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apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2021-09-04 14:01:24 -04:00
parent 0286c3e2be
commit e2d8fd58fa
1 changed files with 118 additions and 137 deletions
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255
src/PYTHON/python_impl.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -25,8 +24,8 @@
#include "python_utils.h"
#include "variable.h"
#include <Python.h> // IWYU pragma: export
#include <cstring>
#include <Python.h> // IWYU pragma: export
#ifdef MLIAP_PYTHON
#include "mliap_model_python.h"
@ -38,8 +37,7 @@
using namespace LAMMPS_NS;
enum{NONE,INT,DOUBLE,STRING,PTR};
enum { NONE, INT, DOUBLE, STRING, PTR };
/* ---------------------------------------------------------------------- */
@ -53,7 +51,7 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
#if PY_MAJOR_VERSION >= 3
#ifndef Py_LIMITED_API
// check for PYTHONUNBUFFERED environment variable
const char * PYTHONUNBUFFERED = getenv("PYTHONUNBUFFERED");
const char *PYTHONUNBUFFERED = getenv("PYTHONUNBUFFERED");
if (PYTHONUNBUFFERED != nullptr && strcmp(PYTHONUNBUFFERED, "1") == 0) {
// Python Global configuration variable
@ -67,7 +65,7 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
// Inform python intialization scheme of the mliappy module.
// This -must- happen before python is initialized.
int err = PyImport_AppendInittab("mliap_model_python_couple", PyInit_mliap_model_python_couple);
if (err) error->all(FLERR,"Could not register MLIAPPY embedded python module.");
if (err) error->all(FLERR, "Could not register MLIAPPY embedded python module.");
#endif
Py_Initialize();
@ -76,15 +74,13 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
// With Python 3.7 this function is now called by Py_Initialize()
// Deprecated since version 3.9, will be removed in version 3.11
#if PY_MAJOR_VERSION < 3 || PY_MINOR_VERSION < 7
if (!PyEval_ThreadsInitialized()) {
PyEval_InitThreads();
}
if (!PyEval_ThreadsInitialized()) { PyEval_InitThreads(); }
#endif
PyUtils::GIL lock;
PyObject *pModule = PyImport_AddModule("__main__");
if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
if (!pModule) error->all(FLERR, "Could not initialize embedded Python");
pyMain = (void *) pModule;
}
@ -98,7 +94,7 @@ PythonImpl::~PythonImpl()
PyUtils::GIL lock;
for (int i = 0; i < nfunc; i++) {
delete [] pfuncs[i].name;
delete[] pfuncs[i].name;
deallocate(i);
Py_CLEAR(pfuncs[i].pFunc);
}
@ -111,39 +107,37 @@ PythonImpl::~PythonImpl()
void PythonImpl::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Invalid python command");
if (narg < 2) error->all(FLERR, "Invalid python command");
// if invoke is only keyword, invoke the previously defined function
if (narg == 2 && strcmp(arg[1],"invoke") == 0) {
if (narg == 2 && strcmp(arg[1], "invoke") == 0) {
int ifunc = find(arg[0]);
if (ifunc < 0) error->all(FLERR,"Python invoke of undefined function");
if (ifunc < 0) error->all(FLERR, "Python invoke of undefined function");
char *str = nullptr;
if (pfuncs[ifunc].noutput) {
str = input->variable->pythonstyle(pfuncs[ifunc].ovarname,
pfuncs[ifunc].name);
if (!str)
error->all(FLERR,"Python variable does not match Python function");
str = input->variable->pythonstyle(pfuncs[ifunc].ovarname, pfuncs[ifunc].name);
if (!str) error->all(FLERR, "Python variable does not match Python function");
}
invoke_function(ifunc,str);
invoke_function(ifunc, str);
return;
}
// if source is only keyword, execute the python code
if (narg == 3 && strcmp(arg[1],"source") == 0) {
if (narg == 3 && strcmp(arg[1], "source") == 0) {
int err;
FILE *fp = fopen(arg[2],"r");
FILE *fp = fopen(arg[2], "r");
if (fp == nullptr)
err = execute_string(arg[2]);
else
err = execute_file(arg[2]);
if (fp) fclose(fp);
if (err) error->all(FLERR,"Could not process Python source command");
if (err) error->all(FLERR, "Could not process Python source command");
return;
}
@ -162,53 +156,53 @@ void PythonImpl::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"input") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
ninput = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (ninput < 0) error->all(FLERR,"Invalid python command");
if (strcmp(arg[iarg], "input") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
ninput = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (ninput < 0) error->all(FLERR, "Invalid python command");
iarg += 2;
delete[] istr;
istr = new char*[ninput];
if (iarg+ninput > narg) error->all(FLERR,"Invalid python command");
for (int i = 0; i < ninput; i++) istr[i] = arg[iarg+i];
istr = new char *[ninput];
if (iarg + ninput > narg) error->all(FLERR, "Invalid python command");
for (int i = 0; i < ninput; i++) istr[i] = arg[iarg + i];
iarg += ninput;
} else if (strcmp(arg[iarg],"return") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
} else if (strcmp(arg[iarg], "return") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
noutput = 1;
delete[] ostr;
ostr = arg[iarg+1];
ostr = arg[iarg + 1];
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
format = utils::strdup(arg[iarg+1]);
} else if (strcmp(arg[iarg], "format") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
format = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg],"length") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
length_longstr = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (length_longstr <= 0) error->all(FLERR,"Invalid python command");
} else if (strcmp(arg[iarg], "length") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
length_longstr = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (length_longstr <= 0) error->all(FLERR, "Invalid python command");
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
} else if (strcmp(arg[iarg], "file") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
delete[] pyfile;
pyfile = utils::strdup(arg[iarg+1]);
pyfile = utils::strdup(arg[iarg + 1]);
iarg += 2;
} else if (strcmp(arg[iarg],"here") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
herestr = arg[iarg+1];
} else if (strcmp(arg[iarg], "here") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Invalid python command");
herestr = arg[iarg + 1];
iarg += 2;
} else if (strcmp(arg[iarg],"exists") == 0) {
} else if (strcmp(arg[iarg], "exists") == 0) {
existflag = 1;
iarg++;
} else error->all(FLERR,"Invalid python command");
} else
error->all(FLERR, "Invalid python command");
}
if (pyfile && herestr) error->all(FLERR,"Invalid python command");
if (pyfile && existflag) error->all(FLERR,"Invalid python command");
if (herestr && existflag) error->all(FLERR,"Invalid python command");
if (pyfile && herestr) error->all(FLERR, "Invalid python command");
if (pyfile && existflag) error->all(FLERR, "Invalid python command");
if (herestr && existflag) error->all(FLERR, "Invalid python command");
// create or overwrite entry in pfuncs vector with name = arg[0]
int ifunc = create_entry(arg[0],ninput,noutput,length_longstr, istr, ostr, format);
int ifunc = create_entry(arg[0], ninput, noutput, length_longstr, istr, ostr, format);
PyUtils::GIL lock;
@ -218,18 +212,18 @@ void PythonImpl::command(int narg, char **arg)
// exist: do nothing, assume code has already been run
if (pyfile) {
FILE *fp = fopen(pyfile,"r");
FILE *fp = fopen(pyfile, "r");
if (fp == nullptr) {
PyUtils::Print_Errors();
error->all(FLERR,"Could not open Python file");
error->all(FLERR, "Could not open Python file");
}
int err = PyRun_SimpleFile(fp,pyfile);
int err = PyRun_SimpleFile(fp, pyfile);
if (err) {
PyUtils::Print_Errors();
error->all(FLERR,"Could not process Python file");
error->all(FLERR, "Could not process Python file");
}
fclose(fp);
@ -238,34 +232,32 @@ void PythonImpl::command(int narg, char **arg)
if (err) {
PyUtils::Print_Errors();
error->all(FLERR,"Could not process Python string");
error->all(FLERR, "Could not process Python string");
}
}
// pFunc = function object for requested function
PyObject *pModule = (PyObject *) pyMain;
PyObject *pFunc = PyObject_GetAttrString(pModule,pfuncs[ifunc].name);
PyObject *pFunc = PyObject_GetAttrString(pModule, pfuncs[ifunc].name);
if (!pFunc) {
PyUtils::Print_Errors();
error->all(FLERR,"Could not find Python function {}",
pfuncs[ifunc].name);
error->all(FLERR, "Could not find Python function {}", pfuncs[ifunc].name);
}
if (!PyCallable_Check(pFunc)) {
PyUtils::Print_Errors();
error->all(FLERR,"Python function {} is not callable",
pfuncs[ifunc].name);
error->all(FLERR, "Python function {} is not callable", pfuncs[ifunc].name);
}
pfuncs[ifunc].pFunc = (void *) pFunc;
// clean-up input storage
delete [] istr;
delete [] format;
delete [] pyfile;
delete[] istr;
delete[] format;
delete[] pyfile;
}
/* ------------------------------------------------------------------ */
@ -283,20 +275,14 @@ void PythonImpl::invoke_function(int ifunc, char *result)
int ninput = pfuncs[ifunc].ninput;
PyObject *pArgs = PyTuple_New(ninput);
if (!pArgs) {
error->all(FLERR,"Could not create Python function arguments");
}
if (!pArgs) { error->all(FLERR, "Could not create Python function arguments"); }
for (int i = 0; i < ninput; i++) {
int itype = pfuncs[ifunc].itype[i];
if (itype == INT) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
if (!str) {
error->all(FLERR,"Could not evaluate Python function input variable");
}
if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); }
pValue = PY_INT_FROM_LONG(atoi(str));
} else {
pValue = PY_INT_FROM_LONG(pfuncs[ifunc].ivalue[i]);
@ -304,11 +290,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
} else if (itype == DOUBLE) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
if (!str) {
error->all(FLERR,"Could not evaluate Python function input variable");
}
if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); }
pValue = PyFloat_FromDouble(atof(str));
} else {
pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]);
@ -316,10 +298,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
} else if (itype == STRING) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
if (!str) {
error->all(FLERR,"Could not evaluate Python function input variable");
}
if (!str) { error->all(FLERR, "Could not evaluate Python function input variable"); }
pValue = PY_STRING_FROM_STRING(str);
} else {
pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]);
@ -327,20 +306,20 @@ void PythonImpl::invoke_function(int ifunc, char *result)
} else if (itype == PTR) {
pValue = PY_VOID_POINTER(lmp);
} else {
error->all(FLERR,"Unsupported variable type");
error->all(FLERR, "Unsupported variable type");
}
PyTuple_SetItem(pArgs,i,pValue);
PyTuple_SetItem(pArgs, i, pValue);
}
// call the Python function
// error check with one() since only some procs may fail
pValue = PyObject_CallObject(pFunc,pArgs);
pValue = PyObject_CallObject(pFunc, pArgs);
Py_CLEAR(pArgs);
if (!pValue) {
PyUtils::Print_Errors();
error->one(FLERR,"Python function evaluation failed");
error->one(FLERR, "Python function evaluation failed");
}
// function returned a value
@ -350,14 +329,15 @@ void PythonImpl::invoke_function(int ifunc, char *result)
if (pfuncs[ifunc].noutput) {
int otype = pfuncs[ifunc].otype;
if (otype == INT) {
sprintf(result,"%ld",PY_INT_AS_LONG(pValue));
sprintf(result, "%ld", PY_INT_AS_LONG(pValue));
} else if (otype == DOUBLE) {
sprintf(result,"%.15g",PyFloat_AsDouble(pValue));
sprintf(result, "%.15g", PyFloat_AsDouble(pValue));
} else if (otype == STRING) {
const char *pystr = PY_STRING_AS_STRING(pValue);
if (pfuncs[ifunc].longstr)
strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr);
else strncpy(result,pystr,Variable::VALUELENGTH-1);
strncpy(pfuncs[ifunc].longstr, pystr, pfuncs[ifunc].length_longstr);
else
strncpy(result, pystr, Variable::VALUELENGTH - 1);
}
}
Py_CLEAR(pValue);
@ -368,19 +348,18 @@ void PythonImpl::invoke_function(int ifunc, char *result)
int PythonImpl::find(const char *name)
{
for (int i = 0; i < nfunc; i++)
if (strcmp(name,pfuncs[i].name) == 0) return i;
if (strcmp(name, pfuncs[i].name) == 0) return i;
return -1;
}
/* ------------------------------------------------------------------ */
int PythonImpl::variable_match(const char *name, const char *varname,
int numeric)
int PythonImpl::variable_match(const char *name, const char *varname, int numeric)
{
int ifunc = find(name);
if (ifunc < 0) return -1;
if (pfuncs[ifunc].noutput == 0) return -1;
if (strcmp(pfuncs[ifunc].ovarname,varname) != 0) return -1;
if (strcmp(pfuncs[ifunc].ovarname, varname) != 0) return -1;
if (numeric && pfuncs[ifunc].otype == STRING) return -1;
return ifunc;
}
@ -394,8 +373,8 @@ char *PythonImpl::long_string(int ifunc)
/* ------------------------------------------------------------------ */
int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_longstr,
char **istr, char *ostr, char *format)
int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_longstr, char **istr,
char *ostr, char *format)
{
// ifunc = index to entry by name in pfuncs vector, can be old or new
// free old vectors if overwriting old pfunc
@ -405,18 +384,18 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
if (ifunc < 0) {
ifunc = nfunc;
nfunc++;
pfuncs = (PyFunc *)
memory->srealloc(pfuncs,nfunc*sizeof(struct PyFunc),"python:pfuncs");
pfuncs = (PyFunc *) memory->srealloc(pfuncs, nfunc * sizeof(struct PyFunc), "python:pfuncs");
pfuncs[ifunc].name = utils::strdup(name);
} else deallocate(ifunc);
} else
deallocate(ifunc);
pfuncs[ifunc].ninput = ninput;
pfuncs[ifunc].noutput = noutput;
if (!format && ninput+noutput)
error->all(FLERR,"Invalid python command");
else if (format && ((int) strlen(format) != ninput+noutput))
error->all(FLERR,"Invalid python command");
if (!format && ninput + noutput)
error->all(FLERR, "Invalid python command");
else if (format && ((int) strlen(format) != ninput + noutput))
error->all(FLERR, "Invalid python command");
// process inputs as values or variables
@ -424,34 +403,34 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
pfuncs[ifunc].ivarflag = new int[ninput];
pfuncs[ifunc].ivalue = new int[ninput];
pfuncs[ifunc].dvalue = new double[ninput];
pfuncs[ifunc].svalue = new char*[ninput];
pfuncs[ifunc].svalue = new char *[ninput];
for (int i = 0; i < ninput; i++) {
pfuncs[ifunc].svalue[i] = nullptr;
char type = format[i];
if (type == 'i') {
pfuncs[ifunc].itype[i] = INT;
if (utils::strmatch(istr[i],"^v_")) {
if (utils::strmatch(istr[i], "^v_")) {
pfuncs[ifunc].ivarflag[i] = 1;
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i]+2);
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i] + 2);
} else {
pfuncs[ifunc].ivarflag[i] = 0;
pfuncs[ifunc].ivalue[i] = utils::inumeric(FLERR,istr[i],false,lmp);
pfuncs[ifunc].ivalue[i] = utils::inumeric(FLERR, istr[i], false, lmp);
}
} else if (type == 'f') {
pfuncs[ifunc].itype[i] = DOUBLE;
if (utils::strmatch(istr[i],"^v_")) {
if (utils::strmatch(istr[i], "^v_")) {
pfuncs[ifunc].ivarflag[i] = 1;
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i]+2);
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i] + 2);
} else {
pfuncs[ifunc].ivarflag[i] = 0;
pfuncs[ifunc].dvalue[i] = utils::numeric(FLERR,istr[i],false,lmp);
pfuncs[ifunc].dvalue[i] = utils::numeric(FLERR, istr[i], false, lmp);
}
} else if (type == 's') {
pfuncs[ifunc].itype[i] = STRING;
if (utils::strmatch(istr[i],"^v_")) {
if (utils::strmatch(istr[i], "^v_")) {
pfuncs[ifunc].ivarflag[i] = 1;
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i]+2);
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i] + 2);
} else {
pfuncs[ifunc].ivarflag[i] = 0;
pfuncs[ifunc].svalue[i] = utils::strdup(istr[i]);
@ -459,10 +438,10 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
} else if (type == 'p') {
pfuncs[ifunc].ivarflag[i] = 0;
pfuncs[ifunc].itype[i] = PTR;
if (strcmp(istr[i],"SELF") != 0)
error->all(FLERR,"Invalid python command");
if (strcmp(istr[i], "SELF") != 0) error->all(FLERR, "Invalid python command");
} else error->all(FLERR,"Invalid python command");
} else
error->all(FLERR, "Invalid python command");
}
// process output as value or variable
@ -472,22 +451,25 @@ int PythonImpl::create_entry(char *name, int ninput, int noutput, int length_lon
if (!noutput) return ifunc;
char type = format[ninput];
if (type == 'i') pfuncs[ifunc].otype = INT;
else if (type == 'f') pfuncs[ifunc].otype = DOUBLE;
else if (type == 's') pfuncs[ifunc].otype = STRING;
else error->all(FLERR,"Invalid python command");
if (type == 'i')
pfuncs[ifunc].otype = INT;
else if (type == 'f')
pfuncs[ifunc].otype = DOUBLE;
else if (type == 's')
pfuncs[ifunc].otype = STRING;
else
error->all(FLERR, "Invalid python command");
if (length_longstr) {
if (pfuncs[ifunc].otype != STRING)
error->all(FLERR,"Python command length keyword "
"cannot be used unless output is a string");
error->all(FLERR, "Python command length keyword cannot be used unless output is a string");
pfuncs[ifunc].length_longstr = length_longstr;
pfuncs[ifunc].longstr = new char[length_longstr+1];
pfuncs[ifunc].longstr = new char[length_longstr + 1];
pfuncs[ifunc].longstr[length_longstr] = '\0';
}
if (strstr(ostr,"v_") != ostr) error->all(FLERR,"Invalid python command");
pfuncs[ifunc].ovarname = utils::strdup(ostr+2);
if (strstr(ostr, "v_") != ostr) error->all(FLERR, "Invalid python command");
pfuncs[ifunc].ovarname = utils::strdup(ostr + 2);
return ifunc;
}
@ -504,11 +486,11 @@ int PythonImpl::execute_string(char *cmd)
int PythonImpl::execute_file(char *fname)
{
FILE *fp = fopen(fname,"r");
FILE *fp = fopen(fname, "r");
if (fp == nullptr) return -1;
PyUtils::GIL lock;
int err = PyRun_SimpleFile(fp,fname);
int err = PyRun_SimpleFile(fp, fname);
if (fp) fclose(fp);
return err;
@ -518,27 +500,26 @@ int PythonImpl::execute_file(char *fname)
void PythonImpl::deallocate(int i)
{
delete [] pfuncs[i].itype;
delete [] pfuncs[i].ivarflag;
delete [] pfuncs[i].ivalue;
delete [] pfuncs[i].dvalue;
for (int j = 0; j < pfuncs[i].ninput; j++)
delete [] pfuncs[i].svalue[j];
delete [] pfuncs[i].svalue;
delete [] pfuncs[i].ovarname;
delete [] pfuncs[i].longstr;
delete[] pfuncs[i].itype;
delete[] pfuncs[i].ivarflag;
delete[] pfuncs[i].ivalue;
delete[] pfuncs[i].dvalue;
for (int j = 0; j < pfuncs[i].ninput; j++) delete[] pfuncs[i].svalue[j];
delete[] pfuncs[i].svalue;
delete[] pfuncs[i].ovarname;
delete[] pfuncs[i].longstr;
}
/* ------------------------------------------------------------------ */
bool PythonImpl::has_minimum_version(int major, int minor)
{
return (PY_MAJOR_VERSION == major && PY_MINOR_VERSION >= minor) || (PY_MAJOR_VERSION > major);
return (PY_MAJOR_VERSION == major && PY_MINOR_VERSION >= minor) || (PY_MAJOR_VERSION > major);
}
/* ------------------------------------------------------------------ */
void PythonImpl::finalize()
{
if (Py_IsInitialized()) Py_Finalize();
if (Py_IsInitialized()) Py_Finalize();
}