Installation of lammps-22Feb18 on macOS High Sierra, 25 February 2018: Twitter@chibafx

In this document, lammps standard packages are employed.

(0) We employ Macbook Pro 15 inch late 2016.

(1) macOS High Sierra 10.13.3 is employed.

(2) You need knowledge of UNIX commands.

If you have never installed Xcode tools:

(3) Xcode.app is needed. It can be obtained from https://developer.apple.com

　　You are required an account of this site.

(4) After installation of Xcode.app, on Terminal.app:

$ xcode-select -install

$ sudo xcodebuild -license

Then gnu tools are enable.

(5a) If you have never used homebrew:

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

(5) On llvm of Apple, OpenMP (is needed for parallel computing) is not available. Then install llvm with openmp by homebrew:

$ brew install llvm

Add the following line

export PATH="/usr/local/opt/llvm/bin:$PATH"

to the end of a file .bash_profile at the home directory.

and

$ source ~/.bash_profile

(6) Installation of gfortran (gfortran is included in GNU Compiler Collection=gcc.):

$ brew install gcc

(7) Installation of OpenMPI (is needed for parallel computing):

$ brew install openmpi

(8) Installation of FFTW (is needed for Fast Fourier Transform):

$ brew install fftw

If you employ Apple BLAS library, skip this step. / BLAS is a library for Matrix calculation.

(9) Installation of OpenBLAS:

$ brew install openblas

Then necessary tools and libraries were installed.

(10) building of lammps-5Nov14

Obtain lammps-22Feb18.tar.gz from http://lammps.sandia.gov/tars/?C=M;O=D

(10.1) extract the tar.gz file and open Terminal.app and change the directory to "lammps-22Feb18/src"

(10.2) build makefiles and source code files as follows (about packages below, see 4. Packages — LAMMPS documentation):

$ make yes-all

Installing package asphere

updating package GPU

updating package USER-OMP

updating package USER-CGDNA

updating package USER-INTEL

Installing package body

Installing package class2

updating package GPU

updating package KOKKOS

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

Installing package colloid

updating package GPU

updating package USER-OMP

Installing package compress

Installing package coreshell

Installing package dipole

updating package USER-MISC

updating package USER-OMP

Installing package gpu

Installing package granular

updating package USER-OMP

Installing package kim

Installing package kokkos

Installing package kspace

updating package CORESHELL

updating package GPU

updating package KOKKOS

updating package OPT

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

updating package USER-INTEL

updating package USER-PHONON

updating package USER-FEP

Installing package latte

Installing package manybody

updating package GPU

updating package KOKKOS

updating package OPT

updating package USER-MISC

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

Installing package mc

Installing package meam

Installing package misc

Installing package molecule

updating package GPU

updating package KOKKOS

updating package USER-MISC

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

updating package USER-FEP

updating package USER-CGDNA

updating package USER-INTEL

Installing package mpiio

Installing package mscg

Installing package opt

Installing package peri

updating package USER-OMP

Installing package poems

Installing package python

Installing package qeq

Installing package reax

Installing package replica

Installing package rigid

updating package USER-OMP

Installing package shock

Installing package snap

updating package KOKKOS

Installing package srd

Installing package voronoi

Installing package user-atc

Installing package user-awpmd

Installing package user-cgdna

Installing package user-cgsdk

updating package GPU

updating package KOKKOS

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

Installing package user-colvars

Installing package user-diffraction

Installing package user-dpd

updating package KOKKOS

Installing package user-drude

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

Installing package user-eff

Installing package user-fep

updating package USER-OMP

Installing package user-h5md

Installing package user-intel

Installing package user-lb

Installing package user-manifold

Installing package user-meamc

Installing package user-meso

Installing package user-mgpt

Installing package user-misc

updating package GPU

updating package USER-OMP

Installing package user-molfile

Installing package user-netcdf

Installing package user-omp

Installing package user-phonon

Installing package user-qmmm

Installing package user-qtb

Installing package user-quip

Installing package user-reaxc

updating package KOKKOS

updating package USER-OMP

updating src/fix_qeq_comb_omp.cpp

updating src/pair_comb_omp.cpp

updating src/fix_qeq_comb_omp.h

updating src/pair_comb_omp.h

Installing package user-smd

Installing package user-smtbq

Installing package user-sph

Installing package user-tally

Installing package user-uef

Installing package user-vtk

(10.3) Uninstalling several packages.

MacBookPro15Late2016:src chibaf$ make no-gpu

Uninstalling package gpu

MacBookPro15Late2016:src chibaf$ make no-kim

Uninstalling package kim

MacBookPro15Late2016:src chibaf$ make no-voronoi

Uninstalling package voronoi

MacBookPro15Late2016:src chibaf$ make no-user-quip

Uninstalling package user-quip

MacBookPro15Late2016:src chibaf$ make no-mscg

Uninstalling package mscg

MacBookPro15Late2016:src chibaf$ make no-latte

Uninstalling package latte

MacBookPro15Late2016:src chibaf$ make no-user-vtk

Uninstalling package user-vtk

Above uninstalling packages are ones with which we couldn't build lammps.

(10.4) making meam library

change directory to "lammps-22Feb18/lib/meam"

$ make -f Makefile.mpi

(10.5) making reax library

change directory to "lammps-22Feb18/lib/reax"

$ make -f Makefile.mpi

(10.5) making reax library

change directory to "lammps-22Feb18/lib/qmmm"

$ make -f Makefile.mpi

(10.6) making colver library

change directory to "lammps-22Feb18/lib/colvers"

$ make -f Makefile.mpi

(10.7) making atc library

change directory to "lammps-22Feb18/lib/atc"

$ make -f Makefile.mpi

(10.8) making linalg library

change directory to "lammps-22Feb18/lib/linalg"

$ make -f Makefile.mpi

(10.8) making awpmd library

change directory to "lammps-22Feb18/lib/awpmd"

$ make -f Makefile.mpi

(10.9) Before building lammps, you need to modify "lammps-22Feb18src/MAKE/Makefile.mpi"

We show only modified lines:

CCFLAGS = -g -O3 -fopenmp

# if you employ OpenBLAS,

LIB = -lgfortran -lgomp -lopenblas

# if you employ Apple BLAS,

LIB = -lgfortran -lgomp -framework Accelerate

#see lammps-22Feb18/lib/kokkos/README

KOKKOS_DEVICES = OpenMP

KOKKOS_ARCH = SKL

#Intel: SNB,HSW,BDW,SKL=Sky Lake, ...

LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64

FFT_INC = -DFFT_FFTW3

FFT_LIB = -lfftw3

If you couldn't link stdc++ library, openblas and gfortran, you might modify as follows. "/usr/local/Cellar/" is a directory for homebrew files. few lines below are examples:

LIB = -L/usr/local/opt/llvm/lib -L/usr/local/Cellar/openblas/0.2.20_1/lib -L/usr/local/Cellar/gcc/7.3.0/lib/gcc/7 -lgfortran -lopenblas -lgomp

We placed this Makefile.mpi (OpenBLAS version) on https://github.com/chibaf/lammps-22Feb18

Then at src,

$ make mpi

If you have four virtual cores:

$ make -j4 mpi

(10.10)

If an error occured as follows:

../compute_smd_tlsph_defgrad.cpp:39:10: fatal error: 'Eigen/Eigen' file not found

#include <Eigen/Eigen>

^~~~~~~~~~~~~

1 error generated.

make[1]: *** [compute_smd_tlsph_defgrad.o] Error 1

make: *** [mpi] Error 2

Please try the follow command at src/:

$ make lib-smd args="-b”

$ make mpi

If build becomes successful, lmp_mpi is generated at src/ as follows:

...........

mpicxx -g -O -L../../lib/qmmm -L../../lib/h5md -L../../lib/colvars -L../../lib/awpmd -L../../lib/atc -L../../lib/reax -L../../lib/poems -L../../lib/meam -L../../lib/linalg -L../../lib/linalg angle.o angle_charmm.o angle_charmm_intel.o angle_charmm_kokkos.o angle_charmm_omp.o angle_class2.o angle_class2_kokkos.o angle_class2_omp.o angle_cosine.o angle_cosine_delta.o angle_cosine_delta_omp.o angle_cosine_omp.o angle_cosine_periodic.o angle_cosine_periodic_omp.o angle_cosine_shift.o angle_cosine_shift_exp.o angle_cosine_shift_exp_omp.o angle_cosine_shift_omp.o angle_cosine_squared.o angle_cosine_squared_omp.o angle_dipole.o angle_dipole_omp.o angle_fourier.o angle_fourier_omp.o angle_fourier_simple.o angle_fourier_simple_omp.o angle_harmonic.o angle_harmonic_intel.o angle_harmonic_kokkos.o angle_harmonic_omp.o angle_hybrid.o angle_quartic.o angle_quartic_omp.o angle_sdk.o angle_sdk_omp.o angle_table.o angle_table_omp.o angle_zero.o atom.o atom_kokkos.o atom_map.o atom_vec.o atom_vec_angle.o atom_vec_angle_kokkos.o atom_vec_atomic.o atom_vec_atomic_kokkos.o atom_vec_body.o atom_vec_bond.o atom_vec_bond_kokkos.o atom_vec_charge.o atom_vec_charge_kokkos.o atom_vec_dipole.o atom_vec_dpd.o atom_vec_dpd_kokkos.o atom_vec_edpd.o atom_vec_electron.o atom_vec_ellipsoid.o atom_vec_full.o atom_vec_full_kokkos.o atom_vec_hybrid.o atom_vec_hybrid_kokkos.o atom_vec_kokkos.o atom_vec_line.o atom_vec_mdpd.o atom_vec_meso.o atom_vec_molecular.o atom_vec_molecular_kokkos.o atom_vec_peri.o atom_vec_smd.o atom_vec_sphere.o atom_vec_tdpd.o atom_vec_template.o atom_vec_tri.o atom_vec_wavepacket.o balance.o body.o body_nparticle.o bond.o bond_class2.o bond_class2_kokkos.o bond_class2_omp.o bond_fene.o bond_fene_expand.o bond_fene_expand_omp.o bond_fene_intel.o bond_fene_kokkos.o bond_fene_omp.o bond_gromos.o bond_gromos_omp.o bond_harmonic.o bond_harmonic_intel.o bond_harmonic_kokkos.o bond_harmonic_omp.o bond_harmonic_shift.o bond_harmonic_shift_cut.o bond_harmonic_shift_cut_omp.o bond_harmonic_shift_omp.o bond_hybrid.o bond_morse.o bond_morse_omp.o bond_nonlinear.o bond_nonlinear_omp.o bond_oxdna2_fene.o bond_oxdna_fene.o bond_quartic.o bond_quartic_omp.o bond_table.o bond_table_omp.o bond_zero.o change_box.o citeme.o colvarproxy_lammps.o comm.o comm_brick.o comm_kokkos.o comm_tiled.o comm_tiled_kokkos.o compute.o compute_ackland_atom.o compute_aggregate_atom.o compute_angle.o compute_angle_local.o compute_angmom_chunk.o compute_basal_atom.o compute_body_local.o compute_bond.o compute_bond_local.o compute_centro_atom.o compute_chunk_atom.o compute_cluster_atom.o compute_cna_atom.o compute_cnp_atom.o compute_com.o compute_com_chunk.o compute_contact_atom.o compute_coord_atom.o compute_damage_atom.o compute_dihedral.o compute_dihedral_local.o compute_dilatation_atom.o compute_dipole_chunk.o compute_displace_atom.o compute_dpd.o compute_dpd_atom.o compute_edpd_temp_atom.o compute_erotate_asphere.o compute_erotate_rigid.o compute_erotate_sphere.o compute_erotate_sphere_atom.o compute_event_displace.o compute_fep.o compute_force_tally.o compute_fragment_atom.o compute_global_atom.o compute_group_group.o compute_gyration.o compute_gyration_chunk.o compute_heat_flux.o compute_heat_flux_tally.o compute_hexorder_atom.o compute_improper.o compute_improper_local.o compute_inertia_chunk.o compute_ke.o compute_ke_atom.o compute_ke_atom_eff.o compute_ke_eff.o compute_ke_rigid.o compute_meso_e_atom.o compute_meso_rho_atom.o compute_meso_t_atom.o compute_msd.o compute_msd_chunk.o compute_msd_nongauss.o compute_omega_chunk.o compute_orientorder_atom.o compute_pair.o compute_pair_local.o compute_pe.o compute_pe_atom.o compute_pe_mol_tally.o compute_pe_tally.o compute_plasticity_atom.o compute_pressure.o compute_pressure_grem.o compute_pressure_uef.o compute_property_atom.o compute_property_chunk.o compute_property_local.o compute_rdf.o compute_reduce.o compute_reduce_region.o compute_rigid_local.o compute_saed.o compute_slice.o compute_smd_contact_radius.o compute_smd_damage.o compute_smd_hourglass_error.o compute_smd_internal_energy.o compute_smd_plastic_strain.o compute_smd_plastic_strain_rate.o compute_smd_rho.o compute_smd_tlsph_defgrad.o compute_smd_tlsph_dt.o compute_smd_tlsph_num_neighs.o compute_smd_tlsph_shape.o compute_smd_tlsph_strain.o compute_smd_tlsph_strain_rate.o compute_smd_tlsph_stress.o compute_smd_triangle_mesh_vertices.o compute_smd_ulsph_effm.o compute_smd_ulsph_num_neighs.o compute_smd_ulsph_strain.o compute_smd_ulsph_strain_rate.o compute_smd_ulsph_stress.o compute_smd_vol.o compute_sna_atom.o compute_snad_atom.o compute_snav_atom.o compute_spec_atom.o compute_stress_atom.o compute_stress_tally.o compute_tdpd_cc_atom.o compute_temp.o compute_temp_asphere.o compute_temp_body.o compute_temp_chunk.o compute_temp_com.o compute_temp_cs.o compute_temp_deform.o compute_temp_deform_eff.o compute_temp_drude.o compute_temp_eff.o compute_temp_kokkos.o compute_temp_partial.o compute_temp_profile.o compute_temp_ramp.o compute_temp_region.o compute_temp_region_eff.o compute_temp_rotate.o compute_temp_sphere.o compute_temp_uef.o compute_ti.o compute_torque_chunk.o compute_vacf.o compute_vcm_chunk.o compute_xrd.o create_atoms.o create_bonds.o create_box.o delete_atoms.o delete_bonds.o dihedral.o dihedral_charmm.o dihedral_charmm_intel.o dihedral_charmm_kokkos.o dihedral_charmm_omp.o dihedral_charmmfsw.o dihedral_class2.o dihedral_class2_kokkos.o dihedral_class2_omp.o dihedral_cosine_shift_exp.o dihedral_cosine_shift_exp_omp.o dihedral_fourier.o dihedral_fourier_omp.o dihedral_harmonic.o dihedral_harmonic_intel.o dihedral_harmonic_omp.o dihedral_helix.o dihedral_helix_omp.o dihedral_hybrid.o dihedral_multi_harmonic.o dihedral_multi_harmonic_omp.o dihedral_nharmonic.o dihedral_nharmonic_omp.o dihedral_opls.o dihedral_opls_intel.o dihedral_opls_kokkos.o dihedral_opls_omp.o dihedral_quadratic.o dihedral_quadratic_omp.o dihedral_spherical.o dihedral_table.o dihedral_table_omp.o dihedral_zero.o displace_atoms.o domain.o domain_kokkos.o domain_omp.o dump.o dump_atom.o dump_atom_gz.o dump_atom_mpiio.o dump_cfg.o dump_cfg_gz.o dump_cfg_mpiio.o dump_cfg_uef.o dump_custom.o dump_custom_gz.o dump_custom_mpiio.o dump_dcd.o dump_h5md.o dump_image.o dump_local.o dump_molfile.o dump_movie.o dump_netcdf.o dump_netcdf_mpiio.o dump_xtc.o dump_xyz.o dump_xyz_gz.o dump_xyz_mpiio.o error.o ewald.o ewald_disp.o ewald_omp.o fft3d.o fft3d_wrap.o finish.o fix.o fix_adapt.o fix_adapt_fep.o fix_addforce.o fix_addtorque.o fix_append_atoms.o fix_atc.o fix_atom_swap.o fix_ave_atom.o fix_ave_chunk.o fix_ave_correlate.o fix_ave_correlate_long.o fix_ave_histo.o fix_ave_histo_weight.o fix_ave_time.o fix_aveforce.o fix_balance.o fix_bond_break.o fix_bond_create.o fix_bond_swap.o fix_box_relax.o fix_cmap.o fix_colvars.o fix_controller.o fix_deform.o fix_deform_kokkos.o fix_deposit.o fix_deprecated.o fix_dpd_energy.o fix_dpd_energy_kokkos.o fix_drag.o fix_drude.o fix_drude_transform.o fix_dt_reset.o fix_edpd_source.o fix_efield.o fix_ehex.o fix_enforce2d.o fix_eos_cv.o fix_eos_table.o fix_eos_table_rx.o fix_eos_table_rx_kokkos.o fix_evaporate.o fix_event.o fix_event_prd.o fix_event_tad.o fix_external.o fix_filter_corotate.o fix_flow_gauss.o fix_freeze.o fix_gcmc.o fix_gld.o fix_gle.o fix_gravity.o fix_gravity_omp.o fix_grem.o fix_group.o fix_halt.o fix_heat.o fix_imd.o fix_indent.o fix_intel.o fix_ipi.o fix_langevin.o fix_langevin_drude.o fix_langevin_eff.o fix_langevin_kokkos.o fix_lb_fluid.o fix_lb_momentum.o fix_lb_pc.o fix_lb_rigid_pc_sphere.o fix_lb_viscous.o fix_lineforce.o fix_manifoldforce.o fix_meso.o fix_meso_stationary.o fix_minimize.o fix_momentum.o fix_momentum_kokkos.o fix_move.o fix_msst.o fix_mvv_dpd.o fix_mvv_edpd.o fix_mvv_tdpd.o fix_neb.o fix_neigh_history.o fix_neigh_history_omp.o fix_nh.o fix_nh_asphere.o fix_nh_asphere_omp.o fix_nh_body.o fix_nh_eff.o fix_nh_intel.o fix_nh_kokkos.o fix_nh_omp.o fix_nh_sphere.o fix_nh_sphere_omp.o fix_nh_uef.o fix_nph.o fix_nph_asphere.o fix_nph_asphere_omp.o fix_nph_body.o fix_nph_eff.o fix_nph_kokkos.o fix_nph_omp.o fix_nph_sphere.o fix_nph_sphere_omp.o fix_nphug.o fix_nphug_omp.o fix_npt.o fix_npt_asphere.o fix_npt_asphere_omp.o fix_npt_body.o fix_npt_eff.o fix_npt_intel.o fix_npt_kokkos.o fix_npt_omp.o fix_npt_sphere.o fix_npt_sphere_omp.o fix_npt_uef.o fix_nve.o fix_nve_asphere.o fix_nve_asphere_intel.o fix_nve_asphere_noforce.o fix_nve_awpmd.o fix_nve_body.o fix_nve_dot.o fix_nve_dotc_langevin.o fix_nve_eff.o fix_nve_intel.o fix_nve_kokkos.o fix_nve_limit.o fix_nve_line.o fix_nve_manifold_rattle.o fix_nve_noforce.o fix_nve_omp.o fix_nve_sphere.o fix_nve_sphere_omp.o fix_nve_tri.o fix_nvk.o fix_nvt.o fix_nvt_asphere.o fix_nvt_asphere_omp.o fix_nvt_body.o fix_nvt_eff.o fix_nvt_intel.o fix_nvt_kokkos.o fix_nvt_manifold_rattle.o fix_nvt_omp.o fix_nvt_sllod.o fix_nvt_sllod_eff.o fix_nvt_sllod_intel.o fix_nvt_sllod_omp.o fix_nvt_sphere.o fix_nvt_sphere_omp.o fix_nvt_uef.o fix_omp.o fix_oneway.o fix_orient_bcc.o fix_orient_fcc.o fix_peri_neigh.o fix_peri_neigh_omp.o fix_phonon.o fix_pimd.o fix_planeforce.o fix_poems.o fix_pour.o fix_press_berendsen.o fix_print.o fix_property_atom.o fix_property_atom_kokkos.o fix_python_invoke.o fix_python_move.o fix_qbmsst.o fix_qeq.o fix_qeq_comb.o fix_qeq_dynamic.o fix_qeq_fire.o fix_qeq_point.o fix_qeq_reax.o fix_qeq_reax_kokkos.o fix_qeq_reax_omp.o fix_qeq_shielded.o fix_qeq_slater.o fix_qmmm.o fix_qtb.o fix_rattle.o fix_read_restart.o fix_reax_bonds.o fix_reaxc.o fix_reaxc_bonds.o fix_reaxc_bonds_kokkos.o fix_reaxc_species.o fix_reaxc_species_kokkos.o fix_recenter.o fix_respa.o fix_restrain.o fix_rhok.o fix_rigid.o fix_rigid_nh.o fix_rigid_nh_omp.o fix_rigid_nh_small.o fix_rigid_nph.o fix_rigid_nph_omp.o fix_rigid_nph_small.o fix_rigid_npt.o fix_rigid_npt_omp.o fix_rigid_npt_small.o fix_rigid_nve.o fix_rigid_nve_omp.o fix_rigid_nve_small.o fix_rigid_nvt.o fix_rigid_nvt_omp.o fix_rigid_nvt_small.o fix_rigid_omp.o fix_rigid_small.o fix_rigid_small_omp.o fix_rx.o fix_rx_kokkos.o fix_saed_vtk.o fix_setforce.o fix_setforce_kokkos.o fix_shake.o fix_shardlow.o fix_shardlow_kokkos.o fix_smd.o fix_smd_adjust_dt.o fix_smd_integrate_tlsph.o fix_smd_integrate_ulsph.o fix_smd_move_triangulated_surface.o fix_smd_setvel.o fix_smd_tlsph_reference_configuration.o fix_smd_wall_surface.o fix_spring.o fix_spring_chunk.o fix_spring_rg.o fix_spring_self.o fix_srd.o fix_srp.o fix_store.o fix_store_force.o fix_store_state.o fix_tdpd_source.o fix_temp_berendsen.o fix_temp_csld.o fix_temp_csvr.o fix_temp_rescale.o fix_temp_rescale_eff.o fix_tfmc.o fix_thermal_conductivity.o fix_ti_spring.o fix_tmd.o fix_ttm.o fix_ttm_mod.o fix_tune_kspace.o fix_vector.o fix_viscosity.o fix_viscous.o fix_wall.o fix_wall_colloid.o fix_wall_ees.o fix_wall_gran.o fix_wall_gran_omp.o fix_wall_gran_region.o fix_wall_harmonic.o fix_wall_lj1043.o fix_wall_lj126.o fix_wall_lj93.o fix_wall_lj93_kokkos.o fix_wall_piston.o fix_wall_reflect.o fix_wall_reflect_kokkos.o fix_wall_region.o fix_wall_region_ees.o fix_wall_srd.o force.o gridcomm.o gridcomm_kokkos.o group.o group_ndx.o image.o imbalance.o imbalance_group.o imbalance_neigh.o imbalance_store.o imbalance_time.o imbalance_var.o improper.o improper_class2.o improper_class2_kokkos.o improper_class2_omp.o improper_cossq.o improper_cossq_omp.o improper_cvff.o improper_cvff_intel.o improper_cvff_omp.o improper_distance.o improper_fourier.o improper_fourier_omp.o improper_harmonic.o improper_harmonic_intel.o improper_harmonic_kokkos.o improper_harmonic_omp.o improper_hybrid.o improper_ring.o improper_ring_omp.o improper_umbrella.o improper_umbrella_omp.o improper_zero.o info.o input.o integrate.o intel_buffers.o irregular.o kokkos.o kspace.o lammps.o lattice.o library.o main.o manifold_cylinder.o manifold_cylinder_dent.o manifold_dumbbell.o manifold_ellipsoid.o manifold_factory.o manifold_gaussian_bump.o manifold_plane.o manifold_plane_wiggle.o manifold_spine.o manifold_thylakoid.o manifold_thylakoid_shared.o manifold_torus.o math_extra.o math_special.o math_special_kokkos.o meam_dens_final.o meam_dens_init.o meam_force.o meam_funcs.o meam_impl.o meam_setup_done.o meam_setup_global.o meam_setup_param.o memory.o mgpt_linalg.o mgpt_readpot.o mgpt_splinetab.o min.o min_cg.o min_fire.o min_hftn.o min_linesearch.o min_quickmin.o min_sd.o minimize.o modify.o modify_kokkos.o molecule.o molfile_interface.o msm.o msm_cg.o msm_cg_omp.o msm_omp.o nbin.o nbin_intel.o nbin_kokkos.o nbin_ssa.o nbin_ssa_kokkos.o nbin_standard.o ndx_group.o neb.o neigh_bond_kokkos.o neigh_list.o neigh_list_kokkos.o neigh_request.o neighbor.o neighbor_kokkos.o npair.o npair_copy.o npair_copy_kokkos.o npair_full_bin.o npair_full_bin_atomonly.o npair_full_bin_atomonly_omp.o npair_full_bin_ghost.o npair_full_bin_ghost_intel.o npair_full_bin_ghost_omp.o npair_full_bin_intel.o npair_full_bin_omp.o npair_full_multi.o npair_full_multi_omp.o npair_full_nsq.o npair_full_nsq_ghost.o npair_full_nsq_ghost_omp.o npair_full_nsq_omp.o npair_half_bin_atomonly_newton.o npair_half_bin_atomonly_newton_omp.o npair_half_bin_newtoff.o npair_half_bin_newtoff_ghost.o npair_half_bin_newtoff_ghost_omp.o npair_half_bin_newtoff_omp.o npair_half_bin_newton.o npair_half_bin_newton_intel.o npair_half_bin_newton_omp.o npair_half_bin_newton_ssa.o npair_half_bin_newton_tri.o npair_half_bin_newton_tri_intel.o npair_half_bin_newton_tri_omp.o npair_half_multi_newtoff.o npair_half_multi_newtoff_omp.o npair_half_multi_newton.o npair_half_multi_newton_omp.o npair_half_multi_newton_tri.o npair_half_multi_newton_tri_omp.o npair_half_nsq_newtoff.o npair_half_nsq_newtoff_ghost.o npair_half_nsq_newtoff_ghost_omp.o npair_half_nsq_newtoff_omp.o npair_half_nsq_newton.o npair_half_nsq_newton_omp.o npair_half_respa_bin_newtoff.o npair_half_respa_bin_newtoff_omp.o npair_half_respa_bin_newton.o npair_half_respa_bin_newton_omp.o npair_half_respa_bin_newton_tri.o npair_half_respa_bin_newton_tri_omp.o npair_half_respa_nsq_newtoff.o npair_half_respa_nsq_newtoff_omp.o npair_half_respa_nsq_newton.o npair_half_respa_nsq_newton_omp.o npair_half_size_bin_newtoff.o npair_half_size_bin_newtoff_omp.o npair_half_size_bin_newton.o npair_half_size_bin_newton_omp.o npair_half_size_bin_newton_tri.o npair_half_size_bin_newton_tri_omp.o npair_half_size_nsq_newtoff.o npair_half_size_nsq_newtoff_omp.o npair_half_size_nsq_newton.o npair_half_size_nsq_newton_omp.o npair_halffull_kokkos.o npair_halffull_newtoff.o npair_halffull_newtoff_omp.o npair_halffull_newton.o npair_halffull_newton_omp.o npair_intel.o npair_kokkos.o npair_skip.o npair_skip_kokkos.o npair_skip_respa.o npair_skip_size.o npair_skip_size_off2on.o npair_skip_size_off2on_oneside.o npair_ssa_kokkos.o nstencil.o nstencil_full_bin_2d.o nstencil_full_bin_3d.o nstencil_full_ghost_bin_2d.o nstencil_full_ghost_bin_3d.o nstencil_full_multi_2d.o nstencil_full_multi_3d.o nstencil_half_bin_2d_newtoff.o nstencil_half_bin_2d_newton.o nstencil_half_bin_2d_newton_ssa.o nstencil_half_bin_2d_newton_tri.o nstencil_half_bin_3d_newtoff.o nstencil_half_bin_3d_newton.o nstencil_half_bin_3d_newton_ssa.o nstencil_half_bin_3d_newton_tri.o nstencil_half_ghost_bin_2d_newtoff.o nstencil_half_ghost_bin_3d_newtoff.o nstencil_half_multi_2d_newtoff.o nstencil_half_multi_2d_newton.o nstencil_half_multi_2d_newton_tri.o nstencil_half_multi_3d_newtoff.o nstencil_half_multi_3d_newton.o nstencil_half_multi_3d_newton_tri.o ntopo.o ntopo_angle_all.o ntopo_angle_partial.o ntopo_angle_template.o ntopo_bond_all.o ntopo_bond_partial.o ntopo_bond_template.o ntopo_dihedral_all.o ntopo_dihedral_partial.o ntopo_dihedral_template.o ntopo_improper_all.o ntopo_improper_partial.o ntopo_improper_template.o output.o pair.o pair_adp.o pair_adp_omp.o pair_agni.o pair_agni_omp.o pair_airebo.o pair_airebo_intel.o pair_airebo_morse.o pair_airebo_morse_intel.o pair_airebo_morse_omp.o pair_airebo_omp.o pair_awpmd_cut.o pair_beck.o pair_beck_omp.o pair_body.o pair_bop.o pair_born.o pair_born_coul_dsf.o pair_born_coul_dsf_cs.o pair_born_coul_long.o pair_born_coul_long_cs.o pair_born_coul_long_omp.o pair_born_coul_msm.o pair_born_coul_msm_omp.o pair_born_coul_wolf.o pair_born_coul_wolf_cs.o pair_born_coul_wolf_omp.o pair_born_omp.o pair_brownian.o pair_brownian_omp.o pair_brownian_poly.o pair_brownian_poly_omp.o pair_buck.o pair_buck_coul_cut.o pair_buck_coul_cut_intel.o pair_buck_coul_cut_kokkos.o pair_buck_coul_cut_omp.o pair_buck_coul_long.o pair_buck_coul_long_cs.o pair_buck_coul_long_intel.o pair_buck_coul_long_kokkos.o pair_buck_coul_long_omp.o pair_buck_coul_msm.o pair_buck_coul_msm_omp.o pair_buck_intel.o pair_buck_kokkos.o pair_buck_long_coul_long.o pair_buck_long_coul_long_omp.o pair_buck_mdf.o pair_buck_omp.o pair_cdeam.o pair_cdeam_omp.o pair_colloid.o pair_colloid_omp.o pair_comb.o pair_comb3.o pair_coul_cut.o pair_coul_cut_kokkos.o pair_coul_cut_omp.o pair_coul_cut_soft.o pair_coul_cut_soft_omp.o pair_coul_debye.o pair_coul_debye_kokkos.o pair_coul_debye_omp.o pair_coul_diel.o pair_coul_diel_omp.o pair_coul_dsf.o pair_coul_dsf_kokkos.o pair_coul_dsf_omp.o pair_coul_long.o pair_coul_long_cs.o pair_coul_long_kokkos.o pair_coul_long_omp.o pair_coul_long_soft.o pair_coul_long_soft_omp.o pair_coul_msm.o pair_coul_msm_omp.o pair_coul_streitz.o pair_coul_wolf.o pair_coul_wolf_cs.o pair_coul_wolf_kokkos.o pair_coul_wolf_omp.o pair_dpd.o pair_dpd_fdt.o pair_dpd_fdt_energy.o pair_dpd_fdt_energy_kokkos.o pair_dpd_intel.o pair_dpd_omp.o pair_dpd_tstat.o pair_dpd_tstat_omp.o pair_dsmc.o pair_eam.o pair_eam_alloy.o pair_eam_alloy_intel.o pair_eam_alloy_kokkos.o pair_eam_alloy_omp.o pair_eam_alloy_opt.o pair_eam_fs.o pair_eam_fs_intel.o pair_eam_fs_kokkos.o pair_eam_fs_omp.o pair_eam_fs_opt.o pair_eam_intel.o pair_eam_kokkos.o pair_eam_omp.o pair_eam_opt.o pair_edip.o pair_edip_multi.o pair_edip_omp.o pair_edpd.o pair_eff_cut.o pair_eim.o pair_eim_omp.o pair_exp6_rx.o pair_exp6_rx_kokkos.o pair_extep.o pair_gauss.o pair_gauss_cut.o pair_gauss_cut_omp.o pair_gauss_omp.o pair_gayberne.o pair_gayberne_intel.o pair_gayberne_omp.o pair_gran_hertz_history.o pair_gran_hertz_history_omp.o pair_gran_hooke.o pair_gran_hooke_history.o pair_gran_hooke_history_omp.o pair_gran_hooke_omp.o pair_gw.o pair_gw_zbl.o pair_hbond_dreiding_lj.o pair_hbond_dreiding_lj_omp.o pair_hbond_dreiding_morse.o pair_hbond_dreiding_morse_omp.o pair_hybrid.o pair_hybrid_kokkos.o pair_hybrid_overlay.o pair_hybrid_overlay_kokkos.o pair_kolmogorov_crespi_z.o pair_lcbop.o pair_lennard_mdf.o pair_line_lj.o pair_list.o pair_lj96_cut.o pair_lj96_cut_omp.o pair_lj_charmm_coul_charmm.o pair_lj_charmm_coul_charmm_implicit.o pair_lj_charmm_coul_charmm_implicit_kokkos.o pair_lj_charmm_coul_charmm_implicit_omp.o pair_lj_charmm_coul_charmm_intel.o pair_lj_charmm_coul_charmm_kokkos.o pair_lj_charmm_coul_charmm_omp.o pair_lj_charmm_coul_long.o pair_lj_charmm_coul_long_intel.o pair_lj_charmm_coul_long_kokkos.o pair_lj_charmm_coul_long_omp.o pair_lj_charmm_coul_long_opt.o pair_lj_charmm_coul_long_soft.o pair_lj_charmm_coul_long_soft_omp.o pair_lj_charmm_coul_msm.o pair_lj_charmm_coul_msm_omp.o pair_lj_charmmfsw_coul_charmmfsh.o pair_lj_charmmfsw_coul_long.o pair_lj_class2.o pair_lj_class2_coul_cut.o pair_lj_class2_coul_cut_kokkos.o pair_lj_class2_coul_cut_omp.o pair_lj_class2_coul_long.o pair_lj_class2_coul_long_kokkos.o pair_lj_class2_coul_long_omp.o pair_lj_class2_kokkos.o pair_lj_class2_omp.o pair_lj_cubic.o pair_lj_cubic_omp.o pair_lj_cut.o pair_lj_cut_coul_cut.o pair_lj_cut_coul_cut_kokkos.o pair_lj_cut_coul_cut_omp.o pair_lj_cut_coul_cut_soft.o pair_lj_cut_coul_cut_soft_omp.o pair_lj_cut_coul_debye.o pair_lj_cut_coul_debye_kokkos.o pair_lj_cut_coul_debye_omp.o pair_lj_cut_coul_dsf.o pair_lj_cut_coul_dsf_kokkos.o pair_lj_cut_coul_dsf_omp.o pair_lj_cut_coul_long.o pair_lj_cut_coul_long_cs.o pair_lj_cut_coul_long_intel.o pair_lj_cut_coul_long_kokkos.o pair_lj_cut_coul_long_omp.o pair_lj_cut_coul_long_opt.o pair_lj_cut_coul_long_soft.o pair_lj_cut_coul_long_soft_omp.o pair_lj_cut_coul_msm.o pair_lj_cut_coul_msm_omp.o pair_lj_cut_coul_wolf.o pair_lj_cut_coul_wolf_omp.o pair_lj_cut_dipole_cut.o pair_lj_cut_dipole_cut_omp.o pair_lj_cut_dipole_long.o pair_lj_cut_intel.o pair_lj_cut_kokkos.o pair_lj_cut_omp.o pair_lj_cut_opt.o pair_lj_cut_soft.o pair_lj_cut_soft_omp.o pair_lj_cut_thole_long.o pair_lj_cut_thole_long_omp.o pair_lj_cut_tip4p_cut.o pair_lj_cut_tip4p_cut_omp.o pair_lj_cut_tip4p_long.o pair_lj_cut_tip4p_long_omp.o pair_lj_cut_tip4p_long_opt.o pair_lj_cut_tip4p_long_soft.o pair_lj_cut_tip4p_long_soft_omp.o pair_lj_expand.o pair_lj_expand_kokkos.o pair_lj_expand_omp.o pair_lj_gromacs.o pair_lj_gromacs_coul_gromacs.o pair_lj_gromacs_coul_gromacs_kokkos.o pair_lj_gromacs_coul_gromacs_omp.o pair_lj_gromacs_kokkos.o pair_lj_gromacs_omp.o pair_lj_long_coul_long.o pair_lj_long_coul_long_intel.o pair_lj_long_coul_long_omp.o pair_lj_long_coul_long_opt.o pair_lj_long_dipole_long.o pair_lj_long_tip4p_long.o pair_lj_long_tip4p_long_omp.o pair_lj_mdf.o pair_lj_sdk.o pair_lj_sdk_coul_long.o pair_lj_sdk_coul_long_omp.o pair_lj_sdk_coul_msm.o pair_lj_sdk_coul_msm_omp.o pair_lj_sdk_kokkos.o pair_lj_sdk_omp.o pair_lj_sf_dipole_sf.o pair_lj_sf_dipole_sf_omp.o pair_lj_smooth.o pair_lj_smooth_linear.o pair_lj_smooth_linear_omp.o pair_lj_smooth_omp.o pair_lubricate.o pair_lubricateU.o pair_lubricateU_poly.o pair_lubricate_omp.o pair_lubricate_poly.o pair_lubricate_poly_omp.o pair_mdpd.o pair_mdpd_rhosum.o pair_meam.o pair_meam_spline.o pair_meam_spline_omp.o pair_meam_sw_spline.o pair_meamc.o pair_mgpt.o pair_mie_cut.o pair_momb.o pair_morse.o pair_morse_kokkos.o pair_morse_omp.o pair_morse_opt.o pair_morse_smooth_linear.o pair_morse_smooth_linear_omp.o pair_morse_soft.o pair_multi_lucy.o pair_multi_lucy_rx.o pair_multi_lucy_rx_kokkos.o pair_nb3b_harmonic.o pair_nb3b_harmonic_omp.o pair_nm_cut.o pair_nm_cut_coul_cut.o pair_nm_cut_coul_cut_omp.o pair_nm_cut_coul_long.o pair_nm_cut_coul_long_omp.o pair_nm_cut_omp.o pair_oxdna2_coaxstk.o pair_oxdna2_dh.o pair_oxdna2_excv.o pair_oxdna2_stk.o pair_oxdna_coaxstk.o pair_oxdna_excv.o pair_oxdna_hbond.o pair_oxdna_stk.o pair_oxdna_xstk.o pair_peri_eps.o pair_peri_lps.o pair_peri_lps_omp.o pair_peri_pmb.o pair_peri_pmb_omp.o pair_peri_ves.o pair_polymorphic.o pair_python.o pair_reax.o pair_reaxc.o pair_reaxc_kokkos.o pair_reaxc_omp.o pair_rebo.o pair_rebo_intel.o pair_rebo_omp.o pair_resquared.o pair_resquared_omp.o pair_smd_hertz.o pair_smd_tlsph.o pair_smd_triangulated_surface.o pair_smd_ulsph.o pair_smtbq.o pair_snap.o pair_snap_kokkos.o pair_soft.o pair_soft_omp.o pair_sph_heatconduction.o pair_sph_idealgas.o pair_sph_lj.o pair_sph_rhosum.o pair_sph_taitwater.o pair_sph_taitwater_morris.o pair_srp.o pair_sw.o pair_sw_intel.o pair_sw_kokkos.o pair_sw_omp.o pair_table.o pair_table_kokkos.o pair_table_omp.o pair_table_rx.o pair_table_rx_kokkos.o pair_tdpd.o pair_tersoff.o pair_tersoff_intel.o pair_tersoff_kokkos.o pair_tersoff_mod.o pair_tersoff_mod_c.o pair_tersoff_mod_c_omp.o pair_tersoff_mod_kokkos.o pair_tersoff_mod_omp.o pair_tersoff_omp.o pair_tersoff_table.o pair_tersoff_table_omp.o pair_tersoff_zbl.o pair_tersoff_zbl_kokkos.o pair_tersoff_zbl_omp.o pair_thole.o pair_tip4p_cut.o pair_tip4p_cut_omp.o pair_tip4p_long.o pair_tip4p_long_omp.o pair_tip4p_long_soft.o pair_tip4p_long_soft_omp.o pair_tri_lj.o pair_ufm.o pair_ufm_omp.o pair_ufm_opt.o pair_vashishta.o pair_vashishta_kokkos.o pair_vashishta_omp.o pair_vashishta_table.o pair_vashishta_table_omp.o pair_yukawa.o pair_yukawa_colloid.o pair_yukawa_colloid_omp.o pair_yukawa_kokkos.o pair_yukawa_omp.o pair_zbl.o pair_zbl_kokkos.o pair_zbl_omp.o pair_zero.o pppm.o pppm_cg.o pppm_cg_omp.o pppm_disp.o pppm_disp_intel.o pppm_disp_omp.o pppm_disp_tip4p.o pppm_disp_tip4p_omp.o pppm_intel.o pppm_kokkos.o pppm_omp.o pppm_stagger.o pppm_tip4p.o pppm_tip4p_omp.o prd.o procmap.o python.o python_impl.o rand_pool_wrap_kokkos.o random_mars.o random_park.o rcb.o read_data.o read_dump.o read_restart.o reader.o reader_molfile.o reader_native.o reader_xyz.o reaxc_allocate.o reaxc_bond_orders.o reaxc_bond_orders_omp.o reaxc_bonds.o reaxc_bonds_omp.o reaxc_control.o reaxc_ffield.o reaxc_forces.o reaxc_forces_omp.o reaxc_hydrogen_bonds.o reaxc_hydrogen_bonds_omp.o reaxc_init_md.o reaxc_init_md_omp.o reaxc_io_tools.o reaxc_list.o reaxc_lookup.o reaxc_multi_body.o reaxc_multi_body_omp.o reaxc_nonbonded.o reaxc_nonbonded_omp.o reaxc_reset_tools.o reaxc_system_props.o reaxc_tool_box.o reaxc_torsion_angles.o reaxc_torsion_angles_omp.o reaxc_traj.o reaxc_valence_angles.o reaxc_valence_angles_omp.o reaxc_vector.o region.o region_block.o region_block_kokkos.o region_cone.o region_cylinder.o region_intersect.o region_plane.o region_prism.o region_sphere.o region_union.o remap.o remap_wrap.o replicate.o rerun.o respa.o respa_omp.o restart_mpiio.o run.o set.o smd_material_models.o sna.o special.o tad.o temper.o temper_grem.o temper_npt.o thermo.o thr_data.o thr_omp.o timer.o uef_utils.o universe.o update.o variable.o velocity.o verlet.o verlet_kokkos.o verlet_lrt_intel.o verlet_split.o write_coeff.o write_data.o write_dump.o write_restart.o xdr_compat.o -lkokkos -ldl -lqmmm -lch5md -lcolvars -lawpmd -latc -lreax -lpoems -lmeam -lfftw3 -L/Users/chibaf/lammps-2018/lammps-22Feb18/src/Obj_mpi -fopenmp=libomp -L/usr/local/Cellar/netcdf/4.6.0/lib -lnetcdf -lhdf5_hl -lhdf5 -lsz -lz -ldl -lm -lcurl -ldl -lhdf5 -llinalg -lgfortran -llinalg -lgfortran -L/Users/chibaf/.pyenv/versions/3.6.3/lib/python3.6/config-3.6m-darwin -lpython3.6m -ldl -framework CoreFoundation -Wl,-stack_size,1000000 -framework CoreFoundation -lz -L/usr/local/opt/llvm/lib -L/usr/local/Cellar/openblas/0.2.20_1/lib -L/usr/local/Cellar/gcc/7.3.0/lib/gcc/7 -lgfortran -lopenblas -lgomp -o ../lmp_mpi

size ../lmp_mpi

__TEXT __DATA __OBJC others dec hex

32894976 1613926400 0 4308336640 5955158016 162f48000

(11) Execution of lammps. You need to set a path to lmp_mpi:

(A) mpirun -np N lmp_mpi < in.lammps

(B) mpirun -x OMP_NUM_THREADS=M -np N lmp_mpi -sf omp -in in.lammps

where N is number of mpi process, M number of OpenMP, and in.lammps is lammps input.

Description of lammps input is found in lammps manual.

lammps examples are found in "lammps-22Feb18/bench".

Example of lammps inputs are also found in http://mathweb.html.xdomain.jp/math/lammps/examples/or the internet.