Merge branch 'master' into openmp-step6
Resolved Conflicts: src/GPU/pppm_gpu.cpp src/KSPACE/ewald.h src/MANYBODY/pair_airebo.cpp src/MANYBODY/pair_comb.cpp src/MANYBODY/pair_comb.h src/MANYBODY/pair_tersoff.h src/MOLECULE/pair_hbond_dreiding_lj.cpp src/MOLECULE/pair_hbond_dreiding_morse.cpp src/USER-CUDA/pppm_cuda.cpp src/USER-OMP/Install.sh src/USER-OMP/Package.sh src/USER-OMP/dihedral_charmm_omp.cpp src/USER-OMP/dihedral_charmm_omp.h src/USER-OMP/dihedral_class2_omp.cpp src/USER-OMP/dihedral_class2_omp.h src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp src/USER-OMP/dihedral_cosine_shift_exp_omp.h src/USER-OMP/dihedral_harmonic_omp.cpp src/USER-OMP/dihedral_harmonic_omp.h src/USER-OMP/dihedral_helix_omp.cpp src/USER-OMP/dihedral_helix_omp.h src/USER-OMP/dihedral_multi_harmonic_omp.cpp src/USER-OMP/dihedral_multi_harmonic_omp.h src/USER-OMP/dihedral_opls_omp.cpp src/USER-OMP/dihedral_opls_omp.h src/USER-OMP/fix_nve_sphere_omp.cpp src/USER-OMP/pair_adp_omp.cpp src/USER-OMP/pair_adp_omp.h src/USER-OMP/pair_born_coul_long_omp.cpp src/USER-OMP/pair_born_coul_long_omp.h src/USER-OMP/pair_born_omp.cpp src/USER-OMP/pair_born_omp.h src/USER-OMP/pair_buck_coul_cut_omp.cpp src/USER-OMP/pair_buck_coul_cut_omp.h src/USER-OMP/pair_buck_coul_long_omp.cpp src/USER-OMP/pair_buck_coul_long_omp.h src/USER-OMP/pair_buck_coul_omp.cpp src/USER-OMP/pair_buck_coul_omp.h src/USER-OMP/pair_buck_omp.cpp src/USER-OMP/pair_buck_omp.h src/USER-OMP/pair_cdeam_omp.cpp src/USER-OMP/pair_cdeam_omp.h src/USER-OMP/pair_colloid_omp.cpp src/USER-OMP/pair_colloid_omp.h src/USER-OMP/pair_coul_cut_omp.cpp src/USER-OMP/pair_coul_cut_omp.h src/USER-OMP/pair_coul_debye_omp.cpp src/USER-OMP/pair_coul_debye_omp.h src/USER-OMP/pair_coul_long_omp.cpp src/USER-OMP/pair_coul_long_omp.h src/USER-OMP/pair_dipole_cut_omp.cpp src/USER-OMP/pair_dipole_cut_omp.h src/USER-OMP/pair_dipole_sf_omp.cpp src/USER-OMP/pair_dipole_sf_omp.h src/USER-OMP/pair_dpd_omp.cpp src/USER-OMP/pair_dpd_omp.h src/USER-OMP/pair_dpd_tstat_omp.cpp src/USER-OMP/pair_dpd_tstat_omp.h src/USER-OMP/pair_eam_omp.cpp src/USER-OMP/pair_eam_omp.h src/USER-OMP/pair_edip_omp.cpp src/USER-OMP/pair_edip_omp.h src/USER-OMP/pair_eim_omp.cpp src/USER-OMP/pair_eim_omp.h src/USER-OMP/pair_gauss_omp.cpp src/USER-OMP/pair_gauss_omp.h src/USER-OMP/pair_gayberne_omp.cpp src/USER-OMP/pair_gayberne_omp.h src/USER-OMP/pair_gran_hertz_history_omp.cpp src/USER-OMP/pair_gran_hertz_history_omp.h src/USER-OMP/pair_gran_hooke_history_omp.cpp src/USER-OMP/pair_gran_hooke_history_omp.h src/USER-OMP/pair_gran_hooke_omp.cpp src/USER-OMP/pair_gran_hooke_omp.h src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp src/USER-OMP/pair_hbond_dreiding_lj_omp.h src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp src/USER-OMP/pair_hbond_dreiding_morse_omp.h src/USER-OMP/pair_lj96_cut_omp.cpp src/USER-OMP/pair_lj96_cut_omp.h src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp src/USER-OMP/pair_lj_charmm_coul_long_omp.h src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp src/USER-OMP/pair_lj_class2_coul_cut_omp.h src/USER-OMP/pair_lj_class2_coul_long_omp.cpp src/USER-OMP/pair_lj_class2_coul_long_omp.h src/USER-OMP/pair_lj_class2_omp.cpp src/USER-OMP/pair_lj_class2_omp.h src/USER-OMP/pair_lj_coul_omp.cpp src/USER-OMP/pair_lj_coul_omp.h src/USER-OMP/pair_lj_cubic_omp.cpp src/USER-OMP/pair_lj_cubic_omp.h src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp src/USER-OMP/pair_lj_cut_coul_cut_omp.h src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp src/USER-OMP/pair_lj_cut_coul_debye_omp.h src/USER-OMP/pair_lj_cut_coul_long_omp.cpp src/USER-OMP/pair_lj_cut_coul_long_omp.h src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h src/USER-OMP/pair_lj_cut_omp.cpp src/USER-OMP/pair_lj_expand_omp.cpp src/USER-OMP/pair_lj_expand_omp.h src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h src/USER-OMP/pair_lj_gromacs_omp.cpp src/USER-OMP/pair_lj_gromacs_omp.h src/USER-OMP/pair_lj_sf_omp.cpp src/USER-OMP/pair_lj_sf_omp.h src/USER-OMP/pair_lj_smooth_omp.cpp src/USER-OMP/pair_lj_smooth_omp.h src/USER-OMP/pair_lubricate_omp.cpp src/USER-OMP/pair_lubricate_omp.h src/USER-OMP/pair_morse_omp.cpp src/USER-OMP/pair_morse_omp.h src/USER-OMP/pair_peri_lps_omp.cpp src/USER-OMP/pair_peri_lps_omp.h src/USER-OMP/pair_peri_pmb_omp.cpp src/USER-OMP/pair_peri_pmb_omp.h src/USER-OMP/pair_resquared_omp.cpp src/USER-OMP/pair_resquared_omp.h src/USER-OMP/pair_soft_omp.cpp src/USER-OMP/pair_soft_omp.h src/USER-OMP/pair_sw_omp.cpp src/USER-OMP/pair_sw_omp.h src/USER-OMP/pair_table_omp.cpp src/USER-OMP/pair_table_omp.h src/USER-OMP/pair_tersoff_omp.cpp src/USER-OMP/pair_tersoff_omp.h src/USER-OMP/pair_yukawa_colloid_omp.cpp src/USER-OMP/pair_yukawa_colloid_omp.h src/USER-OMP/pair_yukawa_omp.cpp src/USER-OMP/pair_yukawa_omp.h src/USER-OMP/thr_omp.cpp src/USER-OMP/thr_omp.h src/read_data.cpp
This commit is contained in:
Axel Kohlmeyer
@ -21,6 +21,8 @@
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_ellipsoid.h"
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#include "atom_vec_line.h"
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#include "atom_vec_tri.h"
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#include "comm.h"
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#include "update.h"
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#include "force.h"
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@ -42,7 +44,10 @@ using namespace LAMMPS_NS;
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#define DELTA 4 // must be 2 or larger
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// customize for new sections
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#define NSECTIONS 21 // change when add to header::section_keywords
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#define NSECTIONS 23 // change when add to header::section_keywords
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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@ -60,6 +65,10 @@ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
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nellipsoids = 0;
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avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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nlines = 0;
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avec_line = (AtomVecLine *) atom->style_match("line");
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ntris = 0;
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avec_tri = (AtomVecTri *) atom->style_match("tri");
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}
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/* ---------------------------------------------------------------------- */
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@ -150,8 +159,18 @@ void ReadData::command(int narg, char **arg)
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} else if (strcmp(keyword,"Ellipsoids") == 0) {
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if (!avec_ellipsoid)
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error->one(FLERR,"Invalid data file section: Ellipsoids");
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if (atomflag == 0) error->one(FLERR,"Must read Atoms before Ellipsoids");
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ellipsoids();
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids");
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bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
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} else if (strcmp(keyword,"Lines") == 0) {
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if (!avec_line)
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error->one(FLERR,"Invalid data file section: Lines");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines");
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bonus(nlines,(AtomVec *) avec_line,"lines");
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} else if (strcmp(keyword,"Triangles") == 0) {
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if (!avec_tri)
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error->one(FLERR,"Invalid data file section: Triangles");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
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bonus(ntris,(AtomVec *) avec_tri,"triangles");
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} else if (strcmp(keyword,"Bonds") == 0) {
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if (atom->avec->bonds_allow == 0)
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@ -222,25 +241,31 @@ void ReadData::command(int narg, char **arg)
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before MiddleBondTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before "
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"MiddleBondTorsion Coeffs");
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dihedralcoeffs(1);
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} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before EndBondTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before EndBondTorsion Coeffs");
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dihedralcoeffs(2);
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} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before AngleTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before AngleTorsion Coeffs");
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dihedralcoeffs(3);
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} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before AngleAngleTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before "
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"AngleAngleTorsion Coeffs");
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dihedralcoeffs(4);
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} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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@ -274,7 +299,8 @@ void ReadData::command(int narg, char **arg)
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// error if natoms > 0 yet no atoms were read
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if (atom->natoms > 0 && atomflag == 0) error->one(FLERR,"No atoms in data file");
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if (atom->natoms > 0 && atomflag == 0)
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error->one(FLERR,"No atoms in data file");
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// create bond topology now that system is defined
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@ -303,7 +329,7 @@ void ReadData::header(int flag)
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// customize for new sections
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char *section_keywords[NSECTIONS] =
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{"Atoms","Velocities","Ellipsoids",
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{"Atoms","Velocities","Ellipsoids","Lines","Triangles",
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"Bonds","Angles","Dihedrals","Impropers",
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"Masses","Pair Coeffs","Bond Coeffs","Angle Coeffs",
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"Dihedral Coeffs","Improper Coeffs",
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@ -373,6 +399,14 @@ void ReadData::header(int flag)
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if (!avec_ellipsoid)
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error->one(FLERR,"No ellipsoids allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&nellipsoids);
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} else if (strstr(line,"lines")) {
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if (!avec_line)
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error->one(FLERR,"No lines allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&nlines);
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} else if (strstr(line,"triangles")) {
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if (!avec_tri)
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error->one(FLERR,"No triangles allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&ntris);
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}
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else if (strstr(line,"xlo xhi"))
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@ -475,7 +509,8 @@ void ReadData::atoms()
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
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}
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if (natoms != atom->natoms) error->all(FLERR,"Did not assign all atoms correctly");
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if (natoms != atom->natoms)
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error->all(FLERR,"Did not assign all atoms correctly");
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// if any atom ID < 0, error
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// if all atom IDs = 0, tag_enable = 0
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@ -568,11 +603,11 @@ void ReadData::velocities()
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}
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/* ----------------------------------------------------------------------
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read all ellipsoids
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read all bonus data
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to find atoms, must build atom map if not a molecular system
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------------------------------------------------------------------------- */
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void ReadData::ellipsoids()
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void ReadData::bonus(bigint nbonus, AtomVec *ptr, char *type)
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{
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int i,m,nchunk;
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@ -585,7 +620,7 @@ void ReadData::ellipsoids()
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}
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bigint nread = 0;
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bigint natoms = nellipsoids;
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bigint natoms = nbonus;
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while (nread < natoms) {
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if (natoms-nread > CHUNK) nchunk = CHUNK;
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@ -603,7 +638,7 @@ void ReadData::ellipsoids()
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MPI_Bcast(&m,1,MPI_INT,0,world);
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MPI_Bcast(buffer,m,MPI_CHAR,0,world);
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atom->data_bonus(nchunk,buffer,avec_ellipsoid);
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atom->data_bonus(nchunk,buffer,ptr);
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nread += nchunk;
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}
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@ -613,8 +648,8 @@ void ReadData::ellipsoids()
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}
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if (me == 0) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " ellipsoids\n",natoms);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " ellipsoids\n",natoms);
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if (screen) fprintf(screen," " BIGINT_FORMAT " %s\n",natoms,type);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " %s\n",natoms,type);
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}
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}
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@ -660,7 +695,8 @@ void ReadData::bonds()
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if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",sum/factor);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor);
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}
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if (sum != factor*atom->nbonds) error->all(FLERR,"Bonds assigned incorrectly");
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if (sum != factor*atom->nbonds)
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error->all(FLERR,"Bonds assigned incorrectly");
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}
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/* ---------------------------------------------------------------------- */
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@ -705,7 +741,8 @@ void ReadData::angles()
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if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",sum/factor);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor);
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}
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if (sum != factor*atom->nangles) error->all(FLERR,"Angles assigned incorrectly");
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if (sum != factor*atom->nangles)
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error->all(FLERR,"Angles assigned incorrectly");
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}
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/* ---------------------------------------------------------------------- */
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@ -1010,6 +1047,8 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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int natoms = static_cast<int> (atom->natoms);
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bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
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int ellipsoid_flag = 0;
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int line_flag = 0;
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int tri_flag = 0;
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// customize for new sections
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// allocate topology counting vector
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@ -1031,6 +1070,14 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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error->one(FLERR,"Invalid data file section: Ellipsoids");
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ellipsoid_flag = 1;
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skip_lines(nellipsoids);
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} else if (strcmp(keyword,"Lines") == 0) {
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if (!avec_line) error->one(FLERR,"Invalid data file section: Lines");
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line_flag = 1;
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skip_lines(nlines);
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} else if (strcmp(keyword,"Triangles") == 0) {
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if (!avec_tri) error->one(FLERR,"Invalid data file section: Triangles");
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tri_flag = 1;
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skip_lines(ntris);
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} else if (strcmp(keyword,"Pair Coeffs") == 0) {
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if (force->pair == NULL)
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@ -1077,25 +1124,31 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before MiddleBondTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before "
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"MiddleBondTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before EndBondTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before EndBondTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before AngleTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before AngleTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->one(FLERR,"Must define dihedral_style before AngleAngleTorsion Coeffs");
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error->one(FLERR,
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"Must define dihedral_style before "
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"AngleAngleTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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@ -1252,6 +1305,10 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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if (nellipsoids && !ellipsoid_flag)
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error->one(FLERR,"Needed bonus data not in data file");
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if (nlines && !line_flag)
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error->one(FLERR,"Needed bonus data not in data file");
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if (ntris && !tri_flag)
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error->one(FLERR,"Needed bonus data not in data file");
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}
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/* ----------------------------------------------------------------------
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