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Merge branch 'develop' into type-labels

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This commit is contained in:
Jacob Gissinger
2022-08-08 17:16:50 -04:00
committed by GitHub
parent e13a70ad2f fb2dd26d45
commit f9717049b1
4100 changed files with 378596 additions and 127634 deletions
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192
src/input.cpp
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@ -169,7 +169,7 @@ Input::~Input()
memory->sfree(line);
memory->sfree(copy);
memory->sfree(work);
if (labelstr) delete[] labelstr;
delete[] labelstr;
memory->sfree(arg);
delete[] infiles;
delete variable;
@ -189,17 +189,20 @@ of the file is reached. The *infile* pointer will usually point to
void Input::file()
{
int m,n;
int m,n,mstart,ntriple,endfile;
while (true) {
// read a line from input script
// n = length of line including str terminator, 0 if end of file
// when done, n = length of line including str terminator, 0 if end of file
// if line ends in continuation char '&', concatenate next line
// if triple quotes are used, read until closing triple quotes
if (me == 0) {
ntriple = 0;
endfile = 0;
m = 0;
while (true) {
if (infile == nullptr) {
@ -207,38 +210,58 @@ void Input::file()
break;
}
if (maxline-m < 2) reallocate(line,maxline,0);
mstart = m;
// end of file reached, so break
// n == 0 if nothing read, else n = line with str terminator
while (1) {
if (maxline-m < 2) reallocate(line,maxline,0);
if (fgets(&line[m],maxline-m,infile) == nullptr) {
if (m) n = strlen(line) + 1;
else n = 0;
// end of file reached, so break
// n == 0 if nothing read, else n = line with str terminator
if (fgets(&line[m],maxline-m,infile) == nullptr) {
endfile = 1;
if (m) n = strlen(line) + 1;
else n = 0;
break;
}
// continue if last char read was not a newline
// can happen if line is very long
m += strlen(&line[m]);
if (line[m-1] != '\n') continue;
break;
}
// continue if last char read was not a newline
// could happen if line is very long
if (endfile) break;
m = strlen(line);
if (line[m-1] != '\n') continue;
// add # of triple quotes in just-read line to ntriple
// continue reading if final printable char is & char
// or if odd number of triple quotes
// else break with n = line with str terminator
ntriple += numtriple(&line[mstart]);
// trim whitespace from end of line
// line[m] = last printable char
m--;
while (m >= 0 && isspace(line[m])) m--;
if (m < 0 || line[m] != '&') {
if (numtriple(line) % 2) {
m += 2;
continue;
}
line[m+1] = '\0';
n = m+2;
break;
// continue reading if final printable char is "&"
if (m >= 0 && line[m] == '&') continue;
// continue reading if odd number of triple quotes
if (ntriple % 2) {
line[m+1] = '\n';
m += 2;
continue;
}
// done, break with n = length of line with str terminator
line[m+1] = '\0';
n = m+2;
break;
}
}
@ -372,8 +395,9 @@ char *Input::one(const std::string &single)
}
/* ----------------------------------------------------------------------
Send text to active echo file pointers
send text to active echo file pointers
------------------------------------------------------------------------- */
void Input::write_echo(const std::string &txt)
{
if (me == 0) {
@ -400,34 +424,35 @@ void Input::parse()
if (n > maxcopy) reallocate(copy,maxcopy,n);
strcpy(copy,line);
// strip any # comment by replacing it with 0
// do not strip from a # inside single/double/triple quotes
// quoteflag = 1,2,3 when encounter first single/double,triple quote
// quoteflag = 0 when encounter matching single/double,triple quote
// strip a # comment by replacing it with 0
// do not treat a # inside single/double/triple quotes as a comment
int quoteflag = 0;
char *ptrmatch;
char *ptr = copy;
while (*ptr) {
if (*ptr == '#' && !quoteflag) {
if (*ptr == '#') {
*ptr = '\0';
break;
}
if (quoteflag == 0) {
if (*ptr == '\'') {
ptrmatch = strchr(ptr+1,'\'');
if (ptrmatch == NULL)
error->all(FLERR,"Unmatched single quote in command");
ptr = ptrmatch + 1;
} else if (*ptr == '"') {
if (strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 3;
ptr += 2;
ptrmatch = strstr(ptr+3,"\"\"\"");
if (ptrmatch == NULL)
error->all(FLERR,"Unmatched triple quote in command");
ptr = ptrmatch + 3;
} else {
ptrmatch = strchr(ptr+1,'"');
if (ptrmatch == NULL)
error->all(FLERR,"Unmatched double quote in command");
ptr = ptrmatch + 1;
}
else if (*ptr == '"') quoteflag = 2;
else if (*ptr == '\'') quoteflag = 1;
} else {
if (quoteflag == 3 && strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 0;
ptr += 2;
}
else if (quoteflag == 2 && *ptr == '"') quoteflag = 0;
else if (quoteflag == 1 && *ptr == '\'') quoteflag = 0;
}
ptr++;
} else ptr++;
}
if (utils::has_utf8(copy)) {
@ -535,16 +560,18 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
{
// use str2 as scratch space to expand str, then copy back to str
// reallocate str and str2 as necessary
// do not replace $ inside single/double/triple quotes
// do not replace variables inside single/double/triple quotes
// var = pts at variable name, ended by null char
// if $ is followed by '{', trailing '}' becomes null char
// else $x becomes x followed by null char
// beyond = points to text following variable
int i,n,paren_count;
int i,n,paren_count,nchars;;
char immediate[256];
char *var,*value,*beyond;
int quoteflag = 0;
char *ptrmatch;
char *ptr = str;
n = strlen(str) + 1;
@ -638,34 +665,41 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
if (echo_log && logfile) fprintf(logfile,"%s%s\n",str2,beyond);
}
continue;
}
// check for single/double/triple quotes and skip past them
// quoteflag = 1,2,3 when encounter first single/double,triple quote
// quoteflag = 0 when encounter matching single/double,triple quote
// copy 2 extra triple quote chars into str2
if (quoteflag == 0) {
} else if (*ptr == '\'') {
ptrmatch = strchr(ptr+1,'\'');
if (ptrmatch == NULL)
error->all(FLERR,"Unmatched single quote in command");
nchars = ptrmatch+1 - ptr;
strncpy(ptr2,ptr,nchars);
ptr += nchars;
ptr2 += nchars;
} else if (*ptr == '"') {
if (strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 3;
*ptr2++ = *ptr++;
*ptr2++ = *ptr++;
ptrmatch = strstr(ptr+3,"\"\"\"");
if (ptrmatch == NULL)
error->all(FLERR,"Unmatched triple quote in command");
nchars = ptrmatch+3 - ptr;
strncpy(ptr2,ptr,nchars);
ptr += nchars;
ptr2 += nchars;
} else {
ptrmatch = strchr(ptr+1,'"');
if (ptrmatch == NULL)
error->all(FLERR,"Unmatched double quote in command");
nchars = ptrmatch+1 - ptr;
strncpy(ptr2,ptr,nchars);
ptr += nchars;
ptr2 += nchars;
}
else if (*ptr == '"') quoteflag = 2;
else if (*ptr == '\'') quoteflag = 1;
} else {
if (quoteflag == 3 && strstr(ptr,"\"\"\"") == ptr) {
quoteflag = 0;
*ptr2++ = *ptr++;
*ptr2++ = *ptr++;
}
else if (quoteflag == 2 && *ptr == '"') quoteflag = 0;
else if (quoteflag == 1 && *ptr == '\'') quoteflag = 0;
}
// copy current character into str2
// else copy current single character into str2
} else *ptr2++ = *ptr++;
// terminate current str2 so variable sub can perform strlen()
*ptr2++ = *ptr++;
*ptr2 = '\0';
}
@ -928,7 +962,7 @@ void Input::ifthenelse()
int ncommands = last-first + 1;
if (ncommands <= 0) error->all(FLERR,"Illegal if command");
char **commands = new char*[ncommands];
auto commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
n = strlen(arg[i]) + 1;
@ -981,7 +1015,7 @@ void Input::ifthenelse()
int ncommands = last-first + 1;
if (ncommands <= 0) error->all(FLERR,"Illegal if command");
char **commands = new char*[ncommands];
auto commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
n = strlen(arg[i]) + 1;
@ -1063,7 +1097,7 @@ void Input::jump()
if (narg == 2) {
label_active = 1;
if (labelstr) delete[] labelstr;
delete[] labelstr;
labelstr = utils::strdup(arg[1]);
}
}
@ -1232,11 +1266,9 @@ void Input::shell()
if (me == 0) {
for (int i = 1; i < narg; i++) {
rv = (platform::mkdir(arg[i]) < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);
errno = err;
if (err != 0)
error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'",
arg[i],utils::getsyserror());
if (rv != 0)
error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'", arg[i],
utils::getsyserror());
}
}
} else if (strcmp(arg[0],"mv") == 0) {
@ -1876,6 +1908,7 @@ void Input::special_bonds()
double lj3 = force->special_lj[3];
double coul2 = force->special_coul[2];
double coul3 = force->special_coul[3];
int onefive = force->special_onefive;
int angle = force->special_angle;
int dihedral = force->special_dihedral;
@ -1886,6 +1919,7 @@ void Input::special_bonds()
if (domain->box_exist && atom->molecular == Atom::MOLECULAR) {
if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||
coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
onefive != force->special_onefive ||
angle != force->special_angle ||
dihedral != force->special_dihedral) {
Special special(lmp);