From 2e0bc27646e800823ed0389518751e8392977e9a Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 29 Jan 2025 15:24:50 -0700 Subject: [PATCH 01/12] adding bpm energy proxy --- doc/src/bond_bpm_spring.rst | 12 +- doc/src/pair_bpm_spring.rst | 4 + src/BPM/bond_bpm_spring.cpp | 14 +- src/BPM/bond_bpm_spring_plastic.cpp | 458 ++++++++++++++++++++++++++++ src/BPM/bond_bpm_spring_plastic.h | 53 ++++ src/BPM/pair_bpm_spring.cpp | 24 +- 6 files changed, 547 insertions(+), 18 deletions(-) create mode 100644 src/BPM/bond_bpm_spring_plastic.cpp create mode 100644 src/BPM/bond_bpm_spring_plastic.h diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 0a43a62159..cde447825a 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -214,12 +214,12 @@ for an overview of LAMMPS output options. The vector or array will be floating point values that correspond to the specified attribute. -The single() function of this bond style returns 0.0 for the energy -of a bonded interaction, since energy is not conserved in these -dissipative potentials. The single() function also calculates an -extra bond quantity, the initial distance :math:`r_0`. This -extra quantity can be accessed by the -:doc:`compute bond/local ` command as *b1*\ . +The potential energy and the single() function of this bond style returns :math:`k (r - r_0)^2 / 2` +for a proxy of the energy of a bonded interaction, ignoring any volumetric/smoothing +factors or dissipative forces. The single() function also calculates an +extra bond quantity, the initial distance :math:`r_0`. This extra quantity +can be accessed by the :doc:`compute bond/local ` +command as *b1*\ . Restrictions """""""""""" diff --git a/doc/src/pair_bpm_spring.rst b/doc/src/pair_bpm_spring.rst index 068efff577..530be8dfba 100644 --- a/doc/src/pair_bpm_spring.rst +++ b/doc/src/pair_bpm_spring.rst @@ -117,6 +117,10 @@ This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*, *middle*, *outer* keywords. +The potential energy and the single() function of this pair style returns +:math:`k (r - r_c)^2 / 2 + k_a (r - r_c)^4 / 4` for a proxy +of the energy of a pair interaction, ignoring any smoothing or dissipative forces. + ---------- Restrictions diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index 0de93fea31..b58b73a43b 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -197,7 +197,7 @@ void BondBPMSpring::compute(int eflag, int vflag) int i1, i2, itmp, n, type; double delx, dely, delz, delvx, delvy, delvz; - double e, rsq, r, r0, rinv, smooth, fbond, dot; + double e, rsq, r, r0, rinv, smooth, fbond, ebond, dot; double vol_sum, vol0_sum, vol_temp; ev_init(eflag, vflag); @@ -264,7 +264,9 @@ void BondBPMSpring::compute(int eflag, int vflag) if (normalize_flag) fbond = -k[type] * e; else - fbond = k[type] * (r0 - r); + fbond = -k[type] * (r - r0); + + if (eflag) ebond = -0.5 * fbond * (r - r0); if (volume_flag) { vol_sum = vol[i1] + vol[i2]; @@ -300,7 +302,7 @@ void BondBPMSpring::compute(int eflag, int vflag) f[i2][2] -= delz * fbond; } - if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, fbond, delx, dely, delz); + if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz); } // Update vol0 to account for any broken bonds @@ -574,7 +576,9 @@ double BondBPMSpring::single(int type, double rsq, int i, int j, double &fforce) if (normalize_flag) fforce = -k[type] * e; else - fforce = k[type] * (r0 - r); + fforce = -k[type] * (r - r0); + + double ebond = -0.5 * fforce * (r - r0); if (volume_flag) { double invdim = 1.0 / domain->dimension; @@ -610,7 +614,7 @@ double BondBPMSpring::single(int type, double rsq, int i, int j, double &fforce) svector[0] = r0; - return 0.0; + return ebond; } /* ---------------------------------------------------------------------- */ diff --git a/src/BPM/bond_bpm_spring_plastic.cpp b/src/BPM/bond_bpm_spring_plastic.cpp new file mode 100644 index 0000000000..1ecc3637d9 --- /dev/null +++ b/src/BPM/bond_bpm_spring_plastic.cpp @@ -0,0 +1,458 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "bond_bpm_spring_plastic.h" + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_bond_history.h" +#include "force.h" +#include "memory.h" +#include "neighbor.h" + +#include +#include + +static constexpr double EPSILON = 1e-10; + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondBPMSpringPlastic::BondBPMSpringPlastic(LAMMPS *_lmp) : + BondBPM(_lmp), k(nullptr), eplastic(nullptr), ecrit(nullptr), gamma(nullptr) +{ + partial_flag = 1; + smooth_flag = 1; + normalize_flag = 0; + writedata = 0; + + nhistory = 2; + update_flag = 1; + id_fix_bond_history = utils::strdup("HISTORY_BPM_SPRING_PLASTIC"); + + single_extra = 2; + svector = new double[2]; +} + +/* ---------------------------------------------------------------------- */ + +BondBPMSpringPlastic::~BondBPMSpringPlastic() +{ + delete[] svector; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(ecrit); + memory->destroy(gamma); + memory->destroy(eplastic); + } +} + +/* ---------------------------------------------------------------------- + Store data for a single bond - if bond added after LAMMPS init (e.g. pour) +------------------------------------------------------------------------- */ + +double BondBPMSpringPlastic::store_bond(int n, int i, int j) +{ + double delx, dely, delz, r; + double **x = atom->x; + double **bondstore = fix_bond_history->bondstore; + tagint *tag = atom->tag; + + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + + r = sqrt(delx * delx + dely * dely + delz * delz); + bondstore[n][0] = r; + + if (i < atom->nlocal) { + for (int m = 0; m < atom->num_bond[i]; m++) { + if (atom->bond_atom[i][m] == tag[j]) { + fix_bond_history->update_atom_value(i, m, 0, r); + fix_bond_history->update_atom_value(i, m, 1, 0); + } + } + } + + if (j < atom->nlocal) { + for (int m = 0; m < atom->num_bond[j]; m++) { + if (atom->bond_atom[j][m] == tag[i]) { + fix_bond_history->update_atom_value(j, m, 0, r); + fix_bond_history->update_atom_value(j, m, 1, 0); + } + } + } + + return r; +} + +/* ---------------------------------------------------------------------- + Store data for all bonds called once +------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::store_data() +{ + int i, j, m, type; + double delx, dely, delz, r; + double **x = atom->x; + int **bond_type = atom->bond_type; + + for (i = 0; i < atom->nlocal; i++) { + for (m = 0; m < atom->num_bond[i]; m++) { + type = bond_type[i][m]; + + //Skip if bond was turned off + if (type < 0) continue; + + // map to find index n + j = atom->map(atom->bond_atom[i][m]); + if (j == -1) error->one(FLERR, "Atom missing in BPM bond"); + + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + + // Get closest image in case bonded with ghost + domain->minimum_image(delx, dely, delz); + r = sqrt(delx * delx + dely * dely + delz * delz); + + fix_bond_history->update_atom_value(i, m, 0, r); + fix_bond_history->update_atom_value(i, m, 1, 0); + } + } + + fix_bond_history->post_neighbor(); +} + +/* ---------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::compute(int eflag, int vflag) +{ + if (!fix_bond_history->stored_flag) { + fix_bond_history->stored_flag = true; + store_data(); + } + + if (hybrid_flag) fix_bond_history->compress_history(); + + int i1, i2, itmp, n, type; + double delx, dely, delz, delvx, delvy, delvz; + double e, ep, rsq, r, r0, rinv, smooth, fbond, dot; + + ev_init(eflag, vflag); + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + tagint *tag = atom->tag; + int **bondlist = neighbor->bondlist; + int nbondlist = neighbor->nbondlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + double **bondstore = fix_bond_history->bondstore; + + for (n = 0; n < nbondlist; n++) { + + // skip bond if already broken + if (bondlist[n][2] <= 0) continue; + + i1 = bondlist[n][0]; + i2 = bondlist[n][1]; + type = bondlist[n][2]; + r0 = bondstore[n][0]; + ep = bondstore[n][1]; + + // Ensure pair is always ordered to ensure numerical operations + // are identical to minimize the possibility that a bond straddling + // an mpi grid (newton off) doesn't break on one proc but not the other + if (tag[i2] < tag[i1]) { + itmp = i1; + i1 = i2; + i2 = itmp; + } + + // If bond hasn't been set - should be initialized to zero + if (r0 < EPSILON || std::isnan(r0)) r0 = store_bond(n, i1, i2); + + delx = x[i1][0] - x[i2][0]; + dely = x[i1][1] - x[i2][1]; + delz = x[i1][2] - x[i2][2]; + + rsq = delx * delx + dely * dely + delz * delz; + r = sqrt(rsq); + e = (r - r0) / r0; + + if ((fabs(e) > ecrit[type]) && break_flag) { + bondlist[n][2] = 0; + process_broken(i1, i2); + continue; + } + + if (e > (ep + eplastic[type])) { + ep = e - eplastic[type]; + bondstore[n][1] = ep; + } + + if (e < (ep - eplastic[type])) { + ep = e + eplastic[type]; + bondstore[n][1] = ep; + } + + rinv = 1.0 / r; + if (normalize_flag) + fbond = -k[type] * (e - ep); + else + fbond = -k[type] * (r - (1.0 + ep) * r0); + + delvx = v[i1][0] - v[i2][0]; + delvy = v[i1][1] - v[i2][1]; + delvz = v[i1][2] - v[i2][2]; + dot = delx * delvx + dely * delvy + delz * delvz; + fbond -= gamma[type] * dot * rinv; + fbond *= rinv; + + if (smooth_flag) { + smooth = (r - r0) / (r0 * ecrit[type]); + smooth *= smooth; + smooth *= smooth; + smooth *= smooth; + smooth = 1 - smooth; + fbond *= smooth; + } + + if (newton_bond || i1 < nlocal) { + f[i1][0] += delx * fbond; + f[i1][1] += dely * fbond; + f[i1][2] += delz * fbond; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= delx * fbond; + f[i2][1] -= dely * fbond; + f[i2][2] -= delz * fbond; + } + + if (evflag) ev_tally(i1, i2, nlocal, newton_bond, 0.0, fbond, delx, dely, delz); + } + + if (hybrid_flag) fix_bond_history->uncompress_history(); +} + +/* ---------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::allocate() +{ + allocated = 1; + const int np1 = atom->nbondtypes + 1; + + memory->create(k, np1, "bond:k"); + memory->create(ecrit, np1, "bond:ecrit"); + memory->create(gamma, np1, "bond:gamma"); + memory->create(eplastic, np1, "bond:eplastic"); + + memory->create(setflag, np1, "bond:setflag"); + for (int i = 1; i < np1; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::coeff(int narg, char **arg) +{ + if (narg != 5) + error->all(FLERR, "Incorrect args for bond coefficients"); + if (!allocated) allocate(); + + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); + + double k_one = utils::numeric(FLERR, arg[1], false, lmp); + double ecrit_one = utils::numeric(FLERR, arg[2], false, lmp); + double gamma_one = utils::numeric(FLERR, arg[3], false, lmp); + double eplastic_one = utils::numeric(FLERR, arg[4], false, lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = k_one; + ecrit[i] = ecrit_one; + gamma[i] = gamma_one; + eplastic[i] = eplastic_one; + setflag[i] = 1; + count++; + + if (1.0 + ecrit[i] > max_stretch) max_stretch = 1.0 + ecrit[i]; + } + + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + check for correct settings and create fix +------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::init_style() +{ + BondBPM::init_style(); + + if (comm->ghost_velocity == 0) + error->all(FLERR, "Bond bpm/spring requires ghost atoms store velocity"); +} + +/* ---------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::settings(int narg, char **arg) +{ + BondBPM::settings(narg, arg); + + int iarg; + for (std::size_t i = 0; i < leftover_iarg.size(); i++) { + iarg = leftover_iarg[i]; + if (strcmp(arg[iarg], "smooth") == 0) { + if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for smooth"); + smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + i += 1; + } else if (strcmp(arg[iarg], "normalize") == 0) { + if (iarg + 1 > narg) + error->all(FLERR, "Illegal bond bpm command, missing option for normalize"); + normalize_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp); + i += 1; + } else { + error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]); + } + } + + if (smooth_flag && !break_flag) + error->all(FLERR, "Illegal bond bpm command, must turn off smoothing with break no option"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::write_restart(FILE *fp) +{ + BondBPM::write_restart(fp); + write_restart_settings(fp); + + fwrite(&k[1], sizeof(double), atom->nbondtypes, fp); + fwrite(&ecrit[1], sizeof(double), atom->nbondtypes, fp); + fwrite(&gamma[1], sizeof(double), atom->nbondtypes, fp); + fwrite(&eplastic[1], sizeof(double), atom->nbondtypes, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::read_restart(FILE *fp) +{ + BondBPM::read_restart(fp); + read_restart_settings(fp); + allocate(); + + if (comm->me == 0) { + utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); + utils::sfread(FLERR, &ecrit[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); + utils::sfread(FLERR, &gamma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); + utils::sfread(FLERR, &eplastic[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); + } + MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&ecrit[1], atom->nbondtypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&gamma[1], atom->nbondtypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&eplastic[1], atom->nbondtypes, MPI_DOUBLE, 0, world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::write_restart_settings(FILE *fp) +{ + fwrite(&smooth_flag, sizeof(int), 1, fp); + fwrite(&normalize_flag, sizeof(int), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void BondBPMSpringPlastic::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR, &smooth_flag, sizeof(int), 1, fp, nullptr, error); + utils::sfread(FLERR, &normalize_flag, sizeof(int), 1, fp, nullptr, error); + } + MPI_Bcast(&smooth_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&normalize_flag, 1, MPI_INT, 0, world); +} + +/* ---------------------------------------------------------------------- */ + +double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &fforce) +{ + if (type <= 0) return 0.0; + + double r0, ep; + for (int n = 0; n < atom->num_bond[i]; n++) { + if (atom->bond_atom[i][n] == atom->tag[j]) { + r0 = fix_bond_history->get_atom_value(i, n, 0); + ep = fix_bond_history->get_atom_value(i, n, 1); + } + } + + double r = sqrt(rsq); + double rinv = 1.0 / r; + double e = (r - r0) / r0; + + if (normalize_flag) + fforce = -k[type] * (e - ep); + else + fforce = -k[type] * (r - (1.0 + ep) * r0); + + double **x = atom->x; + double **v = atom->v; + double delx = x[i][0] - x[j][0]; + double dely = x[i][1] - x[j][1]; + double delz = x[i][2] - x[j][2]; + double delvx = v[i][0] - v[j][0]; + double delvy = v[i][1] - v[j][1]; + double delvz = v[i][2] - v[j][2]; + double dot = delx * delvx + dely * delvy + delz * delvz; + fforce -= gamma[type] * dot * rinv; + fforce *= rinv; + + if (smooth_flag) { + double smooth = (r - r0) / (r0 * ecrit[type]); + smooth *= smooth; + smooth *= smooth; + smooth *= smooth; + smooth = 1 - smooth; + fforce *= smooth; + } + + // set single_extra quantities + + svector[0] = r0; + svector[0] = (1.0 + ep) * r0; + + return 0.0; +} diff --git a/src/BPM/bond_bpm_spring_plastic.h b/src/BPM/bond_bpm_spring_plastic.h new file mode 100644 index 0000000000..0565d5ce01 --- /dev/null +++ b/src/BPM/bond_bpm_spring_plastic.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BOND_CLASS +// clang-format off +BondStyle(bpm/spring/plastic,BondBPMSpringPlastic); +// clang-format on +#else + +#ifndef LMP_BOND_BPM_SPRING_PLASTIC_H +#define LMP_BOND_BPM_SPRING_PLASTIC_H + +#include "bond_bpm.h" + +namespace LAMMPS_NS { + +class BondBPMSpringPlastic : public BondBPM { + public: + BondBPMSpringPlastic(class LAMMPS *); + ~BondBPMSpringPlastic() override; + void compute(int, int) override; + void coeff(int, char **) override; + void init_style() override; + void settings(int, char **) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_restart_settings(FILE *) override; + void read_restart_settings(FILE *) override; + double single(int, double, int, int, double &) override; + + protected: + double *k, *eplastic, *ecrit, *gamma; + int smooth_flag, normalize_flag; + + void allocate(); + void store_data(); + double store_bond(int, int, int); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/src/BPM/pair_bpm_spring.cpp b/src/BPM/pair_bpm_spring.cpp index bf58b9e515..e69b8c7879 100644 --- a/src/BPM/pair_bpm_spring.cpp +++ b/src/BPM/pair_bpm_spring.cpp @@ -54,7 +54,7 @@ void PairBPMSpring::compute(int eflag, int vflag) { int i, j, ii, jj, inum, jnum, itype, jtype; double xtmp, ytmp, ztmp, delx, dely, delz, dr, evdwl, fpair; - double r, rsq, rinv, factor_lj; + double r, rsq, rinv, fa, factor_lj; int *ilist, *jlist, *numneigh, **firstneigh; double vxtmp, vytmp, vztmp, delvx, delvy, delvz, dot, smooth; @@ -112,8 +112,12 @@ void PairBPMSpring::compute(int eflag, int vflag) dr = r - cut[itype][jtype]; fpair = -k[itype][jtype] * dr; - if (anharmonic_flag) - fpair += -ka[itype][jtype] * dr * dr * dr; + if (eflag) evdwl = -0.5 * fpair * dr; + if (anharmonic_flag) { + fa = -ka[itype][jtype] * dr * dr * dr; + fpair += fa; + if (eflag) evdwl += -0.25 * fa * dr; + } smooth = rsq / cutsq[itype][jtype]; smooth *= smooth; @@ -126,7 +130,7 @@ void PairBPMSpring::compute(int eflag, int vflag) fpair -= gamma[itype][jtype] * dot * smooth * rinv; fpair *= factor_lj * rinv; - if (eflag) evdwl = 0.0; + if (eflag) evdwl *= factor_lj; f[i][0] += delx * fpair; f[i][1] += dely * fpair; @@ -378,8 +382,13 @@ double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq, dou dr = r - cut[itype][jtype]; fpair = -k[itype][jtype] * dr; - if (anharmonic_flag) - fpair += -ka[itype][jtype] * dr * dr * dr; + double energy = -0.5 * fpair * (r - cut[itype][jtype]); + + if (anharmonic_flag) { + double fa = -ka[itype][jtype] * dr * dr * dr; + fpair += fa; + energy += -0.25 * fa * dr; + } smooth = rsq / cutsq[itype][jtype]; smooth *= smooth; @@ -394,7 +403,8 @@ double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq, dou fpair -= gamma[itype][jtype] * dot * rinv * smooth; fpair *= factor_lj; + energy *= factor_lj; fforce = fpair; - return 0.0; + return energy; } From 3e587685b6bae174e66f61033945eef6cfb7b2e5 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 29 Jan 2025 15:25:55 -0700 Subject: [PATCH 02/12] Initial plastic BPM bond style --- src/.gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 9431d55913..768730ba6c 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -374,6 +374,8 @@ /bond_bpm_rotational.h /bond_bpm_spring.cpp /bond_bpm_spring.h +/bond_bpm_spring_plastic.cpp +/bond_bpm_spring_plastic.h /compute_nbond_atom.cpp /compute_nbond_atom.h /fix_nve_bpm_sphere.cpp From 080df8cf747c72ad9f6384e8f0eb5a8990bf79ba Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 30 Jan 2025 11:22:06 -0700 Subject: [PATCH 03/12] BPM plastic citation info --- src/BPM/bond_bpm_spring_plastic.cpp | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/BPM/bond_bpm_spring_plastic.cpp b/src/BPM/bond_bpm_spring_plastic.cpp index 1ecc3637d9..07619a8dfc 100644 --- a/src/BPM/bond_bpm_spring_plastic.cpp +++ b/src/BPM/bond_bpm_spring_plastic.cpp @@ -14,6 +14,7 @@ #include "bond_bpm_spring_plastic.h" #include "atom.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" @@ -29,6 +30,18 @@ static constexpr double EPSILON = 1e-10; using namespace LAMMPS_NS; +static const char cite_bpm_plastic[] = + "BPM/spring/plastic bond style: doi:10.1016/j.powtec.2024.120563\n\n" + "@Article{Clemmer2025,\n" + " author = {Clemmer, Joel T. and Lechman, Jeremy B.},\n" + " title = {Onset and impact of plastic deformation in granular compaction},\n" + " journal = {Powder Technology},\n" + " year = 2025,\n" + " volume = 452,\n" + " number = 28,\n" + " pages = {120563}\n" + "}\n\n"; + /* ---------------------------------------------------------------------- */ BondBPMSpringPlastic::BondBPMSpringPlastic(LAMMPS *_lmp) : @@ -45,6 +58,8 @@ BondBPMSpringPlastic::BondBPMSpringPlastic(LAMMPS *_lmp) : single_extra = 2; svector = new double[2]; + + if (lmp->citeme) lmp->citeme->add(cite_bpm_plastic); } /* ---------------------------------------------------------------------- */ From dda72fee76dc8f68cf6836bfa465933f605c5c8e Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 30 Jan 2025 11:42:26 -0700 Subject: [PATCH 04/12] Drafting bpm/plastic doc page --- doc/src/bond_bpm_spring_plastic.rst | 183 ++++++++++++++++++++++++++++ 1 file changed, 183 insertions(+) create mode 100644 doc/src/bond_bpm_spring_plastic.rst diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst new file mode 100644 index 0000000000..06e1846c58 --- /dev/null +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -0,0 +1,183 @@ +.. index:: bond_style bpm/spring/plastic + +bond_style bpm/spring/plastic command +===================================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + bond_style bpm/spring/plastic keyword value attribute1 attribute2 ... + +* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* + + .. parsed-literal:: + + *store/local* values = fix_ID N attributes ... + * fix_ID = ID of associated internal fix to store data + * N = prepare data for output every this many timesteps + * attributes = zero or more of the below attributes may be appended + + *id1, id2* = IDs of two atoms in the bond + *time* = the timestep the bond broke + *x, y, z* = the center of mass position of the two atoms when the bond broke (distance units) + *x/ref, y/ref, z/ref* = the initial center of mass position of the two atoms (distance units) + + *overlay/pair* value = *yes* or *no* + bonded particles will still interact with pair forces + + *smooth* value = *yes* or *no* + smooths bond forces near the breaking point + + *normalize* value = *yes* or *no* + normalizes bond forces by the reference length + + *break* value = *yes* or *no* + indicates whether bonds break during a run + +Examples +"""""""" + +.. code-block:: LAMMPS + + bond_style bpm/spring/plastic + bond_coeff 1 1.0 0.05 0.1 0.02 + + bond_style bpm/spring/plastic myfix 1000 time id1 id2 + dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3] + dump_modify 1 write_header no + +Description +""""""""""" + +.. versionadded:: TBD + +The *bpm/spring/plastic* bond style computes forces based on +deviations from the initial reference state of the two atoms and the +strain history. The reference length of the bond :math:`r_0` is stored +by each bond when it is first computed in the setup of a run. Initially, +the equilibrium length of each bond :math:`r_\mathrm{eq}` is set equal +to :math:`r_0` but can evolve. data is then preserved across run commands +and is written to :doc:`binary restart files ` such that restarting +the system will not modify either of these quantities. + +This bond style only applies central-body forces which conserve the +translational and rotational degrees of freedom of a bonded set of +particles. The force has a magnitude of + +.. math:: + + F = -k (r_\mathrm{eq} - r) w + +where :math:`k` is a stiffness, :math:`r` is the current distance between +the two particles, and :math:`w` is an optional smoothing factor discussed +below. If the bond stretches beyond a strain of :math:`\epsilon_p`, it will +plastically activate and :math:`r_\mathrm{eq}` will evolve to ensure +:math:`|(r-r_\mathrm{eq})/r_\mathrm{eq}|` never exceeds :math:`\epsilon_p`. +Therefore, in pure tension, the force initially grows elastically before +plateauing. See :ref:`(Clemmer) ` for more details on +these mechanics. + +Bonds will break at a strain of :math:`\epsilon_c`. This is done by setting +the bond type to 0 such that forces are no longer computed. + +An additional damping force is applied to the bonded +particles. This forces is proportional to the difference in the +normal velocity of particles: + +.. math:: + + F_D = - \gamma w (\hat{r} \bullet \vec{v}) + +where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the +radial normal vector, and :math:`\vec{v}` is the velocity difference +between the two particles. + +The smoothing factor :math:`w` is constructed such that forces smoothly +go to zero, avoiding discontinuities, as bonds approach the critical +breaking strain + +.. math:: + + w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 . + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data +` or :doc:`read_restart ` commands: + +* :math:`k` (force/distance units) +* :math:`\epsilon_c` (unit less) +* :math:`\gamma` (force/velocity units) +* :math:`\epsilon_p (unit less) + +See the :doc:`bpm/spring doc page ` for information on +the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local* +keywords. + +Note that when unbroken bonds are dumped to a file via the +:doc:`dump local ` command, bonds with type 0 (broken bonds) +are not included. +The :doc:`delete_bonds ` command can also be used to +query the status of broken bonds or permanently delete them, e.g.: + +.. code-block:: LAMMPS + + delete_bonds all stats + delete_bonds all bond 0 remove + +---------- + +Restart and other info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This bond style writes the reference state and plastic history of each +bond to :doc:`binary restart files `. Loading a restart +file will properly restore bonds. However, the reference state is NOT +written to data files. Therefore reading a data file will not +restore bonds and will cause their reference states to be redefined. + +The potential energy and the single() function of this bond style returns zero. +The single() function also calculates two extra bond quantities, the initial +distance :math:`r_0` and the current equilbrium length :math:`r_eq`. These extra +quantities can be accessed by the :doc:`compute bond/local ` +command as *b1* and *b2*\ . + +Restrictions +"""""""""""" + +This bond style is part of the BPM package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. + +By default if pair interactions between bonded atoms are to be disabled, +this bond style requires setting + +.. code-block:: LAMMPS + + special_bonds lj 0 1 1 coul 1 1 1 + +and :doc:`newton ` must be set to bond off. If the *overlay/pair* +keyword is set to *yes*, this bond style alternatively requires setting + +.. code-block:: LAMMPS + + special_bonds lj/coul 1 1 1 + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`bond bpm/spring ` + +Default +""""""" + +The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes* + +---------- + +.. _plastic-Clemmer: + +**(Clemmer)** Clemmer and Lechman, Powder Technology (2025). + From 33c4ce8929ab9337ff26178a0a3e9375766ac70e Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 30 Jan 2025 14:54:59 -0700 Subject: [PATCH 05/12] Adding auxetic/incompressible bpm demo --- doc/src/Examples.rst | 2 +- doc/src/bond_bpm_spring.rst | 3 +- .../bpm/poissons_ratio/in.bpm.poissons_ratio | 90 +++ .../log.19Nov2024.bpm.poissons_ratio.g++.1 | 635 ++++++++++++++++++ 4 files changed, 728 insertions(+), 2 deletions(-) create mode 100644 examples/bpm/poissons_ratio/in.bpm.poissons_ratio create mode 100644 examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 683cbd0500..d80fc8aa4c 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -54,7 +54,7 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | body | body particles, 2d system | +-------------+------------------------------------------------------------------+ -| bpm | BPM simulations of pouring elastic grains and plate impact | +| bpm | simulations of solid elastic/plastic deformation and fracture | +-------------+------------------------------------------------------------------+ | cmap | CMAP 5-body contributions to CHARMM force field | +-------------+------------------------------------------------------------------+ diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index cde447825a..4d958a2a1e 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -141,7 +141,8 @@ calculated using bond lengths squared and the cube root in the above equation is accordingly replaced with a square root. This approximation assumes bonds are evenly distributed on a spherical surface and neglects constant prefactors which are irrelevant since only the ratio of volumes matters. This term may be -used to adjust the Poisson's ratio. +used to adjust the Poisson's ratio. See the simulation in the +examples/bpm/poissons_ratio directory for a demonstration of this effect. If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting (or adding) that bond's contribution. diff --git a/examples/bpm/poissons_ratio/in.bpm.poissons_ratio b/examples/bpm/poissons_ratio/in.bpm.poissons_ratio new file mode 100644 index 0000000000..4f31291a6a --- /dev/null +++ b/examples/bpm/poissons_ratio/in.bpm.poissons_ratio @@ -0,0 +1,90 @@ +# Squish three pillars with different Poisson's ratios +# going from nearly incompressible to auxetic +# from left to right, nu ~ 0.5, 0.25, 0, <0 +# calibration from DOI: 10.1039/d3sm01373a + +units lj +dimension 3 +boundary p p s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +region box block 0 20 -10 10 -1 21 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +mass * 1.0 + +# Create initial disordered geometry somewhat near jamming + +region pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box +region pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box +create_atoms 1 region pillar + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region pillarw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group p1 region r1 +group p2 region r2 +group p3 region r3 +group p4 region r4 + +set group p2 type 2 +set group p3 type 3 +set group p4 type 4 + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many p1 p1 1 0.0 1.5 +create_bonds many p2 p2 2 0.0 1.5 +create_bonds many p3 p3 3 0.0 1.5 +create_bonds many p4 p4 4 0.0 1.5 + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring break no smooth no volume/factor yes +bond_coeff 1 1.0 0 1.0 -0.8 +bond_coeff 2 1.0 0 1.0 0.0 +bond_coeff 3 1.0 0 1.0 2.0 +bond_coeff 4 1.0 0 1.0 10.0 + +# squish + +region b block EDGE EDGE EDGE EDGE -1.0 2.0 units box +region t block EDGE EDGE EDGE EDGE 18.0 21.0 units box +group bot region b +group top region t + +velocity top set 0.0 0.0 -0.0025 +fix 2 bot setforce 0.0 0.0 0.0 +fix 3 top setforce 0.0 0.0 0.0 + +compute zmax all reduce max z + +thermo_style custom step ke pe pxx pyy pzz c_zmax +#dump 1 all custom 100 atomDump id type x y z + +run 10000 diff --git a/examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 b/examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 new file mode 100644 index 0000000000..e4a95e2b70 --- /dev/null +++ b/examples/bpm/poissons_ratio/log.19Nov2024.bpm.poissons_ratio.g++.1 @@ -0,0 +1,635 @@ +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1028-g800a5f6310-modified) +# Squish three pillars with different Poisson's ratios +# from left to right, nu ~ 0.5, nu = 0.25 nu ~ 0, nu << 0 + +units lj +dimension 3 +boundary p p s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +Lattice spacing in x,y,z = 1.4156209 1.4156209 1.4156209 +region box block 0 20 -10 10 -1 21 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (0 -10 -1) to (20 10 21) + 1 by 1 by 1 MPI processor grid +mass * 1.0 + +# Create roughly jammed initial disordered geometry + +region pillar cylinder z 10.0 0.0 7.0 0.0 20.0 units box +region pillarw cylinder z 10.0 0.0 8.0 -1.0 21.0 units box +create_atoms 1 region pillar +Created 4348 atoms + using lattice units in orthogonal box = (0 -10 -1.0022) to (20 10 21.0022) + create_atoms CPU = 0.001 seconds + +velocity all create 0.1 345910 + +pair_style 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6.6606975e-05 6.3318574e-05 5.3065953e-05 + 14700 2.2058311e-05 5.4197187e-08 6.5636138e-05 6.2862183e-05 5.1216722e-05 + 14800 2.2056992e-05 5.3753302e-08 6.4166876e-05 6.2347682e-05 5.1644619e-05 + 14900 2.2055144e-05 5.3731475e-08 6.2886449e-05 6.2665027e-05 5.1085737e-05 + 15000 2.2055534e-05 5.1421678e-08 6.3216438e-05 6.2497955e-05 4.9420052e-05 + 15100 2.2053654e-05 5.02402e-08 6.185253e-05 6.1020856e-05 4.8961501e-05 + 15200 2.2052236e-05 4.9076779e-08 6.1894516e-05 5.8658526e-05 4.9270802e-05 + 15300 2.2050986e-05 4.8464692e-08 6.1632248e-05 5.939126e-05 4.7954422e-05 + 15400 2.2050221e-05 4.7362506e-08 5.9932389e-05 5.8619584e-05 4.8571134e-05 + 15500 2.2049702e-05 4.5776499e-08 5.9343369e-05 5.6908271e-05 4.5799128e-05 + 15600 2.2046842e-05 4.6074337e-08 6.0035433e-05 5.8667997e-05 4.6172612e-05 + 15700 2.2046262e-05 4.542862e-08 5.8703316e-05 5.7704418e-05 4.6189812e-05 + 15800 2.204616e-05 4.3329814e-08 5.6689179e-05 5.6845301e-05 4.5918735e-05 + 15900 2.2044466e-05 4.3332045e-08 5.806419e-05 5.6030356e-05 4.5166944e-05 + 16000 2.2043425e-05 4.2921122e-08 5.6716404e-05 5.5927539e-05 4.5500189e-05 + 16100 2.2041966e-05 4.1774604e-08 5.6210966e-05 5.4580522e-05 4.4615956e-05 + 16200 2.2041126e-05 4.1198995e-08 5.6314084e-05 5.5538584e-05 4.3793702e-05 + 16300 2.2040394e-05 4.0405671e-08 5.6049147e-05 5.5461464e-05 4.1884999e-05 + 16400 2.2040538e-05 3.8384306e-08 5.4398726e-05 5.3601303e-05 4.2580325e-05 + 16500 2.2039103e-05 3.8153339e-08 5.46254e-05 5.3390447e-05 4.2089044e-05 + 16600 2.2036976e-05 3.8358477e-08 5.2955748e-05 5.3742853e-05 4.1975739e-05 + 16700 2.20354e-05 3.8227046e-08 5.3241934e-05 5.2684751e-05 4.1815545e-05 + 16800 2.2034486e-05 3.7612842e-08 5.3915367e-05 5.3101063e-05 3.9996576e-05 + 16900 2.2033757e-05 3.6901749e-08 5.324896e-05 5.2020981e-05 4.0209668e-05 + 17000 2.2032483e-05 3.631797e-08 5.2504044e-05 5.1532024e-05 4.1841265e-05 + 17100 2.2031907e-05 3.5761725e-08 5.2177113e-05 5.1853522e-05 4.0475234e-05 + 17200 2.2030622e-05 3.5615934e-08 5.2153967e-05 5.1680185e-05 4.0255138e-05 + 17300 2.2028906e-05 3.5769817e-08 5.3276095e-05 5.1713123e-05 3.9429947e-05 + 17400 2.2027982e-05 3.5279634e-08 5.1720769e-05 5.1071287e-05 3.946136e-05 + 17500 2.2027385e-05 3.4532852e-08 5.0897208e-05 5.0132128e-05 3.9770047e-05 + 17600 2.2025743e-05 3.4705869e-08 5.1921573e-05 4.9849618e-05 3.9250188e-05 + 17700 2.202442e-05 3.4664237e-08 5.1037538e-05 5.1309699e-05 3.8699028e-05 + 17800 2.2024041e-05 3.3230639e-08 5.0676543e-05 4.9676967e-05 3.6992319e-05 + 17900 2.2024009e-05 3.2185399e-08 4.9624741e-05 4.8805054e-05 3.8163917e-05 + 18000 2.2023291e-05 3.1901464e-08 4.9090832e-05 4.9184392e-05 3.7458065e-05 + 18100 2.202221e-05 3.1698456e-08 4.9178905e-05 4.8243736e-05 3.7166662e-05 + 18200 2.2021437e-05 3.1022506e-08 4.8457604e-05 4.8875433e-05 3.5824097e-05 + 18300 2.2020792e-05 3.0064688e-08 4.909522e-05 4.7180933e-05 3.5355876e-05 + 18400 2.2021113e-05 2.9279611e-08 4.7111226e-05 4.7747191e-05 3.4625046e-05 + 18500 2.2019843e-05 2.9077485e-08 4.7131195e-05 4.633375e-05 3.5061152e-05 + 18600 2.201863e-05 2.9334156e-08 4.7778742e-05 4.7369011e-05 3.4559728e-05 + 18700 2.2018219e-05 2.862088e-08 4.7260131e-05 4.5881586e-05 3.4305681e-05 + 18800 2.2018393e-05 2.7165913e-08 4.6456933e-05 4.5912824e-05 3.3022256e-05 + 18900 2.201532e-05 2.8873682e-08 4.7138874e-05 4.6487853e-05 3.5130117e-05 + 19000 2.2014497e-05 2.8430782e-08 4.7563112e-05 4.6760097e-05 3.3226263e-05 + 19100 2.2014081e-05 2.8050044e-08 4.6431839e-05 4.6219284e-05 3.4248177e-05 + 19200 2.2013576e-05 2.7201031e-08 4.5709989e-05 4.5916792e-05 3.3897641e-05 + 19300 2.2012609e-05 2.7374842e-08 4.561715e-05 4.5693439e-05 3.4284473e-05 + 19400 2.2010667e-05 2.8105102e-08 4.6663945e-05 4.6539017e-05 3.3608877e-05 + 19500 2.2010486e-05 2.6897595e-08 4.5576796e-05 4.6292499e-05 3.2656892e-05 + 19600 2.2010302e-05 2.6248669e-08 4.4996903e-05 4.3675939e-05 3.4540503e-05 + 19700 2.2009254e-05 2.6450724e-08 4.4868007e-05 4.5628545e-05 3.3413034e-05 + 19800 2.2007283e-05 2.721852e-08 4.5939302e-05 4.5327011e-05 3.3411556e-05 + 19900 2.2007538e-05 2.6295204e-08 4.5722301e-05 4.441743e-05 3.4023953e-05 + 20000 2.2006515e-05 2.6089093e-08 4.4621124e-05 4.5449725e-05 3.2126359e-05 +Loop time of 7.03939 on 1 procs for 20000 steps with 4348 atoms + +Performance: 24547586.015 tau/day, 2841.156 timesteps/s, 12.353 Matom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.55 | 4.55 | 4.55 | 0.0 | 64.64 +Bond | 0.00067765 | 0.00067765 | 0.00067765 | 0.0 | 0.01 +Neigh | 0.3745 | 0.3745 | 0.3745 | 0.0 | 5.32 +Comm | 0.013687 | 0.013687 | 0.013687 | 0.0 | 0.19 +Output | 0.006889 | 0.006889 | 0.006889 | 0.0 | 0.10 +Modify | 1.9222 | 1.9222 | 1.9222 | 0.0 | 27.31 +Other | | 0.1715 | | | 2.44 + +Nlocal: 4348 ave 4348 max 4348 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23350 ave 23350 max 23350 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 23350 +Ave neighs/atom = 5.3702852 +Ave special neighs/atom = 0 +Neighbor list builds = 222 +Dangerous builds = 0 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 +Replication is creating a 4x1x1 = 4 times larger system... + orthogonal box = (0 -10 -0.0025658844) to (80 10 20.002511) + 1 by 1 by 1 MPI processor grid + 17392 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 0 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.001 seconds + replicate CPU = 0.003 seconds + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group p1 region r1 +4348 atoms in group p1 +group p2 region r2 +4348 atoms in group p2 +group p3 region r3 +4348 atoms in group p3 +group p4 region r4 +4348 atoms in group p4 + +set group p2 type 2 +Setting atom values ... + 4348 settings made for type +set group p3 type 3 +Setting atom values ... + 4348 settings made for type +set group p4 type 4 +Setting atom values ... + 4348 settings made for type + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many p1 p1 1 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 29229 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many p2 p2 2 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 58458 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.003 seconds +create_bonds many p3 p3 3 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 87687 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.004 seconds +create_bonds many p4 p4 4 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 20 21 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 29229 bonds, new total = 116916 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 19 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.005 seconds + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring break no smooth no volume/factor yes +bond_coeff 1 1.0 0 1.0 -0.8 +bond_coeff 2 1.0 0 1.0 0.0 +bond_coeff 3 1.0 0 1.0 2.0 +bond_coeff 4 1.0 0 1.0 10.0 + +# squish + +region b block EDGE EDGE EDGE EDGE -1.0 2.0 units box +region t block EDGE EDGE EDGE EDGE 18.0 21.0 units box +group bot region b +2040 atoms in group bot +group top region t +2036 atoms in group top + +velocity top set 0.0 0.0 -0.0025 +fix 2 bot setforce 0.0 0.0 0.0 +fix 3 top setforce 0.0 0.0 0.0 + +compute zmax all reduce max z + +thermo_style custom step ke pe pxx pyy pzz c_zmax +dump 1 all custom 100 atomDump id type x y z + +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- BPM bond style: doi:10.1039/D3SM01373A + +@Article{Clemmer2024, + author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, + title = {A soft departure from jamming: the compaction of deformable + granular matter under high pressures}, + journal = {Soft Matter}, + year = 2024, + volume = 20, + number = 8, + pages = {1702--1718} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 124 31 31 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 33.55 | 33.55 | 33.55 Mbytes + Step KinEng PotEng Pxx Pyy Pzz c_zmax + 20000 7.3311514e-07 0 5.5082149e-05 5.6035691e-05 0.00016879881 20.000342 + 20100 3.1226194e-06 4.1766539e-06 -0.00013996263 -0.00014393529 0.0029331928 19.964952 + 20200 2.5567295e-06 1.4988852e-05 -0.00027674096 -0.00027610139 0.0056641847 19.929561 + 20300 2.5665365e-06 3.3513395e-05 -0.00042198157 -0.0004191815 0.0083802213 19.894171 + 20400 2.4143831e-06 5.9638373e-05 -0.00055373017 -0.00055236369 0.011083701 19.85878 + 20500 2.2440232e-06 9.3155125e-05 -0.00070411826 -0.00070166982 0.013871936 19.82339 + 20600 2.3036882e-06 0.00013415012 -0.00084108079 -0.00084004876 0.016564858 19.787999 + 20700 2.4894579e-06 0.00018252868 -0.00098164122 -0.00097848101 0.019243173 19.752609 + 20800 2.3533488e-06 0.0002383092 -0.0011196916 -0.0011163409 0.021906836 19.717218 + 20900 2.3312562e-06 0.000301439 -0.0012662271 -0.0012625903 0.024743687 19.681828 + 21000 2.3806649e-06 0.00037188609 -0.0014035798 -0.0013992731 0.02739958 19.646437 + 21100 2.3212779e-06 0.00044964779 -0.0015396059 -0.0015348733 0.030041098 19.611047 + 21200 2.3908442e-06 0.00053469194 -0.001674797 -0.0016694993 0.03266844 19.575656 + 21300 2.3622478e-06 0.00062699617 -0.001822934 -0.0018167895 0.035552232 19.540266 + 21400 2.349964e-06 0.00072653051 -0.0019569691 -0.0019503123 0.038170924 19.504875 + 21500 2.3567592e-06 0.00083327134 -0.0020899915 -0.0020827032 0.040775314 19.469484 + 21600 2.3616263e-06 0.00094719631 -0.0022220661 -0.0022140075 0.043365368 19.434094 + 21700 2.353721e-06 0.0010682808 -0.0023711759 -0.0023623886 0.046296241 19.398703 + 21800 2.3646799e-06 0.0011965 -0.0025021157 -0.0024925265 0.048877326 19.363313 + 21900 2.3550746e-06 0.0013318277 -0.0026319662 -0.0026215842 0.051443901 19.327922 + 22000 2.3552825e-06 0.0014742397 -0.0027607166 -0.0027495396 0.053995979 19.292532 + 22100 2.3588762e-06 0.0016237112 -0.0028884164 -0.0028763855 0.05653356 19.257141 + 22200 2.3566445e-06 0.0017802179 -0.0030385388 -0.0030255211 0.05951687 19.221751 + 22300 2.3569128e-06 0.0019437341 -0.0031650443 -0.0031511287 0.062044959 19.18636 + 22400 2.3573615e-06 0.0021142342 -0.0032904648 -0.0032756057 0.064558413 19.15097 + 22500 2.3556792e-06 0.0022916926 -0.003414791 -0.0033989599 0.067057238 19.115579 + 22600 2.3559622e-06 0.0024760839 -0.0035658051 -0.0035488398 0.070087637 19.080189 + 22700 2.3565188e-06 0.0026673826 -0.0036888874 -0.0036708796 0.072576558 19.044798 + 22800 2.3554654e-06 0.0028655631 -0.0038108556 -0.0037917743 0.075050709 19.009408 + 22900 2.3556755e-06 0.0030705996 -0.0039317038 -0.0039115206 0.07751008 18.974017 + 23000 2.3553906e-06 0.0032824663 -0.0040835075 -0.0040620186 0.080587643 18.938627 + 23100 2.3549893e-06 0.0035011372 -0.0042030492 -0.0041803845 0.08303667 18.903236 + 23200 2.3549869e-06 0.0037265864 -0.0043214571 -0.004297582 0.085470779 18.867846 + 23300 2.3548674e-06 0.0039587875 -0.0044387217 -0.004413608 0.087889956 18.832455 + 23400 2.3544804e-06 0.0041977141 -0.0045911895 -0.0045645946 0.091014737 18.797065 + 23500 2.3543814e-06 0.0044433399 -0.0047070844 -0.0046791718 0.093423108 18.761674 + 23600 2.3541461e-06 0.0046956382 -0.0048218198 -0.0047925569 0.09581641 18.726284 + 23700 2.3539051e-06 0.0049545823 -0.0049353928 -0.0049047458 0.098194634 18.690893 + 23800 2.3537612e-06 0.0052201456 -0.0050478006 -0.0050157354 0.10055777 18.655502 + 23900 2.3535618e-06 0.0054923012 -0.0052005398 -0.0051667526 0.10373359 18.620112 + 24000 2.353333e-06 0.005771022 -0.0053114912 -0.0052762067 0.10608529 18.584721 + 24100 2.3531619e-06 0.006056281 -0.0054212598 -0.0053844406 0.10842176 18.549331 + 24200 2.3529697e-06 0.0063480511 -0.0055298409 -0.0054914515 0.11074298 18.51394 + 24300 2.352776e-06 0.0066463046 -0.0056829436 -0.0056426256 0.11396569 18.47855 + 24400 2.3526011e-06 0.0069510143 -0.0057899993 -0.0057480274 0.11627496 18.443159 + 24500 2.3524078e-06 0.0072621525 -0.0058958481 -0.0058521853 0.11856882 18.407769 + 24600 2.3522128e-06 0.0075796913 -0.0060004865 -0.0059550957 0.12084728 18.372378 + 24700 2.3520292e-06 0.0079036029 -0.0061538145 -0.0061062726 0.12411681 18.336988 + 24800 2.3518453e-06 0.0082338593 -0.0062568585 -0.0062074978 0.12638278 18.301597 + 24900 2.3516643e-06 0.0085704324 -0.0063586718 -0.0063074546 0.12863317 18.266207 + 25000 2.3514892e-06 0.0089132938 -0.0064592514 -0.0064061393 0.13086797 18.230816 + 25100 2.3513106e-06 0.0092624151 -0.0066126575 -0.0065571568 0.13418421 18.195426 + 25200 2.3511362e-06 0.0096177679 -0.0067115701 -0.0066540785 0.13640596 18.160035 + 25300 2.3509678e-06 0.0099793234 -0.0068092292 -0.0067497066 0.13861195 18.124645 + 25400 2.3508006e-06 0.010347053 -0.0069056318 -0.0068440373 0.14080217 18.089254 + 25500 2.3506356e-06 0.010720927 -0.0070007749 -0.0069370671 0.14297661 18.053864 + 25600 2.3504737e-06 0.011100917 -0.0071536223 -0.0070872122 0.14634153 18.018473 + 25700 2.3503117e-06 0.011486993 -0.007247006 -0.0071783805 0.14850216 17.983083 + 25800 2.3501529e-06 0.011879126 -0.0073391102 -0.0072682259 0.15064682 17.947692 + 25900 2.3499998e-06 0.012277287 -0.0074299315 -0.0073567446 0.1527755 17.912302 + 26000 2.3498505e-06 0.012681445 -0.0075824884 -0.0075063219 0.15618632 17.876911 + 26100 2.3497046e-06 0.013091571 -0.0076714736 -0.0075928957 0.15830056 17.84152 + 26200 2.3495632e-06 0.013507634 -0.0077591555 -0.0076781204 0.16039862 17.80613 + 26300 2.349426e-06 0.013929604 -0.0078455309 -0.0077619923 0.1624805 17.770739 + 26400 2.3492932e-06 0.014357451 -0.0079976262 -0.0079108096 0.16593692 17.735349 + 26500 2.349166e-06 0.014791144 -0.008082087 -0.0079926504 0.16800369 17.699958 + 26600 2.3490444e-06 0.015230653 -0.0081652207 -0.0080731154 0.17005406 17.664568 + 26700 2.3489277e-06 0.015675946 -0.008247024 -0.0081522008 0.17208804 17.629177 + 26800 2.3488161e-06 0.016126992 -0.0083984781 -0.008300055 0.17558967 17.593787 + 26900 2.3487105e-06 0.016583761 -0.0084782861 -0.0083770201 0.17760782 17.558396 + 27000 2.3486117e-06 0.017046219 -0.0085567431 -0.008452582 0.17960935 17.523006 + 27100 2.3485201e-06 0.017514336 -0.0086338458 -0.0085267367 0.18159424 17.487615 + 27200 2.3484365e-06 0.017988079 -0.0087095911 -0.0085994803 0.18356247 17.452225 + 27300 2.3483611e-06 0.018467417 -0.008859495 -0.0087453549 0.18710893 17.416834 + 27400 2.3482941e-06 0.018952317 -0.0089331441 -0.0088158653 0.18906038 17.381444 + 27500 2.3482362e-06 0.019442747 -0.0090054148 -0.0088849402 0.19099494 17.346053 + 27600 2.3481885e-06 0.019938673 -0.009076304 -0.0089525756 0.19291257 17.310663 + 27700 2.3481517e-06 0.020440063 -0.0092251203 -0.0090969772 0.19650266 17.275272 + 27800 2.3481263e-06 0.020946883 -0.0092938279 -0.0091622823 0.1984027 17.239882 + 27900 2.3481132e-06 0.0214591 -0.0093611327 -0.0092261226 0.20028558 17.204491 + 28000 2.3481132e-06 0.02197668 -0.0094270316 -0.0092884939 0.20215126 17.169101 + 28100 2.3481274e-06 0.02249959 -0.0095745512 -0.0094311779 0.20578425 17.13371 + 28200 2.348157e-06 0.023027794 -0.0096381809 -0.0094911175 0.20763145 17.09832 + 28300 2.3482036e-06 0.023561259 -0.0097003831 -0.0095495617 0.20946119 17.062929 + 28400 2.3482687e-06 0.024099949 -0.0097611548 -0.0096065059 0.21127344 17.027538 + 28500 2.3480319e-06 0.024643805 -0.0099071195 -0.0097471709 0.21494867 16.992148 + 28600 2.3475123e-06 0.025192783 -0.0099654368 -0.0098014823 0.21674185 16.956757 + 28700 2.3465283e-06 0.02574682 -0.010022297 -0.0098542782 0.21851751 16.921367 + 28800 2.3462245e-06 0.026305935 -0.010077643 -0.0099055665 0.2202753 16.885976 + 28900 2.3465001e-06 0.026870106 -0.010131548 -0.0099553377 0.22201519 16.850586 + 29000 2.3468383e-06 0.027439281 -0.010274668 -0.010092595 0.22572932 16.815195 + 29100 2.3470511e-06 0.028013406 -0.010326047 -0.010139547 0.22744875 16.779805 + 29200 2.3477211e-06 0.02859243 -0.010375939 -0.01018496 0.22915025 16.744414 + 29300 2.348195e-06 0.029176333 -0.010424252 -0.010228763 0.23083364 16.709024 + 29400 2.3486217e-06 0.02976508 -0.010565133 -0.010363233 0.2345875 16.673633 + 29500 2.3494547e-06 0.030358578 -0.010610824 -0.010404093 0.2362499 16.638243 + 29600 2.350246e-06 0.030956806 -0.010654741 -0.010443743 0.23789521 16.602852 + 29700 2.350645e-06 0.031559783 -0.010697062 -0.01048188 0.23952237 16.567462 + 29800 2.3513205e-06 0.032167468 -0.010835186 -0.010613742 0.24331694 16.532071 + 29900 2.3500682e-06 0.03277985 -0.010874694 -0.010649336 0.2449217 16.496681 + 30000 2.348814e-06 0.033396866 -0.010912585 -0.010683036 0.24650812 16.46129 +Loop time of 96.3898 on 1 procs for 10000 steps with 17392 atoms + +Performance: 896360.661 tau/day, 103.745 timesteps/s, 1.804 Matom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.4048 | 2.4048 | 2.4048 | 0.0 | 2.49 +Bond | 89.472 | 89.472 | 89.472 | 0.0 | 92.82 +Neigh | 0.25526 | 0.25526 | 0.25526 | 0.0 | 0.26 +Comm | 0.0489 | 0.0489 | 0.0489 | 0.0 | 0.05 +Output | 1.6355 | 1.6355 | 1.6355 | 0.0 | 1.70 +Modify | 1.8578 | 1.8578 | 1.8578 | 0.0 | 1.93 +Other | | 0.7153 | | | 0.74 + +Nlocal: 17392 ave 17392 max 17392 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 77 ave 77 max 77 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 102662 ave 102662 max 102662 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 102662 +Ave neighs/atom = 5.9028289 +Ave special neighs/atom = 13.444802 +Neighbor list builds = 23 +Dangerous builds = 0 + 10000 +ERROR: Unknown command: 10000 (../input.cpp:314) +Last input line: 10000 From ed627579f6b78147e952767b65bc95375f8ca21b Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 30 Jan 2025 16:44:11 -0700 Subject: [PATCH 06/12] Adding bpm/plastic demo, fixing mistake in poisson example --- examples/bpm/plasticity/in.bpm.plasticity | 96 + .../log.19Nov2024.bpm.plasticity.g++.1 | 1573 +++++++++++++++++ .../bpm/poissons_ratio/in.bpm.poissons_ratio | 2 +- 3 files changed, 1670 insertions(+), 1 deletion(-) create mode 100644 examples/bpm/plasticity/in.bpm.plasticity create mode 100644 examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 diff --git a/examples/bpm/plasticity/in.bpm.plasticity b/examples/bpm/plasticity/in.bpm.plasticity new file mode 100644 index 0000000000..47e82455ed --- /dev/null +++ b/examples/bpm/plasticity/in.bpm.plasticity @@ -0,0 +1,96 @@ +# Load then unload four cantilevers with different plastic yield strains +# model from DOI: 10.1016/j.powtec.2024.120563 + +units lj +dimension 3 +boundary p s s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +region box block 0 20 -1 41 -5 5 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +mass * 1.0 + +# Create initial disordered geometry somewhat near jamming + +region cantilever block 3.0 12.0 0 40 -2.5 2.5 units box +region cantileverw block 2.0 13.0 -1 41 -3.5 3.5 units box +create_atoms 1 region cantilever + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region cantileverw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group c1 region r1 +group c2 region r2 +group c3 region r3 +group c4 region r4 + +set group c2 type 2 +set group c3 type 3 +set group c4 type 4 + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many c1 c1 1 0.0 1.5 +create_bonds many c2 c2 2 0.0 1.5 +create_bonds many c3 c3 3 0.0 1.5 +create_bonds many c4 c4 4 0.0 1.5 + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring/plastic break no smooth no +bond_coeff 1 1.0 0 1.0 1.0 +bond_coeff 2 1.0 0 1.0 0.03 +bond_coeff 3 1.0 0 1.0 0.02 +bond_coeff 4 1.0 0 1.0 0.01 + +# apply load + +region anchor block EDGE EDGE EDGE 2.0 EDGE EDGE units box +region load block EDGE EDGE 38.0 EDGE EDGE EDGE units box +group anchor region anchor +group load region load + +fix 2 anchor setforce 0.0 0.0 0.0 +fix 3 load addforce 0.0 0.0 -0.0005 +fix 4 all viscous 0.001 + +compute zmin1 c1 reduce min z +compute zmin2 c2 reduce min z +compute zmin3 c3 reduce min z +compute zmin4 c4 reduce min z + +thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4 +#dump 1 all custom 200 atomDump id type x y z + +run 50000 + +# remove load + +unfix 3 +run 50000 diff --git a/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 b/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 new file mode 100644 index 0000000000..45fd829e70 --- /dev/null +++ b/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 @@ -0,0 +1,1573 @@ +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1028-g800a5f6310-modified) +# Load then unload four cantilevers with different plastic yield strains +# model from DOI: 10.1016/j.powtec.2024.120563 + +units lj +dimension 3 +boundary p s s +atom_style bond +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 2.6 +lattice fcc 1.41 +Lattice spacing in x,y,z = 1.4156209 1.4156209 1.4156209 +region box block 0 20 -1 41 -5 5 units box +create_box 4 box bond/types 4 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (0 -1 -5) to (20 41 5) + 1 by 1 by 1 MPI processor grid +mass * 1.0 + +# Create initial disordered geometry somewhat near jamming + +region cantilever block 3.0 12.0 0 40 -2.5 2.5 units box +region cantileverw block 2.0 13.0 -1 41 -3.5 3.5 units box +create_atoms 1 region cantilever +Created 2394 atoms + using lattice units in orthogonal box = (0 -1.0042 -5.001) to (20 41.0042 5.001) + create_atoms CPU = 0.001 seconds + +velocity all create 0.1 345910 + +pair_style bpm/spring +pair_coeff * * 1.0 1.0 1.0 + +fix 1 all nve +fix wtemp all wall/region cantileverw harmonic 1.0 1.0 1.0 + +thermo_style custom step ke pe pxx pyy pzz +thermo 100 + +timestep 0.1 +run 20000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 31 65 16 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.752 | 9.752 | 9.752 Mbytes + Step KinEng PotEng Pxx Pyy Pzz + 0 0.14993734 0 0.071514461 0.070121562 0.071454556 + 100 0.0066788839 0.0029982274 0.016637041 0.016868542 0.015823802 + 200 0.0019715508 0.00071490141 0.007843495 0.0076223765 0.0067662021 + 300 0.00087217257 0.00026043228 0.003985349 0.004259066 0.0040664397 + 400 0.00050307484 0.00011882009 0.0024899485 0.0025393633 0.0024477801 + 500 0.00033241763 6.5955939e-05 0.0016895447 0.0018048761 0.0017308071 + 600 0.00023663671 4.4828066e-05 0.0013515511 0.001353668 0.0013208904 + 700 0.0001837694 2.7185024e-05 0.00094852029 0.0010286312 0.00099370739 + 800 0.00014655165 1.8873405e-05 0.00075979673 0.0008230931 0.00075345331 + 900 0.00012145909 1.4344012e-05 0.00060702604 0.00068683252 0.00061213385 + 1000 0.00010239299 1.2153676e-05 0.00055078741 0.00060838425 0.00054159268 + 1100 8.8075366e-05 9.9954299e-06 0.00045915185 0.00057179945 0.00047014896 + 1200 7.8336822e-05 7.4598572e-06 0.00038286385 0.000423282 0.00040077777 + 1300 6.8617848e-05 7.4071518e-06 0.00038962894 0.00045042653 0.00042176853 + 1400 6.1816066e-05 5.7757188e-06 0.00035626235 0.00037452754 0.00033148835 + 1500 5.5158763e-05 5.3010672e-06 0.00032659745 0.00035059437 0.0003143055 + 1600 5.0680523e-05 4.4203877e-06 0.00027420802 0.00032194903 0.00030193132 + 1700 4.6020086e-05 4.0228214e-06 0.00026909527 0.00029969818 0.00027492066 + 1800 4.1968387e-05 3.9751303e-06 0.00027184181 0.00028203292 0.00026747334 + 1900 3.8741903e-05 3.5539155e-06 0.00024183418 0.00026550737 0.00025356968 + 2000 3.6204768e-05 2.9462894e-06 0.00022277001 0.00025408288 0.0002123446 + 2100 3.3266509e-05 2.8028832e-06 0.00021917117 0.00024069099 0.00020369452 + 2200 3.102664e-05 2.6085678e-06 0.0001882006 0.00023685724 0.00019134947 + 2300 2.903812e-05 2.3143895e-06 0.0001749797 0.00021704715 0.00019021214 + 2400 2.7141792e-05 2.1848123e-06 0.00018014226 0.00020933228 0.00017930569 + 2500 2.5612882e-05 1.8545406e-06 0.00017807794 0.00016882959 0.0001750063 + 2600 2.4068378e-05 1.7104525e-06 0.00015853683 0.000178264 0.00015848288 + 2700 2.2573196e-05 1.7771307e-06 0.00015577573 0.00017747772 0.00016654472 + 2800 2.1422175e-05 1.4847142e-06 0.00014322637 0.00013897114 0.00014490629 + 2900 2.0433268e-05 1.3514585e-06 0.00012745407 0.00014678277 0.000135221 + 3000 1.9204132e-05 1.3849721e-06 0.00012986068 0.00015084177 0.00014142185 + 3100 1.8212704e-05 1.2748732e-06 0.00013317833 0.00014368027 0.00013451894 + 3200 1.7326097e-05 1.3213286e-06 0.00012777819 0.00014793494 0.00012886678 + 3300 1.6615969e-05 1.1158927e-06 0.00011223033 0.00012323335 0.0001210878 + 3400 1.5855041e-05 1.1229014e-06 0.00011468711 0.00013243589 0.00012051018 + 3500 1.532374e-05 8.888678e-07 0.00010638549 0.00011430069 0.00010089698 + 3600 1.467535e-05 8.7654654e-07 8.8094885e-05 0.00011642682 0.00010671988 + 3700 1.4062105e-05 8.1807269e-07 9.4265348e-05 0.0001161673 9.3404926e-05 + 3800 1.3552196e-05 8.3487647e-07 8.6030873e-05 0.00011280194 0.0001010521 + 3900 1.3022591e-05 7.9989391e-07 0.00010119027 0.00010258667 9.1434393e-05 + 4000 1.2525445e-05 8.1520281e-07 9.5211467e-05 0.00010785495 9.97298e-05 + 4100 1.2181734e-05 6.4410557e-07 9.4373715e-05 8.9279858e-05 7.9893316e-05 + 4200 1.1704251e-05 7.0450874e-07 8.0872404e-05 9.4334475e-05 8.8302993e-05 + 4300 1.1280286e-05 7.1408139e-07 9.1119222e-05 8.5870034e-05 8.8445587e-05 + 4400 1.1016643e-05 6.0873467e-07 7.9024773e-05 8.1967988e-05 8.5977338e-05 + 4500 1.0668349e-05 5.8516931e-07 7.8294095e-05 8.0043527e-05 8.4715888e-05 + 4600 1.0331041e-05 5.7376843e-07 7.5679063e-05 8.2398328e-05 7.4278168e-05 + 4700 1.0004816e-05 5.4597537e-07 7.2607537e-05 7.7956907e-05 6.9095147e-05 + 4800 9.7594591e-06 5.2681078e-07 7.6737892e-05 6.79129e-05 7.2013864e-05 + 4900 9.4372215e-06 5.108678e-07 7.1926492e-05 7.6336467e-05 7.2404427e-05 + 5000 9.2301398e-06 4.9943356e-07 6.9272822e-05 7.4437007e-05 6.8591392e-05 + 5100 8.9087719e-06 5.0137676e-07 7.1953364e-05 7.0112306e-05 7.1894235e-05 + 5200 8.6733384e-06 4.6530133e-07 5.9160431e-05 7.2957759e-05 6.7731265e-05 + 5300 8.5237067e-06 4.0166784e-07 5.6976938e-05 6.4780167e-05 6.2493655e-05 + 5400 8.2585748e-06 3.9144457e-07 5.6287251e-05 6.5281415e-05 6.4678701e-05 + 5500 8.1089159e-06 3.5903718e-07 6.2738749e-05 5.8042636e-05 5.1954549e-05 + 5600 7.8605737e-06 3.9176106e-07 6.1198736e-05 6.5959291e-05 5.8081374e-05 + 5700 7.6788462e-06 3.8505614e-07 5.5766462e-05 6.4100303e-05 6.0012403e-05 + 5800 7.5163424e-06 3.4531571e-07 5.326349e-05 6.1833688e-05 4.8218455e-05 + 5900 7.3552892e-06 3.1726542e-07 5.2593444e-05 5.3015093e-05 5.2366381e-05 + 6000 7.1550139e-06 3.188599e-07 4.7713401e-05 5.6322276e-05 5.2424598e-05 + 6100 7.0361757e-06 3.0641052e-07 4.7286992e-05 5.8028248e-05 5.2063931e-05 + 6200 6.8801441e-06 2.7974487e-07 5.3580486e-05 4.6047586e-05 4.7327222e-05 + 6300 6.6802143e-06 3.3499395e-07 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1.687417e-05 + 15400 2.3489693e-06 4.7278336e-08 1.2011731e-05 1.2230688e-05 1.678822e-05 + 15500 2.3284108e-06 5.2715812e-08 1.3176372e-05 1.6503583e-05 1.3955123e-05 + 15600 2.2947375e-06 6.7465869e-08 1.5326712e-05 1.9881502e-05 1.6487331e-05 + 15700 2.3019796e-06 4.8005103e-08 1.4590446e-05 1.4276946e-05 1.4055723e-05 + 15800 2.2826912e-06 4.9641879e-08 1.3481867e-05 1.6276418e-05 1.3419255e-05 + 15900 2.2583072e-06 5.4614844e-08 1.7382114e-05 1.604672e-05 1.4741544e-05 + 16000 2.2430797e-06 4.8420384e-08 1.2843624e-05 1.2618834e-05 1.2491054e-05 + 16100 2.2264678e-06 4.796181e-08 1.4438989e-05 1.5552177e-05 1.2048946e-05 + 16200 2.2123007e-06 5.2907699e-08 1.2747032e-05 1.4431874e-05 1.6152188e-05 + 16300 2.1942666e-06 5.1538008e-08 1.3243122e-05 1.4793006e-05 1.4855916e-05 + 16400 2.1800741e-06 5.0280071e-08 1.1549921e-05 1.5836438e-05 1.5087605e-05 + 16500 2.1718081e-06 4.2144732e-08 1.4603756e-05 1.3084635e-05 1.2983558e-05 + 16600 2.15145e-06 4.6326815e-08 1.4904114e-05 1.4500088e-05 1.2283839e-05 + 16700 2.1563978e-06 3.2862475e-08 1.1841441e-05 1.2463519e-05 1.0662253e-05 + 16800 2.1128692e-06 5.462978e-08 1.3455978e-05 1.6216741e-05 1.4636363e-05 + 16900 2.1178726e-06 3.6500222e-08 1.1666564e-05 1.2789709e-05 9.6393609e-06 + 17000 2.1058751e-06 3.6428095e-08 1.3109685e-05 1.304962e-05 1.0397847e-05 + 17100 2.0817867e-06 5.1894295e-08 1.5527039e-05 1.442429e-05 1.1662417e-05 + 17200 2.0697616e-06 4.8400908e-08 1.2051247e-05 1.4854095e-05 1.4277423e-05 + 17300 2.0496506e-06 5.1765629e-08 1.5484172e-05 1.6516861e-05 1.3787806e-05 + 17400 2.0318945e-06 5.0178134e-08 1.2610435e-05 1.5926848e-05 1.3146463e-05 + 17500 2.0312975e-06 4.2775082e-08 1.1413756e-05 1.2303892e-05 1.332512e-05 + 17600 2.0286562e-06 3.3246228e-08 9.9623166e-06 1.1190246e-05 1.0713751e-05 + 17700 2.0057117e-06 4.1465626e-08 1.28564e-05 1.2354674e-05 1.1732572e-05 + 17800 1.9775891e-06 5.3253383e-08 1.3320474e-05 1.6084721e-05 1.1697579e-05 + 17900 1.9763707e-06 4.0037754e-08 1.0787927e-05 1.0905895e-05 1.2524822e-05 + 18000 1.9659819e-06 4.2213997e-08 1.0786016e-05 1.356023e-05 1.3052018e-05 + 18100 1.962808e-06 3.1950711e-08 1.0829314e-05 1.246617e-05 1.1079602e-05 + 18200 1.9360469e-06 4.3810974e-08 1.382493e-05 1.245849e-05 1.2288243e-05 + 18300 1.9407685e-06 3.0042901e-08 7.3716082e-06 1.109871e-05 1.226921e-05 + 18400 1.910359e-06 4.7042217e-08 1.3644803e-05 1.4884969e-05 1.1956804e-05 + 18500 1.8946497e-06 5.0743345e-08 1.1974771e-05 1.4385508e-05 1.7610709e-05 + 18600 1.8962987e-06 3.9757677e-08 1.0582884e-05 1.2673246e-05 1.3298389e-05 + 18700 1.8742478e-06 4.4718119e-08 1.5344401e-05 1.2546575e-05 1.1764246e-05 + 18800 1.8650878e-06 3.7704721e-08 1.07802e-05 1.2917662e-05 9.5373738e-06 + 18900 1.8685713e-06 3.6504734e-08 1.0815769e-05 1.3268273e-05 9.2228416e-06 + 19000 1.8510631e-06 3.5157873e-08 1.2534306e-05 1.2128038e-05 1.0355377e-05 + 19100 1.844547e-06 3.5807341e-08 1.1011196e-05 1.2288462e-05 1.042938e-05 + 19200 1.8237482e-06 4.4374495e-08 1.0976301e-05 1.0525434e-05 1.3496339e-05 + 19300 1.809658e-06 4.663351e-08 1.0427019e-05 1.2761301e-05 1.2443509e-05 + 19400 1.8047595e-06 3.7730816e-08 1.2549441e-05 9.4564734e-06 1.159109e-05 + 19500 1.7912254e-06 3.9882052e-08 1.3940679e-05 1.220604e-05 1.1210472e-05 + 19600 1.789224e-06 3.7125586e-08 1.0231473e-05 1.2070753e-05 1.1047121e-05 + 19700 1.7845362e-06 3.456485e-08 1.12335e-05 1.042505e-05 9.0484867e-06 + 19800 1.7683141e-06 3.8353201e-08 1.29417e-05 1.0764969e-05 1.116828e-05 + 19900 1.7664071e-06 3.2153664e-08 9.4515931e-06 1.1051242e-05 1.0924767e-05 + 20000 1.7618892e-06 2.2689236e-08 8.4011955e-06 7.5721128e-06 8.9521609e-06 +Loop time of 2.54444 on 1 procs for 20000 steps with 2394 atoms + +Performance: 67912724.488 tau/day, 7860.269 timesteps/s, 18.817 Matom-step/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2052 | 1.2052 | 1.2052 | 0.0 | 47.37 +Bond | 0.00069514 | 0.00069514 | 0.00069514 | 0.0 | 0.03 +Neigh | 0.18155 | 0.18155 | 0.18155 | 0.0 | 7.14 +Comm | 0.0076275 | 0.0076275 | 0.0076275 | 0.0 | 0.30 +Output | 0.0043813 | 0.0043813 | 0.0043813 | 0.0 | 0.17 +Modify | 1.0429 | 1.0429 | 1.0429 | 0.0 | 40.99 +Other | | 0.1021 | | | 4.01 + +Nlocal: 2394 ave 2394 max 2394 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 11170 ave 11170 max 11170 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 11170 +Ave neighs/atom = 4.6658312 +Ave special neighs/atom = 0 +Neighbor list builds = 199 +Dangerous builds = 0 +unfix wtemp + +# Replicate cylinder and add bonds + +replicate 4 1 1 +Replication is creating a 4x1x1 = 4 times larger system... + orthogonal box = (0 -0.0019118212 -2.5018545) to (80 40.003414 2.5021045) + 1 by 1 by 1 MPI processor grid + 9576 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 0 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.002 seconds + +region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box +region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box +region r3 block 40.0 60.0 EDGE EDGE EDGE EDGE side in units box +region r4 block 60.0 80.0 EDGE EDGE EDGE EDGE side in units box + +group c1 region r1 +2394 atoms in group c1 +group c2 region r2 +2394 atoms in group c2 +group c3 region r3 +2394 atoms in group c3 +group c4 region r4 +2394 atoms in group c4 + +set group c2 type 2 +Setting atom values ... + 2394 settings made for type +set group c3 type 3 +Setting atom values ... + 2394 settings made for type +set group c4 type 4 +Setting atom values ... + 2394 settings made for type + +velocity all set 0.0 0.0 0.0 +neighbor 1.0 bin + +create_bonds many c1 c1 1 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 13760 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.001 seconds +create_bonds many c2 c2 2 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 27520 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.002 seconds +create_bonds many c3 c3 3 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 41280 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.003 seconds +create_bonds many c4 c4 4 0.0 1.5 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Bonds are defined but no bond style is set (../force.cpp:197) +WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:199) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2.6 + binsize = 1, bins = 80 41 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Added 13760 bonds, new total = 55040 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 17 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.003 seconds + +neighbor 0.3 bin +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style bpm/spring/plastic break no smooth no +bond_coeff 1 1.0 0 1.0 1.0 +bond_coeff 2 1.0 0 1.0 0.03 +bond_coeff 3 1.0 0 1.0 0.02 +bond_coeff 4 1.0 0 1.0 0.01 + +# apply load + +region anchor block EDGE EDGE EDGE 2.0 EDGE EDGE units box +region load block EDGE EDGE 38.0 EDGE EDGE EDGE units box +group anchor region anchor +512 atoms in group anchor +group load region load +592 atoms in group load + +fix 2 anchor setforce 0.0 0.0 0.0 +fix 3 load addforce 0.0 0.0 -0.0005 +fix 4 all viscous 0.001 + +compute zmin1 c1 reduce min z +compute zmin2 c2 reduce min z +compute zmin3 c3 reduce min z +compute zmin4 c4 reduce min z + +thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4 +#dump 1 all custom 200 atomDump id type x y z + +run 50000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- BPM bond style: doi:10.1039/D3SM01373A + +@Article{Clemmer2024, + author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, + title = {A soft departure from jamming: the compaction of deformable + granular matter under high pressures}, + journal = {Soft Matter}, + year = 2024, + volume = 20, + number = 8, + pages = {1702--1718} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 2.6 + binsize = 0.65, bins = 124 62 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair bpm/spring, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 20.02 | 20.02 | 20.02 Mbytes + Step KinEng c_zmin1 c_zmin2 c_zmin3 c_zmin4 + 20000 0 -2.5009426 -2.5009426 -2.5009426 -2.5009426 + 20100 4.0956567e-07 -2.5160602 -2.5160602 -2.5160602 -2.5160602 + 20200 1.3143434e-06 -2.555086 -2.555086 -2.555086 -2.555086 + 20300 2.5328497e-06 -2.6114806 -2.6114806 -2.6114806 -2.6114806 + 20400 4.0044252e-06 -2.6807339 -2.6807339 -2.6807339 -2.6807339 + 20500 5.683827e-06 -2.7603965 -2.7603965 -2.7603965 -2.7603965 + 20600 7.5588865e-06 -2.8493381 -2.8493381 -2.8493381 -2.8493381 + 20700 9.5460405e-06 -2.9466232 -2.9466232 -2.9466232 -2.9466232 + 20800 1.1434976e-05 -3.0516294 -3.0516294 -3.0516294 -3.0516294 + 20900 1.3298452e-05 -3.1649086 -3.1649086 -3.1649086 -3.1649086 + 21000 1.5334087e-05 -3.2853774 -3.2853774 -3.2853774 -3.2853774 + 21100 1.7644543e-05 -3.4124904 -3.4124904 -3.4124904 -3.4124904 + 21200 2.0249305e-05 -3.5471314 -3.5471314 -3.5471314 -3.5471314 + 21300 2.3096201e-05 -3.6870368 -3.6870368 -3.6870368 -3.6870367 + 21400 2.6137865e-05 -3.8263018 -3.8263018 -3.8263018 -3.8262991 + 21500 2.94271e-05 -3.9605484 -3.9605484 -3.9605484 -3.9605778 + 21600 3.2932776e-05 -4.0900526 -4.0900526 -4.0900526 -4.0902275 + 21700 3.6482197e-05 -4.2183658 -4.2183658 -4.2183658 -4.2187208 + 21800 3.9901933e-05 -4.3498077 -4.3498077 -4.3498077 -4.3503142 + 21900 4.3096586e-05 -4.4878953 -4.4878953 -4.4878953 -4.4885197 + 22000 4.6065281e-05 -4.6348263 -4.6348263 -4.6348263 -4.6355379 + 22100 4.8854721e-05 -4.7916676 -4.7916676 -4.7916676 -4.7924466 + 22200 5.1467377e-05 -4.958865 -4.958865 -4.958865 -4.9597307 + 22300 5.3899117e-05 -5.1366375 -5.1366375 -5.1366375 -5.1376323 + 22400 5.6210492e-05 -5.3246709 -5.3246709 -5.3246709 -5.3257786 + 22500 5.8495105e-05 -5.5216133 -5.5216133 -5.5216133 -5.5227109 + 22600 6.0812028e-05 -5.7258178 -5.7258178 -5.7258178 -5.7265308 + 22700 6.3143749e-05 -5.9368597 -5.9368597 -5.9368595 -5.9365948 + 22800 6.5410125e-05 -6.1554904 -6.1554904 -6.155484 -6.1532615 + 22900 6.7542278e-05 -6.3835712 -6.3835712 -6.3835479 -6.3779477 + 23000 6.9507997e-05 -6.6216992 -6.6216992 -6.6216707 -6.6104365 + 23100 7.1266388e-05 -6.8682926 -6.8682926 -6.8682125 -6.8496968 + 23200 7.2755292e-05 -7.1203614 -7.1203614 -7.1199808 -7.0940328 + 23300 7.3926113e-05 -7.3743208 -7.3743208 -7.3732718 -7.3415245 + 23400 7.477841e-05 -7.6268907 -7.6268907 -7.624851 -7.5907534 + 23500 7.5367785e-05 -7.8755433 -7.8755433 -7.8722996 -7.840737 + 23600 7.5767316e-05 -8.118477 -8.118477 -8.1140037 -8.0907012 + 23700 7.602765e-05 -8.3545004 -8.3545004 -8.3489055 -8.3399761 + 23800 7.6179748e-05 -8.5831449 -8.5831448 -8.5766169 -8.588118 + 23900 7.6254392e-05 -8.8047933 -8.8047901 -8.7975178 -8.8348184 + 24000 7.6282088e-05 -9.0203998 -9.02038 -9.0124888 -9.0799295 + 24100 7.6273769e-05 -9.2308282 -9.2307693 -9.2224638 -9.3235303 + 24200 7.6210421e-05 -9.4363163 -9.4361182 -9.4281809 -9.5657774 + 24300 7.6054129e-05 -9.6364815 -9.6359364 -9.6298499 -9.8069317 + 24400 7.5770911e-05 -9.8308075 -9.8296133 -9.8273813 -10.047332 + 24500 7.5346158e-05 -10.019212 -10.016965 -10.020848 -10.287277 + 24600 7.4773894e-05 -10.202327 -10.198639 -10.21069 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x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.3143 | 6.3143 | 6.3143 | 0.0 | 9.22 +Bond | 50.992 | 50.992 | 50.992 | 0.0 | 74.44 +Neigh | 1.9091 | 1.9091 | 1.9091 | 0.0 | 2.79 +Comm | 0.12117 | 0.12117 | 0.12117 | 0.0 | 0.18 +Output | 0.043458 | 0.043458 | 0.043458 | 0.0 | 0.06 +Modify | 7.4924 | 7.4924 | 7.4924 | 0.0 | 10.94 +Other | | 1.626 | | | 2.37 + +Nlocal: 9576 ave 9576 max 9576 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 44768 ave 44768 max 44768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 44768 +Ave neighs/atom = 4.6750209 +Ave special neighs/atom = 11.495405 +Neighbor list builds = 365 +Dangerous builds = 0 + +# remove load + +unfix 3 +run 50000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 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-33.356853 + 119800 1.8211288e-07 -2.8771001 -6.1941032 -15.131011 -33.35882 + 119900 1.9159516e-07 -2.8587205 -6.1799459 -15.127154 -33.3607 + 120000 2.0075596e-07 -2.8398756 -6.1653354 -15.122793 -33.362492 +Loop time of 66.7366 on 1 procs for 50000 steps with 9576 atoms + +Performance: 6473210.162 tau/day, 749.214 timesteps/s, 7.174 Matom-step/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.3674 | 6.3674 | 6.3674 | 0.0 | 9.54 +Bond | 50.92 | 50.92 | 50.92 | 0.0 | 76.30 +Neigh | 1.1547 | 1.1547 | 1.1547 | 0.0 | 1.73 +Comm | 0.11662 | 0.11662 | 0.11662 | 0.0 | 0.17 +Output | 0.041399 | 0.041399 | 0.041399 | 0.0 | 0.06 +Modify | 6.3682 | 6.3682 | 6.3682 | 0.0 | 9.54 +Other | | 1.768 | | | 2.65 + +Nlocal: 9576 ave 9576 max 9576 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 44738 ave 44738 max 44738 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 44738 +Ave neighs/atom = 4.6718881 +Ave special neighs/atom = 11.495405 +Neighbor list builds = 219 +Dangerous builds = 0 +Total wall time: 0:02:17 diff --git a/examples/bpm/poissons_ratio/in.bpm.poissons_ratio b/examples/bpm/poissons_ratio/in.bpm.poissons_ratio index 4f31291a6a..71052ad417 100644 --- a/examples/bpm/poissons_ratio/in.bpm.poissons_ratio +++ b/examples/bpm/poissons_ratio/in.bpm.poissons_ratio @@ -1,4 +1,4 @@ -# Squish three pillars with different Poisson's ratios +# Squish four pillars with different Poisson's ratios # going from nearly incompressible to auxetic # from left to right, nu ~ 0.5, 0.25, 0, <0 # calibration from DOI: 10.1039/d3sm01373a From edaab05db6c6565ab70f2942ea443ae5c2015e09 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 4 Feb 2025 13:12:35 -0700 Subject: [PATCH 07/12] Tweaking BPM plastic example parameters --- examples/bpm/plasticity/in.bpm.plasticity | 21 +- .../log.19Nov2024.bpm.plasticity.g++.1 | 2553 ++++++++++------- 2 files changed, 1516 insertions(+), 1058 deletions(-) diff --git a/examples/bpm/plasticity/in.bpm.plasticity b/examples/bpm/plasticity/in.bpm.plasticity index 47e82455ed..4cf8f277a8 100644 --- a/examples/bpm/plasticity/in.bpm.plasticity +++ b/examples/bpm/plasticity/in.bpm.plasticity @@ -65,9 +65,9 @@ special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 bond_style bpm/spring/plastic break no smooth no bond_coeff 1 1.0 0 1.0 1.0 -bond_coeff 2 1.0 0 1.0 0.03 -bond_coeff 3 1.0 0 1.0 0.02 -bond_coeff 4 1.0 0 1.0 0.01 +bond_coeff 2 1.0 0 1.0 0.022 +bond_coeff 3 1.0 0 1.0 0.0185 +bond_coeff 4 1.0 0 1.0 0.017 # apply load @@ -76,9 +76,10 @@ region load block EDGE EDGE 38.0 EDGE EDGE EDGE units box group anchor region anchor group load region load +variable fload equal ramp(0.0,-0.0005) fix 2 anchor setforce 0.0 0.0 0.0 -fix 3 load addforce 0.0 0.0 -0.0005 -fix 4 all viscous 0.001 +fix 3 load addforce 0.0 0.0 v_fload +fix 4 all viscous 0.0016 compute zmin1 c1 reduce min z compute zmin2 c2 reduce min z @@ -86,11 +87,17 @@ compute zmin3 c3 reduce min z compute zmin4 c4 reduce min z thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4 -#dump 1 all custom 200 atomDump id type x y z +#dump 1 all custom 1000 atomDump id type x y z +run 30000 + +# hold load + +unfix 3 +fix 3 load addforce 0.0 0.0 -0.0005 run 50000 # remove load unfix 3 -run 50000 +run 60000 diff --git a/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 b/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 index 45fd829e70..e51437b585 100644 --- a/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 +++ b/examples/bpm/plasticity/log.19Nov2024.bpm.plasticity.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1028-g800a5f6310-modified) +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1034-ged627579f6-modified) # Load then unload four cantilevers with different plastic yield strains # model from DOI: 10.1016/j.powtec.2024.120563 @@ -255,21 +255,21 @@ Per MPI rank memory allocation (min/avg/max) = 9.752 | 9.752 | 9.752 Mbytes 19800 1.7683141e-06 3.8353201e-08 1.29417e-05 1.0764969e-05 1.116828e-05 19900 1.7664071e-06 3.2153664e-08 9.4515931e-06 1.1051242e-05 1.0924767e-05 20000 1.7618892e-06 2.2689236e-08 8.4011955e-06 7.5721128e-06 8.9521609e-06 -Loop time of 2.54444 on 1 procs for 20000 steps with 2394 atoms +Loop time of 1.48476 on 1 procs for 20000 steps with 2394 atoms -Performance: 67912724.488 tau/day, 7860.269 timesteps/s, 18.817 Matom-step/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 116382628.128 tau/day, 13470.212 timesteps/s, 32.248 Matom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2052 | 1.2052 | 1.2052 | 0.0 | 47.37 -Bond | 0.00069514 | 0.00069514 | 0.00069514 | 0.0 | 0.03 -Neigh | 0.18155 | 0.18155 | 0.18155 | 0.0 | 7.14 -Comm | 0.0076275 | 0.0076275 | 0.0076275 | 0.0 | 0.30 -Output | 0.0043813 | 0.0043813 | 0.0043813 | 0.0 | 0.17 -Modify | 1.0429 | 1.0429 | 1.0429 | 0.0 | 40.99 -Other | | 0.1021 | | | 4.01 +Pair | 0.63885 | 0.63885 | 0.63885 | 0.0 | 43.03 +Bond | 0.00053413 | 0.00053413 | 0.00053413 | 0.0 | 0.04 +Neigh | 0.15112 | 0.15112 | 0.15112 | 0.0 | 10.18 +Comm | 0.0056225 | 0.0056225 | 0.0056225 | 0.0 | 0.38 +Output | 0.0032158 | 0.0032158 | 0.0032158 | 0.0 | 0.22 +Modify | 0.61597 | 0.61597 | 0.61597 | 0.0 | 41.49 +Other | | 0.06945 | | | 4.68 Nlocal: 2394 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -298,7 +298,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-2 neighbors 101 = max # of special neighbors special bonds CPU = 0.000 seconds - replicate CPU = 0.002 seconds + replicate CPU = 0.001 seconds region r1 block 0.0 20.0 EDGE EDGE EDGE EDGE side in units box region r2 block 20.0 40.0 EDGE EDGE EDGE EDGE side in units box @@ -408,7 +408,7 @@ Finding 1-2 1-3 1-4 neighbors ... special bond factors coul: 0 1 1 17 = max # of 1-2 neighbors 101 = max # of special neighbors - special bonds CPU = 0.003 seconds + special bonds CPU = 0.002 seconds create_bonds many c4 c4 4 0.0 1.5 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule WARNING: Bonds are defined but no bond style is set (../force.cpp:197) @@ -436,16 +436,16 @@ Finding 1-2 1-3 1-4 neighbors ... special bond factors coul: 0 1 1 17 = max # of 1-2 neighbors 101 = max # of special neighbors - special bonds CPU = 0.003 seconds + special bonds CPU = 0.002 seconds neighbor 0.3 bin special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 bond_style bpm/spring/plastic break no smooth no bond_coeff 1 1.0 0 1.0 1.0 -bond_coeff 2 1.0 0 1.0 0.03 -bond_coeff 3 1.0 0 1.0 0.02 -bond_coeff 4 1.0 0 1.0 0.01 +bond_coeff 2 1.0 0 1.0 0.022 +bond_coeff 3 1.0 0 1.0 0.0185 +bond_coeff 4 1.0 0 1.0 0.017 # apply load @@ -456,9 +456,10 @@ group anchor region anchor group load region load 592 atoms in group load +variable fload equal ramp(0.0,-0.0005) fix 2 anchor setforce 0.0 0.0 0.0 -fix 3 load addforce 0.0 0.0 -0.0005 -fix 4 all viscous 0.001 +fix 3 load addforce 0.0 0.0 v_fload +fix 4 all viscous 0.0016 compute zmin1 c1 reduce min z compute zmin2 c2 reduce min z @@ -466,9 +467,9 @@ compute zmin3 c3 reduce min z compute zmin4 c4 reduce min z thermo_style custom step ke c_zmin1 c_zmin2 c_zmin3 c_zmin4 -#dump 1 all custom 200 atomDump id type x y z +dump 1 all custom 1000 atomDump id type x y z -run 50000 +run 30000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -487,6 +488,18 @@ Your simulation uses code contributions which should be cited: pages = {1702--1718} } +- BPM/spring/plastic bond style: doi:10.1016/j.powtec.2024.120563 + +@Article{Clemmer2025, + author = {Clemmer, Joel T. and Lechman, Jeremy B.}, + title = {Onset and impact of plastic deformation in granular compaction}, + journal = {Powder Technology}, + year = 2025, + volume = 452, + number = 28, + pages = {120563} +} + CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule @@ -505,1069 +518,1507 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 20.02 | 20.02 | 20.02 Mbytes Step KinEng c_zmin1 c_zmin2 c_zmin3 c_zmin4 20000 0 -2.5009426 -2.5009426 -2.5009426 -2.5009426 - 20100 4.0956567e-07 -2.5160602 -2.5160602 -2.5160602 -2.5160602 - 20200 1.3143434e-06 -2.555086 -2.555086 -2.555086 -2.555086 - 20300 2.5328497e-06 -2.6114806 -2.6114806 -2.6114806 -2.6114806 - 20400 4.0044252e-06 -2.6807339 -2.6807339 -2.6807339 -2.6807339 - 20500 5.683827e-06 -2.7603965 -2.7603965 -2.7603965 -2.7603965 - 20600 7.5588865e-06 -2.8493381 -2.8493381 -2.8493381 -2.8493381 - 20700 9.5460405e-06 -2.9466232 -2.9466232 -2.9466232 -2.9466232 - 20800 1.1434976e-05 -3.0516294 -3.0516294 -3.0516294 -3.0516294 - 20900 1.3298452e-05 -3.1649086 -3.1649086 -3.1649086 -3.1649086 - 21000 1.5334087e-05 -3.2853774 -3.2853774 -3.2853774 -3.2853774 - 21100 1.7644543e-05 -3.4124904 -3.4124904 -3.4124904 -3.4124904 - 21200 2.0249305e-05 -3.5471314 -3.5471314 -3.5471314 -3.5471314 - 21300 2.3096201e-05 -3.6870368 -3.6870368 -3.6870368 -3.6870367 - 21400 2.6137865e-05 -3.8263018 -3.8263018 -3.8263018 -3.8262991 - 21500 2.94271e-05 -3.9605484 -3.9605484 -3.9605484 -3.9605778 - 21600 3.2932776e-05 -4.0900526 -4.0900526 -4.0900526 -4.0902275 - 21700 3.6482197e-05 -4.2183658 -4.2183658 -4.2183658 -4.2187208 - 21800 3.9901933e-05 -4.3498077 -4.3498077 -4.3498077 -4.3503142 - 21900 4.3096586e-05 -4.4878953 -4.4878953 -4.4878953 -4.4885197 - 22000 4.6065281e-05 -4.6348263 -4.6348263 -4.6348263 -4.6355379 - 22100 4.8854721e-05 -4.7916676 -4.7916676 -4.7916676 -4.7924466 - 22200 5.1467377e-05 -4.958865 -4.958865 -4.958865 -4.9597307 - 22300 5.3899117e-05 -5.1366375 -5.1366375 -5.1366375 -5.1376323 - 22400 5.6210492e-05 -5.3246709 -5.3246709 -5.3246709 -5.3257786 - 22500 5.8495105e-05 -5.5216133 -5.5216133 -5.5216133 -5.5227109 - 22600 6.0812028e-05 -5.7258178 -5.7258178 -5.7258178 -5.7265308 - 22700 6.3143749e-05 -5.9368597 -5.9368597 -5.9368595 -5.9365948 - 22800 6.5410125e-05 -6.1554904 -6.1554904 -6.155484 -6.1532615 - 22900 6.7542278e-05 -6.3835712 -6.3835712 -6.3835479 -6.3779477 - 23000 6.9507997e-05 -6.6216992 -6.6216992 -6.6216707 -6.6104365 - 23100 7.1266388e-05 -6.8682926 -6.8682926 -6.8682125 -6.8496968 - 23200 7.2755292e-05 -7.1203614 -7.1203614 -7.1199808 -7.0940328 - 23300 7.3926113e-05 -7.3743208 -7.3743208 -7.3732718 -7.3415245 - 23400 7.477841e-05 -7.6268907 -7.6268907 -7.624851 -7.5907534 - 23500 7.5367785e-05 -7.8755433 -7.8755433 -7.8722996 -7.840737 - 23600 7.5767316e-05 -8.118477 -8.118477 -8.1140037 -8.0907012 - 23700 7.602765e-05 -8.3545004 -8.3545004 -8.3489055 -8.3399761 - 23800 7.6179748e-05 -8.5831449 -8.5831448 -8.5766169 -8.588118 - 23900 7.6254392e-05 -8.8047933 -8.8047901 -8.7975178 -8.8348184 - 24000 7.6282088e-05 -9.0203998 -9.02038 -9.0124888 -9.0799295 - 24100 7.6273769e-05 -9.2308282 -9.2307693 -9.2224638 -9.3235303 - 24200 7.6210421e-05 -9.4363163 -9.4361182 -9.4281809 -9.5657774 - 24300 7.6054129e-05 -9.6364815 -9.6359364 -9.6298499 -9.8069317 - 24400 7.5770911e-05 -9.8308075 -9.8296133 -9.8273813 -10.047332 - 24500 7.5346158e-05 -10.019212 -10.016965 -10.020848 -10.287277 - 24600 7.4773894e-05 -10.202327 -10.198639 -10.21069 -10.526948 - 24700 7.4050263e-05 -10.381365 -10.375876 -10.397763 -10.766375 - 24800 7.3180356e-05 -10.557735 -10.550055 -10.58316 -11.005505 - 24900 7.2185526e-05 -10.732679 -10.722522 -10.767885 -11.244347 - 25000 7.1106011e-05 -10.907087 -10.894308 -10.952726 -11.483049 - 25100 6.9985212e-05 -11.081419 -11.066111 -11.138362 -11.721873 - 25200 6.8853108e-05 -11.255636 -11.238316 -11.325516 -11.961107 - 25300 6.7725304e-05 -11.429152 -11.410944 -11.514757 -12.201026 - 25400 6.660963e-05 -11.600933 -11.583606 -11.706214 -12.441881 - 25500 6.5511741e-05 -11.769787 -11.755527 -11.899618 -12.683904 - 25600 6.4431312e-05 -11.93471 -11.925846 -12.09448 -12.927272 - 25700 6.3358881e-05 -12.095051 -12.094001 -12.290238 -13.17205 - 25800 6.2279783e-05 -12.250417 -12.259724 -12.486358 -13.41819 - 25900 6.1182597e-05 -12.400395 -12.422931 -12.682434 -13.665588 - 26000 6.0064731e-05 -12.544284 -12.583582 -12.878121 -13.914096 - 26100 5.8931468e-05 -12.681003 -12.74145 -13.072993 -14.163547 - 26200 5.7791958e-05 -12.809231 -12.895994 -13.266591 -14.413818 - 26300 5.6657846e-05 -12.92764 -13.04641 -13.458453 -14.664819 - 26400 5.5543753e-05 -13.035138 -13.191802 -13.648055 -14.916483 - 26500 5.4465863e-05 -13.13102 -13.331331 -13.834847 -15.168771 - 26600 5.3437869e-05 -13.215073 -13.464305 -14.018282 -15.421628 - 26700 5.2467582e-05 -13.287603 -13.590164 -14.197897 -15.674928 - 26800 5.1557173e-05 -13.34938 -13.708555 -14.373328 -15.928477 - 26900 5.0705883e-05 -13.40147 -13.819378 -14.544261 -16.182031 - 27000 4.9911134e-05 -13.444985 -13.922817 -14.710472 -16.435349 - 27100 4.9168609e-05 -13.480839 -14.019362 -14.871829 -16.688246 - 27200 4.8472969e-05 -13.50963 -14.109672 -15.028327 -16.940585 - 27300 4.7820336e-05 -13.53168 -14.194403 -15.180117 -17.192235 - 27400 4.7210393e-05 -13.547187 -14.274111 -15.327496 -17.443055 - 27500 4.6646131e-05 -13.556406 -14.349198 -15.470825 -17.692916 - 27600 4.6131822e-05 -13.55974 -14.419959 -15.61046 -17.941734 - 27700 4.5671463e-05 -13.557748 -14.486644 -15.746709 -18.189438 - 27800 4.526841e-05 -13.55106 -14.549496 -15.879832 -18.435965 - 27900 4.4925027e-05 -13.540261 -14.608781 -16.01005 -18.681274 - 28000 4.4641149e-05 -13.525772 -14.664791 -16.137576 -18.925336 - 28100 4.4413443e-05 -13.507739 -14.717881 -16.262673 -19.168131 - 28200 4.4236093e-05 -13.485997 -14.768473 -16.385611 -19.409639 - 28300 4.4103038e-05 -13.460087 -14.816971 -16.506607 -19.649817 - 28400 4.4009677e-05 -13.429366 -14.863676 -16.625875 -19.88859 - 28500 4.395268e-05 -13.393145 -14.908709 -16.743629 -20.125895 - 28600 4.3929199e-05 -13.35081 -14.952007 -16.860112 -20.361701 - 28700 4.3931357e-05 -13.301876 -14.99336 -16.97559 -20.596003 - 28800 4.3958849e-05 -13.245964 -15.03248 -17.090288 -20.828842 - 28900 4.4017767e-05 -13.182747 -15.069077 -17.204323 -21.060354 - 29000 4.4112107e-05 -13.111905 -15.102891 -17.317673 -21.290863 - 29100 4.4238616e-05 -13.033134 -15.133697 -17.430203 -21.520613 - 29200 4.437609e-05 -12.946196 -15.161312 -17.541762 -21.749803 - 29300 4.4521265e-05 -12.851002 -15.185556 -17.652227 -21.97852 - 29400 4.4663842e-05 -12.747688 -15.206178 -17.761476 -22.206898 - 29500 4.4799305e-05 -12.63667 -15.222853 -17.869356 -22.435207 - 29600 4.4928852e-05 -12.518653 -15.235188 -17.975691 -22.66335 - 29700 4.5048862e-05 -12.394588 -15.242741 -18.080302 -22.89138 - 29800 4.5151469e-05 -12.265571 -15.245083 -18.183038 -23.119178 - 29900 4.5238694e-05 -12.132715 -15.241915 -18.283755 -23.346422 - 30000 4.5310976e-05 -11.997019 -15.23315 -18.382297 -23.572939 - 30100 4.5367895e-05 -11.859285 -15.218941 -18.478497 -23.798746 - 30200 4.5409758e-05 -11.720105 -15.199629 -18.572189 -24.023589 - 30300 4.5437914e-05 -11.579914 -15.175689 -18.663215 -24.246982 - 30400 4.5454781e-05 -11.439079 -15.147661 -18.751468 -24.468408 - 30500 4.546054e-05 -11.297967 -15.116074 -18.8369 -24.687405 - 30600 4.5448468e-05 -11.156981 -15.08141 -18.919516 -24.903683 - 30700 4.5410939e-05 -11.016532 -15.044084 -18.999368 -25.117042 - 30800 4.5339487e-05 -10.876969 -15.004442 -19.076532 -25.32748 - 30900 4.5224936e-05 -10.7385 -14.962771 -19.151114 -25.53528 - 31000 4.5064834e-05 -10.601114 -14.919327 -19.223245 -25.740748 - 31100 4.4858022e-05 -10.464556 -14.874359 -19.293077 -25.944182 - 31200 4.4603577e-05 -10.328349 -14.82811 -19.360777 -26.145888 - 31300 4.4302138e-05 -10.191878 -14.780786 -19.426527 -26.34594 - 31400 4.3955895e-05 -10.054501 -14.732515 -19.490517 -26.544193 - 31500 4.356891e-05 -9.9156707 -14.683313 -19.552928 -26.740381 - 31600 4.3145785e-05 -9.7750191 -14.633087 -19.613944 -26.934353 - 31700 4.2689819e-05 -9.6323955 -14.581655 -19.67376 -27.126104 - 31800 4.2204394e-05 -9.4878602 -14.528796 -19.73257 -27.31555 - 31900 4.169173e-05 -9.3416467 -14.474281 -19.790543 -27.502505 - 32000 4.1153109e-05 -9.1941157 -14.417899 -19.847789 -27.686714 - 32100 4.0588966e-05 -9.0457218 -14.359461 -19.904349 -27.86792 - 32200 3.9998911e-05 -8.8969982 -14.298815 -19.960257 -28.04599 - 32300 3.9382527e-05 -8.7485603 -14.235852 -20.01557 -28.220844 - 32400 3.8739886e-05 -8.6011166 -14.170496 -20.070338 -28.392428 - 32500 3.807179e-05 -8.455473 -14.102695 -20.124582 -28.560692 - 32600 3.7380597e-05 -8.3125174 -14.032425 -20.178286 -28.725584 - 32700 3.6669507e-05 -8.173176 -13.959714 -20.231415 -28.887079 - 32800 3.5942269e-05 -8.0383455 -13.884682 -20.283914 -29.045243 - 32900 3.5203089e-05 -7.9088151 -13.807571 -20.335713 -29.200239 - 33000 3.4455796e-05 -7.7851998 -13.728756 -20.386736 -29.352283 - 33100 3.3703315e-05 -7.6679015 -13.648728 -20.436897 -29.501552 - 33200 3.2947524e-05 -7.5571093 -13.568052 -20.486094 -29.648164 - 33300 3.2188895e-05 -7.4528303 -13.487314 -20.534215 -29.792195 - 33400 3.1427363e-05 -7.3549392 -13.407076 -20.581164 -29.933685 - 33500 3.0663873e-05 -7.2632256 -13.327826 -20.626861 -30.072653 - 33600 2.9898968e-05 -7.1774267 -13.249955 -20.671239 -30.20916 - 33700 2.9133275e-05 -7.0972388 -13.173745 -20.714241 -30.343255 - 33800 2.8368812e-05 -7.0223118 -13.099383 -20.755828 -30.47491 - 33900 2.7609003e-05 -6.9522386 -13.026985 -20.79601 -30.604079 - 34000 2.6857675e-05 -6.8865525 -12.956623 -20.834836 -30.730759 - 34100 2.6118839e-05 -6.8247453 -12.888336 -20.87237 -30.854988 - 34200 2.5396622e-05 -6.7663094 -12.822128 -20.908707 -30.97674 - 34300 2.469467e-05 -6.710799 -12.757955 -20.943955 -31.095936 - 34400 2.4015785e-05 -6.6578961 -12.695711 -20.978205 -31.212492 - 34500 2.3351522e-05 -6.6074644 -12.635225 -21.011508 -31.326423 - 34600 2.2693793e-05 -6.5595753 -12.576275 -21.043901 -31.437755 - 34700 2.2042845e-05 -6.5145006 -12.518607 -21.075419 -31.546556 - 34800 2.1400448e-05 -6.4726739 -12.461972 -21.106109 -31.654648 - 34900 2.076709e-05 -6.4346333 -12.406153 -21.136024 -31.762833 - 35000 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tau/day, 1308.496 timesteps/s, 12.530 Matom-step/s 99.7% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.3143 | 6.3143 | 6.3143 | 0.0 | 9.22 -Bond | 50.992 | 50.992 | 50.992 | 0.0 | 74.44 -Neigh | 1.9091 | 1.9091 | 1.9091 | 0.0 | 2.79 -Comm | 0.12117 | 0.12117 | 0.12117 | 0.0 | 0.18 -Output | 0.043458 | 0.043458 | 0.043458 | 0.0 | 0.06 -Modify | 7.4924 | 7.4924 | 7.4924 | 0.0 | 10.94 -Other | | 1.626 | | | 2.37 +Pair | 2.5727 | 2.5727 | 2.5727 | 0.0 | 11.22 +Bond | 16.951 | 16.951 | 16.951 | 0.0 | 73.94 +Neigh | 0.25843 | 0.25843 | 0.25843 | 0.0 | 1.13 +Comm | 0.037787 | 0.037787 | 0.037787 | 0.0 | 0.16 +Output | 0.17723 | 0.17723 | 0.17723 | 0.0 | 0.77 +Modify | 2.4504 | 2.4504 | 2.4504 | 0.0 | 10.69 +Other | | 0.4793 | | | 2.09 Nlocal: 9576 ave 9576 max 9576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 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0.37652 | 0.0 | 0.90 +Comm | 0.044633 | 0.044633 | 0.044633 | 0.0 | 0.11 +Output | 0.29854 | 0.29854 | 0.29854 | 0.0 | 0.71 +Modify | 4.0413 | 4.0413 | 4.0413 | 0.0 | 9.65 +Other | | 0.8001 | | | 1.91 + +Nlocal: 9576 ave 9576 max 9576 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 44699 ave 44699 max 44699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 44699 +Ave neighs/atom = 4.6678154 +Ave special neighs/atom = 11.495405 +Neighbor list builds = 87 Dangerous builds = 0 # remove load unfix 3 -run 50000 +run 60000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 21.82 | 21.82 | 21.82 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.79 | 22.79 | 22.79 Mbytes Step KinEng c_zmin1 c_zmin2 c_zmin3 c_zmin4 - 70000 2.1813311e-07 -9.2730579 -12.893919 -21.521774 -34.603669 - 70100 2.7416894e-07 -9.2778729 -12.8872 -21.508977 -34.598374 - 70200 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+ 158300 2.6209012e-09 -2.5004006 -5.4272873 -10.729945 -17.250727 + 158400 2.7383439e-09 -2.5004006 -5.4288018 -10.730953 -17.25063 + 158500 2.8505612e-09 -2.5004006 -5.4303597 -10.732 -17.250581 + 158600 2.9568506e-09 -2.5004006 -5.4319595 -10.733086 -17.250577 + 158700 3.0565375e-09 -2.5004006 -5.433599 -10.734209 -17.250618 + 158800 3.1489662e-09 -2.5004006 -5.4352753 -10.73537 -17.250703 + 158900 3.233503e-09 -2.5004006 -5.4369853 -10.736568 -17.250832 + 159000 3.3095496e-09 -2.5004006 -5.438725 -10.737801 -17.251004 + 159100 3.3765645e-09 -2.5004006 -5.4404902 -10.739067 -17.251221 + 159200 3.4340876e-09 -2.5004006 -5.442276 -10.740364 -17.251481 + 159300 3.4817613e-09 -2.5004006 -5.4440776 -10.741689 -17.251787 + 159400 3.519345e-09 -2.5004006 -5.4458896 -10.743039 -17.252137 + 159500 3.5467184e-09 -2.5004006 -5.4477069 -10.74441 -17.252532 + 159600 3.5638745e-09 -2.5004006 -5.4495245 -10.745798 -17.252973 + 159700 3.5709026e-09 -2.5004006 -5.4513374 -10.7472 -17.253459 + 159800 3.5679663e-09 -2.5004006 -5.4531412 -10.74861 -17.25399 + 159900 3.5552803e-09 -2.5004006 -5.4549318 -10.750025 -17.254564 + 160000 3.5330905e-09 -2.5004006 -5.4567055 -10.75144 -17.255181 +Loop time of 49.2753 on 1 procs for 60000 steps with 9576 atoms -Performance: 6473210.162 tau/day, 749.214 timesteps/s, 7.174 Matom-step/s +Performance: 10520476.677 tau/day, 1217.648 timesteps/s, 11.660 Matom-step/s 99.7% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.3674 | 6.3674 | 6.3674 | 0.0 | 9.54 -Bond | 50.92 | 50.92 | 50.92 | 0.0 | 76.30 -Neigh | 1.1547 | 1.1547 | 1.1547 | 0.0 | 1.73 -Comm | 0.11662 | 0.11662 | 0.11662 | 0.0 | 0.17 -Output | 0.041399 | 0.041399 | 0.041399 | 0.0 | 0.06 -Modify | 6.3682 | 6.3682 | 6.3682 | 0.0 | 9.54 -Other | | 1.768 | | | 2.65 +Pair | 6.0276 | 6.0276 | 6.0276 | 0.0 | 12.23 +Bond | 36.671 | 36.671 | 36.671 | 0.0 | 74.42 +Neigh | 0.63507 | 0.63507 | 0.63507 | 0.0 | 1.29 +Comm | 0.063752 | 0.063752 | 0.063752 | 0.0 | 0.13 +Output | 0.3562 | 0.3562 | 0.3562 | 0.0 | 0.72 +Modify | 4.5593 | 4.5593 | 4.5593 | 0.0 | 9.25 +Other | | 0.9622 | | | 1.95 Nlocal: 9576 ave 9576 max 9576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 44738 ave 44738 max 44738 min +Neighs: 44691 ave 44691 max 44691 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 44738 -Ave neighs/atom = 4.6718881 +Total # of neighbors = 44691 +Ave neighs/atom = 4.6669799 Ave special neighs/atom = 11.495405 -Neighbor list builds = 219 +Neighbor list builds = 147 Dangerous builds = 0 -Total wall time: 0:02:17 +Total wall time: 0:01:55 From acb9fdfc247401058e187cefea4437489690b78c Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 4 Feb 2025 15:34:54 -0700 Subject: [PATCH 08/12] fix doc spacing for bpm/spring --- doc/src/bond_bpm_spring.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 4d958a2a1e..45d62fa2b9 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -215,12 +215,12 @@ for an overview of LAMMPS output options. The vector or array will be floating point values that correspond to the specified attribute. -The potential energy and the single() function of this bond style returns :math:`k (r - r_0)^2 / 2` -for a proxy of the energy of a bonded interaction, ignoring any volumetric/smoothing -factors or dissipative forces. The single() function also calculates an -extra bond quantity, the initial distance :math:`r_0`. This extra quantity -can be accessed by the :doc:`compute bond/local ` -command as *b1*\ . +The potential energy and the single() function of this bond style returns +:math:`k (r - r_0)^2 / 2` as a proxy of the energy of a bonded interaction, +ignoring any volumetric/smoothing factors or dissipative forces. The single() +function also calculates an extra bond quantity, the initial distance +:math:`r_0`. This extra quantity can be accessed by the +:doc:`compute bond/local ` command as *b1*\ . Restrictions """""""""""" From 892c20cc2012e523d78a10ac07bbbdfab091fcd0 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 4 Feb 2025 15:36:48 -0700 Subject: [PATCH 09/12] fixing typo --- doc/src/bond_bpm_spring.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 45d62fa2b9..8c5c33e93f 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -215,7 +215,7 @@ for an overview of LAMMPS output options. The vector or array will be floating point values that correspond to the specified attribute. -The potential energy and the single() function of this bond style returns +The potential energy and the single() function of this bond style return :math:`k (r - r_0)^2 / 2` as a proxy of the energy of a bonded interaction, ignoring any volumetric/smoothing factors or dissipative forces. The single() function also calculates an extra bond quantity, the initial distance From 4a3394b300087ca7e553d688ffb9701fec961e15 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 4 Feb 2025 15:42:01 -0700 Subject: [PATCH 10/12] Adding references to bpplastic bpm bond style --- doc/src/Commands_bond.rst | 1 + doc/src/Howto_bpm.rst | 6 ++++-- doc/src/bond_style.rst | 3 ++- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 40532bdef7..05c505b5ee 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -23,6 +23,7 @@ OPT. * * :doc:`bpm/rotational ` * :doc:`bpm/spring ` + * :doc:`bpm/spring/plastic ` * :doc:`class2 (ko) ` * :doc:`fene (iko) ` * :doc:`fene/expand (o) ` diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index f2aa1fc0a3..f632ee6172 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -42,12 +42,14 @@ such as those created by pouring grains using :doc:`fix pour ---------- -Currently, there are two types of bonds included in the BPM package. The +Currently, there are three types of bonds included in the BPM package. The first bond style, :doc:`bond bpm/spring `, only applies pairwise, central body forces. Point particles must have :doc:`bond atom style ` and may be thought of as nodes in a spring network. An optional multibody term can be used to adjust the network's -Poisson's ratio. Alternatively, the second bond style, :doc:`bond bpm/rotational +Poisson's ratio. The :doc:`bpm/spring/plastic ` +bond style is similar except it adds a plastic yield strain. +Alternatively, the third bond style, :doc:`bond bpm/rotational `, resolves tangential forces and torques arising with the shearing, bending, and twisting of the bond due to rotation or displacement of particles. Particles are similar to those used in the diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index 590f7c8cba..a30fb9e812 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -10,7 +10,7 @@ Syntax bond_style style args -* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table* +* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *bpm/spring/plastic* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table* * args = none for any style except *hybrid* @@ -86,6 +86,7 @@ accelerated styles exist. * :doc:`bpm/rotational ` - breakable bond with forces and torques based on deviation from reference state * :doc:`bpm/spring ` - breakable bond with forces based on deviation from reference length +* :doc:`bpm/spring/plastic ` - a similar breakable bond with plastic yield * :doc:`class2 ` - COMPASS (class 2) bond * :doc:`fene ` - FENE (finite-extensible non-linear elastic) bond * :doc:`fene/expand ` - FENE bonds with variable size particles From e178f593be3953870ba6ed6833766d1c0f4e48fd Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 4 Feb 2025 15:49:01 -0700 Subject: [PATCH 11/12] Adding BPM contribution statements --- src/BPM/atom_vec_bpm_sphere.cpp | 4 ++++ src/BPM/bond_bpm.cpp | 4 ++++ src/BPM/bond_bpm_rotational.cpp | 4 ++++ src/BPM/bond_bpm_spring.cpp | 4 ++++ src/BPM/bond_bpm_spring_plastic.cpp | 4 ++++ src/BPM/compute_nbond_atom.cpp | 4 ++++ src/BPM/fix_nve_bpm_sphere.cpp | 4 ++++ src/BPM/fix_update_special_bonds.cpp | 4 ++++ src/BPM/pair_bpm_spring.cpp | 4 ++++ src/fix_bond_history.cpp | 4 ++++ 10 files changed, 40 insertions(+) diff --git a/src/BPM/atom_vec_bpm_sphere.cpp b/src/BPM/atom_vec_bpm_sphere.cpp index 4332d517b4..5a79bb5b00 100644 --- a/src/BPM/atom_vec_bpm_sphere.cpp +++ b/src/BPM/atom_vec_bpm_sphere.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "atom_vec_bpm_sphere.h" #include "atom.h" diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index 24f8be8fd9..db6b96cf05 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "bond_bpm.h" #include "atom.h" diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index abee373c5d..50a9d18b2c 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "bond_bpm_rotational.h" #include "atom.h" diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index b58b73a43b..49ea6ae046 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "bond_bpm_spring.h" #include "atom.h" diff --git a/src/BPM/bond_bpm_spring_plastic.cpp b/src/BPM/bond_bpm_spring_plastic.cpp index 07619a8dfc..cb09ef66fc 100644 --- a/src/BPM/bond_bpm_spring_plastic.cpp +++ b/src/BPM/bond_bpm_spring_plastic.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "bond_bpm_spring_plastic.h" #include "atom.h" diff --git a/src/BPM/compute_nbond_atom.cpp b/src/BPM/compute_nbond_atom.cpp index 31428b1912..4083483faf 100644 --- a/src/BPM/compute_nbond_atom.cpp +++ b/src/BPM/compute_nbond_atom.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "compute_nbond_atom.h" #include "atom.h" diff --git a/src/BPM/fix_nve_bpm_sphere.cpp b/src/BPM/fix_nve_bpm_sphere.cpp index 1766f49c5c..89ea778bbb 100644 --- a/src/BPM/fix_nve_bpm_sphere.cpp +++ b/src/BPM/fix_nve_bpm_sphere.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "fix_nve_bpm_sphere.h" #include "atom.h" diff --git a/src/BPM/fix_update_special_bonds.cpp b/src/BPM/fix_update_special_bonds.cpp index d9a11c7819..3c37769fee 100644 --- a/src/BPM/fix_update_special_bonds.cpp +++ b/src/BPM/fix_update_special_bonds.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "fix_update_special_bonds.h" #include "atom.h" diff --git a/src/BPM/pair_bpm_spring.cpp b/src/BPM/pair_bpm_spring.cpp index e69b8c7879..931ecf590f 100644 --- a/src/BPM/pair_bpm_spring.cpp +++ b/src/BPM/pair_bpm_spring.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "pair_bpm_spring.h" #include "atom.h" diff --git a/src/fix_bond_history.cpp b/src/fix_bond_history.cpp index 38ea497ebe..0fa03e430e 100644 --- a/src/fix_bond_history.cpp +++ b/src/fix_bond_history.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Joel Clemmer (SNL) +------------------------------------------------------------------------- */ + #include "fix_bond_history.h" #include "atom.h" From ba14ce210c5ac0975a69c08cab31ed3a3dd90857 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Tue, 11 Feb 2025 10:42:56 -0700 Subject: [PATCH 12/12] Fixing mistakes & clarifying BPM files --- doc/src/bond_bpm_spring.rst | 2 +- doc/src/bond_bpm_spring_plastic.rst | 16 ++++++++-------- src/BPM/bond_bpm_rotational.cpp | 3 +-- src/BPM/bond_bpm_spring.cpp | 2 +- src/BPM/bond_bpm_spring_plastic.cpp | 2 +- src/BPM/pair_bpm_spring.cpp | 2 +- 6 files changed, 13 insertions(+), 14 deletions(-) diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 77da77bcfc..69d8e2d491 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -10,7 +10,7 @@ Syntax bond_style bpm/spring keyword value attribute1 attribute2 ... -* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor* +* optional keyword = *overlay/pair* or *store/local* or *smooth* or *normalize* or *break* or *volume/factor* .. parsed-literal:: diff --git a/doc/src/bond_bpm_spring_plastic.rst b/doc/src/bond_bpm_spring_plastic.rst index 06e1846c58..fb0c50e9d3 100644 --- a/doc/src/bond_bpm_spring_plastic.rst +++ b/doc/src/bond_bpm_spring_plastic.rst @@ -10,7 +10,7 @@ Syntax bond_style bpm/spring/plastic keyword value attribute1 attribute2 ... -* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* +* optional keyword = *overlay/pair* or *store/local* or *smooth* or *normalize* or *break* .. parsed-literal:: @@ -72,12 +72,12 @@ particles. The force has a magnitude of where :math:`k` is a stiffness, :math:`r` is the current distance between the two particles, and :math:`w` is an optional smoothing factor discussed -below. If the bond stretches beyond a strain of :math:`\epsilon_p`, it will -plastically activate and :math:`r_\mathrm{eq}` will evolve to ensure -:math:`|(r-r_\mathrm{eq})/r_\mathrm{eq}|` never exceeds :math:`\epsilon_p`. -Therefore, in pure tension, the force initially grows elastically before -plateauing. See :ref:`(Clemmer) ` for more details on -these mechanics. +below. If the bond stretches beyond a strain of :math:`\epsilon_p` in compression +or extension, it will plastically activate and :math:`r_\mathrm{eq}` will evolve +to ensure :math:`|(r-r_\mathrm{eq})/r_\mathrm{eq}|` never exceeds :math:`\epsilon_p`. +Therefore, if a bond is continually loaded in either tension or compression, the +force will initially grow elastically before plateauing. See +:ref:`(Clemmer) ` for more details on these mechanics. Bonds will break at a strain of :math:`\epsilon_c`. This is done by setting the bond type to 0 such that forces are no longer computed. @@ -142,7 +142,7 @@ The potential energy and the single() function of this bond style returns zero. The single() function also calculates two extra bond quantities, the initial distance :math:`r_0` and the current equilbrium length :math:`r_eq`. These extra quantities can be accessed by the :doc:`compute bond/local ` -command as *b1* and *b2*\ . +command as *b1* and *b2*, respectively. Restrictions """""""""""" diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index 50a9d18b2c..ad08edb3e9 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -158,7 +158,7 @@ void BondBPMRotational::store_data() type = bond_type[i][m]; //Skip if bond was turned off - if (type < 0) continue; + if (type <= 0) continue; // map to find index n for tag j = atom->map(atom->bond_atom[i][m]); @@ -779,7 +779,6 @@ void BondBPMRotational::read_restart_settings(FILE *fp) double BondBPMRotational::single(int type, double rsq, int i, int j, double &fforce) { - // Not yet enabled if (type <= 0) return 0.0; int flipped = 0; diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index 49ea6ae046..9e007c9372 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -128,7 +128,7 @@ void BondBPMSpring::store_data() type = bond_type[i][m]; //Skip if bond was turned off - if (type < 0) continue; + if (type <= 0) continue; // map to find index n j = atom->map(atom->bond_atom[i][m]); diff --git a/src/BPM/bond_bpm_spring_plastic.cpp b/src/BPM/bond_bpm_spring_plastic.cpp index cb09ef66fc..35fd8e4691 100644 --- a/src/BPM/bond_bpm_spring_plastic.cpp +++ b/src/BPM/bond_bpm_spring_plastic.cpp @@ -136,7 +136,7 @@ void BondBPMSpringPlastic::store_data() type = bond_type[i][m]; //Skip if bond was turned off - if (type < 0) continue; + if (type <= 0) continue; // map to find index n j = atom->map(atom->bond_atom[i][m]); diff --git a/src/BPM/pair_bpm_spring.cpp b/src/BPM/pair_bpm_spring.cpp index 931ecf590f..1ca9362347 100644 --- a/src/BPM/pair_bpm_spring.cpp +++ b/src/BPM/pair_bpm_spring.cpp @@ -386,7 +386,7 @@ double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq, dou dr = r - cut[itype][jtype]; fpair = -k[itype][jtype] * dr; - double energy = -0.5 * fpair * (r - cut[itype][jtype]); + double energy = -0.5 * fpair * dr; if (anharmonic_flag) { double fa = -ka[itype][jtype] * dr * dr * dr;