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Merge pull request #2388 from jrgissing/molecule_fragments_check 

molecule: findfragments correction
This commit is contained in:
Axel Kohlmeyer 2020-09-23 15:54:37 -04:00 committed by GitHub
parent ab4dc9c343 b6d98707ec
commit 85fe94a6dd
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 19 additions and 0 deletions
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6
doc/src/Errors_messages.rst
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@ -5708,6 +5708,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Molecule file has dihedrals but no ndihedrals setting*
Self-explanatory.
*Molecule file has fragments but no nfragments setting*
Self-explanatory.
*Molecule file has impropers but no nimpropers setting*
Self-explanatory.
@ -5717,6 +5720,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Molecule file has no Body Integers section*
Self-explanatory.
*Molecule file has no Fragments section*
Self-explanatory.
*Molecule file has special flags but no bonds*
Self-explanatory.

5
src/molecule.cpp
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@ -535,6 +535,8 @@ void Molecule::read(int flag)
if (flag) molecules(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Fragments") == 0) {
if (nfragments == 0)
error->all(FLERR,"Molecule file has fragments but no nfragments setting");
fragmentflag = 1;
if (flag) fragments(line);
else skip_lines(nfragments,line);
@ -634,6 +636,8 @@ void Molecule::read(int flag)
error->all(FLERR,"Molecule file has no Body Integers section");
if (bodyflag && ndbody && dbodyflag == 0)
error->all(FLERR,"Molecule file has no Body Doubles section");
if (nfragments > 0 && !fragmentflag)
error->all(FLERR,"Molecule file has no Fragments section");
}
// auto-generate special bonds if needed and not in file
@ -1691,6 +1695,7 @@ void Molecule::initialize()
nmolecules = 1;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nibody = ndbody = 0;
nfragments = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
maxspecial = 0;

8
src/molecule.h
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@ -241,6 +241,10 @@ E: Molecule file has impropers but no nimpropers setting
Self-explanatory.
E: Molecule file has fragments but no nfragments setting
Self-explanatory.
E: Molecule file shake flags not before shake atoms
The order of the two sections is important.
@ -277,6 +281,10 @@ E: Molecule file has no Body Doubles section
Self-explanatory.
E: Molecule file has no Fragments section
Self-explanatory.
E: Cannot auto-generate special bonds before simulation box is defined
UNDOCUMENTED