From d8f211c05d6f4e70d380dc16bf34d424f94132d5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 8 Sep 2022 17:15:23 -0600 Subject: [PATCH 01/11] allow fix latte to exclude atoms in a group --- src/LATTE/fix_latte.cpp | 179 +++++++++++++++++++++++++++++++--------- src/LATTE/fix_latte.h | 6 ++ 2 files changed, 147 insertions(+), 38 deletions(-) diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 71df0d0c8b..b72deb6f08 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -24,6 +24,7 @@ #include "domain.h" #include "error.h" #include "force.h" +#include "group.h" #include "memory.h" #include "modify.h" #include "update.h" @@ -63,8 +64,6 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : if (LATTE_ABIVERSION != latte_abiversion()) error->all(FLERR,"LAMMPS is linked against incompatible LATTE library"); - if (narg != 4) error->all(FLERR,"Illegal fix latte command"); - scalar_flag = 1; global_freq = 1; extscalar = 1; @@ -72,21 +71,40 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : virial_global_flag = 1; thermo_energy = thermo_virial = 1; - // store ID of compute pe/atom used to generate Coulomb potential for LATTE - // null pointer means LATTE will compute Coulombic potential - + // process optional args + coulomb = 0; id_pe = nullptr; + exclude = 0; - if (strcmp(arg[3],"NULL") != 0) { - coulomb = 1; - error->all(FLERR,"Fix latte does not yet support a LAMMPS calculation of a Coulomb potential"); + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"coulomb") == 0) { + if (iarg+2 > narg) + utils::missing_cmd_args(FLERR, "fix latte coulomb", error); + coulomb = 1; + error->all(FLERR,"Fix latte does not yet support a " + "LAMMPS calculation of a Coulomb potential"); + id_pe = utils::strdup(arg[3]); + c_pe = modify->get_compute_by_id(id_pe); + if (!c_pe) error->all(FLERR,"Could not find fix latte compute ID {}", id_pe); + if (c_pe->peatomflag == 0) + error->all(FLERR,"Fix latte compute ID does not compute pe/atom"); + iarg += 2; - id_pe = utils::strdup(arg[3]); - c_pe = modify->get_compute_by_id(id_pe); - if (!c_pe) error->all(FLERR,"Could not find fix latte compute ID {}", id_pe); - if (c_pe->peatomflag == 0) - error->all(FLERR,"Fix latte compute ID does not compute pe/atom"); + } else if (strcmp(arg[iarg],"exclude") == 0) { + if (iarg+2 > narg) + utils::missing_cmd_args(FLERR, "fix latte exclude", error); + exclude = 1; + int excludegroup = group->find(arg[iarg+1]); + if (excludegroup == -1) + error->all(FLERR, "Fix latte couldd not find exclude group ID: {}", + arg[iarg+1]); + excludebit = group->bitmask[excludegroup]; + iarg += 2; + + } else + error->all(FLERR, "Unknown fix latte keyword: {}", arg[iarg]); } // initializations @@ -234,37 +252,32 @@ void FixLatte::post_force(int vflag) neighflag = 0; // set flags used by LATTE - // NOTE: LATTE does not compute per-atom energies or virials + // note that LATTE does not compute per-atom energies or virials - int flags[6]; + flags_latte[0] = pbcflag; // 1 for fully periodic, 0 for fully non-periodic + flags_latte[1] = coulombflag; // 1 for LAMMPS computes Coulombics, 0 for LATTE + flags_latte[2] = eflag_atom; // 1 to return per-atom energies, 0 for no + flags_latte[3] = vflag_global && thermo_virial; // 1 to return global/per-atom + flags_latte[4] = vflag_atom && thermo_virial; // virial, 0 for no + flags_latte[5] = neighflag; // 1 to pass neighbor list to LATTE, 0 for no - flags[0] = pbcflag; // 1 for fully periodic, 0 for fully non-periodic - flags[1] = coulombflag; // 1 for LAMMPS computes Coulombics, 0 for LATTE - flags[2] = eflag_atom; // 1 to return per-atom energies, 0 for no - flags[3] = vflag_global && thermo_virial; // 1 to return global/per-atom - flags[4] = vflag_atom && thermo_virial; // virial, 0 for no - flags[5] = neighflag; // 1 to pass neighbor list to LATTE, 0 for no + // setup arguments for latte() function within LATTE lib and invoke it + // either for all atoms or excluding some atoms + // in latter case, need to construct reduced-size per-atom vectors/arrays - // setup LATTE arguments + if (!exclude) latte_wrapper_all(); + else { + int *mask = atom->mask; + int nlocal = atom->nlocal; - int natoms = atom->nlocal; - double *coords = &atom->x[0][0]; - int *type = atom->type; - int ntypes = atom->ntypes; - double *mass = &atom->mass[1]; - double *boxlo = domain->boxlo; - double *boxhi = domain->boxhi; - double *forces; - bool latteerror = false; - if (coulomb) forces = &flatte[0][0]; - else forces = &atom->f[0][0]; - int maxiter = -1; + int anyexclude = 0; + for (int i = 0; i < nlocal; i++) + if (mask[i] & excludebit) anyexclude = 1; - latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy, - &domain->xz,&domain->yz,forces,&maxiter,&latte_energy, - &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); + if (!anyexclude) latte_wrapper_all(); + else latte_wrapper_exclude(); + } - if (latteerror) error->all(FLERR,"Internal LATTE problem"); // sum LATTE forces to LAMMPS forces // e.g. LAMMPS may compute Coulombics at some point @@ -280,6 +293,96 @@ void FixLatte::post_force(int vflag) } } +/* ---------------------------------------------------------------------- + invoke LATTE on all LAMMPS atoms +------------------------------------------------------------------------- */ + +void FixLatte::latte_wrapper_all() +{ + int natoms = atom->nlocal; + double *coords = &atom->x[0][0]; + int *types = atom->type; + int ntypes = atom->ntypes; + double *mass = &atom->mass[1]; + double *boxlo = domain->boxlo; + double *boxhi = domain->boxhi; + double *forces; + bool latteerror = false; + if (coulomb) forces = &flatte[0][0]; + else forces = &atom->f[0][0]; + int maxiter = -1; + + latte(flags_latte,&natoms,coords,types,&ntypes,mass,boxlo,boxhi, + &domain->xy,&domain->xz,&domain->yz,forces,&maxiter,&latte_energy, + &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); + + if (latteerror) error->all(FLERR,"Internal LATTE problem"); +} + +/* ---------------------------------------------------------------------- + invoke LATTE on only LAMMPS atoms not in exclude group +------------------------------------------------------------------------- */ + +void FixLatte::latte_wrapper_exclude() +{ + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int nlatte = 0; + for (int i = 0; i < nlocal; i++) + if (!(mask[i] & excludebit)) nlatte++; + + // created compressed type vectory and coords array + + int *typeinclude; + double **xinclude,**finclude; + memory->create(typeinclude,nlatte,"latte:typeinclude"); + memory->create(xinclude,nlatte,3,"latte:xinclude"); + memory->create(finclude,nlatte,3,"latte:finclude"); + + double **x = atom->x; + int *type = atom->type; + + nlatte = 0; + for (int i = 0; i < nlocal; i++) { + if (mask[i] & excludebit) continue; + typeinclude[nlatte] = type[i]; + x[nlatte][0] = x[i][0]; + x[nlatte][1] = x[i][1]; + x[nlatte][2] = x[i][2]; + nlatte++; + } + + double *coords = &xinclude[0][0]; + int *types = typeinclude; + int ntypes = atom->ntypes; + double *mass = &atom->mass[1]; + double *boxlo = domain->boxlo; + double *boxhi = domain->boxhi; + double *forces = &finclude[0][0]; + bool latteerror = false; + int maxiter = -1; + + latte(flags_latte,&nlatte,coords,types,&ntypes,mass,boxlo,boxhi, + &domain->xy,&domain->xz,&domain->yz,forces,&maxiter,&latte_energy, + &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); + + if (latteerror) error->all(FLERR,"Internal LATTE problem"); + + // expand compressed forces array + + double **f = atom->f; + + int m = 0; + for (int i = 0; i < nlocal; i++) { + if (mask[i] & excludebit) continue; + f[i][0] = forces[m+0]; + f[i][1] = forces[m+1]; + f[i][2] = forces[m+2]; + m += 3; + } +} + /* ---------------------------------------------------------------------- */ void FixLatte::min_post_force(int vflag) diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index 894940e1e2..fdc3fdee40 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -46,8 +46,11 @@ class FixLatte : public Fix { protected: char *id_pe; int coulomb, pbcflag, pe_peratom, virial_global, virial_peratom, neighflag; + int exclude, excludebit; int eflag_caller; + int flags_latte[6]; + int nmax, newsystem; double *qpotential; double **flatte; @@ -55,6 +58,9 @@ class FixLatte : public Fix { class NeighList *list; class Compute *c_pe; + + void latte_wrapper_all(); + void latte_wrapper_exclude(); }; } // namespace LAMMPS_NS From ad05300d25fc9650ed15b04063f2ccd6ddea7d50 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 8 Sep 2022 17:27:53 -0600 Subject: [PATCH 02/11] free memory --- src/LATTE/fix_latte.cpp | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index b72deb6f08..1095b9ab9a 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -328,11 +328,13 @@ void FixLatte::latte_wrapper_exclude() int *mask = atom->mask; int nlocal = atom->nlocal; + // nlatte = number of non-excluded atoms to pass to LATTE + int nlatte = 0; for (int i = 0; i < nlocal; i++) if (!(mask[i] & excludebit)) nlatte++; - // created compressed type vectory and coords array + // created compressed type vector and coords array int *typeinclude; double **xinclude,**finclude; @@ -381,6 +383,10 @@ void FixLatte::latte_wrapper_exclude() f[i][2] = forces[m+2]; m += 3; } + + memory->destroy(typeinclude); + memory->destroy(xinclude); + memory->destroy(finclude); } /* ---------------------------------------------------------------------- */ From 97f8a600e798aeca6d61397b0c40d173444ab4fa Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 8 Sep 2022 17:44:15 -0600 Subject: [PATCH 03/11] initial doc page edits --- doc/src/fix_latte.rst | 47 ++++++++++++++++++++++++++++++++++++------- 1 file changed, 40 insertions(+), 7 deletions(-) diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index 8a6315fa48..6ce84f9d52 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -8,18 +8,27 @@ Syntax .. parsed-literal:: - fix ID group-ID latte peID + fix ID group-ID latte keyword value ... * ID, group-ID are documented in :doc:`fix ` command * latte = style name of this fix command -* peID = NULL or ID of compute used to calculate per-atom energy +* zero or more keyword/value pairs may be appended + + .. parsed-literal:: + + keyword = *coulomb* or *exclude* + *coulomb* value = peID + peID = ID of compute used to calculate per-atom energy + *exclude* value = groupID + groupID = ID of group of atoms to exclude before calling LATTE Examples """""""" .. code-block:: LAMMPS - fix dftb all latte NULL + fix dftb all latte + fix dftb all exclude GCMCmol Description """"""""""" @@ -48,10 +57,34 @@ found in examples/latte. A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial `_ -The *peID* argument is not yet supported by fix latte, so it must be -specified as NULL. Eventually it will be used to enable LAMMPS to -calculate a Coulomb potential as an alternative to LATTE performing -the calculation. +---------- + +The *coulomb* argument is not yet supported by fix latte (as of Sept +2022). Eventually it will be used to enable LAMMPS to calculate a +Coulomb potential as an alternative to LATTE performing the +calculation. + +NOTE: after intitial debugging, change the exclude arg to +be the ID of another fix (GCMC in this case), and extract() +the exclusion group ID from fix gcmc. + +The *exclude argument allows this fix to work in tandem with the +:doc:`fix gcmc ` command which may decide to delete an atom +or molecule as one of its Monte Carlo events. In this case, LAMMPS +needs to pass LATTE the atoms for the system with the atom/molecule +removed. Fix gcmc does not actually remove the atom/molecule until +after the new energy is computed (in this case by LATTE), and a Monte +Carlo accept/reject decision is made for the event. + +The specified groupID must match the group ID which the :doc:`fix gcmc +` command assigns to atoms flagged for possible deletion. +It should be either its default exclusion group ID or group ID used +with its "exclude" keyword option. + +.. note:: + + The fix gcmc command must appear in the input script prior + to the fix latte command for this to work. ---------- From 04bdfb151b808d2c4ef081044129a52060fc78a6 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 9 Sep 2022 12:22:50 -0600 Subject: [PATCH 04/11] refactor how fix latte connects to fix gcmc --- doc/src/fix_latte.rst | 36 ++++++++------------ src/LATTE/fix_latte.cpp | 74 +++++++++++++++++++++++++++++------------ src/LATTE/fix_latte.h | 3 +- src/MC/fix_gcmc.cpp | 14 ++++++++ src/MC/fix_gcmc.h | 51 ++++++++++++++++------------ 5 files changed, 111 insertions(+), 67 deletions(-) diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index 6ce84f9d52..df23027238 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -19,8 +19,8 @@ Syntax keyword = *coulomb* or *exclude* *coulomb* value = peID peID = ID of compute used to calculate per-atom energy - *exclude* value = groupID - groupID = ID of group of atoms to exclude before calling LATTE + *exclude* value = fixID + fixID = ID of fix which potentially excludes atoms before calling LATTE Examples """""""" @@ -28,7 +28,7 @@ Examples .. code-block:: LAMMPS fix dftb all latte - fix dftb all exclude GCMCmol + fix dftb all exclude GCMC Description """"""""""" @@ -64,27 +64,17 @@ The *coulomb* argument is not yet supported by fix latte (as of Sept Coulomb potential as an alternative to LATTE performing the calculation. -NOTE: after intitial debugging, change the exclude arg to -be the ID of another fix (GCMC in this case), and extract() -the exclusion group ID from fix gcmc. +The *exclude argument allows this fix to work in tandem with another +fix which may decide to delete one or more atoms of molecules. The +specified fixID is the ID of the other fix. -The *exclude argument allows this fix to work in tandem with the -:doc:`fix gcmc ` command which may decide to delete an atom -or molecule as one of its Monte Carlo events. In this case, LAMMPS -needs to pass LATTE the atoms for the system with the atom/molecule -removed. Fix gcmc does not actually remove the atom/molecule until -after the new energy is computed (in this case by LATTE), and a Monte -Carlo accept/reject decision is made for the event. - -The specified groupID must match the group ID which the :doc:`fix gcmc -` command assigns to atoms flagged for possible deletion. -It should be either its default exclusion group ID or group ID used -with its "exclude" keyword option. - -.. note:: - - The fix gcmc command must appear in the input script prior - to the fix latte command for this to work. +The one current example of such a fix is the :doc:`fix gcmc +` command which performs Monte Carlo insertions and +deletions. If a trial deletion is performed, then LAMMPS needs to +only pass LATTE the atoms which remain. Fix gcmc does not actually +remove any atoms until after the new energy is computed (in this case +by LATTE), and a Monte Carlo accept/reject decision is made for the +trial deletion. ---------- diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 1095b9ab9a..0ba16a9c61 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -76,6 +76,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : coulomb = 0; id_pe = nullptr; exclude = 0; + id_exclude = nullptr; int iarg = 3; while (iarg < narg) { @@ -85,7 +86,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : coulomb = 1; error->all(FLERR,"Fix latte does not yet support a " "LAMMPS calculation of a Coulomb potential"); - id_pe = utils::strdup(arg[3]); + id_pe = utils::strdup(arg[iarg+1]); c_pe = modify->get_compute_by_id(id_pe); if (!c_pe) error->all(FLERR,"Could not find fix latte compute ID {}", id_pe); if (c_pe->peatomflag == 0) @@ -96,11 +97,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix latte exclude", error); exclude = 1; - int excludegroup = group->find(arg[iarg+1]); - if (excludegroup == -1) - error->all(FLERR, "Fix latte couldd not find exclude group ID: {}", - arg[iarg+1]); - excludebit = group->bitmask[excludegroup]; + id_exclude = utils::strdup(arg[iarg+1]); iarg += 2; } else @@ -121,6 +118,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : FixLatte::~FixLatte() { delete[] id_pe; + delete[] id_exclude; memory->destroy(qpotential); memory->destroy(flatte); } @@ -148,9 +146,9 @@ void FixLatte::init() if (coulomb) { if (atom->q_flag == 0 || force->pair == nullptr || force->kspace == nullptr) error->all(FLERR,"Fix latte cannot compute Coulomb potential"); - c_pe = modify->get_compute_by_id(id_pe); - if (!c_pe) error->all(FLERR,"Could not find fix latte compute ID {}", id_pe); + if (!c_pe) + error->all(FLERR,"Fix latte could not find Coulomb compute ID {}",id_pe); } // must be fully periodic or fully non-periodic @@ -167,6 +165,20 @@ void FixLatte::init() memory->create(qpotential,atom->nlocal,"latte:qpotential"); memory->create(flatte,atom->nlocal,3,"latte:flatte"); } + + // extract pointer to exclusion_group variable from id_exclude + // exclusion_group is index of a group the Fix defines + + if (exclude) { + Fix *f_exclude = modify->get_fix_by_id(id_exclude); + if (!f_exclude) + error->all(FLERR,"Fix latte could not find exclude fix ID {}", id_exclude); + int exclude_group_index,dim; + exclusion_group_ptr = (int *) f_exclude->extract("exclusion_group",dim); + if (!exclusion_group_ptr || dim != 0) + error->all(FLERR,"Fix latte could not query exclude_group of fix ID {}", + id_exclude); + } } /* ---------------------------------------------------------------------- */ @@ -267,12 +279,18 @@ void FixLatte::post_force(int vflag) if (!exclude) latte_wrapper_all(); else { - int *mask = atom->mask; - int nlocal = atom->nlocal; - int anyexclude = 0; - for (int i = 0; i < nlocal; i++) - if (mask[i] & excludebit) anyexclude = 1; + + int exclusion_group = *exclusion_group_ptr; + if (exclusion_group) { + int excludebit = group->bitmask[exclusion_group]; + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & excludebit) anyexclude = 1; + } if (!anyexclude) latte_wrapper_all(); else latte_wrapper_exclude(); @@ -316,6 +334,9 @@ void FixLatte::latte_wrapper_all() &domain->xy,&domain->xz,&domain->yz,forces,&maxiter,&latte_energy, &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); + printf("LATTE ALL: step %ld, natoms %d, LATTE eng %g\n", + update->ntimestep, natoms, latte_energy); + if (latteerror) error->all(FLERR,"Internal LATTE problem"); } @@ -325,6 +346,11 @@ void FixLatte::latte_wrapper_all() void FixLatte::latte_wrapper_exclude() { + int m; + + int exclusion_group = *exclusion_group_ptr; + int excludebit = group->bitmask[exclusion_group]; + int *mask = atom->mask; int nlocal = atom->nlocal; @@ -342,26 +368,29 @@ void FixLatte::latte_wrapper_exclude() memory->create(xinclude,nlatte,3,"latte:xinclude"); memory->create(finclude,nlatte,3,"latte:finclude"); + double *coords = &xinclude[0][0]; + int *types = typeinclude; + double *forces = &finclude[0][0]; + double **x = atom->x; int *type = atom->type; nlatte = 0; + m = 0; for (int i = 0; i < nlocal; i++) { if (mask[i] & excludebit) continue; - typeinclude[nlatte] = type[i]; - x[nlatte][0] = x[i][0]; - x[nlatte][1] = x[i][1]; - x[nlatte][2] = x[i][2]; + types[nlatte] = type[i]; nlatte++; + coords[m+0] = x[i][0]; + coords[m+1] = x[i][1]; + coords[m+2] = x[i][2]; + m += 3; } - double *coords = &xinclude[0][0]; - int *types = typeinclude; int ntypes = atom->ntypes; double *mass = &atom->mass[1]; double *boxlo = domain->boxlo; double *boxhi = domain->boxhi; - double *forces = &finclude[0][0]; bool latteerror = false; int maxiter = -1; @@ -369,13 +398,16 @@ void FixLatte::latte_wrapper_exclude() &domain->xy,&domain->xz,&domain->yz,forces,&maxiter,&latte_energy, &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); + printf("LATTE EXCLUDE: step %ld, natoms %d, LATTE eng %g\n", + update->ntimestep, nlatte, latte_energy); + if (latteerror) error->all(FLERR,"Internal LATTE problem"); // expand compressed forces array double **f = atom->f; - int m = 0; + m = 0; for (int i = 0; i < nlocal; i++) { if (mask[i] & excludebit) continue; f[i][0] = forces[m+0]; diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index fdc3fdee40..0ce6e0f4ce 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -44,10 +44,11 @@ class FixLatte : public Fix { double memory_usage() override; protected: - char *id_pe; int coulomb, pbcflag, pe_peratom, virial_global, virial_peratom, neighflag; int exclude, excludebit; int eflag_caller; + char *id_pe,*id_exclude; + int *exclusion_group_ptr; int flags_latte[6]; diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 0cc6590d5a..ef1ad324b0 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -2573,3 +2573,17 @@ void FixGCMC::grow_molecule_arrays(int nmolatoms) { molq = memory->grow(molq,nmaxmolatoms,"gcmc:molq"); molimage = memory->grow(molimage,nmaxmolatoms,"gcmc:molimage"); } + + +/* ---------------------------------------------------------------------- + extract variable which stores index of exclusion group +------------------------------------------------------------------------- */ + +void *FixGCMC::extract(const char *name, int &dim) +{ + if (strcmp(name,"exclusion_group") == 0) { + dim = 0; + return (void *) &exclusion_group; + } + return nullptr; +} diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index d945b82346..2bdd9eb461 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -31,32 +31,11 @@ class FixGCMC : public Fix { int setmask() override; void init() override; void pre_exchange() override; - void attempt_atomic_translation(); - void attempt_atomic_deletion(); - void attempt_atomic_insertion(); - void attempt_molecule_translation(); - void attempt_molecule_rotation(); - void attempt_molecule_deletion(); - void attempt_molecule_insertion(); - void attempt_atomic_translation_full(); - void attempt_atomic_deletion_full(); - void attempt_atomic_insertion_full(); - void attempt_molecule_translation_full(); - void attempt_molecule_rotation_full(); - void attempt_molecule_deletion_full(); - void attempt_molecule_insertion_full(); - double energy(int, int, tagint, double *); - double molecule_energy(tagint); - double energy_full(); - int pick_random_gas_atom(); - tagint pick_random_gas_molecule(); - void toggle_intramolecular(int); - void update_gas_atoms_list(); double compute_vector(int) override; double memory_usage() override; void write_restart(FILE *) override; void restart(char *) override; - void grow_molecule_arrays(int); + void *extract(const char *, int &); private: int molecule_group, molecule_group_bit; @@ -139,7 +118,35 @@ class FixGCMC : public Fix { class Compute *c_pe; + // private methods + void options(int, char **); + + void attempt_atomic_translation(); + void attempt_atomic_deletion(); + void attempt_atomic_insertion(); + void attempt_molecule_translation(); + void attempt_molecule_rotation(); + void attempt_molecule_deletion(); + void attempt_molecule_insertion(); + void attempt_atomic_translation_full(); + void attempt_atomic_deletion_full(); + void attempt_atomic_insertion_full(); + void attempt_molecule_translation_full(); + void attempt_molecule_rotation_full(); + void attempt_molecule_deletion_full(); + void attempt_molecule_insertion_full(); + + double energy(int, int, tagint, double *); + double energy_full(); + double molecule_energy(tagint); + + int pick_random_gas_atom(); + tagint pick_random_gas_molecule(); + void toggle_intramolecular(int); + void update_gas_atoms_list(); + + void grow_molecule_arrays(int); }; } // namespace LAMMPS_NS From 5e3adfa71046dd4f5cc9b2f289747b9a62907102 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 12 Sep 2022 14:40:10 -0600 Subject: [PATCH 05/11] trigger newsystem in LATTE if atom count changes - e.g. fix gcmc --- src/LATTE/fix_latte.cpp | 30 ++++++++++++++++++------------ src/LATTE/fix_latte.h | 4 +++- 2 files changed, 21 insertions(+), 13 deletions(-) diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 0ba16a9c61..4daaf9d40a 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -192,18 +192,20 @@ void FixLatte::init_list(int /*id*/, NeighList * /*ptr*/) void FixLatte::setup(int vflag) { - newsystem = 1; + natoms_last = -1; + setupflag = 1; post_force(vflag); - newsystem = 0; + setupflag = 0; } /* ---------------------------------------------------------------------- */ void FixLatte::min_setup(int vflag) { - newsystem = 1; + natoms_last = -1; + setupflag = 1; post_force(vflag); - newsystem = 0; + setupflag = 0; } /* ---------------------------------------------------------------------- */ @@ -273,7 +275,15 @@ void FixLatte::post_force(int vflag) flags_latte[4] = vflag_atom && thermo_virial; // virial, 0 for no flags_latte[5] = neighflag; // 1 to pass neighbor list to LATTE, 0 for no - // setup arguments for latte() function within LATTE lib and invoke it + // newsystem flag determines whether LATTE treats snapshot + // as new system (more work) or increment to last system + // if setup or atom count changed then newsystem = 1 + // else newsystem = 0 + + if (setupflag || atom->natoms != natoms_last) newsystem = 1; + else newsystem = 0; + + // setup arguments for latte() function and invoke it // either for all atoms or excluding some atoms // in latter case, need to construct reduced-size per-atom vectors/arrays @@ -296,7 +306,9 @@ void FixLatte::post_force(int vflag) else latte_wrapper_exclude(); } - + newsystem = 0; + natoms_last = atom->natoms; + // sum LATTE forces to LAMMPS forces // e.g. LAMMPS may compute Coulombics at some point @@ -334,9 +346,6 @@ void FixLatte::latte_wrapper_all() &domain->xy,&domain->xz,&domain->yz,forces,&maxiter,&latte_energy, &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); - printf("LATTE ALL: step %ld, natoms %d, LATTE eng %g\n", - update->ntimestep, natoms, latte_energy); - if (latteerror) error->all(FLERR,"Internal LATTE problem"); } @@ -398,9 +407,6 @@ void FixLatte::latte_wrapper_exclude() &domain->xy,&domain->xz,&domain->yz,forces,&maxiter,&latte_energy, &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); - printf("LATTE EXCLUDE: step %ld, natoms %d, LATTE eng %g\n", - update->ntimestep, nlatte, latte_energy); - if (latteerror) error->all(FLERR,"Internal LATTE problem"); // expand compressed forces array diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index 0ce6e0f4ce..18730e7f5e 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -49,10 +49,12 @@ class FixLatte : public Fix { int eflag_caller; char *id_pe,*id_exclude; int *exclusion_group_ptr; + int setupflag, newsystem; + bigint natoms_last; int flags_latte[6]; - int nmax, newsystem; + int nmax; double *qpotential; double **flatte; double latte_energy; From abfdb5bca3851158489c5bdd340c63f099f97a3f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Sep 2022 18:33:27 -0400 Subject: [PATCH 06/11] whitespace --- src/LATTE/fix_latte.cpp | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 4daaf9d40a..8da1db5261 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -72,7 +72,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : thermo_energy = thermo_virial = 1; // process optional args - + coulomb = 0; id_pe = nullptr; exclude = 0; @@ -147,7 +147,7 @@ void FixLatte::init() if (atom->q_flag == 0 || force->pair == nullptr || force->kspace == nullptr) error->all(FLERR,"Fix latte cannot compute Coulomb potential"); c_pe = modify->get_compute_by_id(id_pe); - if (!c_pe) + if (!c_pe) error->all(FLERR,"Fix latte could not find Coulomb compute ID {}",id_pe); } @@ -171,12 +171,12 @@ void FixLatte::init() if (exclude) { Fix *f_exclude = modify->get_fix_by_id(id_exclude); - if (!f_exclude) + if (!f_exclude) error->all(FLERR,"Fix latte could not find exclude fix ID {}", id_exclude); int exclude_group_index,dim; exclusion_group_ptr = (int *) f_exclude->extract("exclusion_group",dim); - if (!exclusion_group_ptr || dim != 0) - error->all(FLERR,"Fix latte could not query exclude_group of fix ID {}", + if (!exclusion_group_ptr || dim != 0) + error->all(FLERR,"Fix latte could not query exclude_group of fix ID {}", id_exclude); } } @@ -308,7 +308,7 @@ void FixLatte::post_force(int vflag) newsystem = 0; natoms_last = atom->natoms; - + // sum LATTE forces to LAMMPS forces // e.g. LAMMPS may compute Coulombics at some point @@ -362,7 +362,7 @@ void FixLatte::latte_wrapper_exclude() int *mask = atom->mask; int nlocal = atom->nlocal; - + // nlatte = number of non-excluded atoms to pass to LATTE int nlatte = 0; From 7dd95db47454c9ecb1f89eeaa35e62dd5d33efe5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 06:22:41 -0400 Subject: [PATCH 07/11] fix typo --- doc/src/fix_latte.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index df23027238..f069c3bddc 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -64,7 +64,7 @@ The *coulomb* argument is not yet supported by fix latte (as of Sept Coulomb potential as an alternative to LATTE performing the calculation. -The *exclude argument allows this fix to work in tandem with another +The *exclude* argument allows this fix to work in tandem with another fix which may decide to delete one or more atoms of molecules. The specified fixID is the ID of the other fix. From 197ce9187e5364e24edc28872e6556a46697f39f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 06:31:49 -0400 Subject: [PATCH 08/11] small programming style updates --- src/LATTE/fix_latte.cpp | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 8da1db5261..f97162cd40 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -55,6 +55,8 @@ extern "C" { FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { + if (narg < 3) utils::missing_cmd_args(FLERR, "fix latte", error); + if (strcmp(update->unit_style,"metal") != 0) error->all(FLERR,"Must use units metal with fix latte command"); @@ -84,19 +86,19 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix latte coulomb", error); coulomb = 1; - error->all(FLERR,"Fix latte does not yet support a " - "LAMMPS calculation of a Coulomb potential"); + error->all(FLERR,"Fix latte does not yet support LAMMPS calculation of a Coulomb potential"); + delete[] id_pe; id_pe = utils::strdup(arg[iarg+1]); c_pe = modify->get_compute_by_id(id_pe); if (!c_pe) error->all(FLERR,"Could not find fix latte compute ID {}", id_pe); - if (c_pe->peatomflag == 0) - error->all(FLERR,"Fix latte compute ID does not compute pe/atom"); + if (c_pe->peatomflag == 0) error->all(FLERR,"Fix latte compute ID does not compute pe/atom"); iarg += 2; } else if (strcmp(arg[iarg],"exclude") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix latte exclude", error); exclude = 1; + delete[] id_exclude; id_exclude = utils::strdup(arg[iarg+1]); iarg += 2; @@ -147,8 +149,7 @@ void FixLatte::init() if (atom->q_flag == 0 || force->pair == nullptr || force->kspace == nullptr) error->all(FLERR,"Fix latte cannot compute Coulomb potential"); c_pe = modify->get_compute_by_id(id_pe); - if (!c_pe) - error->all(FLERR,"Fix latte could not find Coulomb compute ID {}",id_pe); + if (!c_pe) error->all(FLERR,"Fix latte could not find Coulomb compute ID {}",id_pe); } // must be fully periodic or fully non-periodic @@ -171,13 +172,11 @@ void FixLatte::init() if (exclude) { Fix *f_exclude = modify->get_fix_by_id(id_exclude); - if (!f_exclude) - error->all(FLERR,"Fix latte could not find exclude fix ID {}", id_exclude); - int exclude_group_index,dim; - exclusion_group_ptr = (int *) f_exclude->extract("exclusion_group",dim); + if (!f_exclude) error->all(FLERR,"Fix latte could not find exclude fix ID {}", id_exclude); + int dim; + exclusion_group_ptr = (int *) f_exclude->extract("exclusion_group", dim); if (!exclusion_group_ptr || dim != 0) - error->all(FLERR,"Fix latte could not query exclude_group of fix ID {}", - id_exclude); + error->all(FLERR,"Fix latte could not query exclude_group of fix ID {}", id_exclude); } } From b34d45644ee1a53eed7061ee2808398c9d625108 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 13 Sep 2022 09:17:50 -0600 Subject: [PATCH 09/11] update fix latte doc page --- doc/src/fix_latte.rst | 31 +++++++++++++++++++------------ 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index df23027238..22f8614d53 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -57,6 +57,23 @@ found in examples/latte. A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial `_ +Currently, LAMMPS must be run in serial or as a single MPI task, to +use this fix. This is because the version of the LATTE library LAMMPS +uses does not support MPI. On the LAMMPS size, this is typically not +a bottleneck, since LATTE will be doing 99% or more of the work to +compute quantum-accurate forces. On the LATTE side, the LATTE library +does support threaded parallelism via OpenMP. You must build the +LATTE library with OpenMP support, then set the OMP_NUM_THREADS +environment variable before performing a LAMMPS + LATTE simulation to +tell LATTE how many threads to invoke. + +.. note:: + + NEB calculations can be done using this fix using multiple + replicas and running LAMMPS in parallel. However, each replica must + be run on a single MPI task. For details, see the :doc:`neb ` + command page and the :doc:`-partition command-line switch ` + ---------- The *coulomb* argument is not yet supported by fix latte (as of Sept @@ -176,18 +193,8 @@ use this fix. LATTE does not currently compute per-atom energy or per-atom virial contributions. So they will not show up as part of the calculations -performed by the :doc:`compute pe/atom ` or :doc:`compute stress/atom ` commands. - -Currently, LAMMPS must be run in serial or as a single MPI task, to -use this fix. This is typically not a bottleneck, since LATTE will be -doing 99% or more of the work to compute quantum-accurate forces. - -.. note:: - - NEB calculations can be done using this fix using multiple - replicas and running LAMMPS in parallel. However, each replica must - be run on a single MPI task. For details, see the :doc:`neb ` - command page and the :doc:`-partition command-line switch ` +performed by the :doc:`compute pe/atom ` or +:doc:`compute stress/atom ` commands. Related commands """""""""""""""" From f3fa24617946e1615f9fb89bc342a0cce346122c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 11:39:16 -0400 Subject: [PATCH 10/11] update LATTE package examples --- ...hene.boxrel => in.latte.graphene.boxrelax} | 20 +- examples/latte/in.latte.multiple | 8 +- examples/latte/in.latte.sucrose | 40 -- examples/latte/in.latte.sucrose.md | 24 +- examples/latte/in.latte.water | 40 -- examples/latte/in.latte.water.md | 24 +- examples/latte/in.latte.water.min | 22 +- .../log.13Sep22.latte.graphene.boxrelax.g++.1 | 179 ++++++++ .../latte/log.13Sep22.latte.multiple.g++.1 | 189 ++++++++ .../latte/log.13Sep22.latte.sucrose.md.g++.1 | 112 +++++ .../latte/log.13Sep22.latte.water.md.g++.1 | 112 +++++ .../latte/log.13Sep22.latte.water.min.g++.1 | 122 ++++++ .../latte/log.19Sep17.latte.sucrose.md.g++.1 | 406 ------------------ .../latte/log.19Sep17.latte.water.md.g++.1 | 406 ------------------ .../log.21Jun18.latte.graphene.boxrelax.g++.1 | 170 -------- .../latte/log.21Jun18.latte.sucrose.g++.1 | 103 ----- examples/latte/log.21Jun18.latte.water.g++.1 | 103 ----- .../latte/log.21Jun18.latte.water.min.g++.1 | 108 ----- 18 files changed, 763 insertions(+), 1425 deletions(-) rename examples/latte/{in.graphene.boxrel => in.latte.graphene.boxrelax} (68%) delete mode 100644 examples/latte/in.latte.sucrose delete mode 100644 examples/latte/in.latte.water create mode 100644 examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 create mode 100644 examples/latte/log.13Sep22.latte.multiple.g++.1 create mode 100644 examples/latte/log.13Sep22.latte.sucrose.md.g++.1 create mode 100644 examples/latte/log.13Sep22.latte.water.md.g++.1 create mode 100644 examples/latte/log.13Sep22.latte.water.min.g++.1 delete mode 100644 examples/latte/log.19Sep17.latte.sucrose.md.g++.1 delete mode 100644 examples/latte/log.19Sep17.latte.water.md.g++.1 delete mode 100644 examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 delete mode 100644 examples/latte/log.21Jun18.latte.sucrose.g++.1 delete mode 100644 examples/latte/log.21Jun18.latte.water.g++.1 delete mode 100644 examples/latte/log.21Jun18.latte.water.min.g++.1 diff --git a/examples/latte/in.graphene.boxrel b/examples/latte/in.latte.graphene.boxrelax similarity index 68% rename from examples/latte/in.graphene.boxrel rename to examples/latte/in.latte.graphene.boxrelax index 721b7f014f..bd61c358e6 100644 --- a/examples/latte/in.graphene.boxrel +++ b/examples/latte/in.latte.graphene.boxrelax @@ -1,35 +1,35 @@ # Simple water model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.graphene # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all box/relax iso 0.0 vmax 0.001 -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom etotal diff --git a/examples/latte/in.latte.multiple b/examples/latte/in.latte.multiple index 4888d14ebc..1c5dc3d2d3 100644 --- a/examples/latte/in.latte.multiple +++ b/examples/latte/in.latte.multiple @@ -9,7 +9,7 @@ read_data data.water velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes @@ -17,7 +17,7 @@ neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press @@ -44,7 +44,7 @@ read_data data.ch4 velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes @@ -53,7 +53,7 @@ timestep 0.00025 fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press diff --git a/examples/latte/in.latte.sucrose b/examples/latte/in.latte.sucrose deleted file mode 100644 index a10dae5c5e..0000000000 --- a/examples/latte/in.latte.sucrose +++ /dev/null @@ -1,40 +0,0 @@ -# simple sucrose model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.sucrose - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 diff --git a/examples/latte/in.latte.sucrose.md b/examples/latte/in.latte.sucrose.md index a10dae5c5e..53eaf80dd7 100644 --- a/examples/latte/in.latte.sucrose.md +++ b/examples/latte/in.latte.sucrose.md @@ -1,35 +1,35 @@ # simple sucrose model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.sucrose # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 -fix 1 all nve +fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press @@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press # dynamics thermo 10 -run 100 +run 100 diff --git a/examples/latte/in.latte.water b/examples/latte/in.latte.water deleted file mode 100644 index e1185602b4..0000000000 --- a/examples/latte/in.latte.water +++ /dev/null @@ -1,40 +0,0 @@ -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 diff --git a/examples/latte/in.latte.water.md b/examples/latte/in.latte.water.md index e1185602b4..7940b7f992 100644 --- a/examples/latte/in.latte.water.md +++ b/examples/latte/in.latte.water.md @@ -1,35 +1,35 @@ # simple water model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.water # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 -fix 1 all nve +fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press @@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press # dynamics thermo 10 -run 100 +run 100 diff --git a/examples/latte/in.latte.water.min b/examples/latte/in.latte.water.min index 173afee96a..81474a0773 100644 --- a/examples/latte/in.latte.water.min +++ b/examples/latte/in.latte.water.min @@ -1,35 +1,35 @@ # simple water model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.water # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 -fix 1 all nve +fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press diff --git a/examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 b/examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 new file mode 100644 index 0000000000..2350e8ad39 --- /dev/null +++ b/examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 @@ -0,0 +1,179 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.graphene +Reading data file ... + triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 32 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all box/relax iso 0.0 vmax 0.001 + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom etotal + +# minimization + +thermo 1 +fix 3 all print 1 "Total Energy =" +min_style cg +min_modify dmax 0.1 +min_modify line quadratic +minimize 1.0e-4 1.0e-4 10000 10000 +Generated 0 of 0 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 + binsize = 1, bins = 11 9 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.03 | 7.03 | 7.03 Mbytes + TotEng +-247.46002 +-247.67224 +-247.87937 +-248.08148 +-248.27865 +-248.47096 +-248.65851 +-248.84137 +-249.01964 +-249.19342 +-249.36281 +-249.52791 +-249.68883 +-249.8457 +-249.99865 +-250.1478 +-250.29332 +-250.43535 +-250.57409 +-250.70972 +-250.84247 +-250.97258 +-251.10035 +-251.2261 +-251.35021 +-251.47314 +-251.59543 +-251.71776 +-251.84096 +-251.9661 +-252.09459 +-252.22833 +-252.37003 +-252.52371 +-252.69578 +-252.89752 +-253.15197 +-253.52044 +-254.31418 +-255.6175 +-256.8162 +-258.1227 +-259.38401 +-260.74831 +-262.03991 +-263.5463 +-264.70486 +-267.69143 +-267.88682 +-269.0352 +-270.602 +-270.65395 +-270.7429 +-271.55831 +-271.81159 +-271.87447 +-273.03096 +-273.23109 +-273.27869 +-273.34621 +-273.4082 +-273.45599 +-273.53849 +-273.57478 +-273.71381 +-273.74092 +Loop time of 20.5496 on 1 procs for 65 steps with 32 atoms + +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -247.460020562055 -273.713813242259 -273.740918498854 + Force two-norm initial, final = 201.60784 9.4927634 + Force max component initial, final = 188.92406 2.4327308 + Final line search alpha, max atom move = 0.00022885545 0.0005567437 + Iterations, force evaluations = 65 65 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7869e-05 | 7.7869e-05 | 7.7869e-05 | 0.0 | 0.00 +Bond | 3.531e-06 | 3.531e-06 | 3.531e-06 | 0.0 | 0.00 +Neigh | 1.3988e-05 | 1.3988e-05 | 1.3988e-05 | 0.0 | 0.00 +Comm | 0.00014355 | 0.00014355 | 0.00014355 | 0.0 | 0.00 +Output | 0.00071475 | 0.00071475 | 0.00071475 | 0.0 | 0.00 +Modify | 20.547 | 20.547 | 20.547 | 0.0 | 99.99 +Other | | 0.001683 | | | 0.01 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 48 ave 48 max 48 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48 +Ave neighs/atom = 1.5 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:20 diff --git a/examples/latte/log.13Sep22.latte.multiple.g++.1 b/examples/latte/log.13Sep22.latte.multiple.g++.1 new file mode 100644 index 0000000000..ca32c96e15 --- /dev/null +++ b/examples/latte/log.13Sep22.latte.multiple.g++.1 @@ -0,0 +1,189 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Generated 0 of 1 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 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes + Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 +Loop time of 0.334108 on 1 procs for 10 steps with 24 atoms + +Performance: 0.646 ns/day, 37.123 hours/ns, 29.930 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.714e-06 | 3.714e-06 | 3.714e-06 | 0.0 | 0.00 +Bond | 5.02e-07 | 5.02e-07 | 5.02e-07 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.1209e-05 | 1.1209e-05 | 1.1209e-05 | 0.0 | 0.00 +Output | 2.3638e-05 | 2.3638e-05 | 2.3638e-05 | 0.0 | 0.01 +Modify | 0.33404 | 0.33404 | 0.33404 | 0.0 | 99.98 +Other | | 2.795e-05 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.5416667 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# Clear up previus calculation + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 +Reading data file ... + triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Generated 0 of 1 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 + binsize = 1, bins = 20 13 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.902 | 5.902 Mbytes + Step Temp PotEng TotEng Press + 0 0 -23.980353 -23.980353 348.02716 + 10 19.123149 -23.990297 -23.98041 18.774332 +Loop time of 0.0121573 on 1 procs for 10 steps with 5 atoms + +Performance: 17.767 ns/day, 1.351 hours/ns, 822.549 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.224e-06 | 1.224e-06 | 1.224e-06 | 0.0 | 0.01 +Bond | 2.93e-07 | 2.93e-07 | 2.93e-07 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 3.845e-06 | 3.845e-06 | 3.845e-06 | 0.0 | 0.03 +Output | 8.633e-06 | 8.633e-06 | 8.633e-06 | 0.0 | 0.07 +Modify | 0.012132 | 0.012132 | 0.012132 | 0.0 | 99.80 +Other | | 1.089e-05 | | | 0.09 + +Nlocal: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10 +Ave neighs/atom = 2 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/latte/log.13Sep22.latte.sucrose.md.g++.1 b/examples/latte/log.13Sep22.latte.sucrose.md.g++.1 new file mode 100644 index 0000000000..9d3a98b66b --- /dev/null +++ b/examples/latte/log.13Sep22.latte.sucrose.md.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose +Reading data file ... + orthogonal box = (0 0 0) to (17.203 18.009 21.643) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 45 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Generated 0 of 3 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 + binsize = 1, bins = 18 19 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.93 | 5.93 | 5.93 Mbytes + Step Temp PotEng TotEng Press + 0 0 -251.26617 -251.26617 16.617233 + 10 0.025263738 -251.26631 -251.26617 8.0576369 + 20 0.034232485 -251.26636 -251.26617 1.6672772 + 30 0.059079585 -251.2665 -251.26617 11.058355 + 40 0.055499785 -251.26648 -251.26617 14.837599 + 50 0.058499496 -251.2665 -251.26617 6.7180488 + 60 0.071094531 -251.26657 -251.26617 6.6131215 + 70 0.084309398 -251.26665 -251.26617 12.372502 + 80 0.1089929 -251.26679 -251.26617 8.8352747 + 90 0.11378255 -251.26681 -251.26617 5.1175071 + 100 0.13003967 -251.26691 -251.26617 8.2429118 +Loop time of 14.4456 on 1 procs for 100 steps with 45 atoms + +Performance: 0.150 ns/day, 160.507 hours/ns, 6.923 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.5758e-05 | 7.5758e-05 | 7.5758e-05 | 0.0 | 0.00 +Bond | 6.748e-06 | 6.748e-06 | 6.748e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 9.0137e-05 | 9.0137e-05 | 9.0137e-05 | 0.0 | 0.00 +Output | 0.00025976 | 0.00025976 | 0.00025976 | 0.0 | 0.00 +Modify | 14.445 | 14.445 | 14.445 | 0.0 | 99.99 +Other | | 0.0005283 | | | 0.00 + +Nlocal: 45 ave 45 max 45 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: 59 ave 59 max 59 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 59 +Ave neighs/atom = 1.3111111 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:14 diff --git a/examples/latte/log.13Sep22.latte.water.md.g++.1 b/examples/latte/log.13Sep22.latte.water.md.g++.1 new file mode 100644 index 0000000000..04cc99135c --- /dev/null +++ b/examples/latte/log.13Sep22.latte.water.md.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Generated 0 of 1 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 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes + Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 + 20 529.06408 -106.53023 -104.95733 131519.85 + 30 753.62603 -107.19952 -104.959 49296.66 + 40 716.65648 -107.08803 -104.95742 28307.121 + 50 824.04392 -107.40823 -104.95836 102167.59 + 60 933.56146 -107.73479 -104.95933 92508.517 + 70 851.18489 -107.48767 -104.95711 13993.262 + 80 999.8028 -107.93147 -104.95907 36700.736 + 90 998.77488 -107.9257 -104.95636 107233.54 + 100 1281.4438 -108.76963 -104.95992 49702.386 +Loop time of 3.14578 on 1 procs for 100 steps with 24 atoms + +Performance: 0.687 ns/day, 34.953 hours/ns, 31.789 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0818e-05 | 3.0818e-05 | 3.0818e-05 | 0.0 | 0.00 +Bond | 4.704e-06 | 4.704e-06 | 4.704e-06 | 0.0 | 0.00 +Neigh | 1.8668e-05 | 1.8668e-05 | 1.8668e-05 | 0.0 | 0.00 +Comm | 0.00010831 | 0.00010831 | 0.00010831 | 0.0 | 0.00 +Output | 0.00021087 | 0.00021087 | 0.00021087 | 0.0 | 0.01 +Modify | 3.1452 | 3.1452 | 3.1452 | 0.0 | 99.98 +Other | | 0.0002339 | | | 0.01 + +Nlocal: 24 ave 24 max 24 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: 31 ave 31 max 31 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31 +Ave neighs/atom = 1.2916667 +Ave special neighs/atom = 0 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/latte/log.13Sep22.latte.water.min.g++.1 b/examples/latte/log.13Sep22.latte.water.min.g++.1 new file mode 100644 index 0000000000..1b1cc59e10 --- /dev/null +++ b/examples/latte/log.13Sep22.latte.water.min.g++.1 @@ -0,0 +1,122 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# minimization + +thermo 10 + +min_style fire +minimize 1.0e-4 1.0e-4 500 500 +Generated 0 of 1 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 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback + 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes +Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes + Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 853.69689 -106.31143 -103.7734 79191.444 + 20 1112.0893 -107.2723 -103.96607 82675.468 + 30 1897.6249 -108.36769 -102.72608 71447.508 + 40 3068.3491 -110.06452 -100.94237 47627.967 + 50 3.730935 -110.16042 -110.14932 5913.0643 + 60 28.603141 -110.18885 -110.10381 5778.8586 + 66 54.717686 -110.21503 -110.05236 5739.5831 +Loop time of 2.48723 on 1 procs for 66 steps with 24 atoms + +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -104.955957263186 -110.209885831179 -110.215033825672 + Force two-norm initial, final = 19.119006 0.51695213 + Force max component initial, final = 11.775801 0.1663917 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 66 69 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7159e-05 | 2.7159e-05 | 2.7159e-05 | 0.0 | 0.00 +Bond | 3.124e-06 | 3.124e-06 | 3.124e-06 | 0.0 | 0.00 +Neigh | 1.0201e-05 | 1.0201e-05 | 1.0201e-05 | 0.0 | 0.00 +Comm | 0.000109 | 0.000109 | 0.000109 | 0.0 | 0.00 +Output | 0.00010568 | 0.00010568 | 0.00010568 | 0.0 | 0.00 +Modify | 2.4866 | 2.4866 | 2.4866 | 0.0 | 99.98 +Other | | 0.0003552 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 75 ave 75 max 75 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 33 ave 33 max 33 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33 +Ave neighs/atom = 1.375 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 b/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 deleted file mode 100644 index bc8843ef7f..0000000000 --- a/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 +++ /dev/null @@ -1,406 +0,0 @@ - The log file for latte_lib - - CONTROL{ } - - WARNING: variable JobName= is missing. I will use a default value instead ... - WARNING: variable PARAMPATH= is missing. I will use a default value instead ... - WARNING: variable DEBUGON= is missing. I will use a default value instead ... - WARNING: variable FERMIM= is missing. I will use a default value instead ... - WARNING: variable CGORLIB= is missing. I will use a default value instead ... - WARNING: variable NORECS= is missing. I will use a default value instead ... - WARNING: variable VDWON= is missing. I will use a default value instead ... - WARNING: variable ORDERNMOL= is missing. I will use a default value instead ... - WARNING: variable LCNON= is missing. I will use a default value instead ... - WARNING: variable LCNITER= is missing. I will use a default value instead ... - WARNING: variable MDON= is missing. I will use a default value instead ... - WARNING: variable PBCON= is missing. I will use a default value instead ... - WARNING: variable RESTART= is missing. I will use a default value instead ... - WARNING: variable NGPU= is missing. I will use a default value instead ... - WARNING: variable COMPFORCE= is missing. I will use a default value instead ... - WARNING: variable DOSFIT= is missing. I will use a default value instead ... - WARNING: variable INTS2FIT= is missing. I will use a default value instead ... - WARNING: variable NFITSTEP= is missing. I will use a default value instead ... - WARNING: variable QFIT= is missing. I will use a default value instead ... - WARNING: variable PPFITON= is missing. I will use a default value instead ... - WARNING: variable ALLFITON= is missing. I will use a default value instead ... - WARNING: variable PPSTEP= is missing. I will use a default value instead ... - WARNING: variable BISTEP= is missing. I will use a default value instead ... - WARNING: variable PP2FIT= is missing. I will use a default value instead ... - WARNING: variable BINT2FIT= is missing. I will use a default value instead ... - WARNING: variable PPNMOL= is missing. I will use a default value instead ... - WARNING: variable PPNGEOM= is missing. I will use a default value instead ... - WARNING: variable PARREP= is missing. I will use a default value instead ... - WARNING: variable VERBOSE= is missing. I will use a default value instead ... - WARNING: variable MIXER= is missing. I will use a default value instead ... - WARNING: variable RESTARTLIB= is missing. I will use a default value instead ... - WARNING: variable CGTOL= is missing. I will use a default value instead ... - WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ... - WARNING: variable COULACC= is missing. I will use a default value instead ... - WARNING: variable COULCUT= is missing. I will use a default value instead ... - WARNING: variable COULR1= is missing. I will use a default value instead ... - WARNING: variable CHTOL= is missing. I will use a default value instead ... - WARNING: variable BETA= is missing. I will use a default value instead ... - WARNING: variable MCSIGMA= is missing. I will use a default value instead ... - WARNING: variable PPBETA= is missing. I will use a default value instead ... - WARNING: variable PPSIGMA= is missing. I will use a default value instead ... - WARNING: variable ER= is missing. I will use a default value instead ... - WARNING: variable INITIALIZED= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - CONTROL{ - xControl= 1 - DEBUGON= 0 - FERMIM= 6 - CGORLIB= 1 - NORECS= 1 - ENTROPYKIND= 1 - PPOTON= 1 - VDWON= 0 - SPINON= 0 - ELECTRO= 1 - ELECMETH= 0 - MAXSCF= 450 - MINSP2ITER= 22 - FULLQCONV= 1 - QITER= 3 - ORDERNMOL= 0 - SPARSEON= 1 - THRESHOLDON= 1 - FILLINSTOP= 100 - BLKSZ= 4 - MSPARSE= 1500 - LCNON= 0 - LCNITER= 4 - RELAX= 0 - MAXITER= 100000 - MDON= 1 - PBCON= 1 - RESTART= 0 - CHARGE= 0 - XBO= 1 - XBODISON= 1 - XBODISORDER= 5 - NGPU= 2 - KON= 0 - COMPFORCE= 1 - DOSFIT= 0 - INTS2FIT= 1 - NFITSTEP= 5000 - QFIT= 0 - PPFITON= 0 - ALLFITON= 0 - PPSTEP= 500 - BISTEP= 500 - PP2FIT= 2 - BINT2FIT= 6 - PPNMOL= 10 - PPNGEOM= 200 - PARREP= 0 - VERBOSE= 0 - MIXER= 0 - RESTARTLIB= 0 - CGTOL= 9.9999999747524271E-007 - KBT= 0.0000000000000000 - SPINTOL= 1.0000000000000000E-004 - ELEC_ETOL= 1.0000000474974513E-003 - ELEC_QTOL= 1.0000000000000000E-008 - COULACC= 9.9999999747524271E-007 - COULCUT= -500.00000000000000 - COULR1= 500.00000000000000 - BREAKTOL= 9.9999999999999995E-007 - QMIX= 0.25000000000000000 - SPINMIX= 0.25000000000000000 - MDMIX= 0.25000000000000000 - NUMTHRESH= 9.9999999999999995E-007 - CHTOL= 9.9999997764825821E-003 - SKIN= 1.0000000000000000 - RLXFTOL= 9.9999999999999995E-008 - BETA= 1000.0000000000000 - MCSIGMA= 0.20000000298023224 - PPBETA= 1000.0000000000000 - PPSIGMA= 9.9999997764825821E-003 - ER= 1.0000000000000000 - JobName=MyJob - BASISTYPE=NONORTHO - SP2CONV=REL - RELAXTYPE=SD - PARAMPATH=./TBparam - COORDSFILE=./coords.dat - INITIALIZED= F - } - - ./TBparam/electrons.dat - MDCONTROL{ } - - WARNING: variable RNDIST= is missing. I will use a default value instead ... - WARNING: variable SEEDINIT= is missing. I will use a default value instead ... - WARNING: variable NPTTYPE= is missing. I will use a default value instead ... - WARNING: variable UDNEIGH= is missing. I will use a default value instead ... - WARNING: variable DUMPFREQ= is missing. I will use a default value instead ... - WARNING: variable RSFREQ= is missing. I will use a default value instead ... - WARNING: variable WRTFREQ= is missing. I will use a default value instead ... - WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ... - WARNING: variable THERMPER= is missing. I will use a default value instead ... - WARNING: variable THERMRUN= is missing. I will use a default value instead ... - WARNING: variable NVTON= is missing. I will use a default value instead ... - WARNING: variable NPTON= is missing. I will use a default value instead ... - WARNING: variable AVEPER= is missing. I will use a default value instead ... - WARNING: variable SEED= is missing. I will use a default value instead ... - WARNING: variable SHOCKON= is missing. I will use a default value instead ... - WARNING: variable SHOCKSTART= is missing. I will use a default value instead ... - WARNING: variable SHOCKDIR= is missing. I will use a default value instead ... - WARNING: variable MDADAPT= is missing. I will use a default value instead ... - WARNING: variable GETHUG= is missing. I will use a default value instead ... - WARNING: variable RSLEVEL= is missing. I will use a default value instead ... - WARNING: variable DT= is missing. I will use a default value instead ... - WARNING: variable TEMPERATURE= is missing. I will use a default value instead ... - WARNING: variable FRICTION= is missing. I will use a default value instead ... - WARNING: variable PTARGET= is missing. I will use a default value instead ... - WARNING: variable UPARTICLE= is missing. I will use a default value instead ... - WARNING: variable USHOCK= is missing. I will use a default value instead ... - WARNING: variable C0= is missing. I will use a default value instead ... - WARNING: variable E0= is missing. I will use a default value instead ... - WARNING: variable V0= is missing. I will use a default value instead ... - WARNING: variable P0= is missing. I will use a default value instead ... - WARNING: variable DUMMY= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - MDCONTROL{ - MAXITER= -1 - UDNEIGH= 1 - DUMPFREQ= 250 - RSFREQ= 500 - WRTFREQ= 25 - TOINITTEMP5= 1 - THERMPER= 500 - THERMRUN= 50000 - NVTON= 0 - NPTON= 0 - AVEPER= 1000 - SEED= 54 - SHOCKON= 0 - SHOCKSTART= 100000 - SHOCKDIR= 1 - MDADAPT= 0 - GETHUG= 0 - RSLEVEL= 0 - DT= 0.25000000000000000 - TEMPERATURE= 300.00000000000000 - FRICTION= 1000.0000000000000 - PTARGET= 0.0000000000000000 - UPARTICLE= 500.00000000000000 - USHOCK= -4590.0000000000000 - C0= 1300.0000000000000 - E0= -795.72497558593750 - V0= 896.98486328125000 - P0= 8.3149001002311707E-002 - RNDIST=GAUSSIAN - SEEDINIT=UNIFORM - NPTTYPE=ISO - DUMMY= F - } - - LIBCALLS 0 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15165627147849 13.850829743067372 0.0000000000000000 3.9653384620309846 - LIBCALLS 1 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15142147081917 13.850596160685321 0.0000000000000000 3.9653428217526296 - 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I will use a default value instead ... - WARNING: variable PARAMPATH= is missing. I will use a default value instead ... - WARNING: variable DEBUGON= is missing. I will use a default value instead ... - WARNING: variable FERMIM= is missing. I will use a default value instead ... - WARNING: variable CGORLIB= is missing. I will use a default value instead ... - WARNING: variable NORECS= is missing. I will use a default value instead ... - WARNING: variable VDWON= is missing. I will use a default value instead ... - WARNING: variable ORDERNMOL= is missing. I will use a default value instead ... - WARNING: variable LCNON= is missing. I will use a default value instead ... - WARNING: variable LCNITER= is missing. I will use a default value instead ... - WARNING: variable MDON= is missing. I will use a default value instead ... - WARNING: variable PBCON= is missing. I will use a default value instead ... - WARNING: variable RESTART= is missing. I will use a default value instead ... - WARNING: variable NGPU= is missing. I will use a default value instead ... - WARNING: variable COMPFORCE= is missing. I will use a default value instead ... - WARNING: variable DOSFIT= is missing. I will use a default value instead ... - WARNING: variable INTS2FIT= is missing. I will use a default value instead ... - WARNING: variable NFITSTEP= is missing. I will use a default value instead ... - WARNING: variable QFIT= is missing. I will use a default value instead ... - WARNING: variable PPFITON= is missing. I will use a default value instead ... - WARNING: variable ALLFITON= is missing. I will use a default value instead ... - WARNING: variable PPSTEP= is missing. I will use a default value instead ... - WARNING: variable BISTEP= is missing. I will use a default value instead ... - WARNING: variable PP2FIT= is missing. I will use a default value instead ... - WARNING: variable BINT2FIT= is missing. I will use a default value instead ... - WARNING: variable PPNMOL= is missing. I will use a default value instead ... - WARNING: variable PPNGEOM= is missing. I will use a default value instead ... - WARNING: variable PARREP= is missing. I will use a default value instead ... - WARNING: variable VERBOSE= is missing. I will use a default value instead ... - WARNING: variable MIXER= is missing. I will use a default value instead ... - WARNING: variable RESTARTLIB= is missing. I will use a default value instead ... - WARNING: variable CGTOL= is missing. I will use a default value instead ... - WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ... - WARNING: variable COULACC= is missing. I will use a default value instead ... - WARNING: variable COULCUT= is missing. I will use a default value instead ... - WARNING: variable COULR1= is missing. I will use a default value instead ... - WARNING: variable CHTOL= is missing. I will use a default value instead ... - WARNING: variable BETA= is missing. I will use a default value instead ... - WARNING: variable MCSIGMA= is missing. I will use a default value instead ... - WARNING: variable PPBETA= is missing. I will use a default value instead ... - WARNING: variable PPSIGMA= is missing. I will use a default value instead ... - WARNING: variable ER= is missing. I will use a default value instead ... - WARNING: variable INITIALIZED= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - CONTROL{ - xControl= 1 - DEBUGON= 0 - FERMIM= 6 - CGORLIB= 1 - NORECS= 1 - ENTROPYKIND= 1 - PPOTON= 1 - VDWON= 0 - SPINON= 0 - ELECTRO= 1 - ELECMETH= 0 - MAXSCF= 450 - MINSP2ITER= 22 - FULLQCONV= 1 - QITER= 3 - ORDERNMOL= 0 - SPARSEON= 1 - THRESHOLDON= 1 - FILLINSTOP= 100 - BLKSZ= 4 - MSPARSE= 1500 - LCNON= 0 - LCNITER= 4 - RELAX= 0 - MAXITER= 100000 - MDON= 1 - PBCON= 1 - RESTART= 0 - CHARGE= 0 - XBO= 1 - XBODISON= 1 - XBODISORDER= 5 - NGPU= 2 - KON= 0 - COMPFORCE= 1 - DOSFIT= 0 - INTS2FIT= 1 - NFITSTEP= 5000 - QFIT= 0 - PPFITON= 0 - ALLFITON= 0 - PPSTEP= 500 - BISTEP= 500 - PP2FIT= 2 - BINT2FIT= 6 - PPNMOL= 10 - PPNGEOM= 200 - PARREP= 0 - VERBOSE= 0 - MIXER= 0 - RESTARTLIB= 0 - CGTOL= 9.9999999747524271E-007 - KBT= 0.0000000000000000 - SPINTOL= 1.0000000000000000E-004 - ELEC_ETOL= 1.0000000474974513E-003 - ELEC_QTOL= 1.0000000000000000E-008 - COULACC= 9.9999999747524271E-007 - COULCUT= -500.00000000000000 - COULR1= 500.00000000000000 - BREAKTOL= 9.9999999999999995E-007 - QMIX= 0.25000000000000000 - SPINMIX= 0.25000000000000000 - MDMIX= 0.25000000000000000 - NUMTHRESH= 9.9999999999999995E-007 - CHTOL= 9.9999997764825821E-003 - SKIN= 1.0000000000000000 - RLXFTOL= 9.9999999999999995E-008 - BETA= 1000.0000000000000 - MCSIGMA= 0.20000000298023224 - PPBETA= 1000.0000000000000 - PPSIGMA= 9.9999997764825821E-003 - ER= 1.0000000000000000 - JobName=MyJob - BASISTYPE=NONORTHO - SP2CONV=REL - RELAXTYPE=SD - PARAMPATH=./TBparam - COORDSFILE=./coords.dat - INITIALIZED= F - } - - ./TBparam/electrons.dat - MDCONTROL{ } - - WARNING: variable RNDIST= is missing. I will use a default value instead ... - WARNING: variable SEEDINIT= is missing. I will use a default value instead ... - WARNING: variable NPTTYPE= is missing. I will use a default value instead ... - WARNING: variable UDNEIGH= is missing. I will use a default value instead ... - WARNING: variable DUMPFREQ= is missing. I will use a default value instead ... - WARNING: variable RSFREQ= is missing. I will use a default value instead ... - WARNING: variable WRTFREQ= is missing. I will use a default value instead ... - WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ... - WARNING: variable THERMPER= is missing. I will use a default value instead ... - WARNING: variable THERMRUN= is missing. I will use a default value instead ... - WARNING: variable NVTON= is missing. I will use a default value instead ... - WARNING: variable NPTON= is missing. I will use a default value instead ... - WARNING: variable AVEPER= is missing. I will use a default value instead ... - WARNING: variable SEED= is missing. I will use a default value instead ... - WARNING: variable SHOCKON= is missing. I will use a default value instead ... - WARNING: variable SHOCKSTART= is missing. I will use a default value instead ... - WARNING: variable SHOCKDIR= is missing. I will use a default value instead ... - WARNING: variable MDADAPT= is missing. I will use a default value instead ... - WARNING: variable GETHUG= is missing. I will use a default value instead ... - WARNING: variable RSLEVEL= is missing. I will use a default value instead ... - WARNING: variable DT= is missing. I will use a default value instead ... - WARNING: variable TEMPERATURE= is missing. I will use a default value instead ... - WARNING: variable FRICTION= is missing. I will use a default value instead ... - WARNING: variable PTARGET= is missing. I will use a default value instead ... - WARNING: variable UPARTICLE= is missing. I will use a default value instead ... - WARNING: variable USHOCK= is missing. I will use a default value instead ... - WARNING: variable C0= is missing. I will use a default value instead ... - WARNING: variable E0= is missing. I will use a default value instead ... - WARNING: variable V0= is missing. I will use a default value instead ... - WARNING: variable P0= is missing. I will use a default value instead ... - WARNING: variable DUMMY= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - MDCONTROL{ - MAXITER= -1 - UDNEIGH= 1 - DUMPFREQ= 250 - RSFREQ= 500 - WRTFREQ= 25 - TOINITTEMP5= 1 - THERMPER= 500 - THERMRUN= 50000 - NVTON= 0 - NPTON= 0 - AVEPER= 1000 - SEED= 54 - SHOCKON= 0 - SHOCKSTART= 100000 - SHOCKDIR= 1 - MDADAPT= 0 - GETHUG= 0 - RSLEVEL= 0 - DT= 0.25000000000000000 - TEMPERATURE= 300.00000000000000 - FRICTION= 1000.0000000000000 - PTARGET= 0.0000000000000000 - UPARTICLE= 500.00000000000000 - USHOCK= -4590.0000000000000 - C0= 1300.0000000000000 - E0= -795.72497558593750 - V0= 896.98486328125000 - P0= 8.3149001002311707E-002 - RNDIST=GAUSSIAN - SEEDINIT=UNIFORM - NPTTYPE=ISO - DUMMY= F - } - - LIBCALLS 0 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -110.94281402417451 9.3197859655447317 0.0000000000000000 3.3331152608769714 - LIBCALLS 1 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.00875524736128 9.3653691493930946 0.0000000000000000 3.3307590218500454 - 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LIBCALLS 98 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.09218577985371 14.515310319889227 0.0000000000000000 3.0759929793994090 - LIBCALLS 99 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.30969482099719 13.692843612811791 0.0000000000000000 3.1081426979179545 - LIBCALLS 100 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.51358261827596 12.884492109393644 0.0000000000000000 3.1405428597121636 diff --git a/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 b/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 deleted file mode 100644 index 3a37136fd3..0000000000 --- a/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (11 May 2018) -# Simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.graphene.boxrel - triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 32 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all box/relax iso 0.0 vmax 0.001 - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom etotal - -# minimization - -thermo 1 -fix 3 all print 1 "Total Energy =" -min_style cg -min_modify dmax 0.1 -min_modify line quadratic -minimize 1.0e-4 1.0e-4 10000 10000 -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 - binsize = 1, bins = 11 9 20 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes -TotEng - -247.46002 - -247.67224 - -247.87937 - -248.08148 - -248.27865 - -248.47096 - -248.65851 - -248.84137 - -249.01964 - -249.19342 - -249.36281 - -249.52791 - -249.68883 - -249.8457 - -249.99865 - -250.1478 - -250.29332 - -250.43535 - -250.57409 - -250.70972 - -250.84247 - -250.97258 - -251.10035 - -251.2261 - -251.35021 - -251.47314 - -251.59543 - -251.71776 - -251.84096 - -251.9661 - -252.09459 - -252.22833 - -252.37003 - -252.52371 - -252.69578 - -252.89752 - -253.15197 - -253.52044 - -254.31418 - -255.6175 - -256.8162 - -258.1227 - -259.38401 - -260.74831 - -262.03991 - -263.5463 - -264.70486 - -267.69144 - -267.88682 - -269.03519 - -270.60187 - -270.65382 - -270.74279 - -271.55883 - -271.81248 - -271.87529 - -273.01494 - -273.23948 - -273.28719 - -273.35272 - -273.41591 - -273.46274 - -273.54755 - -273.58318 - -273.73111 - -273.75754 -Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms - -1582.4% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -247.460020579 -273.731112592 -273.757543461 - Force two-norm initial, final = 201.608 9.43485 - Force max component initial, final = 188.924 2.41297 - Final line search alpha, max atom move = 0.000223273 0.00053875 - Iterations, force evaluations = 65 65 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.00 -Bond | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 -Neigh | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00 -Comm | 0.00026107 | 0.00026107 | 0.00026107 | 0.0 | 0.00 -Output | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.00 -Modify | 39.412 | 39.412 | 39.412 | 0.0 | 99.99 -Other | | 0.00127 | | | 0.00 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 48 ave 48 max 48 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 48 -Ave neighs/atom = 1.5 -Ave special neighs/atom = 0 -Neighbor list builds = 1 -Dangerous builds = 0 -Total wall time: 0:00:40 diff --git a/examples/latte/log.21Jun18.latte.sucrose.g++.1 b/examples/latte/log.21Jun18.latte.sucrose.g++.1 deleted file mode 100644 index cb4526587c..0000000000 --- a/examples/latte/log.21Jun18.latte.sucrose.g++.1 +++ /dev/null @@ -1,103 +0,0 @@ -LAMMPS (11 May 2018) -# simple sucrose model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.sucrose - orthogonal box = (0 0 0) to (17.203 18.009 21.643) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 45 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 -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 - binsize = 1, bins = 18 19 22 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes -Step Temp PotEng TotEng Press - 0 0 -251.26617 -251.26617 16.617234 - 10 0.025263709 -251.26631 -251.26617 8.0576708 - 20 0.034232467 -251.26636 -251.26617 1.6673442 - 30 0.059079556 -251.2665 -251.26617 11.058458 - 40 0.055499766 -251.26648 -251.26617 14.837775 - 50 0.058499509 -251.2665 -251.26617 6.7183113 - 60 0.071094535 -251.26657 -251.26617 6.6133687 - 70 0.084309439 -251.26665 -251.26617 12.372721 - 80 0.1089929 -251.26679 -251.26617 8.8355516 - 90 0.11378257 -251.26681 -251.26617 5.1177922 - 100 0.13003966 -251.26691 -251.26617 8.2431185 -Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms - -Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s -1799.6% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00 -Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00 -Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 -Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00 -Other | | 0.0005403 | | | 0.00 - -Nlocal: 45 ave 45 max 45 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: 59 ave 59 max 59 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 59 -Ave neighs/atom = 1.31111 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:28 diff --git a/examples/latte/log.21Jun18.latte.water.g++.1 b/examples/latte/log.21Jun18.latte.water.g++.1 deleted file mode 100644 index 0decce1f98..0000000000 --- a/examples/latte/log.21Jun18.latte.water.g++.1 +++ /dev/null @@ -1,103 +0,0 @@ -LAMMPS (11 May 2018) -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - orthogonal box = (0 0 0) to (6.267 6.267 6.267) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 24 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 -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 - binsize = 1, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes -Step Temp PotEng TotEng Press - 0 0 -104.95594 -104.95594 48236.006 - 10 336.5303 -105.96026 -104.95976 97997.303 - 20 529.06385 -106.53021 -104.95731 131520.49 - 30 753.62616 -107.1995 -104.95898 49297.371 - 40 716.6565 -107.08802 -104.95741 28307.272 - 50 824.04417 -107.40822 -104.95835 102167.48 - 60 933.56056 -107.73478 -104.95932 92508.792 - 70 851.18518 -107.48766 -104.95711 13993.28 - 80 999.80265 -107.93146 -104.95906 36700.417 - 90 998.77707 -107.92569 -104.95634 107233.7 - 100 1281.4446 -108.76961 -104.95989 49703.193 -Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms - -Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s -6459.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 | 0.0 | 0.00 -Bond | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 | 0.0 | 0.00 -Neigh | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 -Comm | 0.00031829 | 0.00031829 | 0.00031829 | 0.0 | 0.00 -Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 -Modify | 10.637 | 10.637 | 10.637 | 0.0 | 99.99 -Other | | 0.00052 | | | 0.00 - -Nlocal: 24 ave 24 max 24 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: 31 ave 31 max 31 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 31 -Ave neighs/atom = 1.29167 -Ave special neighs/atom = 0 -Neighbor list builds = 2 -Dangerous builds = 0 -Total wall time: 0:00:10 diff --git a/examples/latte/log.21Jun18.latte.water.min.g++.1 b/examples/latte/log.21Jun18.latte.water.min.g++.1 deleted file mode 100644 index 1c8921fd60..0000000000 --- a/examples/latte/log.21Jun18.latte.water.min.g++.1 +++ /dev/null @@ -1,108 +0,0 @@ -LAMMPS (11 May 2018) -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - orthogonal box = (0 0 0) to (6.267 6.267 6.267) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 24 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# minimization - -thermo 10 - -min_style fire -minimize 1.0e-4 1.0e-4 500 500 -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 - binsize = 1, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes -Step Temp PotEng TotEng Press - 0 0 -104.95594 -104.95594 48236.006 - 10 349.4534 -105.50948 -104.47056 62157.729 - 20 1253.6636 -107.00863 -103.28151 116456.71 - 30 134.64051 -107.56155 -107.16127 59864.196 - 40 2.4044989 -108.1527 -108.14556 32695.648 - 47 137.26885 -108.30413 -107.89603 60177.442 -Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms - -6481.9% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -104.955944301 -108.302982895 -108.304126127 - Force two-norm initial, final = 19.119 3.44609 - Force max component initial, final = 11.7758 1.3408 - Final line search alpha, max atom move = 0 0 - Iterations, force evaluations = 47 47 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00 -Bond | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 0.00 -Output | 0.00012302 | 0.00012302 | 0.00012302 | 0.0 | 0.00 -Modify | 6.426 | 6.426 | 6.426 | 0.0 | 99.99 -Other | | 0.0004699 | | | 0.01 - -Nlocal: 24 ave 24 max 24 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37 ave 37 max 37 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 37 -Ave neighs/atom = 1.54167 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:06 From fe4f7bd46737c62471470707bb6ac737922282d4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 11:43:09 -0400 Subject: [PATCH 11/11] spelling --- doc/src/labelmap.rst | 2 +- doc/src/read_data.rst | 2 +- doc/src/restart.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/labelmap.rst b/doc/src/labelmap.rst index a709bb1104..1f500db6b4 100644 --- a/doc/src/labelmap.rst +++ b/doc/src/labelmap.rst @@ -86,7 +86,7 @@ This command must come after the simulation box is defined by a :doc:`read_data `, :doc:`read_restart `, or :doc:`create_box ` command. -Labelmaps are currently not supported when using the KOKKOS package. +Label maps are currently not supported when using the KOKKOS package. Related commands """""""""""""""" diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index f39e27df90..858029caae 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -1519,7 +1519,7 @@ To read gzipped data files, you must compile LAMMPS with the -DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. -Labelmaps are currently not supported when using the KOKKOS package. +Label maps are currently not supported when using the KOKKOS package. Related commands """""""""""""""" diff --git a/doc/src/restart.rst b/doc/src/restart.rst index 91b920f377..5de2d3d75c 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -12,7 +12,7 @@ Syntax restart N root keyword value ... restart N file1 file2 keyword value ... -* N = write a restart file on timesteps which are multipls of N +* N = write a restart file on timesteps which are multiples of N * N can be a variable (see below) * root = filename to which timestep # is appended * file1,file2 = two full filenames, toggle between them when writing file