Merge branch 'release-2019' into master

Updated reference data that needed updating.

Resolved Conflicts:
	cmake/gmxVersionInfo.cmake
	docs/CMakeLists.txt
	src/gromacs/ewald/pme-gpu-types-host.h
	src/gromacs/ewald/pme-only.cpp
	src/gromacs/gmxana/gmx_make_ndx.cpp
	src/gromacs/mdlib/nbnxn_gpu_common.h
	src/gromacs/mdrun/md.cpp
	src/programs/mdrun/tests/minimize.cpp

Change-Id: Ic5aeae6bf932d190b95366373b64ee3449f4a630

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 46276b3401fa4894d11ddce3dfd4e742c3aa970e..b7159826001e08d5ec754f9f694ebece297e41e0 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -370,6 +370,7 @@ if (SPHINX_FOUND)
         release-notes/2020/major/deprecated-functionality.rst
         release-notes/2020/major/portability.rst
         release-notes/2020/major/miscellaneous.rst
+        release-notes/2019/2019.5.rst
         release-notes/2019/2019.4.rst
         release-notes/2019/2019.3.rst
         release-notes/2019/2019.2.rst

diff --git a/docs/release-notes/2019/2019.3.rst b/docs/release-notes/2019/2019.3.rst
index c5e7b7cd83b10ce8dcb199380ffa199032ee9cec..80f501cb4da12cb1fc7f5be07f77511217b231d7 100644 (file)
--- a/docs/release-notes/2019/2019.3.rst
+++ b/docs/release-notes/2019/2019.3.rst
@@ -67,9 +67,11 @@ Fix gmx wham with angle geometries
 """"""""""""""""""""""""""""""""""
 
 gmx wham would mix up degree and radian units leading to no overlap
-or not-a-number output.
+or not-a-number output. **Note**: this fix is not correct, a correct
+fix is applied in the next patch release.
 
 :issue:`2609`
+:issue:`3094`
 
 Add some information for grompp error with wrong line endings
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

diff --git a/docs/release-notes/2019/2019.4.rst b/docs/release-notes/2019/2019.4.rst
index 1c388402369c92a0ce91bef89d4f3b382189e477..195be46ebcd45f3c144c797215cec4d649b08028 100644 (file)
--- a/docs/release-notes/2019/2019.4.rst
+++ b/docs/release-notes/2019/2019.4.rst
@@ -1,7 +1,7 @@
 GROMACS 2019.4 release notes
 ----------------------------
 
-This version was released on TODO, 2019. These release notes
+This version was released on October 2nd, 2019. These release notes
 document the changes that have taken place in GROMACS since the
 previous 2019.3 version, to fix known issues. It also incorporates all
 fixes made in version 2018.7 and earlier, which you can find described
@@ -54,6 +54,15 @@ other non-local atoms within the pair-list cut-off distance.
 
 :issue:`3063`
 
+Fix incorrect reporting of final kinetic energy and temperature
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+With the leap-frog integrator, the kinetic energy and temperature reported
+for the last step were incorrect when the last step was not divisible by
+nstcalcenergy, nsttcouple or nstpcouple.
+
+:issue:`2950`
+
 Fix segmentation fault in grompp and mdrun with cosine COM pulling
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -72,6 +81,15 @@ but not replaced by angle constraints.
 
 :issue:`3067`
 
+Fix gmx wham with angle and dihedral geometries
+"""""""""""""""""""""""""""""""""""""""""""""""
+
+gmx wham would apply an incorrect radian to degree unit conversion,
+leading to no overlap or not-a-number output.
+
+:issue:`2609`
+:issue:`3094`
+
 Fix bug in gmx xpm2ps
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -100,6 +118,24 @@ Made gmx disre work with non-consecutively labeled restraints
 
 :issue:`2953`
 
+Fixed writing of gro files with index groups
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+An output ``.gro`` file from from e.g. ``gmx editconf -f -n`` would
+take the atom names for the output file in order from the atoms in the
+input file, rather than in order from the atoms indicated by the
+indices in the index file.
+
+:issue:`3107`
+
+Made gmx make_ndx keep chain IDs
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Old style structure file reading caused the chain IDs to be overwritten with
+default values.
+
+:issue:`3070`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/release-notes/2019/2019.5.rst b/docs/release-notes/2019/2019.5.rst
new file mode 100644 (file)
index 0000000..a34b88e
--- /dev/null
+++ b/docs/release-notes/2019/2019.5.rst
@@ -0,0 +1,54 @@
+GROMACS 2019.5 release notes
+----------------------------
+
+This version was released on TODO, 2019. These release notes
+document the changes that have taken place in GROMACS since the
+previous 2019.4 version, to fix known issues. It also incorporates all
+fixes made in version 2018.7 and earlier, which you can find described
+in the :ref:`release-notes`.
+
+.. Note to developers!
+   Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+   otherwise the formatting on the webpage is messed up.
+   Also, please use the syntax :issue:`number` to reference issues on redmine, without the
+   a space between the colon and number!
+
+Fixes where mdrun could behave incorrectly
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fix use of uninitialized data on PME only ranks
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+When building GPU enabled versions of |Gromacs| with clang as either host only or host
+and device side compiler, PME datastructures could be left uninitialized, leading
+to the use of random values for LJ PME energies, virial and pressure.
+
+The effect of this bug was that the potential and total energy could
+be wrong, but not the Coulomb mesh energy. This didn't affect sampling.
+The pressure could also be wrong, which would affect sampling when pressure
+coupling is used, but likely the simulation would explode after a few steps.
+
+This doesn't seem to have affected versions of |Gromacs| built
+with gcc as the host side compiler.
+
+:issue:`3120`
+
+Fix out of range memory access with free-energy calculations
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+With free-energy calculations not using lambda states, an output
+buffer would be accessed one element beyond it's allocated size.
+We don't expect this to have caused incorrect results, but
+a memory checker would complain.
+
+:issue:`3173`
+ 
+Fixes for ``gmx`` tools
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes that affect portability
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Miscellaneous
+^^^^^^^^^^^^^
+

diff --git a/docs/release-notes/index.rst b/docs/release-notes/index.rst
index 3ed1cf3c45354ee65c9d0b47e1ccdec45b6bec3b..af120cc8ae8e53d8720aefee01c74126e5a40eb4 100644 (file)
--- a/docs/release-notes/index.rst
+++ b/docs/release-notes/index.rst
@@ -49,6 +49,7 @@ Patch releases
 .. toctree::
    :maxdepth: 1
 
+   2019/2019.5
    2019/2019.4
    2019/2019.3
    2019/2019.2

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index 79900c51a2f439a6b09863ba2ae9ee434215b697..92c0a0fd20d991350dc74a3470e32ce1539e48e7 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -2048,8 +2048,12 @@ static void read_tpr_header(const char *fn, t_UmbrellaHeader* header, t_Umbrella
         header->pcrd[i].pull_type     = ir->pull->coord[i].eType;
         header->pcrd[i].geometry      = ir->pull->coord[i].eGeom;
         header->pcrd[i].ngroup        = ir->pull->coord[i].ngroup;
-        /* Angle type coordinates are handled fully in degrees in gmx wham */
-        header->pcrd[i].k             = ir->pull->coord[i].k*pull_conversion_factor_internal2userinput(&ir->pull->coord[i]);
+        /* Angle type coordinates are handled fully in degrees in gmx wham.
+         * The pull "distance" appears with a power of -2 in the force constant,
+         * so we need to multiply with the internal units (radians for angle)
+         * to user units (degrees for an angle) with the same power.
+         */
+        header->pcrd[i].k             = ir->pull->coord[i].k/gmx::square(pull_conversion_factor_internal2userinput(&ir->pull->coord[i]));
         header->pcrd[i].init_dist     = ir->pull->coord[i].init;
 
         copy_ivec(ir->pull->coord[i].dim, header->pcrd[i].dim);

diff --git a/src/gromacs/mdlib/mdebin_bar.cpp b/src/gromacs/mdlib/mdebin_bar.cpp
index f0d1651aa7ad7b068647217971144705dbdb386e..6a6d467999fc41f2bfea111955cdb32f8502af67 100644 (file)
--- a/src/gromacs/mdlib/mdebin_bar.cpp
+++ b/src/gromacs/mdlib/mdebin_bar.cpp
@@ -55,6 +55,11 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
+/* Number of entries in subblock_d preceding the lambda components */
+constexpr int c_subblockDNumPreEntries = 5;
+/* Number of entries in subblock_i preceding the lambda components */
+constexpr int c_subblockINumPreEntries = 2;
+
 /* reset the delta_h list to prepare it for new values */
 static void mde_delta_h_reset(t_mde_delta_h *dh)
 {
@@ -430,8 +435,8 @@ void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc, const t_inputrec *ir)
         dhc->lambda_index             = -1;
     }
     /* allocate metadata subblocks */
-    snew(dhc->subblock_d, 5 + dhc->n_lambda_vec);
-    snew(dhc->subblock_i, 1 + dhc->n_lambda_vec);
+    snew(dhc->subblock_d, c_subblockDNumPreEntries + dhc->n_lambda_vec);
+    snew(dhc->subblock_i, c_subblockINumPreEntries + dhc->n_lambda_vec);
 
     /* now decide which data to write out */
     dhc->nlambda     = 0;
@@ -665,11 +670,11 @@ void mde_delta_h_coll_handle_block(t_mde_delta_h_coll *dhc,
     {
         for (i = 0; i < dhc->n_lambda_vec; i++)
         {
-            dhc->subblock_d[5+i] = dhc->native_lambda_vec[i];
+            dhc->subblock_d[c_subblockDNumPreEntries + i] = dhc->native_lambda_vec[i];
         }
     }
     blk->id          = enxDHCOLL;
-    blk->sub[0].nr   = 5 + dhc->n_lambda_vec;
+    blk->sub[0].nr   = c_subblockDNumPreEntries + dhc->n_lambda_vec;
     blk->sub[0].type = xdr_datatype_double;
     blk->sub[0].dval = dhc->subblock_d;
 
@@ -680,9 +685,9 @@ void mde_delta_h_coll_handle_block(t_mde_delta_h_coll *dhc,
         dhc->subblock_i[1] = dhc->n_lambda_vec;
         for (i = 0; i < dhc->n_lambda_vec; i++)
         {
-            dhc->subblock_i[i+2] = dhc->native_lambda_components[i];
+            dhc->subblock_i[c_subblockINumPreEntries + i] = dhc->native_lambda_components[i];
         }
-        blk->sub[1].nr   = 2 + dhc->n_lambda_vec;
+        blk->sub[1].nr   = c_subblockINumPreEntries + dhc->n_lambda_vec;
         blk->sub[1].type = xdr_datatype_int;
         blk->sub[1].ival = dhc->subblock_i;
     }

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 803dfb1103222ed3c3b3da796f41d08331b4cb76..fef7f4850a6af7824b983b2e0cbd804e4e6dbdc6 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -794,6 +794,11 @@ void gmx::LegacySimulator::do_md()
         /* Determine whether or not to do Neighbour Searching */
         bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
 
+        /* Note that the stopHandler will cause termination at nstglobalcomm
+         * steps. Since this concides with nstcalcenergy, nsttcouple and/or
+         * nstpcouple steps, we have computed the half-step kinetic energy
+         * of the previous step and can always output energies at the last step.
+         */
         bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 
         /* do_log triggers energy and virial calculation. Because this leads
@@ -1410,9 +1415,16 @@ void gmx::LegacySimulator::do_md()
         {
             // Organize to do inter-simulation signalling on steps if
             // and when algorithms require it.
-            bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
+            const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
+
+            // With leap-frog we also need to compute the half-step
+            // kinetic energy at the step before we need to write
+            // the full-step kinetic energy
+            const bool needEkinAtNextStep =
+                (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) ||
+                                    step_rel + 1 == ir->nsteps));
 
-            if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
+            if (bGStat || needEkinAtNextStep || doInterSimSignal)
             {
                 // Since we're already communicating at this step, we
                 // can propagate intra-simulation signals. Note that

diff --git a/src/gromacs/tools/make_ndx.cpp b/src/gromacs/tools/make_ndx.cpp
index a3758b259a5feceddceb5a87b318f31b9eeb9154..a97fb81eceac2ed9e95c453cd61f9c8f2add64d7 100644 (file)
--- a/src/gromacs/tools/make_ndx.cpp
+++ b/src/gromacs/tools/make_ndx.cpp
@@ -48,6 +48,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/cstringutil.h"
@@ -1558,7 +1559,7 @@ int gmx_make_ndx(int argc, char *argv[])
     const char       *ndxoutfile;
     gmx_bool          bNatoms;
     int               j;
-    t_atoms          *atoms;
+    t_atoms           atoms;
     rvec             *x, *v;
     int               ePBC;
     matrix            box;
@@ -1587,23 +1588,23 @@ int gmx_make_ndx(int argc, char *argv[])
         gmx_fatal(FARGS, "No input files (structure or index)");
     }
 
+    gmx_mtop_t mtop;
     if (stxfile)
     {
-        t_topology *top;
-        snew(top, 1);
+        bool haveFullTopology = false;
         fprintf(stderr, "\nReading structure file\n");
-        read_tps_conf(stxfile, top, &ePBC, &x, &v, box, FALSE);
-        atoms = &top->atoms;
-        if (atoms->pdbinfo == nullptr)
+        readConfAndTopology(stxfile, &haveFullTopology, &mtop,
+                            &ePBC, &x, &v, box);
+        atoms = gmx_mtop_global_atoms(&mtop);
+        if (atoms.pdbinfo == nullptr)
         {
-            snew(atoms->pdbinfo, atoms->nr);
+            snew(atoms.pdbinfo, atoms.nr);
         }
-        natoms  = atoms->nr;
+        natoms  = atoms.nr;
         bNatoms = TRUE;
     }
     else
     {
-        atoms = nullptr;
         x     = nullptr;
     }
 
@@ -1632,7 +1633,7 @@ int gmx_make_ndx(int argc, char *argv[])
     else
     {
         snew(gnames, 1);
-        analyse(atoms, block, &gnames, FALSE, TRUE);
+        analyse(&atoms, block, &gnames, FALSE, TRUE);
     }
 
     if (!bNatoms)
@@ -1641,7 +1642,7 @@ int gmx_make_ndx(int argc, char *argv[])
         printf("Counted atom numbers up to %d in index file\n", natoms);
     }
 
-    edit_index(natoms, atoms, x, block, &gnames, bVerbose);
+    edit_index(natoms, &atoms, x, block, &gnames, bVerbose);
 
     write_index(ndxoutfile, block, gnames, bDuplicate, natoms);
 

diff --git a/src/programs/mdrun/tests/refdata/Angles1_SimpleMdrunTest_WithinTolerances_0.xml b/src/programs/mdrun/tests/refdata/Angles1_SimpleMdrunTest_WithinTolerances_0.xml
index e6b945db3cfee5293b34067ac7251bc071d5c346..3e723a8d3e952991d9255e17da0b596458ef7afa 100644 (file)
--- a/src/programs/mdrun/tests/refdata/Angles1_SimpleMdrunTest_WithinTolerances_0.xml
+++ b/src/programs/mdrun/tests/refdata/Angles1_SimpleMdrunTest_WithinTolerances_0.xml
@@ -3,53 +3,53 @@
 <ReferenceData>
   <Simulation Name="angles1">
     <Mdrun Name="md">
+      <Energy Name="Pressure">
+        <Real Name="Time 0.000000 Step 0 in frame 0">0.050796915464453078</Real>
+        <Real Name="Time 0.004000 Step 4 in frame 1">0.049668265065138127</Real>
+        <Real Name="Time 0.008000 Step 8 in frame 2">0.051740106421168469</Real>
+        <Real Name="Time 0.012000 Step 12 in frame 3">0.05656710035689768</Real>
+        <Real Name="Time 0.016000 Step 16 in frame 4">0.062737560105270665</Real>
+        <Real Name="Time 0.020000 Step 20 in frame 5">0.068449719298513415</Real>
+        <Real Name="Time 0.024000 Step 24 in frame 6">0.072170660789040553</Real>
+        <Real Name="Time 0.028000 Step 28 in frame 7">0.073111436629933149</Real>
+        <Real Name="Time 0.032000 Step 32 in frame 8">0.0713787995074181</Real>
+        <Real Name="Time 0.036000 Step 36 in frame 9">0.067818279739478599</Real>
+        <Real Name="Time 0.040000 Step 40 in frame 10">0.06366651387852211</Real>
+        <Real Name="Time 0.044000 Step 44 in frame 11">0.060156895239239429</Real>
+        <Real Name="Time 0.048000 Step 48 in frame 12">0.05819249706054485</Real>
+        <Real Name="Time 0.050000 Step 50 in frame 13">0.057930280864272023</Real>
+      </Energy>
       <Energy Name="Kinetic En.">
         <Real Name="Time 0.000000 Step 0 in frame 0">8.8827049229659867</Real>
-        <Real Name="Time 0.004000 Step 4 in frame 1">8.6853411978925212</Real>
-        <Real Name="Time 0.008000 Step 8 in frame 2">9.0476379091109891</Real>
-        <Real Name="Time 0.012000 Step 12 in frame 3">9.8917199248001868</Real>
-        <Real Name="Time 0.016000 Step 16 in frame 4">10.970729795432797</Real>
-        <Real Name="Time 0.020000 Step 20 in frame 5">11.969598016517697</Real>
-        <Real Name="Time 0.024000 Step 24 in frame 6">12.620267943889669</Real>
+        <Real Name="Time 0.004000 Step 4 in frame 1">8.6853411978925283</Real>
+        <Real Name="Time 0.008000 Step 8 in frame 2">9.0476379091110388</Real>
+        <Real Name="Time 0.012000 Step 12 in frame 3">9.8917199248002774</Real>
+        <Real Name="Time 0.016000 Step 16 in frame 4">10.970729795432909</Real>
+        <Real Name="Time 0.020000 Step 20 in frame 5">11.969598016517836</Real>
+        <Real Name="Time 0.024000 Step 24 in frame 6">12.620267943889758</Real>
         <Real Name="Time 0.028000 Step 28 in frame 7">12.784778605942707</Real>
-        <Real Name="Time 0.032000 Step 32 in frame 8">12.481797526143797</Real>
-        <Real Name="Time 0.036000 Step 36 in frame 9">11.859180066366713</Real>
-        <Real Name="Time 0.040000 Step 40 in frame 10">11.133173167819335</Real>
-        <Real Name="Time 0.044000 Step 44 in frame 11">10.519456636414786</Real>
-        <Real Name="Time 0.048000 Step 48 in frame 12">10.175948192781643</Real>
-        <Real Name="Time 0.050000 Step 50 in frame 13">10.141536444106846</Real>
-      </Energy>
-      <Energy Name="Pressure">
-        <Real Name="Time 0.000000 Step 0 in frame 0">0.050796915464453078</Real>
-        <Real Name="Time 0.004000 Step 4 in frame 1">0.049668265065138079</Real>
-        <Real Name="Time 0.008000 Step 8 in frame 2">0.051740106421168025</Real>
-        <Real Name="Time 0.012000 Step 12 in frame 3">0.056567100356897236</Real>
-        <Real Name="Time 0.016000 Step 16 in frame 4">0.062737560105270318</Real>
-        <Real Name="Time 0.020000 Step 20 in frame 5">0.06844971929851254</Real>
-        <Real Name="Time 0.024000 Step 24 in frame 6">0.072170660789039956</Real>
-        <Real Name="Time 0.028000 Step 28 in frame 7">0.073111436629933163</Real>
-        <Real Name="Time 0.032000 Step 32 in frame 8">0.071378799507418461</Real>
-        <Real Name="Time 0.036000 Step 36 in frame 9">0.067818279739479667</Real>
-        <Real Name="Time 0.040000 Step 40 in frame 10">0.063666513878523082</Real>
-        <Real Name="Time 0.044000 Step 44 in frame 11">0.060156895239239817</Real>
-        <Real Name="Time 0.048000 Step 48 in frame 12">0.058192497060544725</Real>
-        <Real Name="Time 0.050000 Step 50 in frame 13">0.057995708953366192</Real>
+        <Real Name="Time 0.032000 Step 32 in frame 8">12.481797526143708</Real>
+        <Real Name="Time 0.036000 Step 36 in frame 9">11.85918006636658</Real>
+        <Real Name="Time 0.040000 Step 40 in frame 10">11.133173167819194</Real>
+        <Real Name="Time 0.044000 Step 44 in frame 11">10.51945663641469</Real>
+        <Real Name="Time 0.048000 Step 48 in frame 12">10.17594819278162</Real>
+        <Real Name="Time 0.050000 Step 50 in frame 13">10.130095229541357</Real>
       </Energy>
       <Energy Name="Potential">
         <Real Name="Time 0.000000 Step 0 in frame 0">4.1472047198540372</Real>
         <Real Name="Time 0.004000 Step 4 in frame 1">4.3456029525254678</Real>
-        <Real Name="Time 0.008000 Step 8 in frame 2">3.9826669068573985</Real>
-        <Real Name="Time 0.012000 Step 12 in frame 3">3.1365732905082528</Real>
-        <Real Name="Time 0.016000 Step 16 in frame 4">2.0549883062523469</Real>
-        <Real Name="Time 0.020000 Step 20 in frame 5">1.053909305545295</Real>
-        <Real Name="Time 0.024000 Step 24 in frame 6">0.40206460374619313</Real>
-        <Real Name="Time 0.028000 Step 28 in frame 7">0.23763430982967265</Real>
-        <Real Name="Time 0.032000 Step 32 in frame 8">0.54173749646261815</Real>
-        <Real Name="Time 0.036000 Step 36 in frame 9">1.1660367172497461</Real>
-        <Real Name="Time 0.040000 Step 40 in frame 10">1.8937346262503456</Real>
-        <Real Name="Time 0.044000 Step 44 in frame 11">2.5086918336925299</Real>
-        <Real Name="Time 0.048000 Step 48 in frame 12">2.852711964582892</Real>
-        <Real Name="Time 0.050000 Step 50 in frame 13">2.8985177691300135</Real>
+        <Real Name="Time 0.008000 Step 8 in frame 2">3.9826669068572804</Real>
+        <Real Name="Time 0.012000 Step 12 in frame 3">3.1365732905081485</Real>
+        <Real Name="Time 0.016000 Step 16 in frame 4">2.0549883062522021</Real>
+        <Real Name="Time 0.020000 Step 20 in frame 5">1.0539093055450899</Real>
+        <Real Name="Time 0.024000 Step 24 in frame 6">0.40206460374611186</Real>
+        <Real Name="Time 0.028000 Step 28 in frame 7">0.23763430982970496</Real>
+        <Real Name="Time 0.032000 Step 32 in frame 8">0.54173749646274727</Real>
+        <Real Name="Time 0.036000 Step 36 in frame 9">1.1660367172499504</Real>
+        <Real Name="Time 0.040000 Step 40 in frame 10">1.8937346262505983</Real>
+        <Real Name="Time 0.044000 Step 44 in frame 11">2.5086918336925828</Real>
+        <Real Name="Time 0.048000 Step 48 in frame 12">2.8527119645828178</Real>
+        <Real Name="Time 0.050000 Step 50 in frame 13">2.8985177691298398</Real>
       </Energy>
       <Vector Name="Time 0.000000 Step 0 F[0]">
         <Real Name="X">10.938095074317319</Real>
@@ -92,224 +92,224 @@
         <Real Name="Z">-155.43795187248847</Real>
       </Vector>
       <Vector Name="Time 0.008000 Step 8 F[0]">
-        <Real Name="X">23.175091525779919</Real>
-        <Real Name="Y">-19.684699303050994</Real>
-        <Real Name="Z">32.068217603600317</Real>
+        <Real Name="X">23.175091525778825</Real>
+        <Real Name="Y">-19.684699303050085</Real>
+        <Real Name="Z">32.068217603598796</Real>
       </Vector>
       <Vector Name="Time 0.008000 Step 8 F[1]">
-        <Real Name="X">-384.67295235829749</Real>
-        <Real Name="Y">-74.107890253924694</Real>
-        <Real Name="Z">-21.330768782037424</Real>
+        <Real Name="X">-384.67295235828954</Real>
+        <Real Name="Y">-74.107890253923756</Real>
+        <Real Name="Z">-21.33076878203557</Real>
       </Vector>
       <Vector Name="Time 0.008000 Step 8 F[2]">
-        <Real Name="X">508.23023246865938</Real>
-        <Real Name="Y">-11.323306055502048</Real>
-        <Real Name="Z">138.18426885013943</Real>
+        <Real Name="X">508.23023246865029</Real>
+        <Real Name="Y">-11.323306055502478</Real>
+        <Real Name="Z">138.18426885013693</Real>
       </Vector>
       <Vector Name="Time 0.008000 Step 8 F[3]">
-        <Real Name="X">-146.73237163614181</Real>
-        <Real Name="Y">105.11589561247773</Real>
-        <Real Name="Z">-148.92171767170231</Real>
+        <Real Name="X">-146.73237163613959</Real>
+        <Real Name="Y">105.11589561247632</Real>
+        <Real Name="Z">-148.92171767170015</Real>
       </Vector>
       <Vector Name="Time 0.012000 Step 12 F[0]">
-        <Real Name="X">19.606862325228409</Real>
-        <Real Name="Y">-16.414806546801842</Real>
-        <Real Name="Z">27.313596732132655</Real>
+        <Real Name="X">19.606862325227326</Real>
+        <Real Name="Y">-16.414806546800946</Real>
+        <Real Name="Z">27.313596732131138</Real>
       </Vector>
       <Vector Name="Time 0.012000 Step 12 F[1]">
-        <Real Name="X">-335.63542363030876</Real>
-        <Real Name="Y">-68.955808848547065</Real>
-        <Real Name="Z">-18.44424868720855</Real>
+        <Real Name="X">-335.63542363030092</Real>
+        <Real Name="Y">-68.955808848546042</Real>
+        <Real Name="Z">-18.444248687206709</Real>
       </Vector>
       <Vector Name="Time 0.012000 Step 12 F[2]">
-        <Real Name="X">443.40685745535319</Real>
-        <Real Name="Y">-6.6985698054608456</Real>
-        <Real Name="Z">124.1640033656024</Real>
+        <Real Name="X">443.40685745534432</Real>
+        <Real Name="Y">-6.6985698054614105</Real>
+        <Real Name="Z">124.16400336559995</Real>
       </Vector>
       <Vector Name="Time 0.012000 Step 12 F[3]">
-        <Real Name="X">-127.37829615027287</Real>
-        <Real Name="Y">92.069185200809756</Real>
-        <Real Name="Z">-133.03335141052651</Real>
+        <Real Name="X">-127.37829615027078</Real>
+        <Real Name="Y">92.069185200808391</Real>
+        <Real Name="Z">-133.03335141052438</Real>
       </Vector>
       <Vector Name="Time 0.016000 Step 16 F[0]">
-        <Real Name="X">10.936701481888193</Real>
-        <Real Name="Y">-9.0594222620341984</Real>
-        <Real Name="Z">15.337114133364635</Real>
+        <Real Name="X">10.936701481886285</Real>
+        <Real Name="Y">-9.0594222620326246</Real>
+        <Real Name="Z">15.337114133361936</Real>
       </Vector>
       <Vector Name="Time 0.016000 Step 16 F[1]">
-        <Real Name="X">-254.29369565940516</Real>
-        <Real Name="Y">-58.536578272057184</Real>
-        <Real Name="Z">-6.7734573229946236</Real>
+        <Real Name="X">-254.29369565939146</Real>
+        <Real Name="Y">-58.536578272055259</Real>
+        <Real Name="Z">-6.7734573229913586</Real>
       </Vector>
       <Vector Name="Time 0.016000 Step 16 F[2]">
-        <Real Name="X">344.4276213065869</Real>
-        <Real Name="Y">-6.5739101403710727</Real>
-        <Real Name="Z">100.47506026189879</Real>
+        <Real Name="X">344.4276213065715</Real>
+        <Real Name="Y">-6.5739101403722024</Real>
+        <Real Name="Z">100.47506026189447</Real>
       </Vector>
       <Vector Name="Time 0.016000 Step 16 F[3]">
-        <Real Name="X">-101.0706271290699</Real>
-        <Real Name="Y">74.169910674462457</Real>
-        <Real Name="Z">-109.0387170722688</Real>
+        <Real Name="X">-101.07062712906634</Real>
+        <Real Name="Y">74.169910674460084</Real>
+        <Real Name="Z">-109.03871707226504</Real>
       </Vector>
       <Vector Name="Time 0.020000 Step 20 F[0]">
-        <Real Name="X">-1.1487885143590644</Real>
-        <Real Name="Y">0.94425702845751291</Real>
-        <Real Name="Z">-1.6210190752303417</Real>
+        <Real Name="X">-1.148788514363047</Real>
+        <Real Name="Y">0.94425702846078807</Real>
+        <Real Name="Z">-1.621019075235957</Real>
       </Vector>
       <Vector Name="Time 0.020000 Step 20 F[1]">
-        <Real Name="X">-151.33525622409871</Real>
-        <Real Name="Y">-42.597492262017155</Real>
-        <Real Name="Z">10.276839538853924</Real>
+        <Real Name="X">-151.33525622407006</Real>
+        <Real Name="Y">-42.597492262012373</Real>
+        <Real Name="Z">10.276839538860115</Real>
       </Vector>
       <Vector Name="Time 0.020000 Step 20 F[2]">
-        <Real Name="X">223.13701175223176</Real>
-        <Real Name="Y">-11.261469518677318</Real>
-        <Real Name="Z">70.282144298824107</Real>
+        <Real Name="X">223.13701175219981</Real>
+        <Real Name="Y">-11.26146951868024</Real>
+        <Real Name="Z">70.282144298815567</Real>
       </Vector>
       <Vector Name="Time 0.020000 Step 20 F[3]">
-        <Real Name="X">-70.652967013773974</Real>
-        <Real Name="Y">52.914704752236958</Real>
-        <Real Name="Z">-78.937964762447692</Real>
+        <Real Name="X">-70.652967013766684</Real>
+        <Real Name="Y">52.914704752231827</Real>
+        <Real Name="Z">-78.937964762439719</Real>
       </Vector>
       <Vector Name="Time 0.024000 Step 24 F[0]">
-        <Real Name="X">-14.792631934835677</Real>
-        <Real Name="Y">12.084501645102721</Real>
-        <Real Name="Z">-20.985856455180208</Real>
+        <Real Name="X">-14.792631934839411</Real>
+        <Real Name="Y">12.084501645105796</Real>
+        <Real Name="Z">-20.985856455185452</Real>
       </Vector>
       <Vector Name="Time 0.024000 Step 24 F[1]">
-        <Real Name="X">-38.508823233299573</Real>
-        <Real Name="Y">-21.773206178588957</Real>
-        <Real Name="Z">28.978581607086344</Real>
+        <Real Name="X">-38.508823233273233</Real>
+        <Real Name="Y">-21.773206178584019</Real>
+        <Real Name="Z">28.978581607091613</Real>
       </Vector>
       <Vector Name="Time 0.024000 Step 24 F[2]">
-        <Real Name="X">92.311360568250592</Real>
-        <Real Name="Y">-20.243825211273709</Real>
-        <Real Name="Z">37.199039838943072</Real>
+        <Real Name="X">92.311360568221545</Real>
+        <Real Name="Y">-20.243825211276956</Real>
+        <Real Name="Z">37.199039838935668</Real>
       </Vector>
       <Vector Name="Time 0.024000 Step 24 F[3]">
-        <Real Name="X">-39.009905400115343</Real>
-        <Real Name="Y">29.932529744759947</Real>
-        <Real Name="Z">-45.191764990849208</Real>
+        <Real Name="X">-39.009905400108892</Real>
+        <Real Name="Y">29.932529744755179</Real>
+        <Real Name="Z">-45.191764990841826</Real>
       </Vector>
       <Vector Name="Time 0.028000 Step 28 F[0]">
-        <Real Name="X">-28.233093664967807</Real>
-        <Real Name="Y">22.92859444472731</Real>
-        <Real Name="Z">-40.223321948721754</Real>
+        <Real Name="X">-28.233093664971499</Real>
+        <Real Name="Y">22.928594444730347</Real>
+        <Real Name="Z">-40.223321948726912</Real>
       </Vector>
       <Vector Name="Time 0.028000 Step 28 F[1]">
-        <Real Name="X">73.021460992109311</Real>
-        <Real Name="Y">2.4029740292514781</Real>
-        <Real Name="Z">46.15342995506451</Real>
+        <Real Name="X">73.021460992134578</Real>
+        <Real Name="Y">2.4029740292567254</Real>
+        <Real Name="Z">46.153429955069178</Real>
       </Vector>
       <Vector Name="Time 0.028000 Step 28 F[2]">
-        <Real Name="X">-36.130408162563846</Real>
-        <Real Name="Y">-32.154073025311916</Real>
-        <Real Name="Z">4.4691445584323635</Real>
+        <Real Name="X">-36.130408162591316</Real>
+        <Real Name="Y">-32.154073025315604</Real>
+        <Real Name="Z">4.4691445584258105</Real>
       </Vector>
       <Vector Name="Time 0.028000 Step 28 F[3]">
-        <Real Name="X">-8.6579591645776546</Real>
-        <Real Name="Y">6.8225045513331253</Real>
-        <Real Name="Z">-10.399252564775118</Real>
+        <Real Name="X">-8.6579591645717695</Real>
+        <Real Name="Y">6.8225045513285316</Real>
+        <Real Name="Z">-10.399252564768073</Real>
       </Vector>
       <Vector Name="Time 0.032000 Step 32 F[0]">
-        <Real Name="X">-39.97789984097686</Real>
-        <Real Name="Y">32.241671576985929</Real>
-        <Real Name="Z">-57.119576941001135</Real>
+        <Real Name="X">-39.977899840980314</Real>
+        <Real Name="Y">32.24167157698875</Real>
+        <Real Name="Z">-57.119576941005896</Real>
       </Vector>
       <Vector Name="Time 0.032000 Step 32 F[1]">
-        <Real Name="X">173.85168027656647</Real>
-        <Real Name="Y">27.749078001711162</Real>
-        <Real Name="Z">59.637350464835151</Real>
+        <Real Name="X">173.85168027659</Real>
+        <Real Name="Y">27.749078001716573</Real>
+        <Real Name="Z">59.637350464838917</Real>
       </Vector>
       <Vector Name="Time 0.032000 Step 32 F[2]">
-        <Real Name="X">-152.36496859639158</Real>
-        <Real Name="Y">-45.012821768681185</Real>
-        <Real Name="Z">-25.518087185941891</Real>
+        <Real Name="X">-152.36496859641699</Real>
+        <Real Name="Y">-45.012821768685001</Real>
+        <Real Name="Z">-25.5180871859476</Real>
       </Vector>
       <Vector Name="Time 0.032000 Step 32 F[3]">
-        <Real Name="X">18.49118816080194</Real>
-        <Real Name="Y">-14.977927810015906</Real>
-        <Real Name="Z">23.000313662107878</Real>
+        <Real Name="X">18.491188160807297</Real>
+        <Real Name="Y">-14.977927810020326</Real>
+        <Real Name="Z">23.000313662114582</Real>
       </Vector>
       <Vector Name="Time 0.036000 Step 36 F[0]">
-        <Real Name="X">-48.881612139197181</Real>
-        <Real Name="Y">39.065295762634229</Real>
-        <Real Name="Z">-69.938279010926436</Real>
+        <Real Name="X">-48.881612139200257</Real>
+        <Real Name="Y">39.065295762636694</Real>
+        <Real Name="Z">-69.938279010930557</Real>
       </Vector>
       <Vector Name="Time 0.036000 Step 36 F[1]">
-        <Real Name="X">256.91883657637214</Real>
-        <Real Name="Y">51.827136837357685</Real>
-        <Real Name="Z">68.316578380756738</Real>
+        <Real Name="X">256.91883657639391</Real>
+        <Real Name="Y">51.827136837363227</Real>
+        <Real Name="Z">68.316578380759381</Real>
       </Vector>
       <Vector Name="Time 0.036000 Step 36 F[2]">
-        <Real Name="X">-249.22935104064919</Real>
-        <Real Name="Y">-56.609707958967739</Real>
-        <Real Name="Z">-51.324820635516417</Real>
+        <Real Name="X">-249.22935104067298</Real>
+        <Real Name="Y">-56.609707958971349</Real>
+        <Real Name="Z">-51.324820635521533</Real>
       </Vector>
       <Vector Name="Time 0.036000 Step 36 F[3]">
-        <Real Name="X">41.192126603474236</Real>
-        <Real Name="Y">-34.282724641024174</Real>
-        <Real Name="Z">52.946521265686115</Real>
+        <Real Name="X">41.192126603479288</Real>
+        <Real Name="Y">-34.282724641028572</Real>
+        <Real Name="Z">52.946521265692709</Real>
       </Vector>
       <Vector Name="Time 0.040000 Step 40 F[0]">
-        <Real Name="X">-54.149503868648566</Real>
-        <Real Name="Y">42.755819150349467</Real>
-        <Real Name="Z">-77.469738353419245</Real>
+        <Real Name="X">-54.149503868651053</Real>
+        <Real Name="Y">42.755819150351471</Real>
+        <Real Name="Z">-77.469738353422414</Real>
       </Vector>
       <Vector Name="Time 0.040000 Step 40 F[1]">
-        <Real Name="X">317.55427307025371</Real>
-        <Real Name="Y">72.337791383415436</Real>
-        <Real Name="Z">71.871971514297229</Real>
+        <Real Name="X">317.55427307027304</Real>
+        <Real Name="Y">72.337791383420608</Real>
+        <Real Name="Z">71.871971514298565</Real>
       </Vector>
       <Vector Name="Time 0.040000 Step 40 F[2]">
-        <Real Name="X">-322.20372287496099</Real>
-        <Real Name="Y">-64.891170578042846</Real>
-        <Real Name="Z">-72.27849537849221</Real>
+        <Real Name="X">-322.2037228749827</Real>
+        <Real Name="Y">-64.891170578045518</Real>
+        <Real Name="Z">-72.278495378496842</Real>
       </Vector>
       <Vector Name="Time 0.040000 Step 40 F[3]">
-        <Real Name="X">58.798953673355882</Real>
-        <Real Name="Y">-50.202439955722056</Real>
-        <Real Name="Z">77.876262217614226</Real>
+        <Real Name="X">58.798953673360693</Real>
+        <Real Name="Y">-50.202439955726554</Real>
+        <Real Name="Z">77.876262217620692</Real>
       </Vector>
       <Vector Name="Time 0.044000 Step 44 F[0]">
-        <Real Name="X">-55.30214765388515</Real>
-        <Real Name="Y">42.989286333517626</Real>
-        <Real Name="Z">-79.007731097948096</Real>
+        <Real Name="X">-55.302147653884383</Real>
+        <Real Name="Y">42.989286333516887</Real>
+        <Real Name="Z">-79.00773109794666</Real>
       </Vector>
       <Vector Name="Time 0.044000 Step 44 F[1]">
-        <Real Name="X">353.20119046090213</Real>
-        <Real Name="Y">87.420405578975277</Real>
-        <Real Name="Z">70.415575063717398</Real>
+        <Real Name="X">353.2011904609036</Real>
+        <Real Name="Y">87.420405578976244</Real>
+        <Real Name="Z">70.41557506371511</Real>
       </Vector>
       <Vector Name="Time 0.044000 Step 44 F[2]">
-        <Real Name="X">-369.03341302494488</Real>
-        <Real Name="Y">-68.257569667105031</Real>
-        <Real Name="Z">-88.161363599526965</Real>
+        <Real Name="X">-369.03341302494869</Real>
+        <Real Name="Y">-68.257569667103468</Real>
+        <Real Name="Z">-88.161363599528485</Real>
       </Vector>
       <Vector Name="Time 0.044000 Step 44 F[3]">
-        <Real Name="X">71.134370217927881</Real>
-        <Real Name="Y">-62.152122245387858</Real>
-        <Real Name="Z">96.753519633757662</Real>
+        <Real Name="X">71.134370217929529</Real>
+        <Real Name="Y">-62.152122245389663</Real>
+        <Real Name="Z">96.753519633760035</Real>
       </Vector>
       <Vector Name="Time 0.048000 Step 48 F[0]">
-        <Real Name="X">-52.13141853615042</Real>
-        <Real Name="Y">39.743487788303739</Real>
-        <Real Name="Z">-74.292830164081394</Real>
+        <Real Name="X">-52.131418536148871</Real>
+        <Real Name="Y">39.743487788302431</Real>
+        <Real Name="Z">-74.292830164078936</Real>
       </Vector>
       <Vector Name="Time 0.048000 Step 48 F[1]">
-        <Real Name="X">363.0139691466951</Real>
-        <Real Name="Y">95.826941958577009</Real>
-        <Real Name="Z">64.166722501371126</Real>
+        <Real Name="X">363.01396914668874</Real>
+        <Real Name="Y">95.826941958575318</Real>
+        <Real Name="Z">64.166722501368355</Real>
       </Vector>
       <Vector Name="Time 0.048000 Step 48 F[2]">
-        <Real Name="X">-389.2319923561339</Real>
-        <Real Name="Y">-65.735297034854213</Real>
-        <Real Name="Z">-98.914481786706801</Real>
+        <Real Name="X">-389.23199235612861</Real>
+        <Real Name="Y">-65.73529703485147</Real>
+        <Real Name="Z">-98.914481786705664</Real>
       </Vector>
       <Vector Name="Time 0.048000 Step 48 F[3]">
-        <Real Name="X">78.349441745589218</Real>
-        <Real Name="Y">-69.835132712026535</Real>
-        <Real Name="Z">109.04058944941707</Real>
+        <Real Name="X">78.349441745588734</Real>
+        <Real Name="Y">-69.835132712026279</Real>
+        <Real Name="Z">109.04058944941626</Real>
       </Vector>
     </Mdrun>
   </Simulation>