org.jmol.adapter.readers.more
public class MopacReader extends AtomSetCollectionReader
Field Summary | |
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int | baseAtomIndex |
boolean | chargesFound |
Method Summary | |
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void | processAtomicCharges()
Reads the section in MOPAC files with atomic charges.
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void | processCoordinates()
Reads the section in MOPAC files with cartesian coordinates.
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void | processTotalEnergy() |
AtomSetCollection | readAtomSetCollection(BufferedReader reader) |
void | readFrequencies()
Interprets the Harmonic frequencies section.
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NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY 1 C -0.077432 4.0774 2 C -0.111917 4.1119 3 C 0.092081 3.9079They are expected to be found in the file before the cartesian coordinate section.
Throws: Exception
CARTESIAN COORDINATES NO. ATOM X Y Z 1 C 0.0000 0.0000 0.0000 2 C 1.3952 0.0000 0.0000 3 C 2.0927 1.2078 0.0000In a MOPAC2002 file the columns are different:
CARTESIAN COORDINATES NO. ATOM X Y Z 1 H 0.00000000 0.00000000 0.00000000 2 O 0.95094500 0.00000000 0.00000000 3 H 1.23995160 0.90598439 0.00000000
Throws: Exception
THE LAST 6 VIBRATIONS ARE THE TRANSLATION AND ROTATION MODES THE FIRST THREE OF THESE BEING TRANSLATIONS IN X, Y, AND Z, RESPECTIVELY NORMAL COORDINATE ANALYSIS ROOT NO. 1 2 3 4 5 6 370.51248 370.82204 618.03031 647.68700 647.74806 744.32662 1 0.00002 0.00001 -0.00002 -0.05890 0.07204 -0.00002 2 0.00001 -0.00006 -0.00001 0.01860 0.13517 0.00000 3 0.00421 -0.11112 0.06838 -0.00002 -0.00003 -0.02449 4 0.00002 0.00001 -0.00002 -0.04779 0.07977 -0.00001 5 -0.00002 0.00002 0.00001 0.13405 -0.02908 0.00004 6 -0.10448 0.05212 -0.06842 -0.00005 -0.00002 -0.02447
The vectors are added to a clone of the last read AtomSet. Only the Frequencies are set as properties for each of the frequency type AtomSet generated.
Throws: Exception If an I/O error occurs