new keywords for read_data: extra/X/per/atoms + changes to docs (38075455) · Commits · 郑智淋 / lammps

doc/src/Section_errors.txt

+25 −20

Original line number	Diff line number	Diff line
		@@ -4696,9 +4696,9 @@ Self-explanatory. :dd

		{Fix bond/create induced too many angles/dihedrals/impropers per atom} :dt

		See the read_data command for info on setting the "extra angle per
		atom", etc header values to allow for additional angles, etc to be
		formed. :dd
		See the read_data command for info on using the "extra/angle/per/atom",
		(or dihedral, improper) keywords to allow for additional
		angles, dihedrals, and impropers to be formed. :dd

		{Fix bond/create needs ghost atoms from further away} :dt

		@@ -7876,18 +7876,20 @@ See the setting for tagint in the src/lmptype.h file. :dd

		{New bond exceeded bonds per atom in create_bonds} :dt

		See the read_data command for info on setting the "extra bond per
		atom" header value to allow for additional bonds to be formed. :dd
		See the read_data command for info on using the "extra/bond/per/atom"
		keyword to allow for additional bonds to be formed

		{New bond exceeded bonds per atom in fix bond/create} :dt

		See the read_data command for info on setting the "extra bond per
		atom" header value to allow for additional bonds to be formed. :dd
		See the read_data command for info on using the "extra/bond/per/atom"
		keyword to allow for additional bonds to be formed :dd

		{New bond exceeded special list size in fix bond/create} :dt

		See the special_bonds extra command for info on how to leave space in
		the special bonds list to allow for additional bonds to be formed. :dd
		See the "special_bonds extra" command
		(or the "read_data extra/special/per/atom" command)
		for info on how to leave space in the special bonds
		list to allow for additional bonds to be formed. :dd

		{Newton bond change after simulation box is defined} :dt

		@@ -9664,9 +9666,10 @@ you are running. :dd

		{Special list size exceeded in fix bond/create} :dt

		See the read_data command for info on setting the "extra special per
		atom" header value to allow for additional special values to be
		stored. :dd
		See the special_bonds extra command
		(or the read_data extra/special/per/atom command)
		for info on how to leave space in the special bonds
		list to allow for additional bonds to be formed. :dd

		{Specified processors != physical processors} :dt

		@@ -9683,23 +9686,25 @@ Self-explanatory. :dd

		{Subsequent read data induced too many angles per atom} :dt

		See the create_box extra/angle/per/atom or read_data "extra angle per
		atom" header value to set this limit larger. :dd
		See the read_data or create_box commands for info on using the
		"extra/angle/per/atom" keyword to allow for additional angles to be formed :dd

		{Subsequent read data induced too many bonds per atom} :dt

		See the create_box extra/bond/per/atom or read_data "extra bond per
		atom" header value to set this limit larger. :dd
		See the read_data or create_box commands for info on using the
		"extra/bond/per/atom" keyword to allow for additional bonds to be formed :dd

		{Subsequent read data induced too many dihedrals per atom} :dt

		See the create_box extra/dihedral/per/atom or read_data "extra
		dihedral per atom" header value to set this limit larger. :dd
		See the read_data or create_box commands for info on using the
		"extra/dihedral/per/atom" keyword to allow for additional
		dihedrals to be formed :dd

		{Subsequent read data induced too many impropers per atom} :dt

		See the create_box extra/improper/per/atom or read_data "extra
		improper per atom" header value to set this limit larger. :dd
		See the read_data or create_box commands for info on using the
		"extra/improper/per/atom" keyword to allow for additional
		impropers to be formed :dd

		{Substitution for illegal variable} :dt

doc/src/read_data.txt

+5 −0

Original line number	Diff line number	Diff line
		@@ -32,6 +32,11 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type
		{extra/angle/types} arg = # of extra angle types
		{extra/dihedral/types} arg = # of extra dihedral types
		{extra/improper/types} arg = # of extra improper types
		{extra/bond/per/atom} arg = leave space for this many new bonds per atom
		{extra/angle/per/atom} arg = leave space for this many new angles per atom
		{extra/dihedral/per/atom} arg = leave space for this many new dihedrals per atom
		{extra/improper/per/atom} arg = leave space for this many new impropers per atom
		{extra/special/per/atom} arg = leave space for extra 1-2,1-3,1-4 interactions per atom
		{group} args = groupID
		groupID = add atoms in data file to this group
		{nocoeff} = ignore force field parameters

src/read_data.cpp

+40 −2

Original line number	Diff line number	Diff line
		@@ -211,13 +211,51 @@ void ReadData::command(int narg, char **arg)
		if (extra_improper_types < 0)
		error->all(FLERR,"Illegal read_data command");
		iarg += 2;

		} else if (strcmp(arg[iarg],"extra/bond/per/atom") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
		if (! atom->molecular)
		error->all(FLERR,"No bonds allowed with this atom style");
		atom->extra_bond_per_atom = force->inumeric(FLERR,arg[iarg+1]);
		if (atom->extra_bond_per_atom < 0)
		error->all(FLERR,"Illegal read_data command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"extra/angle/per/atom") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
		if (! atom->molecular)
		error->all(FLERR,"No angles allowed with this atom style");
		atom->extra_angle_per_atom = force->inumeric(FLERR,arg[iarg+1]);
		if (atom->extra_angle_per_atom < 0)
		error->all(FLERR,"Illegal read_data command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"extra/dihedral/per/atom") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
		if (! atom->molecular)
		error->all(FLERR,"No dihedrals allowed with this atom style");
		atom->extra_dihedral_per_atom = force->inumeric(FLERR,arg[iarg+1]);
		if (atom->extra_dihedral_per_atom < 0)
		error->all(FLERR,"Illegal read_data command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"extra/improper/per/atom") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
		if (! atom->molecular)
		error->all(FLERR,"No impropers allowed with this atom style");
		atom->extra_improper_per_atom = force->inumeric(FLERR,arg[iarg+1]);
		if (atom->extra_improper_per_atom < 0)
		error->all(FLERR,"Illegal read_data command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"extra/special/per/atom") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
		if (! atom->molecular)
		error->all(FLERR,"No bonded interactions allowed with this atom style");
		force->special_extra = force->inumeric(FLERR,arg[iarg+1]);
		if (force->special_extra < 0)
		error->all(FLERR,"Illegal read_data command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"group") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
		int igroup = group->find_or_create(arg[iarg+1]);
		groupbit = group->bitmask[igroup];
		iarg += 2;

		} else if (strcmp(arg[iarg],"fix") == 0) {
		if (iarg+4 > narg)
		error->all(FLERR,"Illegal read_data command");

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