diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 25377ae82827307e8c9e66c98e32382788222221..acd35a1b9c5ee533b1dcc6e256cfd1048fde9e05 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -41,7 +41,7 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
size_border = 11;
size_velocity = 3;
size_data_atom = 9;
- size_data_vel = 7;
+ size_data_vel = 4;
xcol_data = 4;
atom->q_flag = atom->mu_flag = 1;
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index 614dbc4c5c3e8c292ee26f84477225f21c3f222e..5db6b096da4217a61478481098b334c80a114053 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -18,13 +18,12 @@
#include "input.h"
#include "modify.h"
#include "variable.h"
+#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
-#define MAXLINE 1024
-
/* ---------------------------------------------------------------------- */
FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
@@ -40,6 +39,10 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
string = new char[n];
strcpy(string,arg[4]);
+ copy = (char *) memory->smalloc(n*sizeof(char),"fix/print:copy");
+ work = (char *) memory->smalloc(n*sizeof(char),"fix/print:work");
+ maxcopy = maxwork = n;
+
// parse optional args
fp = NULL;
@@ -85,9 +88,6 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
delete [] title;
- copy = new char[MAXLINE];
- work = new char[MAXLINE];
-
// add nfirst to all computes that store invocation times
// since don't know a priori which are invoked via variables by this fix
// once in end_of_step() can set timestep for ones actually invoked
@@ -101,8 +101,8 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
FixPrint::~FixPrint()
{
delete [] string;
- delete [] copy;
- delete [] work;
+ memory->sfree(copy);
+ memory->sfree(work);
if (fp && me == 0) fclose(fp);
}
@@ -128,16 +128,15 @@ void FixPrint::end_of_step()
modify->clearstep_compute();
strcpy(copy,string);
- input->substitute(copy,0);
- strcat(copy,"\n");
+ input->substitute(copy,work,maxcopy,maxwork,0);
modify->addstep_compute(update->ntimestep + nevery);
if (me == 0) {
- if (screenflag && screen) fprintf(screen,"%s",copy);
- if (screenflag && logfile) fprintf(logfile,"%s",copy);
+ if (screenflag && screen) fprintf(screen,"%s\n",copy);
+ if (screenflag && logfile) fprintf(logfile,"%s\n",copy);
if (fp) {
- fprintf(fp,"%s",copy);
+ fprintf(fp,"%s\n",copy);
fflush(fp);
}
}
diff --git a/src/fix_print.h b/src/fix_print.h
index 35c18d78f213a36203682f37a993ffeaef6bd4d1..8cba1093cdf0094876a466832f24f38b177ac92f 100644
--- a/src/fix_print.h
+++ b/src/fix_print.h
@@ -36,6 +36,7 @@ class FixPrint : public Fix {
int me,screenflag;
FILE *fp;
char *string,*copy,*work;
+ int maxcopy,maxwork;
};
}
diff --git a/src/input.cpp b/src/input.cpp
index 3ec89cd44b81232160b0462c09890459d877e845..e1ce2851859e0288482c4356dad2db876875c1d7 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -52,7 +52,7 @@
using namespace LAMMPS_NS;
-#define MAXLINE 8192
+#define DELTALINE 256
#define DELTA 4
/* ---------------------------------------------------------------------- */
@@ -61,9 +61,8 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
- line = new char[MAXLINE];
- copy = new char[MAXLINE];
- work = new char[MAXLINE];
+ maxline = maxcopy = maxwork = 0;
+ line = copy = work = NULL;
narg = maxarg = 0;
arg = NULL;
@@ -112,13 +111,13 @@ Input::~Input()
// don't free command and arg strings
// they just point to other allocated memory
- delete variable;
- delete [] line;
- delete [] copy;
- delete [] work;
+ memory->sfree(line);
+ memory->sfree(copy);
+ memory->sfree(work);
if (labelstr) delete [] labelstr;
memory->sfree(arg);
memory->sfree(infiles);
+ delete variable;
}
/* ----------------------------------------------------------------------
@@ -133,19 +132,28 @@ void Input::file()
while (1) {
// read a line from input script
- // if line ends in continuation char '&', concatenate next line(s)
// n = length of line including str terminator, 0 if end of file
- // m = position of last printable char in line or -1 if blank line
+ // if line ends in continuation char '&', concatenate next line
if (me == 0) {
m = 0;
while (1) {
- if (fgets(&line[m],MAXLINE-m,infile) == NULL) n = 0;
- else n = strlen(line) + 1;
- if (n == 0) break;
- m = n-2;
+ if (maxline-m < 2) reallocate(line,maxline,0);
+ if (fgets(&line[m],maxline-m,infile) == NULL) {
+ if (m) n = strlen(line) + 1;
+ else n = 0;
+ break;
+ }
+ m = strlen(line);
+ if (line[m-1] != '\n') continue;
+
+ m--;
while (m >= 0 && isspace(line[m])) m--;
- if (m < 0 || line[m] != '&') break;
+ if (m < 0 || line[m] != '&') {
+ line[m+1] = '\0';
+ n = m+2;
+ break;
+ }
}
}
@@ -168,16 +176,9 @@ void Input::file()
continue;
}
+ if (n > maxline) reallocate(line,maxline,n);
MPI_Bcast(line,n,MPI_CHAR,0,world);
- // if n = MAXLINE, line is too long
-
- if (n == MAXLINE) {
- char str[MAXLINE+32];
- sprintf(str,"Input line too long: %s",line);
- error->all(FLERR,str);
- }
-
// echo the command unless scanning for label
if (me == 0 && label_active == 0) {
@@ -198,7 +199,7 @@ void Input::file()
// execute the command
if (execute_command()) {
- char str[MAXLINE];
+ char str[maxline+32];
sprintf(str,"Unknown command: %s",line);
error->all(FLERR,str);
}
@@ -260,7 +261,7 @@ char *Input::one(const char *single)
// execute the command and return its name
if (execute_command()) {
- char str[MAXLINE];
+ char str[maxline+32];
sprintf(str,"Unknown command: %s",line);
error->all(FLERR,str);
}
@@ -269,7 +270,7 @@ char *Input::one(const char *single)
}
/* ----------------------------------------------------------------------
- parse copy of command line
+ parse copy of command line by inserting string terminators
strip comment = all chars from # on
replace all $ via variable substitution
command = first word
@@ -280,8 +281,10 @@ char *Input::one(const char *single)
void Input::parse()
{
- // make a copy to work on
+ // duplicate line into copy string to break into words
+ int n = strlen(line) + 1;
+ if (n > maxcopy) reallocate(copy,maxcopy,n);
strcpy(copy,line);
// strip any # comment by replacing it with 0
@@ -302,16 +305,16 @@ void Input::parse()
// perform $ variable substitution (print changes)
// except if searching for a label since earlier variable may not be defined
- if (!label_active) substitute(copy,1);
+ if (!label_active) substitute(copy,work,maxcopy,maxwork,1);
- // command = 1st arg
+ // command = 1st arg in copy string
char *next;
command = nextword(copy,&next);
if (command == NULL) return;
- // point arg[] at each subsequent arg
- // nextword() inserts zeroes in copy to delimit args
+ // point arg[] at each subsequent arg in copy string
+ // nextword() inserts string terminators into copy string to delimit args
// nextword() treats text between single/double quotes as one arg
narg = 0;
@@ -363,23 +366,29 @@ char *Input::nextword(char *str, char **next)
/* ----------------------------------------------------------------------
substitute for $ variables in str and return it
- str assumed to be long enough to hold expanded version
+ reallocate str/str2 to hold expanded version if necessary & reset max1/max2
print updated string if flag is set and not searching for label
+ label_active will be 0 if called from external class
------------------------------------------------------------------------- */
-void Input::substitute(char *str, int flag)
+void Input::substitute(char *&str, char *&str2, int &max1, int &max2, int flag)
{
- // use work[] as scratch space to expand str, then copy back to str
+ // 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 quotes
// var = pts at variable name, ended by NULL
// if $ is followed by '{', trailing '}' becomes NULL
// else $x becomes x followed by NULL
// beyond = pts at text following variable
+ int n;
char *var,*value,*beyond;
char quote = '\0';
char *ptr = str;
+ n = strlen(str) + 1;
+ if (n > max2) reallocate(str2,max2,n);
+
while (*ptr) {
if (*ptr == '$' && !quote) {
if (*(ptr+1) == '{') {
@@ -399,14 +408,13 @@ void Input::substitute(char *str, int flag)
if (value == NULL) error->one(FLERR,"Substitution for illegal variable");
*ptr = '\0';
- strcpy(work,str);
- if (strlen(work)+strlen(value) >= MAXLINE)
- error->one(FLERR,"Input line too long after variable substitution");
- strcat(work,value);
- if (strlen(work)+strlen(beyond) >= MAXLINE)
- error->one(FLERR,"Input line too long after variable substitution");
- strcat(work,beyond);
- strcpy(str,work);
+ strcpy(str2,str);
+ n = strlen(str2) + strlen(value) + strlen(beyond) + 1;
+ if (n > max1) reallocate(str,max1,n);
+ if (n > max2) reallocate(str2,max2,n);
+ strcat(str2,value);
+ strcat(str2,beyond);
+ strcpy(str,str2);
ptr += strlen(value);
if (flag && me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s",str);
@@ -420,6 +428,21 @@ void Input::substitute(char *str, int flag)
}
}
+/* ----------------------------------------------------------------------
+ rellocate a string
+ if n > 0: set max >= n in increments of DELTALINE
+ else just increment max by DELTALINE
+------------------------------------------------------------------------- */
+
+void Input::reallocate(char *&str, int &max, int n)
+{
+ if (n) {
+ while (n > max) max += DELTALINE;
+ } else max += DELTALINE;
+
+ str = (char *) memory->srealloc(str,max*sizeof(char),"input:str");
+}
+
/* ----------------------------------------------------------------------
process a single parsed command
return 0 if successful, -1 if did not recognize command
@@ -565,13 +588,14 @@ void Input::ifthenelse()
// in case expression was enclosed in quotes
// must substitute on copy of arg else will step on subsequent args
- char *scopy = new char[MAXLINE];
- strcpy(scopy,arg[0]);
- substitute(scopy,0);
+ int n = strlen(arg[0]) + 1;
+ if (n > maxline) reallocate(line,maxline,n);
+ strcpy(line,arg[0]);
+ substitute(line,work,maxline,maxwork,0);
// evaluate Boolean expression for "if"
- double btest = variable->evaluate_boolean(scopy);
+ double btest = variable->evaluate_boolean(line);
// bound "then" commands
@@ -606,17 +630,13 @@ void Input::ifthenelse()
for (int i = 0; i < ncommands; i++) delete [] commands[i];
delete [] commands;
- delete [] scopy;
return;
}
// done if no "elif" or "else"
- if (iarg == narg) {
- delete [] scopy;
- return;
- }
+ if (iarg == narg) return;
// check "elif" or "else" until find commands to execute
// substitute for variables and evaluate Boolean expression for "elif"
@@ -626,9 +646,11 @@ void Input::ifthenelse()
while (1) {
if (iarg+2 > narg) error->all(FLERR,"Illegal if command");
if (strcmp(arg[iarg],"elif") == 0) {
- strcpy(scopy,arg[iarg+1]);
- substitute(scopy,0);
- btest = variable->evaluate_boolean(scopy);
+ n = strlen(arg[iarg+1]) + 1;
+ if (n > maxline) reallocate(line,maxline,n);
+ strcpy(line,arg[iarg+1]);
+ substitute(line,work,maxline,maxwork,0);
+ btest = variable->evaluate_boolean(line);
first = iarg+2;
} else {
btest = 1.0;
@@ -664,7 +686,6 @@ void Input::ifthenelse()
for (int i = 0; i < ncommands; i++) delete [] commands[i];
delete [] commands;
- delete [] scopy;
return;
}
@@ -801,12 +822,18 @@ void Input::print()
{
if (narg != 1) error->all(FLERR,"Illegal print command");
+ // copy 1st arg back into line (copy is being used)
+ // check maxline since arg[0] could have been exanded by variables
// substitute for $ variables (no printing) and print arg
- substitute(arg[0],0);
+ int n = strlen(arg[0]) + 1;
+ if (n > maxline) reallocate(line,maxline,n);
+ strcpy(line,arg[0]);
+ substitute(line,work,maxline,maxwork,0);
+
if (me == 0) {
- if (screen) fprintf(screen,"%s\n",arg[0]);
- if (logfile) fprintf(logfile,"%s\n",arg[0]);
+ if (screen) fprintf(screen,"%s\n",line);
+ if (logfile) fprintf(logfile,"%s\n",line);
}
}
@@ -850,15 +877,20 @@ void Input::shell()
if (me == 0)
for (int i = 1; i < narg; i++) rmdir(arg[i]);
- // use work to concat args back into one string separated by spaces
+ // use work string to concat args back into one string separated by spaces
// invoke string in shell via system()
} else {
+ int n = 0;
+ for (int i = 0; i < narg; i++) n += strlen(arg[i]) + 1;
+ if (n > maxwork) reallocate(work,maxwork,n);
+
strcpy(work,arg[0]);
for (int i = 1; i < narg; i++) {
strcat(work," ");
strcat(work,arg[i]);
}
+
if (me == 0) system(work);
}
}
diff --git a/src/input.h b/src/input.h
index fb0fce2d15402bc366c51cf61d754a4f1e55aade..36e6c0c0dd1968caa3883793bae642efe0b271a7 100644
--- a/src/input.h
+++ b/src/input.h
@@ -30,13 +30,15 @@ class Input : protected Pointers {
void file(); // process all input
void file(const char *); // process an input script
char *one(const char *); // process a single command
- void substitute(char *, int); // substitute for variables in a string
+ void substitute(char *&, char *&, int &, int &, int);
+ // substitute for variables in a string
private:
int me; // proc ID
char *command; // ptr to current command
int maxarg; // max # of args in arg
- char *line,*copy,*work; // input line & copy of it
+ char *line,*copy,*work; // input line & copy and work string
+ int maxline,maxcopy,maxwork; // max lengths of char strings
int echo_screen; // 0 = no, 1 = yes
int echo_log; // 0 = no, 1 = yes
int nfile,maxfile; // current # and max # of open input files
@@ -46,9 +48,10 @@ class Input : protected Pointers {
FILE **infiles; // list of open input files
- void parse(); // parse an input text line
- char *nextword(char *, char **); // find next word in string, with quotes
- int execute_command(); // execute a single command
+ void parse(); // parse an input text line
+ char *nextword(char *, char **); // find next word in string with quotes
+ void reallocate(char *&, int &, int); // reallocate a char string
+ int execute_command(); // execute a single command
void clear(); // input script commands
void echo();
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 763e1a175dd69955f5fdfef3d6ecb555470cab7b..0909153adb563fc75331aa466599c07bf1a7938d 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -67,7 +67,6 @@ enum{SCALAR,VECTOR,ARRAY};
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
-#define MAXLINE 32768 // make this 4x longer than Input::MAXLINE
#define DELTA 8
/* ---------------------------------------------------------------------- */
@@ -89,12 +88,19 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
lostbefore = 0;
flushflag = 0;
+ // line string used for 3 tasks
+ // concat of custom style args
+ // one-time thermo output of header line
+ // each line of numeric thermo output
+ // 256 = extra for ONE or MULTI string or multi formatting
+ // 32 = max per-arg chars in header or numeric output
+
+ line = new char[256+32*narg];
+
// set style and corresponding lineflag
// custom style builds its own line of keywords
// customize a new thermo style by adding to if statement
- line = new char[MAXLINE];
-
if (strcmp(style,"one") == 0) {
strcpy(line,ONE);
} else if (strcmp(style,"multi") == 0) {
@@ -337,9 +343,6 @@ void Thermo::compute(int flag)
}
}
- // kludge for RedStorm timing issue
- // if (ntimestep == 100) return;
-
// print line to screen and logfile
if (me == 0) {