add explanations for "before/after simulation box is defined" errors
This commit is contained in:
@ -912,3 +912,29 @@ typically happens when there are multiple fix commands that advance atom
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positions with overlapping groups. Also, for some fix styles it is not
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positions with overlapping groups. Also, for some fix styles it is not
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immediately obvious that they include time integration. Please check
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immediately obvious that they include time integration. Please check
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the documentation carefully.
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the documentation carefully.
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.. _err0033:
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XXX command before simulation box is defined
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--------------------------------------------
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This error happens, when trying to excute a LAMMPS command that requires
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information about the system dimensions, or the number atom, bond,
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angle, dihedral, or improper types, or the number of atoms or similar
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data that is only available *after* the simulation box has been created.
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See the paragraph on :ref:`errors before or after the simulation box is
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created <hint12>` for additional information.
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.. _err0034:
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XXX command after simulation box is defined
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--------------------------------------------
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This error happens, when trying to excute a LAMMPS command that that
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changes a global setting that will be locked in when the simulation box
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is created (for instance defining the :doc:`atom style <atom_style>`,
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:doc:`dimension <dimension>`, :doc:`newton <newton>`, or :doc:`units
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<units>` setting). These settings may only be changed *before* the
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simulation box has been created. See the paragraph on :ref:`errors
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before or after the simulation box is created <hint12>` for additional
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information.
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@ -306,10 +306,10 @@ void PPPMDielectric::qsum_qsq(int warning_flag)
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// so issue warning or error
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// so issue warning or error
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if (fabs(qsum) > SMALL) {
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if (fabs(qsum) > SMALL) {
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std::string message = fmt::format("System is not charge neutral, net "
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std::string message = fmt::format("System is not charge neutral, net charge = {:.8}{}",
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"charge = {:.8}",qsum);
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qsum, utils::errorurl(29));
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if (!warn_nonneutral) error->all(FLERR,message + utils::errorurl(29));
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if (!warn_nonneutral) error->all(FLERR,message);
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if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message + utils::errorurl(29));
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if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message);
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warn_nonneutral = 2;
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warn_nonneutral = 2;
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}
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}
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}
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}
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@ -580,10 +580,10 @@ void PPPMDispDielectric::qsum_qsq(int warning_flag)
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// so issue warning or error
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// so issue warning or error
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if (fabs(qsum) > SMALL) {
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if (fabs(qsum) > SMALL) {
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std::string message = fmt::format("System is not charge neutral, net "
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std::string message = fmt::format("System is not charge neutral, net charge = {:.8}{}",
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"charge = {:.8}",qsum);
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qsum, utils::errorurl(29));
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if (!warn_nonneutral) error->all(FLERR,message + utils::errorurl(29));
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if (!warn_nonneutral) error->all(FLERR,message);
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if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message + utils::errorurl(29));
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if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message);
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warn_nonneutral = 2;
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warn_nonneutral = 2;
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}
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}
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}
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}
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@ -86,7 +86,7 @@ void KimInit::command(int narg, char **arg)
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if ((narg < 2) || (narg > 3)) error->all(FLERR, "Illegal 'kim init' command");
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if ((narg < 2) || (narg > 3)) error->all(FLERR, "Illegal 'kim init' command");
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if (domain->box_exist)
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if (domain->box_exist)
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error->all(FLERR, "Must use 'kim init' command before simulation box is defined");
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error->all(FLERR, "Must use 'kim init' command before simulation box is defined" + utils::errorurl(33));
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char *model_name = utils::strdup(arg[0]);
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char *model_name = utils::strdup(arg[0]);
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char *user_units = utils::strdup(arg[1]);
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char *user_units = utils::strdup(arg[1]);
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@ -112,7 +112,7 @@ void DynamicalMatrix::command(int narg, char **arg)
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MPI_Comm_rank(world,&me);
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MPI_Comm_rank(world,&me);
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"Dynamical_matrix command before simulation box is defined");
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error->all(FLERR,"Dynamical_matrix command before simulation box is defined" + utils::errorurl(33));
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if (narg < 2) error->all(FLERR,"Illegal dynamical_matrix command");
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if (narg < 2) error->all(FLERR,"Illegal dynamical_matrix command");
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lmp->init();
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lmp->init();
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@ -118,7 +118,7 @@ void ThirdOrder::command(int narg, char **arg)
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MPI_Comm_rank(world,&me);
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MPI_Comm_rank(world,&me);
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"third_order command before simulation box is defined");
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error->all(FLERR,"third_order command before simulation box is defined" + utils::errorurl(33));
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if (narg < 2) error->all(FLERR,"Illegal third_order command");
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if (narg < 2) error->all(FLERR,"Illegal third_order command");
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// request a full neighbor list for use by this command
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// request a full neighbor list for use by this command
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@ -336,7 +336,8 @@ void FixQEq::init()
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MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world);
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if ((comm->me == 0) && (fabs(qsum) > QSUMSMALL))
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if ((comm->me == 0) && (fabs(qsum) > QSUMSMALL))
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error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}", style, qsum);
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error->warning(FLERR,"Fix {} group is not charge neutral, net charge = {:.8}{}",
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style, qsum, utils::errorurl(29));
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}
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}
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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@ -52,7 +52,7 @@ void Hyper::command(int narg, char **arg)
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// error checks
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// error checks
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"Hyper command before simulation box is defined");
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error->all(FLERR,"Hyper command before simulation box is defined" + utils::errorurl(33));
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if (narg < 4) error->all(FLERR,"Illegal hyper command");
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if (narg < 4) error->all(FLERR,"Illegal hyper command");
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@ -113,7 +113,7 @@ NEB::~NEB()
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void NEB::command(int narg, char **arg)
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void NEB::command(int narg, char **arg)
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{
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{
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->universe_all(FLERR, "NEB command before simulation box is defined");
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error->universe_all(FLERR, "NEB command before simulation box is defined" + utils::errorurl(33));
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if (narg < 6) error->universe_all(FLERR, "Illegal NEB command: missing argument(s)");
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if (narg < 6) error->universe_all(FLERR, "Illegal NEB command: missing argument(s)");
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@ -60,7 +60,7 @@ void PRD::command(int narg, char **arg)
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// error checks
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// error checks
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"PRD command before simulation box is defined");
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error->all(FLERR,"PRD command before simulation box is defined" + utils::errorurl(33));
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if (universe->nworlds != universe->nprocs &&
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if (universe->nworlds != universe->nprocs &&
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atom->map_style == Atom::MAP_NONE)
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atom->map_style == Atom::MAP_NONE)
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error->all(FLERR,"Cannot use PRD with multi-processor replicas "
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error->all(FLERR,"Cannot use PRD with multi-processor replicas "
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@ -74,7 +74,7 @@ void TAD::command(int narg, char **arg)
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// error checks
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// error checks
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"Tad command before simulation box is defined");
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error->all(FLERR,"Tad command before simulation box is defined" + utils::errorurl(33));
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if (universe->nworlds == 1)
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if (universe->nworlds == 1)
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error->all(FLERR,"Cannot use TAD with a single replica for NEB");
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error->all(FLERR,"Cannot use TAD with a single replica for NEB");
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if (universe->nworlds != universe->nprocs)
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if (universe->nworlds != universe->nprocs)
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@ -64,7 +64,7 @@ void Temper::command(int narg, char **arg)
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if (universe->nworlds == 1)
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if (universe->nworlds == 1)
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error->universe_all(FLERR,"More than one processor partition required for temper command");
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error->universe_all(FLERR,"More than one processor partition required for temper command");
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->universe_all(FLERR,"Temper command before simulation box is defined");
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error->universe_all(FLERR,"Temper command before simulation box is defined" + utils::errorurl(33));
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if (narg != 6 && narg != 7) error->universe_all(FLERR,"Illegal temper command");
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if (narg != 6 && narg != 7) error->universe_all(FLERR,"Illegal temper command");
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int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
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int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
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@ -66,7 +66,7 @@ void TemperGrem::command(int narg, char **arg)
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if (universe->nworlds == 1)
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if (universe->nworlds == 1)
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error->universe_all(FLERR,"More than one processor partition required for temper/grem command");
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error->universe_all(FLERR,"More than one processor partition required for temper/grem command");
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->universe_all(FLERR,"Temper/grem command before simulation box is defined");
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error->universe_all(FLERR,"Temper/grem command before simulation box is defined" + utils::errorurl(33));
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if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/grem command");
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if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/grem command");
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int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
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int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
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@ -66,7 +66,7 @@ void TemperNPT::command(int narg, char **arg)
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if (universe->nworlds == 1)
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if (universe->nworlds == 1)
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error->universe_all(FLERR,"More than one processor partition required for temper/npt command");
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error->universe_all(FLERR,"More than one processor partition required for temper/npt command");
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->universe_all(FLERR,"Temper/npt command before simulation box is defined");
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error->universe_all(FLERR,"Temper/npt command before simulation box is defined" + utils::errorurl(33));
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if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/npt command");
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if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/npt command");
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int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
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int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
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@ -95,7 +95,7 @@ NEBSpin::~NEBSpin()
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void NEBSpin::command(int narg, char **arg)
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void NEBSpin::command(int narg, char **arg)
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{
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{
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"NEBSpin command before simulation box is defined");
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error->all(FLERR,"NEBSpin command before simulation box is defined" + utils::errorurl(33));
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if (narg < 6) error->universe_all(FLERR,"Illegal NEBSpin command");
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if (narg < 6) error->universe_all(FLERR,"Illegal NEBSpin command");
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@ -43,11 +43,11 @@ void AngleWrite::command(int narg, char **arg)
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// sanity checks
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// sanity checks
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR, "Angle_write command before simulation box is defined");
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error->all(FLERR, "Angle_write command before simulation box is defined" + utils::errorurl(33));
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if (atom->avec->angles_allow == 0)
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if (atom->avec->angles_allow == 0)
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error->all(FLERR, "Angle_write command when no angles allowed");
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error->all(FLERR, "Angle_write command when no angles allowed");
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auto angle = force->angle;
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auto angle = force->angle;
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if (angle == nullptr) error->all(FLERR, "Angle_write command before an angle_style is defined");
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if (angle == nullptr) error->all(FLERR, "Angle_write command before an angle_style is defined" + utils::errorurl(33));
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if (angle && (force->angle->writedata == 0))
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if (angle && (force->angle->writedata == 0))
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error->all(FLERR, "Angle style must support writing coeffs to data file for angle_write");
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error->all(FLERR, "Angle style must support writing coeffs to data file for angle_write");
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@ -836,13 +836,15 @@ void Atom::modify_params(int narg, char **arg)
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if (strcmp(arg[iarg],"id") == 0) {
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if (strcmp(arg[iarg],"id") == 0) {
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if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "atom_modify id", error);
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if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "atom_modify id", error);
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if (domain->box_exist)
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if (domain->box_exist)
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error->all(FLERR, idx, "Atom_modify id command after simulation box is defined");
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error->all(FLERR, idx, "Atom_modify id command after simulation box is defined"
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+ utils::errorurl(34));
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tag_enable = utils::logical(FLERR,arg[iarg+1],false,lmp);
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tag_enable = utils::logical(FLERR,arg[iarg+1],false,lmp);
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iarg += 2;
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iarg += 2;
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} else if (strcmp(arg[iarg],"map") == 0) {
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} else if (strcmp(arg[iarg],"map") == 0) {
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if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "atom_modify map", error);
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if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "atom_modify map", error);
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if (domain->box_exist)
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if (domain->box_exist)
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error->all(FLERR, idx, "Atom_modify map command after simulation box is defined");
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error->all(FLERR, idx, "Atom_modify map command after simulation box is defined"
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+ utils::errorurl(34));
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if (strcmp(arg[iarg+1],"array") == 0) map_user = MAP_ARRAY;
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if (strcmp(arg[iarg+1],"array") == 0) map_user = MAP_ARRAY;
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else if (strcmp(arg[iarg+1],"hash") == 0) map_user = MAP_HASH;
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else if (strcmp(arg[iarg+1],"hash") == 0) map_user = MAP_HASH;
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else if (strcmp(arg[iarg+1],"yes") == 0) map_user = MAP_YES;
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else if (strcmp(arg[iarg+1],"yes") == 0) map_user = MAP_YES;
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@ -113,7 +113,7 @@ Balance::~Balance()
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void Balance::command(int narg, char **arg)
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void Balance::command(int narg, char **arg)
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{
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{
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR, -1, "Balance command before simulation box is defined");
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error->all(FLERR, -1, "Balance command before simulation box is defined" + utils::errorurl(33));
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if (comm->me == 0) utils::logmesg(lmp,"Balancing ...\n");
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if (comm->me == 0) utils::logmesg(lmp,"Balancing ...\n");
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@ -45,7 +45,7 @@ void ChangeBox::command(int narg, char **arg)
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int i;
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int i;
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR,"Change_box command before simulation box is defined");
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error->all(FLERR,"Change_box command before simulation box is defined" + utils::errorurl(33));
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if (narg < 2) utils::missing_cmd_args(FLERR, "change_box", error);
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if (narg < 2) utils::missing_cmd_args(FLERR, "change_box", error);
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if (comm->me == 0) utils::logmesg(lmp,"Changing box ...\n");
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if (comm->me == 0) utils::logmesg(lmp,"Changing box ...\n");
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@ -73,7 +73,7 @@ CreateAtoms::CreateAtoms(LAMMPS *lmp) : Command(lmp), basistype(nullptr) {}
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void CreateAtoms::command(int narg, char **arg)
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void CreateAtoms::command(int narg, char **arg)
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{
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{
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR, "Create_atoms command before simulation box is defined");
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error->all(FLERR, "Create_atoms command before simulation box is defined" + utils::errorurl(33));
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if (modify->nfix_restart_peratom)
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if (modify->nfix_restart_peratom)
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error->all(FLERR, "Cannot create_atoms after reading restart file with per-atom info");
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error->all(FLERR, "Cannot create_atoms after reading restart file with per-atom info");
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@ -44,7 +44,7 @@ CreateBonds::CreateBonds(LAMMPS *lmp) : Command(lmp) {}
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void CreateBonds::command(int narg, char **arg)
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void CreateBonds::command(int narg, char **arg)
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{
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{
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if (domain->box_exist == 0)
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if (domain->box_exist == 0)
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error->all(FLERR, "Create_bonds command before simulation box is defined");
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error->all(FLERR, "Create_bonds command before simulation box is defined" + utils::errorurl(33));
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if (atom->tag_enable == 0) error->all(FLERR, "Cannot use create_bonds unless atoms have IDs");
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if (atom->tag_enable == 0) error->all(FLERR, "Cannot use create_bonds unless atoms have IDs");
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if (atom->molecular != Atom::MOLECULAR)
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if (atom->molecular != Atom::MOLECULAR)
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error->all(FLERR, "Cannot use create_bonds with non-molecular system");
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error->all(FLERR, "Cannot use create_bonds with non-molecular system");
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@ -38,7 +38,8 @@ void CreateBox::command(int narg, char **arg)
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{
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{
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if (narg < 2) utils::missing_cmd_args(FLERR, "create_box", error);
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if (narg < 2) utils::missing_cmd_args(FLERR, "create_box", error);
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if (domain->box_exist) error->all(FLERR, "Cannot create_box after simulation box is defined");
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if (domain->box_exist)
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error->all(FLERR, "Cannot create_box after simulation box is defined" + utils::errorurl(34));
|
||||||
if (domain->dimension == 2 && domain->zperiodic == 0)
|
if (domain->dimension == 2 && domain->zperiodic == 0)
|
||||||
error->all(FLERR, "Cannot run 2d simulation with nonperiodic Z dimension");
|
error->all(FLERR, "Cannot run 2d simulation with nonperiodic Z dimension");
|
||||||
|
|
||||||
|
|||||||
@ -52,7 +52,7 @@ DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {}
|
|||||||
void DeleteAtoms::command(int narg, char **arg)
|
void DeleteAtoms::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Delete_atoms command before simulation box is defined");
|
error->all(FLERR, "Delete_atoms command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (narg < 1) utils::missing_cmd_args(FLERR, "delete_atoms", error);
|
if (narg < 1) utils::missing_cmd_args(FLERR, "delete_atoms", error);
|
||||||
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use delete_atoms unless atoms have IDs");
|
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use delete_atoms unless atoms have IDs");
|
||||||
|
|
||||||
|
|||||||
@ -40,7 +40,7 @@ DeleteBonds::DeleteBonds(LAMMPS *lmp) : Command(lmp) {}
|
|||||||
void DeleteBonds::command(int narg, char **arg)
|
void DeleteBonds::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Delete_bonds command before simulation box is defined");
|
error->all(FLERR,"Delete_bonds command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (atom->natoms == 0)
|
if (atom->natoms == 0)
|
||||||
error->all(FLERR,"Delete_bonds command with no atoms existing");
|
error->all(FLERR,"Delete_bonds command with no atoms existing");
|
||||||
if (atom->molecular != Atom::MOLECULAR)
|
if (atom->molecular != Atom::MOLECULAR)
|
||||||
|
|||||||
@ -42,12 +42,12 @@ void DihedralWrite::command(int narg, char **arg)
|
|||||||
// sanity checks
|
// sanity checks
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Dihedral_write command before simulation box is defined");
|
error->all(FLERR, "Dihedral_write command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (atom->avec->dihedrals_allow == 0)
|
if (atom->avec->dihedrals_allow == 0)
|
||||||
error->all(FLERR, "Dihedral_write command when no dihedrals allowed");
|
error->all(FLERR, "Dihedral_write command when no dihedrals allowed");
|
||||||
auto dihedral = force->dihedral;
|
auto dihedral = force->dihedral;
|
||||||
if (dihedral == nullptr)
|
if (dihedral == nullptr)
|
||||||
error->all(FLERR, "Dihedral_write command before an dihedral_style is defined");
|
error->all(FLERR, "Dihedral_write command before an dihedral_style is defined" + utils::errorurl(33));
|
||||||
if (dihedral && (force->dihedral->writedata == 0))
|
if (dihedral && (force->dihedral->writedata == 0))
|
||||||
error->all(FLERR, "Dihedral style must support writing coeffs to data file for dihedral_write");
|
error->all(FLERR, "Dihedral style must support writing coeffs to data file for dihedral_write");
|
||||||
|
|
||||||
|
|||||||
@ -63,7 +63,7 @@ void DisplaceAtoms::command(int narg, char **arg)
|
|||||||
int i;
|
int i;
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Displace_atoms command before simulation box is defined");
|
error->all(FLERR,"Displace_atoms command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
|
if (narg < 2) error->all(FLERR,"Illegal displace_atoms command");
|
||||||
if (modify->nfix_restart_peratom)
|
if (modify->nfix_restart_peratom)
|
||||||
error->all(FLERR,"Cannot displace_atoms after "
|
error->all(FLERR,"Cannot displace_atoms after "
|
||||||
|
|||||||
@ -92,7 +92,7 @@ void Group::assign(int narg, char **arg)
|
|||||||
{
|
{
|
||||||
int i;
|
int i;
|
||||||
|
|
||||||
if (domain->box_exist == 0) error->all(FLERR, "Group command before simulation box is defined");
|
if (domain->box_exist == 0) error->all(FLERR, "Group command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (narg < 2) utils::missing_cmd_args(FLERR, "group", error);
|
if (narg < 2) utils::missing_cmd_args(FLERR, "group", error);
|
||||||
|
|
||||||
// delete the group if not being used elsewhere
|
// delete the group if not being used elsewhere
|
||||||
|
|||||||
@ -1347,7 +1347,7 @@ void Input::variable_command()
|
|||||||
void Input::angle_coeff()
|
void Input::angle_coeff()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Angle_coeff command before simulation box is defined");
|
error->all(FLERR,"Angle_coeff command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (force->angle == nullptr)
|
if (force->angle == nullptr)
|
||||||
error->all(FLERR,"Angle_coeff command before angle_style is defined");
|
error->all(FLERR,"Angle_coeff command before angle_style is defined");
|
||||||
if (atom->avec->angles_allow == 0)
|
if (atom->avec->angles_allow == 0)
|
||||||
@ -1382,7 +1382,7 @@ void Input::atom_style()
|
|||||||
{
|
{
|
||||||
if (narg < 1) utils::missing_cmd_args(FLERR, "atom_style", error);
|
if (narg < 1) utils::missing_cmd_args(FLERR, "atom_style", error);
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Atom_style command after simulation box is defined");
|
error->all(FLERR,"Atom_style command after simulation box is defined" + utils::errorurl(34));
|
||||||
atom->create_avec(arg[0],narg-1,&arg[1],1);
|
atom->create_avec(arg[0],narg-1,&arg[1],1);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1391,7 +1391,7 @@ void Input::atom_style()
|
|||||||
void Input::bond_coeff()
|
void Input::bond_coeff()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Bond_coeff command before simulation box is defined");
|
error->all(FLERR,"Bond_coeff command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (force->bond == nullptr)
|
if (force->bond == nullptr)
|
||||||
error->all(FLERR,"Bond_coeff command before bond_style is defined");
|
error->all(FLERR,"Bond_coeff command before bond_style is defined");
|
||||||
if (atom->avec->bonds_allow == 0)
|
if (atom->avec->bonds_allow == 0)
|
||||||
@ -1429,7 +1429,7 @@ void Input::bond_write()
|
|||||||
void Input::boundary()
|
void Input::boundary()
|
||||||
{
|
{
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Boundary command after simulation box is defined");
|
error->all(FLERR,"Boundary command after simulation box is defined" + utils::errorurl(34));
|
||||||
domain->set_boundary(narg,arg,0);
|
domain->set_boundary(narg,arg,0);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1486,7 +1486,8 @@ void Input::dielectric()
|
|||||||
void Input::dihedral_coeff()
|
void Input::dihedral_coeff()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Dihedral_coeff command before simulation box is defined");
|
error->all(FLERR,"Dihedral_coeff command before simulation box is defined"
|
||||||
|
+ utils::errorurl(33));
|
||||||
if (force->dihedral == nullptr)
|
if (force->dihedral == nullptr)
|
||||||
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
|
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
|
||||||
if (atom->avec->dihedrals_allow == 0)
|
if (atom->avec->dihedrals_allow == 0)
|
||||||
@ -1514,7 +1515,7 @@ void Input::dimension()
|
|||||||
{
|
{
|
||||||
if (narg != 1) error->all(FLERR, "Dimension command expects exactly 1 argument");
|
if (narg != 1) error->all(FLERR, "Dimension command expects exactly 1 argument");
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Dimension command after simulation box is defined");
|
error->all(FLERR,"Dimension command after simulation box is defined" + utils::errorurl(34));
|
||||||
domain->dimension = utils::inumeric(FLERR,arg[0],false,lmp);
|
domain->dimension = utils::inumeric(FLERR,arg[0],false,lmp);
|
||||||
if (domain->dimension != 2 && domain->dimension != 3)
|
if (domain->dimension != 2 && domain->dimension != 3)
|
||||||
error->all(FLERR, "Invalid dimension argument: {}", arg[0]);
|
error->all(FLERR, "Invalid dimension argument: {}", arg[0]);
|
||||||
@ -1565,7 +1566,7 @@ void Input::group_command()
|
|||||||
void Input::improper_coeff()
|
void Input::improper_coeff()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Improper_coeff command before simulation box is defined");
|
error->all(FLERR,"Improper_coeff command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (force->improper == nullptr)
|
if (force->improper == nullptr)
|
||||||
error->all(FLERR,"Improper_coeff command before improper_style is defined");
|
error->all(FLERR,"Improper_coeff command before improper_style is defined");
|
||||||
if (atom->avec->impropers_allow == 0)
|
if (atom->avec->impropers_allow == 0)
|
||||||
@ -1607,7 +1608,8 @@ void Input::kspace_style()
|
|||||||
|
|
||||||
void Input::labelmap()
|
void Input::labelmap()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0) error->all(FLERR,"Labelmap command before simulation box is defined");
|
if (domain->box_exist == 0)
|
||||||
|
error->all(FLERR,"Labelmap command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (!atom->labelmapflag) atom->add_label_map();
|
if (!atom->labelmapflag) atom->add_label_map();
|
||||||
atom->lmap->modify_lmap(narg,arg);
|
atom->lmap->modify_lmap(narg,arg);
|
||||||
}
|
}
|
||||||
@ -1625,7 +1627,7 @@ void Input::mass()
|
|||||||
{
|
{
|
||||||
if (narg != 2) error->all(FLERR,"Illegal mass command: expected 2 arguments but found {}", narg);
|
if (narg != 2) error->all(FLERR,"Illegal mass command: expected 2 arguments but found {}", narg);
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Mass command before simulation box is defined");
|
error->all(FLERR,"Mass command before simulation box is defined" + utils::errorurl(33));
|
||||||
atom->set_mass(FLERR,narg,arg);
|
atom->set_mass(FLERR,narg,arg);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1641,7 +1643,7 @@ void Input::min_modify()
|
|||||||
void Input::min_style()
|
void Input::min_style()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Min_style command before simulation box is defined");
|
error->all(FLERR,"Min_style command before simulation box is defined" + utils::errorurl(33));
|
||||||
update->create_minimize(narg,arg,1);
|
update->create_minimize(narg,arg,1);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1682,7 +1684,7 @@ void Input::newton()
|
|||||||
force->newton_pair = newton_pair;
|
force->newton_pair = newton_pair;
|
||||||
|
|
||||||
if (domain->box_exist && (newton_bond != force->newton_bond))
|
if (domain->box_exist && (newton_bond != force->newton_bond))
|
||||||
error->all(FLERR,"Newton bond change after simulation box is defined");
|
error->all(FLERR,"Newton bond change after simulation box is defined" + utils::errorurl(34));
|
||||||
force->newton_bond = newton_bond;
|
force->newton_bond = newton_bond;
|
||||||
|
|
||||||
if (newton_pair || newton_bond) force->newton = 1;
|
if (newton_pair || newton_bond) force->newton = 1;
|
||||||
@ -1696,8 +1698,8 @@ void Input::newton()
|
|||||||
void Input::package()
|
void Input::package()
|
||||||
{
|
{
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Package command after simulation box is defined");
|
error->all(FLERR,"Package command after simulation box is defined" + utils::errorurl(34));
|
||||||
if (narg < 1) error->all(FLERR,"Illegal package command");
|
if (narg < 1) utils::missing_cmd_args(FLERR, "package", error);
|
||||||
|
|
||||||
// same checks for packages existing as in LAMMPS::post_create()
|
// same checks for packages existing as in LAMMPS::post_create()
|
||||||
// since can be invoked here by package command in input script
|
// since can be invoked here by package command in input script
|
||||||
@ -1739,7 +1741,7 @@ void Input::package()
|
|||||||
void Input::pair_coeff()
|
void Input::pair_coeff()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Pair_coeff command before simulation box is defined");
|
error->all(FLERR,"Pair_coeff command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (force->pair == nullptr) error->all(FLERR,"Pair_coeff command without a pair style");
|
if (force->pair == nullptr) error->all(FLERR,"Pair_coeff command without a pair style");
|
||||||
if (narg < 2) utils::missing_cmd_args(FLERR,"pair_coeff", error);
|
if (narg < 2) utils::missing_cmd_args(FLERR,"pair_coeff", error);
|
||||||
if (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0) || (strcmp(arg[1],"*") != 0)))
|
if (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0) || (strcmp(arg[1],"*") != 0)))
|
||||||
@ -1820,7 +1822,7 @@ void Input::pair_write()
|
|||||||
void Input::processors()
|
void Input::processors()
|
||||||
{
|
{
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Processors command after simulation box is defined");
|
error->all(FLERR,"Processors command after simulation box is defined" + utils::errorurl(34));
|
||||||
comm->set_processors(narg,arg);
|
comm->set_processors(narg,arg);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1850,7 +1852,7 @@ void Input::restart()
|
|||||||
void Input::run_style()
|
void Input::run_style()
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Run_style command before simulation box is defined");
|
error->all(FLERR,"Run_style command before simulation box is defined" + utils::errorurl(33));
|
||||||
update->create_integrate(narg,arg,1);
|
update->create_integrate(narg,arg,1);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -2002,7 +2004,7 @@ void Input::units()
|
|||||||
{
|
{
|
||||||
if (narg != 1) error->all(FLERR,"Illegal units command: expected 1 argument but found {}", narg);
|
if (narg != 1) error->all(FLERR,"Illegal units command: expected 1 argument but found {}", narg);
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Units command after simulation box is defined");
|
error->all(FLERR,"Units command after simulation box is defined" + utils::errorurl(34));
|
||||||
update->set_units(arg[0]);
|
update->set_units(arg[0]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -321,10 +321,10 @@ void KSpace::qsum_qsq(int warning_flag)
|
|||||||
// so issue warning or error
|
// so issue warning or error
|
||||||
|
|
||||||
if (fabs(qsum) > SMALL) {
|
if (fabs(qsum) > SMALL) {
|
||||||
std::string message = fmt::format("System is not charge neutral, net "
|
std::string message = fmt::format("System is not charge neutral, net charge = {:.8}{}",
|
||||||
"charge = {:.8}",qsum);
|
qsum, utils::errorurl(29));
|
||||||
if (!warn_nonneutral) error->all(FLERR,message + utils::errorurl(29));
|
if (!warn_nonneutral) error->all(FLERR,message);
|
||||||
if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message + utils::errorurl(29));
|
if (warn_nonneutral == 1 && comm->me == 0) error->warning(FLERR,message);
|
||||||
warn_nonneutral = 2;
|
warn_nonneutral = 2;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -254,7 +254,7 @@ int LabelMap::find_or_create(const std::string &mylabel, std::vector<std::string
|
|||||||
|
|
||||||
// if label cannot be found or created, need more space reserved
|
// if label cannot be found or created, need more space reserved
|
||||||
|
|
||||||
error->all(FLERR, "Topology type exceeds system topology type");
|
error->all(FLERR, "Topology type exceeds system topology type" + utils::errorurl(25));
|
||||||
|
|
||||||
// never reaches here, just to prevent compiler warning
|
// never reaches here, just to prevent compiler warning
|
||||||
|
|
||||||
|
|||||||
@ -35,7 +35,7 @@ void Minimize::command(int narg, char **arg)
|
|||||||
error->all(FLERR, "Illegal minimize command: expected 4 arguments but found {}", narg);
|
error->all(FLERR, "Illegal minimize command: expected 4 arguments but found {}", narg);
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Minimize command before simulation box is defined");
|
error->all(FLERR, "Minimize command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
// ignore minimize command, if walltime limit was already reached
|
// ignore minimize command, if walltime limit was already reached
|
||||||
if (timer->is_timeout()) return;
|
if (timer->is_timeout()) return;
|
||||||
|
|||||||
@ -896,7 +896,7 @@ void Output::create_thermo(int narg, char **arg)
|
|||||||
// don't allow this so that dipole style can safely allocate inertia vector
|
// don't allow this so that dipole style can safely allocate inertia vector
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Thermo_style command before simulation box is defined");
|
error->all(FLERR,"Thermo_style command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
// warn if previous thermo had been modified via thermo_modify command
|
// warn if previous thermo had been modified via thermo_modify command
|
||||||
|
|
||||||
|
|||||||
@ -339,9 +339,11 @@ void ReadData::command(int narg, char **arg)
|
|||||||
"Reading a data file with shrinkwrap boundaries is not "
|
"Reading a data file with shrinkwrap boundaries is not "
|
||||||
"compatible with a MSM KSpace style");
|
"compatible with a MSM KSpace style");
|
||||||
if (domain->box_exist && !addflag)
|
if (domain->box_exist && !addflag)
|
||||||
error->all(FLERR, "Cannot use read_data without add keyword after simulation box is defined");
|
error->all(FLERR, "Cannot use read_data without add keyword after simulation box is defined"
|
||||||
|
+ utils::errorurl(34));
|
||||||
if (!domain->box_exist && addflag)
|
if (!domain->box_exist && addflag)
|
||||||
error->all(FLERR, "Cannot use read_data add before simulation box is defined");
|
error->all(FLERR, "Cannot use read_data add before simulation box is defined"
|
||||||
|
+ utils::errorurl(33));
|
||||||
if (offsetflag) {
|
if (offsetflag) {
|
||||||
if (addflag == NONE) {
|
if (addflag == NONE) {
|
||||||
error->all(FLERR, "Cannot use read_data offset without add keyword");
|
error->all(FLERR, "Cannot use read_data offset without add keyword");
|
||||||
|
|||||||
@ -80,7 +80,7 @@ ReadDump::~ReadDump()
|
|||||||
void ReadDump::command(int narg, char **arg)
|
void ReadDump::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Read_dump command before simulation box is defined");
|
error->all(FLERR,"Read_dump command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
if (narg < 2) utils::missing_cmd_args(FLERR, "read_dump", error);
|
if (narg < 2) utils::missing_cmd_args(FLERR, "read_dump", error);
|
||||||
|
|
||||||
|
|||||||
@ -52,7 +52,7 @@ void ReadRestart::command(int narg, char **arg)
|
|||||||
if (narg != 1 && narg != 2) error->all(FLERR,"Illegal read_restart command");
|
if (narg != 1 && narg != 2) error->all(FLERR,"Illegal read_restart command");
|
||||||
|
|
||||||
if (domain->box_exist)
|
if (domain->box_exist)
|
||||||
error->all(FLERR,"Cannot read_restart after simulation box is defined");
|
error->all(FLERR,"Cannot read_restart after simulation box is defined" + utils::errorurl(34));
|
||||||
|
|
||||||
MPI_Barrier(world);
|
MPI_Barrier(world);
|
||||||
double time1 = platform::walltime();
|
double time1 = platform::walltime();
|
||||||
|
|||||||
@ -52,7 +52,7 @@ void Replicate::command(int narg, char **arg)
|
|||||||
int i,n;
|
int i,n;
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Replicate command before simulation box is defined");
|
error->all(FLERR,"Replicate command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
|
if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
|
||||||
|
|
||||||
|
|||||||
@ -41,7 +41,7 @@ Rerun::Rerun(LAMMPS *lmp) : Command(lmp) {}
|
|||||||
void Rerun::command(int narg, char **arg)
|
void Rerun::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Rerun command before simulation box is defined");
|
error->all(FLERR,"Rerun command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
if (narg < 2) error->all(FLERR,"Illegal rerun command");
|
if (narg < 2) error->all(FLERR,"Illegal rerun command");
|
||||||
|
|
||||||
|
|||||||
@ -53,7 +53,7 @@ ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp)
|
|||||||
void ResetAtomsID::command(int narg, char **arg)
|
void ResetAtomsID::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Reset_atoms id command before simulation box is defined");
|
error->all(FLERR, "Reset_atoms id command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms id unless atoms have IDs");
|
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms id unless atoms have IDs");
|
||||||
|
|
||||||
for (const auto &ifix : modify->get_fix_list())
|
for (const auto &ifix : modify->get_fix_list())
|
||||||
|
|||||||
@ -39,7 +39,7 @@ ResetAtomsImage::ResetAtomsImage(LAMMPS *lmp) : Command(lmp) {}
|
|||||||
void ResetAtomsImage::command(int narg, char **arg)
|
void ResetAtomsImage::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Reset_atoms image command before simulation box is defined");
|
error->all(FLERR, "Reset_atoms image command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (atom->tag_enable == 0)
|
if (atom->tag_enable == 0)
|
||||||
error->all(FLERR, "Cannot use reset_atoms image unless atoms have IDs");
|
error->all(FLERR, "Cannot use reset_atoms image unless atoms have IDs");
|
||||||
if (atom->avec->bonds_allow == 0)
|
if (atom->avec->bonds_allow == 0)
|
||||||
|
|||||||
@ -61,7 +61,7 @@ ResetAtomsMol::~ResetAtomsMol()
|
|||||||
void ResetAtomsMol::command(int narg, char **arg)
|
void ResetAtomsMol::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Reset_atoms mol command before simulation box is defined");
|
error->all(FLERR, "Reset_atoms mol command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms mol unless atoms have IDs");
|
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms mol unless atoms have IDs");
|
||||||
if (atom->molecular != Atom::MOLECULAR)
|
if (atom->molecular != Atom::MOLECULAR)
|
||||||
error->all(FLERR, "Can only use reset_atoms mol on molecular systems");
|
error->all(FLERR, "Can only use reset_atoms mol on molecular systems");
|
||||||
|
|||||||
@ -39,7 +39,7 @@ void Run::command(int narg, char **arg)
|
|||||||
if (narg < 1) utils::missing_cmd_args(FLERR, "run", error);
|
if (narg < 1) utils::missing_cmd_args(FLERR, "run", error);
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Run command before simulation box is defined");
|
error->all(FLERR,"Run command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
// ignore run command, if walltime limit was already reached
|
// ignore run command, if walltime limit was already reached
|
||||||
|
|
||||||
|
|||||||
@ -51,7 +51,7 @@ void Velocity::command(int narg, char **arg)
|
|||||||
if (narg < 2) utils::missing_cmd_args(FLERR, "velocity", error);
|
if (narg < 2) utils::missing_cmd_args(FLERR, "velocity", error);
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Velocity command before simulation box is defined");
|
error->all(FLERR,"Velocity command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (atom->natoms == 0)
|
if (atom->natoms == 0)
|
||||||
error->all(FLERR,"Velocity command with no atoms existing");
|
error->all(FLERR,"Velocity command with no atoms existing");
|
||||||
|
|
||||||
|
|||||||
@ -39,7 +39,7 @@ static constexpr int BUF_SIZE = 256;
|
|||||||
void WriteCoeff::command(int narg, char **arg)
|
void WriteCoeff::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR, "Write_coeff command before simulation box is defined");
|
error->all(FLERR, "Write_coeff command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
if (narg != 1) utils::missing_cmd_args(FLERR, "write_coeff", error);
|
if (narg != 1) utils::missing_cmd_args(FLERR, "write_coeff", error);
|
||||||
|
|
||||||
|
|||||||
@ -51,7 +51,7 @@ WriteData::WriteData(LAMMPS *lmp) : Command(lmp) {}
|
|||||||
void WriteData::command(int narg, char **arg)
|
void WriteData::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Write_data command before simulation box is defined");
|
error->all(FLERR,"Write_data command before simulation box is defined" + utils::errorurl(33));
|
||||||
|
|
||||||
if (narg < 1) utils::missing_cmd_args(FLERR, "write_data", error);
|
if (narg < 1) utils::missing_cmd_args(FLERR, "write_data", error);
|
||||||
|
|
||||||
|
|||||||
@ -59,7 +59,7 @@ WriteRestart::WriteRestart(LAMMPS *lmp) : Command(lmp)
|
|||||||
void WriteRestart::command(int narg, char **arg)
|
void WriteRestart::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Write_restart command before simulation box is defined");
|
error->all(FLERR,"Write_restart command before simulation box is defined" + utils::errorurl(33));
|
||||||
if (narg < 1) utils::missing_cmd_args(FLERR, "write_restart", error);
|
if (narg < 1) utils::missing_cmd_args(FLERR, "write_restart", error);
|
||||||
|
|
||||||
// if filename contains a "*", replace with current timestep
|
// if filename contains a "*", replace with current timestep
|
||||||
|
|||||||
Reference in New Issue
Block a user