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update colvars to version of 2016-04-20

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This commit is contained in:
Axel Kohlmeyer
2016-04-22 20:50:51 -04:00
parent ec9977f788
commit 5f0578f95a
17 changed files with 236 additions and 211 deletions
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36
lib/colvars/colvar.cpp
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@ -649,7 +649,7 @@ int colvar::parse_analysis(std::string const &conf)
} else {
cvm::log("Unknown type of correlation function, \""+
acf_type_str+"\".\n");
cvm::set_error_bits(INPUT_ERROR);
cvm::set_error_bit(INPUT_ERROR);
}
get_keyval(conf, "corrFuncOffset", acf_offset, 0);
@ -720,11 +720,11 @@ int colvar::calc()
// Note: if anything is added here, it should be added also in the SMP block of calc_colvars()
int error_code = COLVARS_OK;
if (is_enabled(f_cv_active)) {
error_code |= update_cvc_flags();
error_code |= calc_cvcs();
error_code |= collect_cvc_data();
cvm::combine_errors(error_code, update_cvc_flags());
cvm::combine_errors(error_code, calc_cvcs());
cvm::combine_errors(error_code, collect_cvc_data());
}
return COLVARS_OK;
return error_code;
}
@ -735,15 +735,15 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
cvm::log("Calculating colvar \""+this->name+"\", components "+
cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");
error_code |= check_cvc_range(first_cvc, num_cvcs);
cvm::combine_errors(error_code, check_cvc_range(first_cvc, num_cvcs));
if (error_code != COLVARS_OK) {
return error_code;
}
error_code |= calc_cvc_values(first_cvc, num_cvcs);
error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
error_code |= calc_cvc_sys_forces(first_cvc, num_cvcs);
error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
cvm::combine_errors(error_code, calc_cvc_values(first_cvc, num_cvcs));
cvm::combine_errors(error_code, calc_cvc_gradients(first_cvc, num_cvcs));
cvm::combine_errors(error_code, calc_cvc_sys_forces(first_cvc, num_cvcs));
cvm::combine_errors(error_code, calc_cvc_Jacobians(first_cvc, num_cvcs));
if (cvm::debug())
cvm::log("Done calculating colvar \""+this->name+"\".\n");
@ -759,12 +759,12 @@ int colvar::collect_cvc_data()
int error_code = COLVARS_OK;
error_code |= collect_cvc_values();
error_code |= collect_cvc_gradients();
error_code |= collect_cvc_sys_forces();
error_code |= collect_cvc_Jacobians();
cvm::combine_errors(error_code, collect_cvc_values());
cvm::combine_errors(error_code, collect_cvc_gradients());
cvm::combine_errors(error_code, collect_cvc_sys_forces());
cvm::combine_errors(error_code, collect_cvc_Jacobians());
error_code |= calc_colvar_properties();
cvm::combine_errors(error_code, calc_colvar_properties());
if (cvm::debug())
cvm::log("Done calculating colvar \""+this->name+"\"'s properties.\n");
@ -879,6 +879,10 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
cvcs[i]->atom_groups[ig]->calc_fit_gradients();
if (cvcs[i]->is_enabled(f_cvc_debug_gradient)) {
cvcs[i]->debug_gradients(cvcs[i]->atom_groups[ig]);
}
}
}
cvm::decrease_depth();
@ -1297,7 +1301,7 @@ bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) c
if ( (!is_enabled(f_cv_lower_boundary)) || (!is_enabled(f_cv_upper_boundary)) ) {
cvm::log("Error: checking periodicity for collective variable \""+this->name+"\" "
"requires lower and upper boundaries to be defined.\n");
cvm::set_error_bits(INPUT_ERROR);
cvm::set_error_bit(INPUT_ERROR);
}
if (period > 0.0) {