| version 1.20 | version 1.21 |
|---|
| |
| target_dist = NULL; | target_dist = NULL; |
| get_keyval(conf, "ebMeta", ebmeta, false); | get_keyval(conf, "ebMeta", ebmeta, false); |
| if(ebmeta){ | if(ebmeta){ |
| | if (use_grids && expand_grids) { |
| | cvm::fatal_error("Error: expandBoundaries is not supported with " |
| | "ebMeta please allocate wide enough boundaries for " |
| | "each colvar ahead of time and set targetdistfile " |
| | "accordingly. \n"); |
| | } |
| target_dist = new colvar_grid_scalar(); | target_dist = new colvar_grid_scalar(); |
| target_dist->init_from_colvars(colvars); | target_dist->init_from_colvars(colvars); |
| get_keyval(conf, "targetdistfile", target_dist_file); | get_keyval(conf, "targetdistfile", target_dist_file); |
| std::ifstream targetdiststream(target_dist_file.c_str()); | std::ifstream targetdiststream(target_dist_file.c_str()); |
| target_dist->read_multicol(targetdiststream); | target_dist->read_multicol(targetdiststream); |
| | cvm::real min_val = target_dist->minimum_value(); |
| | if(min_val<0){ |
| | cvm::error("Error: Target distribution of ebMeta " |
| | "has negative values!.\n", INPUT_ERROR); |
| | } |
| | cvm::real min_pos_val = target_dist->minimum_pos_value(); |
| | if(min_pos_val<=0){ |
| | cvm::error("Error: Target distribution of ebMeta has negative " |
| | "or zero minimum positive value!.\n", INPUT_ERROR); |
| | } |
| | if(min_val==0){ |
| | cvm::log("WARNING: Target distribution has zero values.\n"); |
| | cvm::log("Zeros will be converted to the minimum positive value.\n"); |
| | target_dist->remove_zeros(min_pos_val); |
| | } |
| // normalize target distribution and multiply by effective volume = exp(differential entropy) | // normalize target distribution and multiply by effective volume = exp(differential entropy) |
| target_dist->multiply_constant(1.0/target_dist->integral()); | target_dist->multiply_constant(1.0/target_dist->integral()); |
| cvm::real volume = std::exp(target_dist->entropy()); | cvm::real volume = std::exp(target_dist->entropy()); |
| |
| | |
| if (ebmeta) { | if (ebmeta) { |
| hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index()); | hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index()); |
| if(cvm::step_absolute() <= ebmeta_equil_steps) { | if(cvm::step_absolute() <= long(ebmeta_equil_steps)) { |
| cvm::real const hills_lambda=(cvm::real(ebmeta_equil_steps - cvm::step_absolute()))/(cvm::real(ebmeta_equil_steps)); | cvm::real const hills_lambda = |
| | (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) / |
| | (cvm::real(ebmeta_equil_steps)); |
| hills_scale = hills_lambda + (1-hills_lambda)*hills_scale; | hills_scale = hills_lambda + (1-hills_lambda)*hills_scale; |
| } | } |
| } | } |