diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1 index 6433d417de..7d5af6aec3 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1 @@ -32,7 +32,6 @@ Reading data file ... 2 = max bonds/atom 10 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 8 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.4 index cf52039af3..da1a98817b 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.4 @@ -32,7 +32,6 @@ Reading data file ... 2 = max bonds/atom 10 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 8 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1 index f69905aa0c..f9b5a909eb 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1 @@ -32,7 +32,6 @@ Reading data file ... 2 = max bonds/atom 16 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 13 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.4 index 7ded7eec79..8744f7b4cd 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.4 @@ -32,7 +32,6 @@ Reading data file ... 2 = max bonds/atom 16 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 13 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.1 index 0c27e603c8..40a6f32d18 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.1 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 10 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 8 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.4 index e787299257..0ab77a2d50 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.4 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 10 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 8 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.1 index 6379401f02..6ad31311d6 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.1 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 16 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 13 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.4 index 5db1bd47b3..0cd4417b42 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.4 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 16 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 13 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.1 index ac55cbd994..965502247e 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.1 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 10 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 8 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.4 index 735559c643..6d5e7669bb 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.4 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 10 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 8 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++1 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++1 index 0193d361af..080db1e84f 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++1 @@ -36,7 +36,6 @@ Reading data file ... 2 = max bonds/atom 26 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 24 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++4 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++4 index eda197670d..e04e7ab623 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++4 @@ -36,7 +36,6 @@ Reading data file ... 2 = max bonds/atom 26 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 24 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++1 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++1 index e6c11be477..64807e1037 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++1 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++1 @@ -36,7 +36,6 @@ Reading data file ... 2 = max bonds/atom 26 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 24 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++4 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++4 index d16e7b4935..2a7b689c6c 100644 --- a/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++4 +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++4 @@ -36,7 +36,6 @@ Reading data file ... 2 = max bonds/atom 26 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 24 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.1 index a3fe688104..9e047a580d 100644 --- a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.1 +++ b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.1 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 16 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 13 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.4 index bbca5e3594..94b722f1da 100644 --- a/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.4 +++ b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.4 @@ -33,7 +33,6 @@ Reading data file ... 2 = max bonds/atom 16 ellipsoids reading bonds ... -Setting oxDNA 3'->5' bond directionality ... 13 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 diff --git a/src/CG-DNA/atom_vec_oxdna.cpp b/src/CG-DNA/atom_vec_oxdna.cpp index 150e9e6d1d..240a38709b 100644 --- a/src/CG-DNA/atom_vec_oxdna.cpp +++ b/src/CG-DNA/atom_vec_oxdna.cpp @@ -66,7 +66,7 @@ void AtomVecOxdna::grow_pointers() } /* ---------------------------------------------------------------------- - initialize atom quantity + initialize atom quantity 5' partner ------------------------------------------------------------------------- */ void AtomVecOxdna::data_atom_post(int ilocal) @@ -80,45 +80,17 @@ void AtomVecOxdna::data_atom_post(int ilocal) store 5' partner to inform 3'->5' bond directionality ------------------------------------------------------------------------- */ -void AtomVecOxdna::data_bonds_post(int n, char *buf, tagint id_offset) +void AtomVecOxdna::data_bonds_post(int m, int num_bond, tagint atom1, + tagint atom2, tagint id_offset) { - - int m,tmp,itype,rv; - tagint atom1,atom2; - char *next; - tagint *id5p = atom->id5p; - if (comm->me == 0) utils::logmesg(lmp,"Setting oxDNA 3'->5' bond directionality ...\n"); + if (id_offset) { + atom1 += id_offset; + atom2 += id_offset; + } - 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 (id_offset) { - atom1 += id_offset; - atom2 += id_offset; - } - - if ((m = atom->map(atom1)) >= 0) { - id5p[m] = atom2; - } - - buf = next + 1; + if ((m = atom->map(atom1)) >= 0) { + id5p[m] = atom2; } } - -/* ---------------------------------------------------------------------- - process bond information as per data file - store 5' partner to inform 3'->5' bond directionality -------------------------------------------------------------------------- */ - -void AtomVecOxdna::data_bonds_post2(int m, int num_bond, tagint atom1, tagint atom2, tagint id_offset) -{ - -printf("CALLED FROM ATOM_VEC_OXDNA\n"); - -} diff --git a/src/CG-DNA/atom_vec_oxdna.h b/src/CG-DNA/atom_vec_oxdna.h index bb8f9a457d..e3297a0482 100644 --- a/src/CG-DNA/atom_vec_oxdna.h +++ b/src/CG-DNA/atom_vec_oxdna.h @@ -30,8 +30,7 @@ class AtomVecOxdna : public AtomVec { ~AtomVecOxdna(); void grow_pointers(); - virtual void data_bonds_post(int, char *, tagint); - virtual void data_bonds_post2(int, int, tagint, tagint, tagint); + virtual void data_bonds_post(int, int, tagint, tagint, tagint); void data_atom_post(int); private: diff --git a/src/atom.cpp b/src/atom.cpp index fbc930dca1..323f88719a 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1288,7 +1288,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, bond_type[m][num_bond[m]] = itype; bond_atom[m][num_bond[m]] = atom2; num_bond[m]++; - avec->data_bonds_post2(m, num_bond[m], atom1, atom2, id_offset); + avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset); } } if (newton_bond == 0) { @@ -1298,6 +1298,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, bond_type[m][num_bond[m]] = itype; bond_atom[m][num_bond[m]] = atom1; num_bond[m]++; + avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset); } } } diff --git a/src/atom_vec.h b/src/atom_vec.h index d65f1f3345..ad3b4c6626 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -129,8 +129,7 @@ class AtomVec : protected Pointers { virtual void data_atom_bonus(int, char **) {} virtual void data_body(int, int, int, int *, double *) {} - virtual void data_bonds_post(int, char *, tagint) {} - virtual void data_bonds_post2(int, int , tagint, tagint, tagint) {} + virtual void data_bonds_post(int, int , tagint, tagint, tagint) {} virtual void pack_data(double **); virtual void write_data(FILE *, int, double **); diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 6df260801c..aa19f14bc8 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -442,11 +442,11 @@ void AtomVecHybrid::data_atom_post(int ilocal) modify what AtomVec::data_bonds() just unpacked or initialize other bond quantities ------------------------------------------------------------------------- */ -void AtomVecHybrid::data_bonds_post2(int m, int num_bond, tagint atom1, tagint atom2, tagint id_offset) +void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1, + tagint atom2, tagint id_offset) { - -printf("CALLED FROM ATOM_VEC_HYBRID\n"); - + for (int k = 0; k < nstyles; k++) + styles[k]->data_bonds_post(m, num_bond, atom1, atom2, id_offset); } /* ---------------------------------------------------------------------- diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index 317dc86338..e596754fb3 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -56,7 +56,7 @@ class AtomVecHybrid : public AtomVec { void create_atom_post(int); void data_atom_post(int); - virtual void data_bonds_post2(int, int, tagint, tagint, tagint); + virtual void data_bonds_post(int, int, tagint, tagint, tagint); void pack_data_pre(int); void pack_data_post(int); diff --git a/src/read_data.cpp b/src/read_data.cpp index af200d3af6..183ef30648 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1342,7 +1342,6 @@ void ReadData::bonds(int firstpass) if (eof) error->all(FLERR,"Unexpected end of data file"); strcpy(buffer_post,buffer); atom->data_bonds(nchunk,buffer,count,id_offset,boffset); - if (!firstpass) avec->data_bonds_post(nchunk,buffer_post,id_offset); nread += nchunk; }