Changeset 606dfb for molecuilder/src/molecules.cpp

Timestamp:

Sep 28, 2009, 6:41:52 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

01e6c5

Parents:

6f1551

git-author:

Frederik Heber <heber@…> (09/28/09 18:39:28)

git-committer:

Frederik Heber <heber@…> (09/28/09 18:41:52)

Message:

Implemenation of embedding merge, untested. LinearInterpolation now has switch for using identity map.

• embed merge in MoleculeListClass determines the non-convex envelope and tries to fill the domain with the filler molecule everywhere outside of this domain
• is added to MergeMolecule in builder.cpp, case 'e'
• in molecule::LinearInterpolationBetweenConfiguration() now has additional parameter to tell whether we have to look for a mapping or use the identity.

File:

• molecuilder/src/molecules.cpp (modified) (3 diffs)

molecuilder/src/molecules.cpp

@@ -662 +662 @@
 {
   int length = 0;
-  char *molname = strrchr(filename, '/')+sizeof(char);  // search for filename without dirs
+  const char *molname = strrchr(filename, '/');
+  if (molname != NULL)
+    molname += sizeof(char);  // search for filename without dirs
+  else
+    molname = filename; // contains no slashes
   char *endname = strchr(molname, '.');
   if ((endname == NULL) || (endname < molname))
@@ -1562 +1566 @@
  * \param endstep stating final configuration in molecule::Trajectories
  * \param &config configuration structure
+ * \param MapByIdentity if true we just use the identity to map atoms in start config to end config, if not we find mapping by \sa MinimiseConstrainedPotential()
  * \return true - success in writing step files, false - error writing files or only one step in molecule::Trajectories
  */
-bool molecule::LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration) 
+bool molecule::LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity)
 {
   molecule *mol = NULL;
@@ -1573 +1578 @@
   atom **PermutationMap = NULL;
   atom *Walker = NULL, *Sprinter = NULL;
-  MinimiseConstrainedPotential(out, PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
+  if (!MapByIdentity)
+    MinimiseConstrainedPotential(out, PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
+  else {
+    PermutationMap = (atom **) Malloc(AtomCount*sizeof(atom *), "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
+    Walker = start;
+    while (Walker->next != end) {
+      Walker = Walker->next;
+      PermutationMap[Walker->nr] = Walker;   // always pick target with the smallest distance
+    }
+  }
 
   // check whether we have sufficient space in Trajectories for each atom