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This commit is contained in:
Axel Kohlmeyer
2022-03-28 07:24:51 -04:00
parent ff107315cb
commit 4545954385
1 changed files with 144 additions and 246 deletions
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390
src/variable.cpp
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@ -131,11 +131,11 @@ Variable::Variable(LAMMPS *lmp) : Pointers(lmp)
Variable::~Variable()
{
for (int i = 0; i < nvar; i++) {
delete [] names[i];
delete[] names[i];
delete reader[i];
if (style[i] == LOOP || style[i] == ULOOP) delete [] data[i][0];
else for (int j = 0; j < num[i]; j++) delete [] data[i][j];
delete [] data[i];
if (style[i] == LOOP || style[i] == ULOOP) delete[] data[i][0];
else for (int j = 0; j < num[i]; j++) delete[] data[i][j];
delete[] data[i];
if (style[i] == VECTOR) memory->destroy(vecs[i].values);
}
memory->sfree(names);
@ -274,8 +274,7 @@ void Variable::set(int narg, char **arg)
if (universe->me == 0) {
FILE *fp = fopen("tmp.lammps.variable","w");
if (fp == nullptr)
error->one(FLERR,"Cannot open temporary file for world counter: "
+ utils::getsyserror());
error->one(FLERR,"Cannot open temporary file for world counter: " + utils::getsyserror());
fprintf(fp,"%d\n",universe->nworlds);
fclose(fp);
fp = nullptr;
@ -284,8 +283,7 @@ void Variable::set(int narg, char **arg)
for (int jvar = 0; jvar < nvar; jvar++)
if (num[jvar] && (style[jvar] == UNIVERSE || style[jvar] == ULOOP) &&
num[nvar] != num[jvar])
error->all(FLERR,
"All universe/uloop variables must have same # of values");
error->all(FLERR,"All universe/uloop variables must have same # of values");
// STRING
// replace pre-existing var if also style STRING (allows it to be reset)
@ -307,7 +305,7 @@ void Variable::set(int narg, char **arg)
if (ivar >= 0) {
if (style[ivar] != STRING)
error->all(FLERR,"Cannot redefine variable as a different style");
delete [] data[ivar][0];
delete[] data[ivar][0];
copy(1,&scopy,data[ivar]);
replaceflag = 1;
} else {
@ -410,7 +408,7 @@ void Variable::set(int narg, char **arg)
if (ivar >= 0) {
if (style[ivar] != EQUAL)
error->all(FLERR,"Cannot redefine variable as a different style");
delete [] data[ivar][0];
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
@ -436,7 +434,7 @@ void Variable::set(int narg, char **arg)
if (ivar >= 0) {
if (style[ivar] != ATOM)
error->all(FLERR,"Cannot redefine variable as a different style");
delete [] data[ivar][0];
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
@ -460,7 +458,7 @@ void Variable::set(int narg, char **arg)
if (ivar >= 0) {
if (style[ivar] != VECTOR)
error->all(FLERR,"Cannot redefine variable as a different style");
delete [] data[ivar][0];
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
@ -486,7 +484,7 @@ void Variable::set(int narg, char **arg)
if (ivar >= 0) {
if (style[ivar] != PYTHON)
error->all(FLERR,"Cannot redefine variable as a different style");
delete [] data[ivar][0];
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
@ -533,8 +531,7 @@ void Variable::set(int narg, char **arg)
if (replaceflag) return;
if (!utils::is_id(arg[0]))
error->all(FLERR,"Variable name '{}' must have only alphanu"
"meric characters or underscores",arg[0]);
error->all(FLERR,"Variable name '{}' must have only letters, numbers, or underscores",arg[0]);
names[nvar] = utils::strdup(arg[0]);
nvar++;
}
@ -567,7 +564,7 @@ void Variable::set(char *name, int narg, char **arg)
newarg[1] = (char *) "index";
for (int i = 0; i < narg; i++) newarg[2+i] = arg[i];
set(2+narg,newarg);
delete [] newarg;
delete[] newarg;
}
/* ----------------------------------------------------------------------
@ -582,7 +579,7 @@ int Variable::set_string(const char *name, const char *str)
int ivar = find(name);
if (ivar < 0) return -1;
if (style[ivar] != STRING) return -1;
delete [] data[ivar][0];
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(str);
return 0;
}
@ -605,8 +602,7 @@ int Variable::next(int narg, char **arg)
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
if (ivar < 0)
error->all(FLERR,"Invalid variable '{}' in next command",
arg[iarg]);
error->all(FLERR,"Invalid variable '{}' in next command",arg[iarg]);
if (style[ivar] == ULOOP && style[find(arg[0])] == UNIVERSE) continue;
else if (style[ivar] == UNIVERSE && style[find(arg[0])] == ULOOP) continue;
else if (style[ivar] != style[find(arg[0])])
@ -631,8 +627,7 @@ int Variable::next(int narg, char **arg)
for (iarg = 0; iarg < narg; iarg++)
if (strcmp(arg[iarg],names[i]) == 0) break;
if (iarg == narg)
error->universe_one(FLERR,"Next command must list all "
"universe and uloop variables");
error->universe_one(FLERR,"Next command must list all universe and uloop variables");
}
// increment all variables in list
@ -724,8 +719,8 @@ int Variable::next(int narg, char **arg)
random = nullptr;
if (nextindex < 0)
error->one(FLERR,"Unexpected error while incrementing uloop "
"style variable. Please contact LAMMPS developers.");
error->one(FLERR,"Unexpected error while incrementing uloop style variable. "
"Please contact the LAMMPS developers.");
//printf("READ %d %d\n",universe->me,nextindex);
fp = fopen("tmp.lammps.variable.lock","w");
@ -735,12 +730,10 @@ int Variable::next(int narg, char **arg)
fp = nullptr;
rename("tmp.lammps.variable.lock","tmp.lammps.variable");
if (universe->uscreen)
fprintf(universe->uscreen,
"Increment via next: value %d on partition %d\n",
fprintf(universe->uscreen, "Increment via next: value %d on partition %d\n",
nextindex+1,universe->iworld);
if (universe->ulogfile)
fprintf(universe->ulogfile,
"Increment via next: value %d on partition %d\n",
fprintf(universe->ulogfile, "Increment via next: value %d on partition %d\n",
nextindex+1,universe->iworld);
}
MPI_Bcast(&nextindex,1,MPI_INT,0,world);
@ -903,7 +896,7 @@ char *Variable::retrieve(const char *name)
sprintf(padstr,"%%0%dd",pad[ivar]);
sprintf(result,padstr,which[ivar]+1);
}
delete [] data[ivar][0];
delete[] data[ivar][0];
str = data[ivar][0] = utils::strdup(result);
} else if (style[ivar] == EQUAL) {
double answer = evaluate(data[ivar][0],nullptr,ivar);
@ -919,13 +912,12 @@ char *Variable::retrieve(const char *name)
} else if (style[ivar] == GETENV) {
const char *result = getenv(data[ivar][0]);
if (result == nullptr) result = (const char *) "";
delete [] data[ivar][1];
delete[] data[ivar][1];
str = data[ivar][1] = utils::strdup(result);
} else if (style[ivar] == PYTHON) {
int ifunc = python->variable_match(data[ivar][0],name,0);
if (ifunc < 0)
error->all(FLERR,"Python variable {} does not match "
"Python function {}", name, data[ivar][0]);
error->all(FLERR,"Python variable {} does not match Python function {}", name, data[ivar][0]);
python->invoke_function(ifunc,data[ivar][1]);
str = data[ivar][1];
// if Python func returns a string longer than VALUELENGTH
@ -993,8 +985,7 @@ double Variable::compute_equal(const std::string &str)
if sumflag, add variable values to existing result
------------------------------------------------------------------------- */
void Variable::compute_atom(int ivar, int igroup,
double *result, int stride, int sumflag)
void Variable::compute_atom(int ivar, int igroup, double *result, int stride, int sumflag)
{
Tree *tree = nullptr;
double *vstore;
@ -1127,10 +1118,10 @@ void Variable::internal_set(int ivar, double value)
void Variable::remove(int n)
{
delete [] names[n];
if (style[n] == LOOP || style[n] == ULOOP) delete [] data[n][0];
else for (int i = 0; i < num[n]; i++) delete [] data[n][i];
delete [] data[n];
delete[] names[n];
if (style[n] == LOOP || style[n] == ULOOP) delete[] data[n][0];
else for (int i = 0; i < num[n]; i++) delete[] data[n][i];
delete[] data[n];
delete reader[n];
for (int i = n+1; i < nvar; i++) {
@ -1261,7 +1252,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = evaluate(contents,nullptr,ivar);
delete [] contents;
delete[] contents;
// ----------------
// number: push value onto stack
@ -1295,7 +1286,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = atof(number);
delete [] number;
delete[] number;
// ----------------
// letter: c_ID, c_ID[], c_ID[][], f_ID, f_ID[], f_ID[][],
@ -1494,8 +1485,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
compute->invoked_flag |= Compute::INVOKED_PERATOM;
}
peratom2global(1,nullptr,compute->vector_atom,1,index1,
tree,treestack,ntreestack,argstack,nargstack);
peratom2global(1,nullptr,compute->vector_atom,1,index1,tree,
treestack,ntreestack,argstack,nargstack);
// c_ID[i][j] = scalar from per-atom array
@ -1503,24 +1494,20 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
compute->size_peratom_cols > 0) {
if (index2 > compute->size_peratom_cols)
print_var_error(FLERR,"Variable formula compute "
"array is accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (update->whichflag == 0) {
if (compute->invoked_peratom != update->ntimestep)
print_var_error(FLERR,"Compute used in variable "
"between runs is not current",ivar);
print_var_error(FLERR,"Compute used in variable between runs is not current",ivar);
} else if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= Compute::INVOKED_PERATOM;
}
if (compute->array_atom)
peratom2global(1,nullptr,&compute->array_atom[0][index2-1],
compute->size_peratom_cols,index1,
peratom2global(1,nullptr,&compute->array_atom[0][index2-1],compute->size_peratom_cols,index1,
tree,treestack,ntreestack,argstack,nargstack);
else
peratom2global(1,nullptr,nullptr,
compute->size_peratom_cols,index1,
peratom2global(1,nullptr,nullptr,compute->size_peratom_cols,index1,
tree,treestack,ntreestack,argstack,nargstack);
// c_ID = vector from per-atom vector
@ -1621,8 +1608,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (nbracket == 0 && fix->scalar_flag && lowercase) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed "
"at a compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
value1 = fix->compute_scalar();
if (tree) {
@ -1638,11 +1624,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > fix->size_vector &&
fix->size_vector_variable == 0)
print_var_error(FLERR,"Variable formula fix vector is "
"accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula fix vector is accessed out-of-range",ivar,0);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed "
"at a compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
value1 = fix->compute_vector(index1-1);
if (tree) {
@ -1658,14 +1642,11 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > fix->size_array_rows &&
fix->size_array_rows_variable == 0)
print_var_error(FLERR,"Variable formula fix array is "
"accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0);
if (index2 > fix->size_array_cols)
print_var_error(FLERR,"Variable formula fix array is "
"accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed at a "
"compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
value1 = fix->compute_array(index1-1,index2-1);
if (tree) {
@ -1680,17 +1661,13 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed at "
"compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
if (tree == nullptr)
print_var_error(FLERR,"Fix global vector in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Fix global vector in equal-style variable formula",ivar);
if (treetype == ATOM)
print_var_error(FLERR,"Fix global vector in "
"atom-style variable formula",ivar);
print_var_error(FLERR,"Fix global vector in atom-style variable formula",ivar);
if (fix->size_vector == 0)
print_var_error(FLERR,"Variable formula "
"fix vector is zero length",ivar);
print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
int nvec = fix->size_vector;
double *vec;
@ -1711,17 +1688,13 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 1 && fix->array_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed "
"at a compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
if (tree == nullptr)
print_var_error(FLERR,"Fix global vector in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Fix global vector in equal-style variable formula",ivar);
if (treetype == ATOM)
print_var_error(FLERR,"Fix global vector in "
"atom-style variable formula",ivar);
print_var_error(FLERR,"Fix global vector in atom-style variable formula",ivar);
if (fix->size_array_rows == 0)
print_var_error(FLERR,"Variable formula fix array is "
"zero length",ivar);
print_var_error(FLERR,"Variable formula fix array is zero length",ivar);
int nvec = fix->size_array_rows;
double *vec;
@ -1744,8 +1717,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
print_var_error(FLERR,"Fix in variable not computed "
"at a compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
peratom2global(1,nullptr,fix->vector_atom,1,index1,
tree,treestack,ntreestack,argstack,nargstack);
@ -1756,20 +1728,16 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols > 0) {
if (index2 > fix->size_peratom_cols)
print_var_error(FLERR,"Variable formula fix array is "
"accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
print_var_error(FLERR,"Fix in variable not computed "
"at a compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
if (fix->array_atom)
peratom2global(1,nullptr,&fix->array_atom[0][index2-1],
fix->size_peratom_cols,index1,
peratom2global(1,nullptr,&fix->array_atom[0][index2-1],fix->size_peratom_cols,index1,
tree,treestack,ntreestack,argstack,nargstack);
else
peratom2global(1,nullptr,nullptr,
fix->size_peratom_cols,index1,
peratom2global(1,nullptr,nullptr,fix->size_peratom_cols,index1,
tree,treestack,ntreestack,argstack,nargstack);
// f_ID = vector from per-atom vector
@ -1778,12 +1746,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols == 0) {
if (tree == nullptr)
print_var_error(FLERR,"Per-atom fix in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
print_var_error(FLERR,"Fix in variable not computed at "
"compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@ -1797,15 +1763,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols > 0) {
if (tree == nullptr)
print_var_error(FLERR,"Per-atom fix in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
if (index1 > fix->size_peratom_cols)
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
print_var_error(FLERR,"Fix in variable not computed at "
"compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@ -1824,8 +1787,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
int ivar = find(word+2);
if (ivar < 0)
print_var_error(FLERR,fmt::format("Invalid variable reference "
"{} in variable formula",word),ivar);
print_var_error(FLERR,fmt::format("Invalid variable reference {} in variable formula",word),
ivar);
if (eval_in_progress[ivar])
print_var_error(FLERR,"has a circular dependency",ivar);
@ -1865,8 +1828,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
char *var = retrieve(word+2);
if (var == nullptr)
print_var_error(FLERR,"Invalid variable evaluation in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar);
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@ -1880,11 +1842,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && style[ivar] == ATOM) {
if (tree == nullptr)
print_var_error(FLERR,"Atom-style variable in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Atom-style variable in equal-style variable formula",ivar);
if (treetype == VECTOR)
print_var_error(FLERR,"Atom-style variable in "
"vector-style variable formula",ivar);
print_var_error(FLERR,"Atom-style variable in vector-style variable formula",ivar);
Tree *newtree = nullptr;
evaluate(data[ivar][0],&newtree,ivar);
@ -1895,11 +1855,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && style[ivar] == ATOMFILE) {
if (tree == nullptr)
print_var_error(FLERR,"Atomfile-style variable in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Atomfile-style variable in equal-style variable formula",ivar);
if (treetype == VECTOR)
print_var_error(FLERR,"Atomfile-style variable in "
"vector-style variable formula",ivar);
print_var_error(FLERR,"Atomfile-style variable in vector-style variable formula",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@ -1913,11 +1871,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && style[ivar] == VECTOR) {
if (tree == nullptr)
print_var_error(FLERR,"Vector-style variable in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Vector-style variable in equal-style variable formula",ivar);
if (treetype == ATOM)
print_var_error(FLERR,"Vector-style variable in "
"atom-style variable formula",ivar);
print_var_error(FLERR,"Vector-style variable in atom-style variable formula",ivar);
double *vec;
int nvec = compute_vector(ivar,&vec);
@ -1938,8 +1894,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
double *result;
memory->create(result,atom->nlocal,"variable:result");
compute_atom(ivar,0,result,1,0);
peratom2global(1,nullptr,result,1,index,
tree,treestack,ntreestack,argstack,nargstack);
peratom2global(1,nullptr,result,1,index,tree,treestack,ntreestack,argstack,nargstack);
memory->destroy(result);
// v_name[N] = scalar from atomfile-style variable
@ -1957,8 +1912,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
double *vec;
int nvec = compute_vector(ivar,&vec);
if (index <= 0 || index > nvec)
print_var_error(FLERR,"Invalid index into "
"vector-style variable",ivar);
print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
int m = index; // convert from tagint to int
if (tree) {
@ -1968,8 +1922,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = vec[m-1];
} else print_var_error(FLERR,"Mismatched variable in "
"variable formula",ivar);
} else print_var_error(FLERR,"Mismatched variable in variable formula",ivar);
// ----------------
// math/group/special function or atom value/vector or
@ -1987,16 +1940,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
i = find_matching_paren(str,i,contents,ivar);
i++;
if (math_function(word,contents,tree,treestack,ntreestack,
argstack,nargstack,ivar));
else if (group_function(word,contents,tree,treestack,ntreestack,
argstack,nargstack,ivar));
else if (special_function(word,contents,tree,treestack,ntreestack,
argstack,nargstack,ivar));
else print_var_error(FLERR,fmt::format("Invalid math/group/special "
"function '{}()'in variable "
"formula", word),ivar);
delete [] contents;
if (math_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar));
else if (group_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar));
else if (special_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar));
else print_var_error(FLERR,fmt::format("Invalid math/group/special function '{}()' "
"in variable formula", word),ivar);
delete[] contents;
// ----------------
// atom value
@ -2004,15 +1953,13 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (str[i] == '[') {
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before "
"simulation box is defined",ivar);
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
ptr = &str[i];
tagint id = int_between_brackets(ptr,1);
i = ptr-str+1;
peratom2global(0,word,nullptr,0,id,
tree,treestack,ntreestack,argstack,nargstack);
peratom2global(0,word,nullptr,0,id,tree,treestack,ntreestack,argstack,nargstack);
// ----------------
// atom vector
@ -2020,8 +1967,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (is_atom_vector(word)) {
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before "
"simulation box is defined",ivar);
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
atom_vector(word,tree,treestack,ntreestack);
@ -2044,13 +1990,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else {
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before "
"simulation box is defined",ivar);
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
int flag = output->thermo->evaluate_keyword(word,&value1);
if (flag)
print_var_error(FLERR,fmt::format("Invalid thermo keyword '{}' in "
"variable formula",word),ivar);
print_var_error(FLERR,fmt::format("Invalid thermo keyword '{}' in variable formula",
word),ivar);
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@ -2060,7 +2005,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
}
}
delete [] word;
delete[] word;
// ----------------
// math operator, including end-of-string
@ -2162,8 +2107,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (value2 == 0.0)
argstack[nargstack++] = 1.0;
else if ((value1 == 0.0) && (value2 < 0.0))
print_var_error(FLERR,"Invalid power expression in "
"variable formula",ivar,0);
print_var_error(FLERR,"Invalid power expression in variable formula",ivar,0);
else argstack[nargstack++] = pow(value1,value2);
} else if (opprevious == UNARY) {
argstack[nargstack++] = -value2;
@ -3103,17 +3047,13 @@ double Variable::eval_tree(Tree *tree, int i)
}
if (tree->type == RMASK) {
if (domain->regions[tree->ivalue1]->match(atom->x[i][0],
atom->x[i][1],
atom->x[i][2])) return 1.0;
if (domain->regions[tree->ivalue1]->match(atom->x[i][0], atom->x[i][1], atom->x[i][2])) return 1.0;
else return 0.0;
}
if (tree->type == GRMASK) {
if ((atom->mask[i] & tree->ivalue1) &&
(domain->regions[tree->ivalue2]->match(atom->x[i][0],
atom->x[i][1],
atom->x[i][2]))) return 1.0;
(domain->regions[tree->ivalue2]->match(atom->x[i][0], atom->x[i][1], atom->x[i][2]))) return 1.0;
else return 0.0;
}
@ -3131,10 +3071,8 @@ int Variable::size_tree_vector(Tree *tree)
{
int nsize = 0;
if (tree->type == VECTORARRAY) nsize = tree->nvector;
if (tree->first) nsize = compare_tree_vector(nsize,
size_tree_vector(tree->first));
if (tree->second) nsize = compare_tree_vector(nsize,
size_tree_vector(tree->second));
if (tree->first) nsize = compare_tree_vector(nsize, size_tree_vector(tree->first));
if (tree->second) nsize = compare_tree_vector(nsize, size_tree_vector(tree->second));
if (tree->nextra) {
for (int i = 0; i < tree->nextra; i++)
nsize = compare_tree_vector(nsize,size_tree_vector(tree->extra[i]));
@ -3164,7 +3102,7 @@ void Variable::free_tree(Tree *tree)
if (tree->second) free_tree(tree->second);
if (tree->nextra) {
for (int i = 0; i < tree->nextra; i++) free_tree(tree->extra[i]);
delete [] tree->extra;
delete[] tree->extra;
}
if (tree->selfalloc) memory->destroy(tree->array);
@ -3223,8 +3161,7 @@ tagint Variable::int_between_brackets(char *&ptr, int varallow)
varflag = 1;
while (*ptr && *ptr != ']') {
if (!isalnum(*ptr) && *ptr != '_')
error->all(FLERR,"Variable name between brackets must be "
"alphanumeric or underscore characters");
error->all(FLERR,"Variable name between brackets must be letters, numbers, or underscores");
ptr++;
}
@ -3278,9 +3215,8 @@ tagint Variable::int_between_brackets(char *&ptr, int varallow)
swiggle(x,y,z),cwiggle(x,y,z)
------------------------------------------------------------------------- */
int Variable::math_function(char *word, char *contents, Tree **tree,
Tree **treestack, int &ntreestack,
double *argstack, int &nargstack, int ivar)
int Variable::math_function(char *word, char *contents, Tree **tree, Tree **treestack,
int &ntreestack, double *argstack, int &nargstack, int ivar)
{
// word not a match to any math function
@ -3349,8 +3285,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = SQRT;
else {
if (value1 < 0.0)
print_var_error(FLERR,"Sqrt of negative value in "
"variable formula",ivar,0);
print_var_error(FLERR,"Sqrt of negative value in variable formula",ivar,0);
argstack[nargstack++] = sqrt(value1);
}
@ -3365,8 +3300,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LN;
else {
if (value1 <= 0.0)
print_var_error(FLERR,"Log of zero/negative value in "
"variable formula",ivar,0);
print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar,0);
argstack[nargstack++] = log(value1);
}
} else if (strcmp(word,"log") == 0) {
@ -3375,8 +3309,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LOG;
else {
if (value1 <= 0.0)
print_var_error(FLERR,"Log of zero/negative value in "
"variable formula",ivar,0);
print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar,0);
argstack[nargstack++] = log10(value1);
}
} else if (strcmp(word,"abs") == 0) {
@ -3481,8 +3414,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
print_var_error(FLERR,"Cannot use ramp in "
"variable formula between runs",ivar);
print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar);
if (tree) newtree->type = RAMP;
else {
double delta = update->ntimestep - update->beginstep;
@ -3648,8 +3580,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
print_var_error(FLERR,"Cannot use vdisplace in "
"variable formula between runs",ivar);
print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar);
if (tree) newtree->type = VDISPLACE;
else {
double delta = update->ntimestep - update->beginstep;
@ -3661,8 +3592,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
print_var_error(FLERR,"Cannot use swiggle in "
"variable formula between runs",ivar);
print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@ -3677,8 +3607,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
print_var_error(FLERR,"Cannot use cwiggle in "
"variable formula between runs",ivar);
print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@ -3692,7 +3621,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
// delete stored args
for (int i = 0; i < narg; i++) delete [] args[i];
for (int i = 0; i < narg; i++) delete[] args[i];
return 1;
}
@ -3710,9 +3639,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
torque(group,dim),inertia(group,dim),omega(group,dim)
------------------------------------------------------------------------- */
int Variable::group_function(char *word, char *contents, Tree **tree,
Tree **treestack, int &ntreestack,
double *argstack, int &nargstack, int ivar)
int Variable::group_function(char *word, char *contents, Tree **tree, Tree **treestack,
int &ntreestack, double *argstack, int &nargstack, int ivar)
{
// word not a match to any group function
@ -3772,8 +3700,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = xcm[0];
else if (strcmp(args[1],"y") == 0) value = xcm[1];
else if (strcmp(args[1],"z") == 0) value = xcm[2];
@ -3789,8 +3716,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->vcm(igroup,masstotal,vcm,iregion);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = vcm[0];
else if (strcmp(args[1],"y") == 0) value = vcm[1];
else if (strcmp(args[1],"z") == 0) value = vcm[2];
@ -3832,8 +3758,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
value = group->gyration(igroup,masstotal,xcm,iregion);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"ke") == 0) {
if (narg == 1) value = group->ke(igroup);
@ -3852,8 +3777,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->angmom(igroup,xcm,lmom,iregion);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = lmom[0];
else if (strcmp(args[1],"y") == 0) value = lmom[1];
else if (strcmp(args[1],"z") == 0) value = lmom[2];
@ -3871,8 +3795,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->torque(igroup,xcm,tq,iregion);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = tq[0];
else if (strcmp(args[1],"y") == 0) value = tq[1];
else if (strcmp(args[1],"z") == 0) value = tq[2];
@ -3890,8 +3813,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->inertia(igroup,xcm,inertia,iregion);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"xx") == 0) value = inertia[0][0];
else if (strcmp(args[1],"yy") == 0) value = inertia[1][1];
else if (strcmp(args[1],"zz") == 0) value = inertia[2][2];
@ -3916,8 +3838,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
group->angmom(igroup,xcm,angmom,iregion);
group->inertia(igroup,xcm,inertia,iregion);
group->omega(angmom,inertia,omega);
} else print_var_error(FLERR,"Invalid group function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = omega[0];
else if (strcmp(args[1],"y") == 0) value = omega[1];
else if (strcmp(args[1],"z") == 0) value = omega[2];
@ -3926,7 +3847,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
// delete stored args
for (int i = 0; i < narg; i++) delete [] args[i];
for (int i = 0; i < narg; i++) delete[] args[i];
// save value in tree or on argstack
@ -3970,9 +3891,8 @@ int Variable::region_function(char *id, int ivar)
gmask(x),rmask(x),grmask(x,y),next(x)
------------------------------------------------------------------------- */
int Variable::special_function(char *word, char *contents, Tree **tree,
Tree **treestack, int &ntreestack,
double *argstack, int &nargstack, int ivar)
int Variable::special_function(char *word, char *contents, Tree **tree, Tree **treestack,
int &ntreestack, double *argstack, int &nargstack, int ivar)
{
double sx,sxx;
double value,sy,sxy;
@ -4085,11 +4005,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
nstride = 1;
} else if (index && fix->array_flag) {
if (index > fix->size_array_cols)
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed at "
"compatible time",ivar);
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
nvec = fix->size_array_rows;
nstride = fix->size_array_cols;
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
@ -4105,15 +4023,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
if (index)
print_var_error(FLERR,"Invalid special function in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
ivar = find(&args[0][2]);
if (ivar < 0)
print_var_error(FLERR,"Invalid special function in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
if (style[ivar] != VECTOR)
print_var_error(FLERR,"Mis-matched special function variable "
"in variable formula",ivar);
print_var_error(FLERR,"Mis-matched special function variable in variable formula",ivar);
if (eval_in_progress[ivar])
print_var_error(FLERR,"has a circular dependency",ivar);
@ -4125,8 +4040,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
print_var_error(FLERR,"Cannot compute average of empty vector",ivar);
} else print_var_error(FLERR,"Invalid special function in "
"variable formula",ivar);
} else print_var_error(FLERR,"Invalid special function in variable formula",ivar);
value = 0.0;
if (method == SLOPE) sx = sxx = sy = sxy = 0.0;
@ -4225,8 +4139,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"gmask") == 0) {
if (tree == nullptr)
print_var_error(FLERR,"Gmask function in equal-style "
"variable formula",ivar);
print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@ -4241,8 +4154,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"rmask") == 0) {
if (tree == nullptr)
print_var_error(FLERR,"Rmask function in equal-style "
"variable formula",ivar);
print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@ -4256,8 +4168,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"grmask") == 0) {
if (tree == nullptr)
print_var_error(FLERR,"Grmask function in equal-style "
"variable formula",ivar);
print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar);
if (narg != 2)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@ -4308,8 +4219,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (style[ivar] == ATOMFILE) {
if (tree == nullptr)
print_var_error(FLERR,"Atomfile variable in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar);
double *result;
memory->create(result,atom->nlocal,"variable:result");
@ -4325,13 +4235,11 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
newtree->selfalloc = 1;
treestack[ntreestack++] = newtree;
} else print_var_error(FLERR,"Invalid variable style in "
"special function next",ivar);
} else print_var_error(FLERR,"Invalid variable style in special function next",ivar);
} else if (strcmp(word,"is_active") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid is_active() function in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar);
Info info(lmp);
value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0;
@ -4347,8 +4255,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_available") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid is_available() function in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar);
Info info(lmp);
value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0;
@ -4364,8 +4271,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_defined") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid is_defined() function in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar);
Info info(lmp);
value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0;
@ -4381,8 +4287,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_file") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid is_file() function in "
"variable formula",ivar);
print_var_error(FLERR,"Invalid is_file() function in variable formula",ivar);
FILE *fp = fopen(args[0],"r");
value = (fp == nullptr) ? 0.0 : 1.0;
@ -4400,7 +4305,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
// delete stored args
for (int i = 0; i < narg; i++) delete [] args[i];
for (int i = 0; i < narg; i++) delete[] args[i];
return 1;
}
@ -4415,17 +4320,14 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
id,mass,type,mol,x,y,z,vx,vy,vz,fx,fy,fz,q
------------------------------------------------------------------------- */
void Variable::peratom2global(int flag, char *word,
double *vector, int nstride, tagint id,
Tree **tree, Tree **treestack, int &ntreestack,
double *argstack, int &nargstack)
void Variable::peratom2global(int flag, char *word, double *vector, int nstride, tagint id, Tree **tree,
Tree **treestack, int &ntreestack, double *argstack, int &nargstack)
{
// error check for ID larger than any atom
// int_between_brackets() already checked for ID <= 0
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,
"Indexed per-atom vector in variable formula without atom map");
error->all(FLERR, "Indexed per-atom vector in variable formula without atom map");
if (id > atom->map_tag_max)
error->all(FLERR,"Variable atom ID is too large");
@ -4515,8 +4417,7 @@ int Variable::is_atom_vector(char *word)
id,mass,type,mol,x,y,z,vx,vy,vz,fx,fy,fz,q
------------------------------------------------------------------------- */
void Variable::atom_vector(char *word, Tree **tree,
Tree **treestack, int &ntreestack)
void Variable::atom_vector(char *word, Tree **tree, Tree **treestack, int &ntreestack)
{
if (tree == nullptr)
error->all(FLERR,"Atom vector in equal-style variable formula");
@ -4712,7 +4613,7 @@ double Variable::evaluate_boolean(char *str)
argstack[nargstack].flag = 0;
nargstack++;
delete [] contents;
delete[] contents;
// ----------------
// number: push value onto stack
@ -4843,8 +4744,8 @@ double Variable::evaluate_boolean(char *str)
} else {
if (strcmp(str1,str2) == 0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
delete [] str1;
delete [] str2;
delete[] str1;
delete[] str2;
}
} else if (opprevious == NE) {
if (flag1 != flag2)
@ -4855,8 +4756,8 @@ double Variable::evaluate_boolean(char *str)
} else {
if (strcmp(str1,str2) != 0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
delete [] str1;
delete [] str2;
delete[] str1;
delete[] str2;
}
} else if (opprevious == LT) {
if (flag2) error->all(FLERR,"Invalid Boolean syntax in if command");
@ -4925,8 +4826,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
if (me == 0) {
fp = fopen(file,"r");
if (fp == nullptr)
error->one(FLERR,"Cannot open file variable file {}: {}",
file, utils::getsyserror());
error->one(FLERR,"Cannot open file variable file {}: {}", file, utils::getsyserror());
}
// if atomfile-style variable, must store per-atom values read from file
@ -4960,8 +4860,8 @@ VarReader::~VarReader()
if (fixstore) {
if (modify) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] buffer;
delete[] id_fix;
delete[] buffer;
}
}
@ -5057,12 +4957,10 @@ int VarReader::read_peratom()
tag = words.next_bigint();
value = words.next_double();
} catch (TokenizerException &e) {
error->all(FLERR,"Invalid atomfile line '{}': {}",
buf,e.what());
error->all(FLERR,"Invalid atomfile line '{}': {}",buf,e.what());
}
if ((tag <= 0) || (tag > map_tag_max))
error->all(FLERR,"Invalid atom ID {} in variable "
"file", tag);
error->all(FLERR,"Invalid atom ID {} in variable file", tag);
if ((m = atom->map(tag)) >= 0) vstore[m] = value;
buf = next + 1;
}