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

add extract_setting special function to variable command

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-03-28 08:00:29 -04:00
parent 4545954385
commit d7f95da8f3
2 changed files with 60 additions and 37 deletions
Download Patch File Download Diff File Expand all files Collapse all files

69
doc/src/variable.rst
View File

@ -65,8 +65,8 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon), bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region), angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region) inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name) special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), extract_setting(name)
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id) feature functions = is_active(category,feature), is_available(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
@ -823,10 +823,15 @@ Special Functions
Special functions take specific kinds of arguments, meaning their Special functions take specific kinds of arguments, meaning their
arguments cannot be formulas themselves. arguments cannot be formulas themselves.
The is_file(x) function is a test whether 'x' is a (readable) file The is_file(name) function is a test whether *name* is a (readable) file
and returns 1 in this case, otherwise it returns 0. For that 'x' and returns 1 in this case, otherwise it returns 0. For that *name*
is taken as a literal string and must not have any blanks in it. is taken as a literal string and must not have any blanks in it.
The extract_setting(name) function allows to access some basic settings
through calling the :cpp:func:`lammps_extract_setting` library function.
For available keywords *name* and their meaning, please see the
documentation of that function.
The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
each take 1 argument which is of the form "c_ID" or "c_ID[N]" or each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
"f_ID" or "f_ID[N]" or "v_name". The first two are computes and the "f_ID" or "f_ID[N]" or "v_name". The first two are computes and the
@ -911,30 +916,30 @@ Feature Functions
----------------- -----------------
Feature functions allow to probe the running LAMMPS executable for Feature functions allow to probe the running LAMMPS executable for
whether specific features are either active, defined, or available. whether specific features are either active, defined, or available. The
The functions take two arguments, a *category* and a corresponding functions take two arguments, a *category* and a corresponding
*argument*\ . The arguments are strings thus cannot be formulas *argument*\ . The arguments are strings and thus cannot be formulas
themselves (only $-style immediate variable expansion is possible). themselves; only $-style immediate variable expansion is possible.
Return value is either 1.0 or 0.0 depending on whether the function Return value is either 1.0 or 0.0 depending on whether the function
evaluates to true or false, respectively. evaluates to true or false, respectively.
The *is_active()* function allows to query for active settings which The *is_active(category,feature)* function allows to query for active
are grouped by categories. Currently supported categories and settings which are grouped by categories. Currently supported categories
arguments are: and arguments are:
* *package* (argument = *gpu* or *intel* or *kokkos* or *omp*\ ) * *package*\ : argument = *gpu* or *intel* or *kokkos* or *omp*
* *newton* (argument = *pair* or *bond* or *any*\ ) * *newton*\ : argument = *pair* or *bond* or *any*
* *pair* (argument = *single* or *respa* or *manybody* or *tail* or *shift*\ ) * *pair*\ : argument = *single* or *respa* or *manybody* or *tail* or *shift*
* *comm_style* (argument = *brick* or *tiled*\ ) * *comm_style*\ : argument = *brick* or *tiled*
* *min_style* (argument = any of the compiled in minimizer styles) * *min_style*\ : argument = any of the compiled in minimizer styles
* *run_style* (argument = any of the compiled in run styles) * *run_style*\ : argument = any of the compiled in run styles
* *atom_style* (argument = any of the compiled in atom styles) * *atom_style*\ : argument = any of the compiled in atom style)
* *pair_style* (argument = any of the compiled in pair styles) * *pair_style*\ : argument = any of the compiled in pair styles
* *bond_style* (argument = any of the compiled in bond styles) * *bond_style*\ : argument = any of the compiled in bond styles
* *angle_style* (argument = any of the compiled in angle styles) * *angle_style*\ : argument = any of the compiled in angle styles
* *dihedral_style* (argument = any of the compiled in dihedral styles) * *dihedral_style*\ : argument = any of the compiled in dihedral styles
* *improper_style* (argument = any of the compiled in improper styles) * *improper_style*\ : argument = any of the compiled in improper styles
* *kspace_style* (argument = any of the compiled in kspace styles) * *kspace_style*\ : argument = any of the compiled in kspace styles
Most of the settings are self-explanatory, the *single* argument in the Most of the settings are self-explanatory, the *single* argument in the
*pair* category allows to check whether a pair style supports a *pair* category allows to check whether a pair style supports a
@ -943,7 +948,9 @@ features or LAMMPS, *respa* allows to check whether the inner/middle/outer
mode of r-RESPA is supported. In the various style categories, mode of r-RESPA is supported. In the various style categories,
the checking is also done using suffix flags, if available and enabled. the checking is also done using suffix flags, if available and enabled.
Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with OPENMP). Example 1: disable use of suffix for pppm when using GPU package
(i.e. run it on the CPU concurrently to running the pair style on the
GPU), but do use the suffix otherwise (e.g. with OPENMP).
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -951,17 +958,15 @@ Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on
if $(is_active(package,gpu)) then "suffix off" if $(is_active(package,gpu)) then "suffix off"
kspace_style pppm kspace_style pppm
Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step Example 2: use r-RESPA with inner/outer cutoff, if supported by pair
style, otherwise fall back to using pair and reducing the outer time
step
.. code-block:: LAMMPS .. code-block:: LAMMPS
timestep $(2.0*(1.0+2.0*is_active(pair,respa)) timestep $(2.0*(1.0+2.0*is_active(pair,respa))
if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3" if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3"
The *is_defined()* function allows to query categories like *compute*,
*dump*, *fix*, *group*, *region*, and *variable* whether an entry
with the provided name or id is defined.
The *is_available(category,name)* function allows to query whether The *is_available(category,name)* function allows to query whether
a specific optional feature is available, i.e. compiled in. a specific optional feature is available, i.e. compiled in.
This currently works for the following categories: *command*, This currently works for the following categories: *command*,
@ -983,6 +988,10 @@ the compiled binary supports it.
if "$(is_available(feature,ffmpeg)" then "dump 3 all movie 25 movie.mp4 type type zoom 1.6 adiam 1.0" if "$(is_available(feature,ffmpeg)" then "dump 3 all movie 25 movie.mp4 type type zoom 1.6 adiam 1.0"
The *is_defined(categoy,id)* function allows to query categories like
*compute*, *dump*, *fix*, *group*, *region*, and *variable* whether an
entry with the provided name or id is defined.
---------- ----------
Atom Values and Vectors Atom Values and Vectors

28
src/variable.cpp
View File

@ -24,6 +24,7 @@
#include "group.h" #include "group.h"
#include "info.h" #include "info.h"
#include "input.h" #include "input.h"
#include "library.h"
#include "lmppython.h" #include "lmppython.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
@ -63,7 +64,7 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY,
SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2, SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2,
RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,LOGFREQ2, RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,LOGFREQ2,
LOGFREQ3,STRIDE,STRIDE2,VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK, LOGFREQ3,STRIDE,STRIDE2,VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,
GRMASK,IS_ACTIVE,IS_DEFINED,IS_AVAILABLE,IS_FILE, GRMASK,IS_ACTIVE,IS_DEFINED,IS_AVAILABLE,IS_FILE,EXTRACT_SETTING,
VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY,VECTORARRAY}; VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY,VECTORARRAY};
// customize by adding a special function // customize by adding a special function
@ -3899,12 +3900,11 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
// word not a match to any special function // word not a match to any special function
if (strcmp(word,"sum") && strcmp(word,"min") && strcmp(word,"max") && if (strcmp(word,"sum") && strcmp(word,"min") && strcmp(word,"max") && strcmp(word,"ave") &&
strcmp(word,"ave") && strcmp(word,"trap") && strcmp(word,"slope") && strcmp(word,"trap") && strcmp(word,"slope") && strcmp(word,"gmask") && strcmp(word,"rmask") &&
strcmp(word,"gmask") && strcmp(word,"rmask") && strcmp(word,"grmask") && strcmp(word,"next") && strcmp(word,"is_active") &&
strcmp(word,"grmask") && strcmp(word,"next") && strcmp(word,"is_defined") && strcmp(word,"is_available") && strcmp(word,"is_file") &&
strcmp(word,"is_active") && strcmp(word,"is_defined") && strcmp(word,"extract_setting"))
strcmp(word,"is_available") && strcmp(word,"is_file"))
return 0; return 0;
// parse contents for comma-separated args // parse contents for comma-separated args
@ -4295,6 +4295,20 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
// save value in tree or on argstack // save value in tree or on argstack
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
} else if (strcmp(word,"extract_setting") == 0) {
if (narg != 1) print_var_error(FLERR,"Invalid extract_setting() function in variable formula",ivar);
value = lammps_extract_setting(lmp, args[0]);
// save value in tree or on argstack
if (tree) { if (tree) {
Tree *newtree = new Tree(); Tree *newtree = new Tree();
newtree->type = VALUE; newtree->type = VALUE;