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bond/react: convert group-ID to group-ID-prefix

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enables consistent syntax when using custom groups
This commit is contained in:
jrgissing
2018-11-03 11:57:46 -06:00
parent 0c7c344e19
commit f7aa01d74a
3 changed files with 40 additions and 38 deletions
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34
doc/src/fix_bond_react.txt
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@ -24,11 +24,11 @@ common_keyword = {stabilization} :l
{stabilization} values = {no} or {yes} {group-ID} {xmax}
{no} = no reaction site stabilization
{yes} = perform reaction site stabilization
{group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
{group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms
{xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
react = mandatory argument indicating new reaction specification :l
react-ID = user-assigned name for the reaction :l
react-group-ID = only atoms in this group are available for the reaction :l
react-group-ID = only atoms in this group are considered for the reaction :l
Nevery = attempt reaction every this many steps :l
Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
@ -51,7 +51,7 @@ react = mandatory argument indicating new reaction specification :l
molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt
fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
molecule mol1 pre_reacted_rxn1.txt
molecule mol2 post_reacted_rxn1.txt
@ -60,7 +60,7 @@ molecule mol4 post_reacted_rxn2.txt
fix 5 all bond/react stabilization yes nvt_grp .03 &
react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre
[Description:]
@ -104,20 +104,22 @@ during the simulation.
The group-ID set using the {stabilization} keyword can be an existing
static group or a previously-unused group-ID. It cannot be specified
as 'all'. If the group-ID is previously unused, fix bond/react command
creates a "dynamic group"_group.html of this name that is initialized
to include all atoms. If the group-ID is that of an existing static
group, the group is converted into a dynamic group, whose atoms are
limited to those belonging to the original static group. In either
case, this dynamic group-ID should then be used by a subsequent
system-wide time integrator such as nvt, npt, or nve, as shown in the
second example above. The time integration command should be placed
after the fix bond/react command due to the internal dynamic grouping
performed by fix bond/react. By specifying an existing group, you may
thermostat non-reacting parts of your system separately.
as 'all'. If the group-ID is previously unused, the fix bond/react
command creates a "dynamic group"_group.html that is initialized to
include all atoms. If the group-ID is that of an existing static
group, the group is used as the parent group of new,
internally-created dynamic group. In both cases, this new dynamic
group is named by appending '_REACT' to the group-ID, e.g.
nvt_grp_REACT. By specifying an existing group, you may thermostat
constant-topology parts of your system separately. The dynamic group
contains only non-reacting atoms at a given timestep, and therefore
should be used by a subsequent system-wide time integrator such as
nvt, npt, or nve, as shown in the second example above. The time
integration command should be placed after the fix bond/react command
due to the internal dynamic grouping performed by fix bond/react.
NOTE: If the group-ID is an existing static group, react-group-IDs
should also be specified as this group, or a subset.
should also be specified as this static group, or a subset.
NOTE: If the group-ID is previously unused, the internally created
group applies to all atoms in the system, i.e. you should generally

38
src/USER-MISC/fix_bond_react.cpp
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@ -78,6 +78,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
fix1 = NULL;
fix2 = NULL;
fix3 = NULL;
if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: "
"too few arguments");
@ -433,10 +434,8 @@ FixBondReact::~FixBondReact()
if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1);
delete [] id_fix1;
if (custom_exclude_flag == 0) {
if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3);
delete [] id_fix3;
}
if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3);
delete [] id_fix3;
}
if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
@ -512,14 +511,14 @@ void FixBondReact::post_constructor()
ifix = modify->find_fix(id_fix3);
if (ifix == -1) {
char **newarg = new char*[6];
newarg[0] = (char *) "bond_react_stabilization_internal";
newarg[0] = (char *) id_fix3;
newarg[1] = (char *) "all"; // group ID is ignored
newarg[2] = (char *) "property/atom";
newarg[3] = (char *) "i_statted_tags";
newarg[4] = (char *) "ghost";
newarg[5] = (char *) "yes";
modify->add_fix(6,newarg);
fix2 = modify->fix[modify->nfix-1];
fix3 = modify->fix[modify->nfix-1];
delete [] newarg;
}
@ -527,17 +526,17 @@ void FixBondReact::post_constructor()
statted_id = new char[len];
strcpy(statted_id,"statted_tags");
// if static group exists, duplicate it, use duplicate as parent group
// original will be converted into dynamic per-atom property group
if (igroup != -1) {
char **newarg;
newarg = new char*[3];
newarg[0] = (char *) "exclude_PARENT_group";
newarg[1] = (char *) "union";
newarg[2] = exclude_group;
group->assign(3,newarg);
delete [] newarg;
}
// if static group exists, use as parent group
// also, rename dynamic exclude_group by appending '_REACT'
char *exclude_PARENT_group;
int n = strlen(exclude_group) + 1;
exclude_PARENT_group = new char[n];
strcpy(exclude_PARENT_group,exclude_group);
n += strlen("_REACT");
delete [] exclude_group;
exclude_group = new char[n];
strcpy(exclude_group,exclude_PARENT_group);
strcat(exclude_group,"_REACT");
group->find_or_create(exclude_group);
char **newarg;
@ -545,16 +544,17 @@ void FixBondReact::post_constructor()
newarg[0] = exclude_group;
newarg[1] = (char *) "dynamic";
if (igroup == -1) newarg[2] = (char *) "all";
else newarg[2] = (char *) "exclude_PARENT_group";
else newarg[2] = (char *) exclude_PARENT_group;
newarg[3] = (char *) "property";
newarg[4] = (char *) "statted_tags";
group->assign(5,newarg);
delete [] newarg;
delete [] exclude_PARENT_group;
// on to statted_tags (system-wide thermostat)
// intialize per-atom statted_flags to 1
// (only if not already initialized by restart)
if (fix2->restart_reset != 1) {
if (fix3->restart_reset != 1) {
int flag;
int index = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index];

6
src/USER-MISC/fix_bond_react.h
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@ -78,9 +78,9 @@ class FixBondReact : public Fix {
class Molecule *onemol; // pre-reacted molecule template
class Molecule *twomol; // post-reacted molecule template
Fix *fix1; // nve/limit used to relax reaction sites
Fix *fix2; // properties/atom used to indicate 1) indicate relaxing atoms
// 2) system-wide thermostat
// 3) to which 'react' atom belongs
Fix *fix2; // properties/atom used to indicate 1) relaxing atoms
// 2) to which 'react' atom belongs
Fix *fix3; // property/atom used for system-wide thermostat
class RanMars **random;
class NeighList *list;