From: <ha...@us...> - 2009-03-28 15:30:56
|
Revision: 10744 http://jmol.svn.sourceforge.net/jmol/?rev=10744&view=rev Author: hansonr Date: 2009-03-28 15:30:17 +0000 (Sat, 28 Mar 2009) Log Message: ----------- version=11.7.31_dev # code -- more documentation and somewhat reorganized adapter section. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-03-28 15:27:38 UTC (rev 10743) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-03-28 15:30:17 UTC (rev 10744) @@ -544,6 +544,7 @@ private final static int SPECIAL_CUBE = 7; private final static int SPECIAL_ALCHEMY = 8; + // these next are needed by the XML reader public final static int SPECIAL_ARGUS_XML = 9; public final static int SPECIAL_CML_XML = 10; @@ -557,7 +558,7 @@ public final static int SPECIAL_MOLPRO_DOM = 17; public final static int SPECIAL_ODYSSEY_DOM = 18; - final public static String[][] specialTags = { + public final static String[][] specialTags = { { "Jme" }, { "MopacGraphf" }, { "V3000" }, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-06-26 07:55:04
|
Revision: 11123 http://jmol.svn.sourceforge.net/jmol/?rev=11123&view=rev Author: hansonr Date: 2009-06-26 07:55:03 +0000 (Fri, 26 Jun 2009) Log Message: ----------- MO reader calculation type Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-06-26 07:51:32 UTC (rev 11122) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-06-26 07:55:03 UTC (rev 11123) @@ -232,15 +232,15 @@ String err = null; try { className = getReaderClassBase(atomSetCollectionReaderName); - atomSetCollectionReaderClass = Class.forName(className);//,true, Thread.currentThread().getContextClassLoader()); + atomSetCollectionReaderClass = Class.forName(className); atomSetCollectionReader = (AtomSetCollectionReader) atomSetCollectionReaderClass .newInstance(); + return atomSetCollectionReader.readData(fullName, htParams, bufferedReader); } catch (Exception e) { err = "File reader was not found:" + className; Logger.error(err); return err; } - return atomSetCollectionReader.readData(fullName, htParams, bufferedReader); } /** @@ -266,12 +266,12 @@ className = classBase + "xml.XmlReader"; atomSetCollectionReaderClass = Class.forName(className); atomSetCollectionReader = (AtomSetCollectionReader) atomSetCollectionReaderClass.newInstance(); + return atomSetCollectionReader.readData("DOM node", htParams, DOMNode); } catch (Exception e) { String err = "File reader was not found:" + className; Logger.error(err, e); return err; } - return atomSetCollectionReader.readData("DOM node", htParams, DOMNode); } ////// PRIVATE METHODS /////// This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-08-25 13:54:51
|
Revision: 11352 http://jmol.svn.sourceforge.net/jmol/?rev=11352&view=rev Author: hansonr Date: 2009-08-25 13:54:44 +0000 (Tue, 25 Aug 2009) Log Message: ----------- aims reader breaks pdb Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-08-25 13:49:00 UTC (rev 11351) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-08-25 13:54:44 UTC (rev 11352) @@ -640,7 +640,9 @@ // AIMS geometry files with indented keywords for ( int i = 0; i<lines.length; i++ ) { String[] tokens = Parser.getTokens(lines[i]); - if ( tokens[0].toLowerCase().startsWith("atom") ) return true; + //No -- can't do this -- it's incompatible with PDB + // for such files you will have to force the reader with "aims::" + // if ( tokens[0].toLowerCase().startsWith("atom") ) return true; if ( tokens[0].toLowerCase().startsWith("lattice_vector") ) return true; } return false; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-08-25 20:27:26
|
Revision: 11365 http://jmol.svn.sourceforge.net/jmol/?rev=11365&view=rev Author: hansonr Date: 2009-08-25 20:27:13 +0000 (Tue, 25 Aug 2009) Log Message: ----------- 11.9.1 aims resolver breaks cif - fixed Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-08-25 20:25:18 UTC (rev 11364) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-08-25 20:27:13 UTC (rev 11365) @@ -638,14 +638,16 @@ // use same tokenizing mechanism as in AimsReader.java to also recognize // AIMS geometry files with indented keywords - for ( int i = 0; i<lines.length; i++ ) { + for (int i = 0; i < lines.length; i++) { String[] tokens = Parser.getTokens(lines[i]); - //No -- can't do this -- it's incompatible with PDB + // No -- can't do this -- it's incompatible with PDB // for such files you will have to force the reader with "aims::" // if ( tokens[0].toLowerCase().startsWith("atom") ) return true; - if ( tokens[0].toLowerCase().startsWith("lattice_vector") ) return true; + if (tokens.length > 0 + && tokens[0].toLowerCase().startsWith("lattice_vector")) + return true; } - return false; + return false; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-09-03 23:48:01
|
Revision: 11453 http://jmol.svn.sourceforge.net/jmol/?rev=11453&view=rev Author: hansonr Date: 2009-09-03 23:47:51 +0000 (Thu, 03 Sep 2009) Log Message: ----------- version=11.8.3 # bug fix: aims/castep readers Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-09-03 23:41:31 UTC (rev 11452) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2009-09-03 23:47:51 UTC (rev 11453) @@ -638,12 +638,11 @@ // use same tokenizing mechanism as in AimsReader.java to also recognize // AIMS geometry files with indented keywords - // "atom" is a VERY generic term. + // "atom" is a VERY generic term; just "atom" breaks HIN reader. for (int i = 0; i < lines.length; i++) { String[] tokens = Parser.getTokens(lines[i]); - if (tokens.length > 0 - && (tokens[0].startsWith("atom") - || tokens[0].startsWith("lattice_vector"))) + if (tokens.length == 5 && tokens[0].startsWith("atom") + || tokens.length == 4 && tokens[0].startsWith("lattice_vector")) return true; } return false; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-19 14:35:44
|
Revision: 12412 http://jmol.svn.sourceforge.net/jmol/?rev=12412&view=rev Author: hansonr Date: 2010-02-19 14:35:37 +0000 (Fri, 19 Feb 2010) Log Message: ----------- preliminary CRYSTAL reader -- requires CRYSTAL:: prefix in LOAD command. -- still needs testing Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-02-19 14:33:22 UTC (rev 12411) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-02-19 14:35:37 UTC (rev 12412) @@ -977,12 +977,15 @@ private final static String[] uicrcifContainsRecords = { "Cif", "Crystallographic Information File"}; + private final static String[] crystalContainsRecords = + { "Crystal", "* CRYSTAL"}; + private final static String[][] containsRecords = { xmlContainsRecords, gaussianContainsRecords, ampacContainsRecords, mopacContainsRecords, qchemContainsRecords, gamessUKContainsRecords, gamessUSContainsRecords, spartanBinaryContainsRecords, spartanContainsRecords, mol2Records, adfContainsRecords, psiContainsRecords, - nwchemContainsRecords, uicrcifContainsRecords, dgridContainsRecords + nwchemContainsRecords, uicrcifContainsRecords, dgridContainsRecords, crystalContainsRecords }; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-19 14:41:21
|
Revision: 12413 http://jmol.svn.sourceforge.net/jmol/?rev=12413&view=rev Author: hansonr Date: 2010-02-19 14:41:15 +0000 (Fri, 19 Feb 2010) Log Message: ----------- preliminary CRYSTAL reader - still needs testing Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-02-19 14:35:37 UTC (rev 12412) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-02-19 14:41:15 UTC (rev 12413) @@ -599,6 +599,8 @@ if (isEnd) { if (checkGromacs(lines)) return "Gromacs"; + if (checkCrystal(lines)) + return "Crystal"; } if (nLines == 1 && lines[0].length() > 0 && Character.isDigit(lines[0].charAt(0))) @@ -638,6 +640,15 @@ return true; } + private static boolean checkCrystal(String[] lines) { + return (lines[1].equals("SLAB") + || lines[1].equals("MOLECULE") + || lines[1].equals("POLYMER") + || lines[3].equals("SLAB") + || lines[3].equals("MOLECULE") + || lines[3].equals("POLYMER")); + } + private static boolean checkWien2k(String[] lines) { return (lines[2].startsWith("MODE OF CALC=") || lines[2].startsWith(" RELA") This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-19 15:20:49
|
Revision: 12415 http://jmol.svn.sourceforge.net/jmol/?rev=12415&view=rev Author: hansonr Date: 2010-02-19 15:20:37 +0000 (Fri, 19 Feb 2010) Log Message: ----------- preliminary CRYSTAL reader - still needs testing Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-02-19 15:19:56 UTC (rev 12414) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-02-19 15:20:37 UTC (rev 12415) @@ -641,12 +641,15 @@ } private static boolean checkCrystal(String[] lines) { - return (lines[1].equals("SLAB") - || lines[1].equals("MOLECULE") - || lines[1].equals("POLYMER") - || lines[3].equals("SLAB") - || lines[3].equals("MOLECULE") - || lines[3].equals("POLYMER")); + if (lines[1].equals("SLAB") || lines[1].equals("MOLECULE") + || lines[1].equals("POLYMER") || lines[3].equals("SLAB") + || lines[3].equals("MOLECULE") || lines[3].equals("POLYMER")) + return true; + for (int i = 0; i < lines.length; i++) { + if (lines[i].equals("OPTGEOM")) + return true; + } + return false; } private static boolean checkWien2k(String[] lines) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2010-11-02 15:33:06
|
Revision: 14565 http://jmol.svn.sourceforge.net/jmol/?rev=14565&view=rev Author: pierocanepa Date: 2010-11-02 15:33:00 +0000 (Tue, 02 Nov 2010) Log Message: ----------- Add VASP outcar functions Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-11-02 15:32:08 UTC (rev 14564) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-11-02 15:33:00 UTC (rev 14565) @@ -52,7 +52,7 @@ "Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;" + "WebMO;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;Mopac;V3000;", - "xtal.", ";Aims;Castep;Crystal;Shelx;Wien2k;" + "xtal.", ";Aims;Castep;Crystal;Shelx;Vasp;Wien2k;" }; public final static String getReaderClassBase(String type) { @@ -547,26 +547,27 @@ private final static int SPECIAL_CASTEP = 10; private final static int SPECIAL_AIMS = 11; private final static int SPECIAL_CRYSTAL = 12; - private final static int SPECIAL_GROMACS = 13; - private final static int SPECIAL_GENNBO = 14; + private final static int SPECIAL_VASP = 13; + private final static int SPECIAL_GROMACS = 14; + private final static int SPECIAL_GENNBO = 15; // these next are needed by the XML reader - public final static int SPECIAL_ARGUS_XML = 15; - public final static int SPECIAL_CML_XML = 16; - public final static int SPECIAL_CHEM3D_XML = 17; - public final static int SPECIAL_MOLPRO_XML = 18; - public final static int SPECIAL_ODYSSEY_XML = 19; - public final static int SPECIAL_XSD_XML = 20; - public final static int SPECIAL_VASP_XML = 21; + public final static int SPECIAL_ARGUS_XML = 16; + public final static int SPECIAL_CML_XML = 17; + public final static int SPECIAL_CHEM3D_XML = 18; + public final static int SPECIAL_MOLPRO_XML = 19; + public final static int SPECIAL_ODYSSEY_XML = 20; + public final static int SPECIAL_XSD_XML = 21; + public final static int SPECIAL_VASP_XML = 22; - public final static int SPECIAL_ARGUS_DOM = 22; - public final static int SPECIAL_CML_DOM = 23; - public final static int SPECIAL_CHEM3D_DOM = 24; - public final static int SPECIAL_MOLPRO_DOM = 25; - public final static int SPECIAL_ODYSSEY_DOM = 26; - public final static int SPECIAL_XSD_DOM = 27; // not implemented - public final static int SPECIAL_VASP_DOM = 28; + public final static int SPECIAL_ARGUS_DOM = 23; + public final static int SPECIAL_CML_DOM = 24; + public final static int SPECIAL_CHEM3D_DOM = 25; + public final static int SPECIAL_MOLPRO_DOM = 26; + public final static int SPECIAL_ODYSSEY_DOM = 27; + public final static int SPECIAL_XSD_DOM = 28; // not implemented + public final static int SPECIAL_VASP_DOM = 29; public final static String[][] specialTags = { { "Jme" }, @@ -584,6 +585,7 @@ { "Castep" }, { "Aims" }, { "Crystal" }, + { "Vasp" }, { "Gromacs" }, { "GenNBO" }, @@ -614,6 +616,8 @@ return specialTags[SPECIAL_GROMACS][0]; if (checkCrystal(lines)) return specialTags[SPECIAL_CRYSTAL][0]; + if (checkVasp(lines)) + return specialTags[SPECIAL_VASP][0]; } if (nLines == 1 && lines[0].length() > 0 && Character.isDigit(lines[0].charAt(0))) @@ -681,6 +685,16 @@ || lines[2].startsWith(" RELA") || lines[2].startsWith(" NREL")); } + + private static boolean checkVasp(String[] lines){ + if(lines[1].startsWith(" vasp.")) + return true; + for(int i =0 ; i < lines.length; i++){ + if(lines[i].startsWith(" INCAR:")) + return true; + } + return false; + } private static boolean checkCastep(String[] lines) { for ( int i = 0; i<lines.length; i++ ) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2010-12-20 12:14:58
|
Revision: 14843 http://jmol.svn.sourceforge.net/jmol/?rev=14843&view=rev Author: pierocanepa Date: 2010-12-20 12:14:51 +0000 (Mon, 20 Dec 2010) Log Message: ----------- Quantum espresso and Gulp update Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-20 12:14:09 UTC (rev 14842) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-20 12:14:51 UTC (rev 14843) @@ -52,7 +52,7 @@ "Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;" + "WebMO;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;Mopac;", - "xtal.", ";Aims;Castep;Crystal;Gulp;Shelx;VaspOutcar;Wien2k;" + "xtal.", ";Aims;Castep;Crystal;Espresso;Gulp;Shelx;VaspOutcar;Wien2k;" }; public final static String getReaderClassBase(String type) { @@ -549,26 +549,27 @@ private final static int SPECIAL_CRYSTAL = 12; private final static int SPECIAL_VASP = 13; private final static int SPECIAL_GULP = 14; - private final static int SPECIAL_GROMACS = 15; - private final static int SPECIAL_GENNBO = 16; + private final static int SPECIAL_ESPRESSO = 15; + private final static int SPECIAL_GROMACS = 16; + private final static int SPECIAL_GENNBO = 17; // these next are needed by the XML reader - public final static int SPECIAL_ARGUS_XML = 17; - public final static int SPECIAL_CML_XML = 18; - public final static int SPECIAL_CHEM3D_XML = 19; - public final static int SPECIAL_MOLPRO_XML = 20; - public final static int SPECIAL_ODYSSEY_XML = 21; - public final static int SPECIAL_XSD_XML = 22; - public final static int SPECIAL_VASP_XML = 23; + public final static int SPECIAL_ARGUS_XML = 18; + public final static int SPECIAL_CML_XML = 19; + public final static int SPECIAL_CHEM3D_XML = 20; + public final static int SPECIAL_MOLPRO_XML = 21; + public final static int SPECIAL_ODYSSEY_XML = 22; + public final static int SPECIAL_XSD_XML = 23; + public final static int SPECIAL_VASP_XML = 24; - public final static int SPECIAL_ARGUS_DOM = 24; - public final static int SPECIAL_CML_DOM = 25; - public final static int SPECIAL_CHEM3D_DOM = 26; - public final static int SPECIAL_MOLPRO_DOM = 27; - public final static int SPECIAL_ODYSSEY_DOM = 28; - public final static int SPECIAL_XSD_DOM = 29; // not implemented - public final static int SPECIAL_VASP_DOM = 30; + public final static int SPECIAL_ARGUS_DOM = 25; + public final static int SPECIAL_CML_DOM = 26; + public final static int SPECIAL_CHEM3D_DOM = 27; + public final static int SPECIAL_MOLPRO_DOM = 28; + public final static int SPECIAL_ODYSSEY_DOM = 29; + public final static int SPECIAL_XSD_DOM = 30; // not implemented + public final static int SPECIAL_VASP_DOM = 31; public final static String[][] specialTags = { { "Jme" }, @@ -588,6 +589,7 @@ { "Crystal" }, { "VaspOutcar" }, { "Gulp" }, + { "Espresso" }, { "Gromacs" }, { "GenNBO" }, @@ -622,6 +624,8 @@ return specialTags[SPECIAL_VASP][0]; if(checkGulp(lines)) return specialTags[SPECIAL_GULP][0]; + if(checkQuantumEspresso(lines)) + return specialTags[SPECIAL_ESPRESSO][0]; } if (nLines == 1 && lines[0].length() > 0 && Character.isDigit(lines[0].charAt(0))) @@ -667,7 +671,25 @@ return false; return true; } - + + private static boolean checkQuantumEspresso(String[] lines) { + if (lines[2].contains("Program PWSCF v")) + return true; + if (lines[2].contains("PHONON ")) + return true; + for (int i = 0; i < lines.length; i++) { + if (lines[i].contains("Quantum ESPRESSO")) + return true; + if (lines[i].contains("http://www.quantum-espresso.org")) + return true; + if (lines[i].contains("Program PWSCF v")) + return true; + if (lines[i].contains("PHONON ")) + return true; + } + return false; + } + private static boolean checkCrystal(String[] lines) { String s = lines[1].trim(); if (s.equals("SLAB") ||s.equals("MOLECULE") This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-21 19:35:53
|
Revision: 14860 http://jmol.svn.sourceforge.net/jmol/?rev=14860&view=rev Author: hansonr Date: 2010-12-21 19:35:47 +0000 (Tue, 21 Dec 2010) Log Message: ----------- Question for Piere Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-21 18:57:52 UTC (rev 14859) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-21 19:35:47 UTC (rev 14860) @@ -673,9 +673,12 @@ } private static boolean checkQuantumEspresso(String[] lines) { - if (lines[2].contains("Program PWSCF v")) + // can't we just use Quantum ESPRESSO and http://... and PWSCF in 'contains' records? + // that catches the whole header. + + if (lines[2].contains("Program PWSCF")) return true; - if (lines[2].contains("PHONON ")) + if (lines[2].contains("PHONON ")) // this may be too general -- is it necessary? Provide an example, please return true; for (int i = 0; i < lines.length; i++) { if (lines[i].contains("Quantum ESPRESSO")) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-22 19:24:07
|
Revision: 14879 http://jmol.svn.sourceforge.net/jmol/?rev=14879&view=rev Author: hansonr Date: 2010-12-22 19:24:00 +0000 (Wed, 22 Dec 2010) Log Message: ----------- version=12.1.27_dev # bug fix: popup menu does not show load {1 1 1} options correctly # new feature: GULP reader Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-22 19:21:06 UTC (rev 14878) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-22 19:24:00 UTC (rev 14879) @@ -675,20 +675,20 @@ private static boolean checkQuantumEspresso(String[] lines) { // can't we just use Quantum ESPRESSO and http://... and PWSCF in 'contains' records? // that catches the whole header. - - if (lines[2].contains("Program PWSCF")) - return true; - if (lines[2].contains("PHONON ")) // this may be too general -- is it necessary? Provide an example, please - return true; + // add more as examples are included in datafiles/quantumEspresso +// if (lines[2].contains("Program PWSCF")) +// return true; +// if (lines[2].contains("PHONON ")) // this may be too general -- is it necessary? Provide an example, please +// return true; for (int i = 0; i < lines.length; i++) { - if (lines[i].contains("Quantum ESPRESSO")) - return true; - if (lines[i].contains("http://www.quantum-espresso.org")) - return true; +// if (lines[i].contains("Quantum ESPRESSO")) +// return true; +// if (lines[i].contains("http://www.quantum-espresso.org")) +// return true; if (lines[i].contains("Program PWSCF")) return true; - if (lines[i].contains("PHONON ")) - return true; +// if (lines[i].contains("PHONON ")) +// return true; } return false; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2010-12-23 00:08:55
|
Revision: 14885 http://jmol.svn.sourceforge.net/jmol/?rev=14885&view=rev Author: pierocanepa Date: 2010-12-23 00:08:48 +0000 (Thu, 23 Dec 2010) Log Message: ----------- I provide more examples for quantum espresso Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-23 00:03:37 UTC (rev 14884) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-23 00:08:48 UTC (rev 14885) @@ -675,10 +675,11 @@ private static boolean checkQuantumEspresso(String[] lines) { // can't we just use Quantum ESPRESSO and http://... and PWSCF in 'contains' records? // that catches the whole header. - // add more as examples are included in datafiles/quantumEspresso + + ///Piero This bit doesn't always appear // if (lines[2].contains("Program PWSCF")) // return true; -// if (lines[2].contains("PHONON ")) // this may be too general -- is it necessary? Provide an example, please +// if (lines[2].contains("Program PHONON ")) // this may be too general -- is it necessary? Provide an example, please // return true; for (int i = 0; i < lines.length; i++) { // if (lines[i].contains("Quantum ESPRESSO")) @@ -687,8 +688,10 @@ // return true; if (lines[i].contains("Program PWSCF")) return true; -// if (lines[i].contains("PHONON ")) -// return true; + + //That's another code within quantum espresso + if (lines[i].contains("Program PHONON")) + return true; } return false; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-04-23 16:32:13
|
Revision: 15401 http://jmol.svn.sourceforge.net/jmol/?rev=15401&view=rev Author: hansonr Date: 2011-04-23 16:32:06 +0000 (Sat, 23 Apr 2011) Log Message: ----------- doctype HTML can be interpreted as cml Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-04-23 15:34:10 UTC (rev 15400) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-04-23 16:32:06 UTC (rev 15401) @@ -497,7 +497,7 @@ if (type.equals("Xml")) { // check for an error message from a server -- certainly not XML // but new CML format includes xmlns:xhtml="http://www.w3.org/1999/xhtml" in <cml> tag. - if (header.indexOf("XHTML") >= 0 || header.indexOf("xhtml") >= 0 && header.indexOf("<cml") < 0) + if (header.indexOf("<!DOCTYPE HTML PUBLIC") >= 0 || header.indexOf("XHTML") >= 0 || header.indexOf("xhtml") >= 0 && header.indexOf("<cml") < 0) break; type = getXmlType(header); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2011-08-31 19:06:19
|
Revision: 16010 http://jmol.svn.sourceforge.net/jmol/?rev=16010&view=rev Author: pierocanepa Date: 2011-08-31 19:06:12 +0000 (Wed, 31 Aug 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-08-31 16:39:53 UTC (rev 16009) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-08-31 19:06:12 UTC (rev 16010) @@ -52,7 +52,7 @@ "Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;" + "WebMO;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;Mopac;", - "xtal.", ";Aims;Castep;Crystal;Espresso;Gulp;Shelx;Siesta;VaspOutcar;Wien2k;" + "xtal.", ";Aims;Castep;Crystal;Dmol;Espresso;Gulp;Shelx;Siesta;VaspOutcar;Wien2k;" }; public final static String getReaderClassBase(String type) { @@ -559,28 +559,29 @@ private final static int SPECIAL_CRYSTAL = 12; private final static int SPECIAL_VASP = 13; private final static int SPECIAL_GULP = 14; - private final static int SPECIAL_ESPRESSO = 15; - private final static int SPECIAL_SIESTA = 16; - private final static int SPECIAL_GROMACS = 17; - private final static int SPECIAL_GENNBO = 18; + private final static int SPECIAL_DMOL = 15; + private final static int SPECIAL_ESPRESSO = 16; + private final static int SPECIAL_SIESTA = 17; + private final static int SPECIAL_GROMACS = 18; + private final static int SPECIAL_GENNBO = 19; // these next are needed by the XML reader - public final static int SPECIAL_ARGUS_XML = 19; - public final static int SPECIAL_CML_XML = 20; - public final static int SPECIAL_CHEM3D_XML = 21; - public final static int SPECIAL_MOLPRO_XML = 22; - public final static int SPECIAL_ODYSSEY_XML = 23; - public final static int SPECIAL_XSD_XML = 24; - public final static int SPECIAL_VASP_XML = 25; + public final static int SPECIAL_ARGUS_XML = 20; + public final static int SPECIAL_CML_XML = 21; + public final static int SPECIAL_CHEM3D_XML = 22; + public final static int SPECIAL_MOLPRO_XML = 23; + public final static int SPECIAL_ODYSSEY_XML = 24; + public final static int SPECIAL_XSD_XML = 25; + public final static int SPECIAL_VASP_XML = 26; - public final static int SPECIAL_ARGUS_DOM = 26; - public final static int SPECIAL_CML_DOM = 27; - public final static int SPECIAL_CHEM3D_DOM = 28; - public final static int SPECIAL_MOLPRO_DOM = 29; - public final static int SPECIAL_ODYSSEY_DOM = 30; - public final static int SPECIAL_XSD_DOM = 31; // not implemented - public final static int SPECIAL_VASP_DOM = 32; + public final static int SPECIAL_ARGUS_DOM = 27; + public final static int SPECIAL_CML_DOM = 28; + public final static int SPECIAL_CHEM3D_DOM = 29; + public final static int SPECIAL_MOLPRO_DOM = 30; + public final static int SPECIAL_ODYSSEY_DOM = 31; + public final static int SPECIAL_XSD_DOM = 32; // not implemented + public final static int SPECIAL_VASP_DOM = 33; public final static String[][] specialTags = { { "Jme" }, @@ -600,6 +601,7 @@ { "Crystal" }, { "VaspOutcar" }, { "Gulp" }, + { "Dmol" }, { "Espresso" }, { "Siesta" }, { "Gromacs" }, @@ -661,6 +663,8 @@ return specialTags[SPECIAL_VASP][0]; if (checkGulp(lines)) return specialTags[SPECIAL_GULP][0]; + if (checkDmol(lines)) + return specialTags[SPECIAL_DMOL][0]; if (checkQuantumEspresso(lines)) return specialTags[SPECIAL_ESPRESSO][0]; if (checkSiesta(lines)) @@ -824,6 +828,19 @@ return false; return true; } + + private static boolean checkDmol(String[] lines) { + if (lines[2].startsWith("Materials Studio DMol^3 version")) + return true; + for (int i = 0; i < lines.length; i++) { + if (lines[i].contains("B. Delley,")) { + return true; + } else if (lines[i].contains("DMol^3")) { + return true; + } + } + return false; + } private static boolean checkGulp(String[] lines) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-24 18:01:26
|
Revision: 16108 http://jmol.svn.sourceforge.net/jmol/?rev=16108&view=rev Author: hansonr Date: 2011-09-24 18:01:20 +0000 (Sat, 24 Sep 2011) Log Message: ----------- version=12.2.RC8_dev # bug fix: MOLDEN reader not reading spherical basis functions Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-09-24 17:57:13 UTC (rev 16107) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-09-24 18:01:20 UTC (rev 16108) @@ -443,13 +443,13 @@ // first check just the first 10 bytes - String leader = llr.getHeader(LEADER_CHAR_MAX); + String leader = llr.getHeader(LEADER_CHAR_MAX).trim(); for (int i = 0; i < fileStartsWithRecords.length; ++i) { String[] recordTags = fileStartsWithRecords[i]; for (int j = 1; j < recordTags.length; ++j) { String recordTag = recordTags[j]; - if (leader.contains(recordTag)) + if (leader.startsWith(recordTag)) return recordTags[0]; } } @@ -910,7 +910,7 @@ private final static int LEADER_CHAR_MAX = 10; private final static String[] cubeFileStartRecords = - {"Cube", "JVXL"}; + {"Cube", "JVXL", "#JVXL"}; private final static String[] mol2Records = {"Mol2", "mol2", "@<TRIPOS>"}; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-08-08 03:49:27
|
Revision: 18523 http://sourceforge.net/p/jmol/code/18523 Author: hansonr Date: 2013-08-08 03:49:24 +0000 (Thu, 08 Aug 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-08 03:21:58 UTC (rev 18522) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-08 03:49:24 UTC (rev 18523) @@ -39,7 +39,7 @@ private final static String classBase = "org.jmol.adapter.readers."; private final static String[] readerSets = new String[] { - "cifpdb.", ";Cif;MMCIF_PDBX;", + "cif.", ";Cif;MMCIF_PDBX;", "molxyz.", ";Mol3D;Mol;Xyz;", "more.", ";BinaryDcd;Gromacs;Jcampdx;MdCrd;MdTop;Mol2;Pqr;P2n;TlsDataOnly;", "quantum.", ";Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GausianWfn;Jaguar;" + This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2013-08-08 11:06:22
|
Revision: 18527 http://sourceforge.net/p/jmol/code/18527 Author: pierocanepa Date: 2013-08-08 11:06:19 +0000 (Thu, 08 Aug 2013) Log Message: ----------- I'm starting developing a redear for Abinit Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-08 04:27:11 UTC (rev 18526) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-08 11:06:19 UTC (rev 18527) @@ -48,7 +48,8 @@ "pdb.", ";Pdb;", "pymol.", ";PyMOL;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;Mopac;MopacArchive;ZMatrix;", - "xtal.", ";Aims;Castep;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;VaspPoscar;Wien2k;Xcrysden;" + "xtal.", ";Abinit;Aims;Castep;Crystal;Dmol;Espresso;Gulp;Magres;Shelx;Siesta;VaspOutcar;" + + "VaspPoscar;Wien2k;Xcrysden;" }; public final static String getReaderClassBase(String type) { @@ -873,9 +874,12 @@ private final static String[] mopacArchiveContainsRecords = { "MopacArchive", "SUMMARY OF PM" }; + private final static String [] abinitContainsRecords = + {"ABINIT", "Louvain", "http://www.abinit.org"}; + private final static String[][] headerContainsRecords = { sptContainsRecords, xmlContainsRecords, gaussianContainsRecords, ampacContainsRecords, mopacContainsRecords, qchemContainsRecords, @@ -883,7 +887,7 @@ spartanBinaryContainsRecords, spartanContainsRecords, mol2Records, adfContainsRecords, psiContainsRecords, nwchemContainsRecords, uicrcifContainsRecords, dgridContainsRecords, crystalContainsRecords, dmolContainsRecords, gulpContainsRecords, espressoContainsRecords, siestaContainsRecords,xcrysDenContainsRecords, - mopacArchiveContainsRecords + mopacArchiveContainsRecords,abinitContainsRecords }; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-08-09 00:09:35
|
Revision: 18532 http://sourceforge.net/p/jmol/code/18532 Author: hansonr Date: 2013-08-09 00:09:29 +0000 (Fri, 09 Aug 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-08 23:30:00 UTC (rev 18531) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-09 00:09:29 UTC (rev 18532) @@ -48,7 +48,7 @@ "pdb.", ";Pdb;", "pymol.", ";PyMOL;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;Mopac;MopacArchive;ZMatrix;", - "xtal.", ";Abinit;Aims;Castep;Crystal;Dmol;Espresso;Gulp;Magres;Shelx;Siesta;VaspOutcar;" + + "xtal.", ";Abinit;Aims;Castep;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;" + "VaspPoscar;Wien2k;Xcrysden;" }; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2013-08-11 10:22:08
|
Revision: 18537 http://sourceforge.net/p/jmol/code/18537 Author: pierocanepa Date: 2013-08-11 10:22:05 +0000 (Sun, 11 Aug 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-11 01:01:29 UTC (rev 18536) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-08-11 10:22:05 UTC (rev 18537) @@ -874,8 +874,8 @@ private final static String[] mopacArchiveContainsRecords = { "MopacArchive", "SUMMARY OF PM" }; - private final static String [] abinitContainsRecords = - {"ABINIT", "Louvain", "http://www.abinit.org"}; + private final static String[] abinitContainsRecords = { "Abinit", + "http://www.abinit.org", "Catholique", "Louvain" }; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-09-19 04:20:07
|
Revision: 18679 http://sourceforge.net/p/jmol/code/18679 Author: hansonr Date: 2013-09-19 04:20:01 +0000 (Thu, 19 Sep 2013) Log Message: ----------- JavaScript PNGJ file loading fix -- need to recognize file containing "JmolManifest" as script file Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-09-18 23:24:06 UTC (rev 18678) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-09-19 04:20:01 UTC (rev 18679) @@ -707,7 +707,7 @@ private final static int LEADER_CHAR_MAX = 64; private final static String[] sptContainsRecords = - { "spt", "# Jmol state", "# Jmol script" }; + { "spt", "# Jmol state", "# Jmol script", "JmolManifest" }; private final static String[] cubeFileStartRecords = {"Cube", "JVXL", "#JVXL"}; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-03-07 18:08:15
|
Revision: 19420 http://sourceforge.net/p/jmol/code/19420 Author: hansonr Date: 2014-03-07 18:08:13 +0000 (Fri, 07 Mar 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-03-06 21:43:48 UTC (rev 19419) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-03-07 18:08:13 UTC (rev 19420) @@ -121,8 +121,8 @@ } } if (readerName.charAt(0) == '\n') - errMsg = "unrecognized file format for file " + fullName + "\n" - + readerName; + errMsg = "unrecognized file format for file\n" + fullName + "\n" + + split(readerName, 50); else if (readerName.equals("spt")) errMsg = JmolAdapter.NOTE_SCRIPT_FILE + fullName + "\n"; else if (!fullName.equals("ligand")) @@ -149,6 +149,14 @@ return atomSetCollectionReader; } + private static String split(String a, int n) { + String s = ""; + int l = a.length(); + for (int i = 0, j = 0; i < l; i = j) + s += a.substring(i, (j = Math.min(i + n, l))) + "\n"; + return s; + } + /** * a largely untested reader of the DOM - where in a browser there is model * actually in XML format already present on the page. -- Egon Willighagen This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <rka...@us...> - 2016-10-04 19:56:42
|
Revision: 21255 http://sourceforge.net/p/jmol/code/21255 Author: rkanters Date: 2016-10-04 19:56:40 +0000 (Tue, 04 Oct 2016) Log Message: ----------- molden itself is able to read files that start with [MOLDEN FORMAT] but Jmol did not. I modified the resolver so it does not only expect Molden Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2016-10-03 05:08:21 UTC (rev 21254) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2016-10-04 19:56:40 UTC (rev 21255) @@ -349,7 +349,7 @@ {"WebMO", "[HEADER]"}; private final static String[] moldenFileStartRecords = - {"Molden", "[Molden"}; + {"Molden", "[Molden", "MOLDEN", "[MOLDEN"}; private final static String[] dcdFileStartRecords = {"BinaryDcd", "T\0\0\0CORD", "\0\0\0TCORD"}; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2017-02-05 22:59:30
|
Revision: 21393 http://sourceforge.net/p/jmol/code/21393 Author: hansonr Date: 2017-02-05 22:59:28 +0000 (Sun, 05 Feb 2017) Log Message: ----------- .nbo files not being read directly Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2017-02-05 22:58:34 UTC (rev 21392) +++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2017-02-05 22:59:28 UTC (rev 21393) @@ -534,6 +534,7 @@ return (leader.indexOf("$GENNBO") >= 0 || lines[1].startsWith(" Basis set information needed for plotting orbitals") || lines[1].indexOf("s in the AO basis:") >= 0 + || lines[1].indexOf("***** NBO ") >= 0 || lines[2].indexOf(" N A T U R A L A T O M I C O R B I T A L") >= 0); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |