||
|
|
||||||
|
## THIRD ORDER TENSOR CALCULATOR
|
||||||
|
|
||||||
|
This directory contains the ingredients to calculate a third order tensor.
|
||||||
|
|
||||||
|
Example:
|
||||||
|
```
|
||||||
|
$THIRD_ORDER=third_order #tensor output file
|
||||||
|
NP=4 #number of processors
|
||||||
|
mpirun -np $NP lmp_mpi < in.silicon > out.silicon
|
||||||
|
combine.sh third_order
|
||||||
|
```
|
||||||
|
|
||||||
|
To test out a different silicon example:
|
||||||
|
```
|
||||||
|
$THIRD_ORDER=third_order
|
||||||
|
$LMP_FILE=amorphous_silicon.lmp
|
||||||
|
cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
|
||||||
|
NP=4 #number of processors
|
||||||
|
mpirun -np $NP lmp_mpi < in.silicon > out.silicon
|
||||||
|
bash combine.sh $THIRD_ORDER
|
||||||
|
```
|
||||||
|
|
||||||
|
## Requires: MANYBODY and MOLECULE packages
|
||||||
66
examples/USER/phonon/third_order_command/Si.opt.tersoff
Executable file
66
examples/USER/phonon/third_order_command/Si.opt.tersoff
Executable file
@ -0,0 +1,66 @@
|
|||||||
|
# Tersoff parameters for various elements and mixtures
|
||||||
|
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
||||||
|
# these entries are in LAMMPS "metal" units:
|
||||||
|
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
|
||||||
|
# other quantities are unitless
|
||||||
|
|
||||||
|
# Aidan Thompson (athomps at sandia.gov) takes full blame for this
|
||||||
|
# file. It specifies various potentials published by J. Tersoff for
|
||||||
|
# silicon, carbon and germanium. Since Tersoff published several
|
||||||
|
# different silicon potentials, I refer to them using atom types
|
||||||
|
# Si(B), Si(C) and Si(D). The last two are almost almost identical but
|
||||||
|
# refer to two different publications. These names should be used in
|
||||||
|
# the LAMMPS command when the file is invoked. For example:
|
||||||
|
# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials
|
||||||
|
# can be used pure silicon, pure carbon, pure germanium, binary SiC,
|
||||||
|
# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
|
||||||
|
# generate an error if this file is used with any combination
|
||||||
|
# involving C and Ge, since there are no entries for the GeC
|
||||||
|
# interactions (Tersoff did not publish parameters for this
|
||||||
|
# cross-interaction.)
|
||||||
|
|
||||||
|
# format of a single entry (one or more lines):
|
||||||
|
# element 1, element 2, element 3,
|
||||||
|
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
|
||||||
|
|
||||||
|
# The original Tersoff potential for Silicon, Si(B)
|
||||||
|
# J. Tersoff, PRB, 37, 6991 (1988)
|
||||||
|
|
||||||
|
Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
|
||||||
|
0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
|
||||||
|
|
||||||
|
# The later Tersoff potential for Silicon, Si(C)
|
||||||
|
# J. Tersoff, PRB, 38, 9902 (1988)
|
||||||
|
|
||||||
|
Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
|
||||||
|
1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
|
||||||
|
|
||||||
|
# The later Tersoff potential for Carbon, Silicon, and Germanium
|
||||||
|
# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
|
||||||
|
# The Si and C parameters are very close to those in SiC.tersoff
|
||||||
|
|
||||||
|
C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6
|
||||||
|
Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
|
||||||
|
Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0
|
||||||
|
|
||||||
|
C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
|
||||||
|
C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0
|
||||||
|
C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
|
||||||
|
|
||||||
|
Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
|
||||||
|
Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
|
||||||
|
Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
|
||||||
|
|
||||||
|
Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
|
||||||
|
Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
|
||||||
|
Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
|
||||||
|
|
||||||
|
Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
|
||||||
|
Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0
|
||||||
|
Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
|
||||||
|
|
||||||
|
# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010)
|
||||||
|
# element 1, element 2, element 3,
|
||||||
|
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
|
||||||
|
C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6
|
||||||
|
|
||||||
17
examples/USER/phonon/third_order_command/combine.sh
Executable file
17
examples/USER/phonon/third_order_command/combine.sh
Executable file
@ -0,0 +1,17 @@
|
|||||||
|
#!/bin/bash
|
||||||
|
|
||||||
|
#This script takes one argument
|
||||||
|
#The argument is the base name for the split up tensor
|
||||||
|
#The script then combines and sorts the tensor
|
||||||
|
#$1 file name
|
||||||
|
|
||||||
|
echo "$1"
|
||||||
|
[ -f $1 ] && rm $1
|
||||||
|
|
||||||
|
for i in $(ls ./$1*); do
|
||||||
|
cat $i >> temp
|
||||||
|
rm $i
|
||||||
|
done
|
||||||
|
|
||||||
|
sort temp | sort -s -n -k 3 | sort -s -n -k 1 > $1
|
||||||
|
rm temp
|
||||||
19
examples/USER/phonon/third_order_command/ff-silicon.lmp
Executable file
19
examples/USER/phonon/third_order_command/ff-silicon.lmp
Executable file
@ -0,0 +1,19 @@
|
|||||||
|
#############################
|
||||||
|
#Atoms types - mass - charge#
|
||||||
|
#############################
|
||||||
|
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
|
||||||
|
|
||||||
|
variable Si equal 1
|
||||||
|
|
||||||
|
#############
|
||||||
|
#Atom Masses#
|
||||||
|
#############
|
||||||
|
|
||||||
|
mass ${Si} 28.08550
|
||||||
|
|
||||||
|
###########################
|
||||||
|
#Pair Potentials - Tersoff#
|
||||||
|
###########################
|
||||||
|
|
||||||
|
pair_style tersoff
|
||||||
|
pair_coeff * * Si.opt.tersoff Si(D)
|
||||||
84
examples/USER/phonon/third_order_command/in.silicon
Executable file
84
examples/USER/phonon/third_order_command/in.silicon
Executable file
@ -0,0 +1,84 @@
|
|||||||
|
###############################mm
|
||||||
|
# Atom style - charge/vdw/bonded#
|
||||||
|
#################################
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
##############################################
|
||||||
|
#Units Metal : eV - ps - angstrom - bar#
|
||||||
|
# Real : kcal/mol - fs - angstrom - atm#
|
||||||
|
##############################################
|
||||||
|
units metal
|
||||||
|
|
||||||
|
############
|
||||||
|
#Run number#
|
||||||
|
############
|
||||||
|
variable run_no equal 0 # is it a restart?
|
||||||
|
variable res_no equal ${run_no}-1 # restart file number
|
||||||
|
|
||||||
|
#######################################
|
||||||
|
#Random Seeds and Domain Decomposition#
|
||||||
|
#######################################
|
||||||
|
variable iseed0 equal 2357
|
||||||
|
variable iseed1 equal 26488
|
||||||
|
variable iseed2 equal 10669
|
||||||
|
processors * * 1
|
||||||
|
|
||||||
|
###########
|
||||||
|
#Data File#
|
||||||
|
###########
|
||||||
|
variable inpfile string silicon_input_file.lmp
|
||||||
|
variable resfile string final_restart.${res_no}
|
||||||
|
variable ff_file string ff-silicon.lmp
|
||||||
|
|
||||||
|
##########
|
||||||
|
#Run Type#
|
||||||
|
##########
|
||||||
|
variable minimise equal 0 #Energy Minimization
|
||||||
|
|
||||||
|
###############################
|
||||||
|
#Molecular Dynamics Parameters#
|
||||||
|
###############################
|
||||||
|
neighbor 1 bin
|
||||||
|
|
||||||
|
################################
|
||||||
|
#Energy Minimization Parameters#
|
||||||
|
################################
|
||||||
|
variable mtraj equal 1 # trajectory output frequency - all system
|
||||||
|
variable etol equal 1e-5 # % change in energy
|
||||||
|
variable ftol equal 1e-5 # max force threshold (force units)
|
||||||
|
variable maxiter equal 10000 # max # of iterations
|
||||||
|
|
||||||
|
########################
|
||||||
|
#3D Periodic Simulation#
|
||||||
|
########################
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
#############################
|
||||||
|
#Reading the input structure#
|
||||||
|
#############################
|
||||||
|
if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
|
||||||
|
|
||||||
|
#############
|
||||||
|
#Force Field#
|
||||||
|
#############
|
||||||
|
include ${ff_file}
|
||||||
|
|
||||||
|
#####################
|
||||||
|
#Energy Minimization#
|
||||||
|
#####################
|
||||||
|
if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
|
||||||
|
print "Doing CG minimisation"
|
||||||
|
dump mdcd all dcd ${mtraj} min.dcd
|
||||||
|
dump_modify mdcd unwrap yes
|
||||||
|
min_style cg
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize ${etol} ${ftol} ${maxiter} ${maxiter}
|
||||||
|
reset_timestep 0
|
||||||
|
undump mdcd
|
||||||
|
label end_minimise
|
||||||
|
|
||||||
|
##################
|
||||||
|
#Dynamical Matrix#
|
||||||
|
##################
|
||||||
|
third_order all ballistico 0.00001 file third_order binary no
|
||||||
|
|
||||||
238
examples/USER/phonon/third_order_command/lmp_bank/silicon_216.lmp
Executable file
238
examples/USER/phonon/third_order_command/lmp_bank/silicon_216.lmp
Executable file
@ -0,0 +1,238 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
216 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 16.293000 xlo xhi
|
||||||
|
0.0000000 16.293000 ylo yhi
|
||||||
|
0.0000000 16.293000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 0.0000000 2.7160000 2.7160000
|
||||||
|
3 3 1 0.0000000 2.7160000 2.7160000 0.0000000
|
||||||
|
4 4 1 0.0000000 2.7160000 0.0000000 2.7160000
|
||||||
|
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
|
||||||
|
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
|
||||||
|
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
|
||||||
|
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
|
||||||
|
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
|
||||||
|
10 10 1 0.0000000 0.0000000 2.7160000 8.1460000
|
||||||
|
11 11 1 0.0000000 2.7160000 2.7160000 5.4310000
|
||||||
|
12 12 1 0.0000000 2.7160000 0.0000000 8.1460000
|
||||||
|
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
|
||||||
|
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
|
||||||
|
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
|
||||||
|
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
|
||||||
|
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
|
||||||
|
18 18 1 0.0000000 0.0000000 2.7160000 13.5780000
|
||||||
|
19 19 1 0.0000000 2.7160000 2.7160000 10.8620000
|
||||||
|
20 20 1 0.0000000 2.7160000 0.0000000 13.5780000
|
||||||
|
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
|
||||||
|
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
|
||||||
|
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
|
||||||
|
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
|
||||||
|
25 25 1 0.0000000 0.0000000 5.4310000 0.0000000
|
||||||
|
26 26 1 0.0000000 0.0000000 8.1460000 2.7160000
|
||||||
|
27 27 1 0.0000000 2.7160000 8.1460000 0.0000000
|
||||||
|
28 28 1 0.0000000 2.7160000 5.4310000 2.7160000
|
||||||
|
29 29 1 0.0000000 4.0730000 6.7890000 4.0730000
|
||||||
|
30 30 1 0.0000000 1.3580000 6.7890000 1.3580000
|
||||||
|
31 31 1 0.0000000 1.3580000 9.5040000 4.0730000
|
||||||
|
32 32 1 0.0000000 4.0730000 9.5040000 1.3580000
|
||||||
|
33 33 1 0.0000000 0.0000000 5.4310000 5.4310000
|
||||||
|
34 34 1 0.0000000 0.0000000 8.1460000 8.1460000
|
||||||
|
35 35 1 0.0000000 2.7160000 8.1460000 5.4310000
|
||||||
|
36 36 1 0.0000000 2.7160000 5.4310000 8.1460000
|
||||||
|
37 37 1 0.0000000 4.0730000 6.7890000 9.5040000
|
||||||
|
38 38 1 0.0000000 1.3580000 6.7890000 6.7890000
|
||||||
|
39 39 1 0.0000000 1.3580000 9.5040000 9.5040000
|
||||||
|
40 40 1 0.0000000 4.0730000 9.5040000 6.7890000
|
||||||
|
41 41 1 0.0000000 0.0000000 5.4310000 10.8620000
|
||||||
|
42 42 1 0.0000000 0.0000000 8.1460000 13.5780000
|
||||||
|
43 43 1 0.0000000 2.7160000 8.1460000 10.8620000
|
||||||
|
44 44 1 0.0000000 2.7160000 5.4310000 13.5780000
|
||||||
|
45 45 1 0.0000000 4.0730000 6.7890000 14.9350000
|
||||||
|
46 46 1 0.0000000 1.3580000 6.7890000 12.2200000
|
||||||
|
47 47 1 0.0000000 1.3580000 9.5040000 14.9350000
|
||||||
|
48 48 1 0.0000000 4.0730000 9.5040000 12.2200000
|
||||||
|
49 49 1 0.0000000 0.0000000 10.8620000 0.0000000
|
||||||
|
50 50 1 0.0000000 0.0000000 13.5780000 2.7160000
|
||||||
|
51 51 1 0.0000000 2.7160000 13.5780000 0.0000000
|
||||||
|
52 52 1 0.0000000 2.7160000 10.8620000 2.7160000
|
||||||
|
53 53 1 0.0000000 4.0730000 12.2200000 4.0730000
|
||||||
|
54 54 1 0.0000000 1.3580000 12.2200000 1.3580000
|
||||||
|
55 55 1 0.0000000 1.3580000 14.9350000 4.0730000
|
||||||
|
56 56 1 0.0000000 4.0730000 14.9350000 1.3580000
|
||||||
|
57 57 1 0.0000000 0.0000000 10.8620000 5.4310000
|
||||||
|
58 58 1 0.0000000 0.0000000 13.5780000 8.1460000
|
||||||
|
59 59 1 0.0000000 2.7160000 13.5780000 5.4310000
|
||||||
|
60 60 1 0.0000000 2.7160000 10.8620000 8.1460000
|
||||||
|
61 61 1 0.0000000 4.0730000 12.2200000 9.5040000
|
||||||
|
62 62 1 0.0000000 1.3580000 12.2200000 6.7890000
|
||||||
|
63 63 1 0.0000000 1.3580000 14.9350000 9.5040000
|
||||||
|
64 64 1 0.0000000 4.0730000 14.9350000 6.7890000
|
||||||
|
65 65 1 0.0000000 0.0000000 10.8620000 10.8620000
|
||||||
|
66 66 1 0.0000000 0.0000000 13.5780000 13.5780000
|
||||||
|
67 67 1 0.0000000 2.7160000 13.5780000 10.8620000
|
||||||
|
68 68 1 0.0000000 2.7160000 10.8620000 13.5780000
|
||||||
|
69 69 1 0.0000000 4.0730000 12.2200000 14.9350000
|
||||||
|
70 70 1 0.0000000 1.3580000 12.2200000 12.2200000
|
||||||
|
71 71 1 0.0000000 1.3580000 14.9350000 14.9350000
|
||||||
|
72 72 1 0.0000000 4.0730000 14.9350000 12.2200000
|
||||||
|
73 73 1 0.0000000 5.4310000 0.0000000 0.0000000
|
||||||
|
74 74 1 0.0000000 5.4310000 2.7160000 2.7160000
|
||||||
|
75 75 1 0.0000000 8.1460000 2.7160000 0.0000000
|
||||||
|
76 76 1 0.0000000 8.1460000 0.0000000 2.7160000
|
||||||
|
77 77 1 0.0000000 9.5040000 1.3580000 4.0730000
|
||||||
|
78 78 1 0.0000000 6.7890000 1.3580000 1.3580000
|
||||||
|
79 79 1 0.0000000 6.7890000 4.0730000 4.0730000
|
||||||
|
80 80 1 0.0000000 9.5040000 4.0730000 1.3580000
|
||||||
|
81 81 1 0.0000000 5.4310000 0.0000000 5.4310000
|
||||||
|
82 82 1 0.0000000 5.4310000 2.7160000 8.1460000
|
||||||
|
83 83 1 0.0000000 8.1460000 2.7160000 5.4310000
|
||||||
|
84 84 1 0.0000000 8.1460000 0.0000000 8.1460000
|
||||||
|
85 85 1 0.0000000 9.5040000 1.3580000 9.5040000
|
||||||
|
86 86 1 0.0000000 6.7890000 1.3580000 6.7890000
|
||||||
|
87 87 1 0.0000000 6.7890000 4.0730000 9.5040000
|
||||||
|
88 88 1 0.0000000 9.5040000 4.0730000 6.7890000
|
||||||
|
89 89 1 0.0000000 5.4310000 0.0000000 10.8620000
|
||||||
|
90 90 1 0.0000000 5.4310000 2.7160000 13.5780000
|
||||||
|
91 91 1 0.0000000 8.1460000 2.7160000 10.8620000
|
||||||
|
92 92 1 0.0000000 8.1460000 0.0000000 13.5780000
|
||||||
|
93 93 1 0.0000000 9.5040000 1.3580000 14.9350000
|
||||||
|
94 94 1 0.0000000 6.7890000 1.3580000 12.2200000
|
||||||
|
95 95 1 0.0000000 6.7890000 4.0730000 14.9350000
|
||||||
|
96 96 1 0.0000000 9.5040000 4.0730000 12.2200000
|
||||||
|
97 97 1 0.0000000 5.4310000 5.4310000 0.0000000
|
||||||
|
98 98 1 0.0000000 5.4310000 8.1460000 2.7160000
|
||||||
|
99 99 1 0.0000000 8.1460000 8.1460000 0.0000000
|
||||||
|
100 100 1 0.0000000 8.1460000 5.4310000 2.7160000
|
||||||
|
101 101 1 0.0000000 9.5040000 6.7890000 4.0730000
|
||||||
|
102 102 1 0.0000000 6.7890000 6.7890000 1.3580000
|
||||||
|
103 103 1 0.0000000 6.7890000 9.5040000 4.0730000
|
||||||
|
104 104 1 0.0000000 9.5040000 9.5040000 1.3580000
|
||||||
|
105 105 1 0.0000000 5.4310000 5.4310000 5.4310000
|
||||||
|
106 106 1 0.0000000 5.4310000 8.1460000 8.1460000
|
||||||
|
107 107 1 0.0000000 8.1460000 8.1460000 5.4310000
|
||||||
|
108 108 1 0.0000000 8.1460000 5.4310000 8.1460000
|
||||||
|
109 109 1 0.0000000 9.5040000 6.7890000 9.5040000
|
||||||
|
110 110 1 0.0000000 6.7890000 6.7890000 6.7890000
|
||||||
|
111 111 1 0.0000000 6.7890000 9.5040000 9.5040000
|
||||||
|
112 112 1 0.0000000 9.5040000 9.5040000 6.7890000
|
||||||
|
113 113 1 0.0000000 5.4310000 5.4310000 10.8620000
|
||||||
|
114 114 1 0.0000000 5.4310000 8.1460000 13.5780000
|
||||||
|
115 115 1 0.0000000 8.1460000 8.1460000 10.8620000
|
||||||
|
116 116 1 0.0000000 8.1460000 5.4310000 13.5780000
|
||||||
|
117 117 1 0.0000000 9.5040000 6.7890000 14.9350000
|
||||||
|
118 118 1 0.0000000 6.7890000 6.7890000 12.2200000
|
||||||
|
119 119 1 0.0000000 6.7890000 9.5040000 14.9350000
|
||||||
|
120 120 1 0.0000000 9.5040000 9.5040000 12.2200000
|
||||||
|
121 121 1 0.0000000 5.4310000 10.8620000 0.0000000
|
||||||
|
122 122 1 0.0000000 5.4310000 13.5780000 2.7160000
|
||||||
|
123 123 1 0.0000000 8.1460000 13.5780000 0.0000000
|
||||||
|
124 124 1 0.0000000 8.1460000 10.8620000 2.7160000
|
||||||
|
125 125 1 0.0000000 9.5040000 12.2200000 4.0730000
|
||||||
|
126 126 1 0.0000000 6.7890000 12.2200000 1.3580000
|
||||||
|
127 127 1 0.0000000 6.7890000 14.9350000 4.0730000
|
||||||
|
128 128 1 0.0000000 9.5040000 14.9350000 1.3580000
|
||||||
|
129 129 1 0.0000000 5.4310000 10.8620000 5.4310000
|
||||||
|
130 130 1 0.0000000 5.4310000 13.5780000 8.1460000
|
||||||
|
131 131 1 0.0000000 8.1460000 13.5780000 5.4310000
|
||||||
|
132 132 1 0.0000000 8.1460000 10.8620000 8.1460000
|
||||||
|
133 133 1 0.0000000 9.5040000 12.2200000 9.5040000
|
||||||
|
134 134 1 0.0000000 6.7890000 12.2200000 6.7890000
|
||||||
|
135 135 1 0.0000000 6.7890000 14.9350000 9.5040000
|
||||||
|
136 136 1 0.0000000 9.5040000 14.9350000 6.7890000
|
||||||
|
137 137 1 0.0000000 5.4310000 10.8620000 10.8620000
|
||||||
|
138 138 1 0.0000000 5.4310000 13.5780000 13.5780000
|
||||||
|
139 139 1 0.0000000 8.1460000 13.5780000 10.8620000
|
||||||
|
140 140 1 0.0000000 8.1460000 10.8620000 13.5780000
|
||||||
|
141 141 1 0.0000000 9.5040000 12.2200000 14.9350000
|
||||||
|
142 142 1 0.0000000 6.7890000 12.2200000 12.2200000
|
||||||
|
143 143 1 0.0000000 6.7890000 14.9350000 14.9350000
|
||||||
|
144 144 1 0.0000000 9.5040000 14.9350000 12.2200000
|
||||||
|
145 145 1 0.0000000 10.8620000 0.0000000 0.0000000
|
||||||
|
146 146 1 0.0000000 10.8620000 2.7160000 2.7160000
|
||||||
|
147 147 1 0.0000000 13.5780000 2.7160000 0.0000000
|
||||||
|
148 148 1 0.0000000 13.5780000 0.0000000 2.7160000
|
||||||
|
149 149 1 0.0000000 14.9350000 1.3580000 4.0730000
|
||||||
|
150 150 1 0.0000000 12.2200000 1.3580000 1.3580000
|
||||||
|
151 151 1 0.0000000 12.2200000 4.0730000 4.0730000
|
||||||
|
152 152 1 0.0000000 14.9350000 4.0730000 1.3580000
|
||||||
|
153 153 1 0.0000000 10.8620000 0.0000000 5.4310000
|
||||||
|
154 154 1 0.0000000 10.8620000 2.7160000 8.1460000
|
||||||
|
155 155 1 0.0000000 13.5780000 2.7160000 5.4310000
|
||||||
|
156 156 1 0.0000000 13.5780000 0.0000000 8.1460000
|
||||||
|
157 157 1 0.0000000 14.9350000 1.3580000 9.5040000
|
||||||
|
158 158 1 0.0000000 12.2200000 1.3580000 6.7890000
|
||||||
|
159 159 1 0.0000000 12.2200000 4.0730000 9.5040000
|
||||||
|
160 160 1 0.0000000 14.9350000 4.0730000 6.7890000
|
||||||
|
161 161 1 0.0000000 10.8620000 0.0000000 10.8620000
|
||||||
|
162 162 1 0.0000000 10.8620000 2.7160000 13.5780000
|
||||||
|
163 163 1 0.0000000 13.5780000 2.7160000 10.8620000
|
||||||
|
164 164 1 0.0000000 13.5780000 0.0000000 13.5780000
|
||||||
|
165 165 1 0.0000000 14.9350000 1.3580000 14.9350000
|
||||||
|
166 166 1 0.0000000 12.2200000 1.3580000 12.2200000
|
||||||
|
167 167 1 0.0000000 12.2200000 4.0730000 14.9350000
|
||||||
|
168 168 1 0.0000000 14.9350000 4.0730000 12.2200000
|
||||||
|
169 169 1 0.0000000 10.8620000 5.4310000 0.0000000
|
||||||
|
170 170 1 0.0000000 10.8620000 8.1460000 2.7160000
|
||||||
|
171 171 1 0.0000000 13.5780000 8.1460000 0.0000000
|
||||||
|
172 172 1 0.0000000 13.5780000 5.4310000 2.7160000
|
||||||
|
173 173 1 0.0000000 14.9350000 6.7890000 4.0730000
|
||||||
|
174 174 1 0.0000000 12.2200000 6.7890000 1.3580000
|
||||||
|
175 175 1 0.0000000 12.2200000 9.5040000 4.0730000
|
||||||
|
176 176 1 0.0000000 14.9350000 9.5040000 1.3580000
|
||||||
|
177 177 1 0.0000000 10.8620000 5.4310000 5.4310000
|
||||||
|
178 178 1 0.0000000 10.8620000 8.1460000 8.1460000
|
||||||
|
179 179 1 0.0000000 13.5780000 8.1460000 5.4310000
|
||||||
|
180 180 1 0.0000000 13.5780000 5.4310000 8.1460000
|
||||||
|
181 181 1 0.0000000 14.9350000 6.7890000 9.5040000
|
||||||
|
182 182 1 0.0000000 12.2200000 6.7890000 6.7890000
|
||||||
|
183 183 1 0.0000000 12.2200000 9.5040000 9.5040000
|
||||||
|
184 184 1 0.0000000 14.9350000 9.5040000 6.7890000
|
||||||
|
185 185 1 0.0000000 10.8620000 5.4310000 10.8620000
|
||||||
|
186 186 1 0.0000000 10.8620000 8.1460000 13.5780000
|
||||||
|
187 187 1 0.0000000 13.5780000 8.1460000 10.8620000
|
||||||
|
188 188 1 0.0000000 13.5780000 5.4310000 13.5780000
|
||||||
|
189 189 1 0.0000000 14.9350000 6.7890000 14.9350000
|
||||||
|
190 190 1 0.0000000 12.2200000 6.7890000 12.2200000
|
||||||
|
191 191 1 0.0000000 12.2200000 9.5040000 14.9350000
|
||||||
|
192 192 1 0.0000000 14.9350000 9.5040000 12.2200000
|
||||||
|
193 193 1 0.0000000 10.8620000 10.8620000 0.0000000
|
||||||
|
194 194 1 0.0000000 10.8620000 13.5780000 2.7160000
|
||||||
|
195 195 1 0.0000000 13.5780000 13.5780000 0.0000000
|
||||||
|
196 196 1 0.0000000 13.5780000 10.8620000 2.7160000
|
||||||
|
197 197 1 0.0000000 14.9350000 12.2200000 4.0730000
|
||||||
|
198 198 1 0.0000000 12.2200000 12.2200000 1.3580000
|
||||||
|
199 199 1 0.0000000 12.2200000 14.9350000 4.0730000
|
||||||
|
200 200 1 0.0000000 14.9350000 14.9350000 1.3580000
|
||||||
|
201 201 1 0.0000000 10.8620000 10.8620000 5.4310000
|
||||||
|
202 202 1 0.0000000 10.8620000 13.5780000 8.1460000
|
||||||
|
203 203 1 0.0000000 13.5780000 13.5780000 5.4310000
|
||||||
|
204 204 1 0.0000000 13.5780000 10.8620000 8.1460000
|
||||||
|
205 205 1 0.0000000 14.9350000 12.2200000 9.5040000
|
||||||
|
206 206 1 0.0000000 12.2200000 12.2200000 6.7890000
|
||||||
|
207 207 1 0.0000000 12.2200000 14.9350000 9.5040000
|
||||||
|
208 208 1 0.0000000 14.9350000 14.9350000 6.7890000
|
||||||
|
209 209 1 0.0000000 10.8620000 10.8620000 10.8620000
|
||||||
|
210 210 1 0.0000000 10.8620000 13.5780000 13.5780000
|
||||||
|
211 211 1 0.0000000 13.5780000 13.5780000 10.8620000
|
||||||
|
212 212 1 0.0000000 13.5780000 10.8620000 13.5780000
|
||||||
|
213 213 1 0.0000000 14.9350000 12.2200000 14.9350000
|
||||||
|
214 214 1 0.0000000 12.2200000 12.2200000 12.2200000
|
||||||
|
215 215 1 0.0000000 12.2200000 14.9350000 14.9350000
|
||||||
|
216 216 1 0.0000000 14.9350000 14.9350000 12.2200000
|
||||||
|
|
||||||
534
examples/USER/phonon/third_order_command/lmp_bank/silicon_512.lmp
Executable file
534
examples/USER/phonon/third_order_command/lmp_bank/silicon_512.lmp
Executable file
@ -0,0 +1,534 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
512 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 21.724000 xlo xhi
|
||||||
|
0.0000000 21.724000 ylo yhi
|
||||||
|
0.0000000 21.724000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 0.0000000 2.7150000 2.7150000
|
||||||
|
3 3 1 0.0000000 2.7150000 2.7150000 0.0000000
|
||||||
|
4 4 1 0.0000000 2.7150000 0.0000000 2.7150000
|
||||||
|
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
|
||||||
|
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
|
||||||
|
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
|
||||||
|
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
|
||||||
|
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
|
||||||
|
10 10 1 0.0000000 0.0000000 2.7150000 8.1460000
|
||||||
|
11 11 1 0.0000000 2.7150000 2.7150000 5.4310000
|
||||||
|
12 12 1 0.0000000 2.7150000 0.0000000 8.1460000
|
||||||
|
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
|
||||||
|
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
|
||||||
|
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
|
||||||
|
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
|
||||||
|
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
|
||||||
|
18 18 1 0.0000000 0.0000000 2.7150000 13.5770000
|
||||||
|
19 19 1 0.0000000 2.7150000 2.7150000 10.8620000
|
||||||
|
20 20 1 0.0000000 2.7150000 0.0000000 13.5770000
|
||||||
|
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
|
||||||
|
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
|
||||||
|
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
|
||||||
|
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
|
||||||
|
25 25 1 0.0000000 0.0000000 0.0000000 16.2930000
|
||||||
|
26 26 1 0.0000000 0.0000000 2.7150000 19.0080000
|
||||||
|
27 27 1 0.0000000 2.7150000 2.7150000 16.2930000
|
||||||
|
28 28 1 0.0000000 2.7150000 0.0000000 19.0080000
|
||||||
|
29 29 1 0.0000000 4.0730000 1.3580000 20.3660000
|
||||||
|
30 30 1 0.0000000 1.3580000 1.3580000 17.6510000
|
||||||
|
31 31 1 0.0000000 1.3580000 4.0730000 20.3660000
|
||||||
|
32 32 1 0.0000000 4.0730000 4.0730000 17.6510000
|
||||||
|
33 33 1 0.0000000 0.0000000 5.4310000 0.0000000
|
||||||
|
34 34 1 0.0000000 0.0000000 8.1460000 2.7150000
|
||||||
|
35 35 1 0.0000000 2.7150000 8.1460000 0.0000000
|
||||||
|
36 36 1 0.0000000 2.7150000 5.4310000 2.7150000
|
||||||
|
37 37 1 0.0000000 4.0730000 6.7890000 4.0730000
|
||||||
|
38 38 1 0.0000000 1.3580000 6.7890000 1.3580000
|
||||||
|
39 39 1 0.0000000 1.3580000 9.5040000 4.0730000
|
||||||
|
40 40 1 0.0000000 4.0730000 9.5040000 1.3580000
|
||||||
|
41 41 1 0.0000000 0.0000000 5.4310000 5.4310000
|
||||||
|
42 42 1 0.0000000 0.0000000 8.1460000 8.1460000
|
||||||
|
43 43 1 0.0000000 2.7150000 8.1460000 5.4310000
|
||||||
|
44 44 1 0.0000000 2.7150000 5.4310000 8.1460000
|
||||||
|
45 45 1 0.0000000 4.0730000 6.7890000 9.5040000
|
||||||
|
46 46 1 0.0000000 1.3580000 6.7890000 6.7890000
|
||||||
|
47 47 1 0.0000000 1.3580000 9.5040000 9.5040000
|
||||||
|
48 48 1 0.0000000 4.0730000 9.5040000 6.7890000
|
||||||
|
49 49 1 0.0000000 0.0000000 5.4310000 10.8620000
|
||||||
|
50 50 1 0.0000000 0.0000000 8.1460000 13.5770000
|
||||||
|
51 51 1 0.0000000 2.7150000 8.1460000 10.8620000
|
||||||
|
52 52 1 0.0000000 2.7150000 5.4310000 13.5770000
|
||||||
|
53 53 1 0.0000000 4.0730000 6.7890000 14.9350000
|
||||||
|
54 54 1 0.0000000 1.3580000 6.7890000 12.2200000
|
||||||
|
55 55 1 0.0000000 1.3580000 9.5040000 14.9350000
|
||||||
|
56 56 1 0.0000000 4.0730000 9.5040000 12.2200000
|
||||||
|
57 57 1 0.0000000 0.0000000 5.4310000 16.2930000
|
||||||
|
58 58 1 0.0000000 0.0000000 8.1460000 19.0080000
|
||||||
|
59 59 1 0.0000000 2.7150000 8.1460000 16.2930000
|
||||||
|
60 60 1 0.0000000 2.7150000 5.4310000 19.0080000
|
||||||
|
61 61 1 0.0000000 4.0730000 6.7890000 20.3660000
|
||||||
|
62 62 1 0.0000000 1.3580000 6.7890000 17.6510000
|
||||||
|
63 63 1 0.0000000 1.3580000 9.5040000 20.3660000
|
||||||
|
64 64 1 0.0000000 4.0730000 9.5040000 17.6510000
|
||||||
|
65 65 1 0.0000000 0.0000000 10.8620000 0.0000000
|
||||||
|
66 66 1 0.0000000 0.0000000 13.5770000 2.7150000
|
||||||
|
67 67 1 0.0000000 2.7150000 13.5770000 0.0000000
|
||||||
|
68 68 1 0.0000000 2.7150000 10.8620000 2.7150000
|
||||||
|
69 69 1 0.0000000 4.0730000 12.2200000 4.0730000
|
||||||
|
70 70 1 0.0000000 1.3580000 12.2200000 1.3580000
|
||||||
|
71 71 1 0.0000000 1.3580000 14.9350000 4.0730000
|
||||||
|
72 72 1 0.0000000 4.0730000 14.9350000 1.3580000
|
||||||
|
73 73 1 0.0000000 0.0000000 10.8620000 5.4310000
|
||||||
|
74 74 1 0.0000000 0.0000000 13.5770000 8.1460000
|
||||||
|
75 75 1 0.0000000 2.7150000 13.5770000 5.4310000
|
||||||
|
76 76 1 0.0000000 2.7150000 10.8620000 8.1460000
|
||||||
|
77 77 1 0.0000000 4.0730000 12.2200000 9.5040000
|
||||||
|
78 78 1 0.0000000 1.3580000 12.2200000 6.7890000
|
||||||
|
79 79 1 0.0000000 1.3580000 14.9350000 9.5040000
|
||||||
|
80 80 1 0.0000000 4.0730000 14.9350000 6.7890000
|
||||||
|
81 81 1 0.0000000 0.0000000 10.8620000 10.8620000
|
||||||
|
82 82 1 0.0000000 0.0000000 13.5770000 13.5770000
|
||||||
|
83 83 1 0.0000000 2.7150000 13.5770000 10.8620000
|
||||||
|
84 84 1 0.0000000 2.7150000 10.8620000 13.5770000
|
||||||
|
85 85 1 0.0000000 4.0730000 12.2200000 14.9350000
|
||||||
|
86 86 1 0.0000000 1.3580000 12.2200000 12.2200000
|
||||||
|
87 87 1 0.0000000 1.3580000 14.9350000 14.9350000
|
||||||
|
88 88 1 0.0000000 4.0730000 14.9350000 12.2200000
|
||||||
|
89 89 1 0.0000000 0.0000000 10.8620000 16.2930000
|
||||||
|
90 90 1 0.0000000 0.0000000 13.5770000 19.0080000
|
||||||
|
91 91 1 0.0000000 2.7150000 13.5770000 16.2930000
|
||||||
|
92 92 1 0.0000000 2.7150000 10.8620000 19.0080000
|
||||||
|
93 93 1 0.0000000 4.0730000 12.2200000 20.3660000
|
||||||
|
94 94 1 0.0000000 1.3580000 12.2200000 17.6510000
|
||||||
|
95 95 1 0.0000000 1.3580000 14.9350000 20.3660000
|
||||||
|
96 96 1 0.0000000 4.0730000 14.9350000 17.6510000
|
||||||
|
97 97 1 0.0000000 0.0000000 16.2930000 0.0000000
|
||||||
|
98 98 1 0.0000000 0.0000000 19.0080000 2.7150000
|
||||||
|
99 99 1 0.0000000 2.7150000 19.0080000 0.0000000
|
||||||
|
100 100 1 0.0000000 2.7150000 16.2930000 2.7150000
|
||||||
|
101 101 1 0.0000000 4.0730000 17.6510000 4.0730000
|
||||||
|
102 102 1 0.0000000 1.3580000 17.6510000 1.3580000
|
||||||
|
103 103 1 0.0000000 1.3580000 20.3660000 4.0730000
|
||||||
|
104 104 1 0.0000000 4.0730000 20.3660000 1.3580000
|
||||||
|
105 105 1 0.0000000 0.0000000 16.2930000 5.4310000
|
||||||
|
106 106 1 0.0000000 0.0000000 19.0080000 8.1460000
|
||||||
|
107 107 1 0.0000000 2.7150000 19.0080000 5.4310000
|
||||||
|
108 108 1 0.0000000 2.7150000 16.2930000 8.1460000
|
||||||
|
109 109 1 0.0000000 4.0730000 17.6510000 9.5040000
|
||||||
|
110 110 1 0.0000000 1.3580000 17.6510000 6.7890000
|
||||||
|
111 111 1 0.0000000 1.3580000 20.3660000 9.5040000
|
||||||
|
112 112 1 0.0000000 4.0730000 20.3660000 6.7890000
|
||||||
|
113 113 1 0.0000000 0.0000000 16.2930000 10.8620000
|
||||||
|
114 114 1 0.0000000 0.0000000 19.0080000 13.5770000
|
||||||
|
115 115 1 0.0000000 2.7150000 19.0080000 10.8620000
|
||||||
|
116 116 1 0.0000000 2.7150000 16.2930000 13.5770000
|
||||||
|
117 117 1 0.0000000 4.0730000 17.6510000 14.9350000
|
||||||
|
118 118 1 0.0000000 1.3580000 17.6510000 12.2200000
|
||||||
|
119 119 1 0.0000000 1.3580000 20.3660000 14.9350000
|
||||||
|
120 120 1 0.0000000 4.0730000 20.3660000 12.2200000
|
||||||
|
121 121 1 0.0000000 0.0000000 16.2930000 16.2930000
|
||||||
|
122 122 1 0.0000000 0.0000000 19.0080000 19.0080000
|
||||||
|
123 123 1 0.0000000 2.7150000 19.0080000 16.2930000
|
||||||
|
124 124 1 0.0000000 2.7150000 16.2930000 19.0080000
|
||||||
|
125 125 1 0.0000000 4.0730000 17.6510000 20.3660000
|
||||||
|
126 126 1 0.0000000 1.3580000 17.6510000 17.6510000
|
||||||
|
127 127 1 0.0000000 1.3580000 20.3660000 20.3660000
|
||||||
|
128 128 1 0.0000000 4.0730000 20.3660000 17.6510000
|
||||||
|
129 129 1 0.0000000 5.4310000 0.0000000 0.0000000
|
||||||
|
130 130 1 0.0000000 5.4310000 2.7150000 2.7150000
|
||||||
|
131 131 1 0.0000000 8.1460000 2.7150000 0.0000000
|
||||||
|
132 132 1 0.0000000 8.1460000 0.0000000 2.7150000
|
||||||
|
133 133 1 0.0000000 9.5040000 1.3580000 4.0730000
|
||||||
|
134 134 1 0.0000000 6.7890000 1.3580000 1.3580000
|
||||||
|
135 135 1 0.0000000 6.7890000 4.0730000 4.0730000
|
||||||
|
136 136 1 0.0000000 9.5040000 4.0730000 1.3580000
|
||||||
|
137 137 1 0.0000000 5.4310000 0.0000000 5.4310000
|
||||||
|
138 138 1 0.0000000 5.4310000 2.7150000 8.1460000
|
||||||
|
139 139 1 0.0000000 8.1460000 2.7150000 5.4310000
|
||||||
|
140 140 1 0.0000000 8.1460000 0.0000000 8.1460000
|
||||||
|
141 141 1 0.0000000 9.5040000 1.3580000 9.5040000
|
||||||
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402 402 1 0.0000000 16.2930000 2.7150000 13.5770000
|
||||||
|
403 403 1 0.0000000 19.0080000 2.7150000 10.8620000
|
||||||
|
404 404 1 0.0000000 19.0080000 0.0000000 13.5770000
|
||||||
|
405 405 1 0.0000000 20.3660000 1.3580000 14.9350000
|
||||||
|
406 406 1 0.0000000 17.6510000 1.3580000 12.2200000
|
||||||
|
407 407 1 0.0000000 17.6510000 4.0730000 14.9350000
|
||||||
|
408 408 1 0.0000000 20.3660000 4.0730000 12.2200000
|
||||||
|
409 409 1 0.0000000 16.2930000 0.0000000 16.2930000
|
||||||
|
410 410 1 0.0000000 16.2930000 2.7150000 19.0080000
|
||||||
|
411 411 1 0.0000000 19.0080000 2.7150000 16.2930000
|
||||||
|
412 412 1 0.0000000 19.0080000 0.0000000 19.0080000
|
||||||
|
413 413 1 0.0000000 20.3660000 1.3580000 20.3660000
|
||||||
|
414 414 1 0.0000000 17.6510000 1.3580000 17.6510000
|
||||||
|
415 415 1 0.0000000 17.6510000 4.0730000 20.3660000
|
||||||
|
416 416 1 0.0000000 20.3660000 4.0730000 17.6510000
|
||||||
|
417 417 1 0.0000000 16.2930000 5.4310000 0.0000000
|
||||||
|
418 418 1 0.0000000 16.2930000 8.1460000 2.7150000
|
||||||
|
419 419 1 0.0000000 19.0080000 8.1460000 0.0000000
|
||||||
|
420 420 1 0.0000000 19.0080000 5.4310000 2.7150000
|
||||||
|
421 421 1 0.0000000 20.3660000 6.7890000 4.0730000
|
||||||
|
422 422 1 0.0000000 17.6510000 6.7890000 1.3580000
|
||||||
|
423 423 1 0.0000000 17.6510000 9.5040000 4.0730000
|
||||||
|
424 424 1 0.0000000 20.3660000 9.5040000 1.3580000
|
||||||
|
425 425 1 0.0000000 16.2930000 5.4310000 5.4310000
|
||||||
|
426 426 1 0.0000000 16.2930000 8.1460000 8.1460000
|
||||||
|
427 427 1 0.0000000 19.0080000 8.1460000 5.4310000
|
||||||
|
428 428 1 0.0000000 19.0080000 5.4310000 8.1460000
|
||||||
|
429 429 1 0.0000000 20.3660000 6.7890000 9.5040000
|
||||||
|
430 430 1 0.0000000 17.6510000 6.7890000 6.7890000
|
||||||
|
431 431 1 0.0000000 17.6510000 9.5040000 9.5040000
|
||||||
|
432 432 1 0.0000000 20.3660000 9.5040000 6.7890000
|
||||||
|
433 433 1 0.0000000 16.2930000 5.4310000 10.8620000
|
||||||
|
434 434 1 0.0000000 16.2930000 8.1460000 13.5770000
|
||||||
|
435 435 1 0.0000000 19.0080000 8.1460000 10.8620000
|
||||||
|
436 436 1 0.0000000 19.0080000 5.4310000 13.5770000
|
||||||
|
437 437 1 0.0000000 20.3660000 6.7890000 14.9350000
|
||||||
|
438 438 1 0.0000000 17.6510000 6.7890000 12.2200000
|
||||||
|
439 439 1 0.0000000 17.6510000 9.5040000 14.9350000
|
||||||
|
440 440 1 0.0000000 20.3660000 9.5040000 12.2200000
|
||||||
|
441 441 1 0.0000000 16.2930000 5.4310000 16.2930000
|
||||||
|
442 442 1 0.0000000 16.2930000 8.1460000 19.0080000
|
||||||
|
443 443 1 0.0000000 19.0080000 8.1460000 16.2930000
|
||||||
|
444 444 1 0.0000000 19.0080000 5.4310000 19.0080000
|
||||||
|
445 445 1 0.0000000 20.3660000 6.7890000 20.3660000
|
||||||
|
446 446 1 0.0000000 17.6510000 6.7890000 17.6510000
|
||||||
|
447 447 1 0.0000000 17.6510000 9.5040000 20.3660000
|
||||||
|
448 448 1 0.0000000 20.3660000 9.5040000 17.6510000
|
||||||
|
449 449 1 0.0000000 16.2930000 10.8620000 0.0000000
|
||||||
|
450 450 1 0.0000000 16.2930000 13.5770000 2.7150000
|
||||||
|
451 451 1 0.0000000 19.0080000 13.5770000 0.0000000
|
||||||
|
452 452 1 0.0000000 19.0080000 10.8620000 2.7150000
|
||||||
|
453 453 1 0.0000000 20.3660000 12.2200000 4.0730000
|
||||||
|
454 454 1 0.0000000 17.6510000 12.2200000 1.3580000
|
||||||
|
455 455 1 0.0000000 17.6510000 14.9350000 4.0730000
|
||||||
|
456 456 1 0.0000000 20.3660000 14.9350000 1.3580000
|
||||||
|
457 457 1 0.0000000 16.2930000 10.8620000 5.4310000
|
||||||
|
458 458 1 0.0000000 16.2930000 13.5770000 8.1460000
|
||||||
|
459 459 1 0.0000000 19.0080000 13.5770000 5.4310000
|
||||||
|
460 460 1 0.0000000 19.0080000 10.8620000 8.1460000
|
||||||
|
461 461 1 0.0000000 20.3660000 12.2200000 9.5040000
|
||||||
|
462 462 1 0.0000000 17.6510000 12.2200000 6.7890000
|
||||||
|
463 463 1 0.0000000 17.6510000 14.9350000 9.5040000
|
||||||
|
464 464 1 0.0000000 20.3660000 14.9350000 6.7890000
|
||||||
|
465 465 1 0.0000000 16.2930000 10.8620000 10.8620000
|
||||||
|
466 466 1 0.0000000 16.2930000 13.5770000 13.5770000
|
||||||
|
467 467 1 0.0000000 19.0080000 13.5770000 10.8620000
|
||||||
|
468 468 1 0.0000000 19.0080000 10.8620000 13.5770000
|
||||||
|
469 469 1 0.0000000 20.3660000 12.2200000 14.9350000
|
||||||
|
470 470 1 0.0000000 17.6510000 12.2200000 12.2200000
|
||||||
|
471 471 1 0.0000000 17.6510000 14.9350000 14.9350000
|
||||||
|
472 472 1 0.0000000 20.3660000 14.9350000 12.2200000
|
||||||
|
473 473 1 0.0000000 16.2930000 10.8620000 16.2930000
|
||||||
|
474 474 1 0.0000000 16.2930000 13.5770000 19.0080000
|
||||||
|
475 475 1 0.0000000 19.0080000 13.5770000 16.2930000
|
||||||
|
476 476 1 0.0000000 19.0080000 10.8620000 19.0080000
|
||||||
|
477 477 1 0.0000000 20.3660000 12.2200000 20.3660000
|
||||||
|
478 478 1 0.0000000 17.6510000 12.2200000 17.6510000
|
||||||
|
479 479 1 0.0000000 17.6510000 14.9350000 20.3660000
|
||||||
|
480 480 1 0.0000000 20.3660000 14.9350000 17.6510000
|
||||||
|
481 481 1 0.0000000 16.2930000 16.2930000 0.0000000
|
||||||
|
482 482 1 0.0000000 16.2930000 19.0080000 2.7150000
|
||||||
|
483 483 1 0.0000000 19.0080000 19.0080000 0.0000000
|
||||||
|
484 484 1 0.0000000 19.0080000 16.2930000 2.7150000
|
||||||
|
485 485 1 0.0000000 20.3660000 17.6510000 4.0730000
|
||||||
|
486 486 1 0.0000000 17.6510000 17.6510000 1.3580000
|
||||||
|
487 487 1 0.0000000 17.6510000 20.3660000 4.0730000
|
||||||
|
488 488 1 0.0000000 20.3660000 20.3660000 1.3580000
|
||||||
|
489 489 1 0.0000000 16.2930000 16.2930000 5.4310000
|
||||||
|
490 490 1 0.0000000 16.2930000 19.0080000 8.1460000
|
||||||
|
491 491 1 0.0000000 19.0080000 19.0080000 5.4310000
|
||||||
|
492 492 1 0.0000000 19.0080000 16.2930000 8.1460000
|
||||||
|
493 493 1 0.0000000 20.3660000 17.6510000 9.5040000
|
||||||
|
494 494 1 0.0000000 17.6510000 17.6510000 6.7890000
|
||||||
|
495 495 1 0.0000000 17.6510000 20.3660000 9.5040000
|
||||||
|
496 496 1 0.0000000 20.3660000 20.3660000 6.7890000
|
||||||
|
497 497 1 0.0000000 16.2930000 16.2930000 10.8620000
|
||||||
|
498 498 1 0.0000000 16.2930000 19.0080000 13.5770000
|
||||||
|
499 499 1 0.0000000 19.0080000 19.0080000 10.8620000
|
||||||
|
500 500 1 0.0000000 19.0080000 16.2930000 13.5770000
|
||||||
|
501 501 1 0.0000000 20.3660000 17.6510000 14.9350000
|
||||||
|
502 502 1 0.0000000 17.6510000 17.6510000 12.2200000
|
||||||
|
503 503 1 0.0000000 17.6510000 20.3660000 14.9350000
|
||||||
|
504 504 1 0.0000000 20.3660000 20.3660000 12.2200000
|
||||||
|
505 505 1 0.0000000 16.2930000 16.2930000 16.2930000
|
||||||
|
506 506 1 0.0000000 16.2930000 19.0080000 19.0080000
|
||||||
|
507 507 1 0.0000000 19.0080000 19.0080000 16.2930000
|
||||||
|
508 508 1 0.0000000 19.0080000 16.2930000 19.0080000
|
||||||
|
509 509 1 0.0000000 20.3660000 17.6510000 20.3660000
|
||||||
|
510 510 1 0.0000000 17.6510000 17.6510000 17.6510000
|
||||||
|
511 511 1 0.0000000 17.6510000 20.3660000 20.3660000
|
||||||
|
512 512 1 0.0000000 20.3660000 20.3660000 17.6510000
|
||||||
|
|
||||||
29
examples/USER/phonon/third_order_command/lmp_bank/silicon_8.lmp
Executable file
29
examples/USER/phonon/third_order_command/lmp_bank/silicon_8.lmp
Executable file
@ -0,0 +1,29 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
8 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 5.4310000 xlo xhi
|
||||||
|
0.0000000 5.4310000 ylo yhi
|
||||||
|
0.0000000 5.4310000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
|
||||||
|
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
|
||||||
|
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
|
||||||
|
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
|
||||||
|
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
|
||||||
|
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
|
||||||
|
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500
|
||||||
58
examples/USER/phonon/third_order_command/results/out.silicon
Executable file
58
examples/USER/phonon/third_order_command/results/out.silicon
Executable file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (16 Jul 2018)
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (5.431 5.431 5.431)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
8 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 4
|
||||||
|
ghost atom cutoff = 4
|
||||||
|
binsize = 2, bins = 3 3 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair tersoff, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Calculating Anharmonic Dynamical Matrix...
|
||||||
|
Third Order calculation took 0.043923 seconds
|
||||||
|
Finished Calculating Third Order Tensor
|
||||||
|
Loop time of 1.22619e+06 on 4 procs for 0 steps with 8 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.013707 | 0.016582 | 0.019588 | 2.2 | 0.00
|
||||||
|
Bond | 8.1341e-05 | 8.7207e-05 | 9.3228e-05 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.019285 | 0.022435 | 0.025684 | 2.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.226e+06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 56 ave 56 max 56 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 32 ave 32 max 32 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 128
|
||||||
|
Ave neighs/atom = 16
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
4608
examples/USER/phonon/third_order_command/results/third_order
Executable file
4608
examples/USER/phonon/third_order_command/results/third_order
Executable file
File diff suppressed because it is too large
Load Diff
29
examples/USER/phonon/third_order_command/silicon_input_file.lmp
Executable file
29
examples/USER/phonon/third_order_command/silicon_input_file.lmp
Executable file
@ -0,0 +1,29 @@
|
|||||||
|
LAMMPS description
|
||||||
|
|
||||||
|
8 atoms
|
||||||
|
0 bonds
|
||||||
|
0 angles
|
||||||
|
0 dihedrals
|
||||||
|
0 impropers
|
||||||
|
|
||||||
|
1 atom types
|
||||||
|
0 bond types
|
||||||
|
0 angle types
|
||||||
|
0 dihedral types
|
||||||
|
0 improper types
|
||||||
|
|
||||||
|
|
||||||
|
0.0000000 5.4310000 xlo xhi
|
||||||
|
0.0000000 5.4310000 ylo yhi
|
||||||
|
0.0000000 5.4310000 zlo zhi
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||||
|
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
|
||||||
|
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
|
||||||
|
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
|
||||||
|
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
|
||||||
|
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
|
||||||
|
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
|
||||||
|
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500
|
||||||
@ -244,7 +244,8 @@ void DynamicalMatrix::calculateMatrix()
|
|||||||
{
|
{
|
||||||
int local_idx; // local index
|
int local_idx; // local index
|
||||||
int local_jdx; // second local index
|
int local_jdx; // second local index
|
||||||
int natoms = atom->natoms;
|
int nlocal = atom->nlocal;
|
||||||
|
bigint natoms = atom->natoms;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
double imass; // dynamical matrix element
|
double imass; // dynamical matrix element
|
||||||
@ -262,13 +263,14 @@ void DynamicalMatrix::calculateMatrix()
|
|||||||
|
|
||||||
for (int i=1; i<=natoms; i++){
|
for (int i=1; i<=natoms; i++){
|
||||||
local_idx = atom->map(i);
|
local_idx = atom->map(i);
|
||||||
|
//if (screen) fprintf(screen, "local idx = %i on proc %i with %i local\n",local_idx, comm->me, nlocal);
|
||||||
if (local_idx >= 0){
|
if (local_idx >= 0){
|
||||||
for (int alpha=0; alpha<3; alpha++){
|
for (int alpha=0; alpha<3; alpha++){
|
||||||
displace_atom(local_idx, alpha, 1);
|
displace_atom(local_idx, alpha, 1);
|
||||||
energy_force(0);
|
energy_force(0);
|
||||||
for (int j=1; j<=natoms; j++){
|
for (int j=1; j<=natoms; j++){
|
||||||
local_jdx = atom->map(j);
|
local_jdx = atom->map(j);
|
||||||
if (local_jdx >= 0){
|
if (local_jdx >= 0 && local_idx < nlocal){
|
||||||
for (int beta=0; beta<3; beta++){
|
for (int beta=0; beta<3; beta++){
|
||||||
dynmat[(i-1)*3+alpha][(j-1)*3+beta] += -f[j-1][beta];
|
dynmat[(i-1)*3+alpha][(j-1)*3+beta] += -f[j-1][beta];
|
||||||
}
|
}
|
||||||
@ -278,7 +280,7 @@ void DynamicalMatrix::calculateMatrix()
|
|||||||
energy_force(0);
|
energy_force(0);
|
||||||
for (int j=1; j<=natoms; j++){
|
for (int j=1; j<=natoms; j++){
|
||||||
local_jdx = atom->map(j);
|
local_jdx = atom->map(j);
|
||||||
if (local_jdx >= 0){
|
if (local_jdx >= 0 && local_idx < nlocal){
|
||||||
for (int beta=0; beta<3; beta++){
|
for (int beta=0; beta<3; beta++){
|
||||||
if (atom->rmass_flag == 1)
|
if (atom->rmass_flag == 1)
|
||||||
imass = sqrt(m[i] * m[j]);
|
imass = sqrt(m[i] * m[j]);
|
||||||
@ -365,31 +367,31 @@ void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
|
|||||||
|
|
||||||
void DynamicalMatrix::energy_force(int resetflag)
|
void DynamicalMatrix::energy_force(int resetflag)
|
||||||
{
|
{
|
||||||
// check for reneighboring
|
//// check for reneighboring
|
||||||
// always communicate since atoms move
|
//// always communicate since atoms move
|
||||||
int nflag = neighbor->check_distance();
|
//int nflag = neighbor->check_distance();
|
||||||
|
//
|
||||||
if (nflag == 0) {
|
//if (nflag == 0) {
|
||||||
//if (comm->me == 0 && screen) fprintf(screen,"b\n");
|
////if (comm->me == 0 && screen) fprintf(screen,"b\n");
|
||||||
timer->stamp();
|
// timer->stamp();
|
||||||
comm->forward_comm();
|
// comm->forward_comm();
|
||||||
timer->stamp(Timer::COMM);
|
// timer->stamp(Timer::COMM);
|
||||||
//if (comm->me == 0 && screen) fprintf(screen,"c\n");
|
////if (comm->me == 0 && screen) fprintf(screen,"c\n");
|
||||||
} else {
|
//} else {
|
||||||
if (triclinic) domain->x2lamda(atom->nlocal);
|
// if (triclinic) domain->x2lamda(atom->nlocal);
|
||||||
domain->pbc();
|
// domain->pbc();
|
||||||
if (domain->box_change) {
|
// if (domain->box_change) {
|
||||||
domain->reset_box();
|
// domain->reset_box();
|
||||||
comm->setup();
|
// comm->setup();
|
||||||
if (neighbor->style) neighbor->setup_bins();
|
// if (neighbor->style) neighbor->setup_bins();
|
||||||
}
|
// }
|
||||||
timer->stamp();
|
// timer->stamp();
|
||||||
comm->borders();
|
// comm->borders();
|
||||||
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
|
// if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
|
||||||
timer->stamp(Timer::COMM);
|
// timer->stamp(Timer::COMM);
|
||||||
neighbor->build(1);
|
// neighbor->build(1);
|
||||||
timer->stamp(Timer::NEIGH);
|
// timer->stamp(Timer::NEIGH);
|
||||||
}
|
//}
|
||||||
force_clear();
|
force_clear();
|
||||||
|
|
||||||
if (pair_compute_flag) {
|
if (pair_compute_flag) {
|
||||||
|
|||||||
Reference in New Issue
Block a user