git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8162 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2012-05-23 16:20:04 +00:00
parent 191c2ca3e5
commit 1cfdda1f82
31 changed files with 17242 additions and 0 deletions
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@ -0,0 +1,91 @@
+#include "colvarmodule.h"
+#include "colvarvalue.h"
+#include "colvar.h"
+#include "colvarcomp.h"
+
+
+
+colvar::cvc::cvc()
+  : sup_coeff (1.0), sup_np (1),
+    b_periodic (false),
+    b_debug_gradients (false),
+    b_inverse_gradients (false),
+    b_Jacobian_derivative (false)
+{}
+
+
+colvar::cvc::cvc (std::string const &conf)
+  : sup_coeff (1.0), sup_np (1),
+    b_periodic (false),
+    b_debug_gradients (false),
+    b_inverse_gradients (false),
+    b_Jacobian_derivative (false)
+{
+  if (cvm::debug())
+    cvm::log ("Initializing cvc base object.\n");
+
+  get_keyval (conf, "name", this->name, std::string (""), parse_silent);
+
+  get_keyval (conf, "componentCoeff", sup_coeff, 1.0);
+  get_keyval (conf, "componentExp", sup_np, 1);
+
+  get_keyval (conf, "period", period, 0.0);
+  get_keyval (conf, "wrapAround", wrap_center, 0.0);
+
+  get_keyval (conf, "debugGradients", b_debug_gradients, false, parse_silent);
+
+  if (cvm::debug())
+    cvm::log ("Done initializing cvc base object.\n");
+}
+
+
+void colvar::cvc::parse_group (std::string const &conf, 
+                               char const *group_key,
+                               cvm::atom_group &group,
+                               bool optional)
+{
+  if (key_lookup (conf, group_key)) {
+    group.parse (conf, group_key);
+  } else {
+    if (! optional) {
+      cvm::fatal_error ("Error: definition for atom group \""+
+                      std::string (group_key)+"\" not found.\n");
+    }
+  }
+}
+
+
+colvar::cvc::~cvc()
+{}
+
+
+void colvar::cvc::calc_force_invgrads()
+{
+  cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
+                    "for colvar components of type \""+function_type+"\".\n");
+}
+
+
+void colvar::cvc::calc_Jacobian_derivative()
+{
+  cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
+                    "for colvar components of type \""+function_type+"\".\n");
+}
+
+
+colvarvalue colvar::cvc::fdiff_change (cvm::atom_group &group)
+{  
+  colvarvalue change (x.type());
+
+  if (group.old_pos.size()) {
+    for (size_t i = 0; i < group.size(); i++) {
+      cvm::rvector const &pold = group.old_pos[i];
+      cvm::rvector const &p = group[i].pos;
+      change += group[i].grad * (p - pold);
+    }
+  }
+
+  // save for next step
+  group.old_pos = group.positions();
+  return change;
+}