bond/react: custom group with stabilization option (5821a5ec) · Commits · 郑智淋 / lammps

doc/src/fix_bond_react.txt

+21 −13

Original line number	Diff line number	Diff line
		@@ -102,19 +102,27 @@ involved in any new reactions. The {xmax} value keyword should
		typically be set to the maximum distance that non-reacting atoms move
		during the simulation.

		The group-ID set using the {stabilization} keyword should be a
		previously unused group-ID. It cannot be specified as 'all'. The fix
		bond/react command creates a "dynamic group"_group.html of this name
		that includes all non-reacting atoms. 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. It is currently
		necessary to place the time integration command after the fix
		bond/react command due to the internal dynamic grouping performed by
		fix bond/react.

		NOTE: The internally created group currently applies to all atoms in
		the system, i.e. you should generally not have a separate thermostat
		which acts on the 'all' group.
		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.

		NOTE: If the group-ID is an existing static group, react-group-IDs
		should also be specified as this 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
		not have a separate thermostat which acts on the 'all' group, or any
		other group.

		The following comments pertain to each {react} argument:

src/USER-MISC/fix_bond_react.cpp

+100 −59

Original line number	Diff line number	Diff line
		@@ -354,6 +354,9 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :

		id_fix1 = NULL;
		id_fix2 = NULL;
		id_fix3 = NULL;
		statted_id = NULL;
		custom_exclude_flag = 0;
		}

		/* ---------------------------------------------------------------------- */
		@@ -426,11 +429,17 @@ FixBondReact::~FixBondReact()
		// check nfix in case all fixes have already been deleted
		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_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
		delete [] id_fix2;

		delete [] statted_id;
		delete [] guess_branch;
		delete [] pioneer_count;
		}
		@@ -461,21 +470,20 @@ void FixBondReact::post_constructor()

		int ifix = modify->find_fix(id_fix2);
		if (ifix == -1) {
		char *newarg = new char[8];
		char *newarg = new char[7];
		newarg[0] = (char *) "bond_react_props_internal";
		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];
		newarg[4] = (char *) "i_react_tags";
		newarg[5] = (char *) "ghost";
		newarg[6] = (char *) "yes";
		modify->add_fix(7,newarg);
		delete [] newarg;
		}

		// create master_group if not already existing
		// NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)
		if (group->find(master_group) == -1) {
		group->find_or_create(master_group);
		char **newarg;
		@@ -489,33 +497,100 @@ void FixBondReact::post_constructor()
		delete [] newarg;
		}

		// on to statted_tags (system-wide thermostat)
		// intialize per-atom statted_flags to 1
		// (only if not already initialized by restart)
		// NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)
		if (fix2->restart_reset != 1) {
		int flag;
		int index = atom->find_custom("statted_tags",flag);
		int *i_statted_tags = atom->ivector[index];
		if (stabilization_flag == 1) {
		int igroup = group->find(exclude_group);
		// create exclude_group if not already existing, or use as parent group if static
		if (igroup == -1 \|\| group->dynamic[igroup] == 0) {
		// create stabilization per-atom property
		len = strlen("bond_react_stabilization_internal") + 1;
		id_fix3 = new char[len];
		strcpy(id_fix3,"bond_react_stabilization_internal");

		ifix = modify->find_fix(id_fix3);
		if (ifix == -1) {
		char *newarg = new char[6];
		newarg[0] = (char *) "bond_react_stabilization_internal";
		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];
		delete [] newarg;
		}

		for (int i = 0; i < atom->nlocal; i++)
		i_statted_tags[i] = 1;
		len = strlen("statted_tags") + 1;
		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 (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";
		if (igroup == -1) newarg[2] = (char *) "all";
		else newarg[2] = (char *) "exclude_PARENT_group";
		newarg[3] = (char *) "property";
		newarg[4] = (char *) "statted_tags";
		group->assign(5,newarg);
		delete [] newarg;

		// 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) {
		int flag;
		int 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;
		}
		} else {
		// sleeping code, for future capabilities
		custom_exclude_flag = 1;
		// first we have to find correct fix group reference
		int n = strlen("GROUP_") + strlen(exclude_group) + 1;
		char *fix_group = new char[n];
		strcpy(fix_group,"GROUP_");
		strcat(fix_group,exclude_group);
		int ifix = modify->find_fix(fix_group);
		Fix *fix = modify->fix[ifix];
		delete [] fix_group;

		// this returns names of corresponding property
		int unused;
		char * idprop;
		idprop = (char *) fix->extract("property",unused);
		if (idprop == NULL)
		error->all(FLERR,"Exclude group must be a per-atom property group");

		len = strlen(idprop) + 1;
		statted_id = new char[len];
		strcpy(statted_id,idprop);

		// intialize per-atom statted_tags to 1
		// need to correct for smooth restarts
		//int flag;
		//int index = atom->find_custom(statted_id,flag);
		//int *i_statted_tags = atom->ivector[index];
		//for (int i = 0; i < atom->nlocal; i++)
		// i_statted_tags[i] = 1;
		}


		// let's create a new nve/limit fix to limit newly reacted atoms
		len = strlen("bond_react_MASTER_nve_limit") + 1;
		@@ -534,40 +609,6 @@ void FixBondReact::post_constructor()
		fix1 = modify->fix[modify->nfix-1];
		delete [] newarg;
		}

		}

		// currently must redefine dynamic groups so they are updated at proper time
		// -> should double check as to why

		int must_redefine_groups = 1;

		if (must_redefine_groups) {
		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;
		}

		if (stabilization_flag == 1) {
		if (must_redefine_groups) {
		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;
		}
		}
		}

		@@ -1812,7 +1853,7 @@ void FixBondReact::limit_bond(int limit_bond_mode)
		int index1 = atom->find_custom("limit_tags",flag);
		int *i_limit_tags = atom->ivector[index1];

		int index2 = atom->find_custom("statted_tags",flag);
		int index2 = atom->find_custom(statted_id,flag);
		int *i_statted_tags = atom->ivector[index2];

		int index3 = atom->find_custom("react_tags",flag);
		@@ -1842,7 +1883,7 @@ void FixBondReact::unlimit_bond()
		int index1 = atom->find_custom("limit_tags",flag);
		int *i_limit_tags = atom->ivector[index1];

		int index2 = atom->find_custom("statted_tags",flag);
		int index2 = atom->find_custom(statted_id,flag);
		int *i_statted_tags = atom->ivector[index2];

		int index3 = atom->find_custom("react_tags",flag);

src/USER-MISC/fix_bond_react.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -57,6 +57,7 @@ class FixBondReact : public Fix {
		double *cutsq,fraction;
		tagint lastcheck;
		int stabilization_flag;
		int custom_exclude_flag;
		int *stabilize_steps_flag;
		int *update_edges_flag;
		int status;
		@@ -88,6 +89,8 @@ class FixBondReact : public Fix {
		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 properties
		char *id_fix3; // id of internally created 'stabilization group' per-atom property fix
		char *statted_id; // name of 'stabilization group' per-atom property
		char *master_group; // group containing relaxing atoms from all fix rxns
		char *exclude_group; // group for system-wide thermostat

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