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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13643 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-07-17 23:20:48 +00:00
parent 6d665f1860
commit 1ebb654b4d
6 changed files with 475 additions and 180 deletions
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94
src/atom.cpp
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@ -516,7 +516,7 @@ void Atom::modify_params(int narg, char **arg)
error->all(FLERR,
"Atom_modify id command after simulation box is defined");
if (strcmp(arg[iarg+1],"yes") == 0) tag_enable = 1;
else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 2;
else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 0;
else error->all(FLERR,"Illegal atom_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"map") == 0) {
@ -559,9 +559,11 @@ void Atom::modify_params(int narg, char **arg)
check that atom IDs are valid
error if any atom ID < 0 or atom ID = MAXTAGINT
if any atom ID > 0, error if any atom ID == 0
if any atom ID > 0, error if tag_enable = 0
if all atom IDs = 0, tag_enable must be 0
OK if atom IDs > natoms
NOTE: not checking that atom IDs are unique
if max atom IDs < natoms, must be duplicates
OK if max atom IDs > natoms
NOTE: not fully checking that atom IDs are unique
------------------------------------------------------------------------- */
void Atom::tag_check()
@ -578,12 +580,16 @@ void Atom::tag_check()
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (minall < 0) error->all(FLERR,"Atom ID is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"Atom ID is too big");
if (maxall > 0 && minall == 0) error->all(FLERR,"Atom ID is zero");
// this last message is wrong
if (maxall == 0 && tag_enable && natoms)
error->all(FLERR,"Not all atom IDs are 0");
if (minall < 0) error->all(FLERR,"One or more Atom IDs is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs is too big");
if (maxall > 0 && minall == 0)
error->all(FLERR,"One or more atom IDs is zero");
if (maxall > 0 && tag_enable == 0)
error->all(FLERR,"Non-zero atom IDs with atom_modify id = no");
if (maxall == 0 && natoms && tag_enable)
error->all(FLERR,"All atom IDs = 0 but atom_modify id = yes");
if (tag_enable && maxall < natoms)
error->all(FLERR,"Duplicate atom IDs exist");
}
/* ----------------------------------------------------------------------
@ -725,7 +731,8 @@ void Atom::deallocate_topology()
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf)
void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
int shiftflag, double *shift)
{
int m,xptr,iptr;
imageint imagedata;
@ -833,6 +840,12 @@ void Atom::data_atoms(int n, char *buf)
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
if (shiftflag) {
xdata[0] += shift[0];
xdata[1] += shift[1];
xdata[2] += shift[2];
}
domain->remap(xdata,imagedata);
if (triclinic) {
domain->x2lamda(xdata,lamda);
@ -841,8 +854,15 @@ void Atom::data_atoms(int n, char *buf)
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
avec->data_atom(xdata,imagedata,values);
if (id_offset) tag[nlocal-1] += id_offset;
if (type_offset) {
type[nlocal-1] += type_offset;
if (type[nlocal-1] > ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
}
}
buf = next + 1;
}
@ -856,7 +876,7 @@ void Atom::data_atoms(int n, char *buf)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_vels(int n, char *buf)
void Atom::data_vels(int n, char *buf, tagint id_offset)
{
int j,m;
tagint tagdata;
@ -883,7 +903,7 @@ void Atom::data_vels(int n, char *buf)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = ATOTAGINT(values[0]);
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
@ -901,7 +921,7 @@ void Atom::data_vels(int n, char *buf)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf, int *count)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2;
@ -913,6 +933,11 @@ void Atom::data_bonds(int n, char *buf, int *count)
*next = '\0';
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
@ -947,7 +972,7 @@ void Atom::data_bonds(int n, char *buf, int *count)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf, int *count)
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3;
@ -959,6 +984,12 @@ void Atom::data_angles(int n, char *buf, int *count)
*next = '\0';
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
@ -1008,7 +1039,7 @@ void Atom::data_angles(int n, char *buf, int *count)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf, int *count)
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3,atom4;
@ -1021,6 +1052,13 @@ void Atom::data_dihedrals(int n, char *buf, int *count)
sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
@ -1086,7 +1124,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf, int *count)
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3,atom4;
@ -1099,6 +1137,13 @@ void Atom::data_impropers(int n, char *buf, int *count)
sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
@ -1163,7 +1208,7 @@ void Atom::data_impropers(int n, char *buf, int *count)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
{
int j,m,tagdata;
char *next;
@ -1189,7 +1234,7 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = ATOTAGINT(values[0]);
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonus section of data file");
@ -1210,7 +1255,8 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
tagint id_offset)
{
int j,m,tagdata,ninteger,ndouble;
@ -1222,8 +1268,8 @@ void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f"));
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f"));
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f")) + id_offset;
ninteger = atoi(strtok(NULL," \t\n\r\f"));
ndouble = atoi(strtok(NULL," \t\n\r\f"));
@ -1260,9 +1306,10 @@ void Atom::allocate_type_arrays()
/* ----------------------------------------------------------------------
set a mass and flag it as set
called from reading of data file
type_offset may be used when reading multiple data files
------------------------------------------------------------------------- */
void Atom::set_mass(const char *str)
void Atom::set_mass(const char *str, int type_offset)
{
if (mass == NULL) error->all(FLERR,"Cannot set mass for this atom style");
@ -1270,6 +1317,7 @@ void Atom::set_mass(const char *str)
double mass_one;
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all(FLERR,"Invalid mass line in data file");
itype += type_offset;
if (itype < 1 || itype > ntypes)
error->all(FLERR,"Invalid type for mass set");