Changeset 88b936 for molecuilder/src/molecules.cpp

Timestamp:

Jul 10, 2009, 9:01:40 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

c95b69

Parents:

598f76

git-author:

Frederik Heber <heber@…> (07/10/09 20:21:12)

git-committer:

Frederik Heber <heber@…> (07/10/09 21:01:40)

Message:

new class ConfigFileBuffer and new overloaded function ParseForParaneter() based on this buffer

• the problem is that we need to use molecuilder for the periodic translating of atoms in a xzy file. However, molecuilder resorts them per element. This destroty the id mapping needed for the DBOND file. The storing was corrected, but also the loading relies on this order.
• To solve this, we have to pull off quite something: Parse file into buffer, resort the Ion_Type ones (via a map only), load atoms and then put them into the molecule in the original order!
• Hence, in config::Load we also have a LinearList (map<int, atom*>) in order to add the atoms after the scanning in their original order into the molecule.
• class ConfigFileBuffer parses a config file line-wise into a buffer and allows for resorting (via a map) of lines containing key_word Ion_Type.
• BUGFIX: molecule::Output...() were writing the wrong elements, as they were numbered during the output and not before in ascending order! (I.e. if the first atom is Si, but there is also H present, then this Si would become Ion_Type1_1 instead of Ion_Type2_1, because the elements are still sorted by their Z value, hence Ion_Type1 is H!)

This is basically tested and seems to work properly

File:

• molecuilder/src/molecules.cpp (modified) (4 diffs)

molecuilder/src/molecules.cpp

@@ -1471 +1471 @@
         atom *walker = NULL;
         int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
-        int CurrentMaxElement = 0;
         CountElements();
 
@@ -1485 +1484 @@
     while (walker->next != end) { // go through every atom of this element
       walker = walker->next;
-      if (ElementNo[walker->type->Z] == 0) // new element
-        ElementNo[walker->type->Z] = ++CurrentMaxElement;
+      ElementNo[walker->type->Z] = 1;
+    }
+    int current=1;
+    for (int i=0;i<MAX_ELEMENTS;++i) {
+      if (ElementNo[i] == 1)
+        ElementNo[i] = current++;
+    }
+    walker = start;
+    while (walker->next != end) { // go through every atom of this element
+      walker = walker->next;
       AtomNo[walker->type->Z]++;
       walker->Output(ElementNo[walker->type->Z], AtomNo[walker->type->Z], out); // removed due to trajectories
@@ -1501 +1508 @@
         atom *walker = NULL;
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
-  int CurrentMaxElement = 0;
         CountElements();
 
@@ -1517 +1523 @@
                     ElementNo[i] = 0;
                   }
-      walker = start;
+    walker = start;
+    while (walker->next != end) { // go through every atom of this element
+      walker = walker->next;
+      ElementNo[walker->type->Z] = 1;
+    }
+    int current=1;
+    for (int i=0;i<MAX_ELEMENTS;++i) {
+      if (ElementNo[i] == 1)
+        ElementNo[i] = current++;
+    }
+    walker = start;
       while (walker->next != end) { // go through every atom of this element
         walker = walker->next;
-        if (ElementNo[walker->type->Z] == 0) // new element
-          ElementNo[walker->type->Z] = ++CurrentMaxElement;
         AtomNo[walker->type->Z]++;
         *out << "Ion_Type" << ElementNo[walker->type->Z] << "_" << AtomNo[walker->type->Z] << "\t"      << fixed << setprecision(9) << showpoint;