From a8eb3ff77f173f1358e7b988b05e9d3b8d49cba9 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Wed, 21 Feb 2018 23:20:17 -0700
Subject: [PATCH] consolidate per-atom property fixes into one
---
src/USER-MISC/fix_bond_react.cpp | 217 ++++++++++++-------------------
src/USER-MISC/fix_bond_react.h | 12 +-
2 files changed, 90 insertions(+), 139 deletions(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 45eab537ab..5a4148f6a7 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -63,8 +63,6 @@ Fix(lmp, narg, arg)
{
fix1 = NULL;
fix2 = NULL;
- fix3 = NULL;
- fix4 = NULL;
if (narg < 8) error->all(FLERR,"Illegal fix bond/react command 0.0");
@@ -284,9 +282,6 @@ Fix(lmp, narg, arg)
id_fix1 = NULL;
id_fix2 = NULL;
- id_fix3 = NULL;
- id_fix4 = NULL;
-
}
/* ---------------------------------------------------------------------- */
@@ -354,12 +349,6 @@ FixBondReact::~FixBondReact()
if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
delete [] id_fix2;
- if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3);
- delete [] id_fix3;
-
- if (id_fix4 == NULL && modify->nfix) modify->delete_fix(id_fix4);
- delete [] id_fix4;
-
delete [] guess_branch;
delete [] pioneer_count;
@@ -385,139 +374,103 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group
void FixBondReact::post_constructor()
{
- //let's add the limit_tags per-atom property fix
- //these are recently reacted atoms being relaxed
- int len = strlen("limit_tags") + 1;
- id_fix2 = new char[len];
- strcpy(id_fix2,"limit_tags"); //note: this is purposefully same as property 'name'
+ //let's add the limit_tags per-atom property fix
+ int len = strlen("per_atom_props") + 1;
+ id_fix2 = new char[len];
+ strcpy(id_fix2,"per_atom_props");
+
+ int ifix = modify->find_fix(id_fix2);
+ if (ifix == -1) {
+ char **newarg = new char*[8];
+ newarg[0] = (char *) "per_atom_props";
+ newarg[1] = (char *) "all"; // group ID is ignored
+ newarg[2] = (char *) "property/atom";
+ newarg[3] = (char *) "i_limit_tags";
+ newarg[4] = (char *) "i_statted_tags";
+ newarg[5] = (char *) "i_react_tags";
+ newarg[6] = (char *) "ghost";
+ newarg[7] = (char *) "yes";
+ modify->add_fix(8,newarg);
+ fix2 = modify->fix[modify->nfix-1];
+ delete [] newarg;
+ }
- int ifix = modify->find_fix(id_fix2);
- if (ifix == -1) {
- char **newarg = new char*[6];
- newarg[0] = (char *) "limit_tags";
- newarg[1] = (char *) "all"; // group ID is ignored
- newarg[2] = (char *) "property/atom";
- newarg[3] = (char *) "i_limit_tags";
- newarg[4] = (char *) "ghost";
- newarg[5] = (char *) "yes";
- modify->add_fix(6,newarg);
- fix2 = modify->fix[modify->nfix-1];
- delete [] newarg;
- }
+ // limit_tags: these are recently reacted atoms being relaxed
+ // per-atom properties already initialized to zero (not in group)
+ // let's do it anyway for clarity
+ int flag;
+ int index = atom->find_custom("limit_tags",flag); //here's where error would happen
+ int *i_limit_tags = atom->ivector[index];
- // per-atom properties already initialized to zero (not in group)
- // let's do it anyway for clarity
- int flag;
- int index = atom->find_custom(id_fix2,flag);
- int *i_limit_tags = atom->ivector[index];
+ for (int i = 0; i < atom->nlocal; i++)
+ i_limit_tags[i] = 0;
- for (int i = 0; i < atom->nlocal; i++)
- i_limit_tags[i] = 0;
+ // create master_group if not already existing
+ if (group->find(master_group) == -1) {
+ group->find_or_create(master_group);
+ char **newarg;
+ newarg = new char*[5];
+ newarg[0] = master_group;
+ newarg[1] = (char *) "dynamic";
+ newarg[2] = (char *) "all";
+ newarg[3] = (char *) "property";
+ newarg[4] = (char *) "limit_tags";
+ group->assign(5,newarg);
+ delete [] newarg;
+ }
+
+ // on to statted_tags (system-wide thermostat)
+ // intialize per-atom statted_flags to 1
+ index = atom->find_custom("statted_tags",flag);
+ int *i_statted_tags = atom->ivector[index];
+
+ for (int i = 0; i < atom->nlocal; i++)
+ i_statted_tags[i] = 1;
- // create master_group if not already existing
- if (group->find(master_group) == -1) {
- group->find_or_create(master_group);
+ if (stabilization_flag == 1) {
+ // create exclude_group if not already existing
+ if (group->find(exclude_group) == -1) {
+ group->find_or_create(exclude_group);
char **newarg;
newarg = new char*[5];
- newarg[0] = master_group;
+ newarg[0] = exclude_group;
newarg[1] = (char *) "dynamic";
newarg[2] = (char *) "all";
newarg[3] = (char *) "property";
- newarg[4] = (char *) "limit_tags";
+ newarg[4] = (char *) "statted_tags";
group->assign(5,newarg);
delete [] newarg;
}
- //let's add the statted_tags per-atom property fix
- //this are atoms subjec to the system-wide thermostat
- len = strlen("statted_tags") + 1;
- id_fix3 = new char[len];
- strcpy(id_fix3,"statted_tags"); //note: this is purposefully same as property 'name'
+ // let's create a new nve/limit fix to limit newly reacted atoms
+ len = strlen("bond_react_MASTER_nve_limit") + 1;
+ id_fix1 = new char[len];
+ strcpy(id_fix1,"bond_react_MASTER_nve_limit");
+
+ ifix = modify->find_fix(id_fix1);
- ifix = modify->find_fix(id_fix3);
if (ifix == -1) {
- char **newarg = new char*[6];
- newarg[0] = (char *) "statted_tags";
- 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);
- fix3 = modify->fix[modify->nfix-1];
+ char **newarg = new char*[4];
+ newarg[0] = id_fix1;
+ newarg[1] = master_group;
+ newarg[2] = (char *) "nve/limit";
+ newarg[3] = nve_limit_xmax;
+ modify->add_fix(4,newarg);
+ fix1 = modify->fix[modify->nfix-1];
delete [] newarg;
}
- //intialize per-atom statted_flags to 1
- index = atom->find_custom(id_fix3,flag);
- int *i_statted_tags = atom->ivector[index];
-
- for (int i = 0; i < atom->nlocal; i++)
- i_statted_tags[i] = 1;
-
- if (stabilization_flag == 1) {
-
- // create exclude_group if not already existing
- if (group->find(exclude_group) == -1) {
- group->find_or_create(exclude_group);
- char **newarg;
- newarg = new char*[5];
- newarg[0] = exclude_group;
- newarg[1] = (char *) "dynamic";
- newarg[2] = (char *) "all";
- newarg[3] = (char *) "property";
- newarg[4] = (char *) "statted_tags";
- group->assign(5,newarg);
- delete [] newarg;
- }
-
- // let's create a new nve/limit fix to limit newly reacted atoms
- len = strlen("bond_react_MASTER_nve_limit") + 1;
- id_fix1 = new char[len];
- strcpy(id_fix1,"bond_react_MASTER_nve_limit");
-
- ifix = modify->find_fix(id_fix1);
-
- if (ifix == -1) {
- char **newarg = new char*[4];
- newarg[0] = id_fix1;
- newarg[1] = master_group;
- newarg[2] = (char *) "nve/limit";
- newarg[3] = nve_limit_xmax;
- modify->add_fix(4,newarg);
- fix1 = modify->fix[modify->nfix-1];
- delete [] newarg;
- }
-
- }
+ }
- //let's add the react_tags per-atom property fix
- //this per-atom property is the ID of the 'react' argument which recently caused atom to react
- //so that atoms which wander between processors may be released to global thermostat at the proper time
- len = strlen("react_tags") + 1;
- id_fix4 = new char[len];
- strcpy(id_fix4,"react_tags"); //note: this is purposefully same as property 'name'
-
- ifix = modify->find_fix(id_fix4);
- if (ifix == -1) { //ifix
- char **newarg = new char*[6];
- newarg[0] = (char *) "react_tags";
- newarg[1] = (char *) "all"; // group ID is ignored
- newarg[2] = (char *) "property/atom";
- newarg[3] = (char *) "i_react_tags";
- newarg[4] = (char *) "ghost";
- newarg[5] = (char *) "yes";
- modify->add_fix(6,newarg);
- fix4 = modify->fix[modify->nfix-1];
- delete [] newarg;
- }
+ //react_tags: this per-atom property is the ID of the 'react' argument which recently caused atom to react
+ //so that atoms which wander between processors may be released to global thermostat at the proper time
- //per-atom values initalized to 0
- index = atom->find_custom(id_fix4,flag);
- int *i_react_tags = atom->ivector[index];
+ //per-atom values initalized to 0
+ index = atom->find_custom("react_tags",flag);
+ int *i_react_tags = atom->ivector[index];
- for (int i = 0; i < atom->nlocal; i++)
- i_react_tags[i] = 0;
+ for (int i = 0; i < atom->nlocal; i++)
+ i_react_tags[i] = 0;
// currently must redefine dynamic groups so they are updated at proper time
// -> should double check as to why
@@ -679,7 +632,7 @@ void FixBondReact::post_integrate()
// per-atom property indicating if in bond/react master group
int flag;
- int index1 = atom->find_custom(id_fix2,flag);
+ int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
int i,j;
@@ -1077,7 +1030,7 @@ void FixBondReact::make_a_guess()
// per-atom property indicating if in bond/react master group
int flag;
- int index1 = atom->find_custom(id_fix2,flag);
+ int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
if (status == GUESSFAIL && avail_guesses == 0) {
@@ -1696,13 +1649,13 @@ void FixBondReact::limit_bond(int limit_bond_mode)
// this will be a new per-atom property!
int flag;
- int index1 = atom->find_custom(id_fix2,flag);
+ int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
- int index2 = atom->find_custom(id_fix3,flag);
+ int index2 = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index2];
- int index3 = atom->find_custom(id_fix4,flag);
+ int index3 = atom->find_custom("react_tags",flag);
int *i_react_tags = atom->ivector[index3];
for (int i = 0; i < temp_limit_num; i++) {
@@ -1725,15 +1678,15 @@ void FixBondReact::unlimit_bond()
{
//let's now unlimit in terms of i_limit_tags
//we just run through all nlocal, looking for > limit_duration
- //then we return i_limit_tag to -1 (which removes from dynamic group)
+ //then we return i_limit_tag to 0 (which removes from dynamic group)
int flag;
- int index1 = atom->find_custom(id_fix2,flag);
+ int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
- int index2 = atom->find_custom(id_fix3,flag); // statted_tags
+ int index2 = atom->find_custom("statted_tags",flag);
int *i_statted_tags = atom->ivector[index2];
- int index3 = atom->find_custom(id_fix4,flag); // statted_tags
+ int index3 = atom->find_custom("react_tags",flag);
int *i_react_tags = atom->ivector[index3];
int num2unlimit = 0;
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index 17856177bc..a0f52c0288 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -75,10 +75,10 @@ class FixBondReact : public Fix {
class Molecule *onemol; // pre-reacted molecule template
class Molecule *twomol; // post-reacted molecule template
- Fix *fix1; // used to relax reaction sites
- Fix *fix2; // used to indicate relaxing atoms
- Fix *fix3; // used to indicate system-wide thermostat
- Fix *fix4; // indicates to which 'react' atom belongs
+ 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
class RanMars **random;
class NeighList *list;
@@ -86,9 +86,7 @@ class FixBondReact : public Fix {
int *limit_duration; // indicates how long to relax
char *nve_limit_xmax; // indicates max distance allowed to move when relaxing
char *id_fix1; // id of internally created fix nve/limit
- char *id_fix2; // id of internally created fix per-atom property (recently reacted)
- char *id_fix3; // id of internally created fix per-atom property (system-wide thermostat)
- char *id_fix4; // id of internally created fix per-atom property (ID of 'react' argument)
+ char *id_fix2; // id of internally created fix per-atom properties
char *master_group; // group containing relaxing atoms from all fix rxns
char *exclude_group; // group for system-wide thermostat
--
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