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<title>[127579] trunk/dports/science/octopus</title>
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<dl class="meta">
<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/127579">127579</a></dd>
<dt>Author</dt> <dd>dstrubbe@macports.org</dd>
<dt>Date</dt> <dd>2014-10-29 12:45:25 -0700 (Wed, 29 Oct 2014)</dd>
</dl>
<h3>Log Message</h3>
<pre>octopus: Add patches to correct test results with libxc 2.1.0. Fix specification of MPIEXEC for test runs. Only OpenMPI needs MPI2 to be disabled; MPICH does not (for this reason I bumped the revision).</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportsscienceoctopusPortfile">trunk/dports/science/octopus/Portfile</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li>trunk/dports/science/octopus/files/</li>
<li><a href="#trunkdportsscienceoctopusfilespatchtestsuitefunctionals03xctestdiff">trunk/dports/science/octopus/files/patch-testsuite-functionals-03-xc.test.diff</a></li>
<li><a href="#trunkdportsscienceoctopusfilespatchtestsuiteperiodic_systems07tb09testdiff">trunk/dports/science/octopus/files/patch-testsuite-periodic_systems-07-tb09.test.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportsscienceoctopusPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/octopus/Portfile (127578 => 127579)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/octopus/Portfile 2014-10-29 19:32:32 UTC (rev 127578)
+++ trunk/dports/science/octopus/Portfile 2014-10-29 19:45:25 UTC (rev 127579)
</span><span class="lines">@@ -6,6 +6,7 @@
</span><span class="cx">
</span><span class="cx"> name octopus
</span><span class="cx"> version 4.1.2
</span><ins>+revision 1
</ins><span class="cx"> categories science
</span><span class="cx"> platforms darwin
</span><span class="cx"> license GPL-2+
</span><span class="lines">@@ -43,15 +44,23 @@
</span><span class="cx"> default_variants +gcc48
</span><span class="cx"> }
</span><span class="cx">
</span><ins>+# Update test results for libxc 2.1.0 (distribution has results for libxc 2.0.0)
+patchfiles patch-testsuite-periodic_systems-07-tb09.test.diff \
+ patch-testsuite-functionals-03-xc.test.diff
+
+
</ins><span class="cx"> pre-configure {
</span><span class="cx"> configure.args-append FCCPP="${configure.cpp} -E -ansi"
</span><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> if {[mpi_variant_isset]} {
</span><span class="cx"> configure.args-delete --disable-mpi
</span><del>- # an in-place allreduce of lxyz_inv in mesh_init.F90 leads to zeroes afterwards with MPI2
- configure.args-append --enable-mpi --without-external_zoltan --disable-mpi2
- test.env-append MPIEXEC=${mpi.exec}
</del><ins>+ configure.args-append --enable-mpi --without-external_zoltan
+
+ if {[variant_isset openmpi] || [variant_isset openmpi-devel]} {
+ # an in-place allreduce of lxyz_inv in mesh_init.F90 leads to zeroes afterwards with OpenMPI and MPI2
+ configure.args-append --disable-mpi2
+ }
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> # More options that could be added:
</span><span class="lines">@@ -64,6 +73,10 @@
</span><span class="cx"> test.run yes
</span><span class="cx"> test.target check-full
</span><span class="cx">
</span><ins>+pre-test {
+ test.env-append MPIEXEC=${prefix}/bin/${mpi.exec}
+}
+
</ins><span class="cx"> variant newuoa description {Build with internal newuoa library for optimal control} {
</span><span class="cx"> configure.args-append --enable-newuoa
</span><span class="cx"> }
</span></span></pre></div>
<a id="trunkdportsscienceoctopusfilespatchtestsuitefunctionals03xctestdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/octopus/files/patch-testsuite-functionals-03-xc.test.diff (0 => 127579)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/octopus/files/patch-testsuite-functionals-03-xc.test.diff (rev 0)
+++ trunk/dports/science/octopus/files/patch-testsuite-functionals-03-xc.test.diff 2014-10-29 19:45:25 UTC (rev 127579)
</span><span class="lines">@@ -0,0 +1,11 @@
</span><ins>+--- testsuite/functionals/03-xc.test.orig 2014-10-29 13:21:12.000000000 -0400
++++ testsuite/functionals/03-xc.test 2014-10-29 13:21:41.000000000 -0400
+@@ -117,7 +117,7 @@
+ match ; gga_x_am05 ; GREP(out, 'Exchange =', 20) ; -0.28774147
+
+ Input: 03-xc.gga_x_pbea.inp
+-match ; gga_x_pbea ; GREP(out, 'Exchange =', 20) ; -0.31167154
++match ; gga_x_pbea ; GREP(out, 'Exchange =', 20) ; -0.31200606
+
+ Input: 03-xc.gga_x_mpbe.inp
+ match ; gga_x_mpbe ; GREP(out, 'Exchange =', 20) ; -0.31887879
</ins></span></pre></div>
<a id="trunkdportsscienceoctopusfilespatchtestsuiteperiodic_systems07tb09testdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/octopus/files/patch-testsuite-periodic_systems-07-tb09.test.diff (0 => 127579)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/octopus/files/patch-testsuite-periodic_systems-07-tb09.test.diff (rev 0)
+++ trunk/dports/science/octopus/files/patch-testsuite-periodic_systems-07-tb09.test.diff 2014-10-29 19:45:25 UTC (rev 127579)
</span><span class="lines">@@ -0,0 +1,117 @@
</span><ins>+--- testsuite/periodic_systems/07-tb09.test.orig 2014-10-29 13:25:46.000000000 -0400
++++ testsuite/periodic_systems/07-tb09.test 2014-10-29 13:25:22.000000000 -0400
+@@ -9,61 +9,62 @@
+ # ground state
+ Input : 07-tb09.01-gs_symm.inp
+
+-match ; Total energy ; GREP(static/info, 'Total =', 20) ; -41.90599902
++match ; Total energy ; GREP(static/info, 'Total =', 20) ; -41.91336041
+ match ; Ion-ion energy ; GREP(static/info, 'Ion-ion =', 20) ; -51.15076275
+-match ; Eigenvalues sum ; GREP(static/info, 'Eigenvalues =', 20) ; -3.64925036
+-match ; Hartree energy ; GREP(static/info, 'Hartree =', 20) ; 3.88116130
++match ; Eigenvalues sum ; GREP(static/info, 'Eigenvalues =', 20) ; -3.66647752
++match ; Hartree energy ; GREP(static/info, 'Hartree =', 20) ; 3.86297517
+ match ; Exchange energy ; GREP(static/info, 'Exchange =', 20) ; 0.00000000
+-match ; Correlation energy ; GREP(static/info, 'Correlation =', 20) ; -1.78030330
+-match ; Kinetic energy ; GREP(static/info, 'Kinetic =', 20) ; 33.20246992
+-match ; External energy ; GREP(static/info, 'External =', 20) ; -26.05856446
+-
+-match ; Eigenvalue [ k=1, n=1 ] ; GREP(static/info, '#k = 1', 12, 2) ; -0.237121
+-match ; Eigenvalue [ k=1, n=8 ] ; GREP(static/info, '#k = 1', 12, 9) ; -0.032776
+-match ; Eigenvalue [ k=1, n=16 ] ; GREP(static/info, '#k = 1', 12, 17) ; 0.432200
+-match ; Eigenvalue [ k=1, n=17 ] ; GREP(static/info, '#k = 1', 12, 18) ; 0.432200
+-
+-match ; Eigenvalue [ k=2, n=1 ] ; GREP(static/info, '#k = 2', 12, 2) ; -0.403851
+-match ; Eigenvalue [ k=2, n=8 ] ; GREP(static/info, '#k = 2', 12, 9) ; -0.081399
+-match ; Eigenvalue [ k=2, n=16 ] ; GREP(static/info, '#k = 2', 12, 17) ; 0.408100
+-match ; Eigenvalue [ k=2, n=17 ] ; GREP(static/info, '#k = 2', 12, 18) ; 0.419803
+-
+-match ; Eigenvalue [ k=3, n=1 ] ; GREP(static/info, '#k = 3', 12, 2) ; -0.370082
+-match ; Eigenvalue [ k=3, n=8 ] ; GREP(static/info, '#k = 3', 12, 9) ; -0.060216
+-match ; Eigenvalue [ k=3, n=16 ] ; GREP(static/info, '#k = 3', 12, 17) ; 0.487729
+-match ; Eigenvalue [ k=3, n=17 ] ; GREP(static/info, '#k = 3', 12, 18) ; 0.508022
+-
+-match ; Eigenvalue [ k=4, n=1 ] ; GREP(static/info, '#k = 4', 12, 2) ; -0.339535
+-match ; Eigenvalue [ k=4, n=8 ] ; GREP(static/info, '#k = 4', 12, 9) ; 0.023254
+-match ; Eigenvalue [ k=4, n=16 ] ; GREP(static/info, '#k = 4', 12, 17) ; 0.506337
+-match ; Eigenvalue [ k=4, n=17 ] ; GREP(static/info, '#k = 4', 12, 18) ; 0.506337
++match ; Correlation energy ; GREP(static/info, 'Correlation =', 20) ; -1.78001693
++match ; Kinetic energy ; GREP(static/info, 'Kinetic =', 20) ; 33.16726539
++match ; External energy ; GREP(static/info, 'External =', 20) ; -26.01282120
++
++match ; Eigenvalue [ k=1, n=1 ] ; GREP(static/info, '#k = 1', 12, 2) ; -0.237687
++match ; Eigenvalue [ k=1, n=8 ] ; GREP(static/info, '#k = 1', 12, 9) ; -0.033387
++match ; Eigenvalue [ k=1, n=16 ] ; GREP(static/info, '#k = 1', 12, 17) ; 0.431539
++match ; Eigenvalue [ k=1, n=17 ] ; GREP(static/info, '#k = 1', 12, 18) ; 0.431539
++
++match ; Eigenvalue [ k=2, n=1 ] ; GREP(static/info, '#k = 2', 12, 2) ; -0.404634
++match ; Eigenvalue [ k=2, n=8 ] ; GREP(static/info, '#k = 2', 12, 9) ; -0.082183
++match ; Eigenvalue [ k=2, n=16 ] ; GREP(static/info, '#k = 2', 12, 17) ; 0.407338
++match ; Eigenvalue [ k=2, n=17 ] ; GREP(static/info, '#k = 2', 12, 18) ; 0.419124
++
++match ; Eigenvalue [ k=3, n=1 ] ; GREP(static/info, '#k = 3', 12, 2) ; -0.370821
++match ; Eigenvalue [ k=3, n=8 ] ; GREP(static/info, '#k = 3', 12, 9) ; -0.060897
++match ; Eigenvalue [ k=3, n=16 ] ; GREP(static/info, '#k = 3', 12, 17) ; 0.486862
++match ; Eigenvalue [ k=3, n=17 ] ; GREP(static/info, '#k = 3', 12, 18) ; 0.507452
++
++match ; Eigenvalue [ k=4, n=1 ] ; GREP(static/info, '#k = 4', 12, 2) ; -0.340194
++match ; Eigenvalue [ k=4, n=8 ] ; GREP(static/info, '#k = 4', 12, 9) ; 0.022912
++match ; Eigenvalue [ k=4, n=16 ] ; GREP(static/info, '#k = 4', 12, 17) ; 0.505459
++match ; Eigenvalue [ k=4, n=17 ] ; GREP(static/info, '#k = 4', 12, 18) ; 0.505459
++
+
+ Input : 07-tb09.02-gs_nosymm.inp
+-match ; Total energy ; GREP(static/info, 'Total =', 20) ; -41.90599990
++match ; Total energy ; GREP(static/info, 'Total =', 20) ; -41.91336038
+ match ; Ion-ion energy ; GREP(static/info, 'Ion-ion =', 20) ; -51.15076275
+-match ; Eigenvalues sum ; GREP(static/info, 'Eigenvalues =', 20) ; -3.64925218
+-match ; Hartree energy ; GREP(static/info, 'Hartree =', 20) ; 3.88116002
++match ; Eigenvalues sum ; GREP(static/info, 'Eigenvalues =', 20) ; -3.66647784
++match ; Hartree energy ; GREP(static/info, 'Hartree =', 20) ; 3.86297499
+ match ; Exchange energy ; GREP(static/info, 'Exchange =', 20) ; 0.00000000
+-match ; Correlation energy ; GREP(static/info, 'Correlation =', 20) ; -1.78030328
+-match ; Kinetic energy ; GREP(static/info, 'Kinetic =', 20) ; 33.20246666
+-match ; External energy ; GREP(static/info, 'External =', 20) ; -26.05856059
+-
+-match ; Eigenvalue [ k=1, n=1 ] ; GREP(static/info, '#k = 1', 12, 2) ; -0.237122
+-match ; Eigenvalue [ k=1, n=8 ] ; GREP(static/info, '#k = 1', 12, 9) ; -0.032776
+-match ; Eigenvalue [ k=1, n=16 ] ; GREP(static/info, '#k = 1', 12, 17) ; 0.432200
+-match ; Eigenvalue [ k=1, n=17 ] ; GREP(static/info, '#k = 1', 12, 18) ; 0.432200
+-
+-match ; Eigenvalue [ k=2, n=1 ] ; GREP(static/info, '#k = 2', 12, 2) ; -0.403851
+-match ; Eigenvalue [ k=2, n=8 ] ; GREP(static/info, '#k = 2', 12, 9) ; -0.081399
+-match ; Eigenvalue [ k=2, n=16 ] ; GREP(static/info, '#k = 2', 12, 17) ; 0.408100
+-match ; Eigenvalue [ k=2, n=17 ] ; GREP(static/info, '#k = 2', 12, 18) ; 0.419803
+-
+-match ; Eigenvalue [ k=8, n=1 ] ; GREP(static/info, '#k = 8', 12, 2) ; -0.370082
+-match ; Eigenvalue [ k=8, n=8 ] ; GREP(static/info, '#k = 8', 12, 9) ; -0.060216
+-match ; Eigenvalue [ k=8, n=16 ] ; GREP(static/info, '#k = 8', 12, 17) ; 0.487729
+-match ; Eigenvalue [ k=8, n=17 ] ; GREP(static/info, '#k = 8', 12, 18) ; 0.508021
+-
+-match ; Eigenvalue [ k=20,n=1 ] ; GREP(static/info, '#k = 20', 12, 2) ; -0.339535
+-match ; Eigenvalue [ k=20,n=8 ] ; GREP(static/info, '#k = 20', 12, 9) ; 0.023254
+-match ; Eigenvalue [ k=20,n=16 ] ; GREP(static/info, '#k = 20', 12, 17) ; 0.506337
+-match ; Eigenvalue [ k=20,n=17 ] ; GREP(static/info, '#k = 20', 12, 18) ; 0.506337
++match ; Correlation energy ; GREP(static/info, 'Correlation =', 20) ; -1.78001693
++match ; Kinetic energy ; GREP(static/info, 'Kinetic =', 20) ; 33.16726427
++match ; External energy ; GREP(static/info, 'External =', 20) ; -26.01281994
++
++match ; Eigenvalue [ k=1, n=1 ] ; GREP(static/info, '#k = 1', 12, 2) ; -0.237687
++match ; Eigenvalue [ k=1, n=8 ] ; GREP(static/info, '#k = 1', 12, 9) ; -0.033387
++match ; Eigenvalue [ k=1, n=16 ] ; GREP(static/info, '#k = 1', 12, 17) ; 0.431539
++match ; Eigenvalue [ k=1, n=17 ] ; GREP(static/info, '#k = 1', 12, 18) ; 0.431539
++
++match ; Eigenvalue [ k=2, n=1 ] ; GREP(static/info, '#k = 2', 12, 2) ; -0.404634
++match ; Eigenvalue [ k=2, n=8 ] ; GREP(static/info, '#k = 2', 12, 9) ; -0.082183
++match ; Eigenvalue [ k=2, n=16 ] ; GREP(static/info, '#k = 2', 12, 17) ; 0.407338
++match ; Eigenvalue [ k=2, n=17 ] ; GREP(static/info, '#k = 2', 12, 18) ; 0.419124
++
++match ; Eigenvalue [ k=8, n=1 ] ; GREP(static/info, '#k = 8', 12, 2) ; -0.370821
++match ; Eigenvalue [ k=8, n=8 ] ; GREP(static/info, '#k = 8', 12, 9) ; -0.060897
++match ; Eigenvalue [ k=8, n=16 ] ; GREP(static/info, '#k = 8', 12, 17) ; 0.486861
++match ; Eigenvalue [ k=8, n=17 ] ; GREP(static/info, '#k = 8', 12, 18) ; 0.507452
++
++match ; Eigenvalue [ k=20,n=1 ] ; GREP(static/info, '#k = 20', 12, 2) ; -0.340194
++match ; Eigenvalue [ k=20,n=8 ] ; GREP(static/info, '#k = 20', 12, 9) ; 0.022912
++match ; Eigenvalue [ k=20,n=16 ] ; GREP(static/info, '#k = 20', 12, 17) ; 0.505459
++match ; Eigenvalue [ k=20,n=17 ] ; GREP(static/info, '#k = 20', 12, 18) ; 0.505459
</ins></span></pre>
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