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dbb23b6006b910cc6c50e67bba494b9b2882f691
lammps/src/variable.cpp
Axel Kohlmeyer 9f88867b37 update parsing of file and atomfile variable files 
this allows to handle comments and empty lines everywhere for atomfile
and file variables and in a consistent manner since it used utils functions.
also error messages are improved and more specific.
2024-04-10 03:08:08 -04:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "variable.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_atom.h"
#include "group.h"
#include "info.h"
#include "input.h"
#include "label_map.h"
#include "library.h"
#include "lmppython.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "output.h"
#include "random_mars.h"
#include "region.h"
#include "thermo.h"
#include "tokenizer.h"
#include "universe.h"
#include "update.h"
#include "fmt/ranges.h"
#include <cctype>
#include <cmath>
#include <cstring>
#include <unordered_map>
using namespace LAMMPS_NS;
using namespace MathConst;
static constexpr int VARDELTA = 4;
static constexpr int MAXLEVEL = 4;
static constexpr int MAXLINE = 256;
static constexpr int CHUNK = 1024;
static constexpr int MAXFUNCARG = 6;
static inline double MYROUND(double a) { return ((a - floor(a)) >= 0.5) ? ceil(a) : floor(a); }
enum{ARG,OP};
// customize by adding a function
// if add before XOR:
// also set precedence level in constructor and precedence length in *.h
enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY,
NOT,EQ,NE,LT,LE,GT,GE,AND,OR,XOR,
SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2,
RANDOM,NORMAL,CEIL,FLOOR,ROUND,TERNARY,
RAMP,STAGGER,LOGFREQ,LOGFREQ2,LOGFREQ3,STRIDE,STRIDE2,
VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,
GRMASK,IS_ACTIVE,IS_DEFINED,IS_AVAILABLE,IS_FILE,EXTRACT_SETTING,
VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY,VECTORARRAY};
// customize by adding a special function
enum{SUM,XMIN,XMAX,AVE,TRAP,SLOPE};
static constexpr double BIG = 1.0e20;
// INT64_MAX cannot be represented with a double. reduce to avoid overflow when casting back
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
static constexpr double MAXBIGINT_DOUBLE = (double) (MAXBIGINT-512);
#else
static constexpr double MAXBIGINT_DOUBLE = (double) MAXBIGINT;
#endif
// constants for variable expressions. customize by adding new items.
// if needed (cf. 'version') initialize in Variable class constructor.
static std::unordered_map<std::string, double> constants = {
{"PI", MY_PI },
{"version", -1 },
{"yes", 1 },
{"no", 0 },
{"on", 1 },
{"off", 0 },
{"true", 1 },
{"false", 0 }
};
/* ---------------------------------------------------------------------- */
Variable::Variable(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
nvar = maxvar = 0;
names = nullptr;
style = nullptr;
num = nullptr;
which = nullptr;
pad = nullptr;
reader = nullptr;
data = nullptr;
dvalue = nullptr;
vecs = nullptr;
eval_in_progress = nullptr;
randomequal = nullptr;
randomatom = nullptr;
// override initializer since LAMMPS class needs to be instantiated
constants["version"] = lmp->num_ver;
// customize by assigning a precedence level
precedence[DONE] = 0;
precedence[OR] = precedence[XOR] = 1;
precedence[AND] = 2;
precedence[EQ] = precedence[NE] = 3;
precedence[LT] = precedence[LE] = precedence[GT] = precedence[GE] = 4;
precedence[ADD] = precedence[SUBTRACT] = 5;
precedence[MULTIPLY] = precedence[DIVIDE] = precedence[MODULO] = 6;
precedence[CARAT] = 7;
precedence[UNARY] = precedence[NOT] = 8;
}
/* ---------------------------------------------------------------------- */
Variable::~Variable()
{
for (int i = 0; i < nvar; 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] == VECTOR) memory->destroy(vecs[i].values);
}
memory->sfree(names);
memory->destroy(style);
memory->destroy(num);
memory->destroy(which);
memory->destroy(pad);
memory->sfree(reader);
memory->sfree(data);
memory->sfree(dvalue);
memory->sfree(vecs);
memory->destroy(eval_in_progress);
delete randomequal;
delete randomatom;
}
/* ----------------------------------------------------------------------
called by variable command in input script
------------------------------------------------------------------------- */
void Variable::set(int narg, char **arg)
{
if (narg < 2) utils::missing_cmd_args(FLERR, "variable", error);
int replaceflag = 0;
// DELETE
// doesn't matter if variable no longer exists
if (strcmp(arg[1],"delete") == 0) {
if (narg != 2)
error->all(FLERR,"Illegal variable delete command: expected 2 arguments but found {}", narg);
if (find(arg[0]) >= 0) remove(find(arg[0]));
return;
// INDEX
// num = listed args, which = 1st value, data = copied args
} else if (strcmp(arg[1],"index") == 0) {
if (narg < 3) utils::missing_cmd_args(FLERR, "variable index", error);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = INDEX;
num[nvar] = narg - 2;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(num[nvar],&arg[2],data[nvar]);
// LOOP
// 1 arg + pad: num = N, which = 1st value, data = single string
// 2 args + pad: num = N2, which = N1, data = single string
} else if (strcmp(arg[1],"loop") == 0) {
if (narg < 3) utils::missing_cmd_args(FLERR, "variable loop", error);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = LOOP;
int nfirst = 0,nlast = 0;
if (narg == 3 || (narg == 4 && strcmp(arg[3],"pad") == 0)) {
nfirst = 1;
nlast = utils::inumeric(FLERR,arg[2],false,lmp);
if (nlast <= 0) error->all(FLERR, "Invalid variable loop argument: {}", nlast);
if (narg == 4 && strcmp(arg[3],"pad") == 0) {
pad[nvar] = fmt::format("{}",nlast).size();
} else pad[nvar] = 0;
} else if (narg == 4 || (narg == 5 && strcmp(arg[4],"pad") == 0)) {
nfirst = utils::inumeric(FLERR,arg[2],false,lmp);
nlast = utils::inumeric(FLERR,arg[3],false,lmp);
if (nfirst > nlast || nlast < 0)
error->all(FLERR,"Illegal variable loop command: {} > {}", nfirst,nlast);
if (narg == 5 && strcmp(arg[4],"pad") == 0) {
pad[nvar] = fmt::format("{}",nlast).size();
} else pad[nvar] = 0;
} else error->all(FLERR,"Illegal variable loop command: too many arguments");
num[nvar] = nlast;
which[nvar] = nfirst-1;
data[nvar] = new char*[1];
data[nvar][0] = nullptr;
// WORLD
// num = listed args, which = partition this proc is in, data = copied args
// error check that num = # of worlds in universe
} else if (strcmp(arg[1],"world") == 0) {
if (narg < 3) utils::missing_cmd_args(FLERR, "variable world", error);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = WORLD;
num[nvar] = narg - 2;
if (num[nvar] != universe->nworlds)
error->all(FLERR,"World variable count doesn't match # of partitions");
which[nvar] = universe->iworld;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(num[nvar],&arg[2],data[nvar]);
// UNIVERSE and ULOOP
// for UNIVERSE: num = listed args, data = copied args
// for ULOOP: num = N, data = single string
// which = partition this proc is in
// universe proc 0 creates lock file
// error check that all other universe/uloop variables are same length
} else if (strcmp(arg[1],"universe") == 0 || strcmp(arg[1],"uloop") == 0) {
if (strcmp(arg[1],"universe") == 0) {
if (narg < 3) utils::missing_cmd_args(FLERR, "variable universe", error);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = UNIVERSE;
num[nvar] = narg - 2;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(num[nvar],&arg[2],data[nvar]);
} else if (strcmp(arg[1],"uloop") == 0) {
if (narg < 3 || narg > 4)
error->all(FLERR,"Illegal variable command: expected 3 or 4 arguments but found {}", narg);
if (narg == 4 && strcmp(arg[3],"pad") != 0)
error->all(FLERR, "Invalid variable uloop argument: {}", arg[3]);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = ULOOP;
num[nvar] = utils::inumeric(FLERR,arg[2],false,lmp);
data[nvar] = new char*[1];
data[nvar][0] = nullptr;
if (narg == 4) pad[nvar] = std::to_string(num[nvar]).size();
else pad[nvar] = 0;
}
if (num[nvar] < universe->nworlds)
error->all(FLERR,"Universe/uloop variable count < # of partitions");
which[nvar] = universe->iworld;
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());
fprintf(fp,"%d\n",universe->nworlds);
fclose(fp);
fp = nullptr;
}
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");
// STRING
// replace pre-existing var if also style STRING (allows it to be reset)
// num = 1, which = 1st value
// data = 1 value, string to eval
} else if (strcmp(arg[1],"string") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
int maxcopy = strlen(arg[2]) + 1;
int maxwork = maxcopy;
auto scopy = (char *) memory->smalloc(maxcopy,"var:string/copy");
auto work = (char *) memory->smalloc(maxwork,"var:string/work");
strcpy(scopy,arg[2]);
input->substitute(scopy,work,maxcopy,maxwork,1);
memory->sfree(work);
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != STRING)
error->all(FLERR,"Cannot redefine variable as a different style");
delete[] data[ivar][0];
copy(1,&scopy,data[ivar]);
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = STRING;
num[nvar] = 1;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(1,&scopy,data[nvar]);
}
memory->sfree(scopy);
// GETENV
// remove pre-existing var if also style GETENV (allows it to be reset)
// num = 1, which = 1st value
// data = 1 value, string to eval
} else if (strcmp(arg[1],"getenv") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
if (find(arg[0]) >= 0) {
if (style[find(arg[0])] != GETENV)
error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) grow();
style[nvar] = GETENV;
num[nvar] = 2;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = utils::strdup(arg[2]);
data[nvar][1] = utils::strdup("(undefined)");
// SCALARFILE for strings or numbers
// which = 1st value
// data = 1 value, string to eval
} else if (strcmp(arg[1],"file") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = SCALARFILE;
num[nvar] = 1;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = new char[MAXLINE];
reader[nvar] = new VarReader(lmp,arg[0],arg[2],SCALARFILE);
int flag = reader[nvar]->read_scalar(data[nvar][0]);
if (flag)
error->all(FLERR,"File variable {} could not read value from {}", arg[0], arg[2]);
// ATOMFILE for numbers
// which = 1st value
// data = nullptr
} else if (strcmp(arg[1],"atomfile") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) grow();
style[nvar] = ATOMFILE;
num[nvar] = 1;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = nullptr;
reader[nvar] = new VarReader(lmp,arg[0],arg[2],ATOMFILE);
int flag = reader[nvar]->read_peratom();
if (flag)
error->all(FLERR,"Atomfile variable {} could not read values from {}", arg[0], arg[2]);
// FORMAT
// num = 3, which = 1st value
// data = 3 values
// 1st is name of variable to eval, 2nd is format string,
// 3rd is filled on retrieval
} else if (strcmp(arg[1],"format") == 0) {
constexpr char validfmt[] = "^% ?-?[0-9]*\\.?[0-9]*[efgEFG]$";
if (narg != 4) error->all(FLERR,"Illegal variable command: expected 4 arguments but found {}", narg);
int ivar = find(arg[0]);
int jvar = find(arg[2]);
if (jvar < 0)
error->all(FLERR, "Variable {}: format variable {} does not exist", arg[0], arg[2]);
if (!equalstyle(jvar))
error->all(FLERR, "Variable {}: format variable {} has incompatible style", arg[0], arg[2]);
if (ivar >= 0) {
if (style[ivar] != FORMAT)
error->all(FLERR,"Cannot redefine variable as a different style");
if (!utils::strmatch(arg[3], validfmt))
error->all(FLERR,"Incorrect conversion in format string");
delete[] data[ivar][0];
delete[] data[ivar][1];
data[ivar][0] = utils::strdup(arg[2]);
data[ivar][1] = utils::strdup(arg[3]);
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = FORMAT;
num[nvar] = 3;
which[nvar] = 0;
pad[nvar] = 0;
if (!utils::strmatch(arg[3], validfmt))
error->all(FLERR,"Incorrect conversion in format string");
data[nvar] = new char*[num[nvar]];
copy(2,&arg[2],data[nvar]);
data[nvar][2] = new char[VALUELENGTH];
strcpy(data[nvar][2],"(undefined)");
}
// EQUAL
// replace pre-existing var if also style EQUAL (allows it to be reset)
// num = 2, which = 1st value
// data = 2 values, 1st is string to eval, 2nd is filled on retrieval
} else if (strcmp(arg[1],"equal") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != EQUAL)
error->all(FLERR,"Cannot redefine variable as a different style");
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = EQUAL;
num[nvar] = 2;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = utils::strdup(arg[2]);
data[nvar][1] = new char[VALUELENGTH];
strcpy(data[nvar][1],"(undefined)");
}
// ATOM
// replace pre-existing var if also style ATOM (allows it to be reset)
// num = 1, which = 1st value
// data = 1 value, string to eval
} else if (strcmp(arg[1],"atom") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != ATOM)
error->all(FLERR,"Cannot redefine variable as a different style");
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = ATOM;
num[nvar] = 1;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = utils::strdup(arg[2]);
}
// VECTOR
// replace pre-existing var if also style VECTOR (allows it to be reset)
// num = 2, which = 1st value
// data = 2 values, 1st is string to eval, 2nd is formatted output string [1,2,3]
// if formula string is [value,value,...] then
// immediately store it as N-length vector and set dynamic flag to 0
} else if (strcmp(arg[1],"vector") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != VECTOR)
error->all(FLERR,"Cannot redefine variable as a different style");
delete[] data[ivar][0];
delete[] data[ivar][1];
data[ivar][0] = utils::strdup(arg[2]);
if (data[ivar][0][0] != '[')
vecs[ivar].dynamic = 1;
else {
vecs[ivar].dynamic = 0;
parse_vector(ivar,data[ivar][0]);
std::vector <double> vec(vecs[ivar].values,vecs[ivar].values + vecs[ivar].n);
data[ivar][1] = utils::strdup(fmt::format("[{}]", fmt::join(vec,",")));
}
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = VECTOR;
num[nvar] = 2;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = utils::strdup(arg[2]);
if (data[nvar][0][0] != '[') {
vecs[nvar].dynamic = 1;
data[nvar][1] = nullptr;
} else {
vecs[nvar].dynamic = 0;
parse_vector(nvar,data[nvar][0]);
std::vector <double> vec(vecs[nvar].values,vecs[nvar].values + vecs[nvar].n);
data[nvar][1] = utils::strdup(fmt::format("[{}]", fmt::join(vec,",")));
}
}
// PYTHON
// replace pre-existing var if also style PYTHON (allows it to be reset)
// num = 2, which = 1st value
// data = 2 values, 1st is Python func to invoke, 2nd is filled by invoke
} else if (strcmp(arg[1],"python") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
if (!python->is_enabled())
error->all(FLERR,"LAMMPS is not built with Python embedded");
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != PYTHON)
error->all(FLERR,"Cannot redefine variable as a different style");
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(arg[2]);
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = PYTHON;
num[nvar] = 2;
which[nvar] = 1;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = utils::strdup(arg[2]);
data[nvar][1] = new char[VALUELENGTH];
strcpy(data[nvar][1],"(undefined)");
}
// TIMER
// stores current walltime as a timestamp in seconds
// replace pre-existing var if also style TIMER (allows reset with current time)
// num = 1, for string representation of dvalue, set by retrieve()
// dvalue = numeric initialization via platform::walltime()
} else if (strcmp(arg[1],"timer") == 0) {
if (narg != 2) error->all(FLERR,"Illegal variable command: expected 2 arguments but found {}", narg);
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != TIMER)
error->all(FLERR,"Cannot redefine variable as a different style");
dvalue[ivar] = platform::walltime();
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = TIMER;
num[nvar] = 1;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = new char[VALUELENGTH];
dvalue[nvar] = platform::walltime();
}
// INTERNAL
// replace pre-existing var if also style INTERNAL (allows it to be reset)
// num = 1, for string representation of dvalue, set by retrieve()
// dvalue = numeric initialization from 2nd arg, reset by internal_set()
} else if (strcmp(arg[1],"internal") == 0) {
if (narg != 3) error->all(FLERR,"Illegal variable command: expected 3 arguments but found {}", narg);
int ivar = find(arg[0]);
if (ivar >= 0) {
if (style[ivar] != INTERNAL)
error->all(FLERR,"Cannot redefine variable as a different style");
dvalue[nvar] = utils::numeric(FLERR,arg[2],false,lmp);
replaceflag = 1;
} else {
if (nvar == maxvar) grow();
style[nvar] = INTERNAL;
num[nvar] = 1;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
data[nvar][0] = new char[VALUELENGTH];
dvalue[nvar] = utils::numeric(FLERR,arg[2],false,lmp);
}
// unrecognized variable style
} else error->all(FLERR,"Unknown variable keyword: {}", arg[1]);
// set name of variable, if not replacing one flagged with replaceflag
// name must be all alphanumeric chars or underscores
if (replaceflag) return;
if (!utils::is_id(arg[0]))
error->all(FLERR,"Variable name '{}' must have only letters, numbers, or underscores",arg[0]);
names[nvar] = utils::strdup(arg[0]);
nvar++;
}
/* ----------------------------------------------------------------------
convenience function to allow defining a variable from a single string
------------------------------------------------------------------------- */
void Variable::set(const std::string &setcmd)
{
std::vector<std::string> args = utils::split_words(setcmd);
auto newarg = new char*[args.size()];
int i=0;
for (const auto &arg : args) {
newarg[i++] = (char *)arg.c_str();
}
set(args.size(),newarg);
delete[] newarg;
}
/* ----------------------------------------------------------------------
INDEX variable created by command-line argument
make it INDEX rather than STRING so cannot be re-defined in input script
------------------------------------------------------------------------- */
void Variable::set(char *name, int narg, char **arg)
{
auto newarg = new char*[2+narg];
newarg[0] = name;
newarg[1] = (char *) "index";
for (int i = 0; i < narg; i++) newarg[2+i] = arg[i];
set(2+narg,newarg);
delete[] newarg;
}
/* ----------------------------------------------------------------------
set existing STRING variable to str
return 0 if successful
return -1 if variable doesn't exist or isn't a STRING variable
called via library interface, so external programs can set variables
------------------------------------------------------------------------- */
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];
data[ivar][0] = utils::strdup(str);
return 0;
}
/* ----------------------------------------------------------------------
increment variable(s)
return 0 if OK if successfully incremented
return 1 if any variable is exhausted, free the variable to allow re-use
------------------------------------------------------------------------- */
int Variable::next(int narg, char **arg)
{
int ivar;
if (narg == 0) error->all(FLERR,"Illegal next command");
// check that variables exist and are all the same style
// exception: UNIVERSE and ULOOP variables can be mixed in same next command
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
if (ivar < 0)
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])])
error->all(FLERR,"All variables in next command must have same style");
}
// invalid styles: STRING, EQUAL, WORLD, GETENV, ATOM, VECTOR,
// FORMAT, PYTHON, TIMER, INTERNAL
int istyle = style[find(arg[0])];
if (istyle == STRING || istyle == EQUAL ||
istyle == WORLD || istyle == GETENV || istyle == ATOM ||
istyle == VECTOR || istyle == FORMAT || istyle == PYTHON ||
istyle == TIMER || istyle == INTERNAL)
error->all(FLERR,"Invalid variable style with next command");
// if istyle = UNIVERSE or ULOOP, ensure all such variables are incremented
if (istyle == UNIVERSE || istyle == ULOOP)
for (int i = 0; i < nvar; i++) {
if (style[i] != UNIVERSE && style[i] != ULOOP) continue;
int iarg = 0;
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");
}
// increment all variables in list
// if any variable is exhausted, set flag = 1 and remove var to allow re-use
int flag = 0;
if (istyle == INDEX || istyle == LOOP) {
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
which[ivar]++;
if (which[ivar] >= num[ivar]) {
flag = 1;
remove(ivar);
}
}
} else if (istyle == SCALARFILE) {
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
int done = reader[ivar]->read_scalar(data[ivar][0]);
if (done) {
flag = 1;
remove(ivar);
}
}
} else if (istyle == ATOMFILE) {
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
int done = reader[ivar]->read_peratom();
if (done) {
flag = 1;
remove(ivar);
}
}
} else if (istyle == UNIVERSE || istyle == ULOOP) {
RanMars *random = nullptr;
uloop_again:
// wait until lock file can be created and owned by proc 0 of this world
// rename() is not atomic in practice, but no known simple fix
// means multiple procs can read/write file at the same time (bad!)
// random delays help
// delay for random fraction of 1 second before first rename() call
// delay for random fraction of 1 second before subsequent tries
// when successful, read next available index and Bcast it within my world
int nextindex = -1;
if (me == 0) {
int seed = 12345 + universe->me + which[find(arg[0])];
if (!random) random = new RanMars(lmp,seed);
int delay = (int) (1000000*random->uniform());
platform::usleep(delay);
while (true) {
if (!rename("tmp.lammps.variable","tmp.lammps.variable.lock")) break;
delay = (int) (1000000*random->uniform());
platform::usleep(delay);
}
// if the file cannot be found, we may have a race with some
// other MPI rank that has called rename at the same time
// and we have to start over.
// if the read is short (we need at least one byte) we try reading again.
FILE *fp;
char buf[64];
for (int loopmax = 0; loopmax < 100; ++loopmax) {
fp = fopen("tmp.lammps.variable.lock","r");
if (fp == nullptr) goto uloop_again;
buf[0] = buf[1] = '\0';
fread(buf,1,64,fp);
fclose(fp);
if (strlen(buf) > 0) {
nextindex = atoi(buf);
break;
}
delay = (int) (1000000*random->uniform());
platform::usleep(delay);
}
delete random;
random = nullptr;
if (nextindex < 0)
error->one(FLERR,"Unexpected error while incrementing uloop style variable. "
"Please contact the LAMMPS developers.");
fp = fopen("tmp.lammps.variable.lock","w");
fprintf(fp,"%d\n",nextindex+1);
fclose(fp);
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",
nextindex+1,universe->iworld);
if (universe->ulogfile)
fprintf(universe->ulogfile, "Increment via next: value %d on partition %d\n",
nextindex+1,universe->iworld);
}
MPI_Bcast(&nextindex,1,MPI_INT,0,world);
// set all variables in list to nextindex
// must increment all UNIVERSE and ULOOP variables here
// error check above tested for this
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
which[ivar] = nextindex;
if (which[ivar] >= num[ivar]) {
flag = 1;
remove(ivar);
}
}
}
return flag;
}
/* ----------------------------------------------------------------------
search for name in list of variables names
return index or -1 if not found
------------------------------------------------------------------------- */
int Variable::find(const char *name)
{
if (name == nullptr) return -1;
for (int i = 0; i < nvar; i++)
if (strcmp(name,names[i]) == 0) return i;
return -1;
}
/* ----------------------------------------------------------------------
initialize one atom's storage values in all VarReaders via fix STORE
called when atom is created
------------------------------------------------------------------------- */
void Variable::set_arrays(int /*i*/)
{
for (int i = 0; i < nvar; i++)
if (reader[i] && style[i] == ATOMFILE)
reader[i]->fixstore->vstore[i] = 0.0;
}
/* ----------------------------------------------------------------------
delete all atomfile style variables.
must scan list in reverse since remove() will compact list.
called from LAMMPS::destroy()
------------------------------------------------------------------------- */
void Variable::purge_atomfile()
{
for (int i = nvar-1; i >= 0; --i)
if (style[i] == ATOMFILE) remove(i);
}
/* ----------------------------------------------------------------------
called by python command in input script
simply pass input script line args to Python class
------------------------------------------------------------------------- */
void Variable::python_command(int narg, char **arg)
{
if (!python->is_enabled())
error->all(FLERR,"LAMMPS is not built with Python embedded");
python->command(narg,arg);
}
/* ----------------------------------------------------------------------
return 1 if variable is EQUAL style, 0 if not
TIMER, INTERNAL, PYTHON qualify as EQUAL style
this is checked before call to compute_equal() to return a double
------------------------------------------------------------------------- */
int Variable::equalstyle(int ivar)
{
if (style[ivar] == EQUAL || style[ivar] == TIMER ||
style[ivar] == INTERNAL) return 1;
if (style[ivar] == PYTHON) {
int ifunc = python->variable_match(data[ivar][0],names[ivar],1);
if (ifunc < 0) return 0;
else return 1;
}
return 0;
}
/* ----------------------------------------------------------------------
return 1 if variable is ATOM or ATOMFILE style, 0 if not
this is checked before call to compute_atom() to return a vector of doubles
------------------------------------------------------------------------- */
int Variable::atomstyle(int ivar)
{
if (style[ivar] == ATOM || style[ivar] == ATOMFILE) return 1;
return 0;
}
/* ----------------------------------------------------------------------
return 1 if variable is VECTOR style, 0 if not
this is checked before call to compute_vector() to return a vector of doubles
------------------------------------------------------------------------- */
int Variable::vectorstyle(int ivar)
{
if (style[ivar] == VECTOR) return 1;
return 0;
}
/* ----------------------------------------------------------------------
check if variable with name is PYTHON and matches funcname
called by Python class before it invokes a Python function
return data storage so Python function can return a value for this variable
return nullptr if not a match
------------------------------------------------------------------------- */
char *Variable::pythonstyle(char *name, char *funcname)
{
int ivar = find(name);
if (ivar < 0) return nullptr;
if (style[ivar] != PYTHON) return nullptr;
if (strcmp(data[ivar][0],funcname) != 0) return nullptr;
return data[ivar][1];
}
/* ----------------------------------------------------------------------
return 1 if variable is INTERNAL style, 0 if not
this is checked before call to set_internal() to assure it can be set
------------------------------------------------------------------------- */
int Variable::internalstyle(int ivar)
{
if (style[ivar] == INTERNAL) return 1;
return 0;
}
/* ----------------------------------------------------------------------
return ptr to the data text associated with a variable
if INDEX or WORLD or UNIVERSE or STRING or SCALARFILE,
return ptr to stored string
if LOOP or ULOOP, write int to data[0] and return ptr to string
if EQUAL, evaluate variable and put result in str
if FORMAT, evaluate its variable and put formatted result in str
if GETENV, query environment and put result in str
if PYTHON, evaluate Python function, it will put result in str
if INTERNAL, convert dvalue and put result in str
if VECTOR, return str = [value,value,...]
if ATOM or ATOMFILE, return nullptr
return nullptr if no variable with name or if which value is bad,
caller must respond
------------------------------------------------------------------------- */
char *Variable::retrieve(const char *name)
{
int ivar = find(name);
if (ivar < 0) return nullptr;
if (which[ivar] >= num[ivar]) return nullptr;
if (eval_in_progress[ivar])
print_var_error(FLERR,"has a circular dependency",ivar);
eval_in_progress[ivar] = 1;
char *str = nullptr;
if (style[ivar] == INDEX || style[ivar] == WORLD ||
style[ivar] == UNIVERSE || style[ivar] == STRING ||
style[ivar] == SCALARFILE) {
str = data[ivar][which[ivar]];
} else if (style[ivar] == LOOP || style[ivar] == ULOOP) {
std::string result;
if (pad[ivar] == 0) result = std::to_string(which[ivar]+1);
else result = fmt::format("{:0>{}d}",which[ivar]+1, pad[ivar]);
delete[] data[ivar][0];
str = data[ivar][0] = utils::strdup(result);
} else if (style[ivar] == EQUAL) {
double answer = evaluate(data[ivar][0],nullptr,ivar);
delete[] data[ivar][1];
data[ivar][1] = utils::strdup(fmt::format("{:.15g}",answer));
str = data[ivar][1];
} else if (style[ivar] == FORMAT) {
int jvar = find(data[ivar][0]);
if (jvar < 0)
error->all(FLERR, "Variable {}: format variable {} does not exist", names[ivar],data[ivar][0]);
if (!equalstyle(jvar))
error->all(FLERR, "Variable {}: format variable {} has incompatible style",
names[ivar],data[ivar][0]);
double answer = compute_equal(jvar);
sprintf(data[ivar][2],data[ivar][1],answer);
str = data[ivar][2];
} else if (style[ivar] == GETENV) {
const char *result = getenv(data[ivar][0]);
if (result == nullptr) result = (const char *) "";
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) {
if (ifunc == -1) {
error->all(FLERR, "Could not find Python function {} linked to variable {}",
data[ivar][0], name);
} else if (ifunc == -2) {
error->all(FLERR, "Python function {} for variable {} does not have a return value",
data[ivar][0], name);
} else if (ifunc == -3) {
error->all(FLERR,"Python variable {} does not match variable name registered with "
"Python function {}", name, data[ivar][0]);
} else {
error->all(FLERR, "Unknown error verifying function {} linked to python style variable {}",
data[ivar][0],name);
}
}
python->invoke_function(ifunc,data[ivar][1]);
str = data[ivar][1];
// if Python func returns a string longer than VALUELENGTH
// then the Python class stores the result, query it via long_string()
char *strlong = python->long_string(ifunc);
if (strlong) str = strlong;
} else if (style[ivar] == TIMER || style[ivar] == INTERNAL) {
delete[] data[ivar][0];
data[ivar][0] = utils::strdup(fmt::format("{:.15g}",dvalue[ivar]));
str = data[ivar][0];
} else if (style[ivar] == VECTOR) {
// check if vector variable needs to be re-computed
// if no, just return previously formatted string in data[ivar][1]
// if yes, invoke compute_vector() and convert vector to formatted string
// must also turn off eval_in_progress b/c compute_vector() checks it
if (vecs[ivar].dynamic || vecs[ivar].currentstep != update->ntimestep) {
eval_in_progress[ivar] = 0;
double *result;
compute_vector(ivar,&result);
delete[] data[ivar][1];
std::vector <double> vectmp(vecs[ivar].values,vecs[ivar].values + vecs[ivar].n);
std::string str = fmt::format("[{}]", fmt::join(vectmp,","));
data[ivar][1] = utils::strdup(str);
}
str = data[ivar][1];
} else if (style[ivar] == ATOM || style[ivar] == ATOMFILE)
return nullptr;
eval_in_progress[ivar] = 0;
return str;
}
/* ----------------------------------------------------------------------
return result of equal-style variable evaluation
can be EQUAL or TIMER or INTERNAL style or PYTHON numeric style
for PYTHON, don't need to check python->variable_match() error return,
since caller will have already checked via equalstyle()
------------------------------------------------------------------------- */
double Variable::compute_equal(int ivar)
{
if (eval_in_progress[ivar])
print_var_error(FLERR,"has a circular dependency",ivar);
eval_in_progress[ivar] = 1;
double value = 0.0;
if (style[ivar] == EQUAL) value = evaluate(data[ivar][0],nullptr,ivar);
else if (style[ivar] == TIMER) value = dvalue[ivar];
else if (style[ivar] == INTERNAL) value = dvalue[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);
python->invoke_function(ifunc,data[ivar][1]);
value = atof(data[ivar][1]);
}
eval_in_progress[ivar] = 0;
return value;
}
/* ----------------------------------------------------------------------
return result of immediate equal-style variable evaluation
called from Input::substitute()
don't need to flag eval_in_progress since is an immediate variable
------------------------------------------------------------------------- */
double Variable::compute_equal(const std::string &str)
{
char *ptr = utils::strdup(str);
double val = evaluate(ptr,nullptr,-1);
delete[] ptr;
return val;
}
/* ----------------------------------------------------------------------
compute result of atom-style and atomfile-style variable evaluation
only computed for atoms in igroup, else result is 0.0
answers are placed every stride locations into result
if sumflag, add variable values to existing result
------------------------------------------------------------------------- */
void Variable::compute_atom(int ivar, int igroup, double *result, int stride, int sumflag)
{
Tree *tree = nullptr;
double *vstore;
if (eval_in_progress[ivar])
print_var_error(FLERR,"has a circular dependency",ivar);
eval_in_progress[ivar] = 1;
if (style[ivar] == ATOM) {
treetype = ATOM;
evaluate(data[ivar][0],&tree,ivar);
collapse_tree(tree);
} else vstore = reader[ivar]->fixstore->vstore;
if (result == nullptr) {
if (style[ivar] == ATOM) free_tree(tree);
eval_in_progress[ivar] = 0;
return;
}
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (style[ivar] == ATOM) {
if (sumflag == 0) {
int m = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) result[m] = eval_tree(tree,i);
else result[m] = 0.0;
m += stride;
}
} else {
int m = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) result[m] += eval_tree(tree,i);
m += stride;
}
}
} else {
if (sumflag == 0) {
int m = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) result[m] = vstore[i];
else result[m] = 0.0;
m += stride;
}
} else {
int m = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) result[m] += vstore[i];
m += stride;
}
}
}
if (style[ivar] == ATOM) free_tree(tree);
eval_in_progress[ivar] = 0;
}
/* ----------------------------------------------------------------------
compute result of vector-style variable evaluation
return length of vector and result pointer to vector values
if length == 0 or -1 (mismatch), generate an error
if necessary, evaluate the formula and its length,
store results in VecVar entry and return them
------------------------------------------------------------------------- */
int Variable::compute_vector(int ivar, double **result)
{
Tree *tree = nullptr;
// if vector is not dynamic, just return stored values
if (!vecs[ivar].dynamic) {
*result = vecs[ivar].values;
return vecs[ivar].n;
}
// if vector already computed on this timestep, just return stored values
if (vecs[ivar].currentstep == update->ntimestep) {
*result = vecs[ivar].values;
return vecs[ivar].n;
}
// evaluate vector variable afresh
if (eval_in_progress[ivar])
print_var_error(FLERR,"has a circular dependency",ivar);
eval_in_progress[ivar] = 1;
treetype = VECTOR;
evaluate(data[ivar][0],&tree,ivar);
collapse_tree(tree);
int nlen = size_tree_vector(tree);
if (nlen == 0)
print_var_error(FLERR,"Vector-style variable has zero length",ivar);
if (nlen < 0)
print_var_error(FLERR,"Inconsistent lengths in vector-style variable",ivar);
// (re)allocate space for results if necessary
if (nlen > vecs[ivar].nmax) {
memory->destroy(vecs[ivar].values);
vecs[ivar].nmax = nlen;
memory->create(vecs[ivar].values,vecs[ivar].nmax,"variable:values");
}
vecs[ivar].n = nlen;
vecs[ivar].currentstep = update->ntimestep;
double *vec = vecs[ivar].values;
for (int i = 0; i < nlen; i++)
vec[i] = eval_tree(tree,i);
free_tree(tree);
eval_in_progress[ivar] = 0;
*result = vec;
return nlen;
}
/* ----------------------------------------------------------------------
set value stored by INTERNAL style ivar
------------------------------------------------------------------------- */
void Variable::internal_set(int ivar, double value)
{
dvalue[ivar] = value;
}
/* ----------------------------------------------------------------------
remove Nth variable from list and compact list
delete reader explicitly if it exists
------------------------------------------------------------------------- */
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 reader[n];
for (int i = n+1; i < nvar; i++) {
names[i-1] = names[i];
style[i-1] = style[i];
num[i-1] = num[i];
which[i-1] = which[i];
pad[i-1] = pad[i];
reader[i-1] = reader[i];
data[i-1] = data[i];
dvalue[i-1] = dvalue[i];
// copy VecVar struct from vecs[i] to vecs[i-1]
memcpy(&vecs[i-1],&vecs[i],sizeof(VecVar));
}
nvar--;
data[nvar] = nullptr;
reader[nvar] = nullptr;
names[nvar] = nullptr;
}
/* ----------------------------------------------------------------------
make space in arrays for new variable
------------------------------------------------------------------------- */
void Variable::grow()
{
int old = maxvar;
maxvar += VARDELTA;
names = (char **) memory->srealloc(names,maxvar*sizeof(char *),"var:names");
memory->grow(style,maxvar,"var:style");
memory->grow(num,maxvar,"var:num");
memory->grow(which,maxvar,"var:which");
memory->grow(pad,maxvar,"var:pad");
reader = (VarReader **)
memory->srealloc(reader,maxvar*sizeof(VarReader *),"var:reader");
for (int i = old; i < maxvar; i++) reader[i] = nullptr;
data = (char ***) memory->srealloc(data,maxvar*sizeof(char **),"var:data");
memory->grow(dvalue,maxvar,"var:dvalue");
vecs = (VecVar *) memory->srealloc(vecs,maxvar*sizeof(VecVar),"var:vecvar");
for (int i = old; i < maxvar; i++) {
vecs[i].n = vecs[i].nmax = 0;
vecs[i].dynamic = 1;
vecs[i].currentstep = -1;
vecs[i].values = nullptr;
}
memory->grow(eval_in_progress,maxvar,"var:eval_in_progress");
for (int i = 0; i < maxvar; i++) eval_in_progress[i] = 0;
}
/* ----------------------------------------------------------------------
copy narg strings from **from to **to, and allocate space for them
------------------------------------------------------------------------- */
void Variable::copy(int narg, char **from, char **to)
{
for (int i = 0; i < narg; i++)
to[i] = utils::strdup(from[i]);
}
/* ----------------------------------------------------------------------
recursive evaluation of a string str
str is an equal-style or atom-style or vector-style formula
containing one or more items:
number = 0.0, -5.45, 2.8e-4, ...
constant = PI, version, yes, no, on, off
thermo keyword = ke, vol, atoms, ...
math operation = (),-x,x+y,x-y,x*y,x/y,x^y,
x==y,x!=y,x<y,x<=y,x>y,x>=y,x&&y,x||y,
sqrt(x),exp(x),ln(x),log(x),abs(x),
sin(x),cos(x),tan(x),asin(x),atan2(y,x),...
group function = count(group), mass(group), xcm(group,x), ...
special function = sum(x),min(x), ...
atom value = x[i], y[i], vx[i], ...
atom vector = x, y, vx, ...
custom atom property = i/d_name, i/d_name[i], i/d2_name[i], i/d2_name[i][j]
compute = c_ID, c_ID[i], c_ID[i][j]
fix = f_ID, f_ID[i], f_ID[i][j]
variable = v_name, v_name[i]
equal-style variables passes in tree = nullptr:
evaluate the formula, return result as a double
atom-style and vector-style variables pass in tree = non-nullptr:
parse the formula but do not evaluate it
create a parse tree and return it
------------------------------------------------------------------------- */
double Variable::evaluate(char *str, Tree **tree, int ivar)
{
int op,opprevious;
double value1,value2;
char onechar;
char *ptr;
double argstack[MAXLEVEL];
Tree *treestack[MAXLEVEL];
int opstack[MAXLEVEL];
int nargstack = 0;
int ntreestack = 0;
int nopstack = 0;
int i = 0;
int expect = ARG;
if (str == nullptr)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
while (true) {
onechar = str[i];
// whitespace: just skip
if (isspace(onechar)) i++;
// ----------------
// parentheses: recursively evaluate contents of parens
// ----------------
else if (onechar == '(') {
if (expect == OP)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
expect = OP;
char *contents = nullptr;
i = find_matching_paren(str,i,contents,ivar);
i++;
// evaluate contents and push on stack
if (tree) {
Tree *newtree = nullptr;
evaluate(contents,&newtree,ivar);
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = evaluate(contents,nullptr,ivar);
delete[] contents;
// ----------------
// number: push value onto stack
// ----------------
} else if (isdigit(onechar) || onechar == '.') {
if (expect == OP)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
expect = OP;
// istop = end of number, including scientific notation
int istart = i;
while (isdigit(str[i]) || str[i] == '.') i++;
if (str[i] == 'e' || str[i] == 'E') {
i++;
if (str[i] == '+' || str[i] == '-') i++;
while (isdigit(str[i])) i++;
}
int istop = i - 1;
int n = istop - istart + 1;
auto number = new char[n+1];
strncpy(number,&str[istart],n);
number[n] = '\0';
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = atof(number);
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = atof(number);
delete[] number;
// ----------------
// letter: c_ID, c_ID[], c_ID[][], f_ID, f_ID[], f_ID[][],
// v_name, v_name[], exp(), xcm(,), x, x[], PI, vol,
// i/d_name, i/d_name[], i/d_name[][],
// i/d2_name, i/d2_name[], i/d2_name[][]
// ----------------
} else if (isalpha(onechar)) {
if (expect == OP)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
expect = OP;
// istop = end of word
// word = all alphanumeric or underscore
int istart = i;
while (isalnum(str[i]) || str[i] == '_') i++;
int istop = i-1;
int n = istop - istart + 1;
auto word = new char[n+1];
strncpy(word,&str[istart],n);
word[n] = '\0';
// ----------------
// compute
// ----------------
if (utils::strmatch(word,"^[Cc]_")) {
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
// uppercase used to access of peratom data by equal-style var
int lowercase = 1;
if (word[0] == 'C') lowercase = 0;
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
// nbracket = # of bracket pairs
// index1,index2 = int inside each bracket pair, possibly an atom ID
int nbracket;
tagint index1,index2;
if (str[i] != '[') nbracket = 0;
else {
nbracket = 1;
ptr = &str[i];
index1 = int_between_brackets(ptr,1);
i = ptr-str+1;
if (str[i] == '[') {
nbracket = 2;
ptr = &str[i];
index2 = int_between_brackets(ptr,1);
i = ptr-str+1;
}
}
// equal-style or immediate variable is being evaluated
if ((ivar < 0) || (style[ivar] == EQUAL)) {
// c_ID = scalar from global scalar
if (lowercase && nbracket == 0) {
if (!compute->scalar_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= Compute::INVOKED_SCALAR;
}
value1 = compute->scalar;
argstack[nargstack++] = value1;
// c_ID[i] = scalar from global vector
} else if (lowercase && nbracket == 1) {
if (!compute->vector_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= Compute::INVOKED_VECTOR;
}
// wait to check index1 until after compute invocation
// to allow for computes with size_vector_variable == 1
if (index1 > compute->size_vector)
print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0);
value1 = compute->vector[index1-1];
argstack[nargstack++] = value1;
// c_ID[i][j] = scalar from global array
} else if (lowercase && nbracket == 2) {
if (!compute->array_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (index2 > compute->size_array_cols)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
}
// wait to check index1 until after compute invocation
// to allow for computes with size_array_rows_variable == 1
if (index1 > compute->size_array_rows)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
value1 = compute->array[index1-1][index2-1];
argstack[nargstack++] = value1;
// C_ID[i] = scalar element of per-atom vector, note uppercase "C"
} else if (!lowercase && nbracket == 1) {
if (!compute->peratom_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (compute->size_peratom_cols)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= Compute::INVOKED_PERATOM;
}
peratom2global(1,nullptr,compute->vector_atom,1,index1,tree,
treestack,ntreestack,argstack,nargstack);
// C_ID[i][j] = scalar element of per-atom array, note uppercase "C"
} else if (!lowercase && nbracket == 2) {
if (!compute->peratom_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->size_peratom_cols)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (index2 > compute->size_peratom_cols)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
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,
tree,treestack,ntreestack,argstack,nargstack);
else
peratom2global(1,nullptr,nullptr,compute->size_peratom_cols,index1,
tree,treestack,ntreestack,argstack,nargstack);
// no other possibilities for equal-style variable, so error
} else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
// vector-style variable is being evaluated
} else if (style[ivar] == VECTOR) {
// c_ID = vector from global vector
if (lowercase && nbracket == 0) {
if (!compute->vector_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= Compute::INVOKED_VECTOR;
}
// wait to check vector size until after compute invocation
// to allow for computes with size_vector_variable == 1
if (compute->size_vector == 0)
print_var_error(FLERR,"Variable formula compute vector is zero length",ivar);
auto newtree = new Tree();
newtree->type = VECTORARRAY;
newtree->array = compute->vector;
newtree->nvector = compute->size_vector;
newtree->nstride = 1;
treestack[ntreestack++] = newtree;
// c_ID[i] = vector from global array
} else if (lowercase && nbracket == 1) {
if (!compute->array_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (index1 > compute->size_array_cols)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
}
// wait to check row count until after compute invocation
// to allow for computes with size_array_rows_variable == 1
if (compute->size_array_rows == 0)
print_var_error(FLERR,"Variable formula compute array has zero rows",ivar);
auto newtree = new Tree();
newtree->type = VECTORARRAY;
newtree->array = &compute->array[0][index1-1];
newtree->nvector = compute->size_array_rows;
newtree->nstride = compute->size_array_cols;
treestack[ntreestack++] = newtree;
// no other possibilities for vector-style variable, so error
} else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
// atom-style variable is being evaluated
} else if (style[ivar] == ATOM) {
// c_ID = vector from per-atom vector
if (lowercase && nbracket == 0) {
if (!compute->peratom_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (compute->size_peratom_cols)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= Compute::INVOKED_PERATOM;
}
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->array = compute->vector_atom;
newtree->nstride = 1;
treestack[ntreestack++] = newtree;
// c_ID[i] = vector from per-atom array
} else if (lowercase && nbracket == 1) {
if (!compute->peratom_flag)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (!compute->size_peratom_cols)
print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
if (index1 > compute->size_peratom_cols)
print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= Compute::INVOKED_PERATOM;
}
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->array = nullptr;
if (compute->array_atom)
newtree->array = &compute->array_atom[0][index1-1];
newtree->nstride = compute->size_peratom_cols;
treestack[ntreestack++] = newtree;
// no other possibilities for atom-style variable, so error
} else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
}
// ----------------
// fix
// ----------------
} else if (utils::strmatch(word,"^[fF]_")) {
if (domain->box_exist == 0)
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
int lowercase = 1;
if (word[0] == 'F') lowercase = 0;
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
// nbracket = # of bracket pairs
// index1,index2 = int inside each bracket pair, possibly an atom ID
int nbracket;
tagint index1,index2;
if (str[i] != '[') nbracket = 0;
else {
nbracket = 1;
ptr = &str[i];
index1 = int_between_brackets(ptr,1);
i = ptr-str+1;
if (str[i] == '[') {
nbracket = 2;
ptr = &str[i];
index2 = int_between_brackets(ptr,1);
i = ptr-str+1;
}
}
// equal-style or immediate variable is being evaluated
if ((ivar < 0) || (style[ivar] == EQUAL)) {
// f_ID = scalar from global scalar
if (lowercase && nbracket == 0) {
if (!fix->scalar_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
value1 = fix->compute_scalar();
argstack[nargstack++] = value1;
// f_ID[i] = scalar from global vector
} else if (lowercase && nbracket == 1) {
if (!fix->vector_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (index1 > fix->size_vector)
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);
value1 = fix->compute_vector(index1-1);
argstack[nargstack++] = value1;
// f_ID[i][j] = scalar from global array
} else if (lowercase && nbracket == 2) {
if (!fix->array_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (index1 > fix->size_array_rows)
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);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
value1 = fix->compute_array(index1-1,index2-1);
argstack[nargstack++] = value1;
// F_ID[i] = scalar element of per-atom vector, note uppercase "F"
} else if (!lowercase && nbracket == 1) {
if (!fix->peratom_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (fix->size_peratom_cols)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
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);
// F_ID[i][j] = scalar element of per-atom array, note uppercase "F"
} else if (!lowercase && nbracket == 2) {
if (!fix->peratom_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (!fix->size_peratom_cols)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (index2 > fix->size_peratom_cols)
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);
if (fix->array_atom)
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,
tree,treestack,ntreestack,argstack,nargstack);
// no other possibilities for equal-style variable, so error
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
// vector-style variable is being evaluated
} else if (style[ivar] == VECTOR) {
// f_ID = vector from global vector
if (lowercase && nbracket == 0) {
if (!fix->vector_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (fix->size_vector == 0)
print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
int nvec = fix->size_vector;
double *vec;
memory->create(vec,nvec,"variable:values");
for (int m = 0; m < nvec; m++)
vec[m] = fix->compute_vector(m);
auto newtree = new Tree();
newtree->type = VECTORARRAY;
newtree->array = vec;
newtree->nvector = nvec;
newtree->nstride = 1;
newtree->selfalloc = 1;
treestack[ntreestack++] = newtree;
// f_ID[i] = vector from global array
} else if (lowercase && nbracket == 1) {
if (!fix->array_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (fix->size_array_rows == 0)
print_var_error(FLERR,"Variable formula fix array is zero length",ivar);
if (index1 > fix->size_array_cols)
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);
int nvec = fix->size_array_rows;
double *vec;
memory->create(vec,nvec,"variable:values");
for (int m = 0; m < nvec; m++)
vec[m] = fix->compute_array(m,index1-1);
auto newtree = new Tree();
newtree->type = VECTORARRAY;
newtree->array = vec;
newtree->nvector = nvec;
newtree->nstride = 1;
newtree->selfalloc = 1;
treestack[ntreestack++] = newtree;
// no other possibilities for vector-style variable, so error
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
// atom-style variable is being evaluated
} else if (style[ivar] == ATOM) {
// f_ID = vector from per-atom vector
if (lowercase && nbracket == 0) {
if (!fix->peratom_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (fix->size_peratom_cols)
print_var_error(FLERR,"Mismatched fix in 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);
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->array = fix->vector_atom;
newtree->nstride = 1;
treestack[ntreestack++] = newtree;
// f_ID[i] = vector from per-atom array
} else if (lowercase && nbracket == 1) {
if (!fix->peratom_flag)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (!fix->size_peratom_cols)
print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
if (index1 > fix->size_peratom_cols)
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);
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->array = nullptr;
if (fix->array_atom)
newtree->array = &fix->array_atom[0][index1-1];
newtree->nstride = fix->size_peratom_cols;
treestack[ntreestack++] = newtree;
// no other possibilities for atom-style variable, so error
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
}
// ----------------
// variable
// ----------------
} else if (strncmp(word,"v_",2) == 0) {
int jvar = find(word+2);
if (jvar < 0)
print_var_error(FLERR,fmt::format("Invalid variable reference {} in variable formula",word),
jvar);
if (eval_in_progress[jvar])
print_var_error(FLERR,"has a circular dependency",jvar);
// parse zero or one trailing brackets
// point i beyond last bracket
// nbracket = # of bracket pairs
// index = int inside bracket, possibly an atom ID
int nbracket;
tagint index;
if (str[i] != '[') nbracket = 0;
else {
nbracket = 1;
ptr = &str[i];
index = int_between_brackets(ptr,1);
i = ptr-str+1;
}
// vname with no bracket
if (nbracket == 0) {
// scalar from internal-style variable
// access value directly
if (style[jvar] == INTERNAL) {
value1 = dvalue[jvar];
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value1;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value1;
// scalar from any style variable except VECTOR, ATOM, ATOMFILE
// access value via retrieve()
} else if (style[jvar] != ATOM && style[jvar] != ATOMFILE && style[jvar] != VECTOR) {
char *var = retrieve(word+2);
if (var == nullptr)
print_var_error(FLERR,"Invalid variable evaluation in variable formula",jvar);
if (!utils::is_double(var))
print_var_error(FLERR,"Non-numeric variable value in variable formula",jvar);
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = atof(var);
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = atof(var);
// vector from vector-style variable
// evaluate the vector-style variable, put result in newtree
} else if (style[jvar] == VECTOR) {
if (tree == nullptr)
print_var_error(FLERR,"Vector-style variable in equal-style variable formula",jvar);
if (treetype == ATOM)
print_var_error(FLERR,"Vector-style variable in atom-style variable formula",jvar);
double *vec;
int nvec = compute_vector(jvar,&vec);
auto newtree = new Tree();
newtree->type = VECTORARRAY;
newtree->array = vec;
newtree->nvector = nvec;
newtree->nstride = 1;
treestack[ntreestack++] = newtree;
// vector from atom-style variable
// evaluate the atom-style variable as newtree
} else if (style[jvar] == ATOM) {
if (tree == nullptr)
print_var_error(FLERR,"Atom-style variable in equal-style variable formula",jvar);
if (treetype == VECTOR)
print_var_error(FLERR,"Atom-style variable in vector-style variable formula",jvar);
Tree *newtree = nullptr;
evaluate(data[jvar][0],&newtree,jvar);
treestack[ntreestack++] = newtree;
// vector from atomfile-style variable
// point to the values in FixStore instance
} else if (style[jvar] == ATOMFILE) {
if (tree == nullptr)
print_var_error(FLERR,"Atomfile-style variable in equal-style variable formula",jvar);
if (treetype == VECTOR)
print_var_error(FLERR,"Atomfile-style variable in vector-style variable formula",jvar);
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->array = reader[jvar]->fixstore->vstore;
newtree->nstride = 1;
treestack[ntreestack++] = newtree;
// no other possibilities for variable with no bracket
} else print_var_error(FLERR,"Mismatched variable in variable formula",jvar);
// vname[i] with one bracket
} else if (nbracket == 1) {
// scalar from vector-style variable
// compute the vector-style variable, extract single value
if (style[jvar] == VECTOR) {
double *vec;
int nvec = compute_vector(jvar,&vec);
if (index <= 0 || index > nvec)
print_var_error(FLERR,"Invalid index into vector-style variable",jvar);
int m = index; // convert from tagint to int
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = vec[m-1];
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = vec[m-1];
// scalar from atom-style variable
// compute the per-atom variable in result
// use peratom2global to extract single value from result
} else if (style[jvar] == ATOM) {
double *result;
memory->create(result,atom->nlocal,"variable:result");
compute_atom(jvar,0,result,1,0);
peratom2global(1,nullptr,result,1,index,tree,treestack,ntreestack,argstack,nargstack);
memory->destroy(result);
// scalar from atomfile-style variable
// use peratom2global to extract single value from FixStore instance
} else if (style[jvar] == ATOMFILE) {
peratom2global(1,nullptr,reader[jvar]->fixstore->vstore,1,index,
tree,treestack,ntreestack,argstack,nargstack);
// no other possibilities for variable with one bracket
} else print_var_error(FLERR,"Mismatched variable in variable formula",jvar);
}
// ----------------
// custom atom property
// ----------------
} else if (utils::strmatch(word,"^[id]2?_")) {
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
int index_custom,type_custom,cols_custom;
if (word[1] == '2') index_custom = atom->find_custom(word+3,type_custom,cols_custom);
else index_custom = atom->find_custom(word+2,type_custom,cols_custom);
if (index_custom < 0)
print_var_error(FLERR,fmt::format("Invalid custom atom property reference {} in variable formula",word),
ivar);
// parse zero or one or two trailing brackets
// point i beyond last bracket
// nbracket = # of bracket pairs
// index1,index2 = int inside each bracket pair, possibly an atom ID
int nbracket;
tagint index1,index2;
if (str[i] != '[') nbracket = 0;
else {
nbracket = 1;
ptr = &str[i];
index1 = int_between_brackets(ptr,1);
i = ptr-str+1;
if (str[i] == '[') {
nbracket = 2;
ptr = &str[i];
index2 = int_between_brackets(ptr,1);
i = ptr-str+1;
}
}
// custom atom property with no bracket
// can only mean use a per-atom vector
if (nbracket == 0) {
if (cols_custom == 0) {
auto newtree = new Tree();
treestack[ntreestack++] = newtree;
if (type_custom == 0) {
newtree->type = INTARRAY;
newtree->iarray = atom->ivector[index_custom];
} else {
newtree->type = ATOMARRAY;
newtree->array = atom->dvector[index_custom];
}
newtree->nstride = 1;
} else if (cols_custom) {
print_var_error(FLERR,fmt::format("Invalid custom atom property reference {} in variable formula",word),
ivar);
}
// custom atom property with one bracket
// can mean either extract a single value from a per-atom vector
// or use a column from a per-atom array
} else if (nbracket == 1) {
if (cols_custom == 0) {
if (type_custom == 0) {
custom2global(atom->ivector[index_custom],nullptr,1,index1,
tree,treestack,ntreestack,argstack,nargstack);
} else {
custom2global(nullptr,atom->dvector[index_custom],1,index1,
tree,treestack,ntreestack,argstack,nargstack);
}
} else if (cols_custom) {
if (index1 <= 0 || index1 > cols_custom)
print_var_error(FLERR,fmt::format("Invalid custom atom property reference {} in variable formula",word),
ivar);
auto newtree = new Tree();
treestack[ntreestack++] = newtree;
if (type_custom == 0) {
newtree->type = INTARRAY;
newtree->iarray = &atom->iarray[index_custom][0][index1-1];
} else {
newtree->type = ATOMARRAY;
newtree->array = &atom->darray[index_custom][0][index1-1];
}
newtree->nstride = cols_custom;
}
// custom atom property with two brackets
// can only mean extract a single value from per-atom array
} else if (nbracket == 2) {
if (cols_custom == 0) {
print_var_error(FLERR,fmt::format("Invalid custom atom property reference {} in variable formula",word),
ivar);
} else if (cols_custom) {
if (index2 <= 0 || index2 > cols_custom)
print_var_error(FLERR,fmt::format("Invalid custom atom property reference {} in variable formula",word),
ivar);
if (type_custom == 0) {
custom2global(&atom->iarray[index_custom][0][index2],nullptr,cols_custom,index1,
tree,treestack,ntreestack,argstack,nargstack);
} else {
custom2global(nullptr,&atom->darray[index_custom][0][index2],cols_custom,index1,
tree,treestack,ntreestack,argstack,nargstack);
}
}
}
// ----------------
// math/group/special/labelmap function or atom value/vector or constant or thermo keyword
// ----------------
} else {
// ----------------
// math or group or special function
// ----------------
if (str[i] == '(') {
char *contents = nullptr;
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 if (feature_function(word,contents,tree,treestack,ntreestack,argstack,nargstack,ivar));
else print_var_error(FLERR,fmt::format("Invalid math/group/special/feature function '{}()' "
"in variable formula", word),ivar);
delete[] contents;
// ----------------
// atom value
// ----------------
} else if (str[i] == '[') {
if (domain->box_exist == 0)
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);
// ----------------
// atom vector
// ----------------
} else if (is_atom_vector(word)) {
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
atom_vector(word,tree,treestack,ntreestack);
// ----------------
// constant
// ----------------
} else if (constants.find(word) != constants.end()) {
value1 = constants[word];
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value1;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value1;
// ----------------
// thermo keyword
// ----------------
} else {
if (domain->box_exist == 0)
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);
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value1;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value1;
}
}
delete[] word;
// ----------------
// math operator, including end-of-string
// ----------------
} else if (strchr("+-*/^<>=!&|%\0",onechar)) {
if (onechar == '+') op = ADD;
else if (onechar == '-') op = SUBTRACT;
else if (onechar == '*') op = MULTIPLY;
else if (onechar == '/') op = DIVIDE;
else if (onechar == '%') op = MODULO;
else if (onechar == '^') op = CARAT;
else if (onechar == '=') {
if (str[i+1] != '=')
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
op = EQ;
i++;
} else if (onechar == '!') {
if (str[i+1] == '=') {
op = NE;
i++;
} else op = NOT;
} else if (onechar == '<') {
if (str[i+1] != '=') op = LT;
else {
op = LE;
i++;
}
} else if (onechar == '>') {
if (str[i+1] != '=') op = GT;
else {
op = GE;
i++;
}
} else if (onechar == '&') {
if (str[i+1] != '&')
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
op = AND;
i++;
} else if (onechar == '|') {
if (str[i+1] == '|') op = OR;
else if (str[i+1] == '^') op = XOR;
else print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
i++;
} else op = DONE;
i++;
if (op == SUBTRACT && expect == ARG) {
opstack[nopstack++] = UNARY;
continue;
}
if (op == NOT && expect == ARG) {
opstack[nopstack++] = op;
continue;
}
if (expect == ARG)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
expect = ARG;
// evaluate stack as deep as possible while respecting precedence
// before pushing current op onto stack
while (nopstack && precedence[opstack[nopstack-1]] >= precedence[op]) {
opprevious = opstack[--nopstack];
if (tree) {
auto newtree = new Tree();
newtree->type = opprevious;
if ((opprevious == UNARY) || (opprevious == NOT)) {
newtree->first = treestack[--ntreestack];
} else {
newtree->second = treestack[--ntreestack];
newtree->first = treestack[--ntreestack];
}
treestack[ntreestack++] = newtree;
} else {
value2 = argstack[--nargstack];
if (opprevious != UNARY && opprevious != NOT)
value1 = argstack[--nargstack];
if (opprevious == ADD)
argstack[nargstack++] = value1 + value2;
else if (opprevious == SUBTRACT)
argstack[nargstack++] = value1 - value2;
else if (opprevious == MULTIPLY)
argstack[nargstack++] = value1 * value2;
else if (opprevious == DIVIDE) {
if (value2 == 0.0)
print_var_error(FLERR,"Divide by 0 in variable formula",ivar,0);
argstack[nargstack++] = value1 / value2;
} else if (opprevious == MODULO) {
if (value2 == 0.0)
print_var_error(FLERR,"Modulo 0 in variable formula",ivar,0);
argstack[nargstack++] = fmod(value1,value2);
} else if (opprevious == CARAT) {
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);
else argstack[nargstack++] = pow(value1,value2);
} else if (opprevious == UNARY) {
argstack[nargstack++] = -value2;
} else if (opprevious == NOT) {
if (value2 == 0.0) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == EQ) {
if (value1 == value2) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == NE) {
if (value1 != value2) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == LT) {
if (value1 < value2) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == LE) {
if (value1 <= value2) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == GT) {
if (value1 > value2) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == GE) {
if (value1 >= value2) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == AND) {
if (value1 != 0.0 && value2 != 0.0) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == OR) {
if (value1 != 0.0 || value2 != 0.0) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
} else if (opprevious == XOR) {
if ((value1 == 0.0 && value2 != 0.0) ||
(value1 != 0.0 && value2 == 0.0)) argstack[nargstack++] = 1.0;
else argstack[nargstack++] = 0.0;
}
}
}
// if end-of-string, break out of entire formula evaluation loop
if (op == DONE) break;
// push current operation onto stack
opstack[nopstack++] = op;
} else print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
}
if (nopstack) print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
// for atom-style and vector-style variable, return remaining tree
// for equal-style variable, return remaining arg
if (tree) {
if (ntreestack != 1)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
*tree = treestack[0];
return 0.0;
} else {
if (nargstack != 1)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
return argstack[0];
}
}
/* ----------------------------------------------------------------------
one-time collapse of an atom-style variable parse tree
tree was created by one-time parsing of formula string via evaluate()
only keep tree nodes that depend on
ATOMARRAY, TYPEARRAY, INTARRAY, BIGINTARRAY, VECTOR
remainder is converted to single VALUE
this enables optimal eval_tree loop over atoms
customize by adding a function:
sqrt(),exp(),ln(),log(),abs(),sin(),cos(),tan(),asin(),acos(),atan(),
atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),ternary(x,y,z),
ramp(x,y),stagger(x,y),logfreq(x,y,z),logfreq2(x,y,z),
logfreq3(x,y,z),stride(x,y,z),stride2(x,y,z,a,b,c),vdisplace(x,y),swiggle(x,y,z),
cwiggle(x,y,z),gmask(x),rmask(x),grmask(x,y)
---------------------------------------------------------------------- */
double Variable::collapse_tree(Tree *tree)
{
double arg1,arg2,arg3;
if (tree->type == VALUE) return tree->value;
if (tree->type == ATOMARRAY) return 0.0;
if (tree->type == TYPEARRAY) return 0.0;
if (tree->type == INTARRAY) return 0.0;
if (tree->type == BIGINTARRAY) return 0.0;
if (tree->type == VECTORARRAY) return 0.0;
if (tree->type == ADD) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = arg1 + arg2;
return tree->value;
}
if (tree->type == SUBTRACT) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = arg1 - arg2;
return tree->value;
}
if (tree->type == MULTIPLY) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = arg1 * arg2;
return tree->value;
}
if (tree->type == DIVIDE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg2 == 0.0) error->one(FLERR,"Divide by 0 in variable formula");
tree->value = arg1 / arg2;
return tree->value;
}
if (tree->type == MODULO) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg2 == 0.0) error->one(FLERR,"Modulo 0 in variable formula");
tree->value = fmod(arg1,arg2);
return tree->value;
}
if (tree->type == CARAT) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg2 == 0.0) error->one(FLERR,"Power by 0 in variable formula");
tree->value = pow(arg1,arg2);
return tree->value;
}
if (tree->type == UNARY) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = -arg1;
return tree->value;
}
if (tree->type == NOT) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 == 0.0) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == EQ) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 == arg2) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == NE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 != arg2) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == LT) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 < arg2) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == LE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 <= arg2) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == GT) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 > arg2) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == GE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 >= arg2) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == AND) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 != 0.0 && arg2 != 0.0) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == OR) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 != 0.0 || arg2 != 0.0) tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == XOR) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if ((arg1 == 0.0 && arg2 != 0.0) || (arg1 != 0.0 && arg2 == 0.0))
tree->value = 1.0;
else tree->value = 0.0;
return tree->value;
}
if (tree->type == SQRT) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 < 0.0)
error->one(FLERR,"Sqrt of negative value in variable formula");
tree->value = sqrt(arg1);
return tree->value;
}
if (tree->type == EXP) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = exp(arg1);
return tree->value;
}
if (tree->type == LN) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
tree->value = log(arg1);
return tree->value;
}
if (tree->type == LOG) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
tree->value = log10(arg1);
return tree->value;
}
if (tree->type == ABS) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = fabs(arg1);
return tree->value;
}
if (tree->type == SIN) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = sin(arg1);
return tree->value;
}
if (tree->type == COS) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = cos(arg1);
return tree->value;
}
if (tree->type == TAN) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = tan(arg1);
return tree->value;
}
if (tree->type == ASIN) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 < -1.0 || arg1 > 1.0)
error->one(FLERR,"Arcsin of invalid value in variable formula");
tree->value = asin(arg1);
return tree->value;
}
if (tree->type == ACOS) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1 < -1.0 || arg1 > 1.0)
error->one(FLERR,"Arccos of invalid value in variable formula");
tree->value = acos(arg1);
return tree->value;
}
if (tree->type == ATAN) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = atan(arg1);
return tree->value;
}
if (tree->type == ATAN2) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = atan2(arg1,arg2);
return tree->value;
}
// random() or normal() do not become a single collapsed value
if (tree->type == RANDOM) {
collapse_tree(tree->first);
collapse_tree(tree->second);
if (randomatom == nullptr) {
int seed = static_cast<int> (collapse_tree(tree->extra[0]));
if (seed <= 0)
error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return 0.0;
}
if (tree->type == NORMAL) {
collapse_tree(tree->first);
double sigma = collapse_tree(tree->second);
if (sigma < 0.0)
error->one(FLERR,"Invalid math function in variable formula");
if (randomatom == nullptr) {
int seed = static_cast<int> (collapse_tree(tree->extra[0]));
if (seed <= 0)
error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return 0.0;
}
if (tree->type == CEIL) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = ceil(arg1);
return tree->value;
}
if (tree->type == FLOOR) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = floor(arg1);
return tree->value;
}
if (tree->type == ROUND) {
arg1 = collapse_tree(tree->first);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
tree->value = MYROUND(arg1);
return tree->value;
}
if (tree->type == TERNARY) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
arg3 = collapse_tree(tree->extra[0]);
if (tree->first->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg1) tree->value = arg2;
else tree->value = arg3;
return tree->value;
}
if (tree->type == RAMP) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (update->whichflag == 0) {
tree->value = arg1;
} else {
double delta = update->ntimestep - update->beginstep;
if ((delta != 0.0) && (update->beginstep != update->endstep))
delta /= update->endstep - update->beginstep;
tree->value = arg1 + delta*(arg2-arg1);
}
return tree->value;
}
if (tree->type == STAGGER) {
auto ivalue1 = static_cast<bigint> (collapse_tree(tree->first));
auto ivalue2 = static_cast<bigint> (collapse_tree(tree->second));
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue1 <= ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
bigint lower = update->ntimestep/ivalue1 * ivalue1;
bigint delta = update->ntimestep - lower;
if (delta < ivalue2) tree->value = lower+ivalue2;
else tree->value = lower+ivalue1;
return tree->value;
}
if (tree->type == LOGFREQ) {
auto ivalue1 = static_cast<bigint> (collapse_tree(tree->first));
auto ivalue2 = static_cast<bigint> (collapse_tree(tree->second));
auto ivalue3 = static_cast<bigint> (collapse_tree(tree->extra[0]));
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 || ivalue2 >= ivalue3)
error->one(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) tree->value = ivalue1;
else {
bigint lower = ivalue1;
while (update->ntimestep >= ivalue3*lower) lower *= ivalue3;
bigint multiple = update->ntimestep/lower;
if (multiple < ivalue2) tree->value = (multiple+1)*lower;
else tree->value = lower*ivalue3;
}
return tree->value;
}
if (tree->type == LOGFREQ2) {
auto ivalue1 = static_cast<bigint> (collapse_tree(tree->first));
auto ivalue2 = static_cast<bigint> (collapse_tree(tree->second));
auto ivalue3 = static_cast<bigint> (collapse_tree(tree->extra[0]));
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0)
error->all(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) tree->value = ivalue1;
else {
tree->value = ivalue1;
double delta = ivalue1*(ivalue3-1.0)/ivalue2;
bigint count = 0;
while (update->ntimestep >= tree->value) {
tree->value += delta;
count++;
if (count % ivalue2 == 0) delta *= ivalue3;
}
}
tree->value = ceil(tree->value);
return tree->value;
}
if (tree->type == LOGFREQ3) {
auto ivalue1 = static_cast<bigint> (collapse_tree(tree->first));
auto ivalue2 = static_cast<bigint> (collapse_tree(tree->second));
auto ivalue3 = static_cast<bigint> (collapse_tree(tree->extra[0]));
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 <= 0 || ivalue2 <= 1 || ivalue3 <= 0 ||
ivalue3-ivalue1+1 < ivalue2 )
error->all(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) tree->value = ivalue1;
//else if (update->ntimestep <= ivalue3) {
else {
tree->value = ivalue1;
double logsp = ivalue1;
double factor = pow(((double)ivalue3)/ivalue1, 1.0/(ivalue2-1));
bigint linsp = ivalue1;
while (update->ntimestep >= (tree->value)) {
logsp *= factor;
linsp++;
if (linsp > logsp) tree->value = linsp;
else tree->value = ceil(logsp)-(((int)ceil(logsp)-1)/ivalue3);
}
}
if (update->ntimestep > ivalue3)
error->all(FLERR,"Calls to variable exceeded limit");
return tree->value;
}
if (tree->type == STRIDE) {
auto ivalue1 = static_cast<bigint> (collapse_tree(tree->first));
auto ivalue2 = static_cast<bigint> (collapse_tree(tree->second));
auto ivalue3 = static_cast<bigint> (collapse_tree(tree->extra[0]));
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE) return 0.0;
tree->type = VALUE;
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) tree->value = ivalue1;
else if (update->ntimestep < ivalue2) {
bigint offset = update->ntimestep - ivalue1;
tree->value = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (tree->value > ivalue2) tree->value = (double) MAXBIGINT_DOUBLE;
} else tree->value = (double) MAXBIGINT_DOUBLE;
return tree->value;
}
if (tree->type == STRIDE2) {
auto ivalue1 = static_cast<bigint> (collapse_tree(tree->first));
auto ivalue2 = static_cast<bigint> (collapse_tree(tree->second));
auto ivalue3 = static_cast<bigint> (collapse_tree(tree->extra[0]));
auto ivalue4 = static_cast<bigint> (collapse_tree(tree->extra[1]));
auto ivalue5 = static_cast<bigint> (collapse_tree(tree->extra[2]));
auto ivalue6 = static_cast<bigint> (collapse_tree(tree->extra[3]));
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE || tree->extra[1]->type != VALUE ||
tree->extra[2]->type != VALUE || tree->extra[3]->type != VALUE)
return 0.0;
tree->type = VALUE;
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < 0 || ivalue5 < 0 || ivalue6 <= 0 || ivalue4 > ivalue5)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < ivalue1 || ivalue5 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
bigint istep, offset;
if (update->ntimestep < ivalue1) istep = ivalue1;
else if (update->ntimestep < ivalue2) {
if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
offset = update->ntimestep - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (update->ntimestep < ivalue2 && istep > ivalue4)
tree->value = ivalue4;
} else {
offset = update->ntimestep - ivalue4;
istep = ivalue4 + (offset/ivalue6)*ivalue6 + ivalue6;
if (istep > ivalue5) {
offset = ivalue5 - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (istep > ivalue2) istep = MAXBIGINT_DOUBLE;
}
}
} else istep = MAXBIGINT_DOUBLE;
tree->value = (double)istep;
return tree->value;
}
if (tree->type == VDISPLACE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0;
tree->type = VALUE;
double delta = update->ntimestep - update->beginstep;
tree->value = arg1 + arg2*delta*update->dt;
return tree->value;
}
if (tree->type == SWIGGLE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
arg3 = collapse_tree(tree->extra[0]);
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg3 == 0.0)
error->one(FLERR,"Invalid swiggle(x,y,z) function in variable formula: z must be > 0");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
tree->value = arg1 + arg2*sin(omega*delta*update->dt);
return tree->value;
}
if (tree->type == CWIGGLE) {
arg1 = collapse_tree(tree->first);
arg2 = collapse_tree(tree->second);
arg3 = collapse_tree(tree->extra[0]);
if (tree->first->type != VALUE || tree->second->type != VALUE ||
tree->extra[0]->type != VALUE) return 0.0;
tree->type = VALUE;
if (arg3 == 0.0)
error->one(FLERR,"Invalid cwiggle(x,y,z) function in variable formula: z must be > 0");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
tree->value = arg1 + arg2*(1.0-cos(omega*delta*update->dt));
return tree->value;
}
// mask functions do not become a single collapsed value
if (tree->type == GMASK) return 0.0;
if (tree->type == RMASK) return 0.0;
if (tree->type == GRMASK) return 0.0;
return 0.0;
}
/* ----------------------------------------------------------------------
evaluate an atom-style or vector-style variable parse tree
index I = atom I or vector index I
tree was created by one-time parsing of formula string via evaluate()
customize by adding a function:
sqrt(),exp(),ln(),log(),sin(),cos(),tan(),asin(),acos(),atan(),
atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),ternary(x,y,z),
ramp(x,y),stagger(x,y),logfreq(x,y,z),logfreq2(x,y,z),
logfreq3(x,y,z),stride(x,y,z),stride2(x,y,z,a,b,c),vdisplace(x,y),
swiggle(x,y,z),cwiggle(x,y,z),gmask(x),rmask(x),grmask(x,y)
---------------------------------------------------------------------- */
double Variable::eval_tree(Tree *tree, int i)
{
double arg,arg1,arg2,arg3;
if (tree->type == VALUE) return tree->value;
if (tree->type == ATOMARRAY) return tree->array[i*tree->nstride];
if (tree->type == TYPEARRAY) return tree->array[atom->type[i]];
if (tree->type == INTARRAY) return (double) tree->iarray[i*tree->nstride];
if (tree->type == BIGINTARRAY) return (double) tree->barray[i*tree->nstride];
if (tree->type == VECTORARRAY) return tree->array[i*tree->nstride];
if (tree->type == ADD)
return eval_tree(tree->first,i) + eval_tree(tree->second,i);
if (tree->type == SUBTRACT)
return eval_tree(tree->first,i) - eval_tree(tree->second,i);
if (tree->type == MULTIPLY)
return eval_tree(tree->first,i) * eval_tree(tree->second,i);
if (tree->type == DIVIDE) {
double denom = eval_tree(tree->second,i);
if (denom == 0.0) error->one(FLERR,"Divide by 0 in variable formula");
return eval_tree(tree->first,i) / denom;
}
if (tree->type == MODULO) {
double denom = eval_tree(tree->second,i);
if (denom == 0.0) error->one(FLERR,"Modulo 0 in variable formula");
return fmod(eval_tree(tree->first,i),denom);
}
if (tree->type == CARAT) {
double exponent = eval_tree(tree->second,i);
if (exponent == 0.0) error->one(FLERR,"Power by 0 in variable formula");
return pow(eval_tree(tree->first,i),exponent);
}
if (tree->type == UNARY) return -eval_tree(tree->first,i);
if (tree->type == NOT) {
if (eval_tree(tree->first,i) == 0.0) return 1.0;
else return 0.0;
}
if (tree->type == EQ) {
if (eval_tree(tree->first,i) == eval_tree(tree->second,i)) return 1.0;
else return 0.0;
}
if (tree->type == NE) {
if (eval_tree(tree->first,i) != eval_tree(tree->second,i)) return 1.0;
else return 0.0;
}
if (tree->type == LT) {
if (eval_tree(tree->first,i) < eval_tree(tree->second,i)) return 1.0;
else return 0.0;
}
if (tree->type == LE) {
if (eval_tree(tree->first,i) <= eval_tree(tree->second,i)) return 1.0;
else return 0.0;
}
if (tree->type == GT) {
if (eval_tree(tree->first,i) > eval_tree(tree->second,i)) return 1.0;
else return 0.0;
}
if (tree->type == GE) {
if (eval_tree(tree->first,i) >= eval_tree(tree->second,i)) return 1.0;
else return 0.0;
}
if (tree->type == AND) {
if (eval_tree(tree->first,i) != 0.0 && eval_tree(tree->second,i) != 0.0)
return 1.0;
else return 0.0;
}
if (tree->type == OR) {
if (eval_tree(tree->first,i) != 0.0 || eval_tree(tree->second,i) != 0.0)
return 1.0;
else return 0.0;
}
if (tree->type == XOR) {
if ((eval_tree(tree->first,i) == 0.0 && eval_tree(tree->second,i) != 0.0)
||
(eval_tree(tree->first,i) != 0.0 && eval_tree(tree->second,i) == 0.0))
return 1.0;
else return 0.0;
}
if (tree->type == SQRT) {
arg1 = eval_tree(tree->first,i);
if (arg1 < 0.0)
error->one(FLERR,"Sqrt of negative value in variable formula");
return sqrt(arg1);
}
if (tree->type == EXP)
return exp(eval_tree(tree->first,i));
if (tree->type == LN) {
arg1 = eval_tree(tree->first,i);
if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
return log(arg1);
}
if (tree->type == LOG) {
arg1 = eval_tree(tree->first,i);
if (arg1 <= 0.0)
error->one(FLERR,"Log of zero/negative value in variable formula");
return log10(arg1);
}
if (tree->type == ABS)
return fabs(eval_tree(tree->first,i));
if (tree->type == SIN)
return sin(eval_tree(tree->first,i));
if (tree->type == COS)
return cos(eval_tree(tree->first,i));
if (tree->type == TAN)
return tan(eval_tree(tree->first,i));
if (tree->type == ASIN) {
arg1 = eval_tree(tree->first,i);
if (arg1 < -1.0 || arg1 > 1.0)
error->one(FLERR,"Arcsin of invalid value in variable formula");
return asin(arg1);
}
if (tree->type == ACOS) {
arg1 = eval_tree(tree->first,i);
if (arg1 < -1.0 || arg1 > 1.0)
error->one(FLERR,"Arccos of invalid value in variable formula");
return acos(arg1);
}
if (tree->type == ATAN)
return atan(eval_tree(tree->first,i));
if (tree->type == ATAN2)
return atan2(eval_tree(tree->first,i),eval_tree(tree->second,i));
if (tree->type == RANDOM) {
double lower = eval_tree(tree->first,i);
double upper = eval_tree(tree->second,i);
if (randomatom == nullptr) {
int seed = static_cast<int> (eval_tree(tree->extra[0],i));
if (seed <= 0)
error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return randomatom->uniform()*(upper-lower)+lower;
}
if (tree->type == NORMAL) {
double mu = eval_tree(tree->first,i);
double sigma = eval_tree(tree->second,i);
if (sigma < 0.0)
error->one(FLERR,"Invalid math function in variable formula");
if (randomatom == nullptr) {
int seed = static_cast<int> (eval_tree(tree->extra[0],i));
if (seed <= 0)
error->one(FLERR,"Invalid math function in variable formula");
randomatom = new RanMars(lmp,seed+me);
}
return mu + sigma*randomatom->gaussian();
}
if (tree->type == CEIL)
return ceil(eval_tree(tree->first,i));
if (tree->type == FLOOR)
return floor(eval_tree(tree->first,i));
if (tree->type == ROUND)
return MYROUND(eval_tree(tree->first,i));
if (tree->type == TERNARY) {
double first = eval_tree(tree->first,i);
double second = eval_tree(tree->second,i);
double third = eval_tree(tree->extra[0],i);
if (first) return second;
else return third;
}
if (tree->type == RAMP) {
arg1 = eval_tree(tree->first,i);
arg2 = eval_tree(tree->second,i);
if (update->whichflag == 0) {
arg = arg1;
} else {
double delta = update->ntimestep - update->beginstep;
if ((delta != 0.0) && (update->beginstep != update->endstep))
delta /= update->endstep - update->beginstep;
arg = arg1 + delta*(arg2-arg1);
}
return arg;
}
if (tree->type == STAGGER) {
auto ivalue1 = static_cast<bigint> (eval_tree(tree->first,i));
auto ivalue2 = static_cast<bigint> (eval_tree(tree->second,i));
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue1 <= ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
bigint lower = update->ntimestep/ivalue1 * ivalue1;
bigint delta = update->ntimestep - lower;
if (delta < ivalue2) arg = lower+ivalue2;
else arg = lower+ivalue1;
return arg;
}
if (tree->type == LOGFREQ) {
auto ivalue1 = static_cast<bigint> (eval_tree(tree->first,i));
auto ivalue2 = static_cast<bigint> (eval_tree(tree->second,i));
auto ivalue3 = static_cast<bigint> (eval_tree(tree->extra[0],i));
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 || ivalue2 >= ivalue3)
error->one(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) arg = ivalue1;
else {
bigint lower = ivalue1;
while (update->ntimestep >= ivalue3*lower) lower *= ivalue3;
bigint multiple = update->ntimestep/lower;
if (multiple < ivalue2) arg = (multiple+1)*lower;
else arg = lower*ivalue3;
}
return arg;
}
if (tree->type == LOGFREQ2) {
auto ivalue1 = static_cast<bigint> (eval_tree(tree->first,i));
auto ivalue2 = static_cast<bigint> (eval_tree(tree->second,i));
auto ivalue3 = static_cast<bigint> (eval_tree(tree->extra[0],i));
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0)
error->all(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) arg = ivalue1;
else {
arg = ivalue1;
double delta = ivalue1*(ivalue3-1.0)/ivalue2;
bigint count = 0;
while (update->ntimestep >= arg) {
arg += delta;
count++;
if (count % ivalue2 == 0) delta *= ivalue3;
}
}
arg = ceil(arg);
return arg;
}
if (tree->type == STRIDE) {
auto ivalue1 = static_cast<bigint> (eval_tree(tree->first,i));
auto ivalue2 = static_cast<bigint> (eval_tree(tree->second,i));
auto ivalue3 = static_cast<bigint> (eval_tree(tree->extra[0],i));
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
if (update->ntimestep < ivalue1) arg = ivalue1;
else if (update->ntimestep < ivalue2) {
bigint offset = update->ntimestep - ivalue1;
arg = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (arg > ivalue2) arg = (double) MAXBIGINT_DOUBLE;
} else arg = (double) MAXBIGINT_DOUBLE;
return arg;
}
if (tree->type == STRIDE2) {
auto ivalue1 = static_cast<bigint> (eval_tree(tree->first,i));
auto ivalue2 = static_cast<bigint> (eval_tree(tree->second,i));
auto ivalue3 = static_cast<bigint> (eval_tree(tree->extra[0],i));
auto ivalue4 = static_cast<bigint> (eval_tree(tree->extra[1],i));
auto ivalue5 = static_cast<bigint> (eval_tree(tree->extra[2],i));
auto ivalue6 = static_cast<bigint> (eval_tree(tree->extra[3],i));
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < 0 || ivalue5 < 0 || ivalue6 <= 0 || ivalue4 > ivalue5)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < ivalue1 || ivalue5 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
bigint istep, offset;
if (update->ntimestep < ivalue1) istep = ivalue1;
else if (update->ntimestep < ivalue2) {
if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
offset = update->ntimestep - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (update->ntimestep < ivalue2 && istep > ivalue4)
tree->value = ivalue4;
} else {
offset = update->ntimestep - ivalue4;
istep = ivalue4 + (offset/ivalue6)*ivalue6 + ivalue6;
if (istep > ivalue5) {
offset = ivalue5 - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (istep > ivalue2) istep = MAXBIGINT_DOUBLE;
}
}
} else istep = MAXBIGINT_DOUBLE;
arg = istep;
return arg;
}
if (tree->type == VDISPLACE) {
arg1 = eval_tree(tree->first,i);
arg2 = eval_tree(tree->second,i);
double delta = update->ntimestep - update->beginstep;
arg = arg1 + arg2*delta*update->dt;
return arg;
}
if (tree->type == SWIGGLE) {
arg1 = eval_tree(tree->first,i);
arg2 = eval_tree(tree->second,i);
arg3 = eval_tree(tree->extra[0],i);
if (arg3 == 0.0)
error->one(FLERR,"Invalid swiggle(x,y,z) function in variable formula: z must be > 0");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
arg = arg1 + arg2*sin(omega*delta*update->dt);
return arg;
}
if (tree->type == CWIGGLE) {
arg1 = eval_tree(tree->first,i);
arg2 = eval_tree(tree->second,i);
arg3 = eval_tree(tree->extra[0],i);
if (arg3 == 0.0)
error->one(FLERR,"Invalid cwiggle(x,y,z) function in variable formula: z must be > 0");
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/arg3;
arg = arg1 + arg2*(1.0-cos(omega*delta*update->dt));
return arg;
}
if (tree->type == GMASK) {
if (atom->mask[i] & tree->ivalue) return 1.0;
else return 0.0;
}
if (tree->type == RMASK) {
if (tree->region->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->ivalue) &&
(tree->region->match(atom->x[i][0], atom->x[i][1], atom->x[i][2]))) return 1.0;
else return 0.0;
}
return 0.0;
}
/* ----------------------------------------------------------------------
scan entire tree, find size of vectors for vector-style variable
return N for consistent vector size
return 0 for no vector size, caller flags as error
return -1 for inconsistent vector size, caller flags as error
------------------------------------------------------------------------- */
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->nextra) {
for (int i = 0; i < tree->nextra; i++)
nsize = compare_tree_vector(nsize,size_tree_vector(tree->extra[i]));
}
return nsize;
}
/* ----------------------------------------------------------------------
compare size of two vectors for vector-style variable
return positive size if same or one has no size 0
return -1 error if one is already error or not same positive size
------------------------------------------------------------------------- */
int Variable::compare_tree_vector(int i, int j)
{
if (i < 0 || j < 0) return -1;
if (i == 0 || j == 0) return MAX(i,j);
if (i != j) return -1;
return i;
}
/* ---------------------------------------------------------------------- */
void Variable::free_tree(Tree *tree)
{
if (tree->first) free_tree(tree->first);
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;
}
if (tree->selfalloc) memory->destroy(tree->array);
delete tree;
}
/* ----------------------------------------------------------------------
find matching parenthesis in str, allocate contents = str between parens
i = left paren
return loc or right paren
------------------------------------------------------------------------- */
int Variable::find_matching_paren(char *str, int i, char *&contents, int ivar)
{
// istop = matching ')' at same level, allowing for nested parens
int istart = i;
int ilevel = 0;
while (true) {
i++;
if (!str[i]) break;
if (str[i] == '(') ilevel++;
else if (str[i] == ')' && ilevel) ilevel--;
else if (str[i] == ')') break;
}
if (!str[i]) print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
int istop = i;
int n = istop - istart - 1;
delete[] contents;
contents = new char[n+1];
strncpy(contents,&str[istart+1],n);
contents[n] = '\0';
return istop;
}
/* ----------------------------------------------------------------------
find int between brackets and return it
return a tagint, since value can be an atom ID
ptr initially points to left bracket
return it pointing to right bracket
error if no right bracket or brackets are empty or index = 0
if varallow = 0: error if any between-bracket chars are non-digits
if varallow = 1: also allow for v_name, where name is variable name
------------------------------------------------------------------------- */
tagint Variable::int_between_brackets(char *&ptr, int varallow)
{
int varflag;
tagint index;
char *start = ++ptr;
if (varallow && utils::strmatch(ptr,"^v_")) {
varflag = 1;
while (*ptr && *ptr != ']') {
if (!isalnum(*ptr) && *ptr != '_')
error->all(FLERR,"Variable name between brackets must be letters, numbers, or underscores");
ptr++;
}
} else {
varflag = 0;
while (*ptr && *ptr != ']') {
if (!isdigit(*ptr))
error->all(FLERR,"Non digit character between brackets in variable");
ptr++;
}
}
if (*ptr != ']') error->all(FLERR,"Mismatched brackets in variable");
if (ptr == start) error->all(FLERR,"Empty brackets in variable");
*ptr = '\0';
// evaluate index as floating point variable or as tagint via ATOTAGINT()
if (varflag) {
char *id = start+2;
int ivar = find(id);
if (ivar < 0)
error->all(FLERR,"Invalid variable name {} in variable formula", id);
char *var = retrieve(id);
if (var == nullptr)
error->all(FLERR,"Invalid variable evaluation for variable {} in variable formula", id);
index = static_cast<tagint> (atof(var));
} else index = ATOTAGINT(start);
*ptr = ']';
if (index <= 0)
error->all(FLERR,"Index between variable brackets must be positive");
return index;
}
/* ----------------------------------------------------------------------
process a math function in formula
push result onto tree or arg stack
word = math function
contents = str between parentheses with comma-separated args
return 0 if not a match, 1 if successfully processed
customize by adding a math function:
sqrt(),exp(),ln(),log(),abs(),sin(),cos(),tan(),asin(),acos(),atan(),
atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),ternary(),
ramp(x,y),stagger(x,y),logfreq(x,y,z),logfreq2(x,y,z),
logfreq3(x,y,z),stride(x,y,z),stride2(x,y,z,a,b,c),vdisplace(x,y),
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)
{
// word not a match to any math function
if (strcmp(word,"sqrt") != 0 && strcmp(word,"exp") && strcmp(word,"ln") != 0 &&
strcmp(word,"log") != 0 && strcmp(word,"abs") != 0 && strcmp(word,"sin") != 0 &&
strcmp(word,"cos") != 0 && strcmp(word,"tan") != 0 && strcmp(word,"asin") != 0 &&
strcmp(word,"acos") != 0 && strcmp(word,"atan") != 0 && strcmp(word,"atan2") != 0 &&
strcmp(word,"random") != 0 && strcmp(word,"normal") != 0 && strcmp(word,"ceil") != 0 &&
strcmp(word,"floor") != 0 && strcmp(word,"round") != 0 && strcmp(word,"ternary") != 0 &&
strcmp(word,"ramp") != 0 && strcmp(word,"stagger") != 0 &&
strcmp(word,"logfreq") != 0 && strcmp(word,"logfreq2") != 0 &&
strcmp(word,"logfreq3") != 0 && strcmp(word,"stride") != 0 &&
strcmp(word,"stride2") != 0 && strcmp(word,"vdisplace") != 0 &&
strcmp(word,"swiggle") != 0 && strcmp(word,"cwiggle") != 0)
return 0;
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
Tree *newtree = nullptr;
double value1,value2;
double values[MAXFUNCARG-2];
if (tree) {
newtree = new Tree();
Tree *argtree = nullptr;
evaluate(args[0],&argtree,ivar);
newtree->first = argtree;
if (narg > 1) {
evaluate(args[1],&argtree,ivar);
newtree->second = argtree;
if (narg > 2) {
newtree->nextra = narg-2;
newtree->extra = new Tree*[narg-2];
for (int i = 2; i < narg; i++) {
evaluate(args[i],&argtree,ivar);
newtree->extra[i-2] = argtree;
}
}
}
treestack[ntreestack++] = newtree;
} else {
value1 = evaluate(args[0],nullptr,ivar);
if (narg > 1) {
value2 = evaluate(args[1],nullptr,ivar);
if (narg > 2) {
for (int i = 2; i < narg; i++)
values[i-2] = evaluate(args[i],nullptr,ivar);
}
}
}
// individual math functions
// customize by adding a function
if (strcmp(word,"sqrt") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = SQRT;
else {
if (value1 < 0.0)
print_var_error(FLERR,"Sqrt of negative value in variable formula",ivar,0);
argstack[nargstack++] = sqrt(value1);
}
} else if (strcmp(word,"exp") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = EXP;
else argstack[nargstack++] = exp(value1);
} else if (strcmp(word,"ln") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = LN;
else {
if (value1 <= 0.0)
print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar,0);
argstack[nargstack++] = log(value1);
}
} else if (strcmp(word,"log") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = LOG;
else {
if (value1 <= 0.0)
print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar,0);
argstack[nargstack++] = log10(value1);
}
} else if (strcmp(word,"abs") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = ABS;
else argstack[nargstack++] = fabs(value1);
} else if (strcmp(word,"sin") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = SIN;
else argstack[nargstack++] = sin(value1);
} else if (strcmp(word,"cos") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = COS;
else argstack[nargstack++] = cos(value1);
} else if (strcmp(word,"tan") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = TAN;
else argstack[nargstack++] = tan(value1);
} else if (strcmp(word,"asin") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = ASIN;
else {
if (value1 < -1.0 || value1 > 1.0)
print_var_error(FLERR,"Arcsin of invalid value in variable formula",ivar,0);
argstack[nargstack++] = asin(value1);
}
} else if (strcmp(word,"acos") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = ACOS;
else {
if (value1 < -1.0 || value1 > 1.0)
print_var_error(FLERR,"Arccos of invalid value in variable formula",ivar,0);
argstack[nargstack++] = acos(value1);
}
} else if (strcmp(word,"atan") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = ATAN;
else argstack[nargstack++] = atan(value1);
} else if (strcmp(word,"atan2") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = ATAN2;
else argstack[nargstack++] = atan2(value1,value2);
} else if (strcmp(word,"random") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = RANDOM;
else {
if (randomequal == nullptr) {
int seed = static_cast<int> (values[0]);
if (seed <= 0)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
randomequal = new RanMars(lmp,seed);
}
argstack[nargstack++] = randomequal->uniform()*(value2-value1) + value1;
}
} else if (strcmp(word,"normal") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = NORMAL;
else {
if (value2 < 0.0)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (randomequal == nullptr) {
int seed = static_cast<int> (values[0]);
if (seed <= 0)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
randomequal = new RanMars(lmp,seed);
}
argstack[nargstack++] = value1 + value2*randomequal->gaussian();
}
} else if (strcmp(word,"ceil") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = CEIL;
else argstack[nargstack++] = ceil(value1);
} else if (strcmp(word,"floor") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = FLOOR;
else argstack[nargstack++] = floor(value1);
} else if (strcmp(word,"round") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = ROUND;
else argstack[nargstack++] = MYROUND(value1);
} else if (strcmp(word,"ternary") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = TERNARY;
else {
if (value1) argstack[nargstack++] = value2;
else argstack[nargstack++] = values[0];
}
} else if (strcmp(word,"ramp") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = RAMP;
else {
if (update->whichflag == 0) {
argstack[nargstack++] = value1;
} else {
double delta = update->ntimestep - update->beginstep;
if ((delta != 0.0) && (update->beginstep != update->endstep))
delta /= update->endstep - update->beginstep;
double value = value1 + delta*(value2-value1);
argstack[nargstack++] = value;
}
}
} else if (strcmp(word,"stagger") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = STAGGER;
else {
auto ivalue1 = static_cast<bigint> (value1);
auto ivalue2 = static_cast<bigint> (value2);
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue1 <= ivalue2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
bigint lower = update->ntimestep/ivalue1 * ivalue1;
bigint delta = update->ntimestep - lower;
double value;
if (delta < ivalue2) value = lower+ivalue2;
else value = lower+ivalue1;
argstack[nargstack++] = value;
}
} else if (strcmp(word,"logfreq") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = LOGFREQ;
else {
auto ivalue1 = static_cast<bigint> (value1);
auto ivalue2 = static_cast<bigint> (value2);
auto ivalue3 = static_cast<bigint> (values[0]);
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 || ivalue2 >= ivalue3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
double value;
if (update->ntimestep < ivalue1) value = ivalue1;
else {
bigint lower = ivalue1;
while (update->ntimestep >= ivalue3*lower) lower *= ivalue3;
bigint multiple = update->ntimestep/lower;
if (multiple < ivalue2) value = (multiple+1)*lower;
else value = lower*ivalue3;
}
argstack[nargstack++] = value;
}
} else if (strcmp(word,"logfreq2") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = LOGFREQ2;
else {
auto ivalue1 = static_cast<bigint> (value1);
auto ivalue2 = static_cast<bigint> (value2);
auto ivalue3 = static_cast<bigint> (values[0]);
if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
double value;
if (update->ntimestep < ivalue1) value = ivalue1;
else {
value = ivalue1;
double delta = ivalue1*(ivalue3-1.0)/ivalue2;
bigint count = 0;
while (update->ntimestep >= value) {
value += delta;
count++;
if (count % ivalue2 == 0) delta *= ivalue3;
}
}
argstack[nargstack++] = ceil(value);
}
} else if (strcmp(word,"logfreq3") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = LOGFREQ3;
else {
auto ivalue1 = static_cast<bigint> (value1);
auto ivalue2 = static_cast<bigint> (value2);
auto ivalue3 = static_cast<bigint> (values[0]);
if (ivalue1 <= 0 || ivalue2 <= 1 || ivalue3 <= 0 ||
ivalue3-ivalue1+1 < ivalue2 )
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
double value;
if (update->ntimestep < ivalue1) value = ivalue1;
else {
value = ivalue1;
double logsp = ivalue1;
double factor = pow(((double)ivalue3)/ivalue1, 1.0/(ivalue2-1));
bigint linsp = ivalue1;
while (update->ntimestep >= value) {
logsp *= factor;
linsp++;
if (linsp > logsp) value = linsp;
else value = ceil(logsp)-(((bigint)ceil(logsp)-1)/ivalue3);
}
}
if (update->ntimestep > ivalue3)
error->all(FLERR,"Calls to variable exceeded limit");
argstack[nargstack++] = value;
}
} else if (strcmp(word,"stride") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = STRIDE;
else {
auto ivalue1 = static_cast<bigint> (value1);
auto ivalue2 = static_cast<bigint> (value2);
auto ivalue3 = static_cast<bigint> (values[0]);
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
double value;
if (update->ntimestep < ivalue1) value = ivalue1;
else if (update->ntimestep < ivalue2) {
bigint offset = update->ntimestep - ivalue1;
value = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (value > ivalue2) value = (double) MAXBIGINT_DOUBLE;
} else value = (double) MAXBIGINT_DOUBLE;
argstack[nargstack++] = value;
}
} else if (strcmp(word,"stride2") == 0) {
if (narg != 6)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (tree) newtree->type = STRIDE2;
else {
auto ivalue1 = static_cast<bigint> (value1);
auto ivalue2 = static_cast<bigint> (value2);
auto ivalue3 = static_cast<bigint> (values[0]);
auto ivalue4 = static_cast<bigint> (values[1]);
auto ivalue5 = static_cast<bigint> (values[2]);
auto ivalue6 = static_cast<bigint> (values[3]);
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < 0 || ivalue5 < 0 || ivalue6 <= 0 || ivalue4 > ivalue5)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < ivalue1 || ivalue5 > ivalue2)
error->one(FLERR,"Invalid math function in variable formula");
bigint istep, offset;
if (update->ntimestep < ivalue1) istep = ivalue1;
else if (update->ntimestep < ivalue2) {
if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
offset = update->ntimestep - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (update->ntimestep < ivalue4 && istep > ivalue4) istep = ivalue4;
} else {
offset = update->ntimestep - ivalue4;
istep = ivalue4 + (offset/ivalue6)*ivalue6 + ivalue6;
if (istep > ivalue5) {
offset = ivalue5 - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
if (istep > ivalue2) istep = MAXBIGINT_DOUBLE;
}
}
} else istep = MAXBIGINT_DOUBLE;
double value = istep;
argstack[nargstack++] = value;
}
} else if (strcmp(word,"vdisplace") == 0) {
if (narg != 2)
print_var_error(FLERR,"Invalid vdisplace function in variable formula: must have 2 arguments",ivar);
if (modify->get_fix_by_style("dt/reset").size() > 0)
print_var_error(FLERR,"Must not use vdisplace(x,y) function with fix dt/reset",ivar);
if (tree) newtree->type = VDISPLACE;
else {
double delta = update->ntimestep - update->beginstep;
double value = value1 + value2*delta*update->dt;
argstack[nargstack++] = value;
}
} else if (strcmp(word,"swiggle") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid swiggle function in variable formula: must have 3 arguments",ivar);
if (modify->get_fix_by_style("dt/reset").size() > 0)
print_var_error(FLERR,"Must not use swiggle(x,y,z) function with fix dt/reset",ivar);
if (tree) newtree->type = SWIGGLE;
else {
if (values[0] == 0.0)
print_var_error(FLERR,"Invalid swiggle(x,y,z) function in variable formula: z must be > 0",ivar);
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/values[0];
double value = value1 + value2*sin(omega*delta*update->dt);
argstack[nargstack++] = value;
}
} else if (strcmp(word,"cwiggle") == 0) {
if (narg != 3)
print_var_error(FLERR,"Invalid cwiggle function in variable formula: must have 3 arguments",ivar);
if (modify->get_fix_by_style("dt/reset").size() > 0)
print_var_error(FLERR,"Must not use cwiggle(x,y,z) function with fix dt/reset",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
print_var_error(FLERR,"Invalid cwiggle(x,y,z) function in variable formula: z must be > 0",ivar);
double delta = update->ntimestep - update->beginstep;
double omega = 2.0*MY_PI/values[0];
double value = value1 + value2*(1.0-cos(omega*delta*update->dt));
argstack[nargstack++] = value;
}
}
// delete stored args
for (int i = 0; i < narg; i++) delete[] args[i];
return 1;
}
/* ----------------------------------------------------------------------
process a group function in formula with optional region arg
push result onto tree or arg stack
word = group function
contents = str between parentheses with one,two,three args
return 0 if not a match, 1 if successfully processed
customize by adding a group function with optional region arg:
count(group),mass(group),charge(group),
xcm(group,dim),vcm(group,dim),fcm(group,dim),
bound(group,xmin),gyration(group),ke(group),angmom(group,dim),
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)
{
// word not a match to any group function
if (strcmp(word,"count") != 0 && strcmp(word,"mass") &&
strcmp(word,"charge") != 0 && strcmp(word,"xcm") != 0 &&
strcmp(word,"vcm") != 0 && strcmp(word,"fcm") != 0 &&
strcmp(word,"bound") != 0 && strcmp(word,"gyration") != 0 &&
strcmp(word,"ke") != 0 && strcmp(word,"angmom") != 0 &&
strcmp(word,"torque") != 0 && strcmp(word,"inertia") != 0 &&
strcmp(word,"omega") != 0)
return 0;
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
// group to operate on
int igroup = group->find(args[0]);
if (igroup == -1) {
const auto errmesg = fmt::format("Group {} in variable formula does not exist", args[0]);
print_var_error(FLERR, errmesg, ivar);
}
// match word to group function
double value = 0.0;
const auto group_errmesg = fmt::format("Invalid {}() function in variable formula", word);
if (strcmp(word,"count") == 0) {
if (narg == 1) value = group->count(igroup);
else if (narg == 2)
value = group->count(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"mass") == 0) {
if (narg == 1) value = group->mass(igroup);
else if (narg == 2) value = group->mass(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"charge") == 0) {
if (narg == 1) value = group->charge(igroup);
else if (narg == 2)
value = group->charge(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"xcm") == 0) {
atom->check_mass(FLERR);
double xcm[3];
if (narg == 2) {
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
} else if (narg == 3) {
auto region = region_function(args[2],ivar);
double masstotal = group->mass(igroup,region);
group->xcm(igroup,masstotal,xcm,region);
} else print_var_error(FLERR,group_errmesg,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];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"vcm") == 0) {
atom->check_mass(FLERR);
double vcm[3];
if (narg == 2) {
double masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vcm);
} else if (narg == 3) {
auto region = region_function(args[2],ivar);
double masstotal = group->mass(igroup,region);
group->vcm(igroup,masstotal,vcm,region);
} else print_var_error(FLERR,group_errmesg,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];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"fcm") == 0) {
double fcm[3];
if (narg == 2) group->fcm(igroup,fcm);
else if (narg == 3) group->fcm(igroup,fcm,region_function(args[2],ivar));
else print_var_error(FLERR,group_errmesg,ivar);
if (strcmp(args[1],"x") == 0) value = fcm[0];
else if (strcmp(args[1],"y") == 0) value = fcm[1];
else if (strcmp(args[1],"z") == 0) value = fcm[2];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"bound") == 0) {
double minmax[6];
if (narg == 2) group->bounds(igroup,minmax);
else if (narg == 3)
group->bounds(igroup,minmax,region_function(args[2],ivar));
else print_var_error(FLERR,group_errmesg,ivar);
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
else if (strcmp(args[1],"xmax") == 0) value = minmax[1];
else if (strcmp(args[1],"ymin") == 0) value = minmax[2];
else if (strcmp(args[1],"ymax") == 0) value = minmax[3];
else if (strcmp(args[1],"zmin") == 0) value = minmax[4];
else if (strcmp(args[1],"zmax") == 0) value = minmax[5];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"gyration") == 0) {
atom->check_mass(FLERR);
double xcm[3];
if (narg == 1) {
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
value = group->gyration(igroup,masstotal,xcm);
} else if (narg == 2) {
auto region = region_function(args[1],ivar);
double masstotal = group->mass(igroup,region);
group->xcm(igroup,masstotal,xcm,region);
value = group->gyration(igroup,masstotal,xcm,region);
} else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"ke") == 0) {
if (narg == 1) value = group->ke(igroup);
else if (narg == 2) value = group->ke(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"angmom") == 0) {
atom->check_mass(FLERR);
double xcm[3],lmom[3];
if (narg == 2) {
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
group->angmom(igroup,xcm,lmom);
} else if (narg == 3) {
auto region = region_function(args[2],ivar);
double masstotal = group->mass(igroup,region);
group->xcm(igroup,masstotal,xcm,region);
group->angmom(igroup,xcm,lmom,region);
} else print_var_error(FLERR,group_errmesg,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];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"torque") == 0) {
atom->check_mass(FLERR);
double xcm[3],tq[3];
if (narg == 2) {
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
group->torque(igroup,xcm,tq);
} else if (narg == 3) {
auto region = region_function(args[2],ivar);
double masstotal = group->mass(igroup,region);
group->xcm(igroup,masstotal,xcm,region);
group->torque(igroup,xcm,tq,region);
} else print_var_error(FLERR,group_errmesg,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];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"inertia") == 0) {
atom->check_mass(FLERR);
double xcm[3],inertia[3][3];
if (narg == 2) {
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
group->inertia(igroup,xcm,inertia);
} else if (narg == 3) {
auto region = region_function(args[2],ivar);
double masstotal = group->mass(igroup,region);
group->xcm(igroup,masstotal,xcm,region);
group->inertia(igroup,xcm,inertia,region);
} else print_var_error(FLERR,group_errmesg,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];
else if (strcmp(args[1],"xy") == 0) value = inertia[0][1];
else if (strcmp(args[1],"yz") == 0) value = inertia[1][2];
else if (strcmp(args[1],"xz") == 0) value = inertia[0][2];
else print_var_error(FLERR,group_errmesg,ivar);
} else if (strcmp(word,"omega") == 0) {
atom->check_mass(FLERR);
double xcm[3],angmom[3],inertia[3][3],omega[3];
if (narg == 2) {
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
group->angmom(igroup,xcm,angmom);
group->inertia(igroup,xcm,inertia);
group->omega(angmom,inertia,omega);
} else if (narg == 3) {
auto region = region_function(args[2],ivar);
double masstotal = group->mass(igroup,region);
group->xcm(igroup,masstotal,xcm,region);
group->angmom(igroup,xcm,angmom,region);
group->inertia(igroup,xcm,inertia,region);
group->omega(angmom,inertia,omega);
} else print_var_error(FLERR,group_errmesg,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];
else print_var_error(FLERR,group_errmesg,ivar);
}
// delete stored args
for (int i = 0; i < narg; i++) delete[] args[i];
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
return 1;
}
/* ---------------------------------------------------------------------- */
Region *Variable::region_function(char *id, int ivar)
{
auto region = domain->get_region_by_id(id);
if (!region)
print_var_error(FLERR, fmt::format("Region {} in variable formula does not exist", id), ivar);
// init region in case sub-regions have been deleted
region->init();
return region;
}
/* ----------------------------------------------------------------------
process a special function in formula
push result onto tree or arg stack
word = special function
contents = str between parentheses with one or more args
return 0 if not a match, 1 if successfully processed
customize by adding a special function:
sum(x),min(x),max(x),ave(x),trap(x),slope(x),
gmask(x),rmask(x),grmask(x,y),next(x),is_file(x),is_ox(x),
extract_setting(x),label2type(x,y),is_typelabel(x,y)
------------------------------------------------------------------------- */
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;
// word is not a match to any special function
if (strcmp(word,"sum") != 0 && strcmp(word,"min") && strcmp(word,"max") != 0 &&
strcmp(word,"ave") != 0 && strcmp(word,"trap") != 0 && strcmp(word,"slope") != 0 &&
strcmp(word,"gmask") != 0 && strcmp(word,"rmask") != 0 && strcmp(word,"grmask") != 0 &&
strcmp(word,"next") != 0 && strcmp(word,"is_file") != 0 && strcmp(word,"is_os") != 0 &&
strcmp(word,"extract_setting") != 0 && strcmp(word,"label2type") != 0 &&
strcmp(word,"is_typelabel") != 0)
return 0;
// process label2type() separately b/c its label arg can have commas in it
if (strcmp(word,"label2type") == 0 || strcmp(word,"is_typelabel") == 0) {
if (!atom->labelmapflag)
print_var_error(FLERR,fmt::format("Cannot use {}() function without a labelmap",word),ivar);
std::string contents_copy(contents);
auto pos = contents_copy.find_first_of(',');
if (pos == std::string::npos) {
if (strcmp(word,"label2type") == 0) {
print_var_error(FLERR, fmt::format("Invalid label2type({}) function in variable formula",
contents_copy), ivar);
} else {
print_var_error(FLERR, fmt::format("Invalid is_typelabel({}) function in variable formula",
contents_copy), ivar);
}
}
std::string typestr = contents_copy.substr(pos+1);
std::string kind = contents_copy.substr(0, pos);
int value = -1;
if (kind == "atom") {
value = atom->lmap->find(typestr,Atom::ATOM);
} else if (kind == "bond") {
value = atom->lmap->find(typestr,Atom::BOND);
} else if (kind == "angle") {
value = atom->lmap->find(typestr,Atom::ANGLE);
} else if (kind == "dihedral") {
value = atom->lmap->find(typestr,Atom::DIHEDRAL);
} else if (kind == "improper") {
value = atom->lmap->find(typestr,Atom::IMPROPER);
} else {
print_var_error(FLERR, fmt::format("Invalid kind {} in {}() in variable", kind, word),ivar);
}
if (strcmp(word,"label2type") == 0) {
if (value == -1)
print_var_error(FLERR, fmt::format("Invalid {} type label {} in label2type() in variable",
kind, typestr), ivar);
} else value = (value == -1) ? 0.0 : 1.0;
// save value in tree or on argstack
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
newtree->first = newtree->second = nullptr;
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
return 1;
}
// process other special functions
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
// special functions that operate on global vectors
if (strcmp(word,"sum") == 0 || strcmp(word,"min") == 0 ||
strcmp(word,"max") == 0 || strcmp(word,"ave") == 0 ||
strcmp(word,"trap") == 0 || strcmp(word,"slope") == 0) {
int method = 0;
if (strcmp(word,"sum") == 0) method = SUM;
else if (strcmp(word,"min") == 0) method = XMIN;
else if (strcmp(word,"max") == 0) method = XMAX;
else if (strcmp(word,"ave") == 0) method = AVE;
else if (strcmp(word,"trap") == 0) method = TRAP;
else if (strcmp(word,"slope") == 0) method = SLOPE;
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
Compute *compute = nullptr;
Fix *fix = nullptr;
int index,nvec,nstride;
char *ptr1,*ptr2;
int ivar = -1;
// argument is compute
if (utils::strmatch(args[0],"^c_")) {
ptr1 = strchr(args[0],'[');
if (ptr1) {
ptr2 = ptr1;
index = (int) int_between_brackets(ptr2,0);
*ptr1 = '\0';
} else index = 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);
}
if (index == 0 && compute->vector_flag) {
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= Compute::INVOKED_VECTOR;
}
nvec = compute->size_vector;
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);
if (!compute->is_initialized())
print_var_error(FLERR,"Variable formula compute cannot be invoked before "
"initialization by a run",ivar);
if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= Compute::INVOKED_ARRAY;
}
nvec = compute->size_array_rows;
nstride = compute->size_array_cols;
} else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
// argument is fix
} else if (utils::strmatch(args[0],"^f_")) {
ptr1 = strchr(args[0],'[');
if (ptr1) {
ptr2 = ptr1;
index = (int) int_between_brackets(ptr2,0);
*ptr1 = '\0';
} else index = 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);
}
if (index == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq) {
std::string mesg = "Fix with ID '";
mesg += (args[0]+2);
mesg += "' in variable formula not computed at compatible time";
print_var_error(FLERR,mesg,ivar);
}
nvec = fix->size_vector;
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);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
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);
// argument is vector-style variable
} else if (utils::strmatch(args[0],"^v_")) {
ptr1 = strchr(args[0],'[');
if (ptr1) {
ptr2 = ptr1;
index = (int) int_between_brackets(ptr2,0);
*ptr1 = '\0';
} else index = 0;
if (index)
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);
if (style[ivar] != VECTOR)
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);
double *vec;
nvec = compute_vector(ivar,&vec);
nstride = 1;
if ((method == AVE) && (nvec == 0))
print_var_error(FLERR,"Cannot compute average of empty vector",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;
else if (method == XMIN) value = BIG;
else if (method == XMAX) value = -BIG;
if (compute) {
double *vec;
if (index) {
if (compute->array) vec = &compute->array[0][index-1];
else vec = nullptr;
} else vec = compute->vector;
int j = 0;
for (int i = 0; i < nvec; i++) {
if (method == SUM) value += vec[j];
else if (method == XMIN) value = MIN(value,vec[j]);
else if (method == XMAX) value = MAX(value,vec[j]);
else if (method == AVE) value += vec[j];
else if (method == TRAP) value += vec[j];
else if (method == SLOPE) {
sx += (double)i;
sy += vec[j];
sxx += (double)i * (double)i;
sxy += (double)i * vec[j];
}
j += nstride;
}
if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1];
}
if (fix) {
double one;
for (int i = 0; i < nvec; i++) {
if (index) one = fix->compute_array(i,index-1);
else one = fix->compute_vector(i);
if (method == SUM) value += one;
else if (method == XMIN) value = MIN(value,one);
else if (method == XMAX) value = MAX(value,one);
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
sx += (double)i;
sy += one;
sxx += (double)i * (double)i;
sxy += (double)i * one;
}
}
if (method == TRAP) {
if (index) value -= 0.5*fix->compute_array(0,index-1) +
0.5*fix->compute_array(nvec-1,index-1);
else value -= 0.5*fix->compute_vector(0) +
0.5*fix->compute_vector(nvec-1);
}
}
if (ivar >= 0) {
double one;
double *vec = vecs[ivar].values;
for (int i = 0; i < nvec; i++) {
one = vec[i];
if (method == SUM) value += one;
else if (method == XMIN) value = MIN(value,one);
else if (method == XMAX) value = MAX(value,one);
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
sx += (double) i;
sy += one;
sxx += (double)i * (double)i;
sxy += (double)i * one;
}
}
if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1];
}
if (method == AVE) value /= nvec;
if (method == SLOPE) {
double numerator = nvec*sxy - sx*sy;
double denominator = nvec*sxx - sx*sx;
if (denominator != 0.0) value = numerator/denominator;
else value = BIG;
}
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
// mask special functions
} else if (strcmp(word,"gmask") == 0) {
if (tree == nullptr)
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);
int igroup = group->find(args[0]);
if (igroup == -1)
print_var_error(FLERR,"Group ID in variable formula does not exist",ivar);
auto newtree = new Tree();
newtree->type = GMASK;
newtree->ivalue = group->bitmask[igroup];
treestack[ntreestack++] = newtree;
} else if (strcmp(word,"rmask") == 0) {
if (tree == nullptr)
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);
auto region = region_function(args[0],ivar);
region->prematch();
auto newtree = new Tree();
newtree->type = RMASK;
newtree->region = region;
treestack[ntreestack++] = newtree;
} else if (strcmp(word,"grmask") == 0) {
if (tree == nullptr)
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);
int igroup = group->find(args[0]);
if (igroup == -1)
print_var_error(FLERR,"Group ID in variable formula does not exist",ivar);
auto region = region_function(args[1],ivar);
region->prematch();
auto newtree = new Tree();
newtree->type = GRMASK;
newtree->ivalue = group->bitmask[igroup];
newtree->region = region;
treestack[ntreestack++] = newtree;
// special function for file-style or atomfile-style variables
} else if (strcmp(word,"next") == 0) {
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
int ivar = find(args[0]);
if (ivar < 0) {
std::string mesg = "Variable ID '";
mesg += args[0];
mesg += "' in variable formula does not exist";
print_var_error(FLERR,mesg,ivar);
}
// SCALARFILE has single current value, read next one
// save value in tree or on argstack
if (style[ivar] == SCALARFILE) {
double value = atof(data[ivar][0]);
int done = reader[ivar]->read_scalar(data[ivar][0]);
if (done) remove(ivar);
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
// ATOMFILE has per-atom values, save values in tree
// copy current per-atom values into result so can read next ones
// set selfalloc = 1 so result will be deleted by free_tree() after eval
} else if (style[ivar] == ATOMFILE) {
if (tree == nullptr)
print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar);
double *result;
memory->create(result,atom->nlocal,"variable:result");
memcpy(result,reader[ivar]->fixstore->vstore,atom->nlocal*sizeof(double));
int done = reader[ivar]->read_peratom();
if (done) remove(ivar);
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->array = result;
newtree->nstride = 1;
newtree->selfalloc = 1;
treestack[ntreestack++] = newtree;
} else print_var_error(FLERR,"Invalid variable style in special function next",ivar);
} else if (strcmp(word,"is_file") == 0) {
if (narg != 1)
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;
if (fp) fclose(fp);
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
} else if (strcmp(word,"is_os") == 0) {
if (narg != 1) print_var_error(FLERR,"Invalid is_os() function in variable formula",ivar);
value = utils::strmatch(platform::os_info(), args[0]) ? 1.0 : 0.0;
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
} else if (strcmp(word,"extract_setting") == 0) {
if (narg != 1) print_var_error(FLERR,"Invalid extract_setting() function in variable formula",ivar);
value = lammps_extract_setting(lmp, args[0]);
if (value < 0) {
auto mesg = fmt::format("Unknown setting {} for extract_setting() function in variable formula",args[0]);
print_var_error(FLERR,mesg,ivar);
}
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
}
// delete stored args
for (int i = 0; i < narg; i++) delete[] args[i];
return 1;
}
/* ----------------------------------------------------------------------
process a feature function in formula
push result onto tree or arg stack
word = special function
contents = str between parentheses with one or more args
return 0 if not a match, 1 if successfully processed
customize by adding a feature function:
is_available(x,y),is_active(x,y),is_defined(x,y),
------------------------------------------------------------------------- */
int Variable::feature_function(char *word, char *contents, Tree **tree, Tree **treestack,
int &ntreestack, double *argstack, int &nargstack, int ivar)
{
double value;
// word is not a match to any feature function
if (strcmp(word,"is_available") && strcmp(word,"is_active") && strcmp(word,"is_defined") != 0)
return 0;
// process feature functions
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
if (strcmp(word,"is_available") == 0) {
if (narg != 2)
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;
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
} else if (strcmp(word,"is_active") == 0) {
if (narg != 2)
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;
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
} else if (strcmp(word,"is_defined") == 0) {
if (narg != 2)
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;
// save value in tree or on argstack
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
}
// delete stored args
for (int i = 0; i < narg; i++) delete[] args[i];
return 1;
}
/* ----------------------------------------------------------------------
extract a global value from a per-atom quantity in a formula
flag = 0 -> word is an atom vector
flag = 1 -> vector is a per-atom compute or fix quantity with nstride
id = global ID of atom, converted here to local index via atom map
push result onto tree or arg stack
customize by adding an atom vector:
id,mass,type,mol,radius,q,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)
{
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR, "Indexed per-atom vector in variable formula without atom map");
// error check for ID larger than any atom
// int_between_brackets() already checked for ID <= 0
if (id > atom->map_tag_max)
error->all(FLERR,"Variable atom ID is too large");
// if ID does not exist, index will be -1 for all procs,
// and mine will be set to 0.0
int index = atom->map(id);
double mine;
if (index >= 0 && index < atom->nlocal) {
if (flag == 0) {
if (strcmp(word,"id") == 0) {
mine = atom->tag[index];
} else if (strcmp(word,"mass") == 0) {
if (atom->rmass) mine = atom->rmass[index];
else mine = atom->mass[atom->type[index]];
} else if (strcmp(word,"type") == 0) {
mine = atom->type[index];
} else if (strcmp(word,"mol") == 0) {
if (!atom->molecule_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
mine = atom->molecule[index];
} else if (strcmp(word,"radius") == 0) {
if (!atom->radius_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
mine = atom->radius[index];
} else if (strcmp(word,"q") == 0) {
if (!atom->q_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
mine = atom->q[index];
}
else if (strcmp(word,"x") == 0) mine = atom->x[index][0];
else if (strcmp(word,"y") == 0) mine = atom->x[index][1];
else if (strcmp(word,"z") == 0) mine = atom->x[index][2];
else if (strcmp(word,"vx") == 0) mine = atom->v[index][0];
else if (strcmp(word,"vy") == 0) mine = atom->v[index][1];
else if (strcmp(word,"vz") == 0) mine = atom->v[index][2];
else if (strcmp(word,"fx") == 0) mine = atom->f[index][0];
else if (strcmp(word,"fy") == 0) mine = atom->f[index][1];
else if (strcmp(word,"fz") == 0) mine = atom->f[index][2];
else error->one(FLERR,"Invalid atom vector {} in variable formula", word);
} else mine = vector[index*nstride];
} else mine = 0.0;
double value;
MPI_Allreduce(&mine,&value,1,MPI_DOUBLE,MPI_SUM,world);
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
}
/* ----------------------------------------------------------------------
extract a global value from a custom atom property in a formula
ivector = ptr to integer per-atom property with nstride
dvector = ptr to floating-point per-atom property with nstride
exactly one if ivector/dvector is non-NULL
id = global ID of atom, converted here to local index via atom map
push result onto tree or arg stack
------------------------------------------------------------------------- */
void Variable::custom2global(int *ivector, double *dvector, int nstride, tagint id, Tree **tree,
Tree **treestack, int &ntreestack, double *argstack, int &nargstack)
{
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR, "Referenced custom atom property in variable formula without atom map");
// error check for ID larger than any atom
// int_between_brackets() already checked for ID <= 0
if (id > atom->map_tag_max)
error->all(FLERR,"Variable atom ID is too large");
// if ID does not exist, index will be -1 for all procs,
// and mine will be set to 0.0
int index = atom->map(id);
double mine;
if (index >= 0 && index < atom->nlocal) {
if (ivector) mine = ivector[index*nstride];
else mine = dvector[index*nstride];
} else mine = 0.0;
double value;
MPI_Allreduce(&mine,&value,1,MPI_DOUBLE,MPI_SUM,world);
if (tree) {
auto newtree = new Tree();
newtree->type = VALUE;
newtree->value = value;
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = value;
}
/* ----------------------------------------------------------------------
check if word matches an atom vector
return 1 if yes, else 0
customize by adding an atom vector:
id,mass,type,mol,radius,q,x,y,z,vx,vy,vz,fx,fy,fz
------------------------------------------------------------------------- */
int Variable::is_atom_vector(char *word)
{
if (strcmp(word,"id") == 0) return 1;
if (strcmp(word,"mass") == 0) return 1;
if (strcmp(word,"type") == 0) return 1;
if (strcmp(word,"mol") == 0) return 1;
if (strcmp(word,"radius") == 0) return 1;
if (strcmp(word,"q") == 0) return 1;
if (strcmp(word,"x") == 0) return 1;
if (strcmp(word,"y") == 0) return 1;
if (strcmp(word,"z") == 0) return 1;
if (strcmp(word,"vx") == 0) return 1;
if (strcmp(word,"vy") == 0) return 1;
if (strcmp(word,"vz") == 0) return 1;
if (strcmp(word,"fx") == 0) return 1;
if (strcmp(word,"fy") == 0) return 1;
if (strcmp(word,"fz") == 0) return 1;
return 0;
}
/* ----------------------------------------------------------------------
process an atom vector in formula
push result onto tree
word = atom vector
customize by adding an atom vector:
id,mass,type,mol,radius,q,x,y,z,vx,vy,vz,fx,fy,fz
------------------------------------------------------------------------- */
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");
auto newtree = new Tree();
newtree->type = ATOMARRAY;
newtree->nstride = 3;
treestack[ntreestack++] = newtree;
if (strcmp(word,"id") == 0) {
if (sizeof(tagint) == sizeof(smallint)) {
newtree->type = INTARRAY;
newtree->iarray = (int *) atom->tag;
} else {
newtree->type = BIGINTARRAY;
newtree->barray = (bigint *) atom->tag;
}
newtree->nstride = 1;
} else if (strcmp(word,"mass") == 0) {
if (atom->rmass) {
newtree->nstride = 1;
newtree->array = atom->rmass;
} else {
newtree->type = TYPEARRAY;
newtree->array = atom->mass;
}
} else if (strcmp(word,"type") == 0) {
newtree->type = INTARRAY;
newtree->nstride = 1;
newtree->iarray = atom->type;
} else if (strcmp(word,"mol") == 0) {
if (!atom->molecule_flag)
error->one(FLERR,"Variable uses atom property 'mol' that isn't allocated");
if (sizeof(tagint) == sizeof(smallint)) {
newtree->type = INTARRAY;
newtree->iarray = (int *) atom->molecule;
} else {
newtree->type = BIGINTARRAY;
newtree->barray = (bigint *) atom->molecule;
}
newtree->nstride = 1;
} else if (strcmp(word,"radius") == 0) {
if (!atom->radius_flag)
error->one(FLERR,"Variable uses atom property 'radius' that isn't allocated");
newtree->array = atom->radius;
newtree->nstride = 1;
} else if (strcmp(word,"q") == 0) {
if (!atom->q_flag)
error->one(FLERR,"Variable uses atom property 'q' that isn't allocated");
newtree->array = atom->q;
newtree->nstride = 1;
}
else if (strcmp(word,"x") == 0) newtree->array = &atom->x[0][0];
else if (strcmp(word,"y") == 0) newtree->array = &atom->x[0][1];
else if (strcmp(word,"z") == 0) newtree->array = &atom->x[0][2];
else if (strcmp(word,"vx") == 0) newtree->array = &atom->v[0][0];
else if (strcmp(word,"vy") == 0) newtree->array = &atom->v[0][1];
else if (strcmp(word,"vz") == 0) newtree->array = &atom->v[0][2];
else if (strcmp(word,"fx") == 0) newtree->array = &atom->f[0][0];
else if (strcmp(word,"fy") == 0) newtree->array = &atom->f[0][1];
else if (strcmp(word,"fz") == 0) newtree->array = &atom->f[0][2];
}
/* ----------------------------------------------------------------------
parse vector string with format [value,value,...] for vector-style variable
store numeric values in vecs[ivar]
------------------------------------------------------------------------- */
void Variable::parse_vector(int ivar, char *str)
{
// check for square brackets, remove them, and split into vector
int nstr = strlen(str)-1;
if ((str[0] != '[') || (str[nstr] != ']'))
error->all(FLERR,"Vector variable formula lacks opening or closing brace: {}", str);
std::vector<std::string> args = Tokenizer(std::string(str+1, str+nstr), ",").as_vector();
int nvec = args.size();
vecs[ivar].n = nvec;
vecs[ivar].nmax = nvec;
vecs[ivar].currentstep = -1;
memory->destroy(vecs[ivar].values);
memory->create(vecs[ivar].values,vecs[ivar].nmax,"variable:values");
for (int i = 0; i < nvec; i++)
vecs[ivar].values[i] = utils::numeric(FLERR, utils::trim(args[i]), false, lmp);
}
/* ----------------------------------------------------------------------
parse string for comma-separated args
store copy of each arg in args array
max allowed # of args = MAXFUNCARG
------------------------------------------------------------------------- */
int Variable::parse_args(char *str, char **args)
{
char *ptrnext;
int narg = 0;
char *ptr = str;
while (ptr && narg < MAXFUNCARG) {
ptrnext = find_next_comma(ptr);
if (ptrnext) *ptrnext = '\0';
args[narg] = utils::strdup(utils::trim(ptr));
narg++;
ptr = ptrnext;
if (ptr) ptr++;
}
if (ptr) error->all(FLERR,"Too many args in variable function");
return narg;
}
/* ----------------------------------------------------------------------
find next comma in str
skip commas inside one or more nested parenthesis
only return ptr to comma at level 0, else nullptr if not found
------------------------------------------------------------------------- */
char *Variable::find_next_comma(char *str)
{
int level = 0;
for (char *p = str; *p; ++p) {
if ('(' == *p) level++;
else if (')' == *p) level--;
else if (',' == *p && !level) return p;
}
return nullptr;
}
/* ----------------------------------------------------------------------
helper routine for printing variable name with error message
------------------------------------------------------------------------- */
void Variable::print_var_error(const std::string &srcfile, const int lineno,
const std::string &errmsg, int ivar, int global)
{
if ((ivar >= 0) && (ivar < nvar)) {
std::string msg = fmt::format("Variable {}: ",names[ivar]) + errmsg;
if (global)
error->all(srcfile,lineno,msg);
else
error->one(srcfile,lineno,msg);
} else {
if (global)
error->all(srcfile,lineno,errmsg);
else
error->one(srcfile,lineno,errmsg);
}
}
/* ----------------------------------------------------------------------
debug routine for printing formula tree recursively
------------------------------------------------------------------------- */
void Variable::print_tree(Tree *tree, int level)
{
printf("TREE %d: %d %g\n",level,tree->type,tree->value);
if (tree->first) print_tree(tree->first,level+1);
if (tree->second) print_tree(tree->second,level+1);
if (tree->nextra)
for (int i = 0; i < tree->nextra; i++) print_tree(tree->extra[i],level+1);
}
/* ----------------------------------------------------------------------
recursive evaluation of string str
called from "if" command in input script
str is a boolean expression containing one or more items:
number = 0.0, -5.45, 2.8e-4, ...
math operation = (),x==y,x!=y,x<y,x<=y,x>y,x>=y,x&&y,x||y
------------------------------------------------------------------------- */
double Variable::evaluate_boolean(char *str)
{
int op,opprevious,flag1,flag2;
double value1,value2;
char onechar;
char *str1,*str2;
struct Arg {
int flag; // 0 for numeric value, 1 for string
double value; // stored numeric value
char *str; // stored string
};
Arg argstack[MAXLEVEL];
int opstack[MAXLEVEL];
int nargstack = 0;
int nopstack = 0;
int i = 0;
int expect = ARG;
while (true) {
onechar = str[i];
// whitespace: just skip
if (isspace(onechar)) i++;
// ----------------
// parentheses: recursively evaluate contents of parens
// ----------------
else if (onechar == '(') {
if (expect == OP)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
char *contents = nullptr;
i = find_matching_paren(str,i,contents,-1);
i++;
// evaluate contents and push on stack
argstack[nargstack].value = evaluate_boolean(contents);
argstack[nargstack].flag = 0;
nargstack++;
delete[] contents;
// ----------------
// number: push value onto stack
// ----------------
} else if (isdigit(onechar) || onechar == '.' || onechar == '-') {
if (expect == OP)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
// set I to end of number, including scientific notation
int istart = i++;
while (isdigit(str[i]) || str[i] == '.') i++;
if (str[i] == 'e' || str[i] == 'E') {
i++;
if (str[i] == '+' || str[i] == '-') i++;
while (isdigit(str[i])) i++;
}
onechar = str[i];
str[i] = '\0';
argstack[nargstack].value = atof(&str[istart]);
str[i] = onechar;
argstack[nargstack++].flag = 0;
// ----------------
// string: push string onto stack
// ----------------
} else if (isalpha(onechar)) {
if (expect == OP)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
// set I to end of string
int istart = i++;
while (isalnum(str[i]) || (str[i] == '_') || (str[i] == '/')) i++;
int n = i - istart + 1;
argstack[nargstack].str = new char[n];
onechar = str[i];
str[i] = '\0';
strcpy(argstack[nargstack].str,&str[istart]);
str[i] = onechar;
argstack[nargstack++].flag = 1;
// ----------------
// Boolean operator, including end-of-string
// ----------------
} else if (strchr("<>=!&|\0",onechar)) {
if (onechar == '=') {
if (str[i+1] != '=')
error->all(FLERR,"Invalid Boolean syntax in if command");
op = EQ;
i++;
} else if (onechar == '!') {
if (str[i+1] == '=') {
op = NE;
i++;
} else op = NOT;
} else if (onechar == '<') {
if (str[i+1] != '=') op = LT;
else {
op = LE;
i++;
}
} else if (onechar == '>') {
if (str[i+1] != '=') op = GT;
else {
op = GE;
i++;
}
} else if (onechar == '&') {
if (str[i+1] != '&')
error->all(FLERR,"Invalid Boolean syntax in if command");
op = AND;
i++;
} else if (onechar == '|') {
if (str[i+1] == '|') op = OR;
else if (str[i+1] == '^') op = XOR;
else error->all(FLERR,"Invalid Boolean syntax in if command");
i++;
} else op = DONE;
i++;
if (op == NOT && expect == ARG) {
opstack[nopstack++] = op;
continue;
}
if (expect == ARG)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = ARG;
// evaluate stack as deep as possible while respecting precedence
// before pushing current op onto stack
while (nopstack && precedence[opstack[nopstack-1]] >= precedence[op]) {
opprevious = opstack[--nopstack];
nargstack--;
flag2 = argstack[nargstack].flag;
value2 = argstack[nargstack].value;
str2 = argstack[nargstack].str;
if (opprevious != NOT) {
nargstack--;
flag1 = argstack[nargstack].flag;
value1 = argstack[nargstack].value;
str1 = argstack[nargstack].str;
}
if (opprevious == NOT) {
if (flag2)
error->all(FLERR,"If command boolean not cannot operate on string");
if (value2 == 0.0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == EQ) {
if (flag1 != flag2)
error->all(FLERR,"If command boolean is comparing string to number");
if (flag2 == 0) {
if (value1 == value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else {
if (strcmp(str1,str2) == 0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
delete[] str1;
delete[] str2;
}
} else if (opprevious == NE) {
if (flag1 != flag2)
error->all(FLERR,"If command boolean is comparing string to number");
if (flag2 == 0) {
if (value1 != value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else {
if (strcmp(str1,str2) != 0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
delete[] str1;
delete[] str2;
}
} else if (opprevious == LT) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 < value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == LE) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 <= value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == GT) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 > value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == GE) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 >= value2) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == AND) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 != 0.0 && value2 != 0.0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == OR) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if (value1 != 0.0 || value2 != 0.0) argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
} else if (opprevious == XOR) {
if (flag1 || flag2)
error->all(FLERR,"If command boolean can only operate on numbers");
if ((value1 == 0.0 && value2 != 0.0) ||
(value1 != 0.0 && value2 == 0.0))
argstack[nargstack].value = 1.0;
else argstack[nargstack].value = 0.0;
}
argstack[nargstack++].flag = 0;
}
// if end-of-string, break out of entire formula evaluation loop
if (op == DONE) break;
// push current operation onto stack
opstack[nopstack++] = op;
} else error->all(FLERR,"Invalid Boolean syntax in if command");
}
if (nopstack) error->all(FLERR,"Invalid Boolean syntax in if command");
if (nargstack != 1) error->all(FLERR,"Invalid Boolean syntax in if command");
// if flag == 1, Boolean expression was a single string with no operator
// error b/c invalid, only single number with no operator is allowed
if (argstack[0].flag == 1)
error->all(FLERR,"If command boolean cannot be single string");
return argstack[0].value;
}
/* ----------------------------------------------------------------------
class to read variable values from a file
for flag = SCALARFILE, reads one value per line
for flag = ATOMFILE, reads set of one value per atom
------------------------------------------------------------------------- */
VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
Pointers(lmp)
{
me = comm->me;
style = flag;
fp = nullptr;
if (me == 0) {
fp = fopen(file,"r");
if (fp == nullptr)
error->one(FLERR,"Cannot open {} variable {} file {}: {}", (style == Variable::ATOMFILE)
? "atomfile" : "file", name, file, utils::getsyserror());
}
// if atomfile-style variable, must store per-atom values read from file
// allocate a new fix STORE, so they persist
// id = variable-ID + VARIABLE_STORE, fix group = all
fixstore = nullptr;
id_fix = nullptr;
buffer = nullptr;
if (style == Variable::ATOMFILE) {
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,"Cannot use atomfile-style variable unless an atom map exists");
id_fix = utils::strdup(std::string(name) + "_VARIABLE_STORE");
fixstore = dynamic_cast<FixStoreAtom *>(
modify->add_fix(std::string(id_fix) + " all STORE/ATOM 1 0 0 0"));
buffer = new char[CHUNK*MAXLINE];
}
}
/* ---------------------------------------------------------------------- */
VarReader::~VarReader()
{
if (me == 0) {
fclose(fp);
fp = nullptr;
}
// check modify in case all fixes have already been deleted
if (fixstore) {
if (modify) modify->delete_fix(id_fix);
delete[] id_fix;
delete[] buffer;
}
}
/* ----------------------------------------------------------------------
read for SCALARFILE style
read next value from file into str for file-style variable
strip comments, skip blank lines
return 0 if successful, 1 if end-of-file
------------------------------------------------------------------------- */
int VarReader::read_scalar(char *str)
{
int n;
char *ptr;
// read one string from file
if (me == 0) {
while (true) {
ptr = fgets(str,MAXLINE,fp);
if (!ptr) { n=0; break; } // end of file
auto line = utils::trim(utils::trim_comment(str));
n = line.size() + 1;
if (n == 1) continue; // skip if blank line
memcpy(str, line.c_str(), n);
break;
}
}
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n == 0) return 1;
MPI_Bcast(str,n,MPI_CHAR,0,world);
return 0;
}
/* ----------------------------------------------------------------------
read snapshot of per-atom values from file
into str for atomfile-style variable
return 0 if successful, 1 if end-of-file
------------------------------------------------------------------------- */
int VarReader::read_peratom()
{
int i,m,nchunk,eof;
tagint tag;
char *ptr;
double value;
// set all per-atom values to 0.0
// values that appear in file will overwrite this
double *vstore = fixstore->vstore;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) vstore[i] = 0.0;
// read one string from file, convert to Nlines
char str[MAXLINE];
bigint nlines = 0;
if (me == 0) {
while (true) {
ptr = fgets(str,MAXLINE,fp);
if (!ptr) { nlines = 0; break; } // end of file
Tokenizer words(utils::trim(utils::trim_comment(str)));
if (words.count() == 0) continue; // skip if blank or comment line
if (words.count() != 1)
error->one(FLERR, "Expected 1 token but found {} when parsing {}", words.count(), str);
nlines = utils::bnumeric(FLERR,words.next(),true,lmp);
break;
}
}
MPI_Bcast(&nlines,1,MPI_LMP_BIGINT,0,world);
if (nlines == 0) return 1;
tagint map_tag_max = atom->map_tag_max;
bigint nread = 0;
while (nread < nlines) {
nchunk = MIN(nlines-nread,CHUNK);
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
if (eof) return 1;
for (const auto &line : utils::split_lines(buffer)) {
try {
ValueTokenizer words(utils::trim_comment(utils::trim(line)));
if (words.count() == 0) continue; // skip comment or empty lines
if (words.count() != 2)
throw TokenizerException(fmt::format("expected 2 tokens but found {}", words.count()), "");
tag = words.next_bigint();
value = words.next_double();
++nread;
} catch (TokenizerException &e) {
error->all(FLERR,"Invalid atomfile line '{}': {}", line, e.what());
}
if ((tag <= 0) || (tag > map_tag_max))
error->all(FLERR,"Invalid atom ID {} in variable file", tag);
if ((m = atom->map(tag)) >= 0) vstore[m] = value;
}
}
return 0;
}
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