/dports/science/lammps/lammps-stable_29Sep2021/src/MOLECULE/ |
H A D | bond_fene_expand.cpp | 134 int n = atom->nbondtypes; in allocate() 205 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 206 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 207 fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 208 fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 209 fwrite(&shift[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 227 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 228 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 230 MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 231 MPI_Bcast(&shift[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() [all …]
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H A D | bond_fene.cpp | 130 int n = atom->nbondtypes; in allocate() 198 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 199 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 200 fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 201 fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 218 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 219 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 220 MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 221 MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 223 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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H A D | bond_morse.cpp | 111 int n = atom->nbondtypes; in allocate() 130 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 163 fwrite(&d0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 164 fwrite(&alpha[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 165 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 177 utils::sfread(FLERR,&d0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 181 MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 182 MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 183 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 185 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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H A D | bond_quartic.cpp | 183 int n = atom->nbondtypes; in allocate() 264 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 265 fwrite(&b1[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 266 fwrite(&b2[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 267 fwrite(&rc[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 268 fwrite(&u0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 286 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 287 MPI_Bcast(&b1[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 288 MPI_Bcast(&b2[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 289 MPI_Bcast(&rc[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() [all …]
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H A D | bond_gromos.cpp | 108 int n = atom->nbondtypes; in allocate() 127 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 158 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 159 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 171 utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 172 utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 174 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 175 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 177 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 186 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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H A D | bond_harmonic.cpp | 109 int n = atom->nbondtypes; in allocate() 128 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 159 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 160 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 172 utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 173 utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 175 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 176 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 178 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 187 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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H A D | atom_vec_template.cpp | 84 atom->nbondtypes = MAX(atom->nbondtypes,onemols[i]->nbondtypes); in process_args()
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/dports/science/lammps/lammps-stable_29Sep2021/src/CLASS2/ |
H A D | bond_class2.cpp | 117 int n = atom->nbondtypes; in allocate() 173 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 174 fwrite(&k2[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 175 fwrite(&k3[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 176 fwrite(&k4[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 193 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 194 MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 195 MPI_Bcast(&k3[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 196 MPI_Bcast(&k4[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 198 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/src/EXTRA-MOLECULE/ |
H A D | bond_harmonic_shift.cpp | 112 int n = atom->nbondtypes; in allocate() 132 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 167 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 168 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 169 fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 181 utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 185 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 186 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 187 MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 189 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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H A D | bond_harmonic_shift_cut.cpp | 114 int n = atom->nbondtypes; in allocate() 134 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 169 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 170 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 171 fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 183 utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 187 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 188 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 189 MPI_Bcast(&r1[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 191 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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H A D | bond_nonlinear.cpp | 108 int n = atom->nbondtypes; in allocate() 127 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 158 fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 159 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 160 fwrite(&lamda[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 173 utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 176 MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 177 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 178 MPI_Bcast(&lamda[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 180 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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H A D | bond_gaussian.cpp | 50 for (int i = 1; i <= atom->nbondtypes; i++) { in ~BondGaussian() 134 int n = atom->nbondtypes; in allocate() 159 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 206 fwrite(&nterms[1],sizeof(int),atom->nbondtypes,fp); in write_restart() 207 for (int i = 1; i <= atom->nbondtypes; i++) { in write_restart() 227 MPI_Bcast(&nterms[1],atom->nbondtypes,MPI_INT,0,world); in read_restart() 230 for (int i = 1; i <= atom->nbondtypes; i++) { in read_restart() 237 for (int i = 1; i <= atom->nbondtypes; i++) { in read_restart() 244 for (int i = 1; i <= atom->nbondtypes; i++) { in read_restart() 250 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/ |
H A D | bond_harmonic.cpp | 137 int n = atom->nbondtypes; in allocate() 156 force->bounds(arg[0],atom->nbondtypes,ilo,ihi); in coeff() 187 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 188 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 200 fread(&k[1],sizeof(double),atom->nbondtypes,fp); in read_restart() 201 fread(&r0[1],sizeof(double),atom->nbondtypes,fp); in read_restart() 203 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 204 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 206 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 215 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/MOLECULE/ |
H A D | bond_harmonic.cpp | 137 int n = atom->nbondtypes; in allocate() 156 force->bounds(arg[0],atom->nbondtypes,ilo,ihi); in coeff() 187 fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 188 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 200 fread(&k[1],sizeof(double),atom->nbondtypes,fp); in read_restart() 201 fread(&r0[1],sizeof(double),atom->nbondtypes,fp); in read_restart() 203 MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 204 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 206 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 215 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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/dports/science/lammps/lammps-stable_29Sep2021/src/ |
H A D | bond_zero.cpp | 69 int n = atom->nbondtypes; in allocate() 88 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 118 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 130 utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 132 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 134 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 143 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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/dports/science/lammps/lammps-stable_29Sep2021/examples/plugins/ |
H A D | bond_zero2.cpp | 69 int n = atom->nbondtypes; in allocate() 88 utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); in coeff() 118 fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp); in write_restart() 130 utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); in read_restart() 132 MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world); in read_restart() 134 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 143 for (int i = 1; i <= atom->nbondtypes; i++) fprintf(fp, "%d %g\n", i, r0[i]); in write_data()
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/dports/science/lammps/lammps-stable_29Sep2021/src/YAFF/ |
H A D | bond_mm3.cpp | 120 int n = atom->nbondtypes; in allocate() 139 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 170 fwrite(&k2[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 171 fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 183 utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 184 utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 186 MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 187 MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 189 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 198 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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/dports/science/lammps/lammps-stable_29Sep2021/src/MISC/ |
H A D | bond_special.cpp | 125 int n = atom->nbondtypes; in allocate() 144 utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); in coeff() 175 fwrite(&factor_lj[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 176 fwrite(&factor_coul[1],sizeof(double),atom->nbondtypes,fp); in write_restart() 188 utils::sfread(FLERR,&factor_lj[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 189 utils::sfread(FLERR,&factor_coul[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); in read_restart() 191 MPI_Bcast(&factor_lj[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 192 MPI_Bcast(&factor_coul[1],atom->nbondtypes,MPI_DOUBLE,0,world); in read_restart() 194 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() 203 for (int i = 1; i <= atom->nbondtypes; i++) in write_data()
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/dports/science/lammps/lammps-stable_29Sep2021/src/CG-DNA/ |
H A D | bond_oxdna_fene.cpp | 266 int n = atom->nbondtypes; in allocate() 286 utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); in coeff() 330 fwrite(&k[1], sizeof(double), atom->nbondtypes, fp); in write_restart() 331 fwrite(&Delta[1], sizeof(double), atom->nbondtypes, fp); in write_restart() 332 fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp); in write_restart() 344 utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); in read_restart() 348 MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world); in read_restart() 349 MPI_Bcast(&Delta[1], atom->nbondtypes, MPI_DOUBLE, 0, world); in read_restart() 350 MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world); in read_restart() 352 for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; in read_restart() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/tools/ |
H A D | micelle2d.f90 | 60 INTEGER :: natoms, maxatom, ntypes, nbonds, nbondtypes, iseed variable 173 nbondtypes = 1 174 IF (nonflag == 1) nbondtypes = 2 178 nbondtypes = 0 192 WRITE (6,*) nbondtypes,' bond types'
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H A D | chain.f90 | 61 INTEGER :: i, n, m, nmolecule, natoms, ntypes, nbonds, nbondtypes variable 263 nbondtypes = 0 267 IF (nbondtype(iset) > nbondtypes) nbondtypes = nbondtype(iset) 283 WRITE (6,*) nbondtypes,' bond types'
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/dports/science/lammps/lammps-stable_29Sep2021/src/INTEL/ |
H A D | bond_harmonic_intel.cpp | 280 const int bp1 = atom->nbondtypes + 1; 292 void BondHarmonicIntel::ForceConst<flt_t>::set_ntypes(const int nbondtypes, argument 294 if (nbondtypes != _nbondtypes) { 298 if (nbondtypes > 0) 299 _memory->create(fc,nbondtypes,"bondharmonicintel.fc"); 301 _nbondtypes = nbondtypes;
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H A D | bond_fene_intel.cpp | 310 const int bp1 = atom->nbondtypes + 1; 324 void BondFENEIntel::ForceConst<flt_t>::set_ntypes(const int nbondtypes, argument 326 if (nbondtypes != _nbondtypes) { 330 if (nbondtypes > 0) 331 _memory->create(fc,nbondtypes,"bondfeneintel.fc"); 333 _nbondtypes = nbondtypes;
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/dports/science/lammps/lammps-stable_29Sep2021/tools/eff/ |
H A D | restart2data-pEFF.cpp | 2173 data.bond_fene_k = new double[data.nbondtypes+1]; in bond() 2174 data.bond_fene_r0 = new double[data.nbondtypes+1]; in bond() 2654 if (nbondtypes) fprintf(fp,"%d bond types\n",nbondtypes); in write() 2873 for (int i = 1; i <= nbondtypes; i++) in write() 2879 for (int i = 1; i <= nbondtypes; i++) in write() 2885 for (int i = 1; i <= nbondtypes; i++) in write() 2892 for (int i = 1; i <= nbondtypes; i++) in write() 2897 for (int i = 1; i <= nbondtypes; i++) in write() 2902 for (int i = 1; i <= nbondtypes; i++) in write() 2908 for (int i = 1; i <= nbondtypes; i++) in write() [all …]
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/dports/science/py-rmf/rmf-1.3.1/plugins/vmd/ |
H A D | Data_read.cpp | 72 float **bondorderptr, int **bondtype, int *nbondtypes, in read_bonds() argument 85 *nbondtypes = 2; in read_bonds() 99 RMF_INTERNAL_CHECK(bt >= 0 && bt < *nbondtypes, "Invalid bond type "); in read_bonds()
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