Hallo,
please find attached the svn diff for the abinit parsing code.
I lightly tested it with some of my outputs.
I noticed that conversion to cif output discards information about
cell orientation, is this a limitation in cif format?
Fulvio
From: Geoffrey Hutchison <geoff.hutchi...@gmail.com>
Subject: Re: [OpenBabel-Devel] abinit parsing
Date: Mon, 15 Apr 2013 13:07:24 -0400
>> I think this is the general pattern, though I am not sure.
>>
>> If you agree with the above, I will gladly patch the code.
>
> Yes, I would agree with this. It's a combination of laziness and not having
> very many abinit files to test.
>
> Thanks!
> -Geoff
>
Index: formats/abinitformat.cpp
===================================================================
--- formats/abinitformat.cpp (revision 5060)
+++ formats/abinitformat.cpp (working copy)
@@ -79,7 +79,7 @@
vector<string> vs;
OBAtom *atom;
- int natom;
+ int natom=-1;
vector<int> atomicNumbers, atomTypes;
double x, y, z;
vector<vector3> atomPositions;
@@ -108,24 +108,32 @@
}
}
// Sometimes Cartesian has lower-case letter
- else if (strstr(buffer, "artesian coordinates")) {
+ else if
+ ((strstr(buffer, "artesian coordinates")) &&
+ (strstr(buffer, "(xcart)")) &&
+ (natom > -1) //be sure natom has already been read
+ )
+ {
double unit = BOHR_TO_ANGSTROM;
if (strstr(buffer, "ngstrom"))
unit = 1.0; // no conversion needed
-
- ifs.getline(buffer,BUFF_SIZE);
- tokenize(vs, buffer);
- while(vs.size() == 3) {
- x = atof(vs[0].c_str()) * unit;
- y = atof(vs[1].c_str()) * unit;
- z = atof(vs[2].c_str()) * unit;
-
- atomPositions.push_back(vector3(x, y, z));
- // get next line
- ifs.getline(buffer,BUFF_SIZE);
- tokenize(vs, buffer);
+ for (int i=0;i<natom;i++)
+ {
+ ifs.getline(buffer,BUFF_SIZE);
+ tokenize(vs, buffer);
+ if (vs.size() != 3) {
+ obErrorLog.ThrowError
+ (__FUNCTION__,
+ "error while parsing coordinates of atoms", obWarning);
+ return(false);
+ }
+ x = atof(vs[0].c_str()) * unit;
+ y = atof(vs[1].c_str()) * unit;
+ z = atof(vs[2].c_str()) * unit;
+ atomPositions.push_back(vector3(x, y, z));
+ // get next line
+ }
}
- }
else if (strstr(buffer, "natom")) {
tokenize(vs, buffer);
if (vs.size() != 2)
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