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Update Colvars to version 2022-05-09

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This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.

Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).

Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers.  Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.

The following pull requests in the Colvars repository are relevant to LAMMPS:

- 475 Remove fatal error condition
  https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)

- 474 Allow normalizing eigenvector vector components to deal with unit change
  https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)

- 470 Better error handling in the initialization of NeuralNetwork CV
  https://github.com/Colvars/colvars/pull/470 (@HanatoK)

- 468 Add examples of histogram configuration, with and without explicit grid parameters
  https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)

- 464 Fix #463 using more fine-grained features
  https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)

- 447 [RFC] New option "scaledBiasingForce" for colvarbias
  https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)

- 444 [RFC] Implementation of dense neural network as CV
  https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)

- 443 Fix explicit gradient dependency of sub-CVs
  https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)

- 442 Persistent bias count
  https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)

- 437 Return type of bias from scripting interface
  https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)

- 434 More flexible use of boundaries from colvars by grids
  https://github.com/Colvars/colvars/pull/434 (@jhenin)

- 433 Prevent double-free in linearCombination
  https://github.com/Colvars/colvars/pull/433 (@HanatoK)

- 428 More complete documentation for index file format (NDX)
  https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)

- 426 Integrate functional version of backup_file() into base proxy class
  https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)

- 424 Track CVC inheritance when documenting feature usage
  https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)

- 419 Generate citation report while running computations
  https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)

- 415 Rebin metadynamics bias from explicit hills when available
  https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)

- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
  https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)

Authors: @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
2022-05-10 11:24:54 -04:00
parent 4737b9efb7
commit 1220bea011
66 changed files with 4040 additions and 1221 deletions
Download Patch File Download Diff File Expand all files Collapse all files

68
lib/colvars/colvarparse.cpp
View File

@ -33,12 +33,14 @@ namespace {
colvarparse::colvarparse()
: keyword_delimiters_left("\n"+std::string(white_space)+"}"),
keyword_delimiters_right("\n"+std::string(white_space)+"{")
{
init();
colvarparse::clear();
}
void colvarparse::init()
void colvarparse::clear()
{
config_string.clear();
clear_keyword_registry();
@ -46,15 +48,17 @@ void colvarparse::init()
colvarparse::colvarparse(const std::string& conf)
: keyword_delimiters_left("\n"+std::string(white_space)+"}"),
keyword_delimiters_right("\n"+std::string(white_space)+"{")
{
init(conf);
colvarparse::set_string(conf);
}
void colvarparse::init(std::string const &conf)
void colvarparse::set_string(std::string const &conf)
{
if (! config_string.size()) {
init();
colvarparse::clear();
config_string = conf;
}
}
@ -62,7 +66,7 @@ void colvarparse::init(std::string const &conf)
colvarparse::~colvarparse()
{
init();
colvarparse::clear();
}
@ -86,7 +90,7 @@ bool colvarparse::get_key_string_value(std::string const &conf,
if (found_count > 1) {
cvm::error("Error: found more than one instance of \""+
std::string(key)+"\".\n", INPUT_ERROR);
std::string(key)+"\".\n", COLVARS_INPUT_ERROR);
}
return b_found_any;
@ -153,10 +157,10 @@ void colvarparse::error_key_required(std::string const &key_str,
}
if (parse_mode & parse_restart) {
cvm::error("Error: keyword \""+key_str+
"\" is missing from the restart.\n", INPUT_ERROR);
"\" is missing from the restart.\n", COLVARS_INPUT_ERROR);
} else {
cvm::error("Error: keyword \""+key_str+
"\" is required.\n", INPUT_ERROR);
"\" is required.\n", COLVARS_INPUT_ERROR);
}
}
@ -178,13 +182,13 @@ int colvarparse::_get_keyval_scalar_value_(std::string const &key_str,
if (value_count == 0) {
return cvm::error("Error: in parsing \""+
key_str+"\".\n", INPUT_ERROR);
key_str+"\".\n", COLVARS_INPUT_ERROR);
}
if (value_count > 1) {
return cvm::error("Error: multiple values "
"are not allowed for keyword \""+
key_str+"\".\n", INPUT_ERROR);
key_str+"\".\n", COLVARS_INPUT_ERROR);
}
return COLVARS_OK;
@ -207,7 +211,7 @@ int colvarparse::_get_keyval_scalar_value_(std::string const &key_str,
set_bool(reinterpret_cast<void *>(&value), false);
} else {
return cvm::error("Error: boolean values only are allowed "
"for \""+key_str+"\".\n", INPUT_ERROR);
"for \""+key_str+"\".\n", COLVARS_INPUT_ERROR);
}
return COLVARS_OK;
}
@ -219,7 +223,7 @@ int colvarparse::_get_keyval_scalar_novalue_(std::string const &key_str,
Parse_Mode const & /* parse_mode */)
{
return cvm::error("Error: improper or missing value "
"for \""+key_str+"\".\n", INPUT_ERROR);
"for \""+key_str+"\".\n", COLVARS_INPUT_ERROR);
}
template<>
@ -318,7 +322,7 @@ bool colvarparse::_get_keyval_vector_(std::string const &conf,
values[i] = x;
} else {
cvm::error("Error: in parsing \""+
key_str+"\".\n", INPUT_ERROR);
key_str+"\".\n", COLVARS_INPUT_ERROR);
}
}
}
@ -329,13 +333,13 @@ bool colvarparse::_get_keyval_vector_(std::string const &conf,
if (b_found_any) {
cvm::error("Error: improper or missing values for \""+
key_str+"\".\n", INPUT_ERROR);
key_str+"\".\n", COLVARS_INPUT_ERROR);
} else {
if ((values.size() > 0) && (values.size() != def_values.size())) {
cvm::error("Error: the number of default values for \""+
key_str+"\" is different from the number of "
"current values.\n", BUG_ERROR);
"current values.\n", COLVARS_BUG_ERROR);
}
if (parse_mode & parse_required) {
@ -621,8 +625,8 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
}
if (!found_keyword) {
cvm::error("Error: keyword \""+uk+"\" is not supported, "
"or not recognized in this context.\n", INPUT_ERROR);
return INPUT_ERROR;
"or not recognized in this context.\n", COLVARS_INPUT_ERROR);
return COLVARS_INPUT_ERROR;
}
}
@ -699,18 +703,26 @@ bool colvarparse::key_lookup(std::string const &conf,
bool b_isolated_left = true, b_isolated_right = true;
if (pos > 0) {
if ( std::string("\n"+std::string(white_space)+
"}").find(conf[pos-1]) ==
std::string::npos ) {
if (keyword_delimiters_left.find(conf[pos-1]) == std::string::npos) {
// none of the valid delimiting characters is on the left of key
b_isolated_left = false;
} else {
size_t const pl = conf_lower.rfind("\n", pos);
size_t const line_begin = (pl == std::string::npos) ? 0 : pl+1;
size_t const pchar =
conf_lower.find_first_not_of(keyword_delimiters_left, line_begin);
size_t const first_text = (pchar == std::string::npos) ? pos : pchar;
if (first_text < pos) {
// There are some non-delimiting characters to the left of the
// keyword on the same line
b_isolated_left = false;
}
}
}
if (pos < conf.size()-key.size()-1) {
if ( std::string("\n"+std::string(white_space)+
"{").find(conf[pos+key.size()]) ==
std::string::npos ) {
if (keyword_delimiters_right.find(conf[pos+key.size()]) ==
std::string::npos) {
// none of the valid delimiting characters is on the right of key
b_isolated_right = false;
}
@ -739,7 +751,7 @@ bool colvarparse::key_lookup(std::string const &conf,
// 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 line_begin = (pl == std::string::npos) ? 0 : pl+1;
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));
@ -792,7 +804,7 @@ bool colvarparse::key_lookup(std::string const &conf,
cvm::error("Parse error: reached the end while "
"looking for closing brace; until now "
"the following was parsed: \"\n"+
line+"\".\n", INPUT_ERROR);
line+"\".\n", COLVARS_INPUT_ERROR);
return false;
}
@ -810,7 +822,7 @@ bool colvarparse::key_lookup(std::string const &conf,
}
if (brace_count < 0) {
cvm::error("Error: found closing brace without opening brace.\n", INPUT_ERROR);
cvm::error("Error: found closing brace without opening brace.\n", COLVARS_INPUT_ERROR);
}
}
@ -920,7 +932,7 @@ int colvarparse::check_braces(std::string const &conf,
if (conf[brace] == '}') brace_count--;
brace++;
}
return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK;
return (brace_count != 0) ? COLVARS_INPUT_ERROR : COLVARS_OK;
}