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Make some CVs (PCVs and NN-based CVs) more robust.
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Return the error code earlier to prevent crashes in interactive
programs.
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@HanatoK
HanatoK committed Mar 12, 2024
1 parent f8a8b6c commit 0a6b87f
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Showing 4 changed files with 27 additions and 13 deletions.
4 changes: 4 additions & 0 deletions src/colvarcomp_apath.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,7 @@ colvar::aspath::aspath()
int colvar::aspath::init(std::string const &conf)
{
int error_code = CartesianBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;
cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
cvm::real p_lambda;
get_keyval(conf, "lambda", p_lambda, -1.0);
Expand Down Expand Up @@ -198,6 +199,7 @@ colvar::azpath::azpath()
int colvar::azpath::init(std::string const &conf)
{
int error_code = CartesianBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;
cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
x.type(colvarvalue::type_scalar);
cvm::real p_lambda;
Expand Down Expand Up @@ -252,6 +254,7 @@ colvar::aspathCV::aspathCV()
int colvar::aspathCV::init(std::string const &conf)
{
int error_code = CVBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;
cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
std::vector<cvm::real> p_weights(cv.size(), 1.0);
get_keyval(conf, "weights", p_weights, std::vector<cvm::real>(cv.size(), 1.0));
Expand Down Expand Up @@ -356,6 +359,7 @@ colvar::azpathCV::azpathCV()
int colvar::azpathCV::init(std::string const &conf)
{
int error_code = CVBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;
cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
std::vector<cvm::real> p_weights(cv.size(), 1.0);
get_keyval(conf, "weights", p_weights, std::vector<cvm::real>(cv.size(), 1.0));
Expand Down
11 changes: 6 additions & 5 deletions src/colvarcomp_combination.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ colvar::linearCombination::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) {
Expand All @@ -40,8 +41,7 @@ int colvar::linearCombination::init(std::string const &conf)
}
// Show useful error messages and prevent crashes if no sub CVC is found
if (cv.size() == 0) {
error_code |=
cvm::error("Error: the CV " + name + " expects one or more nesting components.\n",
return cvm::error("Error: the CV " + name + " expects one or more nesting components.\n",
COLVARS_INPUT_ERROR);
} else {
x.type(cv[0]->value());
Expand Down Expand Up @@ -170,6 +170,7 @@ colvar::customColvar::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;
Expand All @@ -191,7 +192,7 @@ int colvar::customColvar::init(std::string const &conf)
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()));
Expand All @@ -209,7 +210,7 @@ int colvar::customColvar::init(std::string const &conf)
}
}
} 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
Expand All @@ -234,7 +235,7 @@ int colvar::customColvar::init(std::string const &conf)
}
}
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);
Expand Down
13 changes: 11 additions & 2 deletions src/colvarcomp_gpath.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ colvar::CartesianBasedPath::CartesianBasedPath()
int colvar::CartesianBasedPath::init(std::string const &conf)
{
int error_code = cvc::init(conf);
if (error_code != COLVARS_OK) return error_code;

// Parse selected atoms
atoms = parse_group(conf, "atoms");
Expand Down Expand Up @@ -182,6 +183,7 @@ colvar::gspath::gspath()
int colvar::gspath::init(std::string const &conf)
{
int error_code = CartesianBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;

get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
if (use_second_closest_frame == true) {
Expand Down Expand Up @@ -336,6 +338,7 @@ colvar::gzpath::gzpath()
int colvar::gzpath::init(std::string const &conf)
{
int error_code = CartesianBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;

get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
if (use_second_closest_frame == true) {
Expand Down Expand Up @@ -481,6 +484,7 @@ colvar::CVBasedPath::CVBasedPath()
int colvar::CVBasedPath::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) {
Expand Down Expand Up @@ -534,6 +538,7 @@ int colvar::CVBasedPath::init(std::string const &conf)
}
} else {
error_code = cvm::error("Error: incorrect format of path file.\n", COLVARS_INPUT_ERROR);
return error_code;
}
}
if (!fields.empty()) {
Expand All @@ -546,11 +551,13 @@ int colvar::CVBasedPath::init(std::string const &conf)
error_code = cvm::error(
"Error: there is only 1 or 0 reference frame, which doesn't constitute a path.\n",
COLVARS_INPUT_ERROR);
return error_code;
}
if (cv.size() == 0) {
error_code =
cvm::error("Error: the CV " + name + " expects one or more nesting components.\n",
COLVARS_INPUT_ERROR);
return error_code;
}

use_explicit_gradients = true;
Expand Down Expand Up @@ -672,6 +679,7 @@ colvar::gspathCV::gspathCV()
int colvar::gspathCV::init(std::string const &conf)
{
int error_code = CVBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;

cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
// Initialize variables for future calculation
Expand All @@ -688,7 +696,7 @@ int colvar::gspathCV::init(std::string const &conf)
cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
}
if (total_reference_frames < 2) {
error_code |= cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) + " reference frames, but gspathCV requires at least 2 frames.\n", COLVARS_INPUT_ERROR);
return cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) + " reference frames, but gspathCV requires at least 2 frames.\n", COLVARS_INPUT_ERROR);
}
GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame);
return error_code;
Expand Down Expand Up @@ -801,6 +809,7 @@ colvar::gzpathCV::gzpathCV()
int colvar::gzpathCV::init(std::string const &conf) {

int error_code = CVBasedPath::init(conf);
if (error_code != COLVARS_OK) return error_code;

cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
// Initialize variables for future calculation
Expand All @@ -824,7 +833,7 @@ int colvar::gzpathCV::init(std::string const &conf) {
cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
}
if (total_reference_frames < 2) {
error_code |= cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) +
return cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) +
" reference frames, but gzpathCV requires at least 2 frames.\n",
COLVARS_INPUT_ERROR);
}
Expand Down
12 changes: 6 additions & 6 deletions src/colvarcomp_neuralnetwork.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ colvar::neuralNetwork::neuralNetwork()
int colvar::neuralNetwork::init(std::string const &conf)
{
int error_code = linearCombination::init(conf);
if (error_code != COLVARS_OK) return error_code;
// the output of neural network consists of multiple values
// read "output_component" key to determine it
get_keyval(conf, "output_component", m_output_index);
Expand Down Expand Up @@ -73,8 +74,7 @@ int colvar::neuralNetwork::init(std::string const &conf)
std::string function_name;
get_keyval(conf, lookup_key.c_str(), function_name, std::string(""));
if (activation_function_map.find(function_name) == activation_function_map.end()) {
error_code |=
cvm::error("Unknown activation function name: \"" + function_name + "\".\n",
return cvm::error("Unknown activation function name: \"" + function_name + "\".\n",
COLVARS_INPUT_ERROR);
}
activation_functions.push_back(std::make_pair(false, function_name));
Expand All @@ -94,7 +94,7 @@ int colvar::neuralNetwork::init(std::string const &conf)
}
// expect the three numbers are equal
if ((num_layers_weight != num_layers_bias) || (num_layers_bias != num_activation_functions)) {
error_code |= cvm::error(
return cvm::error(
"Error: the numbers of weights, biases and activation functions do not match.\n",
COLVARS_INPUT_ERROR);
}
Expand All @@ -110,7 +110,7 @@ int colvar::neuralNetwork::init(std::string const &conf)
try {
d = denseLayer(weight_files[i_layer], bias_files[i_layer], activation_functions[i_layer].second);
} catch (std::exception &ex) {
error_code |= cvm::error("Error on initializing layer " + cvm::to_str(i_layer) +
return cvm::error("Error on initializing layer " + cvm::to_str(i_layer) +
" (" + ex.what() + ")\n",
COLVARS_INPUT_ERROR);
}
Expand All @@ -122,7 +122,7 @@ int colvar::neuralNetwork::init(std::string const &conf)
try {
d = denseLayer(weight_files[i_layer], bias_files[i_layer], f, df);
} catch (std::exception &ex) {
error_code |= cvm::error("Error on initializing layer " + cvm::to_str(i_layer) +
return cvm::error("Error on initializing layer " + cvm::to_str(i_layer) +
" (" + ex.what() + ")\n",
COLVARS_INPUT_ERROR);
}
Expand All @@ -142,7 +142,7 @@ int colvar::neuralNetwork::init(std::string const &conf)
}
}
} else {
error_code |= cvm::error("Error: error on adding a new dense layer.\n", COLVARS_INPUT_ERROR);
return cvm::error("Error: error on adding a new dense layer.\n", COLVARS_INPUT_ERROR);
}
}
nn->input().resize(cv.size());
Expand Down

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