more changes to merge with current master
This commit is contained in:
Steve Plimpton
@ -1444,54 +1444,15 @@ int DumpCustom::parse_fields(int narg, char **arg)
|
||||
} else if (strcmp(arg[iarg],"tqz") == 0) {
|
||||
if (!atom->torque_flag)
|
||||
error->all(FLERR,"Dumping an atom property that isn't allocated");
|
||||
pack_choice[i] = &DumpCustom::pack_tqz;
|
||||
vtype[i] = Dump::DOUBLE;
|
||||
|
||||
// custom per-atom array = i2_ID or d2_ID, must include bracketed index
|
||||
// OLDSTYLE code - remove this after extend ArgInfo for i2/d2 arrays
|
||||
|
||||
} else if (strncmp(arg[iarg],"i2_",3) == 0 ||
|
||||
strncmp(arg[iarg],"d2_",3) == 0) {
|
||||
int which = 0;
|
||||
if (arg[iarg][0] == 'd') which = 1;
|
||||
|
||||
pack_choice[i] = &DumpCustom::pack_custom;
|
||||
if (!which) vtype[i] = Dump::INT;
|
||||
else vtype[i] = Dump::DOUBLE;
|
||||
|
||||
int n = strlen(arg[iarg]);
|
||||
char *suffix = new char[n];
|
||||
strcpy(suffix,&arg[iarg][3]);
|
||||
|
||||
char *ptr = strchr(suffix,'[');
|
||||
if (ptr) {
|
||||
if (suffix[strlen(suffix)-1] != ']')
|
||||
error->all(FLERR,"Invalid attribute in dump custom command");
|
||||
suffix[strlen(suffix)-1] = '\0';
|
||||
argindex[i] = utils::inumeric(FLERR,ptr+1,true,lmp);
|
||||
*ptr = '\0';
|
||||
} else error->all(FLERR,"Dump custom per-atom custom array is not indexed");
|
||||
|
||||
int flag,cols;
|
||||
n = atom->find_custom(suffix,flag,cols);
|
||||
|
||||
if ((!which && (n < 0 || flag || !cols)) ||
|
||||
(which && (n < 0 || !flag || !cols)))
|
||||
error->all(FLERR,"Dump custom per-atom custom array does not exist");
|
||||
if (argindex[i] <= 0 || argindex[i] > cols)
|
||||
error->all(FLERR,
|
||||
"Dump custom per-atom custom array is accessed out-of-range");
|
||||
|
||||
field2index[i] = add_custom(suffix,which);
|
||||
delete [] suffix;
|
||||
pack_choice[iarg] = &DumpCustom::pack_tqz;
|
||||
vtype[iarg] = Dump::DOUBLE;
|
||||
|
||||
// compute or fix or variable or custom vector/array
|
||||
// NEWSTYLE code - add ArgInfo returns for IVEC, DVEC, IARRAY, DARRAY
|
||||
|
||||
} else {
|
||||
int n,tmp;
|
||||
int n,flag,cols;
|
||||
ArgInfo argi(arg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
|
||||
|ArgInfo::DVEC|ArgInfo::IVEC);
|
||||
|ArgInfo::DNAME|ArgInfo::INAME);
|
||||
argindex[iarg] = argi.get_index1();
|
||||
auto name = argi.get_name();
|
||||
|
||||
@ -1559,50 +1520,58 @@ int DumpCustom::parse_fields(int narg, char **arg)
|
||||
field2index[iarg] = add_variable(name);
|
||||
break;
|
||||
|
||||
// custom per-atom floating point vector = d_ID
|
||||
// custom per-atom floating point vector or array
|
||||
|
||||
case ArgInfo::DVEC:
|
||||
case ArgInfo::DNAME:
|
||||
pack_choice[iarg] = &DumpCustom::pack_custom;
|
||||
vtype[iarg] = Dump::DOUBLE;
|
||||
|
||||
tmp = -1;
|
||||
n = atom->find_custom(name,tmp);
|
||||
n = atom->find_custom(name,flag,cols);
|
||||
|
||||
if (n < 0)
|
||||
error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
|
||||
|
||||
if (tmp != 1)
|
||||
error->all(FLERR,"Custom per-atom property ID {} is not floating point", name);
|
||||
if (argindex[iarg] == 0) {
|
||||
if (!flag || cols)
|
||||
error->all(FLERR,
|
||||
"Property double vector for dump custom does not exist");
|
||||
} else {
|
||||
if (!flag || !cols)
|
||||
error->all(FLERR,
|
||||
"Property double array for dump custom does not exist");
|
||||
if (argindex[iarg] > atom->dcols[n])
|
||||
error->all(FLERR,
|
||||
"Dump custom property array is accessed out-of-range");
|
||||
}
|
||||
|
||||
field2index[iarg] = add_custom(name,1);
|
||||
break;
|
||||
|
||||
// custom per-atom integer vector = i_ID
|
||||
// custom per-atom integer vector or array
|
||||
|
||||
case ArgInfo::IVEC:
|
||||
case ArgInfo::INAME:
|
||||
pack_choice[iarg] = &DumpCustom::pack_custom;
|
||||
vtype[iarg] = Dump::INT;
|
||||
|
||||
tmp = -1;
|
||||
n = atom->find_custom(name,tmp);
|
||||
n = atom->find_custom(name,flag,cols);
|
||||
|
||||
if (n < 0)
|
||||
error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
|
||||
|
||||
if (tmp != 0)
|
||||
error->all(FLERR,"Custom per-atom property ID {} is not integer", name);
|
||||
if (argindex[iarg] == 0) {
|
||||
if (flag || cols)
|
||||
error->all(FLERR,
|
||||
"Property integer vector for dump custom does not exist");
|
||||
} else {
|
||||
if (flag || !cols)
|
||||
error->all(FLERR,
|
||||
"Property integer array for dump custom does not exist");
|
||||
if (argindex[iarg] > atom->icols[n])
|
||||
error->all(FLERR,
|
||||
"Dump custom property array is accessed out-of-range");
|
||||
}
|
||||
|
||||
field2index[iarg] = add_custom(name,0);
|
||||
break;
|
||||
|
||||
// custom per-atom floating point array = d2_ID
|
||||
|
||||
case ArgInfo::DARRAY:
|
||||
return iarg;
|
||||
|
||||
// custom per-atom integer array = i2_ID
|
||||
|
||||
case ArgInfo::IARRAY:
|
||||
return iarg;
|
||||
|
||||
// no match
|
||||
|
||||
default:
|
||||
@ -1915,55 +1884,16 @@ int DumpCustom::modify_param(int narg, char **arg)
|
||||
else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY;
|
||||
else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ;
|
||||
|
||||
// custom per-atom array = i2_ID or d2_ID, must include bracketed index
|
||||
// OLDSTYLE code - remove this after extend ArgInfo for i2/d2 arrays
|
||||
|
||||
else if (strncmp(arg[1],"i2_",3) == 0 || strncmp(arg[1],"d2_",3) == 0) {
|
||||
int which = 0;
|
||||
if (arg[1][0] == 'd') which = 1;
|
||||
|
||||
if (!which) thresh_array[nthresh] = IARRAY;
|
||||
else thresh_array[nthresh] = DARRAY;
|
||||
memory->grow(field2index,nfield+nthresh+1,"dump:field2index");
|
||||
memory->grow(argindex,nfield+nthresh+1,"dump:argindex");
|
||||
|
||||
int n = strlen(arg[1]);
|
||||
char *suffix = new char[n];
|
||||
strcpy(suffix,&arg[1][3]);
|
||||
|
||||
char *ptr = strchr(suffix,'[');
|
||||
if (ptr) {
|
||||
if (suffix[strlen(suffix)-1] != ']')
|
||||
error->all(FLERR,"Invalid attribute in dump custom command");
|
||||
suffix[strlen(suffix)-1] = '\0';
|
||||
argindex[nfield+nthresh] = utils::inumeric(FLERR,ptr+1,true,lmp);
|
||||
*ptr = '\0';
|
||||
} else error->all(FLERR,"Dump_modify per-atom custom array is not indexed");
|
||||
|
||||
int flag,cols;
|
||||
n = atom->find_custom(suffix,flag,cols);
|
||||
|
||||
if ((!which && (n < 0 || flag || !cols)) ||
|
||||
(which && (n < 0 || !flag || !cols)))
|
||||
error->all(FLERR,"Could not find dump_modify per-atom custom array");
|
||||
if (argindex[nfield+nthresh] <= 0 || argindex[nfield+nthresh] > cols)
|
||||
error->all(FLERR,
|
||||
"Dump_modify per-atom custom array is accessed out-of-range");
|
||||
|
||||
field2index[nfield+nthresh] = add_custom(suffix,which);
|
||||
delete [] suffix;
|
||||
|
||||
// compute or fix or variable or custom vector/array
|
||||
// NEWSTYLE code - add ArgInfo returns for IVEC, DVEC, IARRAY, DARRAY
|
||||
// must grow field2index and argindex arrays, since access is beyond nfield
|
||||
|
||||
} else {
|
||||
else {
|
||||
memory->grow(field2index,nfield+nthresh+1,"dump:field2index");
|
||||
memory->grow(argindex,nfield+nthresh+1,"dump:argindex");
|
||||
|
||||
int n,tmp;
|
||||
int n,flag,cols;
|
||||
ArgInfo argi(arg[1],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
|
||||
|ArgInfo::DVEC|ArgInfo::IVEC);
|
||||
|ArgInfo::DNAME|ArgInfo::INAME);
|
||||
argindex[nfield+nthresh] = argi.get_index1();
|
||||
auto name = argi.get_name();
|
||||
|
||||
@ -2026,39 +1956,55 @@ int DumpCustom::modify_param(int narg, char **arg)
|
||||
field2index[nfield+nthresh] = add_variable(name);
|
||||
break;
|
||||
|
||||
// custom per atom floating point value = d_ID
|
||||
// custom per atom floating point vector or array
|
||||
|
||||
case ArgInfo::DVEC:
|
||||
thresh_array[nthresh] = DVEC;
|
||||
tmp = -1;
|
||||
n = atom->find_custom(name,tmp);
|
||||
if ((n < 0) || (tmp != 1))
|
||||
error->all(FLERR,"Could not find dump modify custom atom floating point property ID: {}",name);
|
||||
|
||||
field2index[nfield+nthresh] = add_custom(name,1);
|
||||
break;
|
||||
|
||||
// custom per atom integer value = i_ID
|
||||
|
||||
case ArgInfo::IVEC:
|
||||
thresh_array[nthresh] = IVEC;
|
||||
tmp = -1;
|
||||
n = atom->find_custom(name,tmp);
|
||||
if ((n < 0) || (tmp != 0))
|
||||
error->all(FLERR,"Could not find dump modify custom atom integer property ID: {}",name);
|
||||
case ArgInfo::DNAME:
|
||||
n = atom->find_custom(name,flag,cols);
|
||||
|
||||
if (n < 0)
|
||||
error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
|
||||
if (argindex[nfield+nthresh] == 0) {
|
||||
if (flag || cols)
|
||||
error->all(FLERR,
|
||||
"Property double vector for dump custom does not exist");
|
||||
thresh_array[nthresh] = DVEC;
|
||||
} else {
|
||||
if (flag || !cols)
|
||||
error->all(FLERR,
|
||||
"Property double array for dump custom does not exist");
|
||||
if (argindex[nfield+nthresh] > atom->dcols[n])
|
||||
error->all(FLERR,
|
||||
"Dump custom property array is accessed out-of-range");
|
||||
thresh_array[nthresh] = DARRAY;
|
||||
}
|
||||
|
||||
field2index[nfield+nthresh] = add_custom(name,0);
|
||||
break;
|
||||
|
||||
// custom per-atom floating point array = d2_ID
|
||||
// custom per atom integer vector or array
|
||||
|
||||
case ArgInfo::INAME:
|
||||
n = atom->find_custom(name,flag,cols);
|
||||
|
||||
case ArgInfo::DARRAY:
|
||||
return iarg;
|
||||
if (n < 0)
|
||||
error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
|
||||
if (argindex[nfield+nthresh] == 0) {
|
||||
if (flag || cols)
|
||||
error->all(FLERR,
|
||||
"Property integer vector for dump custom does not exist");
|
||||
thresh_array[nthresh] = IVEC;
|
||||
} else {
|
||||
if (flag || !cols)
|
||||
error->all(FLERR,
|
||||
"Property integer array for dump custom does not exist");
|
||||
if (argindex[nfield+nthresh] > atom->icols[n])
|
||||
error->all(FLERR,
|
||||
"Dump custom property array is accessed out-of-range");
|
||||
thresh_array[nthresh] = IARRAY;
|
||||
}
|
||||
|
||||
// custom per-atom integer array = i2_ID
|
||||
|
||||
case ArgInfo::IARRAY:
|
||||
return iarg;
|
||||
field2index[nfield+nthresh] = add_custom(name,0);
|
||||
break;
|
||||
|
||||
// no match
|
||||
|
||||
@ -2069,7 +2015,7 @@ int DumpCustom::modify_param(int narg, char **arg)
|
||||
}
|
||||
|
||||
// set operation type of threshold
|
||||
|
||||
|
||||
if (strcmp(arg[2],"<") == 0) thresh_op[nthresh] = LT;
|
||||
else if (strcmp(arg[2],"<=") == 0) thresh_op[nthresh] = LE;
|
||||
else if (strcmp(arg[2],">") == 0) thresh_op[nthresh] = GT;
|
||||
@ -2078,11 +2024,11 @@ int DumpCustom::modify_param(int narg, char **arg)
|
||||
else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ;
|
||||
else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
|
||||
else error->all(FLERR,"Invalid dump_modify thresh operator");
|
||||
|
||||
|
||||
// set threshold value as number or special LAST keyword
|
||||
// create FixStore to hold LAST values, should work with restart
|
||||
// id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
|
||||
|
||||
|
||||
if (strcmp(arg[3],"LAST") != 0) {
|
||||
thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
thresh_last[nthresh] = -1;
|
||||
@ -2092,17 +2038,17 @@ int DumpCustom::modify_param(int narg, char **arg)
|
||||
thresh_fixID = (char **)
|
||||
memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
|
||||
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
|
||||
|
||||
|
||||
std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
|
||||
thresh_fixID[nthreshlast] = utils::strdup(threshid);
|
||||
threshid += fmt::format(" {} STORE peratom 1 1", group->names[igroup]);
|
||||
thresh_fix[nthreshlast] = (FixStore *) modify->add_fix(threshid);
|
||||
|
||||
|
||||
thresh_last[nthreshlast] = nthreshlast;
|
||||
thresh_first[nthreshlast] = 1;
|
||||
nthreshlast++;
|
||||
}
|
||||
|
||||
|
||||
nthresh++;
|
||||
return 4;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user