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debugging merged version

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This commit is contained in:
Steve Plimpton
2021-08-18 13:07:49 -06:00
parent e5a194d8d4
commit cf25a586bd
3 changed files with 24 additions and 17 deletions
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33
doc/src/dump.rst
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@ -569,10 +569,11 @@ Nprocs-1) that currently owns the atom. *Procp1* is the proc ID+1,
which can be convenient in place of a *type* attribute (1 to Ntypes)
for coloring atoms in a visualization program. *Type* is the atom
type (1 to Ntypes). *Element* is typically the chemical name of an
element, which you must assign to each type via the :doc:`dump_modify element <dump_modify>` command. More generally, it can be any
string you wish to associated with an atom type. *Mass* is the atom
mass. *Vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components of
atom velocity and force and atomic charge.
element, which you must assign to each type via the :doc:`dump_modify
element <dump_modify>` command. More generally, it can be any string
you wish to associated with an atom type. *Mass* is the atom mass.
*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*, *z* attributes write atom coordinates "unscaled", in the
@ -646,11 +647,12 @@ above for how 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 <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 <fix_ave_atom>` command is one that calculates per-atom
quantities. Since it can time-average per-atom quantities produced by
any :doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
quantities calculated by a :doc:`fix <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
<fix_ave_atom>` command is one that calculates per-atom quantities.
Since it can time-average per-atom quantities produced by any
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
:doc:`variable <variable>`, this allows those time-averaged results to
be written to a dump file.
@ -667,10 +669,10 @@ 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
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
@ -678,7 +680,10 @@ added via the :doc:`fix property/atom <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[2], i2_mySpin[3].
the name in brackets: e.g. d2_xyz[I], i2_mySpin[I], where I is in the
range from 1-M, where M is the number of columns in the custom array.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities

2
src/dump_custom.cpp
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@ -1554,6 +1554,8 @@ int DumpCustom::parse_fields(int narg, char **arg)
n = atom->find_custom(name,flag,cols);
printf("NAME %s\n",name);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
if (argindex[iarg] == 0) {

6
src/utils.cpp
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@ -693,9 +693,9 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
}
}
//printf("NEWARG %d\n",newarg);
//for (int i = 0; i < newarg; i++)
// printf(" arg %d: %s\n",i,earg[i]);
printf("NEWARG %d\n",newarg);
for (int i = 0; i < newarg; i++)
printf(" arg %d: %s\n",i,earg[i]);
return newarg;
}