#include "gromacs/utility/textreader.h"
#include "gromacs/utility/textwriter.h"
-std::vector<t_inpfile>
-read_inpfile(gmx::TextInputStream *stream, const char *fn,
- warninp_t wi)
+std::vector<t_inpfile> read_inpfile(gmx::TextInputStream* stream, const char* fn, warninp_t wi)
{
std::vector<t_inpfile> inp;
auto tokens = gmx::splitAndTrimDelimitedString(line, '=');
if (tokens.size() < 2)
{
- auto message = gmx::formatString("No '=' to separate .mdp parameter key and value was found on line:\n'%s'", line.c_str());
+ auto message = gmx::formatString(
+ "No '=' to separate .mdp parameter key and value was found on line:\n'%s'",
+ line.c_str());
warning_error(wi, message);
continue;
}
GMX_RELEASE_ASSERT(tokens.size() == 2, "Must have tokens for key and value");
if (tokens[0].empty() && tokens[1].empty())
{
- auto message = gmx::formatString("No .mdp parameter name or value was found on line:\n'%s'", line.c_str());
+ auto message = gmx::formatString(
+ "No .mdp parameter name or value was found on line:\n'%s'", line.c_str());
warning_error(wi, message);
continue;
}
if (tokens[0].empty())
{
- auto message = gmx::formatString("No .mdp parameter name was found on the left-hand side of '=' on line:\n'%s'", line.c_str());
+ auto message = gmx::formatString(
+ "No .mdp parameter name was found on the left-hand side of '=' on line:\n'%s'",
+ line.c_str());
warning_error(wi, message);
continue;
}
if (found_index == -1)
{
/* add a new item */
- inp.emplace_back(0, 1, false, false, false,
- tokens[0], tokens[1]);
+ inp.emplace_back(0, 1, false, false, false, tokens[0], tokens[1]);
}
else
{
- auto message = gmx::formatString("Parameter \"%s\" doubly defined\n",
- tokens[0].c_str());
+ auto message = gmx::formatString("Parameter \"%s\" doubly defined\n", tokens[0].c_str());
warning_error(wi, message);
}
}
if (debug)
{
- fprintf(debug, "Done reading MDP file, there were %zu entries in there\n",
- inp.size());
+ fprintf(debug, "Done reading MDP file, there were %zu entries in there\n", inp.size());
}
return inp;
gmx::KeyValueTreeObject flatKeyValueTreeFromInpFile(gmx::ArrayRef<const t_inpfile> inp)
{
- gmx::KeyValueTreeBuilder builder;
- auto root = builder.rootObject();
- for (auto &local : inp)
+ gmx::KeyValueTreeBuilder builder;
+ auto root = builder.rootObject();
+ for (auto& local : inp)
{
root.addValue<std::string>(local.name_, !local.value_.empty() ? local.value_ : "");
}
struct inp_comp
{
- bool operator()(t_inpfile const &a, t_inpfile const &b)
- {
- return a.count_ < b.count_;
- }
+ bool operator()(t_inpfile const& a, t_inpfile const& b) { return a.count_ < b.count_; }
};
-static void sort_inp(std::vector<t_inpfile> *inp)
+static void sort_inp(std::vector<t_inpfile>* inp)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
int mm;
mm = -1;
- for (const auto &local : inpRef)
+ for (const auto& local : inpRef)
{
mm = std::max(mm, local.count_);
}
- for (auto &local : inpRef)
+ for (auto& local : inpRef)
{
if (local.count_ == 0)
{
std::sort(inpRef.begin(), inpRef.end(), inp_comp());
}
-void write_inpfile(gmx::TextOutputStream *stream, const char *fn, std::vector<t_inpfile> *inp,
- gmx_bool bHaltOnUnknown,
- WriteMdpHeader writeHeader,
- warninp_t wi)
+void write_inpfile(gmx::TextOutputStream* stream,
+ const char* fn,
+ std::vector<t_inpfile>* inp,
+ gmx_bool bHaltOnUnknown,
+ WriteMdpHeader writeHeader,
+ warninp_t wi)
{
using gmx::formatString;
settings.linePrefix(";\t");
gmx::printBinaryInformation(&writer, gmx::getProgramContext(), settings);
}
- for (const auto &local : *inp)
+ for (const auto& local : *inp)
{
- if (local.bHandledAsKeyValueTree_)
- {
- }
+ if (local.bHandledAsKeyValueTree_) {}
else if (local.bSet_)
{
if (local.name_[0] == ';' || (local.name_.length() > 2 && local.name_[1] == ';'))
}
else
{
- writer.writeLine(formatString("%-24s = %s", local.name_.c_str(), !local.value_.empty() ? local.value_.c_str() : ""));
+ writer.writeLine(formatString("%-24s = %s", local.name_.c_str(),
+ !local.value_.empty() ? local.value_.c_str() : ""));
}
}
else if (!local.bObsolete_)
{
- auto message = formatString("Unknown left-hand '%s' in parameter file\n",
- local.name_.c_str());
+ auto message =
+ formatString("Unknown left-hand '%s' in parameter file\n", local.name_.c_str());
if (bHaltOnUnknown)
{
warning_error(wi, message.c_str());
check_warning_error(wi, FARGS);
}
-void replace_inp_entry(gmx::ArrayRef<t_inpfile> inp, const char *old_entry, const char *new_entry)
+void replace_inp_entry(gmx::ArrayRef<t_inpfile> inp, const char* old_entry, const char* new_entry)
{
- for (auto &local : inp)
+ for (auto& local : inp)
{
if (gmx_strcasecmp_min(old_entry, local.name_.c_str()) == 0)
{
if (new_entry)
{
- fprintf(stderr, "Replacing old mdp entry '%s' by '%s'\n",
- local.name_.c_str(), new_entry);
+ fprintf(stderr, "Replacing old mdp entry '%s' by '%s'\n", local.name_.c_str(), new_entry);
int foundIndex = search_einp(inp, new_entry);
if (foundIndex >= 0)
{
- gmx_fatal(FARGS, "A parameter is present with both the old name '%s' and the new name '%s'.", local.name_.c_str(), inp[foundIndex].name_.c_str());
+ gmx_fatal(FARGS,
+ "A parameter is present with both the old name '%s' and the new name "
+ "'%s'.",
+ local.name_.c_str(), inp[foundIndex].name_.c_str());
}
local.name_.assign(new_entry);
}
else
{
- fprintf(stderr, "Ignoring obsolete mdp entry '%s'\n",
- local.name_.c_str());
+ fprintf(stderr, "Ignoring obsolete mdp entry '%s'\n", local.name_.c_str());
local.bObsolete_ = TRUE;
}
}
}
}
-int search_einp(gmx::ArrayRef<const t_inpfile> inp, const char *name)
+int search_einp(gmx::ArrayRef<const t_inpfile> inp, const char* name)
{
if (inp.empty())
{
return -1;
}
-void mark_einp_set(gmx::ArrayRef<t_inpfile> inp, const char *name)
+void mark_einp_set(gmx::ArrayRef<t_inpfile> inp, const char* name)
{
- int i = search_einp(inp, name);
+ int i = search_einp(inp, name);
if (i != -1)
{
inp[i].count_ = inp.front().inp_count_++;
}
}
-static int get_einp(std::vector<t_inpfile> *inp, const char *name)
+static int get_einp(std::vector<t_inpfile>* inp, const char* name)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
bool notfound = false;
- int i = search_einp(inpRef, name);
+ int i = search_einp(inpRef, name);
if (i == -1)
{
notfound = true;
- inpRef.emplace_back(0, 0, false, true, false,
- name, "");
+ inpRef.emplace_back(0, 0, false, true, false, name, "");
i = inpRef.size() - 1;
- if (inpRef.size() == 1)
+ if (inpRef.size() == 1)
{
inpRef.front().inp_count_ = 1;
}
}
/* Note that sanitizing the trailing part of inp[ii].value was the responsibility of read_inpfile() */
-int get_eint(std::vector<t_inpfile> *inp, const char *name, int def,
- warninp_t wi)
+int get_eint(std::vector<t_inpfile>* inp, const char* name, int def, warninp_t wi)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
char buf[32], *ptr, warn_buf[STRLEN];
- int ii = get_einp(inp, name);
+ int ii = get_einp(inp, name);
if (ii == -1)
{
int ret = std::strtol(inpRef[ii].value_.c_str(), &ptr, 10);
if (*ptr != '\0')
{
- sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n", inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
+ sprintf(warn_buf,
+ "Right hand side '%s' for parameter '%s' in parameter file is not an integer "
+ "value\n",
+ inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
warning_error(wi, warn_buf);
}
}
}
-int get_eint(std::vector<t_inpfile> *inp, const std::string &name, int def,
- warninp_t wi)
+int get_eint(std::vector<t_inpfile>* inp, const std::string& name, int def, warninp_t wi)
{
return get_eint(inp, name.c_str(), def, wi);
}
/* Note that sanitizing the trailing part of inp[ii].value was the responsibility of read_inpfile() */
-int64_t get_eint64(std::vector<t_inpfile> *inp,
- const char *name, int64_t def,
- warninp_t wi)
+int64_t get_eint64(std::vector<t_inpfile>* inp, const char* name, int64_t def, warninp_t wi)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
char buf[32], *ptr, warn_buf[STRLEN];
- int ii = get_einp(inp, name);
+ int ii = get_einp(inp, name);
if (ii == -1)
{
int64_t ret = str_to_int64_t(inpRef[ii].value_.c_str(), &ptr);
if (*ptr != '\0')
{
- sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n", inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
+ sprintf(warn_buf,
+ "Right hand side '%s' for parameter '%s' in parameter file is not an integer "
+ "value\n",
+ inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
warning_error(wi, warn_buf);
}
}
}
-int64_t get_eint64(std::vector<t_inpfile> *inp,
- const std::string &name, int64_t def,
- warninp_t wi)
+int64_t get_eint64(std::vector<t_inpfile>* inp, const std::string& name, int64_t def, warninp_t wi)
{
return get_eint64(inp, name.c_str(), def, wi);
}
/* Note that sanitizing the trailing part of inp[ii].value was the responsibility of read_inpfile() */
-double get_ereal(std::vector<t_inpfile> *inp, const char *name, double def,
- warninp_t wi)
+double get_ereal(std::vector<t_inpfile>* inp, const char* name, double def, warninp_t wi)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
char buf[32], *ptr, warn_buf[STRLEN];
- int ii = get_einp(inp, name);
+ int ii = get_einp(inp, name);
if (ii == -1)
{
double ret = strtod(inpRef[ii].value_.c_str(), &ptr);
if (*ptr != '\0')
{
- sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not a real value\n", inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
+ sprintf(warn_buf,
+ "Right hand side '%s' for parameter '%s' in parameter file is not a real "
+ "value\n",
+ inpRef[ii].value_.c_str(), inpRef[ii].name_.c_str());
warning_error(wi, warn_buf);
}
}
}
-double get_ereal(std::vector<t_inpfile> *inp, const std::string &name, double def,
- warninp_t wi)
+double get_ereal(std::vector<t_inpfile>* inp, const std::string& name, double def, warninp_t wi)
{
return get_ereal(inp, name.c_str(), def, wi);
}
/* Note that sanitizing the trailing part of inp[ii].value was the responsibility of read_inpfile() */
-const char *get_estr(std::vector<t_inpfile> *inp, const char *name, const char *def)
+const char* get_estr(std::vector<t_inpfile>* inp, const char* name, const char* def)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
char buf[32];
- int ii = get_einp(inp, name);
+ int ii = get_einp(inp, name);
if (ii == -1)
{
}
}
-const char *get_estr(std::vector<t_inpfile> *inp, const std::string &name, const char *def)
+const char* get_estr(std::vector<t_inpfile>* inp, const std::string& name, const char* def)
{
return get_estr(inp, name.c_str(), def);
}
/* Note that sanitizing the trailing part of inp[ii].value was the responsibility of read_inpfile() */
-int get_eeenum(std::vector<t_inpfile> *inp, const char *name, const char **defs,
- warninp_t wi)
+int get_eeenum(std::vector<t_inpfile>* inp, const char* name, const char** defs, warninp_t wi)
{
- std::vector<t_inpfile> &inpRef = *inp;
+ std::vector<t_inpfile>& inpRef = *inp;
int n = 0;
char buf[STRLEN];
- int ii = get_einp(inp, name);
+ int ii = get_einp(inp, name);
if (ii == -1)
{
{
n += sprintf(buf, "Invalid enum '%s' for variable %s, using '%s'\n",
inpRef[ii].value_.c_str(), name, defs[0]);
- n += sprintf(buf+n, "Next time use one of:");
- int j = 0;
+ n += sprintf(buf + n, "Next time use one of:");
+ int j = 0;
while (defs[j])
{
- n += sprintf(buf+n, " '%s'", defs[j]);
+ n += sprintf(buf + n, " '%s'", defs[j]);
j++;
}
if (wi != nullptr)
return i;
}
-int get_eeenum(std::vector<t_inpfile> *inp, const std::string &name, const char **defs,
- warninp_t wi)
+int get_eeenum(std::vector<t_inpfile>* inp, const std::string& name, const char** defs, warninp_t wi)
{
return get_eeenum(inp, name.c_str(), defs, wi);
}
-int get_eenum(std::vector<t_inpfile> *inp, const char *name, const char **defs)
+int get_eenum(std::vector<t_inpfile>* inp, const char* name, const char** defs)
{
return get_eeenum(inp, name, defs, nullptr);
}
-void
-printStringNewline(std::vector<t_inpfile> *inp, const char *line)
+void printStringNewline(std::vector<t_inpfile>* inp, const char* line)
{
std::string tmp("\n; ");
tmp.append(line);
get_estr(inp, tmp.c_str(), nullptr);
}
-void
-printStringNoNewline(std::vector<t_inpfile> *inp, const char *line)
+void printStringNoNewline(std::vector<t_inpfile>* inp, const char* line)
{
std::string tmp("; ");
tmp.append(line);
get_estr(inp, tmp.c_str(), nullptr);
}
-void
-setStringEntry(std::vector<t_inpfile> *inp, const char *name, char *newName, const char *def)
+void setStringEntry(std::vector<t_inpfile>* inp, const char* name, char* newName, const char* def)
{
- const char *found = nullptr;
- found = get_estr(inp, name, def);
+ const char* found = nullptr;
+ found = get_estr(inp, name, def);
if (found != nullptr)
{
std::strcpy(newName, found);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff