Re: [Jmol-developers] CrystalReader and external pressure

2015-07-08 Thread Georg Eickerling
Bob, I just want to confirm that it indeed works and 
thank you for the ultra-fast reply/fix!

cheers

Georg


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Re: [Jmol-developers] CrystalReader and external pressure

2015-07-07 Thread Robert Hanson
found it. Fixed. See

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.07.07b.zip (uploading
shortly)

On Tue, Jul 7, 2015 at 8:49 AM, Georg Eickerling 
georg.eickerl...@physik.uni-augsburg.de wrote:

 Dear all,

 this is a feature request for the CrystalReader of jmol. When doing
 optimizations employing external pressure with CRYSTAL, the output contains
 some additional lines starting with the string TOTAL ENERGY which jmol
 can
 not cope with at the moment:


 TOTAL ENERGY CORRECTED: EXTERNAL STRESS CONTRIBUTION =0.944E+00

 TOTAL ENERGY(DFT)(AU)( 27) -1.2874392471314E+04 DE (AU)   -5.323E-04

 jmol does this ATM in src/org/jmol/adapter/readers/xtal/CrystalReader.java

 line 239:

 if (line.startsWith( TOTAL ENERGY)) {
   readEnergy();
   rd();
   if (line.startsWith( ))
 discardLinesUntilContains(SYMMETRY ALLOWED);
   else if (line.startsWith( ))
 discardLinesUntilContains2(PREDICTED ENERGY CHANGE, HHH);
   return true;
 }


 This will crash if the first of the above lines is present in addition to
 the
 second as most likely readEnergy can not parse the EXTERNAL STRESS stuff.

 I am completely illiterate when it comes to java and even fail to build
 jmol
 from the src using ant on Debian Jessie, so unfortunately I can not
 provide the
 required 2-line fix to simply skip all the EXTERNAL STRESS lines in this
 case.

 regards

 Georg



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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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it is better to take what answer we get.

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[Jmol-developers] CrystalReader and external pressure

2015-07-07 Thread Georg Eickerling
Dear all,

this is a feature request for the CrystalReader of jmol. When doing
optimizations employing external pressure with CRYSTAL, the output contains
some additional lines starting with the string TOTAL ENERGY which jmol can
not cope with at the moment:


TOTAL ENERGY CORRECTED: EXTERNAL STRESS CONTRIBUTION =0.944E+00 

TOTAL ENERGY(DFT)(AU)( 27) -1.2874392471314E+04 DE (AU)   -5.323E-04

jmol does this ATM in src/org/jmol/adapter/readers/xtal/CrystalReader.java

line 239:

if (line.startsWith( TOTAL ENERGY)) {
  readEnergy();
  rd();
  if (line.startsWith( ))
discardLinesUntilContains(SYMMETRY ALLOWED);
  else if (line.startsWith( ))
discardLinesUntilContains2(PREDICTED ENERGY CHANGE, HHH);
  return true;
}


This will crash if the first of the above lines is present in addition to the
second as most likely readEnergy can not parse the EXTERNAL STRESS stuff. 

I am completely illiterate when it comes to java and even fail to build jmol
from the src using ant on Debian Jessie, so unfortunately I can not provide the
required 2-line fix to simply skip all the EXTERNAL STRESS lines in this case.

regards

Georg



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