forked from lijiext/lammps
Merge pull request #554 from jewettaij/master
Have extra/XXX/per/atom set by keyword to the read_data command
This commit is contained in:
sjplimp
GitHub
commit
b79044d4f6
|
|
@ -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 +9686,23 @@ 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 extra/angle/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger :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 extra/bond/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger :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 extra/dihedral/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger :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 extra/improper/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger :dd
|
||||
|
||||
{Substitution for illegal variable} :dt
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -264,11 +269,11 @@ is different than the default.
|
|||
{angle types} = # of angle types in system
|
||||
{dihedral types} = # of dihedral types in system
|
||||
{improper types} = # of improper types in system
|
||||
{extra bond per atom} = leave space for this many new bonds per atom
|
||||
{extra angle per atom} = leave space for this many new angles per atom
|
||||
{extra dihedral per atom} = leave space for this many new dihedrals per atom
|
||||
{extra improper per atom} = leave space for this many new impropers per atom
|
||||
{extra special per atom} = leave space for this many new special bonds per atom
|
||||
{extra bond per atom} = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword)
|
||||
{extra angle per atom} = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword)
|
||||
{extra dihedral per atom} = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword)
|
||||
{extra improper per atom} = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword)
|
||||
{extra special per atom} = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword)
|
||||
{ellipsoids} = # of ellipsoids in system
|
||||
{lines} = # of line segments in system
|
||||
{triangles} = # of triangles in system
|
||||
|
|
@ -367,25 +372,32 @@ read_data command will generate an error in this case.
|
|||
The "extra bond per atom" setting (angle, dihedral, improper) is only
|
||||
needed if new bonds (angles, dihedrals, impropers) will be added to
|
||||
the system when a simulation runs, e.g. by using the "fix
|
||||
bond/create"_fix_bond_create.html command. This will pre-allocate
|
||||
space in LAMMPS data structures for storing the new bonds (angles,
|
||||
bond/create"_fix_bond_create.html command. Using this header flag
|
||||
is deprecated; please use the {extra/bond/per/atom} keyword (and
|
||||
correspondingly for angles, dihedrals and impropers) in the
|
||||
read_data command instead. Either will pre-allocate space in LAMMPS
|
||||
data structures for storing the new bonds (angles,
|
||||
dihedrals, impropers).
|
||||
|
||||
The "extra special per atom" setting is typically only needed if new
|
||||
bonds/angles/etc will be added to the system, e.g. by using the "fix
|
||||
bond/create"_fix_bond_create.html command. Or if entire new molecules
|
||||
will be added to the system, e.g. by using the "fix
|
||||
deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which
|
||||
will have more special 1-2,1-3,1-4 neighbors than any other molecules
|
||||
defined in the data file. Using this setting will pre-allocate space
|
||||
in the LAMMPS data structures for storing these neighbors. See the
|
||||
will be added to the system, e.g. by using the
|
||||
"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands,
|
||||
which will have more special 1-2,1-3,1-4 neighbors than any other
|
||||
molecules defined in the data file. Using this header flag is
|
||||
deprecated; please use the {extra/special/per/atom} keyword instead.
|
||||
Using this setting will pre-allocate space in the LAMMPS data
|
||||
structures for storing these neighbors. See the
|
||||
"special_bonds"_special_bonds.html and "molecule"_molecule.html doc
|
||||
pages for more discussion of 1-2,1-3,1-4 neighbors.
|
||||
|
||||
NOTE: All of the "extra" settings are only used if they appear in the
|
||||
first data file read; see the description of the {add} keyword above
|
||||
for reading multiple data files. If they appear in later data files,
|
||||
they are ignored.
|
||||
NOTE: All of the "extra" settings are only applied in the first data
|
||||
file read and when no simulation box has yet been created; as soon as
|
||||
the simulation box is created (and read_data implies that), these
|
||||
settings are {locked} and cannot be changed anymore. Please see the
|
||||
description of the {add} keyword above for reading multiple data files.
|
||||
If they appear in later data files, they are ignored.
|
||||
|
||||
The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
|
||||
only used with "atom_style ellipsoid or line or tri or
|
||||
|
|
|
|||
|
|
@ -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");
|
||||
|
|
@ -930,6 +968,7 @@ void ReadData::header(int firstpass)
|
|||
// search line for header keyword and set corresponding variable
|
||||
// customize for new header lines
|
||||
// check for triangles before angles so "triangles" not matched as "angles"
|
||||
int extra_flag_value = 0;
|
||||
|
||||
if (strstr(line,"atoms")) {
|
||||
sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
|
|
@ -991,17 +1030,26 @@ void ReadData::header(int firstpass)
|
|||
atom->nimpropertypes = nimpropertypes + extra_improper_types;
|
||||
|
||||
// these settings only used by first data file
|
||||
// also, these are obsolescent. we parse them to maintain backward
|
||||
// compatibility, but the recommended way is to set them via keywords
|
||||
// in the LAMMPS input file. In case these flags are set in both,
|
||||
// the input and the data file, we use the larger of the two.
|
||||
|
||||
} else if (strstr(line,"extra bond per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_bond_per_atom);
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
atom->extra_bond_per_atom = MAX(atom->extra_bond_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra angle per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_angle_per_atom);
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
atom->extra_angle_per_atom = MAX(atom->extra_angle_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra dihedral per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_dihedral_per_atom);
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
atom->extra_dihedral_per_atom = MAX(atom->extra_dihedral_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra improper per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&atom->extra_improper_per_atom);
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
atom->extra_improper_per_atom = MAX(atom->extra_improper_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra special per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&force->special_extra);
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
force->special_extra = MAX(force->special_extra,extra_flag_value);
|
||||
|
||||
// local copy of box info
|
||||
// so can treat differently for first vs subsequent data files
|
||||
|
|
|
|||
|
|
@ -472,8 +472,8 @@ outside a non-periodic simulation box.
|
|||
|
||||
E: Subsequent read data induced too many bonds per atom
|
||||
|
||||
See the create_box extra/bond/per/atom or read_data "extra bond per
|
||||
atom" header value to set this limit larger.
|
||||
See the extra/bond/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger.
|
||||
|
||||
E: Bonds assigned incorrectly
|
||||
|
||||
|
|
@ -482,8 +482,8 @@ This means there is something invalid about the topology definitions.
|
|||
|
||||
E: Subsequent read data induced too many angles per atom
|
||||
|
||||
See the create_box extra/angle/per/atom or read_data "extra angle per
|
||||
atom" header value to set this limit larger.
|
||||
See the extra/angle/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger.
|
||||
|
||||
E: Angles assigned incorrectly
|
||||
|
||||
|
|
@ -493,8 +493,8 @@ definitions.
|
|||
|
||||
E: Subsequent read data induced too many dihedrals per atom
|
||||
|
||||
See the create_box extra/dihedral/per/atom or read_data "extra
|
||||
dihedral per atom" header value to set this limit larger.
|
||||
See the extra/dihedral/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger.
|
||||
|
||||
E: Dihedrals assigned incorrectly
|
||||
|
||||
|
|
@ -504,8 +504,8 @@ definitions.
|
|||
|
||||
E: Subsequent read data induced too many impropers per atom
|
||||
|
||||
See the create_box extra/improper/per/atom or read_data "extra
|
||||
improper per atom" header value to set this limit larger.
|
||||
See the extra/improper/per/atom keyword for the create_box
|
||||
or the read_data command to set this limit larger.
|
||||
|
||||
E: Impropers assigned incorrectly
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue