ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

debugging merged version

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

33
doc/src/dump.rst
View File

@ -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) which can be convenient in place of a *type* attribute (1 to Ntypes)
for coloring atoms in a visualization program. *Type* is the atom for coloring atoms in a visualization program. *Type* is the atom
type (1 to Ntypes). *Element* is typically the chemical name of an 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 element, which you must assign to each type via the :doc:`dump_modify
string you wish to associated with an atom type. *Mass* is the atom element <dump_modify>` command. More generally, it can be any string
mass. *Vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components of you wish to associated with an atom type. *Mass* is the atom mass.
atom velocity and force and atomic charge. *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*, There are several options for outputting atom coordinates. The *x*,
*y*, *z* attributes write atom coordinates "unscaled", in the *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. effectively specify multiple values.
The *f_ID* and *f_ID[I]* attributes allow vector or array per-atom 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 quantities calculated by a :doc:`fix <fix>` to be output. The ID in
attribute should be replaced by the actual ID of the fix that has been the attribute should be replaced by the actual ID of the fix that has
defined previously in the input script. The :doc:`fix ave/atom <fix_ave_atom>` command is one that calculates per-atom been defined previously in the input script. The :doc:`fix ave/atom
quantities. Since it can time-average per-atom quantities produced by <fix_ave_atom>` command is one that calculates per-atom quantities.
any :doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style 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 :doc:`variable <variable>`, this allows those time-averaged results to
be written to a dump file. 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 defined previously in the input script. Only an atom-style variable
can be referenced, since it is the only style that generates per-atom can be referenced, since it is the only style that generates per-atom
values. Variables of style *atom* can reference individual atom values. Variables of style *atom* can reference individual atom
attributes, per-atom attributes, thermodynamic keywords, or attributes, per-atom attributes, thermodynamic keywords, or invoke
invoke other computes, fixes, or variables when they are evaluated, so other computes, fixes, or variables when they are evaluated, so this
this is a very general means of creating quantities to output to a is a very general means of creating quantities to output to a dump
dump file. file.
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
per-atom integer and floating-point vectors or arrays that have been 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 When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name* 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 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 See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities new compute and fix styles to LAMMPS to calculate per-atom quantities

2
src/dump_custom.cpp
View File

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

6
src/utils.cpp
View File

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