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Update Colvars library to version 2024-06-04

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This commit is contained in:
Giacomo Fiorin
2024-08-06 01:07:43 +02:00
parent 278accd9ea
commit 133dee9ac1
74 changed files with 7343 additions and 4676 deletions
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96
lib/colvars/colvarcomp_combination.cpp
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@ -1,4 +1,4 @@
#if (__cplusplus >= 201103L)
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
@ -9,14 +9,26 @@
#include "colvarcomp.h"
colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) {
colvar::linearCombination::linearCombination()
{
set_function_type("linearCombination");
}
int colvar::linearCombination::init(std::string const &conf)
{
int error_code = cvc::init(conf);
if (error_code != COLVARS_OK) return error_code;
// Lookup all available sub-cvcs
for (auto it_cv_map = colvar::get_global_cvc_map().begin(); it_cv_map != colvar::get_global_cvc_map().end(); ++it_cv_map) {
if (key_lookup(conf, it_cv_map->first.c_str())) {
std::vector<std::string> sub_cvc_confs;
get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
cv.push_back((it_cv_map->second)());
cv.back()->init(*(it_sub_cvc_conf));
}
}
}
@ -29,26 +41,11 @@ colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf)
}
// Show useful error messages and prevent crashes if no sub CVC is found
if (cv.size() == 0) {
cvm::error("Error: the CV " + name +
" expects one or more nesting components.\n");
return;
return cvm::error("Error: the CV " + name + " expects one or more nesting components.\n",
COLVARS_INPUT_ERROR);
} else {
// TODO: Maybe we can add an option to allow mixing scalar and vector types,
// but that's a bit complicated so we just require a consistent type
// of nesting CVs.
x.type(cv[0]->value());
x.reset();
for (size_t i_cv = 1; i_cv < cv.size(); ++i_cv) {
const auto type_i = cv[i_cv]->value().type();
if (type_i != x.type()) {
cvm::error("Error: the type of sub-CVC " + cv[i_cv]->name +
" is " + colvarvalue::type_desc(type_i) + ", which is "
"different to the type of the first sub-CVC. Currently "
"only sub-CVCs of the same type are supported to be "
"nested.\n");
return;
}
}
}
use_explicit_gradients = true;
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
@ -59,6 +56,7 @@ colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf)
if (!use_explicit_gradients) {
disable(f_cvc_explicit_gradient);
}
return error_code;
}
cvm::real colvar::linearCombination::getPolynomialFactorOfCVGradient(size_t i_cv) const {
@ -138,8 +136,42 @@ void colvar::linearCombination::apply_force(colvarvalue const &force) {
}
}
colvar::customColvar::customColvar(std::string const &conf): linearCombination(conf) {
use_custom_function = false;
cvm::real colvar::linearCombination::dist2(colvarvalue const &x1, colvarvalue const &x2) const
{
return x1.dist2(x2);
}
colvarvalue colvar::linearCombination::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.dist2_grad(x2);
}
colvarvalue colvar::linearCombination::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x2.dist2_grad(x1);
}
void colvar::linearCombination::wrap(colvarvalue & /* x_unwrapped */) const {}
colvar::customColvar::customColvar()
{
set_function_type("customColvar");
}
int colvar::customColvar::init(std::string const &conf)
{
int error_code = linearCombination::init(conf);
if (error_code != COLVARS_OK) return error_code;
// code swipe from colvar::init_custom_function
std::string expr_in, expr;
size_t pos = 0; // current position in config string
@ -160,7 +192,7 @@ colvar::customColvar::customColvar(std::string const &conf): linearCombination(c
pexpr = Lepton::Parser::parse(expr);
pexprs.push_back(pexpr);
} catch (...) {
cvm::error("Error parsing expression \"" + expr + "\".\n", COLVARS_INPUT_ERROR);
return cvm::error("Error parsing expression \"" + expr + "\".\n", COLVARS_INPUT_ERROR);
}
try {
value_evaluators.push_back(new Lepton::CompiledExpression(pexpr.createCompiledExpression()));
@ -178,7 +210,7 @@ colvar::customColvar::customColvar(std::string const &conf): linearCombination(c
}
}
} catch (...) {
cvm::error("Error compiling expression \"" + expr + "\".\n", COLVARS_INPUT_ERROR);
return cvm::error("Error compiling expression \"" + expr + "\".\n", COLVARS_INPUT_ERROR);
}
} while (key_lookup(conf, "customFunction", &expr_in, &pos));
// Now define derivative with respect to each scalar sub-component
@ -203,7 +235,7 @@ colvar::customColvar::customColvar(std::string const &conf): linearCombination(c
}
}
if (value_evaluators.size() == 0) {
cvm::error("Error: no custom function defined.\n", COLVARS_INPUT_ERROR);
return cvm::error("Error: no custom function defined.\n", COLVARS_INPUT_ERROR);
}
if (value_evaluators.size() != 1) {
x.type(colvarvalue::type_vector);
@ -211,14 +243,17 @@ colvar::customColvar::customColvar(std::string const &conf): linearCombination(c
x.type(colvarvalue::type_scalar);
}
#else
cvm::error("customFunction requires the Lepton library, but it is not enabled during compilation.\n"
"Please refer to the Compilation Notes section of the Colvars manual for more information.\n",
COLVARS_INPUT_ERROR);
return cvm::error(
"customFunction requires the Lepton library, but it is not enabled during compilation.\n"
"Please refer to the Compilation Notes section of the Colvars manual for more "
"information.\n",
COLVARS_NOT_IMPLEMENTED);
#endif
} else {
cvm::log("Warning: no customFunction specified.\n");
cvm::log("Warning: use linear combination instead.\n");
}
return error_code;
}
colvar::customColvar::~customColvar() {
@ -317,7 +352,8 @@ void colvar::customColvar::apply_force(colvarvalue const &force) {
}
} else {
const colvarvalue& current_cv_value = cv[i_cv]->value();
colvarvalue cv_force(current_cv_value.type());
colvarvalue cv_force(current_cv_value);
cv_force.reset();
const cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
for (size_t j_elem = 0; j_elem < current_cv_value.size(); ++j_elem) {
for (size_t c = 0; c < x.size(); ++c) {
@ -340,5 +376,3 @@ void colvar::customColvar::apply_force(colvarvalue const &force) {
#endif
}
}
#endif // __cplusplus >= 201103L