From d8f211c05d6f4e70d380dc16bf34d424f94132d5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 8 Sep 2022 17:15:23 -0600 Subject: [PATCH 01/14] 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 02/14] 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 03/14] 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 04/14] 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 05/14] 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 06/14] 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 cc2b6a35652921cfe2f8460ec7942d53ff49b164 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Sep 2022 19:02:46 -0400 Subject: [PATCH 07/14] reorder punctuation and quotation characters for clarity --- doc/src/Bibliography.rst | 2 +- doc/src/Packages_details.rst | 2 +- doc/src/Run_options.rst | 2 +- doc/src/Speed_intel.rst | 2 +- doc/src/compute_angmom_chunk.rst | 2 +- doc/src/compute_born_matrix.rst | 2 +- doc/src/compute_com.rst | 2 +- doc/src/compute_com_chunk.rst | 2 +- doc/src/compute_dipole.rst | 2 +- doc/src/compute_dipole_chunk.rst | 2 +- doc/src/compute_erotate_asphere.rst | 2 +- doc/src/compute_erotate_rigid.rst | 2 +- doc/src/compute_erotate_sphere.rst | 2 +- doc/src/compute_event_displace.rst | 4 +- doc/src/compute_fep.rst | 2 +- doc/src/compute_group_group.rst | 2 +- doc/src/compute_gyration.rst | 2 +- doc/src/compute_gyration_shape.rst | 2 +- doc/src/compute_gyration_shape_chunk.rst | 2 +- doc/src/compute_heat_flux.rst | 14 +- doc/src/compute_hma.rst | 2 +- doc/src/compute_inertia_chunk.rst | 2 +- doc/src/compute_ke.rst | 2 +- doc/src/compute_ke_rigid.rst | 2 +- doc/src/compute_momentum.rst | 2 +- doc/src/compute_msd.rst | 2 +- doc/src/compute_msd_chunk.rst | 2 +- doc/src/compute_msd_nongauss.rst | 2 +- doc/src/compute_omega_chunk.rst | 2 +- doc/src/compute_pe.rst | 4 +- doc/src/compute_plasticity_atom.rst | 2 +- doc/src/compute_pressure.rst | 6 +- doc/src/compute_property_chunk.rst | 2 +- doc/src/compute_property_local.rst | 2 +- doc/src/compute_rdf.rst | 2 +- doc/src/compute_reduce.rst | 12 +- doc/src/compute_reduce_chunk.rst | 2 +- doc/src/compute_stress_profile.rst | 2 +- doc/src/compute_tally.rst | 2 +- doc/src/compute_temp.rst | 2 +- doc/src/compute_temp_asphere.rst | 4 +- doc/src/compute_temp_body.rst | 4 +- doc/src/compute_temp_chunk.rst | 4 +- doc/src/compute_temp_com.rst | 4 +- doc/src/compute_temp_cs.rst | 4 +- doc/src/compute_temp_deform.rst | 2 +- doc/src/compute_temp_deform_eff.rst | 4 +- doc/src/compute_temp_drude.rst | 4 +- doc/src/compute_temp_eff.rst | 4 +- doc/src/compute_temp_partial.rst | 4 +- doc/src/compute_temp_profile.rst | 4 +- doc/src/compute_temp_ramp.rst | 4 +- doc/src/compute_temp_region.rst | 4 +- doc/src/compute_temp_region_eff.rst | 4 +- doc/src/compute_temp_rotate.rst | 4 +- doc/src/compute_temp_sphere.rst | 4 +- doc/src/compute_ti.rst | 2 +- doc/src/compute_torque_chunk.rst | 2 +- doc/src/compute_vacf.rst | 2 +- doc/src/compute_vcm_chunk.rst | 2 +- doc/src/compute_viscosity_cos.rst | 6 +- doc/src/compute_voronoi_atom.rst | 2 +- doc/src/compute_xrd.rst | 2 +- doc/src/create_atoms.rst | 4 +- doc/src/dump.rst | 233 ++++++++++++----------- doc/src/dump_image.rst | 55 +++--- doc/src/fix_adapt.rst | 56 +++--- doc/src/fix_adapt_fep.rst | 4 +- doc/src/fix_addforce.rst | 2 +- doc/src/fix_addtorque.rst | 2 +- doc/src/fix_amoeba_bitorsion.rst | 2 +- doc/src/fix_amoeba_pitorsion.rst | 2 +- doc/src/fix_atc.rst | 2 +- doc/src/fix_atom_swap.rst | 2 +- doc/src/fix_ave_atom.rst | 8 +- doc/src/fix_ave_chunk.rst | 36 ++-- doc/src/fix_ave_correlate.rst | 6 +- doc/src/fix_ave_histo.rst | 6 +- doc/src/fix_ave_time.rst | 6 +- doc/src/fix_balance.rst | 4 +- doc/src/group.rst | 2 +- doc/src/kim_commands.rst | 2 +- doc/src/pair_zbl.rst | 2 +- 83 files changed, 315 insertions(+), 311 deletions(-) diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index 9f3591dcde..dff457836c 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -1373,7 +1373,7 @@ Bibliography Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). **(Ziegler)** - J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. + J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985. **(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 4e75c5e94a..f89ab00039 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -276,7 +276,7 @@ the barostat as outlined in: N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of -molecular liquids," J. Chem. Phys. 143, 243148 (2015). +molecular liquids", J. Chem. Phys. 143, 243148 (2015). **Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University) diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index d2d7f8c155..f3c7973197 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -495,7 +495,7 @@ run: write_dump group-ID dumpstyle dumpfile arg1 arg2 ... Note that the specified restartfile and dumpfile names may contain -wild-card characters ("\*","%") as explained on the +wild-card characters ("\*" or "%") as explained on the :doc:`read_restart ` and :doc:`write_dump ` doc pages. The use of "%" means that a parallel restart file and/or parallel dump file can be read and/or written. Note that a filename diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 6526f836b2..2b53af8698 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -536,6 +536,6 @@ supported. References """""""""" -* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. +* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. * Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. `_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index 2e98742772..ba3ec526cf 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in mass-velocity-distance :doc:`units `. Restrictions diff --git a/doc/src/compute_born_matrix.rst b/doc/src/compute_born_matrix.rst index 920ae46532..52bed6a357 100644 --- a/doc/src/compute_born_matrix.rst +++ b/doc/src/compute_born_matrix.rst @@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The array values calculated by this compute are all "extensive." +The array values calculated by this compute are all "extensive". Restrictions """""""""""" diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index df5373293e..6fa3fda64c 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The vector values are "intensive." The vector values will be in +The vector values are "intensive". The vector values will be in distance :doc:`units `. Restrictions diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index a2df80d5d8..2556d97b09 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in distance :doc:`units `. Restrictions diff --git a/doc/src/compute_dipole.rst b/doc/src/compute_dipole.rst index 7fb4b54fab..95c5e216f0 100644 --- a/doc/src/compute_dipole.rst +++ b/doc/src/compute_dipole.rst @@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the dipole vector. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The computed values are "intensive." The array values will be in +The computed values are "intensive". The array values will be in dipole units (i.e., charge :doc:`units ` times distance :doc:`units `). diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 24e6442a63..504e6f20d0 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in dipole units (i.e., charge :doc:`units ` times distance :doc:`units `). diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 44415c63cc..35691d8c9a 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." The +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index 1e03a2316c..b1342bf15e 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -48,7 +48,7 @@ of all the rigid bodies). This value can be used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." The +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index 28b0052b89..aae37277a4 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." The +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index f8911e1224..43881460f4 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -40,7 +40,7 @@ further than the threshold distance. If the system is undergoing significant center-of-mass motion, due to thermal motion, an external force, or an initial net momentum, then this compute will not be able to distinguish that motion from - local atom displacements and may generate "false positives." + local atom displacements and may generate "false positives". Output info """"""""""" @@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The +The scalar value calculated by this compute is "intensive". The scalar value will be a 0 or 1 as explained above. Restrictions diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index e2de8d405b..481e4ead91 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -299,7 +299,7 @@ These output results can be used by any command that uses a global scalar or vector from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. For example, the computed values can be averaged using :doc:`fix ave/time `. -The values calculated by this compute are "extensive." +The values calculated by this compute are "extensive". Restrictions """""""""""" diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 87e855ae1e..b4eccf959f 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -140,7 +140,7 @@ vector values from a compute as input. See the options. Both the scalar and vector values calculated by this compute are -"extensive." The scalar value will be in energy :doc:`units `. +"extensive". The scalar value will be in energy :doc:`units `. The vector values will be in force :doc:`units `. Restrictions diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index 5610dd1d98..eaefc3abbb 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -69,7 +69,7 @@ vector values from a compute as input. See the :doc:`Howto output `, respectively. Restrictions diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 892677b0ba..2cbffbbdf4 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -78,7 +78,7 @@ vector values from a compute as input. See the options. The vector values calculated by this compute are -"intensive." The first five vector values will be in +"intensive". The first five vector values will be in distance\ :math:`2` :doc:`units ` while the sixth one is dimensionless. Restrictions diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 2bf8c970e9..62a25b05a3 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -80,7 +80,7 @@ See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array calculated by this compute is -"intensive." The first five columns will be in +"intensive". The first five columns will be in distance\ :math:`^2` :doc:`units ` while the sixth one is dimensionless. Restrictions diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 4302ecddb8..b88cb76260 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -142,14 +142,14 @@ command that uses global vector values from a compute as input. See the :doc:`Howto output ` documentation for an overview of LAMMPS output options. -The vector values calculated by this compute are "extensive," meaning +The vector values calculated by this compute are "extensive", meaning they scale with the number of atoms in the simulation. They can be -divided by the appropriate volume to get a flux, which would then be -an "intensive" value, meaning independent of the number of atoms in -the simulation. Note that if the compute is "all," then the -appropriate volume to divide by is the simulation box volume. -However, if a sub-group is used, it should be the volume containing -those atoms. +divided by the appropriate volume to get a flux, which would then be an +"intensive" value, meaning independent of the number of atoms in the +simulation. Note that if the compute group is "all", then the +appropriate volume to divide by is the simulation box volume. However, +if a group with a subset of atoms is used, it should be the volume +containing those atoms. The vector values will be in energy\*velocity :doc:`units `. Once divided by a volume the units will be that of flux, namely diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 8c0c958ae5..4fa4579651 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea capacity). The elements of the vector can be accessed by indices 1--n by any command that uses global vector values as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The vector values calculated by this compute are "extensive." The +The vector values calculated by this compute are "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 74f59dd7a7..6569c3965d 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in mass\*distance\ :math:`^2` :doc:`units `. Restrictions diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 4eb07b920c..8a19438640 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." The +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index b3e446daf6..e77cabfeb6 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -48,7 +48,7 @@ global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." The +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index 59215c889b..d16d220673 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global vector value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The vector value calculated by this compute is "extensive." The vector +The vector value calculated by this compute is "extensive". The vector value will be in mass\*velocity :doc:`units `. Restrictions diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 77694ca8fc..bc16a3de6f 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The vector values are "intensive." The vector values will be in +The vector values are "intensive". The vector values will be in distance\ :math:`^2` :doc:`units `. Restrictions diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 6be5196782..584453d76b 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -121,7 +121,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in distance\ :math:`^2` :doc:`units `. Restrictions diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 16c4e0b06c..512437a932 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -67,7 +67,7 @@ accessed by indices 1--3 by any command that uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The vector values are "intensive." The first vector value will be in +The vector values are "intensive". The first vector value will be in distance\ :math:`^2` :doc:`units `, the second is in distance\ :math:`^4` units, and the third is dimensionless. diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index 8c32d6491e..7eaddff602 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -84,7 +84,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in velocity/distance :doc:`units `. Restrictions diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 825fe4cba4..a96bdd249e 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -27,7 +27,7 @@ Description """"""""""" Define a computation that calculates the potential energy of the -entire system of atoms. The specified group must be "all." See the +entire system of atoms. The specified group must be "all". See the :doc:`compute pe/atom ` command if you want per-atom energies. These per-atom values could be summed for a group of atoms via the :doc:`compute reduce ` command. @@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." The +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index ad0c22dbf5..45d77d228d 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -73,5 +73,5 @@ none .. _Mitchell: **(Mitchell)** Mitchell, "A non-local, ordinary-state-based -viscoelasticity model for peridynamics," Sandia National Lab Report, +viscoelasticity model for peridynamics", Sandia National Lab Report, 8064:1-28 (2011). diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index c1a9e3d2ec..bf344be270 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -29,7 +29,7 @@ Description """"""""""" Define a computation that calculates the pressure of the entire system -of atoms. The specified group must be "all." See the +of atoms. The specified group must be "all". See the :doc:`compute stress/atom ` command if you want per-atom pressure (stress). These per-atom values could be summed for a group of atoms via the :doc:`compute reduce ` command. @@ -115,7 +115,7 @@ LAMMPS starts up, as if this command were in the input script: compute thermo_press all pressure thermo_temp where thermo_temp is the ID of a similarly defined compute of style -"temp." See the :doc:`thermo_style ` command for more details. +"temp". See the :doc:`thermo_style ` command for more details. ---------- @@ -137,7 +137,7 @@ The ordering of values in the symmetric pressure tensor is as follows: :math:`p_{xz},` :math:`p_{yz}.` The scalar and vector values calculated by this compute are -"intensive." The scalar and vector values will be in pressure +"intensive". The scalar and vector values will be in pressure :doc:`units `. Restrictions diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 6475a4b962..7c06b8d51e 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The vector or array values are "intensive." The values will be +The vector or array values are "intensive". The values will be unitless or in the units discussed above. Restrictions diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 2f74f45bf4..f1234ade09 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -164,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types. The number of bond types is defined in the data file read by the :doc:`read_data ` command. -The attributes that start with "a," "d," and "i" refer to similar values +The attributes that start with "a", "d", and "i" refer to similar values for :doc:`angles `, :doc:`dihedrals `, and :doc:`impropers `. diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 2ccc03cf8f..e40775c6e0 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values calculated by this compute are all "intensive." +The array values calculated by this compute are all "intensive". The first column of array values will be in distance :doc:`units `. The :math:`g(r)` columns of array values are normalized diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index b85b2b7dbb..89554ebece 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -128,7 +128,7 @@ inputs to this fix by using the :doc:`compute property/atom ` command and then specifying an input value from that compute. -If a value begins with "c\_," a compute ID must follow which has been +If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual :doc:`compute ` page for details. If no bracketed integer @@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS `. See the discussion above for how :math:`I` can be specified with a wildcard asterisk to effectively specify multiple values. -If a value begins with "f\_," a fix ID must follow which has been +If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual :doc:`fix ` page for details. Note that some fixes only produce their values on certain @@ -152,7 +152,7 @@ is used. Users can also write code for their own fix style and :math:`I` can be specified with a wildcard asterisk to effectively specify multiple values. -If a value begins with "v\_," a variable name must follow which has +If a value begins with "v\_", a variable name must follow which has been previously defined in the input script. It must be an :doc:`atom-style variable `. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or @@ -197,7 +197,7 @@ global vector of values, the length of which is equal to the number of inputs specified. As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s) -produced by this compute are all "extensive," meaning their value +produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the :doc:`thermo_style custom ` command with @@ -218,9 +218,9 @@ compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are -"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on +"intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on per-atom or local vectors, in which case the calculated values are -"extensive." +"extensive". The scalar or vector values will be in whatever :doc:`units ` the quantities being reduced are in. diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index c988af276f..43fee39cf2 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -102,7 +102,7 @@ The commands below can be added to the examples/in.micelle script. Imagine a collection of polymer chains or small molecules with hydrophobic end groups. All the hydrophobic (HP) atoms are assigned -to a group called "phobic." +to a group called "phobic". These commands will assign a unique cluster ID to all HP atoms within a specified distance of each other. A cluster will contain all HP diff --git a/doc/src/compute_stress_profile.rst b/doc/src/compute_stress_profile.rst index 9761c68b1e..cb4628bd5d 100644 --- a/doc/src/compute_stress_profile.rst +++ b/doc/src/compute_stress_profile.rst @@ -114,7 +114,7 @@ This array can be output with :doc:`fix ave/time `, compute p all stress/cartesian x 0.1 fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector -The values calculated by this compute are "intensive." The stress +The values calculated by this compute are "intensive". The stress values will be in pressure :doc:`units `. The number density values are in inverse volume :doc:`units `. diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index fd979d19a0..6eff1e186e 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -182,7 +182,7 @@ Output info from individual atoms in both groups). Both the scalar and vector values calculated by this compute are -"extensive." +"extensive". Restrictions """""""""""" diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 2e9d4ab362..1d5a62d6f6 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -91,7 +91,7 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The +The scalar value calculated by this compute is "intensive". The vector values are "extensive". The scalar value will be in temperature :doc:`units `. The diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index cef8d573c1..cba52a68b4 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -134,8 +134,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index 42497e34cb..64f5ce9a0f 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -117,8 +117,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index f3d1a83351..c92b4e36e9 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -242,8 +242,8 @@ can be accessed by any command that uses global array values from a compute as input. Again, see the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." The array values are "intensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The array values are "intensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. The array values diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index fde6f701fd..d54fa7dfa6 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -87,8 +87,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 3c9503cf4f..45de17be89 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -101,8 +101,8 @@ vector of length 6 (KE tensor), which can be accessed by indices 1--6. These values can be used by any command that uses global scalar or vector values from a compute as input. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index b2d6b68b17..adf76564a8 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -134,7 +134,7 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The +The scalar value calculated by this compute is "intensive". The vector values are "extensive". The scalar value will be in temperature :doc:`units `. diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 3dd1225299..83535f4727 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -53,8 +53,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 8c50831941..8602bc3589 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -67,8 +67,8 @@ vector values from a compute as input. See the options. Both the scalar value and the first two values of the vector -calculated by this compute are "intensive." The other four vector values -are "extensive." +calculated by this compute are "intensive". The other four vector values +are "extensive". Restrictions """""""""""" diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index c76581fa68..3ec6300ca4 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -88,9 +88,9 @@ thermostatting. Output info """"""""""" -The scalar value calculated by this compute is "intensive," meaning it +The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector -values are "extensive," meaning they scale with the number of atoms in +values are "extensive", meaning they scale with the number of atoms in the simulation. Restrictions diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index 0512311d8f..d5628e0d60 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -94,8 +94,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 9076a6cb14..566d8cf3fc 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -183,8 +183,8 @@ vector or array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." The array values are "intensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The array values are "intensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. The first column diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 13799874ab..5c18243c23 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -106,8 +106,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index c8a3075771..77954e8898 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -99,8 +99,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index ebfc35cbe6..b8cd73f4fd 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -46,8 +46,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index e760a49b00..7c445109a1 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -86,8 +86,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 3f41837013..5c7c73a8d2 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -122,8 +122,8 @@ vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -vector values are "extensive." +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The scalar value will be in temperature :doc:`units `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index a32f0d1b18..f1f2e5d430 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -125,7 +125,7 @@ value can be used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive." +The scalar value calculated by this compute is "extensive". The scalar value will be in energy :doc:`units `. diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index 97c9c127b8..23befe8458 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -83,7 +83,7 @@ array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in force-distance :doc:`units `. Restrictions diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index c94277f43b..704e597e18 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -66,7 +66,7 @@ accessed by indices 1--4 by any command that uses global vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The vector values are "intensive." The vector values will be in +The vector values are "intensive". The vector values will be in velocity\ :math:`^2` :doc:`units `. Restrictions diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index 5579208766..c2960075f0 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -69,7 +69,7 @@ each chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive." The array values will be in +The array values are "intensive". The array values will be in velocity :doc:`units `. Restrictions diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index a3adf3d78b..1bf9bc2588 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -134,9 +134,9 @@ These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive." The -first six elements of vector values are "extensive," -and the seventh element of vector values is "intensive." +The scalar value calculated by this compute is "intensive". The +first six elements of vector values are "extensive", +and the seventh element of vector values is "intensive". The scalar value will be in temperature :doc:`units `. The first six elements of vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index e1f8de0667..699d3f2aaa 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -198,7 +198,7 @@ Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the *occupation* keyword is specified). These values can be accessed by any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output -options. If the *peratom* keyword is set to "no," the per-atom array +options. If the *peratom* keyword is set to "no", the per-atom array is still created, but it is not accessible. If the *edge_histo* keyword is used, then this compute generates a diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index 39dc78a314..10ee35496d 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -219,7 +219,7 @@ The array can be accessed by any command that uses global values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -All array values calculated by this compute are "intensive." +All array values calculated by this compute are "intensive". Restrictions """""""""""" diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 489d4fa5d1..c8f94f7d5e 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -95,7 +95,7 @@ typically created via the :doc:`create_box ` command. Before using this command, a lattice must also be defined using the :doc:`lattice ` command, unless you specify the *single* style with units = box or the *random* style. For the remainder of this doc -page, a created atom or molecule is referred to as a "particle." +page, a created atom or molecule is referred to as a "particle". If created particles are individual atoms, they are assigned the specified atom *type*, though this can be altered via the *basis* @@ -352,7 +352,7 @@ As an example, these commands can be used in a 2d simulation, to create a sinusoidal surface. Note that the surface is "rough" due to individual lattice points being "above" or "below" the mathematical expression for the sinusoidal curve. If a finer lattice were used, -the sinusoid would appear to be "smoother." Also note the use of the +the sinusoid would appear to be "smoother". Also note the use of the "xlat" and "ylat" :doc:`thermo_style ` keywords, which converts lattice spacings to distance. diff --git a/doc/src/dump.rst b/doc/src/dump.rst index fc86fbaaed..21b82de4f0 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -224,30 +224,29 @@ page for details. The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical in command syntax to the corresponding styles without -"gz," however, they generate compressed files using the zlib +"gz", however, they generate compressed files using the zlib library. Thus the filename suffix ".gz" is mandatory. This is an -alternative approach to writing compressed files via a pipe, as done -by the regular dump styles, which may be required on clusters where -the interface to the high-speed network disallows using the fork() -library call (which is needed for a pipe). For the remainder of this -page, you should thus consider the *atom* and *atom/gz* styles -(etc.) to be inter-changeable, with the exception of the required -filename suffix. +alternative approach to writing compressed files via a pipe, as done by +the regular dump styles, which may be required on clusters where the +interface to the high-speed network disallows using the fork() library +call (which is needed for a pipe). For the remainder of this page, you +should thus consider the *atom* and *atom/gz* styles (etc.) to be +inter-changeable, with the exception of the required filename suffix. -Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, -and *xyz/zstd* styles are identical to the gz styles, but use the Zstd +Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and +*xyz/zstd* styles are identical to the gz styles, but use the Zstd compression library instead and require the ".zst" suffix. See the -:doc:`dump_modify ` page for details on how to control -the compression level in both variants. +:doc:`dump_modify ` page for details on how to control the +compression level in both variants. As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and -*xyz/mpiio* styles are identical in command syntax and in the format -of the dump files they create, to the corresponding styles without -"mpiio," except the single dump file they produce is written in -parallel via the MPI-IO library. For the remainder of this page, -you should thus consider the *atom* and *atom/mpiio* styles (etc.) to -be inter-changeable. The one exception is how the filename is -specified for the MPI-IO styles, as explained below. +*xyz/mpiio* styles are identical in command syntax and in the format of +the dump files they create, to the corresponding styles without "mpiio", +except the single dump file they produce is written in parallel via the +MPI-IO library. For the remainder of this page, you should thus +consider the *atom* and *atom/mpiio* styles (etc.) to be +inter-changeable. The one exception is how the filename is specified +for the MPI-IO styles, as explained below. .. warning:: @@ -434,7 +433,7 @@ Below is an example for a YAML format dump created by the following commands. dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e" -The tags "time," "units," and "thermo" are optional and enabled by the +The tags "time", "units", and "thermo" are optional and enabled by the dump_modify command. The list under the "box" tag has three lines for orthogonal boxes and four lines for triclinic boxes, where the first three are the box boundaries and the fourth the three tilt factors (:math:`xy`, @@ -553,15 +552,14 @@ package installed, viz., make yes-mpiio # installs the MPIIO package make mpi # build LAMMPS for your platform -Second, use a dump filename which contains ".mpiio." Note that it -does not have to end in ".mpiio," just contain those characters. -Unlike MPI-IO restart files, which must be both written and read using -MPI-IO, the dump files produced by these MPI-IO styles are identical -in format to the files produced by their non-MPI-IO style -counterparts. This means you can write a dump file using MPI-IO and -use the :doc:`read_dump ` command or perform other -post-processing, just as if the dump file was not written using -MPI-IO. +Second, use a dump filename which contains ".mpiio". Note that it does +not have to end in ".mpiio", just contain those characters. Unlike +MPI-IO restart files, which must be both written and read using MPI-IO, +the dump files produced by these MPI-IO styles are identical in format +to the files produced by their non-MPI-IO style counterparts. This +means you can write a dump file using MPI-IO and use the :doc:`read_dump +` command or perform other post-processing, just as if the +dump file was not written using MPI-IO. .. warning:: @@ -570,37 +568,40 @@ MPI-IO. Note that MPI-IO dump files are one large file which all processors write to. You thus cannot use the "%" wildcard character described -above in the filename since that specifies generation of multiple -files. You can use the ".bin" or ".lammpsbin" suffix described below in an -MPI-IO dump file; again this file will be written in parallel and have the -same binary format as if it were written without MPI-IO. +above in the filename since that specifies generation of multiple files. +You can use the ".bin" or ".lammpsbin" suffix described below in an +MPI-IO dump file; again this file will be written in parallel and have +the same binary format as if it were written without MPI-IO. -If the filename ends with ".bin" or ".lammpsbin," the dump file (or files, if -"\*" or "%" is also used) is written in binary format. A binary dump file -will be about the same size as a text version, but will typically -write out much faster. Of course, when post-processing, you will need -to convert it back to text format (see the :ref:`binary2txt tool `) or -write your own code to read the binary file. The format of the binary file can -be understood by looking at the :file:`tools/binary2txt.cpp` file. This option -is only available for the *atom* and *custom* styles. +If the filename ends with ".bin" or ".lammpsbin", the dump file (or +files, if "\*" or "%" is also used) is written in binary format. A +binary dump file will be about the same size as a text version, but will +typically write out much faster. Of course, when post-processing, you +will need to convert it back to text format (see the :ref:`binary2txt +tool `) or write your own code to read the binary file. The +format of the binary file can be understood by looking at the +:file:`tools/binary2txt.cpp` file. This option is only available for +the *atom* and *custom* styles. -If the filename ends with ".gz," the dump file (or files, if "\*" or "%" -is also used) is written in gzipped format. A gzipped dump file will be about -:math:`3\times` smaller than the text version, but will also take longer -to write. This option is not available for the *dcd* and *xtc* styles. +If the filename ends with ".gz", the dump file (or files, if "\*" or "%" +is also used) is written in gzipped format. A gzipped dump file will be +about :math:`3\times` smaller than the text version, but will also take +longer to write. This option is not available for the *dcd* and *xtc* +styles. ---------- Note that in the discussion which follows, for styles which can -reference values from a compute or fix or custom atom property, like -the *custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "\*" or "\*n" or "m\*" -or "m\*n." If :math:`N` is the number of columns in the array, then an -asterisk with no numeric values means all column indices from 1 to :math:`N`. -A leading asterisk means all indices from 1 to n (inclusive). A -trailing asterisk means all indices from m to :math:`N` (inclusive). A middle -asterisk means all indices from m to n (inclusive). +reference values from a compute or fix or custom atom property, like the +*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` +can be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "\*" or "\*n" or "m\*" or +"m\*n". If :math:`N` is the number of columns in the array, then an +asterisk with no numeric values means all column indices from 1 to +:math:`N`. A leading asterisk means all indices from 1 to n +(inclusive). A trailing asterisk means all indices from m to :math:`N` +(inclusive). A middle asterisk means all indices from m to n +(inclusive). Using a wildcard is the same as if the individual columns of the array had been listed one by one. For example, these two dump commands are @@ -679,37 +680,38 @@ The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*, *Id* is the atom ID. *Mol* is the molecule ID, included in the data file for molecular systems. *Proc* is the ID of the processor (0 to -:math:`N_\text{procs}-1`) that currently owns the atom. -*Procp1* is the proc ID+1, which can be convenient in place of a *type* -attribute (1 to :math:`N_\text{types}`) for coloring atoms in a visualization -program. *Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is -typically the chemical name of an element, which you must assign to each type -via the :doc:`dump_modify element ` command. More generally, it -can be any string you wish to associated with an atom type. *Mass* is the atom -mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components -of atom velocity and force and atomic charge. +:math:`N_\text{procs}-1`) that currently owns the atom. *Procp1* is the +proc ID+1, which can be convenient in place of a *type* attribute (1 to +:math:`N_\text{types}`) for coloring atoms in a visualization program. +*Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is +typically the chemical name of an element, which you must assign to each +type via the :doc:`dump_modify element ` command. More +generally, it can be any string you wish to associated with an atom +type. *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*, +*fy*, *fz*, and *q* are components of atom velocity and force and atomic +charge. There are several options for outputting atom coordinates. The *x*, -*y*, and *z* attributes write atom coordinates "unscaled," in the +*y*, and *z* attributes write atom coordinates "unscaled", in the appropriate distance :doc:`units ` (:math:`\mathrm{\mathring A}`, -:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the coordinates -"scaled" to the box size so that each value is 0.0 to 1.0. If the simulation -box is triclinic (tilted), then all atom coords will still be between 0.0 and -1.0. The actual unscaled :math:`(x,y,z)` coordinate is -:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal -vectors of the simulation box edges, as discussed on the -:doc:`Howto triclinic ` page. +:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the +coordinates "scaled" to the box size so that each value is 0.0 to 1.0. +If the simulation box is triclinic (tilted), then all atom coords will +still be between 0.0 and 1.0. The actual unscaled :math:`(x,y,z)` +coordinate is :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are +the non-orthogonal vectors of the simulation box edges, as discussed on +the :doc:`Howto triclinic ` page. Use *xu*, *yu*, and *zu* if you want the coordinates "unwrapped" by the -image flags for each atom. Unwrapped means that if the atom has -passed through a periodic boundary one or more times, the value is -printed for what the coordinate would be if it had not been wrapped -back into the periodic box. Note that using *xu*, *yu*, and *zu* means -that the coordinate values may be far outside the box bounds printed -with the snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using -*xu*, *yu*, and *zu*, except that the unwrapped coordinates are scaled by -the box size. Atoms that have passed through a periodic boundary will -have the corresponding coordinate increased or decreased by 1.0. +image flags for each atom. Unwrapped means that if the atom has passed +through a periodic boundary one or more times, the value is printed for +what the coordinate would be if it had not been wrapped back into the +periodic box. Note that using *xu*, *yu*, and *zu* means that the +coordinate values may be far outside the box bounds printed with the +snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using *xu*, *yu*, +and *zu*, except that the unwrapped coordinates are scaled by the box +size. Atoms that have passed through a periodic boundary will have the +corresponding coordinate increased or decreased by 1.0. The image flags can be printed directly using the *ix*, *iy*, and *iz* attributes. For periodic dimensions, they specify which image of the @@ -721,8 +723,8 @@ periodic boundaries during the simulation. The *mux*, *muy*, and *muz* attributes are specific to dipolar systems defined with an atom style of *dipole*\ . They give the orientation of -the atom's point dipole moment. The *mu* attribute gives the -magnitude of the atom's dipole moment. +the atom's point dipole moment. The *mu* attribute gives the magnitude +of the atom's dipole moment. The *radius* and *diameter* attributes are specific to spherical particles that have a finite size, such as those defined with an atom @@ -736,17 +738,17 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to finite-size aspherical particles that have an angular momentum. Only the *ellipsoid* atom style defines this quantity. -The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that -can sustain a rotational torque due to interactions with other +The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles +that can sustain a rotational torque due to interactions with other particles. The *c_ID* and *c_ID[I]* attributes allow per-atom vectors or arrays calculated by a :doc:`compute ` to be output. The ID in the attribute should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -:doc:`compute ` command for details. There are computes for -calculating the per-atom energy, stress, centro-symmetry parameter, -and coordination number of individual atoms. +been defined previously in the input script. See the :doc:`compute +` command for details. There are computes for calculating the +per-atom energy, stress, centro-symmetry parameter, and coordination +number of individual atoms. Note that computes which calculate global or local quantities, as opposed to per-atom quantities, cannot be output in a dump custom @@ -754,39 +756,39 @@ command. Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and local quantities can be output by the dump local command. -If *c_ID* is used as a attribute, then the per-atom vector calculated -by the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in -the range from 1 to :math:`M`, which will print the :math:`i`\ th column of the -per-atom array with :math:`M` columns calculated by the compute. See the -discussion above for how :math:`i` can be specified with a wildcard asterisk to -effectively specify multiple values. +If *c_ID* is used as a attribute, then the per-atom vector calculated by +the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in +the range from 1 to :math:`M`, which will print the :math:`i`\ th column +of the per-atom array with :math:`M` columns calculated by the compute. +See the discussion above for how :math:`i` can be specified with a +wildcard asterisk to effectively specify multiple values. The *f_ID* and *f_ID[I]* attributes allow vector or array per-atom -quantities calculated by a :doc:`fix ` to be output. The ID in -the attribute should be replaced by the actual ID of the fix that has -been defined previously in the input script. The :doc:`fix ave/atom +quantities calculated by a :doc:`fix ` to be output. The ID in the +attribute should be replaced by the actual ID of the fix that has been +defined previously in the input script. The :doc:`fix ave/atom ` command is one that calculates per-atom quantities. Since it can time-average per-atom quantities produced by any -:doc:`compute `, :doc:`fix `, or atom-style -:doc:`variable `, this allows those time-averaged results to -be written to a dump file. +:doc:`compute `, :doc:`fix `, or atom-style :doc:`variable +`, this allows those time-averaged results to be written to a +dump file. -If *f_ID* is used as a attribute, then the per-atom vector calculated -by the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the -range from 1 to :math:`M`, which will print the :math:`i`\ th column of the -per-atom array with :math:`M` columns calculated by the fix. See the -discussion above for how :math:`i` can be specified with a wildcard asterisk -to effectively specify multiple values. +If *f_ID* is used as a attribute, then the per-atom vector calculated by +the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the +range from 1 to :math:`M`, which will print the :math:`i`\ th column of +the per-atom array with :math:`M` columns calculated by the fix. See +the discussion above for how :math:`i` can be specified with a wildcard +asterisk to effectively specify multiple values. The *v_name* attribute allows per-atom vectors calculated by a :doc:`variable ` to be output. The name in the attribute should be replaced by the actual name of the variable that has been -defined previously in the input script. Only an atom-style variable -can be referenced, since it is the only style that generates per-atom +defined previously in the input script. Only an atom-style variable can +be referenced, since it is the only style that generates per-atom values. Variables of style *atom* can reference individual atom -attributes, per-atom attributes, thermodynamic keywords, or invoke -other computes, fixes, or variables when they are evaluated, so this -is a very general means of creating quantities to output to a dump file. +attributes, per-atom attributes, thermodynamic keywords, or invoke other +computes, fixes, or variables when they are evaluated, so this is a very +general means of creating quantities to output to a dump file. The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to per-atom integer and floating-point vectors or arrays that have been @@ -794,10 +796,11 @@ added via the :doc:`fix property/atom ` command. When that command is used specific names are given to each attribute which are the "name" portion of these keywords. For arrays *i2_name* and *d2_name*, the column of the array must also be included following -the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is in the -range from 1 to :math:`M`, where :math:`M` is the number of columns in the -custom array). See the discussion above for how :math:`i` can be specified with -a wildcard asterisk to effectively specify multiple values. +the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is +in the range from 1 to :math:`M`, where :math:`M` is the number of +columns in the custom array). See the discussion above for how :math:`i` +can be specified with a wildcard asterisk to effectively specify +multiple values. See the :doc:`Modify ` page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 257f7a87a8..c395f6ef06 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -196,8 +196,8 @@ Only atoms in the specified group are rendered in the image. The alter what atoms are included in the image. The filename suffix determines whether a JPEG, PNG, or PPM file is created with the *image* dump style. If the suffix is ".jpg" or -".jpeg," then a `JPEG format `_ file is created, if the -suffix is ".png," then a `PNG format `_ is created, else +".jpeg", then a `JPEG format `_ file is created, if the +suffix is ".png", then a `PNG format `_ is created, else a `PPM (aka NETPBM) format `_ file is created. The JPEG and PNG files are binary; PPM has a text mode header followed by binary data. JPEG images have lossy compression, PNG has lossless @@ -261,7 +261,7 @@ atoms rendered in the image. They can be any atom attribute defined for the :doc:`dump custom ` command, including *type* and *element*\ . This includes per-atom quantities calculated by a :doc:`compute `, :doc:`fix `, or :doc:`variable `, -which are prefixed by "c\_," "f\_," or "v\_," respectively. Note that the +which are prefixed by "c\_", "f\_", or "v\_", respectively. Note that the *diameter* setting can be overridden with a numeric value applied to all atoms by the optional *adiam* keyword. @@ -297,18 +297,18 @@ and sizes used by the `AtomEye `_ visualization package. If other atom attributes are used for the *color* or *diameter* settings, they are interpreted in the following way. -If "vx," for example, is used as the *color* setting, then the color +If "vx", for example, is used as the *color* setting, then the color of the atom will depend on the x-component of its velocity. The association of a per-atom value with a specific color is determined by -a "color map," which can be specified via the dump_modify command, as +a "color map", which can be specified via the dump_modify command, as described below. The basic idea is that the atom-attribute will be within a range of values, and every value within the range is mapped to a specific color. Depending on how the color map is defined, that mapping can take place via interpolation so that a value of -3.2 is -halfway between "red" and "blue," or discretely so that the value of +halfway between "red" and "blue", or discretely so that the value of -3.2 is "orange". -If "vx," for example, is used as the *diameter* setting, then the atom +If "vx", for example, is used as the *diameter* setting, then the atom will be rendered using the x-component of its velocity as the diameter. If the per-atom value <= 0.0, them the atom will not be drawn. Note that finite-size spherical particles, as defined by @@ -792,14 +792,14 @@ increasing values. Note that numeric values can be specified either as absolute numbers or as fractions (0.0 to 1.0) of the range, depending on the "a" or "f" in the style setting for the color map. -Here is how the entries are used to determine the color of an -individual atom, given the value :math:`X` of its atom attribute. -:math:`X` will fall between 2 of the entry values. The color of the atom is -linearly interpolated (in each of the RGB values) between the 2 colors -associated with those entries. For example, if :math:`X = -5.0` and the two -surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`, -then the atom's color will be halfway between "red" and "blue," which happens -to be "purple." +Here is how the entries are used to determine the color of an individual +atom, given the value :math:`X` of its atom attribute. :math:`X` will +fall between 2 of the entry values. The color of the atom is linearly +interpolated (in each of the RGB values) between the 2 colors associated +with those entries. For example, if :math:`X = -5.0` and the two +surrounding entries are "red" at :math:`-10.0` and "blue" at +:math:`0.0`, then the atom's color will be halfway between "red" and +"blue", which happens to be "purple". For discrete color maps, each entry has a *lo* and *hi* value and a *color*\ . The *lo* and *hi* settings are either numbers within the @@ -807,19 +807,18 @@ range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo* and *hi* settings of the last entry must be *min* and *max*\ . Other entries can have any *lo* and *hi* values and the sub-ranges of different values can overlap. Note that numeric *lo* and *hi* values -can be specified either as absolute numbers or as fractions (0.0 to -1.0) of the range, depending on the "a" or "f" in the style setting -for the color map. +can be specified either as absolute numbers or as fractions (0.0 to 1.0) +of the range, depending on the "a" or "f" in the style setting for the +color map. -Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. The entries -are scanned from first to last. The first time that *lo* <= X <= -*hi*, X is assigned the color associated with that entry. You can -think of the last entry as assigning a default color (since it will -always be matched by X), and the earlier entries as colors that -override the default. Also note that no interpolation of a color RGB -is done. All atoms will be drawn with one of the colors in the list -of entries. +Here is how the entries are used to determine the color of an individual +atom, given the value X of its atom attribute. The entries are scanned +from first to last. The first time that *lo* <= X <= *hi*, X is +assigned the color associated with that entry. You can think of the +last entry as assigning a default color (since it will always be matched +by X), and the earlier entries as colors that override the default. +Also note that no interpolation of a color RGB is done. All atoms will +be drawn with one of the colors in the list of entries. For sequential color maps, each entry has only a *color*\ . Here is how the entries are used to determine the color of an individual atom, @@ -867,7 +866,7 @@ that bonds of each type will be drawn in the image. The specified *type* should be an integer from 1 to :math:`N`, where :math:`N` is the number of bond types. A wildcard asterisk can be used in place of or in conjunction with the *type* argument to specify a range of bond -types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` +types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of bond types, then an asterisk with no numerical values means all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index a782f32331..a0c9c5edea 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -122,7 +122,7 @@ The *pstyle* argument is the name of the pair style. If sub-styles using the same pair style, then *pstyle* should be specified as "style:N", where :math:`N` is which instance of the pair style you wish to adapt (e.g., the first or second). For example, *pstyle* could be -specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2." The +specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2". The *pparam* argument is the name of the parameter to change. This is the current list of pair styles and parameters that can be varied by this fix. See the doc pages for individual pair styles and their energy @@ -245,7 +245,7 @@ the coefficients for the symmetric :math:`J,I` interaction to the same values. A wild-card asterisk can be used in place of or in conjunction with the :math:`I,J` arguments to set the coefficients for multiple pairs of atom -types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` +types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk with no numeric values means all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` @@ -260,17 +260,17 @@ values defined (via the :doc:`pair_coeff ` command) for that sub-style. The *v_name* argument for keyword *pair* is the name of an -:doc:`equal-style variable ` which will be evaluated each -time this fix is invoked to set the parameter to a new value. It -should be specified as v_name, where name is the variable name. -Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo_style ` command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify parameters that change as a function -of time or span consecutive runs in a continuous fashion. For the -latter, see the *start* and *stop* keywords of the :doc:`run ` -command and the *elaplong* keyword of :doc:`thermo_style custom -` for details. +:doc:`equal-style variable ` which will be evaluated each time +this fix is invoked to set the parameter to a new value. It should be +specified as v_name, where name is the variable name. Equal-style +variables can specify formulas with various mathematical functions, and +include :doc:`thermo_style ` command keywords for the +simulation box parameters and timestep and elapsed time. Thus it is +easy to specify parameters that change as a function of time or span +consecutive runs in a continuous fashion. For the latter, see the +*start* and *stop* keywords of the :doc:`run ` command and the +*elaplong* keyword of :doc:`thermo_style custom ` for +details. For example, these commands would change the prefactor coefficient of the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a @@ -288,13 +288,14 @@ a bond coefficient over time, very similar to how the *pair* keyword operates. The only difference is that now a bond coefficient for a given bond type is adapted. -A wild-card asterisk can be used in place of or in conjunction with -the bond type argument to set the coefficients for multiple bond -types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` -is the number of bond types, then an asterisk with no numeric values -means all types from 1 to :math:`N`. A leading asterisk means all types from -1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` -(inclusive). A middle asterisk means all types from m to n (inclusive). +A wild-card asterisk can be used in place of or in conjunction with the +bond type argument to set the coefficients for multiple bond types. +This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is +the number of bond types, then an asterisk with no numeric values means +all types from 1 to :math:`N`. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from m to +:math:`N` (inclusive). A middle asterisk means all types from m to n +(inclusive). Currently *bond* does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The bond styles that currently work @@ -323,13 +324,14 @@ an angle coefficient over time, very similar to how the *pair* keyword operates. The only difference is that now an angle coefficient for a given angle type is adapted. -A wild-card asterisk can be used in place of or in conjunction with -the angle type argument to set the coefficients for multiple angle -types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` -is the number of angle types, then an asterisk with no numeric values -means all types from 1 to :math:`N`. A leading asterisk means all types from -1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` -(inclusive). A middle asterisk means all types from m to n (inclusive). +A wild-card asterisk can be used in place of or in conjunction with the +angle type argument to set the coefficients for multiple angle types. +This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is +the number of angle types, then an asterisk with no numeric values means +all types from 1 to :math:`N`. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from m to +:math:`N` (inclusive). A middle asterisk means all types from m to n +(inclusive). Currently *angle* does not support angle_style hybrid nor angle_style hybrid/overlay as angle styles. The angle styles that currently work diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 2f8a1a9475..c35986de49 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -115,7 +115,7 @@ overrides the parameters. The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be a sub-style name. For example, *pstyle* could be specified as "soft" -or "lubricate." The *pparam* argument is the name of the parameter to +or "lubricate". The *pparam* argument is the name of the parameter to change. This is the current list of pair styles and parameters that can be varied by this fix. See the doc pages for individual pair styles and their energy formulas for the meaning of these parameters: @@ -209,7 +209,7 @@ the coefficients for the symmetric J,I interaction to the same values. A wild-card asterisk can be used in place of or in conjunction with the :math:`I,J` arguments to set the coefficients for multiple pairs of atom -types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` is +types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk with no numeric values means all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from m to :math:`N` diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 8734593b58..4e696f709b 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -153,7 +153,7 @@ which can be accessed by various :doc:`output commands `. The scalar is the potential energy discussed above. The vector is the total force on the group of atoms before the forces on individual atoms are changed by the fix. The scalar and vector -values calculated by this fix are "extensive." +values calculated by this fix are "extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index e90e70a8d3..be2823afcf 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -75,7 +75,7 @@ accessed by various :doc:`output commands `. The scalar is the potential energy discussed above. The vector is the total torque on the group of atoms before the forces on individual atoms are changed by the fix. The scalar and vector values calculated by this -fix are "extensive." +fix are "extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. diff --git a/doc/src/fix_amoeba_bitorsion.rst b/doc/src/fix_amoeba_bitorsion.rst index ebfcf7ad40..a9abaf19ce 100644 --- a/doc/src/fix_amoeba_bitorsion.rst +++ b/doc/src/fix_amoeba_bitorsion.rst @@ -124,7 +124,7 @@ setting for this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the potential energy discussed above. The scalar value calculated by this fix is -"extensive." +"extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. diff --git a/doc/src/fix_amoeba_pitorsion.rst b/doc/src/fix_amoeba_pitorsion.rst index e20324fa0d..484c1015c8 100644 --- a/doc/src/fix_amoeba_pitorsion.rst +++ b/doc/src/fix_amoeba_pitorsion.rst @@ -138,7 +138,7 @@ setting for this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the potential energy discussed above. The scalar value calculated by this fix is -"extensive." +"extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 0aa91dbc6f..c6bde5dcc4 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -135,7 +135,7 @@ fix are listed below. This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the energy -discussed in the previous paragraph. The scalar value is "extensive." +discussed in the previous paragraph. The scalar value is "extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index d6779925a5..0deda8a5f5 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -167,7 +167,7 @@ the following global cumulative quantities: * 1 = swap attempts * 2 = swap accepts -The vector values calculated by this fix are "extensive." +The vector values calculated by this fix are "extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 711aa653e4..e2ca9bf16e 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -70,7 +70,7 @@ per-atom vectors. Note that for values from a compute or fix, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "m\*" or -"m\*n." If :math:`N` is the size of the vector (for *mode* = scalar) or the +"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the number of columns in the array (for *mode* = vector), then an asterisk with no numeric values means all indices from 1 to :math:`N`. A leading asterisk means all indices from 1 to n (inclusive). A trailing @@ -127,7 +127,7 @@ specifying an input value from that compute. :doc:`compute property/atom ` command via its *xu*, *yu*, and *zu* attributes. -If a value begins with "c\_," a compute ID must follow which has been +If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index :math:`I` is appended, the @@ -137,7 +137,7 @@ used. Users can also write code for their own compute styles and :math:`I` can be specified with a wildcard asterisk to effectively specify multiple values. -If a value begins with "f\_," a fix ID must follow which has been previously +If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the per-atom vector calculated by the fix is used. If a bracketed term containing an index :math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array @@ -148,7 +148,7 @@ and :doc:`add them to LAMMPS `. See the discussion above for how :math:`I` can be specified with a wildcard asterisk to effectively specify multiple values. -If a value begins with "v\_," a variable name must follow which has +If a value begins with "v\_", a variable name must follow which has been previously defined in the input script as an :doc:`atom-style variable `. Variables of style *atom* can reference thermodynamic keywords or invoke other computes, fixes, or variables diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index a014e587eb..354c8d8e8b 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -288,7 +288,7 @@ together as one set of atoms to calculate their temperature. The compute allows the center-of-mass velocity of each chunk to be subtracted before calculating the temperature; this fix does not. -If a value begins with "c\_," a compute ID must follow which has been +If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array @@ -297,7 +297,7 @@ their own compute styles and :doc:`add them to LAMMPS `. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. -If a value begins with "f\_," a fix ID must follow which has been +If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array @@ -308,7 +308,7 @@ their own fix styles and :doc:`add them to LAMMPS `. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. -If a value begins with "v\_," a variable name must follow which has +If a value begins with "v\_", a variable name must follow which has been previously defined in the input script. Variables of style *atom* can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they @@ -348,7 +348,7 @@ at each sampling step. If the *norm* setting is *none*, a similar computation as for the *sample* setting is done, except the individual "average sample -values" are "summed sample values." A summed sample value is simply +values" are "summed sample values". A summed sample value is simply the chunk value summed over atoms in the sample, without dividing by the number of atoms in the sample. The output value for the chunk on the :math:`N_\text{freq}` timesteps is the average of the @@ -494,21 +494,21 @@ relevant to this fix. This fix computes a global array of values which can be accessed by various :doc:`output commands `. The values can only be -accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that -is when averaging is performed. The global array has # of rows = the number -of chunks :math:`N_\text{chunk}`, as calculated by the specified -:doc:`compute chunk/atom ` command. The # of columns is -:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`, -depending on whether the optional -columns for OrigID and CoordN are used, as explained above. Following -the optional columns, the next column contains the count of atoms in -the chunk, and the remaining columns are the Nvalue quantities. When -the array is accessed with a row :math:`I` that exceeds the current number of -chunks, than a 0.0 is returned by the fix instead of an error, since -the number of chunks can vary as a simulation runs depending on how -that value is computed by the compute chunk/atom command. +accessed on timesteps that are multiples of :math:`N_\text{freq}`, since +that is when averaging is performed. The global array has # of rows = +the number of chunks :math:`N_\text{chunk}`, as calculated by the +specified :doc:`compute chunk/atom ` command. The # +of columns is :math:`M+1+N_\text{values}`, where :math:`M \in +\{1,\dotsc,4\}`, depending on whether the optional columns for OrigID +and CoordN are used, as explained above. Following the optional +columns, the next column contains the count of atoms in the chunk, and +the remaining columns are the Nvalue quantities. When the array is +accessed with a row :math:`I` that exceeds the current number of chunks, +than a 0.0 is returned by the fix instead of an error, since the number +of chunks can vary as a simulation runs depending on how that value is +computed by the compute chunk/atom command. -The array values calculated by this fix are treated as "intensive," +The array values calculated by this fix are treated as "intensive", since they are typically already normalized by the count of atoms in each chunk. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 82046990e0..1aff749048 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -189,7 +189,7 @@ Also, if the *ave* keyword is set to *one* which is the default, then ---------- -If a value begins with "c\_," a compute ID must follow which has been +If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the :math:`I^\text{th}` element of the global @@ -206,7 +206,7 @@ or :doc:`fix temp/rescale `. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. -If a value begins with "f\_," a fix ID must follow which has been +If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the :math:`I^\text{th}` element of the global @@ -219,7 +219,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. -If a value begins with "v\_," a variable name must follow which has been +If a value begins with "v\_", a variable name must follow which has been previously defined in the input script. Only equal-style or vector-style variables can be referenced; the latter requires a bracketed term to specify the :math:`I^\text{th}` element of the vector calculated by the variable. diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 56671c30f5..e915526aa7 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -193,7 +193,7 @@ inputs to this fix by using the :doc:`compute property/atom ` command and then specifying an input value from that compute. -If a value begins with "c\_," a compute ID must follow which has been +If a value begins with "c\_", a compute ID must follow which has been previously defined in the input script. If *mode* = scalar, then if no bracketed term is appended, the global scalar calculated by the compute is used. If a bracketed term is appended, the Ith element of @@ -215,7 +215,7 @@ these commands which give the IDs of these computes. Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. -If a value begins with "f\_," a fix ID must follow which has been +If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. If *mode* = scalar, then if no bracketed term is appended, the global scalar calculated by the fix is used. If a bracketed term is appended, the Ith element of the @@ -232,7 +232,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will result. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. -If a value begins with "v\_," a variable name must follow which has +If a value begins with "v\_", a variable name must follow which has been previously defined in the input script. If *mode* = scalar, then only equal-style or vector-style variables can be used, which both produce global values. In this mode, a vector-style variable requires diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 782f0850cc..0308ecc92a 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -358,11 +358,11 @@ of rows = length of the input vectors and # of columns = number of inputs. If the fix produces a scalar or vector, then the scalar and each -element of the vector can be either "intensive" or "extensive," +element of the vector can be either "intensive" or "extensive", depending on whether the values contributing to the scalar or vector -element are "intensive" or "extensive." If the fix produces an array, +element are "intensive" or "extensive". If the fix produces an array, then all elements in the array must be the same, either "intensive" or -"extensive." If a compute or fix provides the value being time +"extensive". If a compute or fix provides the value being time averaged, then the compute or fix determines whether the value is intensive or extensive; see the page for that compute or fix for further info. Values produced by a variable are treated as intensive. diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 7afb077881..bf4f77ecd9 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -361,7 +361,7 @@ The "SQUARES" section lists the node IDs of the four vertices in a rectangle for each processor (1 to 4). For a 3d problem, the syntax is similar but with eight vertices listed for -each processor instead of four, and "SQUARES" replaced by "CUBES." +each processor instead of four, and "SQUARES" replaced by "CUBES". ---------- @@ -387,7 +387,7 @@ number of particles (or total weight) per processor. These quantities can be accessed by various :doc:`output commands `. The scalar and vector values calculated -by this fix are "intensive." +by this fix are "intensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during diff --git a/doc/src/group.rst b/doc/src/group.rst index 5cdbfb5c13..4f2a18c8a6 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -318,7 +318,7 @@ Restrictions """""""""""" There can be no more than 32 groups defined at one time, including -"all." +"all". The parent group of a dynamic group cannot itself be a dynamic group. diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index a002b539bd..d886fa7dab 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -981,7 +981,7 @@ In the last example, "new-property.edn" and "/home/mary/marys-kim-properties/dissociation-energy.edn" are the names of files that contain user-defined (local) property definitions. -A KIM property instance takes the form of a "map," i.e. a set of key-value +A KIM property instance takes the form of a "map", i.e. a set of key-value pairs akin to Perl's hash, Python's dictionary, or Java's Hashtable. It consists of a set of property key names, each of which is referred to here by the *key_name* argument, that are defined as part of the relevant KIM Property diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index bbf9f6bc29..6c698b23d2 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -140,4 +140,4 @@ none .. _Ziegler: **(Ziegler)** J.F. Ziegler, J. P. Biersack and U. Littmark, "The -Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. +Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985. From 446cc46bbd86f569c75cf0ed62177ef96c761deb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Sep 2022 19:10:18 -0400 Subject: [PATCH 08/14] spelling --- doc/src/labelmap.rst | 10 +++++----- doc/src/read_data.rst | 2 +- doc/src/restart.rst | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/src/labelmap.rst b/doc/src/labelmap.rst index a709bb1104..98bc4cfbd3 100644 --- a/doc/src/labelmap.rst +++ b/doc/src/labelmap.rst @@ -69,13 +69,13 @@ there is a label defined for *every* numeric type within a given type-kind in order to write out the type label section for that type-kind. -The *clear* option resets the labelmap and thus discards all previous +The *clear* option resets the label map and thus discards all previous settings. The *write* option takes a filename as argument and writes the current -label mappings to a file as labelmap commands, so the file can be copied -into a new LAMMPS input file or read in using the :doc:`include -` command. +label mappings to a file as a sequence of *labelmap* commands, so the +file can be copied into a new LAMMPS input file or read in using the +:doc:`include ` command. ---------- @@ -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 From 7dd95db47454c9ecb1f89eeaa35e62dd5d33efe5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 06:22:41 -0400 Subject: [PATCH 09/14] 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 10/14] 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 11/14] 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 56304fe939c3639988d462da609e8db317c0454e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 11:24:20 -0400 Subject: [PATCH 12/14] move check for Fortran Compiler validity --- unittest/fortran/CMakeLists.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/unittest/fortran/CMakeLists.txt b/unittest/fortran/CMakeLists.txt index c7174d8e6e..7aa2177918 100644 --- a/unittest/fortran/CMakeLists.txt +++ b/unittest/fortran/CMakeLists.txt @@ -6,14 +6,14 @@ endif() include(CheckLanguage) check_language(Fortran) -if(NOT CMAKE_Fortran_COMPILER_ID) - message(STATUS "Skipping Tests for the LAMMPS Fortran Module: cannot identify Fortran compiler") - return() -endif() if(CMAKE_Fortran_COMPILER) enable_language(C) enable_language(Fortran) + if(NOT CMAKE_Fortran_COMPILER_ID) + message(STATUS "Skipping Tests for the LAMMPS Fortran Module: cannot identify Fortran compiler") + return() + endif() get_filename_component(LAMMPS_FORTRAN_MODULE ${LAMMPS_SOURCE_DIR}/../fortran/lammps.f90 ABSOLUTE) if(BUILD_MPI) find_package(MPI REQUIRED) From f3fa24617946e1615f9fb89bc342a0cce346122c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Sep 2022 11:39:16 -0400 Subject: [PATCH 13/14] 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 - LIBCALLS 2 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15072431717670 13.849902902335046 0.0000000000000000 3.9653556077235628 - LIBCALLS 3 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14958682134301 13.848772166382796 0.0000000000000000 3.9653762812719782 - LIBCALLS 4 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14804481054080 13.847240065975685 0.0000000000000000 3.9654039257311324 - LIBCALLS 5 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14614669298459 13.845355347298943 0.0000000000000000 3.9654372593625880 - LIBCALLS 6 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14395200541782 13.843177681164811 0.0000000000000000 3.9654747563744728 - LIBCALLS 7 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14152950027858 13.840775605612510 0.0000000000000000 3.9655146828204026 - LIBCALLS 8 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13895477239572 13.838224210058369 0.0000000000000000 3.9655551214573213 - LIBCALLS 9 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13630808318862 13.835602658269416 0.0000000000000000 3.9655940696401335 - LIBCALLS 10 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13367156672246 13.832991646694552 0.0000000000000000 3.9656294961085377 - LIBCALLS 11 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13112695791978 13.830470890853416 0.0000000000000000 3.9656594331001127 - LIBCALLS 12 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12875304084571 13.828116721514562 0.0000000000000000 3.9656820468287637 - LIBCALLS 13 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12662314462005 13.825999860613845 0.0000000000000000 3.9656956633599689 - LIBCALLS 14 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12480303363179 13.824183432931337 0.0000000000000000 3.9656988576578489 - LIBCALLS 15 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12334906554690 13.822721254684298 0.0000000000000000 3.9656905013961525 - LIBCALLS 16 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12230649281338 13.821656427050725 0.0000000000000000 3.9656697961568699 - LIBCALLS 17 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12170820445976 13.821020251989051 0.0000000000000000 3.9656362957330207 - LIBCALLS 18 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12157378544725 13.820831478957400 0.0000000000000000 3.9655899465557289 - LIBCALLS 19 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12190902409918 13.821095885466233 0.0000000000000000 3.9655310732858191 - LIBCALLS 20 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12270578464654 13.821806190548854 0.0000000000000000 3.9654603894825375 - LIBCALLS 21 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12394226924755 13.822942298269552 0.0000000000000000 3.9653789701528157 - LIBCALLS 22 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12558369933174 13.824471866833779 0.0000000000000000 3.9652882392864672 - LIBCALLS 23 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12758334335854 13.826351196916939 0.0000000000000000 3.9651899208403507 - LIBCALLS 24 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12988392857540 13.828526429544008 0.0000000000000000 3.9650859962581815 - LIBCALLS 25 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13241933900565 13.830935038404082 0.0000000000000000 3.9649786471076300 - LIBCALLS 26 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13511663668885 13.833507593821677 0.0000000000000000 3.9648702062183578 - LIBCALLS 27 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13789821166085 13.836169765592846 0.0000000000000000 3.9647630647732250 - LIBCALLS 28 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14068416314257 13.838844520440762 0.0000000000000000 3.9646596094056243 - LIBCALLS 29 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14339478125902 13.841454456993119 0.0000000000000000 3.9645621614306648 - LIBCALLS 30 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14595299166797 13.843924209084781 0.0000000000000000 3.9644728862209537 - LIBCALLS 31 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14828672908391 13.846182838096166 0.0000000000000000 3.9643937231592781 - LIBCALLS 32 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15033121417270 13.848166127650318 0.0000000000000000 3.9643263326484774 - LIBCALLS 33 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15203097820654 13.849818691045462 0.0000000000000000 3.9642720350529470 - LIBCALLS 34 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15334158494318 13.851095804201121 0.0000000000000000 3.9642317563508436 - LIBCALLS 35 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15423101277941 13.851964884709183 0.0000000000000000 3.9642060118064197 - LIBCALLS 36 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15468060067406 13.852406550643760 0.0000000000000000 3.9641948735126151 - LIBCALLS 37 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15468556770435 13.852415210893483 0.0000000000000000 3.9641979705462513 - LIBCALLS 38 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15425506702360 13.851999160128511 0.0000000000000000 3.9642145018322728 - LIBCALLS 39 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15341177086162 13.851180175004831 0.0000000000000000 3.9642432622019754 - LIBCALLS 40 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15219100341108 13.849992631968849 0.0000000000000000 3.9642826797086155 - LIBCALLS 41 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15063948253476 13.848482189284203 0.0000000000000000 3.9643308764467280 - LIBCALLS 42 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14881366363778 13.846704095034502 0.0000000000000000 3.9643857194231229 - LIBCALLS 43 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14677783841711 13.844721197666447 0.0000000000000000 3.9644449063996254 - LIBCALLS 44 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14460195130079 13.842601745208173 0.0000000000000000 3.9645060327113080 - LIBCALLS 45 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14235930197236 13.840417063344470 0.0000000000000000 3.9645666751650537 - LIBCALLS 46 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14012416839108 13.838239201362184 0.0000000000000000 3.9646244709241216 - LIBCALLS 47 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13796944534135 13.836138629087953 0.0000000000000000 3.9646771958199687 - LIBCALLS 48 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13596436459642 13.834182058508610 0.0000000000000000 3.9647228360374207 - LIBCALLS 49 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13417236277201 13.832430452024822 0.0000000000000000 3.9647596471475066 - LIBCALLS 50 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13264918465853 13.830937266579358 0.0000000000000000 3.9647862263274365 - LIBCALLS 51 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13144121811348 13.829746970164395 0.0000000000000000 3.9648015300858930 - LIBCALLS 52 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13058418584075 13.828893856279002 0.0000000000000000 3.9648049379175174 - LIBCALLS 53 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13010212355317 13.828401171909800 0.0000000000000000 3.9647962482159476 - LIBCALLS 54 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13000675986638 13.828280567696357 0.0000000000000000 3.9647757005033171 - LIBCALLS 55 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13029725443062 13.828531873218640 0.0000000000000000 3.9647439679967813 - LIBCALLS 56 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13096031859556 13.829143196581525 0.0000000000000000 3.9647021412055241 - LIBCALLS 57 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13197071275096 13.830091344339912 0.0000000000000000 3.9646517009757813 - LIBCALLS 58 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13329208290526 13.831342554670950 0.0000000000000000 3.9645944691057076 - LIBCALLS 59 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13487817952188 13.832853532802908 0.0000000000000000 3.9645325717081379 - LIBCALLS 60 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13667431785007 13.834572772174083 0.0000000000000000 3.9644683636269380 - LIBCALLS 61 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13861917436014 13.836442137716100 0.0000000000000000 3.9644043716683206 - LIBCALLS 62 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14064674344610 13.838398678492441 0.0000000000000000 3.9643432117931376 - LIBCALLS 63 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14268847880851 13.840376626541268 0.0000000000000000 3.9642875107994442 - LIBCALLS 64 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14467552446979 13.842309527587247 0.0000000000000000 3.9642398279114381 - LIBCALLS 65 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14654097615647 13.844132438475109 0.0000000000000000 3.9642025589783412 - LIBCALLS 66 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14822207995957 13.845784117078871 0.0000000000000000 3.9641778771678413 - LIBCALLS 67 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14966231911774 13.847209123749478 0.0000000000000000 3.9641676470155103 - LIBCALLS 68 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15081329445576 13.848359751049152 0.0000000000000000 3.9641733618391299 - LIBCALLS 69 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15163634076458 13.849197700537186 0.0000000000000000 3.9641960937768981 - LIBCALLS 70 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15210380659516 13.849695432596437 0.0000000000000000 3.9642364336978391 - LIBCALLS 71 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15219997215792 13.849837127658775 0.0000000000000000 3.9642944914660605 - LIBCALLS 72 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15192153900722 13.849619213627008 0.0000000000000000 3.9643698667021590 - LIBCALLS 73 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15127769530471 13.849050434626310 0.0000000000000000 3.9644616585289247 - LIBCALLS 74 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15028974592457 13.848151458176057 0.0000000000000000 3.9645684873567908 - LIBCALLS 75 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14899032381624 13.846954040343237 0.0000000000000000 3.9646885325372980 - LIBCALLS 76 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14742221364327 13.845499789571511 0.0000000000000000 3.9648195821504211 - LIBCALLS 77 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14563684020112 13.843838588134755 0.0000000000000000 3.9649591055666282 - LIBCALLS 78 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14369246883172 13.842026744273829 0.0000000000000000 3.9651043223068876 - LIBCALLS 79 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14165219754119 13.840124957235691 0.0000000000000000 3.9652522794782556 - LIBCALLS 80 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13958181195608 13.838196181062383 0.0000000000000000 3.9653999492835532 - LIBCALLS 81 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13754757713065 13.836303471774007 0.0000000000000000 3.9655443071963385 - LIBCALLS 82 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13561405478509 13.834507896249461 0.0000000000000000 3.9656824354232736 - LIBCALLS 83 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13384198639028 13.832866571528193 0.0000000000000000 3.9658115908515681 - LIBCALLS 84 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13228634940748 13.831430891696755 0.0000000000000000 3.9659292903699495 - LIBCALLS 85 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13099461122306 13.830244986101496 0.0000000000000000 3.9660333724384569 - LIBCALLS 86 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13000526350720 13.829344440260281 0.0000000000000000 3.9661220782532145 - LIBCALLS 87 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12934661713206 13.828755299191645 0.0000000000000000 3.9661940662588862 - LIBCALLS 88 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12903595764971 13.828493364127572 0.0000000000000000 3.9662484623936765 - LIBCALLS 89 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12907904533250 13.828563786156602 0.0000000000000000 3.9662848954537067 - 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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 14/14] 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