update colvars library to version 2016-07-05

lib/colvars/colvarbias.cpp

@@ -172,6 +172,7 @@ int colvarbias::add_colvar(std::string const &cv_name)
 int colvarbias::update()
 {
   // Note: if anything is added here, it should be added also in the SMP block of calc_biases()
+  // TODO move here debug msg of bias update
   has_data = true;
   return COLVARS_OK;
 }

lib/colvars/colvarbias_abf.cpp

@@ -20,6 +20,8 @@ int colvarbias_abf::init(std::string const &conf)
 {
   colvarbias::init(conf);
 
+  provide(f_cvb_history_dependent);
+
   // TODO relax this in case of VMD plugin
   if (cvm::temperature() == 0.0)
     cvm::log("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");
@@ -27,10 +29,18 @@ int colvarbias_abf::init(std::string const &conf)
   // ************* parsing general ABF options ***********************
 
   get_keyval(conf, "applyBias",  apply_bias, true);
-  if (!apply_bias) cvm::log("WARNING: ABF biases will *not* be applied!\n");
+  if (apply_bias) {
+    enable(f_cvb_apply_force);
+  } else {
+    cvm::log("WARNING: ABF biases will *not* be applied!\n");
+  }
 
   get_keyval(conf, "updateBias",  update_bias, true);
-  if (!update_bias) cvm::log("WARNING: ABF biases will *not* be updated!\n");
+  if (update_bias) {
+    enable(f_cvb_history_dependent);
+  } else {
+    cvm::log("WARNING: ABF biases will *not* be updated!\n");
+  }
 
   get_keyval(conf, "hideJacobian", hide_Jacobian, false);
   if (hide_Jacobian) {
@@ -44,7 +54,7 @@ int colvarbias_abf::init(std::string const &conf)
   min_samples = full_samples / 2;
   // full_samples - min_samples >= 1 is guaranteed
 
-  get_keyval(conf, "inputPrefix",  input_prefix, std::vector<std::string> ());
+  get_keyval(conf, "inputPrefix",  input_prefix, std::vector<std::string>());
   get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
   get_keyval(conf, "historyFreq", history_freq, 0);
   b_history_files = (history_freq > 0);

lib/colvars/colvarbias_alb.cpp

@@ -33,6 +33,8 @@ int colvarbias_alb::init(std::string const &conf)
 {
   colvarbias::init(conf);
 
+  provide(f_cvb_history_dependent);
+
   size_t i;
 
   // get the initial restraint centers
@@ -82,6 +84,8 @@ int colvarbias_alb::init(std::string const &conf)
   if (update_freq == 0)
     cvm::fatal_error("Error: must set updateFrequency to greater than 2.\n");
 
+  enable(f_cvb_history_dependent);
+
   get_keyval(conf, "outputCenters", b_output_centers, false);
   get_keyval(conf, "outputGradient", b_output_grad, false);
   get_keyval(conf, "outputCoupling", b_output_coupling, true);

lib/colvars/colvarbias_histogram.cpp

@@ -17,6 +17,9 @@ int colvarbias_histogram::init(std::string const &conf)
 {
   colvarbias::init(conf);
 
+  provide(f_cvb_history_dependent);
+  enable(f_cvb_history_dependent);
+
   size_t i;
 
   get_keyval(conf, "outputFile", out_name, std::string(""));
@@ -82,7 +85,6 @@ int colvarbias_histogram::init(std::string const &conf)
     }
   }
 
-  cvm::log("Finished histogram setup.\n");
   return COLVARS_OK;
 }
 
@@ -132,7 +134,7 @@ int colvarbias_histogram::update()
     // update indices for scalar values
     size_t i;
     for (i = 0; i < colvars.size(); i++) {
-      bin[i] = grid->value_to_bin_scalar(colvars[i]->value(), i);
+      bin[i] = grid->current_bin_scalar(i);
     }
 
     if (grid->index_ok(bin)) {
@@ -143,7 +145,7 @@ int colvarbias_histogram::update()
     size_t iv, i;
     for (iv = 0; iv < colvar_array_size; iv++) {
       for (i = 0; i < colvars.size(); i++) {
-        bin[i] = grid->value_to_bin_scalar(colvars[i]->value().vector1d_value[iv], i);
+        bin[i] = grid->current_bin_scalar(i, iv);
       }
 
       if (grid->index_ok(bin)) {

lib/colvars/colvarbias_meta.cpp

@@ -37,18 +37,26 @@ int colvarbias_meta::init(std::string const &conf)
 {
   colvarbias::init(conf);
 
-  // TODO this relies on having initialized biases in alphabetical order
-  if (cvm::n_abf_biases > 0)
-    cvm::log("Warning: running ABF and metadynamics together is not recommended unless applyBias is off for ABF.\n");
+  provide(f_cvb_history_dependent);
 
   get_keyval(conf, "hillWeight", hill_weight, 0.0);
-  if (hill_weight <= 0.0) {
+  if (hill_weight > 0.0) {
+    enable(f_cvb_apply_force);
+  } else {
     cvm::error("Error: hillWeight must be provided, and a positive number.\n", INPUT_ERROR);
   }
 
   get_keyval(conf, "newHillFrequency", new_hill_freq, 1000);
+  if (new_hill_freq > 0) {
+    enable(f_cvb_history_dependent);
+  }
 
   get_keyval(conf, "hillWidth", hill_width, std::sqrt(2.0 * PI) / 2.0);
+  cvm::log("Half-widths of the Gaussian hills (sigma's):\n");
+  for (size_t i = 0; i < colvars.size(); i++) {
+    cvm::log(colvars[i]->name+std::string(": ")+
+             cvm::to_str(0.5 * colvars[i]->width * hill_width));
+  }
 
   {
     bool b_replicas = false;

lib/colvars/colvarbias_restraint.cpp

@@ -563,6 +563,7 @@ cvm::real colvarbias_restraint_harmonic::restraint_convert_k(cvm::real k,
 }
 
 
+
 colvarbias_restraint_linear::colvarbias_restraint_linear(char const *key)
   : colvarbias_restraint(key)
 {

lib/colvars/colvardeps.cpp

@@ -210,6 +210,8 @@ void cvm::deps::init_cvb_requires() {
   f_description(f_cvb_get_system_force, "obtain system force");
   f_req_children(f_cvb_get_system_force, f_cv_system_force);
 
+  f_description(f_cvb_history_dependent, "history-dependent");
+
   // Initialize feature_states for each instance
   feature_states.reserve(f_cvb_ntot);
   for (i = 0; i < f_cvb_ntot; i++) {
@@ -217,6 +219,9 @@ void cvm::deps::init_cvb_requires() {
     // Most features are available, so we set them so
     // and list exceptions below
   }
+
+  // some biases are not history-dependent
+  feature_states[f_cvb_history_dependent]->available = false;
 }
 
 

lib/colvars/colvardeps.h

@@ -147,8 +147,9 @@ public:
   enum features_biases {
     /// \brief Bias is active
     f_cvb_active,
-    f_cvb_apply_force,
-    f_cvb_get_system_force,
+    f_cvb_apply_force, // will apply forces
+    f_cvb_get_system_force, // requires system forces
+    f_cvb_history_dependent, // depends on simulation history
     f_cvb_ntot
   };
 

lib/colvars/colvargrid.h

@@ -368,6 +368,14 @@ public:
     return value_to_bin_scalar(actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i);
   }
 
+  /// \brief Report the bin corresponding to the current value of item iv in variable i
+  inline int current_bin_scalar(int const i, int const iv) const
+  {
+    return value_to_bin_scalar(actual_value[i] ?
+        cv[i]->actual_value().vector1d_value[iv] :
+        cv[i]->value().vector1d_value[iv], i);
+  }
+
   /// \brief Use the lower boundary and the width to report which bin
   /// the provided value is in
   inline int value_to_bin_scalar(colvarvalue const &value, const int i) const

lib/colvars/colvarmodule.cpp

@@ -299,12 +299,27 @@ int colvarmodule::parse_biases(std::string const &conf)
     cvm::decrease_depth();
   }
 
-  for (size_t i = 0; i < biases.size(); i++) {
+  size_t i;
+
+  for (i = 0; i < biases.size(); i++) {
     biases[i]->enable(cvm::deps::f_cvb_active);
     if (cvm::debug())
       biases[i]->print_state();
   }
 
+  size_t n_hist_dep_biases = 0;
+  for (i = 0; i < biases.size(); i++) {
+    if (biases[i]->is_enabled(cvm::deps::f_cvb_apply_force) &&
+        biases[i]->is_enabled(cvm::deps::f_cvb_history_dependent)) {
+      n_hist_dep_biases++;
+    }
+  }
+  if (n_hist_dep_biases) {
+    cvm::log("WARNING: there are "+cvm::to_str(n_hist_dep_biases)+
+             " history-dependent biases with non-zero force parameters; "
+             "please make sure that their forces do not counteract each other.\n");
+  }
+
   if (biases.size() || use_scripted_forces) {
     cvm::log(cvm::line_marker);
     cvm::log("Collective variables biases initialized, "+

lib/colvars/colvarmodule.h

@@ -4,7 +4,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-06-23"
+#define COLVARS_VERSION "2016-07-05"
 #endif
 
 #ifndef COLVARS_DEBUG