Merge branch 'develop' into compute_temp_profile_dof
This commit is contained in:
Axel Kohlmeyer
32
src/.clang-format
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32
src/.clang-format
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...
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295
src/.gitignore
vendored
295
src/.gitignore
vendored
@ -1,6 +1,7 @@
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||||
/Makefile.package
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||||
/Makefile.package.settings
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||||
/MAKE/MINE
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/ADIOS/Makefile.lammps
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||||
/Make.py.last
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/lmp_*
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||||
@ -27,11 +28,36 @@
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||||
/*_ssa.h
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||||
/*_ssa.cpp
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||||
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||||
!accelerator_kokkos.h
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||||
!accelerator_omp.h
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||||
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||||
/fix_mdi_engine.cpp
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||||
/fix_mdi_engine.h
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||||
/library_mdi.cpp
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||||
/library_mdi.h
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||||
/mdi_engine.cpp
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||||
/mdi_engine.h
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||||
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||||
/fix_brownian*.cpp
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||||
/fix_brownian*.h
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||||
/fix_propel_self.cpp
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||||
/fix_propel_self.h
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||||
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||||
/kim_*.cpp
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||||
/kim_*.h
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||||
/pair_kim.cpp
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||||
/pair_kim.h
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||||
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||||
/pair_pace.cpp
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||||
/pair_pace.h
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||||
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||||
/fix_polarize*.cpp
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||||
/fix_polarize*.h
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||||
/*_dielectric.cpp
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||||
/*_dielectric.h
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||||
/compute_efield_atom.cpp
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/compute_efield_atom.h
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/superpose3d.h
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/kokkos.cpp
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@ -48,13 +74,14 @@
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||||
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||||
/meam*.h
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||||
/meam*.cpp
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||||
/pair_meamc.cpp
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||||
/pair_meamc.h
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||||
/pair_meam.cpp
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||||
/pair_meam.h
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||||
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||||
/compute_mliap.cpp
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||||
/compute_mliap.h
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||||
/mliap_*.cpp
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||||
/mliap_*.h
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||||
/mliap_model_python_couple.pyx
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/pair_mliap.cpp
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||||
/pair_mliap.h
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||||
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||||
@ -72,6 +99,11 @@
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/fix_pafi*.cpp
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/fix_pafi*.h
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||||
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||||
/pair_rann.cpp
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/pair_rann.h
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/rann_*.cpp
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||||
/rann_*.h
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||||
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||||
/compute_test_nbl.cpp
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||||
/compute_test_nbl.h
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||||
/pair_multi_lucy.cpp
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@ -172,6 +204,9 @@
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||||
/pair_lj_charmmfsw_coul_long.cpp
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||||
/pair_lj_charmmfsw_coul_long.h
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||||
/plugin.cpp
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||||
/plugin.h
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||||
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/atom_vec_spin.cpp
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/atom_vec_spin.h
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/compute_spin.cpp
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||||
@ -219,6 +254,83 @@
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||||
/pair_mesont_tpm.cpp
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||||
/pair_mesont_tpm.h
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||||
/atom_vec_bpm_sphere.cpp
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||||
/atom_vec_bpm_sphere.h
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/bond_bpm.cpp
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/bond_bpm.h
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||||
/bond_bpm_rotational.cpp
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||||
/bond_bpm_rotational.h
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||||
/bond_bpm_spring.cpp
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||||
/bond_bpm_spring.h
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||||
/compute_nbond_atom.cpp
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||||
/compute_nbond_atom.h
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||||
/fix_nve_bpm_sphere.cpp
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||||
/fix_nve_bpm_sphere.h
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||||
/pair_bpm_spring.cpp
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||||
/pair_bpm_spring.h
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||||
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||||
/compute_adf.cpp
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||||
/compute_adf.h
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||||
/compute_contact_atom.cpp
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||||
/compute_contact_atom.h
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||||
/compute_hexorder_atom.cpp
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||||
/compute_hexorder_atom.h
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/dump_dcd.cpp
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/dump_dcd.h
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/fix_controller.cpp
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||||
/fix_controller.h
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/fix_drag.cpp
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/fix_drag.h
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||||
/fix_numdiff.cpp
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||||
/fix_numdiff.h
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||||
/fix_numdiff_virial.cpp
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||||
/fix_numdiff_virial.h
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||||
/fix_spring_rg.cpp
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||||
/fix_spring_rg.h
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||||
/fix_temp_csld.cpp
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||||
/fix_temp_csld.h
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||||
/fix_temp_csvr.cpp
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||||
/fix_temp_csvr.h
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||||
/fix_tmd.cpp
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||||
/fix_tmd.h
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||||
/pair_beck.cpp
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||||
/pair_beck.h
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||||
/pair_born_coul_dsf.cpp
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||||
/pair_born_coul_dsf.h
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||||
/pair_born_coul_wolf.cpp
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||||
/pair_born_coul_wolf.h
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||||
/pair_coul_cut_global.cpp
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||||
/pair_coul_cut_global.h
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||||
/pair_coul_streitz.cpp
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||||
/pair_coul_streitz.h
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||||
/pair_gauss.cpp
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||||
/pair_gauss.h
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||||
/pair_lj96_cut.cpp
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||||
/pair_lj96_cut.h
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||||
/pair_lj_cubic.cpp
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||||
/pair_lj_cubic.h
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||||
/pair_lj_cubic_const.h
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||||
/pair_lj_cut_coul_debye.cpp
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||||
/pair_lj_cut_coul_debye.h
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||||
/pair_lj_cut_coul_dsf.cpp
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||||
/pair_lj_cut_coul_dsf.h
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||||
/pair_lj_cut_coul_wolf.cpp
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/pair_lj_cut_coul_wolf.h
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/pair_lj_gromacs.cpp
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/pair_lj_gromacs.h
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/pair_lj_gromacs_coul_gromacs.cpp
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/pair_lj_gromacs_coul_gromacs.h
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/pair_lj_relres.cpp
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/pair_lj_relres.h
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/pair_lj_smooth.cpp
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/pair_lj_smooth.h
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/pair_lj_smooth_linear.cpp
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/pair_lj_smooth_linear.h
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/pair_mie_cut.cpp
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/pair_mie_cut.h
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/pair_ufm.cpp
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/pair_ufm.h
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/angle_cg_cmm.cpp
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/angle_cg_cmm.h
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/angle_charmm.cpp
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@ -273,8 +385,6 @@
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/atom_vec_dpd.h
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/atom_vec_electron.cpp
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/atom_vec_electron.h
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/atom_vec_ellipsoid.cpp
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/atom_vec_ellipsoid.h
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/atom_vec_full.cpp
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/atom_vec_full.h
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/atom_vec_full_hars.cpp
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@ -283,6 +393,8 @@
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/atom_vec_granular.h
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/atom_vec_molecular.cpp
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/atom_vec_molecular.h
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/atom_vec_oxdna.cpp
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||||
/atom_vec_oxdna.h
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/atom_vec_peri.cpp
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||||
/atom_vec_peri.h
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||||
/atom_vec_template.cpp
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@ -299,6 +411,8 @@
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/bond_fene.h
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/bond_fene_expand.cpp
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/bond_fene_expand.h
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/bond_fene_nm.cpp
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/bond_fene_nm.h
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/bond_gaussian.cpp
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/bond_gaussian.h
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/bond_gromos.cpp
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@ -333,6 +447,8 @@
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/commgrid.h
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/compute_ackland_atom.cpp
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/compute_ackland_atom.h
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/compute_ave_sphere_atom.cpp
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/compute_ave_sphere_atom.h
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/compute_basal_atom.cpp
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/compute_basal_atom.h
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/compute_body_local.cpp
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||||
@ -355,8 +471,12 @@
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||||
/compute_erotate_rigid.h
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/compute_event_displace.cpp
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/compute_event_displace.h
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/compute_fabric.cpp
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||||
/compute_fabric.h
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/compute_fep.cpp
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||||
/compute_fep.h
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/compute_fep_ta.cpp
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/compute_fep_ta.h
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/compute_force_tally.cpp
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/compute_force_tally.h
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/compute_gyration_shape.cpp
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@ -389,8 +509,6 @@
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/compute_plasticity_atom.h
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/compute_pressure_bocs.cpp
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/compute_pressure_bocs.h
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/compute_pressure_cylinder.cpp
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/compute_pressure_cylinder.h
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/compute_pressure_grem.cpp
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/compute_pressure_grem.h
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/compute_ptm_atom.cpp
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@ -401,10 +519,16 @@
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/compute_smd_triangle_vertices.h
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/compute_spec_atom.cpp
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/compute_spec_atom.h
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/compute_stress_cartesian.cpp
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/compute_stress_cartesian.h
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/compute_stress_cylinder.cpp
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/compute_stress_cylinder.h
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/compute_stress_mop.cpp
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/compute_stress_mop.h
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/compute_stress_mop_profile.cpp
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/compute_stress_mop_profile.h
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/compute_stress_spherical.cpp
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/compute_stress_spherical.h
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/compute_stress_tally.cpp
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/compute_stress_tally.h
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/compute_temp_asphere.cpp
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@ -437,8 +561,6 @@
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/dihedral_harmonic.h
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/dihedral_helix.cpp
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/dihedral_helix.h
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/dihedral_hybrid.cpp
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/dihedral_hybrid.h
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/dihedral_multi_harmonic.cpp
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/dihedral_multi_harmonic.h
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/dihedral_nharmonic.cpp
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@ -495,6 +617,8 @@
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/dump_xyz_mpiio.h
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/dump_xyz_zstd.cpp
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/dump_xyz_zstd.h
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/dump_yaml.cpp
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/dump_yaml.h
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/dynamical_matrix.cpp
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/dynamical_matrix.h
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/ewald.cpp
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@ -515,6 +639,8 @@
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/fft3d_wrap.h
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/fix_accelerate_cos.cpp
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/fix_accelerate_cos.h
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/fix_acks2_reaxff.cpp
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/fix_acks2_reaxff.h
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/fix_adapt_fep.cpp
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/fix_adapt_fep.h
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/fix_addtorque.cpp
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@ -537,16 +663,14 @@
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/fix_bond_react.h
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/fix_bond_swap.cpp
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/fix_bond_swap.h
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/fix_charge_regulation.cpp
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/fix_charge_regulation.h
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/fix_client_md.cpp
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/fix_client_md.h
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/fix_cmap.cpp
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/fix_cmap.h
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/fix_deposit.cpp
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/fix_deposit.h
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/fix_dpd_energy.cpp
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/fix_dpd_energy.h
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/fix_efield.cpp
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/fix_efield.h
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/fix_electron_stopping.cpp
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/fix_electron_stopping.h
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/fix_electron_stopping_fit.cpp
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@ -555,8 +679,6 @@
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/fix_eos_cv.h
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/fix_eos_table.cpp
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/fix_eos_table.h
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/fix_evaporate.cpp
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/fix_evaporate.h
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/fix_ffl.cpp
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/fix_ffl.h
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/fix_filter_corotate.cpp
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@ -693,22 +815,20 @@
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/fix_poems.h
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/fix_pour.cpp
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/fix_pour.h
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/fix_propel_self.cpp
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/fix_propel_self.h
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/fix_qeq_comb.cpp
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/fix_qeq_comb.h
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/fix_qeq_reax.cpp
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/fix_qeq_fire.cpp
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/fix_qeq_fire.h
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/fix_qeq_reax.h
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/fix_qeq_reaxff.cpp
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/fix_qeq_reaxff.h
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/fix_qmmm.cpp
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/fix_qmmm.h
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/fix_reaxc.cpp
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/fix_reaxc.h
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/fix_reaxc_bonds.cpp
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/fix_reaxc_bonds.h
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/fix_reaxc_species.cpp
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/fix_reaxc_species.h
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/fix_reaxff.cpp
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/fix_reaxff.h
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/fix_reaxff_bonds.cpp
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/fix_reaxff_bonds.h
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/fix_reaxff_species.cpp
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/fix_reaxff_species.h
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/fix_rhok.cpp
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/fix_rhok.h
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/fix_rigid.cpp
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@ -760,14 +880,10 @@
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/fix_tgnpt_drude.h
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/fix_tgnvt_drude.cpp
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/fix_tgnvt_drude.h
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/fix_thermal_conductivity.cpp
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/fix_thermal_conductivity.h
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/fix_ti_rs.cpp
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/fix_ti_rs.h
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/fix_ti_spring.cpp
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/fix_ti_spring.h
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/fix_ttm.cpp
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/fix_ttm.h
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/fix_tune_kspace.cpp
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/fix_tune_kspace.h
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/fix_wall_body_polygon.cpp
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@ -793,10 +909,10 @@
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/fix_widom.cpp
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/fix_widom.h
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/gpu_extra.h
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/gridcomm.cpp
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/gridcomm.h
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/group_ndx.cpp
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/group_ndx.h
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/gz_file_writer.cpp
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/gz_file_writer.h
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/ndx_group.cpp
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/ndx_group.h
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/hyper.cpp
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/improper_fourier.h
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/improper_harmonic.cpp
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/improper_harmonic.h
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/improper_hybrid.cpp
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/improper_hybrid.h
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/improper_inversion_harmonic.cpp
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/improper_inversion_harmonic.h
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/improper_ring.cpp
|
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/improper_ring.h
|
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/improper_umbrella.cpp
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||||
/improper_umbrella.h
|
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/interlayer_taper.h
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||||
/kissfft.h
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/lj_sdk_common.h
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/math_complex.h
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@ -839,7 +954,8 @@
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/msm_cg.h
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/neb.cpp
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/neb.h
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/netcdf_units.cpp
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/netcdf_units.h
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/pair_adp.cpp
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/pair_adp.h
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/pair_agni.cpp
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@ -900,6 +1016,8 @@
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/pair_cosine_squared.h
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/pair_coul_diel.cpp
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/pair_coul_diel.h
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/pair_coul_exclude.cpp
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/pair_coul_exclude.h
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/pair_coul_long.cpp
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/pair_coul_long.h
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/pair_coul_msm.cpp
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@ -916,8 +1034,6 @@
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/pair_dipole_cut.h
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/pair_dipole_sf.cpp
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/pair_dipole_sf.h
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/pair_dpd_mt.cpp
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/pair_dpd_mt.h
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/pair_dsmc.cpp
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/pair_dsmc.h
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/pair_e3b.cpp
|
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@ -971,8 +1087,12 @@
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/pair_hbond_dreiding_lj.h
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||||
/pair_hbond_dreiding_morse.cpp
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||||
/pair_hbond_dreiding_morse.h
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/pair_hdnnp.cpp
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/pair_hdnnp.h
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/pair_ilp_graphene_hbn.cpp
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/pair_ilp_graphene_hbn.h
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/pair_ilp_tmd.cpp
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/pair_ilp_tmd.h
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/pair_kolmogorov_crespi_full.cpp
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/pair_kolmogorov_crespi_full.h
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/pair_kolmogorov_crespi_z.cpp
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@ -1079,6 +1199,8 @@
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/pair_nm_cut_coul_cut.h
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/pair_nm_cut_coul_long.cpp
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/pair_nm_cut_coul_long.h
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/pair_nm_cut_split.cpp
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/pair_nm_cut_split.h
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/pair_oxdna_*.cpp
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/pair_oxdna_*.h
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/pair_oxdna2_*.cpp
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@ -1086,6 +1208,8 @@
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/pair_oxrna2_*.cpp
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/pair_oxrna2_*.h
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/mf_oxdna.h
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/pair_peri.cpp
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/pair_peri.h
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/pair_peri_eps.cpp
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/pair_peri_eps.h
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/pair_peri_lps.cpp
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@ -1096,12 +1220,14 @@
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/pair_peri_ves.h
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/pair_quip.cpp
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/pair_quip.h
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/pair_reaxc.cpp
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/pair_reaxc.h
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||||
/pair_reaxff.cpp
|
||||
/pair_reaxff.h
|
||||
/pair_rebo.cpp
|
||||
/pair_rebo.h
|
||||
/pair_resquared.cpp
|
||||
/pair_resquared.h
|
||||
/pair_saip_metal.cpp
|
||||
/pair_saip_metal.h
|
||||
/pair_sdpd_taitwater_isothermal.cpp
|
||||
/pair_sdpd_taitwater_isothermal.h
|
||||
/pair_sph_heatconduction.cpp
|
||||
@ -1118,6 +1244,8 @@
|
||||
/pair_sph_taitwater_morris.h
|
||||
/pair_sw.cpp
|
||||
/pair_sw.h
|
||||
/pair_sw_mod.cpp
|
||||
/pair_sw_mod.h
|
||||
/pair_tersoff.cpp
|
||||
/pair_tersoff.h
|
||||
/pair_tersoff_mod.cpp
|
||||
@ -1134,6 +1262,8 @@
|
||||
/pair_tip4p_long.h
|
||||
/pair_tip4p_long_soft.cpp
|
||||
/pair_tip4p_long_soft.h
|
||||
/pair_tracker.h
|
||||
/pair_tracker.cpp
|
||||
/pair_tri_lj.cpp
|
||||
/pair_tri_lj.h
|
||||
/pair_yukawa_colloid.cpp
|
||||
@ -1171,6 +1301,7 @@
|
||||
/python_impl.cpp
|
||||
/python_impl.h
|
||||
/python_compat.h
|
||||
/python_utils.h
|
||||
/fix_python_move.cpp
|
||||
/fix_python_move.h
|
||||
/fix_python_invoke.cpp
|
||||
@ -1181,50 +1312,27 @@
|
||||
/reader_adios.h
|
||||
/reader_molfile.cpp
|
||||
/reader_molfile.h
|
||||
/reaxc_allocate.cpp
|
||||
/reaxc_allocate.h
|
||||
/reaxc_basic_comm.cpp
|
||||
/reaxc_basic_comm.h
|
||||
/reaxc_bond_orders.cpp
|
||||
/reaxc_bond_orders.h
|
||||
/reaxc_bonds.cpp
|
||||
/reaxc_bonds.h
|
||||
/reaxc_control.cpp
|
||||
/reaxc_control.h
|
||||
/reaxc_defs.h
|
||||
/reaxc_ffield.cpp
|
||||
/reaxc_ffield.h
|
||||
/reaxc_forces.cpp
|
||||
/reaxc_forces.h
|
||||
/reaxc_hydrogen_bonds.cpp
|
||||
/reaxc_hydrogen_bonds.h
|
||||
/reaxc_init_md.cpp
|
||||
/reaxc_init_md.h
|
||||
/reaxc_io_tools.cpp
|
||||
/reaxc_io_tools.h
|
||||
/reaxc_list.cpp
|
||||
/reaxc_list.h
|
||||
/reaxc_lookup.cpp
|
||||
/reaxc_lookup.h
|
||||
/reaxc_multi_body.cpp
|
||||
/reaxc_multi_body.h
|
||||
/reaxc_nonbonded.cpp
|
||||
/reaxc_nonbonded.h
|
||||
/reaxc_reset_tools.cpp
|
||||
/reaxc_reset_tools.h
|
||||
/reaxc_system_props.cpp
|
||||
/reaxc_system_props.h
|
||||
/reaxc_tool_box.cpp
|
||||
/reaxc_tool_box.h
|
||||
/reaxc_torsion_angles.cpp
|
||||
/reaxc_torsion_angles.h
|
||||
/reaxc_traj.cpp
|
||||
/reaxc_traj.h
|
||||
/reaxc_types.h
|
||||
/reaxc_valence_angles.cpp
|
||||
/reaxc_valence_angles.h
|
||||
/reaxc_vector.cpp
|
||||
/reaxc_vector.h
|
||||
/reaxff_allocate.cpp
|
||||
/reaxff_bond_orders.cpp
|
||||
/reaxff_bonds.cpp
|
||||
/reaxff_control.cpp
|
||||
/reaxff_ffield.cpp
|
||||
/reaxff_forces.cpp
|
||||
/reaxff_hydrogen_bonds.cpp
|
||||
/reaxff_init_md.cpp
|
||||
/reaxff_list.cpp
|
||||
/reaxff_lookup.cpp
|
||||
/reaxff_multi_body.cpp
|
||||
/reaxff_nonbonded.cpp
|
||||
/reaxff_reset_tools.cpp
|
||||
/reaxff_tool_box.cpp
|
||||
/reaxff_torsion_angles.cpp
|
||||
/reaxff_valence_angles.cpp
|
||||
/reaxff_api.h
|
||||
/reaxff_defs.h
|
||||
/reaxff_inline.h
|
||||
/reaxff_omp.h
|
||||
/reaxff_types.h
|
||||
/remap.cpp
|
||||
/remap.h
|
||||
/remap_wrap.cpp
|
||||
@ -1258,10 +1366,10 @@
|
||||
/thr_data.h
|
||||
/verlet_split.cpp
|
||||
/verlet_split.h
|
||||
/write_dump.cpp
|
||||
/write_dump.h
|
||||
/xdr_compat.cpp
|
||||
/xdr_compat.h
|
||||
/zstd_file_writer.cpp
|
||||
/zstd_file_writer.h
|
||||
|
||||
/atom_vec_smd.cpp
|
||||
/atom_vec_smd.h
|
||||
@ -1327,6 +1435,8 @@
|
||||
/fix_drude_transform.h
|
||||
/fix_langevin_drude.cpp
|
||||
/fix_langevin_drude.h
|
||||
/fix_mol_swap.cpp
|
||||
/fix_mol_swap.h
|
||||
/fix_pimd.cpp
|
||||
/fix_pimd.h
|
||||
/fix_qbmsst.cpp
|
||||
@ -1355,6 +1465,10 @@
|
||||
/fix_srp.h
|
||||
/fix_tfmc.cpp
|
||||
/fix_tfmc.h
|
||||
/fix_ttm.cpp
|
||||
/fix_ttm.h
|
||||
/fix_ttm_grid.cpp
|
||||
/fix_ttm_grid.h
|
||||
/fix_ttm_mod.cpp
|
||||
/fix_ttm_mod.h
|
||||
/pair_born_coul_long_cs.cpp
|
||||
@ -1393,12 +1507,20 @@
|
||||
/pair_thole.h
|
||||
/pair_buck_mdf.cpp
|
||||
/pair_buck_mdf.h
|
||||
/pair_dpd_conservative.cpp
|
||||
/pair_dpd_conservative.h
|
||||
/pair_dpd.cpp
|
||||
/pair_dpd.h
|
||||
/pair_dpd_tstat.cpp
|
||||
/pair_dpd_tstat.h
|
||||
/pair_dpd_ext.cpp
|
||||
/pair_dpd_ext.h
|
||||
/pair_dpd_ext_tstat.cpp
|
||||
/pair_dpd_ext_tstat.h
|
||||
/pair_dpd_fdt.cpp
|
||||
/pair_dpd_fdt.h
|
||||
/pair_dpd_fdt_energy.cpp
|
||||
/pair_dpd_fdt_energy.h
|
||||
/pair_harmonic_cut.cpp
|
||||
/pair_harmonic_cut.h
|
||||
/pair_lennard_mdf.cpp
|
||||
/pair_lennard_mdf.h
|
||||
/pair_lj_cut_coul_long_cs.cpp
|
||||
@ -1415,5 +1537,4 @@
|
||||
/pair_smtbq.h
|
||||
/pair_vashishta*.cpp
|
||||
/pair_vashishta*.h
|
||||
/zstd_file_writer.cpp
|
||||
/zstd_file_writer.h
|
||||
|
||||
|
||||
@ -72,7 +72,7 @@ adios_SYSLIB=${ADIOS2_LIB}
|
||||
sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings
|
||||
# multiline form needed for BSD sed on Macs
|
||||
sed -i -e '4 i \
|
||||
include ../USER-ADIOS/Makefile.lammps
|
||||
include ../ADIOS/Makefile.lammps
|
||||
' ../Makefile.package.settings
|
||||
fi
|
||||
fi
|
||||
@ -8,7 +8,7 @@ Configure LAMMPS with CMake
|
||||
ADIOS2_DIR
|
||||
to the ADIOS 2.x installation path
|
||||
b. use the cmake option
|
||||
-D PKG_USER-ADIOS=yes
|
||||
-D PKG_ADIOS=yes
|
||||
|
||||
The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory);
|
||||
If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket.
|
||||
39
src/ADIOS/adios_common.h
Normal file
39
src/ADIOS/adios_common.h
Normal file
@ -0,0 +1,39 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributed by Norbert Podhorszki (Oak Ridge National Laboratory)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_ADIOS_COMMON_H
|
||||
#define LMP_ADIOS_COMMON_H
|
||||
|
||||
// common definitions for all ADIOS package classes
|
||||
|
||||
static const char default_config[] = "<?xml version=\"1.0\"?>\n"
|
||||
"<adios-config>\n"
|
||||
" <io name=\"atom\">\n"
|
||||
" <engine type=\"BP4\">\n"
|
||||
" <parameter key=\"substreams\" value=\"1\"/>\n"
|
||||
" </engine>\n"
|
||||
" </io>\n"
|
||||
" <io name=\"custom\">\n"
|
||||
" <engine type=\"BP4\">\n"
|
||||
" <parameter key=\"substreams\" value=\"1\"/>\n"
|
||||
" </engine>\n"
|
||||
" </io>\n"
|
||||
" <io name=\"read_dump\">\n"
|
||||
" <engine type=\"BP4\">\n"
|
||||
" </engine>\n"
|
||||
" </io>\n"
|
||||
"</adios-config>\n";
|
||||
|
||||
#endif
|
||||
316
src/ADIOS/dump_atom_adios.cpp
Normal file
316
src/ADIOS/dump_atom_adios.cpp
Normal file
@ -0,0 +1,316 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Norbert Podhorszki (ORNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "dump_atom_adios.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "group.h"
|
||||
#include "memory.h"
|
||||
#include "universe.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
#include "adios2.h"
|
||||
#include "adios_common.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class DumpAtomADIOSInternal {
|
||||
|
||||
public:
|
||||
DumpAtomADIOSInternal(){};
|
||||
~DumpAtomADIOSInternal() = default;
|
||||
|
||||
// name of adios group, referrable in adios2_config.xml
|
||||
const std::string ioName = "atom";
|
||||
adios2::ADIOS *ad = nullptr; // adios object
|
||||
adios2::IO io; // adios group of variables and attributes in this dump
|
||||
adios2::Engine fh; // adios file/stream handle object
|
||||
// one ADIOS output variable we need to change every step
|
||||
adios2::Variable<double> varAtoms;
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpAtomADIOS::DumpAtomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg)
|
||||
{
|
||||
// create a default adios2_config.xml if it doesn't exist yet.
|
||||
FILE *cfgfp = fopen("adios2_config.xml", "r");
|
||||
if (!cfgfp) {
|
||||
cfgfp = fopen("adios2_config.xml", "w");
|
||||
if (cfgfp) fputs(default_config, cfgfp);
|
||||
}
|
||||
if (cfgfp) fclose(cfgfp);
|
||||
|
||||
internal = new DumpAtomADIOSInternal();
|
||||
try {
|
||||
internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON);
|
||||
} catch (std::ios_base::failure &e) {
|
||||
error->all(FLERR, "ADIOS initialization failed with error: {}", e.what());
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpAtomADIOS::~DumpAtomADIOS()
|
||||
{
|
||||
if (internal->fh) internal->fh.Close();
|
||||
delete internal->ad;
|
||||
delete internal;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpAtomADIOS::openfile()
|
||||
{
|
||||
if (multifile) {
|
||||
// if one file per timestep, replace '*' with current timestep
|
||||
auto filecurrent = utils::star_subst(filename, update->ntimestep, padflag);
|
||||
internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write, world);
|
||||
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filecurrent);
|
||||
} else {
|
||||
if (!singlefile_opened) {
|
||||
internal->fh = internal->io.Open(filename, adios2::Mode::Write, world);
|
||||
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filename);
|
||||
singlefile_opened = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpAtomADIOS::write()
|
||||
{
|
||||
if (domain->triclinic == 0) {
|
||||
boxxlo = domain->boxlo[0];
|
||||
boxxhi = domain->boxhi[0];
|
||||
boxylo = domain->boxlo[1];
|
||||
boxyhi = domain->boxhi[1];
|
||||
boxzlo = domain->boxlo[2];
|
||||
boxzhi = domain->boxhi[2];
|
||||
} else {
|
||||
boxxlo = domain->boxlo_bound[0];
|
||||
boxxhi = domain->boxhi_bound[0];
|
||||
boxylo = domain->boxlo_bound[1];
|
||||
boxyhi = domain->boxhi_bound[1];
|
||||
boxzlo = domain->boxlo_bound[2];
|
||||
boxzhi = domain->boxhi_bound[2];
|
||||
boxxy = domain->xy;
|
||||
boxxz = domain->xz;
|
||||
boxyz = domain->yz;
|
||||
}
|
||||
|
||||
// nme = # of dump lines this proc contributes to dump
|
||||
|
||||
nme = count();
|
||||
|
||||
// ntotal = total # of atoms in snapshot
|
||||
// atomOffset = sum of # of atoms up to this proc (exclusive prefix sum)
|
||||
|
||||
bigint bnme = nme;
|
||||
MPI_Allreduce(&bnme, &ntotal, 1, MPI_LMP_BIGINT, MPI_SUM, world);
|
||||
|
||||
bigint atomOffset; // sum of all atoms on processes 0..me-1
|
||||
MPI_Scan(&bnme, &atomOffset, 1, MPI_LMP_BIGINT, MPI_SUM, world);
|
||||
atomOffset -= nme; // exclusive prefix sum needed
|
||||
|
||||
// Now we know the global size and the local subset size and offset
|
||||
// of the atoms table
|
||||
auto nAtomsGlobal = static_cast<size_t>(ntotal);
|
||||
auto startRow = static_cast<size_t>(atomOffset);
|
||||
auto nAtomsLocal = static_cast<size_t>(nme);
|
||||
auto nColumns = static_cast<size_t>(size_one);
|
||||
internal->varAtoms.SetShape({nAtomsGlobal, nColumns});
|
||||
internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}});
|
||||
|
||||
// insure buf is sized for packing
|
||||
// adios does not limit per-process data size so nme*size_one is not
|
||||
// constrained to int
|
||||
// if sorting on IDs also request ID list from pack()
|
||||
// sort buf as needed
|
||||
|
||||
if (nme > maxbuf) {
|
||||
maxbuf = nme;
|
||||
memory->destroy(buf);
|
||||
memory->create(buf, (maxbuf * size_one), "dump:buf");
|
||||
}
|
||||
if (sort_flag && sortcol == 0 && nme > maxids) {
|
||||
maxids = nme;
|
||||
memory->destroy(ids);
|
||||
memory->create(ids, maxids, "dump:ids");
|
||||
}
|
||||
|
||||
if (sort_flag && sortcol == 0)
|
||||
pack(ids);
|
||||
else
|
||||
pack(nullptr);
|
||||
if (sort_flag) sort();
|
||||
|
||||
openfile();
|
||||
internal->fh.BeginStep();
|
||||
// write info on data as scalars (by me==0)
|
||||
if (me == 0) {
|
||||
internal->fh.Put<uint64_t>("ntimestep", update->ntimestep);
|
||||
internal->fh.Put<int>("nprocs", nprocs);
|
||||
|
||||
internal->fh.Put<double>("boxxlo", boxxlo);
|
||||
internal->fh.Put<double>("boxxhi", boxxhi);
|
||||
internal->fh.Put<double>("boxylo", boxylo);
|
||||
internal->fh.Put<double>("boxyhi", boxyhi);
|
||||
internal->fh.Put<double>("boxzlo", boxzlo);
|
||||
internal->fh.Put<double>("boxzhi", boxzhi);
|
||||
|
||||
if (domain->triclinic) {
|
||||
internal->fh.Put<double>("boxxy", boxxy);
|
||||
internal->fh.Put<double>("boxxz", boxxz);
|
||||
internal->fh.Put<double>("boxyz", boxyz);
|
||||
}
|
||||
}
|
||||
// Everyone needs to write scalar variables that are used as dimensions and
|
||||
// offsets of arrays
|
||||
internal->fh.Put<uint64_t>("natoms", ntotal);
|
||||
internal->fh.Put<int>("ncolumns", size_one);
|
||||
internal->fh.Put<uint64_t>("nme", bnme);
|
||||
internal->fh.Put<uint64_t>("offset", atomOffset);
|
||||
// now write the atoms
|
||||
internal->fh.Put<double>(internal->varAtoms, buf);
|
||||
internal->fh.EndStep(); // I/O will happen now...
|
||||
|
||||
if (multifile) internal->fh.Close();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpAtomADIOS::init_style()
|
||||
{
|
||||
if (image_flag == 0)
|
||||
size_one = 5;
|
||||
else
|
||||
size_one = 8;
|
||||
|
||||
// setup boundary string
|
||||
|
||||
domain->boundary_string(boundstr);
|
||||
|
||||
// remove % from filename since ADIOS always writes a global file with
|
||||
// data/metadata.
|
||||
char *ptr = strchr(filename, '%');
|
||||
if (ptr) {
|
||||
while (*ptr) {
|
||||
ptr[0] = ptr[1];
|
||||
++ptr;
|
||||
}
|
||||
}
|
||||
|
||||
// setup column string
|
||||
|
||||
std::vector<std::string> columnNames;
|
||||
|
||||
if (scale_flag == 0 && image_flag == 0) {
|
||||
columns = (char *) "id type x y z";
|
||||
columnNames = {"id", "type", "x", "y", "z"};
|
||||
} else if (scale_flag == 0 && image_flag == 1) {
|
||||
columns = (char *) "id type x y z ix iy iz";
|
||||
columnNames = {"id", "type", "x", "y", "z", "ix", "iy", "iz"};
|
||||
} else if (scale_flag == 1 && image_flag == 0) {
|
||||
columns = (char *) "id type xs ys zs";
|
||||
columnNames = {"id", "type", "xs", "ys", "zs"};
|
||||
} else if (scale_flag == 1 && image_flag == 1) {
|
||||
columns = (char *) "id type xs ys zs ix iy iz";
|
||||
columnNames = {"id", "type", "xs", "ys", "zs", "ix", "iy", "iz"};
|
||||
}
|
||||
|
||||
for (int icol = 0; icol < (int)columnNames.size(); ++icol)
|
||||
if (keyword_user[icol].size()) columnNames[icol] = keyword_user[icol];
|
||||
|
||||
// setup function ptrs
|
||||
|
||||
if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0)
|
||||
pack_choice = &DumpAtomADIOS::pack_scale_noimage;
|
||||
else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0)
|
||||
pack_choice = &DumpAtomADIOS::pack_scale_image;
|
||||
else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1)
|
||||
pack_choice = &DumpAtomADIOS::pack_scale_noimage_triclinic;
|
||||
else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1)
|
||||
pack_choice = &DumpAtomADIOS::pack_scale_image_triclinic;
|
||||
else if (scale_flag == 0 && image_flag == 0)
|
||||
pack_choice = &DumpAtomADIOS::pack_noscale_noimage;
|
||||
else if (scale_flag == 0 && image_flag == 1)
|
||||
pack_choice = &DumpAtomADIOS::pack_noscale_image;
|
||||
|
||||
/* Define the group of variables for the atom style here since it's a fixed
|
||||
* set */
|
||||
internal->io = internal->ad->DeclareIO(internal->ioName);
|
||||
if (!internal->io.InConfigFile()) {
|
||||
// if not defined by user, we can change the default settings
|
||||
// BPFile is the default writer
|
||||
internal->io.SetEngine("BPFile");
|
||||
int num_aggregators = multiproc;
|
||||
if (num_aggregators == 0) num_aggregators = 1;
|
||||
auto nstreams = std::to_string(num_aggregators);
|
||||
internal->io.SetParameters({{"substreams", nstreams}});
|
||||
if (me == 0)
|
||||
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
|
||||
nstreams);
|
||||
}
|
||||
|
||||
internal->io.DefineVariable<uint64_t>("ntimestep");
|
||||
internal->io.DefineVariable<uint64_t>("natoms");
|
||||
|
||||
internal->io.DefineVariable<int>("nprocs");
|
||||
internal->io.DefineVariable<int>("ncolumns");
|
||||
|
||||
internal->io.DefineVariable<double>("boxxlo");
|
||||
internal->io.DefineVariable<double>("boxxhi");
|
||||
internal->io.DefineVariable<double>("boxylo");
|
||||
internal->io.DefineVariable<double>("boxyhi");
|
||||
internal->io.DefineVariable<double>("boxzlo");
|
||||
internal->io.DefineVariable<double>("boxzhi");
|
||||
|
||||
internal->io.DefineVariable<double>("boxxy");
|
||||
internal->io.DefineVariable<double>("boxxz");
|
||||
internal->io.DefineVariable<double>("boxyz");
|
||||
|
||||
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
|
||||
internal->io.DefineAttribute<int>("scaled", scale_flag);
|
||||
internal->io.DefineAttribute<int>("image", image_flag);
|
||||
|
||||
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
|
||||
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
|
||||
|
||||
auto nColumns = static_cast<size_t>(size_one);
|
||||
internal->io.DefineAttribute<std::string>("columns", columnNames.data(), nColumns);
|
||||
internal->io.DefineAttribute<std::string>("columnstr", columns);
|
||||
internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
|
||||
internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "atom");
|
||||
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
|
||||
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
|
||||
|
||||
// local dimension variables
|
||||
internal->io.DefineVariable<uint64_t>("nme", {adios2::LocalValueDim});
|
||||
internal->io.DefineVariable<uint64_t>("offset", {adios2::LocalValueDim});
|
||||
|
||||
// atom table size is not known at the moment
|
||||
// it will be correctly defined at the moment of write
|
||||
size_t UnknownSizeYet = 1;
|
||||
internal->varAtoms = internal->io.DefineVariable<double>(
|
||||
"atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
|
||||
}
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -13,7 +13,7 @@
|
||||
|
||||
#ifdef DUMP_CLASS
|
||||
// clang-format off
|
||||
DumpStyle(atom/adios, DumpAtomADIOS)
|
||||
DumpStyle(atom/adios, DumpAtomADIOS);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
@ -22,32 +22,30 @@ DumpStyle(atom/adios, DumpAtomADIOS)
|
||||
|
||||
#include "dump_atom.h"
|
||||
|
||||
namespace LAMMPS_NS
|
||||
{
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DumpAtomADIOSInternal;
|
||||
|
||||
class DumpAtomADIOS : public DumpAtom
|
||||
{
|
||||
class DumpAtomADIOS : public DumpAtom {
|
||||
|
||||
public:
|
||||
DumpAtomADIOS(class LAMMPS *, int, char **);
|
||||
virtual ~DumpAtomADIOS();
|
||||
public:
|
||||
DumpAtomADIOS(class LAMMPS *, int, char **);
|
||||
~DumpAtomADIOS() override;
|
||||
|
||||
protected:
|
||||
virtual void openfile();
|
||||
virtual void write();
|
||||
virtual void init_style();
|
||||
protected:
|
||||
void openfile() override;
|
||||
void write() override;
|
||||
void init_style() override;
|
||||
|
||||
private:
|
||||
DumpAtomADIOSInternal *internal;
|
||||
private:
|
||||
DumpAtomADIOSInternal *internal;
|
||||
};
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Cannot open dump file %s
|
||||
|
||||
337
src/ADIOS/dump_custom_adios.cpp
Normal file
337
src/ADIOS/dump_custom_adios.cpp
Normal file
@ -0,0 +1,337 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Norbert Podhorszki (ORNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "dump_custom_adios.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix.h"
|
||||
#include "input.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "update.h"
|
||||
#include "variable.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
#include "adios2.h"
|
||||
#include "adios_common.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class DumpCustomADIOSInternal {
|
||||
|
||||
public:
|
||||
DumpCustomADIOSInternal(){};
|
||||
~DumpCustomADIOSInternal() = default;
|
||||
|
||||
// name of adios group, referrable in adios2_config.xml
|
||||
const std::string ioName = "custom";
|
||||
adios2::ADIOS *ad = nullptr; // adios object
|
||||
adios2::IO io; // adios group of variables and attributes in this dump
|
||||
adios2::Engine fh; // adios file/stream handle object
|
||||
// one ADIOS output variable we need to change every step
|
||||
adios2::Variable<double> varAtoms;
|
||||
// list of column names for the atom table
|
||||
// (individual list of 'columns' string)
|
||||
std::vector<std::string> columnNames;
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpCustomADIOS::DumpCustomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg)
|
||||
{
|
||||
// create a default adios2_config.xml if it doesn't exist yet.
|
||||
FILE *cfgfp = fopen("adios2_config.xml", "r");
|
||||
if (!cfgfp) {
|
||||
cfgfp = fopen("adios2_config.xml", "w");
|
||||
if (cfgfp) fputs(default_config, cfgfp);
|
||||
}
|
||||
if (cfgfp) fclose(cfgfp);
|
||||
|
||||
internal = new DumpCustomADIOSInternal();
|
||||
try {
|
||||
internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON);
|
||||
} catch (std::ios_base::failure &e) {
|
||||
error->all(FLERR, "ADIOS initialization failed with error: {}", e.what());
|
||||
}
|
||||
|
||||
internal->columnNames.reserve(nfield);
|
||||
for (int i = 0; i < nfield; ++i) { internal->columnNames.push_back(earg[i]); }
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpCustomADIOS::~DumpCustomADIOS()
|
||||
{
|
||||
internal->columnNames.clear();
|
||||
if (internal->fh) { internal->fh.Close(); }
|
||||
delete internal->ad;
|
||||
delete internal;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomADIOS::openfile()
|
||||
{
|
||||
if (multifile) {
|
||||
// if one file per timestep, replace '*' with current timestep
|
||||
auto filecurrent = utils::star_subst(filename, update->ntimestep, padflag);
|
||||
internal->fh = internal->io.Open(filecurrent, adios2::Mode::Write, world);
|
||||
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filecurrent);
|
||||
} else {
|
||||
if (!singlefile_opened) {
|
||||
internal->fh = internal->io.Open(filename, adios2::Mode::Write, world);
|
||||
if (!internal->fh) error->one(FLERR, "Cannot open dump file {}", filename);
|
||||
singlefile_opened = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomADIOS::write()
|
||||
{
|
||||
if (domain->triclinic == 0) {
|
||||
boxxlo = domain->boxlo[0];
|
||||
boxxhi = domain->boxhi[0];
|
||||
boxylo = domain->boxlo[1];
|
||||
boxyhi = domain->boxhi[1];
|
||||
boxzlo = domain->boxlo[2];
|
||||
boxzhi = domain->boxhi[2];
|
||||
} else {
|
||||
boxxlo = domain->boxlo_bound[0];
|
||||
boxxhi = domain->boxhi_bound[0];
|
||||
boxylo = domain->boxlo_bound[1];
|
||||
boxyhi = domain->boxhi_bound[1];
|
||||
boxzlo = domain->boxlo_bound[2];
|
||||
boxzhi = domain->boxhi_bound[2];
|
||||
boxxy = domain->xy;
|
||||
boxxz = domain->xz;
|
||||
boxyz = domain->yz;
|
||||
}
|
||||
|
||||
// nme = # of dump lines this proc contributes to dump
|
||||
|
||||
nme = count();
|
||||
|
||||
// ntotal = total # of atoms in snapshot
|
||||
// atomOffset = sum of # of atoms up to this proc (exclusive prefix sum)
|
||||
|
||||
bigint bnme = nme;
|
||||
MPI_Allreduce(&bnme, &ntotal, 1, MPI_LMP_BIGINT, MPI_SUM, world);
|
||||
|
||||
bigint atomOffset; // sum of all atoms on processes 0..me-1
|
||||
MPI_Scan(&bnme, &atomOffset, 1, MPI_LMP_BIGINT, MPI_SUM, world);
|
||||
atomOffset -= nme; // exclusive prefix sum needed
|
||||
|
||||
// Now we know the global size and the local subset size and offset
|
||||
// of the atoms table
|
||||
auto nAtomsGlobal = static_cast<size_t>(ntotal);
|
||||
auto startRow = static_cast<size_t>(atomOffset);
|
||||
auto nAtomsLocal = static_cast<size_t>(nme);
|
||||
auto nColumns = static_cast<size_t>(size_one);
|
||||
internal->varAtoms.SetShape({nAtomsGlobal, nColumns});
|
||||
internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}});
|
||||
|
||||
// insure filewriter proc can receive everyone's info
|
||||
// limit nmax*size_one to int since used as arg in MPI_Rsend() below
|
||||
// pack my data into buf
|
||||
// if sorting on IDs also request ID list from pack()
|
||||
// sort buf as needed
|
||||
|
||||
if (nme > maxbuf) {
|
||||
if ((bigint) nme * size_one > MAXSMALLINT) error->all(FLERR, "Too much per-proc info for dump");
|
||||
maxbuf = nme;
|
||||
memory->destroy(buf);
|
||||
memory->create(buf, (maxbuf * size_one), "dump:buf");
|
||||
}
|
||||
if (sort_flag && sortcol == 0 && nme > maxids) {
|
||||
maxids = nme;
|
||||
memory->destroy(ids);
|
||||
memory->create(ids, maxids, "dump:ids");
|
||||
}
|
||||
|
||||
if (sort_flag && sortcol == 0)
|
||||
pack(ids);
|
||||
else
|
||||
pack(nullptr);
|
||||
if (sort_flag) sort();
|
||||
|
||||
openfile();
|
||||
internal->fh.BeginStep();
|
||||
// write info on data as scalars (by me==0)
|
||||
if (me == 0) {
|
||||
internal->fh.Put<uint64_t>("ntimestep", update->ntimestep);
|
||||
internal->fh.Put<int>("nprocs", nprocs);
|
||||
|
||||
internal->fh.Put<double>("boxxlo", boxxlo);
|
||||
internal->fh.Put<double>("boxxhi", boxxhi);
|
||||
internal->fh.Put<double>("boxylo", boxylo);
|
||||
internal->fh.Put<double>("boxyhi", boxyhi);
|
||||
internal->fh.Put<double>("boxzlo", boxzlo);
|
||||
internal->fh.Put<double>("boxzhi", boxzhi);
|
||||
|
||||
if (domain->triclinic) {
|
||||
internal->fh.Put<double>("boxxy", boxxy);
|
||||
internal->fh.Put<double>("boxxz", boxxz);
|
||||
internal->fh.Put<double>("boxyz", boxyz);
|
||||
}
|
||||
}
|
||||
// Everyone needs to write scalar variables that are used as dimensions and
|
||||
// offsets of arrays
|
||||
internal->fh.Put<uint64_t>("natoms", ntotal);
|
||||
internal->fh.Put<int>("ncolumns", size_one);
|
||||
internal->fh.Put<uint64_t>("nme", bnme);
|
||||
internal->fh.Put<uint64_t>("offset", atomOffset);
|
||||
// now write the atoms
|
||||
internal->fh.Put<double>("atoms", buf);
|
||||
internal->fh.EndStep(); // I/O will happen now...
|
||||
|
||||
if (multifile) { internal->fh.Close(); }
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomADIOS::init_style()
|
||||
{
|
||||
// assemble column string from defaults and user values
|
||||
|
||||
delete[] columns;
|
||||
std::string combined;
|
||||
int icol = 0;
|
||||
for (auto item : utils::split_words(columns_default)) {
|
||||
if (combined.size()) combined += " ";
|
||||
if (keyword_user[icol].size()) combined += keyword_user[icol];
|
||||
else combined += item;
|
||||
++icol;
|
||||
}
|
||||
columns = utils::strdup(combined);
|
||||
|
||||
// setup boundary string
|
||||
|
||||
domain->boundary_string(boundstr);
|
||||
|
||||
// remove % from filename since ADIOS always writes a global file with
|
||||
// data/metadata
|
||||
char *ptr = strchr(filename, '%');
|
||||
if (ptr) {
|
||||
while (*ptr) {
|
||||
ptr[0] = ptr[1];
|
||||
++ptr;
|
||||
}
|
||||
}
|
||||
|
||||
/* The next four loops are copied from dump_custom_mpiio, but nothing is
|
||||
* done with them.
|
||||
* It is unclear why we need them here.
|
||||
* For metadata, variable[] will be written out as an ADIOS attribute if
|
||||
* nvariable>0
|
||||
*/
|
||||
// find current ptr for each compute,fix,variable
|
||||
// check that fix frequency is acceptable
|
||||
int icompute;
|
||||
for (int i = 0; i < ncompute; i++) {
|
||||
icompute = modify->find_compute(id_compute[i]);
|
||||
if (icompute < 0) error->all(FLERR, "Could not find dump custom compute ID");
|
||||
compute[i] = modify->compute[icompute];
|
||||
}
|
||||
|
||||
int ifix;
|
||||
for (int i = 0; i < nfix; i++) {
|
||||
ifix = modify->find_fix(id_fix[i]);
|
||||
if (ifix < 0) error->all(FLERR, "Could not find dump custom fix ID");
|
||||
fix[i] = modify->fix[ifix];
|
||||
if (nevery % modify->fix[ifix]->peratom_freq)
|
||||
error->all(FLERR, "Dump custom and fix not computed at compatible times");
|
||||
}
|
||||
|
||||
int ivariable;
|
||||
for (int i = 0; i < nvariable; i++) {
|
||||
ivariable = input->variable->find(id_variable[i]);
|
||||
if (ivariable < 0) error->all(FLERR, "Could not find dump custom variable name");
|
||||
variable[i] = ivariable;
|
||||
}
|
||||
|
||||
// set index and check validity of region
|
||||
if (iregion >= 0) {
|
||||
iregion = domain->find_region(idregion);
|
||||
if (iregion == -1) error->all(FLERR, "Region ID for dump custom does not exist");
|
||||
}
|
||||
|
||||
/* Define the group of variables for the atom style here since it's a fixed
|
||||
* set */
|
||||
internal->io = internal->ad->DeclareIO(internal->ioName);
|
||||
if (!internal->io.InConfigFile()) {
|
||||
// if not defined by user, we can change the default settings
|
||||
// BPFile is the default writer
|
||||
internal->io.SetEngine("BPFile");
|
||||
int num_aggregators = multiproc;
|
||||
if (num_aggregators == 0) num_aggregators = 1;
|
||||
auto nstreams = std::to_string(num_aggregators);
|
||||
internal->io.SetParameters({{"substreams", nstreams}});
|
||||
if (me == 0)
|
||||
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
|
||||
nstreams);
|
||||
}
|
||||
|
||||
internal->io.DefineVariable<uint64_t>("ntimestep");
|
||||
internal->io.DefineVariable<uint64_t>("natoms");
|
||||
|
||||
internal->io.DefineVariable<int>("nprocs");
|
||||
internal->io.DefineVariable<int>("ncolumns");
|
||||
|
||||
internal->io.DefineVariable<double>("boxxlo");
|
||||
internal->io.DefineVariable<double>("boxxhi");
|
||||
internal->io.DefineVariable<double>("boxylo");
|
||||
internal->io.DefineVariable<double>("boxyhi");
|
||||
internal->io.DefineVariable<double>("boxzlo");
|
||||
internal->io.DefineVariable<double>("boxzhi");
|
||||
|
||||
internal->io.DefineVariable<double>("boxxy");
|
||||
internal->io.DefineVariable<double>("boxxz");
|
||||
internal->io.DefineVariable<double>("boxyz");
|
||||
|
||||
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
|
||||
|
||||
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
|
||||
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
|
||||
|
||||
auto nColumns = static_cast<size_t>(size_one);
|
||||
internal->io.DefineAttribute<std::string>("columns", internal->columnNames.data(), nColumns);
|
||||
internal->io.DefineAttribute<std::string>("columnstr", columns);
|
||||
internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
|
||||
internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "custom");
|
||||
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
|
||||
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
|
||||
|
||||
internal->io.DefineVariable<uint64_t>("nme",
|
||||
{adios2::LocalValueDim}); // local dimension variable
|
||||
internal->io.DefineVariable<uint64_t>("offset",
|
||||
{adios2::LocalValueDim}); // local dimension variable
|
||||
|
||||
// atom table size is not known at the moment
|
||||
// it will be correctly defined at the moment of write
|
||||
size_t UnknownSizeYet = 1;
|
||||
internal->varAtoms = internal->io.DefineVariable<double>(
|
||||
"atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
|
||||
}
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -13,7 +13,7 @@
|
||||
|
||||
#ifdef DUMP_CLASS
|
||||
// clang-format off
|
||||
DumpStyle(custom/adios, DumpCustomADIOS)
|
||||
DumpStyle(custom/adios, DumpCustomADIOS);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
@ -22,31 +22,29 @@ DumpStyle(custom/adios, DumpCustomADIOS)
|
||||
|
||||
#include "dump_custom.h"
|
||||
|
||||
namespace LAMMPS_NS
|
||||
{
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DumpCustomADIOSInternal;
|
||||
|
||||
class DumpCustomADIOS : public DumpCustom
|
||||
{
|
||||
public:
|
||||
DumpCustomADIOS(class LAMMPS *, int, char **);
|
||||
virtual ~DumpCustomADIOS();
|
||||
class DumpCustomADIOS : public DumpCustom {
|
||||
public:
|
||||
DumpCustomADIOS(class LAMMPS *, int, char **);
|
||||
~DumpCustomADIOS() override;
|
||||
|
||||
protected:
|
||||
virtual void openfile();
|
||||
virtual void write();
|
||||
virtual void init_style();
|
||||
protected:
|
||||
void openfile() override;
|
||||
void write() override;
|
||||
void init_style() override;
|
||||
|
||||
private:
|
||||
DumpCustomADIOSInternal *internal;
|
||||
private:
|
||||
DumpCustomADIOSInternal *internal;
|
||||
};
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Cannot open dump file %s
|
||||
|
||||
456
src/ADIOS/reader_adios.cpp
Normal file
456
src/ADIOS/reader_adios.cpp
Normal file
@ -0,0 +1,456 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Norbert Podhorszki (Oak Ridge National Laboratory)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "reader_adios.h"
|
||||
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
|
||||
#include "adios2.h"
|
||||
#include "adios_common.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
// also in read_dump.cpp
|
||||
|
||||
enum { ID, TYPE, X, Y, Z, VX, VY, VZ, Q, IX, IY, IZ, FX, FY, FZ };
|
||||
enum { UNSET, NOSCALE_NOWRAP, NOSCALE_WRAP, SCALE_NOWRAP, SCALE_WRAP };
|
||||
|
||||
#define SMALL 1.0e-6
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class ReadADIOSInternal {
|
||||
|
||||
public:
|
||||
ReadADIOSInternal(){};
|
||||
~ReadADIOSInternal() = default;
|
||||
|
||||
// name of adios group, referrable in adios2_config.xml
|
||||
const std::string ioName = "read_dump";
|
||||
adios2::ADIOS *ad = nullptr; // adios object
|
||||
adios2::IO io; // adios group of variables and attributes in this dump
|
||||
adios2::Engine fh; // adios file/stream handle object
|
||||
// ADIOS input variables we need to change every step
|
||||
adios2::Variable<uint64_t> varNtimestep;
|
||||
adios2::Variable<uint64_t> varNatoms;
|
||||
adios2::Variable<double> varAtoms;
|
||||
// list of column names for the atom table
|
||||
// (individual list of 'columns' string)
|
||||
std::vector<std::string> columnNames;
|
||||
float timeout = 0.0;
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ReaderADIOS::ReaderADIOS(LAMMPS *lmp) : Reader(lmp)
|
||||
{
|
||||
fieldindex = nullptr;
|
||||
nAtoms = 0;
|
||||
nAtomsTotal = 0;
|
||||
atomOffset = 0;
|
||||
nstep = 0;
|
||||
nid = 0;
|
||||
me = comm->me;
|
||||
|
||||
// create a default adios2_config.xml if it doesn't exist yet.
|
||||
FILE *cfgfp = fopen("adios2_config.xml", "r");
|
||||
if (!cfgfp) {
|
||||
cfgfp = fopen("adios2_config.xml", "w");
|
||||
if (cfgfp) fputs(default_config, cfgfp);
|
||||
}
|
||||
if (cfgfp) fclose(cfgfp);
|
||||
|
||||
internal = new ReadADIOSInternal();
|
||||
try {
|
||||
internal->ad = new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON);
|
||||
} catch (std::ios_base::failure &e) {
|
||||
error->one(FLERR, "ADIOS initialization failed with error: {}", e.what());
|
||||
}
|
||||
|
||||
/* Define the group holding all variables and attributes */
|
||||
internal->io = internal->ad->DeclareIO(internal->ioName);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ReaderADIOS::~ReaderADIOS()
|
||||
{
|
||||
if (me == 0) memory->destroy(fieldindex);
|
||||
internal->columnNames.clear();
|
||||
if (internal->fh) internal->fh.Close();
|
||||
delete internal->ad;
|
||||
delete internal;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pass on settings to find and load the proper plugin
|
||||
Called by all processors.
|
||||
------------------------------------------------------------------------- */
|
||||
void ReaderADIOS::settings(int narg, char **arg)
|
||||
{
|
||||
int idx = 0;
|
||||
while (idx < narg) {
|
||||
if (!strcmp(arg[idx], "timeout")) {
|
||||
if (idx + 1 < narg) {
|
||||
internal->timeout = std::stof(arg[idx + 1]);
|
||||
internal->io.SetParameter("OpenTimeoutSecs", arg[idx + 1]);
|
||||
++idx;
|
||||
} else {
|
||||
error->one(FLERR, "Missing value for 'timeout' option for ADIOS read_dump command");
|
||||
}
|
||||
}
|
||||
++idx;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
try to open given file
|
||||
Every process must call this Collective operation
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReaderADIOS::open_file(const std::string &file)
|
||||
{
|
||||
// close open file, if needed.
|
||||
if (internal->fh) internal->fh.Close();
|
||||
|
||||
try {
|
||||
internal->fh = internal->io.Open(file, adios2::Mode::Read, world);
|
||||
} catch (std::ios_base::failure &e) {
|
||||
error->one(FLERR, "Error opening file {}: {}", file, e.what());
|
||||
}
|
||||
if (!internal->fh) error->one(FLERR, "Cannot open file {} using ADIOS", file);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
close current file
|
||||
Every process must call this Collective operation
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReaderADIOS::close_file()
|
||||
{
|
||||
// close open file, if needed.
|
||||
if (internal->fh) { internal->fh.Close(); }
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read and return time stamp from dump file
|
||||
if first read reaches end-of-file, return 1 so caller can open next file
|
||||
Called by all processors.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int ReaderADIOS::read_time(bigint &ntimestep)
|
||||
{
|
||||
adios2::StepStatus status = internal->fh.BeginStep(adios2::StepMode::Read, internal->timeout);
|
||||
|
||||
switch (status) {
|
||||
case adios2::StepStatus::EndOfStream:
|
||||
case adios2::StepStatus::NotReady:
|
||||
case adios2::StepStatus::OtherError:
|
||||
return 1;
|
||||
default:
|
||||
break;
|
||||
}
|
||||
|
||||
internal->varNtimestep = internal->io.InquireVariable<uint64_t>("ntimestep");
|
||||
|
||||
if (!internal->varNtimestep)
|
||||
error->one(FLERR, "Did not find 'ntimestep' variable in ADIOS file {}", internal->fh.Name());
|
||||
|
||||
ntimestep = static_cast<bigint>(internal->varNtimestep.Max());
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
skip snapshot for given timestamp
|
||||
Called by all processors.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReaderADIOS::skip()
|
||||
{
|
||||
internal->fh.EndStep();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read remaining header info:
|
||||
return natoms
|
||||
box bounds, triclinic (inferred), fieldflag (1 if any fields not found),
|
||||
xyz flags = from input scaleflag & wrapflag
|
||||
if fieldflag set:
|
||||
match Nfield fields to per-atom column labels
|
||||
allocate and set fieldindex = which column each field maps to
|
||||
fieldtype = X,VX,IZ etc
|
||||
fieldlabel = user-specified label or nullptr if use fieldtype default
|
||||
xyz flag = scaledflag if has fieldlabel name, else set by x,xs,xu,xsu
|
||||
only called by proc 0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bigint ReaderADIOS::read_header(double box[3][3], int &boxinfo, int &triclinic, int fieldinfo,
|
||||
int nfield, int *fieldtype, char **fieldlabel, int scaleflag,
|
||||
int wrapflag, int &fieldflag, int &xflag, int &yflag, int &zflag)
|
||||
{
|
||||
nid = 0;
|
||||
|
||||
// signal that we have no box info at all so far.
|
||||
|
||||
internal->varNatoms = internal->io.InquireVariable<uint64_t>("natoms");
|
||||
if (!internal->varNatoms)
|
||||
error->one(FLERR, "Did not find 'natoms' variable in ADIOS file {}", internal->fh.Name());
|
||||
|
||||
/* nAtoms */
|
||||
nAtomsTotal = internal->varNatoms.Max();
|
||||
uint64_t rem = nAtomsTotal % comm->nprocs;
|
||||
nAtoms = nAtomsTotal / comm->nprocs;
|
||||
atomOffset = comm->me * nAtoms;
|
||||
if (comm->me < (int)rem) {
|
||||
++nAtoms;
|
||||
atomOffset += comm->me;
|
||||
} else {
|
||||
atomOffset += rem;
|
||||
}
|
||||
|
||||
/* triclinic */
|
||||
adios2::Attribute<int32_t> attTriclinic = internal->io.InquireAttribute<int32_t>("triclinic");
|
||||
if (!attTriclinic)
|
||||
error->one(FLERR, "Did not find 'triclinic' attribute in ADIOS file {}", internal->fh.Name());
|
||||
|
||||
triclinic = attTriclinic.Data()[0];
|
||||
|
||||
/* read Box */
|
||||
adios2::Variable<double> varBoxxlo = internal->io.InquireVariable<double>("boxxlo");
|
||||
adios2::Variable<double> varBoxxhi = internal->io.InquireVariable<double>("boxxhi");
|
||||
adios2::Variable<double> varBoxylo = internal->io.InquireVariable<double>("boxylo");
|
||||
adios2::Variable<double> varBoxyhi = internal->io.InquireVariable<double>("boxyhi");
|
||||
adios2::Variable<double> varBoxzlo = internal->io.InquireVariable<double>("boxzlo");
|
||||
adios2::Variable<double> varBoxzhi = internal->io.InquireVariable<double>("boxzhi");
|
||||
|
||||
box[0][0] = varBoxxlo.Max();
|
||||
box[0][1] = varBoxxhi.Max();
|
||||
box[0][2] = 0.0;
|
||||
box[1][0] = varBoxylo.Max();
|
||||
box[1][1] = varBoxyhi.Max();
|
||||
box[1][2] = 0.0;
|
||||
box[2][0] = varBoxzlo.Max();
|
||||
box[2][1] = varBoxzhi.Max();
|
||||
box[2][2] = 0.0;
|
||||
|
||||
if (triclinic) {
|
||||
adios2::Variable<double> varBoxxy = internal->io.InquireVariable<double>("boxxy");
|
||||
adios2::Variable<double> varBoxxz = internal->io.InquireVariable<double>("boxxz");
|
||||
adios2::Variable<double> varBoxyz = internal->io.InquireVariable<double>("boxyz");
|
||||
|
||||
box[0][2] = varBoxxy.Max();
|
||||
box[1][2] = varBoxxz.Max();
|
||||
box[2][2] = varBoxyz.Max();
|
||||
}
|
||||
|
||||
boxinfo = 1;
|
||||
|
||||
// if no field info requested, just return
|
||||
|
||||
if (!fieldinfo) return nAtoms;
|
||||
|
||||
memory->create(fieldindex, nfield, "read_dump:fieldindex");
|
||||
|
||||
/* Columns */
|
||||
adios2::Attribute<std::string> attColumns = internal->io.InquireAttribute<std::string>("columns");
|
||||
|
||||
std::vector<std::string> labelVector = attColumns.Data();
|
||||
int nwords = labelVector.size();
|
||||
std::map<std::string, int> labels;
|
||||
for (int i = 0; i < nwords; ++i) { labels.emplace(labelVector[i], i); }
|
||||
|
||||
int s_index, u_index, su_index;
|
||||
xflag = UNSET;
|
||||
yflag = UNSET;
|
||||
zflag = UNSET;
|
||||
|
||||
// copy fieldtype list for supported fields
|
||||
|
||||
for (int i = 0; i < nfield; i++) {
|
||||
if (fieldlabel[i]) {
|
||||
fieldindex[i] = find_label(fieldlabel[i], labels);
|
||||
if (fieldtype[i] == X)
|
||||
xflag = 2 * scaleflag + wrapflag + 1;
|
||||
else if (fieldtype[i] == Y)
|
||||
yflag = 2 * scaleflag + wrapflag + 1;
|
||||
else if (fieldtype[i] == Z)
|
||||
zflag = 2 * scaleflag + wrapflag + 1;
|
||||
}
|
||||
|
||||
else if (fieldtype[i] == ID)
|
||||
fieldindex[i] = find_label("id", labels);
|
||||
else if (fieldtype[i] == TYPE)
|
||||
fieldindex[i] = find_label("type", labels);
|
||||
|
||||
else if (fieldtype[i] == X) {
|
||||
fieldindex[i] = find_label("x", labels);
|
||||
xflag = NOSCALE_WRAP;
|
||||
if (fieldindex[i] < 0) {
|
||||
fieldindex[i] = nwords;
|
||||
s_index = find_label("xs", labels);
|
||||
u_index = find_label("xu", labels);
|
||||
su_index = find_label("xsu", labels);
|
||||
if (s_index >= 0 && s_index < fieldindex[i]) {
|
||||
fieldindex[i] = s_index;
|
||||
xflag = SCALE_WRAP;
|
||||
}
|
||||
if (u_index >= 0 && u_index < fieldindex[i]) {
|
||||
fieldindex[i] = u_index;
|
||||
xflag = NOSCALE_NOWRAP;
|
||||
}
|
||||
if (su_index >= 0 && su_index < fieldindex[i]) {
|
||||
fieldindex[i] = su_index;
|
||||
xflag = SCALE_NOWRAP;
|
||||
}
|
||||
}
|
||||
if (fieldindex[i] == nwords) fieldindex[i] = -1;
|
||||
|
||||
} else if (fieldtype[i] == Y) {
|
||||
fieldindex[i] = find_label("y", labels);
|
||||
yflag = NOSCALE_WRAP;
|
||||
if (fieldindex[i] < 0) {
|
||||
fieldindex[i] = nwords;
|
||||
s_index = find_label("ys", labels);
|
||||
u_index = find_label("yu", labels);
|
||||
su_index = find_label("ysu", labels);
|
||||
if (s_index >= 0 && s_index < fieldindex[i]) {
|
||||
fieldindex[i] = s_index;
|
||||
yflag = SCALE_WRAP;
|
||||
}
|
||||
if (u_index >= 0 && u_index < fieldindex[i]) {
|
||||
fieldindex[i] = u_index;
|
||||
yflag = NOSCALE_NOWRAP;
|
||||
}
|
||||
if (su_index >= 0 && su_index < fieldindex[i]) {
|
||||
fieldindex[i] = su_index;
|
||||
yflag = SCALE_NOWRAP;
|
||||
}
|
||||
}
|
||||
if (fieldindex[i] == nwords) fieldindex[i] = -1;
|
||||
|
||||
} else if (fieldtype[i] == Z) {
|
||||
fieldindex[i] = find_label("z", labels);
|
||||
zflag = NOSCALE_WRAP;
|
||||
if (fieldindex[i] < 0) {
|
||||
fieldindex[i] = nwords;
|
||||
s_index = find_label("zs", labels);
|
||||
u_index = find_label("zu", labels);
|
||||
su_index = find_label("zsu", labels);
|
||||
if (s_index >= 0 && s_index < fieldindex[i]) {
|
||||
fieldindex[i] = s_index;
|
||||
zflag = SCALE_WRAP;
|
||||
}
|
||||
if (u_index >= 0 && u_index < fieldindex[i]) {
|
||||
fieldindex[i] = u_index;
|
||||
zflag = NOSCALE_NOWRAP;
|
||||
}
|
||||
if (su_index >= 0 && su_index < fieldindex[i]) {
|
||||
fieldindex[i] = su_index;
|
||||
zflag = SCALE_NOWRAP;
|
||||
}
|
||||
}
|
||||
if (fieldindex[i] == nwords) fieldindex[i] = -1;
|
||||
|
||||
} else if (fieldtype[i] == VX)
|
||||
fieldindex[i] = find_label("vx", labels);
|
||||
else if (fieldtype[i] == VY)
|
||||
fieldindex[i] = find_label("vy", labels);
|
||||
else if (fieldtype[i] == VZ)
|
||||
fieldindex[i] = find_label("vz", labels);
|
||||
|
||||
else if (fieldtype[i] == FX)
|
||||
fieldindex[i] = find_label("fx", labels);
|
||||
else if (fieldtype[i] == FY)
|
||||
fieldindex[i] = find_label("fy", labels);
|
||||
else if (fieldtype[i] == FZ)
|
||||
fieldindex[i] = find_label("fz", labels);
|
||||
|
||||
else if (fieldtype[i] == Q)
|
||||
fieldindex[i] = find_label("q", labels);
|
||||
|
||||
else if (fieldtype[i] == IX)
|
||||
fieldindex[i] = find_label("ix", labels);
|
||||
else if (fieldtype[i] == IY)
|
||||
fieldindex[i] = find_label("iy", labels);
|
||||
else if (fieldtype[i] == IZ)
|
||||
fieldindex[i] = find_label("iz", labels);
|
||||
}
|
||||
|
||||
// set fieldflag = -1 if any unfound fields
|
||||
|
||||
fieldflag = 0;
|
||||
for (int i = 0; i < nfield; i++)
|
||||
if (fieldindex[i] < 0) fieldflag = -1;
|
||||
|
||||
return nAtoms;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read N atom lines from dump file
|
||||
stores appropriate values in fields array
|
||||
return 0 if success, 1 if error
|
||||
only called by proc 0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReaderADIOS::read_atoms(int n, int nfield, double **fields)
|
||||
{
|
||||
/* Read Atoms */
|
||||
/* This is the firsts (and last) read of array data, so we
|
||||
* call EndStep() here instead of PerformGets()
|
||||
*/
|
||||
|
||||
adios2::Variable<double> varAtoms = internal->io.InquireVariable<double>("atoms");
|
||||
|
||||
if ((uint64_t)n != nAtoms)
|
||||
error->one(FLERR,
|
||||
"ReaderADIOS::read_atoms() expects 'n={}' equal to the number of "
|
||||
"atoms (={}) for process {} in ADIOS file {}.",
|
||||
n, nAtoms, comm->me, internal->fh.Name());
|
||||
|
||||
size_t ncols = varAtoms.Count()[1];
|
||||
varAtoms.SetSelection({{atomOffset, 0}, {nAtoms, ncols}});
|
||||
|
||||
std::vector<double> table;
|
||||
|
||||
internal->fh.Get<double>(varAtoms, table);
|
||||
// EndStep or PerformGets required to make the read happen
|
||||
internal->fh.EndStep();
|
||||
|
||||
size_t idx;
|
||||
for (uint64_t i = 0; i < nAtoms; i++) {
|
||||
idx = i * ncols;
|
||||
for (int m = 0; m < nfield; m++) { fields[i][m] = table[idx + fieldindex[m]]; }
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
match label to any of N labels
|
||||
return index of match or -1 if no match
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int ReaderADIOS::find_label(const std::string &label, const std::map<std::string, int> &labels)
|
||||
{
|
||||
auto it = labels.find(label);
|
||||
if (it != labels.end()) { return it->second; }
|
||||
return -1;
|
||||
}
|
||||
69
src/ADIOS/reader_adios.h
Normal file
69
src/ADIOS/reader_adios.h
Normal file
@ -0,0 +1,69 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Contributed by Norbert Podhorszki (Oak Ridge National Laboratory)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef READER_CLASS
|
||||
// clang-format off
|
||||
ReaderStyle(adios, ReaderADIOS);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_READER_ADIOS_H
|
||||
#define LMP_READER_ADIOS_H
|
||||
|
||||
#include "reader.h"
|
||||
|
||||
#include <map>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class ReadADIOSInternal;
|
||||
|
||||
class ReaderADIOS : public Reader {
|
||||
public:
|
||||
ReaderADIOS(class LAMMPS *);
|
||||
~ReaderADIOS() override;
|
||||
|
||||
void settings(int, char **) override;
|
||||
|
||||
int read_time(bigint &) override;
|
||||
void skip() override;
|
||||
bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
|
||||
int &, int &, int &) override;
|
||||
void read_atoms(int, int, double **) override;
|
||||
|
||||
void open_file(const std::string &) override;
|
||||
void close_file() override;
|
||||
|
||||
private:
|
||||
int *fieldindex; // mapping of input fields to dump
|
||||
uint64_t nAtomsTotal; // current number of atoms in entire dump step
|
||||
uint64_t nAtoms; // current number of atoms for this process
|
||||
// (Sum(nAtoms)=nAtomsTotal)
|
||||
uint64_t atomOffset; // starting atom position for this process to read
|
||||
|
||||
bigint nstep; // current (time) step number
|
||||
bigint nid; // current atom id.
|
||||
|
||||
int me;
|
||||
ReadADIOSInternal *internal;
|
||||
|
||||
int find_label(const std::string &label, const std::map<std::string, int> &labels);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -42,9 +43,9 @@ void ComputeERotateAsphere::init()
|
||||
{
|
||||
// error check
|
||||
|
||||
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
avec_line = (AtomVecLine *) atom->style_match("line");
|
||||
avec_tri = (AtomVecTri *) atom->style_match("tri");
|
||||
avec_ellipsoid = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
||||
avec_line = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
|
||||
avec_tri = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
|
||||
if (!avec_ellipsoid && !avec_line && !avec_tri)
|
||||
error->all(FLERR,"Compute erotate/asphere requires "
|
||||
"atom style ellipsoid or line or tri");
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(erotate/asphere,ComputeERotateAsphere)
|
||||
|
||||
// clang-format off
|
||||
ComputeStyle(erotate/asphere,ComputeERotateAsphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_EROTATE_ASPHERE_H
|
||||
@ -27,8 +27,8 @@ namespace LAMMPS_NS {
|
||||
class ComputeERotateAsphere : public Compute {
|
||||
public:
|
||||
ComputeERotateAsphere(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
double compute_scalar();
|
||||
void init() override;
|
||||
double compute_scalar() override;
|
||||
|
||||
private:
|
||||
double pfactor;
|
||||
@ -37,7 +37,7 @@ class ComputeERotateAsphere : public Compute {
|
||||
class AtomVecTri *avec_tri;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -58,9 +59,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute temp/asphere command");
|
||||
tempbias = 1;
|
||||
int n = strlen(arg[iarg+1]) + 1;
|
||||
id_bias = new char[n];
|
||||
strcpy(id_bias,arg[iarg+1]);
|
||||
id_bias = utils::strdup(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"dof") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
@ -95,7 +94,7 @@ void ComputeTempAsphere::init()
|
||||
{
|
||||
// error check
|
||||
|
||||
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
||||
if (!avec)
|
||||
error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid");
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(temp/asphere,ComputeTempAsphere)
|
||||
|
||||
// clang-format off
|
||||
ComputeStyle(temp/asphere,ComputeTempAsphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_TEMP_ASPHERE_H
|
||||
@ -27,28 +27,28 @@ namespace LAMMPS_NS {
|
||||
class ComputeTempAsphere : public Compute {
|
||||
public:
|
||||
ComputeTempAsphere(class LAMMPS *, int, char **);
|
||||
~ComputeTempAsphere();
|
||||
void init();
|
||||
void setup();
|
||||
double compute_scalar();
|
||||
void compute_vector();
|
||||
~ComputeTempAsphere() override;
|
||||
void init() override;
|
||||
void setup() override;
|
||||
double compute_scalar() override;
|
||||
void compute_vector() override;
|
||||
|
||||
void remove_bias(int, double *);
|
||||
void restore_bias(int, double *);
|
||||
void remove_bias_thr(int, double *, double *);
|
||||
void restore_bias_thr(int, double *, double *);
|
||||
void remove_bias(int, double *) override;
|
||||
void restore_bias(int, double *) override;
|
||||
void remove_bias_thr(int, double *, double *) override;
|
||||
void restore_bias_thr(int, double *, double *) override;
|
||||
|
||||
private:
|
||||
int mode;
|
||||
double tfactor;
|
||||
char *id_bias;
|
||||
class Compute *tbias; // ptr to additional bias compute
|
||||
class Compute *tbias; // ptr to additional bias compute
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
void dof_compute();
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -35,7 +36,7 @@ FixNHAsphere::FixNHAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
void FixNHAsphere::init()
|
||||
{
|
||||
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
||||
if (!avec)
|
||||
error->all(FLERR,
|
||||
"Compute nvt/nph/npt asphere requires atom style ellipsoid");
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -21,19 +21,18 @@ namespace LAMMPS_NS {
|
||||
class FixNHAsphere : public FixNH {
|
||||
public:
|
||||
FixNHAsphere(class LAMMPS *, int, char **);
|
||||
virtual ~FixNHAsphere() {}
|
||||
void init();
|
||||
void init() override;
|
||||
|
||||
protected:
|
||||
double dtq;
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
void nve_v();
|
||||
void nve_x();
|
||||
void nh_v_temp();
|
||||
void nve_v() override;
|
||||
void nve_x() override;
|
||||
void nh_v_temp() override;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,10 +13,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_nph_asphere.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
#include "modify.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -36,21 +36,15 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp,tcmd.c_str());
|
||||
|
||||
modify->add_compute(tcmd + " all temp/asphere");
|
||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||
modify->add_compute(fmt::format("{} all temp/asphere",id_temp));
|
||||
tcomputeflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
std::string pcmd = id + std::string("_press");
|
||||
id_press = new char[pcmd.size()+1];
|
||||
strcpy(id_press,pcmd.c_str());
|
||||
|
||||
modify->add_compute(pcmd + " all pressure " + std::string(id_temp));
|
||||
id_press = utils::strdup(std::string(id) + "_press");
|
||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
||||
pcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nph/asphere,FixNPHAsphere)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nph/asphere,FixNPHAsphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPH_ASPHERE_H
|
||||
@ -27,10 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNPHAsphere : public FixNHAsphere {
|
||||
public:
|
||||
FixNPHAsphere(class LAMMPS *, int, char **);
|
||||
~FixNPHAsphere() {}
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,10 +13,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_npt_asphere.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
#include "modify.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -35,21 +35,15 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp,tcmd.c_str());
|
||||
|
||||
modify->add_compute(tcmd + " all temp/asphere");
|
||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||
modify->add_compute(fmt::format("{} all temp/asphere",id_temp));
|
||||
tcomputeflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
std::string pcmd = id + std::string("_press");
|
||||
id_press = new char[pcmd.size()+1];
|
||||
strcpy(id_press,pcmd.c_str());
|
||||
|
||||
modify->add_compute(pcmd + " all pressure " + std::string(id_temp));
|
||||
id_press = utils::strdup(std::string(id) + "_press");
|
||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
||||
pcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(npt/asphere,FixNPTAsphere)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(npt/asphere,FixNPTAsphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPT_ASPHERE_H
|
||||
@ -27,10 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNPTAsphere : public FixNHAsphere {
|
||||
public:
|
||||
FixNPTAsphere(class LAMMPS *, int, char **);
|
||||
~FixNPTAsphere() {}
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -16,10 +17,11 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_nve_asphere.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "error.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -35,7 +37,7 @@ FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
void FixNVEAsphere::init()
|
||||
{
|
||||
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
||||
if (!avec)
|
||||
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/asphere,FixNVEAsphere)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/asphere,FixNVEAsphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_ASPHERE_H
|
||||
@ -27,16 +27,16 @@ namespace LAMMPS_NS {
|
||||
class FixNVEAsphere : public FixNVE {
|
||||
public:
|
||||
FixNVEAsphere(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
class AtomVecEllipsoid *avec;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -36,7 +37,7 @@ void FixNVEAsphereNoforce::init()
|
||||
{
|
||||
// error check
|
||||
|
||||
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
||||
if (!atom->ellipsoid_flag)
|
||||
error->all(FLERR,"Fix nve/asphere/noforce requires atom style ellipsoid");
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/asphere/noforce,FixNVEAsphereNoforce)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/asphere/noforce,FixNVEAsphereNoforce);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_ASPHERE_NOFORCE_H
|
||||
@ -27,15 +27,15 @@ namespace LAMMPS_NS {
|
||||
class FixNVEAsphereNoforce : public FixNVENoforce {
|
||||
public:
|
||||
FixNVEAsphereNoforce(class LAMMPS *, int, char **);
|
||||
void initial_integrate(int);
|
||||
void init();
|
||||
void initial_integrate(int) override;
|
||||
void init() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
class AtomVecEllipsoid *avec;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -55,7 +56,7 @@ void FixNVELine::init()
|
||||
{
|
||||
// error checks
|
||||
|
||||
avec = (AtomVecLine *) atom->style_match("line");
|
||||
avec = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
|
||||
if (!avec) error->all(FLERR,"Fix nve/line requires atom style line");
|
||||
|
||||
if (domain->dimension != 2)
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/line,FixNVELine)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/line,FixNVELine);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_LINE_H
|
||||
@ -27,18 +27,17 @@ namespace LAMMPS_NS {
|
||||
class FixNVELine : public FixNVE {
|
||||
public:
|
||||
FixNVELine(class LAMMPS *, int, char **);
|
||||
~FixNVELine() {}
|
||||
int setmask();
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double MINUSPI,TWOPI;
|
||||
double MINUSPI, TWOPI;
|
||||
class AtomVecLine *avec;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -49,7 +50,7 @@ void FixNVETri::init()
|
||||
{
|
||||
// error checks
|
||||
|
||||
avec = (AtomVecTri *) atom->style_match("tri");
|
||||
avec = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
|
||||
if (!avec) error->all(FLERR,"Fix nve/tri requires atom style tri");
|
||||
|
||||
if (domain->dimension != 3)
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/tri,FixNVETri)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/tri,FixNVETri);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_TRI_H
|
||||
@ -27,18 +27,17 @@ namespace LAMMPS_NS {
|
||||
class FixNVETri : public FixNVE {
|
||||
public:
|
||||
FixNVETri(class LAMMPS *, int, char **);
|
||||
~FixNVETri() {}
|
||||
int setmask();
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
class AtomVecTri *avec;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,12 +13,10 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_nvt_asphere.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "error.h"
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -35,11 +34,8 @@ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
|
||||
std::string cmd = id + std::string("_temp");
|
||||
id_temp = new char[cmd.size()+1];
|
||||
strcpy(id_temp,cmd.c_str());
|
||||
|
||||
cmd += fmt::format(" {} temp/asphere",group->names[igroup]);
|
||||
modify->add_compute(cmd);
|
||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||
modify->add_compute(fmt::format("{} {} temp/asphere",
|
||||
id_temp,group->names[igroup]));
|
||||
tcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nvt/asphere,FixNVTAsphere)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nvt/asphere,FixNVTAsphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVT_ASPHERE_H
|
||||
@ -27,10 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNVTAsphere : public FixNHAsphere {
|
||||
public:
|
||||
FixNVTAsphere(class LAMMPS *, int, char **);
|
||||
~FixNVTAsphere() {}
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -17,18 +18,18 @@
|
||||
|
||||
#include "pair_gayberne.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "math_extra.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "citeme.h"
|
||||
#include "memory.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -344,10 +345,10 @@ void PairGayBerne::coeff(int narg, char **arg)
|
||||
|
||||
void PairGayBerne::init_style()
|
||||
{
|
||||
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
||||
if (!avec) error->all(FLERR,"Pair gayberne requires atom style ellipsoid");
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
||||
|
||||
// per-type shape precalculations
|
||||
// require that atom shapes are identical within each type
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(gayberne,PairGayBerne)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(gayberne,PairGayBerne);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_GAYBERNE_H
|
||||
@ -27,52 +27,49 @@ namespace LAMMPS_NS {
|
||||
class PairGayBerne : public Pair {
|
||||
public:
|
||||
PairGayBerne(LAMMPS *lmp);
|
||||
virtual ~PairGayBerne();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
~PairGayBerne() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
|
||||
protected:
|
||||
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
|
||||
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
|
||||
|
||||
double cut_global;
|
||||
double **cut;
|
||||
|
||||
double gamma,upsilon,mu; // Gay-Berne parameters
|
||||
double **shape1; // per-type radii in x, y and z
|
||||
double **shape2; // per-type radii in x, y and z SQUARED
|
||||
double *lshape; // precalculation based on the shape
|
||||
double **well; // well depth scaling along each axis ^ -1.0/mu
|
||||
double **epsilon,**sigma; // epsilon and sigma values for atom-type pairs
|
||||
double gamma, upsilon, mu; // Gay-Berne parameters
|
||||
double **shape1; // per-type radii in x, y and z
|
||||
double **shape2; // per-type radii in x, y and z SQUARED
|
||||
double *lshape; // precalculation based on the shape
|
||||
double **well; // well depth scaling along each axis ^ -1.0/mu
|
||||
double **epsilon, **sigma; // epsilon and sigma values for atom-type pairs
|
||||
|
||||
int **form;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
double **lj1, **lj2, **lj3, **lj4;
|
||||
double **offset;
|
||||
int *setwell;
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
void allocate();
|
||||
double gayberne_analytic(const int i, const int j, double a1[3][3],
|
||||
double a2[3][3], double b1[3][3], double b2[3][3],
|
||||
double g1[3][3], double g2[3][3], double *r12,
|
||||
const double rsq, double *fforce, double *ttor,
|
||||
double gayberne_analytic(const int i, const int j, double a1[3][3], double a2[3][3],
|
||||
double b1[3][3], double b2[3][3], double g1[3][3], double g2[3][3],
|
||||
double *r12, const double rsq, double *fforce, double *ttor,
|
||||
double *rtor);
|
||||
double gayberne_lj(const int i, const int j, double a1[3][3],
|
||||
double b1[3][3],double g1[3][3],double *r12,
|
||||
const double rsq, double *fforce, double *ttor);
|
||||
void compute_eta_torque(double m[3][3], double m2[3][3],
|
||||
double *s, double ans[3][3]);
|
||||
double gayberne_lj(const int i, const int j, double a1[3][3], double b1[3][3], double g1[3][3],
|
||||
double *r12, const double rsq, double *fforce, double *ttor);
|
||||
void compute_eta_torque(double m[3][3], double m2[3][3], double *s, double ans[3][3]);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -300,8 +301,7 @@ void PairLineLJ::compute(int eflag, int vflag)
|
||||
}
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -402,10 +402,10 @@ void PairLineLJ::coeff(int narg, char **arg)
|
||||
|
||||
void PairLineLJ::init_style()
|
||||
{
|
||||
avec = (AtomVecLine *) atom->style_match("line");
|
||||
avec = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
|
||||
if (!avec) error->all(FLERR,"Pair line/lj requires atom style line");
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(line/lj,PairLineLJ)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(line/lj,PairLineLJ);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LINE_LJ_H
|
||||
@ -27,38 +27,38 @@ namespace LAMMPS_NS {
|
||||
class PairLineLJ : public Pair {
|
||||
public:
|
||||
PairLineLJ(class LAMMPS *);
|
||||
virtual ~PairLineLJ();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
~PairLineLJ() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double *subsize;
|
||||
double **epsilon,**sigma,**cutsub,**cutsubsq;
|
||||
double **epsilon, **sigma, **cutsub, **cutsubsq;
|
||||
double **cut;
|
||||
double **lj1,**lj2,**lj3,**lj4; // for sphere/sphere interactions
|
||||
double **lj1, **lj2, **lj3, **lj4; // for sphere/sphere interactions
|
||||
class AtomVecLine *avec;
|
||||
|
||||
double *size; // per-type size of sub-particles to tile line segment
|
||||
double *size; // per-type size of sub-particles to tile line segment
|
||||
|
||||
struct Discrete {
|
||||
double dx,dy;
|
||||
double dx, dy;
|
||||
};
|
||||
Discrete *discrete; // list of all discretes for all lines
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
Discrete *discrete; // list of all discretes for all lines
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
void allocate();
|
||||
void discretize(int, double);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(resquared,PairRESquared)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(resquared,PairRESquared);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_RESQUARED_H
|
||||
@ -27,31 +27,31 @@ namespace LAMMPS_NS {
|
||||
class PairRESquared : public Pair {
|
||||
public:
|
||||
PairRESquared(LAMMPS *lmp);
|
||||
virtual ~PairRESquared();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
~PairRESquared() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
|
||||
protected:
|
||||
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
|
||||
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
|
||||
|
||||
double cut_global;
|
||||
double **cut;
|
||||
|
||||
double **shape1; // per-type radii in x, y and z
|
||||
double **shape2; // per-type radii in x, y and z SQUARED
|
||||
double *lshape; // product of the radii
|
||||
double **well; // well depth scaling along each axis
|
||||
double **epsilon,**sigma; // epsilon and sigma values for atom-type pairs
|
||||
double **shape1; // per-type radii in x, y and z
|
||||
double **shape2; // per-type radii in x, y and z SQUARED
|
||||
double *lshape; // product of the radii
|
||||
double **well; // well depth scaling along each axis
|
||||
double **epsilon, **sigma; // epsilon and sigma values for atom-type pairs
|
||||
|
||||
int **form;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
double **lj1, **lj2, **lj3, **lj4;
|
||||
double **offset;
|
||||
int *setwell;
|
||||
class AtomVecEllipsoid *avec;
|
||||
@ -61,38 +61,35 @@ class PairRESquared : public Pair {
|
||||
struct RE2Vars {
|
||||
// per particle precomputations for energy, force, torque
|
||||
|
||||
double A[3][3]; // Rotation matrix (lab->body)
|
||||
double aTe[3][3]; // A'*E
|
||||
double gamma[3][3]; // A'*S^2*A
|
||||
double A[3][3]; // Rotation matrix (lab->body)
|
||||
double aTe[3][3]; // A'*E
|
||||
double gamma[3][3]; // A'*S^2*A
|
||||
|
||||
// per particle precomputations for torque
|
||||
|
||||
double sa[3][3]; // S^2*A;
|
||||
double lA[3][3][3]; // -A*rotation generator (x,y, or z)
|
||||
double lAtwo[3][3][3]; // A'*S^2*lA
|
||||
double lAsa[3][3][3]; // lAtwo+lA'*sa
|
||||
double sa[3][3]; // S^2*A;
|
||||
double lA[3][3][3]; // -A*rotation generator (x,y, or z)
|
||||
double lAtwo[3][3][3]; // A'*S^2*lA
|
||||
double lAsa[3][3][3]; // lAtwo+lA'*sa
|
||||
};
|
||||
|
||||
void allocate();
|
||||
|
||||
void precompute_i(const int i,RE2Vars &ws);
|
||||
void precompute_i(const int i, RE2Vars &ws);
|
||||
double det_prime(const double m[3][3], const double m2[3][3]);
|
||||
double resquared_analytic(const int i, const int j,
|
||||
const RE2Vars &wi, const RE2Vars &wj,
|
||||
const double *r, const double rsq,
|
||||
double *fforce, double *ttor,
|
||||
double resquared_analytic(const int i, const int j, const RE2Vars &wi, const RE2Vars &wj,
|
||||
const double *r, const double rsq, double *fforce, double *ttor,
|
||||
double *rtor);
|
||||
double resquared_lj(const int i, const int j, const RE2Vars &wi,
|
||||
const double *r, const double rsq, double *fforce,
|
||||
double *ttor, bool calc_torque);
|
||||
double resquared_lj(const int i, const int j, const RE2Vars &wi, const double *r,
|
||||
const double rsq, double *fforce, double *ttor, bool calc_torque);
|
||||
|
||||
double cr60; // 60^1/3
|
||||
double b_alpha; // 45/56
|
||||
double solv_f_a; // 3.0/(4.0*PI*-36)
|
||||
double solv_f_r; // 3.0/(4.0*PI*2025)
|
||||
double cr60; // 60^1/3
|
||||
double b_alpha; // 45/56
|
||||
double solv_f_a; // 3.0/(4.0*PI*-36)
|
||||
double solv_f_r; // 3.0/(4.0*PI*2025)
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -374,8 +375,7 @@ void PairTriLJ::compute(int eflag, int vflag)
|
||||
}
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -467,10 +467,10 @@ void PairTriLJ::coeff(int narg, char **arg)
|
||||
|
||||
void PairTriLJ::init_style()
|
||||
{
|
||||
avec = (AtomVecTri *) atom->style_match("tri");
|
||||
avec = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
|
||||
if (!avec) error->all(FLERR,"Pair tri/lj requires atom style tri");
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(tri/lj,PairTriLJ)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(tri/lj,PairTriLJ);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TRI_LJ_H
|
||||
@ -27,36 +27,36 @@ namespace LAMMPS_NS {
|
||||
class PairTriLJ : public Pair {
|
||||
public:
|
||||
PairTriLJ(class LAMMPS *);
|
||||
virtual ~PairTriLJ();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
~PairTriLJ() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
double **epsilon, **sigma;
|
||||
double **lj1, **lj2, **lj3, **lj4;
|
||||
class AtomVecTri *avec;
|
||||
|
||||
struct Discrete {
|
||||
double dx,dy,dz;
|
||||
double dx, dy, dz;
|
||||
double sigma;
|
||||
};
|
||||
Discrete *discrete; // list of all discretes for all lines
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
Discrete *discrete; // list of all discretes for all lines
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
void allocate();
|
||||
void discretize(int, double, double *, double *, double *);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -31,7 +31,7 @@ action () {
|
||||
|
||||
if (test $1 = 1) then
|
||||
if (test ! -e ../pair_eam.cpp) then
|
||||
echo "Must install MANYBODY package with USER-ATC"
|
||||
echo "Must install MANYBODY package with ATC"
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
@ -54,9 +54,9 @@ if (test $1 = 1) then
|
||||
# sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/atc |' ../Makefile.package
|
||||
# sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/atc$(LIBSOBJDIR) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-latc |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-atc_SYSINC) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-atc_SYSPATH) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(atc_SYSINC) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(atc_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(atc_SYSPATH) |' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
@ -7,7 +7,7 @@ See the doc page for the fix atc command to get started. At the
|
||||
bottom of the doc page are many links to additional documentation
|
||||
contained in the doc/USER/atc directory.
|
||||
|
||||
There are example scripts for using this package in examples/USER/atc.
|
||||
There are example scripts for using this package in examples/PACKAGES/atc.
|
||||
|
||||
This package uses an external library in lib/atc which must be
|
||||
compiled before making LAMMPS. See the lib/atc/README file and the
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/
|
||||
https://www.lammps.org/
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -17,7 +18,6 @@
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "group.h"
|
||||
#include "neigh_request.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include "ATC_Method.h"
|
||||
@ -36,7 +36,7 @@ using namespace FixConst;
|
||||
using std::string;
|
||||
|
||||
#ifdef LAMMPS_BIGBIG
|
||||
#error "The USER-ATC package is not compatible with -DLAMMPS_BIGBIG"
|
||||
#error "The ATC package is not compatible with -DLAMMPS_BIGBIG"
|
||||
#endif
|
||||
|
||||
// main page of doxygen documentation
|
||||
@ -557,11 +557,7 @@ int FixATC::modify_param(int narg, char** arg)
|
||||
void FixATC::init()
|
||||
{
|
||||
// Guarantee construction of full neighborlist
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->pair = 0;
|
||||
neighbor->requests[irequest]->fix = 1;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
neighbor->add_request(this, NeighConst::REQ_FULL);
|
||||
|
||||
// create computes, if necessary
|
||||
atc_->init_computes();
|
||||
@ -574,7 +570,7 @@ void FixATC::min_setup(int vflag)
|
||||
|
||||
void FixATC::setup(int /* vflag */)
|
||||
{
|
||||
comm->forward_comm_fix(this);
|
||||
comm->forward_comm(this);
|
||||
|
||||
try {
|
||||
atc_->initialize();
|
||||
@ -699,20 +695,17 @@ int FixATC::size_restart(int /* nlocal */) {
|
||||
|
||||
void FixATC::write_restart(FILE * /* fp */) {
|
||||
|
||||
char ** args = new char*[2];
|
||||
args[0] = new char[50];
|
||||
args[1] = new char[50];
|
||||
sprintf(args[0],"write_restart");
|
||||
sprintf(args[1],"ATC.restart");
|
||||
char *args[2];
|
||||
args[0] = utils::strdup("write_restart");
|
||||
args[1] = utils::strdup("ATC.restart");
|
||||
|
||||
// Then call all objects I own to write their data
|
||||
if (comm->me == 0) {
|
||||
atc_->modify(2,args);
|
||||
}
|
||||
|
||||
delete [] args[0];
|
||||
delete [] args[1];
|
||||
delete [] args;
|
||||
delete[] args[0];
|
||||
delete[] args[1];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -721,20 +714,17 @@ void FixATC::write_restart(FILE * /* fp */) {
|
||||
|
||||
void FixATC::restart(char * /* buf */) {
|
||||
|
||||
char ** args = new char*[2];
|
||||
args[0] = new char[50];
|
||||
args[1] = new char[50];
|
||||
sprintf(args[0],"read_restart");
|
||||
sprintf(args[1],"ATC.restart");
|
||||
char *args[2];
|
||||
args[0] = utils::strdup("read_restart");
|
||||
args[1] = utils::strdup("ATC.restart");
|
||||
|
||||
// Then call all objects I own to write their data
|
||||
if (comm->me == 0) {
|
||||
atc_->modify(2,args);
|
||||
}
|
||||
|
||||
delete [] args[0];
|
||||
delete [] args[1];
|
||||
delete [] args;
|
||||
delete[] args[0];
|
||||
delete[] args[1];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -819,7 +809,7 @@ void FixATC::pre_neighbor()
|
||||
{
|
||||
try {
|
||||
atc_->pre_neighbor();
|
||||
comm->forward_comm_fix(this);
|
||||
comm->forward_comm(this);
|
||||
}
|
||||
catch (ATC::ATC_Error& atcError) {
|
||||
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
|
||||
142
src/ATC/fix_atc.h
Normal file
142
src/ATC/fix_atc.h
Normal file
@ -0,0 +1,142 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(atc,FixATC);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef FIX_ATC_H
|
||||
#define FIX_ATC_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace ATC {
|
||||
class ATC_Method;
|
||||
}
|
||||
namespace LAMMPS_NS {
|
||||
class NeighList;
|
||||
|
||||
/**
|
||||
* @class FixATC
|
||||
* @brief Class for an atom-to-continuum (ATC) LAMMPS fix.
|
||||
*/
|
||||
|
||||
class FixATC : public Fix {
|
||||
public:
|
||||
/** constructor & destructor */
|
||||
FixATC(class LAMMPS *, int, char **);
|
||||
~FixATC() override;
|
||||
|
||||
/** initialization functions */
|
||||
void init() override;
|
||||
void init_list(int id, NeighList *ptr) override;
|
||||
void setup(int vflag) override;
|
||||
void min_setup(int vflag) override;
|
||||
|
||||
/** setmask: tell LAMMPS which fix methods to call */
|
||||
int setmask() override;
|
||||
|
||||
/** initial_integrate */
|
||||
void initial_integrate(int vflag) override;
|
||||
|
||||
/** after first integrate phase */
|
||||
void post_integrate() override;
|
||||
|
||||
/** final_integrate */
|
||||
void final_integrate() override;
|
||||
|
||||
/** end of step for run or minimize */
|
||||
void end_of_step() override;
|
||||
|
||||
/** pre_exchange is used to modify fix-specific data
|
||||
and is called before domain->pbc() and comm->exchange(). */
|
||||
void setup_pre_exchange() override;
|
||||
void pre_exchange() override;
|
||||
void min_pre_exchange() override;
|
||||
|
||||
double memory_usage() override;
|
||||
void grow_arrays(int) override;
|
||||
void copy_arrays(int, int, int) override;
|
||||
|
||||
/** pack_exchange called from atom_vec->pack_exchange()
|
||||
and packs fix-specific data for a given real (local)
|
||||
atom being sent to another processor. */
|
||||
int pack_exchange(int, double *) override;
|
||||
|
||||
/** unpack_exchange called from atom_vec->unpack_exchange()
|
||||
and unpacks fix-specific data for a given real (local)
|
||||
atom received from another processor. */
|
||||
int unpack_exchange(int, double *) override;
|
||||
|
||||
/** pack_comm called from comm->forward_comm and
|
||||
packs fix-specific data for a given ghost atom
|
||||
from exchange with another proc */
|
||||
int pack_forward_comm(int, int *, double *, int, int *) override;
|
||||
|
||||
/** unpack_comm called from comm->forward_comm and
|
||||
unpacks fix-specific data for a given ghost atom
|
||||
from exchange with another proc */
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
|
||||
/** pre_neighbor is used to modify fix-specific data
|
||||
and is called before neighbor list is built in
|
||||
neighbor->build(). */
|
||||
void pre_neighbor() override;
|
||||
void setup_pre_neighbor() override;
|
||||
|
||||
/** pre/post_force is used to modify fix-specific data
|
||||
and is before/after the various force computations. */
|
||||
void pre_force(int vflag) override;
|
||||
void post_force(int vflag) override;
|
||||
|
||||
/** post_run is called after a run completes */
|
||||
void post_run() override;
|
||||
|
||||
/** min_pre_force is called before forces are calculated in minimize */
|
||||
void min_pre_force(int vflag) override;
|
||||
|
||||
/** min_post_force is called after forces are calculated in minimize */
|
||||
void min_post_force(int vflag) override;
|
||||
|
||||
/** modify atc parameters (parser) */
|
||||
int modify_param(int narg, char **arg) override;
|
||||
|
||||
/** calls ATC_Method to handle restarting/checkpointing */
|
||||
/** these four methods are for writing per-atom quantities */
|
||||
int pack_restart(int, double *) override;
|
||||
void unpack_restart(int, int) override;
|
||||
int size_restart(int) override;
|
||||
int maxsize_restart() override;
|
||||
/** these two methods are for writing all other quantities */
|
||||
void write_restart(FILE *) override;
|
||||
void restart(char *) override;
|
||||
|
||||
/** accessor function for ATC_Method class pointer */
|
||||
const ATC::ATC_Method *atc() { return atc_; }
|
||||
|
||||
protected:
|
||||
LAMMPS *lammps_;
|
||||
|
||||
/** functions for "thermo" output */
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int n) override;
|
||||
double compute_array(int irow, int icol) override;
|
||||
double dtv, dtf;
|
||||
ATC::ATC_Method *atc_;
|
||||
};
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -41,8 +41,8 @@ if (test $1 = 1) then
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/awpmd/ivutils/include -I../../lib/awpmd/systems/interact |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/awpmd |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-lawpmd |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-awpmd_SYSPATH) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-awpmd_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(awpmd_SYSPATH) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(awpmd_SYSLIB) |' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
@ -4,7 +4,7 @@ Wave Packet Molecular Dynamics (AWPMD) method.
|
||||
See the doc page for the pair_style awpmd/cut command to get started.
|
||||
|
||||
There are example scripts for using this package in
|
||||
examples/USER/awpmd.
|
||||
examples/PACKAGES/awpmd.
|
||||
|
||||
This package uses an external library in lib/awpmd which must be
|
||||
compiled before making LAMMPS. See the lib/awpmd/README file and the
|
||||
@ -1,6 +1,6 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -19,8 +19,6 @@
|
||||
|
||||
#include "atom.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -31,33 +29,29 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
|
||||
molecular = Atom::ATOMIC;
|
||||
forceclearflag = 1;
|
||||
|
||||
atom->wavepacket_flag = 1;
|
||||
|
||||
atom->electron_flag = 1; // compatible with eff
|
||||
atom->q_flag = atom->spin_flag = atom->eradius_flag =
|
||||
atom->ervel_flag = atom->erforce_flag = 1;
|
||||
atom->cs_flag = atom->csforce_flag =
|
||||
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
|
||||
atom->wavepacket_flag = atom->q_flag = atom->spin_flag = atom->eradius_flag = 1;
|
||||
atom->ervel_flag = atom->erforce_flag = atom->cs_flag = atom->csforce_flag = 1;
|
||||
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
|
||||
|
||||
// strings with peratom variables to include in each AtomVec method
|
||||
// strings cannot contain fields in corresponding AtomVec default strings
|
||||
// order of fields in a string does not matter
|
||||
// except: fields_data_atom & fields_data_vel must match data file
|
||||
|
||||
fields_grow = (char *)
|
||||
"q spin eradius ervel erforce cs csforce "
|
||||
"vforce ervelforce etag";
|
||||
fields_copy = (char *) "q spin eradius ervel cs etag";
|
||||
fields_comm = (char *) "eradius";
|
||||
fields_comm_vel = (char *) "eradius ervel cs";
|
||||
fields_reverse = (char *) "erforce ervelforce vforce csforce";
|
||||
fields_border = (char *) "q spin eradius etag";
|
||||
fields_border_vel = (char *) "q spin eradius etag ervel cs";
|
||||
fields_exchange = (char *) "q spin eradius ervel etag cs";
|
||||
fields_restart = (char *) "q spin eradius ervel etag cs";
|
||||
fields_create = (char *) "q spin eradius ervel etag cs";
|
||||
fields_data_atom = (char *) "id type q spin eradius etag cs x";
|
||||
fields_data_vel = (char *) "id v ervel";
|
||||
fields_grow = {"q", "spin", "eradius", "ervel", "erforce",
|
||||
"cs", "csforce", "vforce", "ervelforce", "etag"};
|
||||
fields_copy = {"q", "spin", "eradius", "ervel", "cs", "etag"};
|
||||
fields_comm = {"eradius"};
|
||||
fields_comm_vel = {"eradius", "ervel", "cs"};
|
||||
fields_reverse = {"erforce", "ervelforce", "vforce", "csforce"};
|
||||
fields_border = {"q", "spin", "eradius", "etag"};
|
||||
fields_border_vel = {"q", "spin", "eradius", "etag", "ervel", "cs"};
|
||||
fields_exchange = {"q", "spin", "eradius", "ervel", "etag", "cs"};
|
||||
fields_restart = {"q", "spin", "eradius", "ervel", "etag", "cs"};
|
||||
fields_create = {"q", "spin", "eradius", "ervel", "etag", "cs"};
|
||||
fields_data_atom = {"id", "type", "q", "spin", "eradius", "etag", "cs", "x"};
|
||||
fields_data_vel = {"id", "v", "ervel"};
|
||||
|
||||
setup_fields();
|
||||
}
|
||||
@ -83,7 +77,7 @@ void AtomVecWavepacket::grow_pointers()
|
||||
|
||||
void AtomVecWavepacket::force_clear(int n, size_t nbytes)
|
||||
{
|
||||
memset(&erforce[n],0,nbytes);
|
||||
memset(&erforce[n], 0, nbytes);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -111,12 +105,12 @@ void AtomVecWavepacket::data_atom_post(int ilocal)
|
||||
return -1 if name is unknown to this atom style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecWavepacket::property_atom(char *name)
|
||||
int AtomVecWavepacket::property_atom(const std::string &name)
|
||||
{
|
||||
if (strcmp(name,"spin") == 0) return 0;
|
||||
if (strcmp(name,"eradius") == 0) return 1;
|
||||
if (strcmp(name,"ervel") == 0) return 2;
|
||||
if (strcmp(name,"erforce") == 0) return 3;
|
||||
if (name == "spin") return 0;
|
||||
if (name == "eradius") return 1;
|
||||
if (name == "ervel") return 2;
|
||||
if (name == "erforce") return 3;
|
||||
return -1;
|
||||
}
|
||||
|
||||
@ -125,34 +119,41 @@ int AtomVecWavepacket::property_atom(char *name)
|
||||
index maps to data specific to this atom style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecWavepacket::pack_property_atom(int index, double *buf,
|
||||
int nvalues, int groupbit)
|
||||
void AtomVecWavepacket::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int n = 0;
|
||||
if (index == 0) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) buf[n] = spin[i];
|
||||
else buf[n] = 0.0;
|
||||
if (mask[i] & groupbit)
|
||||
buf[n] = spin[i];
|
||||
else
|
||||
buf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
} else if (index == 1) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) buf[n] = eradius[i];
|
||||
else buf[n] = 0.0;
|
||||
if (mask[i] & groupbit)
|
||||
buf[n] = eradius[i];
|
||||
else
|
||||
buf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
} else if (index == 2) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) buf[n] = ervel[i];
|
||||
else buf[n] = 0.0;
|
||||
if (mask[i] & groupbit)
|
||||
buf[n] = ervel[i];
|
||||
else
|
||||
buf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
} else if (index == 3) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) buf[n] = erforce[i];
|
||||
else buf[n] = 0.0;
|
||||
if (mask[i] & groupbit)
|
||||
buf[n] = erforce[i];
|
||||
else
|
||||
buf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef ATOM_CLASS
|
||||
|
||||
AtomStyle(wavepacket,AtomVecWavepacket)
|
||||
|
||||
// clang-format off
|
||||
AtomStyle(wavepacket,AtomVecWavepacket);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_ATOM_VEC_WAVEPACKET_H
|
||||
@ -25,22 +25,22 @@ AtomStyle(wavepacket,AtomVecWavepacket)
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AtomVecWavepacket : public AtomVec {
|
||||
public:
|
||||
public:
|
||||
AtomVecWavepacket(class LAMMPS *);
|
||||
|
||||
void grow_pointers();
|
||||
void force_clear(int, size_t);
|
||||
void create_atom_post(int);
|
||||
void data_atom_post(int);
|
||||
int property_atom(char *);
|
||||
void pack_property_atom(int, double *, int, int);
|
||||
void grow_pointers() override;
|
||||
void force_clear(int, size_t) override;
|
||||
void create_atom_post(int) override;
|
||||
void data_atom_post(int) override;
|
||||
int property_atom(const std::string &) override;
|
||||
void pack_property_atom(int, double *, int, int) override;
|
||||
|
||||
private:
|
||||
int *spin;
|
||||
double *q,*eradius,*ervel,*erforce;
|
||||
double *q, *eradius, *ervel, *erforce;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -60,9 +61,9 @@ void FixNVEAwpmd::init()
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
|
||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||
step_respa = ((Respa *) update->integrate)->step;
|
||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
||||
|
||||
awpmd_pair=(PairAWPMDCut *)force->pair;
|
||||
awpmd_pair=dynamic_cast<PairAWPMDCut *>(force->pair);
|
||||
awpmd_pair->wpmd->norm_needed=1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -16,9 +16,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/awpmd,FixNVEAwpmd)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/awpmd,FixNVEAwpmd);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_awpmd_H
|
||||
@ -31,23 +31,23 @@ namespace LAMMPS_NS {
|
||||
class FixNVEAwpmd : public Fix {
|
||||
public:
|
||||
FixNVEAwpmd(class LAMMPS *, int, char **);
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void initial_integrate_respa(int, int, int);
|
||||
void final_integrate_respa(int, int);
|
||||
void reset_dt();
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
void initial_integrate_respa(int, int, int) override;
|
||||
void final_integrate_respa(int, int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
protected:
|
||||
double dtv,dtf;
|
||||
double dtv, dtf;
|
||||
double *step_respa;
|
||||
int mass_require;
|
||||
|
||||
class PairAWPMDCut *awpmd_pair;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -25,7 +26,6 @@
|
||||
#include "memory.h"
|
||||
#include "min.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
@ -38,7 +38,6 @@
|
||||
#include <cstring>
|
||||
#include <map>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -96,10 +95,7 @@ struct cmp_x{
|
||||
else if (d>tol)
|
||||
return false;
|
||||
d=xx[left.second][2]-xx[right.second][2];
|
||||
if (d<-tol)
|
||||
return true;
|
||||
else
|
||||
return false;
|
||||
return d < -tol;
|
||||
}
|
||||
else
|
||||
return left.first<right.first;
|
||||
@ -150,7 +146,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
|
||||
|
||||
# if 1
|
||||
// mapping of the LAMMPS numbers to the AWPMC numbers
|
||||
vector<int> gmap(ntot,-1);
|
||||
std::vector<int> gmap(ntot,-1);
|
||||
|
||||
for (int ii = 0; ii < inum; ii++) {
|
||||
int i = ilist[ii];
|
||||
@ -226,7 +222,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
|
||||
// prepare the solver object
|
||||
wpmd->reset();
|
||||
|
||||
map<int,vector<int> > etmap;
|
||||
std::map<int,std::vector<int> > etmap;
|
||||
// add particles to the AWPMD solver object
|
||||
for (int i = 0; i < ntot; i++) {
|
||||
//int i = ilist[ii];
|
||||
@ -246,8 +242,8 @@ void PairAWPMDCut::compute(int eflag, int vflag)
|
||||
fi= new Vector_3[wpmd->ni];
|
||||
|
||||
// adding electrons
|
||||
for (map<int,vector<int> >::iterator it=etmap.begin(); it!= etmap.end(); ++it) {
|
||||
vector<int> &el=it->second;
|
||||
for (auto & it : etmap) {
|
||||
std::vector<int> &el=it.second;
|
||||
if (!el.size()) // should not happen
|
||||
continue;
|
||||
int s=spin[el[0]] >0 ? 0 : 1;
|
||||
@ -513,45 +509,18 @@ void PairAWPMDCut::init_style()
|
||||
|
||||
if (!atom->q_flag || !atom->spin_flag ||
|
||||
!atom->eradius_flag || !atom->erforce_flag ) // TO DO: adjust this to match approximation used
|
||||
error->all(FLERR,"Pair awpmd/cut requires atom attributes "
|
||||
"q, spin, eradius, erforce");
|
||||
|
||||
/*
|
||||
if (vflag_atom) { // can't compute virial per atom
|
||||
//warning->
|
||||
error->all(FLERR,"Pair style awpmd can't compute per atom virials");
|
||||
}*/
|
||||
error->all(FLERR,"Pair awpmd/cut requires atom attributes q, spin, eradius, erforce");
|
||||
|
||||
// add hook to minimizer for eradius and erforce
|
||||
|
||||
if (update->whichflag == 2)
|
||||
int ignore = update->minimize->request(this,1,0.01);
|
||||
|
||||
// make sure to use the appropriate timestep when using real units
|
||||
|
||||
/*if (update->whichflag == 1) {
|
||||
if (force->qqr2e == 332.06371 && update->dt == 1.0)
|
||||
error->all(FLERR,"You must lower the default real units timestep for pEFF ");
|
||||
}*/
|
||||
|
||||
// need a half neigh list and optionally a granular history neigh list
|
||||
|
||||
//int irequest = neighbor->request(this,instance_me);
|
||||
|
||||
//if (atom->tag_enable == 0)
|
||||
// error->all(FLERR,"Pair style reax requires atom IDs");
|
||||
|
||||
//if (force->newton_pair == 0)
|
||||
//error->all(FLERR,"Pair style awpmd requires newton pair on");
|
||||
|
||||
//if (strcmp(update->unit_style,"real") != 0 && comm->me == 0)
|
||||
//error->warning(FLERR,"Not using real units with pair reax");
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->newton = 2;
|
||||
neighbor->add_request(this, NeighConst::REQ_NEWTON_OFF);
|
||||
|
||||
if (force->e_mass==0. || force->hhmrr2e==0. || force->mvh2r==0.)
|
||||
error->all(FLERR,"Pair style awpmd requires e_mass and conversions hhmrr2e, mvh2r to be properly set for unit system");
|
||||
error->all(FLERR,"Pair style awpmd requires e_mass and conversions "
|
||||
"hhmrr2e, mvh2r to be properly set for unit system");
|
||||
|
||||
wpmd->me=force->e_mass;
|
||||
wpmd->h2_me=force->hhmrr2e/force->e_mass;
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -14,11 +14,10 @@
|
||||
Contributing author: Ilya Valuev (JIHT RAS)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(awpmd/cut,PairAWPMDCut)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(awpmd/cut,PairAWPMDCut);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_AWPMD_CUT_H
|
||||
@ -26,56 +25,51 @@ PairStyle(awpmd/cut,PairAWPMDCut)
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
|
||||
class AWPMD_split;
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairAWPMDCut : public Pair {
|
||||
friend class FixNVEAwpmd;
|
||||
|
||||
public:
|
||||
PairAWPMDCut(class LAMMPS *);
|
||||
virtual ~PairAWPMDCut();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
~PairAWPMDCut() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
void min_pointers(double **, double **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
|
||||
void min_xf_pointers(int, double **, double **);
|
||||
void min_xf_get(int);
|
||||
void min_x_set(int);
|
||||
double memory_usage();
|
||||
void min_xf_pointers(int, double **, double **) override;
|
||||
void min_xf_get(int) override;
|
||||
void min_x_set(int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
|
||||
|
||||
int flexible_pressure_flag;
|
||||
double cut_global;
|
||||
double **cut;
|
||||
|
||||
|
||||
int nmax; // number of additional variables for minimizer
|
||||
double *min_var,*min_varforce; // additional variables for minimizer
|
||||
int nmax; // number of additional variables for minimizer
|
||||
double *min_var, *min_varforce; // additional variables for minimizer
|
||||
|
||||
void allocate();
|
||||
|
||||
void virial_eradius_compute();
|
||||
|
||||
|
||||
AWPMD_split *wpmd; // solver object
|
||||
double ermscale; // scale of width mass for motion
|
||||
double width_pbc; // setting for width pbc
|
||||
double half_box_length; // calculated by coeff function
|
||||
AWPMD_split *wpmd; // solver object
|
||||
double ermscale; // scale of width mass for motion
|
||||
double width_pbc; // setting for width pbc
|
||||
double half_box_length; // calculated by coeff function
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -7,7 +7,7 @@ molecular liquids," J. Chem. Phys. 143, 243148 (2015).
|
||||
|
||||
doi: 10.1063/1.4937383
|
||||
|
||||
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
|
||||
The BOCS user package for LAMMPS is part of the BOCS software package:
|
||||
https://github.com/noid-group/BOCS
|
||||
|
||||
See the following reference for information about the entire package:
|
||||
@ -16,4 +16,4 @@ Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
|
||||
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
|
||||
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
|
||||
|
||||
Example inputs are in the examples/USER/bocs folder.
|
||||
Example inputs are in the examples/PACKAGES/bocs folder.
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -10,7 +11,7 @@
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -59,9 +60,7 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
|
||||
else {
|
||||
int n = strlen(arg[3]) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,arg[3]);
|
||||
id_temp = utils::strdup(arg[3]);
|
||||
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if (icompute < 0)
|
||||
@ -217,7 +216,7 @@ double ComputePressureBocs::find_index(double * grid, double value)
|
||||
|
||||
if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; }
|
||||
|
||||
error->all(FLERR, fmt::format("find_index could not find value in grid for value: {}", value));
|
||||
error->all(FLERR,"find_index could not find value in grid for value: {}", value);
|
||||
for (int i = 0; i < gridsize; ++i)
|
||||
{
|
||||
fprintf(stderr, "grid %d: %f\n",i,grid[i]);
|
||||
@ -234,23 +233,14 @@ double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
|
||||
double vCG)
|
||||
{
|
||||
int i = find_index(grid[0],vCG);
|
||||
double correction, deltax = vCG - grid[0][i];
|
||||
double deltax = vCG - grid[0][i];
|
||||
|
||||
if (basis_type == BASIS_LINEAR_SPLINE)
|
||||
{
|
||||
correction = grid[1][i] + (deltax) *
|
||||
( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
|
||||
}
|
||||
return grid[1][i] + (deltax) * ( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
|
||||
else if (basis_type == BASIS_CUBIC_SPLINE)
|
||||
{
|
||||
correction = grid[1][i] + (grid[2][i] * deltax) +
|
||||
(grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
|
||||
}
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
|
||||
}
|
||||
return correction;
|
||||
return grid[1][i] + (grid[2][i] * deltax) + (grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
|
||||
else error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -262,11 +252,8 @@ void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
|
||||
double *sent_phi_coeff, int sent_N_mol,
|
||||
double sent_vavg)
|
||||
{
|
||||
if (basis_type == BASIS_ANALYTIC) { p_basis_type = BASIS_ANALYTIC; }
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
|
||||
}
|
||||
if (basis_type == BASIS_ANALYTIC) p_basis_type = BASIS_ANALYTIC;
|
||||
else error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
|
||||
|
||||
p_match_flag = 1;
|
||||
|
||||
@ -446,7 +433,5 @@ void ComputePressureBocs::virial_compute(int n, int ndiag)
|
||||
void ComputePressureBocs::reset_extra_compute_fix(const char *id_new)
|
||||
{
|
||||
delete [] id_temp;
|
||||
int n = strlen(id_new) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id_new);
|
||||
id_temp = utils::strdup(id_new);
|
||||
}
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -10,74 +10,73 @@
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(PRESSURE/BOCS,ComputePressureBocs)
|
||||
|
||||
// clang-format off
|
||||
ComputeStyle(PRESSURE/BOCS,ComputePressureBocs);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
|
||||
#ifndef LMP_COMPUTE_PRESSURE_BOCS_H
|
||||
#define LMP_COMPUTE_PRESSURE_BOCS_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// Enumerate the p_basis_type magic values to improve readability:
|
||||
enum{BASIS_ANALYTIC, BASIS_LINEAR_SPLINE, BASIS_CUBIC_SPLINE};
|
||||
// Enumerate the data file column names to improve readability
|
||||
enum{VOLUME, PRESSURE_CORRECTION};
|
||||
// Declare names for the number of columns in the splines data structure to improve readability
|
||||
const int NUM_LINEAR_SPLINE_COLUMNS = 2; // linear spline columns passed to compute
|
||||
const int NUM_CUBIC_SPLINE_COLUMNS = 5; // cubic spline columns passed to compute
|
||||
// Enumerate the p_basis_type magic values to improve readability:
|
||||
enum { BASIS_ANALYTIC, BASIS_LINEAR_SPLINE, BASIS_CUBIC_SPLINE };
|
||||
// Enumerate the data file column names to improve readability
|
||||
enum { VOLUME, PRESSURE_CORRECTION };
|
||||
// Declare names for the number of columns in the splines data structure to improve readability
|
||||
const int NUM_LINEAR_SPLINE_COLUMNS = 2; // linear spline columns passed to compute
|
||||
const int NUM_CUBIC_SPLINE_COLUMNS = 5; // cubic spline columns passed to compute
|
||||
|
||||
// ComputePressure -> ComputePressureBocs MRD NJD
|
||||
// ComputePressure -> ComputePressureBocs MRD NJD
|
||||
class ComputePressureBocs : public Compute {
|
||||
public:
|
||||
ComputePressureBocs(class LAMMPS *, int, char **);
|
||||
virtual ~ComputePressureBocs();
|
||||
virtual void init();
|
||||
virtual double compute_scalar();
|
||||
virtual void compute_vector();
|
||||
void reset_extra_compute_fix(const char *);
|
||||
~ComputePressureBocs() override;
|
||||
void init() override;
|
||||
double compute_scalar() override;
|
||||
void compute_vector() override;
|
||||
void reset_extra_compute_fix(const char *) override;
|
||||
|
||||
double compute_cg_scalar();
|
||||
double get_cg_p_corr(int, double *, int, double, double);
|
||||
double get_cg_fluct(double, double);
|
||||
void send_cg_info(int, int, double*, int, double);
|
||||
void send_cg_info(int, int, double *, int, double);
|
||||
void send_cg_info(int, double **, int);
|
||||
double get_cg_p_corr(double **, int, double);
|
||||
double find_index(double* , double);
|
||||
double find_index(double *, double);
|
||||
|
||||
protected:
|
||||
double boltz,nktv2p,inv_volume;
|
||||
int nvirial,dimension;
|
||||
double boltz, nktv2p, inv_volume;
|
||||
int nvirial, dimension;
|
||||
double **vptr;
|
||||
double *kspace_virial;
|
||||
Compute *temperature;
|
||||
char *id_temp;
|
||||
double virial[6];
|
||||
int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
|
||||
int fixflag,kspaceflag;
|
||||
int keflag, pairflag, bondflag, angleflag, dihedralflag, improperflag;
|
||||
int fixflag, kspaceflag;
|
||||
|
||||
// NJD MRD
|
||||
// NJD MRD
|
||||
int p_basis_type;
|
||||
int p_match_flag;
|
||||
double vavg;
|
||||
int N_mol;
|
||||
int N_basis;
|
||||
double *phi_coeff;
|
||||
double ** splines;
|
||||
double **splines;
|
||||
int spline_length;
|
||||
|
||||
void virial_compute(int, int);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -10,17 +11,12 @@
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_bocs.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
#include <cmath>
|
||||
#include <vector>
|
||||
|
||||
#include "atom.h"
|
||||
#include "citeme.h"
|
||||
#include "comm.h"
|
||||
@ -29,7 +25,6 @@
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_deform.h"
|
||||
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include "irregular.h"
|
||||
@ -40,11 +35,14 @@
|
||||
#include "respa.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
static const char cite_user_bocs_package[] =
|
||||
"USER-BOCS package:\n\n"
|
||||
"BOCS package:\n\n"
|
||||
"@Article{Dunn2018,\n"
|
||||
" author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n"
|
||||
" title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n"
|
||||
@ -70,7 +68,8 @@ const int NUM_INPUT_DATA_COLUMNS = 2; // columns in the pressure correction
|
||||
|
||||
FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
rfix(nullptr), id_dilate(nullptr), irregular(nullptr), id_temp(nullptr), id_press(nullptr),
|
||||
rfix(nullptr), id_dilate(nullptr), irregular(nullptr),
|
||||
id_temp(nullptr), id_press(nullptr),
|
||||
eta(nullptr), eta_dot(nullptr), eta_dotdot(nullptr),
|
||||
eta_mass(nullptr), etap(nullptr), etap_dot(nullptr), etap_dotdot(nullptr),
|
||||
etap_mass(nullptr)
|
||||
@ -234,9 +233,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"mtk") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
|
||||
else error->all(FLERR,"Illegal fix bocs command");
|
||||
mtk_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"tloop") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
|
||||
@ -403,38 +400,16 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "temp";
|
||||
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
id_temp = utils::strdup(std::string(id)+"_temp");
|
||||
modify->add_compute(fmt::format("{} all temp",id_temp));
|
||||
tcomputeflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
n = strlen(id) + 7;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,id);
|
||||
strcat(id_press,"_press");
|
||||
|
||||
newarg = new char*[4];
|
||||
newarg[0] = id_press;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "PRESSURE/BOCS";
|
||||
newarg[3] = id_temp;
|
||||
modify->add_compute(4,newarg);
|
||||
delete [] newarg;
|
||||
id_press = utils::strdup(std::string(id)+"_press");
|
||||
modify->add_compute(fmt::format("{} all PRESSURE/BOCS {}",id_press,id_temp));
|
||||
pcomputeflag = 1;
|
||||
|
||||
/*~ MRD End of stuff copied from fix_npt.cpp~*/
|
||||
@ -514,7 +489,7 @@ void FixBocs::init()
|
||||
{
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
|
||||
int *dimflag = (dynamic_cast<FixDeform *>( modify->fix[i]))->dimflag;
|
||||
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
|
||||
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
|
||||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
|
||||
@ -548,12 +523,12 @@ void FixBocs::init()
|
||||
{
|
||||
if (p_basis_type == BASIS_ANALYTIC)
|
||||
{
|
||||
((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
|
||||
(dynamic_cast<ComputePressureBocs *>(pressure))->send_cg_info(p_basis_type,
|
||||
N_p_match, p_match_coeffs, N_mol, vavg);
|
||||
}
|
||||
else if (p_basis_type == BASIS_LINEAR_SPLINE || p_basis_type == BASIS_CUBIC_SPLINE)
|
||||
{
|
||||
((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
|
||||
(dynamic_cast<ComputePressureBocs *>(pressure))->send_cg_info(p_basis_type,
|
||||
splines, spline_length);
|
||||
}
|
||||
}
|
||||
@ -613,9 +588,9 @@ void FixBocs::init()
|
||||
if (force->kspace) kspace_flag = 1;
|
||||
else kspace_flag = 0;
|
||||
|
||||
if (strstr(update->integrate_style,"respa")) {
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
step_respa = ((Respa *) update->integrate)->step;
|
||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||
nlevels_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels;
|
||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
||||
dto = 0.5*step_respa[0];
|
||||
}
|
||||
|
||||
@ -652,7 +627,7 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
// NB: LAMMPS coding guidelines prefer cstdio so we are intentionally
|
||||
// foregoing reading with getline
|
||||
if (comm->me == 0) {
|
||||
error->message(FLERR, fmt::format("INFO: About to read data file: {}", filename));
|
||||
error->message(FLERR, "INFO: About to read data file: {}", filename);
|
||||
}
|
||||
|
||||
// Data file lines hold two floating point numbers.
|
||||
@ -662,13 +637,13 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
char line[MAX_F_TABLE_LINE_LENGTH];
|
||||
std::vector<std::string> inputLines;
|
||||
while (fgets(line, MAX_F_TABLE_LINE_LENGTH, fpi)) {
|
||||
inputLines.push_back(std::string(line));
|
||||
inputLines.emplace_back(line);
|
||||
}
|
||||
fclose(fpi);
|
||||
|
||||
numEntries = inputLines.size();
|
||||
if (comm->me == 0) {
|
||||
error->message(FLERR, fmt::format("INFO: Read {} lines from file", numEntries));
|
||||
error->message(FLERR, "INFO: Read {} lines from file", numEntries);
|
||||
}
|
||||
|
||||
|
||||
@ -693,34 +668,23 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
test_sscanf = sscanf(inputLines.at(i).c_str()," %f , %f ",&f1, &f2);
|
||||
if (test_sscanf == 2)
|
||||
{
|
||||
//if (comm->me == 0) {
|
||||
// error->message(FLERR, fmt::format("INFO: f1 = {}, f2 = {}", f1, f2));
|
||||
//}
|
||||
data[VOLUME][i] = (double)f1;
|
||||
data[PRESSURE_CORRECTION][i] = (double)f2;
|
||||
if (i == 1)
|
||||
{
|
||||
// second entry is used to compute the validation interval used below
|
||||
stdVolumeInterval = data[VOLUME][i] - data[VOLUME][i-1];
|
||||
//if (comm->me == 0) {
|
||||
// error->message(FLERR, fmt::format("INFO: standard volume interval computed: {}", stdVolumeInterval));
|
||||
//}
|
||||
}
|
||||
else if (i > 1)
|
||||
{
|
||||
// after second entry, all intervals are validated
|
||||
currVolumeInterval = data[VOLUME][i] - data[VOLUME][i-1];
|
||||
//if (comm->me == 0) {
|
||||
// error->message(FLERR, fmt::format("INFO: current volume interval: {}", currVolumeInterval));
|
||||
//}
|
||||
if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) {
|
||||
if (comm->me == 0) {
|
||||
message = fmt::format("Bad volume interval. Spline analysis requires uniform"
|
||||
" volume distribution, found inconsistent volume"
|
||||
" differential, line {} of file {}\n\tline: {}",
|
||||
lineNum, filename, inputLines.at(i));
|
||||
error->warning(FLERR, message);
|
||||
}
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Bad volume interval. Spline analysis requires uniform"
|
||||
" volume distribution, found inconsistent volume"
|
||||
" differential, line {} of file {}\nWARNING:\tline: {}",
|
||||
lineNum, filename, inputLines.at(i));
|
||||
badInput = true;
|
||||
numBadVolumeIntervals++;
|
||||
}
|
||||
@ -729,12 +693,10 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
}
|
||||
else
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
message = fmt::format("Bad input format: did not find 2 comma separated numeric"
|
||||
" values in line {} of file {}\n\tline: {}",
|
||||
lineNum, filename, inputLines.at(i));
|
||||
error->warning(FLERR, message);
|
||||
}
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Bad input format: did not find 2 comma separated numeric"
|
||||
" values in line {} of file {}\nWARNING:\tline: {}",
|
||||
lineNum, filename, inputLines.at(i));
|
||||
badInput = true;
|
||||
}
|
||||
if (badInput)
|
||||
@ -744,15 +706,15 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
}
|
||||
|
||||
if (numBadVolumeIntervals > 0 && comm->me == 0) {
|
||||
error->message(FLERR, fmt::format("INFO: total number bad volume intervals = {}", numBadVolumeIntervals));
|
||||
error->message(FLERR, "INFO: total number bad volume intervals = {}", numBadVolumeIntervals);
|
||||
}
|
||||
}
|
||||
else {
|
||||
error->all(FLERR,fmt::format("ERROR: Unable to open file: {}", filename));
|
||||
error->all(FLERR,"ERROR: Unable to open file: {}", filename);
|
||||
}
|
||||
|
||||
if (badInput && comm->me == 0) {
|
||||
error->warning(FLERR,fmt::format("Bad volume / pressure-correction data: {}\nSee details above", filename));
|
||||
error->warning(FLERR,"Bad volume / pressure-correction data: {}\nSee details above", filename);
|
||||
}
|
||||
|
||||
if (p_basis_type == BASIS_LINEAR_SPLINE)
|
||||
@ -767,7 +729,7 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
}
|
||||
else
|
||||
{
|
||||
error->all(FLERR,fmt::format("ERROR: invalid p_basis_type value of {} in read_F_table", p_basis_type));
|
||||
error->all(FLERR,"ERROR: invalid p_basis_type value of {} in read_F_table", p_basis_type);
|
||||
}
|
||||
|
||||
memory->destroy(data);
|
||||
@ -775,9 +737,6 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
|
||||
}
|
||||
|
||||
int FixBocs::build_linear_splines(double **data) {
|
||||
//if (comm->me == 0) {
|
||||
//error->message(FLERR, fmt::format("INFO: entering build_linear_splines, spline_length = {}", spline_length));
|
||||
//}
|
||||
splines = (double **) calloc(NUM_LINEAR_SPLINE_COLUMNS,sizeof(double *));
|
||||
splines[VOLUME] = (double *) calloc(spline_length,sizeof(double));
|
||||
splines[PRESSURE_CORRECTION] = (double *) calloc(spline_length,sizeof(double));
|
||||
@ -789,7 +748,7 @@ int FixBocs::build_linear_splines(double **data) {
|
||||
}
|
||||
|
||||
if (comm->me == 0) {
|
||||
error->message(FLERR, fmt::format("INFO: leaving build_linear_splines, spline_length = {}", spline_length));
|
||||
error->message(FLERR, "INFO: leaving build_linear_splines, spline_length = {}", spline_length);
|
||||
}
|
||||
|
||||
return spline_length;
|
||||
@ -797,9 +756,6 @@ int FixBocs::build_linear_splines(double **data) {
|
||||
|
||||
int FixBocs::build_cubic_splines(double **data)
|
||||
{
|
||||
//if (comm->me == 0) {
|
||||
//error->message(FLERR, fmt::format("INFO: entering build_cubic_splines, spline_length = {}", spline_length));
|
||||
//}
|
||||
int n = spline_length;
|
||||
double *a, *b, *d, *h, *alpha, *c, *l, *mu, *z;
|
||||
// 2020-07-17 ag:
|
||||
@ -890,7 +846,7 @@ int FixBocs::build_cubic_splines(double **data)
|
||||
memory->destroy(z);
|
||||
|
||||
if (comm->me == 0) {
|
||||
error->message(FLERR, fmt::format("INFO: leaving build_cubic_splines, numSplines = {}", numSplines));
|
||||
error->message(FLERR, "INFO: leaving build_cubic_splines, numSplines = {}", numSplines);
|
||||
}
|
||||
|
||||
// Tell the caller how many splines we created
|
||||
@ -1141,7 +1097,12 @@ void FixBocs::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/)
|
||||
nve_x();
|
||||
if (pstat_flag) remap();
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixBocs::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/)
|
||||
{
|
||||
// if barostat, redo KSpace coeffs at outermost level,
|
||||
// since volume has changed
|
||||
|
||||
@ -1491,7 +1452,7 @@ int FixBocs::pack_restart_data(double *list)
|
||||
void FixBocs::restart(char *buf)
|
||||
{
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
auto list = (double *) buf;
|
||||
int flag = static_cast<int> (list[n++]);
|
||||
if (flag) {
|
||||
int m = static_cast<int> (list[n++]);
|
||||
@ -1548,9 +1509,7 @@ int FixBocs::modify_param(int narg, char **arg)
|
||||
tcomputeflag = 0;
|
||||
}
|
||||
delete [] id_temp;
|
||||
int n = strlen(arg[1]) + 1;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,arg[1]);
|
||||
id_temp = utils::strdup(arg[1]);
|
||||
|
||||
int icompute = modify->find_compute(arg[1]);
|
||||
if (icompute < 0)
|
||||
@ -1582,9 +1541,7 @@ int FixBocs::modify_param(int narg, char **arg)
|
||||
pcomputeflag = 0;
|
||||
}
|
||||
delete [] id_press;
|
||||
int n = strlen(arg[1]) + 1;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,arg[1]);
|
||||
id_press = utils::strdup(arg[1]);
|
||||
|
||||
int icompute = modify->find_compute(arg[1]);
|
||||
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
|
||||
@ -1594,12 +1551,12 @@ int FixBocs::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (p_basis_type == BASIS_ANALYTIC)
|
||||
{
|
||||
((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match,
|
||||
(dynamic_cast<ComputePressureBocs *>(pressure))->send_cg_info(p_basis_type, N_p_match,
|
||||
p_match_coeffs, N_mol, vavg);
|
||||
}
|
||||
else if (p_basis_type == BASIS_LINEAR_SPLINE || p_basis_type == BASIS_CUBIC_SPLINE )
|
||||
{
|
||||
((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines, spline_length );
|
||||
(dynamic_cast<ComputePressureBocs *>(pressure))->send_cg_info(p_basis_type, splines, spline_length );
|
||||
}
|
||||
}
|
||||
|
||||
@ -1877,7 +1834,7 @@ void FixBocs::reset_dt()
|
||||
|
||||
// If using respa, then remap is performed in innermost level
|
||||
|
||||
if (strstr(update->integrate_style,"respa"))
|
||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||
dto = 0.5*step_respa[0];
|
||||
|
||||
if (pstat_flag)
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -10,15 +10,14 @@
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
|
||||
from The Pennsylvania State University
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(bocs,FixBocs)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(bocs,FixBocs);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_BOCS_H
|
||||
@ -30,119 +29,118 @@ namespace LAMMPS_NS {
|
||||
|
||||
class FixBocs : public Fix {
|
||||
public:
|
||||
FixBocs(class LAMMPS *, int, char **); // MRD NJD
|
||||
virtual ~FixBocs(); // MRD NJD
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void setup(int);
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void initial_integrate_respa(int, int, int);
|
||||
void final_integrate_respa(int, int);
|
||||
virtual void pre_exchange();
|
||||
double compute_scalar();
|
||||
virtual double compute_vector(int);
|
||||
void write_restart(FILE *);
|
||||
virtual int pack_restart_data(double *); // pack restart data
|
||||
virtual void restart(char *);
|
||||
int modify_param(int, char **);
|
||||
void reset_target(double);
|
||||
void reset_dt();
|
||||
virtual void *extract(const char*,int &);
|
||||
double memory_usage();
|
||||
|
||||
FixBocs(class LAMMPS *, int, char **); // MRD NJD
|
||||
~FixBocs() override; // MRD NJD
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void setup(int) override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
void initial_integrate_respa(int, int, int) override;
|
||||
void pre_force_respa(int, int, int) override;
|
||||
void final_integrate_respa(int, int) override;
|
||||
void pre_exchange() override;
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int) override;
|
||||
void write_restart(FILE *) override;
|
||||
virtual int pack_restart_data(double *); // pack restart data
|
||||
void restart(char *) override;
|
||||
int modify_param(int, char **) override;
|
||||
void reset_target(double) override;
|
||||
void reset_dt() override;
|
||||
void *extract(const char *, int &) override;
|
||||
double memory_usage() override;
|
||||
|
||||
protected:
|
||||
int dimension,which;
|
||||
double dtv,dtf,dthalf,dt4,dt8,dto;
|
||||
double boltz,nktv2p,tdof;
|
||||
double vol0; // reference volume
|
||||
double t0; // reference temperature
|
||||
// used for barostat mass
|
||||
double t_start,t_stop;
|
||||
double t_current,t_target,ke_target;
|
||||
int dimension, which;
|
||||
double dtv, dtf, dthalf, dt4, dt8, dto;
|
||||
double boltz, nktv2p, tdof;
|
||||
double vol0; // reference volume
|
||||
double t0; // reference temperature
|
||||
// used for barostat mass
|
||||
double t_start, t_stop;
|
||||
double t_current, t_target, ke_target;
|
||||
double t_freq;
|
||||
|
||||
int tstat_flag; // 1 if control T
|
||||
int pstat_flag; // 1 if control P
|
||||
int tstat_flag; // 1 if control T
|
||||
int pstat_flag; // 1 if control P
|
||||
|
||||
int pstyle,pcouple,allremap;
|
||||
int p_flag[6]; // 1 if control P on this dim, 0 if not
|
||||
double p_start[6],p_stop[6];
|
||||
double p_freq[6],p_target[6];
|
||||
double omega[6],omega_dot[6];
|
||||
int pstyle, pcouple, allremap;
|
||||
int p_flag[6]; // 1 if control P on this dim, 0 if not
|
||||
double p_start[6], p_stop[6];
|
||||
double p_freq[6], p_target[6];
|
||||
double omega[6], omega_dot[6];
|
||||
double omega_mass[6];
|
||||
double p_current[6];
|
||||
double drag,tdrag_factor; // drag factor on particle thermostat
|
||||
double pdrag_factor; // drag factor on barostat
|
||||
int kspace_flag; // 1 if KSpace invoked, 0 if not
|
||||
int nrigid; // number of rigid fixes
|
||||
int dilate_group_bit; // mask for dilation group
|
||||
int *rfix; // indices of rigid fixes
|
||||
char *id_dilate; // group name to dilate
|
||||
class Irregular *irregular; // for migrating atoms after box flips
|
||||
double drag, tdrag_factor; // drag factor on particle thermostat
|
||||
double pdrag_factor; // drag factor on barostat
|
||||
int kspace_flag; // 1 if KSpace invoked, 0 if not
|
||||
int nrigid; // number of rigid fixes
|
||||
int dilate_group_bit; // mask for dilation group
|
||||
int *rfix; // indices of rigid fixes
|
||||
char *id_dilate; // group name to dilate
|
||||
class Irregular *irregular; // for migrating atoms after box flips
|
||||
|
||||
// MRD NJD
|
||||
// MRD NJD
|
||||
int p_basis_type;
|
||||
int p_match_flag;
|
||||
double vavg;
|
||||
int N_mol;
|
||||
int N_p_match;
|
||||
double *p_match_coeffs;
|
||||
double ** splines;
|
||||
double **splines;
|
||||
int spline_length;
|
||||
|
||||
|
||||
int nlevels_respa;
|
||||
double *step_respa;
|
||||
|
||||
char *id_temp,*id_press;
|
||||
class Compute *temperature,*pressure;
|
||||
int tcomputeflag,pcomputeflag; // 1 = compute was created by fix
|
||||
// 0 = created externally
|
||||
char *id_temp, *id_press;
|
||||
class Compute *temperature, *pressure;
|
||||
int tcomputeflag, pcomputeflag; // 1 = compute was created by fix
|
||||
// 0 = created externally
|
||||
|
||||
double *eta,*eta_dot; // chain thermostat for particles
|
||||
double *eta, *eta_dot; // chain thermostat for particles
|
||||
double *eta_dotdot;
|
||||
double *eta_mass;
|
||||
int mtchain; // length of chain
|
||||
int mtchain_default_flag; // 1 = mtchain is default
|
||||
int mtchain; // length of chain
|
||||
int mtchain_default_flag; // 1 = mtchain is default
|
||||
|
||||
double *etap; // chain thermostat for barostat
|
||||
double *etap; // chain thermostat for barostat
|
||||
double *etap_dot;
|
||||
double *etap_dotdot;
|
||||
double *etap_mass;
|
||||
int mpchain; // length of chain
|
||||
int mpchain; // length of chain
|
||||
|
||||
int mtk_flag; // 0 if using Hoover barostat
|
||||
int pdim; // number of barostatted dims
|
||||
double p_freq_max; // maximum barostat frequency
|
||||
int mtk_flag; // 0 if using Hoover barostat
|
||||
int pdim; // number of barostatted dims
|
||||
double p_freq_max; // maximum barostat frequency
|
||||
|
||||
double p_hydro; // hydrostatic target pressure
|
||||
double p_hydro; // hydrostatic target pressure
|
||||
|
||||
int nc_tchain,nc_pchain;
|
||||
int nc_tchain, nc_pchain;
|
||||
double factor_eta;
|
||||
double sigma[6]; // scaled target stress
|
||||
double fdev[6]; // deviatoric force on barostat
|
||||
int deviatoric_flag; // 0 if target stress tensor is hydrostatic
|
||||
double h0_inv[6]; // h_inv of reference (zero strain) box
|
||||
int nreset_h0; // interval for resetting h0
|
||||
double sigma[6]; // scaled target stress
|
||||
double fdev[6]; // deviatoric force on barostat
|
||||
int deviatoric_flag; // 0 if target stress tensor is hydrostatic
|
||||
double h0_inv[6]; // h_inv of reference (zero strain) box
|
||||
int nreset_h0; // interval for resetting h0
|
||||
|
||||
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
|
||||
double mtk_term1, mtk_term2; // Martyna-Tobias-Klein corrections
|
||||
|
||||
int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
|
||||
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
|
||||
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
|
||||
int dipole_flag; // 1 if dipole is updated, 0 if not.
|
||||
int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
|
||||
int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
|
||||
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
|
||||
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
|
||||
int dipole_flag; // 1 if dipole is updated, 0 if not.
|
||||
int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
|
||||
|
||||
int scaleyz; // 1 if yz scaled with lz
|
||||
int scalexz; // 1 if xz scaled with lz
|
||||
int scalexy; // 1 if xy scaled with ly
|
||||
int flipflag; // 1 if box flips are invoked as needed
|
||||
int scaleyz; // 1 if yz scaled with lz
|
||||
int scalexz; // 1 if xz scaled with lz
|
||||
int scalexy; // 1 if xy scaled with ly
|
||||
int flipflag; // 1 if box flips are invoked as needed
|
||||
|
||||
int pre_exchange_flag; // set if pre_exchange needed for box flips
|
||||
int pre_exchange_flag; // set if pre_exchange needed for box flips
|
||||
|
||||
double fixedpoint[3]; // location of dilation fixed-point
|
||||
double fixedpoint[3]; // location of dilation fixed-point
|
||||
|
||||
void couple();
|
||||
virtual void remap();
|
||||
@ -153,7 +151,7 @@ class FixBocs : public Fix {
|
||||
int build_linear_splines(double **);
|
||||
int build_cubic_splines(double **);
|
||||
|
||||
virtual void nve_x(); // may be overwritten by child classes
|
||||
virtual void nve_x(); // may be overwritten by child classes
|
||||
virtual void nve_v();
|
||||
virtual void nh_v_press();
|
||||
virtual void nh_v_temp();
|
||||
@ -167,7 +165,7 @@ class FixBocs : public Fix {
|
||||
void nh_omega_dot();
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,44 +12,44 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BODY_CLASS
|
||||
|
||||
BodyStyle(nparticle,BodyNparticle)
|
||||
|
||||
// clang-format off
|
||||
BodyStyle(nparticle,BodyNparticle);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_BODY_NPARTICLE_H
|
||||
#define LMP_BODY_NPARTICLE_H
|
||||
|
||||
#include "body.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BodyNparticle : public Body {
|
||||
public:
|
||||
BodyNparticle(class LAMMPS *, int, char **);
|
||||
~BodyNparticle();
|
||||
~BodyNparticle() override;
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
int pack_data_body(tagint, int, double *);
|
||||
int write_data_body(FILE *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
void data_body(int, int, int, int *, double *) override;
|
||||
int pack_data_body(tagint, int, double *) override;
|
||||
int write_data_body(FILE *, double *) override;
|
||||
double radius_body(int, int, int *, double *) override;
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
int noutrow(int) override;
|
||||
int noutcol() override;
|
||||
void output(int, int, double *) override;
|
||||
int image(int, double, double, int *&, double **&) override;
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
double **imdata;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,23 +12,23 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BODY_CLASS
|
||||
|
||||
BodyStyle(rounded/polygon,BodyRoundedPolygon)
|
||||
|
||||
// clang-format off
|
||||
BodyStyle(rounded/polygon,BodyRoundedPolygon);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_BODY_ROUNDED_POLYGON_H
|
||||
#define LMP_BODY_ROUNDED_POLYGON_H
|
||||
|
||||
#include "body.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BodyRoundedPolygon : public Body {
|
||||
public:
|
||||
BodyRoundedPolygon(class LAMMPS *, int, char **);
|
||||
~BodyRoundedPolygon();
|
||||
~BodyRoundedPolygon() override;
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
int nedges(struct AtomVecBody::Bonus *);
|
||||
@ -36,24 +36,24 @@ class BodyRoundedPolygon : public Body {
|
||||
double enclosing_radius(struct AtomVecBody::Bonus *);
|
||||
double rounded_radius(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
int pack_data_body(tagint, int, double *);
|
||||
int write_data_body(FILE *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
void data_body(int, int, int, int *, double *) override;
|
||||
int pack_data_body(tagint, int, double *) override;
|
||||
int write_data_body(FILE *, double *) override;
|
||||
double radius_body(int, int, int *, double *) override;
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
int noutrow(int) override;
|
||||
int noutcol() override;
|
||||
void output(int, int, double *) override;
|
||||
int image(int, double, double, int *&, double **&) override;
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
double **imdata;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,23 +12,23 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BODY_CLASS
|
||||
|
||||
BodyStyle(rounded/polyhedron,BodyRoundedPolyhedron)
|
||||
|
||||
// clang-format off
|
||||
BodyStyle(rounded/polyhedron,BodyRoundedPolyhedron);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_BODY_ROUNDED_POLYHEDRON_H
|
||||
#define LMP_BODY_ROUNDED_POLYHEDRON_H
|
||||
|
||||
#include "body.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BodyRoundedPolyhedron : public Body {
|
||||
public:
|
||||
BodyRoundedPolyhedron(class LAMMPS *, int, char **);
|
||||
~BodyRoundedPolyhedron();
|
||||
~BodyRoundedPolyhedron() override;
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
int nedges(struct AtomVecBody::Bonus *);
|
||||
@ -38,24 +38,24 @@ class BodyRoundedPolyhedron : public Body {
|
||||
double enclosing_radius(struct AtomVecBody::Bonus *);
|
||||
double rounded_radius(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
int pack_data_body(tagint, int, double *);
|
||||
int write_data_body(FILE *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
void data_body(int, int, int, int *, double *) override;
|
||||
int pack_data_body(tagint, int, double *) override;
|
||||
int write_data_body(FILE *, double *) override;
|
||||
double radius_body(int, int, int *, double *) override;
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
int noutrow(int) override;
|
||||
int noutcol() override;
|
||||
void output(int, int, double *) override;
|
||||
int image(int, double, double, int *&, double **&) override;
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
double **imdata;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -52,7 +53,7 @@ ComputeBodyLocal::ComputeBodyLocal(LAMMPS *lmp, int narg, char **arg) :
|
||||
}
|
||||
}
|
||||
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec) error->all(FLERR,"Compute body/local requires atom style body");
|
||||
bptr = avec->bptr;
|
||||
|
||||
@ -152,7 +153,7 @@ int ComputeBodyLocal::compute_body(int flag)
|
||||
// perform computation and fill output vector/array
|
||||
|
||||
int m,n,ibonus;
|
||||
double *values = new double[bptr->noutcol()];
|
||||
auto values = new double[bptr->noutcol()];
|
||||
|
||||
double **x = atom->x;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(body/local,ComputeBodyLocal)
|
||||
|
||||
// clang-format off
|
||||
ComputeStyle(body/local,ComputeBodyLocal);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_BODY_LOCAL_H
|
||||
@ -27,14 +27,14 @@ namespace LAMMPS_NS {
|
||||
class ComputeBodyLocal : public Compute {
|
||||
public:
|
||||
ComputeBodyLocal(class LAMMPS *, int, char **);
|
||||
~ComputeBodyLocal();
|
||||
void init();
|
||||
void compute_local();
|
||||
double memory_usage();
|
||||
~ComputeBodyLocal() override;
|
||||
void init() override;
|
||||
void compute_local() override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
int nvalues;
|
||||
int *which,*index;
|
||||
int *which, *index;
|
||||
|
||||
int nmax;
|
||||
|
||||
@ -45,7 +45,7 @@ class ComputeBodyLocal : public Compute {
|
||||
void reallocate(int);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -56,9 +57,7 @@ ComputeTempBody::ComputeTempBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute temp/body command");
|
||||
tempbias = 1;
|
||||
int n = strlen(arg[iarg+1]) + 1;
|
||||
id_bias = new char[n];
|
||||
strcpy(id_bias,arg[iarg+1]);
|
||||
id_bias = utils::strdup(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"dof") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
@ -88,7 +87,7 @@ void ComputeTempBody::init()
|
||||
{
|
||||
// error check
|
||||
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec)
|
||||
error->all(FLERR,"Compute temp/body requires atom style body");
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(temp/body,ComputeTempBody)
|
||||
|
||||
// clang-format off
|
||||
ComputeStyle(temp/body,ComputeTempBody);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_TEMP_BODY_H
|
||||
@ -27,26 +27,26 @@ namespace LAMMPS_NS {
|
||||
class ComputeTempBody : public Compute {
|
||||
public:
|
||||
ComputeTempBody(class LAMMPS *, int, char **);
|
||||
~ComputeTempBody();
|
||||
void init();
|
||||
void setup();
|
||||
double compute_scalar();
|
||||
void compute_vector();
|
||||
~ComputeTempBody() override;
|
||||
void init() override;
|
||||
void setup() override;
|
||||
double compute_scalar() override;
|
||||
void compute_vector() override;
|
||||
|
||||
void remove_bias(int, double *);
|
||||
void restore_bias(int, double *);
|
||||
void remove_bias(int, double *) override;
|
||||
void restore_bias(int, double *) override;
|
||||
|
||||
private:
|
||||
int mode;
|
||||
double tfactor;
|
||||
char *id_bias;
|
||||
class Compute *tbias; // ptr to additional bias compute
|
||||
class Compute *tbias; // ptr to additional bias compute
|
||||
class AtomVecBody *avec;
|
||||
|
||||
void dof_compute();
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -36,7 +37,7 @@ FixNHBody::FixNHBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
void FixNHBody::init()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec)
|
||||
error->all(FLERR,
|
||||
"Compute nvt/nph/npt body requires atom style body");
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -21,19 +21,18 @@ namespace LAMMPS_NS {
|
||||
class FixNHBody : public FixNH {
|
||||
public:
|
||||
FixNHBody(class LAMMPS *, int, char **);
|
||||
virtual ~FixNHBody() {}
|
||||
void init();
|
||||
void init() override;
|
||||
|
||||
protected:
|
||||
double dtq;
|
||||
class AtomVecBody *avec;
|
||||
|
||||
void nve_v();
|
||||
void nve_x();
|
||||
void nh_v_temp();
|
||||
void nve_v() override;
|
||||
void nve_x() override;
|
||||
void nh_v_temp() override;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -16,12 +17,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_nph_body.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "modify.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -41,22 +39,15 @@ FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp,tcmd.c_str());
|
||||
|
||||
tcmd += fmt::format(" {} temp/body",group->names[igroup]);
|
||||
modify->add_compute(tcmd);
|
||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||
modify->add_compute(fmt::format("{} all temp/body",id_temp));
|
||||
tcomputeflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
std::string pcmd = id + std::string("_press");
|
||||
id_press = new char[pcmd.size()+1];
|
||||
strcpy(id_press,pcmd.c_str());
|
||||
|
||||
modify->add_compute(pcmd + " all pressure " + std::string(id_temp));
|
||||
id_press = utils::strdup(std::string(id) + "_press");
|
||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
||||
pcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nph/body,FixNPHBody)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nph/body,FixNPHBody);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPH_BODY_H
|
||||
@ -27,10 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNPHBody : public FixNHBody {
|
||||
public:
|
||||
FixNPHBody(class LAMMPS *, int, char **);
|
||||
~FixNPHBody() {}
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -16,12 +17,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_npt_body.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "modify.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -41,22 +39,15 @@ FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp,tcmd.c_str());
|
||||
|
||||
tcmd += fmt::format(" {} temp/body",group->names[igroup]);
|
||||
modify->add_compute(tcmd);
|
||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||
modify->add_compute(fmt::format("{} all temp/body",id_temp));
|
||||
tcomputeflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
std::string pcmd = id + std::string("_press");
|
||||
id_press = new char[pcmd.size()+1];
|
||||
strcpy(id_press,pcmd.c_str());
|
||||
|
||||
modify->add_compute(pcmd + " all pressure " + std::string(id_temp));
|
||||
id_press = utils::strdup(std::string(id) + "_press");
|
||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
||||
pcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(npt/body,FixNPTBody)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(npt/body,FixNPTBody);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPT_BODY_H
|
||||
@ -27,10 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNPTBody : public FixNHBody {
|
||||
public:
|
||||
FixNPTBody(class LAMMPS *, int, char **);
|
||||
~FixNPTBody() {}
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -29,7 +30,7 @@ FixNVEBody::FixNVEBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
void FixNVEBody::init()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec) error->all(FLERR,"Fix nve/body requires atom style body");
|
||||
|
||||
// check that all particles are bodies
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/body,FixNVEBody)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/body,FixNVEBody);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_BODY_H
|
||||
@ -27,16 +27,16 @@ namespace LAMMPS_NS {
|
||||
class FixNVEBody : public FixNVE {
|
||||
public:
|
||||
FixNVEBody(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
class AtomVecBody *avec;
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
#endif
|
||||
#endif
|
||||
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -16,12 +17,10 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_nvt_body.h"
|
||||
#include <cstring>
|
||||
|
||||
#include "error.h"
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -39,11 +38,8 @@ FixNVTBody::FixNVTBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
|
||||
std::string tcmd = id + std::string("_temp");
|
||||
id_temp = new char[tcmd.size()+1];
|
||||
strcpy(id_temp,tcmd.c_str());
|
||||
|
||||
tcmd += fmt::format(" {} temp/body",group->names[igroup]);
|
||||
modify->add_compute(tcmd);
|
||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||
modify->add_compute(fmt::format("{} {} temp/body",
|
||||
id_temp,group->names[igroup]));
|
||||
tcomputeflag = 1;
|
||||
}
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nvt/body,FixNVTBody)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nvt/body,FixNVTBody);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVT_BODY_H
|
||||
@ -27,10 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNVTBody : public FixNHBody {
|
||||
public:
|
||||
FixNVTBody(class LAMMPS *, int, char **);
|
||||
~FixNVTBody() {}
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -16,18 +17,20 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_wall_body_polygon.h"
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body_rounded_polygon.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -97,7 +100,7 @@ FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) :
|
||||
lo = hi = 0.0;
|
||||
cylradius = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg]));
|
||||
} else error->all(FLERR,"Unknown wall style {}",arg[iarg]);
|
||||
|
||||
// check for trailing keyword/values
|
||||
|
||||
@ -176,13 +179,13 @@ void FixWallBodyPolygon::init()
|
||||
{
|
||||
dt = update->dt;
|
||||
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec)
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires "
|
||||
"body style rounded/polygon");
|
||||
bptr = (BodyRoundedPolygon *) avec->bptr;
|
||||
bptr = dynamic_cast<BodyRoundedPolygon *>( avec->bptr);
|
||||
|
||||
// set pairstyle from body/polygonular pair style
|
||||
|
||||
@ -195,7 +198,7 @@ void FixWallBodyPolygon::init()
|
||||
|
||||
void FixWallBodyPolygon::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
if (utils::strmatch(update->integrate_style,"^verlet"))
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
@ -334,8 +337,7 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
|
||||
|
||||
num_contacts = 0;
|
||||
facc[0] = facc[1] = facc[2] = 0;
|
||||
vertex_against_wall(i, wall_pos, x, f, torque, side,
|
||||
contact_list, num_contacts, facc);
|
||||
vertex_against_wall(i, wall_pos, x, f, torque, side, contact_list, num_contacts, facc);
|
||||
|
||||
if (num_contacts >= 2) {
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(wall/body/polygon,FixWallBodyPolygon)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(wall/body/polygon,FixWallBodyPolygon);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WALL_BODY_POLYGON_H
|
||||
@ -27,74 +27,69 @@ namespace LAMMPS_NS {
|
||||
class FixWallBodyPolygon : public Fix {
|
||||
public:
|
||||
FixWallBodyPolygon(class LAMMPS *, int, char **);
|
||||
virtual ~FixWallBodyPolygon();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
void reset_dt();
|
||||
~FixWallBodyPolygon() override;
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void setup(int) override;
|
||||
void post_force(int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation;// separation at contact
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation; // separation at contact
|
||||
};
|
||||
|
||||
protected:
|
||||
int wallstyle,pairstyle,wiggle,axis;
|
||||
double kn; // normal repulsion strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double lo,hi,cylradius;
|
||||
double amplitude,period,omega;
|
||||
int wallstyle, pairstyle, wiggle, axis;
|
||||
double kn; // normal repulsion strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double lo, hi, cylradius;
|
||||
double amplitude, period, omega;
|
||||
double dt;
|
||||
int time_origin;
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolygon *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
|
||||
void body2space(int);
|
||||
|
||||
int vertex_against_wall(int ibody, double wall_pos, double** x,
|
||||
double** f, double** torque, int side,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double* facc);
|
||||
|
||||
int compute_distance_to_wall(double* x0, double rradi, double wall_pos,
|
||||
int side, double &d, double hi[3], int &contact);
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
void contact_forces(Contact& contact, double j_a, double** x,
|
||||
double** v, double** angmom, double** f, double** torque,
|
||||
double* vwall, double* facc);
|
||||
void sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
void distance(const double* x2, const double* x1, double& r);
|
||||
int vertex_against_wall(int ibody, double wall_pos, double **x, double **f, double **torque,
|
||||
int side, Contact *contact_list, int &num_contacts, double *facc);
|
||||
|
||||
int compute_distance_to_wall(double *x0, double rradi, double wall_pos, int side, double &d,
|
||||
double hi[3], int &contact);
|
||||
double contact_separation(const Contact &c1, const Contact &c2);
|
||||
void contact_forces(Contact &contact, double j_a, double **x, double **v, double **angmom,
|
||||
double **f, double **torque, double *vwall, double *facc);
|
||||
void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
|
||||
void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
|
||||
double *quat, double *vi);
|
||||
void distance(const double *x2, const double *x1, double &r);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -99,7 +100,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg)
|
||||
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
|
||||
else hi = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||
iarg += 3;
|
||||
} else error->all(FLERR,fmt::format("Unknown wall style {}",arg[iarg]));
|
||||
} else error->all(FLERR,"Unknown wall style {}",arg[iarg]);
|
||||
|
||||
// check for trailing keyword/values
|
||||
|
||||
@ -183,13 +184,13 @@ void FixWallBodyPolyhedron::init()
|
||||
{
|
||||
dt = update->dt;
|
||||
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec)
|
||||
error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
||||
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||
"body style rounded/polyhedron");
|
||||
bptr = (BodyRoundedPolyhedron *) avec->bptr;
|
||||
bptr = dynamic_cast<BodyRoundedPolyhedron *>( avec->bptr);
|
||||
|
||||
// set pairstyle from body/polyhedronular pair style
|
||||
|
||||
@ -202,7 +203,7 @@ void FixWallBodyPolyhedron::init()
|
||||
|
||||
void FixWallBodyPolyhedron::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
if (utils::strmatch(update->integrate_style,"^verlet"))
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(wall/body/polyhedron,FixWallBodyPolyhedron)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(wall/body/polyhedron,FixWallBodyPolyhedron);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WALL_BODY_POLYHERON_H
|
||||
@ -27,86 +27,80 @@ namespace LAMMPS_NS {
|
||||
class FixWallBodyPolyhedron : public Fix {
|
||||
public:
|
||||
FixWallBodyPolyhedron(class LAMMPS *, int, char **);
|
||||
virtual ~FixWallBodyPolyhedron();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
void reset_dt();
|
||||
~FixWallBodyPolyhedron() override;
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void setup(int) override;
|
||||
void post_force(int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation;// separation at contact
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation; // separation at contact
|
||||
};
|
||||
|
||||
protected:
|
||||
int wallstyle,pairstyle,wiggle,axis;
|
||||
double kn,c_n,c_t;
|
||||
double lo,hi,cylradius;
|
||||
double amplitude,period,omega;
|
||||
int wallstyle, pairstyle, wiggle, axis;
|
||||
double kn, c_n, c_t;
|
||||
double lo, hi, cylradius;
|
||||
double amplitude, period, omega;
|
||||
double dt;
|
||||
int time_origin;
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolyhedron *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double **face; // list of all edge for all bodies
|
||||
int nface; // number of faces in list
|
||||
int facmax; // allocated size of face list
|
||||
int *facnum; // number of faces per line, 0 if uninit
|
||||
int *facfirst; // index of first face per each line
|
||||
int facnummax; // allocated size of facnum,facfirst vectors
|
||||
double **face; // list of all edge for all bodies
|
||||
int nface; // number of faces in list
|
||||
int facmax; // allocated size of face list
|
||||
int *facnum; // number of faces per line, 0 if uninit
|
||||
int *facfirst; // index of first face per each line
|
||||
int facnummax; // allocated size of facnum,facfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
|
||||
void body2space(int);
|
||||
|
||||
int edge_against_wall(int ibody, double wall_pos, int side, double* vwall,
|
||||
double** x, double** f, double** torque, Contact* contact_list,
|
||||
int &num_contacts, double* facc);
|
||||
int sphere_against_wall(int i, double wall_pos, int side, double* vwall,
|
||||
double** x, double** v, double** f, double** angmom, double** torque);
|
||||
int edge_against_wall(int ibody, double wall_pos, int side, double *vwall, double **x, double **f,
|
||||
double **torque, Contact *contact_list, int &num_contacts, double *facc);
|
||||
int sphere_against_wall(int i, double wall_pos, int side, double *vwall, double **x, double **v,
|
||||
double **f, double **angmom, double **torque);
|
||||
|
||||
int compute_distance_to_wall(int ibody, int edge_index, double *xmi,
|
||||
double rounded_radius_i, double wall_pos, int side,
|
||||
double* vwall, int &contact);
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
void contact_forces(int ibody, double j_a, double *xi, double *xj,
|
||||
double delx, double dely, double delz,
|
||||
double fx, double fy, double fz, double** x, double** v,
|
||||
double** angmom, double** f, double** torque, double* vwall);
|
||||
|
||||
void contact_forces(Contact& contact, double j_a, double** x,
|
||||
double** v, double** angmom, double** f, double** torque,
|
||||
double* vwall, double* facc);
|
||||
void sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
void distance(const double* x2, const double* x1, double& r);
|
||||
int compute_distance_to_wall(int ibody, int edge_index, double *xmi, double rounded_radius_i,
|
||||
double wall_pos, int side, double *vwall, int &contact);
|
||||
double contact_separation(const Contact &c1, const Contact &c2);
|
||||
void contact_forces(int ibody, double j_a, double *xi, double *xj, double delx, double dely,
|
||||
double delz, double fx, double fy, double fz, double **x, double **v,
|
||||
double **angmom, double **f, double **torque, double *vwall);
|
||||
|
||||
void contact_forces(Contact &contact, double j_a, double **x, double **v, double **angmom,
|
||||
double **f, double **torque, double *vwall, double *facc);
|
||||
void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
|
||||
void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
|
||||
double *quat, double *vi);
|
||||
void distance(const double *x2, const double *x1, double &r);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,18 +13,19 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_body_nparticle.h"
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "math_extra.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body_nparticle.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -322,8 +324,7 @@ void PairBodyNparticle::compute(int eflag, int vflag)
|
||||
}
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
@ -415,13 +416,13 @@ void PairBodyNparticle::coeff(int narg, char **arg)
|
||||
|
||||
void PairBodyNparticle::init_style()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"nparticle") != 0)
|
||||
error->all(FLERR,"Pair body/nparticle requires body style nparticle");
|
||||
bptr = (BodyNparticle *) avec->bptr;
|
||||
bptr = dynamic_cast<BodyNparticle *>( avec->bptr);
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
neighbor->add_request(this);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(body/nparticle,PairBodyNparticle)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(body/nparticle,PairBodyNparticle);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BODY_NPARTICLE_H
|
||||
@ -27,34 +27,34 @@ namespace LAMMPS_NS {
|
||||
class PairBodyNparticle : public Pair {
|
||||
public:
|
||||
PairBodyNparticle(class LAMMPS *);
|
||||
~PairBodyNparticle();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
~PairBodyNparticle() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
double **epsilon, **sigma;
|
||||
double **lj1, **lj2, **lj3, **lj4;
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyNparticle *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
void allocate();
|
||||
void body2space(int);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -20,21 +21,21 @@
|
||||
|
||||
#include "pair_body_rounded_polygon.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "math_extra.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body_rounded_polygon.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "fix.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "fix.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -206,8 +207,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
|
||||
if (r > radi + radj + cut_inner) continue;
|
||||
|
||||
if (npi == 1 && npj == 1) {
|
||||
sphere_against_sphere(i, j, delx, dely, delz, rsq,
|
||||
k_nij, k_naij, x, v, f, evflag);
|
||||
sphere_against_sphere(i, j, delx, dely, delz, rsq, k_nij, k_naij, x, v, f, evflag);
|
||||
continue;
|
||||
}
|
||||
|
||||
@ -411,13 +411,13 @@ void PairBodyRoundedPolygon::coeff(int narg, char **arg)
|
||||
|
||||
void PairBodyRoundedPolygon::init_style()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec)
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires "
|
||||
"body style rounded/polygon");
|
||||
bptr = (BodyRoundedPolygon *) avec->bptr;
|
||||
bptr = dynamic_cast<BodyRoundedPolygon *>( avec->bptr);
|
||||
|
||||
if (force->newton_pair == 0)
|
||||
error->all(FLERR,"Pair style body/rounded/polygon requires "
|
||||
@ -427,7 +427,7 @@ void PairBodyRoundedPolygon::init_style()
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires "
|
||||
"ghost atoms store velocity");
|
||||
|
||||
neighbor->request(this);
|
||||
neighbor->add_request(this);
|
||||
|
||||
// find the maximum enclosing radius for each atom type
|
||||
|
||||
@ -570,8 +570,8 @@ void PairBodyRoundedPolygon::body2space(int i)
|
||||
}
|
||||
|
||||
if ((body_num_edges > 0) && (edge_ends == nullptr))
|
||||
error->one(FLERR,fmt::format("Inconsistent edge data for body of atom {}",
|
||||
atom->tag[i]));
|
||||
error->one(FLERR,"Inconsistent edge data for body of atom {}",
|
||||
atom->tag[i]);
|
||||
|
||||
for (int m = 0; m < body_num_edges; m++) {
|
||||
edge[nedge][0] = static_cast<int>(edge_ends[2*m+0]);
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(body/rounded/polygon,PairBodyRoundedPolygon)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(body/rounded/polygon,PairBodyRoundedPolygon);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BODY_ROUNDED_POLYGON_H
|
||||
@ -27,89 +27,84 @@ namespace LAMMPS_NS {
|
||||
class PairBodyRoundedPolygon : public Pair {
|
||||
public:
|
||||
PairBodyRoundedPolygon(class LAMMPS *);
|
||||
~PairBodyRoundedPolygon();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
~PairBodyRoundedPolygon() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation;// separation at contact
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation; // separation at contact
|
||||
};
|
||||
|
||||
protected:
|
||||
double **k_n; // normal repulsion strength
|
||||
double **k_na; // normal attraction strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double mu; // normal friction coefficient during gross sliding
|
||||
double delta_ua; // contact line (area for 3D models) modification factor
|
||||
double cut_inner; // cutoff for interaction between vertex-edge surfaces
|
||||
double **k_n; // normal repulsion strength
|
||||
double **k_na; // normal attraction strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double mu; // normal friction coefficient during gross sliding
|
||||
double delta_ua; // contact line (area for 3D models) modification factor
|
||||
double cut_inner; // cutoff for interaction between vertex-edge surfaces
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolygon *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *maxerad; // per-type maximum enclosing radius
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *maxerad; // per-type maximum enclosing radius
|
||||
|
||||
void allocate();
|
||||
void body2space(int);
|
||||
|
||||
// sphere-sphere interaction
|
||||
void sphere_against_sphere(int i, int j, double delx, double dely, double delz,
|
||||
double rsq, double k_n, double k_na,
|
||||
double** x, double** v, double** f, int evflag);
|
||||
void sphere_against_sphere(int i, int j, double delx, double dely, double delz, double rsq,
|
||||
double k_n, double k_na, double **x, double **v, double **f,
|
||||
int evflag);
|
||||
// vertex-edge interaction
|
||||
int vertex_against_edge(int i, int j, double k_n, double k_na,
|
||||
double** x, double** f, double** torque,
|
||||
tagint* tag, Contact* contact_list,
|
||||
int &num_contacts, double &evdwl, double* facc);
|
||||
int vertex_against_edge(int i, int j, double k_n, double k_na, double **x, double **f,
|
||||
double **torque, tagint *tag, Contact *contact_list, int &num_contacts,
|
||||
double &evdwl, double *facc);
|
||||
// compute distance between a point and an edge from another body
|
||||
int compute_distance_to_vertex(int ibody, int edge_index, double* xmi,
|
||||
double rounded_radius, double* x0,
|
||||
double x0_rounded_radius, double cut_inner,
|
||||
double &d, double hi[3], double &t,
|
||||
int &contact);
|
||||
int compute_distance_to_vertex(int ibody, int edge_index, double *xmi, double rounded_radius,
|
||||
double *x0, double x0_rounded_radius, double cut_inner, double &d,
|
||||
double hi[3], double &t, int &contact);
|
||||
// compute contact forces if contact points are detected
|
||||
void contact_forces(Contact& contact, double j_a,
|
||||
double** x, double** v, double** angmom, double** f,
|
||||
double** torque, double &evdwl, double* facc);
|
||||
void contact_forces(Contact &contact, double j_a, double **x, double **v, double **angmom,
|
||||
double **f, double **torque, double &evdwl, double *facc);
|
||||
|
||||
// compute the separation between two contacts
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
double contact_separation(const Contact &c1, const Contact &c2);
|
||||
|
||||
// accumulate torque to a body given a force at a given point
|
||||
void sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque);
|
||||
void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
|
||||
// helper functions
|
||||
int opposite_sides(double* x1, double* x2, double* a, double* b);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
inline void distance(const double* x2, const double* x1, double& r);
|
||||
int opposite_sides(double *x1, double *x2, double *a, double *b);
|
||||
void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
|
||||
double *quat, double *vi);
|
||||
inline void distance(const double *x2, const double *x1, double &r);
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -22,22 +23,22 @@
|
||||
|
||||
#include "pair_body_rounded_polyhedron.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body_rounded_polyhedron.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "fix.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "math_extra.h"
|
||||
#include "fix.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
@ -389,13 +390,13 @@ void PairBodyRoundedPolyhedron::coeff(int narg, char **arg)
|
||||
|
||||
void PairBodyRoundedPolyhedron::init_style()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
||||
if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||
"atom style body");
|
||||
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
||||
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||
"body style rounded/polyhedron");
|
||||
bptr = (BodyRoundedPolyhedron *) avec->bptr;
|
||||
bptr = dynamic_cast<BodyRoundedPolyhedron *>( avec->bptr);
|
||||
|
||||
if (force->newton_pair == 0)
|
||||
error->all(FLERR,"Pair style body/rounded/polyhedron requires "
|
||||
@ -405,7 +406,7 @@ void PairBodyRoundedPolyhedron::init_style()
|
||||
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||
"ghost atoms store velocity");
|
||||
|
||||
neighbor->request(this);
|
||||
neighbor->add_request(this);
|
||||
|
||||
// find the maximum enclosing radius for each atom type
|
||||
|
||||
@ -557,8 +558,8 @@ void PairBodyRoundedPolyhedron::body2space(int i)
|
||||
}
|
||||
|
||||
if ((body_num_edges > 0) && (edge_ends == nullptr))
|
||||
error->one(FLERR,fmt::format("Inconsistent edge data for body of atom {}",
|
||||
atom->tag[i]));
|
||||
error->one(FLERR,"Inconsistent edge data for body of atom {}",
|
||||
atom->tag[i]);
|
||||
|
||||
for (int m = 0; m < body_num_edges; m++) {
|
||||
edge[nedge][0] = static_cast<int>(edge_ends[2*m+0]);
|
||||
@ -584,8 +585,8 @@ void PairBodyRoundedPolyhedron::body2space(int i)
|
||||
}
|
||||
|
||||
if ((body_num_faces > 0) && (face_pts == nullptr))
|
||||
error->one(FLERR,fmt::format("Inconsistent face data for body of atom {}",
|
||||
atom->tag[i]));
|
||||
error->one(FLERR,"Inconsistent face data for body of atom {}",
|
||||
atom->tag[i]);
|
||||
|
||||
for (int m = 0; m < body_num_faces; m++) {
|
||||
for (int k = 0; k < MAX_FACE_SIZE; k++)
|
||||
@ -1211,10 +1212,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
|
||||
contact_list[num_contacts].unique = 1;
|
||||
num_contacts++;
|
||||
}
|
||||
} else {
|
||||
|
||||
}
|
||||
|
||||
return interact;
|
||||
}
|
||||
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,9 +12,9 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(body/rounded/polyhedron,PairBodyRoundedPolyhedron)
|
||||
|
||||
// clang-format off
|
||||
PairStyle(body/rounded/polyhedron,PairBodyRoundedPolyhedron);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H
|
||||
@ -27,152 +27,138 @@ namespace LAMMPS_NS {
|
||||
class PairBodyRoundedPolyhedron : public Pair {
|
||||
public:
|
||||
PairBodyRoundedPolyhedron(class LAMMPS *);
|
||||
~PairBodyRoundedPolyhedron();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
~PairBodyRoundedPolyhedron() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
virtual void kernel_force(double R, int itype, int jtype,
|
||||
double& energy, double& fpair);
|
||||
virtual void kernel_force(double R, int itype, int jtype, double &energy, double &fpair);
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int type; // 0 = VERTEX-FACE; 1 = EDGE-EDGE
|
||||
double fx,fy,fz; // unscaled cohesive forces at contact
|
||||
double xi[3]; // coordinates of the contact point on ibody
|
||||
double xj[3]; // coordinates of the contact point on jbody
|
||||
double separation; // contact surface separation
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int type; // 0 = VERTEX-FACE; 1 = EDGE-EDGE
|
||||
double fx, fy, fz; // unscaled cohesive forces at contact
|
||||
double xi[3]; // coordinates of the contact point on ibody
|
||||
double xj[3]; // coordinates of the contact point on jbody
|
||||
double separation; // contact surface separation
|
||||
int unique;
|
||||
};
|
||||
|
||||
protected:
|
||||
double **k_n; // normal repulsion strength
|
||||
double **k_na; // normal attraction strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double mu; // normal friction coefficient during gross sliding
|
||||
double A_ua; // characteristic contact area
|
||||
double cut_inner; // cutoff for interaction between vertex-edge surfaces
|
||||
double **k_n; // normal repulsion strength
|
||||
double **k_na; // normal attraction strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double mu; // normal friction coefficient during gross sliding
|
||||
double A_ua; // characteristic contact area
|
||||
double cut_inner; // cutoff for interaction between vertex-edge surfaces
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolyhedron *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double **face; // list of all edge for all bodies
|
||||
int nface; // number of faces in list
|
||||
int facmax; // allocated size of face list
|
||||
int *facnum; // number of faces per line, 0 if uninit
|
||||
int *facfirst; // index of first face per each line
|
||||
int facnummax; // allocated size of facnum,facfirst vectors
|
||||
double **face; // list of all edge for all bodies
|
||||
int nface; // number of faces in list
|
||||
int facmax; // allocated size of face list
|
||||
int *facnum; // number of faces per line, 0 if uninit
|
||||
int *facfirst; // index of first face per each line
|
||||
int facnummax; // allocated size of facnum,facfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *maxerad; // per-type maximum enclosing radius
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *maxerad; // per-type maximum enclosing radius
|
||||
|
||||
void allocate();
|
||||
void body2space(int);
|
||||
|
||||
// sphere-sphere interaction
|
||||
void sphere_against_sphere(int ibody, int jbody, int itype, int jtype,
|
||||
double delx, double dely, double delz, double rsq,
|
||||
double** v, double** f, int evflag);
|
||||
void sphere_against_sphere(int ibody, int jbody, int itype, int jtype, double delx, double dely,
|
||||
double delz, double rsq, double **v, double **f, int evflag);
|
||||
// sphere-edge interaction
|
||||
void sphere_against_edge(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int evflag);
|
||||
void sphere_against_edge(int ibody, int jbody, int itype, int jtype, double **x, double **v,
|
||||
double **f, double **torque, double **angmom, int evflag);
|
||||
// sphere-face interaction
|
||||
void sphere_against_face(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int evflag);
|
||||
void sphere_against_face(int ibody, int jbody, int itype, int jtype, double **x, double **v,
|
||||
double **f, double **torque, double **angmom, int evflag);
|
||||
// edge-edge interactions
|
||||
int edge_against_edge(int ibody, int jbody, int itype, int jtype,
|
||||
double** x,Contact* contact_list, int &num_contacts,
|
||||
double &evdwl, double* facc);
|
||||
int edge_against_edge(int ibody, int jbody, int itype, int jtype, double **x,
|
||||
Contact *contact_list, int &num_contacts, double &evdwl, double *facc);
|
||||
// edge-face interactions
|
||||
int edge_against_face(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, Contact* contact_list, int &num_contacts,
|
||||
double &evdwl, double* facc);
|
||||
int edge_against_face(int ibody, int jbody, int itype, int jtype, double **x,
|
||||
Contact *contact_list, int &num_contacts, double &evdwl, double *facc);
|
||||
|
||||
// a face vs. a single edge
|
||||
int interaction_face_to_edge(int ibody, int face_index, double* xmi,
|
||||
double rounded_radius_i, int jbody, int edge_index,
|
||||
double* xmj, double rounded_radius_j,
|
||||
int itype, int jtype, double cut_inner,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double& energy, double* facc);
|
||||
int interaction_face_to_edge(int ibody, int face_index, double *xmi, double rounded_radius_i,
|
||||
int jbody, int edge_index, double *xmj, double rounded_radius_j,
|
||||
int itype, int jtype, double cut_inner, Contact *contact_list,
|
||||
int &num_contacts, double &energy, double *facc);
|
||||
// an edge vs. an edge from another body
|
||||
int interaction_edge_to_edge(int ibody, int edge_index_i, double* xmi,
|
||||
double rounded_radius_i, int jbody, int edge_index_j,
|
||||
double* xmj, double rounded_radius_j,
|
||||
int itype, int jtype, double cut_inner,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double& energy, double* facc);
|
||||
int interaction_edge_to_edge(int ibody, int edge_index_i, double *xmi, double rounded_radius_i,
|
||||
int jbody, int edge_index_j, double *xmj, double rounded_radius_j,
|
||||
int itype, int jtype, double cut_inner, Contact *contact_list,
|
||||
int &num_contacts, double &energy, double *facc);
|
||||
|
||||
// compute contact forces if contact points are detected
|
||||
void contact_forces(int ibody, int jbody, double *xi, double *xj,
|
||||
double delx, double dely, double delz, double fx, double fy, double fz,
|
||||
double** x, double** v, double** angmom, double** f, double** torque,
|
||||
double* facc);
|
||||
void contact_forces(int ibody, int jbody, double *xi, double *xj, double delx, double dely,
|
||||
double delz, double fx, double fy, double fz, double **x, double **v,
|
||||
double **angmom, double **f, double **torque, double *facc);
|
||||
|
||||
// compute force and torque between two bodies given a pair of interacting points
|
||||
void pair_force_and_torque(int ibody, int jbody, double* pi, double* pj,
|
||||
double r, double contact_dist, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int jflag, double& energy, double* facc);
|
||||
void pair_force_and_torque(int ibody, int jbody, double *pi, double *pj, double r,
|
||||
double contact_dist, int itype, int jtype, double **x, double **v,
|
||||
double **f, double **torque, double **angmom, int jflag,
|
||||
double &energy, double *facc);
|
||||
|
||||
// rescale the cohesive forces if a contact area is detected
|
||||
void rescale_cohesive_forces(double** x, double** f, double** torque,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
int itype, int jtype, double* facc);
|
||||
void rescale_cohesive_forces(double **x, double **f, double **torque, Contact *contact_list,
|
||||
int &num_contacts, int itype, int jtype, double *facc);
|
||||
|
||||
// compute the separation between two contacts
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
double contact_separation(const Contact &c1, const Contact &c2);
|
||||
|
||||
// detect the unique contact points (as there may be double counts)
|
||||
void find_unique_contacts(Contact* contact_list, int& num_contacts);
|
||||
void find_unique_contacts(Contact *contact_list, int &num_contacts);
|
||||
|
||||
// accumulate torque to a body given a force at a given point
|
||||
void sum_torque(double* xm, double *x, double fx, double fy, double fz, double* torque);
|
||||
void sum_torque(double *xm, double *x, double fx, double fy, double fz, double *torque);
|
||||
|
||||
// find the intersection point (if any) between an edge and a face
|
||||
int edge_face_intersect(double* x1, double* x2, double* x3, double* a, double* b,
|
||||
double* hi1, double* hi2, double& d1, double& d2,
|
||||
int& inside_a, int& inside_b);
|
||||
int edge_face_intersect(double *x1, double *x2, double *x3, double *a, double *b, double *hi1,
|
||||
double *hi2, double &d1, double &d2, int &inside_a, int &inside_b);
|
||||
// helper functions
|
||||
int opposite_sides(double* n, double* x0, double* a, double* b);
|
||||
void project_pt_plane(const double* q, const double* p,
|
||||
const double* n, double* q_proj, double &d);
|
||||
void project_pt_plane(const double* q, const double* x1, const double* x2,
|
||||
const double* x3, double* q_proj, double &d, int& inside);
|
||||
void project_pt_line(const double* q, const double* xi1, const double* xi2,
|
||||
double* h, double& d, double& t);
|
||||
void inside_polygon(int ibody, int face_index, double* xmi,
|
||||
const double* q1, const double* q2, int& inside1, int& inside2);
|
||||
int opposite_sides(double *n, double *x0, double *a, double *b);
|
||||
void project_pt_plane(const double *q, const double *p, const double *n, double *q_proj,
|
||||
double &d);
|
||||
void project_pt_plane(const double *q, const double *x1, const double *x2, const double *x3,
|
||||
double *q_proj, double &d, int &inside);
|
||||
void project_pt_line(const double *q, const double *xi1, const double *xi2, double *h, double &d,
|
||||
double &t);
|
||||
void inside_polygon(int ibody, int face_index, double *xmi, const double *q1, const double *q2,
|
||||
int &inside1, int &inside2);
|
||||
|
||||
void distance_bt_edges(const double* x1, const double* x2,
|
||||
const double* x3, const double* x4,
|
||||
double* h1, double* h2, double& t1, double& t2, double& r);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
void distance_bt_edges(const double *x1, const double *x2, const double *x3, const double *x4,
|
||||
double *h1, double *h2, double &t1, double &t2, double &r);
|
||||
void total_velocity(double *p, double *xcm, double *vcm, double *angmom, double *inertia,
|
||||
double *quat, double *vi);
|
||||
void sanity_check();
|
||||
};
|
||||
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
248
src/BPM/atom_vec_bpm_sphere.cpp
Normal file
248
src/BPM/atom_vec_bpm_sphere.cpp
Normal file
@ -0,0 +1,248 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "atom_vec_bpm_sphere.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "fix.h"
|
||||
#include "fix_adapt.h"
|
||||
#include "math_const.h"
|
||||
#include "modify.h"
|
||||
#include "utils.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathConst::MY_PI;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
|
||||
{
|
||||
mass_type = PER_ATOM;
|
||||
molecular = Atom::MOLECULAR;
|
||||
bonds_allow = 1;
|
||||
|
||||
atom->molecule_flag = 1;
|
||||
atom->sphere_flag = 1;
|
||||
atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = atom->quat_flag = 1;
|
||||
|
||||
// strings with peratom variables to include in each AtomVec method
|
||||
// strings cannot contain fields in corresponding AtomVec default strings
|
||||
// order of fields in a string does not matter
|
||||
// except: fields_data_atom & fields_data_vel must match data file
|
||||
|
||||
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special",
|
||||
"radius", "rmass", "omega", "torque", "quat"};
|
||||
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial",
|
||||
"special", "radius", "rmass", "omega", "quat"};
|
||||
fields_comm_vel = {"omega", "quat"};
|
||||
fields_reverse = {"torque"};
|
||||
fields_border = {"molecule", "radius", "rmass"};
|
||||
fields_border_vel = {"molecule", "radius", "rmass", "omega", "quat"};
|
||||
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial",
|
||||
"special", "radius", "rmass", "omega", "quat"};
|
||||
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom",
|
||||
"radius", "rmass", "omega", "quat"};
|
||||
fields_create = {"molecule", "num_bond", "nspecial", "radius", "rmass", "omega", "quat"};
|
||||
fields_data_atom = {"id", "molecule", "type", "radius", "rmass", "x"};
|
||||
fields_data_vel = {"id", "v", "omega"};
|
||||
|
||||
bond_per_atom = 0;
|
||||
bond_negative = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
process sub-style args
|
||||
optional arg = 0/1 for static/dynamic particle radii
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::process_args(int narg, char **arg)
|
||||
{
|
||||
if (narg != 0 && narg != 1) error->all(FLERR, "Illegal atom_style bpm/sphere command");
|
||||
|
||||
radvary = 0;
|
||||
if (narg == 1) {
|
||||
radvary = utils::numeric(FLERR, arg[0], true, lmp);
|
||||
if (radvary < 0 || radvary > 1) error->all(FLERR, "Illegal atom_style bpm/sphere command");
|
||||
}
|
||||
|
||||
// dynamic particle radius and mass must be communicated every step
|
||||
|
||||
if (radvary) {
|
||||
fields_comm = {"radius", "rmass"};
|
||||
fields_comm_vel = {"radius", "rmass", "omega"};
|
||||
}
|
||||
|
||||
// delay setting up of fields until now
|
||||
|
||||
setup_fields();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::init()
|
||||
{
|
||||
AtomVec::init();
|
||||
|
||||
// check if optional radvary setting should have been set to 1
|
||||
|
||||
for (auto ifix : modify->get_fix_by_style("^adapt")) {
|
||||
if (radvary == 0) {
|
||||
if ((strcmp(ifix->style, "adapt") == 0) && (dynamic_cast<FixAdapt *>(ifix)->diamflag))
|
||||
error->all(FLERR, "Fix adapt changes atom radii but atom_style bpm/sphere is not dynamic");
|
||||
// cannot properly check for fix adapt/fep since its header is optional
|
||||
if ((strcmp(ifix->style, "adapt/fep") == 0) && (comm->me == 0))
|
||||
error->warning(
|
||||
FLERR, "Fix adapt/fep may change atom radii but atom_style bpm/sphere is not dynamic");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set local copies of all grow ptrs used by this class, except defaults
|
||||
needed in replicate when 2 atom classes exist and it calls pack_restart()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::grow_pointers()
|
||||
{
|
||||
radius = atom->radius;
|
||||
rmass = atom->rmass;
|
||||
omega = atom->omega;
|
||||
quat = atom->quat;
|
||||
|
||||
num_bond = atom->num_bond;
|
||||
bond_type = atom->bond_type;
|
||||
nspecial = atom->nspecial;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
initialize non-zero atom quantities
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::create_atom_post(int ilocal)
|
||||
{
|
||||
radius[ilocal] = 0.5;
|
||||
rmass[ilocal] = 4.0 * MY_PI / 3.0 * 0.5 * 0.5 * 0.5;
|
||||
|
||||
quat[ilocal][0] = 1.0;
|
||||
quat[ilocal][1] = 0.0;
|
||||
quat[ilocal][2] = 0.0;
|
||||
quat[ilocal][3] = 0.0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
modify values for AtomVec::pack_restart() to pack
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::pack_restart_pre(int ilocal)
|
||||
{
|
||||
// insure bond_negative vector is needed length
|
||||
|
||||
if (bond_per_atom < atom->bond_per_atom) {
|
||||
delete[] bond_negative;
|
||||
bond_per_atom = atom->bond_per_atom;
|
||||
bond_negative = new int[bond_per_atom];
|
||||
}
|
||||
|
||||
// flip any negative types to positive and flag which ones
|
||||
|
||||
any_bond_negative = 0;
|
||||
for (int m = 0; m < num_bond[ilocal]; m++) {
|
||||
if (bond_type[ilocal][m] < 0) {
|
||||
bond_negative[m] = 1;
|
||||
bond_type[ilocal][m] = -bond_type[ilocal][m];
|
||||
any_bond_negative = 1;
|
||||
} else
|
||||
bond_negative[m] = 0;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unmodify values packed by AtomVec::pack_restart()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::pack_restart_post(int ilocal)
|
||||
{
|
||||
// restore the flagged types to their negative values
|
||||
|
||||
if (any_bond_negative) {
|
||||
for (int m = 0; m < num_bond[ilocal]; m++)
|
||||
if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
initialize other atom quantities after AtomVec::unpack_restart()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::unpack_restart_init(int ilocal)
|
||||
{
|
||||
nspecial[ilocal][0] = 0;
|
||||
nspecial[ilocal][1] = 0;
|
||||
nspecial[ilocal][2] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
modify what AtomVec::data_atom() just unpacked
|
||||
or initialize other atom quantities
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::data_atom_post(int ilocal)
|
||||
{
|
||||
radius_one = 0.5 * atom->radius[ilocal];
|
||||
radius[ilocal] = radius_one;
|
||||
if (radius_one > 0.0) rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
|
||||
|
||||
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
|
||||
|
||||
omega[ilocal][0] = 0.0;
|
||||
omega[ilocal][1] = 0.0;
|
||||
omega[ilocal][2] = 0.0;
|
||||
|
||||
quat[ilocal][0] = 1.0;
|
||||
quat[ilocal][1] = 0.0;
|
||||
quat[ilocal][2] = 0.0;
|
||||
quat[ilocal][3] = 0.0;
|
||||
|
||||
num_bond[ilocal] = 0;
|
||||
nspecial[ilocal][0] = 0;
|
||||
nspecial[ilocal][1] = 0;
|
||||
nspecial[ilocal][2] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
modify values for AtomVec::pack_data() to pack
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::pack_data_pre(int ilocal)
|
||||
{
|
||||
radius_one = radius[ilocal];
|
||||
rmass_one = rmass[ilocal];
|
||||
|
||||
radius[ilocal] *= 2.0;
|
||||
if (radius_one != 0.0)
|
||||
rmass[ilocal] = rmass_one / (4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unmodify values packed by AtomVec::pack_data()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBPMSphere::pack_data_post(int ilocal)
|
||||
{
|
||||
radius[ilocal] = radius_one;
|
||||
rmass[ilocal] = rmass_one;
|
||||
}
|
||||
82
src/BPM/atom_vec_bpm_sphere.h
Normal file
82
src/BPM/atom_vec_bpm_sphere.h
Normal file
@ -0,0 +1,82 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef ATOM_CLASS
|
||||
// clang-format off
|
||||
AtomStyle(bpm/sphere,AtomVecBPMSphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_ATOM_VEC_BPM_SPHERE_H
|
||||
#define LMP_ATOM_VEC_BPM_SPHERE_H
|
||||
|
||||
#include "atom_vec.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AtomVecBPMSphere : public AtomVec {
|
||||
public:
|
||||
AtomVecBPMSphere(class LAMMPS *);
|
||||
void process_args(int, char **) override;
|
||||
void init() override;
|
||||
|
||||
void grow_pointers() override;
|
||||
void create_atom_post(int) override;
|
||||
void pack_restart_pre(int) override;
|
||||
void pack_restart_post(int) override;
|
||||
void unpack_restart_init(int) override;
|
||||
void data_atom_post(int) override;
|
||||
void pack_data_pre(int) override;
|
||||
void pack_data_post(int) override;
|
||||
|
||||
private:
|
||||
int *num_bond;
|
||||
int **bond_type;
|
||||
int **nspecial;
|
||||
|
||||
double *radius, *rmass;
|
||||
double **omega, **quat;
|
||||
|
||||
int any_bond_negative;
|
||||
int bond_per_atom;
|
||||
int *bond_negative;
|
||||
|
||||
int radvary;
|
||||
double radius_one, rmass_one;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Per-processor system is too big
|
||||
|
||||
The number of owned atoms plus ghost atoms on a single
|
||||
processor must fit in 32-bit integer.
|
||||
|
||||
E: Invalid atom type in Atoms section of data file
|
||||
|
||||
Atom types must range from 1 to specified # of types.
|
||||
|
||||
E: Invalid radius in Atoms section of data file
|
||||
|
||||
Radius must be >= 0.0.
|
||||
|
||||
E: Invalid density in Atoms section of data file
|
||||
|
||||
Density value cannot be <= 0.0.
|
||||
|
||||
*/
|
||||
415
src/BPM/bond_bpm.cpp
Normal file
415
src/BPM/bond_bpm.cpp
Normal file
@ -0,0 +1,415 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "bond_bpm.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_bond_history.h"
|
||||
#include "fix_store_local.h"
|
||||
#include "fix_update_special_bonds.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <vector>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPM::BondBPM(LAMMPS *_lmp) :
|
||||
Bond(_lmp), id_fix_dummy(nullptr), id_fix_dummy2(nullptr), id_fix_update(nullptr),
|
||||
id_fix_bond_history(nullptr), id_fix_store_local(nullptr), id_fix_prop_atom(nullptr),
|
||||
fix_store_local(nullptr), fix_bond_history(nullptr), fix_update_special_bonds(nullptr),
|
||||
pack_choice(nullptr), output_data(nullptr)
|
||||
|
||||
{
|
||||
overlay_flag = 0;
|
||||
prop_atom_flag = 0;
|
||||
nvalues = 0;
|
||||
|
||||
r0_max_estimate = 0.0;
|
||||
max_stretch = 1.0;
|
||||
|
||||
// create dummy fix as placeholder for FixUpdateSpecialBonds & BondHistory
|
||||
// this is so final order of Modify:fix will conform to input script
|
||||
// BondHistory technically only needs this if updateflag = 1
|
||||
|
||||
id_fix_dummy = utils::strdup("BPM_DUMMY");
|
||||
modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy));
|
||||
|
||||
id_fix_dummy2 = utils::strdup("BPM_DUMMY2");
|
||||
modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy2));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPM::~BondBPM()
|
||||
{
|
||||
delete[] pack_choice;
|
||||
|
||||
if (id_fix_dummy) modify->delete_fix(id_fix_dummy);
|
||||
if (id_fix_dummy2) modify->delete_fix(id_fix_dummy2);
|
||||
if (id_fix_update) modify->delete_fix(id_fix_update);
|
||||
if (id_fix_bond_history) modify->delete_fix(id_fix_bond_history);
|
||||
if (id_fix_store_local) modify->delete_fix(id_fix_store_local);
|
||||
if (id_fix_prop_atom) modify->delete_fix(id_fix_prop_atom);
|
||||
|
||||
delete[] id_fix_dummy;
|
||||
delete[] id_fix_dummy2;
|
||||
delete[] id_fix_update;
|
||||
delete[] id_fix_bond_history;
|
||||
delete[] id_fix_store_local;
|
||||
delete[] id_fix_prop_atom;
|
||||
|
||||
memory->destroy(output_data);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::init_style()
|
||||
{
|
||||
if (id_fix_store_local) {
|
||||
auto ifix = modify->get_fix_by_id(id_fix_store_local);
|
||||
if (!ifix) error->all(FLERR, "Cannot find fix store/local");
|
||||
if (strcmp(ifix->style, "STORE_LOCAL") != 0)
|
||||
error->all(FLERR, "Incorrect fix style matched, not store/local");
|
||||
fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
|
||||
fix_store_local->nvalues = nvalues;
|
||||
}
|
||||
|
||||
if (overlay_flag) {
|
||||
if (force->special_lj[1] != 1.0)
|
||||
error->all(FLERR,
|
||||
"With overlay/pair, BPM bond styles require special_bonds weight of 1.0 for "
|
||||
"first neighbors");
|
||||
if (id_fix_update) {
|
||||
modify->delete_fix(id_fix_update);
|
||||
delete[] id_fix_update;
|
||||
id_fix_update = nullptr;
|
||||
}
|
||||
} else {
|
||||
// Require atoms know about all of their bonds and if they break
|
||||
if (force->newton_bond)
|
||||
error->all(FLERR, "Without overlay/pair, BPM bond styles require Newton bond off");
|
||||
|
||||
// special lj must be 0 1 1 to censor pair forces between bonded particles
|
||||
// special coulomb must be 1 1 1 to ensure all pairs are included in the
|
||||
// neighbor list and 1-3 and 1-4 special bond lists are skipped
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
|
||||
error->all(FLERR,
|
||||
"Without overlay/pair, BPM bond sytles requires special LJ weights = 0,1,1");
|
||||
if (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
|
||||
force->special_coul[3] != 1.0)
|
||||
error->all(FLERR,
|
||||
"Without overlay/pair, BPM bond sytles requires special Coulomb weights = 1,1,1");
|
||||
|
||||
if (id_fix_dummy) {
|
||||
id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
|
||||
fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(modify->replace_fix(
|
||||
id_fix_dummy, fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update), 1));
|
||||
delete[] id_fix_dummy;
|
||||
id_fix_dummy = nullptr;
|
||||
}
|
||||
}
|
||||
|
||||
if (force->angle || force->dihedral || force->improper)
|
||||
error->all(FLERR, "Bond style bpm cannot be used with 3,4-body interactions");
|
||||
if (atom->molecular == 2)
|
||||
error->all(FLERR, "Bond style bpm cannot be used with atom style template");
|
||||
|
||||
// special 1-3 and 1-4 weights must be 1 to prevent building 1-3 and 1-4 special bond lists
|
||||
if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 || force->special_coul[2] != 1.0 ||
|
||||
force->special_coul[3] != 1.0)
|
||||
error->all(FLERR, "Bond style bpm requires 1-3 and 1-4 special weights of 1.0");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
All args before store/local command are saved for potential args
|
||||
for specific bond BPM substyles
|
||||
All args after optional store/local command are variables stored
|
||||
in the compute store/local
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::settings(int narg, char **arg)
|
||||
{
|
||||
leftover_iarg.clear();
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "store/local") == 0) {
|
||||
nvalues = 0;
|
||||
id_fix_store_local = utils::strdup(arg[iarg + 1]);
|
||||
store_local_freq = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
|
||||
pack_choice = new FnPtrPack[narg - iarg - 1];
|
||||
iarg += 3;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "id1") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_id1;
|
||||
} else if (strcmp(arg[iarg], "id2") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_id2;
|
||||
} else if (strcmp(arg[iarg], "time") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_time;
|
||||
} else if (strcmp(arg[iarg], "x") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_x;
|
||||
} else if (strcmp(arg[iarg], "y") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_y;
|
||||
} else if (strcmp(arg[iarg], "z") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_z;
|
||||
} else if (strcmp(arg[iarg], "x/ref") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_x_ref;
|
||||
prop_atom_flag = 1;
|
||||
} else if (strcmp(arg[iarg], "y/ref") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_y_ref;
|
||||
prop_atom_flag = 1;
|
||||
} else if (strcmp(arg[iarg], "z/ref") == 0) {
|
||||
pack_choice[nvalues++] = &BondBPM::pack_z_ref;
|
||||
prop_atom_flag = 1;
|
||||
} else {
|
||||
break;
|
||||
}
|
||||
iarg++;
|
||||
}
|
||||
} else if (strcmp(arg[iarg], "overlay/pair") == 0) {
|
||||
overlay_flag = 1;
|
||||
iarg++;
|
||||
} else {
|
||||
leftover_iarg.push_back(iarg);
|
||||
iarg++;
|
||||
}
|
||||
}
|
||||
|
||||
if (id_fix_store_local) {
|
||||
|
||||
if (nvalues == 0)
|
||||
error->all(FLERR, "Storing local data must include at least one value to output");
|
||||
memory->create(output_data, nvalues, "bond/bpm:output_data");
|
||||
|
||||
auto ifix = modify->get_fix_by_id(id_fix_store_local);
|
||||
if (!ifix)
|
||||
ifix = modify->add_fix(
|
||||
fmt::format("{} all STORE_LOCAL {} {}", id_fix_store_local, store_local_freq, nvalues));
|
||||
fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
|
||||
|
||||
// Use property/atom to save reference positions as it can transfer to ghost atoms
|
||||
// This won't work for instances where bonds are added (e.g. fix pour) but in those cases
|
||||
// a reference state isn't well defined
|
||||
if (prop_atom_flag == 1) {
|
||||
|
||||
id_fix_prop_atom = utils::strdup("BPM_property_atom");
|
||||
char *x_ref_id = utils::strdup("BPM_X_REF");
|
||||
char *y_ref_id = utils::strdup("BPM_Y_REF");
|
||||
char *z_ref_id = utils::strdup("BPM_Z_REF");
|
||||
|
||||
ifix = modify->get_fix_by_id(id_fix_prop_atom);
|
||||
if (!ifix)
|
||||
ifix = modify->add_fix(fmt::format("{} all property/atom {} {} {} ghost yes",
|
||||
id_fix_prop_atom, x_ref_id, y_ref_id, z_ref_id));
|
||||
|
||||
int type_flag;
|
||||
int col_flag;
|
||||
index_x_ref = atom->find_custom(x_ref_id, type_flag, col_flag);
|
||||
index_y_ref = atom->find_custom(y_ref_id, type_flag, col_flag);
|
||||
index_z_ref = atom->find_custom(z_ref_id, type_flag, col_flag);
|
||||
|
||||
delete[] x_ref_id;
|
||||
delete[] y_ref_id;
|
||||
delete[] z_ref_id;
|
||||
|
||||
if (ifix->restart_reset) {
|
||||
ifix->restart_reset = 0;
|
||||
} else {
|
||||
double *x_ref = atom->dvector[index_x_ref];
|
||||
double *y_ref = atom->dvector[index_y_ref];
|
||||
double *z_ref = atom->dvector[index_z_ref];
|
||||
|
||||
double **x = atom->x;
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
x_ref[i] = x[i][0];
|
||||
y_ref[i] = x[i][1];
|
||||
z_ref[i] = x[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
used to check bond communiction cutoff - not perfect, estimates based on local-local only
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondBPM::equilibrium_distance(int /*i*/)
|
||||
{
|
||||
// Ghost atoms may not yet be communicated, this may only be an estimate
|
||||
if (r0_max_estimate == 0) {
|
||||
int type, j;
|
||||
double delx, dely, delz, r;
|
||||
double **x = atom->x;
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
for (int m = 0; m < atom->num_bond[i]; m++) {
|
||||
type = atom->bond_type[i][m];
|
||||
if (type == 0) continue;
|
||||
|
||||
j = atom->map(atom->bond_atom[i][m]);
|
||||
if (j == -1) continue;
|
||||
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
domain->minimum_image(delx, dely, delz);
|
||||
|
||||
r = sqrt(delx * delx + dely * dely + delz * delz);
|
||||
if (r > r0_max_estimate) r0_max_estimate = r;
|
||||
}
|
||||
}
|
||||
|
||||
double temp;
|
||||
MPI_Allreduce(&r0_max_estimate, &temp, 1, MPI_DOUBLE, MPI_MAX, world);
|
||||
r0_max_estimate = temp;
|
||||
}
|
||||
|
||||
// Divide out heuristic prefactor added in comm class
|
||||
return max_stretch * r0_max_estimate / 1.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::process_broken(int i, int j)
|
||||
{
|
||||
if (fix_store_local) {
|
||||
for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
|
||||
|
||||
fix_store_local->add_data(output_data, i, j);
|
||||
}
|
||||
|
||||
if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j);
|
||||
|
||||
// Manually search and remove from atom arrays
|
||||
// need to remove in case special bonds arrays rebuilt
|
||||
int m, n;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
tagint *tag = atom->tag;
|
||||
tagint **bond_atom = atom->bond_atom;
|
||||
int **bond_type = atom->bond_type;
|
||||
int *num_bond = atom->num_bond;
|
||||
|
||||
if (i < nlocal) {
|
||||
for (m = 0; m < num_bond[i]; m++) {
|
||||
if (bond_atom[i][m] == tag[j]) {
|
||||
bond_type[i][m] = 0;
|
||||
n = num_bond[i];
|
||||
bond_type[i][m] = bond_type[i][n - 1];
|
||||
bond_atom[i][m] = bond_atom[i][n - 1];
|
||||
fix_bond_history->shift_history(i, m, n - 1);
|
||||
fix_bond_history->delete_history(i, n - 1);
|
||||
num_bond[i]--;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (j < nlocal) {
|
||||
for (m = 0; m < num_bond[j]; m++) {
|
||||
if (bond_atom[j][m] == tag[i]) {
|
||||
bond_type[j][m] = 0;
|
||||
n = num_bond[j];
|
||||
bond_type[j][m] = bond_type[j][n - 1];
|
||||
bond_atom[j][m] = bond_atom[j][n - 1];
|
||||
fix_bond_history->shift_history(j, m, n - 1);
|
||||
fix_bond_history->delete_history(j, n - 1);
|
||||
num_bond[j]--;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
one method for every keyword bond bpm can output
|
||||
the atom property is packed into array or vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_id1(int n, int i, int /*j*/)
|
||||
{
|
||||
tagint *tag = atom->tag;
|
||||
output_data[n] = tag[i];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_id2(int n, int /*i*/, int j)
|
||||
{
|
||||
tagint *tag = atom->tag;
|
||||
output_data[n] = tag[j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_time(int n, int /*i*/, int /*j*/)
|
||||
{
|
||||
bigint time = update->ntimestep;
|
||||
output_data[n] = time;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_x(int n, int i, int j)
|
||||
{
|
||||
double **x = atom->x;
|
||||
output_data[n] = (x[i][0] + x[j][0]) * 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_y(int n, int i, int j)
|
||||
{
|
||||
double **x = atom->x;
|
||||
output_data[n] = (x[i][1] + x[j][1]) * 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_z(int n, int i, int j)
|
||||
{
|
||||
double **x = atom->x;
|
||||
output_data[n] = (x[i][2] + x[j][2]) * 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_x_ref(int n, int i, int j)
|
||||
{
|
||||
double *x = atom->dvector[index_x_ref];
|
||||
output_data[n] = (x[i] + x[j]) * 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_y_ref(int n, int i, int j)
|
||||
{
|
||||
double *y = atom->dvector[index_y_ref];
|
||||
output_data[n] = (y[i] + y[j]) * 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPM::pack_z_ref(int n, int i, int j)
|
||||
{
|
||||
double *z = atom->dvector[index_z_ref];
|
||||
output_data[n] = (z[i] + z[j]) * 0.5;
|
||||
}
|
||||
98
src/BPM/bond_bpm.h
Normal file
98
src/BPM/bond_bpm.h
Normal file
@ -0,0 +1,98 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_BOND_BPM_H
|
||||
#define LMP_BOND_BPM_H
|
||||
|
||||
#include "bond.h"
|
||||
|
||||
#include <vector>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondBPM : public Bond {
|
||||
public:
|
||||
BondBPM(class LAMMPS *);
|
||||
~BondBPM() override;
|
||||
void compute(int, int) override = 0;
|
||||
void coeff(int, char **) override = 0;
|
||||
void init_style() override;
|
||||
void settings(int, char **) override;
|
||||
double equilibrium_distance(int) override;
|
||||
void write_restart(FILE *) override{};
|
||||
void read_restart(FILE *) override{};
|
||||
void write_data(FILE *) override{};
|
||||
double single(int, double, int, int, double &) override = 0;
|
||||
|
||||
protected:
|
||||
double r0_max_estimate;
|
||||
double max_stretch;
|
||||
int store_local_freq;
|
||||
|
||||
std::vector<int> leftover_iarg;
|
||||
|
||||
char *id_fix_dummy, *id_fix_dummy2;
|
||||
char *id_fix_update, *id_fix_bond_history;
|
||||
char *id_fix_store_local, *id_fix_prop_atom;
|
||||
class FixStoreLocal *fix_store_local;
|
||||
class FixBondHistory *fix_bond_history;
|
||||
class FixUpdateSpecialBonds *fix_update_special_bonds;
|
||||
|
||||
void process_broken(int, int);
|
||||
typedef void (BondBPM::*FnPtrPack)(int, int, int);
|
||||
FnPtrPack *pack_choice; // ptrs to pack functions
|
||||
double *output_data;
|
||||
|
||||
int prop_atom_flag, nvalues, overlay_flag;
|
||||
int index_x_ref, index_y_ref, index_z_ref;
|
||||
|
||||
void pack_id1(int, int, int);
|
||||
void pack_id2(int, int, int);
|
||||
void pack_time(int, int, int);
|
||||
void pack_x(int, int, int);
|
||||
void pack_y(int, int, int);
|
||||
void pack_z(int, int, int);
|
||||
void pack_x_ref(int, int, int);
|
||||
void pack_y_ref(int, int, int);
|
||||
void pack_z_ref(int, int, int);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Cannot find fix store/local
|
||||
|
||||
Fix id cannot be found.
|
||||
|
||||
E: Illegal bond_style command
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Bond style bpm must include at least one value to output
|
||||
|
||||
Must include at least one bond property to store in fix store/local
|
||||
|
||||
E: Bond style bpm cannot be used with 3,4-body interactions
|
||||
|
||||
No angle, dihedral, or improper styles can be defined when using
|
||||
bond style bpm.
|
||||
|
||||
E: Bond style bpm cannot be used with atom style template
|
||||
|
||||
This bond style can change the bond topology which is not
|
||||
allowed with this atom style.
|
||||
|
||||
*/
|
||||
796
src/BPM/bond_bpm_rotational.cpp
Normal file
796
src/BPM/bond_bpm_rotational.cpp
Normal file
@ -0,0 +1,796 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "bond_bpm_rotational.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_bond_history.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
#define EPSILON 1e-10
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPMRotational::BondBPMRotational(LAMMPS *_lmp) : BondBPM(_lmp)
|
||||
{
|
||||
Kr = nullptr;
|
||||
Ks = nullptr;
|
||||
Kt = nullptr;
|
||||
Kb = nullptr;
|
||||
Fcr = nullptr;
|
||||
Fcs = nullptr;
|
||||
Tct = nullptr;
|
||||
Tcb = nullptr;
|
||||
gnorm = nullptr;
|
||||
gslide = nullptr;
|
||||
groll = nullptr;
|
||||
gtwist = nullptr;
|
||||
partial_flag = 1;
|
||||
smooth_flag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPMRotational::~BondBPMRotational()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(Kr);
|
||||
memory->destroy(Ks);
|
||||
memory->destroy(Kt);
|
||||
memory->destroy(Kb);
|
||||
memory->destroy(Fcr);
|
||||
memory->destroy(Fcs);
|
||||
memory->destroy(Tct);
|
||||
memory->destroy(Tcb);
|
||||
memory->destroy(gnorm);
|
||||
memory->destroy(gslide);
|
||||
memory->destroy(groll);
|
||||
memory->destroy(gtwist);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMRotational::acos_limit(double c)
|
||||
{
|
||||
if (c > 1.0) c = 1.0;
|
||||
if (c < -1.0) c = -1.0;
|
||||
return acos(c);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Store data for a single bond - if bond added after LAMMPS init (e.g. pour)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMRotational::store_bond(int n, int i, int j)
|
||||
{
|
||||
double delx, dely, delz, r, rinv;
|
||||
double **x = atom->x;
|
||||
tagint *tag = atom->tag;
|
||||
double **bondstore = fix_bond_history->bondstore;
|
||||
|
||||
if (tag[i] < tag[j]) {
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
} else {
|
||||
delx = x[j][0] - x[i][0];
|
||||
dely = x[j][1] - x[i][1];
|
||||
delz = x[j][2] - x[i][2];
|
||||
}
|
||||
|
||||
r = sqrt(delx * delx + dely * dely + delz * delz);
|
||||
rinv = 1.0 / r;
|
||||
|
||||
bondstore[n][0] = r;
|
||||
bondstore[n][1] = delx * rinv;
|
||||
bondstore[n][2] = dely * rinv;
|
||||
bondstore[n][3] = delz * rinv;
|
||||
|
||||
if (i < atom->nlocal) {
|
||||
for (int m = 0; m < atom->num_bond[i]; m++) {
|
||||
if (atom->bond_atom[i][m] == tag[j]) {
|
||||
fix_bond_history->update_atom_value(i, m, 0, r);
|
||||
fix_bond_history->update_atom_value(i, m, 1, delx * rinv);
|
||||
fix_bond_history->update_atom_value(i, m, 2, dely * rinv);
|
||||
fix_bond_history->update_atom_value(i, m, 3, delz * rinv);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (j < atom->nlocal) {
|
||||
for (int m = 0; m < atom->num_bond[j]; m++) {
|
||||
if (atom->bond_atom[j][m] == tag[i]) {
|
||||
fix_bond_history->update_atom_value(j, m, 0, r);
|
||||
fix_bond_history->update_atom_value(j, m, 1, delx * rinv);
|
||||
fix_bond_history->update_atom_value(j, m, 2, dely * rinv);
|
||||
fix_bond_history->update_atom_value(j, m, 3, delz * rinv);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return r;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Store data for all bonds called once
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::store_data()
|
||||
{
|
||||
int i, j, m, type;
|
||||
double delx, dely, delz, r, rinv;
|
||||
double **x = atom->x;
|
||||
int **bond_type = atom->bond_type;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
for (i = 0; i < atom->nlocal; i++) {
|
||||
for (m = 0; m < atom->num_bond[i]; m++) {
|
||||
type = bond_type[i][m];
|
||||
|
||||
//Skip if bond was turned off
|
||||
if (type < 0) continue;
|
||||
|
||||
// map to find index n for tag
|
||||
j = atom->map(atom->bond_atom[i][m]);
|
||||
if (j == -1) error->one(FLERR, "Atom missing in BPM bond");
|
||||
|
||||
// Save orientation as pointing towards small tag
|
||||
if (tag[i] < tag[j]) {
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
} else {
|
||||
delx = x[j][0] - x[i][0];
|
||||
dely = x[j][1] - x[i][1];
|
||||
delz = x[j][2] - x[i][2];
|
||||
}
|
||||
|
||||
// Get closest image in case bonded with ghost
|
||||
domain->minimum_image(delx, dely, delz);
|
||||
r = sqrt(delx * delx + dely * dely + delz * delz);
|
||||
rinv = 1.0 / r;
|
||||
|
||||
fix_bond_history->update_atom_value(i, m, 0, r);
|
||||
fix_bond_history->update_atom_value(i, m, 1, delx * rinv);
|
||||
fix_bond_history->update_atom_value(i, m, 2, dely * rinv);
|
||||
fix_bond_history->update_atom_value(i, m, 3, delz * rinv);
|
||||
}
|
||||
}
|
||||
|
||||
fix_bond_history->post_neighbor();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate forces using formulation in:
|
||||
1) Y. Wang Acta Geotechnica 2009
|
||||
2) P. Mora & Y. Wang Advances in Geomcomputing 2009
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMRotational::elastic_forces(int i1, int i2, int type, double &Fr, double r_mag,
|
||||
double r0_mag, double r_mag_inv, double * /*rhat*/,
|
||||
double *r, double *r0, double *force1on2,
|
||||
double *torque1on2, double *torque2on1)
|
||||
{
|
||||
double breaking, temp, r0_dot_rb, c, gamma;
|
||||
double psi, theta, cos_phi, sin_phi;
|
||||
double mag_in_plane, mag_out_plane;
|
||||
double Fs_mag, Tt_mag, Tb_mag;
|
||||
|
||||
double q1[4], q2[4];
|
||||
double q2inv[4], mq[4], mqinv[4], qp21[4], q21[4], qtmp[4];
|
||||
double rb[3], rb_x_r0[3], s[3], t[3];
|
||||
double Fs[3], Fsp[3], F_rot[3], Ftmp[3];
|
||||
double Ts[3], Tb[3], Tt[3], Tbp[3], Ttp[3], Tsp[3], T_rot[3], Ttmp[3];
|
||||
|
||||
double **quat = atom->quat;
|
||||
|
||||
q1[0] = quat[i1][0];
|
||||
q1[1] = quat[i1][1];
|
||||
q1[2] = quat[i1][2];
|
||||
q1[3] = quat[i1][3];
|
||||
|
||||
q2[0] = quat[i2][0];
|
||||
q2[1] = quat[i2][1];
|
||||
q2[2] = quat[i2][2];
|
||||
q2[3] = quat[i2][3];
|
||||
|
||||
// Calculate normal forces, rb = bond vector in particle 1's frame
|
||||
MathExtra::qconjugate(q2, q2inv);
|
||||
MathExtra::quatrotvec(q2inv, r, rb);
|
||||
Fr = Kr[type] * (r_mag - r0_mag);
|
||||
|
||||
MathExtra::scale3(Fr * r_mag_inv, rb, F_rot);
|
||||
|
||||
// Calculate forces due to tangential displacements (no rotation)
|
||||
r0_dot_rb = MathExtra::dot3(r0, rb);
|
||||
c = r0_dot_rb * r_mag_inv / r0_mag;
|
||||
gamma = acos_limit(c);
|
||||
|
||||
MathExtra::cross3(rb, r0, rb_x_r0);
|
||||
MathExtra::cross3(rb, rb_x_r0, s);
|
||||
MathExtra::norm3(s);
|
||||
|
||||
MathExtra::scale3(Ks[type] * r_mag * gamma, s, Fs);
|
||||
|
||||
// Calculate torque due to tangential displacements
|
||||
MathExtra::cross3(r0, rb, t);
|
||||
MathExtra::norm3(t);
|
||||
|
||||
MathExtra::scale3(0.5 * r_mag * Ks[type] * r_mag * gamma, t, Ts);
|
||||
|
||||
// Relative rotation force/torque
|
||||
// Use representation of X'Y'Z' rotations from Wang, Mora 2009
|
||||
temp = r_mag + rb[2];
|
||||
if (temp < 0.0) temp = 0.0;
|
||||
mq[0] = sqrt(2) * 0.5 * sqrt(temp * r_mag_inv);
|
||||
|
||||
temp = sqrt(rb[0] * rb[0] + rb[1] * rb[1]);
|
||||
if (temp != 0.0) {
|
||||
mq[1] = -sqrt(2) * 0.5 / temp;
|
||||
temp = r_mag - rb[2];
|
||||
if (temp < 0.0) temp = 0.0;
|
||||
mq[1] *= sqrt(temp * r_mag_inv);
|
||||
mq[2] = -mq[1];
|
||||
mq[1] *= rb[1];
|
||||
mq[2] *= rb[0];
|
||||
} else {
|
||||
// If aligned along z axis, x,y terms zero (r_mag-rb[2] = 0)
|
||||
mq[1] = 0.0;
|
||||
mq[2] = 0.0;
|
||||
}
|
||||
mq[3] = 0.0;
|
||||
|
||||
// qp21 = opposite of r^\circ_21 in Wang
|
||||
// q21 = opposite of r_21 in Wang
|
||||
MathExtra::quatquat(q2inv, q1, qp21);
|
||||
MathExtra::qconjugate(mq, mqinv);
|
||||
MathExtra::quatquat(mqinv, qp21, qtmp);
|
||||
MathExtra::quatquat(qtmp, mq, q21);
|
||||
|
||||
temp = sqrt(q21[0] * q21[0] + q21[3] * q21[3]);
|
||||
if (temp != 0.0) {
|
||||
c = q21[0] / temp;
|
||||
psi = 2.0 * acos_limit(c);
|
||||
} else {
|
||||
c = 0.0;
|
||||
psi = 0.0;
|
||||
}
|
||||
|
||||
// Map negative rotations
|
||||
if (q21[3] < 0.0) // sin = q21[3]/temp
|
||||
psi = -psi;
|
||||
|
||||
if (q21[3] == 0.0) psi = 0.0;
|
||||
|
||||
c = q21[0] * q21[0] - q21[1] * q21[1] - q21[2] * q21[2] + q21[3] * q21[3];
|
||||
theta = acos_limit(c);
|
||||
|
||||
// Separately calculte magnitude of quaternion in x-y and out of x-y planes
|
||||
// to avoid dividing by zero
|
||||
mag_out_plane = (q21[0] * q21[0] + q21[3] * q21[3]);
|
||||
mag_in_plane = (q21[1] * q21[1] + q21[2] * q21[2]);
|
||||
|
||||
if (mag_in_plane == 0.0) {
|
||||
// No rotation => no bending/shear torque or extra shear force
|
||||
// achieve by setting cos/sin = 0
|
||||
cos_phi = 0.0;
|
||||
sin_phi = 0.0;
|
||||
} else if (mag_out_plane == 0.0) {
|
||||
// Calculate angle in plane
|
||||
cos_phi = q21[2] / sqrt(mag_in_plane);
|
||||
sin_phi = -q21[1] / sqrt(mag_in_plane);
|
||||
} else {
|
||||
// Default equations in Mora, Wang 2009
|
||||
cos_phi = q21[1] * q21[3] + q21[0] * q21[2];
|
||||
sin_phi = q21[2] * q21[3] - q21[0] * q21[1];
|
||||
|
||||
cos_phi /= sqrt(mag_out_plane * mag_in_plane);
|
||||
sin_phi /= sqrt(mag_out_plane * mag_in_plane);
|
||||
}
|
||||
|
||||
Tbp[0] = -Kb[type] * theta * sin_phi;
|
||||
Tbp[1] = Kb[type] * theta * cos_phi;
|
||||
Tbp[2] = 0.0;
|
||||
|
||||
Ttp[0] = 0.0;
|
||||
Ttp[1] = 0.0;
|
||||
Ttp[2] = Kt[type] * psi;
|
||||
|
||||
Fsp[0] = -0.5 * Ks[type] * r_mag * theta * cos_phi;
|
||||
Fsp[1] = -0.5 * Ks[type] * r_mag * theta * sin_phi;
|
||||
Fsp[2] = 0.0;
|
||||
|
||||
Tsp[0] = 0.25 * Ks[type] * r_mag * r_mag * theta * sin_phi;
|
||||
Tsp[1] = -0.25 * Ks[type] * r_mag * r_mag * theta * cos_phi;
|
||||
Tsp[2] = 0.0;
|
||||
|
||||
// Rotate forces/torques back to 1st particle's frame
|
||||
|
||||
MathExtra::quatrotvec(mq, Fsp, Ftmp);
|
||||
MathExtra::quatrotvec(mq, Tsp, Ttmp);
|
||||
for (int m = 0; m < 3; m++) {
|
||||
Fs[m] += Ftmp[m];
|
||||
Ts[m] += Ttmp[m];
|
||||
}
|
||||
|
||||
MathExtra::quatrotvec(mq, Tbp, Tb);
|
||||
MathExtra::quatrotvec(mq, Ttp, Tt);
|
||||
|
||||
// Sum forces and calculate magnitudes
|
||||
F_rot[0] += Fs[0];
|
||||
F_rot[1] += Fs[1];
|
||||
F_rot[2] += Fs[2];
|
||||
MathExtra::quatrotvec(q2, F_rot, force1on2);
|
||||
|
||||
T_rot[0] = Ts[0] + Tt[0] + Tb[0];
|
||||
T_rot[1] = Ts[1] + Tt[1] + Tb[1];
|
||||
T_rot[2] = Ts[2] + Tt[2] + Tb[2];
|
||||
MathExtra::quatrotvec(q2, T_rot, torque1on2);
|
||||
|
||||
T_rot[0] = Ts[0] - Tt[0] - Tb[0];
|
||||
T_rot[1] = Ts[1] - Tt[1] - Tb[1];
|
||||
T_rot[2] = Ts[2] - Tt[2] - Tb[2];
|
||||
MathExtra::quatrotvec(q2, T_rot, torque2on1);
|
||||
|
||||
Fs_mag = MathExtra::len3(Fs);
|
||||
Tt_mag = MathExtra::len3(Tt);
|
||||
Tb_mag = MathExtra::len3(Tb);
|
||||
|
||||
breaking = Fr / Fcr[type] + Fs_mag / Fcs[type] + Tb_mag / Tcb[type] + Tt_mag / Tct[type];
|
||||
if (breaking < 0.0) breaking = 0.0;
|
||||
|
||||
return breaking;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate damping using formulation in
|
||||
Y. Wang, F. Alonso-Marroquin, W. Guo 2015
|
||||
Note: n points towards 1 vs pointing towards 2
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::damping_forces(int i1, int i2, int type, double &Fr, double *rhat,
|
||||
double *r, double *force1on2, double *torque1on2,
|
||||
double *torque2on1)
|
||||
{
|
||||
double v1dotr, v2dotr, w1dotr, w2dotr;
|
||||
double s1[3], s2[3], tdamp[3], tmp[3];
|
||||
double vn1[3], vn2[3], vt1[3], vt2[3], vroll[3];
|
||||
double wxn1[3], wxn2[3], wn1[3], wn2[3];
|
||||
|
||||
double **v = atom->v;
|
||||
double **omega = atom->omega;
|
||||
|
||||
// Damp normal velocity difference
|
||||
v1dotr = MathExtra::dot3(v[i1], rhat);
|
||||
v2dotr = MathExtra::dot3(v[i2], rhat);
|
||||
|
||||
MathExtra::scale3(v1dotr, rhat, vn1);
|
||||
MathExtra::scale3(v2dotr, rhat, vn2);
|
||||
|
||||
MathExtra::sub3(vn1, vn2, tmp);
|
||||
MathExtra::scale3(gnorm[type], tmp);
|
||||
Fr = MathExtra::lensq3(tmp);
|
||||
MathExtra::add3(force1on2, tmp, force1on2);
|
||||
|
||||
// Damp tangential objective velocities
|
||||
MathExtra::sub3(v[i1], vn1, vt1);
|
||||
MathExtra::sub3(v[i2], vn2, vt2);
|
||||
|
||||
MathExtra::sub3(vt2, vt1, tmp);
|
||||
MathExtra::scale3(0.5, tmp);
|
||||
|
||||
MathExtra::cross3(omega[i1], r, s1);
|
||||
MathExtra::scale3(-0.5, s1);
|
||||
MathExtra::sub3(s1, tmp, s1); // Eq 12
|
||||
|
||||
MathExtra::cross3(omega[i2], r, s2);
|
||||
MathExtra::scale3(0.5, s2);
|
||||
MathExtra::add3(s2, tmp, s2); // Eq 13
|
||||
|
||||
MathExtra::sub3(s1, s2, tmp);
|
||||
MathExtra::scale3(gslide[type], tmp);
|
||||
MathExtra::add3(force1on2, tmp, force1on2);
|
||||
|
||||
// Apply corresponding torque
|
||||
MathExtra::cross3(r, tmp, tdamp);
|
||||
MathExtra::scale3(0.5, tdamp);
|
||||
MathExtra::add3(torque1on2, tdamp, torque1on2);
|
||||
MathExtra::add3(torque2on1, tdamp, torque2on1);
|
||||
|
||||
// Damp rolling
|
||||
MathExtra::cross3(omega[i1], rhat, wxn1);
|
||||
MathExtra::cross3(omega[i2], rhat, wxn2);
|
||||
MathExtra::sub3(wxn1, wxn2, vroll); // Eq. 31
|
||||
MathExtra::cross3(r, vroll, tdamp);
|
||||
|
||||
MathExtra::scale3(0.5 * groll[type], tdamp);
|
||||
MathExtra::add3(torque1on2, tdamp, torque1on2);
|
||||
MathExtra::scale3(-1.0, tdamp);
|
||||
MathExtra::add3(torque2on1, tdamp, torque2on1);
|
||||
|
||||
// Damp twist
|
||||
w1dotr = MathExtra::dot3(omega[i1], rhat);
|
||||
w2dotr = MathExtra::dot3(omega[i2], rhat);
|
||||
|
||||
MathExtra::scale3(w1dotr, rhat, wn1);
|
||||
MathExtra::scale3(w2dotr, rhat, wn2);
|
||||
|
||||
MathExtra::sub3(wn1, wn2, tdamp); // Eq. 38
|
||||
MathExtra::scale3(0.5 * gtwist[type], tdamp);
|
||||
MathExtra::add3(torque1on2, tdamp, torque1on2);
|
||||
MathExtra::scale3(-1.0, tdamp);
|
||||
MathExtra::add3(torque2on1, tdamp, torque2on1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::compute(int eflag, int vflag)
|
||||
{
|
||||
|
||||
if (!fix_bond_history->stored_flag) {
|
||||
fix_bond_history->stored_flag = true;
|
||||
store_data();
|
||||
}
|
||||
|
||||
int i1, i2, itmp, n, type;
|
||||
double r[3], r0[3], rhat[3];
|
||||
double rsq, r0_mag, r_mag, r_mag_inv;
|
||||
double Fr, breaking, smooth;
|
||||
double force1on2[3], torque1on2[3], torque2on1[3];
|
||||
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double **torque = atom->torque;
|
||||
tagint *tag = atom->tag;
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
double **bondstore = fix_bond_history->bondstore;
|
||||
|
||||
for (n = 0; n < nbondlist; n++) {
|
||||
|
||||
// skip bond if already broken
|
||||
if (bondlist[n][2] <= 0) continue;
|
||||
|
||||
i1 = bondlist[n][0];
|
||||
i2 = bondlist[n][1];
|
||||
type = bondlist[n][2];
|
||||
r0_mag = bondstore[n][0];
|
||||
|
||||
// Ensure pair is always ordered such that r0 points in
|
||||
// a consistent direction and to ensure numerical operations
|
||||
// are identical to minimize the possibility that a bond straddling
|
||||
// an mpi grid (newton off) doesn't break on one proc but not the other
|
||||
if (tag[i2] < tag[i1]) {
|
||||
itmp = i1;
|
||||
i1 = i2;
|
||||
i2 = itmp;
|
||||
}
|
||||
|
||||
// If bond hasn't been set - should be initialized to zero
|
||||
if (r0_mag < EPSILON || std::isnan(r0_mag)) r0_mag = store_bond(n, i1, i2);
|
||||
|
||||
r0[0] = bondstore[n][1];
|
||||
r0[1] = bondstore[n][2];
|
||||
r0[2] = bondstore[n][3];
|
||||
MathExtra::scale3(r0_mag, r0);
|
||||
|
||||
// Note this is the reverse of Mora & Wang
|
||||
MathExtra::sub3(x[i1], x[i2], r);
|
||||
|
||||
rsq = MathExtra::lensq3(r);
|
||||
r_mag = sqrt(rsq);
|
||||
r_mag_inv = 1.0 / r_mag;
|
||||
MathExtra::scale3(r_mag_inv, r, rhat);
|
||||
|
||||
// ------------------------------------------------------//
|
||||
// Calculate forces, check if bond breaks
|
||||
// ------------------------------------------------------//
|
||||
|
||||
breaking = elastic_forces(i1, i2, type, Fr, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
|
||||
torque1on2, torque2on1);
|
||||
|
||||
if (breaking >= 1.0) {
|
||||
bondlist[n][2] = 0;
|
||||
process_broken(i1, i2);
|
||||
continue;
|
||||
}
|
||||
|
||||
damping_forces(i1, i2, type, Fr, rhat, r, force1on2, torque1on2, torque2on1);
|
||||
|
||||
if (smooth_flag) {
|
||||
smooth = breaking * breaking;
|
||||
smooth = 1.0 - smooth * smooth;
|
||||
} else {
|
||||
smooth = 1.0;
|
||||
}
|
||||
|
||||
// ------------------------------------------------------//
|
||||
// Apply forces and torques to particles
|
||||
// ------------------------------------------------------//
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] -= force1on2[0] * smooth;
|
||||
f[i1][1] -= force1on2[1] * smooth;
|
||||
f[i1][2] -= force1on2[2] * smooth;
|
||||
|
||||
torque[i1][0] += torque2on1[0] * smooth;
|
||||
torque[i1][1] += torque2on1[1] * smooth;
|
||||
torque[i1][2] += torque2on1[2] * smooth;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] += force1on2[0] * smooth;
|
||||
f[i2][1] += force1on2[1] * smooth;
|
||||
f[i2][2] += force1on2[2] * smooth;
|
||||
|
||||
torque[i2][0] += torque1on2[0] * smooth;
|
||||
torque[i2][1] += torque1on2[1] * smooth;
|
||||
torque[i2][2] += torque1on2[2] * smooth;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, Fr * smooth, r[0], r[1], r[2]);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(Kr, np1, "bond:Kr");
|
||||
memory->create(Ks, np1, "bond:Ks");
|
||||
memory->create(Kt, np1, "bond:Kt");
|
||||
memory->create(Kb, np1, "bond:Kb");
|
||||
memory->create(Fcr, np1, "bond:Fcr");
|
||||
memory->create(Fcs, np1, "bond:Fcs");
|
||||
memory->create(Tct, np1, "bond:Tct");
|
||||
memory->create(Tcb, np1, "bond:Tcb");
|
||||
memory->create(gnorm, np1, "bond:gnorm");
|
||||
memory->create(gslide, np1, "bond:gslide");
|
||||
memory->create(groll, np1, "bond:groll");
|
||||
memory->create(gtwist, np1, "bond:gtwist");
|
||||
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 13) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double Kr_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double Ks_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double Kt_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double Kb_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double Fcr_one = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
double Fcs_one = utils::numeric(FLERR, arg[6], false, lmp);
|
||||
double Tct_one = utils::numeric(FLERR, arg[7], false, lmp);
|
||||
double Tcb_one = utils::numeric(FLERR, arg[8], false, lmp);
|
||||
double gnorm_one = utils::numeric(FLERR, arg[9], false, lmp);
|
||||
double gslide_one = utils::numeric(FLERR, arg[10], false, lmp);
|
||||
double groll_one = utils::numeric(FLERR, arg[11], false, lmp);
|
||||
double gtwist_one = utils::numeric(FLERR, arg[12], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
Kr[i] = Kr_one;
|
||||
Ks[i] = Ks_one;
|
||||
Kt[i] = Kt_one;
|
||||
Kb[i] = Kb_one;
|
||||
Fcr[i] = Fcr_one;
|
||||
Fcs[i] = Fcs_one;
|
||||
Tct[i] = Tct_one;
|
||||
Tcb[i] = Tcb_one;
|
||||
gnorm[i] = gnorm_one;
|
||||
gslide[i] = gslide_one;
|
||||
groll[i] = groll_one;
|
||||
gtwist[i] = gtwist_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
|
||||
if (Fcr[i] / Kr[i] > max_stretch) max_stretch = Fcr[i] / Kr[i];
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check for correct settings and create fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::init_style()
|
||||
{
|
||||
BondBPM::init_style();
|
||||
|
||||
if (!atom->quat_flag || !atom->sphere_flag)
|
||||
error->all(FLERR, "Bond bpm/rotational requires atom style bpm/sphere");
|
||||
if (comm->ghost_velocity == 0)
|
||||
error->all(FLERR, "Bond bpm/rotational requires ghost atoms store velocity");
|
||||
|
||||
if (domain->dimension == 2)
|
||||
error->warning(FLERR, "Bond style bpm/rotational not intended for 2d use");
|
||||
|
||||
if (!id_fix_bond_history) {
|
||||
id_fix_bond_history = utils::strdup("HISTORY_BPM_ROTATIONAL");
|
||||
fix_bond_history = dynamic_cast<FixBondHistory *>(modify->replace_fix(
|
||||
id_fix_dummy2, fmt::format("{} all BOND_HISTORY 0 4", id_fix_bond_history), 1));
|
||||
delete[] id_fix_dummy2;
|
||||
id_fix_dummy2 = nullptr;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::settings(int narg, char **arg)
|
||||
{
|
||||
BondBPM::settings(narg, arg);
|
||||
|
||||
int iarg;
|
||||
for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
|
||||
iarg = leftover_iarg[i];
|
||||
if (strcmp(arg[iarg], "smooth") == 0) {
|
||||
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command");
|
||||
smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
|
||||
i += 1;
|
||||
} else {
|
||||
error->all(FLERR, "Illegal bond_style command");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&Kr[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Ks[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Kt[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Kb[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Fcr[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Fcs[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Tct[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&Tcb[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&gnorm[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&gslide[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&groll[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(>wist[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR, &Kr[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Ks[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Kt[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Kb[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Fcr[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Fcs[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Tct[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &Tcb[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &gnorm[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &gslide[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &groll[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, >wist[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&Kr[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Ks[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Kt[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Kb[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Fcr[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Fcs[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Tct[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&Tcb[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&gnorm[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&gslide[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&groll[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(>wist[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMRotational::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp, "%d %g %g %g %g %g %g %g %g %g %g %g %g\n", i, Kr[i], Ks[i], Kt[i], Kb[i], Fcr[i],
|
||||
Fcs[i], Tct[i], Tcb[i], gnorm[i], gslide[i], groll[i], gtwist[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMRotational::single(int type, double rsq, int i, int j, double &fforce)
|
||||
{
|
||||
// Not yet enabled
|
||||
if (type <= 0) return 0.0;
|
||||
|
||||
int itmp;
|
||||
if (atom->tag[j] < atom->tag[i]) {
|
||||
itmp = i;
|
||||
i = j;
|
||||
j = itmp;
|
||||
}
|
||||
|
||||
double r0_mag, r_mag, r_mag_inv;
|
||||
double r0[3], r[3], rhat[3];
|
||||
for (int n = 0; n < atom->num_bond[i]; n++) {
|
||||
if (atom->bond_atom[i][n] == atom->tag[j]) {
|
||||
r0_mag = fix_bond_history->get_atom_value(i, n, 0);
|
||||
r0[0] = fix_bond_history->get_atom_value(i, n, 1);
|
||||
r0[1] = fix_bond_history->get_atom_value(i, n, 2);
|
||||
r0[2] = fix_bond_history->get_atom_value(i, n, 3);
|
||||
}
|
||||
}
|
||||
|
||||
double **x = atom->x;
|
||||
MathExtra::scale3(r0_mag, r0);
|
||||
MathExtra::sub3(x[i], x[j], r);
|
||||
|
||||
r_mag = sqrt(rsq);
|
||||
r_mag_inv = 1.0 / r_mag;
|
||||
MathExtra::scale3(r_mag_inv, r, rhat);
|
||||
|
||||
double breaking, smooth, Fr;
|
||||
double force1on2[3], torque1on2[3], torque2on1[3];
|
||||
breaking = elastic_forces(i, j, type, Fr, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
|
||||
torque1on2, torque2on1);
|
||||
fforce = Fr;
|
||||
damping_forces(i, j, type, Fr, rhat, r, force1on2, torque1on2, torque2on1);
|
||||
fforce += Fr;
|
||||
|
||||
if (smooth_flag) {
|
||||
smooth = breaking * breaking;
|
||||
smooth = 1.0 - smooth * smooth;
|
||||
fforce *= smooth;
|
||||
}
|
||||
return 0.0;
|
||||
}
|
||||
83
src/BPM/bond_bpm_rotational.h
Normal file
83
src/BPM/bond_bpm_rotational.h
Normal file
@ -0,0 +1,83 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
// clang-format off
|
||||
BondStyle(bpm/rotational,BondBPMRotational);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_BPM_ROTATIONAL_H
|
||||
#define LMP_BOND_BPM_ROTATIONAL_H
|
||||
|
||||
#include "bond_bpm.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondBPMRotational : public BondBPM {
|
||||
public:
|
||||
BondBPMRotational(class LAMMPS *);
|
||||
~BondBPMRotational() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
void settings(int, char **) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
double single(int, double, int, int, double &) override;
|
||||
|
||||
protected:
|
||||
double *Kr, *Ks, *Kt, *Kb, *gnorm, *gslide, *groll, *gtwist;
|
||||
double *Fcr, *Fcs, *Tct, *Tcb;
|
||||
int smooth_flag;
|
||||
|
||||
double acos_limit(double);
|
||||
|
||||
double elastic_forces(int, int, int, double &, double, double, double, double *, double *,
|
||||
double *, double *, double *, double *);
|
||||
void damping_forces(int, int, int, double &, double *, double *, double *, double *, double *);
|
||||
|
||||
void allocate();
|
||||
void store_data();
|
||||
double store_bond(int, int, int);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Atom missing in BPM bond
|
||||
|
||||
Bonded atom cannot be found
|
||||
|
||||
E: Incorrect args for bond coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Bond bpm/rotational requires atom style bpm/sphere
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Bond style bpm requires 1-3 and 1-4 special weights of 1.0
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: Bond style bpm/rotational not intended for 2d use, may be inefficient
|
||||
|
||||
This bond style will perform a lot of unnecessary calculations in 2d
|
||||
|
||||
*/
|
||||
380
src/BPM/bond_bpm_spring.cpp
Normal file
380
src/BPM/bond_bpm_spring.cpp
Normal file
@ -0,0 +1,380 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "bond_bpm_spring.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_bond_history.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#define EPSILON 1e-10
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPMSpring::BondBPMSpring(LAMMPS *_lmp) : BondBPM(_lmp), k(nullptr), ecrit(nullptr), gamma(nullptr)
|
||||
{
|
||||
partial_flag = 1;
|
||||
smooth_flag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPMSpring::~BondBPMSpring()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(k);
|
||||
memory->destroy(ecrit);
|
||||
memory->destroy(gamma);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Store data for a single bond - if bond added after LAMMPS init (e.g. pour)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMSpring::store_bond(int n, int i, int j)
|
||||
{
|
||||
double delx, dely, delz, r;
|
||||
double **x = atom->x;
|
||||
double **bondstore = fix_bond_history->bondstore;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
|
||||
r = sqrt(delx * delx + dely * dely + delz * delz);
|
||||
bondstore[n][0] = r;
|
||||
|
||||
if (i < atom->nlocal) {
|
||||
for (int m = 0; m < atom->num_bond[i]; m++) {
|
||||
if (atom->bond_atom[i][m] == tag[j]) { fix_bond_history->update_atom_value(i, m, 0, r); }
|
||||
}
|
||||
}
|
||||
|
||||
if (j < atom->nlocal) {
|
||||
for (int m = 0; m < atom->num_bond[j]; m++) {
|
||||
if (atom->bond_atom[j][m] == tag[i]) { fix_bond_history->update_atom_value(j, m, 0, r); }
|
||||
}
|
||||
}
|
||||
|
||||
return r;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Store data for all bonds called once
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::store_data()
|
||||
{
|
||||
int i, j, m, type;
|
||||
double delx, dely, delz, r;
|
||||
double **x = atom->x;
|
||||
int **bond_type = atom->bond_type;
|
||||
|
||||
for (i = 0; i < atom->nlocal; i++) {
|
||||
for (m = 0; m < atom->num_bond[i]; m++) {
|
||||
type = bond_type[i][m];
|
||||
|
||||
//Skip if bond was turned off
|
||||
if (type < 0) continue;
|
||||
|
||||
// map to find index n
|
||||
j = atom->map(atom->bond_atom[i][m]);
|
||||
if (j == -1) error->one(FLERR, "Atom missing in BPM bond");
|
||||
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
|
||||
// Get closest image in case bonded with ghost
|
||||
domain->minimum_image(delx, dely, delz);
|
||||
r = sqrt(delx * delx + dely * dely + delz * delz);
|
||||
|
||||
fix_bond_history->update_atom_value(i, m, 0, r);
|
||||
}
|
||||
}
|
||||
|
||||
fix_bond_history->post_neighbor();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::compute(int eflag, int vflag)
|
||||
{
|
||||
|
||||
if (!fix_bond_history->stored_flag) {
|
||||
fix_bond_history->stored_flag = true;
|
||||
store_data();
|
||||
}
|
||||
|
||||
int i1, i2, itmp, n, type;
|
||||
double delx, dely, delz, delvx, delvy, delvz;
|
||||
double e, rsq, r, r0, rinv, smooth, fbond, dot;
|
||||
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
tagint *tag = atom->tag;
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
double **bondstore = fix_bond_history->bondstore;
|
||||
|
||||
for (n = 0; n < nbondlist; n++) {
|
||||
|
||||
// skip bond if already broken
|
||||
if (bondlist[n][2] <= 0) continue;
|
||||
|
||||
i1 = bondlist[n][0];
|
||||
i2 = bondlist[n][1];
|
||||
type = bondlist[n][2];
|
||||
r0 = bondstore[n][0];
|
||||
|
||||
// Ensure pair is always ordered to ensure numerical operations
|
||||
// are identical to minimize the possibility that a bond straddling
|
||||
// an mpi grid (newton off) doesn't break on one proc but not the other
|
||||
if (tag[i2] < tag[i1]) {
|
||||
itmp = i1;
|
||||
i1 = i2;
|
||||
i2 = itmp;
|
||||
}
|
||||
|
||||
// If bond hasn't been set - should be initialized to zero
|
||||
if (r0 < EPSILON || std::isnan(r0)) r0 = store_bond(n, i1, i2);
|
||||
|
||||
delx = x[i1][0] - x[i2][0];
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
r = sqrt(rsq);
|
||||
e = (r - r0) / r0;
|
||||
|
||||
if (fabs(e) > ecrit[type]) {
|
||||
bondlist[n][2] = 0;
|
||||
process_broken(i1, i2);
|
||||
continue;
|
||||
}
|
||||
|
||||
rinv = 1.0 / r;
|
||||
fbond = k[type] * (r0 - r);
|
||||
|
||||
delvx = v[i1][0] - v[i2][0];
|
||||
delvy = v[i1][1] - v[i2][1];
|
||||
delvz = v[i1][2] - v[i2][2];
|
||||
dot = delx * delvx + dely * delvy + delz * delvz;
|
||||
fbond -= gamma[type] * dot * rinv;
|
||||
fbond *= rinv;
|
||||
|
||||
if (smooth_flag) {
|
||||
smooth = (r - r0) / (r0 * ecrit[type]);
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth = 1 - smooth;
|
||||
fbond *= smooth;
|
||||
}
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx * fbond;
|
||||
f[i1][1] += dely * fbond;
|
||||
f[i1][2] += delz * fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx * fbond;
|
||||
f[i2][1] -= dely * fbond;
|
||||
f[i2][2] -= delz * fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, fbond, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
const int np1 = atom->nbondtypes + 1;
|
||||
|
||||
memory->create(k, np1, "bond:k");
|
||||
memory->create(ecrit, np1, "bond:ecrit");
|
||||
memory->create(gamma, np1, "bond:gamma");
|
||||
|
||||
memory->create(setflag, np1, "bond:setflag");
|
||||
for (int i = 1; i < np1; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double ecrit_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double gamma_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
ecrit[i] = ecrit_one;
|
||||
gamma[i] = gamma_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
|
||||
if (1.0 + ecrit[i] > max_stretch) max_stretch = 1.0 + ecrit[i];
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check for correct settings and create fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::init_style()
|
||||
{
|
||||
BondBPM::init_style();
|
||||
|
||||
if (comm->ghost_velocity == 0)
|
||||
error->all(FLERR, "Bond bpm/spring requires ghost atoms store velocity");
|
||||
|
||||
if (!id_fix_bond_history) {
|
||||
id_fix_bond_history = utils::strdup("HISTORY_BPM_SPRING");
|
||||
fix_bond_history = dynamic_cast<FixBondHistory *>(modify->replace_fix(
|
||||
id_fix_dummy2, fmt::format("{} all BOND_HISTORY 0 1", id_fix_bond_history), 1));
|
||||
delete[] id_fix_dummy2;
|
||||
id_fix_dummy2 = nullptr;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::settings(int narg, char **arg)
|
||||
{
|
||||
BondBPM::settings(narg, arg);
|
||||
|
||||
int iarg;
|
||||
for (std::size_t i = 0; i < leftover_iarg.size(); i++) {
|
||||
iarg = leftover_iarg[i];
|
||||
if (strcmp(arg[iarg], "smooth") == 0) {
|
||||
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command");
|
||||
smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
|
||||
i += 1;
|
||||
} else {
|
||||
error->all(FLERR, "Illegal bond_style command");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&ecrit[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&gamma[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &ecrit[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &gamma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&ecrit[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&gamma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp, "%d %g %g %g\n", i, k[i], ecrit[i], gamma[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMSpring::single(int type, double rsq, int i, int j, double &fforce)
|
||||
{
|
||||
if (type <= 0) return 0.0;
|
||||
|
||||
double r0;
|
||||
for (int n = 0; n < atom->num_bond[i]; n++) {
|
||||
if (atom->bond_atom[i][n] == atom->tag[j]) r0 = fix_bond_history->get_atom_value(i, n, 0);
|
||||
}
|
||||
|
||||
double r = sqrt(rsq);
|
||||
double rinv = 1.0 / r;
|
||||
fforce = k[type] * (r0 - r);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double delx = x[i][0] - x[j][0];
|
||||
double dely = x[i][1] - x[j][1];
|
||||
double delz = x[i][2] - x[j][2];
|
||||
double delvx = v[i][0] - v[j][0];
|
||||
double delvy = v[i][1] - v[j][1];
|
||||
double delvz = v[i][2] - v[j][2];
|
||||
double dot = delx * delvx + dely * delvy + delz * delvz;
|
||||
fforce -= gamma[type] * dot * rinv;
|
||||
fforce *= rinv;
|
||||
|
||||
if (smooth_flag) {
|
||||
double smooth = (r - r0) / (r0 * ecrit[type]);
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth = 1 - smooth;
|
||||
fforce *= smooth;
|
||||
}
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
68
src/BPM/bond_bpm_spring.h
Normal file
68
src/BPM/bond_bpm_spring.h
Normal file
@ -0,0 +1,68 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
// clang-format off
|
||||
BondStyle(bpm/spring,BondBPMSpring);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_BPM_SPRING_H
|
||||
#define LMP_BOND_BPM_SPRING_H
|
||||
|
||||
#include "bond_bpm.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondBPMSpring : public BondBPM {
|
||||
public:
|
||||
BondBPMSpring(class LAMMPS *);
|
||||
~BondBPMSpring() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
void settings(int, char **) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
double single(int, double, int, int, double &) override;
|
||||
|
||||
protected:
|
||||
double *k, *ecrit, *gamma;
|
||||
int smooth_flag;
|
||||
|
||||
void allocate();
|
||||
void store_data();
|
||||
double store_bond(int, int, int);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Atom missing in BPM bond
|
||||
|
||||
Bonded atom cannot be found
|
||||
|
||||
E: Incorrect args for bond coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Bond style bpm requires 1-3 and 1-4 special weights of 1.0
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
145
src/BPM/compute_nbond_atom.cpp
Normal file
145
src/BPM/compute_nbond_atom.cpp
Normal file
@ -0,0 +1,145 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "compute_nbond_atom.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
|
||||
Compute(_lmp, narg, arg), nbond(nullptr)
|
||||
{
|
||||
if (narg < 3) error->all(FLERR, "Illegal compute nbond/atom command");
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 0;
|
||||
peatomflag = 1;
|
||||
timeflag = 1;
|
||||
comm_reverse = 1;
|
||||
|
||||
nmax = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeNBondAtom::~ComputeNBondAtom()
|
||||
{
|
||||
memory->destroy(nbond);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeNBondAtom::compute_peratom()
|
||||
{
|
||||
|
||||
invoked_peratom = update->ntimestep;
|
||||
if (update->eflag_atom != invoked_peratom)
|
||||
error->all(FLERR, "Per-atom nbond was not tallied on needed timestep");
|
||||
|
||||
// grow local nbond array if necessary
|
||||
// needs to be atom->nmax in length
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
memory->destroy(nbond);
|
||||
nmax = atom->nmax;
|
||||
memory->create(nbond, nmax, "nbond/atom:nbond");
|
||||
vector_atom = nbond;
|
||||
}
|
||||
|
||||
// npair includes ghosts if either newton flag is set
|
||||
// b/c some bonds/dihedrals call pair::ev_tally with pairwise info
|
||||
// nbond includes ghosts if newton_bond is set
|
||||
// ntotal includes ghosts if either newton flag is set
|
||||
// KSpace includes ghosts if tip4pflag is set
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
tagint **bond_atom = atom->bond_atom;
|
||||
int **bond_type = atom->bond_type;
|
||||
|
||||
int ntotal = nlocal;
|
||||
if (force->newton) ntotal += atom->nghost;
|
||||
|
||||
// set local nbond array
|
||||
int i, j, k;
|
||||
int *num_bond = atom->num_bond;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
for (i = 0; i < ntotal; i++) nbond[i] = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
for (j = 0; j < num_bond[i]; j++) {
|
||||
if (bond_type[i][j] <= 0) continue;
|
||||
|
||||
k = atom->map(bond_atom[i][j]);
|
||||
if (k < 0) continue;
|
||||
|
||||
nbond[i] += 1;
|
||||
if (newton_bond) nbond[k] += 1;
|
||||
}
|
||||
}
|
||||
|
||||
// communicate ghost nbond between neighbor procs
|
||||
if (force->newton) comm->reverse_comm(this);
|
||||
|
||||
// zero nbond of atoms not in group
|
||||
// only do this after comm since ghost contributions must be included
|
||||
int *mask = atom->mask;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (!(mask[i] & groupbit)) nbond[i] = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int ComputeNBondAtom::pack_reverse_comm(int n, int first, double *buf)
|
||||
{
|
||||
int i, m, last;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) buf[m++] = nbond[i];
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeNBondAtom::unpack_reverse_comm(int n, int *list, double *buf)
|
||||
{
|
||||
int i, j, m;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
nbond[j] += buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeNBondAtom::memory_usage()
|
||||
{
|
||||
double bytes = nmax * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
61
src/BPM/compute_nbond_atom.h
Normal file
61
src/BPM/compute_nbond_atom.h
Normal file
@ -0,0 +1,61 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMPUTE_CLASS
|
||||
// clang-format off
|
||||
ComputeStyle(nbond/atom,ComputeNBondAtom);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_NBOND_ATOM_H
|
||||
#define LMP_COMPUTE_NBOND_ATOM_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeNBondAtom : public Compute {
|
||||
public:
|
||||
ComputeNBondAtom(class LAMMPS *, int, char **);
|
||||
~ComputeNBondAtom() override;
|
||||
void init() override {}
|
||||
void compute_peratom() override;
|
||||
int pack_reverse_comm(int, int, double *) override;
|
||||
void unpack_reverse_comm(int, int *, double *) override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
int nmax;
|
||||
double *nbond;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Per-atom energy was not tallied on needed timestep
|
||||
|
||||
You are using a thermo keyword that requires potentials to
|
||||
have tallied energy, but they didn't on this timestep. See the
|
||||
variable doc page for ideas on how to make this work.
|
||||
|
||||
*/
|
||||
157
src/BPM/fix_nve_bpm_sphere.cpp
Normal file
157
src/BPM/fix_nve_bpm_sphere.cpp
Normal file
@ -0,0 +1,157 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_nve_bpm_sphere.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
using namespace MathExtra;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNVEBPMSphere::FixNVEBPMSphere(LAMMPS *_lmp, int narg, char **arg) : FixNVE(_lmp, narg, arg)
|
||||
{
|
||||
if (narg < 3) error->all(FLERR, "Illegal fix nve/bpm/sphere command");
|
||||
|
||||
time_integrate = 1;
|
||||
|
||||
// process extra keywords
|
||||
// inertia = moment of inertia prefactor for sphere or disc
|
||||
|
||||
inertia = 0.4;
|
||||
|
||||
int iarg = 3;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "disc") == 0) {
|
||||
inertia = 0.5;
|
||||
if (domain->dimension != 2)
|
||||
error->all(FLERR, "Fix nve/bpm/sphere disc requires 2d simulation");
|
||||
iarg++;
|
||||
} else
|
||||
error->all(FLERR, "Illegal fix nve/bpm/sphere command");
|
||||
}
|
||||
|
||||
inv_inertia = 1.0 / inertia;
|
||||
|
||||
// error checks
|
||||
|
||||
if (!atom->quat_flag || !atom->sphere_flag)
|
||||
error->all(FLERR, "Fix nve/bpm/sphere requires atom style bpm/sphere");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVEBPMSphere::init()
|
||||
{
|
||||
FixNVE::init();
|
||||
|
||||
// check that all particles are finite-size spheres
|
||||
// no point particles allowed
|
||||
|
||||
double *radius = atom->radius;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
if (radius[i] == 0.0) error->one(FLERR, "Fix nve/bpm/sphere requires extended particles");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVEBPMSphere::initial_integrate(int /*vflag*/)
|
||||
{
|
||||
double dtq, dtfm, dtirotate, particle_inertia;
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **omega = atom->omega;
|
||||
double **torque = atom->torque;
|
||||
double **quat = atom->quat;
|
||||
double *radius = atom->radius;
|
||||
double *rmass = atom->rmass;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// set timestep here since dt may have changed or come via rRESPA
|
||||
dtq = 0.5 * dtv;
|
||||
|
||||
// update v,x,omega,quat for all particles
|
||||
// d_omega/dt = torque / inertia
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
|
||||
particle_inertia = inertia * (radius[i] * radius[i] * rmass[i]);
|
||||
dtirotate = dtf / particle_inertia;
|
||||
omega[i][0] += dtirotate * torque[i][0];
|
||||
omega[i][1] += dtirotate * torque[i][1];
|
||||
omega[i][2] += dtirotate * torque[i][2];
|
||||
|
||||
MathExtra::richardson_sphere(quat[i], omega[i], dtq);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVEBPMSphere::final_integrate()
|
||||
{
|
||||
double dtfm, dtirotate, particle_inertia;
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **omega = atom->omega;
|
||||
double **torque = atom->torque;
|
||||
double *rmass = atom->rmass;
|
||||
double *radius = atom->radius;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// update v,omega for all particles
|
||||
// d_omega/dt = torque / inertia
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
particle_inertia = inertia * (radius[i] * radius[i] * rmass[i]);
|
||||
dtirotate = dtf / particle_inertia;
|
||||
omega[i][0] += dtirotate * torque[i][0];
|
||||
omega[i][1] += dtirotate * torque[i][1];
|
||||
omega[i][2] += dtirotate * torque[i][2];
|
||||
}
|
||||
}
|
||||
@ -1,6 +1,6 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
@ -12,50 +12,33 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(propel/self,FixPropelSelf)
|
||||
|
||||
// clang-format off
|
||||
FixStyle(nve/bpm/sphere,FixNVEBPMSphere);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_PROPEL_SELF_H
|
||||
#define LMP_FIX_PROPEL_SELF_H
|
||||
#ifndef LMP_FIX_NVE_BPM_SPHERE_H
|
||||
#define LMP_FIX_NVE_BPM_SPHERE_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "fix_nve.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixPropelSelf : public Fix {
|
||||
class FixNVEBPMSphere : public FixNVE {
|
||||
public:
|
||||
FixNVEBPMSphere(class LAMMPS *, int, char **);
|
||||
|
||||
FixPropelSelf(class LAMMPS *, int, char **);
|
||||
virtual ~FixPropelSelf();
|
||||
virtual int setmask();
|
||||
virtual void post_force(int);
|
||||
|
||||
double memory_usage();
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
protected:
|
||||
enum operation_modes {
|
||||
VELOCITY = 0,
|
||||
QUATERNION = 1
|
||||
};
|
||||
|
||||
private:
|
||||
double magnitude;
|
||||
int mode;
|
||||
|
||||
// If 0, apply fix to everything in group. If > 0, apply only to those
|
||||
// types i for which i <= n_types_filter _and_ apply_to_type[i] == 1:
|
||||
int n_types_filter;
|
||||
int *apply_to_type; //< Specifies, per type, if the fix applies to it or not.
|
||||
|
||||
|
||||
int atoms_have_quaternion();
|
||||
|
||||
template <int filter_by_type> void post_force_velocity(int);
|
||||
template <int filter_by_type> void post_force_quaternion(int);
|
||||
double inertia, inv_inertia;
|
||||
int extra;
|
||||
int dlm;
|
||||
};
|
||||
}
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -68,4 +51,21 @@ Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix nve/bpm/sphere disc requires 2d simulation
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix nve/bpm/sphere requires atom style bpm/sphere
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix nve/bpm/sphere update dipole requires atom attribute mu
|
||||
|
||||
An atom style with this attribute is needed.
|
||||
|
||||
E: Fix nve/bpm/sphere requires extended particles
|
||||
|
||||
This fix can only be used for particles of a finite size.
|
||||
|
||||
|
||||
*/
|
||||
326
src/BPM/pair_bpm_spring.cpp
Normal file
326
src/BPM/pair_bpm_spring.cpp
Normal file
@ -0,0 +1,326 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_bpm_spring.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBPMSpring::PairBPMSpring(LAMMPS *_lmp) : Pair(_lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBPMSpring::~PairBPMSpring()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(k);
|
||||
memory->destroy(cut);
|
||||
memory->destroy(gamma);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::compute(int eflag, int vflag)
|
||||
{
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
|
||||
double r, rsq, rinv, factor_lj;
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double vxtmp, vytmp, vztmp, delvx, delvy, delvz, dot, smooth;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
double *special_lj = force->special_lj;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
|
||||
if (factor_lj == 0) continue;
|
||||
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r = sqrt(rsq);
|
||||
|
||||
rinv = 1.0 / r;
|
||||
fpair = k[itype][jtype] * (cut[itype][jtype] - r);
|
||||
|
||||
smooth = rsq / cutsq[itype][jtype];
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth = 1.0 - smooth;
|
||||
delvx = vxtmp - v[j][0];
|
||||
delvy = vytmp - v[j][1];
|
||||
delvz = vztmp - v[j][2];
|
||||
dot = delx * delvx + dely * delvy + delz * delvz;
|
||||
fpair -= gamma[itype][jtype] * dot * smooth * rinv;
|
||||
|
||||
fpair *= factor_lj * rinv;
|
||||
if (eflag) evdwl = 0.0;
|
||||
|
||||
f[i][0] += delx * fpair;
|
||||
f[i][1] += dely * fpair;
|
||||
f[i][2] += delz * fpair;
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair;
|
||||
f[j][1] -= dely * fpair;
|
||||
f[j][2] -= delz * fpair;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
const int np1 = atom->ntypes + 1;
|
||||
|
||||
memory->create(setflag, np1, np1, "pair:setflag");
|
||||
for (int i = 1; i < np1; i++)
|
||||
for (int j = i; j < np1; j++) setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, np1, np1, "pair:cutsq");
|
||||
|
||||
memory->create(k, np1, np1, "pair:k");
|
||||
memory->create(cut, np1, np1, "pair:cut");
|
||||
memory->create(gamma, np1, np1, "pair:gamma");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::settings(int narg, char ** /*arg*/)
|
||||
{
|
||||
if (narg != 0) error->all(FLERR, "Illegal pair_style command");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double cut_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double gamma_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
|
||||
if (cut_one <= 0.0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo, i); j <= jhi; j++) {
|
||||
k[i][j] = k_one;
|
||||
cut[i][j] = cut_one;
|
||||
gamma[i][j] = gamma_one;
|
||||
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairBPMSpring::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
|
||||
k[i][j] = mix_energy(k[i][i], k[j][j], cut[i][i], cut[j][j]);
|
||||
gamma[i][j] = mix_energy(gamma[i][i], gamma[j][j], cut[i][i], cut[j][j]);
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
k[j][i] = k[i][j];
|
||||
gamma[j][i] = gamma[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i, j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j], sizeof(int), 1, fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&k[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&cut[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&gamma[i][j], sizeof(double), 1, fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i, j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
|
||||
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
utils::sfread(FLERR, &k[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &gamma[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&gamma[i][j], 1, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp, "%d %g %g %g\n", i, k[i][i], cut[i][i], gamma[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBPMSpring::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp, "%d %d %g %g %g\n", i, j, k[i][j], cut[i][j], gamma[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq, double /*factor_coul*/,
|
||||
double factor_lj, double &fforce)
|
||||
{
|
||||
double fpair, r, rinv;
|
||||
double delx, dely, delz, delvx, delvy, delvz, dot, smooth;
|
||||
|
||||
if (rsq > cutsq[itype][jtype]) return 0.0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
|
||||
r = sqrt(rsq);
|
||||
rinv = 1.0 / r;
|
||||
|
||||
fpair = k[itype][jtype] * (cut[itype][jtype] - r);
|
||||
|
||||
smooth = rsq / cutsq[itype][jtype];
|
||||
smooth *= smooth;
|
||||
smooth = 1.0 - smooth;
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
delvx = v[i][0] - v[j][0];
|
||||
delvy = v[i][1] - v[j][1];
|
||||
delvz = v[i][2] - v[j][2];
|
||||
dot = delx * delvx + dely * delvy + delz * delvz;
|
||||
fpair -= gamma[itype][jtype] * dot * rinv * smooth;
|
||||
|
||||
fpair *= factor_lj;
|
||||
fforce = fpair;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
64
src/BPM/pair_bpm_spring.h
Normal file
64
src/BPM/pair_bpm_spring.h
Normal file
@ -0,0 +1,64 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(bpm/spring,PairBPMSpring);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BPM_SPRING_H
|
||||
#define LMP_PAIR_BPM_SPRING_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBPMSpring : public Pair {
|
||||
public:
|
||||
PairBPMSpring(class LAMMPS *);
|
||||
~PairBPMSpring() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
double single(int, int, int, int, double, double, double, double &) override;
|
||||
|
||||
protected:
|
||||
double **k, **cut, **gamma;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user