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new accessor APIs for fixes and computes in Modify plus a few applications

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This commit is contained in:
Axel Kohlmeyer
2021-08-08 17:25:06 -04:00
parent ef04f6ca69
commit 5b40e4cb38
20 changed files with 397 additions and 388 deletions
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122
src/variable.cpp
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@ -963,8 +963,7 @@ double Variable::compute_equal(int ivar)
else if (style[ivar] == PYTHON) {
int ifunc = python->find(data[ivar][0]);
if (ifunc < 0)
print_var_error(FLERR,fmt::format("cannot find python function {}",
data[ivar][0]),ivar);
print_var_error(FLERR,fmt::format("cannot find python function {}",data[ivar][0]),ivar);
python->invoke_function(ifunc,data[ivar][1]);
value = atof(data[ivar][1]);
}
@ -1324,10 +1323,9 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
// compute
// ----------------
if (strncmp(word,"c_",2) == 0 || strncmp(word,"C_",2) == 0) {
if (utils::strmatch(word,"^[Cc]_")) {
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);
// uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
@ -1335,14 +1333,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
int lowercase = 1;
if (word[0] == 'C') lowercase = 0;
int icompute = modify->find_compute(word+2);
if (icompute < 0) {
std::string mesg = "Invalid compute ID '";
mesg += (word+2);
mesg += "' in variable formula";
print_var_error(FLERR,mesg,ivar);
}
Compute *compute = modify->compute[icompute];
Compute *compute = modify->get_compute_by_id(word+2);
if (!compute)
print_var_error(FLERR,fmt::format("Invalid compute ID '{}' in variable formula", word+2),ivar);
// parse zero or one or two trailing brackets
// point i beyond last bracket
@ -1371,8 +1365,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (update->whichflag == 0) {
if (compute->invoked_scalar != 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_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= Compute::INVOKED_SCALAR;
@ -1392,12 +1385,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > compute->size_vector &&
compute->size_vector_variable == 0)
print_var_error(FLERR,"Variable formula compute vector "
"is accessed out-of-range",ivar,0);
print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0);
if (update->whichflag == 0) {
if (compute->invoked_vector != 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_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= Compute::INVOKED_VECTOR;
@ -1419,15 +1410,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > compute->size_array_rows &&
compute->size_array_rows_variable == 0)
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 (index2 > compute->size_array_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_array != 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_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
@ -1448,18 +1436,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && compute->vector_flag) {
if (tree == nullptr)
print_var_error(FLERR,"Compute global vector in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Compute global vector in equal-style variable formula",ivar);
if (treetype == ATOM)
print_var_error(FLERR,"Compute global vector in "
"atom-style variable formula",ivar);
print_var_error(FLERR,"Compute global vector in atom-style variable formula",ivar);
if (compute->size_vector == 0)
print_var_error(FLERR,"Variable formula compute "
"vector is zero length",ivar);
print_var_error(FLERR,"Variable formula compute vector is zero length",ivar);
if (update->whichflag == 0) {
if (compute->invoked_vector != 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_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= Compute::INVOKED_VECTOR;
@ -1477,18 +1461,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 1 && compute->array_flag) {
if (tree == nullptr)
print_var_error(FLERR,"Compute global vector in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Compute global vector in equal-style variable formula",ivar);
if (treetype == ATOM)
print_var_error(FLERR,"Compute global vector in "
"atom-style variable formula",ivar);
print_var_error(FLERR,"Compute global vector in atom-style variable formula",ivar);
if (compute->size_array_rows == 0)
print_var_error(FLERR,"Variable formula compute array "
"is zero length",ivar);
print_var_error(FLERR,"Variable formula compute array is zero length",ivar);
if (update->whichflag == 0) {
if (compute->invoked_array != 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_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
@ -1508,8 +1488,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
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;
@ -1550,15 +1529,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
compute->size_peratom_cols == 0) {
if (tree == nullptr)
print_var_error(FLERR,"Per-atom compute in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Per-atom compute in equal-style variable formula",ivar);
if (treetype == VECTOR)
print_var_error(FLERR,"Per-atom compute in "
"vector-style variable formula",ivar);
print_var_error(FLERR,"Per-atom compute in vector-style variable formula",ivar);
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;
@ -1576,18 +1552,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
compute->size_peratom_cols > 0) {
if (tree == nullptr)
print_var_error(FLERR,"Per-atom compute in "
"equal-style variable formula",ivar);
print_var_error(FLERR,"Per-atom compute in equal-style variable formula",ivar);
if (treetype == VECTOR)
print_var_error(FLERR,"Per-atom compute in "
"vector-style variable formula",ivar);
print_var_error(FLERR,"Per-atom compute in vector-style variable formula",ivar);
if (index1 > 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;
@ -1602,17 +1574,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 1 && compute->local_flag) {
print_var_error(FLERR,"Cannot access local data via indexing",ivar);
} else print_var_error(FLERR,
"Mismatched compute in variable formula",ivar);
} else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
// ----------------
// fix
// ----------------
} else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) {
} else if (utils::strmatch(word,"^[fF]_")) {
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);
// uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
@ -1620,11 +1590,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
int lowercase = 1;
if (word[0] == 'F') lowercase = 0;
int ifix = modify->find_fix(word+2);
if (ifix < 0)
print_var_error(FLERR,fmt::format("Invalid fix ID '{}' in variable"
" formula",word+2),ivar);
Fix *fix = modify->fix[ifix];
Fix *fix = modify->get_fix_by_id(word+2);
if (!fix)
print_var_error(FLERR,fmt::format("Invalid fix ID '{}' in variable formula",word+2),ivar);
// parse zero or one or two trailing brackets
// point i beyond last bracket
@ -4057,19 +4026,17 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
*ptr1 = '\0';
} else index = 0;
int icompute = modify->find_compute(&args[0][2]);
if (icompute < 0) {
compute = modify->get_compute_by_id(&args[0][2]);
if (!compute) {
std::string mesg = "Invalid compute ID '";
mesg += (args[0]+2);
mesg += "' in variable formula";
print_var_error(FLERR,mesg,ivar);
}
compute = modify->compute[icompute];
if (index == 0 && compute->vector_flag) {
if (update->whichflag == 0) {
if (compute->invoked_vector != 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_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= Compute::INVOKED_VECTOR;
@ -4078,12 +4045,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
nstride = 1;
} else if (index && compute->array_flag) {
if (index > compute->size_array_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_array != 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_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
@ -4102,14 +4067,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
*ptr1 = '\0';
} else index = 0;
int ifix = modify->find_fix(&args[0][2]);
if (ifix < 0) {
fix = modify->get_fix_by_id(&args[0][2]);
if (!fix) {
std::string mesg = "Invalid fix ID '";
mesg += (args[0]+2);
mesg += "' in variable formula";
print_var_error(FLERR,mesg,ivar);
}
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq) {
std::string mesg = "Fix with ID '";