Difference for src/colvarmodule.C from version 1.29 to 1.30

version 1.29version 1.30
Line 210
Line 210
     catch_input_errors(parse_global_params(extra_conf));     catch_input_errors(parse_global_params(extra_conf));
     catch_input_errors(parse_colvars(extra_conf));     catch_input_errors(parse_colvars(extra_conf));
     catch_input_errors(parse_biases(extra_conf));     catch_input_errors(parse_biases(extra_conf));
      parse->check_keywords(extra_conf, "colvarmodule");
     extra_conf.clear();     extra_conf.clear();
     if (get_error() != COLVARS_OK) return get_error();     if (get_error() != COLVARS_OK) return get_error();
   }   }
Line 672
Line 673
   variables_active()->resize(0);   variables_active()->resize(0);
   variables_active()->reserve(variables()->size());   variables_active()->reserve(variables()->size());
   for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {   for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
     (*cvi)->feature_states[colvardeps::f_cv_active]->enabled =     (*cvi)->set_enabled(colvardeps::f_cv_active,
       (step_absolute() % (*cvi)->get_time_step_factor() == 0);       step_absolute() % (*cvi)->get_time_step_factor() == 0);
     variables_active()->push_back(*cvi);     variables_active()->push_back(*cvi);
   }   }
  
Line 741
Line 742
   std::vector<colvarbias *>::iterator bi;   std::vector<colvarbias *>::iterator bi;
   int error_code = COLVARS_OK;   int error_code = COLVARS_OK;
  
    // Total bias energy is reset before calling scripted biases
    total_bias_energy = 0.0;
  
   // update the list of active biases   // update the list of active biases
   biases_active()->resize(0);   biases_active()->resize(0);
   biases_active()->reserve(biases.size());   biases_active()->reserve(biases.size());
Line 777
Line 781
     cvm::decrease_depth();     cvm::decrease_depth();
   }   }
  
   cvm::real total_bias_energy = 0.0; 
   for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {   for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
     total_bias_energy += (*bi)->get_energy();     total_bias_energy += (*bi)->get_energy();
   }   }
  
   if (cvm::debug()) 
     cvm::log("Adding total bias energy: " + cvm::to_str(total_bias_energy) + "\n"); 
   proxy->add_energy(total_bias_energy); 
   return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);   return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
 } }
  
Line 812
Line 812
     error_code |= calc_scripted_forces();     error_code |= calc_scripted_forces();
   }   }
  
    // Now we have collected energies from both built-in and scripted biases
    if (cvm::debug())
      cvm::log("Adding total bias energy: " + cvm::to_str(total_bias_energy) + "\n");
    proxy->add_energy(total_bias_energy);
  
   cvm::real total_colvar_energy = 0.0;   cvm::real total_colvar_energy = 0.0;
   // sum up the forces for each colvar, including wall forces   // sum up the forces for each colvar, including wall forces
   // and integrate any internal   // and integrate any internal


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changed lines
 Added in v.1.30



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