test restart of orca compound jobs

Author: marco-foscato

src/main/java/autocompchem/run/jobediting/ActionApplier.java

@@ -17,12 +17,10 @@
 import autocompchem.files.FileUtils;
 import autocompchem.run.EvaluationJob;
 import autocompchem.run.Job;
-import autocompchem.run.JobConstants;
 import autocompchem.run.MonitoringJob;
 import autocompchem.run.jobediting.Action.ActionObject;
 import autocompchem.run.jobediting.Action.ActionType;
 import autocompchem.run.jobediting.DataArchivingRule.ArchivingTaskType;
-import autocompchem.utils.NumberUtils;
 import autocompchem.utils.SetUtils;
 import autocompchem.utils.StringUtils;
 import autocompchem.wiro.WIROConstants;

src/main/java/autocompchem/run/jobediting/DataArchivingRule.java

@@ -27,7 +27,7 @@ public class DataArchivingRule
 	/*
 	 * Placeholder for the base name of the file.
 	 */
-	public static final String BASENAME_PLHLD = "BASENAME_PLHLD";
+	public static final String BASENAME_PLHLD = "BASENAME";
 
 	/**
 	 * Defines if a data archiving rule is meant for moving, copying or removing
@@ -116,8 +116,7 @@ public DataArchivingRule(ArchivingTaskType type, String pattern)
 	 * the pathname.
 	 * @param newName the new name for the file. Used only if the type is 
 	 * {@link ArchivingTaskType#RENAME_COPY_LAST_SEQUENTIAL} or
-	 * {@link ArchivingTaskType#RENAME_COPY_INDEXED}
-	 * or {@link ArchivingTaskType#RENAME_COPY_BASENAME_PLHLD}.
+	 * {@link ArchivingTaskType#RENAME_COPY_BASENAME_IDX}
 	 */
 	public DataArchivingRule(ArchivingTaskType type, String pattern, String newName)
 	{

src/main/java/autocompchem/wiro/chem/ChemSoftInputWriter.java

@@ -295,6 +295,10 @@ else if (params.contains(ChemSoftConstants.PARJOBDETAILS))
                     ((AtomContainerSet) geomParamValue).atomContainers().forEach(i -> inMols.add(i));
                 } else if (geomParamValue instanceof IAtomContainer) {
                     inMols.add((IAtomContainer) geomParamValue);
+                } else if (geomParamValue == null) {
+                    throw new IllegalArgumentException("Parameter '" + ChemSoftConstants.PARGEOM 
+                        + "' is expected to be an AtomContainerSet or IAtomContainer, "
+                        + "but is null.");
                 } else {
                     throw new IllegalArgumentException("Parameter '" + ChemSoftConstants.PARGEOM 
                         + "' is expected to be an AtomContainerSet or IAtomContainer, "

test/cli47.check

@@ -33,15 +33,15 @@ if ! grep -q -i "second attempt" "cli47_wdir/restart.densities" ; then not_passe
 if [ ! -f "cli47_wdir/Job_#0.1_1/cli47.out" ] ; then not_passed $LINENO ; fi
 if ! grep -q -i "The optimization did not converge but reached the maximum number" "cli47_wdir/Job_#0.1_1/cli47.out" ; then not_passed $LINENO ; fi
 
-if [ -f cli47_wdir/Job_#0.1_1/restart.gbw ] ; then not_passed $LINENO ; fi # overwritten, so not archived
+if [ -f "cli47_wdir/Job_#0.1_1/restart.gbw" ] ; then not_passed $LINENO ; fi # overwritten, so not archived
 
-if [ ! -f cli47_wdir/Job_#0.1_1/cli47.gbw ] ; then not_passed $LINENO ; fi
+if [ ! -f "cli47_wdir/Job_#0.1_1/cli47.gbw" ] ; then not_passed $LINENO ; fi
 if ! grep -q -i "this should remain" "cli47_wdir/Job_#0.1_1/cli47.gbw" ; then not_passed $LINENO ; fi
 if ! grep -q -i "second attempt" "cli47_wdir/Job_#0.1_1/cli47.gbw" ; then not_passed $LINENO ; fi
 
-if [ -f cli47_wdir/Job_#0.1_1/restart.densities ] ; then not_passed $LINENO ; fi # overwritten, so not archived
+if [ -f "cli47_wdir/Job_#0.1_1/restart.densities" ] ; then not_passed $LINENO ; fi # overwritten, so not archived
 
-if [ ! -f cli47_wdir/Job_#0.1_1/cli47.densities ] ; then not_passed $LINENO ; fi
+if [ ! -f "cli47_wdir/Job_#0.1_1/cli47.densities" ] ; then not_passed $LINENO ; fi
 if ! grep -q -i "this should remain" "cli47_wdir/Job_#0.1_1/cli47.densities" ; then not_passed $LINENO ; fi
 if ! grep -q -i "second attempt" "cli47_wdir/Job_#0.1_1/cli47.densities" ; then not_passed $LINENO ; fi
 

test/cli47_KB/draft_geom_opt_run_out_of_cycles.json

@@ -20,7 +20,7 @@
     "jobEditTasks": [
       {
         "task": "SET_JOB_PARAMETER",
-        "parameter": {"reference": "inputGeometries", "value": "getACCJobsData(#0,JOBOUTPUTDATA,LAST,GEOMETRIES,LAST)"}
+        "parameter": {"reference": "inputGeometries", "value": "getACCJobsData(#0,GEOMETRIES,LAST)"}
       },
       {
         "task": "SET_KEYWORD",
@@ -65,12 +65,12 @@
         "pattern": "*.sdf"
       },
       {
-        "type": "rename_copy_basename",
+        "type": "rename_copy_basename_idx",
         "pattern": "BASENAME.gbw",
         "newName": "restart.gbw"
       },
       {
-        "type": "rename_copy_basename",
+        "type": "rename_copy_basename_idx",
         "pattern": "BASENAME.densities",
         "newName": "restart.densities"
       },