Changeset 88b936 for molecuilder/src/molecules.hpp

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.hpp (modified) (2 diffs)

molecuilder/src/molecules.hpp

@@ -392 +392 @@
 };
 
+class ConfigFileBuffer {
+  public:
+    char **buffer;
+    int *LineMapping;
+    int CurrentLine;
+    int NoLines;
+
+    ConfigFileBuffer();
+    ConfigFileBuffer(char *filename);
+    ~ConfigFileBuffer();
+
+    void InitMapping();
+    void MapIonTypesInBuffer(int NoAtoms);
+};
+
+
 /** The config file.
  * The class contains all parameters that control a dft run also functions to load and save.
@@ -469 +485 @@
 
         int ParseForParameter(int verbose, ifstream *file, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
+        int ParseForParameter(int verbose, struct ConfigFileBuffer *FileBuffer, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
 
         public: