Sam Adams avatar Sam Adams committed c2ae50a

Start work on compchem ATs

Comments (0)

Files changed (9)

acceptance-test-driver/pom.xml

             <groupId>net.chempound</groupId>
             <artifactId>chempound-webapp</artifactId>
         </dependency>
+        <dependency>
+            <groupId>net.chempound.compchem</groupId>
+            <artifactId>compchem-handler</artifactId>
+            <version>0.1-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>net.chempound.compchem</groupId>
+            <artifactId>compchem-importer</artifactId>
+            <version>0.1-SNAPSHOT</version>
+        </dependency>
 
         <dependency>
             <groupId>net.chempound</groupId>

acceptance-test-driver/src/main/java/net/chempound/acceptance/dsl/AbstractAcceptanceTest.java

 import org.junit.BeforeClass;
 
 import java.net.URI;
-import java.util.Collection;
 import java.util.Random;
 
 import static java.util.Arrays.asList;

acceptance-test-driver/src/main/java/net/chempound/acceptance/dsl/ChempoundTestModule.java

 
 import net.chempound.ChempoundConfigurationModule;
 import net.chempound.DefaultChempoundModule;
+import net.chempound.compchem.CompChemModule;
 import net.chempound.config.DefaultChempoundConfiguration;
 import net.chempound.datastore.InMemoryJenaTripleStore;
 import net.chempound.datastore.TripleStore;
     protected void configure() {
         install(new ChempoundConfigurationModule(new DefaultChempoundConfiguration(rootUri, workspace)));
         install(new DefaultChempoundModule());
+        install(new CompChemModule());
         super.configure();
     }
 

acceptance-test-driver/src/main/java/net/chempound/acceptance/dsl/driver/APIDriver.java

         final DepositItemRequest request = new DepositItemRequest()
             .withUri(config.parent != null ? config.parent : context.getContentRoot())
             .withTitle(context.actual(config.title))
-            .withSlug(context.actual(config.slug));
+            .withSlug(context.actual(config.slug))
+            .withMetadata(config.metadata);
 
         if (config.files != null) {
             for (final Resource file : config.files) {
-                request.addResource(createResource(file));
+                request.withFile(createResource(file));
             }
         }
 

acceptance-test-driver/src/main/java/net/chempound/acceptance/dsl/driver/DepositInstruction.java

 package net.chempound.acceptance.dsl.driver;
 
+import com.hp.hpl.jena.rdf.model.Model;
+
 import java.net.URI;
 import java.util.ArrayList;
 import java.util.List;
     boolean multipart;
     List<Resource> files;
     boolean inProgress;
+    Model metadata;
 
     DepositInstruction(final APIDriver driver) {
         this.driver = driver;
         return this;
     }
 
-    public DepositInstruction withInProgress(final boolean inProgress)
-    {
+    public DepositInstruction withInProgress(final boolean inProgress) {
         this.inProgress = inProgress;
         return this;
     }
     public DepositReceipt execute() {
         return driver.depositItem(this);
     }
+
+    public DepositInstruction withMetadata(final Model metadata) {
+        this.metadata = metadata;
+        return this;
+    }
 }

acceptance-tests/src/test/java/net/chempound/acceptance/chemistry/GaussianLogAcceptanceTest.java

+package net.chempound.acceptance.chemistry;
+
+import net.chempound.acceptance.dsl.AbstractAcceptanceTest;
+import net.chempound.acceptance.dsl.driver.APIDriver;
+import net.chempound.acceptance.dsl.driver.DepositInstruction;
+import net.chempound.acceptance.dsl.driver.Resource;
+import net.chempound.compchem.gaussian.GaussianLogImporter;
+import net.chempound.content.DepositRequest;
+import net.chempound.storage.DepositResource;
+import nu.xom.Document;
+import org.apache.commons.io.IOUtils;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.xmlcml.cml.base.CMLBuilder;
+
+import java.io.InputStream;
+
+/**
+ * @author Sam Adams
+ */
+@Ignore
+public class GaussianLogAcceptanceTest extends AbstractAcceptanceTest {
+
+    private APIDriver apiDriver;
+
+    @Before
+    public void setUp() throws Exception {
+        apiDriver = driverFactory.createAPIDriver();
+    }
+
+    @Test
+    public void shouldDepositGaussianLogFile() throws Exception {
+
+        final DepositRequest depositRequest;
+        final InputStream in = getClass().getResourceAsStream("gaussian.log");
+        try {
+            final GaussianLogImporter importer = new GaussianLogImporter();
+            importer.setLogFile(in, "gaussian.log");
+            depositRequest = importer.generateDepositRequest();
+        } finally {
+            IOUtils.closeQuietly(in);
+        }
+
+        final DepositInstruction depositInstruction = apiDriver.depositItem()
+                                                       .withSlug("slug")
+                                                       .withTitle("title")
+                                                       .withMetadata(depositRequest.getMetadataModel());
+        for (DepositResource resource : depositRequest.getAggregatedResources()) {
+            depositInstruction.withFile(new Resource(resource.getURI(), resource.getMimeType().getName(), IOUtils.toByteArray(resource.openInputStream())));
+        }
+        depositInstruction.execute();
+
+        Assert.fail("work in progress");
+    }
+
+}

acceptance-tests/src/test/java/net/chempound/acceptance/chemistry/NwChemLogAcceptanceTest.java

+package net.chempound.acceptance.chemistry;
+
+import net.chempound.acceptance.dsl.AbstractAcceptanceTest;
+import net.chempound.acceptance.dsl.driver.APIDriver;
+import net.chempound.acceptance.dsl.driver.DepositInstruction;
+import net.chempound.acceptance.dsl.driver.Resource;
+import net.chempound.compchem.gaussian.GaussianLogImporter;
+import net.chempound.compchem.nwchem.NWChemLogImporter;
+import net.chempound.content.DepositRequest;
+import net.chempound.storage.DepositResource;
+import org.apache.commons.io.IOUtils;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import java.io.InputStream;
+
+/**
+ * @author Sam Adams
+ */
+@Ignore
+public class NwChemLogAcceptanceTest extends AbstractAcceptanceTest {
+
+    private APIDriver apiDriver;
+
+    @Before
+    public void setUp() throws Exception {
+        apiDriver = driverFactory.createAPIDriver();
+    }
+
+    @Test
+    public void shouldDepositNwChemLogFile() throws Exception {
+
+        final DepositRequest depositRequest;
+        final InputStream in = getClass().getResourceAsStream("h2o_631gs.nwo");
+        try {
+            final NWChemLogImporter importer = new NWChemLogImporter();
+            importer.setLogFile(in, "h2o_631gs.nwo");
+            depositRequest = importer.generateDepositRequest();
+        } finally {
+            IOUtils.closeQuietly(in);
+        }
+
+        final DepositInstruction depositInstruction = apiDriver.depositItem()
+                                                       .withSlug("slug")
+                                                       .withTitle("title")
+                                                       .withMetadata(depositRequest.getMetadataModel());
+        for (DepositResource resource : depositRequest.getAggregatedResources()) {
+            depositInstruction.withFile(new Resource(resource.getURI(), resource.getMimeType().getName(), IOUtils.toByteArray(resource.openInputStream())));
+        }
+        depositInstruction.execute();
+
+        Assert.fail("work in progress");
+    }
+
+}

acceptance-tests/src/test/resources/net/chempound/acceptance/chemistry/gaussian.log

+ Entering Gaussian System, Link 0=/usr/local/gaussian/g03/g03
+ Initial command:
+ /usr/local/gaussian/g03/l1.exe /tmp/webmo/3/Gau-15097.inp -scrdir=/tmp/webmo/3/
+ Entering Link 1 = /usr/local/gaussian/g03/l1.exe PID=     15098.
+  
+ Copyright (c) 1988,1990,1992,1993,1995,1998,2003, Gaussian, Inc.
+                  All Rights Reserved.
+  
+ This is the Gaussian(R) 03 program.  It is based on the
+ the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
+ the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
+ the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
+ the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
+ the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
+ the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
+ University), and the Gaussian 82(TM) system (copyright 1983,
+ Carnegie Mellon University). Gaussian is a federally registered
+ trademark of Gaussian, Inc.
+  
+ This software contains proprietary and confidential information,
+ including trade secrets, belonging to Gaussian, Inc.
+  
+ This software is provided under written license and may be
+ used, copied, transmitted, or stored only in accord with that
+ written license.
+  
+ The following legend is applicable only to US Government
+ contracts under DFARS:
+  
+                    RESTRICTED RIGHTS LEGEND
+  
+ Use, duplication or disclosure by the US Government is subject
+ to restrictions as set forth in subparagraph (c)(1)(ii) of the
+ Rights in Technical Data and Computer Software clause at DFARS
+ 252.227-7013.
+  
+ Gaussian, Inc.
+ Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA
+  
+ The following legend is applicable only to US Government
+ contracts under FAR:
+  
+                    RESTRICTED RIGHTS LEGEND
+  
+ Use, reproduction and disclosure by the US Government is subject
+ to restrictions as set forth in subparagraph (c) of the
+ Commercial Computer Software - Restricted Rights clause at FAR
+ 52.227-19.
+  
+ Gaussian, Inc.
+ Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA
+  
+  
+ ---------------------------------------------------------------
+ Warning -- This program may not be used in any manner that
+ competes with the business of Gaussian, Inc. or will provide
+ assistance to any competitor of Gaussian, Inc.  The licensee
+ of this program is prohibited from giving any competitor of
+ Gaussian, Inc. access to this program.  By using this program,
+ the user acknowledges that Gaussian, Inc. is engaged in the
+ business of creating and licensing software in the field of
+ computational chemistry and represents and warrants to the
+ licensee that it is not a competitor of Gaussian, Inc. and that
+ it will not use this program in any manner prohibited above.
+ ---------------------------------------------------------------
+  
+
+ Cite this work as:
+ Gaussian 03, Revision B.04,
+ M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, 
+ M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, 
+ K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, 
+ V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, 
+ G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, 
+ R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, 
+ H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, 
+ C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, 
+ A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, 
+ K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, 
+ V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, 
+ O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, 
+ J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, 
+ J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, 
+ I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, 
+ C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, 
+ B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, 
+ Gaussian, Inc., Pittsburgh PA, 2003.
+ 
+ *********************************************
+ Gaussian 03:  x86-Linux-G03RevB.04 2-Jun-2003
+                  21-Nov-2006 
+ *********************************************
+ --------------------------
+ #N B3LYP/6-31G(d) OPT FREQ
+ --------------------------
+ 1/14=-1,18=20,26=3,38=1/1,3;
+ 2/9=110,17=6,18=5,40=1/2;
+ 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3;
+ 4//1;
+ 5/5=2,38=5/2;
+ 6/7=2,8=2,9=2,10=2,28=1/1;
+ 7//1,2,3,16;
+ 1/14=-1,18=20/3(1);
+ 99//99;
+ 2/9=110/2;
+ 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3;
+ 4/5=5,16=3/1;
+ 5/5=2,38=5/2;
+ 7//1,2,3,16;
+ 1/14=-1,18=20/3(-5);
+ 2/9=110/2;
+ 6/7=2,8=2,9=2,10=2,19=2,28=1/1;
+ 99/9=1/99;
+ --
+ Cl
+ --
+ Symbolic Z-matrix:
+ Charge =  0 Multiplicity = 2
+ Cl
+ 
+
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+ Berny optimization.
+ Initialization pass.
+ No Z-matrix variables, so optimization will use Cartesian coordinates.
+ Trust Radius=1.00D-01 FncErr=1.00D-07 GrdErr=1.00D-06
+ Number of steps in this run=  20 maximum allowed number of steps= 100.
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+
+                          Input orientation:                          
+ ---------------------------------------------------------------------
+ Center     Atomic     Atomic              Coordinates (Angstroms)
+ Number     Number      Type              X           Y           Z
+ ---------------------------------------------------------------------
+    1         17             0        0.000000    0.000000    0.000000
+ ---------------------------------------------------------------------
+ Stoichiometry    Cl(2)
+ Framework group  OH[O(Cl)]
+ Deg. of freedom     0
+ Full point group                 OH      NOp  48
+ Largest Abelian subgroup         D2H     NOp   8
+ Largest concise Abelian subgroup C1      NOp   1
+                         Standard orientation:                         
+ ---------------------------------------------------------------------
+ Center     Atomic     Atomic              Coordinates (Angstroms)
+ Number     Number      Type              X           Y           Z
+ ---------------------------------------------------------------------
+    1         17             0        0.000000    0.000000    0.000000
+ ---------------------------------------------------------------------
+ Standard basis: 6-31G(d) (6D, 7F)
+ There are     7 symmetry adapted basis functions of AG  symmetry.
+ There are     1 symmetry adapted basis functions of B1G symmetry.
+ There are     1 symmetry adapted basis functions of B2G symmetry.
+ There are     1 symmetry adapted basis functions of B3G symmetry.
+ There are     0 symmetry adapted basis functions of AU  symmetry.
+ There are     3 symmetry adapted basis functions of B1U symmetry.
+ There are     3 symmetry adapted basis functions of B2U symmetry.
+ There are     3 symmetry adapted basis functions of B3U symmetry.
+ Integral buffers will be    262144 words long.
+ Raffenetti 2 integral format.
+ Two-electron integral symmetry is turned on.
+    19 basis functions,    52 primitive gaussians,    19 cartesian basis functions
+     9 alpha electrons        8 beta electrons
+       nuclear repulsion energy         0.0000000000 Hartrees.
+ NAtoms=    1 NActive=    1 NUniq=    1 SFac= 1.00D+00 NAtFMM=   60 Big=F
+ One-electron integrals computed using PRISM.
+ NBasis=    19 RedAO= T  NBF=     7     1     1     1     0     3     3     3
+ NBsUse=    19 1.00D-06 NBFU=     7     1     1     1     0     3     3     3
+ Harris functional with IExCor=  402 diagonalized for initial guess.
+ ExpMin= 1.43D-01 ExpMax= 2.52D+04 ExpMxC= 3.78D+03 IAcc=1 IRadAn=         1 AccDes= 1.00D-06
+ HarFok:  IExCor= 402 AccDes= 1.00D-06 IRadAn=         1 IDoV=1
+ ScaDFX=  1.000000  1.000000  1.000000  1.000000
+ Initial guess orbital symmetries:
+ Alpha Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (A1G) (T1U) (T1U)
+                 (T1U)
+       Virtual   (A1G) (T1U) (T1U) (T1U) (EG) (EG) (T2G) (T2G)
+                 (T2G) (A1G)
+ Beta  Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (A1G) (T1U) (T1U)
+       Virtual   (T1U) (A1G) (T1U) (T1U) (T1U) (EG) (EG) (T2G)
+                 (T2G) (T2G) (A1G)
+ <S**2> of initial guess= 0.7500
+ Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
+ Requested convergence on MAX density matrix=1.00D-06.
+ Requested convergence on             energy=1.00D-06.
+ No special actions if energy rises.
+ Keep R1 and R2 integrals in memory in canonical form, NReq=      496463.
+ Integral accuracy reduced to 1.0D-05 until final iterations.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Initial convergence to 1.0D-05 achieved.  Increase integral accuracy.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ SCF Done:  E(UB+HF-LYP) =  -460.136242222     A.U. after   10 cycles
+             Convg  =    0.8955D-08             -V/T =  2.0031
+             S**2   =   0.7517
+ Annihilation of the first spin contaminant:
+ S**2 before annihilation     0.7517,   after     0.7500
+
+ **********************************************************************
+
+            Population analysis using the SCF density.
+
+ **********************************************************************
+
+ Orbital symmetries:
+ Alpha Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (?A) (?B) (?B) (?B)
+       Virtual   (?A) (?B) (?B) (?B) (?A) (T2G) (T2G) (T2G) (?A)
+                 (A1G)
+ Beta  Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (T2G) (?A) (?A)
+       Virtual   (?A) (A1G) (?A) (?A) (?A) (T2G) (T2G) (T2G) (T2G)
+                 (T2G) (A1G)
+ Unable to determine electronic state:  an orbital has unidentified symmetry.
+ Alpha  occ. eigenvalues -- -101.59790  -9.51080  -7.28568  -7.26232  -7.26232
+ Alpha  occ. eigenvalues --   -0.84502  -0.40765  -0.35224  -0.35224
+ Alpha virt. eigenvalues --    0.32222   0.39579   0.42573   0.42573   0.78069
+ Alpha virt. eigenvalues --    0.79441   0.79441   0.84049   0.84049   4.15353
+  Beta  occ. eigenvalues -- -101.59109  -9.50436  -7.26397  -7.25843  -7.25843
+  Beta  occ. eigenvalues --   -0.79151  -0.33603  -0.33603
+  Beta virt. eigenvalues --   -0.24572   0.33828   0.43208   0.43208   0.43723
+  Beta virt. eigenvalues --    0.84953   0.84953   0.85541   0.85541   0.86478
+  Beta virt. eigenvalues --    4.17523
+          Condensed to atoms (all electrons):
+              1
+     1  Cl  17.000000
+ Mulliken atomic charges:
+              1
+     1  Cl   0.000000
+ Sum of Mulliken charges=   0.00000
+ Atomic charges with hydrogens summed into heavy atoms:
+              1
+     1  Cl   0.000000
+ Sum of Mulliken charges=   0.00000
+          Atomic-Atomic Spin Densities.
+              1
+     1  Cl   1.000000
+ Mulliken atomic spin densities:
+              1
+     1  Cl   1.000000
+ Sum of Mulliken spin densities=   1.00000
+ Electronic spatial extent (au):  <R**2>=    27.2144
+ Charge=     0.0000 electrons
+ Dipole moment (field-independent basis, Debye):
+    X=     0.0000    Y=     0.0000    Z=     0.0000  Tot=     0.0000
+ Quadrupole moment (field-independent basis, Debye-Ang):
+   XX=   -12.9360   YY=   -12.9360   ZZ=   -10.7323
+   XY=     0.0000   XZ=     0.0000   YZ=     0.0000
+ Traceless Quadrupole moment (field-independent basis, Debye-Ang):
+   XX=    -0.7346   YY=    -0.7346   ZZ=     1.4691
+   XY=     0.0000   XZ=     0.0000   YZ=     0.0000
+ Octapole moment (field-independent basis, Debye-Ang**2):
+  XXX=     0.0000  YYY=     0.0000  ZZZ=     0.0000  XYY=     0.0000
+  XXY=     0.0000  XXZ=     0.0000  XZZ=     0.0000  YZZ=     0.0000
+  YYZ=     0.0000  XYZ=     0.0000
+ Hexadecapole moment (field-independent basis, Debye-Ang**3):
+ XXXX=   -14.4264 YYYY=   -14.4264 ZZZZ=   -10.2914 XXXY=     0.0000
+ XXXZ=     0.0000 YYYX=     0.0000 YYYZ=     0.0000 ZZZX=     0.0000
+ ZZZY=     0.0000 XXYY=    -4.8088 XXZZ=    -4.1195 YYZZ=    -4.1195
+ XXYZ=     0.0000 YYXZ=     0.0000 ZZXY=     0.0000
+ N-N= 0.000000000000D+00 E-N=-1.093647653130D+03  KE= 4.587260959574D+02
+ Symmetry AG   KE= 3.234798818474D+02
+ Symmetry B1G  KE= 0.000000000000D+00
+ Symmetry B2G  KE= 0.000000000000D+00
+ Symmetry B3G  KE= 0.000000000000D+00
+ Symmetry AU   KE= 0.000000000000D+00
+ Symmetry B1U  KE= 4.357549325406D+01
+ Symmetry B2U  KE= 4.583536042793D+01
+ Symmetry B3U  KE= 4.583536042793D+01
+                          Isotropic Fermi Contact Couplings
+        Atom                 a.u.       MegaHertz       Gauss      10(-4) cm-1
+     1  Cl(35)             0.04286      18.79305       6.70583       6.26869
+ --------------------------------------------------------
+       Center         ----  Spin Dipole Couplings  ----
+                      3XX-RR        3YY-RR        3ZZ-RR
+ --------------------------------------------------------
+     1   Atom       -2.940531     -2.940531      5.881062
+ --------------------------------------------------------
+                        XY            XZ            YZ
+ --------------------------------------------------------
+     1   Atom        0.000000      0.000000      0.000000
+ --------------------------------------------------------
+
+
+ ---------------------------------------------------------------------------------
+              Anisotropic Spin Dipole Couplings in Principal Axis System
+ ---------------------------------------------------------------------------------
+
+       Atom             a.u.   MegaHertz   Gauss  10(-4) cm-1        Axes
+
+              Baa    -2.9405  -153.900   -54.916   -51.336  0.0000  1.0000  0.0000
+     1 Cl(35) Bbb    -2.9405  -153.900   -54.916   -51.336  1.0000  0.0000  0.0000
+              Bcc     5.8811   307.801   109.831   102.671  0.0000  0.0000  1.0000
+ 
+
+ ---------------------------------------------------------------------------------
+
+ Density matrix has only Abelian symmetry.
+ Density matrix has only Abelian symmetry.
+ ***** Axes restored to original set *****
+ -------------------------------------------------------------------
+ Center     Atomic                   Forces (Hartrees/Bohr)
+ Number     Number              X              Y              Z
+ -------------------------------------------------------------------
+    1         17           0.000000000    0.000000000    0.000000000
+ -------------------------------------------------------------------
+ Cartesian Forces:  Max     0.000000000 RMS     0.000000000
+ ------------------------------------------------------------------------
+           Internal Coordinate Forces (Hartree/Bohr or radian)
+ Cent Atom N1     Length/X     N2     Alpha/Y      N3      Beta/Z       J
+ ------------------------------------------------------------------------
+   1  Cl        0.000000(   1)      0.000000(   2)      0.000000(   3)
+ ------------------------------------------------------------------------
+ Internal  Forces:  Max     0.000000000 RMS     0.000000000
+
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+ Berny optimization.
+ Search for a local minimum.
+ Step number   1 out of a maximum of  20
+ All quantities printed in internal units (Hartrees-Bohrs-Radians)
+ Second derivative matrix not updated -- first step.
+ The second derivative matrix:
+                          X1        Y1        Z1
+           X1           0.00000
+           Y1           0.00000   0.00000
+           Z1           0.00000   0.00000   0.00000
+     Eigenvalues --- 
+ RFO step:  Lambda=-5.96046448D-09.
+ Linear search not attempted -- first point.
+ TrRot=  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
+ Variable       Old X    -DE/DX   Delta X   Delta X   Delta X     New X
+                                 (Linear)    (Quad)   (Total)
+    X1        0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
+    Y1        0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
+    Z1        0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
+         Item               Value     Threshold  Converged?
+ Maximum Force            0.000000     0.000450     YES
+ RMS     Force            0.000000     0.000300     YES
+ Maximum Displacement     0.000000     0.001800     YES
+ RMS     Displacement     0.000000     0.001200     YES
+ Predicted change in Energy= 0.000000D+00
+ Optimization completed.
+    -- Stationary point found.
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+
+ 1\1\GINC-NODE02\FOpt\UB3LYP\6-31G(d)\Cl1(2)\CHS60A\21-Nov-2006\0\\#N B
+ 3LYP/6-31G(D) OPT FREQ\\Cl\\0,2\Cl,0.,0.,0.\\Version=x86-Linux-G03RevB
+ .04\HF=-460.1362422\S2=0.751721\S2-1=0.\S2A=0.750001\RMSD=8.955e-09\RM
+ SF=0.000e+00\Dipole=0.,0.,0.\PG=OH [O(Cl1)]\\@
+
+
+ THERE'S NOTHING SO GREAT AS THE GREAT OUTDOORS.
+
+                                       -- ZIGGY
+ Job cpu time:  0 days  0 hours  0 minutes  6.2 seconds.
+ File lengths (MBytes):  RWF=     11 Int=      0 D2E=      0 Chk=      4 Scr=      1
+ Normal termination of Gaussian 03 at Tue Nov 21 09:54:57 2006.
+ Link1:  Proceeding to internal job step number  2.
+ ------------------------------------------------------------------
+ #N Geom=AllCheck Guess=Read SCRF=Check GenChk UB3LYP/6-31G(d) Freq
+ ------------------------------------------------------------------
+ 1/10=4,29=7,30=1,38=1,40=1,46=1/1,3;
+ 2/40=1/2;
+ 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,70=2,71=2,74=-5/1,2,3;
+ 4/5=1,7=2/1;
+ 5/5=2,38=6/2;
+ 8/6=4,10=90,11=11/1;
+ 11/6=1,8=1,9=11,15=111,16=1/1,2,10;
+ 10/6=1/2;
+ 6/7=2,8=2,9=2,10=2,18=1,28=1/1;
+ 7/8=1,10=1,25=1/1,2,3,16;
+ 1/10=4,30=1,46=1/3;
+ 99//99;
+ --
+ Cl
+ --
+ No Z-matrix found on checkpoint file.
+ Cartesian coordinates read from the checkpoint file:
+ /tmp/webmo/3/Gau-15098.chk
+ Charge =  0 Multiplicity = 2
+  Cl                                                0.000000000000      0.000000000000      0.000000000000
+ Recover connectivity data from disk.
+
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+ Berny optimization.
+ Initialization pass.
+ Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07
+ Number of steps in this run=   2 maximum allowed number of steps=   2.
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+
+                          Input orientation:                          
+ ---------------------------------------------------------------------
+ Center     Atomic     Atomic              Coordinates (Angstroms)
+ Number     Number      Type              X           Y           Z
+ ---------------------------------------------------------------------
+    1         17             0        0.000000    0.000000    0.000000
+ ---------------------------------------------------------------------
+ Stoichiometry    Cl(2)
+ Framework group  OH[O(Cl)]
+ Deg. of freedom     0
+ Full point group                 OH      NOp  48
+ Largest Abelian subgroup         D2H     NOp   8
+ Largest concise Abelian subgroup C1      NOp   1
+                         Standard orientation:                         
+ ---------------------------------------------------------------------
+ Center     Atomic     Atomic              Coordinates (Angstroms)
+ Number     Number      Type              X           Y           Z
+ ---------------------------------------------------------------------
+    1         17             0        0.000000    0.000000    0.000000
+ ---------------------------------------------------------------------
+ Standard basis: 6-31G(d) (6D, 7F)
+ There are     7 symmetry adapted basis functions of AG  symmetry.
+ There are     1 symmetry adapted basis functions of B1G symmetry.
+ There are     1 symmetry adapted basis functions of B2G symmetry.
+ There are     1 symmetry adapted basis functions of B3G symmetry.
+ There are     0 symmetry adapted basis functions of AU  symmetry.
+ There are     3 symmetry adapted basis functions of B1U symmetry.
+ There are     3 symmetry adapted basis functions of B2U symmetry.
+ There are     3 symmetry adapted basis functions of B3U symmetry.
+ Integral buffers will be    262144 words long.
+ Raffenetti 2 integral format.
+ Two-electron integral symmetry is turned on.
+    19 basis functions,    52 primitive gaussians,    19 cartesian basis functions
+     9 alpha electrons        8 beta electrons
+       nuclear repulsion energy         0.0000000000 Hartrees.
+ NAtoms=    1 NActive=    1 NUniq=    1 SFac= 1.00D+00 NAtFMM=   60 Big=F
+ One-electron integrals computed using PRISM.
+ NBasis=    19 RedAO= T  NBF=     7     1     1     1     0     3     3     3
+ NBsUse=    19 1.00D-06 NBFU=     7     1     1     1     0     3     3     3
+ Initial guess read from the checkpoint file:
+ /tmp/webmo/3/Gau-15098.chk
+ Initial guess orbital symmetries:
+ Alpha Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (?A) (?B) (?B) (?B)
+       Virtual   (?A) (?B) (?B) (?B) (?A) (T2G) (T2G) (T2G) (?A)
+                 (A1G)
+ Beta  Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (T2G) (?A) (?A)
+       Virtual   (?A) (A1G) (?A) (?A) (?A) (T2G) (T2G) (T2G) (T2G)
+                 (T2G) (A1G)
+ <S**2> of initial guess= 0.7517
+ Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
+ Requested convergence on MAX density matrix=1.00D-06.
+ Requested convergence on             energy=1.00D-06.
+ No special actions if energy rises.
+ Keep R1 and R2 integrals in memory in canonical form, NReq=      496463.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ Density matrix breaks symmetry, PCut= 1.00D-04
+ Density has only Abelian symmetry.
+ SCF Done:  E(UB+HF-LYP) =  -460.136242222     A.U. after    1 cycles
+             Convg  =    0.4404D-09             -V/T =  2.0031
+             S**2   =   0.7517
+ Annihilation of the first spin contaminant:
+ S**2 before annihilation     0.7517,   after     0.7500
+ Range of M.O.s used for correlation:     1    19
+ NBasis=    19 NAE=     9 NBE=     8 NFC=     0 NFV=     0
+ NROrb=     19 NOA=     9 NOB=     8 NVA=    10 NVB=    11
+
+ **** Warning!!: The smallest beta delta epsilon is  0.90310648D-01
+
+ Symmetrizing basis deriv contribution to polar:
+ IMax=3 JMax=2 DiffMx= 0.00D+00
+ G2DrvN: will do    2 centers at a time, making    1 passes doing MaxLOS=2.
+ FoFDir/FoFCou used for L=0 through L=2.
+          Differentiating once with respect to electric field.
+                with respect to dipole field.
+          Differentiating once with respect to nuclear coordinates.
+          Store integrals in memory, NReq=      466665.
+ CalDSu exits because no D1Ps are significant.
+          There are   6 degrees of freedom in the 1st order CPHF.
+     3 vectors were produced by pass  0.
+ AX will form   3 AO Fock derivatives at one time.
+     3 vectors were produced by pass  1.
+     3 vectors were produced by pass  2.
+     3 vectors were produced by pass  3.
+     3 vectors were produced by pass  4.
+     3 vectors were produced by pass  5.
+     3 vectors were produced by pass  6.
+ Inv2:  IOpt= 1 Iter= 1 AM= 3.76D-16 Conv= 1.00D-12.
+ Inverted reduced A of dimension   21 with in-core refinement.
+ Isotropic polarizability for W=    0.000000        5.63 Bohr**3.
+ End of Minotr Frequency-dependent properties file   721 does not exist.
+
+ **********************************************************************
+
+            Population analysis using the SCF density.
+
+ **********************************************************************
+
+ Orbital symmetries:
+ Alpha Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (?A) (?B) (?B) (?B)
+       Virtual   (?A) (?B) (?B) (?B) (?A) (T2G) (T2G) (T2G) (?A)
+                 (A1G)
+ Beta  Orbitals:
+       Occupied  (A1G) (A1G) (T1U) (T1U) (T1U) (T2G) (?A) (?A)
+       Virtual   (?A) (A1G) (?A) (?A) (?A) (T2G) (T2G) (T2G) (T2G)
+                 (T2G) (A1G)
+ Unable to determine electronic state:  an orbital has unidentified symmetry.
+ Alpha  occ. eigenvalues -- -101.59790  -9.51080  -7.28568  -7.26232  -7.26232
+ Alpha  occ. eigenvalues --   -0.84502  -0.40765  -0.35224  -0.35224
+ Alpha virt. eigenvalues --    0.32222   0.39579   0.42573   0.42573   0.78069
+ Alpha virt. eigenvalues --    0.79441   0.79441   0.84049   0.84049   4.15353
+  Beta  occ. eigenvalues -- -101.59109  -9.50436  -7.26397  -7.25843  -7.25843
+  Beta  occ. eigenvalues --   -0.79151  -0.33603  -0.33603
+  Beta virt. eigenvalues --   -0.24572   0.33828   0.43208   0.43208   0.43723
+  Beta virt. eigenvalues --    0.84953   0.84953   0.85541   0.85541   0.86478
+  Beta virt. eigenvalues --    4.17523
+          Condensed to atoms (all electrons):
+              1
+     1  Cl  17.000000
+ Mulliken atomic charges:
+              1
+     1  Cl   0.000000
+ Sum of Mulliken charges=   0.00000
+ Atomic charges with hydrogens summed into heavy atoms:
+              1
+     1  Cl   0.000000
+ Sum of Mulliken charges=   0.00000
+          Atomic-Atomic Spin Densities.
+              1
+     1  Cl   1.000000
+ Mulliken atomic spin densities:
+              1
+     1  Cl   1.000000
+ Sum of Mulliken spin densities=   1.00000
+ APT atomic charges:
+              1
+     1  Cl   0.000000
+ Sum of APT charges=   0.00000
+ APT Atomic charges with hydrogens summed into heavy atoms:
+              1
+     1  Cl   0.000000
+ Sum of APT charges=   0.00000
+ Electronic spatial extent (au):  <R**2>=    27.2144
+ Charge=     0.0000 electrons
+ Dipole moment (field-independent basis, Debye):
+    X=     0.0000    Y=     0.0000    Z=     0.0000  Tot=     0.0000
+ Quadrupole moment (field-independent basis, Debye-Ang):
+   XX=   -12.9360   YY=   -12.9360   ZZ=   -10.7323
+   XY=     0.0000   XZ=     0.0000   YZ=     0.0000
+ Traceless Quadrupole moment (field-independent basis, Debye-Ang):
+   XX=    -0.7346   YY=    -0.7346   ZZ=     1.4691
+   XY=     0.0000   XZ=     0.0000   YZ=     0.0000
+ Octapole moment (field-independent basis, Debye-Ang**2):
+  XXX=     0.0000  YYY=     0.0000  ZZZ=     0.0000  XYY=     0.0000
+  XXY=     0.0000  XXZ=     0.0000  XZZ=     0.0000  YZZ=     0.0000
+  YYZ=     0.0000  XYZ=     0.0000
+ Hexadecapole moment (field-independent basis, Debye-Ang**3):
+ XXXX=   -14.4264 YYYY=   -14.4264 ZZZZ=   -10.2914 XXXY=     0.0000
+ XXXZ=     0.0000 YYYX=     0.0000 YYYZ=     0.0000 ZZZX=     0.0000
+ ZZZY=     0.0000 XXYY=    -4.8088 XXZZ=    -4.1195 YYZZ=    -4.1195
+ XXYZ=     0.0000 YYXZ=     0.0000 ZZXY=     0.0000
+ N-N= 0.000000000000D+00 E-N=-1.093647653007D+03  KE= 4.587260959030D+02
+ Symmetry AG   KE= 3.234798818318D+02
+ Symmetry B1G  KE= 0.000000000000D+00
+ Symmetry B2G  KE= 0.000000000000D+00
+ Symmetry B3G  KE= 0.000000000000D+00
+ Symmetry AU   KE= 0.000000000000D+00
+ Symmetry B1U  KE= 4.357549324047D+01
+ Symmetry B2U  KE= 4.583536041537D+01
+ Symmetry B3U  KE= 4.583536041537D+01
+  Exact polarizability:   5.542   0.000   5.542   0.000   0.000   5.795
+ Approx polarizability:   6.396   0.000   6.396   0.000   0.000   7.848
+                          Isotropic Fermi Contact Couplings
+        Atom                 a.u.       MegaHertz       Gauss      10(-4) cm-1
+     1  Cl(35)             0.04286      18.79306       6.70583       6.26869
+ --------------------------------------------------------
+       Center         ----  Spin Dipole Couplings  ----
+                      3XX-RR        3YY-RR        3ZZ-RR
+ --------------------------------------------------------
+     1   Atom       -2.940531     -2.940531      5.881062
+ --------------------------------------------------------
+                        XY            XZ            YZ
+ --------------------------------------------------------
+     1   Atom        0.000000      0.000000      0.000000
+ --------------------------------------------------------
+
+
+ ---------------------------------------------------------------------------------
+              Anisotropic Spin Dipole Couplings in Principal Axis System
+ ---------------------------------------------------------------------------------
+
+       Atom             a.u.   MegaHertz   Gauss  10(-4) cm-1        Axes
+
+              Baa    -2.9405  -153.900   -54.916   -51.336  0.0000  1.0000  0.0000
+     1 Cl(35) Bbb    -2.9405  -153.900   -54.916   -51.336  1.0000  0.0000  0.0000
+              Bcc     5.8811   307.801   109.831   102.671  0.0000  0.0000  1.0000
+ 
+
+ ---------------------------------------------------------------------------------
+
+ Density matrix has only Abelian symmetry.
+ Density matrix has only Abelian symmetry.
+ Full mass-weighted force constant matrix:
+ Low frequencies ---   -0.0006    0.0006    0.0008
+ Diagonal vibrational polarizability:
+        0.0000000       0.0000000       0.0000000
+ Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
+ activities (A**4/AMU), depolarization ratios for plane and unpolarized
+ incident light, reduced masses (AMU), force constants (mDyne/A),
+ and normal coordinates:
+
+ -------------------
+ - Thermochemistry -
+ -------------------
+ Temperature   298.150 Kelvin.  Pressure   1.00000 Atm.
+ Atom  1 has atomic number 17 and mass  34.96885
+ Molecular mass:    34.96885 amu.
+ Zero-point vibrational energy          0.0 (Joules/Mol)
+                                    0.00000 (Kcal/Mol)
+ Vibrational temperatures: 
+          (Kelvin)
+ 
+ Zero-point correction=                           0.000000 (Hartree/Particle)
+ Thermal correction to Energy=                    0.001416
+ Thermal correction to Enthalpy=                  0.002360
+ Thermal correction to Gibbs Free Energy=        -0.015677
+ Sum of electronic and zero-point Energies=           -460.136242
+ Sum of electronic and thermal Energies=              -460.134826
+ Sum of electronic and thermal Enthalpies=            -460.133882
+ Sum of electronic and thermal Free Energies=         -460.151919
+ 
+                     E (Thermal)             CV                S
+                      KCal/Mol        Cal/Mol-Kelvin    Cal/Mol-Kelvin
+ Total                    0.889              2.981             37.964
+ Electronic               0.000              0.000              1.377
+ Translational            0.889              2.981             36.586
+ Rotational               0.000              0.000              0.000
+ Vibrational              0.000              0.000              0.000
+                       Q            Log10(Q)             Ln(Q)
+ Total Bot       0.162558D+08          7.211007         16.603958
+ Total V=0       0.162558D+08          7.211007         16.603958
+ Vib (Bot)       0.100000D+01          0.000000          0.000000
+ Vib (V=0)       0.100000D+01          0.000000          0.000000
+ Electronic      0.200000D+01          0.301030          0.693147
+ Translational   0.812788D+07          6.909977         15.910811
+ Rotational      0.100000D+01          0.000000          0.000000
+ ***** Axes restored to original set *****
+ -------------------------------------------------------------------
+ Center     Atomic                   Forces (Hartrees/Bohr)
+ Number     Number              X              Y              Z
+ -------------------------------------------------------------------
+    1         17           0.000000000    0.000000000    0.000000000
+ -------------------------------------------------------------------
+ Cartesian Forces:  Max     0.000000000 RMS     0.000000000
+
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+ Berny optimization.
+ Search for a local minimum.
+ Step number   1 out of a maximum of   2
+ All quantities printed in internal units (Hartrees-Bohrs-Radians)
+ Second derivative matrix not updated -- analytic derivatives used.
+ The second derivative matrix:
+                          X1        Y1        Z1
+           X1           0.00000
+           Y1           0.00000   0.00000
+           Z1           0.00000   0.00000   0.00000
+     Eigenvalues --- 
+ Angle between quadratic step and forces=  90.00 degrees.
+ Linear search not attempted -- first point.
+ TrRot=  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
+ Variable       Old X    -DE/DX   Delta X   Delta X   Delta X     New X
+                                 (Linear)    (Quad)   (Total)
+    X1        0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
+    Y1        0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
+    Z1        0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
+         Item               Value     Threshold  Converged?
+ Maximum Force            0.000000     0.000450     YES
+ RMS     Force            0.000000     0.000300     YES
+ Maximum Displacement     0.000000     0.001800     YES
+ RMS     Displacement     0.000000     0.001200     YES
+ Predicted change in Energy= 0.000000D+00
+ Optimization completed.
+    -- Stationary point found.
+ GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
+
+ 1\1\GINC-NODE02\Freq\UB3LYP\6-31G(d)\Cl1(2)\CHS60A\21-Nov-2006\0\\#N G
+ EOM=ALLCHECK GUESS=READ SCRF=CHECK GENCHK UB3LYP/6-31G(D) FREQ\\Cl\\0,
+ 2\Cl,0.,0.,0.\\Version=x86-Linux-G03RevB.04\HF=-460.1362422\S2=0.75172
+ 1\S2-1=0.\S2A=0.750001\RMSD=4.404e-10\RMSF=0.000e+00\Dipole=0.,0.,0.\D
+ ipoleDeriv=0.,0.,0.,0.,0.,0.,0.,0.,0.\Polar=5.7952054,0.,5.5423764,0.,
+ 0.,5.5423764\PG=OH [O(Cl1)]\NImag=0\\0.,0.,0.,0.,0.,0.\\0.,0.,0.\\\@
+
+
+ FAULTILY FAULTLESS, ICILY REGULAR, SPLENDIDLY NULL...
+           MAUDE BY TENNYSON
+ Job cpu time:  0 days  0 hours  0 minutes  8.9 seconds.
+ File lengths (MBytes):  RWF=     11 Int=      0 D2E=      0 Chk=      4 Scr=      1
+ Normal termination of Gaussian 03 at Tue Nov 21 09:55:07 2006.

acceptance-tests/src/test/resources/net/chempound/acceptance/chemistry/h2o_631gs.nwo

+ argument  1 = h2o_631gs.nw
+
+
+
+============================== echo of input deck ==============================
+echo
+start molecule
+
+title "HF SCF calculation on water with 6-31G* basis"
+
+geometry units angstrom
+O      0.00000000     0.00000000     0.11726921
+H      0.75698224     0.00000000    -0.46907685
+H     -0.75698224     0.00000000    -0.46907685
+end
+
+basis
+  O library 6-31g*
+  H library 6-31g*
+end
+
+task scf
+================================================================================
+
+
+                                         
+                                         
+
+
+              Northwest Computational Chemistry Package (NWChem) 6.1
+              ------------------------------------------------------
+
+
+                    Environmental Molecular Sciences Laboratory
+                       Pacific Northwest National Laboratory
+                                Richland, WA 99352
+
+                              Copyright (c) 1994-2010
+                       Pacific Northwest National Laboratory
+                            Battelle Memorial Institute
+
+             NWChem is an open-source computational chemistry package
+                        distributed under the terms of the
+                      Educational Community License (ECL) 2.0
+             A copy of the license is included with this distribution
+                              in the LICENSE.TXT file
+
+                                  ACKNOWLEDGMENT
+                                  --------------
+
+            This software and its documentation were developed at the
+            EMSL at Pacific Northwest National Laboratory, a multiprogram
+            national laboratory, operated for the U.S. Department of Energy
+            by Battelle under Contract Number DE-AC05-76RL01830. Support
+            for this work was provided by the Department of Energy Office
+            of Biological and Environmental Research, Office of Basic
+            Energy Sciences, and the Office of Advanced Scientific Computing.
+
+
+           Job information
+           ---------------
+
+    hostname      = jmhts-MacBook-Air.local
+    program       = nwchem
+    date          = Sun Apr  1 13:56:19 2012
+
+    compiled      = Sat_Mar_03_17:07:28_2012
+    source        = /Users/jmht/Documents/quixote/nwchem/nwchem-src-2012-Mar-01
+    nwchem branch = Development
+    input         = h2o_631gs.nw
+    prefix        = molecule.
+    data base     = ./molecule.db
+    status        = startup
+    nproc         =        1
+    time left     =     -1s
+
+
+
+           Memory information
+           ------------------
+
+    heap     =   13107201 doubles =    100.0 Mbytes
+    stack    =   13107201 doubles =    100.0 Mbytes
+    global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)
+    total    =   52428802 doubles =    400.0 Mbytes
+    verify   = yes
+    hardfail = no 
+
+
+           Directory information
+           ---------------------
+
+  0 permanent = .
+  0 scratch   = .
+
+
+
+
+                                NWChem Input Module
+                                -------------------
+
+
+                   HF SCF calculation on water with 6-31G* basis
+                   ---------------------------------------------
+
+ Scaling coordinates for geometry "geometry" by  1.889725989
+ (inverse scale =  0.529177249)
+
+ C2V symmetry detected
+
+          ------
+          auto-z
+          ------
+
+
+                             Geometry "geometry" -> ""
+                             -------------------------
+
+ Output coordinates in angstroms (scale by  1.889725989 to convert to a.u.)
+
+  No.       Tag          Charge          X              Y              Z
+ ---- ---------------- ---------- -------------- -------------- --------------
+    1 O                    8.0000     0.00000000     0.00000000     0.11726921
+    2 H                    1.0000     0.75698224     0.00000000    -0.46907685
+    3 H                    1.0000    -0.75698224     0.00000000    -0.46907685
+
+      Atomic Mass 
+      ----------- 
+
+      O                 15.994910
+      H                  1.007825
+
+
+ Effective nuclear repulsion energy (a.u.)       9.1920946687
+
+            Nuclear Dipole moment (a.u.) 
+            ----------------------------
+        X                 Y               Z
+ ---------------- ---------------- ----------------
+     0.0000000000     0.0000000000     0.0000000000
+
+      Symmetry information
+      --------------------
+
+ Group name             C2v       
+ Group number             16
+ Group order               4
+ No. of unique centers     2
+
+      Symmetry unique atoms
+
+     1    2
+
+
+
+                                Z-matrix (autoz)
+                                -------- 
+
+ Units are Angstrom for bonds and degrees for angles
+
+      Type          Name      I     J     K     L     M      Value
+      ----------- --------  ----- ----- ----- ----- ----- ----------
+    1 Stretch                  1     2                       0.95751
+    2 Stretch                  1     3                       0.95751
+    3 Bend                     2     1     3               104.47845
+
+
+            XYZ format geometry
+            -------------------
+     3
+ geometry
+ O                     0.00000000     0.00000000     0.11726921
+ H                     0.75698224     0.00000000    -0.46907685
+ H                    -0.75698224     0.00000000    -0.46907685
+
+ ==============================================================================
+                                internuclear distances
+ ------------------------------------------------------------------------------
+       center one      |      center two      | atomic units |  angstroms
+ ------------------------------------------------------------------------------
+    2 H                |   1 O                |     1.80943  |     0.95751
+    3 H                |   1 O                |     1.80943  |     0.95751
+ ------------------------------------------------------------------------------
+                         number of included internuclear distances:          2
+ ==============================================================================
+
+
+
+ ==============================================================================
+                                 internuclear angles
+ ------------------------------------------------------------------------------
+        center 1       |       center 2       |       center 3       |  degrees
+ ------------------------------------------------------------------------------
+    2 H                |   1 O                |   3 H                |   104.48
+ ------------------------------------------------------------------------------
+                            number of included internuclear angles:          1
+ ==============================================================================
+
+
+
+                      Basis "ao basis" -> "" (cartesian)
+                      -----
+  O (Oxygen)
+  ----------
+            Exponent  Coefficients 
+       -------------- ---------------------------------------------------------
+  1 S  5.48467170E+03  0.001831
+  1 S  8.25234950E+02  0.013950
+  1 S  1.88046960E+02  0.068445
+  1 S  5.29645000E+01  0.232714
+  1 S  1.68975700E+01  0.470193
+  1 S  5.79963530E+00  0.358521
+
+  2 S  1.55396160E+01 -0.110778
+  2 S  3.59993360E+00 -0.148026
+  2 S  1.01376180E+00  1.130767
+
+  3 P  1.55396160E+01  0.070874
+  3 P  3.59993360E+00  0.339753
+  3 P  1.01376180E+00  0.727159
+
+  4 S  2.70005800E-01  1.000000
+
+  5 P  2.70005800E-01  1.000000
+
+  6 D  8.00000000E-01  1.000000
+
+  H (Hydrogen)
+  ------------
+            Exponent  Coefficients 
+       -------------- ---------------------------------------------------------
+  1 S  1.87311370E+01  0.033495
+  1 S  2.82539370E+00  0.234727
+  1 S  6.40121700E-01  0.813757
+
+  2 S  1.61277800E-01  1.000000
+
+
+
+ Summary of "ao basis" -> "" (cartesian)
+ ------------------------------------------------------------------------------
+       Tag                 Description            Shells   Functions and Types
+ ---------------- ------------------------------  ------  ---------------------
+ O                           6-31g*                  6       15   3s2p1d
+ H                           6-31g*                  2        2   2s
+
+
+                                 NWChem SCF Module
+                                 -----------------
+
+
+                   HF SCF calculation on water with 6-31G* basis
+
+
+
+  ao basis        = "ao basis"
+  functions       =    19
+  atoms           =     3
+  closed shells   =     5
+  open shells     =     0
+  charge          =   0.00
+  wavefunction    = RHF 
+  input vectors   = atomic
+  output vectors  = ./molecule.movecs
+  use symmetry    = T
+  symmetry adapt  = T
+
+
+ Summary of "ao basis" -> "ao basis" (cartesian)
+ ------------------------------------------------------------------------------
+       Tag                 Description            Shells   Functions and Types
+ ---------------- ------------------------------  ------  ---------------------
+ O                           6-31g*                  6       15   3s2p1d
+ H                           6-31g*                  2        2   2s
+
+
+      Symmetry analysis of basis
+      --------------------------
+
+        a1         10
+        a2          1
+        b1          5
+        b2          3
+
+
+ Forming initial guess at       0.0s
+
+
+      Superposition of Atomic Density Guess
+      -------------------------------------
+
+ Sum of atomic energies:         -75.75081731
+
+      Non-variational initial energy
+      ------------------------------
+
+ Total energy =     -75.918936
+ 1-e energy   =    -121.729629
+ 2-e energy   =      36.618599
+ HOMO         =      -0.470312
+ LUMO         =       0.114726
+
+
+      Symmetry analysis of molecular orbitals - initial
+      -------------------------------------------------
+
+  Numbering of irreducible representations: 
+
+     1 a1          2 a2          3 b1          4 b2      
+
+  Orbital symmetries:
+
+     1 a1          2 a1          3 b1          4 a1          5 b2      
+     6 a1          7 b1          8 b1          9 a1         10 b2      
+    11 a1         12 b1         13 a1         14 a1         15 a2      
+
+
+ Starting SCF solution at       0.1s
+
+
+
+ ----------------------------------------------
+         Quadratically convergent ROHF
+
+ Convergence threshold     :          1.000E-04
+ Maximum no. of iterations :           30
+ Final Fock-matrix accuracy:          1.000E-07
+ ----------------------------------------------
+
+
+ #quartets = 1.009D+03 #integrals = 5.756D+03 #direct =  0.0% #cached =100.0%
+
+
+ Integral file          = ./molecule.aoints.0
+ Record size in doubles =  65536        No. of integs per rec  =  43688
+ Max. records in memory =      2        Max. records in file   = 150023
+ No. of bits per label  =      8        No. of bits per value  =     64
+
+
+              iter       energy          gnorm     gmax       time
+             ----- ------------------- --------- --------- --------
+                 1      -75.9747320880  8.31D-01  3.41D-01      0.1
+                 2      -76.0080741434  1.84D-01  1.02D-01      0.1
+                 3      -76.0103974428  4.08D-02  2.40D-02      0.1
+                 4      -76.0105156776  1.64D-03  9.33D-04      0.1
+                 5      -76.0105159183  2.31D-06  9.80D-07      0.1
+
+
+       Final RHF  results 
+       ------------------ 
+
+         Total SCF energy =    -76.010515918328
+      One-electron energy =   -123.049668244691
+      Two-electron energy =     37.847057657707
+ Nuclear repulsion energy =      9.192094668657
+
+        Time for solution =      0.1s
+
+
+
+       Symmetry analysis of molecular orbitals - final
+       -----------------------------------------------
+
+  Numbering of irreducible representations: 
+
+     1 a1          2 a2          3 b1          4 b2      
+
+  Orbital symmetries:
+
+     1 a1          2 a1          3 b1          4 a1          5 b2      
+     6 a1          7 b1          8 b1          9 a1         10 b2      
+    11 a1         12 b1         13 a1         14 a1         15 a2      
+
+             Final eigenvalues
+             -----------------
+
+              1      
+    1  -20.5605
+    2   -1.3417
+    3   -0.7067
+    4   -0.5710
+    5   -0.4979
+    6    0.2107
+    7    0.3041
+    8    1.0223
+    9    1.1317
+   10    1.1678
+   11    1.1715
+   12    1.3807
+   13    1.4342
+   14    2.0201
+   15    2.0339
+
+                       ROHF Final Molecular Orbital Analysis
+                       -------------------------------------
+
+ Vector    2  Occ=2.000000D+00  E=-1.341678D+00  Symmetry=a1
+              MO Center= -1.6D-17,  6.3D-17, -5.6D-02, r^2= 5.0D-01
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     2      0.475872  1 O  s                  6      0.439425  1 O  s          
+     1     -0.209688  1 O  s          
+
+ Vector    3  Occ=2.000000D+00  E=-7.067015D-01  Symmetry=b1
+              MO Center= -2.1D-17, -4.2D-37, -1.0D-01, r^2= 7.7D-01
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     3      0.507572  1 O  px                 7      0.306615  1 O  px         
+    16      0.230906  2 H  s                 18     -0.230906  3 H  s          
+
+ Vector    4  Occ=2.000000D+00  E=-5.710391D-01  Symmetry=a1
+              MO Center=  1.7D-16, -2.0D-17,  1.7D-01, r^2= 6.9D-01
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     5      0.555341  1 O  pz                 9      0.403123  1 O  pz         
+     6      0.325491  1 O  s                  2      0.164610  1 O  s          
+
+ Vector    5  Occ=2.000000D+00  E=-4.979013D-01  Symmetry=b2
+              MO Center=  3.9D-17,  2.1D-17,  9.8D-02, r^2= 6.0D-01
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     4      0.639633  1 O  py                 8      0.511452  1 O  py         
+
+ Vector    6  Occ=0.000000D+00  E= 2.106808D-01  Symmetry=a1
+              MO Center=  0.0D+00,  1.8D-17, -6.5D-01, r^2= 2.6D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     6      1.414245  1 O  s                 17     -1.040910  2 H  s          
+    19     -1.040910  3 H  s                  9     -0.508441  1 O  pz         
+     5     -0.217316  1 O  pz         
+
+ Vector    7  Occ=0.000000D+00  E= 3.040839D-01  Symmetry=b1
+              MO Center= -5.6D-16,  1.5D-31, -6.2D-01, r^2= 2.7D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+    17     -1.393942  2 H  s                 19      1.393942  3 H  s          
+     7      0.833469  1 O  px                 3      0.329461  1 O  px         
+
+ Vector    8  Occ=0.000000D+00  E= 1.022345D+00  Symmetry=b1
+              MO Center=  1.9D-16, -6.0D-18, -4.8D-02, r^2= 1.4D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+    16      0.838906  2 H  s                 18     -0.838906  3 H  s          
+     7     -0.660200  1 O  px                17     -0.461185  2 H  s          
+    19      0.461185  3 H  s                 12     -0.343162  1 O  dxz        
+
+ Vector    9  Occ=0.000000D+00  E= 1.131716D+00  Symmetry=a1
+              MO Center= -6.9D-16, -4.9D-18,  2.0D-01, r^2= 1.6D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     6      1.637641  1 O  s                  2     -0.922552  1 O  s          
+     9      0.705400  1 O  pz                16      0.551896  2 H  s          
+    18      0.551896  3 H  s                 17     -0.476743  2 H  s          
+    19     -0.476743  3 H  s                  5     -0.414790  1 O  pz         
+    13     -0.388053  1 O  dyy               15     -0.317805  1 O  dzz        
+
+ Vector   10  Occ=0.000000D+00  E= 1.167778D+00  Symmetry=b2
+              MO Center= -8.8D-17,  2.7D-15,  1.1D-01, r^2= 1.1D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     8      1.036057  1 O  py                 4     -0.962733  1 O  py         
+
+ Vector   11  Occ=0.000000D+00  E= 1.171513D+00  Symmetry=a1
+              MO Center=  6.1D-16, -2.9D-15, -3.4D-02, r^2= 1.1D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     5      0.763201  1 O  pz                16      0.658242  2 H  s          
+    18      0.658242  3 H  s                  6     -0.470200  1 O  s          
+     9     -0.374557  1 O  pz                17     -0.355445  2 H  s          
+    19     -0.355445  3 H  s                 10      0.249943  1 O  dxx        
+
+ Vector   12  Occ=0.000000D+00  E= 1.380728D+00  Symmetry=b1
+              MO Center= -4.0D-16, -7.4D-32,  5.7D-02, r^2= 1.4D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     7      1.536975  1 O  px                 3     -1.037222  1 O  px         
+    17     -0.913963  2 H  s                 19      0.913963  3 H  s          
+
+ Vector   13  Occ=0.000000D+00  E= 1.434167D+00  Symmetry=a1
+              MO Center= -8.3D-17,  1.2D-16, -3.9D-01, r^2= 1.3D+00
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+     6      3.571124  1 O  s                  2     -1.417272  1 O  s          
+     9     -1.175201  1 O  pz                17     -0.783617  2 H  s          
+    19     -0.783617  3 H  s                 10     -0.644426  1 O  dxx        
+     5      0.506756  1 O  pz                15     -0.402252  1 O  dzz        
+    16     -0.323912  2 H  s                 18     -0.323912  3 H  s          
+
+ Vector   14  Occ=0.000000D+00  E= 2.020094D+00  Symmetry=a1
+              MO Center= -3.5D-17, -2.2D-18,  1.6D-01, r^2= 6.2D-01
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+    15      1.008721  1 O  dzz               10     -0.581191  1 O  dxx        
+    13     -0.366144  1 O  dyy                6     -0.226974  1 O  s          
+
+ Vector   15  Occ=0.000000D+00  E= 2.033876D+00  Symmetry=a2
+              MO Center=  3.3D-16,  6.2D-18,  1.2D-01, r^2= 6.1D-01
+   Bfn.  Coefficient  Atom+Function         Bfn.  Coefficient  Atom+Function  
+  ----- ------------  ---------------      ----- ------------  ---------------
+    11      1.732051  1 O  dxy        
+
+
+ center of mass
+ --------------
+ x =   0.00000000 y =   0.00000000 z =   0.09760123
+
+ moments of inertia (a.u.)
+ ------------------
+           2.197735387303           0.000000000000           0.000000000000
+           0.000000000000           6.322357589609           0.000000000000
+           0.000000000000           0.000000000000           4.124622202307
+
+  Mulliken analysis of the total density
+  --------------------------------------
+
+    Atom       Charge   Shell Charges
+ -----------   ------   -------------------------------------------------------
+    1 O    8     8.87   2.00  0.90  2.90  0.92  2.07  0.08
+    2 H    1     0.57   0.46  0.10
+    3 H    1     0.57   0.46  0.10
+
+       Multipole analysis of the density wrt the origin
+       ------------------------------------------------
+
+     L   x y z        total         open         nuclear
+     -   - - -        -----         ----         -------
+     0   0 0 0     -0.000000      0.000000     10.000000
+
+     1   1 0 0     -0.000000      0.000000      0.000000
+     1   0 1 0     -0.000000      0.000000      0.000000
+     1   0 0 1     -0.875704      0.000000      0.000000
+
+     2   2 0 0     -3.072151      0.000000      4.092598
+     2   1 1 0     -0.000000      0.000000      0.000000
+     2   1 0 1      0.000000      0.000000      0.000000
+     2   0 2 0     -5.373173      0.000000      0.000000
+     2   0 1 1      0.000000      0.000000      0.000000
+     2   0 0 2     -4.444080      0.000000      1.964381
+
+
+ Parallel integral file used       1 records with       0 large values
+
+
+ Task  times  cpu:        0.1s     wall:        0.2s
+ Summary of allocated global arrays
+-----------------------------------
+  No active global arrays
+
+
+
+                         GA Statistics for process    0
+                         ------------------------------
+
+       create   destroy   get      put      acc     scatter   gather  read&inc
+calls:  307      307     3167     1391     1746        0        0        0     
+number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
+bytes total:             1.28e+06 7.56e+05 4.33e+05 0.00e+00 0.00e+00 0.00e+00
+bytes remote:            0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
+Max memory consumed for GA by this process: 39432 bytes
+MA_summarize_allocated_blocks: starting scan ...
+MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
+MA usage statistics:
+
+	allocation statistics:
+					      heap	     stack
+					      ----	     -----
+	current number of blocks	         0	         0
+	maximum number of blocks	        18	        14
+	current total bytes		         0	         0
+	maximum total bytes		   1059848	  22509336
+	maximum total K-bytes		      1060	     22510
+	maximum total M-bytes		         2	        23
+
+
+                                NWChem Input Module
+                                -------------------
+
+
+
+
+
+                                     CITATION
+                                     --------
+                Please cite the following reference when publishing
+                           results obtained with NWChem:
+
+                 M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
+              T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
+                        E. Apra, T.L. Windus, W.A. de Jong
+                 "NWChem: a comprehensive and scalable open-source
+                  solution for large scale molecular simulations"
+                      Comput. Phys. Commun. 181, 1477 (2010)
+                           doi:10.1016/j.cpc.2010.04.018
+
+                              AUTHORS & CONTRIBUTORS
+                              ----------------------
+      E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski, T. P. Straatsma,
+     M. Valiev, H. J. J. van Dam, D. Wang, E. Apra, T. L. Windus, J. Hammond,
+    J. Autschbach, F. Aquino, J. Mullin, P. Nichols, S. Hirata, M. T. Hackler,
+   Y. Zhao, P.-D. Fan, R. J. Harrison, M. Dupuis, D. M. A. Smith, K. Glaesemann,
+    J. Nieplocha, V. Tipparaju, M. Krishnan, A. Vazquez-Mayagoitia, L. Jensen,
+      M. Swart, Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby,
+        E. Brown, G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao,
+        R. Kendall, J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell,
+       D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. Deegan,
+        K. Dyall, D. Elwood, E. Glendening, M. Gutowski, A. Hess, J. Jaffe,
+        B. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield,
+    X. Long, B. Meng, T. Nakajima, S. Niu, R. Peverati, L. Pollack, M. Rosing,
+          G. Sandrone, M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe,
+                                A. Wong, Z. Zhang.
+
+ Total times  cpu:        0.1s     wall:        0.2s
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