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pointer and style issues

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This commit is contained in:
jrgissing
2021-01-31 14:59:10 -05:00
parent 2ee6e8f582
commit b92adfaf6f
6 changed files with 58 additions and 44 deletions
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40
src/input.cpp
View File

@ -662,16 +662,17 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
substitute type labels with numeric value substitute type labels with numeric value
reallocate str to hold expanded version if necessary reallocate str to hold expanded version if necessary
if type is a valid numerical string (can include *), do not modify return flag if new pointer, caller will need to delete []
if type is a valid numerical string (can include '*'), do not modify
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Input::readtype(char *&str, int mode) int Input::readtype(char *&str, int mode)
{ {
int numflag = 1; int numflag = 1;
int n = strlen(str); int n = strlen(str);
for (int i = 0; i < n; i++) for (int i = 0; i < n; i++)
if (!isdigit(str[i]) && str[i] != '*') numflag = 0; if (!isdigit(str[i]) && str[i] != '*') numflag = 0;
if (numflag) return; if (numflag) return 0;
if (!atom->labelmapflag) error->all(FLERR,fmt::format("Invalid type {}",str)); if (!atom->labelmapflag) error->all(FLERR,fmt::format("Invalid type {}",str));
int type,max,max2; int type,max,max2;
@ -685,8 +686,13 @@ void Input::readtype(char *&str, int mode)
max = strlen(str) + 1; max = strlen(str) + 1;
max2 = strlen(typechar) + 1; max2 = strlen(typechar) + 1;
if (max2 > max) reallocate(str,max,max2); if (max2 > max) {
strcpy(str,typechar); str = new char[max2];
strcpy(str,typechar);
return 1;
} else strcpy(str,typechar);
return 0;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -1333,8 +1339,9 @@ void Input::angle_coeff()
error->all(FLERR,"Angle_coeff command before angle_style is defined"); error->all(FLERR,"Angle_coeff command before angle_style is defined");
if (atom->avec->angles_allow == 0) if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_coeff command when no angles allowed"); error->all(FLERR,"Angle_coeff command when no angles allowed");
readtype(arg[0],atom->ANGLE); int newflag = readtype(arg[0],Atom::ANGLE);
force->angle->coeff(narg,arg); force->angle->coeff(narg,arg);
if (newflag) delete [] arg[0];
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1375,8 +1382,9 @@ void Input::bond_coeff()
error->all(FLERR,"Bond_coeff command before bond_style is defined"); error->all(FLERR,"Bond_coeff command before bond_style is defined");
if (atom->avec->bonds_allow == 0) if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_coeff command when no bonds allowed"); error->all(FLERR,"Bond_coeff command when no bonds allowed");
readtype(arg[0],atom->BOND); int newflag = readtype(arg[0],Atom::BOND);
force->bond->coeff(narg,arg); force->bond->coeff(narg,arg);
if (newflag) delete [] arg[0];
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1479,8 +1487,9 @@ void Input::dihedral_coeff()
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined"); error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed"); error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
readtype(arg[0],atom->DIHEDRAL); int newflag = readtype(arg[0],Atom::DIHEDRAL);
force->dihedral->coeff(narg,arg); force->dihedral->coeff(narg,arg);
if (newflag) delete [] arg[0];
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1557,8 +1566,9 @@ void Input::improper_coeff()
error->all(FLERR,"Improper_coeff command before improper_style is defined"); error->all(FLERR,"Improper_coeff command before improper_style is defined");
if (atom->avec->impropers_allow == 0) if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_coeff command when no impropers allowed"); error->all(FLERR,"Improper_coeff command when no impropers allowed");
readtype(arg[0],atom->IMPROPER); int newflag = readtype(arg[0],Atom::IMPROPER);
force->improper->coeff(narg,arg); force->improper->coeff(narg,arg);
if (newflag) delete [] arg[0];
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1751,13 +1761,12 @@ void Input::pair_coeff()
error->all(FLERR,"Pair_coeff command before simulation box is defined"); error->all(FLERR,"Pair_coeff command before simulation box is defined");
if (force->pair == nullptr) if (force->pair == nullptr)
error->all(FLERR,"Pair_coeff command before pair_style is defined"); error->all(FLERR,"Pair_coeff command before pair_style is defined");
readtype(arg[0],atom->ATOM); int newflag0 = readtype(arg[0],Atom::ATOM);
readtype(arg[1],atom->ATOM); int newflag1 = readtype(arg[1],Atom::ATOM);
// if arg[1] < arg[0], and neither contain a wildcard, reorder // if arg[1] < arg[0], and neither contain a wildcard, reorder
int itype,jtype; int tmpflag,itype,jtype;
int *ptr;
char *str; char *str;
if (strchr(arg[0],'*') == nullptr && strchr(arg[1],'*') == nullptr) { if (strchr(arg[0],'*') == nullptr && strchr(arg[1],'*') == nullptr) {
itype = utils::numeric(FLERR,arg[0],false,lmp); itype = utils::numeric(FLERR,arg[0],false,lmp);
@ -1766,10 +1775,15 @@ void Input::pair_coeff()
str = arg[0]; str = arg[0];
arg[0] = arg[1]; arg[0] = arg[1];
arg[1] = str; arg[1] = str;
tmpflag = newflag0;
newflag0 = newflag1;
newflag1 = tmpflag;
} }
} }
force->pair->coeff(narg,arg); force->pair->coeff(narg,arg);
if (newflag0) delete [] arg[0];
if (newflag1) delete [] arg[1];
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

2
src/input.h
View File

@ -38,7 +38,7 @@ class Input : protected Pointers {
char *one(const std::string&); // process a single command char *one(const std::string&); // process a single command
void substitute(char *&, char *&, int &, int &, int); void substitute(char *&, char *&, int &, int &, int);
// substitute for variables in a string // substitute for variables in a string
void readtype(char *&, int); // substitute type label with numeric type int readtype(char *&, int); // substitute type label with numeric type
void write_echo(const std::string &); // send text to active echo file pointers void write_echo(const std::string &); // send text to active echo file pointers
protected: protected:

30
src/label_map.cpp
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@ -119,23 +119,23 @@ void LabelMap::modify_lmap(int narg, char **arg)
void LabelMap::merge_lmap(LabelMap *lmap2, int mode) void LabelMap::merge_lmap(LabelMap *lmap2, int mode)
{ {
if (mode == atom->ATOM) if (mode == Atom::ATOM)
for (int i = 0; i < lmap2->natomtypes; i++) for (int i = 0; i < lmap2->natomtypes; i++)
find_or_create(lmap2->typelabel[i],typelabel,natomtypes); find_or_create(lmap2->typelabel[i],typelabel,natomtypes);
if (mode == atom->BOND) if (mode == Atom::BOND)
for (int i = 0; i < lmap2->nbondtypes; i++) for (int i = 0; i < lmap2->nbondtypes; i++)
find_or_create(lmap2->btypelabel[i],btypelabel,nbondtypes); find_or_create(lmap2->btypelabel[i],btypelabel,nbondtypes);
if (mode == atom->ANGLE) if (mode == Atom::ANGLE)
for (int i = 0; i < lmap2->nangletypes; i++) for (int i = 0; i < lmap2->nangletypes; i++)
find_or_create(lmap2->atypelabel[i],atypelabel,nangletypes); find_or_create(lmap2->atypelabel[i],atypelabel,nangletypes);
if (mode == atom->DIHEDRAL) if (mode == Atom::DIHEDRAL)
for (int i = 0; i < lmap2->ndihedraltypes; i++) for (int i = 0; i < lmap2->ndihedraltypes; i++)
find_or_create(lmap2->dtypelabel[i],dtypelabel,ndihedraltypes); find_or_create(lmap2->dtypelabel[i],dtypelabel,ndihedraltypes);
if (mode == atom->IMPROPER) if (mode == Atom::IMPROPER)
for (int i = 0; i < lmap2->nimpropertypes; i++) for (int i = 0; i < lmap2->nimpropertypes; i++)
find_or_create(lmap2->itypelabel[i],itypelabel,nimpropertypes); find_or_create(lmap2->itypelabel[i],itypelabel,nimpropertypes);
} }
@ -147,27 +147,27 @@ void LabelMap::merge_lmap(LabelMap *lmap2, int mode)
void LabelMap::create_lmap2lmap(LabelMap *lmap2, int mode) void LabelMap::create_lmap2lmap(LabelMap *lmap2, int mode)
{ {
if (mode == atom->ATOM) if (mode == Atom::ATOM)
for (int i = 0; i < natomtypes; i++) for (int i = 0; i < natomtypes; i++)
lmap2lmap.atom[i] = search(typelabel[i],lmap2->typelabel, lmap2lmap.atom[i] = search(typelabel[i],lmap2->typelabel,
lmap2->natomtypes); lmap2->natomtypes);
if (mode == atom->BOND) if (mode == Atom::BOND)
for (int i = 0; i < nbondtypes; i++) for (int i = 0; i < nbondtypes; i++)
lmap2lmap.bond[i] = search(btypelabel[i],lmap2->btypelabel, lmap2lmap.bond[i] = search(btypelabel[i],lmap2->btypelabel,
lmap2->nbondtypes); lmap2->nbondtypes);
if (mode == atom->ANGLE) if (mode == Atom::ANGLE)
for (int i = 0; i < nangletypes; i++) for (int i = 0; i < nangletypes; i++)
lmap2lmap.angle[i] = search(atypelabel[i],lmap2->atypelabel, lmap2lmap.angle[i] = search(atypelabel[i],lmap2->atypelabel,
lmap2->nangletypes); lmap2->nangletypes);
if (mode == atom->DIHEDRAL) if (mode == Atom::DIHEDRAL)
for (int i = 0; i < ndihedraltypes; i++) for (int i = 0; i < ndihedraltypes; i++)
lmap2lmap.dihedral[i] = search(dtypelabel[i],lmap2->dtypelabel, lmap2lmap.dihedral[i] = search(dtypelabel[i],lmap2->dtypelabel,
lmap2->ndihedraltypes); lmap2->ndihedraltypes);
if (mode == atom->IMPROPER) if (mode == Atom::IMPROPER)
for (int i = 0; i < nimpropertypes; i++) for (int i = 0; i < nimpropertypes; i++)
lmap2lmap.improper[i] = search(itypelabel[i],lmap2->itypelabel, lmap2lmap.improper[i] = search(itypelabel[i],lmap2->itypelabel,
lmap2->nimpropertypes); lmap2->nimpropertypes);
@ -206,19 +206,19 @@ int LabelMap::find_or_create(std::string mylabel, std::vector<std::string> &labe
int LabelMap::find(std::string mylabel, int mode) int LabelMap::find(std::string mylabel, int mode)
{ {
if (mode == atom->ATOM) if (mode == Atom::ATOM)
return search(mylabel,typelabel,natomtypes); return search(mylabel,typelabel,natomtypes);
if (mode == atom->BOND) if (mode == Atom::BOND)
return search(mylabel,btypelabel,nbondtypes); return search(mylabel,btypelabel,nbondtypes);
if (mode == atom->ANGLE) if (mode == Atom::ANGLE)
return search(mylabel,atypelabel,nangletypes); return search(mylabel,atypelabel,nangletypes);
if (mode == atom->DIHEDRAL) if (mode == Atom::DIHEDRAL)
return search(mylabel,dtypelabel,ndihedraltypes); return search(mylabel,dtypelabel,ndihedraltypes);
if (mode == atom->IMPROPER) if (mode == Atom::IMPROPER)
return search(mylabel,itypelabel,nimpropertypes); return search(mylabel,itypelabel,nimpropertypes);
return -1; return -1;

10
src/molecule.cpp
View File

@ -728,7 +728,7 @@ void Molecule::types(char *line)
typestr = values.next_string(); typestr = values.next_string();
if (!isdigit(typestr[0])) { if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Types section in molecule file"); if (!atom->labelmapflag) error->one(FLERR,"Invalid Types section in molecule file");
type[iatom] = atom->find_label(typestr,atom->ATOM); type[iatom] = atom->find_label(typestr,Atom::ATOM);
if (type[iatom] == -1) error->one(FLERR,"Invalid Types section in molecule file"); if (type[iatom] == -1) error->one(FLERR,"Invalid Types section in molecule file");
} else type[iatom] = utils::inumeric(FLERR,typestr.c_str(),false,lmp); } else type[iatom] = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
type[iatom] += toffset; type[iatom] += toffset;
@ -941,7 +941,7 @@ void Molecule::bonds(int flag, char *line)
typestr = values.next_string(); typestr = values.next_string();
if (!isdigit(typestr[0])) { if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in molecule file"); if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in molecule file");
itype = atom->find_label(typestr,atom->BOND); itype = atom->find_label(typestr,Atom::BOND);
if (itype == -1) error->one(FLERR,"Invalid Bonds section in molecule file"); if (itype == -1) error->one(FLERR,"Invalid Bonds section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp); } else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint(); atom1 = values.next_tagint();
@ -1015,7 +1015,7 @@ void Molecule::angles(int flag, char *line)
typestr = values.next_string(); typestr = values.next_string();
if (!isdigit(typestr[0])) { if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in molecule file"); if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in molecule file");
itype = atom->find_label(typestr,atom->ANGLE); itype = atom->find_label(typestr,Atom::ANGLE);
if (itype == -1) error->one(FLERR,"Invalid Angles section in molecule file"); if (itype == -1) error->one(FLERR,"Invalid Angles section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp); } else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint(); atom1 = values.next_tagint();
@ -1105,7 +1105,7 @@ void Molecule::dihedrals(int flag, char *line)
typestr = values.next_string(); typestr = values.next_string();
if (!isdigit(typestr[0])) { if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in molecule file"); if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in molecule file");
itype = atom->find_label(typestr,atom->DIHEDRAL); itype = atom->find_label(typestr,Atom::DIHEDRAL);
if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in molecule file"); if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp); } else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint(); atom1 = values.next_tagint();
@ -1210,7 +1210,7 @@ void Molecule::impropers(int flag, char *line)
typestr = values.next_string(); typestr = values.next_string();
if (!isdigit(typestr[0])) { if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in molecule file"); if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in molecule file");
itype = atom->find_label(typestr,atom->IMPROPER); itype = atom->find_label(typestr,Atom::IMPROPER);
if (itype == -1) error->one(FLERR,"Invalid Impropers section in molecule file"); if (itype == -1) error->one(FLERR,"Invalid Impropers section in molecule file");
} else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp); } else itype = utils::inumeric(FLERR,typestr.c_str(),false,lmp);
atom1 = values.next_tagint(); atom1 = values.next_tagint();

10
src/read_data.cpp
View File

@ -729,7 +729,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) { if (firstpass) {
if (atomflag == 1) if (atomflag == 1)
error->all(FLERR,"Must read Atom Type Labels before Atoms"); error->all(FLERR,"Must read Atom Type Labels before Atoms");
typelabels(lmap->typelabel,ntypes,atom->ATOM); typelabels(lmap->typelabel,ntypes,Atom::ATOM);
} else skip_lines(ntypes); } else skip_lines(ntypes);
} else if (strcmp(keyword,"Bond Type Labels") == 0) { } else if (strcmp(keyword,"Bond Type Labels") == 0) {
@ -737,7 +737,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) { if (firstpass) {
if (bondflag == 1) if (bondflag == 1)
error->all(FLERR,"Must read Bond Type Labels before Bonds"); error->all(FLERR,"Must read Bond Type Labels before Bonds");
typelabels(lmap->btypelabel,nbondtypes,atom->BOND); typelabels(lmap->btypelabel,nbondtypes,Atom::BOND);
} else skip_lines(nbondtypes); } else skip_lines(nbondtypes);
} }
@ -746,7 +746,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) { if (firstpass) {
if (angleflag == 1) if (angleflag == 1)
error->all(FLERR,"Must read Angle Type Labels before Angles"); error->all(FLERR,"Must read Angle Type Labels before Angles");
typelabels(lmap->atypelabel,nangletypes,atom->ANGLE); typelabels(lmap->atypelabel,nangletypes,Atom::ANGLE);
} else skip_lines(nangletypes); } else skip_lines(nangletypes);
} }
@ -755,7 +755,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) { if (firstpass) {
if (dihedralflag == 1) if (dihedralflag == 1)
error->all(FLERR,"Must read Dihedral Type Labels before Dihedrals"); error->all(FLERR,"Must read Dihedral Type Labels before Dihedrals");
typelabels(lmap->dtypelabel,ndihedraltypes,atom->DIHEDRAL); typelabels(lmap->dtypelabel,ndihedraltypes,Atom::DIHEDRAL);
} else skip_lines(ndihedraltypes); } else skip_lines(ndihedraltypes);
} }
@ -764,7 +764,7 @@ void ReadData::command(int narg, char **arg)
if (firstpass) { if (firstpass) {
if (improperflag == 1) if (improperflag == 1)
error->all(FLERR,"Must read Improper Type Labels before Impropers"); error->all(FLERR,"Must read Improper Type Labels before Impropers");
typelabels(lmap->itypelabel,nimpropertypes,atom->IMPROPER); typelabels(lmap->itypelabel,nimpropertypes,Atom::IMPROPER);
} else skip_lines(nimpropertypes); } else skip_lines(nimpropertypes);
} }

10
src/variable.cpp
View File

@ -4540,19 +4540,19 @@ int Variable::labelmap_function(char *word, char *contents, Tree **tree,
std::string typestr = contents; std::string typestr = contents;
if (strcmp(word,"label") == 0) { if (strcmp(word,"label") == 0) {
value = atom->find_label(typestr,atom->ATOM); value = atom->find_label(typestr,Atom::ATOM);
} else if (strcmp(word,"blabel") == 0) { } else if (strcmp(word,"blabel") == 0) {
value = atom->find_label(typestr,atom->BOND); value = atom->find_label(typestr,Atom::BOND);
} else if (strcmp(word,"alabel") == 0) { } else if (strcmp(word,"alabel") == 0) {
value = atom->find_label(typestr,atom->ANGLE); value = atom->find_label(typestr,Atom::ANGLE);
} else if (strcmp(word,"dlabel") == 0) { } else if (strcmp(word,"dlabel") == 0) {
value = atom->find_label(typestr,atom->DIHEDRAL); value = atom->find_label(typestr,Atom::DIHEDRAL);
} else if (strcmp(word,"ilabel") == 0) { } else if (strcmp(word,"ilabel") == 0) {
value = atom->find_label(typestr,atom->IMPROPER); value = atom->find_label(typestr,Atom::IMPROPER);
} }
if (value == -1) if (value == -1)