Loading doc/src/fix_smd.txt +5 −0 Original line number Diff line number Diff line Loading @@ -101,6 +101,11 @@ See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial no} The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. Loading src/USER-MISC/fix_smd.cpp +29 −0 Original line number Diff line number Diff line Loading @@ -58,6 +58,7 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) : extvector = 1; respa_level_support = 1; ilevel_respa = 0; virial_flag = 1; int argoffs=3; if (strcmp(arg[argoffs],"cvel") == 0) { Loading Loading @@ -181,6 +182,11 @@ void FixSMD::setup(int vflag) void FixSMD::post_force(int vflag) { // energy and virial setup if (vflag) v_setup(vflag); else evflag = 0; if (styleflag & SMD_TETHER) smd_tether(); else smd_couple(); Loading Loading @@ -238,12 +244,15 @@ void FixSMD::smd_tether() // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal double **x = atom->x; double **f = atom->f; imageint *image = atom->image; int *mask = atom->mask; int *type = atom->type; double *mass = atom->mass; double *rmass = atom->rmass; double massfrac; double unwrap[3],v[6]; int nlocal = atom->nlocal; ftotal[0] = ftotal[1] = ftotal[2] = 0.0; Loading @@ -259,6 +268,16 @@ void FixSMD::smd_tether() ftotal[0] -= fx*massfrac; ftotal[1] -= fy*massfrac; ftotal[2] -= fz*massfrac; if (evflag) { domain->unmap(x[i],image[i],unwrap); v[0] = fx*massfrac*unwrap[0]; v[1] = fy*massfrac*unwrap[1]; v[2] = fz*massfrac*unwrap[2]; v[3] = fx*massfrac*unwrap[1]; v[4] = fx*massfrac*unwrap[2]; v[5] = fy*massfrac*unwrap[2]; v_tally(i, v); } } } else { for (int i = 0; i < nlocal; i++) Loading @@ -270,6 +289,16 @@ void FixSMD::smd_tether() ftotal[0] -= fx*massfrac; ftotal[1] -= fy*massfrac; ftotal[2] -= fz*massfrac; if (evflag) { domain->unmap(x[i],image[i],unwrap); v[0] = fx*massfrac*unwrap[0]; v[1] = fy*massfrac*unwrap[1]; v[2] = fz*massfrac*unwrap[2]; v[3] = fx*massfrac*unwrap[1]; v[4] = fx*massfrac*unwrap[2]; v[5] = fy*massfrac*unwrap[2]; v_tally(i, v); } } } } Loading Loading
doc/src/fix_smd.txt +5 −0 Original line number Diff line number Diff line Loading @@ -101,6 +101,11 @@ See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. The "fix_modify"_fix_modify.html {virial} option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial no} The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. Loading
src/USER-MISC/fix_smd.cpp +29 −0 Original line number Diff line number Diff line Loading @@ -58,6 +58,7 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) : extvector = 1; respa_level_support = 1; ilevel_respa = 0; virial_flag = 1; int argoffs=3; if (strcmp(arg[argoffs],"cvel") == 0) { Loading Loading @@ -181,6 +182,11 @@ void FixSMD::setup(int vflag) void FixSMD::post_force(int vflag) { // energy and virial setup if (vflag) v_setup(vflag); else evflag = 0; if (styleflag & SMD_TETHER) smd_tether(); else smd_couple(); Loading Loading @@ -238,12 +244,15 @@ void FixSMD::smd_tether() // apply restoring force to atoms in group // f = -k*(r-r0)*mass/masstotal double **x = atom->x; double **f = atom->f; imageint *image = atom->image; int *mask = atom->mask; int *type = atom->type; double *mass = atom->mass; double *rmass = atom->rmass; double massfrac; double unwrap[3],v[6]; int nlocal = atom->nlocal; ftotal[0] = ftotal[1] = ftotal[2] = 0.0; Loading @@ -259,6 +268,16 @@ void FixSMD::smd_tether() ftotal[0] -= fx*massfrac; ftotal[1] -= fy*massfrac; ftotal[2] -= fz*massfrac; if (evflag) { domain->unmap(x[i],image[i],unwrap); v[0] = fx*massfrac*unwrap[0]; v[1] = fy*massfrac*unwrap[1]; v[2] = fz*massfrac*unwrap[2]; v[3] = fx*massfrac*unwrap[1]; v[4] = fx*massfrac*unwrap[2]; v[5] = fy*massfrac*unwrap[2]; v_tally(i, v); } } } else { for (int i = 0; i < nlocal; i++) Loading @@ -270,6 +289,16 @@ void FixSMD::smd_tether() ftotal[0] -= fx*massfrac; ftotal[1] -= fy*massfrac; ftotal[2] -= fz*massfrac; if (evflag) { domain->unmap(x[i],image[i],unwrap); v[0] = fx*massfrac*unwrap[0]; v[1] = fy*massfrac*unwrap[1]; v[2] = fz*massfrac*unwrap[2]; v[3] = fx*massfrac*unwrap[1]; v[4] = fx*massfrac*unwrap[2]; v[5] = fy*massfrac*unwrap[2]; v_tally(i, v); } } } } Loading
