From e364b80724ae4258e0f3eedbf49236a69fbf0c25 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 16 Dec 2016 10:24:25 -0700
Subject: [PATCH] added length keyword to python command
---
doc/src/python.txt | 15 ++++++++++++++-
src/PYTHON/python.cpp | 28 +++++++++++++++++++++++++++-
src/PYTHON/python.h | 5 ++++-
src/USER-INTEL/fix_intel.cpp | 2 --
src/fix_shear_history.cpp | 2 +-
src/variable.cpp | 4 ++++
6 files changed, 50 insertions(+), 6 deletions(-)
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 773992bddd..7da69a0319 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -14,7 +14,7 @@ python func keyword args ... :pre
func = name of Python function :ulb,l
one or more keyword/args pairs must be appended :l
-keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {exists}
+keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {here} or {exists}
{invoke} arg = none = invoke the previously defined Python function
{input} args = N i1 i2 ... iN
N = # of inputs to function
@@ -29,6 +29,8 @@ keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {ex
M = N+1 if there is a return value
fstring = each character (i,f,s,p) corresponds in order to an input or return value
'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
+ {length} arg = Nlen
+ Nlen = max length of string returned from Python function
{file} arg = filename
filename = file of Python code, which defines func
{here} arg = inline
@@ -165,6 +167,17 @@ equal-style variable as an argument, but only if the output of the
Python function is flagged as a numeric value ("i" or "f") via the
{format} keyword.
+If the {return} keyword is used and the {format} keyword specifies the
+output as a string, then the default maximum length of that string is
+63 characters (64-1 for the string terminator). If you want to return
+a longer string, the {length} keyword can be specified with its {Nlen}
+value set to a larger number (the code allocates space for Nlen+1 to
+include the string terminator). If the Python function generates a
+string longer than the default 63 or the specified {Nlen}, it will be
+trunctated.
+
+:line
+
Either the {file}, {here}, or {exists} keyword must be used, but only
one of them. These keywords specify what Python code to load into the
Python interpreter. The {file} keyword gives the name of a file,
diff --git a/src/PYTHON/python.cpp b/src/PYTHON/python.cpp
index c9947f3521..6c89be6922 100644
--- a/src/PYTHON/python.cpp
+++ b/src/PYTHON/python.cpp
@@ -89,6 +89,7 @@ void Python::command(int narg, char **arg)
istr = NULL;
ostr = NULL;
format = NULL;
+ length_longstr = 0;
char *pyfile = NULL;
char *herestr = NULL;
int existflag = 0;
@@ -115,6 +116,11 @@ void Python::command(int narg, char **arg)
format = new char[n];
strcpy(format,arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"length") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Invalid python command");
+ length_longstr = force->inumeric(FLERR,arg[iarg+1]);
+ 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");
delete[] pyfile;
@@ -249,6 +255,7 @@ void Python::invoke_function(int ifunc, char *result)
// function returned a value
// assign it to result string stored by python-style variable
+ // or if user specified a length, assign it to longstr
if (pfuncs[ifunc].noutput) {
int otype = pfuncs[ifunc].otype;
@@ -258,7 +265,9 @@ void Python::invoke_function(int ifunc, char *result)
sprintf(result,"%.15g",PyFloat_AsDouble(pValue));
} else if (otype == STRING) {
char *pystr = PyString_AsString(pValue);
- strncpy(result,pystr,VALUELENGTH-1);
+ if (pfuncs[ifunc].longstr)
+ strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr);
+ else strncpy(result,pystr,VALUELENGTH-1);
}
Py_DECREF(pValue);
}
@@ -287,6 +296,13 @@ int Python::variable_match(char *name, char *varname, int numeric)
/* ------------------------------------------------------------------ */
+char *Python::long_string(int ifunc)
+{
+ return pfuncs[ifunc].longstr;
+}
+
+/* ------------------------------------------------------------------ */
+
int Python::create_entry(char *name)
{
// ifunc = index to entry by name in pfuncs vector, can be old or new
@@ -370,6 +386,7 @@ int Python::create_entry(char *name)
// process output as value or variable
pfuncs[ifunc].ovarname = NULL;
+ pfuncs[ifunc].longstr = NULL;
if (!noutput) return ifunc;
char type = format[ninput];
@@ -378,6 +395,14 @@ int Python::create_entry(char *name)
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");
+ pfuncs[ifunc].length_longstr = length_longstr;
+ pfuncs[ifunc].longstr = new char[length_longstr+1];
+ }
+
if (strstr(ostr,"v_") != ostr) error->all(FLERR,"Invalid python command");
int n = strlen(&ostr[2]) + 1;
pfuncs[ifunc].ovarname = new char[n];
@@ -398,4 +423,5 @@ void Python::deallocate(int i)
delete [] pfuncs[i].svalue[j];
delete [] pfuncs[i].svalue;
delete [] pfuncs[i].ovarname;
+ delete [] pfuncs[i].longstr;
}
diff --git a/src/PYTHON/python.h b/src/PYTHON/python.h
index d1622728ac..61e5f015e2 100644
--- a/src/PYTHON/python.h
+++ b/src/PYTHON/python.h
@@ -28,9 +28,10 @@ class Python : protected Pointers {
void invoke_function(int, char *);
int find(char *);
int variable_match(char *, char *, int);
+ char *long_string(int);
private:
- int ninput,noutput;
+ int ninput,noutput,length_longstr;
char **istr;
char *ostr,*format;
void *pyMain;
@@ -44,6 +45,8 @@ class Python : protected Pointers {
char **svalue;
int otype;
char *ovarname;
+ char *longstr;
+ int length_longstr;
void *pFunc;
};
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 84f4994901..7c5dd0b34c 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -325,8 +325,6 @@ void FixIntel::init()
error->all(FLERR,
"Currently, cannot use more than one intel style with hybrid.");
- neighbor->fix_intel = (void *)this;
-
check_neighbor_intel();
if (_precision_mode == PREC_MODE_SINGLE)
_single_buffers->zero_ev();
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index 42d088875b..379de9bcd3 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -526,7 +526,7 @@ double FixShearHistory::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
- bytes += nmax * sizeof(int *);
+ bytes += nmax * sizeof(tagint *);
bytes += nmax * sizeof(double *);
int nmypage = comm->nthreads;
diff --git a/src/variable.cpp b/src/variable.cpp
index 2f985a7c8e..67c8951974 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -875,6 +875,10 @@ char *Variable::retrieve(char *name)
error->all(FLERR,"Python variable does not match Python function");
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] == INTERNAL) {
sprintf(data[ivar][0],"%.15g",dvalue[ivar]);
str = data[ivar][0];
--
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