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lammps/lib/colvars/colvarparse.cpp
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colvarparse.cpp
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#include <sstream>
#include <iostream>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
// space & tab
std::string const colvarparse::white_space = " \t";
std::string colvarparse::dummy_string = "";
size_t colvarparse::dummy_pos = 0;
// definition of single-value keyword parsers
template<typename TYPE> bool colvarparse::_get_keyval_scalar_(std::string const &conf,
char const *key,
TYPE &value,
TYPE const &def_value,
Parse_Mode const parse_mode)
{
std::string data;
bool b_found = false, b_found_any = false;
size_t save_pos = 0, found_count = 0;
do {
std::string data_this = "";
b_found = key_lookup(conf, key, data_this, save_pos);
if (b_found) {
if (!b_found_any)
b_found_any = true;
found_count++;
data = data_this;
}
} while (b_found);
if (found_count > 1)
cvm::log("Warning: found more than one instance of \""+
std::string(key)+"\".\n");
if (data.size()) {
std::istringstream is(data);
TYPE x(def_value);
if (is >> x) {
value = x;
} else {
cvm::error("Error: in parsing \""+
std::string(key)+"\".\n", INPUT_ERROR);
}
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = "+
cvm::to_str(value)+"\n");
}
} else {
if (b_found_any) {
cvm::error("Error: improper or missing value "
"for \""+std::string(key)+"\".\n", INPUT_ERROR);
}
value = def_value;
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = "+
cvm::to_str(def_value)+" [default]\n");
}
}
return b_found_any;
}
bool colvarparse::_get_keyval_scalar_string_(std::string const &conf,
char const *key,
std::string &value,
std::string const &def_value,
Parse_Mode const parse_mode)
{
std::string data;
bool b_found = false, b_found_any = false;
size_t save_pos = 0, found_count = 0;
do {
std::string data_this = "";
b_found = key_lookup(conf, key, data_this, save_pos);
if (b_found) {
if (!b_found_any)
b_found_any = true;
found_count++;
data = data_this;
}
} while (b_found);
if (found_count > 1)
cvm::log("Warning: found more than one instance of \""+
std::string(key)+"\".\n");
if (data.size()) {
std::istringstream is(data);
size_t data_count = 0;
std::string x(def_value);
while (is >> x) {
value = x;
data_count++;
}
if (data_count == 0)
cvm::error("Error: in parsing \""+
std::string(key)+"\".\n", INPUT_ERROR);
if (data_count > 1) {
cvm::error("Error: multiple values "
"are not allowed for keyword \""+
std::string(key)+"\".\n", INPUT_ERROR);
}
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = \""+
cvm::to_str(value)+"\"\n");
}
} else {
if (b_found_any) {
cvm::error("Error: improper or missing value "
"for \""+std::string(key)+"\".\n", INPUT_ERROR);
}
value = def_value;
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = \""+
cvm::to_str(def_value)+"\" [default]\n");
}
}
return b_found_any;
}
// multiple-value keyword parsers
template<typename TYPE> bool colvarparse::_get_keyval_vector_(std::string const &conf,
char const *key,
std::vector<TYPE> &values,
std::vector<TYPE> const &def_values,
Parse_Mode const parse_mode)
{
std::string data;
bool b_found = false, b_found_any = false;
size_t save_pos = 0, found_count = 0;
do {
std::string data_this = "";
b_found = key_lookup(conf, key, data_this, save_pos);
if (b_found) {
if (!b_found_any)
b_found_any = true;
found_count++;
data = data_this;
}
} while (b_found);
if (found_count > 1)
cvm::log("Warning: found more than one instance of \""+
std::string(key)+"\".\n");
if (data.size()) {
std::istringstream is(data);
if (values.size() == 0) {
std::vector<TYPE> x;
if (def_values.size())
x = def_values;
else
x.assign(1, TYPE());
for (size_t i = 0;
( is >> x[ ((i<x.size()) ? i : x.size()-1) ] );
i++) {
values.push_back(x[ ((i<x.size()) ? i : x.size()-1) ]);
}
} else {
size_t i = 0;
for ( ; i < values.size(); i++) {
TYPE x(values[i]);
if (is >> x) {
values[i] = x;
} else {
cvm::error("Error: in parsing \""+
std::string(key)+"\".\n", INPUT_ERROR);
}
}
}
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = "+
cvm::to_str(values)+"\n");
}
} else {
if (b_found_any) {
cvm::error("Error: improper or missing values for \""+
std::string(key)+"\".\n", INPUT_ERROR);
}
for (size_t i = 0; i < values.size(); i++)
values[i] = def_values[ (i > def_values.size()) ? 0 : i ];
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = "+
cvm::to_str(def_values)+" [default]\n");
}
}
return b_found_any;
}
// single-value keyword parsers
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
int &value,
int const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<int>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
size_t &value,
size_t const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<size_t>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
long &value,
long const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<long>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::string &value,
std::string const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_string_(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
cvm::real &value,
cvm::real const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<cvm::real>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
cvm::rvector &value,
cvm::rvector const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<cvm::rvector>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
cvm::quaternion &value,
cvm::quaternion const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<cvm::quaternion>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
colvarvalue &value,
colvarvalue const &def_value,
Parse_Mode const parse_mode)
{
return _get_keyval_scalar_<colvarvalue>(conf, key, value, def_value, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
bool &value,
bool const &def_value,
Parse_Mode const parse_mode)
{
std::string data;
bool b_found = false, b_found_any = false;
size_t save_pos = 0, found_count = 0;
do {
std::string data_this = "";
b_found = key_lookup(conf, key, data_this, save_pos);
if (b_found) {
if (!b_found_any)
b_found_any = true;
found_count++;
data = data_this;
}
} while (b_found);
if (found_count > 1)
cvm::log("Warning: found more than one instance of \""+
std::string(key)+"\".\n");
if (data.size()) {
if ( (data == std::string("on")) ||
(data == std::string("yes")) ||
(data == std::string("true")) ) {
value = true;
} else if ( (data == std::string("off")) ||
(data == std::string("no")) ||
(data == std::string("false")) ) {
value = false;
} else
cvm::error("Error: boolean values only are allowed "
"for \""+std::string(key)+"\".\n", INPUT_ERROR);
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = "+
(value ? "on" : "off")+"\n");
}
} else {
if (b_found_any) {
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = on\n");
}
value = true;
} else {
value = def_value;
if (parse_mode != parse_silent) {
cvm::log("# "+std::string(key)+" = "+
(def_value ? "on" : "off")+" [default]\n");
}
}
}
return b_found_any;
}
// multiple-value keyword parsers
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<int> &values,
std::vector<int> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<int>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<size_t> &values,
std::vector<size_t> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<size_t>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<long> &values,
std::vector<long> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<long>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<std::string> &values,
std::vector<std::string> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<std::string>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<cvm::real> &values,
std::vector<cvm::real> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<cvm::real>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<cvm::rvector> &values,
std::vector<cvm::rvector> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<cvm::rvector>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<cvm::quaternion> &values,
std::vector<cvm::quaternion> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<cvm::quaternion>(conf, key, values, def_values, parse_mode);
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
std::vector<colvarvalue> &values,
std::vector<colvarvalue> const &def_values,
Parse_Mode const parse_mode)
{
return _get_keyval_vector_<colvarvalue>(conf, key, values, def_values, parse_mode);
}
void colvarparse::add_keyword(char const *key)
{
for (std::list<std::string>::iterator ki = allowed_keywords.begin();
ki != allowed_keywords.end(); ki++) {
if (to_lower_cppstr(std::string(key)) == *ki)
return;
}
// not found in the list
// if (cvm::debug())
// cvm::log("Registering a new keyword, \""+std::string (key)+"\".\n");
allowed_keywords.push_back(to_lower_cppstr(std::string(key)));
}
void colvarparse::strip_values(std::string &conf)
{
size_t offset = 0;
data_begin_pos.sort();
data_end_pos.sort();
std::list<size_t>::iterator data_begin = data_begin_pos.begin();
std::list<size_t>::iterator data_end = data_end_pos.begin();
for ( ; (data_begin != data_begin_pos.end()) &&
(data_end != data_end_pos.end()) ;
data_begin++, data_end++) {
// std::cerr << "data_begin, data_end "
// << *data_begin << ", " << *data_end
// << "\n";
size_t const nchars = *data_end-*data_begin;
// std::cerr << "conf[data_begin:data_end] = \""
// << std::string (conf, *data_begin - offset, nchars)
// << "\"\n";
conf.erase(*data_begin - offset, nchars);
offset += nchars;
// std::cerr << ("Stripped config = \"\n"+conf+"\"\n");
}
}
void colvarparse::clear_keyword_registry()
{
allowed_keywords.clear();
data_begin_pos.clear();
data_end_pos.clear();
}
int colvarparse::check_keywords(std::string &conf, char const *key)
{
if (cvm::debug())
cvm::log("Configuration string for \""+std::string(key)+
"\": \"\n"+conf+"\".\n");
strip_values(conf);
// after stripping, the config string has either empty lines, or
// lines beginning with a keyword
std::string line;
std::istringstream is(conf);
while (std::getline(is, line)) {
if (line.size() == 0)
continue;
if (line.find_first_not_of(white_space) ==
std::string::npos)
continue;
std::string uk;
std::istringstream line_is(line);
line_is >> uk;
// if (cvm::debug())
// cvm::log ("Checking the validity of \""+uk+"\" from line:\n" + line);
uk = to_lower_cppstr(uk);
bool found_keyword = false;
for (std::list<std::string>::iterator ki = allowed_keywords.begin();
ki != allowed_keywords.end(); ki++) {
if (uk == *ki) {
found_keyword = true;
break;
}
}
if (!found_keyword) {
cvm::error("Error: keyword \""+uk+"\" is not supported, "
"or not recognized in this context.\n", INPUT_ERROR);
return INPUT_ERROR;
}
}
init();
return COLVARS_OK;
}
std::istream & colvarparse::getline_nocomments(std::istream &is,
std::string &line,
char const delim)
{
std::getline(is, line, delim);
size_t const comment = line.find('#');
if (comment != std::string::npos) {
line.erase(comment);
}
return is;
}
bool colvarparse::key_lookup(std::string const &conf,
char const *key_in,
std::string &data,
size_t &save_pos)
{
// add this keyword to the register (in its camelCase version)
add_keyword(key_in);
// use the lowercase version from now on
std::string const key(to_lower_cppstr(key_in));
// "conf_lower" is only used to lookup the keyword, but its value
// will be read from "conf", in order not to mess up file names
std::string const conf_lower(to_lower_cppstr(conf));
// by default, there is no value, unless we found one
data = "";
// when the function is invoked without save_pos, ensure that we
// start from zero
colvarparse::dummy_pos = 0;
// start from the first occurrence of key
size_t pos = conf_lower.find(key, save_pos);
// iterate over all instances until it finds the isolated keyword
while (true) {
if (pos == std::string::npos) {
// no valid instance of the keyword has been found
return false;
}
bool b_isolated_left = true, b_isolated_right = true;
if (pos > 0) {
if ( std::string("\n"+white_space+
"}").find(conf[pos-1]) ==
std::string::npos ) {
// none of the valid delimiting characters is on the left of key
b_isolated_left = false;
}
}
if (pos < conf.size()-key.size()-1) {
if ( std::string("\n"+white_space+
"{").find(conf[pos+key.size()]) ==
std::string::npos ) {
// none of the valid delimiting characters is on the right of key
b_isolated_right = false;
}
}
// check that there are matching braces between here and the end of conf
bool const b_not_within_block = brace_check(conf, pos);
bool const b_isolated = (b_isolated_left && b_isolated_right &&
b_not_within_block);
if (b_isolated) {
// found it
break;
} else {
// try the next occurrence of key
pos = conf_lower.find(key, pos+key.size());
}
}
// save the pointer for a future call (when iterating over multiple
// valid instances of the same keyword)
save_pos = pos + key.size();
// get the remainder of the line
size_t pl = conf.rfind("\n", pos);
size_t line_begin = (pl == std::string::npos) ? 0 : pos;
size_t nl = conf.find("\n", pos);
size_t line_end = (nl == std::string::npos) ? conf.size() : nl;
std::string line(conf, line_begin, (line_end-line_begin));
size_t data_begin = (to_lower_cppstr(line)).find(key) + key.size();
data_begin = line.find_first_not_of(white_space, data_begin+1);
// size_t data_begin_absolute = data_begin + line_begin;
// size_t data_end_absolute = data_begin;
if (data_begin != std::string::npos) {
size_t data_end = line.find_last_not_of(white_space) + 1;
data_end = (data_end == std::string::npos) ? line.size() : data_end;
// data_end_absolute = data_end + line_begin;
if (line.find('{', data_begin) != std::string::npos) {
size_t brace_count = 1;
size_t brace = line.find('{', data_begin); // start from the first opening brace
while (brace_count > 0) {
// find the matching closing brace
brace = line.find_first_of("{}", brace+1);
while (brace == std::string::npos) {
// add a new line
if (line_end >= conf.size()) {
cvm::error("Parse error: reached the end while "
"looking for closing brace; until now "
"the following was parsed: \"\n"+
line+"\".\n", INPUT_ERROR);
return false;
}
size_t const old_end = line.size();
// data_end_absolute += old_end+1;
line_begin = line_end;
nl = conf.find('\n', line_begin+1);
if (nl == std::string::npos)
line_end = conf.size();
else
line_end = nl;
line.append(conf, line_begin, (line_end-line_begin));
brace = line.find_first_of("{}", old_end);
}
if (line[brace] == '{') brace_count++;
if (line[brace] == '}') brace_count--;
}
// set data_begin after the opening brace
data_begin = line.find_first_of('{', data_begin) + 1;
data_begin = line.find_first_not_of(white_space,
data_begin);
// set data_end before the closing brace
data_end = brace;
data_end = line.find_last_not_of(white_space+"}",
data_end) + 1;
// data_end_absolute = line_end;
if (data_end > line.size())
data_end = line.size();
}
data.append(line, data_begin, (data_end-data_begin));
if (data.size() && save_delimiters) {
data_begin_pos.push_back(conf.find(data, pos+key.size()));
data_end_pos.push_back(data_begin_pos.back()+data.size());
// std::cerr << "key = " << key << ", data = \""
// << data << "\", data_begin, data_end = "
// << data_begin_pos.back() << ", " << data_end_pos.back()
// << "\n";
}
}
save_pos = line_end;
return true;
}
std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
{
size_t start_pos = is.tellg();
std::string read_key, next;
if ( !(is >> read_key) || !(read_key == rb.key) ||
!(is >> next) ) {
// the requested keyword has not been found, or it is not possible
// to read data after it
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if (next != "{") {
(*rb.data) = next;
return is;
}
size_t brace_count = 1;
std::string line;
while (colvarparse::getline_nocomments(is, line)) {
size_t br = 0, br_old = 0;
while ( (br = line.find_first_of("{}", br)) != std::string::npos) {
if (line[br] == '{') brace_count++;
if (line[br] == '}') brace_count--;
br_old = br;
br++;
}
if (brace_count) (*rb.data).append(line + "\n");
else {
(*rb.data).append(line, 0, br_old);
break;
}
}
if (brace_count) {
// end-of-file reached
// restore initial position
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
}
return is;
}
bool colvarparse::brace_check(std::string const &conf,
size_t const start_pos)
{
size_t brace_count = 0;
size_t brace = start_pos;
while ( (brace = conf.find_first_of("{}", brace)) != std::string::npos) {
if (conf[brace] == '{') brace_count++;
if (conf[brace] == '}') brace_count--;
brace++;
}
if (brace_count != 0)
return false;
else
return true;
}
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