ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7851 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-02-28 17:41:29 +00:00
parent 3450c008aa
commit c2777b94c2
6 changed files with 92 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
src/create_atoms.cpp
View File

@ -89,6 +89,7 @@ void CreateAtoms::command(int narg, char **arg)
// process optional keywords
int scaleflag = 1;
remapflag = 0;
if (domain->lattice) {
nbasis = domain->lattice->nbasis;
@ -108,6 +109,12 @@ void CreateAtoms::command(int narg, char **arg)
error->all(FLERR,"Illegal create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"yes") == 0) remapflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) remapflag = 0;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
@ -214,6 +221,13 @@ void CreateAtoms::add_single()
{
double *sublo,*subhi;
// remap atom if requested
if (remapflag) {
int imagetmp = (512 << 20) | (512 << 10) | 512;
domain->remap(xone,imagetmp);
}
// sub-domain bounding box, in lamda units if triclinic
if (domain->triclinic == 0) {

1
src/create_atoms.h
View File

@ -33,6 +33,7 @@ class CreateAtoms : protected Pointers {
int itype,style,nregion,nbasis,nrandom,seed;
int *basistype;
double xone[3];
int remapflag;
void add_single();
void add_random();

41
src/delete_bonds.cpp
View File

@ -82,12 +82,14 @@ void DeleteBonds::command(int narg, char **arg)
// grab optional keywords
int any_flag = 0;
int undo_flag = 0;
int remove_flag = 0;
int special_flag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"undo") == 0) undo_flag = 1;
if (strcmp(arg[iarg],"any") == 0) any_flag = 1;
else if (strcmp(arg[iarg],"undo") == 0) undo_flag = 1;
else if (strcmp(arg[iarg],"remove") == 0) remove_flag = 1;
else if (strcmp(arg[iarg],"special") == 0) special_flag = 1;
else error->all(FLERR,"Illegal delete_bonds command");
@ -107,7 +109,7 @@ void DeleteBonds::command(int narg, char **arg)
// set topology interactions either off or on
// criteria for an interaction to potentially be changed (set flag = 1)
// all atoms in interaction must be in group
// all atoms or one atom in interaction must be in group, based on any_flag
// for style = MULTI, no other criteria
// for style = ATOM, at least one atom is specified type
// for style = BOND/ANGLE/DIHEDRAL/IMPROPER, interaction is specified type
@ -120,7 +122,7 @@ void DeleteBonds::command(int narg, char **arg)
int *type = atom->type;
int nlocal = atom->nlocal;
int i,m,n,flag;
int i,m,n,consider,flag;
int atom1,atom2,atom3,atom4;
if (atom->avec->bonds_allow) {
@ -131,7 +133,12 @@ void DeleteBonds::command(int narg, char **arg)
for (m = 0; m < num_bond[i]; m++) {
atom1 = atom->map(atom->bond_atom[i][m]);
if (atom1 == -1) error->one(FLERR,"Bond atom missing in delete_bonds");
if (mask[i] & groupbit && mask[atom1] & groupbit) {
consider = 0;
if (!any_flag && mask[i] & groupbit && mask[atom1] & groupbit)
consider = 1;
if (any_flag && (mask[i] & groupbit || mask[atom1] & groupbit))
consider = 1;
if (consider) {
flag = 0;
if (style == MULTI) flag = 1;
if (style == ATOM &&
@ -159,8 +166,12 @@ void DeleteBonds::command(int narg, char **arg)
atom3 = atom->map(atom->angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
error->one(FLERR,"Angle atom missing in delete_bonds");
if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit) {
consider = 0;
if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit) consider = 1;
if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
mask[atom3] & groupbit)) consider = 1;
if (consider) {
flag = 0;
if (style == MULTI) flag = 1;
if (style == ATOM &&
@ -190,8 +201,13 @@ void DeleteBonds::command(int narg, char **arg)
atom4 = atom->map(atom->dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,"Dihedral atom missing in delete_bonds");
if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit && mask[atom4] & groupbit) {
consider = 0;
if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
mask[atom3] & groupbit || mask[atom4] & groupbit))
consider = 1;
if (consider) {
flag = 0;
if (style == MULTI) flag = 1;
if (style == ATOM &&
@ -221,8 +237,13 @@ void DeleteBonds::command(int narg, char **arg)
atom4 = atom->map(atom->improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,"Improper atom missing in delete_bonds");
if (mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit && mask[atom4] & groupbit) {
consider = 0;
if (!any_flag && mask[atom1] & groupbit && mask[atom2] & groupbit &&
mask[atom3] & groupbit && mask[atom4] & groupbit) consider = 1;
if (any_flag && (mask[atom1] & groupbit || mask[atom2] & groupbit ||
mask[atom3] & groupbit || mask[atom4] & groupbit))
consider = 1;
if (consider) {
flag = 0;
if (style == MULTI) flag = 1;
if (style == ATOM &&

63
src/input.cpp
View File

@ -284,7 +284,7 @@ void Input::parse()
strcpy(copy,line);
// strip any # comment by resetting string terminator
// strip any # comment by replacing it with 0
// do not strip # inside single/double quotes
char quote = '\0';
@ -306,40 +306,59 @@ void Input::parse()
// command = 1st arg
command = strtok(copy," \t\n\r\f");
char *next;
command = nextword(copy,&next);
if (command == NULL) return;
// point arg[] at each subsequent arg
// treat text between single/double quotes as one arg
// insert string terminators in copy to delimit args
quote = '\0';
int iarg,argstart;
// nextword() inserts zeroes in copy to delimit args
// nextword() treats text between single/double quotes as one arg
narg = 0;
while (1) {
ptr = next;
while (ptr) {
if (narg == maxarg) {
maxarg += DELTA;
arg = (char **) memory->srealloc(arg,maxarg*sizeof(char *),"input:arg");
}
arg[narg] = strtok(NULL," \t\n\r\f");
arg[narg] = nextword(ptr,&next);
if (!arg[narg]) break;
if (!quote && (arg[narg][0] == '"' || arg[narg][0] == '\'')) {
quote = arg[narg][0];
argstart = narg;
arg[narg] = &arg[narg][1];
}
if (quote && arg[narg][strlen(arg[narg])-1] == quote) {
for (iarg = argstart; iarg < narg; iarg++)
arg[iarg][strlen(arg[iarg])] = ' ';
arg[narg][strlen(arg[narg])-1] = '\0';
narg = argstart;
quote = '\0';
}
narg++;
ptr = next;
}
}
if (quote) error->all(FLERR,"Unbalanced quotes in input line");
/* ----------------------------------------------------------------------
find next word in str
insert 0 at end of word
ignore leading whitespace
treat text between single/double quotes as one arg
matching quote must be followed by whitespace char if not end of string
strip quotes from returned word
return ptr to start of word
return next = ptr after word or NULL if word ended with 0
return NULL if no word in string
------------------------------------------------------------------------- */
char *Input::nextword(char *str, char **next)
{
char *start,*stop;
start = &str[strspn(str," \t\n\v\f\r")];
if (*start == '\0') return NULL;
if (*start == '"' || *start == '\'') {
stop = strchr(&start[1],*start);
if (!stop) error->all(FLERR,"Unbalanced quotes in input line");
if (stop[1] && !isspace(stop[1]))
error->all(FLERR,"Input line quote not followed by whitespace");
start++;
} else stop = &start[strcspn(start," \t\n\v\f\r")];
if (*stop == '\0') *next = NULL;
else *next = stop+1;
*stop = '\0';
return start;
}
/* ----------------------------------------------------------------------

5
src/input.h
View File

@ -46,8 +46,9 @@ class Input : protected Pointers {
FILE **infiles; // list of open input files
void parse(); // parse an input text line
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
int execute_command(); // execute a single command
void clear(); // input script commands
void echo();

2
src/output.cpp
View File

@ -502,6 +502,8 @@ void Output::create_restart(int narg, char **arg)
restart = new WriteRestart(lmp);
if (narg != 2 && narg != 3) error->all(FLERR,"Illegal restart command");
int n = strlen(arg[1]) + 3;
restart1 = new char[n];
strcpy(restart1,arg[1]);