ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

modernize/correct parsing for Bonus and Bodies sections

Browse Source
This commit is contained in:
Axel Kohlmeyer
2021-12-30 22:58:14 -05:00
parent 8d53cd1e5d
commit e6e9aed385
8 changed files with 58 additions and 62 deletions
Download Patch File Download Diff File Expand all files Collapse all files

63
src/atom.cpp
View File

@ -1198,7 +1198,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
void Atom::data_vels(int n, char *buf, tagint id_offset)
{
int j,m;
tagint tagdata;
char *next;
next = strchr(buf,'\n');
@ -1220,7 +1219,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
if (values.size() != nwords)
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + 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);
@ -1577,7 +1576,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
{
int j,m,tagdata;
int j,m;
char *next;
next = strchr(buf,'\n');
@ -1588,35 +1587,28 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
if (nwords != avec_bonus->size_data_bonus)
error->all(FLERR,"Incorrect bonus data format in data file");
char **values = new char*[nwords];
// loop over lines of bonus atom data
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
if (values.size() != nwords)
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonus section of data file");
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
// since data_bonus() was called with child ptr, and method is virtual
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,values);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -1628,12 +1620,13 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
{
int j,m,nvalues,tagdata,ninteger,ndouble;
int j,m,nvalues,ninteger,ndouble;
int maxint = 0;
int maxdouble = 0;
int *ivalues = nullptr;
double *dvalues = nullptr;
char *next;
if (!unique_tags) unique_tags = new std::set<tagint>;
@ -1642,10 +1635,13 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
// else skip values
for (int i = 0; i < n; i++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
tagdata = utils::tnumeric(FLERR,buf,false,lmp) + id_offset;
buf += strlen(buf)+1;
next = strchr(buf,'\n');
*next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
ninteger = utils::inumeric(FLERR,values[1],false,lmp);
ndouble = utils::inumeric(FLERR,values[2],false,lmp);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
@ -1655,24 +1651,21 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
else
error->one(FLERR,"Duplicate atom ID in Bodies section of data file");
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ninteger = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
if (ninteger < 0)
error->one(FLERR,"Invalid number of integers in Bodies section of data file");
if (ndouble < 0)
error->one(FLERR,"Invalid number of doubles in Bodies section of data file");
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ndouble = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
if ((m = map(tagdata)) >= 0) {
buf = next + 1;
m = map(tagdata);
if (m >= 0) {
if (ninteger > maxint) {
delete [] ivalues;
delete[] ivalues;
maxint = ninteger;
ivalues = new int[maxint];
}
if (ndouble > maxdouble) {
delete [] dvalues;
delete[] dvalues;
maxdouble = ndouble;
dvalues = new double[maxdouble];
}
@ -1703,8 +1696,8 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
}
}
delete [] ivalues;
delete [] dvalues;
delete[] ivalues;
delete[] dvalues;
}
/* ----------------------------------------------------------------------

2
src/atom_vec.h
View File

@ -126,7 +126,7 @@ class AtomVec : protected Pointers {
virtual void data_atom(double *, imageint, const std::vector<std::string> &);
virtual void data_atom_post(int) {}
virtual void data_atom_bonus(int, char **) {}
virtual void data_atom_bonus(int, const std::vector<std::string> &) {}
virtual void data_body(int, int, int, int *, double *) {}
virtual void data_bonds_post(int, int, tagint, tagint, tagint) {}

17
src/atom_vec_ellipsoid.cpp
View File

@ -381,7 +381,7 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
unpack one line from Ellipsoids section of data file
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_atom_bonus(int m, char **values)
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & values)
{
if (ellipsoid[m])
error->one(FLERR,"Assigning ellipsoid parameters to non-ellipsoid atom");
@ -389,17 +389,18 @@ void AtomVecEllipsoid::data_atom_bonus(int m, char **values)
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
shape[0] = 0.5 * utils::numeric(FLERR,values[0],true,lmp);
shape[1] = 0.5 * utils::numeric(FLERR,values[1],true,lmp);
shape[2] = 0.5 * utils::numeric(FLERR,values[2],true,lmp);
int ivalue = 1;
shape[0] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[1] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[2] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0)
error->one(FLERR,"Invalid shape in Ellipsoids section of data file");
double *quat = bonus[nlocal_bonus].quat;
quat[0] = utils::numeric(FLERR,values[3],true,lmp);
quat[1] = utils::numeric(FLERR,values[4],true,lmp);
quat[2] = utils::numeric(FLERR,values[5],true,lmp);
quat[3] = utils::numeric(FLERR,values[6],true,lmp);
quat[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[3] = utils::numeric(FLERR,values[ivalue++],true,lmp);
MathExtra::qnormalize(quat);
// reset ellipsoid mass

2
src/atom_vec_ellipsoid.h
View File

@ -48,7 +48,7 @@ class AtomVecEllipsoid : public AtomVec {
int size_restart_bonus();
int pack_restart_bonus(int, double *);
int unpack_restart_bonus(int, double *);
void data_atom_bonus(int, char **);
void data_atom_bonus(int, const std::vector<std::string> &);
double memory_usage_bonus();
void create_atom_post(int);

11
src/atom_vec_line.cpp
View File

@ -337,16 +337,17 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
unpack one line from Lines section of data file
------------------------------------------------------------------------- */
void AtomVecLine::data_atom_bonus(int m, char **values)
void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (line[m]) error->one(FLERR,"Assigning line parameters to non-line atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double x1 = utils::numeric(FLERR,values[0],true,lmp);
double y1 = utils::numeric(FLERR,values[1],true,lmp);
double x2 = utils::numeric(FLERR,values[2],true,lmp);
double y2 = utils::numeric(FLERR,values[3],true,lmp);
int ivalue = 1;
double x1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double dx = x2 - x1;
double dy = y2 - y1;
double length = sqrt(dx*dx + dy*dy);

2
src/atom_vec_line.h
View File

@ -48,7 +48,7 @@ class AtomVecLine : public AtomVec {
int size_restart_bonus();
int pack_restart_bonus(int, double *);
int unpack_restart_bonus(int, double *);
void data_atom_bonus(int, char **);
void data_atom_bonus(int, const std::vector<std::string> &);
double memory_usage_bonus();
void create_atom_post(int);

21
src/atom_vec_tri.cpp
View File

@ -470,22 +470,23 @@ int AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
unpack one line from Tris section of data file
------------------------------------------------------------------------- */
void AtomVecTri::data_atom_bonus(int m, char **values)
void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (tri[m]) error->one(FLERR,"Assigning tri parameters to non-tri atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double c1[3],c2[3],c3[3];
c1[0] = utils::numeric(FLERR,values[0],true,lmp);
c1[1] = utils::numeric(FLERR,values[1],true,lmp);
c1[2] = utils::numeric(FLERR,values[2],true,lmp);
c2[0] = utils::numeric(FLERR,values[3],true,lmp);
c2[1] = utils::numeric(FLERR,values[4],true,lmp);
c2[2] = utils::numeric(FLERR,values[5],true,lmp);
c3[0] = utils::numeric(FLERR,values[6],true,lmp);
c3[1] = utils::numeric(FLERR,values[7],true,lmp);
c3[2] = utils::numeric(FLERR,values[8],true,lmp);
int ivalue = 1;
c1[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
// check for duplicate points

2
src/atom_vec_tri.h
View File

@ -50,7 +50,7 @@ class AtomVecTri : public AtomVec {
int size_restart_bonus();
int pack_restart_bonus(int, double *);
int unpack_restart_bonus(int, double *);
void data_atom_bonus(int, char **);
void data_atom_bonus(int, const std::vector<std::string> &);
double memory_usage_bonus();
void create_atom_post(int);