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Merge pull request #3072 from akohlmey/refactor-data-file-parsing

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Modernize parsing of topology data sections of data files
This commit is contained in:
Axel Kohlmeyer
2022-01-04 13:21:14 -05:00
committed by GitHub
parent 8ae68d71dd ede7787741
commit 12420181e1
40 changed files with 508 additions and 338 deletions
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31
doc/src/Developer_utils.rst
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@ -56,11 +56,11 @@ String to number conversions with validity check
These functions should be used to convert strings to numbers. They are
are strongly preferred over C library calls like ``atoi()`` or
``atof()`` since they check if the **entire** provided string is a valid
``atof()`` since they check if the **entire** string is a valid
(floating-point or integer) number, and will error out instead of
silently returning the result of a partial conversion or zero in cases
where the string is not a valid number. This behavior allows to more
easily detect typos or issues when processing input files.
where the string is not a valid number. This behavior improves
detecting typos or issues when processing input files.
Similarly the :cpp:func:`logical() <LAMMPS_NS::utils::logical>` function
will convert a string into a boolean and will only accept certain words.
@ -76,19 +76,34 @@ strings for compliance without conversion.
----------
.. doxygenfunction:: numeric
.. doxygenfunction:: numeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: inumeric
.. doxygenfunction:: numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: bnumeric
.. doxygenfunction:: inumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric
.. doxygenfunction:: inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical
.. doxygenfunction:: bnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide

2
doc/src/Developer_write.rst
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@ -55,7 +55,7 @@ of each timestep. First of all, implement a constructor:
if (narg < 4)
error->all(FLERR,"Illegal fix print/vel command");
nevery = force->inumeric(FLERR,arg[3]);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0)
error->all(FLERR,"Illegal fix print/vel command");
}

7
src/KOKKOS/atom_vec_angle_kokkos.cpp
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@ -1630,7 +1630,7 @@ void AtomVecAngleKokkos::create_atom(int itype, double *coord)
------------------------------------------------------------------------- */
void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -1663,9 +1663,10 @@ void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp);
h_num_bond(nlocal) = 0;
h_num_angle(nlocal) = 0;
return 1;

4
src/KOKKOS/atom_vec_angle_kokkos.h
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@ -51,8 +51,8 @@ class AtomVecAngleKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

4
src/KOKKOS/atom_vec_atomic_kokkos.cpp
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@ -821,8 +821,8 @@ void AtomVecAtomicKokkos::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecAtomicKokkos::data_atom(double *coord, tagint imagetmp,
char **values)
void AtomVecAtomicKokkos::data_atom(double *coord, imageint imagetmp,
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);

2
src/KOKKOS/atom_vec_atomic_kokkos.h
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@ -44,7 +44,7 @@ class AtomVecAtomicKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
void pack_data(double **);
void write_data(FILE *, int, double **);
double memory_usage();

7
src/KOKKOS/atom_vec_bond_kokkos.cpp
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@ -1056,7 +1056,7 @@ void AtomVecBondKokkos::create_atom(int itype, double *coord)
------------------------------------------------------------------------- */
void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
const std::vector<std::string> &values)
{
int nlocal = atomKK->nlocal;
if (nlocal == nmax) grow(0);
@ -1088,9 +1088,10 @@ void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecBondKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecBondKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp);
h_num_bond(nlocal) = 0;
return 1;
}

4
src/KOKKOS/atom_vec_bond_kokkos.h
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@ -45,8 +45,8 @@ class AtomVecBondKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

7
src/KOKKOS/atom_vec_charge_kokkos.cpp
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@ -955,7 +955,7 @@ void AtomVecChargeKokkos::create_atom(int itype, double *coord)
------------------------------------------------------------------------- */
void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -987,9 +987,10 @@ void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_q[nlocal] = utils::numeric(FLERR,values[0],true,lmp);
h_q[nlocal] = utils::numeric(FLERR,values[offset],true,lmp);
return 1;
}

4
src/KOKKOS/atom_vec_charge_kokkos.h
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@ -46,8 +46,8 @@ class AtomVecChargeKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int , char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int , const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

9
src/KOKKOS/atom_vec_dpd_kokkos.cpp
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@ -1716,8 +1716,8 @@ void AtomVecDPDKokkos::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp,
char **values)
void AtomVecDPDKokkos::data_atom(double *coord, imageint imagetmp,
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -1759,9 +1759,10 @@ void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecDPDKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecDPDKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_dpdTheta(nlocal) = utils::numeric(FLERR,values[0],true,lmp);
h_dpdTheta(nlocal) = utils::numeric(FLERR,values[offset],true,lmp);
atomKK->modified(Host,DPDTHETA_MASK);

4
src/KOKKOS/atom_vec_dpd_kokkos.h
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@ -54,8 +54,8 @@ class AtomVecDPDKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

9
src/KOKKOS/atom_vec_full_kokkos.cpp
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@ -1488,7 +1488,7 @@ void AtomVecFullKokkos::create_atom(int itype, double *coord)
------------------------------------------------------------------------- */
void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -1525,10 +1525,11 @@ void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecFullKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecFullKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
h_q(nlocal) = utils::numeric(FLERR,values[1],true,lmp);
h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp);
h_q(nlocal) = utils::numeric(FLERR,values[offset+1],true,lmp);
h_num_bond(nlocal) = 0;
h_num_angle(nlocal) = 0;
h_num_dihedral(nlocal) = 0;

4
src/KOKKOS/atom_vec_full_kokkos.h
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@ -45,8 +45,8 @@ class AtomVecFullKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

17
src/KOKKOS/atom_vec_hybrid_kokkos.cpp
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@ -970,7 +970,8 @@ void AtomVecHybridKokkos::create_atom(int itype, double *coord)
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **values)
void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp,
const std::vector<std::string> &values)
{
atomKK->sync(Host,X_MASK|TAG_MASK|TYPE_MASK|IMAGE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
@ -1009,7 +1010,7 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **val
int m = 5;
for (int k = 0; k < nstyles; k++)
m += styles[k]->data_atom_hybrid(nlocal,&values[m]);
m += styles[k]->data_atom_hybrid(nlocal,values,m);
atom->nlocal++;
}
@ -1018,21 +1019,21 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **val
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::data_vel(int m, char **values)
void AtomVecHybridKokkos::data_vel(int m, const std::vector<std::string> &values)
{
atomKK->sync(Host,V_MASK);
h_v(m,0) = utils::numeric(FLERR,values[0],true,lmp);
h_v(m,1) = utils::numeric(FLERR,values[1],true,lmp);
h_v(m,2) = utils::numeric(FLERR,values[2],true,lmp);
int ivalue = 1;
h_v(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_v(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_v(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp);
atomKK->modified(Host,V_MASK);
// each sub-style parses sub-style specific values
int n = 3;
for (int k = 0; k < nstyles; k++)
n += styles[k]->data_vel_hybrid(m,&values[n]);
ivalue += styles[k]->data_vel_hybrid(m,values,ivalue);
}
/* ----------------------------------------------------------------------

6
src/KOKKOS/atom_vec_hybrid_kokkos.h
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@ -57,9 +57,9 @@ class AtomVecHybridKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **) {return 0;}
void data_vel(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int) {return 0;}
void data_vel(int, const std::vector<std::string> &);
void pack_data(double **);
void write_data(FILE *, int, double **);
void pack_vel(double **);

9
src/KOKKOS/atom_vec_kokkos.cpp
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@ -1016,12 +1016,13 @@ void AtomVecKokkos::unpack_reverse(int n, int *list, double *buf)
* unpack one line from Velocities section of data file
* ------------------------------------------------------------------------- */
void AtomVecKokkos::data_vel(int m, char **values)
void AtomVecKokkos::data_vel(int m, const std::vector<std::string> &values)
{
double **v = atom->v;
v[m][0] = utils::numeric(FLERR,values[0],true,lmp);
v[m][1] = utils::numeric(FLERR,values[1],true,lmp);
v[m][2] = utils::numeric(FLERR,values[2],true,lmp);
int ivalue = 1;
v[m][0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
v[m][1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
v[m][2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
atomKK->modified(Host,V_MASK);
}

2
src/KOKKOS/atom_vec_kokkos.h
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@ -44,7 +44,7 @@ class AtomVecKokkos : public AtomVec {
virtual void unpack_comm_vel(int, int, double *);
virtual int pack_reverse(int, int, double *);
virtual void unpack_reverse(int, int *, double *);
virtual void data_vel(int, char **);
virtual void data_vel(int, const std::vector<std::string> &);
virtual void pack_vel(double **);
virtual void write_vel(FILE *, int, double **);

7
src/KOKKOS/atom_vec_molecular_kokkos.cpp
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@ -1889,7 +1889,7 @@ void AtomVecMolecularKokkos::create_atom(int itype, double *coord)
------------------------------------------------------------------------- */
void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -1924,9 +1924,10 @@ void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecMolecularKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecMolecularKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp);
h_num_bond(nlocal) = 0;
h_num_angle(nlocal) = 0;
h_num_dihedral(nlocal) = 0;

4
src/KOKKOS/atom_vec_molecular_kokkos.h
View File

@ -51,8 +51,8 @@ class AtomVecMolecularKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

34
src/KOKKOS/atom_vec_sphere_kokkos.cpp
View File

@ -2543,7 +2543,8 @@ void AtomVecSphereKokkos::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **values)
void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp,
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -2590,13 +2591,14 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
radius[nlocal] = 0.5 * utils::numeric(FLERR,values[0],true,lmp);
radius[nlocal] = 0.5 * utils::numeric(FLERR,values[offset],true,lmp);
if (radius[nlocal] < 0.0)
error->one(FLERR,"Invalid radius in Atoms section of data file");
double density = utils::numeric(FLERR,values[1],true,lmp);
double density = utils::numeric(FLERR,values[offset+1],true,lmp);
if (density <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
@ -2615,15 +2617,16 @@ int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values)
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecSphereKokkos::data_vel(int m, char **values)
void AtomVecSphereKokkos::data_vel(int m, const std::vector<std::string> &values)
{
int ivalue = 1;
atomKK->sync(Host,V_MASK|OMEGA_MASK);
h_v(m,0) = utils::numeric(FLERR,values[0],true,lmp);
h_v(m,1) = utils::numeric(FLERR,values[1],true,lmp);
h_v(m,2) = utils::numeric(FLERR,values[2],true,lmp);
h_omega(m,0) = utils::numeric(FLERR,values[3],true,lmp);
h_omega(m,1) = utils::numeric(FLERR,values[4],true,lmp);
h_omega(m,2) = utils::numeric(FLERR,values[5],true,lmp);
h_v(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_v(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_v(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_omega(m,0) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_omega(m,1) = utils::numeric(FLERR,values[ivalue++],true,lmp);
h_omega(m,2) = utils::numeric(FLERR,values[ivalue++],true,lmp);
atomKK->modified(Host,V_MASK|OMEGA_MASK);
}
@ -2631,12 +2634,13 @@ void AtomVecSphereKokkos::data_vel(int m, char **values)
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecSphereKokkos::data_vel_hybrid(int m, char **values)
int AtomVecSphereKokkos::data_vel_hybrid(int m, const std::vector<std::string> &values,
int offset)
{
atomKK->sync(Host,OMEGA_MASK);
omega[m][0] = utils::numeric(FLERR,values[0],true,lmp);
omega[m][1] = utils::numeric(FLERR,values[1],true,lmp);
omega[m][2] = utils::numeric(FLERR,values[2],true,lmp);
omega[m][0] = utils::numeric(FLERR,values[offset],true,lmp);
omega[m][1] = utils::numeric(FLERR,values[offset+1],true,lmp);
omega[m][2] = utils::numeric(FLERR,values[offset+2],true,lmp);
atomKK->modified(Host,OMEGA_MASK);
return 3;
}

8
src/KOKKOS/atom_vec_sphere_kokkos.h
View File

@ -58,10 +58,10 @@ class AtomVecSphereKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **);
void data_vel(int, char **);
int data_vel_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void data_vel(int, const std::vector<std::string> &);
int data_vel_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

13
src/KOKKOS/atom_vec_spin_kokkos.cpp
View File

@ -1056,7 +1056,7 @@ void AtomVecSpinKokkos::create_atom(int itype, double *coord)
------------------------------------------------------------------------- */
void AtomVecSpinKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
const std::vector<std::string> &values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -1098,12 +1098,13 @@ void AtomVecSpinKokkos::data_atom(double *coord, imageint imagetmp,
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecSpinKokkos::data_atom_hybrid(int nlocal, char **values)
int AtomVecSpinKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
int offset)
{
h_sp(nlocal,3) = utils::numeric(FLERR,values[0],true,lmp);
h_sp(nlocal,0) = utils::numeric(FLERR,values[1],true,lmp);
h_sp(nlocal,1) = utils::numeric(FLERR,values[2],true,lmp);
h_sp(nlocal,2) = utils::numeric(FLERR,values[3],true,lmp);
h_sp(nlocal,3) = utils::numeric(FLERR,values[offset],true,lmp);
h_sp(nlocal,0) = utils::numeric(FLERR,values[offset+1],true,lmp);
h_sp(nlocal,1) = utils::numeric(FLERR,values[offset+2],true,lmp);
h_sp(nlocal,2) = utils::numeric(FLERR,values[offset+3],true,lmp);
double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);

4
src/KOKKOS/atom_vec_spin_kokkos.h
View File

@ -45,8 +45,8 @@ class AtomVecSpinKokkos : public AtomVecKokkos {
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **);
void data_atom(double *, imageint, const std::vector<std::string> &);
int data_atom_hybrid(int, const std::vector<std::string> &, int);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);

33
src/ML-IAP/mliap_descriptor_so3.cpp
View File

@ -125,28 +125,27 @@ void MLIAPDescriptorSO3::read_paramfile(char *paramfilename)
// check for keywords with one value per element
if (strcmp(skeywd.c_str(), "elems") == 0 || strcmp(skeywd.c_str(), "radelems") == 0 ||
strcmp(skeywd.c_str(), "welems") == 0) {
if ((skeywd == "elems") || (skeywd == "radelems") || (skeywd == "welems")) {
if (nelementsflag == 0 || nwords != nelements + 1)
error->all(FLERR, "Incorrect SO3 parameter file");
if (strcmp(skeywd.c_str(), "elems") == 0) {
if (skeywd == "elems") {
for (int ielem = 0; ielem < nelements; ielem++) {
elements[ielem] = utils::strdup(skeyval);
if (ielem < nelements - 1) skeyval = p.next();
}
elementsflag = 1;
} else if (strcmp(skeywd.c_str(), "radelems") == 0) {
} else if (skeywd == "radelems") {
for (int ielem = 0; ielem < nelements; ielem++) {
radelem[ielem] = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
radelem[ielem] = utils::numeric(FLERR, skeyval, false, lmp);
if (ielem < nelements - 1) skeyval = p.next();
}
radelemflag = 1;
} else if (strcmp(skeywd.c_str(), "welems") == 0) {
} else if (skeywd == "welems") {
for (int ielem = 0; ielem < nelements; ielem++) {
wjelem[ielem] = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
wjelem[ielem] = utils::numeric(FLERR, skeyval, false, lmp);
if (ielem < nelements - 1) skeyval = p.next();
}
wjelemflag = 1;
@ -158,23 +157,23 @@ void MLIAPDescriptorSO3::read_paramfile(char *paramfilename)
if (nwords != 2) error->all(FLERR, "Incorrect SO3 parameter file");
if (strcmp(skeywd.c_str(), "nelems") == 0) {
nelements = utils::inumeric(FLERR, skeyval.c_str(), false, lmp);
if (skeywd == "nelems") {
nelements = utils::inumeric(FLERR, skeyval, false, lmp);
elements = new char *[nelements];
memory->create(radelem, nelements, "mliap_so3_descriptor:radelem");
memory->create(wjelem, nelements, "mliap_so3_descriptor:wjelem");
nelementsflag = 1;
} else if (strcmp(skeywd.c_str(), "rcutfac") == 0) {
rcutfac = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
} else if (skeywd == "rcutfac") {
rcutfac = utils::numeric(FLERR, skeyval, false, lmp);
rcutfacflag = 1;
} else if (strcmp(skeywd.c_str(), "nmax") == 0) {
nmax = utils::inumeric(FLERR, skeyval.c_str(), false, lmp);
} else if (skeywd == "nmax") {
nmax = utils::inumeric(FLERR, skeyval, false, lmp);
nmaxflag = 1;
} else if (strcmp(skeywd.c_str(), "lmax") == 0) {
lmax = utils::inumeric(FLERR, skeyval.c_str(), false, lmp);
} else if (skeywd == "lmax") {
lmax = utils::inumeric(FLERR, skeyval, false, lmp);
lmaxflag = 1;
} else if (strcmp(skeywd.c_str(), "alpha") == 0) {
alpha = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
} else if (skeywd == "alpha") {
alpha = utils::numeric(FLERR, skeyval, false, lmp);
alphaflag = 1;
} else
error->all(FLERR, "Incorrect SO3 parameter file");

30
src/ML-RANN/pair_rann.cpp
View File

@ -440,7 +440,7 @@ void PairRANN::read_mass(const std::vector<std::string> &line1, const std::vecto
if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before mass in potential file.");
for (int i=0;i<nelements;i++) {
if (line1[1].compare(elements[i])==0) {
mass[i]=utils::numeric(filename,linenum,line2[0].c_str(),true,lmp);
mass[i]=utils::numeric(filename,linenum,line2[0],true,lmp);
return;
}
}
@ -452,7 +452,7 @@ void PairRANN::read_fpe(std::vector<std::string> line,std::vector<std::string> l
if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before fingerprints per element in potential file.");
for (i=0;i<nelementsp;i++) {
if (line[1].compare(elementsp[i])==0) {
fingerprintperelement[i] = utils::inumeric(filename,linenum,line1[0].c_str(),true,lmp);
fingerprintperelement[i] = utils::inumeric(filename,linenum,line1[0],true,lmp);
fingerprints[i] = new RANN::Fingerprint *[fingerprintperelement[i]];
for (int j=0;j<fingerprintperelement[i];j++) {
fingerprints[i][j]=new RANN::Fingerprint(this);
@ -491,7 +491,7 @@ void PairRANN::read_fingerprints(std::vector<std::string> line,std::vector<std::
fingerprints[i][i1] = create_fingerprint(line1[k].c_str());
if (fingerprints[i][i1]->n_body_type!=nwords-1) {error->one(filename,linenum,"invalid fingerprint for element combination");}
k++;
fingerprints[i][i1]->init(atomtypes,utils::inumeric(filename,linenum,line1[k++].c_str(),true,lmp));
fingerprints[i][i1]->init(atomtypes,utils::inumeric(filename,linenum,line1[k++],true,lmp));
fingerprintcount[i]++;
}
delete[] atomtypes;
@ -523,7 +523,7 @@ void PairRANN::read_fingerprint_constants(std::vector<std::string> line,std::vec
for (j=0;j<n_body_type;j++) {
if (fingerprints[i][k]->atomtypes[j]!=atomtypes[j]) {break;}
if (j==n_body_type-1) {
if (line[nwords-3].compare(fingerprints[i][k]->style)==0 && utils::inumeric(filename,linenum,line[nwords-2].c_str(),true,lmp)==fingerprints[i][k]->id) {
if (line[nwords-3].compare(fingerprints[i][k]->style)==0 && utils::inumeric(filename,linenum,line[nwords-2],true,lmp)==fingerprints[i][k]->id) {
found=true;
i1 = k;
break;
@ -542,7 +542,7 @@ void PairRANN::read_network_layers(std::vector<std::string> line,std::vector<std
if (nelements == -1)error->one(filename,linenum-1,"atom types must be defined before network layers in potential file.");
for (i=0;i<nelements;i++) {
if (line[1].compare(elements[i])==0) {
net[i].layers = utils::inumeric(filename,linenum,line1[0].c_str(),true,lmp);
net[i].layers = utils::inumeric(filename,linenum,line1[0],true,lmp);
if (net[i].layers < 1)error->one(filename,linenum,"invalid number of network layers");
delete[] net[i].dimensions;
weightdefined[i] = new bool [net[i].layers];
@ -570,9 +570,9 @@ void PairRANN::read_layer_size(std::vector<std::string> line,std::vector<std::st
for (i=0;i<nelements;i++) {
if (line[1].compare(elements[i])==0) {
if (net[i].layers==0)error->one(filename,linenum-1,"networklayers for each atom type must be defined before the corresponding layer sizes.");
int j = utils::inumeric(filename,linenum,line[2].c_str(),true,lmp);
int j = utils::inumeric(filename,linenum,line[2],true,lmp);
if (j>=net[i].layers || j<0) {error->one(filename,linenum,"invalid layer in layer size definition");};
net[i].dimensions[j]= utils::inumeric(filename,linenum,line1[0].c_str(),true,lmp);
net[i].dimensions[j]= utils::inumeric(filename,linenum,line1[0],true,lmp);
return;
}
}
@ -587,7 +587,7 @@ void PairRANN::read_weight(std::vector<std::string> line,std::vector<std::string
for (l=0;l<nelements;l++) {
if (line[1].compare(elements[l])==0) {
if (net[l].layers==0)error->one(filename,*linenum-1,"networklayers must be defined before weights.");
i=utils::inumeric(filename,*linenum,line[2].c_str(),true,lmp);
i=utils::inumeric(filename,*linenum,line[2],true,lmp);
if (i>=net[l].layers || i<0)error->one(filename,*linenum-1,"invalid weight layer");
if (net[l].dimensions[i]==0 || net[l].dimensions[i+1]==0) error->one(filename,*linenum-1,"network layer sizes must be defined before corresponding weight");
net[l].Weights[i] = new double[net[l].dimensions[i]*net[l].dimensions[i+1]];
@ -595,7 +595,7 @@ void PairRANN::read_weight(std::vector<std::string> line,std::vector<std::string
nwords = line1.size();
if (nwords != net[l].dimensions[i])error->one(filename,*linenum,"invalid weights per line");
for (k=0;k<net[l].dimensions[i];k++) {
net[l].Weights[i][k] = utils::numeric(filename,*linenum,line1[k].c_str(),true,lmp);
net[l].Weights[i][k] = utils::numeric(filename,*linenum,line1[k],true,lmp);
}
for (j=1;j<net[l].dimensions[i+1];j++) {
ptr = fgets(linetemp,longline,fp);
@ -606,7 +606,7 @@ void PairRANN::read_weight(std::vector<std::string> line,std::vector<std::string
nwords = line1.size();
if (nwords != net[l].dimensions[i])error->one(filename,*linenum,"invalid weights per line");
for (k=0;k<net[l].dimensions[i];k++) {
net[l].Weights[i][j*net[l].dimensions[i]+k] = utils::numeric(filename,*linenum,line1[k].c_str(),true,lmp);
net[l].Weights[i][j*net[l].dimensions[i]+k] = utils::numeric(filename,*linenum,line1[k],true,lmp);
}
}
return;
@ -621,19 +621,19 @@ void PairRANN::read_bias(std::vector<std::string> line,std::vector<std::string>
for (l=0;l<nelements;l++) {
if (line[1].compare(elements[l])==0) {
if (net[l].layers==0)error->one(filename,*linenum-1,"networklayers must be defined before biases.");
i=utils::inumeric(filename,*linenum,line[2].c_str(),true,lmp);
i=utils::inumeric(filename,*linenum,line[2],true,lmp);
if (i>=net[l].layers || i<0)error->one(filename,*linenum-1,"invalid bias layer");
if (net[l].dimensions[i]==0) error->one(filename,*linenum-1,"network layer sizes must be defined before corresponding bias");
biasdefined[l][i] = true;
net[l].Biases[i] = new double[net[l].dimensions[i+1]];
net[l].Biases[i][0] = utils::numeric(filename,*linenum,line1[0].c_str(),true,lmp);
net[l].Biases[i][0] = utils::numeric(filename,*linenum,line1[0],true,lmp);
for (j=1;j<net[l].dimensions[i+1];j++) {
ptr=fgets(linetemp,MAXLINE,fp);
if (ptr==nullptr)error->one(filename,*linenum,"unexpected end of potential file!");
(*linenum)++;
Tokenizer values1 = Tokenizer(linetemp,": ,\t_\n");
line1 = values1.as_vector();
net[l].Biases[i][j] = utils::numeric(filename,*linenum,line1[0].c_str(),true,lmp);
net[l].Biases[i][j] = utils::numeric(filename,*linenum,line1[0],true,lmp);
}
return;
}
@ -680,10 +680,10 @@ void PairRANN::read_screening(std::vector<std::string> line,std::vector<std::str
k = atomtypes[2];
int index = i*nelements*nelements+j*nelements+k;
if (line[4].compare("Cmin")==0) {
screening_min[index] = utils::numeric(filename,linenum,line1[0].c_str(),true,lmp);
screening_min[index] = utils::numeric(filename,linenum,line1[0],true,lmp);
}
else if (line[4].compare("Cmax")==0) {
screening_max[index] = utils::numeric(filename,linenum,line1[0].c_str(),true,lmp);
screening_max[index] = utils::numeric(filename,linenum,line1[0],true,lmp);
}
else error->one(filename,linenum-1,"unrecognized screening keyword");
delete[] atomtypes;

31
src/ML-SNAP/pair_snap.cpp
View File

@ -570,8 +570,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
else
elementflags[jelem] = 1;
radelem[jelem] = utils::numeric(FLERR,words[1].c_str(),false,lmp);
wjelem[jelem] = utils::numeric(FLERR,words[2].c_str(),false,lmp);
radelem[jelem] = utils::numeric(FLERR,words[1],false,lmp);
wjelem[jelem] = utils::numeric(FLERR,words[2],false,lmp);
if (comm->me == 0)
utils::logmesg(lmp,"SNAP Element = {}, Radius {}, Weight {}\n",
@ -672,34 +672,33 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
utils::logmesg(lmp,"SNAP keyword {} {}\n",keywd,keyval);
if (keywd == "rcutfac") {
rcutfac = utils::numeric(FLERR,keyval.c_str(),false,lmp);
rcutfac = utils::numeric(FLERR,keyval,false,lmp);
rcutfacflag = 1;
} else if (keywd == "twojmax") {
twojmax = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
twojmax = utils::inumeric(FLERR,keyval,false,lmp);
twojmaxflag = 1;
} else if (keywd == "rfac0")
rfac0 = utils::numeric(FLERR,keyval.c_str(),false,lmp);
rfac0 = utils::numeric(FLERR,keyval,false,lmp);
else if (keywd == "rmin0")
rmin0 = utils::numeric(FLERR,keyval.c_str(),false,lmp);
rmin0 = utils::numeric(FLERR,keyval,false,lmp);
else if (keywd == "switchflag")
switchflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
switchflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "bzeroflag")
bzeroflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
bzeroflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "quadraticflag")
quadraticflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
quadraticflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "chemflag")
chemflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
chemflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "bnormflag")
bnormflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
bnormflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "wselfallflag")
wselfallflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
wselfallflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "chunksize")
chunksize = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
chunksize = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "parallelthresh")
parallel_thresh = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
parallel_thresh = utils::inumeric(FLERR,keyval,false,lmp);
else
error->all(FLERR,"Unknown parameter '{}' in SNAP "
"parameter file", keywd);
error->all(FLERR,"Unknown parameter '{}' in SNAP parameter file", keywd);
}
if (rcutfacflag == 0 || twojmaxflag == 0)

229
src/atom.cpp
View File

@ -29,6 +29,7 @@
#include "modify.h"
#include "molecule.h"
#include "neighbor.h"
#include "tokenizer.h"
#include "update.h"
#include "variable.h"
@ -1057,6 +1058,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
double *coord;
char *next;
// use the first line to detect and validate the number of words/tokens per line
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::trim_and_count_words(buf);
@ -1065,8 +1067,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
error->all(FLERR,"Incorrect atom format in data file");
char **values = new char*[nwords];
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off
@ -1137,15 +1137,10 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
for (m = 0; m < nwords; m++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
if (strlen(buf) == 0)
error->all(FLERR,"Incorrect atom format in data file");
values[m] = buf;
buf += strlen(buf)+1;
}
*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));
int imx = 0, imy = 0, imz = 0;
if (imageflag) {
@ -1192,7 +1187,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -1204,7 +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');
@ -1215,31 +1208,24 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
if (nwords != avec->size_data_vel)
error->all(FLERR,"Incorrect velocity format in data file");
char **values = new char*[nwords];
// loop over lines of atom velocities
// 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 Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
if ((m = map(tagdata)) >= 0) avec->data_vel(m,values);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -1252,18 +1238,25 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2;
char *next;
int newton_bond = force->newton_bond;
auto location = "Bonds section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (rv != 4)
error->one(FLERR,"Incorrect format of Bonds section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1272,9 +1265,9 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file");
error->one(FLERR,"Invalid bond type in {}: {}", location, utils::trim(buf));
if ((m = map(atom1)) >= 0) {
if (count) count[m]++;
else {
@ -1309,18 +1302,26 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2,atom3;
char *next;
int newton_bond = force->newton_bond;
auto location = "Angles section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (rv != 5)
error->one(FLERR,"Incorrect format of Angles section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1332,9 +1333,9 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
(atom2 <= 0) || (atom2 > map_tag_max) ||
(atom3 <= 0) || (atom3 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->one(FLERR,"Invalid atom ID in Angles section of data file");
error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file");
error->one(FLERR,"Invalid angle type in {}: {}", location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1381,19 +1382,27 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
auto location = "Dihedrals section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
" " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Dihedrals section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1408,10 +1417,9 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
(atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,"Invalid atom ID in Dihedrals section of data file");
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR,
"Invalid dihedral type in Dihedrals section of data file");
error->one(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1472,19 +1480,27 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
auto location = "Impropers section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Impropers section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1499,10 +1515,9 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
(atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,"Invalid atom ID in Impropers section of data file");
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR,
"Invalid improper type in Impropers section of data file");
error->one(FLERR, "Invalid improper type in {}: {}", location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1561,7 +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');
@ -1572,35 +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;
}
/* ----------------------------------------------------------------------
@ -1612,12 +1620,8 @@ 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 maxint = 0;
int maxdouble = 0;
int *ivalues = nullptr;
double *dvalues = nullptr;
std::vector<int> ivalues;
std::vector<double> dvalues;
if (!unique_tags) unique_tags = new std::set<tagint>;
@ -1626,69 +1630,51 @@ 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;
char *next = strchr(buf,'\n');
*next = '\0';
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
int ninteger = utils::inumeric(FLERR,values[1],false,lmp);
int ndouble = utils::inumeric(FLERR,values[2],false,lmp);
if (unique_tags->find(tagdata) == unique_tags->end())
unique_tags->insert(tagdata);
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;
buf = next + 1;
int m = map(tagdata);
if (m >= 0) {
ivalues.resize(ninteger);
dvalues.resize(ndouble);
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) {
if (ninteger > maxint) {
delete [] ivalues;
maxint = ninteger;
ivalues = new int[maxint];
}
if (ndouble > maxdouble) {
delete [] dvalues;
maxdouble = ndouble;
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++) {
for (int j = 0; j < ninteger; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
for (j = 0; j < ndouble; j++) {
for (int j = 0; j < ndouble; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
avec_body->data_body(m,ninteger,ndouble,ivalues.data(),dvalues.data());
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++) {
int nvalues = ninteger + ndouble; // number of values to skip
for (int j = 0; j < nvalues; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
buf += strlen(buf)+1;
}
}
buf += strspn(buf," \t\n\r\f");
}
delete [] ivalues;
delete [] dvalues;
}
/* ----------------------------------------------------------------------
@ -1743,17 +1729,20 @@ void Atom::set_mass(const char *file, int line, const char *str, int type_offset
int itype;
double mass_one;
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all(file,line,"Invalid mass line in data file");
itype += type_offset;
try {
ValueTokenizer values(utils::trim_comment(str));
itype = values.next_int() + type_offset;
mass_one = values.next_double();
if (values.has_next()) throw TokenizerException("Too many tokens", "");
if (itype < 1 || itype > ntypes)
error->all(file,line,"Invalid type for mass set");
if (itype < 1 || itype > ntypes) throw TokenizerException("Invalid atom type", "");
if (mass_one <= 0.0) throw TokenizerException("Invalid mass value", "");
} catch (TokenizerException &e) {
error->all(file,line,"{} in Masses section of data file: {}", e.what(), utils::trim(str));
}
mass[itype] = mass_one;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all(file,line,"Invalid mass value");
}
/* ----------------------------------------------------------------------

12
src/atom_vec.cpp
View File

@ -1707,7 +1707,7 @@ void AtomVec::create_atom(int itype, double *coord)
initialize other peratom quantities
------------------------------------------------------------------------- */
void AtomVec::data_atom(double *coord, imageint imagetmp, char **values)
void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std::string> &values)
{
int m,n,datatype,cols;
void *pdata;
@ -1890,18 +1890,18 @@ void AtomVec::write_data(FILE *fp, int n, double **buf)
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVec::data_vel(int ilocal, char **values)
void AtomVec::data_vel(int ilocal, const std::vector<std::string> &values)
{
int m,n,datatype,cols;
void *pdata;
double **v = atom->v;
v[ilocal][0] = utils::numeric(FLERR,values[0],true,lmp);
v[ilocal][1] = utils::numeric(FLERR,values[1],true,lmp);
v[ilocal][2] = utils::numeric(FLERR,values[2],true,lmp);
int ivalue = 1;
v[ilocal][0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
v[ilocal][1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
v[ilocal][2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
if (ndata_vel > 2) {
int ivalue = 3;
for (n = 2; n < ndata_vel; n++) {
pdata = mdata_vel.pdata[n];
datatype = mdata_vel.datatype[n];

10
src/atom_vec.h
View File

@ -124,9 +124,9 @@ class AtomVec : protected Pointers {
virtual void create_atom(int, double *);
virtual void create_atom_post(int) {}
virtual void data_atom(double *, imageint, char **);
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) {}
@ -136,7 +136,7 @@ class AtomVec : protected Pointers {
virtual void pack_data_pre(int) {}
virtual void pack_data_post(int) {}
virtual void data_vel(int, char **);
virtual void data_vel(int, const std::vector<std::string> &);
virtual void pack_vel(double **);
virtual void write_vel(FILE *, int, double **);
@ -166,8 +166,8 @@ class AtomVec : protected Pointers {
virtual int unpack_reverse_hybrid(int, int *, double *) { return 0; }
virtual int pack_border_hybrid(int, int *, double *) { return 0; }
virtual int unpack_border_hybrid(int, int, double *) { return 0; }
virtual int data_atom_hybrid(int, char **) { return 0; }
virtual int data_vel_hybrid(int, char **) { return 0; }
virtual int data_atom_hybrid(int, const std::vector<std::string> &, int) { return 0; }
virtual int data_vel_hybrid(int, const std::vector<std::string> &, int) { return 0; }
virtual int pack_data_hybrid(int, double *) { return 0; }
virtual int write_data_hybrid(FILE *, double *) { return 0; }
virtual int pack_vel_hybrid(int, double *) { return 0; }

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);

52
src/read_data.cpp
View File

@ -35,6 +35,7 @@
#include "molecule.h"
#include "pair.h"
#include "special.h"
#include "tokenizer.h"
#include "update.h"
#include <cctype>
@ -1088,37 +1089,32 @@ void ReadData::header(int firstpass)
} else if (utils::strmatch(line,"^\\s*\\d+\\s+atom\\s+types\\s")) {
rv = sscanf(line,"%d",&ntypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'atom types' line "
"in data file header");
error->all(FLERR,"Could not parse 'atom types' line in data file header");
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
} else if (utils::strmatch(line,"\\s*\\d+\\s+bond\\s+types\\s")) {
rv = sscanf(line,"%d",&nbondtypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'bond types' line "
"in data file header");
error->all(FLERR,"Could not parse 'bond types' line in data file header");
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angle\\s+types\\s")) {
rv = sscanf(line,"%d",&nangletypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'angle types' line "
"in data file header");
error->all(FLERR,"Could not parse 'angle types' line in data file header");
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedral\\s+types\\s")) {
rv = sscanf(line,"%d",&ndihedraltypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'dihedral types' line "
"in data file header");
error->all(FLERR,"Could not parse 'dihedral types' line in data file header");
if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
} else if (utils::strmatch(line,"^\\s*\\d+\\s+improper\\s+types\\s")) {
rv = sscanf(line,"%d",&nimpropertypes);
if (rv != 1)
error->all(FLERR,"Could not parse 'improper types' line "
"in data file header");
error->all(FLERR,"Could not parse 'improper types' line in data file header");
if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types;
@ -1658,12 +1654,12 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
read all body data
variable amount of info per body, described by ninteger and ndouble
to find atoms, must build atom map if not a molecular system
if not firstpass, just read past data, but no processing of data
if not firstpass, just read past body data and only process body header
------------------------------------------------------------------------- */
void ReadData::bodies(int firstpass, AtomVec *ptr)
{
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp,rv;
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody;
char *eof;
int mapflag = 0;
@ -1677,11 +1673,11 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
// nchunk = actual # read
bigint nread = 0;
bigint natoms = nbodies;
bigint nblocks = nbodies;
while (nread < natoms) {
if (natoms-nread > CHUNK) nmax = CHUNK;
else nmax = natoms-nread;
while (nread < nblocks) {
if (nblocks-nread > CHUNK) nmax = CHUNK;
else nmax = nblocks-nread;
if (me == 0) {
nchunk = 0;
@ -1690,11 +1686,25 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
const char *buf = &buffer[m];
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
if (rv != 3)
error->one(FLERR,"Incorrect format in Bodies section of data file");
m += strlen(&buffer[m]);
try {
auto values = ValueTokenizer(utils::trim_comment(buf));
tagint tagdata = values.next_tagint() + id_offset;
ninteger = values.next_int();
ndouble = values.next_double();
if (tagdata <= 0 || tagdata > atom->map_tag_max)
throw TokenizerException("Invalid atom ID in body header", utils::trim(buf));
if (ninteger < 0)
throw TokenizerException("Invalid number of integers", utils::trim(buf));
if (ndouble < 0)
throw TokenizerException("Invalid number of doubles", utils::trim(buf));
if (values.has_next())
throw TokenizerException("Too many tokens in body header", utils::trim(buf));
} catch (TokenizerException &e) {
error->one(FLERR,std::string(e.what()) + " while reading Bodies section of data file");
}
m += strlen(buf);
// read lines one at a time into buffer and count words
// count to ninteger and ndouble until have enough lines
@ -1754,7 +1764,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
}
if (me == 0 && firstpass)
utils::logmesg(lmp," {} bodies\n",natoms);
utils::logmesg(lmp," {} bodies\n",nblocks);
}
/* ---------------------------------------------------------------------- */

98
src/utils.cpp
View File

@ -298,12 +298,9 @@ std::string utils::check_packages_for_style(const std::string &style, const std:
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
int utils::logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
int utils::logical(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (str.empty()) {
const char msg[] = "Expected boolean parameter instead of NULL or empty string "
"in input script or data file";
if (do_abort)
@ -332,18 +329,28 @@ int utils::logical(const char *file, int line, const char *str, bool do_abort, L
return rv;
}
/* ----------------------------------------------------------------------
wrapper for logical() that accepts a char pointer instead of a string
------------------------------------------------------------------------- */
int utils::logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
{
if (str)
return logical(file, line, std::string(str), do_abort, lmp);
else
return logical(file, line, std::string(""), do_abort, lmp);
}
/* ----------------------------------------------------------------------
read a floating point value from a string
generate an error if not a legitimate floating point value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
double utils::numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
double utils::numeric(const char *file, int line, const std::string &str, bool do_abort,
LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (str.empty()) {
const char msg[] = "Expected floating point parameter instead of"
" NULL or empty string in input script or data file";
if (do_abort)
@ -367,18 +374,27 @@ double utils::numeric(const char *file, int line, const char *str, bool do_abort
return atof(buf.c_str());
}
/* ----------------------------------------------------------------------
wrapper for numeric() that accepts a char pointer instead of a string
------------------------------------------------------------------------- */
double utils::numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
{
if (str)
return numeric(file, line, std::string(str), do_abort, lmp);
else
return numeric(file, line, std::string(""), do_abort, lmp);
}
/* ----------------------------------------------------------------------
read an integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
int utils::inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
int utils::inumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (str.empty()) {
const char msg[] = "Expected integer parameter instead of"
" NULL or empty string in input script or data file";
if (do_abort)
@ -402,18 +418,28 @@ int utils::inumeric(const char *file, int line, const char *str, bool do_abort,
return atoi(buf.c_str());
}
/* ----------------------------------------------------------------------
wrapper for inumeric() that accepts a char pointer instead of a string
------------------------------------------------------------------------- */
int utils::inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
{
if (str)
return inumeric(file, line, std::string(str), do_abort, lmp);
else
return inumeric(file, line, std::string(""), do_abort, lmp);
}
/* ----------------------------------------------------------------------
read a big integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
bigint utils::bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
bigint utils::bnumeric(const char *file, int line, const std::string &str, bool do_abort,
LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (str.empty()) {
const char msg[] = "Expected integer parameter instead of"
" NULL or empty string in input script or data file";
if (do_abort)
@ -437,18 +463,28 @@ bigint utils::bnumeric(const char *file, int line, const char *str, bool do_abor
return ATOBIGINT(buf.c_str());
}
/* ----------------------------------------------------------------------
wrapper for bnumeric() that accepts a char pointer instead of a string
------------------------------------------------------------------------- */
bigint utils::bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
{
if (str)
return bnumeric(file, line, std::string(str), do_abort, lmp);
else
return bnumeric(file, line, std::string(""), do_abort, lmp);
}
/* ----------------------------------------------------------------------
read a tag integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
tagint utils::tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
tagint utils::tnumeric(const char *file, int line, const std::string &str, bool do_abort,
LAMMPS *lmp)
{
int n = 0;
if (str) n = strlen(str);
if (n == 0) {
if (str.empty()) {
const char msg[] = "Expected integer parameter instead of"
" NULL or empty string in input script or data file";
if (do_abort)
@ -472,6 +508,18 @@ tagint utils::tnumeric(const char *file, int line, const char *str, bool do_abor
return ATOTAGINT(buf.c_str());
}
/* ----------------------------------------------------------------------
wrapper for tnumeric() that accepts a char pointer instead of a string
------------------------------------------------------------------------- */
tagint utils::tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
{
if (str)
return tnumeric(file, line, std::string(str), do_abort, lmp);
else
return tnumeric(file, line, std::string(""), do_abort, lmp);
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterisk
------------------------------------------------------------------------- */

55
src/utils.h
View File

@ -169,6 +169,17 @@ namespace utils {
* \param lmp pointer to top-level LAMMPS class instance
* \return 1 if string resolves to "true", otherwise 0 */
int logical(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp);
/*! \overload
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to logical
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return 1 if string resolves to "true", otherwise 0 */
int logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to a floating point number while checking
@ -181,6 +192,17 @@ namespace utils {
* \param lmp pointer to top-level LAMMPS class instance
* \return double precision floating point number */
double numeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp);
/*! \overload
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return double precision floating point number */
double numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to an integer number while checking
@ -193,6 +215,17 @@ namespace utils {
* \param lmp pointer to top-level LAMMPS class instance
* \return integer number (regular int) */
int inumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp);
/*! \overload
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return double precision floating point number */
int inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to an integer number while checking
@ -205,6 +238,17 @@ namespace utils {
* \param lmp pointer to top-level LAMMPS class instance
* \return integer number (bigint) */
bigint bnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp);
/*! \overload
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return double precision floating point number */
bigint bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Convert a string to an integer number while checking
@ -217,6 +261,17 @@ namespace utils {
* \param lmp pointer to top-level LAMMPS class instance
* \return integer number (tagint) */
tagint tnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp);
/*! \overload
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str string to be converted to number
* \param do_abort determines whether to call Error::one() or Error::all()
* \param lmp pointer to top-level LAMMPS class instance
* \return double precision floating point number */
tagint tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp);
/*! Compute index bounds derived from a string with a possible wildcard

39
unittest/formats/test_input_convert.cpp
View File

@ -49,6 +49,15 @@ TEST_F(InputConvertTest, logical)
EXPECT_EQ(utils::logical(FLERR, "off", false, lmp), 0);
EXPECT_EQ(utils::logical(FLERR, "0", false, lmp), 0);
EXPECT_EQ(utils::logical(FLERR, std::string("yes"), false, lmp), 1);
EXPECT_EQ(utils::logical(FLERR, std::string("true"), false, lmp), 1);
EXPECT_EQ(utils::logical(FLERR, std::string("on"), false, lmp), 1);
EXPECT_EQ(utils::logical(FLERR, std::string("1"), false, lmp), 1);
EXPECT_EQ(utils::logical(FLERR, std::string("no"), false, lmp), 0);
EXPECT_EQ(utils::logical(FLERR, std::string("false"), false, lmp), 0);
EXPECT_EQ(utils::logical(FLERR, std::string("off"), false, lmp), 0);
EXPECT_EQ(utils::logical(FLERR, std::string("0"), false, lmp), 0);
TEST_FAILURE(".*ERROR: Expected boolean parameter instead of.*",
utils::logical(FLERR, "YES", false, lmp););
TEST_FAILURE(".*ERROR: Expected boolean parameter instead of.*",
@ -94,6 +103,15 @@ TEST_F(InputConvertTest, numeric)
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, "10000000000", false, lmp), 1e10);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, "2.56E+3", false, lmp), 2560);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("0"), false, lmp), 0);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("0.1"), false, lmp), 0.1);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("-.232"), false, lmp), -0.232);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string(".2e5"), false, lmp), 20000.0);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("2.5e-10"), false, lmp), 2.5e-10);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("+0.3"), false, lmp), 0.3);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("10000000000"), false, lmp), 1e10);
EXPECT_DOUBLE_EQ(utils::numeric(FLERR, std::string("2.56E+3"), false, lmp), 2560);
TEST_FAILURE(".*ERROR: Expected floating point.*", utils::numeric(FLERR, "yay", false, lmp););
TEST_FAILURE(".*ERROR: Expected floating point.*", utils::numeric(FLERR, "", false, lmp););
TEST_FAILURE(".*ERROR: Expected floating point.*", utils::numeric(FLERR, nullptr, false, lmp););
@ -110,6 +128,13 @@ TEST_F(InputConvertTest, inumeric)
EXPECT_EQ(utils::inumeric(FLERR, "-0", false, lmp), 0);
EXPECT_EQ(utils::inumeric(FLERR, "0100", false, lmp), 100);
EXPECT_EQ(utils::inumeric(FLERR, std::string("0"), false, lmp), 0);
EXPECT_EQ(utils::inumeric(FLERR, std::string("-1"), false, lmp), -1);
EXPECT_EQ(utils::inumeric(FLERR, std::string("10000"), false, lmp), 10000);
EXPECT_EQ(utils::inumeric(FLERR, std::string("-532410"), false, lmp), -532410);
EXPECT_EQ(utils::inumeric(FLERR, std::string("-0"), false, lmp), 0);
EXPECT_EQ(utils::inumeric(FLERR, std::string("0100"), false, lmp), 100);
TEST_FAILURE(".*ERROR: Expected integer.*", utils::inumeric(FLERR, "yay", false, lmp););
TEST_FAILURE(".*ERROR: Expected integer.*", utils::inumeric(FLERR, "0.1", false, lmp););
TEST_FAILURE(".*ERROR: Expected integer.*", utils::inumeric(FLERR, "1.1", false, lmp););
@ -128,6 +153,13 @@ TEST_F(InputConvertTest, bnumeric)
EXPECT_EQ(utils::bnumeric(FLERR, "-0", false, lmp), 0);
EXPECT_EQ(utils::bnumeric(FLERR, "0100", false, lmp), 100);
EXPECT_EQ(utils::bnumeric(FLERR, std::string("0"), false, lmp), 0);
EXPECT_EQ(utils::bnumeric(FLERR, std::string("-1"), false, lmp), -1);
EXPECT_EQ(utils::bnumeric(FLERR, std::string("10000"), false, lmp), 10000);
EXPECT_EQ(utils::bnumeric(FLERR, std::string("-532410"), false, lmp), -532410);
EXPECT_EQ(utils::bnumeric(FLERR, std::string("-0"), false, lmp), 0);
EXPECT_EQ(utils::bnumeric(FLERR, std::string("0100"), false, lmp), 100);
TEST_FAILURE(".*ERROR: Expected integer.*", utils::bnumeric(FLERR, "yay", false, lmp););
TEST_FAILURE(".*ERROR: Expected integer.*", utils::bnumeric(FLERR, "0.1", false, lmp););
TEST_FAILURE(".*ERROR: Expected integer.*", utils::bnumeric(FLERR, "1.1", false, lmp););
@ -146,6 +178,13 @@ TEST_F(InputConvertTest, tnumeric)
EXPECT_EQ(utils::tnumeric(FLERR, "-0", false, lmp), 0);
EXPECT_EQ(utils::tnumeric(FLERR, "0100", false, lmp), 100);
EXPECT_EQ(utils::tnumeric(FLERR, std::string("0"), false, lmp), 0);
EXPECT_EQ(utils::tnumeric(FLERR, std::string("-1"), false, lmp), -1);
EXPECT_EQ(utils::tnumeric(FLERR, std::string("10000"), false, lmp), 10000);
EXPECT_EQ(utils::tnumeric(FLERR, std::string("-532410"), false, lmp), -532410);
EXPECT_EQ(utils::tnumeric(FLERR, std::string("-0"), false, lmp), 0);
EXPECT_EQ(utils::tnumeric(FLERR, std::string("0100"), false, lmp), 100);
TEST_FAILURE(".*ERROR: Expected integer.*", utils::tnumeric(FLERR, "yay", false, lmp););
TEST_FAILURE(".*ERROR: Expected integer.*", utils::tnumeric(FLERR, "0.1", false, lmp););
TEST_FAILURE(".*ERROR: Expected integer.*", utils::tnumeric(FLERR, "1.1", false, lmp););