mirror of
https://github.com/nwchemgit/nwchem.git
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Update java tools to reflect new segment file format
This commit is contained in:
Tjerk Straatsma
parent
f7ae019e58
commit
ca56bf2acd
9 changed files with 249 additions and 79 deletions
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@ -6,7 +6,25 @@ public class AngleDefinition{
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public int type, source;
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public int source1,source2,source3;
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public double angle1,angle2,angle3,force1,force2,force3;
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public AngleDefinition(String card1, String card2, String card3, String card4){
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atomi=Integer.parseInt(card1.substring(5,10).trim());
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atomj=Integer.parseInt(card1.substring(10,15).trim());
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atomk=Integer.parseInt(card1.substring(15,20).trim());
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type=Integer.parseInt(card1.substring(20,25).trim());
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source3=Integer.parseInt(card1.substring(29,30).trim());
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source1=source3;
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source2=source3;
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if(card1.charAt(27)!=' ') source1=Integer.parseInt(card1.substring(25,28).trim());
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if(card1.charAt(28)!=' ') source2=Integer.parseInt(card1.substring(28,29).trim());
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source=source1;
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angle1=Double.valueOf(card2.substring(0,10)).doubleValue();
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angle2=Double.valueOf(card3.substring(0,10)).doubleValue();
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angle3=Double.valueOf(card4.substring(0,10)).doubleValue();
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force1=Double.valueOf(card2.substring(10,22)).doubleValue();
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force2=Double.valueOf(card3.substring(10,22)).doubleValue();
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force3=Double.valueOf(card4.substring(10,22)).doubleValue();
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}
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public AngleDefinition(String card1, String card2){
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atomi=Integer.parseInt(card1.substring(5,10).trim());
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atomj=Integer.parseInt(card1.substring(10,15).trim());
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@ -19,11 +37,11 @@ public class AngleDefinition{
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if(card1.charAt(28)!=' ') source2=Integer.parseInt(card1.substring(28,29).trim());
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source=source1;
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angle1=Double.valueOf(card2.substring(0,10)).doubleValue();
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angle2=Double.valueOf(card2.substring(22,32)).doubleValue();
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angle3=Double.valueOf(card2.substring(44,54)).doubleValue();
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angle2=angle1;
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angle3=angle1;
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force1=Double.valueOf(card2.substring(10,22)).doubleValue();
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force2=Double.valueOf(card2.substring(32,44)).doubleValue();
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force3=Double.valueOf(card2.substring(54,66)).doubleValue();
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force2=force1;
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force3=force1;
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}
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}
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@ -5,21 +5,37 @@ public class AtomDefinition{
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public int cgroup, pgroup, link, type;
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public double q1,q2,q3,p1,p2,p3;
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public AtomDefinition(String card1, String card2, String card3, String card4){
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Name=card1.substring(5,10);
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link=Integer.parseInt(card1.substring(11,16).trim());
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type=Integer.parseInt(card1.substring(16,21).trim());
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cgroup=Integer.parseInt(card1.substring(26,31).trim());
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pgroup=Integer.parseInt(card1.substring(31,36).trim());
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Type1=card2.substring(5,11);
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Type2=card3.substring(5,11);
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Type3=card4.substring(5,11);
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q1=Double.valueOf(card2.substring(11,23)).doubleValue();
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q2=Double.valueOf(card3.substring(11,23)).doubleValue();
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q3=Double.valueOf(card4.substring(11,23)).doubleValue();
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p1=Double.valueOf(card2.substring(23,35)).doubleValue();
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p2=Double.valueOf(card3.substring(23,35)).doubleValue();
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p3=Double.valueOf(card4.substring(23,35)).doubleValue();
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}
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public AtomDefinition(String card1, String card2){
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Name=card1.substring(5,10);
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Type1=card1.substring(11,17);
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Type2=card1.substring(17,23);
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Type3=card1.substring(23,29);
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cgroup=Integer.parseInt(card1.substring(29,33).trim());
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pgroup=Integer.parseInt(card1.substring(33,37).trim());
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link=Integer.parseInt(card1.substring(37,41).trim());
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type=Integer.parseInt(card1.substring(41,45).trim());
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q1=Double.valueOf(card2.substring(0,12)).doubleValue();
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q2=Double.valueOf(card2.substring(24,36)).doubleValue();
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q3=Double.valueOf(card2.substring(48,60)).doubleValue();
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p1=Double.valueOf(card2.substring(12,24)).doubleValue();
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p2=Double.valueOf(card2.substring(36,48)).doubleValue();
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p3=Double.valueOf(card2.substring(60,72)).doubleValue();
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link=Integer.parseInt(card1.substring(11,16).trim());
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type=Integer.parseInt(card1.substring(16,21).trim());
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cgroup=Integer.parseInt(card1.substring(26,31).trim());
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pgroup=Integer.parseInt(card1.substring(31,36).trim());
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Type1=card2.substring(5,11);
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Type2=Type1;
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Type3=Type1;
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q1=Double.valueOf(card2.substring(11,23)).doubleValue();
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q2=q1;
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q3=q1;
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p1=Double.valueOf(card2.substring(23,35)).doubleValue();
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p2=p2;
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p3=p2;
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}
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public AtomDefinition(String card){
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Name=card.substring(5,10);
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@ -7,6 +7,24 @@ public class BondDefinition{
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public int source1,source2,source3;
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public double bond1,bond2,bond3,force1,force2,force3;
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public BondDefinition(String card1, String card2, String card3, String card4){
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atomi=Integer.parseInt(card1.substring(5,10).trim());
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atomj=Integer.parseInt(card1.substring(10,15).trim());
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type=Integer.parseInt(card1.substring(15,20).trim());
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source3=Integer.parseInt(card1.substring(24,25).trim());
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source1=source3;
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source2=source3;
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if(card1.charAt(22)!=' ') source1=Integer.parseInt(card1.substring(20,23).trim());
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if(card1.charAt(23)!=' ') source2=Integer.parseInt(card1.substring(23,24).trim());
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source=source1;
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bond1=Double.valueOf(card2.substring(0,12)).doubleValue();
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bond2=Double.valueOf(card3.substring(0,12)).doubleValue();
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bond3=Double.valueOf(card4.substring(0,12)).doubleValue();
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force1=Double.valueOf(card2.substring(12,24)).doubleValue();
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force2=Double.valueOf(card3.substring(12,24)).doubleValue();
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force3=Double.valueOf(card4.substring(12,24)).doubleValue();
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};
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public BondDefinition(String card1, String card2){
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atomi=Integer.parseInt(card1.substring(5,10).trim());
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atomj=Integer.parseInt(card1.substring(10,15).trim());
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@ -18,11 +36,11 @@ public class BondDefinition{
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if(card1.charAt(23)!=' ') source2=Integer.parseInt(card1.substring(23,24).trim());
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source=source1;
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bond1=Double.valueOf(card2.substring(0,12)).doubleValue();
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bond2=Double.valueOf(card2.substring(24,36)).doubleValue();
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bond3=Double.valueOf(card2.substring(48,60)).doubleValue();
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bond2=bond1;
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bond3=bond1;
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force1=Double.valueOf(card2.substring(12,24)).doubleValue();
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force2=Double.valueOf(card2.substring(36,48)).doubleValue();
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force3=Double.valueOf(card2.substring(60,72)).doubleValue();
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force2=force1;
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force3=force1;
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};
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public BondDefinition(String card){
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@ -1,8 +1,9 @@
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#
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# $Id: GNUmakefile,v 1.22 2002-01-29 04:49:31 d3j191 Exp $
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# $Id: GNUmakefile,v 1.23 2008-01-25 01:15:18 d3j191 Exp $
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#
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OBJ_CLASS = nwchem.class nwchem_Main.class nwchem_Filter.class \
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OBJ_CLASS = PrintfFormat.class PrintfWriter.class PrintfStream.class\
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nwchem.class nwchem_Main.class nwchem_Filter.class \
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nwchem_Task.class nwchem_Job.class nwchem_MD.class \
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nwchem_MD_energy.class nwchem_MD_optimize.class \
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nwchem_MD_dynamics.class nwchem_MD_thermo.class \
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@ -13,7 +14,8 @@ OBJ_CLASS = nwchem.class nwchem_Main.class nwchem_Filter.class \
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nwchem_Prepare_topology.class nwchem_Prepare_restart.class\
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nwchem_Prepare.class nwchem_Rama.class nwchem_Param.class nwchem_Segment.class nwchem_Fragment.class\
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IntegerField.class DoubleField.class Graph.class \
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Atom.class Cros.class Bond.class Angle.class Torsion.class Improper.class Rule.class Segment.class Fragment.class TimingSet.class
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Atom.class Cros.class Bond.class Angle.class Torsion.class Improper.class Rule.class Segment.class Fragment.class TimingSet.class\
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AtomDefinition.class BondDefinition.class AngleDefinition.class TorsionDefinition.class ImproperDefinition.class
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CLASS_PATH = .:${MYCLASSES}:$(PTPLOT_APPLICATION)
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@ -8,6 +8,29 @@ public class ImproperDefinition{
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public int source1,source2,source3;
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public double improper1,improper2,improper3,force1,force2,force3;
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public ImproperDefinition(String card1, String card2, String card3, String card4){
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atomi=Integer.parseInt(card1.substring(5,10).trim());
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atomj=Integer.parseInt(card1.substring(10,15).trim());
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atomk=Integer.parseInt(card1.substring(15,20).trim());
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atoml=Integer.parseInt(card1.substring(20,25).trim());
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type=Integer.parseInt(card1.substring(25,30).trim());
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source3=Integer.parseInt(card1.substring(34,35).trim());
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source1=source3;
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source2=source3;
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if(card1.charAt(32)!=' ') source1=Integer.parseInt(card1.substring(30,33).trim());
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if(card1.charAt(33)!=' ') source2=Integer.parseInt(card1.substring(33,34).trim());
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source=source1;
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multi1=Integer.parseInt(card2.substring(0,3).trim());
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multi2=Integer.parseInt(card3.substring(0,3).trim());
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multi3=Integer.parseInt(card4.substring(0,3).trim());
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improper1=Double.valueOf(card2.substring(3,13)).doubleValue();
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improper2=Double.valueOf(card3.substring(3,13)).doubleValue();
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improper3=Double.valueOf(card4.substring(3,13)).doubleValue();
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force1=Double.valueOf(card2.substring(13,25)).doubleValue();
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force2=Double.valueOf(card3.substring(13,25)).doubleValue();
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force3=Double.valueOf(card4.substring(13,25)).doubleValue();
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}
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public ImproperDefinition(String card1, String card2){
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atomi=Integer.parseInt(card1.substring(5,10).trim());
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atomj=Integer.parseInt(card1.substring(10,15).trim());
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@ -21,14 +44,14 @@ public class ImproperDefinition{
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if(card1.charAt(33)!=' ') source2=Integer.parseInt(card1.substring(33,34).trim());
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source=source1;
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multi1=Integer.parseInt(card2.substring(0,3).trim());
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multi2=Integer.parseInt(card2.substring(25,28).trim());
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multi3=Integer.parseInt(card2.substring(50,53).trim());
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multi2=multi1;
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multi3=multi1;
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improper1=Double.valueOf(card2.substring(3,13)).doubleValue();
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improper2=Double.valueOf(card2.substring(28,38)).doubleValue();
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improper3=Double.valueOf(card2.substring(53,63)).doubleValue();
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improper2=improper1;
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improper3=improper1;
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force1=Double.valueOf(card2.substring(13,25)).doubleValue();
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force2=Double.valueOf(card2.substring(38,50)).doubleValue();
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force3=Double.valueOf(card2.substring(63,75)).doubleValue();
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force2=force1;
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force3=force1;
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}
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}
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@ -1,7 +1,7 @@
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import java.io.*;
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public class Segment{
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public int numAtoms, numBonds, numAngles, numTorsions, numImpropers, numZmatrix;
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public int numAtoms, numBonds, numAngles, numTorsions, numImpropers, numZmatrix, numParms, iParms;
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public AtomDefinition[] atom;
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public BondDefinition[] bond;
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@ -15,54 +15,78 @@ public class Segment{
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};
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void read(String fileName){
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// System.out.println("Reading file "+fileName);
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// System.out.println("Reading file "+fileName);
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try{
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BufferedReader br = new BufferedReader(new FileReader(fileName));
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String card1;
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String card2;
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String card3;
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String card4;
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card1=br.readLine();
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while(card1.startsWith("$") || card1.startsWith("#")){
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if(card1.startsWith("#")) title=card1;
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card1=br.readLine();
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};
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card1=br.readLine();
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numAtoms=Integer.parseInt(card1.substring(0,5).trim());
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numBonds=Integer.parseInt(card1.substring(5,10).trim());
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numAngles=Integer.parseInt(card1.substring(10,15).trim());
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numTorsions=Integer.parseInt(card1.substring(15,20).trim());
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numImpropers=Integer.parseInt(card1.substring(20,25).trim());
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try{
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numZmatrix=Integer.parseInt(card1.substring(61,66).trim());
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} catch(Exception ez) {numZmatrix=0;};
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numZmatrix=Integer.parseInt(card1.substring(25,30).trim());
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numParms=Integer.parseInt(card1.substring(30,35).trim());
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iParms=Integer.parseInt(card1.substring(35,40).trim());
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atom = new AtomDefinition[numAtoms];
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bond = new BondDefinition[numBonds];
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angle = new AngleDefinition[numAngles];
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torsion = new TorsionDefinition[numTorsions];
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improper = new ImproperDefinition[numImpropers];
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zmatrix = new ZmatrixDefinition[numZmatrix];
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card1=br.readLine();
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for(int i=0; i<numAtoms; i++){
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card1=br.readLine();
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card2=br.readLine();
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atom[i] = new AtomDefinition(card1,card2);
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card3=card2;
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card4=card2;
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if(numParms>1){card3=br.readLine();};
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if(numParms>2){card4=br.readLine();};
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atom[i] = new AtomDefinition(card1,card2,card3,card4);
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};
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for(int i=0; i<numBonds; i++){
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card1=br.readLine();
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card2=br.readLine();
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bond[i] = new BondDefinition(card1,card2);
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card3=card2;
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card4=card2;
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if(numParms>1){card3=br.readLine();};
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if(numParms>2){card4=br.readLine();};
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bond[i] = new BondDefinition(card1,card2,card3,card4);
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};
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for(int i=0; i<numAngles; i++){
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card1=br.readLine();
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card2=br.readLine();
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angle[i] = new AngleDefinition(card1,card2);
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card3=card2;
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card4=card2;
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if(numParms>1){card3=br.readLine();};
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if(numParms>2){card4=br.readLine();};
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angle[i] = new AngleDefinition(card1,card2,card3,card4);
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};
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for(int i=0; i<numTorsions; i++){
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card1=br.readLine();
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card2=br.readLine();
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torsion[i] = new TorsionDefinition(card1,card2);
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card3=card2;
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card4=card2;
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if(numParms>1){card3=br.readLine();};
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if(numParms>2){card4=br.readLine();};
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torsion[i] = new TorsionDefinition(card1,card2,card3,card4);
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};
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for(int i=0; i<numImpropers; i++){
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card1=br.readLine();
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card2=br.readLine();
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improper[i] = new ImproperDefinition(card1,card2);
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card3=card2;
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card4=card2;
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if(numParms>1){card3=br.readLine();};
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if(numParms>2){card4=br.readLine();};
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improper[i] = new ImproperDefinition(card1,card2,card3,card4);
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};
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for(int i=0; i<numZmatrix; i++){
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card1=br.readLine();
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@ -138,28 +162,35 @@ public class Segment{
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try{
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PrintfWriter file = new PrintfWriter(new FileWriter(filename));
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file.println(title);
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file.println(" 4.600000");
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file.printf("%5d",numAtoms);
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file.printf("%5d",numBonds);
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file.printf("%5d",numAngles);
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file.printf("%5d",numTorsions);
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file.printf("%5d",numImpropers);
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file.printf("%41d",numZmatrix);
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file.printf("%5d",numZmatrix);
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file.printf("%5d",3);
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file.printf("%5d",1);
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file.println();
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file.println(" 0.000000");
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for(int i=0; i<numAtoms; i++){
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file.printf("%5d",i+1);
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file.print(atom[i].Name+" ");
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file.print(atom[i].Type1);
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file.print(atom[i].Type2);
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file.print(atom[i].Type3);
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file.printf("%4d",atom[i].cgroup);
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file.printf("%4d",atom[i].pgroup);
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file.printf("%4d",atom[i].link);
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file.printf("%4d",atom[i].type);
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file.printf("%5d",atom[i].link);
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file.printf("%5d",atom[i].type);
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file.printf("%5d",0);
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file.printf("%5d",atom[i].cgroup);
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file.printf("%5d",atom[i].pgroup);
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file.println();
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file.print(" "+atom[i].Type1);
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file.printf("%12.6f",atom[i].q1);
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file.printf("%12.5E",atom[i].p1);
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file.println();
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file.print(" "+atom[i].Type2);
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file.printf("%12.6f",atom[i].q2);
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file.printf("%12.5E",atom[i].p2);
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file.println();
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file.print(" "+atom[i].Type3);
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file.printf("%12.6f",atom[i].q3);
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file.printf("%12.5E",atom[i].p3);
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file.println();
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@ -175,8 +206,10 @@ public class Segment{
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file.println();
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file.printf("%12.6f",bond[i].bond1);
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file.printf("%12.5E",bond[i].force1);
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file.println();
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file.printf("%12.6f",bond[i].bond2);
|
||||
file.printf("%12.5E",bond[i].force2);
|
||||
file.println();
|
||||
file.printf("%12.6f",bond[i].bond3);
|
||||
file.printf("%12.5E",bond[i].force3);
|
||||
file.println();
|
||||
|
|
@ -235,9 +268,11 @@ public class Segment{
|
|||
file.printf("%3d",improper[i].multi1);
|
||||
file.printf("%10.6f",improper[i].improper1);
|
||||
file.printf("%12.5E",improper[i].force1);
|
||||
file.println();
|
||||
file.printf("%3d",improper[i].multi2);
|
||||
file.printf("%10.6f",improper[i].improper2);
|
||||
file.printf("%12.5E",improper[i].force2);
|
||||
file.println();
|
||||
file.printf("%3d",improper[i].multi3);
|
||||
file.printf("%10.6f",improper[i].improper3);
|
||||
file.printf("%12.5E",improper[i].force3);
|
||||
|
|
|
|||
|
|
@ -8,6 +8,29 @@ public class TorsionDefinition{
|
|||
public int source1,source2,source3;
|
||||
public double torsion1,torsion2,torsion3,force1,force2,force3;
|
||||
|
||||
public TorsionDefinition(String card1, String card2, String card3, String card4){
|
||||
atomi=Integer.parseInt(card1.substring(5,10).trim());
|
||||
atomj=Integer.parseInt(card1.substring(10,15).trim());
|
||||
atomk=Integer.parseInt(card1.substring(15,20).trim());
|
||||
atoml=Integer.parseInt(card1.substring(20,25).trim());
|
||||
type=Integer.parseInt(card1.substring(25,30).trim());
|
||||
source3=Integer.parseInt(card1.substring(34,35).trim());
|
||||
source1=source3;
|
||||
source2=source3;
|
||||
if(card1.charAt(32)!=' ') source1=Integer.parseInt(card1.substring(30,33).trim());
|
||||
if(card1.charAt(33)!=' ') source2=Integer.parseInt(card1.substring(33,34).trim());
|
||||
source=source1;
|
||||
multi1=Integer.parseInt(card2.substring(0,3).trim());
|
||||
multi2=Integer.parseInt(card3.substring(0,3).trim());
|
||||
multi3=Integer.parseInt(card4.substring(0,3).trim());
|
||||
torsion1=Double.valueOf(card2.substring(3,13)).doubleValue();
|
||||
torsion2=Double.valueOf(card3.substring(3,13)).doubleValue();
|
||||
torsion3=Double.valueOf(card4.substring(3,13)).doubleValue();
|
||||
force1=Double.valueOf(card2.substring(13,25)).doubleValue();
|
||||
force2=Double.valueOf(card3.substring(13,25)).doubleValue();
|
||||
force3=Double.valueOf(card4.substring(13,25)).doubleValue();
|
||||
}
|
||||
|
||||
public TorsionDefinition(String card1, String card2){
|
||||
atomi=Integer.parseInt(card1.substring(5,10).trim());
|
||||
atomj=Integer.parseInt(card1.substring(10,15).trim());
|
||||
|
|
@ -21,14 +44,14 @@ public class TorsionDefinition{
|
|||
if(card1.charAt(33)!=' ') source2=Integer.parseInt(card1.substring(33,34).trim());
|
||||
source=source1;
|
||||
multi1=Integer.parseInt(card2.substring(0,3).trim());
|
||||
multi2=Integer.parseInt(card2.substring(25,28).trim());
|
||||
multi3=Integer.parseInt(card2.substring(50,53).trim());
|
||||
multi2=multi1;
|
||||
multi3=multi1;
|
||||
torsion1=Double.valueOf(card2.substring(3,13)).doubleValue();
|
||||
torsion2=Double.valueOf(card2.substring(28,38)).doubleValue();
|
||||
torsion3=Double.valueOf(card2.substring(53,63)).doubleValue();
|
||||
torsion2=torsion1;
|
||||
torsion3=torsion1;
|
||||
force1=Double.valueOf(card2.substring(13,25)).doubleValue();
|
||||
force2=Double.valueOf(card2.substring(38,50)).doubleValue();
|
||||
force3=Double.valueOf(card2.substring(63,75)).doubleValue();
|
||||
force2=force1;
|
||||
force3=force1;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -309,6 +309,7 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
try{
|
||||
PrintfWriter sgmFile = new PrintfWriter(new FileWriter("TEMP.sgm"));
|
||||
sgmFile.println("# Merged Segment File for "+frName+" to "+toName);
|
||||
sgmFile.println(" 4.600000");
|
||||
sgmFile.printf("%5d",atmNumber);
|
||||
// count new number of bonds
|
||||
int number=0;
|
||||
|
|
@ -450,8 +451,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
};
|
||||
if(!found) number++;
|
||||
};
|
||||
sgmFile.printf("%41d",number);
|
||||
sgmFile.printf("%5d",number);
|
||||
sgmFile.printf("%5d",3);
|
||||
sgmFile.printf("%5d",1);
|
||||
sgmFile.println();
|
||||
sgmFile.println(" 0.000000");
|
||||
int polgrp= 1;
|
||||
int chgrp = 1;
|
||||
double charge1 = 0.0;
|
||||
|
|
@ -461,24 +465,25 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%5d",k+1);
|
||||
if(id[k][0]>=0){
|
||||
sgmFile.print(FrSgm.atom[id[k][0]].Name+" ");
|
||||
sgmFile.print(FrSgm.atom[id[k][0]].Type1);
|
||||
sgmFile.print(FrSgm.atom[id[k][0]].Type1);
|
||||
if(id[k][1]>=0){
|
||||
sgmFile.print(ToSgm.atom[id[k][1]].Type1);
|
||||
} else {
|
||||
sgmFile.print(FrSgm.atom[id[k][0]].Type1.substring(0,5)+"D");
|
||||
};
|
||||
sgmFile.printf("%4d",chgrp);
|
||||
sgmFile.printf("%4d",polgrp);
|
||||
// sgmFile.printf("%4d",FrSgm.atom[id[k][0]].cgroup);
|
||||
// sgmFile.printf("%4d",FrSgm.atom[id[k][0]].pgroup);
|
||||
sgmFile.printf("%4d",FrSgm.atom[id[k][0]].link);
|
||||
sgmFile.printf("%4d",FrSgm.atom[id[k][0]].type);
|
||||
sgmFile.printf("%5d",FrSgm.atom[id[k][0]].link);
|
||||
sgmFile.printf("%5d",FrSgm.atom[id[k][0]].type);
|
||||
sgmFile.printf("%5d",0);
|
||||
sgmFile.printf("%5d",chgrp);
|
||||
sgmFile.printf("%5d",polgrp);
|
||||
sgmFile.println();
|
||||
sgmFile.print(" "+FrSgm.atom[id[k][0]].Type1);
|
||||
sgmFile.printf("%12.6f",FrSgm.atom[id[k][0]].q1);
|
||||
sgmFile.printf("%12.5E",FrSgm.atom[id[k][0]].p1);
|
||||
sgmFile.println();
|
||||
sgmFile.print(" "+FrSgm.atom[id[k][0]].Type1);
|
||||
sgmFile.printf("%12.6f",FrSgm.atom[id[k][0]].q1);
|
||||
sgmFile.printf("%12.5E",FrSgm.atom[id[k][0]].p1);
|
||||
sgmFile.println();
|
||||
if(id[k][1]>=0){
|
||||
sgmFile.print(" "+ToSgm.atom[id[k][1]].Type1);
|
||||
} else {
|
||||
sgmFile.print(" "+FrSgm.atom[id[k][0]].Type1.substring(0,5)+"D");
|
||||
};
|
||||
charge1=charge1+FrSgm.atom[id[k][0]].q1;
|
||||
if(id[k][1]>=0){
|
||||
sgmFile.printf("%12.6f",ToSgm.atom[id[k][1]].q1);
|
||||
|
|
@ -491,20 +496,21 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.println();
|
||||
} else {
|
||||
sgmFile.print(ToSgm.atom[id[k][1]].Name+" ");
|
||||
sgmFile.print(ToSgm.atom[id[k][1]].Type1.substring(0,5)+"D");
|
||||
sgmFile.print(ToSgm.atom[id[k][1]].Type1.substring(0,5)+"D");
|
||||
sgmFile.print(ToSgm.atom[id[k][1]].Type1);
|
||||
sgmFile.printf("%4d",chgrp);
|
||||
sgmFile.printf("%4d",polgrp);
|
||||
// sgmFile.printf("%4d",ToSgm.atom[id[k][1]].cgroup);
|
||||
// sgmFile.printf("%4d",ToSgm.atom[id[k][1]].pgroup);
|
||||
sgmFile.printf("%4d",ToSgm.atom[id[k][1]].link);
|
||||
sgmFile.printf("%4d",ToSgm.atom[id[k][1]].type);
|
||||
sgmFile.printf("%5d",ToSgm.atom[id[k][1]].link);
|
||||
sgmFile.printf("%5d",ToSgm.atom[id[k][1]].type);
|
||||
sgmFile.printf("%5d",0);
|
||||
sgmFile.printf("%5d",chgrp);
|
||||
sgmFile.printf("%5d",polgrp);
|
||||
sgmFile.println();
|
||||
sgmFile.print(" "+ToSgm.atom[id[k][1]].Type1.substring(0,5)+"D");
|
||||
sgmFile.printf("%12.6f",0.0);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
sgmFile.println();
|
||||
sgmFile.print(" "+ToSgm.atom[id[k][1]].Type1.substring(0,5)+"D");
|
||||
sgmFile.printf("%12.6f",0.0);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
sgmFile.println();
|
||||
sgmFile.print(" "+ToSgm.atom[id[k][1]].Type1);
|
||||
sgmFile.printf("%12.6f",ToSgm.atom[id[k][1]].q1);
|
||||
sgmFile.printf("%12.5E",ToSgm.atom[id[k][1]].p1);
|
||||
charge3=charge3+ToSgm.atom[id[k][1]].q1;
|
||||
|
|
@ -539,8 +545,10 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%1d",ToSgm.bond[jfound].source); sgmFile.println();
|
||||
sgmFile.printf("%12.6f",FrSgm.bond[i].bond1);
|
||||
sgmFile.printf("%12.5E",FrSgm.bond[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",FrSgm.bond[i].bond2);
|
||||
sgmFile.printf("%12.5E",FrSgm.bond[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",ToSgm.bond[jfound].bond1);
|
||||
sgmFile.printf("%12.5E",ToSgm.bond[jfound].force1);
|
||||
} else {
|
||||
|
|
@ -554,8 +562,10 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",FrSgm.bond[i].bond1);
|
||||
sgmFile.printf("%12.5E",FrSgm.bond[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",FrSgm.bond[i].bond2);
|
||||
sgmFile.printf("%12.5E",FrSgm.bond[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",FrSgm.bond[i].bond3);
|
||||
if(id[ida[number][0]][1]>=0 && id[ida[number][1]][1]>=0) {
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
|
|
@ -585,6 +595,7 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%1d",ToSgm.bond[i].source); sgmFile.println();
|
||||
sgmFile.printf("%12.6f",ToSgm.bond[i].bond1);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",ToSgm.bond[i].bond2);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
} else {
|
||||
|
|
@ -592,9 +603,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%1d",ToSgm.bond[i].source); sgmFile.println();
|
||||
sgmFile.printf("%12.6f",ToSgm.bond[i].bond1);
|
||||
sgmFile.printf("%12.5E",ToSgm.bond[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",ToSgm.bond[i].bond2);
|
||||
sgmFile.printf("%12.5E",ToSgm.bond[i].force2);
|
||||
};
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%12.6f",ToSgm.bond[i].bond3);
|
||||
sgmFile.printf("%12.5E",ToSgm.bond[i].force3);
|
||||
sgmFile.println();
|
||||
|
|
@ -632,8 +645,10 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%1d",ToSgm.angle[jfound].source); sgmFile.println();
|
||||
sgmFile.printf("%10.6f",FrSgm.angle[i].angle1);
|
||||
sgmFile.printf("%12.5E",FrSgm.angle[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",FrSgm.angle[i].angle2);
|
||||
sgmFile.printf("%12.5E",FrSgm.angle[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",ToSgm.angle[jfound].angle1);
|
||||
sgmFile.printf("%12.5E",ToSgm.angle[jfound].force1);
|
||||
} else {
|
||||
|
|
@ -647,8 +662,10 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",FrSgm.angle[i].angle1);
|
||||
sgmFile.printf("%12.5E",FrSgm.angle[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",FrSgm.angle[i].angle2);
|
||||
sgmFile.printf("%12.5E",FrSgm.angle[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",FrSgm.angle[i].angle3);
|
||||
if(id[ida[number][0]][1]>=0 && id[ida[number][1]][1]>=0 && id[ida[number][2]][1]>=0) {
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
|
|
@ -680,6 +697,7 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%1d",ToSgm.angle[i].source); sgmFile.println();
|
||||
sgmFile.printf("%10.6f",ToSgm.angle[i].angle1);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",ToSgm.angle[i].angle2);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
} else {
|
||||
|
|
@ -687,9 +705,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%1d",ToSgm.angle[i].source); sgmFile.println();
|
||||
sgmFile.printf("%10.6f",ToSgm.angle[i].angle1);
|
||||
sgmFile.printf("%12.5E",ToSgm.angle[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",ToSgm.angle[i].angle2);
|
||||
sgmFile.printf("%12.5E",ToSgm.angle[i].force2);
|
||||
};
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%10.6f",ToSgm.angle[i].angle3);
|
||||
sgmFile.printf("%12.5E",ToSgm.angle[i].force3);
|
||||
sgmFile.println();
|
||||
|
|
@ -730,9 +750,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",FrSgm.torsion[i].multi1);
|
||||
sgmFile.printf("%10.6f",FrSgm.torsion[i].torsion1);
|
||||
sgmFile.printf("%12.5E",FrSgm.torsion[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",FrSgm.torsion[i].multi2);
|
||||
sgmFile.printf("%10.6f",FrSgm.torsion[i].torsion2);
|
||||
sgmFile.printf("%12.5E",FrSgm.torsion[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.torsion[jfound].multi1);
|
||||
sgmFile.printf("%10.6f",ToSgm.torsion[jfound].torsion1);
|
||||
sgmFile.printf("%12.5E",ToSgm.torsion[jfound].force1);
|
||||
|
|
@ -748,9 +770,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",FrSgm.torsion[i].multi1);
|
||||
sgmFile.printf("%10.6f",FrSgm.torsion[i].torsion1);
|
||||
sgmFile.printf("%12.5E",FrSgm.torsion[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",FrSgm.torsion[i].multi2);
|
||||
sgmFile.printf("%10.6f",FrSgm.torsion[i].torsion2);
|
||||
sgmFile.printf("%12.5E",FrSgm.torsion[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",FrSgm.torsion[i].multi3);
|
||||
sgmFile.printf("%10.6f",FrSgm.torsion[i].torsion3);
|
||||
if(id[ida[number][0]][1]>=0 && id[ida[number][1]][1]>=0 && id[ida[number][2]][1]>=0 && id[ida[number][3]][1]>=0) {
|
||||
|
|
@ -786,6 +810,7 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",ToSgm.torsion[i].multi1);
|
||||
sgmFile.printf("%10.6f",ToSgm.torsion[i].torsion1);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.torsion[i].multi2);
|
||||
sgmFile.printf("%10.6f",ToSgm.torsion[i].torsion2);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
|
|
@ -795,10 +820,12 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",ToSgm.torsion[i].multi1);
|
||||
sgmFile.printf("%10.6f",ToSgm.torsion[i].torsion1);
|
||||
sgmFile.printf("%12.5E",ToSgm.torsion[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.torsion[i].multi2);
|
||||
sgmFile.printf("%10.6f",ToSgm.torsion[i].torsion2);
|
||||
sgmFile.printf("%12.5E",ToSgm.torsion[i].force2);
|
||||
};
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.torsion[i].multi3);
|
||||
sgmFile.printf("%10.6f",ToSgm.torsion[i].torsion3);
|
||||
sgmFile.printf("%12.5E",ToSgm.torsion[i].force3);
|
||||
|
|
@ -852,9 +879,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",FrSgm.improper[i].multi1);
|
||||
sgmFile.printf("%10.6f",FrSgm.improper[i].improper1);
|
||||
sgmFile.printf("%12.5E",FrSgm.improper[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",FrSgm.improper[i].multi2);
|
||||
sgmFile.printf("%10.6f",FrSgm.improper[i].improper2);
|
||||
sgmFile.printf("%12.5E",FrSgm.improper[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.improper[jfound].multi1);
|
||||
sgmFile.printf("%10.6f",ToSgm.improper[jfound].improper1);
|
||||
sgmFile.printf("%12.5E",ToSgm.improper[jfound].force1);
|
||||
|
|
@ -870,9 +899,11 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",FrSgm.improper[i].multi1);
|
||||
sgmFile.printf("%10.6f",FrSgm.improper[i].improper1);
|
||||
sgmFile.printf("%12.5E",FrSgm.improper[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",FrSgm.improper[i].multi2);
|
||||
sgmFile.printf("%10.6f",FrSgm.improper[i].improper2);
|
||||
sgmFile.printf("%12.5E",FrSgm.improper[i].force2);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",FrSgm.improper[i].multi3);
|
||||
sgmFile.printf("%10.6f",FrSgm.improper[i].improper3);
|
||||
if(id[ida[number][0]][1]>=0 && id[ida[number][1]][1]>=0 && id[ida[number][2]][1]>=0 && id[ida[number][3]][1]>=0) {
|
||||
|
|
@ -912,6 +943,7 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",ToSgm.improper[i].multi1);
|
||||
sgmFile.printf("%10.6f",ToSgm.improper[i].improper1);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.improper[i].multi2);
|
||||
sgmFile.printf("%10.6f",ToSgm.improper[i].improper2);
|
||||
sgmFile.printf("%12.5E",0.0);
|
||||
|
|
@ -921,10 +953,12 @@ class nwchem_Segment extends JFrame implements ActionListener, ChangeListener, W
|
|||
sgmFile.printf("%3d",ToSgm.improper[i].multi1);
|
||||
sgmFile.printf("%10.6f",ToSgm.improper[i].improper1);
|
||||
sgmFile.printf("%12.5E",ToSgm.improper[i].force1);
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.improper[i].multi2);
|
||||
sgmFile.printf("%10.6f",ToSgm.improper[i].improper2);
|
||||
sgmFile.printf("%12.5E",ToSgm.improper[i].force2);
|
||||
};
|
||||
sgmFile.println();
|
||||
sgmFile.printf("%3d",ToSgm.improper[i].multi3);
|
||||
sgmFile.printf("%10.6f",ToSgm.improper[i].improper3);
|
||||
sgmFile.printf("%12.5E",ToSgm.improper[i].force3);
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
// $Id: whichjava.java,v 1.4 2005-04-27 19:02:26 marat Exp $
|
||||
// $Id: whichjava.java,v 1.5 2008-01-25 01:15:18 d3j191 Exp $
|
||||
|
||||
public class whichjava implements Runnable {
|
||||
public static void main(String[] args){
|
||||
|
|
@ -6,6 +6,7 @@ public class whichjava implements Runnable {
|
|||
if (System.getProperty("java.version").indexOf("1.2")>=0){System.exit((int)0);};
|
||||
if (System.getProperty("java.version").indexOf("1.3")>=0){System.exit((int)0);};
|
||||
if (System.getProperty("java.version").indexOf("1.4")>=0){System.exit((int)0);};
|
||||
if (System.getProperty("java.version").indexOf("1.5")>=0){System.exit((int)0);};
|
||||
System.out.println (" This code requires Java 1.2 or greater"); System.exit((int)1);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue