improve data file section parsing
- avoid segfaults when dereferencing a null pointer on short files - allow skipping over empty and comment-only lines.
This commit is contained in:
Axel Kohlmeyer
610
src/atom.cpp
610
src/atom.cpp
@ -1137,54 +1137,57 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
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for (int i = 0; i < n; i++) {
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next = strchr(buf,'\n');
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if (!next) error->all(FLERR, "Missing data in Atoms section of data file");
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*next = '\0';
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auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
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if ((int)values.size() != nwords)
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if (values.size() == 0) {
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// skip over empty of comment lines
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} else if ((int)values.size() != nwords) {
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error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
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int imx = 0, imy = 0, imz = 0;
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if (imageflag) {
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imx = utils::inumeric(FLERR,values[iptr],false,lmp);
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imy = utils::inumeric(FLERR,values[iptr+1],false,lmp);
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imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
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if ((domain->dimension == 2) && (imz != 0))
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error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
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if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; }
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if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; }
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if ((!domain->zperiodic) && (imz != 0)) { reset_image_flag[2] = true; imz = 0; }
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}
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imagedata = ((imageint) (imx + IMGMAX) & IMGMASK) |
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} else {
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int imx = 0, imy = 0, imz = 0;
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if (imageflag) {
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imx = utils::inumeric(FLERR,values[iptr],false,lmp);
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imy = utils::inumeric(FLERR,values[iptr+1],false,lmp);
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imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
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if ((domain->dimension == 2) && (imz != 0))
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error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
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if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; }
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if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; }
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if ((!domain->zperiodic) && (imz != 0)) { reset_image_flag[2] = true; imz = 0; }
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}
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imagedata = ((imageint) (imx + IMGMAX) & IMGMASK) |
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(((imageint) (imy + IMGMAX) & IMGMASK) << IMGBITS) |
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(((imageint) (imz + IMGMAX) & IMGMASK) << IMG2BITS);
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xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp);
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xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp);
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xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp);
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if (shiftflag) {
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xdata[0] += shift[0];
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xdata[1] += shift[1];
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xdata[2] += shift[2];
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}
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xdata[0] = utils::numeric(FLERR,values[xptr],false,lmp);
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xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp);
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xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp);
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if (shiftflag) {
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xdata[0] += shift[0];
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xdata[1] += shift[1];
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xdata[2] += shift[2];
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}
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domain->remap(xdata,imagedata);
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if (triclinic) {
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domain->x2lamda(xdata,lamda);
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coord = lamda;
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} else coord = xdata;
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domain->remap(xdata,imagedata);
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if (triclinic) {
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domain->x2lamda(xdata,lamda);
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coord = lamda;
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} else coord = xdata;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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avec->data_atom(xdata,imagedata,values);
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if (id_offset) tag[nlocal-1] += id_offset;
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if (mol_offset) molecule[nlocal-1] += mol_offset;
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if (type_offset) {
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type[nlocal-1] += type_offset;
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if (type[nlocal-1] > ntypes)
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error->one(FLERR,"Invalid atom type in Atoms section of data file");
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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avec->data_atom(xdata,imagedata,values);
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if (id_offset) tag[nlocal-1] += id_offset;
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if (mol_offset) molecule[nlocal-1] += mol_offset;
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if (type_offset) {
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type[nlocal-1] += type_offset;
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if (type[nlocal-1] > ntypes)
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error->one(FLERR,"Invalid atom type in Atoms section of data file");
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}
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}
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}
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buf = next + 1;
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}
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}
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@ -1200,30 +1203,25 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
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int m;
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char *next;
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next = strchr(buf,'\n');
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*next = '\0';
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int nwords = utils::trim_and_count_words(buf);
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*next = '\n';
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if (nwords != avec->size_data_vel)
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error->all(FLERR,"Incorrect velocity format in data file");
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// loop over lines of atom velocities
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// tokenize the line into values
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// if I own atom tag, unpack its values
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for (int i = 0; i < n; i++) {
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next = strchr(buf,'\n');
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if (!next) error->all(FLERR, "Missing data in Velocities section of data file");
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*next = '\0';
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auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
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if ((int)values.size() != nwords)
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error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
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tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
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if (tagdata <= 0 || tagdata > map_tag_max)
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error->one(FLERR,"Invalid atom ID in Velocities section of data file");
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if ((m = map(tagdata)) >= 0) avec->data_vel(m,values);
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if (values.size() == 0) {
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// skip over empty or comment lines
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} else if ((int)values.size() != avec->size_data_vel) {
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error->all(FLERR, "Incorrect velocity format in data file: {}", utils::trim(buf));
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} else {
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tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
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if (tagdata <= 0 || tagdata > map_tag_max)
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error->one(FLERR,"Invalid atom ID {} in Velocities section of data file: {}", tagdata, buf);
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if ((m = map(tagdata)) >= 0) avec->data_vel(m,values);
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}
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buf = next + 1;
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}
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}
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@ -1246,47 +1244,51 @@ void Atom::data_bonds(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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if (!next) error->all(FLERR, "Missing data in Bonds section of data file");
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*next = '\0';
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try {
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ValueTokenizer values(utils::trim_comment(buf));
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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if (values.has_next()) throw TokenizerException("Too many tokens","");
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} catch (TokenizerException &e) {
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error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
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}
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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}
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itype += type_offset;
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if ((atom1 <= 0) || (atom1 > map_tag_max) ||
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(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
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error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
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if (itype <= 0 || itype > nbondtypes)
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error->one(FLERR,"Invalid bond type in {}: {}", location, utils::trim(buf));
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if ((m = map(atom1)) >= 0) {
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if (count) count[m]++;
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else {
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bond_type[m][num_bond[m]] = itype;
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bond_atom[m][num_bond[m]] = atom2;
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num_bond[m]++;
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avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
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ValueTokenizer values(utils::trim_comment(buf));
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// skip over empty of comment lines
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if (values.has_next()) {
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try {
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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if (values.has_next()) throw TokenizerException("Too many tokens","");
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} catch (TokenizerException &e) {
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error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
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}
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}
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if (newton_bond == 0) {
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if ((m = map(atom2)) >= 0) {
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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}
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itype += type_offset;
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if ((atom1 <= 0) || (atom1 > map_tag_max) ||
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(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
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error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
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if (itype <= 0 || itype > nbondtypes)
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error->one(FLERR,"Invalid bond type in {}: {}", location, utils::trim(buf));
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if ((m = map(atom1)) >= 0) {
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if (count) count[m]++;
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else {
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bond_type[m][num_bond[m]] = itype;
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bond_atom[m][num_bond[m]] = atom1;
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bond_atom[m][num_bond[m]] = atom2;
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num_bond[m]++;
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avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
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}
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}
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if (newton_bond == 0) {
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if ((m = map(atom2)) >= 0) {
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if (count) count[m]++;
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else {
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bond_type[m][num_bond[m]] = itype;
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bond_atom[m][num_bond[m]] = atom1;
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num_bond[m]++;
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avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
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}
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}
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}
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}
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buf = next + 1;
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}
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@ -1310,44 +1312,36 @@ void Atom::data_angles(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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if (!next) error->all(FLERR, "Missing data in Angles section of data file");
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*next = '\0';
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try {
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ValueTokenizer values(utils::trim_comment(buf));
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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atom3 = values.next_tagint();
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if (values.has_next()) throw TokenizerException("Too many tokens","");
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} catch (TokenizerException &e) {
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error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
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}
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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atom3 += id_offset;
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}
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itype += type_offset;
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if ((atom1 <= 0) || (atom1 > map_tag_max) ||
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(atom2 <= 0) || (atom2 > map_tag_max) ||
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(atom3 <= 0) || (atom3 > map_tag_max) ||
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(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
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error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
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if (itype <= 0 || itype > nangletypes)
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error->one(FLERR,"Invalid angle type in {}: {}", location, utils::trim(buf));
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if ((m = map(atom2)) >= 0) {
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if (count) count[m]++;
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else {
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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ValueTokenizer values(utils::trim_comment(buf));
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// skip over empty of comment lines
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if (values.has_next()) {
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try {
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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atom3 = values.next_tagint();
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if (values.has_next()) throw TokenizerException("Too many tokens","");
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} catch (TokenizerException &e) {
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error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
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}
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}
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if (newton_bond == 0) {
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if ((m = map(atom1)) >= 0) {
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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atom3 += id_offset;
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}
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itype += type_offset;
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if ((atom1 <= 0) || (atom1 > map_tag_max) ||
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(atom2 <= 0) || (atom2 > map_tag_max) ||
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(atom3 <= 0) || (atom3 > map_tag_max) ||
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(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
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error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
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if (itype <= 0 || itype > nangletypes)
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error->one(FLERR,"Invalid angle type in {}: {}", location, utils::trim(buf));
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if ((m = map(atom2)) >= 0) {
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if (count) count[m]++;
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else {
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angle_type[m][num_angle[m]] = itype;
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@ -1357,14 +1351,26 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
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num_angle[m]++;
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}
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}
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if ((m = map(atom3)) >= 0) {
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if (count) count[m]++;
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else {
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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if (newton_bond == 0) {
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if ((m = map(atom1)) >= 0) {
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if (count) count[m]++;
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else {
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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}
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}
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if ((m = map(atom3)) >= 0) {
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if (count) count[m]++;
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else {
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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}
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}
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}
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}
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@ -1390,49 +1396,40 @@ 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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if (!next) error->all(FLERR, "Missing data in Dihedrals section of data file");
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*next = '\0';
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try {
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ValueTokenizer values(utils::trim_comment(buf));
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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atom3 = values.next_tagint();
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atom4 = values.next_tagint();
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if (values.has_next()) throw TokenizerException("Too many tokens","");
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} catch (TokenizerException &e) {
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error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
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}
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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atom3 += id_offset;
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atom4 += id_offset;
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}
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itype += type_offset;
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ValueTokenizer values(utils::trim_comment(buf));
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// skip over empty of comment lines
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if (values.has_next()) {
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try {
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values.next_int();
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itype = values.next_int();
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atom1 = values.next_tagint();
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atom2 = values.next_tagint();
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atom3 = values.next_tagint();
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atom4 = values.next_tagint();
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if (values.has_next()) throw TokenizerException("Too many tokens","");
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} catch (TokenizerException &e) {
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error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
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}
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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atom3 += id_offset;
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atom4 += id_offset;
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}
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itype += type_offset;
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if ((atom1 <= 0) || (atom1 > map_tag_max) ||
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(atom2 <= 0) || (atom2 > map_tag_max) ||
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(atom3 <= 0) || (atom3 > map_tag_max) ||
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(atom4 <= 0) || (atom4 > map_tag_max) ||
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(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
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(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
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error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
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if (itype <= 0 || itype > ndihedraltypes)
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error->one(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(buf));
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if ((m = map(atom2)) >= 0) {
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||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
||||
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
||||
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
||||
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
||||
num_dihedral[m]++;
|
||||
}
|
||||
}
|
||||
if (newton_bond == 0) {
|
||||
if ((m = map(atom1)) >= 0) {
|
||||
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
|
||||
(atom2 <= 0) || (atom2 > map_tag_max) ||
|
||||
(atom3 <= 0) || (atom3 > map_tag_max) ||
|
||||
(atom4 <= 0) || (atom4 > map_tag_max) ||
|
||||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
|
||||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
|
||||
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
|
||||
if (itype <= 0 || itype > ndihedraltypes)
|
||||
error->one(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(buf));
|
||||
if ((m = map(atom2)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
@ -1443,26 +1440,39 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
|
||||
num_dihedral[m]++;
|
||||
}
|
||||
}
|
||||
if ((m = map(atom3)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
||||
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
||||
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
||||
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
||||
num_dihedral[m]++;
|
||||
if (newton_bond == 0) {
|
||||
if ((m = map(atom1)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
||||
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
||||
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
||||
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
||||
num_dihedral[m]++;
|
||||
}
|
||||
}
|
||||
}
|
||||
if ((m = map(atom4)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
||||
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
||||
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
||||
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
||||
num_dihedral[m]++;
|
||||
if ((m = map(atom3)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
||||
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
||||
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
||||
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
||||
num_dihedral[m]++;
|
||||
}
|
||||
}
|
||||
if ((m = map(atom4)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
dihedral_type[m][num_dihedral[m]] = itype;
|
||||
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
||||
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
||||
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
||||
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
||||
num_dihedral[m]++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1488,49 +1498,40 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
if (!next) error->all(FLERR, "Missing data in Impropers section of data file");
|
||||
*next = '\0';
|
||||
try {
|
||||
ValueTokenizer values(utils::trim_comment(buf));
|
||||
values.next_int();
|
||||
itype = values.next_int();
|
||||
atom1 = values.next_tagint();
|
||||
atom2 = values.next_tagint();
|
||||
atom3 = values.next_tagint();
|
||||
atom4 = values.next_tagint();
|
||||
if (values.has_next()) throw TokenizerException("Too many tokens","");
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
|
||||
}
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
atom3 += id_offset;
|
||||
atom4 += id_offset;
|
||||
}
|
||||
itype += type_offset;
|
||||
ValueTokenizer values(utils::trim_comment(buf));
|
||||
// skip over empty of comment lines
|
||||
if (values.has_next()) {
|
||||
try {
|
||||
values.next_int();
|
||||
itype = values.next_int();
|
||||
atom1 = values.next_tagint();
|
||||
atom2 = values.next_tagint();
|
||||
atom3 = values.next_tagint();
|
||||
atom4 = values.next_tagint();
|
||||
if (values.has_next()) throw TokenizerException("Too many tokens","");
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
|
||||
}
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
atom3 += id_offset;
|
||||
atom4 += id_offset;
|
||||
}
|
||||
itype += type_offset;
|
||||
|
||||
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
|
||||
(atom2 <= 0) || (atom2 > map_tag_max) ||
|
||||
(atom3 <= 0) || (atom3 > map_tag_max) ||
|
||||
(atom4 <= 0) || (atom4 > map_tag_max) ||
|
||||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
|
||||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
|
||||
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
|
||||
if (itype <= 0 || itype > nimpropertypes)
|
||||
error->one(FLERR, "Invalid improper type in {}: {}", location, utils::trim(buf));
|
||||
if ((m = map(atom2)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
}
|
||||
if (newton_bond == 0) {
|
||||
if ((m = map(atom1)) >= 0) {
|
||||
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
|
||||
(atom2 <= 0) || (atom2 > map_tag_max) ||
|
||||
(atom3 <= 0) || (atom3 > map_tag_max) ||
|
||||
(atom4 <= 0) || (atom4 > map_tag_max) ||
|
||||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
|
||||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
|
||||
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
|
||||
if (itype <= 0 || itype > nimpropertypes)
|
||||
error->one(FLERR, "Invalid improper type in {}: {}", location, utils::trim(buf));
|
||||
if ((m = map(atom2)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
@ -1541,26 +1542,39 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
|
||||
num_improper[m]++;
|
||||
}
|
||||
}
|
||||
if ((m = map(atom3)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
if (newton_bond == 0) {
|
||||
if ((m = map(atom1)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
}
|
||||
}
|
||||
if ((m = map(atom4)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
if ((m = map(atom3)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
}
|
||||
if ((m = map(atom4)) >= 0) {
|
||||
if (count) count[m]++;
|
||||
else {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1579,34 +1593,29 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
|
||||
int m;
|
||||
char *next;
|
||||
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
int nwords = utils::trim_and_count_words(buf);
|
||||
*next = '\n';
|
||||
|
||||
if (nwords != avec_bonus->size_data_bonus)
|
||||
error->all(FLERR,"Incorrect bonus data format in data file");
|
||||
|
||||
// loop over lines of bonus atom data
|
||||
// tokenize the line into values
|
||||
// if I own atom tag, unpack its values
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
if (!next) error->all(FLERR, "Missing data in Bonus section of data file");
|
||||
*next = '\0';
|
||||
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
|
||||
if ((int)values.size() != nwords)
|
||||
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
|
||||
if (values.size() == 0) {
|
||||
// skip over empty of comment lines
|
||||
} else if ((int)values.size() != avec_bonus->size_data_bonus) {
|
||||
error->all(FLERR, "Incorrect bonus data format in data file: {}", utils::trim(buf));
|
||||
} else {
|
||||
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
|
||||
if (tagdata <= 0 || tagdata > map_tag_max)
|
||||
error->one(FLERR,"Invalid atom ID in Bonus section of data file");
|
||||
|
||||
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
|
||||
if (tagdata <= 0 || tagdata > map_tag_max)
|
||||
error->one(FLERR,"Invalid atom ID in Bonus section of data file");
|
||||
|
||||
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
|
||||
// since data_bonus() was called with child ptr, and method is virtual
|
||||
|
||||
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,values);
|
||||
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
|
||||
// since data_bonus() was called with child ptr, and method is virtual
|
||||
|
||||
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,values);
|
||||
}
|
||||
buf = next + 1;
|
||||
}
|
||||
}
|
||||
@ -1631,46 +1640,49 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
char *next = strchr(buf,'\n');
|
||||
if (!next) error->all(FLERR, "Missing data in Bodies section of data file");
|
||||
*next = '\0';
|
||||
|
||||
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
|
||||
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
|
||||
int ninteger = utils::inumeric(FLERR,values[1],false,lmp);
|
||||
int ndouble = utils::inumeric(FLERR,values[2],false,lmp);
|
||||
if (values.size()) {
|
||||
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
|
||||
int ninteger = utils::inumeric(FLERR,values[1],false,lmp);
|
||||
int ndouble = utils::inumeric(FLERR,values[2],false,lmp);
|
||||
|
||||
if (unique_tags->find(tagdata) == unique_tags->end())
|
||||
unique_tags->insert(tagdata);
|
||||
else
|
||||
error->one(FLERR,"Duplicate atom ID in Bodies section of data file");
|
||||
if (unique_tags->find(tagdata) == unique_tags->end())
|
||||
unique_tags->insert(tagdata);
|
||||
else
|
||||
error->one(FLERR,"Duplicate atom ID {} in Bodies section of data file", tagdata);
|
||||
|
||||
buf = next + 1;
|
||||
int m = map(tagdata);
|
||||
if (m >= 0) {
|
||||
ivalues.resize(ninteger);
|
||||
dvalues.resize(ndouble);
|
||||
buf = next + 1;
|
||||
int m = map(tagdata);
|
||||
if (m >= 0) {
|
||||
ivalues.resize(ninteger);
|
||||
dvalues.resize(ndouble);
|
||||
|
||||
for (int j = 0; j < ninteger; j++) {
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
buf[strcspn(buf," \t\n\r\f")] = '\0';
|
||||
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
|
||||
buf += strlen(buf)+1;
|
||||
}
|
||||
for (int j = 0; j < ninteger; j++) {
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
buf[strcspn(buf," \t\n\r\f")] = '\0';
|
||||
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
|
||||
buf += strlen(buf)+1;
|
||||
}
|
||||
|
||||
for (int j = 0; j < ndouble; j++) {
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
buf[strcspn(buf," \t\n\r\f")] = '\0';
|
||||
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
|
||||
buf += strlen(buf)+1;
|
||||
}
|
||||
for (int j = 0; j < ndouble; j++) {
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
buf[strcspn(buf," \t\n\r\f")] = '\0';
|
||||
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
|
||||
buf += strlen(buf)+1;
|
||||
}
|
||||
|
||||
avec_body->data_body(m,ninteger,ndouble,ivalues.data(),dvalues.data());
|
||||
avec_body->data_body(m,ninteger,ndouble,ivalues.data(),dvalues.data());
|
||||
|
||||
} else {
|
||||
int nvalues = ninteger + ndouble; // number of values to skip
|
||||
for (int j = 0; j < nvalues; j++) {
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
buf[strcspn(buf," \t\n\r\f")] = '\0';
|
||||
buf += strlen(buf)+1;
|
||||
} else {
|
||||
int nvalues = ninteger + ndouble; // number of values to skip
|
||||
for (int j = 0; j < nvalues; j++) {
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
buf[strcspn(buf," \t\n\r\f")] = '\0';
|
||||
buf += strlen(buf)+1;
|
||||
}
|
||||
}
|
||||
}
|
||||
buf += strspn(buf," \t\n\r\f");
|
||||
|
||||
Reference in New Issue
Block a user