include 2 use cases in doc page
This commit is contained in:
Steve Plimpton
174
src/.gitignore
vendored
174
src/.gitignore
vendored
@ -52,7 +52,7 @@
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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.j
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/compute_efield_atom.h
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/superpose3d.h
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@ -70,13 +70,14 @@
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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
|
||||
/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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@ -250,6 +251,68 @@
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/pair_mesont_tpm.cpp
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/pair_mesont_tpm.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_nve_noforce.cpp
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/fix_nve_noforce.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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@ -314,6 +377,8 @@
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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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@ -386,6 +451,8 @@
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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_force_tally.cpp
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@ -574,12 +641,8 @@
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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
|
||||
/fix_dpd_energy.cpp
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/fix_dpd_energy.h
|
||||
/fix_efield.cpp
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||||
/fix_efield.h
|
||||
/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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@ -588,8 +651,6 @@
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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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@ -718,6 +779,8 @@
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/fix_orient_eco.h
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||||
/fix_orient_fcc.cpp
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/fix_orient_fcc.h
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||||
/fix_pair_tracker.cpp
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||||
/fix_pair_tracker.h
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||||
/fix_peri_neigh.cpp
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||||
/fix_peri_neigh.h
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||||
/fix_phonon.cpp
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@ -728,18 +791,18 @@
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/fix_pour.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
|
||||
/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
|
||||
/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
|
||||
/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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@ -791,8 +854,6 @@
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/fix_tgnpt_drude.h
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/fix_tgnvt_drude.cpp
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/fix_tgnvt_drude.h
|
||||
/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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@ -1129,8 +1190,8 @@
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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
|
||||
/pair_reaxc.h
|
||||
/pair_reaxff.cpp
|
||||
/pair_reaxff.h
|
||||
/pair_rebo.cpp
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||||
/pair_rebo.h
|
||||
/pair_resquared.cpp
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||||
@ -1167,6 +1228,8 @@
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||||
/pair_tip4p_long.h
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||||
/pair_tip4p_long_soft.cpp
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||||
/pair_tip4p_long_soft.h
|
||||
/pair_tracker.h
|
||||
/pair_tracker.cpp
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||||
/pair_tri_lj.cpp
|
||||
/pair_tri_lj.h
|
||||
/pair_yukawa_colloid.cpp
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@ -1215,50 +1278,27 @@
|
||||
/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
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||||
/reaxc_ffield.h
|
||||
/reaxc_forces.cpp
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||||
/reaxc_forces.h
|
||||
/reaxc_hydrogen_bonds.cpp
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||||
/reaxc_hydrogen_bonds.h
|
||||
/reaxc_init_md.cpp
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||||
/reaxc_init_md.h
|
||||
/reaxc_io_tools.cpp
|
||||
/reaxc_io_tools.h
|
||||
/reaxc_list.cpp
|
||||
/reaxc_list.h
|
||||
/reaxc_lookup.cpp
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||||
/reaxc_lookup.h
|
||||
/reaxc_multi_body.cpp
|
||||
/reaxc_multi_body.h
|
||||
/reaxc_nonbonded.cpp
|
||||
/reaxc_nonbonded.h
|
||||
/reaxc_reset_tools.cpp
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||||
/reaxc_reset_tools.h
|
||||
/reaxc_system_props.cpp
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||||
/reaxc_system_props.h
|
||||
/reaxc_tool_box.cpp
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||||
/reaxc_tool_box.h
|
||||
/reaxc_torsion_angles.cpp
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||||
/reaxc_torsion_angles.h
|
||||
/reaxc_traj.cpp
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||||
/reaxc_traj.h
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||||
/reaxc_types.h
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||||
/reaxc_valence_angles.cpp
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||||
/reaxc_valence_angles.h
|
||||
/reaxc_vector.cpp
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||||
/reaxc_vector.h
|
||||
/reaxff_allocate.cpp
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||||
/reaxff_bond_orders.cpp
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||||
/reaxff_bonds.cpp
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||||
/reaxff_control.cpp
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||||
/reaxff_ffield.cpp
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||||
/reaxff_forces.cpp
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||||
/reaxff_hydrogen_bonds.cpp
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||||
/reaxff_init_md.cpp
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/reaxff_list.cpp
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/reaxff_lookup.cpp
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/reaxff_multi_body.cpp
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/reaxff_nonbonded.cpp
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/reaxff_reset_tools.cpp
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||||
/reaxff_tool_box.cpp
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||||
/reaxff_torsion_angles.cpp
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||||
/reaxff_valence_angles.cpp
|
||||
/reaxff_api.h
|
||||
/reaxff_defs.h
|
||||
/reaxff_inline.h
|
||||
/reaxff_omp.h
|
||||
/reaxff_types.h
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||||
/remap.cpp
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||||
/remap.h
|
||||
/remap_wrap.cpp
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||||
@ -1429,6 +1469,10 @@
|
||||
/pair_thole.h
|
||||
/pair_buck_mdf.cpp
|
||||
/pair_buck_mdf.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
|
||||
|
||||
@ -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.
|
||||
File diff suppressed because it is too large
Load Diff
@ -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
|
||||
@ -37,7 +37,7 @@ 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
|
||||
@ -700,20 +700,17 @@ 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];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -722,20 +719,17 @@ 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];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -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
|
||||
@ -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.
|
||||
@ -11,7 +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
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
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
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -11,7 +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
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -43,7 +43,7 @@ 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"
|
||||
@ -1100,7 +1100,12 @@ 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
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
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
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -37,6 +37,7 @@ class FixBocs : public Fix {
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void initial_integrate_respa(int, int, int);
|
||||
void pre_force_respa(int, int, int);
|
||||
void final_integrate_respa(int, int);
|
||||
virtual void pre_exchange();
|
||||
double compute_scalar();
|
||||
@ -21,21 +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;
|
||||
|
||||
|
||||
@ -23,22 +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;
|
||||
@ -1212,10 +1212,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
|
||||
contact_list[num_contacts].unique = 1;
|
||||
num_contacts++;
|
||||
}
|
||||
} else {
|
||||
|
||||
}
|
||||
|
||||
return interact;
|
||||
}
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||
Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
|
||||
|
||||
Contributing author: Sam Cameron (University of Bristol)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||
Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
|
||||
|
||||
Contributing author: Sam Cameron (University of Bristol)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||
Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
|
||||
|
||||
Contributing author: Sam Cameron (University of Bristol)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||
Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
|
||||
|
||||
Contributing author: Sam Cameron (University of Bristol)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -26,8 +26,25 @@ action () {
|
||||
fi
|
||||
}
|
||||
|
||||
# the CG-DNA package cannot be used without
|
||||
# the MOLECULE and ASPHERE packages installed.
|
||||
|
||||
if (test $1 = 1) then
|
||||
if (test ! -e ../bond_harmonic.cpp) then
|
||||
echo "Must install MOLECULE package with CG-DNA"
|
||||
exit 1
|
||||
fi
|
||||
if (test ! -e ../fix_nve_asphere.cpp) then
|
||||
echo "Must install ASPHERE package with CG-DNA"
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
|
||||
|
||||
# list of files with dependcies
|
||||
|
||||
action atom_vec_oxdna.cpp
|
||||
action atom_vec_oxdna.h
|
||||
action bond_oxdna_fene.cpp bond_fene.h
|
||||
action bond_oxdna2_fene.cpp bond_fene.h
|
||||
action bond_oxrna2_fene.cpp bond_fene.h
|
||||
@ -40,13 +40,13 @@ gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
|
||||
144114 (2015).
|
||||
|
||||
Example input and data files can be found in
|
||||
/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
|
||||
examples/PACKAGES/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
|
||||
Python setup tools which create single straight or helical DNA or RNA
|
||||
strands as well as DNA or RNA duplexes or arrays of duplexes can be
|
||||
found in /examples/USER/cgdna/util/. A technical report with more
|
||||
found in examples/PACKAGES/cgdna/util/. A technical report with more
|
||||
general information on the model, its implementation and performance
|
||||
as well as the structure of the data and input file can be found
|
||||
in /doc/src/PDF/USER-CGDNA.pdf.
|
||||
in doc/src/PDF/CG-DNA.pdf.
|
||||
|
||||
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
|
||||
with the MOLECULE and ASPHERE packages. These should be included in
|
||||
95
src/CG-DNA/atom_vec_oxdna.cpp
Normal file
95
src/CG-DNA/atom_vec_oxdna.cpp
Normal file
@ -0,0 +1,95 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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_oxdna.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
|
||||
{
|
||||
molecular = Atom::MOLECULAR;
|
||||
bonds_allow = 1;
|
||||
mass_type = PER_TYPE;
|
||||
|
||||
atom->molecule_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 *) "id5p";
|
||||
fields_copy = (char *) "id5p";
|
||||
fields_comm = (char *) "";
|
||||
fields_comm_vel = (char *) "";
|
||||
fields_reverse = (char *) "";
|
||||
fields_border = (char *) "id5p";
|
||||
fields_border_vel = (char *) "";
|
||||
fields_exchange = (char *) "id5p";
|
||||
fields_restart = (char *) "id5p";
|
||||
fields_create = (char *) "";
|
||||
fields_data_atom = (char *) "id type x";
|
||||
fields_data_vel = (char *) "id v";
|
||||
|
||||
setup_fields();
|
||||
|
||||
if(!force->newton_bond) error->warning(FLERR,"Write_data command requires newton on to preserve 3'->5' bond polarity");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
AtomVecOxdna::~AtomVecOxdna() {}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
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 AtomVecOxdna::grow_pointers()
|
||||
{
|
||||
id5p = atom->id5p;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
initialize atom quantity 5' partner
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecOxdna::data_atom_post(int ilocal)
|
||||
{
|
||||
tagint *id5p = atom->id5p;
|
||||
id5p[ilocal] = -1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
process bond information as per data file
|
||||
store 5' partner to inform 3'->5' bond directionality
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecOxdna::data_bonds_post(int /*m*/, int /*num_bond*/, tagint atom1, tagint atom2,
|
||||
tagint id_offset)
|
||||
{
|
||||
int n;
|
||||
tagint *id5p = atom->id5p;
|
||||
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
}
|
||||
|
||||
if ((n = atom->map(atom1)) >= 0) { id5p[n] = atom2; }
|
||||
}
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -12,33 +11,37 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
#ifdef ATOM_CLASS
|
||||
// clang-format off
|
||||
FixStyle(reax/c/species/kk,FixReaxCSpeciesKokkos);
|
||||
FixStyle(reax/c/species/kk/device,FixReaxCSpeciesKokkos);
|
||||
FixStyle(reax/c/species/kk/host,FixReaxCSpeciesKokkos);
|
||||
AtomStyle(oxdna,AtomVecOxdna);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_REAXC_SPECIES_KOKKOS_H
|
||||
#define LMP_FIX_REAXC_SPECIES_KOKKOS_H
|
||||
#ifndef LMP_ATOM_VEC_OXDNA_H
|
||||
#define LMP_ATOM_VEC_OXDNA_H
|
||||
|
||||
#include "fix_reaxc_species.h"
|
||||
|
||||
#define BUFLEN 1000
|
||||
#include "atom_vec.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixReaxCSpeciesKokkos : public FixReaxCSpecies {
|
||||
class AtomVecOxdna : public AtomVec {
|
||||
public:
|
||||
FixReaxCSpeciesKokkos(class LAMMPS *, int, char **);
|
||||
virtual ~FixReaxCSpeciesKokkos();
|
||||
void init();
|
||||
AtomVecOxdna(class LAMMPS *);
|
||||
~AtomVecOxdna();
|
||||
|
||||
void grow_pointers();
|
||||
void data_atom_post(int);
|
||||
void data_bonds_post(int, int, tagint, tagint, tagint);
|
||||
|
||||
private:
|
||||
void FindMolecule();
|
||||
tagint *id5p;
|
||||
};
|
||||
}
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
*/
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -19,30 +18,16 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxdna2Fene::BondOxdna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxdna2Fene::~BondOxdna2Fene()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
|
||||
------------------------------------------------------------------------- */
|
||||
void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3],
|
||||
double /*e3*/[3], double r[3])
|
||||
void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3],
|
||||
double r[3]) const
|
||||
{
|
||||
double d_cs_x=-0.34, d_cs_y=+0.3408;
|
||||
|
||||
r[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
|
||||
r[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
|
||||
r[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
|
||||
constexpr double d_cs_x = -0.34;
|
||||
constexpr double d_cs_y = +0.3408;
|
||||
|
||||
r[0] = d_cs_x * e1[0] + d_cs_y * e2[0];
|
||||
r[1] = d_cs_x * e1[1] + d_cs_y * e2[1];
|
||||
r[2] = d_cs_x * e1[2] + d_cs_y * e2[2];
|
||||
}
|
||||
@ -26,9 +26,9 @@ namespace LAMMPS_NS {
|
||||
|
||||
class BondOxdna2Fene : public BondOxdnaFene {
|
||||
public:
|
||||
BondOxdna2Fene(class LAMMPS *);
|
||||
virtual ~BondOxdna2Fene();
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *);
|
||||
BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
|
||||
virtual ~BondOxdna2Fene() {}
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -17,7 +16,6 @@
|
||||
|
||||
#include "bond_oxdna_fene.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "comm.h"
|
||||
@ -29,26 +27,19 @@
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxdnaFene::BondOxdnaFene(LAMMPS *lmp) : Bond(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxdnaFene::~BondOxdnaFene()
|
||||
{
|
||||
if (allocated) {
|
||||
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(k);
|
||||
memory->destroy(Delta);
|
||||
memory->destroy(r0);
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@ -57,14 +48,13 @@ BondOxdnaFene::~BondOxdnaFene()
|
||||
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
|
||||
------------------------------------------------------------------------- */
|
||||
void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3],
|
||||
double /*e3*/[3], double r[3])
|
||||
double /*e3*/[3], double r[3]) const
|
||||
{
|
||||
double d_cs=-0.4;
|
||||
constexpr double d_cs=-0.4;
|
||||
|
||||
r[0] = d_cs*e1[0];
|
||||
r[1] = d_cs*e1[1];
|
||||
r[2] = d_cs*e1[2];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -218,11 +208,8 @@ void BondOxdnaFene::compute(int eflag, int vflag)
|
||||
// if r > 2*Delta something serious is wrong, abort
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
char str[128];
|
||||
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
|
||||
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
|
||||
update->ntimestep,atom->tag[a],atom->tag[b],r);
|
||||
error->warning(FLERR,str);
|
||||
error->warning(FLERR,"FENE bond too long: {} {} {} {}",
|
||||
update->ntimestep,atom->tag[a],atom->tag[b],r);
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
@ -398,10 +385,8 @@ double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/,
|
||||
// if r > 2*Delta something serious is wrong, abort
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
char str[128];
|
||||
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
|
||||
update->ntimestep,sqrt(rsq));
|
||||
error->warning(FLERR,str);
|
||||
error->warning(FLERR,"FENE bond too long: {} {:.8}",
|
||||
update->ntimestep,sqrt(rsq));
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
@ -26,9 +26,9 @@ namespace LAMMPS_NS {
|
||||
|
||||
class BondOxdnaFene : public Bond {
|
||||
public:
|
||||
BondOxdnaFene(class LAMMPS *);
|
||||
BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {}
|
||||
virtual ~BondOxdnaFene();
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *);
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
|
||||
virtual void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -19,30 +18,17 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxrna2Fene::~BondOxrna2Fene()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
|
||||
------------------------------------------------------------------------- */
|
||||
void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3],
|
||||
double e3[3], double r[3])
|
||||
|
||||
void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3],
|
||||
double r[3]) const
|
||||
{
|
||||
double d_cs_x=-0.4, d_cs_z=+0.2;
|
||||
|
||||
r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
|
||||
r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
|
||||
r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
|
||||
constexpr double d_cs_x = -0.4;
|
||||
constexpr double d_cs_z = +0.2;
|
||||
|
||||
r[0] = d_cs_x * e1[0] + d_cs_z * e3[0];
|
||||
r[1] = d_cs_x * e1[1] + d_cs_z * e3[1];
|
||||
r[2] = d_cs_x * e1[2] + d_cs_z * e3[2];
|
||||
}
|
||||
@ -26,9 +26,10 @@ namespace LAMMPS_NS {
|
||||
|
||||
class BondOxrna2Fene : public BondOxdnaFene {
|
||||
public:
|
||||
BondOxrna2Fene(class LAMMPS *);
|
||||
virtual ~BondOxrna2Fene();
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *);
|
||||
BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
|
||||
virtual ~BondOxrna2Fene() {}
|
||||
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -19,34 +18,19 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxdna2Excv::PairOxdna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxdna2Excv::~PairOxdna2Excv()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-excluded volume interaction sites in oxDNA2
|
||||
------------------------------------------------------------------------- */
|
||||
void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3],
|
||||
double /*e3*/[3], double rs[3], double rb[3])
|
||||
void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3],
|
||||
double rs[3], double rb[3])
|
||||
{
|
||||
double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4;
|
||||
double d_cs_x = -0.34, d_cs_y = +0.3408, d_cb = +0.4;
|
||||
|
||||
rs[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
|
||||
rs[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
|
||||
rs[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
|
||||
|
||||
rb[0] = d_cb*e1[0];
|
||||
rb[1] = d_cb*e1[1];
|
||||
rb[2] = d_cb*e1[2];
|
||||
rs[0] = d_cs_x * e1[0] + d_cs_y * e2[0];
|
||||
rs[1] = d_cs_x * e1[1] + d_cs_y * e2[1];
|
||||
rs[2] = d_cs_x * e1[2] + d_cs_y * e2[2];
|
||||
|
||||
rb[0] = d_cb * e1[0];
|
||||
rb[1] = d_cb * e1[1];
|
||||
rb[2] = d_cb * e1[2];
|
||||
}
|
||||
@ -26,8 +26,8 @@ namespace LAMMPS_NS {
|
||||
|
||||
class PairOxdna2Excv : public PairOxdnaExcv {
|
||||
public:
|
||||
PairOxdna2Excv(class LAMMPS *);
|
||||
virtual ~PairOxdna2Excv();
|
||||
PairOxdna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
|
||||
virtual ~PairOxdna2Excv() {}
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
|
||||
};
|
||||
|
||||
@ -17,19 +17,20 @@
|
||||
|
||||
#include "pair_oxdna_stk.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "atom_vec_oxdna.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "mf_oxdna.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include <utility>
|
||||
#include "mf_oxdna.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MFOxdna;
|
||||
@ -42,26 +43,26 @@ PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp)
|
||||
writedata = 1;
|
||||
|
||||
// sequence-specific stacking strength
|
||||
// A:0 C:1 G:2 T:3, 5'- [i][j] -3'
|
||||
// A:0 C:1 G:2 T:3, 3'- [i][j] -5'
|
||||
|
||||
eta_st[0][0] = 1.11960;
|
||||
eta_st[0][1] = 1.00852;
|
||||
eta_st[0][2] = 0.96950;
|
||||
eta_st[0][3] = 0.99632;
|
||||
eta_st[1][0] = 1.00852;
|
||||
eta_st[2][0] = 0.96950;
|
||||
eta_st[3][0] = 0.99632;
|
||||
|
||||
eta_st[1][0] = 1.01889;
|
||||
eta_st[0][1] = 1.01889;
|
||||
eta_st[1][1] = 0.97804;
|
||||
eta_st[1][2] = 1.02681;
|
||||
eta_st[1][3] = 0.96950;
|
||||
eta_st[2][1] = 1.02681;
|
||||
eta_st[3][1] = 0.96950;
|
||||
|
||||
eta_st[2][0] = 0.98169;
|
||||
eta_st[2][1] = 1.05913;
|
||||
eta_st[0][2] = 0.98169;
|
||||
eta_st[1][2] = 1.05913;
|
||||
eta_st[2][2] = 0.97804;
|
||||
eta_st[2][3] = 1.00852;
|
||||
eta_st[3][2] = 1.00852;
|
||||
|
||||
eta_st[3][0] = 0.94694;
|
||||
eta_st[3][1] = 0.98169;
|
||||
eta_st[3][2] = 1.01889;
|
||||
eta_st[0][3] = 0.94694;
|
||||
eta_st[1][3] = 0.98169;
|
||||
eta_st[2][3] = 1.01889;
|
||||
eta_st[3][3] = 0.96383;
|
||||
|
||||
}
|
||||
@ -244,15 +245,16 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
|
||||
tagint *id5p = atom->id5p;
|
||||
|
||||
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
|
||||
int a,b,in,atype,btype;
|
||||
int a,b,btemp,in,atype,btype;
|
||||
|
||||
double f1,f4t4,f4t5,f4t6,f5c1,f5c2;
|
||||
double df1,df4t4,df4t5,df4t6,df5c1,df5c2;
|
||||
double tptofp;
|
||||
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
@ -261,8 +263,19 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
|
||||
for (in = 0; in < nbondlist; in++) {
|
||||
|
||||
a = bondlist[in][1];
|
||||
b = bondlist[in][0];
|
||||
a = bondlist[in][0];
|
||||
b = bondlist[in][1];
|
||||
|
||||
// directionality test: a -> b is 3' -> 5'
|
||||
if(atom->tag[b] != id5p[a]) {
|
||||
|
||||
btemp = b;
|
||||
b = a;
|
||||
a = btemp;
|
||||
|
||||
}
|
||||
|
||||
// a now in 3' direction, b in 5' direction
|
||||
|
||||
qa=bonus[ellipsoid[a]].quat;
|
||||
MathExtra::q_to_exyz(qa,ax,ay,az);
|
||||
@ -279,30 +292,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
rb_cst[1] = d_cst*bx[1];
|
||||
rb_cst[2] = d_cst*bx[2];
|
||||
|
||||
// vector stacking site b to a
|
||||
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
|
||||
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
|
||||
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
|
||||
// vector stacking site a to b
|
||||
delr_st[0] = x[b][0] + rb_cst[0] - x[a][0] - ra_cst[0];
|
||||
delr_st[1] = x[b][1] + rb_cst[1] - x[a][1] - ra_cst[1];
|
||||
delr_st[2] = x[b][2] + rb_cst[2] - x[a][2] - ra_cst[2];
|
||||
|
||||
// test for directionality of vector b to a
|
||||
tptofp = MFOxdna::is_3pto5p(delr_st,bz);
|
||||
|
||||
// if b to a is 5' to 3' we need to swap roles of a and b
|
||||
if (tptofp == -1) {
|
||||
|
||||
std::swap(a,b);
|
||||
std::swap(ax,bx);
|
||||
std::swap(ay,by);
|
||||
std::swap(az,bz);
|
||||
std::swap(ra_cst,rb_cst);
|
||||
|
||||
delr_st[0] *= -1;
|
||||
delr_st[1] *= -1;
|
||||
delr_st[2] *= -1;
|
||||
|
||||
}
|
||||
|
||||
// a now in 5' direction, b in 3' direction
|
||||
atype = type[a];
|
||||
btype = type[b];
|
||||
|
||||
@ -325,9 +319,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
rb_cs[2] = d_cs*bx[2];
|
||||
|
||||
// vector backbone site b to a
|
||||
delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
|
||||
delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
|
||||
delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
|
||||
delr_ss[0] = (x[b][0] + rb_cs[0] - x[a][0] - ra_cs[0]);
|
||||
delr_ss[1] = (x[b][1] + rb_cs[1] - x[a][1] - ra_cs[1]);
|
||||
delr_ss[2] = (x[b][2] + rb_cs[2] - x[a][2] - ra_cs[2]);
|
||||
|
||||
rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
|
||||
r_ss = sqrt(rsq_ss);
|
||||
@ -345,7 +339,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (f1) {
|
||||
|
||||
// theta4 angle and correction
|
||||
cost4 = MathExtra::dot3(az,bz);
|
||||
cost4 = MathExtra::dot3(bz,az);
|
||||
if (cost4 > 1.0) cost4 = 1.0;
|
||||
if (cost4 < -1.0) cost4 = -1.0;
|
||||
theta4 = acos(cost4);
|
||||
@ -357,7 +351,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (f4t4) {
|
||||
|
||||
// theta5 angle and correction
|
||||
cost5p = MathExtra::dot3(delr_st_norm,az);
|
||||
cost5p = MathExtra::dot3(delr_st_norm,bz);
|
||||
if (cost5p > 1.0) cost5p = 1.0;
|
||||
if (cost5p < -1.0) cost5p = -1.0;
|
||||
theta5p = acos(cost5p);
|
||||
@ -368,16 +362,16 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
// early rejection criterium
|
||||
if (f4t5) {
|
||||
|
||||
cost6p = MathExtra::dot3(delr_st_norm,bz);
|
||||
cost6p = MathExtra::dot3(delr_st_norm,az);
|
||||
if (cost6p > 1.0) cost6p = 1.0;
|
||||
if (cost6p < -1.0) cost6p = -1.0;
|
||||
theta6p = acos(cost6p);
|
||||
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,by);
|
||||
if (cosphi1 > 1.0) cosphi1 = 1.0;
|
||||
if (cosphi1 < -1.0) cosphi1 = -1.0;
|
||||
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,by);
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
if (cosphi2 > 1.0) cosphi2 = 1.0;
|
||||
if (cosphi2 < -1.0) cosphi2 = -1.0;
|
||||
|
||||
@ -385,11 +379,10 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
b_st6[atype][btype], dtheta_st6_c[atype][btype]);
|
||||
|
||||
f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
evdwl = f1 * f4t4 * f4t5 * f4t6 * f5c1 * f5c2;
|
||||
|
||||
@ -410,10 +403,10 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
b_st6[atype][btype], dtheta_st6_c[atype][btype])/sin(theta6p);
|
||||
|
||||
df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
|
||||
// force, torque and virial contribution for forces between stacking sites
|
||||
@ -446,9 +439,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - bz[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -458,28 +451,27 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - az[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cst,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cst,delf,deltb);
|
||||
|
||||
@ -487,16 +479,16 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -505,7 +497,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
|
||||
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// force, torque and virial contribution for forces between backbone sites
|
||||
|
||||
@ -529,9 +521,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - by[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -541,28 +533,27 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - ay[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cs,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cs,delf,deltb);
|
||||
|
||||
@ -570,22 +561,22 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
// increment virial only
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// pure torques not expressible as r x f
|
||||
|
||||
@ -600,7 +591,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (theta4) {
|
||||
|
||||
tpair = -f1 * df4t4 * f4t5 * f4t6 * f5c1 * f5c2;
|
||||
MathExtra::cross3(bz,az,t4dir);
|
||||
MathExtra::cross3(az,bz,t4dir);
|
||||
|
||||
delta[0] += t4dir[0]*tpair;
|
||||
delta[1] += t4dir[1]*tpair;
|
||||
@ -616,11 +607,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (theta5p) {
|
||||
|
||||
tpair = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,az,t5pdir);
|
||||
MathExtra::cross3(delr_st_norm,bz,t5pdir);
|
||||
|
||||
delta[0] += t5pdir[0] * tpair;
|
||||
delta[1] += t5pdir[1] * tpair;
|
||||
delta[2] += t5pdir[2] * tpair;
|
||||
deltb[0] += t5pdir[0] * tpair;
|
||||
deltb[1] += t5pdir[1] * tpair;
|
||||
deltb[2] += t5pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -628,11 +619,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (theta6p) {
|
||||
|
||||
tpair = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,bz,t6pdir);
|
||||
MathExtra::cross3(delr_st_norm,az,t6pdir);
|
||||
|
||||
deltb[0] -= t6pdir[0] * tpair;
|
||||
deltb[1] -= t6pdir[1] * tpair;
|
||||
deltb[2] -= t6pdir[2] * tpair;
|
||||
delta[0] -= t6pdir[0] * tpair;
|
||||
delta[1] -= t6pdir[1] * tpair;
|
||||
delta[2] -= t6pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -640,11 +631,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (cosphi1) {
|
||||
|
||||
tpair = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi1dir);
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi1dir);
|
||||
|
||||
delta[0] += cosphi1dir[0] * tpair;
|
||||
delta[1] += cosphi1dir[1] * tpair;
|
||||
delta[2] += cosphi1dir[2] * tpair;
|
||||
deltb[0] += cosphi1dir[0] * tpair;
|
||||
deltb[1] += cosphi1dir[1] * tpair;
|
||||
deltb[2] += cosphi1dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -652,27 +643,27 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (cosphi2) {
|
||||
|
||||
tpair = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2;
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi2dir);
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi2dir);
|
||||
|
||||
deltb[0] -= cosphi2dir[0] * tpair;
|
||||
deltb[1] -= cosphi2dir[1] * tpair;
|
||||
deltb[2] -= cosphi2dir[2] * tpair;
|
||||
delta[0] -= cosphi2dir[0] * tpair;
|
||||
delta[1] -= cosphi2dir[1] * tpair;
|
||||
delta[2] -= cosphi2dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
// increment torques
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -935,6 +926,17 @@ void PairOxdnaStk::coeff(int narg, char **arg)
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
atom_style hybrid bond ellipsoid oxdna required
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairOxdnaStk::init_style()
|
||||
{
|
||||
if (!atom->style_match("oxdna")) {
|
||||
error->all(FLERR,"Must use 'atom_style hybrid bond ellipsoid oxdna' with pair style oxdna/stk, oxdna2/stk or oxrna2/stk");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
neighbor callback to inform pair style of neighbor list to use regular
|
||||
------------------------------------------------------------------------- */
|
||||
@ -32,6 +32,7 @@ class PairOxdnaStk : public Pair {
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -19,30 +18,15 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxrna2Dh::PairOxrna2Dh(LAMMPS *lmp) : PairOxdna2Dh(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxrna2Dh::~PairOxrna2Dh()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-sugar-phosphate backbone interaction site in oxRNA2
|
||||
------------------------------------------------------------------------- */
|
||||
void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3],
|
||||
double e3[3], double r[3])
|
||||
void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3],
|
||||
double r[3])
|
||||
{
|
||||
double d_cs_x=-0.4, d_cs_z=+0.2;
|
||||
|
||||
r[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
|
||||
r[1] = d_cs_x*e1[1] + d_cs_z*e3[1];
|
||||
r[2] = d_cs_x*e1[2] + d_cs_z*e3[2];
|
||||
double d_cs_x = -0.4, d_cs_z = +0.2;
|
||||
|
||||
r[0] = d_cs_x * e1[0] + d_cs_z * e3[0];
|
||||
r[1] = d_cs_x * e1[1] + d_cs_z * e3[1];
|
||||
r[2] = d_cs_x * e1[2] + d_cs_z * e3[2];
|
||||
}
|
||||
@ -26,8 +26,8 @@ namespace LAMMPS_NS {
|
||||
|
||||
class PairOxrna2Dh : public PairOxdna2Dh {
|
||||
public:
|
||||
PairOxrna2Dh(class LAMMPS *);
|
||||
virtual ~PairOxrna2Dh();
|
||||
PairOxrna2Dh(class LAMMPS *lmp) : PairOxdna2Dh(lmp) {}
|
||||
virtual ~PairOxrna2Dh() {}
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *);
|
||||
};
|
||||
|
||||
@ -21,20 +21,6 @@
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxrna2Excv::PairOxrna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxrna2Excv::~PairOxrna2Excv()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-excluded volume interaction sites in oxRNA2
|
||||
------------------------------------------------------------------------- */
|
||||
@ -26,8 +26,8 @@ namespace LAMMPS_NS {
|
||||
|
||||
class PairOxrna2Excv : public PairOxdnaExcv {
|
||||
public:
|
||||
PairOxrna2Excv(class LAMMPS *);
|
||||
virtual ~PairOxrna2Excv();
|
||||
PairOxrna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
|
||||
virtual ~PairOxrna2Excv() {}
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
|
||||
};
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -48,12 +47,4 @@ PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp)
|
||||
alpha_hb[3][1] = 1.00000;
|
||||
alpha_hb[3][2] = 0.58655;
|
||||
alpha_hb[3][3] = 1.00000;
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxrna2Hbond::~PairOxrna2Hbond()
|
||||
{
|
||||
|
||||
}
|
||||
@ -27,7 +27,7 @@ namespace LAMMPS_NS {
|
||||
class PairOxrna2Hbond : public PairOxdnaHbond {
|
||||
public:
|
||||
PairOxrna2Hbond(class LAMMPS *);
|
||||
virtual ~PairOxrna2Hbond();
|
||||
virtual ~PairOxrna2Hbond() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
@ -19,6 +19,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "atom_vec_oxdna.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
@ -44,26 +45,26 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp)
|
||||
writedata = 1;
|
||||
|
||||
// sequence-specific stacking strength
|
||||
// A:0 C:1 G:2 U:3, 5'- [i][j] -3'
|
||||
// A:0 C:1 G:2 U:3, 3'- [i][j] -5'
|
||||
|
||||
eta_st[0][0] = 0.93851;
|
||||
eta_st[0][1] = 1.12901;
|
||||
eta_st[0][2] = 1.15626;
|
||||
eta_st[0][3] = 0.88850;
|
||||
eta_st[1][0] = 1.12901;
|
||||
eta_st[2][0] = 1.15626;
|
||||
eta_st[3][0] = 0.88850;
|
||||
|
||||
eta_st[1][0] = 0.86331;
|
||||
eta_st[0][1] = 0.86331;
|
||||
eta_st[1][1] = 1.05060;
|
||||
eta_st[1][2] = 0.90982;
|
||||
eta_st[1][3] = 0.83252;
|
||||
eta_st[2][1] = 0.90982;
|
||||
eta_st[3][1] = 0.83252;
|
||||
|
||||
eta_st[2][0] = 0.99407;
|
||||
eta_st[2][1] = 1.14333;
|
||||
eta_st[0][2] = 0.99407;
|
||||
eta_st[1][2] = 1.14333;
|
||||
eta_st[2][2] = 1.06573;
|
||||
eta_st[2][3] = 0.91705;
|
||||
eta_st[3][2] = 0.91705;
|
||||
|
||||
eta_st[3][0] = 0.98804;
|
||||
eta_st[3][1] = 1.04949;
|
||||
eta_st[3][2] = 1.12063;
|
||||
eta_st[0][3] = 0.98804;
|
||||
eta_st[1][3] = 1.04949;
|
||||
eta_st[2][3] = 1.12063;
|
||||
eta_st[3][3] = 0.83818;
|
||||
|
||||
}
|
||||
@ -261,15 +262,16 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
|
||||
tagint *id5p = atom->id5p;
|
||||
|
||||
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
|
||||
int a,b,in,atype,btype;
|
||||
int a,b,btemp,in,atype,btype;
|
||||
|
||||
double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2;
|
||||
double df1,df4t5,df4t6,df4t9,df4t10,df5c1,df5c2;
|
||||
double tptofp;
|
||||
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
@ -278,62 +280,43 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
|
||||
for (in = 0; in < nbondlist; in++) {
|
||||
|
||||
a = bondlist[in][1];
|
||||
b = bondlist[in][0];
|
||||
a = bondlist[in][0];
|
||||
b = bondlist[in][1];
|
||||
|
||||
// directionality test: a -> b is 3' -> 5'
|
||||
if(atom->tag[b] != id5p[a]) {
|
||||
|
||||
btemp = b;
|
||||
b = a;
|
||||
a = btemp;
|
||||
|
||||
}
|
||||
|
||||
// a now in 3' direction, b in 5' direction
|
||||
|
||||
qa=bonus[ellipsoid[a]].quat;
|
||||
MathExtra::q_to_exyz(qa,ax,ay,az);
|
||||
qb=bonus[ellipsoid[b]].quat;
|
||||
MathExtra::q_to_exyz(qb,bx,by,bz);
|
||||
|
||||
// vector COM a - 3'-stacking site a
|
||||
ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
|
||||
ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
|
||||
ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
|
||||
// vector COM a - 5'-stacking site a
|
||||
ra_cst[0] = d_cst_x_5p*ax[0] + d_cst_y_5p*ay[0];
|
||||
ra_cst[1] = d_cst_x_5p*ax[1] + d_cst_y_5p*ay[1];
|
||||
ra_cst[2] = d_cst_x_5p*ax[2] + d_cst_y_5p*ay[2];
|
||||
|
||||
// vector COM b - 5'-stacking site b
|
||||
rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
|
||||
rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
|
||||
rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
|
||||
// vector COM b - 3'-stacking site b
|
||||
rb_cst[0] = d_cst_x_3p*bx[0] + d_cst_y_3p*by[0];
|
||||
rb_cst[1] = d_cst_x_3p*bx[1] + d_cst_y_3p*by[1];
|
||||
rb_cst[2] = d_cst_x_3p*bx[2] + d_cst_y_3p*by[2];
|
||||
|
||||
// vector 5'-stacking site b to 3'-stacking site a
|
||||
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
|
||||
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
|
||||
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
|
||||
// vector 5'-stacking site a to 3'-stacking site b
|
||||
delr_st[0] = x[b][0] + rb_cst[0] - x[a][0] - ra_cst[0];
|
||||
delr_st[1] = x[b][1] + rb_cst[1] - x[a][1] - ra_cst[1];
|
||||
delr_st[2] = x[b][2] + rb_cst[2] - x[a][2] - ra_cst[2];
|
||||
|
||||
// test for directionality of vector b to a
|
||||
tptofp = MFOxdna::is_3pto5p(delr_st,bz);
|
||||
|
||||
// if b to a is 5' to 3' we need to swap roles of a and b
|
||||
if (tptofp == -1) {
|
||||
|
||||
std::swap(a,b);
|
||||
std::swap(ax,bx);
|
||||
std::swap(ay,by);
|
||||
std::swap(az,bz);
|
||||
|
||||
}
|
||||
|
||||
// a now in 5' direction, b in 3' direction
|
||||
atype = type[a];
|
||||
btype = type[b];
|
||||
|
||||
// calculate again
|
||||
// vector COM a - 3'-stacking site a
|
||||
ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
|
||||
ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
|
||||
ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
|
||||
|
||||
// vector COM b - 5'-stacking site b
|
||||
rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
|
||||
rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
|
||||
rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
|
||||
|
||||
// vector 5'-stacking site b to 3'-stacking site a
|
||||
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
|
||||
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
|
||||
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
|
||||
|
||||
rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2];
|
||||
r_st = sqrt(rsq_st);
|
||||
rinv_st = 1.0/r_st;
|
||||
@ -352,10 +335,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
rb_cs[1] = d_cs_x*bx[1] + d_cs_z*bz[1];
|
||||
rb_cs[2] = d_cs_x*bx[2] + d_cs_z*bz[2];
|
||||
|
||||
// vector backbone site b to a
|
||||
delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
|
||||
delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
|
||||
delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
|
||||
// vector backbone site a to b
|
||||
delr_ss[0] = (x[b][0] + rb_cs[0] - x[a][0] - ra_cs[0]);
|
||||
delr_ss[1] = (x[b][1] + rb_cs[1] - x[a][1] - ra_cs[1]);
|
||||
delr_ss[2] = (x[b][2] + rb_cs[2] - x[a][2] - ra_cs[2]);
|
||||
|
||||
rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
|
||||
r_ss = sqrt(rsq_ss);
|
||||
@ -373,7 +356,7 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (f1) {
|
||||
|
||||
// theta5 angle and correction
|
||||
cost5p = MathExtra::dot3(delr_st_norm,az);
|
||||
cost5p = MathExtra::dot3(delr_st_norm,bz);
|
||||
if (cost5p > 1.0) cost5p = 1.0;
|
||||
if (cost5p < -1.0) cost5p = -1.0;
|
||||
theta5p = acos(cost5p);
|
||||
@ -384,18 +367,18 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
// early rejection criterium
|
||||
if (f4t5) {
|
||||
|
||||
cost6p = MathExtra::dot3(delr_st_norm,bz);
|
||||
cost6p = MathExtra::dot3(delr_st_norm,az);
|
||||
if (cost6p > 1.0) cost6p = 1.0;
|
||||
if (cost6p < -1.0) cost6p = -1.0;
|
||||
theta6p = acos(cost6p);
|
||||
|
||||
aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0];
|
||||
aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1];
|
||||
aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2];
|
||||
aux5p[0] = d5p_x * ax[0] + d5p_y * ay[0] + d5p_z * az[0];
|
||||
aux5p[1] = d5p_x * ax[1] + d5p_y * ay[1] + d5p_z * az[1];
|
||||
aux5p[2] = d5p_x * ax[2] + d5p_y * ay[2] + d5p_z * az[2];
|
||||
|
||||
aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0];
|
||||
aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1];
|
||||
aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2];
|
||||
aux3p[0] = d3p_x * bx[0] + d3p_y * by[0] + d3p_z * bz[0];
|
||||
aux3p[1] = d3p_x * bx[1] + d3p_y * by[1] + d3p_z * bz[1];
|
||||
aux3p[2] = d3p_x * bx[2] + d3p_y * by[2] + d3p_z * bz[2];
|
||||
|
||||
cost9 = MathExtra::dot3(delr_ss_norm,aux3p);
|
||||
if (cost9 > 1.0) cost9 = 1.0;
|
||||
@ -407,11 +390,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (cost10 < -1.0) cost10 = -1.0;
|
||||
theta10 = acos(cost10);
|
||||
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,by);
|
||||
if (cosphi1 > 1.0) cosphi1 = 1.0;
|
||||
if (cosphi1 < -1.0) cosphi1 = -1.0;
|
||||
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,by);
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
if (cosphi2 > 1.0) cosphi2 = 1.0;
|
||||
if (cosphi2 < -1.0) cosphi2 = -1.0;
|
||||
|
||||
@ -425,10 +408,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
b_st10[atype][btype], dtheta_st10_c[atype][btype]);
|
||||
|
||||
f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
|
||||
evdwl = f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
|
||||
@ -453,10 +436,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
b_st10[atype][btype], dtheta_st10_c[atype][btype])/sin(theta10);
|
||||
|
||||
df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
|
||||
// force, torque and virial contribution for forces between stacking sites
|
||||
@ -489,9 +472,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - bz[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -501,28 +484,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - az[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cst,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cst,delf,deltb);
|
||||
|
||||
@ -530,16 +512,16 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -547,8 +529,8 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
// NOTE: The virial is calculated on the 'molecular' basis.
|
||||
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
|
||||
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
if (evflag) ev_tally_xyz(b,a,nlocal,newton_bond,evdwl,
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// force, torque and virial contribution for forces between backbone sites
|
||||
|
||||
@ -596,9 +578,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - by[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -608,28 +590,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - ay[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cs,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cs,delf,deltb);
|
||||
|
||||
@ -637,22 +618,22 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
// increment virial only
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
if (evflag) ev_tally_xyz(b,a,nlocal,newton_bond,0.0,
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// pure torques not expressible as r x f
|
||||
|
||||
@ -667,11 +648,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (theta5p) {
|
||||
|
||||
tpair = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,az,t5pdir);
|
||||
MathExtra::cross3(delr_st_norm,bz,t5pdir);
|
||||
|
||||
delta[0] += t5pdir[0] * tpair;
|
||||
delta[1] += t5pdir[1] * tpair;
|
||||
delta[2] += t5pdir[2] * tpair;
|
||||
deltb[0] += t5pdir[0] * tpair;
|
||||
deltb[1] += t5pdir[1] * tpair;
|
||||
deltb[2] += t5pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -679,11 +660,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (theta6p) {
|
||||
|
||||
tpair = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,bz,t6pdir);
|
||||
MathExtra::cross3(delr_st_norm,az,t6pdir);
|
||||
|
||||
deltb[0] -= t6pdir[0] * tpair;
|
||||
deltb[1] -= t6pdir[1] * tpair;
|
||||
deltb[2] -= t6pdir[2] * tpair;
|
||||
delta[0] -= t6pdir[0] * tpair;
|
||||
delta[1] -= t6pdir[1] * tpair;
|
||||
delta[2] -= t6pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -693,9 +674,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
tpair = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,aux3p,t9dir);
|
||||
|
||||
delta[0] += t9dir[0] * tpair;
|
||||
delta[1] += t9dir[1] * tpair;
|
||||
delta[2] += t9dir[2] * tpair;
|
||||
deltb[0] += t9dir[0] * tpair;
|
||||
deltb[1] += t9dir[1] * tpair;
|
||||
deltb[2] += t9dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -705,9 +686,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
tpair = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,aux5p,t10dir);
|
||||
|
||||
deltb[0] -= t10dir[0] * tpair;
|
||||
deltb[1] -= t10dir[1] * tpair;
|
||||
deltb[2] -= t10dir[2] * tpair;
|
||||
delta[0] -= t10dir[0] * tpair;
|
||||
delta[1] -= t10dir[1] * tpair;
|
||||
delta[2] -= t10dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -715,11 +696,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (cosphi1) {
|
||||
|
||||
tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi1dir);
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi1dir);
|
||||
|
||||
delta[0] += cosphi1dir[0] * tpair;
|
||||
delta[1] += cosphi1dir[1] * tpair;
|
||||
delta[2] += cosphi1dir[2] * tpair;
|
||||
deltb[0] += cosphi1dir[0] * tpair;
|
||||
deltb[1] += cosphi1dir[1] * tpair;
|
||||
deltb[2] += cosphi1dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -727,27 +708,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (cosphi2) {
|
||||
|
||||
tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2;
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi2dir);
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi2dir);
|
||||
|
||||
deltb[0] -= cosphi2dir[0] * tpair;
|
||||
deltb[1] -= cosphi2dir[1] * tpair;
|
||||
deltb[2] -= cosphi2dir[2] * tpair;
|
||||
delta[0] -= cosphi2dir[0] * tpair;
|
||||
delta[1] -= cosphi2dir[1] * tpair;
|
||||
delta[2] -= cosphi2dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
// increment torques
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -1027,6 +1008,17 @@ void PairOxrna2Stk::coeff(int narg, char **arg)
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
atom_style hybrid bond ellipsoid oxdna required
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairOxrna2Stk::init_style()
|
||||
{
|
||||
if (!atom->style_match("oxdna")) {
|
||||
error->all(FLERR,"Must use 'atom_style hybrid bond ellipsoid oxdna' with pair style oxdna/stk, oxdna2/stk or oxrna2/stk");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
neighbor callback to inform pair style of neighbor list to use regular
|
||||
------------------------------------------------------------------------- */
|
||||
@ -31,6 +31,7 @@ class PairOxrna2Stk : public Pair {
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
@ -1,8 +1,9 @@
|
||||
This package implements 3 commands which can be used in a LAMMPS input
|
||||
This package implements 4 commands which can be used in a LAMMPS input
|
||||
script:
|
||||
|
||||
pair_style lj/sdk
|
||||
pair_style lj/sdk/coul/long
|
||||
pair_style lj/sdk/coul/msm
|
||||
angle_style sdk
|
||||
|
||||
These styles allow coarse grained MD simulations with the
|
||||
@ -13,7 +14,7 @@ lipids and charged amino acids.
|
||||
See the doc pages for these commands for details.
|
||||
|
||||
There are example scripts for using this package in
|
||||
examples/USER/cgsdk
|
||||
examples/PACKAGES/cgsdk
|
||||
|
||||
This is the second generation implementation reducing the the clutter
|
||||
of the previous version. For many systems with long range
|
||||
@ -13,7 +13,7 @@ on building LAMMPS with external libraries. The settings in the
|
||||
Makefile.lammps file in that directory must be correct for LAMMPS to
|
||||
build correctly with this package installed.
|
||||
|
||||
The files in the USER-COLVARS package folder implement an interface
|
||||
The files in the COLVARS package folder implement an interface
|
||||
between LAMMPS and Colvars, originally written by Axel Kohlmeyer
|
||||
(akohlmey@gmail.com) and maintained by Giacomo Fiorin
|
||||
(giacomo.fiorin@gmail.com).
|
||||
@ -36,7 +36,7 @@ which also includes citations to the articles documenting the various
|
||||
methods that make use Colvars.
|
||||
|
||||
There are also example scripts for using this package in the folder
|
||||
examples/USER/colvars, as well as the GitHub page for Colvars.
|
||||
examples/PACKAGES/colvars, as well as the GitHub page for Colvars.
|
||||
|
||||
Please contact Giacomo Fiorin (giacomo.fiorin@gmail.com) for questions
|
||||
regarding this package.
|
||||
3
src/COLVARS/colvarproxy_lammps_version.h
Normal file
3
src/COLVARS/colvarproxy_lammps_version.h
Normal file
@ -0,0 +1,3 @@
|
||||
#ifndef COLVARPROXY_VERSION
|
||||
#define COLVARPROXY_VERSION "2021-03-02"
|
||||
#endif
|
||||
@ -480,7 +480,7 @@ void FixColvars::one_time_init()
|
||||
memory->create(force_buf,3*num_coords,"colvars:force_buf");
|
||||
|
||||
if (me == 0) {
|
||||
std::vector<int> &tl = *(proxy->modify_atom_ids());
|
||||
std::vector<int> const &tl = *(proxy->get_atom_ids());
|
||||
inthash_t *hashtable=new inthash_t;
|
||||
inthash_init(hashtable, num_coords);
|
||||
idmap = (void *)hashtable;
|
||||
@ -563,7 +563,7 @@ void FixColvars::setup(int vflag)
|
||||
|
||||
if (me == 0) {
|
||||
|
||||
std::vector<int> &id = *(proxy->modify_atom_ids());
|
||||
std::vector<int> const &id = *(proxy->get_atom_ids());
|
||||
std::vector<int> &tp = *(proxy->modify_atom_types());
|
||||
std::vector<cvm::atom_pos> &cd = *(proxy->modify_atom_positions());
|
||||
std::vector<cvm::rvector> &of = *(proxy->modify_atom_total_forces());
|
||||
@ -836,7 +836,7 @@ void FixColvars::post_force(int /*vflag*/)
|
||||
|
||||
if (me == 0) {
|
||||
|
||||
std::vector<cvm::rvector> &fo = *(proxy->modify_atom_new_colvar_forces());
|
||||
std::vector<cvm::rvector> &fo = *(proxy->modify_atom_applied_forces());
|
||||
|
||||
double *fbuf = force_buf;
|
||||
for (int j=0; j < num_coords; ++j) {
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user