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Remove GMX_CONSTRVIR
authorMark Abraham <mark.j.abraham@gmail.com>
Mon, 24 May 2021 03:58:19 +0000 (05:58 +0200)
committerArtem Zhmurov <zhmurov@gmail.com>
Mon, 24 May 2021 07:30:12 +0000 (07:30 +0000)
Simplifies handling of energy output by removing a feature that was
likely useful only during debugging yet incurred function-call
overhead every MD step even when not used.

Resolves previous TODO

Updates tests to no longer check such output while not changing
the numerical output previously written.

19 files changed:
docs/user-guide/environment-variables.rst patch | blob | history
src/gromacs/mdlib/energyoutput.cpp patch | blob | history
src/gromacs/mdlib/energyoutput.h patch | blob | history
src/gromacs/mdlib/tests/energyoutput.cpp patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml patch | blob | history
src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml patch | blob | history
src/gromacs/mdrun/md.cpp patch | blob | history
src/gromacs/mdrun/mimic.cpp patch | blob | history
src/gromacs/mdrun/minimize.cpp patch | blob | history
src/gromacs/mdrun/rerun.cpp patch | blob | history
src/gromacs/modularsimulator/energydata.cpp patch | blob | history

diff --git a/docs/user-guide/environment-variables.rst b/docs/user-guide/environment-variables.rst
index ecd06e671e8c4296836a168b57254cd83795d6e5..026654d36988a1309164adcebbd62c3573a7bb68 100644 (file)
--- a/docs/user-guide/environment-variables.rst
+++ b/docs/user-guide/environment-variables.rst
@@ -22,9 +22,6 @@ you should consult your local documentation for details.
 
 Output Control
 --------------
-``GMX_CONSTRAINTVIR``
-        Print constraint virial and force virial energy terms.
-
 ``GMX_DUMP_NL``
         Neighbour list dump level; default 0.
 
diff --git a/src/gromacs/mdlib/energyoutput.cpp b/src/gromacs/mdlib/energyoutput.cpp
index cc19e024dfcdcff19b9eabe3c3ae8896ce30ec96..fa5b8dca1075c0a3851f74502701af9784e03df2 100644 (file)
--- a/src/gromacs/mdlib/energyoutput.cpp
+++ b/src/gromacs/mdlib/energyoutput.cpp
@@ -132,7 +132,6 @@ namespace gmx
  * be written out to the .edr file.
  *
  * \todo Use more std containers.
- * \todo Remove GMX_CONSTRAINTVIR
  * \todo Write free-energy output also to energy file (after adding more tests)
  */
 EnergyOutput::EnergyOutput(ener_file*                fp_ene,
@@ -148,12 +147,6 @@ EnergyOutput::EnergyOutput(ener_file*                fp_ene,
     const char*        ener_nm[F_NRE];
     static const char* vir_nm[]   = { "Vir-XX", "Vir-XY", "Vir-XZ", "Vir-YX", "Vir-YY",
                                     "Vir-YZ", "Vir-ZX", "Vir-ZY", "Vir-ZZ" };
-    static const char* sv_nm[]    = { "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
-                                   "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
-                                   "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ" };
-    static const char* fv_nm[]    = { "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
-                                   "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
-                                   "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ" };
     static const char* pres_nm[]  = { "Pres-XX", "Pres-XY", "Pres-XZ", "Pres-YX", "Pres-YY",
                                      "Pres-YZ", "Pres-ZX", "Pres-ZY", "Pres-ZZ" };
     static const char* surft_nm[] = { "#Surf*SurfTen" };
@@ -186,7 +179,6 @@ EnergyOutput::EnergyOutput(ener_file*                fp_ene,
     ncon         = gmx_mtop_ftype_count(mtop, F_CONSTR);
     nset         = gmx_mtop_ftype_count(mtop, F_SETTLE);
     bool bConstr = (ncon > 0 || nset > 0) && !isRerun;
-    bConstrVir_  = false;
     nCrmsd_      = 0;
     if (bConstr)
     {
@@ -194,7 +186,6 @@ EnergyOutput::EnergyOutput(ener_file*                fp_ene,
         {
             nCrmsd_ = 1;
         }
-        bConstrVir_ = (getenv("GMX_CONSTRAINTVIR") != nullptr);
     }
     else
     {
@@ -319,11 +310,6 @@ EnergyOutput::EnergyOutput(ener_file*                fp_ene,
             ienthalpy_ = get_ebin_space(ebin_, 1, enthalpy_nm, unit_energy);
         }
     }
-    if (bConstrVir_)
-    {
-        isvir_ = get_ebin_space(ebin_, asize(sv_nm), sv_nm, unit_energy);
-        ifvir_ = get_ebin_space(ebin_, asize(fv_nm), fv_nm, unit_energy);
-    }
     if (bPres_)
     {
         ivir_   = get_ebin_space(ebin_, asize(vir_nm), vir_nm, unit_energy);
@@ -852,8 +838,6 @@ void EnergyOutput::addDataAtEnergyStep(bool                    bDoDHDL,
                                        const matrix            box,
                                        PTCouplingArrays        ptCouplingArrays,
                                        int                     fep_state,
-                                       const tensor            svir,
-                                       const tensor            fvir,
                                        const tensor            vir,
                                        const tensor            pres,
                                        const gmx_ekindata_t*   ekind,
@@ -916,11 +900,6 @@ void EnergyOutput::addDataAtEnergyStep(bool                    bDoDHDL,
             add_ebin(ebin_, ienthalpy_, 1, &enthalpy, bSum);
         }
     }
-    if (bConstrVir_)
-    {
-        add_ebin(ebin_, isvir_, 9, svir[0], bSum);
-        add_ebin(ebin_, ifvir_, 9, fvir[0], bSum);
-    }
     if (bPres_)
     {
         add_ebin(ebin_, ivir_, 9, vir[0], bSum);
@@ -1356,15 +1335,6 @@ void EnergyOutput::printAverages(FILE* log, const SimulationGroups* groups)
             pr_ebin(log, ebin_, ib_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(), 5, eprAVER, true);
             fprintf(log, "\n");
         }
-        if (bConstrVir_)
-        {
-            fprintf(log, "   Constraint Virial (%s)\n", unit_energy);
-            pr_ebin(log, ebin_, isvir_, 9, 3, eprAVER, false);
-            fprintf(log, "\n");
-            fprintf(log, "   Force Virial (%s)\n", unit_energy);
-            pr_ebin(log, ebin_, ifvir_, 9, 3, eprAVER, false);
-            fprintf(log, "\n");
-        }
         if (bPres_)
         {
             fprintf(log, "   Total Virial (%s)\n", unit_energy);
diff --git a/src/gromacs/mdlib/energyoutput.h b/src/gromacs/mdlib/energyoutput.h
index c2d5fd571c6019a356e3b4d3d50606d71c945f43..6c5805514e5a7ed919e8f8e2a90ede3dbf033209 100644 (file)
--- a/src/gromacs/mdlib/energyoutput.h
+++ b/src/gromacs/mdlib/energyoutput.h
@@ -129,7 +129,6 @@ struct PTCouplingArrays
  * be written out to the .edr file.
  *
  * \todo Use more std containers.
- * \todo Remove GMX_CONSTRAINTVIR
  * \todo Write free-energy output also to energy file (after adding more tests)
  */
 class EnergyOutput
@@ -173,8 +172,6 @@ public:
      * \param[in] lastbox           PBC data.
      * \param[in] ptCouplingArrays  Arrays connected to pressure and temperature coupling.
      * \param[in] fep_state         The current alchemical state we are in.
-     * \param[in] svir              Constraint virial.
-     * \param[in] fvir              Force virial.
      * \param[in] vir               Total virial.
      * \param[in] pres              Pressure.
      * \param[in] ekind             Kinetic energy data.
@@ -191,8 +188,6 @@ public:
                              const matrix            lastbox,
                              PTCouplingArrays        ptCouplingArrays,
                              int                     fep_state,
-                             const tensor            svir,
-                             const tensor            fvir,
                              const tensor            vir,
                              const tensor            pres,
                              const gmx_ekindata_t*   ekind,
@@ -347,14 +342,6 @@ private:
     //! Index for entalpy (pV + total energy)
     int ienthalpy_ = 0;
 
-    /*! \brief If the constraints virial should be printed.
-     * Can only be true if "GMX_CONSTRAINTVIR" environmental variable is set */
-    bool bConstrVir_ = false;
-    //! Index for constrains virial
-    int isvir_ = 0;
-    //! Index for force virial
-    int ifvir_ = 0;
-
     //! If we have pressure computed
     bool bPres_ = false;
     //! Index for total virial
diff --git a/src/gromacs/mdlib/tests/energyoutput.cpp b/src/gromacs/mdlib/tests/energyoutput.cpp
index 51a06b9f769d93837b2399ba68fab5371452be6f..f75136b5a1ede53555c34e56bd9ef93e6891e0ac 100644 (file)
--- a/src/gromacs/mdlib/tests/energyoutput.cpp
+++ b/src/gromacs/mdlib/tests/energyoutput.cpp
@@ -162,10 +162,6 @@ public:
     t_state state_;
     //! PBC box
     matrix box_;
-    //! Virial from constraints
-    tensor constraintsVirial_;
-    //! Virial from force computation
-    tensor forceVirial_;
     //! Total virial
     tensor totalVirial_;
     //! Pressure
@@ -237,9 +233,6 @@ public:
         // Dipole (mu)
         inputrec_.ewald_geometry = EwaldGeometry::ThreeDC;
 
-        // GMX_CONSTRAINTVIR environment variable should also be
-        // set to print constraints and force virials separately.
-        gmxSetenv("GMX_CONSTRAINTVIR", "true", 1);
         // To print constrain RMSD, constraints algorithm should be set to LINCS.
         inputrec_.eConstrAlg = ConstraintAlgorithm::Lincs;
 
@@ -463,25 +456,9 @@ public:
         box_[ZZ][YY] = (*testValue += 0.1);
         box_[ZZ][ZZ] = (*testValue += 0.1);
 
-        constraintsVirial_[XX][XX] = (*testValue += 0.1);
-        constraintsVirial_[XX][YY] = (*testValue += 0.1);
-        constraintsVirial_[XX][ZZ] = (*testValue += 0.1);
-        constraintsVirial_[YY][XX] = (*testValue += 0.1);
-        constraintsVirial_[YY][YY] = (*testValue += 0.1);
-        constraintsVirial_[YY][ZZ] = (*testValue += 0.1);
-        constraintsVirial_[ZZ][XX] = (*testValue += 0.1);
-        constraintsVirial_[ZZ][YY] = (*testValue += 0.1);
-        constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1);
-
-        forceVirial_[XX][XX] = (*testValue += 0.1);
-        forceVirial_[XX][YY] = (*testValue += 0.1);
-        forceVirial_[XX][ZZ] = (*testValue += 0.1);
-        forceVirial_[YY][XX] = (*testValue += 0.1);
-        forceVirial_[YY][YY] = (*testValue += 0.1);
-        forceVirial_[YY][ZZ] = (*testValue += 0.1);
-        forceVirial_[ZZ][XX] = (*testValue += 0.1);
-        forceVirial_[ZZ][YY] = (*testValue += 0.1);
-        forceVirial_[ZZ][ZZ] = (*testValue += 0.1);
+        // Removing GMX_CONSTRVIR removed a total increment of 1.8
+        // To avoid unnecessary changes in reference data, we keep the increment
+        (*testValue += 1.8);
 
         totalVirial_[XX][XX] = (*testValue += 0.1);
         totalVirial_[XX][YY] = (*testValue += 0.1);
@@ -648,8 +625,6 @@ TEST_P(EnergyOutputTest, CheckOutput)
                                                              state_.nhpres_xi,
                                                              state_.nhpres_vxi }),
                                           state_.fep_state,
-                                          constraintsVirial_,
-                                          forceVirial_,
                                           totalVirial_,
                                           pressure_,
                                           &ekindata_,
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml
index f100a6bc7f634178f233751ca1b5ec0038d168d8..2f0e42906750077873610b688eaae568d815ee38 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">91</Int>
+      <Int Name="Length">73</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -92,78 +92,6 @@
         <String Name="Name">Constr. rmsd</String>
         <String Name="Units"></String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -377,7 +305,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -466,78 +394,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -746,7 +602,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">91</Int>
+  <Int Name="Number of Energy Terms">73</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -783,16 +639,6 @@ Current ref_t for group Lipid:     25.8
  dVrestraint/dl   Constr. rmsd
     1.22000e+01    0.00000e+00
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml
index e7d41dbf15807d5e3970ec3812b5612a78654673..03e27d25f8b27c2106f1a40ef0c9fbb022c4aac6 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">102</Int>
+      <Int Name="Length">84</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -124,78 +124,6 @@
         <String Name="Name">Enthalpy</String>
         <String Name="Units">kJ/mol</String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -421,7 +349,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">102</Int>
+          <Int Name="Length">84</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -542,78 +470,6 @@
             <String Name="Name">Enthalpy</String>
             <Real Name="Value">10.699999999999998</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -834,7 +690,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">102</Int>
+  <Int Name="Number of Energy Terms">84</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -874,16 +730,6 @@ Current ref_t for group Lipid:     25.8
           Box-X          Box-Y          Box-Z
     1.99000e+01    2.03000e+01    2.07000e+01
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml
index f100a6bc7f634178f233751ca1b5ec0038d168d8..2f0e42906750077873610b688eaae568d815ee38 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">91</Int>
+      <Int Name="Length">73</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -92,78 +92,6 @@
         <String Name="Name">Constr. rmsd</String>
         <String Name="Units"></String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -377,7 +305,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -466,78 +394,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -746,7 +602,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">91</Int>
+  <Int Name="Number of Energy Terms">73</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -783,16 +639,6 @@ Current ref_t for group Lipid:     25.8
  dVrestraint/dl   Constr. rmsd
     1.22000e+01    0.00000e+00
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml
index 5376fc9a0aa6db0b9683020f03b1523218befeda..6f57ceb0a62fb95b8afe37660958730041a93e3e 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
 <ReferenceData>
-  <Int Name="Number of Energy Terms">91</Int>
+  <Int Name="Number of Energy Terms">73</Int>
   <String Name="log">Current ref_t for group Water:      0.0
 Current ref_t for group Lipid:      0.0
 
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml
index efc4d8958ba513cf04a005cd11fe1cb1da9be23f..d01bbf372ef92f64998e421a7a31b7455593be28 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">91</Int>
+      <Int Name="Length">73</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -92,78 +92,6 @@
         <String Name="Name">Constr. rmsd</String>
         <String Name="Units"></String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
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-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
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-        <String Name="Name">ShakeVir-ZY</String>
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-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
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-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
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-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
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-      </EnergyTerm>
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-      </EnergyTerm>
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-        <String Name="Name">ForceVir-YX</String>
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-        <String Name="Name">ForceVir-YY</String>
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       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
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         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
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+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -466,78 +394,6 @@
             <String Name="Name">Constr. rmsd</String>
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           </EnergyTerm>
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           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
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         <String Name="Step">100</String>
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         <Sequence Name="EnergyTerms">
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           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">28.900000000000162</Real>
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             <String Name="Name">Constr. rmsd</String>
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           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">40.00000000000032</Real>
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         <String Name="Step">200</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
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+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">46.300000000000409</Real>
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             <String Name="Name">Constr. rmsd</String>
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           </EnergyTerm>
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           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">57.400000000000567</Real>
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         <String Name="Step">300</String>
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         <Sequence Name="EnergyTerms">
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             <String Name="Name">LJ-14</String>
             <Real Name="Value">63.700000000000657</Real>
@@ -1585,78 +1297,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
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           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
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             <String Name="Name">LJ-14</String>
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             <String Name="Name">Constr. rmsd</String>
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             <String Name="Name">Vir-XX</String>
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-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">107.99999999999815</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">108.09999999999815</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">108.19999999999814</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">108.29999999999814</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">108.39999999999813</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">108.49999999999812</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">108.59999999999812</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">108.69999999999811</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">108.79999999999811</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">108.8999999999981</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">108.9999999999981</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">109.09999999999809</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">109.19999999999808</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">109.29999999999808</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">109.39999999999807</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">109.49999999999807</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">109.59999999999806</Real>
@@ -2615,7 +2111,7 @@
         <String Name="Step">600</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">115.8999999999977</Real>
@@ -2704,78 +2200,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">125.19999999999717</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">125.29999999999717</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">125.39999999999716</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">125.49999999999716</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">125.59999999999715</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">125.69999999999715</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">125.79999999999714</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">125.89999999999714</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">125.99999999999713</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">126.09999999999712</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">126.19999999999712</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">126.29999999999711</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">126.39999999999711</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">126.4999999999971</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">126.5999999999971</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">126.69999999999709</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">126.79999999999708</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">126.89999999999708</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">126.99999999999707</Real>
@@ -2988,7 +2412,7 @@
         <String Name="Step">700</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">133.29999999999671</Real>
@@ -3077,78 +2501,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">142.59999999999619</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">142.69999999999618</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">142.79999999999617</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">142.89999999999617</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">142.99999999999616</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">143.09999999999616</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">143.19999999999615</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">143.29999999999615</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">143.39999999999614</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">143.49999999999613</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">143.59999999999613</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">143.69999999999612</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">143.79999999999612</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">143.89999999999611</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">143.99999999999611</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">144.0999999999961</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">144.19999999999609</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">144.29999999999609</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">144.39999999999608</Real>
@@ -3361,7 +2713,7 @@
         <String Name="Step">800</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">150.69999999999573</Real>
@@ -3450,78 +2802,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">159.9999999999952</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">160.09999999999519</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">160.19999999999519</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">160.29999999999518</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">160.39999999999517</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">160.49999999999517</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">160.59999999999516</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">160.69999999999516</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">160.79999999999515</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">160.89999999999515</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">160.99999999999514</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">161.09999999999513</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">161.19999999999513</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">161.29999999999512</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">161.39999999999512</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">161.49999999999511</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">161.59999999999511</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">161.6999999999951</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">161.79999999999509</Real>
@@ -3734,7 +3014,7 @@
         <String Name="Step">900</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">168.09999999999474</Real>
@@ -3823,78 +3103,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">177.39999999999421</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">177.4999999999942</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">177.5999999999942</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">177.69999999999419</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">177.79999999999418</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">177.89999999999418</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">177.99999999999417</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">178.09999999999417</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">178.19999999999416</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">178.29999999999416</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">178.39999999999415</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">178.49999999999415</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">178.59999999999414</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">178.69999999999413</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">178.79999999999413</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">178.89999999999412</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">178.99999999999412</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">179.09999999999411</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">179.19999999999411</Real>
@@ -4103,7 +3311,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">91</Int>
+  <Int Name="Number of Energy Terms">73</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -4275,16 +3483,6 @@ Current ref_t for group Lipid:    182.4
  dVrestraint/dl   Constr. rmsd
     9.05000e+01    0.00000e+00
 
-   Constraint Virial (kJ/mol)
-    9.91000e+01    9.92000e+01    9.93000e+01
-    9.94000e+01    9.95000e+01    9.96000e+01
-    9.97000e+01    9.98000e+01    9.99000e+01
-
-   Force Virial (kJ/mol)
-    1.00000e+02    1.00100e+02    1.00200e+02
-    1.00300e+02    1.00400e+02    1.00500e+02
-    1.00600e+02    1.00700e+02    1.00800e+02
-
    Total Virial (kJ/mol)
     1.00900e+02    1.01000e+02    1.01100e+02
     1.01200e+02    1.01300e+02    1.01400e+02
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml
index 43e5ca6aebdd78614ced6d2f383ab05db698dbae..47a1d4daa69148aee2e82bd8bf74077e060433fb 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">95</Int>
+      <Int Name="Length">77</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -96,78 +96,6 @@
         <String Name="Name">Constr. rmsd</String>
         <String Name="Units"></String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -393,7 +321,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">95</Int>
+          <Int Name="Length">77</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -486,78 +414,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -778,7 +634,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">95</Int>
+  <Int Name="Number of Energy Terms">77</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -815,16 +671,6 @@ Current ref_t for group Lipid:     25.8
     dVbonded/dl dVrestraint/dl   Constr. rmsd
     1.21000e+01    1.22000e+01    0.00000e+00
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml
index 73ca7a122f4a3c76105b6f297b31dbff8bdc3c23..e1aaee38df79e82668ac34ab75b0229771d452bb 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">98</Int>
+      <Int Name="Length">80</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -96,78 +96,6 @@
         <String Name="Name">Constr. rmsd</String>
         <String Name="Units"></String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -405,7 +333,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">98</Int>
+          <Int Name="Length">80</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -498,78 +426,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -802,7 +658,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">98</Int>
+  <Int Name="Number of Energy Terms">80</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -839,16 +695,6 @@ Current ref_t for group Lipid:     25.8
     dVbonded/dl dVrestraint/dl   Constr. rmsd
     1.21000e+01    1.22000e+01    0.00000e+00
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml
index e7d41dbf15807d5e3970ec3812b5612a78654673..03e27d25f8b27c2106f1a40ef0c9fbb022c4aac6 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">102</Int>
+      <Int Name="Length">84</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -124,78 +124,6 @@
         <String Name="Name">Enthalpy</String>
         <String Name="Units">kJ/mol</String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -421,7 +349,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">102</Int>
+          <Int Name="Length">84</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -542,78 +470,6 @@
             <String Name="Name">Enthalpy</String>
             <Real Name="Value">10.699999999999998</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -834,7 +690,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">102</Int>
+  <Int Name="Number of Energy Terms">84</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -874,16 +730,6 @@ Current ref_t for group Lipid:     25.8
           Box-X          Box-Y          Box-Z
     1.99000e+01    2.03000e+01    2.07000e+01
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml
index e7d41dbf15807d5e3970ec3812b5612a78654673..03e27d25f8b27c2106f1a40ef0c9fbb022c4aac6 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">102</Int>
+      <Int Name="Length">84</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -124,78 +124,6 @@
         <String Name="Name">Enthalpy</String>
         <String Name="Units">kJ/mol</String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -421,7 +349,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">102</Int>
+          <Int Name="Length">84</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -542,78 +470,6 @@
             <String Name="Name">Enthalpy</String>
             <Real Name="Value">10.699999999999998</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -834,7 +690,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">102</Int>
+  <Int Name="Number of Energy Terms">84</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -874,16 +730,6 @@ Current ref_t for group Lipid:     25.8
           Box-X          Box-Y          Box-Z
     1.99000e+01    2.03000e+01    2.07000e+01
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml
index f100a6bc7f634178f233751ca1b5ec0038d168d8..2f0e42906750077873610b688eaae568d815ee38 100644 (file)
--- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml
+++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml
@@ -3,7 +3,7 @@
 <ReferenceData>
   <File Name="EnergyFile">
     <Sequence Name="EnergyTerms">
-      <Int Name="Length">91</Int>
+      <Int Name="Length">73</Int>
       <EnergyTerm>
         <String Name="Name">LJ-14</String>
         <String Name="Units">kJ/mol</String>
@@ -92,78 +92,6 @@
         <String Name="Name">Constr. rmsd</String>
         <String Name="Units"></String>
       </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ShakeVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-XZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-YZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZX</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZY</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
-      <EnergyTerm>
-        <String Name="Name">ForceVir-ZZ</String>
-        <String Name="Units">kJ/mol</String>
-      </EnergyTerm>
       <EnergyTerm>
         <String Name="Name">Vir-XX</String>
         <String Name="Units">kJ/mol</String>
@@ -377,7 +305,7 @@
         <String Name="Step">0</String>
         <String Name="NumSteps">0</String>
         <Sequence Name="EnergyTerms">
-          <Int Name="Length">91</Int>
+          <Int Name="Length">73</Int>
           <EnergyTerm>
             <String Name="Name">LJ-14</String>
             <Real Name="Value">11.499999999999995</Real>
@@ -466,78 +394,6 @@
             <String Name="Name">Constr. rmsd</String>
             <Real Name="Value">0</Real>
           </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XX</String>
-            <Real Name="Value">20.800000000000047</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XY</String>
-            <Real Name="Value">20.900000000000048</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-XZ</String>
-            <Real Name="Value">21.00000000000005</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YX</String>
-            <Real Name="Value">21.100000000000051</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YY</String>
-            <Real Name="Value">21.200000000000053</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-YZ</String>
-            <Real Name="Value">21.300000000000054</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZX</String>
-            <Real Name="Value">21.400000000000055</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZY</String>
-            <Real Name="Value">21.500000000000057</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ShakeVir-ZZ</String>
-            <Real Name="Value">21.600000000000058</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XX</String>
-            <Real Name="Value">21.70000000000006</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XY</String>
-            <Real Name="Value">21.800000000000061</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-XZ</String>
-            <Real Name="Value">21.900000000000063</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YX</String>
-            <Real Name="Value">22.000000000000064</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YY</String>
-            <Real Name="Value">22.100000000000065</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-YZ</String>
-            <Real Name="Value">22.200000000000067</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZX</String>
-            <Real Name="Value">22.300000000000068</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZY</String>
-            <Real Name="Value">22.40000000000007</Real>
-          </EnergyTerm>
-          <EnergyTerm>
-            <String Name="Name">ForceVir-ZZ</String>
-            <Real Name="Value">22.500000000000071</Real>
-          </EnergyTerm>
           <EnergyTerm>
             <String Name="Name">Vir-XX</String>
             <Real Name="Value">22.600000000000072</Real>
@@ -746,7 +602,7 @@
       </Frame>
     </Sequence>
   </File>
-  <Int Name="Number of Energy Terms">91</Int>
+  <Int Name="Number of Energy Terms">73</Int>
   <String Name="log">Current ref_t for group Water:     25.7
 Current ref_t for group Lipid:     25.8
 
@@ -783,16 +639,6 @@ Current ref_t for group Lipid:     25.8
  dVrestraint/dl   Constr. rmsd
     1.22000e+01    0.00000e+00
 
-   Constraint Virial (kJ/mol)
-    2.08000e+01    2.09000e+01    2.10000e+01
-    2.11000e+01    2.12000e+01    2.13000e+01
-    2.14000e+01    2.15000e+01    2.16000e+01
-
-   Force Virial (kJ/mol)
-    2.17000e+01    2.18000e+01    2.19000e+01
-    2.20000e+01    2.21000e+01    2.22000e+01
-    2.23000e+01    2.24000e+01    2.25000e+01
-
    Total Virial (kJ/mol)
     2.26000e+01    2.27000e+01    2.28000e+01
     2.29000e+01    2.30000e+01    2.31000e+01
diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 92c51459b85cceac7366b4b6e5f8a09c7b6261d0..810606ed223d46a312a82cca50d3510cbf6ea977 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -1863,8 +1863,6 @@ void gmx::LegacySimulator::do_md()
                                                                    state->nhpres_xi,
                                                                    state->nhpres_vxi },
                                                  state->fep_state,
-                                                 shake_vir,
-                                                 force_vir,
                                                  total_vir,
                                                  pres,
                                                  ekind,
diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index c014f5ae2573ca99e87dd875df20e71bde844601..24661da9ac0118d0b4efd16b8fe5aeb1d0aa1949 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -715,8 +715,6 @@ void gmx::LegacySimulator::do_mimic()
                                                                 state->nhpres_xi,
                                                                 state->nhpres_vxi }),
                                              state->fep_state,
-                                             shake_vir,
-                                             force_vir,
                                              total_vir,
                                              pres,
                                              ekind,
diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp
index a1d42aa6c1f5eddd7e033dd7dc6c6bba03ca0aeb..6784cfeb0bad3d855a3f78f5c75b635f7c151d6b 100644 (file)
--- a/src/gromacs/mdrun/minimize.cpp
+++ b/src/gromacs/mdrun/minimize.cpp
@@ -1368,8 +1368,6 @@ void LegacySimulator::do_cg()
                                          nullBox,
                                          PTCouplingArrays(),
                                          0,
-                                         nullptr,
-                                         nullptr,
                                          vir,
                                          pres,
                                          nullptr,
@@ -1819,8 +1817,6 @@ void LegacySimulator::do_cg()
                                              nullBox,
                                              PTCouplingArrays(),
                                              0,
-                                             nullptr,
-                                             nullptr,
                                              vir,
                                              pres,
                                              nullptr,
@@ -2107,8 +2103,6 @@ void LegacySimulator::do_lbfgs()
                                          nullBox,
                                          PTCouplingArrays(),
                                          0,
-                                         nullptr,
-                                         nullptr,
                                          vir,
                                          pres,
                                          nullptr,
@@ -2631,8 +2625,6 @@ void LegacySimulator::do_lbfgs()
                                              nullBox,
                                              PTCouplingArrays(),
                                              0,
-                                             nullptr,
-                                             nullptr,
                                              vir,
                                              pres,
                                              nullptr,
@@ -2909,8 +2901,6 @@ void LegacySimulator::do_steep()
                                                  nullBox,
                                                  PTCouplingArrays(),
                                                  0,
-                                                 nullptr,
-                                                 nullptr,
                                                  vir,
                                                  pres,
                                                  nullptr,
diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index 78271fae4824e620cf3969fc14ce6097ad9a40e2..fd712581491fff60d533e0987508c53c9f9bb514 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -797,8 +797,6 @@ void gmx::LegacySimulator::do_rerun()
                                                                 state->nhpres_xi,
                                                                 state->nhpres_vxi }),
                                              state->fep_state,
-                                             shake_vir,
-                                             force_vir,
                                              total_vir,
                                              pres,
                                              ekind,
diff --git a/src/gromacs/modularsimulator/energydata.cpp b/src/gromacs/modularsimulator/energydata.cpp
index 4396f3f1b175126676ffcb3e919b402a3019be12..5553ec2b8d7d02eeac5628617ad5fb8e76878b63 100644 (file)
--- a/src/gromacs/modularsimulator/energydata.cpp
+++ b/src/gromacs/modularsimulator/energydata.cpp
@@ -266,8 +266,6 @@ void EnergyData::doStep(Step step, Time time, bool isEnergyCalculationStep, bool
                                {},
                                {} }),
             freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0,
-            shakeVirial_,
-            forceVirial_,
             totalVirial_,
             pressure_,
             ekind_,
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