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Searched refs:nbondtypes (Results 1 – 25 of 110) sorted by relevance

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/dports/science/lammps/lammps-stable_29Sep2021/src/MOLECULE/
H A Dbond_fene_expand.cpp134 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 …]
H A Dbond_fene.cpp130 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()
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H A Dbond_morse.cpp111 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 …]
H A Dbond_quartic.cpp183 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 …]
H A Dbond_gromos.cpp108 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()
H A Dbond_harmonic.cpp109 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()
H A Datom_vec_template.cpp84 atom->nbondtypes = MAX(atom->nbondtypes,onemols[i]->nbondtypes); in process_args()
/dports/science/lammps/lammps-stable_29Sep2021/src/CLASS2/
H A Dbond_class2.cpp117 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 …]
/dports/science/lammps/lammps-stable_29Sep2021/src/EXTRA-MOLECULE/
H A Dbond_harmonic_shift.cpp112 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 …]
H A Dbond_harmonic_shift_cut.cpp114 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 …]
H A Dbond_nonlinear.cpp108 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()
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H A Dbond_gaussian.cpp50 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 …]
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/
H A Dbond_harmonic.cpp137 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()
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/MOLECULE/
H A Dbond_harmonic.cpp137 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()
/dports/science/lammps/lammps-stable_29Sep2021/src/
H A Dbond_zero.cpp69 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()
/dports/science/lammps/lammps-stable_29Sep2021/examples/plugins/
H A Dbond_zero2.cpp69 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()
/dports/science/lammps/lammps-stable_29Sep2021/src/YAFF/
H A Dbond_mm3.cpp120 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()
/dports/science/lammps/lammps-stable_29Sep2021/src/MISC/
H A Dbond_special.cpp125 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()
/dports/science/lammps/lammps-stable_29Sep2021/src/CG-DNA/
H A Dbond_oxdna_fene.cpp266 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 …]
/dports/science/lammps/lammps-stable_29Sep2021/tools/
H A Dmicelle2d.f9060 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'
H A Dchain.f9061 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'
/dports/science/lammps/lammps-stable_29Sep2021/src/INTEL/
H A Dbond_harmonic_intel.cpp280 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;
H A Dbond_fene_intel.cpp310 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;
/dports/science/lammps/lammps-stable_29Sep2021/tools/eff/
H A Drestart2data-pEFF.cpp2173 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 …]
/dports/science/py-rmf/rmf-1.3.1/plugins/vmd/
H A DData_read.cpp72 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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