From 94fdd3103c1a8d8a59e4d8437c22eaf36cf0a728 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Fri, 2 Dec 2022 11:03:30 +0100
Subject: [PATCH 01/13] First version of NAMD lambda-dynamics

Save pointer to NAMD Controller in proxy

this is necessary for accessing the Controller from threads other than 0

Simplify accelMD call

Use alch lambda value from state file

Dependencies updates and fixes

- distinguish f_cv_gradient and f_cv_apply_force
- rename external cvs "driven"
- fix bug where error messages were not informative for complex
dependency resolution failures

Lambda-dynamics improvements

- add total_force_current_step feature
- follow lambda value from back-end

Remove unused variables

Enable scriptedColvarforces in ABMD script

Allow scripted forces on external param

Print unscaled biasing force in MTS
---
 colvartools/abmd.tcl               |  2 +-
 namd/src/colvarproxy_namd.C        | 57 +++++++++++++++++++----
 namd/src/colvarproxy_namd.h        | 15 ++++++
 src/colvar.cpp                     | 75 ++++++++++++++++++++----------
 src/colvar.h                       |  2 +-
 src/colvarbias.cpp                 | 11 +++--
 src/colvarbias_abf.cpp             | 41 ++++++++--------
 src/colvarcomp.cpp                 |  3 +-
 src/colvarcomp.h                   |  3 +-
 src/colvarcomp_alchlambda.cpp      | 32 ++++++++++---
 src/colvardeps.cpp                 | 34 ++++++++------
 src/colvardeps.h                   | 20 ++++++--
 src/colvarmodule.cpp               |  2 +-
 src/colvarproxy_system.h           |  5 ++
 src/colvarscript_commands.h        |  2 +-
 src/colvarscript_commands_colvar.h |  1 +
 16 files changed, 216 insertions(+), 89 deletions(-)

diff --git a/colvartools/abmd.tcl b/colvartools/abmd.tcl
index 17fb4453e..3bca4d6d0 100644
--- a/colvartools/abmd.tcl
+++ b/colvartools/abmd.tcl
@@ -53,7 +53,7 @@ proc calc_z_max_gradient { args } { return 0 }
 proc calc_z_min_gradient { args } { return 0 }
 
 proc setup_ABMD { colvar force_k z_stop {direction up} } {
-  # cv config "scriptedColvarForces on"
+  cv config "scriptedColvarForces on"
 
   namespace eval ::ABMD {}
   set ::ABMD::cvname $colvar
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 4e44f63a3..41a32ae70 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -345,6 +345,8 @@ void colvarproxy_namd::calculate()
     colvars->update_engine_parameters();
     colvars->setup_input();
     colvars->setup_output();
+    // Controller is only available after full startup phase, so now
+    controller = &Node::Object()->state->getController();
 
     first_timestep = false;
 
@@ -373,7 +375,7 @@ void colvarproxy_namd::calculate()
   }
 
   previous_NAMD_step = step;
-  update_accelMD_info();
+  if (accelMDOn) update_accelMD_info();
 
   {
     Vector const a = lattice->a();
@@ -605,14 +607,8 @@ void colvarproxy_namd::calculate()
 }
 
 void colvarproxy_namd::update_accelMD_info() {
-  if (accelMDOn == false) {
-    return;
-  }
-  const Controller& c = Node::Object()->state->getController();
   // This aMD factor is from previous step!
-  amd_weight_factor = std::exp(c.accelMDdV /
-                               (target_temperature() * boltzmann()));
-//   std::cout << "Step: " << cvm::to_str(colvars->it) << " accelMD dV in colvars: " << c.accelMDdV << std::endl;
+  amd_weight_factor = std::exp(controller->accelMDdV / (target_temperature() * boltzmann()));
 }
 
 
@@ -1651,3 +1647,48 @@ int colvarproxy_namd::replica_comm_send(char* msg_data, int msg_len,
   replica_send(msg_data, msg_len, dest_rep, CkMyPe());
   return msg_len;
 }
+
+
+/// Request energy computation every freq steps
+int colvarproxy_namd::request_alch_energy_freq(int const freq) {
+  // This test is only valid for NAMD3
+  if (freq % simparams->computeEnergies) {
+    cvm::error("computeEnergies must be a divisor of lambda-dynamics period (" + cvm::to_str(freq) + ").\n");
+    return COLVARS_INPUT_ERROR;
+  }
+  if (!simparams->alchOn) {
+    cvm::error("alch must be enabled for lambda-dynamics.\n");
+    return COLVARS_INPUT_ERROR;
+  }
+  if (!simparams->alchThermIntOn) {
+    cvm::error("alchType must be set to TI for lambda-dynamics.\n");
+    return COLVARS_INPUT_ERROR;
+  }
+  return COLVARS_OK;
+}
+
+
+/// Get value of alchemical lambda parameter from back-end
+int colvarproxy_namd::get_alch_lambda(cvm::real* lambda) {
+  *lambda = simparams->alchLambda;
+  return COLVARS_OK;
+}
+
+
+/// Set value of alchemical lambda parameter in back-end
+int colvarproxy_namd::send_alch_lambda(void) {
+  simparams->alchLambda = cached_alch_lambda;
+  return COLVARS_OK;
+}
+
+
+/// Get energy derivative with respect to lambda
+int colvarproxy_namd::get_dE_dlambda(cvm::real* dE_dlambda) {
+  // Force data at step zero is garbage in NAMD3, zero in NAMD2
+  if (cvm::step_relative() > 0) {
+    *dE_dlambda = controller->getTIderivative();
+  } else {
+    *dE_dlambda = 0.0;
+  }
+  return COLVARS_OK;
+}
diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index 3aff50295..85986dc01 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -46,6 +46,9 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster {
   /// Pointer to the NAMD simulation input object
   SimParameters *simparams;
 
+  /// Pointer to Controller object
+  Controller const *controller;
+
   /// NAMD-style PRNG object
   Random random;
 
@@ -266,6 +269,18 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster {
 
   int backup_file(char const *filename) override;
 
+  /// Get value of alchemical lambda parameter from back-end
+  int get_alch_lambda(cvm::real* lambda);
+
+  /// Set value of alchemical lambda parameter in back-end
+  int send_alch_lambda(void);
+
+  /// Request energy computation every freq steps
+  int request_alch_energy_freq(int const freq);
+
+  /// Get energy derivative with respect to lambda
+  int get_dE_dlambda(cvm::real* dE_dlambda);
+
 };
 
 
diff --git a/src/colvar.cpp b/src/colvar.cpp
index 7e85eeb3b..e670e0adc 100644
--- a/src/colvar.cpp
+++ b/src/colvar.cpp
@@ -182,12 +182,6 @@ int colvar::init(std::string const &conf)
 
   set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar));
 
-  // If using scripted biases, any colvar may receive bias forces
-  // and will need its gradient
-  if (cvm::scripted_forces()) {
-    enable(f_cv_gradient);
-  }
-
   // check for linear combinations
   {
     bool lin = !(is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function));
@@ -320,6 +314,11 @@ int colvar::init(std::string const &conf)
     enable(f_cv_external);
   }
 
+  // If using scripted biases, any colvar may receive bias forces
+  if (cvm::scripted_forces()) {
+    enable(f_cv_apply_force);
+  }
+
   error_code |= init_extended_Lagrangian(conf);
   error_code |= init_output_flags(conf);
 
@@ -693,14 +692,15 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
     x_ext.type(colvarvalue::type_notset);
     v_ext.type(value());
     fr.type(value());
-    const bool temp_provided = get_keyval(conf, "extendedTemp", temp,
-                                          proxy->target_temperature());
+    const bool temp_provided = get_keyval(conf, "extendedTemp", temp, proxy->target_temperature());
     if (is_enabled(f_cv_external)) {
-      // In the case of an "external" coordinate, there is no coupling potential:
+      // In the case of a driven external parameter in the back-end, there is no coupling potential:
       // only the fictitious mass is meaningful
       get_keyval(conf, "extendedMass", ext_mass);
       // Ensure that the computed restraint energy term is zero
       ext_force_k = 0.0;
+      // Then we need forces from the back-end
+      enable(f_cv_total_force_calc);
     } else {
       // Standard case of coupling to a geometric colvar
       if (temp <= 0.0) { // Then a finite temperature is required
@@ -1135,6 +1135,9 @@ int colvar::init_dependencies() {
     init_feature(f_cv_gradient, "gradient", f_type_dynamic);
     require_feature_children(f_cv_gradient, f_cvc_gradient);
 
+    init_feature(f_cv_apply_force, "apply_force", f_type_dynamic);
+    require_feature_alt(f_cv_apply_force, f_cv_gradient, f_cv_external);
+
     init_feature(f_cv_collect_gradient, "collect_gradient", f_type_dynamic);
     require_feature_self(f_cv_collect_gradient, f_cv_gradient);
     require_feature_self(f_cv_collect_gradient, f_cv_scalar);
@@ -1153,6 +1156,8 @@ int colvar::init_dependencies() {
     init_feature(f_cv_total_force, "total_force", f_type_dynamic);
     require_feature_alt(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
 
+    init_feature(f_cv_total_force_current_step, "total_force_current_step", f_type_dynamic);
+
     // Deps for explicit total force calculation
     init_feature(f_cv_total_force_calc, "total_force_calculation", f_type_dynamic);
     require_feature_self(f_cv_total_force_calc, f_cv_scalar);
@@ -1171,13 +1176,15 @@ int colvar::init_dependencies() {
 
     init_feature(f_cv_extended_Lagrangian, "extended_Lagrangian", f_type_user);
     require_feature_self(f_cv_extended_Lagrangian, f_cv_scalar);
-    require_feature_self(f_cv_extended_Lagrangian, f_cv_gradient);
+    require_feature_self(f_cv_extended_Lagrangian, f_cv_apply_force);
 
     init_feature(f_cv_Langevin, "Langevin_dynamics", f_type_user);
     require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian);
 
-    init_feature(f_cv_external, "external", f_type_user);
+    init_feature(f_cv_external, "external_parameter", f_type_static);
     require_feature_self(f_cv_external, f_cv_single_cvc);
+    // External parameters always report the total force for current step
+    require_feature_self(f_cv_external, f_cv_total_force_current_step);
 
     init_feature(f_cv_single_cvc, "single_component", f_type_static);
 
@@ -1238,10 +1245,16 @@ int colvar::init_dependencies() {
     init_feature(f_cv_linear, "linear", f_type_static);
     init_feature(f_cv_homogeneous, "homogeneous", f_type_static);
 
-    // because total forces are obtained from the previous time step,
-    // we cannot (currently) have colvar values and total forces for the same timestep
     init_feature(f_cv_multiple_ts, "multiple_timestep", f_type_static);
-    exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
+
+    // when total atomic forces are obtained from the previous time step,
+    // we cannot (currently) have colvar values and projected total forces for the same timestep
+    // TODO this will need refining for driven alchemical parameters
+    // ie. the combination of f_cv_total_force_calc and f_cv_multiple_ts requires f_cv_total_force_current_step
+    // or we need to anticipate the total force request by one timestep
+    if (!cvm::main()->proxy->total_forces_same_step()) {
+      exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
+    }
 
     // check that everything is initialized
     for (i = 0; i < colvardeps::f_cv_ntot; i++) {
@@ -1262,6 +1275,10 @@ int colvar::init_dependencies() {
   feature_states[f_cv_fdiff_velocity].available =
     cvm::main()->proxy->simulation_running();
 
+  // Some back-ends report current total forces for all colvars
+  if (cvm::main()->proxy->total_forces_same_step())
+    enable(f_cv_total_force_current_step);
+
   return COLVARS_OK;
 }
 
@@ -1388,7 +1405,6 @@ 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");
 
-  colvarproxy *proxy = cvm::main()->proxy;
   int error_code = COLVARS_OK;
 
   error_code |= check_cvc_range(first_cvc, num_cvcs);
@@ -1396,7 +1412,7 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
     return error_code;
   }
 
-  if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
+  if ((cvm::step_relative() > 0) && (!is_enabled(f_cv_total_force_current_step))){
     // Use Jacobian derivative from previous timestep
     error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
   }
@@ -1404,7 +1420,7 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
   error_code |= calc_cvc_values(first_cvc, num_cvcs);
   error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
   error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
-  if (proxy->total_forces_same_step()){
+  if (is_enabled(f_cv_total_force_current_step)){
     // Use Jacobian derivative from this timestep
     error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
   }
@@ -1421,10 +1437,9 @@ int colvar::collect_cvc_data()
   if (cvm::debug())
     cvm::log("Calculating colvar \""+this->name+"\"'s properties.\n");
 
-  colvarproxy *proxy = cvm::main()->proxy;
   int error_code = COLVARS_OK;
 
-  if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
+  if ((cvm::step_relative() > 0) && (!is_enabled(f_cv_total_force_current_step))){
     // Total force depends on Jacobian derivative from previous timestep
     // collect_cvc_total_forces() uses the previous value of jd
     error_code |= collect_cvc_total_forces();
@@ -1432,7 +1447,7 @@ int colvar::collect_cvc_data()
   error_code |= collect_cvc_values();
   error_code |= collect_cvc_gradients();
   error_code |= collect_cvc_Jacobians();
-  if (proxy->total_forces_same_step()){
+  if (is_enabled(f_cv_total_force_current_step)){
     // Use Jacobian derivative from this timestep
     error_code |= collect_cvc_total_forces();
   }
@@ -1871,13 +1886,13 @@ void colvar::update_extended_Lagrangian()
     f += fb_actual;
   }
 
-  // fr: bias force on extended variable (without harmonic spring), for output in trajectory
-  fr = f;
-
   // External force has been scaled for an inner-timestep impulse (for the back-end integrator)
   // here we scale it back because this integrator uses only the outer (long) timestep
   f_ext = f / cvm::real(time_step_factor);
 
+  // fr: bias force on extended variable (without harmonic spring), for output in trajectory
+  fr = f_ext;
+
   colvarvalue f_system(fr.type()); // force exterted by the system on the extended DOF
 
   if (is_enabled(f_cv_external)) {
@@ -2382,6 +2397,10 @@ int colvar::set_state_params(std::string const &conf)
              cvm::to_str(x)+"\n");
     x_restart = x;
     after_restart = true;
+    // Externally driven cv (e.g. alchemical lambda) is imposed by restart value
+    if (is_enabled(f_cv_external) && is_enabled(f_cv_extended_Lagrangian)) {
+      cvcs[0]->set_value(x);
+    }
   }
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
@@ -2524,8 +2543,14 @@ std::string const colvar::get_state_params() const
   os << "  name " << name << "\n"
      << "  x "
      << std::setprecision(cvm::cv_prec)
-     << std::setw(cvm::cv_width)
-     << x << "\n";
+     << std::setw(cvm::cv_width);
+  if (is_enabled(f_cv_external)) {
+    // For an external colvar, x is one timestep in the future after integration
+    // write x at beginning of timestep
+    os << x_reported << "\n";
+  } else {
+    os << x << "\n";
+  }
 
   if (is_enabled(f_cv_output_velocity)) {
     os << "  v "
diff --git a/src/colvar.h b/src/colvar.h
index 3c08b5cc5..1db313f41 100644
--- a/src/colvar.h
+++ b/src/colvar.h
@@ -760,7 +760,7 @@ inline colvarvalue const & colvar::total_force() const
 
 inline void colvar::add_bias_force(colvarvalue const &force)
 {
-  check_enabled(f_cv_gradient,
+  check_enabled(f_cv_apply_force,
                 std::string("applying a force to the variable \""+name+"\""));
   if (cvm::debug()) {
     cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp
index be3e3f37d..606c772b6 100644
--- a/src/colvarbias.cpp
+++ b/src/colvarbias.cpp
@@ -93,11 +93,18 @@ int colvarbias::init(std::string const &conf)
     cvm::log("Reinitializing bias \""+name+"\".\n");
   }
 
+  feature_states[f_cvb_step_zero_data].available = true;
+
   colvar_values.resize(num_variables());
   for (i = 0; i < num_variables(); i++) {
     colvar_values[i].type(colvars[i]->value().type());
     colvar_forces[i].type(colvar_values[i].type());
     previous_colvar_forces[i].type(colvar_values[i].type());
+    if (!colvars[i]->is_enabled(f_cv_total_force_current_step)) {
+      // If any colvar does not have current-step total force, then
+      // we can't do step 0 data
+      feature_states[f_cvb_step_zero_data].available = false;
+    }
   }
 
   output_prefix = cvm::output_prefix();
@@ -157,7 +164,7 @@ int colvarbias::init_dependencies() {
     init_feature(f_cvb_step_zero_data, "step_zero_data", f_type_user);
 
     init_feature(f_cvb_apply_force, "apply_force", f_type_user);
-    require_feature_children(f_cvb_apply_force, f_cv_gradient);
+    require_feature_children(f_cvb_apply_force, f_cv_apply_force);
 
     init_feature(f_cvb_bypass_ext_lagrangian, "bypass_extended_Lagrangian_coordinates", f_type_user);
 
@@ -221,8 +228,6 @@ int colvarbias::init_dependencies() {
   // The feature f_cvb_bypass_ext_lagrangian is only implemented by some derived classes
   // (initially, harmonicWalls)
   feature_states[f_cvb_bypass_ext_lagrangian].available = false;
-  // disabled by default; can be changed by derived classes that implement it
-  feature_states[f_cvb_bypass_ext_lagrangian].enabled = false;
 
   return COLVARS_OK;
 }
diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp
index db6ee6d57..7f4fd2e09 100644
--- a/src/colvarbias_abf.cpp
+++ b/src/colvarbias_abf.cpp
@@ -130,10 +130,11 @@ int colvarbias_abf::init(std::string const &conf)
       colvars[i]->enable(f_cv_hide_Jacobian);
     }
 
-    // If any colvar is extended-system, we need to collect the extended
-    // system gradient
-    if (colvars[i]->is_enabled(f_cv_extended_Lagrangian))
+    // If any colvar is extended-system (restrained, not driven external param), we are running eABF
+    if (colvars[i]->is_enabled(f_cv_extended_Lagrangian)
+        && !colvars[i]->is_enabled(f_cv_external)) {
       enable(f_cvb_extended);
+    }
 
     // Cannot mix and match coarse time steps with ABF because it gives
     // wrong total force averages - total force needs to be averaged over
@@ -321,17 +322,25 @@ int colvarbias_abf::update()
   size_t i;
   for (i = 0; i < num_variables(); i++) {
     bin[i] = samples->current_bin_scalar(i);
+    if (colvars[i]->is_enabled(f_cv_total_force_current_step)) {
+      force_bin[i] = bin[i];
+    }
   }
 
-
   // ***********************************************************
   // ******  ABF Part I: update the FE gradient estimate  ******
   // ***********************************************************
 
 
-  if (cvm::proxy->total_forces_same_step()) {
-    // e.g. in LAMMPS, total forces are current
-    force_bin = bin;
+  // Share data first, so that 2d/3d PMF is refreshed using new data for mw-pABF.
+  // shared_on can be true with shared_freq 0 if we are sharing via script
+  if (shared_on && shared_freq &&
+      shared_last_step >= 0 &&                    // we have already collected some data
+      cvm::step_absolute() > shared_last_step &&  // time has passed since the last sharing timestep
+                                                  // (avoid re-sharing at last and first ts of successive run statements)
+      cvm::step_absolute() % shared_freq == 0) {
+    // Share gradients and samples for shared ABF.
+    replica_share();
   }
 
   if (can_accumulate_data() && is_enabled(f_cvb_history_dependent)) {
@@ -374,21 +383,11 @@ int colvarbias_abf::update()
     }
   }
 
-  if (!(cvm::proxy->total_forces_same_step())) {
-    // e.g. in NAMD, total forces will be available for next timestep
-    // hence we store the current colvar bin
-    force_bin = bin;
-  }
+  // In some cases, total forces are stored for next timestep
+  // hence we store the current colvar bin - this is overwritten on a per-colvar basis
+  // at the top of update()
+  force_bin = bin;
 
-  // Share data after force sample is collected for this time step
-  // shared_on can be true with shared_freq 0 if we are sharing via script
-  if (shared_on && shared_freq &&
-      cvm::step_absolute() > shared_last_step &&  // time has passed since the last sharing timestep
-                                                  // (avoid re-sharing at last and first ts of successive run statements)
-      cvm::step_absolute() % shared_freq == 0) {
-    // Share gradients and samples for shared ABF.
-    replica_share();
-  }
 
   // ******************************************************************
   // ******  ABF Part II: calculate and apply the biasing force  ******
diff --git a/src/colvarcomp.cpp b/src/colvarcomp.cpp
index 024c00e50..9a056f7dd 100644
--- a/src/colvarcomp.cpp
+++ b/src/colvarcomp.cpp
@@ -261,7 +261,6 @@ int colvar::cvc::init_dependencies() {
     require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient);
 
     init_feature(f_cvc_inv_gradient, "inverse_gradient", f_type_dynamic);
-    require_feature_self(f_cvc_inv_gradient, f_cvc_gradient);
 
     init_feature(f_cvc_debug_gradient, "debug_gradient", f_type_user);
     require_feature_self(f_cvc_debug_gradient, f_cvc_gradient);
@@ -525,7 +524,7 @@ void colvar::cvc::calc_force_invgrads()
 
 void colvar::cvc::calc_Jacobian_derivative()
 {
-  cvm::error("Error: calculation of inverse gradients is not implemented "
+  cvm::error("Error: calculation of Jacobian derivatives is not implemented "
              "for colvar components of type \""+function_type()+"\".\n",
              COLVARS_NOT_IMPLEMENTED);
 }
diff --git a/src/colvarcomp.h b/src/colvarcomp.h
index 334fdc1f6..e47a2a76d 100644
--- a/src/colvarcomp.h
+++ b/src/colvarcomp.h
@@ -1214,7 +1214,8 @@ class colvar::alch_lambda
   alch_lambda();
   virtual ~alch_lambda() {}
   virtual void calc_value();
-  virtual void calc_gradients();
+  virtual void calc_force_invgrads();
+  virtual void calc_Jacobian_derivative();
   virtual void apply_force(colvarvalue const &force);
 };
 
diff --git a/src/colvarcomp_alchlambda.cpp b/src/colvarcomp_alchlambda.cpp
index a175ea43e..d9d08df5c 100644
--- a/src/colvarcomp_alchlambda.cpp
+++ b/src/colvarcomp_alchlambda.cpp
@@ -20,19 +20,32 @@ colvar::alch_lambda::alch_lambda()
 {
   set_function_type("alchLambda");
 
-  disable(f_cvc_explicit_gradient);
-  disable(f_cvc_gradient);
+  provide(f_cvc_explicit_gradient, false);
+  provide(f_cvc_gradient, false); // Cannot apply forces on this CVC
+  provide(f_cvc_collect_atom_ids, false);
+
+  provide(f_cvc_inv_gradient); // Projected force is TI derivative
+  provide(f_cvc_Jacobian);     // Zero
 
   x.type(colvarvalue::type_scalar);
-  // Query initial value from back-end
+
+  // We need calculation every time step
+  // default in Tinker-HP and NAMD2, must be enforced in NAMD3
+  // Also checks back-end settings, ie. that alchemy is enabled
+  // (in NAMD3: alchType TI, computeEnergies at the right frequency)
+  cvm::proxy->request_alch_energy_freq(1);
+  // TODO examine how this breaks everything - whereas alchOutFreq seems to work
+
+  // Query initial value from back-end; will be overwritten if restarting from a state file
   cvm::proxy->get_alch_lambda(&x.real_value);
 }
 
 
 void colvar::alch_lambda::calc_value()
 {
-  // Special workflow:
-  // at the beginning of the timestep we get a force instead of calculating the value
+  // By default, follow external parameter
+  // This might get overwritten by driving extended dynamics
+  cvm::proxy->get_alch_lambda(&x.real_value);
 
   cvm::proxy->get_dE_dlambda(&ft.real_value);
   ft.real_value *= -1.0; // Energy derivative to force
@@ -43,8 +56,15 @@ void colvar::alch_lambda::calc_value()
 }
 
 
-void colvar::alch_lambda::calc_gradients()
+void colvar::alch_lambda::calc_force_invgrads()
+{
+  // All the work is done in calc_value()
+}
+
+
+void colvar::alch_lambda::calc_Jacobian_derivative()
 {
+  jd = 0.0;
 }
 
 
diff --git a/src/colvardeps.cpp b/src/colvardeps.cpp
index 46b791756..56d285a21 100644
--- a/src/colvardeps.cpp
+++ b/src/colvardeps.cpp
@@ -92,6 +92,8 @@ void colvardeps::restore_children_deps() {
 
 void colvardeps::provide(int feature_id, bool truefalse) {
   feature_states[feature_id].available = truefalse;
+  // Make sure that we don't leave this feature enabled
+  if (!truefalse) disable(feature_id);
 }
 
 
@@ -123,8 +125,9 @@ bool colvardeps::get_keyval_feature(colvarparse *cvp,
 
 
 int colvardeps::enable(int feature_id,
-                       bool dry_run /* default: false */,
-                       bool toplevel /* default: true */)
+                       bool dry_run  /* default: false */,
+                       bool toplevel /* default: true */,
+                       bool error    /*default: false */)
 {
   int res;
   size_t i, j;
@@ -137,9 +140,12 @@ int colvardeps::enable(int feature_id,
   feature *f = features()[feature_id];
   feature_state *fs = &feature_states[feature_id];
 
+  // dry_run can be true because parent object is not active, yet we are displaying an error message
+  // then error is set to true
+
   if (cvm::debug()) {
     cvm::log("DEPS: " + description +
-      (dry_run ? " testing " : " enabling ") +
+      (dry_run ? " testing " : " enabling ") +  (error ? " [error] " : "") +
       "\"" + f->description +"\"\n");
   }
 
@@ -159,7 +165,7 @@ int colvardeps::enable(int feature_id,
     (is_dynamic(feature_id) ? "Dynamic" : "User-controlled");
 
   if (!fs->available) {
-    if (!dry_run) {
+    if (!dry_run || error) {
       if (toplevel) {
         cvm::error("Error: " + feature_type_descr + " feature unavailable: \""
           + f->description + "\" in " + description + ".\n");
@@ -172,7 +178,7 @@ int colvardeps::enable(int feature_id,
   }
 
   if (!toplevel && !is_dynamic(feature_id)) {
-    if (!dry_run) {
+    if (!dry_run || error) {
       cvm::log(feature_type_descr + " feature \"" + f->description
         + "\" cannot be enabled automatically in " + description + ".\n");
       if (is_user(feature_id)) {
@@ -189,7 +195,7 @@ int colvardeps::enable(int feature_id,
     if (cvm::debug())
       cvm::log(f->description + " requires exclude " + g->description + "\n");
     if (is_enabled(f->requires_exclude[i])) {
-      if (!dry_run) {
+      if (!dry_run || error) {
         cvm::log("Feature \"" + f->description + "\" is incompatible with \""
         + g->description + "\" in " + description + ".\n");
         if (toplevel) {
@@ -204,9 +210,9 @@ int colvardeps::enable(int feature_id,
   for (i=0; i<f->requires_self.size(); i++) {
     if (cvm::debug())
       cvm::log(f->description + " requires self " + features()[f->requires_self[i]]->description + "\n");
-    res = enable(f->requires_self[i], dry_run, false);
+    res = enable(f->requires_self[i], dry_run, false, error);
     if (res != COLVARS_OK) {
-      if (!dry_run) {
+      if (!dry_run || error) {
         cvm::log("...required by \"" + f->description + "\" in " + description + "\n");
         if (toplevel) {
           cvm::error("Error: Failed dependency in " + description + ".\n");
@@ -225,11 +231,11 @@ int colvardeps::enable(int feature_id,
       int g = f->requires_alt[i][j];
       if (cvm::debug())
         cvm::log(f->description + " requires alt " + features()[g]->description + "\n");
-      res = enable(g, true, false);  // see if available
+      res = enable(g, true, false, error);  // see if available
       if (res == COLVARS_OK) {
         ok = true;
-        if (!dry_run) {
-          enable(g, false, false); // Require again, for real
+        if (!dry_run || error) {
+          enable(g, false, false, error); // Require again, for real
           fs->alternate_refs.push_back(g); // We remember we enabled this
           // so we can free it if this feature gets disabled
         }
@@ -245,7 +251,7 @@ int colvardeps::enable(int feature_id,
         for (j=0; j<f->requires_alt[i].size(); j++) {
           int g = f->requires_alt[i][j];
           cvm::log(cvm::to_str(j+1) + ". " + features()[g]->description + "\n");
-          enable(g, false, false); // Just for printing error output
+          enable(g, false, false, true); // Just for printing error output
         }
         cvm::decrease_depth();
         cvm::log("-----------------------------------------\n");
@@ -264,9 +270,9 @@ int colvardeps::enable(int feature_id,
   for (i=0; i<f->requires_children.size(); i++) {
     int g = f->requires_children[i];
     for (j=0; j<children.size(); j++) {
-      res = children[j]->enable(g, dry_run || !is_enabled(), false);
+      res = children[j]->enable(g, dry_run || !is_enabled(), false, error);
       if (res != COLVARS_OK) {
-        if (!dry_run) {
+        if (!dry_run || error) {
           cvm::log("...required by \"" + f->description + "\" in " + description + "\n");
           if (toplevel) {
             cvm::error("Error: Failed dependency in " + description + ".\n");
diff --git a/src/colvardeps.h b/src/colvardeps.h
index 1bd304b54..3878e54ec 100644
--- a/src/colvardeps.h
+++ b/src/colvardeps.h
@@ -198,7 +198,9 @@ class colvardeps {
   /// \param toplevel False if this is called as part of a chain of dependency resolution.
   /// This is used to diagnose failed dependencies by displaying the full stack:
   /// only the toplevel dependency will throw a fatal error.
-  int enable(int f, bool dry_run = false, bool toplevel = true);
+  /// \param error Recursively enable, printing error messages along the way
+  /// Necessary when propagating errors across alternate dependencies
+  int enable(int f, bool dry_run = false, bool toplevel = true, bool error = false);
 
   /// Disable a feature, decrease the reference count of its dependencies
   /// and recursively disable them as applicable
@@ -263,8 +265,11 @@ class colvardeps {
     f_cv_active,
     /// \brief Colvar is awake (active on its own accord) this timestep
     f_cv_awake,
-    /// \brief Gradients are calculated and temporarily stored, so
-    /// that external forces can be applied
+    /// \brief External force can be applied, either to atoms or to an
+    /// extended DOF
+    f_cv_apply_force,
+    /// \brief Gradients are calculated and temporarily stored,
+    /// so that external forces can be propagated to atoms
     f_cv_gradient,
     /// \brief Collect atomic gradient data from all cvcs into vector
     /// atomic_gradient
@@ -277,7 +282,10 @@ class colvardeps {
     /// forces on the inverse gradient
     f_cv_total_force,
     /// \brief Calculate total force from atomic forces
+    /// or get it from the back-end for an external parameter
     f_cv_total_force_calc,
+    /// \brief Total force is that of current time step
+    f_cv_total_force_current_step,
     /// \brief Subtract the applied force from the total force
     f_cv_subtract_applied_force,
     /// \brief Estimate Jacobian derivative
@@ -289,8 +297,10 @@ class colvardeps {
     /// center with fictitious mass; bias forces will be applied to
     /// the center
     f_cv_extended_Lagrangian,
-    /// \brief An extended variable that sets an external variable in the
-    /// back-end (eg. an alchemical coupling parameter for lambda-dynamics)
+    /// \brief A variable that constrains or follows an external parameter
+    /// in the back-end (eg. an alchemical coupling parameter for lambda-dynamics)
+    /// If extended Lagrangian, then we drive the external parameter
+    /// Otherwise we follow it
     /// Can have a single component
     f_cv_external,
     /// \brief The extended system coordinate undergoes Langevin dynamics
diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp
index 4a52017b7..256ed1a5a 100644
--- a/src/colvarmodule.cpp
+++ b/src/colvarmodule.cpp
@@ -1111,7 +1111,7 @@ int colvarmodule::update_colvar_forces()
     cvm::log("Communicating forces from the colvars to the atoms.\n");
   cvm::increase_depth();
   for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
-    if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
+    if ((*cvi)->is_enabled(colvardeps::f_cv_apply_force)) {
       (*cvi)->communicate_forces();
       if (cvm::get_error()) {
         return COLVARS_ERROR;
diff --git a/src/colvarproxy_system.h b/src/colvarproxy_system.h
index 67d0938e5..6caf9473e 100644
--- a/src/colvarproxy_system.h
+++ b/src/colvarproxy_system.h
@@ -109,6 +109,11 @@ class colvarproxy_system {
   /// Send cached value of alchemical lambda parameter to back-end (if available)
   virtual int send_alch_lambda();
 
+  /// Request energy computation every freq steps (necessary for NAMD3, not all back-ends)
+  virtual int request_alch_energy_freq(int const freq) {
+    return COLVARS_OK;
+  }
+
   /// Get energy derivative with respect to lambda (if available)
   virtual int get_dE_dlambda(cvm::real* dE_dlambda);
 
diff --git a/src/colvarscript_commands.h b/src/colvarscript_commands.h
index f873f7793..191724dd0 100644
--- a/src/colvarscript_commands.h
+++ b/src/colvarscript_commands.h
@@ -674,7 +674,7 @@ CVSCRIPT(cv_version,
          )
 
 // This guard allows compiling colvar and bias function bodies in their
-// respecitve files instead of colvarscript_commands.o
+// respective files instead of colvarscript_commands.o
 #ifndef COLVARSCRIPT_COMMANDS_GLOBAL
 #include "colvarscript_commands_colvar.h"
 #include "colvarscript_commands_bias.h"
diff --git a/src/colvarscript_commands_colvar.h b/src/colvarscript_commands_colvar.h
index f6bb6b8c9..c641b321d 100644
--- a/src/colvarscript_commands_colvar.h
+++ b/src/colvarscript_commands_colvar.h
@@ -23,6 +23,7 @@ CVSCRIPT(colvar_addforce,
            script->add_error_msg("addforce : error parsing force value");
            return COLVARSCRIPT_ERROR;
          }
+         this_colvar->enable(colvardeps::f_cv_apply_force);
          this_colvar->add_bias_force(force);
          script->set_result_colvarvalue(force);
          return COLVARS_OK;

From 8cc7672f129ed774ab14895d1d55f5baa8503583 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Fri, 1 Mar 2024 18:31:40 +0100
Subject: [PATCH 02/13] Better dependency failure messages for toplevel

---
 src/colvardeps.cpp | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/colvardeps.cpp b/src/colvardeps.cpp
index 56d285a21..3ba320900 100644
--- a/src/colvardeps.cpp
+++ b/src/colvardeps.cpp
@@ -213,7 +213,11 @@ int colvardeps::enable(int feature_id,
     res = enable(f->requires_self[i], dry_run, false, error);
     if (res != COLVARS_OK) {
       if (!dry_run || error) {
-        cvm::log("...required by \"" + f->description + "\" in " + description + "\n");
+        if (toplevel) {
+          cvm::log("Cannot enable \"" + f->description + "\" in " + description + "\n");
+        } else {
+          cvm::log("...required by \"" + f->description + "\" in " + description + "\n");
+        }
         if (toplevel) {
           cvm::error("Error: Failed dependency in " + description + ".\n");
         }
@@ -273,7 +277,11 @@ int colvardeps::enable(int feature_id,
       res = children[j]->enable(g, dry_run || !is_enabled(), false, error);
       if (res != COLVARS_OK) {
         if (!dry_run || error) {
-          cvm::log("...required by \"" + f->description + "\" in " + description + "\n");
+          if (toplevel) {
+            cvm::log("Cannot enable \"" + f->description + "\" in " + description + "\n");
+          } else {
+            cvm::log("...required by \"" + f->description + "\" in " + description + "\n");
+          }
           if (toplevel) {
             cvm::error("Error: Failed dependency in " + description + ".\n");
           }

From d3c34e0ed7fe860390ddd1355a6a93dbe05ce78e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Wed, 13 Mar 2024 14:33:51 +0100
Subject: [PATCH 03/13] Fix classic ABF in Tinker-HP

---
 src/colvar.cpp                | 5 +++--
 src/colvarbias.cpp            | 3 ++-
 src/colvarbias_abf.cpp        | 6 +++++-
 src/colvarcomp_alchlambda.cpp | 4 ++--
 4 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/colvar.cpp b/src/colvar.cpp
index e670e0adc..4cb34206b 100644
--- a/src/colvar.cpp
+++ b/src/colvar.cpp
@@ -1790,7 +1790,7 @@ int colvar::calc_colvar_properties()
 
   } else {
 
-    if (is_enabled(f_cv_subtract_applied_force)) {
+    if (is_enabled(f_cv_subtract_applied_force) && !cvm::proxy->total_forces_same_step()) {
       // correct the total force only if it has been measured
       // TODO add a specific test instead of relying on sq norm
       if (ft.norm2() > 0.0) {
@@ -1877,7 +1877,8 @@ void colvar::update_extended_Lagrangian()
   // Integrate with slow timestep (if time_step_factor != 1)
   cvm::real dt = cvm::dt() * cvm::real(time_step_factor);
 
-  colvarvalue f_ext(fr.type()); // force acting on the extended variable
+  // Force acting on the extended variable
+  colvarvalue f_ext(fr.type());
   f_ext.reset();
 
   if (is_enabled(f_cv_external)) {
diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp
index 606c772b6..b30bdb181 100644
--- a/src/colvarbias.cpp
+++ b/src/colvarbias.cpp
@@ -899,8 +899,9 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
   if ((cvm::step_relative() > 0) || proxy->total_forces_same_step()) {
     if (ti_avg_forces->index_ok(ti_bin)) {
       for (i = 0; i < num_variables(); i++) {
-        if (variables(i)->is_enabled(f_cv_subtract_applied_force)) {
+        if (variables(i)->is_enabled(f_cv_subtract_applied_force) || proxy->total_forces_same_step()) {
           // this colvar is already subtracting all applied forces
+          // or the "total force" is really a system force at current step
           ti_system_forces[i] = variables(i)->total_force();
         } else {
           ti_system_forces[i] = variables(i)->total_force() -
diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp
index 7f4fd2e09..5beb24a67 100644
--- a/src/colvarbias_abf.cpp
+++ b/src/colvarbias_abf.cpp
@@ -457,8 +457,12 @@ int colvarbias_abf::update_system_force()
   // System force from atomic forces (or extended Lagrangian if applicable)
 
   for (i = 0; i < num_variables(); i++) {
-    if (colvars[i]->is_enabled(f_cv_subtract_applied_force)) {
+    if (colvars[i]->is_enabled(f_cv_subtract_applied_force) ||
+       (cvm::proxy->total_forces_same_step() && !colvars[i]->is_enabled(f_cv_external))) {
       // this colvar is already subtracting the ABF force
+      // or the "total force" is really a system force at current step
+      // (For external parameters, the total force contains biasing forces
+      // unless f_cv_subtract_applied_force is enabled)
       system_force[i] = colvars[i]->total_force().real_value;
     } else {
       system_force[i] = colvars[i]->total_force().real_value
diff --git a/src/colvarcomp_alchlambda.cpp b/src/colvarcomp_alchlambda.cpp
index d9d08df5c..cd928e823 100644
--- a/src/colvarcomp_alchlambda.cpp
+++ b/src/colvarcomp_alchlambda.cpp
@@ -45,10 +45,11 @@ void colvar::alch_lambda::calc_value()
 {
   // By default, follow external parameter
   // This might get overwritten by driving extended dynamics
+  // (in apply_force() below)
   cvm::proxy->get_alch_lambda(&x.real_value);
 
   cvm::proxy->get_dE_dlambda(&ft.real_value);
-  ft.real_value *= -1.0; // Energy derivative to force
+  ft.real_value *= -1.0; // Convert energy derivative to force
 
   // Include any force due to bias on Flambda
   ft.real_value += cvm::proxy->indirect_lambda_biasing_force;
@@ -75,7 +76,6 @@ void colvar::alch_lambda::apply_force(colvarvalue const & /* force */)
 }
 
 
-
 colvar::alch_Flambda::alch_Flambda()
 {
   set_function_type("alch_Flambda");

From a31fd8e89e0aa25ee2e58cea9895518613284f41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Thu, 14 Mar 2024 23:10:56 +0100
Subject: [PATCH 04/13] Port ABF fix to TI bias

Select correct force bin on a per-colvar basis
---
 src/colvarbias.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp
index b30bdb181..490a07811 100644
--- a/src/colvarbias.cpp
+++ b/src/colvarbias.cpp
@@ -889,8 +889,8 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
 
   size_t i;
 
-  if (proxy->total_forces_same_step()) {
-    for (i = 0; i < num_variables(); i++) {
+  for (i = 0; i < num_variables(); i++) {
+    if (variables(i)->is_enabled(f_cv_total_force_current_step)) {
       ti_bin[i] = ti_avg_forces->current_bin_scalar(i);
     }
   }
@@ -899,7 +899,8 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
   if ((cvm::step_relative() > 0) || proxy->total_forces_same_step()) {
     if (ti_avg_forces->index_ok(ti_bin)) {
       for (i = 0; i < num_variables(); i++) {
-        if (variables(i)->is_enabled(f_cv_subtract_applied_force) || proxy->total_forces_same_step()) {
+        if (variables(i)->is_enabled(f_cv_subtract_applied_force) ||
+          (cvm::proxy->total_forces_same_step() && !variables(i)->is_enabled(f_cv_external))) {
           // this colvar is already subtracting all applied forces
           // or the "total force" is really a system force at current step
           ti_system_forces[i] = variables(i)->total_force();
@@ -915,9 +916,9 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
     }
   }
 
-  if (!proxy->total_forces_same_step()) {
-    // Set the index for use in the next iteration, when total forces come in
-    for (i = 0; i < num_variables(); i++) {
+  for (i = 0; i < num_variables(); i++) {
+    if (!variables(i)->is_enabled(f_cv_total_force_current_step)) {
+      // Set the index for use in the next iteration, when total forces come in
       ti_bin[i] = ti_avg_forces->current_bin_scalar(i);
     }
   }

From 1b103129dda665b2f7c5c14a11ecb42d0af044bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Thu, 28 Mar 2024 14:18:53 +0100
Subject: [PATCH 05/13] Fix total_forces_same_step flag for LAMMPS

So far is was erroneously set to true, but its effects were not fully
implemented in ABF.
---
 lammps/src/COLVARS/colvarproxy_lammps.h | 3 ++-
 src/colvarproxy_system.h                | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/lammps/src/COLVARS/colvarproxy_lammps.h b/lammps/src/COLVARS/colvarproxy_lammps.h
index 7ed469baa..e9571bd65 100644
--- a/lammps/src/COLVARS/colvarproxy_lammps.h
+++ b/lammps/src/COLVARS/colvarproxy_lammps.h
@@ -64,7 +64,8 @@ class colvarproxy_lammps : public colvarproxy {
  public:
 
   bool total_forces_enabled() const override { return total_force_requested; };
-  bool total_forces_same_step() const override { return true; };
+  // Total forces are saved at end of step, only processed at the next step
+  bool total_forces_same_step() const override { return false; };
   bool want_exit() const { return do_exit; };
 
   // perform colvars computation. returns biasing energy
diff --git a/src/colvarproxy_system.h b/src/colvarproxy_system.h
index 6caf9473e..bf2ad2ea8 100644
--- a/src/colvarproxy_system.h
+++ b/src/colvarproxy_system.h
@@ -94,6 +94,7 @@ class colvarproxy_system {
   virtual bool total_forces_enabled() const;
 
   /// Are total forces from the current step available?
+  /// in which case they are really system forces
   virtual bool total_forces_same_step() const;
 
   /// Get the molecule ID when called in VMD; raise error otherwise

From 5d1544fbd63b8184b93ea21b5de4e006d95140f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Wed, 10 Apr 2024 16:35:59 +0200
Subject: [PATCH 06/13] Update LAMMPS regression tests for TI/ABF fix

---
 .../AutoDiff/test.colvars.out                 | 39 +++++++--------
 .../AutoDiff/test.colvars.state.stripped      | 12 ++---
 .../AutoDiff/test.colvars.traj                | 30 ++++++------
 .../000_distance-grid_abf/AutoDiff/test.grad  |  2 +-
 .../000_distance-grid_abf/AutoDiff/test.pmf   | 14 +++---
 .../AutoDiff/test.restart.colvars.out         | 48 ++++++++++---------
 .../test.restart.colvars.state.stripped       | 12 ++---
 .../AutoDiff/test.restart.colvars.traj        | 42 ++++++++--------
 .../AutoDiff/test.restart.grad                |  2 +-
 .../AutoDiff/test.restart.pmf                 | 14 +++---
 .../000_distance-grid_abf/lammps-version.txt  |  2 +-
 .../AutoDiff/test.colvars.out                 | 37 +++++++-------
 .../AutoDiff/test.colvars.state.stripped      | 14 +++---
 .../AutoDiff/test.restart.colvars.out         | 44 +++++++++--------
 .../test.restart.colvars.state.stripped       | 14 +++---
 .../AutoDiff/test.restart.colvars.traj        |  6 +--
 .../lammps-version.txt                        |  2 +-
 .../AutoDiff/test.colvars.out                 | 36 +++++++-------
 .../AutoDiff/test.colvars.state.stripped      |  8 ++--
 .../AutoDiff/test.restart.colvars.out         | 43 +++++++++--------
 .../test.restart.colvars.state.stripped       |  8 ++--
 .../AutoDiff/test.restart.colvars.traj        |  6 +--
 .../lammps-version.txt                        |  2 +-
 .../AutoDiff/test.colvars.out                 | 35 +++++++-------
 .../AutoDiff/test.colvars.state.stripped      | 34 ++++++-------
 .../AutoDiff/test.colvars.traj                | 22 ++++-----
 .../AutoDiff/test.restart.colvars.out         | 44 +++++++++--------
 .../test.restart.colvars.state.stripped       | 32 +++++++------
 .../AutoDiff/test.restart.colvars.traj        | 24 +++++-----
 .../lammps-version.txt                        |  2 +-
 lammps/tests/library/run_tests.sh             |  4 +-
 31 files changed, 329 insertions(+), 305 deletions(-)

diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out
index ccb1dec72..502a4cd97 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.out
@@ -1,10 +1,12 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +58,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,19 +106,20 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "abf" instance.
 colvars:   # name = "abf1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
 colvars:   WARNING: ABF should not be run without a thermostat or at 0 Kelvin!
 colvars:   # applyBias = on [default]
-colvars:   # updateBias = on [default]
 colvars:   # hideJacobian = off [default]
 colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
 colvars:   # fullSamples = 10
+colvars:   # minSamples = 5 [default]
 colvars:   # inputPrefix =  [default]
 colvars:   # historyFreq = 0 [default]
 colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
 colvars:   # maxForce =  [default]
 colvars:   # integrate = on [default]
 colvars:   Finished ABF setup.
@@ -125,16 +128,14 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
-colvars: Opening trajectory file "test.colvars.traj".
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
 colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
 colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
-colvars:   Prepared sample and gradient buffers at step 0.
+colvars: The final output state file will be "test.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
 colvars: Saving collective variables state to "test.colvars.state".
-colvars: Resetting the Collective Variables module.
+colvars: Saving collective variables state to "test.colvars.state".
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped
index 814e325f5..7c60a0d34 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.state.stripped
@@ -5,13 +5,13 @@ configuration {
 
 colvar {
   name one
-  x  3.20036069218762e+00
+  x       3.2003843562355
 }
 
 abf {
   configuration {
-    step 20
-    name abf1
+step 20
+name abf1
   }
 
 samples
@@ -20,8 +20,8 @@ samples
  0 0 0 0
 
 gradient
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -1.12776581376024e-01 0.00000000000000e+00
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0 0 0 0 0 0 -0.10385485654788 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
 }
 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj
index 31bc87f2f..1c9b3d776 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.colvars.traj
@@ -5,18 +5,18 @@
            3    3.20405779931486e+00  0.00000000000000e+00 
            4    3.20488715757478e+00  0.00000000000000e+00 
            5    3.20630753860023e+00  0.00000000000000e+00 
-           6    3.20822521484009e+00 -6.61626791923408e+00 
-           7    3.21041717634450e+00 -1.27156541500808e+01 
-           8    3.21265147474750e+00 -1.78199101059935e+01 
-           9    3.21470018041825e+00 -2.15984911523814e+01 
-          10    3.21635524474136e+00 -2.38649655797079e+01 
-          11    3.21744175542164e+00 -2.04771085292232e+01 
-          12    3.21789227153408e+00 -1.70074606132688e+01 
-          13    3.21766748124389e+00 -1.36104049871579e+01 
-          14    3.21676135390922e+00 -1.04308363259766e+01 
-          15    3.21520071953742e+00 -7.58252414070870e+00 
-          16    3.21304286766655e+00 -5.14775867496289e+00 
-          17    3.21037093904356e+00 -3.17629358378122e+00 
-          18    3.20728794724505e+00 -1.68764750172374e+00 
-          19    3.20391020908566e+00 -6.75514681148352e-01 
-          20    3.20036069218762e+00 -1.12776581376024e-01 
+           6    3.20822521484009e+00 -6.61157190854750e+00 
+           7    3.21041724907750e+00 -1.27050301328157e+01 
+           8    3.21265178240395e+00 -1.78028628544160e+01 
+           9    3.21470098068744e+00 -2.15753129933168e+01 
+          10    3.21635688320852e+00 -2.38366465889628e+01 
+          11    3.21744464629897e+00 -2.04504671342194e+01 
+          12    3.21789678756116e+00 -1.69832533952049e+01 
+          13    3.21767393972780e+00 -1.35890910889714e+01 
+          14    3.21677000635471e+00 -1.04125653142527e+01 
+          15    3.21521174831218e+00 -7.56715843574337e+00 
+          16    3.21305638863422e+00 -5.13491652636543e+00 
+          17    3.21038700938995e+00 -3.16541313007834e+00 
+          18    3.20730657726304e+00 -1.67806747099744e+00 
+          19    3.20393137633088e+00 -6.66563054214209e-01 
+          20    3.20038435623547e+00 -1.03854856547883e-01 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.grad b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.grad
index b29f49b8a..2291bdea6 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.grad
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.grad
@@ -7,7 +7,7 @@
   1.75000000000000e+00   0.00000000000000e+00
   2.25000000000000e+00   0.00000000000000e+00
   2.75000000000000e+00   0.00000000000000e+00
-  3.25000000000000e+00  -1.12776581375979e-01
+  3.25000000000000e+00  -1.03854856547883e-01
   3.75000000000000e+00   0.00000000000000e+00
   4.25000000000000e+00   0.00000000000000e+00
   4.75000000000000e+00   0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.pmf b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.pmf
index 2b0f3c6f5..8dd132ee4 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.pmf
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.pmf
@@ -1,13 +1,13 @@
 # 1
 # -2.50000000000000e-01  5.00000000000000e-01         21  0
 
-  0.00000000000000e+00   5.63882906879895e-02
-  5.00000000000000e-01   5.63882906879895e-02
-  1.00000000000000e+00   5.63882906879895e-02
-  1.50000000000000e+00   5.63882906879895e-02
-  2.00000000000000e+00   5.63882906879895e-02
-  2.50000000000000e+00   5.63882906879895e-02
-  3.00000000000000e+00   5.63882906879895e-02
+  0.00000000000000e+00   5.19274282739416e-02
+  5.00000000000000e-01   5.19274282739416e-02
+  1.00000000000000e+00   5.19274282739416e-02
+  1.50000000000000e+00   5.19274282739416e-02
+  2.00000000000000e+00   5.19274282739416e-02
+  2.50000000000000e+00   5.19274282739416e-02
+  3.00000000000000e+00   5.19274282739416e-02
   3.50000000000000e+00   0.00000000000000e+00
   4.00000000000000e+00   0.00000000000000e+00
   4.50000000000000e+00   0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out
index f235c1e6b..62b5a9a56 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.out
@@ -1,10 +1,13 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
+colvars: Will read input state from file "test.colvars.state"
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +59,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,19 +107,20 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "abf" instance.
 colvars:   # name = "abf1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
 colvars:   WARNING: ABF should not be run without a thermostat or at 0 Kelvin!
 colvars:   # applyBias = on [default]
-colvars:   # updateBias = on [default]
 colvars:   # hideJacobian = off [default]
 colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
 colvars:   # fullSamples = 10
+colvars:   # minSamples = 5 [default]
 colvars:   # inputPrefix =  [default]
 colvars:   # historyFreq = 0 [default]
 colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
 colvars:   # maxForce =  [default]
 colvars:   # integrate = on [default]
 colvars:   Finished ABF setup.
@@ -125,21 +129,19 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
+colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "test.colvars.state".
-colvars:   Restarting collective variable "one" from value: 3.20036
-colvars:   Restarting abf bias "abf1" from step number 20.
+colvars: Loading state from text file "test.colvars.state".
+colvars:   Restarting collective variable "one" from value: 3.20038
+colvars:   Restarted abf bias "abf1" with step number 20.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
 colvars: The final output state file will be "test.restart.colvars.state".
-colvars: Opening trajectory file "test.restart.colvars.traj".
-colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
-colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
-colvars:   Prepared sample and gradient buffers at step 20.
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
 colvars: Saving collective variables state to "test.restart.colvars.state".
-colvars: Resetting the Collective Variables module.
+colvars: Saving collective variables state to "test.restart.colvars.state".
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped
index 59f390b59..b9f26a9c1 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.state.stripped
@@ -5,13 +5,13 @@ configuration {
 
 colvar {
   name one
-  x  3.17582252688381e+00
+  x       3.1758939206034
 }
 
 abf {
   configuration {
-    step 40
-    name abf1
+step 40
+name abf1
   }
 
 samples
@@ -20,8 +20,8 @@ samples
  0 0 0 0
 
 gradient
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 -8.67716293178495e+00 0.00000000000000e+00
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0 0 0 0 0 0 -8.6637911275798 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
 }
 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj
index 82200b242..ced9762f9 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.colvars.traj
@@ -1,22 +1,22 @@
 # step         one                   fa_one                
-          20    3.20036076583879e+00 -1.12776581376024e-01 
-          21    3.19676250595523e+00 -1.12776581376024e-01 
-          22    3.19323015858381e+00 -2.99226657105897e-01 
-          23    3.18986878033029e+00 -7.71570670388436e-01 
-          24    3.18676635816465e+00 -1.45966444381162e+00 
-          25    3.18399012323985e+00 -2.29255009605800e+00 
-          26    3.18158461659959e+00 -3.20291155852885e+00 
-          27    3.17957172980453e+00 -4.13119762789999e+00 
-          28    3.17795242533882e+00 -5.02830487271041e+00 
-          29    3.17670962516017e+00 -5.85665418044438e+00 
-          30    3.17581173522468e+00 -6.58995308174671e+00 
-          31    3.17521643416185e+00 -7.21224165778954e+00 
-          32    3.17487456266985e+00 -7.71677976467746e+00 
-          33    3.17473400751618e+00 -8.10491399457095e+00 
-          34    3.17474340422162e+00 -8.38478985628265e+00 
-          35    3.17485538125568e+00 -8.56974337269324e+00 
-          36    3.17502906896877e+00 -8.67642273989548e+00 
-          37    3.17523173654562e+00 -8.72292739505557e+00 
-          38    3.17543964478384e+00 -8.72734418672621e+00 
-          39    3.17563832893481e+00 -8.70683028310459e+00 
-          40    3.17582252688381e+00 -8.67716293178495e+00 
+          20    3.20038442890979e+00 -1.03854856547880e-01 
+          21    3.19678862154174e+00 -1.03854856547880e-01 
+          22    3.19325868201096e+00 -2.89577637067747e-01 
+          23    3.18989968114783e+00 -7.61101440554271e-01 
+          24    3.18679962469704e+00 -1.44844736047144e+00 
+          25    3.18402576202599e+00 -2.28077446479501e+00 
+          26    3.18162264923830e+00 -3.19083007934240e+00 
+          27    3.17961218770411e+00 -4.11907208902965e+00 
+          28    3.17799534343587e+00 -5.01636137209204e+00 
+          29    3.17675503558160e+00 -5.84505314310151e+00 
+          30    3.17585966166561e+00 -6.57877537042113e+00 
+          31    3.17526688749274e+00 -7.20148861595175e+00 
+          32    3.17492753806785e+00 -7.70638297502586e+00 
+          33    3.17478948326253e+00 -8.09475011416048e+00 
+          34    3.17480134217557e+00 -8.37469681855967e+00 
+          35    3.17491572893043e+00 -8.55953599790606e+00 
+          36    3.17509176298755e+00 -8.66590727775137e+00 
+          37    3.17529670713715e+00 -8.71191545508902e+00 
+          38    3.17550682085422e+00 -8.71566657237990e+00 
+          39    3.17570764320513e+00 -8.69435074482412e+00 
+          40    3.17589392060342e+00 -8.66379112757977e+00 
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad
index ec20a8621..7d7f6dc06 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.grad
@@ -7,7 +7,7 @@
   1.75000000000000e+00   0.00000000000000e+00
   2.25000000000000e+00   0.00000000000000e+00
   2.75000000000000e+00   0.00000000000000e+00
-  3.25000000000000e+00  -8.67716293178499e+00
+  3.25000000000000e+00  -8.66379112757977e+00
   3.75000000000000e+00   0.00000000000000e+00
   4.25000000000000e+00   0.00000000000000e+00
   4.75000000000000e+00   0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf
index 980be4de1..18c4a1926 100644
--- a/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf
+++ b/lammps/tests/library/000_distance-grid_abf/AutoDiff/test.restart.pmf
@@ -1,13 +1,13 @@
 # 1
 # -2.50000000000000e-01  5.00000000000000e-01         21  0
 
-  0.00000000000000e+00   4.33858146589250e+00
-  5.00000000000000e-01   4.33858146589250e+00
-  1.00000000000000e+00   4.33858146589250e+00
-  1.50000000000000e+00   4.33858146589250e+00
-  2.00000000000000e+00   4.33858146589250e+00
-  2.50000000000000e+00   4.33858146589250e+00
-  3.00000000000000e+00   4.33858146589250e+00
+  0.00000000000000e+00   4.33189556378988e+00
+  5.00000000000000e-01   4.33189556378988e+00
+  1.00000000000000e+00   4.33189556378988e+00
+  1.50000000000000e+00   4.33189556378988e+00
+  2.00000000000000e+00   4.33189556378988e+00
+  2.50000000000000e+00   4.33189556378988e+00
+  3.00000000000000e+00   4.33189556378988e+00
   3.50000000000000e+00   0.00000000000000e+00
   4.00000000000000e+00   0.00000000000000e+00
   4.50000000000000e+00   0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_abf/lammps-version.txt b/lammps/tests/library/000_distance-grid_abf/lammps-version.txt
index 308cf25eb..8b1378917 100644
--- a/lammps/tests/library/000_distance-grid_abf/lammps-version.txt
+++ b/lammps/tests/library/000_distance-grid_abf/lammps-version.txt
@@ -1 +1 @@
-LAMMPS (19 Mar 2020)
+
diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out
index 6cdfac061..60f8d8ab5 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out
+++ b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.out
@@ -1,10 +1,12 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +58,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,7 +106,7 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
 colvars:   # name = "harmonic1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = on
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
@@ -112,11 +114,13 @@ colvars:   # writeTISamples = off [default]
 colvars:   # writeTIPMF = on
 colvars:   # centers = { 0.1 }
 colvars:   # targetCenters = { 0.2 }
+colvars:   Initial step for restraint change: 0
 colvars:   # targetNumSteps = 10
 colvars:   # targetNumStages = 0 [default]
 colvars:   # outputAccumulatedWork = on
 colvars:   # outputCenters = on
 colvars:   # forceConstant = 0.001
+colvars:   # decoupling = off [default]
 colvars:   # targetForceConstant = -1 [default]
 colvars:   The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5).
 colvars: ----------------------------------------------------------------------
@@ -124,17 +128,16 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
-colvars: Opening trajectory file "test.colvars.traj".
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
 colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
 colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
+colvars: The final output state file will be "test.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars:   Writing TI PMF to file "test.harmonic1.ti.pmf".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars:   Writing TI PMF to file "test.harmonic1.ti.pmf".
 colvars: Saving collective variables state to "test.colvars.state".
-colvars: Resetting the Collective Variables module.
diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped
index 02bd32580..95b778174 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.colvars.state.stripped
@@ -5,16 +5,16 @@ configuration {
 
 colvar {
   name one
-  x  3.21927610288861e+00
+  x       3.2192761028886
 }
 
 restraint {
   configuration {
-    step 20
-    name harmonic1
-    firstStep            0
-    centers   2.00000000000000e-01
-    accumulatedWork -1.22156562115015e-03
+step 20
+name harmonic1
+firstStep            0
+centers   2.00000000000000e-01
+accumulatedWork -1.22156562115015e-03
   }
 
 histogram
@@ -29,7 +29,7 @@ histogram
 system_forces
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- -2.90562076256866e+00 0.00000000000000e+00 0.00000000000000e+00
+ -2.91094223405173e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out
index 8f922dcfa..69bb3a784 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out
+++ b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.out
@@ -1,10 +1,13 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
+colvars: Will read input state from file "test.colvars.state"
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +59,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,7 +107,7 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
 colvars:   # name = "harmonic1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = on
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
@@ -112,11 +115,13 @@ colvars:   # writeTISamples = off [default]
 colvars:   # writeTIPMF = on
 colvars:   # centers = { 0.1 }
 colvars:   # targetCenters = { 0.2 }
+colvars:   Initial step for restraint change: 0
 colvars:   # targetNumSteps = 10
 colvars:   # targetNumStages = 0 [default]
 colvars:   # outputAccumulatedWork = on
 colvars:   # outputCenters = on
 colvars:   # forceConstant = 0.001
+colvars:   # decoupling = off [default]
 colvars:   # targetForceConstant = -1 [default]
 colvars:   The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5).
 colvars: ----------------------------------------------------------------------
@@ -124,22 +129,21 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
+colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "test.colvars.state".
+colvars: Loading state from text file "test.colvars.state".
 colvars:   Restarting collective variable "one" from value: 3.21928
-colvars:   Restarting harmonic bias "harmonic1" from step number 20.
+colvars:   Restarted harmonic bias "harmonic1" with step number 20.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
 colvars: The final output state file will be "test.restart.colvars.state".
-colvars: Opening trajectory file "test.restart.colvars.traj".
-colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
-colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars:   Writing TI PMF to file "test.restart.harmonic1.ti.pmf".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars:   Writing TI PMF to file "test.restart.harmonic1.ti.pmf".
 colvars: Saving collective variables state to "test.restart.colvars.state".
-colvars: Resetting the Collective Variables module.
diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped
index 072172249..bfe487f97 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.state.stripped
@@ -5,16 +5,16 @@ configuration {
 
 colvar {
   name one
-  x  3.21816782210277e+00
+  x       3.2181678221028
 }
 
 restraint {
   configuration {
-    step 40
-    name harmonic1
-    firstStep            0
-    centers   2.00000000000000e-01
-    accumulatedWork -1.22156562115015e-03
+step 40
+name harmonic1
+firstStep            0
+centers   2.00000000000000e-01
+accumulatedWork -1.22156562115015e-03
   }
 
 histogram
@@ -29,7 +29,7 @@ histogram
 system_forces
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 4.14032182279623e+00 0.00000000000000e+00 0.00000000000000e+00
+ 4.13477803678241e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj
index 92ad6def5..cf945fde8 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj
+++ b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/AutoDiff/test.restart.colvars.traj
@@ -1,5 +1,5 @@
 # step         one                   fa_one                 E_harmonic1           x0_one                W_harmonic1          
-          20    3.21927610420272e+00 -1.20771044168109e-02   1.82320563868192e-02  2.00000000000000e-01 -1.22156562115015e-03
+          20    3.21927610420273e+00 -1.20771044168109e-02   1.82320563868192e-02  2.00000000000000e-01 -1.22156562115015e-03
           21    3.21712493217757e+00 -1.20684997287103e-02   1.82060857127351e-02  2.00000000000000e-01 -1.22156562115015e-03
           22    3.21491957781060e+00 -1.20596783112424e-02   1.81794801213313e-02  2.00000000000000e-01 -1.22156562115015e-03
           23    3.21277838638075e+00 -1.20511135455230e-02   1.81536672108860e-02  2.00000000000000e-01 -1.22156562115015e-03
@@ -8,12 +8,12 @@
           26    3.20772353744991e+00 -1.20308941497996e-02   1.80928017554604e-02  2.00000000000000e-01 -1.22156562115015e-03
           27    3.20672256044185e+00 -1.20268902417674e-02   1.80807611109400e-02  2.00000000000000e-01 -1.22156562115015e-03
           28    3.20611979984341e+00 -1.20244791993736e-02   1.80735125020211e-02  2.00000000000000e-01 -1.22156562115015e-03
-          29    3.20591518168161e+00 -1.20236607267264e-02   1.80710521589280e-02  2.00000000000000e-01 -1.22156562115015e-03
+          29    3.20591518168161e+00 -1.20236607267264e-02   1.80710521589279e-02  2.00000000000000e-01 -1.22156562115015e-03
           30    3.20608917462516e+00 -1.20243566985006e-02   1.80731442515971e-02  2.00000000000000e-01 -1.22156562115015e-03
           31    3.20660613772624e+00 -1.20264245509050e-02   1.80793609348262e-02  2.00000000000000e-01 -1.22156562115015e-03
           32    3.20741824461812e+00 -1.20296729784725e-02   1.80891289961239e-02  2.00000000000000e-01 -1.22156562115015e-03
           33    3.20846986624845e+00 -1.20338794649938e-02   1.81017818722499e-02  2.00000000000000e-01 -1.22156562115015e-03
-          34    3.20970218001743e+00 -1.20388087200697e-02   1.81166144248033e-02  2.00000000000000e-01 -1.22156562115015e-03
+          34    3.20970218001742e+00 -1.20388087200697e-02   1.81166144248033e-02  2.00000000000000e-01 -1.22156562115015e-03
           35    3.21105763094978e+00 -1.20442305237991e-02   1.81329361138018e-02  2.00000000000000e-01 -1.22156562115015e-03
           36    3.21248380017773e+00 -1.20499352007109e-02   1.81501172926665e-02  2.00000000000000e-01 -1.22156562115015e-03
           37    3.21393637834814e+00 -1.20557455133925e-02   1.81676249854606e-02  2.00000000000000e-01 -1.22156562115015e-03
diff --git a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/lammps-version.txt b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/lammps-version.txt
index 308cf25eb..8b1378917 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/lammps-version.txt
+++ b/lammps/tests/library/000_distance-grid_harmonic-centers-moving-ti/lammps-version.txt
@@ -1 +1 @@
-LAMMPS (19 Mar 2020)
+
diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out
index 7b1e4f787..b07731c0f 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out
+++ b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.out
@@ -1,10 +1,12 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +58,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,7 +106,7 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
 colvars:   # name = "harmonic1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
@@ -114,6 +116,7 @@ colvars:   # centers = { 0.1 }
 colvars:   # targetCenters = { 0.1 } [default]
 colvars:   # outputCenters = off [default]
 colvars:   # forceConstant = 0.001
+colvars:   # decoupling = off [default]
 colvars:   # targetForceConstant = -1 [default]
 colvars:   The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5).
 colvars: ----------------------------------------------------------------------
@@ -121,17 +124,16 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
-colvars: Opening trajectory file "test.colvars.traj".
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
 colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
 colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
+colvars: The final output state file will be "test.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars:   Writing TI PMF to file "test.harmonic1.ti.pmf".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars:   Writing TI PMF to file "test.harmonic1.ti.pmf".
 colvars: Saving collective variables state to "test.colvars.state".
-colvars: Resetting the Collective Variables module.
diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped
index a35c8ee23..cd1638600 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.colvars.state.stripped
@@ -5,13 +5,13 @@ configuration {
 
 colvar {
   name one
-  x  3.21927552466352e+00
+  x       3.2192755246635
 }
 
 restraint {
   configuration {
-    step 20
-    name harmonic1
+step 20
+name harmonic1
   }
 
 histogram
@@ -26,7 +26,7 @@ histogram
 system_forces
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- -2.90553316335430e+00 0.00000000000000e+00 0.00000000000000e+00
+ -2.91085463660568e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out
index 513279fe8..fe531fd6e 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out
+++ b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.out
@@ -1,10 +1,13 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
+colvars: Will read input state from file "test.colvars.state"
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +59,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,7 +107,7 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
 colvars:   # name = "harmonic1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
@@ -114,6 +117,7 @@ colvars:   # centers = { 0.1 }
 colvars:   # targetCenters = { 0.1 } [default]
 colvars:   # outputCenters = off [default]
 colvars:   # forceConstant = 0.001
+colvars:   # decoupling = off [default]
 colvars:   # targetForceConstant = -1 [default]
 colvars:   The force constant for colvar "one" will be rescaled to 0.004 according to the specified width (0.5).
 colvars: ----------------------------------------------------------------------
@@ -121,22 +125,21 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
+colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "test.colvars.state".
+colvars: Loading state from text file "test.colvars.state".
 colvars:   Restarting collective variable "one" from value: 3.21928
-colvars:   Restarting harmonic bias "harmonic1" from step number 20.
+colvars:   Restarted harmonic bias "harmonic1" with step number 20.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
 colvars: The final output state file will be "test.restart.colvars.state".
-colvars: Opening trajectory file "test.restart.colvars.traj".
-colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
-colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars:   Writing TI PMF to file "test.restart.harmonic1.ti.pmf".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars:   Writing TI PMF to file "test.restart.harmonic1.ti.pmf".
 colvars: Saving collective variables state to "test.restart.colvars.state".
-colvars: Resetting the Collective Variables module.
diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped
index ffe43b4e0..0f6d646be 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.state.stripped
@@ -5,13 +5,13 @@ configuration {
 
 colvar {
   name one
-  x  3.21816571931147e+00
+  x       3.2181657193115
 }
 
 restraint {
   configuration {
-    step 40
-    name harmonic1
+step 40
+name harmonic1
   }
 
 histogram
@@ -26,7 +26,7 @@ histogram
 system_forces
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 4.14054595271419e+00 0.00000000000000e+00 0.00000000000000e+00
+ 4.13500215076519e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj
index d6db29cb9..fde91a8ee 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj
+++ b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/AutoDiff/test.restart.colvars.traj
@@ -9,13 +9,13 @@
           27    3.20672148778391e+00 -1.24268859511357e-02 
           28    3.20611865018057e+00 -1.24244746007223e-02 
           29    3.20591395386379e+00 -1.24236558154552e-02 
-          30    3.20608786769079e+00 -1.24243514707632e-02 
+          30    3.20608786769079e+00 -1.24243514707631e-02 
           31    3.20660475092205e+00 -1.24264190036882e-02 
           32    3.20741677741603e+00 -1.24296671096641e-02 
           33    3.20846831835692e+00 -1.24338732734277e-02 
           34    3.20970055138465e+00 -1.24388022055386e-02 
-          35    3.21105592175671e+00 -1.24442236870269e-02 
-          36    3.21248201082058e+00 -1.24499280432823e-02 
+          35    3.21105592175671e+00 -1.24442236870268e-02 
+          36    3.21248201082057e+00 -1.24499280432823e-02 
           37    3.21393450941138e+00 -1.24557380376455e-02 
           38    3.21537923153366e+00 -1.24615169261346e-02 
           39    3.21679330254328e+00 -1.24671732101731e-02 
diff --git a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/lammps-version.txt b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/lammps-version.txt
index 308cf25eb..8b1378917 100644
--- a/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/lammps-version.txt
+++ b/lammps/tests/library/000_distance-grid_harmonic-fixed-ti/lammps-version.txt
@@ -1 +1 @@
-LAMMPS (19 Mar 2020)
+
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out
index 9f67f0dfd..f7d142022 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.out
@@ -1,10 +1,12 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +58,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,7 +106,7 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "metadynamics" instance.
 colvars:   # name = "metadynamics1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
@@ -132,17 +134,16 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "test.colvars.state".
-colvars: Opening trajectory file "test.colvars.traj".
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
 colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
 colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
+colvars: The final output state file will be "test.colvars.state".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars:   Writing TI PMF to file "test.metadynamics1.ti.pmf".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
 colvars:   Writing TI PMF to file "test.metadynamics1.ti.pmf".
 colvars: Saving collective variables state to "test.colvars.state".
-colvars: Resetting the Collective Variables module.
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped
index 43a9f1078..9cf83ad73 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.state.stripped
@@ -5,40 +5,42 @@ configuration {
 
 colvar {
   name one
-  x  3.21930432522528e+00
+  x       3.2193043252253
 }
 
 metadynamics {
   configuration {
-    step 20
-    name metadynamics1
+step 20
+name metadynamics1
   }
-  hills_energy
+
+hills_energy
 grid_parameters {
   n_colvars 1
-  lower_boundaries  0.00000000000000e+00
-  upper_boundaries  1.00000000000000e+01
-  widths  5.00000000000000e-01
+  lower_boundaries  0
+  upper_boundaries  10
+  widths  0.5
   sizes  20
 }
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 3.38514518045129e-08 1.67980873239227e-05 6.53166613975910e-04
- 1.99007630938374e-03 4.75113192446023e-04 8.88804117170131e-06
+ 3.38514518045131e-08 1.67980873239228e-05 6.53166613975911e-04
+ 1.99007630938374e-03 4.75113192446022e-04 8.88804117170127e-06
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00
-  hills_energy_gradients
+
+hills_energy_gradients
 grid_parameters {
   n_colvars 1
-  lower_boundaries  0.00000000000000e+00
-  upper_boundaries  1.00000000000000e+01
-  widths  5.00000000000000e-01
+  lower_boundaries  0
+  upper_boundaries  10
+  widths  0.5
   sizes  20
 }
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 5.06436271151796e-07 1.65756901208920e-04 3.11865061690916e-03
- -6.33399841494236e-04 -2.57094275931607e-03 -9.33614419730819e-05
+ 5.06436271151799e-07 1.65756901208920e-04 3.11865061690917e-03
+ -6.33399841494245e-04 -2.57094275931606e-03 -9.33614419730815e-05
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
@@ -56,7 +58,7 @@ histogram
 system_forces
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- -2.91090719796639e+00 0.00000000000000e+00 0.00000000000000e+00
+ -2.91622858016849e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj
index 2a6b58e0b..29c7da327 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.colvars.traj
@@ -9,14 +9,14 @@
            7    3.21051965076451e+00  0.00000000000000e+00 
            8    3.21305004618829e+00  0.00000000000000e+00 
            9    3.21566301892414e+00  0.00000000000000e+00 
-          10    3.21820151179421e+00  3.22233053233233e-04 
-          11    3.22051469810240e+00  3.22233053233233e-04 
-          12    3.22246811428391e+00  3.22233053233233e-04 
-          13    3.22395287819937e+00  3.22233053233233e-04 
-          14    3.22489272676255e+00  3.22233053233233e-04 
-          15    3.22524801388741e+00  3.22233053233233e-04 
-          16    3.22501642539137e+00  3.22233053233233e-04 
-          17    3.22423078880002e+00  3.22233053233233e-04 
-          18    3.22295471902996e+00  3.22233053233233e-04 
-          19    3.22127686703542e+00  3.22233053233233e-04 
-          20    3.21930432522528e+00  6.33399841494236e-04 
+          10    3.21820151179421e+00  3.22233053233242e-04 
+          11    3.22051469810240e+00  3.22233053233242e-04 
+          12    3.22246811428391e+00  3.22233053233242e-04 
+          13    3.22395287819937e+00  3.22233053233242e-04 
+          14    3.22489272676255e+00  3.22233053233242e-04 
+          15    3.22524801388741e+00  3.22233053233242e-04 
+          16    3.22501642539137e+00  3.22233053233242e-04 
+          17    3.22423078880002e+00  3.22233053233242e-04 
+          18    3.22295471902996e+00  3.22233053233242e-04 
+          19    3.22127686703542e+00  3.22233053233242e-04 
+          20    3.21930432522528e+00  6.33399841494245e-04 
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out
index e96e7f4a8..0b3b2c692 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.out
@@ -1,10 +1,13 @@
-colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
 colvars: Please cite Fiorin et al, Mol Phys 2013:
-colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
-colvars: in any publication based on this calculation.
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
 colvars: This version was built with the C++11 standard or higher.
-colvars: Using LAMMPS interface, version "2020-04-07".
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 2)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: not available
+colvars: Will read input state from file "test.colvars.state"
 colvars: ----------------------------------------------------------------------
 colvars: Reading new configuration from file "test.in":
 colvars: # units = "" [default]
@@ -56,27 +59,27 @@ colvars:     # forceNoPBC = off [default]
 colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group1"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group1" defined with 4 atoms requested.
 colvars:       Initializing atom group "group2".
 colvars:       # name = "" [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
+colvars:       # centerToOrigin = off [default]
+colvars:       # centerToReference = off [default]
+colvars:       # rotateToReference = off [default]
 colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "group2"
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
-colvars:       # enableForces = on [default]
 colvars:       # enableFitGradients = on [default]
 colvars:       # printAtomIDs = off [default]
 colvars:       Atom group "group2" defined with 4 atoms requested.
@@ -104,7 +107,7 @@ colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "metadynamics" instance.
 colvars:   # name = "metadynamics1" [default]
 colvars:   # colvars = { one }
-colvars:   # zeroStepData = off [default]
+colvars:   # stepZeroData = off [default]
 colvars:   # outputEnergy = off [default]
 colvars:   # outputFreq = 10 [default]
 colvars:   # timeStepFactor = 1 [default]
@@ -132,22 +135,23 @@ colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
+colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "test.colvars.state".
+colvars: Loading state from text file "test.colvars.state".
 colvars:   Restarting collective variable "one" from value: 3.2193
-colvars:   Restarting metadynamics bias "metadynamics1" from step number 20.
+colvars:     successfully read the biasing potential and its gradients from grids.
+colvars:     successfully read 0 explicit hills from state.
+colvars:   Restarted metadynamics bias "metadynamics1" with step number 20.
 colvars: ----------------------------------------------------------------------
-colvars: The restart output state file will be "rest.colvars.state".
 colvars: The final output state file will be "test.restart.colvars.state".
-colvars: Opening trajectory file "test.restart.colvars.traj".
-colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
-colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars:   Writing TI PMF to file "test.restart.metadynamics1.ti.pmf".
 colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
-colvars: Saving collective variables state to "rest.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
 colvars:   Writing TI PMF to file "test.restart.metadynamics1.ti.pmf".
 colvars: Saving collective variables state to "test.restart.colvars.state".
-colvars: Resetting the Collective Variables module.
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped
index b2e45880d..8fd94ae17 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.state.stripped
@@ -5,39 +5,41 @@ configuration {
 
 colvar {
   name one
-  x  3.21824609730369e+00
+  x       3.2182460973037
 }
 
 metadynamics {
   configuration {
-    step 40
-    name metadynamics1
+step 40
+name metadynamics1
   }
-  hills_energy
+
+hills_energy
 grid_parameters {
   n_colvars 1
-  lower_boundaries  0.00000000000000e+00
-  upper_boundaries  1.00000000000000e+01
-  widths  5.00000000000000e-01
+  lower_boundaries  0
+  upper_boundaries  10
+  widths  0.5
   sizes  20
 }
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 7.13281977740248e-08 3.47432719684774e-05 1.32710969531751e-03
- 3.97520584607863e-03 9.33724923614962e-04 1.71978626509194e-05
+ 7.13281977740245e-08 3.47432719684773e-05 1.32710969531751e-03
+ 3.97520584607863e-03 9.33724923614963e-04 1.71978626509194e-05
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00
-  hills_energy_gradients
+
+hills_energy_gradients
 grid_parameters {
   n_colvars 1
-  lower_boundaries  0.00000000000000e+00
-  upper_boundaries  1.00000000000000e+01
-  widths  5.00000000000000e-01
+  lower_boundaries  0
+  upper_boundaries  10
+  widths  0.5
   sizes  20
 }
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 1.06439936442365e-06 3.41569090091749e-04 6.29030566258467e-03
+ 1.06439936442365e-06 3.41569090091748e-04 6.29030566258467e-03
  -1.39755890530190e-03 -5.08230090961957e-03 -1.81171853765071e-04
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
@@ -56,7 +58,7 @@ histogram
 system_forces
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
- 4.13122374770899e+00 0.00000000000000e+00 0.00000000000000e+00
+ 4.12568041118547e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
  0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj
index eb3fc8a80..1fe1c9d89 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/AutoDiff/test.restart.colvars.traj
@@ -1,22 +1,22 @@
 # step         one                   fa_one                
-          20    3.21930432520045e+00  6.33399841494236e-04 
-          21    3.21715548774701e+00  6.33399841494236e-04 
-          22    3.21495252438721e+00  6.33399841494236e-04 
-          23    3.21281377542992e+00  6.33399841494236e-04 
-          24    3.21084656658218e+00  6.33399841494236e-04 
-          25    3.20914116190983e+00  6.33399841494236e-04 
-          26    3.20776651114698e+00  6.33399841494236e-04 
-          27    3.20676812466764e+00  6.33399841494236e-04 
-          28    3.20616797192082e+00  6.33399841494236e-04 
-          29    3.20596596977028e+00  6.33399841494236e-04 
+          20    3.21930432520045e+00  6.33399841494245e-04 
+          21    3.21715548774701e+00  6.33399841494245e-04 
+          22    3.21495252438721e+00  6.33399841494245e-04 
+          23    3.21281377542992e+00  6.33399841494245e-04 
+          24    3.21084656658218e+00  6.33399841494245e-04 
+          25    3.20914116190983e+00  6.33399841494245e-04 
+          26    3.20776651114698e+00  6.33399841494245e-04 
+          27    3.20676812466765e+00  6.33399841494245e-04 
+          28    3.20616797192082e+00  6.33399841494245e-04 
+          29    3.20596596977028e+00  6.33399841494245e-04 
           30    3.20614257752035e+00  1.07577301998646e-03 
           31    3.20666215184123e+00  1.07577301998646e-03 
           32    3.20747685740396e+00  1.07577301998646e-03 
           33    3.20853105712263e+00  1.07577301998646e-03 
           34    3.20976592143065e+00  1.07577301998646e-03 
-          35    3.21112388983557e+00  1.07577301998646e-03 
+          35    3.21112388983558e+00  1.07577301998646e-03 
           36    3.21255253963151e+00  1.07577301998646e-03 
-          37    3.21400755940122e+00  1.07577301998646e-03 
+          37    3.21400755940123e+00  1.07577301998646e-03 
           38    3.21545476262327e+00  1.07577301998646e-03 
           39    3.21687127560958e+00  1.07577301998646e-03 
           40    3.21824609730369e+00  1.39755890530190e-03 
diff --git a/lammps/tests/library/000_distance-grid_metadynamics-ti/lammps-version.txt b/lammps/tests/library/000_distance-grid_metadynamics-ti/lammps-version.txt
index 308cf25eb..8b1378917 100644
--- a/lammps/tests/library/000_distance-grid_metadynamics-ti/lammps-version.txt
+++ b/lammps/tests/library/000_distance-grid_metadynamics-ti/lammps-version.txt
@@ -1 +1 @@
-LAMMPS (19 Mar 2020)
+
diff --git a/lammps/tests/library/run_tests.sh b/lammps/tests/library/run_tests.sh
index ad2e15311..b772766f6 100755
--- a/lammps/tests/library/run_tests.sh
+++ b/lammps/tests/library/run_tests.sh
@@ -293,11 +293,11 @@ else
   echo "$(${TPUT_RED})There were failed tests.$(${TPUT_CLEAR})"
   if [ ${#failed_tests[@]} -gt 0 ]; then
     echo "The following tests are failed:"
-    printf "%s\n" "${failed_tests[@]}"
+    printf "%s\n" "${failed_tests[@]}" | sort -u
   fi
   if [ ${#failed_tests_low_prec[@]} -gt 0 ]; then
     echo "The following tests are failed, but passed at low precisions:"
-    printf "%s\n" "${failed_tests_low_prec[@]}"
+    printf "%s\n" "${failed_tests_low_prec[@]}" | sort -u
   fi
   exit 1
 fi

From b99011a70e7500521ab558f83d86a9967a9146a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Tue, 16 Apr 2024 16:24:20 +0200
Subject: [PATCH 07/13] Fix parsing of white-space only blocks

---
 src/colvarparse.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/colvarparse.cpp b/src/colvarparse.cpp
index 76b5c694c..cf3096ba5 100644
--- a/src/colvarparse.cpp
+++ b/src/colvarparse.cpp
@@ -592,7 +592,7 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
 {
   if (cvm::debug())
     cvm::log("Configuration string for \""+std::string(key)+
-             "\": \"\n"+conf+"\".\n");
+             "\":\n\""+conf+"\".\n");
 
   strip_values(conf);
   // after stripping, the config string has either empty lines, or
@@ -833,7 +833,8 @@ bool colvarparse::key_lookup(std::string const &conf,
                                        data_end) + 1;
     }
 
-    if (data != NULL) {
+    // data_end < data_begin means that the data or block contains only whitespace
+    if (data != NULL && data_end > data_begin) {
       data->append(line, data_begin, (data_end-data_begin));
 
       if (cvm::debug()) {

From 299dbf0272c92127d920160fcfe30207d159f58a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Tue, 16 Apr 2024 16:43:02 +0200
Subject: [PATCH 08/13] NAMD doc for lambda-dynamics

[update-doc]
---
 doc/colvars-code-refs.bib   | 13 ++++++++++++
 doc/colvars-refman-main.tex | 40 +++++++++++++++++++++++++------------
 doc/colvars-refman-namd.tex |  2 +-
 src/colvarmodule_refs.h     | 23 +++++++++++++++++++++
 4 files changed, 64 insertions(+), 14 deletions(-)

diff --git a/doc/colvars-code-refs.bib b/doc/colvars-code-refs.bib
index 84cfa1be8..8e2570f0e 100644
--- a/doc/colvars-code-refs.bib
+++ b/doc/colvars-code-refs.bib
@@ -255,6 +255,19 @@ @article{Humphrey1996
   url = {https://doi.org/10.1016/0263-7855(96)00018-5}
 }
 
+% alchLambda colvar component
+% alchFLambda colvar component
+% Tinker-HP interface
+@misc{Lagardere2023,
+      title={Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations},
+      author={Louis Lagard\`ere and Lise Maurin and Olivier Adjoua and Krystel El Hage and Pierre Monmarch\'e and Jean-Philip Piquemal and J\'er\^ome H\'enin},
+      year={2023},
+      eprint={2307.08006},
+      archivePrefix={arXiv},
+      primaryClass={physics.chem-ph},
+      url = {https://arxiv.org/abs/2307.08006}
+}
+
 % eABF implementation
 % CZAR eABF estimator
 @article{Lesage2017,
diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex
index 0e510c5db..f4224497c 100644
--- a/doc/colvars-refman-main.tex
+++ b/doc/colvars-refman-main.tex
@@ -3042,32 +3042,46 @@
 \cvsubsubsec{\texttt{alchLambda}: alchemical lambda parameter.}{sec:cvc_alchlambda}
 \labelkey{colvar|alchLambda}
 
-The \texttt{alchLambda~\{\}} block defines a component returning the alchemical lambda parameter
-of the back-end simulation in \MDENGINE{}, provided that it is enabled using the appropriate options
-of \MDENGINE{}. This coordinate is obtained from the back-end at the beginning of a simulation, and
-synchronized from Colvars to \MDENGINE{} at every time step. This enables lambda-dynamics simulations.
-The \texttt{alchLambda} block itself takes no parameters, it should be left empty.
-In contrast, the \texttt{colvar} block containing it should define the relevant extended-system parameters
-to enable lambda dynamics, primarily \refkey{extendedMass}{colvar|extendedMass}:
+The \texttt{alchLambda} block defines a component returning the alchemical lambda parameter
+of the back-end simulation in \MDENGINE{}, provided that it is enabled within that software.
+\cvnamdonly{Specifically, the flag \texttt{alchOn} should be enabled, and \texttt{alchType}
+should be set to \texttt{TI}.}
+The current lambda value is obtained from the back-end at the beginning of a simulation, and
+synchronized from Colvars to \MDENGINE{} at every following time step.
+This enables lambda-dynamics simulations as documented in detail in \cite{Lagardere2023}.
+The \texttt{alchLambda} keyword itself takes no parameters.
+
+To run lambda-dynamics, the enclosing \texttt{colvar} block should contain extended-system
+parameters (\ref{sec:colvar_extended}) as in the following example:
 
 \begin{cvexampleinput}
 \-colvar~\{\\
 \-~~name~lambda\\
 \-~~extendedLagrangian~on\\
-\-~~extendedMass~400\\
-\-\\
-\-~~alchLambda~\{~\#~Keep~the~line~break\\
-\-~~\}\\
+\-~~extendedMass~150000\\
+\-~~extendedLangevinDamping~1000\\
+\\
+\-~~lowerBoundary~0\\
+\-~~upperBoundary~1\\
+\-~~reflectingLowerBoundary\\
+\-~~reflectingUpperBoundary\\
+\\
+\-~~alchLambda\\
 \-\}
 \end{cvexampleinput}
 
+These parameter values have been found  to give stable dynamics for a wide range of applications\cite{Lagardere2023}.
+Reflecting boundary conditions are recommended for lambda-dynamics to ensure that the alchemical
+variable remains precisely within its physical range.
+
+
 \cvsubsubsec{\texttt{alchFlambda}: Force on the alchemical lambda parameter.}{sec:cvc_alchFlambda}
 \labelkey{colvar|alchFlambda}
 
 The \texttt{alchFlambda~\{\}} block defines a component returning the force exterted on the alchemical
 lambda parameter of the back-end simulation in \MDENGINE{}, provided that it is enabled using the appropriate options
 of \MDENGINE{}. This coordinate is obtained from the back-end at each time step of a simulation.
-The \texttt{alchfLambda} block itself takes no parameters, it should be left empty.
+The \texttt{alchFlambda} block itself takes no parameters, it should be left empty.
 } % end of \cvalchlambdaonly
 
 \cvsubsec{Raw data: building blocks for custom functions}{sec:cvc_raw}
@@ -4508,7 +4522,7 @@
     positive decimal}{%
     This parameter specifies the fictitious mass in the case of an alchemical
     variable used in lambda-dynamics (\refkey{alchLambda}{colvar|alchLambda}).
-    Note that the dimension is not that of a usual mass. Its unit is the energy unit
+    Note that the dimension is not that of a usual mass: its unit is the energy unit
     (\ref{sec:units}) times fs$^2$.
     }
 }
diff --git a/doc/colvars-refman-namd.tex b/doc/colvars-refman-namd.tex
index 6e30e6861..c1b56c631 100644
--- a/doc/colvars-refman-namd.tex
+++ b/doc/colvars-refman-namd.tex
@@ -32,7 +32,7 @@
 \newcommand{\cvnamebasedonly}[1]{#1}
 
 % only in programs were the alchemical coordinate (alchLambda) is available
-\newcommand{\cvalchlambdaonly}[1]{}
+\newcommand{\cvalchlambdaonly}[1]{#1}
 
 % File output prefixes
 \newcommand{\outputName}{\emph{outputName}}
diff --git a/src/colvarmodule_refs.h b/src/colvarmodule_refs.h
index 7af4656e6..031756750 100644
--- a/src/colvarmodule_refs.h
+++ b/src/colvarmodule_refs.h
@@ -244,6 +244,20 @@
     "  url = {https://doi.org/10.1016/0263-7855(96)00018-5}\n"
     "}\n";
 
+  paper_count_[std::string("Lagardere2023")] = 0;
+  paper_url_[std::string("Lagardere2023")] = "https://arxiv.org/abs/2307.08006";
+  paper_bibtex_[std::string("Lagardere2023")] =
+    "\n"
+    "@misc{Lagardere2023,\n"
+    "      title={Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations},\n"
+    "      author={Louis Lagard\\`ere and Lise Maurin and Olivier Adjoua and Krystel El Hage and Pierre Monmarch\\'e and Jean-Philip Piquemal and J\\'er\\^ome H\\'enin},\n"
+    "      year={2023},\n"
+    "      eprint={2307.08006},\n"
+    "      archivePrefix={arXiv},\n"
+    "      primaryClass={physics.chem-ph},\n"
+    "      url = {https://arxiv.org/abs/2307.08006}\n"
+    "}\n";
+
   paper_count_[std::string("Lesage2017")] = 0;
   paper_url_[std::string("Lesage2017")] = "https://doi.org/10.1021/acs.jpcb.6b10055";
   paper_bibtex_[std::string("Lesage2017")] =
@@ -617,6 +631,15 @@
   feature_count_[std::string("VMD engine")] = 0;
   feature_paper_map_[std::string("VMD engine")] = "Humphrey1996";
 
+  feature_count_[std::string("alchLambda colvar component")] = 0;
+  feature_paper_map_[std::string("alchLambda colvar component")] = "Lagardere2023";
+
+  feature_count_[std::string("alchFLambda colvar component")] = 0;
+  feature_paper_map_[std::string("alchFLambda colvar component")] = "Lagardere2023";
+
+  feature_count_[std::string("Tinker-HP interface")] = 0;
+  feature_paper_map_[std::string("Tinker-HP interface")] = "Lagardere2023";
+
   feature_count_[std::string("eABF implementation")] = 0;
   feature_paper_map_[std::string("eABF implementation")] = "Lesage2017";
 

From c01fb5d6ff7a95c27b2aabeb9ccf454426d4b9ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Fri, 7 Jun 2024 11:37:55 +0200
Subject: [PATCH 09/13] Finer choice of files to update in regtest script

removes spurious error messages
---
 namd/tests/library/run_tests.sh | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh
index 95f64c676..3136239e2 100755
--- a/namd/tests/library/run_tests.sh
+++ b/namd/tests/library/run_tests.sh
@@ -102,7 +102,7 @@ cleanup_files() {
     fi
     for f in ${script%.namd}.*diff; do if [ ! -s $f ]; then rm -f $f; fi; done # remove empty diffs only
     rm -f ${script%.namd}.*{BAK,old,backup}
-    for f in ${script%.namd}.*{state,state.stripped,out,traj,coor,vel,xsc,dcd,pmf,hills,grad,force,count,histogram?.dat,hist.dat,corrfunc.dat,histogram?.dx,count.dx,pmf.dx,output.dat,kernels.dat}
+    for f in ${script%.namd}.*{state,state.stripped,out,traj,coor,vel,xsc,dcd,pmf,hills,grad,force,count,histogram?.dat,hist.dat,corrfunc.dat,histogram?.dx,count.dx,pmf.dx,output.dat,ti,kernels.dat}
     do
       if [ ! -f "$f.diff" ]; then rm -f $f; fi # keep files that have a non-empty diff
     done
@@ -230,8 +230,11 @@ for dir in ${DIRLIST} ; do
       fi
 
       # Update any additional files with current versions
-      for file in AutoDiff/*; do
-        cp -uf `basename ${file}` AutoDiff/
+      for file in AutoDiff/${basename}*; do
+        source=`basename ${file}`
+        if [ -f ${source} ] ; then
+          cp -uf ${source} AutoDiff/
+        fi
       done
     fi
 

From 9ab0c43b51d07e10be22892f3a1f240a149af505 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Mon, 10 Jun 2024 13:53:31 +0200
Subject: [PATCH 10/13] First step towards MTS support in lambda-dynamics

---
 namd/src/colvarproxy_namd.C      |  4 +-
 namd/tests/library/Common/da.pdb | 22 ++++-----
 src/colvar.cpp                   | 79 +++++++++++++++++++-------------
 src/colvarbias_abf.cpp           | 14 +++---
 src/colvarcomp.h                 |  1 +
 src/colvarcomp_alchlambda.cpp    | 18 ++++++--
 6 files changed, 82 insertions(+), 56 deletions(-)

diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 41a32ae70..e0c2cf389 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -1649,7 +1649,7 @@ int colvarproxy_namd::replica_comm_send(char* msg_data, int msg_len,
 }
 
 
-/// Request energy computation every freq steps
+/// Request alchemical energy computation every freq steps
 int colvarproxy_namd::request_alch_energy_freq(int const freq) {
   // This test is only valid for NAMD3
   if (freq % simparams->computeEnergies) {
@@ -1657,7 +1657,7 @@ int colvarproxy_namd::request_alch_energy_freq(int const freq) {
     return COLVARS_INPUT_ERROR;
   }
   if (!simparams->alchOn) {
-    cvm::error("alch must be enabled for lambda-dynamics.\n");
+    cvm::error("alchOn must be enabled for lambda-dynamics.\n");
     return COLVARS_INPUT_ERROR;
   }
   if (!simparams->alchThermIntOn) {
diff --git a/namd/tests/library/Common/da.pdb b/namd/tests/library/Common/da.pdb
index 368cc7619..64a49cb27 100644
--- a/namd/tests/library/Common/da.pdb
+++ b/namd/tests/library/Common/da.pdb
@@ -1,15 +1,15 @@
 CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
-ATOM      1  N   ALA B   1       6.652  -0.764  -1.333  1.00  0.00      BH    
-ATOM      2  HT2 ALA B   1       5.760  -0.450  -1.766  1.00  0.00      BH    
-ATOM      3  HT3 ALA B   1       7.342  -1.305  -1.892  1.00  0.00      BH    
-ATOM      4  CA  ALA B   1       7.306   0.408  -0.585  1.00  0.00      BH    
-ATOM      5  HA  ALA B   1       8.253  -0.035  -0.313  1.00  0.00      BH    
-ATOM      6  CB  ALA B   1       7.329   1.530  -1.594  1.00  0.00      BH    
-ATOM      7  HB1 ALA B   1       7.786   2.446  -1.164  1.00  0.00      BH    
-ATOM      8  HB2 ALA B   1       7.862   1.113  -2.475  1.00  0.00      BH    
-ATOM      9  HB3 ALA B   1       6.363   1.945  -1.952  1.00  0.00      BH    
-ATOM     10  C   ALA B   1       6.475   0.890   0.649  1.00  0.00      BH    
-ATOM     11  O   ALA B   1       5.256   1.022   0.506  1.00  0.00      BH    
+ATOM      1  N   ALA B   1       6.652  -0.764  -1.333  1.00 -1.00      BH    
+ATOM      2  HT2 ALA B   1       5.760  -0.450  -1.766  1.00 -1.00      BH    
+ATOM      3  HT3 ALA B   1       7.342  -1.305  -1.892  1.00 -1.00      BH    
+ATOM      4  CA  ALA B   1       7.306   0.408  -0.585  1.00 -1.00      BH    
+ATOM      5  HA  ALA B   1       8.253  -0.035  -0.313  1.00 -1.00      BH    
+ATOM      6  CB  ALA B   1       7.329   1.530  -1.594  1.00 -1.00      BH    
+ATOM      7  HB1 ALA B   1       7.786   2.446  -1.164  1.00 -1.00      BH    
+ATOM      8  HB2 ALA B   1       7.862   1.113  -2.475  1.00 -1.00      BH    
+ATOM      9  HB3 ALA B   1       6.363   1.945  -1.952  1.00 -1.00      BH    
+ATOM     10  C   ALA B   1       6.475   0.890   0.649  1.00 -1.00      BH    
+ATOM     11  O   ALA B   1       5.256   1.022   0.506  1.00 -1.00      BH    
 ATOM     12  N   ALA B   2       7.106   1.140   1.813  1.00  0.00      BH    
 ATOM     13  HN  ALA B   2       8.097   1.077   1.900  1.00  0.00      BH    
 ATOM     14  CA  ALA B   2       6.403   1.216   3.045  1.00  0.00      BH    
diff --git a/src/colvar.cpp b/src/colvar.cpp
index 4cb34206b..62c156765 100644
--- a/src/colvar.cpp
+++ b/src/colvar.cpp
@@ -312,6 +312,8 @@ int colvar::init(std::string const &conf)
   // Detect if we have a single component that is an alchemical lambda
   if (is_enabled(f_cv_single_cvc) && cvcs[0]->function_type() == "alchLambda") {
     enable(f_cv_external);
+
+    static_cast<colvar::alch_lambda *>(cvcs[0].get())->init_alchemy(time_step_factor);
   }
 
   // If using scripted biases, any colvar may receive bias forces
@@ -320,6 +322,17 @@ int colvar::init(std::string const &conf)
   }
 
   error_code |= init_extended_Lagrangian(conf);
+
+  // when total atomic forces are obtained from the previous time step,
+  // we cannot (currently) have colvar values and projected total forces for the same timestep
+  // (that would require anticipating the total force request by one timestep)
+  // i.e. the combination of f_cv_total_force_calc and f_cv_multiple_ts requires f_cv_total_force_current_step
+  // Because f_cv_total_force_current_step is static, we can hard-code this, once other features are set
+  // that is f_cv_external and f_cv_extended_Lagrangian
+  if (!is_enabled(f_cv_total_force_current_step)) {
+    exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
+  }
+
   error_code |= init_output_flags(conf);
 
   // Now that the children are defined we can solve dependencies
@@ -1156,6 +1169,8 @@ int colvar::init_dependencies() {
     init_feature(f_cv_total_force, "total_force", f_type_dynamic);
     require_feature_alt(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
 
+    // If this is active, the total force reported to biases (ABF / TI) is from the current step
+    // therefore it does not include Colvars biases -> it is a "system force"
     init_feature(f_cv_total_force_current_step, "total_force_current_step", f_type_dynamic);
 
     // Deps for explicit total force calculation
@@ -1247,15 +1262,6 @@ int colvar::init_dependencies() {
 
     init_feature(f_cv_multiple_ts, "multiple_timestep", f_type_static);
 
-    // when total atomic forces are obtained from the previous time step,
-    // we cannot (currently) have colvar values and projected total forces for the same timestep
-    // TODO this will need refining for driven alchemical parameters
-    // ie. the combination of f_cv_total_force_calc and f_cv_multiple_ts requires f_cv_total_force_current_step
-    // or we need to anticipate the total force request by one timestep
-    if (!cvm::main()->proxy->total_forces_same_step()) {
-      exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
-    }
-
     // check that everything is initialized
     for (i = 0; i < colvardeps::f_cv_ntot; i++) {
       if (is_not_set(i)) {
@@ -1661,22 +1667,20 @@ int colvar::collect_cvc_total_forces()
   if (is_enabled(f_cv_total_force_calc)) {
     ft.reset();
 
-    if (cvm::step_relative() > 0) {
-      // get from the cvcs the total forces from the PREVIOUS step
-      for (size_t i = 0; i < cvcs.size();  i++) {
-        if (!cvcs[i]->is_enabled()) continue;
-            if (cvm::debug())
-            cvm::log("Colvar component no. "+cvm::to_str(i+1)+
-                " within colvar \""+this->name+"\" has total force "+
-                cvm::to_str((cvcs[i])->total_force(),
-                cvm::cv_width, cvm::cv_prec)+".\n");
-        // linear combination is assumed
-        ft += (cvcs[i])->total_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
-      }
+    for (size_t i = 0; i < cvcs.size();  i++) {
+      if (!cvcs[i]->is_enabled()) continue;
+          if (cvm::debug())
+          cvm::log("Colvar component no. "+cvm::to_str(i+1)+
+              " within colvar \""+this->name+"\" has total force "+
+              cvm::to_str((cvcs[i])->total_force(),
+              cvm::cv_width, cvm::cv_prec)+".\n");
+      // linear combination is assumed
+      ft += (cvcs[i])->total_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
     }
 
     if (!(is_enabled(f_cv_hide_Jacobian) && is_enabled(f_cv_subtract_applied_force))) {
-      // add the Jacobian force to the total force, and don't apply any silent
+      // This is by far the most common case
+      // Add the Jacobian force to the total force, and don't apply any silent
       // correction internally: biases such as colvarbias_abf will handle it
       // If f_cv_hide_Jacobian is enabled, a force of -fj is present in ft due to the
       // Jacobian-compensating force
@@ -1684,6 +1688,10 @@ int colvar::collect_cvc_total_forces()
     }
   }
 
+  if (is_enabled(f_cv_total_force_current_step)) {
+   // Report total force value without waiting for calc_colvar_properties()
+    ft_reported = ft;
+  }
   return COLVARS_OK;
 }
 
@@ -1785,9 +1793,12 @@ int colvar::calc_colvar_properties()
     // But we report values at the beginning of the timestep (value at t=0 on the first timestep)
     x_reported = x_ext;
     v_reported = v_ext;
-    // the "total force" with the extended Lagrangian is
-    // calculated in update_forces_energy() below
 
+    // the "total force" for the extended Lagrangian is calculated in update_forces_energy() below
+    // A future improvement could compute a "system force" here, borrowing a part of update_extended_Lagrangian()
+    // this would change the behavior of eABF with respect to other biases
+    // by enabling f_cv_total_force_current_step, and reducing the total force to a system force
+    // giving the behavior of f_cv_subtract_applied_force - this is correct for WTM-eABF etc.
   } else {
 
     if (is_enabled(f_cv_subtract_applied_force) && !cvm::proxy->total_forces_same_step()) {
@@ -1916,14 +1927,18 @@ void colvar::update_extended_Lagrangian()
   }
   f_ext += f_system;
 
-  if (is_enabled(f_cv_subtract_applied_force)) {
-    // Report a "system" force without the biases on this colvar
-    // that is, just the spring force (or alchemical force)
-    ft_reported = f_system;
-  } else {
-    // The total force acting on the extended variable is f_ext
-    // This will be used in the next timestep
-    ft_reported = f_ext;
+  if ( ! is_enabled(f_cv_total_force_current_step)) {
+    if (is_enabled(f_cv_subtract_applied_force)) {
+      // Report a "system" force without the biases on this colvar
+      // that is, just the spring force (or alchemical force)
+      ft_reported = f_system;
+    } else {
+      // The total force acting on the extended variable is f_ext
+      // This will be used in the next timestep
+      ft_reported = f_ext;
+    }
+    // Since biases have already been updated, this ft_reported will only be
+    // communicated to biases at the next timestep
   }
 
   // backup in case we need to revert this integration timestep
diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp
index 5beb24a67..ae598ce39 100644
--- a/src/colvarbias_abf.cpp
+++ b/src/colvarbias_abf.cpp
@@ -346,11 +346,12 @@ int colvarbias_abf::update()
   if (can_accumulate_data() && is_enabled(f_cvb_history_dependent)) {
 
     if (cvm::step_relative() > 0 || cvm::proxy->total_forces_same_step()) {
+      // Note: this will skip step 0 data when available in some cases (extended system),
+      // but not doing so would make the code more complex
       if (samples->index_ok(force_bin)) {
         // Only if requested and within bounds of the grid...
 
-        // get total forces (lagging by 1 timestep) from colvars
-        // and subtract previous ABF force if necessary
+        // get total force and subtract previous ABF force if necessary
         update_system_force();
 
         gradients->acc_force(force_bin, system_force);
@@ -457,14 +458,13 @@ int colvarbias_abf::update_system_force()
   // System force from atomic forces (or extended Lagrangian if applicable)
 
   for (i = 0; i < num_variables(); i++) {
-    if (colvars[i]->is_enabled(f_cv_subtract_applied_force) ||
-       (cvm::proxy->total_forces_same_step() && !colvars[i]->is_enabled(f_cv_external))) {
+    if (colvars[i]->is_enabled(f_cv_subtract_applied_force)
+      || colvars[i]->is_enabled(f_cv_total_force_current_step)) {
       // this colvar is already subtracting the ABF force
-      // or the "total force" is really a system force at current step
-      // (For external parameters, the total force contains biasing forces
-      // unless f_cv_subtract_applied_force is enabled)
+      // or the "total force" is from current step and cannot possibly contain Colvars biases
       system_force[i] = colvars[i]->total_force().real_value;
     } else {
+      // Subtract previous step's bias force from previous step's total force
       system_force[i] = colvars[i]->total_force().real_value
         - colvar_forces[i].real_value;
     }
diff --git a/src/colvarcomp.h b/src/colvarcomp.h
index e47a2a76d..9d6887666 100644
--- a/src/colvarcomp.h
+++ b/src/colvarcomp.h
@@ -1212,6 +1212,7 @@ class colvar::alch_lambda
   // No atom groups needed
 public:
   alch_lambda();
+  int init_alchemy(int time_step_factor);
   virtual ~alch_lambda() {}
   virtual void calc_value();
   virtual void calc_force_invgrads();
diff --git a/src/colvarcomp_alchlambda.cpp b/src/colvarcomp_alchlambda.cpp
index cd928e823..dad3a1cd1 100644
--- a/src/colvarcomp_alchlambda.cpp
+++ b/src/colvarcomp_alchlambda.cpp
@@ -29,15 +29,25 @@ colvar::alch_lambda::alch_lambda()
 
   x.type(colvarvalue::type_scalar);
 
+  // Query initial value from back-end; will be overwritten if restarting from a state file
+  cvm::proxy->get_alch_lambda(&x.real_value);
+}
+
+
+int colvar::alch_lambda::init_alchemy(int factor)
+{
   // We need calculation every time step
   // default in Tinker-HP and NAMD2, must be enforced in NAMD3
   // Also checks back-end settings, ie. that alchemy is enabled
   // (in NAMD3: alchType TI, computeEnergies at the right frequency)
-  cvm::proxy->request_alch_energy_freq(1);
-  // TODO examine how this breaks everything - whereas alchOutFreq seems to work
 
-  // Query initial value from back-end; will be overwritten if restarting from a state file
-  cvm::proxy->get_alch_lambda(&x.real_value);
+  // Forbid MTS until fully implemented
+  if (factor != 1) {
+    return cvm::error("Error: timeStepFactor > 1 is not yet supported for alchemical variables.");
+  }
+  cvm::proxy->request_alch_energy_freq(factor);
+
+  return COLVARS_OK;
 }
 
 

From 875ea4fac9a449766e90f4c4aee8cb5d56fe5278 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Fri, 30 Aug 2024 19:05:03 +0200
Subject: [PATCH 11/13] Regression test for lambda-ABF in NAMD

Had to force single-thread calculation to work around unreliable results on the singel timestep level
---
 .../AutoDiff/test.colvars.out                 | 122 +++++++++++++++++
 .../AutoDiff/test.colvars.state.stripped      |  25 ++++
 .../AutoDiff/test.colvars.traj                |  22 +++
 .../009_lambda_dynamics/AutoDiff/test.count   |   4 +
 .../009_lambda_dynamics/AutoDiff/test.grad    |   4 +
 .../009_lambda_dynamics/AutoDiff/test.pmf     |   5 +
 .../AutoDiff/test.restart.colvars.out         | 126 ++++++++++++++++++
 .../test.restart.colvars.state.stripped       |  25 ++++
 .../AutoDiff/test.restart.colvars.traj        |  22 +++
 .../AutoDiff/test.restart.count               |   4 +
 .../AutoDiff/test.restart.grad                |   4 +
 .../AutoDiff/test.restart.pmf                 |   5 +
 .../interface/009_lambda_dynamics/alchemy.tcl |  11 ++
 .../009_lambda_dynamics/namd-version.txt      |   3 +
 .../interface/009_lambda_dynamics/no_smp      |   0
 .../interface/009_lambda_dynamics/test.in     |  22 +++
 .../interface/009_lambda_dynamics/test.namd   |  22 +++
 .../009_lambda_dynamics/test.restart.namd     |  30 +++++
 namd/tests/library/run_tests.sh               |  15 ++-
 19 files changed, 466 insertions(+), 5 deletions(-)
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.out
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.state.stripped
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.traj
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.count
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.grad
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.pmf
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.out
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.state.stripped
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.traj
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.count
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.grad
 create mode 100644 namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.pmf
 create mode 100644 namd/tests/interface/009_lambda_dynamics/alchemy.tcl
 create mode 100644 namd/tests/interface/009_lambda_dynamics/namd-version.txt
 create mode 100644 namd/tests/interface/009_lambda_dynamics/no_smp
 create mode 100644 namd/tests/interface/009_lambda_dynamics/test.in
 create mode 100644 namd/tests/interface/009_lambda_dynamics/test.namd
 create mode 100644 namd/tests/interface/009_lambda_dynamics/test.restart.namd

diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.out b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.out
new file mode 100644
index 000000000..e4dc33a7b
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.out
@@ -0,0 +1,122 @@
+colvars: ----------------------------------------------------------------------
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
+colvars: This version was built with the C++11 standard or higher.
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 1)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: available
+colvars: Redefining the Tcl "cv" command to the new script interface.
+colvars: The restart output state file will be "test.tmp.colvars.state".
+colvars: The final output state file will be "test.colvars.state".
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "test.in":
+colvars: # units = "" [default]
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 10
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: # sourceTclFile = "" [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "lambda"
+colvars:   Initializing a new "alchLambda" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0
+colvars:   # upperBoundary = 1
+colvars:   # hardLowerBoundary = off [default]
+colvars:   # hardUpperBoundary = off [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = on
+colvars:     Enabling the extended Lagrangian term for colvar "lambda".
+colvars:     # extendedTemp = 300 [default]
+colvars:     # extendedMass = 150000
+colvars:     # outputEnergy = off [default]
+colvars:     # extendedLangevinDamping = 1 [default]
+colvars:     # reflectingLowerBoundary = on
+colvars:     # reflectingUpperBoundary = on
+colvars:     # outputValue = on [default]
+colvars:     # outputVelocity = off [default]
+colvars:     # outputTotalForce = on
+colvars:     # outputAppliedForce = on
+colvars:     # subtractAppliedForce = off [default]
+colvars:     # runAve = off [default]
+colvars:     # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "abf" instance.
+colvars:   # name = "abf1" [default]
+colvars:   # colvars = { lambda }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # applyBias = on [default]
+colvars:   # hideJacobian = off [default]
+colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
+colvars:   # fullSamples = 0
+colvars:   # minSamples = 0 [default]
+colvars:   # inputPrefix =  [default]
+colvars:   # historyFreq = 0 [default]
+colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
+colvars:   # maxForce =  [default]
+colvars:   # integrate = on [default]
+colvars:   Finished ABF setup.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (0 scalable groups, 0 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: 
+colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
+colvars: 
+colvars: - BAOA integrator:
+colvars:   BouRabee2010 https://doi.org/10.1137/090758842
+colvars: 
+colvars: - Colvars module:
+colvars: - Colvars-NAMD interface:
+colvars:   Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
+colvars: 
+colvars: - ABF colvar bias implementation:
+colvars: - Internal-forces free energy estimator:
+colvars:   Henin2010 https://doi.org/10.1021/ct9004432
+colvars: 
+colvars: - alchLambda colvar component:
+colvars:   Lagardere2023 https://arxiv.org/abs/2307.08006
+colvars: 
+colvars: - NAMD engine:
+colvars:   Phillips2020 https://doi.org/10.1063/5.0014475
+colvars: 
+colvars: updating target temperature (T = 300 K).
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (0 scalable groups, 0 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: updating target temperature (T = 300 K).
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: The restart output state file will be "test.tmp.colvars.state".
+colvars:   Initializing extended coordinate to colvar value.
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Saving collective variables state to "test.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Saving collective variables state to "test.tmp.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.state.stripped b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.state.stripped
new file mode 100644
index 000000000..dd42615aa
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.state.stripped
@@ -0,0 +1,25 @@
+configuration {
+  step           20
+  dt 1.000000e+00
+}
+
+colvar {
+  name lambda
+  x      0.20245122980265
+  extended_x      0.20245122980265
+  extended_v   0.00015391572142221
+}
+
+abf {
+  configuration {
+    step 20
+    name abf1
+  }
+
+samples
+ 20
+
+gradient
+ -8.0141711538951
+}
+
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.traj b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.traj
new file mode 100644
index 000000000..2cce7e646
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.colvars.traj
@@ -0,0 +1,22 @@
+# step         lambda                ft_lambda             fa_lambda             
+           0    2.00000000000000e-01  0.00000000000000e+00  0.00000000000000e+00 
+           1    1.99992395820152e-01  7.96684221784716e+00 -7.96684221784716e+00 
+           2    1.99901022015639e-01  7.88324824580072e+00 -7.92504523182394e+00 
+           3    1.99800875537990e-01  7.80665457013810e+00 -7.88558167792866e+00 
+           4    1.99762218563404e-01  7.73048537492151e+00 -7.84680760217688e+00 
+           5    1.99769367689661e-01  7.65449840553533e+00 -7.80834576284857e+00 
+           6    1.99807952653923e-01  7.58324655116611e+00 -7.77082922756816e+00 
+           7    1.99845484395962e-01  7.52736002846028e+00 -7.73604791340989e+00 
+           8    1.99869775547569e-01  7.50005661145498e+00 -7.70654900066553e+00 
+           9    1.99836075126736e-01  7.51578941134210e+00 -7.68535349074070e+00 
+          10    1.99812694785606e-01  7.57995782043818e+00 -7.67481392371045e+00 
+          11    1.99873218443446e-01  7.69049228724148e+00 -7.67623922948600e+00 
+          12    2.00011013975393e-01  7.84032662263539e+00 -7.68991317891511e+00 
+          13    2.00168434974116e-01  8.01767282114353e+00 -7.71512545908653e+00 
+          14    2.00359096146772e-01  8.20385566003222e+00 -7.75003475915408e+00 
+          15    2.00679173048730e-01  8.37628507963051e+00 -7.79178478051917e+00 
+          16    2.01074279279389e-01  8.52227734901836e+00 -7.83744056605037e+00 
+          17    2.01467672933468e-01  8.63554749590671e+00 -7.88438803251251e+00 
+          18    2.01869356438853e-01  8.71184768812576e+00 -7.93035801337991e+00 
+          19    2.02221179933948e-01  8.75639425563999e+00 -7.97383360507781e+00 
+          20    2.02451229802647e-01  8.78058458142414e+00 -8.01417115389513e+00 
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.count b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.count
new file mode 100644
index 000000000..5a113f218
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.count
@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01                     20
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.grad b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.grad
new file mode 100644
index 000000000..f82f75df5
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.grad
@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01  -8.01417115389513e+00
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.pmf b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.pmf
new file mode 100644
index 000000000..607462679
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.pmf
@@ -0,0 +1,5 @@
+# 1
+# -5.00000000000000e-01  1.00000000000000e+00          2  0
+
+  0.00000000000000e+00   8.01417115389513e+00
+  1.00000000000000e+00   0.00000000000000e+00
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.out b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.out
new file mode 100644
index 000000000..0dc63e526
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.out
@@ -0,0 +1,126 @@
+colvars: ----------------------------------------------------------------------
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
+colvars: This version was built with the C++11 standard or higher.
+colvars: Summary of compile-time features available in this build:
+colvars:   - SMP parallelism: enabled (num. threads = 1)
+colvars:   - Lepton custom functions: available
+colvars:   - Tcl interpreter: available
+colvars: Redefining the Tcl "cv" command to the new script interface.
+colvars: The restart output state file will be "test.restart.tmp.colvars.state".
+colvars: The final output state file will be "test.restart.colvars.state".
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "test.in":
+colvars: # units = "" [default]
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 10
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: # sourceTclFile = "" [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "lambda"
+colvars:   Initializing a new "alchLambda" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0
+colvars:   # upperBoundary = 1
+colvars:   # hardLowerBoundary = off [default]
+colvars:   # hardUpperBoundary = off [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = on
+colvars:     Enabling the extended Lagrangian term for colvar "lambda".
+colvars:     # extendedTemp = 300 [default]
+colvars:     # extendedMass = 150000
+colvars:     # outputEnergy = off [default]
+colvars:     # extendedLangevinDamping = 1 [default]
+colvars:     # reflectingLowerBoundary = on
+colvars:     # reflectingUpperBoundary = on
+colvars:     # outputValue = on [default]
+colvars:     # outputVelocity = off [default]
+colvars:     # outputTotalForce = on
+colvars:     # outputAppliedForce = on
+colvars:     # subtractAppliedForce = off [default]
+colvars:     # runAve = off [default]
+colvars:     # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "abf" instance.
+colvars:   # name = "abf1" [default]
+colvars:   # colvars = { lambda }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # applyBias = on [default]
+colvars:   # hideJacobian = off [default]
+colvars:   Jacobian (geometric) forces will be included in reported free energy gradients.
+colvars:   # fullSamples = 0
+colvars:   # minSamples = 0 [default]
+colvars:   # inputPrefix =  [default]
+colvars:   # historyFreq = 0 [default]
+colvars:   # shared = off [default]
+colvars:   # updateBias = on [default]
+colvars:   # maxForce =  [default]
+colvars:   # integrate = on [default]
+colvars:   Finished ABF setup.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (0 scalable groups, 0 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: 
+colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
+colvars: 
+colvars: - BAOA integrator:
+colvars:   BouRabee2010 https://doi.org/10.1137/090758842
+colvars: 
+colvars: - Colvars module:
+colvars: - Colvars-NAMD interface:
+colvars:   Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
+colvars: 
+colvars: - ABF colvar bias implementation:
+colvars: - Internal-forces free energy estimator:
+colvars:   Henin2010 https://doi.org/10.1021/ct9004432
+colvars: 
+colvars: - alchLambda colvar component:
+colvars:   Lagardere2023 https://arxiv.org/abs/2307.08006
+colvars: 
+colvars: - NAMD engine:
+colvars:   Phillips2020 https://doi.org/10.1063/5.0014475
+colvars: 
+colvars: updating target temperature (T = 300 K).
+colvars: ----------------------------------------------------------------------
+colvars: Loading state from text file "test.colvars.state".
+colvars:   Restarting collective variable "lambda" from value: 0.202451
+colvars:   Restarted abf bias "abf1" with step number 20.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (0 scalable groups, 0 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: updating target temperature (T = 300 K).
+colvars: Current simulation parameters: initial step = 20, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: The restart output state file will be "test.restart.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
+colvars: Saving collective variables state to "test.restart.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj".
+colvars: Saving collective variables state to "test.restart.tmp.colvars.state".
+colvars: Saving collective variables state to "test.restart.colvars.state".
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.state.stripped
new file mode 100644
index 000000000..bbd7a6f52
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.state.stripped
@@ -0,0 +1,25 @@
+configuration {
+  step           40
+  dt 1.000000e+00
+}
+
+colvar {
+  name lambda
+  x      0.20836051020006
+  extended_x      0.20836051020006
+  extended_v    0.0004528018356754
+}
+
+abf {
+  configuration {
+    step 40
+    name abf1
+  }
+
+samples
+ 40
+
+gradient
+ -9.1800383003581
+}
+
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.traj b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.traj
new file mode 100644
index 000000000..2c8ac13ef
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.colvars.traj
@@ -0,0 +1,22 @@
+# step         lambda                ft_lambda             fa_lambda             
+          20    2.02451229802650e-01  0.00000000000000e+00 -8.01417115389510e+00 
+          21    2.02544063317688e-01  8.79677173742116e+00 -8.05143784834872e+00 
+          22    2.02557993229958e-01  8.81441210482505e+00 -8.08611849637037e+00 
+          23    2.02568176589621e-01  8.83952439255414e+00 -8.11887527446532e+00 
+          24    2.02645067021906e-01  8.87347035441114e+00 -8.15031673612973e+00 
+          25    2.02773241774165e-01  8.91763592471448e+00 -8.18100950367312e+00 
+          26    2.02938664924388e-01  8.97161705686943e+00 -8.21141748648836e+00 
+          27    2.03109223468217e-01  9.03911380941207e+00 -8.24207290585590e+00 
+          28    2.03273109969140e-01  9.13005964298271e+00 -8.27378671789615e+00 
+          29    2.03385946933364e-01  9.26505411891078e+00 -8.30796835241389e+00 
+          30    2.03516464758499e-01  9.46339797126387e+00 -8.34648267304223e+00 
+          31    2.03738807200153e-01  9.74220853201881e+00 -8.39150608784792e+00 
+          32    2.04047164987984e-01  1.01132685590046e+01 -8.44531116507157e+00 
+          33    2.04385089669305e-01  1.05741725498844e+01 -8.50982211612650e+00 
+          34    2.04767813595167e-01  1.10964359033778e+01 -8.58589899222213e+00 
+          35    2.05293465871353e-01  1.16275890959526e+01 -8.67280442375728e+00 
+          36    2.05909736002440e-01  1.21203178221254e+01 -8.76856868482306e+00 
+          37    2.06541843034024e-01  1.25351891085928e+01 -8.87036923681684e+00 
+          38    2.07201416018228e-01  1.28409084557337e+01 -8.97485711099886e+00 
+          39    2.07831424699300e-01  1.30323135766731e+01 -9.07889445627256e+00 
+          40    2.08360510200055e-01  1.31246482196932e+01 -9.18003830035808e+00 
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.count b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.count
new file mode 100644
index 000000000..04982258b
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.count
@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01                     40
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.grad b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.grad
new file mode 100644
index 000000000..511481847
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.grad
@@ -0,0 +1,4 @@
+# 1
+#  0.00000000000000e+00  1.00000000000000e+00          1  0
+
+  5.00000000000000e-01  -9.18003830035807e+00
diff --git a/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.pmf b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.pmf
new file mode 100644
index 000000000..01192537c
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/AutoDiff/test.restart.pmf
@@ -0,0 +1,5 @@
+# 1
+# -5.00000000000000e-01  1.00000000000000e+00          2  0
+
+  0.00000000000000e+00   9.18003830035808e+00
+  1.00000000000000e+00   0.00000000000000e+00
diff --git a/namd/tests/interface/009_lambda_dynamics/alchemy.tcl b/namd/tests/interface/009_lambda_dynamics/alchemy.tcl
new file mode 100644
index 000000000..2016c8fe4
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/alchemy.tcl
@@ -0,0 +1,11 @@
+
+langevin                on
+langevinTemp            300.0
+langevinDamping         0.000000001
+
+alch on
+alchType TI
+alchFile ../Common/da.pdb
+alchCol  B
+alchLambda 0.2
+
diff --git a/namd/tests/interface/009_lambda_dynamics/namd-version.txt b/namd/tests/interface/009_lambda_dynamics/namd-version.txt
new file mode 100644
index 000000000..e1d311c69
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/namd-version.txt
@@ -0,0 +1,3 @@
+Info: NAMD 3.1alpha2 for Linux-x86_64-multicore
+colvars: Initializing the collective variables module, version 2024-06-04.
+colvars: Using NAMD interface, version "2023-12-05".
diff --git a/namd/tests/interface/009_lambda_dynamics/no_smp b/namd/tests/interface/009_lambda_dynamics/no_smp
new file mode 100644
index 000000000..e69de29bb
diff --git a/namd/tests/interface/009_lambda_dynamics/test.in b/namd/tests/interface/009_lambda_dynamics/test.in
new file mode 100644
index 000000000..00f9a1906
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/test.in
@@ -0,0 +1,22 @@
+colvarsTrajFrequency 1
+colvarsRestartFrequency 10
+
+colvar {
+  name lambda
+  extendedLagrangian on
+  extendedMass 150000
+
+  lowerBoundary 0
+  upperBoundary 1
+  reflectingLowerBoundary
+  reflectingUpperBoundary
+
+  alchLambda
+  outputTotalForce
+  outputAppliedForce
+}
+
+abf {
+    colvars     lambda
+    fullSamples 0
+}
diff --git a/namd/tests/interface/009_lambda_dynamics/test.namd b/namd/tests/interface/009_lambda_dynamics/test.namd
new file mode 100644
index 000000000..7e8b1149f
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/test.namd
@@ -0,0 +1,22 @@
+# -*- tcl -*-
+
+# Note: see also test.restart.namd, test.legacy.namd, test.restart.legacy.namd
+
+source ../Common/common.namd
+source alchemy.tcl
+
+colvars on
+
+cv configfile test.in
+
+if { [file exists test.prerun.tcl] > 0 } {
+    source test.prerun.tcl
+}
+
+run ${numsteps}
+
+if { [file exists test.postprocess.tcl] > 0 } {
+    source test.postprocess.tcl
+}
+
+source ../Common/delete_tmp_files.tcl
diff --git a/namd/tests/interface/009_lambda_dynamics/test.restart.namd b/namd/tests/interface/009_lambda_dynamics/test.restart.namd
new file mode 100644
index 000000000..4a1e140ff
--- /dev/null
+++ b/namd/tests/interface/009_lambda_dynamics/test.restart.namd
@@ -0,0 +1,30 @@
+# -*- tcl -*-
+
+# Note: see also test.restart.namd, test.legacy.namd, test.restart.legacy.namd
+
+set output_name "test.restart"
+set coor_bin_file "test.coor"
+set vel_bin_file "test.vel"
+
+source ../Common/common.namd
+source alchemy.tcl
+
+# Enforce GPU resident to avoid synchronization issues in parallel
+#GPUresident on
+
+colvars                 on
+
+cv configfile test.in
+cv load test.colvars.state
+
+if { [file exists test.restart.prerun.tcl] > 0 } {
+    source test.restart.prerun.tcl
+}
+
+run ${numsteps}
+
+if { [file exists test.restart.postprocess.tcl] > 0 } {
+    source test.restart.postprocess.tcl
+}
+
+source ../Common/delete_tmp_files.tcl
diff --git a/namd/tests/library/run_tests.sh b/namd/tests/library/run_tests.sh
index 3136239e2..b26de8b6c 100755
--- a/namd/tests/library/run_tests.sh
+++ b/namd/tests/library/run_tests.sh
@@ -69,12 +69,12 @@ CHARM_ARCH=$(${BINARY} 2>&1 | grep 'Info: Based on Charm++/Converse' | cut -d' '
 if [ "x${CHARM_ARCH}" == "xmpi-linux-x86_64" ] && source ${TOPDIR}/devel-tools/load-openmpi.sh ; then
   NUM_TASKS=${NUM_THREADS}
   NUM_THREADS=1
-  BINARY="mpirun -n ${NUM_TASKS} -oversubscribe $BINARY"
+  CMD="mpirun -n ${NUM_TASKS} -oversubscribe $BINARY"
 else
-  BINARY="$BINARY +p ${NUM_THREADS}"
+  CMD="$BINARY +p ${NUM_THREADS}"
 fi
 
-echo "Running NAMD as: $BINARY"
+echo "Running NAMD as: $CMD"
 
 TPUT_RED='true'
 TPUT_GREEN='true'
@@ -188,8 +188,13 @@ for dir in ${DIRLIST} ; do
       fi
     fi
 
-    # Run the test (use a subshell to avoid cluttering stdout)
-    NAMD_CUDASOA=$CUDASOA $BINARY $script > ${basename}.out
+    if [ -f no_smp ]; then
+      # Force the test to run serially
+      NAMD_CUDASOA=$CUDASOA $BINARY +p1 $script > ${basename}.out
+    else
+      # Run the test (use a subshell to avoid cluttering stdout)
+      NAMD_CUDASOA=$CUDASOA $CMD $script > ${basename}.out
+    fi
 
     # Output of Colvars module, minus the version numbers
     grep "^colvars:" ${basename}.out | grep -v 'Initializing the collective variables module' \

From 5e37f65d764c38eec892fadd753095747eeb37d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Fri, 18 Oct 2024 16:54:35 +0200
Subject: [PATCH 12/13] Doc improvements for NAMD/lambda-dyn

---
 doc/colvars-refman-main.tex | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex
index f4224497c..c529f0818 100644
--- a/doc/colvars-refman-main.tex
+++ b/doc/colvars-refman-main.tex
@@ -3074,6 +3074,36 @@
 Reflecting boundary conditions are recommended for lambda-dynamics to ensure that the alchemical
 variable remains precisely within its physical range.
 
+\cvnamdonly{
+The NAMD configuration file should also contain the parameters for setting up the alchemical simulation, for example:
+\begin{cvexampleinput}
+computeEnergies~~~~~~~~~1\\
+\\
+alch~~~~~~~~~~~~~~~~~~~~on\\
+alchType~~~~~~~~~~~~~~~~TI\\
+alchFile~~~~~~~~~~~~~~~~\$\{alchFile\}.pdb\\
+alchCol~~~~~~~~~~~~~~~~~B\\
+alchOutFile~~~~~~~~~~~~~\$\{outName\}.fepout\\
+alchOutFreq~~~~~~~~~~~~~100\\
+alchVdwLambdaEnd~~~~~~~~0.5\\
+alchElecLambdaStart~~~~~0.5\\
+alchVdWShiftCoeff~~~~~~~6.0\\
+alchlambda~~~~~~~~~~~~~~0\\
+\end{cvexampleinput}
+
+Here, the value of 1 for \texttt{computeEnergies} and TI for \texttt{alchType} are mandatory.
+All other parameters can be chosen freely as documented in the NAMD User's Guide.
+
+\paragraph{Special considerations for running lambda-dynamics in NAMD/Colvars.}
+As of NAMD 3.0, lambda-dynamics is not compatible with multiple timestepping. We recommend applying
+hydrogen mass repartitioning (HMR) to the topology and increasing the base timestep to 2~fs
+to limit the performance impact of disabling multiple timestepping.
+When running in parallel on CPUs, synchronization issues prevent lambda-dynamics trajectories from being
+fully reproducible.
+This can be circumvented by running NAMD in GPU-resident mode.
+} % end of \cvnamdonly
+
+
 
 \cvsubsubsec{\texttt{alchFlambda}: Force on the alchemical lambda parameter.}{sec:cvc_alchFlambda}
 \labelkey{colvar|alchFlambda}
@@ -3082,8 +3112,12 @@
 lambda parameter of the back-end simulation in \MDENGINE{}, provided that it is enabled using the appropriate options
 of \MDENGINE{}. This coordinate is obtained from the back-end at each time step of a simulation.
 The \texttt{alchFlambda} block itself takes no parameters, it should be left empty.
+
+
 } % end of \cvalchlambdaonly
 
+
+
 \cvsubsec{Raw data: building blocks for custom functions}{sec:cvc_raw}
 
 \cvsubsubsec{\texttt{cartesian}: vector of atomic Cartesian coordinates.}{sec:cvc_cartesian}

From d6fc186ed678c85b93304ba987f76d5ff1367e37 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= <heninj@gmail.com>
Date: Tue, 17 Dec 2024 00:03:19 +0100
Subject: [PATCH 13/13] Feature fixes after PR review

- move step zero data test from colvarbias.cpp to ABF
- properly test for driven external parameter
---
 src/colvar.cpp         | 2 +-
 src/colvarbias.cpp     | 5 -----
 src/colvarbias_abf.cpp | 6 ++++++
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/colvar.cpp b/src/colvar.cpp
index 62c156765..be623a5a0 100644
--- a/src/colvar.cpp
+++ b/src/colvar.cpp
@@ -2560,7 +2560,7 @@ std::string const colvar::get_state_params() const
      << "  x "
      << std::setprecision(cvm::cv_prec)
      << std::setw(cvm::cv_width);
-  if (is_enabled(f_cv_external)) {
+  if (is_enabled(f_cv_external) && is_enabled(f_cv_extended_Lagrangian)) {
     // For an external colvar, x is one timestep in the future after integration
     // write x at beginning of timestep
     os << x_reported << "\n";
diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp
index 490a07811..7de84e0d5 100644
--- a/src/colvarbias.cpp
+++ b/src/colvarbias.cpp
@@ -100,11 +100,6 @@ int colvarbias::init(std::string const &conf)
     colvar_values[i].type(colvars[i]->value().type());
     colvar_forces[i].type(colvar_values[i].type());
     previous_colvar_forces[i].type(colvar_values[i].type());
-    if (!colvars[i]->is_enabled(f_cv_total_force_current_step)) {
-      // If any colvar does not have current-step total force, then
-      // we can't do step 0 data
-      feature_states[f_cvb_step_zero_data].available = false;
-    }
   }
 
   output_prefix = cvm::output_prefix();
diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp
index ae598ce39..db140181a 100644
--- a/src/colvarbias_abf.cpp
+++ b/src/colvarbias_abf.cpp
@@ -136,6 +136,12 @@ int colvarbias_abf::init(std::string const &conf)
       enable(f_cvb_extended);
     }
 
+    if (!colvars[i]->is_enabled(f_cv_total_force_current_step)) {
+      // If any colvar does not have current-step total force, then
+      // we can't do step 0 data
+      provide(f_cvb_step_zero_data, false);
+    }
+
     // Cannot mix and match coarse time steps with ABF because it gives
     // wrong total force averages - total force needs to be averaged over
     // every time step