add more strict checking of data when parsing molecule files to detect format errors (2a7d2dee) · Commits · 郑智淋 / lammps

src/molecule.cpp

+213 −220

Original line number	Diff line number	Diff line
		@@ -427,47 +427,61 @@ void Molecule::read(int flag)

		// search line for header keywords and set corresponding variable

		if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
		else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
		else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
		else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
		else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);

		else if (strstr(line,"mass")) {
		int nmatch = 0;
		int nwant = 0;
		if (strstr(line,"atoms")) {
		nmatch = sscanf(line,"%d",&natoms);
		nwant = 1;
		} else if (strstr(line,"bonds")) {
		nmatch = sscanf(line,"%d",&nbonds);
		nwant = 1;
		} else if (strstr(line,"angles")) {
		nmatch = sscanf(line,"%d",&nangles);
		nwant = 1;
		} else if (strstr(line,"dihedrals")) {
		nmatch = sscanf(line,"%d",&ndihedrals);
		nwant = 1;
		} else if (strstr(line,"impropers")) {
		nmatch = sscanf(line,"%d",&nimpropers);
		nwant = 1;
		} else if (strstr(line,"mass")) {
		massflag = 1;
		sscanf(line,"%lg",&masstotal);
		nmatch = sscanf(line,"%lg",&masstotal);
		nwant = 1;
		masstotal = sizescalesizescale*sizescale;
		}
		else if (strstr(line,"com")) {
		} else if (strstr(line,"com")) {
		comflag = 1;
		sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
		nmatch = sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
		nwant = 3;
		com[0] *= sizescale;
		com[1] *= sizescale;
		com[2] *= sizescale;
		if (domain->dimension == 2 && com[2] != 0.0)
		error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d");
		}
		else if (strstr(line,"inertia")) {
		} else if (strstr(line,"inertia")) {
		inertiaflag = 1;
		sscanf(line,"%lg %lg %lg %lg %lg %lg",
		nmatch = sscanf(line,"%lg %lg %lg %lg %lg %lg",
		&itensor[0],&itensor[1],&itensor[2],
		&itensor[3],&itensor[4],&itensor[5]);
		itensor[0] = sizescalesizescalesizescalesizescale*sizescale;
		itensor[1] = sizescalesizescalesizescalesizescale*sizescale;
		itensor[2] = sizescalesizescalesizescalesizescale*sizescale;
		itensor[3] = sizescalesizescalesizescalesizescale*sizescale;
		itensor[4] = sizescalesizescalesizescalesizescale*sizescale;
		itensor[5] = sizescalesizescalesizescalesizescale*sizescale;
		}
		else if (strstr(line,"body")) {
		nwant = 6;
		const double scale5 = sizescalesizescalesizescalesizescalesizescale;
		itensor[0] *= scale5;
		itensor[1] *= scale5;
		itensor[2] *= scale5;
		itensor[3] *= scale5;
		itensor[4] *= scale5;
		itensor[5] *= scale5;
		} else if (strstr(line,"body")) {
		bodyflag = 1;
		avec_body = (AtomVecBody *) atom->style_match("body");
		if (!avec_body)
		error->all(FLERR,"Molecule file requires atom style body");
		sscanf(line,"%d %d",&nibody,&ndbody);
		}
		nmatch = sscanf(line,"%d %d",&nibody,&ndbody);
		nwant = 2;
		} else break;

		else break;
		if (nmatch != nwant)
		error->all(FLERR,"Invalid header in molecule file");
		}

		// error checks
		@@ -493,7 +507,7 @@ void Molecule::read(int flag)

		// loop over sections of molecule file

		while (strlen(keyword)) {
		while (strlen(keyword) > 0) {
		if (strcmp(keyword,"Coords") == 0) {
		xflag = 1;
		if (flag) coords(line);
		@@ -641,12 +655,9 @@ void Molecule::coords(char *line)
		int tmp;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 4)
		if (4 != sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]))
		error->all(FLERR,"Invalid Coords section in molecule file");
		}
		sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]);

		x[i][0] *= sizescale;
		x[i][1] *= sizescale;
		x[i][2] *= sizescale;
		@@ -669,12 +680,8 @@ void Molecule::types(char *line)
		int tmp;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 2)
		if (2 != sscanf(line,"%d %d",&tmp,&type[i]))
		error->all(FLERR,"Invalid Types section in molecule file");
		}
		sscanf(line,"%d %d",&tmp,&type[i]);
		type[i] += toffset;
		}

		@@ -695,13 +702,9 @@ void Molecule::charges(char *line)
		int tmp;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 2)
		if (2 != sscanf(line,"%d %lg",&tmp,&q[i]))
		error->all(FLERR,"Invalid Charges section in molecule file");
		}
		sscanf(line,"%d %lg",&tmp,&q[i]);
		}
		}

		/* ----------------------------------------------------------------------
		@@ -714,12 +717,8 @@ void Molecule::diameters(char *line)
		maxradius = 0.0;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 2)
		if (2 != sscanf(line,"%d %lg",&tmp,&radius[i]))
		error->all(FLERR,"Invalid Diameters section in molecule file");
		}
		sscanf(line,"%d %lg",&tmp,&radius[i]);
		radius[i] *= sizescale;
		radius[i] *= 0.5;
		maxradius = MAX(maxradius,radius[i]);
		@@ -739,12 +738,8 @@ void Molecule::masses(char *line)
		int tmp;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 2)
		if (2 != sscanf(line,"%d %lg",&tmp,&rmass[i]))
		error->all(FLERR,"Invalid Masses section in molecule file");
		}
		sscanf(line,"%d %lg",&tmp,&rmass[i]);
		rmass[i] = sizescalesizescale*sizescale;
		}

		@@ -773,13 +768,9 @@ void Molecule::bonds(int flag, char *line)

		for (int i = 0; i < nbonds; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 4)
		if (4 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&itype,&atom1,&atom2))
		error->all(FLERR,"Invalid Bonds section in molecule file");
		}
		sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&itype,&atom1,&atom2);
		itype += boffset;

		if (atom1 <= 0 \|\| atom1 > natoms \|\|
		@@ -835,13 +826,9 @@ void Molecule::angles(int flag, char *line)

		for (int i = 0; i < nangles; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 5)
		if (5 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&itype,&atom1,&atom2,&atom3))
		error->all(FLERR,"Invalid Angles section in molecule file");
		}
		sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&itype,&atom1,&atom2,&atom3);
		itype += aoffset;

		if (atom1 <= 0 \|\| atom1 > natoms \|\|
		@@ -911,14 +898,10 @@ void Molecule::dihedrals(int flag, char *line)

		for (int i = 0; i < ndihedrals; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 6)
		error->all(FLERR,"Invalid Dihedrals section in molecule file");
		}
		sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
		if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
		TAGINT_FORMAT " " TAGINT_FORMAT " ",
		&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
		&tmp,&itype,&atom1,&atom2,&atom3,&atom4))
		error->all(FLERR,"Invalid Dihedrals section in molecule file");
		itype += doffset;

		if (atom1 <= 0 \|\| atom1 > natoms \|\|
		@@ -1002,14 +985,10 @@ void Molecule::impropers(int flag, char *line)

		for (int i = 0; i < nimpropers; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 6)
		error->all(FLERR,"Invalid Impropers section in molecule file");
		}
		sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
		if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
		TAGINT_FORMAT " " TAGINT_FORMAT " ",
		&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
		&tmp,&itype,&atom1,&atom2,&atom3,&atom4))
		error->all(FLERR,"Invalid Impropers section in molecule file");
		itype += ioffset;

		if (atom1 <= 0 \|\| atom1 > natoms \|\|
		@@ -1087,13 +1066,9 @@ void Molecule::nspecial_read(int flag, char *line)

		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (i == 0) {
		int nwords = atom->count_words(line);
		if (nwords != 4)
		if (4 != sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3))
		error->all(FLERR,"Invalid Special Bond Counts section in "
		"molecule file");
		}
		sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3);

		if (flag) {
		nspecial[i][0] = c1;
		@@ -1229,7 +1204,8 @@ void Molecule::shakeflag_read(char *line)
		int tmp;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		sscanf(line,"%d %d",&tmp,&shake_flag[i]);
		if (2 != sscanf(line,"%d %d",&tmp,&shake_flag[i]))
		error->all(FLERR,"Invalid Shake Flags section in molecule file");
		}

		for (int i = 0; i < natoms; i++)
		@@ -1243,23 +1219,32 @@ void Molecule::shakeflag_read(char *line)

		void Molecule::shakeatom_read(char *line)
		{
		int tmp;
		int tmp, nmatch, nwant;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (shake_flag[i] == 1)
		sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
		else if (shake_flag[i] == 2)
		sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
		if (shake_flag[i] == 1) {
		nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT
		" " TAGINT_FORMAT,&tmp,&shake_atom[i][0],
		&shake_atom[i][1],&shake_atom[i][2]);
		nwant = 4;
		} else if (shake_flag[i] == 2) {
		nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&shake_atom[i][0],&shake_atom[i][1]);
		else if (shake_flag[i] == 3)
		sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
		else if (shake_flag[i] == 4)
		sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
		nwant = 3;
		} else if (shake_flag[i] == 3) {
		nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT
		" " TAGINT_FORMAT,&tmp,&shake_atom[i][0],
		&shake_atom[i][1],&shake_atom[i][2]);
		nwant = 4;
		} else if (shake_flag[i] == 4) {
		nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
		TAGINT_FORMAT " " TAGINT_FORMAT,
		&tmp,&shake_atom[i][0],&shake_atom[i][1],
		&shake_atom[i][2],&shake_atom[i][3]);
		nwant = 5;
		}
		if (nmatch != nwant)
		error->all(FLERR,"Invalid shake atom in molecule file");
		}

		for (int i = 0; i < natoms; i++) {
		@@ -1277,19 +1262,27 @@ void Molecule::shakeatom_read(char *line)

		void Molecule::shaketype_read(char *line)
		{
		int tmp;
		int tmp,nmatch,nwant;
		for (int i = 0; i < natoms; i++) {
		readline(line);
		if (shake_flag[i] == 1)
		sscanf(line,"%d %d %d %d",&tmp,
		&shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
		else if (shake_flag[i] == 2)
		sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
		else if (shake_flag[i] == 3)
		sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],&shake_type[i][1]);
		else if (shake_flag[i] == 4)
		sscanf(line,"%d %d %d %d",&tmp,
		&shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
		if (shake_flag[i] == 1) {
		nmatch = sscanf(line,"%d %d %d %d",&tmp,&shake_type[i][0],
		&shake_type[i][1],&shake_type[i][2]);
		nwant = 4;
		} else if (shake_flag[i] == 2) {
		nmatch = sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
		nwant = 2;
		} else if (shake_flag[i] == 3) {
		nmatch = sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],
		&shake_type[i][1]);
		nwant = 3;
		} else if (shake_flag[i] == 4) {
		nmatch = sscanf(line,"%d %d %d %d",&tmp,&shake_type[i][0],
		&shake_type[i][1],&shake_type[i][2]);
		nwant = 4;
		}
		if (nmatch != nwant)
		error->all(FLERR,"Invalid shake type data in molecule file");
		}

		for (int i = 0; i < natoms; i++) {

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