changes in package files to match new find_custom() syntax (76725731) · Commits · 郑智淋 / lammps

doc/src/fix_rigid.rst

+11 −10

Original line number	Diff line number	Diff line
		@@ -64,7 +64,7 @@ Syntax
		single args = none
		molecule args = none
		custom args = i_propname or v_varname
		i_propname = an integer property defined via fix property/atom
		i_propname = a custom integer vector defined via fix property/atom
		v_varname = an atom-style or atomfile-style variable
		group args = N groupID1 groupID2 ...
		N = # of groups
		@@ -287,15 +287,16 @@ includes atoms you want to be part of rigid bodies.

		Bodystyle custom is similar to bodystyle molecule except that it
		is more flexible in using other per-atom properties to define the sets
		of atoms that form rigid bodies. An integer vector defined by the
		:doc:`fix property/atom <fix_property_atom>` command can be used. Or an
		:doc:`atom-style or atomfile-style variable <variable>` can be used; the
		floating-point value produced by the variable is rounded to an
		integer. As with bodystyle molecule\ , each set of atoms in the fix
		groups with the same integer value is treated as a different rigid
		body. Since fix property/atom vectors and atom-style variables
		produce values for all atoms, you should be careful to use a fix group
		that only includes atoms you want to be part of rigid bodies.
		of atoms that form rigid bodies. A custom per-atom integer vector
		defined by the :doc:`fix property/atom <fix_property_atom>` command
		can be used. Or an :doc:`atom-style or atomfile-style variable
		<variable>` can be used; the floating-point value produced by the
		variable is rounded to an integer. As with bodystyle molecule\ ,
		each set of atoms in the fix groups with the same integer value is
		treated as a different rigid body. Since fix property/atom custom
		vectors and atom-style variables produce values for all atoms, you
		should be careful to use a fix group that only includes atoms you want
		to be part of rigid bodies.

		.. note::

src/RIGID/fix_rigid.cpp

+4 −8

Original line number	Diff line number	Diff line
		@@ -129,14 +129,10 @@ FixRigid::FixRigid(LAMMPS lmp, int narg, char *arg) :
		// determine whether atom-style variable or atom property is used

		if (strstr(arg[4],"i_") == arg[4]) {
		int is_double=0;
		int custom_index = atom->find_custom(arg[4]+2,is_double);
		if (custom_index == -1)
		error->all(FLERR,"Fix rigid custom requires "
		"previously defined property/atom");
		else if (is_double)
		error->all(FLERR,"Fix rigid custom requires "
		"integer-valued property/atom");
		int flag,cols;
		int custom_index = atom->find_custom(arg[4]+2,flag,cols);
		if (custom_index < 0 \|\| !flag \|\| cols)
		error->all(FLERR,"Fix rigid custom requires custom integer vector");
		int minval = INT_MAX;
		int *value = atom->ivector[custom_index];
		for (i = 0; i < nlocal; i++)

src/RIGID/fix_rigid_small.cpp

+4 −9

Original line number	Diff line number	Diff line
		@@ -113,15 +113,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS lmp, int narg, char *arg) :
		// determine whether atom-style variable or atom property is used

		if (strstr(arg[4],"i_") == arg[4]) {
		int is_double=0;
		int custom_index = atom->find_custom(arg[4]+2,is_double);
		if (custom_index == -1)
		error->all(FLERR,"Fix rigid/small custom requires "
		"previously defined property/atom");
		else if (is_double)
		error->all(FLERR,"Fix rigid/small custom requires "
		"integer-valued property/atom");

		int flag,cols;
		int custom_index = atom->find_custom(arg[4]+2,flag,cols);
		if (custom_index < 0 \|\| !flag \|\| cols)
		error->all(FLERR,"Fix rigid custom requires custom integer vector");
		int minval = INT_MAX;
		int *value = atom->ivector[custom_index];
		for (i = 0; i < nlocal; i++)

src/USER-REACTION/fix_bond_react.cpp

+18 −18

Original line number	Diff line number	Diff line
		@@ -683,8 +683,8 @@ void FixBondReact::post_constructor()
		// initialize per-atom statted_flags to 1
		// (only if not already initialized by restart)
		if (fix3->restart_reset != 1) {
		int flag;
		int index = atom->find_custom("statted_tags",flag);
		int flag,cols;
		int index = atom->find_custom("statted_tags",flag,cols);
		int *i_statted_tags = atom->ivector[index];

		for (int i = 0; i < atom->nlocal; i++)
		@@ -715,8 +715,8 @@ void FixBondReact::post_constructor()

		// initialize per-atom statted_tags to 1
		// need to correct for smooth restarts
		//int flag;
		//int index = atom->find_custom(statted_id,flag);
		//int flag,cols;
		//int index = atom->find_custom(statted_id,flag,cols);
		//int *i_statted_tags = atom->ivector[index];
		//for (int i = 0; i < atom->nlocal; i++)
		// i_statted_tags[i] = 1;
		@@ -1021,8 +1021,8 @@ void FixBondReact::far_partner()
		firstneigh = list->firstneigh;

		// per-atom property indicating if in bond/react master group
		int flag;
		int index1 = atom->find_custom("limit_tags",flag);
		int flag,cols;
		int index1 = atom->find_custom("limit_tags",flag,cols);
		int *i_limit_tags = atom->ivector[index1];

		int i,j;
		@@ -1108,8 +1108,8 @@ void FixBondReact::close_partner()
		int *mask = atom->mask;

		// per-atom property indicating if in bond/react master group
		int flag;
		int index1 = atom->find_custom("limit_tags",flag);
		int flag,cols;
		int index1 = atom->find_custom("limit_tags",flag,cols);
		int *i_limit_tags = atom->ivector[index1];

		// loop over special list
		@@ -1377,8 +1377,8 @@ void FixBondReact::make_a_guess()
		int nfirst_neighs = onemol_nxspecial[pion][0];

		// per-atom property indicating if in bond/react master group
		int flag;
		int index1 = atom->find_custom("limit_tags",flag);
		int flag,cols;
		int index1 = atom->find_custom("limit_tags",flag,cols);
		int *i_limit_tags = atom->ivector[index1];

		if (status == GUESSFAIL && avail_guesses == 0) {
		@@ -2341,17 +2341,17 @@ void FixBondReact::limit_bond(int limit_bond_mode)
		// we must keep our own list of limited atoms
		// this will be a new per-atom property!

		int flag;
		int index1 = atom->find_custom("limit_tags",flag);
		int flag,cols;
		int index1 = atom->find_custom("limit_tags",flag,cols);
		int *i_limit_tags = atom->ivector[index1];

		int *i_statted_tags;
		if (stabilization_flag == 1) {
		int index2 = atom->find_custom(statted_id,flag);
		int index2 = atom->find_custom(statted_id,flag,cols);
		i_statted_tags = atom->ivector[index2];
		}

		int index3 = atom->find_custom("react_tags",flag);
		int index3 = atom->find_custom("react_tags",flag,cols);
		int *i_react_tags = atom->ivector[index3];

		for (int i = 0; i < temp_limit_num; i++) {
		@@ -2374,17 +2374,17 @@ 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 0 (which removes from dynamic group)
		int flag;
		int index1 = atom->find_custom("limit_tags",flag);
		int flag,cols;
		int index1 = atom->find_custom("limit_tags",flag,cols);
		int *i_limit_tags = atom->ivector[index1];

		int *i_statted_tags;
		if (stabilization_flag == 1) {
		int index2 = atom->find_custom(statted_id,flag);
		int index2 = atom->find_custom(statted_id,flag,cols);
		i_statted_tags = atom->ivector[index2];
		}

		int index3 = atom->find_custom("react_tags",flag);
		int index3 = atom->find_custom("react_tags",flag,cols);
		int *i_react_tags = atom->ivector[index3];

		for (int i = 0; i < atom->nlocal; i++) {

src/USER-VTK/dump_vtk.cpp

+59 −33

Original line number	Diff line number	Diff line
		@@ -237,9 +237,15 @@ void DumpVTK::init_style()

		int icustom;
		for (int i = 0; i < ncustom; i++) {
		icustom = atom->find_custom(id_custom[i],flag_custom[i]);
		int flag,cols;
		icustom = atom->find_custom(id_custom[i],flag,cols);
		if (icustom < 0)
		error->all(FLERR,"Could not find custom per-atom property ID");
		error->all(FLERR,"Could not find dump vtk atom property name");
		custom[i] = icustom;
		if (!flag && !cols) custom_flag[i] = IVEC;
		else if (flag && !cols) custom_flag[i] = DVEC;
		else if (!flag && cols) custom_flag[i] = IARRAY;
		else if (flag && cols) custom_flag[i] = DARRAY;
		}

		// set index and check validity of region
		@@ -1511,6 +1517,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
		name[Z] = "z";

		// customize by adding to if statement

		int i;
		for (int iarg = 5; iarg < narg; iarg++) {
		i = iarg-5;
		@@ -1825,49 +1832,67 @@ int DumpVTK::parse_fields(int narg, char **arg)
		name[ATTRIBUTES+i] = suffix;
		delete [] suffix;

		// custom per-atom floating point value = d_ID
		// custom per-atom integer value = i_ID or d_ID

		} else if (strncmp(arg[iarg],"i_",2) == 0 \|\|
		strncmp(arg[iarg],"d_",2) == 0) {
		int which = 0;
		if (arg[iarg][0] == 'd') which = 1;

		} else if (strncmp(arg[iarg],"d_",2) == 0) {
		pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
		vtype[ATTRIBUTES+i] = Dump::DOUBLE;
		if (!which) vtype[ATTRIBUTES+i] = Dump::INT;
		else vtype[ATTRIBUTES+i] = Dump::DOUBLE;

		int n = strlen(arg[iarg]);
		char *suffix = new char[n];
		strcpy(suffix,&arg[iarg][2]);
		argindex[ATTRIBUTES+i] = 0;

		int tmp = -1;
		n = atom->find_custom(suffix,tmp);
		if (n < 0)
		error->all(FLERR,"Could not find custom per-atom property ID");

		if (tmp != 1)
		error->all(FLERR,"Custom per-atom property ID is not floating point");
		int flag,cols;
		n = atom->find_custom(suffix,flag,cols);
		if ((!which && (n < 0 \|\| flag \|\| cols)) \|\|
		(which && (n < 0 \|\| !flag \|\| cols)))
		error->all(FLERR,"Dump vtk per-atom custom vector does not exist");

		field2index[ATTRIBUTES+i] = add_custom(suffix,1);
		field2index[ATTRIBUTES+i] = add_custom(suffix);
		name[ATTRIBUTES+i] = suffix;
		delete [] suffix;

		// custom per-atom integer value = i_ID
		// custom per-atom array = i2_ID or d2_ID, must include bracketed index

		} else if (strncmp(arg[iarg],"i2_",3) == 0 \|\|
		strncmp(arg[iarg],"d2_",3) == 0) {
		int which = 0;
		if (arg[iarg][0] == 'd') which = 1;

		} else if (strncmp(arg[iarg],"i_",2) == 0) {
		pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
		vtype[ATTRIBUTES+i] = Dump::INT;
		if (!which) vtype[ATTRIBUTES+i] = Dump::INT;
		else vtype[ATTRIBUTES+i] = Dump::DOUBLE;

		int n = strlen(arg[iarg]);
		char *suffix = new char[n];
		strcpy(suffix,&arg[iarg][2]);
		argindex[ATTRIBUTES+i] = 0;
		strcpy(suffix,&arg[iarg][3]);

		int tmp = -1;
		n = atom->find_custom(suffix,tmp);
		if (n < 0)
		error->all(FLERR,"Could not find custom per-atom property ID");
		char *ptr = strchr(suffix,'[');
		if (ptr) {
		if (suffix[strlen(suffix)-1] != ']')
		error->all(FLERR,"Invalid attribute in dump custom command");
		suffix[strlen(suffix)-1] = '\0';
		argindex[ATTRIBUTES+i] = utils::inumeric(FLERR,ptr+1,true,lmp);
		*ptr = '\0';
		} else error->all(FLERR,"Dump custom per-atom custom array is not indexed");

		if (tmp != 0)
		error->all(FLERR,"Custom per-atom property ID is not integer");
		int flag,cols;
		n = atom->find_custom(suffix,flag,cols);

		field2index[ATTRIBUTES+i] = add_custom(suffix,0);
		if ((!which && (n < 0 \|\| flag \|\| !cols)) \|\|
		(which && (n < 0 \|\| !flag \|\| !cols)))
		error->all(FLERR,"Dump vtk per-atom custom array does not exist");
		if (argindex[i] <= 0 \|\| argindex[i] > cols)
		error->all(FLERR,
		"Dump vtk per-atom custom array is accessed out-of-range");

		field2index[i] = add_custom(suffix);
		name[ATTRIBUTES+i] = suffix;
		delete [] suffix;

		@@ -2006,27 +2031,28 @@ int DumpVTK::add_variable(char *id)

		/* ----------------------------------------------------------------------
		add custom atom property to list used by dump
		return index of where this property is in list
		return index of where this property is in Atom class custom lists
		if already in list, do not add, just return index, else add to list
		------------------------------------------------------------------------- */

		int DumpVTK::add_custom(char *id, int flag)
		int DumpVTK::add_custom(char *id)
		{
		int icustom;
		for (icustom = 0; icustom < ncustom; icustom++)
		if ((strcmp(id,id_custom[icustom]) == 0)
		&& (flag == flag_custom[icustom])) break;
		if (strcmp(id,id_custom[icustom]) == 0) break;
		if (icustom < ncustom) return icustom;

		id_custom = (char **)
		memory->srealloc(id_custom,(ncustom+1)sizeof(char ),"dump:id_custom");
		flag_custom = (int *)
		memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");

		delete [] custom;
		custom = new int[ncustom+1];
		delete [] custom_flag;
		custom_flag = new int[ncustom+1];

		int n = strlen(id) + 1;
		id_custom[ncustom] = new char[n];
		strcpy(id_custom[ncustom],id);
		flag_custom[ncustom] = flag;

		ncustom++;
		return ncustom-1;

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