From 959da9de013d29d9e58bb4d2c4b6d8a48308bdc5 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Sat, 16 Feb 2019 14:49:44 +0000 Subject: [PATCH 1/8] Create a compute for the momentum of a group of atoms --- src/Makefile.list | 4 +-- src/compute_momentum.cpp | 59 ++++++++++++++++++++++++++++++++++++++++ src/compute_momentum.h | 36 ++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 2 deletions(-) create mode 100644 src/compute_momentum.cpp create mode 100644 src/compute_momentum.h diff --git a/src/Makefile.list b/src/Makefile.list index 65bbebca09..6e4c9726a6 100644 --- a/src/Makefile.list +++ b/src/Makefile.list @@ -7,9 +7,9 @@ SHELL = /bin/sh ROOT = lmp EXE = $(ROOT)_$@ -SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp +SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_momentum.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp -INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h +INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_momentum.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h OBJ = $(SRC:.cpp=.o) diff --git a/src/compute_momentum.cpp b/src/compute_momentum.cpp new file mode 100644 index 0000000000..f8fc0ec6ab --- /dev/null +++ b/src/compute_momentum.cpp @@ -0,0 +1,59 @@ + +#include +#include "compute_momentum.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "domain.h" +#include "group.h" +#include "error.h" + +using namespace LAMMPS_NS; + +ComputeMomentum::ComputeMomentum(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute momentum command"); + + vector_flag = 1; + size_vector = 3; + extvector = 1; + vector = new double[size_vector]; +} + +ComputeMomentum::~ComputeMomentum() { + delete[] vector; +} + +void ComputeMomentum::init() +{ +} + +void ComputeMomentum::compute_vector() +{ + invoked_vector = update->ntimestep; + + double **v = atom->v; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + + double mom[3] = {0.0, 0.0, 0.0}; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + for(int j = 0; j < 3; ++j) + mom[j] += rmass[i] * v[i][j]; + } + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + for(int j = 0; j < 3; ++j) + mom[j] += mass[type[i]] * v[i][j]; + } + + MPI_Allreduce(&mom, vector, 3, MPI_DOUBLE, MPI_SUM, world); +} diff --git a/src/compute_momentum.h b/src/compute_momentum.h new file mode 100644 index 0000000000..1e0c52c045 --- /dev/null +++ b/src/compute_momentum.h @@ -0,0 +1,36 @@ +#ifdef COMPUTE_CLASS + +ComputeStyle(momentum,ComputeMomentum) + +#else + +#ifndef LMP_COMPUTE_MOMENTUM_H +#define LMP_COMPUTE_MOMENTUM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeMomentum : public Compute { + public: + ComputeMomentum(class LAMMPS *, int, char **); + virtual ~ComputeMomentum(); + + virtual void init(); + virtual void compute_vector(); +}; + +} + +#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. + +*/ From 26347ec80ce8a33a4162d5d5275d8be52d6666fa Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Wed, 19 Jun 2019 13:55:10 +0100 Subject: [PATCH 2/8] Add docs for compute momentum --- doc/src/Commands_compute.txt | 1 + doc/src/compute.txt | 1 + doc/src/compute_momentum.txt | 45 ++++++++++++++++++++++++++++++++++++ doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + 5 files changed, 49 insertions(+) create mode 100644 doc/src/compute_momentum.txt diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index f566702609..0817f44adf 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -80,6 +80,7 @@ KOKKOS, o = USER-OMP, t = OPT. "meso/e/atom"_compute_meso_e_atom.html, "meso/rho/atom"_compute_meso_rho_atom.html, "meso/t/atom"_compute_meso_t_atom.html, +"momentum"_compute_momentum.html, "msd"_compute_msd.html, "msd/chunk"_compute_msd_chunk.html, "msd/nongauss"_compute_msd_nongauss.html, diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 87dbee57d6..12c6b141b7 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -229,6 +229,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "meso/e/atom"_compute_meso_e_atom.html - "meso/rho/atom"_compute_meso_rho_atom.html - "meso/t/atom"_compute_meso_t_atom.html - +"momentum"_compute_momentum.html - translational momentum "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt new file mode 100644 index 0000000000..4db171d42d --- /dev/null +++ b/doc/src/compute_momentum.txt @@ -0,0 +1,45 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute momentum command :h3 + +[Syntax:] + +compute ID group-ID momentum :pre + +ID, group-ID are documented in "compute"_compute.html command +momentum = style name of this compute command :ul + +[Examples:] + +compute 1 all momentum :pre + +[Description:] + +Define a computation that calculates the translational momentum +of a group of particles. + +The momentum of each particles is computed as m v, where m and v are +the mass and velocity of the particle. + +[Output info:] + +This compute calculates a global vector (the summed momentum) on +length 3. This value can be used by any command that uses a global +vector value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The vector value calculated by this compute is "extensive". The vector +value will be in momentum "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +[Default:] none diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 926b8da222..1c914365b1 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -57,6 +57,7 @@ Computes :h1 compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom + compute_momentum compute_msd compute_msd_chunk compute_msd_nongauss diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 2738c9b051..816acd3521 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -468,6 +468,7 @@ compute_ke_rigid.html compute_meso_e_atom.html compute_meso_rho_atom.html compute_meso_t_atom.html +compute_momentum.html compute_msd.html compute_msd_chunk.html compute_msd_nongauss.html From 1bb18ebde4dec8dab43741b4b9c005f732200214 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Fri, 21 Jun 2019 15:50:52 +0100 Subject: [PATCH 3/8] rollback unneeded change to Makefile.list per review --- src/Makefile.list | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Makefile.list b/src/Makefile.list index 6e4c9726a6..65bbebca09 100644 --- a/src/Makefile.list +++ b/src/Makefile.list @@ -7,9 +7,9 @@ SHELL = /bin/sh ROOT = lmp EXE = $(ROOT)_$@ -SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_momentum.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp +SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp -INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_momentum.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h +INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h OBJ = $(SRC:.cpp=.o) From e9e7d995b270fd4abf7041474fd0c667453f4e99 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 1 Jul 2019 11:37:13 +0100 Subject: [PATCH 4/8] move to user-misc --- src/USER-MISC/README | 1 + src/{ => USER-MISC}/compute_momentum.cpp | 0 src/{ => USER-MISC}/compute_momentum.h | 0 3 files changed, 1 insertion(+) rename src/{ => USER-MISC}/compute_momentum.cpp (100%) rename src/{ => USER-MISC}/compute_momentum.h (100%) diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 219e19673d..7c48640e2a 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -31,6 +31,7 @@ compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 +compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019 compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 diff --git a/src/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp similarity index 100% rename from src/compute_momentum.cpp rename to src/USER-MISC/compute_momentum.cpp diff --git a/src/compute_momentum.h b/src/USER-MISC/compute_momentum.h similarity index 100% rename from src/compute_momentum.h rename to src/USER-MISC/compute_momentum.h From fb5e7e6f3badd73feb79768d6f4dbd0ed0c1c2de Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 1 Jul 2019 12:06:40 +0100 Subject: [PATCH 5/8] add note about USER-MISC package --- doc/src/compute_momentum.txt | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt index 4db171d42d..fc5243583e 100644 --- a/doc/src/compute_momentum.txt +++ b/doc/src/compute_momentum.txt @@ -36,9 +36,13 @@ output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector value calculated by this compute is "extensive". The vector -value will be in momentum "units"_units.html. +value will be in mass*velocity "units"_units.html. -[Restrictions:] none +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] From 32728375b97714dbbe42e68fc2c14b5a0c770aa8 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 1 Jul 2019 13:39:32 +0100 Subject: [PATCH 6/8] add test script for compute momentum --- examples/USER/misc/momentum/in.momentum | 65 +++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 examples/USER/misc/momentum/in.momentum diff --git a/examples/USER/misc/momentum/in.momentum b/examples/USER/misc/momentum/in.momentum new file mode 100644 index 0000000000..5adcbfeff6 --- /dev/null +++ b/examples/USER/misc/momentum/in.momentum @@ -0,0 +1,65 @@ +# Test compute momentum with by comparing it's output with compute reduce + +# Script will output the two computations of the total momentum as +# thermo vars - they should be identical + +# 3D LJ Poiseuille flow simulation +dimension 3 +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry +lattice hcp 0.5 +region box block 0 20 0 10 0 10 +create_box 3 box +create_atoms 1 box + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 + +# LJ potentials +pair_style lj/cut 1.0 +pair_coeff * * 1.0 1.0 1.0 + +# define groups +region 1 block INF INF INF 1.0 INF INF +group lower region 1 +region 2 block INF INF 9.0 INF INF INF +group upper region 2 +group boundary union lower upper +group liquid subtract all boundary + +set group lower type 2 +set group upper type 3 + +# temperature settings +compute mobile liquid temp +velocity liquid create 1.0 100 temp mobile +fix 1 all nve +fix 2 liquid temp/rescale 200 1.0 2.0 0.02 1.0 +fix_modify 2 temp mobile + +velocity boundary set 0.0 0.0 0.0 +fix 4 lower setforce 0.0 0.0 0.0 +fix 5 upper setforce 0.0 0.0 0.0 +fix 6 liquid addforce 0.1 0.0 0.0 + +# Compute total momentum +compute mom liquid momentum + +# Comparison (momentum variables + compute reduce) +variable mx atom mass*vx +variable my atom mass*vy +variable mz atom mass*vz +compute mom_red liquid reduce sum v_mx v_my v_mz + +# Run +timestep 0.003 +thermo 1000 +thermo_style custom step c_mom_red[*] c_mom[*] + +run 100000 From c831cee21dad5e5009960498930e0543f692c2a2 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 22 Jul 2019 09:46:01 +0100 Subject: [PATCH 7/8] Fix typos in documentation --- doc/src/compute_momentum.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt index fc5243583e..2c6ec78cf3 100644 --- a/doc/src/compute_momentum.txt +++ b/doc/src/compute_momentum.txt @@ -29,7 +29,7 @@ the mass and velocity of the particle. [Output info:] -This compute calculates a global vector (the summed momentum) on +This compute calculates a global vector (the summed momentum) of length 3. This value can be used by any command that uses a global vector value from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output From 4289dbb78d3fe8267e2a91881e30a92c6dbbd461 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 22:28:29 -0400 Subject: [PATCH 8/8] clean up includes and whitespace --- src/USER-MISC/compute_momentum.cpp | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp index f8fc0ec6ab..541b52d9c0 100644 --- a/src/USER-MISC/compute_momentum.cpp +++ b/src/USER-MISC/compute_momentum.cpp @@ -1,12 +1,9 @@ -#include #include "compute_momentum.h" +#include #include "atom.h" -#include "update.h" -#include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; @@ -45,14 +42,14 @@ void ComputeMomentum::compute_vector() if (rmass) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - for(int j = 0; j < 3; ++j) - mom[j] += rmass[i] * v[i][j]; + for(int j = 0; j < 3; ++j) + mom[j] += rmass[i] * v[i][j]; } } else { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) - for(int j = 0; j < 3; ++j) - mom[j] += mass[type[i]] * v[i][j]; + for(int j = 0; j < 3; ++j) + mom[j] += mass[type[i]] * v[i][j]; } MPI_Allreduce(&mom, vector, 3, MPI_DOUBLE, MPI_SUM, world);