Loading examples/USER/phonon/dynamical_matrix_command/Manual.md 0 → 100755 +48 −0 Original line number Diff line number Diff line # dynamical_matrix command ## Syntax ``` dynamical_matrix group-ID style args keyword value ... ``` * group-ID = ID of group of atoms to displace * style = *regular* or *eskm* ``` *regular* args = gamma gamma = finite difference displacement length *eskm* 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 = *yes* or *no* or *gzip* ``` ## Examples ``` dynamical_matrix 1 regular 0.000001 dynamical_matrix 1 eskm 0.000001 dynamical_matrix 3 regular 0.00004 file dynmat.dat dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes ``` ## Description Calculate the dynamical matrix of the selected group. ## Restrictions None ## Related commands None ## Default The option defaults are file = "dynmat.dyn", binary = no examples/USER/phonon/dynamical_matrix_command/README.md 0 → 100755 +21 −0 Original line number Diff line number Diff line # LAMMPS LATTICE DYNAMICS COMMANDS ## DYNAMICAL MATRIX CALCULATOR This directory contains the ingredients to calculate a dynamical matrix. Example: ``` NP=4 #number of processors mpirun -np $NP lmp_mpi < in.silicon > out.silicon ``` To test out a different silicon example: ``` LMP_FILE=amorphous_silicon.lmp cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp NP=4 #number of processors mpirun -np $NP lmp_mpi < in.silicon > out.silicon ``` ## Requires: MANYBODY and MOLECULE packages examples/USER/phonon/dynamical_matrix_command/Si.opt.tersoff 0 → 100755 +66 −0 Original line number Diff line number Diff line # 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 examples/USER/phonon/dynamical_matrix_command/ff-silicon.lmp 0 → 100755 +19 −0 Original line number Diff line number Diff line ############################# #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) examples/USER/phonon/dynamical_matrix_command/in.silicon 0 → 100755 +89 −0 Original line number Diff line number Diff line ###############################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 ${run_no}-1 # restart file number ####################################### #Random Seeds and Domain Decomposition# ####################################### variable iseed0 equal 2357 variable iseed1 equal 26488 variable iseed2 equal 10669 processors * * * ########### #Data File# ########### variable inpfile string silicon_input_file.lmp variable resfile string final_restart.${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 ${ff_file} ###################### #Thermodynamic Output# ###################### variable str_basic string 'step time pe temp press' ##################### #Energy Minimization# ##################### if "${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# ################## dynamical_matrix all eskm 0.000001 file dynmat.dat binary no Loading
examples/USER/phonon/dynamical_matrix_command/Manual.md 0 → 100755 +48 −0 Original line number Diff line number Diff line # dynamical_matrix command ## Syntax ``` dynamical_matrix group-ID style args keyword value ... ``` * group-ID = ID of group of atoms to displace * style = *regular* or *eskm* ``` *regular* args = gamma gamma = finite difference displacement length *eskm* 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 = *yes* or *no* or *gzip* ``` ## Examples ``` dynamical_matrix 1 regular 0.000001 dynamical_matrix 1 eskm 0.000001 dynamical_matrix 3 regular 0.00004 file dynmat.dat dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes ``` ## Description Calculate the dynamical matrix of the selected group. ## Restrictions None ## Related commands None ## Default The option defaults are file = "dynmat.dyn", binary = no
examples/USER/phonon/dynamical_matrix_command/README.md 0 → 100755 +21 −0 Original line number Diff line number Diff line # LAMMPS LATTICE DYNAMICS COMMANDS ## DYNAMICAL MATRIX CALCULATOR This directory contains the ingredients to calculate a dynamical matrix. Example: ``` NP=4 #number of processors mpirun -np $NP lmp_mpi < in.silicon > out.silicon ``` To test out a different silicon example: ``` LMP_FILE=amorphous_silicon.lmp cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp NP=4 #number of processors mpirun -np $NP lmp_mpi < in.silicon > out.silicon ``` ## Requires: MANYBODY and MOLECULE packages
examples/USER/phonon/dynamical_matrix_command/Si.opt.tersoff 0 → 100755 +66 −0 Original line number Diff line number Diff line # 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
examples/USER/phonon/dynamical_matrix_command/ff-silicon.lmp 0 → 100755 +19 −0 Original line number Diff line number Diff line ############################# #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)
examples/USER/phonon/dynamical_matrix_command/in.silicon 0 → 100755 +89 −0 Original line number Diff line number Diff line ###############################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 ${run_no}-1 # restart file number ####################################### #Random Seeds and Domain Decomposition# ####################################### variable iseed0 equal 2357 variable iseed1 equal 26488 variable iseed2 equal 10669 processors * * * ########### #Data File# ########### variable inpfile string silicon_input_file.lmp variable resfile string final_restart.${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 ${ff_file} ###################### #Thermodynamic Output# ###################### variable str_basic string 'step time pe temp press' ##################### #Energy Minimization# ##################### if "${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# ################## dynamical_matrix all eskm 0.000001 file dynmat.dat binary no
