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avoid segfault and print more meaningful error message with empty lines in coeff sections

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Axel Kohlmeyer
2019-05-20 14:15:04 -04:00
parent 50082c287d
commit 55116db8fb
3 changed files with 34 additions and 26 deletions
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20
doc/src/Errors_messages.txt
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@ -9990,25 +9990,25 @@ quote. :dd
Self-explanatory. :dd Self-explanatory. :dd
{Unexpected end of AngleCoeffs section} :dt {Unexpected empty line in AngleCoeffs section} :dt
Read a blank line. :dd Read a blank line where there should be coefficient data. :dd
{Unexpected end of BondCoeffs section} :dt {Unexpected empty line in BondCoeffs section} :dt
Read a blank line. :dd Read a blank line where there should be coefficient data. :dd
{Unexpected end of DihedralCoeffs section} :dt {Unexpected empty line in DihedralCoeffs section} :dt
Read a blank line. :dd Read a blank line where there should be coefficient data. :dd
{Unexpected end of ImproperCoeffs section} :dt {Unexpected empty line in ImproperCoeffs section} :dt
Read a blank line. :dd Read a blank line where there should be coefficient data. :dd
{Unexpected end of PairCoeffs section} :dt {Unexpected empty line in PairCoeffs section} :dt
Read a blank line. :dd Read a blank line where there should be coefficient data. :dd
{Unexpected end of custom file} :dt {Unexpected end of custom file} :dt

20
src/read_data.cpp
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@ -1768,7 +1768,8 @@ void ReadData::paircoeffs()
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
parse_coeffs(buf,NULL,1,2,toffset); parse_coeffs(buf,NULL,1,2,toffset);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section"); if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg); force->pair->coeff(narg,arg);
buf = next + 1; buf = next + 1;
} }
@ -1794,7 +1795,8 @@ void ReadData::pairIJcoeffs()
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
parse_coeffs(buf,NULL,0,2,toffset); parse_coeffs(buf,NULL,0,2,toffset);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section"); if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg); force->pair->coeff(narg,arg);
buf = next + 1; buf = next + 1;
} }
@ -1818,7 +1820,8 @@ void ReadData::bondcoeffs()
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
parse_coeffs(buf,NULL,0,1,boffset); parse_coeffs(buf,NULL,0,1,boffset);
if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section"); if (narg == 0)
error->all(FLERR,"Unexpected empty line in BondCoeffs section");
force->bond->coeff(narg,arg); force->bond->coeff(narg,arg);
buf = next + 1; buf = next + 1;
} }
@ -1844,7 +1847,7 @@ void ReadData::anglecoeffs(int which)
if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset); if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset);
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset); else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset);
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset); else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset);
if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section"); if (narg == 0) error->all(FLERR,"Unexpected empty line in AngleCoeffs section");
force->angle->coeff(narg,arg); force->angle->coeff(narg,arg);
buf = next + 1; buf = next + 1;
} }
@ -1873,7 +1876,8 @@ void ReadData::dihedralcoeffs(int which)
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset); else if (which == 3) parse_coeffs(buf,"at",0,1,doffset);
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset); else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset);
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset); else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset);
if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section"); if (narg == 0)
error->all(FLERR,"Unexpected empty line in DihedralCoeffs section");
force->dihedral->coeff(narg,arg); force->dihedral->coeff(narg,arg);
buf = next + 1; buf = next + 1;
} }
@ -1898,7 +1902,7 @@ void ReadData::impropercoeffs(int which)
*next = '\0'; *next = '\0';
if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset); if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset);
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset); else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset);
if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section"); if (narg == 0) error->all(FLERR,"Unexpected empty line in ImproperCoeffs section");
force->improper->coeff(narg,arg); force->improper->coeff(narg,arg);
buf = next + 1; buf = next + 1;
} }
@ -2092,6 +2096,10 @@ void ReadData::parse_coeffs(char *line, const char *addstr,
word = strtok(NULL," \t\n\r\f"); word = strtok(NULL," \t\n\r\f");
} }
// to avoid segfaults on empty lines
if (narg == 0) return;
if (noffset) { if (noffset) {
int value = force->inumeric(FLERR,arg[0]); int value = force->inumeric(FLERR,arg[0]);
sprintf(argoffset1,"%d",value+offset); sprintf(argoffset1,"%d",value+offset);

20
src/read_data.h
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@ -533,25 +533,25 @@ E: Too many lines in one body in data file - boost MAXBODY
MAXBODY is a setting at the top of the src/read_data.cpp file. MAXBODY is a setting at the top of the src/read_data.cpp file.
Set it larger and re-compile the code. Set it larger and re-compile the code.
E: Unexpected end of PairCoeffs section E: Unexpected empty line in PairCoeffs section
Read a blank line. Read a blank line where there should be coefficient data.
E: Unexpected end of BondCoeffs section E: Unexpected empty line in BondCoeffs section
Read a blank line. Read a blank line where there should be coefficient data.
E: Unexpected end of AngleCoeffs section E: Unexpected empty line in AngleCoeffs section
Read a blank line. Read a blank line where there should be coefficient data.
E: Unexpected end of DihedralCoeffs section E: Unexpected empty line in DihedralCoeffs section
Read a blank line. Read a blank line where there should be coefficient data.
E: Unexpected end of ImproperCoeffs section E: Unexpected empty line in ImproperCoeffs section
Read a blank line. Read a blank line where there should be coefficient data.
E: Cannot open gzipped file E: Cannot open gzipped file