sync with GH
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15561 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -83,7 +83,9 @@ int colvarmodule::read_config_file(char const *config_filename)
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std::string conf = "";
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std::string line;
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while (colvarparse::getline_nocomments(config_s, line)) {
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conf.append(line+"\n");
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// Delete lines that contain only white space after removing comments
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if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
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conf.append(line+"\n");
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}
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config_s.close();
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@ -101,7 +103,9 @@ int colvarmodule::read_config_string(std::string const &config_str)
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std::string conf = "";
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std::string line;
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while (colvarparse::getline_nocomments(config_s, line)) {
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conf.append(line+"\n");
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// Delete lines that contain only white space after removing comments
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if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
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conf.append(line+"\n");
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}
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return parse_config(conf);
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}
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@ -302,7 +306,7 @@ int colvarmodule::parse_biases(std::string const &conf)
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size_t i;
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for (i = 0; i < biases.size(); i++) {
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biases[i]->enable(cvm::deps::f_cvb_active);
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biases[i]->enable(colvardeps::f_cvb_active);
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if (cvm::debug())
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biases[i]->print_state();
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}
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@ -310,8 +314,8 @@ int colvarmodule::parse_biases(std::string const &conf)
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size_t n_hist_dep_biases = 0;
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std::vector<std::string> hist_dep_biases_names;
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for (i = 0; i < biases.size(); i++) {
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if (biases[i]->is_enabled(cvm::deps::f_cvb_apply_force) &&
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biases[i]->is_enabled(cvm::deps::f_cvb_history_dependent)) {
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if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
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biases[i]->is_enabled(colvardeps::f_cvb_history_dependent)) {
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n_hist_dep_biases++;
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hist_dep_biases_names.push_back(biases[i]->name);
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}
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@ -340,8 +344,8 @@ int colvarmodule::parse_biases(std::string const &conf)
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int colvarmodule::catch_input_errors(int result)
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{
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if (result != COLVARS_OK || get_error()) {
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set_error_bit(result);
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set_error_bit(INPUT_ERROR);
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set_error_bits(result);
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set_error_bits(INPUT_ERROR);
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parse->init();
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return get_error();
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}
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@ -493,27 +497,27 @@ int colvarmodule::calc()
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cvm::to_str(cvm::step_absolute())+"\n");
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}
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combine_errors(error_code, calc_colvars());
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error_code |= calc_colvars();
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// set biasing forces to zero before biases are calculated and summed over
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for (std::vector<colvar *>::iterator cvi = colvars.begin();
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cvi != colvars.end(); cvi++) {
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(*cvi)->reset_bias_force();
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}
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combine_errors(error_code, calc_biases());
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combine_errors(error_code, update_colvar_forces());
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error_code |= calc_biases();
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error_code |= update_colvar_forces();
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if (cvm::b_analysis) {
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combine_errors(error_code, analyze());
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error_code |= analyze();
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}
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// write trajectory files, if needed
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if (cv_traj_freq && cv_traj_name.size()) {
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combine_errors(error_code, write_traj_files());
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error_code |= write_traj_files();
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}
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// write restart files, if needed
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if (restart_out_freq && restart_out_name.size()) {
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combine_errors(error_code, write_restart_files());
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error_code |= write_restart_files();
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}
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return error_code;
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@ -531,7 +535,7 @@ int colvarmodule::calc_colvars()
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// Determine which colvars are active at this time step
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for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
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(*cvi)->feature_states[cvm::deps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
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(*cvi)->feature_states[colvardeps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
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}
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// if SMP support is available, split up the work
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@ -551,7 +555,7 @@ int colvarmodule::calc_colvars()
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for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
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if (!(*cvi)->is_enabled()) continue;
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combine_errors(error_code, (*cvi)->update_cvc_flags());
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error_code |= (*cvi)->update_cvc_flags();
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size_t num_items = (*cvi)->num_active_cvcs();
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colvars_smp.reserve(colvars_smp.size() + num_items);
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@ -566,12 +570,12 @@ int colvarmodule::calc_colvars()
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cvm::decrease_depth();
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// calculate colvar components in parallel
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combine_errors(error_code, proxy->smp_colvars_loop());
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error_code |= proxy->smp_colvars_loop();
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cvm::increase_depth();
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for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
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if (!(*cvi)->is_enabled()) continue;
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combine_errors(error_code, (*cvi)->collect_cvc_data());
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error_code |= (*cvi)->collect_cvc_data();
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}
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cvm::decrease_depth();
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@ -581,7 +585,7 @@ int colvarmodule::calc_colvars()
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cvm::increase_depth();
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for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
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if (!(*cvi)->is_enabled()) continue;
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combine_errors(error_code, (*cvi)->calc());
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error_code |= (*cvi)->calc();
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if (cvm::get_error()) {
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return COLVARS_ERROR;
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}
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@ -589,7 +593,7 @@ int colvarmodule::calc_colvars()
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cvm::decrease_depth();
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}
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combine_errors(error_code, cvm::get_error());
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error_code |= cvm::get_error();
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return error_code;
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}
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@ -609,21 +613,21 @@ int colvarmodule::calc_biases()
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if (use_scripted_forces && !scripting_after_biases) {
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// calculate biases and scripted forces in parallel
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combine_errors(error_code, proxy->smp_biases_script_loop());
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error_code |= proxy->smp_biases_script_loop();
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} else {
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// calculate biases in parallel
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combine_errors(error_code, proxy->smp_biases_loop());
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error_code |= proxy->smp_biases_loop();
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}
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} else {
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if (use_scripted_forces && !scripting_after_biases) {
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combine_errors(error_code, calc_scripted_forces());
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error_code |= calc_scripted_forces();
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}
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cvm::increase_depth();
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for (bi = biases.begin(); bi != biases.end(); bi++) {
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combine_errors(error_code, (*bi)->update());
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error_code |= (*bi)->update();
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if (cvm::get_error()) {
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return COLVARS_ERROR;
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}
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@ -661,7 +665,7 @@ int colvarmodule::update_colvar_forces()
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cvm::decrease_depth();
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if (use_scripted_forces && scripting_after_biases) {
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combine_errors(error_code, calc_scripted_forces());
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error_code |= calc_scripted_forces();
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}
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cvm::real total_colvar_energy = 0.0;
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@ -689,7 +693,7 @@ int colvarmodule::update_colvar_forces()
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cvm::log("Communicating forces from the colvars to the atoms.\n");
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cvm::increase_depth();
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for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
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if ((*cvi)->is_enabled(cvm::deps::f_cv_gradient)) {
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if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
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if (!(*cvi)->is_enabled()) continue;
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(*cvi)->communicate_forces();
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if (cvm::get_error()) {
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@ -913,17 +917,17 @@ int colvarmodule::setup_output()
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std::string(""));
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if (cv_traj_freq && cv_traj_name.size()) {
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combine_errors(error_code, open_traj_file(cv_traj_name));
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error_code |= open_traj_file(cv_traj_name);
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}
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for (std::vector<colvarbias *>::iterator bi = biases.begin();
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bi != biases.end();
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bi++) {
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combine_errors(error_code, (*bi)->setup_output());
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error_code |= (*bi)->setup_output();
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}
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if (error_code != COLVARS_OK || cvm::get_error()) {
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set_error_bit(FILE_ERROR);
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set_error_bits(FILE_ERROR);
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}
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return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
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@ -1259,29 +1263,20 @@ size_t & cvm::depth()
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}
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void colvarmodule::set_error_bit(int code)
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void colvarmodule::set_error_bits(int code)
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{
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if (code > 0) {
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cvm::fatal_error("Error: set_error_bit() received positive error code.\n");
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if (code < 0) {
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cvm::fatal_error("Error: set_error_bits() received negative error code.\n");
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return;
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}
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proxy->smp_lock();
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errorCode = -1 * ((-1 * errorCode) | (-1 * code) | (-1 * COLVARS_ERROR));
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errorCode |= code | COLVARS_ERROR;
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proxy->smp_unlock();
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}
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bool colvarmodule::get_error_bit(int code)
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{
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return bool((-1 * errorCode) & (-1 * code));
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}
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void colvarmodule::combine_errors(int &target, int const code)
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{
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if (code > 0 || target > 0) {
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cvm::fatal_error("Error: combine_errors() received positive error code.\n");
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return;
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}
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target = -1 * ((-1 * target) | (-1 * code));
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return bool(errorCode & code);
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}
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void colvarmodule::clear_error()
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@ -1294,7 +1289,7 @@ void colvarmodule::clear_error()
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void cvm::error(std::string const &message, int code)
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{
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set_error_bit(code);
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set_error_bits(code);
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proxy->error(message);
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}
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@ -1303,7 +1298,7 @@ void cvm::fatal_error(std::string const &message)
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{
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// TODO once all non-fatal errors have been set to be handled by error(),
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// set DELETE_COLVARS here for VMD to handle it
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set_error_bit(FATAL_ERROR);
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set_error_bits(FATAL_ERROR);
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proxy->fatal_error(message);
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}
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