forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14165 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -638,6 +638,7 @@ int colvar::enable(colvar::task const &t)
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case task_output_system_force:
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enable(task_system_force);
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tasks[t] = true;
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break;
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case task_report_Jacobian_force:
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@ -646,6 +647,7 @@ int colvar::enable(colvar::task const &t)
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if (cvm::debug())
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cvm::log("Adding the Jacobian force to the system force, "
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"rather than applying its opposite silently.\n");
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tasks[t] = true;
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break;
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case task_Jacobian_force:
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@ -669,6 +671,7 @@ int colvar::enable(colvar::task const &t)
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"on this colvar.\n");
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}
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fj.type(value());
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tasks[t] = true;
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break;
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case task_system_force:
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@ -683,6 +686,7 @@ int colvar::enable(colvar::task const &t)
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}
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ft.type(value());
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ft_reported.type(value());
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tasks[t] = true;
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break;
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case task_output_applied_force:
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@ -690,16 +694,19 @@ int colvar::enable(colvar::task const &t)
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case task_upper_wall:
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// all of the above require gradients
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enable(task_gradients);
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tasks[t] = true;
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break;
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case task_fdiff_velocity:
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x_old.type(value());
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v_fdiff.type(value());
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v_reported.type(value());
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tasks[t] = true;
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break;
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case task_output_velocity:
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enable(task_fdiff_velocity);
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tasks[t] = true;
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break;
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case task_grid:
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@ -708,11 +715,13 @@ int colvar::enable(colvar::task const &t)
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this->name+"\", because its value is not a scalar number.\n",
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INPUT_ERROR);
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}
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tasks[t] = true;
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break;
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case task_extended_lagrangian:
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enable(task_gradients);
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v_reported.type(value());
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tasks[t] = true;
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break;
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case task_lower_boundary:
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@ -722,16 +731,17 @@ int colvar::enable(colvar::task const &t)
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"and cannot produce a grid.\n",
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INPUT_ERROR);
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}
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tasks[t] = true;
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break;
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case task_output_value:
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case task_runave:
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case task_corrfunc:
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case task_ntot:
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case task_langevin:
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case task_output_energy:
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case task_scripted:
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case task_gradients:
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tasks[t] = true;
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break;
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case task_collect_gradients:
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@ -745,10 +755,13 @@ int colvar::enable(colvar::task const &t)
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if (atom_ids.size() == 0) {
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build_atom_list();
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}
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tasks[t] = true;
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break;
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default:
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break;
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}
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tasks[t] = true;
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return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
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}
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@ -763,23 +776,28 @@ void colvar::disable(colvar::task const &t)
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disable(task_output_applied_force);
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disable(task_system_force);
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disable(task_Jacobian_force);
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tasks[t] = false;
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break;
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case task_system_force:
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disable(task_output_system_force);
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tasks[t] = false;
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break;
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case task_Jacobian_force:
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disable(task_report_Jacobian_force);
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tasks[t] = false;
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break;
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case task_fdiff_velocity:
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disable(task_output_velocity);
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tasks[t] = false;
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break;
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case task_lower_boundary:
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case task_upper_boundary:
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disable(task_grid);
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tasks[t] = false;
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break;
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case task_extended_lagrangian:
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@ -793,15 +811,17 @@ void colvar::disable(colvar::task const &t)
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case task_grid:
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case task_lower_wall:
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case task_upper_wall:
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case task_ntot:
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case task_langevin:
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case task_output_energy:
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case task_collect_gradients:
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case task_scripted:
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tasks[t] = false;
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break;
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default:
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break;
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}
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tasks[t] = false;
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}
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@ -1106,44 +1126,6 @@ cvm::real colvar::update()
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f += fb;
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if (tasks[task_lower_wall] || tasks[task_upper_wall]) {
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// wall force
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colvarvalue fw(value());
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fw.reset();
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if (cvm::debug())
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cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n");
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// if the two walls are applied concurrently, decide which is the
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// closer one (on a periodic colvar, both walls may be applicable
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// at the same time)
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if ( (!tasks[task_upper_wall]) ||
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(this->dist2(x_reported, lower_wall) < this->dist2(x_reported, upper_wall)) ) {
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cvm::real const grad = this->dist2_lgrad(x_reported, lower_wall);
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if (grad < 0.0) {
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fw = -0.5 * lower_wall_k * grad;
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if (cvm::debug())
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cvm::log("Applying a lower wall force("+
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cvm::to_str(fw)+") to \""+this->name+"\".\n");
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f += fw;
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}
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} else {
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cvm::real const grad = this->dist2_lgrad(x_reported, upper_wall);
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if (grad > 0.0) {
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fw = -0.5 * upper_wall_k * grad;
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if (cvm::debug())
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cvm::log("Applying an upper wall force("+
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cvm::to_str(fw)+") to \""+this->name+"\".\n");
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f += fw;
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}
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}
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}
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if (tasks[task_Jacobian_force]) {
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size_t i;
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for (i = 0; i < cvcs.size(); i++) {
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@ -1178,10 +1160,11 @@ cvm::real colvar::update()
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// the total force is applied to the fictitious mass, while the
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// atoms only feel the harmonic force
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// fr: extended coordinate force (without harmonic spring), for output in trajectory
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// fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
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// f_ext: total force on extended coordinate (including harmonic spring)
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// f: - initially, external biasing force
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// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
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// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
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// (note: wall potential is added to f after this block)
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fr = f;
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f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
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f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
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@ -1203,6 +1186,44 @@ cvm::real colvar::update()
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}
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// Adding wall potential to "true" colvar force, whether or not an extended coordinate is in use
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if (tasks[task_lower_wall] || tasks[task_upper_wall]) {
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// Wall force
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colvarvalue fw(x);
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fw.reset();
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if (cvm::debug())
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cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n");
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// For a periodic colvar, both walls may be applicable at the same time
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// in which case we pick the closer one
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if ( (!tasks[task_upper_wall]) ||
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(this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) {
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cvm::real const grad = this->dist2_lgrad(x, lower_wall);
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if (grad < 0.0) {
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fw = -0.5 * lower_wall_k * grad;
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f += fw;
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if (cvm::debug())
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cvm::log("Applying a lower wall force("+
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cvm::to_str(fw)+") to \""+this->name+"\".\n");
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}
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} else {
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cvm::real const grad = this->dist2_lgrad(x, upper_wall);
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if (grad > 0.0) {
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fw = -0.5 * upper_wall_k * grad;
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f += fw;
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if (cvm::debug())
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cvm::log("Applying an upper wall force("+
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cvm::to_str(fw)+") to \""+this->name+"\".\n");
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}
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}
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}
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if (tasks[task_fdiff_velocity]) {
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// set it for the next step
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x_old = x;
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@ -4,7 +4,7 @@
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#define COLVARMODULE_H
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#ifndef COLVARS_VERSION
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#define COLVARS_VERSION "2015-09-03"
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#define COLVARS_VERSION "2015-09-16"
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#endif
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#ifndef COLVARS_DEBUG
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/// shared between all object instances) to be accessed from other
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/// objects.
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// Internal method return codes
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#define COLVARS_NOT_IMPLEMENTED -2
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#define COLVARS_ERROR -1
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// Error codes
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#define COLVARS_OK 0
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// On error, values of the colvars module error register
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#define GENERAL_ERROR 1
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#define FILE_ERROR (1<<1)
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#define MEMORY_ERROR (1<<2)
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#define BUG_ERROR (1<<3) // Inconsistent state indicating bug
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#define INPUT_ERROR (1<<4) // out of bounds or inconsistent input
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#define DELETE_COLVARS (1<<5) // Instruct the caller to delete cvm
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#define FATAL_ERROR (1<<6) // Should be set, or not, together with other bits
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#define COLVARS_ERROR -1
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#define GENERAL_ERROR -1 // TODO this can be simply merged with COLVARS_ERROR
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#define COLVARS_NOT_IMPLEMENTED (-1<<1)
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#define INPUT_ERROR (-1<<2) // out of bounds or inconsistent input
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#define BUG_ERROR (-1<<3) // Inconsistent state indicating bug
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#define FILE_ERROR (-1<<4)
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#define MEMORY_ERROR (-1<<5)
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#define FATAL_ERROR (-1<<6) // Should be set, or not, together with other bits
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#define DELETE_COLVARS (-1<<7) // Instruct the caller to delete cvm
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#include <iostream>
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@ -388,6 +388,7 @@ Input and output:\n\
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list -- return a list of all variables\n\
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list biases -- return a list of all biases\n\
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load <file name> -- load a state file (requires configuration)\n\
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save <file name> -- save a state file (requires configuration)\n\
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update -- recalculate colvars and biases based\n\
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printframe -- return a summary of the current frame\n\
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printframelabels -- return labels to annotate printframe's output\n";
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@ -406,6 +407,7 @@ Accessing collective variables:\n\
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colvar <name> delete -- delete colvar <name>\n\
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colvar <name> addforce <F> -- apply given force on colvar <name>\n\
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colvar <name> getconfig -- return config string of colvar <name>\n\
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colvar <name> cvcflags <fl> -- enable or disable cvcs according to 0/1 flags\n\
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\n\
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Accessing biases:\n\
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bias <name> energy -- return the current energy of bias <name>\n\
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