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Merge branch 'develop' of https://github.com/lammps/lammps into lammps-develop

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This commit is contained in:
Jacob Gissinger
2021-11-04 21:20:29 -04:00
parent 67ae6eb7b6 a4ceda9706
commit 8d4956046b
727 changed files with 31087 additions and 8662 deletions
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141
src/variable.cpp
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@ -39,7 +39,6 @@
#include <cctype>
#include <cmath>
#include <cstring>
#include <unistd.h>
#include <unordered_map>
using namespace LAMMPS_NS;
@ -692,11 +691,11 @@ int Variable::next(int narg, char **arg)
int seed = 12345 + universe->me + which[find(arg[0])];
if (!random) random = new RanMars(lmp,seed);
int delay = (int) (1000000*random->uniform());
usleep(delay);
while (1) {
platform::usleep(delay);
while (true) {
if (!rename("tmp.lammps.variable","tmp.lammps.variable.lock")) break;
delay = (int) (1000000*random->uniform());
usleep(delay);
platform::usleep(delay);
}
// if the file cannot be found, we may have a race with some
@ -719,7 +718,7 @@ int Variable::next(int narg, char **arg)
break;
}
delay = (int) (1000000*random->uniform());
usleep(delay);
platform::usleep(delay);
}
delete random;
random = nullptr;
@ -964,8 +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]);
}
@ -1235,7 +1233,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (str == nullptr)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
while (1) {
while (true) {
onechar = str[i];
// whitespace: just skip
@ -1325,10 +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
@ -1336,14 +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
@ -1372,8 +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;
@ -1393,12 +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;
@ -1420,15 +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;
@ -1449,18 +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;
@ -1478,18 +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;
@ -1509,8 +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;
@ -1551,15 +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;
@ -1577,18 +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;
@ -1603,17 +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
@ -1621,11 +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
@ -3217,7 +3185,7 @@ int Variable::find_matching_paren(char *str, int i, char *&contents, int ivar)
int istart = i;
int ilevel = 0;
while (1) {
while (true) {
i++;
if (!str[i]) break;
if (str[i] == '(') ilevel++;
@ -4060,19 +4028,17 @@ 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;
@ -4081,12 +4047,10 @@ 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;
@ -4105,14 +4069,13 @@ 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 '";
@ -4788,7 +4751,7 @@ double Variable::evaluate_boolean(char *str)
int i = 0;
int expect = ARG;
while (1) {
while (true) {
onechar = str[i];
// whitespace: just skip
@ -5082,7 +5045,7 @@ int VarReader::read_scalar(char *str)
// read one string from file
if (me == 0) {
while (1) {
while (true) {
ptr = fgets(str,MAXLINE,fp);
if (!ptr) { n=0; break; } // end of file
ptr[strcspn(ptr,"#")] = '\0'; // strip comment
@ -5125,7 +5088,7 @@ int VarReader::read_peratom()
char str[MAXLINE];
if (me == 0) {
while (1) {
while (true) {
ptr = fgets(str,MAXLINE,fp);
if (!ptr) { n=0; break; } // end of file
ptr[strcspn(ptr,"#")] = '\0'; // strip comment