Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
# Resolved Conflicts: # doc/Manual.html # doc/Manual.txt # src/REAX/fix_reax_bonds.cpp # src/REAX/fix_reax_bonds.h # src/REAX/pair_reax.cpp # src/USER-MGPT/pair_mgpt.cpp # src/USER-SMTBQ/pair_smtbq.cpp # src/lammps.cpp # src/timer.cpp
This commit is contained in:
Axel Kohlmeyer
46
src/atom.cpp
46
src/atom.cpp
@ -11,12 +11,12 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "limits.h"
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#include <mpi.h>
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <limits.h>
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#include "atom.h"
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#include "style_atom.h"
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#include "atom_vec.h"
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@ -611,11 +611,11 @@ void Atom::tag_check()
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if (minall < 0) error->all(FLERR,"One or more Atom IDs is negative");
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if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs is too big");
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if (maxall > 0 && minall == 0)
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if (maxall > 0 && minall == 0)
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error->all(FLERR,"One or more atom IDs is zero");
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if (maxall > 0 && tag_enable == 0)
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error->all(FLERR,"Non-zero atom IDs with atom_modify id = no");
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if (maxall == 0 && natoms && tag_enable)
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if (maxall == 0 && natoms && tag_enable)
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error->all(FLERR,"All atom IDs = 0 but atom_modify id = yes");
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if (tag_enable && maxall < natoms)
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error->all(FLERR,"Duplicate atom IDs exist");
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@ -735,23 +735,23 @@ void Atom::deallocate_topology()
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memory->destroy(atom->angle_atom3);
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atom->angle_type = NULL;
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atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
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memory->destroy(atom->dihedral_type);
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memory->destroy(atom->dihedral_atom1);
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memory->destroy(atom->dihedral_atom2);
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memory->destroy(atom->dihedral_atom3);
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memory->destroy(atom->dihedral_atom4);
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atom->dihedral_type = NULL;
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atom->dihedral_atom1 = atom->dihedral_atom2 =
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atom->dihedral_atom1 = atom->dihedral_atom2 =
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atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
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memory->destroy(atom->improper_type);
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memory->destroy(atom->improper_atom1);
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memory->destroy(atom->improper_atom2);
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memory->destroy(atom->improper_atom3);
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memory->destroy(atom->improper_atom4);
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atom->improper_type = NULL;
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atom->improper_atom1 = atom->improper_atom2 =
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atom->improper_atom1 = atom->improper_atom2 =
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atom->improper_atom3 = atom->improper_atom4 = NULL;
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}
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@ -760,7 +760,7 @@ void Atom::deallocate_topology()
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call style-specific routine to parse line
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------------------------------------------------------------------------- */
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void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
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void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
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int shiftflag, double *shift)
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{
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int m,xptr,iptr;
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@ -865,7 +865,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
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(((imageint) (atoi(values[iptr+2]) + IMGMAX) & IMGMASK) << IMG2BITS);
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else imagedata = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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xdata[0] = atof(values[xptr]);
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xdata[1] = atof(values[xptr+1]);
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xdata[2] = atof(values[xptr+2]);
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@ -951,7 +951,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
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------------------------------------------------------------------------- */
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void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
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int type_offset)
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int type_offset)
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{
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int m,tmp,itype;
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tagint atom1,atom2;
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@ -1004,7 +1004,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
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------------------------------------------------------------------------- */
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void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
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int type_offset)
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int type_offset)
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{
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int m,tmp,itype;
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tagint atom1,atom2,atom3;
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@ -1083,7 +1083,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
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for (int i = 0; i < n; i++) {
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next = strchr(buf,'\n');
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*next = '\0';
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sscanf(buf,"%d %d "
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sscanf(buf,"%d %d "
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TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
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&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
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if (id_offset) {
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@ -1170,7 +1170,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
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for (int i = 0; i < n; i++) {
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next = strchr(buf,'\n');
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*next = '\0';
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sscanf(buf,"%d %d "
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sscanf(buf,"%d %d "
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TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
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&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
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if (id_offset) {
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@ -1292,7 +1292,7 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
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call style-specific routine to parse line
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------------------------------------------------------------------------- */
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void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
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void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
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tagint id_offset)
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{
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int j,m,tagdata,ninteger,ndouble;
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@ -1501,7 +1501,7 @@ void Atom::add_molecule(int narg, char **arg)
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{
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if (narg < 1) error->all(FLERR,"Illegal molecule command");
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if (find_molecule(arg[0]) >= 0)
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if (find_molecule(arg[0]) >= 0)
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error->all(FLERR,"Reuse of molecule template ID");
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// 1st molecule in set stores nset = # of mols, others store nset = 0
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@ -1548,7 +1548,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
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if (onemol->qflag && q_flag) q[ilocal] = onemol->q[iatom];
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if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
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if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
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else if (rmass_flag)
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else if (rmass_flag)
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rmass[ilocal] = 4.0*MY_PI/3.0 *
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radius[ilocal]*radius[ilocal]*radius[ilocal];
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@ -2050,9 +2050,9 @@ void *Atom::extract(char *name)
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if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
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if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
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if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress;
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if (strcmp(name, "eff_plastic_strain") == 0)
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if (strcmp(name, "eff_plastic_strain") == 0)
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return (void *) eff_plastic_strain;
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if (strcmp(name, "eff_plastic_strain_rate") == 0)
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if (strcmp(name, "eff_plastic_strain_rate") == 0)
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return (void *) eff_plastic_strain_rate;
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if (strcmp(name, "damage") == 0) return (void *) damage;
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