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provide error information for two more cases

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This commit is contained in:
Axel Kohlmeyer
2025-03-13 05:31:41 -04:00
parent 0f10741f71
commit 9d70c8b8ae
4 changed files with 82 additions and 16 deletions
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73
doc/src/Errors_details.rst
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@ -521,6 +521,47 @@ Most likely, one or more atoms have been blown out of the simulation
box to a great distance or a fix (like fix deform or a barostat) has
excessively grown the simulation box.
.. _err0018:
Step X: (h)bondchk failed
-------------------------
This error is a consequence of the heuristic memory allocations for
buffers of the regular ReaxFF version. In ReaxFF simulation the lists
of bonds and hydrogen bonds can change due to chemical reactions. The
default approach, however, assumes that these changes are not very
large, so it allocates buffers for the current system setup plus a
safety margin. This can be adjusted with the :doc:`safezone, mincap,
and minhbonds settings of pair style <pair_reaxff>`, but only to some
extent. When equilibrating a new system, or simulating a sparse system
in parallel, this can be difficult to control and become wasteful. A
simple workaround is often to break a simulation down in multiple
chunks. A better approach, however, is to compile and use the KOKKOS
package version of ReaxFF (you don't need a GPU for that, but can also
compile it in serial or OpenMP mode), which uses are much more robust
memory allocation approach.
.. _err0019:
Numeric index X is out of bounds
--------------------------------
This error most commonly happens, when setting force field coefficients
with either the :doc:`pair_coeff <pair_coeff>`, the :doc:`bond_coeff
<bond_coeff>`, the :doc:`angle_coeff <angle_coeff>`, the
:doc:`dihedral_coeff <dihedral_coeff>`, or the :doc:`improper_coeff
<improper_coeff>` command. These commands accept type labels,
explicit numbers and wildcards for ranges of numbers. If the numeric
value of any of these is outside the valid range (defined by the number
of corresponding types), LAMMPS will stop with this error. Also
a few other commands and styles allow ranges of numbers and check
using the same method and thus print the same kind of error.
The cause is almost always a typo in the input or a logic error
when defining the values or ranges. So one needs to carefully
review the input. Along with the error, LAMMPS will print the
valid range as a hint.
.. _err0020:
Variable formula X is accessed out-of-range
@ -613,20 +654,40 @@ Another cause is requesting a quantity on a timestep that is not
a thermo or dump output timestep. This can often be
remedied by increasing the frequency of thermo or dump output.
.. _err0023:
Molecule auto special bond generation overflow
----------------------------------------------
In order to correctly apply the :doc:`special_bonds <special_bonds>`
settings (also known as "exclusions"), LAMMPS needs to maintain for each
atom a list of atoms that are connected to this atom either with a bond
or are connected to a bonded atom. The purpose is to either remove or
tag those pairs of atoms in the neighbor list. This information is stored with individual
atoms and thus the maximum number of such "special" neighbors is set
when the simulation box is created. When reading (relative) geometry
and topology of a 'molecule' from a :doc:`molecule file <molecule>`,
LAMMPS will build the list of such "special" for the molecule atom
(if not given in the molecule file explicitly). The error is triggered
when the resulting list is too long for the space reserved when
creating the simulation box. The solution is to increase the
corresponding setting. Overestimating this value will only consume
more memory, and is thus a safe choice.
.. _err0024:
Molecule topology/atom exceeds system topology/atom
---------------------------------------------------
LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to distribute data
(i.e. atoms) across the MPI processes in parallel runs. This includes topology
data, that is data about bonds, angles, dihedrals, impropers and :doc:`"special"
neighbors <special_bonds>`.
LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to
distribute data (i.e. atoms) across the MPI processes in parallel
runs. This includes topology data, that is data about bonds, angles,
dihedrals, impropers and :doc:`"special" neighbors <special_bonds>`.
This information is stored with either one or all atoms involved in such
a topology entry (which of the two option applies depends on the
:doc:`newton <newton>` setting for bonds. When reading a data file,
LAMMPS analyzes the requirements for this file and then the values
are "locked in" and cannot be extended.
LAMMPS analyzes the requirements for this file and then the values are
"locked in" and cannot be extended.
So loading a molecule file that requires more of the topology per atom
storage or adding a data file with such needs will lead to an error. To

9
src/REAXFF/reaxff_forces.cpp
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@ -31,6 +31,9 @@
#include <cstring>
#include "error.h"
#include "utils.h"
using LAMMPS_NS::utils::errorurl;
namespace ReaxFF {
@ -95,7 +98,8 @@ namespace ReaxFF {
if (End_Index(i, bonds) > comp)
system->error_ptr->one(FLERR, fmt::format("step {}: bondchk failed: "
"i={} end(i)={} str(i+1)={}\n",
"i={} end(i)={} str(i+1)={}\n"
+ errorurl(18),
step,i,End_Index(i,bonds),comp));
}
}
@ -117,7 +121,8 @@ namespace ReaxFF {
if (End_Index(Hindex, hbonds) > comp)
system->error_ptr->one(FLERR, fmt::format("step {}: hbondchk failed: "
"H={} end(H)={} str(H+1)={}\n",
"H={} end(H)={} str(H+1)={}\n"
+ errorurl(18),
step, Hindex,End_Index(Hindex,hbonds),comp));
}
}

8
src/molecule.cpp
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@ -1554,7 +1554,7 @@ void Molecule::special_generate()
nspecial[i][0]++;
nspecial[atom2][0]++;
if (count[i] >= atom->maxspecial || count[atom2] >= atom->maxspecial)
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow");
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23));
tmpspecial[i][count[i]++] = atom2 + 1;
tmpspecial[atom2][count[atom2]++] = i + 1;
}
@ -1566,7 +1566,7 @@ void Molecule::special_generate()
atom1 = i;
atom2 = bond_atom[i][j];
if (count[atom1] >= atom->maxspecial)
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow");
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23));
tmpspecial[i][count[atom1]++] = atom2;
}
}
@ -1589,7 +1589,7 @@ void Molecule::special_generate()
}
if (!dedup) {
if (count[i] >= atom->maxspecial)
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow");
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23));
tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m] - 1][j];
nspecial[i][1]++;
}
@ -1613,7 +1613,7 @@ void Molecule::special_generate()
}
if (!dedup) {
if (count[i] >= atom->maxspecial)
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow");
error->all(FLERR, fileiarg, "Molecule auto special bond generation overflow" + utils::errorurl(23));
tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m] - 1][j];
nspecial[i][2]++;
}

8
src/utils.cpp
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@ -807,13 +807,13 @@ void utils::bounds(const char *file, int line, const std::string &str,
if (error) {
if ((nlo <= 0) || (nhi <= 0))
error->all(file, line, failed, "Invalid range string: {}", str);
constexpr char fmt[] = "Numeric index {} is out of bounds ({}-{}){}";
if (nlo < nmin)
error->all(file, line, failed, "Numeric index {} is out of bounds ({}-{})", nlo, nmin, nmax);
error->all(file, line, failed, fmt, nlo, nmin, nmax, errorurl(19));
else if (nhi > nmax)
error->all(file, line, failed, "Numeric index {} is out of bounds ({}-{})", nhi, nmin, nmax);
error->all(file, line, failed, fmt, nhi, nmin, nmax, errorurl(19));
else if (nlo > nhi)
error->all(file, line, failed, "Numeric index {} is out of bounds ({}-{})", nlo, nmin, nhi);
error->all(file, line, failed, fmt, nlo, nmin, nhi, errorurl(19));
}
}